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/*
* $Id: TestPluginManager.java,v 1.26 2003-12-23 00:37:32 tlipkis Exp $
*/
package org.lockss.plugin;
import java.io.*;
import java.net.*;
import java.util.*;
import junit.framework.*;
import org.lockss.daemon.*;
import org.lockss.plugin.*;
import org.lockss.poller.*;
import org.lockss.util.*;
import org.lockss.test.*;
import org.lockss.repository.*;
import org.lockss.poller.PollSpec;
/**
* Test class for org.lockss.plugin.PluginManager
*/
public class TestPluginManager extends LockssTestCase {
private MockLockssDaemon theDaemon;
static String mockPlugKey = "org|lockss|test|MockPlugin";
static Properties props1 = new Properties();
static Properties props2 = new Properties();
static {
props1.setProperty(MockPlugin.CONFIG_PROP_1, "val1");
props1.setProperty(MockPlugin.CONFIG_PROP_2, "val2");
props2.setProperty(MockPlugin.CONFIG_PROP_1, "val1");
props2.setProperty(MockPlugin.CONFIG_PROP_2, "va.l3");//auid contains a dot
}
static String mauauidKey1 = PropUtil.propsToCanonicalEncodedString(props1);
static String mauauid1 = mockPlugKey+"&"+ mauauidKey1;
// static String m
static String mauauidKey2 = PropUtil.propsToCanonicalEncodedString(props2);
static String mauauid2 = mockPlugKey+"&"+mauauidKey2;
static String p1param =
PluginManager.PARAM_AU_TREE + "." + mockPlugKey + ".";
static String p1a1param = p1param + mauauidKey1 + ".";
static String p1a2param = p1param + mauauidKey2 + ".";
static String configStr =
p1a1param + MockPlugin.CONFIG_PROP_1 + "=val1\n" +
p1a1param + MockPlugin.CONFIG_PROP_2 + "=val2\n" +
p1a2param + MockPlugin.CONFIG_PROP_1 + "=val1\n" +
p1a2param + MockPlugin.CONFIG_PROP_2 + "=va.l3\n" + // value contains a dot
// needed to allow PluginManager to register AUs
// leave value blank to allow 'doConfig()' to fill it in dynamically
LockssRepositoryImpl.PARAM_CACHE_LOCATION + "=";
PluginManager mgr;
public TestPluginManager(String msg) {
super(msg);
}
public void setUp() throws Exception {
super.setUp();
theDaemon = new MockLockssDaemon();
mgr = new PluginManager();
theDaemon.setPluginManager(mgr);
theDaemon.setDaemonInited(true);
mgr.initService(theDaemon);
}
public void tearDown() throws Exception {
mgr.stopService();
theDaemon.stopDaemon();
super.tearDown();
}
private void doConfig() throws Exception {
mgr.startService();
String localConfig = configStr + getTempDir().getAbsolutePath() +
File.separator;
ConfigurationUtil.setCurrentConfigFromString(localConfig);
}
private void minimalConfig() throws Exception {
mgr.startService();
ConfigurationUtil.setFromArgs(LockssRepositoryImpl.PARAM_CACHE_LOCATION,
getTempDir().getAbsolutePath() +
File.separator);
}
public void testNameFromKey() {
assertEquals("org.lockss.Foo", PluginManager.pluginNameFromKey("org|lockss|Foo"));
}
public void testKeyFromName() {
assertEquals("org|lockss|Foo", PluginManager.pluginKeyFromName("org.lockss.Foo"));
}
public void testKeyFromId() {
assertEquals("org|lockss|Foo", PluginManager.pluginKeyFromId("org.lockss.Foo"));
}
public void testEnsurePluginLoaded() throws Exception {
// non-existent class shouldn't load
String key = "org|lockss|NoSuchClass";
assertFalse(mgr.ensurePluginLoaded(key));
assertNull(mgr.getPlugin(key));
// MockPlugin should load
assertTrue(mgr.ensurePluginLoaded(mockPlugKey));
Plugin p = mgr.getPlugin(mockPlugKey);
assertTrue(p.toString(), p instanceof MockPlugin);
MockPlugin mpi = (MockPlugin)mgr.getPlugin(mockPlugKey);
assertNotNull(mpi);
assertEquals(1, mpi.getInitCtr()); // should have been inited once
// second time shouldn't reload, reinstantiate, or reinitialize plugin
assertTrue(mgr.ensurePluginLoaded(mockPlugKey));
MockPlugin mpi2 = (MockPlugin)mgr.getPlugin(mockPlugKey);
assertSame(mpi, mpi2);
assertEquals(1, mpi.getInitCtr());
}
public void testInitPluginRegistry() {
String n1 = "org.lockss.test.MockPlugin";
String n2 = ThrowingMockPlugin.class.getName();
assertEmpty(mgr.getRegisteredPlugins());
ConfigurationUtil.setFromArgs(PluginManager.PARAM_PLUGIN_REGISTRY,
n1 + ";" + n2);
Plugin p1 = mgr.getPlugin(mgr.pluginKeyFromName(n1));
assertNotNull(p1);
assertTrue(p1.toString(), p1 instanceof MockPlugin);
Plugin p2 = mgr.getPlugin(mgr.pluginKeyFromName(n2));
assertNotNull(p2);
assertTrue(p2.toString(), p2 instanceof ThrowingMockPlugin);
assertEquals(2, mgr.getRegisteredPlugins().size());
ConfigurationUtil.setFromArgs(PluginManager.PARAM_PLUGIN_REGISTRY, n1);
assertEquals(1, mgr.getRegisteredPlugins().size());
assertNull(mgr.getPlugin(mgr.pluginKeyFromName(n2)));
assertNotNull(mgr.getPlugin(mgr.pluginKeyFromName(n1)));
assertTrue(mgr.getPlugin(mgr.pluginKeyFromName(n1)) instanceof MockPlugin);
}
public void testInitTitleDB() {
Properties p = new Properties();
p.put("org.lockss.title.1.foo", "foo1");
p.put("org.lockss.title.1.bar", "bar1");
p.put("org.lockss.title.2.bar", "bar2");
ConfigurationUtil.setCurrentConfigFromProps(p);
}
public void testStop() throws Exception {
doConfig();
MockPlugin mpi = (MockPlugin)mgr.getPlugin(mockPlugKey);
assertEquals(0, mpi.getStopCtr());
mgr.stopService();
assertEquals(1, mpi.getStopCtr());
}
public void testAuConfig() throws Exception {
doConfig();
MockPlugin mpi = (MockPlugin)mgr.getPlugin(mockPlugKey);
// plugin should be registered
assertNotNull(mpi);
// should have been inited once
assertEquals(1, mpi.getInitCtr());
// get the two archival units
ArchivalUnit au1 = mgr.getAuFromId(mauauid1);
ArchivalUnit au2 = mgr.getAuFromId(mauauid2);
// verify the plugin's set of all AUs is {au1, au2}
Collection aus = mpi.getAllAus();
assertEquals(SetUtil.set(au1, au2), new HashSet(mgr.getAllAus()));
// verify au1's configuration
assertEquals(mauauid1, au1.getAuId());
MockArchivalUnit mau1 = (MockArchivalUnit)au1;
Configuration c1 = mau1.getConfiguration();
assertEquals("val1", c1.get(MockPlugin.CONFIG_PROP_1));
assertEquals("val2", c1.get(MockPlugin.CONFIG_PROP_2));
// verify au1's configuration
assertEquals(mauauid2, au2.getAuId());
MockArchivalUnit mau2 = (MockArchivalUnit)au2;
Configuration c2 = mau2.getConfiguration();
assertEquals("val1", c2.get(MockPlugin.CONFIG_PROP_1));
assertEquals("va.l3", c2.get(MockPlugin.CONFIG_PROP_2));
assertEquals(au1, mgr.getAuFromId(mauauid1));
}
public void testCreateAu() throws Exception {
minimalConfig();
String pid = new ThrowingMockPlugin().getPluginId();
String key = PluginManager.pluginKeyFromId(pid);
assertTrue(mgr.ensurePluginLoaded(key));
ThrowingMockPlugin mpi = (ThrowingMockPlugin)mgr.getPlugin(key);
assertNotNull(mpi);
Configuration config = ConfigurationUtil.fromArgs("a", "b");
ArchivalUnit au = mgr.createAu(mpi, config);
// verify put in PluginManager map
String auid = au.getAuId();
ArchivalUnit aux = mgr.getAuFromId(auid);
assertSame(au, aux);
// verify got right config
Configuration auConfig = au.getConfiguration();
assertEquals("b", auConfig.get("a"));
assertEquals(1, auConfig.keySet().size());
assertEquals(mpi, au.getPlugin());
// verify turns RuntimeException into ArchivalUnit.ConfigurationException
mpi.setCfgEx(new ArchivalUnit.ConfigurationException("should be thrown"));
try {
ArchivalUnit au2 = mgr.createAu(mpi, config);
fail("createAU should have thrown ArchivalUnit.ConfigurationException");
} catch (ArchivalUnit.ConfigurationException e) {
}
mpi.setRtEx(new ExpectedRuntimeException("Ok if in log"));
try {
ArchivalUnit au2 = mgr.createAu(mpi, config);
fail("createAU should have thrown ArchivalUnit.ConfigurationException");
} catch (ArchivalUnit.ConfigurationException e) {
// this is what's expected
} catch (RuntimeException e) {
fail("createAU threw RuntimeException");
}
}
public void testConfigureAu() throws Exception {
minimalConfig();
String pid = new ThrowingMockPlugin().getPluginId();
String key = PluginManager.pluginKeyFromId(pid);
assertTrue(mgr.ensurePluginLoaded(key));
ThrowingMockPlugin mpi = (ThrowingMockPlugin)mgr.getPlugin(key);
assertNotNull(mpi);
Configuration config = ConfigurationUtil.fromArgs("a", "b");
ArchivalUnit au = mgr.createAu(mpi, config);
String auid = au.getAuId();
ArchivalUnit aux = mgr.getAuFromId(auid);
assertSame(au, aux);
// verify can reconfig
mgr.configureAu(mpi, ConfigurationUtil.fromArgs("a", "c"), auid);
Configuration auConfig = au.getConfiguration();
assertEquals("c", auConfig.get("a"));
assertEquals(1, auConfig.keySet().size());
// verify turns RuntimeException into ArchivalUnit.ConfigurationException
mpi.setCfgEx(new ArchivalUnit.ConfigurationException("should be thrown"));
try {
mgr.configureAu(mpi, config, auid);
fail("configureAU should have thrown ArchivalUnit.ConfigurationException");
} catch (ArchivalUnit.ConfigurationException e) {
}
mpi.setRtEx(new ExpectedRuntimeException("Ok if in log"));
try {
mgr.configureAu(mpi, config, auid);
fail("configureAU should have thrown ArchivalUnit.ConfigurationException");
} catch (ArchivalUnit.ConfigurationException e) {
// this is what's expected
} catch (RuntimeException e) {
fail("createAU threw RuntimeException");
}
}
static class ThrowingMockPlugin extends MockPlugin {
RuntimeException rtEx;
ArchivalUnit.ConfigurationException cfgEx;;
public void setRtEx(RuntimeException rtEx) {
this.rtEx = rtEx;
}
public void setCfgEx(ArchivalUnit.ConfigurationException cfgEx) {
this.cfgEx = cfgEx;
}
public ArchivalUnit createAu(Configuration config)
throws ArchivalUnit.ConfigurationException {
if (rtEx != null) {
throw rtEx;
} else if (cfgEx != null) {
throw cfgEx;
} else {
return super.createAu(config);
}
}
public ArchivalUnit configureAu(Configuration config, ArchivalUnit au)
throws ArchivalUnit.ConfigurationException {
if (rtEx != null) {
throw rtEx;
} else if (cfgEx != null) {
throw cfgEx;
} else {
return super.configureAu(config, au);
}
}
}
public void testFindCus() throws Exception {
String url = "http://foo.bar/";
String lower = "abc";
String upper = "xyz";
doConfig();
MockPlugin mpi = (MockPlugin)mgr.getPlugin(mockPlugKey);
// make a PollSpec with info from a manually created CUS, which should
// match one of the registered AUs
CachedUrlSet protoCus = makeCus(mpi, mauauid1, url, lower, upper);
PollSpec ps1 = new PollSpec(protoCus);
// verify PluginManager can make a CUS for the PollSpec
CachedUrlSet cus = mgr.findCachedUrlSet(ps1);
assertNotNull(cus);
// verify the CUS's CUSS
CachedUrlSetSpec cuss = cus.getSpec();
assertEquals(url, cuss.getUrl());
RangeCachedUrlSetSpec rcuss = (RangeCachedUrlSetSpec)cuss;
assertEquals(lower, rcuss.getLowerBound());
assertEquals(upper, rcuss.getUpperBound());
assertEquals(mauauid1, cus.getArchivalUnit().getAuId());
// can't test protoCus.getArchivalUnit() .equals( cus.getArchivalUnit() )
// as we made a fake mock one to build PollSpec, and PluginManager will
// have created & configured a real mock one.
CachedUrlSet protoAuCus = makeAuCus(mpi, mauauid1);
PollSpec ps2 = new PollSpec(protoAuCus);
CachedUrlSet aucus = mgr.findCachedUrlSet(ps2);
assertNotNull(aucus);
CachedUrlSetSpec aucuss = aucus.getSpec();
assertTrue(aucuss instanceof AuCachedUrlSetSpec);
}
public void testFindSingleNodeCus() throws Exception {
String url = "http://foo.bar/";
String lower = PollSpec.SINGLE_NODE_LWRBOUND;
doConfig();
MockPlugin mpi = (MockPlugin)mgr.getPlugin(mockPlugKey);
// make a PollSpec with info from a manually created CUS, which should
// match one of the registered AUs
CachedUrlSet protoCus = makeCus(mpi, mauauid1, url, lower, null);
PollSpec ps1 = new PollSpec(protoCus);
// verify PluginManager can make a CUS for the PollSpec
CachedUrlSet cus = mgr.findCachedUrlSet(ps1);
assertNotNull(cus);
// verify the CUS's CUSS
CachedUrlSetSpec cuss = cus.getSpec();
assertTrue(cuss instanceof SingleNodeCachedUrlSetSpec);
assertEquals(url, cuss.getUrl());
}
public void testFindMostRecentCachedUrl() throws Exception {
String prefix = "http://foo.bar/";
String url1 = "http://foo.bar/baz";
String url2 = "http://foo.bar/not";
doConfig();
MockPlugin mpi = (MockPlugin)mgr.getPlugin(mockPlugKey);
// get the two archival units
MockArchivalUnit au1 = (MockArchivalUnit)mgr.getAuFromId(mauauid1);
ArchivalUnit au2 = mgr.getAuFromId(mauauid2);
assertNull(mgr.findMostRecentCachedUrl(url1));
CachedUrlSetSpec cuss = new MockCachedUrlSetSpec(prefix, null);
MockCachedUrlSet mcuss = new MockCachedUrlSet(au1, cuss);
mcuss.addUrl("foo", url1, true, true, null);
au1.setAuCachedUrlSet(mcuss);
CachedUrl cu = mgr.findMostRecentCachedUrl(url1);
assertNotNull(cu);
assertEquals(url1, cu.getUrl());
assertNull(mgr.findMostRecentCachedUrl(url2));
}
public void testGenerateAuId() {
Properties props = new Properties();
props.setProperty("key&1", "val=1");
props.setProperty("key2", "val 2");
props.setProperty("key.3", "val:3");
props.setProperty("key4", "val.4");
String pluginId = "org|lockss|plugin|Blah";
String actual = PluginManager.generateAuId(pluginId, props);
String expected =
pluginId+"&"+
"key%261~val%3D1&"+
"key%2E3~val%3A3&"+
"key2~val+2&"+
"key4~val%2E4";
assertEquals(expected, actual);
}
public void testConfigKeyFromAuId() {
String pluginId = "org|lockss|plugin|Blah";
String auId = "base_url~foo&volume~123";
String totalId = PluginManager.generateAuId(pluginId, auId);
String expectedStr = pluginId + "." + auId;
assertEquals(expectedStr, PluginManager.configKeyFromAuId(totalId));
}
public CachedUrlSet makeCus(Plugin plugin, String auid, String url,
String lower, String upper) {
MockArchivalUnit au = new MockArchivalUnit();
au.setAuId(auid);
au.setPlugin(plugin);
au.setPluginId(plugin.getPluginId());
CachedUrlSet cus = new MockCachedUrlSet(au,
new RangeCachedUrlSetSpec(url,
lower,
upper));
return cus;
}
public CachedUrlSet makeAuCus(Plugin plugin, String auid) {
MockArchivalUnit au = new MockArchivalUnit();
au.setAuId(auid);
au.setPlugin(plugin);
au.setPluginId(plugin.getPluginId());
CachedUrlSet cus = new MockCachedUrlSet(au, new AuCachedUrlSetSpec());
return cus;
}
private static String wkey = "org|lockss|plugin|wrapper|WrappedPlugin";
public void testWrappedAu() {
if (WrapperState.isUsingWrapping()) {
try {
mgr.startService();
String localConfig = p1a1param + MockPlugin.CONFIG_PROP_1 + "=val1\n" +
p1a1param + MockPlugin.CONFIG_PROP_2 + "=val2\n" +
p1a1param + "reserved.wrapper=true\n" +
LockssRepositoryImpl.PARAM_CACHE_LOCATION + "=" +
getTempDir().getAbsolutePath() + File.separator + "\n";
ConfigurationUtil.setCurrentConfigFromString(localConfig);
ArchivalUnit wau = (ArchivalUnit) mgr.getAuFromId(
mauauid1);
Plugin wplug = (Plugin) wau.getPlugin();
MockPlugin mock = (MockPlugin) WrapperState.getOriginal(wplug);
assertSame(mock,wplug);
MockArchivalUnit mau = (MockArchivalUnit) WrapperState.getOriginal(wau);
assertSame(mock, mau.getPlugin());
assertSame(mau,wau);
} catch (IOException e) {
fail(e.getMessage());
} catch (ClassCastException e) {
fail("WrappedArchivalUnit not found.");
}
}
}
public static Test suite() {
TestSuite suite = new TestSuite();
suite.addTestSuite(TestPluginManager.class);
return suite;
}
} |
package de.zib.gndms.model.gorfx;
import de.zib.gndms.model.common.PermissionInfo;
import de.zib.gndms.model.common.PersistentContract;
import de.zib.gndms.model.common.TimedGridResource;
import de.zib.gndms.model.gorfx.types.TaskState;
import de.zib.gndms.stuff.copy.Copier;
import de.zib.gndms.stuff.copy.CopyMode;
import de.zib.gndms.stuff.copy.Copyable;
import de.zib.gndms.stuff.mold.Mold;
import de.zib.gndms.stuff.mold.Molder;
import org.jetbrains.annotations.NotNull;
import javax.persistence.*;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.LinkedList;
import java.util.List;
@MappedSuperclass
@Copyable(CopyMode.MOLD)
public abstract class AbstractTask extends TimedGridResource {
private OfferType offerType;
private String description;
private byte[] serializedCredential;
private PersistentContract contract;
private boolean broken = false;
private TaskState state = TaskState.CREATED;
private boolean done = false;
private int progress = 0;
private int maxProgress = 100;
@Basic private Serializable orq;
@Basic private String faultString;
/**
* Payload depending on state, either task results or a detailed task failure
**/
@Basic private Serializable data;
@Basic private String wid;
private PermissionInfo permissions;
List<SubTask> subTasks = new ArrayList<SubTask>();
public void transit(final TaskState newState) {
final @NotNull TaskState goalState = newState == null ? getState() : newState;
final @NotNull TaskState transitState = getState().transit(goalState);
assert transitState != null;
setState(transitState);
}
public void fail (final @NotNull Exception e) {
setState(getState().transit(TaskState.FAILED));
setFaultString(e.getMessage());
setData(e);
setProgress(0);
}
public void finish(final Serializable result) {
setState(getState().transit(TaskState.FINISHED));
setFaultString("");
setData(result);
setProgress(maxProgress);
}
public void add ( SubTask st ) {
if( subTasks == null );
subTasks = new LinkedList<SubTask>( );
subTasks.add( st );
}
// TODO veryify "(D) this"
@SuppressWarnings({"unchecked"})
public <D> Molder<D> molder(@NotNull final Class<D> moldedClazz) {
return Mold.newMolderProxy( (Class<D>) getClass(), (D) this, moldedClazz);
}
public void mold(final @NotNull AbstractTask instance) {
instance.setId( getId() );
instance.setTerminationTime( getTerminationTime() );
instance.description = description;
instance.wid = wid;
instance.faultString = faultString;
instance.done = done;
instance.state = state;
instance.broken = broken;
instance.progress = progress;
instance.maxProgress = maxProgress;
instance.contract = Copier.copy(false, contract);
/* shallow therefore needs refresh */
instance.offerType = offerType;
instance.orq = Copier.copySerializable(orq);
instance.data = Copier.copySerializable(data);
instance.permissions = Copier.copyViaConstructor( permissions );
if (subTasks == null)
instance.subTasks = null;
else {
instance.subTasks = new LinkedList<SubTask>();
instance.subTasks.addAll(subTasks);
}
}
public void refresh(final @NotNull EntityManager em) {
if (offerType != null)
offerType = em.find(OfferType.class, offerType.getOfferTypeKey());
}
/* Nullable for testing purposes */
@ManyToOne(fetch=FetchType.EAGER) @JoinColumn(name="offerTypeKey", nullable=false, updatable=false, columnDefinition="VARCHAR")
public OfferType getOfferType() {
return offerType;
}
@Column(name="descr", nullable=false, updatable=false, columnDefinition="VARCHAR")
public String getDescription() {
return description;
}
@Column(name="cred", nullable=true, updatable=true, columnDefinition="BLOB")
@Lob
public byte[] getSerializedCredential() {
return serializedCredential;
}
/* always this.tod >= this.validity */
@Embedded
@AttributeOverrides({
@AttributeOverride(name="accepted", column=@Column(name="accepted", nullable=false, updatable=false)),
@AttributeOverride(name="deadline", column=@Column(name="deadline", nullable=true, updatable=false)),
@AttributeOverride(name="resultValidity", column=@Column(name="validity", nullable=true, updatable=false))
})
public PersistentContract getContract() {
return contract;
}
@Column(name="broken", updatable=true)
public boolean isBroken() {
return broken;
}
@Enumerated(EnumType.STRING)
@Column(name="state", nullable=false, updatable=true)
public TaskState getState() {
return state;
}
@Column(name = "done", nullable=false, updatable=true)
public boolean isDone() {
return done;
}
@Column(name = "done", nullable=false, updatable=true)
public int getProgress() {
return progress;
}
@Column(name="max_progress", nullable=false, updatable=false)
public int getMaxProgress() {
return maxProgress;
}
@Column(name="orq", nullable=false, updatable=true)
public Serializable getOrq() {
return orq;
}
@Column(name="fault", nullable=true, updatable=true, columnDefinition="VARCHAR", length=5000 )
public String getFaultString() {
return faultString;
}
@Column(name="data", nullable=true, updatable=true)
public Serializable getData() {
return data;
}
@Column(name="wid", nullable=true, updatable=false)
public String getWid() {
return wid;
}
@Embedded
public PermissionInfo getPermissions() {
return permissions;
}
@OneToMany( targetEntity=SubTask.class, cascade={CascadeType.REMOVE}, fetch=FetchType.EAGER )
public List<SubTask> getSubTasks() {
return subTasks;
}
public void setOfferType( OfferType offerType ) {
this.offerType = offerType;
}
public void setDescription( String description ) {
this.description = description;
}
public void setSerializedCredential( byte[] serializedCredential ) {
this.serializedCredential = serializedCredential;
}
public void setContract( PersistentContract contract ) {
this.contract = contract;
}
public void setBroken( boolean broken ) {
this.broken = broken;
}
public void setState( TaskState state ) {
this.state = state;
}
public void setDone( boolean done ) {
this.done = done;
}
public void setProgress( int progress ) {
this.progress = progress;
}
public void setMaxProgress( int maxProgress ) {
this.maxProgress = maxProgress;
}
public void setOrq( Serializable orq ) {
this.orq = orq;
}
public void setFaultString( String faultString ) {
this.faultString = faultString;
}
public void setData( Serializable data ) {
this.data = data;
}
public void setWid( String wid ) {
this.wid = wid;
}
public void setPermissions( PermissionInfo permissions ) {
this.permissions = permissions;
}
public void setSubTasks( List<SubTask> subTasks ) {
this.subTasks = subTasks;
}
} |
package jme3test.network;
import com.jme3.network.Client;
import com.jme3.network.Message;
import com.jme3.network.MessageConnection;
import com.jme3.network.MessageListener;
import com.jme3.network.Network;
import com.jme3.network.Server;
import com.jme3.network.serializing.Serializable;
import com.jme3.network.serializing.Serializer;
import java.io.IOException;
public class TestThroughput implements MessageListener<MessageConnection> { //extends MessageAdapter {
private static long lastTime = -1;
private static long counter = 0;
private static long total = 0;
private static Client client;
// Change this flag to test UDP instead of TCP
private static boolean testReliable = true;
private boolean isOnServer;
public TestThroughput( boolean isOnServer ) {
this.isOnServer = isOnServer;
}
@Override
public void messageReceived( MessageConnection source, Message msg){
if( !isOnServer ) {
// It's local to the client so we got it back
counter++;
total++;
long time = System.currentTimeMillis();
//System.out.println( "total:" + total + " counter:" + counter + " lastTime:" + lastTime + " time:" + time );
if( lastTime < 0 ) {
lastTime = time;
} else if( time - lastTime > 1000 ) {
long delta = time - lastTime;
double scale = delta / 1000.0;
double pps = counter / scale;
System.out.println( "messages per second:" + pps + " total messages:" + total );
counter = 0;
lastTime = time;
}
} else {
if( source == null ) {
System.out.println( "Received a message from a not fully connected source, msg:"+ msg );
} else {
//System.out.println( "sending:" + msg + " back to client:" + source );
// The 'reliable' flag is transient and the server doesn't
// (yet) reset this value for us.
((com.jme3.network.message.Message)msg).setReliable(testReliable);
source.send(msg);
}
}
}
public static void main(String[] args) throws IOException, InterruptedException{
Serializer.registerClass(TestMessage.class);
Server server = Network.createServer( 5110 );
server.start();
Client client = Network.connectToServer( "localhost", 5110, 5000 );
client.start();
client.addMessageListener(new TestThroughput(false), TestMessage.class);
server.addMessageListener(new TestThroughput(true), TestMessage.class);
Thread.sleep(1);
TestMessage test = new TestMessage();
// for( int i = 0; i < 10; i++ ) {
while( true ) {
//System.out.println( "sending." );
client.send(test);
}
//Thread.sleep(5000);
}
@Serializable
public static class TestMessage extends com.jme3.network.message.Message {
public TestMessage(){
setReliable(testReliable);
}
}
} |
package org.neo4j.helpers;
/**
* Utility to handle pairs of objects.
*/
public final class Pair<T1, T2>
{
private final T1 first;
private final T2 other;
public Pair( T1 first, T2 other )
{
this.first = first;
this.other = other;
}
public T1 first()
{
return first;
}
public T2 other()
{
return other;
}
@Override
public String toString()
{
return "(" + first + ", " + other + ")";
}
@Override
public int hashCode()
{
return ( 31 * hashCode( first ) ) | hashCode( other );
}
@SuppressWarnings( "unchecked" )
@Override
public boolean equals( Object obj )
{
if ( this == obj ) return true;
if ( obj instanceof Pair )
{
Pair that = (Pair) obj;
return equals( this.first, that.first ) && equals( this.other, that.other );
}
return false;
}
private static int hashCode( Object obj )
{
return obj == null ? 0 : obj.hashCode();
}
private static boolean equals( Object obj1, Object obj2 )
{
return ( obj1 == obj2 ) || ( obj1 != null && obj1.equals( obj2 ) );
}
} |
package org.pcap4j.util;
import static java.nio.ByteOrder.*;
import java.net.Inet4Address;
import java.net.Inet6Address;
import java.net.InetAddress;
import java.net.UnknownHostException;
import java.nio.ByteOrder;
import java.util.regex.Pattern;
/**
* @author Kaito Yamada
* @since pcap4j 0.9.1
*/
public final class ByteArrays {
public static final int BYTE_SIZE_IN_BYTES = 1;
public static final int SHORT_SIZE_IN_BYTES = 2;
public static final int INT_SIZE_IN_BYTES = 4;
public static final int LONG_SIZE_IN_BYTES = 8;
public static final int INET4_ADDRESS_SIZE_IN_BYTES = 4;
public static final int INET6_ADDRESS_SIZE_IN_BYTES = 16;
public static final int BYTE_SIZE_IN_BITS = 8;
private static final Pattern NO_SEPARATOR_HEX_STRING_PATTERN
= Pattern.compile("\\A([0-9a-fA-F][0-9a-fA-F])+\\z");
private ByteArrays() { throw new AssertionError(); }
/**
*
* @param array
* @return a new array containing specified array's elements in reverse order.
*/
public static byte[] reverse(byte[] array) {
byte[] rarray = new byte[array.length];
for (int i = 0; i < array.length; i++) {
rarray[i] = array[array.length - i - 1];
}
return rarray;
}
/**
*
* @param array
* @param offset
* @return byte value.
*/
public static byte getByte(byte[] array, int offset) {
validateBounds(array, offset, BYTE_SIZE_IN_BYTES);
return array[offset];
}
/**
*
* @param value
* @return byte array
*/
public static byte[] toByteArray(byte value) {
return new byte[] { value };
}
/**
*
* @param value
* @param separator
* @return hex string
*/
public static String toHexString(byte value, String separator) {
return toHexString(toByteArray(value), separator);
}
/**
*
* @param array
* @param offset
* @return short value
*/
public static short getShort(byte[] array, int offset) {
return getShort(array, offset, ByteOrder.BIG_ENDIAN);
}
/**
*
* @param array
* @param offset
* @param bo
* @return short value
*/
public static short getShort(byte[] array, int offset, ByteOrder bo) {
validateBounds(array, offset, SHORT_SIZE_IN_BYTES);
if (bo == null) {
throw new NullPointerException(" bo: " + bo);
}
if (bo.equals(LITTLE_ENDIAN)) {
return (short)(
(( array[offset + 1]) << (BYTE_SIZE_IN_BITS * 1))
| ((0xFF & array[offset ]) )
);
}
else {
return (short)(
(( array[offset ]) << (BYTE_SIZE_IN_BITS * 1))
| ((0xFF & array[offset + 1]) )
);
}
}
/**
*
* @param value
* @return byte array
*/
public static byte[] toByteArray(short value) {
return toByteArray(value, ByteOrder.BIG_ENDIAN);
}
/**
*
* @param value
* @param bo
* @return byte array
*/
public static byte[] toByteArray(short value, ByteOrder bo) {
if (bo.equals(LITTLE_ENDIAN)) {
return new byte[] {
(byte)(value ),
(byte)(value >> BYTE_SIZE_IN_BITS * 1)
};
}
else {
return new byte[] {
(byte)(value >> BYTE_SIZE_IN_BITS * 1),
(byte)(value )
};
}
}
/**
*
* @param value
* @param separator
* @return hex string
*/
public static String toHexString(short value, String separator) {
return toHexString(value, separator, ByteOrder.BIG_ENDIAN);
}
/**
*
* @param value
* @param separator
* @param bo
* @return hex string
*/
public static String toHexString(short value, String separator, ByteOrder bo) {
return toHexString(toByteArray(value, bo), separator);
}
/**
*
* @param array
* @param offset
* @return int value.
*/
public static int getInt(byte[] array, int offset) {
return getInt(array, offset, ByteOrder.BIG_ENDIAN);
}
/**
*
* @param array
* @param offset
* @param bo
* @return int value.
*/
public static int getInt(byte[] array, int offset, ByteOrder bo) {
validateBounds(array, offset, INT_SIZE_IN_BYTES);
if (bo == null) {
throw new NullPointerException(" bo: " + bo);
}
if (bo.equals(LITTLE_ENDIAN)) {
return (( array[offset + 3]) << (BYTE_SIZE_IN_BITS * 3))
| ((0xFF & array[offset + 2]) << (BYTE_SIZE_IN_BITS * 2))
| ((0xFF & array[offset + 1]) << (BYTE_SIZE_IN_BITS * 1))
| ((0xFF & array[offset ]) );
}
else {
return (( array[offset ]) << (BYTE_SIZE_IN_BITS * 3))
| ((0xFF & array[offset + 1]) << (BYTE_SIZE_IN_BITS * 2))
| ((0xFF & array[offset + 2]) << (BYTE_SIZE_IN_BITS * 1))
| ((0xFF & array[offset + 3]) );
}
}
/**
* @param array
* @param offset
* @param length
* @return int value.
*/
public static int getInt(byte[] array, int offset, int length) {
return getInt(array, offset, length, ByteOrder.BIG_ENDIAN);
}
/**
* @param array
* @param offset
* @param length
* @param bo
* @return int value.
*/
public static int getInt(byte[] array, int offset, int length, ByteOrder bo) {
validateBounds(array, offset, length);
if (length > INT_SIZE_IN_BYTES) {
StringBuilder sb
= new StringBuilder(30)
.append("length must be equal or less than ")
.append(INT_SIZE_IN_BYTES)
.append(", but is: ")
.append(length);
throw new IllegalArgumentException(sb.toString());
}
if (bo == null) {
throw new NullPointerException(" bo: " + bo);
}
int value = 0;
if (bo.equals(LITTLE_ENDIAN)) {
for (int i = offset + length - 1; i >= offset; i
value <<= BYTE_SIZE_IN_BITS;
value |= 0xFF & array[i];
}
}
else {
for (int i = offset; i < offset + length; i++) {
value <<= BYTE_SIZE_IN_BITS;
value |= 0xFF & array[i];
}
}
return value;
}
/**
*
* @param value
* @return byte array
*/
public static byte[] toByteArray(int value) {
return toByteArray(value, ByteOrder.BIG_ENDIAN);
}
/**
*
* @param value
* @param bo
* @return byte array
*/
public static byte[] toByteArray(int value, ByteOrder bo) {
if (bo.equals(LITTLE_ENDIAN)) {
return new byte[] {
(byte)(value ),
(byte)(value >> BYTE_SIZE_IN_BITS * 1),
(byte)(value >> BYTE_SIZE_IN_BITS * 2),
(byte)(value >> BYTE_SIZE_IN_BITS * 3),
};
}
else {
return new byte[] {
(byte)(value >> BYTE_SIZE_IN_BITS * 3),
(byte)(value >> BYTE_SIZE_IN_BITS * 2),
(byte)(value >> BYTE_SIZE_IN_BITS * 1),
(byte)(value )
};
}
}
/**
* @param value
* @param length
* @return byte array
*/
public static byte[] toByteArray(int value, int length) {
return toByteArray(value, length, ByteOrder.BIG_ENDIAN);
}
/**
* @param value
* @param length
* @param bo
* @return byte array
*/
public static byte[] toByteArray(int value, int length, ByteOrder bo) {
if (length > INT_SIZE_IN_BYTES) {
StringBuilder sb
= new StringBuilder(30)
.append("length must be equal or less than ")
.append(INT_SIZE_IN_BYTES)
.append(", but is: ")
.append(length);
throw new IllegalArgumentException(sb.toString());
}
byte[] arr = new byte[length];
if (bo.equals(LITTLE_ENDIAN)) {
for (int i = 0; i < length; i++) {
arr[length - i - 1] = (byte)(value >> BYTE_SIZE_IN_BITS * i);
}
}
else {
for (int i = 0; i < length; i++) {
arr[i] = (byte)(value >> BYTE_SIZE_IN_BITS * i);
}
}
return arr;
}
/**
*
* @param value
* @param separator
* @return hex string
*/
public static String toHexString(int value, String separator) {
return toHexString(value, separator, ByteOrder.BIG_ENDIAN);
}
/**
*
* @param value
* @param separator
* @param bo
* @return hex string
*/
public static String toHexString(int value, String separator, ByteOrder bo) {
return toHexString(toByteArray(value, bo), separator);
}
/**
*
* @param array
* @param offset
* @return long value
*/
public static long getLong(byte[] array, int offset) {
return getLong(array, offset, ByteOrder.BIG_ENDIAN);
}
/**
*
* @param array
* @param offset
* @param bo
* @return long value
*/
public static long getLong(byte[] array, int offset, ByteOrder bo) {
validateBounds(array, offset, LONG_SIZE_IN_BYTES);
if (bo == null) {
throw new NullPointerException(" bo: " + bo);
}
if (bo.equals(LITTLE_ENDIAN)) {
return (( (long)array[offset + 7]) << (BYTE_SIZE_IN_BITS * 7))
| ((0xFFL & array[offset + 6]) << (BYTE_SIZE_IN_BITS * 6))
| ((0xFFL & array[offset + 5]) << (BYTE_SIZE_IN_BITS * 5))
| ((0xFFL & array[offset + 4]) << (BYTE_SIZE_IN_BITS * 4))
| ((0xFFL & array[offset + 3]) << (BYTE_SIZE_IN_BITS * 3))
| ((0xFFL & array[offset + 2]) << (BYTE_SIZE_IN_BITS * 2))
| ((0xFFL & array[offset + 1]) << (BYTE_SIZE_IN_BITS * 1))
| ((0xFFL & array[offset ]) );
}
else {
return (( (long)array[offset ]) << (BYTE_SIZE_IN_BITS * 7))
| ((0xFFL & array[offset + 1]) << (BYTE_SIZE_IN_BITS * 6))
| ((0xFFL & array[offset + 2]) << (BYTE_SIZE_IN_BITS * 5))
| ((0xFFL & array[offset + 3]) << (BYTE_SIZE_IN_BITS * 4))
| ((0xFFL & array[offset + 4]) << (BYTE_SIZE_IN_BITS * 3))
| ((0xFFL & array[offset + 5]) << (BYTE_SIZE_IN_BITS * 2))
| ((0xFFL & array[offset + 6]) << (BYTE_SIZE_IN_BITS * 1))
| ((0xFFL & array[offset + 7]) );
}
}
/**
*
* @param value
* @return byte array
*/
public static byte[] toByteArray(long value) {
return toByteArray(value, ByteOrder.BIG_ENDIAN);
}
/**
*
* @param value
* @param bo
* @return byte array
*/
public static byte[] toByteArray(long value, ByteOrder bo) {
if (bo.equals(LITTLE_ENDIAN)) {
return new byte[] {
(byte)(value ),
(byte)(value >> BYTE_SIZE_IN_BITS * 1),
(byte)(value >> BYTE_SIZE_IN_BITS * 2),
(byte)(value >> BYTE_SIZE_IN_BITS * 3),
(byte)(value >> BYTE_SIZE_IN_BITS * 4),
(byte)(value >> BYTE_SIZE_IN_BITS * 5),
(byte)(value >> BYTE_SIZE_IN_BITS * 6),
(byte)(value >> BYTE_SIZE_IN_BITS * 7)
};
}
else {
return new byte[] {
(byte)(value >> BYTE_SIZE_IN_BITS * 7),
(byte)(value >> BYTE_SIZE_IN_BITS * 6),
(byte)(value >> BYTE_SIZE_IN_BITS * 5),
(byte)(value >> BYTE_SIZE_IN_BITS * 4),
(byte)(value >> BYTE_SIZE_IN_BITS * 3),
(byte)(value >> BYTE_SIZE_IN_BITS * 2),
(byte)(value >> BYTE_SIZE_IN_BITS * 1),
(byte)(value )
};
}
}
/**
*
* @param value
* @param separator
* @return hex string
*/
public static String toHexString(long value, String separator) {
return toHexString(value, separator, ByteOrder.BIG_ENDIAN);
}
/**
*
* @param value
* @param separator
* @param bo
* @return hex string
*/
public static String toHexString(long value, String separator, ByteOrder bo) {
return toHexString(toByteArray(value, bo), separator);
}
/**
*
* @param array
* @param offset
* @return a new MacAddress object.
*/
public static MacAddress getMacAddress(byte[] array, int offset) {
return getMacAddress(array, offset, ByteOrder.BIG_ENDIAN);
}
/**
*
* @param array
* @param offset
* @param bo
* @return a new MacAddress object.
*/
public static MacAddress getMacAddress(
byte[] array, int offset, ByteOrder bo
) {
validateBounds(array, offset, MacAddress.SIZE_IN_BYTES);
if (bo == null) {
throw new NullPointerException(" bo: " + bo);
}
if (bo.equals(LITTLE_ENDIAN)) {
return MacAddress.getByAddress(
reverse(getSubArray(array, offset, MacAddress.SIZE_IN_BYTES))
);
}
else {
return MacAddress.getByAddress(
getSubArray(array, offset, MacAddress.SIZE_IN_BYTES)
);
}
}
/**
*
* @param value
* @return byte array
*/
public static byte[] toByteArray(MacAddress value) {
return toByteArray(value, ByteOrder.BIG_ENDIAN);
}
/**
*
* @param value
* @param bo
* @return byte array
*/
public static byte[] toByteArray(MacAddress value, ByteOrder bo) {
if (bo.equals(LITTLE_ENDIAN)) {
return reverse(value.getAddress());
}
else {
return value.getAddress();
}
}
/**
*
* @param array
* @param offset
* @param length
* @return a new LinkLayerAddress object.
*/
public static LinkLayerAddress getLinkLayerAddress(byte[] array, int offset, int length) {
return getLinkLayerAddress(array, offset, length, ByteOrder.BIG_ENDIAN);
}
/**
*
* @param array
* @param offset
* @param length
* @param bo
* @return a new LinkLayerAddress object.
*/
public static LinkLayerAddress getLinkLayerAddress(
byte[] array, int offset, int length, ByteOrder bo
) {
validateBounds(array, offset, length);
if (bo == null) {
throw new NullPointerException(" bo: " + bo);
}
if (bo.equals(LITTLE_ENDIAN)) {
return LinkLayerAddress.getByAddress(
reverse(getSubArray(array, offset, length))
);
}
else {
return LinkLayerAddress.getByAddress(
getSubArray(array, offset, length)
);
}
}
/**
*
* @param value
* @return byte array
*/
public static byte[] toByteArray(LinkLayerAddress value) {
return toByteArray(value, ByteOrder.BIG_ENDIAN);
}
/**
*
* @param value
* @param bo
* @return byte array
*/
public static byte[] toByteArray(LinkLayerAddress value, ByteOrder bo) {
if (bo.equals(LITTLE_ENDIAN)) {
return reverse(value.getAddress());
}
else {
return value.getAddress();
}
}
/**
*
* @param array
* @param offset
* @return a new Inet4Address object.
*/
public static Inet4Address getInet4Address(byte[] array, int offset) {
return getInet4Address(array, offset, ByteOrder.BIG_ENDIAN);
}
/**
*
* @param array
* @param offset
* @param bo
* @return a new Inet4Address object.
*/
public static Inet4Address getInet4Address(
byte[] array, int offset, ByteOrder bo
) {
validateBounds(array, offset, INET4_ADDRESS_SIZE_IN_BYTES);
if (bo == null) {
throw new NullPointerException(" bo: " + bo);
}
try {
if (bo.equals(LITTLE_ENDIAN)) {
return (Inet4Address)InetAddress.getByAddress(
reverse(
getSubArray(
array,
offset,
INET4_ADDRESS_SIZE_IN_BYTES
)
)
);
}
else {
return (Inet4Address)InetAddress.getByAddress(
getSubArray(
array,
offset,
INET4_ADDRESS_SIZE_IN_BYTES
)
);
}
} catch (UnknownHostException e) {
throw new AssertionError(e);
}
}
/**
*
* @param array
* @param offset
* @return a new Inet6Address object.
*/
public static Inet6Address getInet6Address(byte[] array, int offset) {
return getInet6Address(array, offset, ByteOrder.BIG_ENDIAN);
}
/**
*
* @param array
* @param offset
* @param bo
* @return a new Inet6Address object.
*/
public static Inet6Address getInet6Address(
byte[] array, int offset, ByteOrder bo
) {
validateBounds(array, offset, INET6_ADDRESS_SIZE_IN_BYTES);
if (bo == null) {
throw new NullPointerException(" bo: " + bo);
}
try {
if (bo.equals(LITTLE_ENDIAN)) {
return (Inet6Address)InetAddress.getByAddress(
reverse(
getSubArray(
array,
offset,
INET6_ADDRESS_SIZE_IN_BYTES
)
)
);
}
else {
return (Inet6Address)InetAddress.getByAddress(
getSubArray(
array,
offset,
INET6_ADDRESS_SIZE_IN_BYTES
)
);
}
} catch (UnknownHostException e) {
throw new AssertionError(e);
}
}
/**
*
* @param value
* @return byte array
*/
public static byte[] toByteArray(InetAddress value) {
return toByteArray(value, ByteOrder.BIG_ENDIAN);
}
/**
*
* @param value
* @param bo
* @return byte array
*/
public static byte[] toByteArray(InetAddress value, ByteOrder bo) {
if (bo.equals(LITTLE_ENDIAN)) {
return reverse(value.getAddress());
}
else {
return value.getAddress();
}
}
/**
*
* @param array
* @param offset
* @param length
* @return sub array
*/
public static byte[] getSubArray(byte[] array, int offset, int length) {
validateBounds(array, offset, length);
byte[] subArray = new byte[length];
System.arraycopy(array, offset, subArray, 0, length);
return subArray;
}
/**
*
* @param array
* @param offset
* @return sub array
*/
public static byte[] getSubArray(byte[] array, int offset) {
return getSubArray(array, offset, array.length - offset);
}
/**
*
* @param array
* @param separator
* @return hex string
*/
public static String toHexString(byte[] array, String separator) {
StringBuffer buf = new StringBuffer();
for (int i = 0; i < array.length; i++) {
buf.append(String.format("%02x", array[i]));
buf.append(separator);
}
if (separator.length() != 0 && array.length > 0) {
buf.delete(buf.lastIndexOf(separator), buf.length());
}
return buf.toString();
}
/**
*
* @param array
* @param separator
* @param offset
* @param length
* @return hex string
*/
public static String toHexString(
byte[] array, String separator, int offset, int length
) {
validateBounds(array, offset, length);
StringBuffer buf = new StringBuffer();
for (int i = offset; i < offset + length; i++) {
buf.append(String.format("%02x", array[i]));
buf.append(separator);
}
if (separator.length() != 0 && length > 0) {
buf.delete(buf.lastIndexOf(separator), buf.length());
}
return buf.toString();
}
/**
*
* @param data
* @return checksum
*/
public static short calcChecksum(byte[] data) {
int sum = 0;
for (int i = 0; i < data.length; i += SHORT_SIZE_IN_BYTES) {
sum += (0xFFFF) & getShort(data, i);
}
sum
= (0xFFFF & sum)
+ ((0xFFFF0000 & sum) >> (BYTE_SIZE_IN_BITS * SHORT_SIZE_IN_BYTES));
sum
= (0xFFFF & sum)
+ ((0xFFFF0000 & sum) >> (BYTE_SIZE_IN_BITS * SHORT_SIZE_IN_BYTES));
return (short)(0xFFFF & ~sum);
}
/**
*
* @param hexString
* @param separator
* @return a new byte array.
*/
public static byte[] parseByteArray(String hexString, String separator) {
if (
hexString == null
|| separator == null
) {
StringBuilder sb = new StringBuilder();
sb.append("hexString: ")
.append(hexString)
.append(" separator: ")
.append(separator);
throw new NullPointerException(sb.toString());
}
if (hexString.startsWith("0x")) {
hexString = hexString.substring(2);
}
String noSeparatorHexString;
if (separator.length() == 0) {
if (
!NO_SEPARATOR_HEX_STRING_PATTERN.matcher(hexString).matches()
) {
StringBuilder sb = new StringBuilder(100);
sb.append("invalid hex string(")
.append(hexString)
.append("), not match pattern(")
.append(NO_SEPARATOR_HEX_STRING_PATTERN.pattern())
.append(")");
throw new IllegalArgumentException(sb.toString());
}
noSeparatorHexString = hexString;
}
else {
StringBuilder patternSb = new StringBuilder(60);
patternSb.append("\\A[0-9a-fA-F][0-9a-fA-F](")
.append(Pattern.quote(separator))
.append("[0-9a-fA-F][0-9a-fA-F])*\\z");
String patternString = patternSb.toString();
Pattern pattern = Pattern.compile(patternString);
if (!pattern.matcher(hexString).matches()) {
StringBuilder sb = new StringBuilder(150);
sb.append("invalid hex string(")
.append(hexString)
.append("), not match pattern(")
.append(patternString)
.append(")");
throw new IllegalArgumentException(sb.toString());
}
noSeparatorHexString
= hexString.replaceAll(Pattern.quote(separator), "");
}
int arrayLength = noSeparatorHexString.length() / 2;
byte[] array = new byte[arrayLength];
for (int i = 0; i < arrayLength; i++) {
array[i]
= (byte)Integer.parseInt(
noSeparatorHexString.substring(i * 2, i * 2 + 2),
16
);
}
return array;
}
/**
*
* @param array
* @return a clone of array
*/
public static byte[] clone(byte[] array) {
byte[] clone = new byte[array.length];
System.arraycopy(array, 0, clone, 0, array.length);
return clone;
}
public static void validateBounds(byte[] arr, int offset, int len) {
if (arr == null) {
throw new NullPointerException("arr must not be null.");
}
if (arr.length == 0) {
throw new IllegalArgumentException("arr is empty.");
}
if (len == 0) {
throw new IllegalArgumentException("length is zero.");
}
if (offset < 0 || len < 0 || offset + len > arr.length) {
StringBuilder sb = new StringBuilder(100);
sb.append("arr.length: ")
.append(arr.length)
.append(", offset: ")
.append(offset)
.append(", len: ")
.append(len);
throw new ArrayIndexOutOfBoundsException(sb.toString());
}
}
} |
/**
* @author cdr
*/
package com.intellij.unscramble;
import com.intellij.execution.ExecutionManager;
import com.intellij.execution.ExecutionRegistry;
import com.intellij.execution.impl.ConsoleViewImpl;
import com.intellij.execution.runners.JavaProgramRunner;
import com.intellij.execution.ui.*;
import com.intellij.ide.util.PropertiesComponent;
import com.intellij.openapi.actionSystem.*;
import com.intellij.openapi.application.ApplicationManager;
import com.intellij.openapi.command.CommandProcessor;
import com.intellij.openapi.editor.Document;
import com.intellij.openapi.editor.Editor;
import com.intellij.openapi.editor.EditorFactory;
import com.intellij.openapi.editor.EditorSettings;
import com.intellij.openapi.fileChooser.FileChooser;
import com.intellij.openapi.fileChooser.FileChooserDescriptor;
import com.intellij.openapi.fileChooser.FileChooserDescriptorFactory;
import com.intellij.openapi.project.Project;
import com.intellij.openapi.ui.DialogWrapper;
import com.intellij.openapi.util.Comparing;
import com.intellij.openapi.util.io.FileUtil;
import com.intellij.openapi.util.text.StringUtil;
import com.intellij.openapi.vfs.VirtualFile;
import com.intellij.ui.GuiUtils;
import com.intellij.ui.TextFieldWithHistory;
import com.intellij.util.ArrayUtil;
import javax.swing.*;
import java.awt.*;
import java.awt.datatransfer.DataFlavor;
import java.awt.datatransfer.Transferable;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.util.ArrayList;
import java.util.List;
public class UnscrambleDialog extends DialogWrapper{
private static final String PROPERTY_LOG_FILE_HISTORY_URLS = "UNSCRAMBLE_LOG_FILE_URL";
private static final String PROPERTY_LOG_FILE_LAST_URL = "UNSCRAMBLE_LOG_FILE_LAST_URL";
private static final String PROPERTY_UNSCRAMBLER_NAME_USED = "UNSCRAMBLER_NAME_USED";
private final Project myProject;
private JPanel myEditorPanel;
private JPanel myLogFileChooserPanel;
private JComboBox myUnscrambleChooser;
private JPanel myPanel;
private Editor myEditor;
private TextFieldWithHistory myLogFile;
private JCheckBox myUseUnscrambler;
private JPanel myUnscramblePanel;
public UnscrambleDialog(Project project) {
super(false);
myProject = project;
populateRegisteredUnscramblerList();
myUnscrambleChooser.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
UnscrambleSupport unscrambleSupport = getSelectedUnscrambler();
GuiUtils.enableChildren(myLogFileChooserPanel, unscrambleSupport != null, null);
}
});
myUseUnscrambler.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
useUnscramblerChanged();
}
});
createLogFileChooser();
createEditor();
reset();
setTitle("Analyze Stacktrace");
init();
}
private void useUnscramblerChanged() {
boolean selected = myUseUnscrambler.isSelected();
GuiUtils.enableChildren(myUnscramblePanel, selected, new JComponent[]{myUseUnscrambler});
}
private void reset() {
final List<String> savedUrls = getSavedLogFileUrls();
myLogFile.setHistory(savedUrls);
String lastUrl = getLastUsedLogUrl();
if (lastUrl == null && savedUrls.size() != 0) {
lastUrl = savedUrls.get(savedUrls.size() - 1);
}
if (lastUrl != null) {
myLogFile.setText(lastUrl);
myLogFile.setSelectedItem(lastUrl);
}
final UnscrambleSupport selectedUnscrambler = getSavedUnscrambler();
final int count = myUnscrambleChooser.getItemCount();
int index = 0;
if (selectedUnscrambler != null) {
for (int i = 0; i < count; i++) {
final UnscrambleSupport unscrambleSupport = (UnscrambleSupport)myUnscrambleChooser.getItemAt(i);
if (unscrambleSupport != null && Comparing.strEqual(unscrambleSupport.getPresentableName(), selectedUnscrambler.getPresentableName())) {
index = i;
break;
}
}
}
if (count > 0) {
myUseUnscrambler.setEnabled(true);
myUnscrambleChooser.setSelectedIndex(index);
myUseUnscrambler.setSelected(selectedUnscrambler != null);
}
else {
myUseUnscrambler.setEnabled(false);
}
useUnscramblerChanged();
pasteTextFromClipboard();
}
public static String getLastUsedLogUrl() {
String lastUrl = PropertiesComponent.getInstance().getValue(PROPERTY_LOG_FILE_LAST_URL);
return lastUrl;
}
public static UnscrambleSupport getSavedUnscrambler() {
final List<UnscrambleSupport> registeredUnscramblers = getRegisteredUnscramblers();
final String savedUnscramblerName = PropertiesComponent.getInstance().getValue(PROPERTY_UNSCRAMBLER_NAME_USED);
UnscrambleSupport selectedUnscrambler = null;
for (int i = 0; i < registeredUnscramblers.size(); i++) {
final UnscrambleSupport unscrambleSupport = registeredUnscramblers.get(i);
if (Comparing.strEqual(unscrambleSupport.getPresentableName(), savedUnscramblerName)) {
selectedUnscrambler = unscrambleSupport;
}
}
return selectedUnscrambler;
}
public static List<String> getSavedLogFileUrls() {
final List<String> res = new ArrayList<String>();
final String savedUrl = PropertiesComponent.getInstance().getValue(PROPERTY_LOG_FILE_HISTORY_URLS);
final String[] strings = savedUrl == null ? ArrayUtil.EMPTY_STRING_ARRAY : savedUrl.split(":::");
for (int i = 0; i != strings.length; ++i) {
res.add(strings[i]);
}
return res;
}
private void pasteTextFromClipboard() {
String text = getTextInClipboard();
if (text != null) {
final String text1 = text;
Runnable runnable = new Runnable() {
public void run() {
ApplicationManager.getApplication().runWriteAction(new Runnable() {
public void run() {
myEditor.getDocument().insertString(0, StringUtil.convertLineSeparators(text1));
}
});
}
};
CommandProcessor.getInstance().executeCommand(myProject, runnable, "", this);
}
}
public static String getTextInClipboard() {
String text = null;
try {
Transferable contents = Toolkit.getDefaultToolkit().getSystemClipboard().getContents(UnscrambleDialog.class);
if (contents != null) {
text = (String)contents.getTransferData(DataFlavor.stringFlavor);
}
}
catch (Exception ex) {
}
return text;
}
private UnscrambleSupport getSelectedUnscrambler() {
if (!myUseUnscrambler.isSelected()) return null;
return (UnscrambleSupport)myUnscrambleChooser.getSelectedItem();
}
private void createEditor() {
EditorFactory editorFactory = EditorFactory.getInstance();
Document document = editorFactory.createDocument("");
myEditor = editorFactory.createEditor(document);
EditorSettings settings = myEditor.getSettings();
settings.setFoldingOutlineShown(false);
settings.setLineMarkerAreaShown(false);
settings.setLineNumbersShown(false);
settings.setRightMarginShown(false);
EditorPanel editorPanel = new EditorPanel(myEditor);
editorPanel.setPreferredSize(new Dimension(600, 400));
myEditorPanel.setLayout(new BorderLayout());
myEditorPanel.add(editorPanel, BorderLayout.CENTER);
}
protected Action[] createActions(){
return new Action[]{new SplitAction(), getOKAction(), getCancelAction()};
}
private void createLogFileChooser() {
myLogFile = new TextFieldWithHistory();
JPanel panel = GuiUtils.constructFieldWithBrowseButton(myLogFile, new ActionListener() {
public void actionPerformed(ActionEvent e) {
FileChooserDescriptor descriptor = FileChooserDescriptorFactory.createSingleFileNoJarsDescriptor();
VirtualFile[] files = FileChooser.chooseFiles(myLogFile, descriptor);
if (files.length != 0) {
myLogFile.setText(FileUtil.toSystemDependentName(files[files.length-1].getPath()));
}
}
});
myLogFileChooserPanel.setLayout(new BorderLayout());
myLogFileChooserPanel.add(panel, BorderLayout.CENTER);
}
private void populateRegisteredUnscramblerList() {
List<UnscrambleSupport> unscrambleComponents = getRegisteredUnscramblers();
//myUnscrambleChooser.addItem(null);
for (int i = 0; i < unscrambleComponents.size(); i++) {
final UnscrambleSupport unscrambleSupport = unscrambleComponents.get(i);
myUnscrambleChooser.addItem(unscrambleSupport);
}
myUnscrambleChooser.setRenderer(new DefaultListCellRenderer() {
public Component getListCellRendererComponent(JList list, Object value, int index, boolean isSelected, boolean cellHasFocus) {
super.getListCellRendererComponent(list, value, index, isSelected, cellHasFocus);
UnscrambleSupport unscrambleSupport = (UnscrambleSupport)value;
setText(unscrambleSupport == null ? "<Do not unscramble>" : unscrambleSupport.getPresentableName());
return this;
}
});
}
private static List<UnscrambleSupport> getRegisteredUnscramblers() {
List<UnscrambleSupport> unscrambleComponents = new ArrayList<UnscrambleSupport>();
Class[] interfaces = ApplicationManager.getApplication().getComponentInterfaces();
for (final Class anInterface : interfaces) {
Object component = ApplicationManager.getApplication().getComponent(anInterface);
if (component instanceof UnscrambleSupport) {
unscrambleComponents.add((UnscrambleSupport)component);
}
}
return unscrambleComponents;
}
protected JComponent createCenterPanel() {
return myPanel;
}
public void dispose() {
EditorFactory editorFactory = EditorFactory.getInstance();
editorFactory.releaseEditor(myEditor);
if (isOK()){
final List list = myLogFile.getHistory();
String res = null;
for (int i = 0; i < list.size(); i++) {
final String s = (String)list.get(i);
if (res == null) {
res = s;
}
else {
res = res + ":::" + s;
}
}
PropertiesComponent.getInstance().setValue(PROPERTY_LOG_FILE_HISTORY_URLS, res);
UnscrambleSupport selectedUnscrambler = getSelectedUnscrambler();
PropertiesComponent.getInstance().setValue(PROPERTY_UNSCRAMBLER_NAME_USED, selectedUnscrambler == null ? null : selectedUnscrambler.getPresentableName());
PropertiesComponent.getInstance().setValue(PROPERTY_LOG_FILE_LAST_URL, myLogFile.getText());
}
super.dispose();
}
private final class SplitAction extends AbstractAction {
public SplitAction(){
putValue(Action.NAME, "&Normalize");
putValue(DEFAULT_ACTION, Boolean.FALSE);
}
public void actionPerformed(ActionEvent e){
String text = myEditor.getDocument().getText();
// move 'at' to the line start
text = text.replaceAll("(\\S)[\\s&&[^\\n]]*at ", "$1\n at ");
text = text.replaceAll("(\\S)\\nat ", "$1\n at ");
// merge (inadvertently) splitted lines
text = text.replaceAll("\\s*\\n\\s*(([\\S&&[^a]])([\\S&&[^t]])?)", "$1");
final String newText = text;
CommandProcessor.getInstance().executeCommand(
myProject, new Runnable() {
public void run(){
ApplicationManager.getApplication().runWriteAction(new Runnable() {
public void run(){
myEditor.getDocument().replaceString(0, myEditor.getDocument().getTextLength(), newText);
}
});
}
},
"",
null
);
}
}
private static final class EditorPanel extends JPanel implements DataProvider{
private final Editor myEditor;
public EditorPanel(Editor editor) {
super(new BorderLayout());
myEditor = editor;
add(myEditor.getComponent());
}
public Object getData(String dataId) {
if (DataConstants.EDITOR.equals(dataId)) {
return myEditor;
}
return null;
}
}
protected void doOKAction() {
if (performUnscramble()) {
myLogFile.addCurrentTextToHistory();
close(OK_EXIT_CODE);
}
}
private boolean performUnscramble() {
UnscrambleSupport selectedUnscrambler = getSelectedUnscrambler();
return showUnscrambledText(selectedUnscrambler, myLogFile.getText(), myProject, myEditor.getDocument().getText());
}
static boolean showUnscrambledText(UnscrambleSupport unscrambleSupport, String logName, Project project, String textToUnscramble) {
String unscrambledTrace = unscrambleSupport == null ? textToUnscramble : unscrambleSupport.unscramble(project,textToUnscramble, logName);
if (unscrambledTrace == null) return false;
final ConsoleView consoleView = addConsole(project);
consoleView.print(unscrambledTrace+"\n", ConsoleViewContentType.ERROR_OUTPUT);
consoleView.performWhenNoDeferredOutput(
new Runnable() {
public void run() {
consoleView.scrollTo(0);
}
}
);
return true;
}
private static ConsoleView addConsole(final Project project){
final ConsoleView consoleView = new ConsoleViewImpl(project);
final JavaProgramRunner defaultRunner = ExecutionRegistry.getInstance().getDefaultRunner();
final DefaultActionGroup toolbarActions = new DefaultActionGroup();
final RunContentDescriptor descriptor =
new RunContentDescriptor(consoleView, null, new MyConsolePanel(consoleView, toolbarActions), "<Unscrambled Stacktrace>") {
public boolean isContentReuseProhibited() {
return true;
}
};
toolbarActions.add(new CloseAction(defaultRunner, descriptor, project));
ExecutionManager.getInstance(project).getContentManager().showRunContent(defaultRunner, descriptor);
return consoleView;
}
private static final class MyConsolePanel extends JPanel {
public MyConsolePanel(ExecutionConsole consoleView, ActionGroup toolbarActions) {
super(new BorderLayout());
JPanel toolbarPanel = new JPanel(new BorderLayout());
toolbarPanel.add(ActionManager.getInstance().createActionToolbar(ActionPlaces.UNKNOWN, toolbarActions,false).getComponent());
add(toolbarPanel, BorderLayout.WEST);
add(consoleView.getComponent(), BorderLayout.CENTER);
}
}
protected String getDimensionServiceKey(){
return "#com.intellij.unscramble.UnscrambleDialog";
}
public JComponent getPreferredFocusedComponent() {
return myEditor.getContentComponent();
}
} |
package net.malisis.core.client.gui.icon;
import java.util.Arrays;
import net.malisis.core.renderer.icon.MalisisIcon;
/**
* @author Ordinastie
*
*/
public class GuiIcon extends MalisisIcon
{
protected MalisisIcon[] icons;
public GuiIcon(MalisisIcon icon)
{
this.icons = new MalisisIcon[] { icon };
}
public GuiIcon(MalisisIcon[] icons)
{
this.icons = icons;
}
public MalisisIcon getIcon(int index)
{
if (icons == null || icons.length == 0)
return null;
return icons[index % icons.length];
}
@Override
public MalisisIcon flip(boolean horizontal, boolean vertical)
{
for (MalisisIcon icon : icons)
icon.flip(horizontal, vertical);
return super.flip(horizontal, vertical);
}
@Override
public void setRotation(int rotation)
{
for (MalisisIcon icon : icons)
icon.setRotation(rotation);
super.setRotation(rotation);
}
@Override
public MalisisIcon clip(float offsetXFactor, float offsetYFactor, float widthFactor, float heightFactor)
{
for (MalisisIcon icon : icons)
icon.clip(offsetXFactor, offsetYFactor, widthFactor, heightFactor);
return super.clip(offsetXFactor, offsetYFactor, widthFactor, heightFactor);
}
@Override
public MalisisIcon clip(int offsetX, int offsetY, int width, int height)
{
for (MalisisIcon icon : icons)
icon.clip(offsetX, offsetY, width, height);
return super.clip(offsetX, offsetY, width, height);
}
@Override
public String toString()
{
return Arrays.toString(icons);
}
} |
package me.buildcarter8.iBukkit.utils;
import java.util.Arrays;
import java.util.List;
import java.util.Random;
import org.bukkit.ChatColor;
public class Colors
{
private static final Random RANDOM = new Random();
public static final List<ChatColor> CHAT_COLOR_POOL = Arrays.asList(
ChatColor.DARK_BLUE,
ChatColor.DARK_GREEN,
ChatColor.DARK_AQUA,
ChatColor.DARK_RED,
ChatColor.DARK_PURPLE,
ChatColor.GOLD,
ChatColor.BLUE,
ChatColor.GREEN,
ChatColor.AQUA,
ChatColor.RED,
ChatColor.LIGHT_PURPLE,
ChatColor.YELLOW);
//Allows random chat colors
public static ChatColor randChatColor()
{
return CHAT_COLOR_POOL.get(RANDOM.nextInt(CHAT_COLOR_POOL.size()));
}
} |
package net.jforum.drivers.generic;
import java.security.NoSuchAlgorithmException;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.Timestamp;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
import net.jforum.JForum;
import net.jforum.drivers.external.LoginAuthenticator;
import net.jforum.entities.Group;
import net.jforum.entities.KarmaStatus;
import net.jforum.entities.User;
import net.jforum.model.DataAccessDriver;
import net.jforum.util.preferences.ConfigKeys;
import net.jforum.util.preferences.SystemGlobals;
/**
* @author Rafael Steil
* @version $Id: UserModel.java,v 1.29 2005/02/07 10:56:29 andowson Exp $
*/
public class UserModel extends AutoKeys implements net.jforum.model.UserModel
{
private static LoginAuthenticator loginAuthenticator;
public UserModel()
{
String className = SystemGlobals.getValue(ConfigKeys.LOGIN_AUTHENTICATOR);
try {
loginAuthenticator = (LoginAuthenticator)Class.forName(className).newInstance();
loginAuthenticator.setUserModel(this);
}
catch (Exception e) {
throw new RuntimeException("Error while trying to instantiate a "
+ "login.authenticator instance (" + className + "): " + e);
}
}
/**
* @see net.jforum.model.UserModel#selectById(int)
*/
public User selectById(int userId) throws Exception
{
String q = SystemGlobals.getSql("UserModel.selectById");
PreparedStatement p = JForum.getConnection().prepareStatement(q);
p.setInt(1, userId);
ResultSet rs = p.executeQuery();
User u = new User();
if (rs.next()) {
this.fillUserFromResultSet(u, rs);
u.setPrivateMessagesCount(rs.getInt("private_messages"));
// User groups
p = JForum.getConnection().prepareStatement(SystemGlobals.getSql("UserModel.selectGroups"));
p.setInt(1, userId);
rs = p.executeQuery();
while (rs.next()) {
Group g = new Group();
g.setName(rs.getString("group_name"));
g.setId(rs.getInt("group_id"));
u.getGroupsList().add(g);
}
}
rs.close();
p.close();
return u;
}
public User selectByName(String username) throws Exception
{
PreparedStatement p = JForum.getConnection().prepareStatement(SystemGlobals.getSql("UserModel.selectByName"));
p.setString(1, username);
ResultSet rs = p.executeQuery();
User u = null;
if (rs.next()) {
u = new User();
fillUserFromResultSet(u, rs);
}
rs.close();
p.close();
return u;
}
protected void fillUserFromResultSet(User u, ResultSet rs) throws Exception
{
u.setAim(rs.getString("user_aim"));
u.setAvatar(rs.getString("user_avatar"));
u.setGender(rs.getString("gender"));
u.setRankId(rs.getInt("rank_id"));
u.setThemeId(rs.getInt("themes_id"));
u.setPrivateMessagesEnabled("1".equals(rs.getString("user_allow_pm")));
u.setNotifyOnMessagesEnabled("1".equals(rs.getString("user_notify")));
u.setViewOnlineEnabled("1".equals(rs.getString("user_viewonline")));
u.setPassword(rs.getString("user_password"));
u.setViewEmailEnabled("1".equals(rs.getString("user_viewemail")));
u.setViewOnlineEnabled("1".equals(rs.getString("user_allow_viewonline")));
u.setAvatarEnabled("1".equals(rs.getString("user_allowavatar")));
u.setBbCodeEnabled("1".equals(rs.getString("user_allowbbcode")));
u.setHtmlEnabled("1".equals(rs.getString("user_allowhtml")));
u.setSmiliesEnabled("1".equals(rs.getString("user_allowsmilies")));
u.setEmail(rs.getString("user_email"));
u.setFrom(rs.getString("user_from"));
u.setIcq(rs.getString("user_icq"));
u.setId(rs.getInt("user_id"));
u.setInterests(rs.getString("user_interests"));
u.setLastVisit(rs.getTimestamp("user_lastvisit"));
u.setOccupation(rs.getString("user_occ"));
u.setTotalPosts(rs.getInt("user_posts"));
u.setRegistrationDate(rs.getTimestamp("user_regdate"));
u.setSignature(rs.getString("user_sig"));
u.setWebSite(rs.getString("user_website"));
u.setYim(rs.getString("user_yim"));
u.setUsername(rs.getString("username"));
u.setAttachSignatureEnabled(rs.getInt("user_attachsig") == 1);
u.setMsnm(rs.getString("user_msnm"));
u.setLang(rs.getString("user_lang"));
u.setActive(rs.getInt("user_active"));
u.setKarma(new KarmaStatus(u.getId(), rs.getDouble("user_karma")));
String actkey = rs.getString("user_actkey");
u.setActivationKey(actkey == null || "".equals(actkey) ? null : actkey);
u.setDeleted(rs.getInt("deleted"));
}
/**
* @see net.jforum.model.UserModel#delete(int)
*/
public void delete(int userId) throws Exception
{
PreparedStatement p = JForum.getConnection().prepareStatement(SystemGlobals.getSql("UserModel.deletedStatus"));
p.setInt(1, 1);
p.setInt(2, userId);
p.executeUpdate();
p.close();
}
/**
* @see net.jforum.model.UserModel#update(net.jforum.User)
*/
public void update(User user) throws Exception
{
PreparedStatement p = JForum.getConnection().prepareStatement(SystemGlobals.getSql("UserModel.update"));
p.setString(1, user.getAim());
p.setString(2, user.getAvatar());
p.setString(3, user.getGender());
p.setInt(4, user.getThemeId());
p.setInt(5, user.isPrivateMessagesEnabled() ? 1 : 0);
p.setInt(6, user.isAvatarEnabled() ? 1 : 0);
p.setInt(7, user.isBbCodeEnabled() ? 1 : 0);
p.setInt(8, user.isHtmlEnabled() ? 1 : 0);
p.setInt(9, user.isSmiliesEnabled() ? 1 : 0);
p.setString(10, user.getEmail());
p.setString(11, user.getFrom());
p.setString(12, user.getIcq());
p.setString(13, user.getInterests());
p.setString(14, user.getOccupation());
p.setString(15, user.getSignature());
p.setString(16, user.getWebSite());
p.setString(17, user.getYim());
p.setString(18, user.getMsnm());
p.setString(19, user.getPassword());
p.setInt(20, user.isViewEmailEnabled() ? 1 : 0);
p.setInt(21, user.isViewOnlineEnabled() ? 1 : 0);
p.setInt(22, user.isNotifyOnMessagesEnabled() ? 1 : 0);
p.setInt(23, user.getAttachSignatureEnabled() ? 1 : 0);
p.setString(24, user.getUsername());
p.setString(25, user.getLang());
p.setInt(26, user.getId());
p.executeUpdate();
p.close();
}
/**
* @see net.jforum.model.UserModel#addNew(net.jforum.User)
*/
public int addNew(User user) throws Exception
{
PreparedStatement p = this.getStatementForAutoKeys("UserModel.addNew");
this.initNewUser(user, p);
int id = this.executeAutoKeysQuery(p);
p.close();
this.addToGroup(id, new int[] { SystemGlobals.getIntValue(ConfigKeys.DEFAULT_USER_GROUP) });
return id;
}
protected void initNewUser(User user, PreparedStatement p) throws Exception
{
p.setString(1, user.getUsername());
p.setString(2, user.getPassword());
p.setString(3, user.getEmail());
p.setTimestamp(4, new Timestamp(System.currentTimeMillis()));
p.setString(5, user.getActivationKey());
}
/**
* @see net.jforum.model.UserModel#addNewWithId(net.jforum.User)
*/
public void addNewWithId(User user) throws Exception
{
PreparedStatement p = this.getStatementForAutoKeys("UserModel.addNewWithId");
this.initNewUser(user, p);
p.setInt(6, user.getId());
p.executeUpdate();
p.close();
}
/**
* @see net.jforum.model.UserModel#decrementPosts(int)
*/
public void decrementPosts(int userId) throws Exception
{
PreparedStatement p = JForum.getConnection().prepareStatement(SystemGlobals.getSql("UserModel.decrementPosts"));
p.setInt(1, userId);
p.executeUpdate();
p.close();
}
/**
* @see net.jforum.model.UserModel#incrementPosts(int)
*/
public void incrementPosts(int userId) throws Exception
{
PreparedStatement p = JForum.getConnection().prepareStatement(SystemGlobals.getSql("UserModel.incrementPosts"));
p.setInt(1, userId);
p.executeUpdate();
p.close();
}
/**
* @see net.jforum.model.UserModel#incrementRanking(int)
*/
public void setRanking(int userId, int rankingId) throws Exception
{
PreparedStatement p = JForum.getConnection().prepareStatement(SystemGlobals.getSql("UserModel.rankingId"));
p.setInt(1, rankingId);
p.setInt(2, userId);
p.executeUpdate();
p.close();
}
/**
* @see net.jforum.model.UserModel#setActive(int, boolean)
*/
public void setActive(int userId, boolean active) throws Exception
{
PreparedStatement p = JForum.getConnection().prepareStatement(SystemGlobals.getSql("UserModel.activeStatus"));
p.setInt(1, active ? 1 : 0);
p.setInt(2, userId);
p.executeUpdate();
p.close();
}
/**
* @see net.jforum.model.UserModel#undelete(int)
*/
public void undelete(int userId) throws Exception
{
PreparedStatement p = JForum.getConnection().prepareStatement(SystemGlobals.getSql("UserModel.deletedStatus"));
p.setInt(1, 0);
p.setInt(2, userId);
p.executeUpdate();
p.close();
}
/**
* @see net.jforum.model.UserModel#selectAll()
*/
public List selectAll() throws Exception
{
return selectAll(0, 0);
}
/**
* @see net.jforum.model.UserModel#selectAll(int, int)
*/
public List selectAll(int startFrom, int count) throws Exception
{
PreparedStatement p;
if (count > 0) {
p = JForum.getConnection().prepareStatement(SystemGlobals.getSql("UserModel.selectAllByLimit"));
p.setInt(1, startFrom);
p.setInt(2, count);
}
else {
p = JForum.getConnection().prepareStatement(SystemGlobals.getSql("UserModel.selectAll"));
}
ResultSet rs = p.executeQuery();
List list = this.processSelectAll(rs);
rs.close();
p.close();
return list;
}
/**
* @see net.jforum.model.UserModel#selectAllWithKarma()
*/
public List selectAllWithKarma() throws Exception
{
return selectAllWithKarma(0, 0);
}
/**
* @see net.jforum.model.UserModel#selectAllWithKarma(int, int)
*/
public List selectAllWithKarma(int startFrom, int count) throws Exception
{
return this.loadKarma( this.selectAll(startFrom, count) );
}
protected List processSelectAll(ResultSet rs) throws Exception
{
List list = new ArrayList();
while (rs.next()) {
User u = new User();
u.setEmail(rs.getString("user_email"));
u.setId(rs.getInt("user_id"));
u.setTotalPosts(rs.getInt("user_posts"));
u.setRegistrationDate(rs.getTimestamp("user_regdate"));
u.setUsername(rs.getString("username"));
u.setDeleted(rs.getInt("deleted"));
KarmaStatus karma = new KarmaStatus();
karma.setKarmaPoints(rs.getInt("user_karma"));
u.setKarma( karma );
u.setFrom(rs.getString("user_from"));
u.setWebSite(rs.getString("user_website"));
list.add(u);
}
return list;
}
/**
* @see net.jforum.model.UserModel#getLastUserInfo()
*/
public User getLastUserInfo() throws Exception
{
User u = new User();
PreparedStatement p = JForum.getConnection().prepareStatement(SystemGlobals.getSql("UserModel.lastUserRegistered"));
ResultSet rs = p.executeQuery();
rs.next();
u.setUsername(rs.getString("username"));
u.setId(rs.getInt("user_id"));
rs.close();
p.close();
return u;
}
/**
* @see net.jforum.model.UserModel#getTotalUsers()
*/
public int getTotalUsers() throws Exception
{
PreparedStatement p = JForum.getConnection().prepareStatement(SystemGlobals.getSql("UserModel.totalUsers"));
ResultSet rs = p.executeQuery();
rs.next();
int total = rs.getInt("total_users");
rs.close();
p.close();
return total;
}
/**
* @see net.jforum.model.UserModel#isDeleted(int user_id)
*/
public boolean isDeleted(int userId) throws Exception
{
PreparedStatement p = JForum.getConnection().prepareStatement(SystemGlobals.getSql("UserModel.isDeleted"));
p.setInt(1, userId);
int deleted = 0;
ResultSet rs = p.executeQuery();
if (rs.next()) {
deleted = rs.getInt("deleted");
}
rs.close();
p.close();
return deleted == 1;
}
/**
* @see net.jforum.model.UserModel#isUsernameRegistered(java.lang.String)
*/
public boolean isUsernameRegistered(String username) throws Exception
{
boolean status = false;
PreparedStatement p = JForum.getConnection().prepareStatement(SystemGlobals.getSql("UserModel.isUsernameRegistered"));
p.setString(1, username);
ResultSet rs = p.executeQuery();
if (rs.next() && rs.getInt("registered") > 0) {
status = true;
}
rs.close();
p.close();
return status;
}
/**
* @see net.jforum.model.UserModel#validateLogin(java.lang.String, java.lang.String)
*/
public User validateLogin(String username, String password) throws NoSuchAlgorithmException, Exception
{
return loginAuthenticator.validateLogin(username, password);
}
/**
* @see net.jforum.model.UserModel#addToGroup(int, int[])
*/
public void addToGroup(int userId, int[] groupId) throws Exception
{
PreparedStatement p = JForum.getConnection().prepareStatement(SystemGlobals.getSql("UserModel.addToGroup"));
p.setInt(1, userId);
for (int i = 0; i < groupId.length; i++) {
p.setInt(2, groupId[i]);
p.executeUpdate();
}
p.close();
}
/**
* @see net.jforum.model.UserModel#removeFromGroup(int, int[])
*/
public void removeFromGroup(int userId, int[] groupId) throws Exception
{
PreparedStatement p = JForum.getConnection().prepareStatement(SystemGlobals.getSql("UserModel.removeFromGroup"));
p.setInt(1, userId);
for (int i = 0; i < groupId.length; i++) {
p.setInt(2, groupId[i]);
p.executeUpdate();
}
p.close();
}
/**
* @see net.jforum.model.UserModel#saveNewPassword(java.lang.String, java.lang.String)
*/
public void saveNewPassword(String password, String email) throws Exception
{
PreparedStatement p = JForum.getConnection().prepareStatement(SystemGlobals.getSql("UserModel.saveNewPassword"));
p.setString(1, password);
p.setString(2, email);
p.executeUpdate();
p.close();
}
/**
* @see net.jforum.model.UserModel#validateLostPasswordHash(java.lang.String, java.lang.String)
*/
public boolean validateLostPasswordHash(String email, String hash) throws Exception
{
PreparedStatement p = JForum.getConnection().prepareStatement(SystemGlobals.getSql("UserModel.validateLostPasswordHash"));
p.setString(1, hash);
p.setString(2, email);
boolean status = false;
ResultSet rs = p.executeQuery();
if (rs.next() && rs.getInt("valid") == 1) {
status = true;
this.writeLostPasswordHash(email, "");
}
rs.close();
p.close();
return status;
}
/**
* @see net.jforum.model.UserModel#writeLostPasswordHash(java.lang.String, java.lang.String)
*/
public void writeLostPasswordHash(String email, String hash) throws Exception
{
PreparedStatement p = JForum.getConnection().prepareStatement(SystemGlobals.getSql("UserModel.writeLostPasswordHash"));
p.setString(1, hash);
p.setString(2, email);
p.executeUpdate();
p.close();
}
/**
* @see net.jforum.model.UserModel#getUsernameByEmail(java.lang.String)
*/
public String getUsernameByEmail(String email) throws Exception
{
PreparedStatement p = JForum.getConnection().prepareStatement(SystemGlobals.getSql("UserModel.getUsernameByEmail"));
p.setString(1, email);
String username = "";
ResultSet rs = p.executeQuery();
if (rs.next()) {
username = rs.getString("username");
}
rs.close();
p.close();
return username;
}
/**
* @see net.jforum.model.UserModel#findByName(java.lang.String, boolean)
*/
public List findByName(String input, boolean exactMatch) throws Exception
{
List namesList = new ArrayList();
PreparedStatement p = JForum.getConnection().prepareStatement(SystemGlobals.getSql("UserModel.findByName"));
p.setString(1, exactMatch ? input : "%" + input + "%");
ResultSet rs = p.executeQuery();
while (rs.next()) {
User u = new User();
u.setId(rs.getInt("user_id"));
u.setUsername(rs.getString("username"));
u.setEmail(rs.getString("user_email"));
namesList.add(u);
}
rs.close();
p.close();
return namesList;
}
/**
* @see net.jforum.model.UserModel#validateActivationKeyHash(int, java.lang.String)
*/
public boolean validateActivationKeyHash(int userId , String hash) throws Exception
{
PreparedStatement p = JForum.getConnection().prepareStatement(SystemGlobals.getSql("UserModel.validateActivationKeyHash"));
p.setString(1, hash);
p.setInt(2, userId);
boolean status = false;
ResultSet rs = p.executeQuery();
if (rs.next() && rs.getInt("valid") == 1) {
status = true;
}
rs.close();
p.close();
return status;
}
/**
* @see net.jforum.model.UserModel#writeUserActive(int)
*/
public void writeUserActive(int userId) throws Exception
{
PreparedStatement p = JForum.getConnection().prepareStatement(SystemGlobals.getSql("UserModel.writeUserActive"));
p.setInt(1, userId);
p.executeUpdate();
p.close();
}
/**
* @see net.jforum.model.UserModel#updateUsername(int, String)
*/
public void updateUsername(int userId, String username) throws Exception
{
PreparedStatement p = JForum.getConnection().prepareStatement(SystemGlobals.getSql("UserModel.updateUsername"));
p.setString(1, username);
p.setInt(2, userId);
p.executeUpdate();
p.close();
}
/**
* @see net.jforum.model.UserModel#hasUsernameChanged(int, java.lang.String)
*/
public boolean hasUsernameChanged(int userId, String usernameToCheck) throws Exception
{
boolean status = false;
PreparedStatement p = JForum.getConnection().prepareStatement(SystemGlobals.getSql("UserModel.getUsername"));
p.setString(1, usernameToCheck);
p.setInt(2, userId);
String dbUsername = null;
ResultSet rs = p.executeQuery();
if (rs.next()) {
dbUsername = rs.getString("username");
}
if (!usernameToCheck.equals(dbUsername)) {
status = true;
}
rs.close();
p.close();
return status;
}
/**
* Load KarmaStatus from a list of users.
* @param users
* @return
* @throws Exception
*/
protected List loadKarma(List users) throws Exception{
List result = new ArrayList(users.size());
User user = null;
Iterator iter = users.iterator();
while (iter.hasNext()) {
user = (User) iter.next();
//load Karma
DataAccessDriver.getInstance().newKarmaModel().getUserTotalKarma(user);
result.add(user);
}
return result;
}
} |
package netspy.components.logging;
import java.text.DateFormat;
import java.text.SimpleDateFormat;
import java.util.Date;
import netspy.components.filehandling.manager.FileManager;
import netspy.components.mailing.Email;
/**
* The Class LogManager.
*/
public class LogManager {
/** The date format logging. */
public final String LOG_FORMAT = "dd-MM-yyyy HH:mm:ss";
/** The Constant LOG_FILE_PREFIX. */
public final String LOG_FILE_PREFIX = "log_";
/** The Constant LOG_FILE_EXTENSION. */
public final String LOG_FILE_EXTENSION = ".txt";
/** The Constant LOG_PATH. */
public final String LOG_PATH = "log/";
/** The Constant LOG_ENTRY_SEPARATOR. */
private static final String LOG_ENTRY_SEPARATOR = " | ";
/**
* Log.
*
* @param scanResult the scan result
*/
public void log(Email email) {
String logLine = "Scan vom: " + new SimpleDateFormat(LOG_FORMAT).format(new Date());
logLine += LOG_ENTRY_SEPARATOR;
logLine += "Gesendet am: " + email.getSendingDate();
logLine += LOG_ENTRY_SEPARATOR;
logLine += "Betreff: " + email.getSubject();
logLine += LOG_ENTRY_SEPARATOR;
logLine += "Absender: " + email.getSender();
logLine += LOG_ENTRY_SEPARATOR;
logLine += "Empfänger: " + email.getReceiver();
logLine += LOG_ENTRY_SEPARATOR;
logLine += "Dateiname: " + email.getFilename();
logLine += LOG_ENTRY_SEPARATOR;
logLine += "Gefundene Wörter: " + email.getHitMap().entrySet().toString();
new FileManager().createLogfile();
new FileManager().log(FileManager.LOG_FILE, logLine);
}
/**
* Gets the formatted date.
*
* @param dateFormat the date format
* @return the formatted date as String
*/
} |
package com.intellij.util;
import com.intellij.openapi.util.SystemInfo;
import org.jetbrains.annotations.ApiStatus;
import org.jetbrains.annotations.NotNull;
import org.jetbrains.annotations.Nullable;
import org.jetbrains.annotations.TestOnly;
/**
* Utility wrappers for accessing system properties.
*
* @see SystemInfo
* @author yole
*/
public class SystemProperties {
private static String ourTestUserName;
private SystemProperties() { }
@NotNull
public static String getUserHome() {
return System.getProperty("user.home");
}
public static String getUserName() {
return ourTestUserName != null ? ourTestUserName : System.getProperty("user.name");
}
@TestOnly
public static void setTestUserName(@Nullable String name) {
ourTestUserName = name;
}
public static String getLineSeparator() {
return System.getProperty("line.separator");
}
/** @deprecated use {@link SystemInfo#OS_NAME} (to be removed in IDEA 2020) */
@Deprecated
@ApiStatus.ScheduledForRemoval(inVersion = "2020")
public static String getOsName() {
return SystemInfo.OS_NAME;
}
/** @deprecated use {@link SystemInfo#JAVA_VERSION} (to be removed in IDEA 2020) */
@Deprecated
public static String getJavaVersion() {
return SystemInfo.JAVA_VERSION;
}
/** @deprecated use {@link SystemInfo#JAVA_VENDOR} (to be removed in IDEA 2020) */
@Deprecated
@ApiStatus.ScheduledForRemoval(inVersion = "2020")
public static String getJavaVmVendor() {
return SystemInfo.JAVA_VENDOR;
}
public static String getJavaHome() {
return System.getProperty("java.home");
}
/**
* Returns the value of given property as integer, or {@code defaultValue} if the property is not specified or malformed.
*/
public static int getIntProperty(@NotNull final String key, final int defaultValue) {
final String value = System.getProperty(key);
if (value != null) {
try {
return Integer.parseInt(value);
}
catch (NumberFormatException ignored) { }
}
return defaultValue;
}
public static float getFloatProperty(@NotNull String key, float defaultValue) {
String value = System.getProperty(key);
if (value != null) {
try {
return Float.parseFloat(value);
}
catch (NumberFormatException ignored) {
}
}
return defaultValue;
}
/**
* Returns the value of given property as a boolean, or {@code defaultValue} if the property is not specified or malformed.
*/
public static boolean getBooleanProperty(@NotNull final String key, final boolean defaultValue) {
final String value = System.getProperty(key);
if (value != null) {
return Boolean.parseBoolean(value);
}
return defaultValue;
}
/** @deprecated use {@link SystemInfo#JAVA_VENDOR} (to be removed in IDEA 2020) */
@Deprecated
@ApiStatus.ScheduledForRemoval(inVersion = "2020")
public static String getJavaVendor() {
return SystemInfo.JAVA_VENDOR;
}
public static boolean is(String key) {
return getBooleanProperty(key, false);
}
public static boolean has(String key) {
return System.getProperty(key) != null;
}
public static boolean isTrueSmoothScrollingEnabled() {
return getBooleanProperty("idea.true.smooth.scrolling", false);
}
} |
package soot.jimple.spark.sets;
import soot.Type;
import soot.util.BitSetIterator;
import soot.util.BitVector;
import soot.jimple.spark.pag.Node;
import soot.jimple.spark.pag.PAG;
import java.util.*;
/*
* Possible sources of inefficiency:
* -It seems like there must be a way to immediately know which subset bitvector
* will exist, since sets are shared when a node with a smaller points-to set is
* pointing to another node. Why not just take that node's bitvector as a base?
* -addAll could probably use many improvements.
* -Cast masking - calling typeManager.get
* -An interesting problem is that when merging a bitvector into an overflow list, if
* the one being merged
* in has a bitvector, the mask or exclude might mask it down to a bitvector with very
* few ones. (In fact, this might even result in one with 0 ones!)
* Should that new bitvector stay as a bitvector, or be converted to an
* overflow list? And how can we tell when it will have few ones? (Modify BitVector?)
*
*/
/**
* A shared representation of a points-to set which uses a bit vector + a list
* of extra elements, an "overflow list", to make adding single elements fast in
* most cases.
*
* The bit vector may be shared by multiple points-to sets, while the overflow
* list is specific to each points-to set.
*
* To facilitate sharing of the bitvectors, there is a "hash table" of all
* existing bitvectors kept, called BitVectorLookupMap, where the ith element
* contains a list of all existing bitvectors of cardinality i (i.e. has i one
* bits).
*
* @author Adam Richard
*
*/
public class SharedHybridSet extends PointsToSetInternal {
public SharedHybridSet(Type type, PAG pag) {
// I'm not sure what "type" is for, but this is the way the other set
// representations
// did it
super(type);
this.pag = pag;
}
// The following 2 constants should be tweaked for efficiency
public final static int OVERFLOW_SIZE = 20;
/**
* The max number of elements allowed in the set before creating a new
* bitvector for it.
*/
public final static int OVERFLOW_THRESHOLD = 5;
/**
* When the overflow list overflows, the maximum number of elements that may
* remain in the overflow list (the rest are moved into the base bit vector)
*/
public boolean contains(Node n) {
// Which should be checked first, bitVector or overflow? (for
// performance)
// I think the bit vector, since it only takes O(1) to check many
// elements
// Check the bit vector
if (bitVector != null && bitVector.contains(n))
return true;
// Check overflow
if (overflow.contains(n))
return true;
return false;
}
public boolean isEmpty() {
return numElements == 0;
}
/**
* @return an overflow list of all elements in a that aren't in b (b is
* assumed to be a subset of a)
*/
private OverflowList remainder(PointsToBitVector a, PointsToBitVector b) {
// Since a contains everything b contains, doing an XOR will give
// everything
// in a not in b
PointsToBitVector xorResult = new PointsToBitVector(a);
xorResult.xor(b);
// xorResult must now contain <= 20 elements, assuming
// OVERFLOW_THRESHOLD <= OVERFLOW_SIZE
return new OverflowList(xorResult);
}
// Look for an existing bitvector in the lookupMap which is a subset of the
// newBitVector (the bitVector to set as the new points-to set), with only a
// few
// elements missing. If we find one, make that set the new `bitVector', and
// the leftovers the new `overflow'
//szBitVector is the size of the ORIGINAL bit vector, NOT the size of newBitVector
private void findAppropriateBitVector(PointsToBitVector newBitVector, PointsToBitVector otherBitVector, int otherSize, int szBitvector) {
//First check "other" and "this"'s bitvector, to maximize sharing and
//minimize searching for a new bitvector
if (otherBitVector != null &&
otherSize <= numElements &&
otherSize + OVERFLOW_THRESHOLD >= numElements &&
otherBitVector.isSubsetOf(newBitVector))
{
setNewBitVector(szBitvector, otherBitVector);
overflow = remainder(newBitVector, otherBitVector);
}
else if (bitVector != null &&
szBitvector <= numElements &&
szBitvector + OVERFLOW_THRESHOLD >= numElements &&
bitVector.isSubsetOf(newBitVector))
{
overflow = remainder(newBitVector, bitVector);
}
else
{
for (int overFlowSize = 0; overFlowSize < OVERFLOW_THRESHOLD; ++overFlowSize)
{
int bitVectorCardinality = numElements - overFlowSize;
if (bitVectorCardinality < 0) break; //We might be trying to add a bitvector
//with <OVERFLOW_THRESHOLD ones (in fact, there might be bitvectors with 0
//ones). This results from merging bitvectors and masking out certain values.
if (bitVectorCardinality < AllSharedHybridNodes.v().lookupMap.map.length
&& AllSharedHybridNodes.v().lookupMap.map[bitVectorCardinality] != null)
{
ListIterator i = AllSharedHybridNodes.v().lookupMap.map[bitVectorCardinality]
.listIterator();
while (i.hasNext()) {
// for each existing bit vector with bitVectorCardinality
// ones
PointsToBitVector candidate = (PointsToBitVector) (i.next());
if (candidate.isSubsetOf(newBitVector)) {
setNewBitVector(szBitvector, candidate);
overflow = remainder(newBitVector, candidate);
return;
}
}
}
}
// Didn't find an appropriate bit vector to use as a base; add the new
// bit vector to the map of all bit vectors and set it as the new base
// bit vector
setNewBitVector(szBitvector, newBitVector);
overflow.removeAll();
AllSharedHybridNodes.v().lookupMap.add(numElements, newBitVector);
}
}
//Allows for reference counting and deleting the old bit vector if it
//isn't being shared
private void setNewBitVector(int size, PointsToBitVector newBitVector)
{
newBitVector.incRefCount();
if (bitVector != null)
{
bitVector.decRefCount();
if (bitVector.unused())
{
//delete bitVector from lookupMap
AllSharedHybridNodes.v().lookupMap.remove(size, bitVector);
}
}
bitVector = newBitVector;
}
public boolean add(Node n)
{
/*
* This algorithm is described in the paper "IBM Research Report: Fast
* Pointer Analysis" by Hirzel, Dincklage, Diwan, and Hind, pg. 11
*/
if (contains(n))
return false;
++numElements;
if (!overflow.full()) {
overflow.add(n);
} else {
// Put everything in the bitvector
PointsToBitVector newBitVector;
if (bitVector == null)
newBitVector = new PointsToBitVector(pag.getAllocNodeNumberer()
.size());
else
newBitVector = new PointsToBitVector(bitVector);
newBitVector.add(n); // add n to it
newBitVector.add(overflow.overflow, overflow.size()); // add
// overflow
// newBitVector
// Now everything is in newBitVector, and it must have numElements
// ones
// The algorithm would still work without this step, but wouldn't be
// shared implmentation at all.
findAppropriateBitVector(newBitVector, null, 0, numElements - overflow.size() - 1);
}
return true;
}
private boolean nativeAddAll(SharedHybridSet other, SharedHybridSet exclude) {
/*
* If one of the shared hybrid sets has a bitvector but the other
* doesn't, set that bitvector as the base bitvector and add the stuff
* from the other overflow list. If they both have a bitvector, AND them
* together, then add it to the lookupMap. If neither of them has a
* bitvector, just combine the overflow lists.
*/
BitVector mask = getBitMask(other, pag);
if (exclude != null)
{
if (exclude.overflow.size() > 0)
{
// Make exclude only a bitvector, for simplicity
PointsToBitVector newBitVector;
if (exclude.bitVector == null) {
newBitVector = new PointsToBitVector(pag.getAllocNodeNumberer()
.size());
} else {
newBitVector = new PointsToBitVector(exclude.bitVector);
}
newBitVector
.add(exclude.overflow.overflow, exclude.overflow.size());
exclude = new SharedHybridSet(type, pag);
exclude.bitVector = newBitVector;
}
//It's possible at this point that exclude could have been passed in non-null,
//but with no elements. Simplify the rest of the algorithm by setting it to null
//in that case.
else if (exclude.bitVector == null) exclude = null;
}
int originalSize = size(),
originalOnes = originalSize - overflow.size(),
otherBitVectorSize = other.size() - other.overflow.size();
// Decide on the base bitvector
if (bitVector == null) {
bitVector = other.bitVector;
if (bitVector != null) { // Maybe both bitvectors were null; in
// that case, no need to do this
bitVector.incRefCount();
// Since merging in new bits might add elements that
// were
// already in the overflow list, we have to remove and re-add
// them all.
// TODO: Can this be avoided somehow?
// Maybe by allowing an element to be both in the overflow set
// and
// the bitvector?
// Or could it be better done by checking just the bitvector and
// removing elements that are there?
OverflowList toReAdd = overflow;
overflow = new OverflowList();
boolean newBitVectorCreated = false; //whether a new bit vector
//was created, which is used to decide whether to re-add the
//overflow list as an overflow list again or merge it into the
//new bit vector.
numElements = otherBitVectorSize;
if (exclude != null || mask != null)
{
PointsToBitVector result = new PointsToBitVector(bitVector);
if (exclude != null) result.andNot(exclude.bitVector);
if (mask != null) result.and(mask);
if (!result.equals(bitVector))
{
result.add(toReAdd.overflow, toReAdd.size());
int newBitVectorSize = result.cardinality();
numElements = newBitVectorSize;
findAppropriateBitVector(result, other.bitVector, otherBitVectorSize, otherBitVectorSize);
newBitVectorCreated = true;
}
}
if (!newBitVectorCreated) //if it was, then toReAdd has
//already been re-added
{
for (int i = 0; i < toReAdd.size(); ++i) {
add(toReAdd.overflow[i]);
}
}
}
} else if (other.bitVector != null) {
// Now both bitvectors are non-null; merge them
PointsToBitVector newBitVector = new PointsToBitVector(other.bitVector);
if (exclude != null)
newBitVector.andNot(exclude.bitVector);
if (mask != null) newBitVector.and(mask);
newBitVector.or(bitVector);
if (!newBitVector.equals(bitVector)) // if some elements were
// actually added
{
//At this point newBitVector is bitVector + some new bits
// Have to make a tough choice - is it better at this point to
// put both overflow lists into this bitvector (which involves
// recalculating bitVector.cardinality() again since there might
// have been overlap), or is it better to re-add both the
// overflow lists to the set?
// I suspect the former, so I'll do that.
// Basically we now want to merge both overflow lists into this
// new
// bitvector (if it is indeed a new bitvector), then add that
// resulting
// huge bitvector to the lookupMap, unless a subset of it is
// already there.
if (other.overflow.size() != 0) {
PointsToBitVector toAdd =
new PointsToBitVector(newBitVector.size());
toAdd.add(other.overflow.overflow, other.overflow.size());
if (mask != null) toAdd.and(mask);
if (exclude != null) toAdd.andNot(exclude.bitVector);
newBitVector.or(toAdd);
}
//At this point newBitVector is still bitVector + some new bits
int numOnes = newBitVector.cardinality(); //# of bits in the
//new bitvector
int numAdded = newBitVector.add(overflow.overflow, overflow.size());
numElements += numOnes - originalOnes //number of new bits
+ numAdded - overflow.size(); //might be negative due to
//elements in overflow already being in the new bits
if (size() > originalSize)
{
findAppropriateBitVector(newBitVector, other.bitVector, otherBitVectorSize, originalOnes);
//checkSize();
return true;
}
else
{
//checkSize();
return false; //It might happen that the bitvector being merged in adds some bits
//to the existing bitvector, but that those new bits are all elements that were already
//in the overflow list. In that case, the set might not change, and if not we return false.
//We also leave the set the way it was by not calling findAppropriateBitvector,
//which maximizes sharing and is fastest in the short term. I'm not sure whether it
//would be faster overall to keep the already calculated bitvector anyway.
}
}
}
// Add all the elements in the overflow list of other, unless they're in
// exclude
OverflowList overflow = other.overflow;
for (int i = 0; i < overflow.size(); ++i) {
Node nodeToMaybeAdd = overflow.overflow[i]; // Here's where
// overloaded operators
// would be better
if ((exclude == null) || !exclude.contains(nodeToMaybeAdd)) {
if (mask == null || mask.get(nodeToMaybeAdd.getNumber()))
{
add(nodeToMaybeAdd);
}
}
}
//checkSize();
return size() > originalSize;
}
//A class invariant - numElements correctly holds the size
//Only used for testing
private void checkSize()
{
int realSize = overflow.size();
if (bitVector != null) realSize += bitVector.cardinality();
if (numElements != realSize)
{
throw new RuntimeException("Assertion failed.");
}
}
public boolean addAll(PointsToSetInternal other,
final PointsToSetInternal exclude) {
// Look at the sort of craziness we have to do just because of a lack of
// multimethods
if (other == null)
return false;
if ((!(other instanceof SharedHybridSet))
|| (exclude != null && !(exclude instanceof SharedHybridSet))) {
return super.addAll(other, exclude);
} else {
return nativeAddAll((SharedHybridSet) other,
(SharedHybridSet) exclude);
}
}
public boolean forall(P2SetVisitor v) {
// Iterate through the bit vector. Ripped from BitPointsToSet again.
// It seems there should be a way to share code between BitPointsToSet
// and
// SharedHybridSet, but I don't know how at the moment.
if (bitVector != null) {
for (BitSetIterator it = bitVector.iterator(); it.hasNext();) {
v.visit((Node) pag.getAllocNodeNumberer().get(it.next()));
}
}
// Iterate through the overflow list
for (int i = 0; i < overflow.size(); ++i) {
v.visit(overflow.overflow[i]);
}
return v.getReturnValue();
}
// Ripped from the other points-to sets - returns a factory that can be
// used to construct SharedHybridSets
public final static P2SetFactory getFactory() {
return new P2SetFactory() {
public final PointsToSetInternal newSet(Type type, PAG pag) {
return new SharedHybridSet(type, pag);
}
};
}
private PointsToBitVector bitVector = null; // Shared with other points-to
// sets
private OverflowList overflow = new OverflowList();
private PAG pag; // I think this is needed to get the size of the bit
// vector and the mask for casting
private int numElements = 0; // # of elements in the set
public int size() {
return numElements;
}
private class OverflowList {
public OverflowList() {
}
public OverflowList(PointsToBitVector bv) {
BitSetIterator it = bv.iterator(); // Iterates over only the 1 bits
while (it.hasNext()) {
// Get the next node in the bitset by looking it up in the
// pointer assignment graph.
// Ripped from BitPointsToSet.
Node n = (Node) (pag.getAllocNodeNumberer().get(it.next()));
add(n);
}
}
public void add(Node n) {
if (full())
throw new RuntimeException(
"Can't add an element to a full overflow list.");
overflow[overflowElements] = n;
overflowElements++;
}
public int size() {
return overflowElements;
}
public boolean full() {
return overflowElements == OVERFLOW_SIZE;
}
public boolean contains(Node n) {
for (int i = 0; i < overflowElements; ++i) {
if (n == overflow[i])
return true;
}
return false;
}
public void removeAll() {
overflow = new Node[OVERFLOW_SIZE];
overflowElements = 0;
}
public Node[] overflow = new Node[OVERFLOW_SIZE]; // Not shared with
// other
// points-to sets - the extra elements besides the ones in bitVector
private int overflowElements = 0; // # of elements actually in the
// array `overflow'
}
} |
/*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package robot;
import edu.wpi.first.wpilibj.DriverStation;
import edu.wpi.first.wpilibj.Joystick;
import edu.wpi.first.wpilibj.Timer;
import edu.wpi.first.wpilibj.Victor;
/**
* Class that owns the intake system of the robot. Includes belts and unobtanium.
*
* @author Tanner Smith (creator)
* @package robot
*/
public class Intake {
private Joystick joystick;
private Victor beltMotorOne, beltMotorTwo, unobtaniumMotor;
private int intakeMode, previousMode;
private DriverStation driverStation;
private ButtonChange intakeButton;
/**
* Creates our intake system.
* @param joystick Joystick of which it is to be controlled by.
* @param intakeMotorOne First belt motor.
* @param intakeMotorTwo Second belt motor.
* @param unobtaniumMotor Unobtanium motor.
*/
public Intake(Joystick joystick, Victor beltMotorOne, Victor beltMotorTwo, Victor unobtaniumMotor) {
this.joystick = joystick;
this.beltMotorOne = beltMotorOne;
this.beltMotorTwo = beltMotorTwo;
this.unobtaniumMotor = unobtaniumMotor;
//Set our mode to nothing so we don't go anywhere until they, the enlightened ones, tell us to.
intakeMode = 0;
previousMode = 0;
driverStation = DriverStation.getInstance();
//Initialize button change object
intakeButton = new ButtonChange(joystick, 3);
}
/**
* Perform the actions that the mode we are in requires.
*/
public void doAction() {
double beltSpeed = 0;
double unobtaniumSpeed = 0;
//Set the mode of the system, based on our button input
if (intakeButton.didButtonChange(true)) {
//Intake Button - Only do this if we let go of the button
if (intakeMode == 1) {
//Mode is at intake, ergo stop.
intakeMode = 0;
} else {
//Mode is not at intake
intakeMode = 1;
}
} else {
//Reverse Button
toggleModeFromJoystickButton(2, -1);
//Fire Button
toggleModeFromJoystickButton(1, 2);
}
//Put our chosen mode into action!
switch (intakeMode) {
case -1:
//Reverse mode
beltSpeed = 1;
unobtaniumSpeed = 0;
break;
case 0:
//Stop mode
beltSpeed = 0;
unobtaniumSpeed = 0;
break;
case 1:
//Intake mode
beltSpeed = -1;
unobtaniumSpeed = 0.5;
break;
case 2:
//Fire mode
beltSpeed = -1;
unobtaniumSpeed = -1;
break;
default:
//Ahhh! mode
beltSpeed = 0;
unobtaniumSpeed = 0;
break;
}
//Put mode into action
setBeltSpeed(beltSpeed);
setUnobtaniumSpeed(unobtaniumSpeed);
intakeButton.setPreviousState();
}
/**
* Switch the mode using the desired joystick button like a toggle switch.
* i.e. Press once turns it on or off depending on its current state
* @param joystickButton The joystick button you plan to use as a toggle button
* @param desiredMode The mode you want to goto with the toggle switch
*/
public void toggleModeFromJoystickButton(int joystickButton, int desiredMode)
{
if (joystick.getRawButton(joystickButton)) {
//Joystick button was hit
if (intakeMode != desiredMode)
{
//Don't set the previous mode if I'm already in the new mode
//i.e. - No infinite loops!
previousMode = intakeMode;
}
intakeMode = desiredMode;
} else if (!joystick.getRawButton(joystickButton) && intakeMode == desiredMode) {
//We don't want to be acting anymore
intakeMode = previousMode;
previousMode = 0;
}
}
/**
* Set the speed of the both belt motors.
* @param speed Value of motor speed from -1 to 1
*/
public void setBeltSpeed(double speed) {
//As a safety measure of un-tested code, the following line is commented out to prevent *boom*
beltMotorOne.set(speed);
beltMotorTwo.set(speed);
}
/**
* Set the speed of the unobtanium motor for easy access.
* @param speed Value of motor speed from -1 to 1
*/
public void setUnobtaniumSpeed(double speed) {
unobtaniumMotor.set(speed);
}
} |
package com.ecyrd.jspwiki;
import junit.framework.*;
import java.io.*;
import java.util.*;
import javax.servlet.*;
public class TranslatorReaderTest extends TestCase
{
Properties props = new Properties();
Vector created = new Vector();
static final String PAGE_NAME = "testpage";
TestEngine testEngine;
public TranslatorReaderTest( String s )
{
super( s );
}
public void setUp()
throws Exception
{
props.load( getClass().getClassLoader().getResourceAsStream("/jspwiki.properties") );
props.setProperty( "jspwiki.translatorReader.matchEnglishPlurals", "true" );
testEngine = new TestEngine( props );
}
public void tearDown()
{
deleteCreatedPages();
}
private void newPage( String name )
{
testEngine.saveText( name, "<test>" );
created.addElement( name );
}
private void deleteCreatedPages()
{
for( Iterator i = created.iterator(); i.hasNext(); )
{
String name = (String) i.next();
testEngine.deletePage(name);
}
created.clear();
}
private String translate( String src )
throws IOException,
NoRequiredPropertyException,
ServletException
{
WikiContext context = new WikiContext( testEngine,
PAGE_NAME );
Reader r = new TranslatorReader( context,
new BufferedReader( new StringReader(src)) );
StringWriter out = new StringWriter();
int c;
while( ( c=r.read()) != -1 )
{
out.write( c );
}
return out.toString();
}
public void testHyperlinks2()
throws Exception
{
newPage("Hyperlink");
String src = "This should be a [hyperlink]";
assertEquals( "This should be a <A CLASS=\"wikipage\" HREF=\"Wiki.jsp?page=Hyperlink\">hyperlink</A>\n",
translate(src) );
}
public void testHyperlinks3()
throws Exception
{
newPage("HyperlinkToo");
String src = "This should be a [hyperlink too]";
assertEquals( "This should be a <A CLASS=\"wikipage\" HREF=\"Wiki.jsp?page=HyperlinkToo\">hyperlink too</A>\n",
translate(src) );
}
public void testHyperlinks4()
throws Exception
{
newPage("HyperLink");
String src = "This should be a [HyperLink]";
assertEquals( "This should be a <A CLASS=\"wikipage\" HREF=\"Wiki.jsp?page=HyperLink\">HyperLink</A>\n",
translate(src) );
}
public void testHyperlinks5()
throws Exception
{
newPage("HyperLink");
String src = "This should be a [here|HyperLink]";
assertEquals( "This should be a <A CLASS=\"wikipage\" HREF=\"Wiki.jsp?page=HyperLink\">here</A>\n",
translate(src) );
}
/** When using CC links, this seems to crash 1.9.2. */
public void testHyperLinks6()
throws Exception
{
newPage("DiscussionAboutWiki");
newPage("WikiMarkupDevelopment");
String src = "[DiscussionAboutWiki] [WikiMarkupDevelopment].";
assertEquals( "<A CLASS=\"wikipage\" HREF=\"Wiki.jsp?page=DiscussionAboutWiki\">DiscussionAboutWiki</A> <A CLASS=\"wikipage\" HREF=\"Wiki.jsp?page=WikiMarkupDevelopment\">WikiMarkupDevelopment</A>.\n",
translate(src) );
}
public void testHyperlinksCC()
throws Exception
{
newPage("HyperLink");
String src = "This should be a HyperLink.";
assertEquals( "This should be a <A CLASS=\"wikipage\" HREF=\"Wiki.jsp?page=HyperLink\">HyperLink</A>.\n",
translate(src) );
}
public void testHyperlinksCCNonExistant()
throws Exception
{
String src = "This should be a HyperLink.";
assertEquals( "This should be a <U>HyperLink</U><A HREF=\"Edit.jsp?page=HyperLink\">?</A>.\n",
translate(src) );
}
/**
* Check if the CC hyperlink translator gets confused with
* unorthodox bracketed links.
*/
public void testHyperlinksCC2()
throws Exception
{
newPage("HyperLink");
String src = "This should be a [ HyperLink ].";
assertEquals( "This should be a <A CLASS=\"wikipage\" HREF=\"Wiki.jsp?page=HyperLink\"> HyperLink </A>.\n",
translate(src) );
}
public void testHyperlinksCC3()
throws Exception
{
String src = "This should be a nonHyperLink.";
assertEquals( "This should be a nonHyperLink.\n",
translate(src) );
}
/** Two links on same line. */
public void testHyperlinksCC4()
throws Exception
{
newPage("HyperLink");
newPage("ThisToo");
String src = "This should be a HyperLink, and ThisToo.";
assertEquals( "This should be a <A CLASS=\"wikipage\" HREF=\"Wiki.jsp?page=HyperLink\">HyperLink</A>, and <A CLASS=\"wikipage\" HREF=\"Wiki.jsp?page=ThisToo\">ThisToo</A>.\n",
translate(src) );
}
/** Two mixed links on same line. */
public void testHyperlinksCC5()
throws Exception
{
newPage("HyperLink");
newPage("ThisToo");
String src = "This should be a [HyperLink], and ThisToo.";
assertEquals( "This should be a <A CLASS=\"wikipage\" HREF=\"Wiki.jsp?page=HyperLink\">HyperLink</A>, and <A CLASS=\"wikipage\" HREF=\"Wiki.jsp?page=ThisToo\">ThisToo</A>.\n",
translate(src) );
}
/** Closing tags only. */
public void testHyperlinksCC6()
throws Exception
{
newPage("HyperLink");
newPage("ThisToo");
String src = "] This ] should be a HyperLink], and ThisToo.";
assertEquals( "] This ] should be a <A CLASS=\"wikipage\" HREF=\"Wiki.jsp?page=HyperLink\">HyperLink</A>], and <A CLASS=\"wikipage\" HREF=\"Wiki.jsp?page=ThisToo\">ThisToo</A>.\n",
translate(src) );
}
/** First and last words on line. */
public void testHyperlinksCCFirstAndLast()
throws Exception
{
newPage("HyperLink");
newPage("ThisToo");
String src = "HyperLink, and ThisToo";
assertEquals( "<A CLASS=\"wikipage\" HREF=\"Wiki.jsp?page=HyperLink\">HyperLink</A>, and <A CLASS=\"wikipage\" HREF=\"Wiki.jsp?page=ThisToo\">ThisToo</A>\n",
translate(src) );
}
/** Hyperlinks inside URIs. */
public void testHyperlinksCCURLs()
throws Exception
{
String src = "http:
assertEquals( "http:
translate(src) );
}
public void testHyperlinksCCNegated()
throws Exception
{
String src = "This should not be a ~HyperLink.";
assertEquals( "This should not be a HyperLink.\n",
translate(src) );
}
public void testHyperlinksCCNegated2()
throws Exception
{
String src = "~HyperLinks should not be matched.";
assertEquals( "HyperLinks should not be matched.\n",
translate(src) );
}
public void testHyperlinksExt()
throws Exception
{
String src = "This should be a [http:
assertEquals( "This should be a <A CLASS=\"external\" HREF=\"http:
translate(src) );
}
public void testHyperlinksExt2()
throws Exception
{
String src = "This should be a [link|http:
assertEquals( "This should be a <A CLASS=\"external\" HREF=\"http:
translate(src) );
}
public void testHyperlinksPluralMatch()
throws Exception
{
String src = "This should be a [HyperLinks]";
newPage("HyperLink");
assertEquals( "This should be a <A CLASS=\"wikipage\" HREF=\"Wiki.jsp?page=HyperLink\">HyperLinks</A>\n",
translate(src) );
}
public void testHyperlinksPluralMatch2()
throws Exception
{
String src = "This should be a [HyperLinks]";
assertEquals( "This should be a <U>HyperLinks</U><A HREF=\"Edit.jsp?page=HyperLinks\">?</A>\n",
translate(src) );
}
public void testHyperlinksPluralMatch3()
throws Exception
{
String src = "This should be a [HyperLink]";
newPage("HyperLinks");
assertEquals( "This should be a <A CLASS=\"wikipage\" HREF=\"Wiki.jsp?page=HyperLinks\">HyperLink</A>\n",
translate(src) );
}
public void testHyperlinkJS1()
throws Exception
{
String src = "This should be a [link|http:
assertEquals( "This should be a <A CLASS=\"external\" HREF=\"http:
translate(src) );
}
public void testHyperlinksInterWiki1()
throws Exception
{
String src = "This should be a [link|JSPWiki:HyperLink]";
assertEquals( "This should be a <A CLASS=\"interwiki\" HREF=\"http:
translate(src) );
}
public void testNoHyperlink()
throws Exception
{
newPage("HyperLink");
String src = "This should not be a [[HyperLink]";
assertEquals( "This should not be a [HyperLink]\n",
translate(src) );
}
public void testNoHyperlink2()
throws Exception
{
String src = "This should not be a [[[[HyperLink]";
assertEquals( "This should not be a [[[HyperLink]\n",
translate(src) );
}
public void testNoHyperlink3()
throws Exception
{
String src = "[[HyperLink], and this [[Neither].";
assertEquals( "[HyperLink], and this [Neither].\n",
translate(src) );
}
public void testErroneousHyperlink()
throws Exception
{
String src = "What if this is the last char [";
assertEquals( "What if this is the last char \n",
translate(src) );
}
public void testErroneousHyperlink2()
throws Exception
{
String src = "What if this is the last char [[";
assertEquals( "What if this is the last char [\n",
translate(src) );
}
public void testExtraPagename1()
throws Exception
{
String src = "Link [test_page]";
newPage("Test_page");
assertEquals("Link <A CLASS=\"wikipage\" HREF=\"Wiki.jsp?page=Test_page\">test_page</A>\n",
translate(src) );
}
public void testExtraPagename2()
throws Exception
{
String src = "Link [test.page]";
newPage("Test.page");
assertEquals("Link <A CLASS=\"wikipage\" HREF=\"Wiki.jsp?page=Test.page\">test.page</A>\n",
translate(src) );
}
public void testExtraPagename3()
throws Exception
{
String src = "Link [.testpage_]";
newPage(".testpage_");
assertEquals("Link <A CLASS=\"wikipage\" HREF=\"Wiki.jsp?page=.testpage_\">.testpage_</A>\n",
translate(src) );
}
public void testInlineImages()
throws Exception
{
String src = "Link [test|http:
assertEquals("Link <IMG CLASS=\"inline\" SRC=\"http:
translate(src) );
}
public void testInlineImages2()
throws Exception
{
String src = "Link [test|http:
assertEquals("Link <A CLASS=\"external\" HREF=\"http:
translate(src) );
}
public void testInlineImages3()
throws Exception
{
String src = "Link [test|http://images.com/testi]";
assertEquals("Link <IMG CLASS=\"inline\" SRC=\"http://images.com/testi\" ALT=\"test\">\n",
translate(src) );
}
public void testInlineImages4()
throws Exception
{
String src = "Link [test|http://foobar.jpg]";
assertEquals("Link <IMG CLASS=\"inline\" SRC=\"http://foobar.jpg\" ALT=\"test\">\n",
translate(src) );
}
// No link text should be just embedded link.
public void testInlineImagesLink2()
throws Exception
{
String src = "Link [http://foobar.jpg]";
assertEquals("Link <IMG CLASS=\"inline\" SRC=\"http:
translate(src) );
}
public void testInlineImagesLink()
throws Exception
{
String src = "Link [http:
assertEquals("Link <A HREF=\"http:
translate(src) );
}
public void testInlineImagesLink3()
throws Exception
{
String src = "Link [SandBox|http://foobar.jpg]";
newPage("SandBox");
assertEquals("Link <A CLASS=\"wikipage\" HREF=\"Wiki.jsp?page=SandBox\"><IMG CLASS=\"inline\" SRC=\"http://foobar.jpg\" ALT=\"SandBox\"></A>\n",
translate(src) );
}
public void testScandicPagename1()
throws Exception
{
String src = "Link [Test]";
newPage("Test"); // FIXME: Should be capital
assertEquals("Link <A CLASS=\"wikipage\" HREF=\"Wiki.jsp?page=%C5%E4Test\">Test</A>\n",
translate(src));
}
public void testParagraph()
throws Exception
{
String src = "1\n\n2\n\n3";
assertEquals( "1\n<P>\n2\n<P>\n3\n", translate(src) );
}
public void testLinebreak()
throws Exception
{
String src = "1\\\\2";
assertEquals( "1<BR>2\n", translate(src) );
}
public void testTT()
throws Exception
{
String src = "1{{2345}}6";
assertEquals( "1<TT>2345</TT>6\n", translate(src) );
}
public void testTTAcrossLines()
throws Exception
{
String src = "1{{\n2345\n}}6";
assertEquals( "1<TT>\n2345\n</TT>6\n", translate(src) );
}
public void testTTLinks()
throws Exception
{
String src = "1{{\n2345\n[a link]\n}}6";
newPage("ALink");
assertEquals( "1<TT>\n2345\n<A CLASS=\"wikipage\" HREF=\"Wiki.jsp?page=ALink\">a link</A>\n</TT>6\n", translate(src) );
}
public void testPre()
throws Exception
{
String src = "1{{{2345}}}6";
assertEquals( "1<PRE>2345</PRE>6\n", translate(src) );
}
public void testPre2()
throws Exception
{
String src = "1 {{{ {{{ 2345 }}} }}} 6";
assertEquals( "1 <PRE> {{{ 2345 </PRE> }}} 6\n", translate(src) );
}
public void testList1()
throws Exception
{
String src = "A list:\n* One\n* Two\n* Three\n";
assertEquals( "A list:\n<UL>\n<LI> One\n<LI> Two\n<LI> Three\n</UL>\n",
translate(src) );
}
/** Plain multi line testing:
<pre>
* One
continuing
* Two
* Three
</pre>
*/
public void testMultilineList1()
throws Exception
{
String src = "A list:\n* One\n continuing.\n* Two\n* Three\n";
assertEquals( "A list:\n<UL>\n<LI> One\n continuing.\n<LI> Two\n<LI> Three\n</UL>\n",
translate(src) );
}
public void testMultilineList2()
throws Exception
{
String src = "A list:\n* One\n continuing.\n* Two\n* Three\nShould be normal.";
assertEquals( "A list:\n<UL>\n<LI> One\n continuing.\n<LI> Two\n<LI> Three\n</UL>\nShould be normal.\n",
translate(src) );
}
public void testHTML()
throws Exception
{
String src = "<B>Test</B>";
assertEquals( "<B>Test</B>\n", translate(src) );
}
public void testHTML2()
throws Exception
{
String src = "<P>";
assertEquals( "<P>\n", translate(src) );
}
public void testQuotes()
throws Exception
{
String src = "\"Test\"\"";
assertEquals( ""Test""\n", translate(src) );
}
public void testItalicAcrossLinebreak()
throws Exception
{
String src="''This is a\ntest.''";
assertEquals( "<I>This is a\ntest.</I>\n", translate(src) );
}
public void testBoldAcrossLinebreak()
throws Exception
{
String src="__This is a\ntest.__";
assertEquals( "<B>This is a\ntest.</B>\n", translate(src) );
}
public void testBoldItalic()
throws Exception
{
String src="__This ''is'' a test.__";
assertEquals( "<B>This <I>is</I> a test.</B>\n", translate(src) );
}
public void testFootnote1()
throws Exception
{
String src="Footnote[1]";
assertEquals( "Footnote<A CLASS=\"footnoteref\" HREF=\"#ref-testpage-1\">[1]</A>\n",
translate(src) );
}
public void testFootnote2()
throws Exception
{
String src="[#2356] Footnote.";
assertEquals( "<A CLASS=\"footnote\" NAME=\"ref-testpage-2356\">[#2356]</A> Footnote.\n",
translate(src) );
}
/** Check an reported error condition where empty list items could cause crashes */
public void testEmptySecondLevelList()
throws Exception
{
String src="A\n\n**\n\nB";
assertEquals( "A\n<P>\n<UL>\n<UL>\n<LI>\n</UL>\n</UL>\n<P>\nB\n",
translate(src) );
}
public void testEmptySecondLevelList2()
throws Exception
{
String src="A\n\n##\n\nB";
assertEquals( "A\n<P>\n<OL>\n<OL>\n<LI>\n</OL>\n</OL>\n<P>\nB\n",
translate(src) );
}
/**
* <pre>
* *Item A
* ##Numbered 1
* ##Numbered 2
* *Item B
* </pre>
*
* would come out as:
*<ul>
* <li>Item A
* </ul>
* <ol>
* <ol>
* <li>Numbered 1
* <li>Numbered 2
* <ul>
* <li></ol>
* </ol>
* Item B
* </ul>
*
* (by Mahlen Morris).
*/
// FIXME: does not run - code base is too screwed for that.
/*
public void testMixedList()
throws Exception
{
String src="*Item A\n##Numbered 1\n##Numbered 2\n*Item B\n";
String result = translate(src);
// Remove newlines for easier parsing.
result = TextUtil.replaceString( result, "\n", "" );
assertEquals( "<UL><LI>Item A"+
"<OL><OL><LI>Numbered 1"+
"<LI>Numbered 2"+
"</OL></OL>"+
"<LI>Item B"+
"</UL>",
result );
}
*/
/**
* Like testMixedList() but the list types have been reversed.
*/
// FIXME: does not run - code base is too screwed for that.
/*
public void testMixedList2()
throws Exception
{
String src="#Item A\n**Numbered 1\n**Numbered 2\n#Item B\n";
String result = translate(src);
// Remove newlines for easier parsing.
result = TextUtil.replaceString( result, "\n", "" );
assertEquals( "<OL><LI>Item A"+
"<UL><UL><LI>Numbered 1"+
"<LI>Numbered 2"+
"</UL></UL>"+
"<LI>Item B"+
"</OL>",
result );
}
*/
public void testPluginInsert()
throws Exception
{
String src="[{INSERT com.ecyrd.jspwiki.plugin.SamplePlugin WHERE text=test}]";
assertEquals( "test\n", translate(src) );
}
public void testPluginNoInsert()
throws Exception
{
String src="[{SamplePlugin text=test}]";
assertEquals( "test\n", translate(src) );
}
public void testPluginInsertJS()
throws Exception
{
String src="Today: [{INSERT JavaScriptPlugin}] ''day''.";
assertEquals( "Today: <script language=\"JavaScript\"><!--\nfoo='';\n--></script>\n <I>day</I>.\n", translate(src) );
}
public void testShortPluginInsert()
throws Exception
{
String src="[{INSERT SamplePlugin WHERE text=test}]";
assertEquals( "test\n", translate(src) );
}
/**
* Test two plugins on same row.
*/
public void testShortPluginInsert2()
throws Exception
{
String src="[{INSERT SamplePlugin WHERE text=test}] [{INSERT SamplePlugin WHERE text=test2}]";
assertEquals( "test test2\n", translate(src) );
}
public void testPluginQuotedArgs()
throws Exception
{
String src="[{INSERT SamplePlugin WHERE text='test me now'}]";
assertEquals( "test me now\n", translate(src) );
}
public void testPluginDoublyQuotedArgs()
throws Exception
{
String src="[{INSERT SamplePlugin WHERE text='test \\'me too\\' now'}]";
assertEquals( "test 'me too' now\n", translate(src) );
}
public void testPluginQuotedArgs2()
throws Exception
{
String src="[{INSERT SamplePlugin WHERE text=foo}] [{INSERT SamplePlugin WHERE text='test \\'me too\\' now'}]";
assertEquals( "foo test 'me too' now\n", translate(src) );
}
/**
* Plugin output must not be parsed as Wiki text.
*/
public void testPluginWikiText()
throws Exception
{
String src="[{INSERT SamplePlugin WHERE text=PageContent}]";
assertEquals( "PageContent\n", translate(src) );
}
public void testMultilinePlugin1()
throws Exception
{
String src="Test [{INSERT SamplePlugin\nWHERE text=PageContent}]";
assertEquals( "Test PageContent\n", translate(src) );
}
public void testMultilinePluginBodyContent()
throws Exception
{
String src="Test [{INSERT SamplePlugin\ntext=PageContent\n\n123\n456\n}]";
assertEquals( "Test PageContent (123+456+)\n", translate(src) );
}
public void testMultilinePluginBodyContent2()
throws Exception
{
String src="Test [{INSERT SamplePlugin\ntext=PageContent\n\n\n123\n456\n}]";
assertEquals( "Test PageContent (+123+456+)\n", translate(src) );
}
public void testVariableInsert()
throws Exception
{
String src="[{$pagename}]";
assertEquals( PAGE_NAME+"\n", translate(src) );
}
public void testTable1()
throws Exception
{
String src="|| heading || heading2 \n| Cell 1 | Cell 2 \n| Cell 3 | Cell 4\n\n";
assertEquals( "<TABLE CLASS=\"wikitable\" BORDER=\"1\">\n"+
"<TR><TH> heading <TH> heading2 </TR>\n"+
"<TR><TD> Cell 1 <TD> Cell 2 </TR>\n"+
"<TR><TD> Cell 3 <TD> Cell 4</TR>\n"+
"</TABLE><P>\n",
translate(src) );
}
public void testTable2()
throws Exception
{
String src="||heading||heading2\n|Cell 1| Cell 2\n| Cell 3 |Cell 4\n\n";
assertEquals( "<TABLE CLASS=\"wikitable\" BORDER=\"1\">\n"+
"<TR><TH>heading<TH>heading2</TR>\n"+
"<TR><TD>Cell 1<TD> Cell 2</TR>\n"+
"<TR><TD> Cell 3 <TD>Cell 4</TR>\n"+
"</TABLE><P>\n",
translate(src) );
}
public void testTable3()
throws Exception
{
String src="|Cell 1| Cell 2\n| Cell 3 |Cell 4\n\n";
assertEquals( "<TABLE CLASS=\"wikitable\" BORDER=\"1\">\n"+
"<TR><TD>Cell 1<TD> Cell 2</TR>\n"+
"<TR><TD> Cell 3 <TD>Cell 4</TR>\n"+
"</TABLE><P>\n",
translate(src) );
}
public void testTableLink()
throws Exception
{
String src="|Cell 1| Cell 2\n|[Cell 3|ReallyALink]|Cell 4\n\n";
newPage("ReallyALink");
assertEquals( "<TABLE CLASS=\"wikitable\" BORDER=\"1\">\n"+
"<TR><TD>Cell 1<TD> Cell 2</TR>\n"+
"<TR><TD><A CLASS=\"wikipage\" HREF=\"Wiki.jsp?page=ReallyALink\">Cell 3</A><TD>Cell 4</TR>\n"+
"</TABLE><P>\n",
translate(src) );
}
public void testDescription()
throws Exception
{
String src=";:Foo";
assertEquals( "<DL>\n<DT></DT><DD>Foo</DD>\n</DL>\n",
translate(src) );
}
public void testDescription2()
throws Exception
{
String src=";Bar:Foo";
assertEquals( "<DL>\n<DT>Bar</DT><DD>Foo</DD>\n</DL>\n",
translate(src) );
}
public void testDescription3()
throws Exception
{
String src=";:";
assertEquals( "<DL>\n<DT></DT><DD></DD>\n</DL>\n",
translate(src) );
}
public void testRuler()
throws Exception
{
String src="
assertEquals( "<HR />\n",
translate(src) );
}
public static Test suite()
{
return new TestSuite( TranslatorReaderTest.class );
}
} |
package com.ecyrd.jspwiki;
import junit.framework.*;
import java.io.*;
import java.util.*;
public class TranslatorReaderTest extends TestCase
{
Properties props = new Properties();
public TranslatorReaderTest( String s )
{
super( s );
}
public void setUp()
throws Exception
{
props.load( getClass().getClassLoader().getResourceAsStream("/jspwiki.properties") );
}
public void tearDown()
{
}
private String translate( String src )
throws IOException,
NoRequiredPropertyException
{
Reader r = new TranslatorReader( new TestEngine( props ),
new BufferedReader( new StringReader(src)) );
StringWriter out = new StringWriter();
int c;
while( ( c=r.read()) != -1 )
{
out.write( c );
}
return out.toString();
}
public void testHyperlinks2()
throws Exception
{
String src = "This should be a [hyperlink]";
assertEquals( "This should be a <A CLASS=\"wikipage\" HREF=\"Wiki.jsp?page=Hyperlink\">hyperlink</A>\n",
translate(src) );
}
public void testHyperlinks3()
throws Exception
{
String src = "This should be a [hyperlink too]";
assertEquals( "This should be a <A CLASS=\"wikipage\" HREF=\"Wiki.jsp?page=HyperlinkToo\">hyperlink too</A>\n",
translate(src) );
}
public void testHyperlinks4()
throws Exception
{
String src = "This should be a [HyperLink]";
assertEquals( "This should be a <A CLASS=\"wikipage\" HREF=\"Wiki.jsp?page=HyperLink\">HyperLink</A>\n",
translate(src) );
}
public void testHyperlinks5()
throws Exception
{
String src = "This should be a [here|HyperLink]";
assertEquals( "This should be a <A CLASS=\"wikipage\" HREF=\"Wiki.jsp?page=HyperLink\">here</A>\n",
translate(src) );
}
public void testHyperlinksExt()
throws Exception
{
String src = "This should be a [http:
assertEquals( "This should be a <A CLASS=\"external\" HREF=\"http:
translate(src) );
}
public void testHyperlinksExt2()
throws Exception
{
String src = "This should be a [link|http:
assertEquals( "This should be a <A CLASS=\"external\" HREF=\"http:
translate(src) );
}
public void testHyperlinkJS1()
throws Exception
{
String src = "This should be a [link|http:
assertEquals( "This should be a <A CLASS=\"external\" HREF=\"http:
translate(src) );
}
public void testHyperlinksInterWiki1()
throws Exception
{
String src = "This should be a [link|JSPWiki:HyperLink]";
assertEquals( "This should be a <A CLASS=\"interwiki\" HREF=\"http:
translate(src) );
}
public void testExtraPagename1()
throws Exception
{
String src = "Link [test_page]";
assertEquals("Link <A CLASS=\"wikipage\" HREF=\"Wiki.jsp?page=Test_page\">test_page</A>\n",
translate(src) );
}
public void testExtraPagename2()
throws Exception
{
String src = "Link [test.page]";
assertEquals("Link <A CLASS=\"wikipage\" HREF=\"Wiki.jsp?page=Test.page\">test.page</A>\n",
translate(src) );
}
public void testExtraPagename3()
throws Exception
{
String src = "Link [.testpage_]";
assertEquals("Link <A CLASS=\"wikipage\" HREF=\"Wiki.jsp?page=.testpage_\">.testpage_</A>\n",
translate(src) );
}
public void testInlineImages()
throws Exception
{
String src = "Link [test|http:
assertEquals("Link <IMG CLASS=\"inline\" SRC=\"http:
translate(src) );
}
public void testInlineImages2()
throws Exception
{
String src = "Link [test|http:
assertEquals("Link <A CLASS=\"external\" HREF=\"http:
translate(src) );
}
public void testInlineImages3()
throws Exception
{
String src = "Link [test|http://images.com/testi]";
assertEquals("Link <IMG CLASS=\"inline\" SRC=\"http://images.com/testi\" ALT=\"test\">\n",
translate(src) );
}
public void testInlineImages4()
throws Exception
{
String src = "Link [test|http://foobar.jpg]";
assertEquals("Link <IMG CLASS=\"inline\" SRC=\"http://foobar.jpg\" ALT=\"test\">\n",
translate(src) );
}
public void testScandicPagename1()
throws Exception
{
String src = "Link [Test]";
assertEquals("Link <A CLASS=\"wikipage\" HREF=\"Wiki.jsp?page=%C5%E4Test\">Test</A>\n",
translate(src));
}
public void testParagraph()
throws Exception
{
String src = "1\n\n2\n\n3";
assertEquals( "1\n<P>\n2\n<P>\n3\n", translate(src) );
}
public void testLinebreak()
throws Exception
{
String src = "1\\\\2";
assertEquals( "1<BR>2\n", translate(src) );
}
public void testTT()
throws Exception
{
String src = "1{{2345}}6";
assertEquals( "1<TT>2345</TT>6\n", translate(src) );
}
public void testPre()
throws Exception
{
String src = "1{{{2345}}}6";
assertEquals( "1<PRE>2345</PRE>6\n", translate(src) );
}
public void testPre2()
throws Exception
{
String src = "1 {{{ {{{ 2345 }}} }}} 6";
assertEquals( "1 <PRE> {{{ 2345 </PRE> }}} 6\n", translate(src) );
}
public void testList1()
throws Exception
{
String src = "A list:\n* One\n* Two\n* Three\n";
assertEquals( "A list:\n<UL>\n<LI> One\n<LI> Two\n<LI> Three\n</UL>\n",
translate(src) );
}
/** Plain multi line testing:
<pre>
* One
continuing
* Two
* Three
</pre>
*/
public void testMultilineList1()
throws Exception
{
String src = "A list:\n* One\n continuing.\n* Two\n* Three\n";
assertEquals( "A list:\n<UL>\n<LI> One\n continuing.\n<LI> Two\n<LI> Three\n</UL>\n",
translate(src) );
}
public void testMultilineList2()
throws Exception
{
String src = "A list:\n* One\n continuing.\n* Two\n* Three\nShould be normal.";
assertEquals( "A list:\n<UL>\n<LI> One\n continuing.\n<LI> Two\n<LI> Three\n</UL>\nShould be normal.\n",
translate(src) );
}
public void testHTML()
throws Exception
{
String src = "<B>Test</B>";
assertEquals( "<B>Test</B>\n", translate(src) );
}
public void testHTML2()
throws Exception
{
String src = "<P>";
assertEquals( "<P>\n", translate(src) );
}
public void testItalicAcrossLinebreak()
throws Exception
{
String src="''This is a\ntest.''";
assertEquals( "<I>This is a\ntest.</I>\n", translate(src) );
}
public void testBoldAcrossLinebreak()
throws Exception
{
String src="__This is a\ntest.__";
assertEquals( "<B>This is a\ntest.</B>\n", translate(src) );
}
public void testBoldItalic()
throws Exception
{
String src="__This ''is'' a test.__";
assertEquals( "<B>This <I>is</I> a test.</B>\n", translate(src) );
}
public void testFootnote1()
throws Exception
{
String src="Footnote[1]";
assertEquals( "Footnote<A CLASS=\"footnoteref\" HREF=\"#ref1\">[1]</A>\n",
translate(src) );
}
public void testFootnote2()
throws Exception
{
String src="[#2356] Footnote.";
assertEquals( "<A CLASS=\"footnote\" NAME=\"ref2356\">[#2356]</A> Footnote.\n",
translate(src) );
}
public static Test suite()
{
return new TestSuite( TranslatorReaderTest.class );
}
} |
package scal.io.liger;
import timber.log.Timber;
import android.content.Context;
import android.os.Environment;
import android.support.annotation.NonNull;
import android.support.annotation.Nullable;
import android.util.Log;
import com.android.vending.expansion.zipfile.APKExpansionSupport;
import com.android.vending.expansion.zipfile.ZipResourceFile;
import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.Set;
import scal.io.liger.model.ExpansionIndexItem;
import scal.io.liger.model.sqlbrite.InstalledIndexItemDao;
/**
* @author Matt Bogner
* @author Josh Steiner
*/
public class ZipHelper {
public static final String TAG = "ZipHelper";
@NonNull
public static String getExpansionZipFilename(Context ctx, String mainOrPatch, int version) {
String packageName = ctx.getPackageName();
return mainOrPatch + "." + version + "." + packageName + ".obb";
}
@Nullable
public static String getExpansionZipDirectory(Context ctx, String mainOrPatch, int version) {
// basically a wrapper for getExpansionFileFolder, but defaults to files directory
String filePath = getExpansionFileFolder(ctx, mainOrPatch, version);
if (filePath == null) {
return getFileFolderName(ctx);
} else {
return filePath;
}
}
@NonNull
public static String getObbFolderName(Context ctx) {
String packageName = ctx.getPackageName();
File root = Environment.getExternalStorageDirectory();
return root.toString() + "/Android/obb/" + packageName + "/";
}
@Nullable
public static String getFileFolderName(Context ctx) {
// TODO Why doesn't this use ctx.getExternalFilesDir(null) (like JsonHelper)?
// String packageName = ctx.getPackageName();
// File root = Environment.getExternalStorageDirectory();
// return root.toString() + "/Android/data/" + packageName + "/files/";
File file = StorageHelper.getActualStorageDirectory(ctx);
String path = null;
if (file != null) {
path = file.getPath() + "/";
}
return path;
}
@Nullable
public static String getFileFolderName(Context context, String fileName) {
// need to account for patch files
if (fileName.contains(Constants.PATCH)) {
fileName = fileName.replace(Constants.PATCH, Constants.MAIN);
}
ExpansionIndexItem expansionIndexItem = IndexManager.loadInstalledFileIndex(context).get(fileName);
if (expansionIndexItem == null) {
Timber.e("FAILED TO LOCATE EXPANSION INDEX ITEM FOR " + fileName);
return null;
}
// TODO - switching to the new storage method ignores the value set in the expansion index item
// File root = Environment.getExternalStorageDirectory();
// return root.toString() + File.separator + expansionIndexItem.getExpansionFilePath();
File file = StorageHelper.getActualStorageDirectory(context);
if (file != null) {
return file.getPath() + "/";
} else {
return null;
}
}
public static String getFileFolderName(Context context, String fileName, ExpansionIndexItem item) {
// need to account for patch files
if (fileName.contains(Constants.PATCH)) {
fileName.replace(Constants.PATCH, Constants.MAIN);
}
// TODO - switching to the new storage method ignores the value set in the expansion index item
// File root = Environment.getExternalStorageDirectory();
// return root.toString() + File.separator + item.getExpansionFilePath();
return StorageHelper.getActualStorageDirectory(context).getPath() + "/";
}
// supressing messages for less text during polling
@Nullable
public static String getExpansionFileFolder(Context ctx, String mainOrPatch, int version) {
if (Environment.getExternalStorageState().equals(Environment.MEDIA_MOUNTED)) {
// check and/or attempt to create obb folder
String checkPath = getObbFolderName(ctx);
File checkDir = new File(checkPath);
if (checkDir.isDirectory() || checkDir.mkdirs()) {
File checkFile = new File(checkPath + getExpansionZipFilename(ctx, mainOrPatch, version));
if (checkFile.exists()) {
Timber.d("FOUND " + mainOrPatch + " " + version + " IN OBB DIRECTORY: " + checkFile.getPath());
return checkPath;
}
}
// check and/or attempt to create files folder
checkPath = getFileFolderName(ctx);
checkDir = new File(checkPath);
if (checkDir.isDirectory() || checkDir.mkdirs()) {
File checkFile = new File(checkPath + getExpansionZipFilename(ctx, mainOrPatch, version));
if (checkFile.exists()) {
Timber.d("FOUND " + mainOrPatch + " " + version + " IN FILES DIRECTORY: " + checkFile.getPath());
return checkPath;
}
}
}
Timber.e(mainOrPatch + " " + version + " NOT FOUND IN OBB DIRECTORY OR FILES DIRECTORY");
return null;
}
// for additional expansion files, check files folder for specified file
@Nullable
public static String getExpansionFileFolder(Context ctx, String fileName) {
if (Environment.getExternalStorageState().equals(Environment.MEDIA_MOUNTED)) {
// check and/or attempt to create files folder
String checkPath = getFileFolderName(ctx, fileName);
if (checkPath == null) {
return null;
}
File checkDir = new File(checkPath);
if (checkDir.isDirectory() || checkDir.mkdirs()) {
File checkFile = new File(checkPath + fileName);
if (checkFile.exists()) {
Timber.d("FOUND " + fileName + " IN DIRECTORY: " + checkFile.getPath());
return checkPath;
}
}
}
Timber.e(fileName + " NOT FOUND");
return null;
}
@Nullable
public static String getExpansionFileFolder(Context ctx, String fileName, ExpansionIndexItem item) {
if (Environment.getExternalStorageState().equals(Environment.MEDIA_MOUNTED)) {
// check and/or attempt to create files folder
String checkPath = getFileFolderName(ctx, fileName, item);
if (checkPath == null) {
return null;
}
File checkDir = new File(checkPath);
if (checkDir.isDirectory() || checkDir.mkdirs()) {
File checkFile = new File(checkPath + fileName);
if (checkFile.exists()) {
Timber.d("FOUND " + fileName + " IN DIRECTORY: " + checkFile.getPath());
return checkPath;
}
}
}
Timber.e(fileName + " NOT FOUND");
return null;
}
@Nullable
public static ZipResourceFile getResourceFile(Context context) {
try {
// resource file contains main file and patch file
ArrayList<String> paths = getExpansionPaths(context);
ZipResourceFile resourceFile = APKExpansionSupport.getResourceZipFile(paths.toArray(new String[paths.size()]));
return resourceFile;
} catch (IOException ioe) {
Timber.e("Could not open resource file (main version " + Constants.MAIN_VERSION + ", patch version " + Constants.PATCH_VERSION + ")");
return null;
}
}
@Nullable
public static InputStream getFileInputStream(String path, Context context, String language) {
String localizedFilePath = path;
// check language setting and insert country code if necessary
if (language != null) {
// just in case, check whether country code has already been inserted
if (path.lastIndexOf("-" + language + path.substring(path.lastIndexOf("."))) < 0) {
// if not already appended, don't bother to append -en
if (!"en".equals(language)) {
localizedFilePath = path.substring(0, path.lastIndexOf(".")) + "-" + language + path.substring(path.lastIndexOf("."));
Timber.d("getFileInputStream() - TRYING LOCALIZED PATH: " + localizedFilePath);
} else {
Timber.d("getFileInputStream() - TRYING PATH: " + localizedFilePath);
}
} else {
Timber.d("getFileInputStream() - TRYING LOCALIZED PATH: " + localizedFilePath);
}
} else {
Timber.d("getFileInputStream() - TRYING PATH: " + localizedFilePath);
}
InputStream fileStream = getFileInputStream(localizedFilePath, context);
// if there is no result with the localized path, retry with default path
if (fileStream == null) {
if (localizedFilePath.contains("-")) {
localizedFilePath = localizedFilePath.substring(0, localizedFilePath.lastIndexOf("-")) + localizedFilePath.substring(localizedFilePath.lastIndexOf("."));
Timber.d("getFileInputStream() - NO RESULT WITH LOCALIZED PATH, TRYING DEFAULT PATH: " + localizedFilePath);
fileStream = ZipHelper.getFileInputStream(localizedFilePath, context);
}
} else {
return fileStream;
}
if (fileStream == null) {
Timber.d("getFileInputStream() - NO RESULT WITH DEFAULT PATH: " + localizedFilePath);
} else {
return fileStream;
}
return null;
}
@Nullable
public static InputStream getFileInputStreamForExpansionAndPath(@NonNull ExpansionIndexItem expansion,
@NonNull String path,
@NonNull Context context) {
return getFileInputStreamFromFile(IndexManager.buildFileAbsolutePath(expansion, Constants.MAIN, context), path, context);
}
@Nullable
public static InputStream getThumbnailInputStreamForItem(@NonNull ExpansionIndexItem item, @NonNull Context context) {
ZipResourceFile resourceFile = null;
try {
resourceFile = APKExpansionSupport.getResourceZipFile(new String[]{IndexManager.buildFileAbsolutePath(item, Constants.MAIN, context)});
return resourceFile.getInputStream(item.getThumbnailPath());
} catch (IOException e) {
e.printStackTrace();
}
return null;
}
// private static ArrayList<String> expansionPaths;
/**
* @return an absolute path to an expansion file with the given expansionId, or null if no
* match could be made.
*/
// unused, removing for now
/*
public static @Nullable String getExpansionPathForExpansionId(Context context, String expansionId) {
String targetExpansionPath = null;
ArrayList<String> expansionPaths = getExpansionPaths(context);
for (String expansionPath : expansionPaths) {
if (expansionPath.contains(expansionId)) {
targetExpansionPath = expansionPath;
break;
}
}
return targetExpansionPath;
}
*/
public static void clearCache() {
// expansionPaths = null;
}
/**
* @return a list of absolute paths to all available expansion files.
*/
@NonNull
private static ArrayList<String> getExpansionPaths(@NonNull Context context) {
//if (expansionPaths == null) {
ArrayList<String> expansionPaths = new ArrayList<>();
File mainFile = new File(getExpansionFileFolder(context, Constants.MAIN, Constants.MAIN_VERSION) + getExpansionZipFilename(context, Constants.MAIN, Constants.MAIN_VERSION));
if (mainFile.exists() && (mainFile.length() > 0)) {
expansionPaths.add(mainFile.getPath());
} else {
Timber.e(mainFile.getPath() + " IS MISSING OR EMPTY, EXCLUDING FROM ZIP RESOURCE");
}
if (Constants.PATCH_VERSION > 0) {
// if the main file is newer than the patch file, do not apply a patch file
if (Constants.PATCH_VERSION < Constants.MAIN_VERSION) {
Timber.d("PATCH VERSION " + Constants.PATCH_VERSION + " IS OUT OF DATE (MAIN VERSION IS " + Constants.MAIN_VERSION + ")");
} else {
Timber.d("APPLYING PATCH VERSION " + Constants.PATCH_VERSION + " (MAIN VERSION IS " + Constants.MAIN_VERSION + ")");
File patchFile = new File(getExpansionFileFolder(context, Constants.PATCH, Constants.PATCH_VERSION) + getExpansionZipFilename(context, Constants.PATCH, Constants.PATCH_VERSION));
if (patchFile.exists() && (patchFile.length() > 0)) {
expansionPaths.add(patchFile.getPath());
}else {
Timber.e(patchFile.getPath() + " IS MISSING OR EMPTY, EXCLUDING FROM ZIP RESOURCE");
}
}
}
// need db access to get installed files
InstalledIndexItemDao dao = null;
if (context instanceof MainActivity) {
dao = ((MainActivity)context).getInstalledIndexItemDao(); // FIXME this isn't a safe cast as context can sometimes not be an activity (getApplicationContext())
} else {
Timber.e("NO DAO IN getExpansionPaths");
}
// add 3rd party stuff
HashMap<String, scal.io.liger.model.sqlbrite.ExpansionIndexItem> expansionIndex = StorymakerIndexManager.loadInstalledOrderIndex(context, dao);
// need to sort patch order keys, numbers may not be consecutive
ArrayList<String> orderNumbers = new ArrayList<String>(expansionIndex.keySet());
Collections.sort(orderNumbers);
for (String orderNumber : orderNumbers) {
scal.io.liger.model.sqlbrite.ExpansionIndexItem item = expansionIndex.get(orderNumber);
if (item == null) {
Timber.d("EXPANSION FILE ENTRY MISSING AT PATCH ORDER NUMBER " + orderNumber);
} else {
// construct name
String pathName = StorymakerIndexManager.buildFilePath(item, context);
String fileName = StorymakerIndexManager.buildFileName(item, Constants.MAIN);
File checkFile = new File(pathName + fileName);
// should be able to do this locally
// if (DownloadHelper.checkExpansionFiles(context, fileName)) {
if (checkFile.exists() && (checkFile.length() > 0)) {
Timber.d("EXPANSION FILE " + checkFile.getPath() + " FOUND, ADDING TO ZIP");
expansionPaths.add(checkFile.getPath());
if ((item.getPatchFileVersion() != null) &&
(item.getExpansionFileVersion() != null) &&
(Integer.parseInt(item.getPatchFileVersion()) > 0) &&
(Integer.parseInt(item.getPatchFileVersion()) >= Integer.parseInt(item.getExpansionFileVersion()))) {
// construct name
String patchName = StorymakerIndexManager.buildFileName(item, Constants.PATCH);
checkFile = new File(pathName + patchName);
// should be able to do this locally
// if (DownloadHelper.checkExpansionFiles(context, patchName)) {
if (checkFile.exists() && (checkFile.length() > 0)) {
Timber.d("EXPANSION FILE " + checkFile.getPath() + " FOUND, ADDING TO ZIP");
expansionPaths.add(checkFile.getPath());
} else {
Timber.e(checkFile.getPath() + " IS MISSING OR EMPTY, EXCLUDING FROM ZIP RESOURCE");
}
}
} else {
Timber.e(checkFile.getPath() + " IS MISSING OR EMPTY, EXCLUDING FROM ZIP RESOURCE");
}
}
}
return expansionPaths;
}
/**
* @return the {@link scal.io.liger.model.ExpansionIndexItem} which is likely to contain the
* given path.
*
* This method is useful as an optimization step until StoryPathLibrarys hold reference
* to the ExpansionIndexItem from which they were created, if applicable. The inspection
* is performed by searching for installed ExpansionIndexItem expansionId values
* within the given path parameter, and does not involve inspection of the files belonging to
* each ExpansionIndexItem.
*
*/
@Nullable
public static ExpansionIndexItem guessExpansionIndexItemForPath(@NonNull String path, @NonNull Context context) {
// need db access to get list of installed content packs
if (context instanceof MainActivity) {
InstalledIndexItemDao dao = ((MainActivity)context).getInstalledIndexItemDao(); // FIXME this isn't a safe cast as context can sometimes not be an activity (getApplicationContext())
HashMap<String, scal.io.liger.model.sqlbrite.ExpansionIndexItem> expansions = StorymakerIndexManager.loadInstalledIdIndex(context, dao);
Set<String> expansionIds = expansions.keySet();
for(String expansionId : expansionIds) {
if (path.contains(expansionId)) {
// turning this into an instance of the non sql-brite class to minimize impact
ExpansionIndexItem eii = new ExpansionIndexItem((expansions.get(expansionId)));
return eii;
}
}
} else {
Timber.e("could not find a dao to access the installed item list in the db");
}
return null;
}
/**
* @return an {@link java.io.InputStream} corresponding to the given path which must reside within
* one of the installed index items. On disk this corresponds to a zip archive packaged as an .obb file.
*
*/
@Deprecated
@Nullable
public static InputStream getFileInputStream(@NonNull String path, @NonNull Context context) {
// resource file contains main file and patch file
ArrayList<String> allExpansionPaths = getExpansionPaths(context);
ArrayList<String> targetExpansionPaths = new ArrayList<>();
// try to extract expansion id from target path
// assumes format org.storymaker.app/learning_guide/content_metadata-en.json
String[] parts = path.split("/");
for (String expansionPath : allExpansionPaths) {
if (expansionPath.contains(parts[1])) {
Timber.d("FOUND MATCH FOR " + parts[1] + " IN PATH " + expansionPath);
targetExpansionPaths.add(expansionPath);
}
}
// this shouldn't happen...
if (targetExpansionPaths.size() == 0) {
Timber.d("NO MATCHES FOR " + parts[1] + ", USING ALL PATHS");
targetExpansionPaths = allExpansionPaths;
}
StringBuilder paths = new StringBuilder();
for (String expansionPath : targetExpansionPaths) {
paths.append(expansionPath);
paths.append(", ");
}
paths.delete(paths.length()-2, paths.length());
Timber.d(String.format("Searching for %s in %s", path, paths));
return getFileInputStreamFromFiles(targetExpansionPaths, path, context);
}
@Nullable
public static InputStream getFileInputStreamFromFile(String zipPath, String filePath, Context context) {
ArrayList<String> zipPaths = new ArrayList<String>();
zipPaths.add(zipPath);
return getFileInputStreamFromFiles(zipPaths, filePath, context);
}
@Nullable
public static InputStream getFileInputStreamFromFiles(ArrayList<String> zipPaths, String filePath, Context context) {
try {
ZipResourceFile resourceFile = APKExpansionSupport.getResourceZipFile(zipPaths.toArray(new String[zipPaths.size()]));
if (resourceFile == null) {
return null;
}
// file path must be relative to the root of the resource file
InputStream resourceStream = resourceFile.getInputStream(filePath);
if (resourceStream == null) {
Timber.d("Could not find file " + filePath + " within resource file (main version " + Constants.MAIN_VERSION + ", patch version " + Constants.PATCH_VERSION + ")");
} else {
Timber.d("Found file " + filePath + " within resource file (main version " + Constants.MAIN_VERSION + ", patch version " + Constants.PATCH_VERSION + ")");
}
return resourceStream;
} catch (IOException ioe) {
Timber.e("Could not find file " + filePath + " within resource file (main version " + Constants.MAIN_VERSION + ", patch version " + Constants.PATCH_VERSION + ")");
return null;
}
}
/**
* Copy the expansion asset at path to a temporary file within tempPath. If
* a temp file exists for the given arguments it will be deleted and remade.
*/
@Deprecated
@Nullable
public static File getTempFile(String path, String tempPath, Context context) {
String extension = path.substring(path.lastIndexOf("."));
File tempFile = new File(tempPath + File.separator + "TEMP" + extension);
try {
if (tempFile.exists()) {
tempFile.delete();
Timber.d("Deleted temp file " + tempFile.getPath());
}
tempFile.createNewFile();
Timber.d("Made temp file " + tempFile.getPath());
} catch (IOException ioe) {
Timber.e("Failed to clean up existing temp file " + tempFile.getPath() + ", " + ioe.getMessage());
return null;
}
InputStream zipInput = getFileInputStream(path, context);
if (zipInput == null) {
Timber.e("Failed to open input stream for " + path + " in .zip file");
return null;
}
try {
FileOutputStream tempOutput = new FileOutputStream(tempFile);
byte[] buf = new byte[1024];
int i;
while((i = zipInput.read(buf)) > 0) {
tempOutput.write(buf, 0, i);
}
tempOutput.close();
zipInput.close();
Timber.d("Wrote temp file " + tempFile.getPath());
} catch (IOException ioe) {
Timber.e("Failed to write to temp file " + tempFile.getPath() + ", " + ioe.getMessage());
return null;
}
Timber.e("Created temp file " + tempFile.getPath());
return tempFile;
}
} |
package scal.io.liger.view;
import android.app.Activity;
import android.content.Intent;
import android.graphics.Point;
import android.graphics.Rect;
import android.support.v7.widget.LinearLayoutManager;
import android.view.ActionMode;
import android.view.Display;
import android.view.Gravity;
import android.view.LayoutInflater;
import android.view.Menu;
import android.view.MenuInflater;
import android.view.MenuItem;
import android.view.View;
import android.view.ViewGroup;
import android.view.Window;
import android.widget.PopupWindow;
import android.widget.Toast;
import java.util.ArrayList;
import java.util.List;
import scal.io.liger.Constants;
import scal.io.liger.MainActivity;
import scal.io.liger.R;
import scal.io.liger.adapter.OrderMediaAdapter;
import scal.io.liger.model.AudioClip;
import scal.io.liger.model.AudioClipFull;
import scal.io.liger.model.Card;
import scal.io.liger.model.FullMetadata;
import scal.io.liger.model.StoryPath;
public class Util {
/**
* @return a String of form "MM:SS:MS" from a raw ms value
*/
public static String makeTimeString(long timeMs) {
long millisecond = timeMs % 1000;
long second = (timeMs / 1000) % 60;
long minute = (timeMs / (1000 * 60)) % 60;
return String.format("%02d:%02d:%02d", minute, second, millisecond);
}
public static void startPublishActivity(Activity host, StoryPath storyPath) {
ArrayList<FullMetadata> exportMetadata = storyPath.exportAllMetadata(); // TODO : Place in AsyncTask?
ArrayList<AudioClipFull> exportAudioClipsMetadata = storyPath.exportAudioClips();
if (exportMetadata.size() > 0) {
Intent i = new Intent();
i.setAction(Constants.ACTION_PUBLISH);
i.putExtra(Constants.EXTRA_STORY_TITLE, storyPath.getTitle());
i.putExtra(Constants.EXTRA_STORY_INSTANCE_PATH, storyPath.getStoryPathLibraryFile());
// i.putExtra(Constants.EXTRA_REQUIRED_UPLOAD_TARGETS, storyPath.getRequiredUploadTargets());
// i.putExtra(Constants.EXTRA_REQUIRED_PUBLISH_TARGETS, storyPath.getRequiredPublishTargets());
// i.putExtra(Constants.EXTRA_REQUIRED_TAGS, storyPath.getRequiredTags());
i.putParcelableArrayListExtra(Constants.EXTRA_EXPORT_CLIPS, exportMetadata);
if (exportAudioClipsMetadata != null) {
i.putParcelableArrayListExtra(Constants.EXTRA_EXPORT_AUDIOCLIPS, exportAudioClipsMetadata);
}
host.startActivity(i);
host.finish(); // Do we definitely want to finish the host Activity?
} else {
Toast.makeText(host, host.getString(R.string.this_story_has_no_clips_to_publish), Toast.LENGTH_LONG).show();
}
}
public static int safeLongToInt(long l) {
if (l < Integer.MIN_VALUE || l > Integer.MAX_VALUE) {
throw new IllegalArgumentException
(l + " cannot be cast to int without changing its value.");
}
return (int) l;
}
} |
package org.apache.fop.fo.flow;
// FOP
import org.apache.fop.fo.*;
import org.apache.fop.fo.properties.*;
import org.apache.fop.fo.pagination.*;
import org.apache.fop.layout.Area;
import org.apache.fop.apps.FOPException;
// Java
import java.util.Enumeration;
public class StaticContent extends Flow {
public StaticContent(FONode parent) {
super(parent);
((PageSequence)parent).setIsFlowSet(false); // hacquery of sorts
}
public Status layout(Area area) throws FOPException {
return layout(area, null);
}
public Status layout(Area area, Region region) throws FOPException {
// int numChildren = this.children.size();
// // Set area absolute height so that link rectangles will be drawn correctly in xsl-before and xsl-after
// String regionClass = "none";
// if (region != null) {
// regionClass = region.getRegionClass();
// } else {
// if (getFlowName().equals("xsl-region-before")) {
// regionClass = RegionBefore.REGION_CLASS;
// } else if (getFlowName().equals("xsl-region-after")) {
// regionClass = RegionAfter.REGION_CLASS;
// } else if (getFlowName().equals("xsl-region-start")) {
// regionClass = RegionStart.REGION_CLASS;
// } else if (getFlowName().equals("xsl-region-end")) {
// regionClass = RegionEnd.REGION_CLASS;
// if (area instanceof org.apache.fop.layout.AreaContainer)
// ((org.apache.fop.layout.AreaContainer)area).setAreaName(regionClass);
// if (regionClass.equals(RegionBefore.REGION_CLASS)) {
// area.setAbsoluteHeight(-area.getMaxHeight());
// } else if (regionClass.equals(RegionAfter.REGION_CLASS)) {
// area.setAbsoluteHeight(area.getPage().getBody().getMaxHeight());
// setContentWidth(area.getContentWidth());
// for (int i = 0; i < numChildren; i++) {
// FObj fo = (FObj)children.elementAt(i);
// Status status;
// if ((status = fo.layout(area)).isIncomplete()) {
// // in fact all should be laid out and clip, error etc depending on 'overflow'
// log.warn("Some static content could not fit in the area.");
// this.marker = i;
// if ((i != 0) && (status.getCode() == Status.AREA_FULL_NONE)) {
// status = new Status(Status.AREA_FULL_SOME);
// return (status);
// resetMarker();
return new Status(Status.OK);
}
protected String getElementName() {
return "fo:static-content";
}
// flowname checking is more stringient for static content currently
protected void setFlowName(String name) throws FOPException {
if (name == null || name.equals("")) {
throw new FOPException("A 'flow-name' is required for "
+ getElementName() + ".");
} else {
super.setFlowName(name);
}
}
} |
package org.appwork.controlling;
import java.util.ArrayList;
import java.util.HashMap;
import org.appwork.utils.logging.Log;
public class StateMachine {
private static State checkState(final State state) {
State finalState = null;
for (final State s : state.getChildren()) {
final State ret = StateMachine.checkState(s);
if (finalState == null) {
finalState = ret;
}
if (finalState != ret) { throw new StateConflictException("States do not all result in one common final state"); }
}
if (finalState == null) { throw new StateConflictException(state + " is a blind state (has no children)"); }
return finalState;
}
/**
* validates a statechain and checks if all states can be reached, and if
* all chans result in one common finalstate
*
* @param initState
* @throws StateConflictException
*/
public static void validateStateChain(final State initState) {
if (initState.getParents().size() > 0) { throw new StateConflictException("initState must not have a parent"); }
StateMachine.checkState(initState);
}
private final State initState;
private volatile State currentState;
private final StateEventsender eventSender;
private final State finalState;
private final ArrayList<StatePathEntry> path;
private final StateMachineInterface owner;
private final Object lock = new Object();
private final Object lock2 = new Object();
private final HashMap<State, Throwable> exceptionMap;
public StateMachine(final StateMachineInterface interfac, final State startState, final State endState) {
this.owner = interfac;
this.initState = startState;
this.currentState = startState;
this.finalState = endState;
this.exceptionMap = new HashMap<State, Throwable>();
this.eventSender = new StateEventsender();
this.path = new ArrayList<StatePathEntry>();
this.path.add(new StatePathEntry(this.initState));
}
public void addListener(final StateEventListener listener) {
this.eventSender.addListener(listener);
}
/*
* synchronized hasPassed/addListener to start run when state has
* reached/passed
*/
public void executeOnceOnState(final Runnable run, final State state) {
if (run == null || state == null) { return; }
boolean reached = false;
synchronized (this.lock) {
if (this.hasPassed(state)) {
reached = true;
} else {
this.addListener(new StateListener(state) {
@Override
public void onStateReached(final StateEvent event) {
StateMachine.this.removeListener(this);
run.run();
}
});
}
}
if (reached) {
run.run();
}
}
/**
* synchronized execution of a runnable if statemachine is currently in a
* given state
*
* @param run
* @param state
* @return
*/
public boolean executeIfOnState(final Runnable run, final State state) {
if (run == null || state == null) { return false; }
synchronized (this.lock) {
if (this.isState(state)) {
run.run();
return true;
}
}
return false;
}
public void fireUpdate(final State currentState) {
if (currentState != null) {
synchronized (this.lock) {
if (this.currentState != currentState) { throw new StateConflictException("Cannot update state " + currentState + " because current state is " + this.currentState); }
}
}
final StateEvent event = new StateEvent(this, StateEvent.Types.UPDATED, currentState, currentState);
this.eventSender.fireEvent(event);
}
public void forceState(final State newState) {
StateEvent event;
synchronized (this.lock) {
if (this.currentState == newState) { return; }
event = new StateEvent(this, StateEvent.Types.CHANGED, this.currentState, newState);
synchronized (this.lock2) {
this.path.add(new StatePathEntry(newState));
}
Log.L.finest(this.owner + " State changed " + this.currentState + " -> " + newState);
this.currentState = newState;
}
this.eventSender.fireEvent(event);
}
public Throwable getCause(final State newState) {
return this.exceptionMap.get(newState);
}
/**
* TODO: not synchronized
*
* @param failedState
* @return
*/
public StatePathEntry getLatestStateEntry(final State failedState) {
try {
StatePathEntry entry = null;
synchronized (this.lock2) {
for (int i = this.path.size() - 1; i >= 0; i
entry = this.path.get(i);
if (entry.getState() == failedState) { return entry; }
}
}
} catch (final Exception e) {
}
return null;
}
public StateMachineInterface getOwner() {
return this.owner;
}
/**
* @return the path
*/
public ArrayList<StatePathEntry> getPath() {
return this.path;
}
public State getState() {
return this.currentState;
}
// public void forceState(int id) {
// State newState;
// synchronized (lock) {
// newState = getStateById(this.initState, id, null);
// if (newState == null) throw new
// StateConflictException("No State with ID " + id);
// forceState(newState);
public boolean hasPassed(final State... states) {
synchronized (this.lock2) {
for (final State s : states) {
for (final StatePathEntry e : this.path) {
if (e.getState() == s) { return true; }
}
}
}
return false;
}
// private State getStateById(State startState, int id, ArrayList<State>
// foundStates) {
// if (foundStates == null) foundStates = new ArrayList<State>();
// if (foundStates.contains(startState)) return null;
// foundStates.add(startState);
// State ret = null;
// for (State s : startState.getChildren()) {
// if (s.getID() == id) return s;
// ret = getStateById(s, id, foundStates);
// if (ret != null) return ret;
// return null;
public boolean isFinal() {
synchronized (this.lock) {
return this.finalState == this.currentState;
}
}
/**
* returns if the statemachine is in startstate currently
*/
public boolean isStartState() {
synchronized (this.lock) {
return this.currentState == this.initState;
}
}
public boolean isState(final State... states) {
synchronized (this.lock) {
for (final State s : states) {
if (s == this.currentState) { return true; }
}
}
return false;
}
public void removeListener(final StateEventListener listener) {
this.eventSender.removeListener(listener);
}
public void reset() {
StateEvent event;
synchronized (this.lock) {
if (this.currentState == this.initState) { return; }
if (this.finalState != this.currentState) { throw new StateConflictException("Cannot reset from state " + this.currentState); }
event = new StateEvent(this, StateEvent.Types.CHANGED, this.currentState, this.initState);
Log.L.finest(this.owner + " State changed (reset) " + this.currentState + " -> " + this.initState);
this.currentState = this.initState;
synchronized (this.lock2) {
this.path.clear();
this.path.add(new StatePathEntry(this.initState));
}
}
this.eventSender.fireEvent(event);
}
public void setCause(final State failedState, final Throwable e) {
this.exceptionMap.put(failedState, e);
}
public void setStatus(final State newState) {
synchronized (this.lock) {
if (this.currentState == newState) { return; }
if (!this.currentState.getChildren().contains(newState)) { throw new StateConflictException("Cannot change state from " + this.currentState + " to " + newState); }
}
this.forceState(newState);
}
} |
package org.egordorichev.lasttry.world;
import org.egordorichev.lasttry.LastTry;
import org.egordorichev.lasttry.entity.Enemy;
import org.egordorichev.lasttry.entity.Entity;
import org.egordorichev.lasttry.item.Block;
import org.egordorichev.lasttry.item.Item;
import org.egordorichev.lasttry.item.Wall;
import org.egordorichev.lasttry.util.FileReader;
import org.egordorichev.lasttry.util.FileWriter;
import org.egordorichev.lasttry.util.Rectangle;
import org.egordorichev.lasttry.world.tile.TileData;
import java.io.FileNotFoundException;
import java.util.ArrayList;
import java.util.List;
public class World {
/**
* Current world version generated by the game. Future versions may
* increment this number.
*/
public static final int CURENT_VERSION = 0;
/**
* Value indicating if the world has been fully loaded <i>(Entities placed,
* tiles added, dimensions set, etc.)</i>
*/
private boolean loaded;
/**
* World width in tiles.
*/
private int width;
/**
* World height in tiles.
*/
private int height;
/**
* World version.
*/
private int version;
/**
* World name.
*/
private String name;
/**
* Array of tile data. 2D coordinates are encoded by:
*
* <pre>
* index = x + y * world - width
* </pre>
*/
private TileData[] tiles;
/**
* List of entities in the world.
*/
private List<Entity> entities;
public World(String name) {
this.loaded = false;
this.name = name;
this.entities = new ArrayList<>();
Block.preload();
Wall.preload();
this.load();
spawnEnemy(Enemy.SLIME_GREEN, 10, 90);
spawnEnemy(Enemy.SLIME_BLUE, 40, 90);
}
/**
* Render the world.
*/
public void render() {
int windowWidth = LastTry.getWindowWidth();
int windowHeight = LastTry.getWindowHeight();
int tww = windowWidth / Block.TEX_SIZE;
int twh = windowHeight / Block.TEX_SIZE;
int tcx = (int) LastTry.camera.getX() / Block.TEX_SIZE;
int tcy = (int) LastTry.camera.getY() / Block.TEX_SIZE;
int minY = Math.max(0, tcy - 2);
int maxY = Math.min(this.height - 1, tcy + twh + 2);
int minX = Math.max(0, tcx - 2);
int maxX = Math.min(this.width - 1, tcx + tww + 2);
// Iterate coordinates, exclude ones not visible to the camera
for (int y = minY; y < maxY; y++) {
for (int x = minX; x < maxX; x++) {
TileData tileData = this.getTile(x, y);
tileData.render(x, y);
}
}
// Render entities, exclude ones not visible to the camera
for (Entity entity : this.entities) {
int gx = entity.getGridX();
int gy = entity.getGridY();
if ((gx > minX && gx < maxX) && (gy > minY && gy < maxY)) {
entity.render();
}
}
}
/**
* Update the world.
*
* @param dt
* The milliseconds passed since the last update.
*/
public void update(int dt) {
for (Entity entity : this.entities) {
entity.update(dt);
}
}
/**
* Spawn an enemy in the world <i>(Type dictated by the name)</i>
*
* @param name
* Name of the type of entity to spawn.
* @param x
* X-position to spawn entity at.
* @param y
* Y-position to spawn entity at.
* @return
*/
public Enemy spawnEnemy(String name, int x, int y) {
Enemy enemy = Enemy.create(name);
enemy.spawn(x, y);
this.entities.add(enemy);
return enemy;
}
/**
* Return the TileData for the given position.
*
* @param x
* X-position of the world.
* @param y
* Y-position of the world.
* @return
*/
public TileData getTile(int x, int y) {
return this.tiles[x + y * this.width];
}
/**
* Set a block in the world at the given position.
*
* @param block
* Block to place.
* @param x
* X-position of the world.
* @param y
* Y-position of the world.
*/
public void setBlock(Block block, int x, int y) {
TileData data = this.getTile(x, y);
data.block = block;
data.blockHp = data.maxHp;
data.data = 0;
}
/**
* Set a wall in the world at the given position.
*
* @param wall
* Wall to place.
* @param x
* X-position of the world.
* @param y
* Y-position of the world.
*/
public void setWall(Wall wall, int x, int y) {
TileData data = this.getTile(x, y);
data.wall = wall;
data.wallHp = data.maxHp;
data.data = 0;
}
/**
* Set the data tag of the tile in the world at the given position.
*
* @param data
* Tag value.
* @param x
* X-position of the world.
* @param y
* Y-position of the world.
*/
public void setData(byte data, int x, int y) {
TileData tileData = this.getTile(x, y);
tileData.data = data;
}
/**
* Return the data tag of the tile in the world at the given position.
*
* @param x
* X-position of the world.
* @param y
* Y-position of the world.
* @returnd Data tag value.
*/
public byte getData(int x, int y) {
TileData tileData = this.getTile(x, y);
return tileData.data;
}
/**
* Return the block in the world at the given position.
*
* @param x
* X-position of the world.
* @param y
* Y-position of the world.
* @return Block in world.
*/
public Block getBlock(int x, int y) {
TileData data = this.getTile(x, y);
return data.block;
}
/**
* Return the wall in the world at the given position.
*
* @param x
* X-position of the world.
* @param y
* Y-position of the world.
* @return Wall in world.
*/
public Wall getWall(int x, int y) {
TileData data = this.getTile(x, y);
return data.wall;
}
/**
* Return the ID of the block in the world at the given position.
*
* @param x
* X-position of the world.
* @param y
* Y-position of the world.
* @return Block ID in world.
*/
public int getBlockId(int x, int y) {
if (!this.isInside(x, y)) {
return 0;
}
TileData data = this.getTile(x, y);
if (data.block == null) {
return 0;
}
return data.block.getId();
}
/**
* Return the ID of the wall in the world at the given position.
*
* @param x
* X-position of the world.
* @param y
* Y-position of the world.
* @return Wall ID in world.
*/
public int getWallId(int x, int y) {
if (!this.isInside(x, y)) {
return 0;
}
TileData data = this.getTile(x, y);
if (data.wall == null) {
return 0;
}
return data.wall.getId();
}
/**
* Check if the given bounds collide with blocks in the world.
*
* @param bounds
* Bounds to check collision for.
* @return If bounds collide with world's blocks.
*/
public boolean isColliding(Rectangle bounds) {
Rectangle gridBounds = new Rectangle(bounds.x, bounds.y, bounds.width, bounds.height);
gridBounds.x /= Block.TEX_SIZE;
gridBounds.y /= Block.TEX_SIZE;
gridBounds.width /= Block.TEX_SIZE;
gridBounds.height /= Block.TEX_SIZE;
for (int y = (int) gridBounds.y - 1; y < gridBounds.y + gridBounds.height + 1; y++) {
for (int x = (int) gridBounds.x - 1; x < gridBounds.x + gridBounds.width + 1; x++) {
if (!this.isInside(x, y)) {
return true;
}
TileData data = this.getTile(x, y);
if (data.block == null || !data.block.isSolid()) {
continue;
}
Rectangle blockRect = new Rectangle(x * Block.TEX_SIZE, y * Block.TEX_SIZE, Block.TEX_SIZE,
Block.TEX_SIZE);
if (blockRect.intersects(bounds)) {
return true;
}
}
}
return false;
}
/**
* Check if the world has been loaded.
