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34.1k
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stringlengths 73
34.1k
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stringlengths 3
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339
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|---|---|---|---|---|---|---|---|---|---|---|---|
9,100
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/journal/helpers/ParameterHelper.java
|
ParameterHelper.getOptionalStringParameter
|
public static String getOptionalStringParameter(Map<String, String> parameters,
String parameterName,
String defaultValue) {
validateParameters(parameters);
validateParameterName(parameterName);
String value = parameters.get(parameterName);
return value == null ? defaultValue : value;
}
|
java
|
public static String getOptionalStringParameter(Map<String, String> parameters,
String parameterName,
String defaultValue) {
validateParameters(parameters);
validateParameterName(parameterName);
String value = parameters.get(parameterName);
return value == null ? defaultValue : value;
}
|
[
"public",
"static",
"String",
"getOptionalStringParameter",
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"String",
"defaultValue",
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] |
Get an optional String parameter, If not found, use the default value.
@throws NullPointerException
if either 'parameters' or 'parameterName' is null.
|
[
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"optional",
"String",
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"If",
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"use",
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"value",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/journal/helpers/ParameterHelper.java#L48-L56
|
9,101
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/journal/helpers/ParameterHelper.java
|
ParameterHelper.getOptionalBooleanParameter
|
public static boolean getOptionalBooleanParameter(Map<String, String> parameters,
String parameterName,
boolean defaultValue)
throws JournalException {
validateParameters(parameters);
validateParameterName(parameterName);
String string = parameters.get(parameterName);
if (string == null) {
return defaultValue;
} else if (string.equals(VALUE_FALSE)) {
return false;
} else if (string.equals(VALUE_TRUE)) {
return true;
} else {
throw new JournalException("'" + parameterName
+ "' parameter must be '" + VALUE_FALSE + "'(default) or '"
+ VALUE_TRUE + "'");
}
}
|
java
|
public static boolean getOptionalBooleanParameter(Map<String, String> parameters,
String parameterName,
boolean defaultValue)
throws JournalException {
validateParameters(parameters);
validateParameterName(parameterName);
String string = parameters.get(parameterName);
if (string == null) {
return defaultValue;
} else if (string.equals(VALUE_FALSE)) {
return false;
} else if (string.equals(VALUE_TRUE)) {
return true;
} else {
throw new JournalException("'" + parameterName
+ "' parameter must be '" + VALUE_FALSE + "'(default) or '"
+ VALUE_TRUE + "'");
}
}
|
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"}"
] |
Get an optional boolean parameter. If not found, use the default value.
@throws JournalException
if a value is supplied that is neither "true" nor "false".
@throws NullPointerException
if either 'parameters' or 'parameterName' is null.
|
[
"Get",
"an",
"optional",
"boolean",
"parameter",
".",
"If",
"not",
"found",
"use",
"the",
"default",
"value",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/journal/helpers/ParameterHelper.java#L66-L86
|
9,102
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/journal/helpers/ParameterHelper.java
|
ParameterHelper.parseParametersForWritableDirectory
|
public static File parseParametersForWritableDirectory(Map<String, String> parameters,
String parameterName)
throws JournalException {
String directoryString = parameters.get(parameterName);
if (directoryString == null) {
throw new JournalException("'" + parameterName + "' is required.");
}
File directory = new File(directoryString);
if (!directory.exists()) {
throw new JournalException("Directory '" + directory
+ "' does not exist.");
}
if (!directory.isDirectory()) {
throw new JournalException("Directory '" + directory
+ "' is not a directory.");
}
if (!directory.canWrite()) {
throw new JournalException("Directory '" + directory
+ "' is not writable.");
}
return directory;
}
|
java
|
public static File parseParametersForWritableDirectory(Map<String, String> parameters,
String parameterName)
throws JournalException {
String directoryString = parameters.get(parameterName);
if (directoryString == null) {
throw new JournalException("'" + parameterName + "' is required.");
}
File directory = new File(directoryString);
if (!directory.exists()) {
throw new JournalException("Directory '" + directory
+ "' does not exist.");
}
if (!directory.isDirectory()) {
throw new JournalException("Directory '" + directory
+ "' is not a directory.");
}
if (!directory.canWrite()) {
throw new JournalException("Directory '" + directory
+ "' is not writable.");
}
return directory;
}
|
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] |
Look in the parameters for the path to a writable directory. The
parameter is required.
|
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"required",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/journal/helpers/ParameterHelper.java#L92-L113
|
9,103
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/journal/helpers/ParameterHelper.java
|
ParameterHelper.parseParametersForFilenamePrefix
|
public static String parseParametersForFilenamePrefix(Map<String, String> parameters) {
return getOptionalStringParameter(parameters,
PARAMETER_JOURNAL_FILENAME_PREFIX,
DEFAULT_FILENAME_PREFIX);
}
|
java
|
public static String parseParametersForFilenamePrefix(Map<String, String> parameters) {
return getOptionalStringParameter(parameters,
PARAMETER_JOURNAL_FILENAME_PREFIX,
DEFAULT_FILENAME_PREFIX);
}
|
[
"public",
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"parseParametersForFilenamePrefix",
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"(",
"parameters",
",",
"PARAMETER_JOURNAL_FILENAME_PREFIX",
",",
"DEFAULT_FILENAME_PREFIX",
")",
";",
"}"
] |
Look for a string to use as a prefix for the names of the journal files.
Default is "fedoraJournal"
|
[
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"for",
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"string",
"to",
"use",
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"prefix",
"for",
"the",
"names",
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"the",
"journal",
"files",
".",
"Default",
"is",
"fedoraJournal"
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/journal/helpers/ParameterHelper.java#L119-L123
|
9,104
|
fcrepo3/fcrepo
|
fcrepo-client/fcrepo-client-admin/src/main/java/org/fcrepo/client/NewObjectDialog.java
|
NewObjectDialog.itemStateChanged
|
public void itemStateChanged(ItemEvent e) {
if (e.getStateChange() == ItemEvent.DESELECTED) {
// disable text entry
m_customPIDField.setEditable(false);
} else if (e.getStateChange() == ItemEvent.SELECTED) {
// enable text entry
m_customPIDField.setEditable(true);
}
}
|
java
|
public void itemStateChanged(ItemEvent e) {
if (e.getStateChange() == ItemEvent.DESELECTED) {
// disable text entry
m_customPIDField.setEditable(false);
} else if (e.getStateChange() == ItemEvent.SELECTED) {
// enable text entry
m_customPIDField.setEditable(true);
}
}
|
[
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"}"
] |
for the checkbox
|
[
"for",
"the",
"checkbox"
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-client/fcrepo-client-admin/src/main/java/org/fcrepo/client/NewObjectDialog.java#L63-L71
|
9,105
|
fcrepo3/fcrepo
|
fcrepo-security/fcrepo-security-pdp/src/main/java/org/fcrepo/server/security/xacml/pdp/data/PolicyIndexBase.java
|
PolicyIndexBase.handleDocument
|
protected AbstractPolicy handleDocument(Document doc, PolicyFinder policyFinder) throws ParsingException {
// handle the policy, if it's a known type
Element root = doc.getDocumentElement();
String name = root.getTagName();
// see what type of policy this is
if (name.equals("Policy")) {
return Policy.getInstance(root);
} else if (name.equals("PolicySet")) {
return PolicySet.getInstance(root, policyFinder);
} else {
// this isn't a root type that we know how to handle
throw new ParsingException("Unknown root document type: " + name);
}
}
|
java
|
protected AbstractPolicy handleDocument(Document doc, PolicyFinder policyFinder) throws ParsingException {
// handle the policy, if it's a known type
Element root = doc.getDocumentElement();
String name = root.getTagName();
// see what type of policy this is
if (name.equals("Policy")) {
return Policy.getInstance(root);
} else if (name.equals("PolicySet")) {
return PolicySet.getInstance(root, policyFinder);
} else {
// this isn't a root type that we know how to handle
throw new ParsingException("Unknown root document type: " + name);
}
}
|
[
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] |
A private method that handles reading the policy and creates the correct
kind of AbstractPolicy.
Because this makes use of the policyFinder, it cannot be reused between finders.
Consider moving to policyManager, which is not intended to be reused outside
of a policyFinderModule, which is not intended to be reused amongst PolicyFinder instances.
|
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] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-security/fcrepo-security-pdp/src/main/java/org/fcrepo/server/security/xacml/pdp/data/PolicyIndexBase.java#L271-L285
|
9,106
|
fcrepo3/fcrepo
|
fcrepo-security/fcrepo-security-pdp/src/main/java/org/fcrepo/server/security/xacml/pdp/data/PolicyIndexBase.java
|
PolicyIndexBase.makeComponents
|
protected static String[] makeComponents(String resourceId) {
if (resourceId == null || resourceId.isEmpty()
|| !resourceId.startsWith("/")) {
return null;
}
List<String> components = new ArrayList<String>();
String[] parts = resourceId.split("\\/");
int bufPrimer = 0;
for (int x = 1; x < parts.length; x++) {
bufPrimer = Math.max(bufPrimer, (parts[x].length() + 1));
StringBuilder sb = new StringBuilder(bufPrimer);
for (int y = 0; y < x; y++) {
sb.append("/");
sb.append(parts[y + 1]);
}
String componentBase = sb.toString();
bufPrimer = componentBase.length() + 16;
components.add(componentBase);
if (x != parts.length - 1) {
components.add(componentBase.concat("/.*"));
} else {
components.add(componentBase.concat("$"));
}
}
return components.toArray(parts);
}
|
java
|
protected static String[] makeComponents(String resourceId) {
if (resourceId == null || resourceId.isEmpty()
|| !resourceId.startsWith("/")) {
return null;
}
List<String> components = new ArrayList<String>();
String[] parts = resourceId.split("\\/");
int bufPrimer = 0;
for (int x = 1; x < parts.length; x++) {
bufPrimer = Math.max(bufPrimer, (parts[x].length() + 1));
StringBuilder sb = new StringBuilder(bufPrimer);
for (int y = 0; y < x; y++) {
sb.append("/");
sb.append(parts[y + 1]);
}
String componentBase = sb.toString();
bufPrimer = componentBase.length() + 16;
components.add(componentBase);
if (x != parts.length - 1) {
components.add(componentBase.concat("/.*"));
} else {
components.add(componentBase.concat("$"));
}
}
return components.toArray(parts);
}
|
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")",
";",
"}"
] |
Splits a XACML hierarchical resource-id value into a set of resource-id values
that can be matched against a policy.
Eg an incoming request for /res1/res2/res3/.* should match
/res1/.*
/res1/res2/.*
/res1/res2/res3/.*
in policies.
@param resourceId XACML hierarchical resource-id value
@return array of individual resource-id values that can be used to match against policies
|
[
"Splits",
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"hierarchical",
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"-",
"id",
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"that",
"can",
"be",
"matched",
"against",
"a",
"policy",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-security/fcrepo-security-pdp/src/main/java/org/fcrepo/server/security/xacml/pdp/data/PolicyIndexBase.java#L301-L332
|
9,107
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/errors/ServerException.java
|
ServerException.getDetails
|
public String[] getDetails(Locale locale) {
if (m_details == null || m_details.length == 0) {
return s_emptyStringArray;
}
String[] ret = new String[m_details.length];
for (int i = 0; i < m_details.length; i++) {
ret[i] = getLocalizedOrCode(m_bundleName, locale, m_code, null);
}
return ret;
}
|
java
|
public String[] getDetails(Locale locale) {
if (m_details == null || m_details.length == 0) {
return s_emptyStringArray;
}
String[] ret = new String[m_details.length];
for (int i = 0; i < m_details.length; i++) {
ret[i] = getLocalizedOrCode(m_bundleName, locale, m_code, null);
}
return ret;
}
|
[
"public",
"String",
"[",
"]",
"getDetails",
"(",
"Locale",
"locale",
")",
"{",
"if",
"(",
"m_details",
"==",
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"m_details",
".",
"length",
"==",
"0",
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"{",
"return",
"s_emptyStringArray",
";",
"}",
"String",
"[",
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"ret",
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"new",
"String",
"[",
"m_details",
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";",
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"ret",
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"i",
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"getLocalizedOrCode",
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",",
"locale",
",",
"m_code",
",",
"null",
")",
";",
"}",
"return",
"ret",
";",
"}"
] |
Gets any detail messages, preferring the provided locale.
@return The detail messages, with {num}-indexed placeholders populated,
if needed.
|
[
"Gets",
"any",
"detail",
"messages",
"preferring",
"the",
"provided",
"locale",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/errors/ServerException.java#L176-L185
|
9,108
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/errors/ServerException.java
|
ServerException.getLocalizedOrCode
|
private static String getLocalizedOrCode(String bundleName,
Locale locale,
String code,
String[] values) {
ResourceBundle bundle = null;
if (bundleName != null) {
bundle = ResourceBundle.getBundle(bundleName, locale);
}
if (bundle == null) {
return code;
}
String locMessage = bundle.getString(code);
if (locMessage == null) {
return code;
}
if (values == null) {
return locMessage;
}
return MessageFormat.format(locMessage, (Object[]) values);
}
|
java
|
private static String getLocalizedOrCode(String bundleName,
Locale locale,
String code,
String[] values) {
ResourceBundle bundle = null;
if (bundleName != null) {
bundle = ResourceBundle.getBundle(bundleName, locale);
}
if (bundle == null) {
return code;
}
String locMessage = bundle.getString(code);
if (locMessage == null) {
return code;
}
if (values == null) {
return locMessage;
}
return MessageFormat.format(locMessage, (Object[]) values);
}
|
[
"private",
"static",
"String",
"getLocalizedOrCode",
"(",
"String",
"bundleName",
",",
"Locale",
"locale",
",",
"String",
"code",
",",
"String",
"[",
"]",
"values",
")",
"{",
"ResourceBundle",
"bundle",
"=",
"null",
";",
"if",
"(",
"bundleName",
"!=",
"null",
")",
"{",
"bundle",
"=",
"ResourceBundle",
".",
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"(",
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",",
"locale",
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"}",
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"String",
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"format",
"(",
"locMessage",
",",
"(",
"Object",
"[",
"]",
")",
"values",
")",
";",
"}"
] |
Gets the message from the resource bundle, formatting it if needed, and
on failure, just returns the code.
@param bundleName
The ResourceBundle where the message is defined.
@param locale
The preferred locale.
@param code
The message key.
@param values
The replacement values, assumed empty if null.
@return The detail messages, with {num}-indexed placeholders populated,
if needed.
|
[
"Gets",
"the",
"message",
"from",
"the",
"resource",
"bundle",
"formatting",
"it",
"if",
"needed",
"and",
"on",
"failure",
"just",
"returns",
"the",
"code",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/errors/ServerException.java#L202-L221
|
9,109
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/journal/entry/CreatorJournalEntry.java
|
CreatorJournalEntry.invokeAndClose
|
public Object invokeAndClose(ManagementDelegate delegate,
JournalWriter writer) throws ServerException,
JournalException {
Object result = invokeMethod(delegate, writer);
close();
return result;
}
|
java
|
public Object invokeAndClose(ManagementDelegate delegate,
JournalWriter writer) throws ServerException,
JournalException {
Object result = invokeMethod(delegate, writer);
close();
return result;
}
|
[
"public",
"Object",
"invokeAndClose",
"(",
"ManagementDelegate",
"delegate",
",",
"JournalWriter",
"writer",
")",
"throws",
"ServerException",
",",
"JournalException",
"{",
"Object",
"result",
"=",
"invokeMethod",
"(",
"delegate",
",",
"writer",
")",
";",
"close",
"(",
")",
";",
"return",
"result",
";",
"}"
] |
A convenience method that invokes the management method and then closes
the JournalEntry, thereby cleaning up any temp files.
|
[
"A",
"convenience",
"method",
"that",
"invokes",
"the",
"management",
"method",
"and",
"then",
"closes",
"the",
"JournalEntry",
"thereby",
"cleaning",
"up",
"any",
"temp",
"files",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/journal/entry/CreatorJournalEntry.java#L70-L76
|
9,110
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/storage/translation/DOTranslationUtility.java
|
DOTranslationUtility.setDatastreamDefaults
|
public static Datastream setDatastreamDefaults(Datastream ds)
throws ObjectIntegrityException {
if ((ds.DSMIME == null || ds.DSMIME.isEmpty())
&& ds.DSControlGrp.equalsIgnoreCase("X")) {
ds.DSMIME = "text/xml";
}
if (ds.DSState == null || ds.DSState.isEmpty()) {
ds.DSState = "A";
}
// For METS backward compatibility
if (ds.DSInfoType == null || ds.DSInfoType.isEmpty()
|| ds.DSInfoType.equalsIgnoreCase("OTHER")) {
ds.DSInfoType = "UNSPECIFIED";
}
// LOOK! For METS backward compatibility:
// If we have a METS MDClass value, and DSFormatURI isn't already
// assigned, preserve MDClass and MDType in a DSFormatURI.
// Note that the system is taking over the DSFormatURI in this case.
// Therefore, if a client subsequently modifies the DSFormatURI
// this METS legacy informatin will be lost, in which case the inline
// datastream will default to amdSec/techMD in a subsequent METS export.
if (ds.DSControlGrp.equalsIgnoreCase("X")) {
if (((DatastreamXMLMetadata) ds).DSMDClass != 0
&& ds.DSFormatURI == null) {
String mdClassName = "";
String mdType = ds.DSInfoType;
String otherType = "";
if (((DatastreamXMLMetadata) ds).DSMDClass == 1) {
mdClassName = "techMD";
} else if (((DatastreamXMLMetadata) ds).DSMDClass == 2) {
mdClassName = "sourceMD";
} else if (((DatastreamXMLMetadata) ds).DSMDClass == 3) {
mdClassName = "rightsMD";
} else if (((DatastreamXMLMetadata) ds).DSMDClass == 4) {
mdClassName = "digiprovMD";
} else if (((DatastreamXMLMetadata) ds).DSMDClass == 5) {
mdClassName = "descMD";
}
if (!mdType.equals("MARC") && !mdType.equals("EAD")
&& !mdType.equals("DC") && !mdType.equals("NISOIMG")
&& !mdType.equals("LC-AV") && !mdType.equals("VRA")
&& !mdType.equals("TEIHDR") && !mdType.equals("DDI")
&& !mdType.equals("FGDC")) {
mdType = "OTHER";
otherType = ds.DSInfoType;
}
ds.DSFormatURI =
"info:fedora/fedora-system:format/xml.mets."
+ mdClassName + "." + mdType + "." + otherType;
}
}
return ds;
}
|
java
|
public static Datastream setDatastreamDefaults(Datastream ds)
throws ObjectIntegrityException {
if ((ds.DSMIME == null || ds.DSMIME.isEmpty())
&& ds.DSControlGrp.equalsIgnoreCase("X")) {
ds.DSMIME = "text/xml";
}
if (ds.DSState == null || ds.DSState.isEmpty()) {
ds.DSState = "A";
}
// For METS backward compatibility
if (ds.DSInfoType == null || ds.DSInfoType.isEmpty()
|| ds.DSInfoType.equalsIgnoreCase("OTHER")) {
ds.DSInfoType = "UNSPECIFIED";
}
// LOOK! For METS backward compatibility:
// If we have a METS MDClass value, and DSFormatURI isn't already
// assigned, preserve MDClass and MDType in a DSFormatURI.
// Note that the system is taking over the DSFormatURI in this case.
// Therefore, if a client subsequently modifies the DSFormatURI
// this METS legacy informatin will be lost, in which case the inline
// datastream will default to amdSec/techMD in a subsequent METS export.
if (ds.DSControlGrp.equalsIgnoreCase("X")) {
if (((DatastreamXMLMetadata) ds).DSMDClass != 0
&& ds.DSFormatURI == null) {
String mdClassName = "";
String mdType = ds.DSInfoType;
String otherType = "";
if (((DatastreamXMLMetadata) ds).DSMDClass == 1) {
mdClassName = "techMD";
} else if (((DatastreamXMLMetadata) ds).DSMDClass == 2) {
mdClassName = "sourceMD";
} else if (((DatastreamXMLMetadata) ds).DSMDClass == 3) {
mdClassName = "rightsMD";
} else if (((DatastreamXMLMetadata) ds).DSMDClass == 4) {
mdClassName = "digiprovMD";
} else if (((DatastreamXMLMetadata) ds).DSMDClass == 5) {
mdClassName = "descMD";
}
if (!mdType.equals("MARC") && !mdType.equals("EAD")
&& !mdType.equals("DC") && !mdType.equals("NISOIMG")
&& !mdType.equals("LC-AV") && !mdType.equals("VRA")
&& !mdType.equals("TEIHDR") && !mdType.equals("DDI")
&& !mdType.equals("FGDC")) {
mdType = "OTHER";
otherType = ds.DSInfoType;
}
ds.DSFormatURI =
"info:fedora/fedora-system:format/xml.mets."
+ mdClassName + "." + mdType + "." + otherType;
}
}
return ds;
}
|
[
"public",
"static",
"Datastream",
"setDatastreamDefaults",
"(",
"Datastream",
"ds",
")",
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"ObjectIntegrityException",
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"if",
"(",
"(",
"ds",
".",
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"(",
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"&&",
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"\"X\"",
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"\"text/xml\"",
";",
"}",
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")",
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"{",
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")",
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"(",
"\"OTHER\"",
")",
")",
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"// assigned, preserve MDClass and MDType in a DSFormatURI.",
"// Note that the system is taking over the DSFormatURI in this case.",
"// Therefore, if a client subsequently modifies the DSFormatURI",
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"}",
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"(",
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")",
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"\"OTHER\"",
";",
"otherType",
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";",
"}",
"ds",
".",
"DSFormatURI",
"=",
"\"info:fedora/fedora-system:format/xml.mets.\"",
"+",
"mdClassName",
"+",
"\".\"",
"+",
"mdType",
"+",
"\".\"",
"+",
"otherType",
";",
"}",
"}",
"return",
"ds",
";",
"}"
] |
Check for null values in attributes and set them to empty string so
'null' does not appear in XML attribute values. This helps in XML
validation of required attributes. If 'null' is the attribute value then
validation would incorrectly consider in a valid non-empty value. Also,
we set some other default values here.
@param ds
The Datastream object to work on.
@return The Datastream value with default set.
@throws ObjectIntegrityException
|
[
"Check",
"for",
"null",
"values",
"in",
"attributes",
"and",
"set",
"them",
"to",
"empty",
"string",
"so",
"null",
"does",
"not",
"appear",
"in",
"XML",
"attribute",
"values",
".",
"This",
"helps",
"in",
"XML",
"validation",
"of",
"required",
"attributes",
".",
"If",
"null",
"is",
"the",
"attribute",
"value",
"then",
"validation",
"would",
"incorrectly",
"consider",
"in",
"a",
"valid",
"non",
"-",
"empty",
"value",
".",
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"we",
"set",
"some",
"other",
"default",
"values",
"here",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/storage/translation/DOTranslationUtility.java#L618-L674
|
9,111
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/storage/translation/DOTranslationUtility.java
|
DOTranslationUtility.appendXMLStream
|
protected static void appendXMLStream(InputStream in,
PrintWriter writer,
String encoding)
throws ObjectIntegrityException, UnsupportedEncodingException,
StreamIOException {
if (in == null) {
throw new ObjectIntegrityException("Object's inline xml "
+ "stream cannot be null.");
}
try {
InputStreamReader chars =
new InputStreamReader(in, Charset.forName(encoding));
/* Content buffer */
char[] charBuf = new char[4096];
/* Beginning/ending whitespace buffer */
char[] wsBuf = new char[4096];
int len;
int start;
int end;
int wsLen = 0;
boolean atBeginning = true;
while ((len = chars.read(charBuf)) != -1) {
start = 0;
end = len - 1;
/* Strip out any leading whitespace */
if (atBeginning) {
while (start < len) {
if (charBuf[start] > 0x20) break;
start++;
}
if (start < len) atBeginning = false;
}
/*
* Hold aside any whitespace at the end of the current chunk. If
* we make it to the next chunk, then append our whitespace to
* the buffer. Using this methodology, we may "trim" at most
* {buffer length} characters from the end.
*/
if (wsLen > 0) {
/* Commit previous ending whitespace */
writer.write(wsBuf, 0, wsLen);
wsLen = 0;
}
while (end > start) {
/* Buffer current ending whitespace */
if (charBuf[end] > 0x20) break;
wsBuf[wsLen] = charBuf[end];
wsLen++;
end--;
}
if (start < len) {
writer.write(charBuf, start, end + 1 - start);
}
}
} catch (UnsupportedEncodingException uee) {
throw uee;
} catch (IOException ioe) {
throw new StreamIOException("Error reading from inline xml datastream.");
} finally {
try {
in.close();
} catch (IOException closeProb) {
throw new StreamIOException("Error closing read stream.");
}
}
}
|
java
|
protected static void appendXMLStream(InputStream in,
PrintWriter writer,
String encoding)
throws ObjectIntegrityException, UnsupportedEncodingException,
StreamIOException {
if (in == null) {
throw new ObjectIntegrityException("Object's inline xml "
+ "stream cannot be null.");
}
try {
InputStreamReader chars =
new InputStreamReader(in, Charset.forName(encoding));
/* Content buffer */
char[] charBuf = new char[4096];
/* Beginning/ending whitespace buffer */
char[] wsBuf = new char[4096];
int len;
int start;
int end;
int wsLen = 0;
boolean atBeginning = true;
while ((len = chars.read(charBuf)) != -1) {
start = 0;
end = len - 1;
/* Strip out any leading whitespace */
if (atBeginning) {
while (start < len) {
if (charBuf[start] > 0x20) break;
start++;
}
if (start < len) atBeginning = false;
}
/*
* Hold aside any whitespace at the end of the current chunk. If
* we make it to the next chunk, then append our whitespace to
* the buffer. Using this methodology, we may "trim" at most
* {buffer length} characters from the end.
*/
if (wsLen > 0) {
/* Commit previous ending whitespace */
writer.write(wsBuf, 0, wsLen);
wsLen = 0;
}
while (end > start) {
/* Buffer current ending whitespace */
if (charBuf[end] > 0x20) break;
wsBuf[wsLen] = charBuf[end];
wsLen++;
end--;
}
if (start < len) {
writer.write(charBuf, start, end + 1 - start);
}
}
} catch (UnsupportedEncodingException uee) {
throw uee;
} catch (IOException ioe) {
throw new StreamIOException("Error reading from inline xml datastream.");
} finally {
try {
in.close();
} catch (IOException closeProb) {
throw new StreamIOException("Error closing read stream.");
}
}
}
|
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"static",
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",",
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"writer",
",",
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"throws",
"ObjectIntegrityException",
",",
"UnsupportedEncodingException",
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".",
"forName",
"(",
"encoding",
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")",
";",
"/* Content buffer */",
"char",
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"charBuf",
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"0",
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"/* Commit previous ending whitespace */",
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"0",
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"0",
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"}",
"}",
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"(",
"UnsupportedEncodingException",
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"throw",
"uee",
";",
"}",
"catch",
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"ioe",
")",
"{",
"throw",
"new",
"StreamIOException",
"(",
"\"Error reading from inline xml datastream.\"",
")",
";",
"}",
"finally",
"{",
"try",
"{",
"in",
".",
"close",
"(",
")",
";",
"}",
"catch",
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"IOException",
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")",
"{",
"throw",
"new",
"StreamIOException",
"(",
"\"Error closing read stream.\"",
")",
";",
"}",
"}",
"}"
] |
Appends XML to a PrintWriter. Essentially, just appends all text content
of the inputStream, trimming any leading and trailing whitespace. It does
his in a streaming fashion, with resource consumption entirely comprised
of fixed internal buffers.
@param in
InputStreaming containing serialized XML.
@param writer
PrintWriter to write XML content to.
@param encoding
Character set encoding.
|
[
"Appends",
"XML",
"to",
"a",
"PrintWriter",
".",
"Essentially",
"just",
"appends",
"all",
"text",
"content",
"of",
"the",
"inputStream",
"trimming",
"any",
"leading",
"and",
"trailing",
"whitespace",
".",
"It",
"does",
"his",
"in",
"a",
"streaming",
"fashion",
"with",
"resource",
"consumption",
"entirely",
"comprised",
"of",
"fixed",
"internal",
"buffers",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/storage/translation/DOTranslationUtility.java#L689-L762
|
9,112
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/storage/translation/DOTranslationUtility.java
|
DOTranslationUtility.validateAudit
|
protected static void validateAudit(AuditRecord audit)
throws ObjectIntegrityException {
if (audit.id == null || audit.id.isEmpty()) {
throw new ObjectIntegrityException("Audit record must have id.");
}
if (audit.date == null) {
throw new ObjectIntegrityException("Audit record must have date.");
}
if (audit.processType == null || audit.processType.isEmpty()) {
throw new ObjectIntegrityException("Audit record must have processType.");
}
if (audit.action == null || audit.action.isEmpty()) {
throw new ObjectIntegrityException("Audit record must have action.");
}
if (audit.componentID == null) {
audit.componentID = ""; // for backwards compatibility, no error on null
// throw new ObjectIntegrityException("Audit record must have componentID.");
}
if (audit.responsibility == null || audit.responsibility.isEmpty()) {
throw new ObjectIntegrityException("Audit record must have responsibility.");
}
}
|
java
|
protected static void validateAudit(AuditRecord audit)
throws ObjectIntegrityException {
if (audit.id == null || audit.id.isEmpty()) {
throw new ObjectIntegrityException("Audit record must have id.");
}
if (audit.date == null) {
throw new ObjectIntegrityException("Audit record must have date.");
}
if (audit.processType == null || audit.processType.isEmpty()) {
throw new ObjectIntegrityException("Audit record must have processType.");
}
if (audit.action == null || audit.action.isEmpty()) {
throw new ObjectIntegrityException("Audit record must have action.");
}
if (audit.componentID == null) {
audit.componentID = ""; // for backwards compatibility, no error on null
// throw new ObjectIntegrityException("Audit record must have componentID.");
}
if (audit.responsibility == null || audit.responsibility.isEmpty()) {
throw new ObjectIntegrityException("Audit record must have responsibility.");
}
}
|
[
"protected",
"static",
"void",
"validateAudit",
"(",
"AuditRecord",
"audit",
")",
"throws",
"ObjectIntegrityException",
"{",
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"audit",
".",
"id",
"==",
"null",
"||",
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".",
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".",
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")",
")",
"{",
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")",
";",
"}",
"if",
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"audit",
".",
"date",
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"null",
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"processType",
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"componentID",
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"null",
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"audit",
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"\"\"",
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"// for backwards compatibility, no error on null",
"// throw new ObjectIntegrityException(\"Audit record must have componentID.\");",
"}",
"if",
"(",
"audit",
".",
"responsibility",
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"null",
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".",
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")",
"{",
"throw",
"new",
"ObjectIntegrityException",
"(",
"\"Audit record must have responsibility.\"",
")",
";",
"}",
"}"
] |
The audit record is created by the system, so programmatic validation
here is o.k. Normally, validation takes place via XML Schema and
Schematron.
@param audit
@throws ObjectIntegrityException
|
[
"The",
"audit",
"record",
"is",
"created",
"by",
"the",
"system",
"so",
"programmatic",
"validation",
"here",
"is",
"o",
".",
"k",
".",
"Normally",
"validation",
"takes",
"place",
"via",
"XML",
"Schema",
"and",
"Schematron",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/storage/translation/DOTranslationUtility.java#L917-L938
|
9,113
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/config/Parameter.java
|
Parameter.getValue
|
public String getValue(boolean asAbsolutePath) {
String path = m_value;
if (asAbsolutePath) {
if (path != null && m_isFilePath) {
File f = new File(path);
if (!f.isAbsolute()) {
path = FEDORA_HOME + File.separator + path;
}
}
}
return path;
}
|
java
|
public String getValue(boolean asAbsolutePath) {
String path = m_value;
if (asAbsolutePath) {
if (path != null && m_isFilePath) {
File f = new File(path);
if (!f.isAbsolute()) {
path = FEDORA_HOME + File.separator + path;
}
}
}
return path;
}
|
[
"public",
"String",
"getValue",
"(",
"boolean",
"asAbsolutePath",
")",
"{",
"String",
"path",
"=",
"m_value",
";",
"if",
"(",
"asAbsolutePath",
")",
"{",
"if",
"(",
"path",
"!=",
"null",
"&&",
"m_isFilePath",
")",
"{",
"File",
"f",
"=",
"new",
"File",
"(",
"path",
")",
";",
"if",
"(",
"!",
"f",
".",
"isAbsolute",
"(",
")",
")",
"{",
"path",
"=",
"FEDORA_HOME",
"+",
"File",
".",
"separator",
"+",
"path",
";",
"}",
"}",
"}",
"return",
"path",
";",
"}"
] |
Gets the value of the parameter. Prepends the location of FEDORA_HOME if
asAbsolutePath is true and the parameter location does not already
specify an absolute pathname.
@param asAbsolutePath
Whether to return the parameter value as an absolute file path
relative to FEDORA_HOME.
