input
stringlengths 205
73.3k
| output
stringlengths 64
73.2k
| instruction
stringclasses 1
value |
|---|---|---|
#vulnerable code
@Override
public List<BxDocument> getDocuments() throws TransformationException {
List<BxDocument> documents = new ArrayList<BxDocument>();
TrueVizToBxDocumentReader tvReader = new TrueVizToBxDocumentReader();
Enumeration<? extends ZipEntry> entries = zipFile.entries();
while (entries.hasMoreElements()) {
ZipEntry zipEntry = (ZipEntry) entries.nextElement();
if (zipEntry.getName().endsWith("xml")) {
try {
List<BxPage> pages = tvReader.read(new InputStreamReader(zipFile.getInputStream(zipEntry)));
BxDocument newDoc = new BxDocument();
for (BxPage page : pages) {
page.setParent(newDoc);
}
newDoc.setFilename(zipEntry.getName());
newDoc.setPages(pages);
documents.add(newDoc);
} catch (IOException ex) {
throw new TransformationException("Cannot read file!", ex);
}
}
}
return documents;
}
#location 11
#vulnerability type RESOURCE_LEAK
|
#fixed code
@Override
public List<BxDocument> getDocuments() throws TransformationException {
List<BxDocument> documents = new ArrayList<BxDocument>();
TrueVizToBxDocumentReader tvReader = new TrueVizToBxDocumentReader();
Enumeration<? extends ZipEntry> entries = zipFile.entries();
while (entries.hasMoreElements()) {
ZipEntry zipEntry = (ZipEntry) entries.nextElement();
if (zipEntry.getName().endsWith("xml")) {
try {
List<BxPage> pages = tvReader.read(new InputStreamReader(zipFile.getInputStream(zipEntry), "UTF-8"));
BxDocument newDoc = new BxDocument();
for (BxPage page : pages) {
page.setParent(newDoc);
}
newDoc.setFilename(zipEntry.getName());
newDoc.setPages(pages);
documents.add(newDoc);
} catch (IOException ex) {
throw new TransformationException("Cannot read file!", ex);
}
}
}
return documents;
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
public void loadModelFromFile(String modelFilePath, String rangeFilePath) throws IOException {
BufferedReader modelFile = new BufferedReader(new InputStreamReader(new FileInputStream(modelFilePath)));
BufferedReader rangeFile = null;
if (rangeFilePath != null) {
rangeFile = new BufferedReader(new InputStreamReader(new FileInputStream(rangeFilePath)));
}
loadModelFromFile(modelFile, rangeFile);
}
#location 7
#vulnerability type RESOURCE_LEAK
|
#fixed code
public void loadModelFromFile(String modelFilePath, String rangeFilePath) throws IOException {
BufferedReader modelFile = new BufferedReader(new InputStreamReader(new FileInputStream(modelFilePath), "UTF-8"));
BufferedReader rangeFile = null;
if (rangeFilePath != null) {
rangeFile = new BufferedReader(new InputStreamReader(new FileInputStream(rangeFilePath), "UTF-8"));
}
loadModelFromFile(modelFile, rangeFile);
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
public static void main(String[] args) throws JDOMException, IOException, AnalysisException {
if (args.length != 3) {
System.err.println("USAGE: ReferenceParsingEvaluator <foldness> <model_path> <test_path>");
System.exit(1);
}
int foldness = Integer.parseInt(args[0]);
String modelPathSuffix = args[1];
String testPathSuffix = args[2];
Map<String, List<Result>> results = new HashMap<String, List<Result>>();
for (int i = 0; i < foldness; i++) {
System.out.println("Fold "+i);
String modelPath = modelPathSuffix + i;
CRFBibReferenceParser parser = new CRFBibReferenceParser(modelPath);
String testPath = testPathSuffix + i;
File testFile = new File(testPath);
List<Citation> testCitations;
InputStream testIS = null;
try {
testIS = new FileInputStream(testFile);
InputSource testSource = new InputSource(testIS);
testCitations = NlmCitationExtractor.extractCitations(testSource);
} finally {
if (testIS != null) {
testIS.close();
}
}
System.out.println(testCitations.size());
List<BibEntry> testEntries = new ArrayList<BibEntry>();
for (Citation c : testCitations) {
BibEntry entry = CitationUtils.citationToBibref(c);