*
* @return World loaded.
*/
public boolean isLoaded() {
return this.loaded;
}
/**
* Check if the given position resides within the world's bounds.
*
* @param x
* X-position to check.
* @param y
* Y-position to check.
* @return Position is inside world.
*/
public boolean isInside(int x, int y) {
return (x >= 0 && x < this.width && y >= 0 && y < this.height);
}
/**
* Return the world's width.
*
* @return World width.
*/
public int getWidth() {
return this.width;
}
/**
* Return the world's height.
*
* @return World height.
*/
public int getHeight() {
return this.height;
}
/**
* Return the world's name.
*
* @return World name.
*/
public String getName() {
return this.name;
}
/**
* Return the world's file path.
*
* @return World file path.
*/
public String getFilePath() {
return "assets/worlds/" + this.name + ".wld";
}
/**
* Generate the world.
*/
private void generate() {
this.width = 500;
this.height = 500;
this.version = World.CURENT_VERSION;
int totalSize = this.width * this.height;
this.tiles = new TileData[totalSize];
int tiles[][] = new int[this.width][this.height];
for (int y = 0; y < this.height; y++) {
for (int x = 0; x < this.width; x++) {
if (y == 120) {
tiles[x][y] = Block.GRASS_BLOCK;
} else if (y > 120) {
tiles[x][y] = Block.DIRT_BLOCK;
} else {
tiles[x][y] = 0;
}
}
}
for (int y = 0; y < this.height; y++) {
for (int x = 0; x < this.width; x++) {
int id = tiles[x][y];
this.tiles[x + y * this.width] = new TileData((Block) Item.fromId(id), Wall.getForBlockId(id));
}
}
System.out.println("done generating!");
this.loaded = true;
}
private void load() {
try {
FileReader stream = new FileReader(this.getFilePath());
// Header
int version = stream.readInt32();
if (version > World.CURENT_VERSION) {
throw new RuntimeException("Unsupported version");
}
String worldName = stream.readString();
this.name = worldName;
this.width = stream.readInt32();
this.height = stream.readInt32();
// Tile data
int totalSize = this.width * this.height;
this.tiles = new TileData[totalSize];
for (int i = 0; i < totalSize; i++) {
this.tiles[i] = new TileData((Block) Item.fromId(stream.readInt32()),
(Wall) Item.fromId(stream.readInt32()));
// TODO: RLE
}
if (stream.readBoolean() == false) {
throw new RuntimeException("Verification failed");
}
worldName = stream.readString();
if (!worldName.equals(this.name)) {
throw new RuntimeException("Verification failed");
}
// Verification
} catch (FileNotFoundException exception) {
this.generate();
// this.save();
}
System.out.println("done loading!");
this.loaded = true;
}
public void save() {
FileWriter stream = new FileWriter(this.getFilePath());
// Header
stream.writeInt32(this.version);
stream.writeString(this.name);
stream.writeInt32(this.width);
stream.writeInt32(this.height);
// Tile data
int totalSize = this.width * this.height;
for (int i = 0; i < totalSize; i++) {
TileData data = this.tiles[i];
int blockId = 0;
int wallId = 0;
if (data.block != null) {
blockId = data.block.getId();
}
if (data.wall != null) {
wallId = data.wall.getId();
}
stream.writeInt32(blockId);
stream.writeInt32(wallId);
// TODO: RLE
}
// Verification
stream.writeBoolean(true);
stream.writeString(this.name);
stream.close();
System.out.println("done saving!");
}
} |
import java.util.HashSet;
import java.util.List;
import java.util.ArrayList;
import java.util.Set;
import java.util.Date;
import java.lang.Math;
import com.amazonaws.AmazonClientException;
import com.amazonaws.AmazonServiceException;
import com.amazonaws.auth.AWSCredentials;
import com.amazonaws.auth.profile.ProfileCredentialsProvider;
import com.amazonaws.services.ec2.AmazonEC2;
import com.amazonaws.services.ec2.AmazonEC2Client;
import com.amazonaws.services.cloudwatch.AmazonCloudWatchClient;
import com.amazonaws.services.ec2.model.DescribeInstancesResult;
import com.amazonaws.services.ec2.model.RunInstancesRequest;
import com.amazonaws.services.ec2.model.RunInstancesResult;
import com.amazonaws.services.ec2.model.Instance;
import com.amazonaws.services.ec2.model.Reservation;
import com.amazonaws.services.cloudwatch.model.Dimension;
import com.amazonaws.services.cloudwatch.model.GetMetricStatisticsRequest;
import com.amazonaws.services.cloudwatch.model.GetMetricStatisticsResult;
import com.amazonaws.services.cloudwatch.model.Datapoint;
import com.amazonaws.services.ec2.model.TerminateInstancesRequest;
public class AutoScaler {
private static AmazonEC2 ec2;
private static AmazonCloudWatchClient cloudWatch;
private static Set<Instance> instances;
private static final int INCR_POLICY_PERIOD = 60 * 1; //in seconds
private static final long INCR_DATAPOINTS_OFFSET = 1000 * (INCR_POLICY_PERIOD * 2 + 30); //Max number of the last datapoints retrieved
private static final int DECR_POLICY_PERIOD = 60 * 7; //in seconds
private static final long DECR_DATAPOINTS_OFFSET = 1000 * (DECR_POLICY_PERIOD * 2 + 30);
private static final int MAX_N_INSTANCES = 5;
private static final int MIN_N_INSTANCES = 2;
private static final long COOLDOWN_PERIOD = 1000 * 30; //in miliseconds
private static final long POOLING_PERIOD = 1000 * 60 * 1; //in miliseconds
private static final double MAX_CPU_UTILIZATION = 60.0; //in percentage
private static final double MIN_CPU_UTILIZATION = 30.0; //in percentage
private static final String WEBSERVER_AMI_ID = "ami-7808840b";
private static final String KEY_PAIR_NAME = "CNV-proj-AWS";
private static final String SECGROUP_NAME = "CNV-ssh+http";
/**
* The only information needed to create a client are security credentials
* consisting of the AWS Access Key ID and Secret Access Key. All other
* configuration, such as the service endpoints, are performed
* automatically. Client parameters, such as proxies, can be specified in an
* optional ClientConfiguration object when constructing a client.
*
* @see com.amazonaws.auth.BasicAWSCredentials
* @see com.amazonaws.auth.PropertiesCredentials
* @see com.amazonaws.ClientConfiguration
*/
private static void init() throws Exception {
AWSCredentials credentials = null;
try {
credentials = new ProfileCredentialsProvider().getCredentials();
} catch (Exception e) {
throw new AmazonClientException(
"Cannot load the credentials from the credential profiles file. " +
"Please make sure that your credentials file is at the correct " +
"location (~/.aws/credentials), and is in valid format.",
e);
}
ec2 = new AmazonEC2Client(credentials);
cloudWatch = new AmazonCloudWatchClient(credentials);
instances = new HashSet<Instance>();
// Using AWS Ireland. Pick the zone where you have AMI, key and secgroup
ec2.setEndpoint("ec2.eu-west-1.amazonaws.com");
cloudWatch.setEndpoint("monitoring.eu-west-1.amazonaws.com");
}
private static Instance launchNewInstance(){
RunInstancesRequest runInstancesRequest = new RunInstancesRequest();
//check if the following options match with the desired AMI and Security Group at AWS
runInstancesRequest.withImageId(WEBSERVER_AMI_ID)
.withInstanceType("t2.micro")
.withMinCount(1)
.withMaxCount(1)
.withKeyName(KEY_PAIR_NAME)
.withSecurityGroups(SECGROUP_NAME)
.withMonitoring(true);
RunInstancesResult runInstancesResult = ec2.runInstances(runInstancesRequest);
Instance newInstance = runInstancesResult.getReservation().getInstances().get(0);
System.out.println("Starting a new instance with id = " + newInstance.getInstanceId());
return newInstance;
}
private static void terminateInstance(String instanceId){
System.out.println("Terminating instance with id = " + instanceId);
TerminateInstancesRequest termInstanceReq = new TerminateInstancesRequest();
termInstanceReq.withInstanceIds(instanceId);
ec2.terminateInstances(termInstanceReq);
}
private static boolean checkIncreaseGroupSizePolicy(List<Datapoint> datapoints) {
//when CPU utilization > 60% for 60 seconds
System.out.println("checkIncreaseGroupSizePolicy:");
for (Datapoint dp : datapoints) {
double cpuUtilization = Math.floor(dp.getAverage() * 100) / 100;
System.out.println(" CPU utilization = " + cpuUtilization + " with time = " + dp.getTimestamp().toString());
if(cpuUtilization <= MAX_CPU_UTILIZATION){
return false;
}
}
//decrease group size
launchNewInstance();
return true;
//TODO: TIMER
}
private static boolean checkDecreaseGroupSizePolicy(List<Datapoint> datapoints, String instanceId) {
//when CPU utilization < 30% for 2 consecutive 7 minutes period
System.out.println("checkDecreaseGroupSizePolicy:");
for (Datapoint dp : datapoints) {
double cpuUtilization = Math.floor(dp.getAverage() * 100) / 100;
System.out.println(" CPU utilization = " + cpuUtilization + " with time = " + dp.getTimestamp().toString());
if(cpuUtilization >= MIN_CPU_UTILIZATION){
return false;
}
}
//decrease group size
terminateInstance(instanceId);
return true;
//TODO: TIMER
}
public static void main(String[] args) throws Exception {
System.out.println("===========================================");
System.out.println("Welcome to the AWS Java SDK!");
System.out.println("===========================================");
try {
init();
//Uncomment below if you need to start an instance
//launchNewInstance();
//Pooling the information about all WebServer instances
DescribeInstancesResult describeInstancesResult = ec2.describeInstances();
List<Reservation> reservations = describeInstancesResult.getReservations();
System.out.println("total reservations = " + reservations.size());
for (Reservation reservation : reservations) {
for (Instance instance : reservation.getInstances()) {
if(!instance.getState().getName().equals("terminated") && instance.getImageId().equals(WEBSERVER_AMI_ID)){
instances.add(instance);
}
}
}
System.out.println("total instances = " + instances.size());
while (instances.size() < MIN_N_INSTANCES){
instances.add(launchNewInstance());
}
System.out.println("total instances = " + instances.size());
Dimension instanceDimension = new Dimension();
instanceDimension.setName("InstanceId");
//auto scaling monitoring loop
long offsetInMilliseconds = 0;
GetMetricStatisticsRequest request;
GetMetricStatisticsResult getMetricStatisticsResult;
List<Datapoint> datapoints;
for(;;){
for (Instance instance : instances) {
String name = instance.getInstanceId();
String state = instance.getState().getName();
System.out.println("Instance Name : " + name +".");
System.out.println("Instance State : " + state +".");
if (state.equals("running")) {
instanceDimension.setValue(name);
//Get metrics to check the increase policy
if (instances.size() < MAX_N_INSTANCES) {
offsetInMilliseconds = INCR_DATAPOINTS_OFFSET;
request = new GetMetricStatisticsRequest()
.withStartTime(new Date(new Date().getTime() - offsetInMilliseconds))
.withNamespace("AWS/EC2")
.withPeriod(INCR_POLICY_PERIOD)
.withMetricName("CPUUtilization")
.withStatistics("Average")
.withUnit("Percent")
.withDimensions(instanceDimension)
.withEndTime(new Date());
getMetricStatisticsResult = cloudWatch.getMetricStatistics(request);
datapoints = getMetricStatisticsResult.getDatapoints();
System.out.println("datapoints size = " + datapoints.size());
if(datapoints.size() >= 2){
if(checkIncreaseGroupSizePolicy(datapoints)){
System.out.println("Coolling down for : " + COOLDOWN_PERIOD +" miliseconds.");
Thread.sleep(COOLDOWN_PERIOD);
System.out.println("Cooldown period expired!");
break;
}
}
}
//Get metrics to check the decrease policy
if (instances.size() > MIN_N_INSTANCES) {
offsetInMilliseconds = DECR_DATAPOINTS_OFFSET;
request = new GetMetricStatisticsRequest()
.withStartTime(new Date(new Date().getTime() - offsetInMilliseconds))
.withNamespace("AWS/EC2")
.withPeriod(DECR_POLICY_PERIOD)
.withMetricName("CPUUtilization")
.withStatistics("Average")
.withUnit("Percent")
.withDimensions(instanceDimension)
.withEndTime(new Date());
getMetricStatisticsResult = cloudWatch.getMetricStatistics(request);
datapoints = getMetricStatisticsResult.getDatapoints();
System.out.println("datapoints size = " + datapoints.size());
if(datapoints.size() >= 2){
if(checkDecreaseGroupSizePolicy(datapoints, name)){
System.out.println("Coolling down for : " + COOLDOWN_PERIOD +" miliseconds.");
Thread.sleep(COOLDOWN_PERIOD);
System.out.println("Cooldown period expired!");
break;
}
}
}
}
else {
System.out.println("Instance id = " + name + " is not running!");
}
}
//Stop pooling for 1 minute
System.out.println("Waiting: " + POOLING_PERIOD +" miliseconds for the next pooling.");
Thread.sleep(POOLING_PERIOD);
System.out.println("===========================================");
//Pooling the information about all WebServer instances
describeInstancesResult = ec2.describeInstances();
reservations = describeInstancesResult.getReservations();
instances = new HashSet<Instance>();
System.out.println("total reservations = " + reservations.size());
for (Reservation reservation : reservations) {
for (Instance instance : reservation.getInstances()) {
if(!instance.getState().getName().equals("terminated") && instance.getImageId().equals(WEBSERVER_AMI_ID)){
instances.add(instance);
}
}
}
System.out.println("total instances = " + instances.size());
}
} catch (AmazonServiceException ase) {
System.out.println("Caught Exception: " + ase.getMessage());
System.out.println("Reponse Status Code: " + ase.getStatusCode());
System.out.println("Error Code: " + ase.getErrorCode());
System.out.println("Request ID: " + ase.getRequestId());
}
}
} |
// -*- mode:java; encoding:utf-8 -*-
// vim:set fileencoding=utf-8:
// @homepage@
package example;
import java.awt.*;
import java.util.Collections;
import javax.swing.*;
import javax.swing.table.DefaultTableModel;
import javax.swing.table.TableModel;
public final class MainPanel extends JPanel {
private MainPanel() {
super(new BorderLayout());
String[] columnNames = {"String", "Integer", "Boolean"};
Object[][] data = {
{"aaa", 12, true}, {"bbb", 5, false},
{"CCC", 92, true}, {"DDD", 0, false}
};
TableModel model = new DefaultTableModel(data, columnNames) {
@Override public Class<?> getColumnClass(int column) {
return getValueAt(0, column).getClass();
}
};
JTable table = new JTable(model);
table.setAutoCreateRowSorter(true);
int index = 0;
// table.getRowSorter().toggleSortOrder(index); // SortOrder.ASCENDING
table.getRowSorter().setSortKeys(Collections.singletonList(new RowSorter.SortKey(index, SortOrder.DESCENDING)));
add(new JScrollPane(table));
setPreferredSize(new Dimension(320, 240));
}
public static void main(String[] args) {
EventQueue.invokeLater(MainPanel::createAndShowGui);
}
private static void createAndShowGui() {
try {
UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
} catch (ClassNotFoundException | InstantiationException | IllegalAccessException | UnsupportedLookAndFeelException ex) {
ex.printStackTrace();
Toolkit.getDefaultToolkit().beep();
}
JFrame frame = new JFrame("@title@");
frame.setDefaultCloseOperation(WindowConstants.EXIT_ON_CLOSE);
frame.getContentPane().add(new MainPanel());
frame.pack();
frame.setLocationRelativeTo(null);
frame.setVisible(true);
}
} |
package org.hcjf.properties;
import com.google.gson.JsonArray;
import com.google.gson.JsonObject;
import com.google.gson.JsonParser;
import org.hcjf.log.Log;
import java.text.DecimalFormat;
import java.text.DecimalFormatSymbols;
import java.text.SimpleDateFormat;
import java.util.*;
/**
* This class overrides the system properties default implementation adding
* some default values and properties definitions for the service-oriented platforms
* works.
* @author javaito
* @email javaito@gmail.com
*/
public final class SystemProperties extends Properties {
public static final String HCJF_DEFAULT_DATE_FORMAT = "hcjf.default.date.format";
public static final String HCJF_DEFAULT_NUMBER_FORMAT = "hcjf.default.number.format";
public static final String HCJF_DEFAULT_DECIMAL_SEPARATOR = "hcjf.default.decimal.separator";
public static final String HCJF_DEFAULT_GROUPING_SEPARATOR = "hcjf.default.grouping.separator";
public static final String HCJF_DEFAULT_LOCALE = "hcjf.default.locale";
public static final String HCJF_DEFAULT_PROPERTIES_FILE_PATH = "hcjf.default.properties.file.path";
public static final String HCJF_DEFAULT_PROPERTIES_FILE_XML = "hcjf.default.properties.file.xml";
public static final String SERVICE_THREAD_POOL_CORE_SIZE = "hcjf.service.thread.pool.core.size";
public static final String SERVICE_THREAD_POOL_MAX_SIZE = "hcfj.service.thread.pool.max.size";
public static final String SERVICE_THREAD_POOL_KEEP_ALIVE_TIME = "hcfj.service.thread.pool.keep.alive.time";
public static final String SERVICE_GUEST_SESSION_NAME = "hcjf.service.guest.session.name";
public static final String SERVICE_SHUTDOWN_TIME_OUT = "hcjf.service.shutdown.time.out";
public static final String LOG_FILE_PREFIX = "hcfj.log.file.prefix";
public static final String LOG_ERROR_FILE = "hcfj.log.error.file";
public static final String LOG_WARNING_FILE = "hcfj.log.warning.file";
public static final String LOG_INFO_FILE = "hcfj.log.info.file";
public static final String LOG_DEBUG_FILE = "hcfj.log.debug.file";
public static final String LOG_LEVEL= "hcfj.log.level";
public static final String LOG_DATE_FORMAT = "hcfj.log.date.format";
public static final String LOG_CONSUMERS = "hcjf.log.consumers";
public static final String LOG_SYSTEM_OUT_ENABLED = "hcjf.log.system.out.enabled";
public static final String LOG_QUEUE_INITIAL_SIZE = "hcjf.log.queue.initial.size";
public static final String LOG_TRUNCATE_TAG = "hcjf.log.truncate.tag";
public static final String LOG_TRUNCATE_TAG_SIZE = "hcjf.log.truncate.tag.size";
public static final String NET_INPUT_BUFFER_SIZE = "hcfj.net.input.buffer.size";
public static final String NET_OUTPUT_BUFFER_SIZE = "hcfj.net.output.buffer.size";
public static final String NET_DISCONNECT_AND_REMOVE = "hcfj.net.disconnect.and.remove";
public static final String NET_CONNECTION_TIMEOUT_AVAILABLE = "hcfj.net.connection.timeout.available";
public static final String NET_CONNECTION_TIMEOUT = "hcfj.net.connection.timeout";
public static final String NET_WRITE_TIMEOUT = "hcjf.net.write.timeout";
public static final String NET_IO_THREAD_POOL_KEEP_ALIVE_TIME = "hcjf.net.io.thread.pool.keep.alive.time";
public static final String NET_IO_THREAD_POOL_MAX_SIZE = "hcjf.net.io.thread.pool.max.size";
public static final String NET_IO_THREAD_POOL_CORE_SIZE = "hcjf.net.io.thread.pool.core.size";
public static final String NET_DEFAULT_INPUT_BUFFER_SIZE = "hcjf.net.default.input.buffer.size";
public static final String NET_DEFAULT_OUTPUT_BUFFER_SIZE = "hcjf.net.default.output.buffer.size";
public static final String NET_IO_THREAD_DIRECT_ALLOCATE_MEMORY = "hcjf.net.io.thread.direct.allocate.memory";
public static final String NET_SSL_MAX_IO_THREAD_POOL_SIZE = "hcjf.net.ssl.max.io.thread.pool.size";
public static final String HTTP_SERVER_NAME = "hcjf.http.server.name";
public static final String HTTP_RESPONSE_DATE_HEADER_FORMAT_VALUE = "hcjf.http.response.date.header.format.value";
public static final String HTTP_INPUT_LOG_BODY_MAX_LENGTH = "hcjf.http.input.log.body.max.length";
public static final String HTTP_OUTPUT_LOG_BODY_MAX_LENGTH = "hcjf.http.output.log.body.max.length";
public static final String HTTP_DEFAULT_SERVER_PORT = "hcjf.http.default.server.port";
public static final String HTTP_DEFAULT_CLIENT_PORT = "hcjf.http.default.client.port";
public static final String HTTP_STREAMING_LIMIT_FILE_SIZE = "hcjf.http.streaming.limit.file.size";
public static final String HTTP_DEFAULT_ERROR_FORMAT_SHOW_STACK = "hcjf.http.default.error.format.show.stack";
public static final String HTTP_DEFAULT_CLIENT_CONNECT_TIMEOUT = "hcjf.http.default.client.connect.timeout";
public static final String HTTP_DEFAULT_CLIENT_READ_TIMEOUT = "hcjf.http.default.client.read.timeout";
public static final String HTTP_DEFAULT_CLIENT_WRITE_TIMEOUT = "hcjf.http.default.client.write.timeout";
public static final String HTTP_DEFAULT_GUEST_SESSION_NAME = "hcjf.http.default.guest.session.name";
public static final String HTTPS_DEFAULT_SERVER_PORT = "hcjf.https.default.server.port";
public static final String HTTPS_DEFAULT_CLIENT_PORT = "hcjf.https.default.server.port";
public static final String REST_DEFAULT_MIME_TYPE = "hcjf.rest.default.mime.type";
public static final String REST_DEFAULT_ENCODING_IMPL = "hcjf.rest.default.encoding.impl";
public static final String REST_QUERY_PATH = "hcjf.rest.query.path";
public static final String REST_QUERY_PARAMETER_PATH = "hcjf.rest.query.parameter.path";
public static final String QUERY_DEFAULT_LIMIT = "hcjf.query.default.limit";
public static final String QUERY_DEFAULT_DESC_ORDER = "hcjf.query.default.desc.order";
public static final String CLOUD_IMPL = "hcjf.cloud.impl";
//Java property names
public static final String FILE_ENCODING = "file.encoding";
private static final SystemProperties instance;
static {
instance = new SystemProperties();
}
private final Map<String, Object> instancesCache;
private final JsonParser jsonParser;
private SystemProperties() {
super(new Properties());
instancesCache = new HashMap<>();
jsonParser = new JsonParser();
defaults.put(HCJF_DEFAULT_DATE_FORMAT, "yyyy-MM-dd HH:mm:ss");
defaults.put(HCJF_DEFAULT_NUMBER_FORMAT, "0.000");
defaults.put(HCJF_DEFAULT_DECIMAL_SEPARATOR, ".");
defaults.put(HCJF_DEFAULT_GROUPING_SEPARATOR, ",");
defaults.put(HCJF_DEFAULT_LOCALE, "EN");
defaults.put(HCJF_DEFAULT_PROPERTIES_FILE_XML, "false");
defaults.put(SERVICE_THREAD_POOL_CORE_SIZE, "100");
defaults.put(SERVICE_THREAD_POOL_MAX_SIZE, Integer.toString(Integer.MAX_VALUE));
defaults.put(SERVICE_THREAD_POOL_KEEP_ALIVE_TIME, "10");
defaults.put(SERVICE_GUEST_SESSION_NAME, "Guest");
defaults.put(SERVICE_SHUTDOWN_TIME_OUT, "200");
defaults.put(LOG_FILE_PREFIX, "hcfj");
defaults.put(LOG_ERROR_FILE, "false");
defaults.put(LOG_WARNING_FILE, "false");
defaults.put(LOG_INFO_FILE, "false");
defaults.put(LOG_DEBUG_FILE, "false");
defaults.put(LOG_LEVEL, "1");
defaults.put(LOG_DATE_FORMAT, "yyyy-MM-dd HH:mm:ss,SSS");
defaults.put(LOG_CONSUMERS, "[]");
defaults.put(LOG_SYSTEM_OUT_ENABLED, "false");
defaults.put(LOG_QUEUE_INITIAL_SIZE, "10000");
defaults.put(LOG_TRUNCATE_TAG, "false");
defaults.put(LOG_TRUNCATE_TAG_SIZE, "35");
defaults.put(NET_INPUT_BUFFER_SIZE, "1024");
defaults.put(NET_OUTPUT_BUFFER_SIZE, "1024");
defaults.put(NET_CONNECTION_TIMEOUT_AVAILABLE, "true");
defaults.put(NET_CONNECTION_TIMEOUT, "30000");
defaults.put(NET_DISCONNECT_AND_REMOVE, "true");
defaults.put(NET_WRITE_TIMEOUT, "100");
defaults.put(NET_IO_THREAD_POOL_KEEP_ALIVE_TIME, "120");
defaults.put(NET_IO_THREAD_POOL_MAX_SIZE, "10000");
defaults.put(NET_IO_THREAD_POOL_CORE_SIZE, "100");
defaults.put(NET_DEFAULT_INPUT_BUFFER_SIZE, "5000");
defaults.put(NET_DEFAULT_OUTPUT_BUFFER_SIZE, "5000");
defaults.put(NET_IO_THREAD_DIRECT_ALLOCATE_MEMORY, "false");
defaults.put(NET_SSL_MAX_IO_THREAD_POOL_SIZE, "2");
defaults.put(HTTP_SERVER_NAME, "HCJF Web Server");
defaults.put(HTTP_RESPONSE_DATE_HEADER_FORMAT_VALUE, "EEE, dd MMM yyyy HH:mm:ss z");
defaults.put(HTTP_INPUT_LOG_BODY_MAX_LENGTH, "128");
defaults.put(HTTP_OUTPUT_LOG_BODY_MAX_LENGTH, "128");
defaults.put(HTTP_DEFAULT_SERVER_PORT, "80");
defaults.put(HTTP_DEFAULT_CLIENT_PORT, "80");
defaults.put(HTTP_STREAMING_LIMIT_FILE_SIZE, "10240");
defaults.put(HTTP_DEFAULT_ERROR_FORMAT_SHOW_STACK, "true");
defaults.put(HTTP_DEFAULT_CLIENT_CONNECT_TIMEOUT, "10000");
defaults.put(HTTP_DEFAULT_CLIENT_READ_TIMEOUT, "10000");
defaults.put(HTTP_DEFAULT_CLIENT_WRITE_TIMEOUT, "10000");
defaults.put(HTTP_DEFAULT_GUEST_SESSION_NAME, "Http guest session");
defaults.put(HTTPS_DEFAULT_SERVER_PORT, "443");
defaults.put(HTTPS_DEFAULT_CLIENT_PORT, "443");
defaults.put(REST_DEFAULT_MIME_TYPE, "application/json");
defaults.put(REST_DEFAULT_ENCODING_IMPL, "hcjf");
defaults.put(REST_QUERY_PATH, "query");
defaults.put(REST_QUERY_PARAMETER_PATH, "q");
defaults.put(QUERY_DEFAULT_LIMIT, "1000");
defaults.put(QUERY_DEFAULT_DESC_ORDER, "false");
Properties system = System.getProperties();
putAll(system);
System.setProperties(this);
}
/**
* Put the default value for a property.
* @param propertyName Property name.
* @param defaultValue Property default value.
* @throws NullPointerException Throw a {@link NullPointerException} when the
* property name or default value are null.
*/
public static void putDefaultValue(String propertyName, String defaultValue) {
if(propertyName == null) {
throw new NullPointerException("Invalid property name null");
}
if(defaultValue == null) {
throw new NullPointerException("Invalid default value null");
}
instance.defaults.put(propertyName, defaultValue);
}
/**
* Calls the <tt>Hashtable</tt> method {@code put}. Provided for
* parallelism with the <tt>getProperty</tt> method. Enforces use of
* strings for property keys and values. The value returned is the
* result of the <tt>Hashtable</tt> call to {@code put}.
*
* @param key the key to be placed into this property list.
* @param value the value corresponding to <tt>key</tt>.
* @return the previous value of the specified key in this property
* list, or {@code null} if it did not have one.
* @see #getProperty
* @since 1.2
*/
@Override
public synchronized Object setProperty(String key, String value) {
Object result = super.setProperty(key, value);
synchronized (instancesCache) {
instancesCache.remove(key);
}
try {
//TODO: Create listeners
} catch (Exception ex){}
return result;
}
/**
* This method return the string value of the system property
* named like the parameter.
* @param propertyName Name of the find property.
* @param validator
* @return Return the value of the property or null if the property is no defined.
*/
public static String get(String propertyName, PropertyValueValidator<String> validator) {
String result = System.getProperty(propertyName);
if(result == null) {
Log.d("Property not found: $1", propertyName);
}
if(validator != null) {
if(!validator.validate(result)){
throw new IllegalPropertyValueException(propertyName + "=" + result);
}
}
return result;
}
/**
* This method return the string value of the system property
* named like the parameter.
* @param propertyName Name of the find property.
* @return Return the value of the property or null if the property is no defined.
*/
public static String get(String propertyName) {
return get(propertyName, null);
}
/**
* This method return the value of the system property as boolean.
* @param propertyName Name of the find property.
* @return Value of the system property as boolean, or null if the property is not found.
*/
public static Boolean getBoolean(String propertyName) {
Boolean result = null;
String propertyValue = get(propertyName);
try {
if (propertyValue != null) {
result = Boolean.valueOf(propertyValue);
}
} catch (Exception ex) {
throw new IllegalArgumentException("The property value has not a boolean valid format: '"
+ propertyName + ":" + propertyValue + "'", ex);
}
return result;
}
/**
* This method return the value of the system property as integer.
* @param propertyName Name of the find property.
* @return Value of the system property as integer, or null if the property is not found.
*/
public static Integer getInteger(String propertyName) {
Integer result = null;
String propertyValue = get(propertyName);
try {
if(propertyValue != null) {
result = Integer.decode(propertyValue);
}
} catch (Exception ex) {
throw new IllegalArgumentException("The property value has not a integer valid format: '"
+ propertyName + ":" + propertyValue + "'", ex);
}
return result;
}
/**
* This method return the value of the system property as long.
* @param propertyName Name of the find property.
* @return Value of the system property as long, or null if the property is not found.
*/
public static Long getLong(String propertyName) {
Long result = null;
String propertyValue = get(propertyName);
try {
if (propertyValue != null) {
result = Long.decode(propertyValue);
}
} catch (Exception ex) {
throw new IllegalArgumentException("The property value has not a long valid format: '"
+ propertyName + ":" + propertyValue + "'", ex);
}
return result;
}
/**
* This method return the value of the system property as double.
* @param propertyName Name of the find property.
* @return Value of the system property as double, or null if the property is not found.
*/
public static Double getDouble(String propertyName) {
Double result = null;
String propertyValue = get(propertyName);
try {
if (propertyValue != null) {
result = Double.valueOf(propertyValue);
}
} catch (Exception ex) {
throw new IllegalArgumentException("The property value has not a double valid format: '"
+ propertyName + ":" + propertyValue + "'", ex);
}
return result;
}
/**
* This method return the value of the system property as class.
* @param propertyName Name of the find property.
* @param <O> Type of the class instance expected.
* @return Class instance.
*/
public static <O extends Object> Class<O> getClass(String propertyName) {
Class<O> result;
String propertyValue = get(propertyName);
try {
result = (Class<O>) Class.forName(propertyValue);
} catch (Exception ex) {
throw new IllegalArgumentException("The property value has not a class name valid format: '"
+ propertyName + ":" + propertyValue + "'", ex);
}
return result;
}
/**
* Return the default charset of the JVM instance.
* @return Default charset.
*/
public static String getDefaultCharset() {
return System.getProperty(FILE_ENCODING);
}
/**
* This method return the value of the property as Locale instance.
* The instance returned will be stored on near cache and will be removed when the
* value of the property has been updated.
* @param propertyName Name of the property that contains locale representation.
* @return Locale instance.
*/
public static Locale getLocale(String propertyName) {
Locale result;
synchronized (instance.instancesCache) {
result = (Locale) instance.instancesCache.get(propertyName);
if(result == null) {
String propertyValue = get(propertyName);
try {
result = Locale.forLanguageTag(propertyValue);
instance.instancesCache.put(propertyName, result);
} catch (Exception ex) {
throw new IllegalArgumentException("The property value has not a locale tag valid format: '"
+ propertyName + ":" + propertyValue + "'", ex);
}
}
}
return result;
}
/**
* This method return the valuo of the property called 'hcjf.default.locale' as a locale instance.
* The instance returned will be stored on near cache and will be removed when the
* value of the property has been updated.
* @return Locale instance.
*/
public static Locale getLocale() {
return getLocale(HCJF_DEFAULT_LOCALE);
}
/**
* This method return the value of the property as a DecimalFormat instnace.
* The instance returned will be stored on near cache and will be removed when the
* value of the property has been updated.
* @param propertyName Name of the property that contains decimal pattern.
* @return DecimalFormat instance.
*/
public static DecimalFormat getDecimalFormat(String propertyName) {
DecimalFormat result;
synchronized (instance.instancesCache) {
result = (DecimalFormat) instance.instancesCache.get(propertyName);
if(result == null) {
String propertyValue = get(propertyName);
try {
DecimalFormatSymbols symbols = new DecimalFormatSymbols();
symbols.setDecimalSeparator(get(HCJF_DEFAULT_DECIMAL_SEPARATOR).charAt(0));
symbols.setGroupingSeparator(get(HCJF_DEFAULT_GROUPING_SEPARATOR).charAt(0));
result = new DecimalFormat(propertyValue, symbols);
instance.instancesCache.put(propertyName, result);
} catch (Exception ex) {
throw new IllegalArgumentException("The property value has not a decimal pattern valid format: '"
+ propertyName + ":" + propertyValue + "'", ex);
}
}
}
return result;
}
/**
* This method return the value of the property as a SimpleDateFormat instance.
* The instance returned will be stored on near cache and will be removed when the
* value of the property has been updated.
* @param propertyName Name of the property that contains date representation.
* @return Simple date format instance.
*/
public static SimpleDateFormat getDateFormat(String propertyName) {
SimpleDateFormat result;
synchronized (instance.instancesCache) {
result = (SimpleDateFormat) instance.instancesCache.get(propertyName);
if(result == null) {
String propertyValue = get(propertyName);
try {
result = new SimpleDateFormat(get(propertyName));
instance.instancesCache.put(propertyName, result);
} catch (Exception ex) {
throw new IllegalArgumentException("The property value has not a date pattern valid format: '"
+ propertyName + ":" + propertyValue + "'", ex);
}
}
}
return result;
}
/**
* This method return the value of the property as instance of list.
* @param propertyName Name of the property that contains the json array representation.
* @return List instance.
*/
public static List<String> getList(String propertyName) {
String propertyValue = get(propertyName);
List<String> result = new ArrayList<>();
if(instance.instancesCache.containsKey(propertyName)) {
result.addAll((List<? extends String>) instance.instancesCache.get(propertyName));
} else {
try {
JsonArray array = (JsonArray) instance.jsonParser.parse(propertyValue);
array.forEach(A -> result.add(A.getAsString()));
List<String> cachedResult = new ArrayList<>();
cachedResult.addAll(result);
instance.instancesCache.put(propertyName, cachedResult);
} catch (Exception ex) {
throw new IllegalArgumentException("The property value has not a json array valid format: '"
+ propertyName + ":" + propertyValue + "'", ex);
}
}
return result;
}
/**
* This method return the value of the property as instance of set.
* @param propertyName Name of the property that contains the json array representation.
* @return Set instance.
*/
public static Set<String> getSet(String propertyName) {
String propertyValue = get(propertyName);
Set<String> result = new TreeSet<>();
if(instance.instancesCache.containsKey(propertyName)) {
result.addAll((List<? extends String>) instance.instancesCache.get(propertyName));
} else {
try {
JsonArray array = (JsonArray) instance.jsonParser.parse(propertyValue);
array.forEach(A -> result.add(A.getAsString()));
List<String> cachedResult = new ArrayList<>();
cachedResult.addAll(result);
instance.instancesCache.put(propertyName, cachedResult);
} catch (Exception ex) {
throw new IllegalArgumentException("The property value has not a json array valid format: '"
+ propertyName + ":" + propertyValue + "'", ex);
}
}
return result;
}
/**
* This method return the value of the property as instance of map.
* @param propertyName The name of the property that contains the json object representation.
* @return Map instance.
*/
public static Map<String, String> getMap(String propertyName) {
String propertyValue = get(propertyName);
Map<String, String> result = new HashMap<>();
if(instance.instancesCache.containsKey(propertyName)) {
result.putAll((Map<String, String>) instance.instancesCache.get(propertyName));
} else {
try {
JsonObject object = (JsonObject) instance.jsonParser.parse(propertyValue);
object.entrySet().forEach(S -> result.put(S.getKey(), object.get(S.getKey()).getAsString()));
Map<String, String> cachedResult = new HashMap<>();
cachedResult.putAll(result);
instance.instancesCache.put(propertyName, cachedResult);
} catch (Exception ex) {
throw new IllegalArgumentException("The property value has not a json object valid format: '"
+ propertyName + ":" + propertyValue + "'", ex);
}
}
return result;
}
} |
package org.helioviewer.jhv.opengl;
import java.nio.Buffer;
import java.nio.ByteBuffer;
import java.nio.ByteOrder;
import java.nio.FloatBuffer;
import java.util.Arrays;
import org.helioviewer.jhv.math.Vec3;
public class BufVertex {
private static final int chunk = 1024;
private int multiplier = 1;
private final byte[] byteLast = new byte[16];
private final FloatBuffer bufferLast = ByteBuffer.wrap(byteLast).order(ByteOrder.nativeOrder()).asFloatBuffer();
private int count;
private ByteBuffer vertxBuffer;
private byte[] arrayVertx;
private int lengthVertx;
private ByteBuffer colorBuffer;
private byte[] arrayColor;
private int lengthColor;
public BufVertex(int size) {
arrayVertx = new byte[size < 16 ? 16 : size];
vertxBuffer = ByteBuffer.wrap(arrayVertx);
size /= 4;
arrayColor = new byte[size < 4 ? 4 : size];
colorBuffer = ByteBuffer.wrap(arrayColor);
}
private void ensureVertx(int nbytes) {
int size = arrayVertx.length;
if (lengthVertx + nbytes > size) {
arrayVertx = Arrays.copyOf(arrayVertx, size + chunk * multiplier++);
vertxBuffer = ByteBuffer.wrap(arrayVertx);
}
}
private void ensureColor(int nbytes) {
int size = arrayColor.length;
if (lengthColor + nbytes > size) {
arrayColor = Arrays.copyOf(arrayColor, size + chunk * multiplier++);
colorBuffer = ByteBuffer.wrap(arrayColor);
}
}
public void putVertex(Vec3 v, byte[] b) {
putVertex((float) v.x, (float) v.y, (float) v.z, 1, b);
}
public void putVertex(float x, float y, float z, float w, byte[] b) {
bufferLast.put(0, x).put(1, y).put(2, z).put(3, w);
repeatVertex(b);
}
public void repeatVertex(byte[] b) {
ensureVertx(16);
System.arraycopy(byteLast, 0, arrayVertx, lengthVertx, 16);
lengthVertx += 16;
ensureColor(4);
arrayColor[lengthColor] = b[0];
arrayColor[lengthColor + 1] = b[1];
arrayColor[lengthColor + 2] = b[2];
arrayColor[lengthColor + 3] = b[3];
lengthColor += 4;
count++;
}
public int getCount() {
return count;
}
public void clear() {
lengthVertx = 0;
lengthColor = 0;
count = 0;
}
public Buffer toVertexBuffer() {
return vertxBuffer.limit(lengthVertx);
}
public Buffer toColorBuffer() {
return colorBuffer.limit(lengthColor);
}
} |
package org.jgroups.blocks;
import org.jgroups.*;
import org.jgroups.logging.Log;
import org.jgroups.logging.LogFactory;
import org.jgroups.protocols.TP;
import org.jgroups.stack.Protocol;
import org.jgroups.stack.StateTransferInfo;
import org.jgroups.util.*;
import java.io.InputStream;
import java.io.OutputStream;
import java.io.Serializable;
import java.util.*;
/**
* Provides synchronous and asynchronous message sending with request-response
* correlation; i.e., matching responses with the original request.
* It also offers push-style message reception (by internally using the PullPushAdapter).
* <p>
* Channels are simple patterns to asynchronously send a receive messages.
* However, a significant number of communication patterns in group communication
* require synchronous communication. For example, a sender would like to send a
* message to the group and wait for all responses. Or another application would
* like to send a message to the group and wait only until the majority of the
* receivers have sent a response, or until a timeout occurred. MessageDispatcher
* offers a combination of the above pattern with other patterns.
* <p>
* Used on top of channel to implement group requests. Client's <code>handle()</code>
* method is called when request is received. Is the equivalent of RpcProtocol on
* the application instead of protocol level.
*
* @author Bela Ban
* @version $Id: MessageDispatcher.java,v 1.103 2010/04/21 09:02:46 belaban Exp $
*/
public class MessageDispatcher implements RequestHandler {
protected Channel channel=null;
protected RequestCorrelator corr=null;
protected MessageListener msg_listener=null;
protected MembershipListener membership_listener=null;
protected RequestHandler req_handler=null;
protected ProtocolAdapter prot_adapter=null;
protected TransportAdapter transport_adapter=null;
protected final Collection<Address> members=new TreeSet<Address>();
protected Address local_addr=null;
protected PullPushAdapter adapter=null;
protected PullPushHandler handler=null;
protected Serializable id=null;
protected final Log log=LogFactory.getLog(getClass());
protected boolean hardware_multicast_supported=false;
public MessageDispatcher() {
}
public MessageDispatcher(Channel channel, MessageListener l, MembershipListener l2) {
this.channel=channel;
prot_adapter=new ProtocolAdapter();
if(channel != null) {
local_addr=channel.getAddress();
}
setMessageListener(l);
setMembershipListener(l2);
if(channel != null) {
channel.setUpHandler(prot_adapter);
}
start();
}
@Deprecated
public MessageDispatcher(Channel channel, MessageListener l, MembershipListener l2, boolean deadlock_detection) {
this.channel=channel;
prot_adapter=new ProtocolAdapter();
if(channel != null) {
local_addr=channel.getAddress();
}
setMessageListener(l);
setMembershipListener(l2);
if(channel != null) {
channel.setUpHandler(prot_adapter);
}
start();
}
@Deprecated
public MessageDispatcher(Channel channel, MessageListener l, MembershipListener l2,
boolean deadlock_detection, boolean concurrent_processing) {
this.channel=channel;
prot_adapter=new ProtocolAdapter();
if(channel != null) {
local_addr=channel.getAddress();
}
setMessageListener(l);
setMembershipListener(l2);
if(channel != null) {
channel.setUpHandler(prot_adapter);
}
start();
}
public MessageDispatcher(Channel channel, MessageListener l, MembershipListener l2, RequestHandler req_handler) {
this(channel, l, l2);
setRequestHandler(req_handler);
}
@Deprecated
public MessageDispatcher(Channel channel, MessageListener l, MembershipListener l2, RequestHandler req_handler,
boolean deadlock_detection) {
this(channel, l, l2, deadlock_detection, false);
setRequestHandler(req_handler);
}
@Deprecated
public MessageDispatcher(Channel channel, MessageListener l, MembershipListener l2, RequestHandler req_handler,
boolean deadlock_detection, boolean concurrent_processing) {
this(channel, l, l2, deadlock_detection, concurrent_processing);
setRequestHandler(req_handler);
}
@Deprecated
public MessageDispatcher(PullPushAdapter adapter, Serializable id, MessageListener l, MembershipListener l2) {
this.adapter=adapter;
this.id=id;
setMembers(((Channel) adapter.getTransport()).getView().getMembers());
setMessageListener(l);
setMembershipListener(l2);
handler=new PullPushHandler();
transport_adapter=new TransportAdapter();
adapter.addMembershipListener(handler); // remove in stop()
if(id == null) { // no other building block around, let's become the main consumer of this PullPushAdapter
adapter.setListener(handler);
}
else {
adapter.registerListener(id, handler);
}
Transport tp;
if((tp=adapter.getTransport()) instanceof Channel) {
local_addr=((Channel) tp).getAddress();
}
start();
}
@Deprecated
public MessageDispatcher(PullPushAdapter adapter, Serializable id,
MessageListener l, MembershipListener l2,
RequestHandler req_handler) {
this.adapter=adapter;
this.id=id;
setMembers(((Channel) adapter.getTransport()).getView().getMembers());
setRequestHandler(req_handler);
setMessageListener(l);
setMembershipListener(l2);
handler=new PullPushHandler();
transport_adapter=new TransportAdapter();
adapter.addMembershipListener(handler);
if(id == null) { // no other building block around, let's become the main consumer of this PullPushAdapter
adapter.setListener(handler);
}
else {
adapter.registerListener(id, handler);
}
Transport tp;
if((tp=adapter.getTransport()) instanceof Channel) {
local_addr=((Channel) tp).getAddress(); // fixed bug #800774
}
start();
}
@Deprecated
public MessageDispatcher(PullPushAdapter adapter, Serializable id,
MessageListener l, MembershipListener l2,
RequestHandler req_handler, boolean concurrent_processing) {
this.adapter=adapter;
this.id=id;
setMembers(((Channel) adapter.getTransport()).getView().getMembers());
setRequestHandler(req_handler);
setMessageListener(l);
setMembershipListener(l2);
handler=new PullPushHandler();
transport_adapter=new TransportAdapter();
adapter.addMembershipListener(handler);
if(id == null) { // no other building block around, let's become the main consumer of this PullPushAdapter
adapter.setListener(handler);
}
else {
adapter.registerListener(id, handler);
}
Transport tp;
if((tp=adapter.getTransport()) instanceof Channel) {
local_addr=((Channel) tp).getAddress(); // fixed bug #800774
}
start();
}
public UpHandler getProtocolAdapter() {
return prot_adapter;
}
/** Returns a copy of members */
protected Collection getMembers() {
synchronized(members) {
return new ArrayList(members);
}
}
/**
* If this dispatcher is using a user-provided PullPushAdapter, then need to set the members from the adapter
* initially since viewChange has most likely already been called in PullPushAdapter.
*/
private void setMembers(Vector new_mbrs) {
if(new_mbrs != null) {
synchronized(members) {
members.clear();
members.addAll(new_mbrs);
}
}
}
@Deprecated
public boolean getDeadlockDetection() {return false;}
@Deprecated
public void setDeadlockDetection(boolean flag) {
}
@Deprecated
public boolean getConcurrentProcessing() {return false;}
@Deprecated
public void setConcurrentProcessing(boolean flag) {
}
public void start() {
if(corr == null) {
if(transport_adapter != null) {
corr=createRequestCorrelator(transport_adapter, this, local_addr);
}
else {
corr=createRequestCorrelator(prot_adapter, this, local_addr);
}
}
correlatorStarted();
corr.start();
if(channel != null) {
Vector tmp_mbrs=channel.getView() != null ? channel.getView().getMembers() : null;
setMembers(tmp_mbrs);
if(channel instanceof JChannel) {
TP transport=channel.getProtocolStack().getTransport();
corr.registerProbeHandler(transport);
}
TP transport=channel.getProtocolStack().getTransport();
hardware_multicast_supported=transport.supportsMulticasting();
}
}
protected RequestCorrelator createRequestCorrelator(Object transport, RequestHandler handler, Address local_addr) {
return new RequestCorrelator(transport, handler, local_addr);
}
protected void correlatorStarted() {
;
}
public void stop() {
if(corr != null) {
corr.stop();
}
if(channel instanceof JChannel) {
TP transport=channel.getProtocolStack().getTransport();
corr.unregisterProbeHandler(transport);
}
if(adapter != null && handler != null) {
adapter.removeMembershipListener(handler);
}
}
public final void setMessageListener(MessageListener l) {
msg_listener=l;
}
/**
* Gives access to the currently configured MessageListener. Returns null if there is no
* configured MessageListener.
*/
public MessageListener getMessageListener() {
return msg_listener;
}
public final void setMembershipListener(MembershipListener l) {
membership_listener=l;
}
public final void setRequestHandler(RequestHandler rh) {
req_handler=rh;
}
/**
* Offers access to the underlying Channel.
* @return a reference to the underlying Channel.
*/
public Channel getChannel() {
return channel;
}
public void setChannel(Channel ch) {
if(ch == null)
return;
this.channel=ch;
local_addr=channel.getAddress();
if(prot_adapter == null)
prot_adapter=new ProtocolAdapter();
if (channel.getUpHandler() == null) {
channel.setUpHandler(prot_adapter);
}
}
@Deprecated
public void send(Message msg) throws ChannelNotConnectedException, ChannelClosedException {
if(channel != null) {
channel.send(msg);
return;
}
if(adapter != null) {
try {
if(id != null)
adapter.send(id, msg);
else
adapter.send(msg);
}
catch(Throwable ex) {
log.error("exception=" + Util.print(ex));
}
}
else {
log.error("channel == null");
}
}
@Deprecated
public RspList castMessage(final Vector dests, Message msg, int mode, long timeout) {
return castMessage(dests, msg, new RequestOptions(mode, timeout, false, null));
}
@Deprecated
public RspList castMessage(final Vector dests, Message msg, int mode, long timeout, boolean use_anycasting) {
return castMessage(dests, msg, new RequestOptions(mode, timeout, use_anycasting, null));
}
// used by Infinispan
@Deprecated
/**
* @deprecated Use {@link #castMessage(java.util.Collection, org.jgroups.Message, RequestOptions)} instead
*/
public RspList castMessage(final Vector dests, Message msg, int mode, long timeout, boolean use_anycasting,
RspFilter filter) {
RequestOptions opts=new RequestOptions(mode, timeout, use_anycasting, filter);
return castMessage(dests, msg, opts);
}
/**
* Sends a message to the members listed in dests. If dests is null, the message is sent to all current group
* members.
* @param dests A list of group members. The message is sent to all members of the current group if null
* @param msg The message to be sent
* @param options A set of options that govern the call. See {@link org.jgroups.blocks.RequestOptions} for details
* @return
* @since 2.9
*/
public RspList castMessage(final Collection<Address> dests, Message msg, RequestOptions options) {
GroupRequest req=cast(dests, msg, options, true);
return req != null? req.getResults() : RspList.EMPTY_RSP_LIST;
}
@Deprecated
public NotifyingFuture<RspList> castMessageWithFuture(final Vector dests, Message msg, int mode, long timeout, boolean use_anycasting,
RspFilter filter) {
return castMessageWithFuture(dests, msg, new RequestOptions(mode, timeout, use_anycasting, filter));
}
public NotifyingFuture<RspList> castMessageWithFuture(final Collection<Address> dests, Message msg, RequestOptions options) {
GroupRequest req=cast(dests, msg, options, false);
return req != null? req : new NullFuture(RspList.EMPTY_RSP_LIST);
}
protected GroupRequest cast(final Collection<Address> dests, Message msg, RequestOptions options, boolean block_for_results) {
List<Address> real_dests;
// we need to clone because we don't want to modify the original
// (we remove ourselves if LOCAL is false, see below) !
// real_dests=dests != null ? (Vector) dests.clone() : (members != null ? new Vector(members) : null);
if(dests != null) {
real_dests=new ArrayList<Address>(dests);
real_dests.retainAll(this.members);
}
else {
synchronized(members) {
real_dests=new ArrayList(members);
}
}
// if local delivery is off, then we should not wait for the message from the local member.
// therefore remove it from the membership
Channel tmp=channel;
if(tmp == null) {
if(adapter != null && adapter.getTransport() instanceof Channel) {
tmp=(Channel) adapter.getTransport();
}
}
if(tmp != null && tmp.getOpt(Channel.LOCAL).equals(Boolean.FALSE)) {
if(local_addr == null) {
local_addr=tmp.getAddress();
}
if(local_addr != null) {
real_dests.remove(local_addr);
}
}
// don't even send the message if the destination list is empty
if(log.isTraceEnabled())
log.trace("real_dests=" + real_dests);
if(real_dests.isEmpty()) {
if(log.isTraceEnabled())
log.trace("destination list is empty, won't send message");
return null;
}
GroupRequest req=new GroupRequest(msg, corr, real_dests, options);
req.setResponseFilter(options.getRspFilter());
req.setBlockForResults(block_for_results);
// we override anycasting and always send a multicast if the transport supports IP multicasting
// boolean use_anycasting=options.getAnycasting() && !hardware_multicast_supported;
// req.setAnycasting(use_anycasting);
req.setAnycasting(options.getAnycasting());
try {
req.execute();
return req;
}
catch(Exception ex) {
throw new RuntimeException("failed executing request " + req, ex);
}
}
public void done(long req_id) {
corr.done(req_id);
}
/**
* Sends a message to a single member (destination = msg.dest) and returns the response. The message's destination
* must be non-zero !
* @deprecated Use {@link #sendMessage(org.jgroups.Message, RequestOptions)} instead
*/
@Deprecated
public Object sendMessage(Message msg, int mode, long timeout) throws TimeoutException, SuspectedException {
return sendMessage(msg, new RequestOptions(mode, timeout, false, null));
}
public Object sendMessage(Message msg, RequestOptions opts) throws TimeoutException, SuspectedException {
Address dest=msg.getDest();
if(dest == null) {
if(log.isErrorEnabled())
log.error("the message's destination is null, cannot send message");
return null;
}
UnicastRequest req=new UnicastRequest(msg, corr, dest, opts);
try {
req.execute();
}
catch(Exception t) {
throw new RuntimeException("failed executing request " + req, t);
}
if(opts.getMode() == Request.GET_NONE)
return null;
Rsp rsp=req.getResult();
if(rsp.wasSuspected())
throw new SuspectedException(dest);
if(!rsp.wasReceived())
throw new TimeoutException("timeout sending message to " + dest);
return rsp.getValue();
}
@Deprecated
public <T> NotifyingFuture<T> sendMessageWithFuture(Message msg, int mode, long timeout) throws TimeoutException, SuspectedException {
return sendMessageWithFuture(msg, new RequestOptions(mode, timeout, false, null));
}
public <T> NotifyingFuture<T> sendMessageWithFuture(Message msg, RequestOptions options) throws TimeoutException, SuspectedException {
Address dest=msg.getDest();
if(dest == null) {
if(log.isErrorEnabled())
log.error("the message's destination is null, cannot send message");
return null;
}
UnicastRequest req=new UnicastRequest(msg, corr, dest, options);
req.setBlockForResults(false);
try {
req.execute();
if(options.getMode() == Request.GET_NONE)
return new NullFuture(null);
return req;
}
catch(Exception t) {
throw new RuntimeException("failed executing request " + req, t);
}
}
public Object handle(Message msg) {
if(req_handler != null) {
return req_handler.handle(msg);
}
else {
return null;
}
}
class ProtocolAdapter extends Protocol implements UpHandler {
public String getName() {
return "MessageDispatcher";
}
private Object handleUpEvent(Event evt) {
switch(evt.getType()) {
case Event.MSG:
if(msg_listener != null) {
msg_listener.receive((Message) evt.getArg());
}
break;
case Event.GET_APPLSTATE: // reply with GET_APPLSTATE_OK
StateTransferInfo info=(StateTransferInfo)evt.getArg();
String state_id=info.state_id;
byte[] tmp_state=null;
if(msg_listener != null) {
try {
if(msg_listener instanceof ExtendedMessageListener && state_id!=null) {
tmp_state=((ExtendedMessageListener)msg_listener).getState(state_id);
}
else {
tmp_state=msg_listener.getState();
}
}
catch(Throwable t) {
this.log.error("failed getting state from message listener (" + msg_listener + ')', t);
}
}
return new StateTransferInfo(null, state_id, 0L, tmp_state);
case Event.GET_STATE_OK:
if(msg_listener != null) {
try {
info=(StateTransferInfo)evt.getArg();
String id=info.state_id;
if(msg_listener instanceof ExtendedMessageListener && id!=null) {
((ExtendedMessageListener)msg_listener).setState(id, info.state);
}
else {
msg_listener.setState(info.state);
}
}
catch(ClassCastException cast_ex) {
if(this.log.isErrorEnabled())
this.log.error("received SetStateEvent, but argument " +
evt.getArg() + " is not serializable. Discarding message.");
}
}
break;
case Event.STATE_TRANSFER_OUTPUTSTREAM:
StateTransferInfo sti=(StateTransferInfo)evt.getArg();
OutputStream os=sti.outputStream;
if(msg_listener instanceof ExtendedMessageListener) {
if(os != null && msg_listener instanceof ExtendedMessageListener) {
if(sti.state_id == null)
((ExtendedMessageListener)msg_listener).getState(os);
else
((ExtendedMessageListener)msg_listener).getState(sti.state_id, os);
}
return new StateTransferInfo(null, os, sti.state_id);
}
else if(msg_listener instanceof MessageListener){
if(log.isWarnEnabled()){
log.warn("Channel has STREAMING_STATE_TRANSFER, however,"
+ " application does not implement ExtendedMessageListener. State is not transfered");
Util.close(os);
}
}
break;
case Event.STATE_TRANSFER_INPUTSTREAM:
sti=(StateTransferInfo)evt.getArg();
InputStream is=sti.inputStream;
if(msg_listener instanceof ExtendedMessageListener) {
if(is!=null && msg_listener instanceof ExtendedMessageListener) {
if(sti.state_id == null)
((ExtendedMessageListener)msg_listener).setState(is);
else
((ExtendedMessageListener)msg_listener).setState(sti.state_id, is);
}
}
else if(msg_listener instanceof MessageListener){
if(log.isWarnEnabled()){
log.warn("Channel has STREAMING_STATE_TRANSFER, however,"
+ " application does not implement ExtendedMessageListener. State is not transfered");
Util.close(is);
}
}
break;
case Event.VIEW_CHANGE:
View v=(View) evt.getArg();
Vector new_mbrs=v.getMembers();
setMembers(new_mbrs);
if(membership_listener != null) {
membership_listener.viewAccepted(v);
}
break;
case Event.SET_LOCAL_ADDRESS:
if(log.isTraceEnabled())
log.trace("setting local_addr (" + local_addr + ") to " + evt.getArg());
local_addr=(Address)evt.getArg();
break;
case Event.SUSPECT:
if(membership_listener != null) {
membership_listener.suspect((Address) evt.getArg());
}
break;
case Event.BLOCK:
if(membership_listener != null) {
membership_listener.block();
}
channel.blockOk();
break;
case Event.UNBLOCK:
if(membership_listener instanceof ExtendedMembershipListener) {
((ExtendedMembershipListener)membership_listener).unblock();
}
break;
}
return null;
}
/**
* Called by channel (we registered before) when event is received. This is the UpHandler interface.
*/
public Object up(Event evt) {
if(corr != null) {
if(!corr.receive(evt)) {
return handleUpEvent(evt);
}
}
else {
if(log.isErrorEnabled()) { //Something is seriously wrong, correlator should not be null since latch is not locked!
log.error("correlator is null, event will be ignored (evt=" + evt + ")");
}
}
return null;
}
public Object down(Event evt) {
if(channel != null) {
// if(!channel.isOpen() || !channel.isConnected())
// throw new RuntimeException("channel is closed or not connected");
return channel.downcall(evt);
}
else
if(this.log.isWarnEnabled()) {
this.log.warn("channel is null, discarding event " + evt);
}
return null;
}
}
@Deprecated
class TransportAdapter implements Transport {
public void send(Message msg) throws Exception {
if(channel != null) {
channel.send(msg);
}
else
if(adapter != null) {
try {
if(id != null) {
adapter.send(id, msg);
}
else {
adapter.send(msg);
}
}
catch(Throwable ex) {
if(log.isErrorEnabled()) {
log.error("exception=" + Util.print(ex));
}
}
}
else {
if(log.isErrorEnabled()) {
log.error("channel == null");
}
}
}
public Object receive(long timeout) throws Exception {
return null; // not supported and not needed
}
}
@Deprecated
class PullPushHandler implements ExtendedMessageListener, MembershipListener {
public void receive(Message msg) {
boolean consumed=false;
if(corr != null) {
consumed=corr.receiveMessage(msg);
}
if(!consumed) { // pass on to MessageListener
if(msg_listener != null) {
msg_listener.receive(msg);
}
}
}
public byte[] getState() {
return msg_listener != null ? msg_listener.getState() : null;
}
public byte[] getState(String state_id) {
if(msg_listener == null) return null;
if(msg_listener instanceof ExtendedMessageListener && state_id!=null) {
return ((ExtendedMessageListener)msg_listener).getState(state_id);
}
else {
return msg_listener.getState();
}
}
public void setState(byte[] state) {
if(msg_listener != null) {
msg_listener.setState(state);
}
}
public void setState(String state_id, byte[] state) {
if(msg_listener != null) {
if(msg_listener instanceof ExtendedMessageListener && state_id!=null) {
((ExtendedMessageListener)msg_listener).setState(state_id, state);
}
else {
msg_listener.setState(state);
}
}
}
public void getState(OutputStream ostream) {
if (msg_listener instanceof ExtendedMessageListener) {
((ExtendedMessageListener) msg_listener).getState(ostream);
}
}
public void getState(String state_id, OutputStream ostream) {
if (msg_listener instanceof ExtendedMessageListener && state_id!=null) {
((ExtendedMessageListener) msg_listener).getState(state_id,ostream);
}
}
public void setState(InputStream istream) {
if (msg_listener instanceof ExtendedMessageListener) {
((ExtendedMessageListener) msg_listener).setState(istream);
}
}
public void setState(String state_id, InputStream istream) {
if (msg_listener instanceof ExtendedMessageListener && state_id != null) {
((ExtendedMessageListener) msg_listener).setState(state_id,istream);
}
}
public void viewAccepted(View v) {
if(corr != null) {
corr.receiveView(v);
}
Vector new_mbrs=v.getMembers();
setMembers(new_mbrs);
if(membership_listener != null) {
membership_listener.viewAccepted(v);
}
}
public void suspect(Address suspected_mbr) {
if(corr != null) {
corr.receiveSuspect(suspected_mbr);
}
if(membership_listener != null) {
membership_listener.suspect(suspected_mbr);
}
}
public void block() {
if(membership_listener != null) {
membership_listener.block();
}
}
// @todo: receive SET_LOCAL_ADDR event and call corr.setLocalAddress(addr)
}
} |
package org.jitsi.service.neomedia;
/**
* The <tt>MediaType</tt> enumeration contains a list of media types
* currently known to and handled by the <tt>MediaService</tt>.
*
* @author Emil Ivov
*/
public enum MediaType
{
/**
* Represents an AUDIO media type.
*/
AUDIO("audio"),
/**
* Represents a (chat-) MESSAGE media type.
*/
MESSAGE("message"),
/**
* Represents a VIDEO media type.
*/
VIDEO("video");
/**
* The name of this <tt>MediaType</tt>.
*/
private final String mediaTypeName;
/**
* Creates a <tt>MediaType</tt> instance with the specified name.
*
* @param mediaTypeName the name of the <tt>MediaType</tt> we'd like to
* create.
*/
private MediaType(String mediaTypeName)
{
this.mediaTypeName = mediaTypeName;
}
/**
* Returns the name of this MediaType (e.g. "audio", "message" or "video").
* The name returned by this method is meant for use by session description
* mechanisms such as SIP/SDP or XMPP/Jingle.
*
* @return the name of this MediaType (e.g. "audio" or "video").
*/
@Override
public String toString()
{
return mediaTypeName;
}
public static MediaType parseString(String mediaTypeName)
throws IllegalArgumentException
{
if(AUDIO.toString().equals(mediaTypeName))
return AUDIO;
if(MESSAGE.toString().equals(mediaTypeName))
return MESSAGE;
if(VIDEO.toString().equals(mediaTypeName))
return VIDEO;
throw new IllegalArgumentException(
mediaTypeName + " is not a currently supported MediaType");
}
} |
package org.jmist.framework.services;
import java.io.IOException;
import java.util.zip.ZipOutputStream;
import org.jmist.framework.AbstractParallelizableJob;
import org.jmist.framework.TaskWorker;
import org.jmist.framework.reporting.ProgressMonitor;
/**
* A <code>ParallelizableJob</code> whose <code>TaskWorker</code>s idle for a
* specified amount of time.
* @author bkimmel
*/
public final class IdleJob extends AbstractParallelizableJob {
/**
* Creates a new <code>IdleJob</code>.
*/
public IdleJob() {
/* nothing to do. */
}
public IdleJob(int idleSeconds) throws IllegalArgumentException {
if (idleSeconds < 0) {
throw new IllegalArgumentException("idleSeconds must be non-negative.");
}
this.idleSeconds = idleSeconds;
}
public void setIdleTime(int idleSeconds) throws IllegalArgumentException {
if (idleSeconds < 0) {
throw new IllegalArgumentException("idleSeconds must be non-negative.");
}
this.idleSeconds = idleSeconds;
}
/* (non-Javadoc)
* @see org.jmist.framework.ParallelizableJob#getNextTask()
*/
@Override
public Object getNextTask() {
return this.idleSeconds;
}
/* (non-Javadoc)
* @see org.jmist.framework.ParallelizableJob#isComplete()
*/
@Override
public boolean isComplete() {
return false;
}
/* (non-Javadoc)
* @see org.jmist.framework.ParallelizableJob#submitTaskResults(java.lang.Object, java.lang.Object, org.jmist.framework.reporting.ProgressMonitor)
*/
@Override
public void submitTaskResults(Object task, Object results,
ProgressMonitor monitor) {
monitor.notifyIndeterminantProgress();
}
/* (non-Javadoc)
* @see org.jmist.framework.ParallelizableJob#worker()
*/
@Override
public TaskWorker worker() {
return worker;
}
/* (non-Javadoc)
* @see org.jmist.framework.ParallelizableJob#writeJobResults(java.util.zip.ZipOutputStream)
*/
@Override
public void writeJobResults(ZipOutputStream stream) throws IOException {
assert(false);
}
/**
* A <code>TaskWorker</code> that sleeps for the specified amount of time
* (in seconds), waking up each second to notify the
* <code>ProgressMonitor</code>.
* @author bkimmel
*/
private static class IdleTaskWorker implements TaskWorker {
/* (non-Javadoc)
* @see org.jmist.framework.TaskWorker#performTask(java.lang.Object, org.jmist.framework.reporting.ProgressMonitor)
*/
@Override
public Object performTask(Object task, ProgressMonitor monitor) {
int seconds = (Integer) task;
monitor.notifyStatusChanged("Idling...");
for (int i = 0; i < seconds; i++) {
if (!monitor.notifyProgress(i, seconds)) {
monitor.notifyCancelled();
return null;
}
this.sleep();
}
monitor.notifyProgress(seconds, seconds);
monitor.notifyComplete();
return null;
}
/**
* Sleeps for one second.
*/
private void sleep() {
try {
Thread.sleep(1000);
} catch (InterruptedException e) {
e.printStackTrace();
}
}
/**
* Serialization version ID.
*/
private static final long serialVersionUID = 4249862961124801480L;
}
/** The amount of time (in seconds) that workers should idle. */
private int idleSeconds = DEFAULT_IDLE_SECONDS;
/** The <code>TaskWorker</code> that idles for the given amount of time. */
private static final TaskWorker worker = new IdleTaskWorker();
/** The default amount of time (in seconds) that workers should idle. */
private static final int DEFAULT_IDLE_SECONDS = 60;
} |
package org.openid4java.server;
import org.openid4java.message.*;
import org.openid4java.association.AssociationSessionType;
import org.openid4java.association.AssociationException;
import org.openid4java.association.DiffieHellmanSession;
import org.openid4java.association.Association;
import org.openid4java.OpenIDException;
import java.net.URL;
import java.net.MalformedURLException;
import org.apache.log4j.Logger;
/**
* Manages OpenID communications with an OpenID Relying Party (Consumer).
*
* @author Marius Scurtescu, Johnny Bufu
*/
public class ServerManager
{
private static Logger _log = Logger.getLogger(ServerManager.class);
private static final boolean DEBUG = _log.isDebugEnabled();
/**
* Keeps track of the associations established with consumer sites.
*/
private ServerAssociationStore _sharedAssociations = new InMemoryServerAssociationStore();
/**
* Keeps track of private (internal) associations created for signing
* authentication responses for stateless consumer sites.
*/
private ServerAssociationStore _privateAssociations = new InMemoryServerAssociationStore();
/**
* Nonce generator implementation.
*/
private NonceGenerator _nonceGenerator = new IncrementalNonceGenerator();
/**
* The lowest encryption level session accepted for association sessions
*/
private AssociationSessionType _minAssocSessEnc
= AssociationSessionType.NO_ENCRYPTION_SHA1MAC;
/**
* The preferred association session type; will be attempted first.
*/
private AssociationSessionType _prefAssocSessEnc
= AssociationSessionType.DH_SHA256;
/**
* Expiration time (in seconds) for associations.
*/
private int _expireIn = 1800;
/**
* In OpenID 1.x compatibility mode, the URL at the OpenID Provider where
* the user should be directed when a immediate authentication request
* fails.
* <p>
* MUST be configured in order for the OpenID provider to be able to
* respond correctly with AuthImmediateFailure messages in compatibility
* mode.
*/
private String _userSetupUrl = null;
/**
* List of coma-separated fields to be signed in authentication responses.
*/
private String _signFields;
/**
* Array of extension namespace URIs that the consumer manager will sign,
* if present in auth responses.
*/
private String[] _signExtensions;
/**
* Used to perform verify realms against return_to URLs.
*/
private RealmVerifier _realmVerifier;
/**
* The OpenID Provider's endpoint URL, where it accepts OpenID
* authentication requests.
* <p>
* This is a global setting for the ServerManager; can also be set on a
* per message basis.
*
* @see #authResponse(org.openid4java.message.ParameterList, String, String, boolean, String)
*/
private String _opEndpointUrl;
/**
* Gets the store implementation used for keeping track of the generated
* associations established with consumer sites.
*
* @see ServerAssociationStore
*/
public ServerAssociationStore getSharedAssociations()
{
return _sharedAssociations;
}
/**
* Sets the store implementation that will be used for keeping track of
* the generated associations established with consumer sites.
*
* @param sharedAssociations ServerAssociationStore implementation
* @see ServerAssociationStore
*/
public void setSharedAssociations(ServerAssociationStore sharedAssociations)
{
_sharedAssociations = sharedAssociations;
}
/**
* Gets the store implementation used for keeping track of the generated
* private associations (used for signing responses to stateless consumer
* sites).
*
* @see ServerAssociationStore
*/
public ServerAssociationStore getPrivateAssociations()
{
return _privateAssociations;
}
/**
* Sets the store implementation that will be used for keeping track of
* the generated private associations (used for signing responses to
* stateless consumer sites).
*
* @param privateAssociations ServerAssociationStore implementation
* @see ServerAssociationStore
*/
public void setPrivateAssociations(ServerAssociationStore privateAssociations)
{
_privateAssociations = privateAssociations;
}
/**
* Gets the minimum level of encryption configured for association sessions.
* <p>
* Default: no-encryption session, SHA1 MAC association
*/
public AssociationSessionType getMinAssocSessEnc()
{
return _minAssocSessEnc;
}
/**
* Gets the NonceGenerator used for generating nonce tokens to uniquely
* identify authentication responses.
*
* @see NonceGenerator
*/
public NonceGenerator getNonceGenerator()
{
return _nonceGenerator;
}
/**
* Sets the NonceGenerator implementation that will be used to generate
* nonce tokens to uniquely identify authentication responses.
*
* @see NonceGenerator
*/
public void setNonceGenerator(NonceGenerator nonceGenerator)
{
_nonceGenerator = nonceGenerator;
}
/**
* Configures the minimum level of encryption accepted for association
* sessions.
* <p>
* Default: no-encryption session, SHA1 MAC association
*/
public void setMinAssocSessEnc(AssociationSessionType minAssocSessEnc)
{
this._minAssocSessEnc = minAssocSessEnc;
}
/**
* Gets the preferred association / session type.
*/
public AssociationSessionType getPrefAssocSessEnc()
{
return _prefAssocSessEnc;
}
/**
* Sets the preferred association / session type.
*
* @see AssociationSessionType
*/
public void setPrefAssocSessEnc(AssociationSessionType type)
throws ServerException
{
if (! Association.isHmacSupported(type.getAssociationType()) ||
! DiffieHellmanSession.isDhSupported(type) )
throw new ServerException("Unsupported association / session type: "
+ type.getSessionType() + " : " + type.getAssociationType());
if (_minAssocSessEnc.isBetter(type) )
throw new ServerException(
"Minimum encryption settings cannot be better than the preferred");
this._prefAssocSessEnc = type;
}
/**
* Gets the expiration time (in seconds) for the generated associations
*/
public int getExpireIn()
{
return _expireIn;
}
/**
* Sets the expiration time (in seconds) for the generated associations
*/
public void setExpireIn(int _expireIn)
{
this._expireIn = _expireIn;
}
/**
* Gets the URL at the OpenID Provider where the user should be directed
* when a immediate authentication request fails.
*/
public String getUserSetupUrl()
{
return _userSetupUrl;
}
/**
* Sets the URL at the OpenID Provider where the user should be directed
* when a immediate authentication request fails.
*/
public void setUserSetupUrl(String userSetupUrl)
{
this._userSetupUrl = userSetupUrl;
}
/**
* Sets the list of parameters that the OpenID Provider will sign when
* generating authentication responses.
* <p>
* The fields in the list must be coma-separated and must not include the
* 'openid.' prefix. Fields that are required to be signed are automatically
* added by the underlying logic, so that a valid message is generated,
* regardles if they are included in the user-supplied list or not.
*/
public void setSignFields(String signFields)
{
this._signFields = signFields;
}
/**
* Gets the list of parameters that the OpenID Provider will sign when
* generating authentication responses.
* <p>
* Coma-separated list.
*/
public String getSignFields()
{
return _signFields;
}
public void setSignExtensions(String[] extensins)
{
_signExtensions = extensins;
}
public String[] getSignExtensions()
{
return _signExtensions;
}
/**
* Gets the RealmVerifier used to verify realms against return_to URLs.
*/
public RealmVerifier getRealmVerifier()
{
return _realmVerifier;
}
/**
* Sets the RealmVerifier used to verify realms against return_to URLs.
*/
public void setRealmVerifier(RealmVerifier realmVerifier)
{
this._realmVerifier = realmVerifier;
}
/**
* Gets OpenID Provider's endpoint URL, where it accepts OpenID
* authentication requests.
* <p>
* This is a global setting for the ServerManager; can also be set on a
* per message basis.
*
* @see #authResponse(org.openid4java.message.ParameterList, String, String, boolean, String)
*/
public String getOPEndpointUrl()
{
return _opEndpointUrl;
}
/**
* Sets the OpenID Provider's endpoint URL, where it accepts OpenID
* authentication requests.
* <p>
* This is a global setting for the ServerManager; can also be set on a
* per message basis.
*
* @see #authResponse(org.openid4java.message.ParameterList, String, String, boolean, String)
*/
public void setOPEndpointUrl(String opEndpointUrl)
{
this._opEndpointUrl = opEndpointUrl;
}
/**
* Constructs a ServerManager with default settings.
*/
public ServerManager()
{
// initialize a default realm verifier
_realmVerifier = new RealmVerifier();
}
/**
* Processes a Association Request and returns a Association Response
* message, according to the request parameters and the preferences
* configured for the OpenID Provider
*
* @return AssociationResponse upon successfull association,
* or AssociationError if no association
* was established
*
*/
public Message associationResponse(ParameterList requestParams)
{
boolean isVersion2 = requestParams.hasParameter("openid.ns");
_log.info("Processing association request...");
try
{
// build request message from response params (+ integrity check)
AssociationRequest assocReq =
AssociationRequest.createAssociationRequest(requestParams);
isVersion2 = assocReq.isVersion2();
AssociationSessionType type = assocReq.getType();
// is supported / allowed ?
if (! Association.isHmacSupported(type.getAssociationType()) ||
! DiffieHellmanSession.isDhSupported(type) ||
_minAssocSessEnc.isBetter(type))
{
throw new AssociationException("Unable create association for: "
+ type.getSessionType() + " / "
+ type.getAssociationType() );
}
else // all ok, go ahead
{
Association assoc = _sharedAssociations.generate(
type.getAssociationType(), _expireIn);
_log.info("Returning shared association; handle: " + assoc.getHandle());
return AssociationResponse.createAssociationResponse(assocReq, assoc);
}
}
catch (OpenIDException e)
{
// association failed, respond accordingly
if (isVersion2)
{
_log.warn("Cannot establish association, " +
"responding with an OpenID2 association error.", e);
return AssociationError.createAssociationError(
e.getMessage(), _prefAssocSessEnc);
}
else
{
_log.warn("Error processing an OpenID1 association request; " +
"responding with a dummy association", e);
try
{
// generate dummy association & no-encryption response
// for compatibility mode
Association dummyAssoc = _sharedAssociations.generate(
Association.TYPE_HMAC_SHA1, 0);
AssociationRequest dummyRequest =
AssociationRequest.createAssociationRequest(
AssociationSessionType.NO_ENCRYPTION_COMPAT_SHA1MAC);
return AssociationResponse.createAssociationResponse(
dummyRequest, dummyAssoc);
}
catch (OpenIDException ee)
{
_log.error("Error creating negative OpenID1 association response.", e);
return null;
}
}
}
}
/**
* Processes a Authentication Request received from a consumer site.
* <p>
* Uses ServerManager's global OpenID Provider endpoint URL.
*
* @return An signed positive Authentication Response if successfull,
* or an IndirectError / DirectError message.
* @see #authResponse(org.openid4java.message.ParameterList, String, String,
* boolean, String, boolean)
*/
public Message authResponse(ParameterList requestParams,
String userSelId,
String userSelClaimed,
boolean authenticatedAndApproved)
{
return authResponse(requestParams, userSelId, userSelClaimed,
authenticatedAndApproved, _opEndpointUrl, true);
}
/**
* Processes a Authentication Request received from a consumer site.
* <p>
* Uses ServerManager's global OpenID Provider endpoint URL.
*
* @return A positive Authentication Response if successfull,
* or an IndirectError / DirectError message.
* @see #authResponse(org.openid4java.message.ParameterList, String, String,
* boolean, String, boolean)
*/
public Message authResponse(ParameterList requestParams,
String userSelId,
String userSelClaimed,
boolean authenticatedAndApproved,
boolean signNow)
{
return authResponse(requestParams, userSelId, userSelClaimed,
authenticatedAndApproved, _opEndpointUrl, signNow);
}
/**
* Processes a Authentication Request received from a consumer site.
* <p>
*
* @return An signed positive Authentication Response if successfull,
* or an IndirectError / DirectError message.
* @see #authResponse(org.openid4java.message.ParameterList, String, String,
* boolean, String, boolean)
*/
public Message authResponse(ParameterList requestParams,
String userSelId,
String userSelClaimed,
boolean authenticatedAndApproved,
String opEndpoint)
{
return authResponse(requestParams, userSelId, userSelClaimed,
authenticatedAndApproved, opEndpoint, true);
}
/**
* Processes a Authentication Request received from a consumer site.
*
* @param opEndpoint The endpoint URL where the OP accepts OpenID
* authentication requests.
* @param requestParams The parameters contained
* in the authentication request message received
* from a consumer site.
* @param userSelId OP-specific Identifier selected by the user at
* the OpenID Provider; if present it will override
* the one received in the authentication request.
* @param userSelClaimed Claimed Identifier selected by the user at
* the OpenID Provider; if present it will override
* the one received in the authentication request.
* @param authenticatedAndApproved Flag indicating that the IdP has
* authenticated the user and the user
* has approved the authentication
* transaction
* @param signNow If true, the returned AuthSuccess will be signed.
* If false, the signature will not be computed and
* set - this will have to be performed later,
* using #sign(org.openid4java.message.Message).
*
* @return <ul><li> AuthSuccess, if authenticatedAndApproved
* <li> AuthFailure (negative response) if either
* of authenticatedAndApproved is false;
* <li> A IndirectError or DirectError message
* if the authentication could not be performed, or
* <li> Null if there was no return_to parameter
* specified in the AuthRequest.</ul>
*/
public Message authResponse(ParameterList requestParams,
String userSelId,
String userSelClaimed,
boolean authenticatedAndApproved,
String opEndpoint,
boolean signNow)
{
_log.info("Processing authentication request...");
boolean isVersion2 = true;
try
{
new URL(opEndpoint);
}
catch (MalformedURLException e)
{
_log.error("Invalid OP-endpoint configured; " +
"cannot issue OpenID authentication responses." + opEndpoint);
return DirectError.createDirectError(
"Invalid OpenID Provider endpoint URL; " +
"cannot issue authentication response", isVersion2);
}
try
{
// build request message from response params (+ integrity check)
AuthRequest authReq = AuthRequest.createAuthRequest(
requestParams, _realmVerifier);
isVersion2 = authReq.isVersion2();
if (authReq.getReturnTo() == null)
{
_log.error("Received valid auth request, but no return_to " +
"specified; authResponse() should not be called.");
return null;
}
String id;
String claimed;
if (AuthRequest.SELECT_ID.equals(authReq.getIdentity()))
{
id = userSelId;
claimed = userSelClaimed;
}
else
{
id = userSelId != null ? userSelId : authReq.getIdentity();
claimed = userSelClaimed != null ? userSelClaimed :
authReq.getClaimed();
}
if (id == null)
throw new ServerException(
"No identifier provided by the authntication request" +
"or by the OpenID Provider");
if (DEBUG) _log.debug("Using ClaimedID: " + claimed +
" OP-specific ID: " + id);
if (authenticatedAndApproved) // positive response
{
Association assoc = null;
String handle = authReq.getHandle();
String invalidateHandle = null;
if (handle != null)
{
assoc = _sharedAssociations.load(handle);
if (assoc == null)
{
_log.info("Invalidating handle: " + handle);
invalidateHandle = handle;
}
else
_log.info("Loaded shared association; hadle: " + handle);
}
if (assoc == null)
{
assoc = _privateAssociations.generate(
_prefAssocSessEnc.getAssociationType(),
_expireIn);
_log.info("Generated private association; handle: "
+ assoc.getHandle());
}
AuthSuccess response = AuthSuccess.createAuthSuccess(
opEndpoint, claimed, id, !isVersion2,
authReq.getReturnTo(),
isVersion2 ? _nonceGenerator.next() : null,
invalidateHandle, assoc, false);
if (_signFields != null)
response.setSignFields(_signFields);
if (_signExtensions != null)
response.setSignExtensions(_signExtensions);
if (signNow)
response.setSignature(assoc.sign(response.getSignedText()));
_log.info("Returning positive assertion for " +
response.getReturnTo());
return response;
}
else // negative response
{
if (authReq.isImmediate())
{
_log.error("Responding with immediate authentication " +
"failure to " + authReq.getReturnTo());
return AuthImmediateFailure.createAuthImmediateFailure(
_userSetupUrl, authReq.getReturnTo(), ! isVersion2);
}
else
{
_log.error("Responding with authentication failure to " +
authReq.getReturnTo());
return new AuthFailure(! isVersion2, authReq.getReturnTo());
}
}
}
catch (OpenIDException e)
{
if (requestParams.hasParameter("openid.return_to"))
{
_log.error("Error processing an authentication request; " +
"responding with an indirect error message.", e);
return IndirectError.createIndirectError(e.getMessage(),
requestParams.getParameterValue("openid.return_to"),
! isVersion2 );
}
else
{
_log.error("Error processing an authentication request; " +
"responding with an direct error message.", e);
return DirectError.createDirectError( e.getMessage(), isVersion2 );
}
}
}
/**
* Signs an AuthSuccess message, using the association identified by the
* handle specified within the message.
*/
public void sign(Message msg) throws ServerException, AssociationException
{
if (! (msg instanceof AuthSuccess) ) throw new ServerException(
"Cannot sign message of type: " + msg.getClass());
AuthSuccess authResp = (AuthSuccess) msg;
String handle = authResp.getHandle();
// try shared associations first, then private
Association assoc = _sharedAssociations.load(handle);
if (assoc == null)
assoc = _privateAssociations.load(handle);
if (assoc == null) throw new ServerException(
"No association found for handle: " + handle);
authResp.setSignature(assoc.sign(authResp.getSignedText()));
}
/**
* Responds to a verification request from the consumer.
*
* @param requestParams ParameterList containing the parameters received
* in a verification request from a consumer site.
* @return VerificationResponse to be sent back to the
* consumer site.
*/
public Message verify(ParameterList requestParams)
{
_log.info("Processing verification request...");
boolean isVersion2 = true;
try
{
// build request message from response params (+ ntegrity check)
VerifyRequest vrfyReq = VerifyRequest.createVerifyRequest(requestParams);
isVersion2 = vrfyReq.isVersion2();
String handle = vrfyReq.getHandle();
boolean verified = false;
Association assoc = _privateAssociations.load(handle);
if (assoc != null) // verify the signature
{
_log.info("Loaded private association; handle: " + handle);
verified = assoc.verifySignature(
vrfyReq.getSignedText(),
vrfyReq.getSignature());
// remove the association so that the request
// cannot be verified more than once
_privateAssociations.remove(handle);
}
VerifyResponse vrfyResp =
VerifyResponse.createVerifyResponse(! vrfyReq.isVersion2());
vrfyResp.setSignatureVerified(verified);
if (verified)
{
String invalidateHandle = vrfyReq.getInvalidateHandle();
if (invalidateHandle != null &&
_sharedAssociations.load(invalidateHandle) == null) {
_log.info("Confirming shared association invalidate handle: "
+ invalidateHandle);
vrfyResp.setInvalidateHandle(invalidateHandle);
}
}
else
_log.error("Signature verification failed, handle: " + handle);
_log.info("Responding with " + (verified? "positive" : "negative")
+ " verification response");
return vrfyResp;
}
catch (OpenIDException e)
{
_log.error("Error processing verification request; " +
"responding with verificatioin error.", e);
return DirectError.createDirectError(e.getMessage(), ! isVersion2);
}
}
} |
package org.spine3.examples.todolist.c.aggregates.definition;
import com.google.protobuf.Message;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.DisplayName;
import org.junit.jupiter.api.Test;
import org.spine3.base.CommandContext;
import org.spine3.examples.todolist.TaskId;
import org.spine3.examples.todolist.c.aggregates.TaskDefinitionPart;
import org.spine3.examples.todolist.c.commands.CreateBasicTask;
import org.spine3.examples.todolist.c.events.TaskCreated;
import java.util.List;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotNull;
import static org.spine3.examples.todolist.testdata.TestTaskCommandFactory.DESCRIPTION;
import static org.spine3.examples.todolist.testdata.TestTaskCommandFactory.createTaskInstance;
/**
* @author Illia Shepilov
*/
@DisplayName("CreateBasicTask command")
public class CreateBasicTaskTest extends TaskDefinitionCommandTest<CreateBasicTask> {
private final CommandContext commandContext = createCommandContext();
private TaskDefinitionPart aggregate;
private TaskId taskId;
@Override
@BeforeEach
public void setUp() {
taskId = createTaskId();
aggregate = createTaskDefinitionPart(taskId);
}
@Test
@DisplayName("produces TaskCreated event")
public void producesEvent() {
final CreateBasicTask createTaskCmd = createTaskInstance(taskId, DESCRIPTION);
final List<? extends Message> messageList =
aggregate.dispatchForTest(createTaskCmd, commandContext);
assertNotNull(aggregate.getState()
.getCreated());
assertNotNull(aggregate.getId());
final int expectedListSize = 1;
assertEquals(expectedListSize, messageList.size());
assertEquals(TaskCreated.class, messageList.get(0)
.getClass());
final TaskCreated taskCreated = (TaskCreated) messageList.get(0);
assertEquals(taskId, taskCreated.getId());
assertEquals(DESCRIPTION, taskCreated.getDetails()
.getDescription());
}
} |
import org.junit.Test;
import org.junit.Ignore;
import java.util.Arrays;
import java.util.List;
import java.util.Collections;
import static org.junit.Assert.assertEquals;
public class AllergiesTest {
@Test
public void noAllergiesMeansNotAllergicToAnything() {
Allergies allergies = new Allergies(0);
assertEquals(false, allergies.isAllergicTo(Allergen.EGGS));
assertEquals(false, allergies.isAllergicTo(Allergen.PEANUTS));
assertEquals(false, allergies.isAllergicTo(Allergen.STRAWBERRIES));
assertEquals(false, allergies.isAllergicTo(Allergen.CATS));
}
@Ignore("Remove to run test")
@Test
public void allergicToEggs() {
Allergies allergies = new Allergies(1);
assertEquals(true, allergies.isAllergicTo(Allergen.EGGS));
}
@Ignore("Remove to run test")
@Test
public void allergicToPeanuts() {
Allergies allergies = new Allergies(2);
assertEquals(true, allergies.isAllergicTo(Allergen.PEANUTS));
}
@Ignore("Remove to run test")
@Test
public void allergicToShellfish() {
Allergies allergies = new Allergies(4);
assertEquals(true, allergies.isAllergicTo(Allergen.SHELLFISH));
}
@Ignore("Remove to run test")
@Test
public void allergicToStrawberries() {
Allergies allergies = new Allergies(8);
assertEquals(true, allergies.isAllergicTo(Allergen.STRAWBERRIES));
}
@Ignore("Remove to run test")
@Test
public void allergicToTomatoes() {
Allergies allergies = new Allergies(16);
assertEquals(true, allergies.isAllergicTo(Allergen.TOMATOES));
}
@Ignore("Remove to run test")
@Test
public void allergicToChocolate() {
Allergies allergies = new Allergies(32);
assertEquals(true, allergies.isAllergicTo(Allergen.CHOCOLATE));
}
@Ignore("Remove to run test")
@Test
public void allergicToPollen() {
Allergies allergies = new Allergies(64);
assertEquals(true, allergies.isAllergicTo(Allergen.POLLEN));
}
@Ignore("Remove to run test")
@Test
public void allergicToCats() {
Allergies allergies = new Allergies(128);
assertEquals(true, allergies.isAllergicTo(Allergen.CATS));
}
@Ignore("Remove to run test")
@Test
public void isAllergicToEggsInAdditionToOtherStuff() {
Allergies allergies = new Allergies(5);
assertEquals(true, allergies.isAllergicTo(Allergen.EGGS));
assertEquals(true, allergies.isAllergicTo(Allergen.SHELLFISH));
assertEquals(false, allergies.isAllergicTo(Allergen.STRAWBERRIES));
}
@Ignore("Remove to run test")
@Test
public void noAllergies() {
Allergies allergies = new Allergies(0);
assertEquals(0, allergies.getList().size());
}
@Ignore("Remove to run test")
@Test
public void isAllergicToJustEggs() {
Allergies allergies = new Allergies(1);
List<Allergen> expectedAllergens = Collections.singletonList(Allergen.EGGS);
assertEquals(expectedAllergens, allergies.getList());
}
@Ignore("Remove to run test")
@Test
public void isAllergicToJustPeanuts() {
Allergies allergies = new Allergies(2);
List<Allergen> expectedAllergens = Collections.singletonList(Allergen.PEANUTS);
assertEquals(expectedAllergens, allergies.getList());
}
@Ignore("Remove to run test")
@Test
public void isAllergicToJustStrawberries() {
Allergies allergies = new Allergies(8);
List<Allergen> expectedAllergens = Collections.singletonList(Allergen.STRAWBERRIES);
assertEquals(expectedAllergens, allergies.getList());
}
@Ignore("Remove to run test")
@Test
public void isAllergicToEggsAndPeanuts() {
Allergies allergies = new Allergies(3);
List<Allergen> expectedAllergens = Arrays.asList(
Allergen.EGGS,
Allergen.PEANUTS
);
assertEquals(expectedAllergens, allergies.getList());
}
@Ignore("Remove to run test")
@Test
public void isAllergicToEggsAndShellfish() {
Allergies allergies = new Allergies(5);
List<Allergen> expectedAllergens = Arrays.asList(
Allergen.EGGS,
Allergen.SHELLFISH
);
assertEquals(expectedAllergens, allergies.getList());
}
@Ignore("Remove to run test")
@Test
public void isAllergicToLotsOfStuff() {
Allergies allergies = new Allergies(248);
List<Allergen> expectedAllergens = Arrays.asList(
Allergen.STRAWBERRIES,
Allergen.TOMATOES,
Allergen.CHOCOLATE,
Allergen.POLLEN,
Allergen.CATS
);
assertEquals(expectedAllergens, allergies.getList());
}
@Ignore("Remove to run test")
@Test
public void isAllergicToEverything() {
Allergies allergies = new Allergies(255);
List<Allergen> expectedAllergens = Arrays.asList(
Allergen.EGGS,
Allergen.PEANUTS,
Allergen.SHELLFISH,
Allergen.STRAWBERRIES,
Allergen.TOMATOES,
Allergen.CHOCOLATE,
Allergen.POLLEN,
Allergen.CATS
);
assertEquals(expectedAllergens, allergies.getList());
}
@Ignore("Remove to run test")
@Test
public void ignoreNonAllergenScoreParts() {
Allergies allergies = new Allergies(509);
List<Allergen> expectedAllergens = Arrays.asList(
Allergen.EGGS,
Allergen.SHELLFISH,
Allergen.STRAWBERRIES,
Allergen.TOMATOES,
Allergen.CHOCOLATE,
Allergen.POLLEN,
Allergen.CATS
);
assertEquals(expectedAllergens, allergies.getList());
}
} |
package org.phenoscape.io;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.util.Comparator;
import java.util.List;
import org.phenoscape.model.Character;
import org.phenoscape.model.DataSet;
import org.phenoscape.model.Phenotype;
import org.phenoscape.model.Specimen;
import org.phenoscape.model.State;
import org.phenoscape.model.Taxon;
import com.eekboom.utils.Strings;
import phenote.datamodel.OboUtil;
import ca.odell.glazedlists.SortedList;
public class TabDelimitedWriter {
private static final String TTO = "http://bioportal.bioontology.org/virtual/1081/";
private static final String TAO = "http://bioportal.bioontology.org/virtual/1110/";
private static final String PATO = "http://bioportal.bioontology.org/virtual/1107/";
private static final String LINK_FORMAT = "=HYPERLINK(\"%s\", \"%s\")";
private DataSet data;
public void setDataSet(DataSet data) {
this.data = data;
}
public void write(File aFile) throws IOException {
final BufferedWriter writer = new BufferedWriter(new FileWriter(aFile));
writer.write(this.getTaxonHeader());
writer.newLine();
for (Taxon taxon : this.data.getTaxa()) {
writer.write(this.getTaxonRow(taxon));
writer.newLine();
}
writer.newLine();
writer.newLine();
writer.write(this.getCharacterHeader());
writer.newLine();
int i = 1;
for (Character character : this.data.getCharacters()) {
writer.write(i + "\t");
i++;
writer.write(this.getCharacterRow(character));
writer.newLine();
}
writer.close();
}
private String getTaxonHeader() {
return "Publication Taxon\tTTO Taxon\tMatrix Taxon\tTaxon Comment\tSpecimens\t" + this.getColumnHeadings();
}
private String getColumnHeadings() {
final StringBuffer sb = new StringBuffer();
for (int i = 1; i <= data.getCharacters().size(); i++) {
sb.append(i);
if (i < data.getCharacters().size()) sb.append("\t");
}
return sb.toString();
}
private String getTaxonRow(Taxon taxon) {
final StringBuffer sb = new StringBuffer();
sb.append(taxon.getPublicationName());
sb.append("\t");
if (taxon.getValidName() != null) {
sb.append(String.format(LINK_FORMAT, TTO + taxon.getValidName().getID(), taxon.getValidName().getName()));
}
sb.append("\t");
sb.append(taxon.getMatrixTaxonName());
sb.append("\t");
sb.append(taxon.getComment());
sb.append("\t");
sb.append(this.getSpecimens(taxon));
sb.append("\t");
sb.append(this.getMatrix(taxon));
return sb.toString();
}
private String getSpecimens(Taxon taxon) {
final StringBuffer sb = new StringBuffer();
boolean first = true;
for (Specimen specimen : taxon.getSpecimens()) {
if (!first) sb.append(", ");
first = false;
sb.append(specimen.getCollectionCode() != null ? specimen.getCollectionCode().getName() + " " : "");
sb.append(specimen.getCatalogID());
}
return sb.toString();
}
private String getMatrix(Taxon taxon) {
final StringBuffer sb = new StringBuffer();
boolean first = true;
for (Character character : this.data.getCharacters()) {
if (!first) sb.append("\t");
first = false;
final State state = this.data.getStateForTaxon(taxon, character);
sb.append(state != null ? state.getSymbol() : "?");
}
return sb.toString();
}
private String getCharacterHeader() {
return "Character Number\tCharacter Description\tCharacter Comment\tState Number\tState Description\tState Comment\tEntity\tQuality\tRelated Entity\tCount\tComment";
}
private String getCharacterRow(Character character) {
final StringBuffer sb = new StringBuffer();
sb.append(character.getLabel());
sb.append("\t");
sb.append(character.getComment());
sb.append("\t");
sb.append(this.getStates(character));
return sb.toString();
}
private String getStates(Character character) {
final StringBuffer sb = new StringBuffer();
boolean first = true;
final List<State> sortedStates = new SortedList<State>(character.getStates(), new Comparator<State>() {
public int compare(State o1, State o2) {
return Strings.compareNatural(o1.getSymbol(), o2.getSymbol());
}});
for (State state : sortedStates) {
if (!first) sb.append("\n\t\t\t");
first = false;
sb.append(state.getSymbol());
sb.append("\t");
sb.append(state.getLabel());
sb.append("\t");
sb.append(state.getComment());
sb.append("\t");
sb.append(this.getPhenotypes(state));
}
return sb.toString();
}
private String getPhenotypes(State state) {
final StringBuffer sb = new StringBuffer();
boolean first = true;
for (Phenotype phenotype : state.getPhenotypes()) {
if (!first) sb.append("\n\t\t\t\t\t\t");
first = false;
if (phenotype.getEntity() != null) {
if (!OboUtil.isPostCompTerm(phenotype.getEntity())) {
sb.append(String.format(LINK_FORMAT, TAO + phenotype.getEntity().getID(), phenotype.getEntity().getName()));
} else {
sb.append(phenotype.getEntity().getName());
}
}
sb.append("\t");
if (phenotype.getQuality() != null) {
if (!OboUtil.isPostCompTerm(phenotype.getQuality())) {
sb.append(String.format(LINK_FORMAT, PATO + phenotype.getQuality().getID(), phenotype.getQuality().getName()));
} else {
sb.append(phenotype.getQuality().getName());
}
}
sb.append("\t");
if (phenotype.getRelatedEntity() != null) {
if (!OboUtil.isPostCompTerm(phenotype.getRelatedEntity())) {
sb.append(String.format(LINK_FORMAT, TAO + phenotype.getRelatedEntity().getID(), phenotype.getRelatedEntity().getName()));
} else {
sb.append(phenotype.getRelatedEntity().getName());
}
}
sb.append("\t");
sb.append(phenotype.getCount() != null ? phenotype.getCount() : "");
sb.append("\t");
sb.append(phenotype.getComment() != null ? phenotype.getComment() : "");
}
return sb.toString();
}
} |
package org.sugr.gearshift;
import java.util.Comparator;
import org.sugr.gearshift.G.SortBy;
import org.sugr.gearshift.G.SortOrder;
public class TorrentComparator implements Comparator<Torrent> {
private SortBy mSortBy = SortBy.STATUS;
private SortOrder mSortOrder = SortOrder.ASCENDING;
private SortBy mBaseSort = SortBy.AGE;
public void setSortingMethod(SortBy by, SortOrder order) {
mSortBy = by;
mSortOrder = order;
}
public SortBy getSortBy() {
return mSortBy;
}
public SortOrder getSortOrder() {
return mSortOrder;
}
public void setBaseComparator(SortBy by) {
mBaseSort = by;
}
public SortBy getBaseComparator() {
return mBaseSort;
}
@Override
public int compare(Torrent a, Torrent b) {
int ret = compare(a, b, mSortBy, mSortOrder);
if (ret == 0 && mBaseSort != mSortBy) {
ret = compare(a, b, mBaseSort, mSortOrder);
}
return ret;
}
private int compare(Torrent a, Torrent b, SortBy sort, SortOrder order) {
int ret = 0;
float delta;
switch(sort) {
case NAME:
ret = a.getName() == null && b.getName() == null
? 0 : a.getName() == null
? -1 : a.getName().compareToIgnoreCase(b.getName());
break;
case SIZE:
ret = (int) (a.getTotalSize() - b.getTotalSize());
break;
case STATUS:
ret = (a.getStatus() == Torrent.Status.STOPPED
? a.getStatus() + 100 : a.getStatus() == Torrent.Status.CHECK_WAITING
? a.getStatus() + 10 : a.getStatus() == Torrent.Status.DOWNLOAD_WAITING
? a.getStatus() + 20 : a.getStatus() == Torrent.Status.SEED_WAITING
? a.getStatus() + 30 : a.getStatus())
- (b.getStatus() == Torrent.Status.STOPPED
? b.getStatus() + 100 : b.getStatus() == Torrent.Status.CHECK_WAITING
? b.getStatus() + 10 : b.getStatus() == Torrent.Status.DOWNLOAD_WAITING
? b.getStatus() + 20 : b.getStatus() == Torrent.Status.SEED_WAITING
? b.getStatus() + 30 : b.getStatus());
break;
case ACTIVITY:
ret = (int) ((b.getRateDownload() + b.getRateUpload()) - (a.getRateDownload() + a.getRateUpload()));
break;
case AGE:
ret = (int) (b.getAddedDate() - a.getAddedDate());
break;
case LOCATION:
ret = a.getDownloadDir() == null && b.getDownloadDir() == null
? 0 : a.getDownloadDir() == null
? -1 : a.getDownloadDir().compareToIgnoreCase(b.getDownloadDir());
break;
case PEERS:
ret = a.getPeersConnected() - b.getPeersConnected();
break;
case PROGRESS:
delta = a.getPercentDone() - b.getPercentDone();
ret = delta < 0 ? -1 : delta > 0 ? 1 : 0;
break;
case QUEUE:
ret = a.getQueuePosition() - b.getQueuePosition();
break;
case RATE_DOWNLOAD:
ret = (int) (a.getRateDownload() - b.getRateDownload());
break;
case RATE_UPLOAD:
ret = (int) (a.getRateUpload() - b.getRateUpload());
break;
case RATIO:
delta = b.getUploadRatio() - a.getUploadRatio();
ret = delta < 0 ? -1 : delta > 0 ? 1 : 0;
break;
default:
break;
}
return order == SortOrder.ASCENDING ? ret : -ret;
}
} |
package main;
import gcm.gui.GCM2SBMLEditor;
import gcm.gui.modelview.movie.MovieContainer;
import gcm.network.GeneticNetwork;
import gcm.parser.CompatibilityFixer;
import gcm.parser.GCMFile;
import gcm.parser.GCMParser;
import gcm.util.GlobalConstants;
import lpn.gui.*;
import lpn.parser.LhpnFile;
import lpn.parser.Lpn2verilog;
import lpn.parser.Translator;
import graph.Graph;
import java.awt.AWTError;
import java.awt.BorderLayout;
import java.awt.Component;
import java.awt.Dimension;
import java.awt.FlowLayout;
import java.awt.Font;
import java.awt.GridLayout;
import java.awt.KeyEventDispatcher;
import java.awt.KeyboardFocusManager;
import java.awt.Toolkit;
import java.awt.Point;
import java.awt.Container;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.KeyEvent;
import java.awt.event.MouseEvent;
import java.awt.event.MouseListener;
import java.awt.event.MouseMotionListener;
import java.awt.event.MouseWheelListener;
import java.awt.event.MouseWheelEvent;
import java.awt.event.WindowEvent;
import java.awt.event.WindowListener;
import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.FileWriter;
import java.io.FileReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStreamWriter;
import java.util.ArrayList;
import java.util.Properties;
import java.util.Scanner;
import java.util.prefs.Preferences;
import java.util.regex.Pattern;
import java.util.regex.Matcher;
import javax.swing.ImageIcon;
import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JComboBox;
import javax.swing.JFileChooser;
import javax.swing.JFrame;
import javax.swing.JLabel;
import javax.swing.JList;
import javax.swing.JMenu;
import javax.swing.JMenuBar;
import javax.swing.JMenuItem;
import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JTabbedPane;
import javax.swing.JToolBar;
import javax.swing.JPopupMenu;
import javax.swing.JScrollPane;
import javax.swing.JTextArea;
import javax.swing.JTextField;
import javax.swing.KeyStroke;
import javax.swing.JTree;
import javax.swing.ListSelectionModel;
import javax.swing.SwingUtilities;
import javax.swing.AbstractAction;
import javax.swing.JViewport;
import javax.swing.UIManager;
import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;
import com.apple.eawt.ApplicationAdapter;
import com.apple.eawt.ApplicationEvent;
import com.apple.eawt.Application;
import java.io.Writer;
import learn.LearnGCM;
import learn.LearnLHPN;
import synthesis.Synthesis;
import verification.*;
import org.sbml.libsbml.*;
import reb2sac.Reb2Sac;
import reb2sac.Run;
import sbmleditor.SBML_Editor;
import sbol.SbolBrowser;
import datamanager.DataManager;
import java.net.*;
import uk.ac.ebi.biomodels.*;
import util.Utility;
import util.tabs.CloseAndMaxTabbedPane;
/**
* This class creates a GUI for the Tstubd program. It implements the
* ActionListener class. This allows the GUI to perform actions when menu items
* are selected.
*
* @author Curtis Madsen
*/
public class Gui implements MouseListener, ActionListener, MouseMotionListener, MouseWheelListener {
public static JFrame frame; // Frame where components of the GUI are
// displayed
private JMenuBar menuBar;
private JMenu file, edit, view, tools, help, importMenu, exportMenu, newMenu, viewModel; // The
// file
// menu
private JMenuItem newProj; // The new menu item
private JMenuItem newSBMLModel; // The new menu item
private JMenuItem newGCMModel; // The new menu item
private JMenuItem newVhdl; // The new vhdl menu item
private JMenuItem newS; // The new assembly file menu item
private JMenuItem newInst; // The new instruction file menu item
private JMenuItem newLhpn; // The new lhpn menu item
private JMenuItem newG; // The new petri net menu item
private JMenuItem newCsp; // The new csp menu item
private JMenuItem newHse; // The new handshaking extension menu item
private JMenuItem newUnc; // The new extended burst mode menu item
private JMenuItem newRsg; // The new rsg menu item
private JMenuItem newSpice; // The new spice circuit item
private JMenuItem exit; // The exit menu item
private JMenuItem importSbol;
private JMenuItem importSbml; // The import sbml menu item
private JMenuItem importBioModel; // The import sbml menu item
private JMenuItem importDot; // The import dot menu item
private JMenuItem importVhdl; // The import vhdl menu item
private JMenuItem importS; // The import assembly file menu item
private JMenuItem importInst; // The import instruction file menu item
private JMenuItem importLpn; // The import lpn menu item
private JMenuItem importG; // The import .g file menu item
private JMenuItem importCsp; // The import csp menu item
private JMenuItem importHse; // The import handshaking extension menu
// item
private JMenuItem importUnc; // The import extended burst mode menu item
private JMenuItem importRsg; // The import rsg menu item
private JMenuItem importSpice; // The import spice circuit item
private JMenuItem manual; // The manual menu item
private JMenuItem about; // The about menu item
private JMenuItem openProj; // The open menu item
private JMenuItem pref; // The preferences menu item
private JMenuItem graph; // The graph menu item
private JMenuItem probGraph, exportCsv, exportDat, exportEps, exportJpg, exportPdf, exportPng, exportSvg, exportTsd,
exportSBML, exportSBOL;
private String root; // The root directory
private FileTree tree; // FileTree
private CloseAndMaxTabbedPane tab; // JTabbedPane for different tools
private JToolBar toolbar; // Tool bar for common options
private JButton saveButton, runButton, refreshButton, saveasButton, checkButton, exportButton; // Tool
// Bar
// options
private JPanel mainPanel; // the main panel
private static Boolean LPN2SBML = true;
public Log log; // the log
private JPopupMenu popup; // popup menu
private String separator;
private KeyEventDispatcher dispatcher;
private JMenuItem recentProjects[];
private String recentProjectPaths[];
private int numberRecentProj;
private int ShortCutKey;
public boolean checkUndeclared, checkUnits;
public static String SBMLLevelVersion;
private JCheckBox Undeclared, Units;
private JComboBox LevelVersion;
private JTextField viewerField;
private JLabel viewerLabel;
private Pattern IDpat = Pattern.compile("([a-zA-Z]|_)([a-zA-Z]|[0-9]|_)*");
private boolean async;
// treeSelected
// = false;
public boolean atacs, lema;
private String viewer;
private String[] BioModelIds = null;
private JMenuItem copy, rename, delete, save, saveAs, saveSBOL, check, run, refresh, viewCircuit, viewRules, viewTrace, viewLog, viewCoverage, viewLHPN,
saveModel, saveAsVerilog, viewSG, viewModGraph, viewLearnedModel, viewModBrowser, createAnal, createLearn, createSbml, createSynth,
createVer, close, closeAll;
public String ENVVAR;
public static int SBML_LEVEL = 3;
public static int SBML_VERSION = 1;
public static final Object[] OPTIONS = { "Yes", "No", "Yes To All", "No To All", "Cancel" };
public static final int YES_OPTION = JOptionPane.YES_OPTION;
public static final int NO_OPTION = JOptionPane.NO_OPTION;
public static final int YES_TO_ALL_OPTION = JOptionPane.CANCEL_OPTION;
public static final int NO_TO_ALL_OPTION = 3;
public static final int CANCEL_OPTION = 4;
public static Object ICON_EXPAND = UIManager.get("Tree.expandedIcon");
public static Object ICON_COLLAPSE = UIManager.get("Tree.collapsedIcon");
public class MacOSAboutHandler extends Application {
public MacOSAboutHandler() {
addApplicationListener(new AboutBoxHandler());
}
class AboutBoxHandler extends ApplicationAdapter {
public void handleAbout(ApplicationEvent event) {
about();
event.setHandled(true);
}
}
}
public class MacOSPreferencesHandler extends Application {
public MacOSPreferencesHandler() {
addApplicationListener(new PreferencesHandler());
}
class PreferencesHandler extends ApplicationAdapter {
public void handlePreferences(ApplicationEvent event) {
preferences();
event.setHandled(true);
}
}
}
public class MacOSQuitHandler extends Application {
public MacOSQuitHandler() {
addApplicationListener(new QuitHandler());
}
class QuitHandler extends ApplicationAdapter {
public void handleQuit(ApplicationEvent event) {
exit();
event.setHandled(true);
}
}
}
/**
* This is the constructor for the Proj class. It initializes all the input
* fields, puts them on panels, adds the panels to the frame, and then
* displays the frame.
*
* @throws Exception
*/
public Gui(boolean lema, boolean atacs, boolean LPN2SBML) {
this.lema = lema;
this.atacs = atacs;
this.LPN2SBML = LPN2SBML;
async = lema || atacs;
if (File.separator.equals("\\")) {
separator = "\\\\";
}
else {
separator = File.separator;
}
if (atacs) {
ENVVAR = System.getenv("ATACSGUI");
}
else if (lema) {
ENVVAR = System.getenv("LEMA");
}
else {
ENVVAR = System.getenv("BIOSIM");
}
// Creates a new frame
if (lema) {
frame = new JFrame("LEMA");
frame.setIconImage(new ImageIcon(ENVVAR + separator + "gui" + separator + "icons" + separator + "LEMA.png").getImage());
}
else if (atacs) {
frame = new JFrame("ATACS");
frame.setIconImage(new ImageIcon(ENVVAR + separator + "gui" + separator + "icons" + separator + "ATACS.png").getImage());
}
else {
frame = new JFrame("iBioSim");
frame.setIconImage(new ImageIcon(ENVVAR + separator + "gui" + separator + "icons" + separator + "iBioSim.png").getImage());
}
// Makes it so that clicking the x in the corner closes the program
WindowListener w = new WindowListener() {
public void windowClosing(WindowEvent arg0) {
exit.doClick();
}
public void windowOpened(WindowEvent arg0) {
}
public void windowClosed(WindowEvent arg0) {
}
public void windowIconified(WindowEvent arg0) {
}
public void windowDeiconified(WindowEvent arg0) {
}
public void windowActivated(WindowEvent arg0) {
}
public void windowDeactivated(WindowEvent arg0) {
}
};
frame.addWindowListener(w);
frame.setDefaultCloseOperation(JFrame.DO_NOTHING_ON_CLOSE);
popup = new JPopupMenu();
popup.addMouseListener(this);
// popup.addFocusListener(this);
// popup.addComponentListener(this);
// Sets up the Tool Bar
toolbar = new JToolBar();
String imgName = ENVVAR + separator + "gui" + separator + "icons" + separator + "save.png";
saveButton = makeToolButton(imgName, "save", "Save", "Save");
// toolButton = new JButton("Save");
toolbar.add(saveButton);
imgName = ENVVAR + separator + "gui" + separator + "icons" + separator + "saveas.png";
saveasButton = makeToolButton(imgName, "saveas", "Save As", "Save As");
toolbar.add(saveasButton);
imgName = ENVVAR + separator + "gui" + separator + "icons" + separator + "savecheck.png";
checkButton = makeToolButton(imgName, "check", "Save and Check", "Save and Check");
toolbar.add(checkButton);
imgName = ENVVAR + separator + "gui" + separator + "icons" + separator + "export.jpg";
exportButton = makeToolButton(imgName, "export", "Export", "Export");
toolbar.add(exportButton);
imgName = ENVVAR + separator + "gui" + separator + "icons" + separator + "run-icon.jpg";
runButton = makeToolButton(imgName, "run", "Save and Run", "Run");
toolbar.add(runButton);
imgName = ENVVAR + separator + "gui" + separator + "icons" + separator + "refresh.jpg";
refreshButton = makeToolButton(imgName, "refresh", "Refresh", "Refresh");
toolbar.add(refreshButton);
saveButton.setEnabled(false);
runButton.setEnabled(false);
refreshButton.setEnabled(false);
saveasButton.setEnabled(false);
checkButton.setEnabled(false);
exportButton.setEnabled(false);
// Creates a menu for the frame
menuBar = new JMenuBar();
file = new JMenu("File");
help = new JMenu("Help");
edit = new JMenu("Edit");
importMenu = new JMenu("Import");
exportMenu = new JMenu("Export");
newMenu = new JMenu("New");
view = new JMenu("View");
viewModel = new JMenu("Model");
tools = new JMenu("Tools");
menuBar.add(file);
menuBar.add(edit);
if (lema) {
menuBar.add(view);
}
menuBar.add(tools);
menuBar.add(help);
// menuBar.addFocusListener(this);
// menuBar.addMouseListener(this);
// file.addMouseListener(this);
// edit.addMouseListener(this);
// view.addMouseListener(this);
// tools.addMouseListener(this);
// help.addMouseListener(this);
copy = new JMenuItem("Copy");
rename = new JMenuItem("Rename");
delete = new JMenuItem("Delete");
manual = new JMenuItem("Manual");
about = new JMenuItem("About");
openProj = new JMenuItem("Open Project");
close = new JMenuItem("Close");
closeAll = new JMenuItem("Close All");
pref = new JMenuItem("Preferences");
newProj = new JMenuItem("Project");
newGCMModel = new JMenuItem("Model");
newSBMLModel = new JMenuItem("SBML Model");
newSpice = new JMenuItem("Spice Circuit");
newVhdl = new JMenuItem("VHDL Model");
newS = new JMenuItem("Assembly File");
newInst = new JMenuItem("Instruction File");
newLhpn = new JMenuItem("LPN Model");
newG = new JMenuItem("Petri Net");
newCsp = new JMenuItem("CSP Model");
newHse = new JMenuItem("Handshaking Expansion");
newUnc = new JMenuItem("Extended Burst Mode Machine");
newRsg = new JMenuItem("Reduced State Graph");
graph = new JMenuItem("TSD Graph");
probGraph = new JMenuItem("Histogram");
importSbol = new JMenuItem("SBOL File");
importSbml = new JMenuItem("SBML Model");
importBioModel = new JMenuItem("BioModel");
importDot = new JMenuItem("iBioSim Model");
importG = new JMenuItem("Petri Net");
importLpn = new JMenuItem("LPN Model");
importVhdl = new JMenuItem("VHDL Model");
importS = new JMenuItem("Assembly File");
importInst = new JMenuItem("Instruction File");
importSpice = new JMenuItem("Spice Circuit");
importCsp = new JMenuItem("CSP Model");
importHse = new JMenuItem("Handshaking Expansion");
importUnc = new JMenuItem("Extended Burst Mode Machine");
importRsg = new JMenuItem("Reduced State Graph");
/*
exportSBML = new JMenuItem("Systems Biology Markup Language (SBML)");
exportSBOL = new JMenuItem("Synthetic Biology Open Language (SBOL)");
exportCsv = new JMenuItem("Comma Separated Values (csv)");
exportDat = new JMenuItem("Tab Delimited Data (dat)");
exportEps = new JMenuItem("Encapsulated Postscript (eps)");
exportJpg = new JMenuItem("JPEG (jpg)");
exportPdf = new JMenuItem("Portable Document Format (pdf)");
exportPng = new JMenuItem("Portable Network Graphics (png)");
exportSvg = new JMenuItem("Scalable Vector Graphics (svg)");
exportTsd = new JMenuItem("Time Series Data (tsd)");
*/
exportSBML = new JMenuItem("SBML");
exportSBOL = new JMenuItem("SBOL");
exportCsv = new JMenuItem("CSV");
exportDat = new JMenuItem("DAT");
exportEps = new JMenuItem("EPS");
exportJpg = new JMenuItem("JPG");
exportPdf = new JMenuItem("PDF");
exportPng = new JMenuItem("PNG");
exportSvg = new JMenuItem("SVG");
exportTsd = new JMenuItem("TSD");
save = new JMenuItem("Save");
if (async) {
saveModel = new JMenuItem("Save Learned LPN");
}
else {
saveModel = new JMenuItem("Save Learned Model");
}
saveAsVerilog = new JMenuItem("Save as Verilog");
saveAsVerilog.addActionListener(this);
saveAsVerilog.setActionCommand("saveAsVerilog");
saveAsVerilog.setEnabled(false);
saveAs = new JMenuItem("Save As");
run = new JMenuItem("Save and Run");
check = new JMenuItem("Save and Check");
saveSBOL = new JMenuItem("Save SBOL");
refresh = new JMenuItem("Refresh");
viewCircuit = new JMenuItem("Circuit");
viewRules = new JMenuItem("Production Rules");
viewTrace = new JMenuItem("Error Trace");
viewLog = new JMenuItem("Log");
viewCoverage = new JMenuItem("Coverage Report");
viewLHPN = new JMenuItem("Model");
viewModGraph = new JMenuItem("Model");
viewLearnedModel = new JMenuItem("Learned Model");
viewModBrowser = new JMenuItem("Model in Browser");
viewSG = new JMenuItem("State Graph");
createAnal = new JMenuItem("Analysis Tool");
createLearn = new JMenuItem("Learn Tool");
createSbml = new JMenuItem("Create SBML File");
createSynth = new JMenuItem("Synthesis Tool");
createVer = new JMenuItem("Verification Tool");
exit = new JMenuItem("Exit");
copy.addActionListener(this);
rename.addActionListener(this);
delete.addActionListener(this);
openProj.addActionListener(this);
close.addActionListener(this);
closeAll.addActionListener(this);
pref.addActionListener(this);
manual.addActionListener(this);
newProj.addActionListener(this);
newGCMModel.addActionListener(this);
newSBMLModel.addActionListener(this);
newVhdl.addActionListener(this);
newS.addActionListener(this);
newInst.addActionListener(this);
newLhpn.addActionListener(this);
newG.addActionListener(this);
newCsp.addActionListener(this);
newHse.addActionListener(this);
newUnc.addActionListener(this);
newRsg.addActionListener(this);
newSpice.addActionListener(this);
exit.addActionListener(this);
about.addActionListener(this);
importSbol.addActionListener(this);
importSbml.addActionListener(this);
importBioModel.addActionListener(this);
importDot.addActionListener(this);
importVhdl.addActionListener(this);
importS.addActionListener(this);
importInst.addActionListener(this);
importLpn.addActionListener(this);
importG.addActionListener(this);
importCsp.addActionListener(this);
importHse.addActionListener(this);
importUnc.addActionListener(this);
importRsg.addActionListener(this);
importSpice.addActionListener(this);
exportSBML.addActionListener(this);
exportSBOL.addActionListener(this);
exportCsv.addActionListener(this);
exportDat.addActionListener(this);
exportEps.addActionListener(this);
exportJpg.addActionListener(this);
exportPdf.addActionListener(this);
exportPng.addActionListener(this);
exportSvg.addActionListener(this);
exportTsd.addActionListener(this);
graph.addActionListener(this);
probGraph.addActionListener(this);
save.addActionListener(this);
saveAs.addActionListener(this);
saveSBOL.addActionListener(this);
run.addActionListener(this);
check.addActionListener(this);
refresh.addActionListener(this);
saveModel.addActionListener(this);
viewCircuit.addActionListener(this);
viewRules.addActionListener(this);
viewTrace.addActionListener(this);
viewLog.addActionListener(this);
viewCoverage.addActionListener(this);
viewLHPN.addActionListener(this);
viewModGraph.addActionListener(this);
viewLearnedModel.addActionListener(this);
viewModBrowser.addActionListener(this);
viewSG.addActionListener(this);
createAnal.addActionListener(this);
createLearn.addActionListener(this);
createSbml.addActionListener(this);
createSynth.addActionListener(this);
createVer.addActionListener(this);
save.setActionCommand("save");
saveAs.setActionCommand("saveas");
saveSBOL.setActionCommand("saveSBOL");
run.setActionCommand("run");
check.setActionCommand("check");
refresh.setActionCommand("refresh");
if (atacs) {
viewModGraph.setActionCommand("viewModel");
}
else {
viewModGraph.setActionCommand("graph");
}
viewLHPN.setActionCommand("viewModel");
viewModBrowser.setActionCommand("browse");
viewSG.setActionCommand("stateGraph");
createLearn.setActionCommand("createLearn");
createSbml.setActionCommand("createSBML");
createSynth.setActionCommand("createSynthesis");
createVer.setActionCommand("createVerify");
ShortCutKey = Toolkit.getDefaultToolkit().getMenuShortcutKeyMask();
newProj.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_P, ShortCutKey));
openProj.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_O, ShortCutKey));
close.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_W, ShortCutKey));
closeAll.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_W, ShortCutKey | KeyEvent.SHIFT_MASK));
save.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_S, ShortCutKey));
saveAs.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_S, ShortCutKey | KeyEvent.SHIFT_MASK));
run.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_R, ShortCutKey));
if (lema) {
} else {
check.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_K, ShortCutKey));
saveSBOL.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_S, ShortCutKey | KeyEvent.ALT_MASK));
refresh.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_F5, 0));
newGCMModel.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_M, ShortCutKey));
createAnal.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_A, ShortCutKey | KeyEvent.SHIFT_MASK));
createLearn.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_L, ShortCutKey | KeyEvent.SHIFT_MASK));
}
newLhpn.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_L, ShortCutKey));
graph.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_G, ShortCutKey));
probGraph.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_H, ShortCutKey | KeyEvent.SHIFT_MASK));
copy.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_C, ShortCutKey | KeyEvent.SHIFT_MASK));
rename.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_V, ShortCutKey | KeyEvent.SHIFT_MASK));
delete.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_X, ShortCutKey | KeyEvent.SHIFT_MASK));
manual.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_M, ShortCutKey | KeyEvent.SHIFT_MASK));
exit.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_X, ShortCutKey));
pref.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_COMMA, ShortCutKey));
/*
if (lema) {
viewLHPN.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_F1, 0));
viewTrace.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_F6, 0));
}
else {
viewCircuit.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_F1, 0));
refresh.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_F5, 0));
}
viewLog.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_F3, 0));
Action newAction = new NewAction();
Action importAction = new ImportAction();
Action exportAction = new ExportAction();
Action modelAction = new ModelAction();
newMenu.getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW)
.put(KeyStroke.getKeyStroke(KeyEvent.VK_N, ShortCutKey | KeyEvent.ALT_DOWN_MASK), "new");
newMenu.getActionMap().put("new", newAction);
importMenu.getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW).put(KeyStroke.getKeyStroke(KeyEvent.VK_I, ShortCutKey | KeyEvent.ALT_DOWN_MASK),
"import");
importMenu.getActionMap().put("import", importAction);
exportMenu.getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW).put(KeyStroke.getKeyStroke(KeyEvent.VK_E, ShortCutKey | KeyEvent.ALT_DOWN_MASK),
"export");
exportMenu.getActionMap().put("export", exportAction);
viewModel.getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW).put(KeyStroke.getKeyStroke(KeyEvent.VK_M, ShortCutKey | KeyEvent.ALT_DOWN_MASK),
"model");
viewModel.getActionMap().put("model", modelAction);
newMenu.setMnemonic(KeyEvent.VK_N);
importMenu.setMnemonic(KeyEvent.VK_I);
exportMenu.setMnemonic(KeyEvent.VK_E);
viewModel.setMnemonic(KeyEvent.VK_M);
copy.setMnemonic(KeyEvent.VK_C);
rename.setMnemonic(KeyEvent.VK_R);
delete.setMnemonic(KeyEvent.VK_D);
exit.setMnemonic(KeyEvent.VK_X);
newProj.setMnemonic(KeyEvent.VK_P);
openProj.setMnemonic(KeyEvent.VK_O);
close.setMnemonic(KeyEvent.VK_W);
newGCMModel.setMnemonic(KeyEvent.VK_G);
newSBMLModel.setMnemonic(KeyEvent.VK_S);
newVhdl.setMnemonic(KeyEvent.VK_V);
newLhpn.setMnemonic(KeyEvent.VK_L);
newG.setMnemonic(KeyEvent.VK_N);
//newSpice.setMnemonic(KeyEvent.VK_P);
about.setMnemonic(KeyEvent.VK_A);
manual.setMnemonic(KeyEvent.VK_M);
graph.setMnemonic(KeyEvent.VK_T);
probGraph.setMnemonic(KeyEvent.VK_H);
if (!async) {
importDot.setMnemonic(KeyEvent.VK_G);
}
else {
importLpn.setMnemonic(KeyEvent.VK_L);
}
//importSbol.setMnemonic(KeyEvent.VK_O);
importSbml.setMnemonic(KeyEvent.VK_S);
importVhdl.setMnemonic(KeyEvent.VK_V);
//importSpice.setMnemonic(KeyEvent.VK_P);
save.setMnemonic(KeyEvent.VK_S);
run.setMnemonic(KeyEvent.VK_R);
check.setMnemonic(KeyEvent.VK_K);
exportCsv.setMnemonic(KeyEvent.VK_C);
exportEps.setMnemonic(KeyEvent.VK_E);
exportDat.setMnemonic(KeyEvent.VK_D);
exportJpg.setMnemonic(KeyEvent.VK_J);
exportPdf.setMnemonic(KeyEvent.VK_F);
exportPng.setMnemonic(KeyEvent.VK_G);
exportSvg.setMnemonic(KeyEvent.VK_S);
exportTsd.setMnemonic(KeyEvent.VK_T);
//pref.setMnemonic(KeyEvent.VK_P);
viewModGraph.setMnemonic(KeyEvent.VK_G);
viewModBrowser.setMnemonic(KeyEvent.VK_B);
createAnal.setMnemonic(KeyEvent.VK_A);
createLearn.setMnemonic(KeyEvent.VK_L);
*/
importDot.setEnabled(false);
importSbol.setEnabled(false);
importSbml.setEnabled(false);
importBioModel.setEnabled(false);
importVhdl.setEnabled(false);
importS.setEnabled(false);
importInst.setEnabled(false);
importLpn.setEnabled(false);
importG.setEnabled(false);
importCsp.setEnabled(false);
importHse.setEnabled(false);
importUnc.setEnabled(false);
importRsg.setEnabled(false);
importSpice.setEnabled(false);
exportMenu.setEnabled(false);
exportSBML.setEnabled(false);
exportSBOL.setEnabled(false);
exportCsv.setEnabled(false);
exportDat.setEnabled(false);
exportEps.setEnabled(false);
exportJpg.setEnabled(false);
exportPdf.setEnabled(false);
exportPng.setEnabled(false);
exportSvg.setEnabled(false);
exportTsd.setEnabled(false);
newGCMModel.setEnabled(false);
newSBMLModel.setEnabled(false);
newVhdl.setEnabled(false);
newS.setEnabled(false);
newInst.setEnabled(false);
newLhpn.setEnabled(false);
newG.setEnabled(false);
newCsp.setEnabled(false);
newHse.setEnabled(false);
newUnc.setEnabled(false);
newRsg.setEnabled(false);
newSpice.setEnabled(false);
graph.setEnabled(false);
probGraph.setEnabled(false);
save.setEnabled(false);
saveModel.setEnabled(false);
saveAs.setEnabled(false);
saveSBOL.setEnabled(false);
run.setEnabled(false);
check.setEnabled(false);
refresh.setEnabled(false);
copy.setEnabled(false);
rename.setEnabled(false);
delete.setEnabled(false);
viewCircuit.setEnabled(false);
viewRules.setEnabled(false);
viewTrace.setEnabled(false);
viewLog.setEnabled(false);
viewCoverage.setEnabled(false);
viewLHPN.setEnabled(false);
viewModel.setEnabled(false);
viewModGraph.setEnabled(false);
viewLearnedModel.setEnabled(false);
viewModBrowser.setEnabled(false);
viewSG.setEnabled(false);
createAnal.setEnabled(false);
createLearn.setEnabled(false);
createSbml.setEnabled(false);
createSynth.setEnabled(false);
createVer.setEnabled(false);
edit.add(copy);
edit.add(rename);
edit.add(delete);
file.add(newMenu);
newMenu.add(newProj);
if (!async) {
newMenu.add(newGCMModel);
newMenu.add(newLhpn);
}
else if (atacs) {
newMenu.add(newVhdl);
newMenu.add(newG);
newMenu.add(newLhpn);
newMenu.add(newCsp);
newMenu.add(newHse);
newMenu.add(newUnc);
newMenu.add(newRsg);
}
else {
newMenu.add(newVhdl);
newMenu.add(newS);
newMenu.add(newInst);
newMenu.add(newLhpn);
// newMenu.add(newSpice);
}
newMenu.add(graph);
newMenu.add(probGraph);
file.add(openProj);
// openMenu.add(openProj);
file.addSeparator();
file.add(close);
file.add(closeAll);
file.addSeparator();
file.add(save);
file.add(saveAs);
if (!async) {
file.add(saveSBOL);
file.add(check);
}
file.add(run);
if (lema) {
file.add(saveAsVerilog);
} else {
file.addSeparator();
file.add(refresh);
}
if (lema) {
file.add(saveModel);
}
file.addSeparator();
file.add(importMenu);
if (!async) {
importMenu.add(importDot);
importMenu.add(importSbml);
importMenu.add(importBioModel);
importMenu.add(importLpn);
importMenu.add(importSbol);
}
else if (atacs) {
importMenu.add(importVhdl);
importMenu.add(importG);
importMenu.add(importLpn);
importMenu.add(importCsp);
importMenu.add(importHse);
importMenu.add(importUnc);
importMenu.add(importRsg);
}
else {
importMenu.add(importVhdl);
importMenu.add(importS);
importMenu.add(importInst);
importMenu.add(importLpn);
// importMenu.add(importSpice);
}
file.add(exportMenu);
exportMenu.add(exportSBML);
exportMenu.add(exportSBOL);
exportMenu.addSeparator();
exportMenu.add(exportTsd);
exportMenu.add(exportCsv);
exportMenu.add(exportDat);
exportMenu.add(exportEps);
exportMenu.add(exportJpg);
exportMenu.add(exportPdf);
exportMenu.add(exportPng);
exportMenu.add(exportSvg);
file.addSeparator();
help.add(manual);
if (System.getProperty("os.name").toLowerCase().startsWith("mac os")) {
new MacOSAboutHandler();
new MacOSPreferencesHandler();
new MacOSQuitHandler();
Application application = new Application();
application.addPreferencesMenuItem();
application.setEnabledPreferencesMenu(true);
}
else {
edit.addSeparator();
edit.add(pref);
file.add(exit);
file.addSeparator();
help.add(about);
}
if (lema) {
// view.add(viewVHDL);
// view.add(viewVerilog);
view.add(viewLHPN);
view.addSeparator();
view.add(viewLearnedModel);
view.add(viewCoverage);
view.add(viewLog);
view.add(viewTrace);
}
else if (atacs) {
view.add(viewModGraph);
view.add(viewCircuit);
view.add(viewRules);
view.add(viewTrace);
view.add(viewLog);
}
else {
view.add(viewModGraph);
//view.add(viewModBrowser);
view.add(viewLearnedModel);
view.add(viewSG);
view.add(viewLog);
//view.addSeparator();
//view.add(refresh);
}
if (LPN2SBML) {
tools.add(createAnal);
}
if (!atacs) {
tools.add(createLearn);
}
if (atacs) {
tools.add(createSynth);
}
if (async) {
tools.add(createVer);
}
// else {
// tools.add(createSbml);
root = null;
// Create recent project menu items
numberRecentProj = 0;
recentProjects = new JMenuItem[10];
recentProjectPaths = new String[10];
for (int i = 0; i < 10; i++) {
recentProjects[i] = new JMenuItem();
recentProjects[i].addActionListener(this);
recentProjects[i].setActionCommand("recent" + i);
recentProjectPaths[i] = "";
}
recentProjects[0].setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_0, ShortCutKey));
recentProjects[0].setMnemonic(KeyEvent.VK_0);
recentProjects[1].setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_1, ShortCutKey));
recentProjects[1].setMnemonic(KeyEvent.VK_1);
recentProjects[2].setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_2, ShortCutKey));
recentProjects[2].setMnemonic(KeyEvent.VK_2);
recentProjects[3].setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_3, ShortCutKey));
recentProjects[3].setMnemonic(KeyEvent.VK_3);
recentProjects[4].setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_4, ShortCutKey));
recentProjects[4].setMnemonic(KeyEvent.VK_4);
recentProjects[5].setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_5, ShortCutKey));
recentProjects[5].setMnemonic(KeyEvent.VK_5);
recentProjects[6].setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_6, ShortCutKey));
recentProjects[6].setMnemonic(KeyEvent.VK_6);
recentProjects[7].setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_7, ShortCutKey));
recentProjects[7].setMnemonic(KeyEvent.VK_7);
recentProjects[8].setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_8, ShortCutKey));
recentProjects[8].setMnemonic(KeyEvent.VK_8);
recentProjects[9].setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_9, ShortCutKey));
recentProjects[9].setMnemonic(KeyEvent.VK_9);
Preferences biosimrc = Preferences.userRoot();
viewer = biosimrc.get("biosim.general.viewer", "");
for (int i = 0; i < 10; i++) {
if (atacs) {
recentProjects[i].setText(biosimrc.get("atacs.recent.project." + i, ""));
recentProjectPaths[i] = biosimrc.get("atacs.recent.project.path." + i, "");
if (!recentProjectPaths[i].equals("")) {
file.add(recentProjects[i]);
numberRecentProj = i + 1;
}
}
else if (lema) {
recentProjects[i].setText(biosimrc.get("lema.recent.project." + i, ""));
recentProjectPaths[i] = biosimrc.get("lema.recent.project.path." + i, "");
if (!recentProjectPaths[i].equals("")) {
file.add(recentProjects[i]);
numberRecentProj = i + 1;
}
}
else {
recentProjects[i].setText(biosimrc.get("biosim.recent.project." + i, ""));
recentProjectPaths[i] = biosimrc.get("biosim.recent.project.path." + i, "");
if (!recentProjectPaths[i].equals("")) {
file.add(recentProjects[i]);
numberRecentProj = i + 1;
}
}
}
if (System.getProperty("os.name").toLowerCase().startsWith("mac os")) {
new MacOSAboutHandler();
new MacOSPreferencesHandler();
new MacOSQuitHandler();
Application application = new Application();
application.addPreferencesMenuItem();
application.setEnabledPreferencesMenu(true);
}
else {
// file.add(pref);
// file.add(exit);
help.add(about);
}
if (biosimrc.get("biosim.sbml.level_version", "").equals("L2V4")) {
SBMLLevelVersion = "L2V4";
SBML_LEVEL = 2;
SBML_VERSION = 4;
}
else {
SBMLLevelVersion = "L3V1";
SBML_LEVEL = 3;
SBML_VERSION = 1;
}
if (biosimrc.get("biosim.check.undeclared", "").equals("false")) {
checkUndeclared = false;
}
else {
checkUndeclared = true;
}
if (biosimrc.get("biosim.check.units", "").equals("false")) {
checkUnits = false;
}
else {
checkUnits = true;
}
if (biosimrc.get("biosim.general.file_browser", "").equals("")) {
biosimrc.put("biosim.general.file_browser", "JFileChooser");
}
if (biosimrc.get("biosim.gcm.KREP_VALUE", "").equals("")) {
biosimrc.put("biosim.gcm.KREP_VALUE", ".5");
}
if (biosimrc.get("biosim.gcm.KACT_VALUE", "").equals("")) {
biosimrc.put("biosim.gcm.KACT_VALUE", ".0033");
}
if (biosimrc.get("biosim.gcm.KBIO_VALUE", "").equals("")) {
biosimrc.put("biosim.gcm.KBIO_VALUE", ".05");
}
if (biosimrc.get("biosim.gcm.PROMOTER_COUNT_VALUE", "").equals("")) {
biosimrc.put("biosim.gcm.PROMOTER_COUNT_VALUE", "2");
}
if (biosimrc.get("biosim.gcm.KASSOCIATION_VALUE", "").equals("")) {
biosimrc.put("biosim.gcm.KASSOCIATION_VALUE", ".05");
}
if (biosimrc.get("biosim.gcm.KBASAL_VALUE", "").equals("")) {
biosimrc.put("biosim.gcm.KBASAL_VALUE", ".0001");
}
if (biosimrc.get("biosim.gcm.OCR_VALUE", "").equals("")) {
biosimrc.put("biosim.gcm.OCR_VALUE", ".05");
}
if (biosimrc.get("biosim.gcm.KDECAY_VALUE", "").equals("")) {
biosimrc.put("biosim.gcm.KDECAY_VALUE", ".0075");
}
if (biosimrc.get("biosim.gcm.KECDECAY_VALUE", "").equals("")) {
biosimrc.put("biosim.gcm.KECDECAY_VALUE", ".005");
}
if (biosimrc.get("biosim.gcm.RNAP_VALUE", "").equals("")) {
biosimrc.put("biosim.gcm.RNAP_VALUE", "30");
}
if (biosimrc.get("biosim.gcm.RNAP_BINDING_VALUE", "").equals("")) {
biosimrc.put("biosim.gcm.RNAP_BINDING_VALUE", ".033");
}
if (biosimrc.get("biosim.gcm.ACTIVATED_RNAP_BINDING_VALUE", "").equals("")) {
biosimrc.put("biosim.gcm.ACTIVATED_RNAP_BINDING_VALUE", "1");
}
if (biosimrc.get("biosim.gcm.STOICHIOMETRY_VALUE", "").equals("")) {
biosimrc.put("biosim.gcm.STOICHIOMETRY_VALUE", "10");
}
if (biosimrc.get("biosim.gcm.KCOMPLEX_VALUE", "").equals("")) {
biosimrc.put("biosim.gcm.KCOMPLEX_VALUE", "0.05");
}
if (biosimrc.get("biosim.gcm.COOPERATIVITY_VALUE", "").equals("")) {
biosimrc.put("biosim.gcm.COOPERATIVITY_VALUE", "2");
}
if (biosimrc.get("biosim.gcm.ACTIVED_VALUE", "").equals("")) {
biosimrc.put("biosim.gcm.ACTIVED_VALUE", ".25");
}
if (biosimrc.get("biosim.gcm.MAX_DIMER_VALUE", "").equals("")) {
biosimrc.put("biosim.gcm.MAX_DIMER_VALUE", "1");
}
if (biosimrc.get("biosim.gcm.INITIAL_VALUE", "").equals("")) {
biosimrc.put("biosim.gcm.INITIAL_VALUE", "0");
}
if (biosimrc.get("biosim.gcm.MEMDIFF_VALUE", "").equals("")) {
biosimrc.put("biosim.gcm.MEMDIFF_VALUE", "1.0/0.01");
}
if (biosimrc.get("biosim.gcm.KECDIFF_VALUE", "").equals("")) {
biosimrc.put("biosim.gcm.KECDIFF_VALUE", "1.0");
}
if (biosimrc.get("biosim.sim.abs", "").equals("")) {
biosimrc.put("biosim.sim.abs", "None");
}
if (biosimrc.get("biosim.sim.type", "").equals("")) {
biosimrc.put("biosim.sim.type", "ODE");
}
if (biosimrc.get("biosim.sim.sim", "").equals("")) {
biosimrc.put("biosim.sim.sim", "rkf45");
}
if (biosimrc.get("biosim.sim.limit", "").equals("")) {
biosimrc.put("biosim.sim.limit", "100.0");
}
if (biosimrc.get("biosim.sim.useInterval", "").equals("")) {
biosimrc.put("biosim.sim.useInterval", "Print Interval");
}
if (biosimrc.get("biosim.sim.interval", "").equals("")) {
biosimrc.put("biosim.sim.interval", "1.0");
}
if (biosimrc.get("biosim.sim.step", "").equals("")) {
biosimrc.put("biosim.sim.step", "inf");
}
if (biosimrc.get("biosim.sim.min.step", "").equals("")) {
biosimrc.put("biosim.sim.min.step", "0");
}
if (biosimrc.get("biosim.sim.error", "").equals("")) {
biosimrc.put("biosim.sim.error", "1.0E-9");
}
if (biosimrc.get("biosim.sim.seed", "").equals("")) {
biosimrc.put("biosim.sim.seed", "314159");
}
if (biosimrc.get("biosim.sim.runs", "").equals("")) {
biosimrc.put("biosim.sim.runs", "1");
}
if (biosimrc.get("biosim.sim.rapid1", "").equals("")) {
biosimrc.put("biosim.sim.rapid1", "0.1");
}
if (biosimrc.get("biosim.sim.rapid2", "").equals("")) {
biosimrc.put("biosim.sim.rapid2", "0.1");
}
if (biosimrc.get("biosim.sim.qssa", "").equals("")) {
biosimrc.put("biosim.sim.qssa", "0.1");
}
if (biosimrc.get("biosim.sim.concentration", "").equals("")) {
biosimrc.put("biosim.sim.concentration", "15");
}
if (biosimrc.get("biosim.learn.tn", "").equals("")) {
biosimrc.put("biosim.learn.tn", "2");
}
if (biosimrc.get("biosim.learn.tj", "").equals("")) {
biosimrc.put("biosim.learn.tj", "2");
}
if (biosimrc.get("biosim.learn.ti", "").equals("")) {
biosimrc.put("biosim.learn.ti", "0.5");
}
if (biosimrc.get("biosim.learn.bins", "").equals("")) {
biosimrc.put("biosim.learn.bins", "4");
}
if (biosimrc.get("biosim.learn.equaldata", "").equals("")) {
biosimrc.put("biosim.learn.equaldata", "Equal Data Per Bins");
}
if (biosimrc.get("biosim.learn.autolevels", "").equals("")) {
biosimrc.put("biosim.learn.autolevels", "Auto");
}
if (biosimrc.get("biosim.learn.ta", "").equals("")) {
biosimrc.put("biosim.learn.ta", "1.15");
}
if (biosimrc.get("biosim.learn.tr", "").equals("")) {
biosimrc.put("biosim.learn.tr", "0.75");
}
if (biosimrc.get("biosim.learn.tm", "").equals("")) {
biosimrc.put("biosim.learn.tm", "0.0");
}
if (biosimrc.get("biosim.learn.tt", "").equals("")) {
biosimrc.put("biosim.learn.tt", "0.025");
}
if (biosimrc.get("biosim.learn.debug", "").equals("")) {
biosimrc.put("biosim.learn.debug", "0");
}
if (biosimrc.get("biosim.learn.succpred", "").equals("")) {
biosimrc.put("biosim.learn.succpred", "Successors");
}
if (biosimrc.get("biosim.learn.findbaseprob", "").equals("")) {
biosimrc.put("biosim.learn.findbaseprob", "False");
}
// Open .biosimrc here
// Packs the frame and displays it
mainPanel = new JPanel(new BorderLayout());
tree = new FileTree(null, this, lema, atacs);
if (biosimrc.get("biosim.general.tree_icons", "").equals("")) {
biosimrc.put("biosim.general.tree_icons", "default");
}
else if (biosimrc.get("biosim.general.tree_icons", "").equals("plus_minus")) {
tree.setExpandibleIcons(false);
}
log = new Log();
tab = new CloseAndMaxTabbedPane(false, this);
tab.setPreferredSize(new Dimension(1100, 550));
// tab.getPaneUI().addMouseListener(this);
mainPanel.add(tree, "West");
mainPanel.add(tab, "Center");
mainPanel.add(log, "South");
mainPanel.add(toolbar, "North");
frame.setContentPane(mainPanel);
frame.setJMenuBar(menuBar);
// frame.getGlassPane().setVisible(true);
// frame.getGlassPane().addMouseListener(this);
// frame.getGlassPane().addMouseMotionListener(this);
// frame.getGlassPane().addMouseWheelListener(this);
frame.addMouseListener(this);
menuBar.addMouseListener(this);
frame.pack();
Dimension screenSize;
try {
Toolkit tk = Toolkit.getDefaultToolkit();
screenSize = tk.getScreenSize();
}
catch (AWTError awe) {
screenSize = new Dimension(640, 480);
}
Dimension frameSize = frame.getSize();
if (frameSize.height > screenSize.height) {
frameSize.height = screenSize.height;
frame.setSize(frameSize);
}
if (frameSize.width > screenSize.width) {
frameSize.width = screenSize.width;
frame.setSize(frameSize);
}
int x = screenSize.width / 2 - frameSize.width / 2;
int y = screenSize.height / 2 - frameSize.height / 2;
frame.setLocation(x, y);
frame.setVisible(true);
dispatcher = new KeyEventDispatcher() {
public boolean dispatchKeyEvent(KeyEvent e) {
if (e.getID() == KeyEvent.KEY_TYPED) {
if (e.getKeyChar() == '') {
if (tab.getTabCount() > 0) {
KeyboardFocusManager.getCurrentKeyboardFocusManager().removeKeyEventDispatcher(dispatcher);
if (save(tab.getSelectedIndex(), 0) != 0) {
tab.remove(tab.getSelectedIndex());
}
KeyboardFocusManager.getCurrentKeyboardFocusManager().addKeyEventDispatcher(dispatcher);
}
}
}
return false;
}
};
KeyboardFocusManager.getCurrentKeyboardFocusManager().addKeyEventDispatcher(dispatcher);
}
// builds the edit>preferences panel
public void preferences() {
if (!async) {
// sbml preferences
String[] Versions = { "L2V4", "L3V1" };
JLabel SBMLlabel = new JLabel("SBML Level/Version");
LevelVersion = new JComboBox(Versions);
if (SBMLLevelVersion.equals("L2V4")) {
LevelVersion.setSelectedItem("L2V4");
}
else {
LevelVersion.setSelectedItem("L3V1");
}
Undeclared = new JCheckBox("Check for undeclared units in SBML");
if (checkUndeclared) {
Undeclared.setSelected(true);
}
else {
Undeclared.setSelected(false);
}
Units = new JCheckBox("Check units in SBML");
if (checkUnits) {
Units.setSelected(true);
}
else {
Units.setSelected(false);
}
Preferences biosimrc = Preferences.userRoot();
// general preferences
JCheckBox dialog = new JCheckBox("Use File Dialog");
if (biosimrc.get("biosim.general.file_browser", "").equals("FileDialog")) {
dialog.setSelected(true);
}
else {
dialog.setSelected(false);
}
JCheckBox icons = new JCheckBox("Use Plus/Minus For Expanding/Collapsing File Tree");
if (biosimrc.get("biosim.general.tree_icons", "").equals("default")) {
icons.setSelected(false);
}
else {
icons.setSelected(true);
}
// create sbml preferences panel
JPanel levelPrefs = new JPanel(new GridLayout(1, 2));
levelPrefs.add(SBMLlabel);
levelPrefs.add(LevelVersion);
// gcm preferences
final JTextField ACTIVED_VALUE = new JTextField(biosimrc.get("biosim.gcm.ACTIVED_VALUE", ""));
final JTextField KACT_VALUE = new JTextField(biosimrc.get("biosim.gcm.KACT_VALUE", ""));
final JTextField KBASAL_VALUE = new JTextField(biosimrc.get("biosim.gcm.KBASAL_VALUE", ""));
final JTextField KBIO_VALUE = new JTextField(biosimrc.get("biosim.gcm.KBIO_VALUE", ""));
final JTextField KDECAY_VALUE = new JTextField(biosimrc.get("biosim.gcm.KDECAY_VALUE", ""));
final JTextField KECDECAY_VALUE = new JTextField(biosimrc.get("biosim.gcm.KECDECAY_VALUE", ""));
final JTextField COOPERATIVITY_VALUE = new JTextField(biosimrc.get("biosim.gcm.COOPERATIVITY_VALUE", ""));
final JTextField KASSOCIATION_VALUE = new JTextField(biosimrc.get("biosim.gcm.KASSOCIATION_VALUE", ""));
final JTextField RNAP_VALUE = new JTextField(biosimrc.get("biosim.gcm.RNAP_VALUE", ""));
final JTextField PROMOTER_COUNT_VALUE = new JTextField(biosimrc.get("biosim.gcm.PROMOTER_COUNT_VALUE", ""));
final JTextField INITIAL_VALUE = new JTextField(biosimrc.get("biosim.gcm.INITIAL_VALUE", ""));
final JTextField MAX_DIMER_VALUE = new JTextField(biosimrc.get("biosim.gcm.MAX_DIMER_VALUE", ""));
final JTextField OCR_VALUE = new JTextField(biosimrc.get("biosim.gcm.OCR_VALUE", ""));
final JTextField RNAP_BINDING_VALUE = new JTextField(biosimrc.get("biosim.gcm.RNAP_BINDING_VALUE", ""));
final JTextField ACTIVATED_RNAP_BINDING_VALUE = new JTextField(biosimrc.get("biosim.gcm.ACTIVATED_RNAP_BINDING_VALUE", ""));
final JTextField KREP_VALUE = new JTextField(biosimrc.get("biosim.gcm.KREP_VALUE", ""));
final JTextField STOICHIOMETRY_VALUE = new JTextField(biosimrc.get("biosim.gcm.STOICHIOMETRY_VALUE", ""));
final JTextField KCOMPLEX_VALUE = new JTextField(biosimrc.get("biosim.gcm.KCOMPLEX_VALUE", ""));
final JTextField MEMDIFF_VALUE = new JTextField(biosimrc.get("biosim.gcm.MEMDIFF_VALUE", ""));
final JTextField KECDIFF_VALUE = new JTextField(biosimrc.get("biosim.gcm.KECDIFF_VALUE", ""));
JPanel labels = new JPanel(new GridLayout(19, 1));
labels.add(SBMLlabel);
labels.add(Undeclared);
labels.add(new JLabel(CompatibilityFixer.getGuiName(GlobalConstants.ACTIVED_STRING) + " (" + GlobalConstants.ACTIVED_STRING + "):"));
labels.add(new JLabel(CompatibilityFixer.getGuiName(GlobalConstants.KACT_STRING) + " (" + GlobalConstants.KACT_STRING + "):"));
labels.add(new JLabel(CompatibilityFixer.getGuiName(GlobalConstants.KBASAL_STRING) + " (" + GlobalConstants.KBASAL_STRING + "):"));
labels.add(new JLabel(CompatibilityFixer.getGuiName(GlobalConstants.KDECAY_STRING) + " (" + GlobalConstants.KDECAY_STRING + "):"));
labels.add(new JLabel(CompatibilityFixer.getGuiName(GlobalConstants.KECDECAY_STRING) + " (" + GlobalConstants.KECDECAY_STRING + "):"));
labels.add(new JLabel(CompatibilityFixer.getGuiName(GlobalConstants.COOPERATIVITY_STRING) + " (" + GlobalConstants.COOPERATIVITY_STRING
+ "):"));
labels.add(new JLabel(CompatibilityFixer.getGuiName(GlobalConstants.RNAP_STRING) + " (" + GlobalConstants.RNAP_STRING + "):"));
labels.add(new JLabel(CompatibilityFixer.getGuiName(GlobalConstants.PROMOTER_COUNT_STRING) + " (" + GlobalConstants.PROMOTER_COUNT_STRING
+ "):"));
labels.add(new JLabel(CompatibilityFixer.getGuiName(GlobalConstants.INITIAL_STRING) + " (" + GlobalConstants.INITIAL_STRING + "):"));
labels.add(new JLabel(CompatibilityFixer.getGuiName(GlobalConstants.OCR_STRING) + " (" + GlobalConstants.OCR_STRING + "):"));
labels.add(new JLabel(CompatibilityFixer.getGuiName(GlobalConstants.RNAP_BINDING_STRING) + " (" + GlobalConstants.RNAP_BINDING_STRING
+ "):"));
labels.add(new JLabel(CompatibilityFixer.getGuiName(GlobalConstants.ACTIVATED_RNAP_BINDING_STRING) + " ("
+ GlobalConstants.ACTIVATED_RNAP_BINDING_STRING + "):"));
labels.add(new JLabel(CompatibilityFixer.getGuiName(GlobalConstants.KREP_STRING) + " (" + GlobalConstants.KREP_STRING + "):"));
labels.add(new JLabel(CompatibilityFixer.getGuiName(GlobalConstants.STOICHIOMETRY_STRING) + " (" + GlobalConstants.STOICHIOMETRY_STRING
+ "):"));
labels.add(new JLabel(CompatibilityFixer.getGuiName(GlobalConstants.KCOMPLEX_STRING) + " (" + GlobalConstants.KCOMPLEX_STRING + "):"));
labels.add(new JLabel(CompatibilityFixer.getGuiName(GlobalConstants.MEMDIFF_STRING) + " (" + GlobalConstants.MEMDIFF_STRING + "):"));
labels.add(new JLabel(CompatibilityFixer.getGuiName(GlobalConstants.KECDIFF_STRING) + " (" + GlobalConstants.KECDIFF_STRING + "):"));
JPanel fields = new JPanel(new GridLayout(19, 1));
fields.add(LevelVersion);
fields.add(Units);
fields.add(ACTIVED_VALUE);
fields.add(KACT_VALUE);
fields.add(KBASAL_VALUE);
fields.add(KDECAY_VALUE);
fields.add(KECDECAY_VALUE);
fields.add(COOPERATIVITY_VALUE);
fields.add(RNAP_VALUE);
fields.add(PROMOTER_COUNT_VALUE);
fields.add(INITIAL_VALUE);
fields.add(OCR_VALUE);
fields.add(RNAP_BINDING_VALUE);
fields.add(ACTIVATED_RNAP_BINDING_VALUE);
fields.add(KREP_VALUE);
fields.add(STOICHIOMETRY_VALUE);
fields.add(KCOMPLEX_VALUE);
fields.add(MEMDIFF_VALUE);
fields.add(KECDIFF_VALUE);
// create gcm preferences panel
JPanel gcmPrefs = new JPanel(new GridLayout(1, 2));
gcmPrefs.add(labels);
gcmPrefs.add(fields);
// analysis preferences
String[] choices = { "None", "Abstraction", "Logical Abstraction" };
JTextField simCommand = new JTextField(biosimrc.get("biosim.sim.command", ""));
final JComboBox abs = new JComboBox(choices);
abs.setSelectedItem(biosimrc.get("biosim.sim.abs", ""));
if (abs.getSelectedItem().equals("None")) {
choices = new String[] { "ODE", "Monte Carlo", "SBML", "Network", "Browser" };
}
else if (abs.getSelectedItem().equals("Abstraction")) {
choices = new String[] { "ODE", "Monte Carlo", "SBML", "Network", "Browser" };
}
else {
choices = new String[] { "Monte Carlo", "Markov", "SBML", "Network", "Browser", "LPN" };
}
final JComboBox type = new JComboBox(choices);
type.setSelectedItem(biosimrc.get("biosim.sim.type", ""));
if (type.getSelectedItem().equals("ODE")) {
choices = new String[] { "euler", "gear1", "gear2", "rk4imp", "rk8pd", "rkf45" };
}
else if (type.getSelectedItem().equals("Monte Carlo")) {
choices = new String[] { "gillespie", "gillespieJava", "mpde", "mp", "mp-adaptive", "mp-event", "emc-sim", "bunker", "nmc" };
}
else if (type.getSelectedItem().equals("Markov")) {
choices = new String[] { "steady-state-markov-chain-analysis", "transient-markov-chain-analysis", "reachability-analysis", "atacs",
"ctmc-transient" };
}
else {
choices = new String[] { "euler", "gear1", "gear2", "rk4imp", "rk8pd", "rkf45" };
}
final JComboBox sim = new JComboBox(choices);
sim.setSelectedItem(biosimrc.get("biosim.sim.sim", ""));
abs.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
if (abs.getSelectedItem().equals("None")) {
Object o = type.getSelectedItem();
type.removeAllItems();
type.addItem("ODE");
type.addItem("Monte Carlo");
type.addItem("Model");
type.addItem("Network");
type.addItem("Browser");
type.setSelectedItem(o);
}
else if (abs.getSelectedItem().equals("Abstraction")) {
Object o = type.getSelectedItem();
type.removeAllItems();
type.addItem("ODE");
type.addItem("Monte Carlo");
type.addItem("Model");
type.addItem("Network");
type.addItem("Browser");
type.setSelectedItem(o);
}
else {
Object o = type.getSelectedItem();
type.removeAllItems();
type.addItem("Monte Carlo");
type.addItem("Markov");
type.addItem("Model");
type.addItem("Network");
type.addItem("Browser");
type.addItem("LPN");
type.setSelectedItem(o);
}
}
});
type.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
if (type.getSelectedItem() == null) {
}
else if (type.getSelectedItem().equals("ODE")) {
Object o = sim.getSelectedItem();
sim.removeAllItems();
sim.addItem("euler");
sim.addItem("gear1");
sim.addItem("gear2");
sim.addItem("rk4imp");
sim.addItem("rk8pd");
sim.addItem("rkf45");
sim.setSelectedIndex(5);
sim.setSelectedItem(o);
}
else if (type.getSelectedItem().equals("Monte Carlo")) {
Object o = sim.getSelectedItem();
sim.removeAllItems();
sim.addItem("gillespie");
sim.addItem("gillespieJava");
sim.addItem("mpde");
sim.addItem("mp");
sim.addItem("mp-adaptive");
sim.addItem("mp-event");
sim.addItem("emc-sim");
sim.addItem("bunker");
sim.addItem("nmc");
sim.setSelectedItem(o);
}
else if (type.getSelectedItem().equals("Markov")) {
Object o = sim.getSelectedItem();
sim.removeAllItems();
sim.addItem("steady-state-markov-chain-analysis");
sim.addItem("transient-markov-chain-analysis");
sim.addItem("reachability-analysis");
sim.addItem("atacs");
sim.addItem("ctmc-transient");
sim.setSelectedItem(o);
}
else {
Object o = sim.getSelectedItem();
sim.removeAllItems();
sim.addItem("euler");
sim.addItem("gear1");
sim.addItem("gear2");
sim.addItem("rk4imp");
sim.addItem("rk8pd");
sim.addItem("rkf45");
sim.setSelectedIndex(5);
sim.setSelectedItem(o);
}
}
});
JTextField limit = new JTextField(biosimrc.get("biosim.sim.limit", ""));
JTextField interval = new JTextField(biosimrc.get("biosim.sim.interval", ""));
JTextField minStep = new JTextField(biosimrc.get("biosim.sim.min.step", ""));
JTextField step = new JTextField(biosimrc.get("biosim.sim.step", ""));
JTextField error = new JTextField(biosimrc.get("biosim.sim.error", ""));
JTextField seed = new JTextField(biosimrc.get("biosim.sim.seed", ""));
JTextField runs = new JTextField(biosimrc.get("biosim.sim.runs", ""));
JTextField rapid1 = new JTextField(biosimrc.get("biosim.sim.rapid1", ""));
JTextField rapid2 = new JTextField(biosimrc.get("biosim.sim.rapid2", ""));
JTextField qssa = new JTextField(biosimrc.get("biosim.sim.qssa", ""));
JTextField concentration = new JTextField(biosimrc.get("biosim.sim.concentration", ""));
choices = new String[] { "Print Interval", "Minimum Print Interval", "Number Of Steps" };
JComboBox useInterval = new JComboBox(choices);
useInterval.setSelectedItem(biosimrc.get("biosim.sim.useInterval", ""));
JPanel analysisLabels = new JPanel(new GridLayout(15, 1));
analysisLabels.add(new JLabel("Simulation Command:"));
analysisLabels.add(new JLabel("Abstraction:"));
analysisLabels.add(new JLabel("Simulation Type:"));
analysisLabels.add(new JLabel("Possible Simulators/Analyzers:"));
analysisLabels.add(new JLabel("Time Limit:"));
analysisLabels.add(useInterval);
analysisLabels.add(new JLabel("Minimum Time Step:"));
analysisLabels.add(new JLabel("Maximum Time Step:"));
analysisLabels.add(new JLabel("Absolute Error:"));
analysisLabels.add(new JLabel("Random Seed:"));
analysisLabels.add(new JLabel("Runs:"));
analysisLabels.add(new JLabel("Rapid Equilibrium Condition 1:"));
analysisLabels.add(new JLabel("Rapid Equilibrium Cojdition 2:"));
analysisLabels.add(new JLabel("QSSA Condition:"));
analysisLabels.add(new JLabel("Max Concentration Threshold:"));
JPanel analysisFields = new JPanel(new GridLayout(15, 1));
analysisFields.add(simCommand);
analysisFields.add(abs);
analysisFields.add(type);
analysisFields.add(sim);
analysisFields.add(limit);
analysisFields.add(interval);
analysisFields.add(minStep);
analysisFields.add(step);
analysisFields.add(error);
analysisFields.add(seed);
analysisFields.add(runs);
analysisFields.add(rapid1);
analysisFields.add(rapid2);
analysisFields.add(qssa);
analysisFields.add(concentration);
// create analysis preferences panel
JPanel analysisPrefs = new JPanel(new GridLayout(1, 2));
analysisPrefs.add(analysisLabels);
analysisPrefs.add(analysisFields);
// learning preferences
final JTextField tn = new JTextField(biosimrc.get("biosim.learn.tn", ""));
final JTextField tj = new JTextField(biosimrc.get("biosim.learn.tj", ""));
final JTextField ti = new JTextField(biosimrc.get("biosim.learn.ti", ""));
choices = new String[] { "0", "1", "2", "3", "4", "5", "6", "7", "8", "9" };
final JComboBox bins = new JComboBox(choices);
bins.setSelectedItem(biosimrc.get("biosim.learn.bins", ""));
choices = new String[] { "Equal Data Per Bins", "Equal Spacing Of Bins" };
final JComboBox equaldata = new JComboBox(choices);
equaldata.setSelectedItem(biosimrc.get("biosim.learn.equaldata", ""));
choices = new String[] { "Auto", "User" };
final JComboBox autolevels = new JComboBox(choices);
autolevels.setSelectedItem(biosimrc.get("biosim.learn.autolevels", ""));
final JTextField ta = new JTextField(biosimrc.get("biosim.learn.ta", ""));
final JTextField tr = new JTextField(biosimrc.get("biosim.learn.tr", ""));
final JTextField tm = new JTextField(biosimrc.get("biosim.learn.tm", ""));
final JTextField tt = new JTextField(biosimrc.get("biosim.learn.tt", ""));
choices = new String[] { "0", "1", "2", "3" };
final JComboBox debug = new JComboBox(choices);
debug.setSelectedItem(biosimrc.get("biosim.learn.debug", ""));
choices = new String[] { "Successors", "Predecessors", "Both" };
final JComboBox succpred = new JComboBox(choices);
succpred.setSelectedItem(biosimrc.get("biosim.learn.succpred", ""));
choices = new String[] { "True", "False" };
final JComboBox findbaseprob = new JComboBox(choices);
findbaseprob.setSelectedItem(biosimrc.get("biosim.learn.findbaseprob", ""));
JPanel learnLabels = new JPanel(new GridLayout(13, 1));
learnLabels.add(new JLabel("Minimum Number Of Initial Vectors (Tn):"));
learnLabels.add(new JLabel("Maximum Influence Vector Size (Tj):"));
learnLabels.add(new JLabel("Score For Empty Influence Vector (Ti):"));
learnLabels.add(new JLabel("Number Of Bins:"));
learnLabels.add(new JLabel("Divide Bins:"));
learnLabels.add(new JLabel("Generate Levels:"));
learnLabels.add(new JLabel("Ratio For Activation (Ta):"));
learnLabels.add(new JLabel("Ratio For Repression (Tr):"));
learnLabels.add(new JLabel("Merge Influence Vectors Delta (Tm):"));
learnLabels.add(new JLabel("Relax Thresholds Delta (Tt):"));
learnLabels.add(new JLabel("Debug Level:"));
learnLabels.add(new JLabel("Successors Or Predecessors:"));
learnLabels.add(new JLabel("Basic FindBaseProb:"));
JPanel learnFields = new JPanel(new GridLayout(13, 1));
learnFields.add(tn);
learnFields.add(tj);
learnFields.add(ti);
learnFields.add(bins);
learnFields.add(equaldata);
learnFields.add(autolevels);
learnFields.add(ta);
learnFields.add(tr);
learnFields.add(tm);
learnFields.add(tt);
learnFields.add(debug);
learnFields.add(succpred);
learnFields.add(findbaseprob);
// create learning preferences panel
JPanel learnPrefs = new JPanel(new GridLayout(1, 2));
learnPrefs.add(learnLabels);
learnPrefs.add(learnFields);
// create general preferences panel
JPanel generalPrefsBordered = new JPanel(new BorderLayout());
JPanel generalPrefs = new JPanel();
generalPrefsBordered.add(dialog, "North");
generalPrefsBordered.add(icons, "Center");
generalPrefs.add(generalPrefsBordered);
((FlowLayout) generalPrefs.getLayout()).setAlignment(FlowLayout.LEFT);
// create tabs
JTabbedPane prefTabs = new JTabbedPane();
prefTabs.addTab("General Preferences", generalPrefs);
prefTabs.addTab("Model Preferences", gcmPrefs);
prefTabs.addTab("Analysis Preferences", analysisPrefs);
prefTabs.addTab("Learn Preferences", learnPrefs);
Object[] options = { "Save", "Cancel" };
int value = JOptionPane.showOptionDialog(frame, prefTabs, "Preferences", JOptionPane.YES_NO_OPTION, JOptionPane.PLAIN_MESSAGE, null,
options, options[0]);
// if user hits "save", store and/or check new data
if (value == JOptionPane.YES_OPTION) {
if (dialog.isSelected()) {
biosimrc.put("biosim.general.file_browser", "FileDialog");
}
else {
biosimrc.put("biosim.general.file_browser", "JFileChooser");
}
if (icons.isSelected()) {
biosimrc.put("biosim.general.tree_icons", "plus_minus");
tree.setExpandibleIcons(false);
}
else {
biosimrc.put("biosim.general.tree_icons", "default");
tree.setExpandibleIcons(true);
}
if (LevelVersion.getSelectedItem().equals("L2V4")) {
SBMLLevelVersion = "L2V4";
SBML_LEVEL = 2;
SBML_VERSION = 4;
biosimrc.put("biosim.sbml.level_version", "L2V4");
}
else {
SBMLLevelVersion = "L3V1";
SBML_LEVEL = 3;
SBML_VERSION = 1;
biosimrc.put("biosim.sbml.level_version", "L3V1");
}
if (Undeclared.isSelected()) {
checkUndeclared = true;
biosimrc.put("biosim.check.undeclared", "true");
}
else {
checkUndeclared = false;
biosimrc.put("biosim.check.undeclared", "false");
}
if (Units.isSelected()) {
checkUnits = true;
biosimrc.put("biosim.check.units", "true");
}
else {
checkUnits = false;
biosimrc.put("biosim.check.units", "false");
}
try {
Double.parseDouble(KREP_VALUE.getText().trim());
biosimrc.put("biosim.gcm.KREP_VALUE", KREP_VALUE.getText().trim());
}
catch (Exception e1) {
}
try {
Double.parseDouble(KACT_VALUE.getText().trim());
biosimrc.put("biosim.gcm.KACT_VALUE", KACT_VALUE.getText().trim());
}
catch (Exception e1) {
}
try {
Double.parseDouble(KBIO_VALUE.getText().trim());
biosimrc.put("biosim.gcm.KBIO_VALUE", KBIO_VALUE.getText().trim());
}
catch (Exception e1) {
}
try {
Double.parseDouble(PROMOTER_COUNT_VALUE.getText().trim());
biosimrc.put("biosim.gcm.PROMOTER_COUNT_VALUE", PROMOTER_COUNT_VALUE.getText().trim());
}
catch (Exception e1) {
}
try {
Double.parseDouble(KASSOCIATION_VALUE.getText().trim());
biosimrc.put("biosim.gcm.KASSOCIATION_VALUE", KASSOCIATION_VALUE.getText().trim());
}
catch (Exception e1) {
}
try {
Double.parseDouble(KBASAL_VALUE.getText().trim());
biosimrc.put("biosim.gcm.KBASAL_VALUE", KBASAL_VALUE.getText().trim());
}
catch (Exception e1) {
}
try {
Double.parseDouble(OCR_VALUE.getText().trim());
biosimrc.put("biosim.gcm.OCR_VALUE", OCR_VALUE.getText().trim());
}
catch (Exception e1) {
}
try {
Double.parseDouble(KDECAY_VALUE.getText().trim());
biosimrc.put("biosim.gcm.KDECAY_VALUE", KDECAY_VALUE.getText().trim());
}
catch (Exception e1) {
}
try {
Double.parseDouble(KECDECAY_VALUE.getText().trim());
biosimrc.put("biosim.gcm.KECDECAY_VALUE", KECDECAY_VALUE.getText().trim());
}
catch (Exception e1) {
}
try {
Double.parseDouble(RNAP_VALUE.getText().trim());
biosimrc.put("biosim.gcm.RNAP_VALUE", RNAP_VALUE.getText().trim());
}
catch (Exception e1) {
}
try {
Double.parseDouble(RNAP_BINDING_VALUE.getText().trim());
biosimrc.put("biosim.gcm.RNAP_BINDING_VALUE", RNAP_BINDING_VALUE.getText().trim());
}
catch (Exception e1) {
}
try {
Double.parseDouble(ACTIVATED_RNAP_BINDING_VALUE.getText().trim());
biosimrc.put("biosim.gcm.ACTIVATED_RNAP_BINDING_VALUE", ACTIVATED_RNAP_BINDING_VALUE.getText().trim());
}
catch (Exception e1) {
}
try {
Double.parseDouble(STOICHIOMETRY_VALUE.getText().trim());
biosimrc.put("biosim.gcm.STOICHIOMETRY_VALUE", STOICHIOMETRY_VALUE.getText().trim());
}
catch (Exception e1) {
}
try {
Double.parseDouble(KCOMPLEX_VALUE.getText().trim());
biosimrc.put("biosim.gcm.KCOMPLEX_VALUE", KCOMPLEX_VALUE.getText().trim());
}
catch (Exception e1) {
}
try {
Double.parseDouble(COOPERATIVITY_VALUE.getText().trim());
biosimrc.put("biosim.gcm.COOPERATIVITY_VALUE", COOPERATIVITY_VALUE.getText().trim());
}
catch (Exception e1) {
}
try {
Double.parseDouble(ACTIVED_VALUE.getText().trim());
biosimrc.put("biosim.gcm.ACTIVED_VALUE", ACTIVED_VALUE.getText().trim());
}
catch (Exception e1) {
}
try {
Double.parseDouble(MAX_DIMER_VALUE.getText().trim());
biosimrc.put("biosim.gcm.MAX_DIMER_VALUE", MAX_DIMER_VALUE.getText().trim());
}
catch (Exception e1) {
}
try {
Double.parseDouble(INITIAL_VALUE.getText().trim());
biosimrc.put("biosim.gcm.INITIAL_VALUE", INITIAL_VALUE.getText().trim());
}
catch (Exception e1) {
}
try {
String[] fdrv = MEMDIFF_VALUE.getText().trim().split("/");
//if the user specifies a forward and reverse rate
if (fdrv.length == 2) {
biosimrc.put("biosim.gcm.MEMDIFF_VALUE",
Double.parseDouble(fdrv[0]) + "/" + Double.parseDouble(fdrv[1]));
}
else if (fdrv.length == 1) {
Double.parseDouble(MEMDIFF_VALUE.getText().trim());
biosimrc.put("biosim.gcm.MEMDIFF_VALUE", MEMDIFF_VALUE.getText().trim());
}
}
catch (Exception e1) {
}
try {
Double.parseDouble(KECDIFF_VALUE.getText().trim());
biosimrc.put("biosim.gcm.KECDIFF_VALUE", KECDIFF_VALUE.getText().trim());
}
catch (Exception e1) {
}
try {
biosimrc.put("biosim.sim.command", simCommand.getText().trim());
}
catch (Exception e1) {
}
try {
Double.parseDouble(limit.getText().trim());
biosimrc.put("biosim.sim.limit", limit.getText().trim());
}
catch (Exception e1) {
}
try {
Double.parseDouble(interval.getText().trim());
biosimrc.put("biosim.sim.interval", interval.getText().trim());
}
catch (Exception e1) {
}
try {
Double.parseDouble(minStep.getText().trim());
biosimrc.put("biosim.min.sim.step", minStep.getText().trim());
}
catch (Exception e1) {
}
try {
if (step.getText().trim().equals("inf")) {
biosimrc.put("biosim.sim.step", step.getText().trim());
}
else {
Double.parseDouble(step.getText().trim());
biosimrc.put("biosim.sim.step", step.getText().trim());
}
}
catch (Exception e1) {
}
try {
Double.parseDouble(error.getText().trim());
biosimrc.put("biosim.sim.error", error.getText().trim());
}
catch (Exception e1) {
}
try {
Long.parseLong(seed.getText().trim());
biosimrc.put("biosim.sim.seed", seed.getText().trim());
}
catch (Exception e1) {
}
try {
Integer.parseInt(runs.getText().trim());
biosimrc.put("biosim.sim.runs", runs.getText().trim());
}
catch (Exception e1) {
}
try {
Double.parseDouble(rapid1.getText().trim());
biosimrc.put("biosim.sim.rapid1", rapid1.getText().trim());
}
catch (Exception e1) {
}
try {
Double.parseDouble(rapid2.getText().trim());
biosimrc.put("biosim.sim.rapid2", rapid2.getText().trim());
}
catch (Exception e1) {
}
try {
Double.parseDouble(qssa.getText().trim());
biosimrc.put("biosim.sim.qssa", qssa.getText().trim());
}
catch (Exception e1) {
}
try {
Integer.parseInt(concentration.getText().trim());
biosimrc.put("biosim.sim.concentration", concentration.getText().trim());
}
catch (Exception e1) {
}
biosimrc.put("biosim.sim.useInterval", (String) useInterval.getSelectedItem());
biosimrc.put("biosim.sim.abs", (String) abs.getSelectedItem());
biosimrc.put("biosim.sim.type", (String) type.getSelectedItem());
biosimrc.put("biosim.sim.sim", (String) sim.getSelectedItem());
try {
Integer.parseInt(tn.getText().trim());
biosimrc.put("biosim.learn.tn", tn.getText().trim());
}
catch (Exception e1) {
}
try {
Integer.parseInt(tj.getText().trim());
biosimrc.put("biosim.learn.tj", tj.getText().trim());
}
catch (Exception e1) {
}
try {
Double.parseDouble(ti.getText().trim());
biosimrc.put("biosim.learn.ti", ti.getText().trim());
}
catch (Exception e1) {
}
biosimrc.put("biosim.learn.bins", (String) bins.getSelectedItem());
biosimrc.put("biosim.learn.equaldata", (String) equaldata.getSelectedItem());
biosimrc.put("biosim.learn.autolevels", (String) autolevels.getSelectedItem());
try {
Double.parseDouble(ta.getText().trim());
biosimrc.put("biosim.learn.ta", ta.getText().trim());
}
catch (Exception e1) {
}
try {
Double.parseDouble(tr.getText().trim());
biosimrc.put("biosim.learn.tr", tr.getText().trim());
}
catch (Exception e1) {
}
try {
Double.parseDouble(tm.getText().trim());
biosimrc.put("biosim.learn.tm", tm.getText().trim());
}
catch (Exception e1) {
}
try {
Double.parseDouble(tt.getText().trim());
biosimrc.put("biosim.learn.tt", tt.getText().trim());
}
catch (Exception e1) {
}
biosimrc.put("biosim.learn.debug", (String) debug.getSelectedItem());
biosimrc.put("biosim.learn.succpred", (String) succpred.getSelectedItem());
biosimrc.put("biosim.learn.findbaseprob", (String) findbaseprob.getSelectedItem());
for (int i = 0; i < tab.getTabCount(); i++) {
if (tab.getTitleAt(i).contains(".gcm")) {
((GCM2SBMLEditor) tab.getComponentAt(i)).getGCM().loadDefaultParameters();
((GCM2SBMLEditor) tab.getComponentAt(i)).reloadParameters();
}
}
}
// if user clicks "cancel"
else {
}
}
// if (async)
else {
Preferences biosimrc = Preferences.userRoot();
JPanel prefPanel = new JPanel(new GridLayout(0, 2));
JLabel verCmdLabel = new JLabel("Verification command:");
JTextField verCmd = new JTextField(biosimrc.get("biosim.verification.command", ""));
viewerLabel = new JLabel("External Editor for non-LPN files:");
viewerField = new JTextField(biosimrc.get("biosim.general.viewer", ""));
prefPanel.add(verCmdLabel);
prefPanel.add(verCmd);
prefPanel.add(viewerLabel);
prefPanel.add(viewerField);
// Preferences biosimrc = Preferences.userRoot();
// JPanel vhdlPrefs = new JPanel();
// JPanel lhpnPrefs = new JPanel();
// JTabbedPane prefTabsNoLema = new JTabbedPane();
// prefTabsNoLema.addTab("VHDL Preferences", vhdlPrefs);
// prefTabsNoLema.addTab("LPN Preferences", lhpnPrefs);
JCheckBox dialog = new JCheckBox("Use File Dialog");
if (biosimrc.get("biosim.general.file_browser", "").equals("FileDialog")) {
dialog.setSelected(true);
}
else {
dialog.setSelected(false);
}
JCheckBox icons = new JCheckBox("Use Plus/Minus For Expanding/Collapsing File Tree");
if (biosimrc.get("biosim.general.tree_icons", "").equals("default")) {
icons.setSelected(false);
}
else {
icons.setSelected(true);
}
JPanel generalPrefsBordered = new JPanel(new BorderLayout());
JPanel generalPrefs = new JPanel();
generalPrefsBordered.add(dialog, "North");
generalPrefsBordered.add(icons, "Center");
generalPrefs.add(generalPrefsBordered);
((FlowLayout) generalPrefs.getLayout()).setAlignment(FlowLayout.LEFT);
prefPanel.add(generalPrefs);
Object[] options = { "Save", "Cancel" };
int value = JOptionPane.showOptionDialog(frame, prefPanel, "Preferences", JOptionPane.YES_NO_OPTION, JOptionPane.PLAIN_MESSAGE, null,
options, options[0]);
if (value == JOptionPane.YES_OPTION) {
viewer = viewerField.getText();
biosimrc.put("biosim.general.viewer", viewer);
biosimrc.put("biosim.verification.command", verCmd.getText());
if (dialog.isSelected()) {
biosimrc.put("biosim.general.file_browser", "FileDialog");
}
else {
biosimrc.put("biosim.general.file_browser", "JFileChooser");
}
if (icons.isSelected()) {
biosimrc.put("biosim.general.tree_icons", "plus_minus");
tree.setExpandibleIcons(false);
}
else {
biosimrc.put("biosim.general.tree_icons", "default");
tree.setExpandibleIcons(true);
}
}
}
}
public void about() {
final JFrame f = new JFrame("About");
// frame.setIconImage(new ImageIcon(ENVVAR +
// File.separator
// + "gui"
// + File.separator + "icons" + File.separator +
// "iBioSim.png").getImage());
JLabel name;
JLabel version;
final String developers;
if (lema) {
name = new JLabel("LEMA", JLabel.CENTER);
version = new JLabel("Version 1.9", JLabel.CENTER);
developers = "Satish Batchu\nKevin Jones\nScott Little\nCurtis Madsen\nChris Myers\nNicholas Seegmiller\n"
+ "Robert Thacker\nDavid Walter";
}
else if (atacs) {
name = new JLabel("ATACS", JLabel.CENTER);
version = new JLabel("Version 6.9", JLabel.CENTER);
developers = "Wendy Belluomini\nJeff Cuthbert\nHans Jacobson\nKevin Jones\nSung-Tae Jung\n"
+ "Christopher Krieger\nScott Little\nCurtis Madsen\nEric Mercer\nChris Myers\n"
+ "Curt Nelson\nEric Peskin\nNicholas Seegmiller\nDavid Walter\nHao Zheng";
}
else {
name = new JLabel("iBioSim", JLabel.CENTER);
version = new JLabel("Version 2.0", JLabel.CENTER);
developers = "Nathan Barker\nKevin Jones\nHiroyuki Kuwahara\n"
+ "Curtis Madsen\nChris Myers\nNam Nguyen\nNicholas Roehner\nTyler Patterson";
}
Font font = name.getFont();
font = font.deriveFont(Font.BOLD, 36.0f);
name.setFont(font);
JLabel uOfU = new JLabel("University of Utah", JLabel.CENTER);
JButton credits = new JButton("Credits");
credits.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
Object[] options = { "Close" };
JOptionPane.showOptionDialog(f, developers, "Credits", JOptionPane.YES_OPTION, JOptionPane.PLAIN_MESSAGE, null, options, options[0]);
}
});
JButton close = new JButton("Close");
close.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
f.dispose();
}
});
JPanel buttons = new JPanel();
buttons.add(credits);
buttons.add(close);
JPanel aboutPanel = new JPanel(new BorderLayout());
JPanel uOfUPanel = new JPanel(new BorderLayout());
uOfUPanel.add(name, "North");
uOfUPanel.add(version, "Center");
uOfUPanel.add(uOfU, "South");
if (lema) {
aboutPanel.add(new javax.swing.JLabel(
new javax.swing.ImageIcon(ENVVAR + separator + "gui" + separator + "icons" + separator + "LEMA.png")), "North");
}
else if (atacs) {
aboutPanel.add(new javax.swing.JLabel(new javax.swing.ImageIcon(ENVVAR + separator + "gui" + separator + "icons" + separator
+ "ATACS.png")), "North");
}
else {
aboutPanel.add(new javax.swing.JLabel(new javax.swing.ImageIcon(ENVVAR + separator + "gui" + separator + "icons" + separator
+ "iBioSim.png")), "North");
}
// aboutPanel.add(bioSim, "North");
aboutPanel.add(uOfUPanel, "Center");
aboutPanel.add(buttons, "South");
f.setContentPane(aboutPanel);
f.pack();
Dimension screenSize;
try {
Toolkit tk = Toolkit.getDefaultToolkit();
screenSize = tk.getScreenSize();
}
catch (AWTError awe) {
screenSize = new Dimension(640, 480);
}
Dimension frameSize = f.getSize();
if (frameSize.height > screenSize.height) {
frameSize.height = screenSize.height;
}
if (frameSize.width > screenSize.width) {
frameSize.width = screenSize.width;
}
int x = screenSize.width / 2 - frameSize.width / 2;
int y = screenSize.height / 2 - frameSize.height / 2;
f.setLocation(x, y);
f.setVisible(true);
}
public void exit() {
int autosave = 0;
for (int i = 0; i < tab.getTabCount(); i++) {
int save = save(i, autosave);
if (save == 0) {
return;
}
else if (save == 2) {
autosave = 1;
}
else if (save == 3) {
autosave = 2;
}
}
Preferences biosimrc = Preferences.userRoot();
for (int i = 0; i < numberRecentProj; i++) {
if (atacs) {
biosimrc.put("atacs.recent.project." + i, recentProjects[i].getText());
biosimrc.put("atacs.recent.project.path." + i, recentProjectPaths[i]);
}
else if (lema) {
biosimrc.put("lema.recent.project." + i, recentProjects[i].getText());
biosimrc.put("lema.recent.project.path." + i, recentProjectPaths[i]);
}
else {
biosimrc.put("biosim.recent.project." + i, recentProjects[i].getText());
biosimrc.put("biosim.recent.project.path." + i, recentProjectPaths[i]);
}
}
System.exit(1);
}
/**
* This method performs different functions depending on what menu items are
* selected.