@return The value, null if undefined.
|
[
"Gets",
"the",
"value",
"of",
"the",
"parameter",
".",
"Prepends",
"the",
"location",
"of",
"FEDORA_HOME",
"if",
"asAbsolutePath",
"is",
"true",
"and",
"the",
"parameter",
"location",
"does",
"not",
"already",
"specify",
"an",
"absolute",
"pathname",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/config/Parameter.java#L73-L84
|
9,114
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/journal/entry/JournalEntry.java
|
JournalEntry.addArgument
|
public void addArgument(String key, InputStream stream)
throws JournalException {
checkOpen();
if (stream == null) {
arguments.put(key, null);
} else {
try {
File tempFile = JournalHelper.copyToTempFile(stream);
arguments.put(key, tempFile);
} catch (IOException e) {
throw new JournalException(e);
}
}
}
|
java
|
public void addArgument(String key, InputStream stream)
throws JournalException {
checkOpen();
if (stream == null) {
arguments.put(key, null);
} else {
try {
File tempFile = JournalHelper.copyToTempFile(stream);
arguments.put(key, tempFile);
} catch (IOException e) {
throw new JournalException(e);
}
}
}
|
[
"public",
"void",
"addArgument",
"(",
"String",
"key",
",",
"InputStream",
"stream",
")",
"throws",
"JournalException",
"{",
"checkOpen",
"(",
")",
";",
"if",
"(",
"stream",
"==",
"null",
")",
"{",
"arguments",
".",
"put",
"(",
"key",
",",
"null",
")",
";",
"}",
"else",
"{",
"try",
"{",
"File",
"tempFile",
"=",
"JournalHelper",
".",
"copyToTempFile",
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"stream",
")",
";",
"arguments",
".",
"put",
"(",
"key",
",",
"tempFile",
")",
";",
"}",
"catch",
"(",
"IOException",
"e",
")",
"{",
"throw",
"new",
"JournalException",
"(",
"e",
")",
";",
"}",
"}",
"}"
] |
If handed an InputStream as an argument, copy it to a temp file and store
that File in the arguments map instead. If the InputStream is null, store
null in the arguments map.
|
[
"If",
"handed",
"an",
"InputStream",
"as",
"an",
"argument",
"copy",
"it",
"to",
"a",
"temp",
"file",
"and",
"store",
"that",
"File",
"in",
"the",
"arguments",
"map",
"instead",
".",
"If",
"the",
"InputStream",
"is",
"null",
"store",
"null",
"in",
"the",
"arguments",
"map",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/journal/entry/JournalEntry.java#L93-L106
|
9,115
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/journal/entry/JournalEntry.java
|
JournalEntry.getStreamArgument
|
public InputStream getStreamArgument(String name) throws JournalException {
checkOpen();
File file = (File) arguments.get(name);
if (file == null) {
return null;
} else {
try {
return new FileInputStream(file);
} catch (FileNotFoundException e) {
throw new JournalException(e);
}
}
}
|
java
|
public InputStream getStreamArgument(String name) throws JournalException {
checkOpen();
File file = (File) arguments.get(name);
if (file == null) {
return null;
} else {
try {
return new FileInputStream(file);
} catch (FileNotFoundException e) {
throw new JournalException(e);
}
}
}
|
[
"public",
"InputStream",
"getStreamArgument",
"(",
"String",
"name",
")",
"throws",
"JournalException",
"{",
"checkOpen",
"(",
")",
";",
"File",
"file",
"=",
"(",
"File",
")",
"arguments",
".",
"get",
"(",
"name",
")",
";",
"if",
"(",
"file",
"==",
"null",
")",
"{",
"return",
"null",
";",
"}",
"else",
"{",
"try",
"{",
"return",
"new",
"FileInputStream",
"(",
"file",
")",
";",
"}",
"catch",
"(",
"FileNotFoundException",
"e",
")",
"{",
"throw",
"new",
"JournalException",
"(",
"e",
")",
";",
"}",
"}",
"}"
] |
If they ask for an InputStream argument, get the File from the arguments
map and create an InputStream on that file. If the value from the map is
null, return null.
|
[
"If",
"they",
"ask",
"for",
"an",
"InputStream",
"argument",
"get",
"the",
"File",
"from",
"the",
"arguments",
"map",
"and",
"create",
"an",
"InputStream",
"on",
"that",
"file",
".",
"If",
"the",
"value",
"from",
"the",
"map",
"is",
"null",
"return",
"null",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/journal/entry/JournalEntry.java#L153-L165
|
9,116
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/journal/entry/JournalEntry.java
|
JournalEntry.close
|
public void close() {
checkOpen();
open = false;
for (Object arg : arguments.values()) {
if (arg instanceof File) {
File file = (File) arg;
if (JournalHelper.isTempFile(file)) {
if (file.exists()) {
file.delete();
}
}
}
}
}
|
java
|
public void close() {
checkOpen();
open = false;
for (Object arg : arguments.values()) {
if (arg instanceof File) {
File file = (File) arg;
if (JournalHelper.isTempFile(file)) {
if (file.exists()) {
file.delete();
}
}
}
}
}
|
[
"public",
"void",
"close",
"(",
")",
"{",
"checkOpen",
"(",
")",
";",
"open",
"=",
"false",
";",
"for",
"(",
"Object",
"arg",
":",
"arguments",
".",
"values",
"(",
")",
")",
"{",
"if",
"(",
"arg",
"instanceof",
"File",
")",
"{",
"File",
"file",
"=",
"(",
"File",
")",
"arg",
";",
"if",
"(",
"JournalHelper",
".",
"isTempFile",
"(",
"file",
")",
")",
"{",
"if",
"(",
"file",
".",
"exists",
"(",
")",
")",
"{",
"file",
".",
"delete",
"(",
")",
";",
"}",
"}",
"}",
"}",
"}"
] |
This should be called when usage of the object is complete, to clean up
any temporary files that were created for the journal entry to use.
|
[
"This",
"should",
"be",
"called",
"when",
"usage",
"of",
"the",
"object",
"is",
"complete",
"to",
"clean",
"up",
"any",
"temporary",
"files",
"that",
"were",
"created",
"for",
"the",
"journal",
"entry",
"to",
"use",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/journal/entry/JournalEntry.java#L171-L186
|
9,117
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/journal/readerwriter/multifile/JournalOutputFile.java
|
JournalOutputFile.createTempFilename
|
private File createTempFilename(File permanentFile, File journalDirectory) {
String tempFilename = "_" + permanentFile.getName();
File file2 = new File(journalDirectory, tempFilename);
return file2;
}
|
java
|
private File createTempFilename(File permanentFile, File journalDirectory) {
String tempFilename = "_" + permanentFile.getName();
File file2 = new File(journalDirectory, tempFilename);
return file2;
}
|
[
"private",
"File",
"createTempFilename",
"(",
"File",
"permanentFile",
",",
"File",
"journalDirectory",
")",
"{",
"String",
"tempFilename",
"=",
"\"_\"",
"+",
"permanentFile",
".",
"getName",
"(",
")",
";",
"File",
"file2",
"=",
"new",
"File",
"(",
"journalDirectory",
",",
"tempFilename",
")",
";",
"return",
"file2",
";",
"}"
] |
The "temporary" filename is the permanent name preceded by an underscore.
|
[
"The",
"temporary",
"filename",
"is",
"the",
"permanent",
"name",
"preceded",
"by",
"an",
"underscore",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/journal/readerwriter/multifile/JournalOutputFile.java#L131-L135
|
9,118
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/journal/readerwriter/multifile/JournalOutputFile.java
|
JournalOutputFile.createTempFile
|
private FileWriter createTempFile(File tempfile) throws IOException,
JournalException {
boolean created = tempfile.createNewFile();
if (!created) {
throw new JournalException("Unable to create file '"
+ tempfile.getPath() + "'.");
}
return new FileWriter(tempfile);
}
|
java
|
private FileWriter createTempFile(File tempfile) throws IOException,
JournalException {
boolean created = tempfile.createNewFile();
if (!created) {
throw new JournalException("Unable to create file '"
+ tempfile.getPath() + "'.");
}
return new FileWriter(tempfile);
}
|
[
"private",
"FileWriter",
"createTempFile",
"(",
"File",
"tempfile",
")",
"throws",
"IOException",
",",
"JournalException",
"{",
"boolean",
"created",
"=",
"tempfile",
".",
"createNewFile",
"(",
")",
";",
"if",
"(",
"!",
"created",
")",
"{",
"throw",
"new",
"JournalException",
"(",
"\"Unable to create file '\"",
"+",
"tempfile",
".",
"getPath",
"(",
")",
"+",
"\"'.\"",
")",
";",
"}",
"return",
"new",
"FileWriter",
"(",
"tempfile",
")",
";",
"}"
] |
Create and open the temporary file.
|
[
"Create",
"and",
"open",
"the",
"temporary",
"file",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/journal/readerwriter/multifile/JournalOutputFile.java#L140-L148
|
9,119
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/journal/readerwriter/multifile/JournalOutputFile.java
|
JournalOutputFile.createXmlEventWriter
|
private XMLEventWriter createXmlEventWriter(FileWriter fileWriter)
throws FactoryConfigurationError, XMLStreamException {
XMLOutputFactory factory = XMLOutputFactory.newInstance();
return new IndentingXMLEventWriter(factory
.createXMLEventWriter(fileWriter));
}
|
java
|
private XMLEventWriter createXmlEventWriter(FileWriter fileWriter)
throws FactoryConfigurationError, XMLStreamException {
XMLOutputFactory factory = XMLOutputFactory.newInstance();
return new IndentingXMLEventWriter(factory
.createXMLEventWriter(fileWriter));
}
|
[
"private",
"XMLEventWriter",
"createXmlEventWriter",
"(",
"FileWriter",
"fileWriter",
")",
"throws",
"FactoryConfigurationError",
",",
"XMLStreamException",
"{",
"XMLOutputFactory",
"factory",
"=",
"XMLOutputFactory",
".",
"newInstance",
"(",
")",
";",
"return",
"new",
"IndentingXMLEventWriter",
"(",
"factory",
".",
"createXMLEventWriter",
"(",
"fileWriter",
")",
")",
";",
"}"
] |
Create an XMLEventWriter for this file. Make it a pretty, indenting
writer.
|
[
"Create",
"an",
"XMLEventWriter",
"for",
"this",
"file",
".",
"Make",
"it",
"a",
"pretty",
"indenting",
"writer",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/journal/readerwriter/multifile/JournalOutputFile.java#L154-L159
|
9,120
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/journal/readerwriter/multifile/JournalOutputFile.java
|
JournalOutputFile.closeIfAppropriate
|
public void closeIfAppropriate() throws JournalException {
synchronized (JournalWriter.SYNCHRONIZER) {
if (!open) {
return;
}
// if the size limit is 0 or negative, treat it as "no limit".
long currentSize = tempFile.length();
if (sizeLimit > 0 && currentSize > sizeLimit) {
close();
}
}
}
|
java
|
public void closeIfAppropriate() throws JournalException {
synchronized (JournalWriter.SYNCHRONIZER) {
if (!open) {
return;
}
// if the size limit is 0 or negative, treat it as "no limit".
long currentSize = tempFile.length();
if (sizeLimit > 0 && currentSize > sizeLimit) {
close();
}
}
}
|
[
"public",
"void",
"closeIfAppropriate",
"(",
")",
"throws",
"JournalException",
"{",
"synchronized",
"(",
"JournalWriter",
".",
"SYNCHRONIZER",
")",
"{",
"if",
"(",
"!",
"open",
")",
"{",
"return",
";",
"}",
"// if the size limit is 0 or negative, treat it as \"no limit\".",
"long",
"currentSize",
"=",
"tempFile",
".",
"length",
"(",
")",
";",
"if",
"(",
"sizeLimit",
">",
"0",
"&&",
"currentSize",
">",
"sizeLimit",
")",
"{",
"close",
"(",
")",
";",
"}",
"}",
"}"
] |
Check the size limit and see whether the file is big enough to close. We
could also check the age limit here, but we trust the timer to handle
that.
|
[
"Check",
"the",
"size",
"limit",
"and",
"see",
"whether",
"the",
"file",
"is",
"big",
"enough",
"to",
"close",
".",
"We",
"could",
"also",
"check",
"the",
"age",
"limit",
"here",
"but",
"we",
"trust",
"the",
"timer",
"to",
"handle",
"that",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/journal/readerwriter/multifile/JournalOutputFile.java#L191-L203
|
9,121
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/journal/readerwriter/multifile/JournalOutputFile.java
|
JournalOutputFile.close
|
public void close() throws JournalException {
synchronized (JournalWriter.SYNCHRONIZER) {
if (!open) {
return;
}
try {
parent.getDocumentTrailer(xmlWriter);
xmlWriter.close();
fileWriter.close();
timer.cancel();
/*
* java.io.File.renameTo() has a known bug when working across
* file-systems, see:
* http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=4073756 So
* instead of this call: tempFile.renameTo(file); We use the
* following line, and check for exception...
*/
try {
FileMovingUtil.move(tempFile, file);
} catch (IOException e) {
throw new JournalException("Failed to rename file from '"
+ tempFile.getPath() + "' to '" + file.getPath()
+ "'", e);
}
open = false;
} catch (XMLStreamException e) {
throw new JournalException(e);
} catch (IOException e) {
throw new JournalException(e);
}
}
}
|
java
|
public void close() throws JournalException {
synchronized (JournalWriter.SYNCHRONIZER) {
if (!open) {
return;
}
try {
parent.getDocumentTrailer(xmlWriter);
xmlWriter.close();
fileWriter.close();
timer.cancel();
/*
* java.io.File.renameTo() has a known bug when working across
* file-systems, see:
* http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=4073756 So
* instead of this call: tempFile.renameTo(file); We use the
* following line, and check for exception...
*/
try {
FileMovingUtil.move(tempFile, file);
} catch (IOException e) {
throw new JournalException("Failed to rename file from '"
+ tempFile.getPath() + "' to '" + file.getPath()
+ "'", e);
}
open = false;
} catch (XMLStreamException e) {
throw new JournalException(e);
} catch (IOException e) {
throw new JournalException(e);
}
}
}
|
[
"public",
"void",
"close",
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")",
"throws",
"JournalException",
"{",
"synchronized",
"(",
"JournalWriter",
".",
"SYNCHRONIZER",
")",
"{",
"if",
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"!",
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"{",
"return",
";",
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"try",
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"getDocumentTrailer",
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"fileWriter",
".",
"close",
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";",
"timer",
".",
"cancel",
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"/*\n * java.io.File.renameTo() has a known bug when working across\n * file-systems, see:\n * http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=4073756 So\n * instead of this call: tempFile.renameTo(file); We use the\n * following line, and check for exception...\n */",
"try",
"{",
"FileMovingUtil",
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"move",
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"file",
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"getPath",
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"e",
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"{",
"throw",
"new",
"JournalException",
"(",
"e",
")",
";",
"}",
"}",
"}"
] |
Write the document trailer, clean up everything and rename the file. Set
the flag saying we are closed.
|
[
"Write",
"the",
"document",
"trailer",
"clean",
"up",
"everything",
"and",
"rename",
"the",
"file",
".",
"Set",
"the",
"flag",
"saying",
"we",
"are",
"closed",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/journal/readerwriter/multifile/JournalOutputFile.java#L218-L252
|
9,122
|
fcrepo3/fcrepo
|
fcrepo-security/fcrepo-security-pdp/src/main/java/org/fcrepo/server/security/xacml/pdp/HierarchicalLowestChildDenyOverridesPolicyAlg.java
|
HierarchicalLowestChildDenyOverridesPolicyAlg.combine
|
@Override
@SuppressWarnings("unchecked")
public Result combine(EvaluationCtx context,
@SuppressWarnings("rawtypes") List parameters,
@SuppressWarnings("rawtypes") List policyElements) {
logger.info("Combining using: " + getIdentifier());
boolean atLeastOneError = false;
boolean atLeastOnePermit = false;
Set<Set<?>> denyObligations = new HashSet<Set<?>>();
Status firstIndeterminateStatus = null;
Set<AbstractPolicy> matchedPolicies = new HashSet<AbstractPolicy>();
Iterator<?> it = policyElements.iterator();
while (it.hasNext()) {
AbstractPolicy policy =
((PolicyCombinerElement) it.next()).getPolicy();
// make sure that the policy matches the context
MatchResult match = policy.match(context);
if (match.getResult() == MatchResult.INDETERMINATE) {
atLeastOneError = true;
// keep track of the first error, regardless of cause
if (firstIndeterminateStatus == null) {
firstIndeterminateStatus = match.getStatus();
}
} else if (match.getResult() == MatchResult.MATCH) {
matchedPolicies.add(policy);
}
}
Set<AbstractPolicy> applicablePolicies =
getApplicablePolicies(context, matchedPolicies);
for (AbstractPolicy policy : applicablePolicies) {
Result result = policy.evaluate(context);
int effect = result.getDecision();
if (effect == Result.DECISION_DENY) {
denyObligations.addAll(result.getObligations());
return new Result(Result.DECISION_DENY, context.getResourceId()
.encode(), denyObligations);
}
if (effect == Result.DECISION_PERMIT) {
atLeastOnePermit = true;
} else if (effect == Result.DECISION_INDETERMINATE) {
atLeastOneError = true;
// keep track of the first error, regardless of cause
if (firstIndeterminateStatus == null) {
firstIndeterminateStatus = result.getStatus();
}
}
}
// if we got a PERMIT, return it
if (atLeastOnePermit) {
return new Result(Result.DECISION_PERMIT, context.getResourceId()
.encode());
}
// if we got an INDETERMINATE, return it
if (atLeastOneError) {
return new Result(Result.DECISION_INDETERMINATE,
firstIndeterminateStatus,
context.getResourceId().encode());
}
// if we got here, then nothing applied to us
return new Result(Result.DECISION_NOT_APPLICABLE, context
.getResourceId().encode());
}
|
java
|
@Override
@SuppressWarnings("unchecked")
public Result combine(EvaluationCtx context,
@SuppressWarnings("rawtypes") List parameters,
@SuppressWarnings("rawtypes") List policyElements) {
logger.info("Combining using: " + getIdentifier());
boolean atLeastOneError = false;
boolean atLeastOnePermit = false;
Set<Set<?>> denyObligations = new HashSet<Set<?>>();
Status firstIndeterminateStatus = null;
Set<AbstractPolicy> matchedPolicies = new HashSet<AbstractPolicy>();
Iterator<?> it = policyElements.iterator();
while (it.hasNext()) {
AbstractPolicy policy =
((PolicyCombinerElement) it.next()).getPolicy();
// make sure that the policy matches the context
MatchResult match = policy.match(context);
if (match.getResult() == MatchResult.INDETERMINATE) {
atLeastOneError = true;
// keep track of the first error, regardless of cause
if (firstIndeterminateStatus == null) {
firstIndeterminateStatus = match.getStatus();
}
} else if (match.getResult() == MatchResult.MATCH) {
matchedPolicies.add(policy);
}
}
Set<AbstractPolicy> applicablePolicies =
getApplicablePolicies(context, matchedPolicies);
for (AbstractPolicy policy : applicablePolicies) {
Result result = policy.evaluate(context);
int effect = result.getDecision();
if (effect == Result.DECISION_DENY) {
denyObligations.addAll(result.getObligations());
return new Result(Result.DECISION_DENY, context.getResourceId()
.encode(), denyObligations);
}
if (effect == Result.DECISION_PERMIT) {
atLeastOnePermit = true;
} else if (effect == Result.DECISION_INDETERMINATE) {
atLeastOneError = true;
// keep track of the first error, regardless of cause
if (firstIndeterminateStatus == null) {
firstIndeterminateStatus = result.getStatus();
}
}
}
// if we got a PERMIT, return it
if (atLeastOnePermit) {
return new Result(Result.DECISION_PERMIT, context.getResourceId()
.encode());
}
// if we got an INDETERMINATE, return it
if (atLeastOneError) {
return new Result(Result.DECISION_INDETERMINATE,
firstIndeterminateStatus,
context.getResourceId().encode());
}
// if we got here, then nothing applied to us
return new Result(Result.DECISION_NOT_APPLICABLE, context
.getResourceId().encode());
}
|
[
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",",
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"DECISION_DENY",
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"addAll",
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"getObligations",
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"{",
"atLeastOnePermit",
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"true",
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"true",
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"(",
"firstIndeterminateStatus",
"==",
"null",
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"{",
"firstIndeterminateStatus",
"=",
"result",
".",
"getStatus",
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")",
";",
"}",
"}",
"}",
"// if we got a PERMIT, return it",
"if",
"(",
"atLeastOnePermit",
")",
"{",
"return",
"new",
"Result",
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"DECISION_PERMIT",
",",
"context",
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"}",
"// if we got an INDETERMINATE, return it",
"if",
"(",
"atLeastOneError",
")",
"{",
"return",
"new",
"Result",
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"DECISION_INDETERMINATE",
",",
"firstIndeterminateStatus",
",",
"context",
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"getResourceId",
"(",
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"// if we got here, then nothing applied to us",
"return",
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"Result",
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"DECISION_NOT_APPLICABLE",
",",
"context",
".",
"getResourceId",
"(",
")",
".",
"encode",
"(",
")",
")",
";",
"}"
] |
Applies the combining rule to the set of policies based on the evaluation
context.
@param context
the context from the request
@param parameters
a (possibly empty) non-null <code>List</code> of
<code>CombinerParameter</code>s
@param policyElements
the policies to combine
@return the result of running the combining algorithm
|
[
"Applies",
"the",
"combining",
"rule",
"to",
"the",
"set",
"of",
"policies",
"based",
"on",
"the",
"evaluation",
"context",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-security/fcrepo-security-pdp/src/main/java/org/fcrepo/server/security/xacml/pdp/HierarchicalLowestChildDenyOverridesPolicyAlg.java#L106-L181
|
9,123
|
fcrepo3/fcrepo
|
fcrepo-security/fcrepo-security-pdp/src/main/java/org/fcrepo/server/security/xacml/pdp/decorator/PolicyIndexInvocationHandler.java
|
PolicyIndexInvocationHandler.invokeTarget
|
private Object invokeTarget(Object target, Method method, Object[] args) throws Throwable {
Object returnValue;
try {
returnValue = method.invoke(target, args);
} catch(InvocationTargetException ite) {
throw ite.getTargetException();
}
return returnValue;
}
|
java
|
private Object invokeTarget(Object target, Method method, Object[] args) throws Throwable {
Object returnValue;
try {
returnValue = method.invoke(target, args);
} catch(InvocationTargetException ite) {
throw ite.getTargetException();
}
return returnValue;
}
|
[
"private",
"Object",
"invokeTarget",
"(",
"Object",
"target",
",",
"Method",
"method",
",",
"Object",
"[",
"]",
"args",
")",
"throws",
"Throwable",
"{",
"Object",
"returnValue",
";",
"try",
"{",
"returnValue",
"=",
"method",
".",
"invoke",
"(",
"target",
",",
"args",
")",
";",
"}",
"catch",
"(",
"InvocationTargetException",
"ite",
")",
"{",
"throw",
"ite",
".",
"getTargetException",
"(",
")",
";",
"}",
"return",
"returnValue",
";",
"}"
] |
Invoke the underlying method, catching any InvocationTargetException and rethrowing the target exception
|
[
"Invoke",
"the",
"underlying",
"method",
"catching",
"any",
"InvocationTargetException",
"and",
"rethrowing",
"the",
"target",
"exception"
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-security/fcrepo-security-pdp/src/main/java/org/fcrepo/server/security/xacml/pdp/decorator/PolicyIndexInvocationHandler.java#L313-L321
|
9,124
|
fcrepo3/fcrepo
|
fcrepo-security/fcrepo-security-pdp/src/main/java/org/fcrepo/server/security/xacml/pdp/decorator/PolicyIndexInvocationHandler.java
|
PolicyIndexInvocationHandler.deletePolicy
|
private void deletePolicy(String pid) throws GeneralException {
LOG.debug("Deleting policy " + pid);
try {
// in case the policy doesn't exist (corrupt policy index, failed to add because invalid, etc)
m_policyIndex.deletePolicy(pid);
} catch (PolicyIndexException e) {
throw new GeneralException("Error deleting policy " + pid + " from policy index: " + e.getMessage(), e);
}
}
|
java
|
private void deletePolicy(String pid) throws GeneralException {
LOG.debug("Deleting policy " + pid);
try {
// in case the policy doesn't exist (corrupt policy index, failed to add because invalid, etc)
m_policyIndex.deletePolicy(pid);
} catch (PolicyIndexException e) {
throw new GeneralException("Error deleting policy " + pid + " from policy index: " + e.getMessage(), e);
}
}
|
[
"private",
"void",
"deletePolicy",
"(",
"String",
"pid",
")",
"throws",
"GeneralException",
"{",
"LOG",
".",
"debug",
"(",
"\"Deleting policy \"",
"+",
"pid",
")",
";",
"try",
"{",
"// in case the policy doesn't exist (corrupt policy index, failed to add because invalid, etc)",
"m_policyIndex",
".",
"deletePolicy",
"(",
"pid",
")",
";",
"}",
"catch",
"(",
"PolicyIndexException",
"e",
")",
"{",
"throw",
"new",
"GeneralException",
"(",
"\"Error deleting policy \"",
"+",
"pid",
"+",
"\" from policy index: \"",
"+",
"e",
".",
"getMessage",
"(",
")",
",",
"e",
")",
";",
"}",
"}"
] |
Remove the specified policy from the cache
@param pid
@throws PolicyIndexException
|
[
"Remove",
"the",
"specified",
"policy",
"from",
"the",
"cache"
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-security/fcrepo-security-pdp/src/main/java/org/fcrepo/server/security/xacml/pdp/decorator/PolicyIndexInvocationHandler.java#L366-L375
|
9,125
|
fcrepo3/fcrepo
|
fcrepo-common/src/main/java/org/fcrepo/utilities/NormalizedURI.java
|
NormalizedURI.defaultPort
|
private final static int defaultPort(String scheme) {
if (scheme == null) {
return -1;
}
Integer port = defaultPorts.get(scheme.trim().toLowerCase());
return (port != null) ? port.intValue() : -1;
}
|
java
|
private final static int defaultPort(String scheme) {
if (scheme == null) {
return -1;
}
Integer port = defaultPorts.get(scheme.trim().toLowerCase());
return (port != null) ? port.intValue() : -1;
}
|
[
"private",
"final",
"static",
"int",
"defaultPort",
"(",
"String",
"scheme",
")",
"{",
"if",
"(",
"scheme",
"==",
"null",
")",
"{",
"return",
"-",
"1",
";",
"}",
"Integer",
"port",
"=",
"defaultPorts",
".",
"get",
"(",
"scheme",
".",
"trim",
"(",
")",
".",
"toLowerCase",
"(",
")",
")",
";",
"return",
"(",
"port",
"!=",
"null",
")",
"?",
"port",
".",
"intValue",
"(",
")",
":",
"-",
"1",
";",
"}"
] |
Return the default port used by a given scheme.
@param the scheme, e.g. http
@return the port number, or -1 if unknown
|
[
"Return",
"the",
"default",
"port",
"used",
"by",
"a",
"given",
"scheme",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-common/src/main/java/org/fcrepo/utilities/NormalizedURI.java#L231-L237
|
9,126
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/storage/types/DeploymentDSBindRule.java
|
DeploymentDSBindRule.describeAllowedMimeTypes
|
public String describeAllowedMimeTypes() {
if (bindingMIMETypes == null || bindingMIMETypes.length == 0) {
return ANY_MIME_TYPE;
}
StringBuffer out = new StringBuffer();
for (int i = 0; i < bindingMIMETypes.length; i++) {
String allowed = bindingMIMETypes[i];
if (allowed == null) {
return ANY_MIME_TYPE;
}
if (allowed.equals("*/*")) {
return ANY_MIME_TYPE;
}
if (allowed.equals("*")) {
return ANY_MIME_TYPE;
}
if (i > 0) {
if (i < bindingMIMETypes.length - 1) {
out.append(", ");
} else {
if (i > 1) {
out.append(",");
}
out.append(" or ");
}
}
out.append(allowed);
}
return out.toString();
}
|
java
|
public String describeAllowedMimeTypes() {
if (bindingMIMETypes == null || bindingMIMETypes.length == 0) {
return ANY_MIME_TYPE;
}
StringBuffer out = new StringBuffer();
for (int i = 0; i < bindingMIMETypes.length; i++) {
String allowed = bindingMIMETypes[i];
if (allowed == null) {
return ANY_MIME_TYPE;
}
if (allowed.equals("*/*")) {
return ANY_MIME_TYPE;
}
if (allowed.equals("*")) {
return ANY_MIME_TYPE;
}
if (i > 0) {
if (i < bindingMIMETypes.length - 1) {
out.append(", ");
} else {
if (i > 1) {
out.append(",");
}
out.append(" or ");
}
}
out.append(allowed);
}
return out.toString();
}
|
[
"public",
"String",
"describeAllowedMimeTypes",
"(",
")",
"{",
"if",
"(",
"bindingMIMETypes",
"==",
"null",
"||",
"bindingMIMETypes",
".",
"length",
"==",
"0",
")",
"{",
"return",
"ANY_MIME_TYPE",
";",
"}",
"StringBuffer",
"out",
"=",
"new",
"StringBuffer",
"(",
")",
";",
"for",
"(",
"int",
"i",
"=",
"0",
";",
"i",
"<",
"bindingMIMETypes",
".",
"length",
";",
"i",
"++",
")",
"{",
"String",
"allowed",
"=",
"bindingMIMETypes",
"[",
"i",
"]",
";",
"if",
"(",
"allowed",
"==",
"null",
")",
"{",
"return",
"ANY_MIME_TYPE",
";",
"}",
"if",
"(",
"allowed",
".",
"equals",
"(",
"\"*/*\"",
")",
")",
"{",
"return",
"ANY_MIME_TYPE",
";",
"}",
"if",
"(",
"allowed",
".",
"equals",
"(",
"\"*\"",
")",
")",
"{",
"return",
"ANY_MIME_TYPE",
";",
"}",
"if",
"(",
"i",
">",
"0",
")",
"{",
"if",
"(",
"i",
"<",
"bindingMIMETypes",
".",
"length",
"-",
"1",
")",
"{",
"out",
".",
"append",
"(",
"\", \"",
")",
";",
"}",
"else",
"{",
"if",
"(",
"i",
">",
"1",
")",
"{",
"out",
".",
"append",
"(",
"\",\"",
")",
";",
"}",
"out",
".",
"append",
"(",
"\" or \"",
")",
";",
"}",
"}",
"out",
".",
"append",
"(",
"allowed",
")",
";",
"}",
"return",
"out",
".",
"toString",
"(",
")",
";",
"}"
] |
In human readable string, describe which mime types are allowed.
|
[
"In",
"human",
"readable",
"string",
"describe",
"which",
"mime",
"types",
"are",
"allowed",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/storage/types/DeploymentDSBindRule.java#L42-L71
|
9,127
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/journal/Journaler.java
|
Journaler.postInitModule
|
@Override
public void postInitModule() throws ModuleInitializationException {
ManagementDelegate delegate = serverInterface.getManagementDelegate();
if (delegate == null) {
throw new ModuleInitializationException("Can't get a ManagementDelegate from Server.getModule()",
getRole());
}
worker.setManagementDelegate(delegate);
}
|
java
|
@Override
public void postInitModule() throws ModuleInitializationException {
ManagementDelegate delegate = serverInterface.getManagementDelegate();
if (delegate == null) {
throw new ModuleInitializationException("Can't get a ManagementDelegate from Server.getModule()",
getRole());
}
worker.setManagementDelegate(delegate);
}
|
[
"@",
"Override",
"public",
"void",
"postInitModule",
"(",
")",
"throws",
"ModuleInitializationException",
"{",
"ManagementDelegate",
"delegate",
"=",
"serverInterface",
".",
"getManagementDelegate",
"(",
")",
";",
"if",
"(",
"delegate",
"==",
"null",
")",
"{",
"throw",
"new",
"ModuleInitializationException",
"(",
"\"Can't get a ManagementDelegate from Server.getModule()\"",
",",
"getRole",
"(",
")",
")",
";",
"}",
"worker",
".",
"setManagementDelegate",
"(",
"delegate",
")",
";",
"}"
] |
Get the ManagementDelegate module and pass it to the worker.
|
[
"Get",
"the",
"ManagementDelegate",
"module",
"and",
"pass",
"it",
"to",
"the",
"worker",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/journal/Journaler.java#L81-L89
|
9,128
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/journal/Journaler.java
|
Journaler.copyPropertiesOverParameters
|
private void copyPropertiesOverParameters(Map<String, String> parameters) {
Properties properties = System.getProperties();
for (Object object : properties.keySet()) {
String key = (String) object;
if (key.startsWith(SYSTEM_PROPERTY_PREFIX)) {
parameters.put(key.substring(SYSTEM_PROPERTY_PREFIX.length()),
properties.getProperty(key));
}
}
}
|
java
|
private void copyPropertiesOverParameters(Map<String, String> parameters) {
Properties properties = System.getProperties();
for (Object object : properties.keySet()) {
String key = (String) object;
if (key.startsWith(SYSTEM_PROPERTY_PREFIX)) {
parameters.put(key.substring(SYSTEM_PROPERTY_PREFIX.length()),
properties.getProperty(key));
}
}
}
|
[
"private",
"void",
"copyPropertiesOverParameters",
"(",
"Map",
"<",
"String",
",",
"String",
">",
"parameters",
")",
"{",
"Properties",
"properties",
"=",
"System",
".",
"getProperties",
"(",
")",
";",
"for",
"(",
"Object",
"object",
":",
"properties",
".",
"keySet",
"(",
")",
")",
"{",
"String",
"key",
"=",
"(",
"String",
")",
"object",
";",
"if",
"(",
"key",
".",
"startsWith",
"(",
"SYSTEM_PROPERTY_PREFIX",
")",
")",
"{",
"parameters",
".",
"put",
"(",
"key",
".",
"substring",
"(",
"SYSTEM_PROPERTY_PREFIX",
".",
"length",
"(",
")",
")",
",",
"properties",
".",
"getProperty",
"(",
"key",
")",
")",
";",
"}",
"}",
"}"
] |
Augment, and perhaps override, the server parameters, using any System
Property whose name begins with "fedora.journal.". So, for example, a
System Property of "fedora.journal.mode" will override a server parameter
of "mode".
|
[
"Augment",
"and",
"perhaps",
"override",
"the",
"server",
"parameters",
"using",
"any",
"System",
"Property",
"whose",
"name",
"begins",
"with",
"fedora",
".",
"journal",
".",
".",
"So",
"for",
"example",
"a",
"System",
"Property",
"of",
"fedora",
".",
"journal",
".",
"mode",
"will",
"override",
"a",
"server",
"parameter",
"of",
"mode",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/journal/Journaler.java#L105-L114
|
9,129
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/journal/Journaler.java
|
Journaler.parseParameters
|
private void parseParameters(Map<String, String> parameters)
throws ModuleInitializationException {
logger.info("Parameters: " + parameters);
String mode = parameters.get(PARAMETER_JOURNAL_MODE);
if (mode == null) {
inRecoveryMode = false;
} else if (mode.equals(VALUE_JOURNAL_MODE_NORMAL)) {
inRecoveryMode = false;
} else if (mode.equals(VALUE_JOURNAL_MODE_RECOVER)) {
inRecoveryMode = true;
} else {
throw new ModuleInitializationException("'"
+ PARAMETER_JOURNAL_MODE + "' parameter must be '"
+ VALUE_JOURNAL_MODE_NORMAL + "'(default) or '"
+ VALUE_JOURNAL_MODE_RECOVER + "'", getRole());
}
}
|
java
|
private void parseParameters(Map<String, String> parameters)
throws ModuleInitializationException {
logger.info("Parameters: " + parameters);
String mode = parameters.get(PARAMETER_JOURNAL_MODE);
if (mode == null) {
inRecoveryMode = false;
} else if (mode.equals(VALUE_JOURNAL_MODE_NORMAL)) {
inRecoveryMode = false;
} else if (mode.equals(VALUE_JOURNAL_MODE_RECOVER)) {
inRecoveryMode = true;
} else {
throw new ModuleInitializationException("'"
+ PARAMETER_JOURNAL_MODE + "' parameter must be '"
+ VALUE_JOURNAL_MODE_NORMAL + "'(default) or '"
+ VALUE_JOURNAL_MODE_RECOVER + "'", getRole());
}
}
|
[
"private",
"void",
"parseParameters",
"(",
"Map",
"<",
"String",
",",
"String",
">",
"parameters",
")",
"throws",
"ModuleInitializationException",
"{",
"logger",
".",
"info",
"(",
"\"Parameters: \"",
"+",
"parameters",
")",
";",
"String",
"mode",
"=",
"parameters",
".",
"get",
"(",
"PARAMETER_JOURNAL_MODE",
")",
";",
"if",
"(",
"mode",
"==",
"null",
")",
"{",
"inRecoveryMode",
"=",
"false",
";",
"}",
"else",
"if",
"(",
"mode",
".",
"equals",
"(",
"VALUE_JOURNAL_MODE_NORMAL",
")",
")",
"{",
"inRecoveryMode",
"=",
"false",
";",
"}",
"else",
"if",
"(",
"mode",
".",
"equals",
"(",
"VALUE_JOURNAL_MODE_RECOVER",
")",
")",
"{",
"inRecoveryMode",
"=",
"true",
";",
"}",
"else",
"{",
"throw",
"new",
"ModuleInitializationException",
"(",
"\"'\"",
"+",
"PARAMETER_JOURNAL_MODE",
"+",
"\"' parameter must be '\"",
"+",
"VALUE_JOURNAL_MODE_NORMAL",
"+",
"\"'(default) or '\"",
"+",
"VALUE_JOURNAL_MODE_RECOVER",
"+",
"\"'\"",
",",
"getRole",
"(",
")",
")",
";",
"}",
"}"
] |
Check the parameters for required values and for acceptable values. At
this point, the only parameter we care about is "mode".