testEntries.add(entry);
for (String key : entry.getFieldKeys()) {
if (results.get(key) == null) {
results.put(key, new ArrayList<Result>());
}
}
}
int j = 0;
for (BibEntry orig : testEntries) {
BibEntry test = parser.parseBibReference(orig.getText());
System.out.println();
System.out.println();
System.out.println(orig.toBibTeX());
System.out.println(test.toBibTeX());
Map<String, Result> map = new HashMap<String, Result>();
for (String s : orig.getFieldKeys()) {
if (map.get(s) == null) {
map.put(s, new Result());
}
map.get(s).addOrig(orig.getAllFieldValues(s).size());
}
for (String s : test.getFieldKeys()) {
if (map.get(s) == null) {
map.put(s, new Result());
}
map.get(s).addExtr(test.getAllFieldValues(s).size());
}
for (String s : test.getFieldKeys()) {
List<String> origVals = orig.getAllFieldValues(s);
for (String testVal : test.getAllFieldValues(s)) {
boolean found = false;
if (origVals.contains(testVal)) {
map.get(s).addSuccess();
origVals.remove(testVal);
found = true;
}
if (!found) {
System.out.println("WRONG "+s);
}
}
}
for (Map.Entry<String, Result> s : map.entrySet()) {
System.out.println("");
System.out.println(s.getKey());
System.out.println(s.getValue());
System.out.println(s.getValue().getPrecision());
System.out.println(s.getValue().getRecall());
results.get(s.getKey()).add(s.getValue());
}
j++;
System.out.println("Tested "+j+" out of "+testEntries.size());
}
}
for (String s : results.keySet()) {
System.out.println("");
System.out.println(s);
System.out.println(results.get(s).size());
double precision = 0;
int precisionCount = 0;
double recall = 0;
int recallCount = 0;
for (Result r : results.get(s)) {
if (r.getPrecision() != null) {
precision += r.getPrecision();
precisionCount++;
}
if (r.getRecall() != null) {
recall += r.getRecall();
recallCount++;
}
}
System.out.println("Precision count "+precisionCount);
System.out.println("Mean precision "+(precision / precisionCount));
System.out.println("Recall count "+recallCount);
System.out.println("Mean recall "+(recall / recallCount));
}
}
#location 103
#vulnerability type NULL_DEREFERENCE
|
#fixed code
public static void main(String[] args) throws JDOMException, IOException, AnalysisException {
if (args.length != 3) {
System.err.println("USAGE: ReferenceParsingEvaluator <foldness> <model_path> <test_path>");
System.exit(1);
}
int foldness = Integer.parseInt(args[0]);
String modelPathSuffix = args[1];
String testPathSuffix = args[2];
Map<String, List<Result>> results = new HashMap<String, List<Result>>();
for (int i = 0; i < foldness; i++) {
System.out.println("Fold "+i);
String modelPath = modelPathSuffix + i;
CRFBibReferenceParser parser = new CRFBibReferenceParser(modelPath);
String testPath = testPathSuffix + i;
File testFile = new File(testPath);
List<Citation> testCitations;
InputStream testIS = null;
try {
testIS = new FileInputStream(testFile);
InputSource testSource = new InputSource(testIS);
testCitations = NlmCitationExtractor.extractCitations(testSource);
} finally {
if (testIS != null) {
testIS.close();
}
}
System.out.println(testCitations.size());
List<BibEntry> testEntries = new ArrayList<BibEntry>();
for (Citation c : testCitations) {
BibEntry entry = CitationUtils.citationToBibref(c);
testEntries.add(entry);
for (String key : entry.getFieldKeys()) {
if (results.get(key) == null) {
results.put(key, new ArrayList<Result>());
}
}
}
int j = 0;
for (BibEntry orig : testEntries) {
BibEntry test = parser.parseBibReference(orig.getText());
System.out.println();
System.out.println();
System.out.println(orig.toBibTeX());
System.out.println(test.toBibTeX());
Map<String, Result> map = new HashMap<String, Result>();
for (String s : orig.getFieldKeys()) {
if (map.get(s) == null) {
map.put(s, new Result());
}
map.get(s).addOrig(orig.getAllFieldValues(s).size());
}
for (String s : test.getFieldKeys()) {
if (map.get(s) == null) {