*/
public void actionPerformed(ActionEvent e) {
if (e.getSource() == viewCircuit) {
Component comp = tab.getSelectedComponent();
if (comp instanceof JTabbedPane) {
Component component = ((JTabbedPane) comp).getSelectedComponent();
if (component instanceof LearnGCM) {
((LearnGCM) component).viewGcm();
}
else if (component instanceof LearnLHPN) {
((LearnLHPN) component).viewLhpn();
}
}
else if (comp instanceof LHPNEditor) {
((LHPNEditor) comp).viewLhpn();
}
else if (comp instanceof JPanel) {
Component[] array = ((JPanel) comp).getComponents();
if (array[0] instanceof Verification) {
((Verification) array[0]).viewCircuit();
}
else if (array[0] instanceof Synthesis) {
((Synthesis) array[0]).viewCircuit();
}
}
}
else if (e.getSource() == viewLog) {
Component comp = tab.getSelectedComponent();
if (comp instanceof Verification) {
((Verification) comp).viewLog();
}
else if (comp instanceof JPanel) {
Component[] array = ((JPanel) comp).getComponents();
if (array[0] instanceof Synthesis) {
((Synthesis) array[0]).viewLog();
}
}
else if (comp instanceof JTabbedPane) {
for (int i = 0; i < ((JTabbedPane) comp).getTabCount(); i++) {
Component component = ((JTabbedPane) comp).getComponent(i);
if (component instanceof LearnGCM) {
((LearnGCM) component).viewLog();
return;
}
else if (component instanceof LearnLHPN) {
((LearnLHPN) component).viewLog();
return;
}
}
}
}
else if (e.getSource() == viewCoverage) {
Component comp = tab.getSelectedComponent();
for (int i = 0; i < ((JTabbedPane) comp).getTabCount(); i++) {
Component component = ((JTabbedPane) comp).getComponent(i);
if (component instanceof LearnLHPN) {
((LearnLHPN) component).viewCoverage();
return;
}
}
}
else if (e.getSource() == saveModel) {
Component comp = tab.getSelectedComponent();
if (comp instanceof JTabbedPane) {
for (Component component : ((JTabbedPane) comp).getComponents()) {
if (component instanceof LearnGCM) {
((LearnGCM) component).saveGcm();
}
else if (component instanceof LearnLHPN) {
((LearnLHPN) component).saveLhpn();
}
}
}
}
else if (e.getSource() == saveAsVerilog) {
new Lpn2verilog(tree.getFile());
String theFile = "";
if (tree.getFile().lastIndexOf('/') >= 0) {
theFile = tree.getFile().substring(tree.getFile().lastIndexOf('/') + 1);
}
if (tree.getFile().lastIndexOf('\\') >= 0) {
theFile = tree.getFile().substring(tree.getFile().lastIndexOf('\\') + 1);
}
addToTree(theFile.replace(".lpn", ".sv"));
}
else if (e.getSource() == close && tab.getSelectedComponent() != null) {
Component comp = tab.getSelectedComponent();
Point point = comp.getLocation();
tab.fireCloseTabEvent(new MouseEvent(comp, e.getID(), e.getWhen(), e.getModifiers(), point.x, point.y, 0, false), tab.getSelectedIndex());
}
else if (e.getSource() == closeAll) {
while (tab.getSelectedComponent() != null) {
int index = tab.getSelectedIndex();
Component comp = tab.getComponent(index);
Point point = comp.getLocation();
tab.fireCloseTabEvent(new MouseEvent(comp, e.getID(), e.getWhen(), e.getModifiers(), point.x, point.y, 0, false), index);
}
}
else if (e.getSource() == viewRules) {
Component comp = tab.getSelectedComponent();
Component[] array = ((JPanel) comp).getComponents();
((Synthesis) array[0]).viewRules();
}
else if (e.getSource() == viewTrace) {
Component comp = tab.getSelectedComponent();
if (comp instanceof Verification) {
((Verification) comp).viewTrace();
}
else if (comp instanceof Synthesis) {
((Synthesis) comp).viewTrace();
}
}
else if (e.getSource() == exportSBML) {
Component comp = tab.getSelectedComponent();
if (comp instanceof GCM2SBMLEditor) {
((GCM2SBMLEditor) comp).exportSBML();
}
}
else if (e.getSource() == exportSBOL) {
Component comp = tab.getSelectedComponent();
if (comp instanceof GCM2SBMLEditor) {
((GCM2SBMLEditor) comp).exportSBOL();
}
}
else if (e.getSource() == saveSBOL) {
Component comp = tab.getSelectedComponent();
if (comp instanceof GCM2SBMLEditor) {
((GCM2SBMLEditor) comp).saveSBOL();
}
}
else if (e.getSource() == exportCsv) {
Component comp = tab.getSelectedComponent();
if (comp instanceof Graph) {
((Graph) comp).export(5);
}
else if (comp instanceof JTabbedPane) {
((Graph) ((JTabbedPane) comp).getSelectedComponent()).export(5);
}
}
else if (e.getSource() == exportDat) {
Component comp = tab.getSelectedComponent();
if (comp instanceof Graph) {
((Graph) comp).export(6);
}
else if (comp instanceof JTabbedPane) {
((Graph) ((JTabbedPane) comp).getSelectedComponent()).export();
}
}
else if (e.getSource() == exportEps) {
Component comp = tab.getSelectedComponent();
if (comp instanceof Graph) {
((Graph) comp).export(3);
}
else if (comp instanceof JTabbedPane) {
((Graph) ((JTabbedPane) comp).getSelectedComponent()).export(3);
}
}
else if (e.getSource() == exportJpg) {
Component comp = tab.getSelectedComponent();
if (comp instanceof Graph) {
((Graph) comp).export(0);
}
else if (comp instanceof JTabbedPane) {
((Graph) ((JTabbedPane) comp).getSelectedComponent()).export(0);
}
}
else if (e.getSource() == exportPdf) {
Component comp = tab.getSelectedComponent();
if (comp instanceof Graph) {
((Graph) comp).export(2);
}
else if (comp instanceof JTabbedPane) {
((Graph) ((JTabbedPane) comp).getSelectedComponent()).export(2);
}
}
else if (e.getSource() == exportPng) {
Component comp = tab.getSelectedComponent();
if (comp instanceof Graph) {
((Graph) comp).export(1);
}
else if (comp instanceof JTabbedPane) {
((Graph) ((JTabbedPane) comp).getSelectedComponent()).export(1);
}
}
else if (e.getSource() == exportSvg) {
Component comp = tab.getSelectedComponent();
if (comp instanceof Graph) {
((Graph) comp).export(4);
}
else if (comp instanceof JTabbedPane) {
((Graph) ((JTabbedPane) comp).getSelectedComponent()).export(4);
}
}
else if (e.getSource() == exportTsd) {
Component comp = tab.getSelectedComponent();
if (comp instanceof Graph) {
((Graph) comp).export(7);
}
else if (comp instanceof JTabbedPane) {
((Graph) ((JTabbedPane) comp).getSelectedComponent()).export(7);
}
}
else if (e.getSource() == about) {
about();
}
else if (e.getSource() == manual) {
try {
String directory = "";
String theFile = "";
if (!async) {
theFile = "iBioSim.html";
}
else if (atacs) {
theFile = "ATACS.html";
}
else {
theFile = "LEMA.html";
}
String command = "";
if (System.getProperty("os.name").contentEquals("Linux")) {
directory = ENVVAR + "/docs/";
command = "gnome-open ";
}
else if (System.getProperty("os.name").toLowerCase().startsWith("mac os")) {
directory = ENVVAR + "/docs/";
command = "open ";
}
else {
directory = ENVVAR + "\\docs\\";
command = "cmd /c start ";
}
File work = new File(directory);
log.addText("Executing:\n" + command + directory + theFile + "\n");
Runtime exec = Runtime.getRuntime();
exec.exec(command + theFile, null, work);
}
catch (IOException e1) {
JOptionPane.showMessageDialog(frame, "Unable to open manual.", "Error", JOptionPane.ERROR_MESSAGE);
}
}
// if the exit menu item is selected
else if (e.getSource() == exit) {
exit();
}
// if the open popup menu is selected on a sim directory
else if (e.getActionCommand().equals("openSim")) {
try {
openSim();
}
catch (Exception e0) {
}
}
else if (e.getActionCommand().equals("openLearn")) {
if (lema) {
openLearnLHPN();
}
else {
openLearn();
}
}
else if (e.getActionCommand().equals("openSynth")) {
openSynth();
}
else if (e.getActionCommand().equals("openVerification")) {
openVerify();
}
else if (e.getActionCommand().equals("convertToSBML")) {
Translator t1 = new Translator();
t1.BuildTemplate(tree.getFile(), "");
t1.outputSBML();
String theFile = "";
if (tree.getFile().lastIndexOf('/') >= 0) {
theFile = tree.getFile().substring(tree.getFile().lastIndexOf('/') + 1);
}
if (tree.getFile().lastIndexOf('\\') >= 0) {
theFile = tree.getFile().substring(tree.getFile().lastIndexOf('\\') + 1);
}
updateOpenSBML(theFile.replace(".lpn", ".xml"));
addToTree(theFile.replace(".lpn", ".xml"));
}
else if (e.getActionCommand().equals("convertToVerilog")) {
new Lpn2verilog(tree.getFile());
String theFile = "";
if (tree.getFile().lastIndexOf('/') >= 0) {
theFile = tree.getFile().substring(tree.getFile().lastIndexOf('/') + 1);
}
if (tree.getFile().lastIndexOf('\\') >= 0) {
theFile = tree.getFile().substring(tree.getFile().lastIndexOf('\\') + 1);
}
addToTree(theFile.replace(".lpn", ".sv"));
}
else if (e.getActionCommand().equals("createAnalysis")) {
try {
simulate(2);
}
catch (Exception e1) {
e1.printStackTrace();
JOptionPane.showMessageDialog(frame, "You must select a valid lpn file for simulation.", "Error", JOptionPane.ERROR_MESSAGE);
}
}
// if the create simulation popup menu is selected on a dot file
else if (e.getActionCommand().equals("createSim")) {
try {
simulate(1);
}
catch (Exception e1) {
e1.printStackTrace();
JOptionPane.showMessageDialog(frame, "You must select a valid gcm file for simulation.", "Error", JOptionPane.ERROR_MESSAGE);
}
}
// if the simulate popup menu is selected on an sbml file
else if (e.getActionCommand().equals("simulate")) {
try {
simulate(0);
}
catch (Exception e1) {
e1.printStackTrace();
JOptionPane.showMessageDialog(frame, "You must select a valid sbml file for simulation.", "Error", JOptionPane.ERROR_MESSAGE);
}
}
// if the synthesis popup menu is selected on a vhdl or lhpn file
else if (e.getActionCommand().equals("createSynthesis")) {
if (root != null) {
for (int i = 0; i < tab.getTabCount(); i++) {
if (tab.getTitleAt(i).equals(tree.getFile().split(separator)[tree.getFile().split(separator).length - 1])) {
tab.setSelectedIndex(i);
if (save(i, 0) == 0) {
return;
}
break;
}
}
String synthName = JOptionPane.showInputDialog(frame, "Enter Synthesis ID:", "Synthesis View ID", JOptionPane.PLAIN_MESSAGE);
if (synthName != null && !synthName.trim().equals("")) {
synthName = synthName.trim();
try {
if (overwrite(root + separator + synthName, synthName)) {
new File(root + separator + synthName).mkdir();
String sbmlFile = tree.getFile();
String[] getFilename = sbmlFile.split(separator);
String circuitFileNoPath = getFilename[getFilename.length - 1];
try {
FileOutputStream out = new FileOutputStream(new File(root + separator + synthName.trim() + separator
+ synthName.trim() + ".syn"));
out.write(("synthesis.file=" + circuitFileNoPath + "\n").getBytes());
out.close();
}
catch (IOException e1) {
JOptionPane
.showMessageDialog(frame, "Unable to save parameter file!", "Error Saving File", JOptionPane.ERROR_MESSAGE);
}
try {
FileInputStream in = new FileInputStream(new File(root + separator + circuitFileNoPath));
FileOutputStream out = new FileOutputStream(new File(root + separator + synthName.trim() + separator
+ circuitFileNoPath));
int read = in.read();
while (read != -1) {
out.write(read);
read = in.read();
}
in.close();
out.close();
}
catch (Exception e1) {
JOptionPane.showMessageDialog(frame, "Unable to copy circuit file!", "Error Saving File", JOptionPane.ERROR_MESSAGE);
}
addToTree(synthName.trim());
String work = root + separator + synthName;
String circuitFile = root + separator + synthName.trim() + separator + circuitFileNoPath;
JPanel synthPane = new JPanel();
Synthesis synth = new Synthesis(work, circuitFile, log, this);
synthPane.add(synth);
addTab(synthName, synthPane, "Synthesis");
}
}
catch (Exception e1) {
JOptionPane.showMessageDialog(frame, "Unable to create Synthesis View directory.", "Error", JOptionPane.ERROR_MESSAGE);
}
}
}
else {
JOptionPane.showMessageDialog(frame, "You must open or create a project first.", "Error", JOptionPane.ERROR_MESSAGE);
}
}
// if the verify popup menu is selected on a vhdl or lhpn file
else if (e.getActionCommand().equals("createVerify")) {
if (root != null) {
for (int i = 0; i < tab.getTabCount(); i++) {
if (tab.getTitleAt(i).equals(tree.getFile().split(separator)[tree.getFile().split(separator).length - 1])) {
tab.setSelectedIndex(i);
if (save(i, 0) == 0) {
return;
}
break;
}
}
String verName = JOptionPane.showInputDialog(frame, "Enter Verification ID:", "Verification View ID", JOptionPane.PLAIN_MESSAGE);
if (verName != null && !verName.trim().equals("")) {
verName = verName.trim();
// try {
if (overwrite(root + separator + verName, verName)) {
new File(root + separator + verName).mkdir();
String sbmlFile = tree.getFile();
String[] getFilename = sbmlFile.split(separator);
String circuitFileNoPath = getFilename[getFilename.length - 1];
try {
FileOutputStream out = new FileOutputStream(new File(root + separator + verName.trim() + separator + verName.trim()
+ ".ver"));
out.write(("verification.file=" + circuitFileNoPath + "\n").getBytes());
out.close();
}
catch (IOException e1) {
JOptionPane.showMessageDialog(frame, "Unable to save parameter file!", "Error Saving File", JOptionPane.ERROR_MESSAGE);
}
addToTree(verName.trim());
Verification verify = new Verification(root + separator + verName, verName, circuitFileNoPath, log, this, lema, atacs);
verify.save();
addTab(verName, verify, "Verification");
}
}
}
else {
JOptionPane.showMessageDialog(frame, "You must open or create a project first.", "Error", JOptionPane.ERROR_MESSAGE);
}
}
// if the delete popup menu is selected
else if (e.getActionCommand().contains("delete") || e.getSource() == delete) {
delete();
}
else if (e.getActionCommand().equals("openLPN")) {
openLPN();
}
else if (e.getActionCommand().equals("browseSbol")) {
openSBOL();
}
// if the edit popup menu is selected on a dot file
else if (e.getActionCommand().equals("gcmEditor")) {
openGCM(false);
}
// if the edit popup menu is selected on a dot file
else if (e.getActionCommand().equals("gcmTextEditor")) {
openGCM(true);
}
// if the edit popup menu is selected on an sbml file
else if (e.getActionCommand().equals("sbmlEditor")) {
openSBML(tree.getFile());
}
else if (e.getActionCommand().equals("stateGraph")) {
try {
String directory = root + separator + tab.getTitleAt(tab.getSelectedIndex());
File work = new File(directory);
for (String f : new File(directory).list()) {
if (f.contains("_sg.dot")) {
Runtime exec = Runtime.getRuntime();
if (System.getProperty("os.name").contentEquals("Linux")) {
log.addText("Executing:\ndotty " + directory + separator + f + "\n");
exec.exec("dotty " + f, null, work);
}
else if (System.getProperty("os.name").toLowerCase().startsWith("mac os")) {
log.addText("Executing:\nopen " + directory + separator + f + "\n");
exec.exec("open " + f, null, work);
}
else {
log.addText("Executing:\ndotty " + directory + separator + f + "\n");
exec.exec("dotty " + f, null, work);
}
return;
}
}
JOptionPane.showMessageDialog(frame, "State graph file has not been generated.", "Error", JOptionPane.ERROR_MESSAGE);
}
catch (Exception e1) {
JOptionPane.showMessageDialog(frame, "Error viewing state graph.", "Error", JOptionPane.ERROR_MESSAGE);
}
}
else if (e.getActionCommand().equals("graphTree")) {
String directory = "";
String theFile = "";
String filename = tree.getFile();
if (filename.lastIndexOf('/') >= 0) {
directory = filename.substring(0, filename.lastIndexOf('/') + 1);
theFile = filename.substring(filename.lastIndexOf('/') + 1);
}
if (filename.lastIndexOf('\\') >= 0) {
directory = filename.substring(0, filename.lastIndexOf('\\') + 1);
theFile = filename.substring(filename.lastIndexOf('\\') + 1);
}
for (int i = 0; i < tab.getTabCount(); i++) {
if (tab.getTitleAt(i).equals(tree.getFile().split(separator)[tree.getFile().split(separator).length - 1])) {
tab.setSelectedIndex(i);
if (save(i, 0) == 0) {
return;
}
break;
}
}
File work = new File(directory);
String out = theFile;
try {
if (out.contains(".lpn")) {
String file = theFile;
String[] findTheFile = file.split("\\.");
theFile = findTheFile[0] + ".dot";
File dot = new File(root + separator + theFile);
dot.delete();
LhpnFile lhpn = new LhpnFile(log);
lhpn.load(directory + separator + theFile);
lhpn.printDot(directory + separator + file);
// String cmd = "atacs -cPllodpl " + file;
Runtime exec = Runtime.getRuntime();
// Process ATACS = exec.exec(cmd, null, work);
// ATACS.waitFor();
// log.addText("Executing:\n" + cmd);
if (dot.exists()) {
String command = "";
if (System.getProperty("os.name").contentEquals("Linux")) {
// directory = ENVVAR + "/docs/";
command = "gnome-open ";
}
else if (System.getProperty("os.name").toLowerCase().startsWith("mac os")) {
// directory = ENVVAR + "/docs/";
command = "open ";
}
else {
// directory = ENVVAR + "\\docs\\";
command = "dotty start ";
}
log.addText(command + root + separator + theFile + "\n");
exec.exec(command + theFile, null, work);
}
else {
File log = new File(root + separator + "atacs.log");
BufferedReader input = new BufferedReader(new FileReader(log));
String line = null;
JTextArea messageArea = new JTextArea();
while ((line = input.readLine()) != null) {
messageArea.append(line);
messageArea.append(System.getProperty("line.separator"));
}
input.close();
messageArea.setLineWrap(true);
messageArea.setWrapStyleWord(true);
messageArea.setEditable(false);
JScrollPane scrolls = new JScrollPane();
scrolls.setMinimumSize(new Dimension(500, 500));
scrolls.setPreferredSize(new Dimension(500, 500));
scrolls.setViewportView(messageArea);
JOptionPane.showMessageDialog(frame, scrolls, "Log", JOptionPane.INFORMATION_MESSAGE);
}
return;
}
if (out.length() > 4 && out.substring(out.length() - 5, out.length()).equals(".sbml")) {
out = out.substring(0, out.length() - 5);
}
else if (out.length() > 3 && out.substring(out.length() - 4, out.length()).equals(".xml")) {
out = out.substring(0, out.length() - 4);
}
else if (out.length() > 3 && out.substring(out.length() - 4, out.length()).equals(".gcm")) {
try {
if (System.getProperty("os.name").contentEquals("Linux")) {
log.addText("Executing:\ndotty " + directory + theFile + "\n");
Runtime exec = Runtime.getRuntime();
exec.exec("dotty " + theFile, null, work);
}
else if (System.getProperty("os.name").toLowerCase().startsWith("mac os")) {
log.addText("Executing:\nopen " + directory + theFile + "\n");
Runtime exec = Runtime.getRuntime();
exec.exec("cp " + theFile + " " + theFile + ".dot", null, work);
exec = Runtime.getRuntime();
exec.exec("open " + theFile + ".dot", null, work);
}
else {
log.addText("Executing:\ndotty " + directory + theFile + "\n");
Runtime exec = Runtime.getRuntime();
exec.exec("dotty " + theFile, null, work);
}
return;
}
catch (Exception e1) {
JOptionPane.showMessageDialog(frame, "Unable to view this gcm file.", "Error", JOptionPane.ERROR_MESSAGE);
return;
}
}
Run run = new Run(null);
JCheckBox dummy = new JCheckBox();
dummy.setSelected(false);
JList empty = new JList();
run.createProperties(0, "Print Interval", 1, 1, 1, 1, directory, 314159, 1, new String[0], new String[0], "tsd.printer", "amount",
(directory + theFile).split(separator), "none", frame, directory + theFile, 0.1, 0.1, 0.1, 15, dummy, "", dummy, null, empty,
empty, empty, null);
log.addText("Executing:\nreb2sac --target.encoding=dot --out=" + directory + out + ".dot " + directory + theFile + "\n");
Runtime exec = Runtime.getRuntime();
Process graph = exec.exec("reb2sac --target.encoding=dot --out=" + out + ".dot " + theFile, null, work);
String error = "";
String output = "";
InputStream reb = graph.getErrorStream();
int read = reb.read();
while (read != -1) {
error += (char) read;
read = reb.read();
}
reb.close();
reb = graph.getInputStream();
read = reb.read();
while (read != -1) {
output += (char) read;
read = reb.read();
}
reb.close();
if (!output.equals("")) {
log.addText("Output:\n" + output + "\n");
}
if (!error.equals("")) {
log.addText("Errors:\n" + error + "\n");
}
graph.waitFor();
if (error.equals("")) {
if (System.getProperty("os.name").contentEquals("Linux")) {
log.addText("Executing:\ndotty " + directory + out + ".dot\n");
exec.exec("dotty " + out + ".dot", null, work);
}
else if (System.getProperty("os.name").toLowerCase().startsWith("mac os")) {
log.addText("Executing:\nopen " + directory + out + ".dot\n");
exec.exec("open " + out + ".dot", null, work);
}
else {
log.addText("Executing:\ndotty " + directory + out + ".dot\n");
exec.exec("dotty " + out + ".dot", null, work);
}
}
String remove;
if (theFile.substring(theFile.length() - 4).equals("sbml")) {
remove = (directory + theFile).substring(0, (directory + theFile).length() - 4) + "properties";
}
else {
remove = (directory + theFile).substring(0, (directory + theFile).length() - 4) + ".properties";
}
System.gc();
new File(remove).delete();
}
catch (InterruptedException e1) {
JOptionPane.showMessageDialog(frame, "Error graphing SBML file.", "Error", JOptionPane.ERROR_MESSAGE);
}
catch (IOException e1) {
JOptionPane.showMessageDialog(frame, "Error graphing SBML file.", "Error", JOptionPane.ERROR_MESSAGE);
}
}
else if (e.getSource() == viewLearnedModel) {
Component comp = tab.getSelectedComponent();
for (int i = 0; i < ((JTabbedPane) comp).getTabCount(); i++) {
Component component = ((JTabbedPane) comp).getComponent(i);
if (component instanceof LearnGCM) {
((LearnGCM) component).viewGcm();
return;
}
else if (component instanceof LearnLHPN) {
((LearnLHPN) component).viewLhpn();
return;
}
}
}
// if the graph popup menu is selected on an sbml file
else if (e.getActionCommand().equals("graph")) {
String directory = "";
String theFile = "";
String filename = tree.getFile();
if (filename.lastIndexOf('/') >= 0) {
directory = filename.substring(0, filename.lastIndexOf('/') + 1);
theFile = filename.substring(filename.lastIndexOf('/') + 1);
}
if (filename.lastIndexOf('\\') >= 0) {
directory = filename.substring(0, filename.lastIndexOf('\\') + 1);
theFile = filename.substring(filename.lastIndexOf('\\') + 1);
}
for (int i = 0; i < tab.getTabCount(); i++) {
if (tab.getTitleAt(i).equals(tree.getFile().split(separator)[tree.getFile().split(separator).length - 1])) {
tab.setSelectedIndex(i);
if (save(i, 0) == 0) {
return;
}
break;
}
}
File work = new File(directory);
String out = theFile;
try {
if (out.contains(".lpn")) {
String file = theFile;
String[] findTheFile = file.split("\\.");
theFile = findTheFile[0] + ".dot";
File dot = new File(root + separator + theFile);
dot.delete();
LhpnFile lhpn = new LhpnFile(log);
lhpn.load(root + separator + file);
lhpn.printDot(root + separator + theFile);
// String cmd = "atacs -cPllodpl " + file;
Runtime exec = Runtime.getRuntime();
// Process ATACS = exec.exec(cmd, null, work);
// ATACS.waitFor();
// log.addText("Executing:\n" + cmd);
if (dot.exists()) {
String command = "";
if (System.getProperty("os.name").contentEquals("Linux")) {
// directory = ENVVAR + "/docs/";
command = "gnome-open ";
}
else if (System.getProperty("os.name").toLowerCase().startsWith("mac os")) {
// directory = ENVVAR + "/docs/";
command = "open ";
}
else {
// directory = ENVVAR + "\\docs\\";
command = "dotty start ";
}
log.addText(command + root + separator + theFile + "\n");
exec.exec(command + theFile, null, work);
}
else {
File log = new File(root + separator + "atacs.log");
BufferedReader input = new BufferedReader(new FileReader(log));
String line = null;
JTextArea messageArea = new JTextArea();
while ((line = input.readLine()) != null) {
messageArea.append(line);
messageArea.append(System.getProperty("line.separator"));
}
input.close();
messageArea.setLineWrap(true);
messageArea.setWrapStyleWord(true);
messageArea.setEditable(false);
JScrollPane scrolls = new JScrollPane();
scrolls.setMinimumSize(new Dimension(500, 500));
scrolls.setPreferredSize(new Dimension(500, 500));
scrolls.setViewportView(messageArea);
JOptionPane.showMessageDialog(frame, scrolls, "Log", JOptionPane.INFORMATION_MESSAGE);
}
return;
}
if (out.length() > 4 && out.substring(out.length() - 5, out.length()).equals(".sbml")) {
out = out.substring(0, out.length() - 5);
}
else if (out.length() > 3 && out.substring(out.length() - 4, out.length()).equals(".xml")) {
out = out.substring(0, out.length() - 4);
}
else if (out.length() > 3 && out.substring(out.length() - 4, out.length()).equals(".gcm")) {
try {
if (System.getProperty("os.name").contentEquals("Linux")) {
log.addText("Executing:\ndotty " + directory + theFile + "\n");
Runtime exec = Runtime.getRuntime();
exec.exec("dotty " + theFile, null, work);
}
else if (System.getProperty("os.name").toLowerCase().startsWith("mac os")) {
log.addText("Executing:\nopen " + directory + theFile + "\n");
Runtime exec = Runtime.getRuntime();
exec.exec("cp " + theFile + " " + theFile + ".dot", null, work);
exec = Runtime.getRuntime();
exec.exec("open " + theFile + ".dot", null, work);
}
else {
log.addText("Executing:\ndotty " + directory + theFile + "\n");
Runtime exec = Runtime.getRuntime();
exec.exec("dotty " + theFile, null, work);
}
return;
}
catch (Exception e1) {
JOptionPane.showMessageDialog(frame, "Unable to view this gcm file.", "Error", JOptionPane.ERROR_MESSAGE);
return;
}
}
Run run = new Run(null);
JCheckBox dummy = new JCheckBox();
dummy.setSelected(false);
JList empty = new JList();
run.createProperties(0, "Print Interval", 1, 1, 1, 1, directory, 314159, 1, new String[0], new String[0], "tsd.printer", "amount",
(directory + theFile).split(separator), "none", frame, directory + theFile, 0.1, 0.1, 0.1, 15, dummy, "", dummy, null, empty,
empty, empty, null);
log.addText("Executing:\nreb2sac --target.encoding=dot --out=" + directory + out + ".dot " + directory + theFile + "\n");
Runtime exec = Runtime.getRuntime();
Process graph = exec.exec("reb2sac --target.encoding=dot --out=" + out + ".dot " + theFile, null, work);
String error = "";
String output = "";
InputStream reb = graph.getErrorStream();
int read = reb.read();
while (read != -1) {
error += (char) read;
read = reb.read();
}
reb.close();
reb = graph.getInputStream();
read = reb.read();
while (read != -1) {
output += (char) read;
read = reb.read();
}
reb.close();
if (!output.equals("")) {
log.addText("Output:\n" + output + "\n");
}
if (!error.equals("")) {
log.addText("Errors:\n" + error + "\n");
}
graph.waitFor();
if (error.equals("")) {
if (System.getProperty("os.name").contentEquals("Linux")) {
log.addText("Executing:\ndotty " + directory + out + ".dot\n");
exec.exec("dotty " + out + ".dot", null, work);
}
else if (System.getProperty("os.name").toLowerCase().startsWith("mac os")) {
log.addText("Executing:\nopen " + directory + out + ".dot\n");
exec.exec("open " + out + ".dot", null, work);
}
else {
log.addText("Executing:\ndotty " + directory + out + ".dot\n");
exec.exec("dotty " + out + ".dot", null, work);
}
}
String remove;
if (theFile.substring(theFile.length() - 4).equals("sbml")) {
remove = (directory + theFile).substring(0, (directory + theFile).length() - 4) + "properties";
}
else {
remove = (directory + theFile).substring(0, (directory + theFile).length() - 4) + ".properties";
}
System.gc();
new File(remove).delete();
}
catch (IOException e1) {
JOptionPane.showMessageDialog(frame, "Error graphing sbml file.", "Error", JOptionPane.ERROR_MESSAGE);
}
catch (InterruptedException e1) {
JOptionPane.showMessageDialog(frame, "Error graphing sbml file.", "Error", JOptionPane.ERROR_MESSAGE);
}
}
// if the browse popup menu is selected on an sbml file
else if (e.getActionCommand().equals("browse")) {
String directory;
String theFile;
String filename = tree.getFile();
directory = "";
theFile = "";
if (filename.lastIndexOf('/') >= 0) {
directory = filename.substring(0, filename.lastIndexOf('/') + 1);
theFile = filename.substring(filename.lastIndexOf('/') + 1);
}
if (filename.lastIndexOf('\\') >= 0) {
directory = filename.substring(0, filename.lastIndexOf('\\') + 1);
theFile = filename.substring(filename.lastIndexOf('\\') + 1);
}
for (int i = 0; i < tab.getTabCount(); i++) {
if (tab.getTitleAt(i).equals(tree.getFile().split(separator)[tree.getFile().split(separator).length - 1])) {
tab.setSelectedIndex(i);
if (save(i, 0) == 0) {
return;
}
break;
}
}
File work = new File(directory);
String out = theFile;
if (out.length() > 4 && out.substring(out.length() - 5, out.length()).equals(".sbml")) {
out = out.substring(0, out.length() - 5);
}
else if (out.length() > 3 && out.substring(out.length() - 4, out.length()).equals(".xml")) {
out = out.substring(0, out.length() - 4);
}
try {
Run run = new Run(null);
JCheckBox dummy = new JCheckBox();
JList empty = new JList();
dummy.setSelected(false);
run.createProperties(0, "Print Interval", 1, 1, 1, 1, directory, 314159, 1, new String[0], new String[0], "tsd.printer", "amount",
(directory + theFile).split(separator), "none", frame, directory + theFile, 0.1, 0.1, 0.1, 15, dummy, "", dummy, null, empty,
empty, empty, null);
log.addText("Executing:\nreb2sac --target.encoding=xhtml --out=" + directory + out + ".xhtml " + directory + theFile + "\n");
Runtime exec = Runtime.getRuntime();
Process browse = exec.exec("reb2sac --target.encoding=xhtml --out=" + out + ".xhtml " + theFile, null, work);
String error = "";
String output = "";
InputStream reb = browse.getErrorStream();
int read = reb.read();
while (read != -1) {
error += (char) read;
read = reb.read();
}
reb.close();
reb = browse.getInputStream();
read = reb.read();
while (read != -1) {
output += (char) read;
read = reb.read();
}
reb.close();
if (!output.equals("")) {
log.addText("Output:\n" + output + "\n");
}
if (!error.equals("")) {
log.addText("Errors:\n" + error + "\n");
}
browse.waitFor();
String command = "";
if (error.equals("")) {
if (System.getProperty("os.name").contentEquals("Linux")) {
command = "gnome-open ";
}
else if (System.getProperty("os.name").toLowerCase().startsWith("mac os")) {
command = "open ";
}
else {
command = "cmd /c start ";
}
log.addText("Executing:\n" + command + directory + out + ".xhtml\n");
exec.exec(command + out + ".xhtml", null, work);
}
String remove;
if (theFile.substring(theFile.length() - 4).equals("sbml")) {
remove = (directory + theFile).substring(0, (directory + theFile).length() - 4) + "properties";
}
else {
remove = (directory + theFile).substring(0, (directory + theFile).length() - 4) + ".properties";
}
System.gc();
new File(remove).delete();
}
catch (Exception e1) {
JOptionPane.showMessageDialog(frame, "Error viewing SBML file in a browser.", "Error", JOptionPane.ERROR_MESSAGE);
}
}
// if the save button is pressed on the Tool Bar
else if (e.getActionCommand().equals("save")) {
Component comp = tab.getSelectedComponent();
// int index = tab.getSelectedIndex();
if (comp instanceof LHPNEditor) {
((LHPNEditor) comp).save();
}
else if (comp instanceof GCM2SBMLEditor) {
((GCM2SBMLEditor) comp).save("Save GCM");
}
else if (comp instanceof SBML_Editor) {
((SBML_Editor) comp).save(false, "", true, true);
}
else if (comp instanceof Graph) {
((Graph) comp).save();
}
else if (comp instanceof Verification) {
((Verification) comp).save();
}
else if (comp instanceof JTabbedPane) {
for (Component component : ((JTabbedPane) comp).getComponents()) {
int index = ((JTabbedPane) comp).getSelectedIndex();
if (component instanceof Graph) {
((Graph) component).save();
}
else if (component instanceof LearnGCM) {
((LearnGCM) component).save();
}
else if (component instanceof LearnLHPN) {
((LearnLHPN) component).save();
}
else if (component instanceof DataManager) {
((DataManager) component).saveChanges(((JTabbedPane) comp).getTitleAt(index));
}
else if (component instanceof SBML_Editor) {
((SBML_Editor) component).save(false, "", true, true);
}
else if (component instanceof GCM2SBMLEditor) {
((GCM2SBMLEditor) component).saveParams(false, "", true);
}
else if (component instanceof Reb2Sac) {
((Reb2Sac) component).save();
}
else if (component instanceof MovieContainer) {
((MovieContainer) component).savePreferences();
}
}
}
if (comp instanceof JPanel) {
if (comp.getName().equals("Synthesis")) {
// ((Synthesis) tab.getSelectedComponent()).save();
Component[] array = ((JPanel) comp).getComponents();
((Synthesis) array[0]).save();
}
}
else if (comp instanceof JScrollPane) {
String fileName = tab.getTitleAt(tab.getSelectedIndex());
try {
File output = new File(root + separator + fileName);
output.createNewFile();
FileOutputStream outStream = new FileOutputStream(output);
Component[] array = ((JScrollPane) comp).getComponents();
array = ((JViewport) array[0]).getComponents();
if (array[0] instanceof JTextArea) {
String text = ((JTextArea) array[0]).getText();
char[] chars = text.toCharArray();
for (int j = 0; j < chars.length; j++) {
outStream.write((int) chars[j]);
}
}
outStream.close();
log.addText("Saving file:\n" + root + separator + fileName);
this.updateAsyncViews(fileName);
}
catch (Exception e1) {
JOptionPane.showMessageDialog(frame, "Error saving file " + fileName, "Error", JOptionPane.ERROR_MESSAGE);
}
}
}
// if the save as button is pressed on the Tool Bar
else if (e.getActionCommand().equals("saveas")) {
Component comp = tab.getSelectedComponent();
// int index = tab.getSelectedIndex();
if (comp instanceof LHPNEditor) {
String newName = JOptionPane.showInputDialog(frame, "Enter LPN name:", "LPN Name", JOptionPane.PLAIN_MESSAGE);
if (newName == null) {
return;
}
if (!newName.endsWith(".lpn")) {
newName = newName + ".lpn";
}
((LHPNEditor) comp).saveAs(newName);
tab.setTitleAt(tab.getSelectedIndex(), newName);
}
else if (comp instanceof GCM2SBMLEditor) {
String newName = JOptionPane.showInputDialog(frame, "Enter GCM name:", "GCM Name", JOptionPane.PLAIN_MESSAGE);
if (newName == null) {
return;
}
if (newName.contains(".gcm")) {
newName = newName.replace(".gcm", "");
}
((GCM2SBMLEditor) comp).saveAs(newName);
}
else if (comp instanceof SBML_Editor) {
((SBML_Editor) comp).saveAs();
}
else if (comp instanceof Graph) {
((Graph) comp).saveAs();
}
else if (comp instanceof Verification) {
((Verification) comp).saveAs();
}
else if (comp instanceof JTabbedPane) {
Component component = ((JTabbedPane) comp).getSelectedComponent();
if (component instanceof Graph) {
((Graph) component).saveAs();
}
}
else if (comp instanceof JPanel) {
if (comp.getName().equals("Synthesis")) {
Component[] array = ((JPanel) comp).getComponents();
((Synthesis) array[0]).saveAs();
}
}
else if (comp instanceof JScrollPane) {
String fileName = tab.getTitleAt(tab.getSelectedIndex());
String newName = "";
if (fileName.endsWith(".vhd")) {
newName = JOptionPane.showInputDialog(frame, "Enter VHDL name:", "VHDL Name", JOptionPane.PLAIN_MESSAGE);
if (newName == null) {
return;
}
if (!newName.endsWith(".vhd")) {
newName = newName + ".vhd";
}
}
else if (fileName.endsWith(".s")) {
newName = JOptionPane.showInputDialog(frame, "Enter Assembly File Name:", "Assembly File Name", JOptionPane.PLAIN_MESSAGE);
if (newName == null) {
return;
}
if (!newName.endsWith(".s")) {
newName = newName + ".s";
}
}
else if (fileName.endsWith(".inst")) {
newName = JOptionPane.showInputDialog(frame, "Enter Instruction File Name:", "Instruction File Name", JOptionPane.PLAIN_MESSAGE);
if (newName == null) {
return;
}
if (!newName.endsWith(".inst")) {
newName = newName + ".inst";
}
}
else if (fileName.endsWith(".g")) {
newName = JOptionPane.showInputDialog(frame, "Enter Petri net name:", "Petri net Name", JOptionPane.PLAIN_MESSAGE);
if (newName == null) {
return;
}
if (!newName.endsWith(".g")) {
newName = newName + ".g";
}
}
else if (fileName.endsWith(".csp")) {
newName = JOptionPane.showInputDialog(frame, "Enter CSP name:", "CSP Name", JOptionPane.PLAIN_MESSAGE);
if (newName == null) {
return;
}
if (!newName.endsWith(".csp")) {
newName = newName + ".csp";
}
}
else if (fileName.endsWith(".hse")) {
newName = JOptionPane.showInputDialog(frame, "Enter HSE name:", "HSE Name", JOptionPane.PLAIN_MESSAGE);
if (newName == null) {
return;
}
if (!newName.endsWith(".hse")) {
newName = newName + ".hse";
}
}
else if (fileName.endsWith(".unc")) {
newName = JOptionPane.showInputDialog(frame, "Enter UNC name:", "UNC Name", JOptionPane.PLAIN_MESSAGE);
if (newName == null) {
return;
}
if (!newName.endsWith(".unc")) {
newName = newName + ".unc";
}
}
else if (fileName.endsWith(".rsg")) {
newName = JOptionPane.showInputDialog(frame, "Enter RSG name:", "RSG Name", JOptionPane.PLAIN_MESSAGE);
if (newName == null) {
return;
}
if (!newName.endsWith(".rsg")) {
newName = newName + ".rsg";
}
}
try {
File output = new File(root + separator + newName);
output.createNewFile();
FileOutputStream outStream = new FileOutputStream(output);
Component[] array = ((JScrollPane) comp).getComponents();
array = ((JViewport) array[0]).getComponents();
if (array[0] instanceof JTextArea) {
String text = ((JTextArea) array[0]).getText();
char[] chars = text.toCharArray();
for (int j = 0; j < chars.length; j++) {
outStream.write((int) chars[j]);
}
}
outStream.close();
log.addText("Saving file:\n" + root + separator + newName);
File oldFile = new File(root + separator + fileName);
oldFile.delete();
tab.setTitleAt(tab.getSelectedIndex(), newName);
addToTree(newName);
}
catch (Exception e1) {
JOptionPane.showMessageDialog(frame, "Error saving file " + newName, "Error", JOptionPane.ERROR_MESSAGE);
}
}
}
// if the run button is selected on the tool bar
else if (e.getActionCommand().equals("run")) {
Component comp = tab.getSelectedComponent();
// int index = tab.getSelectedIndex();
if (comp instanceof JTabbedPane) {
// int index = -1;
for (int i = 0; i < ((JTabbedPane) comp).getTabCount(); i++) {
Component component = ((JTabbedPane) comp).getComponent(i);
if (component instanceof Reb2Sac) {
((Reb2Sac) component).getRunButton().doClick();
break;
}
else if (component instanceof LearnGCM) {
((LearnGCM) component).save();
new Thread((LearnGCM) component).start();
break;
}
else if (component instanceof LearnLHPN) {
((LearnLHPN) component).save();
((LearnLHPN) component).learn();
break;
}
}
}
else if (comp instanceof Verification) {
((Verification) comp).save();
new Thread((Verification) comp).start();
}
else if (comp instanceof Synthesis) {
((Synthesis) comp).save();
new Thread((Synthesis) comp).start();
}
}
else if (e.getActionCommand().equals("refresh")) {
Component comp = tab.getSelectedComponent();
if (comp instanceof JTabbedPane) {
Component component = ((JTabbedPane) comp).getSelectedComponent();
if (component instanceof Graph) {
((Graph) component).refresh();
}
}
else if (comp instanceof Graph) {
((Graph) comp).refresh();
}
}
else if (e.getActionCommand().equals("check")) {
Component comp = tab.getSelectedComponent();
if (comp instanceof SBML_Editor) {
((SBML_Editor) comp).save(true, "", true, true);
((SBML_Editor) comp).check();
}
else if (comp instanceof GCM2SBMLEditor) {
((GCM2SBMLEditor) comp).save("Save and Check GCM");
}
}
else if (e.getActionCommand().equals("export")) {
Component comp = tab.getSelectedComponent();
if (comp instanceof Graph) {
((Graph) comp).export();
} else if (comp instanceof GCM2SBMLEditor) {
((GCM2SBMLEditor) comp).exportSBML();
// TODO: should give choice of SBML or SBOL
}
else if (comp instanceof JTabbedPane) {
Component component = ((JTabbedPane) comp).getSelectedComponent();
if (component instanceof Graph) {
((Graph) component).export();
}
}
}
// if the new menu item is selected
else if (e.getSource() == newProj) {
int autosave = 0;
for (int i = 0; i < tab.getTabCount(); i++) {
int save = save(i, autosave);
if (save == 0) {
return;
}
else if (save == 2) {
autosave = 1;
}
else if (save == 3) {
autosave = 2;
}
}
File file;
Preferences biosimrc = Preferences.userRoot();
if (biosimrc.get("biosim.general.project_dir", "").equals("")) {
file = null;
}
else {
file = new File(biosimrc.get("biosim.general.project_dir", ""));
}
String filename = Utility.browse(frame, file, null, JFileChooser.DIRECTORIES_ONLY, "New", -1);
if (!filename.trim().equals("")) {
filename = filename.trim();
biosimrc.put("biosim.general.project_dir", filename);
File f = new File(filename);
if (f.exists()) {
Object[] options = { "Overwrite", "Cancel" };
int value = JOptionPane.showOptionDialog(frame, "File already exists." + "\nDo you want to overwrite?", "Overwrite",
JOptionPane.YES_NO_OPTION, JOptionPane.PLAIN_MESSAGE, null, options, options[0]);
if (value == JOptionPane.YES_OPTION) {
File dir = new File(filename);
if (dir.isDirectory()) {
deleteDir(dir);
}
else {
System.gc();
dir.delete();
}
}
else {
return;
}
}
new File(filename).mkdir();
try {
if (lema) {
new FileWriter(new File(filename + separator + "LEMA.prj")).close();
}
else if (atacs) {
new FileWriter(new File(filename + separator + "ATACS.prj")).close();
}
else {
new FileWriter(new File(filename + separator + "BioSim.prj")).close();
}
}
catch (IOException e1) {
JOptionPane.showMessageDialog(frame, "Unable to create a new project.", "Error", JOptionPane.ERROR_MESSAGE);
return;
}
root = filename;
refresh();
tab.removeAll();
addRecentProject(filename);
importDot.setEnabled(true);
importSbol.setEnabled(true);
importSbml.setEnabled(true);
importBioModel.setEnabled(true);
importVhdl.setEnabled(true);
importS.setEnabled(true);
importInst.setEnabled(true);
importLpn.setEnabled(true);
importG.setEnabled(true);
importCsp.setEnabled(true);
importHse.setEnabled(true);
importUnc.setEnabled(true);
importRsg.setEnabled(true);
importSpice.setEnabled(true);
newGCMModel.setEnabled(true);
newSBMLModel.setEnabled(true);
newVhdl.setEnabled(true);
newS.setEnabled(true);
newInst.setEnabled(true);
newLhpn.setEnabled(true);
newG.setEnabled(true);
newCsp.setEnabled(true);
newHse.setEnabled(true);
newUnc.setEnabled(true);
newRsg.setEnabled(true);
newSpice.setEnabled(true);
graph.setEnabled(true);
probGraph.setEnabled(true);
}
}
// if the open project menu item is selected
else if (e.getSource() == pref) {
preferences();
}
else if ((e.getSource() == openProj) || (e.getSource() == recentProjects[0]) || (e.getSource() == recentProjects[1])
|| (e.getSource() == recentProjects[2]) || (e.getSource() == recentProjects[3]) || (e.getSource() == recentProjects[4])
|| (e.getSource() == recentProjects[5]) || (e.getSource() == recentProjects[6]) || (e.getSource() == recentProjects[7])
|| (e.getSource() == recentProjects[8]) || (e.getSource() == recentProjects[9])) {
int autosave = 0;
for (int i = 0; i < tab.getTabCount(); i++) {
int save = save(i, autosave);
if (save == 0) {
return;
}
else if (save == 2) {
autosave = 1;
}
else if (save == 3) {
autosave = 2;
}
}
Preferences biosimrc = Preferences.userRoot();
String projDir = "";
if (e.getSource() == openProj) {
File file;
if (biosimrc.get("biosim.general.project_dir", "").equals("")) {
file = null;
}
else {
file = new File(biosimrc.get("biosim.general.project_dir", ""));
}
projDir = Utility.browse(frame, file, null, JFileChooser.DIRECTORIES_ONLY, "Open", -1);
if (projDir.endsWith(".prj")) {
biosimrc.put("biosim.general.project_dir", projDir);
String[] tempArray = projDir.split(separator);
projDir = "";
for (int i = 0; i < tempArray.length - 1; i++) {
projDir = projDir + tempArray[i] + separator;
}
}
}
else if (e.getSource() == recentProjects[0]) {
projDir = recentProjectPaths[0];
}
else if (e.getSource() == recentProjects[1]) {
projDir = recentProjectPaths[1];
}
else if (e.getSource() == recentProjects[2]) {
projDir = recentProjectPaths[2];
}
else if (e.getSource() == recentProjects[3]) {
projDir = recentProjectPaths[3];
}
else if (e.getSource() == recentProjects[4]) {
projDir = recentProjectPaths[4];
}
else if (e.getSource() == recentProjects[5]) {
projDir = recentProjectPaths[5];
}
else if (e.getSource() == recentProjects[6]) {
projDir = recentProjectPaths[6];
}
else if (e.getSource() == recentProjects[7]) {
projDir = recentProjectPaths[7];
}
else if (e.getSource() == recentProjects[8]) {
projDir = recentProjectPaths[8];
}
else if (e.getSource() == recentProjects[9]) {
projDir = recentProjectPaths[9];
}
// log.addText(projDir);
if (!projDir.equals("")) {
biosimrc.put("biosim.general.project_dir", projDir);
if (new File(projDir).isDirectory()) {
boolean isProject = false;
for (String temp : new File(projDir).list()) {
if (temp.equals(".prj")) {
isProject = true;
}
if (lema && temp.equals("LEMA.prj")) {
isProject = true;
}
else if (atacs && temp.equals("ATACS.prj")) {
isProject = true;
}
else if (temp.equals("BioSim.prj")) {
isProject = true;
}
}
if (isProject) {
root = projDir;
refresh();
tab.removeAll();
addRecentProject(projDir);
importDot.setEnabled(true);
importSbol.setEnabled(true);
importSbml.setEnabled(true);
importBioModel.setEnabled(true);
importVhdl.setEnabled(true);
importS.setEnabled(true);
importInst.setEnabled(true);
importLpn.setEnabled(true);
importG.setEnabled(true);
importCsp.setEnabled(true);
importHse.setEnabled(true);
importUnc.setEnabled(true);
importRsg.setEnabled(true);
importSpice.setEnabled(true);
newGCMModel.setEnabled(true);
newSBMLModel.setEnabled(true);
newVhdl.setEnabled(true);
newS.setEnabled(true);
newInst.setEnabled(true);
newLhpn.setEnabled(true);
newG.setEnabled(true);
newCsp.setEnabled(true);
newHse.setEnabled(true);
newUnc.setEnabled(true);
newRsg.setEnabled(true);
newSpice.setEnabled(true);
graph.setEnabled(true);
probGraph.setEnabled(true);
}
else {
JOptionPane.showMessageDialog(frame, "You must select a valid project.", "Error", JOptionPane.ERROR_MESSAGE);
}
}
else {
JOptionPane.showMessageDialog(frame, "You must select a valid project.", "Error", JOptionPane.ERROR_MESSAGE);
}
}
}
// if the new circuit model menu item is selected
else if (e.getSource() == newGCMModel) {
createGCM();
}
// if the new SBML model menu item is selected
else if (e.getSource() == newSBMLModel) {
createSBML();
}
// if the new vhdl menu item is selected
else if (e.getSource() == newVhdl) {
newModel("VHDL", ".vhd");
}
// if the new assembly menu item is selected
else if (e.getSource() == newS) {
newModel("Assembly", ".s");
}
// if the new instruction file menu item is selected
else if (e.getSource() == newInst) {
newModel("Instruction", ".inst");
}
// if the new petri net menu item is selected
else if (e.getSource() == newG) {
newModel("Petri Net", ".g");
}
// if the new lhpn menu item is selected
else if (e.getSource() == newLhpn) {
createLPN();
}
// if the new csp menu item is selected
else if (e.getSource() == newCsp) {
newModel("CSP", ".csp");
}
// if the new hse menu item is selected
else if (e.getSource() == newHse) {
newModel("Handshaking Expansion", ".hse");
}
// if the new unc menu item is selected
else if (e.getSource() == newUnc) {
newModel("Extended Burst Mode Machine", ".unc");
}
// if the new rsg menu item is selected
else if (e.getSource() == newRsg) {
newModel("Reduced State Graph", ".rsg");
}
// if the new rsg menu item is selected
else if (e.getSource() == newSpice) {
newModel("Spice Circuit", ".cir");
}
else if (e.getSource().equals(importSbol)) {
importFile("SBOL", ".rdf");
}
// if the import sbml menu item is selected
else if (e.getSource() == importSbml) {
importSBML(null);
}
else if (e.getSource() == importBioModel) {
importBioModel();
}
// if the import dot menu item is selected
else if (e.getSource() == importDot) {
importGCM();
}
// if the import vhdl menu item is selected
else if (e.getSource() == importVhdl) {
importFile("VHDL", ".vhd");
}
else if (e.getSource() == importS) {
importFile("Assembly", ".s");
}
else if (e.getSource() == importInst) {
importFile("Instruction", ".inst");
}
else if (e.getSource() == importLpn) {
importLPN();
}
else if (e.getSource() == importG) {
importFile("Petri Net", ".g");
}
// if the import csp menu item is selected
else if (e.getSource() == importCsp) {
importFile("CSP", ".csp");
}
// if the import hse menu item is selected
else if (e.getSource() == importHse) {
importFile("Handshaking Expansion", ".hse");
}
// if the import unc menu item is selected
else if (e.getSource() == importUnc) {
importFile("Extended Burst State Machine", ".unc");
}
// if the import rsg menu item is selected
else if (e.getSource() == importRsg) {
importFile("Reduced State Graph", ".rsg");
}
// if the import spice menu item is selected
else if (e.getSource() == importSpice) {
importFile("Spice Circuit", ".cir");
}
// if the Graph data menu item is clicked
else if (e.getSource() == graph) {
createGraph();
}
else if (e.getSource() == probGraph) {
createHistogram();
}
else if (e.getActionCommand().equals("createLearn")) {
createLearn();
}
else if (e.getActionCommand().equals("viewModel")) {
viewModel();
}
else if (e.getActionCommand().equals("copy") || e.getSource() == copy) {
copy();
}
else if (e.getActionCommand().equals("rename") || e.getSource() == rename) {
rename();
}
else if (e.getActionCommand().equals("openGraph")) {
openGraph();
}
else if (e.getActionCommand().equals("openHistogram")) {
openHistogram();
}
enableTabMenu(tab.getSelectedIndex());
enableTreeMenu();
}
private void delete() {
if (!tree.getFile().equals(root)) {
if (new File(tree.getFile()).isDirectory()) {
String dirName = tree.getFile().split(separator)[tree.getFile().split(separator).length - 1];
for (int i = 0; i < tab.getTabCount(); i++) {
if (tab.getTitleAt(i).equals(dirName)) {
tab.remove(i);
}
}
File dir = new File(tree.getFile());
if (dir.isDirectory()) {
deleteDir(dir);
}
else {
System.gc();
dir.delete();
}
deleteFromTree(dirName);
}
else {
String[] views = canDelete(tree.getFile().split(separator)[tree.getFile().split(separator).length - 1]);
if (views.length == 0) {
String fileName = tree.getFile().split(separator)[tree.getFile().split(separator).length - 1];
for (int i = 0; i < tab.getTabCount(); i++) {
if (tab.getTitleAt(i).equals(fileName)) {
tab.remove(i);
}
}
System.gc();
if (tree.getFile().endsWith(".gcm")) {
new File(tree.getFile().replace(".gcm", ".xml")).delete();
}
new File(tree.getFile()).delete();
deleteFromTree(fileName);
}
else {
String view = "";
String gcms = "";
for (int i = 0; i < views.length; i++) {
if (views[i].endsWith(".gcm")) {
gcms += views[i] + "\n";
}
else {
view += views[i] + "\n";
}
}
String message;
if (gcms.equals("")) {
message = "Unable to delete the selected file." + "\nIt is linked to the following views:\n" + view
+ "Delete these views first.";
}
else if (view.equals("")) {
message = "Unable to delete the selected file." + "\nIt is linked to the following gcms:\n" + gcms
+ "Delete these gcms first.";
}
else {
message = "Unable to delete the selected file." + "\nIt is linked to the following views:\n" + view
+ "It is also linked to the following gcms:\n" + gcms + "Delete these views and gcms first.";
}
JTextArea messageArea = new JTextArea(message);
messageArea.setEditable(false);
JScrollPane scroll = new JScrollPane();
scroll.setMinimumSize(new Dimension(300, 300));
scroll.setPreferredSize(new Dimension(300, 300));
scroll.setViewportView(messageArea);
JOptionPane.showMessageDialog(frame, scroll, "Unable To Delete File", JOptionPane.ERROR_MESSAGE);
}
}
}
}
private void importBioModel() {
final BioModelsWSClient client = new BioModelsWSClient();
if (BioModelIds == null) {
try {
BioModelIds = client.getAllCuratedModelsId();
}
catch (BioModelsWSException e2) {
JOptionPane.showMessageDialog(frame, "Error Contacting BioModels Database", "Error", JOptionPane.ERROR_MESSAGE);
return;
}
}
JPanel BioModelsPanel = new JPanel(new BorderLayout());
final JList ListOfBioModels = new JList();
sort(BioModelIds);
ListOfBioModels.setListData(BioModelIds);
ListOfBioModels.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
JLabel TextBioModels = new JLabel("List of BioModels");
JScrollPane ScrollBioModels = new JScrollPane();
ScrollBioModels.setMinimumSize(new Dimension(520, 250));
ScrollBioModels.setPreferredSize(new Dimension(552, 250));
ScrollBioModels.setViewportView(ListOfBioModels);
JPanel GetButtons = new JPanel();
JButton GetNames = new JButton("Get Names");
JButton GetDescription = new JButton("Get Description");
JButton GetReference = new JButton("Get Reference");
GetNames.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
for (int i = 0; i < BioModelIds.length; i++) {
try {
BioModelIds[i] += " " + client.getModelNameById(BioModelIds[i]);
}
catch (BioModelsWSException e1) {
JOptionPane.showMessageDialog(frame, "Error Contacting BioModels Database", "Error", JOptionPane.ERROR_MESSAGE);
}
}
ListOfBioModels.setListData(BioModelIds);
}
});
GetDescription.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
String SelectedModel = ((String) ListOfBioModels.getSelectedValue()).split(" ")[0];
String command = "";
if (System.getProperty("os.name").contentEquals("Linux")) {
command = "gnome-open http:
}
else if (System.getProperty("os.name").toLowerCase().startsWith("mac os")) {
command = "open http:
}
else {
command = "cmd /c start http:
}
log.addText("Executing:\n" + command + "\n");
Runtime exec = Runtime.getRuntime();
try {
exec.exec(command);
}
catch (IOException e1) {
JOptionPane.showMessageDialog(frame, "Unable to open model description.", "Error", JOptionPane.ERROR_MESSAGE);
}
}
});
GetReference.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
String SelectedModel = ((String) ListOfBioModels.getSelectedValue()).split(" ")[0];
try {
String Pub = (client.getSimpleModelById(SelectedModel)).getPublicationId();
String command = "";
if (System.getProperty("os.name").contentEquals("Linux")) {
command = "gnome-open http:
}
else if (System.getProperty("os.name").toLowerCase().startsWith("mac os")) {
command = "open http:
}
else {
command = "cmd /c start http:
}
log.addText("Executing:\n" + command + "\n");
Runtime exec = Runtime.getRuntime();
exec.exec(command);
}
catch (BioModelsWSException e2) {
JOptionPane.showMessageDialog(frame, "Error Contacting BioModels Database", "Error", JOptionPane.ERROR_MESSAGE);
}
catch (IOException e1) {
JOptionPane.showMessageDialog(frame, "Unable to open model description.", "Error", JOptionPane.ERROR_MESSAGE);
}
}
});
GetButtons.add(GetNames);
GetButtons.add(GetDescription);
GetButtons.add(GetReference);
BioModelsPanel.add(TextBioModels, "North");
BioModelsPanel.add(ScrollBioModels, "Center");
BioModelsPanel.add(GetButtons, "South");
Object[] options = { "OK", "Cancel" };
int value = JOptionPane.showOptionDialog(frame, BioModelsPanel, "List of BioModels", JOptionPane.YES_NO_OPTION, JOptionPane.PLAIN_MESSAGE,
null, options, options[0]);
if (value == JOptionPane.YES_OPTION && ListOfBioModels.getSelectedValue() != null) {
String ModelId = ((String) ListOfBioModels.getSelectedValue()).split(" ")[0];
String filename = ModelId + ".xml";
try {
if (overwrite(root + separator + filename, filename)) {
String model = client.getModelSBMLById(ModelId);
Writer out = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(root + separator + filename), "UTF-8"));
out.write(model);
out.close();
String[] file = filename.trim().split(separator);
SBMLDocument document = readSBML(root + separator + filename.trim());
long numErrors = document.checkConsistency();
if (numErrors > 0) {
final JFrame f = new JFrame("SBML Errors and Warnings");
JTextArea messageArea = new JTextArea();
messageArea.append("Imported SBML file contains the errors listed below. ");
messageArea.append("It is recommended that you fix them before using this model or you may get unexpected results.\n\n");
for (long i = 0; i < numErrors; i++) {
String error = document.getError(i).getMessage();
messageArea.append(i + ":" + error + "\n");
}
messageArea.setLineWrap(true);
messageArea.setEditable(false);
messageArea.setSelectionStart(0);
messageArea.setSelectionEnd(0);
JScrollPane scroll = new JScrollPane();
scroll.setMinimumSize(new Dimension(600, 600));
scroll.setPreferredSize(new Dimension(600, 600));
scroll.setViewportView(messageArea);
JButton close = new JButton("Dismiss");
close.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
f.dispose();
}
});
JPanel consistencyPanel = new JPanel(new BorderLayout());
consistencyPanel.add(scroll, "Center");
consistencyPanel.add(close, "South");
f.setContentPane(consistencyPanel);
f.pack();
Dimension screenSize;
try {
Toolkit tk = Toolkit.getDefaultToolkit();
screenSize = tk.getScreenSize();
}
catch (AWTError awe) {
screenSize = new Dimension(640, 480);
}
Dimension frameSize = f.getSize();
if (frameSize.height > screenSize.height) {
frameSize.height = screenSize.height;
}
if (frameSize.width > screenSize.width) {
frameSize.width = screenSize.width;
}
int x = screenSize.width / 2 - frameSize.width / 2;
int y = screenSize.height / 2 - frameSize.height / 2;
f.setLocation(x, y);
f.setVisible(true);
}
SBMLWriter writer = new SBMLWriter();
writer.writeSBML(document, root + separator + file[file.length - 1]);
addToTree(file[file.length - 1]);
openSBML(root + separator + file[file.length - 1]);
}
}
catch (MalformedURLException e1) {
JOptionPane.showMessageDialog(frame, e1.toString(), "Error", JOptionPane.ERROR_MESSAGE);
filename = "";
}
catch (IOException e1) {
JOptionPane.showMessageDialog(frame, filename + " not found.", "Error", JOptionPane.ERROR_MESSAGE);
filename = "";
}
catch (Exception e1) {
JOptionPane.showMessageDialog(frame, "Unable to import file.", "Error", JOptionPane.ERROR_MESSAGE);
}
}
}
private void createLPN() {
try {
String lhpnName = JOptionPane.showInputDialog(frame, "Enter LPN Model ID:", "Model ID", JOptionPane.PLAIN_MESSAGE);
if (lhpnName != null && !lhpnName.trim().equals("")) {
lhpnName = lhpnName.trim();
if (lhpnName.length() > 3) {
if (!lhpnName.substring(lhpnName.length() - 4).equals(".lpn")) {
lhpnName += ".lpn";
}
}
else {
lhpnName += ".lpn";
}
String modelID = "";
if (lhpnName.length() > 3) {
if (lhpnName.substring(lhpnName.length() - 4).equals(".lpn")) {
modelID = lhpnName.substring(0, lhpnName.length() - 4);
}
else {
modelID = lhpnName.substring(0, lhpnName.length() - 3);
}
}
if (!(IDpat.matcher(modelID).matches())) {
JOptionPane.showMessageDialog(frame, "A model ID can only contain letters, numbers, and underscores.", "Invalid ID",
JOptionPane.ERROR_MESSAGE);
}
else {
if (overwrite(root + separator + lhpnName, lhpnName)) {
File f = new File(root + separator + lhpnName);
f.createNewFile();
new LhpnFile(log).save(f.getAbsolutePath());
int i = getTab(f.getName());
if (i != -1) {
tab.remove(i);
}
LHPNEditor lhpn = new LHPNEditor(root + separator, f.getName(), null, this, log);
// lhpn.addMouseListener(this);
addTab(f.getName(), lhpn, "LHPN Editor");
addToTree(f.getName());
}
}
}
}
catch (IOException e1) {
JOptionPane.showMessageDialog(frame, "Unable to create new model.", "Error", JOptionPane.ERROR_MESSAGE);
}
}
private void importLPN() {
File importFile;
Preferences biosimrc = Preferences.userRoot();
if (biosimrc.get("biosim.general.import_dir", "").equals("")) {
importFile = null;
}
else {
importFile = new File(biosimrc.get("biosim.general.import_dir", ""));
}
String filename = Utility.browse(frame, importFile, null, JFileChooser.FILES_ONLY, "Import LPN", -1);
if ((filename.length() > 1 && !filename.substring(filename.length() - 2, filename.length()).equals(".g"))
&& (filename.length() > 3 && !filename.substring(filename.length() - 4, filename.length()).equals(".lpn"))) {
JOptionPane.showMessageDialog(frame, "You must select a valid LPN file to import.", "Error", JOptionPane.ERROR_MESSAGE);
return;
}
else if (!filename.equals("")) {
biosimrc.put("biosim.general.import_dir", filename);
String[] file = filename.split(separator);
try {
if (new File(filename).exists()) {
file[file.length - 1] = file[file.length - 1].replaceAll("[^a-zA-Z0-9_.]+", "_");
if (checkFiles(root + separator + file[file.length - 1], filename.trim())) {
if (overwrite(root + separator + file[file.length - 1], file[file.length - 1])) {
FileOutputStream out = new FileOutputStream(new File(root + separator + file[file.length - 1]));
FileInputStream in = new FileInputStream(new File(filename));
// log.addText(filename);
int read = in.read();
while (read != -1) {
out.write(read);
read = in.read();
}
in.close();
out.close();
addToTree(file[file.length - 1]);
}
}
}
if (filename.substring(filename.length() - 2, filename.length()).equals(".g")) {
// log.addText(filename + file[file.length - 1]);
File work = new File(root);
String oldName = root + separator + file[file.length - 1];
// String newName = oldName.replace(".lpn",
// "_NEW.g");
Process atacs = Runtime.getRuntime().exec("atacs -lgsl " + oldName, null, work);
atacs.waitFor();
String lpnName = oldName.replace(".g", ".lpn");
String newName = oldName.replace(".g", "_NEW.lpn");
atacs = Runtime.getRuntime().exec("atacs -llsl " + lpnName, null, work);
atacs.waitFor();
lpnName = lpnName.replaceAll("[^a-zA-Z0-9_.]+", "_");
FileOutputStream out = new FileOutputStream(new File(lpnName));
FileInputStream in = new FileInputStream(new File(newName));
int read = in.read();
while (read != -1) {
out.write(read);
read = in.read();
}
in.close();
out.close();
new File(newName).delete();
addToTree(file[file.length - 1].replace(".g", ".lpn"));
}
}
catch (Exception e1) {
e1.printStackTrace();
JOptionPane.showMessageDialog(frame, "Unable to import file.", "Error", JOptionPane.ERROR_MESSAGE);
}
}
}
private void importGCM() {
File importFile;
Preferences biosimrc = Preferences.userRoot();
if (biosimrc.get("biosim.general.import_dir", "").equals("")) {
importFile = null;
}
else {
importFile = new File(biosimrc.get("biosim.general.import_dir", ""));
}
String filename = Utility.browse(frame, importFile, null, JFileChooser.FILES_AND_DIRECTORIES, "Import Genetic Circuit", -1);
if (filename != null && !filename.trim().equals("")) {
biosimrc.put("biosim.general.import_dir", filename.trim());
}
if (new File(filename.trim()).isDirectory()) {
for (String s : new File(filename.trim()).list()) {
if (!(filename.trim() + separator + s).equals("")
&& (filename.trim() + separator + s).length() > 3
&& (filename.trim() + separator + s).substring((filename.trim() + separator + s).length() - 4,
(filename.trim() + separator + s).length()).equals(".gcm")) {
try {
// GCMParser parser =
new GCMParser((filename.trim() + separator + s));
s = s.replaceAll("[^a-zA-Z0-9_.]+", "_");
if (overwrite(root + separator + s, s)) {
FileOutputStream out = new FileOutputStream(new File(root + separator + s));
FileInputStream in = new FileInputStream(new File((filename.trim() + separator + s)));
int read = in.read();
while (read != -1) {
out.write(read);
read = in.read();
}
in.close();
out.close();
addToTree(s);
importSBML(filename.trim().replace(".gcm", ".xml"));
}
}
catch (Exception e1) {
JOptionPane.showMessageDialog(frame, "Unable to import file.", "Error", JOptionPane.ERROR_MESSAGE);
}
}
}
}
else {
if (filename.trim().length() > 3 && !filename.trim().substring(filename.trim().length() - 4, filename.trim().length()).equals(".gcm")) {
JOptionPane.showMessageDialog(frame, "You must select a valid gcm file to import.", "Error", JOptionPane.ERROR_MESSAGE);
return;
}
else if (!filename.trim().equals("")) {
String[] file = filename.trim().split(separator);
try {
// GCMParser parser =
new GCMParser(filename.trim());
file[file.length - 1] = file[file.length - 1].replaceAll("[^a-zA-Z0-9_.]+", "_");
if (checkFiles(root + separator + file[file.length - 1], filename.trim())) {
if (overwrite(root + separator + file[file.length - 1], file[file.length - 1])) {
FileOutputStream out = new FileOutputStream(new File(root + separator + file[file.length - 1]));
FileInputStream in = new FileInputStream(new File(filename.trim()));
int read = in.read();
while (read != -1) {
out.write(read);
read = in.read();
}
in.close();
out.close();
addToTree(file[file.length - 1]);
importSBML(filename.trim().replace(".gcm", ".xml"));
}
}
}
catch (Exception e1) {
JOptionPane.showMessageDialog(frame, "Unable to import file.", "Error", JOptionPane.ERROR_MESSAGE);
}
}
}
}
private void createSBML() {
try {
String simName = JOptionPane.showInputDialog(frame, "Enter SBML Model ID:", "Model ID", JOptionPane.PLAIN_MESSAGE);
if (simName != null && !simName.trim().equals("")) {
simName = simName.trim();
if (simName.length() > 4) {
if (!simName.substring(simName.length() - 5).equals(".sbml") && !simName.substring(simName.length() - 4).equals(".xml")) {
simName += ".xml";
}
}
else {
simName += ".xml";
}
String modelID = "";
if (simName.length() > 4) {
if (simName.substring(simName.length() - 5).equals(".sbml")) {
modelID = simName.substring(0, simName.length() - 5);
}
else {
modelID = simName.substring(0, simName.length() - 4);
}
}
if (!(IDpat.matcher(modelID).matches())) {
JOptionPane.showMessageDialog(frame, "A model ID can only contain letters, numbers, and underscores.", "Invalid ID",
JOptionPane.ERROR_MESSAGE);
}
else {
if (overwrite(root + separator + simName, simName)) {
String f = new String(root + separator + simName);
SBMLDocument document = new SBMLDocument(Gui.SBML_LEVEL, Gui.SBML_VERSION);
document.createModel();
Compartment c = document.getModel().createCompartment();
c.setId("default");
c.setSize(1.0);
c.setSpatialDimensions(3);
document.getModel().setId(modelID);
SBMLWriter writer = new SBMLWriter();
writer.writeSBML(document, root + separator + simName);
SBML_Editor sbml = new SBML_Editor(f, null, log, this, null, null);
addTab(f.split(separator)[f.split(separator).length - 1], sbml, "SBML Editor");
addToTree(f.split(separator)[f.split(separator).length - 1]);
}
}
}
}
catch (Exception e1) {
JOptionPane.showMessageDialog(frame, "Unable to create new model.", "Error", JOptionPane.ERROR_MESSAGE);
}
}
private void createGCM() {
if (root != null) {
try {
String simName = null;
JTextField modelChooser = new JTextField("");
modelChooser.setColumns(20);
JCheckBox gridCheckBox = new JCheckBox("Make Grid");
JPanel modelPanel = new JPanel(new GridLayout(2, 2));
modelPanel.add(new JLabel("Enter Model ID: "));
modelPanel.add(modelChooser);
modelPanel.add(gridCheckBox);
frame.add(modelPanel);
String[] options = {GlobalConstants.OK, GlobalConstants.CANCEL};
int okCancel = JOptionPane.showOptionDialog(frame, modelPanel, "Model ID",
JOptionPane.YES_NO_OPTION, JOptionPane.PLAIN_MESSAGE, null, options, options[0]);
//if the user clicks "ok" on the panel
if (okCancel == JOptionPane.OK_OPTION) {
simName = modelChooser.getText();
}
else return;
//String simName = JOptionPane.showInputDialog(frame, "Enter Model ID:", "Model ID", JOptionPane.PLAIN_MESSAGE);
if (simName != null && !simName.trim().equals("")) {
simName = simName.trim();
if (simName.length() > 3) {
if (!simName.substring(simName.length() - 4).equals(".gcm")) {
simName += ".gcm";
}
}
else {
simName += ".gcm";
}
String modelID = "";
if (simName.length() > 3) {
if (simName.substring(simName.length() - 4).equals(".gcm")) {
modelID = simName.substring(0, simName.length() - 4);
}
else {
modelID = simName.substring(0, simName.length() - 3);
}
}
if (!(IDpat.matcher(modelID).matches())) {
JOptionPane.showMessageDialog(frame, "A model ID can only contain letters, numbers, and underscores.", "Invalid ID",
JOptionPane.ERROR_MESSAGE);
}
else {
if (overwrite(root + separator + simName, simName)) {
File f = new File(root + separator + simName);
f.createNewFile();
new GCMFile(root).save(f.getAbsolutePath());
int i = getTab(f.getName());
if (i != -1) {
tab.remove(i);
}
/*
SBMLDocument document = new SBMLDocument(Gui.SBML_LEVEL, Gui.SBML_VERSION);
Model m = document.createModel();
document.setModel(m);
m.setId(simName);
Compartment c = m.createCompartment();
c.setId("default");
c.setSize(1);
c.setSpatialDimensions(3);
c.setConstant(true);
SBMLWriter writer = new SBMLWriter();
writer.writeSBML(document, root + separator + simName.replace(".gcm", ".xml"));
addToTree(simName.replace(".gcm", ".xml"));
*/
GCM2SBMLEditor gcm2sbml = new GCM2SBMLEditor(root + separator, f.getName(), this, log, false, null, null, null, false);
// gcm2sbml.addMouseListener(this);
addTab(f.getName(), gcm2sbml, "GCM Editor");
addToTree(f.getName());
if (gridCheckBox.isSelected())
gcm2sbml.launchGridPanel();
}
}
}
}
catch (Exception e1) {
JOptionPane.showMessageDialog(frame, "Unable to create new model.", "Error", JOptionPane.ERROR_MESSAGE);
}
}
}
private void importSBML(String filename) {
Preferences biosimrc = Preferences.userRoot();
if (filename == null) {
File importFile;
if (biosimrc.get("biosim.general.import_dir", "").equals("")) {
importFile = null;
}
else {
importFile = new File(biosimrc.get("biosim.general.import_dir", ""));
}
filename = Utility.browse(frame, importFile, null, JFileChooser.FILES_AND_DIRECTORIES, "Import SBML", -1);
}
if (!filename.trim().equals("")) {
biosimrc.put("biosim.general.import_dir", filename.trim());
if (new File(filename.trim()).isDirectory()) {
JTextArea messageArea = new JTextArea();
messageArea.append("Imported SBML files contain the errors listed below. ");
messageArea.append("It is recommended that you fix them before using these models or you may get " + "unexpected results.\n\n");
boolean display = false;
for (String s : new File(filename.trim()).list()) {
if (s.endsWith(".xml") || s.endsWith(".sbml")) {
try {
SBMLDocument document = readSBML(filename.trim() + separator + s);
checkModelCompleteness(document);
if (overwrite(root + separator + s, s)) {
long numErrors = document.checkConsistency();
if (numErrors > 0) {
display = true;
messageArea.append("
+ "
messageArea.append(s);
messageArea.append("\n
+ "
for (long i = 0; i < numErrors; i++) {
String error = document.getError(i).getMessage();
messageArea.append(i + ":" + error + "\n");
}
}
SBMLWriter writer = new SBMLWriter();
s = s.replaceAll("[^a-zA-Z0-9_.]+", "_");
writer.writeSBML(document, root + separator + s);
}
}
catch (Exception e1) {
JOptionPane.showMessageDialog(frame, "Unable to import files.", "Error", JOptionPane.ERROR_MESSAGE);
}
}
addToTree(s);
}
if (display) {
final JFrame f = new JFrame("SBML Errors and Warnings");
messageArea.setLineWrap(true);
messageArea.setEditable(false);
messageArea.setSelectionStart(0);
messageArea.setSelectionEnd(0);
JScrollPane scroll = new JScrollPane();
scroll.setMinimumSize(new Dimension(600, 600));
scroll.setPreferredSize(new Dimension(600, 600));
scroll.setViewportView(messageArea);
JButton close = new JButton("Dismiss");
close.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
f.dispose();
}
});
JPanel consistencyPanel = new JPanel(new BorderLayout());
consistencyPanel.add(scroll, "Center");
consistencyPanel.add(close, "South");
f.setContentPane(consistencyPanel);
f.pack();
Dimension screenSize;
try {
Toolkit tk = Toolkit.getDefaultToolkit();
screenSize = tk.getScreenSize();
}
catch (AWTError awe) {
screenSize = new Dimension(640, 480);
}
Dimension frameSize = f.getSize();
if (frameSize.height > screenSize.height) {
frameSize.height = screenSize.height;
}
if (frameSize.width > screenSize.width) {
frameSize.width = screenSize.width;
}
int x = screenSize.width / 2 - frameSize.width / 2;
int y = screenSize.height / 2 - frameSize.height / 2;
f.setLocation(x, y);
f.setVisible(true);
}
}
else {
String[] file = filename.trim().split(separator);
try {
SBMLDocument document = readSBML(filename.trim());
if (overwrite(root + separator + file[file.length - 1], file[file.length - 1])) {
checkModelCompleteness(document);
long numErrors = document.checkConsistency();
if (numErrors > 0) {
final JFrame f = new JFrame("SBML Errors and Warnings");
JTextArea messageArea = new JTextArea();
messageArea.append("Imported SBML file contains the errors listed below. ");
messageArea.append("It is recommended that you fix them before using this model or you may get unexpected results.\n\n");
for (long i = 0; i < numErrors; i++) {
String error = document.getError(i).getMessage();
messageArea.append(i + ":" + error + "\n");
}
messageArea.setLineWrap(true);
messageArea.setEditable(false);
messageArea.setSelectionStart(0);
messageArea.setSelectionEnd(0);
JScrollPane scroll = new JScrollPane();
scroll.setMinimumSize(new Dimension(600, 600));
scroll.setPreferredSize(new Dimension(600, 600));
scroll.setViewportView(messageArea);
JButton close = new JButton("Dismiss");
close.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
f.dispose();
}
});
JPanel consistencyPanel = new JPanel(new BorderLayout());
consistencyPanel.add(scroll, "Center");
consistencyPanel.add(close, "South");
f.setContentPane(consistencyPanel);
f.pack();
Dimension screenSize;
try {
Toolkit tk = Toolkit.getDefaultToolkit();
screenSize = tk.getScreenSize();
}
catch (AWTError awe) {
screenSize = new Dimension(640, 480);
}
Dimension frameSize = f.getSize();
if (frameSize.height > screenSize.height) {
frameSize.height = screenSize.height;
}
if (frameSize.width > screenSize.width) {
frameSize.width = screenSize.width;
}
int x = screenSize.width / 2 - frameSize.width / 2;
int y = screenSize.height / 2 - frameSize.height / 2;
f.setLocation(x, y);
f.setVisible(true);
}
SBMLWriter writer = new SBMLWriter();
String newFile = file[file.length - 1];
newFile = newFile.replaceAll("[^a-zA-Z0-9_.]+", "_");
writer.writeSBML(document, root + separator + newFile);
addToTree(newFile);
openSBML(root + separator + newFile);
}
}
catch (Exception e1) {
JOptionPane.showMessageDialog(frame, "Unable to import file.", "Error", JOptionPane.ERROR_MESSAGE);
}
}
}
}
private void importFile(String fileType, String extension) {
File importFile;
Preferences biosimrc = Preferences.userRoot();
if (biosimrc.get("biosim.general.import_dir", "").equals("")) {
importFile = null;
}
else {
importFile = new File(biosimrc.get("biosim.general.import_dir", ""));
}
String filename = Utility.browse(frame, importFile, null, JFileChooser.FILES_ONLY, "Import " + fileType, -1);
if (filename.length() > 1 && !filename.substring(filename.length() - 4, filename.length()).equals(extension)) {
JOptionPane.showMessageDialog(frame, "You must select a valid " + fileType + " file to import.", "Error", JOptionPane.ERROR_MESSAGE);
return;
}
else if (!filename.equals("")) {
biosimrc.put("biosim.general.import_dir", filename);
String[] file = filename.split(separator);
try {
file[file.length - 1] = file[file.length - 1].replaceAll("[^a-zA-Z0-9_.]+", "_");
if (checkFiles(root + separator + file[file.length - 1], filename.trim())) {
if (overwrite(root + separator + file[file.length - 1], file[file.length - 1])) {
FileOutputStream out = new FileOutputStream(new File(root + separator + file[file.length - 1]));
FileInputStream in = new FileInputStream(new File(filename));
int read = in.read();
while (read != -1) {
out.write(read);
read = in.read();
}
in.close();
out.close();
addToTree(file[file.length - 1]);
}
}
}
catch (Exception e1) {
JOptionPane.showMessageDialog(frame, "Unable to import file.", "Error", JOptionPane.ERROR_MESSAGE);
}
}
}
private void createGraph() {
String graphName = JOptionPane.showInputDialog(frame, "Enter A Name For The TSD Graph:", "TSD Graph Name", JOptionPane.PLAIN_MESSAGE);
if (graphName != null && !graphName.trim().equals("")) {
graphName = graphName.trim();
if (graphName.length() > 3) {
if (!graphName.substring(graphName.length() - 4).equals(".grf")) {
graphName += ".grf";
}
}
else {
graphName += ".grf";
}
if (overwrite(root + separator + graphName, graphName)) {
Graph g = new Graph(null, "Number of molecules", graphName.trim().substring(0, graphName.length() - 4), "tsd.printer", root, "Time",
this, null, log, graphName.trim(), true, false);
addTab(graphName.trim(), g, "TSD Graph");
g.save();
addToTree(graphName.trim());
}
}
}
private void createHistogram() {
String graphName = JOptionPane.showInputDialog(frame, "Enter A Name For The Histogram:", "Histogram Name", JOptionPane.PLAIN_MESSAGE);
if (graphName != null && !graphName.trim().equals("")) {
graphName = graphName.trim();
if (graphName.length() > 3) {
if (!graphName.substring(graphName.length() - 4).equals(".prb")) {
graphName += ".prb";
}
}
else {
graphName += ".prb";
}
if (overwrite(root + separator + graphName, graphName)) {
Graph g = new Graph(null, "Number of Molecules", graphName.trim().substring(0, graphName.length() - 4), "tsd.printer", root, "Time",
this, null, log, graphName.trim(), false, false);
addTab(graphName.trim(), g, "Histogram");
g.save();
addToTree(graphName.trim());
}
}
}
private void createLearn() {
if (root != null) {
for (int i = 0; i < tab.getTabCount(); i++) {
if (tab.getTitleAt(i).equals(tree.getFile().split(separator)[tree.getFile().split(separator).length - 1])) {
tab.setSelectedIndex(i);
if (save(i, 0) == 0) {
return;
}
break;
}
}
String lrnName = JOptionPane.showInputDialog(frame, "Enter Learn ID:", "Learn View ID", JOptionPane.PLAIN_MESSAGE);
if (lrnName != null && !lrnName.trim().equals("")) {
lrnName = lrnName.trim();
// try {
if (overwrite(root + separator + lrnName, lrnName)) {
new File(root + separator + lrnName).mkdir();
// new FileWriter(new File(root + separator +
// lrnName + separator
// ".lrn")).close();
String sbmlFile = tree.getFile();
String[] getFilename = sbmlFile.split(separator);
String sbmlFileNoPath = getFilename[getFilename.length - 1];
if (sbmlFileNoPath.endsWith(".vhd")) {
try {
File work = new File(root);
Runtime.getRuntime().exec("atacs -lvsl " + sbmlFileNoPath, null, work);
sbmlFileNoPath = sbmlFileNoPath.replace(".vhd", ".lpn");
log.addText("atacs -lvsl " + sbmlFileNoPath + "\n");
}
catch (IOException e1) {
JOptionPane.showMessageDialog(frame, "Unable to generate LPN from VHDL file!", "Error Generating File",
JOptionPane.ERROR_MESSAGE);
}
}
try {
FileOutputStream out = new FileOutputStream(new File(root + separator + lrnName.trim() + separator + lrnName.trim() + ".lrn"));
if (lema) {
out.write(("learn.file=" + sbmlFileNoPath + "\n").getBytes());
}
else {
out.write(("genenet.file=" + sbmlFileNoPath + "\n").getBytes());
}
out.close();
}
catch (IOException e1) {
JOptionPane.showMessageDialog(frame, "Unable to save parameter file!", "Error Saving File", JOptionPane.ERROR_MESSAGE);
}
addToTree(lrnName);
JTabbedPane lrnTab = new JTabbedPane();
lrnTab.addMouseListener(this);
DataManager data = new DataManager(root + separator + lrnName, this, lema);
lrnTab.addTab("Data Manager", data);
lrnTab.getComponentAt(lrnTab.getComponents().length - 1).setName("Data Manager");
if (lema) {
LearnLHPN learn = new LearnLHPN(root + separator + lrnName, log, this);
lrnTab.addTab("Learn", learn);
lrnTab.getComponentAt(lrnTab.getComponents().length - 1).setName("Learn");
lrnTab.addTab("Advanced Options", learn.getAdvancedOptionsPanel());
lrnTab.getComponentAt(lrnTab.getComponents().length - 1).setName("Advanced Options");
}
else {
LearnGCM learn = new LearnGCM(root + separator + lrnName, log, this);
lrnTab.addTab("Learn", learn);
lrnTab.getComponentAt(lrnTab.getComponents().length - 1).setName("Learn");
lrnTab.addTab("Advanced Options", learn.getAdvancedOptionsPanel());
lrnTab.getComponentAt(lrnTab.getComponents().length - 1).setName("Advanced Options");
}
Graph tsdGraph;
tsdGraph = new Graph(null, "Number of molecules", lrnName + " data", "tsd.printer", root + separator + lrnName, "Time", this,
null, log, null, true, false);
lrnTab.addTab("TSD Graph", tsdGraph);
lrnTab.getComponentAt(lrnTab.getComponents().length - 1).setName("TSD Graph");
addTab(lrnName, lrnTab, null);
}
}
}
else {
JOptionPane.showMessageDialog(frame, "You must open or create a project first.", "Error", JOptionPane.ERROR_MESSAGE);
}
}
private void viewModel() {
try {
if (tree.getFile().length() >= 4 && tree.getFile().substring(tree.getFile().length() - 4).equals(".lpn")) {
String filename = tree.getFile().split(separator)[tree.getFile().split(separator).length - 1];
String[] findTheFile = filename.split("\\.");
String theFile = findTheFile[0] + ".dot";
File dot = new File(root + separator + theFile);
dot.delete();
LhpnFile lhpn = new LhpnFile(log);
lhpn.load(tree.getFile());
lhpn.printDot(root + separator + theFile);
File work = new File(root);
Runtime exec = Runtime.getRuntime();
if (dot.exists()) {
String command = "";
if (System.getProperty("os.name").contentEquals("Linux")) {
command = "gnome-open ";
}
else if (System.getProperty("os.name").toLowerCase().startsWith("mac os")) {
command = "open ";
}
else {
command = "dotty start ";
}
log.addText(command + root + separator + theFile + "\n");
exec.exec(command + theFile, null, work);
}
else {
File log = new File(root + separator + "atacs.log");
BufferedReader input = new BufferedReader(new FileReader(log));
String line = null;
JTextArea messageArea = new JTextArea();
while ((line = input.readLine()) != null) {
messageArea.append(line);
messageArea.append(System.getProperty("line.separator"));
}
input.close();
messageArea.setLineWrap(true);
messageArea.setWrapStyleWord(true);
messageArea.setEditable(false);
JScrollPane scrolls = new JScrollPane();
scrolls.setMinimumSize(new Dimension(500, 500));
scrolls.setPreferredSize(new Dimension(500, 500));
scrolls.setViewportView(messageArea);
JOptionPane.showMessageDialog(frame, scrolls, "Log", JOptionPane.INFORMATION_MESSAGE);
}
}
else if (tree.getFile().length() >= 2 && tree.getFile().substring(tree.getFile().length() - 2).equals(".g")) {
String filename = tree.getFile().split(separator)[tree.getFile().split(separator).length - 1];
String[] findTheFile = filename.split("\\.");
String theFile = findTheFile[0] + ".dot";
File dot = new File(root + separator + theFile);
dot.delete();
String cmd = "atacs -cPlgodpe " + filename;
File work = new File(root);
Runtime exec = Runtime.getRuntime();
Process ATACS = exec.exec(cmd, null, work);
ATACS.waitFor();
log.addText("Executing:\n" + cmd);
if (dot.exists()) {
String command = "";
if (System.getProperty("os.name").contentEquals("Linux")) {
command = "gnome-open ";
}
else if (System.getProperty("os.name").toLowerCase().startsWith("mac os")) {
command = "open ";
}
else {
command = "dotty start ";
}
log.addText(command + root + separator + theFile + "\n");
exec.exec(command + theFile, null, work);
}
else {
File log = new File(root + separator + "atacs.log");
BufferedReader input = new BufferedReader(new FileReader(log));
String line = null;
JTextArea messageArea = new JTextArea();
while ((line = input.readLine()) != null) {
messageArea.append(line);
messageArea.append(System.getProperty("line.separator"));
}
input.close();
messageArea.setLineWrap(true);
messageArea.setWrapStyleWord(true);
messageArea.setEditable(false);
JScrollPane scrolls = new JScrollPane();
scrolls.setMinimumSize(new Dimension(500, 500));
scrolls.setPreferredSize(new Dimension(500, 500));
scrolls.setViewportView(messageArea);
JOptionPane.showMessageDialog(frame, scrolls, "Log", JOptionPane.INFORMATION_MESSAGE);
}
}
else if (tree.getFile().length() >= 4 && tree.getFile().substring(tree.getFile().length() - 4).equals(".vhd")) {
try {
String vhdFile = tree.getFile();
if (new File(vhdFile).exists()) {
File vhdlAmsFile = new File(vhdFile);
BufferedReader input = new BufferedReader(new FileReader(vhdlAmsFile));
String line = null;
JTextArea messageArea = new JTextArea();
while ((line = input.readLine()) != null) {
messageArea.append(line);
messageArea.append(System.getProperty("line.separator"));
}
input.close();
messageArea.setLineWrap(true);
messageArea.setWrapStyleWord(true);
messageArea.setEditable(false);
JScrollPane scrolls = new JScrollPane();
scrolls.setMinimumSize(new Dimension(800, 500));
scrolls.setPreferredSize(new Dimension(800, 500));
scrolls.setViewportView(messageArea);
JOptionPane.showMessageDialog(frame, scrolls, "VHDL Model", JOptionPane.INFORMATION_MESSAGE);
}
else {
JOptionPane.showMessageDialog(frame, "VHDL model does not exist.", "Error", JOptionPane.ERROR_MESSAGE);
}
}
catch (Exception e1) {
JOptionPane.showMessageDialog(frame, "Unable to view VHDL model.", "Error", JOptionPane.ERROR_MESSAGE);
}
}
else if (tree.getFile().length() >= 5 && tree.getFile().substring(tree.getFile().length() - 5).equals(".vams")) {
try {
String vamsFileName = tree.getFile();
if (new File(vamsFileName).exists()) {
File vamsFile = new File(vamsFileName);
BufferedReader input = new BufferedReader(new FileReader(vamsFile));
String line = null;
JTextArea messageArea = new JTextArea();
while ((line = input.readLine()) != null) {
messageArea.append(line);
messageArea.append(System.getProperty("line.separator"));
}
input.close();
messageArea.setLineWrap(true);
messageArea.setWrapStyleWord(true);
messageArea.setEditable(false);
JScrollPane scrolls = new JScrollPane();
scrolls.setMinimumSize(new Dimension(800, 500));
scrolls.setPreferredSize(new Dimension(800, 500));
scrolls.setViewportView(messageArea);
JOptionPane.showMessageDialog(frame, scrolls, "Verilog-AMS Model", JOptionPane.INFORMATION_MESSAGE);
}
else {
JOptionPane.showMessageDialog(frame, "Verilog-AMS model does not exist.", "Error", JOptionPane.ERROR_MESSAGE);
}
}
catch (Exception e1) {
JOptionPane.showMessageDialog(frame, "Unable to view Verilog-AMS model.", "Error", JOptionPane.ERROR_MESSAGE);
}
}
else if (tree.getFile().length() >= 3 && tree.getFile().substring(tree.getFile().length() - 3).equals(".sv")) {
try {
String svFileName = tree.getFile();
if (new File(svFileName).exists()) {
File svFile = new File(svFileName);
BufferedReader input = new BufferedReader(new FileReader(svFile));
String line = null;
JTextArea messageArea = new JTextArea();
while ((line = input.readLine()) != null) {
messageArea.append(line);
messageArea.append(System.getProperty("line.separator"));
}
input.close();
messageArea.setLineWrap(true);
messageArea.setWrapStyleWord(true);
messageArea.setEditable(false);
JScrollPane scrolls = new JScrollPane();
scrolls.setMinimumSize(new Dimension(800, 500));
scrolls.setPreferredSize(new Dimension(800, 500));
scrolls.setViewportView(messageArea);
JOptionPane.showMessageDialog(frame, scrolls, "SystemVerilog Model", JOptionPane.INFORMATION_MESSAGE);
}
else {
JOptionPane.showMessageDialog(frame, "SystemVerilog model does not exist.", "Error", JOptionPane.ERROR_MESSAGE);
}
}
catch (Exception e1) {
JOptionPane.showMessageDialog(frame, "Unable to view SystemVerilog model.", "Error", JOptionPane.ERROR_MESSAGE);
}
}
else if (tree.getFile().length() >= 4 && tree.getFile().substring(tree.getFile().length() - 4).equals(".csp")) {
String filename = tree.getFile().split(separator)[tree.getFile().split(separator).length - 1];
String cmd = "atacs -lcslllodpl " + filename;
File work = new File(root);
Runtime exec = Runtime.getRuntime();
Process view = exec.exec(cmd, null, work);
log.addText("Executing:\n" + cmd);
view.waitFor();
String[] findTheFile = filename.split("\\.");
// String directory = "";
String theFile = findTheFile[0] + ".dot";
if (new File(root + separator + theFile).exists()) {
String command = "";
if (System.getProperty("os.name").contentEquals("Linux")) {
// directory = ENVVAR + "/docs/";
command = "gnome-open ";
}
else if (System.getProperty("os.name").toLowerCase().startsWith("mac os")) {
// directory = ENVVAR + "/docs/";
command = "open ";
}
else {
// directory = ENVVAR + "\\docs\\";
command = "dotty start ";
}
log.addText(command + root + theFile + "\n");
exec.exec(command + theFile, null, work);
}
else {
File log = new File(root + separator + "atacs.log");
BufferedReader input = new BufferedReader(new FileReader(log));
String line = null;
JTextArea messageArea = new JTextArea();
while ((line = input.readLine()) != null) {
messageArea.append(line);
messageArea.append(System.getProperty("line.separator"));
}
input.close();
messageArea.setLineWrap(true);
messageArea.setWrapStyleWord(true);
messageArea.setEditable(false);
JScrollPane scrolls = new JScrollPane();
scrolls.setMinimumSize(new Dimension(500, 500));
scrolls.setPreferredSize(new Dimension(500, 500));
scrolls.setViewportView(messageArea);
JOptionPane.showMessageDialog(frame, scrolls, "Log", JOptionPane.INFORMATION_MESSAGE);
}
}
else if (tree.getFile().length() >= 4 && tree.getFile().substring(tree.getFile().length() - 4).equals(".hse")) {
String filename = tree.getFile().split(separator)[tree.getFile().split(separator).length - 1];
String cmd = "atacs -lhslllodpl " + filename;
File work = new File(root);
Runtime exec = Runtime.getRuntime();
Process view = exec.exec(cmd, null, work);
log.addText("Executing:\n" + cmd);
view.waitFor();
String[] findTheFile = filename.split("\\.");
// String directory = "";
String theFile = findTheFile[0] + ".dot";
if (new File(root + separator + theFile).exists()) {
String command = "";
if (System.getProperty("os.name").contentEquals("Linux")) {
// directory = ENVVAR + "/docs/";
command = "gnome-open ";
}
else if (System.getProperty("os.name").toLowerCase().startsWith("mac os")) {
// directory = ENVVAR + "/docs/";
command = "open ";
}
else {
// directory = ENVVAR + "\\docs\\";
command = "dotty start ";
}
log.addText(command + root + theFile + "\n");
exec.exec(command + theFile, null, work);
}
else {
File log = new File(root + separator + "atacs.log");
BufferedReader input = new BufferedReader(new FileReader(log));
String line = null;
JTextArea messageArea = new JTextArea();
while ((line = input.readLine()) != null) {
messageArea.append(line);
messageArea.append(System.getProperty("line.separator"));
}
input.close();
messageArea.setLineWrap(true);
messageArea.setWrapStyleWord(true);
messageArea.setEditable(false);
JScrollPane scrolls = new JScrollPane();
scrolls.setMinimumSize(new Dimension(500, 500));
scrolls.setPreferredSize(new Dimension(500, 500));
scrolls.setViewportView(messageArea);
JOptionPane.showMessageDialog(frame, scrolls, "Log", JOptionPane.INFORMATION_MESSAGE);
}
}
else if (tree.getFile().length() >= 4 && tree.getFile().substring(tree.getFile().length() - 4).equals(".unc")) {
String filename = tree.getFile().split(separator)[tree.getFile().split(separator).length - 1];
String cmd = "atacs -lxodps " + filename;
File work = new File(root);
Runtime exec = Runtime.getRuntime();
Process view = exec.exec(cmd, null, work);
log.addText("Executing:\n" + cmd);
view.waitFor();
String[] findTheFile = filename.split("\\.");
// String directory = "";
String theFile = findTheFile[0] + ".dot";
if (new File(root + separator + theFile).exists()) {
String command = "";
if (System.getProperty("os.name").contentEquals("Linux")) {
// directory = ENVVAR + "/docs/";
command = "gnome-open ";
}
else if (System.getProperty("os.name").toLowerCase().startsWith("mac os")) {
// directory = ENVVAR + "/docs/";
command = "open ";
}
else {
// directory = ENVVAR + "\\docs\\";
command = "dotty start ";
}
log.addText(command + root + theFile + "\n");
exec.exec(command + theFile, null, work);
}
else {
File log = new File(root + separator + "atacs.log");
BufferedReader input = new BufferedReader(new FileReader(log));
String line = null;
JTextArea messageArea = new JTextArea();
while ((line = input.readLine()) != null) {
messageArea.append(line);
messageArea.append(System.getProperty("line.separator"));
}
input.close();
messageArea.setLineWrap(true);
messageArea.setWrapStyleWord(true);
messageArea.setEditable(false);
JScrollPane scrolls = new JScrollPane();
scrolls.setMinimumSize(new Dimension(500, 500));
scrolls.setPreferredSize(new Dimension(500, 500));
scrolls.setViewportView(messageArea);
JOptionPane.showMessageDialog(frame, scrolls, "Log", JOptionPane.INFORMATION_MESSAGE);
}
}
else if (tree.getFile().length() >= 4 && tree.getFile().substring(tree.getFile().length() - 4).equals(".rsg")) {
String filename = tree.getFile().split(separator)[tree.getFile().split(separator).length - 1];
String cmd = "atacs -lsodps " + filename;
File work = new File(root);
Runtime exec = Runtime.getRuntime();
Process view = exec.exec(cmd, null, work);
log.addText("Executing:\n" + cmd);
view.waitFor();
String[] findTheFile = filename.split("\\.");
// String directory = "";
String theFile = findTheFile[0] + ".dot";
if (new File(root + separator + theFile).exists()) {
String command = "";
if (System.getProperty("os.name").contentEquals("Linux")) {
// directory = ENVVAR + "/docs/";
command = "gnome-open ";
}
else if (System.getProperty("os.name").toLowerCase().startsWith("mac os")) {
// directory = ENVVAR + "/docs/";
command = "open ";
}
else {
// directory = ENVVAR + "\\docs\\";
command = "dotty start ";
}
log.addText(command + root + theFile + "\n");
exec.exec(command + theFile, null, work);
}
else {
File log = new File(root + separator + "atacs.log");
BufferedReader input = new BufferedReader(new FileReader(log));
String line = null;
JTextArea messageArea = new JTextArea();
while ((line = input.readLine()) != null) {
messageArea.append(line);
messageArea.append(System.getProperty("line.separator"));
}
input.close();
messageArea.setLineWrap(true);
messageArea.setWrapStyleWord(true);
messageArea.setEditable(false);
JScrollPane scrolls = new JScrollPane();
scrolls.setMinimumSize(new Dimension(500, 500));
scrolls.setPreferredSize(new Dimension(500, 500));
scrolls.setViewportView(messageArea);
JOptionPane.showMessageDialog(frame, scrolls, "Log", JOptionPane.INFORMATION_MESSAGE);
}
}
}
catch (IOException e1) {
e1.printStackTrace();
JOptionPane.showMessageDialog(frame, "File cannot be read", "Error", JOptionPane.ERROR_MESSAGE);
}
catch (InterruptedException e2) {
e2.printStackTrace();
}
}
private void copy() {
if (!tree.getFile().equals(root)) {
for (int i = 0; i < tab.getTabCount(); i++) {
if (tab.getTitleAt(i).equals(tree.getFile().split(separator)[tree.getFile().split(separator).length - 1])) {
tab.setSelectedIndex(i);
if (save(i, 0) == 0) {
return;
}
break;
}
}
String copy = JOptionPane.showInputDialog(frame, "Enter a New Filename:", "Copy", JOptionPane.PLAIN_MESSAGE);
if (copy == null || copy.equals("")) {
return;
}
copy = copy.trim();
if (tree.getFile().contains(".")) {
String extension = tree.getFile().substring(tree.getFile().lastIndexOf("."), tree.getFile().length());
if (!copy.endsWith(extension)) {
copy += extension;
}
}
if (copy.equals(tree.getFile().split(separator)[tree.getFile().split(separator).length - 1])) {
JOptionPane.showMessageDialog(frame, "Unable to copy file." + "\nNew filename must be different than old filename.", "Error",
JOptionPane.ERROR_MESSAGE);
return;
}
try {
if (overwrite(root + separator + copy, copy)) {
if (copy.endsWith(".xml")) {
SBMLDocument document = readSBML(tree.getFile());
document.getModel().setId(copy.substring(0, copy.lastIndexOf(".")));
SBMLWriter writer = new SBMLWriter();
writer.writeSBML(document, root + separator + copy);
}
else if (copy.endsWith(".gcm")) {
SBMLDocument document = readSBML(tree.getFile().replace(".gcm", ".xml"));
document.getModel().setId(copy.substring(0, copy.lastIndexOf(".")));
SBMLWriter writer = new SBMLWriter();
writer.writeSBML(document, root + separator + copy.replace(".gcm", ".xml"));
addToTree(copy.replace(".gcm", ".xml"));
GCMFile gcm = new GCMFile(root);
gcm.load(tree.getFile());
gcm.setSBMLFile(copy.replace(".gcm", ".xml"));
gcm.save(root + separator + copy);
}
else if (copy.contains(".")) {
FileOutputStream out = new FileOutputStream(new File(root + separator + copy));
FileInputStream in = new FileInputStream(new File(tree.getFile()));
int read = in.read();
while (read != -1) {
out.write(read);
read = in.read();
}
in.close();
out.close();
}
else {
boolean sim = false;
for (String s : new File(tree.getFile()).list()) {
if (s.length() > 3 && s.substring(s.length() - 4).equals(".sim")) {
sim = true;
}
}
if (sim) {
new File(root + separator + copy).mkdir();
String[] s = new File(tree.getFile()).list();
for (String ss : s) {
if (ss.length() > 4 && ss.substring(ss.length() - 5).equals(".sbml") || ss.length() > 3
&& ss.substring(ss.length() - 4).equals(".xml")) {
SBMLDocument document = readSBML(tree.getFile() + separator + ss);
SBMLWriter writer = new SBMLWriter();
writer.writeSBML(document, root + separator + copy + separator + ss);
}
else if (ss.length() > 10 && ss.substring(ss.length() - 11).equals(".properties")) {
FileOutputStream out = new FileOutputStream(new File(root + separator + copy + separator + ss));
FileInputStream in = new FileInputStream(new File(tree.getFile() + separator + ss));
int read = in.read();
while (read != -1) {
out.write(read);
read = in.read();
}
in.close();
out.close();
}
else if (ss.length() > 3
&& (ss.substring(ss.length() - 4).equals(".tsd") || ss.substring(ss.length() - 4).equals(".dat")
|| ss.substring(ss.length() - 4).equals(".sad") || ss.substring(ss.length() - 4).equals(".pms") || ss
.substring(ss.length() - 4).equals(".sim")) && !ss.equals(".sim")) {
FileOutputStream out;
if (ss.substring(ss.length() - 4).equals(".pms")) {
out = new FileOutputStream(new File(root + separator + copy + separator + copy + ".sim"));
}
else if (ss.substring(ss.length() - 4).equals(".sim")) {
out = new FileOutputStream(new File(root + separator + copy + separator + copy + ".sim"));
}
else {
out = new FileOutputStream(new File(root + separator + copy + separator + ss));
}
FileInputStream in = new FileInputStream(new File(tree.getFile() + separator + ss));
int read = in.read();
while (read != -1) {
out.write(read);
read = in.read();
}
in.close();
out.close();
}
}
}
else {
new File(root + separator + copy).mkdir();
String[] s = new File(tree.getFile()).list();
for (String ss : s) {
if (ss.length() > 3 && (ss.substring(ss.length() - 4).equals(".tsd") || ss.substring(ss.length() - 4).equals(".lrn"))) {
FileOutputStream out;
if (ss.substring(ss.length() - 4).equals(".lrn")) {
out = new FileOutputStream(new File(root + separator + copy + separator + copy + ".lrn"));
}
else {
out = new FileOutputStream(new File(root + separator + copy + separator + ss));
}
FileInputStream in = new FileInputStream(new File(tree.getFile() + separator + ss));
int read = in.read();
while (read != -1) {
out.write(read);
read = in.read();
}
in.close();
out.close();
}
}
}
}
addToTree(copy);
}
}
catch (Exception e1) {
JOptionPane.showMessageDialog(frame, "Unable to copy file.", "Error", JOptionPane.ERROR_MESSAGE);
}
}
}
private void rename() {
if (!tree.getFile().equals(root)) {
String oldName = tree.getFile().split(separator)[tree.getFile().split(separator).length - 1];
for (int i = 0; i < tab.getTabCount(); i++) {
if (tab.getTitleAt(i).equals(tree.getFile().split(separator)[tree.getFile().split(separator).length - 1])) {
tab.setSelectedIndex(i);
if (save(i, 0) == 0) {
return;
}
break;
}
}
String rename = JOptionPane.showInputDialog(frame, "Enter a New Filename:", "Rename", JOptionPane.PLAIN_MESSAGE);
if (rename == null || rename.equals("")) {
return;
}
rename = rename.trim();
if (tree.getFile().contains(".")) {
String extension = tree.getFile().substring(tree.getFile().lastIndexOf("."), tree.getFile().length());
if (!rename.endsWith(extension)) {
rename += extension;
}
}
if (rename.equals(tree.getFile().split(separator)[tree.getFile().split(separator).length - 1])) {
JOptionPane.showMessageDialog(frame, "Unable to rename file." + "\nNew filename must be different than old filename.", "Error",
JOptionPane.ERROR_MESSAGE);
return;
}
String modelID = rename.substring(0, rename.lastIndexOf("."));
try {
if (overwrite(root + separator + rename, rename)) {
if (tree.getFile().endsWith(".sbml") || tree.getFile().endsWith(".xml") || tree.getFile().endsWith(".gcm")
|| tree.getFile().endsWith(".lpn") || tree.getFile().endsWith(".vhd") || tree.getFile().endsWith(".csp")
|| tree.getFile().endsWith(".hse") || tree.getFile().endsWith(".unc") || tree.getFile().endsWith(".rsg")) {
reassignViews(oldName, rename);
}
if (tree.getFile().endsWith(".gcm")) {
String newSBMLfile = rename.replace(".gcm", ".xml");
new File(tree.getFile()).renameTo(new File(root + separator + rename));
new File(tree.getFile().replace(".gcm", ".xml")).renameTo(new File(root + separator + newSBMLfile));
GCMFile gcm = new GCMFile(root);
gcm.load(root + separator + rename);
gcm.setSBMLFile(newSBMLfile);
gcm.save(root + separator + rename);
SBMLDocument document = readSBML(root + separator + newSBMLfile);
document.getModel().setId(modelID);
SBMLWriter writer = new SBMLWriter();
writer.writeSBML(document, root + separator + newSBMLfile);
deleteFromTree(oldName.replace(".gcm", ".xml"));
addToTree(newSBMLfile);
}
else if (tree.getFile().endsWith(".xml")) {
new File(tree.getFile()).renameTo(new File(root + separator + rename));
SBMLDocument document = readSBML(root + separator + rename);
document.getModel().setId(modelID);
SBMLWriter writer = new SBMLWriter();
writer.writeSBML(document, root + separator + rename);
}
else {
new File(tree.getFile()).renameTo(new File(root + separator + rename));
}
if (rename.length() >= 4 && rename.substring(rename.length() - 4).equals(".gcm")) {
for (String s : new File(root).list()) {
if (s.endsWith(".gcm")) {
BufferedReader in = new BufferedReader(new FileReader(root + separator + s));
String line = null;
String file = "";
while ((line = in.readLine()) != null) {
line = line.replace(oldName, rename);
file += line;
file += "\n";
}
in.close();
BufferedWriter out = new BufferedWriter(new FileWriter(root + separator + s));
out.write(file);
out.close();
}
}
}
if (tree.getFile().endsWith(".sbml") || tree.getFile().endsWith(".xml") || tree.getFile().endsWith(".gcm")
|| tree.getFile().endsWith(".lpn") || tree.getFile().endsWith(".vhd") || tree.getFile().endsWith(".csp")
|| tree.getFile().endsWith(".hse") || tree.getFile().endsWith(".unc") || tree.getFile().endsWith(".rsg")) {
updateAsyncViews(rename);
}
if (new File(root + separator + rename).isDirectory()) {
if (new File(root + separator + rename + separator
+ tree.getFile().split(separator)[tree.getFile().split(separator).length - 1] + ".sim").exists()) {
new File(root + separator + rename + separator
+ tree.getFile().split(separator)[tree.getFile().split(separator).length - 1] + ".sim").renameTo(new File(root
+ separator + rename + separator + rename + ".sim"));
}
else if (new File(root + separator + rename + separator
+ tree.getFile().split(separator)[tree.getFile().split(separator).length - 1] + ".pms").exists()) {
new File(root + separator + rename + separator
+ tree.getFile().split(separator)[tree.getFile().split(separator).length - 1] + ".pms").renameTo(new File(root
+ separator + rename + separator + rename + ".sim"));
}
if (new File(root + separator + rename + separator
+ tree.getFile().split(separator)[tree.getFile().split(separator).length - 1] + ".lrn").exists()) {
new File(root + separator + rename + separator
+ tree.getFile().split(separator)[tree.getFile().split(separator).length - 1] + ".lrn").renameTo(new File(root
+ separator + rename + separator + rename + ".lrn"));
}
if (new File(root + separator + rename + separator
+ tree.getFile().split(separator)[tree.getFile().split(separator).length - 1] + ".ver").exists()) {
new File(root + separator + rename + tree.getFile().split(separator)[tree.getFile().split(separator).length - 1] + ".ver")
.renameTo(new File(root + separator + rename + separator + rename + ".ver"));
}
if (new File(root + separator + rename + separator
+ tree.getFile().split(separator)[tree.getFile().split(separator).length - 1] + ".grf").exists()) {
new File(root + separator + rename + separator
+ tree.getFile().split(separator)[tree.getFile().split(separator).length - 1] + ".grf").renameTo(new File(root
+ separator + rename + separator + rename + ".grf"));
}
if (new File(root + separator + rename + separator
+ tree.getFile().split(separator)[tree.getFile().split(separator).length - 1] + ".prb").exists()) {
new File(root + separator + rename + separator
+ tree.getFile().split(separator)[tree.getFile().split(separator).length - 1] + ".prb").renameTo(new File(root
+ separator + rename + separator + rename + ".prb"));
}
}
for (int i = 0; i < tab.getTabCount(); i++) {
if (tab.getTitleAt(i).equals(tree.getFile().split(separator)[tree.getFile().split(separator).length - 1])) {
if (tree.getFile().length() > 4 && tree.getFile().substring(tree.getFile().length() - 5).equals(".sbml")
|| tree.getFile().length() > 3 && tree.getFile().substring(tree.getFile().length() - 4).equals(".xml")) {
((SBML_Editor) tab.getComponentAt(i)).setModelID(modelID);
((SBML_Editor) tab.getComponentAt(i)).setFile(root + separator + rename);
tab.setTitleAt(i, rename);
}
else if (tree.getFile().length() > 3
&& (tree.getFile().substring(tree.getFile().length() - 4).equals(".grf") || tree.getFile()
.substring(tree.getFile().length() - 4).equals(".prb"))) {
((Graph) tab.getComponentAt(i)).setGraphName(rename);
tab.setTitleAt(i, rename);
}
else if (tree.getFile().length() > 3 && tree.getFile().substring(tree.getFile().length() - 4).equals(".gcm")) {
((GCM2SBMLEditor) tab.getComponentAt(i)).reload(rename.substring(0, rename.length() - 4));
}
else if (tree.getFile().length() > 3 && tree.getFile().substring(tree.getFile().length() - 4).equals(".rdf")) {
tab.setTitleAt(i, rename);
}
else if (tree.getFile().length() > 3 && tree.getFile().substring(tree.getFile().length() - 4).equals(".lpn")) {
((LHPNEditor) tab.getComponentAt(i)).reload(rename.substring(0, rename.length() - 4));
tab.setTitleAt(i, rename);
}
else if (tab.getComponentAt(i) instanceof JTabbedPane) {
JTabbedPane t = new JTabbedPane();
t.addMouseListener(this);
int selected = ((JTabbedPane) tab.getComponentAt(i)).getSelectedIndex();
boolean analysis = false;
ArrayList<Component> comps = new ArrayList<Component>();
for (int j = 0; j < ((JTabbedPane) tab.getComponentAt(i)).getTabCount(); j++) {
Component c = ((JTabbedPane) tab.getComponentAt(i)).getComponent(j);
comps.add(c);
}
SBML_Editor sbml = null;
Reb2Sac reb2sac = null;
for (Component c : comps) {
if (c instanceof Reb2Sac) {
((Reb2Sac) c).setSim(rename);
analysis = true;
}
else if (c instanceof SBML_Editor) {
String properties = root + separator + rename + separator + rename + ".sim";
new File(properties).renameTo(new File(properties.replace(".sim", ".temp")));
try {
boolean dirty = ((SBML_Editor) c).isDirty();
((SBML_Editor) c).setParamFileAndSimDir(properties, root + separator + rename);
((SBML_Editor) c).save(false, "", true, true);
((SBML_Editor) c).updateSBML(i, 0);
((SBML_Editor) c).setDirty(dirty);
}
catch (Exception e1) {
e1.printStackTrace();
}
new File(properties).delete();
new File(properties.replace(".sim", ".temp")).renameTo(new File(properties));
}
else if (c instanceof Graph) {
// c.addMouseListener(this);
Graph g = ((Graph) c);
g.setDirectory(root + separator + rename);
if (g.isTSDGraph()) {
g.setGraphName(rename + ".grf");
}
else {
g.setGraphName(rename + ".prb");
}
}
else if (c instanceof LearnGCM) {
LearnGCM l = ((LearnGCM) c);
l.setDirectory(root + separator + rename);
}
else if (c instanceof DataManager) {
DataManager d = ((DataManager) c);
d.setDirectory(root + separator + rename);
}
if (analysis) {
if (c instanceof Reb2Sac) {
reb2sac = (Reb2Sac) c;
t.addTab("Simulation Options", c);
t.getComponentAt(t.getComponents().length - 1).setName("Simulate");
}
else if (c instanceof MovieContainer) {
t.addTab("Schematic", c);
t.getComponentAt(t.getComponents().length - 1).setName("ModelViewMovie");
}
else if (c instanceof SBML_Editor) {
sbml = (SBML_Editor) c;
t.addTab("Parameter Editor", c);
t.getComponentAt(t.getComponents().length - 1).setName("SBML Editor");
}
else if (c instanceof GCM2SBMLEditor) {
GCM2SBMLEditor gcm = (GCM2SBMLEditor) c;
if (!gcm.getSBMLFile().equals("--none
sbml = new SBML_Editor(root + separator + gcm.getSBMLFile(), reb2sac, log, this, root + separator
+ rename, root + separator + rename + separator + rename + ".sim");
}
t.addTab("Parameters", c);
t.getComponentAt(t.getComponents().length - 1).setName("GCM Editor");
}
else if (c instanceof Graph) {
if (((Graph) c).isTSDGraph()) {
t.addTab("TSD Graph", c);
t.getComponentAt(t.getComponents().length - 1).setName("TSD Graph");
}
else {
t.addTab("Histogram", c);
t.getComponentAt(t.getComponents().length - 1).setName("ProbGraph");
}
}
else if (c instanceof JScrollPane) {
if (sbml != null) {
t.addTab("SBML Elements", sbml.getElementsPanel());
t.getComponentAt(t.getComponents().length - 1).setName("");
}
else {
JScrollPane scroll = new JScrollPane();
scroll.setViewportView(new JPanel());
t.addTab("SBML Elements", scroll);
t.getComponentAt(t.getComponents().length - 1).setName("");
}
}
else {
t.addTab("Abstraction Options", c);
t.getComponentAt(t.getComponents().length - 1).setName("");
}
}
}
if (analysis) {
t.setSelectedIndex(selected);
tab.setComponentAt(i, t);
}
tab.setTitleAt(i, rename);
tab.getComponentAt(i).setName(rename);
}
else {
tab.setTitleAt(i, rename);
tab.getComponentAt(i).setName(rename);
}
}
else if (tab.getComponentAt(i) instanceof JTabbedPane) {
ArrayList<Component> comps = new ArrayList<Component>();
for (int j = 0; j < ((JTabbedPane) tab.getComponentAt(i)).getTabCount(); j++) {
Component c = ((JTabbedPane) tab.getComponentAt(i)).getComponent(j);
comps.add(c);
}
for (Component c : comps) {
if (c instanceof Reb2Sac && ((Reb2Sac) c).getBackgroundFile().equals(oldName)) {
((Reb2Sac) c).updateBackgroundFile(rename);
}
else if (c instanceof LearnGCM && ((LearnGCM) c).getBackgroundFile().equals(oldName)) {
((LearnGCM) c).updateBackgroundFile(rename);
}
}
}
}
// updateAsyncViews(rename);
updateViewNames(tree.getFile(), rename);
deleteFromTree(oldName);
addToTree(rename);
}
}
catch (Exception e1) {
JOptionPane.showMessageDialog(frame, "Unable to rename selected file.", "Error", JOptionPane.ERROR_MESSAGE);
}
}
}
private void openGCM(boolean textBased) {
String file = tree.getFile();
String filename = "";
if (file.lastIndexOf('/') >= 0) {
filename = file.substring(file.lastIndexOf('/') + 1);
}
if (file.lastIndexOf('\\') >= 0) {
filename = file.substring(file.lastIndexOf('\\') + 1);
}
openGCM(filename, textBased);
}
public void openGCM(String filename, boolean textBased) {
try {
File work = new File(root);
int i = getTab(filename);
if (i == -1) {
i = getTab(filename.replace(".gcm", ".xml"));
}
if (i != -1) {
tab.setSelectedIndex(i);
}
else {
String path = work.getAbsolutePath();
/*
* GCMFile gcmFile = new GCMFile(path); String gcmname =
* theFile.replace(".gcm", ""); gcmFile.load(filename); if
* ((gcmFile.getSBMLFile() == null ||
* !gcmFile.getSBMLFile().equals(gcmname + ".xml")) && new
* File(path + separator + gcmname + ".xml").exists()) {
* Object[] options = { "Overwrite", "Cancel" }; int value;
* value = JOptionPane.showOptionDialog(Gui.frame, gcmname +
* ".xml already exists." + "\nDo you want to overwrite?",
* "Overwrite", JOptionPane.YES_NO_OPTION,
* JOptionPane.PLAIN_MESSAGE, null, options, options[0]); if
* (value == JOptionPane.YES_OPTION) { GCM2SBMLEditor gcm = new
* GCM2SBMLEditor(path, theFile, this, log, false, null, null,
* null, textBased); addTab(theFile, gcm, "GCM Editor"); } }
* else {
*/
try {
GCM2SBMLEditor gcm = new GCM2SBMLEditor(path, filename, this, log, false, null, null, null, textBased);
addTab(filename, gcm, "GCM Editor");
}
catch (Exception e) {
e.printStackTrace();
}
}
}
catch (Exception e1) {
e1.printStackTrace();
JOptionPane.showMessageDialog(frame, "Unable to open this GCM file.", "Error", JOptionPane.ERROR_MESSAGE);
}
}
private void openSBML(String fullPath) {
try {
boolean done = false;
String theSBMLFile = fullPath.split(separator)[fullPath.split(separator).length - 1];
String theGCMFile = theSBMLFile.replace(".xml", ".gcm");
for (int i = 0; i < tab.getTabCount(); i++) {
if (tab.getTitleAt(i).equals(theSBMLFile) || tab.getTitleAt(i).equals(theGCMFile)) {
tab.setSelectedIndex(i);
done = true;
break;
}
}
if (!done) {
createGCMFromSBML(root, fullPath, theSBMLFile, theGCMFile, false);
addToTree(theGCMFile);
GCM2SBMLEditor gcm = new GCM2SBMLEditor(root + separator, theGCMFile, this, log, false, null, null, null, false);
addTab(theGCMFile, gcm, "GCM Editor");
}
}
catch (Exception e1) {
JOptionPane.showMessageDialog(frame, "You must select a valid SBML file.", "Error", JOptionPane.ERROR_MESSAGE);
}
}
public static boolean createGCMFromSBML(String root, String fullPath, String theSBMLFile, String theGCMFile, boolean force) {
if (force || !new File(fullPath.replace(".xml", ".gcm").replace(".sbml", ".gcm")).exists()) {
SBMLDocument document = readSBML(fullPath);
Model m = document.getModel();
GCMFile gcmFile = new GCMFile(root);
int x = 50;
int y = 50;
if (m != null) {
for (int i = 0; i < m.getNumSpecies(); i++) {
gcmFile.createSpecies(document.getModel().getSpecies(i).getId(), x, y);
if (m.getSpecies(i).isSetInitialAmount()) {
gcmFile.getSpecies().get(m.getSpecies(i).getId())
.setProperty(GlobalConstants.INITIAL_STRING, m.getSpecies(i).getInitialAmount() + "");
}
else {
gcmFile.getSpecies().get(m.getSpecies(i).getId())
.setProperty(GlobalConstants.INITIAL_STRING, "[" + m.getSpecies(i).getInitialConcentration() + "]");
}
gcmFile.getSpecies().get(m.getSpecies(i).getId()).setProperty(GlobalConstants.KDECAY_STRING, "0.0");
x += 50;
y += 50;
}
}
gcmFile.setSBMLDocument(document);
gcmFile.setSBMLFile(theSBMLFile);
gcmFile.save(fullPath.replace(".xml", ".gcm").replace(".sbml", ".gcm"));
return true;
}
else
return false;
}
private void openSBOL() {
String filePath = tree.getFile();
String fileName = "";
String mySeparator = File.separator;
int spacer = 1;
if (mySeparator.equals("\\")) {
mySeparator = "\\\\";
spacer = 2;
}
fileName = filePath.substring(filePath.lastIndexOf(mySeparator) + spacer);
int i = getTab(fileName);
if (i != -1) {
tab.setSelectedIndex(i);
}
else {
SbolBrowser browser = new SbolBrowser(filePath, this);
}
}
private void openGraph() {
boolean done = false;
for (int i = 0; i < tab.getTabCount(); i++) {
if (tab.getTitleAt(i).equals(tree.getFile().split(separator)[tree.getFile().split(separator).length - 1])) {
tab.setSelectedIndex(i);
done = true;
}
}
if (!done) {
addTab(tree.getFile().split(separator)[tree.getFile().split(separator).length - 1], new Graph(null, "Number of molecules", "title",
"tsd.printer", root, "Time", this, tree.getFile(), log,
tree.getFile().split(separator)[tree.getFile().split(separator).length - 1], true, false), "TSD Graph");
}
}
private void openHistogram() {
boolean done = false;
for (int i = 0; i < tab.getTabCount(); i++) {
if (tab.getTitleAt(i).equals(tree.getFile().split(separator)[tree.getFile().split(separator).length - 1])) {
tab.setSelectedIndex(i);
done = true;
}
}
if (!done) {
addTab(tree.getFile().split(separator)[tree.getFile().split(separator).length - 1], new Graph(null, "Percent", "title", "tsd.printer",
root, "Time", this, tree.getFile(), log, tree.getFile().split(separator)[tree.getFile().split(separator).length - 1], false,
false), "Histogram");
}
}
private void openLPN() {
try {
String filename = tree.getFile();
String directory = "";
String theFile = "";
if (filename.lastIndexOf('/') >= 0) {
directory = filename.substring(0, filename.lastIndexOf('/') + 1);
theFile = filename.substring(filename.lastIndexOf('/') + 1);
}
if (filename.lastIndexOf('\\') >= 0) {
directory = filename.substring(0, filename.lastIndexOf('\\') + 1);
theFile = filename.substring(filename.lastIndexOf('\\') + 1);
}
LhpnFile lhpn = new LhpnFile(log);
File work = new File(directory);
int i = getTab(theFile);
if (i != -1) {
tab.setSelectedIndex(i);
}
else {
LHPNEditor editor = new LHPNEditor(work.getAbsolutePath(), theFile, lhpn, this, log);
addTab(theFile, editor, "LHPN Editor");
}
}
catch (Exception e1) {
e1.printStackTrace();
JOptionPane.showMessageDialog(frame, "Unable to view this LPN file.", "Error", JOptionPane.ERROR_MESSAGE);
}
}
private void newModel(String fileType, String extension) {
if (root != null) {
try {
String modelID = JOptionPane.showInputDialog(frame, "Enter " + fileType + " Model ID:", "Model ID", JOptionPane.PLAIN_MESSAGE);
if (modelID != null && !modelID.trim().equals("")) {
String fileName;
modelID = modelID.trim();
if (modelID.length() >= extension.length()) {
if (!modelID.substring(modelID.length() - extension.length()).equals(extension)) {
fileName = modelID + extension;
}
else {
fileName = modelID;
modelID = modelID.substring(0, modelID.length() - extension.length());
}
}
else {
fileName = modelID + extension;
}
if (!(IDpat.matcher(modelID).matches())) {
JOptionPane.showMessageDialog(frame, "A model ID can only contain letters, numbers, and underscores.", "Invalid ID",
JOptionPane.ERROR_MESSAGE);
}
else {
File f = new File(root + separator + fileName);
f.createNewFile();
addToTree(fileName);
if (!viewer.equals("")) {
String command = viewer + " " + root + separator + fileName;
Runtime exec = Runtime.getRuntime();
try {
exec.exec(command);
}
catch (Exception e1) {
JOptionPane.showMessageDialog(frame, "Unable to open external editor.", "Error Opening Editor",
JOptionPane.ERROR_MESSAGE);
}
}
else {
JTextArea text = new JTextArea("");
text.setEditable(true);
text.setLineWrap(true);
JScrollPane scroll = new JScrollPane(text);
addTab(fileName, scroll, fileType + " Editor");
}
}
}
}
catch (IOException e1) {
JOptionPane.showMessageDialog(frame, "Unable to create new model.", "Error", JOptionPane.ERROR_MESSAGE);
}
}
}
private void openModel(String fileType) {
try {
String filename = tree.getFile();
String directory = "";
String theFile = "";
if (filename.lastIndexOf('/') >= 0) {
directory = filename.substring(0, filename.lastIndexOf('/') + 1);
theFile = filename.substring(filename.lastIndexOf('/') + 1);
}
if (filename.lastIndexOf('\\') >= 0) {
directory = filename.substring(0, filename.lastIndexOf('\\') + 1);
theFile = filename.substring(filename.lastIndexOf('\\') + 1);
}
File work = new File(directory);
int i = getTab(theFile);
if (i != -1) {
tab.setSelectedIndex(i);
}
else {
if (!viewer.equals("")) {
String command = viewer + " " + directory + separator + theFile;
Runtime exec = Runtime.getRuntime();
try {
exec.exec(command);
}
catch (Exception e1) {
JOptionPane.showMessageDialog(frame, "Unable to open external editor.", "Error Opening Editor", JOptionPane.ERROR_MESSAGE);
}
}
else {
File file = new File(work + separator + theFile);
String input = "";
FileReader in = new FileReader(file);
int read = in.read();
while (read != -1) {
input += (char) read;
read = in.read();
}
in.close();
JTextArea text = new JTextArea(input);
text.setEditable(true);
text.setLineWrap(true);
JScrollPane scroll = new JScrollPane(text);
addTab(theFile, scroll, fileType + " Editor");
}
}
}
catch (Exception e1) {
JOptionPane.showMessageDialog(frame, "Unable to view this " + fileType + " file.", "Error", JOptionPane.ERROR_MESSAGE);
}
}
public int getTab(String name) {
for (int i = 0; i < tab.getTabCount(); i++) {
if (tab.getTitleAt(i).equals(name)) {
return i;
}
}
return -1;
}
public void deleteDir(File dir) {
int count = 0;
do {
File[] list = dir.listFiles();
System.gc();
for (int i = 0; i < list.length; i++) {
if (list[i].isDirectory()) {
deleteDir(list[i]);
}
else {
list[i].delete();
}
}
count++;
}
while (!dir.delete() && count != 100);
if (count == 100) {
JOptionPane.showMessageDialog(frame, "Unable to delete.", "Error", JOptionPane.ERROR_MESSAGE);
}
}
/**
* This method adds a new project to recent list
*/
public void addRecentProject(String projDir) {
// boolean newOne = true;
for (int i = 0; i < numberRecentProj; i++) {
if (recentProjectPaths[i].equals(projDir)) {
for (int j = 0; j <= i; j++) {
String save = recentProjectPaths[j];
recentProjects[j].setText(projDir.split(separator)[projDir.split(separator).length - 1]);
if (file.getItem(file.getItemCount() - 1) == exit) {
file.insert(recentProjects[j], file.getItemCount() - 3 - numberRecentProj);
}
else {
file.add(recentProjects[j]);
}
recentProjectPaths[j] = projDir;
projDir = save;
}
for (int j = i + 1; j < numberRecentProj; j++) {
if (file.getItem(file.getItemCount() - 1) == exit) {
file.insert(recentProjects[j], file.getItemCount() - 3 - numberRecentProj);
}
else {
file.add(recentProjects[j]);
}
}
return;
}
}
if (numberRecentProj < 10) {
numberRecentProj++;
}
for (int i = 0; i < numberRecentProj; i++) {
String save = recentProjectPaths[i];
recentProjects[i].setText(projDir.split(separator)[projDir.split(separator).length - 1]);
if (file.getItem(file.getItemCount() - 1) == exit) {
file.insert(recentProjects[i], file.getItemCount() - 3 - numberRecentProj);
}
else {
file.add(recentProjects[i]);
}
recentProjectPaths[i] = projDir;
projDir = save;
}
}
/**
* This method refreshes the menu.
*/
public void refresh() {
mainPanel.remove(tree);
tree = new FileTree(new File(root), this, lema, atacs);
mainPanel.add(tree, "West");
mainPanel.validate();
}
/**
* This method refreshes the tree.
*/
public void refreshTree() {
mainPanel.remove(tree);
tree = new FileTree(new File(root), this, lema, atacs);
mainPanel.add(tree, "West");
//updateGCM();
mainPanel.validate();
}
public void addToTree(String item) {
tree.addToTree(item, root);
//updateGCM();
mainPanel.validate();
}
public void addToTreeNoUpdate(String item) {
tree.addToTree(item, root);
mainPanel.validate();
}
public void deleteFromTree(String item) {
tree.deleteFromTree(item);
//updateGCM();
mainPanel.validate();
}
public FileTree getFileTree() {
return tree;
}
/**
* This method adds the given Component to a tab.
*/
public void addTab(String name, Component panel, String tabName) {
tab.addTab(name, panel);
// panel.addMouseListener(this);
if (tabName != null) {
tab.getComponentAt(tab.getTabCount() - 1).setName(tabName);
}
else {
tab.getComponentAt(tab.getTabCount() - 1).setName(name);
}
tab.setSelectedIndex(tab.getTabCount() - 1);
}
/**
* This method removes the given component from the tabs.
*/
public void removeTab(Component component) {
tab.remove(component);
if (tab.getTabCount() > 0) {
tab.setSelectedIndex(tab.getTabCount() - 1);
enableTabMenu(tab.getSelectedIndex());
}
else {
enableTreeMenu();
}
}
public JTabbedPane getTab() {
return tab;
}
/**
* Prompts the user to save work that has been done.