|
[
"Check",
"the",
"parameters",
"for",
"required",
"values",
"and",
"for",
"acceptable",
"values",
".",
"At",
"this",
"point",
"the",
"only",
"parameter",
"we",
"care",
"about",
"is",
"mode",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/journal/Journaler.java#L120-L137
|
9,130
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/journal/JournalReader.java
|
JournalReader.getInstance
|
public static JournalReader getInstance(Map<String, String> parameters,
String role,
JournalRecoveryLog recoveryLog,
ServerInterface server)
throws ModuleInitializationException {
try {
Object journalReader =
JournalHelper
.createInstanceAccordingToParameter(PARAMETER_JOURNAL_READER_CLASSNAME,
new Class[] {
Map.class,
String.class,
JournalRecoveryLog.class,
ServerInterface.class},
new Object[] {
parameters,
role,
recoveryLog,
server},
parameters);
logger.info("JournalReader is " + journalReader.toString());
return (JournalReader) journalReader;
} catch (JournalException e) {
String msg = "Can't create JournalReader";
logger.error(msg, e);
throw new ModuleInitializationException(msg, role, e);
}
}
|
java
|
public static JournalReader getInstance(Map<String, String> parameters,
String role,
JournalRecoveryLog recoveryLog,
ServerInterface server)
throws ModuleInitializationException {
try {
Object journalReader =
JournalHelper
.createInstanceAccordingToParameter(PARAMETER_JOURNAL_READER_CLASSNAME,
new Class[] {
Map.class,
String.class,
JournalRecoveryLog.class,
ServerInterface.class},
new Object[] {
parameters,
role,
recoveryLog,
server},
parameters);
logger.info("JournalReader is " + journalReader.toString());
return (JournalReader) journalReader;
} catch (JournalException e) {
String msg = "Can't create JournalReader";
logger.error(msg, e);
throw new ModuleInitializationException(msg, role, e);
}
}
|
[
"public",
"static",
"JournalReader",
"getInstance",
"(",
"Map",
"<",
"String",
",",
"String",
">",
"parameters",
",",
"String",
"role",
",",
"JournalRecoveryLog",
"recoveryLog",
",",
"ServerInterface",
"server",
")",
"throws",
"ModuleInitializationException",
"{",
"try",
"{",
"Object",
"journalReader",
"=",
"JournalHelper",
".",
"createInstanceAccordingToParameter",
"(",
"PARAMETER_JOURNAL_READER_CLASSNAME",
",",
"new",
"Class",
"[",
"]",
"{",
"Map",
".",
"class",
",",
"String",
".",
"class",
",",
"JournalRecoveryLog",
".",
"class",
",",
"ServerInterface",
".",
"class",
"}",
",",
"new",
"Object",
"[",
"]",
"{",
"parameters",
",",
"role",
",",
"recoveryLog",
",",
"server",
"}",
",",
"parameters",
")",
";",
"logger",
".",
"info",
"(",
"\"JournalReader is \"",
"+",
"journalReader",
".",
"toString",
"(",
")",
")",
";",
"return",
"(",
"JournalReader",
")",
"journalReader",
";",
"}",
"catch",
"(",
"JournalException",
"e",
")",
"{",
"String",
"msg",
"=",
"\"Can't create JournalReader\"",
";",
"logger",
".",
"error",
"(",
"msg",
",",
"e",
")",
";",
"throw",
"new",
"ModuleInitializationException",
"(",
"msg",
",",
"role",
",",
"e",
")",
";",
"}",
"}"
] |
Create an instance of the proper JournalReader child class, as determined
by the server parameters.
|
[
"Create",
"an",
"instance",
"of",
"the",
"proper",
"JournalReader",
"child",
"class",
"as",
"determined",
"by",
"the",
"server",
"parameters",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/journal/JournalReader.java#L66-L94
|
9,131
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/journal/JournalReader.java
|
JournalReader.checkRepositoryHash
|
protected void checkRepositoryHash(String hash) throws JournalException {
if (!server.hasInitialized()) {
throw new IllegalStateException("The repository has is not available until "
+ "the server is fully initialized.");
}
JournalException hashException = null;
if (hash == null) {
hashException =
new JournalException("'" + QNAME_TAG_JOURNAL
+ "' tag must have a '"
+ QNAME_ATTR_REPOSITORY_HASH + "' attribute.");
} else {
try {
String currentHash = server.getRepositoryHash();
if (hash.equals(currentHash)) {
recoveryLog.log("Validated repository hash: '" + hash
+ "'.");
} else {
hashException =
new JournalException("'"
+ QNAME_ATTR_REPOSITORY_HASH
+ "' attribute in '"
+ QNAME_TAG_JOURNAL
+ "' tag does not match current repository hash: '"
+ hash + "' vs. '" + currentHash + "'.");
}
} catch (ServerException e) {
hashException = new JournalException(e);
}
}
if (hashException != null) {
if (ignoreHashErrors) {
recoveryLog.log("WARNING: " + hashException.getMessage());
} else {
throw hashException;
}
}
}
|
java
|
protected void checkRepositoryHash(String hash) throws JournalException {
if (!server.hasInitialized()) {
throw new IllegalStateException("The repository has is not available until "
+ "the server is fully initialized.");
}
JournalException hashException = null;
if (hash == null) {
hashException =
new JournalException("'" + QNAME_TAG_JOURNAL
+ "' tag must have a '"
+ QNAME_ATTR_REPOSITORY_HASH + "' attribute.");
} else {
try {
String currentHash = server.getRepositoryHash();
if (hash.equals(currentHash)) {
recoveryLog.log("Validated repository hash: '" + hash
+ "'.");
} else {
hashException =
new JournalException("'"
+ QNAME_ATTR_REPOSITORY_HASH
+ "' attribute in '"
+ QNAME_TAG_JOURNAL
+ "' tag does not match current repository hash: '"
+ hash + "' vs. '" + currentHash + "'.");
}
} catch (ServerException e) {
hashException = new JournalException(e);
}
}
if (hashException != null) {
if (ignoreHashErrors) {
recoveryLog.log("WARNING: " + hashException.getMessage());
} else {
throw hashException;
}
}
}
|
[
"protected",
"void",
"checkRepositoryHash",
"(",
"String",
"hash",
")",
"throws",
"JournalException",
"{",
"if",
"(",
"!",
"server",
".",
"hasInitialized",
"(",
")",
")",
"{",
"throw",
"new",
"IllegalStateException",
"(",
"\"The repository has is not available until \"",
"+",
"\"the server is fully initialized.\"",
")",
";",
"}",
"JournalException",
"hashException",
"=",
"null",
";",
"if",
"(",
"hash",
"==",
"null",
")",
"{",
"hashException",
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"new",
"JournalException",
"(",
"\"'\"",
"+",
"QNAME_TAG_JOURNAL",
"+",
"\"' tag must have a '\"",
"+",
"QNAME_ATTR_REPOSITORY_HASH",
"+",
"\"' attribute.\"",
")",
";",
"}",
"else",
"{",
"try",
"{",
"String",
"currentHash",
"=",
"server",
".",
"getRepositoryHash",
"(",
")",
";",
"if",
"(",
"hash",
".",
"equals",
"(",
"currentHash",
")",
")",
"{",
"recoveryLog",
".",
"log",
"(",
"\"Validated repository hash: '\"",
"+",
"hash",
"+",
"\"'.\"",
")",
";",
"}",
"else",
"{",
"hashException",
"=",
"new",
"JournalException",
"(",
"\"'\"",
"+",
"QNAME_ATTR_REPOSITORY_HASH",
"+",
"\"' attribute in '\"",
"+",
"QNAME_TAG_JOURNAL",
"+",
"\"' tag does not match current repository hash: '\"",
"+",
"hash",
"+",
"\"' vs. '\"",
"+",
"currentHash",
"+",
"\"'.\"",
")",
";",
"}",
"}",
"catch",
"(",
"ServerException",
"e",
")",
"{",
"hashException",
"=",
"new",
"JournalException",
"(",
"e",
")",
";",
"}",
"}",
"if",
"(",
"hashException",
"!=",
"null",
")",
"{",
"if",
"(",
"ignoreHashErrors",
")",
"{",
"recoveryLog",
".",
"log",
"(",
"\"WARNING: \"",
"+",
"hashException",
".",
"getMessage",
"(",
")",
")",
";",
"}",
"else",
"{",
"throw",
"hashException",
";",
"}",
"}",
"}"
] |
Compare the repository hash from the journal file with the current hash
obtained from the server. If they do not match, either throw an exception
or simply log it, depending on the parameters. This method must not be
called before the server has completed initialization. That's the only
way we can be confident that the DOManager is present, and ready to
create the repository has that we will compare to.
|
[
"Compare",
"the",
"repository",
"hash",
"from",
"the",
"journal",
"file",
"with",
"the",
"current",
"hash",
"obtained",
"from",
"the",
"server",
".",
"If",
"they",
"do",
"not",
"match",
"either",
"throw",
"an",
"exception",
"or",
"simply",
"log",
"it",
"depending",
"on",
"the",
"parameters",
".",
"This",
"method",
"must",
"not",
"be",
"called",
"before",
"the",
"server",
"has",
"completed",
"initialization",
".",
"That",
"s",
"the",
"only",
"way",
"we",
"can",
"be",
"confident",
"that",
"the",
"DOManager",
"is",
"present",
"and",
"ready",
"to",
"create",
"the",
"repository",
"has",
"that",
"we",
"will",
"compare",
"to",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/journal/JournalReader.java#L150-L191
|
9,132
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/journal/JournalReader.java
|
JournalReader.getJournalEntryStartTag
|
private StartElement getJournalEntryStartTag(XMLEventReader reader)
throws XMLStreamException, JournalException {
XMLEvent event = reader.nextTag();
if (!isStartTagEvent(event, QNAME_TAG_JOURNAL_ENTRY)) {
throw getNotStartTagException(QNAME_TAG_JOURNAL_ENTRY, event);
}
return event.asStartElement();
}
|
java
|
private StartElement getJournalEntryStartTag(XMLEventReader reader)
throws XMLStreamException, JournalException {
XMLEvent event = reader.nextTag();
if (!isStartTagEvent(event, QNAME_TAG_JOURNAL_ENTRY)) {
throw getNotStartTagException(QNAME_TAG_JOURNAL_ENTRY, event);
}
return event.asStartElement();
}
|
[
"private",
"StartElement",
"getJournalEntryStartTag",
"(",
"XMLEventReader",
"reader",
")",
"throws",
"XMLStreamException",
",",
"JournalException",
"{",
"XMLEvent",
"event",
"=",
"reader",
".",
"nextTag",
"(",
")",
";",
"if",
"(",
"!",
"isStartTagEvent",
"(",
"event",
",",
"QNAME_TAG_JOURNAL_ENTRY",
")",
")",
"{",
"throw",
"getNotStartTagException",
"(",
"QNAME_TAG_JOURNAL_ENTRY",
",",
"event",
")",
";",
"}",
"return",
"event",
".",
"asStartElement",
"(",
")",
";",
"}"
] |
Get the next event and complain if it isn't a JournalEntry start tag.
|
[
"Get",
"the",
"next",
"event",
"and",
"complain",
"if",
"it",
"isn",
"t",
"a",
"JournalEntry",
"start",
"tag",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/journal/JournalReader.java#L218-L225
|
9,133
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/journal/JournalReader.java
|
JournalReader.readArguments
|
private void readArguments(XMLEventReader reader, ConsumerJournalEntry cje)
throws XMLStreamException, JournalException {
while (true) {
XMLEvent nextTag = reader.nextTag();
if (isStartTagEvent(nextTag, QNAME_TAG_ARGUMENT)) {
readArgument(nextTag, reader, cje);
} else if (isEndTagEvent(nextTag, QNAME_TAG_JOURNAL_ENTRY)) {
return;
} else {
throw getNotNextMemberOrEndOfGroupException(QNAME_TAG_JOURNAL_ENTRY,
QNAME_TAG_ARGUMENT,
nextTag);
}
}
}
|
java
|
private void readArguments(XMLEventReader reader, ConsumerJournalEntry cje)
throws XMLStreamException, JournalException {
while (true) {
XMLEvent nextTag = reader.nextTag();
if (isStartTagEvent(nextTag, QNAME_TAG_ARGUMENT)) {
readArgument(nextTag, reader, cje);
} else if (isEndTagEvent(nextTag, QNAME_TAG_JOURNAL_ENTRY)) {
return;
} else {
throw getNotNextMemberOrEndOfGroupException(QNAME_TAG_JOURNAL_ENTRY,
QNAME_TAG_ARGUMENT,
nextTag);
}
}
}
|
[
"private",
"void",
"readArguments",
"(",
"XMLEventReader",
"reader",
",",
"ConsumerJournalEntry",
"cje",
")",
"throws",
"XMLStreamException",
",",
"JournalException",
"{",
"while",
"(",
"true",
")",
"{",
"XMLEvent",
"nextTag",
"=",
"reader",
".",
"nextTag",
"(",
")",
";",
"if",
"(",
"isStartTagEvent",
"(",
"nextTag",
",",
"QNAME_TAG_ARGUMENT",
")",
")",
"{",
"readArgument",
"(",
"nextTag",
",",
"reader",
",",
"cje",
")",
";",
"}",
"else",
"if",
"(",
"isEndTagEvent",
"(",
"nextTag",
",",
"QNAME_TAG_JOURNAL_ENTRY",
")",
")",
"{",
"return",
";",
"}",
"else",
"{",
"throw",
"getNotNextMemberOrEndOfGroupException",
"(",
"QNAME_TAG_JOURNAL_ENTRY",
",",
"QNAME_TAG_ARGUMENT",
",",
"nextTag",
")",
";",
"}",
"}",
"}"
] |
Read arguments and add them to the event, until we hit the end tag for
the event.
|
[
"Read",
"arguments",
"and",
"add",
"them",
"to",
"the",
"event",
"until",
"we",
"hit",
"the",
"end",
"tag",
"for",
"the",
"event",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/journal/JournalReader.java#L231-L245
|
9,134
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/journal/JournalReader.java
|
JournalReader.readStreamArgument
|
private void readStreamArgument(XMLEventReader reader,
ConsumerJournalEntry journalEntry,
String name) throws XMLStreamException,
JournalException {
try {
File tempFile = JournalHelper.createTempFile();
DecodingBase64OutputStream decoder =
new DecodingBase64OutputStream(new FileOutputStream(tempFile));
while (true) {
XMLEvent event = reader.nextEvent();
if (event.isCharacters()) {
decoder.write(event.asCharacters().getData());
} else if (isEndTagEvent(event, QNAME_TAG_ARGUMENT)) {
break;
} else {
throw getUnexpectedEventInArgumentException(name,
ARGUMENT_TYPE_STREAM,
journalEntry
.getMethodName(),
event);
}
}
decoder.close();
journalEntry.addArgument(name, tempFile);
} catch (IOException e) {
throw new JournalException("failed to write stream argument to temp file",
e);
}
}
|
java
|
private void readStreamArgument(XMLEventReader reader,
ConsumerJournalEntry journalEntry,
String name) throws XMLStreamException,
JournalException {
try {
File tempFile = JournalHelper.createTempFile();
DecodingBase64OutputStream decoder =
new DecodingBase64OutputStream(new FileOutputStream(tempFile));
while (true) {
XMLEvent event = reader.nextEvent();
if (event.isCharacters()) {
decoder.write(event.asCharacters().getData());
} else if (isEndTagEvent(event, QNAME_TAG_ARGUMENT)) {
break;
} else {
throw getUnexpectedEventInArgumentException(name,
ARGUMENT_TYPE_STREAM,
journalEntry
.getMethodName(),
event);
}
}
decoder.close();
journalEntry.addArgument(name, tempFile);
} catch (IOException e) {
throw new JournalException("failed to write stream argument to temp file",
e);
}
}
|
[
"private",
"void",
"readStreamArgument",
"(",
"XMLEventReader",
"reader",
",",
"ConsumerJournalEntry",
"journalEntry",
",",
"String",
"name",
")",
"throws",
"XMLStreamException",
",",
"JournalException",
"{",
"try",
"{",
"File",
"tempFile",
"=",
"JournalHelper",
".",
"createTempFile",
"(",
")",
";",
"DecodingBase64OutputStream",
"decoder",
"=",
"new",
"DecodingBase64OutputStream",
"(",
"new",
"FileOutputStream",
"(",
"tempFile",
")",
")",
";",
"while",
"(",
"true",
")",
"{",
"XMLEvent",
"event",
"=",
"reader",
".",
"nextEvent",
"(",
")",
";",
"if",
"(",
"event",
".",
"isCharacters",
"(",
")",
")",
"{",
"decoder",
".",
"write",
"(",
"event",
".",
"asCharacters",
"(",
")",
".",
"getData",
"(",
")",
")",
";",
"}",
"else",
"if",
"(",
"isEndTagEvent",
"(",
"event",
",",
"QNAME_TAG_ARGUMENT",
")",
")",
"{",
"break",
";",
"}",
"else",
"{",
"throw",
"getUnexpectedEventInArgumentException",
"(",
"name",
",",
"ARGUMENT_TYPE_STREAM",
",",
"journalEntry",
".",
"getMethodName",
"(",
")",
",",
"event",
")",
";",
"}",
"}",
"decoder",
".",
"close",
"(",
")",
";",
"journalEntry",
".",
"addArgument",
"(",
"name",
",",
"tempFile",
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"}",
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"IOException",
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")",
"{",
"throw",
"new",
"JournalException",
"(",
"\"failed to write stream argument to temp file\"",
",",
"e",
")",
";",
"}",
"}"
] |
An InputStream argument appears as a Base64-encoded String. It must be
decoded and written to a temp file, so it can be presented to the
management method as an InputStream again.
|
[
"An",
"InputStream",
"argument",
"appears",
"as",
"a",
"Base64",
"-",
"encoded",
"String",
".",
"It",
"must",
"be",
"decoded",
"and",
"written",
"to",
"a",
"temp",
"file",
"so",
"it",
"can",
"be",
"presented",
"to",
"the",
"management",
"method",
"as",
"an",
"InputStream",
"again",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/journal/JournalReader.java#L405-L434
|
9,135
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/journal/JournalReader.java
|
JournalReader.getUnexpectedEventInArgumentException
|
private JournalException getUnexpectedEventInArgumentException(String name,
String argumentType,
String methodName,
XMLEvent event) {
return new JournalException("Unexpected event while processing '"
+ name + "' argument (type = '" + argumentType + "') for '"
+ methodName + "' method call: event is '" + event + "'");
}
|
java
|
private JournalException getUnexpectedEventInArgumentException(String name,
String argumentType,
String methodName,
XMLEvent event) {
return new JournalException("Unexpected event while processing '"
+ name + "' argument (type = '" + argumentType + "') for '"
+ methodName + "' method call: event is '" + event + "'");
}
|
[
"private",
"JournalException",
"getUnexpectedEventInArgumentException",
"(",
"String",
"name",
",",
"String",
"argumentType",
",",
"String",
"methodName",
",",
"XMLEvent",
"event",
")",
"{",
"return",
"new",
"JournalException",
"(",
"\"Unexpected event while processing '\"",
"+",
"name",
"+",
"\"' argument (type = '\"",
"+",
"argumentType",
"+",
"\"') for '\"",
"+",
"methodName",
"+",
"\"' method call: event is '\"",
"+",
"event",
"+",
"\"'\"",
")",
";",
"}"
] |
If we encounter an unexpected event when reading the a method argument,
create an exception with all of the pertinent information.
|
[
"If",
"we",
"encounter",
"an",
"unexpected",
"event",
"when",
"reading",
"the",
"a",
"method",
"argument",
"create",
"an",
"exception",
"with",
"all",
"of",
"the",
"pertinent",
"information",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/journal/JournalReader.java#L482-L489
|
9,136
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/storage/SimpleDOWriter.java
|
SimpleDOWriter.addDatastream
|
public void addDatastream(Datastream datastream, boolean addNewVersion)
throws ServerException {
assertNotInvalidated();
assertNotPendingRemoval();
// use this call to handle versionable
m_obj.addDatastreamVersion(datastream, addNewVersion);
}
|
java
|
public void addDatastream(Datastream datastream, boolean addNewVersion)
throws ServerException {
assertNotInvalidated();
assertNotPendingRemoval();
// use this call to handle versionable
m_obj.addDatastreamVersion(datastream, addNewVersion);
}
|
[
"public",
"void",
"addDatastream",
"(",
"Datastream",
"datastream",
",",
"boolean",
"addNewVersion",
")",
"throws",
"ServerException",
"{",
"assertNotInvalidated",
"(",
")",
";",
"assertNotPendingRemoval",
"(",
")",
";",
"// use this call to handle versionable",
"m_obj",
".",
"addDatastreamVersion",
"(",
"datastream",
",",
"addNewVersion",
")",
";",
"}"
] |
Adds a datastream to the object.
@param datastream
The datastream.
@throws ServerException
If any type of error occurred fulfilling the request.
|
[
"Adds",
"a",
"datastream",
"to",
"the",
"object",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/storage/SimpleDOWriter.java#L167-L173
|
9,137
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/storage/SimpleDOWriter.java
|
SimpleDOWriter.removeDatastream
|
public Date[] removeDatastream(String id, Date start, Date end)
throws ServerException {
assertNotInvalidated();
assertNotPendingRemoval();
ArrayList<Datastream> removeList = new ArrayList<Datastream>();
for (Datastream ds : m_obj.datastreams(id)) {
boolean doRemove = false;
if (start != null) {
if (end != null) {
if (ds.DSCreateDT.compareTo(start) >= 0
&& ds.DSCreateDT.compareTo(end) <= 0) {
doRemove = true;
}
} else {
if (ds.DSCreateDT.compareTo(start) >= 0) {
doRemove = true;
}
}
} else {
if (end != null) {
if (ds.DSCreateDT.compareTo(end) <= 0) {
doRemove = true;
}
} else {
doRemove = true;
}
}
if (doRemove) {
// Note: We don't remove old audit records by design.
// add this datastream to the datastream to-be-removed list.
removeList.add(ds);
}
}
/* Now that we've identified all ds versions to remove, remove 'em */
for (Datastream toRemove : removeList) {
m_obj.removeDatastreamVersion(toRemove);
}
// finally, return the dates of each deleted item
Date[] deletedDates = new Date[removeList.size()];
for (int i = 0; i < removeList.size(); i++) {
deletedDates[i] = (removeList.get(i)).DSCreateDT;
}
return deletedDates;
}
|
java
|
public Date[] removeDatastream(String id, Date start, Date end)
throws ServerException {
assertNotInvalidated();
assertNotPendingRemoval();
ArrayList<Datastream> removeList = new ArrayList<Datastream>();
for (Datastream ds : m_obj.datastreams(id)) {
boolean doRemove = false;
if (start != null) {
if (end != null) {
if (ds.DSCreateDT.compareTo(start) >= 0
&& ds.DSCreateDT.compareTo(end) <= 0) {
doRemove = true;
}
} else {
if (ds.DSCreateDT.compareTo(start) >= 0) {
doRemove = true;
}
}
} else {
if (end != null) {
if (ds.DSCreateDT.compareTo(end) <= 0) {
doRemove = true;
}
} else {
doRemove = true;
}
}
if (doRemove) {
// Note: We don't remove old audit records by design.
// add this datastream to the datastream to-be-removed list.
removeList.add(ds);
}
}
/* Now that we've identified all ds versions to remove, remove 'em */
for (Datastream toRemove : removeList) {
m_obj.removeDatastreamVersion(toRemove);
}
// finally, return the dates of each deleted item
Date[] deletedDates = new Date[removeList.size()];
for (int i = 0; i < removeList.size(); i++) {
deletedDates[i] = (removeList.get(i)).DSCreateDT;
}
return deletedDates;
}
|
[
"public",
"Date",
"[",
"]",
"removeDatastream",
"(",
"String",
"id",
",",
"Date",
"start",
",",
"Date",
"end",
")",
"throws",
"ServerException",
"{",
"assertNotInvalidated",
"(",
")",
";",
"assertNotPendingRemoval",
"(",
")",
";",
"ArrayList",
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"removeList",
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"new",
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"<",
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">",
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";",
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"{",
"boolean",
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"=",
"false",
";",
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"compareTo",
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"compareTo",
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"}",
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">=",
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".",
"compareTo",
"(",
"end",
")",
"<=",
"0",
")",
"{",
"doRemove",
"=",
"true",
";",
"}",
"}",
"else",
"{",
"doRemove",
"=",
"true",
";",
"}",
"}",
"if",
"(",
"doRemove",
")",
"{",
"// Note: We don't remove old audit records by design.",
"// add this datastream to the datastream to-be-removed list.",
"removeList",
".",
"add",
"(",
"ds",
")",
";",
"}",
"}",
"/* Now that we've identified all ds versions to remove, remove 'em */",
"for",
"(",
"Datastream",
"toRemove",
":",
"removeList",
")",
"{",
"m_obj",
".",
"removeDatastreamVersion",
"(",
"toRemove",
")",
";",
"}",
"// finally, return the dates of each deleted item",
"Date",
"[",
"]",
"deletedDates",
"=",
"new",
"Date",
"[",
"removeList",
".",
"size",
"(",
")",
"]",
";",
"for",
"(",
"int",
"i",
"=",
"0",
";",
"i",
"<",
"removeList",
".",
"size",
"(",
")",
";",
"i",
"++",
")",
"{",
"deletedDates",
"[",
"i",
"]",
"=",
"(",
"removeList",
".",
"get",
"(",
"i",
")",
")",
".",
"DSCreateDT",
";",
"}",
"return",
"deletedDates",
";",
"}"
] |
Removes a datastream from the object.
@param id
The id of the datastream.
@param start
The start date (inclusive) of versions to remove. If
<code>null</code>, this is taken to be the smallest possible
value.
@param end
The end date (inclusive) of versions to remove. If
<code>null</code>, this is taken to be the greatest possible
value.
@throws ServerException
If any type of error occurred fulfilling the request.
|
[
"Removes",
"a",
"datastream",
"from",
"the",
"object",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/storage/SimpleDOWriter.java#L191-L237
|
9,138
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/storage/SimpleDOWriter.java
|
SimpleDOWriter.resolveSubjectToDatastream
|
private String resolveSubjectToDatastream(String subject) throws ServerException{
String pidURI = PID.toURI(m_obj.getPid());
if (subject.startsWith(pidURI)) {
if (subject.length() == pidURI.length()) {
return "RELS-EXT";
}
if (subject.charAt(pidURI.length()) == '/') {
return "RELS-INT";
}
}
throw new GeneralException("Cannot determine which relationship datastream to update for subject " + subject + ". Relationship subjects must be the URI of the object or the URI of a datastream within the object.");
}
|
java
|
private String resolveSubjectToDatastream(String subject) throws ServerException{
String pidURI = PID.toURI(m_obj.getPid());
if (subject.startsWith(pidURI)) {
if (subject.length() == pidURI.length()) {
return "RELS-EXT";
}
if (subject.charAt(pidURI.length()) == '/') {
return "RELS-INT";
}
}
throw new GeneralException("Cannot determine which relationship datastream to update for subject " + subject + ". Relationship subjects must be the URI of the object or the URI of a datastream within the object.");
}
|
[
"private",
"String",
"resolveSubjectToDatastream",
"(",
"String",
"subject",
")",
"throws",
"ServerException",
"{",
"String",
"pidURI",
"=",
"PID",
".",
"toURI",
"(",
"m_obj",
".",
"getPid",
"(",
")",
")",
";",
"if",
"(",
"subject",
".",
"startsWith",
"(",
"pidURI",
")",
")",
"{",
"if",
"(",
"subject",
".",
"length",
"(",
")",
"==",
"pidURI",
".",
"length",
"(",
")",
")",
"{",
"return",
"\"RELS-EXT\"",
";",
"}",
"if",
"(",
"subject",
".",
"charAt",
"(",
"pidURI",
".",
"length",
"(",
")",
")",
"==",
"'",
"'",
")",
"{",
"return",
"\"RELS-INT\"",
";",
"}",
"}",
"throw",
"new",
"GeneralException",
"(",
"\"Cannot determine which relationship datastream to update for subject \"",
"+",
"subject",
"+",
"\". Relationship subjects must be the URI of the object or the URI of a datastream within the object.\"",
")",
";",
"}"
] |
from the relationship subject, determine which datastream to modify etc
|
[
"from",
"the",
"relationship",
"subject",
"determine",
"which",
"datastream",
"to",
"modify",
"etc"
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/storage/SimpleDOWriter.java#L240-L251
|
9,139
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/storage/SimpleDOWriter.java
|
SimpleDOWriter.commit
|
public void commit(String logMessage) throws ServerException {
assertNotInvalidated();
m_mgr.doCommit(Server.USE_DEFINITIVE_STORE,
m_context,
m_obj,
logMessage,
m_pendingRemoval);
m_committed = true;
invalidate();
}
|
java
|
public void commit(String logMessage) throws ServerException {
assertNotInvalidated();
m_mgr.doCommit(Server.USE_DEFINITIVE_STORE,
m_context,
m_obj,
logMessage,
m_pendingRemoval);
m_committed = true;
invalidate();
}
|
[
"public",
"void",
"commit",
"(",
"String",
"logMessage",
")",
"throws",
"ServerException",
"{",
"assertNotInvalidated",
"(",
")",
";",
"m_mgr",
".",
"doCommit",
"(",
"Server",
".",
"USE_DEFINITIVE_STORE",
",",
"m_context",
",",
"m_obj",
",",
"logMessage",
",",
"m_pendingRemoval",
")",
";",
"m_committed",
"=",
"true",
";",
"invalidate",
"(",
")",
";",
"}"
] |
Saves the changes thus far to the permanent copy of the digital object.
@param logMessage
An explanation of the change(s).
@throws ServerException
If any type of error occurred fulfilling the request.
|
[
"Saves",
"the",
"changes",
"thus",
"far",
"to",
"the",
"permanent",
"copy",
"of",
"the",
"digital",
"object",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/storage/SimpleDOWriter.java#L510-L519
|
9,140
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/journal/readerwriter/multicast/rmi/RmiTransportWriter.java
|
RmiTransportWriter.write
|
@Override
public void write(char[] cbuf, int off, int len) throws IOException {
try {
String indexedHash =
RmiJournalReceiverHelper.figureIndexedHash(repositoryHash,
itemIndex);
receiver.writeText(indexedHash, new String(cbuf, off, len));
itemIndex++;
} catch (JournalException e) {
throw new IOException(e);
}
}
|
java
|
@Override
public void write(char[] cbuf, int off, int len) throws IOException {
try {
String indexedHash =
RmiJournalReceiverHelper.figureIndexedHash(repositoryHash,
itemIndex);
receiver.writeText(indexedHash, new String(cbuf, off, len));
itemIndex++;
} catch (JournalException e) {
throw new IOException(e);
}
}
|
[
"@",
"Override",
"public",
"void",
"write",
"(",
"char",
"[",
"]",
"cbuf",
",",
"int",
"off",
",",
"int",
"len",
")",
"throws",
"IOException",
"{",
"try",
"{",
"String",
"indexedHash",
"=",
"RmiJournalReceiverHelper",
".",
"figureIndexedHash",
"(",
"repositoryHash",
",",
"itemIndex",
")",
";",
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",",
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"e",
")",
"{",
"throw",
"new",
"IOException",
"(",
"e",
")",
";",
"}",
"}"
] |
Each time characters are written, send them to the receiver. Keep track
of how many writes, so we can create a proper item hash.
|
[
"Each",
"time",
"characters",
"are",
"written",
"send",
"them",
"to",
"the",
"receiver",
".",
"Keep",
"track",
"of",
"how",
"many",
"writes",
"so",
"we",
"can",
"create",
"a",
"proper",
"item",
"hash",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/journal/readerwriter/multicast/rmi/RmiTransportWriter.java#L62-L73
|
9,141
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/journal/readerwriter/multicast/rmi/RmiTransportWriter.java
|
RmiTransportWriter.close
|
@Override
public void close() throws IOException {
try {
if (!m_closed) {
receiver.closeFile();
m_closed= true;
}
} catch (JournalException e) {
throw new IOException(e);
}
}
|
java
|
@Override
public void close() throws IOException {
try {
if (!m_closed) {
receiver.closeFile();
m_closed= true;
}
} catch (JournalException e) {
throw new IOException(e);
}
}
|
[
"@",
"Override",
"public",
"void",
"close",
"(",
")",
"throws",
"IOException",
"{",
"try",
"{",
"if",
"(",
"!",
"m_closed",
")",
"{",
"receiver",
".",
"closeFile",
"(",
")",
";",
"m_closed",
"=",
"true",
";",
"}",
"}",
"catch",
"(",
"JournalException",
"e",
")",
"{",
"throw",
"new",
"IOException",
"(",
"e",
")",
";",
"}",
"}"
] |
Time to close the file? Tell the receiver.
|
[
"Time",
"to",
"close",
"the",
"file?",
"Tell",
"the",
"receiver",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/journal/readerwriter/multicast/rmi/RmiTransportWriter.java#L78-L88
|
9,142
|
fcrepo3/fcrepo
|
fcrepo-security/fcrepo-security-jaas/src/main/java/org/fcrepo/server/security/jaas/util/SubjectUtils.java
|
SubjectUtils.getAttributes
|
@SuppressWarnings("unchecked")
public static Map<String, Set<String>> getAttributes(Subject subject) {
Map<String, Set<String>> attributes = null;
if (subject.getPublicCredentials() == null) {
return new HashMap<String, Set<String>>();
}
@SuppressWarnings("rawtypes")
Iterator<HashMap> credentialObjects = subject.getPublicCredentials(HashMap.class).iterator();
while (attributes == null && credentialObjects.hasNext()) {
HashMap<?,?> credentialObject = credentialObjects.next();
if (logger.isDebugEnabled()) {
logger.debug("checking for attributes (class name): "
+ credentialObject.getClass().getName());
}
Object key = null;
Iterator<?> keys = null;
keys = credentialObject.keySet().iterator();
if (!keys.hasNext()) {
continue;
}
key = keys.next();
if (logger.isDebugEnabled()) {
logger.debug("checking for attributes (key object name): "
+ key.getClass().getName());
}
if (!(key instanceof String)) {
continue;
}
keys = credentialObject.values().iterator();
if (!keys.hasNext()) {
continue;
}
key = keys.next();
if (logger.isDebugEnabled()) {
logger.debug("checking for attributes (value object name): "
+ key.getClass().getName());
}
if (!(key instanceof HashSet)) {
continue;
}
attributes = (Map<String, Set<String>>) credentialObject;
}
if (attributes == null) {
attributes = new HashMap<String, Set<String>>();
subject.getPublicCredentials().add(attributes);
}
return attributes;
}
|
java
|
@SuppressWarnings("unchecked")
public static Map<String, Set<String>> getAttributes(Subject subject) {
Map<String, Set<String>> attributes = null;
if (subject.getPublicCredentials() == null) {
return new HashMap<String, Set<String>>();
}
@SuppressWarnings("rawtypes")
Iterator<HashMap> credentialObjects = subject.getPublicCredentials(HashMap.class).iterator();
while (attributes == null && credentialObjects.hasNext()) {
HashMap<?,?> credentialObject = credentialObjects.next();
if (logger.isDebugEnabled()) {
logger.debug("checking for attributes (class name): "
+ credentialObject.getClass().getName());
}
Object key = null;
Iterator<?> keys = null;
keys = credentialObject.keySet().iterator();
if (!keys.hasNext()) {
continue;
}
key = keys.next();
if (logger.isDebugEnabled()) {
logger.debug("checking for attributes (key object name): "
+ key.getClass().getName());
}
if (!(key instanceof String)) {
continue;
}
keys = credentialObject.values().iterator();
if (!keys.hasNext()) {
continue;
}
key = keys.next();
if (logger.isDebugEnabled()) {
logger.debug("checking for attributes (value object name): "
+ key.getClass().getName());
}
if (!(key instanceof HashSet)) {
continue;
}
attributes = (Map<String, Set<String>>) credentialObject;
}
if (attributes == null) {
attributes = new HashMap<String, Set<String>>();
subject.getPublicCredentials().add(attributes);
}
return attributes;
}
|
[
"@",
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"(",
"\"unchecked\"",
")",
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">",
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"(",
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"+",
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";",
"if",
"(",
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".",
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"(",
")",
")",
"{",
"logger",
".",
"debug",
"(",
"\"checking for attributes (key object name): \"",
"+",
"key",
".",
"getClass",
"(",
")",
".",
"getName",
"(",
")",
")",
";",
"}",
"if",
"(",
"!",
"(",
"key",
"instanceof",
"String",
")",
")",
"{",
"continue",
";",
"}",
"keys",
"=",
"credentialObject",
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"(",
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"(",
")",
";",
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"keys",
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"hasNext",
"(",
")",
")",
"{",
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";",
"}",
"key",
"=",
"keys",
".",
"next",
"(",
")",
";",
"if",
"(",
"logger",
".",
"isDebugEnabled",
"(",
")",
")",
"{",
"logger",
".",
"debug",
"(",
"\"checking for attributes (value object name): \"",
"+",
"key",
".",
"getClass",
"(",
")",
".",
"getName",
"(",
")",
")",
";",
"}",
"if",
"(",
"!",
"(",
"key",
"instanceof",
"HashSet",
")",
")",
"{",
"continue",
";",
"}",
"attributes",
"=",
"(",
"Map",
"<",
"String",
",",
"Set",
"<",
"String",
">",
">",
")",
"credentialObject",
";",
"}",
"if",
"(",
"attributes",
"==",
"null",
")",
"{",
"attributes",
"=",
"new",
"HashMap",
"<",
"String",
",",
"Set",
"<",
"String",
">",
">",
"(",
")",
";",
"subject",
".",
"getPublicCredentials",
"(",
")",
".",
"add",
"(",
"attributes",
")",
";",
"}",
"return",
"attributes",
";",
"}"
] |
Get the attribute map of String keys to Set<String> values
This method will not return a null
@param subject
@return Map<String, Set<String>>
|
[
"Get",
"the",
"attribute",
"map",
"of",
"String",
"keys",
"to",
"Set<",
";",
"String>",
";",
"values",
"This",
"method",
"will",
"not",
"return",
"a",
"null"
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-security/fcrepo-security-jaas/src/main/java/org/fcrepo/server/security/jaas/util/SubjectUtils.java#L44-L106
|
9,143
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/journal/readerwriter/multifile/JournalInputFile.java
|
JournalInputFile.closeAndRename
|
public void closeAndRename(File archiveDirectory) throws JournalException {
try {
xmlReader.close();
fileReader.close();
File archiveFile = new File(archiveDirectory, file.getName());
/*
* java.io.File.renameTo() has a known bug when working across
* file-systems, see:
* http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=4073756 So
* instead of this call: file.renameTo(archiveFile); We use the
* following line, and check for exception...