map.put(s, new Result());
}
map.get(s).addExtr(test.getAllFieldValues(s).size());
}
for (String s : test.getFieldKeys()) {
List<String> origVals = orig.getAllFieldValues(s);
for (String testVal : test.getAllFieldValues(s)) {
boolean found = false;
if (origVals.contains(testVal)) {
map.get(s).addSuccess();
origVals.remove(testVal);
found = true;
}
if (!found) {
System.out.println("WRONG "+s);
}
}
}
for (Map.Entry<String, Result> s : map.entrySet()) {
System.out.println("");
System.out.println(s.getKey());
System.out.println(s.getValue());
System.out.println(s.getValue().getPrecision());
System.out.println(s.getValue().getRecall());
results.get(s.getKey()).add(s.getValue());
}
j++;
System.out.println("Tested "+j+" out of "+testEntries.size());
}
}
for (Map.Entry<String, List<Result>> e : results.entrySet()) {
System.out.println("");
System.out.println(e.getKey());
System.out.println(e.getValue().size());
double precision = 0;
int precisionCount = 0;
double recall = 0;
int recallCount = 0;
for (Result r : e.getValue()) {
if (r.getPrecision() != null) {
precision += r.getPrecision();
precisionCount++;
}
if (r.getRecall() != null) {
recall += r.getRecall();
recallCount++;
}
}
System.out.println("Precision count "+precisionCount);
System.out.println("Mean precision "+(precision / precisionCount));
System.out.println("Recall count "+recallCount);
System.out.println("Mean recall "+(recall / recallCount));
}
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
@Test
public void deepCloneTest() throws TransformationException {
InputStream stream = BxModelUtilsTest.class.getResourceAsStream(EXP_STR_LAB_1);
TrueVizToBxDocumentReader reader = new TrueVizToBxDocumentReader();
BxDocument doc = new BxDocument().setPages(reader.read(new InputStreamReader(stream)));
BxDocument copy = BxModelUtils.deepClone(doc);
assertFalse(doc == copy);
assertTrue(BxModelUtils.areEqual(doc, copy));
Stack<BxPage> pages = new Stack<BxPage>();
Stack<BxZone> zones = new Stack<BxZone>();
Stack<BxLine> lines = new Stack<BxLine>();
Stack<BxWord> words = new Stack<BxWord>();
Stack<BxChunk> chunks = new Stack<BxChunk>();
for (BxPage page : copy) {
assertTrue(page.getParent() == copy);
for (BxZone zone : page) {
assertTrue(zone.getParent() == page);
for (BxLine line : zone) {
assertTrue(line.getParent() == zone);
for (BxWord word : line) {
assertTrue(word.getParent() == line);
for (BxChunk chunk : word) {
assertTrue(chunk.getParent() == word);
}
}
}
}
}
BxPage page = copy.getFirstChild();
while (page != null) {
pages.push(page);
page = page.getNext();
}
page = pages.peek();
BxZone zone = copy.getFirstChild().getFirstChild();
while (zone != null) {
zones.push(zone);
zone = zone.getNext();
}
zone = zones.peek();
BxLine line = copy.getFirstChild().getFirstChild().getFirstChild();
while (line != null) {
lines.push(line);
line = line.getNext();
}
line = lines.peek();
BxWord word = copy.getFirstChild().getFirstChild().getFirstChild().getFirstChild();
while (word != null) {
words.push(word);
word = word.getNext();
}
word = words.peek();
BxChunk chunk = copy.getFirstChild().getFirstChild().getFirstChild().getFirstChild().getFirstChild();
while (chunk != null) {
chunks.push(chunk);
chunk = chunk.getNext();
}
chunk = chunks.peek();
while (!pages.empty() && !zones.empty() && !lines.empty()
&& !words.empty() && !chunks.empty()) {
BxChunk ch = chunks.pop();
assertTrue(ch.getParent() == words.peek());
assertTrue(words.peek().getParent() == lines.peek());
assertTrue(lines.peek().getParent() == zones.peek());
assertTrue(zones.peek().getParent() == pages.peek());
if (chunks.empty()) {
words.pop();
lines.pop();
zones.pop();
pages.pop();
} else if (ch.getParent() != chunks.peek().getParent()) {
BxWord w = words.pop();
assertFalse(words.empty());
if (w.getParent() != words.peek().getParent()) {
BxLine l = lines.pop();
assertFalse(lines.empty());