*/
public int save(int index, int autosave) {
if (tab.getComponentAt(index).getName().contains(("GCM")) || tab.getComponentAt(index).getName().contains("LHPN")) {
if (tab.getComponentAt(index) instanceof GCM2SBMLEditor) {
GCM2SBMLEditor editor = (GCM2SBMLEditor) tab.getComponentAt(index);
if (editor.isDirty()) {
if (autosave == 0) {
int value = JOptionPane.showOptionDialog(frame, "Do you want to save changes to " + tab.getTitleAt(index) + "?",
"Save Changes", JOptionPane.YES_NO_CANCEL_OPTION, JOptionPane.PLAIN_MESSAGE, null, OPTIONS, OPTIONS[0]);
if (value == YES_OPTION) {
editor.save("gcm");
return 1;
}
else if (value == NO_OPTION) {
return 1;
}
else if (value == CANCEL_OPTION) {
return 0;
}
else if (value == YES_TO_ALL_OPTION) {
editor.save("gcm");
return 2;
}
else if (value == NO_TO_ALL_OPTION) {
return 3;
}
}
else if (autosave == 1) {
editor.save("gcm");
return 2;
}
else {
return 3;
}
}
}
else if (tab.getComponentAt(index) instanceof LHPNEditor) {
LHPNEditor editor = (LHPNEditor) tab.getComponentAt(index);
if (editor.isDirty()) {
if (autosave == 0) {
int value = JOptionPane.showOptionDialog(frame, "Do you want to save changes to " + tab.getTitleAt(index) + "?",
"Save Changes", JOptionPane.YES_NO_CANCEL_OPTION, JOptionPane.PLAIN_MESSAGE, null, OPTIONS, OPTIONS[0]);
if (value == YES_OPTION) {
editor.save();
return 1;
}
else if (value == NO_OPTION) {
return 1;
}
else if (value == CANCEL_OPTION) {
return 0;
}
else if (value == YES_TO_ALL_OPTION) {
editor.save();
return 2;
}
else if (value == NO_TO_ALL_OPTION) {
return 3;
}
}
else if (autosave == 1) {
editor.save();
return 2;
}
else {
return 3;
}
}
}
if (autosave == 0) {
return 1;
}
else if (autosave == 1) {
return 2;
}
else {
return 3;
}
}
else if (tab.getComponentAt(index).getName().equals("SBML Editor")) {
if (tab.getComponentAt(index) instanceof SBML_Editor) {
if (((SBML_Editor) tab.getComponentAt(index)).isDirty()) {
if (autosave == 0) {
int value = JOptionPane.showOptionDialog(frame, "Do you want to save changes to " + tab.getTitleAt(index) + "?",
"Save Changes", JOptionPane.YES_NO_CANCEL_OPTION, JOptionPane.PLAIN_MESSAGE, null, OPTIONS, OPTIONS[0]);
if (value == YES_OPTION) {
((SBML_Editor) tab.getComponentAt(index)).save(false, "", true, true);
return 1;
}
else if (value == NO_OPTION) {
return 1;
}
else if (value == CANCEL_OPTION) {
return 0;
}
else if (value == YES_TO_ALL_OPTION) {
((SBML_Editor) tab.getComponentAt(index)).save(false, "", true, true);
return 2;
}
else if (value == NO_TO_ALL_OPTION) {
return 3;
}
}
else if (autosave == 1) {
((SBML_Editor) tab.getComponentAt(index)).save(false, "", true, true);
return 2;
}
else {
return 3;
}
}
}
if (autosave == 0) {
return 1;
}
else if (autosave == 1) {
return 2;
}
else {
return 3;
}
}
else if (tab.getComponentAt(index).getName().contains("Graph") || tab.getComponentAt(index).getName().equals("Histogram")) {
if (tab.getComponentAt(index) instanceof Graph) {
if (((Graph) tab.getComponentAt(index)).hasChanged()) {
if (autosave == 0) {
int value = JOptionPane.showOptionDialog(frame, "Do you want to save changes to " + tab.getTitleAt(index) + "?",
"Save Changes", JOptionPane.YES_NO_CANCEL_OPTION, JOptionPane.PLAIN_MESSAGE, null, OPTIONS, OPTIONS[0]);
if (value == YES_OPTION) {
((Graph) tab.getComponentAt(index)).save();
return 1;
}
else if (value == NO_OPTION) {
return 1;
}
else if (value == CANCEL_OPTION) {
return 0;
}
else if (value == YES_TO_ALL_OPTION) {
((Graph) tab.getComponentAt(index)).save();
return 2;
}
else if (value == NO_TO_ALL_OPTION) {
return 3;
}
}
else if (autosave == 1) {
((Graph) tab.getComponentAt(index)).save();
return 2;
}
else {
return 3;
}
}
}
if (autosave == 0) {
return 1;
}
else if (autosave == 1) {
return 2;
}
else {
return 3;
}
}
else {
if (tab.getComponentAt(index) instanceof JTabbedPane) {
for (int i = 0; i < ((JTabbedPane) tab.getComponentAt(index)).getTabCount(); i++) {
if (((JTabbedPane) tab.getComponentAt(index)).getComponentAt(i).getName() != null) {
if (((JTabbedPane) tab.getComponentAt(index)).getComponentAt(i).getName().equals("Simulate")) {
if (((Reb2Sac) ((JTabbedPane) tab.getComponentAt(index)).getComponent(i)).hasChanged()) {
if (autosave == 0) {
int value = JOptionPane.showOptionDialog(frame,
"Do you want to save simulation option changes for " + tab.getTitleAt(index) + "?", "Save Changes",
JOptionPane.YES_NO_CANCEL_OPTION, JOptionPane.PLAIN_MESSAGE, null, OPTIONS, OPTIONS[0]);
if (value == YES_OPTION) {
((Reb2Sac) ((JTabbedPane) tab.getComponentAt(index)).getComponent(i)).save();
}
else if (value == CANCEL_OPTION) {
return 0;
}
else if (value == YES_TO_ALL_OPTION) {
((Reb2Sac) ((JTabbedPane) tab.getComponentAt(index)).getComponent(i)).save();
autosave = 1;
}
else if (value == NO_TO_ALL_OPTION) {
autosave = 2;
}
}
else if (autosave == 1) {
((Reb2Sac) ((JTabbedPane) tab.getComponentAt(index)).getComponent(i)).save();
}
}
}
else if (((JTabbedPane) tab.getComponentAt(index)).getComponent(i).getName().equals("SBML Editor")) {
if (((SBML_Editor) ((JTabbedPane) tab.getComponentAt(index)).getComponent(i)).isDirty()) {
if (autosave == 0) {
int value = JOptionPane.showOptionDialog(frame,
"Do you want to save parameter changes for " + tab.getTitleAt(index) + "?", "Save Changes",
JOptionPane.YES_NO_CANCEL_OPTION, JOptionPane.PLAIN_MESSAGE, null, OPTIONS, OPTIONS[0]);
if (value == YES_OPTION) {
((SBML_Editor) ((JTabbedPane) tab.getComponentAt(index)).getComponent(i)).save(false, "", true, true);
}
else if (value == CANCEL_OPTION) {
return 0;
}
else if (value == YES_TO_ALL_OPTION) {
((SBML_Editor) ((JTabbedPane) tab.getComponentAt(index)).getComponent(i)).save(false, "", true, true);
autosave = 1;
}
else if (value == NO_TO_ALL_OPTION) {
autosave = 2;
}
}
else if (autosave == 1) {
((SBML_Editor) ((JTabbedPane) tab.getComponentAt(index)).getComponent(i)).save(false, "", true, true);
}
}
}
/*
* else if (((JTabbedPane)
* tab.getComponentAt(index)).getComponent(i)
* .getName().equals("GCM Editor")) { if
* (((GCM2SBMLEditor) ((JTabbedPane)
* tab.getComponentAt(index))
* .getComponent(i)).isDirty()) { if (autosave == 0) {
* int value = JOptionPane.showOptionDialog(frame,
* "Do you want to save parameter changes for " +
* tab.getTitleAt(index) + "?", "Save Changes",
* JOptionPane.YES_NO_CANCEL_OPTION,
* JOptionPane.PLAIN_MESSAGE, null, OPTIONS,
* OPTIONS[0]); if (value == YES_OPTION) {
* ((GCM2SBMLEditor) ((JTabbedPane)
* tab.getComponentAt(index))
* .getComponent(i)).saveParams(false, ""); } else if
* (value == CANCEL_OPTION) { return 0; } else if (value
* == YES_TO_ALL_OPTION) { ((GCM2SBMLEditor)
* ((JTabbedPane) tab.getComponentAt(index))
* .getComponent(i)).saveParams(false, ""); autosave =
* 1; } else if (value == NO_TO_ALL_OPTION) { autosave =
* 2; } } else if (autosave == 1) { ((GCM2SBMLEditor)
* ((JTabbedPane) tab.getComponentAt(index))
* .getComponent(i)).saveParams(false, ""); } } }
*/
else if (((JTabbedPane) tab.getComponentAt(index)).getComponent(i) instanceof MovieContainer) {
if (((MovieContainer) ((JTabbedPane) tab.getComponentAt(index)).getComponent(i)).getGCM2SBMLEditor().isDirty()
|| ((MovieContainer) ((JTabbedPane) tab.getComponentAt(index)).getComponent(i)).getIsDirty()) {
if (autosave == 0) {
int value = JOptionPane.showOptionDialog(frame,
"Do you want to save parameter changes for " + tab.getTitleAt(index) + "?", "Save Changes",
JOptionPane.YES_NO_CANCEL_OPTION, JOptionPane.PLAIN_MESSAGE, null, OPTIONS, OPTIONS[0]);
if (value == YES_OPTION) {
((MovieContainer) ((JTabbedPane) tab.getComponentAt(index)).getComponent(i)).savePreferences();
}
else if (value == CANCEL_OPTION) {
return 0;
}
else if (value == YES_TO_ALL_OPTION) {
((MovieContainer) ((JTabbedPane) tab.getComponentAt(index)).getComponent(i)).savePreferences();
autosave = 1;
}
else if (value == NO_TO_ALL_OPTION) {
autosave = 2;
}
}
else if (autosave == 1) {
((MovieContainer) ((JTabbedPane) tab.getComponentAt(index)).getComponent(i)).savePreferences();
}
}
}
else if (((JTabbedPane) tab.getComponentAt(index)).getComponent(i).getName().equals("Learn")) {
if (((JTabbedPane) tab.getComponentAt(index)).getComponent(i) instanceof LearnGCM) {
if (((LearnGCM) ((JTabbedPane) tab.getComponentAt(index)).getComponent(i)).hasChanged()) {
if (autosave == 0) {
int value = JOptionPane.showOptionDialog(frame,
"Do you want to save learn option changes for " + tab.getTitleAt(index) + "?", "Save Changes",
JOptionPane.YES_NO_CANCEL_OPTION, JOptionPane.PLAIN_MESSAGE, null, OPTIONS, OPTIONS[0]);
if (value == YES_OPTION) {
if (((JTabbedPane) tab.getComponentAt(index)).getComponent(i) instanceof LearnGCM) {
((LearnGCM) ((JTabbedPane) tab.getComponentAt(index)).getComponent(i)).save();
}
}
else if (value == CANCEL_OPTION) {
return 0;
}
else if (value == YES_TO_ALL_OPTION) {
if (((JTabbedPane) tab.getComponentAt(index)).getComponent(i) instanceof LearnGCM) {
((LearnGCM) ((JTabbedPane) tab.getComponentAt(index)).getComponent(i)).save();
}
autosave = 1;
}
else if (value == NO_TO_ALL_OPTION) {
autosave = 2;
}
}
else if (autosave == 1) {
if (((JTabbedPane) tab.getComponentAt(index)).getComponent(i) instanceof LearnGCM) {
((LearnGCM) ((JTabbedPane) tab.getComponentAt(index)).getComponent(i)).save();
}
}
}
}
if (((JTabbedPane) tab.getComponentAt(index)).getComponent(i) instanceof LearnLHPN) {
if (((LearnLHPN) ((JTabbedPane) tab.getComponentAt(index)).getComponent(i)).hasChanged()) {
if (autosave == 0) {
int value = JOptionPane.showOptionDialog(frame,
"Do you want to save learn option changes for " + tab.getTitleAt(index) + "?", "Save Changes",
JOptionPane.YES_NO_CANCEL_OPTION, JOptionPane.PLAIN_MESSAGE, null, OPTIONS, OPTIONS[0]);
if (value == YES_OPTION) {
if (((JTabbedPane) tab.getComponentAt(index)).getComponent(i) instanceof LearnLHPN) {
((LearnLHPN) ((JTabbedPane) tab.getComponentAt(index)).getComponent(i)).save();
}
}
else if (value == CANCEL_OPTION) {
return 0;
}
else if (value == YES_TO_ALL_OPTION) {
if (((JTabbedPane) tab.getComponentAt(index)).getComponent(i) instanceof LearnLHPN) {
((LearnLHPN) ((JTabbedPane) tab.getComponentAt(index)).getComponent(i)).save();
}
autosave = 1;
}
else if (value == NO_TO_ALL_OPTION) {
autosave = 2;
}
}
else if (autosave == 1) {
if (((JTabbedPane) tab.getComponentAt(index)).getComponent(i) instanceof LearnLHPN) {
((LearnLHPN) ((JTabbedPane) tab.getComponentAt(index)).getComponent(i)).save();
}
}
}
}
}
else if (((JTabbedPane) tab.getComponentAt(index)).getComponent(i).getName().equals("Data Manager")) {
if (((JTabbedPane) tab.getComponentAt(index)).getComponent(i) instanceof DataManager) {
((DataManager) ((JTabbedPane) tab.getComponentAt(index)).getComponent(i)).saveChanges(tab.getTitleAt(index));
}
}
else if (((JTabbedPane) tab.getComponentAt(index)).getComponent(i).getName().contains("Graph")) {
if (((JTabbedPane) tab.getComponentAt(index)).getComponent(i) instanceof Graph) {
if (((Graph) ((JTabbedPane) tab.getComponentAt(index)).getComponent(i)).hasChanged()) {
if (autosave == 0) {
int value = JOptionPane.showOptionDialog(frame,
"Do you want to save graph changes for " + tab.getTitleAt(index) + "?", "Save Changes",
JOptionPane.YES_NO_CANCEL_OPTION, JOptionPane.PLAIN_MESSAGE, null, OPTIONS, OPTIONS[0]);
if (value == YES_OPTION) {
if (((JTabbedPane) tab.getComponentAt(index)).getComponent(i) instanceof Graph) {
Graph g = ((Graph) ((JTabbedPane) tab.getComponentAt(index)).getComponent(i));
g.save();
}
}
else if (value == CANCEL_OPTION) {
return 0;
}
else if (value == YES_TO_ALL_OPTION) {
if (((JTabbedPane) tab.getComponentAt(index)).getComponent(i) instanceof Graph) {
Graph g = ((Graph) ((JTabbedPane) tab.getComponentAt(index)).getComponent(i));
g.save();
}
autosave = 1;
}
else if (value == NO_TO_ALL_OPTION) {
autosave = 2;
}
}
else if (autosave == 1) {
if (((JTabbedPane) tab.getComponentAt(index)).getComponent(i) instanceof Graph) {
Graph g = ((Graph) ((JTabbedPane) tab.getComponentAt(index)).getComponent(i));
g.save();
}
}
}
}
}
}
}
}
else if (tab.getComponentAt(index) instanceof JPanel) {
if ((tab.getComponentAt(index)).getName().equals("Synthesis")) {
Component[] array = ((JPanel) tab.getComponentAt(index)).getComponents();
if (array[0] instanceof Synthesis) {
if (((Synthesis) array[0]).hasChanged()) {
if (autosave == 0) {
int value = JOptionPane.showOptionDialog(frame,
"Do you want to save synthesis option changes for " + tab.getTitleAt(index) + "?", "Save Changes",
JOptionPane.YES_NO_CANCEL_OPTION, JOptionPane.PLAIN_MESSAGE, null, OPTIONS, OPTIONS[0]);
if (value == YES_OPTION) {
if (array[0] instanceof Synthesis) {
((Synthesis) array[0]).save();
}
}
else if (value == CANCEL_OPTION) {
return 0;
}
else if (value == YES_TO_ALL_OPTION) {
if (array[0] instanceof Synthesis) {
((Synthesis) array[0]).save();
}
autosave = 1;
}
else if (value == NO_TO_ALL_OPTION) {
autosave = 2;
}
}
else if (autosave == 1) {
if (array[0] instanceof Synthesis) {
((Synthesis) array[0]).save();
}
}
}
}
}
else if (tab.getComponentAt(index).getName().equals("Verification")) {
Component[] array = ((JPanel) tab.getComponentAt(index)).getComponents();
if (array[0] instanceof Verification) {
if (((Verification) array[0]).hasChanged()) {
if (autosave == 0) {
int value = JOptionPane.showOptionDialog(frame,
"Do you want to save verification option changes for " + tab.getTitleAt(index) + "?", "Save Changes",
JOptionPane.YES_NO_CANCEL_OPTION, JOptionPane.PLAIN_MESSAGE, null, OPTIONS, OPTIONS[0]);
if (value == YES_OPTION) {
((Verification) array[0]).save();
}
else if (value == CANCEL_OPTION) {
return 0;
}
else if (value == YES_TO_ALL_OPTION) {
((Verification) array[0]).save();
autosave = 1;
}
else if (value == NO_TO_ALL_OPTION) {
autosave = 2;
}
}
else if (autosave == 1) {
((Verification) array[0]).save();
}
}
}
}
}
if (autosave == 0) {
return 1;
}
else if (autosave == 1) {
return 2;
}
else {
return 3;
}
}
}
/**
* Saves a circuit from a learn view to the project view
*/
public void saveGcm(String filename, String path) {
try {
if (overwrite(root + separator + filename, filename)) {
FileOutputStream out = new FileOutputStream(new File(root + separator + filename));
FileInputStream in = new FileInputStream(new File(path));
int read = in.read();
while (read != -1) {
out.write(read);
read = in.read();
}
in.close();
out.close();
addToTree(filename);
}
}
catch (Exception e1) {
JOptionPane.showMessageDialog(frame, "Unable to save genetic circuit.", "Error", JOptionPane.ERROR_MESSAGE);
}
}
/**
* Saves a circuit from a learn view to the project view
*/
public void saveLhpn(String filename, String path) {
try {
if (overwrite(root + separator + filename, filename)) {
BufferedWriter out = new BufferedWriter(new FileWriter(root + separator + filename));
BufferedReader in = new BufferedReader(new FileReader(path));
String str;
while ((str = in.readLine()) != null) {
out.write(str + "\n");
}
in.close();
out.close();
addToTree(filename);
}
}
catch (IOException e1) {
JOptionPane.showMessageDialog(frame, "Unable to save LPN.", "Error", JOptionPane.ERROR_MESSAGE);
}
}
public void copySFiles(String filename, String directory) {
StringBuffer data = new StringBuffer();
try {
BufferedReader in = new BufferedReader(new FileReader(directory + separator + filename));
String str;
while ((str = in.readLine()) != null) {
data.append(str + "\n");
}
in.close();
}
catch (IOException e) {
e.printStackTrace();
throw new IllegalStateException("Error opening file");
}
Pattern sLinePattern = Pattern.compile(SFILELINE);
Matcher sLineMatcher = sLinePattern.matcher(data);
while (sLineMatcher.find()) {
String sFilename = sLineMatcher.group(1);
try {
File newFile = new File(directory + separator + sFilename);
newFile.createNewFile();
FileOutputStream copyin = new FileOutputStream(newFile);
FileInputStream copyout = new FileInputStream(new File(root + separator + sFilename));
int read = copyout.read();
while (read != -1) {
copyin.write(read);
read = copyout.read();
}
copyin.close();
copyout.close();
}
catch (IOException e) {
e.printStackTrace();
JOptionPane.showMessageDialog(Gui.frame, "Cannot copy file " + sFilename, "Copy Error", JOptionPane.ERROR_MESSAGE);
}
}
}
public void updateMenu(boolean logEnabled, boolean othersEnabled) {
viewLearnedModel.setEnabled(othersEnabled);
viewCoverage.setEnabled(othersEnabled);
save.setEnabled(othersEnabled);
viewLog.setEnabled(logEnabled);
// Do saveas & save button too
}
public void mousePressed(MouseEvent e) {
executePopupMenu(e);
}
public void mouseReleased(MouseEvent e) {
executePopupMenu(e);
}
public void executePopupMenu(MouseEvent e) {
if (e.getSource() instanceof JTree && tree.getFile() != null && e.isPopupTrigger()) {
// frame.getGlassPane().setVisible(false);
popup.removeAll();
if (tree.getFile().length() > 4 && tree.getFile().substring(tree.getFile().length() - 5).equals(".sbml") || tree.getFile().length() > 3
&& tree.getFile().substring(tree.getFile().length() - 4).equals(".xml")) {
JMenuItem edit = new JMenuItem("View/Edit");
edit.addActionListener(this);
edit.addMouseListener(this);
edit.setActionCommand("sbmlEditor");
JMenuItem graph = new JMenuItem("View Model");
graph.addActionListener(this);
graph.addMouseListener(this);
graph.setActionCommand("graphTree");
JMenuItem browse = new JMenuItem("View Model in Browser");
browse.addActionListener(this);
browse.addMouseListener(this);
browse.setActionCommand("browse");
JMenuItem simulate = new JMenuItem("Create Analysis View");
simulate.addActionListener(this);
simulate.addMouseListener(this);
simulate.setActionCommand("simulate");
JMenuItem createLearn = new JMenuItem("Create Learn View");
createLearn.addActionListener(this);
createLearn.addMouseListener(this);
createLearn.setActionCommand("createLearn");
JMenuItem delete = new JMenuItem("Delete");
delete.addActionListener(this);
delete.addMouseListener(this);
delete.setActionCommand("delete");
JMenuItem copy = new JMenuItem("Copy");
copy.addActionListener(this);
copy.addMouseListener(this);
copy.setActionCommand("copy");
JMenuItem rename = new JMenuItem("Rename");
rename.addActionListener(this);
rename.addMouseListener(this);
rename.setActionCommand("rename");
popup.add(simulate);
popup.add(createLearn);
popup.addSeparator();
popup.add(graph);
popup.add(browse);
popup.addSeparator();
popup.add(edit);
popup.add(copy);
popup.add(rename);
popup.add(delete);
}
else if (tree.getFile().length() > 3 && tree.getFile().substring(tree.getFile().length() - 4).equals(".rdf")) {
JMenuItem view = new JMenuItem("View");
view.addActionListener(this);
view.addMouseListener(this);
view.setActionCommand("browseSbol");
JMenuItem copy = new JMenuItem("Copy");
copy.addActionListener(this);
copy.addMouseListener(this);
copy.setActionCommand("copy");
JMenuItem rename = new JMenuItem("Rename");
rename.addActionListener(this);
rename.addMouseListener(this);
rename.setActionCommand("rename");
JMenuItem delete = new JMenuItem("Delete");
delete.addActionListener(this);
delete.addMouseListener(this);
delete.setActionCommand("delete");
popup.add(view);
popup.add(copy);
popup.add(rename);
popup.add(delete);
}
else if (tree.getFile().length() > 3 && tree.getFile().substring(tree.getFile().length() - 4).equals(".gcm")) {
JMenuItem create = new JMenuItem("Create Analysis View");
create.addActionListener(this);
create.addMouseListener(this);
create.setActionCommand("createSim");
JMenuItem createLearn = new JMenuItem("Create Learn View");
createLearn.addActionListener(this);
createLearn.addMouseListener(this);
createLearn.setActionCommand("createLearn");
JMenuItem edit = new JMenuItem("View/Edit (graphical)");
edit.addActionListener(this);
edit.addMouseListener(this);
edit.setActionCommand("gcmEditor");
JMenuItem editText = new JMenuItem("View/Edit (tabular)");
editText.addActionListener(this);
editText.addMouseListener(this);
editText.setActionCommand("gcmTextEditor");
//JMenuItem graph = new JMenuItem("View Model");
//graph.addActionListener(this);
//graph.addMouseListener(this);
//graph.setActionCommand("graphTree");
JMenuItem delete = new JMenuItem("Delete");
delete.addActionListener(this);
delete.addMouseListener(this);
delete.setActionCommand("delete");
JMenuItem copy = new JMenuItem("Copy");
copy.addActionListener(this);
copy.addMouseListener(this);
copy.setActionCommand("copy");
JMenuItem rename = new JMenuItem("Rename");
rename.addActionListener(this);
rename.addMouseListener(this);
rename.setActionCommand("rename");
popup.add(create);
popup.add(createLearn);
popup.addSeparator();
//popup.add(graph);
//popup.addSeparator();
popup.add(edit);
popup.add(editText);
popup.add(copy);
popup.add(rename);
popup.add(delete);
}
else if (tree.getFile().length() > 3 && tree.getFile().substring(tree.getFile().length() - 4).equals(".vhd")) {
JMenuItem createSynthesis = new JMenuItem("Create Synthesis View");
createSynthesis.addActionListener(this);
createSynthesis.addMouseListener(this);
createSynthesis.setActionCommand("createSynthesis");
JMenuItem createAnalysis = new JMenuItem("Create Analysis View");
createAnalysis.addActionListener(this);
createAnalysis.addMouseListener(this);
createAnalysis.setActionCommand("createAnalysis");
JMenuItem createLearn = new JMenuItem("Create Learn View");
createLearn.addActionListener(this);
createLearn.addMouseListener(this);
createLearn.setActionCommand("createLearn");
JMenuItem createVerification = new JMenuItem("Create Verification View");
createVerification.addActionListener(this);
createVerification.addMouseListener(this);
createVerification.setActionCommand("createVerify");
JMenuItem viewModel = new JMenuItem("View Model");
viewModel.addActionListener(this);
viewModel.addMouseListener(this);
viewModel.setActionCommand("viewModel");
JMenuItem delete = new JMenuItem("Delete");
delete.addActionListener(this);
delete.addMouseListener(this);
delete.setActionCommand("delete");
JMenuItem copy = new JMenuItem("Copy");
copy.addActionListener(this);
copy.addMouseListener(this);
copy.setActionCommand("copy");
JMenuItem rename = new JMenuItem("Rename");
rename.addActionListener(this);
rename.addMouseListener(this);
rename.setActionCommand("rename");
if (atacs) {
popup.add(createSynthesis);
}
// popup.add(createAnalysis);
if (lema) {
popup.add(createLearn);
}
popup.add(createVerification);
popup.addSeparator();
popup.add(viewModel);
popup.addSeparator();
popup.add(copy);
popup.add(rename);
popup.add(delete);
}
else if (tree.getFile().length() > 4 && tree.getFile().substring(tree.getFile().length() - 5).equals(".vams")) {
JMenuItem viewModel = new JMenuItem("View Model");
viewModel.addActionListener(this);
viewModel.addMouseListener(this);
viewModel.setActionCommand("viewModel");
JMenuItem delete = new JMenuItem("Delete");
delete.addActionListener(this);
delete.addMouseListener(this);
delete.setActionCommand("delete");
JMenuItem copy = new JMenuItem("Copy");
copy.addActionListener(this);
copy.addMouseListener(this);
copy.setActionCommand("copy");
JMenuItem rename = new JMenuItem("Rename");
rename.addActionListener(this);
rename.addMouseListener(this);
rename.setActionCommand("rename");
if (lema) {
popup.add(viewModel);
popup.addSeparator();
popup.add(copy);
popup.add(rename);
popup.add(delete);
}
}
else if (tree.getFile().length() > 2 && tree.getFile().substring(tree.getFile().length() - 3).equals(".sv")) {
JMenuItem viewModel = new JMenuItem("View Model");
viewModel.addActionListener(this);
viewModel.addMouseListener(this);
viewModel.setActionCommand("viewModel");
JMenuItem delete = new JMenuItem("Delete");
delete.addActionListener(this);
delete.addMouseListener(this);
delete.setActionCommand("delete");
JMenuItem copy = new JMenuItem("Copy");
copy.addActionListener(this);
copy.addMouseListener(this);
copy.setActionCommand("copy");
JMenuItem rename = new JMenuItem("Rename");
rename.addActionListener(this);
rename.addMouseListener(this);
rename.setActionCommand("rename");
if (lema) {
popup.add(viewModel);
popup.addSeparator();
popup.add(copy);
popup.add(rename);
popup.add(delete);
}
}
else if (tree.getFile().length() > 1 && tree.getFile().substring(tree.getFile().length() - 2).equals(".g")) {
JMenuItem createSynthesis = new JMenuItem("Create Synthesis View");
createSynthesis.addActionListener(this);
createSynthesis.addMouseListener(this);
createSynthesis.setActionCommand("createSynthesis");
JMenuItem createAnalysis = new JMenuItem("Create Analysis View");
createAnalysis.addActionListener(this);
createAnalysis.addMouseListener(this);
createAnalysis.setActionCommand("createAnalysis");
JMenuItem createLearn = new JMenuItem("Create Learn View");
createLearn.addActionListener(this);
createLearn.addMouseListener(this);
createLearn.setActionCommand("createLearn");
JMenuItem createVerification = new JMenuItem("Create Verification View");
createVerification.addActionListener(this);
createVerification.addMouseListener(this);
createVerification.setActionCommand("createVerify");
JMenuItem viewModel = new JMenuItem("View Model");
viewModel.addActionListener(this);
viewModel.addMouseListener(this);
viewModel.setActionCommand("viewModel");
JMenuItem delete = new JMenuItem("Delete");
delete.addActionListener(this);
delete.addMouseListener(this);
delete.setActionCommand("delete");
JMenuItem copy = new JMenuItem("Copy");
copy.addActionListener(this);
copy.addMouseListener(this);
copy.setActionCommand("copy");
JMenuItem rename = new JMenuItem("Rename");
rename.addActionListener(this);
rename.addMouseListener(this);
rename.setActionCommand("rename");
if (atacs) {
popup.add(createSynthesis);
}
// popup.add(createAnalysis);
// if (lema) {
// popup.add(createLearn);
popup.add(createVerification);
popup.addSeparator();
popup.add(viewModel);
popup.addSeparator();
popup.add(copy);
popup.add(rename);
popup.add(delete);
}
else if (tree.getFile().length() > 3 && tree.getFile().substring(tree.getFile().length() - 4).equals(".lpn")) {
JMenuItem createSynthesis = new JMenuItem("Create Synthesis View");
createSynthesis.addActionListener(this);
createSynthesis.addMouseListener(this);
createSynthesis.setActionCommand("createSynthesis");
JMenuItem createAnalysis = new JMenuItem("Create Analysis View");
createAnalysis.addActionListener(this);
createAnalysis.addMouseListener(this);
createAnalysis.setActionCommand("createAnalysis");
JMenuItem createLearn = new JMenuItem("Create Learn View");
createLearn.addActionListener(this);
createLearn.addMouseListener(this);
createLearn.setActionCommand("createLearn");
JMenuItem createVerification = new JMenuItem("Create Verification View");
createVerification.addActionListener(this);
createVerification.addMouseListener(this);
createVerification.setActionCommand("createVerify");
JMenuItem convertToSBML = new JMenuItem("Convert To SBML");
convertToSBML.addActionListener(this);
convertToSBML.addMouseListener(this);
convertToSBML.setActionCommand("convertToSBML");
JMenuItem convertToVerilog = new JMenuItem("Save as Verilog");
convertToVerilog.addActionListener(this);
convertToVerilog.addMouseListener(this);
convertToVerilog.setActionCommand("convertToVerilog");
JMenuItem viewModel = new JMenuItem("View Model");
viewModel.addActionListener(this);
viewModel.addMouseListener(this);
viewModel.setActionCommand("viewModel");
JMenuItem view = new JMenuItem("View/Edit");
view.addActionListener(this);
view.addMouseListener(this);
view.setActionCommand("openLPN");
JMenuItem delete = new JMenuItem("Delete");
delete.addActionListener(this);
delete.addMouseListener(this);
delete.setActionCommand("delete");
JMenuItem copy = new JMenuItem("Copy");
copy.addActionListener(this);
copy.addMouseListener(this);
copy.setActionCommand("copy");
JMenuItem rename = new JMenuItem("Rename");
rename.addActionListener(this);
rename.addMouseListener(this);
rename.setActionCommand("rename");
if (atacs) {
popup.add(createSynthesis);
}
if (LPN2SBML) {
popup.add(createAnalysis);
}
if (lema) {
popup.add(createLearn);
popup.addSeparator();
popup.add(viewModel);
}
if (atacs || lema) {
popup.add(createVerification);
}
// popup.add(createAnalysis); // TODO
// popup.add(viewStateGraph);
/*
if (!atacs && !lema && LPN2SBML) {
popup.add(convertToSBML); // changed the order. SB
}
*/
if (atacs || lema) {
popup.add(convertToVerilog);
}
// popup.add(markovAnalysis);
popup.addSeparator();
popup.add(view);
popup.add(copy);
popup.add(rename);
popup.add(delete);
}
else if (tree.getFile().length() > 1 && tree.getFile().substring(tree.getFile().length() - 2).equals(".s")) {
JMenuItem createAnalysis = new JMenuItem("Create Analysis View");
createAnalysis.addActionListener(this);
createAnalysis.addMouseListener(this);
createAnalysis.setActionCommand("createAnalysis");
JMenuItem createVerification = new JMenuItem("Create Verification View");
createVerification.addActionListener(this);
createVerification.addMouseListener(this);
createVerification.setActionCommand("createVerify");
JMenuItem delete = new JMenuItem("Delete");
delete.addActionListener(this);
delete.addMouseListener(this);
delete.setActionCommand("delete");
JMenuItem copy = new JMenuItem("Copy");
copy.addActionListener(this);
copy.addMouseListener(this);
copy.setActionCommand("copy");
JMenuItem rename = new JMenuItem("Rename");
rename.addActionListener(this);
rename.addMouseListener(this);
rename.setActionCommand("rename");
popup.add(createAnalysis);
popup.add(createVerification);
popup.addSeparator();
popup.add(copy);
popup.add(rename);
popup.add(delete);
}
else if (tree.getFile().length() > 4 && tree.getFile().substring(tree.getFile().length() - 5).equals(".inst")) {
JMenuItem delete = new JMenuItem("Delete");
delete.addActionListener(this);
delete.addMouseListener(this);
delete.setActionCommand("delete");
JMenuItem copy = new JMenuItem("Copy");
copy.addActionListener(this);
copy.addMouseListener(this);
copy.setActionCommand("copy");
JMenuItem rename = new JMenuItem("Rename");
rename.addActionListener(this);
rename.addMouseListener(this);
rename.setActionCommand("rename");
popup.add(copy);
popup.add(rename);
popup.add(delete);
}
else if (tree.getFile().length() > 3 && tree.getFile().substring(tree.getFile().length() - 4).equals(".csp")) {
JMenuItem createSynthesis = new JMenuItem("Create Synthesis View");
createSynthesis.addActionListener(this);
createSynthesis.addMouseListener(this);
createSynthesis.setActionCommand("createSynthesis");
JMenuItem createAnalysis = new JMenuItem("Create Analysis View");
createAnalysis.addActionListener(this);
createAnalysis.addMouseListener(this);
createAnalysis.setActionCommand("createAnalysis");
JMenuItem createLearn = new JMenuItem("Create Learn View");
createLearn.addActionListener(this);
createLearn.addMouseListener(this);
createLearn.setActionCommand("createLearn");
JMenuItem createVerification = new JMenuItem("Create Verification View");
createVerification.addActionListener(this);
createVerification.addMouseListener(this);
createVerification.setActionCommand("createVerify");
JMenuItem viewModel = new JMenuItem("View Model");
viewModel.addActionListener(this);
viewModel.addMouseListener(this);
viewModel.setActionCommand("viewModel");
JMenuItem delete = new JMenuItem("Delete");
delete.addActionListener(this);
delete.addMouseListener(this);
delete.setActionCommand("delete");
JMenuItem copy = new JMenuItem("Copy");
copy.addActionListener(this);
copy.addMouseListener(this);
copy.setActionCommand("copy");
JMenuItem rename = new JMenuItem("Rename");
rename.addActionListener(this);
rename.addMouseListener(this);
rename.setActionCommand("rename");
if (atacs) {
popup.add(createSynthesis);
}
// popup.add(createAnalysis);
if (lema) {
popup.add(createLearn);
}
popup.add(createVerification);
popup.addSeparator();
popup.add(viewModel);
popup.addSeparator();
popup.add(copy);
popup.add(rename);
popup.add(delete);
}
else if (tree.getFile().length() > 3 && tree.getFile().substring(tree.getFile().length() - 4).equals(".hse")) {
JMenuItem createSynthesis = new JMenuItem("Create Synthesis View");
createSynthesis.addActionListener(this);
createSynthesis.addMouseListener(this);
createSynthesis.setActionCommand("createSynthesis");
JMenuItem createAnalysis = new JMenuItem("Create Analysis View");
createAnalysis.addActionListener(this);
createAnalysis.addMouseListener(this);
createAnalysis.setActionCommand("createAnalysis");
JMenuItem createLearn = new JMenuItem("Create Learn View");
createLearn.addActionListener(this);
createLearn.addMouseListener(this);
createLearn.setActionCommand("createLearn");
JMenuItem createVerification = new JMenuItem("Create Verification View");
createVerification.addActionListener(this);
createVerification.addMouseListener(this);
createVerification.setActionCommand("createVerify");
JMenuItem viewModel = new JMenuItem("View Model");
viewModel.addActionListener(this);
viewModel.addMouseListener(this);
viewModel.setActionCommand("viewModel");
JMenuItem delete = new JMenuItem("Delete");
delete.addActionListener(this);
delete.addMouseListener(this);
delete.setActionCommand("delete");
JMenuItem copy = new JMenuItem("Copy");
copy.addActionListener(this);
copy.addMouseListener(this);
copy.setActionCommand("copy");
JMenuItem rename = new JMenuItem("Rename");
rename.addActionListener(this);
rename.addMouseListener(this);
rename.setActionCommand("rename");
if (atacs) {
popup.add(createSynthesis);
}
// popup.add(createAnalysis);
if (lema) {
popup.add(createLearn);
}
popup.add(createVerification);
popup.addSeparator();
popup.add(viewModel);
popup.addSeparator();
popup.add(copy);
popup.add(rename);
popup.add(delete);
}
else if (tree.getFile().length() > 3 && tree.getFile().substring(tree.getFile().length() - 4).equals(".unc")) {
JMenuItem createSynthesis = new JMenuItem("Create Synthesis View");
createSynthesis.addActionListener(this);
createSynthesis.addMouseListener(this);
createSynthesis.setActionCommand("createSynthesis");
JMenuItem viewModel = new JMenuItem("View Model");
viewModel.addActionListener(this);
viewModel.addMouseListener(this);
viewModel.setActionCommand("viewModel");
JMenuItem delete = new JMenuItem("Delete");
delete.addActionListener(this);
delete.addMouseListener(this);
delete.setActionCommand("delete");
JMenuItem copy = new JMenuItem("Copy");
copy.addActionListener(this);
copy.addMouseListener(this);
copy.setActionCommand("copy");
JMenuItem rename = new JMenuItem("Rename");
rename.addActionListener(this);
rename.addMouseListener(this);
rename.setActionCommand("rename");
popup.add(createSynthesis);
popup.addSeparator();
popup.add(viewModel);
popup.addSeparator();
popup.add(copy);
popup.add(rename);
popup.add(delete);
}
else if (tree.getFile().length() > 3 && tree.getFile().substring(tree.getFile().length() - 4).equals(".rsg")) {
JMenuItem createSynthesis = new JMenuItem("Create Synthesis View");
createSynthesis.addActionListener(this);
createSynthesis.addMouseListener(this);
createSynthesis.setActionCommand("createSynthesis");
JMenuItem viewModel = new JMenuItem("View Model");
viewModel.addActionListener(this);
viewModel.addMouseListener(this);
viewModel.setActionCommand("viewModel");
JMenuItem delete = new JMenuItem("Delete");
delete.addActionListener(this);
delete.addMouseListener(this);
delete.setActionCommand("delete");
JMenuItem copy = new JMenuItem("Copy");
copy.addActionListener(this);
copy.addMouseListener(this);
copy.setActionCommand("copy");
JMenuItem rename = new JMenuItem("Rename");
rename.addActionListener(this);
rename.addMouseListener(this);
rename.setActionCommand("rename");
popup.add(createSynthesis);
popup.addSeparator();
popup.add(viewModel);
popup.addSeparator();
popup.add(copy);
popup.add(rename);
popup.add(delete);
}
else if (tree.getFile().length() > 3 && tree.getFile().substring(tree.getFile().length() - 4).equals(".grf")) {
JMenuItem edit = new JMenuItem("View/Edit");
edit.addActionListener(this);
edit.addMouseListener(this);
edit.setActionCommand("openGraph");
JMenuItem delete = new JMenuItem("Delete");
delete.addActionListener(this);
delete.addMouseListener(this);
delete.setActionCommand("delete");
JMenuItem copy = new JMenuItem("Copy");
copy.addActionListener(this);
copy.addMouseListener(this);
copy.setActionCommand("copy");
JMenuItem rename = new JMenuItem("Rename");
rename.addActionListener(this);
rename.addMouseListener(this);
rename.setActionCommand("rename");
popup.add(edit);
popup.add(copy);
popup.add(rename);
popup.add(delete);
}
else if (tree.getFile().length() > 3 && tree.getFile().substring(tree.getFile().length() - 4).equals(".prb")) {
JMenuItem edit = new JMenuItem("View/Edit");
edit.addActionListener(this);
edit.addMouseListener(this);
edit.setActionCommand("openHistogram");
JMenuItem delete = new JMenuItem("Delete");
delete.addActionListener(this);
delete.addMouseListener(this);
delete.setActionCommand("delete");
JMenuItem copy = new JMenuItem("Copy");
copy.addActionListener(this);
copy.addMouseListener(this);
copy.setActionCommand("copy");
JMenuItem rename = new JMenuItem("Rename");
rename.addActionListener(this);
rename.addMouseListener(this);
rename.setActionCommand("rename");
popup.add(edit);
popup.add(copy);
popup.add(rename);
popup.add(delete);
}
else if (new File(tree.getFile()).isDirectory() && !tree.getFile().equals(root)) {
boolean sim = false;
boolean synth = false;
boolean ver = false;
boolean learn = false;
for (String s : new File(tree.getFile()).list()) {
if (s.length() > 3 && s.substring(s.length() - 4).equals(".sim")) {
sim = true;
}
if (s.length() > 3 && s.substring(s.length() - 4).equals(".syn")) {
synth = true;
}
if (s.length() > 3 && s.substring(s.length() - 4).equals(".ver")) {
ver = true;
}
if (s.length() > 3 && s.substring(s.length() - 4).equals(".lrn")) {
learn = true;
}
}
JMenuItem open;
if (sim) {
open = new JMenuItem("Open Analysis View");
open.addActionListener(this);
open.addMouseListener(this);
open.setActionCommand("openSim");
popup.add(open);
}
else if (synth) {
open = new JMenuItem("Open Synthesis View");
open.addActionListener(this);
open.addMouseListener(this);
open.setActionCommand("openSynth");
popup.add(open);
}
else if (ver) {
open = new JMenuItem("Open Verification View");
open.addActionListener(this);
open.addMouseListener(this);
open.setActionCommand("openVerification");
popup.add(open);
}
else if (learn) {
open = new JMenuItem("Open Learn View");
open.addActionListener(this);
open.addMouseListener(this);
open.setActionCommand("openLearn");
popup.add(open);
}
if (sim || ver || synth || learn) {
JMenuItem delete = new JMenuItem("Delete");
delete.addActionListener(this);
delete.addMouseListener(this);
delete.setActionCommand("deleteSim");
JMenuItem copy = new JMenuItem("Copy");
copy.addActionListener(this);
copy.addMouseListener(this);
copy.setActionCommand("copy");
JMenuItem rename = new JMenuItem("Rename");
rename.addActionListener(this);
rename.addMouseListener(this);
rename.setActionCommand("rename");
popup.addSeparator();
popup.add(copy);
popup.add(rename);
popup.add(delete);
}
}
if (popup.getComponentCount() != 0) {
popup.show(e.getComponent(), e.getX(), e.getY());
}
}
}
public void executeMouseClickEvent(MouseEvent e) {
if (!(e.getSource() instanceof JTree)) {
enableTabMenu(tab.getSelectedIndex());
// frame.getGlassPane().setVisible(true);
}
else if (e.getButton() == MouseEvent.BUTTON1 && e.getClickCount() == 2 && e.getSource() instanceof JTree && tree.getFile() != null) {
if (tree.getFile().length() >= 5 && tree.getFile().substring(tree.getFile().length() - 5).equals(".sbml") || tree.getFile().length() >= 4
&& tree.getFile().substring(tree.getFile().length() - 4).equals(".xml")) {
openSBML(tree.getFile());
}
else if (tree.getFile().length() >= 4 && tree.getFile().substring(tree.getFile().length() - 4).equals(".gcm")) {
openGCM(false);
}
else if (tree.getFile().length() >= 4 && tree.getFile().substring(tree.getFile().length() - 4).equals(".rdf")) {
openSBOL();
}
else if (tree.getFile().length() >= 4 && tree.getFile().substring(tree.getFile().length() - 4).equals(".vhd")) {
openModel("VHDL");
}
else if (tree.getFile().length() >= 2 && tree.getFile().substring(tree.getFile().length() - 2).equals(".s")) {
openModel("Assembly File");
}
else if (tree.getFile().length() >= 5 && tree.getFile().substring(tree.getFile().length() - 5).equals(".inst")) {
openModel("Instruction File");
}
else if (tree.getFile().length() >= 5 && tree.getFile().substring(tree.getFile().length() - 5).equals(".vams")) {
openModel("Verilog-AMS");
}
else if (tree.getFile().length() >= 3 && tree.getFile().substring(tree.getFile().length() - 3).equals(".sv")) {
openModel("SystemVerilog");
}
else if (tree.getFile().length() >= 2 && tree.getFile().substring(tree.getFile().length() - 2).equals(".g")) {
openModel("Petri Net");
}
else if (tree.getFile().length() >= 4 && tree.getFile().substring(tree.getFile().length() - 4).equals(".lpn")) {
openLPN();
}
else if (tree.getFile().length() >= 4 && tree.getFile().substring(tree.getFile().length() - 4).equals(".csp")) {
openModel("CSP");
}
else if (tree.getFile().length() >= 4 && tree.getFile().substring(tree.getFile().length() - 4).equals(".hse")) {
openModel("Handshaking Expansion");
}
else if (tree.getFile().length() >= 4 && tree.getFile().substring(tree.getFile().length() - 4).equals(".unc")) {
openModel("Extended Burst-Mode Machine");
}
else if (tree.getFile().length() >= 4 && tree.getFile().substring(tree.getFile().length() - 4).equals(".rsg")) {
openModel("Reduced State Graph");
}
else if (tree.getFile().length() >= 4 && tree.getFile().substring(tree.getFile().length() - 4).equals(".cir")) {
openModel("Spice Circuit");
}
else if (tree.getFile().length() >= 4 && tree.getFile().substring(tree.getFile().length() - 4).equals(".grf")) {
openGraph();
}
else if (tree.getFile().length() >= 4 && tree.getFile().substring(tree.getFile().length() - 4).equals(".prb")) {
openHistogram();
}
else if (new File(tree.getFile()).isDirectory() && !tree.getFile().equals(root)) {
boolean sim = false;
boolean synth = false;
boolean ver = false;
boolean learn = false;
for (String s : new File(tree.getFile()).list()) {
if (s.length() > 3 && s.substring(s.length() - 4).equals(".sim")) {
sim = true;
}
else if (s.length() > 3 && s.substring(s.length() - 4).equals(".syn")) {
synth = true;
}
else if (s.length() > 3 && s.substring(s.length() - 4).equals(".ver")) {
ver = true;
}
else if (s.length() > 3 && s.substring(s.length() - 4).equals(".lrn")) {
learn = true;
}
}
if (sim) {
try {
openSim();
}
catch (Exception e0) {
}
}
else if (synth) {
openSynth();
}
else if (ver) {
openVerify();
}
else if (learn) {
if (lema) {
openLearnLHPN();
}
else {
openLearn();
}
}
}
}
else {
enableTreeMenu();
return;
}
enableTabMenu(tab.getSelectedIndex());
}
public void mouseMoved(MouseEvent e) {
}
public void mouseWheelMoved(MouseWheelEvent e) {
Component glassPane = frame.getGlassPane();
Point glassPanePoint = e.getPoint();
// Component component = e.getComponent();
Container container = frame.getContentPane();
Point containerPoint = SwingUtilities.convertPoint(glassPane, glassPanePoint, frame.getContentPane());
if (containerPoint.y < 0) { // we're not in the content pane
if (containerPoint.y + menuBar.getHeight() >= 0) {
Component component = menuBar.getComponentAt(glassPanePoint);
Point componentPoint = SwingUtilities.convertPoint(glassPane, glassPanePoint, component);
component.dispatchEvent(new MouseWheelEvent(component, e.getID(), e.getWhen(), e.getModifiers(), componentPoint.x, componentPoint.y,
e.getClickCount(), e.isPopupTrigger(), e.getScrollType(), e.getScrollAmount(), e.getWheelRotation()));
frame.getGlassPane().setVisible(false);
}
}
else {
Component deepComponent = SwingUtilities.getDeepestComponentAt(container, containerPoint.x, containerPoint.y);
Point componentPoint = SwingUtilities.convertPoint(glassPane, glassPanePoint, deepComponent);
// if (deepComponent instanceof ScrollableTabPanel) {
// deepComponent = tab.findComponentAt(componentPoint);
deepComponent.dispatchEvent(new MouseWheelEvent(deepComponent, e.getID(), e.getWhen(), e.getModifiers(), componentPoint.x,
componentPoint.y, e.getClickCount(), e.isPopupTrigger(), e.getScrollType(), e.getScrollAmount(), e.getWheelRotation()));
}
}
private void simulate(int fileType) throws Exception {
for (int i = 0; i < tab.getTabCount(); i++) {
if (tab.getTitleAt(i).equals(tree.getFile().split(separator)[tree.getFile().split(separator).length - 1])) {
tab.setSelectedIndex(i);
if (save(i, 0) == 0) {
return;
}
break;
}
}
if (fileType == 0) {
readSBML(tree.getFile());
}
String simName = JOptionPane.showInputDialog(frame, "Enter analysis id:", "Analysis ID", JOptionPane.PLAIN_MESSAGE);
if (simName != null && !simName.trim().equals("")) {
simName = simName.trim();
if (overwrite(root + separator + simName, simName)) {
new File(root + separator + simName).mkdir();
// new FileWriter(new File(root + separator + simName +
// separator +
// ".sim")).close();
String sbmlFile = tree.getFile();
String[] sbml1 = tree.getFile().split(separator);
String sbmlFileProp;
//ArrayList<String> interestingSpecies = new ArrayList<String>();
if (fileType == 1) {
sbmlFile = (sbml1[sbml1.length - 1].substring(0, sbml1[sbml1.length - 1].length() - 3) + "xml");
//GCMParser parser = new GCMParser(tree.getFile());
//GeneticNetwork network = parser.buildNetwork();
//interestingSpecies.addAll(network.getInterestingSpecies());
//GeneticNetwork.setRoot(root + separator);
//network.mergeSBML(root + separator + simName + separator + sbmlFile);
new File(root + separator + simName + separator + sbmlFile).createNewFile();
sbmlFileProp = root + separator + simName + separator
+ (sbml1[sbml1.length - 1].substring(0, sbml1[sbml1.length - 1].length() - 3) + "xml");
sbmlFile = sbmlFileProp;
}
else if (fileType == 2) {
sbmlFile = (sbml1[sbml1.length - 1].substring(0, sbml1[sbml1.length - 1].length() - 3) + "xml");
Translator t1 = new Translator();
t1.BuildTemplate(tree.getFile(), "");
t1.setFilename(root + separator + simName + separator + sbmlFile);
t1.outputSBML();
sbmlFileProp = root + separator + simName + separator
+ (sbml1[sbml1.length - 1].substring(0, sbml1[sbml1.length - 1].length() - 3) + "xml");
sbmlFile = sbmlFileProp;
}
else {
sbmlFileProp = root + separator + simName + separator + sbml1[sbml1.length - 1];
new FileOutputStream(new File(sbmlFileProp)).close();
}
try {
FileOutputStream out = new FileOutputStream(new File(root + separator + simName.trim() + separator + simName.trim() + ".sim"));
out.write((sbml1[sbml1.length - 1] + "\n").getBytes());
out.close();
}
catch (IOException e1) {
JOptionPane.showMessageDialog(frame, "Unable to save parameter file!", "Error Saving File", JOptionPane.ERROR_MESSAGE);
}
/*
* try { FileOutputStream out = new FileOutputStream(new
* File(sbmlFile)); SBMLWriter writer = new SBMLWriter(); String
* doc = writer.writeToString(document); byte[] output =
* doc.getBytes(); out.write(output); out.close(); } catch
* (Exception e1) { JOptionPane.showMessageDialog(frame, "Unable
* to copy sbml file to output location.", "Error",
* JOptionPane.ERROR_MESSAGE); }
*/
addToTree(simName);
JTabbedPane simTab = new JTabbedPane();
simTab.addMouseListener(this);
Reb2Sac reb2sac = new Reb2Sac(sbmlFile, sbmlFileProp, root, this, simName.trim(), log, simTab, null, sbml1[sbml1.length - 1], null,
null);
// reb2sac.addMouseListener(this);
simTab.addTab("Simulation Options", reb2sac);
simTab.getComponentAt(simTab.getComponents().length - 1).setName("Simulate");
// abstraction.addMouseListener(this);
if (fileType == 2) {
simTab.addTab("Abstraction Options", new AbstPane(root, sbml1[sbml1.length - 1], log, this, false, false));
}
else {
// System.out.println(fileType);
simTab.addTab("Abstraction Options", reb2sac.getAdvanced());
}
simTab.getComponentAt(simTab.getComponents().length - 1).setName("");
// simTab.addTab("Advanced Options",
// reb2sac.getProperties());
// simTab.getComponentAt(simTab.getComponents().length -
// 1).setName("");boolean
if (sbml1[sbml1.length - 1].contains(".gcm")) {
GCM2SBMLEditor gcm = new GCM2SBMLEditor(root + separator, sbml1[sbml1.length - 1], this, log, true, simName.trim(), root
+ separator + simName.trim() + separator + simName.trim() + ".sim", reb2sac, false);
reb2sac.setGcm(gcm);
// sbml.addMouseListener(this);
addModelViewTab(reb2sac, simTab, gcm);
simTab.addTab("Parameters", gcm);
simTab.getComponentAt(simTab.getComponents().length - 1).setName("GCM Editor");
if (!gcm.getSBMLFile().equals("--none
SBML_Editor sbml = new SBML_Editor(root + separator + gcm.getSBMLFile(), reb2sac, log, this, root + separator
+ simName.trim(), root + separator + simName.trim() + separator + simName.trim() + ".sim");
simTab.addTab("SBML Elements", sbml.getElementsPanel());
simTab.getComponentAt(simTab.getComponents().length - 1).setName("");
gcm.setSBMLParamFile(sbml);
}
else {
JScrollPane scroll = new JScrollPane();
scroll.setViewportView(new JPanel());
simTab.addTab("SBML Elements", scroll);
simTab.getComponentAt(simTab.getComponents().length - 1).setName("");
gcm.setSBMLParamFile(null);
}
}
else if (sbml1[sbml1.length - 1].contains(".sbml") || sbml1[sbml1.length - 1].contains(".xml")) {
SBML_Editor sbml = new SBML_Editor(sbmlFile, reb2sac, log, this, root + separator + simName.trim(), root + separator
+ simName.trim() + separator + simName.trim() + ".sim");
reb2sac.setSbml(sbml);
// sbml.addMouseListener(this);
simTab.addTab("Parameter Editor", sbml);
simTab.getComponentAt(simTab.getComponents().length - 1).setName("SBML Editor");
simTab.addTab("SBML Elements", sbml.getElementsPanel());
simTab.getComponentAt(simTab.getComponents().length - 1).setName("");
}
Graph tsdGraph = reb2sac.createGraph(null);
// tsdGraph.addMouseListener(this);
simTab.addTab("TSD Graph", tsdGraph);
simTab.getComponentAt(simTab.getComponents().length - 1).setName("TSD Graph");
Graph probGraph = reb2sac.createProbGraph(null);
// probGraph.addMouseListener(this);
simTab.addTab("Histogram", probGraph);
simTab.getComponentAt(simTab.getComponents().length - 1).setName("ProbGraph");
/*
* JLabel noData = new JLabel("No data available"); Font font =
* noData.getFont(); font = font.deriveFont(Font.BOLD, 42.0f);
* noData.setFont(font);
* noData.setHorizontalAlignment(SwingConstants.CENTER);
* simTab.addTab("TSD Graph", noData);
* simTab.getComponentAt(simTab.getComponents().length -
* 1).setName("TSD Graph"); JLabel noData1 = new JLabel("No data
* available"); Font font1 = noData1.getFont(); font1 =
* font1.deriveFont(Font.BOLD, 42.0f); noData1.setFont(font1);
* noData1.setHorizontalAlignment(SwingConstants.CENTER);
* simTab.addTab("Histogram", noData1);
* simTab.getComponentAt(simTab.getComponents().length -
* 1).setName("ProbGraph");
*/
addTab(simName, simTab, null);
}
}
}
private void openLearn() {
boolean done = false;
for (int i = 0; i < tab.getTabCount(); i++) {
if (tab.getTitleAt(i).equals(tree.getFile().split(separator)[tree.getFile().split(separator).length - 1])) {
tab.setSelectedIndex(i);
done = true;
}
}
if (!done) {
JTabbedPane lrnTab = new JTabbedPane();
lrnTab.addMouseListener(this);
// String graphFile = "";
String open = null;
if (new File(tree.getFile()).isDirectory()) {
String[] list = new File(tree.getFile()).list();
int run = 0;
for (int i = 0; i < list.length; i++) {
if (!(new File(list[i]).isDirectory()) && list[i].length() > 4) {
String end = "";
for (int j = 1; j < 5; j++) {
end = list[i].charAt(list[i].length() - j) + end;
}
if (end.equals(".tsd") || end.equals(".dat") || end.equals(".csv")) {
if (list[i].contains("run-")) {
int tempNum = Integer.parseInt(list[i].substring(4, list[i].length() - end.length()));
if (tempNum > run) {
run = tempNum;
// graphFile = tree.getFile() + separator +
// list[i];
}
}
}
else if (end.equals(".grf")) {
open = tree.getFile() + separator + list[i];
}
}
}
}
String lrnFile = tree.getFile() + separator + tree.getFile().split(separator)[tree.getFile().split(separator).length - 1] + ".lrn";
String lrnFile2 = tree.getFile() + separator + ".lrn";
Properties load = new Properties();
String learnFile = "";
try {
if (new File(lrnFile2).exists()) {
FileInputStream in = new FileInputStream(new File(lrnFile2));
load.load(in);
in.close();
new File(lrnFile2).delete();
}
if (new File(lrnFile).exists()) {
FileInputStream in = new FileInputStream(new File(lrnFile));
load.load(in);
in.close();
if (load.containsKey("genenet.file")) {
learnFile = load.getProperty("genenet.file");
learnFile = learnFile.split(separator)[learnFile.split(separator).length - 1];
if (learnFile.endsWith(".xml")) {
learnFile = learnFile.replace(".xml", ".gcm");
load.setProperty("genenet.file", learnFile);
}
}
}
FileOutputStream out = new FileOutputStream(new File(lrnFile));
load.store(out, learnFile);
out.close();
}
catch (Exception e) {
JOptionPane.showMessageDialog(frame, "Unable to load properties file!", "Error Loading Properties", JOptionPane.ERROR_MESSAGE);
}
for (int i = 0; i < tab.getTabCount(); i++) {
if (tab.getTitleAt(i).equals(learnFile)) {
tab.setSelectedIndex(i);
if (save(i, 0) == 0) {
return;
}
break;
}
}
if (!(new File(root + separator + learnFile).exists())) {
JOptionPane.showMessageDialog(frame, "Unable to open view because " + learnFile + " is missing.", "Error", JOptionPane.ERROR_MESSAGE);
return;
}
// if (!graphFile.equals("")) {
DataManager data = new DataManager(tree.getFile(), this, lema);
// data.addMouseListener(this);
lrnTab.addTab("Data Manager", data);
lrnTab.getComponentAt(lrnTab.getComponents().length - 1).setName("Data Manager");
LearnGCM learn = new LearnGCM(tree.getFile(), log, this);
// learn.addMouseListener(this);
lrnTab.addTab("Learn", learn);
lrnTab.getComponentAt(lrnTab.getComponents().length - 1).setName("Learn");
lrnTab.addTab("Advanced Options", learn.getAdvancedOptionsPanel());
lrnTab.getComponentAt(lrnTab.getComponents().length - 1).setName("Advanced Options");
Graph tsdGraph = new Graph(null, "Number of molecules", tree.getFile().split(separator)[tree.getFile().split(separator).length - 1]
+ " data", "tsd.printer", tree.getFile(), "Time", this, open, log, null, true, true);
// tsdGraph.addMouseListener(this);
lrnTab.addTab("TSD Graph", tsdGraph);
lrnTab.getComponentAt(lrnTab.getComponents().length - 1).setName("TSD Graph");
addTab(tree.getFile().split(separator)[tree.getFile().split(separator).length - 1], lrnTab, null);
}
}
private void openLearnLHPN() {
boolean done = false;
for (int i = 0; i < tab.getTabCount(); i++) {
if (tab.getTitleAt(i).equals(tree.getFile().split(separator)[tree.getFile().split(separator).length - 1])) {
tab.setSelectedIndex(i);
done = true;
}
}
if (!done) {
JTabbedPane lrnTab = new JTabbedPane();
lrnTab.addMouseListener(this);
// String graphFile = "";
String open = null;
if (new File(tree.getFile()).isDirectory()) {
String[] list = new File(tree.getFile()).list();
int run = 0;
for (int i = 0; i < list.length; i++) {
if (!(new File(list[i]).isDirectory()) && list[i].length() > 4) {
String end = "";
for (int j = 1; j < 5; j++) {
end = list[i].charAt(list[i].length() - j) + end;
}
if (end.equals(".tsd") || end.equals(".dat") || end.equals(".csv")) {
if (list[i].contains("run-")) {
int tempNum = Integer.parseInt(list[i].substring(4, list[i].length() - end.length()));
if (tempNum > run) {
run = tempNum;
// graphFile = tree.getFile() + separator +
// list[i];
}
}
}
else if (end.equals(".grf")) {
open = tree.getFile() + separator + list[i];
}
}
}
}
String lrnFile = tree.getFile() + separator + tree.getFile().split(separator)[tree.getFile().split(separator).length - 1] + ".lrn";
String lrnFile2 = tree.getFile() + separator + ".lrn";
Properties load = new Properties();
String learnFile = "";
try {
if (new File(lrnFile2).exists()) {
FileInputStream in = new FileInputStream(new File(lrnFile2));
load.load(in);
in.close();
new File(lrnFile2).delete();
}
if (new File(lrnFile).exists()) {
FileInputStream in = new FileInputStream(new File(lrnFile));
load.load(in);
in.close();
if (load.containsKey("genenet.file")) {
learnFile = load.getProperty("genenet.file");
learnFile = learnFile.split(separator)[learnFile.split(separator).length - 1];
}
}
FileOutputStream out = new FileOutputStream(new File(lrnFile));
load.store(out, learnFile);
out.close();
}
catch (Exception e) {
JOptionPane.showMessageDialog(frame, "Unable to load properties file!", "Error Loading Properties", JOptionPane.ERROR_MESSAGE);
}
for (int i = 0; i < tab.getTabCount(); i++) {
if (tab.getTitleAt(i).equals(learnFile)) {
tab.setSelectedIndex(i);
if (save(i, 0) == 0) {
return;
}
break;
}
}
if (!(new File(root + separator + learnFile).exists())) {
JOptionPane.showMessageDialog(frame, "Unable to open view because " + learnFile + " is missing.", "Error", JOptionPane.ERROR_MESSAGE);
return;
}
DataManager data = new DataManager(tree.getFile(), this, lema);
lrnTab.addTab("Data Manager", data);
lrnTab.getComponentAt(lrnTab.getComponents().length - 1).setName("Data Manager");
LearnLHPN learn = new LearnLHPN(tree.getFile(), log, this);
lrnTab.addTab("Learn", learn);
lrnTab.getComponentAt(lrnTab.getComponents().length - 1).setName("Learn");
lrnTab.addTab("Advanced Options", learn.getAdvancedOptionsPanel());
lrnTab.getComponentAt(lrnTab.getComponents().length - 1).setName("Advanced Options");
Graph tsdGraph = new Graph(null, "Number of molecules", tree.getFile().split(separator)[tree.getFile().split(separator).length - 1]
+ " data", "tsd.printer", tree.getFile(), "Time", this, open, log, null, true, true);
lrnTab.addTab("TSD Graph", tsdGraph);
lrnTab.getComponentAt(lrnTab.getComponents().length - 1).setName("TSD Graph");
addTab(tree.getFile().split(separator)[tree.getFile().split(separator).length - 1], lrnTab, null);
}
}
private void openSynth() {
boolean done = false;
for (int i = 0; i < tab.getTabCount(); i++) {
if (tab.getTitleAt(i).equals(tree.getFile().split(separator)[tree.getFile().split(separator).length - 1])) {
tab.setSelectedIndex(i);
done = true;
}
}
if (!done) {
JPanel synthPanel = new JPanel();
// String graphFile = "";
if (new File(tree.getFile()).isDirectory()) {
String[] list = new File(tree.getFile()).list();
int run = 0;
for (int i = 0; i < list.length; i++) {
if (!(new File(list[i]).isDirectory()) && list[i].length() > 4) {
String end = "";
for (int j = 1; j < 5; j++) {
end = list[i].charAt(list[i].length() - j) + end;
}
if (end.equals(".tsd") || end.equals(".dat") || end.equals(".csv")) {
if (list[i].contains("run-")) {
int tempNum = Integer.parseInt(list[i].substring(4, list[i].length() - end.length()));
if (tempNum > run) {
run = tempNum;
// graphFile = tree.getFile() + separator +
// list[i];
}
}
}
}
}
}
String synthFile = tree.getFile() + separator + tree.getFile().split(separator)[tree.getFile().split(separator).length - 1] + ".syn";
String synthFile2 = tree.getFile() + separator + ".syn";
Properties load = new Properties();
String synthesisFile = "";
try {
if (new File(synthFile2).exists()) {
FileInputStream in = new FileInputStream(new File(synthFile2));
load.load(in);
in.close();
new File(synthFile2).delete();
}
if (new File(synthFile).exists()) {
FileInputStream in = new FileInputStream(new File(synthFile));
load.load(in);
in.close();
if (load.containsKey("synthesis.file")) {
synthesisFile = load.getProperty("synthesis.file");
synthesisFile = synthesisFile.split(separator)[synthesisFile.split(separator).length - 1];
}
}
FileOutputStream out = new FileOutputStream(new File(synthesisFile));
load.store(out, synthesisFile);
out.close();
}
catch (Exception e) {
JOptionPane.showMessageDialog(frame, "Unable to load properties file!", "Error Loading Properties", JOptionPane.ERROR_MESSAGE);
}
for (int i = 0; i < tab.getTabCount(); i++) {
if (tab.getTitleAt(i).equals(synthesisFile)) {
tab.setSelectedIndex(i);
if (save(i, 0) == 0) {
return;
}
break;
}
}
if (!(new File(root + separator + synthesisFile).exists())) {
JOptionPane.showMessageDialog(frame, "Unable to open view because " + synthesisFile + " is missing.", "Error",
JOptionPane.ERROR_MESSAGE);
return;
}
// if (!graphFile.equals("")) {
Synthesis synth = new Synthesis(tree.getFile(), "flag", log, this);
// synth.addMouseListener(this);
synthPanel.add(synth);
addTab(tree.getFile().split(separator)[tree.getFile().split(separator).length - 1], synthPanel, "Synthesis");
}
}
private void openVerify() {
boolean done = false;
for (int i = 0; i < tab.getTabCount(); i++) {
if (tab.getTitleAt(i).equals(tree.getFile().split(separator)[tree.getFile().split(separator).length - 1])) {
tab.setSelectedIndex(i);
done = true;
}
}
if (!done) {
// JPanel verPanel = new JPanel();
// JPanel abstPanel = new JPanel();
// JPanel verTab = new JTabbedPane();
// String graphFile = "";
/*
* if (new File(tree.getFile()).isDirectory()) { String[] list = new
* File(tree.getFile()).list(); int run = 0; for (int i = 0; i <
* list.length; i++) { if (!(new File(list[i]).isDirectory()) &&
* list[i].length() > 4) { String end = ""; for (int j = 1; j < 5;
* j++) { end = list[i].charAt(list[i].length() - j) + end; } if
* (end.equals(".tsd") || end.equals(".dat") || end.equals(".csv"))
* { if (list[i].contains("run-")) { int tempNum =
* Integer.parseInt(list[i].substring(4, list[i] .length() -
* end.length())); if (tempNum > run) { run = tempNum; // graphFile
* = tree.getFile() + separator + // list[i]; } } } } } }
*/
String verName = tree.getFile().split(separator)[tree.getFile().split(separator).length - 1];
String verFile = tree.getFile() + separator + verName + ".ver";
Properties load = new Properties();
String verifyFile = "";
try {
if (new File(verFile).exists()) {
FileInputStream in = new FileInputStream(new File(verFile));
load.load(in);
in.close();
if (load.containsKey("verification.file")) {
verifyFile = load.getProperty("verification.file");
verifyFile = verifyFile.split(separator)[verifyFile.split(separator).length - 1];
}
}
// FileOutputStream out = new FileOutputStream(new
// File(verifyFile));
// load.store(out, verifyFile);
// out.close();
}
catch (Exception e) {
JOptionPane.showMessageDialog(frame, "Unable to load properties file!", "Error Loading Properties", JOptionPane.ERROR_MESSAGE);
}
for (int i = 0; i < tab.getTabCount(); i++) {
if (tab.getTitleAt(i).equals(verifyFile)) {
tab.setSelectedIndex(i);
if (save(i, 0) == 0) {
return;
}
break;
}
}
if (!(new File(verFile).exists())) {
JOptionPane
.showMessageDialog(frame, "Unable to open view because " + verifyFile + " is missing.", "Error", JOptionPane.ERROR_MESSAGE);
return;
}
// if (!graphFile.equals("")) {
Verification ver = new Verification(root + separator + verName, verName, "flag", log, this, lema, atacs);
// ver.addMouseListener(this);
// verPanel.add(ver);
// AbstPane abst = new AbstPane(root + separator + verName, ver,
// "flag", log, this, lema,
// atacs);
// abstPanel.add(abst);
// verTab.add("verify", verPanel);
// verTab.add("abstract", abstPanel);
addTab(tree.getFile().split(separator)[tree.getFile().split(separator).length - 1], ver, "Verification");
}
}
private void openSim() throws Exception {
String filename = tree.getFile();
boolean done = false;
for (int i = 0; i < tab.getTabCount(); i++) {
if (tab.getTitleAt(i).equals(filename.split(separator)[filename.split(separator).length - 1])) {
tab.setSelectedIndex(i);
done = true;
}
}
if (!done) {
if (filename != null && !filename.equals("")) {
if (new File(filename).isDirectory()) {
if (new File(filename + separator + ".sim").exists()) {
new File(filename + separator + ".sim").delete();
}
String[] list = new File(filename).list();
String getAFile = "";
// String probFile = "";
String openFile = "";
// String graphFile = "";
String open = null;
String openProb = null;
int run = 0;
for (int i = 0; i < list.length; i++) {
if (!(new File(list[i]).isDirectory()) && list[i].length() > 4) {
String end = "";
for (int j = 1; j < 5; j++) {
end = list[i].charAt(list[i].length() - j) + end;
}
if (end.equals(".xml")) {
getAFile = filename + separator + list[i];
}
else if (end.equals("sbml") && getAFile.equals("")) {
getAFile = filename + separator + list[i];
}
else if (end.equals(".txt") && list[i].contains("sim-rep")) {
// probFile = filename + separator + list[i];
}
else if (end.equals("ties") && list[i].contains("properties") && !(list[i].equals("species.properties"))) {
openFile = filename + separator + list[i];
}
else if (end.equals(".tsd") || end.equals(".dat") || end.equals(".csv") || end.contains("=")) {
if (list[i].contains("run-")) {
int tempNum = Integer.parseInt(list[i].substring(4, list[i].length() - end.length()));
if (tempNum > run) {
run = tempNum;
// graphFile = filename + separator +
// list[i];
}
}
else if (list[i].contains("euler-run.") || list[i].contains("gear1-run.") || list[i].contains("gear2-run.")
|| list[i].contains("rk4imp-run.") || list[i].contains("rk8pd-run.") || list[i].contains("rkf45-run.")) {
// graphFile = filename + separator +
// list[i];
}
else if (end.contains("=")) {
// graphFile = filename + separator +
// list[i];
}
}
else if (end.equals(".grf")) {
open = filename + separator + list[i];
}
else if (end.equals(".prb")) {
openProb = filename + separator + list[i];
}
}
else if (new File(filename + separator + list[i]).isDirectory()) {
String[] s = new File(filename + separator + list[i]).list();
for (int j = 0; j < s.length; j++) {
if (s[j].contains("sim-rep")) {
// probFile = filename + separator + list[i]
// + separator +
}
else if (s[j].contains(".tsd")) {
// graphFile = filename + separator +
// list[i] + separator +
}
}
}
}
if (!getAFile.equals("")) {
String[] split = filename.split(separator);
String simFile = root + separator + split[split.length - 1].trim() + separator + split[split.length - 1].trim() + ".sim";
String pmsFile = root + separator + split[split.length - 1].trim() + separator + split[split.length - 1].trim() + ".pms";
if (new File(pmsFile).exists()) {
if (new File(simFile).exists()) {
new File(pmsFile).delete();
}
else {
new File(pmsFile).renameTo(new File(simFile));
}
}
String sbmlLoadFile = "";
String gcmFile = "";
// ArrayList<String> interestingSpecies = new
// ArrayList<String>();
if (new File(simFile).exists()) {
try {
Scanner s = new Scanner(new File(simFile));
if (s.hasNextLine()) {
sbmlLoadFile = s.nextLine();
sbmlLoadFile = sbmlLoadFile.split(separator)[sbmlLoadFile.split(separator).length - 1];
if (sbmlLoadFile.contains(".xml"))
sbmlLoadFile = sbmlLoadFile.replace(".xml", ".gcm");
if (sbmlLoadFile.equals("")) {
JOptionPane.showMessageDialog(frame, "Unable to open view because "
+ "the sbml linked to this view is missing.", "Error", JOptionPane.ERROR_MESSAGE);
return;
}
else if (!(new File(root + separator + sbmlLoadFile).exists())) {
JOptionPane.showMessageDialog(frame, "Unable to open view because " + sbmlLoadFile + " is missing.", "Error",
JOptionPane.ERROR_MESSAGE);
return;
}
gcmFile = sbmlLoadFile;
if (sbmlLoadFile.contains(".gcm")) {
//GCMParser parser = new GCMParser(root + separator + sbmlLoadFile);
//GeneticNetwork network = parser.buildNetwork();
// interestingSpecies.addAll(network.getInterestingSpecies());
//GeneticNetwork.setRoot(root + separator);
sbmlLoadFile = root + separator + split[split.length - 1].trim() + separator
+ sbmlLoadFile.replace(".gcm", ".xml");
//network.mergeSBML(sbmlLoadFile);
}
else if (sbmlLoadFile.contains(".lpn")) {
//Translator t1 = new Translator();
//t1.BuildTemplate(root + separator + sbmlLoadFile, "");
sbmlLoadFile = root + separator + split[split.length - 1].trim() + separator
+ sbmlLoadFile.replace(".lpn", ".xml");
//t1.setFilename(sbmlLoadFile);
//t1.outputSBML();
}
else {
sbmlLoadFile = root + separator + sbmlLoadFile;
}
}
while (s.hasNextLine()) {
s.nextLine();
}
s.close();
File f = new File(sbmlLoadFile);
if (!f.exists()) {
sbmlLoadFile = root + separator + f.getName();
}
}
catch (Exception e) {
e.printStackTrace();
JOptionPane.showMessageDialog(frame, "Unable to load sbml file.", "Error", JOptionPane.ERROR_MESSAGE);
return;
}
}
else {
sbmlLoadFile = root + separator + getAFile.split(separator)[getAFile.split(separator).length - 1];
if (!new File(sbmlLoadFile).exists()) {
sbmlLoadFile = getAFile;
/*
* JOptionPane.showMessageDialog(frame, "Unable
* to load sbml file.", "Error",
* JOptionPane.ERROR_MESSAGE); return;
*/
}
}
if (!new File(sbmlLoadFile).exists()) {
JOptionPane.showMessageDialog(frame,
"Unable to open view because " + sbmlLoadFile.split(separator)[sbmlLoadFile.split(separator).length - 1]
+ " is missing.", "Error", JOptionPane.ERROR_MESSAGE);
return;
}
for (int i = 0; i < tab.getTabCount(); i++) {
if (tab.getTitleAt(i).equals(sbmlLoadFile.split(separator)[sbmlLoadFile.split(separator).length - 1])) {
tab.setSelectedIndex(i);
if (save(i, 0) == 0) {
return;
}
break;
}
}
JTabbedPane simTab = new JTabbedPane();
simTab.addMouseListener(this);
AbstPane lhpnAbstraction = new AbstPane(root, gcmFile, log, this, false, false);
Reb2Sac reb2sac;
if (gcmFile.contains(".lpn")) {
reb2sac = new Reb2Sac(sbmlLoadFile, getAFile, root, this, split[split.length - 1].trim(), log, simTab, openFile, gcmFile,
lhpnAbstraction, null);
}
else {
reb2sac = new Reb2Sac(sbmlLoadFile, getAFile, root, this, split[split.length - 1].trim(), log, simTab, openFile, gcmFile,
null, null);
}
simTab.addTab("Simulation Options", reb2sac);
simTab.getComponentAt(simTab.getComponents().length - 1).setName("Simulate");
if (gcmFile.contains(".lpn")) {
simTab.addTab("Abstraction Options", lhpnAbstraction);
}
else {
simTab.addTab("Abstraction Options", reb2sac.getAdvanced());
}
simTab.getComponentAt(simTab.getComponents().length - 1).setName("");
// simTab.addTab("Advanced Options",
// reb2sac.getProperties());
// simTab.getComponentAt(simTab.getComponents().length -
// 1).setName("");
if (gcmFile.contains(".gcm")) {
GCM2SBMLEditor gcm = new GCM2SBMLEditor(root + separator, gcmFile, this, log, true, split[split.length - 1].trim(), root
+ separator + split[split.length - 1].trim() + separator + split[split.length - 1].trim() + ".sim", reb2sac,
false);
reb2sac.setGcm(gcm);
// sbml.addMouseListener(this);
addModelViewTab(reb2sac, simTab, gcm);
simTab.addTab("Parameters", gcm);
simTab.getComponentAt(simTab.getComponents().length - 1).setName("GCM Editor");
if (!gcm.getSBMLFile().equals("--none
SBML_Editor sbml = new SBML_Editor(root + separator + gcm.getSBMLFile(), reb2sac, log, this, root + separator
+ split[split.length - 1].trim(), root + separator + split[split.length - 1].trim() + separator
+ split[split.length - 1].trim() + ".sim");
simTab.addTab("SBML Elements", sbml.getElementsPanel());
simTab.getComponentAt(simTab.getComponents().length - 1).setName("");
gcm.setSBMLParamFile(sbml);
}
else {
JScrollPane scroll = new JScrollPane();
scroll.setViewportView(new JPanel());
simTab.addTab("SBML Elements", scroll);
simTab.getComponentAt(simTab.getComponents().length - 1).setName("");
gcm.setSBMLParamFile(null);
}
}
else if (gcmFile.contains(".sbml") || gcmFile.contains(".xml")) {
SBML_Editor sbml = new SBML_Editor(sbmlLoadFile, reb2sac, log, this, root + separator + split[split.length - 1].trim(),
root + separator + split[split.length - 1].trim() + separator + split[split.length - 1].trim() + ".sim");
reb2sac.setSbml(sbml);
// sbml.addMouseListener(this);
simTab.addTab("Parameter Editor", sbml);
simTab.getComponentAt(simTab.getComponents().length - 1).setName("SBML Editor");
simTab.addTab("SBML Elements", sbml.getElementsPanel());
simTab.getComponentAt(simTab.getComponents().length - 1).setName("");
}
Graph tsdGraph = reb2sac.createGraph(open);
simTab.addTab("TSD Graph", tsdGraph);
simTab.getComponentAt(simTab.getComponents().length - 1).setName("TSD Graph");
Graph probGraph = reb2sac.createProbGraph(openProb);
simTab.addTab("Histogram", probGraph);
simTab.getComponentAt(simTab.getComponents().length - 1).setName("ProbGraph");
addTab(split[split.length - 1], simTab, null);
}
}
}
}
}
/**
* adds the tab for the modelview and the correct listener.
*
* @return
*/
private void addModelViewTab(Reb2Sac reb2sac, JTabbedPane tabPane, GCM2SBMLEditor gcm2sbml) {
// Add the modelview tab
MovieContainer movieContainer = new MovieContainer(reb2sac, gcm2sbml.getGCM(), this, gcm2sbml);
tabPane.addTab("Schematic", movieContainer);
tabPane.getComponentAt(tabPane.getComponents().length - 1).setName("ModelViewMovie");
// When the Graphical View panel gets clicked on, tell it to display
// itself.
tabPane.addChangeListener(new ChangeListener() {
public void stateChanged(ChangeEvent e) {
JTabbedPane selectedTab = (JTabbedPane) (e.getSource());
if (!(selectedTab.getComponent(selectedTab.getSelectedIndex()) instanceof JScrollPane)) {
JPanel selectedPanel = (JPanel) selectedTab.getComponent(selectedTab.getSelectedIndex());
String className = selectedPanel.getClass().getName();
// The new Schematic
if (className.indexOf("MovieContainer") >= 0) {
((MovieContainer) selectedPanel).display();
}
}
}
});
}
private class NewAction extends AbstractAction {
private static final long serialVersionUID = 1L;
NewAction() {
super();
}
public void actionPerformed(ActionEvent e) {
popup.add(newProj);
if (!async) {
popup.add(newGCMModel);
popup.add(newSBMLModel);
}
else if (atacs) {
popup.add(newVhdl);
popup.add(newLhpn);
popup.add(newCsp);
popup.add(newHse);
popup.add(newUnc);
popup.add(newRsg);
}
else {
popup.add(newVhdl);
popup.add(newLhpn);
popup.add(newSpice);
}
popup.add(graph);
popup.add(probGraph);
if (popup.getComponentCount() != 0) {
popup.show(mainPanel, mainPanel.getMousePosition().x, mainPanel.getMousePosition().y);
}
}
}
private class ImportAction extends AbstractAction {
private static final long serialVersionUID = 1L;
ImportAction() {
super();
}
public void actionPerformed(ActionEvent e) {
if (!lema) {
popup.add(importDot);
popup.add(importSbol);
popup.add(importSbml);
popup.add(importBioModel);
}
else if (atacs) {
popup.add(importVhdl);
popup.add(importLpn);
popup.add(importCsp);
popup.add(importHse);
popup.add(importUnc);
popup.add(importRsg);
}
else {
popup.add(importVhdl);
popup.add(importS);
popup.add(importInst);
popup.add(importLpn);
popup.add(importSpice);
}
if (popup.getComponentCount() != 0) {
popup.show(mainPanel, mainPanel.getMousePosition().x, mainPanel.getMousePosition().y);
}
}
}
private class ExportAction extends AbstractAction {
private static final long serialVersionUID = 1L;
ExportAction() {
super();
}
public void actionPerformed(ActionEvent e) {
popup.add(exportCsv);
popup.add(exportDat);
popup.add(exportEps);
popup.add(exportJpg);
popup.add(exportPdf);
popup.add(exportPng);
popup.add(exportSvg);
popup.add(exportTsd);
if (popup.getComponentCount() != 0) {
popup.show(mainPanel, mainPanel.getMousePosition().x, mainPanel.getMousePosition().y);
}
}
}
private class ModelAction extends AbstractAction {
private static final long serialVersionUID = 1L;
ModelAction() {
super();
}
public void actionPerformed(ActionEvent e) {
popup.add(viewModGraph);
popup.add(viewModBrowser);
if (popup.getComponentCount() != 0) {
popup.show(mainPanel, mainPanel.getMousePosition().x, mainPanel.getMousePosition().y);
}
}
}
public void mouseClicked(MouseEvent e) {
executeMouseClickEvent(e);
}
public void mouseEntered(MouseEvent e) {
}
public void mouseExited(MouseEvent e) {
}
public void mouseDragged(MouseEvent e) {
Component glassPane = frame.getGlassPane();
Point glassPanePoint = e.getPoint();
// Component component = e.getComponent();
Container container = frame.getContentPane();
Point containerPoint = SwingUtilities.convertPoint(glassPane, glassPanePoint, frame.getContentPane());
if (containerPoint.y < 0) { // we're not in the content pane
if (containerPoint.y + menuBar.getHeight() >= 0) {
Component component = menuBar.getComponentAt(glassPanePoint);
Point componentPoint = SwingUtilities.convertPoint(glassPane, glassPanePoint, component);
component.dispatchEvent(new MouseEvent(component, e.getID(), e.getWhen(), e.getModifiers(), componentPoint.x, componentPoint.y, e
.getClickCount(), e.isPopupTrigger()));
frame.getGlassPane().setVisible(false);
}
}
else {
try {
Component deepComponent = SwingUtilities.getDeepestComponentAt(container, containerPoint.x, containerPoint.y);
Point componentPoint = SwingUtilities.convertPoint(glassPane, glassPanePoint, deepComponent);
deepComponent.dispatchEvent(new MouseEvent(deepComponent, e.getID(), e.getWhen(), e.getModifiers(), componentPoint.x,
componentPoint.y, e.getClickCount(), e.isPopupTrigger()));
}
catch (Exception e1) {
}
}
}
public void windowLostFocus(WindowEvent e) {
}
public JMenuItem getExitButton() {
return exit;
}
/**
* This is the main method. It excecutes the BioSim GUI FrontEnd program.
*/
public static void main(String args[]) {
boolean lemaFlag = false, atacsFlag = false, LPN2SBML = true;
if (args.length > 0) {
for (int i = 0; i < args.length; i++) {
if (args[i].equals("-lema")) {
lemaFlag = true;
}
else if (args[i].equals("-atacs")) {
atacsFlag = true;
}
}
}
if (!lemaFlag && !atacsFlag) {
String varname;
if (System.getProperty("mrj.version") != null)
varname = "DYLD_LIBRARY_PATH"; // We're on a Mac.
else
varname = "LD_LIBRARY_PATH"; // We're not on a Mac.
try {
System.loadLibrary("sbmlj");
// For extra safety, check that the jar file is in the
// classpath.
Class.forName("org.sbml.libsbml.libsbml");
}
catch (UnsatisfiedLinkError e) {
System.err.println("Error: could not link with the libSBML library." + " It is likely\nyour " + varname
+ " environment variable does not include\nthe" + " directory containing the libsbml library file.");
System.exit(1);
}
catch (ClassNotFoundException e) {
System.err.println("Error: unable to load the file libsbmlj.jar." + " It is likely\nyour " + varname + " environment"
+ " variable or CLASSPATH variable\ndoes not include" + " the directory containing the libsbmlj.jar file.");
System.exit(1);
}
catch (SecurityException e) {
System.err.println("Could not load the libSBML library files due to a" + " security exception.");
System.exit(1);
}
}
else {
/*
* String varname; if (System.getProperty("mrj.version") != null)
* varname = "DYLD_LIBRARY_PATH"; // We're on a Mac. else varname =
* "LD_LIBRARY_PATH"; // We're not on a Mac.
*/
try {
System.loadLibrary("sbmlj");
// For extra safety, check that the jar file is in the
// classpath.
Class.forName("org.sbml.libsbml.libsbml");
}
catch (UnsatisfiedLinkError e) {
LPN2SBML = false;
}
catch (ClassNotFoundException e) {
LPN2SBML = false;
}
catch (SecurityException e) {
LPN2SBML = false;
}
}
new Gui(lemaFlag, atacsFlag, LPN2SBML);
}
public void copySim(String newSim) {
try {
new File(root + separator + newSim).mkdir();
// new FileWriter(new File(root + separator + newSim + separator +
// ".sim")).close();
String oldSim = tab.getTitleAt(tab.getSelectedIndex());
String[] s = new File(root + separator + oldSim).list();
String sbmlFile = "";
String propertiesFile = "";
String sbmlLoadFile = null;
String gcmFile = null;
for (String ss : s) {
if (ss.length() > 4 && ss.substring(ss.length() - 5).equals(".sbml") || ss.length() > 3
&& ss.substring(ss.length() - 4).equals(".xml")) {
SBMLDocument document = readSBML(root + separator + oldSim + separator + ss);
SBMLWriter writer = new SBMLWriter();
writer.writeSBML(document, root + separator + newSim + separator + ss);
sbmlFile = root + separator + newSim + separator + ss;
}
else if (ss.length() > 10 && ss.substring(ss.length() - 11).equals(".properties")) {
FileOutputStream out = new FileOutputStream(new File(root + separator + newSim + separator + ss));
FileInputStream in = new FileInputStream(new File(root + separator + oldSim + separator + ss));
int read = in.read();
while (read != -1) {
out.write(read);
read = in.read();
}
in.close();
out.close();
propertiesFile = root + separator + newSim + separator + ss;
}
else if (ss.length() > 3
&& (ss.substring(ss.length() - 4).equals(".dat") || ss.substring(ss.length() - 4).equals(".sad")
|| ss.substring(ss.length() - 4).equals(".pms") || ss.substring(ss.length() - 4).equals(".sim"))
&& !ss.equals(".sim")) {
FileOutputStream out;
if (ss.substring(ss.length() - 4).equals(".pms")) {
out = new FileOutputStream(new File(root + separator + newSim + separator + newSim + ".sim"));
}
else if (ss.substring(ss.length() - 4).equals(".sim")) {
out = new FileOutputStream(new File(root + separator + newSim + separator + newSim + ".sim"));
}
else {
out = new FileOutputStream(new File(root + separator + newSim + separator + ss));
}
FileInputStream in = new FileInputStream(new File(root + separator + oldSim + separator + ss));
int read = in.read();
while (read != -1) {
out.write(read);
read = in.read();
}
in.close();
out.close();
if (ss.substring(ss.length() - 4).equals(".pms")) {
if (new File(root + separator + newSim + separator + ss.substring(0, ss.length() - 4) + ".sim").exists()) {
new File(root + separator + newSim + separator + ss).delete();
}
else {
new File(root + separator + newSim + separator + ss).renameTo(new File(root + separator + newSim + separator
+ ss.substring(0, ss.length() - 4) + ".sim"));
}
ss = ss.substring(0, ss.length() - 4) + ".sim";
}
if (ss.substring(ss.length() - 4).equals(".sim")) {
try {
Scanner scan = new Scanner(new File(root + separator + newSim + separator + ss));
if (scan.hasNextLine()) {
sbmlLoadFile = scan.nextLine();
sbmlLoadFile = sbmlLoadFile.split(separator)[sbmlLoadFile.split(separator).length - 1];
gcmFile = sbmlLoadFile;
if (sbmlLoadFile.contains(".gcm")) {
//GCMParser parser = new GCMParser(root + separator + sbmlLoadFile);
//GeneticNetwork network = parser.buildNetwork();
//GeneticNetwork.setRoot(root + separator);
sbmlLoadFile = root + separator + newSim + separator + sbmlLoadFile.replace(".gcm", ".sbml");
//network.mergeSBML(sbmlLoadFile);
}
else {
sbmlLoadFile = root + separator + sbmlLoadFile;
}
}
while (scan.hasNextLine()) {
scan.nextLine();
}
scan.close();
}
catch (Exception e) {
e.printStackTrace();
JOptionPane.showMessageDialog(frame, "Unable to load sbml file.", "Error", JOptionPane.ERROR_MESSAGE);
}
}
}
}
addToTree(newSim);
JTabbedPane simTab = new JTabbedPane();
simTab.addMouseListener(this);
Reb2Sac reb2sac = new Reb2Sac(sbmlLoadFile, sbmlFile, root, this, newSim, log, simTab, propertiesFile, gcmFile, null, null);
simTab.addTab("Simulation Options", reb2sac);
simTab.getComponentAt(simTab.getComponents().length - 1).setName("Simulate");
simTab.addTab("Abstraction Options", reb2sac.getAdvanced());
simTab.getComponentAt(simTab.getComponents().length - 1).setName("");
// simTab.addTab("Advanced Options", reb2sac.getProperties());
// simTab.getComponentAt(simTab.getComponents().length -
// 1).setName("");
if (gcmFile.contains(".gcm")) {
GCM2SBMLEditor gcm = new GCM2SBMLEditor(root + separator, gcmFile, this, log, true, newSim, root + separator + newSim + separator
+ newSim + ".sim", reb2sac, false);
reb2sac.setGcm(gcm);
// sbml.addMouseListener(this);
addModelViewTab(reb2sac, simTab, gcm);
simTab.addTab("Parameters", gcm);
simTab.getComponentAt(simTab.getComponents().length - 1).setName("GCM Editor");
if (!gcm.getSBMLFile().equals("--none
SBML_Editor sbml = new SBML_Editor(root + separator + gcm.getSBMLFile(), reb2sac, log, this, root + separator + newSim, root
+ separator + newSim + separator + newSim + ".sim");
simTab.addTab("SBML Elements", sbml.getElementsPanel());
simTab.getComponentAt(simTab.getComponents().length - 1).setName("");
gcm.setSBMLParamFile(sbml);
}
else {
JScrollPane scroll = new JScrollPane();
scroll.setViewportView(new JPanel());
simTab.addTab("SBML Elements", scroll);
simTab.getComponentAt(simTab.getComponents().length - 1).setName("");
gcm.setSBMLParamFile(null);
}
}
else {
SBML_Editor sbml = new SBML_Editor(sbmlLoadFile, reb2sac, log, this, root + separator + newSim, root + separator + newSim + separator
+ newSim + ".sim");
reb2sac.setSbml(sbml);
// sbml.addMouseListener(this);
simTab.addTab("Parameter Editor", sbml);
simTab.getComponentAt(simTab.getComponents().length - 1).setName("SBML Editor");
simTab.addTab("SBML Elements", sbml.getElementsPanel());
simTab.getComponentAt(simTab.getComponents().length - 1).setName("");
}
Graph tsdGraph = reb2sac.createGraph(null);
// tsdGraph.addMouseListener(this);
simTab.addTab("TSD Graph", tsdGraph);
simTab.getComponentAt(simTab.getComponents().length - 1).setName("TSD Graph");
Graph probGraph = reb2sac.createProbGraph(null);
// probGraph.addMouseListener(this);
simTab.addTab("Histogram", probGraph);
simTab.getComponentAt(simTab.getComponents().length - 1).setName("ProbGraph");
tab.setComponentAt(tab.getSelectedIndex(), simTab);
tab.setTitleAt(tab.getSelectedIndex(), newSim);
tab.getComponentAt(tab.getSelectedIndex()).setName(newSim);
}
catch (Exception e) {
JOptionPane.showMessageDialog(frame, "Unable to copy simulation.", "Error", JOptionPane.ERROR_MESSAGE);
}
}
public void refreshLearn(String learnName, boolean data) {
for (int i = 0; i < tab.getTabCount(); i++) {
if (tab.getTitleAt(i).equals(learnName)) {
for (int j = 0; j < ((JTabbedPane) tab.getComponentAt(i)).getComponentCount(); j++) {
if (((JTabbedPane) tab.getComponentAt(i)).getComponentAt(j).getName().equals("TSD Graph")) {
// if (data) {
if (((JTabbedPane) tab.getComponentAt(i)).getComponentAt(j) instanceof Graph) {
((Graph) ((JTabbedPane) tab.getComponentAt(i)).getComponentAt(j)).refresh();
}
else {
((JTabbedPane) tab.getComponentAt(i)).setComponentAt(j, new Graph(null, "Number of molecules", learnName + " data",
"tsd.printer", root + separator + learnName, "Time", this, null, log, null, true, true));
((JTabbedPane) tab.getComponentAt(i)).getComponentAt(j).setName("TSD Graph");
}
}
else if (((JTabbedPane) tab.getComponentAt(i)).getComponentAt(j).getName().equals("Learn")) {
if (((JTabbedPane) tab.getComponentAt(i)).getComponentAt(j) instanceof LearnGCM) {
}
else {
if (lema) {
((JTabbedPane) tab.getComponentAt(i)).setComponentAt(j, new LearnLHPN(root + separator + learnName, log, this));
}
else {
((JTabbedPane) tab.getComponentAt(i)).setComponentAt(j, new LearnGCM(root + separator + learnName, log, this));
}
((JTabbedPane) tab.getComponentAt(i)).getComponentAt(j).setName("Learn");
}
}
}
}
}
}
private void updateGCM() {
for (int i = 0; i < tab.getTabCount(); i++) {
if (tab.getTitleAt(i).contains(".gcm")) {
((GCM2SBMLEditor) tab.getComponentAt(i)).reloadFiles();
tab.setTitleAt(i, ((GCM2SBMLEditor) tab.getComponentAt(i)).getFilename());
}
}
}
public boolean updateOpenGCM(String gcmName) {
for (int i = 0; i < tab.getTabCount(); i++) {
String tab = this.tab.getTitleAt(i);
if (gcmName.equals(tab)) {
if (this.tab.getComponentAt(i) instanceof GCM2SBMLEditor) {
try {
GCM2SBMLEditor gcm = new GCM2SBMLEditor(root + separator, gcmName, this, log, false, null, null, null, false);
this.tab.setComponentAt(i, gcm);
this.tab.getComponentAt(i).setName("GCM Editor");
// gcm.save(false, "", false, true);
}
catch (Exception e) {
e.printStackTrace();
}
return true;
}
}
}
return false;
}
public void updateAsyncViews(String updatedFile) {
for (int i = 0; i < tab.getTabCount(); i++) {
String tab = this.tab.getTitleAt(i);
String properties = root + separator + tab + separator + tab + ".ver";
String properties1 = root + separator + tab + separator + tab + ".synth";
String properties2 = root + separator + tab + separator + tab + ".lrn";
if (new File(properties).exists()) {
Verification verify = ((Verification) (this.tab.getComponentAt(i)));
verify.reload(updatedFile);
}
if (new File(properties1).exists()) {
JTabbedPane sim = ((JTabbedPane) (this.tab.getComponentAt(i)));
for (int j = 0; j < sim.getTabCount(); j++) {
if (sim.getComponentAt(j).getName().equals("Synthesis")) {
((Synthesis) (sim.getComponentAt(j))).reload(updatedFile);
}
}
}
if (new File(properties2).exists()) {
String check = "";
try {
Properties p = new Properties();
FileInputStream load = new FileInputStream(new File(properties2));
p.load(load);
load.close();
if (p.containsKey("learn.file")) {
String[] getProp = p.getProperty("learn.file").split(separator);
check = getProp[getProp.length - 1];
}
else {
check = "";
}
}
catch (Exception e) {
JOptionPane.showMessageDialog(frame, "Unable to load background file.", "Error", JOptionPane.ERROR_MESSAGE);
check = "";
}
if (check.equals(updatedFile)) {
JTabbedPane learn = ((JTabbedPane) (this.tab.getComponentAt(i)));
for (int j = 0; j < learn.getTabCount(); j++) {
if (learn.getComponentAt(j).getName().equals("Data Manager")) {
((DataManager) (learn.getComponentAt(j))).updateSpecies();
}
else if (learn.getComponentAt(j).getName().equals("Learn")) {
((LearnLHPN) (learn.getComponentAt(j))).updateSpecies(root + separator + updatedFile);
((LearnLHPN) (learn.getComponentAt(j))).reload(updatedFile);
}
else if (learn.getComponentAt(j).getName().contains("Graph")) {
((Graph) (learn.getComponentAt(j))).refresh();
}
}
}
}
}
}
public void updateViews(String updatedFile) {
for (int i = 0; i < tab.getTabCount(); i++) {
String tab = this.tab.getTitleAt(i);
String properties = root + separator + tab + separator + tab + ".sim";
String properties2 = root + separator + tab + separator + tab + ".lrn";
if (new File(properties).exists()) {
String check = "";
try {
Scanner s = new Scanner(new File(properties));
if (s.hasNextLine()) {
check = s.nextLine();
check = check.split(separator)[check.split(separator).length - 1];
}
s.close();
}
catch (Exception e) {
e.printStackTrace();
}
if (check.equals(updatedFile)) {
JTabbedPane sim = ((JTabbedPane) (this.tab.getComponentAt(i)));
for (int j = 0; j < sim.getTabCount(); j++) {
// String tabName = sim.getComponentAt(j).getName();
// boolean b =
// sim.getComponentAt(j).getName().equals("ModelViewMovie");
if (sim.getComponentAt(j) instanceof Reb2Sac) {
((Reb2Sac) sim.getComponentAt(j)).updateProperties();
}
else if (sim.getComponentAt(j).getName().equals("SBML Editor")) {
new File(properties).renameTo(new File(properties.replace(".sim", ".temp")));
try {
boolean dirty = ((SBML_Editor) (sim.getComponentAt(j))).isDirty();
((SBML_Editor) (sim.getComponentAt(j))).save(false, "", true, true);
if (updatedFile.contains(".gcm")) {
//GCMParser parser = new GCMParser(root + separator + updatedFile);
//GeneticNetwork network = parser.buildNetwork();
//GeneticNetwork.setRoot(root + separator);
//network.mergeSBML(root + separator + tab + separator + updatedFile.replace(".gcm", ".xml"));
((SBML_Editor) (sim.getComponentAt(j))).updateSBML(i, j,
root + separator + tab + separator + updatedFile.replace(".gcm", ".xml"));
}
else {
((SBML_Editor) (sim.getComponentAt(j))).updateSBML(i, j, root + separator + updatedFile);
}
((SBML_Editor) (sim.getComponentAt(j))).setDirty(dirty);
}
catch (Exception e) {
e.printStackTrace();
}
new File(properties).delete();
new File(properties.replace(".sim", ".temp")).renameTo(new File(properties));
sim.setComponentAt(j + 1, ((SBML_Editor) (sim.getComponentAt(j))).getElementsPanel());
sim.getComponentAt(j + 1).setName("");
}
else if (sim.getComponentAt(j).getName().equals("GCM Editor")) {
new File(properties).renameTo(new File(properties.replace(".sim", ".temp")));
try {
boolean dirty = ((GCM2SBMLEditor) (sim.getComponentAt(j))).isDirty();
((GCM2SBMLEditor) (sim.getComponentAt(j))).saveParams(false, "", true);
((GCM2SBMLEditor) (sim.getComponentAt(j))).reload(check.replace(".gcm", ""));
((GCM2SBMLEditor) (sim.getComponentAt(j))).refresh();
((GCM2SBMLEditor) (sim.getComponentAt(j))).loadParams();
((GCM2SBMLEditor) (sim.getComponentAt(j))).setDirty(dirty);
}
catch (Exception e) {
e.printStackTrace();
}
new File(properties).delete();
new File(properties.replace(".sim", ".temp")).renameTo(new File(properties));
if (!((GCM2SBMLEditor) (sim.getComponentAt(j))).getSBMLFile().equals("--none
SBML_Editor sbml = new SBML_Editor(root + separator + ((GCM2SBMLEditor) (sim.getComponentAt(j))).getSBMLFile(),
((Reb2Sac) sim.getComponentAt(0)), log, this, root + separator + tab, root + separator + tab + separator
+ tab + ".sim");
sim.setComponentAt(j + 1, sbml.getElementsPanel());
sim.getComponentAt(j + 1).setName("");
((GCM2SBMLEditor) (sim.getComponentAt(j))).setSBMLParamFile(sbml);
}
else {
JScrollPane scroll = new JScrollPane();
scroll.setViewportView(new JPanel());
sim.setComponentAt(j + 1, scroll);
sim.getComponentAt(j + 1).setName("");
((GCM2SBMLEditor) (sim.getComponentAt(j))).setSBMLParamFile(null);
}
for (int k = 0; k < sim.getTabCount(); k++) {
if (sim.getComponentAt(k) instanceof MovieContainer) {
//display the schematic and reload the grid
((MovieContainer) (sim.getComponentAt(k))).display();
((MovieContainer) (sim.getComponentAt(k))).reloadGrid();
}
}
}
}
}
}
if (new File(properties2).exists()) {
String check = "";
try {
Properties p = new Properties();
FileInputStream load = new FileInputStream(new File(properties2));
p.load(load);
load.close();
if (p.containsKey("genenet.file")) {
String[] getProp = p.getProperty("genenet.file").split(separator);
check = getProp[getProp.length - 1];
}
else {
check = "";
}
}
catch (Exception e) {
JOptionPane.showMessageDialog(frame, "Unable to load background file.", "Error", JOptionPane.ERROR_MESSAGE);
check = "";
}
if (check.equals(updatedFile)) {
JTabbedPane learn = ((JTabbedPane) (this.tab.getComponentAt(i)));
for (int j = 0; j < learn.getTabCount(); j++) {
if (learn.getComponentAt(j).getName().equals("Data Manager")) {
((DataManager) (learn.getComponentAt(j))).updateSpecies();
}
else if (learn.getComponentAt(j).getName().equals("Learn")) {
((LearnGCM) (learn.getComponentAt(j))).updateSpecies(root + separator + updatedFile);
}
else if (learn.getComponentAt(j).getName().contains("Graph")) {
((Graph) (learn.getComponentAt(j))).refresh();
}
}
}
}
// ArrayList<String> saved = new ArrayList<String>();
// if (this.tab.getComponentAt(i) instanceof GCM2SBMLEditor) {
// saved.add(this.tab.getTitleAt(i));
// GCM2SBMLEditor gcm = (GCM2SBMLEditor) this.tab.getComponentAt(i);
// if (gcm.getSBMLFile().equals(updatedFile)) {
// gcm.save("save");
// String[] files = new File(root).list();
// for (String s : files) {
// if (s.endsWith(".gcm") && !saved.contains(s)) {
// GCMFile gcm = new GCMFile(root);
// gcm.load(root + separator + s);
// if (gcm.getSBMLFile().equals(updatedFile)) {
// updateViews(s);
}
}
private void updateViewNames(String oldname, String newname) {
File work = new File(root);
String[] fileList = work.list();
String[] temp = oldname.split(separator);
oldname = temp[temp.length - 1];
for (int i = 0; i < fileList.length; i++) {
String tabTitle = fileList[i];
String properties = root + separator + tabTitle + separator + tabTitle + ".ver";
String properties1 = root + separator + tabTitle + separator + tabTitle + ".synth";
String properties2 = root + separator + tabTitle + separator + tabTitle + ".lrn";
if (new File(properties).exists()) {
String check;
Properties p = new Properties();
try {
FileInputStream load = new FileInputStream(new File(properties));
p.load(load);
load.close();
if (p.containsKey("verification.file")) {
String[] getProp = p.getProperty("verification.file").split(separator);
check = getProp[getProp.length - 1];
}
else {
check = "";
}
if (check.equals(oldname)) {
p.setProperty("verification.file", newname);
FileOutputStream out = new FileOutputStream(new File(properties));
p.store(out, properties);
}
}
catch (Exception e) {
// log.addText("verification");
// e.printStackTrace();
JOptionPane.showMessageDialog(frame, "Unable to load background file.", "Error", JOptionPane.ERROR_MESSAGE);
check = "";
}
}
if (new File(properties1).exists()) {
String check;
try {
Properties p = new Properties();
FileInputStream load = new FileInputStream(new File(properties1));
p.load(load);
load.close();
if (p.containsKey("synthesis.file")) {
String[] getProp = p.getProperty("synthesis.file").split(separator);
check = getProp[getProp.length - 1];
}
else {
check = "";
}
if (check.equals(oldname)) {
p.setProperty("synthesis.file", newname);
FileOutputStream out = new FileOutputStream(new File(properties1));
p.store(out, properties1);
}
}
catch (Exception e) {
// log.addText("synthesis");
// e.printStackTrace();
JOptionPane.showMessageDialog(frame, "Unable to load background file.", "Error", JOptionPane.ERROR_MESSAGE);
check = "";
}
}
if (new File(properties2).exists()) {
String check = "";
try {
Properties p = new Properties();
FileInputStream load = new FileInputStream(new File(properties2));
p.load(load);
load.close();
if (p.containsKey("learn.file")) {
String[] getProp = p.getProperty("learn.file").split(separator);
check = getProp[getProp.length - 1];
}
else {
check = "";
}
if (check.equals(oldname)) {
p.setProperty("learn.file", newname);
FileOutputStream out = new FileOutputStream(new File(properties2));
p.store(out, properties2);
}
}
catch (Exception e) {
// e.printStackTrace();
JOptionPane.showMessageDialog(frame, "Unable to load background file.", "Error", JOptionPane.ERROR_MESSAGE);
check = "";
}
}
}
updateAsyncViews(newname);
}
public void enableTabMenu(int selectedTab) {
saveButton.setEnabled(false);
saveasButton.setEnabled(false);
runButton.setEnabled(false);
refreshButton.setEnabled(false);
checkButton.setEnabled(false);
exportButton.setEnabled(false);
save.setEnabled(false);
saveAs.setEnabled(false);
saveSBOL.setEnabled(false);
saveModel.setEnabled(false);
run.setEnabled(false);
check.setEnabled(false);
exportMenu.setEnabled(false);
exportSBML.setEnabled(false);
exportSBOL.setEnabled(false);
exportCsv.setEnabled(false);
exportDat.setEnabled(false);
exportEps.setEnabled(false);
exportJpg.setEnabled(false);
exportPdf.setEnabled(false);
exportPng.setEnabled(false);
exportSvg.setEnabled(false);
exportTsd.setEnabled(false);
saveAsVerilog.setEnabled(false);
viewCircuit.setEnabled(false);
viewSG.setEnabled(false);
viewLog.setEnabled(false);
viewCoverage.setEnabled(false);
viewLearnedModel.setEnabled(false);
refresh.setEnabled(false);
if (selectedTab != -1) {
tab.setSelectedIndex(selectedTab);
}
Component comp = tab.getSelectedComponent();
if (comp instanceof GCM2SBMLEditor) {
saveButton.setEnabled(true);
saveasButton.setEnabled(true);
checkButton.setEnabled(true);
exportButton.setEnabled(true);
save.setEnabled(true);
saveAs.setEnabled(true);
saveSBOL.setEnabled(true);
check.setEnabled(true);
exportMenu.setEnabled(true);
exportSBML.setEnabled(true);
exportSBOL.setEnabled(true);
}
else if (comp instanceof SbolBrowser) {
//save.setEnabled(true);
}
else if (comp instanceof LHPNEditor) {
saveButton.setEnabled(true);
saveasButton.setEnabled(true);
save.setEnabled(true);
saveAs.setEnabled(true);
viewCircuit.setEnabled(true);
exportMenu.setEnabled(true);
exportSBML.setEnabled(true);
}
else if (comp instanceof SBML_Editor) {
saveButton.setEnabled(true);
saveasButton.setEnabled(true);
checkButton.setEnabled(true);
save.setEnabled(true);
saveAs.setEnabled(true);
check.setEnabled(true);
}
else if (comp instanceof Graph) {
saveButton.setEnabled(true);
saveasButton.setEnabled(true);
refreshButton.setEnabled(true);
exportButton.setEnabled(true);
save.setEnabled(true);
saveAs.setEnabled(true);
refresh.setEnabled(true);
exportMenu.setEnabled(true);
if (((Graph) comp).isTSDGraph()) {
exportCsv.setEnabled(true);
exportDat.setEnabled(true);
exportTsd.setEnabled(true);
}
else {
exportCsv.setEnabled(false);
exportDat.setEnabled(false);
exportTsd.setEnabled(false);
}
exportEps.setEnabled(true);
exportJpg.setEnabled(true);
exportPdf.setEnabled(true);
exportPng.setEnabled(true);
exportSvg.setEnabled(true);
}
else if (comp instanceof JTabbedPane) {
Component component = ((JTabbedPane) comp).getSelectedComponent();
Component learnComponent = null;
Boolean learn = false;
Boolean learnLHPN = false;
for (String s : new File(root + separator + tab.getTitleAt(tab.getSelectedIndex())).list()) {
if (s.contains("_sg.dot")) {
viewSG.setEnabled(true);
}
}
for (Component c : ((JTabbedPane) comp).getComponents()) {
if (c instanceof LearnGCM) {
learn = true;
learnComponent = c;
}
else if (c instanceof LearnLHPN) {
learnLHPN = true;
learnComponent = c;
}
}
if (component instanceof Graph) {
saveButton.setEnabled(true);
saveasButton.setEnabled(true);
runButton.setEnabled(true);
refreshButton.setEnabled(true);
exportButton.setEnabled(true);
save.setEnabled(true);
run.setEnabled(true);
if (learn) {
if (new File(root + separator + tab.getTitleAt(tab.getSelectedIndex()) + separator + "method.gcm").exists()) {
viewLearnedModel.setEnabled(true);
}
run.setEnabled(true);
saveModel.setEnabled(((LearnGCM) learnComponent).getViewGcmEnabled());
saveAsVerilog.setEnabled(false);
viewCircuit.setEnabled(((LearnGCM) learnComponent).getViewGcmEnabled());
viewLog.setEnabled(((LearnGCM) learnComponent).getViewLogEnabled());
}
else if (learnLHPN) {
run.setEnabled(true);
saveModel.setEnabled(((LearnLHPN) learnComponent).getViewLhpnEnabled());
saveAsVerilog.setEnabled(false);
viewLearnedModel.setEnabled(((LearnLHPN) learnComponent).getViewLhpnEnabled());
viewCircuit.setEnabled(((LearnLHPN) learnComponent).getViewLhpnEnabled());
viewLog.setEnabled(((LearnLHPN) learnComponent).getViewLogEnabled());
viewCoverage.setEnabled(((LearnLHPN) learnComponent).getViewCoverageEnabled());
}
saveAs.setEnabled(true);
refresh.setEnabled(true);
exportMenu.setEnabled(true);
if (((Graph) component).isTSDGraph()) {
exportCsv.setEnabled(true);
exportDat.setEnabled(true);
exportTsd.setEnabled(true);
}
else {
exportCsv.setEnabled(false);
exportDat.setEnabled(false);
exportTsd.setEnabled(false);
}
exportEps.setEnabled(true);
exportJpg.setEnabled(true);
exportPdf.setEnabled(true);
exportPng.setEnabled(true);
exportSvg.setEnabled(true);
}
else if (component instanceof Reb2Sac) {
saveButton.setEnabled(true);
runButton.setEnabled(true);
save.setEnabled(true);
run.setEnabled(true);
}
else if (component instanceof SBML_Editor) {
saveButton.setEnabled(true);
runButton.setEnabled(true);
save.setEnabled(true);
run.setEnabled(true);
}
else if (component instanceof GCM2SBMLEditor) {
saveButton.setEnabled(true);
runButton.setEnabled(true);
save.setEnabled(true);
run.setEnabled(true);
}
else if (component instanceof LearnGCM) {
if (new File(root + separator + tab.getTitleAt(tab.getSelectedIndex()) + separator + "method.gcm").exists()) {
viewLearnedModel.setEnabled(true);
}
saveButton.setEnabled(true);
runButton.setEnabled(true);
save.setEnabled(true);
run.setEnabled(true);
viewCircuit.setEnabled(((LearnGCM) component).getViewGcmEnabled());
viewLog.setEnabled(((LearnGCM) component).getViewLogEnabled());
saveModel.setEnabled(((LearnGCM) component).getViewGcmEnabled());
}
else if (component instanceof LearnLHPN) {
saveButton.setEnabled(true);
runButton.setEnabled(true);
save.setEnabled(true);
run.setEnabled(true);
viewLearnedModel.setEnabled(((LearnLHPN) component).getViewLhpnEnabled());
viewCircuit.setEnabled(((LearnLHPN) component).getViewLhpnEnabled());
viewLog.setEnabled(((LearnLHPN) component).getViewLogEnabled());
viewCoverage.setEnabled(((LearnLHPN) component).getViewCoverageEnabled());
saveModel.setEnabled(((LearnLHPN) learnComponent).getViewLhpnEnabled());
}
else if (component instanceof DataManager) {
saveButton.setEnabled(true);
runButton.setEnabled(true);
save.setEnabled(true);
saveAs.setEnabled(true);
if (learn) {
if (new File(root + separator + tab.getTitleAt(tab.getSelectedIndex()) + separator + "method.gcm").exists()) {
viewLearnedModel.setEnabled(true);
}
run.setEnabled(true);
saveModel.setEnabled(((LearnGCM) learnComponent).getViewGcmEnabled());
viewCircuit.setEnabled(((LearnGCM) learnComponent).getViewGcmEnabled());
viewLog.setEnabled(((LearnGCM) learnComponent).getViewLogEnabled());
}
else if (learnLHPN) {
run.setEnabled(true);
saveModel.setEnabled(((LearnLHPN) learnComponent).getViewLhpnEnabled());
viewLearnedModel.setEnabled(((LearnLHPN) learnComponent).getViewLhpnEnabled());
viewCircuit.setEnabled(((LearnLHPN) learnComponent).getViewLhpnEnabled());
viewLog.setEnabled(((LearnLHPN) learnComponent).getViewLogEnabled());
viewCoverage.setEnabled(((LearnLHPN) learnComponent).getViewCoverageEnabled());
}
}
else if (component instanceof JPanel) {
saveButton.setEnabled(true);
runButton.setEnabled(true);
save.setEnabled(true);
run.setEnabled(true);
if (learn) {
if (new File(root + separator + tab.getTitleAt(tab.getSelectedIndex()) + separator + "method.gcm").exists()) {
viewLearnedModel.setEnabled(true);
}
run.setEnabled(true);
saveModel.setEnabled(((LearnGCM) learnComponent).getViewGcmEnabled());
viewCircuit.setEnabled(((LearnGCM) learnComponent).getViewGcmEnabled());
viewLog.setEnabled(((LearnGCM) learnComponent).getViewLogEnabled());
}
else if (learnLHPN) {
run.setEnabled(true);
saveModel.setEnabled(((LearnLHPN) learnComponent).getViewLhpnEnabled());
viewLearnedModel.setEnabled(((LearnLHPN) learnComponent).getViewLhpnEnabled());
viewCircuit.setEnabled(((LearnLHPN) learnComponent).getViewLhpnEnabled());
viewLog.setEnabled(((LearnLHPN) learnComponent).getViewLogEnabled());
viewCoverage.setEnabled(((LearnLHPN) learnComponent).getViewCoverageEnabled());
}
}
else if (component instanceof JScrollPane) {
saveButton.setEnabled(true);
runButton.setEnabled(true);
save.setEnabled(true);
run.setEnabled(true);
}
}
else if (comp instanceof JPanel) {
if (comp.getName().equals("Verification")) {
saveButton.setEnabled(true);
saveasButton.setEnabled(true);
runButton.setEnabled(true);
save.setEnabled(true);
run.setEnabled(true);
viewTrace.setEnabled(((Verification) comp).getViewTraceEnabled());
viewLog.setEnabled(((Verification) comp).getViewLogEnabled());
}
else if (comp.getName().equals("Synthesis")) {
saveButton.setEnabled(true);
saveasButton.setEnabled(true);
runButton.setEnabled(true);
save.setEnabled(true);
run.setEnabled(true);
viewRules.setEnabled(((Synthesis) comp).getViewRulesEnabled());
viewTrace.setEnabled(((Synthesis) comp).getViewTraceEnabled());
viewCircuit.setEnabled(((Synthesis) comp).getViewCircuitEnabled());
viewLog.setEnabled(((Synthesis) comp).getViewLogEnabled());
}
}
else if (comp instanceof JScrollPane) {
saveButton.setEnabled(true);
saveasButton.setEnabled(true);
save.setEnabled(true);
saveAs.setEnabled(true);
}
}
private void enableTreeMenu() {
viewModGraph.setEnabled(false);
viewModBrowser.setEnabled(false);
createAnal.setEnabled(false);
createLearn.setEnabled(false);
createVer.setEnabled(false);
createSbml.setEnabled(false);
check.setEnabled(false);
copy.setEnabled(false);
rename.setEnabled(false);
delete.setEnabled(false);
viewModel.setEnabled(false);
viewRules.setEnabled(false);
viewTrace.setEnabled(false);
viewCircuit.setEnabled(false);
viewLHPN.setEnabled(false);
saveAsVerilog.setEnabled(false);
if (tree.getFile() != null) {
if (tree.getFile().equals(root)) {
}
else if (tree.getFile().length() > 4 && tree.getFile().substring(tree.getFile().length() - 5).equals(".sbml")
|| tree.getFile().length() > 3 && tree.getFile().substring(tree.getFile().length() - 4).equals(".xml")) {
viewModGraph.setEnabled(true);
viewModGraph.setActionCommand("graph");
viewModBrowser.setEnabled(true);
createAnal.setEnabled(true);
createAnal.setActionCommand("simulate");
createLearn.setEnabled(true);
copy.setEnabled(true);
rename.setEnabled(true);
delete.setEnabled(true);
viewModel.setEnabled(true);
}
else if (tree.getFile().length() > 3 && tree.getFile().substring(tree.getFile().length() - 4).equals(".gcm")) {
viewModGraph.setEnabled(true);
createAnal.setEnabled(true);
createAnal.setActionCommand("createSim");
createLearn.setEnabled(true);
createSbml.setEnabled(true);
copy.setEnabled(true);
rename.setEnabled(true);
delete.setEnabled(true);
viewModel.setEnabled(true);
}
else if (tree.getFile().length() > 3
&& (tree.getFile().substring(tree.getFile().length() - 4).equals(".rdf") || tree.getFile().substring(tree.getFile().length() - 4)
.equals(".grf"))) {
copy.setEnabled(true);
rename.setEnabled(true);
delete.setEnabled(true);
}
else if (tree.getFile().length() > 4 && tree.getFile().substring(tree.getFile().length() - 5).equals(".vams")) {
copy.setEnabled(true);
rename.setEnabled(true);
delete.setEnabled(true);
}
else if (tree.getFile().length() > 2 && tree.getFile().substring(tree.getFile().length() - 3).equals(".sv")) {
copy.setEnabled(true);
rename.setEnabled(true);
delete.setEnabled(true);
}
else if (tree.getFile().length() > 1 && tree.getFile().substring(tree.getFile().length() - 2).equals(".g")) {
viewModel.setEnabled(true);
viewModGraph.setEnabled(true);
createSynth.setEnabled(true);
createVer.setEnabled(true);
copy.setEnabled(true);
rename.setEnabled(true);
delete.setEnabled(true);
viewLHPN.setEnabled(true);
}
else if (tree.getFile().length() > 3 && tree.getFile().substring(tree.getFile().length() - 4).equals(".lpn")) {
viewModel.setEnabled(true);
viewModGraph.setEnabled(true);
createAnal.setEnabled(true);
createAnal.setActionCommand("createAnalysis");
if (lema) {
createLearn.setEnabled(true);
}
createSynth.setEnabled(true);
createVer.setEnabled(true);
copy.setEnabled(true);
rename.setEnabled(true);
delete.setEnabled(true);
viewLHPN.setEnabled(true);
saveAsVerilog.setEnabled(true);
}
else if (tree.getFile().length() > 3
&& (tree.getFile().substring(tree.getFile().length() - 4).equals(".hse")
|| tree.getFile().substring(tree.getFile().length() - 4).equals(".unc")
|| tree.getFile().substring(tree.getFile().length() - 4).equals(".csp")
|| tree.getFile().substring(tree.getFile().length() - 4).equals(".vhd") || tree.getFile()
.substring(tree.getFile().length() - 4).equals(".rsg"))) {
viewModel.setEnabled(true);
viewModGraph.setEnabled(true);
createSynth.setEnabled(true);
createVer.setEnabled(true);
copy.setEnabled(true);
rename.setEnabled(true);
delete.setEnabled(true);
viewLHPN.setEnabled(true);
}
else if (tree.getFile().length() > 1 && tree.getFile().substring(tree.getFile().length() - 2).equals(".s") || tree.getFile().length() > 4
&& tree.getFile().substring(tree.getFile().length() - 5).equals(".inst")) {
createAnal.setEnabled(true);
createVer.setEnabled(true);
copy.setEnabled(true);
rename.setEnabled(true);
delete.setEnabled(true);
viewLHPN.setEnabled(true);
}
else if (new File(tree.getFile()).isDirectory()) {
boolean sim = false;
boolean synth = false;
boolean ver = false;
boolean learn = false;
for (String s : new File(tree.getFile()).list()) {
if (s.length() > 3 && s.substring(s.length() - 4).equals(".sim")) {
sim = true;
}
else if (s.length() > 4 && s.substring(s.length() - 4).equals(".syn")) {
synth = true;
}
else if (s.length() > 4 && s.substring(s.length() - 4).equals(".ver")) {
ver = true;
}
else if (s.length() > 4 && s.substring(s.length() - 4).equals(".lrn")) {
learn = true;
}
}
if (sim || synth || ver || learn) {
copy.setEnabled(true);
rename.setEnabled(true);
delete.setEnabled(true);
}
}
}
}
public String getRoot() {
return root;
}
public boolean checkFiles(String input, String output) {
input = input.replaceAll("
output = output.replaceAll("
if (input.equals(output)) {
Object[] options = { "Ok" };
JOptionPane.showOptionDialog(frame, "Files are the same.", "Files Same", JOptionPane.YES_NO_OPTION, JOptionPane.PLAIN_MESSAGE, null,
options, options[0]);
return false;
}
return true;
}
public boolean overwrite(String fullPath, String name) {
if (new File(fullPath).exists()) {
String[] views = canDelete(name);
Object[] options = { "Overwrite", "Cancel" };
int value;
if (views.length == 0) {
value = JOptionPane.showOptionDialog(frame, name + " already exists." + "\nDo you want to overwrite?", "Overwrite",
JOptionPane.YES_NO_OPTION, JOptionPane.PLAIN_MESSAGE, null, options, options[0]);
}
else {
String view = "";
String gcms = "";
for (int i = 0; i < views.length; i++) {
if (views[i].endsWith(".gcm")) {
gcms += views[i] + "\n";
}
else {
view += views[i] + "\n";
}
}
String message;
if (gcms.equals("")) {
message = "The file, " + name + ", already exists, and\nit is linked to the following views:\n\n" + view
+ "\n\nAre you sure you want to overwrite?";
}
else if (view.equals("")) {
message = "The file, " + name + ", already exists, and\nit is linked to the following gcms:\n\n" + gcms
+ "\n\nAre you sure you want to overwrite?";
}
else {
message = "The file, " + name + ", already exists, and\nit is linked to the following views:\n\n" + views
+ "\n\nand\nit is linked to the following gcms:\n\n" + gcms + "\n\nAre you sure you want to overwrite?";
}
JTextArea messageArea = new JTextArea(message);
messageArea.setEditable(false);
JScrollPane scroll = new JScrollPane();
scroll.setMinimumSize(new Dimension(300, 300));
scroll.setPreferredSize(new Dimension(300, 300));
scroll.setViewportView(messageArea);
value = JOptionPane.showOptionDialog(frame, scroll, "Overwrite", JOptionPane.YES_NO_OPTION, JOptionPane.PLAIN_MESSAGE, null, options,
options[0]);
value = JOptionPane.NO_OPTION;
}
if (value == JOptionPane.YES_OPTION) {
for (int i = 0; i < tab.getTabCount(); i++) {
if (tab.getTitleAt(i).equals(name)) {
tab.remove(i);
}
}
File dir = new File(fullPath);
if (dir.isDirectory()) {
deleteDir(dir);
}
else {
System.gc();
dir.delete();
}
return true;
}
else {
return false;
}
}
else {
return true;
}
}
public boolean updateOpenSBML(String sbmlName) {
for (int i = 0; i < tab.getTabCount(); i++) {
String tab = this.tab.getTitleAt(i);
if (sbmlName.equals(tab)) {
if (this.tab.getComponentAt(i) instanceof SBML_Editor) {
SBML_Editor newSBML = new SBML_Editor(root + separator + sbmlName, null, log, this, null, null);
this.tab.setComponentAt(i, newSBML);
this.tab.getComponentAt(i).setName("SBML Editor");
newSBML.save(false, "", false, true);
return true;
}
}
}
return false;
}
public void updateTabName(String oldName, String newName) {
for (int i = 0; i < tab.getTabCount(); i++) {
String tab = this.tab.getTitleAt(i);
if (oldName.equals(tab)) {
this.tab.setTitleAt(i, newName);
}
}
}
public boolean updateOpenLHPN(String lhpnName) {
for (int i = 0; i < tab.getTabCount(); i++) {
String tab = this.tab.getTitleAt(i);
if (lhpnName.equals(tab)) {
if (this.tab.getComponentAt(i) instanceof LHPNEditor) {
LHPNEditor newLHPN = new LHPNEditor(root, lhpnName, null, this, log);
this.tab.setComponentAt(i, newLHPN);
this.tab.getComponentAt(i).setName("LHPN Editor");
return true;
}
}
}
return false;
}
private String[] canDelete(String filename) {
ArrayList<String> views = new ArrayList<String>();
String[] files = new File(root).list();
for (String s : files) {
if (new File(root + separator + s).isDirectory()) {
String check = "";
if (new File(root + separator + s + separator + s + ".sim").exists()) {
try {
Scanner scan = new Scanner(new File(root + separator + s + separator + s + ".sim"));
if (scan.hasNextLine()) {
check = scan.nextLine();
check = check.split(separator)[check.split(separator).length - 1];
}
scan.close();
}
catch (Exception e) {
}
}
else if (new File(root + separator + s + separator + s + ".lrn").exists()) {
try {
Properties p = new Properties();
FileInputStream load = new FileInputStream(new File(root + separator + s + separator + s + ".lrn"));
p.load(load);
load.close();
if (p.containsKey("genenet.file")) {
String[] getProp = p.getProperty("genenet.file").split(separator);
check = getProp[getProp.length - 1];
}
else if (p.containsKey("learn.file")) {
String[] getProp = p.getProperty("learn.file").split(separator);
check = getProp[getProp.length - 1];
}
else {
check = "";
}
}
catch (Exception e) {
check = "";
}
}
else if (new File(root + separator + s + separator + s + ".ver").exists()) {
try {
Properties p = new Properties();
FileInputStream load = new FileInputStream(new File(root + separator + s + separator + s + ".lrn"));
p.load(load);
load.close();
if (p.containsKey("verification.file")) {
String[] getProp = p.getProperty("verification.file").split(separator);
check = getProp[getProp.length - 1];
}
else {
check = "";
}
}
catch (Exception e) {
check = "";
}
}
else if (new File(root + separator + s + separator + s + ".synth").exists()) {
try {
Properties p = new Properties();
FileInputStream load = new FileInputStream(new File(root + separator + s + separator + s + ".lrn"));
p.load(load);
load.close();
if (p.containsKey("synthesis.file")) {
String[] getProp = p.getProperty("synthesis.file").split(separator);
check = getProp[getProp.length - 1];
}
else {
check = "";
}
}
catch (Exception e) {
check = "";
}
}
if (check.equals(filename)) {
views.add(s);
}
}
else if (s.endsWith(".gcm") && (filename.endsWith(".gcm") || filename.endsWith(".xml") || filename.endsWith(".sbml"))) {
GCMFile gcm = new GCMFile(root);
gcm.load(root + separator + s);
if (gcm.getSBMLFile().equals(filename)) {
views.add(s);
}
for (String comp : gcm.getComponents().keySet()) {
if (gcm.getComponents().get(comp).getProperty("gcm").equals(filename)) {
views.add(s);
break;
}
}
}
}
String[] usingViews = views.toArray(new String[0]);
sort(usingViews);
return usingViews;
}
private void sort(String[] sort) {
int i, j;
String index;
for (i = 1; i < sort.length; i++) {
index = sort[i];
j = i;
while ((j > 0) && sort[j - 1].compareToIgnoreCase(index) > 0) {
sort[j] = sort[j - 1];
j = j - 1;
}
sort[j] = index;
}
}
private void reassignViews(String oldName, String newName) {
String[] files = new File(root).list();
for (String s : files) {
if (new File(root + separator + s).isDirectory()) {
String check = "";
if (new File(root + separator + s + separator + s + ".sim").exists()) {
try {
ArrayList<String> copy = new ArrayList<String>();
Scanner scan = new Scanner(new File(root + separator + s + separator + s + ".sim"));
if (scan.hasNextLine()) {
check = scan.nextLine();
check = check.split(separator)[check.split(separator).length - 1];
if (check.equals(oldName)) {
while (scan.hasNextLine()) {
copy.add(scan.nextLine());
}
scan.close();
FileOutputStream out = new FileOutputStream(new File(root + separator + s + separator + s + ".sim"));
out.write((newName + "\n").getBytes());
for (String cop : copy) {
out.write((cop + "\n").getBytes());
}
out.close();
}
else {
scan.close();
}
}
}
catch (Exception e) {
}
}
else if (new File(root + separator + s + separator + s + ".lrn").exists()) {
try {
Properties p = new Properties();
FileInputStream load = new FileInputStream(new File(root + separator + s + separator + s + ".lrn"));
p.load(load);
load.close();
if (p.containsKey("genenet.file")) {
String[] getProp = p.getProperty("genenet.file").split(separator);
check = getProp[getProp.length - 1];
if (check.equals(oldName)) {
p.setProperty("genenet.file", newName);
FileOutputStream store = new FileOutputStream(new File(root + separator + s + separator + s + ".lrn"));
p.store(store, "Learn File Data");
store.close();
}
}
}
catch (Exception e) {
}
}
}
}
}
protected JButton makeToolButton(String imageName, String actionCommand, String toolTipText, String altText) {
JButton button = new JButton();
button.setActionCommand(actionCommand);
button.setToolTipText(toolTipText);
button.addActionListener(this);
button.setIcon(new ImageIcon(imageName));
return button;
}
public static SBMLDocument readSBML(String filename) {
SBMLReader reader = new SBMLReader();
SBMLDocument document = reader.readSBML(filename);
JTextArea messageArea = new JTextArea();
messageArea.append("Conversion to SBML level " + SBML_LEVEL + " version " + SBML_VERSION + " produced the errors listed below. ");
messageArea.append("It is recommended that you fix them before using these models or you may get unexpected results.\n\n");
boolean display = false;
long numErrors = 0;
if (SBMLLevelVersion.equals("L2V4")) {
numErrors = document.checkL2v4Compatibility();
}
else {
numErrors = document.checkL3v1Compatibility();
}
if (numErrors > 0) {
display = true;
messageArea.append("
messageArea.append(filename);
messageArea.append("\n
for (long i = 0; i < numErrors; i++) {
String error = document.getError(i).getMessage();
messageArea.append(i + ":" + error + "\n");
}
}
if (display) {
final JFrame f = new JFrame("SBML Conversion Errors and Warnings");
messageArea.setLineWrap(true);
messageArea.setEditable(false);
messageArea.setSelectionStart(0);
messageArea.setSelectionEnd(0);
JScrollPane scroll = new JScrollPane();
scroll.setMinimumSize(new Dimension(600, 600));
scroll.setPreferredSize(new Dimension(600, 600));
scroll.setViewportView(messageArea);
JButton close = new JButton("Dismiss");
close.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
f.dispose();
}
});
JPanel consistencyPanel = new JPanel(new BorderLayout());
consistencyPanel.add(scroll, "Center");
consistencyPanel.add(close, "South");
f.setContentPane(consistencyPanel);
f.pack();
Dimension screenSize;
try {
Toolkit tk = Toolkit.getDefaultToolkit();
screenSize = tk.getScreenSize();
}
catch (AWTError awe) {
screenSize = new Dimension(640, 480);
}
Dimension frameSize = f.getSize();
if (frameSize.height > screenSize.height) {
frameSize.height = screenSize.height;
}
if (frameSize.width > screenSize.width) {
frameSize.width = screenSize.width;
}
int x = screenSize.width / 2 - frameSize.width / 2;
int y = screenSize.height / 2 - frameSize.height / 2;
f.setLocation(x, y);
f.setVisible(true);
}
if (document.getLevel() < SBML_LEVEL || document.getVersion() < SBML_VERSION) {
document.setLevelAndVersion(SBML_LEVEL, SBML_VERSION);
SBMLWriter writer = new SBMLWriter();
writer.writeSBML(document, filename);
document = reader.readSBML(filename);
}
return document;
}
public static void checkModelCompleteness(SBMLDocument document) {
JTextArea messageArea = new JTextArea();
messageArea.append("Model is incomplete. Cannot be simulated until the following information is provided.\n");
boolean display = false;
Model model = document.getModel();
ListOf list = model.getListOfCompartments();
for (int i = 0; i < model.getNumCompartments(); i++) {
Compartment compartment = (Compartment) list.get(i);
if (!compartment.isSetSize()) {
messageArea.append("
messageArea.append("Compartment " + compartment.getId() + " needs a size.\n");
display = true;
}
}
list = model.getListOfSpecies();
for (int i = 0; i < model.getNumSpecies(); i++) {
Species species = (Species) list.get(i);
if (!(species.isSetInitialAmount()) && !(species.isSetInitialConcentration())) {
messageArea.append("
messageArea.append("Species " + species.getId() + " needs an initial amount or concentration.\n");
display = true;
}
}
list = model.getListOfParameters();
for (int i = 0; i < model.getNumParameters(); i++) {
Parameter parameter = (Parameter) list.get(i);
if (!(parameter.isSetValue())) {
messageArea.append("
messageArea.append("Parameter " + parameter.getId() + " needs an initial value.\n");
display = true;
}
}
list = model.getListOfReactions();
for (int i = 0; i < model.getNumReactions(); i++) {
Reaction reaction = (Reaction) list.get(i);
if (!(reaction.isSetKineticLaw())) {
messageArea.append("
messageArea.append("Reaction " + reaction.getId() + " needs a kinetic law.\n");
display = true;
}
else {
ListOf params = reaction.getKineticLaw().getListOfParameters();
for (int j = 0; j < reaction.getKineticLaw().getNumParameters(); j++) {
Parameter param = (Parameter) params.get(j);
if (!(param.isSetValue())) {
messageArea.append("
messageArea.append("Local parameter " + param.getId() + " for reaction " + reaction.getId() + " needs an initial value.\n");
display = true;
}
}
}
}
if (display) {
final JFrame f = new JFrame("SBML Model Completeness Errors");
messageArea.setLineWrap(true);
messageArea.setEditable(false);
messageArea.setSelectionStart(0);
messageArea.setSelectionEnd(0);
JScrollPane scroll = new JScrollPane();
scroll.setMinimumSize(new Dimension(600, 600));
scroll.setPreferredSize(new Dimension(600, 600));
scroll.setViewportView(messageArea);
JButton close = new JButton("Dismiss");
close.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
f.dispose();
}
});
JPanel consistencyPanel = new JPanel(new BorderLayout());
consistencyPanel.add(scroll, "Center");
consistencyPanel.add(close, "South");
f.setContentPane(consistencyPanel);
f.pack();
Dimension screenSize;
try {
Toolkit tk = Toolkit.getDefaultToolkit();
screenSize = tk.getScreenSize();
}
catch (AWTError awe) {
screenSize = new Dimension(640, 480);
}
Dimension frameSize = f.getSize();
if (frameSize.height > screenSize.height) {
frameSize.height = screenSize.height;
}
if (frameSize.width > screenSize.width) {
frameSize.width = screenSize.width;
}
int x = screenSize.width / 2 - frameSize.width / 2;
int y = screenSize.height / 2 - frameSize.height / 2;
f.setLocation(x, y);
f.setVisible(true);
}
}
static final String SFILELINE = "input (\\S+?)\n";
} |
package org.treetank.pagelayer;
import org.treetank.api.IPage;
import org.treetank.utils.FastByteArrayReader;
import org.treetank.utils.FastByteArrayWriter;
public class PageReference {
private boolean mIsDirty;
private IPage mPage;
private long mStart;
private int mLength;
private long mChecksum;
public PageReference() {
this(null, -1L, -1, -1L);
}
public PageReference(final PageReference pageReference) {
this(
pageReference.mPage,
pageReference.mStart,
pageReference.mLength,
pageReference.mChecksum);
mIsDirty = true;
}
public PageReference(
final IPage page,
final long start,
final int length,
final long checksum) {
mIsDirty = false;
mPage = page;
mStart = start;
mLength = length;
mChecksum = checksum;
}
public PageReference(final FastByteArrayReader in) throws Exception {
this(null, in.readVarLong(), in.readVarInt(), in.readVarLong());
}
public final boolean isInstantiated() {
return (mPage != null);
}
public final boolean isCommitted() {
return (mStart != -1L);
}
public final boolean isDirty() {
return mIsDirty;
}
public final long getChecksum() {
return mChecksum;
}
public final void setChecksum(final long checksum) {
mChecksum = checksum;
}
public final IPage getPage() {
return mPage;
}
public final void setPage(final IPage page) {
mPage = page;
mIsDirty = true;
}
public final int getLength() {
return mLength;
}
public final void setLength(final int length) {
mLength = length;
}
public final long getStart() {
return mStart;
}
public final void setStart(final long start) {
mStart = start;
}
public final void serialize(final FastByteArrayWriter out) throws Exception {
mIsDirty = false;
out.writeVarLong(mStart);
out.writeVarInt(mLength);
out.writeVarLong(mChecksum);
}
@Override
public final boolean equals(final Object object) {
final PageReference pageReference = (PageReference) object;
return ((mChecksum == pageReference.mChecksum)
&& (mStart == pageReference.mStart) && (mLength == pageReference.mLength));
}
@Override
public final String toString() {
return "start="
+ mStart
+ ", length="
+ mLength
+ ", checksum="
+ mChecksum;
}
} |
package org.opencms.ugc.client;
import org.opencms.ugc.client.export.CmsXmlContentUgcApi;
import org.timepedia.exporter.client.ExporterUtil;
import com.google.gwt.core.client.EntryPoint;
/**
* Entry point for client-side form handling code for user-generated content module.<p>
*/
public class CmsUgcEntryPoint implements EntryPoint {
/**
* Exports the API objects as native Javascript objects.<p>
*
* @param api the API to expose as Javascript object
*/
public native void installJavascriptApi(CmsXmlContentUgcApi api) /*-{
$wnd.OpenCmsUgc = new $wnd.opencms.CmsXmlContentUgcApi(api);
}-*/;
/**
* @see com.google.gwt.core.client.EntryPoint#onModuleLoad()
*/
public void onModuleLoad() {
ExporterUtil.exportAll();
CmsXmlContentUgcApi api = new CmsXmlContentUgcApi();
installJavascriptApi(api);
callInitFunction();
}
/**
* Calls the init form method after the API has been exported.<p>
*/
private native void callInitFunction() /*-{
if ($wnd.initUgc != undefined && typeof $wnd.initUgc == 'function') {
$wnd.initUgc();
}
}-*/;
} |
package org.elasticsearch.gradle.internal.info;
import org.apache.commons.io.IOUtils;
import org.elasticsearch.gradle.internal.BwcVersions;
import org.elasticsearch.gradle.OS;
import org.elasticsearch.gradle.internal.conventions.info.GitInfo;
import org.elasticsearch.gradle.internal.conventions.info.ParallelDetector;
import org.elasticsearch.gradle.internal.conventions.util.Util;
import org.gradle.api.GradleException;
import org.gradle.api.JavaVersion;
import org.gradle.api.Plugin;
import org.gradle.api.Project;
import org.gradle.api.logging.Logger;
import org.gradle.api.logging.Logging;
import org.gradle.api.provider.Provider;
import org.gradle.api.provider.ProviderFactory;
import org.gradle.internal.jvm.Jvm;
import org.gradle.internal.jvm.inspection.JvmInstallationMetadata;
import org.gradle.internal.jvm.inspection.JvmMetadataDetector;
import org.gradle.internal.jvm.inspection.JvmVendor;
import org.gradle.jvm.toolchain.internal.InstallationLocation;
import org.gradle.jvm.toolchain.internal.JavaInstallationRegistry;
import org.gradle.util.GradleVersion;
import javax.inject.Inject;
import java.io.BufferedReader;
import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileReader;
import java.io.IOException;
import java.io.InputStreamReader;
import java.io.UncheckedIOException;
import java.nio.file.Files;
import java.time.ZoneOffset;
import java.time.ZonedDateTime;
import java.util.Arrays;
import java.util.HashMap;
import java.util.List;
import java.util.Locale;
import java.util.Map;
import java.util.Random;
import java.util.stream.Collectors;
import java.util.stream.Stream;
public class GlobalBuildInfoPlugin implements Plugin<Project> {
private static final Logger LOGGER = Logging.getLogger(GlobalBuildInfoPlugin.class);
private static final String DEFAULT_VERSION_JAVA_FILE_PATH = "server/src/main/java/org/elasticsearch/Version.java";
private static Integer _defaultParallel = null;
private final JavaInstallationRegistry javaInstallationRegistry;
private final JvmMetadataDetector metadataDetector;
private final ProviderFactory providers;
@Inject
public GlobalBuildInfoPlugin(
JavaInstallationRegistry javaInstallationRegistry,
JvmMetadataDetector metadataDetector,
ProviderFactory providers
) {
this.javaInstallationRegistry = javaInstallationRegistry;
this.metadataDetector = new ErrorTraceMetadataDetector(metadataDetector);
this.providers = providers;
}
@Override
public void apply(Project project) {
if (project != project.getRootProject()) {
throw new IllegalStateException(this.getClass().getName() + " can only be applied to the root project.");
}
GradleVersion minimumGradleVersion = GradleVersion.version(getResourceContents("/minimumGradleVersion"));
if (GradleVersion.current().compareTo(minimumGradleVersion) < 0) {
throw new GradleException("Gradle " + minimumGradleVersion.getVersion() + "+ is required");
}
JavaVersion minimumCompilerVersion = JavaVersion.toVersion(getResourceContents("/minimumCompilerVersion"));
JavaVersion minimumRuntimeVersion = JavaVersion.toVersion(getResourceContents("/minimumRuntimeVersion"));
File runtimeJavaHome = findRuntimeJavaHome();
File rootDir = project.getRootDir();
GitInfo gitInfo = GitInfo.gitInfo(rootDir);
BuildParams.init(params -> {
params.reset();
params.setRuntimeJavaHome(runtimeJavaHome);
params.setRuntimeJavaVersion(determineJavaVersion("runtime java.home", runtimeJavaHome, minimumRuntimeVersion));
params.setIsRuntimeJavaHomeSet(Jvm.current().getJavaHome().equals(runtimeJavaHome) == false);
JvmInstallationMetadata runtimeJdkMetaData = metadataDetector.getMetadata(getJavaInstallation(runtimeJavaHome).getLocation());
params.setRuntimeJavaDetails(formatJavaVendorDetails(runtimeJdkMetaData));
params.setJavaVersions(getAvailableJavaVersions());
params.setMinimumCompilerVersion(minimumCompilerVersion);
params.setMinimumRuntimeVersion(minimumRuntimeVersion);
params.setGradleJavaVersion(Jvm.current().getJavaVersion());
params.setGitRevision(gitInfo.getRevision());
params.setGitOrigin(gitInfo.getOrigin());
params.setBuildDate(ZonedDateTime.now(ZoneOffset.UTC));
params.setTestSeed(getTestSeed());
params.setIsCi(System.getenv("JENKINS_URL") != null);
params.setDefaultParallel(ParallelDetector.findDefaultParallel(project));
params.setInFipsJvm(Util.getBooleanProperty("tests.fips.enabled", false));
params.setIsSnapshotBuild(Util.getBooleanProperty("build.snapshot", true));
params.setBwcVersions(providers.provider(() -> resolveBwcVersions(rootDir)));
});
// Enforce the minimum compiler version
assertMinimumCompilerVersion(minimumCompilerVersion);
// Print global build info header just before task execution
project.getGradle().getTaskGraph().whenReady(graph -> logGlobalBuildInfo());
}
private String formatJavaVendorDetails(JvmInstallationMetadata runtimeJdkMetaData) {
JvmVendor vendor = runtimeJdkMetaData.getVendor();
return runtimeJdkMetaData.getVendor().getKnownVendor().name() + "/" + vendor.getRawVendor();
}
/* Introspect all versions of ES that may be tested against for backwards
* compatibility. It is *super* important that this logic is the same as the
* logic in VersionUtils.java. */
private static BwcVersions resolveBwcVersions(File root) {
File versionsFile = new File(root, DEFAULT_VERSION_JAVA_FILE_PATH);
try {
List<String> versionLines = IOUtils.readLines(new FileInputStream(versionsFile), "UTF-8");
return new BwcVersions(versionLines);
} catch (IOException e) {
throw new IllegalStateException("Unable to resolve to resolve bwc versions from versionsFile.", e);
}
}
private void logGlobalBuildInfo() {
final String osName = System.getProperty("os.name");
final String osVersion = System.getProperty("os.version");
final String osArch = System.getProperty("os.arch");
final Jvm gradleJvm = Jvm.current();
JvmInstallationMetadata gradleJvmMetadata = metadataDetector.getMetadata(gradleJvm.getJavaHome());
final String gradleJvmVendorDetails = gradleJvmMetadata.getVendor().getDisplayName();
final String gradleJvmImplementationVersion = gradleJvmMetadata.getImplementationVersion();
LOGGER.quiet("=======================================");
LOGGER.quiet("Elasticsearch Build Hamster says Hello!");
LOGGER.quiet(" Gradle Version : " + GradleVersion.current().getVersion());
LOGGER.quiet(" OS Info : " + osName + " " + osVersion + " (" + osArch + ")");
if (BuildParams.getIsRuntimeJavaHomeSet()) {
JvmInstallationMetadata runtimeJvm = metadataDetector.getMetadata(BuildParams.getRuntimeJavaHome());
final String runtimeJvmVendorDetails = runtimeJvm.getVendor().getDisplayName();
final String runtimeJvmImplementationVersion = runtimeJvm.getImplementationVersion();
LOGGER.quiet(" Runtime JDK Version : " + runtimeJvmImplementationVersion + " (" + runtimeJvmVendorDetails + ")");
LOGGER.quiet(" Runtime java.home : " + BuildParams.getRuntimeJavaHome());
LOGGER.quiet(" Gradle JDK Version : " + gradleJvmImplementationVersion + " (" + gradleJvmVendorDetails + ")");
LOGGER.quiet(" Gradle java.home : " + gradleJvm.getJavaHome());
} else {
LOGGER.quiet(" JDK Version : " + gradleJvmImplementationVersion + " (" + gradleJvmVendorDetails + ")");
LOGGER.quiet(" JAVA_HOME : " + gradleJvm.getJavaHome());
}
LOGGER.quiet(" Random Testing Seed : " + BuildParams.getTestSeed());
LOGGER.quiet(" In FIPS 140 mode : " + BuildParams.isInFipsJvm());
LOGGER.quiet("=======================================");
}
private JavaVersion determineJavaVersion(String description, File javaHome, JavaVersion requiredVersion) {
InstallationLocation installation = getJavaInstallation(javaHome);
JavaVersion actualVersion = metadataDetector.getMetadata(installation.getLocation()).getLanguageVersion();
if (actualVersion.isCompatibleWith(requiredVersion) == false) {
throwInvalidJavaHomeException(
description,
javaHome,
Integer.parseInt(requiredVersion.getMajorVersion()),
Integer.parseInt(actualVersion.getMajorVersion())
);
}
return actualVersion;
}
private InstallationLocation getJavaInstallation(File javaHome) {
return getAvailableJavaInstallationLocationSteam().filter(installationLocation -> isSameFile(javaHome, installationLocation))
.findFirst()
.orElseThrow(() -> new GradleException("Could not locate available Java installation in Gradle registry at: " + javaHome));
}
private boolean isSameFile(File javaHome, InstallationLocation installationLocation) {
try {
return Files.isSameFile(installationLocation.getLocation().toPath(), javaHome.toPath());
} catch (IOException ioException) {
throw new UncheckedIOException(ioException);
}
}
/**
* We resolve all available java versions using auto detected by gradles tool chain
* To make transition more reliable we only take env var provided installations into account for now
*/
private List<JavaHome> getAvailableJavaVersions() {
return getAvailableJavaInstallationLocationSteam().map(installationLocation -> {
File installationDir = installationLocation.getLocation();
JvmInstallationMetadata metadata = metadataDetector.getMetadata(installationDir);
int actualVersion = Integer.parseInt(metadata.getLanguageVersion().getMajorVersion());
return JavaHome.of(actualVersion, providers.provider(() -> installationDir));
}).collect(Collectors.toList());
}
private Stream<InstallationLocation> getAvailableJavaInstallationLocationSteam() {
return Stream.concat(
javaInstallationRegistry.listInstallations().stream(),
Stream.of(new InstallationLocation(Jvm.current().getJavaHome(), "Current JVM"))
);
}
private static String getTestSeed() {
String testSeedProperty = System.getProperty("tests.seed");
final String testSeed;
if (testSeedProperty == null) {
long seed = new Random(System.currentTimeMillis()).nextLong();
testSeed = Long.toUnsignedString(seed, 16).toUpperCase(Locale.ROOT);
} else {
testSeed = testSeedProperty;
}
return testSeed;
}
private static void throwInvalidJavaHomeException(String description, File javaHome, int expectedVersion, int actualVersion) {
String message = String.format(
Locale.ROOT,
"The %s must be set to a JDK installation directory for Java %d but is [%s] corresponding to [%s]",
description,
expectedVersion,
javaHome,
actualVersion
);
throw new GradleException(message);
}
private static void assertMinimumCompilerVersion(JavaVersion minimumCompilerVersion) {
JavaVersion currentVersion = Jvm.current().getJavaVersion();
if (System.getProperty("idea.active", "false").equals("true") == false && minimumCompilerVersion.compareTo(currentVersion) > 0) {
throw new GradleException(
"Project requires Java version of " + minimumCompilerVersion + " or newer but Gradle JAVA_HOME is " + currentVersion
);
}
}
private File findRuntimeJavaHome() {
String runtimeJavaProperty = System.getProperty("runtime.java");
if (runtimeJavaProperty != null) {
return new File(findJavaHome(runtimeJavaProperty));
}
return System.getenv("RUNTIME_JAVA_HOME") == null ? Jvm.current().getJavaHome() : new File(System.getenv("RUNTIME_JAVA_HOME"));
}
private String findJavaHome(String version) {
Provider<String> javaHomeNames = providers.gradleProperty("org.gradle.java.installations.fromEnv").forUseAtConfigurationTime();
String javaHomeEnvVar = getJavaHomeEnvVarName(version);
// Provide a useful error if we're looking for a Java home version that we haven't told Gradle about yet
Arrays.stream(javaHomeNames.get().split(","))
.filter(s -> s.equals(javaHomeEnvVar))
.findFirst()
.orElseThrow(
() -> new GradleException(
"Environment variable '"
+ javaHomeEnvVar
+ "' is not registered with Gradle installation supplier. Ensure 'org.gradle.java.installations.fromEnv' is "
+ "updated in gradle.properties file."
)
);
String versionedJavaHome = System.getenv(javaHomeEnvVar);
if (versionedJavaHome == null) {
final String exceptionMessage = String.format(
Locale.ROOT,
"$%s must be set to build Elasticsearch. "
+ "Note that if the variable was just set you "
+ "might have to run `./gradlew --stop` for "
+ "it to be picked up. See https://github.com/elastic/elasticsearch/issues/31399 details.",
javaHomeEnvVar
);
throw new GradleException(exceptionMessage);
}
return versionedJavaHome;
}
private static String getJavaHomeEnvVarName(String version) {
return "JAVA" + version + "_HOME";
}
private static int findDefaultParallel(Project project) {
// Since it costs IO to compute this, and is done at configuration time we want to cache this if possible
// It's safe to store this in a static variable since it's just a primitive so leaking memory isn't an issue
if (_defaultParallel == null) {
File cpuInfoFile = new File("/proc/cpuinfo");
if (cpuInfoFile.exists()) {
// Count physical cores on any Linux distro ( don't count hyper-threading )
Map<String, Integer> socketToCore = new HashMap<>();
String currentID = "";
try (BufferedReader reader = new BufferedReader(new FileReader(cpuInfoFile))) {
for (String line = reader.readLine(); line != null; line = reader.readLine()) {
if (line.contains(":")) {
List<String> parts = Arrays.stream(line.split(":", 2)).map(String::trim).collect(Collectors.toList());
String name = parts.get(0);
String value = parts.get(1);
// the ID of the CPU socket
if (name.equals("physical id")) {
currentID = value;
}
// Number of cores not including hyper-threading
if (name.equals("cpu cores")) {
assert currentID.isEmpty() == false;
socketToCore.put("currentID", Integer.valueOf(value));
currentID = "";
}
}
}
} catch (IOException e) {
throw new UncheckedIOException(e);
}
_defaultParallel = socketToCore.values().stream().mapToInt(i -> i).sum();
} else if (OS.current() == OS.MAC) {
// Ask macOS to count physical CPUs for us
ByteArrayOutputStream stdout = new ByteArrayOutputStream();
project.exec(spec -> {
spec.setExecutable("sysctl");
spec.args("-n", "hw.physicalcpu");
spec.setStandardOutput(stdout);
});
_defaultParallel = Integer.parseInt(stdout.toString().trim());
}
_defaultParallel = Runtime.getRuntime().availableProcessors() / 2;
}
return _defaultParallel;
}
public static String getResourceContents(String resourcePath) {
try (
BufferedReader reader = new BufferedReader(new InputStreamReader(GlobalBuildInfoPlugin.class.getResourceAsStream(resourcePath)))
) {
StringBuilder b = new StringBuilder();
for (String line = reader.readLine(); line != null; line = reader.readLine()) {
if (b.length() != 0) {
b.append('\n');
}
b.append(line);
}
return b.toString();
} catch (IOException e) {
throw new UncheckedIOException("Error trying to read classpath resource: " + resourcePath, e);
}
}
private static class ErrorTraceMetadataDetector implements JvmMetadataDetector {
private final JvmMetadataDetector delegate;
ErrorTraceMetadataDetector(JvmMetadataDetector delegate) {
this.delegate = delegate;
}
@Override
public JvmInstallationMetadata getMetadata(File file) {
JvmInstallationMetadata metadata = delegate.getMetadata(file);
if(metadata instanceof JvmInstallationMetadata.FailureInstallationMetadata) {
throw new GradleException("Jvm Metadata cannot be resolved for " + metadata.getJavaHome().toString());
}
return metadata;
}
}
} |
package gov.nih.nci.cagrid.dorian.gridca.common;
import gov.nih.nci.cagrid.common.FaultUtil;
import gov.nih.nci.cagrid.gridca.common.CRLEntry;
import gov.nih.nci.cagrid.gridca.common.CertUtil;
import gov.nih.nci.cagrid.gridca.common.KeyUtil;
import java.io.File;
import java.io.FileInputStream;
import java.io.InputStream;
import java.security.KeyPair;
import java.security.PrivateKey;
import java.security.cert.X509CRL;
import java.security.cert.X509Certificate;
import java.util.Calendar;
import java.util.Date;
import java.util.GregorianCalendar;
import junit.framework.TestCase;
import org.bouncycastle.asn1.x509.CRLReason;
import org.bouncycastle.asn1.x509.X509Name;
import org.bouncycastle.jce.PKCS10CertificationRequest;
/**
* @author <A href="mailto:langella@bmi.osu.edu">Stephen Langella </A>
* @author <A href="mailto:oster@bmi.osu.edu">Scott Oster </A>
* @author <A href="mailto:hastings@bmi.osu.edu">Shannon Hastings </A>
* @version $Id: ArgumentManagerTable.java,v 1.2 2004/10/15 16:35:16 langella
* Exp $
*/
public class TestCertUtil extends TestCase {
public void testCreateCertificateSimpleCARoot() {
try {
InputStream certLocation = TestCase.class.getResourceAsStream(Constants.SIMPLECA_CACERT);
InputStream keyLocation = TestCase.class.getResourceAsStream(Constants.SIMPLECA_CAKEY);
String keyPassword = "gomets123";
X509Certificate[] certs = createCertificateSpecifyRootCA(certLocation, keyLocation, keyPassword, "John Doe");
assertEquals(2, certs.length);
String rootSub = "O=caBIG,OU=Ohio State University,OU=Department of Biomedical Informatics,CN=caBIG Certificate Authority";
String issuedSub = "O=caBIG,OU=Ohio State University,OU=Department of Biomedical Informatics,CN=John Doe";
X509Certificate rootCert = certs[1];
X509Certificate issuedCert = certs[0];
checkCert(rootCert, rootSub, rootSub);
checkCert(issuedCert, rootSub, issuedSub);
checkWriteReadCertificate(rootCert);
checkWriteReadCertificate(issuedCert);
} catch (Exception e) {
FaultUtil.printFault(e);
assertTrue(false);
}
}
public void testCreateCertificateDorianCARoot() {
try {
InputStream certLocation = TestCase.class.getResourceAsStream(Constants.BMI_CACERT);
InputStream keyLocation = TestCase.class.getResourceAsStream(Constants.BMI_CAKEY);
String keyPassword = "gomets123";
X509Certificate[] certs = createCertificateSpecifyRootCA(certLocation, keyLocation, keyPassword, "John Doe");
assertEquals(2, certs.length);
String rootSub = "O=Ohio State University,OU=BMI,OU=MSCL,CN=BMI Certificate Authority";
String issuedSub = "O=Ohio State University,OU=BMI,OU=MSCL,CN=John Doe";
X509Certificate rootCert = certs[1];
X509Certificate issuedCert = certs[0];
checkCert(rootCert, rootSub, rootSub);
checkCert(issuedCert, rootSub, issuedSub);
checkWriteReadCertificate(rootCert);
checkWriteReadCertificate(issuedCert);
} catch (Exception e) {
FaultUtil.printFault(e);
assertTrue(false);
}
}
public void testCreateCertificateNewDorianCARootCert() {
try {
KeyPair rootPair = KeyUtil.generateRSAKeyPair1024();
assertNotNull(rootPair);
String rootSub = "O=Ohio State University,OU=BMI,OU=MSCL,CN=Temp Certificate Authority";
X509Name rootSubject = new X509Name(rootSub);
X509Certificate root = CertUtil.generateCACertificate(rootSubject, new Date(System.currentTimeMillis()),
new Date(System.currentTimeMillis() + 500000000), rootPair);
assertNotNull(root);
String certLocation = "temp-cacert.pem";
String keyLocation = "temp-cakey.pem";
String keyPassword = "gomets123";
KeyUtil.writePrivateKey(rootPair.getPrivate(), new File(keyLocation), keyPassword);
CertUtil.writeCertificate(root, new File(certLocation));
X509Certificate[] certs = createCertificateSpecifyRootCA(certLocation, keyLocation, keyPassword, "John Doe");
File f1 = new File(certLocation);
f1.delete();
File f2 = new File(keyLocation);
f2.delete();
assertEquals(2, certs.length);
String issuedSub = "O=Ohio State University,OU=BMI,OU=MSCL,CN=John Doe";
X509Certificate rootCert = certs[1];
X509Certificate issuedCert = certs[0];
checkCert(rootCert, rootSub, rootSub);
checkCert(issuedCert, rootSub, issuedSub);
checkWriteReadCertificate(rootCert);
checkWriteReadCertificate(issuedCert);
} catch (Exception e) {
FaultUtil.printFault(e);
assertTrue(false);
}
}
public void testCreateCertificateExpiredRootCert() {
try {
KeyPair rootPair = KeyUtil.generateRSAKeyPair1024();
assertNotNull(rootPair);
String rootSub = "O=Ohio State University,OU=BMI,OU=MSCL,CN=Temp Certificate Authority";
X509Name rootSubject = new X509Name(rootSub);
X509Certificate root = CertUtil.generateCACertificate(rootSubject, new Date(System.currentTimeMillis()),
new Date(System.currentTimeMillis()), rootPair);
Thread.sleep(10);
assertNotNull(root);
String certLocation = "temp-cacert.pem";
String keyLocation = "temp-cakey.pem";
String keyPassword = "gomets123";
KeyUtil.writePrivateKey(rootPair.getPrivate(), new File(keyLocation), keyPassword);
CertUtil.writeCertificate(root, new File(certLocation));
checkCert(root, rootSub, rootSub);
checkWriteReadCertificate(root);
try {
createCertificateSpecifyRootCA(certLocation, keyLocation, keyPassword, "John Doe");
assertTrue(false);
} catch (Exception e) {
assertEquals("Root Certificate Expired.", e.getMessage());
}
File f1 = new File(certLocation);
f1.delete();
File f2 = new File(keyLocation);
f2.delete();
} catch (Exception e) {
FaultUtil.printFault(e);
assertTrue(false);
}
}
public void testCreateCertificateNotYetValidRootCert() {
try {
KeyPair rootPair = KeyUtil.generateRSAKeyPair1024();
assertNotNull(rootPair);
String rootSub = "O=Ohio State University,OU=BMI,OU=MSCL,CN=Temp Certificate Authority";
X509Name rootSubject = new X509Name(rootSub);
X509Certificate root = CertUtil.generateCACertificate(rootSubject, new Date(
System.currentTimeMillis() + 50000), new Date(System.currentTimeMillis() + 500000), rootPair);
assertNotNull(root);
String certLocation = "temp-cacert.pem";
String keyLocation = "temp-cakey.pem";
String keyPassword = "gomets123";
KeyUtil.writePrivateKey(rootPair.getPrivate(), new File(keyLocation), keyPassword);
CertUtil.writeCertificate(root, new File(certLocation));
checkCert(root, rootSub, rootSub);
checkWriteReadCertificate(root);
try {
createCertificateSpecifyRootCA(certLocation, keyLocation, keyPassword, "John Doe");
assertTrue(false);
} catch (Exception e) {
assertEquals("Root Certificate not yet valid.", e.getMessage());
}
File f1 = new File(certLocation);
f1.delete();
File f2 = new File(keyLocation);
f2.delete();
} catch (Exception e) {
FaultUtil.printFault(e);
assertTrue(false);
}
}
private void checkWriteReadCertificate(X509Certificate cert) throws Exception {
String temp = "temp.pem";
CertUtil.writeCertificate(cert, new File(temp));
X509Certificate in = CertUtil.loadCertificate(new File(temp));
assertEquals(cert, in);
File f = new File(temp);
f.delete();
}
private void checkCert(X509Certificate cert, String issuer, String subject) {
assertEquals(subject, cert.getSubjectDN().toString());
assertEquals(issuer, cert.getIssuerDN().toString());
}
public X509Certificate[] createCertificateSpecifyRootCA(String certLocation, String keyLocation,
String keyPassword, String cn) throws Exception {
return createCertificateSpecifyRootCA(getFileInputStream(certLocation), getFileInputStream(keyLocation),
keyPassword, cn);
}
public X509Certificate[] createCertificateSpecifyRootCA(InputStream certLocation, InputStream keyLocation,
String keyPassword, String cn) throws Exception {
// Load a root certificate
PrivateKey rootKey = KeyUtil.loadPrivateKey(keyLocation, keyPassword);
assertNotNull(rootKey);
X509Certificate rootCert = CertUtil.loadCertificate(certLocation);
assertNotNull(rootCert);
String rootSub = rootCert.getSubjectDN().toString();
Date now = new Date(System.currentTimeMillis());
if (now.after(rootCert.getNotAfter())) {
throw new Exception("Root Certificate Expired.");
}
if (now.before(rootCert.getNotBefore())) {
throw new Exception("Root Certificate not yet valid.");
}
// create the certification request
KeyPair pair = KeyUtil.generateRSAKeyPair1024();
assertNotNull(pair);
int index = rootSub.lastIndexOf(",");
String sub = rootSub.substring(0, index) + ",CN=" + cn;
PKCS10CertificationRequest request = CertUtil.generateCertficateRequest(sub, pair);
// validate the certification request
if (!request.verify("BC")) {
System.out.println("request failed to verify!");
System.exit(1);
}
X509Certificate issuedCert = CertUtil.signCertificateRequest(request, new Date(System.currentTimeMillis()),
new Date(System.currentTimeMillis() + 500000000), rootCert, rootKey);
assertNotNull(issuedCert);
return new X509Certificate[]{issuedCert, rootCert};
}
public void testCRL() {
try {
String rootSub = "O=Ohio State University,OU=BMI,OU=MSCL,CN=TestCA";
String user1Sub = "O=Ohio State University,OU=BMI,OU=MSCL,CN=John Doe";
String user2Sub = "O=Ohio State University,OU=BMI,OU=MSCL,CN=Jane Doe";
String user3Sub = "O=Ohio State University,OU=BMI,OU=MSCL,CN=Tom Doe";
KeyPair rootKeys = KeyUtil.generateRSAKeyPair512();
assertNotNull(rootKeys);
Calendar c = new GregorianCalendar();
Date now = c.getTime();
c.add(Calendar.YEAR, 1);
Date end = c.getTime();
X509Certificate cacert = CertUtil.generateCACertificate(new X509Name(rootSub), now, end, rootKeys);
checkCert(cacert, rootSub, rootSub);
checkWriteReadCertificate(cacert);
KeyPair user1Keys = KeyUtil.generateRSAKeyPair512();
assertNotNull(user1Keys);
X509Certificate user1 = CertUtil.generateCertificate(new X509Name(user1Sub), now, end, user1Keys
.getPublic(), cacert, rootKeys.getPrivate());
checkCert(user1, rootSub, user1Sub);
checkWriteReadCertificate(user1);
KeyPair user2Keys = KeyUtil.generateRSAKeyPair512();
assertNotNull(user2Keys);
X509Certificate user2 = CertUtil.generateCertificate(new X509Name(user2Sub), now, end, user2Keys
.getPublic(), cacert, rootKeys.getPrivate());
checkCert(user2, rootSub, user2Sub);
checkWriteReadCertificate(user2);
KeyPair user3Keys = KeyUtil.generateRSAKeyPair512();
assertNotNull(user3Keys);
X509Certificate user3 = CertUtil.generateCertificate(new X509Name(user3Sub), now, end, user3Keys
.getPublic(), cacert, rootKeys.getPrivate());
checkCert(user3, rootSub, user3Sub);
checkWriteReadCertificate(user3);
CRLEntry[] crls = new CRLEntry[2];
crls[0] = new CRLEntry(user1.getSerialNumber(), CRLReason.PRIVILEGE_WITHDRAWN);
crls[1] = new CRLEntry(user3.getSerialNumber(), CRLReason.PRIVILEGE_WITHDRAWN);
X509CRL crl = CertUtil.createCRL(cacert, rootKeys.getPrivate(), crls, cacert.getNotAfter());
assertNotNull(crl);
// Test validity of CRL
crl.verify(cacert.getPublicKey());
try {
crl.verify(user1.getPublicKey());
fail("CRL verified against invalid certificate");
} catch (Exception ex) {
}
assertTrue(crl.isRevoked(user1));
assertTrue(!crl.isRevoked(user2));
assertTrue(crl.isRevoked(user3));
// Test validity after reading writing to string
String crlStr = CertUtil.writeCRL(crl);
X509CRL crl2 = CertUtil.loadCRL(crlStr);
assertEquals(crl, crl2);
crl2.verify(cacert.getPublicKey());
try {
crl2.verify(user1.getPublicKey());
fail("CRL verified against invalid certificate");
} catch (Exception ex) {
}
assertTrue(crl2.isRevoked(user1));
assertTrue(!crl2.isRevoked(user2));
assertTrue(crl2.isRevoked(user3));
// Test validity after reading writing to file
File f = new File("temp-crl.pem");
CertUtil.writeCRL(crl,f);
X509CRL crl3 = CertUtil.loadCRL(f);
assertEquals(crl, crl3);
crl3.verify(cacert.getPublicKey());
try {
crl3.verify(user1.getPublicKey());
fail("CRL verified against invalid certificate");
} catch (Exception ex) {
}
assertTrue(crl3.isRevoked(user1));
assertTrue(!crl3.isRevoked(user2));
assertTrue(crl3.isRevoked(user3));
f.delete();
} catch (Exception e) {
FaultUtil.printFault(e);
assertTrue(false);
}
}
private static FileInputStream getFileInputStream(String file) throws Exception {
return new FileInputStream(new File(file));
}
} |
package com.ForgeEssentials.chat;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.List;
import java.util.TreeSet;
import java.util.regex.Matcher;
import net.minecraft.entity.player.EntityPlayer;
import net.minecraft.network.packet.NetHandler;
import net.minecraft.network.packet.Packet3Chat;
import net.minecraftforge.event.ForgeSubscribe;
import net.minecraftforge.event.ServerChatEvent;
import com.ForgeEssentials.core.PlayerInfo;
import com.ForgeEssentials.permission.Group;
import com.ForgeEssentials.permission.APIHelper;
import com.ForgeEssentials.permission.SqlHelper;
import com.ForgeEssentials.permission.Zone;
import com.ForgeEssentials.permission.ZoneManager;
import com.ForgeEssentials.permission.query.PermQueryPlayer;
import com.ForgeEssentials.util.FEChatFormatCodes;
import com.ForgeEssentials.util.FunctionHelper;
import com.ForgeEssentials.util.OutputHandler;
import com.ForgeEssentials.util.AreaSelector.Point;
import cpw.mods.fml.common.network.IChatListener;
public class Chat implements IChatListener
{
public static List<String> bannedWords = new ArrayList<String>();
public static boolean censor;
@ForgeSubscribe
public void chatEvent(ServerChatEvent event)
{
/*
* Mute?
*/
if (event.player.getEntityData().getCompoundTag(EntityPlayer.PERSISTED_NBT_TAG).getBoolean("mute"))
{
event.setCanceled(true);
event.player.sendChatToPlayer("You are muted.");
return;
}
String message = event.message;
String nickname = event.username;
//Perhaps add option to completely remove message?
/*if (censor && remove)
{
event.setCanceled(true);
event.player.sendChatToPlayer("Such language is not tolerated.");
return;
}*/
if (censor)
{
for (String word : bannedWords)
{
message = replaceAllIgnoreCase(message, word, "
}
}
/*
* Nickname
*/
if (event.player.getEntityData().getCompoundTag(EntityPlayer.PERSISTED_NBT_TAG).hasKey("nickname"))
{
nickname = event.player.getEntityData().getCompoundTag(EntityPlayer.PERSISTED_NBT_TAG).getString("nickname");
}
/*
* Colorize!
*/
if (event.message.contains("&"))
{
if (APIHelper.checkPermAllowed(new PermQueryPlayer(event.player, "ForgeEssentials.chat.usecolor")))
{
message = FunctionHelper.formatColors(event.message);
}
}
String rank = "";
String zoneID = "";
String gPrefix = "";
String gSuffix = "";
PlayerInfo info = PlayerInfo.getPlayerInfo(event.player);
String playerPrefix = info.prefix == null ? "" : FunctionHelper.formatColors(info.prefix).trim();
String playerSuffix = info.suffix == null ? "" : FunctionHelper.formatColors(info.suffix).trim();
Zone zone = ZoneManager.getWhichZoneIn(new Point(event.player), event.player.worldObj);
zoneID = zone.getZoneName();
// Group stuff!!! DO NOT TOUCH!!!
{
rank = getGroupRankString(event.username);
gPrefix = getGroupPrefixString(event.username);
gPrefix = FunctionHelper.formatColors(gPrefix).trim();
gSuffix = getGroupSuffixString(event.username);
gSuffix = FunctionHelper.formatColors(gSuffix).trim();
}
//It may be beneficial to make this a public function. -RlonRyan
String format = ConfigChat.chatFormat;
format = ConfigChat.chatFormat == null || ConfigChat.chatFormat.trim().isEmpty() ? "<%username>%message" : ConfigChat.chatFormat;
// replace group, zone, and rank
format = replaceAllIgnoreCase(format, "%rank", rank);
format = replaceAllIgnoreCase(format, "%zone", zoneID);
format = replaceAllIgnoreCase(format, "%groupPrefix", gPrefix);
format = replaceAllIgnoreCase(format, "%groupSuffix", gSuffix);
// replace colors
format = replaceAllIgnoreCase(format, "%red", FEChatFormatCodes.RED.toString());
format = replaceAllIgnoreCase(format, "%yellow", FEChatFormatCodes.YELLOW.toString());
format = replaceAllIgnoreCase(format, "%black", FEChatFormatCodes.BLACK.toString());
format = replaceAllIgnoreCase(format, "%darkblue", FEChatFormatCodes.DARKBLUE.toString());
format = replaceAllIgnoreCase(format, "%darkgreen", FEChatFormatCodes.DARKGREEN.toString());
format = replaceAllIgnoreCase(format, "%darkaqua", FEChatFormatCodes.DARKAQUA.toString());
format = replaceAllIgnoreCase(format, "%darkred", FEChatFormatCodes.DARKRED.toString());
format = replaceAllIgnoreCase(format, "%purple", FEChatFormatCodes.PURPLE.toString());
format = replaceAllIgnoreCase(format, "%gold", FEChatFormatCodes.GOLD.toString());
format = replaceAllIgnoreCase(format, "%grey", FEChatFormatCodes.GREY.toString());
format = replaceAllIgnoreCase(format, "%darkgrey", FEChatFormatCodes.DARKGREY.toString());
format = replaceAllIgnoreCase(format, "%indigo", FEChatFormatCodes.INDIGO.toString());
format = replaceAllIgnoreCase(format, "%green", FEChatFormatCodes.GREEN.toString());
format = replaceAllIgnoreCase(format, "%aqua", FEChatFormatCodes.AQUA.toString());
format = replaceAllIgnoreCase(format, "%pink", FEChatFormatCodes.PINK.toString());
format = replaceAllIgnoreCase(format, "%white", FEChatFormatCodes.WHITE.toString());
// replace MC formating
format = replaceAllIgnoreCase(format, "%random", FEChatFormatCodes.RANDOM.toString());
format = replaceAllIgnoreCase(format, "%bold", FEChatFormatCodes.BOLD.toString());
format = replaceAllIgnoreCase(format, "%strike", FEChatFormatCodes.STRIKE.toString());
format = replaceAllIgnoreCase(format, "%underline", FEChatFormatCodes.UNDERLINE.toString());
format = replaceAllIgnoreCase(format, "%italics", FEChatFormatCodes.ITALICS.toString());
format = replaceAllIgnoreCase(format, "%reset", FEChatFormatCodes.RESET.toString());
// random nice things...
format = replaceAllIgnoreCase(format, "%health", "" + event.player.getHealth());
// essentials
format = replaceAllIgnoreCase(format, "%playerPrefix", playerPrefix);
format = replaceAllIgnoreCase(format, "%playerSuffix", playerSuffix);
format = replaceAllIgnoreCase(format, "%username", nickname);
format = format.replace("%message", message);
// finally make it the chat line.
event.line = format;
}
@Override
public Packet3Chat serverChat(NetHandler handler, Packet3Chat message)
{
return message;
}
@Override
public Packet3Chat clientChat(NetHandler handler, Packet3Chat message)
{
return message;
}
private String replaceAllIgnoreCase(String text, String search, String replacement)
{
if (search.equals(replacement))
{
return text;
}
StringBuilder buffer = new StringBuilder(text);
String lowerSearch = search.toLowerCase();
int i = 0;
int prev = 0;
while ((i = buffer.toString().toLowerCase().indexOf(lowerSearch, prev)) > -1)
{
buffer.replace(i, i + search.length(), replacement);
prev = i + replacement.length();
}
return buffer.toString();
}
private String getGroupRankString(String username)
{
Matcher match = ConfigChat.groupRegex.matcher(ConfigChat.groupRankFormat);
ArrayList<TreeSet<Group>> list = getGroupsList(match, username);
String end = "";
StringBuilder temp = new StringBuilder();
for (TreeSet<Group> set : list)
{
for (Group g: set)
temp.append(g.name);
end = match.replaceFirst(temp.toString());
temp = new StringBuilder();
}
return end;
}
private String getGroupPrefixString(String username)
{
Matcher match = ConfigChat.groupRegex.matcher(ConfigChat.groupPrefixFormat);
ArrayList<TreeSet<Group>> list = getGroupsList(match, username);
String end = "";
StringBuilder temp = new StringBuilder();
for (TreeSet<Group> set : list)
{
for (Group g: set)
temp.insert(0, g.prefix);
end = match.replaceFirst(temp.toString());
temp = new StringBuilder();
}
return end;
}
private String getGroupSuffixString(String username)
{
Matcher match = ConfigChat.groupRegex.matcher(ConfigChat.groupSuffixFormat);
ArrayList<TreeSet<Group>> list = getGroupsList(match, username);
String end = "";
StringBuilder temp = new StringBuilder();
for (TreeSet<Group> set : list)
{
for (Group g: set)
temp.append(g.suffix);
end = match.replaceFirst(temp.toString());
temp = new StringBuilder();
}
return end;
}
private ArrayList<TreeSet<Group>> getGroupsList(Matcher match, String username)
{
ArrayList<TreeSet<Group>> list = new ArrayList<TreeSet<Group>>();
String whole;
String[] p;
TreeSet<Group> set;
while (match.find())
{
whole = match.group();
whole = whole.replaceAll("\\{", "").replaceAll("\\}", "");
p = whole.split("\\<\\:\\>", 2);
if (p[0].equalsIgnoreCase("..."))
p[0] = null;
if (p[1].equalsIgnoreCase("..."))
p[1] = null;
set = SqlHelper.getGroupsForChat(p[0], p[1], username);
if (set != null)
list.add(set);
}
list = removeDuplicates(list);
return list;
}
private ArrayList<TreeSet<Group>> removeDuplicates(ArrayList<TreeSet<Group>> list)
{
HashSet<Group> used = new HashSet<Group>();
for (TreeSet set: list)
{
for (Group g : used)
set.remove(g);
// add all the remaining...
used.addAll(set);
}
return list;
}
} |
package org.jgroups.tests;
import org.jgroups.Channel;
import org.jgroups.Global;
import org.jgroups.JChannel;
import org.jgroups.Message;
import org.jgroups.util.Util;
import org.testng.annotations.Test;
import java.io.*;
import java.util.Collections;
import java.util.HashMap;
import java.util.Map;
import java.util.Set;
import java.util.concurrent.Semaphore;
import java.util.concurrent.TimeUnit;
/**
* Tests correct state transfer while other members continue sending messages to the group
* @author Bela Ban
* @version $Id: StateTransferTest.java,v 1.35 2009/10/01 21:09:55 vlada Exp $
*/
@Test(groups=Global.STACK_DEPENDENT,sequential=false)
public class StateTransferTest extends ChannelTestBase {
static final int MSG_SEND_COUNT=5000;
static final String[] names= { "A", "B", "C", "D"};
static final int APP_COUNT=names.length;
@Test
public void testStateTransferFromSelfWithRegularChannel() throws Exception {
Channel ch=createChannel(true);
ch.connect("StateTransferTest");
try {
boolean rc=ch.getState(null, 2000);
assert !rc : "getState() on singleton should return false";
}
finally {
ch.close();
}
}
@Test
public void testStateTransferWhileSending() throws Exception {
StateTransferApplication[] apps=new StateTransferApplication[APP_COUNT];
try {
Semaphore semaphore=new Semaphore(APP_COUNT);
semaphore.acquire(APP_COUNT);
int from=0, to=MSG_SEND_COUNT;
for(int i=0;i < apps.length;i++) {
if(i == 0)
apps[i]=new StateTransferApplication(semaphore, names[i], from, to);
else
apps[i]=new StateTransferApplication((JChannel)apps[0].getChannel(), semaphore, names[i], from, to);
from+=MSG_SEND_COUNT;
to+=MSG_SEND_COUNT;
}
for(int i=0;i < apps.length;i++) {
StateTransferApplication app=apps[i];
app.start();
semaphore.release();
//avoid merge
Util.sleep(3000);
}
// Make sure everyone is in sync
Channel[] tmp=new Channel[apps.length];
for(int i=0; i < apps.length; i++)
tmp[i]=apps[i].getChannel();
Util.blockUntilViewsReceived(60000, 1000, tmp);
// Reacquire the semaphore tickets; when we have them all
// we know the threads are done
boolean acquired=semaphore.tryAcquire(apps.length, 30, TimeUnit.SECONDS);
if(!acquired) {
log.warn("Most likely a bug, analyse the stack below:");
log.warn(Util.dumpThreads());
}
// Sleep to ensure async messages arrive
System.out.println("Waiting for all channels to have received the " + MSG_SEND_COUNT * APP_COUNT + " messages:");
long end_time=System.currentTimeMillis() + 40000L;
while(System.currentTimeMillis() < end_time) {
boolean terminate=true;
for(StateTransferApplication app: apps) {
Map map=app.getMap();
if(map.size() != MSG_SEND_COUNT * APP_COUNT) {
terminate=false;
break;
}
}
if(terminate)
break;
else
Util.sleep(500);
}
// have we received all and the correct messages?
System.out.println("++++++++++++++++++++++++++++++++++++++");
for(int i=0;i < apps.length;i++) {
StateTransferApplication w=apps[i];
Map m=w.getMap();
log.info("map has " + m.size() + " elements");
assert m.size() == MSG_SEND_COUNT * APP_COUNT;
}
System.out.println("++++++++++++++++++++++++++++++++++++++");
Set keys=apps[0].getMap().keySet();
for(int i=0;i < apps.length;i++) {
StateTransferApplication app=apps[i];
Map m=app.getMap();
Set s=m.keySet();
assert keys.equals(s);
}
}
finally {
for(StateTransferApplication app: apps)
app.getChannel().setReceiver(null);
for(StateTransferApplication app: apps)
app.cleanup();
}
}
protected class StateTransferApplication extends PushChannelApplicationWithSemaphore {
private final Map<Object,Object> map=new HashMap<Object,Object>(MSG_SEND_COUNT * APP_COUNT);
private int from, to;
public StateTransferApplication(Semaphore semaphore, String name, int from, int to) throws Exception {
super(name, semaphore);
this.from=from;
this.to=to;
}
public StateTransferApplication(JChannel copySource,Semaphore semaphore, String name, int from, int to) throws Exception {
super(copySource,name, semaphore);
this.from=from;
this.to=to;
}
public Map<Object,Object> getMap() {
synchronized(map) {
return Collections.unmodifiableMap(map);
}
}
public void receive(Message msg) {
Object[] data=(Object[])msg.getObject();
int num_received=0;
boolean changed=false;
synchronized(map) {
int tmp_size=map.size();
map.put(data[0], data[1]);
num_received=map.size();
changed=tmp_size != num_received;
}
if(changed && num_received % 1000 == 0)
log.info(channel.getAddress() + ": received " + num_received);
// are we done?
if(num_received >= MSG_SEND_COUNT * APP_COUNT)
semaphore.release();
}
public byte[] getState() {
synchronized(map) {
try {
return Util.objectToByteBuffer(map);
}
catch(Exception e) {
e.printStackTrace();
}
}
return null;
}
@SuppressWarnings("unchecked")
public void setState(byte[] state) {
synchronized(map) {
try {
Map<Object,Object> tmp=(Map<Object,Object>)Util.objectFromByteBuffer(state);
map.putAll(tmp);
log.info(channel.getAddress() + ": received state, map has " + map.size() + " elements");
}
catch(Exception e) {
e.printStackTrace();
}
}
}
public void getState(OutputStream ostream) {
synchronized(map) {
try {
ObjectOutputStream out=new ObjectOutputStream(ostream);
out.writeObject(map);
out.close();
}
catch(IOException e) {
e.printStackTrace();
}
}
}
@SuppressWarnings("unchecked")
public void setState(InputStream istream) {
synchronized(map) {
try {
ObjectInputStream in=new ObjectInputStream(istream);
Map<Object,Object> tmp=(Map<Object,Object>)in.readObject();
Util.close(in);
map.putAll(tmp);
log.info(channel.getAddress() + ": received state, map has " + map.size() + " elements");
}
catch(Exception e) {
e.printStackTrace();
}
}
}
public void run() {
boolean acquired=false;
try {
acquired=semaphore.tryAcquire(60000L, TimeUnit.MILLISECONDS);
if(!acquired) {
throw new Exception(channel.getAddress() + " cannot acquire semaphore");
}
useChannel();
}
catch(Exception e) {
log.error(channel.getAddress() + ": " + e.getLocalizedMessage(), e);
exception=e;
}
}
protected void useChannel() throws Exception {
System.out.println(channel.getName() + ": connecting and fetching the state");
channel.connect("StateTransferTest", null, null, 30000);
System.out.println(channel.getName() + ": state transfer is done");
Object[] data=new Object[2];
for(int i=from; i < to; i++) {
data[0]=new Integer(i);
data[1]="Value
try {
channel.send(null, null, data);
if(i % 100 == 0)
Util.sleep(50);
if(i % 1000 == 0)
log.info(channel.getAddress() + ": sent " + i);
}
catch(Exception e) {
e.printStackTrace();
break;
}
}
}
}
} |
package org.jfree.chart.junit;
import junit.framework.Test;
import junit.framework.TestCase;
import junit.framework.TestSuite;
import org.jfree.chart.annotations.junit.AnnotationsPackageTests;
import org.jfree.chart.axis.junit.AxisPackageTests;
import org.jfree.chart.block.junit.BlockPackageTests;
import org.jfree.chart.entity.junit.EntityPackageTests;
import org.jfree.chart.labels.junit.LabelsPackageTests;
import org.jfree.chart.needle.junit.NeedlePackageTests;
import org.jfree.chart.plot.junit.PlotPackageTests;
import org.jfree.chart.renderer.category.junit.RendererCategoryPackageTests;
import org.jfree.chart.renderer.junit.RendererPackageTests;
import org.jfree.chart.renderer.xy.junit.RendererXYPackageTests;
import org.jfree.chart.title.junit.TitlePackageTests;
import org.jfree.chart.urls.junit.UrlsPackageTests;
import org.jfree.chart.util.junit.UtilPackageTests;
import org.jfree.data.category.junit.DataCategoryPackageTests;
import org.jfree.data.gantt.junit.DataGanttPackageTests;
import org.jfree.data.junit.DataPackageTests;
import org.jfree.data.statistics.junit.DataStatisticsPackageTests;
import org.jfree.data.time.junit.DataTimePackageTests;
import org.jfree.data.time.ohlc.junit.OHLCPackageTests;
import org.jfree.data.xy.junit.DataXYPackageTests;
public class JFreeChartTestSuite extends TestCase {
/**
* Returns a test suite to the JUnit test runner.
*
* @return The test suite.
*/
public static Test suite() {
TestSuite suite = new TestSuite("JFreeChart");
suite.addTest(ChartPackageTests.suite());
suite.addTest(AnnotationsPackageTests.suite());
suite.addTest(AxisPackageTests.suite());
suite.addTest(BlockPackageTests.suite());
suite.addTest(EntityPackageTests.suite());
suite.addTest(LabelsPackageTests.suite());
suite.addTest(NeedlePackageTests.suite());
suite.addTest(PlotPackageTests.suite());
suite.addTest(RendererPackageTests.suite());
suite.addTest(RendererCategoryPackageTests.suite());
suite.addTest(RendererXYPackageTests.suite());
suite.addTest(TitlePackageTests.suite());
suite.addTest(UrlsPackageTests.suite());
suite.addTest(UtilPackageTests.suite());
suite.addTest(DataPackageTests.suite());
suite.addTest(DataCategoryPackageTests.suite());
suite.addTest(DataStatisticsPackageTests.suite());
suite.addTest(DataTimePackageTests.suite());
suite.addTest(OHLCPackageTests.suite());
suite.addTest(DataXYPackageTests.suite());
suite.addTest(DataGanttPackageTests.suite());
return suite;
}
/**
* Runs the test suite using JUnit's text-based runner.
*
* @param args ignored.