*/
try {
FileMovingUtil.move(file, archiveFile);
} catch (IOException e) {
throw new JournalException("Failed to rename file from '"
+ file.getPath() + "' to '" + archiveFile.getPath()
+ "'", e);
}
} catch (XMLStreamException e) {
throw new JournalException(e);
} catch (IOException e) {
throw new JournalException(e);
}
}
|
java
|
public void closeAndRename(File archiveDirectory) throws JournalException {
try {
xmlReader.close();
fileReader.close();
File archiveFile = new File(archiveDirectory, file.getName());
/*
* java.io.File.renameTo() has a known bug when working across
* file-systems, see:
* http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=4073756 So
* instead of this call: file.renameTo(archiveFile); We use the
* following line, and check for exception...
*/
try {
FileMovingUtil.move(file, archiveFile);
} catch (IOException e) {
throw new JournalException("Failed to rename file from '"
+ file.getPath() + "' to '" + archiveFile.getPath()
+ "'", e);
}
} catch (XMLStreamException e) {
throw new JournalException(e);
} catch (IOException e) {
throw new JournalException(e);
}
}
|
[
"public",
"void",
"closeAndRename",
"(",
"File",
"archiveDirectory",
")",
"throws",
"JournalException",
"{",
"try",
"{",
"xmlReader",
".",
"close",
"(",
")",
";",
"fileReader",
".",
"close",
"(",
")",
";",
"File",
"archiveFile",
"=",
"new",
"File",
"(",
"archiveDirectory",
",",
"file",
".",
"getName",
"(",
")",
")",
";",
"/*\n * java.io.File.renameTo() has a known bug when working across\n * file-systems, see:\n * http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=4073756 So\n * instead of this call: file.renameTo(archiveFile); We use the\n * following line, and check for exception...\n */",
"try",
"{",
"FileMovingUtil",
".",
"move",
"(",
"file",
",",
"archiveFile",
")",
";",
"}",
"catch",
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"IOException",
"e",
")",
"{",
"throw",
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"JournalException",
"(",
"\"Failed to rename file from '\"",
"+",
"file",
".",
"getPath",
"(",
")",
"+",
"\"' to '\"",
"+",
"archiveFile",
".",
"getPath",
"(",
")",
"+",
"\"'\"",
",",
"e",
")",
";",
"}",
"}",
"catch",
"(",
"XMLStreamException",
"e",
")",
"{",
"throw",
"new",
"JournalException",
"(",
"e",
")",
";",
"}",
"catch",
"(",
"IOException",
"e",
")",
"{",
"throw",
"new",
"JournalException",
"(",
"e",
")",
";",
"}",
"}"
] |
When we have processed the file, move it to the archive directory.
|
[
"When",
"we",
"have",
"processed",
"the",
"file",
"move",
"it",
"to",
"the",
"archive",
"directory",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/journal/readerwriter/multifile/JournalInputFile.java#L63-L88
|
9,144
|
fcrepo3/fcrepo
|
fcrepo-client/fcrepo-client-admin/src/main/java/org/fcrepo/client/objecteditor/DatastreamsPane.java
|
DatastreamsPane.doNew
|
public void doNew(String[] dropdownMimeTypes, boolean makeSelected) {
int i = getTabIndex("New...");
m_tabbedPane
.setComponentAt(i, new NewDatastreamPane(dropdownMimeTypes));
i = getTabIndex("New...");
m_tabbedPane.setToolTipTextAt(i, "Add a new datastream to this object");
m_tabbedPane.setIconAt(i, newIcon);
m_tabbedPane.setBackgroundAt(i, Administrator.DEFAULT_COLOR);
if (makeSelected) {
m_tabbedPane.setSelectedIndex(i);
}
}
|
java
|
public void doNew(String[] dropdownMimeTypes, boolean makeSelected) {
int i = getTabIndex("New...");
m_tabbedPane
.setComponentAt(i, new NewDatastreamPane(dropdownMimeTypes));
i = getTabIndex("New...");
m_tabbedPane.setToolTipTextAt(i, "Add a new datastream to this object");
m_tabbedPane.setIconAt(i, newIcon);
m_tabbedPane.setBackgroundAt(i, Administrator.DEFAULT_COLOR);
if (makeSelected) {
m_tabbedPane.setSelectedIndex(i);
}
}
|
[
"public",
"void",
"doNew",
"(",
"String",
"[",
"]",
"dropdownMimeTypes",
",",
"boolean",
"makeSelected",
")",
"{",
"int",
"i",
"=",
"getTabIndex",
"(",
"\"New...\"",
")",
";",
"m_tabbedPane",
".",
"setComponentAt",
"(",
"i",
",",
"new",
"NewDatastreamPane",
"(",
"dropdownMimeTypes",
")",
")",
";",
"i",
"=",
"getTabIndex",
"(",
"\"New...\"",
")",
";",
"m_tabbedPane",
".",
"setToolTipTextAt",
"(",
"i",
",",
"\"Add a new datastream to this object\"",
")",
";",
"m_tabbedPane",
".",
"setIconAt",
"(",
"i",
",",
"newIcon",
")",
";",
"m_tabbedPane",
".",
"setBackgroundAt",
"(",
"i",
",",
"Administrator",
".",
"DEFAULT_COLOR",
")",
";",
"if",
"(",
"makeSelected",
")",
"{",
"m_tabbedPane",
".",
"setSelectedIndex",
"(",
"i",
")",
";",
"}",
"}"
] |
Set the content of the "New..." JPanel to a fresh new datastream entry
panel, and switch to it, if needed.
|
[
"Set",
"the",
"content",
"of",
"the",
"New",
"...",
"JPanel",
"to",
"a",
"fresh",
"new",
"datastream",
"entry",
"panel",
"and",
"switch",
"to",
"it",
"if",
"needed",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-client/fcrepo-client-admin/src/main/java/org/fcrepo/client/objecteditor/DatastreamsPane.java#L158-L170
|
9,145
|
fcrepo3/fcrepo
|
fcrepo-client/fcrepo-client-admin/src/main/java/org/fcrepo/client/objecteditor/DatastreamsPane.java
|
DatastreamsPane.updateNewRelsExt
|
public void updateNewRelsExt(String pid) throws Exception {
if (!hasRelsExt() && getTabIndex("New RELS-EXT...") == -1) {
m_tabbedPane.insertTab("New RELS-EXT...",
newIcon,
new NewRelsExtDatastreamPane(m_owner,
pid,
this),
"Add a RELS-EXT datastream to this object",
getTabIndex("New..."));
int i = getTabIndex("New RELS-EXT...");
m_tabbedPane.setBackgroundAt(i, Administrator.DEFAULT_COLOR);
} else if (hasRelsExt() && getTabIndex("New RELS-EXT...") != -1) {
m_tabbedPane.remove(getTabIndex("New RELS-EXT..."));
}
}
|
java
|
public void updateNewRelsExt(String pid) throws Exception {
if (!hasRelsExt() && getTabIndex("New RELS-EXT...") == -1) {
m_tabbedPane.insertTab("New RELS-EXT...",
newIcon,
new NewRelsExtDatastreamPane(m_owner,
pid,
this),
"Add a RELS-EXT datastream to this object",
getTabIndex("New..."));
int i = getTabIndex("New RELS-EXT...");
m_tabbedPane.setBackgroundAt(i, Administrator.DEFAULT_COLOR);
} else if (hasRelsExt() && getTabIndex("New RELS-EXT...") != -1) {
m_tabbedPane.remove(getTabIndex("New RELS-EXT..."));
}
}
|
[
"public",
"void",
"updateNewRelsExt",
"(",
"String",
"pid",
")",
"throws",
"Exception",
"{",
"if",
"(",
"!",
"hasRelsExt",
"(",
")",
"&&",
"getTabIndex",
"(",
"\"New RELS-EXT...\"",
")",
"==",
"-",
"1",
")",
"{",
"m_tabbedPane",
".",
"insertTab",
"(",
"\"New RELS-EXT...\"",
",",
"newIcon",
",",
"new",
"NewRelsExtDatastreamPane",
"(",
"m_owner",
",",
"pid",
",",
"this",
")",
",",
"\"Add a RELS-EXT datastream to this object\"",
",",
"getTabIndex",
"(",
"\"New...\"",
")",
")",
";",
"int",
"i",
"=",
"getTabIndex",
"(",
"\"New RELS-EXT...\"",
")",
";",
"m_tabbedPane",
".",
"setBackgroundAt",
"(",
"i",
",",
"Administrator",
".",
"DEFAULT_COLOR",
")",
";",
"}",
"else",
"if",
"(",
"hasRelsExt",
"(",
")",
"&&",
"getTabIndex",
"(",
"\"New RELS-EXT...\"",
")",
"!=",
"-",
"1",
")",
"{",
"m_tabbedPane",
".",
"remove",
"(",
"getTabIndex",
"(",
"\"New RELS-EXT...\"",
")",
")",
";",
"}",
"}"
] |
Set the content of the "New Rels-Ext..." JPanel to a fresh new datastream
entry panel, and switch to it, if needed.
@throws Exception
|
[
"Set",
"the",
"content",
"of",
"the",
"New",
"Rels",
"-",
"Ext",
"...",
"JPanel",
"to",
"a",
"fresh",
"new",
"datastream",
"entry",
"panel",
"and",
"switch",
"to",
"it",
"if",
"needed",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-client/fcrepo-client-admin/src/main/java/org/fcrepo/client/objecteditor/DatastreamsPane.java#L178-L192
|
9,146
|
fcrepo3/fcrepo
|
fcrepo-client/fcrepo-client-admin/src/main/java/org/fcrepo/client/objecteditor/DatastreamsPane.java
|
DatastreamsPane.getDatastreamPaneIndex
|
private int getDatastreamPaneIndex(String id) {
int index = -1;
for (int i=0; i < m_datastreamPanes.length; i++)
{
if(m_datastreamPanes[i].getItemId().equals(id)){
index = i;
break;
}
}
return index;
}
|
java
|
private int getDatastreamPaneIndex(String id) {
int index = -1;
for (int i=0; i < m_datastreamPanes.length; i++)
{
if(m_datastreamPanes[i].getItemId().equals(id)){
index = i;
break;
}
}
return index;
}
|
[
"private",
"int",
"getDatastreamPaneIndex",
"(",
"String",
"id",
")",
"{",
"int",
"index",
"=",
"-",
"1",
";",
"for",
"(",
"int",
"i",
"=",
"0",
";",
"i",
"<",
"m_datastreamPanes",
".",
"length",
";",
"i",
"++",
")",
"{",
"if",
"(",
"m_datastreamPanes",
"[",
"i",
"]",
".",
"getItemId",
"(",
")",
".",
"equals",
"(",
"id",
")",
")",
"{",
"index",
"=",
"i",
";",
"break",
";",
"}",
"}",
"return",
"index",
";",
"}"
] |
Gets the index of the pane containing the
datastream with the given id.
@return index, or -1 if index is not found
|
[
"Gets",
"the",
"index",
"of",
"the",
"pane",
"containing",
"the",
"datastream",
"with",
"the",
"given",
"id",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-client/fcrepo-client-admin/src/main/java/org/fcrepo/client/objecteditor/DatastreamsPane.java#L207-L217
|
9,147
|
fcrepo3/fcrepo
|
fcrepo-client/fcrepo-client-admin/src/main/java/org/fcrepo/client/objecteditor/DatastreamsPane.java
|
DatastreamsPane.refresh
|
protected void refresh(String dsID) {
int i = getTabIndex(dsID);
try {
List<Datastream> versions =
Administrator.APIM.getDatastreamHistory(m_pid, dsID);
m_currentVersionMap.put(dsID, versions.get(i));
logger.debug("New create date is: " + versions.get(i).getCreateDate());
DatastreamPane replacement =
new DatastreamPane(m_owner, m_pid, versions, this);
m_datastreamPanes[i] = replacement;
m_tabbedPane.setComponentAt(i, replacement);
m_tabbedPane.setToolTipTextAt(i, versions.get(i).getMIMEType() + " - "
+ versions.get(i).getLabel() + " ("
+ versions.get(i).getControlGroup().toString() + ")");
colorTabForState(dsID, versions.get(i).getState());
setDirty(dsID, false);
} catch (Exception e) {
Administrator
.showErrorDialog(Administrator.getDesktop(),
"Error while refreshing",
e.getMessage()
+ "\nTry re-opening the object viewer.",
e);
}
}
|
java
|
protected void refresh(String dsID) {
int i = getTabIndex(dsID);
try {
List<Datastream> versions =
Administrator.APIM.getDatastreamHistory(m_pid, dsID);
m_currentVersionMap.put(dsID, versions.get(i));
logger.debug("New create date is: " + versions.get(i).getCreateDate());
DatastreamPane replacement =
new DatastreamPane(m_owner, m_pid, versions, this);
m_datastreamPanes[i] = replacement;
m_tabbedPane.setComponentAt(i, replacement);
m_tabbedPane.setToolTipTextAt(i, versions.get(i).getMIMEType() + " - "
+ versions.get(i).getLabel() + " ("
+ versions.get(i).getControlGroup().toString() + ")");
colorTabForState(dsID, versions.get(i).getState());
setDirty(dsID, false);
} catch (Exception e) {
Administrator
.showErrorDialog(Administrator.getDesktop(),
"Error while refreshing",
e.getMessage()
+ "\nTry re-opening the object viewer.",
e);
}
}
|
[
"protected",
"void",
"refresh",
"(",
"String",
"dsID",
")",
"{",
"int",
"i",
"=",
"getTabIndex",
"(",
"dsID",
")",
";",
"try",
"{",
"List",
"<",
"Datastream",
">",
"versions",
"=",
"Administrator",
".",
"APIM",
".",
"getDatastreamHistory",
"(",
"m_pid",
",",
"dsID",
")",
";",
"m_currentVersionMap",
".",
"put",
"(",
"dsID",
",",
"versions",
".",
"get",
"(",
"i",
")",
")",
";",
"logger",
".",
"debug",
"(",
"\"New create date is: \"",
"+",
"versions",
".",
"get",
"(",
"i",
")",
".",
"getCreateDate",
"(",
")",
")",
";",
"DatastreamPane",
"replacement",
"=",
"new",
"DatastreamPane",
"(",
"m_owner",
",",
"m_pid",
",",
"versions",
",",
"this",
")",
";",
"m_datastreamPanes",
"[",
"i",
"]",
"=",
"replacement",
";",
"m_tabbedPane",
".",
"setComponentAt",
"(",
"i",
",",
"replacement",
")",
";",
"m_tabbedPane",
".",
"setToolTipTextAt",
"(",
"i",
",",
"versions",
".",
"get",
"(",
"i",
")",
".",
"getMIMEType",
"(",
")",
"+",
"\" - \"",
"+",
"versions",
".",
"get",
"(",
"i",
")",
".",
"getLabel",
"(",
")",
"+",
"\" (\"",
"+",
"versions",
".",
"get",
"(",
"i",
")",
".",
"getControlGroup",
"(",
")",
".",
"toString",
"(",
")",
"+",
"\")\"",
")",
";",
"colorTabForState",
"(",
"dsID",
",",
"versions",
".",
"get",
"(",
"i",
")",
".",
"getState",
"(",
")",
")",
";",
"setDirty",
"(",
"dsID",
",",
"false",
")",
";",
"}",
"catch",
"(",
"Exception",
"e",
")",
"{",
"Administrator",
".",
"showErrorDialog",
"(",
"Administrator",
".",
"getDesktop",
"(",
")",
",",
"\"Error while refreshing\"",
",",
"e",
".",
"getMessage",
"(",
")",
"+",
"\"\\nTry re-opening the object viewer.\"",
",",
"e",
")",
";",
"}",
"}"
] |
Refresh the content of the tab for the indicated datastream with the
latest information from the server.
|
[
"Refresh",
"the",
"content",
"of",
"the",
"tab",
"for",
"the",
"indicated",
"datastream",
"with",
"the",
"latest",
"information",
"from",
"the",
"server",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-client/fcrepo-client-admin/src/main/java/org/fcrepo/client/objecteditor/DatastreamsPane.java#L233-L257
|
9,148
|
fcrepo3/fcrepo
|
fcrepo-client/fcrepo-client-admin/src/main/java/org/fcrepo/client/objecteditor/DatastreamsPane.java
|
DatastreamsPane.addDatastreamTab
|
protected void addDatastreamTab(String dsID, boolean reInitNewPanel)
throws Exception {
DatastreamPane[] newArray =
new DatastreamPane[m_datastreamPanes.length + 1];
for (int i = 0; i < m_datastreamPanes.length; i++) {
newArray[i] = m_datastreamPanes[i];
}
List<Datastream> versions =
Administrator.APIM.getDatastreamHistory(m_pid, dsID);
m_currentVersionMap.put(dsID, versions.get(0));
newArray[m_datastreamPanes.length] =
new DatastreamPane(m_owner, m_pid, versions, this);
// swap the arrays
m_datastreamPanes = newArray;
int newIndex = getTabIndex("New...");
m_tabbedPane.add(m_datastreamPanes[m_datastreamPanes.length - 1],
newIndex);
m_tabbedPane.setTitleAt(newIndex, dsID);
m_tabbedPane.setToolTipTextAt(newIndex, versions.get(0).getMIMEType()
+ " - " + versions.get(0).getLabel() + " ("
+ versions.get(0).getControlGroup().toString() + ")");
colorTabForState(dsID, versions.get(0).getState());
if (reInitNewPanel) {
doNew(XML_MIMETYPE, false);
}
updateNewRelsExt(m_pid);
m_tabbedPane.setSelectedIndex(getTabIndex(dsID));
}
|
java
|
protected void addDatastreamTab(String dsID, boolean reInitNewPanel)
throws Exception {
DatastreamPane[] newArray =
new DatastreamPane[m_datastreamPanes.length + 1];
for (int i = 0; i < m_datastreamPanes.length; i++) {
newArray[i] = m_datastreamPanes[i];
}
List<Datastream> versions =
Administrator.APIM.getDatastreamHistory(m_pid, dsID);
m_currentVersionMap.put(dsID, versions.get(0));
newArray[m_datastreamPanes.length] =
new DatastreamPane(m_owner, m_pid, versions, this);
// swap the arrays
m_datastreamPanes = newArray;
int newIndex = getTabIndex("New...");
m_tabbedPane.add(m_datastreamPanes[m_datastreamPanes.length - 1],
newIndex);
m_tabbedPane.setTitleAt(newIndex, dsID);
m_tabbedPane.setToolTipTextAt(newIndex, versions.get(0).getMIMEType()
+ " - " + versions.get(0).getLabel() + " ("
+ versions.get(0).getControlGroup().toString() + ")");
colorTabForState(dsID, versions.get(0).getState());
if (reInitNewPanel) {
doNew(XML_MIMETYPE, false);
}
updateNewRelsExt(m_pid);
m_tabbedPane.setSelectedIndex(getTabIndex(dsID));
}
|
[
"protected",
"void",
"addDatastreamTab",
"(",
"String",
"dsID",
",",
"boolean",
"reInitNewPanel",
")",
"throws",
"Exception",
"{",
"DatastreamPane",
"[",
"]",
"newArray",
"=",
"new",
"DatastreamPane",
"[",
"m_datastreamPanes",
".",
"length",
"+",
"1",
"]",
";",
"for",
"(",
"int",
"i",
"=",
"0",
";",
"i",
"<",
"m_datastreamPanes",
".",
"length",
";",
"i",
"++",
")",
"{",
"newArray",
"[",
"i",
"]",
"=",
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"[",
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"]",
";",
"}",
"List",
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"Datastream",
">",
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"=",
"Administrator",
".",
"APIM",
".",
"getDatastreamHistory",
"(",
"m_pid",
",",
"dsID",
")",
";",
"m_currentVersionMap",
".",
"put",
"(",
"dsID",
",",
"versions",
".",
"get",
"(",
"0",
")",
")",
";",
"newArray",
"[",
"m_datastreamPanes",
".",
"length",
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"=",
"new",
"DatastreamPane",
"(",
"m_owner",
",",
"m_pid",
",",
"versions",
",",
"this",
")",
";",
"// swap the arrays",
"m_datastreamPanes",
"=",
"newArray",
";",
"int",
"newIndex",
"=",
"getTabIndex",
"(",
"\"New...\"",
")",
";",
"m_tabbedPane",
".",
"add",
"(",
"m_datastreamPanes",
"[",
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".",
"length",
"-",
"1",
"]",
",",
"newIndex",
")",
";",
"m_tabbedPane",
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"setTitleAt",
"(",
"newIndex",
",",
"dsID",
")",
";",
"m_tabbedPane",
".",
"setToolTipTextAt",
"(",
"newIndex",
",",
"versions",
".",
"get",
"(",
"0",
")",
".",
"getMIMEType",
"(",
")",
"+",
"\" - \"",
"+",
"versions",
".",
"get",
"(",
"0",
")",
".",
"getLabel",
"(",
")",
"+",
"\" (\"",
"+",
"versions",
".",
"get",
"(",
"0",
")",
".",
"getControlGroup",
"(",
")",
".",
"toString",
"(",
")",
"+",
"\")\"",
")",
";",
"colorTabForState",
"(",
"dsID",
",",
"versions",
".",
"get",
"(",
"0",
")",
".",
"getState",
"(",
")",
")",
";",
"if",
"(",
"reInitNewPanel",
")",
"{",
"doNew",
"(",
"XML_MIMETYPE",
",",
"false",
")",
";",
"}",
"updateNewRelsExt",
"(",
"m_pid",
")",
";",
"m_tabbedPane",
".",
"setSelectedIndex",
"(",
"getTabIndex",
"(",
"dsID",
")",
")",
";",
"}"
] |
Add a new tab with a new datastream.
|
[
"Add",
"a",
"new",
"tab",
"with",
"a",
"new",
"datastream",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-client/fcrepo-client-admin/src/main/java/org/fcrepo/client/objecteditor/DatastreamsPane.java#L262-L290
|
9,149
|
fcrepo3/fcrepo
|
fcrepo-security/fcrepo-security-jaas/src/main/java/org/fcrepo/server/security/jaas/AuthFilterJAAS.java
|
AuthFilterJAAS.loginForm
|
private void loginForm(HttpServletResponse response) throws IOException {
response.reset();
response.addHeader("WWW-Authenticate",
"Basic realm=\"!!Fedora Repository Server\"");
response.setStatus(HttpServletResponse.SC_UNAUTHORIZED);
OutputStream out = response.getOutputStream();
out.write("Fedora: 401 ".getBytes());
out.flush();
out.close();
}
|
java
|
private void loginForm(HttpServletResponse response) throws IOException {
response.reset();
response.addHeader("WWW-Authenticate",
"Basic realm=\"!!Fedora Repository Server\"");
response.setStatus(HttpServletResponse.SC_UNAUTHORIZED);
OutputStream out = response.getOutputStream();
out.write("Fedora: 401 ".getBytes());
out.flush();
out.close();
}
|
[
"private",
"void",
"loginForm",
"(",
"HttpServletResponse",
"response",
")",
"throws",
"IOException",
"{",
"response",
".",
"reset",
"(",
")",
";",
"response",
".",
"addHeader",
"(",
"\"WWW-Authenticate\"",
",",
"\"Basic realm=\\\"!!Fedora Repository Server\\\"\"",
")",
";",
"response",
".",
"setStatus",
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"HttpServletResponse",
".",
"SC_UNAUTHORIZED",
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"out",
".",
"flush",
"(",
")",
";",
"out",
".",
"close",
"(",
")",
";",
"}"
] |
Sends a 401 error to the browser. This forces a login box to be displayed
allowing the user to login.
@param response
the response to set the headers and status
|
[
"Sends",
"a",
"401",
"error",
"to",
"the",
"browser",
".",
"This",
"forces",
"a",
"login",
"box",
"to",
"be",
"displayed",
"allowing",
"the",
"user",
"to",
"login",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-security/fcrepo-security-jaas/src/main/java/org/fcrepo/server/security/jaas/AuthFilterJAAS.java#L349-L358
|
9,150
|
fcrepo3/fcrepo
|
fcrepo-security/fcrepo-security-jaas/src/main/java/org/fcrepo/server/security/jaas/AuthFilterJAAS.java
|
AuthFilterJAAS.authenticate
|
private Subject authenticate(HttpServletRequest req) {
String authorization = req.getHeader("authorization");
if (authorization == null || authorization.trim().isEmpty()) {
return null;
}
// subject from session instead of re-authenticating
// can't change username/password for this session.
Subject subject =
(Subject) req.getSession().getAttribute(authorization);
if (subject != null) {
return subject;
}
String auth = null;
try {
byte[] data = Base64.decode(authorization.substring(6));
auth = new String(data);
} catch (IOException e) {
logger.error(e.toString());
return null;
}
String username = auth.substring(0, auth.indexOf(':'));
String password = auth.substring(auth.indexOf(':') + 1);
if (logger.isDebugEnabled()) {
logger.debug("auth username: " + username);
}
LoginContext loginContext = null;
try {
CallbackHandler handler =
new UsernamePasswordCallbackHandler(username, password);
loginContext = new LoginContext(jaasConfigName, handler);
loginContext.login();
} catch (LoginException le) {
logger.error(le.toString());
return null;
}
// successfully logged in
subject = loginContext.getSubject();
// object accessable by a fixed key for usage
req.getSession().setAttribute(SESSION_SUBJECT_KEY, subject);
// object accessable only by base64 encoded username:password that was
// initially used - prevents some dodgy stuff
req.getSession().setAttribute(authorization, subject);
return subject;
}
|
java
|
private Subject authenticate(HttpServletRequest req) {
String authorization = req.getHeader("authorization");
if (authorization == null || authorization.trim().isEmpty()) {
return null;
}
// subject from session instead of re-authenticating
// can't change username/password for this session.
Subject subject =
(Subject) req.getSession().getAttribute(authorization);
if (subject != null) {
return subject;
}
String auth = null;
try {
byte[] data = Base64.decode(authorization.substring(6));
auth = new String(data);
} catch (IOException e) {
logger.error(e.toString());
return null;
}
String username = auth.substring(0, auth.indexOf(':'));
String password = auth.substring(auth.indexOf(':') + 1);
if (logger.isDebugEnabled()) {
logger.debug("auth username: " + username);
}
LoginContext loginContext = null;
try {
CallbackHandler handler =
new UsernamePasswordCallbackHandler(username, password);
loginContext = new LoginContext(jaasConfigName, handler);
loginContext.login();
} catch (LoginException le) {
logger.error(le.toString());
return null;
}
// successfully logged in
subject = loginContext.getSubject();
// object accessable by a fixed key for usage
req.getSession().setAttribute(SESSION_SUBJECT_KEY, subject);
// object accessable only by base64 encoded username:password that was
// initially used - prevents some dodgy stuff
req.getSession().setAttribute(authorization, subject);
return subject;
}
|
[
"private",
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")",
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"// successfully logged in",
"subject",
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"(",
")",
";",
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"req",
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"(",
"SESSION_SUBJECT_KEY",
",",
"subject",
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".",
"setAttribute",
"(",
"authorization",
",",
"subject",
")",
";",
"return",
"subject",
";",
"}"
] |
Performs the authentication. Once a Subject is obtained, it is stored in
the users session. Subsequent requests check for the existence of this
object before performing the authentication again.
@param req
the servlet request.
@return a user principal that was extracted from the login context.
|
[
"Performs",
"the",
"authentication",
".",
"Once",
"a",
"Subject",
"is",
"obtained",
"it",
"is",
"stored",
"in",
"the",
"users",
"session",
".",
"Subsequent",
"requests",
"check",
"for",
"the",
"existence",
"of",
"this",
"object",
"before",
"performing",
"the",
"authentication",
"again",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-security/fcrepo-security-jaas/src/main/java/org/fcrepo/server/security/jaas/AuthFilterJAAS.java#L369-L421
|
9,151
|
fcrepo3/fcrepo
|
fcrepo-security/fcrepo-security-jaas/src/main/java/org/fcrepo/server/security/jaas/AuthFilterJAAS.java
|
AuthFilterJAAS.getUserPrincipal
|
private Principal getUserPrincipal(Subject subject) {
Principal userPrincipal = null;
Set<Principal> principals = subject.getPrincipals();
// try and get userPrincipal based on userClassNames
if (userClassNames != null && userClassNames.size() > 0) {
for (Principal p : principals) {
if (userPrincipal == null
&& userClassNames.contains(p.getClass().getName())) {
userPrincipal = p;
}
}
}
// no userPrincipal found using userClassNames, just grab first principal
if (userPrincipal == null) {
Iterator<Principal> i = principals.iterator();
// should always have 1 at least and 1st should be user principal
if (i.hasNext()) {
userPrincipal = i.next();
}
}
if (logger.isDebugEnabled()) {
logger.debug("found userPrincipal [{}]: {}",
userPrincipal.getClass().getName(),
userPrincipal.getName());
}
return userPrincipal;
}
|
java
|
private Principal getUserPrincipal(Subject subject) {
Principal userPrincipal = null;
Set<Principal> principals = subject.getPrincipals();
// try and get userPrincipal based on userClassNames
if (userClassNames != null && userClassNames.size() > 0) {
for (Principal p : principals) {
if (userPrincipal == null
&& userClassNames.contains(p.getClass().getName())) {
userPrincipal = p;
}
}
}
// no userPrincipal found using userClassNames, just grab first principal
if (userPrincipal == null) {
Iterator<Principal> i = principals.iterator();
// should always have 1 at least and 1st should be user principal
if (i.hasNext()) {
userPrincipal = i.next();
}
}
if (logger.isDebugEnabled()) {
logger.debug("found userPrincipal [{}]: {}",
userPrincipal.getClass().getName(),
userPrincipal.getName());
}
return userPrincipal;
}
|
[
"private",
"Principal",
"getUserPrincipal",
"(",
"Subject",
"subject",
")",
"{",
"Principal",
"userPrincipal",
"=",
"null",
";",
"Set",
"<",
"Principal",
">",
"principals",
"=",
"subject",
".",
"getPrincipals",
"(",
")",
";",
"// try and get userPrincipal based on userClassNames",
"if",
"(",
"userClassNames",
"!=",
"null",
"&&",
"userClassNames",
".",
"size",
"(",
")",
">",
"0",
")",
"{",
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"principals",
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"contains",
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"p",
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"getClass",
"(",
")",
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"getName",
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")",
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")",
"{",
"userPrincipal",
"=",
"p",
";",
"}",
"}",
"}",
"// no userPrincipal found using userClassNames, just grab first principal",
"if",
"(",
"userPrincipal",
"==",
"null",
")",
"{",
"Iterator",
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"i",
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"(",
")",
";",
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"if",
"(",
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"(",
")",
")",
"{",
"userPrincipal",
"=",
"i",
".",
"next",
"(",
")",
";",
"}",
"}",
"if",
"(",
"logger",
".",
"isDebugEnabled",
"(",
")",
")",
"{",
"logger",
".",
"debug",
"(",
"\"found userPrincipal [{}]: {}\"",
",",
"userPrincipal",
".",
"getClass",
"(",
")",
".",
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"(",
")",
",",
"userPrincipal",
".",
"getName",
"(",
")",
")",
";",
"}",
"return",
"userPrincipal",
";",
"}"
] |
Given a subject, obtain the userPrincipal from it. The user principal is
defined by a Principal class that can be defined in the web.xml file. If
this is undefined, the first principal found is assumed to be the
userPrincipal.
@param subject
the subject returned from authentication.