if (l.getParent() != lines.peek().getParent()) {
BxZone z = zones.pop();
assertFalse(zones.empty());
if (z.getParent() != zones.peek().getParent()) {
pages.pop();
assertFalse(pages.empty());
}
}
}
}
}
assertTrue(pages.empty());
assertTrue(zones.empty());
assertTrue(lines.empty());
assertTrue(words.empty());
assertTrue(chunks.empty());
while (page != null) {
pages.push(page);
page = page.getPrev();
}
while (zone != null) {
zones.push(zone);
zone = zone.getPrev();
}
while (line != null) {
lines.push(line);
line = line.getPrev();
}
while (word != null) {
words.push(word);
word = word.getPrev();
}
while (chunk != null) {
chunks.push(chunk);
chunk = chunk.getPrev();
}
while (!pages.empty() && !zones.empty() && !lines.empty()
&& !words.empty() && !chunks.empty()) {
BxChunk ch = chunks.pop();
assertTrue(ch.getParent() == words.peek());
assertTrue(words.peek().getParent() == lines.peek());
assertTrue(lines.peek().getParent() == zones.peek());
assertTrue(zones.peek().getParent() == pages.peek());
if (chunks.empty()) {
words.pop();
lines.pop();
zones.pop();
pages.pop();
} else if (ch.getParent() != chunks.peek().getParent()) {
BxWord w = words.pop();
assertFalse(words.empty());
if (w.getParent() != words.peek().getParent()) {
BxLine l = lines.pop();
assertFalse(lines.empty());
if (l.getParent() != lines.peek().getParent()) {
BxZone z = zones.pop();
assertFalse(zones.empty());
if (z.getParent() != zones.peek().getParent()) {
pages.pop();
assertFalse(pages.empty());
}
}
}
}
}
assertTrue(pages.empty());
assertTrue(zones.empty());
assertTrue(lines.empty());
assertTrue(words.empty());
assertTrue(chunks.empty());
}
#location 5
#vulnerability type RESOURCE_LEAK
|
#fixed code
@Test
public void deepCloneTest() throws TransformationException, UnsupportedEncodingException {
InputStream stream = BxModelUtilsTest.class.getResourceAsStream(EXP_STR_LAB_1);
TrueVizToBxDocumentReader reader = new TrueVizToBxDocumentReader();
BxDocument doc = new BxDocument().setPages(reader.read(new InputStreamReader(stream, "UTF-8")));
BxDocument copy = BxModelUtils.deepClone(doc);
assertFalse(doc == copy);
assertTrue(BxModelUtils.areEqual(doc, copy));
Stack<BxPage> pages = new Stack<BxPage>();
Stack<BxZone> zones = new Stack<BxZone>();
Stack<BxLine> lines = new Stack<BxLine>();
Stack<BxWord> words = new Stack<BxWord>();
Stack<BxChunk> chunks = new Stack<BxChunk>();
for (BxPage page : copy) {
assertTrue(page.getParent() == copy);
for (BxZone zone : page) {
assertTrue(zone.getParent() == page);
for (BxLine line : zone) {
assertTrue(line.getParent() == zone);
for (BxWord word : line) {
assertTrue(word.getParent() == line);
for (BxChunk chunk : word) {
assertTrue(chunk.getParent() == word);
}
}
}
}
}
BxPage page = copy.getFirstChild();
while (page != null) {
pages.push(page);
page = page.getNext();
}
page = pages.peek();
BxZone zone = copy.getFirstChild().getFirstChild();
while (zone != null) {
zones.push(zone);
zone = zone.getNext();
}
zone = zones.peek();
BxLine line = copy.getFirstChild().getFirstChild().getFirstChild();
while (line != null) {
lines.push(line);
line = line.getNext();
}
line = lines.peek();
BxWord word = copy.getFirstChild().getFirstChild().getFirstChild().getFirstChild();
while (word != null) {
words.push(word);
word = word.getNext();
}
word = words.peek();
BxChunk chunk = copy.getFirstChild().getFirstChild().getFirstChild().getFirstChild().getFirstChild();
while (chunk != null) {
chunks.push(chunk);
chunk = chunk.getNext();
}
chunk = chunks.peek();
while (!pages.empty() && !zones.empty() && !lines.empty()
&& !words.empty() && !chunks.empty()) {
BxChunk ch = chunks.pop();
assertTrue(ch.getParent() == words.peek());
assertTrue(words.peek().getParent() == lines.peek());
assertTrue(lines.peek().getParent() == zones.peek());
assertTrue(zones.peek().getParent() == pages.peek());
if (chunks.empty()) {
words.pop();
lines.pop();
zones.pop();