*/
public static void main(String[] args) {
junit.textui.TestRunner.run(suite());
}
} |
package cgeo.geocaching.files;
import cgeo.geocaching.SearchResult;
import cgeo.geocaching.Settings;
import cgeo.geocaching.cgCache;
import cgeo.geocaching.cgeoapplication;
import cgeo.geocaching.enumerations.LoadFlags;
import cgeo.geocaching.test.AbstractResourceInstrumentationTestCase;
import cgeo.geocaching.test.R;
import cgeo.geocaching.utils.CancellableHandler;
import cgeo.geocaching.utils.Log;
import android.net.Uri;
import android.os.Message;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Iterator;
import java.util.List;
public class GPXImporterTest extends AbstractResourceInstrumentationTestCase {
private TestHandler importStepHandler = new TestHandler();
private TestHandler progressHandler = new TestHandler();
private int listId;
private File tempDir;
private boolean importCacheStaticMaps;
private boolean importWpStaticMaps;
public void testGetWaypointsFileNameForGpxFile() throws IOException {
String[] gpxFiles = new String[] { "1234567.gpx", "1.gpx", "1234567.9.gpx",
"1234567.GPX", "gpx.gpx.gpx", ".gpx",
"1234567_query.gpx", "123-4.gpx", "123(5).gpx" };
String[] wptsFiles = new String[] { "1234567-wpts.gpx", "1-wpts.gpx", "1234567.9-wpts.gpx",
"1234567-wpts.GPX", "gpx.gpx-wpts.gpx", "-wpts.gpx",
"1234567_query-wpts.gpx", "123-wpts-4.gpx", "123-wpts(5).gpx" };
for (int i = 0; i < gpxFiles.length; i++) {
String gpxFileName = gpxFiles[i];
String wptsFileName = wptsFiles[i];
File gpx = new File(tempDir, gpxFileName);
File wpts = new File(tempDir, wptsFileName);
// the files need to exist - we create them
assertTrue(gpx.createNewFile());
assertTrue(wpts.createNewFile());
// the "real" method check
assertEquals(wptsFileName, GPXImporter.getWaypointsFileNameForGpxFile(gpx));
// they also need to be deleted, because of case sensitive tests that will not work correct on case insensitive file systems
gpx.delete();
wpts.delete();
}
File gpx1 = new File(tempDir, "abc.gpx");
assertNull(GPXImporter.getWaypointsFileNameForGpxFile(gpx1));
}
public void testImportGpx() throws IOException {
File gc31j2h = new File(tempDir, "gc31j2h.gpx");
copyResourceToFile(R.raw.gc31j2h, gc31j2h);
GPXImporter.ImportGpxFileThread importThread = new GPXImporter.ImportGpxFileThread(gc31j2h, listId, importStepHandler, progressHandler);
runImportThread(importThread);
assertEquals(5, importStepHandler.messages.size());
Iterator<Message> iMsg = importStepHandler.messages.iterator();
assertEquals(GPXImporter.IMPORT_STEP_START, iMsg.next().what);
assertEquals(GPXImporter.IMPORT_STEP_READ_FILE, iMsg.next().what);
assertEquals(GPXImporter.IMPORT_STEP_STORE_CACHES, iMsg.next().what);
assertEquals(GPXImporter.IMPORT_STEP_STORE_STATIC_MAPS, iMsg.next().what);
assertEquals(GPXImporter.IMPORT_STEP_FINISHED, iMsg.next().what);
SearchResult search = (SearchResult) importStepHandler.messages.get(4).obj;
assertEquals(Collections.singletonList("GC31J2H"), new ArrayList<String>(search.getGeocodes()));
cgCache cache = cgeoapplication.getInstance().loadCache("GC31J2H", LoadFlags.LOAD_CACHE_OR_DB);
assertCacheProperties(cache);
// can't assert, for whatever reason the waypoints are remembered in DB
// assertNull(cache.waypoints);
}
private void runImportThread(GPXImporter.ImportThread importThread) {
importThread.start();
try {
importThread.join();
} catch (InterruptedException e) {
Log.e("GPXImporterTest.runImportThread", e);
}
importStepHandler.waitForCompletion();
}
public void testImportGpxWithWaypoints() throws IOException {
File gc31j2h = new File(tempDir, "gc31j2h.gpx");
copyResourceToFile(R.raw.gc31j2h, gc31j2h);
copyResourceToFile(R.raw.gc31j2h_wpts, new File(tempDir, "gc31j2h-wpts.gpx"));
GPXImporter.ImportGpxFileThread importThread = new GPXImporter.ImportGpxFileThread(gc31j2h, listId, importStepHandler, progressHandler);
runImportThread(importThread);
assertImportStepMessages(GPXImporter.IMPORT_STEP_START, GPXImporter.IMPORT_STEP_READ_FILE, GPXImporter.IMPORT_STEP_READ_WPT_FILE, GPXImporter.IMPORT_STEP_STORE_CACHES, GPXImporter.IMPORT_STEP_STORE_STATIC_MAPS, GPXImporter.IMPORT_STEP_FINISHED);
SearchResult search = (SearchResult) importStepHandler.messages.get(5).obj;
assertEquals(Collections.singletonList("GC31J2H"), new ArrayList<String>(search.getGeocodes()));
cgCache cache = cgeoapplication.getInstance().loadCache("GC31J2H", LoadFlags.LOAD_CACHE_OR_DB);
assertCacheProperties(cache);
assertEquals(2, cache.getWaypoints().size());
}
public void testImportGpxWithLowercaseNames() throws IOException {
final File tc2012 = new File(tempDir, "tc2012.gpx");
copyResourceToFile(R.raw.tc2012, tc2012);
final GPXImporter.ImportGpxFileThread importThread = new GPXImporter.ImportGpxFileThread(tc2012, listId, importStepHandler, progressHandler);
runImportThread(importThread);
assertImportStepMessages(GPXImporter.IMPORT_STEP_START, GPXImporter.IMPORT_STEP_READ_FILE, GPXImporter.IMPORT_STEP_STORE_CACHES, GPXImporter.IMPORT_STEP_STORE_STATIC_MAPS, GPXImporter.IMPORT_STEP_FINISHED);
final cgCache cache = cgeoapplication.getInstance().loadCache("AID1", LoadFlags.LOAD_CACHE_OR_DB);
assertCacheProperties(cache);
assertEquals("First Aid Station #1", cache.getName());
}
private void assertImportStepMessages(int... importSteps) {
for (int i = 0; i < Math.min(importSteps.length, importStepHandler.messages.size()); i++) {
assertEquals(importSteps[i], importStepHandler.messages.get(i).what);
}
assertEquals(importSteps.length, importStepHandler.messages.size());
}
public void testImportLoc() throws IOException {
File oc5952 = new File(tempDir, "oc5952.loc");
copyResourceToFile(R.raw.oc5952_loc, oc5952);
GPXImporter.ImportLocFileThread importThread = new GPXImporter.ImportLocFileThread(oc5952, listId, importStepHandler, progressHandler);
runImportThread(importThread);
assertImportStepMessages(GPXImporter.IMPORT_STEP_START, GPXImporter.IMPORT_STEP_READ_FILE, GPXImporter.IMPORT_STEP_STORE_CACHES, GPXImporter.IMPORT_STEP_STORE_STATIC_MAPS, GPXImporter.IMPORT_STEP_FINISHED);
SearchResult search = (SearchResult) importStepHandler.messages.get(4).obj;
assertEquals(Collections.singletonList("OC5952"), new ArrayList<String>(search.getGeocodes()));
cgCache cache = cgeoapplication.getInstance().loadCache("OC5952", LoadFlags.LOAD_CACHE_OR_DB);
assertCacheProperties(cache);
}
private static void assertCacheProperties(cgCache cache) {
assertNotNull(cache);
assertFalse(cache.getLocation().startsWith(","));
assertTrue(cache.isReliableLatLon());
}
public void testImportGpxError() throws IOException {
File gc31j2h = new File(tempDir, "gc31j2h.gpx");
copyResourceToFile(R.raw.gc31j2h_err, gc31j2h);
GPXImporter.ImportGpxFileThread importThread = new GPXImporter.ImportGpxFileThread(gc31j2h, listId, importStepHandler, progressHandler);
runImportThread(importThread);
assertImportStepMessages(GPXImporter.IMPORT_STEP_START, GPXImporter.IMPORT_STEP_READ_FILE, GPXImporter.IMPORT_STEP_READ_FILE, GPXImporter.IMPORT_STEP_FINISHED_WITH_ERROR);
}
public void testImportGpxCancel() throws IOException {
File gc31j2h = new File(tempDir, "gc31j2h.gpx");
copyResourceToFile(R.raw.gc31j2h, gc31j2h);
progressHandler.cancel();
GPXImporter.ImportGpxFileThread importThread = new GPXImporter.ImportGpxFileThread(gc31j2h, listId, importStepHandler, progressHandler);
runImportThread(importThread);
assertImportStepMessages(GPXImporter.IMPORT_STEP_START, GPXImporter.IMPORT_STEP_READ_FILE, GPXImporter.IMPORT_STEP_CANCELED);
}
public void testImportGpxAttachment() {
Uri uri = Uri.parse("android.resource://cgeo.geocaching.test/raw/gc31j2h");
GPXImporter.ImportGpxAttachmentThread importThread = new GPXImporter.ImportGpxAttachmentThread(uri, getInstrumentation().getContext().getContentResolver(), listId, importStepHandler, progressHandler);
runImportThread(importThread);
assertImportStepMessages(GPXImporter.IMPORT_STEP_START, GPXImporter.IMPORT_STEP_READ_FILE, GPXImporter.IMPORT_STEP_STORE_CACHES, GPXImporter.IMPORT_STEP_STORE_STATIC_MAPS, GPXImporter.IMPORT_STEP_FINISHED);
SearchResult search = (SearchResult) importStepHandler.messages.get(4).obj;
assertEquals(Collections.singletonList("GC31J2H"), new ArrayList<String>(search.getGeocodes()));
cgCache cache = cgeoapplication.getInstance().loadCache("GC31J2H", LoadFlags.LOAD_CACHE_OR_DB);
assertCacheProperties(cache);
// can't assert, for whatever reason the waypoints are remembered in DB
// assertNull(cache.waypoints);
}
public void testImportGpxZip() throws IOException {
File pq7545915 = new File(tempDir, "7545915.zip");
copyResourceToFile(R.raw.pq7545915, pq7545915);
GPXImporter.ImportGpxZipFileThread importThread = new GPXImporter.ImportGpxZipFileThread(pq7545915, listId, importStepHandler, progressHandler);
runImportThread(importThread);
assertImportStepMessages(GPXImporter.IMPORT_STEP_START, GPXImporter.IMPORT_STEP_READ_FILE, GPXImporter.IMPORT_STEP_READ_WPT_FILE, GPXImporter.IMPORT_STEP_STORE_CACHES, GPXImporter.IMPORT_STEP_STORE_STATIC_MAPS, GPXImporter.IMPORT_STEP_FINISHED);
SearchResult search = (SearchResult) importStepHandler.messages.get(5).obj;
assertEquals(Collections.singletonList("GC31J2H"), new ArrayList<String>(search.getGeocodes()));
cgCache cache = cgeoapplication.getInstance().loadCache("GC31J2H", LoadFlags.LOAD_CACHE_OR_DB);
assertCacheProperties(cache);
assertEquals(1, cache.getWaypoints().size()); // this is the original pocket query result without test waypoint
}
public void testImportGpxZipErr() throws IOException {
File pqError = new File(tempDir, "pq_error.zip");
copyResourceToFile(R.raw.pq_error, pqError);
GPXImporter.ImportGpxZipFileThread importThread = new GPXImporter.ImportGpxZipFileThread(pqError, listId, importStepHandler, progressHandler);
runImportThread(importThread);
assertImportStepMessages(GPXImporter.IMPORT_STEP_START, GPXImporter.IMPORT_STEP_FINISHED_WITH_ERROR);
}
public void testImportGpxZipAttachment() {
Uri uri = Uri.parse("android.resource://cgeo.geocaching.test/raw/pq7545915");
GPXImporter.ImportGpxZipAttachmentThread importThread = new GPXImporter.ImportGpxZipAttachmentThread(uri, getInstrumentation().getContext().getContentResolver(), listId, importStepHandler, progressHandler);
runImportThread(importThread);
assertImportStepMessages(GPXImporter.IMPORT_STEP_START, GPXImporter.IMPORT_STEP_READ_FILE, GPXImporter.IMPORT_STEP_READ_WPT_FILE, GPXImporter.IMPORT_STEP_STORE_CACHES, GPXImporter.IMPORT_STEP_STORE_STATIC_MAPS, GPXImporter.IMPORT_STEP_FINISHED);
SearchResult search = (SearchResult) importStepHandler.messages.get(5).obj;
assertEquals(Collections.singletonList("GC31J2H"), new ArrayList<String>(search.getGeocodes()));
cgCache cache = cgeoapplication.getInstance().loadCache("GC31J2H", LoadFlags.LOAD_CACHE_OR_DB);
assertCacheProperties(cache);
assertEquals(1, cache.getWaypoints().size()); // this is the original pocket query result without test waypoint
}
static class TestHandler extends CancellableHandler {
private final List<Message> messages = new ArrayList<Message>();
private long lastMessage = System.currentTimeMillis();
@Override
public synchronized void handleRegularMessage(Message msg) {
final Message msg1 = Message.obtain();
msg1.copyFrom(msg);
messages.add(msg1);
lastMessage = System.currentTimeMillis();
notify();
}
public synchronized void waitForCompletion(final long milliseconds, final int maxMessages) {
try {
while (System.currentTimeMillis() - lastMessage <= milliseconds && messages.size() <= maxMessages) {
wait(milliseconds);
}
} catch (InterruptedException e) {
// intentionally left blank
}
}
public void waitForCompletion() {
// Use reasonable defaults
waitForCompletion(1000, 10);
}
}
@Override
protected void setUp() throws Exception {
super.setUp();
tempDir = new File(System.getProperty("java.io.tmpdir"), "cgeogpxesTest");
tempDir.mkdir();
// workaround to get storage initialized
cgeoapplication.getInstance().getAllHistoricCachesCount();
listId = cgeoapplication.getInstance().createList("cgeogpxesTest");
importCacheStaticMaps = Settings.isStoreOfflineMaps();
Settings.setStoreOfflineMaps(true);
importWpStaticMaps = Settings.isStoreOfflineWpMaps();
Settings.setStoreOfflineWpMaps(true);
}
@Override
protected void tearDown() throws Exception {
cgeoapplication.getInstance().removeList(listId);
deleteDirectory(tempDir);
Settings.setStoreOfflineMaps(importCacheStaticMaps);
Settings.setStoreOfflineWpMaps(importWpStaticMaps);
super.tearDown();
}
private static void deleteDirectory(File dir) {
for (File f : dir.listFiles()) {
if (f.isFile()) {
f.delete();
} else if (f.isDirectory()) {
deleteDirectory(f);
}
}
dir.delete();
}
} |
package SimpleSocketTwimeClient;
import org.agrona.concurrent.UnsafeBuffer;
import sbe.*;
import java.io.IOException;
import java.math.BigDecimal;
import java.nio.ByteBuffer;
import java.nio.channels.Channels;
import java.nio.channels.WritableByteChannel;
public class AbstractTwimeClient implements Runnable{
private MessageHeaderDecoder messageHeaderDecoder = new MessageHeaderDecoder();
protected long receivedSequenceNum = 0;
protected long retransmissionCount = 0;
private TwimeHeartBeatProcess heartBeatProcess = null;
private long intervalMsec = 0;
private WritableByteChannel outputChannel = null;
private String userAccount = null;
private String clientId = null;
private long lastSendTime = 0;
private int socketReadTimeoutMsec = 10000;
private ByteBuffer byteBuffer = ByteBuffer.allocateDirect(4096);
private UnsafeBuffer directBuffer = new UnsafeBuffer(byteBuffer);
private int bufferOffset = 0;
private int encodingLength = 0;
private String hostAddress = null;
private int connectionPort;
//decoders
private EstablishmentAckDecoder establishmentAckDecoder = new EstablishmentAckDecoder();
private EstablishmentRejectDecoder establishmentRejectDecoder = new EstablishmentRejectDecoder();
private SequenceDecoder sequenceDecoder = new SequenceDecoder();
private TerminateDecoder terminateDecoder = new TerminateDecoder();
private OrderMassCancelResponseDecoder orderMassCancelResponseDecoder = new OrderMassCancelResponseDecoder();
private SessionRejectDecoder sessionRejectDecoder = new SessionRejectDecoder();
private RetransmissionDecoder retransmissionDecoder = new RetransmissionDecoder();
private NewOrderRejectDecoder newOrderRejectDecoder = new NewOrderRejectDecoder();
private NewOrderSingleResponseDecoder newOrderSingleResponseDecoder = new NewOrderSingleResponseDecoder();
private OrderCancelResponseDecoder orderCancelResponseDecoder = new OrderCancelResponseDecoder();
private ExecutionSingleReportDecoder executionSingleReportDecoder = new ExecutionSingleReportDecoder();
private SystemEventDecoder systemEventDecoder = new SystemEventDecoder();
private EmptyBookDecoder emptyBookDecoder = new EmptyBookDecoder();
private OrderReplaceResponseDecoder orderReplaceResponseDecoder = new OrderReplaceResponseDecoder();
//encoders
private MessageHeaderEncoder headerEncoder = new MessageHeaderEncoder();
private EstablishEncoder establishEncoder = new EstablishEncoder();
private RetransmitRequestEncoder retransmitRequestEncoder = new RetransmitRequestEncoder();
private OrderMassCancelRequestEncoder orderMassCancelRequestEncoder = new OrderMassCancelRequestEncoder();
private NewOrderSingleEncoder newOrderSingleEncoder = new NewOrderSingleEncoder();
private OrderCancelRequestEncoder orderCancelRequestEncoder = new OrderCancelRequestEncoder();
private OrderReplaceRequestEncoder orderReplaceRequestEncoder = new OrderReplaceRequestEncoder();
protected BigDecimal priceMultiplier = new BigDecimal(100000);
private ReadSocketProcess readSocketProcess = null;
@Override
public void run() {
SimpleSocketClient simpleSocketClient = new SimpleSocketClient(this.hostAddress, this.connectionPort);
simpleSocketClient.doConnect();
if (simpleSocketClient.isConnected()){
try {
outputChannel = Channels.newChannel(simpleSocketClient.getSocket().getOutputStream());
readSocketProcess = new ReadSocketProcess(simpleSocketClient.getSocket(), socketReadTimeoutMsec){
@Override
protected void processMessage(int actualReaded) {
super.processMessage(actualReaded);
int currentOffset = 0;
while(currentOffset < actualReaded) {
currentOffset = AbstractTwimeClient.this.decodeMessage(unsafeBuffer, currentOffset);
}
}
@Override
protected void onStop() {
super.onStop();
AbstractTwimeClient.this.stopHeartBeatProcess();
}
};
Thread connectionThread = new Thread(readSocketProcess);
connectionThread.start();
this.sendEstablish();
try {
connectionThread.join();
} catch (InterruptedException e) {
e.printStackTrace();
}
AbstractTwimeClient.this.stopHeartBeatProcess();
simpleSocketClient.doDisconnect();
} catch (IOException e) {
e.printStackTrace();
}
}
}
public void stopConnectionProcess(){
if (readSocketProcess != null && !readSocketProcess.isStopped()){
readSocketProcess.setStopped(true);
}
}
private void initSender(int templateId, int blockLength){
bufferOffset = encodingLength = 0;
byteBuffer.clear();
headerEncoder.wrap(directBuffer, bufferOffset)
.blockLength(blockLength)
.templateId(templateId)
.schemaId(establishEncoder.sbeSchemaId())
.version(establishEncoder.sbeSchemaVersion());
bufferOffset += headerEncoder.encodedLength();
encodingLength += headerEncoder.encodedLength();
}
public void sendNewOrderSingle(long clOrdId, int securityId, double price, long amount, int clOrdLinkId, TimeInForceEnum timeInForce, SideEnum side) throws IOException {
initSender(newOrderSingleEncoder.sbeTemplateId(), newOrderSingleEncoder.sbeBlockLength());
newOrderSingleEncoder.wrap(directBuffer, bufferOffset);
long longPrice = new BigDecimal(price).multiply(priceMultiplier).longValue();
newOrderSingleEncoder.price().mantissa(longPrice);
newOrderSingleEncoder.account(userAccount).clOrdID(clOrdId).clOrdLinkID(clOrdLinkId).orderQty(amount).securityID(securityId).timeInForce(timeInForce).side(side).checkLimit(CheckLimitEnum.Check).expireDate(NewOrderSingleEncoder.expireDateNullValue());
encodingLength += newOrderSingleEncoder.encodedLength();
sendBuffer(encodingLength);
}
public void sendOrderMassCancelRequest(long clOrdId, int clOrdLinkID, int securityId, SecurityTypeEnum securityTypeEnum, SideEnum sideEnum, String securityGroup) throws IOException {
initSender(orderMassCancelRequestEncoder.sbeTemplateId(), orderMassCancelRequestEncoder.sbeBlockLength());
orderMassCancelRequestEncoder.wrap(directBuffer, bufferOffset).account(userAccount).clOrdID(clOrdId).clOrdLinkID(clOrdLinkID).securityID(securityId).securityType(securityTypeEnum).side(sideEnum).securityGroup(securityGroup);
encodingLength += orderMassCancelRequestEncoder.encodedLength();
sendBuffer(encodingLength);
}
public void sendOrderCancelRequest(long clOrdId, long orderId) throws IOException {
initSender(orderCancelRequestEncoder.sbeTemplateId(), orderCancelRequestEncoder.sbeBlockLength());
orderCancelRequestEncoder.wrap(directBuffer, bufferOffset);
orderCancelRequestEncoder.account(userAccount).clOrdID(clOrdId).orderID(orderId);
encodingLength += orderCancelRequestEncoder.encodedLength();
sendBuffer(encodingLength);
}
public void sendOrderReplaceRequest(long clOrdId, long orderId, double newPrice, long newAmount, int clOrdLinkId, ModeEnum mode) throws IOException {
initSender(orderReplaceRequestEncoder.sbeTemplateId(), orderReplaceRequestEncoder.sbeBlockLength());
orderReplaceRequestEncoder.wrap(directBuffer, bufferOffset);
long longPrice = new BigDecimal(newPrice).multiply(priceMultiplier).longValue();
orderReplaceRequestEncoder.price().mantissa(longPrice);
orderReplaceRequestEncoder.account(userAccount).clOrdID(clOrdId).orderID(orderId).orderQty(newAmount).clOrdLinkID(clOrdLinkId).mode(mode);
encodingLength += orderReplaceRequestEncoder.encodedLength();
sendBuffer(encodingLength);
}
public void sendEstablish() throws IOException {
if (outputChannel != null) {
initSender(establishEncoder.sbeTemplateId(), establishEncoder.sbeBlockLength());
establishEncoder.wrap(directBuffer, bufferOffset).credentials(clientId).keepaliveInterval(intervalMsec).timestamp(System.currentTimeMillis());
encodingLength += establishEncoder.encodedLength();
sendBuffer(encodingLength);
}
}
public void sendRetransmitRequest(long timestamp, long fromSeqNum, long count) throws IOException{
initSender(retransmitRequestEncoder.sbeTemplateId(), retransmitRequestEncoder.sbeBlockLength());
retransmitRequestEncoder.wrap(directBuffer, bufferOffset).timestamp(timestamp).fromSeqNo(fromSeqNum).count(count);
encodingLength += retransmitRequestEncoder.encodedLength();
sendBuffer(encodingLength);
}
private void sendBuffer(int length) throws IOException {
byteBuffer.limit(length);
outputChannel.write(byteBuffer);
lastSendTime = System.currentTimeMillis();
}
private void increaseSequence(){
if (retransmissionCount > 0) {
System.out.println("
retransmissionCount
}
receivedSequenceNum ++;
}
public synchronized int decodeMessage(UnsafeBuffer unsafeBuffer, int startOffset){
int bytesOffset = startOffset;
messageHeaderDecoder.wrap(unsafeBuffer, bytesOffset);
int templateId = messageHeaderDecoder.templateId();
int schemaId = messageHeaderDecoder.schemaId();
int version = messageHeaderDecoder.version();
int blockLength = messageHeaderDecoder.blockLength();
bytesOffset += messageHeaderDecoder.encodedLength();
if (templateId > 0 && version > 0) {
if (SequenceDecoder.TEMPLATE_ID != templateId) {
System.out.println(" <<<< AbstractTwimeClient decodeMessage, schemaId: " + schemaId + " |version: " + version + " |templateId: " + templateId + " |blockLength: " + blockLength + " |bytesOffset: " + bytesOffset);
}
switch (templateId) {
case EstablishmentAckDecoder.TEMPLATE_ID:
establishmentAckDecoder.wrap(unsafeBuffer, bytesOffset, blockLength, version);
onEstablishmentAck(establishmentAckDecoder);
break;
case EstablishmentRejectDecoder.TEMPLATE_ID:
establishmentRejectDecoder.wrap(unsafeBuffer, bytesOffset, blockLength, version);
onEstablishmentReject(establishmentRejectDecoder);
break;
case SequenceDecoder.TEMPLATE_ID://heartbeat (sequence)
sequenceDecoder.wrap(unsafeBuffer, bytesOffset, blockLength, version);
onSequence(sequenceDecoder);
break;
case TerminateDecoder.TEMPLATE_ID: //terminate
terminateDecoder.wrap(unsafeBuffer, bytesOffset, blockLength, version);
onTerminate(terminateDecoder);
break;
case SessionRejectDecoder.TEMPLATE_ID:
sessionRejectDecoder.wrap(unsafeBuffer, bytesOffset, blockLength, version);
onSessionReject(sessionRejectDecoder);
break;
case RetransmissionDecoder.TEMPLATE_ID:
retransmissionDecoder.wrap(unsafeBuffer, bytesOffset, blockLength, version);
retransmissionCount = retransmissionDecoder.count();
onRetransmission(retransmissionDecoder);
break;
case OrderMassCancelResponseDecoder.TEMPLATE_ID:
orderMassCancelResponseDecoder.wrap(unsafeBuffer, bytesOffset, blockLength, version);
onOrderMassCancelResponse(orderMassCancelResponseDecoder);
increaseSequence();
break;
case NewOrderRejectDecoder.TEMPLATE_ID:
newOrderRejectDecoder.wrap(unsafeBuffer, bytesOffset, blockLength, version);
onNewOrderReject(newOrderRejectDecoder);
increaseSequence();
break;
case NewOrderSingleResponseDecoder.TEMPLATE_ID:
newOrderSingleResponseDecoder.wrap(unsafeBuffer, bytesOffset, blockLength, version);
onNewOrderSingleResponse(newOrderSingleResponseDecoder);
increaseSequence();
break;
case OrderCancelResponseDecoder.TEMPLATE_ID:
orderCancelResponseDecoder.wrap(unsafeBuffer, bytesOffset, blockLength, version);
onOrderCancelResponse(orderCancelResponseDecoder);
increaseSequence();
break;
case ExecutionSingleReportDecoder.TEMPLATE_ID:
executionSingleReportDecoder.wrap(unsafeBuffer, bytesOffset, blockLength, version);
onExecutionSingleReport(executionSingleReportDecoder);
increaseSequence();
break;
case OrderReplaceRequestDecoder.TEMPLATE_ID:
orderReplaceResponseDecoder.wrap(unsafeBuffer, bytesOffset, blockLength, version);
onOrderReplaceResponse(orderReplaceResponseDecoder);
increaseSequence();
break;
case SystemEventDecoder.TEMPLATE_ID:
systemEventDecoder.wrap(unsafeBuffer, bytesOffset, blockLength, version);
onSystemEvent(systemEventDecoder);
increaseSequence();
break;
case EmptyBookDecoder.TEMPLATE_ID:
emptyBookDecoder.wrap(unsafeBuffer, bytesOffset, blockLength, version);
onEmptyBook(emptyBookDecoder);
increaseSequence();
break;
}
bytesOffset += blockLength;
}
return bytesOffset;
}
protected void onEstablishmentAck(EstablishmentAckDecoder decoder){
if (heartBeatProcess == null) {
heartBeatProcess = new TwimeHeartBeatProcess(outputChannel, intervalMsec);
}
new Thread(heartBeatProcess).start();
}
protected void onTerminate(TerminateDecoder decoder){}
protected void onOrderMassCancelResponse(OrderMassCancelResponseDecoder decoder){}
protected void onSessionReject(SessionRejectDecoder decoder){}
protected void onEstablishmentReject(EstablishmentRejectDecoder decoder){}
protected void onSequence(SequenceDecoder decoder){}
protected void onRetransmission(RetransmissionDecoder decoder){}
protected void onNewOrderReject(NewOrderRejectDecoder decoder){}
protected void onNewOrderSingleResponse(NewOrderSingleResponseDecoder decoder){}
protected void onOrderCancelResponse(OrderCancelResponseDecoder decoder){}
protected void onOrderReplaceResponse(OrderReplaceResponseDecoder decoder){}
protected void onExecutionSingleReport(ExecutionSingleReportDecoder decoder){}
protected void onSystemEvent(SystemEventDecoder decoder){}
protected void onEmptyBook(EmptyBookDecoder decoder){}
public TwimeHeartBeatProcess getHeartBeatProcess() {
return heartBeatProcess;
}
public long getIntervalMsec() {
return intervalMsec;
}
public AbstractTwimeClient setIntervalMsec(long intervalMsec) {
this.intervalMsec = intervalMsec;
return this;
}
public String getUserAccount() {
return userAccount;
}
public AbstractTwimeClient setUserAccount(String userAccount) {
this.userAccount = userAccount;
return this;
}
public String getClientId() {
return clientId;
}
public AbstractTwimeClient setClientId(String clientId) {
this.clientId = clientId;
return this;
}
public long getLastSendTime() {
return lastSendTime;
}
public void stopHeartBeatProcess(){
if (this.getHeartBeatProcess() != null && !this.getHeartBeatProcess().isStopped()) {
this.getHeartBeatProcess().setStopped(true);
}
}
public long generateNewClientOrderId(){
return System.currentTimeMillis();
}
public String getHostAddress() {
return hostAddress;
}
public AbstractTwimeClient setHostAddress(String hostAddress) {
this.hostAddress = hostAddress;
return this;
}
public int getConnectionPort() {
return connectionPort;
}
public AbstractTwimeClient setConnectionPort(int connectionPort) {
this.connectionPort = connectionPort;
return this;
}
public long getReceivedSequenceNum() {
return receivedSequenceNum;
}
public AbstractTwimeClient setReceivedSequenceNum(long receivedSequenceNum) {
this.receivedSequenceNum = receivedSequenceNum;
return this;
}
public long getRetransmissionCount() {
return retransmissionCount;
}
public int getSocketReadTimeoutMsec() {
return socketReadTimeoutMsec;
}
public AbstractTwimeClient setSocketReadTimeoutMsec(int socketReadTimeoutMsec) {
this.socketReadTimeoutMsec = socketReadTimeoutMsec;
return this;
}
} |
package arez.processor;
import com.squareup.javapoet.AnnotationSpec;
import com.squareup.javapoet.FieldSpec;
import com.squareup.javapoet.MethodSpec;
import com.squareup.javapoet.ParameterSpec;
import com.squareup.javapoet.TypeName;
import com.squareup.javapoet.TypeSpec;
import com.squareup.javapoet.TypeVariableName;
import java.util.ArrayList;
import java.util.Collection;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import java.util.stream.Collectors;
import javax.annotation.Nonnull;
import javax.annotation.Nullable;
import javax.lang.model.AnnotatedConstruct;
import javax.lang.model.element.AnnotationMirror;
import javax.lang.model.element.AnnotationValue;
import javax.lang.model.element.Element;
import javax.lang.model.element.ElementKind;
import javax.lang.model.element.ExecutableElement;
import javax.lang.model.element.Modifier;
import javax.lang.model.element.PackageElement;
import javax.lang.model.element.TypeElement;
import javax.lang.model.element.VariableElement;
import javax.lang.model.type.DeclaredType;
import javax.lang.model.type.ExecutableType;
import javax.lang.model.type.TypeKind;
import javax.lang.model.type.TypeMirror;
import javax.lang.model.type.TypeVariable;
import javax.lang.model.util.Elements;
import javax.lang.model.util.Types;
final class ProcessorUtil
{
static final String SENTINEL_NAME = "<default>";
private ProcessorUtil()
{
}
@Nonnull
static List<TypeElement> getSuperTypes( @Nonnull final TypeElement element )
{
final List<TypeElement> superTypes = new ArrayList<>();
enumerateSuperTypes( element, superTypes );
return superTypes;
}
private static void enumerateSuperTypes( @Nonnull final TypeElement element,
@Nonnull final List<TypeElement> superTypes )
{
final TypeMirror superclass = element.getSuperclass();
if ( TypeKind.NONE != superclass.getKind() )
{
final TypeElement superclassElement = (TypeElement) ( (DeclaredType) superclass ).asElement();
superTypes.add( superclassElement );
enumerateSuperTypes( superclassElement, superTypes );
}
for ( final TypeMirror interfaceType : element.getInterfaces() )
{
final TypeElement interfaceElement = (TypeElement) ( (DeclaredType) interfaceType ).asElement();
enumerateSuperTypes( interfaceElement, superTypes );
}
}
@Nonnull
static PackageElement getPackageElement( @Nonnull final TypeElement element )
{
Element enclosingElement = element.getEnclosingElement();
while ( null != enclosingElement )
{
if ( enclosingElement instanceof PackageElement )
{
return (PackageElement) enclosingElement;
}
enclosingElement = enclosingElement.getEnclosingElement();
}
assert false;
return null;
}
@Nonnull
static List<TypeVariableName> getTypeArgumentsAsNames( @Nonnull final DeclaredType declaredType )
{
final List<TypeVariableName> variables = new ArrayList<>();
for ( final TypeMirror argument : declaredType.getTypeArguments() )
{
variables.add( TypeVariableName.get( (TypeVariable) argument ) );
}
return variables;
}
@Nonnull
static List<VariableElement> getFieldElements( @Nonnull final TypeElement element )
{
final Map<String, VariableElement> methodMap = new LinkedHashMap<>();
enumerateFieldElements( element, methodMap );
return new ArrayList<>( methodMap.values() );
}
private static void enumerateFieldElements( @Nonnull final TypeElement element,
@Nonnull final Map<String, VariableElement> fields )
{
final TypeMirror superclass = element.getSuperclass();
if ( TypeKind.NONE != superclass.getKind() )
{
enumerateFieldElements( (TypeElement) ( (DeclaredType) superclass ).asElement(), fields );
}
for ( final Element member : element.getEnclosedElements() )
{
if ( member.getKind() == ElementKind.FIELD )
{
fields.put( member.getSimpleName().toString(), (VariableElement) member );
}
}
}
@Nonnull
static List<ExecutableElement> getMethods( @Nonnull final TypeElement element,
@Nonnull final Elements elementUtils,
@Nonnull final Types typeUtils )
{
final Map<String, ArrayList<ExecutableElement>> methodMap = new LinkedHashMap<>();
enumerateMethods( element, elementUtils, typeUtils, element, methodMap );
return methodMap.values().stream().flatMap( Collection::stream ).collect( Collectors.toList() );
}
private static void enumerateMethods( @Nonnull final TypeElement scope,
@Nonnull final Elements elementUtils,
@Nonnull final Types typeUtils,
@Nonnull final TypeElement element,
@Nonnull final Map<String, ArrayList<ExecutableElement>> methods )
{
final TypeMirror superclass = element.getSuperclass();
if ( TypeKind.NONE != superclass.getKind() )
{
final TypeElement superclassElement = (TypeElement) ( (DeclaredType) superclass ).asElement();
enumerateMethods( scope, elementUtils, typeUtils, superclassElement, methods );
}
for ( final TypeMirror interfaceType : element.getInterfaces() )
{
final TypeElement interfaceElement = (TypeElement) ( (DeclaredType) interfaceType ).asElement();
enumerateMethods( scope, elementUtils, typeUtils, interfaceElement, methods );
}
for ( final Element member : element.getEnclosedElements() )
{
if ( member.getKind() == ElementKind.METHOD )
{
final ExecutableElement method = (ExecutableElement) member;
processMethod( elementUtils, typeUtils, scope, methods, method );
}
}
}
private static void processMethod( @Nonnull final Elements elementUtils,
@Nonnull final Types typeUtils,
@Nonnull final TypeElement typeElement,
@Nonnull final Map<String, ArrayList<ExecutableElement>> methods,
@Nonnull final ExecutableElement method )
{
final ExecutableType methodType =
(ExecutableType) typeUtils.asMemberOf( (DeclaredType) typeElement.asType(), method );
final String key = method.getSimpleName().toString();
final ArrayList<ExecutableElement> elements = methods.computeIfAbsent( key, k -> new ArrayList<>() );
boolean found = false;
final int size = elements.size();
for ( int i = 0; i < size; i++ )
{
final ExecutableElement executableElement = elements.get( i );
if ( method.equals( executableElement ) )
{
found = true;
break;
}
else if ( isSubsignature( typeUtils, typeElement, methodType, executableElement ) )
{
if ( !isAbstractInterfaceMethod( method ) )
{
elements.set( i, method );
}
found = true;
break;
}
else if ( elementUtils.overrides( method, executableElement, typeElement ) )
{
elements.set( i, method );
found = true;
break;
}
}
if ( !found )
{
elements.add( method );
}
}
private static boolean isAbstractInterfaceMethod( final @Nonnull ExecutableElement method )
{
return method.getModifiers().contains( Modifier.ABSTRACT ) &&
ElementKind.INTERFACE == method.getEnclosingElement().getKind();
}
private static boolean isSubsignature( @Nonnull final Types typeUtils,
@Nonnull final TypeElement typeElement,
@Nonnull final ExecutableType methodType,
@Nonnull final ExecutableElement candidate )
{
final ExecutableType candidateType =
(ExecutableType) typeUtils.asMemberOf( (DeclaredType) typeElement.asType(), candidate );
final boolean isEqual = methodType.equals( candidateType );
final boolean isSubsignature = typeUtils.isSubsignature( methodType, candidateType );
return isSubsignature || isEqual;
}
@Nonnull
static List<ExecutableElement> getConstructors( @Nonnull final TypeElement element )
{
return element.getEnclosedElements().stream().
filter( m -> m.getKind() == ElementKind.CONSTRUCTOR ).
map( m -> (ExecutableElement) m ).
collect( Collectors.toList() );
}
static void copyAccessModifiers( @Nonnull final TypeElement element, @Nonnull final TypeSpec.Builder builder )
{
if ( element.getModifiers().contains( Modifier.PUBLIC ) )
{
builder.addModifiers( Modifier.PUBLIC );
}
}
static void copyAccessModifiers( @Nonnull final TypeElement element, @Nonnull final MethodSpec.Builder builder )
{
if ( element.getModifiers().contains( Modifier.PUBLIC ) )
{
builder.addModifiers( Modifier.PUBLIC );
}
}
static void copyAccessModifiers( @Nonnull final ExecutableElement element, @Nonnull final MethodSpec.Builder builder )
{
if ( element.getModifiers().contains( Modifier.PUBLIC ) )
{
builder.addModifiers( Modifier.PUBLIC );
}
else if ( element.getModifiers().contains( Modifier.PROTECTED ) )
{
builder.addModifiers( Modifier.PROTECTED );
}
}
static void copyWhitelistedAnnotations( @Nonnull final AnnotatedConstruct element,
@Nonnull final MethodSpec.Builder builder )
{
for ( final AnnotationMirror annotation : element.getAnnotationMirrors() )
{
if ( shouldCopyAnnotation( annotation.getAnnotationType().toString() ) )
{
builder.addAnnotation( AnnotationSpec.get( annotation ) );
}
}
}
static void copyWhitelistedAnnotations( @Nonnull final AnnotatedConstruct element,
@Nonnull final ParameterSpec.Builder builder )
{
for ( final AnnotationMirror annotation : element.getAnnotationMirrors() )
{
if ( shouldCopyAnnotation( annotation.getAnnotationType().toString() ) )
{
builder.addAnnotation( AnnotationSpec.get( annotation ) );
}
}
}
static void copyWhitelistedAnnotations( @Nonnull final AnnotatedConstruct element,
@Nonnull final FieldSpec.Builder builder )
{
for ( final AnnotationMirror annotation : element.getAnnotationMirrors() )
{
if ( shouldCopyAnnotation( annotation.getAnnotationType().toString() ) )
{
builder.addAnnotation( AnnotationSpec.get( annotation ) );
}
}
}
private static boolean shouldCopyAnnotation( @Nonnull final String classname )
{
return Constants.NONNULL_ANNOTATION_CLASSNAME.equals( classname ) ||
Constants.NULLABLE_ANNOTATION_CLASSNAME.equals( classname ) ||
Constants.DEPRECATED_ANNOTATION_CLASSNAME.equals( classname );
}
static void copyExceptions( @Nonnull final ExecutableType method, @Nonnull final MethodSpec.Builder builder )
{
for ( final TypeMirror thrownType : method.getThrownTypes() )
{
builder.addException( TypeName.get( thrownType ) );
}
}
static void copyTypeParameters( @Nonnull final ExecutableType action, @Nonnull final MethodSpec.Builder builder )
{
for ( final TypeVariable typeParameter : action.getTypeVariables() )
{
builder.addTypeVariable( TypeVariableName.get( typeParameter ) );
}
}
@Nullable
static String deriveName( @Nonnull final ExecutableElement method,
@Nonnull final Pattern pattern,
@Nonnull final String name )
throws ArezProcessorException
{
if ( isSentinelName( name ) )
{
final String methodName = method.getSimpleName().toString();
final Matcher matcher = pattern.matcher( methodName );
if ( matcher.find() )
{
final String candidate = matcher.group( 1 );
return firstCharacterToLowerCase( candidate );
}
else
{
return null;
}
}
else
{
return name;
}
}
@Nonnull
static String firstCharacterToLowerCase( @Nonnull final String name )
{
return Character.toLowerCase( name.charAt( 0 ) ) + name.substring( 1 );
}
static boolean isSentinelName( @Nonnull final String name )
{
return SENTINEL_NAME.equals( name );
}
@SuppressWarnings( { "unchecked", "SameParameterValue" } )
@Nonnull
static List<TypeMirror> getTypeMirrorsAnnotationParameter( @Nonnull final Elements elements,
@Nonnull final TypeElement typeElement,
@Nonnull final String annotationClassName,
@Nonnull final String parameterName )
{
final AnnotationValue annotationValue =
getAnnotationValue( elements, typeElement, annotationClassName, parameterName );
return ( (List<AnnotationValue>) annotationValue.getValue() )
.stream()
.map( v -> (TypeMirror) v.getValue() ).collect( Collectors.toList() );
}
@Nonnull
static AnnotationValue getAnnotationValue( @Nonnull final Elements elements,
@Nonnull final AnnotatedConstruct annotated,
@Nonnull final String annotationClassName,
@Nonnull final String parameterName )
{
final AnnotationValue value = findAnnotationValue( elements, annotated, annotationClassName, parameterName );
assert null != value;
return value;
}
@Nullable
private static AnnotationValue findAnnotationValue( @Nonnull final Elements elements,
@Nonnull final AnnotatedConstruct annotated,
@Nonnull final String annotationClassName,
@Nonnull final String parameterName )
{
final AnnotationMirror mirror = findAnnotationByType( annotated, annotationClassName );
return null == mirror ? null : findAnnotationValue( elements, mirror, parameterName );
}
@Nullable
private static AnnotationValue findAnnotationValue( @Nonnull final Elements elements,
@Nonnull final AnnotationMirror annotation,
@Nonnull final String parameterName )
{
final Map<? extends ExecutableElement, ? extends AnnotationValue> values =
elements.getElementValuesWithDefaults( annotation );
final ExecutableElement annotationKey = values.keySet().stream().
filter( k -> parameterName.equals( k.getSimpleName().toString() ) ).findFirst().orElse( null );
return values.get( annotationKey );
}
@SuppressWarnings( "SameParameterValue" )
@Nullable
static AnnotationValue findAnnotationValueNoDefaults( @Nonnull final AnnotationMirror annotation,
@Nonnull final String parameterName )
{
final Map<? extends ExecutableElement, ? extends AnnotationValue> values = annotation.getElementValues();
final ExecutableElement annotationKey = values.keySet().stream().
filter( k -> parameterName.equals( k.getSimpleName().toString() ) ).findFirst().orElse( null );
return values.get( annotationKey );
}
@SuppressWarnings( "unchecked" )
@Nonnull
static <T> T getAnnotationValue( @Nonnull final Elements elements,
@Nonnull final AnnotationMirror annotation,
@Nonnull final String parameterName )
{
final AnnotationValue value = findAnnotationValue( elements, annotation, parameterName );
assert null != value;
return (T) value.getValue();
}
@SuppressWarnings( "SameParameterValue" )
@Nonnull
static AnnotationMirror getAnnotationByType( @Nonnull final Element typeElement,
@Nonnull final String annotationClassName )
{
AnnotationMirror mirror = findAnnotationByType( typeElement, annotationClassName );
assert null != mirror;
return mirror;
}
@Nullable
static AnnotationMirror findAnnotationByType( @Nonnull final AnnotatedConstruct annotated,
@Nonnull final String annotationClassName )
{
return annotated.getAnnotationMirrors().stream().
filter( a -> a.getAnnotationType().toString().equals( annotationClassName ) ).findFirst().orElse( null );
}
@Nonnull
static String toSimpleName( @Nonnull final String annotationName )
{
return annotationName.replaceAll( ".*\\.", "" );
}
static boolean isDisposableTrackableRequired( @Nonnull final Elements elementUtils,
@Nonnull final Element element )
{
final VariableElement variableElement = (VariableElement)
getAnnotationValue( elementUtils,
element,
Constants.COMPONENT_ANNOTATION_CLASSNAME,
"disposeNotifier" ).getValue();
switch ( variableElement.getSimpleName().toString() )
{
case "ENABLE":
return true;
case "DISABLE":
return false;
default:
return null == findAnnotationByType( element, Constants.SINGLETON_ANNOTATION_CLASSNAME );
}
}
} |
package gov.nih.nci.nbia.lookup;
import org.apache.http.impl.client.DefaultHttpClient;
import org.apache.http.HttpResponse;
import org.apache.http.client.methods.HttpGet;
import org.apache.http.util.EntityUtils;
import org.apache.log4j.Logger;
import org.springframework.security.oauth2.common.DefaultOAuth2AccessToken;
import gov.nih.nci.nbia.dto.StudyDTO;
import gov.nih.nci.nbia.dto.ImageDTO;
import gov.nih.nci.nbia.dynamicsearch.DynamicSearchCriteria;
import org.codehaus.jackson.JsonParseException;
import org.codehaus.jackson.map.JsonMappingException;
import org.codehaus.jackson.map.ObjectMapper;
import org.codehaus.jackson.type.TypeReference;
import org.codehaus.jackson.annotate.*;
import gov.nih.nci.nbia.searchresult.APIURLHolder;
import gov.nih.nci.nbia.searchresult.PatientSearchResult;
import gov.nih.nci.nbia.searchresult.PatientSearchResultImpl;
import javax.ws.rs.core.MultivaluedMap;
import com.sun.jersey.core.util.MultivaluedMapImpl;
import com.sun.jersey.api.representation.Form;
import com.sun.jersey.api.client.Client;
import com.sun.jersey.api.client.WebResource;
import com.sun.jersey.api.client.ClientResponse;
import com.sun.jersey.api.client.config.*;
import com.sun.jersey.api.client.filter.*;
import java.io.IOException;
import java.util.*;
import javax.ws.rs.core.MediaType;
import gov.nih.nci.nbia.dto.StudyDTO;
import org.codehaus.jackson.jaxrs.JacksonJsonProvider;
public class RESTUtil {
private static Map<String, String> userMap = new HashMap<String, String>();
private static ObjectMapper mapper = new ObjectMapper();
private static Logger logger = Logger.getLogger(RESTUtil.class);
public static List<PatientSearchResult> getDynamicSearch(List<DynamicSearchCriteria> criteria,
String stateRelation,
String userToken)
{
// Use a form because there are an unknown number of values
MultivaluedMap form = new MultivaluedMapImpl();
// stateRelation is how the criteria are logically related "AND", "OR"
form.add("stateRelation", stateRelation);
form.add("userName",userToken);
int i=0;
// Step through all criteria given, the form fields are appended with an integer
// to maintain grouping in REST call (dataGroup0, dataGroup1...)
for (DynamicSearchCriteria dcriteria:criteria){
form.add("sourceName"+i,dcriteria.getDataGroup());
form.add("itemName"+i,dcriteria.getField());
form.add("operator"+i,dcriteria.getOperator().getValue());
form.add("value"+i,dcriteria.getValue());
i++;
}
ClientConfig cc = new DefaultClientConfig();
cc.getClasses().add(JacksonJsonProvider.class);
Client client = Client.create();
client.addFilter(new LoggingFilter(System.out));
WebResource resource = client.resource(APIURLHolder.getUrl()
+"/nbia-api/services/getDynamicSearch");
ClientResponse response = resource.accept(MediaType.APPLICATION_JSON)
.type(MediaType.APPLICATION_FORM_URLENCODED)
.header("Authorization", "Bearer "+userToken)
.post(ClientResponse.class, form);
// check response status code
if (response.getStatus() != 200) {
throw new RuntimeException("Failed : HTTP error code : "
+ response.getStatus());
}
// display response
String output = response.getEntity(String.class);
List<PatientSearchResultImpl> myObjects;
try {
Object json = mapper.readValue(output, Object.class);
String indented = mapper.writerWithDefaultPrettyPrinter().writeValueAsString(json);
logger.info("Returned JSON\n"+indented);
myObjects = mapper.readValue(output, new TypeReference<List<PatientSearchResultImpl>>(){});
} catch (Exception e) {
e.printStackTrace();
return null;
}
List<PatientSearchResult> returnValue=new ArrayList<PatientSearchResult>();
for (PatientSearchResultImpl result:myObjects)
{
returnValue.add(result);
}
return returnValue;
}
public static List<StudyDTO> getStudyDrillDown(List<Integer> criteria, String userToken)
{
Form form = new Form();
form.add("userName",userToken);
// Add all selected studies to the list
for (Integer dcriteria:criteria){
form.add("list",dcriteria.toString());
}
ClientConfig cc = new DefaultClientConfig();
cc.getClasses().add(JacksonJsonProvider.class);
Client client = Client.create();
WebResource resource = client.resource(APIURLHolder.getUrl()
+"/nbia-api/services/getStudyDrillDown");
ClientResponse response = resource.accept(MediaType.APPLICATION_JSON).
header("Authorization", "Bearer "+userToken).
type(MediaType.APPLICATION_FORM_URLENCODED).
post(ClientResponse.class, form);
// check response status code
if (response.getStatus() != 200) {
throw new RuntimeException("Failed : HTTP error code : "
+ response.getStatus());
}
// display response
String output = response.getEntity(String.class);
List<StudyDTO> myObjects;
try {
Object json = mapper.readValue(output, Object.class);
String indented = mapper.writerWithDefaultPrettyPrinter().writeValueAsString(json);
logger.info("Returned JSON\n"+indented);
myObjects = mapper.readValue(output, new TypeReference<List<StudyDTO>>(){});
} catch (Exception e) {
e.printStackTrace();
return null;
}
return myObjects;
}
public static DefaultOAuth2AccessToken getToken(String userName, String password)
{
Form form = new Form();
form.add("username",userName);
form.add("password",password);
form.add("client_id","nbiaRestAPIClient");
form.add("client_secret","ItsBetweenUAndMe");
form.add("grant_type","password");
ClientConfig cc = new DefaultClientConfig();
cc.getClasses().add(JacksonJsonProvider.class);
Client client = Client.create();
WebResource resource = client.resource(APIURLHolder.getUrl()
+"/nbia-api/oauth/token");
ClientResponse response = resource.accept(MediaType.APPLICATION_JSON).
type(MediaType.APPLICATION_FORM_URLENCODED).post(ClientResponse.class, form);
// check response status code
if (response.getStatus() != 200) {
throw new RuntimeException("Failed : HTTP error code : "
+ response.getStatus());
}
// display response
String output = response.getEntity(String.class);
output="["+output+"]";
System.out.println(output);
List<DefaultOAuth2AccessToken> myObjects;
try {
Object json = mapper.readValue(output, Object.class);
String indented = mapper.writerWithDefaultPrettyPrinter().writeValueAsString(json);
logger.info("Returned JSON\n"+indented);
myObjects = mapper.readValue(output, new TypeReference<List<DefaultOAuth2AccessToken>>(){});
} catch (Exception e) {
e.printStackTrace();
return null;
}
return myObjects.get(0);
}
public static List<ImageDTO> getImageDrillDown(List<Integer> criteria, String userToken)
{
Form form = new Form();
form.add("userName",userToken);
int i=0;
// List of selected series
for (Integer dcriteria:criteria){
form.add("list",dcriteria.toString());
}
ClientConfig cc = new DefaultClientConfig();
cc.getClasses().add(JacksonJsonProvider.class);
Client client = Client.create();
WebResource resource = client.resource(APIURLHolder.getUrl()
+"/nbia-api/services/getImageDrillDown");
ClientResponse response = resource.accept(MediaType.APPLICATION_JSON).
header("Authorization", "Bearer "+userToken).
type(MediaType.APPLICATION_FORM_URLENCODED).post(ClientResponse.class, form);
// check response status code
if (response.getStatus() != 200) {
throw new RuntimeException("Failed : HTTP error code : "
+ response.getStatus());
}
// display response
String output = response.getEntity(String.class);
List<ImageDTO> myObjects;
try {
Object json = mapper.readValue(output, Object.class);
String indented = mapper.writerWithDefaultPrettyPrinter().writeValueAsString(json);
logger.info("Returned JSON\n"+indented);
myObjects = mapper.readValue(output, new TypeReference<List<ImageDTO>>(){});
} catch (Exception e) {
e.printStackTrace();
return null;
}
return myObjects;
}
public static List<PatientSearchResult> getJNLP(List<DynamicSearchCriteria> criteria,
String stateRelation,
String userToken,
List<BasketSeriesItemBean> seriesItems)
{
// Use a form because there are an unknown number of values
MultivaluedMap form = new MultivaluedMapImpl();
int i=0;
// Step through all data in series items for display in download manager
for (BasketSeriesItemBean item:seriesItems){
form.add("collection"+i,item.getProject());
form.add("patientId"+i,item.getPatientId());
form.add("annotation"+i,item.getAnnotated());
form.add("seriesInstanceUid"+i,item.getSeriesId());
i++;
}
ClientConfig cc = new DefaultClientConfig();
cc.getClasses().add(JacksonJsonProvider.class);
Client client = Client.create();
client.addFilter(new LoggingFilter(System.out));
WebResource resource = client.resource(APIURLHolder.getUrl()
+"/nbia-api/services/getDynamicSearch");
ClientResponse response = resource.accept(MediaType.APPLICATION_JSON)
.type(MediaType.APPLICATION_FORM_URLENCODED)
.header("Authorization", "Bearer "+userToken)
.post(ClientResponse.class, form);
// check response status code
if (response.getStatus() != 200) {
throw new RuntimeException("Failed : HTTP error code : "
+ response.getStatus());
}
// display response
String output = response.getEntity(String.class);
List<PatientSearchResultImpl> myObjects;
try {
Object json = mapper.readValue(output, Object.class);
String indented = mapper.writerWithDefaultPrettyPrinter().writeValueAsString(json);
logger.info("Returned JSON\n"+indented);
myObjects = mapper.readValue(output, new TypeReference<List<PatientSearchResultImpl>>(){});
} catch (Exception e) {
e.printStackTrace();
return null;
}
List<PatientSearchResult> returnValue=new ArrayList<PatientSearchResult>();
for (PatientSearchResultImpl result:myObjects)
{
returnValue.add(result);
}
return returnValue;
}
} |
package net.sf.farrago.ddl;
import java.util.*;
import net.sf.farrago.catalog.*;
import net.sf.farrago.fem.security.*;
import net.sf.farrago.session.*;
import org.eigenbase.sql.*;
/**
* DdlGrantRoleStmt represents a DDL GRANT ROLE statement.
*
* @author Quoc Tai Tran
* @version $Id$
*/
public class DdlGrantRoleStmt
extends DdlGrantStmt
{
protected List<SqlIdentifier> roleList;
/**
* Constructs a new DdlGrantRoleStmt.
*/
public DdlGrantRoleStmt()
{
super();
}
// implement DdlStmt
public void visit(DdlVisitor visitor)
{
visitor.visit(this);
}
// implement FarragoSessionDdlStmt
public void preValidate(FarragoSessionDdlValidator ddlValidator)
{
FarragoRepos repos = ddlValidator.getRepos();
FemAuthId grantorAuthId = determineGrantor(ddlValidator);
// TODO: Check that for all roles to be granted (a) the grantor must be
// the owner. Or (b) the owner has been granted with Admin Option. Need
// model change!
for (SqlIdentifier granteeId : granteeList) {
// REVIEW: SWZ: 2008-07-29: getAuthIdByName most certainly does
// not create an AuthId if it does not exist. An optimization
// here would be to modify newRoleGrant to accept AuthId instances
// instead of re-doing the lookup for granteeId for each role in
// the roleList.
// Find the repository element id for the grantee, create one if
// it does not exist
FemAuthId granteeAuthId =
FarragoCatalogUtil.getAuthIdByName(
repos,
granteeId.getSimple());
// for each role in the list, we instantiate a repository
// element. Note that this makes it easier to revoke the privs on
// the individual basis.
for (SqlIdentifier roleId : roleList) {
// create a privilege object and set its properties
FemGrant grant =
FarragoCatalogUtil.newRoleGrant(
repos,
grantorAuthId.getName(),
granteeId.getSimple(),
roleId.getSimple());
// set the privilege name (i.e. action) and properties
grant.setWithGrantOption(grantOption);
}
}
}
public void setRoleList(List<SqlIdentifier> roleList)
{
this.roleList = roleList;
}
}
// End DdlGrantRoleStmt.java |
package com.intellij.openapi.editor.impl;
import com.intellij.openapi.diagnostic.Logger;
import com.intellij.openapi.editor.FoldRegion;
import com.intellij.openapi.editor.RangeMarker;
import com.intellij.openapi.editor.colors.EditorColors;
import com.intellij.openapi.editor.ex.HighlighterIterator;
import com.intellij.openapi.editor.ex.MarkupModelEx;
import com.intellij.openapi.editor.markup.*;
import org.jetbrains.annotations.Nullable;
import java.awt.*;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Comparator;
import java.util.List;
@SuppressWarnings({"ForLoopReplaceableByForEach"}) // Way too many garbage in AbrstractList.iterator() produced otherwise.
public class IterationState {
private static final Logger LOG = Logger.getInstance("#com.intellij.openapi.editor.impl.IterationState");
private TextAttributes myMergedAttributes = new TextAttributes();
private HighlighterIterator myHighlighterIterator;
private ArrayList<RangeHighlighterImpl> myViewHighlighters;
private int myCurrentViewHighlighterIdx;
private ArrayList<RangeHighlighterImpl> myDocumentHighlighters;
private int myCurrentDocHighlighterIdx;
private int myStartOffset;
private int myEndOffset;
private int myEnd;
private int mySelectionStart;
private int mySelectionEnd;
private ArrayList<RangeHighlighterImpl> myCurrentHighlighters;
private RangeHighlighterImpl myNextViewHighlighter = null;
private RangeHighlighterImpl myNextDocumentHighlighter = null;
private FoldingModelImpl myFoldingModel = null;
private boolean hasSelection = false;
private FoldRegion myCurrentFold = null;
private TextAttributes myFoldTextAttributes = null;
private TextAttributes mySelectionAttributes = null;
private TextAttributes myCaretRowAttributes = null;
private Color myDefaultBackground = null;
private Color myDefaultForeground = null;
private int myCaretRowStart;
private int myCaretRowEnd;
private ArrayList<TextAttributes> myCachedAttributesList;
private DocumentImpl myDocument;
private EditorImpl myEditor;
private Color myReadOnlyColor;
public IterationState(EditorImpl editor, int start, boolean useCaretAndSelection) {
myDocument = (DocumentImpl)editor.getDocument();
myStartOffset = start;
myEnd = editor.getDocument().getTextLength();
myEditor = editor;
LOG.assertTrue(myStartOffset <= myEnd);
myHighlighterIterator = editor.getHighlighter().createIterator(start);
HighlighterList editorList = ((MarkupModelEx)editor.getMarkupModel()).getHighlighterList();
int longestViewHighlighterLength = editorList == null ? 0 : editorList.getLongestHighlighterLength();
myViewHighlighters = editorList == null ? null : editorList.getSortedHighlighters();
final MarkupModelEx docMarkup = (MarkupModelEx)editor.getDocument().getMarkupModel(editor.myProject);
final HighlighterList docList = docMarkup.getHighlighterList();
myDocumentHighlighters = docList != null
? docList.getSortedHighlighters()
: new ArrayList<RangeHighlighterImpl>();
int longestDocHighlighterLength = docList != null
? docList.getLongestHighlighterLength()
: 0;
hasSelection = useCaretAndSelection && editor.getSelectionModel().hasSelection();
mySelectionStart = hasSelection ? editor.getSelectionModel().getSelectionStart() : -1;
mySelectionEnd = hasSelection ? editor.getSelectionModel().getSelectionEnd() : -1;
myFoldingModel = (FoldingModelImpl)editor.getFoldingModel();
myFoldTextAttributes = myFoldingModel.getPlaceholderAttributes();
mySelectionAttributes = ((SelectionModelImpl)editor.getSelectionModel()).getTextAttributes();
myReadOnlyColor = myEditor.getColorsScheme().getColor(EditorColors.READONLY_FRAGMENT_BACKGROUND_COLOR);
CaretModelImpl caretModel = (CaretModelImpl)editor.getCaretModel();
myCaretRowAttributes = editor.isRendererMode() ? null : caretModel.getTextAttributes();
myDefaultBackground = editor.getColorsScheme().getDefaultBackground();
myDefaultForeground = editor.getForegroundColor();
myCurrentHighlighters = new ArrayList<RangeHighlighterImpl>();
myCurrentViewHighlighterIdx = initHighlighterIterator(start, myViewHighlighters, longestViewHighlighterLength);
while (myCurrentViewHighlighterIdx < myViewHighlighters.size()) {
myNextViewHighlighter = myViewHighlighters.get(myCurrentViewHighlighterIdx);
if (!skipHighlighter(myNextViewHighlighter)) break;
myCurrentViewHighlighterIdx++;
}
if (myCurrentViewHighlighterIdx == myViewHighlighters.size()) myNextViewHighlighter = null;
myCurrentDocHighlighterIdx = initHighlighterIterator(start, myDocumentHighlighters, longestDocHighlighterLength);
myNextDocumentHighlighter = null;
while (myCurrentDocHighlighterIdx < myDocumentHighlighters.size()) {
myNextDocumentHighlighter = myDocumentHighlighters.get(myCurrentDocHighlighterIdx);
if (!skipHighlighter(myNextDocumentHighlighter)) break;
myCurrentDocHighlighterIdx++;
}
if (myCurrentDocHighlighterIdx == myDocumentHighlighters.size()) myNextDocumentHighlighter = null;
advanceSegmentHighlighters();
myCaretRowStart = caretModel.getVisualLineStart();
myCaretRowEnd = caretModel.getVisualLineEnd();
myEndOffset = Math.min(getHighlighterEnd(myStartOffset), getSelectionEnd(myStartOffset));
myEndOffset = Math.min(myEndOffset, getSegmentHighlightersEnd());
myEndOffset = Math.min(myEndOffset, getFoldRangesEnd(myStartOffset));
myEndOffset = Math.min(myEndOffset, getCaretEnd(myStartOffset));
myEndOffset = Math.min(myEndOffset, getGuardedBlockEnd(myStartOffset));
myCurrentFold = myFoldingModel.getCollapsedRegionAtOffset(myStartOffset);
if (myCurrentFold != null) {
myEndOffset = myCurrentFold.getEndOffset();
}
myCachedAttributesList = new ArrayList<TextAttributes>(5);
reinit();
}
private int initHighlighterIterator(int start, ArrayList<RangeHighlighterImpl> sortedHighlighters, int longestHighlighterLength) {
int low = 0;
int high = sortedHighlighters.size();
int search = myDocument.getLineStartOffset(myDocument.getLineNumber(start)) -
longestHighlighterLength - 1;
if (search > 0) {
while (low < high) {
int mid = (low + high) / 2;
while (mid > 0 && !sortedHighlighters.get(mid).isValid()) mid
if (mid < low + 1) break;
RangeHighlighterImpl midHighlighter = sortedHighlighters.get(mid);
if (midHighlighter.getStartOffset() < search) {
low = mid + 1;
}
else {
high = mid - 1;
}
}
}
for (int i = low == high ? low : 0; i < sortedHighlighters.size(); i++) {
RangeHighlighterImpl rangeHighlighter = sortedHighlighters.get(i);
if (!skipHighlighter(rangeHighlighter) &&
rangeHighlighter.getAffectedAreaEndOffset() >= start) {
return i;
}
}
return sortedHighlighters.size();
}
private boolean skipHighlighter(RangeHighlighterImpl highlighter) {
return !highlighter.isValid() ||
highlighter.isAfterEndOfLine() ||
highlighter.getTextAttributes() == null ||
myFoldingModel.isOffsetCollapsed(highlighter.getAffectedAreaStartOffset()) ||
myFoldingModel.isOffsetCollapsed(highlighter.getAffectedAreaEndOffset()) ||
!highlighter.getEditorFilter().avaliableIn(myEditor);
}
public void advance() {
myCurrentFold = null;
myStartOffset = myEndOffset;
FoldRegion range = myFoldingModel.fetchOutermost(myStartOffset);
if (range != null) {
myEndOffset = range.getEndOffset();
myCurrentFold = range;
}
else {
advanceSegmentHighlighters();
myEndOffset = Math.min(getHighlighterEnd(myStartOffset), getSelectionEnd(myStartOffset));
myEndOffset = Math.min(myEndOffset, getSegmentHighlightersEnd());
myEndOffset = Math.min(myEndOffset, getFoldRangesEnd(myStartOffset));
myEndOffset = Math.min(myEndOffset, getCaretEnd(myStartOffset));
myEndOffset = Math.min(myEndOffset, getGuardedBlockEnd(myStartOffset));
}
reinit();
}
private int getHighlighterEnd(int start) {
while (!myHighlighterIterator.atEnd()) {
int end = myHighlighterIterator.getEnd();
if (end > start) {
return end;
}
myHighlighterIterator.advance();
}
return myEnd;
}
private int getCaretEnd(int start) {
if (myCaretRowStart > start) {
return myCaretRowStart;
}
if (myCaretRowEnd > start) {
return myCaretRowEnd;
}
return myEnd;
}
private int getGuardedBlockEnd(int start) {
List<RangeMarker> blocks = myDocument.getGuardedBlocks();
int min = myEnd;
for (int i = 0; i < blocks.size(); i++) {
RangeMarker block = blocks.get(i);
if (block.getStartOffset() > start) {
min = Math.min(min, block.getStartOffset());
}
else if (block.getEndOffset() > start) {
min = Math.min(min, block.getEndOffset());
}
}
return min;
}
private int getSelectionEnd(int start) {
if (!hasSelection) {
return myEnd;
}
if (mySelectionStart > start) {
return mySelectionStart;
}
if (mySelectionEnd > start) {
return mySelectionEnd;
}
return myEnd;
}
private void advanceSegmentHighlighters() {
if (myNextDocumentHighlighter != null) {
if (myNextDocumentHighlighter.getAffectedAreaStartOffset() <= myStartOffset) {
myCurrentHighlighters.add(myNextDocumentHighlighter);
myNextDocumentHighlighter = null;
}
}
if (myNextViewHighlighter != null) {
if (myNextViewHighlighter.getAffectedAreaStartOffset() <= myStartOffset) {
myCurrentHighlighters.add(myNextViewHighlighter);
myNextViewHighlighter = null;
}
}
RangeHighlighterImpl highlighter;
final int docHighlightersSize = myDocumentHighlighters.size();
while (myNextDocumentHighlighter == null && myCurrentDocHighlighterIdx < docHighlightersSize) {
highlighter = myDocumentHighlighters.get(myCurrentDocHighlighterIdx++);
if (!skipHighlighter(highlighter)) {
if (highlighter.getAffectedAreaStartOffset() > myStartOffset) {
myNextDocumentHighlighter = highlighter;
break;
}
else {
myCurrentHighlighters.add(highlighter);
}
}
}
final int viewHighlightersSize = myViewHighlighters.size();
while (myNextViewHighlighter == null && myCurrentViewHighlighterIdx < viewHighlightersSize) {
highlighter = myViewHighlighters.get(myCurrentViewHighlighterIdx++);
if (!skipHighlighter(highlighter)) {
if (highlighter.getAffectedAreaStartOffset() > myStartOffset) {
myNextViewHighlighter = highlighter;
break;
}
else {
myCurrentHighlighters.add(highlighter);
}
}
}
if (myCurrentHighlighters.size() == 1) {
//Optimization
if (myCurrentHighlighters.get(0).getAffectedAreaEndOffset() <= myStartOffset) {
myCurrentHighlighters = new ArrayList<RangeHighlighterImpl>();
}
}
else if (!myCurrentHighlighters.isEmpty()) {
ArrayList<RangeHighlighterImpl> copy = new ArrayList<RangeHighlighterImpl>(myCurrentHighlighters.size());
for (int i = 0; i < myCurrentHighlighters.size(); i++) {
highlighter = myCurrentHighlighters.get(i);
if (highlighter.getAffectedAreaEndOffset() > myStartOffset) {
copy.add(highlighter);
}
}
myCurrentHighlighters = copy;
}
}
private int getFoldRangesEnd(int startOffset) {
int end = myEnd;
FoldRegion[] topLevelCollapsed = myFoldingModel.fetchTopLevel();
if (topLevelCollapsed != null) {
for (int i = myFoldingModel.getLastCollapsedRegionBefore(startOffset) + 1;
i >= 0 && i < topLevelCollapsed.length;
i++) {
FoldRegion range = topLevelCollapsed[i];
if (!range.isValid()) continue;
int rangeEnd = range.getStartOffset();
if (rangeEnd > startOffset) {
if (rangeEnd < end) {
end = rangeEnd;
}
else {
break;
}
}
}
}
return end;
}
private int getSegmentHighlightersEnd() {
int end = myEnd;
for (RangeHighlighterImpl highlighter : myCurrentHighlighters) {
if (highlighter.getAffectedAreaEndOffset() < end) {
end = highlighter.getAffectedAreaEndOffset();
}
}
if (myNextDocumentHighlighter != null && myNextDocumentHighlighter.getAffectedAreaStartOffset() < end) {
end = myNextDocumentHighlighter.getAffectedAreaStartOffset();
}
if (myNextViewHighlighter != null && myNextViewHighlighter.getAffectedAreaStartOffset() < end) {
end = myNextViewHighlighter.getAffectedAreaStartOffset();
}
return end;
}
private void reinit() {
if (myHighlighterIterator.atEnd()) {
return;
}
boolean isInSelection = hasSelection && myStartOffset >= mySelectionStart && myStartOffset < mySelectionEnd;
boolean isInCaretRow = myStartOffset >= myCaretRowStart && myStartOffset < myCaretRowEnd;
boolean isInGuardedBlock = myDocument.getOffsetGuard(myStartOffset) != null;
TextAttributes syntax = myHighlighterIterator.getTextAttributes();
TextAttributes selection = isInSelection ? mySelectionAttributes : null;
TextAttributes caret = isInCaretRow ? myCaretRowAttributes : null;
TextAttributes fold = myCurrentFold != null ? myFoldTextAttributes : null;
TextAttributes guard = isInGuardedBlock
? new TextAttributes(null, myReadOnlyColor, null, EffectType.BOXED, Font.PLAIN)
: null;
final int size = myCurrentHighlighters.size();
if (size > 1) {
Collections.sort(myCurrentHighlighters, LayerComparator.INSTANCE);
}
myCachedAttributesList.clear();
for (int i = 0; i < size; i++) {
RangeHighlighterImpl highlighter = myCurrentHighlighters.get(i);
if (selection != null && highlighter.getLayer() < HighlighterLayer.SELECTION) {
myCachedAttributesList.add(selection);
selection = null;
}
if (syntax != null && highlighter.getLayer() < HighlighterLayer.SYNTAX) {
if (fold != null) {
myCachedAttributesList.add(fold);
fold = null;
}
myCachedAttributesList.add(syntax);
syntax = null;
}
if (guard != null && highlighter.getLayer() < HighlighterLayer.GUARDED_BLOCKS) {
myCachedAttributesList.add(guard);
guard = null;
}
if (caret != null && highlighter.getLayer() < HighlighterLayer.CARET_ROW) {
myCachedAttributesList.add(caret);
caret = null;
}
TextAttributes textAttributes = highlighter.getTextAttributes();
if (textAttributes != null) {
myCachedAttributesList.add(textAttributes);
}
}
if (selection != null) myCachedAttributesList.add(selection);
if (fold != null) myCachedAttributesList.add(fold);
if (guard != null) myCachedAttributesList.add(guard);
if (syntax != null) myCachedAttributesList.add(syntax);
if (caret != null) myCachedAttributesList.add(caret);
Color fore = null;
Color back = isInGuardedBlock ? myReadOnlyColor : null;
Color effect = null;
EffectType effectType = null;
int fontType = TextAttributes.TRANSPARENT;
for (int i = 0; i < myCachedAttributesList.size(); i++) {
TextAttributes attrs = myCachedAttributesList.get(i);
if (fore == null) {
fore = attrs.getForegroundColor();
}
if (back == null) {
back = attrs.getBackgroundColor();
}
if (fontType == TextAttributes.TRANSPARENT) {
fontType = attrs.getRawFontType();
}
if (effect == null) {
effect = attrs.getEffectColor();
effectType = attrs.getEffectType();
}
}
if (fore == null) fore = myDefaultForeground;
if (back == null) back = myDefaultBackground;
if (fontType == TextAttributes.TRANSPARENT) fontType = Font.PLAIN;
if (effectType == null) effectType = EffectType.BOXED;
myMergedAttributes.setForegroundColor(fore);
myMergedAttributes.setBackgroundColor(back);
myMergedAttributes.setFontType(fontType);
myMergedAttributes.setEffectColor(effect);
myMergedAttributes.setEffectType(effectType);
}
public boolean atEnd() {
return myStartOffset >= myEnd;
}
public int getStartOffset() {
return myStartOffset;
}
public int getEndOffset() {
return myEndOffset;
}
public TextAttributes getMergedAttributes() {
return myMergedAttributes;
}
public FoldRegion getCurrentFold() {
return myCurrentFold;
}
@Nullable
public Color getPastFileEndBackground() {
boolean isInCaretRow = myEditor.getCaretModel().getLogicalPosition().line >= myDocument.getLineCount() - 1;
Color caret = isInCaretRow && myCaretRowAttributes != null ? myCaretRowAttributes.getBackgroundColor() : null;
if (myCurrentHighlighters.size() > 1) {
Collections.sort(myCurrentHighlighters, LayerComparator.INSTANCE);
}
for (int i = 0; i < myCurrentHighlighters.size(); i++) {
RangeHighlighterImpl highlighter = myCurrentHighlighters.get(i);
if (caret != null && highlighter.getLayer() < HighlighterLayer.CARET_ROW) {
return caret;
}
if (highlighter.getTargetArea() != HighlighterTargetArea.LINES_IN_RANGE
|| myDocument.getLineNumber(highlighter.getEndOffset()) < myDocument.getLineCount() - 1) {
continue;
}
TextAttributes textAttributes = highlighter.getTextAttributes();
if (textAttributes != null) {
Color backgroundColor = textAttributes.getBackgroundColor();
if (backgroundColor != null) return backgroundColor;
}
}
return caret;
}
private static class LayerComparator implements Comparator<RangeHighlighterImpl> {
private static final LayerComparator INSTANCE = new LayerComparator();
public int compare(RangeHighlighterImpl o1, RangeHighlighterImpl o2) {
int layerDiff = o2.getLayer() - o1.getLayer();
if (layerDiff != 0) {
return layerDiff;
}
// prefer more specific region
int o1Length = o1.getEndOffset() - o1.getStartOffset();
int o2Length = o2.getEndOffset() - o2.getStartOffset();
return o1Length - o2Length;
}
}
} |
package liquid;
import java.awt.geom.Rectangle2D;
import java.lang.InterruptedException;
import java.util.Random;
import java.util.concurrent.Executors;
import java.util.concurrent.ScheduledExecutorService;
import java.util.concurrent.TimeUnit;
import javax.swing.JFrame;
import lombok.extern.java.Log;
import lombok.val;
import org.jbox2d.collision.shapes.CircleShape;
import org.jbox2d.collision.shapes.PolygonShape;
import org.jbox2d.common.Vec2;
import org.jbox2d.dynamics.Body;
import org.jbox2d.dynamics.BodyDef;
import org.jbox2d.dynamics.BodyType;
import org.jbox2d.dynamics.FixtureDef;
import org.jbox2d.dynamics.World;
@Log
public class Launcher {
/* Solver */
private static final float DT = 1f / 15f; // seconds
private static final int V_ITERATIONS = 8;
private static final int P_ITERATIONS = 3;
/* World */
private static final float WIDTH = 50f;
private static final float HEIGHT = 70f;
private static final float THICKNESS = 1f;
private static final Vec2 GRAVITY = new Vec2(0, -0.005f);
private static final Rectangle2D VIEW =
new Rectangle2D.Float(WIDTH / -2, HEIGHT / -2, WIDTH, HEIGHT);
private static final long FLIP_RATE = 1500L;
/* Balls */
private static final int BALLS = 100;
private static final float BALL_RADIUS = 0.75f;
private static final float BALL_DENSITY = 1f;
private static final float BALL_FRICTION = 0.1f;
private static final float BALL_RESTITUTION = 0.6f;
public static void main(String[] args) {
/* Fix for poor OpenJDK performance. */
System.setProperty("sun.java2d.pmoffscreen", "false");
val world = new World(GRAVITY, false);
val viewer = new Viewer(world, VIEW);
JFrame frame = new JFrame("Fun Liquid");
frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
frame.add(viewer);
frame.setResizable(false);
frame.pack();
frame.setVisible(true);
/* Set up the containment box. */
buildContainer(world);
/* Add a ball. */
Random rng = new Random();
for (int i = 0; i < BALLS; i++) {
addBall(world,
(rng.nextFloat() - 0.5f) * (WIDTH - BALL_RADIUS),
(rng.nextFloat() - 0.5f) * (HEIGHT - BALL_RADIUS));
}
val exec = Executors.newSingleThreadScheduledExecutor();
exec.scheduleAtFixedRate(new Runnable() {
public void run() {
while (true) {
world.step(DT, V_ITERATIONS, P_ITERATIONS);
viewer.repaint();
if (System.currentTimeMillis() / FLIP_RATE % 2 == 0) {
world.setGravity(GRAVITY.negate());
} else {
world.setGravity(GRAVITY);
}
}
}
}, 0L, (long) (DT * 1000.0), TimeUnit.MILLISECONDS);
}
private static void buildContainer(World world) {
BodyDef def = new BodyDef();
PolygonShape box = new PolygonShape();
Body side;
def.position = new Vec2(WIDTH / 2, 0);
box.setAsBox(THICKNESS / 2, HEIGHT / 2);
world.createBody(def).createFixture(box, 0f);
def.position = new Vec2(-WIDTH / 2, 0);
box.setAsBox(THICKNESS / 2, HEIGHT / 2);
world.createBody(def).createFixture(box, 0f);
def.position = new Vec2(0, HEIGHT / 2);
box.setAsBox(WIDTH / 2, THICKNESS / 2);
world.createBody(def).createFixture(box, 0f);
def.position = new Vec2(0, -HEIGHT / 2);
box.setAsBox(WIDTH / 2, THICKNESS / 2);
world.createBody(def).createFixture(box, 0f);
}
private static void addBall(World world, float x, float y) {
BodyDef def = new BodyDef();
def.position = new Vec2(x, y);
def.type = BodyType.DYNAMIC;
CircleShape circle = new CircleShape();
circle.m_radius = BALL_RADIUS;
FixtureDef mass = new FixtureDef();
mass.shape = circle;
mass.density = BALL_DENSITY;
mass.friction = BALL_FRICTION;
mass.restitution = BALL_RESTITUTION;
world.createBody(def).createFixture(mass);
}
} |
package tlc2.tool.distributed;
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.net.InetAddress;
import java.net.URI;
import java.rmi.AccessException;
import java.rmi.ConnectException;
import java.rmi.NoSuchObjectException;
import java.rmi.NotBoundException;
import java.rmi.RemoteException;
import java.rmi.ServerException;
import java.rmi.registry.LocateRegistry;
import java.rmi.registry.Registry;
import java.rmi.server.UnicastRemoteObject;
import java.util.ArrayList;
import java.util.ConcurrentModificationException;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.concurrent.ConcurrentHashMap;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
import java.util.concurrent.atomic.AtomicLong;
import model.InJarFilenameToStream;
import model.ModelInJar;
import tlc2.TLC;
import tlc2.TLCGlobals;
import tlc2.output.EC;
import tlc2.output.MP;
import tlc2.tool.EvalException;
import tlc2.tool.IStateFunctor;
import tlc2.tool.ModelChecker;
import tlc2.tool.TLCState;
import tlc2.tool.TLCTrace;
import tlc2.tool.distributed.fp.FPSetManager;
import tlc2.tool.distributed.fp.FPSetRMI;
import tlc2.tool.distributed.fp.IFPSetManager;
import tlc2.tool.distributed.fp.NonDistributedFPSetManager;
import tlc2.tool.distributed.management.TLCServerMXWrapper;
import tlc2.tool.distributed.selector.BlockSelectorFactory;
import tlc2.tool.distributed.selector.IBlockSelector;
import tlc2.tool.fp.FPSet;
import tlc2.tool.fp.FPSetFactory;
import tlc2.tool.management.TLCStandardMBean;
import tlc2.tool.queue.DiskStateQueue;
import tlc2.tool.queue.IStateQueue;
import tlc2.util.FP64;
import util.Assert;
import util.FileUtil;
import util.MailSender;
import util.UniqueString;
@SuppressWarnings("serial")
public class TLCServer extends UnicastRemoteObject implements TLCServerRMI,
InternRMI {
/**
* Name by which {@link FPSetRMI} lookup the {@link TLCServer} (master).
*/
public static final String SERVER_NAME = "TLCServer";
/**
* Name by which {@link TLCWorker} lookup the {@link TLCServer} (master).
*/
public static final String SERVER_WORKER_NAME = SERVER_NAME + "WORKER";
/**
* Prefix master and worker heavy workload threads with this prefix and an incrementing counter to
* make the threads identifiable in jmx2munin statistics, which uses simple string matching.
*/
public static final String THREAD_NAME_PREFIX = "TLCWorkerThread-";
/**
* Used by TLCStatistics which are collected after the {@link FPSet} or {@link FPSetManager} shut down.
*/
static long finalNumberOfDistinctStates = -1L;
/**
* the port # for tlc server
*/
public static int Port = Integer.getInteger(TLCServer.class.getName() + ".port", 10997);
/**
* show statistics every 1 minutes
*/
private static final int REPORT_INTERVAL = Integer.getInteger(TLCServer.class.getName() + ".report", 1 * 60 * 1000);
/**
* If the state/ dir should be cleaned up after a successful model run
*/
private static final boolean VETO_CLEANUP = Boolean.getBoolean(TLCServer.class.getName() + ".vetoCleanup");
/**
* The amount of FPset servers to use (use a non-distributed FPSet server on
* master node if unset).
*/
private static final int expectedFPSetCount = Integer.getInteger(TLCServer.class.getName() + ".expectedFPSetCount", 0);
/**
* Performance metric: distinct states per minute
*/
private long distinctStatesPerMinute;
/**
* Performance metric: states per minute
*/
private long statesPerMinute;
/**
* A counter used to count the states generated by (remote)
* {@link TLCWorker}s but which have been skipped due to a worker-local
* fingerprint cache hit.
*/
protected final AtomicLong workerStatesGenerated = new AtomicLong(0);
/**
* A thread pool used to execute tasks
*/
private final ExecutorService es = Executors.newCachedThreadPool();
public final IFPSetManager fpSetManager;
public final IStateQueue stateQueue;
public final TLCTrace trace;
private final DistApp work;
private final String metadir;
private final String filename;
private TLCState errState = null;
private boolean done = false;
private boolean keepCallStack = false;
/**
* Main data structure used to maintain the list of active workers (ref
* {@link TLCWorkerRMI}) and the corresponding local {@link TLCServerThread}
* .
* <p>
* A worker ({@link TLCWorkerRMI}) requires a local thread counterpart to do
* its work concurrently.
* <p>
* The implementation uses a {@link ConcurrentHashMap}, to allow concurrent
* access during the end game phase. It is the phase when
* {@link TLCServer#modelCheck()} cleans up threadsToWorkers by waiting
* {@link Thread#join()} on the various {@link TLCServerThread}s. If this
* action is overlapped with a worker registering - calling
* {@link TLCServer#registerWorker(TLCWorkerRMI)} - which would cause a
* {@link ConcurrentModificationException}.
*/
private final Map<TLCServerThread, TLCWorkerRMI> threadsToWorkers = new ConcurrentHashMap<TLCServerThread, TLCWorkerRMI>();
private final IBlockSelector blockSelector;
/**
* @param work
* @throws IOException
* @throws NotBoundException
*/
public TLCServer(TLCApp work) throws IOException, NotBoundException {
// LL modified error message on 7 April 2012
Assert.check(work != null, "TLC server found null work.");
// TLCApp which calculates the next state relation
this.metadir = work.getMetadir();
int end = this.metadir.length();
if (this.metadir.endsWith(FileUtil.separator)) {
end
}
int start = this.metadir.lastIndexOf(FileUtil.separator, end - 1);
this.filename = this.metadir.substring(start + 1, end);
this.work = work;
// State Queue of unexplored states
this.stateQueue = new DiskStateQueue(this.metadir);
// State trace file
this.trace = new TLCTrace(this.metadir, this.work.getFileName(),
this.work);
// FPSet
this.fpSetManager = getFPSetManagerImpl(work, metadir, expectedFPSetCount);
// Determines the size of the state queue subset handed out to workers
blockSelector = BlockSelectorFactory.getBlockSelector(this);
}
/**
* The {@link IFPSetManager} implementation to be used by the
* {@link TLCServer} implementation. Subclass may want to return specialized
* {@link IFPSetManager}s with different functionality.
* @param expectedfpsetcount2
*/
protected IFPSetManager getFPSetManagerImpl(final TLCApp work,
final String metadir, final int fpsetCount) throws IOException {
// A single FPSet server running on the master node
final FPSet fpSet = FPSetFactory.getFPSet(work.getFPSetConfiguration());
fpSet.init(1, metadir, work.getFileName());
return new NonDistributedFPSetManager(fpSet, InetAddress.getLocalHost()
.getCanonicalHostName());
}
/* (non-Javadoc)
* @see tlc2.tool.distributed.TLCServerRMI#getCheckDeadlock()
*/
public final Boolean getCheckDeadlock() {
return this.work.getCheckDeadlock();
}
/* (non-Javadoc)
* @see tlc2.tool.distributed.TLCServerRMI#getPreprocess()
*/
public final Boolean getPreprocess() {
return this.work.getPreprocess();
}
/* (non-Javadoc)
* @see tlc2.tool.distributed.TLCServerRMI#getFPSetManager()
*/
public IFPSetManager getFPSetManager() {
return this.fpSetManager;
}
/* (non-Javadoc)
* @see tlc2.tool.distributed.TLCServerRMI#getIrredPolyForFP()
*/
public final long getIrredPolyForFP() {
return FP64.getIrredPoly();
}
/* (non-Javadoc)
* @see tlc2.tool.distributed.InternRMI#intern(java.lang.String)
*/
public final UniqueString intern(String str) {
// SZ 11.04.2009: changed access method
return UniqueString.uniqueStringOf(str);
}
/* (non-Javadoc)
* @see tlc2.tool.distributed.TLCServerRMI#registerWorker(tlc2.tool.distributed.TLCWorkerRMI)
*/
public synchronized final void registerWorker(TLCWorkerRMI worker
) throws IOException {
// Wake up potentially stuck TLCServerThreads (in
// tlc2.tool.queue.StateQueue.isAvail()) to avoid a deadlock.
// Obviously stuck TLCServerThreads will never be reported to
// users if resumeAllStuck() is not call by a new worker.
stateQueue.resumeAllStuck();
// create new server thread for given worker
final TLCServerThread thread = new TLCServerThread(worker, worker.getURI(), this, es, blockSelector);
threadsToWorkers.put(thread, worker);
thread.start();
MP.printMessage(EC.TLC_DISTRIBUTED_WORKER_REGISTERED, worker.getURI().toString());
}
/* (non-Javadoc)
* @see tlc2.tool.distributed.TLCServerRMI#registerFPSet(tlc2.tool.distributed.fp.FPSetRMI, java.lang.String)
*/
public synchronized void registerFPSet(FPSetRMI fpSet, String hostname) throws RemoteException {
throw new UnsupportedOperationException("Not applicable for non-distributed TLCServer");
}
/**
* An (idempotent) method to remove a (dead) TLCServerThread from the TLCServer.
*
* @see Map#remove(Object)
* @param thread
* @return
*/
public TLCWorkerRMI removeTLCServerThread(final TLCServerThread thread) {
final TLCWorkerRMI worker = threadsToWorkers.remove(thread);
if (worker != null) {
MP.printMessage(EC.TLC_DISTRIBUTED_WORKER_DEREGISTERED, thread.getUri().toString());
}
return worker;
}
/**
* @param s
* @param keep
* @return true iff setting the error state has succeeded. This is the case
* for the first worker to call
* {@link TLCServer#setErrState(TLCState, boolean)}. Subsequent
* calls by other workers will be ignored. This implies that other
* error states are ignored.
*/
public synchronized final boolean setErrState(TLCState s, boolean keep) {
if (this.done) {
return false;
}
this.done = true;
this.errState = s;
this.keepCallStack = keep;
return true;
}
/**
* Indicates the completion of model checking. This is called by
* {@link TLCServerThread}s once they find an empty {@link IStateQueue}. An
* empty {@link IStateQueue} is the termination condition.
*/
public final void setDone() {
this.done = true;
}
/**
* Number of states generated by (remote) {@link TLCWorker}s but which have
* been skipped due to a worker-local fingerprint cache hit.
* <p>
* We count them here to still report the correct amount of states generated
* overall. {@link IFPSetManager#getStatesSeen()} will not count these
* states.
*/
public void addStatesGeneratedDelta(long delta) {
workerStatesGenerated.addAndGet(delta);
}
/**
* Creates a checkpoint for the currently running model run
* @throws IOException
* @throws InterruptedException
*/
public void checkpoint() throws IOException, InterruptedException {
if (this.stateQueue.suspendAll()) {
// Checkpoint:
MP.printMessage(EC.TLC_CHECKPOINT_START, "-- Checkpointing of run " + this.metadir
+ " compl");
// start checkpointing:
this.stateQueue.beginChkpt();
this.trace.beginChkpt();
this.fpSetManager.checkpoint(this.filename);
this.stateQueue.resumeAll();
UniqueString.internTbl.beginChkpt(this.metadir);
// commit:
this.stateQueue.commitChkpt();
this.trace.commitChkpt();
UniqueString.internTbl.commitChkpt(this.metadir);
this.fpSetManager.commitChkpt();
MP.printMessage(EC.TLC_CHECKPOINT_END, "eted.");
}
}
/**
* Recovers a model run
* @throws IOException
* @throws InterruptedException
*/
public final void recover() throws IOException, InterruptedException {
this.trace.recover();
this.stateQueue.recover();
this.fpSetManager.recover(this.filename);
}
/**
* @throws Throwable
*/
private final void doInit() throws Throwable {
final DoInitFunctor functor = new DoInitFunctor();
work.getInitStates(functor);
// Iff one of the init states' checks violates any properties, the
// functor will record it.
if (functor.e != null) {
throw functor.e;
}
}
/**
* @param cleanup
* @throws IOException
*/
public final void close(boolean cleanup) throws IOException {
this.trace.close();
this.fpSetManager.close(cleanup);
if (cleanup && !VETO_CLEANUP) {
FileUtil.deleteDir(new File(this.metadir), true);
}
}
/**
* @param server
* @throws IOException
* @throws InterruptedException
* @throws NotBoundException
*/
protected void modelCheck() throws IOException, InterruptedException, NotBoundException {
final long startTime = System.currentTimeMillis();
/*
* Before we initialize the server, we check if recovery is requested
*/
boolean recovered = false;
if (work.canRecover()) {
MP.printMessage(EC.TLC_CHECKPOINT_RECOVER_START, metadir);
recover();
MP.printMessage(EC.TLC_CHECKPOINT_RECOVER_END, new String[] { String.valueOf(fpSetManager.size()),
String.valueOf(stateQueue.size())});
recovered = true;
}
// Create the central naming authority that is used by _all_ nodes
String hostname = InetAddress.getLocalHost().getHostName();
Registry rg = LocateRegistry.createRegistry(Port);
rg.rebind(SERVER_NAME, this);
MP.printMessage(EC.TLC_DISTRIBUTED_SERVER_RUNNING, hostname);
// First register TLCSERVER with RMI and only then wait for all FPSets
// to become registered. This only waits if we use distributed
// fingerprint set (FPSet) servers which have to partition the
// distributed hash table (fingerprint space) prior to starting model
// checking.
waitForFPSetManager();
/*
* Start initializing the server by calculating the init state(s)
*/
if (!recovered) {
// Initialize with the initial states:
try {
MP.printMessage(EC.TLC_COMPUTING_INIT);
doInit();
MP.printMessage(EC.TLC_INIT_GENERATED1,
new String[] { String.valueOf(stateQueue.size()), "(s)" });
} catch (Throwable e) {
// Assert.printStack(e);
done = true;
// Distributed TLC does not support TLCGet/TLCSet operator. It
// would require synchronization among all (distributed)
// workers. In distributed mode, it is of limited use anyway.
if (e instanceof EvalException
&& ((EvalException) e).getErrorCode() == EC.TLC_MODULE_VALUE_JAVA_METHOD_OVERRIDE
&& (((EvalException) e).getMessage().contains("tlc2.module.TLC.TLCSet")
|| ((EvalException) e).getMessage().contains("tlc2.module.TLC.TLCGet"))) {
MP.printError(EC.TLC_FEATURE_UNSUPPORTED,
"TLCSet & TLCGet operators not supported by distributed TLC.");
} else {
String msg = e.getMessage();
if (msg == null) {
msg = e.toString();
}
if (!this.hasNoErrors()) {
MP.printError(EC.TLC_INITIAL_STATE, new String[] { msg, this.errState.toString() });
} else {
MP.printError(EC.GENERAL, msg);
}
// We redo the work on the error state, recording the call
// stack.
work.setCallStack();
try {
doInit();
} catch (Throwable e1) {
// Assert.printStack(e);
MP.printError(EC.TLC_NESTED_EXPRESSION, work.printCallStack());
}
}
}
}
if (done) {
printSummary(1, 0, stateQueue.size(), fpSetManager.size(), false);
MP.printMessage(EC.TLC_FINISHED,
TLC.convertRuntimeToHumanReadable(System.currentTimeMillis() - startTime));
es.shutdown();
// clean up before exit:
close(false);
return;
}
// Init states have been computed successfully which marks the point in
// time where workers can start generating and exploring next states.
rg.rebind(SERVER_WORKER_NAME, this);
/*
* This marks the end of the master and FPSet server initialization.
* Model checking can start now.
*/
// Model checking results to be collected after model checking has finished
long oldNumOfGenStates = 0;
long oldFPSetSize = 0;
// Wait for completion, but print out progress report and checkpoint
// periodically.
synchronized (this) { //TODO convert to do/while to move initial wait into loop
wait(REPORT_INTERVAL);
}
while (true) {
if (TLCGlobals.doCheckPoint()) {
// Periodically create a checkpoint assuming it is activated
checkpoint();
}
synchronized (this) {
if (!done) {
final long numOfGenStates = getStatesGenerated();
final long fpSetSize = fpSetManager.size();
// print progress showing states per minute metric (spm)
final double factor = REPORT_INTERVAL / 60000d;
statesPerMinute = (long) ((numOfGenStates - oldNumOfGenStates) / factor);
distinctStatesPerMinute = (long) ((fpSetSize - oldFPSetSize) / factor);
// print to system.out
MP.printMessage(EC.TLC_PROGRESS_STATS, new String[] { String.valueOf(trace.getLevelForReporting()),
String.valueOf(numOfGenStates), String.valueOf(fpSetSize),
String.valueOf(getNewStates()), String.valueOf(statesPerMinute), String.valueOf(distinctStatesPerMinute) });
// Make the TLCServer main thread sleep for one report interval
wait(REPORT_INTERVAL);
// keep current values as old values
oldFPSetSize = fpSetSize;
oldNumOfGenStates = numOfGenStates;
}
if (done) {
break;
}
}
}
// Either model checking has found an error/violation or no
// violation has been found represented by an empty state queue.
Assert.check(!hasNoErrors() || stateQueue.isEmpty(), EC.GENERAL);
/*
* From this point on forward, we expect model checking to be done. What
* is left open, is to collect results and clean up
*/
// Wait for all the server threads to die.
for (final Entry<TLCServerThread, TLCWorkerRMI> entry : threadsToWorkers.entrySet()) {
final TLCServerThread thread = entry.getKey();
final TLCWorkerRMI worker = entry.getValue();
thread.join();
// print worker stats
int sentStates = thread.getSentStates();
int receivedStates = thread.getReceivedStates();
double cacheHitRatio = thread.getCacheRateRatio();
URI name = thread.getUri();
MP.printMessage(EC.TLC_DISTRIBUTED_WORKER_STATS,
new String[] { name.toString(), Integer.toString(sentStates), Integer.toString(receivedStates),
cacheHitRatio < 0 ? "n/a" : String.format("%1$,.2f", cacheHitRatio) });
try {
worker.exit();
} catch (NoSuchObjectException e) {
// worker might have been lost in the meantime
MP.printWarning(EC.GENERAL, "Ignoring attempt to exit dead worker");
} catch (ConnectException e) {
// worker might have been lost in the meantime
MP.printWarning(EC.GENERAL, "Ignoring attempt to exit dead worker");
} catch (ServerException e) {
// worker might have been lost in the meantime
MP.printWarning(EC.GENERAL, "Ignoring attempt to exit dead worker");
} finally {
threadsToWorkers.remove(thread);
}
}
// Only shutdown the thread pool if we exit gracefully
es.shutdown();
// Collect model checking results before exiting remote workers
finalNumberOfDistinctStates = fpSetManager.size();
final long statesGenerated = getStatesGenerated();
final long statesLeftInQueue = getNewStates();
final int level = trace.getLevelForReporting();
statesPerMinute = 0;
distinctStatesPerMinute = 0;
// Postprocessing:
if (hasNoErrors()) {
// We get here because the checking has succeeded.
final double actualProb = fpSetManager.checkFPs();
final long statesSeen = fpSetManager.getStatesSeen();
ModelChecker.reportSuccess(finalNumberOfDistinctStates, actualProb, statesSeen);
} else if (keepCallStack) {
// We redo the work on the error state, recording the call stack.
work.setCallStack();
}
// Finally print the results
printSummary(level, statesGenerated, statesLeftInQueue, finalNumberOfDistinctStates, hasNoErrors());
MP.printMessage(EC.TLC_FINISHED,
TLC.convertRuntimeToHumanReadable(System.currentTimeMillis() - startTime));
MP.flush();
// Close trace and (distributed) _FPSet_ servers!
close(hasNoErrors());
// dispose RMI leftovers
rg.unbind(SERVER_WORKER_NAME);
rg.unbind(SERVER_NAME);
UnicastRemoteObject.unexportObject(this, false);
}
/**
* Makes the flow of control wait for the IFPSetManager implementation to
* become fully initialized.<p>
* For the non-distributed FPSet implementation, this is true right away.
*/
protected void waitForFPSetManager() throws InterruptedException {
// no-op
}
public long getStatesGeneratedPerMinute() {
return statesPerMinute;
}
public long getDistinctStatesGeneratedPerMinute() {
return distinctStatesPerMinute;
}
public long getAverageBlockCnt() {
return blockSelector.getAverageBlockCnt();
}
/**
* @return true iff model checking has not found an error state
*/
private boolean hasNoErrors() {
return errState == null;
}
/**
* @return
*/
public synchronized long getNewStates() {
long res = stateQueue.size();
for (TLCServerThread thread : threadsToWorkers.keySet()) {
res += thread.getCurrentSize();
}
return res;
}
public long getStatesGenerated() {
return workerStatesGenerated.get() + fpSetManager.getStatesSeen();
}
/**
* This allows the toolbox to easily display the last set
* of state space statistics by putting them in the same
* form as all other progress statistics.
* @param workerOverallCacheRate
*/
public static final void printSummary(int level, long statesGenerated, long statesLeftInQueue, long distinctStates, boolean success) throws IOException
{
if (TLCGlobals.tool) {
MP.printMessage(EC.TLC_PROGRESS_STATS, new String[] { String.valueOf(level),
String.valueOf(statesGenerated), String.valueOf(distinctStates),
String.valueOf(statesLeftInQueue), "0", "0" });
}
MP.printMessage(EC.TLC_STATS, new String[] { String.valueOf(statesGenerated),
String.valueOf(distinctStates), String.valueOf(statesLeftInQueue) });
if (success) {
MP.printMessage(EC.TLC_SEARCH_DEPTH, String.valueOf(level));
}
}
public static void main(String argv[]) {
MP.printMessage(EC.TLC_VERSION, "TLC Server " + TLCGlobals.versionOfTLC);
TLCStandardMBean tlcServerMXWrapper = TLCStandardMBean.getNullTLCStandardMBean();
MailSender mail = null;
TLCServer server = null;
TLCApp app = null;
try {
TLCGlobals.setNumWorkers(0);
app = TLCApp.create(argv);
mail = new MailSender(app.getFileName());
if (expectedFPSetCount > 0) {
server = new DistributedFPSetTLCServer(app, expectedFPSetCount);
} else {
server = new TLCServer(app);
}
tlcServerMXWrapper = new TLCServerMXWrapper(server);
if(server != null) {
Runtime.getRuntime().addShutdownHook(new Thread(new WorkerShutdownHook(server)));
server.modelCheck();
}
} catch (Throwable e) {
System.gc();
// Assert.printStack(e);
if (e instanceof StackOverflowError) {
MP.printError(EC.SYSTEM_STACK_OVERFLOW, e);
} else if (e instanceof OutOfMemoryError) {
MP.printError(EC.SYSTEM_OUT_OF_MEMORY, e);
} else {
MP.printError(EC.GENERAL, e);
}
if (server != null) {
try {
server.close(false);
} catch (Exception e1) {
MP.printError(EC.GENERAL, e1);
}
}
} finally {
if (!server.es.isShutdown()) {
server.es.shutdownNow();
}
tlcServerMXWrapper.unregister();
// When creation of TLCApp fails, we get here as well.
if (mail != null) {
List<File> files = new ArrayList<File>();
if (app != null) {
files = app.getModuleFiles();
}
boolean send = mail.send(files);
// In case sending the mail has failed we treat this as an error.
// This is needed when TLC runs on another host and email is
// the only means for the user to get access to the model checking
// results.
// With distributed TLC and CloudDistributedTLCJob in particular,
// the cloud node is immediately turned off once the TLC process has
// finished. If we were to shutdown the node even when sending out
// the email has failed, the result would be lost.
if (!send) {
MP.printMessage(EC.GENERAL, "Sending result mail failed.");
System.exit(1);
}
}
}
}
/**
* @return Number of currently registered workers
*/
public int getWorkerCount() {
return threadsToWorkers.size();
}
/**
* @return
*/
synchronized TLCServerThread[] getThreads() {
return threadsToWorkers.keySet().toArray(new TLCServerThread[threadsToWorkers.size()]);
}
public boolean isRunning() {
return !done;
}
/* (non-Javadoc)
* @see tlc2.tool.distributed.TLCServerRMI#isDone()
*/
public boolean isDone() throws RemoteException {
return done;
}
/* (non-Javadoc)
* @see tlc2.tool.distributed.TLCServerRMI#getSpec()
*/
public String getSpecFileName() throws RemoteException {
return this.work.getFileName();
}
/* (non-Javadoc)
* @see tlc2.tool.distributed.TLCServerRMI#getConfig()
*/
public String getConfigFileName() throws RemoteException {
return this.work.getConfigName();
}
/* (non-Javadoc)
* @see tlc2.tool.distributed.TLCServerRMI#getFile(java.lang.String)
*/
public byte[] getFile(final String file) throws RemoteException {
// sanitize file to only last part of the path
// to make sure to not load files outside of spec dir
String name = new File(file).getName();
// Resolve all
File f = new InJarFilenameToStream(ModelInJar.PATH).resolve(name);
return read(f);
}
private byte[] read(final File file) {
if (file.isDirectory())
throw new RuntimeException("Unsupported operation, file "
+ file.getAbsolutePath() + " is a directory");
if (file.length() > Integer.MAX_VALUE)
throw new RuntimeException("Unsupported operation, file "
+ file.getAbsolutePath() + " is too big");
Throwable pending = null;
FileInputStream in = null;
final byte buffer[] = new byte[(int) file.length()];
try {
in = new FileInputStream(file);
in.read(buffer);
} catch (Exception e) {
pending = new RuntimeException("Exception occured on reading file "
+ file.getAbsolutePath(), e);
} finally {
if (in != null) {
try {
in.close();
} catch (Exception e) {
if (pending == null) {
pending = new RuntimeException(
"Exception occured on closing file"
+ file.getAbsolutePath(), e);
}
}
}
if (pending != null) {
throw new RuntimeException(pending);
}
}
return buffer;
}
private class DoInitFunctor implements IStateFunctor {
private Throwable e;
/* (non-Javadoc)
* @see tlc2.tool.IStateFunctor#addElement(tlc2.tool.TLCState)
*/
public Object addElement(final TLCState curState) {
if (e != null) {
return curState;
}
try {
final boolean inConstraints = work.isInModel(curState);
boolean seen = false;
if (inConstraints) {
long fp = curState.fingerPrint();
seen = fpSetManager.put(fp);
if (!seen) {
curState.uid = trace.writeState(fp);
stateQueue.enqueue(curState);
}
}
if (!inConstraints || !seen) {
work.checkState(null, curState);
}
} catch (Exception e) {
if (setErrState(curState, true)) {
this.e = e;
}
}
return curState;
}
}
/**
* Tries to exit all connected workers
*/
private static class WorkerShutdownHook implements Runnable {
private final TLCServer server;
public WorkerShutdownHook(final TLCServer aServer) {
server = aServer;
}
/* (non-Javadoc)
* @see java.lang.Runnable#run()
*/
public void run() {
if (server.threadsToWorkers.isEmpty()) {
// Nothing to be done here.
return;
}
try {
// No need to attempt to exit workers if the server itself
// isn't registered any longer. It won't be able to connect to
// workers anyway.
LocateRegistry.getRegistry(Port).lookup(SERVER_NAME);
} catch (AccessException e1) {
return;
} catch (RemoteException e1) {
return;
} catch (NotBoundException e1) {
return;
}
for (TLCWorkerRMI worker : server.threadsToWorkers.values()) {
try {
worker.exit();
} catch (java.rmi.ConnectException e) {
// happens if worker has exited already
} catch (java.rmi.NoSuchObjectException e) {
// happens if worker has exited already
} catch (IOException e) {
//TODO handle more gracefully
MP.printError(EC.GENERAL, e);
}
}
}
}
} |
package etomica.normalmode;
import java.awt.Color;
import etomica.action.BoxInflate;
import etomica.action.IAction;
import etomica.action.activity.ActivityIntegrate;
import etomica.api.IAtom;
import etomica.api.IAtomList;
import etomica.api.IAtomType;
import etomica.api.IBoundary;
import etomica.api.IBox;
import etomica.api.IIntegratorEvent;
import etomica.api.IIntegratorListener;
import etomica.api.IVector;
import etomica.api.IVectorMutable;
import etomica.atom.DiameterHash;
import etomica.box.Box;
import etomica.data.AccumulatorAverageBlockless;
import etomica.data.AccumulatorHistogram;
import etomica.data.AccumulatorHistory;
import etomica.data.DataDistributer;
import etomica.data.DataFork;
import etomica.data.DataPumpListener;
import etomica.data.DataSourceCountSteps;
import etomica.data.DataSplitter.IDataSinkFactory;
import etomica.data.DataTag;
import etomica.data.IData;
import etomica.data.IDataSink;
import etomica.data.meter.MeterNMolecules;
import etomica.data.meter.MeterPressure;
import etomica.graphics.ColorScheme;
import etomica.graphics.DeviceBox;
import etomica.graphics.DeviceButton;
import etomica.graphics.DisplayPlot;
import etomica.graphics.DisplayTextBox;
import etomica.graphics.SimulationGraphic;
import etomica.graphics.SimulationPanel;
import etomica.integrator.IntegratorMC;
import etomica.integrator.mcmove.MCMoveAtom;
import etomica.integrator.mcmove.MCMoveIDBiasAction;
import etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy;
import etomica.integrator.mcmove.MCMoveOverlapListener;
import etomica.integrator.mcmove.MCMoveVolume;
import etomica.lattice.crystal.Basis;
import etomica.lattice.crystal.BasisCubicFcc;
import etomica.lattice.crystal.PrimitiveCubic;
import etomica.listener.IntegratorListenerAction;
import etomica.modifier.Modifier;
import etomica.nbr.cell.Api1ACell;
import etomica.nbr.cell.PotentialMasterCell;
import etomica.normalmode.DataSourceMuRoot.DataSourceMuRootVacancyConcentration;
import etomica.potential.P2LennardJones;
import etomica.potential.P2SoftSphericalTruncated;
import etomica.simulation.Simulation;
import etomica.space.BoundaryRectangularPeriodic;
import etomica.space3d.Space3D;
import etomica.species.SpeciesSpheresMono;
import etomica.statmech.LennardJones;
import etomica.units.Dimension;
import etomica.units.Null;
import etomica.util.HistogramDiscrete;
import etomica.util.HistoryCollapsingAverage;
import etomica.util.HistoryCollapsingDiscard;
import etomica.util.ParameterBase;
import etomica.util.ParseArgs;
/**
* Simple Lennard-Jones molecular dynamics simulation in 3D
*/
public class SimLJVacancy extends Simulation {
public final PotentialMasterCell potentialMaster;
public final ActivityIntegrate ai;
public IntegratorMC integrator;
public SpeciesSpheresMono species;
public IBox box;
public P2LennardJones p2LJ;
public P2SoftSphericalTruncated potential;
public MCMoveVolume mcMoveVolume;
public MCMoveInsertDeleteLatticeVacancy mcMoveID;
public SimLJVacancy(final int numAtoms, double temperature, double density, double rc, final int fixedN, final int maxDN, final double bmu) {
super(Space3D.getInstance());
species = new SpeciesSpheresMono(this, space);
species.setIsDynamic(true);
addSpecies(species);
box = new Box(space);
addBox(box);
box.setNMolecules(species, numAtoms);
double L = Math.pow(4.0/density, 1.0/3.0);
int n = (int)Math.round(Math.pow(numAtoms/4, 1.0/3.0));
PrimitiveCubic primitive = new PrimitiveCubic(space, n*L);
int[] nCells = new int[]{n,n,n};
IBoundary boundary = new BoundaryRectangularPeriodic(space, n * L);
Basis basisFCC = new BasisCubicFcc();
BasisBigCell basis = new BasisBigCell(space, basisFCC, nCells);
box.setBoundary(boundary);
potentialMaster = new PotentialMasterCell(this, rc, space);
potentialMaster.setCellRange(2);
integrator = new IntegratorMC(this, potentialMaster);
integrator.setTemperature(temperature);
MCMoveAtom move = new MCMoveAtom(random, potentialMaster, space);
move.setStepSize(0.2);
// ((MCMoveStepTracker)move.getTracker()).setNoisyAdjustment(true);
integrator.getMoveManager().addMCMove(move);
ai = new ActivityIntegrate(integrator);
getController().addAction(ai);
BoxInflate inflater = new BoxInflate(box, space);
inflater.setTargetDensity(density);
inflater.actionPerformed();
if (rc > 0.49*box.getBoundary().getBoxSize().getX(0)) {
throw new RuntimeException("rc is too large");
}
double nbr1 = L/Math.sqrt(2);
double y = 1.25*nbr1; //nbr1+(L-nbr1)*0.6+0.06;
p2LJ = new P2LennardJones(space, 1, 1);
potential = new P2SoftSphericalTruncated(space, p2LJ, rc);
IAtomType leafType = species.getLeafType();
potentialMaster.addPotential(potential,new IAtomType[]{leafType,leafType});
integrator.setBox(box);
CoordinateDefinitionLeaf coordinateDefinition = new CoordinateDefinitionLeaf(box, primitive, basis, space);
coordinateDefinition.initializeCoordinates(new int[]{1,1,1});
// we just needed this to initial coordinates, to keep track of lattice positions of atoms
coordinateDefinition = null;
integrator.getMoveEventManager().addListener(potentialMaster.getNbrCellManager(box).makeMCMoveListener());
potentialMaster.getNbrCellManager(box).assignCellAll();
mcMoveID = new MCMoveInsertDeleteLatticeVacancy(potentialMaster, random, space, integrator, y, fixedN, maxDN);
double x = nbr1/40.0;
mcMoveID.setMaxInsertDistance(x);
mcMoveID.makeFccVectors(nbr1);
mcMoveID.setMu(bmu);
mcMoveID.setSpecies(species);
integrator.getMoveManager().addMCMove(mcMoveID);
integrator.getMoveManager().setFrequency(mcMoveID, 0.1);
integrator.getMoveEventManager().addListener(mcMoveID);
}
public static void main(String[] args) {
LJParams params = new LJParams();
ParseArgs.doParseArgs(params, args);
if (args.length==0) {
params.graphics = true;
params.numAtoms = 500;
params.steps = 1000000;
params.density = 1.0;
params.temperature = 0.7;
params.numV = 4;
}
final int numAtoms = params.numAtoms;
final double density = params.density;
final double temperature = params.temperature;
final double rc = params.rc*Math.pow(density, -1.0/3.0);
long steps = params.steps;
boolean graphics = params.graphics;
int maxDN = (params.numV+1)/2;
int fixedN = params.numAtoms - maxDN;
double mu = params.mu;
double Alat = params.Alat;
System.out.println("Running N="+params.numAtoms+" at rho="+density);
if (Double.isNaN(mu)) {
// this should get us pretty close
Alat = Math.log(density)-1.0 + (LennardJones.aResidualFcc(temperature, density))/temperature;
double zLat = LennardJones.ZFcc(temperature, density);
System.out.println("lattice pressure "+zLat);
mu = (Alat + zLat);
System.out.println("beta mu "+mu);
}
else if (Double.isNaN(Alat)) {
// this should get us pretty close
Alat = Math.log(density)-1.0 + (LennardJones.aResidualFcc(temperature, density))/temperature;
}
double daDef = params.daDef;
if (Double.isNaN(daDef)) {
// use a correlation. this should be with ~1
double Y = temperature/Math.pow(density, 4)/4;
double v2 = 1/(density*density);
daDef = (-3.6 - 10.5*Y + 8.2*v2)/Y;
System.out.println("estimated defect free energy: "+daDef);
}
else {
System.out.println("using defect free energy: "+daDef);
}
System.out.println("Running LJ MC");
System.out.println("N: "+numAtoms);
System.out.println("T: "+temperature);
System.out.println("density: "+density);
System.out.println("steps: "+steps);
final SimLJVacancy sim = new SimLJVacancy(numAtoms, temperature, density, rc, fixedN, maxDN, mu);
final int biasInterval = 10*numAtoms;
final MCMoveOverlapListener mcMoveOverlapMeter = new MCMoveOverlapListener(sim.mcMoveID, 11, daDef, numAtoms, 6);
mcMoveOverlapMeter.setTemperature(temperature);
sim.integrator.getMoveEventManager().addListener(mcMoveOverlapMeter);
final MeterPressure meterP = new MeterPressure(sim.getSpace());
meterP.setIntegrator(sim.integrator);
DataDistributer.Indexer indexer = new DataDistributer.Indexer() {
public int getIndex() {
return numAtoms-sim.box.getNMolecules(sim.species);
}
};
final DataDistributer pSplitter = new DataDistributer(indexer, new IDataSinkFactory() {
public IDataSink makeDataSink(int i) {
return new AccumulatorAverageBlockless();
}
});
pSplitter.putDataInfo(meterP.getDataInfo());
// collect pressure data before any insert/delete trials
sim.integrator.getEventManager().addListener(new IIntegratorListener() {
long countDown = numAtoms, interval = numAtoms;
public void integratorInitialized(IIntegratorEvent e) {}
public void integratorStepStarted(IIntegratorEvent e) {}
public void integratorStepFinished(IIntegratorEvent e) {
countDown
if (countDown==0) {
// everything really wants beta P
IData pData = meterP.getData();
pData.TE(1.0/temperature);
pSplitter.putData(pData);
countDown=interval;
}
}
});
final MCMoveIDBiasAction mcMoveBiasAction;
final IntegratorListenerAction mcMoveBiasListener;
if (params.doReweight) {
mcMoveBiasAction = new MCMoveIDBiasAction(sim.integrator, sim.mcMoveID, maxDN,
fixedN, mu, mcMoveOverlapMeter, numAtoms, 1);
mcMoveBiasAction.setNMaxReweight(numAtoms);
mcMoveBiasAction.setDefaultDaDef(daDef);
mcMoveBiasListener = new IntegratorListenerAction(mcMoveBiasAction, biasInterval);
sim.integrator.getEventManager().addListener(mcMoveBiasListener);
}
else {
mcMoveBiasAction = null;
mcMoveBiasListener = null;
}
if (graphics) {
MeterNMolecules meterN = new MeterNMolecules();
meterN.setBox(sim.box);
final AccumulatorHistogram nHistogram = new AccumulatorHistogram(new HistogramDiscrete(0.1));
DataPumpListener nPump = new DataPumpListener(meterN, nHistogram, numAtoms);
sim.integrator.getEventManager().addListener(nPump);
final String APP_NAME = "LJ Vacancy";
final SimulationGraphic simGraphic = new SimulationGraphic(sim, SimulationGraphic.TABBED_PANE, APP_NAME, numAtoms, sim.space, sim.getController());
final int nc = (int)Math.round(Math.pow(numAtoms/4, 1.0/3.0));
ColorScheme colorScheme = new ColorScheme() {
public Color getAtomColor(IAtom a) {
float x = (float)a.getPosition().getX(0);
float L = (float)sim.box.getBoundary().getBoxSize().getX(0);
x = nc*2*(x/L+0.5f);
if (nc%2==0) x+=0.5f;
while (x>3) x-=3;
float r = 0f, g = 0f, b = 0f;
if (x < 1) {
r = 1-x;
if (r>1) r=1;
g = x;
if (g<0) g=0;
}
else if (x < 2) {
g = 2-x;
b = x-1;
}
else {
b = 3-x;
if (b<0) b=0;
r = x-2;
if (r>1) r=1;
}
return new Color(r, g, b);
}
};
colorScheme = new ColorScheme() {
IVectorMutable dr = sim.space.makeVector();
double rMax = sim.mcMoveID.getMaxDistance();
double rc2 = rMax*rMax;
int nmax = 12;
Api1ACell iter = new Api1ACell(3, rMax, sim.potentialMaster.getCellAgentManager());
public Color getAtomColor(IAtom a) {
if (!sim.integrator.getEventManager().firingEvent() && !sim.ai.isPaused()) return new Color(1.0f, 1.0f, 1.0f);
IVector pi = a.getPosition();
iter.setBox(sim.box);
iter.setDirection(null);
iter.setTarget(a);
iter.reset();
IBoundary boundary = sim.box.getBoundary();
int n = 0;
for (IAtomList pair = iter.next(); pair!=null; pair=iter.next()) {
IAtom nbrj = pair.getAtom(0);
if (nbrj==a) nbrj=pair.getAtom(1);
dr.Ev1Mv2(pi, nbrj.getPosition());
boundary.nearestImage(dr);
double r2 = dr.squared();
if (r2 < rc2) {
n++;
}
}
if (n < nmax) return Color.RED;
if (n == nmax) return Color.BLUE;
return Color.BLUE;
}
};
simGraphic.getDisplayBox(sim.box).setColorScheme(colorScheme);
DiameterHash dh = new DiameterHash() {
IVectorMutable dr = sim.space.makeVector();
double rMax = sim.mcMoveID.getMaxDistance();
double rc2 = rc*rc;
int nmax = 12;
Api1ACell iter = new Api1ACell(3, rMax, sim.potentialMaster.getCellAgentManager());
public double getDiameter(IAtom a) {
IVector pi = a.getPosition();
IBoundary boundary = sim.box.getBoundary();
iter.setBox(sim.box);
iter.setDirection(null);
iter.setTarget(a);
try {
iter.reset();
}
catch (NullPointerException ex) {
// during addition
return 0;
}
int n = 0;
for (IAtomList pair = iter.next(); pair!=null; pair=iter.next()) {
IAtom nbrj = pair.getAtom(0);
if (nbrj==a) nbrj=pair.getAtom(1);
dr.Ev1Mv2(pi, nbrj.getPosition());
boundary.nearestImage(dr);
double r2 = dr.squared();
if (r2 < rc2) {
n++;
}
}
if (n < nmax) return 1.0;
if (n == nmax) return 0.1;
return 0.1;
}
};
// simGraphic.getDisplayBox(sim.box).setDiameterHash(dh);
simGraphic.getController().getReinitButton().setPostAction(simGraphic.getPaintAction(sim.box));
simGraphic.makeAndDisplayFrame(APP_NAME);
final AccumulatorHistory nHistory = new AccumulatorHistory(new HistoryCollapsingAverage());
DataSourceCountSteps timeDataSource = new DataSourceCountSteps(sim.integrator);
nHistory.setTimeDataSource(timeDataSource);
nHistory.setPushInterval(1);
DataFork nFork = new DataFork();
nPump.setDataSink(nFork);
nFork.addDataSink(nHistogram);
nFork.addDataSink(nHistory);
DisplayPlot nHistoryPlot = new DisplayPlot();
nHistoryPlot.setLabel("N history");
nHistoryPlot.setDoLegend(false);
nHistory.setDataSink(nHistoryPlot.getDataSet().makeDataSink());
simGraphic.add(nHistoryPlot);
DisplayPlot nPlot = new DisplayPlot();
nPlot.setLabel("N histogram");
nPlot.getPlot().setYLog(true);
nHistogram.setDataSink(nPlot.getDataSet().makeDataSink());
nPlot.setLegend(new DataTag[]{nHistogram.getTag()}, "visited");
simGraphic.add(nPlot);
final DataSourceFEHistogram feHistogram = new DataSourceFEHistogram(mcMoveOverlapMeter, mu);
DataPumpListener feHistPump = new DataPumpListener(feHistogram, nPlot.getDataSet().makeDataSink(), numAtoms);
sim.integrator.getEventManager().addListener(feHistPump);
nPlot.setLegend(new DataTag[]{feHistogram.getTag()}, "measured");
final DataSourceImposedFEHistogram feHistogramImposed = new DataSourceImposedFEHistogram(mcMoveOverlapMeter, sim.mcMoveID, mu);
DataPumpListener feHistImposedPump = new DataPumpListener(feHistogramImposed, nPlot.getDataSet().makeDataSink(), numAtoms);
nPlot.setLegend(new DataTag[]{feHistogramImposed.getTag()}, "imposed");
sim.integrator.getEventManager().addListener(feHistImposedPump);
final DataSourceImposedFEFit feHistogramFit = new DataSourceImposedFEFit(mcMoveOverlapMeter, sim.mcMoveID, mu);
DataPumpListener feHistFitPump = new DataPumpListener(feHistogramFit, nPlot.getDataSet().makeDataSink(), numAtoms);
nPlot.setLegend(new DataTag[]{feHistogramFit.getTag()}, "fit");
sim.integrator.getEventManager().addListener(feHistFitPump);
DisplayPlot fePlot = new DisplayPlot();
final DataSourceFE dsfe = new DataSourceFE(mcMoveOverlapMeter);
DataPumpListener fePump = new DataPumpListener(dsfe, fePlot.getDataSet().makeDataSink(), numAtoms);
sim.integrator.getEventManager().addListener(fePump);
fePlot.setLegend(new DataTag[]{dsfe.getTag()}, "FE");
final DataSourceFE dsfe2 = new DataSourceFE(mcMoveOverlapMeter);
dsfe2.setSubtractComb(true);
DataPumpListener fe2Pump = new DataPumpListener(dsfe2, fePlot.getDataSet().makeDataSink(), numAtoms);
sim.integrator.getEventManager().addListener(fe2Pump);
fePlot.setLegend(new DataTag[]{dsfe2.getTag()}, "FEdef");
final DataSourceFE dsfe3 = new DataSourceFE(mcMoveOverlapMeter);
dsfe3.setSubtractComb(true);
dsfe3.setAvgDef(true);
DataPumpListener fe3Pump = new DataPumpListener(dsfe3, fePlot.getDataSet().makeDataSink(), numAtoms);
sim.integrator.getEventManager().addListener(fe3Pump);
fePlot.setLegend(new DataTag[]{dsfe3.getTag()}, "FEdefAvg");
fePlot.setLabel("FE");
simGraphic.add(fePlot);
DisplayTextBox pDisplayBox = new DisplayTextBox();
pDisplayBox.setLabel("Measured pressure");
pDisplayBox.setPrecision(5);
DisplayTextBox pDisplayBox2 = new DisplayTextBox();
pDisplayBox2.setLabel("Pressure");
pDisplayBox2.setPrecision(5);
final DataSourceAvgPressure avgP = new DataSourceAvgPressure(pSplitter, mcMoveOverlapMeter, mu);
DataPumpListener avgPPump = new DataPumpListener(avgP, pDisplayBox, numAtoms);
sim.integrator.getEventManager().addListener(avgPPump);
final DataSourceAvgPressure2 avgP2 = new DataSourceAvgPressure2(mcMoveOverlapMeter, mu, Alat, density, numAtoms/density);
DataPumpListener avgPPump2 = new DataPumpListener(avgP2, pDisplayBox2, numAtoms);
sim.integrator.getEventManager().addListener(avgPPump2);
simGraphic.add(pDisplayBox);
simGraphic.add(pDisplayBox2);
DisplayPlot pmuPlot = new DisplayPlot();
pmuPlot.setDoLegend(false);
pmuPlot.setLabel("dP vs. mu");
final DataSourcePMu pmu = new DataSourcePMu(mcMoveOverlapMeter, 0.2, 21, mu, pSplitter, Alat, density, numAtoms/density, false);
DataPumpListener pmuPump = new DataPumpListener(pmu, pmuPlot.getDataSet().makeDataSink(), numAtoms);
sim.integrator.getEventManager().addListener(pmuPump);
simGraphic.add(pmuPlot);
DisplayPlot muMuPlot = new DisplayPlot();
muMuPlot.setDoLegend(false);
muMuPlot.setLabel("mu vs. mu");
final DataSourcePMu muMu = new DataSourcePMu(mcMoveOverlapMeter, 0.2, 21, mu, pSplitter, Alat, density, numAtoms/density, true);
DataPumpListener muMuPump = new DataPumpListener(muMu, muMuPlot.getDataSet().makeDataSink(), numAtoms);
sim.integrator.getEventManager().addListener(muMuPump);
simGraphic.add(muMuPlot);
DeviceBox muBox = new DeviceBox();
muBox.setPrecision(8);
muBox.setEditable(true);
muBox.setLabel("mu");
muBox.setModifier(new Modifier() {
public void setValue(double newValue) {
sim.mcMoveID.setMu(newValue);
feHistogram.setMu(newValue);
feHistogramImposed.setMu(newValue);
avgP.setMu(newValue);
avgP2.setBetaMu(newValue);
pmu.setMu(newValue);
mcMoveBiasAction.setMu(newValue);
}
public double getValue() {
return sim.mcMoveID.getMu();
}
public String getLabel() {
return "your mom";
}
public Dimension getDimension() {
return Null.DIMENSION;
}
});
simGraphic.add(muBox);
DataSourceMuRoot dsmr = new DataSourceMuRoot(mcMoveOverlapMeter, mu, pSplitter, Alat, density, numAtoms/density);
final AccumulatorHistory dsmrHistory = new AccumulatorHistory(new HistoryCollapsingDiscard());
dsmrHistory.setTimeDataSource(timeDataSource);
DataPumpListener dsmrPump = new DataPumpListener(dsmr, dsmrHistory, numAtoms);
sim.integrator.getEventManager().addListener(dsmrPump);
DisplayPlot dsmrPlot = new DisplayPlot();
dsmrPlot.setLabel("mu*");
dsmrPlot.setLegend(new DataTag[]{dsmr.getTag()},"avg");
dsmrHistory.setDataSink(dsmrPlot.getDataSet().makeDataSink());
simGraphic.add(dsmrPlot);
DataSourceMuRoot1 dsmr1 = null;
final AccumulatorHistory dsmr1History;
dsmr1 = new DataSourceMuRoot1(mcMoveOverlapMeter, mu, pSplitter, Alat, density, numAtoms/density);
dsmr1.setMinMu(10);
dsmr1History = new AccumulatorHistory(new HistoryCollapsingDiscard());
dsmr1History.setTimeDataSource(timeDataSource);
DataPumpListener dsmr1Pump = new DataPumpListener(dsmr1, dsmr1History, numAtoms);
sim.integrator.getEventManager().addListener(dsmr1Pump);
dsmr1History.setDataSink(dsmrPlot.getDataSet().makeDataSink());
dsmrPlot.setLegend(new DataTag[]{dsmr1.getTag()},"v1");
DataSourcePN dataSourcePN = new DataSourcePN(pSplitter, numAtoms);
DisplayPlot plotPN = new DisplayPlot();
DataPumpListener pumpPN = new DataPumpListener(dataSourcePN, plotPN.getDataSet().makeDataSink(), numAtoms);
sim.integrator.getEventManager().addListener(pumpPN);
plotPN.setLabel("P vs. N");
plotPN.setDoLegend(false);
simGraphic.add(plotPN);
DataSourceMuRootVacancyConcentration dsmrvc = dsmr.new DataSourceMuRootVacancyConcentration();
final AccumulatorHistory dsmrvcHistory = new AccumulatorHistory(new HistoryCollapsingDiscard());
dsmrvcHistory.setTimeDataSource(timeDataSource);
DataPumpListener dsmrvcPump = new DataPumpListener(dsmrvc, dsmrvcHistory, numAtoms);
sim.integrator.getEventManager().addListener(dsmrvcPump);
DisplayPlot vPlot = new DisplayPlot();
vPlot.setLabel("vacancies");
dsmrvcHistory.setDataSink(vPlot.getDataSet().makeDataSink());
vPlot.setLegend(new DataTag[]{dsmrvc.getTag()}, "avg");
simGraphic.add(vPlot);
final AccumulatorHistory dsmrvc1History;
DataSourceMuRoot1.DataSourceMuRootVacancyConcentration dsmrvc1 = dsmr1.new DataSourceMuRootVacancyConcentration();
dsmrvc1History = new AccumulatorHistory(new HistoryCollapsingDiscard());
dsmrvc1History.setTimeDataSource(timeDataSource);
DataPumpListener dsmrvc1Pump = new DataPumpListener(dsmrvc1, dsmrvc1History, numAtoms);
sim.integrator.getEventManager().addListener(dsmrvc1Pump);
dsmrvc1History.setDataSink(vPlot.getDataSet().makeDataSink());
vPlot.setLegend(new DataTag[]{dsmrvc1.getTag()}, "v1");
final DeviceButton resetButton = new DeviceButton(sim.getController());
IAction resetAction = new IAction() {
boolean enabled = true;
public void actionPerformed() {
if (enabled) {
mcMoveOverlapMeter.reset();
sim.integrator.resetStepCount();
nHistogram.reset();
nHistory.reset();
dsmrHistory.reset();
if (dsmr1History != null) {
dsmr1History.reset();
dsmrvc1History.reset();
}
dsmrvcHistory.reset();
for (int i=0; i<pSplitter.getNumDataSinks(); i++) {
AccumulatorAverageBlockless avg = (AccumulatorAverageBlockless)pSplitter.getDataSink(i);
if (avg != null) avg.reset();
}
sim.integrator.getEventManager().removeListener(mcMoveBiasListener);
enabled = false;
resetButton.setLabel("Reweight");
}
else {
sim.integrator.getEventManager().addListener(mcMoveBiasListener);
enabled = true;
resetButton.setLabel("Reset");
}
}
};
resetButton.setAction(resetAction);
resetButton.setLabel("Reset");
simGraphic.getPanel().controlPanel.add(resetButton.graphic(),SimulationPanel.getVertGBC());
return;
}
final DataSourceFE dsfe3 = new DataSourceFE(mcMoveOverlapMeter);
dsfe3.setSubtractComb(true);
dsfe3.setAvgDef(true);
// equilibrate off the lattice
sim.ai.setMaxSteps(steps/40);
sim.ai.actionPerformed();
IData dsfe3Data = dsfe3.getData();
if (dsfe3Data.getLength() == 0) {
throw new RuntimeException("no data after initial equilibration");
}
double daDefAvg = dsfe3Data.getValue(0);
System.out.println("very initial daDef = "+daDefAvg);
// throw away our data
mcMoveOverlapMeter.reset();
sim.integrator.resetStepCount();
for (int i=0; i<pSplitter.getNumDataSinks(); i++) {
AccumulatorAverageBlockless avg = (AccumulatorAverageBlockless)pSplitter.getDataSink(i);
if (avg != null) avg.reset();
}
sim.integrator.resetStepCount();
if (params.doReweight) {
// update weights
mcMoveBiasAction.actionPerformed();
// and stop adjusting them
sim.integrator.getEventManager().removeListener(mcMoveBiasListener);
}
final long finalSteps = steps;
sim.integrator.getEventManager().addListener(new IIntegratorListener() {
boolean reenabled = false;
public void integratorStepStarted(IIntegratorEvent e) {}
public void integratorStepFinished(IIntegratorEvent e) {
if (!reenabled && sim.integrator.getStepCount() >= finalSteps/40) {
sim.integrator.getEventManager().addListener(mcMoveBiasListener);
reenabled = true;
}
}
public void integratorInitialized(IIntegratorEvent e) {}
});
sim.ai.setMaxSteps(steps/10);
sim.ai.actionPerformed();
if (params.doReweight) {
dsfe3Data = dsfe3.getData();
daDefAvg = dsfe3Data.getValue(0);
System.out.println("using daDef = "+daDefAvg);
// update weights
mcMoveBiasAction.actionPerformed();
// and stop adjusting them (permanently this time)
sim.integrator.getEventManager().removeListener(mcMoveBiasListener);
}
// and throw away data again
mcMoveOverlapMeter.reset();
for (int i=0; i<pSplitter.getNumDataSinks(); i++) {
AccumulatorAverageBlockless avg = (AccumulatorAverageBlockless)pSplitter.getDataSink(i);
if (avg != null) avg.reset();
}
sim.integrator.resetStepCount();
sim.integrator.getMoveManager().setEquilibrating(false);
// take real data
long t1 = System.currentTimeMillis();
sim.ai.setMaxSteps(steps);
sim.getController().actionPerformed();
long t2 = System.currentTimeMillis();
System.out.println();
DataSourceMuRoot dsmr = new DataSourceMuRoot(mcMoveOverlapMeter, mu, pSplitter, Alat, density, numAtoms/density);
double muRoot = dsmr.getDataAsScalar();
// histogram of # of atoms based on free energy differences
final DataSourceFEHistogram feHistogram = new DataSourceFEHistogram(mcMoveOverlapMeter, muRoot);
// actual free energy differences
final DataSourceFE dsfe = new DataSourceFE(mcMoveOverlapMeter);
final DataSourceFE dsfe2 = new DataSourceFE(mcMoveOverlapMeter);
// subtract off combinatorial entropy
dsfe2.setSubtractComb(true);
IData nData = feHistogram.getIndependentData(0);
IData fenData = feHistogram.getData();
IData dsfeData = dsfe.getData();
IData dsfe2Data = dsfe2.getData();
dsfe3Data = dsfe3.getData();
double[] nHistogram = mcMoveOverlapMeter.getHistogram();
for (int i=0; i<nData.getLength(); i++) {
int n = (int)Math.round(nData.getValue(i));
double pAvg = Double.NaN;
if (numAtoms-n < pSplitter.getNumDataSinks()) {
AccumulatorAverageBlockless pAcc = (AccumulatorAverageBlockless)pSplitter.getDataSink(numAtoms-n);
pAvg = pAcc == null ? Double.NaN : pAcc.getData().getValue(pAcc.AVERAGE.index);
}
if (dsfeData.getLength() > i) {
System.out.println(String.format("%6d %20.15e %20.15e %20.15e %20.15e %20.15e", n, nHistogram[i], fenData.getValue(i), pAvg, dsfeData.getValue(i), dsfe2Data.getValue(i)));
}
else {
System.out.println(String.format("%6d %20.15e %20.15e %20.15e", n, nHistogram[i], fenData.getValue(i), pAvg));
}
}
double pAccept = sim.mcMoveID.getTracker().acceptanceProbability();
System.out.println("\nInsert/delete acceptance "+pAccept);
System.out.println("final daDef: "+dsfe3Data.getValue(0));
System.out.println("mu: "+muRoot);
double pRoot = dsmr.getLastPressure();
double vRoot = dsmr.getLastVacancyConcentration();
System.out.println("pressure: "+pRoot);
double deltaP = dsmr.getLastDPressure();
System.out.println("delta P: "+deltaP);
System.out.println("vacancy fraction: "+vRoot);
double tot = dsmr.getLastTot();
double deltaA = -(1-vRoot)*Math.log(tot)/numAtoms - vRoot/density*deltaP/temperature;
// free energy change per lattice site
System.out.println("delta betaA: "+deltaA);
System.out.println("time: "+(t2-t1)/1000.0+" seconds");
}
public static class LJParams extends ParameterBase {
public int numAtoms = 500;
public double density = 1.0;
public double temperature = 0.8;
public long steps = 1000000;
public boolean graphics = false;
public double mu = Double.NaN;
public double Alat = Double.NaN;
public int numV = 5;
public boolean doReweight = true;
public double daDef = Double.NaN;
public double rc = 3;
}
} |
package etomica.virial.cluster;
import etomica.math.SpecialFunctions;
import etomica.utility.Arrays;
import etomica.virial.Cluster;
import etomica.virial.ClusterAbstract;
import etomica.virial.ClusterSum;
import etomica.virial.MayerFunction;
import etomica.virial.Cluster.BondGroup;
/**
* @author kofke
*
* Class that provides some standard pair sets (via static methods or fields of
* integer arrays) used in specification of clusters.
*/
public final class Standard {
/**
* Private constructor to prevent instantiation.
*/
private Standard() {
super();
}
/**
* Returns a chain of bonds, {{0,1},{1,2},...{n-2,n-1}}
* @param n number of points in chain
* @return int[][] array describing chain of bonds
*/
public static int[][] chain(int n) {
int[][] array = new int[n-1][];
for(int i=0; i<n-1; i++) {
array[i] = new int[] {i,i+1};
}
return array;
}
/**
* Returns a ring of bonds, {{0,1},{1,2},...{n-2,n-1},{n-1,0}}
* @param n number of points in ring
* @return int[][] array describing ring of bonds
*/
public static int[][] ring(int n) {
int[][] array = new int[n][];
for(int i=0; i<n-1; i++) {
array[i] = new int[] {i,i+1};
}
array[n-1] = new int[] {0,n-1};
return array;
}
/**
* Returns a full set of bonds, such that each of the n points is joined to
* each of the others. Starts labeling points at 0.
*/
public static int[][] full(int n) {
return full(n, 0);
}
/**
* Returns a full set of bonds, such that each of the n points is joined to
* each of the others; starts labeling of point using the given index
* <first>. For example, full(3,2) returns {{2,3},{2,4},{3,4}}, which can
* be compared to full(3), which returns {{0,1},{0,2},{1,2}}
*/
public static int[][] full(int n, int first) {
int[][] array = new int[n*(n-1)/2][];
int k = 0;
for(int i=0; i<n-1; i++) {
for(int j=i+1; j<n; j++) {
array[k++] = new int[] {i+first,j+first};
}
}
return array;
}
/** Prepares a set of bond pairs for a clusters
* formed from a disconnected set of fully connected subclusters.
* @param iSet element [k] describes the number of subclusters having k
* points
* @return int[][] the bond array built to the given specification
*/
public static int[][] product(int[] iSet) {
int n = 0;
for(int i=1; i<=iSet.length; i++) n += iSet[i-1]*i*(i-1)/2;
int[][] array = new int[n][];
int j = 0;
int first = iSet[0];//only single points (Q1) (no integer pairs) for number of points equal to iSet[0]
for(int i=2; i<=iSet.length; i++) { //{1, 2, 0, 0, 0} = {Q1, 2Q2, etc} start with Q2
for(int k=0; k<iSet[i-1]; k++) {//e.g. make 2 Q2 sets {0,1}, {2,3}
int[][] a = full(i, first);
for(int m=0; m<a.length; m++) array[j++] = a[m];//add integer pairs for this group to array of all pairs
first += i;
}
}
return array;
}
public static ClusterAbstract virialCluster(int nBody, MayerFunction f) {
return virialCluster(nBody,f,true);
}
public static ClusterAbstract virialCluster(int nBody, MayerFunction f, boolean usePermutations) {
ClusterDiagram clusterD = new ClusterDiagram(nBody,0);
ClusterGenerator generator = new ClusterGenerator(clusterD);
generator.setAllPermutations(!usePermutations);
generator.setOnlyDoublyConnected(true);
generator.setExcludeArticulationPoint(false);
generator.setExcludeArticulationPair(false);
generator.setExcludeNodalPoint(false);
generator.reset();
ClusterAbstract[] clusters = new ClusterAbstract[0];
double[] weights = new double[0];
int fullSymmetry = usePermutations ? SpecialFunctions.factorial(nBody) : 1;
double weightPrefactor = -fullSymmetry*nBody/(double)(nBody-1);
do {
int numBonds = clusterD.getNumConnections();
int[][] bondList = new int[numBonds][2];
int iBond = 0;
for (int i = 0; i < nBody; i++) {
int[] iConnections = clusterD.mConnections[i];
for (int j = 0; j < nBody - 1 && iConnections[j] != -1; j++) {
if (i < iConnections[j]) {
bondList[iBond][0] = i;
bondList[iBond++][1] = iConnections[j];
}
}
}
// only use permutations if the diagram has permutations
boolean thisUsePermutations = usePermutations && clusterD.mNumIdenticalPermutations < fullSymmetry;
clusters = (ClusterAbstract[])Arrays.addObject(clusters,new Cluster(nBody, new BondGroup[] {new BondGroup(f, bondList)}, thisUsePermutations));
double [] newWeights = new double[weights.length+1];
System.arraycopy(weights,0,newWeights,0,weights.length);
newWeights[weights.length] = weightPrefactor/(usePermutations ? clusterD.mNumIdenticalPermutations : 1);
weights = newWeights;
} while (generator.advance());
if (clusters.length == 1) return clusters[0];
return new ClusterSum(clusters,weights);
}
public static final int[][] B2 = new int[][] {{0,1}};
public static final int[][] C3 = ring(3);
public static final int[][] D4 = ring(4);
public static final int[][] D5 = new int[][] {{0,1},{0,2},{0,3},{1,2},{2,3}};
public static final int[][] D6 = full(4);
public static double B2HS(double sigma) {
return 2.0*Math.PI/3.0 * sigma*sigma*sigma;
}
public static double C3HS(double sigma) {
double b0 = B2HS(sigma);
return 5./8. * b0 * b0;
}
public static double D4HS(double sigma) {
double b0 = B2HS(sigma);
return (219.0*Math.sqrt(2.0)/2240.0/Math.PI-89.0/280.0+4131.0/2240.0/Math.PI*Math.atan(Math.sqrt(2.0)))*b0*b0*b0;
}
public static Cluster[] B6Clusters(MayerFunction f) {
int[][] FRH1 = new int[][] {{0,1},{0,2},{0,4},{0,5},{1,2},{1,3},{1,5}
,{2,3},{2,4},{2,5},{3,4},{3,5},{4,5}};
int[][] FRH2 = new int[][] {{0,2},{0,3},{0,4},{0,5},{1,2},{1,3},{1,4},{1,5}
,{2,4},{2,5},{3,4},{3,5}};
int[][] FRH3 = new int[][] {{0,2},{0,3},{0,4},{1,2},{1,3},{1,4},{1,5}
,{2,3},{2,5},{3,4},{3,5},{4,5}};
int[][] FRH4 = new int[][] {{0,1},{0,2},{0,3},{0,4},{1,3},{1,4},{1,5}
,{2,4},{2,5},{3,4},{3,5}};
int[][] FRH5 = new int[][] {{0,2},{0,3},{0,4},{0,5},{1,2},{1,3},{1,4},{1,5}
,{2,4},{2,5},{3,5}};
int[][] FRH6 = new int[][] {{0,1},{0,2},{0,3},{1,2},{1,4},{1,5}
,{2,3},{2,4},{2,5},{3,4},{3,5}};
int[][] FRH7 = new int[][] {{0,1},{0,3},{0,4},{0,5},{1,2},{1,3},{1,5}
,{2,3},{2,4},{2,5},{3,5}};
int[][] FRH8 = new int[][] {{0,2},{0,3},{0,4},{1,3},{1,4},{1,5}
,{2,4},{2,5},{3,4},{3,5}};
int[][] FRH9 = new int[][] {{0,2},{0,3},{0,4},{0,5},{1,2},{1,3},{1,4},{1,5}
,{2,4},{3,5}};
int[][] FRH10 = new int[][] {{0,2},{0,3},{0,4},{1,3},{1,4},{1,5}
,{2,3},{2,5},{3,4},{3,5}};
int[][] FRH11 = new int[][] {{0,1},{0,3},{0,4},{0,5},{1,2},{1,3},{1,5}
,{2,3},{2,4},{2,5}};
int[][] FRH12 = new int[][] {{0,2},{0,3},{0,4},{1,3},{1,4},{1,5}
,{2,4},{2,5},{3,5}};
int[][] FRH13 = new int[][] {{0,2},{0,3},{1,3},{1,4},{1,5}
,{2,4},{2,5},{3,4},{3,5}};
int[][] FRH14 = new int[][] {{0,2},{0,3},{0,4},{1,3},{1,4},{1,5}
,{2,5},{3,4},{3,5}};
int[][] FRH15 = new int[][] {{0,2},{0,3},{0,4},{1,4},{1,5}
,{2,4},{2,5},{3,5}};
int[][] FRH16 = new int[][] {{0,2},{0,3},{1,4},{1,5}
,{2,4},{2,5},{3,4},{3,5}};
//error int[][] FRH17 = new int[][] {{0,2},{0,3},{0,4},{1,3},{1,4},{1,5}
//error ,{2,5},{3,5}};
int[][] FRH17 = new int[][] {{0,2},{0,3},{0,4},{1,3},{1,4},{1,5}
,{2,5},{3,4}};
int[][] FRH18 = new int[][] {{0,2},{0,3},{0,4},{1,3},{1,4},{1,5}
,{2,5}};
int[][] FRH19 = new int[][] {{0,2},{0,3},{1,4},{1,5}
,{2,4},{3,5}};
// rest which are negligible in hard spheres
int[][] FRH20 = new int[][]{{0,1},{0,2},{0,3},{1,4},{1,5},{2,4},{2,5}
,{3,4},{3,5}};
int[][] FRH21 = new int[][]{{0,2},{0,3},{0,4},{0,5},{1,2},{1,3},{1,4},{1,5}
,{2,4}};
//error int[][] FRH22 = new int[][]{{0,2},{0,3},{0,4},{0,5},{1,3},{1,4},{1,5}};
int[][] FRH22 = new int[][]{{0,2},{0,3},{0,4},{0,5},{1,2},{1,3},{1,4},{1,5}};
Cluster f0 = new Cluster(6, new Cluster.BondGroup(f, Standard.full(6)));
Cluster f1 = new ReeHoover(6, new Cluster.BondGroup(f, FRH1));
Cluster f2 = new ReeHoover(6, new Cluster.BondGroup(f, FRH2));
Cluster f3 = new ReeHoover(6, new Cluster.BondGroup(f, FRH3));
Cluster f4 = new ReeHoover(6, new Cluster.BondGroup(f, FRH4));
Cluster f5 = new ReeHoover(6, new Cluster.BondGroup(f, FRH5));
Cluster f6 = new ReeHoover(6, new Cluster.BondGroup(f, FRH6));
Cluster f7 = new ReeHoover(6, new Cluster.BondGroup(f, FRH7));
Cluster f8 = new ReeHoover(6, new Cluster.BondGroup(f, FRH8));
Cluster f9 = new ReeHoover(6, new Cluster.BondGroup(f, FRH9));
Cluster f10 = new ReeHoover(6, new Cluster.BondGroup(f, FRH10));
Cluster f11 = new ReeHoover(6, new Cluster.BondGroup(f, FRH11));
Cluster f12 = new ReeHoover(6, new Cluster.BondGroup(f, FRH12));
Cluster f13 = new ReeHoover(6, new Cluster.BondGroup(f, FRH13));
Cluster f14 = new ReeHoover(6, new Cluster.BondGroup(f, FRH14));
Cluster f15 = new ReeHoover(6, new Cluster.BondGroup(f, FRH15));
Cluster f16 = new ReeHoover(6, new Cluster.BondGroup(f, FRH16));
Cluster f17 = new ReeHoover(6, new Cluster.BondGroup(f, FRH17));
Cluster f18 = new ReeHoover(6, new Cluster.BondGroup(f, FRH18));
Cluster f19 = new ReeHoover(6, new Cluster.BondGroup(f, FRH19));
Cluster f20 = new ReeHoover(6, new Cluster.BondGroup(f, FRH20));
Cluster f21 = new ReeHoover(6, new Cluster.BondGroup(f, FRH21));
Cluster f22 = new ReeHoover(6, new Cluster.BondGroup(f, FRH22));
Cluster[] clusters = new Cluster[] {f0,f1,f2,f3,f4,f5,f6,f7,f8,f9,f10,f11,f12,f13,f14,f15,f16,f17,f18,f19,f20,f21,f22};
for(int i=0; i<clusters.length; i++) clusters[i].setUsePermutations(true);
return clusters;
}
public static double[] B6ClusterWeights() {
double[] weights = new double[]{-24, -240, -1440, -360, 900, 240, 360, 360, -180, 288, -540, -240, -360, -1080, 720, 90, 360, -180, -60, -40, -180, -15};
for (int i=0; i<weights.length; i++) {
weights[i] /= 144.0;
}
return weights;
}
public static void main(String[] args) {
int[] iSet = new int[] {5,0,0,0,0};
int[][] array = product(iSet);
int n = array.length;
String string = "(";
for(int i=0; i<n-1; i++) string += "{"+array[i][0]+","+array[i][1]+"}, ";
if(n>0) string += "{"+array[n-1][0]+","+array[n-1][1]+"}";
string += ")";
System.out.println(string);
}
// 24 (5, 0, 0, 0, 0)
// -60 (3, 1, 0, 0, 0)
// 30 (1, 2, 0, 0, 0)
// 20 (2, 0, 1, 0, 0)
// -10 (0, 1, 1, 0, 0)
// -5 (1, 0, 0, 1, 0)
// 1 (0, 0, 0, 0, 1)
} |
package swarm.client.view.cell;
import java.util.logging.Logger;
import swarm.client.app.smClientAppConfig;
import swarm.client.app.smAppContext;
import swarm.client.entities.smCamera;
import swarm.client.entities.smBufferCell;
import swarm.client.entities.smE_CodeStatus;
import swarm.client.input.smClickManager;
import swarm.client.input.smI_ClickHandler;
import swarm.client.managers.smCameraManager;
import swarm.client.navigation.smBrowserNavigator;
import swarm.client.navigation.smU_CameraViewport;
import swarm.client.states.camera.Action_Camera_SnapToPoint;
import swarm.client.states.camera.Action_Camera_SetViewSize;
import swarm.client.states.camera.Action_Camera_SnapToAddress;
import swarm.client.states.camera.Action_Camera_SnapToCoordinate;
import swarm.client.states.camera.Action_ViewingCell_Refresh;
import swarm.client.states.camera.StateMachine_Camera;
import swarm.client.states.camera.State_CameraSnapping;
import swarm.client.states.camera.State_ViewingCell;
import swarm.client.states.code.Action_EditingCode_Preview;
import swarm.client.states.code.Action_EditingCode_Save;
import swarm.client.view.smE_ZIndex;
import swarm.client.view.smI_UIElement;
import swarm.client.view.smU_Css;
import swarm.client.view.smViewContext;
import swarm.client.view.tooltip.smE_ToolTipType;
import swarm.client.view.tooltip.smToolTipConfig;
import swarm.client.view.tooltip.smToolTipManager;
import swarm.client.view.widget.smSpriteButton;
import swarm.shared.app.smS_App;
import swarm.shared.debugging.smU_Debug;
import swarm.shared.entities.smA_Grid;
import swarm.shared.entities.smE_CodeType;
import swarm.shared.statemachine.smA_Action;
import swarm.shared.statemachine.smA_State;
import swarm.shared.statemachine.smE_StateTimeType;
import swarm.shared.statemachine.smStateEvent;
import swarm.shared.structs.smGridCoordinate;
import swarm.shared.structs.smPoint;
import swarm.shared.structs.smVector;
import swarm.shared.utils.smU_Math;
import com.google.gwt.dom.client.Element;
import com.google.gwt.dom.client.Style.Unit;
import com.google.gwt.event.dom.client.ClickEvent;
import com.google.gwt.event.dom.client.ClickHandler;
import com.google.gwt.user.client.ui.FlowPanel;
import com.google.gwt.user.client.ui.HasHorizontalAlignment;
import com.google.gwt.user.client.ui.HasVerticalAlignment;
import com.google.gwt.user.client.ui.HorizontalPanel;
import com.google.gwt.user.client.ui.Panel;
import com.google.gwt.user.client.ui.HasHorizontalAlignment.HorizontalAlignmentConstant;
public class smVisualCellHud extends FlowPanel implements smI_UIElement
{
private static final Logger s_logger = Logger.getLogger(smVisualCellHud.class.getName());
private static final smPoint s_utilPoint1 = new smPoint();
private static final smPoint s_utilPoint2 = new smPoint();
private static final smVector s_utilVector = new smVector();
private class smHudButton extends smSpriteButton
{
private smHudButton(String spriteId)
{
super(spriteId);
this.addStyleName("sm_hud_button");
}
}
private final HorizontalPanel m_innerContainer = new HorizontalPanel();
private final HorizontalPanel m_leftDock = new HorizontalPanel();
private final HorizontalPanel m_rightDock = new HorizontalPanel();
private final smHudButton m_back = new smHudButton("back");
private final smHudButton m_forward = new smHudButton("forward");
private final smHudButton m_refresh = new smHudButton("refresh");
private final smHudButton m_close = new smHudButton("close");
private boolean m_waitingForBeingRefreshableAgain = false;
private final smViewContext m_viewContext;
private final smClientAppConfig m_appConfig;
private final Action_Camera_SnapToPoint.Args m_args_SetCameraTarget = new Action_Camera_SnapToPoint.Args();
private final double m_minWidth = 169;// TODO: GHETTO
private double m_width = 0;
private double m_baseAlpha;
private double m_alpha;
private final double m_fadeOutTime_seconds;
private String m_lastTranslation = "";
private final smPoint m_lastWorldPositionOnDoubleSnap = new smPoint();
private final smPoint m_lastWorldPosition = new smPoint();
private final smGridCoordinate m_lastSnapCoord = new smGridCoordinate();
private boolean m_performedDoubleSnap;
public smVisualCellHud(smViewContext viewContext, smClientAppConfig appConfig)
{
m_viewContext = viewContext;
m_appConfig = appConfig;
m_fadeOutTime_seconds = m_viewContext.viewConfig.hudFadeOutTime_seconds;
m_alpha = m_baseAlpha = 0.0;
this.addStyleName("sm_cell_hud");
smE_ZIndex.CELL_HUD.assignTo(this);
this.setVisible(false);
m_innerContainer.setWidth("100%");
this.getElement().getStyle().setProperty("minWidth", m_minWidth + "px");
smU_Css.setTransformOrigin(this.getElement(), "0% 0%");
m_innerContainer.setVerticalAlignment(HasVerticalAlignment.ALIGN_MIDDLE);
m_leftDock.setVerticalAlignment(HasVerticalAlignment.ALIGN_MIDDLE);
m_rightDock.setVerticalAlignment(HasVerticalAlignment.ALIGN_MIDDLE);
m_leftDock.add(m_back);
m_leftDock.add(m_forward);
m_leftDock.add(m_refresh);
m_rightDock.add(m_close);
m_innerContainer.add(m_leftDock);
m_innerContainer.add(m_rightDock);
m_innerContainer.setCellHorizontalAlignment(m_rightDock, HasHorizontalAlignment.ALIGN_RIGHT);
this.add(m_innerContainer);
m_viewContext.clickMngr.addClickHandler(m_back, new smI_ClickHandler()
{
@Override
public void onClick(int x, int y)
{
if( !m_back.isEnabled() ) return;
m_viewContext.browserNavigator.go(-1);
}
});
m_viewContext.clickMngr.addClickHandler(m_forward, new smI_ClickHandler()
{
@Override
public void onClick(int x, int y)
{
if( !m_forward.isEnabled() ) return;
m_viewContext.browserNavigator.go(1);
}
});
m_viewContext.clickMngr.addClickHandler(m_refresh, new smI_ClickHandler()
{
@Override
public void onClick(int x, int y)
{
if( !m_refresh.isEnabled() ) return;
smVisualCellHud.this.m_viewContext.cellMngr.clearAlerts();
m_viewContext.stateContext.performAction(Action_ViewingCell_Refresh.class);
}
});
m_viewContext.clickMngr.addClickHandler(m_close, new smI_ClickHandler()
{
@Override
public void onClick(int x, int y)
{
if( !m_close.isEnabled() ) return;
s_utilPoint1.copy(smVisualCellHud.this.m_viewContext.appContext.cameraMngr.getCamera().getPosition());
s_utilPoint1.incZ(m_appConfig.backOffDistance);
m_args_SetCameraTarget.init(s_utilPoint1, false, true);
m_viewContext.stateContext.performAction(Action_Camera_SnapToPoint.class, m_args_SetCameraTarget);
}
});
smToolTipManager toolTipper = m_viewContext.toolTipMngr;
toolTipper.addTip(m_back, new smToolTipConfig(smE_ToolTipType.MOUSE_OVER, "Go back."));
toolTipper.addTip(m_forward, new smToolTipConfig(smE_ToolTipType.MOUSE_OVER, "Go forward."));
toolTipper.addTip(m_refresh, new smToolTipConfig(smE_ToolTipType.MOUSE_OVER, "Refresh this cell."));
toolTipper.addTip(m_close, new smToolTipConfig(smE_ToolTipType.MOUSE_OVER, "Back off."));
}
private void setAlpha(double alpha)
{
m_alpha = alpha <= 0 ? 0 : alpha;
//s_logger.severe(m_alpha + "");
this.getElement().getStyle().setOpacity(m_alpha);
}
private void updateCloseButton()
{
State_ViewingCell viewingState = m_viewContext.stateContext.getEnteredState(State_ViewingCell.class);
State_CameraSnapping snappingState = m_viewContext.stateContext.getEnteredState(State_CameraSnapping.class);
if( viewingState != null || snappingState != null && snappingState.getPreviousState() == State_ViewingCell.class )
{
m_close.setEnabled(true);
}
else
{
m_close.setEnabled(false);
}
}
private void updateRefreshButton()
{
boolean canRefresh = m_viewContext.stateContext.isActionPerformable(Action_ViewingCell_Refresh.class);
m_refresh.setEnabled(canRefresh);
if( !canRefresh )
{
m_waitingForBeingRefreshableAgain = true;
}
else
{
m_waitingForBeingRefreshableAgain = false;
}
}
private void updatePositionFromScreenPoint(smA_Grid grid, smPoint screenPoint)
{
smCamera camera = m_viewContext.appContext.cameraMngr.getCamera();
camera.calcWorldPoint(screenPoint, m_lastWorldPosition);
boolean has3dTransforms = m_viewContext.appContext.platformInfo.has3dTransforms();
m_lastTranslation = smU_Css.createTranslateTransform(screenPoint.getX(), screenPoint.getY(), has3dTransforms);
double scaling = m_viewContext.cellMngr.getLastScaling();
String scaleProperty = smU_Css.createScaleTransform(scaling, has3dTransforms);
smU_Css.setTransform(this.getElement(), m_lastTranslation + " " + scaleProperty);
}
private void updateScalingOnly()
{
boolean has3dTransforms = m_viewContext.appContext.platformInfo.has3dTransforms();
double scaling = m_viewContext.cellMngr.getLastScaling();
String scaleProperty = smU_Css.createScaleTransform(scaling, has3dTransforms);
smU_Css.setTransform(this.getElement(), m_lastTranslation + " " + scaleProperty);
}
private void updatePositionFromWorldPoint(smA_Grid grid, smPoint worldPoint)
{
smCamera camera = m_viewContext.appContext.cameraMngr.getCamera();
camera.calcScreenPoint(worldPoint, s_utilPoint2);
this.updatePositionFromScreenPoint(grid, s_utilPoint2);
}
private void updatePosition(smA_Grid grid, smGridCoordinate coord)
{
this.calcScreenPositionFromCoord(grid, coord, s_utilPoint2);
this.updatePositionFromScreenPoint(grid, s_utilPoint2);
}
private void calcScreenPositionFromCoord(smA_Grid grid, smGridCoordinate coord, smPoint point_out)
{
smCamera camera = m_viewContext.appContext.cameraMngr.getCamera();
coord.calcPoint(s_utilPoint1, grid.getCellWidth(), grid.getCellHeight(), grid.getCellPadding(), 1);
camera.calcScreenPoint(s_utilPoint1, point_out);
Element scrollElement = this.getParent().getElement();
double scrollX = scrollElement.getScrollLeft();
double scrollY = scrollElement.getScrollTop();
double x = point_out.getX() + scrollX*2;
double viewWidth = getViewWidth(camera, grid);
double hudWidth = Math.max(m_width, m_minWidth);
if( hudWidth > viewWidth )
{
double scrollWidth = scrollElement.getScrollWidth();
double clientWidth = scrollElement.getClientWidth();
double diff = (hudWidth - viewWidth) + smU_CameraViewport.getViewPadding(grid)/2.0;
double scrollRatio = scrollX / (scrollWidth-clientWidth);
x -= diff * scrollRatio;
}
double scaling = m_viewContext.cellMngr.getLastScaling();
double y = point_out.getY()-(m_appConfig.cellHudHeight+grid.getCellPadding())*scaling;
y -= 1*scaling; // account for margin...sigh
y += scrollY * scaling;
point_out.set(x, y, 0);
}
private void updatePositionFromState(State_CameraSnapping state)
{
smA_Grid grid = m_viewContext.appContext.gridMngr.getGrid(); // TODO: Can be more than one grid in the future
smGridCoordinate coord = state.getTargetCoordinate();
this.updatePosition(grid, coord);
}
private void updatePositionFromState(State_ViewingCell state)
{
smBufferCell cell = ((State_ViewingCell)state).getCell();
smA_Grid grid = cell.getGrid();
smGridCoordinate coord = cell.getCoordinate();
this.updatePosition(grid, coord);
}
private void updateHistoryButtons()
{
State_ViewingCell viewingState = m_viewContext.stateContext.getEnteredState(State_ViewingCell.class);
State_CameraSnapping snappingState = m_viewContext.stateContext.getEnteredState(State_CameraSnapping.class);
if( viewingState != null || snappingState != null && snappingState.getPreviousState() == State_ViewingCell.class )
{
m_back.setEnabled(m_viewContext.browserNavigator.hasBack());
m_forward.setEnabled(m_viewContext.browserNavigator.hasForward());
}
else
{
m_back.setEnabled(false);
m_forward.setEnabled(false);
}
}
private double getViewWidth(smCamera camera, smA_Grid grid)
{
double viewPadding = smU_CameraViewport.getViewPadding(grid);
double viewWidth = camera.getViewWidth() - viewPadding*2;
return viewWidth;
}
private void updateSize(State_ViewingCell state)
{
smA_Grid grid = state.getCell().getGrid();
smCamera camera = m_viewContext.appContext.cameraMngr.getCamera();
double viewWidth = getViewWidth(camera, grid);
double cellWidth = grid.getCellWidth();
double hudWidth = Math.min(viewWidth, cellWidth);
m_width = hudWidth - 9; // TODO: GHETTO...takes into account padding or something.
//m_width = Math.max(m_width, m_minWidth);
//s_logger.severe("hud width: " + m_width);
this.getElement().getStyle().setWidth(m_width, Unit.PX);
}
private void onDoubleSnap()
{
m_lastWorldPositionOnDoubleSnap.copy(m_lastWorldPosition);
m_performedDoubleSnap = true;
}
@Override
public void onStateEvent(smStateEvent event)
{
switch( event.getType() )
{
case DID_ENTER:
{
if( event.getState() instanceof State_ViewingCell )
{
this.updateSize((State_ViewingCell) event.getState());
this.updatePositionFromState((State_ViewingCell) event.getState());
this.updateCloseButton();
this.updateHistoryButtons();
this.setAlpha(1);
m_baseAlpha = m_alpha;
}
else if( event.getState() instanceof State_CameraSnapping )
{
if( event.getState().getPreviousState() != State_ViewingCell.class )
{
if( m_alpha <= 0 )
{
this.updatePositionFromState((State_CameraSnapping)event.getState());
}
this.setVisible(true);
m_baseAlpha = m_alpha;
// s_logger.severe("BASE ALPHA: " + m_baseAlpha);
}
this.updateCloseButton();
this.updateHistoryButtons();
m_performedDoubleSnap = false;
}
break;
}
case DID_FOREGROUND:
{
if( event.getState() instanceof State_ViewingCell )
{
this.updateHistoryButtons();
this.updateRefreshButton();
}
break;
}
case DID_UPDATE:
{
if( event.getState().getParent() instanceof StateMachine_Camera )
{
if( event.getState() instanceof State_ViewingCell )
{
State_ViewingCell viewingState = (State_ViewingCell) event.getState();
if( m_waitingForBeingRefreshableAgain )
{
if( viewingState.isForegrounded() )
{
updateRefreshButton();
}
}
}
else if( event.getState() instanceof State_CameraSnapping )
{
State_CameraSnapping cameraSnapping = m_viewContext.stateContext.getEnteredState(State_CameraSnapping.class);
if( cameraSnapping != null )
{
if( cameraSnapping.getPreviousState() != State_ViewingCell.class )
{
//s_logger.severe(cameraSnapping.getOverallSnapProgress() + "");
this.setAlpha(m_baseAlpha + (1-m_baseAlpha) * cameraSnapping.getOverallSnapProgress());
//this.setAlpha((1 - m_baseAlpha) * (1 - ));
}
if( !m_performedDoubleSnap && cameraSnapping.getPreviousState() != State_ViewingCell.class)
{
this.updatePositionFromState((State_CameraSnapping)event.getState());
}
else
{
smA_Grid grid = m_viewContext.appContext.gridMngr.getGrid();
smGridCoordinate coord = cameraSnapping.getTargetCoordinate();
smCameraManager cameraMngr = m_viewContext.appContext.cameraMngr;
smCamera camera = cameraMngr.getCamera();
this.calcScreenPositionFromCoord(grid, coord, s_utilPoint2);
camera.calcWorldPoint(s_utilPoint2, s_utilPoint2);
s_utilPoint2.calcDifference(m_lastWorldPositionOnDoubleSnap, s_utilVector);
double progress = cameraMngr.getSnapProgressRatio();
s_utilVector.scaleByNumber(progress);
s_utilPoint2.copy(m_lastWorldPositionOnDoubleSnap);
s_utilPoint2.translate(s_utilVector);
this.updatePositionFromWorldPoint(grid, s_utilPoint2);
}
}
}
else if( !(event.getState() instanceof State_ViewingCell) )
{
if( m_alpha <= 1 )
{
if( event.getState().isEntered() )
{
if( m_alpha > 0 )
{
double timeMantissa = event.getState().getTimeInState(smE_StateTimeType.TOTAL) / m_fadeOutTime_seconds;
timeMantissa = smU_Math.clamp(timeMantissa, 0, 1);
this.setAlpha(m_baseAlpha * (1-timeMantissa));
smA_Grid grid = m_viewContext.appContext.gridMngr.getGrid();
this.updatePositionFromWorldPoint(grid, m_lastWorldPosition);
if( m_alpha <= 0 )
{
this.setVisible(false);
}
}
}
}
}
}
break;
}
case DID_EXIT:
{
if( event.getState() instanceof State_ViewingCell || event.getState() instanceof State_CameraSnapping )
{
m_baseAlpha = m_alpha;
smCamera camera = m_viewContext.appContext.cameraMngr.getCamera();
if( event.getState() instanceof State_ViewingCell )
{
m_waitingForBeingRefreshableAgain = false;
this.updateCloseButton();
this.updateHistoryButtons();
this.updateRefreshButton();
}
else if( event.getState() instanceof State_CameraSnapping )
{
m_lastSnapCoord.set(-1, -1);
}
}
break;
}
case DID_PERFORM_ACTION:
{
if( event.getAction() == Action_Camera_SetViewSize.class )
{
State_ViewingCell state = event.getContext().getEnteredState(State_ViewingCell.class);
if( state != null )
{
this.updateSize(state);
Action_Camera_SetViewSize.Args args = event.getActionArgs();
if( args.updateBuffer() )
{
this.updatePositionFromState(state);
}
}
else if( event.getContext().isEntered(State_CameraSnapping.class) )
{
this.onDoubleSnap();
}
}
else if( event.getAction() == Action_Camera_SnapToPoint.class )
{
State_ViewingCell state = event.getContext().getEnteredState(State_ViewingCell.class);
if( state != null )
{
Action_Camera_SnapToPoint.Args args = event.getActionArgs();
if( args.isInstant() )
{
this.updatePositionFromState(state);
}
}
}
else if( event.getAction() == Action_Camera_SnapToCoordinate.class )
{s_logger.severe("snap to coord");
State_CameraSnapping state = event.getContext().getEnteredState(State_CameraSnapping.class);
//if( state != null && (state.getUpdateCount() > 0 )
{
//if( !m_lastSnapCoord.isEqualTo(state.getTargetCoordinate()) )
{s_logger.severe("double");
this.onDoubleSnap();
}
}
m_lastSnapCoord.copy(state.getTargetCoordinate());
}
else if(( event.getAction() == Action_ViewingCell_Refresh.class ||
event.getAction() == Action_EditingCode_Save.class ||
event.getAction() == Action_EditingCode_Preview.class ||
event.getAction() == Action_Camera_SnapToAddress.class ||
event.getAction() == Action_Camera_SnapToCoordinate.class ))
{
updateRefreshButton();
}
break;
}
}
}
} |
import javafx.application.Application;
import javafx.geometry.Insets;
import javafx.geometry.Pos;
import javafx.scene.Scene;
import javafx.scene.control.Button;
import javafx.scene.layout.HBox;
import javafx.scene.layout.GridPane;
import javafx.stage.Stage;
public class Game extends Application {
public static void main(String[] args) {
launch(args);
}
@Override
public void start(Stage primaryStage) {
primaryStage.setTitle("Puzzle");
GridPane grid = new GridPane();
grid.setAlignment(Pos.CENTER);
grid.setHgap(10);
grid.setVgap(10);
grid.setPadding(new Insets(25,25,25,25));
String gridBName = "";
for (int i = 0; i<10; i++) {
for (int j = 0; j<10; j++) {
gridBName = "Button" + i + j;
Button = new Button(gridBName);
grid.add();
}
}
Button StartOver = new Button("Start Over");
Button Hint = new Button("Hint");
HBox hbBtn = new HBox(10);
hbBtn.setAlignment(Pos.BASELINE_CENTER);
hbBtn.getChildren().add(Hint);
hbBtn.getChildren().add(StartOver);
grid.add(hbBtn,1,10);
primaryStage.setScene(new Scene(grid, 300, 300));
primaryStage.show();
}
} |
import java.security.MessageDigest;
import java.security.NoSuchAlgorithmException;
import java.util.concurrent.TimeUnit;
import static spark.Spark.*;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.common.cache.Cache;
import com.google.common.cache.CacheBuilder;
import com.philihp.weblabora.model.*;
import org.apache.commons.codec.binary.Hex;
public class Main {
private static ObjectMapper objectMapper = new ObjectMapper();
private static Cache<String, String> cache =
CacheBuilder.newBuilder()
.maximumSize(100000)
.expireAfterAccess(7, TimeUnit.DAYS)
.build();
public static void main(String[] args) {
port(Integer.valueOf(System.getenv("PORT")));
get("/:hash", "application/json", (request, response) -> {
String hash = request.params(":hash");
return cache.get(hash, () -> {
response.status(404);
return "{\"error\":\"Forgot state of board. Please retry.\"}";
});
});
get("/", "application/json", (request, response) -> {;
return Boolean.FALSE;
});
post("/", "application/json", (request, response) -> {
String hash = hash(request.body());
Board board = new Board();
String[] tokens = request.body().split("\n+");
for (String token : tokens) {
MoveProcessor.processMove(board, token);
}
cache.put(hash, objectMapper.valueToTree(board).toString());
response.redirect("/" + hash, 303); // very important to use 303
return null;
}); |
import static javax.measure.unit.SI.KILOGRAM;
import javax.measure.quantity.Mass;
import org.jscience.physics.model.RelativisticModel;
import org.jscience.physics.amount.Amount;
import java.sql.*;
import java.util.HashMap;
import java.util.ArrayList;
import java.util.Map;
import java.net.URI;
import java.net.URISyntaxException;
import static spark.Spark.*;
import spark.template.freemarker.FreeMarkerEngine;
import spark.ModelAndView;
import static spark.Spark.get;
import com.heroku.sdk.jdbc.DatabaseUrl;
public class Main {
public static void main(String[] args) {
port(Integer.valueOf(System.getenv("PORT")));
staticFileLocation("/public");
get("/hello", (req, res) -> "Hello World");
get("/", (request, response) -> {
Map<String, Object> attributes = new HashMap<>();
attributes.put("message", "Hello World!");
return new ModelAndView(attributes, "index.ftl");
}, new FreeMarkerEngine());
get("/db", (req, res) -> {
Connection connection = null;
Map<String, Object> attributes = new HashMap<>();
try {
connection = DatabaseUrl.extract().getConnection();
Statement stmt = connection.createStatement();
stmt.executeUpdate("CREATE TABLE IF NOT EXISTS ticks (tick timestamp)");
stmt.executeUpdate("INSERT INTO ticks VALUES (now())");
ResultSet rs = stmt.executeQuery("SELECT tick FROM ticks");
ArrayList<String> output = new ArrayList<String>();
while (rs.next()) {
output.add( "Read from DB: " + rs.getTimestamp("tick"));
}
attributes.put("results", output);
return new ModelAndView(attributes, "db.ftl");
} catch (Exception e) {
attributes.put("message", "There was an error: " + e);
return new ModelAndView(attributes, "error.ftl");
} finally {
if (connection != null) try{connection.close();} catch(SQLException e){}
}
}, new FreeMarkerEngine());
}
} |
// import static javax.measure.unit.SI.KILOGRAM;
// import javax.measure.quantity.Mass;
// import org.jscience.physics.model.RelativisticModel;
// import org.jscience.physics.amount.Amount;
import java.sql.*;
import java.util.HashMap;
import java.util.ArrayList;
import java.util.Map;
import java.net.URI;
import java.net.URISyntaxException;
import static spark.Spark.*;
import spark.template.freemarker.FreeMarkerEngine;
import spark.ModelAndView;
import static spark.Spark.get;
import com.heroku.sdk.jdbc.DatabaseUrl;
public class Main {
public static void main(String[] args) {
port(Integer.valueOf(System.getenv("PORT")));
staticFileLocation("/public");
// get("/hello", (req, res) -> {
// RelativisticModel.select();
// String energy = System.getenv().get("ENERGY");
// Amount<Mass> m = Amount.valueOf(energy).to(KILOGRAM);
// return "E=mc^2: " + energy + " = " + m.toString();
get("/", (request, response) -> {
Map<String, Object> attributes = new HashMap<>();
attributes.put("message", "Hello World!");
return new ModelAndView(attributes, "index.ftl");
}, new FreeMarkerEngine());
get("/db", (req, res) -> {
Connection connection = null;
Map<String, Object> attributes = new HashMap<>();
try {
connection = DatabaseUrl.extract().getConnection();
Statement stmt = connection.createStatement();
stmt.executeUpdate("CREATE TABLE IF NOT EXISTS ticks (tick timestamp)");
stmt.executeUpdate("INSERT INTO ticks VALUES (now())");
ResultSet rs = stmt.executeQuery("SELECT tick FROM ticks");
ArrayList<String> output = new ArrayList<String>();
while (rs.next()) {
output.add( "Read from DB: " + rs.getTimestamp("tick"));
}
attributes.put("results", output);
return new ModelAndView(attributes, "db.ftl");
} catch (Exception e) {
attributes.put("message", "There was an error: " + e);
return new ModelAndView(attributes, "error.ftl");
} finally {
if (connection != null) try{connection.close();} catch(SQLException e){}
}
}, new FreeMarkerEngine());
}
} |
package nl.cwi.monetdb.jdbc;
import java.sql.*;
import java.util.*;
/**
* A DatabaseMetaData object suitable for the Monet database
* <br /><br />
*
* @author Fabian Groffen <Fabian.Groffen@cwi.nl>
* @version 0.3 (beta release)
*/
public class MonetDatabaseMetaData implements DatabaseMetaData {
private Connection con;
private Driver driver;
private Statement stmt;
private Map envs;
public MonetDatabaseMetaData(Connection parent) {
con = parent;
driver = new MonetDriver();
}
private synchronized Statement getStmt() throws SQLException {
if (stmt == null) stmt = con.createStatement();
return(stmt);
}
private synchronized Map getEnvMap() throws SQLException {
if (envs == null) {
// make the env map
envs = new HashMap();
ResultSet env = getStmt().executeQuery("SELECT * FROM env");
while (env.next()) {
envs.put(env.getString("name"), env.getString("value"));
}
env.close();
}
return(envs);
}
/**
* Can all the procedures returned by getProcedures be called
* by the current user?
*
* @return true if so
*/
public boolean allProceduresAreCallable() {
return(true);
}
/**
* Can all the tables returned by getTable be SELECTed by
* the current user?
*
* @return true because we only have one user a.t.m.
*/
public boolean allTablesAreSelectable() {
return(true);
}
/**
* What is the URL for this database?
*
* @return a reconstructed connection string
* @throws SQLException if a database access error occurs
*/
public String getURL() throws SQLException {
Map env = getEnvMap();
return("jdbc:monetdb://" + (String)env.get("host") +
":" + (String)env.get("sql_port") + "/" +
(String)env.get("gdk_dbname"));
}
/**
* What is our user name as known to the database?
*
* @return sql user
* @throws SQLException if a database access error occurs
*/
public String getUserName() throws SQLException {
Map env = getEnvMap();
return((String)env.get("sql_user"));
}
/**
* Is the database in read-only mode?
*
* @return always false for now
*/
public boolean isReadOnly() {
return(false);
}
/**
* Are NULL values sorted high?
*
* @return true because Monet puts NULL values on top upon ORDER BY
*/
public boolean nullsAreSortedHigh() {
return(true);
}
/**
* Are NULL values sorted low?
*
* @return negative of nullsAreSortedHigh()
* @see #nullsAreSortedHigh()
*/
public boolean nullsAreSortedLow() {
return(!nullsAreSortedHigh());
}
/**
* Are NULL values sorted at the start regardless of sort order?
*
* @return false, since Monet doesn't do this
*/
public boolean nullsAreSortedAtStart() {
return(false);
}
/**
* Are NULL values sorted at the end regardless of sort order?
*
* @return false, since Monet doesn't do this
*/
public boolean nullsAreSortedAtEnd() {
return(false);
}
/**
* What is the name of this database product - this should be MonetDB
* of course, so we return that explicitly.
*
* @return the database product name
*/
public String getDatabaseProductName() {
return "MonetDB";
}
/**
* What is the version of this database product.
*
* @return a fixed version number, yes it's quick and dirty
* @throws SQLException if a database access error occurs
*/
public String getDatabaseProductVersion() throws SQLException {
Map env = getEnvMap();
return((String)env.get("gdk_version"));
}
/**
* What is the name of this JDBC driver? If we don't know this
* we are doing something wrong!
*
* @return the JDBC driver name
*/
public String getDriverName() {
return("MonetDB Native Driver");
}
/**
* What is the version string of this JDBC driver? Again, this is
* static.
*
* @return the JDBC driver name.
*/
public String getDriverVersion() {
return(((MonetDriver)driver).getDriverVersion());
}
/**
* What is this JDBC driver's major version number?
*
* @return the JDBC driver major version
*/
public int getDriverMajorVersion() {
return(driver.getMajorVersion());
}
/**
* What is this JDBC driver's minor version number?
*
* @return the JDBC driver minor version
*/
public int getDriverMinorVersion() {
return(driver.getMinorVersion());
}
/**
* Does the database store tables in a local file? No - it
* stores them in a file on the server.
*
* @return false because that's what Monet is for
*/
public boolean usesLocalFiles() {
return(false);
}
/**
* Does the database use a local file for each table? Well, not really,
* since it doesn't use local files.
*
* @return false for it doesn't
*/
public boolean usesLocalFilePerTable() {
return(false);
}
/**
* Does the database treat mixed case unquoted SQL identifiers
* as case sensitive and as a result store them in mixed case?
* A JDBC-Compliant driver will always return false.
*
* @return false
*/
public boolean supportsMixedCaseIdentifiers() {
return(false);
}
/**
* Does the database treat mixed case unquoted SQL identifiers as
* case insensitive and store them in upper case?
*
* @return true if so
*/
public boolean storesUpperCaseIdentifiers() {
return(false);
}
/**
* Does the database treat mixed case unquoted SQL identifiers as
* case insensitive and store them in lower case?
*
* @return true if so
*/
public boolean storesLowerCaseIdentifiers() {
return(true);
}
/**
* Does the database treat mixed case unquoted SQL identifiers as
* case insensitive and store them in mixed case?
*
* @return true if so
*/
public boolean storesMixedCaseIdentifiers() {
return(false);
}
/**
* Does the database treat mixed case quoted SQL identifiers as
* case sensitive and as a result store them in mixed case? A
* JDBC compliant driver will always return true.
*
* @return true if so
*/
public boolean supportsMixedCaseQuotedIdentifiers() {
return(true);
}
/**
* Does the database treat mixed case quoted SQL identifiers as
* case insensitive and store them in upper case?
*
* @return true if so
*/
public boolean storesUpperCaseQuotedIdentifiers() {
return(false);
}
/**
* Does the database treat mixed case quoted SQL identifiers as case
* insensitive and store them in lower case?
*
* @return true if so
*/
public boolean storesLowerCaseQuotedIdentifiers() {
return(false);
}
/**
* Does the database treat mixed case quoted SQL identifiers as case
* insensitive and store them in mixed case?
*
* @return true if so
*/
public boolean storesMixedCaseQuotedIdentifiers() {
return(false);
}
/**
* What is the string used to quote SQL identifiers? This returns
* a space if identifier quoting isn't supported. A JDBC Compliant
* driver will always use a double quote character.
*
* @return the quoting string
*/
public String getIdentifierQuoteString() {
return("\"");
}
/**
* Get a comma separated list of all a database's SQL keywords that
* are NOT also SQL92 keywords.
* <br /><br />
* Wasn't MonetDB fully standards compliant? So no extra keywords...
*
* @return a comma separated list of keywords we use (none)
*/
public String getSQLKeywords() {
return("");
}
public String getNumericFunctions() {
return("");
}
public String getStringFunctions() {
return("");
}
public String getSystemFunctions() {
return("");
}
public String getTimeDateFunctions() {
return("");
}
/**
* This is the string that can be used to escape '_' and '%' in
* a search string pattern style catalog search parameters
*
* @return the string used to escape wildcard characters
*/
public String getSearchStringEscape() {
return("\\");
}
/**
* Get all the "extra" characters that can be used in unquoted
* identifier names (those beyond a-zA-Z0-9 and _)
* Monet has no extras
*
* @return a string containing the extra characters
*/
public String getExtraNameCharacters() {
return("");
}
/**
* Is "ALTER TABLE" with an add column supported?
*
* @return true if so
*/
public boolean supportsAlterTableWithAddColumn() {
return(true);
}
/**
* Is "ALTER TABLE" with a drop column supported?
*
* @return true if so
* @exception SQLException if a database access error occurs
*/
public boolean supportsAlterTableWithDropColumn() {
return(true);
}
public boolean supportsColumnAliasing() {
return(true);
}
/**
* Are concatenations between NULL and non-NULL values NULL? A
* JDBC Compliant driver always returns true
*
* @return true if so
* @throws SQLException if a database access error occurs
*/
public boolean nullPlusNonNullIsNull() {
return(true);
}
public boolean supportsConvert() {
return(false);
}
public boolean supportsConvert(int fromType, int toType) {
return(false);
}
/**
* Are table correlation names supported? A JDBC Compliant
* driver always returns true.
*
* @return true if so
*/
public boolean supportsTableCorrelationNames() {
return(true);
}
/**
* If table correlation names are supported, are they restricted to
* be different from the names of the tables?
*
* @return true if so; false otherwise
*/
public boolean supportsDifferentTableCorrelationNames() {
return(false);
}
/**
* Are expressions in "ORDER BY" lists supported?
*
* <br>e.g. select * from t order by a + b;
*
* MonetDB does not support this (yet?)
*
* @return true if so
*/
public boolean supportsExpressionsInOrderBy() {
return(false);
}
/**
* Can an "ORDER BY" clause use columns not in the SELECT?
* Monet = SQL99 = false
*
* @return true if so
*/
public boolean supportsOrderByUnrelated() {
return(false);
}
/**
* Is some form of "GROUP BY" clause supported?
*
* @return true since MonetDB supports it
* @exception SQLException if a database access error occurs
*/
public boolean supportsGroupBy() {
return(true);
}
/**
* Can a "GROUP BY" clause use columns not in the SELECT?
*
* @return true since that also is supported
* @exception SQLException if a database access error occurs
*/
public boolean supportsGroupByUnrelated() {
return(true);
}
/**
* Can a "GROUP BY" clause add columns not in the SELECT provided
* it specifies all the columns in the SELECT?
*
* (Monet already supports the more difficult supportsGroupByUnrelated(),
* so this is a piece of cake)
*
* @return true if so
*/
public boolean supportsGroupByBeyondSelect() {
return(true);
}
/**
* Is the escape character in "LIKE" clauses supported? A
* JDBC compliant driver always returns true.
*
* @return true if so
*/
public boolean supportsLikeEscapeClause() {
return(true);
}
/**
* Are multiple ResultSets from a single execute supported?
* MonetDB probably supports it, but I don't
*
* @return true if so
*/
public boolean supportsMultipleResultSets() {
return(false);
}
/**
* Can we have multiple transactions open at once (on different
* connections?)
* This is the main idea behind the Connection, is it?
*
* @return true if so
* @exception SQLException if a database access error occurs
*/
public boolean supportsMultipleTransactions() {
return(true);
}
/**
* Can columns be defined as non-nullable. A JDBC Compliant driver
* always returns true.
*
* @return true if so
*/
public boolean supportsNonNullableColumns() {
return(true);
}
public boolean supportsMinimumSQLGrammar() {
return(true);
}
/**
* Does this driver support the Core ODBC SQL grammar. We need
* SQL-92 conformance for this.
*
* @return true if so
*/
public boolean supportsCoreSQLGrammar() {
return(true);
}
/**
* Does this driver support the Extended (Level 2) ODBC SQL
* grammar. We don't conform to the Core (Level 1), so we can't
* conform to the Extended SQL Grammar.
*
* @return true if so
*/
public boolean supportsExtendedSQLGrammar() {
return(false);
}
/**
* Does this driver support the ANSI-92 entry level SQL grammar?
* All JDBC Compliant drivers must return true. We should be this
* compliant, so let's 'act' like we are.
*
* @return true if so
*/
public boolean supportsANSI92EntryLevelSQL() {
return(true);
}
/**
* Does this driver support the ANSI-92 intermediate level SQL
* grammar?
* probably not
*
* @return true if so
*/
public boolean supportsANSI92IntermediateSQL() {
return(false);
}
/**
* Does this driver support the ANSI-92 full SQL grammar?
* Would be good if it was like that
*
* @return true if so
* @exception SQLException if a database access error occurs
*/
public boolean supportsANSI92FullSQL() {
return(false);
}
/**
* Is the SQL Integrity Enhancement Facility supported?
* Our best guess is that this means support for constraints
*
* @return true if so
*/
public boolean supportsIntegrityEnhancementFacility() {
return(true);
}
/**
* Is some form of outer join supported?
*
* @return true if so
* @exception SQLException if a database access error occurs
*/
public boolean supportsOuterJoins(){
return(true);
}
/**
* Are full nexted outer joins supported?
*
* @return true if so
* @exception SQLException if a database access error occurs
*/
public boolean supportsFullOuterJoins() {
return(true);
}
/**
* Is there limited support for outer joins?
*
* @return true if so
* @exception SQLException if a database access error occurs
*/
public boolean supportsLimitedOuterJoins() {
return(false);
}
/**
* What is the database vendor's preferred term for "schema"?
* MonetDB uses the term "schema".
*
* @return the vendor term
*/
public String getSchemaTerm() {
return("schema");
}
/**
* What is the database vendor's preferred term for "procedure"?
* Traditionally, "function" has been used.
*
* @return the vendor term
*/
public String getProcedureTerm() {
return("function");
}
/**
* What is the database vendor's preferred term for "catalog"?
* MonetDB doesn't really have them (from driver accessible) but
* from the monetdb.conf file the term "database" sounds best
*
* @return the vendor term
*/
public String getCatalogTerm() {
return("database");
}
/**
* Does a catalog appear at the start of a qualified table name?
* (Otherwise it appears at the end).
* Currently there is no catalog support at all in MonetDB
*
* @return true if so
*/
public boolean isCatalogAtStart() {
// return true here; we return false for every other catalog function
// so it won't matter what we return here
return(true);
}
/**
* What is the Catalog separator.
*
* @return the catalog separator string
*/
public String getCatalogSeparator() {
// Give them something to work with here
// everything else returns false so it won't matter what we return here
return(".");
}
/**
* Can a schema name be used in a data manipulation statement?
*
* @return true if so
*/
public boolean supportsSchemasInDataManipulation() {
return(true);
}
/**
* Can a schema name be used in a procedure call statement?
* Ohw probably, but I don't know of procedures in Monet
*
* @return true if so
*/
public boolean supportsSchemasInProcedureCalls() {
return(true);
}
/**
* Can a schema be used in a table definition statement?
*
* @return true if so
*/
public boolean supportsSchemasInTableDefinitions() {
return(true);
}
/**
* Can a schema name be used in an index definition statement?
*
* @return true if so
*/
public boolean supportsSchemasInIndexDefinitions() {
return(true);
}
/**
* Can a schema name be used in a privilege definition statement?
*
* @return true if so
*/
public boolean supportsSchemasInPrivilegeDefinitions() {
return(true);
}
/**
* Can a catalog name be used in a data manipulation statement?
*
* @return true if so
*/
public boolean supportsCatalogsInDataManipulation() {
return(false);
}
/**
* Can a catalog name be used in a procedure call statement?
*
* @return true if so
*/
public boolean supportsCatalogsInProcedureCalls() {
return(false);
}
/**
* Can a catalog name be used in a table definition statement?
*
* @return true if so
*/
public boolean supportsCatalogsInTableDefinitions() {
return(false);
}
/**
* Can a catalog name be used in an index definition?
*
* @return true if so
*/
public boolean supportsCatalogsInIndexDefinitions() {
return(false);
}
/**
* Can a catalog name be used in a privilege definition statement?
*
* @return true if so
*/
public boolean supportsCatalogsInPrivilegeDefinitions() {
return(false);
}
/**
* MonetDB doesn't support positioned DELETEs I guess
*
* @return true if so
*/
public boolean supportsPositionedDelete() {
return(false);
}
/**
* Is positioned UPDATE supported? (same as above)
*
* @return true if so
*/
public boolean supportsPositionedUpdate() {
return(false);
}
/**
* Is SELECT FOR UPDATE supported?
* My test resulted in a negative answer
*
* @return true if so; false otherwise
*/
public boolean supportsSelectForUpdate(){
return(false);
}
/**
* Are stored procedure calls using the stored procedure escape
* syntax supported?
*
* @return true if so; false otherwise
*/
public boolean supportsStoredProcedures() {
return(false);
}
/**
* Are subqueries in comparison expressions supported? A JDBC
* Compliant driver always returns true. MonetDB also supports this
*
* @return true if so; false otherwise
*/
public boolean supportsSubqueriesInComparisons() {
return(true);
}
/**
* Are subqueries in 'exists' expressions supported? A JDBC
* Compliant driver always returns true.
*
* @return true if so; false otherwise
*/
public boolean supportsSubqueriesInExists() {
return(true);
}
/**
* Are subqueries in 'in' statements supported? A JDBC
* Compliant driver always returns true.
*
* @return true if so; false otherwise
*/
public boolean supportsSubqueriesInIns() {
return(true);
}
/**
* Are subqueries in quantified expressions supported? A JDBC
* Compliant driver always returns true.
*
* (No idea what this is, but we support a good deal of
* subquerying.)
*
* @return true if so; false otherwise
*/
public boolean supportsSubqueriesInQuantifieds() {
return(true);
}
/**
* Are correlated subqueries supported? A JDBC Compliant driver
* always returns true.
*
* (a.k.a. subselect in from?)
*
* @return true if so; false otherwise
*/
public boolean supportsCorrelatedSubqueries() {
return(true);
}
/**
* Is SQL UNION supported?
* since 2004-03-20
*
* @return true if so
*/
public boolean supportsUnion() {
return(true);
}
/**
* Is SQL UNION ALL supported?
* since 2004-03-20
*
* @return true if so
*/
public boolean supportsUnionAll() {
return(true);
}
/**
* ResultSet objects (cursors) are not closed upon explicit or
* implicit commit.
*
* @return true if so
*/
public boolean supportsOpenCursorsAcrossCommit() {
return(true);
}
/**
* Same as above
*
* @return true if so
*/
public boolean supportsOpenCursorsAcrossRollback() {
return(true);
}
/**
* Can statements remain open across commits? They may, but
* this driver cannot guarentee that. In further reflection.
* we are taking a Statement object here, so the answer is
* yes, since the Statement is only a vehicle to execute some SQL
*
* @return true if they always remain open; false otherwise
*/
public boolean supportsOpenStatementsAcrossCommit() {
return(true);
}
/**
* Can statements remain open across rollbacks? They may, but
* this driver cannot guarentee that. In further contemplation,
* we are taking a Statement object here, so the answer is yes again.
*
* @return true if they always remain open; false otherwise
*/
public boolean supportsOpenStatementsAcrossRollback() {
return(true);
}
/**
* How many hex characters can you have in an inline binary literal
* I honestly wouldn't know...
*
* @return the max literal length
*/
public int getMaxBinaryLiteralLength() {
return(0); // no limit
}
/**
* What is the maximum length for a character literal
* Is there a max?
*
* @return the max literal length
*/
public int getMaxCharLiteralLength() {
return(0); // no limit
}
/**
* Whats the limit on column name length.
* I take some safety here, but it's just a varchar in MonetDB
*
* @return the maximum column name length
*/
public int getMaxColumnNameLength() {
return(256);
}
/**
* What is the maximum number of columns in a "GROUP BY" clause?
*
* @return the max number of columns
*/
public int getMaxColumnsInGroupBy() {
return(0); // no limit
}
/**
* What's the maximum number of columns allowed in an index?
*
* @return max number of columns
*/
public int getMaxColumnsInIndex() {
return(0); // unlimited I guess
}
/**
* What's the maximum number of columns in an "ORDER BY clause?
*
* @return the max columns
*/
public int getMaxColumnsInOrderBy() {
return(0); // unlimited I guess
}
/**
* What is the maximum number of columns in a "SELECT" list?