@return the userPrincipal associated with the given subject.
|
[
"Given",
"a",
"subject",
"obtain",
"the",
"userPrincipal",
"from",
"it",
".",
"The",
"user",
"principal",
"is",
"defined",
"by",
"a",
"Principal",
"class",
"that",
"can",
"be",
"defined",
"in",
"the",
"web",
".",
"xml",
"file",
".",
"If",
"this",
"is",
"undefined",
"the",
"first",
"principal",
"found",
"is",
"assumed",
"to",
"be",
"the",
"userPrincipal",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-security/fcrepo-security-jaas/src/main/java/org/fcrepo/server/security/jaas/AuthFilterJAAS.java#L433-L464
|
9,152
|
fcrepo3/fcrepo
|
fcrepo-security/fcrepo-security-jaas/src/main/java/org/fcrepo/server/security/jaas/AuthFilterJAAS.java
|
AuthFilterJAAS.getUserRoles
|
private Set<String> getUserRoles(Subject subject) {
Set<String> userRoles = null;
// get roles from specified classes
Set<Principal> principals = subject.getPrincipals();
if (roleClassNames != null && roleClassNames.size() > 0) {
for (Principal p : principals) {
if (roleClassNames.contains(p.getClass().getName())) {
if (userRoles == null) userRoles = new HashSet<String>();
userRoles.add(p.getName());
}
}
}
// get roles from specified attributes
Map<String, Set<String>> attributes =
SubjectUtils.getAttributes(subject);
for (String key : attributes.keySet()) {
if (roleAttributeNames.contains(key)) {
if (userRoles == null) userRoles = new HashSet<String>();
userRoles.addAll(attributes.get(key));
}
}
if (userRoles == null) userRoles = Collections.emptySet();
if (logger.isDebugEnabled()) {
for (String r : userRoles) {
logger.debug("found role: {}", r);
}
}
return userRoles;
}
|
java
|
private Set<String> getUserRoles(Subject subject) {
Set<String> userRoles = null;
// get roles from specified classes
Set<Principal> principals = subject.getPrincipals();
if (roleClassNames != null && roleClassNames.size() > 0) {
for (Principal p : principals) {
if (roleClassNames.contains(p.getClass().getName())) {
if (userRoles == null) userRoles = new HashSet<String>();
userRoles.add(p.getName());
}
}
}
// get roles from specified attributes
Map<String, Set<String>> attributes =
SubjectUtils.getAttributes(subject);
for (String key : attributes.keySet()) {
if (roleAttributeNames.contains(key)) {
if (userRoles == null) userRoles = new HashSet<String>();
userRoles.addAll(attributes.get(key));
}
}
if (userRoles == null) userRoles = Collections.emptySet();
if (logger.isDebugEnabled()) {
for (String r : userRoles) {
logger.debug("found role: {}", r);
}
}
return userRoles;
}
|
[
"private",
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"<",
"String",
">",
"getUserRoles",
"(",
"Subject",
"subject",
")",
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"String",
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"userRoles",
"=",
"null",
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"<",
"Principal",
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"principals",
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",",
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")",
";",
"}",
"}",
"return",
"userRoles",
";",
"}"
] |
Obtains the roles for the user based on the class names and attribute
names provided in the web.xml file.
@param subject
the subject returned from authentication.
@return a set of strings that represent the users roles.
|
[
"Obtains",
"the",
"roles",
"for",
"the",
"user",
"based",
"on",
"the",
"class",
"names",
"and",
"attribute",
"names",
"provided",
"in",
"the",
"web",
".",
"xml",
"file",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-security/fcrepo-security-jaas/src/main/java/org/fcrepo/server/security/jaas/AuthFilterJAAS.java#L474-L506
|
9,153
|
fcrepo3/fcrepo
|
fcrepo-security/fcrepo-security-jaas/src/main/java/org/fcrepo/server/security/jaas/AuthFilterJAAS.java
|
AuthFilterJAAS.addRolesToSubject
|
private void addRolesToSubject(Subject subject, Set<String> userRoles) {
if (userRoles == null) {
userRoles = Collections.emptySet();
}
Map<String, Set<String>> attributes =
SubjectUtils.getAttributes(subject);
Set<String> roles = attributes.get(ROLE_KEY);
if (roles == null) {
roles = new HashSet<String>(userRoles);
attributes.put(ROLE_KEY, roles);
} else {
roles.addAll(userRoles);
}
if (logger.isDebugEnabled()) {
for (String role : userRoles) {
logger.debug("added role: {}", role);
}
}
}
|
java
|
private void addRolesToSubject(Subject subject, Set<String> userRoles) {
if (userRoles == null) {
userRoles = Collections.emptySet();
}
Map<String, Set<String>> attributes =
SubjectUtils.getAttributes(subject);
Set<String> roles = attributes.get(ROLE_KEY);
if (roles == null) {
roles = new HashSet<String>(userRoles);
attributes.put(ROLE_KEY, roles);
} else {
roles.addAll(userRoles);
}
if (logger.isDebugEnabled()) {
for (String role : userRoles) {
logger.debug("added role: {}", role);
}
}
}
|
[
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"{",
"roles",
"=",
"new",
"HashSet",
"<",
"String",
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"(",
"userRoles",
")",
";",
"attributes",
".",
"put",
"(",
"ROLE_KEY",
",",
"roles",
")",
";",
"}",
"else",
"{",
"roles",
".",
"addAll",
"(",
"userRoles",
")",
";",
"}",
"if",
"(",
"logger",
".",
"isDebugEnabled",
"(",
")",
")",
"{",
"for",
"(",
"String",
"role",
":",
"userRoles",
")",
"{",
"logger",
".",
"debug",
"(",
"\"added role: {}\"",
",",
"role",
")",
";",
"}",
"}",
"}"
] |
Adds roles to the Subject object.
@param subject
the subject that was returned from authentication.
@param userRoles
the set of user roles that were found.
|
[
"Adds",
"roles",
"to",
"the",
"Subject",
"object",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-security/fcrepo-security-jaas/src/main/java/org/fcrepo/server/security/jaas/AuthFilterJAAS.java#L516-L536
|
9,154
|
fcrepo3/fcrepo
|
fcrepo-security/fcrepo-security-jaas/src/main/java/org/fcrepo/server/security/jaas/AuthFilterJAAS.java
|
AuthFilterJAAS.populateFedoraAttributes
|
private void populateFedoraAttributes(Subject subject,
Set<String> userRoles,
HttpServletRequest request) {
Map<String, Set<String>> attributes =
SubjectUtils.getAttributes(subject);
// get the fedoraRole attribute or create it.
Set<String> roles = attributes.get(FEDORA_ROLE_KEY);
if (roles == null) {
roles = new HashSet<String>(userRoles);
attributes.put(FEDORA_ROLE_KEY, roles);
} else {
roles.addAll(userRoles);
}
request.setAttribute(FEDORA_ATTRIBUTES_KEY, attributes);
}
|
java
|
private void populateFedoraAttributes(Subject subject,
Set<String> userRoles,
HttpServletRequest request) {
Map<String, Set<String>> attributes =
SubjectUtils.getAttributes(subject);
// get the fedoraRole attribute or create it.
Set<String> roles = attributes.get(FEDORA_ROLE_KEY);
if (roles == null) {
roles = new HashSet<String>(userRoles);
attributes.put(FEDORA_ROLE_KEY, roles);
} else {
roles.addAll(userRoles);
}
request.setAttribute(FEDORA_ATTRIBUTES_KEY, attributes);
}
|
[
"private",
"void",
"populateFedoraAttributes",
"(",
"Subject",
"subject",
",",
"Set",
"<",
"String",
">",
"userRoles",
",",
"HttpServletRequest",
"request",
")",
"{",
"Map",
"<",
"String",
",",
"Set",
"<",
"String",
">",
">",
"attributes",
"=",
"SubjectUtils",
".",
"getAttributes",
"(",
"subject",
")",
";",
"// get the fedoraRole attribute or create it.",
"Set",
"<",
"String",
">",
"roles",
"=",
"attributes",
".",
"get",
"(",
"FEDORA_ROLE_KEY",
")",
";",
"if",
"(",
"roles",
"==",
"null",
")",
"{",
"roles",
"=",
"new",
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"userRoles",
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"put",
"(",
"FEDORA_ROLE_KEY",
",",
"roles",
")",
";",
"}",
"else",
"{",
"roles",
".",
"addAll",
"(",
"userRoles",
")",
";",
"}",
"request",
".",
"setAttribute",
"(",
"FEDORA_ATTRIBUTES_KEY",
",",
"attributes",
")",
";",
"}"
] |
Add roles and other subject attributes where Fedora expects them - a Map
called FEDORA_AUX_SUBJECT_ATTRIBUTES. Roles will be put in "fedoraRole"
and others will be named as-is.
@param subject
the subject from authentication.
@param userRoles
the set of user roles.
@param request
the request in which to place the attributes.
|
[
"Add",
"roles",
"and",
"other",
"subject",
"attributes",
"where",
"Fedora",
"expects",
"them",
"-",
"a",
"Map",
"called",
"FEDORA_AUX_SUBJECT_ATTRIBUTES",
".",
"Roles",
"will",
"be",
"put",
"in",
"fedoraRole",
"and",
"others",
"will",
"be",
"named",
"as",
"-",
"is",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-security/fcrepo-security-jaas/src/main/java/org/fcrepo/server/security/jaas/AuthFilterJAAS.java#L550-L567
|
9,155
|
fcrepo3/fcrepo
|
fcrepo-security/fcrepo-security-pep/src/main/java/org/fcrepo/server/security/xacml/pep/rest/PEP.java
|
PEP.denyAccess
|
private void denyAccess(HttpServletResponse response, String message)
throws IOException {
StringBuilder sb = new StringBuilder();
sb.append("Fedora: 403 ").append(message.toUpperCase());
response.reset();
response.setStatus(HttpServletResponse.SC_FORBIDDEN);
response.setContentType("text/plain");
response.setContentLength(sb.length());
ServletOutputStream out = response.getOutputStream();
out.write(sb.toString().getBytes());
out.flush();
out.close();
}
|
java
|
private void denyAccess(HttpServletResponse response, String message)
throws IOException {
StringBuilder sb = new StringBuilder();
sb.append("Fedora: 403 ").append(message.toUpperCase());
response.reset();
response.setStatus(HttpServletResponse.SC_FORBIDDEN);
response.setContentType("text/plain");
response.setContentLength(sb.length());
ServletOutputStream out = response.getOutputStream();
out.write(sb.toString().getBytes());
out.flush();
out.close();
}
|
[
"private",
"void",
"denyAccess",
"(",
"HttpServletResponse",
"response",
",",
"String",
"message",
")",
"throws",
"IOException",
"{",
"StringBuilder",
"sb",
"=",
"new",
"StringBuilder",
"(",
")",
";",
"sb",
".",
"append",
"(",
"\"Fedora: 403 \"",
")",
".",
"append",
"(",
"message",
".",
"toUpperCase",
"(",
")",
")",
";",
"response",
".",
"reset",
"(",
")",
";",
"response",
".",
"setStatus",
"(",
"HttpServletResponse",
".",
"SC_FORBIDDEN",
")",
";",
"response",
".",
"setContentType",
"(",
"\"text/plain\"",
")",
";",
"response",
".",
"setContentLength",
"(",
"sb",
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"length",
"(",
")",
")",
";",
"ServletOutputStream",
"out",
"=",
"response",
".",
"getOutputStream",
"(",
")",
";",
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".",
"write",
"(",
"sb",
".",
"toString",
"(",
")",
".",
"getBytes",
"(",
")",
")",
";",
"out",
".",
"flush",
"(",
")",
";",
"out",
".",
"close",
"(",
")",
";",
"}"
] |
Outputs an access denied message.
@param out
the output stream to send the message to
@param message
the message to send
|
[
"Outputs",
"an",
"access",
"denied",
"message",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-security/fcrepo-security-pep/src/main/java/org/fcrepo/server/security/xacml/pep/rest/PEP.java#L266-L279
|
9,156
|
fcrepo3/fcrepo
|
fcrepo-security/fcrepo-security-pep/src/main/java/org/fcrepo/server/security/xacml/pep/rest/PEP.java
|
PEP.loginForm
|
private void loginForm(HttpServletResponse response) {
response.reset();
response.addHeader("WWW-Authenticate",
"Basic realm=\"!!Fedora Repository Server\"");
response.setStatus(HttpServletResponse.SC_UNAUTHORIZED);
}
|
java
|
private void loginForm(HttpServletResponse response) {
response.reset();
response.addHeader("WWW-Authenticate",
"Basic realm=\"!!Fedora Repository Server\"");
response.setStatus(HttpServletResponse.SC_UNAUTHORIZED);
}
|
[
"private",
"void",
"loginForm",
"(",
"HttpServletResponse",
"response",
")",
"{",
"response",
".",
"reset",
"(",
")",
";",
"response",
".",
"addHeader",
"(",
"\"WWW-Authenticate\"",
",",
"\"Basic realm=\\\"!!Fedora Repository Server\\\"\"",
")",
";",
"response",
".",
"setStatus",
"(",
"HttpServletResponse",
".",
"SC_UNAUTHORIZED",
")",
";",
"}"
] |
Sends a 401 error to the browser. This forces a login screen to be
displayed allowing the user to login.
@param response
the response to set the headers and status
|
[
"Sends",
"a",
"401",
"error",
"to",
"the",
"browser",
".",
"This",
"forces",
"a",
"login",
"screen",
"to",
"be",
"displayed",
"allowing",
"the",
"user",
"to",
"login",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-security/fcrepo-security-pep/src/main/java/org/fcrepo/server/security/xacml/pep/rest/PEP.java#L288-L293
|
9,157
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/journal/JournalConsumer.java
|
JournalConsumer.shutdown
|
public void shutdown() throws ModuleShutdownException {
try {
consumerThread.shutdown();
reader.shutdown();
recoveryLog.shutdown("Server is shutting down.");
} catch (JournalException e) {
throw new ModuleShutdownException("Error closing journal reader.",
role,
e);
}
}
|
java
|
public void shutdown() throws ModuleShutdownException {
try {
consumerThread.shutdown();
reader.shutdown();
recoveryLog.shutdown("Server is shutting down.");
} catch (JournalException e) {
throw new ModuleShutdownException("Error closing journal reader.",
role,
e);
}
}
|
[
"public",
"void",
"shutdown",
"(",
")",
"throws",
"ModuleShutdownException",
"{",
"try",
"{",
"consumerThread",
".",
"shutdown",
"(",
")",
";",
"reader",
".",
"shutdown",
"(",
")",
";",
"recoveryLog",
".",
"shutdown",
"(",
"\"Server is shutting down.\"",
")",
";",
"}",
"catch",
"(",
"JournalException",
"e",
")",
"{",
"throw",
"new",
"ModuleShutdownException",
"(",
"\"Error closing journal reader.\"",
",",
"role",
",",
"e",
")",
";",
"}",
"}"
] |
Tell the thread, the reader and the log to shut down.
|
[
"Tell",
"the",
"thread",
"the",
"reader",
"and",
"the",
"log",
"to",
"shut",
"down",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/journal/JournalConsumer.java#L82-L92
|
9,158
|
fcrepo3/fcrepo
|
fcrepo-common/src/main/java/org/fcrepo/common/PID.java
|
PID.getInstance
|
public static PID getInstance(String pidString) {
try {
return new PID(pidString);
} catch (MalformedPIDException e) {
throw new FaultException("Malformed PID: " + e.getMessage(), e);
}
}
|
java
|
public static PID getInstance(String pidString) {
try {
return new PID(pidString);
} catch (MalformedPIDException e) {
throw new FaultException("Malformed PID: " + e.getMessage(), e);
}
}
|
[
"public",
"static",
"PID",
"getInstance",
"(",
"String",
"pidString",
")",
"{",
"try",
"{",
"return",
"new",
"PID",
"(",
"pidString",
")",
";",
"}",
"catch",
"(",
"MalformedPIDException",
"e",
")",
"{",
"throw",
"new",
"FaultException",
"(",
"\"Malformed PID: \"",
"+",
"e",
".",
"getMessage",
"(",
")",
",",
"e",
")",
";",
"}",
"}"
] |
Factory method that throws an unchecked exception if it's not
well-formed.
@param pidString the String value of the PID
@return PID
|
[
"Factory",
"method",
"that",
"throws",
"an",
"unchecked",
"exception",
"if",
"it",
"s",
"not",
"well",
"-",
"formed",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-common/src/main/java/org/fcrepo/common/PID.java#L82-L88
|
9,159
|
fcrepo3/fcrepo
|
fcrepo-common/src/main/java/org/fcrepo/common/PID.java
|
PID.normalize
|
public static String normalize(String pidString)
throws MalformedPIDException {
if (pidString == null) {
throw new MalformedPIDException("PID is null.");
}
return normalize(pidString, 0, pidString.length());
}
|
java
|
public static String normalize(String pidString)
throws MalformedPIDException {
if (pidString == null) {
throw new MalformedPIDException("PID is null.");
}
return normalize(pidString, 0, pidString.length());
}
|
[
"public",
"static",
"String",
"normalize",
"(",
"String",
"pidString",
")",
"throws",
"MalformedPIDException",
"{",
"if",
"(",
"pidString",
"==",
"null",
")",
"{",
"throw",
"new",
"MalformedPIDException",
"(",
"\"PID is null.\"",
")",
";",
"}",
"return",
"normalize",
"(",
"pidString",
",",
"0",
",",
"pidString",
".",
"length",
"(",
")",
")",
";",
"}"
] |
Return the normalized form of the given pid string, or throw a
MalformedPIDException.
@param pidString
@return String normalized version of the pid
@throws MalformedPIDException
|
[
"Return",
"the",
"normalized",
"form",
"of",
"the",
"given",
"pid",
"string",
"or",
"throw",
"a",
"MalformedPIDException",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-common/src/main/java/org/fcrepo/common/PID.java#L113-L120
|
9,160
|
fcrepo3/fcrepo
|
fcrepo-common/src/main/java/org/fcrepo/common/PID.java
|
PID.toURIReference
|
public static SimpleURIReference toURIReference(String pidString) {
SimpleURIReference ref = null;
try {
ref = new SimpleURIReference(new URI(toURI(pidString)));
} catch (URISyntaxException e) {
// assumes pid is well-formed
throw new Error(e);
}
return ref;
}
|
java
|
public static SimpleURIReference toURIReference(String pidString) {
SimpleURIReference ref = null;
try {
ref = new SimpleURIReference(new URI(toURI(pidString)));
} catch (URISyntaxException e) {
// assumes pid is well-formed
throw new Error(e);
}
return ref;
}
|
[
"public",
"static",
"SimpleURIReference",
"toURIReference",
"(",
"String",
"pidString",
")",
"{",
"SimpleURIReference",
"ref",
"=",
"null",
";",
"try",
"{",
"ref",
"=",
"new",
"SimpleURIReference",
"(",
"new",
"URI",
"(",
"toURI",
"(",
"pidString",
")",
")",
")",
";",
"}",
"catch",
"(",
"URISyntaxException",
"e",
")",
"{",
"// assumes pid is well-formed",
"throw",
"new",
"Error",
"(",
"e",
")",
";",
"}",
"return",
"ref",
";",
"}"
] |
Return a URIReference of some PID string, assuming it is well-formed.
|
[
"Return",
"a",
"URIReference",
"of",
"some",
"PID",
"string",
"assuming",
"it",
"is",
"well",
"-",
"formed",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-common/src/main/java/org/fcrepo/common/PID.java#L245-L254
|
9,161
|
fcrepo3/fcrepo
|
fcrepo-common/src/main/java/org/fcrepo/common/PID.java
|
PID.main
|
public static void main(String[] args) throws Exception {
if (args.length > 0) {
PID p = new PID(args[0]);
System.out.println("Normalized : " + p.toString());
System.out.println("To filename : " + p.toFilename());
System.out.println("From filename : "
+ PID.fromFilename(p.toFilename()).toString());
} else {
System.out.println("--------------------------------------");
System.out.println("PID Syntax Checker - Interactive mode");
System.out.println("--------------------------------------");
boolean done = false;
BufferedReader reader =
new BufferedReader(new InputStreamReader(System.in));
while (!done) {
try {
System.out.print("Enter a PID (ENTER to exit): ");
String line = reader.readLine();
if (line.isEmpty()) {
done = true;
} else {
PID p = new PID(line);
System.out.println("Normalized : " + p.toString());
System.out.println("To filename : " + p.toFilename());
System.out.println("From filename : "
+ PID.fromFilename(p.toFilename()).toString());
}
} catch (MalformedPIDException e) {
System.out.println("ERROR: " + e.getMessage());
}
}
}
}
|
java
|
public static void main(String[] args) throws Exception {
if (args.length > 0) {
PID p = new PID(args[0]);
System.out.println("Normalized : " + p.toString());
System.out.println("To filename : " + p.toFilename());
System.out.println("From filename : "
+ PID.fromFilename(p.toFilename()).toString());
} else {
System.out.println("--------------------------------------");
System.out.println("PID Syntax Checker - Interactive mode");
System.out.println("--------------------------------------");
boolean done = false;
BufferedReader reader =
new BufferedReader(new InputStreamReader(System.in));
while (!done) {
try {
System.out.print("Enter a PID (ENTER to exit): ");
String line = reader.readLine();
if (line.isEmpty()) {
done = true;
} else {
PID p = new PID(line);
System.out.println("Normalized : " + p.toString());
System.out.println("To filename : " + p.toFilename());
System.out.println("From filename : "
+ PID.fromFilename(p.toFilename()).toString());
}
} catch (MalformedPIDException e) {
System.out.println("ERROR: " + e.getMessage());
}
}
}
}
|
[
"public",
"static",
"void",
"main",
"(",
"String",
"[",
"]",
"args",
")",
"throws",
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"args",
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"\"From filename : \"",
"+",
"PID",
".",
"fromFilename",
"(",
"p",
".",
"toFilename",
"(",
")",
")",
".",
"toString",
"(",
")",
")",
";",
"}",
"}",
"catch",
"(",
"MalformedPIDException",
"e",
")",
"{",
"System",
".",
"out",
".",
"println",
"(",
"\"ERROR: \"",
"+",
"e",
".",
"getMessage",
"(",
")",
")",
";",
"}",
"}",
"}",
"}"
] |
Command-line interactive tester. If one arg given, prints normalized form
of that PID and exits. If no args, enters interactive mode.
|
[
"Command",
"-",
"line",
"interactive",
"tester",
".",
"If",
"one",
"arg",
"given",
"prints",
"normalized",
"form",
"of",
"that",
"PID",
"and",
"exits",
".",
"If",
"no",
"args",
"enters",
"interactive",
"mode",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-common/src/main/java/org/fcrepo/common/PID.java#L303-L335
|
9,162
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/search/FieldSearchResultSQLImpl.java
|
FieldSearchResultSQLImpl.getObjectFields
|
private ObjectFields getObjectFields(String pid)
throws UnrecognizedFieldException, ObjectIntegrityException,
RepositoryConfigurationException, StreamIOException,
ServerException {
DOReader r =
m_repoReader.getReader(Server.USE_DEFINITIVE_STORE,
ReadOnlyContext.EMPTY,
pid);
ObjectFields f;
// If there's a DC record available, use SAX to parse the most
// recent version of it into f.
Datastream dcmd = null;
try {
dcmd = r.GetDatastream("DC", null);
} catch (ClassCastException cce) {
throw new ObjectIntegrityException("Object " + r.GetObjectPID()
+ " has a DC datastream, but it's not inline XML.");
}
if (dcmd != null) {
f = new ObjectFields(m_resultFields, dcmd.getContentStream());
// add dcmDate if wanted
for (String element : m_resultFields) {
if (element.equals("dcmDate")) {
f.setDCMDate(dcmd.DSCreateDT);
}
}
} else {
f = new ObjectFields();
}
// add non-dc values from doReader for the others in m_resultFields[]
// Disseminator[] disses=null;
for (String n : m_resultFields) {
if (n.equals("pid")) {
f.setPid(pid);
}
if (n.equals("label")) {
f.setLabel(r.GetObjectLabel());
}
if (n.equals("state")) {
f.setState(r.GetObjectState());
}
if (n.equals("ownerId")) {
f.setOwnerId(r.getOwnerId());
}
if (n.equals("cDate")) {
f.setCDate(r.getCreateDate());
}
if (n.equals("mDate")) {
f.setMDate(r.getLastModDate());
}
}
return f;
}
|
java
|
private ObjectFields getObjectFields(String pid)
throws UnrecognizedFieldException, ObjectIntegrityException,
RepositoryConfigurationException, StreamIOException,
ServerException {
DOReader r =
m_repoReader.getReader(Server.USE_DEFINITIVE_STORE,
ReadOnlyContext.EMPTY,
pid);
ObjectFields f;
// If there's a DC record available, use SAX to parse the most
// recent version of it into f.
Datastream dcmd = null;
try {
dcmd = r.GetDatastream("DC", null);
} catch (ClassCastException cce) {
throw new ObjectIntegrityException("Object " + r.GetObjectPID()
+ " has a DC datastream, but it's not inline XML.");
}
if (dcmd != null) {
f = new ObjectFields(m_resultFields, dcmd.getContentStream());
// add dcmDate if wanted
for (String element : m_resultFields) {
if (element.equals("dcmDate")) {
f.setDCMDate(dcmd.DSCreateDT);
}
}
} else {
f = new ObjectFields();
}
// add non-dc values from doReader for the others in m_resultFields[]
// Disseminator[] disses=null;
for (String n : m_resultFields) {
if (n.equals("pid")) {
f.setPid(pid);
}
if (n.equals("label")) {
f.setLabel(r.GetObjectLabel());
}
if (n.equals("state")) {
f.setState(r.GetObjectState());
}
if (n.equals("ownerId")) {
f.setOwnerId(r.getOwnerId());
}
if (n.equals("cDate")) {
f.setCDate(r.getCreateDate());
}
if (n.equals("mDate")) {
f.setMDate(r.getLastModDate());
}
}
return f;
}
|
[
"private",
"ObjectFields",
"getObjectFields",
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"String",
"pid",
")",
"throws",
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",",
"ObjectIntegrityException",
",",
"RepositoryConfigurationException",
",",
"StreamIOException",
",",
"ServerException",
"{",
"DOReader",
"r",
"=",
"m_repoReader",
".",
"getReader",
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"Server",
".",
"USE_DEFINITIVE_STORE",
",",
"ReadOnlyContext",
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"EMPTY",
",",
"pid",
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";",
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"// If there's a DC record available, use SAX to parse the most",
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"{",
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"GetDatastream",
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")",
";",
"}",
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"dcmd",
"!=",
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"f",
"=",
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",",
"dcmd",
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")",
")",
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"// add dcmDate if wanted",
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"String",
"element",
":",
"m_resultFields",
")",
"{",
"if",
"(",
"element",
".",
"equals",
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"\"dcmDate\"",
")",
")",
"{",
"f",
".",
"setDCMDate",
"(",
"dcmd",
".",
"DSCreateDT",
")",
";",
"}",
"}",
"}",
"else",
"{",
"f",
"=",
"new",
"ObjectFields",
"(",
")",
";",
"}",
"// add non-dc values from doReader for the others in m_resultFields[]",
"// Disseminator[] disses=null;",
"for",
"(",
"String",
"n",
":",
"m_resultFields",
")",
"{",
"if",
"(",
"n",
".",
"equals",
"(",
"\"pid\"",
")",
")",
"{",
"f",
".",
"setPid",
"(",
"pid",
")",
";",
"}",
"if",
"(",
"n",
".",
"equals",
"(",
"\"label\"",
")",
")",
"{",
"f",
".",
"setLabel",
"(",
"r",
".",
"GetObjectLabel",
"(",
")",
")",
";",
"}",
"if",
"(",
"n",
".",
"equals",
"(",
"\"state\"",
")",
")",
"{",
"f",
".",
"setState",
"(",
"r",
".",
"GetObjectState",
"(",
")",
")",
";",
"}",
"if",
"(",
"n",
".",
"equals",
"(",
"\"ownerId\"",
")",
")",
"{",
"f",
".",
"setOwnerId",
"(",
"r",
".",
"getOwnerId",
"(",
")",
")",
";",
"}",
"if",
"(",
"n",
".",
"equals",
"(",
"\"cDate\"",
")",
")",
"{",
"f",
".",
"setCDate",
"(",
"r",
".",
"getCreateDate",
"(",
")",
")",
";",
"}",
"if",
"(",
"n",
".",
"equals",
"(",
"\"mDate\"",
")",
")",
"{",
"f",
".",
"setMDate",
"(",
"r",
".",
"getLastModDate",
"(",
")",
")",
";",
"}",
"}",
"return",
"f",
";",
"}"
] |
For the given pid, get a reader on the object from the repository and
return an ObjectFields object with resultFields fields populated.
@param pid
the unique identifier of the object for which the information is
requested.
@return ObjectFields populated with the requested fields
@throws UnrecognizedFieldException
if a resultFields value isn't valid
@throws ObjectIntegrityException
if the underlying digital object can't be parsed
@throws RepositoryConfigurationException
if the sax parser can't be constructed
@throws StreamIOException
if an error occurs while reading the serialized digital object
stream
@throws ServerException
if any other kind of error occurs while reading the underlying
object
|
[
"For",
"the",
"given",
"pid",
"get",
"a",
"reader",
"on",
"the",
"object",
"from",
"the",
"repository",
"and",
"return",
"an",
"ObjectFields",
"object",
"with",
"resultFields",
"fields",
"populated",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/search/FieldSearchResultSQLImpl.java#L481-L533
|
9,163
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/search/FieldSearchResultSQLImpl.java
|
FieldSearchResultSQLImpl.isDCProp
|
private static final boolean isDCProp(String in) {//2004.05.18 wdn5e wasn't static final
if (in.equals("mDate") || in.equals("dcmDate")) {
return false;
}
for (String n : FieldSearchSQLImpl.DB_COLUMN_NAMES) {
if (n.startsWith("dc")
&& n.toLowerCase().indexOf(in.toLowerCase()) == 2) { //2004.05.18 wdn5e (was -1)
return true;
}
}
return false;
}
|
java
|
private static final boolean isDCProp(String in) {//2004.05.18 wdn5e wasn't static final
if (in.equals("mDate") || in.equals("dcmDate")) {
return false;
}
for (String n : FieldSearchSQLImpl.DB_COLUMN_NAMES) {
if (n.startsWith("dc")
&& n.toLowerCase().indexOf(in.toLowerCase()) == 2) { //2004.05.18 wdn5e (was -1)
return true;
}
}
return false;
}
|
[
"private",
"static",
"final",
"boolean",
"isDCProp",
"(",
"String",
"in",
")",
"{",
"//2004.05.18 wdn5e wasn't static final",
"if",
"(",
"in",
".",
"equals",
"(",
"\"mDate\"",
")",
"||",
"in",
".",
"equals",
"(",
"\"dcmDate\"",
")",
")",
"{",
"return",
"false",
";",
"}",
"for",
"(",
"String",
"n",
":",
"FieldSearchSQLImpl",
".",
"DB_COLUMN_NAMES",
")",
"{",
"if",
"(",
"n",
".",
"startsWith",
"(",
"\"dc\"",
")",
"&&",
"n",
".",
"toLowerCase",
"(",
")",
".",
"indexOf",
"(",
"in",
".",
"toLowerCase",
"(",
")",
")",
"==",
"2",
")",
"{",
"//2004.05.18 wdn5e (was -1)",
"return",
"true",
";",
"}",
"}",
"return",
"false",
";",
"}"
] |
Tell whether a field name, as given in the search request, is a dublin
core field.
@param the
field
@return whether it's a dublin core field
|
[
"Tell",
"whether",
"a",
"field",
"name",
"as",
"given",
"in",
"the",
"search",
"request",
"is",
"a",
"dublin",
"core",
"field",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/search/FieldSearchResultSQLImpl.java#L712-L723
|
9,164
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/resourceIndex/ModelBasedTripleGenerator.java
|
ModelBasedTripleGenerator.getTriplesForObject
|
public Set<Triple> getTriplesForObject(DOReader reader)
throws ResourceIndexException {
Set<Triple> objectTriples = new HashSet<Triple>();
try {
for (String modelRelobject:reader.getContentModels()){
if (m_generators.containsKey(modelRelobject)) {
objectTriples.addAll(m_generators.get(modelRelobject)
.getTriplesForObject(reader));
}
}
} catch (ServerException e) {
throw new ResourceIndexException("Could not read object's content model",
e);
}
return objectTriples;
}
|
java
|
public Set<Triple> getTriplesForObject(DOReader reader)
throws ResourceIndexException {
Set<Triple> objectTriples = new HashSet<Triple>();
try {
for (String modelRelobject:reader.getContentModels()){
if (m_generators.containsKey(modelRelobject)) {
objectTriples.addAll(m_generators.get(modelRelobject)
.getTriplesForObject(reader));
}
}
} catch (ServerException e) {
throw new ResourceIndexException("Could not read object's content model",
e);
}
return objectTriples;
}
|
[
"public",
"Set",
"<",
"Triple",
">",
"getTriplesForObject",
"(",
"DOReader",
"reader",
")",
"throws",
"ResourceIndexException",
"{",
"Set",
"<",
"Triple",
">",
"objectTriples",
"=",
"new",
"HashSet",
"<",
"Triple",
">",
"(",
")",
";",
"try",
"{",
"for",
"(",
"String",
"modelRelobject",
":",
"reader",
".",
"getContentModels",
"(",
")",
")",
"{",
"if",
"(",
"m_generators",
".",
"containsKey",
"(",
"modelRelobject",
")",
")",
"{",
"objectTriples",
".",
"addAll",
"(",
"m_generators",
".",
"get",
"(",
"modelRelobject",
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".",
"getTriplesForObject",
"(",
"reader",
")",
")",
";",
"}",
"}",
"}",
"catch",
"(",
"ServerException",
"e",
")",
"{",
"throw",
"new",
"ResourceIndexException",
"(",
"\"Could not read object's content model\"",
",",
"e",
")",
";",
"}",
"return",
"objectTriples",
";",
"}"
] |
Gets all triples implied by the object's models.
@param reader
Reads the current object
@return Set of all triples implied by the object's models.
|
[
"Gets",
"all",
"triples",
"implied",
"by",
"the",
"object",
"s",
"models",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/resourceIndex/ModelBasedTripleGenerator.java#L90-L109
|
9,165
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/validation/DOValidatorSchematron.java
|
DOValidatorSchematron.validate
|
public void validate(StreamSource objectSource) throws ServerException {
DOValidatorSchematronResult result = null;
try {
// Create a transformer that uses the validating stylesheet.
// Run the Schematron validation of the Fedora object and
// output results in DOM format.
Transformer vtransformer =
validatingStyleSheet.newTransformer();
DOMResult validationResult = new DOMResult();
vtransformer.transform(objectSource, validationResult);
result = new DOValidatorSchematronResult(validationResult);
} catch (Exception e) {
Validation validation = new Validation("unknown");
String problem = "Schematron validation failed:".concat(e.getMessage());
validation.setObjectProblems(Collections.singletonList(problem));
logger.error("Schematron validation failed", e);
throw new ObjectValidityException(e.getMessage(), validation);
}
if (!result.isValid()) {
String msg = null;
try {
msg = result.getXMLResult();
} catch (Exception e) {
logger.warn("Error getting XML result of schematron validation failure", e);
}
Validation validation = new Validation("unknown");
if (msg == null) {
msg = "Unknown schematron error. Error getting XML results of schematron validation";
}
validation.setObjectProblems(Collections.singletonList(msg));
throw new ObjectValidityException(msg, validation);
}
}
|
java
|
public void validate(StreamSource objectSource) throws ServerException {
DOValidatorSchematronResult result = null;
try {
// Create a transformer that uses the validating stylesheet.
// Run the Schematron validation of the Fedora object and
// output results in DOM format.