*
* @return the max columns
*/
public int getMaxColumnsInSelect() {
return(0); // unlimited I guess
}
/**
* What is the maximum number of columns in a table?
* wasn't Monet designed for datamining? (= much columns)
*
* @return the max columns
*/
public int getMaxColumnsInTable() {
return(0);
}
/**
* How many active connections can we have at a time to this
* database? Well, since it depends on Mserver, which just listens
* for new connections and creates a new thread for each connection,
* this number can be very high, and theoretically till the system
* runs out of resources. However, knowing Monet is knowing that you
* should handle it a little bit with care, so I give a very minimalistic
* number here.
*
* @return the maximum number of connections
*/
public int getMaxConnections() {
return(16);
}
/**
* What is the maximum cursor name length
* Actually we do not do named cursors, so I keep the value small as
* a precaution for maybe the future.
*
* @return max cursor name length in bytes
*/
public int getMaxCursorNameLength() {
return(256);
}
/**
* Retrieves the maximum number of bytes for an index, including all
* of the parts of the index.
*
* @return max index length in bytes, which includes the composite
* of all the constituent parts of the index; a result of zero
* means that there is no limit or the limit is not known
*/
public int getMaxIndexLength() {
return(0); // I assume it is large, but I don't know
}
/**
* Retrieves the maximum number of characters that this database
* allows in a schema name.
*
* @return the number of characters or 0 if there is no limit, or the
* limit is unknown.
*/
public int getMaxSchemaNameLength() {
return(0); // I don't know...
}
/**
* What is the maximum length of a procedure name
*
* @return the max name length in bytes
*/
public int getMaxProcedureNameLength() {
return(0); // unknown
}
/**
* What is the maximum length of a catalog
*
* @return the max length
*/
public int getMaxCatalogNameLength() {
return(0);
}
/**
* What is the maximum length of a single row?
*
* @return max row size in bytes
*/
public int getMaxRowSize() {
return(0); // very long I hope...
}
/**
* Did getMaxRowSize() include LONGVARCHAR and LONGVARBINARY
* blobs?
* Yes I thought so...
*
* @return true if so
*/
public boolean doesMaxRowSizeIncludeBlobs() {
return(true);
}
/**
* What is the maximum length of a SQL statement?
* Till a programmer makes a mistake and causes a segmentation fault
* on a string overflow...
*
* @return max length in bytes
*/
public int getMaxStatementLength() {
return(0); // actually whatever fits in size_t
}
/**
* How many active statements can we have open at one time to
* this database? Basically, since each Statement downloads
* the results as the query is executed, we can have many.
*
* @return the maximum
*/
public int getMaxStatements() {
return(0);
}
/**
* What is the maximum length of a table name
*
* @return max name length in bytes
*/
public int getMaxTableNameLength() {
return(0);
}
/**
* What is the maximum number of tables that can be specified
* in a SELECT?
*
* @return the maximum
*/
public int getMaxTablesInSelect() {
return(0); // no limit
}
/**
* What is the maximum length of a user name
*
* @return the max name length in bytes
* @exception SQLException if a database access error occurs
*/
public int getMaxUserNameLength() {
return(0); // no limit
}
/**
* What is the database's default transaction isolation level?
* We only see commited data, nonrepeatable reads and phantom
* reads can occur.
*
* @return the default isolation level
* @see Connection
*/
public int getDefaultTransactionIsolation() {
return(Connection.TRANSACTION_SERIALIZABLE);
}
/**
* Are transactions supported? If not, commit and rollback are noops
* and the isolation level is TRANSACTION_NONE. We do support
* transactions.
*
* @return true if transactions are supported
*/
public boolean supportsTransactions() {
return(true);
}
/**
* Does the database support the given transaction isolation level?
* We only support TRANSACTION_READ_COMMITTED as far as I know
*
* @param level the values are defined in java.sql.Connection
* @return true if so
* @see Connection
*/
public boolean supportsTransactionIsolationLevel(int level) {
return(level == Connection.TRANSACTION_SERIALIZABLE);
}
/**
* Are both data definition and data manipulation transactions
* supported?
* Supposedly that data definition is like CREATE or ALTER TABLE
* yes it is.
*
* @return true if so
*/
public boolean supportsDataDefinitionAndDataManipulationTransactions() {
return(true);
}
/**
* Are only data manipulation statements withing a transaction
* supported?
*
* @return true if so
*/
public boolean supportsDataManipulationTransactionsOnly() {
return(false);
}
/**
* Does a data definition statement within a transaction force
* the transaction to commit? I think this means something like:
*
* <p><pre>
* CREATE TABLE T (A INT);
* INSERT INTO T (A) VALUES (2);
* BEGIN;
* UPDATE T SET A = A + 1;
* CREATE TABLE X (A INT);
* SELECT A FROM T INTO X;
* COMMIT;
* </pre><p>
*
* does the CREATE TABLE call cause a commit? The answer is no.
*
* @return true if so
*/
public boolean dataDefinitionCausesTransactionCommit() {
return(false);
}
/**
* Is a data definition statement within a transaction ignored?
*
* @return true if so
* @exception SQLException if a database access error occurs
*/
public boolean dataDefinitionIgnoredInTransactions() {
return(false);
}
/**
* Get a description of stored procedures available in a catalog
* Currently not applicable and not implemented, returns null
*
* <p>Only procedure descriptions matching the schema and procedure
* name criteria are returned. They are ordered by PROCEDURE_SCHEM
* and PROCEDURE_NAME
*
* <p>Each procedure description has the following columns:
* <ol>
* <li><b>PROCEDURE_CAT</b> String => procedure catalog (may be null)
* <li><b>PROCEDURE_SCHEM</b> String => procedure schema (may be null)
* <li><b>PROCEDURE_NAME</b> String => procedure name
* <li><b>Field 4</b> reserved (make it null)
* <li><b>Field 5</b> reserved (make it null)
* <li><b>Field 6</b> reserved (make it null)
* <li><b>REMARKS</b> String => explanatory comment on the procedure
* <li><b>PROCEDURE_TYPE</b> short => kind of procedure
* <ul>
* <li> procedureResultUnknown - May return a result
* <li> procedureNoResult - Does not return a result
* <li> procedureReturnsResult - Returns a result
* </ul>
* </ol>
*
* @param catalog - a catalog name; "" retrieves those without a
* catalog; null means drop catalog name from criteria
* @param schemaPattern - a schema name pattern; "" retrieves those
* without a schema - we ignore this parameter
* @param procedureNamePattern - a procedure name pattern
* @return ResultSet - each row is a procedure description
* @throws SQLException if a database access error occurs
*/
public ResultSet getProcedures(
String catalog,
String schemaPattern,
String procedureNamePattern
) throws SQLException
{
String query =
"SELECT null AS \"PROCEDURE_CAT\", null AS \"PROCEDURE_SCHEM\", " +
"'' AS \"PROCEDURE_NAME\", null AS \"Field4\", " +
"null AS \"Field5\", null AS \"Field6\", " +
"'' AS \"REMARKS\", 0 AS \"PROCEDURE_TYPE\" " +
"WHERE 1 = 0";
return(getStmt().executeQuery(query));
}
/**
* Get a description of a catalog's stored procedure parameters
* and result columns.
* Currently not applicable and not implemented, returns null
*
* <p>Only descriptions matching the schema, procedure and parameter
* name criteria are returned. They are ordered by PROCEDURE_SCHEM
* and PROCEDURE_NAME. Within this, the return value, if any, is
* first. Next are the parameter descriptions in call order. The
* column descriptions follow in column number order.
*
* <p>Each row in the ResultSet is a parameter description or column
* description with the following fields:
* <ol>
* <li><b>PROCEDURE_CAT</b> String => procedure catalog (may be null)
* <li><b>PROCEDURE_SCHEM</b> String => procedure schema (may be null)
* <li><b>PROCEDURE_NAME</b> String => procedure name
* <li><b>COLUMN_NAME</b> String => column/parameter name
* <li><b>COLUMN_TYPE</b> Short => kind of column/parameter:
* <ul><li>procedureColumnUnknown - nobody knows
* <li>procedureColumnIn - IN parameter
* <li>procedureColumnInOut - INOUT parameter
* <li>procedureColumnOut - OUT parameter
* <li>procedureColumnReturn - procedure return value
* <li>procedureColumnResult - result column in ResultSet
* </ul>
* <li><b>DATA_TYPE</b> short => SQL type from java.sql.Types
* <li><b>TYPE_NAME</b> String => Data source specific type name
* <li><b>PRECISION</b> int => precision
* <li><b>LENGTH</b> int => length in bytes of data
* <li><b>SCALE</b> short => scale
* <li><b>RADIX</b> short => radix
* <li><b>NULLABLE</b> short => can it contain NULL?
* <ul><li>procedureNoNulls - does not allow NULL values
* <li>procedureNullable - allows NULL values
* <li>procedureNullableUnknown - nullability unknown
* <li><b>REMARKS</b> String => comment describing parameter/column
* </ol>
* @param catalog This is ignored in org.postgresql, advise this is set to null
* @param schemaPattern
* @param procedureNamePattern a procedure name pattern
* @param columnNamePattern a column name pattern, this is currently ignored because postgresql does not name procedure parameters.
* @return each row is a stored procedure parameter or column description
* @throws SQLException if a database-access error occurs
* @see #getSearchStringEscape
*/
public ResultSet getProcedureColumns(
String catalog,
String schemaPattern,
String procedureNamePattern,
String columnNamePattern
) throws SQLException
{
String query =
"SELECT null AS \"PROCEDURE_CAT\", null AS \"PROCEDURE_SCHEM\", " +
"'' AS \"PROCEDURE_NAME\", '' AS \"COLUMN_NAME\", " +
"0 AS \"COLUMN_TYPE\", 0 AS \"DATA_TYPE\", " +
"'' AS \"TYPE_NAME\", 0 AS \"PRECISION\", " +
"0 AS \"LENGTH\", 0 AS \"SCALE\", 0 AS \"RADIX\", " +
"0 AS \"NULLABLE\", '' AS \"REMARKS\" " +
"WHERE 1 = 0";
return(getStmt().executeQuery(query));
}
//== this is a helper method which does not belong to the interface
/**
* returns the given string where all slashes and single quotes are
* escaped with a slash.
*
* @param in the string to escape
* @return the escaped string
*/
private static String escapeQuotes(String in) {
return(in.replaceAll("\\\\", "\\\\\\\\").replaceAll("'", "\\\\'"));
}
/**
* returns the given string between two double quotes for usage as
* exact column or table name in SQL queries.
*
* @param in the string to quote
* @return the quoted string
*/
private static String dq(String in) {
return("\"" + in.replaceAll("\\\\", "\\\\\\\\").replaceAll("\"", "\\\\\"") + "\"");
}
//== end helper methods
/**
* Get a description of tables available in a catalog.
*
* <p>Only table descriptions matching the catalog, schema, table
* name and type criteria are returned. They are ordered by
* TABLE_TYPE, TABLE_SCHEM and TABLE_NAME.
*
* <p>Each table description has the following columns:
*
* <ol>
* <li><b>TABLE_CAT</b> String => table catalog (may be null)
* <li><b>TABLE_SCHEM</b> String => table schema (may be null)
* <li><b>TABLE_NAME</b> String => table name
* <li><b>TABLE_TYPE</b> String => table type. Typical types are "TABLE",
* "VIEW", "SYSTEM TABLE", "GLOBAL TEMPORARY", "LOCAL
* TEMPORARY", "ALIAS", "SYNONYM".
* <li><b>REMARKS</b> String => explanatory comment on the table
* </ol>
*
* <p>The valid values for the types parameter are:
* "TABLE", "INDEX", "SEQUENCE", "VIEW",
* "SYSTEM TABLE", "SYSTEM INDEX", "SYSTEM VIEW",
* "SYSTEM TOAST TABLE", "SYSTEM TOAST INDEX",
* "TEMPORARY TABLE", and "TEMPORARY VIEW"
*
* @param catalog a catalog name; this parameter is currently ignored
* @param schemaPattern a schema name pattern
* @param tableNamePattern a table name pattern. For all tables this should be "%"
* @param types a list of table types to include; null returns all types;
* this parameter is currently ignored
* @return each row is a table description
* @throws SQLException if a database-access error occurs.
*/
public ResultSet getTables(
String catalog,
String schemaPattern,
String tableNamePattern,
String types[]
) throws SQLException
{
String select;
String orderby;
String cat = (String)(getEnvMap().get("gdk_dbname"));
select =
"SELECT * FROM ( " +
"SELECT '" + cat + "' AS \"TABLE_CAT\", \"schemas\".\"name\" AS \"TABLE_SCHEM\", \"tables\".\"name\" AS \"TABLE_NAME\", " +
"CASE WHEN \"tables\".\"system\" = true AND \"tables\".\"istable\" = true THEN 'SYSTEM TABLE' " +
" WHEN \"tables\".\"system\" = true AND \"tables\".\"istable\" = false THEN 'SYSTEM VIEW' " +
" WHEN \"tables\".\"system\" = false AND \"tables\".\"istable\" = true THEN 'TABLE' " +
" WHEN \"tables\".\"system\" = false AND \"tables\".\"istable\" = false THEN 'VIEW' " +
"END AS \"TABLE_TYPE\", '' AS \"REMARKS\", null AS \"TYPE_CAT\", null AS \"TYPE_SCHEM\", " +
"null AS \"TYPE_NAME\", 'rowid' AS \"SELF_REFERENCING_COL_NAME\", 'SYSTEM' AS \"REF_GENERATION\" " +
"FROM \"tables\", \"schemas\" WHERE \"tables\".\"schema_id\" = \"schemas\".\"id\"" +
"UNION ALL " +
"SELECT '" + cat + "' AS \"TABLE_CAT\", \"schemas\".\"name\" AS \"TABLE_SCHEM\", \"tables\".\"name\" AS \"TABLE_NAME\", " +
"CASE WHEN \"tables\".\"system\" = true AND \"tables\".\"istable\" = true THEN 'SYSTEM SESSION TABLE' " +
" WHEN \"tables\".\"system\" = true AND \"tables\".\"istable\" = false THEN 'SYSTEM SESSION VIEW' " +
" WHEN \"tables\".\"system\" = false AND \"tables\".\"istable\" = true THEN 'SESSION TABLE' " +
" WHEN \"tables\".\"system\" = false AND \"tables\".\"istable\" = false THEN 'SESSION VIEW' " +
"END AS \"TABLE_TYPE\", '' AS \"REMARKS\", null AS \"TYPE_CAT\", null AS \"TYPE_SCHEM\", " +
"null AS \"TYPE_NAME\", 'rowid' AS \"SELF_REFERENCING_COL_NAME\", 'SYSTEM' AS \"REF_GENERATION\" " +
"FROM \"tmp_tables\" AS \"tables\", \"schemas\" WHERE \"tables\".\"schema_id\" = \"schemas\".\"id\"" +
") AS \"tables\" WHERE 1 = 1 ";
if (tableNamePattern != null) {
select += "AND \"TABLE_NAME\" LIKE '" + escapeQuotes(tableNamePattern) + "' ";
}
if (schemaPattern != null) {
select += "AND \"TABLE_SCHEM\" LIKE '" + escapeQuotes(schemaPattern) + "' ";
}
if (types != null) {
select += "AND (";
for (int i = 0; i < types.length; i++) {
select += (i == 0 ? "" : " OR ") + "\"TABLE_TYPE\" LIKE '" + escapeQuotes(types[i]) + "'";
}
select += ") ";
}
orderby = "ORDER BY \"TABLE_TYPE\", \"TABLE_SCHEM\", \"TABLE_NAME\" ";
return(getStmt().executeQuery(select + orderby));
}
/**
* Get the schema names available in this database. The results
* are ordered by schema name.
*
* <P>The schema column is:
* <OL>
* <LI><B>TABLE_SCHEM</B> String => schema name
* <LI><B>TABLE_CATALOG</B> String => catalog name (may be null)
* </OL>
*
* @return ResultSet each row has a single String column that is a
* schema name
* @throws SQLException if a database error occurs
*/
public ResultSet getSchemas() throws SQLException {
String cat = (String)(getEnvMap().get("gdk_dbname"));
String query =
"SELECT \"name\" AS \"TABLE_SCHEM\", '" + cat + "' AS \"TABLE_CATALOG\" " +
"FROM \"schemas\" " +
"ORDER BY \"TABLE_SCHEM\"";
return(getStmt().executeQuery(query));
}
/**
* Get the catalog names available in this database. The results
* are ordered by catalog name.
*
* <P>The catalog column is:
* <OL>
* <LI><B>TABLE_CAT</B> String => catalog name
* </OL>
*
* Note: this will return a resultset with 'default', since there are no catalogs
* in Monet
*
* @return ResultSet each row has a single String column that is a
* catalog name
* @throws SQLException if a database error occurs
*/
public ResultSet getCatalogs() throws SQLException {
Map env = getEnvMap();
String query =
"SELECT '" + ((String)env.get("gdk_dbname")) + "' AS \"TABLE_CAT\"";
// some applications need a database or catalog...
return(getStmt().executeQuery(query));
}
/**
* Get the table types available in this database. The results
* are ordered by table type.
*
* <P>The table type is:
* <OL>
* <LI><B>TABLE_TYPE</B> String => table type. Typical types are "TABLE",
* "VIEW", "SYSTEM TABLE", "GLOBAL TEMPORARY",
* "LOCAL TEMPORARY", "ALIAS", "SYNONYM".
* </OL>
*
* @return ResultSet each row has a single String column that is a
* table type
* @throws SQLException if a database error occurs
*/
public ResultSet getTableTypes() throws SQLException {
String[] columns, types;
String[][] results;
columns = new String[1];
types = new String[1];
results = new String[8][1];
columns[0] = "TABLE_TYPE";
types[0] = "varchar";
results[0][0] = "SYSTEM TABLE";
results[1][0] = "TABLE";
results[2][0] = "SYSTEM VIEW";
results[3][0] = "VIEW";
results[4][0] = "SYSTEM SESSION TABLE";
results[5][0] = "SESSION TABLE";
results[6][0] = "SYSTEM SESSION VIEW";
results[7][0] = "SESSION VIEW";
try {
return(new MonetVirtualResultSet(columns, types, results));
} catch (IllegalArgumentException e) {
throw new SQLException("Internal driver error: " + e.getMessage());
}
}
/**
* Get a description of table columns available in a catalog.
*
* <P>Only column descriptions matching the catalog, schema, table
* and column name criteria are returned. They are ordered by
* TABLE_SCHEM, TABLE_NAME and ORDINAL_POSITION.
*
* <P>Each column description has the following columns:
* <OL>
* <LI><B>TABLE_CAT</B> String => table catalog (may be null)
* <LI><B>TABLE_SCHEM</B> String => table schema (may be null)
* <LI><B>TABLE_NAME</B> String => table name
* <LI><B>COLUMN_NAME</B> String => column name
* <LI><B>DATA_TYPE</B> short => SQL type from java.sql.Types
* <LI><B>TYPE_NAME</B> String => Data source dependent type name
* <LI><B>COLUMN_SIZE</B> int => column size. For char or date
* types this is the maximum number of characters, for numeric or
* decimal types this is precision.
* <LI><B>BUFFER_LENGTH</B> is not used.
* <LI><B>DECIMAL_DIGITS</B> int => the number of fractional digits
* <LI><B>NUM_PREC_RADIX</B> int => Radix (typically either 10 or 2)
* <LI><B>NULLABLE</B> int => is NULL allowed?
* <UL>
* <LI> columnNoNulls - might not allow NULL values
* <LI> columnNullable - definitely allows NULL values
* <LI> columnNullableUnknown - nullability unknown
* </UL>
* <LI><B>REMARKS</B> String => comment describing column (may be null)
* <LI><B>COLUMN_DEF</B> String => default value (may be null)
* <LI><B>SQL_DATA_TYPE</B> int => unused
* <LI><B>SQL_DATETIME_SUB</B> int => unused
* <LI><B>CHAR_OCTET_LENGTH</B> int => for char types the
* maximum number of bytes in the column
* <LI><B>ORDINAL_POSITION</B> int => index of column in table
* (starting at 1)
* <LI><B>IS_NULLABLE</B> String => "NO" means column definitely
* does not allow NULL values; "YES" means the column might
* allow NULL values. An empty string means nobody knows.
* </OL>
*
* @param catalog a catalog name; "" retrieves those without a catalog;
* currently ignored
* @param schemaPattern a schema name pattern; "" retrieves those
* without a schema
* @param tableNamePattern a table name pattern
* @param columnNamePattern a column name pattern
* @return ResultSet each row is a column description
* @see #getSearchStringEscape
* @throws SQLException if a database error occurs
*/
public ResultSet getColumns(
String catalog,
String schemaPattern,
String tableNamePattern,
String columnNamePattern
) throws SQLException
{
String cat = (String)(getEnvMap().get("gdk_dbname"));
String query =
"SELECT '" + cat + "' AS \"TABLE_CAT\", \"schemas\".\"name\" AS \"TABLE_SCHEM\", " +
"\"tables\".\"name\" AS \"TABLE_NAME\", \"columns\".\"name\" AS \"COLUMN_NAME\", " +
"CASE \"columns\".\"type\" " +
"WHEN 'table' THEN " + Types.ARRAY + " " +
"WHEN 'boolean' THEN " + Types.BOOLEAN + " " +
"WHEN 'bool' THEN " + Types.BOOLEAN + " " +
"WHEN 'ubyte' THEN " + Types.CHAR + " " +
"WHEN 'char' THEN " + Types.CHAR + " " +
"WHEN 'character' THEN " + Types.CHAR + " " +
"WHEN 'varchar' THEN " + Types.VARCHAR + " " +
"WHEN 'text' THEN " + Types.LONGVARCHAR + " " +
"WHEN 'tinytext' THEN " + Types.LONGVARCHAR + " " +
"WHEN 'string' THEN " + Types.LONGVARCHAR + " " +
"WHEN 'tinyint' THEN " + Types.TINYINT + " " +
"WHEN 'smallint' THEN " + Types.SMALLINT + " " +
"WHEN 'mediumint' THEN " + Types.INTEGER + " " +
"WHEN 'oid' THEN " + Types.OTHER + " " +
"WHEN 'int' THEN " + Types.INTEGER + " " +
"WHEN 'integer' THEN " + Types.INTEGER + " " +
"WHEN 'bigint' THEN " + Types.BIGINT + " " +
"WHEN 'number' THEN " + Types.INTEGER + " " +
"WHEN 'decimal' THEN " + Types.DECIMAL + " " +
"WHEN 'numeric' THEN " + Types.NUMERIC + " " +
"WHEN 'float' THEN " + Types.FLOAT + " " +
"WHEN 'double' THEN " + Types.DOUBLE + " " +
"WHEN 'real' THEN " + Types.DOUBLE + " " +
"WHEN 'month_interval' THEN " + Types.INTEGER + " " +
"WHEN 'sec_interval' THEN " + Types.BIGINT + " " +
"WHEN 'date' THEN " + Types.DATE + " " +
"WHEN 'time' THEN " + Types.TIME + " " +
"WHEN 'datetime' THEN " + Types.TIMESTAMP + " " +
"WHEN 'timestamp' THEN " + Types.TIMESTAMP + " " +
"WHEN 'blob' THEN " + Types.BLOB + " " +
"ELSE " + Types.OTHER + " " +
"END AS \"DATA_TYPE\", " +
"\"columns\".\"type\" AS \"TYPE_NAME\", \"columns\".\"type_digits\" AS \"COLUMN_SIZE\", " +
"\"columns\".\"type_scale\" AS \"DECIMAL_DIGITS\", 0 AS \"BUFFER_LENGTH\", " +
"10 AS \"NUM_PREC_RADIX\", " +
"CASE \"null\" " +
"WHEN true THEN " + ResultSetMetaData.columnNullable + " " +
"WHEN false THEN " + ResultSetMetaData.columnNoNulls + " " +
"END AS \"NULLABLE\", null AS \"REMARKS\", " +
"\"columns\".\"default\" AS \"COLUMN_DEF\", 0 AS \"SQL_DATA_TYPE\", " +
"0 AS \"SQL_DATETIME_SUB\", 0 AS \"CHAR_OCTET_LENGTH\", " +
"\"columns\".\"number\" + 1 AS \"ORDINAL_POSITION\", null AS \"SCOPE_CATALOG\", " +
"null AS \"SCOPE_SCHEMA\", null AS \"SCOPE_TABLE\", " + ((MonetDriver)driver).getJavaType("other") + " AS \"SOURCE_DATA_TYPE\", " +
"CASE \"null\" " +
"WHEN true THEN CAST ('YES' AS varchar) " +
"WHEN false THEN CAST ('NO' AS varchar) " +
"END AS \"IS_NULLABLE\" " +
"FROM ( " +
"SELECT * FROM \"columns\" " +
"UNION ALL " +
"SELECT * FROM \"tmp_columns\" " +
") AS \"columns\", ( " +
"SELECT * FROM \"tables\" " +
"UNION ALL " +
"SELECT * FROM \"tmp_tables\" " +
") AS \"tables\", \"schemas\" " +
"WHERE \"columns\".\"table_id\" = \"tables\".\"id\" " +
"AND \"tables\".\"schema_id\" = \"schemas\".\"id\" ";
if (schemaPattern != null) {
query += "AND \"schemas\".\"name\" LIKE '" + escapeQuotes(schemaPattern) + "' ";
}
if (tableNamePattern != null) {
query += "AND \"tables\".\"name\" LIKE '" + escapeQuotes(tableNamePattern) + "' ";
}
if (columnNamePattern != null) {
query += "AND \"columns\".\"name\" LIKE '" + escapeQuotes(columnNamePattern) + "' ";
}
query += "ORDER BY \"TABLE_SCHEM\", \"TABLE_NAME\", \"ORDINAL_POSITION\"";
return(getStmt().executeQuery(query));
}
/**
* Get a description of the access rights for a table's columns.
* Not implemented since,Monet knows no access rights
*
* <P>Only privileges matching the column name criteria are
* returned. They are ordered by COLUMN_NAME and PRIVILEGE.
*
* <P>Each privilige description has the following columns:
* <OL>
* <LI><B>TABLE_CAT</B> String => table catalog (may be null)
* <LI><B>TABLE_SCHEM</B> String => table schema (may be null)
* <LI><B>TABLE_NAME</B> String => table name
* <LI><B>COLUMN_NAME</B> String => column name
* <LI><B>GRANTOR</B> => grantor of access (may be null)
* <LI><B>GRANTEE</B> String => grantee of access
* <LI><B>PRIVILEGE</B> String => name of access (SELECT,
* INSERT, UPDATE, REFRENCES, ...)
* <LI><B>IS_GRANTABLE</B> String => "YES" if grantee is permitted
* to grant to others; "NO" if not; null if unknown
* </OL>
*
* @param catalog a catalog name; "" retrieves those without a catalog
* @param schema a schema name; "" retrieves those without a schema
* @param table a table name
* @param columnNamePattern a column name pattern
* @return ResultSet each row is a column privilege description
* @see #getSearchStringEscape
* @throws SQLException if a database error occurs
*/
public ResultSet getColumnPrivileges(
String catalog,
String schema,
String table,
String columnNamePattern
) throws SQLException
{
String[] columns = {
"TABLE_CAT", "TABLE_SCHEM", "TABLE_NAME", "COLUMN_NAME",
"GRANTOR", "GRANTEE", "PRIVILEGE", "IS_GRANTABLE"
};
String[] types = {
"varchar", "varchar", "varchar", "varchar", "varchar",
"varchar", "varchar", "varchar"
};
String[][] results = new String[0][columns.length];
try {
return(new MonetVirtualResultSet(columns, types, results));
} catch (IllegalArgumentException e) {
throw new SQLException("Internal driver error: " + e.getMessage());
}
}
/**
* Get a description of the access rights for each table available
* in a catalog.
* Not implemented since Monet knows no access rights
*
* <P>Only privileges matching the schema and table name
* criteria are returned. They are ordered by TABLE_SCHEM,
* TABLE_NAME, and PRIVILEGE.
*
* <P>Each privilige description has the following columns:
* <OL>
* <LI><B>TABLE_CAT</B> String => table catalog (may be null)
* <LI><B>TABLE_SCHEM</B> String => table schema (may be null)
* <LI><B>TABLE_NAME</B> String => table name
* <LI><B>GRANTOR</B> => grantor of access (may be null)
* <LI><B>GRANTEE</B> String => grantee of access
* <LI><B>PRIVILEGE</B> String => name of access (SELECT,
* INSERT, UPDATE, REFRENCES, ...)
* <LI><B>IS_GRANTABLE</B> String => "YES" if grantee is permitted
* to grant to others; "NO" if not; null if unknown
* </OL>
*
* @param catalog a catalog name; "" retrieves those without a catalog
* @param schemaPattern a schema name pattern; "" retrieves those
* without a schema
* @param tableNamePattern a table name pattern
* @return ResultSet each row is a table privilege description
* @see #getSearchStringEscape
* @throws SQLException if a database error occurs
*/
public ResultSet getTablePrivileges(
String catalog,
String schemaPattern,
String tableNamePattern
) throws SQLException
{
String[] columns = {
"TABLE_CAT", "TABLE_SCHEM", "TABLE_NAME", "COLUMN_NAME",
"GRANTOR", "GRANTEE", "PRIVILEGE", "IS_GRANTABLE"
};
String[] types = {
"varchar", "varchar", "varchar", "varchar", "varchar",
"varchar", "varchar", "varchar"
};
String[][] results = new String[0][columns.length];
try {
return(new MonetVirtualResultSet(columns, types, results));
} catch (IllegalArgumentException e) {
throw new SQLException("Internal driver error: " + e.getMessage());
}
}
/**
* Get a description of a table's optimal set of columns that
* uniquely identifies a row. They are ordered by SCOPE.
*
* <P>Each column description has the following columns:
* <OL>
* <LI><B>SCOPE</B> short => actual scope of result
* <UL>
* <LI> bestRowTemporary - very temporary, while using row
* <LI> bestRowTransaction - valid for remainder of current transaction
* <LI> bestRowSession - valid for remainder of current session
* </UL>
* <LI><B>COLUMN_NAME</B> String => column name
* <LI><B>DATA_TYPE</B> short => SQL data type from java.sql.Types
* <LI><B>TYPE_NAME</B> String => Data source dependent type name
* <LI><B>COLUMN_SIZE</B> int => precision
* <LI><B>BUFFER_LENGTH</B> int => not used
* <LI><B>DECIMAL_DIGITS</B> short => scale
* <LI><B>PSEUDO_COLUMN</B> short => is this a pseudo column
* like an Oracle ROWID
* <UL>
* <LI> bestRowUnknown - may or may not be pseudo column
* <LI> bestRowNotPseudo - is NOT a pseudo column
* <LI> bestRowPseudo - is a pseudo column
* </UL>
* </OL>
*
* @param catalog a catalog name; "" retrieves those without a catalog
* @param schema a schema name; "" retrieves those without a schema
* @param table a table name
* @param scope the scope of interest; use same values as SCOPE
* @param nullable include columns that are nullable?
* @return ResultSet each row is a column description
* @throws SQLException if a database error occurs
*/
public ResultSet getBestRowIdentifier(
String catalog,
String schema,
String table,
int scope,
boolean nullable
) throws SQLException
{
String query =
"SELECT \"columns\".\"name\" AS \"COLUMN_NAME\", \"columns\".\"type\" AS \"TYPE_NAME\", " +
"\"columns\".\"type_digits\" AS \"COLUMN_SIZE\", 0 AS \"BUFFER_LENGTH\", " +
"\"columns\".\"type_scale\" AS \"DECIMAL_DIGITS\", \"keys\".\"type\" AS \"keytype\" " +
"FROM \"keys\", \"keycolumns\", ( " +
"SELECT * FROM \"columns\" " +
"UNION ALL " +
"SELECT * FROM \"tmp_columns\" " +
") AS \"columns\", ( " +
"SELECT * FROM \"tables\" " +
"UNION ALL " +
"SELECT * FROM \"tmp_tables\" " +
") AS \"tables\", \"schemas\" " +
"WHERE \"keys\".\"id\" = \"keycolumns\".\"id\" AND \"keys\".\"table_id\" = \"tables\".\"id\" " +
"AND \"keys\".\"table_id\" = \"columns\".\"table_id\" " +
"AND \"keycolumns\".\"column\" = \"columns\".\"name\" " +
"AND \"tables\".\"schema_id\" = \"schemas\".\"id\" " +
"AND \"keys\".\"type\" IN (0, 1) ";
// SCOPE, DATA_TYPE, PSEUDO_COLUMN have to be generated with Java logic
if (schema != null) {
query += "AND \"schemas\".\"name\" LIKE '" + escapeQuotes(schema) + "' ";
}
if (table != null) {
query += "AND \"tables\".\"name\" LIKE '" + escapeQuotes(table) + "' ";
}
if (!nullable) {
query += "AND \"columns\".\"null\" = false ";
}
query += "ORDER BY \"keytype\"";
String columns[] = {
"SCOPE", "COLUMN_NAME", "DATA_TYPE", "TYPE_NAME", "COLUMN_SIZE",
"BUFFER_LENGTH", "DECIMAL_DIGITS", "PSEUDO_COLUMN"
};
String types[] = {
"mediumint", "varchar", "mediumint", "varchar", "mediumint",
"mediumint", "mediumint", "mediumint"
};
String[][] results;
ArrayList tmpRes = new ArrayList();
ResultSet rs = getStmt().executeQuery(query);
while (rs.next()) {
String[] result = new String[8];
result[0] = "" + DatabaseMetaData.bestRowSession;
result[1] = rs.getString("column_name");
result[2] = "" + ((MonetDriver)driver).getJavaType(rs.getString("type_name"));
result[3] = rs.getString("type_name");
result[4] = rs.getString("column_size");
result[5] = rs.getString("buffer_length");
result[6] = rs.getString("decimal_digits");
result[7] = "" + DatabaseMetaData.bestRowNotPseudo;
tmpRes.add(result);
}
rs.close();
results = (String[][])tmpRes.toArray(new String[tmpRes.size()][]);
try {
return(new MonetVirtualResultSet(columns, types, results));
} catch (IllegalArgumentException e) {
throw new SQLException("Internal driver error: " + e.getMessage());
}
}
/**
* Get a description of a table's columns that are automatically
* updated when any value in a row is updated. They are
* unordered.
*
* <P>Each column description has the following columns:
* <OL>
* <LI><B>SCOPE</B> short => is not used
* <LI><B>COLUMN_NAME</B> String => column name
* <LI><B>DATA_TYPE</B> short => SQL data type from java.sql.Types
* <LI><B>TYPE_NAME</B> String => Data source dependent type name
* <LI><B>COLUMN_SIZE</B> int => precision
* <LI><B>BUFFER_LENGTH</B> int => length of column value in bytes
* <LI><B>DECIMAL_DIGITS</B> short => scale
* <LI><B>PSEUDO_COLUMN</B> short => is this a pseudo column
* like an Oracle ROWID
* <UL>
* <LI> versionColumnUnknown - may or may not be pseudo column
* <LI> versionColumnNotPseudo - is NOT a pseudo column
* <LI> versionColumnPseudo - is a pseudo column
* </UL>
* </OL>
*
* @param catalog a catalog name; "" retrieves those without a catalog
* @param schema a schema name; "" retrieves those without a schema
* @param table a table name
* @return ResultSet each row is a column description
* @throws SQLException if a database error occurs
*/
public ResultSet getVersionColumns(
String catalog,
String schema,
String table
) throws SQLException
{
// I don't know of columns which update themselves, except maybe on the
// system tables
String columns[] = {
"SCOPE", "COLUMN_NAME", "DATA_TYPE", "TYPE_NAME", "COLUMN_SIZE",
"BUFFER_LENGTH", "DECIMAL_DIGITS", "PSEUDO_COLUMN"
};
String types[] = {
"mediumint", "varchar", "mediumint", "varchar", "mediumint",
"mediumint", "mediumint", "mediumint"
};
String[][] results = new String[0][columns.length];
try {
return(new MonetVirtualResultSet(columns, types, results));
} catch (IllegalArgumentException e) {
throw new SQLException("Internal driver error: " + e.getMessage());
}
}
/**
* Get a description of a table's primary key columns. They
* are ordered by COLUMN_NAME.
*
* <P>Each column description has the following columns:
* <OL>
* <LI><B>TABLE_CAT</B> String => table catalog (may be null)
* <LI><B>TABLE_SCHEM</B> String => table schema (may be null)
* <LI><B>TABLE_NAME</B> String => table name
* <LI><B>COLUMN_NAME</B> String => column name
* <LI><B>KEY_SEQ</B> short => sequence number within primary key
* <LI><B>PK_NAME</B> String => primary key name (may be null)
* </OL>
*
* @param catalog a catalog name; "" retrieves those without a catalog
* @param schema a schema name pattern; "" retrieves those
* without a schema
* @param table a table name
* @return ResultSet each row is a primary key column description
* @throws SQLException if a database error occurs
*/
public ResultSet getPrimaryKeys(
String catalog,
String schema,
String table
) throws SQLException
{
String query =
"SELECT null AS \"TABLE_CAT\", \"schemas\".\"name\" AS \"TABLE_SCHEM\", " +
"\"tables\".\"name\" AS \"TABLE_NAME\", \"keycolumns\".\"column\" AS \"COLUMN_NAME\", " +
"\"keys\".\"type\" AS \"KEY_SEQ\", \"keys\".\"name\" AS \"PK_NAME\" " +
"FROM \"keys\", \"keycolumns\", ( " +
"SELECT * FROM \"tables\" " +
"UNION ALL " +
"SELECT * FROM \"tmp_tables\" " +
") AS \"tables\", \"schemas\" " +
"WHERE \"keys\".\"id\" = \"keycolumns\".\"id\" AND \"keys\".\"table_id\" = \"tables\".\"id\" " +
"AND \"tables\".\"schema_id\" = \"schemas\".\"id\" " +
"AND \"keys\".\"type\" = 0 ";
if (schema != null) {
query += "AND \"schemas\".\"name\" LIKE '" + escapeQuotes(schema) + "' ";
}
if (table != null) {
query += "AND \"tables\".\"name\" LIKE '" + escapeQuotes(table) + "' ";
}
query += "ORDER BY \"COLUMN_NAME\"";
return(getStmt().executeQuery(query));
}
final static String keyQuery =
", \"pkschema\".\"name\" AS \"PKTABLE_SCHEM\", " +
"\"pktable\".\"name\" AS \"PKTABLE_NAME\", \"pkkeycol\".\"column\" AS \"PKCOLUMN_NAME\", " +
"\"fkschema\".\"name\" AS \"FKTABLE_SCHEM\", " +
"\"fktable\".\"name\" AS \"FKTABLE_NAME\", \"fkkeycol\".\"column\" AS \"FKCOLUMN_NAME\", " +
"\"fkkey\".\"type\" AS \"KEY_SEQ\", " + DatabaseMetaData.importedKeyNoAction + " AS \"UPDATE_RULE\", " +
"" + DatabaseMetaData.importedKeyNoAction + " AS \"DELETE_RULE\", " +
"\"fkkey\".\"name\" AS \"FK_NAME\", \"pkkey\".\"name\" AS \"PK_NAME\", " +
"" + DatabaseMetaData.importedKeyNotDeferrable + " AS \"DEFERRABILITY\" " +
"FROM \"keys\" AS \"fkkey\", \"keys\" AS \"pkkey\", \"keycolumns\" AS \"fkkeycol\", " +
"\"keycolumns\" AS \"pkkeycol\", ( " +
"SELECT * FROM \"tables\" " +
"UNION ALL " +
"SELECT * FROM \"tmp_tables\" " +
") AS \"fktable\", ( " +
"SELECT * FROM \"tables\" " +
"UNION ALL " +
"SELECT * FROM \"tmp_tables\" " +
") AS \"pktable\", " +
"\"schemas\" AS \"fkschema\", \"schemas\" AS \"pkschema\" " +
"WHERE \"fktable\".\"id\" = \"fkkey\".\"table_id\" AND \"pktable\".\"id\" = \"pkkey\".\"table_id\" AND " +
"\"fkkey\".\"id\" = \"fkkeycol\".\"id\" AND \"pkkey\".\"id\" = \"pkkeycol\".\"id\" AND " +
"\"fkschema\".\"id\" = \"fktable\".\"schema_id\" AND \"pkschema\".\"id\" = \"pktable\".\"schema_id\" AND " +
"\"fkkey\".\"rkey\" > -1 AND \"fkkey\".\"rkey\" = \"pkkey\".\"id\" ";
static String keyQuery(String cat) {
return("SELECT '" + cat + "' AS \"PKTABLE_CAT\", '" + cat + "' AS \"FKTABLE_CAT\"" + keyQuery);
}
/**
* Get a description of the primary key columns that are
* referenced by a table's foreign key columns (the primary keys
* imported by a table). They are ordered by PKTABLE_CAT,
* PKTABLE_SCHEM, PKTABLE_NAME, and KEY_SEQ.
*
* <P>Each primary key column description has the following columns:
* <OL>
* <LI><B>PKTABLE_CAT</B> String => primary key table catalog
* being imported (may be null)
* <LI><B>PKTABLE_SCHEM</B> String => primary key table schema
* being imported (may be null)
* <LI><B>PKTABLE_NAME</B> String => primary key table name
* being imported
* <LI><B>PKCOLUMN_NAME</B> String => primary key column name
* being imported
* <LI><B>FKTABLE_CAT</B> String => foreign key table catalog (may be null)
* <LI><B>FKTABLE_SCHEM</B> String => foreign key table schema (may be null)
* <LI><B>FKTABLE_NAME</B> String => foreign key table name
* <LI><B>FKCOLUMN_NAME</B> String => foreign key column name
* <LI><B>KEY_SEQ</B> short => sequence number within foreign key
* <LI><B>UPDATE_RULE</B> short => What happens to
* foreign key when primary is updated:
* <UL>
* <LI> importedKeyCascade - change imported key to agree
* with primary key update
* <LI> importedKeyRestrict - do not allow update of primary
* key if it has been imported
* <LI> importedKeySetNull - change imported key to NULL if
* its primary key has been updated
* </UL>
* <LI><B>DELETE_RULE</B> short => What happens to
* the foreign key when primary is deleted.
* <UL>
* <LI> importedKeyCascade - delete rows that import a deleted key
* <LI> importedKeyRestrict - do not allow delete of primary
* key if it has been imported
* <LI> importedKeySetNull - change imported key to NULL if
* its primary key has been deleted
* </UL>
* <LI><B>FK_NAME</B> String => foreign key name (may be null)
* <LI><B>PK_NAME</B> String => primary key name (may be null)
* </OL>
*
* @param catalog a catalog name; "" retrieves those without a catalog
* @param schema a schema name pattern; "" retrieves those
* without a schema
* @param table a table name
* @return ResultSet each row is a primary key column description
* @see #getExportedKeys
* @throws SQLException if a database error occurs
*/
public ResultSet getImportedKeys(String catalog, String schema, String table)
throws SQLException
{
String cat = (String)(getEnvMap().get("gdk_dbname"));
String query = keyQuery(cat);
if (schema != null) {
query += "AND \"fkschema\".\"name\" LIKE '" + escapeQuotes(schema) + "' ";
}
if (table != null) {
query += "AND \"fktable\".\"name\" LIKE '" + escapeQuotes(table) + "' ";
}
query += "ORDER BY \"PKTABLE_CAT\", \"PKTABLE_SCHEM\", \"PKTABLE_NAME\", \"KEY_SEQ\"";
return(getStmt().executeQuery(query));
}
/**
* Get a description of a foreign key columns that reference a
* table's primary key columns (the foreign keys exported by a
* table). They are ordered by FKTABLE_CAT, FKTABLE_SCHEM,
* FKTABLE_NAME, and KEY_SEQ.
*
* <P>Each foreign key column description has the following columns:
* <OL>
* <LI><B>PKTABLE_CAT</B> String => primary key table catalog (may be null)
* <LI><B>PKTABLE_SCHEM</B> String => primary key table schema (may be null)
* <LI><B>PKTABLE_NAME</B> String => primary key table name
* <LI><B>PKCOLUMN_NAME</B> String => primary key column name
* <LI><B>FKTABLE_CAT</B> String => foreign key table catalog (may be null)
* being exported (may be null)
* <LI><B>FKTABLE_SCHEM</B> String => foreign key table schema (may be null)
* being exported (may be null)
* <LI><B>FKTABLE_NAME</B> String => foreign key table name
* being exported
* <LI><B>FKCOLUMN_NAME</B> String => foreign key column name
* being exported
* <LI><B>KEY_SEQ</B> short => sequence number within foreign key
* <LI><B>UPDATE_RULE</B> short => What happens to
* foreign key when primary is updated:
* <UL>
* <LI> importedKeyCascade - change imported key to agree
* with primary key update
* <LI> importedKeyRestrict - do not allow update of primary
* key if it has been imported
* <LI> importedKeySetNull - change imported key to NULL if
* its primary key has been updated
* </UL>
* <LI><B>DELETE_RULE</B> short => What happens to
* the foreign key when primary is deleted.
* <UL>
* <LI> importedKeyCascade - delete rows that import a deleted key
* <LI> importedKeyRestrict - do not allow delete of primary
* key if it has been imported
* <LI> importedKeySetNull - change imported key to NULL if
* its primary key has been deleted
* </UL>
* <LI><B>FK_NAME</B> String => foreign key identifier (may be null)
* <LI><B>PK_NAME</B> String => primary key identifier (may be null)
* </OL>
*
* @param catalog a catalog name; "" retrieves those without a catalog
* @param schema a schema name pattern; "" retrieves those
* without a schema
* @param table a table name
* @return ResultSet each row is a foreign key column description
* @see #getImportedKeys
* @throws SQLException if a database error occurs
*/
public ResultSet getExportedKeys(String catalog, String schema, String table)
throws SQLException
{
String cat = (String)(getEnvMap().get("gdk_dbname"));
String query = keyQuery(cat);
if (schema != null) {
query += "AND \"pkschema\".\"name\" LIKE '" + escapeQuotes(schema) + "' ";
}
if (table != null) {
query += "AND \"pktable\".\"name\" LIKE '" + escapeQuotes(table) + "' ";
}
query += "ORDER BY \"FKTABLE_CAT\", \"FKTABLE_SCHEM\", \"FKTABLE_NAME\", \"KEY_SEQ\"";
return(getStmt().executeQuery(query));
}
/**
* Get a description of the foreign key columns in the foreign key
* table that reference the primary key columns of the primary key
* table (describe how one table imports another's key.) This
* should normally return a single foreign key/primary key pair
* (most tables only import a foreign key from a table once.) They
* are ordered by FKTABLE_CAT, FKTABLE_SCHEM, FKTABLE_NAME, and
* KEY_SEQ.
*
* This method is currently unimplemented.
*
* <P>Each foreign key column description has the following columns:
* <OL>
* <LI><B>PKTABLE_CAT</B> String => primary key table catalog (may be null)
* <LI><B>PKTABLE_SCHEM</B> String => primary key table schema (may be null)
* <LI><B>PKTABLE_NAME</B> String => primary key table name
* <LI><B>PKCOLUMN_NAME</B> String => primary key column name
* <LI><B>FKTABLE_CAT</B> String => foreign key table catalog (may be null)
* being exported (may be null)
* <LI><B>FKTABLE_SCHEM</B> String => foreign key table schema (may be null)
* being exported (may be null)
* <LI><B>FKTABLE_NAME</B> String => foreign key table name
* being exported
* <LI><B>FKCOLUMN_NAME</B> String => foreign key column name
* being exported
* <LI><B>KEY_SEQ</B> short => sequence number within foreign key
* <LI><B>UPDATE_RULE</B> short => What happens to
* foreign key when primary is updated:
* <UL>
* <LI> importedKeyCascade - change imported key to agree
* with primary key update
* <LI> importedKeyRestrict - do not allow update of primary
* key if it has been imported
* <LI> importedKeySetNull - change imported key to NULL if
* its primary key has been updated
* </UL>
* <LI><B>DELETE_RULE</B> short => What happens to
* the foreign key when primary is deleted.
* <UL>
* <LI> importedKeyCascade - delete rows that import a deleted key
* <LI> importedKeyRestrict - do not allow delete of primary
* key if it has been imported
* <LI> importedKeySetNull - change imported key to NULL if
* its primary key has been deleted
* </UL>
* <LI><B>FK_NAME</B> String => foreign key identifier (may be null)
* <LI><B>PK_NAME</B> String => primary key identifier (may be null)
* </OL>
*
* @param pcatalog primary key catalog name; "" retrieves those without a catalog
* @param pschema primary key schema name pattern; "" retrieves those
* without a schema
* @param ptable primary key table name
* @param fcatalog foreign key catalog name; "" retrieves those without a catalog
* @param fschema foreign key schema name pattern; "" retrieves those
* without a schema
* @param ftable koreign key table name
* @return ResultSet each row is a foreign key column description
* @throws SQLException if a database error occurs
* @see #getImportedKeys
*/
public ResultSet getCrossReference(
String pcatalog,
String pschema,
String ptable,
String fcatalog,
String fschema,
String ftable
) throws SQLException
{
String cat = (String)(getEnvMap().get("gdk_dbname"));
String query = keyQuery(cat);
if (pschema != null) {
query += "AND \"pkschema\".\"name\" LIKE '" + escapeQuotes(pschema) + "' ";
}
if (ptable != null) {
query += "AND \"pktable\".\"name\" LIKE '" + escapeQuotes(ptable) + "' ";
}
if (fschema != null) {
query += "AND \"fkschema\".\"name\" LIKE '" + escapeQuotes(fschema) + "' ";
}
if (ftable != null) {
query += "AND \"fktable\".\"name\" LIKE '" + escapeQuotes(ftable) + "' ";
}
query += "ORDER BY \"FKTABLE_CAT\", \"FKTABLE_SCHEM\", \"FKTABLE_NAME\", \"KEY_SEQ\"";
return(getStmt().executeQuery(query));
}
/**
* Get a description of all the standard SQL types supported by
* this database. They are ordered by DATA_TYPE and then by how
* closely the data type maps to the corresponding JDBC SQL type.
*
* <P>Each type description has the following columns:
* <OL>
* <LI><B>TYPE_NAME</B> String => Type name
* <LI><B>DATA_TYPE</B> short => SQL data type from java.sql.Types
* <LI><B>PRECISION</B> int => maximum precision
* <LI><B>LITERAL_PREFIX</B> String => prefix used to quote a literal
* (may be null)
* <LI><B>LITERAL_SUFFIX</B> String => suffix used to quote a literal
* (may be null)
* <LI><B>CREATE_PARAMS</B> String => parameters used in creating
* the type (may be null)
* <LI><B>NULLABLE</B> short => can you use NULL for this type?
* <UL>
* <LI> typeNoNulls - does not allow NULL values
* <LI> typeNullable - allows NULL values
* <LI> typeNullableUnknown - nullability unknown
* </UL>
* <LI><B>CASE_SENSITIVE</B> boolean=> is it case sensitive?
* <LI><B>SEARCHABLE</B> short => can you use "WHERE" based on this type:
* <UL>
* <LI> typePredNone - No support
* <LI> typePredChar - Only supported with WHERE .. LIKE
* <LI> typePredBasic - Supported except for WHERE .. LIKE
* <LI> typeSearchable - Supported for all WHERE ..
* </UL>
* <LI><B>UNSIGNED_ATTRIBUTE</B> boolean => is it unsigned?
* <LI><B>FIXED_PREC_SCALE</B> boolean => can it be a money value?
* <LI><B>AUTO_INCREMENT</B> boolean => can it be used for an
* auto-increment value?
* <LI><B>LOCAL_TYPE_NAME</B> String => localized version of type name
* (may be null)
* <LI><B>MINIMUM_SCALE</B> short => minimum scale supported
* <LI><B>MAXIMUM_SCALE</B> short => maximum scale supported
* <LI><B>SQL_DATA_TYPE</B> int => unused
* <LI><B>SQL_DATETIME_SUB</B> int => unused
* <LI><B>NUM_PREC_RADIX</B> int => usually 2 or 10
* </OL>
*
* @return ResultSet each row is a SQL type description
* @throws Exception if the developer made a Boo-Boo
*/
public ResultSet getTypeInfo() throws SQLException {
String columns[] = {
"TYPE_NAME", "DATA_TYPE", "PRECISION", "LITERAL_PREFIX",
"LITERAL_SUFFIX", "CREATE_PARAMS", "NULLABLE", "CASE_SENSITIVE",
"SEARCHABLE", "UNSIGNED_ATTRIBUTE", "FIXED_PREC_SCALE", "AUTO_INCREMENT",
"LOCAL_TYPE_NAME", "MINIMUM_SCALE", "MAXIMUM_SCALE", "SQL_DATA_TYPE",
"SQL_DATETIME_SUB", "NUM_PREC_RADIX"
};
String types[] = {
"varchar", "mediumint", "mediumint", "varchar", "varchar",
"varchar", "tinyint", "boolean", "tinyint", "boolean",
"boolean", "boolean", "varchar", "tinyint", "tinyint",
"mediumint", "mediumint", "mediumint"
};
String results[][] = {
// type_name data_type prec. pre suff crte nullable casesns searchable unsign fixprec autoinc name min max sql sql radix
{"table", "" + Types.ARRAY, "0", null, null, null, "" + DatabaseMetaData.typeNullable, "false", "" + DatabaseMetaData.typePredNone, "true", "false", "false", "bat", "0", "0", "0", "0", "0"},
{"boolean", "" + Types.BOOLEAN, "1", null, null, null, "" + DatabaseMetaData.typeNullable, "false", "" + DatabaseMetaData.typePredBasic, "true", "false", "false", "bit", "0", "0", "0", "0", "2"},
{"bool", "" + Types.BOOLEAN, "1", null, null, null, "" + DatabaseMetaData.typeNullable, "false", "" + DatabaseMetaData.typePredBasic, "true", "false", "false", "bit", "0", "0", "0", "0", "2"},
{"blob", "" + Types.BLOB, "0", null, null, null, "" + DatabaseMetaData.typeNullable, "false", "" + DatabaseMetaData.typePredNone, "true", "false", "false", "blob", "0", "0", "0", "0", "0"},
{"char", "" + Types.CHAR, "0", null, null, null, "" + DatabaseMetaData.typeNullable, "false", "" + DatabaseMetaData.typePredChar, "true", "false", "false", "str", "0", "0", "0", "0", "0"},
{"character", "" + Types.CHAR, "0", null, null, null, "" + DatabaseMetaData.typeNullable, "false", "" + DatabaseMetaData.typePredChar, "true", "false", "false", "str", "0", "0", "0", "0", "0"},
{"ubyte", "" + Types.CHAR, "2", null, null, null, "" + DatabaseMetaData.typeNullable, "false", "" + DatabaseMetaData.typePredNone, "true", "false", "false", "uchr", "0", "0", "0", "0", "2"},
{"date", "" + Types.DATE, "0", null, null, null, "" + DatabaseMetaData.typeNullable, "false", "" + DatabaseMetaData.typePredBasic, "true", "false", "false", "date", "0", "0", "0", "0", "0"},
{"decimal", "" + Types.DECIMAL, "4", null, null, null, "" + DatabaseMetaData.typeNullable, "false", "" + DatabaseMetaData.typePredBasic, "false", "true", "false", "sht", "1", "0", "0", "0", "10"},
{"decimal", "" + Types.DECIMAL, "9", null, null, null, "" + DatabaseMetaData.typeNullable, "false", "" + DatabaseMetaData.typePredBasic, "false", "true", "false", "int", "1", "0", "0", "0", "10"},
{"decimal", "" + Types.DECIMAL,"19", null, null, null, "" + DatabaseMetaData.typeNullable, "false", "" + DatabaseMetaData.typePredBasic, "false", "true", "false", "lng", "1", "0", "0", "0", "10"},
{"double", "" + Types.DOUBLE, "51", null, null, null, "" + DatabaseMetaData.typeNullable, "false", "" + DatabaseMetaData.typePredBasic, "false", "false", "false", "dbl", "2", "0", "0", "0", "2"},
{"float", "" + Types.REAL, "23", null, null, null, "" + DatabaseMetaData.typeNullable, "false", "" + DatabaseMetaData.typePredBasic, "false", "false", "false", "flt", "2", "0", "0", "0", "2"},
{"float", "" + Types.FLOAT, "51", null, null, null, "" + DatabaseMetaData.typeNullable, "false", "" + DatabaseMetaData.typePredBasic, "false", "false", "false", "dbl", "2", "0", "0", "0", "2"},
{"integer", "" + Types.INTEGER, "9", null, null, null, "" + DatabaseMetaData.typeNullable, "false", "" + DatabaseMetaData.typePredBasic, "false", "false", "false", "int", "0", "0", "0", "0", "2"},
{"number", "" + Types.INTEGER, "9", null, null, null, "" + DatabaseMetaData.typeNullable, "false", "" + DatabaseMetaData.typePredBasic, "false", "false", "false", "int", "0", "0", "0", "0", "2"},
{"mediumint", "" + Types.INTEGER, "9", null, null, null, "" + DatabaseMetaData.typeNullable, "false", "" + DatabaseMetaData.typePredBasic, "false", "false", "false", "int", "0", "0", "0", "0", "2"},
{"int", "" + Types.INTEGER, "9", null, null, null, "" + DatabaseMetaData.typeNullable, "false", "" + DatabaseMetaData.typePredBasic, "false", "false", "false", "int", "0", "0", "0", "0", "2"},
{"tinyint", "" + Types.TINYINT, "2", null, null, null, "" + DatabaseMetaData.typeNullable, "false", "" + DatabaseMetaData.typePredBasic, "false", "false", "false", "sht", "0", "0", "0", "0", "2"},
{"smallint", "" + Types.SMALLINT,"4", null, null, null, "" + DatabaseMetaData.typeNullable, "false", "" + DatabaseMetaData.typePredBasic, "false", "false", "false", "sht", "0", "0", "0", "0", "2"},
{"int", "" + Types.INTEGER, "4", null, null, null, "" + DatabaseMetaData.typeNullable, "false", "" + DatabaseMetaData.typePredBasic, "false", "false", "false", "sht", "0", "0", "0", "0", "2"},
{"int", "" + Types.BIGINT, "19", null, null, null, "" + DatabaseMetaData.typeNullable, "false", "" + DatabaseMetaData.typePredBasic, "false", "false", "false", "lng", "0", "0", "0", "0", "2"},
{"bigint", "" + Types.BIGINT, "19", null, null, null, "" + DatabaseMetaData.typeNullable, "false", "" + DatabaseMetaData.typePredBasic, "false", "false", "false", "lng", "0", "0", "0", "0", "2"},
{"text", "" + Types.LONGVARCHAR,"0",null,null,null, "" + DatabaseMetaData.typeNullable, "false", "" + DatabaseMetaData.typePredChar, "true", "false", "false", "str", "0", "0", "0", "0", "0"},
{"tinytext", "" + Types.LONGVARCHAR,"0",null,null,null, "" + DatabaseMetaData.typeNullable, "false", "" + DatabaseMetaData.typePredChar, "true", "false", "false", "str", "0", "0", "0", "0", "0"},
{"string", "" + Types.LONGVARCHAR,"0",null,null,null, "" + DatabaseMetaData.typeNullable, "false", "" + DatabaseMetaData.typePredChar, "true", "false", "false", "str", "0", "0", "0", "0", "0"},
{"numeric", "" + Types.NUMERIC, "4", null, null, null, "" + DatabaseMetaData.typeNullable, "false", "" + DatabaseMetaData.typePredBasic, "false", "false", "false", "sht", "1", "0", "0", "0", "10"},
{"numeric", "" + Types.NUMERIC, "9", null, null, null, "" + DatabaseMetaData.typeNullable, "false", "" + DatabaseMetaData.typePredBasic, "false", "false", "false", "int", "1", "0", "0", "0", "10"},
{"numeric", "" + Types.NUMERIC,"19", null, null, null, "" + DatabaseMetaData.typeNullable, "false", "" + DatabaseMetaData.typePredBasic, "false", "false", "false", "lng", "1", "0", "0", "0", "10"},
{"oid", "" + Types.OTHER, "9", null, null, null, "" + DatabaseMetaData.typeNullable, "false", "" + DatabaseMetaData.typePredNone, "true", "false", "true", "lng", "0", "0", "0", "0", "2"},
{"month_interval",""+Types.INTEGER,"0",null, null, null, "" + DatabaseMetaData.typeNullable, "false", "" + DatabaseMetaData.typePredNone, "false", "false", "false", "int", "0", "0", "0", "0", "10"},
{"sec_interval",""+Types.BIGINT, "0", null, null, null, "" + DatabaseMetaData.typeNullable, "false", "" + DatabaseMetaData.typePredNone, "false", "false", "false", "lng", "0", "0", "0", "0", "10"},
{"real", "" + Types.DOUBLE, "51", null, null, null, "" + DatabaseMetaData.typeNullable, "false", "" + DatabaseMetaData.typePredBasic, "false", "false", "false", "dbl", "2", "0", "0", "0", "2"},
{"time", "" + Types.TIME, "0", null, null, null, "" + DatabaseMetaData.typeNullable, "false", "" + DatabaseMetaData.typePredBasic, "true", "false", "false", "daytime","0","0","0", "0", "0"},
{"datetime", "" + Types.TIMESTAMP,"0",null, null, null, "" + DatabaseMetaData.typeNullable, "false", "" + DatabaseMetaData.typePredBasic, "true", "false", "false", "timestamp","0","0","0","0", "0"},
{"timestamp", "" + Types.TIMESTAMP,"0",null, null, null, "" + DatabaseMetaData.typeNullable, "false", "" + DatabaseMetaData.typePredBasic, "true", "false", "false", "timestamp","0","0","0","0", "0"},
{"varchar", "" + Types.VARCHAR, "0", null, null, null, "" + DatabaseMetaData.typeNullable, "false", "" + DatabaseMetaData.typePredChar, "true", "false", "false", "str", "0", "0", "0", "0", "0"}
};
try {
return(new MonetVirtualResultSet(columns, types, results));
} catch (IllegalArgumentException e) {
throw new SQLException("Internal driver error: " + e.getMessage());
}
}
/**
* Get a description of a table's indices and statistics. They are
* ordered by NON_UNIQUE, TYPE, INDEX_NAME, and ORDINAL_POSITION.
*
* <P>Each index column description has the following columns:
* <OL>
* <LI><B>TABLE_CAT</B> String => table catalog (may be null)
* <LI><B>TABLE_SCHEM</B> String => table schema (may be null)
* <LI><B>TABLE_NAME</B> String => table name
* <LI><B>NON_UNIQUE</B> boolean => Can index values be non-unique?
* false when TYPE is tableIndexStatistic
* <LI><B>INDEX_QUALIFIER</B> String => index catalog (may be null);
* null when TYPE is tableIndexStatistic
* <LI><B>INDEX_NAME</B> String => index name; null when TYPE is
* tableIndexStatistic
* <LI><B>TYPE</B> short => index type:
* <UL>
* <LI> tableIndexStatistic - this identifies table statistics that are
* returned in conjuction with a table's index descriptions
* <LI> tableIndexClustered - this is a clustered index
* <LI> tableIndexHashed - this is a hashed index
* <LI> tableIndexOther - this is some other style of index
* </UL>
* <LI><B>ORDINAL_POSITION</B> short => column sequence number
* within index; zero when TYPE is tableIndexStatistic
* <LI><B>COLUMN_NAME</B> String => column name; null when TYPE is
* tableIndexStatistic
* <LI><B>ASC_OR_DESC</B> String => column sort sequence, "A" => ascending
* "D" => descending, may be null if sort sequence is not supported;
* null when TYPE is tableIndexStatistic
* <LI><B>CARDINALITY</B> int => When TYPE is tableIndexStatisic then
* this is the number of rows in the table; otherwise it is the
* number of unique values in the index.
* <LI><B>PAGES</B> int => When TYPE is tableIndexStatisic then
* this is the number of pages used for the table, otherwise it
* is the number of pages used for the current index.
* <LI><B>FILTER_CONDITION</B> String => Filter condition, if any.
* (may be null)
* </OL>
*
* @param catalog a catalog name; "" retrieves those without a catalog
* @param schema a schema name pattern; "" retrieves those without a schema
* @param table a table name
* @param unique when true, return only indices for unique values;
* when false, return indices regardless of whether unique or not
* @param approximate when true, result is allowed to reflect approximate
* or out of data values; when false, results are requested to be
* accurate
* @return ResultSet each row is an index column description
* @throws SQLException if a database occurs
*/
public ResultSet getIndexInfo(
String catalog,
String schema,
String table,
boolean unique,
boolean approximate
) throws SQLException
{
String cat = (String)(getEnvMap().get("gdk_dbname"));
String query =
"SELECT * FROM ( " +
"SELECT '" + cat + "' AS \"TABLE_CAT\", " +
"\"idxs\".\"name\" AS \"INDEX_NAME\", " +
"\"tables\".\"name\" AS \"TABLE_NAME\", " +
"\"schemas\".\"name\" AS \"TABLE_SCHEM\", " +
"CASE WHEN \"keys\".\"name\" IS NULL THEN true ELSE false END AS \"NON_UNIQUE\", " +
"CASE \"idxs\".\"type\" WHEN 0 THEN " + DatabaseMetaData. tableIndexHashed + " ELSE " + DatabaseMetaData. tableIndexOther + " END AS \"TYPE\", " +
"\"keycolumns\".\"nr\" AS \"ORDINAL_POSITION\", " +
"\"columns\".\"name\" as \"COLUMN_NAME\", " +
"null AS \"INDEX_QUALIFIER\", " +
"null AS \"ASC_OR_DESC\", " +
"0 AS \"PAGES\", " +
"null AS \"FILTER_CONDITION\" " +
"FROM \"idxs\" LEFT JOIN \"keys\" ON \"idxs\".\"name\" = \"keys\".\"name\", \"schemas\", \"keycolumns\", ( " +
"SELECT * FROM \"columns\" " +
"UNION ALL " +
"SELECT * FROM \"tmp_columns\" " +
") AS \"columns\", ( " +
"SELECT * FROM \"tables\" " +
"UNION ALL " +
"SELECT * FROM \"tmp_tables\" " +
") AS \"tables\" " +
"WHERE \"idxs\".\"table_id\" = \"tables\".\"id\" " +
"AND \"tables\".\"schema_id\" = \"schemas\".\"id\" " +
"AND \"idxs\".\"id\" = \"keycolumns\".\"id\" " +
"AND \"tables\".\"id\" = \"columns\".\"table_id\" " +
"AND \"keycolumns\".\"column\" = \"columns\".\"name\" " +
"AND (\"keys\".\"type\" IS NULL OR \"keys\".\"type\" = 1) " +
") AS jdbcquery " +
"WHERE 1 = 1 ";
if (schema != null) {
query += "AND \"TABLE_SCHEM\" LIKE '" + escapeQuotes(schema) + "' ";
}
if (table != null) {
query += "AND \"TABLE_NAME\" LIKE '" + escapeQuotes(table) + "' ";
}
if (unique) {
query += "AND \"NON_UNIQUE\" = false ";
}
query += "ORDER BY \"NON_UNIQUE\", \"TYPE\", \"INDEX_NAME\", \"ORDINAL_POSITION\"";
String columns[] = {
"TABLE_CAT", "TABLE_SCHEM", "TABLE_NAME", "NON_UNIQUE",
"INDEX_QUALIFIER", "INDEX_NAME", "TYPE", "ORDINAL_POSITION",
"COLUMN_NAME", "ASC_OR_DESC", "CARDINALITY", "PAGES",
"FILTER_CONDITION"
};
String types[] = {
"varchar", "varchar", "varchar", "boolean",
"varchar", "varchar", "mediumint", "mediumint",
"varchar", "varchar", "mediumint", "mediumint", "varchar"
};
String[][] results;
ArrayList tmpRes = new ArrayList();
Statement sub = null;
if (!approximate) sub = con.createStatement();
ResultSet rs = getStmt().executeQuery(query);
while (rs.next()) {
String[] result = new String[13];
result[0] = null;
result[1] = rs.getString("table_schem");
result[2] = rs.getString("table_name");
result[3] = rs.getString("non_unique");
result[4] = rs.getString("index_qualifier");
result[5] = rs.getString("index_name");
result[6] = rs.getString("type");
result[7] = rs.getString("ordinal_position");
result[8] = rs.getString("column_name");
result[9] = rs.getString("asc_or_desc");
if (approximate) {
result[10] = "0";
} else {
ResultSet count = sub.executeQuery("SELECT COUNT(*) AS \"CARDINALITY\" FROM \"" + rs.getString("table_schem") + "\".\"" + rs.getString("table_name") + "\"");
if (count.next()) {
result[10] = count.getString("cardinality");
} else {
result[10] = "0";
}
}
result[11] = rs.getString("pages");
result[12] = rs.getString("filter_condition");
tmpRes.add(result);
}
if (!approximate) sub.close();
rs.close();
results = (String[][])tmpRes.toArray(new String[tmpRes.size()][]);
try {
return(new MonetVirtualResultSet(columns, types, results));
} catch (IllegalArgumentException e) {
throw new SQLException("Internal driver error: " + e.getMessage());
}
}
// ** JDBC 2 Extensions **
/**
* Does the database support the given result set type?
*
* @param type - defined in java.sql.ResultSet
* @return true if so; false otherwise
* @throws SQLException - if a database access error occurs
*/
public boolean supportsResultSetType(int type) throws SQLException {
// The only type we don't support
return(type != ResultSet.TYPE_SCROLL_SENSITIVE);
}
/**
* Does the database support the concurrency type in combination
* with the given result set type?
*
* @param type - defined in java.sql.ResultSet
* @param concurrency - type defined in java.sql.ResultSet
* @return true if so; false otherwise
* @throws SQLException - if a database access error occurs
*/
public boolean supportsResultSetConcurrency(int type, int concurrency)
throws SQLException
{
// These combinations are not supported!
if (type == ResultSet.TYPE_SCROLL_SENSITIVE)
return(false);
// We do only support Read Only ResultSets
if (concurrency != ResultSet.CONCUR_READ_ONLY)
return(false);
// Everything else we do (well, what's left of it :) )
return(true);
}
/* lots of unsupported stuff... (no updatable ResultSet!) */
public boolean ownUpdatesAreVisible(int type) {
return(false);
}
public boolean ownDeletesAreVisible(int type) {
return(false);
}
public boolean ownInsertsAreVisible(int type) {
return(false);
}
public boolean othersUpdatesAreVisible(int type) {
return(false);
}
public boolean othersDeletesAreVisible(int i) {
return(false);
}
public boolean othersInsertsAreVisible(int type) {
return(false);
}
public boolean updatesAreDetected(int type) {
return(false);
}
public boolean deletesAreDetected(int i) {
return(false);
}
public boolean insertsAreDetected(int type) {
return(false);
}
/**
* Indicates whether the driver supports batch updates.
* Not yet, but I want to do them in the near future
*/
public boolean supportsBatchUpdates() {
return(false);
}
/**
* Return user defined types in a schema
* Probably not possible within Monet
*
* @throws SQLException if I made a Boo-Boo
*/
public ResultSet getUDTs(
String catalog,
String schemaPattern,
String typeNamePattern,
int[] types
) throws SQLException
{
String cat = (String)(getEnvMap().get("gdk_dbname"));
String query =
"SELECT '" + cat + "' AS \"TYPE_CAT\", '' AS \"TYPE_SCHEM\", '' AS \"TYPE_NAME\", " +
"'java.lang.Object' AS \"CLASS_NAME\", 0 AS \"DATA_TYPE\", " +
"'' AS \"REMARKS\", 0 AS \"BASE_TYPE\" WHERE 1 = 0";
return(getStmt().executeQuery(query));
}
/**
* Retrieves the connection that produced this metadata object.
*
* @return the connection that produced this metadata object
*/
public Connection getConnection() {
return(con);
}
/* I don't find these in the spec!?! */
public boolean rowChangesAreDetected(int type) {
return(false);
}
public boolean rowChangesAreVisible(int type) {
return(false);
}
// ** JDBC 3 extensions **
/**
* Retrieves whether this database supports savepoints.
*
* @return <code>true</code> if savepoints are supported;
* <code>false</code> otherwise
*/
public boolean supportsSavepoints() {
return(true);
}
/**
* Retrieves whether this database supports named parameters to callable
* statements.
*
* @return <code>true</code> if named parameters are supported;
* <code>false</code> otherwise
*/
public boolean supportsNamedParameters() {
return(false);
}
/**
* Retrieves whether it is possible to have multiple <code>ResultSet</code> objects
* returned from a <code>CallableStatement</code> object
* simultaneously.
*
* @return <code>true</code> if a <code>CallableStatement</code> object
* can return multiple <code>ResultSet</code> objects
* simultaneously; <code>false</code> otherwise
*/
public boolean supportsMultipleOpenResults() {
return(false);
}
/**
* Retrieves whether auto-generated keys can be retrieved after
* a statement has been executed.
*
* @return <code>true</code> if auto-generated keys can be retrieved
* after a statement has executed; <code>false</code> otherwise
*/
public boolean supportsGetGeneratedKeys() {
return(false);
}
/**
* Retrieves a description of the user-defined type (UDT) hierarchies defined in a
* particular schema in this database. Only the immediate super type/
* sub type relationship is modeled.
* <P>
* Only supertype information for UDTs matching the catalog,
* schema, and type name is returned. The type name parameter
* may be a fully-qualified name. When the UDT name supplied is a
* fully-qualified name, the catalog and schemaPattern parameters are
* ignored.
* <P>
* If a UDT does not have a direct super type, it is not listed here.
* A row of the <code>ResultSet</code> object returned by this method
* describes the designated UDT and a direct supertype. A row has the following
* columns:
* <OL>
* <LI><B>TYPE_CAT</B> String => the UDT's catalog (may be <code>null</code>)
* <LI><B>TYPE_SCHEM</B> String => UDT's schema (may be <code>null</code>)
* <LI><B>TYPE_NAME</B> String => type name of the UDT
* <LI><B>SUPERTYPE_CAT</B> String => the direct super type's catalog
* (may be <code>null</code>)
* <LI><B>SUPERTYPE_SCHEM</B> String => the direct super type's schema
* (may be <code>null</code>)
* <LI><B>SUPERTYPE_NAME</B> String => the direct super type's name
* </OL>
*
* <P><B>Note:</B> If the driver does not support type hierarchies, an
* empty result set is returned.
*
* @param catalog a catalog name; "" retrieves those without a catalog;
* <code>null</code> means drop catalog name from the selection criteria
* @param schemaPattern a schema name pattern; "" retrieves those
* without a schema
* @param typeNamePattern a UDT name pattern; may be a fully-qualified
* name
* @return a <code>ResultSet</code> object in which a row gives information
* about the designated UDT
* @throws SQLException if a database access error occurs
*/
public ResultSet getSuperTypes(
String catalog,
String schemaPattern,
String typeNamePattern
) throws SQLException
{
String cat = (String)(getEnvMap().get("gdk_dbname"));
String query =
"SELECT '" + cat + "' AS \"TYPE_CAT\", '' AS \"TYPE_SCHEM\", '' AS \"TYPE_NAME\", " +
"'' AS \"SUPERTYPE_CAT\", '' AS \"SUPERTYPE_SCHEM\", " +
"'' AS \"SUPERTYPE_NAME\" WHERE 1 = 0";
return(getStmt().executeQuery(query));
}
/**
* Retrieves a description of the table hierarchies defined in a particular
* schema in this database.
*
* <P>Only supertable information for tables matching the catalog, schema
* and table name are returned. The table name parameter may be a fully-
* qualified name, in which case, the catalog and schemaPattern parameters
* are ignored. If a table does not have a super table, it is not listed here.
* Supertables have to be defined in the same catalog and schema as the
* sub tables. Therefore, the type description does not need to include
* this information for the supertable.
*
* <P>Each type description has the following columns:
* <OL>
* <LI><B>TABLE_CAT</B> String => the type's catalog (may be <code>null</code>)
* <LI><B>TABLE_SCHEM</B> String => type's schema (may be <code>null</code>)
* <LI><B>TABLE_NAME</B> String => type name
* <LI><B>SUPERTABLE_NAME</B> String => the direct super type's name
* </OL>
*
* <P><B>Note:</B> If the driver does not support type hierarchies, an
* empty result set is returned.
*
* @param catalog a catalog name; "" retrieves those without a catalog;
* <code>null</code> means drop catalog name from the selection criteria
* @param schemaPattern a schema name pattern; "" retrieves those
* without a schema
* @param tableNamePattern a table name pattern; may be a fully-qualified
* name
* @return a <code>ResultSet</code> object in which each row is a type description
* @throws SQLException if a database access error occurs
*/
public ResultSet getSuperTables(
String catalog,
String schemaPattern,
String tableNamePattern
) throws SQLException
{
String cat = (String)(getEnvMap().get("gdk_dbname"));
String query =
"SELECT '" + cat + "' AS \"TABLE_CAT\", '' AS \"TABLE_SCHEM\", '' AS \"TABLE_NAME\", " +
"'' AS \"SUPERTABLE_NAME\" WHERE 1 = 0";
return(getStmt().executeQuery(query));
}
/**
* Retrieves a description of the given attribute of the given type
* for a user-defined type (UDT) that is available in the given schema
* and catalog.
* <P>
* Descriptions are returned only for attributes of UDTs matching the
* catalog, schema, type, and attribute name criteria. They are ordered by
* TYPE_SCHEM, TYPE_NAME and ORDINAL_POSITION. This description
* does not contain inherited attributes.
* <P>
* The <code>ResultSet</code> object that is returned has the following
* columns:
* <OL>
* <LI><B>TYPE_CAT</B> String => type catalog (may be <code>null</code>)
* <LI><B>TYPE_SCHEM</B> String => type schema (may be <code>null</code>)
* <LI><B>TYPE_NAME</B> String => type name
* <LI><B>ATTR_NAME</B> String => attribute name
* <LI><B>DATA_TYPE</B> short => attribute type SQL type from java.sql.Types
* <LI><B>ATTR_TYPE_NAME</B> String => Data source dependent type name.
* For a UDT, the type name is fully qualified. For a REF, the type name is
* fully qualified and represents the target type of the reference type.
* <LI><B>ATTR_SIZE</B> int => column size. For char or date
* types this is the maximum number of characters; for numeric or
* decimal types this is precision.
* <LI><B>DECIMAL_DIGITS</B> int => the number of fractional digits
* <LI><B>NUM_PREC_RADIX</B> int => Radix (typically either 10 or 2)
* <LI><B>NULLABLE</B> int => whether NULL is allowed
* <UL>
* <LI> attributeNoNulls - might not allow NULL values
* <LI> attributeNullable - definitely allows NULL values
* <LI> attributeNullableUnknown - nullability unknown
* </UL>
* <LI><B>REMARKS</B> String => comment describing column (may be <code>null</code>)
* <LI><B>ATTR_DEF</B> String => default value (may be <code>null</code>)
* <LI><B>SQL_DATA_TYPE</B> int => unused
* <LI><B>SQL_DATETIME_SUB</B> int => unused
* <LI><B>CHAR_OCTET_LENGTH</B> int => for char types the
* maximum number of bytes in the column
* <LI><B>ORDINAL_POSITION</B> int => index of column in table
* (starting at 1)
* <LI><B>IS_NULLABLE</B> String => "NO" means column definitely
* does not allow NULL values; "YES" means the column might
* allow NULL values. An empty string means unknown.
* <LI><B>SCOPE_CATALOG</B> String => catalog of table that is the
* scope of a reference attribute (<code>null</code> if DATA_TYPE isn't REF)
* <LI><B>SCOPE_SCHEMA</B> String => schema of table that is the
* scope of a reference attribute (<code>null</code> if DATA_TYPE isn't REF)
* <LI><B>SCOPE_TABLE</B> String => table name that is the scope of a
* reference attribute (<code>null</code> if the DATA_TYPE isn't REF)
* <LI><B>SOURCE_DATA_TYPE</B> short => source type of a distinct type or user-generated
* Ref type,SQL type from java.sql.Types (<code>null</code> if DATA_TYPE
* isn't DISTINCT or user-generated REF)
* </OL>
* @param catalog a catalog name; must match the catalog name as it
* is stored in the database; "" retrieves those without a catalog;
* <code>null</code> means that the catalog name should not be used to narrow
* the search
* @param schemaPattern a schema name pattern; must match the schema name
* as it is stored in the database; "" retrieves those without a schema;
* <code>null</code> means that the schema name should not be used to narrow
* the search
* @param typeNamePattern a type name pattern; must match the
* type name as it is stored in the database
* @param attributeNamePattern an attribute name pattern; must match the attribute
* name as it is declared in the database
* @return a <code>ResultSet</code> object in which each row is an
* attribute description
* @throws SQLException if a database access error occurs
*/
public ResultSet getAttributes(
String catalog,
String schemaPattern,
String typeNamePattern,
String attributeNamePattern
) throws SQLException
{
String cat = (String)(getEnvMap().get("gdk_dbname"));
String query =
"SELECT '" + cat + "' AS \"TYPE_CAT\", '' AS \"TYPE_SCHEM\", '' AS \"TYPE_NAME\", " +
"'' AS \"ATTR_NAME\", '' AS \"ATTR_TYPE_NAME\", 0 AS \"ATTR_SIZE\", " +
"0 AS \"DECIMAL_DIGITS\", 0 AS \"NUM_PREC_RADIX\", 0 AS \"NULLABLE\", " +
"'' AS \"REMARKS\", '' AS \"ATTR_DEF\", 0 AS \"SQL_DATA_TYPE\", " +
"0 AS \"SQL_DATETIME_SUB\", 0 AS \"CHAR_OCTET_LENGTH\", " +
"0 AS \"ORDINAL_POSITION\", 'YES' AS \"IS_NULLABLE\", " +
"'' AS \"SCOPE_CATALOG\", '' AS \"SCOPE_SCHEMA\", '' AS \"SCOPE_TABLE\", " +
"0 AS \"SOURCE_DATA_TYPE\" WHERE 1 = 0";
return(getStmt().executeQuery(query));
}
/**
* Retrieves whether this database supports the given result set holdability.
*
* @param holdability one of the following constants:
* <code>ResultSet.HOLD_CURSORS_OVER_COMMIT</code> or
* <code>ResultSet.CLOSE_CURSORS_AT_COMMIT<code>
* @return <code>true</code> if so; <code>false</code> otherwise
* @see Connection
*/
public boolean supportsResultSetHoldability(int holdability) {
// we don't close ResultSets at commit; and we don't do updateable
// result sets, so comes closest to hold cursors over commit
return(holdability == ResultSet.HOLD_CURSORS_OVER_COMMIT);
}
/**
* Retrieves the default holdability of this <code>ResultSet</code>
* object.
*
* @return the default holdability; either
* <code>ResultSet.HOLD_CURSORS_OVER_COMMIT</code> or
* <code>ResultSet.CLOSE_CURSORS_AT_COMMIT</code>
*/
public int getResultSetHoldability() {
return(ResultSet.HOLD_CURSORS_OVER_COMMIT);
}
/**
* Retrieves the major version number of the underlying database.
*
* @return the underlying database's major version
* @throws SQLException if a database access error occurs
*/
public int getDatabaseMajorVersion() throws SQLException {
Map env = getEnvMap();
String version = (String)env.get("gdk_version");
int major = 0;
try {
major = Integer.parseInt(version.substring(0, version.indexOf(".")));
} catch (NumberFormatException e) {
// baaaaaaaaaa
}
return(major);
}
/**
* Retrieves the minor version number of the underlying database.
*
* @return underlying database's minor version
* @throws SQLException if a database access error occurs
*/
public int getDatabaseMinorVersion() throws SQLException {
Map env = getEnvMap();
String version = (String)env.get("gdk_version");
int minor = 0;
try {
int start = version.indexOf(".");
minor = Integer.parseInt(version.substring(start + 1, version.indexOf(".", start + 1)));
} catch (NumberFormatException e) {
// baaaaaaaaaa
}
return(minor);
}
/**
* Retrieves the major JDBC version number for this
* driver.
*
* @return JDBC version major number
*/
public int getJDBCMajorVersion() {
return(3); // This class implements JDBC 3.0 (at least we try to)
}
/**
* Retrieves the minor JDBC version number for this
* driver.
*
* @return JDBC version minor number
*/
public int getJDBCMinorVersion() {
return(0); // This class implements JDBC 3.0 (at least we try to)
}
/**
* Indicates whether the SQLSTATEs returned by <code>SQLException.getSQLState</code>
* is X/Open (now known as Open Group) SQL CLI or SQL99.
* @return the type of SQLSTATEs, one of:
* sqlStateXOpen or
* sqlStateSQL99
*/
public int getSQLStateType() {
// we conform to the SQL99 standard, so...
return(DatabaseMetaData.sqlStateSQL99);
}
/**
* Indicates whether updates made to a LOB are made on a copy or directly
* to the LOB.
* @return <code>true</code> if updates are made to a copy of the LOB;
* <code>false</code> if updates are made directly to the LOB
*/
public boolean locatorsUpdateCopy() {
// not that we have it, but in a transaction it will be copy-on-write
return(true);
}
/**
* Retrieves whether this database supports statement pooling.
*
* @return <code>true</code> is so;
<code>false</code> otherwise
*/
public boolean supportsStatementPooling() {
// For the moment, I don't think so
return(false);
}
//== end methods interface DatabaseMetaData
/**
* make sure our related statement is closed upon garbage collect
*/
protected void finalize() throws Throwable {
try {
if (stmt != null) stmt.close();
} catch (SQLException e) { /* ignore */ }
super.finalize();
}
}
/**
* This class is not intended for normal use. Therefore it is restricted to
* classes from the very same package only. Because it is used only in the
* MonetDatabaseMetaData class it is placed here.
*
* Any use of this class is disencouraged.
*/
class MonetVirtualResultSet extends MonetResultSet {
private String results[][];
private boolean closed;
MonetVirtualResultSet(
String[] columns,
String[] types,
String[][] results
) throws IllegalArgumentException {
super(columns, types, results.length);
this.results = results;
closed = false;
}
/**
* This method is overridden in order to let it use the results array
* instead of the cache in the Statement object that created it.
*
* @param row the number of the row to which the cursor should move. A
* positive number indicates the row number counting from the
* beginning of the result set; a negative number indicates the row
* number counting from the end of the result set
* @return true if the cursor is on the result set; false otherwise
* @throws SQLException if a database error occurs
*/
public boolean absolute(int row) throws SQLException {
if (closed) throw new SQLException("ResultSet is closed!");
// first calculate what the JDBC row is
if (row < 0) {
// calculate the negatives...
row = tupleCount + row + 1;
}
// now place the row not farther than just before or after the result
if (row < 0) row = 0; // before first
else if (row > tupleCount + 1) row = tupleCount + 1; // after last
// store it
curRow = row;
// see if we have the row
if (row < 1 || row > tupleCount) return(false);
result = results[row - 1];
return(true);
}
/**
* Mainly here to prevent errors when the close method is called. There
* is no real need for this object to close it. We simply remove our
* resultset data.
*/
public void close() {
if (!closed) {
closed = true;
results = null;
// types and columns are MonetResultSets private parts
}
}
/**
* Retrieves the fetch size for this ResultSet object, which will be
* zero, since it's a virtual set.
*
* @return the current fetch size for this ResultSet object
* @throws SQLException if a database access error occurs
*/
public int getFetchSize() throws SQLException {
return(0);
}
} |
public class Test{
//This is just a comment
public static void main(String[] args){
System.out.println("Hello World!!");
}
} |
package com.experitest.auto;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.IOException;
import java.lang.reflect.Method;
import java.net.URL;
import java.util.Properties;
import org.openqa.selenium.Capabilities;
import org.openqa.selenium.remote.DesiredCapabilities;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
import io.appium.java_client.AppiumDriver;
import io.appium.java_client.ios.IOSDriver;
import io.appium.java_client.ios.IOSElement;
import io.appium.java_client.remote.IOSMobileCapabilityType;
import io.appium.java_client.remote.MobileCapabilityType;
public class BaseTest {
public static String buildId = System.getenv("BUILD_NUMBER");
public static String accessKey = System.getenv("access.key");
public static String deviceQuery = System.getenv("device.query");
protected IOSDriver<IOSElement> driver = null;
protected DesiredCapabilities dc = new DesiredCapabilities();
public void init(String deviceQuery) throws Exception {
initCloudProperties();
dc.setCapability("deviceQuery", adhocDevice(deviceQuery));
String cname = className.split("\\.")[className.split("\\.").length - 1];
dc.setCapability("testName", cname + "." + testName);
dc.setCapability("build", String.valueOf(getBuild()));
dc.setCapability(MobileCapabilityType.ORIENTATION, "portrait");
//dc.setCapability(MobileCapabilityType.APP, "cloud:com.experitest.ExperiBank");
//dc.setCapability(IOSMobileCapabilityType.BUNDLE_ID, "com.experitest.ExperiBank");
dc.setCapability("accessKey", accessKey);
dc.setCapability("autoAcceptAlerts", true);
dc.setCapability("stream", "demo4");
dc.setCapability("reportDirectory", "reports");
dc.setCapability("reportFormat", "xml");
dc.setCapability("project", getProperty("project", cloudProperties));
dc.setCapability("instrumentApp", true);
driver = new IOSDriver<>(new URL("https://stage.experitest.com/wd/hub"), dc);
Thread.sleep(2000);
driver.executeScript("client:client.install(\"cloud:com.experitest.ExperiBank\", true, false);");
driver.executeScript("client:client.launch(\"com.experitest.ExperiBank\", true, true);");
}
protected String getProperty(String property, Properties props) throws FileNotFoundException, IOException {
if (System.getProperty(property) != null) {
return System.getProperty(property);
} else if (System.getenv().containsKey(property)) {
return System.getenv(property);
} else if (props != null) {
return props.getProperty(property);
}
return null;
}
protected Properties cloudProperties = new Properties();
String testName = "unknown";
String className = "unknown";
@BeforeMethod
public void handleTestMethodName(Method method)
{
testName = method.getName();
}
@BeforeClass
public void beforeClass() {
className = this.getClass().getName();
}
private void initCloudProperties() throws FileNotFoundException, IOException {
FileReader fr = new FileReader("cloud.properties");
cloudProperties.load(fr);
fr.close();
}
private static synchronized String adhocDevice(String deviceQuery) {
try {
File jarLocation = (System.getProperty("os.name").toUpperCase().contains("WIN"))
? new File(System.getenv("APPDATA"), ".mobiledata")
: new File(System.getProperty("user.home") + "/Library/Application " + "Support", ".mobiledata");
File adhocProperties = new File(jarLocation, "adhoc.properties");
if (adhocProperties.exists()) {
Properties prop = new Properties();
FileReader reader = new FileReader(adhocProperties);
try {
prop.load(reader);
} finally {
reader.close();
}
adhocProperties.delete();
return "@serialnumber='" + prop.getProperty("serial") + "'";
}
} catch (Exception e) {
e.printStackTrace();
}
return deviceQuery;
}
public synchronized static String getBuild() {
if(buildId == null) {
buildId = "-1";
}
return buildId;
}
public void shouldFailTest(AppiumDriver<?> driver) {
Capabilities c = driver.getCapabilities();
try {
Thread.sleep(5000);
} catch (InterruptedException e) {
e.printStackTrace();
}
// if("11.x".equals(c.getCapability("device.majorVersion"))) { |
package org.collectionspace.chain.csp.persistence.services.user;
import java.io.IOException;
import java.io.UnsupportedEncodingException;
import java.net.URLDecoder;
import java.net.URLEncoder;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Set;
import org.collectionspace.chain.csp.persistence.services.XmlJsonConversion;
import org.collectionspace.chain.csp.persistence.services.connection.ConnectionException;
import org.collectionspace.chain.csp.persistence.services.connection.RequestMethod;
import org.collectionspace.chain.csp.persistence.services.connection.ReturnedDocument;
import org.collectionspace.chain.csp.persistence.services.connection.ReturnedMultipartDocument;
import org.collectionspace.chain.csp.persistence.services.connection.ReturnedURL;
import org.collectionspace.chain.csp.persistence.services.connection.ServicesConnection;
import org.collectionspace.chain.csp.persistence.services.vocab.URNProcessor;
import org.collectionspace.chain.csp.schema.Field;
import org.collectionspace.chain.csp.schema.FieldSet;
import org.collectionspace.chain.csp.schema.Record;
import org.collectionspace.csp.api.core.CSPRequestCache;
import org.collectionspace.csp.api.core.CSPRequestCredentials;
import org.collectionspace.csp.api.persistence.ExistException;
import org.collectionspace.csp.api.persistence.Storage;
import org.collectionspace.csp.api.persistence.UnderlyingStorageException;
import org.collectionspace.csp.api.persistence.UnimplementedException;
import org.collectionspace.csp.helper.persistence.ContextualisedStorage;
import org.dom4j.Document;
import org.dom4j.DocumentException;
import org.dom4j.Element;
import org.dom4j.Node;
import org.json.JSONException;
import org.json.JSONObject;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.sun.org.apache.xerces.internal.impl.dv.util.Base64;
/** Implements user service connection over service layer. Generally simply a much simpler version of regular record storage, but also uses non-multiparts.
*
* @author dan
*
*/
public class UserStorage implements ContextualisedStorage {
private static final Logger log=LoggerFactory.getLogger(UserStorage.class);
private ServicesConnection conn;
private Record r;
private Map<String,String> view_good=new HashMap<String,String>();
private Map<String,String> view_map=new HashMap<String,String>();
private Set<String> xxx_view_deurn=new HashSet<String>();
public UserStorage(Record r,ServicesConnection conn) throws DocumentException, IOException {
this.conn=conn;
this.r=r;
}
private void setGleanedValue(CSPRequestCache cache,String path,String key,String value) {
cache.setCached(getClass(),new String[]{"glean",path,key},value);
}
private String getGleanedValue(CSPRequestCache cache,String path,String key) {
return (String)cache.getCached(getClass(),new String[]{"glean",path,key});
}
private JSONObject correctPassword(JSONObject in) throws JSONException, UnderlyingStorageException {
try {
if(in.has("password")){
String password=in.getString("password");
in.remove("password");
password=Base64.encode(password.getBytes("UTF-8"));
while(password.endsWith("\n") || password.endsWith("\r"))
password=password.substring(0,password.length()-1);
in.put("password",password);
}
return in;
} catch (UnsupportedEncodingException e) {
throw new UnderlyingStorageException("Error generating Base 64",e);
}
}
/* XXX FIXME in here until we fix the UI layer to pass the data correctly */
private JSONObject correctScreenName(JSONObject in) throws JSONException, UnderlyingStorageException {
if(in.has("userName") && !in.has("screenName")){
String username=in.getString("userName");
in.remove("userName");
in.put("screenName",username);
}
return in;
}
/* XXX FIXME in here until we fix the UI layer to pass the data correctly */
private JSONObject correctUserId(JSONObject in) throws JSONException, UnderlyingStorageException {
if(!in.has("userId")){
String userId=in.getString("email");
in.remove("userId");
in.put("userId",userId);
}
return in;
}
public String autocreateJSON(ContextualisedStorage root,CSPRequestCredentials creds,CSPRequestCache cache,String filePath, JSONObject jsonObject) throws ExistException, UnimplementedException, UnderlyingStorageException {
try {
jsonObject=correctPassword(jsonObject);
jsonObject= correctScreenName(jsonObject);
jsonObject= correctUserId(jsonObject);
Document doc=XmlJsonConversion.convertToXml(r,jsonObject,"common");
ReturnedURL url = conn.getURL(RequestMethod.POST,r.getServicesURL()+"/",doc,creds,cache);
if(url.getStatus()>299 || url.getStatus()<200)
throw new UnderlyingStorageException("Bad response "+url.getStatus());
return url.getURLTail();
} catch (ConnectionException e) {
throw new UnderlyingStorageException("Service layer exception",e);
} catch (JSONException e) {
throw new UnimplementedException("JSONException",e);
}
}
public void createJSON(ContextualisedStorage root,CSPRequestCredentials creds,CSPRequestCache cache,String filePath, JSONObject jsonObject)
throws ExistException, UnimplementedException, UnderlyingStorageException {
throw new UnimplementedException("Cannot post to full path");
}
public void deleteJSON(ContextualisedStorage root,CSPRequestCredentials creds,CSPRequestCache cache,String filePath) throws ExistException,
UnimplementedException, UnderlyingStorageException {
try {
int status=conn.getNone(RequestMethod.DELETE,r.getServicesURL()+"/"+filePath,null,creds,cache);
if(status>299 || status<200) // XXX CSPACE-73, should be 404
throw new UnderlyingStorageException("Service layer exception status="+status);
} catch (ConnectionException e) {
throw new UnderlyingStorageException("Service layer exception",e);
}
}
@SuppressWarnings("unchecked")
public String[] getPaths(ContextualisedStorage root,CSPRequestCredentials creds,CSPRequestCache cache,String rootPath,JSONObject restrictions) throws ExistException, UnimplementedException, UnderlyingStorageException {
try {
List<String> out=new ArrayList<String>();
Iterator rit=restrictions.keys();
StringBuffer args=new StringBuffer();
while(rit.hasNext()) {
String key=(String)rit.next();
FieldSet fs=r.getField(key);
if(!(fs instanceof Field))
continue;
String filter=((Field)fs).getServicesFilterParam();
if(filter==null)
continue;
args.append('&');
args.append(filter);
args.append('=');
args.append(URLEncoder.encode(restrictions.getString(key),"UTF-8"));
}
//pagination
String url=r.getServicesURL()+"/";
String postfix = "?";
String tail=args.toString();
if(tail.length()>0) {
postfix += tail.substring(1) +"&";
}
if(restrictions!=null){
if(restrictions.has("pageSize")){
postfix += "pgSz="+restrictions.getString("pageSize")+"&";
}
if(restrictions.has("pageNum")){
postfix += "pgNum="+restrictions.getString("pageNum")+"&";
}
}
postfix = postfix.substring(0, postfix.length()-1);
ReturnedDocument doc=conn.getXMLDocument(RequestMethod.GET,r.getServicesURL()+"/"+postfix,null,creds,cache);
if(doc.getStatus()<200 || doc.getStatus()>399)
throw new UnderlyingStorageException("Cannot retrieve account list");
Document list=doc.getDocument();
List<Node> objects=list.selectNodes(r.getServicesListPath());
for(Node object : objects) {
List<Node> fields=object.selectNodes("*");
String csid=object.selectSingleNode("csid").getText();
for(Node field : fields) {
if("csid".equals(field.getName())) {
int idx=csid.lastIndexOf("/");
if(idx!=-1)
csid=csid.substring(idx+1);
out.add(csid);
} else if("uri".equals(field.getName())) {
// Skip!
} else {
String json_name=view_map.get(field.getName());
if(json_name!=null) {
String value=field.getText();
// XXX hack to cope with multi values
if(value==null || "".equals(value)) {
List<Node> inners=field.selectNodes("*");
for(Node n : inners) {
value+=n.getText();
}
}
setGleanedValue(cache,r.getServicesURL()+"/"+csid,json_name,value);
}
}
}
}
return out.toArray(new String[0]);
} catch (ConnectionException e) {
throw new UnderlyingStorageException("Service layer exception",e);
} catch (UnsupportedEncodingException e) {
throw new UnderlyingStorageException("Exception building query",e);
} catch (JSONException e) {
throw new UnderlyingStorageException("Exception building query",e);
}
}
// XXX support URNs for reference
private JSONObject miniForURI(ContextualisedStorage storage,CSPRequestCredentials creds,CSPRequestCache cache,String refname,String uri) throws ExistException, UnimplementedException, UnderlyingStorageException, JSONException {
return storage.retrieveJSON(storage,creds,cache,"direct/urn/"+uri+"/"+refname);
}
public JSONObject refViewRetrieveJSON(ContextualisedStorage storage,CSPRequestCredentials creds,CSPRequestCache cache,String filePath) throws ExistException,UnimplementedException, UnderlyingStorageException, JSONException {
try {
ReturnedDocument all = conn.getXMLDocument(RequestMethod.GET,r.getServicesURL()+"/"+filePath+"/authorityrefs",null,creds,cache);
if(all.getStatus()!=200)
throw new ConnectionException("Bad request during identifier cache map update: status not 200");
Document list=all.getDocument();
JSONObject out=new JSONObject();
for(Object node : list.selectNodes("authority-ref-list/authority-ref-item")) {
if(!(node instanceof Element))
continue;
String key=((Element)node).selectSingleNode("sourceField").getText();
String uri=((Element)node).selectSingleNode("uri").getText();
String refname=((Element)node).selectSingleNode("refName").getText();
if(uri!=null && uri.startsWith("/"))
uri=uri.substring(1);
JSONObject data=miniForURI(storage,creds,cache,refname,uri);
out.put(key,data);
}
return out;
} catch (ConnectionException e) {
throw new UnderlyingStorageException("Connection problem",e);
}
}
public JSONObject retrieveJSON(ContextualisedStorage root,CSPRequestCredentials creds,CSPRequestCache cache,String filePath) throws ExistException,
UnimplementedException, UnderlyingStorageException {
try {
ReturnedDocument doc = conn.getXMLDocument(RequestMethod.GET,r.getServicesURL()+"/"+filePath,null,creds,cache);
JSONObject out=new JSONObject();
if((doc.getStatus()<200 || doc.getStatus()>=300))
throw new ExistException("Does not exist "+filePath);
out=XmlJsonConversion.convertToJson(r,doc.getDocument());
return out;
} catch (ConnectionException e) {
throw new UnderlyingStorageException("Service layer exception",e);
} catch (JSONException e) {
throw new UnderlyingStorageException("Service layer exception",e);
}
}
private JSONObject xxx_cspace1458_fix(String filePath,JSONObject in,CSPRequestCredentials creds,CSPRequestCache cache) throws ConnectionException, UnderlyingStorageException, JSONException {
// We need to also specify status and createdAt (revealed by GET) because of CSPACE-1458.
ReturnedDocument doc = conn.getXMLDocument(RequestMethod.GET,r.getServicesURL()+"/"+filePath,null,creds,cache);
if(doc.getStatus()>299 || doc.getStatus()<200)
throw new UnderlyingStorageException("Bad response "+doc.getStatus());
System.err.println(doc.getDocument().asXML());
String created_at=doc.getDocument().selectSingleNode("accounts_common/createdAt").getText();
String status=doc.getDocument().selectSingleNode("accounts_common/status").getText();
in.put("createdAt",created_at);
if(!in.has("status"))
in.put("status",status);
//in.remove("password");
return in;
}
public void updateJSON(ContextualisedStorage root,CSPRequestCredentials creds,CSPRequestCache cache,String filePath, JSONObject jsonObject)
throws ExistException, UnimplementedException, UnderlyingStorageException {
try {
// XXX when CSPACE-1458 is fixed, remove the call to xxx_cspace1458_fix, and just pass jsonObject as this arg. (fao Chris or somoeone else at CARET).
jsonObject=correctPassword(jsonObject);
Document in=XmlJsonConversion.convertToXml(r,xxx_cspace1458_fix(filePath,jsonObject,creds,cache),"common");
System.err.println("Sending: "+in.asXML());
ReturnedDocument doc = conn.getXMLDocument(RequestMethod.PUT,r.getServicesURL()+"/"+filePath,in,creds,cache);
if(doc.getStatus()==404)
throw new ExistException("Not found: "+r.getServicesURL()+"/"+filePath);
if(doc.getStatus()>299 || doc.getStatus()<200)
throw new UnderlyingStorageException("Bad response "+doc.getStatus());
} catch (ConnectionException e) {
throw new UnderlyingStorageException("Service layer exception",e);
} catch (JSONException e) {
throw new UnimplementedException("JSONException",e);
}
}
} |
package gov.cdc.sdp.cbr;
import static org.junit.Assert.*;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.IOException;
import java.io.LineNumberReader;
import java.sql.ResultSet;
import java.util.List;
import java.util.Map;
import javax.sql.DataSource;
import org.apache.camel.CamelContext;
import org.apache.camel.EndpointInject;
import org.apache.camel.Exchange;
import org.apache.camel.Message;
import org.apache.camel.Produce;
import org.apache.camel.ProducerTemplate;
import org.apache.camel.component.mock.MockEndpoint;
import org.apache.camel.impl.DefaultExchange;
import org.apache.camel.impl.DefaultMessage;
import org.apache.camel.test.spring.CamelSpringJUnit4ClassRunner;
import org.apache.camel.test.spring.CamelTestContextBootstrapper;
import org.junit.Test;
import org.junit.runner.RunWith;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.annotation.PropertySource;
import org.springframework.jdbc.core.JdbcTemplate;
import org.springframework.test.context.BootstrapWith;
import org.springframework.test.context.ContextConfiguration;
@RunWith(CamelSpringJUnit4ClassRunner.class)
@BootstrapWith(CamelTestContextBootstrapper.class)
@ContextConfiguration(locations = { "classpath:PhinMSDBTest-context.xml" })
@PropertySource("classpath:application.properties")
public class PhinMSDBTest {
@Autowired
protected CamelContext camelContext;
@EndpointInject(uri = "mock:phinmsDb")
protected MockEndpoint phinMSDb;
@Produce(uri = "direct:phinms")
protected ProducerTemplate template;
private final String file_name = "phinms_input.csv";
private final String input_file_path = "src/test/resources/" + file_name;
@Test
public void testPhinMSProducer() {
MockEndpoint.resetMocks(camelContext);
JdbcTemplate jdbcTemplate = null;
int count = -1;
try {
DataSource ds = (DataSource) camelContext.getRegistry().lookupByName("phinMSDataSource");
jdbcTemplate = new JdbcTemplate(ds);
count = jdbcTemplate.queryForObject("select count(*) from message_inq", Integer.class);
Exchange exchange = new DefaultExchange(camelContext);
Message msg = new DefaultMessage();
String expected_content = readFile(input_file_path);
msg.setBody(expected_content);
exchange.setIn(msg);
phinMSDb.expectedMessageCount(1);
template.send(exchange);
MockEndpoint.assertIsSatisfied(camelContext);
int linesInFile = getLinesInFile(input_file_path);
int countDelta = jdbcTemplate.queryForObject("select count(*) from message_inq", Integer.class) - count;
assertEquals(linesInFile-1, countDelta);
} catch (IOException e) {
fail("Could not read input file");
} catch (InterruptedException e) {
fail("Interrupted Exception thrown");
} finally {
if (jdbcTemplate != null) {
jdbcTemplate.execute("DELETE from message_inq where fromPartyId='testPhinMS_Producer'");
if (count > 0) {
assertEquals(count, (int)jdbcTemplate.queryForObject("select count(*) from message_inq", Integer.class));
}
}
}
}
@Test
public void testPhinMSProducerMultiLine() {
MockEndpoint.resetMocks(camelContext);
JdbcTemplate jdbcTemplate = null;
int count = -1;
try {
DataSource ds = (DataSource) camelContext.getRegistry().lookupByName("phinMSDataSource");
jdbcTemplate = new JdbcTemplate(ds);
count = jdbcTemplate.queryForObject("select count(*) from message_inq", Integer.class);
String fileName = "phinms_input_multi.csv";
String inputFilePath = "src/test/resources/" + fileName;
Exchange exchange = new DefaultExchange(camelContext);
Message msg = new DefaultMessage();
String expected_content = readFile(inputFilePath);
msg.setBody(expected_content);
exchange.setIn(msg);
phinMSDb.expectedMessageCount(1);
template.send(exchange);
MockEndpoint.assertIsSatisfied(camelContext);
int countDelta = jdbcTemplate.queryForObject("select count(*) from message_inq", Integer.class) - count;
assertEquals(13, countDelta);
} catch (IOException e) {
fail("Could not read input file");
} catch (InterruptedException e) {
fail("Interrupted Exception thrown");
} finally {
if (jdbcTemplate != null) {
jdbcTemplate.execute("DELETE from message_inq where fromPartyId='TEST'");
if (count > 0) {
assertEquals(count, (int)jdbcTemplate.queryForObject("select count(*) from message_inq", Integer.class));
}
}
}
}
private String readFile(String file) throws IOException {
return new String(java.nio.file.Files.readAllBytes(java.nio.file.Paths.get(file)));
}
private int getLinesInFile(String file) throws IOException {
LineNumberReader lnr = null;
try {
lnr = new LineNumberReader(new FileReader(new File(file)));
lnr.skip(Long.MAX_VALUE);
int lines = lnr.getLineNumber();
return lines;
} finally {
if (lnr != null)
lnr.close();
}
}
} |
package jcifs.tests;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNull;
import java.net.MalformedURLException;
import java.net.UnknownHostException;
import org.junit.Test;
import jcifs.CIFSContext;
import jcifs.CIFSException;
import jcifs.DfsReferralData;
import jcifs.SmbConstants;
import jcifs.SmbResource;
import jcifs.SmbResourceLocator;
import jcifs.config.BaseConfiguration;
import jcifs.context.BaseContext;
import jcifs.smb.SmbFile;
import jcifs.smb.SmbResourceLocatorInternal;
/**
* @author mbechler
*
*/
@SuppressWarnings ( "javadoc" )
public class FileLocationTest {
@Test
public void testRoot () throws MalformedURLException, CIFSException {
try ( SmbResource p = new SmbFile("smb://", getContext()) ) {
SmbResourceLocator fl = p.getLocator();
assertNull(fl.getServer());
assertNull(fl.getShare());
assertEquals(SmbConstants.TYPE_WORKGROUP, fl.getType());
assertEquals("\\", fl.getUNCPath());
assertEquals("smb://", fl.getCanonicalURL());
assertEquals("/", fl.getURLPath());
}
}
@Test
public void testEmpty () throws MalformedURLException, CIFSException {
try ( SmbResource p = new SmbFile("smb:", getContext()) ) {
SmbResourceLocator fl = p.getLocator();
assertNull(fl.getServer());
assertNull(fl.getShare());
assertEquals(SmbConstants.TYPE_WORKGROUP, fl.getType());
assertEquals("\\", fl.getUNCPath());
assertEquals("smb://", fl.getCanonicalURL());
assertEquals("/", fl.getURLPath());
}
}
@Test
public void testChildHost () throws MalformedURLException, CIFSException, UnknownHostException {
try ( SmbFile p = new SmbFile("smb://", getContext());
SmbResource c = new SmbFile(p, "1.2.3.4") ) {
SmbResourceLocator fl = c.getLocator();
assertEquals("1.2.3.4", fl.getServer());
assertEquals(SmbConstants.TYPE_SERVER, fl.getType());
assertNull(fl.getShare());
assertEquals("\\", fl.getUNCPath());
assertEquals("smb://1.2.3.4/", fl.getCanonicalURL());
assertEquals("/", fl.getURLPath());
}
}
@Test
public void testChildShare () throws MalformedURLException, CIFSException, UnknownHostException {
try ( SmbFile p = new SmbFile("smb://1.2.3.4/", getContext());
SmbResource c = new SmbFile(p, "share/") ) {
SmbResourceLocator fl = c.getLocator();
assertEquals("1.2.3.4", fl.getServer());
assertEquals(SmbConstants.TYPE_SHARE, fl.getType());
assertEquals("share", fl.getShare());
assertEquals("\\", fl.getUNCPath());
assertEquals("smb://1.2.3.4/share/", fl.getCanonicalURL());
assertEquals("/share/", fl.getURLPath());
}
}
@Test
public void testChildShareCombined () throws MalformedURLException, CIFSException, UnknownHostException {
try ( SmbFile p = new SmbFile("smb://", getContext());
SmbResource c = new SmbFile(p, "1.2.3.4/share/") ) {
SmbResourceLocator fl = c.getLocator();
assertEquals("1.2.3.4", fl.getServer());
assertEquals(SmbConstants.TYPE_SHARE, fl.getType());
assertEquals("share", fl.getShare());
assertEquals("\\", fl.getUNCPath());
assertEquals("smb://1.2.3.4/share/", fl.getCanonicalURL());
assertEquals("/share/", fl.getURLPath());
}
}
@Test
public void testChildPath () throws MalformedURLException, CIFSException, UnknownHostException {
try ( SmbFile p = new SmbFile("smb://1.2.3.4/share/", getContext());
SmbResource c = new SmbFile(p, "foo/") ) {
SmbResourceLocator fl = c.getLocator();
assertEquals("1.2.3.4", fl.getServer());
assertEquals(SmbConstants.TYPE_FILESYSTEM, fl.getType());
assertEquals("share", fl.getShare());
assertEquals("\\foo\\", fl.getUNCPath());
assertEquals("smb://1.2.3.4/share/foo/", fl.getCanonicalURL());
assertEquals("/share/foo/", fl.getURLPath());
}
}
@Test
public void testChildMultiPath () throws MalformedURLException, CIFSException, UnknownHostException {
try ( SmbFile p = new SmbFile("smb://1.2.3.4/share/", getContext());
SmbResource c = new SmbFile(p, "foo/bar/") ) {
SmbResourceLocator fl = c.getLocator();
assertEquals("1.2.3.4", fl.getServer());
assertEquals(SmbConstants.TYPE_FILESYSTEM, fl.getType());
assertEquals("share", fl.getShare());
assertEquals("\\foo\\bar\\", fl.getUNCPath());
assertEquals("smb://1.2.3.4/share/foo/bar/", fl.getCanonicalURL());
assertEquals("/share/foo/bar/", fl.getURLPath());
}
}
@Test
public void testChildPathCombined () throws MalformedURLException, CIFSException, UnknownHostException {
try ( SmbFile p = new SmbFile("smb://", getContext());
SmbResource c = new SmbFile(p, "1.2.3.4/share/foo/") ) {
SmbResourceLocator fl = c.getLocator();
assertEquals("1.2.3.4", fl.getServer());
assertEquals(SmbConstants.TYPE_FILESYSTEM, fl.getType());
assertEquals("share", fl.getShare());
assertEquals("\\foo\\", fl.getUNCPath());
assertEquals("smb://1.2.3.4/share/foo/", fl.getCanonicalURL());
assertEquals("/share/foo/", fl.getURLPath());
}
}
@Test
public void testParentRoot () throws MalformedURLException, CIFSException {
try ( SmbFile p = new SmbFile("smb://", getContext());
SmbResource pp = new SmbFile(p.getParent(), getContext()) ) {
assertEquals("smb://", p.getLocator().getParent());
assertEquals(SmbConstants.TYPE_WORKGROUP, pp.getLocator().getType());
assertNull(pp.getLocator().getServer());
assertNull(pp.getLocator().getShare());
}
}
@Test
public void testParentServer () throws MalformedURLException, CIFSException {
try ( SmbFile p = new SmbFile("smb://1.2.3.4/", getContext());
SmbResource pp = new SmbFile(p.getParent(), getContext()) ) {
assertEquals("smb://", p.getLocator().getParent());
SmbResourceLocator fl = pp.getLocator();
assertEquals(SmbConstants.TYPE_WORKGROUP, fl.getType());
assertNull(fl.getServer());
assertNull(fl.getShare());
}
}
@Test
public void testParentShare () throws MalformedURLException, CIFSException {
try ( SmbFile p = new SmbFile("smb://1.2.3.4/share/", getContext());
SmbResource pp = new SmbFile(p.getParent(), getContext()) ) {
assertEquals("smb://1.2.3.4/", p.getLocator().getParent());
SmbResourceLocator fl = pp.getLocator();
assertEquals(SmbConstants.TYPE_SERVER, fl.getType());
assertEquals("1.2.3.4", fl.getServer());
assertNull(fl.getShare());
assertEquals("\\", fl.getUNCPath());
assertEquals("/", fl.getURLPath());
}
}
@Test
public void testParentPath1 () throws MalformedURLException, CIFSException {
try ( SmbFile p = new SmbFile("smb://1.2.3.4/share/foo/", getContext());
SmbResource pp = new SmbFile(p.getParent(), getContext()) ) {
assertEquals("smb://1.2.3.4/share/", p.getLocator().getParent());
SmbResourceLocator fl = pp.getLocator();
assertEquals(SmbConstants.TYPE_SHARE, fl.getType());
assertEquals("1.2.3.4", fl.getServer());
assertEquals("share", fl.getShare());
assertEquals("\\", fl.getUNCPath());
assertEquals("/share/", fl.getURLPath());
}
}
@Test
public void testParentPath2 () throws MalformedURLException, CIFSException {
try ( SmbFile p = new SmbFile("smb://1.2.3.4/share/foo/bar/", getContext());
SmbResource pp = new SmbFile(p.getParent(), getContext()) ) {
assertEquals("smb://1.2.3.4/share/foo/", p.getLocator().getParent());
SmbResourceLocator fl = pp.getLocator();
assertEquals(SmbConstants.TYPE_FILESYSTEM, fl.getType());
assertEquals("1.2.3.4", fl.getServer());
assertEquals("share", fl.getShare());
assertEquals("\\foo\\", fl.getUNCPath());
assertEquals("/share/foo/", fl.getURLPath());
}
}
@Test
public void testDfsReferralServer () throws MalformedURLException, CIFSException {
try ( SmbResource p = new SmbFile("smb://1.2.3.4/share/foo/bar/", getContext()) ) {
DfsReferralData dr = new TestDfsReferral("2.3.4.5", null, "", 0);
String reqPath = "\\foo\\bar\\";
SmbResourceLocator fl = p.getLocator();
assertEquals(reqPath, ( (SmbResourceLocatorInternal) fl ).handleDFSReferral(dr, reqPath));
assertEquals("1.2.3.4", fl.getServer());
assertEquals("2.3.4.5", fl.getServerWithDfs());
assertEquals("share", fl.getShare());
assertEquals("\\foo\\bar\\", fl.getUNCPath());
assertEquals("/share/foo/bar/", fl.getURLPath());
}
}
@Test
public void testDfsReferralShare () throws MalformedURLException, CIFSException {
try ( SmbResource p = new SmbFile("smb://1.2.3.4/share/foo/bar/", getContext()) ) {
DfsReferralData dr = new TestDfsReferral("1.2.3.4", "other", "", 0);
String reqPath = "\\foo\\bar\\";
SmbResourceLocator fl = p.getLocator();
assertEquals(reqPath, ( (SmbResourceLocatorInternal) fl ).handleDFSReferral(dr, reqPath));
assertEquals("1.2.3.4", fl.getServer());
assertEquals("1.2.3.4", fl.getServerWithDfs());
assertEquals("other", fl.getShare());
assertEquals("\\foo\\bar\\", fl.getUNCPath());
// this intentionally sticks to the old name
assertEquals("/share/foo/bar/", fl.getURLPath());
}
}
@Test
public void testDfsReferralShareNested () throws MalformedURLException, CIFSException {
try ( SmbResource p = new SmbFile("smb://1.2.3.4/dfs/share/bar/", getContext()) ) {
DfsReferralData dr = new TestDfsReferral("1.2.3.4", "target", "", 6); // consumes the /share dfs root path
String reqPath = "\\share\\bar\\";
SmbResourceLocator fl = p.getLocator();
assertEquals("\\bar\\", ( (SmbResourceLocatorInternal) fl ).handleDFSReferral(dr, reqPath));
assertEquals("1.2.3.4", fl.getServer());
assertEquals("1.2.3.4", fl.getServerWithDfs());
assertEquals("target", fl.getShare());
assertEquals("\\bar\\", fl.getUNCPath());
// this intentionally sticks to the old name
assertEquals("/dfs/share/bar/", fl.getURLPath());
}
}
@Test
public void testDfsReferralAfterUncPath () throws MalformedURLException, CIFSException {
try ( SmbResource p = new SmbFile("smb://1.2.3.4/share/foo/bar/", getContext()) ) {
p.getLocator().getUNCPath();
DfsReferralData dr = new TestDfsReferral("1.2.3.5", "other", "", 0);
String reqPath = "\\foo\\bar\\";
SmbResourceLocator fl = p.getLocator();
assertEquals(reqPath, ( (SmbResourceLocatorInternal) fl ).handleDFSReferral(dr, reqPath));
assertEquals("1.2.3.4", fl.getServer());
assertEquals("1.2.3.5", fl.getServerWithDfs());
assertEquals("other", fl.getShare());
assertEquals("\\foo\\bar\\", fl.getUNCPath());
// this intentionally sticks to the old name
assertEquals("/share/foo/bar/", fl.getURLPath());
}
}
@Test
public void testDfsReferralChildResource () throws MalformedURLException, CIFSException {
try ( SmbResource p = new SmbFile("smb://1.2.3.4/share/foo/", getContext()) ) {
DfsReferralData dr = new TestDfsReferral("1.2.3.5", "other", "", 0);
String reqPath = "\\foo\\";
SmbResourceLocator fl = p.getLocator();
assertEquals(reqPath, ( (SmbResourceLocatorInternal) fl ).handleDFSReferral(dr, reqPath));
assertEquals("1.2.3.4", fl.getServer());
assertEquals("1.2.3.5", fl.getServerWithDfs());
assertEquals("other", fl.getShare());
assertEquals("\\foo\\", fl.getUNCPath());
// this intentionally sticks to the old name
assertEquals("/share/foo/", fl.getURLPath());
try ( SmbResource c = p.resolve("bar/") ) {
SmbResourceLocator fl2 = c.getLocator();
reqPath = fl2.getUNCPath();
assertEquals(reqPath, ( (SmbResourceLocatorInternal) fl2 ).handleDFSReferral(dr, reqPath));
}
}
}
@Test
public void testDfsReferralMultiLink () throws MalformedURLException, CIFSException {
try ( SmbResource p = new SmbFile("smb://1.2.3.4/share/foo/", getContext()) ) {
DfsReferralData dr = new TestDfsReferral("1.2.3.5", "otherdfs", "", 0);
String reqPath = "\\foo\\";
SmbResourceLocator fl = p.getLocator();
assertEquals(reqPath, ( (SmbResourceLocatorInternal) fl ).handleDFSReferral(dr, reqPath));
assertEquals("1.2.3.4", fl.getServer());
assertEquals("1.2.3.5", fl.getServerWithDfs());
assertEquals("otherdfs", fl.getShare());
assertEquals("\\foo\\", fl.getUNCPath());
// this intentionally sticks to the old name
assertEquals("/share/foo/", fl.getURLPath());
try ( SmbResource c = p.resolve("bar/") ) {
DfsReferralData dr2 = new TestDfsReferral("1.2.3.6", "target", "", 0);
SmbResourceLocator fl2 = c.getLocator();
reqPath = fl2.getUNCPath();
assertEquals(reqPath, ( (SmbResourceLocatorInternal) fl2 ).handleDFSReferral(dr2, reqPath));
assertEquals("1.2.3.4", fl2.getServer());
assertEquals("1.2.3.6", fl2.getServerWithDfs());
assertEquals("target", fl2.getShare());
assertEquals("\\foo\\bar\\", fl2.getUNCPath());
// this intentionally sticks to the old name
assertEquals("/share/foo/bar/", fl2.getURLPath());
}
}
}
// test case for
@Test ( expected = MalformedURLException.class )
public void testInvalid () throws MalformedURLException, CIFSException {
try ( SmbResource p = new SmbFile("smb:a", getContext()) ) {
p.getType();
}
}
//
@Test
public void testGetName () throws MalformedURLException, CIFSException {
try ( SmbResource p = new SmbFile("smb://MYSERVER/Public/MyVideo.mkv", getContext()) ) {
SmbResourceLocator fl = p.getLocator();
assertEquals("MYSERVER", fl.getServer());
assertEquals("MYSERVER", fl.getServerWithDfs());
assertEquals("Public", fl.getShare());
assertEquals("\\MyVideo.mkv", fl.getUNCPath());
assertEquals("/Public/MyVideo.mkv", fl.getURLPath());
assertEquals("MyVideo.mkv", p.getName());
}
}
//
@Test
public void testGetNameShare () throws MalformedURLException, CIFSException {
try ( SmbResource r = new SmbFile("smb://MYSERVER/Public/", getContext());
SmbResource p = r.resolve("MyVideo.mkv") ) {
SmbResourceLocator fl = p.getLocator();
assertEquals("MYSERVER", fl.getServer());
assertEquals("MYSERVER", fl.getServerWithDfs());
assertEquals("Public", fl.getShare());
assertEquals("\\MyVideo.mkv", fl.getUNCPath());
assertEquals("/Public/MyVideo.mkv", fl.getURLPath());
assertEquals("MyVideo.mkv", p.getName());
}
}
//
@Test
public void testGetNameServer () throws MalformedURLException, CIFSException {
try ( SmbResource r = new SmbFile("smb://0.0.0.0/", getContext());
SmbResource s = r.resolve("Public/");
SmbResource p = s.resolve("MyVideo.mkv"); ) {
SmbResourceLocator fl = p.getLocator();
assertEquals("0.0.0.0", fl.getServer());
assertEquals("0.0.0.0", fl.getServerWithDfs());
assertEquals("Public", fl.getShare());
assertEquals("\\MyVideo.mkv", fl.getUNCPath());
assertEquals("/Public/MyVideo.mkv", fl.getURLPath());
assertEquals("MyVideo.mkv", p.getName());
}
}
//
@Test
public void testIPCHidden () throws MalformedURLException, CIFSException {
try ( SmbResource r = new SmbFile("smb://0.0.0.0/IPC$/", getContext()) ) {
assert ( r.isHidden() );
}
}
private static class TestDfsReferral implements DfsReferralData {
private String server;
private String share;
private String path;
private int pathConsumed;
public TestDfsReferral ( String server, String share, String path, int pathConsumed ) {
this.server = server;
this.share = share;
this.path = path;
this.pathConsumed = pathConsumed;
}
/**
* {@inheritDoc}
*
* @see jcifs.DfsReferralData#unwrap(java.lang.Class)
*/
@SuppressWarnings ( "unchecked" )
@Override
public <T extends DfsReferralData> T unwrap ( Class<T> type ) {
if ( type.isAssignableFrom(this.getClass()) ) {
return (T) this;
}
throw new ClassCastException();
}
/**
* {@inheritDoc}
*
* @see jcifs.DfsReferralData#getServer()
*/
@Override
public String getServer () {
return this.server;
}
/**
* {@inheritDoc}
*
* @see jcifs.DfsReferralData#getDomain()
*/
@Override
public String getDomain () {
return null;
}
/**
* {@inheritDoc}
*
* @see jcifs.DfsReferralData#getLink()
*/
@Override
public String getLink () {
return null;
}
/**
* {@inheritDoc}
*
* @see jcifs.DfsReferralData#getShare()
*/
@Override
public String getShare () {
return this.share;
}
/**
* {@inheritDoc}
*
* @see jcifs.DfsReferralData#getPathConsumed()
*/
@Override
public int getPathConsumed () {
return this.pathConsumed;
}
/**
* {@inheritDoc}
*
* @see jcifs.DfsReferralData#getPath()
*/
@Override
public String getPath () {
return this.path;
}
/**
* {@inheritDoc}
*
* @see jcifs.DfsReferralData#getExpiration()
*/
@Override
public long getExpiration () {
return 0;
}
/**
* {@inheritDoc}
*
* @see jcifs.DfsReferralData#next()
*/
@Override
public DfsReferralData next () {
return this;
}
}
/**
* @return
* @throws CIFSException
*/
private static CIFSContext getContext () throws CIFSException {
return new BaseContext(new BaseConfiguration(true));
}
} |
package org.drools.benchmark.manners;
import java.io.BufferedReader;
import java.io.ByteArrayInputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.StringWriter;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Iterator;
import java.util.List;
import java.util.Random;
import java.util.StringTokenizer;
import org.drools.KnowledgeBase;
import org.drools.KnowledgeBaseFactory;
import org.drools.builder.KnowledgeBuilder;
import org.drools.builder.KnowledgeBuilderConfiguration;
import org.drools.builder.KnowledgeBuilderFactory;
import org.drools.builder.KnowledgeType;
import org.drools.definition.KnowledgePackage;
import org.drools.io.ResourceFactory;
import org.drools.runtime.StatefulKnowledgeSession;
public class MannersBenchmark {
/** Number of guests at the dinner (default: 16). */
private static int numGuests = 16;
/** Number of seats at the table (default: 16). */
private static int numSeats = 16;
/** Minimum number of hobbies each guest should have (default: 2). */
private static int minHobbies = 2;
/** Maximun number of hobbies each guest should have (default: 3). */
private static int maxHobbies = 3;
public static void main(final String[] args) throws Exception {
KnowledgeBuilderConfiguration kbuilderConfig = KnowledgeBuilderFactory.newKnowledgeBuilderConfiguration();
KnowledgeBuilder kbuilder = KnowledgeBuilderFactory.newKnowledgeBuilder( kbuilderConfig );
kbuilder.add( ResourceFactory.newClassPathResource( "manners.drl",
MannersBenchmark.class ),
KnowledgeType.DRL );
Collection<KnowledgePackage> pkgs = kbuilder.getKnowledgePackages();
// add the package to a rulebase
final KnowledgeBase kbase = KnowledgeBaseFactory.newKnowledgeBase();
kbase.addKnowledgePackages( pkgs );
for ( int i = 0; i < 10; i++ ) {
StatefulKnowledgeSession ksession = kbase.newStatefulKnowledgeSession();
String filename;
if ( args.length != 0 ) {
String arg = args[0];
filename = arg;
} else {
filename = "manners128.dat";
}
InputStream is = MannersBenchmark.class.getResourceAsStream( filename );
List list = getInputObjects( is );
for ( Iterator it = list.iterator(); it.hasNext(); ) {
Object object = it.next();
ksession.insert( object );
}
ksession.insert( new Count( 1 ) );
long start = System.currentTimeMillis();
ksession.fireAllRules();
System.err.println( System.currentTimeMillis() - start );
ksession.dispose();
}
}
/**
* Convert the facts from the <code>InputStream</code> to a list of
* objects.
*/
protected static List<Object> getInputObjects(InputStream inputStream) throws IOException {
List<Object> list = new ArrayList<Object>();
BufferedReader br = new BufferedReader( new InputStreamReader( inputStream ) );
String line;
while ( (line = br.readLine()) != null ) {
if ( line.trim().length() == 0 || line.trim().startsWith( ";" ) ) {
continue;
}
StringTokenizer st = new StringTokenizer( line,
"() " );
String type = st.nextToken();
if ( "guest".equals( type ) ) {
if ( !"name".equals( st.nextToken() ) ) {
throw new IOException( "expected 'name' in: " + line );
}
String name = st.nextToken();
if ( !"sex".equals( st.nextToken() ) ) {
throw new IOException( "expected 'sex' in: " + line );
}
String sex = st.nextToken();
if ( !"hobby".equals( st.nextToken() ) ) {
throw new IOException( "expected 'hobby' in: " + line );
}
String hobby = st.nextToken();
Guest guest = new Guest( name,
Sex.resolve( sex ),
Hobby.resolve( hobby ) );
list.add( guest );
}
if ( "last_seat".equals( type ) ) {
if ( !"seat".equals( st.nextToken() ) ) {
throw new IOException( "expected 'seat' in: " + line );
}
list.add( new LastSeat( new Integer( st.nextToken() ).intValue() ) );
}
if ( "context".equals( type ) ) {
if ( !"state".equals( st.nextToken() ) ) {
throw new IOException( "expected 'state' in: " + line );
}
list.add( new Context( st.nextToken() ) );
}
}
inputStream.close();
return list;
}
public static InputStream generateData() {
final String LINE_SEPARATOR = System.getProperty( "line.separator" );
StringWriter writer = new StringWriter();
int maxMale = numGuests / 2;
int maxFemale = numGuests / 2;
int maleCount = 0;
int femaleCount = 0;
// init hobbies
List<String> hobbyList = new ArrayList<String>();
for ( int i = 1; i <= maxHobbies; i++ ) {
hobbyList.add( "h" + i );
}
Random rnd = new Random();
for ( int i = 1; i <= numGuests; i++ ) {
char sex = rnd.nextBoolean() ? 'm' : 'f';
if ( sex == 'm' && maleCount == maxMale ) {
sex = 'f';
}
if ( sex == 'f' && femaleCount == maxFemale ) {
sex = 'm';
}
if ( sex == 'm' ) {
maleCount++;
}
if ( sex == 'f' ) {
femaleCount++;
}
List<String> guestHobbies = new ArrayList<String>( hobbyList );
int numHobbies = minHobbies + rnd.nextInt( maxHobbies - minHobbies + 1 );
for ( int j = 0; j < numHobbies; j++ ) {
int hobbyIndex = rnd.nextInt( guestHobbies.size() );
String hobby = (String) guestHobbies.get( hobbyIndex );
writer.write( "(guest (name n" + i + ") (sex " + sex + ") (hobby " + hobby + "))" + LINE_SEPARATOR );
guestHobbies.remove( hobbyIndex );
}
}
writer.write( "(last_seat (seat " + numSeats + "))" + LINE_SEPARATOR );
writer.write( LINE_SEPARATOR );
writer.write( "(context (state start))" + LINE_SEPARATOR );
return new ByteArrayInputStream( writer.getBuffer().toString().getBytes() );
}
} |
package net.pixelcop.sewer;
import java.io.IOException;
import java.text.DecimalFormat;
import java.text.NumberFormat;
import java.util.ArrayList;
import java.util.List;
import java.util.Properties;
import net.pixelcop.sewer.node.AbstractNodeTest;
import net.pixelcop.sewer.node.NodeConfig;
import net.pixelcop.sewer.node.TestableNode;
import net.pixelcop.sewer.sink.buffer.DisruptorSink;
import net.pixelcop.sewer.source.debug.ThreadedEventGeneratorSource;
import net.pixelcop.sewer.util.HdfsUtil;
import org.apache.hadoop.io.compress.CompressionCodec;
import org.apache.hadoop.io.compress.CompressionCodecFactory;
import org.junit.Test;
import org.junit.runner.JUnitCore;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
public class Benchmark extends AbstractNodeTest {
class Result {
double duration;
double count;
double opsPerSec;
String source;
String sink;
String notes;
}
private static final long TEST_WARMUP = 10000;
private static final long TEST_DURATION = 30000;
protected static final Logger LOG = LoggerFactory.getLogger(Benchmark.class);
protected static final List<String> waitStrategies = new ArrayList<>();
static {
waitStrategies.add(DisruptorSink.WAIT_BLOCKING);
waitStrategies.add(DisruptorSink.WAIT_BUSYSPIN);
waitStrategies.add(DisruptorSink.WAIT_SLEEPING);
waitStrategies.add(DisruptorSink.WAIT_TIMEOUT);
waitStrategies.add(DisruptorSink.WAIT_YIELDING);
}
private String compressor = null;
public static void main(String[] args) {
JUnitCore.main(Benchmark.class.getName());
}
@Test
public void testPerf() throws InterruptedException, IOException {
Properties props = new Properties();
props.setProperty(DisruptorSink.CONF_THREADS, "1");
props.setProperty(DisruptorSink.CONF_TIMEOUT_MS, "1");
String source = "tgen(256)";
List<Result> results = new ArrayList<>();
// null tests
runAllTests(props, source, "null", results);
// i/o tests
List<Class<? extends CompressionCodec>> codecs = CompressionCodecFactory.getCodecClasses(loadTestConfig(false, ""));
for (Class<? extends CompressionCodec> codec : codecs) {
props.put(HdfsUtil.CONFIG_COMPRESSION, codec.getName());
compressor = codec.getSimpleName();
runAllTests(props, source, "seqfile('/tmp/sewer-bench')", results);
}
compressor = null;
// print results
NumberFormat f = DecimalFormat.getIntegerInstance();
System.err.println("\n\n\n\n\n\n");
System.err.println("sink\tmsgs\tops/sec\t\tnotes");
for (Result result : results) {
System.err.print(result.sink);
System.err.print("\t");
System.err.print(f.format(result.count));
System.err.print("\t");
System.err.print(f.format(result.opsPerSec));
System.err.print("\t\t");
System.err.print(result.notes);
System.err.print("\n");
}
System.err.println("\n\n\n\n\n\n");
}
private void runAllTests(Properties props, String source, String dest, List<Result> results)
throws InterruptedException, IOException {
// basic tests
results.add(runTest(source, dest));
results.add(runTest(source, "buffer > " + dest));
// disruptor > null
runDisruptorTests(props, source, "disruptor > " + dest, results);
// meter before
results.add(runTest(source, "meter > " + dest));
results.add(runTest(source, "meter > buffer > " + dest));
runDisruptorTests(props, source, "meter > disruptor > " + dest, results);
// meter after
results.add(runTest(source, "buffer > meter > " + dest));
runDisruptorTests(props, source, "disruptor > meter > " + dest, results);
// meter before & after
results.add(runTest(source, "meter > buffer > meter > " + dest));
runDisruptorTests(props, source, "meter > disruptor > meter > " + dest, results);
}
private void runDisruptorTests(Properties props, String source, String sink, List<Result> results)
throws InterruptedException, IOException {
for (String strat : waitStrategies) {
props.setProperty(DisruptorSink.CONF_WAIT_STRATEGY, strat);
results.add(runTest(source, sink, props, strat));
}
}
private Result runTest(String source, String sink) throws InterruptedException, IOException {
return runTest(source, sink, null, "");
}
private Result runTest(String source, String sink, Properties props, String notes) throws InterruptedException, IOException {
// add compressor to notes
if (compressor != null) {
if (notes == null) {
notes = "" + compressor;
} else {
notes = notes + ", " + compressor;
}
}
Result r = new Result();
r.source = source;
r.sink = sink;
r.notes = notes;
NodeConfig conf = loadTestConfig(false, "");
if (props != null) {
conf.addResource(props);
}
TestableNode node = createNode(source, sink, null, conf);
// start node, opens source
node.start();
LOG.info("warming up...");
Thread.sleep(TEST_WARMUP);
double startTime = System.nanoTime();
((ThreadedEventGeneratorSource) node.getSource()).resetCounters();
Thread.sleep(TEST_DURATION);
node.await();
node.cleanup();
r.count = ((ThreadedEventGeneratorSource) node.getSource()).getTotalCount();
r.duration = System.nanoTime() - startTime;
r.opsPerSec = (1000L * 1000L * 1000L * r.count) / r.duration;
System.gc(); // why not
return r;
}
} |
package controller;
import boundary.PlayerApplication;
import boundary.PlayerLevelView;
import java.awt.EventQueue;
import java.awt.event.MouseEvent;
import java.awt.event.MouseListener;
import java.awt.event.MouseMotionListener;
import model.CellType;
import model.Move;
import model.PlayerModel;
import model.PlayerState;
import model.Point;
/**
* @author Eli Skeggs, Nick Chaput
*
* TODO: implement "Swap" special move, add validity checks to basic moves
*/
public class PlayerBoardMouseCtrl implements MouseListener, MouseMotionListener
{
PlayerApplication app;
PlayerModel model;
PlayerRemoveCtrl removeCtrl;
PlayerSwapCtrl swapCtrl;
PlayerExpandMoveCtrl expandMoveCtrl;
PlayerFinishMoveCtrl finishMoveCtrl;
PlayerStartMoveCtrl startMoveCtrl;
public PlayerBoardMouseCtrl(PlayerApplication app, PlayerModel model) {
this.app = app;
this.model = model;
removeCtrl = new PlayerRemoveCtrl(app, model);
swapCtrl = new PlayerSwapCtrl(app, model);
expandMoveCtrl = new PlayerExpandMoveCtrl(app, model);
finishMoveCtrl = new PlayerFinishMoveCtrl(app, model);
startMoveCtrl = new PlayerStartMoveCtrl(app, model);
}
Point identifyPoint(MouseEvent event) {
PlayerLevelView view = (PlayerLevelView) app.getView();
return view.boardView.identifyPoint(event.getX(), event.getY());
}
protected void fizzleMove() {
// make the move fizzle
model.playerState = PlayerState.NONE;
model.move = new Move();
if (model.counter > 0) {
model.counter
}
// ends the level from here
if (model.counter == 0) {
EventQueue.invokeLater(new PlayerEndLevelCtrl(app, model, true));
}
}
@Override
public void mouseClicked(MouseEvent event) {
Point point;
if (event.getButton() != MouseEvent.BUTTON1 ||
(point = identifyPoint(event)) == null
|| isNullTile(point)){
return;
}
switch (model.playerState) {
case REMOVE:
removeCtrl.mouseClicked(point);
break;
case SWAP:
swapCtrl.startSwap(point);
break;
default:
// do nothing!
}
}
@Override
public void mouseEntered(MouseEvent event) {}
@Override
public void mouseExited(MouseEvent event) {
if (model.playerState == PlayerState.SELECT) {
fizzleMove();
((PlayerLevelView) app.getView()).update();
}
}
@Override
public void mousePressed(MouseEvent event) {
Point point;
if (event.getButton() == MouseEvent.BUTTON1 &&
model.playerState == PlayerState.NONE &&
(point = identifyPoint(event)) != null) {
startMoveCtrl.startMove(point);
}
((PlayerLevelView) app.getView()).repaint();
}
@Override
public void mouseReleased(MouseEvent event) {
Point point;
if (event.getButton() == MouseEvent.BUTTON1 &&
model.playerState == PlayerState.SELECT &&
(point = identifyPoint(event)) != null) {
finishMoveCtrl.finishMove(point);
}
}
@Override
public void mouseDragged(MouseEvent event) {
if (model.playerState == PlayerState.SELECT) {
Point point = identifyPoint(event);
if (point != null) {
expandMoveCtrl.expandMove(point);
} else {
fizzleMove();
((PlayerLevelView)app.getView()).update();
}
}
}
@Override
public void mouseMoved(MouseEvent event) {}
public boolean isNullTile (Point point) {
return (model.level.currentBoard.grid[point.x][point.y].tile == null
|| model.level.currentBoard.grid[point.x][point.y].type == CellType.BUCKET
|| model.level.currentBoard.grid[point.x][point.y].type == CellType.INERT);
}
} |
package org.eclipse.birt.report.engine.parser;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.logging.Logger;
import org.eclipse.birt.data.engine.api.IConditionalExpression;
import org.eclipse.birt.data.engine.api.querydefn.ConditionalExpression;
import org.eclipse.birt.report.engine.api.IParameterDefnBase;
import org.eclipse.birt.report.engine.api.IScalarParameterDefn;
import org.eclipse.birt.report.engine.api.impl.CascadingParameterGroupDefn;
import org.eclipse.birt.report.engine.api.impl.ParameterGroupDefn;
import org.eclipse.birt.report.engine.api.impl.ParameterSelectionChoice;
import org.eclipse.birt.report.engine.api.impl.ScalarParameterDefn;
import org.eclipse.birt.report.engine.content.IStyle;
import org.eclipse.birt.report.engine.css.dom.StyleDeclaration;
import org.eclipse.birt.report.engine.css.engine.CSSEngine;
import org.eclipse.birt.report.engine.ir.ActionDesign;
import org.eclipse.birt.report.engine.ir.CellDesign;
import org.eclipse.birt.report.engine.ir.ColumnDesign;
import org.eclipse.birt.report.engine.ir.DataItemDesign;
import org.eclipse.birt.report.engine.ir.DimensionType;
import org.eclipse.birt.report.engine.ir.DrillThroughActionDesign;
import org.eclipse.birt.report.engine.ir.EngineIRConstants;
import org.eclipse.birt.report.engine.ir.Expression;
import org.eclipse.birt.report.engine.ir.ExtendedItemDesign;
import org.eclipse.birt.report.engine.ir.FreeFormItemDesign;
import org.eclipse.birt.report.engine.ir.GraphicMasterPageDesign;
import org.eclipse.birt.report.engine.ir.GridItemDesign;
import org.eclipse.birt.report.engine.ir.GroupDesign;
import org.eclipse.birt.report.engine.ir.HighlightDesign;
import org.eclipse.birt.report.engine.ir.HighlightRuleDesign;
import org.eclipse.birt.report.engine.ir.ImageItemDesign;
import org.eclipse.birt.report.engine.ir.LabelItemDesign;
import org.eclipse.birt.report.engine.ir.ListBandDesign;
import org.eclipse.birt.report.engine.ir.ListGroupDesign;
import org.eclipse.birt.report.engine.ir.ListItemDesign;
import org.eclipse.birt.report.engine.ir.ListingDesign;
import org.eclipse.birt.report.engine.ir.MapDesign;
import org.eclipse.birt.report.engine.ir.MapRuleDesign;
import org.eclipse.birt.report.engine.ir.MasterPageDesign;
import org.eclipse.birt.report.engine.ir.MultiLineItemDesign;
import org.eclipse.birt.report.engine.ir.PageSetupDesign;
import org.eclipse.birt.report.engine.ir.Report;
import org.eclipse.birt.report.engine.ir.ReportElementDesign;
import org.eclipse.birt.report.engine.ir.ReportItemDesign;
import org.eclipse.birt.report.engine.ir.RowDesign;
import org.eclipse.birt.report.engine.ir.SimpleMasterPageDesign;
import org.eclipse.birt.report.engine.ir.StylePropertyMapping;
import org.eclipse.birt.report.engine.ir.StyledElementDesign;
import org.eclipse.birt.report.engine.ir.TableBandDesign;
import org.eclipse.birt.report.engine.ir.TableGroupDesign;
import org.eclipse.birt.report.engine.ir.TableItemDesign;
import org.eclipse.birt.report.engine.ir.TemplateDesign;
import org.eclipse.birt.report.engine.ir.TextItemDesign;
import org.eclipse.birt.report.engine.ir.VisibilityDesign;
import org.eclipse.birt.report.engine.ir.VisibilityRuleDesign;
import org.eclipse.birt.report.model.api.ActionHandle;
import org.eclipse.birt.report.model.api.CascadingParameterGroupHandle;
import org.eclipse.birt.report.model.api.CellHandle;
import org.eclipse.birt.report.model.api.ColumnHandle;
import org.eclipse.birt.report.model.api.DataItemHandle;
import org.eclipse.birt.report.model.api.DataSetHandle;
import org.eclipse.birt.report.model.api.DesignElementHandle;
import org.eclipse.birt.report.model.api.DesignVisitor;
import org.eclipse.birt.report.model.api.DimensionHandle;
import org.eclipse.birt.report.model.api.ExtendedItemHandle;
import org.eclipse.birt.report.model.api.FactoryPropertyHandle;
import org.eclipse.birt.report.model.api.FreeFormHandle;
import org.eclipse.birt.report.model.api.GraphicMasterPageHandle;
import org.eclipse.birt.report.model.api.GridHandle;
import org.eclipse.birt.report.model.api.GroupHandle;
import org.eclipse.birt.report.model.api.HideRuleHandle;
import org.eclipse.birt.report.model.api.HighlightRuleHandle;
import org.eclipse.birt.report.model.api.ImageHandle;
import org.eclipse.birt.report.model.api.LabelHandle;
import org.eclipse.birt.report.model.api.ListGroupHandle;
import org.eclipse.birt.report.model.api.ListHandle;
import org.eclipse.birt.report.model.api.ListingHandle;
import org.eclipse.birt.report.model.api.MapRuleHandle;
import org.eclipse.birt.report.model.api.MasterPageHandle;
import org.eclipse.birt.report.model.api.MemberHandle;
import org.eclipse.birt.report.model.api.ParamBindingHandle;
import org.eclipse.birt.report.model.api.ParameterGroupHandle;
import org.eclipse.birt.report.model.api.PropertyHandle;
import org.eclipse.birt.report.model.api.ReportDesignHandle;
import org.eclipse.birt.report.model.api.ReportElementHandle;
import org.eclipse.birt.report.model.api.ReportItemHandle;
import org.eclipse.birt.report.model.api.RowHandle;
import org.eclipse.birt.report.model.api.ScalarParameterHandle;
import org.eclipse.birt.report.model.api.SelectionChoiceHandle;
import org.eclipse.birt.report.model.api.SimpleMasterPageHandle;
import org.eclipse.birt.report.model.api.SlotHandle;
import org.eclipse.birt.report.model.api.StructureHandle;
import org.eclipse.birt.report.model.api.StyleHandle;
import org.eclipse.birt.report.model.api.TableGroupHandle;
import org.eclipse.birt.report.model.api.TableHandle;
import org.eclipse.birt.report.model.api.TemplateReportItemHandle;
import org.eclipse.birt.report.model.api.TextDataHandle;
import org.eclipse.birt.report.model.api.TextItemHandle;
import org.eclipse.birt.report.model.api.core.UserPropertyDefn;
import org.eclipse.birt.report.model.api.elements.DesignChoiceConstants;
import org.eclipse.birt.report.model.api.elements.structures.HighlightRule;
import org.eclipse.birt.report.model.api.metadata.DimensionValue;
import org.eclipse.birt.report.model.api.metadata.IPropertyType;
import org.eclipse.birt.report.model.elements.Style;
class EngineIRVisitor extends DesignVisitor
{
/**
* logger used to log the error.
*/
protected static Logger logger = Logger.getLogger( EngineIRVisitor.class
.getName( ) );
protected Object currentElement;
/**
* default unit used by this report
*/
protected String defaultUnit;
protected Report report;
/**
* report design handle
*/
protected ReportDesignHandle handle;
/**
* the CSSEngine
*/
protected CSSEngine cssEngine;
/**
* the inheritable report style
*/
StyleDeclaration nonInheritableReportStyle;
/**
* the non-inheritable report style
*/
StyleDeclaration inheritableReportStyle;
/**
* constructor
*
* @param handle
* the entry point to the DE report design IR
*
*/
EngineIRVisitor( ReportDesignHandle handle )
{
super( );
this.handle = handle;
}
/**
* translate the DE's IR to FPE's IR.
*
* @return FPE's IR.
*/
public Report translate( )
{
report = new Report( );
cssEngine = report.getCSSEngine( );
report.setReportDesign( handle );
apply( handle );
return report;
}
/*
* (non-Javadoc)
*
* @see org.eclipse.birt.report.model.api.DesignVisitor#visitReportDesign(org.eclipse.birt.report.model.api.ReportDesignHandle)
*/
public void visitReportDesign( ReportDesignHandle handle )
{
report.setUnit( handle.getDefaultUnits( ) );
if ( handle.getBase( ) != null && !handle.getBase( ).equals( "" ) ) //$NON-NLS-1$
{
report.setBasePath( handle.getBase( ) );
}
defaultUnit = report.getUnit( );
setupNamedExpressions( handle, report.getNamedExpressions( ) );
// INCLUDE LIBRARY
// INCLUDE SCRIPT
// CODE MODULES
// Sets the report default style
StyleHandle defaultStyle = handle.findStyle( "report" );//$NON-NLS-1$
createReportDefaultStyles( defaultStyle );
// TODO: add report style
// report.addStyle( );
// COLOR-PALETTE
// METHOD
// STYLES
// We needn't handle the style slot, it will be handled for each
// element.
// Handle Master Page
PageSetupDesign pageSetup = new PageSetupDesign( );
SlotHandle pageSlot = handle.getMasterPages( );
for ( int i = 0; i < pageSlot.getCount( ); i++ )
{
apply( pageSlot.get( i ) );
if ( currentElement != null )
{
pageSetup.addMasterPage( (MasterPageDesign) currentElement );
}
}
// FIXME: add page sequence support
// Handle Page Sequence
// SlotHandle seqSlot = handle.getPageSequences( );
// for ( int i = 0; i < seqSlot.getCount( ); i++ )
// apply( seqSlot.get( i ) );
// assert ( currentElement != null );
// pageSetup.addPageSequence( (PageSequenceDesign) currentElement );
report.setPageSetup( pageSetup );
// COMPONENTS
// Handle Report Body
SlotHandle bodySlot = handle.getBody( );
for ( int i = 0; i < bodySlot.getCount( ); i++ )
{
apply( bodySlot.get( i ) );
if ( currentElement != null )
{
report.addContent( (ReportItemDesign) currentElement );
}
}
// SCRATCH-PAD
// CONFIG-VARS
// TRANSLATIONS
// IMAGES
// CUSTOM
}
/**
* setup the named expression map
*
* @param userProperties
* user defined named expressions in design file
* @param namedExpressions
* the data structure that hold named expressions
*/
private void setupNamedExpressions( DesignElementHandle handle,
Map namedExpressions )
{
List userProperties = handle.getUserProperties( );
if ( userProperties == null || namedExpressions == null )
return;
for ( int i = 0; i < userProperties.size( ); i++ )
{
UserPropertyDefn userDef = (UserPropertyDefn) userProperties
.get( i );
if ( userDef.getTypeCode( ) == IPropertyType.EXPRESSION_TYPE )
{
String name = userDef.getName( );
String exprString = handle.getStringProperty( name );
if ( exprString != null && !exprString.trim( ).equals( "" ) )
{
//Expression expression = new Expression( exprString );
namedExpressions.put( name, exprString );
}
}
}
}
/**
* setup the master page object from the base master page handle.
*
* @param page
* page object
* @param handle
* page handle
*/
private void setupMasterPage( MasterPageDesign page, MasterPageHandle handle )
{
setupStyledElement( page, handle );
String styleName = setupBodyStyle( page );
if (styleName != null)
{
page.setBodyStyleName( styleName );
}
page.setPageType( handle.getPageType( ) );
// Master page width and height
DimensionValue effectWidth = handle.getEffectiveWidth( );
DimensionValue effectHeight = handle.getEffectiveHeight( );
DimensionType width = null;
DimensionType height = null;
if ( effectWidth != null )
{
width = new DimensionType( effectWidth.getMeasure( ), effectWidth
.getUnits( ) );
}
if ( effectHeight != null )
{
height = new DimensionType( effectHeight.getMeasure( ),
effectHeight.getUnits( ) );
}
page.setPageSize( width, height );
page.setOrientation( handle.getOrientation( ) );
// Master page margins
DimensionType top = createDimension( handle.getTopMargin( ) );
DimensionType left = createDimension( handle.getLeftMargin( ) );
DimensionType bottom = createDimension( handle.getBottomMargin( ) );
DimensionType right = createDimension( handle.getRightMargin( ) );
page.setMargin( top, left, bottom, right );
}
protected void visitDesignElement( DesignElementHandle obj )
{
// any unsupported element
currentElement = null;
}
public void visitGraphicMasterPage( GraphicMasterPageHandle handle )
{
GraphicMasterPageDesign page = new GraphicMasterPageDesign( );
setupMasterPage( page, handle );
// Multi-column properties
page.setColumns( handle.getColumnCount( ) );
DimensionType spacing = createDimension( handle.getColumnSpacing( ) );
page.setColumnSpacing( spacing );
// Master page content
SlotHandle contentSlot = handle.getContent( );
for ( int i = 0; i < contentSlot.getCount( ); i++ )
{
apply( contentSlot.get( i ) );
if ( currentElement != null )
{
page.addContent( (ReportItemDesign) currentElement );
}
}
currentElement = page;
}
public void visitSimpleMasterPage( SimpleMasterPageHandle handle )
{
SimpleMasterPageDesign page = new SimpleMasterPageDesign( );
// setup the base master page property.
setupMasterPage( page, handle );
page.setHeaderHeight( createDimension( handle.getHeaderHeight( ) ) );
page.setFooterHeight( createDimension( handle.getFooterHeight( ) ) );
page.setShowFooterOnLast( handle.showFooterOnLast( ) );
page.setShowHeaderOnFirst( handle.showHeaderOnFirst( ) );
page.setFloatingFooter( handle.isFloatingFooter( ) );
SlotHandle headerSlot = handle.getPageHeader( );
for ( int i = 0; i < headerSlot.getCount( ); i++ )
{
apply( headerSlot.get( i ) );
if ( currentElement != null )
{
page.addHeader( (ReportItemDesign) currentElement );
}
}
SlotHandle footerSlot = handle.getPageFooter( );
for ( int i = 0; i < footerSlot.getCount( ); i++ )
{
apply( footerSlot.get( i ) );
if ( currentElement != null )
{
page.addFooter( (ReportItemDesign) currentElement );
}
}
currentElement = page;
}
public void visitList( ListHandle handle )
{
// Create ListItem
ListItemDesign listItem = new ListItemDesign( );
setupListingItem( listItem, handle );
// Header
SlotHandle headerSlot = handle.getHeader( );
listItem.setHeader( createListBand( headerSlot ) );
// Multiple groups
SlotHandle groupsSlot = handle.getGroups( );
for ( int i = 0; i < groupsSlot.getCount( ); i++ )
{
apply( groupsSlot.get( i ) );
if ( currentElement != null )
{
listItem.addGroup( (ListGroupDesign) currentElement );
}
}
// List detail
SlotHandle detailSlot = handle.getDetail( );
listItem.setDetail( createListBand( detailSlot ) );
// List Footer
SlotHandle footerSlot = handle.getFooter( );
listItem.setFooter( createListBand( footerSlot ) );
currentElement = listItem;
}
public void visitFreeForm( FreeFormHandle handle )
{
// Create Free form element
FreeFormItemDesign container = new FreeFormItemDesign( );
setupReportItem( container, handle );
// Set up each individual item in a free form container
SlotHandle slot = handle.getReportItems( );
for ( int i = 0; i < slot.getCount( ); i++ )
{
apply( slot.get( i ) );
if ( currentElement != null )
{
container.addItem( (ReportItemDesign) currentElement );
}
}
currentElement = container;
}
public void visitTextDataItem( TextDataHandle handle )
{
MultiLineItemDesign multiLineItem = new MultiLineItemDesign( );
setupReportItem( multiLineItem, handle );
String valueExpr = handle.getValueExpr( );
String contentType = handle.getContentType( );
multiLineItem.setContent( createExpression( valueExpr ) );
multiLineItem.setContentType( contentType );
setHighlight( multiLineItem, valueExpr );
setMap( multiLineItem, valueExpr );
currentElement = multiLineItem;
}
public void visitParameterGroup( ParameterGroupHandle handle )
{
ParameterGroupDefn paramGroup = new ParameterGroupDefn( );
paramGroup.setHandle( handle );
paramGroup.setParameterType( IParameterDefnBase.PARAMETER_GROUP );
paramGroup.setName( handle.getName( ) );
paramGroup.setDisplayName( handle.getDisplayName( ) );
paramGroup.setDisplayNameKey( handle.getDisplayNameKey( ) );
paramGroup.setHelpText( handle.getHelpText( ) );
paramGroup.setHelpTextKey( handle.getHelpTextKey( ) );
SlotHandle parameters = handle.getParameters( );
// set custom properties
List properties = handle.getUserProperties( );
for ( int i = 0; i < properties.size( ); i++ )
{
UserPropertyDefn p = (UserPropertyDefn) properties.get( i );
paramGroup.addUserProperty( p.getName( ), handle.getProperty( p
.getName( ) ) );
}
int size = parameters.getCount( );
for ( int n = 0; n < size; n++ )
{
apply( parameters.get( n ) );
if ( currentElement != null )
{
paramGroup.addParameter( (IParameterDefnBase) currentElement );
}
}
currentElement = paramGroup;
}
public void visitCascadingParameterGroup(
CascadingParameterGroupHandle handle )
{
CascadingParameterGroupDefn paramGroup = new CascadingParameterGroupDefn( );
paramGroup.setHandle( handle );
paramGroup
.setParameterType( IParameterDefnBase.CASCADING_PARAMETER_GROUP );
paramGroup.setName( handle.getName( ) );
paramGroup.setDisplayName( handle.getDisplayName( ) );
paramGroup.setDisplayNameKey( handle.getDisplayNameKey( ) );
paramGroup.setHelpText( handle.getHelpText( ) );
paramGroup.setHelpTextKey( handle.getHelpTextKey( ) );
DataSetHandle dset = handle.getDataSet( );
if ( dset != null )
{
paramGroup.setDataSet( dset.getName( ) );
}
SlotHandle parameters = handle.getParameters( );
// set custom properties
List properties = handle.getUserProperties( );
for ( int i = 0; i < properties.size( ); i++ )
{
UserPropertyDefn p = (UserPropertyDefn) properties.get( i );
paramGroup.addUserProperty( p.getName( ), handle.getProperty( p
.getName( ) ) );
}
int size = parameters.getCount( );
for ( int n = 0; n < size; n++ )
{
apply( parameters.get( n ) );
if ( currentElement != null )
{
paramGroup.addParameter( (IParameterDefnBase) currentElement );
}
}
currentElement = paramGroup;
}
public void visitScalarParameter( ScalarParameterHandle handle )
{
assert ( handle.getName( ) != null );
// Create Parameter
ScalarParameterDefn scalarParameter = new ScalarParameterDefn( );
scalarParameter.setHandle( handle );
scalarParameter.setParameterType( IParameterDefnBase.SCALAR_PARAMETER );
scalarParameter.setName( handle.getName( ) );
// set custom properties
List properties = handle.getUserProperties( );
for ( int i = 0; i < properties.size( ); i++ )
{
UserPropertyDefn p = (UserPropertyDefn) properties.get( i );
scalarParameter.addUserProperty( p.getName( ), handle
.getProperty( p.getName( ) ) );
}
String align = handle.getAlignment( );
if ( DesignChoiceConstants.SCALAR_PARAM_ALIGN_CENTER.equals( align ) )
scalarParameter.setAlignment( IScalarParameterDefn.CENTER );
else if ( DesignChoiceConstants.SCALAR_PARAM_ALIGN_LEFT.equals( align ) )
scalarParameter.setAlignment( IScalarParameterDefn.LEFT );
else if ( DesignChoiceConstants.SCALAR_PARAM_ALIGN_RIGHT.equals( align ) )
scalarParameter.setAlignment( IScalarParameterDefn.RIGHT );
else
scalarParameter.setAlignment( IScalarParameterDefn.AUTO );
scalarParameter.setAllowBlank( handle.allowBlank( ) );
scalarParameter.setAllowNull( handle.allowNull( ) );
String controlType = handle.getControlType( );
if ( DesignChoiceConstants.PARAM_CONTROL_CHECK_BOX.equals( controlType ) )
scalarParameter.setControlType( IScalarParameterDefn.CHECK_BOX );
else if ( DesignChoiceConstants.PARAM_CONTROL_LIST_BOX
.equals( controlType ) )
scalarParameter.setControlType( IScalarParameterDefn.LIST_BOX );
else if ( DesignChoiceConstants.PARAM_CONTROL_RADIO_BUTTON
.equals( controlType ) )
scalarParameter.setControlType( IScalarParameterDefn.RADIO_BUTTON );
else
scalarParameter.setControlType( IScalarParameterDefn.TEXT_BOX );
scalarParameter.setDefaultValue( handle.getDefaultValue( ) );
scalarParameter.setDisplayName( handle.getDisplayName( ) );
scalarParameter.setDisplayNameKey( handle.getDisplayNameKey( ) );
scalarParameter.setFormat( handle.getFormat( ) );
scalarParameter.setHelpText( handle.getHelpText( ) );
scalarParameter.setHelpTextKey( handle.getHelpTextKey( ) );
scalarParameter.setPromptText( handle.getPromptText( ) );
scalarParameter.setIsHidden( handle.isHidden( ) );
scalarParameter.setName( handle.getName( ) );
String valueType = handle.getDataType( );
if ( DesignChoiceConstants.PARAM_TYPE_BOOLEAN.equals( valueType ) )
scalarParameter.setDataType( IScalarParameterDefn.TYPE_BOOLEAN );
else if ( DesignChoiceConstants.PARAM_TYPE_DATETIME.equals( valueType ) )
scalarParameter.setDataType( IScalarParameterDefn.TYPE_DATE_TIME );
else if ( DesignChoiceConstants.PARAM_TYPE_DECIMAL.equals( valueType ) )
scalarParameter.setDataType( IScalarParameterDefn.TYPE_DECIMAL );
else if ( DesignChoiceConstants.PARAM_TYPE_FLOAT.equals( valueType ) )
scalarParameter.setDataType( IScalarParameterDefn.TYPE_FLOAT );
else if ( DesignChoiceConstants.PARAM_TYPE_STRING.equals( valueType ) )
scalarParameter.setDataType( IScalarParameterDefn.TYPE_STRING );
else
scalarParameter.setDataType( IScalarParameterDefn.TYPE_ANY );
ArrayList values = new ArrayList( );
Iterator selectionIter = handle.choiceIterator( );
while ( selectionIter.hasNext( ) )
{
SelectionChoiceHandle selection = (SelectionChoiceHandle) selectionIter
.next( );
ParameterSelectionChoice selectionChoice = new ParameterSelectionChoice(
this.handle );
selectionChoice.setLabel( selection.getLabelKey( ), selection
.getLabel( ) );
selectionChoice.setValue( selection.getValue( ), scalarParameter
.getDataType( ) );
values.add( selectionChoice );
}
scalarParameter.setSelectionList( values );
scalarParameter.setAllowNewValues( !handle.isMustMatch( ) );
scalarParameter.setFixedOrder( handle.isFixedOrder( ) );
if ( scalarParameter.getSelectionList( ) != null
&& scalarParameter.getSelectionList( ).size( ) > 0 )
scalarParameter
.setSelectionListType( IScalarParameterDefn.SELECTION_LIST_STATIC );
else
scalarParameter
.setSelectionListType( IScalarParameterDefn.SELECTION_LIST_NONE );
scalarParameter.setValueConcealed( handle.isConcealValue( ) );
currentElement = scalarParameter;
}
public void visitLabel( LabelHandle handle )
{
// Create Label Item
LabelItemDesign labelItem = new LabelItemDesign( );
setupReportItem( labelItem, handle );
// Text
String text = handle.getText( );
String textKey = handle.getTextKey( );
labelItem.setText( textKey, text );
// Handle Action
ActionHandle action = handle.getActionHandle( );
if ( action != null )
{
labelItem.setAction( createAction( action ) );
}
// Fill in help text
labelItem.setHelpText( handle.getHelpTextKey( ), handle.getHelpText( ) );
currentElement = labelItem;
}
public void visitDataItem( DataItemHandle handle )
{
// Create data item
DataItemDesign data = new DataItemDesign( );
setupReportItem( data, handle );
data.setName( handle.getName( ) );
// Fill in data expression,
//String expr = handle.getValueExpr( );
String expr = handle.getResultSetColumn( );
if (expr != null && expr.trim( ).length( ) > 0)
{
expr = "row[\"" + expr.replaceAll( "\"", "\\\\\"") + "\"]";
data.setValue( expr );
}
// Handle Action
ActionHandle action = handle.getActionHandle( );
if ( action != null )
{
data.setAction( createAction( action ) );
}
// Fill in help text
data.setHelpText( handle.getHelpTextKey( ), handle.getHelpText( ) );
setHighlight( data, expr );
setMap( data, expr );
currentElement = data;
}
public void visitGrid( GridHandle handle )
{
// Create Grid Item
GridItemDesign grid = new GridItemDesign( );
setupReportItem( grid, handle );
// Handle Columns
SlotHandle columnSlot = handle.getColumns( );
for ( int i = 0; i < columnSlot.getCount( ); i++ )
{
ColumnHandle columnHandle = (ColumnHandle) columnSlot.get( i );
apply( columnHandle );
if ( currentElement != null )
{
ColumnDesign columnDesign = (ColumnDesign) currentElement;
for ( int j = 0; j < columnHandle.getRepeatCount( ); j++ )
{
grid.addColumn( columnDesign );
}
}
}
// Handle Rows
SlotHandle rowSlot = handle.getRows( );
for ( int i = 0; i < rowSlot.getCount( ); i++ )
{
apply( rowSlot.get( i ) );
if ( currentElement != null )
{
grid.addRow( (RowDesign) currentElement );
}
}
new TableItemDesignLayout( ).layout( grid );
currentElement = grid;
}
public void visitImage( ImageHandle handle )
{
// Create Image Item
ImageItemDesign image = new ImageItemDesign( );
setupReportItem( image, handle );
// Handle Action
ActionHandle action = handle.getActionHandle( );
if ( action != null )
{
image.setAction( createAction( action ) );
}
// Alternative text for image
image.setAltText( handle.getAltTextKey( ), handle.getAltText( ) );
// Help text for image
image.setHelpText( handle.getHelpTextKey( ), handle.getHelpText( ) );
// Handle Image Source
String imageSrc = handle.getSource( );
if ( EngineIRConstants.IMAGE_REF_TYPE_URL.equals( imageSrc ) )
{
image.setImageUri( createExpression( handle.getURI( ) ) );
}
else if ( EngineIRConstants.IMAGE_REF_TYPE_EXPR.equals( imageSrc ) )
{
String valueExpr = handle.getValueExpression( );
String typeExpr = handle.getTypeExpression( );
String imageValue = createExpression( valueExpr );
String imageType = createExpression( typeExpr );
image.setImageExpression( imageValue, imageType );
}
else if ( EngineIRConstants.IMAGE_REF_TYPE_EMBED.equals( imageSrc ) )
{
image.setImageName( handle.getImageName( ) );
}
else if ( EngineIRConstants.IMAGE_REF_TYPE_FILE.equals( imageSrc ) )
{
image.setImageFile( createExpression( handle.getURI( ) ) );
}
else
{
assert false;
}
currentElement = image;
}
public void visitTable( TableHandle handle )
{
// Create Table Item
TableItemDesign table = new TableItemDesign( );
table.setRepeatHeader( handle.repeatHeader( ) );
setupListingItem( table, handle );
// Handle table caption
String caption = handle.getCaption( );
String captionKey = handle.getCaptionKey( );
if ( caption != null || captionKey != null )
{
table.setCaption( captionKey, caption );
}
// Handle table Columns
SlotHandle columnSlot = handle.getColumns( );
for ( int i = 0; i < columnSlot.getCount( ); i++ )
{
ColumnHandle columnHandle = (ColumnHandle) columnSlot.get( i );
apply( columnHandle );
if ( currentElement != null )
{
ColumnDesign columnDesign = (ColumnDesign) currentElement;
for ( int j = 0; j < columnHandle.getRepeatCount( ); j++ )
{
table.addColumn( columnDesign );
}
}
}
// Handle Table Header
SlotHandle headerSlot = handle.getHeader( );
TableBandDesign header = createTableBand( headerSlot );
table.setHeader( header );
// Handle grouping in table
SlotHandle groupSlot = handle.getGroups( );
for ( int i = 0; i < groupSlot.getCount( ); i++ )
{
apply( groupSlot.get( i ) );
if ( currentElement != null )
{
table.addGroup( (TableGroupDesign) currentElement );
}
}
// Handle detail section
SlotHandle detailSlot = handle.getDetail( );
TableBandDesign detail = createTableBand( detailSlot );
table.setDetail( detail );
// Handle table footer
SlotHandle footerSlot = handle.getFooter( );
TableBandDesign footer = createTableBand( footerSlot );
table.setFooter( footer );
new TableItemDesignLayout( ).layout( table );
//setup the supressDuplicate property of the data items in the
//detail band
detail = table.getDetail( );
for ( int i = 0; i < detail.getRowCount( ); i++ )
{
RowDesign row = detail.getRow(i);
for (int j = 0; j < row.getCellCount( ); j++)
{
CellDesign cell = row.getCell( j );
ColumnDesign column = table.getColumn( cell.getColumn( ) );
if ( column.getSuppressDuplicate( ) )
{
for ( int k = 0; k < cell.getContentCount( ); k++ )
{
ReportItemDesign item = cell.getContent( k );
if ( item instanceof DataItemDesign )
{
DataItemDesign dataItem = ( DataItemDesign )item;
dataItem.setSuppressDuplicate( true );
}
}
}
}
}
currentElement = table;
}
public void visitColumn( ColumnHandle handle )
{
// Create a Column, mostly used in Table or Grid
ColumnDesign col = new ColumnDesign( );
setupStyledElement( col, handle );
// Column Width
DimensionType width = createDimension( handle.getWidth( ) );
col.setWidth( width );
boolean supress = handle.suppressDuplicates( );
col.setSuppressDuplicate( supress );
currentElement = col;
}
public void visitRow( RowHandle handle )
{
// Create a Row, mostly used in Table and Grid Item
RowDesign row = new RowDesign( );
setupStyledElement( row, handle );
// Row Height
DimensionType height = createDimension( handle.getHeight( ) );
row.setHeight( height );
// Book mark
String bookmark = handle.getBookmark( );
row.setBookmark( createExpression( bookmark ) );
// Visibility
VisibilityDesign visibility = createVisibility( handle
.visibilityRulesIterator( ) );
row.setVisibility( visibility );
// Cells in a row
SlotHandle cellSlot = handle.getCells( );
for ( int i = 0; i < cellSlot.getCount( ); i++ )
{
apply( cellSlot.get( i ) );
if ( currentElement != null )
{
row.addCell( (CellDesign) currentElement );
}
}
String onCreate = handle.getOnCreate( );
row.setOnCreate( createExpression( onCreate ) );
row.setOnRender( ( (RowHandle) handle ).getOnRender( ) );
setHighlight( row, null );
currentElement = row;
}
private boolean isContainer( ReportElementHandle handle )
{
if ( handle instanceof TextItemHandle )
{
return false;
}
if ( handle instanceof DataItemHandle )
{
return false;
}
if ( handle instanceof LabelHandle )
{
return false;
}
if ( handle instanceof TextDataHandle )
{
return false;
}
if ( handle instanceof ExtendedItemHandle )
{
return false;
}
if ( handle instanceof ImageHandle )
{
return false;
}
return true;
}
/**
* Sets up cell element's style attribute.
*
* @param cell
* engine's styled cell element.
* @param handle
* DE's styled cell element.
*/
protected void setupStyledElement( StyledElementDesign design,
ReportElementHandle handle )
{
// Styled element is a report element
setupReportElement( design, handle );
StyleDeclaration style = createPrivateStyle( handle,
isContainer( handle ) );
if ( style != null && !style.isEmpty( ) )
{
design.setStyleName( assignStyleName( style ) );
}
}
public void visitCell( CellHandle handle )
{
// Create a Cell
CellDesign cell = new CellDesign( );
setupStyledElement( cell, handle );
// Cell contents
SlotHandle contentSlot = handle.getContent( );
for ( int i = 0; i < contentSlot.getCount( ); i++ )
{
apply( contentSlot.get( i ) );
if ( currentElement != null )
{
cell.addContent( (ReportItemDesign) currentElement );
}
}
// Span, Drop properties of a cell
// FIXME: change the colspan/rowspan after MODEL fix the bug
// cell.setColSpan( LayoutUtil.getEffectiveColumnSpan( handle ) );
cell.setColSpan( handle.getColumnSpan( ) );
int columnId = handle.getColumn( ) - 1;
if ( columnId < 0 )
{
columnId = -1;
}
cell.setColumn( columnId );
// cell.setRowSpan( LayoutUtil.getEffectiveRowSpan( handle ) );
cell.setRowSpan( handle.getRowSpan( ) );
cell.setDrop( handle.getDrop( ) );
String onCreate = handle.getOnCreate( );
cell.setOnCreate( createExpression( onCreate ) );
cell.setOnRender( handle.getOnRender( ) );
setHighlight( cell, null );
currentElement = cell;
}
/**
* create a list band using the items in slot.
*
* @param elements
* items in DE's IR
* @return ListBand.
*/
private ListBandDesign createListBand( SlotHandle elements )
{
ListBandDesign band = new ListBandDesign( );
for ( int i = 0; i < elements.getCount( ); i++ )
{
apply( elements.get( i ) );
if ( currentElement != null )
{
band.addContent( (ReportItemDesign) currentElement );
}
}
return band;
}
/**
* create a list group using the DE's ListGroup.
*
* @param handle
* De's list group
* @return engine's list group
*/
public void visitListGroup( ListGroupHandle handle )
{
ListGroupDesign listGroup = new ListGroupDesign( );
setupGroup( listGroup, handle );
ListBandDesign header = createListBand( handle.getHeader( ) );
listGroup.setHeader( header );
// flatten TOC on group to the first report item in group header
String tocExpr = handle.getTocExpression( );
if ( null != tocExpr && !"".equals( tocExpr.trim( ) ) ) //$NON-NLS-1$
{
if ( header.getContentCount( ) > 0 )
{
ReportItemDesign item = (ReportItemDesign) header
.getContent( 0 );
item.setTOC( createExpression( tocExpr ) );
}
}
ListBandDesign footer = createListBand( handle.getFooter( ) );
listGroup.setFooter( footer );
boolean hideDetail = handle.hideDetail( );
listGroup.setHideDetail( hideDetail );
currentElement = listGroup;
}
/**
* create a table group using the DE's TableGroup.