Transformer vtransformer =
validatingStyleSheet.newTransformer();
DOMResult validationResult = new DOMResult();
vtransformer.transform(objectSource, validationResult);
result = new DOValidatorSchematronResult(validationResult);
} catch (Exception e) {
Validation validation = new Validation("unknown");
String problem = "Schematron validation failed:".concat(e.getMessage());
validation.setObjectProblems(Collections.singletonList(problem));
logger.error("Schematron validation failed", e);
throw new ObjectValidityException(e.getMessage(), validation);
}
if (!result.isValid()) {
String msg = null;
try {
msg = result.getXMLResult();
} catch (Exception e) {
logger.warn("Error getting XML result of schematron validation failure", e);
}
Validation validation = new Validation("unknown");
if (msg == null) {
msg = "Unknown schematron error. Error getting XML results of schematron validation";
}
validation.setObjectProblems(Collections.singletonList(msg));
throw new ObjectValidityException(msg, validation);
}
}
|
[
"public",
"void",
"validate",
"(",
"StreamSource",
"objectSource",
")",
"throws",
"ServerException",
"{",
"DOValidatorSchematronResult",
"result",
"=",
"null",
";",
"try",
"{",
"// Create a transformer that uses the validating stylesheet.",
"// Run the Schematron validation of the Fedora object and",
"// output results in DOM format.",
"Transformer",
"vtransformer",
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"validatingStyleSheet",
".",
"newTransformer",
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")",
";",
"DOMResult",
"validationResult",
"=",
"new",
"DOMResult",
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"vtransformer",
".",
"transform",
"(",
"objectSource",
",",
"validationResult",
")",
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"result",
"=",
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"validationResult",
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"catch",
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"error",
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",",
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")",
",",
"validation",
")",
";",
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")",
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"logger",
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"warn",
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"\"Error getting XML result of schematron validation failure\"",
",",
"e",
")",
";",
"}",
"Validation",
"validation",
"=",
"new",
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"(",
"\"unknown\"",
")",
";",
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"(",
"msg",
"==",
"null",
")",
"{",
"msg",
"=",
"\"Unknown schematron error. Error getting XML results of schematron validation\"",
";",
"}",
"validation",
".",
"setObjectProblems",
"(",
"Collections",
".",
"singletonList",
"(",
"msg",
")",
")",
";",
"throw",
"new",
"ObjectValidityException",
"(",
"msg",
",",
"validation",
")",
";",
"}",
"}"
] |
Run the Schematron validation on a Fedora object.
@param objectSource
the Fedora object as an StreamSource
@throws ServerException
|
[
"Run",
"the",
"Schematron",
"validation",
"on",
"a",
"Fedora",
"object",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/validation/DOValidatorSchematron.java#L107-L140
|
9,166
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/validation/DOValidatorSchematron.java
|
DOValidatorSchematron.setUp
|
private Templates setUp(String preprocessorPath,
String fedoraschemaPath,
String phase)
throws ObjectValidityException, TransformerException {
String key = fedoraschemaPath + "#" + phase;
Templates templates =
generatedStyleSheets.get(key);
if (templates == null) {
rulesSource = fileToStreamSource(fedoraschemaPath);
preprocessorSource = fileToStreamSource(preprocessorPath);
templates = createValidatingStyleSheet(rulesSource,
preprocessorSource, phase);
generatedStyleSheets.put(key, templates);
}
return templates;
}
|
java
|
private Templates setUp(String preprocessorPath,
String fedoraschemaPath,
String phase)
throws ObjectValidityException, TransformerException {
String key = fedoraschemaPath + "#" + phase;
Templates templates =
generatedStyleSheets.get(key);
if (templates == null) {
rulesSource = fileToStreamSource(fedoraschemaPath);
preprocessorSource = fileToStreamSource(preprocessorPath);
templates = createValidatingStyleSheet(rulesSource,
preprocessorSource, phase);
generatedStyleSheets.put(key, templates);
}
return templates;
}
|
[
"private",
"Templates",
"setUp",
"(",
"String",
"preprocessorPath",
",",
"String",
"fedoraschemaPath",
",",
"String",
"phase",
")",
"throws",
"ObjectValidityException",
",",
"TransformerException",
"{",
"String",
"key",
"=",
"fedoraschemaPath",
"+",
"\"#\"",
"+",
"phase",
";",
"Templates",
"templates",
"=",
"generatedStyleSheets",
".",
"get",
"(",
"key",
")",
";",
"if",
"(",
"templates",
"==",
"null",
")",
"{",
"rulesSource",
"=",
"fileToStreamSource",
"(",
"fedoraschemaPath",
")",
";",
"preprocessorSource",
"=",
"fileToStreamSource",
"(",
"preprocessorPath",
")",
";",
"templates",
"=",
"createValidatingStyleSheet",
"(",
"rulesSource",
",",
"preprocessorSource",
",",
"phase",
")",
";",
"generatedStyleSheets",
".",
"put",
"(",
"key",
",",
"templates",
")",
";",
"}",
"return",
"templates",
";",
"}"
] |
Run setup to prepare for Schematron validation. This entails dynamically
creating the validating stylesheet using the preprocessor and the schema.
@param preprocessorPath
the location of the Schematron preprocessor
@param fedoraschemaPath
the URL of the Schematron schema
@param phase
the phase in the fedora object lifecycle to which validation
should pertain. (Currently options are "ingest" and "store")
@return StreamSource
@throws ObjectValidityException
|
[
"Run",
"setup",
"to",
"prepare",
"for",
"Schematron",
"validation",
".",
"This",
"entails",
"dynamically",
"creating",
"the",
"validating",
"stylesheet",
"using",
"the",
"preprocessor",
"and",
"the",
"schema",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/validation/DOValidatorSchematron.java#L156-L171
|
9,167
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/validation/DOValidatorSchematron.java
|
DOValidatorSchematron.createValidatingStyleSheet
|
private Templates createValidatingStyleSheet(StreamSource rulesSource,
StreamSource preprocessorSource,
String phase)
throws ObjectValidityException, TransformerException {
ReadableCharArrayWriter out = new ReadableCharArrayWriter(4096);
try {
// Create a transformer for that uses the Schematron preprocessor stylesheet.
// Transform the Schematron schema (rules) into a validating stylesheet.
Transformer ptransformer =
XmlTransformUtility.getTransformer(preprocessorSource);
ptransformer.setParameter("phase", phase);
ptransformer.transform(rulesSource, new StreamResult(out));
out.close();
} catch (Exception e) {
logger.error("Schematron validation failed", e);
throw new ObjectValidityException(e.getMessage());
}
return XmlTransformUtility.getTemplates(
new StreamSource(out.toReader()));
}
|
java
|
private Templates createValidatingStyleSheet(StreamSource rulesSource,
StreamSource preprocessorSource,
String phase)
throws ObjectValidityException, TransformerException {
ReadableCharArrayWriter out = new ReadableCharArrayWriter(4096);
try {
// Create a transformer for that uses the Schematron preprocessor stylesheet.
// Transform the Schematron schema (rules) into a validating stylesheet.
Transformer ptransformer =
XmlTransformUtility.getTransformer(preprocessorSource);
ptransformer.setParameter("phase", phase);
ptransformer.transform(rulesSource, new StreamResult(out));
out.close();
} catch (Exception e) {
logger.error("Schematron validation failed", e);
throw new ObjectValidityException(e.getMessage());
}
return XmlTransformUtility.getTemplates(
new StreamSource(out.toReader()));
}
|
[
"private",
"Templates",
"createValidatingStyleSheet",
"(",
"StreamSource",
"rulesSource",
",",
"StreamSource",
"preprocessorSource",
",",
"String",
"phase",
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"throws",
"ObjectValidityException",
",",
"TransformerException",
"{",
"ReadableCharArrayWriter",
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"new",
"ReadableCharArrayWriter",
"(",
"4096",
")",
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"// Create a transformer for that uses the Schematron preprocessor stylesheet.",
"// Transform the Schematron schema (rules) into a validating stylesheet.",
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"ptransformer",
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"XmlTransformUtility",
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"}",
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";",
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"e",
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")",
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"getTemplates",
"(",
"new",
"StreamSource",
"(",
"out",
".",
"toReader",
"(",
")",
")",
")",
";",
"}"
] |
Create the validating stylesheet which will be used to perform the actual
Schematron validation. The validating stylesheet is created dynamically
using the preprocessor stylesheet and the Schematron schema for Fedora.
The phase is key. The stylesheet is created for the appropriate phase as
specified in the Schematron rules schema. Valid work flow phases are
currently "ingest" and "store." Different schematron rules apply to
different phases of the object lifecycle. Some rules are applied when an
object is first being ingested into the repository. Other rules apply
before the object is put into permanent storage.
@param rulesSource
the location of the rules
@param preprocessorSource
the location of the Schematron preprocessor
@param phase
the phase in the fedora object lifecycle to which validation
should pertain. (Currently options are "ingest" and "store"
@return A ByteArrayOutputStream containing the stylesheet
@throws ObjectValidityException
@throws TransformerException
|
[
"Create",
"the",
"validating",
"stylesheet",
"which",
"will",
"be",
"used",
"to",
"perform",
"the",
"actual",
"Schematron",
"validation",
".",
"The",
"validating",
"stylesheet",
"is",
"created",
"dynamically",
"using",
"the",
"preprocessor",
"stylesheet",
"and",
"the",
"Schematron",
"schema",
"for",
"Fedora",
".",
"The",
"phase",
"is",
"key",
".",
"The",
"stylesheet",
"is",
"created",
"for",
"the",
"appropriate",
"phase",
"as",
"specified",
"in",
"the",
"Schematron",
"rules",
"schema",
".",
"Valid",
"work",
"flow",
"phases",
"are",
"currently",
"ingest",
"and",
"store",
".",
"Different",
"schematron",
"rules",
"apply",
"to",
"different",
"phases",
"of",
"the",
"object",
"lifecycle",
".",
"Some",
"rules",
"are",
"applied",
"when",
"an",
"object",
"is",
"first",
"being",
"ingested",
"into",
"the",
"repository",
".",
"Other",
"rules",
"apply",
"before",
"the",
"object",
"is",
"put",
"into",
"permanent",
"storage",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/validation/DOValidatorSchematron.java#L195-L215
|
9,168
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/storage/lowlevel/DBPathRegistry.java
|
DBPathRegistry.exists
|
@Override
public boolean exists(String pid)
throws LowlevelStorageException {
Connection connection = null;
PreparedStatement statement = null;
ResultSet rs = null;
try {
connection = connectionPool.getReadOnlyConnection();
statement = connection.prepareStatement(selectByIdQuery);
statement.setString(1,pid);
rs =
statement.executeQuery();
return rs.next();
} catch (SQLException e1) {
throw new LowlevelStorageException(true, "sql failure (get)", e1);
} finally {
try {
if (rs != null) {
rs.close();
}
if (statement != null) {
statement.close();
}
if (connection != null) {
connectionPool.free(connection);
}
} catch (Exception e2) { // purposely general to include uninstantiated statement, connection
throw new LowlevelStorageException(true,
"sql failure closing statement, connection, pool (get)",
e2);
} finally {
rs = null;
statement = null;
connection = null;
}
}
}
|
java
|
@Override
public boolean exists(String pid)
throws LowlevelStorageException {
Connection connection = null;
PreparedStatement statement = null;
ResultSet rs = null;
try {
connection = connectionPool.getReadOnlyConnection();
statement = connection.prepareStatement(selectByIdQuery);
statement.setString(1,pid);
rs =
statement.executeQuery();
return rs.next();
} catch (SQLException e1) {
throw new LowlevelStorageException(true, "sql failure (get)", e1);
} finally {
try {
if (rs != null) {
rs.close();
}
if (statement != null) {
statement.close();
}
if (connection != null) {
connectionPool.free(connection);
}
} catch (Exception e2) { // purposely general to include uninstantiated statement, connection
throw new LowlevelStorageException(true,
"sql failure closing statement, connection, pool (get)",
e2);
} finally {
rs = null;
statement = null;
connection = null;
}
}
}
|
[
"@",
"Override",
"public",
"boolean",
"exists",
"(",
"String",
"pid",
")",
"throws",
"LowlevelStorageException",
"{",
"Connection",
"connection",
"=",
"null",
";",
"PreparedStatement",
"statement",
"=",
"null",
";",
"ResultSet",
"rs",
"=",
"null",
";",
"try",
"{",
"connection",
"=",
"connectionPool",
".",
"getReadOnlyConnection",
"(",
")",
";",
"statement",
"=",
"connection",
".",
"prepareStatement",
"(",
"selectByIdQuery",
")",
";",
"statement",
".",
"setString",
"(",
"1",
",",
"pid",
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"rs",
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"statement",
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"executeQuery",
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"next",
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"true",
",",
"\"sql failure (get)\"",
",",
"e1",
")",
";",
"}",
"finally",
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"try",
"{",
"if",
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"rs",
"!=",
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"rs",
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")",
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"}",
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"statement",
"!=",
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"statement",
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"close",
"(",
")",
";",
"}",
"if",
"(",
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"!=",
"null",
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"free",
"(",
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")",
";",
"}",
"}",
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"Exception",
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"// purposely general to include uninstantiated statement, connection",
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"null",
";",
"statement",
"=",
"null",
";",
"connection",
"=",
"null",
";",
"}",
"}",
"}"
] |
Checks to see whether a pid exists in the registry.
Makes no audits of the number of registrations or
the paths registered.
|
[
"Checks",
"to",
"see",
"whether",
"a",
"pid",
"exists",
"in",
"the",
"registry",
".",
"Makes",
"no",
"audits",
"of",
"the",
"number",
"of",
"registrations",
"or",
"the",
"paths",
"registered",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/storage/lowlevel/DBPathRegistry.java#L91-L127
|
9,169
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/storage/translation/ConvertObjectSerialization.java
|
ConvertObjectSerialization.setObjectDefaults
|
private void setObjectDefaults(DigitalObject obj) {
if (obj.getCreateDate() == null) obj.setCreateDate(m_now);
if (obj.getLastModDate() == null) obj.setLastModDate(m_now);
Iterator<String> dsIds = obj.datastreamIdIterator();
while (dsIds.hasNext()) {
String dsid = dsIds.next();
for (Datastream ds : obj.datastreams(dsid)) {
ds.DSSize = 0;
if (ds.DSCreateDT == null) {
ds.DSCreateDT = m_now;
}
}
}
}
|
java
|
private void setObjectDefaults(DigitalObject obj) {
if (obj.getCreateDate() == null) obj.setCreateDate(m_now);
if (obj.getLastModDate() == null) obj.setLastModDate(m_now);
Iterator<String> dsIds = obj.datastreamIdIterator();
while (dsIds.hasNext()) {
String dsid = dsIds.next();
for (Datastream ds : obj.datastreams(dsid)) {
ds.DSSize = 0;
if (ds.DSCreateDT == null) {
ds.DSCreateDT = m_now;
}
}
}
}
|
[
"private",
"void",
"setObjectDefaults",
"(",
"DigitalObject",
"obj",
")",
"{",
"if",
"(",
"obj",
".",
"getCreateDate",
"(",
")",
"==",
"null",
")",
"obj",
".",
"setCreateDate",
"(",
"m_now",
")",
";",
"if",
"(",
"obj",
".",
"getLastModDate",
"(",
")",
"==",
"null",
")",
"obj",
".",
"setLastModDate",
"(",
"m_now",
")",
";",
"Iterator",
"<",
"String",
">",
"dsIds",
"=",
"obj",
".",
"datastreamIdIterator",
"(",
")",
";",
"while",
"(",
"dsIds",
".",
"hasNext",
"(",
")",
")",
"{",
"String",
"dsid",
"=",
"dsIds",
".",
"next",
"(",
")",
";",
"for",
"(",
"Datastream",
"ds",
":",
"obj",
".",
"datastreams",
"(",
"dsid",
")",
")",
"{",
"ds",
".",
"DSSize",
"=",
"0",
";",
"if",
"(",
"ds",
".",
"DSCreateDT",
"==",
"null",
")",
"{",
"ds",
".",
"DSCreateDT",
"=",
"m_now",
";",
"}",
"}",
"}",
"}"
] |
- Sets datastream sizes to 0
|
[
"-",
"Sets",
"datastream",
"sizes",
"to",
"0"
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/storage/translation/ConvertObjectSerialization.java#L175-L189
|
9,170
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/storage/translation/ConvertObjectSerialization.java
|
ConvertObjectSerialization.main
|
public static void main(String[] args) throws ClassNotFoundException {
LogConfig.initMinimal();
if (args.length < 4 || args.length > 7) {
die("Expected 4 to 7 arguments", true);
}
File sourceDir = new File(args[0]);
if (!sourceDir.isDirectory()) {
die("Not a directory: " + sourceDir.getPath(), false);
}
File destDir = new File(args[1]);
@SuppressWarnings("unchecked")
Class<DODeserializer> deserializer = (Class<DODeserializer>) Class.forName(args[2]);
@SuppressWarnings("unchecked")
Class<DOSerializer> serializer = (Class<DOSerializer>) Class.forName(args[3]);
// So DOTranslationUtility works...
System.setProperty("fedora.hostname", "localhost");
System.setProperty("fedora.port", "8080");
System.setProperty("fedora.appServerContext", Constants.FEDORA_DEFAULT_APP_CONTEXT);
boolean pretty = args.length > 4 && args[4].equals("true");
String inExt = "xml";
if (args.length > 5) inExt = args[5];
String outExt = "xml";
if (args.length > 6) outExt = args[6];
ConvertObjectSerialization converter =
new ConvertObjectSerialization(deserializer,
serializer,
pretty,
inExt,
outExt);
converter.convert(sourceDir, destDir);
TripleIteratorFactory.defaultInstance().shutdown();
}
|
java
|
public static void main(String[] args) throws ClassNotFoundException {
LogConfig.initMinimal();
if (args.length < 4 || args.length > 7) {
die("Expected 4 to 7 arguments", true);
}
File sourceDir = new File(args[0]);
if (!sourceDir.isDirectory()) {
die("Not a directory: " + sourceDir.getPath(), false);
}
File destDir = new File(args[1]);
@SuppressWarnings("unchecked")
Class<DODeserializer> deserializer = (Class<DODeserializer>) Class.forName(args[2]);
@SuppressWarnings("unchecked")
Class<DOSerializer> serializer = (Class<DOSerializer>) Class.forName(args[3]);
// So DOTranslationUtility works...
System.setProperty("fedora.hostname", "localhost");
System.setProperty("fedora.port", "8080");
System.setProperty("fedora.appServerContext", Constants.FEDORA_DEFAULT_APP_CONTEXT);
boolean pretty = args.length > 4 && args[4].equals("true");
String inExt = "xml";
if (args.length > 5) inExt = args[5];
String outExt = "xml";
if (args.length > 6) outExt = args[6];
ConvertObjectSerialization converter =
new ConvertObjectSerialization(deserializer,
serializer,
pretty,
inExt,
outExt);
converter.convert(sourceDir, destDir);
TripleIteratorFactory.defaultInstance().shutdown();
}
|
[
"public",
"static",
"void",
"main",
"(",
"String",
"[",
"]",
"args",
")",
"throws",
"ClassNotFoundException",
"{",
"LogConfig",
".",
"initMinimal",
"(",
")",
";",
"if",
"(",
"args",
".",
"length",
"<",
"4",
"||",
"args",
".",
"length",
">",
"7",
")",
"{",
"die",
"(",
"\"Expected 4 to 7 arguments\"",
",",
"true",
")",
";",
"}",
"File",
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"[",
"0",
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";",
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"isDirectory",
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")",
")",
"{",
"die",
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"\"Not a directory: \"",
"+",
"sourceDir",
".",
"getPath",
"(",
")",
",",
"false",
")",
";",
"}",
"File",
"destDir",
"=",
"new",
"File",
"(",
"args",
"[",
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"]",
")",
";",
"@",
"SuppressWarnings",
"(",
"\"unchecked\"",
")",
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">",
"deserializer",
"=",
"(",
"Class",
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"DODeserializer",
">",
")",
"Class",
".",
"forName",
"(",
"args",
"[",
"2",
"]",
")",
";",
"@",
"SuppressWarnings",
"(",
"\"unchecked\"",
")",
"Class",
"<",
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">",
"serializer",
"=",
"(",
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">",
")",
"Class",
".",
"forName",
"(",
"args",
"[",
"3",
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")",
";",
"// So DOTranslationUtility works...",
"System",
".",
"setProperty",
"(",
"\"fedora.hostname\"",
",",
"\"localhost\"",
")",
";",
"System",
".",
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"(",
"\"fedora.port\"",
",",
"\"8080\"",
")",
";",
"System",
".",
"setProperty",
"(",
"\"fedora.appServerContext\"",
",",
"Constants",
".",
"FEDORA_DEFAULT_APP_CONTEXT",
")",
";",
"boolean",
"pretty",
"=",
"args",
".",
"length",
">",
"4",
"&&",
"args",
"[",
"4",
"]",
".",
"equals",
"(",
"\"true\"",
")",
";",
"String",
"inExt",
"=",
"\"xml\"",
";",
"if",
"(",
"args",
".",
"length",
">",
"5",
")",
"inExt",
"=",
"args",
"[",
"5",
"]",
";",
"String",
"outExt",
"=",
"\"xml\"",
";",
"if",
"(",
"args",
".",
"length",
">",
"6",
")",
"outExt",
"=",
"args",
"[",
"6",
"]",
";",
"ConvertObjectSerialization",
"converter",
"=",
"new",
"ConvertObjectSerialization",
"(",
"deserializer",
",",
"serializer",
",",
"pretty",
",",
"inExt",
",",
"outExt",
")",
";",
"converter",
".",
"convert",
"(",
"sourceDir",
",",
"destDir",
")",
";",
"TripleIteratorFactory",
".",
"defaultInstance",
"(",
")",
".",
"shutdown",
"(",
")",
";",
"}"
] |
Command-line utility to convert objects from one format to another.
@param args command-line args.
|
[
"Command",
"-",
"line",
"utility",
"to",
"convert",
"objects",
"from",
"one",
"format",
"to",
"another",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/storage/translation/ConvertObjectSerialization.java#L196-L234
|
9,171
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/messaging/AtomAPIMMessage.java
|
AtomAPIMMessage.objectToString
|
private String objectToString(Object obj, String xsdType) {
if (obj == null) {
return "null";
}
String javaType = obj.getClass().getCanonicalName();
String term;
if (javaType != null && javaType.equals("java.util.Date")) { // several circumstances yield null canonical names
term = DateUtility.convertDateToXSDString((Date) obj);
} else if (xsdType.equals("fedora-types:ArrayOfString")) {
term = array2string(obj);
} else if (xsdType.equals("xsd:boolean")) {
term = obj.toString();
} else if (xsdType.equals("xsd:nonNegativeInteger")) {
term = obj.toString();
} else if (xsdType.equals("fedora-types:RelationshipTuple")) {
RelationshipTuple[] tuples = (RelationshipTuple[]) obj;
TupleArrayTripleIterator iter =
new TupleArrayTripleIterator(new ArrayList<RelationshipTuple>(Arrays
.asList(tuples)));
ReadableByteArrayOutputStream os = new ReadableByteArrayOutputStream();
try {
iter.toStream(os, RDFFormat.NOTATION_3, false);
} catch (TrippiException e) {
e.printStackTrace();
}
term = os.getString(Charset.forName("UTF-8"));
} else if (javaType != null && javaType.equals("java.lang.String")) {
term = (String) obj;
term = term.replaceAll("\"", "'");
} else {
term = "[OMITTED]";
}
return term;
}
|
java
|
private String objectToString(Object obj, String xsdType) {
if (obj == null) {
return "null";
}
String javaType = obj.getClass().getCanonicalName();
String term;
if (javaType != null && javaType.equals("java.util.Date")) { // several circumstances yield null canonical names
term = DateUtility.convertDateToXSDString((Date) obj);
} else if (xsdType.equals("fedora-types:ArrayOfString")) {
term = array2string(obj);
} else if (xsdType.equals("xsd:boolean")) {
term = obj.toString();
} else if (xsdType.equals("xsd:nonNegativeInteger")) {
term = obj.toString();
} else if (xsdType.equals("fedora-types:RelationshipTuple")) {
RelationshipTuple[] tuples = (RelationshipTuple[]) obj;
TupleArrayTripleIterator iter =
new TupleArrayTripleIterator(new ArrayList<RelationshipTuple>(Arrays
.asList(tuples)));
ReadableByteArrayOutputStream os = new ReadableByteArrayOutputStream();
try {
iter.toStream(os, RDFFormat.NOTATION_3, false);
} catch (TrippiException e) {
e.printStackTrace();
}
term = os.getString(Charset.forName("UTF-8"));
} else if (javaType != null && javaType.equals("java.lang.String")) {
term = (String) obj;
term = term.replaceAll("\"", "'");
} else {
term = "[OMITTED]";
}
return term;
}
|
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"\"[OMITTED]\"",
";",
"}",
"return",
"term",
";",
"}"
] |
Get the String value of an object based on its class or
XML Schema Datatype.
@param obj
@param xsdType
@return
|
[
"Get",
"the",
"String",
"value",
"of",
"an",
"object",
"based",
"on",
"its",
"class",
"or",
"XML",
"Schema",
"Datatype",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/messaging/AtomAPIMMessage.java#L253-L286
|
9,172
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/security/impl/BasicRequestCtx.java
|
BasicRequestCtx.encodeAttributes
|
private void encodeAttributes(List attributes, PrintStream out,
Indenter indenter) {
Iterator it = attributes.iterator();
while (it.hasNext()) {
Attribute attr = (Attribute)(it.next());
attr.encode(out, indenter);
}
}
|
java
|
private void encodeAttributes(List attributes, PrintStream out,
Indenter indenter) {
Iterator it = attributes.iterator();
while (it.hasNext()) {
Attribute attr = (Attribute)(it.next());
attr.encode(out, indenter);
}
}
|
[
"private",
"void",
"encodeAttributes",
"(",
"List",
"attributes",
",",
"PrintStream",
"out",
",",
"Indenter",
"indenter",
")",
"{",
"Iterator",
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".",
"iterator",
"(",
")",
";",
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")",
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")",
")",
";",
"attr",
".",
"encode",
"(",
"out",
",",
"indenter",
")",
";",
"}",
"}"
] |
Private helper function to encode the attribute sets
|
[
"Private",
"helper",
"function",
"to",
"encode",
"the",
"attribute",
"sets"
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/security/impl/BasicRequestCtx.java#L496-L503
|
9,173
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/security/impl/BasicRequestCtx.java
|
BasicRequestCtx.encodeSubject
|
private void encodeSubject(Subject subject, PrintStream out,
Indenter indenter) {
char [] indent = indenter.makeString().toCharArray();
out.print(indent);
out.append("<Subject SubjectCategory=\"")
.append(subject.getCategory().toString()).append('"');
List subjectAttrs = subject.getAttributesAsList();
if (subjectAttrs.size() == 0) {
// there's nothing in this Subject, so just close the tag
out.println("/>");
} else {
// there's content, so fill it in
out.println('>');
encodeAttributes(subjectAttrs, out, indenter);
out.print(indent);
out.println("</Subject>");
}
}
|
java
|
private void encodeSubject(Subject subject, PrintStream out,
Indenter indenter) {
char [] indent = indenter.makeString().toCharArray();
out.print(indent);
out.append("<Subject SubjectCategory=\"")
.append(subject.getCategory().toString()).append('"');
List subjectAttrs = subject.getAttributesAsList();
if (subjectAttrs.size() == 0) {
// there's nothing in this Subject, so just close the tag
out.println("/>");
} else {
// there's content, so fill it in
out.println('>');
encodeAttributes(subjectAttrs, out, indenter);
out.print(indent);
out.println("</Subject>");
}
}
|
[
"private",
"void",
"encodeSubject",
"(",
"Subject",
"subject",
",",
"PrintStream",
"out",
",",
"Indenter",
"indenter",
")",
"{",
"char",
"[",
"]",
"indent",
"=",
"indenter",
".",
"makeString",
"(",
")",
".",
"toCharArray",
"(",
")",
";",
"out",
".",
"print",
"(",
"indent",
")",
";",
"out",
".",
"append",
"(",
"\"<Subject SubjectCategory=\\\"\"",
")",
".",
"append",
"(",
"subject",
".",
"getCategory",
"(",
")",
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"toString",
"(",
")",
")",
".",
"append",
"(",
"'",
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")",
";",
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"(",
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";",
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"subjectAttrs",
".",
"size",
"(",
")",
"==",
"0",
")",
"{",
"// there's nothing in this Subject, so just close the tag",
"out",
".",
"println",
"(",
"\"/>\"",
")",
";",
"}",
"else",
"{",
"// there's content, so fill it in",
"out",
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"println",
"(",
"'",
"'",
")",
";",
"encodeAttributes",
"(",
"subjectAttrs",
",",
"out",
",",
"indenter",
")",
";",
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"print",
"(",
"indent",
")",
";",
"out",
".",
"println",
"(",
"\"</Subject>\"",
")",
";",
"}",
"}"
] |
Private helper function to encode the subjects
|
[
"Private",
"helper",
"function",
"to",
"encode",
"the",
"subjects"
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/security/impl/BasicRequestCtx.java#L508-L529
|
9,174
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/security/servletfilters/ldap/FilterLdap.java
|
FilterLdap.init
|
@Override
public void init(FilterConfig filterConfig) {
String m = "L init() ";
try {
logger.debug(m + ">");
super.init(filterConfig);
m = FilterSetup.getFilterNameAbbrev(FILTER_NAME) + " init() ";
inited = false;
if (!initErrors) {
Set<String> temp = new HashSet<String>();
if (ATTRIBUTES2RETURN == null) {
ATTRIBUTES2RETURN = EMPTY_STRING_ARRAY;
} else {
for (String element : ATTRIBUTES2RETURN) {
temp.add(element);
}
}
if (AUTHENTICATE && PASSWORD != null && !PASSWORD.isEmpty()) {
temp.add(PASSWORD);
}
DIRECTORY_ATTRIBUTES_NEEDED =
(String[]) temp.toArray(StringArrayPrototype);
boolean haveBindMethod = false;
if (SECURITY_AUTHENTICATION != null
&& !SECURITY_AUTHENTICATION.isEmpty()) {
haveBindMethod = true;
}
boolean haveSuperUser = false;
if (SECURITY_PRINCIPAL != null
&& !SECURITY_PRINCIPAL.isEmpty()) {
haveSuperUser = true;
}
boolean haveSuperUserPassword = false;
if (SECURITY_CREDENTIALS != null
&& !SECURITY_CREDENTIALS.isEmpty()) {
haveSuperUserPassword = true;
}
if (haveBindMethod && haveSuperUserPassword) {
initErrors = !haveSuperUser;
}
}
if (initErrors) {
logger.error(m + "not initialized; see previous error");
}
inited = true;
} finally {
logger.debug("{}<", m);
}
}
|
java
|
@Override
public void init(FilterConfig filterConfig) {
String m = "L init() ";
try {
logger.debug(m + ">");
super.init(filterConfig);
m = FilterSetup.getFilterNameAbbrev(FILTER_NAME) + " init() ";
inited = false;
if (!initErrors) {
Set<String> temp = new HashSet<String>();
if (ATTRIBUTES2RETURN == null) {
ATTRIBUTES2RETURN = EMPTY_STRING_ARRAY;
} else {
for (String element : ATTRIBUTES2RETURN) {
temp.add(element);
}
}
if (AUTHENTICATE && PASSWORD != null && !PASSWORD.isEmpty()) {
temp.add(PASSWORD);
}
DIRECTORY_ATTRIBUTES_NEEDED =
(String[]) temp.toArray(StringArrayPrototype);
boolean haveBindMethod = false;
if (SECURITY_AUTHENTICATION != null
&& !SECURITY_AUTHENTICATION.isEmpty()) {
haveBindMethod = true;
}
boolean haveSuperUser = false;
if (SECURITY_PRINCIPAL != null
&& !SECURITY_PRINCIPAL.isEmpty()) {
haveSuperUser = true;
}
boolean haveSuperUserPassword = false;
if (SECURITY_CREDENTIALS != null
&& !SECURITY_CREDENTIALS.isEmpty()) {
haveSuperUserPassword = true;
}
if (haveBindMethod && haveSuperUserPassword) {
initErrors = !haveSuperUser;
}
}
if (initErrors) {
logger.error(m + "not initialized; see previous error");
}
inited = true;
} finally {
logger.debug("{}<", m);
}
}
|
[
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"(",
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"}",
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"+",
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")",
";",
"}",
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"logger",
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"(",
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",",
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")",
";",
"}",
"}"
] |
public Boolean REQUIRE_RETURNED_ATTRS = Boolean.FALSE;
|
[
"public",
"Boolean",
"REQUIRE_RETURNED_ATTRS",
"=",
"Boolean",
".",
"FALSE",
";"
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/security/servletfilters/ldap/FilterLdap.java#L99-L152
|
9,175
|
fcrepo3/fcrepo
|
fcrepo-client/fcrepo-client-admin/src/main/java/org/fcrepo/client/Uploader.java
|
Uploader.upload
|
public String upload(final File file) throws IOException {
if (Administrator.INSTANCE == null) {
return fc.uploadFile(file);
} else {
// paint initial status to the progress bar
String msg =
"Uploading " + file.length() + " bytes to "
+ fc.getUploadURL();
Dimension d = Administrator.PROGRESS.getSize();
Administrator.PROGRESS.setString(msg);
Administrator.PROGRESS.setValue(100);
Administrator.PROGRESS.paintImmediately(0,
0,
(int) d.getWidth() - 1,
(int) d.getHeight() - 1);
// then start the thread, passing parms in
SwingWorker<String> worker = new SwingWorker<String>() {
@Override
public String construct() {
try {
return fc.uploadFile(file);
} catch (IOException e) {
thrownException = e;
return "";
}
}
};
worker.start();
// keep updating status till the worker's finished
int ms = 200;
while (!worker.done) {
try {
Administrator.PROGRESS.setValue(ms);
Administrator.PROGRESS.paintImmediately(0, 0, (int) d
.getWidth() - 1, (int) d.getHeight() - 1);
Thread.sleep(100);
ms = ms + 100;
if (ms >= 2000) {
ms = 200;
}
} catch (InterruptedException ie) {
}
}
// reset the status bar to normal
Administrator.PROGRESS.setValue(2000);
Administrator.PROGRESS.paintImmediately(0,
0,
(int) d.getWidth() - 1,
(int) d.getHeight() - 1);
try {
Thread.sleep(100);
} catch (InterruptedException ie) {
}
// report if there was an error; otherwise return the response
if (worker.thrownException != null) {
throw (IOException) worker.thrownException;
} else {
return (String) worker.getValue();
}
}
}
|
java
|
public String upload(final File file) throws IOException {
if (Administrator.INSTANCE == null) {
return fc.uploadFile(file);
} else {
// paint initial status to the progress bar
String msg =
"Uploading " + file.length() + " bytes to "
+ fc.getUploadURL();
Dimension d = Administrator.PROGRESS.getSize();
Administrator.PROGRESS.setString(msg);
Administrator.PROGRESS.setValue(100);
Administrator.PROGRESS.paintImmediately(0,
0,
(int) d.getWidth() - 1,
(int) d.getHeight() - 1);
// then start the thread, passing parms in
SwingWorker<String> worker = new SwingWorker<String>() {
@Override
public String construct() {
try {
return fc.uploadFile(file);
} catch (IOException e) {
thrownException = e;
return "";
}
}
};
worker.start();
// keep updating status till the worker's finished
int ms = 200;
while (!worker.done) {
try {
Administrator.PROGRESS.setValue(ms);
Administrator.PROGRESS.paintImmediately(0, 0, (int) d
.getWidth() - 1, (int) d.getHeight() - 1);
Thread.sleep(100);
ms = ms + 100;
if (ms >= 2000) {
ms = 200;
}
} catch (InterruptedException ie) {
}
}
// reset the status bar to normal
Administrator.PROGRESS.setValue(2000);
Administrator.PROGRESS.paintImmediately(0,
0,
(int) d.getWidth() - 1,
(int) d.getHeight() - 1);
try {
Thread.sleep(100);
} catch (InterruptedException ie) {
}
// report if there was an error; otherwise return the response
if (worker.thrownException != null) {
throw (IOException) worker.thrownException;
} else {
return (String) worker.getValue();
}
}
}
|
[
"public",
"String",
"upload",
"(",
"final",
"File",
"file",
")",
"throws",
"IOException",
"{",
"if",
"(",
"Administrator",
".",
"INSTANCE",
"==",
"null",
")",
"{",
"return",
"fc",
".",
"uploadFile",
"(",
"file",
")",
";",
"}",
"else",
"{",
"// paint initial status to the progress bar",
"String",
"msg",
"=",
"\"Uploading \"",
"+",
"file",
".",
"length",
"(",
")",
"+",
"\" bytes to \"",
"+",
"fc",
".",
"getUploadURL",
"(",
")",
";",
"Dimension",
"d",
"=",
"Administrator",
".",
"PROGRESS",
".",
"getSize",
"(",
")",
";",
"Administrator",
".",
"PROGRESS",
".",
"setString",
"(",
"msg",
")",
";",
"Administrator",
".",
"PROGRESS",
".",
"setValue",
"(",
"100",
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";",
"Administrator",
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"PROGRESS",
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"-",
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"start",
"(",
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"// keep updating status till the worker's finished",
"int",
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"// reset the status bar to normal",
"Administrator",
".",
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"-",
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"return",
"(",
"String",
")",
"worker",
".",
"getValue",
"(",
")",
";",
"}",
"}",
"}"
] |
Send a file to the server, getting back the identifier.