*
* @param handle
* De's table group
* @return engine's table group
*/
public void visitTableGroup( TableGroupHandle handle )
{
TableGroupDesign tableGroup = new TableGroupDesign( );
setupGroup( tableGroup, handle );
TableBandDesign header = createTableBand( handle.getHeader( ) );
tableGroup.setHeader( header );
// flatten TOC on group to the first report item in group header
String toc = handle.getTocExpression( );
if ( null != toc && !"".equals( toc.trim( ) ) ) //$NON-NLS-1$
{
if ( header.getRowCount( ) > 0 )
{
RowDesign row = header.getRow( 0 );
row.setTOC( createExpression( toc ) );
}
}
TableBandDesign footer = createTableBand( handle.getFooter( ) );
tableGroup.setFooter( footer );
boolean hideDetail = handle.hideDetail( );
tableGroup.setHideDetail( hideDetail );
currentElement = tableGroup;
}
public void visitTextItem( TextItemHandle handle )
{
// Create Text Item
TextItemDesign textItem = new TextItemDesign( );
setupReportItem( textItem, handle );
String contentType = handle.getContentType( );
if ( contentType != null )
{
textItem.setTextType( contentType );
}
textItem.setText( handle.getContentKey( ), handle.getContent( ) );
currentElement = textItem;
}
/*
* (non-Javadoc)
*
* @see org.eclipse.birt.report.model.api.DesignVisitor#visitExtendedItem(org.eclipse.birt.report.model.api.ExtendedItemHandle)
*/
protected void visitExtendedItem( ExtendedItemHandle obj )
{
ExtendedItemDesign extendedItem = new ExtendedItemDesign( );
setupReportItem( extendedItem, obj );
currentElement = extendedItem;
}
public void visitTemplateReportItem( TemplateReportItemHandle obj )
{
TemplateDesign template = new TemplateDesign( );
setupReportElement( template, obj );
template.setPromptText( obj.getDescription( ) );
template.setPromptTextKey( obj.getDescriptionKey( ) );
template.setAllowedType( obj.getAllowedType( ) );
currentElement = template;
}
protected void setupGroup( GroupDesign group, GroupHandle handle )
{
// name
group.setName( handle.getName( ) );
String pageBreakBefore = handle
.getStringProperty( StyleHandle.PAGE_BREAK_BEFORE_PROP );
String pageBreakAfter = handle
.getStringProperty( StyleHandle.PAGE_BREAK_AFTER_PROP );
group.setPageBreakBefore( pageBreakBefore );
group.setPageBreakAfter( pageBreakAfter );
}
/**
* create a table band using the items in slot.
*
* @param elements
* items in DE's IR
* @return TableBand.
*/
private TableBandDesign createTableBand( SlotHandle elements )
{
TableBandDesign band = new TableBandDesign( );
for ( int i = 0; i < elements.getCount( ); i++ )
{
apply( elements.get( i ) );
if ( currentElement != null )
{
band.addRow( (RowDesign) currentElement );
}
}
return band;
}
/**
* Creates the property visibility
*
* @param visibilityRulesIterator
* the handle's rules iterator
* @return null only if the iterator is null or it contains no rules,
* otherwise VisibilityDesign
*/
protected VisibilityDesign createVisibility(
Iterator visibilityRulesIterator )
{
if ( visibilityRulesIterator != null )
{
VisibilityDesign visibility = new VisibilityDesign( );
while ( visibilityRulesIterator.hasNext( ) )
{
VisibilityRuleDesign hide = createHide( (HideRuleHandle) visibilityRulesIterator
.next( ) );
visibility.addRule( hide );
}
if ( visibility.count( ) == 0 )
{
return null;
}
return visibility;
}
return null;
}
/**
* Creates the visibility rule( i.e. the hide)
*
* @param handle
* the DE's handle
* @return the created visibility rule
*/
protected VisibilityRuleDesign createHide( HideRuleHandle handle )
{
VisibilityRuleDesign rule = new VisibilityRuleDesign( );
rule.setExpression( createExpression( handle.getExpression( ) ) );
rule.setFormat( handle.getFormat( ) );
return rule;
}
/**
* setup the attribute of report item
*
* @param item
* Engine's Report Item
* @param handle
* DE's report item.
*/
private void setupReportItem( ReportItemDesign item, ReportItemHandle handle )
{
setupStyledElement( item, handle );
// x, y, width & height
DimensionType height = createDimension( handle.getHeight( ) );
DimensionType width = createDimension( handle.getWidth( ) );
DimensionType x = createDimension( handle.getX( ) );
DimensionType y = createDimension( handle.getY( ) );
item.setHeight( height );
item.setWidth( width );
item.setX( x );
item.setY( y );
// setup TOC expression
String toc = handle.getTocExpression( );
item.setTOC( createExpression( toc ) );
// setup book mark
String bookmark = handle.getBookmark( );
item.setBookmark( createExpression( bookmark ) );
String onCreate = handle.getOnCreate( );
item.setOnCreate( createExpression( onCreate ) );
item.setOnRender( handle.getOnRender( ) );
// Sets up the visibility
Iterator visibilityIter = handle.visibilityRulesIterator( );
VisibilityDesign visibility = createVisibility( visibilityIter );
item.setVisibility( visibility );
setHighlight( item, null );
}
/**
* setup report element attribute
*
* @param elem
* engine's report element
* @param handle
* DE's report element
*/
private void setupReportElement( ReportElementDesign element,
DesignElementHandle handle )
{
element.setHandle( handle );
element.setName( handle.getName( ) );
element.setID( handle.getID( ) );
DesignElementHandle extend = handle.getExtends( );
if ( extend != null )
{
element.setExtends( extend.getName( ) );
}
// handle the properties
Iterator iter = handle.getPropertyIterator( );
if ( iter != null )
{
PropertyHandle propHandle = (PropertyHandle) iter.next( );
if ( propHandle != null && propHandle.isSet( ) )
{
String name = propHandle.getDefn( ).getName( );
Object value = propHandle.getValue( );
assert name != null;
assert value != null;
Map properties = element.getCustomProperties( );
assert properties != null;
properties.put( name, value );
}
}
setupNamedExpressions( handle, element.getNamedExpressions( ) );
setupElementIDMap( element );
}
protected String createExpression( String expr )
{
if ( expr != null && !expr.trim( ).equals( "" ) )
{
return expr;
}
return null;
}
/**
* create a Action.
*
* @param handle
* action in DE
* @return action in Engine.
*/
protected ActionDesign createAction( ActionHandle handle )
{
ActionDesign action = new ActionDesign( );
String linkType = handle.getLinkType( );
if ( EngineIRConstants.ACTION_LINK_TYPE_HYPERLINK.equals( linkType ) )
{
action.setHyperlink( createExpression( handle.getURI( ) ) );
action.setTargetWindow( handle.getTargetWindow( ) );
}
else if ( EngineIRConstants.ACTION_LINK_TYPE_BOOKMARK_LINK
.equals( linkType ) )
{
action
.setBookmark( createExpression( handle.getTargetBookmark( ) ) );
}
else if ( EngineIRConstants.ACTION_LINK_TYPE_DRILL_THROUGH
.equals( linkType ) )
{
action.setTargetWindow( handle.getTargetWindow( ) );
DrillThroughActionDesign drillThrough = new DrillThroughActionDesign( );
action.setDrillThrough( drillThrough );
drillThrough.setReportName( handle.getReportName( ) );
drillThrough.setFormat( handle.getFormatType( ) );
drillThrough.setBookmark( createExpression( handle
.getTargetBookmark( ) ) );
Map params = new HashMap( );
Iterator paramIte = handle.paramBindingsIterator( );
while ( paramIte.hasNext( ) )
{
ParamBindingHandle member = (ParamBindingHandle) paramIte
.next( );
params.put( member.getParamName( ), createExpression( member
.getExpression( ) ) );
}
drillThrough.setParameters( params );
// XXX Search criteria is not supported yet.
// Map search = new HashMap( );
// Iterator searchIte = handle.searchIterator( );
// while ( searchIte.hasNext( ) )
// SearchKeyHandle member = (SearchKeyHandle) paramIte.next( );
// params
// .put( member., member
// .getValue( ) );
// drillThrough.setSearch( search );
}
else
{
assert ( false );
}
return action;
}
/**
* create a highlight rule from a structure handle.
*
* @param ruleHandle
* rule in the MODEL.
* @return rule design, null if exist any error.
*/
protected HighlightRuleDesign createHighlightRule(
StructureHandle ruleHandle, String defaultStr )
{
HighlightRuleDesign rule = new HighlightRuleDesign( );
MemberHandle hOperator = ruleHandle
.getMember( HighlightRule.OPERATOR_MEMBER );
MemberHandle hValue1 = ruleHandle
.getMember( HighlightRule.VALUE1_MEMBER );
MemberHandle hValue2 = ruleHandle
.getMember( HighlightRule.VALUE2_MEMBER );
MemberHandle hTestExpr = ruleHandle
.getMember( HighlightRule.TEST_EXPR_MEMBER );
String oper = hOperator.getStringValue( );
String value1 = hValue1.getStringValue( );
String value2 = hValue2.getStringValue( );
String testExpr = hTestExpr.getStringValue( );
rule.setExpression( oper, value1, value2 );
if ( testExpr != null && testExpr.length( ) > 0 )
{
rule.setTestExpression( testExpr );
}
else if ( ( defaultStr != null ) && defaultStr.length( ) > 0 )
{
rule.setTestExpression( defaultStr );
}
else
{
// test expression is null
return null;
}
// all other properties are style properties,
// copy those properties into a style design.
StyleDeclaration style = new StyleDeclaration( cssEngine );
setupStyle( ruleHandle, style );
// this rule is empty, so we can drop it safely.
if ( style.isEmpty( ) )
{
return null;
}
rule.setStyle( style );
ConditionalExpression condExpr = new ConditionalExpression( rule
.getTestExpression( ),
toDteFilterOperator( rule.getOperator( ) ), rule.getValue1( ),
rule.getValue2( ) );
rule.setConditionExpr( condExpr );
return rule;
}
/**
* create highlight defined in the handle.
*
* @param item
* styled item.
*/
protected void setHighlight( StyledElementDesign item, String defaultStr )
{
StyleHandle handle = item.getHandle( ).getPrivateStyle( );
if ( handle == null )
{
return;
}
// hightlight Rules
Iterator iter = handle.highlightRulesIterator( );
if ( iter == null )
{
return;
}
HighlightDesign highlight = new HighlightDesign( );
while ( iter.hasNext( ) )
{
HighlightRuleHandle ruleHandle = (HighlightRuleHandle) iter.next( );
HighlightRuleDesign rule = createHighlightRule( ruleHandle,
defaultStr );
if ( rule != null )
{
highlight.addRule( rule );
}
}
if ( highlight.getRuleCount( ) > 0 )
{
item.setHighlight( highlight );
}
}
/**
* setup a Map.
*
* @param item
* styled item;
*/
protected void setMap( StyledElementDesign item, String defaultStr )
{
StyleHandle handle = item.getHandle( ).getPrivateStyle( );
if ( handle == null )
{
return;
}
Iterator iter = handle.mapRulesIterator( );
if ( iter == null )
{
return;
}
MapDesign map = new MapDesign( );
while ( iter.hasNext( ) )
{
MapRuleHandle ruleHandle = (MapRuleHandle) iter.next( );
MapRuleDesign rule = createMapRule( ruleHandle, defaultStr );
if ( rule != null )
{
map.addRule( rule );
}
}
if ( map.getRuleCount( ) > 0 )
{
item.setMap( map );
}
}
/**
* create a map rule.
*
* @param obj
* map rule in DE.
* @return map rule in ENGINE.
*/
protected MapRuleDesign createMapRule( MapRuleHandle handle,
String defaultStr )
{
MapRuleDesign rule = new MapRuleDesign( );
rule.setExpression( handle.getOperator( ), handle.getValue1( ), handle
.getValue2( ) );
rule.setDisplayText( handle.getDisplayKey( ), handle.getDisplay( ) );
String testExpr = handle.getTestExpression( );
if ( testExpr != null && testExpr.length( ) > 0 )
{
rule.setTestExpression( testExpr );
}
else if ( ( defaultStr != null ) && defaultStr.length( ) > 0 )
{
rule.setTestExpression( defaultStr );
}
else
{
// test expression is null
return null;
}
ConditionalExpression condExpr = new ConditionalExpression( rule
.getTestExpression( ),
toDteFilterOperator( rule.getOperator( ) ), rule.getValue1( ),
rule.getValue2( ) );
rule.setConditionExpr( condExpr );
return rule;
}
/**
* Checks if a given style is in report's style list, if not, assign a
* unique name to it and then add it to the style list.
*
* @param style
* The <code>StyleDeclaration</code> object.
* @return the name of the style.
*/
private String assignStyleName( StyleDeclaration style )
{
if ( style == null || style.isEmpty( ) )
{
return null;
}
// Check if the style is already in report's style list
for ( int i = 0; i < report.getStyleCount( ); i++ )
{
// Cast the type mandatorily
StyleDeclaration cachedStyle = (StyleDeclaration) report
.getStyle( i );
if ( cachedStyle.equals( style ) )
{
// There exist a style which has same properties with this
// one,
style = cachedStyle;
return Report.PREFIX_STYLE_NAME + i;
}
}
// the style is a new style, we need create a unique name for
// it, and
// add it into the report's style list.
String styleName = Report.PREFIX_STYLE_NAME + report.getStyleCount( );
report.addStyle( styleName, style );
return styleName;
}
protected String getElementProperty( ReportElementHandle handle, String name )
{
return getElementProperty( handle, name, false );
}
protected String getElementProperty( ReportElementHandle handle,
String name, boolean isColorProperty )
{
FactoryPropertyHandle prop = handle.getFactoryPropertyHandle( name );
if ( prop != null && prop.isSet( ) )
{
if ( isColorProperty )
{
return prop.getColorValue( );
}
return prop.getStringValue( );
}
return null;
}
String getElementColorProperty( ReportElementHandle handle, String name )
{
FactoryPropertyHandle prop = handle.getFactoryPropertyHandle( name );
if ( prop != null && prop.isSet( ) )
{
return prop.getColorValue( );
}
return null;
}
protected StyleDeclaration createPrivateStyle( ReportElementHandle handle )
{
return createPrivateStyle( handle, true );
}
protected String decodePageBreak( String pageBreak )
{
if ( pageBreak == null )
{
return null;
}
if ( DesignChoiceConstants.PAGE_BREAK_AFTER_ALWAYS.equals( pageBreak ) )
{
return IStyle.CSS_ALWAYS_VALUE;
}
if ( DesignChoiceConstants.PAGE_BREAK_AFTER_ALWAYS_EXCLUDING_LAST
.equals( pageBreak ) )
{
return IStyle.CSS_ALWAYS_VALUE;
}
if ( DesignChoiceConstants.PAGE_BREAK_AFTER_AUTO.equals( pageBreak ) )
{
return IStyle.CSS_AUTO_VALUE;
}
if ( DesignChoiceConstants.PAGE_BREAK_AFTER_AVOID.equals( pageBreak ) )
{
return IStyle.CSS_AVOID_VALUE;
}
if ( DesignChoiceConstants.PAGE_BREAK_BEFORE_ALWAYS.equals( pageBreak ) )
{
return IStyle.CSS_ALWAYS_VALUE;
}
if ( DesignChoiceConstants.PAGE_BREAK_BEFORE_ALWAYS_EXCLUDING_FIRST
.equals( pageBreak ) )
{
return IStyle.CSS_ALWAYS_VALUE;
}
if ( DesignChoiceConstants.PAGE_BREAK_BEFORE_AUTO.equals( pageBreak ) )
{
return IStyle.CSS_AUTO_VALUE;
}
if ( DesignChoiceConstants.PAGE_BREAK_BEFORE_AVOID.equals( pageBreak ) )
{
return IStyle.CSS_AVOID_VALUE;
}
return IStyle.CSS_AUTO_VALUE;
}
protected StyleDeclaration createPrivateStyle( ReportElementHandle handle,
boolean isContainer )
{
// Background
StyleDeclaration style = new StyleDeclaration( cssEngine );
style.setBackgroundColor( getElementProperty( handle,
Style.BACKGROUND_COLOR_PROP, true ) );
style.setBackgroundImage( getElementProperty( handle,
Style.BACKGROUND_IMAGE_PROP ) );
style.setBackgroundPositionX( getElementProperty( handle,
Style.BACKGROUND_POSITION_X_PROP ) );
style.setBackgroundPositionY( getElementProperty( handle,
Style.BACKGROUND_POSITION_Y_PROP ) );
style.setBackgroundRepeat( getElementProperty( handle,
Style.BACKGROUND_REPEAT_PROP ) );
// Text related
style
.setTextAlign( getElementProperty( handle,
Style.TEXT_ALIGN_PROP ) );
style
.setTextIndent( getElementProperty( handle,
Style.TEXT_INDENT_PROP ) );
style.setTextUnderline( getElementProperty( handle,
Style.TEXT_UNDERLINE_PROP ) );
style.setTextLineThrough( getElementProperty( handle,
Style.TEXT_LINE_THROUGH_PROP ) );
style.setTextOverline( getElementProperty( handle,
Style.TEXT_OVERLINE_PROP ) );
style.setLetterSpacing( getElementProperty( handle,
Style.LETTER_SPACING_PROP ) );
style
.setLineHeight( getElementProperty( handle,
Style.LINE_HEIGHT_PROP ) );
style.setOrphans( getElementProperty( handle, Style.ORPHANS_PROP ) );
style.setTextTransform( getElementProperty( handle,
Style.TEXT_TRANSFORM_PROP ) );
style.setVerticalAlign( getElementProperty( handle,
Style.VERTICAL_ALIGN_PROP ) );
style
.setWhiteSpace( getElementProperty( handle,
Style.WHITE_SPACE_PROP ) );
style.setWidows( getElementProperty( handle, Style.WIDOWS_PROP ) );
style.setWordSpacing( getElementProperty( handle,
Style.WORD_SPACING_PROP ) );
// Section properties
style.setDisplay( getElementProperty( handle, Style.DISPLAY_PROP ) );
style
.setMasterPage( getElementProperty( handle,
Style.MASTER_PAGE_PROP ) );
String pageBreakAfter = getElementProperty(handle, StyleHandle.PAGE_BREAK_AFTER_PROP);
style.setPageBreakAfter( decodePageBreak(pageBreakAfter) );
String pageBreakBefore = getElementProperty( handle,
StyleHandle.PAGE_BREAK_BEFORE_PROP );
style.setPageBreakBefore( decodePageBreak(pageBreakBefore) );
style.setPageBreakInside( getElementProperty( handle,
Style.PAGE_BREAK_INSIDE_PROP ) );
// Font related
style
.setFontFamily( getElementProperty( handle,
Style.FONT_FAMILY_PROP ) );
style.setColor( getElementProperty( handle, Style.COLOR_PROP, true ) );
style.setFontSize( getElementProperty( handle, Style.FONT_SIZE_PROP ) );
style
.setFontStyle( getElementProperty( handle,
Style.FONT_STYLE_PROP ) );
style
.setFontWeight( getElementProperty( handle,
Style.FONT_WEIGHT_PROP ) );
style.setFontVariant( getElementProperty( handle,
Style.FONT_VARIANT_PROP ) );
// Border
style.setBorderBottomColor( getElementProperty( handle,
Style.BORDER_BOTTOM_COLOR_PROP, true ) );
style.setBorderBottomStyle( getElementProperty( handle,
Style.BORDER_BOTTOM_STYLE_PROP ) );
style.setBorderBottomWidth( getElementProperty( handle,
Style.BORDER_BOTTOM_WIDTH_PROP ) );
style.setBorderLeftColor( getElementProperty( handle,
Style.BORDER_LEFT_COLOR_PROP, true ) );
style.setBorderLeftStyle( getElementProperty( handle,
Style.BORDER_LEFT_STYLE_PROP ) );
style.setBorderLeftWidth( getElementProperty( handle,
Style.BORDER_LEFT_WIDTH_PROP ) );
style.setBorderRightColor( getElementProperty( handle,
Style.BORDER_RIGHT_COLOR_PROP, true ) );
style.setBorderRightStyle( getElementProperty( handle,
Style.BORDER_RIGHT_STYLE_PROP ) );
style.setBorderRightWidth( getElementProperty( handle,
Style.BORDER_RIGHT_WIDTH_PROP ) );
style.setBorderTopColor( getElementProperty( handle,
Style.BORDER_TOP_COLOR_PROP, true ) );
style.setBorderTopStyle( getElementProperty( handle,
Style.BORDER_TOP_STYLE_PROP ) );
style.setBorderTopWidth( getElementProperty( handle,
Style.BORDER_TOP_WIDTH_PROP ) );
// Margin
style
.setMarginTop( getElementProperty( handle,
Style.MARGIN_TOP_PROP ) );
style
.setMarginLeft( getElementProperty( handle,
Style.MARGIN_LEFT_PROP ) );
style.setMarginBottom( getElementProperty( handle,
Style.MARGIN_BOTTOM_PROP ) );
style.setMarginRight( getElementProperty( handle,
Style.MARGIN_RIGHT_PROP ) );
// Padding
style
.setPaddingTop( getElementProperty( handle,
Style.PADDING_TOP_PROP ) );
style.setPaddingLeft( getElementProperty( handle,
Style.PADDING_LEFT_PROP ) );
style.setPaddingBottom( getElementProperty( handle,
Style.PADDING_BOTTOM_PROP ) );
style.setPaddingRight( getElementProperty( handle,
Style.PADDING_RIGHT_PROP ) );
// Data Formatting
style.setNumberAlign( getElementProperty( handle,
Style.NUMBER_ALIGN_PROP ) );
style.setDateFormat( getElementProperty( handle,
Style.DATE_TIME_FORMAT_PROP ) );
style.setNumberFormat( getElementProperty( handle,
Style.NUMBER_FORMAT_PROP ) );
style.setStringFormat( getElementProperty( handle,
Style.STRING_FORMAT_PROP ) );
// Others
style
.setCanShrink( getElementProperty( handle,
Style.CAN_SHRINK_PROP ) );
style.setShowIfBlank( getElementProperty( handle,
Style.SHOW_IF_BLANK_PROP ) );
return style;
}
String getMemberProperty( StructureHandle handle, String name )
{
MemberHandle prop = handle.getMember( name );
if ( prop != null )
{
return prop.getStringValue( );
}
return null;
}
IStyle setupStyle( StructureHandle highlight, IStyle style )
{
// Background
style.setBackgroundColor( getMemberProperty( highlight,
HighlightRule.BACKGROUND_COLOR_MEMBER ) );
// style.setBackgroundPositionX(getMemberProperty(highlight,
// HighlightRule.BACKGROUND_POSITION_X_MEMBER));
// style.setBackgroundPositionY(getMemberProperty(highlight,
// HighlightRule.BACKGROUND_POSITION_Y_MEMBER));
// style.setBackgroundRepeat(getMemberProperty(highlight,
// HighlightRule.BACKGROUND_REPEAT_MEMBER));
// Text related
style.setTextAlign( getMemberProperty( highlight,
HighlightRule.TEXT_ALIGN_MEMBER ) );
style.setTextIndent( getMemberProperty( highlight,
HighlightRule.TEXT_INDENT_MEMBER ) );
style.setTextUnderline( getMemberProperty( highlight,
Style.TEXT_UNDERLINE_PROP ) );
style.setTextLineThrough( getMemberProperty( highlight,
Style.TEXT_LINE_THROUGH_PROP ) );
style.setTextOverline( getMemberProperty( highlight,
Style.TEXT_OVERLINE_PROP ) );
// style.setLetterSpacing(getMemberProperty(highlight,
// HighlightRule.LETTER_SPACING_MEMBER));
// style.setLineHeight(getMemberProperty(highlight,
// HighlightRule.LINE_HEIGHT_MEMBER));
// style.setOrphans(getMemberProperty(highlight,
// HighlightRule.ORPHANS_MEMBER));
style.setTextTransform( getMemberProperty( highlight,
HighlightRule.TEXT_TRANSFORM_MEMBER ) );
// style.setVerticalAlign(getMemberProperty(highlight,
// HighlightRule.VERTICAL_ALIGN_MEMBER));
// style.setWhiteSpace(getMemberProperty(highlight,
// HighlightRule.WHITE_SPACE_MEMBER));
// style.setWidows(getMemberProperty(highlight,
// HighlightRule.WIDOWS_MEMBER));
// style.setWordSpacing(getMemberProperty(highlight,
// HighlightRule.WORD_SPACING_MEMBER));
// Section properties
// style.setDisplay(getMemberProperty(highlight,
// HighlightRule.DISPLAY_MEMBER));
// style.setMasterPage(getMemberProperty(highlight,
// HighlightRule.MASTER_PAGE_MEMBER));
// style.setPageBreakAfter(getMemberProperty(highlight,
// HighlightRule.PAGE_BREAK_AFTER_MEMBER));
// style.setPageBreakBefore(getMemberProperty(highlight,
// HighlightRule.PAGE_BREAK_BEFORE_MEMBER));
// style.setPageBreakInside(getMemberProperty(highlight,
// HighlightRule.PAGE_BREAK_INSIDE_MEMBER));
// Font related
style.setFontFamily( getMemberProperty( highlight,
HighlightRule.FONT_FAMILY_MEMBER ) );
style.setColor( getMemberProperty( highlight,
HighlightRule.COLOR_MEMBER ) );
style.setFontSize( getMemberProperty( highlight,
HighlightRule.FONT_SIZE_MEMBER ) );
style.setFontStyle( getMemberProperty( highlight,
HighlightRule.FONT_STYLE_MEMBER ) );
style.setFontWeight( getMemberProperty( highlight,
HighlightRule.FONT_WEIGHT_MEMBER ) );
style.setFontVariant( getMemberProperty( highlight,
HighlightRule.FONT_VARIANT_MEMBER ) );
// Border
style.setBorderBottomColor( getMemberProperty( highlight,
HighlightRule.BORDER_BOTTOM_COLOR_MEMBER ) );
style.setBorderBottomStyle( getMemberProperty( highlight,
HighlightRule.BORDER_BOTTOM_STYLE_MEMBER ) );
style.setBorderBottomWidth( getMemberProperty( highlight,
HighlightRule.BORDER_BOTTOM_WIDTH_MEMBER ) );
style.setBorderLeftColor( getMemberProperty( highlight,
HighlightRule.BORDER_LEFT_COLOR_MEMBER ) );
style.setBorderLeftStyle( getMemberProperty( highlight,
HighlightRule.BORDER_LEFT_STYLE_MEMBER ) );
style.setBorderLeftWidth( getMemberProperty( highlight,
HighlightRule.BORDER_LEFT_WIDTH_MEMBER ) );
style.setBorderRightColor( getMemberProperty( highlight,
HighlightRule.BORDER_RIGHT_COLOR_MEMBER ) );
style.setBorderRightStyle( getMemberProperty( highlight,
HighlightRule.BORDER_RIGHT_STYLE_MEMBER ) );
style.setBorderRightWidth( getMemberProperty( highlight,
HighlightRule.BORDER_RIGHT_WIDTH_MEMBER ) );
style.setBorderTopColor( getMemberProperty( highlight,
HighlightRule.BORDER_TOP_COLOR_MEMBER ) );
style.setBorderTopStyle( getMemberProperty( highlight,
HighlightRule.BORDER_TOP_STYLE_MEMBER ) );
style.setBorderTopWidth( getMemberProperty( highlight,
HighlightRule.BORDER_TOP_WIDTH_MEMBER ) );
// Margin
// style.setMarginTop(getMemberProperty(highlight,
// HighlightRule.MARGIN_TOP_MEMBER));
// style.setMarginLeft(getMemberProperty(highlight,
// HighlightRule.MARGIN_LEFT_MEMBER));
// style.setMarginBottom(getMemberProperty(highlight,
// HighlightRule.MARGIN_BOTTOM_MEMBER));
// style.setMarginRight(getMemberProperty(highlight,
// HighlightRule.MARGIN_RIGHT_MEMBER));
// Padding
// style.setPaddingTop(getMemberProperty(highlight,
// HighlightRule.PADDING_TOP_MEMBER));
// style.setPaddingLeft(getMemberProperty(highlight,
// HighlightRule.PADDING_LEFT_MEMBER));
// style.setPaddingBottom(getMemberProperty(highlight,
// HighlightRule.PADDING_BOTTOM_MEMBER));
// style.setPaddingRight(getMemberProperty(highlight,
// HighlightRule.PADDING_RIGHT_MEMBER));
// Data Formatting
style.setNumberAlign( getMemberProperty( highlight,
HighlightRule.NUMBER_ALIGN_MEMBER ) );
style.setDateFormat( getMemberProperty( highlight,
HighlightRule.DATE_TIME_FORMAT_MEMBER ) );
style.setNumberFormat( getMemberProperty( highlight,
HighlightRule.NUMBER_FORMAT_MEMBER ) );
style.setStringFormat( getMemberProperty( highlight,
HighlightRule.STRING_FORMAT_MEMBER ) );
// Others
// style.setCanShrink(getMemberProperty(highlight,
// HighlightRule.CAN_SHRINK_MEMBER));
// style.setShowIfBlank(getMemberProperty(highlight,
// HighlightRule.SHOW_IF_BLANK_MEMBER));
return style;
}
protected DimensionType createDimension( DimensionHandle handle )
{
if ( handle == null || !handle.isSet( ) )
{
return null;
}
// Extended Choice
if ( handle.isKeyword( ) )
{
return new DimensionType( handle.getStringValue( ) );
}
// set measure and unit
double measure = handle.getMeasure( );
String unit = handle.getUnits( );
if ( DimensionValue.DEFAULT_UNIT.equals( unit ) )
{
unit = defaultUnit;
}
return new DimensionType( measure, unit );
}
protected void setupListingItem( ListingDesign listing, ListingHandle handle )
{
// setup related scripts
setupReportItem( listing, handle );
listing.setPageBreakInterval( handle.getPageBreakInterval( ) );
// setup scripts
// listing.setOnStart( handle.getOnStart( ) );
// listing.setOnRow( handle.getOnRow( ) );
// listing.setOnFinish( handle.getOnFinish( ) );
}
// Convert model operator value to DtE IColumnFilter enum value
protected int toDteFilterOperator( String modelOpr )
{
if ( modelOpr.equals( DesignChoiceConstants.FILTER_OPERATOR_EQ ) )
return IConditionalExpression.OP_EQ;
if ( modelOpr.equals( DesignChoiceConstants.FILTER_OPERATOR_NE ) )
return IConditionalExpression.OP_NE;
if ( modelOpr.equals( DesignChoiceConstants.FILTER_OPERATOR_LT ) )
return IConditionalExpression.OP_LT;
if ( modelOpr.equals( DesignChoiceConstants.FILTER_OPERATOR_LE ) )
return IConditionalExpression.OP_LE;
if ( modelOpr.equals( DesignChoiceConstants.FILTER_OPERATOR_GE ) )
return IConditionalExpression.OP_GE;
if ( modelOpr.equals( DesignChoiceConstants.FILTER_OPERATOR_GT ) )
return IConditionalExpression.OP_GT;
if ( modelOpr.equals( DesignChoiceConstants.FILTER_OPERATOR_BETWEEN ) )
return IConditionalExpression.OP_BETWEEN;
if ( modelOpr
.equals( DesignChoiceConstants.FILTER_OPERATOR_NOT_BETWEEN ) )
return IConditionalExpression.OP_NOT_BETWEEN;
if ( modelOpr.equals( DesignChoiceConstants.FILTER_OPERATOR_NULL ) )
return IConditionalExpression.OP_NULL;
if ( modelOpr.equals( DesignChoiceConstants.FILTER_OPERATOR_NOT_NULL ) )
return IConditionalExpression.OP_NOT_NULL;
if ( modelOpr.equals( DesignChoiceConstants.FILTER_OPERATOR_TRUE ) )
return IConditionalExpression.OP_TRUE;
if ( modelOpr.equals( DesignChoiceConstants.FILTER_OPERATOR_FALSE ) )
return IConditionalExpression.OP_FALSE;
if ( modelOpr.equals( DesignChoiceConstants.FILTER_OPERATOR_LIKE ) )
return IConditionalExpression.OP_LIKE;
if ( modelOpr.equals( DesignChoiceConstants.FILTER_OPERATOR_TOP_N ) )
return IConditionalExpression.OP_TOP_N;
if ( modelOpr.equals( DesignChoiceConstants.FILTER_OPERATOR_BOTTOM_N ) )
return IConditionalExpression.OP_BOTTOM_N;
if ( modelOpr
.equals( DesignChoiceConstants.FILTER_OPERATOR_TOP_PERCENT ) )
return IConditionalExpression.OP_TOP_PERCENT;
if ( modelOpr
.equals( DesignChoiceConstants.FILTER_OPERATOR_BOTTOM_PERCENT ) )
return IConditionalExpression.OP_BOTTOM_PERCENT;
if ( modelOpr.equals( DesignChoiceConstants.FILTER_OPERATOR_NOT_LIKE ))
return IConditionalExpression.OP_NOT_LIKE;
if ( modelOpr.equals( DesignChoiceConstants.FILTER_OPERATOR_NOT_MATCH ))
return IConditionalExpression.OP_NOT_MATCH;
/* if ( modelOpr.equals( DesignChoiceConstants.FILTER_OPERATOR_ANY ) )
return IConditionalExpression.OP_ANY;*/
return IConditionalExpression.OP_NONE;
}
protected void addReportDefaultPropertyValue( String name,
StyleHandle handle )
{
addReportDefaultPropertyValue( name, handle, false );
}
protected void addReportDefaultPropertyValue( String name,
StyleHandle handle, boolean isColorProperty )
{
Object value = null;
int index = StylePropertyMapping.getPropertyID( name );
if ( StylePropertyMapping.canInherit( name ) )
{
if ( handle != null )
{
if ( isColorProperty )
{
value = handle.getColorProperty( name ).getStringValue( );
}
else
{
value = handle.getProperty( name );
}
}
if ( value == null )
{
value = StylePropertyMapping.getDefaultValue( name );
}
inheritableReportStyle.setCssText( index, value == null
? null
: value.toString( ) );
}
else
{
value = StylePropertyMapping.getDefaultValue( name );
nonInheritableReportStyle.setCssText( index, value == null
? null
: value.toString( ) );
}
}
/**
* Creates Report default styles
*/
protected void createReportDefaultStyles( StyleHandle handle )
{
nonInheritableReportStyle = new StyleDeclaration( cssEngine );
inheritableReportStyle = new StyleDeclaration( cssEngine );
// Background
addReportDefaultPropertyValue( Style.BACKGROUND_COLOR_PROP, handle,
true );
addReportDefaultPropertyValue( Style.BACKGROUND_IMAGE_PROP, handle );
addReportDefaultPropertyValue( Style.BACKGROUND_POSITION_X_PROP, handle );
addReportDefaultPropertyValue( Style.BACKGROUND_POSITION_Y_PROP, handle );
addReportDefaultPropertyValue( Style.BACKGROUND_REPEAT_PROP, handle );
// Text related
addReportDefaultPropertyValue( Style.TEXT_ALIGN_PROP, handle );
addReportDefaultPropertyValue( Style.TEXT_INDENT_PROP, handle );
addReportDefaultPropertyValue( Style.LETTER_SPACING_PROP, handle );
addReportDefaultPropertyValue( Style.LINE_HEIGHT_PROP, handle );
addReportDefaultPropertyValue( Style.ORPHANS_PROP, handle );
addReportDefaultPropertyValue( Style.TEXT_TRANSFORM_PROP, handle );
addReportDefaultPropertyValue( Style.VERTICAL_ALIGN_PROP, handle );
addReportDefaultPropertyValue( Style.WHITE_SPACE_PROP, handle );
addReportDefaultPropertyValue( Style.WIDOWS_PROP, handle );
addReportDefaultPropertyValue( Style.WORD_SPACING_PROP, handle );
// Section properties
addReportDefaultPropertyValue( Style.DISPLAY_PROP, handle );
addReportDefaultPropertyValue( Style.MASTER_PAGE_PROP, handle );
addReportDefaultPropertyValue( Style.PAGE_BREAK_AFTER_PROP, handle );
addReportDefaultPropertyValue( Style.PAGE_BREAK_BEFORE_PROP, handle );
addReportDefaultPropertyValue( Style.PAGE_BREAK_INSIDE_PROP, handle );
// Font related
addReportDefaultPropertyValue( Style.FONT_FAMILY_PROP, handle );
addReportDefaultPropertyValue( Style.COLOR_PROP, handle, true );
addReportDefaultPropertyValue( Style.FONT_SIZE_PROP, handle );
addReportDefaultPropertyValue( Style.FONT_STYLE_PROP, handle );
addReportDefaultPropertyValue( Style.FONT_WEIGHT_PROP, handle );
addReportDefaultPropertyValue( Style.FONT_VARIANT_PROP, handle );
// Text decoration
addReportDefaultPropertyValue( Style.TEXT_LINE_THROUGH_PROP, handle );
addReportDefaultPropertyValue( Style.TEXT_OVERLINE_PROP, handle );
addReportDefaultPropertyValue( Style.TEXT_UNDERLINE_PROP, handle );
// Border
addReportDefaultPropertyValue( Style.BORDER_BOTTOM_COLOR_PROP, handle,
true );
addReportDefaultPropertyValue( Style.BORDER_BOTTOM_STYLE_PROP, handle );
addReportDefaultPropertyValue( Style.BORDER_BOTTOM_WIDTH_PROP, handle );
addReportDefaultPropertyValue( Style.BORDER_LEFT_COLOR_PROP, handle,
true );
addReportDefaultPropertyValue( Style.BORDER_LEFT_STYLE_PROP, handle );
addReportDefaultPropertyValue( Style.BORDER_LEFT_WIDTH_PROP, handle );
addReportDefaultPropertyValue( Style.BORDER_RIGHT_COLOR_PROP, handle,
true );
addReportDefaultPropertyValue( Style.BORDER_RIGHT_STYLE_PROP, handle );
addReportDefaultPropertyValue( Style.BORDER_RIGHT_WIDTH_PROP, handle );
addReportDefaultPropertyValue( Style.BORDER_TOP_COLOR_PROP, handle,
true );
addReportDefaultPropertyValue( Style.BORDER_TOP_STYLE_PROP, handle );
addReportDefaultPropertyValue( Style.BORDER_TOP_WIDTH_PROP, handle );
// Margin
addReportDefaultPropertyValue( Style.MARGIN_TOP_PROP, handle );
addReportDefaultPropertyValue( Style.MARGIN_LEFT_PROP, handle );
addReportDefaultPropertyValue( Style.MARGIN_BOTTOM_PROP, handle );
addReportDefaultPropertyValue( Style.MARGIN_RIGHT_PROP, handle );
// Padding
addReportDefaultPropertyValue( Style.PADDING_TOP_PROP, handle );
addReportDefaultPropertyValue( Style.PADDING_LEFT_PROP, handle );
addReportDefaultPropertyValue( Style.PADDING_BOTTOM_PROP, handle );
addReportDefaultPropertyValue( Style.PADDING_RIGHT_PROP, handle );
report.setRootStyleName( assignStyleName( inheritableReportStyle ) );
if ( nonInheritableReportStyle.isEmpty( ) )
{
nonInheritableReportStyle = null;
}
else
{
report.setDefaultStyle( nonInheritableReportStyle );
}
}
/**
* Creates the body style for master page.
*
* @param design
* the master page design
* @return the content style
*/
protected String setupBodyStyle( MasterPageDesign design )
{
String styleName = design.getStyleName( );
IStyle style = report.findStyle( styleName );
if ( style == null || style.isEmpty( ) )
{
return null;
}
StyleDeclaration contentStyle = new StyleDeclaration( cssEngine );
contentStyle.setProperty( IStyle.STYLE_BACKGROUND_COLOR, style
.getProperty( IStyle.STYLE_BACKGROUND_COLOR ) );
contentStyle.setProperty( IStyle.STYLE_BACKGROUND_IMAGE, style
.getProperty( IStyle.STYLE_BACKGROUND_IMAGE ) );
contentStyle.setProperty( IStyle.STYLE_BACKGROUND_POSITION_Y, style
.getProperty( IStyle.STYLE_BACKGROUND_POSITION_Y ) );
contentStyle.setProperty( IStyle.STYLE_BACKGROUND_POSITION_X, style
.getProperty( IStyle.STYLE_BACKGROUND_POSITION_X ) );
contentStyle.setProperty( IStyle.STYLE_BACKGROUND_REPEAT, style
.getProperty( IStyle.STYLE_BACKGROUND_REPEAT ) );
String bodyStyleName = assignStyleName( contentStyle );
return bodyStyleName;
}
private void setupElementIDMap( ReportElementDesign rptElement )
{
report.setReportItemInstanceID( rptElement.getID( ), rptElement );
}
} |
package org.mariadb.jdbc;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertTrue;
import java.sql.Connection;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.sql.SQLNonTransientConnectionException;
import java.sql.Statement;
import java.util.Random;
import org.junit.Ignore;
import org.junit.Test;
public class TimeoutTest extends BaseTest {
/**
* CONJ-79
*
* @throws SQLException
*/
@Test
public void resultSetAfterSocketTimeoutTest() throws SQLException {
setConnection("&connectTimeout=5&socketTimeout=5");
boolean bugReproduced = false;
int exc = 0;
int went = 0;
for (int i = 0; i < 10000; i++) {
try {
int v1 = selectValue(connection, 1);
int v2 = selectValue(connection, 2);
if (v1 != 1 || v2 != 2) {
bugReproduced = true;
break;
}
assertTrue(v1 == 1 && v2 == 2);
went++;
} catch (Exception e) {
exc++;
}
}
assertFalse(bugReproduced); // either Exception or fine
assertTrue(went > 0);
assertTrue(went + exc == 10000);
}
private static int selectValue(Connection conn, int value)
throws SQLException {
Statement stmt = null;
ResultSet rs = null;
try {
stmt = conn.createStatement();
rs = stmt.executeQuery("select " + value);
rs.next();
return rs.getInt(1);
} finally {
if (rs != null) {
rs.close();
}
if (stmt != null) {
stmt.close();
}
}
}
/**
* CONJ-79
*
* @throws SQLException
*/
@Test
public void socketTimeoutTest() throws SQLException {
int exceptionCount = 0;
// set a short connection timeout
setConnection("&connectTimeout=5&socketTimeout=5");
PreparedStatement ps = connection.prepareStatement("SELECT 1");
ResultSet rs = ps.executeQuery();
rs.next();
logInfo(rs.getString(1));
// wait for the connection to time out
ps = connection.prepareStatement("SELECT sleep(1)");
// a timeout should occur here
try
{
rs = ps.executeQuery();
} catch (SQLException e) {
// check that it's a timeout that occurs
if (e.getMessage().contains("timed out"))
exceptionCount++;
}
ps = connection.prepareStatement("SELECT 2");
// connection should be closed here, exception expected
try
{
rs = ps.executeQuery();
rs.next();
} catch (SQLException e) {
// check that it's a execute "called on closed" exception that occurs
if (e.getMessage().contains("called on closed"))
exceptionCount++;
}
// the connection should be closed
assertTrue(connection.isClosed());
// there should have been two exceptions
assertTrue(exceptionCount == 2);
}
@Test
public void waitTimeoutStatementTest() throws SQLException, InterruptedException {
Statement statement = connection.createStatement();
statement.execute("set session wait_timeout=1");
Thread.sleep(3000); // Wait for the server to kill the connection
logInfo(connection.toString());
// here a SQLNonTransientConnectionException is expected
// "Could not read resultset: unexpected end of stream, ..."
try
{
statement.execute("SELECT 1");
} catch (SQLException e) {
// verify that the correct type of exception is thrown
assertTrue(e.getMessage().contains("Could not read resultset"));
}
statement.close();
connection.close();
connection = null;
}
@Test
public void waitTimeoutResultSetTest() throws SQLException, InterruptedException {
Statement stmt = connection.createStatement();
ResultSet rs = stmt.executeQuery("SELECT 1");
rs.next();
stmt.execute("set session wait_timeout=1");
Thread.sleep(3000); // Wait for the server to kill the connection
// here a SQLNonTransientConnectionException is expected
// "Could not read resultset: unexpected end of stream, ..."
try
{
rs = stmt.executeQuery("SELECT 2");
rs.next();
} catch (SQLException e) {
// verify that the correct type of exception is thrown
assertTrue(e.getMessage().contains("Could not read resultset"));
}
}
// CONJ-68
// TODO: this test is not yet able to repeat the bug. Ignore until then.
@Ignore
@Test
public void lastPacketFailedTest() throws SQLException
{
Statement stmt = connection.createStatement();
stmt.execute("DROP TABLE IF EXISTS `pages_txt`");
stmt.execute("CREATE TABLE `pages_txt` (`id` INT(10) UNSIGNED NOT NULL, `title` TEXT NOT NULL, `txt` MEDIUMTEXT NOT NULL, PRIMARY KEY (`id`)) COLLATE='utf8_general_ci' ENGINE=MyISAM;");
//create arbitrary long strings
String chars = "0123456789abcdefghijklmnopqrstuvwxyzåäöABCDEFGHIJKLMNOPQRSTUVWXYZÅÄÖ,;.:-_*¨^+?!<>
StringBuffer outputBuffer = null;
Random r = null;
for(int i = 1; i < 2001; i++)
{
r = new Random();
outputBuffer = new StringBuffer(i);
for (int j = 0; j < i; j++){
outputBuffer.append(chars.charAt(r.nextInt(chars.length())));
}
stmt.execute("insert into pages_txt values (" + i + ", '" + outputBuffer.toString() + "' , 'txt')");
}
}
} |
package org.geomajas.gwt2.example.client.sample.general;
import org.geomajas.command.dto.TransformGeometryRequest;
import org.geomajas.command.dto.TransformGeometryResponse;
import org.geomajas.geometry.Bbox;
import org.geomajas.gwt.client.command.AbstractCommandCallback;
import org.geomajas.gwt.client.command.GwtCommand;
import org.geomajas.gwt2.client.GeomajasImpl;
import org.geomajas.gwt2.client.GeomajasServerExtension;
import org.geomajas.gwt2.client.event.MapInitializationEvent;
import org.geomajas.gwt2.client.event.MapInitializationHandler;
import org.geomajas.gwt2.client.map.MapConfiguration;
import org.geomajas.gwt2.client.map.MapPresenter;
import org.geomajas.gwt2.client.map.layer.Layer;
import org.geomajas.gwt2.example.base.client.ExampleBase;
import org.geomajas.gwt2.example.base.client.sample.SamplePanel;
import com.google.gwt.core.client.Callback;
import com.google.gwt.core.client.GWT;
import com.google.gwt.event.dom.client.ClickEvent;
import com.google.gwt.event.dom.client.KeyCodes;
import com.google.gwt.event.dom.client.KeyUpEvent;
import com.google.gwt.event.dom.client.KeyUpHandler;
import com.google.gwt.event.logical.shared.ValueChangeEvent;
import com.google.gwt.event.logical.shared.ValueChangeHandler;
import com.google.gwt.geolocation.client.Geolocation;
import com.google.gwt.geolocation.client.Position;
import com.google.gwt.geolocation.client.PositionError;
import com.google.gwt.uibinder.client.UiBinder;
import com.google.gwt.uibinder.client.UiField;
import com.google.gwt.uibinder.client.UiHandler;
import com.google.gwt.user.client.Window;
import com.google.gwt.user.client.ui.CheckBox;
import com.google.gwt.user.client.ui.DecoratorPanel;
import com.google.gwt.user.client.ui.ResizeLayoutPanel;
import com.google.gwt.user.client.ui.TextBox;
import com.google.gwt.user.client.ui.VerticalPanel;
import com.google.gwt.user.client.ui.Widget;
/**
* ContentPanel that demonstrates some options regarding map navigation.
*
* @author Pieter De Graef
*/
public class NavigationOptionPanel implements SamplePanel {
/**
* UI binder for this widget.
*
* @author Pieter De Graef
*/
interface MyUiBinder extends UiBinder<Widget, NavigationOptionPanel> {
}
private static final MyUiBinder UI_BINDER = GWT.create(MyUiBinder.class);
private final int defaultMillis = 400;
private final int defaultFadeInMillis = 250;
private MapPresenter mapPresenter;
@UiField
protected TextBox millisBox;
@UiField
protected TextBox fadeInBox;
@UiField
protected CheckBox cancelAnimationSupport;
@UiField
protected VerticalPanel layerPanel;
@UiField
protected ResizeLayoutPanel mapPanel;
public Widget asWidget() {
Widget layout = UI_BINDER.createAndBindUi(this);
// Initialize the map, and return the layout:
mapPresenter = GeomajasImpl.getInstance().createMapPresenter();
mapPresenter.setSize(480, 480);
mapPresenter.getEventBus().addMapInitializationHandler(new MyMapInitializationHandler());
GeomajasServerExtension.getInstance().initializeMap(mapPresenter, "gwt-app", "mapCountries");
DecoratorPanel mapDecorator = new DecoratorPanel();
mapDecorator.add(mapPresenter.asWidget());
mapPanel.add(mapDecorator);
// Make sure the text box also reacts to the "Enter" key:
millisBox.addKeyUpHandler(new KeyUpHandler() {
public void onKeyUp(KeyUpEvent event) {
if (event.getNativeKeyCode() == KeyCodes.KEY_ENTER) {
changeAnimationMillis();
}
}
});
fadeInBox.addKeyUpHandler(new KeyUpHandler() {
public void onKeyUp(KeyUpEvent event) {
if (event.getNativeKeyCode() == KeyCodes.KEY_ENTER) {
changeFadeInMillis();
}
}
});
cancelAnimationSupport.addValueChangeHandler(new ValueChangeHandler<Boolean>() {
public void onValueChange(ValueChangeEvent<Boolean> event) {
mapPresenter.getConfiguration().setHintValue(MapConfiguration.ANIMATION_CANCEL_SUPPORT,
cancelAnimationSupport.getValue());
}
});
return layout;
}
@UiHandler("millisBtn")
protected void onMillisButtonClicked(ClickEvent event) {
changeAnimationMillis();
}
@UiHandler("fadeInBtn")
protected void onFadeInButtonClicked(ClickEvent event) {
changeFadeInMillis();
}
@UiHandler("currentLocationBtn")
protected void onCurrentLocationButtonClicked(ClickEvent event) {
if (Geolocation.isSupported()) {
Geolocation.getIfSupported().getCurrentPosition(new Callback<Position, PositionError>() {
@Override
public void onSuccess(Position result) {
TransformGeometryRequest request = new TransformGeometryRequest();
request.setBounds(new Bbox(result.getCoordinates().getLongitude(), result.getCoordinates()
.getLatitude(), 0, 0));
request.setSourceCrs("EPSG:4326");
request.setTargetCrs(mapPresenter.getViewPort().getCrs());
GwtCommand command = new GwtCommand(TransformGeometryRequest.COMMAND);
command.setCommandRequest(request);
GeomajasServerExtension.getInstance().getCommandService()
.execute(command, new AbstractCommandCallback<TransformGeometryResponse>() {
@Override
public void execute(TransformGeometryResponse response) {
mapPresenter.getViewPort().applyBounds(response.getBounds());
}
});
};
@Override
public void onFailure(PositionError reason) {
// TODO Auto-generated method stub
}
});
}
}
private void changeAnimationMillis() {
String txt = millisBox.getValue();
int time = defaultMillis;
try {
time = Integer.parseInt(txt);
} catch (Exception e) { // NOSONAR
Window.alert("Could not parse milliseconds... Default value of " + defaultMillis + " is used");
mapPresenter.getConfiguration().setHintValue(MapConfiguration.ANIMATION_TIME, defaultMillis);
millisBox.setValue(defaultMillis + "");
}
mapPresenter.getConfiguration().setHintValue(MapConfiguration.ANIMATION_TIME, time);
}
private void changeFadeInMillis() {
String txt = fadeInBox.getValue();
int time = defaultFadeInMillis;
try {
time = Integer.parseInt(txt);
} catch (Exception e) { // NOSONAR
Window.alert("Could not parse milliseconds... Default value of " + defaultFadeInMillis + " is used");
mapPresenter.getConfiguration().setHintValue(MapConfiguration.FADE_IN_TIME, defaultMillis);
fadeInBox.setValue(defaultFadeInMillis + "");
}
mapPresenter.getConfiguration().setHintValue(MapConfiguration.FADE_IN_TIME, time);
}
/**
* Map initialization handler that adds checkboxes for every layer to enable/disable animated rendering for those
* layers.
*
* @author Pieter De Graef
*/
private class MyMapInitializationHandler implements MapInitializationHandler {
public void onMapInitialized(MapInitializationEvent event) {
// Add layer specific animation CheckBoxes:
for (int i = 0; i < mapPresenter.getLayersModel().getLayerCount(); i++) {
final Layer layer = mapPresenter.getLayersModel().getLayer(i);
CheckBox cb = new CheckBox("Animate: " + layer.getTitle());
cb.setValue(mapPresenter.getLayersModelRenderer().isAnimated(layer));
cb.addValueChangeHandler(new ValueChangeHandler<Boolean>() {
public void onValueChange(ValueChangeEvent<Boolean> event) {
mapPresenter.getLayersModelRenderer().setAnimated(layer, event.getValue());
}
});
layerPanel.add(cb);
}
// Zoom in (scale times 4), to get a better view:
mapPresenter.getViewPort().applyBounds(ExampleBase.BBOX_AFRICA);
}
}
} |
package com.yox89.ld32.actors;
import javax.swing.plaf.basic.BasicScrollPaneUI.HSBChangeListener;
import box2dLight.PointLight;
import com.badlogic.gdx.Gdx;
import com.badlogic.gdx.Input.Keys;
import com.badlogic.gdx.graphics.Color;
import com.badlogic.gdx.graphics.Texture;
import com.badlogic.gdx.graphics.g2d.Animation;
import com.badlogic.gdx.graphics.g2d.Animation.PlayMode;
import com.badlogic.gdx.graphics.g2d.Batch;
import com.badlogic.gdx.graphics.g2d.BitmapFont;
import com.badlogic.gdx.graphics.g2d.TextureRegion;
import com.badlogic.gdx.maps.MapProperties;
import com.badlogic.gdx.math.Interpolation;
import com.badlogic.gdx.math.Vector2;
import com.badlogic.gdx.physics.box2d.Body;
import com.badlogic.gdx.physics.box2d.BodyDef;
import com.badlogic.gdx.physics.box2d.BodyDef.BodyType;
import com.badlogic.gdx.physics.box2d.CircleShape;
import com.badlogic.gdx.physics.box2d.FixtureDef;
import com.badlogic.gdx.scenes.scene2d.Stage;
import com.badlogic.gdx.scenes.scene2d.Touchable;
import com.badlogic.gdx.scenes.scene2d.actions.Actions;
import com.badlogic.gdx.scenes.scene2d.ui.Label;
import com.badlogic.gdx.scenes.scene2d.ui.Label.LabelStyle;
import com.yox89.ld32.Physics;
import com.yox89.ld32.util.Collision;
import com.yox89.ld32.util.Ui;
public class PlayerActor extends PhysicsActor {
private static final float ROTATION_UP = 90;
private static final float ROTATION_DOWN = -90;
private static final float ROTATION_RIGHT = 0;
private static final float ROTATION_LEFT = 180;
private static final float ANIMATION_START = 10f;
private static final float ANIMATION_DURATION = 2.30f;
private static final String MAP_PROPERTIES_FLUFF = "fluff";
private static final int URGE_TO_MUTTER = 70;
private float speed;
private float angularSpeed;
private Animation animation;
private float rotationPriority = 0f;
private boolean moving;
private float stateTime = ANIMATION_START;
private PointLight mLight;
private Ui ui;
public boolean mBlockInput;
private MapProperties mapProperties;
private int urgeToMutter = 0;
private boolean hasMuttered = false;
public PlayerActor(Physics physics, Ui ui, MapProperties mapProperties) {
setTouchable(Touchable.disabled);
this.ui = ui;
this.mapProperties = mapProperties;
this.animation = setupAnimation();
this.speed = 5f;
this.angularSpeed = 10f;
setSize(1.3f, 1.3f);
initPhysicsBody(createBody(physics, BodyType.DynamicBody,
Collision.PLAYER, (short) (Collision.WORLD | Collision.GHOST_VISION)));
mLight = new PointLight(physics.rayHandler, 10, new Color(1f, 1f, 1f,
0.5f), 1.5f, 0f, 0f);
}
private Animation setupAnimation() {
int frameRows = 4;
int frameColumns = 4;
Texture walkSheet = new Texture(
Gdx.files.internal("animation_sheet2.png"));
TextureRegion[][] tmp = TextureRegion.split(walkSheet,
walkSheet.getWidth() / frameColumns, walkSheet.getHeight()
/ frameRows);
TextureRegion[] walkFrames = new TextureRegion[frameColumns * frameRows];
int index = 0;
for (int i = 0; i < frameRows; i++) {
for (int j = 0; j < frameColumns; j++) {
walkFrames[index++] = tmp[i][j];
}
}
animation = new Animation(ANIMATION_DURATION, walkFrames);
animation.setPlayMode(PlayMode.LOOP);
return animation;
}
@Override
public void act(float delta) {
super.act(delta);
final Vector2 movement = new Vector2();
if (!mBlockInput) {
if (Gdx.input.isKeyPressed(Keys.UP) || Gdx.input.isKeyPressed(Keys.W)) {
movement.y++;
rotationPriority = ROTATION_UP;
}
if (Gdx.input.isKeyPressed(Keys.DOWN) || Gdx.input.isKeyPressed(Keys.S)) {
movement.y
rotationPriority = ROTATION_DOWN;
}
if (Gdx.input.isKeyPressed(Keys.RIGHT)
|| Gdx.input.isKeyPressed(Keys.D)) {
movement.x++;
rotationPriority = ROTATION_RIGHT;
}
if (Gdx.input.isKeyPressed(Keys.LEFT) || Gdx.input.isKeyPressed(Keys.A)) {
movement.x
rotationPriority = ROTATION_LEFT;
}
}
if(movement.x != 0 || movement.y != 0){
moving = true;
ui.removeFluffText();
mutter();
} else {
moving = false;
stateTime = ANIMATION_START;
}
movement.nor().scl(delta * speed);
rotateTowards(rotationPriority,
getCurrentRotationNegative180ToPositive180(), angularSpeed);
moveBy(movement.x, movement.y);
mLight.setPosition(getX(), getY());
}
private void rotateTowards(float rotationGoal,
float currentRotationNegative180ToPositive180, float rotationChange) {
float currentRotation = currentRotationNegative180ToPositive180;
boolean leftSemi = currentRotation < -90 || currentRotation > 90;
boolean lowerSemi = currentRotation < 0;
int clockWise = 1;
if (rotationGoal == ROTATION_UP) {
clockWise = leftSemi ? -1 : 1;
} else if (rotationGoal == ROTATION_DOWN) {
clockWise = leftSemi ? 1 : -1;
} else if (rotationGoal == ROTATION_LEFT) {
clockWise = lowerSemi ? -1 : 1;
} else if (rotationGoal == ROTATION_RIGHT) {
clockWise = lowerSemi ? 1 : -1;
}
rotationChange = (Math.abs(rotationGoal - currentRotation) < rotationChange) ? 0
: rotationChange;
rotateBy(rotationChange * clockWise);
}
private float getCurrentRotationNegative180ToPositive180() {
float currentRotation = getRotation() % 360;
if (currentRotation > 180) {
currentRotation = -180 + (currentRotation - 180);
} else if (currentRotation < -180) {
currentRotation = 180 + (currentRotation + 180);
}
return currentRotation;
}
private void mutter() {
if(!hasMuttered ){
urgeToMutter++;
if(urgeToMutter > URGE_TO_MUTTER){
if(urgeToMutter%URGE_TO_MUTTER == 0 && Math.random() < 0.4f){
ui.showMutter(mapProperties.containsKey(MAP_PROPERTIES_FLUFF)?""+mapProperties.get(MAP_PROPERTIES_FLUFF):"Urgh...", new Vector2(getX(),getY()));
hasMuttered = true;
}
}
}
}
@Override
public void draw(Batch batch, float parentAlpha) {
batch.draw(animation.getKeyFrame((moving ? ++stateTime : 10)), getX()
- (getWidth() / 2), getY() - (getHeight() / 2), getOriginX()
+ (getWidth() / 2), getOriginY() + (getHeight() / 2),
getWidth(), getHeight(), getScaleX(), getScaleY(),
getRotation(), true);
}
public static Body createBody(Physics physics, BodyType bodyType,
short collisionType, short collisionMask) {
final BodyDef bd = new BodyDef();
bd.type = bodyType;
bd.position.set(0.0f, 10.0f);
bd.linearDamping = 0.2f;
final Body body = physics.world.createBody(bd);
final FixtureDef fd = new FixtureDef();
fd.density = 0.0f;
fd.filter.categoryBits = collisionType;
fd.filter.maskBits = collisionMask;
fd.restitution = 0.0f;
fd.friction = 0.0f;
final CircleShape shape = new CircleShape();
shape.setRadius(0.4f);
fd.shape = shape;
body.createFixture(fd);
shape.dispose();
return body;
}
} |
//@@author A0144939R
package seedu.task.testutil;
import seedu.task.model.tag.UniqueTagList;
import seedu.task.model.task.*;
/**
* A mutable task object. For testing only.
*/
public class TestTask implements ReadOnlyTask {
private Name name;
private DateTime openTime;
private DateTime closeTime;
private UniqueTagList tags;
private boolean isImportant;
private boolean isCompleted;
public TestTask() {
tags = new UniqueTagList();
}
//@@author A0141052Y
/**
* Creates a duplicate (copy) of an existing TestTask
* @param task the TestTask to copy from
*/
public TestTask(TestTask task) {
this.name = task.getName();
this.openTime = task.getOpenTime();
this.closeTime = task.getCloseTime();
this.isCompleted = task.getComplete();
this.isImportant = task.getImportance();
this.tags = new UniqueTagList(task.getTags());
}
//@@author
public void setName(Name name) {
this.name = name;
}
//@@author A0153467Y
public void setIsImportant(boolean isImportant){
this.isImportant=isImportant;
}
//@@author
public void setOpenTime(DateTime openTime) {
this.openTime = openTime;
}
public void setCloseTime(DateTime closeTime) {
this.closeTime = closeTime;
}
//@@author A0153467Y
public void setIsCompleted(boolean isCompleted){
this.isCompleted = isCompleted;
}
@Override
public Name getName() {
return name;
}
//@@author A0153467Y
@Override
public boolean getComplete() {
return isCompleted;
}
//@@author
@Override
public DateTime getOpenTime() {
return openTime;
}
@Override
public DateTime getCloseTime() {
return closeTime;
}
@Override
public UniqueTagList getTags() {
return tags;
}
//@@author A0153467Y
@Override
public boolean getImportance() {
return isImportant;
}
//@@author
@Override
public String toString() {
return getAsText();
}
public String getAddCommand() {
StringBuilder sb = new StringBuilder();
sb.append("add " + this.getName().taskName + " ");
sb.append("starts " + this.getOpenTime().toPrettyString() + " ");
sb.append("ends " + this.getCloseTime().toPrettyString() + " ");
this.getTags().getInternalList().stream().forEach(s -> sb.append("tag " + s.tagName + " "));
System.out.println("COMMAND" +sb.toString());
return sb.toString();
}
public String getArgs() {
StringBuilder sb = new StringBuilder();
sb.append(" "+this.getName().taskName + " ");
sb.append("starts " + this.getOpenTime().toPrettyString() + " ");
sb.append("ends " + this.getCloseTime().toPrettyString() + " ");
this.getTags().getInternalList().stream().forEach(s -> sb.append("tag " + s.tagName + " "));
return sb.toString();
}
} |
package org.monarchinitiative.exomiser.core.model.pathogenicity;
import com.google.common.collect.ImmutableMap;
import com.google.common.collect.Sets;
import java.util.*;
public class ClinVarData {
private static final ClinVarData EMPTY = new Builder().build();
public enum ClinSig {
// ACMG/AMP-based
BENIGN,
BENIGN_OR_LIKELY_BENIGN,
LIKELY_BENIGN,
UNCERTAIN_SIGNIFICANCE,
LIKELY_PATHOGENIC,
PATHOGENIC_OR_LIKELY_PATHOGENIC,
PATHOGENIC,
CONFLICTING_PATHOGENICITY_INTERPRETATIONS,
//Non-ACMG-based
AFFECTS,
ASSOCIATION,
DRUG_RESPONSE,
NOT_PROVIDED,
OTHER,
PROTECTIVE,
RISK_FACTOR;
}
private final String alleleId;
private final ClinSig primaryInterpretation;
private final Set<ClinSig> secondaryInterpretations;
private final String reviewStatus;
private final Map<String, ClinSig> includedAlleles;
private ClinVarData(Builder builder) {
this.alleleId = builder.alleleId;
this.primaryInterpretation = builder.primaryInterpretation;
this.secondaryInterpretations = Sets.immutableEnumSet(builder.secondaryInterpretations);
this.reviewStatus = builder.reviewStatus;
this.includedAlleles = ImmutableMap.copyOf(builder.includedAlleles);
}
public static ClinVarData empty() {
return EMPTY;
}
public boolean isEmpty() {
return this.equals(EMPTY);
}
public String getAlleleId() {
return alleleId;
}
public ClinSig getPrimaryInterpretation() {
return primaryInterpretation;
}
public Set<ClinSig> getSecondaryInterpretations() {
return secondaryInterpretations;
}
public String getReviewStatus() {
return reviewStatus;
}
public Map<String, ClinSig> getIncludedAlleles() {
return includedAlleles;
}
@Override
public boolean equals(Object o) {
if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false;
ClinVarData that = (ClinVarData) o;
return Objects.equals(alleleId, that.alleleId) &&
primaryInterpretation == that.primaryInterpretation &&
Objects.equals(secondaryInterpretations, that.secondaryInterpretations) &&
Objects.equals(reviewStatus, that.reviewStatus) &&
Objects.equals(includedAlleles, that.includedAlleles);
}
@Override
public int hashCode() {
return Objects.hash(alleleId, primaryInterpretation, secondaryInterpretations, reviewStatus, includedAlleles);
}
@Override
public String toString() {
return "ClinVarData{" +
"alleleId='" + alleleId + '\'' +
", primaryInterpretation=" + primaryInterpretation +
", secondaryInterpretations=" + secondaryInterpretations +
", reviewStatus='" + reviewStatus + '\'' +
", includedAlleles=" + includedAlleles +
'}';
}
public static Builder builder() {
return new Builder();
}
public static class Builder {
private String alleleId = "";
private ClinSig primaryInterpretation = ClinSig.NOT_PROVIDED;
private Set<ClinSig> secondaryInterpretations = EnumSet.noneOf(ClinSig.class);
private String reviewStatus = "";
private Map<String, ClinSig> includedAlleles = Collections.emptyMap();
public Builder alleleId(String alleleId) {
Objects.requireNonNull(alleleId);
this.alleleId = alleleId;
return this;
}
public Builder primaryInterpretation(ClinSig primaryInterpretation) {
Objects.requireNonNull(primaryInterpretation);
this.primaryInterpretation = primaryInterpretation;
return this;
}
public Builder secondaryInterpretations(Set<ClinSig> secondaryInterpretations) {
Objects.requireNonNull(secondaryInterpretations);
this.secondaryInterpretations = secondaryInterpretations;
return this;
}
public Builder reviewStatus(String reviewStatus) {
Objects.requireNonNull(reviewStatus);
this.reviewStatus = reviewStatus;
return this;
}
public Builder includedAlleles(Map<String, ClinSig> includedAlleles) {
Objects.requireNonNull(includedAlleles);
this.includedAlleles = includedAlleles;
return this;
}
public ClinVarData build() {
return new ClinVarData(this);
}
}
} |
package org.eclipse.persistence.config;
import org.eclipse.persistence.descriptors.ClassDescriptor;
/**
* PUBLIC:
* This interface is to allow extra customization on a EclipseLink Session
*/
public interface DescriptorCustomizer {
public void customize(ClassDescriptor descriptor) throws Exception;
} |
package de.stefanocke.japkit.roo.japkit;
import java.util.Date;
import javax.lang.model.element.Modifier;
import javax.validation.constraints.NotNull;
import de.stefanocke.japkit.annotations.RuntimeMetadata;
import de.stefanocke.japkit.metaannotations.Annotation;
import de.stefanocke.japkit.metaannotations.Case;
import de.stefanocke.japkit.metaannotations.CodeFragment;
import de.stefanocke.japkit.metaannotations.Constructor;
import de.stefanocke.japkit.metaannotations.Field;
import de.stefanocke.japkit.metaannotations.Getter;
import de.stefanocke.japkit.metaannotations.InnerClass;
import de.stefanocke.japkit.metaannotations.Matcher;
import de.stefanocke.japkit.metaannotations.Method;
import de.stefanocke.japkit.metaannotations.ParamNames;
import de.stefanocke.japkit.metaannotations.Setter;
import de.stefanocke.japkit.metaannotations.Template;
import de.stefanocke.japkit.metaannotations.Var;
import de.stefanocke.japkit.metaannotations.classselectors.ClassSelector;
import de.stefanocke.japkit.metaannotations.classselectors.ClassSelectorKind;
import de.stefanocke.japkit.metaannotations.classselectors.GeneratedClass;
import de.stefanocke.japkit.metaannotations.classselectors.SrcType;
@RuntimeMetadata
@Template(vars = {
@Var(name = "validationFragment", code = @CodeFragment(activation = @Matcher(annotations = NotNull.class),
code = "if(#{src.simpleName}==null){\n"
+ " throw new IllegalArgumentException(\"#{src.simpleName} must not be null.\");\n" + "}")),
@Var(name = "defensiveCopyFragment", code = @CodeFragment(imports = Date.class, cases = { @Case(matcher = @Matcher(
type = Date.class), expr = "new Date(#{surrounded}.getTime())") }, linebreak = false))
// @Var(name = "tryFinallyTest", code = @CodeFragment(expr="try {\n" +
// "#{surrounded}" +
// "} finally {\n" +
})
public abstract class ValueObjectTemplate {
@InnerClass(fields = @Field(src = "#{properties}", modifiers = Modifier.PRIVATE,
annotations = @Annotation(copyAnnotationsFromPackages = { "javax.persistence", "javax.validation.constraints",
"org.springframework.format.annotation" }), getter = @Getter(fluent = true), setter = @Setter(fluent = true,
chain = true), commentFromSrc = true))
@ClassSelector(kind = ClassSelectorKind.INNER_CLASS_NAME, enclosing = GeneratedClass.class)
public static abstract class Builder {
@ClassSelector(kind = ClassSelectorKind.EXPR, expr = "#{currentGenClass.enclosingElement.asType()}")
abstract static class EnclosingClass {
}
@Method(bodyCode = "return new #{genElement.returnType.code}(this);")
public abstract EnclosingClass build();
}
@Field(src = "#{properties}", annotations = @Annotation(copyAnnotationsFromPackages = { "javax.persistence",
"javax.validation.constraints", "org.springframework.format.annotation" }), commentFromSrc = true, getter = @Getter(
fluent = true, surroundReturnExprFragments = "defensiveCopyFragment",
commentExpr = "Getter for #{src.simpleName}. \n@returns #{src.simpleName}\n"))
private SrcType $srcElementName$;
@Constructor(bodyCode = "//Some ctor code")
private ValueObjectTemplate() {
};
@Constructor(vars = {
@Var(name = "rhs", code = @CodeFragment(code = "builder.#{src.simpleName}", surroundingFragments = "defensiveCopyFragment",
linebreak = false)),
@Var(name = "assignment", code = @CodeFragment(code = "this.#{src.simpleName} = #{rhs.code()};",
beforeFragments = "validationFragment")) }, bodyIterator = "properties", bodyCode = "assignment")
@ParamNames("builder")
private ValueObjectTemplate(Builder builder) {
}
} |
package com.intellij.psi.impl.source.resolve.graphInference;
import com.intellij.psi.*;
import com.intellij.psi.util.PsiTreeUtil;
import com.intellij.psi.util.PsiUtil;
import com.intellij.psi.util.TypeConversionUtil;
import org.jetbrains.annotations.NotNull;
import org.jetbrains.annotations.Nullable;
import java.util.Arrays;
import java.util.HashSet;
import java.util.Set;
import java.util.function.Function;
public class PsiPolyExpressionUtil {
public static boolean hasStandaloneForm(PsiExpression expression) {
return !(expression instanceof PsiFunctionalExpression) &&
!(expression instanceof PsiParenthesizedExpression) &&
!(expression instanceof PsiConditionalExpression) &&
!(expression instanceof PsiSwitchExpression) &&
!(expression instanceof PsiCallExpression);
}
public static boolean isPolyExpression(final PsiExpression expression) {
if (expression instanceof PsiFunctionalExpression) {
return true;
}
if (expression instanceof PsiParenthesizedExpression) {
return isPolyExpression(((PsiParenthesizedExpression)expression).getExpression());
}
if (expression instanceof PsiNewExpression && PsiDiamondType.hasDiamond((PsiNewExpression)expression)) {
return isInAssignmentOrInvocationContext(expression);
}
if (expression instanceof PsiMethodCallExpression) {
return isMethodCallPolyExpression(expression, expr -> ((PsiMethodCallExpression)expr).resolveMethod());
}
if (expression instanceof PsiConditionalExpression) {
final ConditionalKind conditionalKind = isBooleanOrNumeric(expression);
if (conditionalKind == null) {
return isInAssignmentOrInvocationContext(expression);
}
}
if (expression instanceof PsiSwitchExpression) {
return isInAssignmentOrInvocationContext(expression);
}
return false;
}
public static boolean isMethodCallPolyExpression(PsiExpression expression, final PsiMethod method) {
return isMethodCallPolyExpression(expression, e -> method);
}
private static boolean isMethodCallPolyExpression(PsiExpression expression, Function<? super PsiExpression, ? extends PsiMethod> methodResolver) {
if (isInAssignmentOrInvocationContext(expression) && ((PsiCallExpression)expression).getTypeArguments().length == 0) {
PsiMethod method = methodResolver.apply(expression);
return method == null || isMethodCallTypeDependsOnInference(expression, method);
}
return false;
}
private static boolean isMethodCallTypeDependsOnInference(PsiExpression expression, PsiMethod method) {
final Set<PsiTypeParameter> typeParameters = new HashSet<>(Arrays.asList(method.getTypeParameters()));
if (!typeParameters.isEmpty()) {
final PsiType returnType = method.getReturnType();
if (returnType != null) {
return mentionsTypeParameters(returnType, typeParameters);
}
}
else if (method.isConstructor() && expression instanceof PsiNewExpression && PsiDiamondType.hasDiamond((PsiNewExpression)expression)) {
return true;
}
return false;
}
public static Boolean mentionsTypeParameters(@Nullable PsiType returnType, final Set<PsiTypeParameter> typeParameters) {
if (returnType == null) return false;
return returnType.accept(new PsiTypeVisitor<Boolean>() {
@NotNull
@Override
public Boolean visitType(PsiType type) {
return false;
}
@Nullable
@Override
public Boolean visitWildcardType(PsiWildcardType wildcardType) {
final PsiType bound = wildcardType.getBound();
if (bound != null) {
return bound.accept(this);
}
return false;
}
@NotNull
@Override
public Boolean visitClassType(PsiClassType classType) {
PsiClassType.ClassResolveResult result = classType.resolveGenerics();
final PsiClass psiClass = result.getElement();
if (psiClass != null) {
PsiSubstitutor substitutor = result.getSubstitutor();
for (PsiTypeParameter parameter : PsiUtil.typeParametersIterable(psiClass)) {
PsiType type = substitutor.substitute(parameter);
if (type != null && type.accept(this)) return true;
}
}
return psiClass instanceof PsiTypeParameter && typeParameters.contains(psiClass);
}
@Nullable
@Override
public Boolean visitArrayType(PsiArrayType arrayType) {
return arrayType.getComponentType().accept(this);
}
});
}
private static boolean isInAssignmentOrInvocationContext(PsiExpression expr) {
final PsiElement context = PsiUtil.skipParenthesizedExprUp(expr.getParent());
return context instanceof PsiExpressionList ||
context instanceof PsiArrayInitializerExpression ||
context instanceof PsiConditionalExpression && (expr instanceof PsiCallExpression || isPolyExpression((PsiExpression)context)) ||
isSwitchExpressionAssignmentOrInvocationContext(expr) ||
isAssignmentContext(expr, context);
}
private static boolean isSwitchExpressionAssignmentOrInvocationContext(PsiExpression expr) {
PsiElement parent = PsiUtil.skipParenthesizedExprUp(expr).getParent();
if (parent instanceof PsiExpressionStatement && parent.getParent() instanceof PsiSwitchLabeledRuleStatement ||
parent instanceof PsiBreakStatement ||
parent instanceof PsiThrowStatement) {
PsiSwitchExpression switchExpression = PsiTreeUtil.getParentOfType(expr, PsiSwitchExpression.class, true, PsiMember.class, PsiLambdaExpression.class);
return switchExpression != null &&
PsiUtil.getSwitchResultExpressions(switchExpression).contains(expr) &&
isInAssignmentOrInvocationContext(switchExpression);
}
return false;
}
private static boolean isAssignmentContext(PsiExpression expr, PsiElement context) {
return PsiUtil.isCondition(expr, context) ||
context instanceof PsiReturnStatement ||
context instanceof PsiAssignmentExpression && ((PsiAssignmentExpression)context).getOperationTokenType() == JavaTokenType.EQ ||
context instanceof PsiVariable && !isVarContext((PsiVariable)context) ||
context instanceof PsiLambdaExpression;
}
private static boolean isVarContext(PsiVariable variable) {
if (PsiUtil.isLanguageLevel10OrHigher(variable)) {
PsiTypeElement typeElement = variable.getTypeElement();
if (typeElement != null && typeElement.isInferredType()) {
return true;
}
}
return false;
}
public static boolean isExpressionOfPrimitiveType(@Nullable PsiExpression arg) {
if (arg != null && !isPolyExpression(arg)) {
final PsiType type = arg.getType();
return type instanceof PsiPrimitiveType && type != PsiType.NULL;
}
else if (arg instanceof PsiNewExpression || arg instanceof PsiFunctionalExpression) {
return false;
}
else if (arg instanceof PsiParenthesizedExpression) {
return isExpressionOfPrimitiveType(((PsiParenthesizedExpression)arg).getExpression());
}
else if (arg instanceof PsiConditionalExpression) {
return isBooleanOrNumeric(arg) != null;
}
else if (arg instanceof PsiMethodCallExpression) {
final PsiMethod method = ((PsiMethodCallExpression)arg).resolveMethod();
return method != null && method.getReturnType() instanceof PsiPrimitiveType;
}
else if (arg instanceof PsiSwitchExpression) {
return isBooleanOrNumeric(arg) != null;
}
else {
assert false : arg;
return false;
}
}
private enum ConditionalKind {
BOOLEAN, NUMERIC, NULL
}
private static ConditionalKind isBooleanOrNumeric(PsiExpression expr) {
if (expr instanceof PsiParenthesizedExpression) {
return isBooleanOrNumeric(((PsiParenthesizedExpression)expr).getExpression());
}
if (expr == null) return null;
PsiType type = null;
//A class instance creation expression (p15.9) for a class that is convertible to a numeric type.
//As numeric classes do not have type parameters, at this point expressions with diamonds could be ignored
if (expr instanceof PsiNewExpression && !PsiDiamondType.hasDiamond((PsiNewExpression)expr) ||
hasStandaloneForm(expr)) {
type = expr.getType();
}
else if (expr instanceof PsiMethodCallExpression) {
final PsiMethod method = ((PsiMethodCallExpression)expr).resolveMethod();
if (method != null) {
type = method.getReturnType();
}
}
final ConditionalKind kind = isBooleanOrNumericType(type);
if (kind != null) {
return kind;
}
if (expr instanceof PsiConditionalExpression) {
final PsiExpression thenExpression = ((PsiConditionalExpression)expr).getThenExpression();
final PsiExpression elseExpression = ((PsiConditionalExpression)expr).getElseExpression();
final ConditionalKind thenKind = isBooleanOrNumeric(thenExpression);
final ConditionalKind elseKind = isBooleanOrNumeric(elseExpression);
if (thenKind == elseKind || elseKind == ConditionalKind.NULL) return thenKind;
if (thenKind == ConditionalKind.NULL) return elseKind;
}
if (expr instanceof PsiSwitchExpression) {
ConditionalKind switchKind = null;
for (PsiExpression resultExpression : PsiUtil.getSwitchResultExpressions((PsiSwitchExpression)expr)) {
ConditionalKind resultKind = isBooleanOrNumeric(resultExpression);
if (resultKind == null) return null;
if (switchKind == null) {
switchKind = resultKind;
}
else if (switchKind != resultKind) {
if (switchKind == ConditionalKind.NULL) {
switchKind = resultKind;
}
else if (resultKind != ConditionalKind.NULL) {
return null;
}
}
}
}
return null;
}
@Nullable
private static ConditionalKind isBooleanOrNumericType(PsiType type) {
if (type == PsiType.NULL) {
return ConditionalKind.NULL;
}
final PsiClass psiClass = PsiUtil.resolveClassInClassTypeOnly(type);
if (TypeConversionUtil.isNumericType(type)) return ConditionalKind.NUMERIC;
if (TypeConversionUtil.isBooleanType(type)) return ConditionalKind.BOOLEAN;
if (psiClass instanceof PsiTypeParameter) {
for (PsiClassType classType : psiClass.getExtendsListTypes()) {
final ConditionalKind kind = isBooleanOrNumericType(classType);
if (kind != null) {
return kind;
}
}
}
return null;
}
} |
package com.ore.infinium;
import com.badlogic.ashley.core.ComponentMapper;
import com.badlogic.ashley.core.Entity;
import com.badlogic.ashley.core.Family;
import com.badlogic.ashley.core.PooledEngine;
import com.badlogic.ashley.utils.ImmutableArray;
import com.badlogic.gdx.Gdx;
import com.badlogic.gdx.Input;
import com.badlogic.gdx.assets.AssetManager;
import com.badlogic.gdx.graphics.OrthographicCamera;
import com.badlogic.gdx.graphics.g2d.TextureAtlas;
import com.badlogic.gdx.math.MathUtils;
import com.badlogic.gdx.math.Rectangle;
import com.badlogic.gdx.math.Vector2;
import com.badlogic.gdx.math.Vector3;
import com.badlogic.gdx.utils.Array;
import com.badlogic.gdx.utils.Disposable;
import com.ore.infinium.components.*;
import com.ore.infinium.systems.*;
import java.util.HashMap;
public class World implements Disposable {
public static final float PIXELS_PER_METER = 50.0f;
public static final float GRAVITY_ACCEL = 9.8f / PIXELS_PER_METER / 3.0f;
public static final float GRAVITY_ACCEL_CLAMP = 9.8f / PIXELS_PER_METER / 3.0f;
public static final float BLOCK_SIZE = (16.0f / PIXELS_PER_METER);
public static final float BLOCK_SIZE_PIXELS = 16.0f;
public static final int WORLD_COLUMNCOUNT = 1000; //2400
public static final int WORLD_ROWCOUNT = 1000; //8400
public static final int WORLD_SEA_LEVEL = 50;
public static final HashMap<Block.BlockType, BlockStruct> blockTypes = new HashMap<>();
static {
blockTypes.put(Block.BlockType.NullBlockType, new BlockStruct("", false));
blockTypes.put(Block.BlockType.DirtBlockType, new BlockStruct("dirt", true));
blockTypes.put(Block.BlockType.StoneBlockType, new BlockStruct("stone", true));
}
private static final int zoomInterval = 50;
private static OreTimer m_zoomTimer = new OreTimer();
public Block[] blocks;
public PooledEngine engine;
public Array<Entity> m_players = new Array<>();
public Entity m_mainPlayer;
public OreServer m_server;
public AssetManager assetManager;
public OreClient m_client;
public OrthographicCamera m_camera;
//fixme remove in favor of the render system
public TextureAtlas m_atlas;
protected TileRenderer m_tileRenderer;
PowerOverlayRenderSystem m_powerOverlaySystem;
private ComponentMapper<PlayerComponent> playerMapper = ComponentMapper.getFor(PlayerComponent.class);
private ComponentMapper<SpriteComponent> spriteMapper = ComponentMapper.getFor(SpriteComponent.class);
private ComponentMapper<ControllableComponent> controlMapper = ComponentMapper.getFor(ControllableComponent.class);
private ComponentMapper<ItemComponent> itemMapper = ComponentMapper.getFor(ItemComponent.class);
private ComponentMapper<VelocityComponent> velocityMapper = ComponentMapper.getFor(VelocityComponent.class);
private ComponentMapper<JumpComponent> jumpMapper = ComponentMapper.getFor(JumpComponent.class);
private ComponentMapper<BlockComponent> blockMapper = ComponentMapper.getFor(BlockComponent.class);
private ComponentMapper<AirGeneratorComponent> airGeneratorMapper = ComponentMapper.getFor(AirGeneratorComponent.class);
private ComponentMapper<ToolComponent> toolMapper = ComponentMapper.getFor(ToolComponent.class);
private ComponentMapper<AirComponent> airMapper = ComponentMapper.getFor(AirComponent.class);
private ComponentMapper<TagComponent> tagMapper = ComponentMapper.getFor(TagComponent.class);
private ComponentMapper<HealthComponent> healthMapper = ComponentMapper.getFor(HealthComponent.class);
private ComponentMapper<TorchComponent> torchMapper = ComponentMapper.getFor(TorchComponent.class);
private boolean m_noClipEnabled;
private Entity m_blockPickingCrosshair;
private Entity m_itemPlacementGhost;
private com.artemis.World artemisWorld;
public World(OreClient client, OreServer server) {
m_client = client;
m_server = server;
if (isClient()) {
float w = Gdx.graphics.getWidth();
float h = Gdx.graphics.getHeight();
}
blocks = new Block[WORLD_ROWCOUNT * WORLD_COLUMNCOUNT];
// assetManager = new AssetManager();
// TextureAtlas m_blockAtlas = assetManager.get("data/", TextureAtlas.class);
// assetManager.finishLoading();
engine = new PooledEngine(2000, 2000, 2000, 2000);
engine.addSystem(new MovementSystem(this));
engine.addSystem(new PlayerSystem(this));
m_camera = new OrthographicCamera(1600 / World.PIXELS_PER_METER, 900 / World.PIXELS_PER_METER);//30, 30 * (h / w));
m_camera.setToOrtho(true, 1600 / World.PIXELS_PER_METER, 900 / World.PIXELS_PER_METER);
// m_camera.position.set(m_camera.viewportWidth / 2f, m_camera.viewportHeight / 2f, 0);
assert isClient() ^ isServer();
if (isClient()) {
m_atlas = new TextureAtlas(Gdx.files.internal("packed/entities.atlas"));
initializeWorld();
m_blockPickingCrosshair = engine.createEntity();
TagComponent tagComponent = engine.createComponent(TagComponent.class);
tagComponent.tag = "crosshair";
m_blockPickingCrosshair.add(tagComponent);
SpriteComponent spriteComponent = engine.createComponent(SpriteComponent.class);
m_blockPickingCrosshair.add(spriteComponent);
spriteComponent.sprite.setSize(BLOCK_SIZE, BLOCK_SIZE);
spriteComponent.sprite.setRegion(m_atlas.findRegion("crosshair-blockpicking"));
}
if (isServer()) {
generateWorld();
}
}
protected void clientInventoryItemSelected() {
assert !isServer();
PlayerComponent playerComponent = playerMapper.get(m_mainPlayer);
Entity entity = playerComponent.equippedPrimaryItem();
if (entity == null) {
return;
}
if (m_itemPlacementGhost != null) {
engine.removeEntity(m_itemPlacementGhost);
}
//this item is placeable, show a ghost of it so we can see where we're going to place it
m_itemPlacementGhost = cloneEntity(entity);
ItemComponent itemComponent = itemMapper.get(m_itemPlacementGhost);
itemComponent.state = ItemComponent.State.InWorldState;
SpriteComponent spriteComponent = spriteMapper.get(m_itemPlacementGhost);
TagComponent tag = engine.createComponent(TagComponent.class);
tag.tag = "itemPlacementGhost";
m_itemPlacementGhost.add(tag);
engine.addEntity(m_itemPlacementGhost);
}
public void initServer() {
}
public void initClient(Entity mainPlayer) {
m_mainPlayer = mainPlayer;
// velocityMapper.get(m_mainPlayer);
engine.addSystem(m_tileRenderer = new TileRenderer(m_camera, this, 1f / 60f));
engine.addSystem(new SpriteRenderSystem(this));
engine.addSystem(m_powerOverlaySystem = new PowerOverlayRenderSystem(this));
SpriteComponent playerSprite = spriteMapper.get(m_mainPlayer);
playerSprite.sprite.setRegion(m_atlas.findRegion("player-32x64"));
playerSprite.sprite.flip(false, true);
}
/**
* adding entity to the world is callers responsibility
*
* @param playerName
* @param connectionId
* @return
*/
public Entity createPlayer(String playerName, int connectionId) {
Entity player = engine.createEntity();
SpriteComponent playerSprite = engine.createComponent(SpriteComponent.class);
player.add(playerSprite);
player.add(engine.createComponent(VelocityComponent.class));
PlayerComponent playerComponent = engine.createComponent(PlayerComponent.class);
playerComponent.connectionId = connectionId;
playerComponent.noClip = m_noClipEnabled;
playerComponent.playerName = playerName;
playerComponent.loadedViewport.setRect(new Rectangle(0, 0, LoadedViewport.MAX_VIEWPORT_WIDTH, LoadedViewport.MAX_VIEWPORT_HEIGHT));
playerComponent.loadedViewport.centerOn(new Vector2(playerSprite.sprite.getX(), playerSprite.sprite.getY()));
player.add(playerComponent);
playerSprite.sprite.setSize(World.BLOCK_SIZE * 2, World.BLOCK_SIZE * 3);
player.add(engine.createComponent(ControllableComponent.class));
playerSprite.textureName = "player1Standing1";
playerSprite.category = SpriteComponent.EntityCategory.Character;
player.add(engine.createComponent(JumpComponent.class));
HealthComponent healthComponent = engine.createComponent(HealthComponent.class);
healthComponent.health = healthComponent.maxHealth;
player.add(healthComponent);
AirComponent airComponent = engine.createComponent(AirComponent.class);
airComponent.air = airComponent.maxAir;
player.add(airComponent);
return player;
}
private void generateWorld() {
generateOres();
}
private void initializeWorld() {
for (int x = 0; x < WORLD_COLUMNCOUNT; ++x) {
for (int y = 0; y < WORLD_ROWCOUNT; ++y) {
int index = x * WORLD_ROWCOUNT + y;
blocks[index] = new Block();
blocks[index].blockType = Block.BlockType.StoneBlockType;
}
}
}
private void generateOres() {
for (int x = 0; x < WORLD_COLUMNCOUNT; ++x) {
for (int y = 0; y < WORLD_ROWCOUNT; ++y) {
int index = x * WORLD_ROWCOUNT + y;
//java wants me to go through each and every block and initialize them..
blocks[index] = new Block();
blocks[index].blockType = Block.BlockType.NullBlockType;
//create some sky
if (y <= seaLevel()) {
continue;
}
switch (MathUtils.random(0, 3)) {
case 0:
blocks[index].blockType = Block.BlockType.NullBlockType;
break;
case 1:
blocks[index].blockType = Block.BlockType.DirtBlockType;
break;
case 2:
blocks[index].blockType = Block.BlockType.StoneBlockType;
break;
}
// blocks[dragSourceIndex].wallType = Block::Wall
}
}
// for (int x = 0; x < WORLD_COLUMNCOUNT; ++x) {
// for (int y = seaLevel(); y < WORLD_ROWCOUNT; ++y) {
// Block block = blockAt(x, y);
// block.blockType = Block.BlockType.DirtBlockType;
}
public boolean isServer() {
return m_server != null;
}
public boolean isClient() {
return m_client != null;
}
public Block blockAtPosition(Vector2 pos) {
return blockAt((int) (pos.x / BLOCK_SIZE), (int) (pos.y / BLOCK_SIZE));
}
public Block blockAt(int x, int y) {
assert x >= 0 && y >= 0 && x <= WORLD_COLUMNCOUNT && y <= WORLD_ROWCOUNT;
return blocks[x * WORLD_ROWCOUNT + y];
}
public boolean isBlockSolid(int x, int y) {
boolean solid = true;
Block.BlockType type = blockAt(x, y).blockType;
if (type == Block.BlockType.NullBlockType) {
solid = false;
}
return solid;
}
public boolean canPlaceBlock(int x, int y) {
boolean canPlace = blockAt(x, y).blockType == Block.BlockType.NullBlockType;
//TODO: check collision with other entities...
return canPlace;
}
public void dispose() {
}
public void zoom(float factor) {
m_camera.zoom *= factor;
}
public void update(double elapsed) {
if (isClient()) {
if (m_mainPlayer == null) {
return;
}
// playerSprite.sprite.setOriginCenter();
// m_camera.position.set(playerSprite.sprite.getX() + playerSprite.sprite.getWidth() * 0.5f, playerSprite.sprite.getY() + playerSprite.sprite.getHeight() * 0.5f, 0);
final float zoomAmount = 0.004f;
if (Gdx.input.isKeyPressed(Input.Keys.MINUS)) {
if (m_zoomTimer.milliseconds() >= zoomInterval) {
//zoom out
zoom(1.0f + zoomAmount);
m_zoomTimer.reset();
}
}
if (Gdx.input.isKeyPressed(Input.Keys.EQUALS)) {
if (m_zoomTimer.milliseconds() >= zoomInterval) {
zoom(1.0f - zoomAmount);
m_zoomTimer.reset();
}
}
updateCrosshair();
updateItemPlacementGhost();
}
if (isServer()) {
}
//todo explicitly call update on systems, me thinks...otherwise the render and update steps are coupled
engine.update((float) elapsed);
}
private void handleLeftMousePrimaryAttack() {
Vector2 mouse = mousePositionWorldCoords();
PlayerComponent playerComponent = playerMapper.get(m_mainPlayer);
Entity item = playerComponent.equippedPrimaryItem();
if (item == null) {
return;
}
ToolComponent toolComponent = toolMapper.get(item);
if (toolComponent != null) {
if (toolComponent.type != ToolComponent.ToolType.Drill) {
return;
}
int x = (int) (mouse.x / BLOCK_SIZE);
int y = (int) (mouse.y / BLOCK_SIZE);
Block block = blockAt(x, y);
//attempt to destroy it if it's not already destroyed...
if (block.blockType != Block.BlockType.NullBlockType) {
block.blockType = Block.BlockType.NullBlockType;
m_client.sendBlockPick(x, y);
}
//action performed
return;
}
BlockComponent blockComponent = blockMapper.get(item);
if (blockComponent != null) {
int x = (int) (mouse.x / BLOCK_SIZE);
int y = (int) (mouse.y / BLOCK_SIZE);
Block block = blockAt(x, y);
//attempt to place one if the area is empty
if (block.blockType == Block.BlockType.NullBlockType) {
block.blockType = blockComponent.blockType;
m_client.sendBlockPlace(x, y);
}
//action performed
return;
}
ItemComponent itemComponent = itemMapper.get(item);
if (itemComponent != null) {
//place the item
Entity placedItem = cloneEntity(playerComponent.equippedPrimaryItem());
ItemComponent placedItemComponent = itemMapper.get(placedItem);
placedItemComponent.state = ItemComponent.State.InWorldState;
SpriteComponent spriteComponent = spriteMapper.get(placedItem);
spriteComponent.sprite.setPosition(mouse.x, mouse.y);
engine.addEntity(placedItem);
//hack, do more validation..
m_client.sendItemPlace(mouse.x, mouse.y);
}
}
public void render(double elapsed) {
if (m_mainPlayer == null) {
return;
}
// m_camera.zoom *= 0.9;
//m_lightRenderer->renderToFBO();
if (m_client.m_renderTiles) {
//m_tileRenderer.render(elapsed);
} else {
}
//FIXME: incorporate entities into the pre-lit gamescene FBO, then render lighting as last pass
//m_lightRenderer->renderToBackbuffer();
//FIXME: take lighting into account, needs access to fbos though.
// m_fluidRenderer->render();
// m_particleRenderer->render();
//FIXME unused m_quadTreeRenderer->render();
updateCrosshair();
updateItemPlacementGhost();
}
private void updateCrosshair() {
//PlayerComponent playerComponent = playerMapper.get(m_mainPlayer);
//playerComponent
SpriteComponent spriteComponent = spriteMapper.get(m_blockPickingCrosshair);
Vector2 mouse = mousePositionWorldCoords();
Vector2 crosshairPosition = new Vector2(BLOCK_SIZE * MathUtils.floor(mouse.x / BLOCK_SIZE), BLOCK_SIZE * MathUtils.floor(mouse.y / BLOCK_SIZE));
Vector2 crosshairOriginOffset = new Vector2(spriteComponent.sprite.getWidth() * 0.5f, spriteComponent.sprite.getHeight() * 0.5f);
Vector2 crosshairFinalPosition = crosshairPosition.add(crosshairOriginOffset);
spriteComponent.sprite.setPosition(crosshairFinalPosition.x, crosshairFinalPosition.y);
}
private Vector2 mousePositionWorldCoords() {
Vector3 mouse = new Vector3(Gdx.input.getX(), Gdx.input.getY(), 0f);
Vector3 finalMouse = m_camera.unproject(mouse);
return new Vector2(finalMouse.x, finalMouse.y);
}
private void updateItemPlacementGhost() {
if (m_itemPlacementGhost == null) {
return;
}
Vector2 mouse = mousePositionWorldCoords();
alignPositionToBlocks(mouse);
SpriteComponent spriteComponent = spriteMapper.get(m_itemPlacementGhost);
spriteComponent.sprite.setPosition(mouse.x, mouse.y);
spriteComponent.placementValid = isPlacementValid(m_itemPlacementGhost);
}
private void alignPositionToBlocks(Vector2 pos) {
pos.set(BLOCK_SIZE * MathUtils.floor(pos.x / BLOCK_SIZE), BLOCK_SIZE * MathUtils.floor(pos.y / BLOCK_SIZE));
}
public int seaLevel() {
return WORLD_SEA_LEVEL;
}
public void createBlockItem(Entity block) {
block.add(engine.createComponent(VelocityComponent.class));
BlockComponent blockComponent = engine.createComponent(BlockComponent.class);
blockComponent.blockType = Block.BlockType.StoneBlockType;
block.add(blockComponent);
SpriteComponent blockSprite = engine.createComponent(SpriteComponent.class);
blockSprite.textureName = blockTypes.get(blockComponent.blockType).textureName;
//warning fixme size is fucked
blockSprite.sprite.setSize(32 / World.PIXELS_PER_METER, 32 / World.PIXELS_PER_METER);
block.add(blockSprite);
ItemComponent itemComponent = engine.createComponent(ItemComponent.class);
itemComponent.stackSize = 800;
itemComponent.maxStackSize = 900;
block.add(itemComponent);
}
public Entity createAirGenerator() {
Entity air = engine.createEntity();
ItemComponent itemComponent = engine.createComponent(ItemComponent.class);
itemComponent.stackSize = 800;
itemComponent.maxStackSize = 900;
air.add(itemComponent);
SpriteComponent airSprite = engine.createComponent(SpriteComponent.class);
airSprite.textureName = "air-generator-64x64";
//warning fixme size is fucked
airSprite.sprite.setSize(BLOCK_SIZE * 4, BLOCK_SIZE * 4);
air.add(airSprite);
AirGeneratorComponent airComponent = engine.createComponent(AirGeneratorComponent.class);
airComponent.airOutputRate = 100;
air.add(airComponent);
return air;
}
private boolean isPlacementValid(Entity entity) {
SpriteComponent spriteComponent = spriteMapper.get(entity);
Vector2 pos = new Vector2(spriteComponent.sprite.getX(), spriteComponent.sprite.getY());
Vector2 size = new Vector2(spriteComponent.sprite.getWidth(), spriteComponent.sprite.getHeight());
float epsilon = 0.001f;
int startX = (int) ((pos.x - (size.x * 0.5f)) / BLOCK_SIZE + epsilon);
int startY = (int) ((pos.y - (size.y * 0.5f)) / BLOCK_SIZE + epsilon);
int endX = (int) ((pos.x + (size.x * 0.5f)) / BLOCK_SIZE + 0);
int endY = (int) ((pos.y + (size.y * 0.5f - epsilon)) / BLOCK_SIZE + 1);
if (!(startX >= 0 && startY >= 0 && endX <= WORLD_COLUMNCOUNT && endY <= WORLD_ROWCOUNT)) {
//fixme
//not sure why, but this ends up giving me some way way invalid values. likely due to mouse being outside
//of valid range, *somehow*. sometimes does it on startup etc
return false;
}
for (int column = startX; column < endX; ++column) {
for (int row = startY; row < endY; ++row) {
if (blockAt(column, row).blockType != Block.BlockType.NullBlockType) {
return false;
}
}
}
//float x = Math.min(pos.x - (BLOCK_SIZE * 20), 0.0f);
//float y = Math.min(pos.y - (BLOCK_SIZE * 20), 0.0f);
//float x2 = Math.min(pos.x + (BLOCK_SIZE * 20), WORLD_COLUMNCOUNT * BLOCK_SIZE);
//float y2 = Math.min(pos.y + (BLOCK_SIZE * 20), WORLD_ROWCOUNT * BLOCK_SIZE);
ImmutableArray<Entity> entities = engine.getEntitiesFor(Family.all(SpriteComponent.class).get());
for (int i = 0; i < entities.size(); ++i) {
//it's us, don't count a collision with ourselves
if (entities.get(i) == entity) {
continue;
}
//ignore players, aka don't count them as colliding when placing static objects.
// if (e.has_component<PlayerComponent>()) {
// continue;
ItemComponent itemComponent = itemMapper.get(entities.get(i));
if (itemComponent != null) {
if (itemComponent.state == ItemComponent.State.DroppedInWorld) {
continue;
}
}
if (entityCollides(entities.get(i), entity)) {
return false;
}
}
return true;
}
private boolean entityCollides(Entity first, Entity second) {
SpriteComponent spriteComponent1 = spriteMapper.get(first);
SpriteComponent spriteComponent2 = spriteMapper.get(second);
Vector2 pos1 = new Vector2(spriteComponent1.sprite.getX(), spriteComponent1.sprite.getY());
Vector2 pos2 = new Vector2(spriteComponent2.sprite.getX(), spriteComponent2.sprite.getY());
Vector2 size1 = new Vector2(spriteComponent1.sprite.getWidth(), spriteComponent1.sprite.getHeight());
Vector2 size2 = new Vector2(spriteComponent2.sprite.getWidth(), spriteComponent2.sprite.getHeight());
float epsilon = 0.0001f;
float left1 = pos1.x - (size1.x * 0.5f) + epsilon;
float right1 = pos1.x + (size1.x * 0.5f) - epsilon;
float top1 = pos1.y - (size1.y * 0.5f) + epsilon;
float bottom1 = pos1.y + (size1.y * 0.5f) - epsilon;
float left2 = pos2.x - (size2.x * 0.5f) + epsilon;
float right2 = pos2.x + (size2.x * 0.5f) - epsilon;
float top2 = pos2.y - (size2.y * 0.5f) + epsilon;
float bottom2 = pos2.y + (size2.y * 0.5f) - epsilon;
boolean collides = !(left2 > right1
|| right2 < left1
|| top2 > bottom1
|| bottom2 < top1);
return collides;
}
public void loadBlockRegion(Network.BlockRegion region) {
int sourceIndex = 0;
for (int row = region.y; row < region.y2; ++row) {
for (int col = region.x; col < region.x2; ++col) {
int index = col * WORLD_ROWCOUNT + row;
Block origBlock = blocks[index];
Network.SingleBlock srcBlock = region.blocks.get(sourceIndex);
origBlock.blockType = srcBlock.blockType;
//fixme wall type as well
++sourceIndex;
}
}
}
/**
* Clone everything about the entity. Does *not* add it to the engine
*
* @param entity to clone
* @return the cloned entity
*/
public Entity cloneEntity(Entity entity) {
Entity clonedEntity = engine.createEntity();
//sorted alphabetically for your pleasure
AirComponent airComponent = airMapper.get(entity);
if (airComponent != null) {
AirComponent clonedComponent = new AirComponent(airComponent);
clonedEntity.add(clonedComponent);
}
AirGeneratorComponent airGeneratorComponent = airGeneratorMapper.get(entity);
if (airGeneratorComponent != null) {
AirGeneratorComponent clonedComponent = new AirGeneratorComponent(airGeneratorComponent);
clonedEntity.add(clonedComponent);
}
BlockComponent blockComponent = blockMapper.get(entity);
if (blockComponent != null) {
BlockComponent clonedComponent = new BlockComponent(blockComponent);
clonedEntity.add(clonedComponent);
}
ControllableComponent controllableComponent = controlMapper.get(entity);
if (controllableComponent != null) {
ControllableComponent clonedComponent = new ControllableComponent(controllableComponent);
clonedEntity.add(clonedComponent);
}
HealthComponent healthComponent = healthMapper.get(entity);
if (healthComponent != null) {
HealthComponent clonedComponent = new HealthComponent(healthComponent);
clonedEntity.add(clonedComponent);
}
ItemComponent itemComponent = itemMapper.get(entity);
if (itemComponent != null) {
ItemComponent clonedComponent = new ItemComponent(itemComponent);
clonedEntity.add(clonedComponent);
}
JumpComponent jumpComponent = jumpMapper.get(entity);
if (jumpComponent != null) {
JumpComponent clonedComponent = new JumpComponent(jumpComponent);
clonedEntity.add(clonedComponent);
}
//player, unneeded
assert playerMapper.get(entity) == null;
SpriteComponent spriteComponent = spriteMapper.get(entity);
if (spriteComponent != null) {
SpriteComponent clonedComponent = new SpriteComponent(spriteComponent);
clonedEntity.add(clonedComponent);
}
TagComponent tagComponent = tagMapper.get(entity);
if (tagComponent != null) {
TagComponent clonedComponent = new TagComponent(tagComponent);
clonedEntity.add(clonedComponent);
}
ToolComponent toolComponent = toolMapper.get(entity);
if (toolComponent != null) {
ToolComponent clonedComponent = new ToolComponent(toolComponent);
clonedEntity.add(clonedComponent);
}
TorchComponent torchComponent = torchMapper.get(entity);
if (torchComponent != null) {
TorchComponent clonedComponent = new TorchComponent(torchComponent);
clonedEntity.add(clonedComponent);
}
VelocityComponent velocityComponent = velocityMapper.get(entity);
if (velocityComponent != null) {
VelocityComponent clonedComponent = new VelocityComponent(velocityComponent);
clonedEntity.add(clonedComponent);
}
return clonedEntity;
}
public void addPlayer(Entity player) {
m_players.add(player);
}
public Entity playerForID(int playerIdWhoDropped) {
assert !isClient();
ImmutableArray<Entity> entities = engine.getEntitiesFor(Family.all(PlayerComponent.class).get());
PlayerComponent playerComponent;
for (int i = 0; i < entities.size(); ++i) {
playerComponent = playerMapper.get(entities.get(i));
if (playerComponent.connectionId == playerIdWhoDropped) {
return entities.get(i);
}
}
throw new IllegalStateException("player id attempted to be obtained from item, but this player does not exist");
}
public boolean touchDown(int screenX, int screenY, int pointer, int button) {
if (button != Input.Buttons.LEFT) {
return false;
}
if (m_powerOverlaySystem.overlayVisible) {
m_powerOverlaySystem.leftMouseReleased();
return true;
} else {
handleLeftMousePrimaryAttack();
return true;
}
//return false;
}
public boolean touchUp(int screenX, int screenY, int pointer, int button) {
if (button != Input.Buttons.LEFT) {
return false;
}
if (m_powerOverlaySystem.overlayVisible) {
m_powerOverlaySystem.leftMouseReleased();
return true;
} else {
}
return false;
}
public static class BlockStruct {
public String textureName; //e.g. "dirt", "stone", etc.
boolean collides;
BlockStruct(String _textureName, boolean _collides) {
textureName = _textureName;
collides = _collides;
}
}
} |
package com.ch;
import com.ch.components.FreeLook;
import com.ch.components.FreeMove;
import com.ch.components.GameComponent;
import com.ch.core.renderer.Renderer3D;
import com.ch.core.scene.Scene;
import com.ch.core.GameObject;
import com.ch.core.Window;
import com.ch.math.Matrix4f;
import com.ch.math.Quaternion;
import com.ch.math.Vector3f;
import com.ch.rendering.Material;
import com.ch.rendering.Mesh;
import com.ch.rendering.Texture;
import com.ch.rendering.components.Camera;
import com.ch.rendering.components.Camera3D;
import com.ch.rendering.components.MeshRenderer;
import com.ch.rendering.components.light.DirectionalLight;
import com.ch.rendering.components.light.PointLight;
import com.ch.rendering.light.Attenuation;
import com.tp.physics.RigidBody;
public class TestGame extends Scene {
public void init() {
setMainRenderer(new Renderer3D());
Mesh mesh = new Mesh("plane3.obj");
Material material2 = new Material(new Texture("crate.png"), 1f, 1, new Texture("crate_normal.png"), new Texture("default_disp.png"), 0.03f, -0.5f);
Material material1 = new Material(new Texture("bricks2.jpg"), .3f, 1, new Texture("bricks2_normal.jpg"), new Texture("bricks2_disp.jpg"), .03f, -.50f);
Material material = new Material(new Texture("bricks.jpg"), .3f, 1, new Texture("bricks_normal.jpg"), new Texture("bricks_disp.png"), 0.04f, -1.0f);
Mesh tempMesh = new Mesh("crate.obj");
MeshRenderer meshRenderer = new MeshRenderer(mesh, material1);
GameObject planeObject = new GameObject();
planeObject.addComponent(meshRenderer);
planeObject.getTransform().getPos().set(0, 0, 0);
// planeObject.getTransform().getScale().set(3, 3, 3);
GameObject directionalLightObject = new GameObject();
DirectionalLight directionalLight = new DirectionalLight(new Vector3f(1f, 1f, 1f), 1f);
directionalLightObject.addComponent(directionalLight);
directionalLight.getTransform().rotate(new Vector3f(0, 0, 1), (float) Math.toRadians(0));
addObject(directionalLightObject);
// GameObject pointLightObject = new GameObject();
// PointLight l = new PointLight(new Vector3f(1, 1, 0.7f), 400f, new Attenuation(0, 0, 1f)) {
// @Override
// public void update(float dt) {
// this.color = this.color.lerp(new Vector3f((float) Math.random(), (float) Math.random(), (float) Math.random()), .1f);
// super.update(dt);
// pointLightObject.addComponent(l);
// addObject(pointLightObject);
// pointLightObject.getTransform().getPos().set(0, 10, 0);
GameObject pointLightObject = new GameObject();
pointLightObject.addComponent(new PointLight(new Vector3f(0, 0.4f, .9f), .4f, new Attenuation(0, 0, .1f)));
addObject(pointLightObject);
pointLightObject.getTransform().getPos().set(0, 2, 0);
// GameObject pointLightObject1 = new GameObject();
// pointLightObject1.addComponent(new PointLight(new Vector3f(1, .7f, 0), .4f, new Attenuation(0, 0, .1f)));
// addObject(pointLightObject1);
// pointLightObject1.getTransform().getPos().set(3, 2, 0);
// GameObject pointLightObject2 = new GameObject();
// pointLightObject2.addComponent(new PointLight(new Vector3f(0, 0, 1), .4f, new Attenuation(0, 0, .1f)));
// addObject(pointLightObject2);
// pointLightObject2.getTransform().getPos().set(-3, 2f, 0);
// GameObject pointLightObject3 = new GameObject();
// pointLightObject3.addComponent(new PointLight(new Vector3f(1, 0.4f, 0), .4f, new Attenuation(0, 0, .1f)));
// addObject(pointLightObject3);
// pointLightObject3.getTransform().getPos().set(6, 2, 0);
// GameObject pointLightObject4 = new GameObject();
// pointLightObject4.addComponent(new PointLight(new Vector3f(1, 0.1f, 0.9f), .4f, new Attenuation(0, 0, .1f)));
// addObject(pointLightObject4);
// pointLightObject4.getTransform().getPos().set(-6, 2, 0);
// SpotLight spotLight = new SpotLight(new Vector3f(1, 0.6f, 0.0f), 10f, new Attenuation(0, 0, 1f), .8f);
// GameObject spotLightObject = new GameObject();
// spotLightObject.addComponent(spotLight);
// spotLightObject.getTransform().getPos().set(0, 2, 5);
// spotLightObject.getTransform().setRot(new Quaternion(new Vector3f(1, 0, 0), (float) Math.toRadians(90.0f)));
// spotLightObject.getTransform().rotate(new Vector3f(0, 0, 1), (float) Math.toRadians(-30.0f));
// spotLightObject.addComponent(new GameComponent() {
// float time = 0;
// @Override
// public void update(float dt) {
// // time += dt;
// getTransform().rotate(new Vector3f(0, 0, 1), 2 * dt);
// addObject(spotLightObject);
// SpotLight spotLight1 = new SpotLight(new Vector3f(0, 0.6f, 0.8f), 10f, new Attenuation(0, 0, 1f), .8f);
// GameObject spotLightObject1 = new GameObject();
// spotLightObject1.addComponent(spotLight1);
// spotLightObject1.getTransform().getPos().set(0, 2, 5);
// spotLightObject1.getTransform().setRot(new Quaternion(new Vector3f(1, 0, 0), (float) Math.toRadians(90.0f)));
// spotLightObject1.getTransform().rotate(new Vector3f(0, 0, 1), (float) Math.toRadians(30.0f));
// spotLightObject1.addComponent(new GameComponent() {
// float time = 0;
// @Override
// public void update(float dt) {
// // time += dt;
// getTransform().rotate(new Vector3f(0, 0, 1), 2f * dt);
// addObject(spotLightObject1);
// SpotLight spotLight2 = new SpotLight(new Vector3f(0.9f, 0.3f, 0.2f), 10f, new Attenuation(0, 0, 1f), .8f);
// GameObject spotLightObject2 = new GameObject();
// spotLightObject2.addComponent(spotLight2);
// spotLightObject2.getTransform().getPos().set(0, 2, 5);
// spotLightObject2.getTransform().setRot(new Quaternion(new Vector3f(1, 0, 0), (float) Math.toRadians(90.0f)));
// spotLightObject2.getTransform().rotate(new Vector3f(0, 0, 1), (float) Math.toRadians(-90.0f));
// spotLightObject2.addComponent(new GameComponent() {
// float time = 0;
// @Override
// public void update(float dt) {
// // time += dt;
// getTransform().rotate(new Vector3f(0, 0, 1), 2f * dt);
// addObject(spotLightObject2);
// SpotLight spotLight3 = new SpotLight(new Vector3f(0.2f, 0.9f, 0.3f), 10f, new Attenuation(0, 0, 1f), .8f);
// GameObject spotLightObject3 = new GameObject();
// spotLightObject3.addComponent(spotLight3);
// spotLightObject3.getTransform().getPos().set(0, 2, 5);
// spotLightObject3.getTransform().setRot(new Quaternion(new Vector3f(1, 0, 0), (float) Math.toRadians(90.0f)));
// spotLightObject3.getTransform().rotate(new Vector3f(0, 0, 1), (float) Math.toRadians(-90.0f - 60.0f));
// spotLightObject3.addComponent(new GameComponent() {
// float time = 0;
// @Override
// public void update(float dt) {
// // time += dt;
// getTransform().rotate(new Vector3f(0, 0, 1), 2f * dt);
// addObject(spotLightObject3);
addObject(planeObject);
GameObject testMesh3 = new GameObject()
// .addComponent(new LookAtComponent())
.addComponent(new MeshRenderer(tempMesh, material2));
addObject(new GameObject().addComponent(new FreeLook(0.3f)).addComponent(new FreeMove(6.0f))
.addComponent(new Camera3D((float) Math.toRadians(70.0f), (float) Window.getWidth() / (float) Window.getHeight(), 0.01f, 1000.0f)));
// AddObject(
// addObject(new GameObject().addComponent(new FreeLook(0.3f)).addComponent(new FreeMove(6.0f))
// .addComponent(new Camera2D(Window.getWidth() / 100, Window.getHeight() / 100, 100, -100)));
addObject(testMesh3);
testMesh3.getTransform().getPos().set(2, 0, 2);
// testMesh3.getTransform().getScale().set(.3f, .3f, .3f);
testMesh3.getTransform().setRot(new Quaternion(new Vector3f(0, 1, 0), (float) Math.toRadians(-70.0f)));
// int i;
// for (i = 0; i < 7; i++) {
for (int i = 0; i < 1; i++) {
MeshRenderer r = new MeshRenderer(new Mesh("cube.obj"), material2);
//5629
GameObject go = new GameObject().addComponent(r);
go.getTransform().getPos().set(0, 10.0f, 0);
go.addComponent(new RigidBody());
addObject(go);
}
GameComponent c;
// final int offset = i = 0;
// final Vector3f posI = new Vector3f(0, -2, 0);
// go.addComponent(new GameComponent() {
// float time = 0;
// @Override
// public void update(float dt) {
// time += 3 * dt;
// getTransform().getPos().set(posI.add((new Vector3f(8 * (float)
// Math.cos(time + offset), 0, 2 * (float) Math.sin(time +
// offset))).mul(0.2f)));
// r.getTransform().getScale().set(.1f, .1f, .1f);
}
} |
package manager;
import java.awt.Point;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import backend.Board;
import backend.Box;
import backend.Content;
import backend.Floor;
import backend.Ice;
import backend.Interruptor;
import backend.Player;
import backend.Target;
import backend.Tree;
import exceptions.ParsingException;
public class Parser {
private int columns = 0;
private int rows = 0;
private Board board;
boolean playerExists = false;
private static final char PLAYER = '@';
private static final char BOX = 'B';
private static final char TARGET = 'G';
private static final char TREE = 'T';
private static final char WATER = '
private static final char ICE = 'C';
private static final char INTERRUPTOR = 'K';
/**
* This method parses a file to check if all the data is correct.
*
* @param file
* An input file where to obtain the data from.
* @return A board created with the data from the file.
* @throws IOException
* If the file couldn't be opened.
*/
public Board parse(File file) throws IOException {
String line;
BufferedReader buffer = null;
try {
buffer = new BufferedReader(new FileReader(file));
while ((line = (buffer.readLine())) != null) {
line = deleteTabs(line);
if (line.length() > 1) {
if (columns == 0) {
columns = line.length();
}
if (line.length() != columns) {
throw new ParsingException();
}
rows++;
}
}
System.out.println(rows);
System.out.println(columns);
board = new Board(rows, columns);
if (buffer != null) {
buffer.close();
}
buffer = new BufferedReader(new FileReader(file));
rows = 0;
while ((line = (buffer.readLine())) != null) {
line = deleteTabs(line);
checkElementsValues(line, rows);
rows++;
}
return board;
} finally {
if (buffer != null) {
buffer.close();
}
}
}
/**
* This method deletes every tab from a string.
*
* @param line
* A string representing a line of the file.
* @return A new string without tabs.
*/
private String deleteTabs(String line) {
char aux;
String resp = new String();
for (int i = 0; i < line.length(); i++) {
if ((aux = line.charAt(i)) != '\t')
resp += aux;
}
return resp;
}
/**
* This method checks each element values to see if they are correct.
*
* @param line
* An array of strings representing each of the parameters of a
* line separated by a comma.
*/
private void checkElementsValues(String line, int rowActual) {
int index = 0;
Content element = null;
Point p;
char symbol;
if (line.length() != columns) {
throw new ParsingException();
}
while (index < columns) {
p = new Point(rowActual, index);
symbol = line.charAt(index);
checkSymbolExistance(symbol);
switch (symbol) {
case PLAYER: {
board.putCell(new Floor(), p);
element = new Player(p, board);
board.putContent(element, p);
board.setPlayer((Player) element);
playerExists = true;
break;
}
case BOX: {
board.putCell(new Floor(), p);
element = new Box(p, board);
board.putContent(element, p);
break;
}
case TARGET: {
board.putCell(new Target(), p);
break;
}
case TREE: {
board.putCell(new Tree(), p);
break;
}
case WATER: {
board.putCell(new Tree(), p);
break;
}
case ICE: {
board.putCell(new Floor(), p);
element = new Ice(p, board);
board.putContent(element, p);
break;
}
case INTERRUPTOR: {
board.putCell(new Interruptor(), p);
break;
}
}
index++;
}
}
/**
* This method checks if the element is an existing type of element.
*
* @param symbol
* A char representing the type of element.
*/
public void checkSymbolExistance(char symbol) {
System.out.println(symbol);
if (symbol != 'G' && symbol != 'T' && symbol != '#' && symbol != 'B'
&& symbol != 'C' && symbol != ' ' && symbol != '@'
&& symbol != 'K') {
throw new ParsingException();
}
}
} |
package bartMachine;
import gnu.trove.list.array.TDoubleArrayList;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashSet;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
import java.util.concurrent.TimeUnit;
import OpenSourceExtensions.UnorderedPair;
/**
* This class handles the parallelization of many Gibbs chains over many CPU cores
* to create one BART regression model. It also handles all operations on the completed model.
*
* @author Adam Kapelner and Justin Bleich
*/
public class bartMachineRegressionMultThread extends Classifier implements Serializable {
/** the number of CPU cores to build many different Gibbs chain within a BART model */
protected int num_cores = 1; //default
/** the number of trees in this BART model on all Gibbs chains */
protected int num_trees = 50; //default
/** the collection of <code>num_cores</code> BART models which will run separate Gibbs chains */
protected bartMachineRegression[] bart_gibbs_chain_threads;
/** this is the combined gibbs samples after burn in from all of the <code>num_cores</code> chains */
protected bartMachineTreeNode[][] gibbs_samples_of_bart_trees_after_burn_in;
/** the estimate of some upper limit of the variance of the response which is usually the MSE from a a linear regression */
private Double sample_var_y;
/** the number of burn-in samples in each Gibbs chain */
protected int num_gibbs_burn_in = 250; //default
/** the total number of gibbs samples where each chain gets a number of burn-in and then the difference from the total divided by <code>num_cores</code> */
protected int num_gibbs_total_iterations = 1250; //default
/** the total number of Gibbs samples for each of the <code>num_cores</code> chains */
protected int total_iterations_multithreaded;
/** The probability vector that samples covariates for selecting split rules */
protected double[] cov_split_prior;
/** A hyperparameter that controls how easy it is to grow new nodes in a tree independent of depth */
protected Double alpha = 0.95;
/** A hyperparameter that controls how easy it is to grow new nodes in a tree dependent on depth which makes it more difficult as the tree gets deeper */
protected Double beta = 2.0;
/** this controls where to set <code>hyper_sigsq_mu</code> by forcing the variance to be this number of standard deviations on the normal CDF */
protected Double hyper_k = 2.0;
/** At a fixed <code>hyper_nu</code>, this controls where to set <code>hyper_lambda</code> by forcing q proportion to be at that value in the inverse gamma CDF */
protected Double hyper_q = 0.9;
/** half the shape parameter and half the multiplicand of the scale parameter of the inverse gamma prior on the variance */
protected Double hyper_nu = 3.0;
/** the hyperparameter of the probability of picking a grow step during the Metropolis-Hastings tree proposal */
protected Double prob_grow = 2.5 / 9.0;
/** the hyperparameter of the probability of picking a prune step during the Metropolis-Hastings tree proposal */
protected Double prob_prune = 2.5 / 9.0;
/** should we print select messages to the screen */
protected boolean verbose = true;
/**
* whether or not we use the memory cache feature
*
* @see Section 3.1 of Kapelner, A and Bleich, J. bartMachine: A Powerful Tool for Machine Learning in R. ArXiv e-prints, 2013
*/
protected boolean mem_cache_for_speed = true;
/** the default constructor sets the number of total iterations each Gibbs chain is charged with sampling */
public bartMachineRegressionMultThread(){
setNumGibbsTotalIterations(num_gibbs_total_iterations);
}
/**
* This is a simple setter for the number of total Gibbs samples and
* it also sets the total iterations per Gibbs chain running on each CPU
* core (see formula in the code)
*
* @param num_gibbs_total_iterations The number of total Gibbs iterations to set
*/
public void setNumGibbsTotalIterations(int num_gibbs_total_iterations){
this.num_gibbs_total_iterations = num_gibbs_total_iterations;
total_iterations_multithreaded = num_gibbs_burn_in + (int)Math.ceil((num_gibbs_total_iterations - num_gibbs_burn_in) / (double) num_cores);
}
/** The number of samples after burning is simply the title minus the burn-in */
public int numSamplesAfterBurning(){
return num_gibbs_total_iterations - num_gibbs_burn_in;
}
/** Set up an array of regression BARTs with length equal to <code>num_cores</code>, the number of CPU cores requested */
protected void SetupBARTModels() {
bart_gibbs_chain_threads = new bartMachineRegression[num_cores];
for (int t = 0; t < num_cores; t++){
bartMachineRegression bart = new bartMachineRegression();
SetupBartModel(bart, t);
}
}
/**
* Initialize one of the <code>num_cores</code> BART models by setting
* all its custom parameters
*
* @param bart The BART model to initialize
* @param t The number of the core this BART model corresponds to
*/
protected void SetupBartModel(bartMachineRegression bart, int t) {
bart.setVerbose(verbose);
//now set specs on each of the bart models
bart.num_trees = num_trees;
bart.num_gibbs_total_iterations = total_iterations_multithreaded;
bart.num_gibbs_burn_in = num_gibbs_burn_in;
bart.sample_var_y = sample_var_y;
//now some hyperparams
bart.setAlpha(alpha);
bart.setBeta(beta);
bart.setK(hyper_k);
bart.setProbGrow(prob_grow);
bart.setProbPrune(prob_prune);
//set thread num and data
bart.setThreadNum(t);
bart.setTotalNumThreads(num_cores);
bart.setMemCacheForSpeed(mem_cache_for_speed);
//set features
if (cov_split_prior != null){
bart.setCovSplitPrior(cov_split_prior);
}
//do special stuff for regression model
if (!(bart instanceof bartMachineClassification)){
bart.setNu(hyper_nu);
bart.setQ(hyper_q);
}
//once the params are set, now you can set the data
bart.setData(X_y);
bart_gibbs_chain_threads[t] = bart;
}
/**
* Takes a library of standard normal samples provided external and caches them
*
* @param norm_samples The externally provided cache
*/
public void setNormSamples(double[] norm_samples){
bartMachine_b_hyperparams.samps_std_normal = norm_samples;
bartMachine_b_hyperparams.samps_std_normal_length = norm_samples.length;
}
/**
* Takes a library of chi-squared samples provided external and caches them
*
* @param gamma_samples The externally provided cache
*/
public void setGammaSamples(double[] gamma_samples){
bartMachine_b_hyperparams.samps_chi_sq_df_eq_nu_plus_n = gamma_samples;
bartMachine_b_hyperparams.samps_chi_sq_df_eq_nu_plus_n_length = gamma_samples.length;
}
/** This function actually initiates the Gibbs sampling to build all the BART models */
public void Build() {
SetupBARTModels();
//run a build on all threads
long t0 = System.currentTimeMillis();
if (verbose){
System.out.println("building BART " + (mem_cache_for_speed ? "with" : "without") + " mem-cache speedup...");
}
BuildOnAllThreads();
long t1 = System.currentTimeMillis();
if (verbose){
System.out.println("done building BART in " + ((t1 - t0) / 1000.0) + " sec \n");
}
//once it's done, now put together the chains
ConstructBurnedChainForTreesAndOtherInformation();
}
/** Create a post burn-in chain for ease of manipulation later */
protected void ConstructBurnedChainForTreesAndOtherInformation() {
gibbs_samples_of_bart_trees_after_burn_in = new bartMachineTreeNode[numSamplesAfterBurning()][num_trees];
if (verbose){
System.out.print("burning and aggregating chains from all threads... ");
}
//go through each thread and get the tail and put them together
for (int t = 0; t < num_cores; t++){
bartMachineRegression bart_model = bart_gibbs_chain_threads[t];
for (int i = num_gibbs_burn_in; i < total_iterations_multithreaded; i++){
int offset = t * (total_iterations_multithreaded - num_gibbs_burn_in);
int g = offset + (i - num_gibbs_burn_in);
if (g >= numSamplesAfterBurning()){
break;
}
gibbs_samples_of_bart_trees_after_burn_in[g] = bart_model.gibbs_samples_of_bart_trees[i];
}
}
if (verbose){
System.out.print("done\n");
}
}
/** This is the core of BART's parallelization for model creation: build one BART model on each CPU core in parallel */
private void BuildOnAllThreads(){
ExecutorService bart_gibbs_chain_pool = Executors.newFixedThreadPool(num_cores);
for (int t = 0; t < num_cores; t++){
final int tf = t;
bart_gibbs_chain_pool.execute(new Runnable(){
public void run() {
bart_gibbs_chain_threads[tf].Build();
}
});
}
bart_gibbs_chain_pool.shutdown();
try {
bart_gibbs_chain_pool.awaitTermination(Long.MAX_VALUE, TimeUnit.SECONDS); //effectively infinity
} catch (InterruptedException ignored){}
}
/**
* Return the predictions from each tree for each burned-in Gibbs sample
*
* @param records the observations / records for which to return predictions
* @param num_cores_evaluate The number of CPU cores to use during evaluation
* @return Predictions for all records further indexed by Gibbs sample
*/
protected double[][] getGibbsSamplesForPrediction(final double[][] records, final int num_cores_evaluate){
final int num_samples_after_burn_in = numSamplesAfterBurning();
final bartMachineRegression first_bart = bart_gibbs_chain_threads[0];
final int n = records.length;
final double[][] y_hats = new double[n][records[0].length];
//this is really ugly, but it's faster (we've checked in a Profiler)
if (num_cores_evaluate == 1){
for (int i = 0; i < n; i++){
double[] y_gibbs_samples = new double[num_samples_after_burn_in];
for (int g = 0; g < num_samples_after_burn_in; g++){
bartMachineTreeNode[] trees = gibbs_samples_of_bart_trees_after_burn_in[g];
double yt_i = 0;
for (int m = 0; m < num_trees; m++){
yt_i += trees[m].Evaluate(records[i]); //sum of trees, right?
}
//just make sure we switch it back to really what y is for the user
y_gibbs_samples[g] = first_bart.un_transform_y(yt_i);
}
y_hats[i] = y_gibbs_samples;
}
}
else {
Thread[] fixed_thread_pool = new Thread[num_cores_evaluate];
for (int t = 0; t < num_cores_evaluate; t++){
final int final_t = t;
Thread thread = new Thread(){
public void run(){
for (int i = 0; i < n; i++){
if (i % num_cores_evaluate == final_t){
double[] y_gibbs_samples = new double[num_samples_after_burn_in];
for (int g = 0; g < num_samples_after_burn_in; g++){
bartMachineTreeNode[] trees = gibbs_samples_of_bart_trees_after_burn_in[g];
double yt_i = 0;
for (int m = 0; m < num_trees; m++){ //sum of trees right?
yt_i += trees[m].Evaluate(records[i]);
}
//just make sure we switch it back to really what y is for the user
y_gibbs_samples[g] = first_bart.un_transform_y(yt_i);
}
y_hats[i] = y_gibbs_samples;
}
}
}
};
thread.start();
fixed_thread_pool[t] = thread;
}
for (int t = 0; t < num_cores_evaluate; t++){
try {
fixed_thread_pool[t].join();
} catch (InterruptedException e) {}
}
}
return y_hats;
}
/**
* Using the {@link #getGibbsSamplesForPrediction} function, return a credible interval at a specified
* level of coverage
*
* @param record The record for which to obtain an interval
* @param coverage The desired coverage
* @param num_cores_evaluate The number of CPU cores to use during evaluation
* @return A double pair which represents the upper and lower bound of coverage
*/
protected double[] getPostPredictiveIntervalForPrediction(double[] record, double coverage, int num_cores_evaluate){
double[][] data = new double[1][record.length];
data[0] = record;
//get all gibbs samples sorted
double[][] y_gibbs_samples_sorted_matrix = getGibbsSamplesForPrediction(data, num_cores_evaluate);
double[] y_gibbs_samples_sorted = y_gibbs_samples_sorted_matrix[0];
Arrays.sort(y_gibbs_samples_sorted);
//calculate index of the CI_a and CI_b
int n_bottom = (int)Math.round((1 - coverage) / 2 * y_gibbs_samples_sorted.length) - 1; //-1 because arrays start at zero
int n_top = (int)Math.round(((1 - coverage) / 2 + coverage) * y_gibbs_samples_sorted.length) - 1; //-1 because arrays start at zero
double[] conf_interval = {y_gibbs_samples_sorted[n_bottom], y_gibbs_samples_sorted[n_top]};
return conf_interval;
}
/**
* Using the {@link #getPostPredictiveIntervalForPrediction} function, return a 95\% credible interval
*
* @param record The record for which to obtain an interval
* @param num_cores_evaluate The number of CPU cores to use during evaluation
* @return A double pair which represents the upper and lower bound of coverage
*/
protected double[] get95PctPostPredictiveIntervalForPrediction(double[] record, int num_cores_evaluate){
return getPostPredictiveIntervalForPrediction(record, 0.95, num_cores_evaluate);
}
public double[] getGibbsSamplesSigsqs(){
TDoubleArrayList sigsqs_to_export = new TDoubleArrayList(num_gibbs_total_iterations);
for (int t = 0; t < num_cores; t++){
TDoubleArrayList sigsqs_to_export_by_thread = new TDoubleArrayList(bart_gibbs_chain_threads[t].getGibbsSamplesSigsqs());
if (t == 0){
sigsqs_to_export.addAll(sigsqs_to_export_by_thread);
}
else {
sigsqs_to_export.addAll(sigsqs_to_export_by_thread.subList(num_gibbs_burn_in, total_iterations_multithreaded));
}
}
return sigsqs_to_export.toArray();
}
/**
* Returns a record of Metropolis-Hastings acceptances or rejections for all trees during burn-in
*
* @return Yes/No's for acceptances for all Gibbs samples further indexed by tree
*/
public boolean[][] getAcceptRejectMHsBurnin(){
boolean[][] accept_reject_mh_first_thread = bart_gibbs_chain_threads[0].getAcceptRejectMH();
boolean[][] accept_reject_mh_burn_ins = new boolean[num_gibbs_burn_in][num_trees];
for (int g = 1; g < num_gibbs_burn_in + 1; g++){
accept_reject_mh_burn_ins[g - 1] = accept_reject_mh_first_thread[g];
}
return accept_reject_mh_burn_ins;
}
/**
* Returns a record of Metropolis-Hastings acceptances or rejections for all trees after burn-in
*
* @param thread_num Which CPU core's acceptance / rejection record should be returned
* @return Yes/No's for acceptances for all Gibbs samples further indexed by tree
*/
public boolean[][] getAcceptRejectMHsAfterBurnIn(int thread_num){
boolean[][] accept_reject_mh_by_core = bart_gibbs_chain_threads[thread_num - 1].getAcceptRejectMH();
boolean[][] accept_reject_mh_after_burn_ins = new boolean[total_iterations_multithreaded - num_gibbs_burn_in][num_trees];
for (int g = num_gibbs_burn_in; g < total_iterations_multithreaded; g++){
accept_reject_mh_after_burn_ins[g - num_gibbs_burn_in] = accept_reject_mh_by_core[g];
}
return accept_reject_mh_after_burn_ins;
}
/**
* Return the number of times each of the attributes were used during the construction of the sum-of-trees
* by Gibbs sample.
*
* @param type Either "splits" or "trees" ("splits" means total number and "trees" means sum of binary values of whether or not it has appeared in the tree)
* @return The counts for all Gibbs samples further indexed by the attribute 1, ..., p
*/
public int[][] getCountsForAllAttribute(final String type) {
final int[][] variable_counts_all_gibbs = new int[num_gibbs_total_iterations - num_gibbs_burn_in][p];
for (int g = 0; g < num_gibbs_total_iterations - num_gibbs_burn_in; g++){
final bartMachineTreeNode[] trees = gibbs_samples_of_bart_trees_after_burn_in[g];
int[] variable_counts_one_gibbs = new int[p];
for (bartMachineTreeNode tree : trees){
if (type.equals("splits")){
variable_counts_one_gibbs = Tools.add_arrays(variable_counts_one_gibbs, tree.attribute_split_counts);
}
else if (type.equals("trees")){
variable_counts_one_gibbs = Tools.binary_add_arrays(variable_counts_one_gibbs, tree.attribute_split_counts);
}
}
variable_counts_all_gibbs[g] = variable_counts_one_gibbs;
}
return variable_counts_all_gibbs;
}
/**
* Return the proportion of times each of the attributes were used (count over total number of splits)
* during the construction of the sum-of-trees by Gibbs sample.
*
* @param type Either "splits" or "trees" ("splits" means total number and "trees" means sum of binary values of whether or not it has appeared in the tree)
* @return The proportion of splits for all Gibbs samples further indexed by the attribute 1, ..., p
*/
public double[] getAttributeProps(final String type) {
int[][] variable_counts_all_gibbs = getCountsForAllAttribute(type);
double[] attribute_counts = new double[p];
for (int g = 0; g < num_gibbs_total_iterations - num_gibbs_burn_in; g++){
attribute_counts = Tools.add_arrays(attribute_counts, variable_counts_all_gibbs[g]);
}
Tools.normalize_array(attribute_counts); //will turn it into proportions
return attribute_counts;
}
/**
* For all Gibbs samples after burn in, calculate the set of interaction counts (consider a split on x_j
* and a daughter node splits on x_k and that would be considered an "interaction")
*
* @return A matrix of size p x p where the row is top split and the column is a bottom split. It is recommended to triangularize the matrix after ignoring the order.
*/
public int[][] getInteractionCounts(){
int[][] interaction_count_matrix = new int[p][p];
for (int g = 0; g < gibbs_samples_of_bart_trees_after_burn_in.length; g++){
bartMachineTreeNode[] trees = gibbs_samples_of_bart_trees_after_burn_in[g];
for (bartMachineTreeNode tree : trees){
//get the set of pairs of interactions
HashSet<UnorderedPair<Integer>> set_of_interaction_pairs = new HashSet<UnorderedPair<Integer>>(p * p);
//find all interactions
tree.findInteractions(set_of_interaction_pairs);
//now tabulate these interactions in our count matrix
for (UnorderedPair<Integer> pair : set_of_interaction_pairs){
interaction_count_matrix[pair.getFirst()][pair.getSecond()]++;
}
}
}
return interaction_count_matrix;
}
/** Flush all unnecessary data from the Gibbs chains to conserve RAM */
protected void FlushData() {
for (int t = 0; t < num_cores; t++){
bart_gibbs_chain_threads[t].FlushData();
}
}
/**
* The default BART evaluation of a new observations is done via sample average of the
* posterior predictions. Other functions can be used here such as median, mode, etc.
* Default is to use one CPU core.
*
* @param record The observation to be evaluated / predicted
*/
public double Evaluate(double[] record) {
return EvaluateViaSampAvg(record, 1);
}
/**
* The default BART evaluation of a new observations is done via sample average of the
* posterior predictions. Other functions can be used here such as median, mode, etc.
*
* @param record The observation to be evaluated / predicted
* @param num_cores_evaluate The number of CPU cores to use during evaluation
*/
public double Evaluate(double[] record, int num_cores_evaluate) {
return EvaluateViaSampAvg(record, num_cores_evaluate);
}
/**
* Evaluates a new observations via sample average of the posterior predictions.
*
* @param record The observation to be evaluated / predicted
* @param num_cores_evaluate The number of CPU cores to use during evaluation
*/
public double EvaluateViaSampAvg(double[] record, int num_cores_evaluate) {
double[][] data = new double[1][record.length];
data[0] = record;
double[][] gibbs_samples = getGibbsSamplesForPrediction(data, num_cores_evaluate);
return StatToolbox.sample_average(gibbs_samples[0]);
}
/**
* Evaluates a new observations via sample median of the posterior predictions.
*
* @param record The observation to be evaluated / predicted
* @param num_cores_evaluate The number of CPU cores to use during evaluation
*/
public double EvaluateViaSampMed(double[] record, int num_cores_evaluate) {
double[][] data = new double[1][record.length];
data[0] = record;
double[][] gibbs_samples = getGibbsSamplesForPrediction(data, num_cores_evaluate);
return StatToolbox.sample_median(gibbs_samples[0]);
}
/**
* After burn in, find the depth (greatest generation of a terminal node) of each tree for each Gibbs sample
*
* @param thread_num which CPU core (which Gibbs chain) to return results for
* @return for each Gibbs chain return a vector of depths for all <code>num_trees</code> chains
*/
public int[][] getDepthsForTreesInGibbsSampAfterBurnIn(int thread_num){
return bart_gibbs_chain_threads[thread_num - 1].getDepthsForTrees(num_gibbs_burn_in, total_iterations_multithreaded);
}
/**
* After burn in, return the number of total nodes (internal plus terminal) of each tree for each Gibbs sample
*
* @param thread_num which CPU core (which Gibbs chain) to return results for
* @return for each Gibbs chain return a vector of number of nodes for all <code>num_trees</code> chains
*/
public int[][] getNumNodesAndLeavesForTreesInGibbsSampAfterBurnIn(int thread_num){
return bart_gibbs_chain_threads[thread_num - 1].getNumNodesAndLeavesForTrees(num_gibbs_burn_in, total_iterations_multithreaded);
}
public void setData(ArrayList<double[]> X_y){
this.X_y = X_y;
n = X_y.size();
p = X_y.get(0).length - 1;
}
public void setCovSplitPrior(double[] cov_split_prior){
this.cov_split_prior = cov_split_prior;
}
public void setNumGibbsBurnIn(int num_gibbs_burn_in){
this.num_gibbs_burn_in = num_gibbs_burn_in;
}
public void setNumTrees(int num_trees){
this.num_trees = num_trees;
}
public void setSampleVarY(double sample_var_y){
this.sample_var_y = sample_var_y;
}
public void setAlpha(double alpha){
this.alpha = alpha;
}
public void setBeta(double beta){
this.beta = beta;
}
public void setK(double hyper_k) {
this.hyper_k = hyper_k;
}
public void setQ(double hyper_q) {
this.hyper_q = hyper_q;
}
public void setNU(double hyper_nu) {
this.hyper_nu = hyper_nu;
}
public void setProbGrow(double prob_grow) {
this.prob_grow = prob_grow;
}
public void setProbPrune(double prob_prune) {
this.prob_prune = prob_prune;
}
public void setVerbose(boolean verbose){
this.verbose = verbose;
}
public void setNumCores(int num_cores){
this.num_cores = num_cores;
}
public void setMemCacheForSpeed(boolean mem_cache_for_speed){
this.mem_cache_for_speed = mem_cache_for_speed;
}
/** Must be implemented, but does nothing */
public void StopBuilding() {}
} |
package org.multibit.hd.ui.views.components.enter_recipient;
import com.google.common.base.Optional;
import net.miginfocom.swing.MigLayout;
import org.multibit.hd.core.dto.Recipient;
import org.multibit.hd.ui.gravatar.Gravatars;
import org.multibit.hd.ui.utils.ClipboardUtils;
import org.multibit.hd.ui.views.components.*;
import org.multibit.hd.ui.views.components.auto_complete.AutoCompleteFilter;
import org.multibit.hd.ui.views.components.auto_complete.AutoCompleteFilters;
import javax.swing.*;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.image.BufferedImage;
/**
* <p>View to provide the following to UI:</p>
* <ul>
* <li>Presentation of a dual-purpose combobox</li>
* <li>Support for locating contacts by name</li>
* <li>Support for entering recipient Bitcoin address representations (address, seed, key etc)</li>
* </ul>
*
* @since 0.0.1
*
*/
public class EnterRecipientView extends AbstractComponentView<EnterRecipientModel> {
// View components
private JComboBox<Recipient> recipientComboBox;
private JLabel imageLabel;
private JButton pasteButton;
/**
* @param model The model backing this view
*/
public EnterRecipientView(EnterRecipientModel model) {
super(model);
}
@Override
public JPanel newComponentPanel() {
AutoCompleteFilter<Recipient> filter = AutoCompleteFilters.newRecipientFilter();
// Bind a key listener to allow instant update of UI to matched passwords
recipientComboBox = ComboBoxes.newRecipientComboBox(filter);
recipientComboBox.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
updateModelFromView();
}
});
pasteButton = Buttons.newPasteButton(getPasteAction());
JPanel panel = Panels.newPanel(new MigLayout(
"fillx,insets 0", // Layout
"[][][][]", // Columns
"[]" // Rows
));
// Start with an invisible label
imageLabel = Labels.newImageLabel(Optional.<BufferedImage>absent());
imageLabel.setVisible(false);
panel.add(Labels.newRecipient());
// Specify minimum width for consistent appearance across contact names and locales
panel.add(recipientComboBox, "growx,w min:350:,push");
panel.add(pasteButton, "shrink");
panel.add(imageLabel, "shrink,wrap");
return panel;
}
@Override
public void updateModelFromView() {
Object selectedItem = recipientComboBox.getSelectedItem();
Optional<Recipient> currentRecipient = getModel().get().getRecipient();
boolean showGravatar = false;
if (selectedItem instanceof Recipient) {
// We have a select from the drop down
Recipient selectedRecipient = (Recipient) selectedItem;
// Avoid double events triggering calls
if (currentRecipient.isPresent() && currentRecipient.get().equals(selectedRecipient)) {
return;
}
// Update the current with the selected
currentRecipient = Optional.of(selectedRecipient);
getModel().get().setValue(selectedRecipient);
// Display a gravatar if we have a contact
if (selectedRecipient.getContact().isPresent()) {
if (selectedRecipient.getContact().get().getEmail().isPresent()) {
// We have an email address
String emailAddress = selectedRecipient.getContact().get().getEmail().get();
Optional<BufferedImage> image = Gravatars.retrieveGravatar(emailAddress);
if (image.isPresent()) {
imageLabel.setIcon(new ImageIcon(image.get()));
imageLabel.setVisible(true);
showGravatar = true;
}
}
}
} else {
// Create a recipient based on the text entry
currentRecipient = Optional.of(new Recipient((String) selectedItem));
}
// There is no gravatar to show
if (!showGravatar) {
imageLabel.setVisible(false);
}
// Update the model
getModel().get().setValue(currentRecipient.get());
}
/**
* @return A new action for pasting the recipient information
*/
private Action getPasteAction() {
// Show or hide the seed phrase
return new AbstractAction() {
@Override
public void actionPerformed(ActionEvent e) {
Optional<String> pastedText = ClipboardUtils.pasteStringFromClipboard();
if (pastedText.isPresent()) {
recipientComboBox.getEditor().setItem(pastedText.get());
}
}
};
}
} |
package org.n52.movingcode.runtime.coderepository;
import java.io.File;
import java.io.IOException;
import java.util.Collection;
import java.util.HashMap;
import java.util.Timer;
import java.util.TimerTask;
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.filefilter.FileFilterUtils;
import org.apache.jackrabbit.uuid.UUID;
import org.apache.xmlbeans.XmlException;
import org.joda.time.DateTime;
import org.n52.movingcode.runtime.codepackage.Constants;
import org.n52.movingcode.runtime.codepackage.MovingCodePackage;
import org.n52.movingcode.runtime.codepackage.PackageID;
import de.tudresden.gis.geoprocessing.movingcode.schema.PackageDescriptionDocument;
/**
* This class implements an {@link IMovingCodeRepository} for local (unzipped) packages, stored
* in a flat folder structure. This folder structure shall have the following appearance:
*
* <absPath>-<folder1>-<packagedescription.xml>
* | \<package.id>
* | \<workspacefolder1>
* |
* -<folder2>-<packagedescription.xml>
* | \<package.id>
* | \<workspacefolder2>
* |
* -<folder3>-<packagedescription.xml>
* | \<package.id>
* | \<workspacefolder3>
* |
* ...
* |
* -<folderN>-<processdescriptionN>
* \<package.id>
* \<workspacefolderN>
*
* For any sub-folders found in <absPath> it will be assumed that it contains a plain (unzipped)
* Moving Code package.
*
* The file <packagedescription.xml> contains the description of the MovingCode package.
*
* The file <package.id> contains the hierarchical ID of that package, usually a URL path or path fragment.
* The following layout / mapping is used:
* (mapping to {@link PackageID})
*
* <packageroot>/<username>/<collectionname>/<packagename>/<timestamp>
*
* pageroot => namespace
* identifier => <username>/<collectionname>/<packagename>
* timestamp => version
*
* Performs occasional checks for updated content.
* (Interval for periodical checks is given by {@link IMovingCodeRepository#localPollingInterval})
*
* @author Matthias Mueller, TU Dresden
*
*/
public class LocalVersionedFileRepository extends AbstractRepository {
private final File directory;
private String fingerprint;
private Timer timerDaemon;
private static final HashMap<PackageID,String> packageFolders = new HashMap<PackageID,String>();
/**
*
* Constructor for file system based repositories. Scans all sub-directories of a given sourceDirectory
* for valid workspaces and attempt to interpret them as MovingCodePackages.
* Incomplete or malformed packages will be ignored.
*
* @param sourceDirectory {@link File} - the directory to be scanned for Moving Code Packages.
*
*/
public LocalVersionedFileRepository(File sourceDirectory) {
this.directory = sourceDirectory;
// compute directory fingerprint
fingerprint = RepositoryUtils.directoryFingerprint(directory);
// load packages from folder
load();
// start timer daemon
timerDaemon = new Timer(true);
timerDaemon.scheduleAtFixedRate(new CheckFolder(), 0, IMovingCodeRepository.localPollingInterval);
}
public synchronized void addPackage(File workspace, PackageDescriptionDocument pd, PackageID pid){
// 1. create moving code packe object
// 2. make new directory with UUID
// 3. put packagedescription XML in place
// 4. dump workspace to repo
// 5. dump packageid to repo
MovingCodePackage mcp = new MovingCodePackage(workspace, pd, new DateTime(pid.getVersion()));
File targetDir = makeNewDirectory();
mcp.dumpWorkspace(targetDir);
mcp.dumpDescription(new File(targetDir.getAbsolutePath() + File.separator + Constants.PACKAGE_DESCRIPTION_XML));
pid.dump(targetDir);
// 6. register package
register(mcp, pid);
packageFolders.put(pid, targetDir.getAbsolutePath());
}
public synchronized void addPackage(MovingCodePackage mcp, PackageID pid){
File targetDir = makeNewDirectory();
mcp.dumpWorkspace(targetDir);
mcp.dumpDescription(new File(targetDir.getAbsolutePath() + File.separator + Constants.PACKAGE_DESCRIPTION_XML));
pid.dump(targetDir);
// finally: register package
register(mcp, pid);
}
/**
* Remove a package with a given ID from this repository
*
* @param pid
* @return
*/
public boolean removePackage(PackageID pid){
// 1. unregister package, so it cannot be found any longer
// 2. remove directory
// 3. TODO: care for errors in case something goes wrong to make sure we are
// not left in an undefined state
unregister(pid);
File packageDir = new File(packageFolders.get(pid));
try {
FileUtils.cleanDirectory(packageDir);
FileUtils.deleteDirectory(packageDir);
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
return false;
}
// 4. remove folder from inventory
packageFolders.remove(pid);
return true;
}
/**
* private method that encapsulates the logic for loading zipped
* MovingCode packages from a local folder.
*/
private final void load(){
// recursively obtain all zipfiles in sourceDirectory
Collection<File> packageFolders = scanForFolders(directory);
logger.info("Scanning directory: " + directory.getAbsolutePath());
for (File currentFolder : packageFolders) {
// attempt to read packageDescription XML
File packageDescriptionFile = new File(currentFolder, Constants.PACKAGE_DESCRIPTION_XML);
if (!packageDescriptionFile.exists()){
continue; // skip this and immediately jump to the next iteration
}
PackageDescriptionDocument pd;
try {
pd = PackageDescriptionDocument.Factory.parse(packageDescriptionFile);
} catch (XmlException e) {
// silently skip this and immediately jump to the next iteration
continue;
} catch (IOException e) {
// silently skip this and immediately jump to the next iteration
continue;
}
// attempt to read package.id
File packageIdFile = new File(currentFolder, Constants.PACKAGE_ID_FILE);
PackageID packageId = PackageID.parse(packageIdFile);
// packageID = absolute path
logger.info("Found package: " + currentFolder + "; using ID: " + packageId.toString());
// attempt to access workspace root folder
String workspace = pd.getPackageDescription().getWorkspace().getWorkspaceRoot();
if (workspace.startsWith("./")){
workspace = workspace.substring(2); // remove leading "./" if it exists
}
File workspaceDir = new File(currentFolder, workspace);
if (!workspaceDir.exists()){
continue; // skip this and immediately jump to the next iteration
}
MovingCodePackage mcPackage = new MovingCodePackage(workspaceDir, pd, null);
// validate
// and add to package map
// and add current file to zipFiles map
if (mcPackage.isValid()) {
register(mcPackage, packageId);
}
else {
logger.error(currentFolder.getAbsolutePath() + " is an invalid package.");
}
}
}
/**
* Scans a directory for subfolders (i.e. immediate child folders) and adds them
* to the resulting Collection.
*
* @param directory {@link File} - parent directory to scan.
* @return {@link Collection} of {@link File} - the directories found
*/
private static final Collection<File> scanForFolders(File directory) {
return FileUtils.listFiles(directory, FileFilterUtils.directoryFileFilter(), null);
}
/**
* Generate a new directory.
*
* @return
*/
private final File makeNewDirectory(){
String dirName = directory.getAbsolutePath() + File.separator + UUID.randomUUID().toString();
File newDir = new File(dirName);
newDir.mkdirs();
return newDir;
}
/**
* A task which re-computes the directory's fingerprint and
* triggers a content reload if required.
*
* @author Matthias Mueller
*
*/
private final class CheckFolder extends TimerTask {
@Override
public void run() {
String newFingerprint = RepositoryUtils.directoryFingerprint(directory);
if (!newFingerprint.equals(fingerprint)){
logger.info("Repository content has silently changed. Running update ...");
// set new fingerprint
fingerprint = newFingerprint;
// clear an reload
clear();
load();
logger.info("Reload finished. Calling Repository Change Listeners.");
informRepositoryChangeListeners();
}
}
}
} |
package main;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
/**
* Collection of Options
*
* @author nhan
*
*/
public class Options implements Iterable<Option> {
private Map<OptionType, Collection<Option>> optionTable;
public boolean add(Option opt) {
OptionType optType = OptionType.fromOption(opt);
Collection<Option> options = null;
if (optionTable.containsKey(optType)) {
options = optionTable.get(optType);
} else {
options = new ArrayList<Option>();
}
options.add(opt);
optionTable.put(optType, options);
return true;
}
/**
* Query if this collection contains a particular option
*
* @param opt the Option to query
* @return boolean flag if the matching option exists in the collection
*/
public boolean hasOption(Option opt) {
OptionType optType = OptionType.fromOption(opt);
if (optionTable.containsKey(optType)) {
Collection<Option> options = optionTable.get(optType);
return options.contains(opt);
} else {
return false;
}
}
/**
* Query if this collection contains an option name
*
* @param optName String name for the option
* @return boolean flag if a certain option type exists.
*/
public boolean hasOption(String optName) {
return optionTable.containsKey(OptionType.fromString(optName));
}
/**
* Retrieve a passed Option if it exists in this collection
*
* @param opt an Option to search for in the collection
* @return an Option object that exists in the collection
*/
public Option getOption(Option opt) {
OptionType optType = OptionType.fromOption(opt);
for (Option o: optionTable.get(optType)) {
if (opt.equals(o)) {
return o;
}
}
return null;
}
/**
* Retrieve the collection of Option that has the same type
*
* @param optName an alias of the option to specify OptionType
* @return a collection of all the options of that OptionType
*/
public Collection<Option> getOptions(String optName) {
OptionType optType = OptionType.fromString(optName);
return optionTable.get(optType);
}
public boolean hasAmbiguity() {
return false;
}
@Override
public Iterator<Option> iterator() {
// TODO Auto-generated method stub
return null;
}
} |
package org.kevoree.modeling.abs;
import org.kevoree.modeling.KCallback;
import org.kevoree.modeling.KObject;
import org.kevoree.modeling.KObjectInfer;
import org.kevoree.modeling.defer.KDefer;
import org.kevoree.modeling.memory.manager.KMemoryManager;
import org.kevoree.modeling.meta.*;
import org.kevoree.modeling.traversal.KTraversalIndexResolver;
public class AbstractKObjectInfer extends AbstractKObject implements KObjectInfer {
public AbstractKObjectInfer(long p_universe, long p_time, long p_uuid, KMetaClass p_metaClass, KMemoryManager p_manager) {
super(p_universe, p_time, p_uuid, p_metaClass, p_manager);
}
@Override
public void train(KObject[] dependencies, Object[] expectedOutputs, KCallback callback) {
final KObjectInfer selfObject = this;
if (dependencies.length != _metaClass.dependencies().dependencies().length || expectedOutputs.length != _metaClass.outputs().length) {
throw new RuntimeException("Bad number of arguments for dependencies");
}
KDefer waiter = this.manager().model().defer();
KTraversalIndexResolver resolver = new KTraversalIndexResolver() {
@Override
public KObject[] resolve(String indexName) {
KMetaDependency dependency = _metaClass.dependencies().dependencyByName(indexName);
if (dependency != null) {
KObject[] single = new KObject[1];
single[0] = dependencies[dependency.index()];
return single;
}
return null;
}
};
for (int i = 0; i < _metaClass.inputs().length; i++) {
_metaClass.inputs()[i].extractor().exec(null, resolver, waiter.wait("" + i));
}
waiter.then(new KCallback() {
@Override
public void on(Object o) {
double[][] extractedInputs = new double[1][_metaClass.inputs().length];
for (int i = 0; i < _metaClass.inputs().length; i++) {
try {
extractedInputs[0][i] = (double) waiter.getResult("" + i);
} catch (Exception e) {
e.printStackTrace();
}
}
double[][] extractedOutputs = new double[1][_metaClass.outputs().length];
for (int i = 0; i < _metaClass.outputs().length; i++) {
KMetaInferOutput metaInferOutput = _metaClass.outputs()[i];
extractedOutputs[0][i] = internalConvertOutput(expectedOutputs[i], metaInferOutput);
}
_metaClass.inferAlg().train(extractedInputs, extractedOutputs, selfObject);
if (callback != null) {
callback.on(null);
}
}
});
}
private double internalConvertOutput(Object output, KMetaInferOutput metaOutput) {
if (metaOutput.type().equals(KPrimitiveTypes.BOOL)) {
if (output.equals(true)) {
return 1.0;
} else {
return 0.0;
}
} else {
//TODO implement here all the case study
//default case
return 0;
}
}
@Override
public void trainAll(KObject[][] p_trainingSet, Object[][] p_expectedResultSet, KCallback callback) {
//if(p_trainingSet)
}
@Override
public void infer(KObject[] features, KCallback<Object[]> callback) {
//TODO
}
@Override
public void inferAll(KObject[][] features, KCallback<Object[][]> callback) {
}
@Override
public void resetLearning() {
//TODO
throw new RuntimeException("Not Implemented Yet!");
}
} |
package com.intellij.openapi.roots.ui.configuration.projectRoot;
import com.intellij.openapi.actionSystem.AnAction;
import com.intellij.openapi.actionSystem.AnActionEvent;
import com.intellij.openapi.actionSystem.DefaultActionGroup;
import com.intellij.openapi.application.ApplicationManager;
import com.intellij.openapi.diagnostic.Logger;
import com.intellij.openapi.options.ConfigurationException;
import com.intellij.openapi.project.DumbAwareAction;
import com.intellij.openapi.project.Project;
import com.intellij.openapi.project.ProjectBundle;
import com.intellij.openapi.projectRoots.*;
import com.intellij.openapi.projectRoots.impl.ProjectJdkImpl;
import com.intellij.openapi.projectRoots.impl.SdkConfigurationUtil;
import com.intellij.openapi.roots.ProjectRootManager;
import com.intellij.openapi.ui.MasterDetailsComponent;
import com.intellij.openapi.ui.Messages;
import com.intellij.openapi.util.Comparing;
import com.intellij.openapi.util.Condition;
import com.intellij.openapi.util.io.FileUtil;
import com.intellij.util.ArrayUtilRt;
import com.intellij.util.Consumer;
import com.intellij.util.EventDispatcher;
import com.intellij.util.containers.ContainerUtil;
import org.jetbrains.annotations.Nls;
import org.jetbrains.annotations.NotNull;
import org.jetbrains.annotations.Nullable;
import javax.swing.*;
import java.util.*;
/**
* @author anna
*/
public class ProjectSdksModel implements SdkModel {
private static final Logger LOG = Logger.getInstance(ProjectSdksModel.class);
private final HashMap<Sdk, Sdk> myProjectSdks = new HashMap<>();
private final EventDispatcher<Listener> mySdkEventsDispatcher = EventDispatcher.create(Listener.class);
private boolean myModified;
private Sdk myProjectSdk;
private boolean myInitialized;
@NotNull
@Override
public Listener getMulticaster() {
return mySdkEventsDispatcher.getMulticaster();
}
@NotNull
@Override
public Sdk[] getSdks() {
return myProjectSdks.values().toArray(new Sdk[0]);
}
@Override
@Nullable
public Sdk findSdk(@NotNull String sdkName) {
for (Sdk projectJdk : myProjectSdks.values()) {
if (sdkName.equals(projectJdk.getName())) return projectJdk;
}
return null;
}
@Override
public void addListener(@NotNull Listener listener) {
mySdkEventsDispatcher.addListener(listener);
}
@Override
public void removeListener(@NotNull Listener listener) {
mySdkEventsDispatcher.removeListener(listener);
}
public void reset(@Nullable Project project) {
myProjectSdks.clear();
final Sdk[] projectSdks = ProjectJdkTable.getInstance().getAllJdks();
for (Sdk sdk : projectSdks) {
try {
Sdk editable = (Sdk)sdk.clone();
myProjectSdks.put(sdk, editable);
SdkDownloadTracker.getInstance().registerEditableSdk(sdk, editable);
}
catch (CloneNotSupportedException e) {
LOG.error(e);
}
}
if (project != null) {
String sdkName = ProjectRootManager.getInstance(project).getProjectSdkName();
myProjectSdk = sdkName == null ? null : findSdk(sdkName);
}
myModified = false;
myInitialized = true;
}
public void disposeUIResources() {
myProjectSdks.clear();
myInitialized = false;
}
@NotNull
public HashMap<Sdk, Sdk> getProjectSdks() {
return myProjectSdks;
}
public boolean isModified() {
return myModified;
}
public void apply() throws ConfigurationException {
apply(null);
}
public void apply(@Nullable MasterDetailsComponent configurable) throws ConfigurationException {
apply(configurable, false);
}
public void apply(@Nullable MasterDetailsComponent configurable, boolean addedOnly) throws ConfigurationException {
String[] errorString = new String[1];
if (!canApply(errorString, configurable, addedOnly)) {
throw new ConfigurationException(errorString[0]);
}
doApply();
myModified = false;
}
private void doApply() {
ApplicationManager.getApplication().runWriteAction(() -> {
final ArrayList<Sdk> itemsInTable = new ArrayList<>();
final ProjectJdkTable jdkTable = ProjectJdkTable.getInstance();
final Sdk[] allFromTable = jdkTable.getAllJdks();
// Delete removed and fill itemsInTable
for (final Sdk tableItem : allFromTable) {
if (myProjectSdks.containsKey(tableItem)) {
itemsInTable.add(tableItem);
}
else {
jdkTable.removeJdk(tableItem);
}
}
// Now all removed items are deleted from table, itemsInTable contains all items in table
for (Sdk originalJdk : itemsInTable) {
final Sdk modifiedJdk = myProjectSdks.get(originalJdk);
LOG.assertTrue(modifiedJdk != null);
LOG.assertTrue(originalJdk != modifiedJdk);
jdkTable.updateJdk(originalJdk, modifiedJdk);
}
// Add new items to table
final Sdk[] allJdks = jdkTable.getAllJdks();
for (final Sdk projectJdk : myProjectSdks.keySet()) {
LOG.assertTrue(projectJdk != null);
if (ArrayUtilRt.find(allJdks, projectJdk) == -1) {
jdkTable.addJdk(projectJdk);
jdkTable.updateJdk(projectJdk, myProjectSdks.get(projectJdk));
}
}
});
}
private boolean canApply(@NotNull String[] errorString, @Nullable MasterDetailsComponent rootConfigurable, boolean addedOnly) throws ConfigurationException {
Map<Sdk, Sdk> sdks = new LinkedHashMap<>(myProjectSdks);
if (addedOnly) {
Sdk[] allJdks = ProjectJdkTable.getInstance().getAllJdks();
for (Sdk jdk : allJdks) {
sdks.remove(jdk);
}
}
ArrayList<String> allNames = new ArrayList<>();
Sdk itemWithError = null;
for (Sdk currItem : sdks.values()) {
String currName = currItem.getName();
if (currName.isEmpty()) {
itemWithError = currItem;
errorString[0] = ProjectBundle.message("sdk.list.name.required.error");
break;
}
if (allNames.contains(currName)) {
itemWithError = currItem;
errorString[0] = ProjectBundle.message("sdk.list.unique.name.required.error");
break;
}
final SdkAdditionalData sdkAdditionalData = currItem.getSdkAdditionalData();
if (sdkAdditionalData instanceof ValidatableSdkAdditionalData) {
try {
((ValidatableSdkAdditionalData)sdkAdditionalData).checkValid(this);
}
catch (ConfigurationException e) {
if (rootConfigurable != null) {
final Object projectJdk = rootConfigurable.getSelectedObject();
if (!(projectJdk instanceof Sdk) ||
!Comparing.strEqual(((Sdk)projectJdk).getName(), currName)) { //do not leave current item with current name
rootConfigurable.selectNodeInTree(currName);
}
}
throw new ConfigurationException(ProjectBundle.message("sdk.configuration.exception", currName) + " " + e.getMessage());
}
}
allNames.add(currName);
}
if (itemWithError == null) return true;
if (rootConfigurable != null) {
rootConfigurable.selectNodeInTree(itemWithError.getName());
}
return false;
}
public void removeSdk(@NotNull Sdk editableObject) {
Sdk projectJdk = null;
for (Sdk jdk : myProjectSdks.keySet()) {
if (myProjectSdks.get(jdk) == editableObject) {
projectJdk = jdk;
break;
}
}
if (projectJdk != null) {
myProjectSdks.remove(projectJdk);
SdkDownloadTracker.getInstance().onSdkRemoved(projectJdk);
mySdkEventsDispatcher.getMulticaster().beforeSdkRemove(projectJdk);
myModified = true;
}
}
public void createAddActions(@NotNull DefaultActionGroup group,
@NotNull final JComponent parent,
@NotNull final Consumer<? super Sdk> updateTree,
@Nullable Condition<? super SdkTypeId> filter) {
createAddActions(group, parent, null, updateTree, filter);
}
@NotNull
private static List<SdkType> getAddableSdkTypes(@Nullable Condition<? super SdkTypeId> filter) {
return ContainerUtil.filter(SdkType.getAllTypes(), type ->
type.allowCreationByUser() && (filter == null || filter.value(type))
);
}
public void createAddActions(@NotNull DefaultActionGroup group,
@NotNull final JComponent parent,
@Nullable final Sdk selectedSdk,
@NotNull final Consumer<? super Sdk> updateTree,
@Nullable Condition<? super SdkTypeId> filter) {
Map<SdkType, NewSdkAction> downloadActions = createDownloadActions(parent, selectedSdk, updateTree, filter);
Map<SdkType, NewSdkAction> defaultAddActions = createAddActions(parent, selectedSdk, updateTree, filter);
for (SdkType type : getAddableSdkTypes(filter)) {
AnAction downloadAction = downloadActions.get(type);
if (downloadAction != null) {
group.add(downloadAction);
}
AnAction defaultAction = defaultAddActions.get(type);
if (defaultAction != null) {
group.add(defaultAction);
}
}
}
public static abstract class NewSdkAction extends DumbAwareAction {
private final SdkType mySdkType;
private NewSdkAction(@NotNull SdkType sdkType,
@Nls(capitalization = Nls.Capitalization.Title) @Nullable String text,
@Nullable Icon icon) {
super(text, null, icon);
mySdkType = sdkType;
}
@NotNull
public SdkType getSdkType() {
return mySdkType;
}
}
@NotNull
public Map<SdkType, NewSdkAction> createDownloadActions(@NotNull final JComponent parent,
@Nullable final Sdk selectedSdk,
@NotNull final Consumer<? super Sdk> updateTree,
@Nullable Condition<? super SdkTypeId> filter) {
Map<SdkType, NewSdkAction> result = new LinkedHashMap<>();
for (final SdkType type : getAddableSdkTypes(filter)) {
SdkDownload downloadExtension = SdkDownload.EP_NAME.findFirstSafe(it -> it.supportsDownload(type));
if (downloadExtension == null) continue;
String downloadText = ProjectBundle.message("sdk.configure.download.action", type.getPresentableName());
NewSdkAction downloadAction = new NewSdkAction(type, downloadText, downloadExtension.getIconForDownloadAction(type)) {
@Override
public void actionPerformed(@NotNull AnActionEvent e) {
doDownload(downloadExtension, parent, selectedSdk, type, updateTree);
}
};
result.put(type, downloadAction);
}
return result;
}
@NotNull
public Map<SdkType, NewSdkAction> createAddActions(@NotNull final JComponent parent,
@Nullable final Sdk selectedSdk,
@NotNull final Consumer<? super Sdk> updateTree,
@Nullable Condition<? super SdkTypeId> filter) {
Map<SdkType, NewSdkAction> result = new LinkedHashMap<>();
for (final SdkType type : getAddableSdkTypes(filter)) {
String addOnDiskText = ProjectBundle.message("sdk.configure.add.default.action", type.getPresentableName());
NewSdkAction addAction = new NewSdkAction(type, addOnDiskText, type.getIconForAddAction()) {
@Override
public void actionPerformed(@NotNull AnActionEvent e) {
if (type.supportsCustomCreateUI()) {
type.showCustomCreateUI(ProjectSdksModel.this, parent, selectedSdk, sdk -> setupSdk(sdk, updateTree));
} else {
SdkConfigurationUtil.selectSdkHome(type, home -> addSdk(type, home, updateTree));
}
}
};
result.put(type, addAction);
}
return result;
}
public void doAdd(@NotNull JComponent parent, @NotNull final SdkType type, @NotNull final Consumer<? super Sdk> callback) {
doAdd(parent, null, type, callback);
}
public void doDownload(@NotNull SdkDownload downloadExtension,
@NotNull JComponent parent,
@Nullable final Sdk selectedSdk,
@NotNull final SdkType type,
@NotNull final Consumer<? super Sdk> callback) {
LOG.assertTrue(downloadExtension.supportsDownload(type));
myModified = true;
downloadExtension.showDownloadUI(type, this, parent, selectedSdk, sdk -> setupInstallableSdk(type, sdk, callback));
}
public void doAdd(@NotNull JComponent parent, @Nullable final Sdk selectedSdk, @NotNull final SdkType type, @NotNull final Consumer<? super Sdk> callback) {
myModified = true;
if (type.supportsCustomCreateUI()) {
type.showCustomCreateUI(this, parent, selectedSdk, sdk -> setupSdk(sdk, callback));
}
else {
SdkConfigurationUtil.selectSdkHome(type, home -> addSdk(type, home, callback));
}
}
public void addSdk(@NotNull SdkType type, @NotNull String home, @Nullable Consumer<? super Sdk> callback) {
final Sdk newJdk = createSdk(type, home);
setupSdk(newJdk, callback);
}
@NotNull
public Sdk createSdk(@NotNull SdkType type, @NotNull String home) {
String newSdkName = SdkConfigurationUtil.createUniqueSdkName(type, home, myProjectSdks.values());
return createSdkInternal(type, newSdkName, home);
}
@NotNull
public Sdk createSdk(@NotNull SdkType type, @NotNull String suggestedName, @NotNull String home) {
String newSdkName = SdkConfigurationUtil.createUniqueSdkName(suggestedName, myProjectSdks.values());
return createSdkInternal(type, newSdkName, home);
}
@NotNull
private static Sdk createSdkInternal(@NotNull SdkType type,
@NotNull String newSdkName,
@NotNull String home) {
final ProjectJdkImpl newJdk = new ProjectJdkImpl(newSdkName, type);
newJdk.setHomePath(home);
return newJdk;
}
public void setupInstallableSdk(@NotNull SdkType type,
@NotNull SdkDownloadTask item,
@Nullable Consumer<? super Sdk> callback) {
// we do not ask the SdkType to set up the SDK for us, instead, we return an incomplete SDK to the
// model with an expectation it would be updated later on
String suggestedName = item.getSuggestedSdkName();
String homeDir = FileUtil.toSystemIndependentName(item.getPlannedHomeDir());
Sdk sdk = createSdk(type, suggestedName, homeDir);
SdkDownloadTracker.configureSdk(sdk, item);
SdkDownloadTracker tracker = SdkDownloadTracker.getInstance();
tracker.registerSdkDownload(sdk, item);
Sdk editableSdk = doAddInternal(sdk, callback);
if (editableSdk != null) {
tracker.registerEditableSdk(sdk, editableSdk);
}
tracker.startSdkDownloadIfNeeded(sdk);
}
private void setupSdk(@NotNull Sdk newJdk, @Nullable Consumer<? super Sdk> callback) {
String home = newJdk.getHomePath();
SdkType sdkType = (SdkType)newJdk.getSdkType();
if (!sdkType.setupSdkPaths(newJdk, this)) return;
if (newJdk.getVersionString() == null) {
String message = ProjectBundle.message("sdk.java.corrupt.error", home);
Messages.showMessageDialog(message, ProjectBundle.message("sdk.java.corrupt.title"), Messages.getErrorIcon());
}
doAdd(newJdk, callback);
}
@Override
public void addSdk(@NotNull Sdk sdk) {
doAdd(sdk, null);
}
public void doAdd(@NotNull Sdk newSdk, @Nullable Consumer<? super Sdk> updateTree) {
doAddInternal(newSdk, updateTree);
}
@Nullable
private Sdk doAddInternal(@NotNull Sdk newSdk, @Nullable Consumer<? super Sdk> updateTree) {
myModified = true;
try {
Sdk editableCopy = (Sdk)newSdk.clone();
myProjectSdks.put(newSdk, editableCopy);
if (updateTree != null) {
updateTree.consume(editableCopy);
}
mySdkEventsDispatcher.getMulticaster().sdkAdded(editableCopy);
return editableCopy;
}
catch (CloneNotSupportedException e) {
LOG.error(e);
return null;
}
}
@Nullable
public Sdk findSdk(@Nullable final Sdk modelJdk) {
for (Map.Entry<Sdk, Sdk> entry : myProjectSdks.entrySet()) {
Sdk jdk = entry.getKey();
if (Comparing.equal(entry.getValue(), modelJdk)) {
return jdk;
}
}
return null;
}
@Nullable
public Sdk getProjectSdk() {
if (!myProjectSdks.containsValue(myProjectSdk)) return null;
return myProjectSdk;
}
public void setProjectSdk(final Sdk projectSdk) {
myProjectSdk = projectSdk;
}
public boolean isInitialized() {
return myInitialized;
}
} |
package uk.ac.horizon.observer.vc;
import java.util.List;
import uk.ac.horizon.observer.model.Places;
import uk.ac.horizon.observer.model.Task;
import uk.ac.horizon.observer.model.TaskBin;
import android.os.Bundle;
import android.support.v4.app.ListFragment;
import android.view.View;
import android.widget.AdapterView;
import android.widget.AdapterView.OnItemClickListener;
import android.widget.ArrayAdapter;
import android.widget.ListView;
import android.widget.Toast;
/**
* A fragment representing a single Place's tasks. This fragment is either
* contained in a {@link PlacesActivity} in two-pane mode (on tablets) or a
* {@link TasksActivity} on handsets.
*/
public class TaskFragment extends ListFragment {
/**
* The fragment argument representing the Place ID that the tasks are for.
*/
public static final String ARG_ITEM_ID = "item_id";
/**
* The tasks
*/
private List<Task> myTasks = null;
/**
* Mandatory empty constructor for the fragment manager to instantiate the
* fragment (e.g. upon screen orientation changes).