|
[
"Send",
"a",
"file",
"to",
"the",
"server",
"getting",
"back",
"the",
"identifier",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-client/fcrepo-client-admin/src/main/java/org/fcrepo/client/Uploader.java#L86-L152
|
9,176
|
fcrepo3/fcrepo
|
fcrepo-client/fcrepo-client-admin/src/main/java/org/fcrepo/client/Uploader.java
|
Uploader.main
|
public static void main(String[] args) {
try {
if (args.length == 5 || args.length == 6) {
String protocol = args[0];
int port = Integer.parseInt(args[1]);
String user = args[2];
String password = args[3];
String fileName = args[4];
String context = Constants.FEDORA_DEFAULT_APP_CONTEXT;
if (args.length == 6 && !args[5].isEmpty()) {
context = args[5];
}
Uploader uploader =
new Uploader(protocol, port, context, user, password);
File f = new File(fileName);
System.out.println(uploader.upload(new FileInputStream(f)));
System.out.println(uploader.upload(f));
uploader =
new Uploader(protocol,
port,
context,
user + "test",
password);
System.out.println(uploader.upload(f));
} else {
System.err
.println("Usage: Uploader host port user password file [context]");
}
} catch (Exception e) {
System.err.println("ERROR: " + e.getMessage());
}
}
|
java
|
public static void main(String[] args) {
try {
if (args.length == 5 || args.length == 6) {
String protocol = args[0];
int port = Integer.parseInt(args[1]);
String user = args[2];
String password = args[3];
String fileName = args[4];
String context = Constants.FEDORA_DEFAULT_APP_CONTEXT;
if (args.length == 6 && !args[5].isEmpty()) {
context = args[5];
}
Uploader uploader =
new Uploader(protocol, port, context, user, password);
File f = new File(fileName);
System.out.println(uploader.upload(new FileInputStream(f)));
System.out.println(uploader.upload(f));
uploader =
new Uploader(protocol,
port,
context,
user + "test",
password);
System.out.println(uploader.upload(f));
} else {
System.err
.println("Usage: Uploader host port user password file [context]");
}
} catch (Exception e) {
System.err.println("ERROR: " + e.getMessage());
}
}
|
[
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"System",
".",
"err",
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"println",
"(",
"\"ERROR: \"",
"+",
"e",
".",
"getMessage",
"(",
")",
")",
";",
"}",
"}"
] |
Test this class by uploading the given file three times. First, with the
provided credentials, as an InputStream. Second, with the provided
credentials, as a File. Third, with bogus credentials, as a File.
|
[
"Test",
"this",
"class",
"by",
"uploading",
"the",
"given",
"file",
"three",
"times",
".",
"First",
"with",
"the",
"provided",
"credentials",
"as",
"an",
"InputStream",
".",
"Second",
"with",
"the",
"provided",
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"as",
"a",
"File",
".",
"Third",
"with",
"bogus",
"credentials",
"as",
"a",
"File",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-client/fcrepo-client-admin/src/main/java/org/fcrepo/client/Uploader.java#L159-L193
|
9,177
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/SpringServlet.java
|
SpringServlet.getFedoraHomeDir
|
private File getFedoraHomeDir() throws ServletException {
String fedoraHome = Constants.FEDORA_HOME;
if (fedoraHome == null) {
failStartup("FEDORA_HOME was not configured properly. It must be "
+ "set via the fedora.home servlet init-param (preferred), "
+ "the fedora.home system property, or the FEDORA_HOME "
+ "environment variable.", null);
}
File fedoraHomeDir = new File(fedoraHome);
if (!fedoraHomeDir.isDirectory()) {
failStartup("The FEDORA_HOME directory, " + fedoraHomeDir.getPath()
+ " does not exist", null);
}
File writeTest = new File(fedoraHomeDir, "writeTest.tmp");
String writeErrorMessage =
"The FEDORA_HOME directory, " + fedoraHomeDir.getPath()
+ " is not writable by " + "the current user, "
+ System.getProperty("user.name");
try {
writeTest.createNewFile();
if (!writeTest.exists()) {
throw new IOException("");
}
writeTest.delete();
} catch (IOException e) {
failStartup(writeErrorMessage, null);
}
return fedoraHomeDir;
}
|
java
|
private File getFedoraHomeDir() throws ServletException {
String fedoraHome = Constants.FEDORA_HOME;
if (fedoraHome == null) {
failStartup("FEDORA_HOME was not configured properly. It must be "
+ "set via the fedora.home servlet init-param (preferred), "
+ "the fedora.home system property, or the FEDORA_HOME "
+ "environment variable.", null);
}
File fedoraHomeDir = new File(fedoraHome);
if (!fedoraHomeDir.isDirectory()) {
failStartup("The FEDORA_HOME directory, " + fedoraHomeDir.getPath()
+ " does not exist", null);
}
File writeTest = new File(fedoraHomeDir, "writeTest.tmp");
String writeErrorMessage =
"The FEDORA_HOME directory, " + fedoraHomeDir.getPath()
+ " is not writable by " + "the current user, "
+ System.getProperty("user.name");
try {
writeTest.createNewFile();
if (!writeTest.exists()) {
throw new IOException("");
}
writeTest.delete();
} catch (IOException e) {
failStartup(writeErrorMessage, null);
}
return fedoraHomeDir;
}
|
[
"private",
"File",
"getFedoraHomeDir",
"(",
")",
"throws",
"ServletException",
"{",
"String",
"fedoraHome",
"=",
"Constants",
".",
"FEDORA_HOME",
";",
"if",
"(",
"fedoraHome",
"==",
"null",
")",
"{",
"failStartup",
"(",
"\"FEDORA_HOME was not configured properly. It must be \"",
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"\"set via the fedora.home servlet init-param (preferred), \"",
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"\"the fedora.home system property, or the FEDORA_HOME \"",
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"\"user.name\"",
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";",
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".",
"createNewFile",
"(",
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"writeErrorMessage",
",",
"null",
")",
";",
"}",
"return",
"fedoraHomeDir",
";",
"}"
] |
Validates and returns the value of FEDORA_HOME.
@return the FEDORA_HOME directory.
@throws ServletException
if FEDORA_HOME (or fedora.home) was not set, does not denote an
existing directory, or is not writable by the current user.
|
[
"Validates",
"and",
"returns",
"the",
"value",
"of",
"FEDORA_HOME",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/SpringServlet.java#L85-L115
|
9,178
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/management/DefaultManagement.java
|
DefaultManagement.validate
|
@Override
public Validation validate(Context context,
String pid,
Date asOfDateTime) throws ServerException {
try {
logger.debug("Entered validate");
m_authz.enforceValidate(context,
pid,
asOfDateTime);
return ecmValidator.validate(context, pid, asOfDateTime);
} finally {
// Logger completion
if (logger.isInfoEnabled()) {
StringBuilder logMsg =
new StringBuilder("Completed validate(");
logMsg.append("pid: ").append(pid);
logMsg.append(", asOfDateTime: ").append(asOfDateTime);
logMsg.append(")");
logger.info(logMsg.toString());
}
logger.debug("Exiting validate");
}
}
|
java
|
@Override
public Validation validate(Context context,
String pid,
Date asOfDateTime) throws ServerException {
try {
logger.debug("Entered validate");
m_authz.enforceValidate(context,
pid,
asOfDateTime);
return ecmValidator.validate(context, pid, asOfDateTime);
} finally {
// Logger completion
if (logger.isInfoEnabled()) {
StringBuilder logMsg =
new StringBuilder("Completed validate(");
logMsg.append("pid: ").append(pid);
logMsg.append(", asOfDateTime: ").append(asOfDateTime);
logMsg.append(")");
logger.info(logMsg.toString());
}
logger.debug("Exiting validate");
}
}
|
[
"@",
"Override",
"public",
"Validation",
"validate",
"(",
"Context",
"context",
",",
"String",
"pid",
",",
"Date",
"asOfDateTime",
")",
"throws",
"ServerException",
"{",
"try",
"{",
"logger",
".",
"debug",
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"\"Entered validate\"",
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"m_authz",
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",",
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".",
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"}",
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"debug",
"(",
"\"Exiting validate\"",
")",
";",
"}",
"}"
] |
Validate the object against the datacontracts from the objects content model. This method just delegates the validation
to EcmValidator
@param context the call context
@param pid the pid of the object to validate
@param asOfDateTime the datetime to get to object as
@return The result of the validation
@see org.fcrepo.server.validation.ecm.EcmValidator
|
[
"Validate",
"the",
"object",
"against",
"the",
"datacontracts",
"from",
"the",
"objects",
"content",
"model",
".",
"This",
"method",
"just",
"delegates",
"the",
"validation",
"to",
"EcmValidator"
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/management/DefaultManagement.java#L1834-L1862
|
9,179
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/management/DefaultManagement.java
|
DefaultManagement.addAuditRecord
|
private void addAuditRecord(Context context,
DOWriter w,
String action,
String componentID,
String justification,
Date nowUTC) throws ServerException {
AuditRecord audit = new AuditRecord();
audit.id = w.newAuditRecordID();
audit.processType = "Fedora API-M";
audit.action = action;
audit.componentID = componentID;
audit.responsibility =
context.getSubjectValue(Constants.SUBJECT.LOGIN_ID.uri);
audit.date = nowUTC;
audit.justification = justification;
w.getAuditRecords().add(audit);
}
|
java
|
private void addAuditRecord(Context context,
DOWriter w,
String action,
String componentID,
String justification,
Date nowUTC) throws ServerException {
AuditRecord audit = new AuditRecord();
audit.id = w.newAuditRecordID();
audit.processType = "Fedora API-M";
audit.action = action;
audit.componentID = componentID;
audit.responsibility =
context.getSubjectValue(Constants.SUBJECT.LOGIN_ID.uri);
audit.date = nowUTC;
audit.justification = justification;
w.getAuditRecords().add(audit);
}
|
[
"private",
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",",
"String",
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",",
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",",
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"w",
".",
"getAuditRecords",
"(",
")",
".",
"add",
"(",
"audit",
")",
";",
"}"
] |
Creates a new audit record and adds it to the digital object audit trail.
|
[
"Creates",
"a",
"new",
"audit",
"record",
"and",
"adds",
"it",
"to",
"the",
"digital",
"object",
"audit",
"trail",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/management/DefaultManagement.java#L1868-L1884
|
9,180
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/management/DefaultManagement.java
|
DefaultManagement.appendAltIDs
|
private static void appendAltIDs(StringBuilder logMsg, String[] altIDs) {
logMsg.append(", altIDs: ");
if (altIDs == null) {
logMsg.append("null");
} else {
for (String altID : altIDs) {
logMsg.append("'").append(altID).append("'");
}
}
}
|
java
|
private static void appendAltIDs(StringBuilder logMsg, String[] altIDs) {
logMsg.append(", altIDs: ");
if (altIDs == null) {
logMsg.append("null");
} else {
for (String altID : altIDs) {
logMsg.append("'").append(altID).append("'");
}
}
}
|
[
"private",
"static",
"void",
"appendAltIDs",
"(",
"StringBuilder",
"logMsg",
",",
"String",
"[",
"]",
"altIDs",
")",
"{",
"logMsg",
".",
"append",
"(",
"\", altIDs: \"",
")",
";",
"if",
"(",
"altIDs",
"==",
"null",
")",
"{",
"logMsg",
".",
"append",
"(",
"\"null\"",
")",
";",
"}",
"else",
"{",
"for",
"(",
"String",
"altID",
":",
"altIDs",
")",
"{",
"logMsg",
".",
"append",
"(",
"\"'\"",
")",
".",
"append",
"(",
"altID",
")",
".",
"append",
"(",
"\"'\"",
")",
";",
"}",
"}",
"}"
] |
Appends alt IDs to the log message.
|
[
"Appends",
"alt",
"IDs",
"to",
"the",
"log",
"message",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/management/DefaultManagement.java#L1889-L1898
|
9,181
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/validation/DOObjectValidatorModule.java
|
DOObjectValidatorModule.setValidators
|
public void setValidators(Map<String,? extends DOObjectValidator> validators){
logger.info("Adding {} object validators", validators.size());
m_validators.putAll(validators);
if (m_validators.size() > 0) {
m_enabled = true;
}
}
|
java
|
public void setValidators(Map<String,? extends DOObjectValidator> validators){
logger.info("Adding {} object validators", validators.size());
m_validators.putAll(validators);
if (m_validators.size() > 0) {
m_enabled = true;
}
}
|
[
"public",
"void",
"setValidators",
"(",
"Map",
"<",
"String",
",",
"?",
"extends",
"DOObjectValidator",
">",
"validators",
")",
"{",
"logger",
".",
"info",
"(",
"\"Adding {} object validators\"",
",",
"validators",
".",
"size",
"(",
")",
")",
";",
"m_validators",
".",
"putAll",
"(",
"validators",
")",
";",
"if",
"(",
"m_validators",
".",
"size",
"(",
")",
">",
"0",
")",
"{",
"m_enabled",
"=",
"true",
";",
"}",
"}"
] |
spring config of the validators
|
[
"spring",
"config",
"of",
"the",
"validators"
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/validation/DOObjectValidatorModule.java#L74-L80
|
9,182
|
fcrepo3/fcrepo
|
fcrepo-installer/src/main/java/org/fcrepo/utilities/install/Installer.java
|
Installer.install
|
public void install() throws InstallationFailedException {
installDir.mkdirs();
// Write out the install options used to a properties file in the install directory
try {
OutputStream out =
new FileOutputStream(new File(installDir,
"install.properties"));
_opts.dump(out);
out.close();
} catch (Exception e) {
throw new InstallationFailedException(e.getMessage(), e);
}
new FedoraHome(_dist, _opts).install();
if (!_opts.getValue(InstallOptions.INSTALL_TYPE)
.equals(InstallOptions.INSTALL_CLIENT)) {
Container container = ContainerFactory.getContainer(_dist, _opts);
container.install();
container.deploy(buildWAR());
if (_opts.getBooleanValue(InstallOptions.DEPLOY_LOCAL_SERVICES,
true)) {
deployLocalService(container, Distribution.FOP_WAR);
deployLocalService(container, Distribution.IMAGEMANIP_WAR);
deployLocalService(container, Distribution.SAXON_WAR);
deployLocalService(container, Distribution.DEMO_WAR);
}
Database database = new Database(_dist, _opts);
database.install();
}
System.out.println("Installation complete.");
if (!_opts.getValue(InstallOptions.INSTALL_TYPE)
.equals(InstallOptions.INSTALL_CLIENT)
&& _opts.getValue(InstallOptions.SERVLET_ENGINE)
.equals(InstallOptions.OTHER)) {
System.out
.println("\n"
+ "----------------------------------------------------------------------\n"
+ "The Fedora Installer cannot automatically deploy the Web ARchives to \n"
+ "the selected servlet container. You must deploy the WAR files \n"
+ "manually. You can find fedora.war plus several sample back-end \n"
+ "services and a demonstration object package in: \n"
+ "\t" + fedoraHome.getAbsolutePath()
+ File.separator + "install");
}
System.out
.println("\n"
+ "----------------------------------------------------------------------\n"
+ "Before starting Fedora, please ensure that any required environment\n"
+ "variables are correctly defined\n"
+ "\t(e.g. FEDORA_HOME, JAVA_HOME, JAVA_OPTS, CATALINA_HOME).\n"
+ "For more information, please consult the Installation & Configuration\n"
+ "Guide in the online documentation.\n"
+ "----------------------------------------------------------------------\n");
}
|
java
|
public void install() throws InstallationFailedException {
installDir.mkdirs();
// Write out the install options used to a properties file in the install directory
try {
OutputStream out =
new FileOutputStream(new File(installDir,
"install.properties"));
_opts.dump(out);
out.close();
} catch (Exception e) {
throw new InstallationFailedException(e.getMessage(), e);
}
new FedoraHome(_dist, _opts).install();
if (!_opts.getValue(InstallOptions.INSTALL_TYPE)
.equals(InstallOptions.INSTALL_CLIENT)) {
Container container = ContainerFactory.getContainer(_dist, _opts);
container.install();
container.deploy(buildWAR());
if (_opts.getBooleanValue(InstallOptions.DEPLOY_LOCAL_SERVICES,
true)) {
deployLocalService(container, Distribution.FOP_WAR);
deployLocalService(container, Distribution.IMAGEMANIP_WAR);
deployLocalService(container, Distribution.SAXON_WAR);
deployLocalService(container, Distribution.DEMO_WAR);
}
Database database = new Database(_dist, _opts);
database.install();
}
System.out.println("Installation complete.");
if (!_opts.getValue(InstallOptions.INSTALL_TYPE)
.equals(InstallOptions.INSTALL_CLIENT)
&& _opts.getValue(InstallOptions.SERVLET_ENGINE)
.equals(InstallOptions.OTHER)) {
System.out
.println("\n"
+ "----------------------------------------------------------------------\n"
+ "The Fedora Installer cannot automatically deploy the Web ARchives to \n"
+ "the selected servlet container. You must deploy the WAR files \n"
+ "manually. You can find fedora.war plus several sample back-end \n"
+ "services and a demonstration object package in: \n"
+ "\t" + fedoraHome.getAbsolutePath()
+ File.separator + "install");
}
System.out
.println("\n"
+ "----------------------------------------------------------------------\n"
+ "Before starting Fedora, please ensure that any required environment\n"
+ "variables are correctly defined\n"
+ "\t(e.g. FEDORA_HOME, JAVA_HOME, JAVA_OPTS, CATALINA_HOME).\n"
+ "For more information, please consult the Installation & Configuration\n"
+ "Guide in the online documentation.\n"
+ "----------------------------------------------------------------------\n");
}
|
[
"public",
"void",
"install",
"(",
")",
"throws",
"InstallationFailedException",
"{",
"installDir",
".",
"mkdirs",
"(",
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";",
"// Write out the install options used to a properties file in the install directory",
"try",
"{",
"OutputStream",
"out",
"=",
"new",
"FileOutputStream",
"(",
"new",
"File",
"(",
"installDir",
",",
"\"install.properties\"",
")",
")",
";",
"_opts",
".",
"dump",
"(",
"out",
")",
";",
"out",
".",
"close",
"(",
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";",
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"{",
"throw",
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"install",
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".",
"getValue",
"(",
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"INSTALL_TYPE",
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".",
"equals",
"(",
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".",
"INSTALL_CLIENT",
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"Container",
"container",
"=",
"ContainerFactory",
".",
"getContainer",
"(",
"_dist",
",",
"_opts",
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";",
"container",
".",
"install",
"(",
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"container",
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"deploy",
"(",
"buildWAR",
"(",
")",
")",
";",
"if",
"(",
"_opts",
".",
"getBooleanValue",
"(",
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".",
"DEPLOY_LOCAL_SERVICES",
",",
"true",
")",
")",
"{",
"deployLocalService",
"(",
"container",
",",
"Distribution",
".",
"FOP_WAR",
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";",
"deployLocalService",
"(",
"container",
",",
"Distribution",
".",
"IMAGEMANIP_WAR",
")",
";",
"deployLocalService",
"(",
"container",
",",
"Distribution",
".",
"SAXON_WAR",
")",
";",
"deployLocalService",
"(",
"container",
",",
"Distribution",
".",
"DEMO_WAR",
")",
";",
"}",
"Database",
"database",
"=",
"new",
"Database",
"(",
"_dist",
",",
"_opts",
")",
";",
"database",
".",
"install",
"(",
")",
";",
"}",
"System",
".",
"out",
".",
"println",
"(",
"\"Installation complete.\"",
")",
";",
"if",
"(",
"!",
"_opts",
".",
"getValue",
"(",
"InstallOptions",
".",
"INSTALL_TYPE",
")",
".",
"equals",
"(",
"InstallOptions",
".",
"INSTALL_CLIENT",
")",
"&&",
"_opts",
".",
"getValue",
"(",
"InstallOptions",
".",
"SERVLET_ENGINE",
")",
".",
"equals",
"(",
"InstallOptions",
".",
"OTHER",
")",
")",
"{",
"System",
".",
"out",
".",
"println",
"(",
"\"\\n\"",
"+",
"\"----------------------------------------------------------------------\\n\"",
"+",
"\"The Fedora Installer cannot automatically deploy the Web ARchives to \\n\"",
"+",
"\"the selected servlet container. You must deploy the WAR files \\n\"",
"+",
"\"manually. You can find fedora.war plus several sample back-end \\n\"",
"+",
"\"services and a demonstration object package in: \\n\"",
"+",
"\"\\t\"",
"+",
"fedoraHome",
".",
"getAbsolutePath",
"(",
")",
"+",
"File",
".",
"separator",
"+",
"\"install\"",
")",
";",
"}",
"System",
".",
"out",
".",
"println",
"(",
"\"\\n\"",
"+",
"\"----------------------------------------------------------------------\\n\"",
"+",
"\"Before starting Fedora, please ensure that any required environment\\n\"",
"+",
"\"variables are correctly defined\\n\"",
"+",
"\"\\t(e.g. FEDORA_HOME, JAVA_HOME, JAVA_OPTS, CATALINA_HOME).\\n\"",
"+",
"\"For more information, please consult the Installation & Configuration\\n\"",
"+",
"\"Guide in the online documentation.\\n\"",
"+",
"\"----------------------------------------------------------------------\\n\"",
")",
";",
"}"
] |
Install the distribution based on the options.
|
[
"Install",
"the",
"distribution",
"based",
"on",
"the",
"options",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-installer/src/main/java/org/fcrepo/utilities/install/Installer.java#L44-L100
|
9,183
|
fcrepo3/fcrepo
|
fcrepo-installer/src/main/java/org/fcrepo/utilities/install/Installer.java
|
Installer.main
|
public static void main(String[] args) {
LogConfig.initMinimal();
try {
Distribution dist = new ClassLoaderDistribution();
InstallOptions opts = null;
if (args.length == 0) {
opts = new InstallOptions(dist);
} else {
Map<String, String> props = new HashMap<String, String>();
for (String file : args) {
props.putAll(FileUtils.loadMap(new File(file)));
}
opts = new InstallOptions(dist, props);
}
// set fedora.home
System.setProperty("fedora.home", opts
.getValue(InstallOptions.FEDORA_HOME));
new Installer(dist, opts).install();
} catch (Exception e) {
printException(e);
System.exit(1);
}
}
|
java
|
public static void main(String[] args) {
LogConfig.initMinimal();
try {
Distribution dist = new ClassLoaderDistribution();
InstallOptions opts = null;
if (args.length == 0) {
opts = new InstallOptions(dist);
} else {
Map<String, String> props = new HashMap<String, String>();
for (String file : args) {
props.putAll(FileUtils.loadMap(new File(file)));
}
opts = new InstallOptions(dist, props);
}
// set fedora.home
System.setProperty("fedora.home", opts
.getValue(InstallOptions.FEDORA_HOME));
new Installer(dist, opts).install();
} catch (Exception e) {
printException(e);
System.exit(1);
}
}
|
[
"public",
"static",
"void",
"main",
"(",
"String",
"[",
"]",
"args",
")",
"{",
"LogConfig",
".",
"initMinimal",
"(",
")",
";",
"try",
"{",
"Distribution",
"dist",
"=",
"new",
"ClassLoaderDistribution",
"(",
")",
";",
"InstallOptions",
"opts",
"=",
"null",
";",
"if",
"(",
"args",
".",
"length",
"==",
"0",
")",
"{",
"opts",
"=",
"new",
"InstallOptions",
"(",
"dist",
")",
";",
"}",
"else",
"{",
"Map",
"<",
"String",
",",
"String",
">",
"props",
"=",
"new",
"HashMap",
"<",
"String",
",",
"String",
">",
"(",
")",
";",
"for",
"(",
"String",
"file",
":",
"args",
")",
"{",
"props",
".",
"putAll",
"(",
"FileUtils",
".",
"loadMap",
"(",
"new",
"File",
"(",
"file",
")",
")",
")",
";",
"}",
"opts",
"=",
"new",
"InstallOptions",
"(",
"dist",
",",
"props",
")",
";",
"}",
"// set fedora.home",
"System",
".",
"setProperty",
"(",
"\"fedora.home\"",
",",
"opts",
".",
"getValue",
"(",
"InstallOptions",
".",
"FEDORA_HOME",
")",
")",
";",
"new",
"Installer",
"(",
"dist",
",",
"opts",
")",
".",
"install",
"(",
")",
";",
"}",
"catch",
"(",
"Exception",
"e",
")",
"{",
"printException",
"(",
"e",
")",
";",
"System",
".",
"exit",
"(",
"1",
")",
";",
"}",
"}"
] |
Command-line entry point.
|
[
"Command",
"-",
"line",
"entry",
"point",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-installer/src/main/java/org/fcrepo/utilities/install/Installer.java#L170-L195
|
9,184
|
fcrepo3/fcrepo
|
fcrepo-installer/src/main/java/org/fcrepo/utilities/install/Installer.java
|
Installer.printException
|
private static void printException(Exception e) {
if (e instanceof InstallationCancelledException) {
System.out.println("Installation cancelled.");
return;
}
boolean recognized = false;
String msg = "ERROR: ";
if (e instanceof InstallationFailedException) {
msg += "Installation failed: " + e.getMessage();
recognized = true;
} else if (e instanceof OptionValidationException) {
OptionValidationException ove = (OptionValidationException) e;
msg +=
"Bad value for '" + ove.getOptionId() + "': "
+ e.getMessage();
recognized = true;
}
if (recognized) {
System.err.println(msg);
if (e.getCause() != null) {
System.err.println("Caused by: ");
e.getCause().printStackTrace(System.err);
}
} else {
System.err.println(msg + "Unexpected error; installation aborted.");
e.printStackTrace();
}
}
|
java
|
private static void printException(Exception e) {
if (e instanceof InstallationCancelledException) {
System.out.println("Installation cancelled.");
return;
}
boolean recognized = false;
String msg = "ERROR: ";
if (e instanceof InstallationFailedException) {
msg += "Installation failed: " + e.getMessage();
recognized = true;
} else if (e instanceof OptionValidationException) {
OptionValidationException ove = (OptionValidationException) e;
msg +=
"Bad value for '" + ove.getOptionId() + "': "
+ e.getMessage();
recognized = true;
}
if (recognized) {
System.err.println(msg);
if (e.getCause() != null) {
System.err.println("Caused by: ");
e.getCause().printStackTrace(System.err);
}
} else {
System.err.println(msg + "Unexpected error; installation aborted.");
e.printStackTrace();
}
}
|
[
"private",
"static",
"void",
"printException",
"(",
"Exception",
"e",
")",
"{",
"if",
"(",
"e",
"instanceof",
"InstallationCancelledException",
")",
"{",
"System",
".",
"out",
".",
"println",
"(",
"\"Installation cancelled.\"",
")",
";",
"return",
";",
"}",
"boolean",
"recognized",
"=",
"false",
";",
"String",
"msg",
"=",
"\"ERROR: \"",
";",
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"(",
"e",
"instanceof",
"InstallationFailedException",
")",
"{",
"msg",
"+=",
"\"Installation failed: \"",
"+",
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";",
"}",
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"OptionValidationException",
")",
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"msg",
"+=",
"\"Bad value for '\"",
"+",
"ove",
".",
"getOptionId",
"(",
")",
"+",
"\"': \"",
"+",
"e",
".",
"getMessage",
"(",
")",
";",
"recognized",
"=",
"true",
";",
"}",
"if",
"(",
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")",
"{",
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".",
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"(",
"msg",
")",
";",
"if",
"(",
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".",
"getCause",
"(",
")",
"!=",
"null",
")",
"{",
"System",
".",
"err",
".",
"println",
"(",
"\"Caused by: \"",
")",
";",
"e",
".",
"getCause",
"(",
")",
".",
"printStackTrace",
"(",
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"err",
")",
";",
"}",
"}",
"else",
"{",
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"err",
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"(",
"msg",
"+",
"\"Unexpected error; installation aborted.\"",
")",
";",
"e",
".",
"printStackTrace",
"(",
")",
";",
"}",
"}"
] |
Print a message appropriate for the given exception in as human-readable
way as possible.
|
[
"Print",
"a",
"message",
"appropriate",
"for",
"the",
"given",
"exception",
"in",
"as",
"human",
"-",
"readable",
"way",
"as",
"possible",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-installer/src/main/java/org/fcrepo/utilities/install/Installer.java#L201-L231
|
9,185
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/journal/JournalConsumerThread.java
|
JournalConsumerThread.run
|
@Override
public void run() {
try {
waitUntilServerIsInitialized();
recoveryLog.log("Start recovery.");
while (true) {
if (shutdown) {
break;
}
ConsumerJournalEntry cje = reader.readJournalEntry();
if (cje == null) {
break;
}
cje.invokeMethod(delegate, recoveryLog);
cje.close();
}
reader.shutdown();
recoveryLog.log("Recovery complete.");
} catch (Throwable e) {
/*
* It makes sense to catch Exception here, because any uncaught
* exception will not be reported - there is no console to print the
* stack trace! It might not be appropriate to catch Throwable, but
* it's the only way we can know about missing class files and such.
* Of course, if we catch an OutOfMemoryError or a
* VirtualMachineError, all bets are off.
*/
logger.error("Error during Journal recovery", e);
String stackTrace = JournalHelper.captureStackTrace(e);
recoveryLog.log("PROBLEM: " + stackTrace);
recoveryLog.log("Recovery terminated prematurely.");
} finally {
recoveryLog.shutdown();
}
}
|
java
|
@Override
public void run() {
try {
waitUntilServerIsInitialized();
recoveryLog.log("Start recovery.");
while (true) {
if (shutdown) {
break;
}
ConsumerJournalEntry cje = reader.readJournalEntry();
if (cje == null) {
break;
}
cje.invokeMethod(delegate, recoveryLog);
cje.close();
}
reader.shutdown();
recoveryLog.log("Recovery complete.");
} catch (Throwable e) {
/*
* It makes sense to catch Exception here, because any uncaught
* exception will not be reported - there is no console to print the
* stack trace! It might not be appropriate to catch Throwable, but
* it's the only way we can know about missing class files and such.
* Of course, if we catch an OutOfMemoryError or a
* VirtualMachineError, all bets are off.