*/
public TaskFragment() {
}
/*
* @Override public void onCreate(Bundle savedInstanceState) {
* super.onCreate(savedInstanceState);
*
* if (getArguments().containsKey(ARG_ITEM_ID)) { // Load the dummy content
* specified by the fragment // arguments. In a real-world scenario, use a
* Loader // to load content from a content provider. mItem =
* DummyContent.ITEM_MAP.get(getArguments().getString( ARG_ITEM_ID)); } }
*
* @Override public View onCreateView(LayoutInflater inflater, ViewGroup
* container, Bundle savedInstanceState) { View rootView =
* inflater.inflate(R.layout.fragment_place_detail, container, false);
*
* // Show the dummy content as text in a TextView. if (mItem != null) {
* ((TextView) rootView.findViewById(R.id.place_detail))
* .setText(mItem.content); }
*
* return rootView; }
*/
/**
* On create set the tasks to the ones for the corresponding Place
* @author Jesse
*/
@Override
public void onCreate(Bundle savedInstanceState) {
super.onCreate(savedInstanceState);
myTasks = Places.getTasksforCurrentPlace(); // can be null
}
/**
* Display a multipe choice selection list of the tasks available for the given Place
* @author Jesse
*/
@Override
public void onActivityCreated(Bundle savedInstanceState) {
super.onActivityCreated(savedInstanceState);
if(null != myTasks){
if(myTasks.isEmpty()){
Toast.makeText(this.getActivity(),
String.valueOf("No tasks to select for " + Places.getCurrentPlaceName()),
Toast.LENGTH_LONG).show();
}
ArrayAdapter<Task> adapter = new ArrayAdapter<Task>(
this.getActivity(),
android.R.layout.simple_list_item_activated_1, myTasks);
setListAdapter(adapter);
ListView lv = getListView();
lv.setChoiceMode(ListView.CHOICE_MODE_MULTIPLE);
lv.setOnItemClickListener(new OnItemClickListener() {
public void onItemClick(AdapterView<?> parent, View view, int position, long id) {
getListView().getChildAt(0).setEnabled(false);
}
});
}
}
/**
* Add values of clicked items to the click queue
*/
@Override
public void onListItemClick(ListView l, View v, int position, long id) {
super.onListItemClick(l, v, position, id);
Task tmp = myTasks.get(position);
Task task = new Task(tmp.getName(), Places.getCurrentPlace());
TaskBin.getInstance().addTask(task);
//task.addObservation(this.getActivity());
//Log the insertion of the new row
//long lastobs = task.addObservation(this.getActivity());
//Toast.makeText(this.getActivity(), "lastobs: " + lastobs, Toast.LENGTH_SHORT)
// .show();
}
} |
package edu.umd.cs.findbugs;
import java.io.FileInputStream;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.HashSet;
import java.util.Iterator;
import java.util.LinkedHashSet;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Set;
import javax.annotation.CheckForNull;
import javax.annotation.Nonnull;
import org.apache.bcel.classfile.ClassFormatException;
import org.dom4j.DocumentException;
import edu.umd.cs.findbugs.asm.FBClassReader;
import edu.umd.cs.findbugs.ba.AnalysisContext;
import edu.umd.cs.findbugs.ba.AnalysisFeatures;
import edu.umd.cs.findbugs.ba.ObjectTypeFactory;
import edu.umd.cs.findbugs.ba.SourceInfoMap;
import edu.umd.cs.findbugs.ba.XClass;
import edu.umd.cs.findbugs.ba.XFactory;
import edu.umd.cs.findbugs.ba.XField;
import edu.umd.cs.findbugs.ba.jsr305.TypeQualifierAnnotation;
import edu.umd.cs.findbugs.ba.jsr305.TypeQualifierApplications;
import edu.umd.cs.findbugs.ba.jsr305.TypeQualifierValue;
import edu.umd.cs.findbugs.bugReporter.BugReporterDecorator;
import edu.umd.cs.findbugs.classfile.CheckedAnalysisException;
import edu.umd.cs.findbugs.classfile.ClassDescriptor;
import edu.umd.cs.findbugs.classfile.DescriptorFactory;
import edu.umd.cs.findbugs.classfile.Global;
import edu.umd.cs.findbugs.classfile.IAnalysisCache;
import edu.umd.cs.findbugs.classfile.IAnalysisEngineRegistrar;
import edu.umd.cs.findbugs.classfile.IClassFactory;
import edu.umd.cs.findbugs.classfile.IClassObserver;
import edu.umd.cs.findbugs.classfile.IClassPath;
import edu.umd.cs.findbugs.classfile.IClassPathBuilder;
import edu.umd.cs.findbugs.classfile.ICodeBase;
import edu.umd.cs.findbugs.classfile.ICodeBaseEntry;
import edu.umd.cs.findbugs.classfile.MissingClassException;
import edu.umd.cs.findbugs.classfile.impl.ClassFactory;
import edu.umd.cs.findbugs.config.AnalysisFeatureSetting;
import edu.umd.cs.findbugs.config.UserPreferences;
import edu.umd.cs.findbugs.detect.NoteSuppressedWarnings;
import edu.umd.cs.findbugs.filter.FilterException;
import edu.umd.cs.findbugs.log.Profiler;
import edu.umd.cs.findbugs.log.YourKitController;
import edu.umd.cs.findbugs.plan.AnalysisPass;
import edu.umd.cs.findbugs.plan.ExecutionPlan;
import edu.umd.cs.findbugs.plan.OrderingConstraintException;
import edu.umd.cs.findbugs.util.ClassName;
import edu.umd.cs.findbugs.util.TopologicalSort.OutEdges;
/**
* FindBugs driver class. Orchestrates the analysis of a project, collection of
* results, etc.
*
* @author David Hovemeyer
*/
public class FindBugs2 implements IFindBugsEngine {
private static final boolean LIST_ORDER = SystemProperties.getBoolean("findbugs.listOrder");
private static final boolean VERBOSE = SystemProperties.getBoolean("findbugs.verbose");
public static final boolean DEBUG = VERBOSE || SystemProperties.getBoolean("findbugs.debug");
public static final boolean PROGRESS = DEBUG || SystemProperties.getBoolean("findbugs.progress");
private static final boolean SCREEN_FIRST_PASS_CLASSES = SystemProperties.getBoolean("findbugs.screenFirstPass");
public static final String PROP_FINDBUGS_HOST_APP = "findbugs.hostApp";
public static final String PROP_FINDBUGS_HOST_APP_VERSION = "findbugs.hostAppVersion";
private int rankThreshold;
private List<IClassObserver> classObserverList;
private BugReporter bugReporter;
private ErrorCountingBugReporter errorCountingBugReporter;
private Project project;
private IClassFactory classFactory;
private IClassPath classPath;
private List<ClassDescriptor> appClassList;
private Collection<ClassDescriptor> referencedClassSet;
private DetectorFactoryCollection detectorFactoryCollection;
private ExecutionPlan executionPlan;
private final YourKitController yourkitController = new YourKitController();
private String currentClassName;
private FindBugsProgress progress;
private IClassScreener classScreener;
private final AnalysisOptions analysisOptions = new AnalysisOptions(true);
/**
* Constructor.
*/
public FindBugs2() {
this.classObserverList = new LinkedList<IClassObserver>();
this.analysisOptions.analysisFeatureSettingList = FindBugs.DEFAULT_EFFORT;
this.progress = new NoOpFindBugsProgress();
// By default, do not exclude any classes via the class screener
this.classScreener = new IClassScreener() {
/*
* (non-Javadoc)
*
* @see edu.umd.cs.findbugs.IClassScreener#matches(java.lang.String)
*/
public boolean matches(String fileName) {
return true;
}
public boolean vacuous() {
return true;
}
};
String hostApp = System.getProperty(PROP_FINDBUGS_HOST_APP);
String hostAppVersion = null;
if (hostApp == null || hostApp.trim().length() <= 0) {
hostApp = "FindBugs TextUI";
hostAppVersion = System.getProperty(PROP_FINDBUGS_HOST_APP_VERSION);
}
if (hostAppVersion == null)
hostAppVersion = "";
Version.registerApplication(hostApp, hostAppVersion);
// By default, we do not want to scan nested archives
this.analysisOptions.scanNestedArchives = false;
// bug 2815983: no bugs are reported anymore
// there is no info which value should be default, so using the any one
rankThreshold = BugRanker.VISIBLE_RANK_MAX;
}
/**
* Set the detector factory collection to be used by this FindBugs2 engine.
* This method should be called before the execute() method is called.
*
* @param detectorFactoryCollection
* The detectorFactoryCollection to set.
*/
public void setDetectorFactoryCollection(DetectorFactoryCollection detectorFactoryCollection) {
this.detectorFactoryCollection = detectorFactoryCollection;
}
/**
* Execute the analysis. For obscure reasons, CheckedAnalysisExceptions are
* re-thrown as IOExceptions. However, these can only happen during the
* setup phase where we scan codebases for classes.
*
* @throws IOException
* @throws InterruptedException
*/
public void execute() throws IOException, InterruptedException {
if (FindBugs.isNoAnalysis())
throw new UnsupportedOperationException("This FindBugs invocation was started without analysis capabilities");
Profiler profiler = bugReporter.getProjectStats().getProfiler();
try {
try {
// Get the class factory for creating classpath/codebase/etc.
classFactory = ClassFactory.instance();
// The class path object
createClassPath();
progress.reportNumberOfArchives(project.getFileCount() + project.getNumAuxClasspathEntries());
profiler.start(this.getClass());
// The analysis cache object
createAnalysisCache();
// Create BCEL compatibility layer
createAnalysisContext(project, appClassList, analysisOptions.sourceInfoFileName);
// Discover all codebases in classpath and
// enumerate all classes (application and non-application)
buildClassPath();
// Build set of classes referenced by application classes
buildReferencedClassSet();
// Create BCEL compatibility layer
setAppClassList(appClassList);
// Configure the BugCollection (if we are generating one)
FindBugs.configureBugCollection(this);
// Enable/disabled relaxed reporting mode
FindBugsAnalysisFeatures.setRelaxedMode(analysisOptions.relaxedReportingMode);
FindBugsDisplayFeatures.setAbridgedMessages(analysisOptions.abridgedMessages);
// Configure training databases
FindBugs.configureTrainingDatabases(this);
// Configure analysis features
configureAnalysisFeatures();
// Create the execution plan (which passes/detectors to execute)
createExecutionPlan();
for (Plugin p : detectorFactoryCollection.plugins()) {
for (ComponentPlugin<BugReporterDecorator> brp
: p.getComponentPlugins(BugReporterDecorator.class)) {
if (brp.isEnabledByDefault() && !brp.isNamed(explicitlyDisabledBugReporterDecorators)
|| brp.isNamed(explicitlyEnabledBugReporterDecorators))
bugReporter = BugReporterDecorator.construct(brp, bugReporter);
}
}
if (!classScreener.vacuous()) {
bugReporter = new DelegatingBugReporter(bugReporter) {
@Override
public void reportBug(@Nonnull BugInstance bugInstance) {
String className = bugInstance.getPrimaryClass().getClassName();
String resourceName = className.replace('.', '/') + ".class";
if (classScreener.matches(resourceName)) {
this.getDelegate().reportBug(bugInstance);
}
}
};
}
if (executionPlan.isActive(NoteSuppressedWarnings.class)) {
SuppressionMatcher m = AnalysisContext.currentAnalysisContext().getSuppressionMatcher();
bugReporter = new FilterBugReporter(bugReporter, m, false);
}
if (appClassList.size() == 0) {
Map<String, ICodeBaseEntry> codebase = classPath.getApplicationCodebaseEntries();
if (analysisOptions.noClassOk) {
System.err.println("No classfiles specified; output will have no warnings");
} else if (codebase.isEmpty()) {
throw new IOException("No files to analyze could be opened");
} else {
throw new NoClassesFoundToAnalyzeException(classPath);
}
}
// Analyze the application
analyzeApplication();
} catch (CheckedAnalysisException e) {
IOException ioe = new IOException("IOException while scanning codebases");
ioe.initCause(e);
throw ioe;
} catch (OutOfMemoryError e) {
System.err.println("Out of memory");
System.err.println("Total memory: " + Runtime.getRuntime().maxMemory() / 1000000 + "M");
System.err.println(" free memory: " + Runtime.getRuntime().freeMemory() / 1000000 + "M");
for (String s : project.getFileList()) {
System.err.println("Analyzed: " + s);
}
for (String s : project.getAuxClasspathEntryList()) {
System.err.println(" Aux: " + s);
}
throw e;
} finally {
clearCaches();
profiler.end(this.getClass());
profiler.report();
}
} catch (IOException e) {
bugReporter.reportQueuedErrors();
throw e;
}
}
/**
* Protected to allow Eclipse plugin remember some cache data for later reuse
*/
protected void clearCaches() {
DescriptorFactory.clearInstance();
ObjectTypeFactory.clearInstance();
TypeQualifierApplications.clearInstance();
TypeQualifierAnnotation.clearInstance();
TypeQualifierValue.clearInstance();
// Make sure the codebases on the classpath are closed
AnalysisContext.removeCurrentAnalysisContext();
Global.removeAnalysisCacheForCurrentThread();
if (classPath != null) {
classPath.close();
}
}
/**
* To avoid cyclic cross-references and allow GC after engine is not more
* needed. (used by Eclipse plugin)
*/
public void dispose() {
if (executionPlan != null)
executionPlan.dispose();
if (appClassList != null)
appClassList.clear();
if (classObserverList != null)
classObserverList.clear();
if (referencedClassSet != null)
referencedClassSet.clear();
analysisOptions.analysisFeatureSettingList = null;
bugReporter = null;
classFactory = null;
classPath = null;
classScreener = null;
detectorFactoryCollection = null;
executionPlan = null;
progress = null;
project = null;
analysisOptions.userPreferences = null;
}
/*
* (non-Javadoc)
*
* @see edu.umd.cs.findbugs.IFindBugsEngine#getBugReporter()
*/
public BugReporter getBugReporter() {
return bugReporter;
}
/*
* (non-Javadoc)
*
* @see edu.umd.cs.findbugs.IFindBugsEngine#getProject()
*/
public Project getProject() {
return project;
}
/*
* (non-Javadoc)
*
* @see
* edu.umd.cs.findbugs.IFindBugsEngine#addClassObserver(edu.umd.cs.findbugs
* .classfile.IClassObserver)
*/
public void addClassObserver(IClassObserver classObserver) {
classObserverList.add(classObserver);
}
/*
* (non-Javadoc)
*
* @see edu.umd.cs.findbugs.IFindBugsEngine#addFilter(java.lang.String,
* boolean)
*/
public void addFilter(String filterFileName, boolean include) throws IOException, FilterException {
bugReporter = FindBugs.configureFilter(bugReporter, filterFileName, include);
}
/*
* (non-Javadoc)
*
* @see
* edu.umd.cs.findbugs.IFindBugsEngine#addBaselineBugs(java.lang.String)
*/
public void excludeBaselineBugs(String baselineBugs) throws IOException, DocumentException {
bugReporter = FindBugs.configureBaselineFilter(bugReporter, baselineBugs);
}
/*
* (non-Javadoc)
*
* @see
* edu.umd.cs.findbugs.IFindBugsEngine#enableTrainingInput(java.lang.String)
*/
public void enableTrainingInput(String trainingInputDir) {
this.analysisOptions.trainingInputDir = trainingInputDir;
}
/*
* (non-Javadoc)
*
* @see
* edu.umd.cs.findbugs.IFindBugsEngine#enableTrainingOutput(java.lang.String
* )
*/
public void enableTrainingOutput(String trainingOutputDir) {
this.analysisOptions.trainingOutputDir = trainingOutputDir;
}
/*
* (non-Javadoc)
*
* @see edu.umd.cs.findbugs.IFindBugsEngine#getBugCount()
*/
public int getBugCount() {
return errorCountingBugReporter.getBugCount();
}
/*
* (non-Javadoc)
*
* @see edu.umd.cs.findbugs.IFindBugsEngine#getCurrentClass()
*/
public String getCurrentClass() {
return currentClassName;
}
/*
* (non-Javadoc)
*
* @see edu.umd.cs.findbugs.IFindBugsEngine#getErrorCount()
*/
public int getErrorCount() {
return errorCountingBugReporter.getErrorCount();
}
/*
* (non-Javadoc)
*
* @see edu.umd.cs.findbugs.IFindBugsEngine#getMissingClassCount()
*/
public int getMissingClassCount() {
return errorCountingBugReporter.getMissingClassCount();
}
/*
* (non-Javadoc)
*
* @see edu.umd.cs.findbugs.IFindBugsEngine#getReleaseName()
*/
public String getReleaseName() {
return analysisOptions.releaseName;
}
public String getProjectName() {
return analysisOptions.projectName;
}
public void setProjectName(String name) {
analysisOptions.projectName = name;
}
/*
* (non-Javadoc)
*
* @see
* edu.umd.cs.findbugs.IFindBugsEngine#setAnalysisFeatureSettings(edu.umd
* .cs.findbugs.config.AnalysisFeatureSetting[])
*/
public void setAnalysisFeatureSettings(AnalysisFeatureSetting[] settingList) {
this.analysisOptions.analysisFeatureSettingList = settingList;
}
/*
* (non-Javadoc)
*
* @see
* edu.umd.cs.findbugs.IFindBugsEngine#setBugReporter(edu.umd.cs.findbugs
* .BugReporter)
*/
public void setBugReporter(BugReporter bugReporter) {
this.bugReporter = this.errorCountingBugReporter = new ErrorCountingBugReporter(bugReporter);
addClassObserver(bugReporter);
}
/*
* (non-Javadoc)
*
* @see
* edu.umd.cs.findbugs.IFindBugsEngine#setClassScreener(edu.umd.cs.findbugs
* .ClassScreener)
*/
public void setClassScreener(IClassScreener classScreener) {
this.classScreener = classScreener;
}
/*
* (non-Javadoc)
*
* @see
* edu.umd.cs.findbugs.IFindBugsEngine#setProgressCallback(edu.umd.cs.findbugs
* .FindBugsProgress)
*/
public void setProgressCallback(FindBugsProgress progressCallback) {
this.progress = progressCallback;
}
/*
* (non-Javadoc)
*
* @see
* edu.umd.cs.findbugs.IFindBugsEngine#setProject(edu.umd.cs.findbugs.Project
* )
*/
public void setProject(Project project) {
this.project = project;
}
/*
* (non-Javadoc)
*
* @see edu.umd.cs.findbugs.IFindBugsEngine#setRelaxedReportingMode(boolean)
*/
public void setRelaxedReportingMode(boolean relaxedReportingMode) {
this.analysisOptions.relaxedReportingMode = relaxedReportingMode;
}
/*
* (non-Javadoc)
*
* @see edu.umd.cs.findbugs.IFindBugsEngine#setReleaseName(java.lang.String)
*/
public void setReleaseName(String releaseName) {
this.analysisOptions.releaseName = releaseName;
}
/*
* (non-Javadoc)
*
* @see
* edu.umd.cs.findbugs.IFindBugsEngine#setSourceInfoFile(java.lang.String)
*/
public void setSourceInfoFile(String sourceInfoFile) {
this.analysisOptions.sourceInfoFileName = sourceInfoFile;
}
public void setUserPreferences(UserPreferences userPreferences) {
this.analysisOptions.userPreferences = userPreferences;
// TODO should set it here too, but gui2 seems to have issues with it
// setAnalysisFeatureSettings(userPreferences.getAnalysisFeatureSettings());
configureFilters(userPreferences);
}
protected void configureFilters(UserPreferences userPreferences) {
IllegalArgumentException deferredError = null;
Set<Entry<String, Boolean>> excludeBugFiles = userPreferences.getExcludeBugsFiles().entrySet();
for (Entry<String, Boolean> entry : excludeBugFiles) {
if (entry.getValue() == null || !entry.getValue()) {
continue;
}
try {
excludeBaselineBugs(entry.getKey());
} catch (Exception e) {
String message = "Unable to read filter: " + entry.getKey() + " : " + e.getMessage();
if (getBugReporter() != null) {
getBugReporter().logError(message, e);
} else if (deferredError == null){
deferredError = new IllegalArgumentException(message, e);
}
}
}
Set<Entry<String, Boolean>> includeFilterFiles = userPreferences.getIncludeFilterFiles().entrySet();
for (Entry<String, Boolean> entry : includeFilterFiles) {
if (entry.getValue() == null || !entry.getValue()) {
continue;
}
try {
addFilter(entry.getKey(), true);
} catch (Exception e) {
String message = "Unable to read filter: " + entry.getKey() + " : " + e.getMessage();
if (getBugReporter() != null) {
getBugReporter().logError(message, e);
} else if (deferredError == null){
deferredError = new IllegalArgumentException(message, e);
}
}
}
Set<Entry<String, Boolean>> excludeFilterFiles = userPreferences.getExcludeFilterFiles().entrySet();
for (Entry<String, Boolean> entry : excludeFilterFiles) {
Boolean value = entry.getValue();
if (value == null || !value) {
continue;
}
String excludeFilterFile = entry.getKey();
try {
addFilter(excludeFilterFile, false);
} catch (Exception e) {
String message = "Unable to read filter: " + excludeFilterFile + " : " + e.getMessage();
if (getBugReporter() != null) {
getBugReporter().logError(message, e);
} else if (deferredError == null){
deferredError = new IllegalArgumentException(message, e);
}
}
}
if (deferredError != null)
throw deferredError;
}
/*
* (non-Javadoc)
*
* @see edu.umd.cs.findbugs.IFindBugsEngine#emitTrainingOutput()
*/
public boolean emitTrainingOutput() {
return analysisOptions.trainingOutputDir != null;
}
/*
* (non-Javadoc)
*
* @see edu.umd.cs.findbugs.IFindBugsEngine#getUserPreferences()
*/
public UserPreferences getUserPreferences() {
return analysisOptions.userPreferences;
}
/**
* Create the classpath object.
*/
private void createClassPath() {
classPath = classFactory.createClassPath();
}
/*
* (non-Javadoc)
*
* @see edu.umd.cs.findbugs.IFindBugsEngine#getTrainingInputDir()
*/
public String getTrainingInputDir() {
return analysisOptions.trainingInputDir;
}
/*
* (non-Javadoc)
*
* @see edu.umd.cs.findbugs.IFindBugsEngine#getTrainingOutputDir()
*/
public String getTrainingOutputDir() {
return analysisOptions.trainingOutputDir;
}
/*
* (non-Javadoc)
*
* @see edu.umd.cs.findbugs.IFindBugsEngine#useTrainingInput()
*/
public boolean useTrainingInput() {
return analysisOptions.trainingInputDir != null;
}
/*
* (non-Javadoc)
*
* @see edu.umd.cs.findbugs.IFindBugsEngine#setScanNestedArchives(boolean)
*/
public void setScanNestedArchives(boolean scanNestedArchives) {
this.analysisOptions.scanNestedArchives = scanNestedArchives;
}
/*
* (non-Javadoc)
*
* @see edu.umd.cs.findbugs.IFindBugsEngine#setNoClassOk(boolean)
*/
public void setNoClassOk(boolean noClassOk) {
this.analysisOptions.noClassOk = noClassOk;
}
/**
* Create the analysis cache object and register it for current execution thread.
* <p>
* This method is protected to allow clients override it and possibly reuse
* some previous analysis data (for Eclipse interactive re-build)
*
* @throws IOException
* if error occurs registering analysis engines in a plugin
*/
protected IAnalysisCache createAnalysisCache() throws IOException {
IAnalysisCache analysisCache = ClassFactory.instance().createAnalysisCache(classPath, bugReporter);
// Register the "built-in" analysis engines
registerBuiltInAnalysisEngines(analysisCache);
// Register analysis engines in plugins
registerPluginAnalysisEngines(detectorFactoryCollection, analysisCache);
// Install the DetectorFactoryCollection as a database
analysisCache.eagerlyPutDatabase(DetectorFactoryCollection.class, detectorFactoryCollection);
Global.setAnalysisCacheForCurrentThread(analysisCache);
return analysisCache;
}
/**
* Register the "built-in" analysis engines with given IAnalysisCache.
*
* @param analysisCache
* an IAnalysisCache
*/
@SuppressWarnings({"UnusedDeclaration"})
public static void registerBuiltInAnalysisEngines(IAnalysisCache analysisCache) {
new edu.umd.cs.findbugs.classfile.engine.EngineRegistrar().registerAnalysisEngines(analysisCache);
new edu.umd.cs.findbugs.classfile.engine.asm.EngineRegistrar().registerAnalysisEngines(analysisCache);
new edu.umd.cs.findbugs.classfile.engine.bcel.EngineRegistrar().registerAnalysisEngines(analysisCache);
}
/**
* Register all of the analysis engines defined in the plugins contained in
* a DetectorFactoryCollection with an IAnalysisCache.
*
* @param detectorFactoryCollection
* a DetectorFactoryCollection
* @param analysisCache
* an IAnalysisCache
* @throws IOException
*/
@SuppressWarnings({"UnusedDeclaration"})
public static void registerPluginAnalysisEngines(DetectorFactoryCollection detectorFactoryCollection,
IAnalysisCache analysisCache) throws IOException {
for (Iterator<Plugin> i = detectorFactoryCollection.pluginIterator(); i.hasNext();) {
Plugin plugin = i.next();
Class<? extends IAnalysisEngineRegistrar> engineRegistrarClass = plugin.getEngineRegistrarClass();
if (engineRegistrarClass != null) {
try {
IAnalysisEngineRegistrar engineRegistrar = engineRegistrarClass.newInstance();
engineRegistrar.registerAnalysisEngines(analysisCache);
} catch (InstantiationException e) {
IOException ioe = new IOException("Could not create analysis engine registrar for plugin "
+ plugin.getPluginId());
ioe.initCause(e);
throw ioe;
} catch (IllegalAccessException e) {
IOException ioe = new IOException("Could not create analysis engine registrar for plugin "
+ plugin.getPluginId());
ioe.initCause(e);
throw ioe;
}
}
}
}
/**
* Build the classpath from project codebases and system codebases.
*
* @throws InterruptedException
* if the analysis thread is interrupted
* @throws IOException
* if an I/O error occurs
* @throws CheckedAnalysisException
*/
private void buildClassPath() throws InterruptedException, IOException, CheckedAnalysisException {
IClassPathBuilder builder = classFactory.createClassPathBuilder(bugReporter);
for (String path : project.getFileArray()) {
builder.addCodeBase(classFactory.createFilesystemCodeBaseLocator(path), true);
}
for (String path : project.getAuxClasspathEntryList()) {
builder.addCodeBase(classFactory.createFilesystemCodeBaseLocator(path), false);
}
builder.scanNestedArchives(analysisOptions.scanNestedArchives);
builder.build(classPath, progress);
appClassList = builder.getAppClassList();
if (PROGRESS) {
System.out.println(appClassList.size() + " classes scanned");
}
// If any of the application codebases contain source code,
// add them to the source path.
// Also, use the last modified time of application codebases
// to set the project timestamp.
for (Iterator<? extends ICodeBase> i = classPath.appCodeBaseIterator(); i.hasNext();) {
ICodeBase appCodeBase = i.next();
if (appCodeBase.containsSourceFiles()) {
String pathName = appCodeBase.getPathName();
if (pathName != null) {
project.addSourceDir(pathName);
}
}
project.addTimestamp(appCodeBase.getLastModifiedTime());
}
}
private void buildReferencedClassSet() throws CheckedAnalysisException, InterruptedException {
// XXX: should drive progress dialog (scanning phase)?
if (PROGRESS) {
System.out.println("Adding referenced classes");
}
Set<String> referencedPackageSet = new HashSet<String>();
LinkedList<ClassDescriptor> workList = new LinkedList<ClassDescriptor>();
workList.addAll(appClassList);
Set<ClassDescriptor> seen = new HashSet<ClassDescriptor>();
Set<ClassDescriptor> appClassSet = new HashSet<ClassDescriptor>(appClassList);
Set<ClassDescriptor> badAppClassSet = new HashSet<ClassDescriptor>();
HashSet<ClassDescriptor> knownDescriptors = new HashSet<ClassDescriptor>(DescriptorFactory.instance()
.getAllClassDescriptors());
int count = 0;
Set<ClassDescriptor> addedToWorkList = new HashSet<ClassDescriptor>(appClassList);
// add fields
//noinspection ConstantIfStatement
if (false)
for (ClassDescriptor classDesc : appClassList) {
try {
XClass classNameAndInfo = Global.getAnalysisCache().getClassAnalysis(XClass.class, classDesc);
for (XField f : classNameAndInfo.getXFields()) {
String sig = f.getSignature();
ClassDescriptor d = DescriptorFactory.createClassDescriptorFromFieldSignature(sig);
if (d != null && addedToWorkList.add(d))
workList.addLast(d);
}
} catch (RuntimeException e) {
bugReporter.logError("Error scanning " + classDesc + " for referenced classes", e);
if (appClassSet.contains(classDesc)) {
badAppClassSet.add(classDesc);
}
} catch (MissingClassException e) {
// Just log it as a missing class
bugReporter.reportMissingClass(e.getClassDescriptor());
if (appClassSet.contains(classDesc)) {
badAppClassSet.add(classDesc);
}
}
}
while (!workList.isEmpty()) {
if (Thread.interrupted()) {
throw new InterruptedException();
}
ClassDescriptor classDesc = workList.removeFirst();
if (seen.contains(classDesc)) {
continue;
}
seen.add(classDesc);
if (!knownDescriptors.contains(classDesc)) {
count++;
if (PROGRESS && count % 5000 == 0) {
System.out.println("Adding referenced class " + classDesc);
}
}
referencedPackageSet.add(classDesc.getPackageName());
// Get list of referenced classes and add them to set.
// Add superclasses and superinterfaces to worklist.
try {
XClass classNameAndInfo = Global.getAnalysisCache().getClassAnalysis(XClass.class, classDesc);
ClassDescriptor superclassDescriptor = classNameAndInfo.getSuperclassDescriptor();
if (superclassDescriptor != null && addedToWorkList.add(superclassDescriptor)) {
workList.addLast(superclassDescriptor);
}
for (ClassDescriptor ifaceDesc : classNameAndInfo.getInterfaceDescriptorList()) {
if (addedToWorkList.add(ifaceDesc))
workList.addLast(ifaceDesc);
}
ClassDescriptor enclosingClass = classNameAndInfo.getImmediateEnclosingClass();
if (enclosingClass != null && addedToWorkList.add(enclosingClass))
workList.addLast(enclosingClass);
} catch (RuntimeException e) {
bugReporter.logError("Error scanning " + classDesc + " for referenced classes", e);
if (appClassSet.contains(classDesc)) {
badAppClassSet.add(classDesc);
}
} catch (MissingClassException e) {
// Just log it as a missing class
bugReporter.reportMissingClass(e.getClassDescriptor());
if (appClassSet.contains(classDesc)) {
badAppClassSet.add(classDesc);
}
} catch (CheckedAnalysisException e) {
// continue
bugReporter.logError("Error scanning " + classDesc + " for referenced classes", e);
if (appClassSet.contains(classDesc)) {
badAppClassSet.add(classDesc);
}
}
}
// Delete any application classes that could not be read
appClassList.removeAll(badAppClassSet);
DescriptorFactory.instance().purge(badAppClassSet);
for (ClassDescriptor d : DescriptorFactory.instance().getAllClassDescriptors()) {
referencedPackageSet.add(d.getPackageName());
}
referencedClassSet = new ArrayList<ClassDescriptor>(DescriptorFactory.instance().getAllClassDescriptors());
// Based on referenced packages, add any resolvable package-info classes
// to the set of referenced classes.
if (PROGRESS) {
referencedPackageSet.remove("");
System.out.println("Added " + count + " referenced classes");
System.out.println("Total of " + referencedPackageSet.size() + " packages");
for (ClassDescriptor d : referencedClassSet)
System.out.println(" " + d);
}
}
public List<ClassDescriptor> sortByCallGraph(Collection<ClassDescriptor> classList, OutEdges<ClassDescriptor> outEdges) {
List<ClassDescriptor> evaluationOrder = edu.umd.cs.findbugs.util.TopologicalSort.sortByCallGraph(classList, outEdges);
edu.umd.cs.findbugs.util.TopologicalSort.countBadEdges(evaluationOrder, outEdges);
return evaluationOrder;
}
@SuppressWarnings({"UnusedDeclaration"})
public static void clearAnalysisContext() {
AnalysisContext.removeCurrentAnalysisContext();
}
/**
* Create the AnalysisContext that will serve as the BCEL-compatibility
* layer over the AnalysisCache.
*
* @param project
* The project
* @param appClassList
* list of ClassDescriptors identifying application classes
* @param sourceInfoFileName
* name of source info file (null if none)
*/
@SuppressWarnings({"UnusedDeclaration"})
public static void createAnalysisContext(Project project, List<ClassDescriptor> appClassList,
@CheckForNull String sourceInfoFileName) throws IOException {
AnalysisContext analysisContext = new AnalysisContext();
// Make this the current analysis context
AnalysisContext.setCurrentAnalysisContext(analysisContext);
// Make the AnalysisCache the backing store for
// the BCEL Repository
analysisContext.clearRepository();
// If needed, load SourceInfoMap
if (sourceInfoFileName != null) {
SourceInfoMap sourceInfoMap = analysisContext.getSourceInfoMap();
sourceInfoMap.read(new FileInputStream(sourceInfoFileName));
}
analysisContext.setProject(project);
}
public static void setAppClassList(List<ClassDescriptor> appClassList) {
AnalysisContext analysisContext = AnalysisContext
.currentAnalysisContext();
analysisContext.setAppClassList(appClassList);
}
/**
* Configure analysis feature settings.
*/
private void configureAnalysisFeatures() {
for (AnalysisFeatureSetting setting : analysisOptions.analysisFeatureSettingList) {
setting.configure(AnalysisContext.currentAnalysisContext());
}
AnalysisContext.currentAnalysisContext().setBoolProperty(AnalysisFeatures.MERGE_SIMILAR_WARNINGS,
analysisOptions.mergeSimilarWarnings);
}
/**
* Create an execution plan.
*
* @throws OrderingConstraintException
* if the detector ordering constraints are inconsistent
*/
private void createExecutionPlan() throws OrderingConstraintException {
executionPlan = new ExecutionPlan();
// Use user preferences to decide which detectors are enabled.
DetectorFactoryChooser detectorFactoryChooser = new DetectorFactoryChooser() {
HashSet<DetectorFactory> forcedEnabled = new HashSet<DetectorFactory>();
/*
* (non-Javadoc)
*
* @see
* edu.umd.cs.findbugs.DetectorFactoryChooser#choose(edu.umd.cs.
* findbugs.DetectorFactory)
*/
public boolean choose(DetectorFactory factory) {
boolean result = FindBugs.isDetectorEnabled(FindBugs2.this, factory, rankThreshold) || forcedEnabled.contains(factory);
if (ExecutionPlan.DEBUG)
System.out.printf(" %6s %s %n", result, factory.getShortName());
return result;
}
public void enable(DetectorFactory factory) {
forcedEnabled.add(factory);
factory.setEnabledButNonReporting(true);
}
};
executionPlan.setDetectorFactoryChooser(detectorFactoryChooser);
if (ExecutionPlan.DEBUG)
System.out.println("rank threshold is " + rankThreshold);
// Add plugins
for (Iterator<Plugin> i = detectorFactoryCollection.pluginIterator(); i.hasNext();) {
Plugin plugin = i.next();
if (DEBUG) {
System.out.println("Adding plugin " + plugin.getPluginId() + " to execution plan");
}
executionPlan.addPlugin(plugin);
}
// Build the execution plan
executionPlan.build();
// Stash the ExecutionPlan in the AnalysisCache.
Global.getAnalysisCache().eagerlyPutDatabase(ExecutionPlan.class, executionPlan);
if (PROGRESS) {
System.out.println(executionPlan.getNumPasses() + " passes in execution plan");
}
}
/**
* Analyze the classes in the application codebase.
*/
private void analyzeApplication() throws InterruptedException {
int passCount = 0;
Profiler profiler = bugReporter.getProjectStats().getProfiler();
profiler.start(this.getClass());
AnalysisContext.currentXFactory().canonicalizeAll();
try {
boolean multiplePasses = executionPlan.getNumPasses() > 1;
if (executionPlan.getNumPasses() == 0) {
throw new AssertionError("no analysis passes");
}
int[] classesPerPass = new int[executionPlan.getNumPasses()];
classesPerPass[0] = referencedClassSet.size();
for (int i = 0; i < classesPerPass.length; i++) {
classesPerPass[i] = i == 0 ? referencedClassSet.size() : appClassList.size();
}
progress.predictPassCount(classesPerPass);
XFactory factory = AnalysisContext.currentXFactory();
Collection<ClassDescriptor> badClasses = new LinkedList<ClassDescriptor>();
for (ClassDescriptor desc : referencedClassSet) {
try {
XClass info = Global.getAnalysisCache().getClassAnalysis(XClass.class, desc);
factory.intern(info);
} catch (CheckedAnalysisException e) {
AnalysisContext.logError("Couldn't get class info for " + desc, e);
badClasses.add(desc);
} catch (RuntimeException e) {
AnalysisContext.logError("Couldn't get class info for " + desc, e);
badClasses.add(desc);
}
}
if (!badClasses.isEmpty()) {
referencedClassSet = new LinkedHashSet<ClassDescriptor>(referencedClassSet);
referencedClassSet.removeAll(badClasses);
}
long startTime = System.currentTimeMillis();
bugReporter.getProjectStats().setReferencedClasses(referencedClassSet.size());
for (Iterator<AnalysisPass> passIterator = executionPlan.passIterator(); passIterator.hasNext();) {
AnalysisPass pass = passIterator.next();
yourkitController.advanceGeneration("Pass " + passCount);
// The first pass is generally a non-reporting pass which
// gathers information about referenced classes.
boolean isNonReportingFirstPass = multiplePasses && passCount == 0;
// Instantiate the detectors
Detector2[] detectorList = pass.instantiateDetector2sInPass(bugReporter);
// If there are multiple passes, then on the first pass,
// we apply detectors to all classes referenced by the
// application classes.
// On subsequent passes, we apply detector only to application
// classes.
Collection<ClassDescriptor> classCollection = (isNonReportingFirstPass) ? referencedClassSet : appClassList;
AnalysisContext.currentXFactory().canonicalizeAll();
if (PROGRESS || LIST_ORDER) {
System.out.printf("%6d : Pass %d: %d classes%n", (System.currentTimeMillis() - startTime)/1000, passCount, classCollection.size());
if (DEBUG)
XFactory.profile();
}
if (!isNonReportingFirstPass) {
OutEdges<ClassDescriptor> outEdges = new OutEdges<ClassDescriptor>() {
public Collection<ClassDescriptor> getOutEdges(ClassDescriptor e) {
try {
XClass classNameAndInfo = Global.getAnalysisCache().getClassAnalysis(XClass.class, e);
return classNameAndInfo.getCalledClassDescriptors();
} catch (CheckedAnalysisException e2) {
AnalysisContext.logError("error while analyzing " + e.getClassName(), e2);
return Collections.emptyList();
}
}
};
classCollection = sortByCallGraph(classCollection, outEdges);
}
if (LIST_ORDER) {
System.out.println("Analysis order:");
for (ClassDescriptor c : classCollection) {
System.out.println(" " + c);
}
}
AnalysisContext currentAnalysisContext = AnalysisContext.currentAnalysisContext();
currentAnalysisContext.updateDatabases(passCount);
progress.startAnalysis(classCollection.size());
int count = 0;
Global.getAnalysisCache().purgeAllMethodAnalysis();
Global.getAnalysisCache().purgeClassAnalysis(FBClassReader.class);
for (ClassDescriptor classDescriptor : classCollection) {
long classStartNanoTime = 0;
if (PROGRESS) {
classStartNanoTime = System.nanoTime();
System.out.printf("%6d %d/%d %d/%d %s%n", (System.currentTimeMillis() - startTime)/1000,
passCount, executionPlan.getNumPasses(), count,
classCollection.size(), classDescriptor);
}
count++;
// Check to see if class is excluded by the class screener.
// In general, we do not want to screen classes from the
// first pass, even if they would otherwise be excluded.
if ((SCREEN_FIRST_PASS_CLASSES || !isNonReportingFirstPass)
&& !classScreener.matches(classDescriptor.toResourceName())) {
if (DEBUG) {
System.out.println("*** Excluded by class screener");
}
continue;
}
boolean isHuge = currentAnalysisContext.isTooBig(classDescriptor);
if (isHuge && currentAnalysisContext.isApplicationClass(classDescriptor)) {
bugReporter.reportBug(new BugInstance("SKIPPED_CLASS_TOO_BIG", Priorities.NORMAL_PRIORITY)
.addClass(classDescriptor));
}
currentClassName = ClassName.toDottedClassName(classDescriptor.getClassName());
notifyClassObservers(classDescriptor);
profiler.startContext(currentClassName);
currentAnalysisContext.setClassBeingAnalyzed(classDescriptor);
try {
for (Detector2 detector : detectorList) {
if (Thread.interrupted()) {
throw new InterruptedException();
}
if (isHuge && !FirstPassDetector.class.isAssignableFrom(detector.getClass())) {
continue;
}
if (DEBUG) {
System.out.println("Applying " + detector.getDetectorClassName() + " to " + classDescriptor);
// System.out.println("foo: " +
// NonReportingDetector.class.isAssignableFrom(detector.getClass())
// + ", bar: " + detector.getClass().getName());
}
try {
profiler.start(detector.getClass());
detector.visitClass(classDescriptor);
} catch (ClassFormatException e) {
logRecoverableException(classDescriptor, detector, e);
} catch (MissingClassException e) {
Global.getAnalysisCache().getErrorLogger().reportMissingClass(e.getClassDescriptor());
} catch (CheckedAnalysisException e) {
logRecoverableException(classDescriptor, detector, e);
} catch (RuntimeException e) {
logRecoverableException(classDescriptor, detector, e);
} finally {
profiler.end(detector.getClass());
}
}
} finally {
progress.finishClass();
profiler.endContext(currentClassName);
currentAnalysisContext.clearClassBeingAnalyzed();
if (PROGRESS) {
long usecs = (System.nanoTime() - classStartNanoTime)/1000;
if (usecs > 15000) {
int classSize = currentAnalysisContext.getClassSize(classDescriptor);
long speed = usecs /classSize;
if (speed > 15)
System.out.printf(" %6d usecs/byte %6d msec %6d bytes %d pass %s%n", speed, usecs/1000, classSize, passCount,
classDescriptor);
}
}
}
}
if (!passIterator.hasNext())
yourkitController.captureMemorySnapshot();
// Call finishPass on each detector
for (Detector2 detector : detectorList) {
detector.finishPass();
}
progress.finishPerClassAnalysis();
passCount++;
}
} finally {
bugReporter.finish();
bugReporter.reportQueuedErrors();
profiler.end(this.getClass());
if (PROGRESS)
System.out.println("Analysis completed");
}
}
/**
* Notify all IClassObservers that we are visiting given class.
*
* @param classDescriptor
* the class being visited
*/
private void notifyClassObservers(ClassDescriptor classDescriptor) {
for (IClassObserver observer : classObserverList) {
observer.observeClass(classDescriptor);
}
}
/**
* Report an exception that occurred while analyzing a class with a
* detector.
*
* @param classDescriptor
* class being analyzed
* @param detector
* detector doing the analysis
* @param e
* the exception
*/
private void logRecoverableException(ClassDescriptor classDescriptor, Detector2 detector, Throwable e) {
bugReporter.logError(
"Exception analyzing " + classDescriptor.toDottedClassName() + " using detector "
+ detector.getDetectorClassName(), e);
}
public static void main(String[] args) throws Exception {
// Sanity-check the loaded BCEL classes
if (!CheckBcel.check()) {
System.exit(1);
}
// Create FindBugs2 engine
FindBugs2 findBugs = new FindBugs2();
// Parse command line and configure the engine
TextUICommandLine commandLine = new TextUICommandLine();
FindBugs.processCommandLine(commandLine, args, findBugs);
boolean justPrintConfiguration = commandLine.justPrintConfiguration();
if (justPrintConfiguration || commandLine.justPrintVersion()) {
Version.printVersion(justPrintConfiguration);
return;
}
// Away we go!
FindBugs.runMain(findBugs, commandLine);
}
public void setAbridgedMessages(boolean xmlWithAbridgedMessages) {
analysisOptions.abridgedMessages = xmlWithAbridgedMessages;
}
public void setMergeSimilarWarnings(boolean mergeSimilarWarnings) {
this.analysisOptions.mergeSimilarWarnings = mergeSimilarWarnings;
}
public void setApplySuppression(boolean applySuppression) {
this.analysisOptions.applySuppression = applySuppression;
}
public void setRankThreshold(int rankThreshold) {
this.rankThreshold = rankThreshold;
}
public void finishSettings() {
if (analysisOptions.applySuppression) {
bugReporter = new FilterBugReporter(bugReporter, getProject().getSuppressionFilter(), false);
}
}
@Nonnull
Set<String> explicitlyEnabledBugReporterDecorators = Collections.emptySet();
@Nonnull
Set<String> explicitlyDisabledBugReporterDecorators = Collections.emptySet();
public void setBugReporterDecorators(Set<String> explicitlyEnabled, Set<String> explicitlyDisabled) {
explicitlyEnabledBugReporterDecorators = explicitlyEnabled;
explicitlyDisabledBugReporterDecorators = explicitlyDisabled;
}
} |
package uk.co.johnjtaylor.events.generic;
import java.util.EventObject;
import uk.co.johnjtaylor.events.EventImportance;
import uk.co.johnjtaylor.events.EventType;
/**
* Base representation of an Event; extended
* into either a SortEvent type or Tester event to
* then be further defined into an individual event class.
*
* @author John
*/
public abstract class Event extends EventObject {
private static final long serialVersionUID = -8983402706390183976L;
private EventType type;
private EventImportance importance;
/**
* @param source Source creating this event (EventObject constr.)
* @param type EventType (enum) of the event instance
* @param importance EventImportance (enum) of the event significance
*/
public Event(Object source, EventType type, EventImportance importance) {
super(source);
this.type = type;
this.importance = importance;
}
/**
* @return EventType (enum) representation of which Event this is
*/
public EventType getEventType() {
return type;
}
/**
* @return EventImportance (enum) representation of the significance of the occuring event
*/
public EventImportance getEventImportance() {
return importance;
}
/**
* @return A string representing the name of this event instance
*/
public abstract String getEventName();
} |
package com.yahoo.vespa.flags;
import com.yahoo.component.Vtag;
import com.yahoo.vespa.defaults.Defaults;
import java.time.Instant;
import java.time.LocalDate;
import java.time.ZoneOffset;
import java.time.format.DateTimeFormatter;
import java.util.List;
import java.util.Optional;
import java.util.TreeMap;
import static com.yahoo.vespa.flags.FetchVector.Dimension.APPLICATION_ID;
import static com.yahoo.vespa.flags.FetchVector.Dimension.CONSOLE_USER_EMAIL;
import static com.yahoo.vespa.flags.FetchVector.Dimension.HOSTNAME;
import static com.yahoo.vespa.flags.FetchVector.Dimension.NODE_TYPE;
import static com.yahoo.vespa.flags.FetchVector.Dimension.TENANT_ID;
import static com.yahoo.vespa.flags.FetchVector.Dimension.VESPA_VERSION;
import static com.yahoo.vespa.flags.FetchVector.Dimension.ZONE_ID;
/**
* Definitions of feature flags.
*
* <p>To use feature flags, define the flag in this class as an "unbound" flag, e.g. {@link UnboundBooleanFlag}
* or {@link UnboundStringFlag}. At the location you want to get the value of the flag, you need the following:</p>
*
* <ol>
* <li>The unbound flag</li>
* <li>A {@link FlagSource}. The flag source is typically available as an injectable component. Binding
* an unbound flag to a flag source produces a (bound) flag, e.g. {@link BooleanFlag} and {@link StringFlag}.</li>
* <li>If you would like your flag value to be dependent on e.g. the application ID, then 1. you should
* declare this in the unbound flag definition in this file (referring to
* {@link FetchVector.Dimension#APPLICATION_ID}), and 2. specify the application ID when retrieving the value, e.g.
* {@link BooleanFlag#with(FetchVector.Dimension, String)}. See {@link FetchVector} for more info.</li>
* </ol>
*
* <p>Once the code is in place, you can override the flag value. This depends on the flag source, but typically
* there is a REST API for updating the flags in the config server, which is the root of all flag sources in the zone.</p>
*
* @author hakonhall
*/
public class Flags {
private static volatile TreeMap<FlagId, FlagDefinition> flags = new TreeMap<>();
public static final UnboundDoubleFlag DEFAULT_TERM_WISE_LIMIT = defineDoubleFlag(
"default-term-wise-limit", 1.0,
List.of("baldersheim"), "2020-12-02", "2022-02-01",
"Default limit for when to apply termwise query evaluation",
"Takes effect at redeployment",
ZONE_ID, APPLICATION_ID);
public static final UnboundDoubleFlag TLS_SIZE_FRACTION = defineDoubleFlag(
"tls-size-fraction", 0.07,
List.of("baldersheim"), "2021-12-20", "2022-02-01",
"Fraction of disk available for transaction log",
"Takes effect at redeployment",
ZONE_ID, APPLICATION_ID);
public static final UnboundStringFlag FEED_SEQUENCER_TYPE = defineStringFlag(
"feed-sequencer-type", "LATENCY",
List.of("baldersheim"), "2020-12-02", "2022-02-01",
"Selects type of sequenced executor used for feeding in proton, valid values are LATENCY, ADAPTIVE, THROUGHPUT",
"Takes effect at redeployment (requires restart)",
ZONE_ID, APPLICATION_ID);
public static final UnboundIntFlag FEED_TASK_LIMIT = defineIntFlag(
"feed-task-limit", 1000,
List.of("geirst, baldersheim"), "2021-10-14", "2022-02-01",
"The task limit used by the executors handling feed in proton",
"Takes effect at redeployment",
ZONE_ID, APPLICATION_ID);
public static final UnboundIntFlag FEED_MASTER_TASK_LIMIT = defineIntFlag(
"feed-master-task-limit", 0,
List.of("geirst, baldersheim"), "2021-11-18", "2022-02-01",
"The task limit used by the master thread in each document db in proton. Ignored when set to 0.",
"Takes effect at redeployment",
ZONE_ID, APPLICATION_ID);
public static final UnboundStringFlag SHARED_FIELD_WRITER_EXECUTOR = defineStringFlag(
"shared-field-writer-executor", "NONE",
List.of("geirst, baldersheim"), "2021-11-05", "2022-02-01",
"Whether to use a shared field writer executor for the document database(s) in proton. " +
"Valid values: NONE, INDEX, INDEX_AND_ATTRIBUTE, DOCUMENT_DB",
"Takes effect at redeployment (requires restart)",
ZONE_ID, APPLICATION_ID);
public static final UnboundIntFlag MAX_UNCOMMITTED_MEMORY = defineIntFlag(
"max-uncommitted-memory", 130000,
List.of("geirst, baldersheim"), "2021-10-21", "2022-02-01",
"Max amount of memory holding updates to an attribute before we do a commit.",
"Takes effect at redeployment",
ZONE_ID, APPLICATION_ID);
public static final UnboundStringFlag RESPONSE_SEQUENCER_TYPE = defineStringFlag(
"response-sequencer-type", "ADAPTIVE",
List.of("baldersheim"), "2020-12-02", "2022-02-01",
"Selects type of sequenced executor used for mbus responses, valid values are LATENCY, ADAPTIVE, THROUGHPUT",
"Takes effect at redeployment",
ZONE_ID, APPLICATION_ID);
public static final UnboundIntFlag RESPONSE_NUM_THREADS = defineIntFlag(
"response-num-threads", 2,
List.of("baldersheim"), "2020-12-02", "2022-02-01",
"Number of threads used for mbus responses, default is 2, negative number = numcores/4",
"Takes effect at redeployment",
ZONE_ID, APPLICATION_ID);
public static final UnboundBooleanFlag SKIP_COMMUNICATIONMANAGER_THREAD = defineFeatureFlag(
"skip-communicationmanager-thread", false,
List.of("baldersheim"), "2020-12-02", "2022-02-01",
"Should we skip the communicationmanager thread",
"Takes effect at redeployment",
ZONE_ID, APPLICATION_ID);
public static final UnboundBooleanFlag SKIP_MBUS_REQUEST_THREAD = defineFeatureFlag(
"skip-mbus-request-thread", false,
List.of("baldersheim"), "2020-12-02", "2022-02-01",
"Should we skip the mbus request thread",
"Takes effect at redeployment",
ZONE_ID, APPLICATION_ID);
public static final UnboundBooleanFlag SKIP_MBUS_REPLY_THREAD = defineFeatureFlag(
"skip-mbus-reply-thread", false,
List.of("baldersheim"), "2020-12-02", "2022-02-01",
"Should we skip the mbus reply thread",
"Takes effect at redeployment",
ZONE_ID, APPLICATION_ID);
public static final UnboundBooleanFlag USE_THREE_PHASE_UPDATES = defineFeatureFlag(
"use-three-phase-updates", false,
List.of("vekterli"), "2020-12-02", "2022-02-01",
"Whether to enable the use of three-phase updates when bucket replicas are out of sync.",
"Takes effect at redeployment",
ZONE_ID, APPLICATION_ID);
public static final UnboundBooleanFlag HIDE_SHARED_ROUTING_ENDPOINT = defineFeatureFlag(
"hide-shared-routing-endpoint", false,
List.of("tokle", "bjormel"), "2020-12-02", "2022-02-01",
"Whether the controller should hide shared routing layer endpoint",
"Takes effect immediately",
APPLICATION_ID
);
public static final UnboundBooleanFlag USE_ASYNC_MESSAGE_HANDLING_ON_SCHEDULE = defineFeatureFlag(
"async-message-handling-on-schedule", false,
List.of("baldersheim"), "2020-12-02", "2022-02-01",
"Optionally deliver async messages in own thread",
"Takes effect at redeployment",
ZONE_ID, APPLICATION_ID);
public static final UnboundDoubleFlag FEED_CONCURRENCY = defineDoubleFlag(
"feed-concurrency", 0.5,
List.of("baldersheim"), "2020-12-02", "2022-02-01",
"How much concurrency should be allowed for feed",
"Takes effect at redeployment",
ZONE_ID, APPLICATION_ID);
public static final UnboundDoubleFlag DISK_BLOAT_FACTOR = defineDoubleFlag(
"disk-bloat-factor", 0.2,
List.of("baldersheim"), "2021-10-08", "2022-02-01",
"Amount of bloat allowed before compacting file",
"Takes effect at redeployment",
ZONE_ID, APPLICATION_ID);
public static final UnboundIntFlag DOCSTORE_COMPRESSION_LEVEL = defineIntFlag(
"docstore-compression-level", 3,
List.of("baldersheim"), "2021-10-08", "2022-02-01",
"Default compression level used for document store",
"Takes effect at redeployment",
ZONE_ID, APPLICATION_ID);
public static final UnboundIntFlag NUM_DEPLOY_HELPER_THREADS = defineIntFlag(
"num-model-builder-threads", -1,
List.of("balder"), "2021-09-09", "2022-02-01",
"Number of threads used for speeding up building of models.",
"Takes effect on first (re)start of config server");
public static final UnboundBooleanFlag ENABLE_FEED_BLOCK_IN_DISTRIBUTOR = defineFeatureFlag(
"enable-feed-block-in-distributor", true,
List.of("geirst"), "2021-01-27", "2022-01-31",
"Enables blocking of feed in the distributor if resource usage is above limit on at least one content node",
"Takes effect at redeployment",
ZONE_ID, APPLICATION_ID);
public static final UnboundBooleanFlag CONTAINER_DUMP_HEAP_ON_SHUTDOWN_TIMEOUT = defineFeatureFlag(
"container-dump-heap-on-shutdown-timeout", false,
List.of("baldersheim"), "2021-09-25", "2022-02-01",
"Will trigger a heap dump during if container shutdown times out",
"Takes effect at redeployment",
ZONE_ID, APPLICATION_ID);
public static final UnboundDoubleFlag CONTAINER_SHUTDOWN_TIMEOUT = defineDoubleFlag(
"container-shutdown-timeout", 50.0,
List.of("baldersheim"), "2021-09-25", "2022-02-01",
"Timeout for shutdown of a jdisc container",
"Takes effect at redeployment",
ZONE_ID, APPLICATION_ID);
public static final UnboundListFlag<String> ALLOWED_ATHENZ_PROXY_IDENTITIES = defineListFlag(
"allowed-athenz-proxy-identities", List.of(), String.class,
List.of("bjorncs", "tokle"), "2021-02-10", "2022-02-01",
"Allowed Athenz proxy identities",
"takes effect at redeployment");
public static final UnboundBooleanFlag GENERATE_NON_MTLS_ENDPOINT = defineFeatureFlag(
"generate-non-mtls-endpoint", true,
List.of("tokle"), "2021-02-18", "2022-02-01",
"Whether to generate the non-mtls endpoint",
"Takes effect on next internal redeployment",
APPLICATION_ID);
public static final UnboundIntFlag MAX_ACTIVATION_INHIBITED_OUT_OF_SYNC_GROUPS = defineIntFlag(
"max-activation-inhibited-out-of-sync-groups", 0,
List.of("vekterli"), "2021-02-19", "2022-02-01",
"Allows replicas in up to N content groups to not be activated " +
"for query visibility if they are out of sync with a majority of other replicas",
"Takes effect at redeployment",
ZONE_ID, APPLICATION_ID);
public static final UnboundIntFlag MAX_CONCURRENT_MERGES_PER_NODE = defineIntFlag(
"max-concurrent-merges-per-node", 128,
List.of("balder", "vekterli"), "2021-06-06", "2022-02-01",
"Specifies max concurrent merges per content node.",
"Takes effect at redeploy",
ZONE_ID, APPLICATION_ID);
public static final UnboundIntFlag MAX_MERGE_QUEUE_SIZE = defineIntFlag(
"max-merge-queue-size", 1024,
List.of("balder", "vekterli"), "2021-06-06", "2022-02-01",
"Specifies max size of merge queue.",
"Takes effect at redeploy",
ZONE_ID, APPLICATION_ID);
public static final UnboundBooleanFlag IGNORE_MERGE_QUEUE_LIMIT = defineFeatureFlag(
"ignore-merge-queue-limit", false,
List.of("vekterli", "geirst"), "2021-10-06", "2022-03-01",
"Specifies if merges that are forwarded (chained) from another content node are always " +
"allowed to be enqueued even if the queue is otherwise full.",
"Takes effect at redeploy",
ZONE_ID, APPLICATION_ID);
public static final UnboundIntFlag LARGE_RANK_EXPRESSION_LIMIT = defineIntFlag(
"large-rank-expression-limit", 8192,
List.of("baldersheim"), "2021-06-09", "2022-02-01",
"Limit for size of rank expressions distributed by filedistribution",
"Takes effect on next internal redeployment",
APPLICATION_ID);
public static final UnboundDoubleFlag MIN_NODE_RATIO_PER_GROUP = defineDoubleFlag(
"min-node-ratio-per-group", 0.0,
List.of("geirst", "vekterli"), "2021-07-16", "2022-03-01",
"Minimum ratio of nodes that have to be available (i.e. not Down) in any hierarchic content cluster group for the group to be Up",
"Takes effect at redeployment",
ZONE_ID, APPLICATION_ID);
public static final UnboundIntFlag METRICSPROXY_NUM_THREADS = defineIntFlag(
"metricsproxy-num-threads", 2,
List.of("balder"), "2021-09-01", "2022-02-01",
"Number of threads for metrics proxy",
"Takes effect at redeployment",
ZONE_ID, APPLICATION_ID);
public static final UnboundBooleanFlag ENABLED_HORIZON_DASHBOARD = defineFeatureFlag(
"enabled-horizon-dashboard", false,
List.of("olaa"), "2021-09-13", "2022-02-01",
"Enable Horizon dashboard",
"Takes effect immediately",
TENANT_ID, CONSOLE_USER_EMAIL
);
public static final UnboundBooleanFlag ENABLE_ONPREM_TENANT_S3_ARCHIVE = defineFeatureFlag(
"enable-onprem-tenant-s3-archive", false,
List.of("bjorncs"), "2021-09-14", "2022-02-01",
"Enable tenant S3 buckets in cd/main. Must be set on controller cluster only.",
"Takes effect immediately",
ZONE_ID, TENANT_ID
);
public static final UnboundBooleanFlag DELETE_UNMAINTAINED_CERTIFICATES = defineFeatureFlag(
"delete-unmaintained-certificates", false,
List.of("andreer"), "2021-09-23", "2022-02-01",
"Whether to delete certificates that are known by provider but not by controller",
"Takes effect on next run of EndpointCertificateMaintainer"
);
public static final UnboundBooleanFlag USE_NEW_ENDPOINT_CERTIFICATE_PROVIDER_URL = defineFeatureFlag(
"use-new-endpoint-certificate-provider-url", true,
List.of("andreer"), "2021-12-14", "2022-01-14",
"Use the new URL for the endpoint certificate provider API",
"Takes effect immediately"
);
public static final UnboundBooleanFlag ENABLE_TENANT_DEVELOPER_ROLE = defineFeatureFlag(
"enable-tenant-developer-role", false,
List.of("bjorncs"), "2021-09-23", "2022-02-01",
"Enable tenant developer Athenz role in cd/main. Must be set on controller cluster only.",
"Takes effect immediately",
TENANT_ID
);
public static final UnboundBooleanFlag ENABLE_ROUTING_REUSE_PORT = defineFeatureFlag(
"enable-routing-reuse-port", true,
List.of("mortent"), "2021-09-29", "2022-02-01",
"Enable reuse port in routing configuration",
"Takes effect on container restart",
HOSTNAME
);
public static final UnboundBooleanFlag ENABLE_TENANT_OPERATOR_ROLE = defineFeatureFlag(
"enable-tenant-operator-role", false,
List.of("bjorncs"), "2021-09-29", "2022-02-01",
"Enable tenant specific operator roles in public systems. For controllers only.",
"Takes effect on subsequent maintainer invocation",
TENANT_ID
);
public static final UnboundIntFlag DISTRIBUTOR_MERGE_BUSY_WAIT = defineIntFlag(
"distributor-merge-busy-wait", 10,
List.of("geirst", "vekterli"), "2021-10-04", "2022-03-01",
"Number of seconds that scheduling of new merge operations in the distributor should be inhibited " +
"towards a content node that has indicated merge busy",
"Takes effect at redeploy",
ZONE_ID, APPLICATION_ID);
public static final UnboundBooleanFlag DISTRIBUTOR_ENHANCED_MAINTENANCE_SCHEDULING = defineFeatureFlag(
"distributor-enhanced-maintenance-scheduling", false,
List.of("vekterli", "geirst"), "2021-10-14", "2022-01-31",
"Enable enhanced maintenance operation scheduling semantics on the distributor",
"Takes effect at redeploy",
ZONE_ID, APPLICATION_ID);
public static final UnboundBooleanFlag ASYNC_APPLY_BUCKET_DIFF = defineFeatureFlag(
"async-apply-bucket-diff", false,
List.of("geirst", "vekterli"), "2021-10-22", "2022-01-31",
"Whether portions of apply bucket diff handling will be performed asynchronously",
"Takes effect at redeploy",
ZONE_ID, APPLICATION_ID);
public static final UnboundBooleanFlag UNORDERED_MERGE_CHAINING = defineFeatureFlag(
"unordered-merge-chaining", false,
List.of("vekterli", "geirst"), "2021-11-15", "2022-03-01",
"Enables the use of unordered merge chains for data merge operations",
"Takes effect at redeploy",
ZONE_ID, APPLICATION_ID);
public static final UnboundStringFlag JDK_VERSION = defineStringFlag(
"jdk-version", "11",
List.of("hmusum"), "2021-10-25", "2022-03-01",
"JDK version to use on host and inside containers. Note application-id dimension only applies for container, " +
"while hostname and node type applies for host.",
"Takes effect on restart for Docker container and on next host-admin tick for host",
APPLICATION_ID,
TENANT_ID,
HOSTNAME,
NODE_TYPE);
public static final UnboundBooleanFlag IGNORE_THREAD_STACK_SIZES = defineFeatureFlag(
"ignore-thread-stack-sizes", false,
List.of("arnej"), "2021-11-12", "2022-01-31",
"Whether C++ thread creation should ignore any requested stack size",
"Triggers restart, takes effect immediately",
ZONE_ID, APPLICATION_ID);
public static final UnboundBooleanFlag USE_V8_GEO_POSITIONS = defineFeatureFlag(
"use-v8-geo-positions", false,
List.of("arnej"), "2021-11-15", "2022-12-31",
"Use Vespa 8 types and formats for geographical positions",
"Takes effect at redeployment",
ZONE_ID, APPLICATION_ID);
public static final UnboundBooleanFlag USE_LEGACY_LB_SERVICES = defineFeatureFlag(
"use-legacy-lb-services", false,
List.of("tokle"), "2021-11-22", "2022-02-01",
"Whether to generate routing table based on legacy lb-services config",
"Takes effect on container reboot",
ZONE_ID, HOSTNAME);
public static final UnboundBooleanFlag USE_V8_DOC_MANAGER_CFG = defineFeatureFlag(
"use-v8-doc-manager-cfg", false,
List.of("arnej", "baldersheim"), "2021-12-09", "2022-12-31",
"Use new (preparing for Vespa 8) section in documentmanager.def",
"Takes effect at redeployment",
ZONE_ID, APPLICATION_ID);
public static final UnboundIntFlag MAX_COMPACT_BUFFERS = defineIntFlag(
"max-compact-buffers", 1,
List.of("baldersheim", "geirst", "toregge"), "2021-12-15", "2022-03-31",
"Upper limit of buffers to compact in a data store at the same time for each reason (memory usage, address space usage)",
"Takes effect at redeployment",
ZONE_ID, APPLICATION_ID);
public static final UnboundBooleanFlag FAIL_DEPLOYMENT_WITH_INVALID_JVM_OPTIONS = defineFeatureFlag(
"fail-deployment-with-invalid-jvm-options", false,
List.of("hmusum"), "2021-12-20", "2022-01-20",
"Whether to fail deployments with invalid JVM options in services.xml",
"Takes effect at redeployment",
ZONE_ID, APPLICATION_ID);
/** WARNING: public for testing: All flags should be defined in {@link Flags}. */
public static UnboundBooleanFlag defineFeatureFlag(String flagId, boolean defaultValue, List<String> owners,
String createdAt, String expiresAt, String description,
String modificationEffect, FetchVector.Dimension... dimensions) {
return define(UnboundBooleanFlag::new, flagId, defaultValue, owners, createdAt, expiresAt, description, modificationEffect, dimensions);
}
/** WARNING: public for testing: All flags should be defined in {@link Flags}. */
public static UnboundStringFlag defineStringFlag(String flagId, String defaultValue, List<String> owners,
String createdAt, String expiresAt, String description,
String modificationEffect, FetchVector.Dimension... dimensions) {
return define(UnboundStringFlag::new, flagId, defaultValue, owners, createdAt, expiresAt, description, modificationEffect, dimensions);
}
/** WARNING: public for testing: All flags should be defined in {@link Flags}. */
public static UnboundIntFlag defineIntFlag(String flagId, int defaultValue, List<String> owners,
String createdAt, String expiresAt, String description,
String modificationEffect, FetchVector.Dimension... dimensions) {
return define(UnboundIntFlag::new, flagId, defaultValue, owners, createdAt, expiresAt, description, modificationEffect, dimensions);
}
/** WARNING: public for testing: All flags should be defined in {@link Flags}. */
public static UnboundLongFlag defineLongFlag(String flagId, long defaultValue, List<String> owners,
String createdAt, String expiresAt, String description,
String modificationEffect, FetchVector.Dimension... dimensions) {
return define(UnboundLongFlag::new, flagId, defaultValue, owners, createdAt, expiresAt, description, modificationEffect, dimensions);
}
/** WARNING: public for testing: All flags should be defined in {@link Flags}. */
public static UnboundDoubleFlag defineDoubleFlag(String flagId, double defaultValue, List<String> owners,
String createdAt, String expiresAt, String description,
String modificationEffect, FetchVector.Dimension... dimensions) {
return define(UnboundDoubleFlag::new, flagId, defaultValue, owners, createdAt, expiresAt, description, modificationEffect, dimensions);
}
/** WARNING: public for testing: All flags should be defined in {@link Flags}. */
public static <T> UnboundJacksonFlag<T> defineJacksonFlag(String flagId, T defaultValue, Class<T> jacksonClass, List<String> owners,
String createdAt, String expiresAt, String description,
String modificationEffect, FetchVector.Dimension... dimensions) {
return define((id2, defaultValue2, vector2) -> new UnboundJacksonFlag<>(id2, defaultValue2, vector2, jacksonClass),
flagId, defaultValue, owners, createdAt, expiresAt, description, modificationEffect, dimensions);
}
/** WARNING: public for testing: All flags should be defined in {@link Flags}. */
public static <T> UnboundListFlag<T> defineListFlag(String flagId, List<T> defaultValue, Class<T> elementClass,
List<String> owners, String createdAt, String expiresAt,
String description, String modificationEffect, FetchVector.Dimension... dimensions) {
return define((fid, dval, fvec) -> new UnboundListFlag<>(fid, dval, elementClass, fvec),
flagId, defaultValue, owners, createdAt, expiresAt, description, modificationEffect, dimensions);
}
@FunctionalInterface
private interface TypedUnboundFlagFactory<T, U extends UnboundFlag<?, ?, ?>> {
U create(FlagId id, T defaultVale, FetchVector defaultFetchVector);
}
/**
* Defines a Flag.
*
* @param factory Factory for creating unbound flag of type U
* @param flagId The globally unique FlagId.
* @param defaultValue The default value if none is present after resolution.
* @param description Description of how the flag is used.
* @param modificationEffect What is required for the flag to take effect? A restart of process? immediately? etc.
* @param dimensions What dimensions will be set in the {@link FetchVector} when fetching
* the flag value in
* {@link FlagSource#fetch(FlagId, FetchVector) FlagSource::fetch}.
* For instance, if APPLICATION is one of the dimensions here, you should make sure
* APPLICATION is set to the ApplicationId in the fetch vector when fetching the RawFlag
* from the FlagSource.
* @param <T> The boxed type of the flag value, e.g. Boolean for flags guarding features.
* @param <U> The type of the unbound flag, e.g. UnboundBooleanFlag.
* @return An unbound flag with {@link FetchVector.Dimension#HOSTNAME HOSTNAME} and
* {@link FetchVector.Dimension#VESPA_VERSION VESPA_VERSION} already set. The ZONE environment
* is typically implicit.
*/
private static <T, U extends UnboundFlag<?, ?, ?>> U define(TypedUnboundFlagFactory<T, U> factory,
String flagId,
T defaultValue,
List<String> owners,
String createdAt,
String expiresAt,
String description,
String modificationEffect,
FetchVector.Dimension[] dimensions) {
FlagId id = new FlagId(flagId);
FetchVector vector = new FetchVector()
.with(HOSTNAME, Defaults.getDefaults().vespaHostname())
// Warning: In unit tests and outside official Vespa releases, the currentVersion is e.g. 7.0.0
// (determined by the current major version). Consider not setting VESPA_VERSION if minor = micro = 0.
.with(VESPA_VERSION, Vtag.currentVersion.toFullString());
U unboundFlag = factory.create(id, defaultValue, vector);
FlagDefinition definition = new FlagDefinition(
unboundFlag, owners, parseDate(createdAt), parseDate(expiresAt), description, modificationEffect, dimensions);
flags.put(id, definition);
return unboundFlag;
}
private static Instant parseDate(String rawDate) {
return DateTimeFormatter.ISO_DATE.parse(rawDate, LocalDate::from).atStartOfDay().toInstant(ZoneOffset.UTC);
}
public static List<FlagDefinition> getAllFlags() {
return List.copyOf(flags.values());
}
public static Optional<FlagDefinition> getFlag(FlagId flagId) {
return Optional.ofNullable(flags.get(flagId));
}
/**
* Allows the statically defined flags to be controlled in a test.
*
* <p>Returns a Replacer instance to be used with e.g. a try-with-resources block. Within the block,
* the flags starts out as cleared. Flags can be defined, etc. When leaving the block, the flags from
* before the block is reinserted.
*
* <p>NOT thread-safe. Tests using this cannot run in parallel.
*/
public static Replacer clearFlagsForTesting(FlagId... flagsToKeep) {
return new Replacer(flagsToKeep);
}
public static class Replacer implements AutoCloseable {
private static volatile boolean flagsCleared = false;
private final TreeMap<FlagId, FlagDefinition> savedFlags;
private Replacer(FlagId... flagsToKeep) {
verifyAndSetFlagsCleared(true);
this.savedFlags = Flags.flags;
Flags.flags = new TreeMap<>();
List.of(flagsToKeep).forEach(id -> Flags.flags.put(id, savedFlags.get(id)));
}
@Override
public void close() {
verifyAndSetFlagsCleared(false);
Flags.flags = savedFlags;
}
/**
* Used to implement a simple verification that Replacer is not used by multiple threads.
* For instance two different tests running in parallel cannot both use Replacer.
*/
private static void verifyAndSetFlagsCleared(boolean newValue) {
if (flagsCleared == newValue) {
throw new IllegalStateException("clearFlagsForTesting called while already cleared - running tests in parallell!?");
}
flagsCleared = newValue;
}
}
} |
package us.kbase.userprofile;
import java.util.HashMap;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import us.kbase.common.service.JsonServerMethod;
import us.kbase.common.service.JsonServerServlet;
//BEGIN_HEADER
import java.util.ArrayList;
import us.kbase.auth.AuthService;
import us.kbase.auth.AuthToken;
import us.kbase.auth.UserDetail;
import org.ini4j.Ini;
import java.io.File;
//END_HEADER
/**
* <p>Original spec-file module name: UserProfile</p>
* <pre>
* </pre>
*/
public class UserProfileServer extends JsonServerServlet {
private static final long serialVersionUID = 1L;
//BEGIN_CLASS_HEADER
public static final String VERSION = "0.1.0";
public static final String SYS_PROP_KB_DEPLOYMENT_CONFIG = "KB_DEPLOYMENT_CONFIG";
public static final String SERVICE_DEPLOYMENT_NAME = "UserProfile";
public static final String CFG_MONGO_HOST = "mongodb-host";
public static final String CFG_MONGO_DB = "mongodb-database";
public static final String CFG_MONGO_USER = "mongodb-user";
public static final String CFG_MONGO_PSWD = "mongodb-pwd";
public static final String CFG_MONGO_RETRY = "mongodb-retry";
public static final String CFG_ADMIN = "admin";
private static Throwable configError = null;
private static Map<String, String> config = null;
public static Map<String, String> config() {
if (config != null)
return config;
if (configError != null)
throw new IllegalStateException("There was an error while loading configuration", configError);
String configPath = System.getProperty(SYS_PROP_KB_DEPLOYMENT_CONFIG);
if (configPath == null)
configPath = System.getenv(SYS_PROP_KB_DEPLOYMENT_CONFIG);
if (configPath == null) {
configError = new IllegalStateException("Configuration file was not defined");
} else {
System.out.println(UserProfileServer.class.getName() + ": Deployment config path was defined: " + configPath);
try {
config = new Ini(new File(configPath)).get(SERVICE_DEPLOYMENT_NAME);
} catch (Throwable ex) {
System.out.println(UserProfileServer.class.getName() + ": Error loading deployment config-file: " + ex.getMessage());
configError = ex;
}
}
if (config == null)
throw new IllegalStateException("There was unknown error in service initialization when checking"
+ "the configuration: is the ["+SERVICE_DEPLOYMENT_NAME+"] config group defined?");
return config;
}
private String getConfig(String configName) {
String ret = config().get(configName);
if (ret == null)
throw new IllegalStateException("Parameter " + configName + " is not defined in configuration");
return ret;
}
private final MongoController db;
//END_CLASS_HEADER
public UserProfileServer() throws Exception {
super("UserProfile");
//BEGIN_CONSTRUCTOR
System.out.println(UserProfileServer.class.getName() + ": " + CFG_MONGO_HOST +" = " + getConfig(CFG_MONGO_HOST));
System.out.println(UserProfileServer.class.getName() + ": " + CFG_MONGO_DB +" = " + getConfig(CFG_MONGO_DB));
System.out.println(UserProfileServer.class.getName() + ": " + CFG_MONGO_RETRY +" = " + getConfig(CFG_MONGO_RETRY));
System.out.println(UserProfileServer.class.getName() + ": " + CFG_ADMIN +" = " + getConfig(CFG_ADMIN));
String mongoUser = ""; boolean useMongoAuth = true;
try{
mongoUser = getConfig(CFG_MONGO_USER);
} catch (Exception e) {
useMongoAuth = false;
}
if(useMongoAuth) {
db = new MongoController(
getConfig(CFG_MONGO_HOST),
getConfig(CFG_MONGO_DB),
Integer.parseInt(getConfig(CFG_MONGO_RETRY)),
mongoUser,
getConfig(CFG_MONGO_PSWD)
);
} else {
db = new MongoController(
getConfig(CFG_MONGO_HOST),
getConfig(CFG_MONGO_DB),
Integer.parseInt(getConfig(CFG_MONGO_RETRY)));
}
//END_CONSTRUCTOR
}
/**
* <p>Original spec-file function name: ver</p>
* <pre>
* </pre>
* @return instance of String
*/
@JsonServerMethod(rpc = "UserProfile.ver")
public String ver() throws Exception {
String returnVal = null;
//BEGIN ver
returnVal = VERSION;
//END ver
return returnVal;
}
/**
* <p>Original spec-file function name: filter_users</p>
* <pre>
* Returns a list of users matching the filter. If the 'filter' field
* is empty or null, then this will return all Users. The filter will
* match substrings in usernames and realnames.
* </pre>
* @param p instance of type {@link us.kbase.userprofile.FilterParams FilterParams}
* @return parameter "users" of list of type {@link us.kbase.userprofile.User User}
*/
@JsonServerMethod(rpc = "UserProfile.filter_users")
public List<User> filterUsers(FilterParams p) throws Exception {
List<User> returnVal = null;
//BEGIN filter_users
returnVal = db.filterUsers(p.getFilter());
//END filter_users
return returnVal;
}
/**
* <p>Original spec-file function name: get_user_profile</p>
* <pre>
* Given a list of usernames, returns a list of UserProfiles in the same order.
* If no UserProfile was found for a username, the UserProfile at that position will
* be null.
* </pre>
* @param usernames instance of list of original type "username"
* @return parameter "profiles" of list of type {@link us.kbase.userprofile.UserProfile UserProfile}
*/
@JsonServerMethod(rpc = "UserProfile.get_user_profile")
public List<UserProfile> getUserProfile(List<String> usernames) throws Exception {
List<UserProfile> returnVal = null;
//BEGIN get_user_profile
returnVal = new ArrayList<UserProfile>();
for(int k=0; k<usernames.size(); k++) {
// todo: make this one single batch query
returnVal.add(db.getProfile(usernames.get(k)));
}
//END get_user_profile
return returnVal;
}
/**
* <p>Original spec-file function name: set_user_profile</p>
* <pre>
* Set the UserProfile for the user indicated in the User field of the UserProfile
* object. This operation can only be performed if authenticated as the user in
* the UserProfile or as the admin account of this service.
* If the profile does not exist, one will be created. If it does already exist,
* then the entire user profile will be replaced with the new profile.
* </pre>
* @param p instance of type {@link us.kbase.userprofile.SetUserProfileParams SetUserProfileParams}
*/
@JsonServerMethod(rpc = "UserProfile.set_user_profile")
public void setUserProfile(SetUserProfileParams p, AuthToken authPart) throws Exception {
//BEGIN set_user_profile
if(p.getProfile()==null)
throw new Exception("'profile' field must be set.");
if(p.getProfile().getUser()==null)
throw new Exception("'profile.user' field must be set.");
if(p.getProfile().getUser().getUsername()==null)
throw new Exception("'profile.user.username' field must be set.");
if(!authPart.getUserName().equals(p.getProfile().getUser().getUsername()) &&
!authPart.getUserName().equals(getConfig(CFG_ADMIN))) {
throw new Exception("only the user '"+p.getProfile().getUser().getUsername()+
"'or an admin can update this profile");
}
db.setProfile(p.getProfile());
//END set_user_profile
}
/**
* <p>Original spec-file function name: update_user_profile</p>
* <pre>
* Update the UserProfile for the user indicated in the User field of the UserProfile
* object. This operation can only be performed if authenticated as the user in
* the UserProfile or as the admin account of this service.
* If the profile does not exist, one will be created. If it does already exist,
* then the specified top-level fields in profile will be updated.
* todo: add some way to remove fields. Fields in profile can only be modified or added.
* </pre>
* @param p instance of type {@link us.kbase.userprofile.SetUserProfileParams SetUserProfileParams}
*/
@JsonServerMethod(rpc = "UserProfile.update_user_profile")
public void updateUserProfile(SetUserProfileParams p, AuthToken authPart) throws Exception {
//BEGIN update_user_profile
if(p.getProfile()==null)
throw new Exception("'profile' field must be set.");
if(p.getProfile().getUser()==null)
throw new Exception("'profile.user' field must be set.");
if(p.getProfile().getUser().getUsername()==null)
throw new Exception("'profile.user.username' field must be set.");
if(!authPart.getUserName().equals(p.getProfile().getUser().getUsername()) &&
!authPart.getUserName().equals(getConfig(CFG_ADMIN))) {
throw new Exception("only the user '"+p.getProfile().getUser().getUsername()+
"'or an admin can update this profile");
}
db.updateProfile(p.getProfile());
//END update_user_profile
}
/**
* <p>Original spec-file function name: lookup_globus_user</p>
* <pre>
* </pre>
* @param usernames instance of list of original type "username"
* @return parameter "users" of mapping from original type "username" to type {@link us.kbase.userprofile.GlobusUser GlobusUser}
*/
@JsonServerMethod(rpc = "UserProfile.lookup_globus_user")
public Map<String,GlobusUser> lookupGlobusUser(List<String> usernames, AuthToken authPart) throws Exception {
Map<String,GlobusUser> returnVal = null;
//BEGIN lookup_globus_user
Map<String, UserDetail> data = AuthService.fetchUserDetail(usernames, authPart);
Map<String, GlobusUser> ret = new HashMap<String, GlobusUser>(data.size());
for (UserDetail ud : data.values()) {
ret.put(ud.getUserName(),
new GlobusUser()
.withEmail(ud.getEmail())
.withFullName(ud.getFullName())
.withUserName(ud.getUserName()));
}
//END lookup_globus_user
return returnVal;
}
public static void main(String[] args) throws Exception {
if (args.length != 1) {
System.out.println("Usage: <program> <server_port>");
return;
}
new UserProfileServer().startupServer(Integer.parseInt(args[0]));
}
} |
package com.psddev.dari.util;
import java.lang.reflect.Field;
import java.util.ArrayList;
import java.util.Date;
import java.util.List;
import java.util.concurrent.Future;
import java.util.concurrent.TimeUnit;
import java.util.concurrent.atomic.AtomicBoolean;
import java.util.concurrent.atomic.AtomicLong;
import java.util.concurrent.atomic.AtomicReference;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.google.common.cache.CacheBuilder;
import com.google.common.cache.CacheLoader;
import com.google.common.cache.LoadingCache;
/**
* Skeletal runnable implementation that contains basic execution control
* and status methods. Subclasses must implement:
*
* <ul>
* <li>{@link #doTask}
* </ul>
*/
public abstract class Task implements Comparable<Task>, Runnable {
private static final Logger LOGGER = LoggerFactory.getLogger(Task.class);
private final TaskExecutor executor;
private final String name;
private final AtomicReference<Future<?>> future = new AtomicReference<Future<?>>();
private final AtomicBoolean isRunning = new AtomicBoolean();
private final AtomicBoolean isPauseRequested = new AtomicBoolean();
private final AtomicBoolean isStopRequested = new AtomicBoolean();
private volatile Thread thread;
private volatile long lastRunBegin = -1;
private volatile long lastRunEnd = -1;
private volatile String progress;
private volatile long progressIndex;
private volatile long progressTotal = -1;
private volatile Throwable lastException;
private final AtomicLong runCount = new AtomicLong();
/**
* Creates an instance that will run in the given
* {@code initialExecutor} with the given {@code initialName}.
*
* @param initialExecutor If {@code null}, this task will run in the
* default executor.
* @param initialName If blank, this task will be named based on its
* class name and the count of all instances created so far.
*/
protected Task(String initialExecutor, String initialName) {
executor = TaskExecutor.Static.getInstance(initialExecutor);
if (ObjectUtils.isBlank(initialName)) {
initialName = getClass().getName();
}
name = initialName + " #" + TASK_INDEXES.getUnchecked(initialName).incrementAndGet();
}
private static final LoadingCache<String, AtomicLong> TASK_INDEXES = CacheBuilder.
newBuilder().
build(new CacheLoader<String, AtomicLong>() {
@Override
public AtomicLong load(String name) {
return new AtomicLong();
}
});
/**
* Creates an instance that will run in the default executor
* anonymously.
*/
protected Task() {
this(null);
}
/**
* Returns the executor that will run this task.
*
* @return Never {@code null}.
*/
public TaskExecutor getExecutor() {
return executor;
}
/**
* Returns the name.
*
* @return Never blank.
*/
public String getName() {
return name;
}
/**
* Returns the future.
*
* @return {@code null} if this task hasn't been started or scheduled.
*/
public Future<?> getFuture() {
return future.get();
}
private boolean isSubmittable() {
Future<?> future = getFuture();
return future == null || future.isDone();
}
private static long nano(double seconds) {
return (long) (seconds * 1e9);
}
/**
* Submits this task to run immediately. Does nothing if this task is
* already scheduled to run.
*/
public void submit() {
synchronized (future) {
if (isSubmittable()) {
future.set(getExecutor().submit(this));
}
}
}
/**
* Schedule this task to run after the given {@code initialDelay}.
* Does nothing if this task is already scheduled to run.
*
* @param initialDelay In seconds.
*/
public void schedule(double initialDelay) {
synchronized (future) {
if (isSubmittable()) {
future.set(getExecutor().schedule(this, nano(initialDelay), TimeUnit.NANOSECONDS));
}
}
}
/**
* Schedule this task to run after the given {@code initialDelay} and
* forever after. Each subsequent runs will be scheduled to execute after
* the given {@code periodicDelay} once the current one finishes. Does
* nothing if this task is already scheduled to run.
*
* @param initialDelay In seconds.
* @param periodicDelay In seconds.
*/
public void scheduleWithFixedDelay(double initialDelay, double periodicDelay) {
synchronized (future) {
if (isSubmittable()) {
future.set(getExecutor().scheduleWithFixedDelay(this, nano(initialDelay), nano(periodicDelay), TimeUnit.NANOSECONDS));
}
}
}
/**
* Schedule this task to run after the given {@code initialDelay} and
* forever after every given {@code periodicDelay}. Does nothing if this
* task is already scheduled to run.
*
* @param initialDelay In seconds.
* @param periodicDelay In seconds.
*/
public void scheduleAtFixedRate(double initialDelay, double periodicDelay) {
synchronized (future) {
if (isSubmittable()) {
future.set(getExecutor().scheduleAtFixedRate(this, nano(initialDelay), nano(periodicDelay), TimeUnit.NANOSECONDS));
}
}
}
/**
* Returns the thread where this task is running.
*
* @return {@code null} if this task isn't running.
*/
public Thread getThread() {
return thread;
}
/**
* Returns {@code true} if the thread running this task has been
* interrupted.
*
* @return Always {@code false} if this task isn't running.
*/
public boolean isInterrupted() {
Thread thread = getThread();
return thread != null && thread.isInterrupted();
}
/** Returns {@code true} if this task is currently running. */
public boolean isRunning() {
return isRunning.get();
}
/**
* Returns {@code true} if {@link #pause} has been called on this
* task.
*/
public boolean isPauseRequested() {
return isPauseRequested.get();
}
/** Tries to pause this task. */
public void pause() {
if (isPauseRequested.compareAndSet(false, true)) {
LOGGER.debug("Pausing [{}]", getName());
}
}
/** Resumes this task if it's paused. */
public void resume() {
if (isPauseRequested.compareAndSet(true, false)) {
LOGGER.debug("Resuming [{}]", getName());
synchronized (isPauseRequested) {
isPauseRequested.notifyAll();
}
}
}
/**
* Returns {@code true} if {@link #stop} has been called on this
* task.
*/
public boolean isStopRequested() {
return isStopRequested.get();
}
/** Tries to stop this task. */
public void stop() {
if (isStopRequested.compareAndSet(false, true)) {
LOGGER.debug("Stopping [{}]", getName());
synchronized (future) {
Future<?> f = getFuture();
if (f != null && f.cancel(true)) {
return;
}
}
Thread t = getThread();
if (t != null) {
t.interrupt();
}
}
}
/**
* Returns the time when the last run of this task began.
*
* @return Milliseconds since the epoch. {@code -1} if this task
* never ran.
*/
public long getLastRunBegin() {
return lastRunBegin;
}
/**
* Returns the time when the last run of this task ended.
*
* @return Milliseconds since the epoch. {@code -1} if this task
* is currenting running.
*/
public long getLastRunEnd() {
return lastRunEnd;
}
/**
* Returns the run duration for this task. If it's not currently
* running, this method returns the measurement from the last run.
*
* @return In milliseconds. {@code -1} if this task never ran.
*/
public long getRunDuration() {
long runBegin = getLastRunBegin();
if (runBegin < 0) {
return -1;
} else {
long lastRunEnd = getLastRunEnd();
long runEnd = lastRunEnd > 0 ? lastRunEnd : System.currentTimeMillis();
return runEnd - runBegin;
}
}
/**
* Returns the progress.
*
* @return {@code null} if the progress isn't available.
*/
public String getProgress() {
return progress;
}
/**
* Sets the progress. For numeric progress, consider using
* {@link #setProgressIndex} and {@link #setProgressTotal} instead.
*/
public void setProgress(String newProgress) {
progress = newProgress;
}
/**
* Returns the progress index.
*
* @return {@code -1} if the progress index isn't available.
*/
public long getProgressIndex() {
return progressIndex;
}
/** Sets the progress index. Also updates the progress string. */
public void setProgressIndex(long newProgressIndex) {
progressIndex = newProgressIndex;
setProgressAutomatically();
}
/**
* Adds the given {@code amount} to the progress index. Also updates
* the progress string.
*/
public void addProgressIndex(long amount) {
setProgressIndex(getProgressIndex() + amount);
}
/**
* Returns the progress total.
*
* @return {@code -1} if the progress total isn't available.
*/
public long getProgressTotal() {
return progressTotal;
}
/** Sets the progress total. Also updates the progress string. */
public void setProgressTotal(long newProgressTotal) {
progressTotal = newProgressTotal;
setProgressAutomatically();
}
private void setProgressAutomatically() {
StringBuilder progress = new StringBuilder();
long index = getProgressIndex();
progress.append(index);
progress.append('/');
long total = getProgressTotal();
if (total < 0) {
progress.append('?');
} else {
progress.append(total);
progress.append(" (");
progress.append(index / (double) total * 100.0);
progress.append(')');
}
setProgress(progress.toString());
}
/**
* Returns the exception thrown from the last run of this task.
*
* @return {@code null} if there wasn't an error.
*/
public Throwable getLastException() {
return lastException;
}
/** Returns the number of times that this task ran. */
public long getRunCount() {
return runCount.get();
}
@Override
public int compareTo(Task other) {
return getName().compareTo(other.getName());
}
/** Returns {@code true} if this task should continue running. */
protected boolean shouldContinue() {
if (isInterrupted() || isStopRequested()) {
return false;
}
synchronized (isPauseRequested) {
while (isPauseRequested()) {
try {
isPauseRequested.wait();
} catch (InterruptedException ex) {
return false;
}
}
}
return true;
}
/** Called by {@link #run} to execute the actual task logic. */
protected abstract void doTask() throws Exception;
@Override
public final void run() {
if (!isRunning.compareAndSet(false, true)) {
LOGGER.debug("[{}] already running!", getName());
return;
}
// If running in Tomcat and this task belongs to an undeployed
// application, stop running immediately.
ClassLoader loader = getClass().getClassLoader();
Class<?> loaderClass = loader.getClass();
String loaderClassName = loaderClass.getName();
if ("org.apache.catalina.loader.WebappClassLoader".equals(loaderClassName)) {
try {
Field startedField = loaderClass.getDeclaredField("started");
startedField.setAccessible(true);
if (Boolean.FALSE.equals(startedField.get(loader))) {
stop();
return;
}
} catch (IllegalAccessException error) {
// This should never happen since #setAccessible is called
// on the field.
} catch (NoSuchFieldException error) {
// In case this code is used on future versions of Tomcat that
// doesn't use the field any more.
}
}
try {
LOGGER.debug("Begin running [{}]", getName());
thread = Thread.currentThread();
lastRunBegin = System.currentTimeMillis();
lastRunEnd = -1;
progress = null;
progressIndex = 0;
progressTotal = -1;
lastException = null;
if (shouldContinue()) {
doTask();
}
} catch (Throwable ex) {
LOGGER.warn(String.format("Error running [%s]!", getName()), ex);
lastException = ex;
} finally {
LOGGER.debug("End running [{}]", getName());
thread = null;
lastRunEnd = System.currentTimeMillis();
runCount.incrementAndGet();
isRunning.set(false);
isPauseRequested.set(false);
isStopRequested.set(false);
}
}
/**
* @deprecated Use {@link TaskExecutor.Static#getAll} and
* {@link TaskExecutor#getTasks} instead.
*/
@Deprecated
public static List<Task> getInstances() {
List<Task> tasks = new ArrayList<Task>();
for (TaskExecutor executor : TaskExecutor.Static.getAll()) {
for (Object taskObject : executor.getTasks()) {
if (taskObject instanceof Task) {
tasks.add((Task) taskObject);
}
}
}
return tasks;
}
/**
* Creates an instance that will run in the default executor
* with the given {@code name}.
*
* @param name If blank, this task will be named based on its
* class name and the count of all instances created so far.
*
* @deprecated Use {@link #Task(String, String)} instead.
*/
@Deprecated
protected Task(String name) {
this(null, name);
}
/** @deprecated Use {@link #getLastRunBegin} instead. */
@Deprecated
public Date getStartTime() {
return new Date(lastRunBegin);
}
/** @deprecated Use {@link #getLastRunEnd} instead. */
@Deprecated
public Date getStopTime() {
return new Date(lastRunEnd);
}
/** @deprecated Use {@link #getRunDuration} instead. */
@Deprecated
public Long getDuration() {
long runDuration = getRunDuration();
return runDuration > 0 ? runDuration : null;
}
/** @deprecated Use {@link #getRunCount} instead. */
@Deprecated
public long getCount() {
return runCount.get();
}
/** @deprecated Use {@link #submit} instead. */
@Deprecated
public void start() {
submit();
}
/** @deprecated Use {@link #schedule(double)} instead. */
@Deprecated
public void scheduleOnce(double initialDelay) {
schedule(initialDelay);
}
/** @deprecated Use {@link #scheduleWithFixedDelay} instead. */
@Deprecated
public void schedule(double initialDelay, double periodicDelay) {
scheduleWithFixedDelay(initialDelay, periodicDelay);
}
} |
package main;
public class BlankClass {
public static void main(String[] args) {
}
} |
import java.util.* ;
import java.io.* ;
import java.lang.* ;
public class PlayGame
{
public static int nodes ;
/**
* print the possible actions
*/
public static void printActions ( Vector v )
{
Iterator< int [] > itSucc = v.iterator () ;
for ( ; itSucc.hasNext () ; )
{
int [] pair = itSucc.next () ;
System.out.println ( pair [ 0 ] + ", " + pair [ 1 ] ) ;
}
}
/**
* testPlay: this test the actions, the
*/
public static void testPlay ()
{
State board = new State () ;
Vector actions = new Vector< int [] > () ;
System.out.println ( board.toString () ) ;
while ( board.terminal () == false )
{
System.out.println ( board.toString () ) ;
System.out.println ( "Player " + board.getPlayer () ) ;
actions = board.action () ;
Iterator< int [] > itSucc = actions.iterator () ;
printActions ( actions ) ;
int [] a = new int [ 2 ] ;
int player = board.getPlayer () ;
a = itSucc.next () ;
// play the first available move
State c = board.result ( player , a [ 0 ] , a [ 1 ] ) ;
board = c ;
}
System.out.println ( "Final? " + board.terminal () ) ;
System.out.println ( "Value? " + board.utility () ) ;
}
public static void testPlayOptimal ()
{
// State board = new State();
//State board = new State ( 2 , 1 , 0 , 0 , 1 , 0 , 0 , 2 , 0 ) ;
nodes = 0 ;
State board = new State ( 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 ) ;
while ( board.terminal () == false )
{
int [] move = minimax ( board ) ;
System.out.println ( "Player: " + board.getPlayer () +
"\nMove: (" + move [ 0 ] + "," + move [ 1 ] +
") => value " + move [ 2 ] ) ;
State c = board.result ( board.getPlayer () , move [ 0 ] , move [ 1 ] ) ;
board = c.copy () ;
System.out.println ( "Board \n" + board.toString () ) ;
}
System.out.println ( "Final? " + board.terminal () ) ;
System.out.println ( "Value? " + board.utility () ) ;
System.out.println ( "Nodes created: " + nodes ) ;
System.out.println ( "\n\n\n\n" ) ;
nodes = 0 ;
board = new State ( 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 ) ;
//board = new State ( 2 , 1 , 0 , 0 , 1 , 0 , 0 , 2 , 0 ) ;
while ( board.terminal () == false )
{
int [] move = alphabeta ( board ) ;
System.out.println ( "Player: " + board.getPlayer () +
"\nMove: (" + move [ 0 ] + "," + move [ 1 ] +
") => value " + move [ 2 ] ) ;
State c = board.result ( board.getPlayer () , move [ 0 ] , move [ 1 ] ) ;
board = c.copy () ;
System.out.println ( "Board \n" + board.toString () ) ;
}
System.out.println ( "Final? " + board.terminal () ) ;
System.out.println ( "Value? " + board.utility () ) ;
System.out.println ( "Nodes created: " + nodes ) ;
}
/**
* testAction used for testing the computation of
* possible actions in a given configuration
*/
public static void testAction ()
{
State board = new State () ;
Vector actions = new Vector<int[]> () ;
System.out.println ( board.toString () ) ;
actions = board.action () ;
printActions ( actions ) ;
System.out.println ( "After setting 1 at 0 0" ) ;
board.setAt ( 1 , 0 , 0 ) ;
actions = board.action () ;
printActions ( actions ) ;
}
/**
* Test the utility function
*/
public static void testUtility ()
{
State board = new State ( 1 , 1 , 1 , 2 , 2 , 0 , 0 , 0 , 0 ) ;
System.out.println ( board.toString () ) ;
System.out.println ( "Final? " + board.terminal () ) ;
System.out.println ( "Value? " + board.utility () ) ;
board = new State ( 1 , 1 , 0 , 2 , 2 , 2 , 1 , 0 , 0 ) ;
System.out.println ( board.toString () ) ;
System.out.println ( "Final? " + board.terminal () ) ;
System.out.println ( "Value? " + board.utility () ) ;
board = new State ( 1 , 1 , 2 , 2 , 2 , 2 , 1 , 1 , 0 ) ;
System.out.println ( board.toString () ) ;
System.out.println ( "Final? " + board.terminal () ) ;
System.out.println ( "Value? " + board.utility () ) ;
board = new State ( 1 , 1 , 2 , 1 , 2 , 1 , 2 , 1 , 2 ) ;
System.out.println ( board.toString () ) ;
System.out.println ( "Final? " + board.terminal () ) ;
System.out.println ( "Value? " + board.utility () ) ;
}
/**
* Minimax
*
* This generates a gametree that calculates every possible move recursively
* to discover the move which is most beneficial to make. This will block a
* move that exists and allows the opposing player to win the game as well
* as win the game if a game winning move exists.
*
* @param s state the current state of the board
* @return returns the result of the serach.
* move[0]: the row to make the move
* move[1]: the column to make the move
* move[2]: the utility cost of the move
*/
public static int [] minimax ( State s )
{
Vector< int [] > actions = s.action () ;
int [] result = new int [ 3 ] ;
// start the result at "negative infinity"
result [ 2 ] = Integer.MIN_VALUE ;
for ( int i = 0 ; i < actions.size () ; i ++ )
{
nodes ++ ; // track nodes created, used for testing
int [] move = actions.elementAt ( i ) ;
int value = minvalue ( s.result (
s.getPlayer () , move [ 0 ] , move [ 1 ] ) ) ;
if ( value > result [ 2 ] )
{
result [ 0 ] = move [ 0 ] ;
result [ 1 ] = move [ 1 ] ;
result [ 2 ] = value ;
}
}
return result ;
}
/**
* MinValue
*
* Recursively finds the minimum maximum value from available actions.
*
* @param s state the current state of the board
* @return the utility score of the best move
*/
public static int minvalue ( State s )
{
if ( s.terminal () == true )
{
// if player 1, negate the result to get the MIN perspective
if ( s.getPlayer () == 1 )
return -s.utility () ;
return s.utility () ;
}
Vector< int [] > actions = s.action () ;
// start score at "possitive infinity"
int score = Integer.MAX_VALUE ;
int [] move = new int [ 2 ] ;
for ( int i = 0 ; i < actions.size () ; i ++ )
{
nodes ++ ; // track nodes created, used for testing
move = actions.elementAt ( i ) ;
score = Math.min ( score,
maxvalue ( s.result (
s.getPlayer () , move [ 0 ] , move [ 1 ] ) ) ) ;
}
return score ;
}
/**
* MaxValue
*
* Recursively finds the maximum minimum value from available actions.
*
* @param s state the current state of the board
* @return the utility score of the best move
*/
public static int maxvalue ( State s )
{
if ( s.terminal () == true )
{
if ( s.getPlayer () == 1 )
return s.utility () ;
// if player 2, negate the result to get MIN perspective
return -s.utility () ;
}
Vector< int [] > actions = s.action () ;
// start score at "negative infinity"
int score = Integer.MIN_VALUE ;
int [] move = new int [ 2 ] ;
for ( int i = 0 ; i < actions.size () ; i ++ )
{
nodes ++ ; // track nodes created, used for testing
move = actions.elementAt ( i ) ;
score = Math.max ( score ,
minvalue ( s.result (
s.getPlayer () , move [ 0 ] , move [ 1 ] ) ) ) ;
}
return score ;
}
/**
* Alpha-Beta Pruning
*
* This generates a gametree that prunes the results as soon as it has found
* a minimum that is lower than another branch of the subtree.
*
* @param s state the current state of the board
* @return returns the result of the serach.
* move[0]: the row to make the move
* move[1]: the column to make the move
* move[2]: the utility cost of the move
*/
public static int [] alphabeta ( State s )
{
Vector< int [] > actions = s.action () ;
int [] result = new int [ 3 ] ;
// start score at "negative infinity"
result [ 2 ] = Integer.MIN_VALUE ;
for ( int i = 0 ; i < actions.size () ; i ++ )
{
nodes ++ ; // track nodes created, used for testing
int [] move = actions.elementAt ( i ) ;
int value = abMinValue ( s.result (
s.getPlayer () , move [ 0 ] , move [ 1 ] ) ,
Integer.MIN_VALUE , Integer.MAX_VALUE ) ;
if ( value > result [ 2 ] )
{
result [ 0 ] = move [ 0 ] ;
result [ 1 ] = move [ 1 ] ;
result [ 2 ] = value ;
}
}
return result ;
}
/**
* Alpha-Beta MaxValue
*
* Recursively finds the maximum minimum value from available actions.
*
* @param s state the current state of the board
* @param a alpha the maximum value found in the chains
* @param b beta the minimum value found in the chains
* @return the utility score of the best move
*/
public static int abMaxValue ( State s , int a , int b )
{
if ( s.terminal () == true )
{
if ( s.getPlayer () == 1 )
return s.utility () ;
// if player 2, negate the result to get MIN perspective
return -s.utility () ;
}
Vector< int [] > actions = s.action () ;
// start score at "negative infinity"
int score = Integer.MIN_VALUE ;
int [] move = new int [ 2 ] ;
for ( int i = 0 ; i < actions.size () ; i ++ )
{
nodes ++ ; // track nodes created, used for testing
move = actions.elementAt ( i ) ;
score = Math.max ( score ,
abMinValue ( s.result (
s.getPlayer () , move [ 0 ] , move [ 1 ] ) , a , b ) ) ;
if ( score >= b )
return score ;
a = Math.max ( a , score ) ;
}
return score ;
}
/**
* Alpha-Beta MinValue
*
* Recursively finds the minimum maximum value from available actions.
*
* @param s state the current state of the board
* @param a alpha the maximum value found in the chains
* @param b beta the minimum value found in the chains
* @return the utility score of the best move
*/
public static int abMinValue ( State s , int a , int b )
{
if ( s.terminal () == true )
{
// if player 1, negate the result to get the MIN perspective
if ( s.getPlayer () == 1 )
return -s.utility () ;
return s.utility () ;
}
Vector< int [] > actions = s.action () ;
// start score at "possitive infinity"
int score = Integer.MAX_VALUE ;
int [] move = new int [ 2 ] ;
for ( int i = 0 ; i < actions.size () ; i ++ )
{
nodes ++ ; // track nodes created, used for testing
move = actions.elementAt ( i ) ;
score = Math.min ( score,
abMaxValue ( s.result (
s.getPlayer () , move [ 0 ] , move [ 1 ] ) , a , b ) ) ;
if ( score <= a )
return score ;
b = Math.min ( b , score ) ;
}
return score ;
}
/**
* @param args
*/
public static void main ( String [] args )
{
//testAction();
//testUtility();
testPlayOptimal();
/*State board = new State(2,1,1,0,1,0,0,2,0);
board.setPlayer(2);
int[] move = minvalue(board);
System.out.println(board.toString());
System.out.println("Move: ("+move[0]+","+move[1]+") => value " + move[2]);
*/
}
} |
import java.awt.Image;
import java.net.URL;
public class MediaCheck {
public static void media(URL url) {
Image image = null;
}
} |
package cpw.mods.fml.server;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.Collections;
import java.util.List;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import java.util.zip.ZipEntry;
import java.util.zip.ZipFile;
import org.apache.commons.io.IOUtils;
import com.google.common.collect.ImmutableList;
import com.google.common.collect.MapDifference;
import net.minecraft.entity.Entity;
import net.minecraft.network.INetworkManager;
import net.minecraft.network.packet.NetHandler;
import net.minecraft.network.packet.Packet;
import net.minecraft.network.packet.Packet131MapData;
import net.minecraft.server.MinecraftServer;
import net.minecraft.util.StringTranslate;
import net.minecraft.world.World;
import cpw.mods.fml.common.FMLCommonHandler;
import cpw.mods.fml.common.FMLLog;
import cpw.mods.fml.common.IFMLSidedHandler;
import cpw.mods.fml.common.Loader;
import cpw.mods.fml.common.ModContainer;
import cpw.mods.fml.common.ObfuscationReflectionHelper;
import cpw.mods.fml.common.network.EntitySpawnAdjustmentPacket;
import cpw.mods.fml.common.network.EntitySpawnPacket;
import cpw.mods.fml.common.network.ModMissingPacket;
import cpw.mods.fml.common.registry.EntityRegistry.EntityRegistration;
import cpw.mods.fml.common.registry.GameData;
import cpw.mods.fml.common.registry.GameRegistry;
import cpw.mods.fml.common.registry.ItemData;
import cpw.mods.fml.common.registry.LanguageRegistry;
import cpw.mods.fml.relauncher.Side;
/**
* Handles primary communication from hooked code into the system
*
* The FML entry point is {@link #beginServerLoading(MinecraftServer)} called from
* {@link net.minecraft.server.dedicated.DedicatedServer}
*
* Obfuscated code should focus on this class and other members of the "server"
* (or "client") code
*
* The actual mod loading is handled at arms length by {@link Loader}
*
* It is expected that a similar class will exist for each target environment:
* Bukkit and Client side.
*
* It should not be directly modified.
*
* @author cpw
*
*/
public class FMLServerHandler implements IFMLSidedHandler
{
/**
* The singleton
*/
private static final FMLServerHandler INSTANCE = new FMLServerHandler();
/**
* A reference to the server itself
*/
private MinecraftServer server;
private FMLServerHandler()
{
FMLCommonHandler.instance().beginLoading(this);
}
/**
* Called to start the whole game off from
* {@link MinecraftServer#startServer}
*
* @param minecraftServer
*/
public void beginServerLoading(MinecraftServer minecraftServer)
{
server = minecraftServer;
Loader.instance().loadMods();
}
/**
* Called a bit later on during server initialization to finish loading mods
*/
public void finishServerLoading()
{
Loader.instance().initializeMods();
LanguageRegistry.reloadLanguageTable();
GameData.initializeServerGate(1);
}
@Override
public void haltGame(String message, Throwable exception)
{
throw new RuntimeException(message, exception);
}
/**
* Get the server instance
*/
public MinecraftServer getServer()
{
return server;
}
/**
* @return the instance
*/
public static FMLServerHandler instance()
{
return INSTANCE;
}
/* (non-Javadoc)
* @see cpw.mods.fml.common.IFMLSidedHandler#getAdditionalBrandingInformation()
*/
@Override
public List<String> getAdditionalBrandingInformation()
{
return ImmutableList.<String>of();
}
/* (non-Javadoc)
* @see cpw.mods.fml.common.IFMLSidedHandler#getSide()
*/
@Override
public Side getSide()
{
return Side.SERVER;
}
@Override
public void showGuiScreen(Object clientGuiElement)
{
}
@Override
public Entity spawnEntityIntoClientWorld(EntityRegistration er, EntitySpawnPacket packet)
{
// NOOP
return null;
}
@Override
public void adjustEntityLocationOnClient(EntitySpawnAdjustmentPacket entitySpawnAdjustmentPacket)
{
// NOOP
}
@Override
public void sendPacket(Packet packet)
{
throw new RuntimeException("You cannot send a bare packet without a target on the server!");
}
@Override
public void displayMissingMods(ModMissingPacket modMissingPacket)
{
// NOOP on server
}
@Override
public void handleTinyPacket(NetHandler handler, Packet131MapData mapData)
{
// NOOP on server
}
@Override
public void setClientCompatibilityLevel(byte compatibilityLevel)
{
// NOOP on server
}
@Override
public byte getClientCompatibilityLevel()
{
return 0;
}
@Override
public boolean shouldServerShouldBeKilledQuietly()
{
return false;
}
@Override
public void disconnectIDMismatch(MapDifference<Integer, ItemData> s, NetHandler handler, INetworkManager mgr)
{
}
@Override
public void addModAsResource(ModContainer container)
{
File source = container.getSource();
try
{
if (source.isDirectory())
{
searchDirForENUSLanguage(source,"");
}
else
{
searchZipForENUSLanguage(source);
}
}
catch (IOException ioe)
{
}
}
private static final Pattern assetENUSLang = Pattern.compile("assets/(.*)/lang/en_US.lang");
private void searchZipForENUSLanguage(File source) throws IOException
{
ZipFile zf = new ZipFile(source);
for (ZipEntry ze : Collections.list(zf.entries()))
{
Matcher matcher = assetENUSLang.matcher(ze.getName());
if (matcher.matches())
{
FMLLog.fine("Injecting found translation data in zip file %s at %s into language system", source.getName(), ze.getName());
StringTranslate.inject(zf.getInputStream(ze));
}
}
zf.close();
}
private void searchDirForENUSLanguage(File source, String path) throws IOException
{
for (File file : source.listFiles())
{
String currPath = path+file.getName();
if (file.isDirectory())
{
searchDirForENUSLanguage(file, currPath+'/');
}
Matcher matcher = assetENUSLang.matcher(currPath);
if (matcher.matches())
{
FMLLog.fine("Injecting found translation data at %s into language system", currPath);
StringTranslate.inject(new FileInputStream(file));
}
}
}
@Override
public void updateResourcePackList()
{
}
} |
package com.ecyrd.jspwiki.providers;
import java.io.IOException;
import java.util.*;
import org.apache.log4j.Logger;
import com.ecyrd.jspwiki.*;
import com.ecyrd.jspwiki.parser.MarkupParser;
import com.ecyrd.jspwiki.render.RenderingManager;
import com.ecyrd.jspwiki.util.ClassUtil;
import com.opensymphony.oscache.base.Cache;
import com.opensymphony.oscache.base.NeedsRefreshException;
import com.opensymphony.oscache.base.events.*;
/**
* Provides a caching page provider. This class rests on top of a
* real provider class and provides a cache to speed things up. Only
* if the cache copy of the page text has expired, we fetch it from
* the provider.
* <p>
* This class also detects if someone has modified the page
* externally, not through JSPWiki routines, and throws the proper
* RepositoryModifiedException.
* <p>
* Heavily based on ideas by Chris Brooking.
* <p>
* Since 2.1.52 uses the OSCache library from OpenSymphony.
*
* @author Janne Jalkanen
* @since 1.6.4
* @see RepositoryModifiedException
*/
// FIXME: Synchronization is a bit inconsistent in places.
// FIXME: A part of the stuff is now redundant, since we could easily use the text cache
// for a lot of things. RefactorMe.
public class CachingProvider
implements WikiPageProvider, VersioningProvider
{
private static final Logger log = Logger.getLogger(CachingProvider.class);
private WikiPageProvider m_provider;
// FIXME: Find another way to the search engine to use instead of from WikiEngine?
private WikiEngine m_engine;
private Cache m_cache;
private Cache m_negCache; // Cache for holding non-existing pages
private Cache m_textCache;
private Cache m_historyCache;
private long m_cacheMisses = 0;
private long m_cacheHits = 0;
private long m_historyCacheMisses = 0;
private long m_historyCacheHits = 0;
private int m_expiryPeriod = 30;
/**
* This can be very long, as normally all modifications are noticed in an earlier
* stage.
*/
private int m_pageContentExpiryPeriod = 24*60*60;
// FIXME: This MUST be cached somehow.
private boolean m_gotall = false;
private CacheItemCollector m_allCollector = new CacheItemCollector();
/**
* Defines, in seconds, the amount of time a text will live in the cache
* at most before requiring a refresh.
*/
public static final String PROP_CACHECHECKINTERVAL = "jspwiki.cachingProvider.cacheCheckInterval";
public static final String PROP_CACHECAPACITY = "jspwiki.cachingProvider.capacity";
private static final int DEFAULT_CACHECAPACITY = 1000; // Good most wikis
private static final String OSCACHE_ALGORITHM = "com.opensymphony.oscache.base.algorithm.LRUCache";
public void initialize( WikiEngine engine, Properties properties )
throws NoRequiredPropertyException,
IOException
{
log.debug("Initing CachingProvider");
// engine is used for getting the search engine
m_engine = engine;
// Cache consistency checks
m_expiryPeriod = TextUtil.getIntegerProperty( properties,
PROP_CACHECHECKINTERVAL,
m_expiryPeriod );
log.debug("Cache expiry period is "+m_expiryPeriod+" s");
// Text cache capacity
int capacity = TextUtil.getIntegerProperty( properties,
PROP_CACHECAPACITY,
DEFAULT_CACHECAPACITY );
log.debug("Cache capacity "+capacity+" pages.");
m_cache = new Cache( true, false, false );
// OSCache documentation sucks big time. The clazz-parameter is completely
// undefined; I had to read the source code to figure out that you need
// to declare what type of a listener you are adding by sending the type
// of the interface.
m_cache.addCacheEventListener( m_allCollector, CacheEntryEventListener.class );
// FIXME: There's an interesting issue here... It would probably be
// possible to DOS a JSPWiki instance by bombarding it with names that
// do not exist, as they would fill the negcache. Will need to
// think about this some more...
m_negCache = new Cache( true, false, false );
m_textCache = new Cache( true, false, false,
false,
OSCACHE_ALGORITHM,
capacity );
m_historyCache = new Cache( true, false, false, false,
OSCACHE_ALGORITHM,
capacity );
// Find and initialize real provider.
String classname = WikiEngine.getRequiredProperty( properties,
PageManager.PROP_PAGEPROVIDER );
try
{
Class providerclass = ClassUtil.findClass( "com.ecyrd.jspwiki.providers",
classname );
m_provider = (WikiPageProvider)providerclass.newInstance();
log.debug("Initializing real provider class "+m_provider);
m_provider.initialize( engine, properties );
}
catch( ClassNotFoundException e )
{
log.error("Unable to locate provider class "+classname,e);
throw new IllegalArgumentException("no provider class");
}
catch( InstantiationException e )
{
log.error("Unable to create provider class "+classname,e);
throw new IllegalArgumentException("faulty provider class");
}
catch( IllegalAccessException e )
{
log.error("Illegal access to provider class "+classname,e);
throw new IllegalArgumentException("illegal provider class");
}
}
private WikiPage getPageInfoFromCache( String name )
throws ProviderException,
RepositoryModifiedException
{
boolean wasUpdated = false;
// Sanity check; seems to occur sometimes
if( name == null ) return null;
try
{
WikiPage item = (WikiPage)m_cache.getFromCache( name, m_expiryPeriod );
wasUpdated = true;
if( item != null )
return item;
return null;
}
catch( NeedsRefreshException e )
{
WikiPage cached = (WikiPage)e.getCacheContent();
// int version = (cached != null) ? cached.getVersion() : WikiPageProvider.LATEST_VERSION;
WikiPage refreshed;
// Just be careful that we don't accidentally leave the cache in a
// hung state
refreshed = m_provider.getPageInfo( name, WikiPageProvider.LATEST_VERSION );
if( refreshed == null && cached != null )
{
// Page has been removed evilly by a goon from outer space
log.debug("Page "+name+" has been removed externally.");
m_cache.putInCache( name, null );
m_textCache.putInCache( name, null );
m_historyCache.putInCache( name, null );
// We cache a page miss
m_negCache.putInCache( name, name );
wasUpdated = true;
throw new RepositoryModifiedException( "Removed: "+name, name );
}
else if( cached == null )
{
// The page did not exist in the first place
if( refreshed != null )
{
// We must now add it
m_cache.putInCache( name, refreshed );
// Requests for this page are now no longer denied
m_negCache.putInCache( name, null );
wasUpdated = true;
throw new RepositoryModifiedException( "Added: "+name, name );
}
// Cache page miss
m_negCache.putInCache( name, name );
}
else if( cached.getVersion() != refreshed.getVersion() )
{
// The newest version has been deleted, but older versions still remain
log.debug("Page "+cached.getName()+" newest version deleted, reloading...");
m_cache.putInCache( name, refreshed );
// Requests for this page are now no longer denied
m_negCache.putInCache( name, null );
m_textCache.flushEntry( name );
m_historyCache.flushEntry( name );
wasUpdated = true;
return refreshed;
}
else if( Math.abs(refreshed.getLastModified().getTime()-cached.getLastModified().getTime()) > 1000L )
{
// Yes, the page has been modified externally and nobody told us
log.info("Page "+cached.getName()+" changed, reloading...");
m_cache.putInCache( name, refreshed );
// Requests for this page are now no longer denied
m_negCache.putInCache( name, null );
m_textCache.flushEntry( name );
m_historyCache.flushEntry( name );
wasUpdated = true;
throw new RepositoryModifiedException( "Modified: "+name, name );
}
else
{
// Refresh the cache by putting the same object back
m_cache.putInCache( name, cached );
// Requests for this page are now no longer denied
m_negCache.putInCache( name, null );
wasUpdated = true;
}
return cached;
}
finally
{
if( !wasUpdated )
m_cache.cancelUpdate(name);
}
}
public boolean pageExists( String pageName, int version )
{
if( pageName == null ) return false;
// First, check the negative cache if we've seen it before
try
{
String isNonExistant = (String) m_negCache.getFromCache( pageName, m_expiryPeriod );
if( isNonExistant != null ) return false; // No such page
}
catch( NeedsRefreshException e )
{
m_negCache.cancelUpdate(pageName);
}
WikiPage p = null;
try
{
p = getPageInfoFromCache( pageName );
}
catch( RepositoryModifiedException e )
{
// The repository was modified, we need to check now if the page was removed or
// added.
// TODO: This information would be available in the exception, but we would
// need to subclass.
try
{
p = getPageInfoFromCache( pageName );
}
catch( Exception ex ) { return false; } // This should not happen
}
catch( ProviderException e )
{
log.info("Provider failed while trying to check if page exists: "+pageName);
return false;
}
if( p != null )
{
int latestVersion = p.getVersion();
if( version == latestVersion || version == LATEST_VERSION )
{
return true;
}
if( m_provider instanceof VersioningProvider )
return ((VersioningProvider) m_provider).pageExists( pageName, version );
}
try
{
return getPageInfo( pageName, version ) != null;
}
catch( ProviderException e )
{}
return false;
}
public boolean pageExists( String pageName )
{
if( pageName == null ) return false;
// First, check the negative cache if we've seen it before
try
{
String isNonExistant = (String) m_negCache.getFromCache( pageName, m_expiryPeriod );
if( isNonExistant != null ) return false; // No such page
}
catch( NeedsRefreshException e )
{
m_negCache.cancelUpdate(pageName);
}
WikiPage p = null;
try
{
p = getPageInfoFromCache( pageName );
}
catch( RepositoryModifiedException e )
{
// The repository was modified, we need to check now if the page was removed or
// added.
// TODO: This information would be available in the exception, but we would
// need to subclass.
try
{
p = getPageInfoFromCache( pageName );
}
catch( Exception ex ) { return false; } // This should not happen
}
catch( ProviderException e )
{
log.info("Provider failed while trying to check if page exists: "+pageName);
return false;
}
// A null item means that the page either does not
// exist, or has not yet been cached; a non-null
// means that the page does exist.
if( p != null )
{
return true;
}
// If we have a list of all pages in memory, then any page
// not in the cache must be non-existent.
// FIXME: There's a problem here; if someone modifies the
// repository by adding a page outside JSPWiki,
// we won't notice it.
if( m_gotall )
{
return false;
}
// We could add the page to the cache here as well,
// but in order to understand whether that is a
// good thing or not we would need to analyze
// the JSPWiki calling patterns extensively. Presumably
// it would be a good thing if pageExists() is called
// many times before the first getPageText() is called,
// and the whole page is cached.
return m_provider.pageExists( pageName );
}
/**
* @throws RepositoryModifiedException If the page has been externally modified.
*/
public String getPageText( String pageName, int version )
throws ProviderException,
RepositoryModifiedException
{
String result = null;
if( pageName == null ) return null;
if( version == WikiPageProvider.LATEST_VERSION )
{
result = getTextFromCache( pageName );
}
else
{
WikiPage p = getPageInfoFromCache( pageName );
// Or is this the latest version fetched by version number?
if( p != null && p.getVersion() == version )
{
result = getTextFromCache( pageName );
}
else
{
result = m_provider.getPageText( pageName, version );
}
}
return result;
}
/**
* @throws RepositoryModifiedException If the page has been externally modified.
*/
private String getTextFromCache( String pageName )
throws ProviderException,
RepositoryModifiedException
{
String text;
boolean wasUpdated = false;
if( pageName == null ) return null;
WikiPage page = getPageInfoFromCache( pageName );
try
{
text = (String)m_textCache.getFromCache( pageName,
m_pageContentExpiryPeriod );
wasUpdated = true;
if( text == null )
{
if( page != null )
{
text = m_provider.getPageText( pageName, WikiPageProvider.LATEST_VERSION );
m_textCache.putInCache( pageName, text );
m_cacheMisses++;
}
else
{
return null;
}
}
else
{
m_cacheHits++;
}
}
catch( NeedsRefreshException e )
{
if( pageExists(pageName) )
{
text = m_provider.getPageText( pageName, WikiPageProvider.LATEST_VERSION );
m_textCache.putInCache( pageName, text );
wasUpdated = true;
m_cacheMisses++;
}
else
{
m_textCache.putInCache( pageName, null );
wasUpdated = true;
return null; // No page exists
}
}
finally
{
if( !wasUpdated )
m_textCache.cancelUpdate(pageName);
}
return text;
}
public void putPageText( WikiPage page, String text )
throws ProviderException
{
synchronized(this)
{
m_provider.putPageText( page, text );
page.setLastModified( new Date() );
// Refresh caches properly
m_cache.flushEntry( page.getName() );
m_textCache.flushEntry( page.getName() );
m_historyCache.flushEntry( page.getName() );
m_negCache.flushEntry( page.getName() );
// Refresh caches
try
{
getPageInfoFromCache( page.getName() );
}
catch(RepositoryModifiedException e) {} // Expected
}
}
public Collection getAllPages()
throws ProviderException
{
Collection all;
if( m_gotall == false )
{
all = m_provider.getAllPages();
// Make sure that all pages are in the cache.
synchronized(this)
{
for( Iterator i = all.iterator(); i.hasNext(); )
{
WikiPage p = (WikiPage) i.next();
m_cache.putInCache( p.getName(), p );
// Requests for this page are now no longer denied
m_negCache.putInCache( p.getName(), null );
}
m_gotall = true;
}
}
else
{
all = m_allCollector.getAllItems();
}
return all;
}
public Collection getAllChangedSince( Date date )
{
return m_provider.getAllChangedSince( date );
}
public int getPageCount()
throws ProviderException
{
return m_provider.getPageCount();
}
public Collection findPages( QueryItem[] query )
{
// If the provider is a fast searcher, then
// just pass this request through.
return m_provider.findPages( query );
// FIXME: Does not implement fast searching
}
// FIXME: Kludge: make sure that the page is also parsed and it gets all the
// necessary variables.
private void refreshMetadata( WikiPage page )
{
if( page != null && !page.hasMetadata() )
{
RenderingManager mgr = m_engine.getRenderingManager();
try
{
String data = m_provider.getPageText(page.getName(), page.getVersion());
WikiContext ctx = new WikiContext( m_engine, page );
MarkupParser parser = mgr.getParser( ctx, data );
parser.parse();
}
catch( Exception ex )
{
log.debug("Failed to retrieve variables for wikipage "+page);
}
}
}
public WikiPage getPageInfo( String pageName, int version )
throws ProviderException,
RepositoryModifiedException
{
WikiPage page = null;
WikiPage cached = getPageInfoFromCache( pageName );
int latestcached = (cached != null) ? cached.getVersion() : Integer.MIN_VALUE;
if( version == WikiPageProvider.LATEST_VERSION ||
version == latestcached )
{
if( cached == null )
{
WikiPage data = m_provider.getPageInfo( pageName, version );
if( data != null )
{
m_cache.putInCache( pageName, data );
// Requests for this page are now no longer denied
m_negCache.putInCache( pageName, null );
}
page = data;
}
else
{
page = cached;
}
}
else
{
// We do not cache old versions.
page = m_provider.getPageInfo( pageName, version );
//refreshMetadata( page );
}
refreshMetadata( page );
return page;
}
public List getVersionHistory( String pageName )
throws ProviderException
{
List history = null;
boolean wasUpdated = false;
if( pageName == null ) return null;
try
{
history = (List)m_historyCache.getFromCache( pageName,
m_expiryPeriod );
log.debug("History cache hit for page "+pageName);
m_historyCacheHits++;
wasUpdated = true;
}
catch( NeedsRefreshException e )
{
history = m_provider.getVersionHistory( pageName );
m_historyCache.putInCache( pageName, history );
log.debug("History cache miss for page "+pageName);
m_historyCacheMisses++;
wasUpdated = true;
}
finally
{
if( !wasUpdated ) m_historyCache.cancelUpdate( pageName );
}
return history;
}
public synchronized String getProviderInfo()
{
return("Real provider: "+m_provider.getClass().getName()+
". Cache misses: "+m_cacheMisses+
". Cache hits: "+m_cacheHits+
". History cache hits: "+m_historyCacheHits+
". History cache misses: "+m_historyCacheMisses+
". Cache consistency checks: "+m_expiryPeriod+"s");
}
public void deleteVersion( String pageName, int version )
throws ProviderException
{
// Luckily, this is such a rare operation it is okay
// to synchronize against the whole thing.
synchronized( this )
{
WikiPage cached = getPageInfoFromCache( pageName );
int latestcached = (cached != null) ? cached.getVersion() : Integer.MIN_VALUE;
// If we have this version cached, remove from cache.
if( version == WikiPageProvider.LATEST_VERSION ||
version == latestcached )
{
m_cache.flushEntry( pageName );
m_textCache.putInCache( pageName, null );
m_historyCache.putInCache( pageName, null );
}
m_provider.deleteVersion( pageName, version );
}
}
public void deletePage( String pageName )
throws ProviderException
{
// See note in deleteVersion().
synchronized(this)
{
m_cache.putInCache( pageName, null );
m_textCache.putInCache( pageName, null );
m_historyCache.putInCache( pageName, null );
m_negCache.putInCache( pageName, pageName );
m_provider.deletePage( pageName );
}
}
public void movePage( String from,
String to )
throws ProviderException
{
m_provider.movePage( from, to );
synchronized(this)
{
// Clear any cached version of the old page
log.debug("Removing page "+from+" from cache");
m_cache.flushEntry( from );
// Clear the cache for the to page, if that page already exists
//if ( m_cache.get( to ) != null )
log.debug("Removing page "+to+" from cache");
m_cache.flushEntry( to );
}
}
/**
* Returns the actual used provider.
* @since 2.0
*/
public WikiPageProvider getRealProvider()
{
return m_provider;
}
/**
* This is a simple class that keeps a list of all WikiPages that
* we have in memory. Because the OSCache cannot give us a list
* of all pages currently in cache, we'll have to check this
* ourselves.
*
* @author jalkanen
*
* @since 2.4
*/
private class CacheItemCollector
implements CacheEntryEventListener
{
private Map m_allItems = new HashMap();
/**
* Returns a clone of the set - you cannot manipulate this.
*
* @return
*/
public Set getAllItems()
{
Set ret = new TreeSet();
ret.addAll(m_allItems.values());
return ret;
}
public void cacheEntryAdded( CacheEntryEvent arg0 )
{
cacheEntryUpdated( arg0 );
}
public void cachePatternFlushed( CachePatternEvent ev )
{
}
public void cacheGroupFlushed( CacheGroupEvent ev )
{
}
public void cacheFlushed( CachewideEvent ev )
{
}
public void cacheEntryFlushed( CacheEntryEvent arg0 )
{
cacheEntryRemoved( arg0 );
}
public void cacheEntryRemoved( CacheEntryEvent arg0 )
{
WikiPage item = (WikiPage) arg0.getEntry().getContent();
if( item != null )
{
m_allItems.remove( item );
}
}
public void cacheEntryUpdated( CacheEntryEvent arg0 )
{
WikiPage item = (WikiPage) arg0.getEntry().getContent();
if( item != null )
{
// Item added or replaced.
m_allItems.put( item.getName(), item );
}
else
{
// Removed item
// FIXME: If the page system is changed during this time, we'll just fail gracefully
m_allItems.remove( arg0.getKey() );
}
}
}
} |
package com.gmail.harleenssahni.mbr;
import java.util.List;
import java.util.concurrent.Executors;
import java.util.concurrent.ScheduledExecutorService;
import java.util.concurrent.ScheduledFuture;
import java.util.concurrent.TimeUnit;
import android.app.ListActivity;
import android.content.BroadcastReceiver;
import android.content.ComponentName;
import android.content.Context;
import android.content.Intent;
import android.content.IntentFilter;
import android.content.pm.PackageManager;
import android.content.pm.ResolveInfo;
import android.media.MediaPlayer;
import android.media.MediaPlayer.OnCompletionListener;
import android.os.Bundle;
import android.os.PowerManager;
import android.os.PowerManager.WakeLock;
import android.speech.tts.TextToSpeech;
import android.speech.tts.TextToSpeech.OnInitListener;
import android.util.Log;
import android.view.KeyEvent;
import android.view.LayoutInflater;
import android.view.View;
import android.view.View.OnClickListener;
import android.view.ViewGroup;
import android.view.WindowManager;
import android.widget.BaseAdapter;
import android.widget.ImageView;
import android.widget.ListView;
import android.widget.TextView;
import com.gmail.harleenssahni.mbr.receivers.MediaButtonReceiver;
/**
* Allows the user to choose which media receiver will handle a media button
* press. Can be navigated via touch screen or media button keys. Provides voice
* feedback.
*
* @author harleenssahni@gmail.com
*/
public class MediaButtonList extends ListActivity implements OnInitListener {
private class SweepBroadcastReceiver extends BroadcastReceiver {
String name;
public SweepBroadcastReceiver(String name) {
this.name = name;
}
@Override
public void onReceive(Context context, Intent intent) {
Log.i(TAG, "After running broadcast receiver " + name + "have resultcode: " + getResultCode()
+ " result Data: " + getResultData());
}
}
/** Our tag for logging purposes and identification purposes. */
private static final String TAG = "MediaButtonRouter.Selector";
/**
* Key used to store and retrieve last selected receiver.
*/
private static final String SELECTION_KEY = "btButtonSelection";
/**
* Number of seconds to wait before timing out and just cancelling.
*/
private static final long TIMEOUT_TIME = 7;
/**
* The media button event that {@link MediaButtonReceiver} captured, and
* that we will be forwarding to a music player's {@code BroadcastReceiver}
* on selection.
*/
private KeyEvent trappedKeyEvent;
/**
* The {@code BroadcastReceiver}'s registered in the system for *
* {@link Intent.ACTION_MEDIA_BUTTON}.
*/
private List<ResolveInfo> receivers;
/** The intent filter for registering our local {@code BroadcastReceiver}. */
private IntentFilter uiIntentFilter;
/** The text to speech engine used to announce navigation to the user. */
private TextToSpeech textToSpeech;
/**
* The receiver currently selected by bluetooth next/prev navigation. We
* track this ourselves because there isn't persisted selection w/ touch
* screen interfaces.
*/
private int btButtonSelection;
/**
* Whether we've done the start up announcement to the user using the text
* to speech. Tracked so we don't repeat ourselves on orientation change.
*/
private boolean announced;
/**
* The power manager used to wake the device with a wake lock so that we can
* handle input. Allows us to have a regular activity life cycle when media
* buttons are pressed when and the screen is off.
*/
private PowerManager powerManager;
/**
* Used to wake up screen so that we can navigate our UI and select an app
* to handle media button presses when display is off.
*/
private WakeLock wakeLock;
/**
* Local broadcast receiver that allows us to handle media button events for
* navigation inside the activity.
*/
private BroadcastReceiver uiMediaReceiver = new BroadcastReceiver() {
@Override
public void onReceive(Context context, Intent intent) {
if (Intent.ACTION_MEDIA_BUTTON.equals(intent.getAction())) {
KeyEvent navigationKeyEvent = (KeyEvent) intent.getExtras().get(Intent.EXTRA_KEY_EVENT);
int keyCode = navigationKeyEvent.getKeyCode();
if (Utils.isMediaButton(keyCode)) {
Log.i(TAG, "Media Button Selector UI is directly handling key: " + navigationKeyEvent);
if (navigationKeyEvent.getAction() == KeyEvent.ACTION_UP) {
switch (keyCode) {
case KeyEvent.KEYCODE_MEDIA_NEXT:
moveSelection(1);
break;
case KeyEvent.KEYCODE_MEDIA_PREVIOUS:
moveSelection(-1);
break;
case KeyEvent.KEYCODE_MEDIA_PLAY_PAUSE:
select();
break;
case KeyEvent.KEYCODE_MEDIA_STOP:
// just cancel
finish();
break;
default:
break;
}
}
abortBroadcast();
}
}
}
};
/**
* ScheduledExecutorService used to time out and close activity if the user
* doesn't make a selection within certain amount of time. Resets on user
* interaction.
*/
private ScheduledExecutorService timeoutExecutor;
/**
* ScheduledFuture of timeout.
*/
private ScheduledFuture<?> timeoutScheduledFuture;
private View cancelButton;
private ImageView mediaImage;
private TextView header;
/**
* {@inheritDoc}
*/
@Override
public void onInit(int status) {
// text to speech initialized
// XXX This is where we announce to the user what we're handling. It's
// not clear that this will always get called. I don't know how else to
// query if the text to speech is started though.
// Only annouce if we haven't before
if (!announced && trappedKeyEvent != null) {
String actionText = "";
switch (trappedKeyEvent.getKeyCode()) {
case KeyEvent.KEYCODE_MEDIA_PLAY_PAUSE:
// This is just play even though the keycode is both play/pause,
// the app shouldn't handle
// pause if music is already playing, it should go to whoever is
// playing the music.
actionText = "Play";
break;
case KeyEvent.KEYCODE_MEDIA_NEXT:
actionText = "Next";
break;
case KeyEvent.KEYCODE_MEDIA_PREVIOUS:
actionText = "Previous";
break;
case KeyEvent.KEYCODE_MEDIA_STOP:
actionText = "Stop";
break;
}
String textToSpeak = null;
if (btButtonSelection > 0 && btButtonSelection < receivers.size()) {
textToSpeak = "Select app to use for " + actionText + ", currently "
+ getAppName(receivers.get(btButtonSelection));
} else {
textToSpeak = "Select app to use for " + actionText;
}
textToSpeech.speak(textToSpeak, TextToSpeech.QUEUE_FLUSH, null);
announced = true;
}
}
/**
* {@inheritDoc}
*/
@Override
protected void onCreate(Bundle savedInstanceState) {
super.onCreate(savedInstanceState);
Log.d(TAG, "On Create Called");
getWindow().addFlags(WindowManager.LayoutParams.FLAG_SHOW_WHEN_LOCKED);
setContentView(R.layout.media_button_list);
uiIntentFilter = new IntentFilter(Intent.ACTION_MEDIA_BUTTON);
uiIntentFilter.setPriority(Integer.MAX_VALUE);
// TODO Handle text engine not installed, etc. Documented on android
// developer guide
textToSpeech = new TextToSpeech(this, this);
powerManager = (PowerManager) getSystemService(Context.POWER_SERVICE);
// XXX Is mode private right? Will this result in the selection being
// stored in different places for this
// and MediaButtonListLocked
// btButtonSelection = savedInstanceState != null ?
// savedInstanceState.getInt(SELECTION_KEY, -1) : -1;
btButtonSelection = getPreferences(MODE_PRIVATE).getInt(SELECTION_KEY, -1);
Intent mediaButtonIntent = new Intent(Intent.ACTION_MEDIA_BUTTON);
receivers = getPackageManager().queryBroadcastReceivers(mediaButtonIntent,
PackageManager.GET_INTENT_FILTERS | PackageManager.GET_RESOLVED_FILTER);
Boolean lastAnnounced = (Boolean) getLastNonConfigurationInstance();
if (lastAnnounced != null) {
announced = lastAnnounced;
}
// Remove our app's receiver from the list so users can't select it.
// NOTE: Our local receiver isn't registered at this point so we don't
// have to remove it.
if (receivers != null) {
for (int i = 0; i < receivers.size(); i++) {
if (MediaButtonReceiver.class.getName().equals(receivers.get(i).activityInfo.name)) {
receivers.remove(i);
break;
}
}
}
// TODO MAYBE sort receivers by MRU so user doesn't have to skip as many
// apps,
// right now apps are sorted by priority (not set by the user, set by
// the app authors.. )
setListAdapter(new BaseAdapter() {
@Override
public int getCount() {
return receivers.size();
}
@Override
public Object getItem(int position) {
return receivers.get(position);
}
@Override
public long getItemId(int position) {
return 0;
}
@Override
public View getView(int position, View convertView, ViewGroup parent) {
View view = convertView;
if (view == null) {
LayoutInflater vi = (LayoutInflater) getSystemService(Context.LAYOUT_INFLATER_SERVICE);
view = vi.inflate(R.layout.media_receiver_view, null);
}
ResolveInfo resolveInfo = receivers.get(position);
ImageView imageView = (ImageView) view.findViewById(R.id.receiverAppImage);
imageView.setImageDrawable(resolveInfo.loadIcon(getPackageManager()));
TextView textView = (TextView) view.findViewById(R.id.receiverAppName);
textView.setText(getAppName(resolveInfo));
return view;
}
});
header = (TextView) findViewById(R.id.dialogHeader);
cancelButton = findViewById(R.id.cancelButton);
cancelButton.setOnClickListener(new OnClickListener() {
@Override
public void onClick(View v) {
finish();
}
});
mediaImage = (ImageView) findViewById(R.id.mediaImage);
Log.i(TAG, "Media button selector created.");
}
/**
* {@inheritDoc}
*/
@Override
protected void onDestroy() {
super.onDestroy();
textToSpeech.shutdown();
Log.d(TAG, "Media button selector destroyed.");
}
/**
* {@inheritDoc}
*/
@Override
protected void onListItemClick(ListView l, View v, int position, long id) {
btButtonSelection = position;
forwardToMediaReceiver(position);
}
/**
* {@inheritDoc}
*/
@Override
protected void onPause() {
super.onPause();
Log.d(TAG, "onPause");
Log.d(TAG, "unegistered UI receiver");
unregisterReceiver(uiMediaReceiver);
if (wakeLock.isHeld()) {
wakeLock.release();
}
textToSpeech.stop();
timeoutExecutor.shutdownNow();
getPreferences(MODE_PRIVATE).edit().putInt(SELECTION_KEY, btButtonSelection).commit();
}
@Override
protected void onStart() {
super.onStart();
Log.d(TAG, "On Start called");
// TODO Originally thought most work should happen onResume and onPause.
// I don't know if the onResume part is
// right since you can't actually ever get back to this view, single
// instance, and not shown in recents. Maybe it's possible if ANOTHER
// dialog opens in front of ours?
}
/**
* {@inheritDoc}
*/
@Override
protected void onResume() {
super.onResume();
Log.d(TAG, "onResume");
// TODO Clean this up, figure out which things need to be set on the
// list view and which don't.
if (getIntent().getExtras() != null && getIntent().getExtras().get(Intent.EXTRA_KEY_EVENT) != null) {
trappedKeyEvent = (KeyEvent) getIntent().getExtras().get(Intent.EXTRA_KEY_EVENT);
Log.i(TAG, "Media button selector handling event: " + trappedKeyEvent + " from intent:" + getIntent());
getListView().setChoiceMode(ListView.CHOICE_MODE_SINGLE);
getListView().setClickable(true);
getListView().setFocusable(true);
getListView().setFocusableInTouchMode(true);
switch (trappedKeyEvent.getKeyCode()) {
case KeyEvent.KEYCODE_MEDIA_PLAY_PAUSE:
header.setText("Android Media Router: Play");
break;
case KeyEvent.KEYCODE_MEDIA_NEXT:
header.setText("Android Media Router: Next");
break;
case KeyEvent.KEYCODE_MEDIA_PREVIOUS:
header.setText("Android Media Router: Previous");
break;
case KeyEvent.KEYCODE_MEDIA_STOP:
header.setText("Android Media Router: Stop");
break;
}
} else {
Log.i(TAG, "Media button selector launched without key event, started with intent: " + getIntent());
trappedKeyEvent = null;
getListView().setClickable(false);
getListView().setChoiceMode(ListView.CHOICE_MODE_NONE);
getListView().setFocusable(false);
getListView().setFocusableInTouchMode(false);
}
Log.d(TAG, "Registered UI receiver");
registerReceiver(uiMediaReceiver, uiIntentFilter);
// power on device's screen so we can interact with it, otherwise on
// pause gets called immediately.
// alternative would be to change all of the selection logic to happen
// in a service?? don't know if that process life cycle would fit well
// -- look into
// added On after release so screen stays on a little longer instead of
// immediately to try and stop resume pause cycle that sometimes
// happens.
wakeLock = powerManager.newWakeLock(PowerManager.ACQUIRE_CAUSES_WAKEUP | PowerManager.SCREEN_DIM_WAKE_LOCK
| PowerManager.ON_AFTER_RELEASE, TAG);
wakeLock.setReferenceCounted(false);
// FIXME The wakelock is too late here. We end up doing multiple
// resume/pause cycles (at least three) before the screen turns on and
// our app is stable (not flickering). What to do?
wakeLock.acquire();
timeoutExecutor = Executors.newSingleThreadScheduledExecutor();
resetTimeout();
}
/**
* {@inheritDoc}
*/
@Override
public Object onRetainNonConfigurationInstance() {
return announced;
}
private void resetTimeout() {
if (timeoutScheduledFuture != null) {
timeoutScheduledFuture.cancel(false);
}
// TODO Clean this up
timeoutScheduledFuture = timeoutExecutor.schedule(new Runnable() {
@Override
public void run() {
runOnUiThread(new Runnable() {
@Override
public void run() {
onTimeout();
}
});
}
}, TIMEOUT_TIME, TimeUnit.SECONDS);
}
/**
* {@inheritDoc}
*/
@Override
public void onUserInteraction() {
super.onUserInteraction();
// Reset timeout to finish
if (!timeoutExecutor.isShutdown()) {
resetTimeout();
}
}
// /**
// * {@inheritDoc}
// */
// @Override
// protected void onSaveInstanceState(Bundle outState) {
// super.onSaveInstanceState(outState);
// outState.putInt(SELECTION_KEY, btButtonSelection);
// Log.d(TAG, "Saving selection state, selected is " + btButtonSelection);
/**
* Forwards the {@code #trappedKeyEvent} to the receiver at specified
* position.
*
* @param position
* The index of the receiver to select. Must be in bounds.
*/
private void forwardToMediaReceiver(int position) {
ResolveInfo resolveInfo = receivers.get(position);
if (resolveInfo != null) {
if (trappedKeyEvent != null) {
ComponentName selectedReceiver = new ComponentName(resolveInfo.activityInfo.packageName,
resolveInfo.activityInfo.name);
Utils.forwardKeyCodeToComponent(this, selectedReceiver, true, trappedKeyEvent.getKeyCode(),
new SweepBroadcastReceiver(selectedReceiver.toString()));
finish();
}
}
}
/**
* Returns the name of the application of the broadcast receiver specified
* by {@code resolveInfo}.
*
* @param resolveInfo
* The receiver.
* @return The name of the application.
*/
private String getAppName(ResolveInfo resolveInfo) {
return resolveInfo.activityInfo.applicationInfo.loadLabel(getPackageManager()).toString();
}
/**
* Moves selection by the amount specified in the list. If we're already at
* the last item and we're moving forward, wraps to the first item. If we're
* already at the first item, and we're moving backwards, wraps to the last
* item.
*
* @param amount
* The amount to move, may be positive or negative.
*/
private void moveSelection(int amount) {
resetTimeout();
btButtonSelection += amount;
if (btButtonSelection >= receivers.size()) {
// wrap
btButtonSelection = 0;
} else if (btButtonSelection < 0) {
// wrap
btButtonSelection = receivers.size() - 1;
}
// May not highlight, but will scroll to item
getListView().setSelection(btButtonSelection);
// todo scroll to item, highlight it
textToSpeech.speak(getAppName(receivers.get(btButtonSelection)), TextToSpeech.QUEUE_FLUSH, null);
}
/**
* Select the currently selected receiver.
*/
private void select() {
// TODO if there is no selection, we should either forward to whoever
// would have handled if we didn't exist, or to mru
if (btButtonSelection == -1) {
finish();
} else {
forwardToMediaReceiver(btButtonSelection);
}
}
/**
* Takes appropriate action to notify user and dismiss activity on timeout.
*/
private void onTimeout() {
Log.d(TAG, "Timed out waiting for user interaction, finishing activity");
final MediaPlayer timeoutPlayer = MediaPlayer.create(this, R.raw.dismiss);
timeoutPlayer.start();
// not having an on error listener results in on completion listener
// being called anyway
timeoutPlayer.setOnCompletionListener(new OnCompletionListener() {
public void onCompletion(MediaPlayer mp) {
timeoutPlayer.release();
}
});
finish();
}
} |
package com.ibm.nmon.data.definition;
import java.util.Collection;
import java.util.List;
import com.ibm.nmon.data.DataSet;
import com.ibm.nmon.data.DataType;
import com.ibm.nmon.data.matcher.HostMatcher;
import com.ibm.nmon.data.matcher.TypeMatcher;
import com.ibm.nmon.data.matcher.FieldMatcher;
import com.ibm.nmon.analysis.Statistic;
/**
* Base class for programmatically defining a set of data. A definition can match any number of
* hosts (via {@link DataSet DataSets}), {@link DataType DataTypes}, or fields. This class also
* supports renaming these values as well. Finally, a {@link Statistic}, which defaults to
* <code>AVERAGE</code>, can be specified for clients that need aggregated data.
*/
public abstract class DataDefinition {
private final Statistic stat;
private final boolean useSecondaryYAxis;
public static DataDefinition ALL_DATA = new DataDefinition() {
public List<DataSet> getMatchingHosts(Collection<DataSet> toMatch) {
return HostMatcher.ALL.getMatchingHosts(toMatch);
};
public List<DataType> getMatchingTypes(DataSet data) {
return TypeMatcher.ALL.getMatchingTypes(data);
};
public List<String> getMatchingFields(DataType type) {
return FieldMatcher.ALL.getMatchingFields(type);
}
};
protected DataDefinition() {
this(null, false);
}
protected DataDefinition(Statistic stat, boolean useSecondaryYAxis) {
if (stat == null) {
stat = Statistic.AVERAGE;
}
this.stat = stat;
this.useSecondaryYAxis = useSecondaryYAxis;
}
public Statistic getStatistic() {
return stat;
}
public boolean usesSecondaryYAxis() {
return useSecondaryYAxis;
}
/**
* Does the definition match the given host?
*
* @return <code>true</code>; by default matches all hosts
*/
public boolean matchesHost(DataSet data) {
return HostMatcher.ALL.matchesHost(data);
}
/**
* Given a list of <code>DataSet</code>s, return a new list containing the ones that match this
* definition.
*/
public abstract List<DataSet> getMatchingHosts(Collection<DataSet> toMatch);
/**
* Given a list of <code>DataType</code>s, return a new list containing the ones that match this
* definition.
*/
public abstract List<DataType> getMatchingTypes(DataSet data);
/**
* Given a <code>DataType</code>, return a new list containing the fields that match this
* definition.
*/
public abstract List<String> getMatchingFields(DataType type);
/**
* Get a new hostname for the given <code>DataSet</code>.
*
* @return {@link DataSet#getHostname()} by default
*/
public String renameHost(DataSet data) {
return data.getHostname();
}
/**
* Get a new name for the given <code>DataType</code>.
*
* @return {@link DataType#toString()} by default
*/
public String renameType(DataType type) {
return type.toString();
}
/**
* Get a new name for the given field.
*
* @return the same field name by default
*/
public String renameField(String field) {
return field;
}
} |
package com.lassedissing.gamenight.events;
import com.jme3.math.Vector3f;
import com.jme3.network.serializing.Serializable;
import com.lassedissing.gamenight.eventmanagning.EventClosure;
import com.lassedissing.gamenight.world.Entity;
import java.util.ArrayList;
import java.util.List;
@Serializable
public class FlagEvent extends Event {
private int flagId;
private int playerId;
private boolean reset;
private boolean isMove;
private Vector3f newLocation = new Vector3f();
public FlagEvent(int playerId, int flagId) {
this.playerId = playerId;
this.flagId = flagId;
}
public FlagEvent(int flagId, boolean reset) {
this.reset = reset;
}
public FlagEvent(int flagId, Vector3f newLocation) {
this.newLocation.set(newLocation);
}
public int getPlayerId() {
return this.playerId;
}
public int getFlagId() {
return this.flagId;
}
public boolean isReset() {
return reset;
}
public boolean isMove() {
return isMove;
}
public Vector3f getLocation() {
return newLocation;
}
/**
* Serialization
*/
public FlagEvent() {
}
//ClosureHolder section
private static List<EventClosure> closures = new ArrayList<>();
@Override
public int getClosureLevel() {
return 1;
}
@Override
public List<EventClosure> getClosures(int level) {
switch (level) {
case 0: return super.getClosures(level);
case 1: return closures;
default: throw new UnsupportedOperationException("Level " + level + " is not supported by " + getEventName());
}
}
} |
package com.mebigfatguy.fbcontrib.debug;
import java.io.FileWriter;
import java.io.IOException;
import java.io.PrintWriter;
import org.apache.bcel.Constants;
import org.apache.bcel.classfile.Code;
import org.apache.bcel.classfile.Method;
import edu.umd.cs.findbugs.BugReporter;
import edu.umd.cs.findbugs.BytecodeScanningDetector;
import edu.umd.cs.findbugs.OpcodeStack;
import edu.umd.cs.findbugs.ba.ClassContext;
public class OCSDebugger extends BytecodeScanningDetector {
private static final String OCS_OUTPUT_FILE = "fb-contrib.ocs.output";
private static final String OCS_METHOD_DESC = "fb-contrib.ocs.method";
private static final String OUTPUT_FILE_NAME = System.getProperty(OCS_OUTPUT_FILE);
private static final String METHOD_DESC = System.getProperty(OCS_METHOD_DESC);
private OpcodeStack stack = new OpcodeStack();
private PrintWriter pw = null;
public OCSDebugger(BugReporter bugReporter) {
}
public void visitClassContext(ClassContext classContext) {
if ((OUTPUT_FILE_NAME != null) && (METHOD_DESC != null))
super.visitClassContext(classContext);
}
public void visitCode(Code obj) {
Method m = getMethod();
String curMethodDesc = getClassContext().getJavaClass().getClassName() + "." + m.getName() + m.getSignature();
if (curMethodDesc.equals(METHOD_DESC)) {
try {
pw = new PrintWriter(new FileWriter(OUTPUT_FILE_NAME));
stack.resetForMethodEntry(this);
super.visitCode(obj);
} catch (IOException e) {
} finally {
pw.close();
pw = null;
}
}
}
public void sawOpcode(int seen) {
stack.precomputation(this);
stack.sawOpcode(this, seen);
pw.println(String.format("After executing: %-16s at PC: %-5d Stack Size: %-3d", Constants.OPCODE_NAMES[getOpcode()], getPC(), stack.getStackDepth()));
}
} |
package com.miracle.intermediate.visitor;
import com.miracle.MiracleOption;
import com.miracle.intermediate.Root;
import com.miracle.intermediate.instruction.*;
import com.miracle.intermediate.instruction.arithmetic.BinaryArithmetic;
import com.miracle.intermediate.instruction.arithmetic.UnaryArithmetic;
import com.miracle.intermediate.instruction.fork.BinaryBranch;
import com.miracle.intermediate.instruction.fork.Jump;
import com.miracle.intermediate.instruction.fork.Return;
import com.miracle.intermediate.instruction.fork.UnaryBranch;
import com.miracle.intermediate.number.*;
import com.miracle.intermediate.number.Number;
import com.miracle.intermediate.structure.BasicBlock;
import com.miracle.intermediate.structure.Function;
import com.miracle.intermediate.visitor.printer.IRPrinter;
import org.apache.commons.io.FileUtils;
import java.io.IOException;
import java.util.*;
import static com.miracle.MiracleOption.CallingConvention;
import static com.miracle.intermediate.number.PhysicalRegister.*;
public class X64Printer implements IRPrinter {
private StringBuilder builder;
private Set<BasicBlock> blockProcessed;
private String builtinPath;
private Function curFunction;
public X64Printer(String builtinPath) {
this.builtinPath = builtinPath;
}
@Override
public String getOutput() throws IOException {
builder.append(FileUtils.readFileToString(
new java.io.File(builtinPath),
"utf-8"
));
return builder.toString();
}
private List<String> divideStringIntoByte(String value) {
List<String> list = new ArrayList<>();
value = value.substring(1, value.length() - 1);
for (int i = 0, length = value.length(); i < length; i++) {
if (i + 1 < value.length() && value.charAt(i) == '\\' && value.charAt(i + 1) == 'n') {
list.add(String.valueOf(10));
i++;
} else {
list.add(String.valueOf((int) value.charAt(i)));
}
}
return list;
}
@Override
public void visit(Root ir) {
blockProcessed = new HashSet<>();
builder = new StringBuilder();
builder.append("; Code generated by Kipsora").append('\n');
builder.append('\n').append("default rel").append('\n');
builder.append('\n').append("extern").append(' ').append("malloc");
builder.append('\n').append("extern").append(' ').append("scanf").append('\n');
builder.append('\n').append("global").append(' ').append("main").append('\n');
builder.append('\n').append("section .bss").append('\n');
ir.globalVariable.forEach((key, value) ->
builder.append(key).append(':').append('\t')
.append("resb").append(' ').append(value.size).append('\n')
);
builder.append("int$buf").append(':').append('\t')
.append("resw").append(' ').append('1').append('\n');
builder.append('\n').append("section .data").append('\n');
ir.globalString.forEach((key, value) -> {
List<String> bytes = divideStringIntoByte(value.value);
builder.append('\t').append("dq").append(' ').append(bytes.size()).append('\n');
builder.append(value.name).append(':').append('\t');
if (!bytes.isEmpty()) {
builder.append("db").append(' ').append(String.join(", ", bytes));
}
builder.append('\n');
});
builder.append("int$fmt").append(':').append('\t')
.append("db").append(' ').append("25H").append(", ")
.append("64H").append(", ").append("00H").append('\n');
builder.append("str$fmt").append(':').append('\t')
.append("db").append(' ').append("25H").append(", ")
.append("73H").append(", ").append("00H").append('\n');
builder.append("fln$fmt").append(':').append('\t')
.append("db").append(' ').append("10").append('\n');
builder.append('\n').append("section .text").append('\n');
ir.globalFunction.forEach((key, value) -> {
value.accept(this);
builder.append('\n');
});
}
@Override
public void visit(BinaryArithmetic binaryArithmetic) {
if (binaryArithmetic.operator.equals(BinaryArithmetic.Types.SHL) ||
binaryArithmetic.operator.equals(BinaryArithmetic.Types.SHR)) {
builder.append('\t').append("mov").append(' ')
.append(PhysicalRegister.getBy16BITName("RCX", binaryArithmetic.getSource().getNumberSize()))
.append(", ").append(binaryArithmetic.getSource()).append('\n');
} else if (binaryArithmetic.operator.equals(BinaryArithmetic.Types.DIV)) {
/*
* Div Instruction: DIV RAX, src (src != RDX, RAX, imm) RAX /= src
* - src cannot be immediate number -> processed in MLIRTransformer
* - src cannot be RDX and RAX -> TODO: in Register Allocator
* - tar must be RAX -> TODO: in Register Allocator
* cdq
* idiv src
*/
builder.append('\t').append("mov").append(' ')
.append(PhysicalRegister.getBy16BITName("RAX", binaryArithmetic.getSource().getNumberSize()))
.append(", ").append(binaryArithmetic.getTarget()).append('\n');
builder.append('\t').append("cdq").append('\n');
builder.append('\t').append("idiv").append(' ').append(binaryArithmetic.getSource()).append('\n');
builder.append('\t').append("mov")
.append(' ').append(binaryArithmetic.getTarget())
.append(", ").append(getBy16BITName("RAX", binaryArithmetic.getTarget().size)).append('\n');
} else if (binaryArithmetic.operator.equals(BinaryArithmetic.Types.MOD)) {
/*
* Div Instruction: MOD RAX, src RAX /= src
* - src cannot be immediate number -> processed in MLIRTransformer
* - src cannot be RDX and RAX -> TODO: in Register Allocator
* - tar must be RAX -> TODO: in Register Allocator
* cdq
* idiv src
* mov RAX, RDX
*/
builder.append('\t').append("mov").append(' ')
.append(PhysicalRegister.getBy16BITName("RAX", binaryArithmetic.getSource().getNumberSize()))
.append(", ").append(binaryArithmetic.getTarget()).append('\n');
builder.append('\t').append("cdq").append('\n');
builder.append('\t').append("idiv").append(' ').append(binaryArithmetic.getSource()).append('\n');
builder.append('\t').append("mov")
.append(' ').append(binaryArithmetic.getTarget())
.append(", ").append(getBy16BITName("RDX", binaryArithmetic.getTarget().size)).append('\n');
} else {
/*
* Other Arithmetic Instruction: OP tar, src (tar != src) tar OP= src
* - tar and src cannot be both indirect registers -> TODO: in Register Allocator
* EXCEPTION:
* >>, <<: target must be physical registers -> TODO: in Register Allocator
* *: source cannot be indirect registers -> TODO: in Register Allocator
*/
builder.append('\t').append(binaryArithmetic.operator)
.append(' ').append(binaryArithmetic.getTarget())
.append(", ").append(binaryArithmetic.getSource())
.append('\n');
}
}
@Override
public void visit(Move move) {
/*
* Move Instruction:
* tar and src cannot be both indirect registers -> TODO: in Register Allocator
*/
if (move.getSource().toString().equals(move.getTarget().toString())) return;
if (move.getSource().getNumberSize() > move.getTarget().getNumberSize()) {
builder.append('\t').append("movsx").append(' ').append(move.getTarget())
.append(", ").append(move.getSource()).append('\n');
} else if (move.getSource().getNumberSize() > move.getTarget().getNumberSize()) {
builder.append('\t').append("movzx").append(' ').append(move.getTarget())
.append(", ").append(move.getSource()).append('\n');
} else {
builder.append('\t').append("mov").append(' ').append(move.getTarget())
.append(", ").append(move.getSource()).append('\n');
}
}
@Override
public void visit(Function function) {
curFunction = function;
builder.append(function.identifier).append(':').append('\n');
function.getEntryBasicBlock().accept(this);
curFunction = null;
}
private int get16Multiplier(int totalSize) {
return (totalSize + 15) / 16 * 16;
}
@Override
public void visit(BasicBlock block) {
if (blockProcessed.contains(block)) return;
blockProcessed.add(block);
builder.append(block.name).append(':').append('\n');
if (block.isFunctionEntryBlock()) {
if (curFunction.buffer.getSpillSize() > 0 || !curFunction.buffer.getCalleeSaveRegisters().isEmpty()) {
builder.append('\t').append("push").append(' ').append(RBP.getELF64Name()).append('\n');
builder.append('\t').append("mov").append(' ').append(RBP).append(", ")
.append(RSP).append('\n');
if (curFunction.buffer.getSpillSize() > 0) {
builder.append('\t').append("sub").append(' ').append(RSP).append(", ")
.append(get16Multiplier(block.blockFrom.buffer.getSpillSize()))
.append('\n');
}
curFunction.buffer.getCalleeSaveRegisters().forEach(element -> {
builder.append('\t').append("push").append(' ')
.append(element.getELF64Name()).append('\n');
});
for (int i = 0, size = curFunction.parameters.size(); i < size && i < MiracleOption.CallingConvention.size(); i++) {
if (!(curFunction.parameters.get(i) instanceof PhysicalRegister) ||
!((PhysicalRegister) curFunction.parameters.get(i)).indexName.equals(MiracleOption.CallingConvention.get(i))) {
builder.append('\t').append("mov").append(' ').append(curFunction.parameters.get(i)).append(", ")
.append(PhysicalRegister.getBy16BITName(
MiracleOption.CallingConvention.get(i),
curFunction.parameters.get(i).size
)).append('\n');
}
}
}
}
for (BasicBlock.Node it = block.getHead(); it != block.tail; it = it.getSucc()) {
it.instruction.accept(this);
}
block.getSuccBasicBlock().forEach(element -> element.accept(this));
}
@Override
public void visit(Call call) {
/*
* CALL instruction:
* returnRegister must be null or RAX -> TODO: in Register Allocator
* The last 6 parameters must follow calling conventions -> TODO: in Register Allocator
*/
List<PhysicalRegister> registers = new LinkedList<>(call.callerSave);
registers.forEach(element -> {
if (element.isCallerSave) {
builder.append('\t').append("push")
.append(' ').append(element.getELF64Name()).append('\n');
}
});
List<Number> parameters = call.parameters;
int spillSize = 0;
for (int i = CallingConvention.size(), size = parameters.size(); i < size; i++) {
spillSize += parameters.get(i).getNumberSize();
}
int fitSize = get16Multiplier(spillSize);
if (fitSize != 0) { // if there are more than 6 args
builder.append('\t').append("sub").append(' ').append(RSP)
.append(", ").append(fitSize).append('\n');
spillSize = 0;
for (int i = CallingConvention.size(), size = parameters.size(); i < size; i++) {
spillSize += parameters.get(i).getNumberSize();
if (parameters.get(i) instanceof IndirectRegister) {
builder.append('\t').append("mov").append(' ')
.append(PhysicalRegister.getBy16BITName("RDI", parameters.get(i).getNumberSize()))
.append(", ").append(parameters.get(i)).append('\n');
builder.append('\t').append("mov").append(' ')
.append(new OffsetRegister(
RSP, fitSize - spillSize,
null, null,
parameters.get(i).getNumberSize()
))
.append(", ")
.append(PhysicalRegister.getBy16BITName("RDI", parameters.get(i).getNumberSize()))
.append('\n');
} else {
builder.append('\t').append("mov").append(' ')
.append(new OffsetRegister(
RSP, fitSize - spillSize,
null, null,
parameters.get(i).getNumberSize()
))
.append(", ").append(parameters.get(i)).append('\n');
}
}
}
for (int i = 0; i < parameters.size() && i < MiracleOption.CallingConvention.size(); i++) {
if (!(parameters.get(i) instanceof PhysicalRegister) ||
!((PhysicalRegister) parameters.get(i)).indexName.equals(MiracleOption.CallingConvention.get(i))) {
builder.append('\t').append("push").append(' ').append(parameters.get(i)).append('\n');
}
}
for (int i = Math.min(parameters.size() - 1, MiracleOption.CallingConvention.size() - 1); i >= 0; i
if (!(parameters.get(i) instanceof PhysicalRegister) ||
!((PhysicalRegister) parameters.get(i)).indexName.equals(MiracleOption.CallingConvention.get(i))) {
builder.append('\t').append("pop").append(' ').append(PhysicalRegister.getBy16BITName(MiracleOption.CallingConvention.get(i), parameters.get(i).getNumberSize())).append('\n');
}
}
builder.append('\t').append("call").append(' ')
.append(call.function.identifier).append('\n');
if (fitSize != 0) {
builder.append('\t').append("add").append(' ').append(RSP)
.append(", ").append(fitSize).append('\n');
}
Collections.reverse(registers);
registers.forEach(element -> {
if (element.isCallerSave) {
builder.append('\t').append("pop")
.append(' ').append(element.getELF64Name()).append('\n');
}
});
if (call.getTarget() != null) {
builder.append('\t').append("mov").append(' ')
.append(call.getTarget()).append(", ")
.append(PhysicalRegister.getBy16BITName(
"RAX",
call.getTarget().size
)).append('\n');
}
}
@Override
public void visit(UnaryArithmetic prefixArithmetic) {
/*
* UnaryArithmetic Instruction:
* NO LIMITS
*/
builder.append('\t').append(prefixArithmetic.operator).append(' ')
.append(prefixArithmetic.getTarget()).append('\n');
}
@Override
public void visit(UnaryBranch unaryBranch) {
/*
* UnaryBranch Instruction:
* expression cannot be immediate number -> processed in MLIRTransformer
*/
builder.append('\t').append("cmp").append(' ').append(unaryBranch.getExpression())
.append(", ").append(0).append('\n');
builder.append('\t').append("jnz").append(' ')
.append(unaryBranch.getBranchTrue().name).append('\n');
}
@Override
public void visit(Return irReturn) {
/*
* Return Instruction:
* - value must be null -> processed in LLIRTransformer
*/
List<PhysicalRegister> registers = new LinkedList<>(curFunction.buffer.getCalleeSaveRegisters());
Collections.reverse(registers);
registers.forEach(element -> {
builder.append('\t').append("pop").append(' ').append(element.getELF64Name()).append('\n');
});
if (curFunction.buffer.getSpillSize() > 0 || !curFunction.buffer.getCalleeSaveRegisters().isEmpty()) {
builder.append('\t').append("leave").append('\n');
}
builder.append('\t').append("ret").append('\n');
}
@Override
public void visit(Jump jump) {
builder.append('\t').append("jmp").append(' ')
.append(jump.block.name).append('\n');
}
@Override
public void visit(Compare compare) {
/*
* Compare Instruction:
* - srcA, srcB cannot be both immediate number -> processed in MLIRTransformer
* - srcA, srcB cannot be both indirect registers -> TODO: in Register Allocator
*/
builder.append('\t').append("cmp").append(' ').append(compare.getSourceA())
.append(", ").append(compare.getSourceB()).append('\n');
builder.append('\t').append(compare.getOperator()).append(' ')
.append(compare.getTarget()).append('\n');
}
@Override
public void visit(HeapAllocate allocate) {
/*
* HeapAllocate Instruction:
* - size must be one -> processed in MLIRTransformer
*/
allocate.callerSave.forEach(element ->
builder.append('\t').append("push").append(' ')
.append(element).append('\n')
);
builder.append('\t').append("mov").append(' ').append("rdi").append(", ")
.append(allocate.getNumber()).append('\n');
builder.append('\t').append("call").append(' ').append("malloc").append('\n');
allocate.callerSave.forEach(element ->
builder.append('\t').append("pop").append(' ')
.append(element).append('\n')
);
builder.append('\t').append("mov").append(' ').append(allocate.getTarget())
.append(", ").append(PhysicalRegister.getBy16BITName("RAX", allocate.getTarget().size))
.append("\n");
}
@Override
public void visit(BinaryBranch binaryBranch) {
/*
* BinaryBranch expression:
* - expA and expB cannot be both immediate number -> processed in MLIRTransformer
* - expA and expB cannot be both indirect registers -> TODO: in Register Allocator
*/
builder.append('\t').append("cmp")
.append(' ').append(binaryBranch.getExpressionA())
.append(", ").append(binaryBranch.getExpressionB())
.append('\n');
builder.append('\t').append(binaryBranch.getOperator())
.append(' ').append(binaryBranch.getBranchTrue().name).append('\n');
}
@Override
public void visit(PhiInstruction phiInstruction) {
throw new RuntimeException("unprocessed phis");
}
} |
package com.ram.kainterview;
import java.util.HashMap;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import javax.swing.JButton;
import javax.swing.JTextField;
import org.graphstream.graph.Graph;
import org.graphstream.ui.view.Viewer;
import org.graphstream.ui.view.ViewerListener;
import org.graphstream.ui.view.ViewerPipe;
import com.ram.kainterview.user.User;
/**
* Controller of the infection model
*/
public class InfectionControllerImpl implements InfectionController {
/**
* Map of all id's to users in the user base
*/
private Map<String,User> users;
/**
* Manages GraphStream's ViewerPipe pump requests
*/
private boolean loop;
/**
* Constructs a controller with the given user base
*/
public InfectionControllerImpl(List<User> users) {
this.users = new HashMap<>();
for (User user : users)
this.users.put(user.id(), user);
loop = true;
}
@Override
public void init(GraphView view, Graph graph, Viewer viewer) {
for (Entry<String,User> entry : users.entrySet()) {
User user = entry.getValue();
// build ids of adjacent nodes
List<String> toIds = new LinkedList<String>();
List<String> fromIds = new LinkedList<String>();
for (User coach : user.coaches())
toIds.add(coach.id());
for (User student : user.students())
fromIds.add(student.id());
view.addNode(user.id(),user.version(), toIds, fromIds);
}
ViewerPipe fromViewer = viewer.newViewerPipe();
fromViewer.addViewerListener(new ViewerListener() {
@Override
public void buttonPushed(String id) {
// unused as only a release event indicates a complete click
// TODO highlight outline of selected node
}
@Override
public void buttonReleased(String id) {
users.get(id).totalInfect(users.get(id).version()+1);
for (Entry<String,User> entry : users.entrySet())
view.updateNode(entry.getKey(), entry.getValue().version());
}
@Override
public void viewClosed(String id) {
loop = false;
}
});
// connect the graph to the viewer
fromViewer.addSink(graph);
fromViewer.removeElementSink(graph); // for issue in library
// run on separate thread to prevent UI thread blocking
new Thread(() -> {
while (loop) {
// request the pipe to check if the viewer thread sent events
try {
fromViewer.blockingPump();
} catch (InterruptedException e) {
e.printStackTrace();
}
}
}).start();
}
@Override
public void registerInfectField(JTextField textField) {
// TODO
}
@Override
public void registerInfectButton(JButton button) {
button.addActionListener((event) -> {
// TODO (toggle for different infection types)
});
}
@Override
public void registerExecuteButton(JButton button) {
button.addActionListener((event) -> {
// TODO
});
}
@Override
public void registerHelpButton(JButton button) {
button.addActionListener((event) -> {
// TODO
});
}
} |
package com.syncleus.dann.associativemap;
import java.io.Serializable;
import java.util.List;
public class Hyperpoint implements Serializable
{
private double[] coordinates;
public Hyperpoint(int dimensions)
{
if(dimensions <= 0)
throw new IllegalArgumentException("dimensions can not be less than or equal to zero");
this.coordinates = new double[dimensions];
}
public Hyperpoint(double[] coordinates)
{
if(coordinates == null)
throw new NullPointerException("coordinates can not be null!");
if(coordinates.length <= 0)
throw new IllegalArgumentException("coordinates must have atleast one member, 0 dimensions isnt valid!");
this.coordinates = (double[]) coordinates.clone();
}
public Hyperpoint(List<Double> coordinates)
{
if(coordinates == null)
throw new NullPointerException("coordinates can not be null!");
if(coordinates.size() <= 0)
throw new IllegalArgumentException("coordinates must have atleast one member, 0 dimensions isnt valid!");
this.coordinates = new double[coordinates.size()];
int coordinatesIndex = 0;
for(Double coordinate : coordinates)
{
this.coordinates[coordinatesIndex++] = coordinate.doubleValue();
}
}
public Hyperpoint(Hyperpoint copy)
{
this.coordinates = (double[]) copy.coordinates.clone();
}
public int getDimensions()
{
return this.coordinates.length;
}
public void setCoordinate(double coordinate, int dimension)
{
if(dimension <= 0)
throw new IllegalArgumentException("dimensions can not be less than or equal to zero");
if(dimension >= this.coordinates.length)
throw new IllegalArgumentException("dimensions is larger than the dimensionality of this point");
this.coordinates[dimension-1] = coordinate;
}
public double getCoordinate(int dimension)
{
if(dimension <= 0)
throw new IllegalArgumentException("dimensions can not be less than or equal to zero");
if(dimension > this.coordinates.length)
throw new IllegalArgumentException("dimensions is larger than the dimensionality of this point");
return this.coordinates[dimension-1];
}
public void setDistance(double distance)
{
double[] newCoords = (double[]) this.coordinates.clone();
for(int coordinateIndex = 0; coordinateIndex < this.getDimensions(); coordinateIndex++)
{
double sphericalProducts = distance;
for(int angleDimension = 1; angleDimension - 1 < (coordinateIndex + 1);angleDimension++)
{
if( angleDimension < (coordinateIndex + 1))
sphericalProducts *= Math.sin(this.getAngularComponent(angleDimension));
else
{
if((coordinateIndex + 1) == this.getDimensions())
sphericalProducts *= Math.sin(this.getAngularComponent(angleDimension));
else
sphericalProducts *= Math.cos(this.getAngularComponent(angleDimension));
}
}
newCoords[coordinateIndex] = sphericalProducts;
}
this.coordinates = newCoords;
}
public void setAngularComponent(double angle, int dimension)
{
if(dimension <= 0)
throw new IllegalArgumentException("dimensions can not be less than or equal to zero");
if((dimension-2) >= this.coordinates.length)
throw new IllegalArgumentException("dimensions is larger than the dimensionality (minus 1) of this point");
double[] newCoords = (double[]) this.coordinates.clone();
for(int coordinateIndex = dimension-1; coordinateIndex < this.getDimensions(); coordinateIndex++)
{
double sphericalProducts = this.getDistance();
for(int angleDimension = 1; angleDimension - 1 < (coordinateIndex + 1);angleDimension++)
{
if( angleDimension < (coordinateIndex + 1))
sphericalProducts *= Math.sin(this.getAngularComponent(angleDimension));
else
{
if((coordinateIndex + 1) == this.getDimensions())
sphericalProducts *= Math.sin(this.getAngularComponent(angleDimension));
else
sphericalProducts *= Math.cos(this.getAngularComponent(angleDimension));
}
}
newCoords[coordinateIndex] = sphericalProducts;
}
this.coordinates = newCoords;
}
public double getDistance()
{
double squaredSum = 0.0;
for(double coordinate : this.coordinates)
squaredSum += Math.pow(coordinate,2);
return Math.sqrt(squaredSum);
}
public double getAngularComponent(int dimension)
{
if(dimension <= 0)
throw new IllegalArgumentException("dimensions can not be less than or equal to zero");
if((dimension-2) >= this.coordinates.length)
throw new IllegalArgumentException("dimensions is larger than the dimensionality (minus 1) of this point");
double squaredSum = 0.0;
for(int coordinateIndex = this.coordinates.length-1; coordinateIndex >= (dimension); coordinateIndex
squaredSum += Math.pow(this.coordinates[coordinateIndex], 2.0);
return Math.atan2(Math.sqrt(squaredSum), this.coordinates[dimension-1]);
}
public Hyperpoint calculateRelativeTo(Hyperpoint absolutePoint)
{
if(absolutePoint == null)
throw new NullPointerException("absolutePoint can not be null!");
if(absolutePoint.getDimensions() != this.getDimensions())
throw new IllegalArgumentException("absolutePoint must have the same dimensions as this point");
double[] relativeCoords = new double[this.coordinates.length];
for(int coordIndex = 0; coordIndex < this.coordinates.length; coordIndex++)
{
relativeCoords[coordIndex] = this.coordinates[coordIndex] - absolutePoint.getCoordinate(coordIndex+1);
}
return new Hyperpoint(relativeCoords);
}
public Hyperpoint add(Hyperpoint pointToAdd)
{
if(pointToAdd == null)
throw new NullPointerException("pointToAdd can not be null!");
if(pointToAdd.getDimensions() != this.getDimensions())
throw new IllegalArgumentException("pointToAdd must have the same dimensions as this point");
double[] relativeCoords = new double[this.coordinates.length];
for(int coordIndex = 0; coordIndex < this.coordinates.length; coordIndex++)
{
relativeCoords[coordIndex] = this.coordinates[coordIndex] + pointToAdd.getCoordinate(coordIndex+1);
}
return new Hyperpoint(relativeCoords);
}
} |
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