*/
logger.error("Error during Journal recovery", e);
String stackTrace = JournalHelper.captureStackTrace(e);
recoveryLog.log("PROBLEM: " + stackTrace);
recoveryLog.log("Recovery terminated prematurely.");
} finally {
recoveryLog.shutdown();
}
}
|
[
"@",
"Override",
"public",
"void",
"run",
"(",
")",
"{",
"try",
"{",
"waitUntilServerIsInitialized",
"(",
")",
";",
"recoveryLog",
".",
"log",
"(",
"\"Start recovery.\"",
")",
";",
"while",
"(",
"true",
")",
"{",
"if",
"(",
"shutdown",
")",
"{",
"break",
";",
"}",
"ConsumerJournalEntry",
"cje",
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"reader",
".",
"readJournalEntry",
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")",
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"}",
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".",
"invokeMethod",
"(",
"delegate",
",",
"recoveryLog",
")",
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"cje",
".",
"close",
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";",
"}",
"reader",
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";",
"}",
"catch",
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"Throwable",
"e",
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"{",
"/*\n * It makes sense to catch Exception here, because any uncaught\n * exception will not be reported - there is no console to print the\n * stack trace! It might not be appropriate to catch Throwable, but\n * it's the only way we can know about missing class files and such.\n * Of course, if we catch an OutOfMemoryError or a\n * VirtualMachineError, all bets are off.\n */",
"logger",
".",
"error",
"(",
"\"Error during Journal recovery\"",
",",
"e",
")",
";",
"String",
"stackTrace",
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"JournalHelper",
".",
"captureStackTrace",
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"\"PROBLEM: \"",
"+",
"stackTrace",
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".",
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"(",
"\"Recovery terminated prematurely.\"",
")",
";",
"}",
"finally",
"{",
"recoveryLog",
".",
"shutdown",
"(",
")",
";",
"}",
"}"
] |
Wait until the server completes its initialization, then process journal
entries until the reader says there are no more, or until a shutdown is
requested.
|
[
"Wait",
"until",
"the",
"server",
"completes",
"its",
"initialization",
"then",
"process",
"journal",
"entries",
"until",
"the",
"reader",
"says",
"there",
"are",
"no",
"more",
"or",
"until",
"a",
"shutdown",
"is",
"requested",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/journal/JournalConsumerThread.java#L68-L105
|
9,186
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/journal/JournalConsumerThread.java
|
JournalConsumerThread.waitUntilServerIsInitialized
|
private void waitUntilServerIsInitialized() {
int i = 0;
for (; i < 60; i++) {
if (server.hasInitialized() || shutdown) {
return;
}
try {
Thread.sleep(1000);
} catch (InterruptedException e) {
logger.warn("Thread was interrupted");
}
}
logger.error("Can't recover from the Journal - "
+ "the server hasn't initialized after " + i + " seconds.");
shutdown = true;
}
|
java
|
private void waitUntilServerIsInitialized() {
int i = 0;
for (; i < 60; i++) {
if (server.hasInitialized() || shutdown) {
return;
}
try {
Thread.sleep(1000);
} catch (InterruptedException e) {
logger.warn("Thread was interrupted");
}
}
logger.error("Can't recover from the Journal - "
+ "the server hasn't initialized after " + i + " seconds.");
shutdown = true;
}
|
[
"private",
"void",
"waitUntilServerIsInitialized",
"(",
")",
"{",
"int",
"i",
"=",
"0",
";",
"for",
"(",
";",
"i",
"<",
"60",
";",
"i",
"++",
")",
"{",
"if",
"(",
"server",
".",
"hasInitialized",
"(",
")",
"||",
"shutdown",
")",
"{",
"return",
";",
"}",
"try",
"{",
"Thread",
".",
"sleep",
"(",
"1000",
")",
";",
"}",
"catch",
"(",
"InterruptedException",
"e",
")",
"{",
"logger",
".",
"warn",
"(",
"\"Thread was interrupted\"",
")",
";",
"}",
"}",
"logger",
".",
"error",
"(",
"\"Can't recover from the Journal - \"",
"+",
"\"the server hasn't initialized after \"",
"+",
"i",
"+",
"\" seconds.\"",
")",
";",
"shutdown",
"=",
"true",
";",
"}"
] |
Wait for the server to initialize. If we wait too long, give up and shut
down the thread.
|
[
"Wait",
"for",
"the",
"server",
"to",
"initialize",
".",
"If",
"we",
"wait",
"too",
"long",
"give",
"up",
"and",
"shut",
"down",
"the",
"thread",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/journal/JournalConsumerThread.java#L111-L126
|
9,187
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/security/PolicyParser.java
|
PolicyParser.getSchema
|
private static Schema getSchema(InputStream schemaStream) throws SAXException {
Schema result;
synchronized(SCHEMA_FACTORY){
result = SCHEMA_FACTORY.newSchema(new StreamSource(schemaStream));
}
return result;
}
|
java
|
private static Schema getSchema(InputStream schemaStream) throws SAXException {
Schema result;
synchronized(SCHEMA_FACTORY){
result = SCHEMA_FACTORY.newSchema(new StreamSource(schemaStream));
}
return result;
}
|
[
"private",
"static",
"Schema",
"getSchema",
"(",
"InputStream",
"schemaStream",
")",
"throws",
"SAXException",
"{",
"Schema",
"result",
";",
"synchronized",
"(",
"SCHEMA_FACTORY",
")",
"{",
"result",
"=",
"SCHEMA_FACTORY",
".",
"newSchema",
"(",
"new",
"StreamSource",
"(",
"schemaStream",
")",
")",
";",
"}",
"return",
"result",
";",
"}"
] |
Schema Factory is not thread safe
@return
|
[
"Schema",
"Factory",
"is",
"not",
"thread",
"safe"
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/security/PolicyParser.java#L80-L86
|
9,188
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/security/PolicyParser.java
|
PolicyParser.parse
|
public AbstractPolicy parse(InputStream policyStream,
boolean schemaValidate)
throws ValidationException {
// Parse; die if not well-formed
Document doc = null;
DocumentBuilder domParser = null;
try {
domParser = XmlTransformUtility.borrowDocumentBuilder();
domParser.setErrorHandler(THROW_ALL);
doc = domParser.parse(policyStream);
} catch (Exception e) {
throw new ValidationException("Policy invalid; malformed XML", e);
} finally {
if (domParser != null) {
XmlTransformUtility.returnDocumentBuilder(domParser);
}
}
if (schemaValidate) {
// XSD-validate; die if not schema-valid
Validator validator = null;
try {
validator = m_validators.borrowObject();
validator.validate(new DOMSource(doc));
} catch (Exception e) {
throw new ValidationException("Policy invalid; schema"
+ " validation failed", e);
} finally {
if (validator != null) try {
m_validators.returnObject(validator);
} catch (Exception e) {
logger.warn(e.getMessage(), e);
}
}
}
// Construct AbstractPolicy from doc; die if root isn't "Policy[Set]"
Element root = doc.getDocumentElement();
String rootName = root.getTagName();
try {
if (rootName.equals("Policy")) {
return Policy.getInstance(root);
} else if (rootName.equals("PolicySet")) {
return PolicySet.getInstance(root);
} else {
throw new ValidationException("Policy invalid; root element is "
+ rootName + ", but should be "
+ "Policy or PolicySet");
}
} catch (ParsingException e) {
throw new ValidationException("Policy invalid; failed parsing by "
+ "Sun XACML implementation", e);
}
}
|
java
|
public AbstractPolicy parse(InputStream policyStream,
boolean schemaValidate)
throws ValidationException {
// Parse; die if not well-formed
Document doc = null;
DocumentBuilder domParser = null;
try {
domParser = XmlTransformUtility.borrowDocumentBuilder();
domParser.setErrorHandler(THROW_ALL);
doc = domParser.parse(policyStream);
} catch (Exception e) {
throw new ValidationException("Policy invalid; malformed XML", e);
} finally {
if (domParser != null) {
XmlTransformUtility.returnDocumentBuilder(domParser);
}
}
if (schemaValidate) {
// XSD-validate; die if not schema-valid
Validator validator = null;
try {
validator = m_validators.borrowObject();
validator.validate(new DOMSource(doc));
} catch (Exception e) {
throw new ValidationException("Policy invalid; schema"
+ " validation failed", e);
} finally {
if (validator != null) try {
m_validators.returnObject(validator);
} catch (Exception e) {
logger.warn(e.getMessage(), e);
}
}
}
// Construct AbstractPolicy from doc; die if root isn't "Policy[Set]"
Element root = doc.getDocumentElement();
String rootName = root.getTagName();
try {
if (rootName.equals("Policy")) {
return Policy.getInstance(root);
} else if (rootName.equals("PolicySet")) {
return PolicySet.getInstance(root);
} else {
throw new ValidationException("Policy invalid; root element is "
+ rootName + ", but should be "
+ "Policy or PolicySet");
}
} catch (ParsingException e) {
throw new ValidationException("Policy invalid; failed parsing by "
+ "Sun XACML implementation", e);
}
}
|
[
"public",
"AbstractPolicy",
"parse",
"(",
"InputStream",
"policyStream",
",",
"boolean",
"schemaValidate",
")",
"throws",
"ValidationException",
"{",
"// Parse; die if not well-formed",
"Document",
"doc",
"=",
"null",
";",
"DocumentBuilder",
"domParser",
"=",
"null",
";",
"try",
"{",
"domParser",
"=",
"XmlTransformUtility",
".",
"borrowDocumentBuilder",
"(",
")",
";",
"domParser",
".",
"setErrorHandler",
"(",
"THROW_ALL",
")",
";",
"doc",
"=",
"domParser",
".",
"parse",
"(",
"policyStream",
")",
";",
"}",
"catch",
"(",
"Exception",
"e",
")",
"{",
"throw",
"new",
"ValidationException",
"(",
"\"Policy invalid; malformed XML\"",
",",
"e",
")",
";",
"}",
"finally",
"{",
"if",
"(",
"domParser",
"!=",
"null",
")",
"{",
"XmlTransformUtility",
".",
"returnDocumentBuilder",
"(",
"domParser",
")",
";",
"}",
"}",
"if",
"(",
"schemaValidate",
")",
"{",
"// XSD-validate; die if not schema-valid",
"Validator",
"validator",
"=",
"null",
";",
"try",
"{",
"validator",
"=",
"m_validators",
".",
"borrowObject",
"(",
")",
";",
"validator",
".",
"validate",
"(",
"new",
"DOMSource",
"(",
"doc",
")",
")",
";",
"}",
"catch",
"(",
"Exception",
"e",
")",
"{",
"throw",
"new",
"ValidationException",
"(",
"\"Policy invalid; schema\"",
"+",
"\" validation failed\"",
",",
"e",
")",
";",
"}",
"finally",
"{",
"if",
"(",
"validator",
"!=",
"null",
")",
"try",
"{",
"m_validators",
".",
"returnObject",
"(",
"validator",
")",
";",
"}",
"catch",
"(",
"Exception",
"e",
")",
"{",
"logger",
".",
"warn",
"(",
"e",
".",
"getMessage",
"(",
")",
",",
"e",
")",
";",
"}",
"}",
"}",
"// Construct AbstractPolicy from doc; die if root isn't \"Policy[Set]\"",
"Element",
"root",
"=",
"doc",
".",
"getDocumentElement",
"(",
")",
";",
"String",
"rootName",
"=",
"root",
".",
"getTagName",
"(",
")",
";",
"try",
"{",
"if",
"(",
"rootName",
".",
"equals",
"(",
"\"Policy\"",
")",
")",
"{",
"return",
"Policy",
".",
"getInstance",
"(",
"root",
")",
";",
"}",
"else",
"if",
"(",
"rootName",
".",
"equals",
"(",
"\"PolicySet\"",
")",
")",
"{",
"return",
"PolicySet",
".",
"getInstance",
"(",
"root",
")",
";",
"}",
"else",
"{",
"throw",
"new",
"ValidationException",
"(",
"\"Policy invalid; root element is \"",
"+",
"rootName",
"+",
"\", but should be \"",
"+",
"\"Policy or PolicySet\"",
")",
";",
"}",
"}",
"catch",
"(",
"ParsingException",
"e",
")",
"{",
"throw",
"new",
"ValidationException",
"(",
"\"Policy invalid; failed parsing by \"",
"+",
"\"Sun XACML implementation\"",
",",
"e",
")",
";",
"}",
"}"
] |
Parses the given policy and optionally schema validates it.
@param policyStream
the serialized XACML policy
@param schemaValidate
whether to schema validate
@return the parsed policy.
@throws ValidationException
if the given xml is not a valid policy. This will occur if it
is not well-formed XML, its root element is not named
<code>Policy</code> or <code>PolicySet</code>, it triggers
a parse exception in the Sun libraries when constructing an
<code>AbstractPolicy</code> from the DOM, or (if validation
is true) it is not schema-valid.
|
[
"Parses",
"the",
"given",
"policy",
"and",
"optionally",
"schema",
"validates",
"it",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/security/PolicyParser.java#L113-L167
|
9,189
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/journal/readerwriter/multicast/rmi/RmiJournalReceiver.java
|
RmiJournalReceiver.exportAndBind
|
public void exportAndBind() throws RemoteException, AlreadyBoundException,
InterruptedException {
Registry registry =
LocateRegistry
.createRegistry(arguments.getRegistryPortNumber());
registry.rebind(RMI_BINDING_NAME, this);
Thread.sleep(2000);
logger.info("RmiJournalReceiver is ready - journal directory is '"
+ arguments.getDirectoryPath().getAbsolutePath() + "'");
}
|
java
|
public void exportAndBind() throws RemoteException, AlreadyBoundException,
InterruptedException {
Registry registry =
LocateRegistry
.createRegistry(arguments.getRegistryPortNumber());
registry.rebind(RMI_BINDING_NAME, this);
Thread.sleep(2000);
logger.info("RmiJournalReceiver is ready - journal directory is '"
+ arguments.getDirectoryPath().getAbsolutePath() + "'");
}
|
[
"public",
"void",
"exportAndBind",
"(",
")",
"throws",
"RemoteException",
",",
"AlreadyBoundException",
",",
"InterruptedException",
"{",
"Registry",
"registry",
"=",
"LocateRegistry",
".",
"createRegistry",
"(",
"arguments",
".",
"getRegistryPortNumber",
"(",
")",
")",
";",
"registry",
".",
"rebind",
"(",
"RMI_BINDING_NAME",
",",
"this",
")",
";",
"Thread",
".",
"sleep",
"(",
"2000",
")",
";",
"logger",
".",
"info",
"(",
"\"RmiJournalReceiver is ready - journal directory is '\"",
"+",
"arguments",
".",
"getDirectoryPath",
"(",
")",
".",
"getAbsolutePath",
"(",
")",
"+",
"\"'\"",
")",
";",
"}"
] |
Create an RMI registry, and bind this object to the expected name.
|
[
"Create",
"an",
"RMI",
"registry",
"and",
"bind",
"this",
"object",
"to",
"the",
"expected",
"name",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/journal/readerwriter/multicast/rmi/RmiJournalReceiver.java#L78-L87
|
9,190
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/resourceIndex/ResourceIndexImpl.java
|
ResourceIndexImpl.updateTriples
|
private void updateTriples(Set<Triple> set, boolean delete)
throws ResourceIndexException {
try {
if (delete) {
_writer.delete(getTripleIterator(set), _syncUpdates);
} else {
_writer.add(getTripleIterator(set), _syncUpdates);
}
} catch (Exception e) {
throw new ResourceIndexException("Error updating triples", e);
}
}
|
java
|
private void updateTriples(Set<Triple> set, boolean delete)
throws ResourceIndexException {
try {
if (delete) {
_writer.delete(getTripleIterator(set), _syncUpdates);
} else {
_writer.add(getTripleIterator(set), _syncUpdates);
}
} catch (Exception e) {
throw new ResourceIndexException("Error updating triples", e);
}
}
|
[
"private",
"void",
"updateTriples",
"(",
"Set",
"<",
"Triple",
">",
"set",
",",
"boolean",
"delete",
")",
"throws",
"ResourceIndexException",
"{",
"try",
"{",
"if",
"(",
"delete",
")",
"{",
"_writer",
".",
"delete",
"(",
"getTripleIterator",
"(",
"set",
")",
",",
"_syncUpdates",
")",
";",
"}",
"else",
"{",
"_writer",
".",
"add",
"(",
"getTripleIterator",
"(",
"set",
")",
",",
"_syncUpdates",
")",
";",
"}",
"}",
"catch",
"(",
"Exception",
"e",
")",
"{",
"throw",
"new",
"ResourceIndexException",
"(",
"\"Error updating triples\"",
",",
"e",
")",
";",
"}",
"}"
] |
Applies the given adds or deletes to the triplestore. If _syncUpdates is
true, changes will be flushed before returning.
|
[
"Applies",
"the",
"given",
"adds",
"or",
"deletes",
"to",
"the",
"triplestore",
".",
"If",
"_syncUpdates",
"is",
"true",
"changes",
"will",
"be",
"flushed",
"before",
"returning",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/resourceIndex/ResourceIndexImpl.java#L159-L170
|
9,191
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/resourceIndex/ResourceIndexImpl.java
|
ResourceIndexImpl.updateTripleDiffs
|
private void updateTripleDiffs(Set<Triple> existing, Set<Triple> desired)
throws ResourceIndexException {
// Delete any existing triples that are no longer desired,
// leaving the ones we want in place
HashSet<Triple> obsoleteTriples = new HashSet<Triple>(existing);
obsoleteTriples.removeAll(desired);
updateTriples(obsoleteTriples, true);
// Add only new desired triples
HashSet<Triple> newTriples = new HashSet<Triple>(desired);
newTriples.removeAll(existing);
updateTriples(newTriples, false);
}
|
java
|
private void updateTripleDiffs(Set<Triple> existing, Set<Triple> desired)
throws ResourceIndexException {
// Delete any existing triples that are no longer desired,
// leaving the ones we want in place
HashSet<Triple> obsoleteTriples = new HashSet<Triple>(existing);
obsoleteTriples.removeAll(desired);
updateTriples(obsoleteTriples, true);
// Add only new desired triples
HashSet<Triple> newTriples = new HashSet<Triple>(desired);
newTriples.removeAll(existing);
updateTriples(newTriples, false);
}
|
[
"private",
"void",
"updateTripleDiffs",
"(",
"Set",
"<",
"Triple",
">",
"existing",
",",
"Set",
"<",
"Triple",
">",
"desired",
")",
"throws",
"ResourceIndexException",
"{",
"// Delete any existing triples that are no longer desired,",
"// leaving the ones we want in place",
"HashSet",
"<",
"Triple",
">",
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"=",
"new",
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"removeAll",
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",",
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"(",
"existing",
")",
";",
"updateTriples",
"(",
"newTriples",
",",
"false",
")",
";",
"}"
] |
Computes the difference between the given sets and applies the
appropriate deletes and adds to the triplestore. If _syncUpdates is true,
changes will be flushed before returning.
|
[
"Computes",
"the",
"difference",
"between",
"the",
"given",
"sets",
"and",
"applies",
"the",
"appropriate",
"deletes",
"and",
"adds",
"to",
"the",
"triplestore",
".",
"If",
"_syncUpdates",
"is",
"true",
"changes",
"will",
"be",
"flushed",
"before",
"returning",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/resourceIndex/ResourceIndexImpl.java#L177-L191
|
9,192
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/resourceIndex/ResourceIndexImpl.java
|
ResourceIndexImpl.getTripleIterator
|
private TripleIterator getTripleIterator(final Set<Triple> set) {
return new TripleIterator() {
private final Iterator<Triple> _iter = set.iterator();
@Override
public boolean hasNext() {
return _iter.hasNext();
}
@Override
public Triple next() {
return getLocalizedTriple(_iter.next());
}
@Override
public void close() {
}
};
}
|
java
|
private TripleIterator getTripleIterator(final Set<Triple> set) {
return new TripleIterator() {
private final Iterator<Triple> _iter = set.iterator();
@Override
public boolean hasNext() {
return _iter.hasNext();
}
@Override
public Triple next() {
return getLocalizedTriple(_iter.next());
}
@Override
public void close() {
}
};
}
|
[
"private",
"TripleIterator",
"getTripleIterator",
"(",
"final",
"Set",
"<",
"Triple",
">",
"set",
")",
"{",
"return",
"new",
"TripleIterator",
"(",
")",
"{",
"private",
"final",
"Iterator",
"<",
"Triple",
">",
"_iter",
"=",
"set",
".",
"iterator",
"(",
")",
";",
"@",
"Override",
"public",
"boolean",
"hasNext",
"(",
")",
"{",
"return",
"_iter",
".",
"hasNext",
"(",
")",
";",
"}",
"@",
"Override",
"public",
"Triple",
"next",
"(",
")",
"{",
"return",
"getLocalizedTriple",
"(",
"_iter",
".",
"next",
"(",
")",
")",
";",
"}",
"@",
"Override",
"public",
"void",
"close",
"(",
")",
"{",
"}",
"}",
";",
"}"
] |
Gets a Trippi TripleIterator for the given set.
|
[
"Gets",
"a",
"Trippi",
"TripleIterator",
"for",
"the",
"given",
"set",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/resourceIndex/ResourceIndexImpl.java#L196-L215
|
9,193
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/resourceIndex/ResourceIndexImpl.java
|
ResourceIndexImpl.getLocalizedTriple
|
private Triple getLocalizedTriple(Triple triple) {
try {
return _connector.getElementFactory().createTriple(
getLocalizedResource(triple.getSubject()),
getLocalizedResource(triple.getPredicate()),
getLocalizedObject(triple.getObject()));
} catch (GraphElementFactoryException e) {
throw new RuntimeException("Error localizing triple", e);
}
}
|
java
|
private Triple getLocalizedTriple(Triple triple) {
try {
return _connector.getElementFactory().createTriple(
getLocalizedResource(triple.getSubject()),
getLocalizedResource(triple.getPredicate()),
getLocalizedObject(triple.getObject()));
} catch (GraphElementFactoryException e) {
throw new RuntimeException("Error localizing triple", e);
}
}
|
[
"private",
"Triple",
"getLocalizedTriple",
"(",
"Triple",
"triple",
")",
"{",
"try",
"{",
"return",
"_connector",
".",
"getElementFactory",
"(",
")",
".",
"createTriple",
"(",
"getLocalizedResource",
"(",
"triple",
".",
"getSubject",
"(",
")",
")",
",",
"getLocalizedResource",
"(",
"triple",
".",
"getPredicate",
"(",
")",
")",
",",
"getLocalizedObject",
"(",
"triple",
".",
"getObject",
"(",
")",
")",
")",
";",
"}",
"catch",
"(",
"GraphElementFactoryException",
"e",
")",
"{",
"throw",
"new",
"RuntimeException",
"(",
"\"Error localizing triple\"",
",",
"e",
")",
";",
"}",
"}"
] |
Gets a Triple appropriate for writing to the store.
|
[
"Gets",
"a",
"Triple",
"appropriate",
"for",
"writing",
"to",
"the",
"store",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/resourceIndex/ResourceIndexImpl.java#L220-L229
|
9,194
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/resourceIndex/ResourceIndexImpl.java
|
ResourceIndexImpl.getLocalizedResource
|
private URIReference getLocalizedResource(Node n)
throws GraphElementFactoryException {
if (n instanceof URIReference) {
URIReference u = (URIReference) n;
return _connector.getElementFactory().createResource(u.getURI());
} else {
throw new RuntimeException("Error localizing triple; "
+ n.getClass().getName() + " is not a URIReference");
}
}
|
java
|
private URIReference getLocalizedResource(Node n)
throws GraphElementFactoryException {
if (n instanceof URIReference) {
URIReference u = (URIReference) n;
return _connector.getElementFactory().createResource(u.getURI());
} else {
throw new RuntimeException("Error localizing triple; "
+ n.getClass().getName() + " is not a URIReference");
}
}
|
[
"private",
"URIReference",
"getLocalizedResource",
"(",
"Node",
"n",
")",
"throws",
"GraphElementFactoryException",
"{",
"if",
"(",
"n",
"instanceof",
"URIReference",
")",
"{",
"URIReference",
"u",
"=",
"(",
"URIReference",
")",
"n",
";",
"return",
"_connector",
".",
"getElementFactory",
"(",
")",
".",
"createResource",
"(",
"u",
".",
"getURI",
"(",
")",
")",
";",
"}",
"else",
"{",
"throw",
"new",
"RuntimeException",
"(",
"\"Error localizing triple; \"",
"+",
"n",
".",
"getClass",
"(",
")",
".",
"getName",
"(",
")",
"+",
"\" is not a URIReference\"",
")",
";",
"}",
"}"
] |
Gets a localized URIReference based on the given Node.
|
[
"Gets",
"a",
"localized",
"URIReference",
"based",
"on",
"the",
"given",
"Node",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/resourceIndex/ResourceIndexImpl.java#L234-L243
|
9,195
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/resourceIndex/ResourceIndexImpl.java
|
ResourceIndexImpl.getLocalizedObject
|
private ObjectNode getLocalizedObject(Node n)
throws GraphElementFactoryException {
if (n instanceof URIReference) {
return getLocalizedResource(n);
} else if (n instanceof Literal) {
Literal l = (Literal) n;
GraphElementFactory elementFactory = _connector.getElementFactory();
if (l.getDatatypeURI() != null) {
return elementFactory.createLiteral(l.getLexicalForm(),
l.getDatatypeURI());
} else if (l.getLanguage() != null) {
return elementFactory.createLiteral(l.getLexicalForm(),
l.getLanguage());
} else {
return elementFactory.createLiteral(l.getLexicalForm());
}
} else {
throw new RuntimeException("Error localizing triple; "
+ n.getClass().getName() + " is not a URIReference "
+ "or a Literal");
}
}
|
java
|
private ObjectNode getLocalizedObject(Node n)
throws GraphElementFactoryException {
if (n instanceof URIReference) {
return getLocalizedResource(n);
} else if (n instanceof Literal) {
Literal l = (Literal) n;
GraphElementFactory elementFactory = _connector.getElementFactory();
if (l.getDatatypeURI() != null) {
return elementFactory.createLiteral(l.getLexicalForm(),
l.getDatatypeURI());
} else if (l.getLanguage() != null) {
return elementFactory.createLiteral(l.getLexicalForm(),
l.getLanguage());
} else {
return elementFactory.createLiteral(l.getLexicalForm());
}
} else {
throw new RuntimeException("Error localizing triple; "
+ n.getClass().getName() + " is not a URIReference "
+ "or a Literal");
}
}
|
[
"private",
"ObjectNode",
"getLocalizedObject",
"(",
"Node",
"n",
")",
"throws",
"GraphElementFactoryException",
"{",
"if",
"(",
"n",
"instanceof",
"URIReference",
")",
"{",
"return",
"getLocalizedResource",
"(",
"n",
")",
";",
"}",
"else",
"if",
"(",
"n",
"instanceof",
"Literal",
")",
"{",
"Literal",
"l",
"=",
"(",
"Literal",
")",
"n",
";",
"GraphElementFactory",
"elementFactory",
"=",
"_connector",
".",
"getElementFactory",
"(",
")",
";",
"if",
"(",
"l",
".",
"getDatatypeURI",
"(",
")",
"!=",
"null",
")",
"{",
"return",
"elementFactory",
".",
"createLiteral",
"(",
"l",
".",
"getLexicalForm",
"(",
")",
",",
"l",
".",
"getDatatypeURI",
"(",
")",
")",
";",
"}",
"else",
"if",
"(",
"l",
".",
"getLanguage",
"(",
")",
"!=",
"null",
")",
"{",
"return",
"elementFactory",
".",
"createLiteral",
"(",
"l",
".",
"getLexicalForm",
"(",
")",
",",
"l",
".",
"getLanguage",
"(",
")",
")",
";",
"}",
"else",
"{",
"return",
"elementFactory",
".",
"createLiteral",
"(",
"l",
".",
"getLexicalForm",
"(",
")",
")",
";",
"}",
"}",
"else",
"{",
"throw",
"new",
"RuntimeException",
"(",
"\"Error localizing triple; \"",
"+",
"n",
".",
"getClass",
"(",
")",
".",
"getName",
"(",
")",
"+",
"\" is not a URIReference \"",
"+",
"\"or a Literal\"",
")",
";",
"}",
"}"
] |
Gets a localized URIReference or Literal based on the given Node.
|
[
"Gets",
"a",
"localized",
"URIReference",
"or",
"Literal",
"based",
"on",
"the",
"given",
"Node",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/resourceIndex/ResourceIndexImpl.java#L248-L269
|
9,196
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/journal/readerwriter/multifile/MultiFileJournalReader.java
|
MultiFileJournalReader.scanThroughFilesForNextJournalEntry
|
private void scanThroughFilesForNextJournalEntry() throws JournalException {
try {
while (true) {
if (currentFile != null) {
// Check to see whether the current file contains any more
// entries.
advancePastWhitespace(currentFile.getReader());
XMLEvent next = currentFile.getReader().peek();
if (isStartTagEvent(next, QNAME_TAG_JOURNAL_ENTRY)) {
// found it
return;
} else if (isEndTagEvent(next, QNAME_TAG_JOURNAL)) {
// need to get the next file
closeCurrentFile();
} else {
// problems
throw getNotNextMemberOrEndOfGroupException(QNAME_TAG_JOURNAL,
QNAME_TAG_JOURNAL_ENTRY,
next);
}
}
// If we don't have a file open, try to open one.
if (currentFile == null) {
currentFile = openNextFile();
}
// If we still don't have a file open, we're finished.
if (currentFile == null) {
// if there was no next file, we're done.
return;
}
// A new file needs to be advanced before using.
advanceIntoFile(currentFile.getReader());
}
} catch (XMLStreamException e) {
throw new JournalException(e);
}
}
|
java
|
private void scanThroughFilesForNextJournalEntry() throws JournalException {
try {
while (true) {
if (currentFile != null) {
// Check to see whether the current file contains any more
// entries.
advancePastWhitespace(currentFile.getReader());
XMLEvent next = currentFile.getReader().peek();
if (isStartTagEvent(next, QNAME_TAG_JOURNAL_ENTRY)) {
// found it
return;
} else if (isEndTagEvent(next, QNAME_TAG_JOURNAL)) {
// need to get the next file
closeCurrentFile();
} else {
// problems
throw getNotNextMemberOrEndOfGroupException(QNAME_TAG_JOURNAL,
QNAME_TAG_JOURNAL_ENTRY,
next);
}
}
// If we don't have a file open, try to open one.
if (currentFile == null) {
currentFile = openNextFile();
}
// If we still don't have a file open, we're finished.
if (currentFile == null) {
// if there was no next file, we're done.
return;
}
// A new file needs to be advanced before using.
advanceIntoFile(currentFile.getReader());
}
} catch (XMLStreamException e) {
throw new JournalException(e);
}
}
|
[
"private",
"void",
"scanThroughFilesForNextJournalEntry",
"(",
")",
"throws",
"JournalException",
"{",
"try",
"{",
"while",
"(",
"true",
")",
"{",
"if",
"(",
"currentFile",
"!=",
"null",
")",
"{",
"// Check to see whether the current file contains any more",
"// entries. ",
"advancePastWhitespace",
"(",
"currentFile",
".",
"getReader",
"(",
")",
")",
";",
"XMLEvent",
"next",
"=",
"currentFile",
".",
"getReader",
"(",
")",
".",
"peek",
"(",
")",
";",
"if",
"(",
"isStartTagEvent",
"(",
"next",
",",
"QNAME_TAG_JOURNAL_ENTRY",
")",
")",
"{",
"// found it",
"return",
";",
"}",
"else",
"if",
"(",
"isEndTagEvent",
"(",
"next",
",",
"QNAME_TAG_JOURNAL",
")",
")",
"{",
"// need to get the next file",
"closeCurrentFile",
"(",
")",
";",
"}",
"else",
"{",
"// problems",
"throw",
"getNotNextMemberOrEndOfGroupException",
"(",
"QNAME_TAG_JOURNAL",
",",
"QNAME_TAG_JOURNAL_ENTRY",
",",
"next",
")",
";",
"}",
"}",
"// If we don't have a file open, try to open one.",
"if",
"(",
"currentFile",
"==",
"null",
")",
"{",
"currentFile",
"=",
"openNextFile",
"(",
")",
";",
"}",
"// If we still don't have a file open, we're finished.",
"if",
"(",
"currentFile",
"==",
"null",
")",
"{",
"// if there was no next file, we're done.",
"return",
";",
"}",
"// A new file needs to be advanced before using.",
"advanceIntoFile",
"(",
"currentFile",
".",
"getReader",
"(",
")",
")",
";",
"}",
"}",
"catch",
"(",
"XMLStreamException",
"e",
")",
"{",
"throw",
"new",
"JournalException",
"(",
"e",
")",
";",
"}",
"}"
] |
Advance to the next journal entry if there is one. If we find one, the
current file will be pointing to it. If we don't find one, there will be
no current file.
|
[
"Advance",
"to",
"the",
"next",
"journal",
"entry",
"if",
"there",
"is",
"one",
".",
"If",
"we",
"find",
"one",
"the",
"current",
"file",
"will",
"be",
"pointing",
"to",
"it",
".",
"If",
"we",
"don",
"t",
"find",
"one",
"there",
"will",
"be",
"no",
"current",
"file",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/journal/readerwriter/multifile/MultiFileJournalReader.java#L144-L184
|
9,197
|
fcrepo3/fcrepo
|
fcrepo-server/src/main/java/org/fcrepo/server/journal/readerwriter/multifile/MultiFileJournalReader.java
|
MultiFileJournalReader.openNextFile
|
protected JournalInputFile openNextFile() throws JournalException {
File[] journalFiles =
MultiFileJournalHelper
.getSortedArrayOfJournalFiles(journalDirectory,
filenamePrefix);
if (journalFiles.length == 0) {
return null;
}
JournalInputFile nextFile = new JournalInputFile(journalFiles[0]);
recoveryLog.log("Opening journal file: '" + nextFile.getFilename()
+ "'");
return nextFile;
}
|
java
|
protected JournalInputFile openNextFile() throws JournalException {
File[] journalFiles =
MultiFileJournalHelper
.getSortedArrayOfJournalFiles(journalDirectory,
filenamePrefix);
if (journalFiles.length == 0) {
return null;
}
JournalInputFile nextFile = new JournalInputFile(journalFiles[0]);
recoveryLog.log("Opening journal file: '" + nextFile.getFilename()
+ "'");
return nextFile;
}
|
[
"protected",
"JournalInputFile",
"openNextFile",
"(",
")",
"throws",
"JournalException",
"{",
"File",
"[",
"]",
"journalFiles",
"=",
"MultiFileJournalHelper",
".",
"getSortedArrayOfJournalFiles",
"(",
"journalDirectory",
",",
"filenamePrefix",
")",
";",
"if",
"(",
"journalFiles",
".",
"length",
"==",
"0",
")",
"{",
"return",
"null",
";",
"}",
"JournalInputFile",
"nextFile",
"=",
"new",
"JournalInputFile",
"(",
"journalFiles",
"[",
"0",
"]",
")",
";",
"recoveryLog",
".",
"log",
"(",
"\"Opening journal file: '\"",
"+",
"nextFile",
".",
"getFilename",
"(",
")",
"+",
"\"'\"",
")",
";",
"return",
"nextFile",
";",
"}"
] |
Look in the directory for files that match the prefix. If there are none,
leave with currentFile still null. If we find one, advance into it.
|
[
"Look",
"in",
"the",
"directory",
"for",
"files",
"that",
"match",
"the",
"prefix",
".",
"If",
"there",
"are",
"none",
"leave",
"with",
"currentFile",
"still",
"null",
".",
"If",
"we",
"find",
"one",
"advance",
"into",
"it",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-server/src/main/java/org/fcrepo/server/journal/readerwriter/multifile/MultiFileJournalReader.java#L190-L204
|
9,198
|
fcrepo3/fcrepo
|
fcrepo-common/src/main/java/org/fcrepo/common/rdf/JRDF.java
|
JRDF.sameResource
|
public static boolean sameResource(URIReference u1, String u2) {
return u1.getURI().toString().equals(u2);
}
|
java
|
public static boolean sameResource(URIReference u1, String u2) {
return u1.getURI().toString().equals(u2);
}
|
[
"public",
"static",
"boolean",
"sameResource",
"(",
"URIReference",
"u1",
",",
"String",
"u2",
")",
"{",
"return",
"u1",
".",
"getURI",
"(",
")",
".",
"toString",
"(",
")",
".",
"equals",
"(",
"u2",
")",
";",
"}"
] |
Tells whether the given resources are equivalent, with one given as a URI
string.
@param u1
first resource.
@param u2
second resource, given as a URI string.
@return true if equivalent, false otherwise.
|
[
"Tells",
"whether",
"the",
"given",
"resources",
"are",
"equivalent",
"with",
"one",
"given",
"as",
"a",
"URI",
"string",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-common/src/main/java/org/fcrepo/common/rdf/JRDF.java#L70-L72
|
9,199
|
fcrepo3/fcrepo
|
fcrepo-common/src/main/java/org/fcrepo/common/rdf/JRDF.java
|
JRDF.sameLiteral
|
public static boolean sameLiteral(Literal l1,
String l2,
URI type,
String lang) {
if (l1.getLexicalForm().equals(l2) && eq(l1.getLanguage(), lang)) {
if (l1.getDatatypeURI() == null) {
return type == null;
} else {
return type != null
&& type.equals(l1.getDatatypeURI());
}
} else {
return false;
}
}
|
java
|
public static boolean sameLiteral(Literal l1,
String l2,
URI type,
String lang) {
if (l1.getLexicalForm().equals(l2) && eq(l1.getLanguage(), lang)) {
if (l1.getDatatypeURI() == null) {
return type == null;
} else {
return type != null
&& type.equals(l1.getDatatypeURI());
}
} else {
return false;
}
}
|
[
"public",
"static",
"boolean",
"sameLiteral",
"(",
"Literal",
"l1",
",",
"String",
"l2",
",",
"URI",
"type",
",",
"String",
"lang",
")",
"{",
"if",
"(",
"l1",
".",
"getLexicalForm",
"(",
")",
".",
"equals",
"(",
"l2",
")",
"&&",
"eq",
"(",
"l1",
".",
"getLanguage",
"(",
")",
",",
"lang",
")",
")",
"{",
"if",
"(",
"l1",
".",
"getDatatypeURI",
"(",
")",
"==",
"null",
")",
"{",
"return",
"type",
"==",
"null",
";",
"}",
"else",
"{",
"return",
"type",
"!=",
"null",
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"type",
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"l1",
".",
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"(",
")",
")",
";",
"}",
"}",
"else",
"{",
"return",
"false",
";",
"}",
"}"
] |
Tells whether the given literals are equivalent, with one given as a set
of simple values.
@param l1
first literal.
@param l2
second literal's lexical value.
@param type
second literal's datatype URI string, if applicable.
@param lang
second literal's language tag string, if applicable.
@return true if equivalent, false otherwise.
|
[
"Tells",
"whether",
"the",
"given",
"literals",
"are",
"equivalent",
"with",
"one",
"given",
"as",
"a",
"set",
"of",
"simple",
"values",
"."
] |
37df51b9b857fd12c6ab8269820d406c3c4ad774
|
https://github.com/fcrepo3/fcrepo/blob/37df51b9b857fd12c6ab8269820d406c3c4ad774/fcrepo-common/src/main/java/org/fcrepo/common/rdf/JRDF.java#L105-L119
|
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