pages.pop();
} else if (ch.getParent() != chunks.peek().getParent()) {
BxWord w = words.pop();
assertFalse(words.empty());
if (w.getParent() != words.peek().getParent()) {
BxLine l = lines.pop();
assertFalse(lines.empty());
if (l.getParent() != lines.peek().getParent()) {
BxZone z = zones.pop();
assertFalse(zones.empty());
if (z.getParent() != zones.peek().getParent()) {
pages.pop();
assertFalse(pages.empty());
}
}
}
}
}
assertTrue(pages.empty());
assertTrue(zones.empty());
assertTrue(lines.empty());
assertTrue(words.empty());
assertTrue(chunks.empty());
while (page != null) {
pages.push(page);
page = page.getPrev();
}
while (zone != null) {
zones.push(zone);
zone = zone.getPrev();
}
while (line != null) {
lines.push(line);
line = line.getPrev();
}
while (word != null) {
words.push(word);
word = word.getPrev();
}
while (chunk != null) {
chunks.push(chunk);
chunk = chunk.getPrev();
}
while (!pages.empty() && !zones.empty() && !lines.empty()
&& !words.empty() && !chunks.empty()) {
BxChunk ch = chunks.pop();
assertTrue(ch.getParent() == words.peek());
assertTrue(words.peek().getParent() == lines.peek());
assertTrue(lines.peek().getParent() == zones.peek());
assertTrue(zones.peek().getParent() == pages.peek());
if (chunks.empty()) {
words.pop();
lines.pop();
zones.pop();
pages.pop();
} else if (ch.getParent() != chunks.peek().getParent()) {
BxWord w = words.pop();
assertFalse(words.empty());
if (w.getParent() != words.peek().getParent()) {
BxLine l = lines.pop();
assertFalse(lines.empty());
if (l.getParent() != lines.peek().getParent()) {
BxZone z = zones.pop();
assertFalse(zones.empty());
if (z.getParent() != zones.peek().getParent()) {
pages.pop();
assertFalse(pages.empty());
}
}
}
}
}
assertTrue(pages.empty());
assertTrue(zones.empty());
assertTrue(lines.empty());
assertTrue(words.empty());
assertTrue(chunks.empty());
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
public void loadModelFromResources(String modelFilePath, String rangeFilePath) throws IOException
{
InputStreamReader modelISR = new InputStreamReader(SVMClassifier.class
.getResourceAsStream(modelFilePath));
BufferedReader modelFile = new BufferedReader(modelISR);
BufferedReader rangeFile = null;
if (rangeFilePath != null) {
InputStreamReader rangeISR = new InputStreamReader(SVMClassifier.class
.getResourceAsStream(rangeFilePath));
rangeFile = new BufferedReader(rangeISR);
}
loadModelFromFile(modelFile, rangeFile);
}
#location 13
#vulnerability type RESOURCE_LEAK
|
#fixed code
public void loadModelFromResources(String modelFilePath, String rangeFilePath) throws IOException
{
InputStreamReader modelISR = new InputStreamReader(this.getClass().getResourceAsStream(modelFilePath));
BufferedReader modelFile = new BufferedReader(modelISR);
InputStreamReader rangeISR = new InputStreamReader(this.getClass().getResourceAsStream(rangeFilePath));
BufferedReader rangeFile = new BufferedReader(rangeISR);
loadModelFromFile(modelFile, rangeFile);
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
public static List<TrainingSample<BxZoneLabel>> loadProblem(File file, FeatureVectorBuilder<BxZone, BxPage> fvb) throws IOException {
List<TrainingSample<BxZoneLabel>> ret = new ArrayList<TrainingSample<BxZoneLabel>>();
BufferedReader br = new BufferedReader(new InputStreamReader(new FileInputStream(file)));
String line;
final Pattern partsPattern = Pattern.compile(" ");
final Pattern twopartPattern = Pattern.compile(":");
while ((line = br.readLine()) != null) {
String[] parts = partsPattern.split(line);
BxZoneLabel label = BxZoneLabel.values()[Integer.parseInt(parts[0])];
FeatureVector fv = new FeatureVector();
List<String> featureNames = fvb.getFeatureNames();
for (int partIdx = 1; partIdx < parts.length; ++partIdx) {
String[] subparts = twopartPattern.split(parts[partIdx]);
fv.addFeature(featureNames.get(partIdx - 1), Double.parseDouble(subparts[1]));
}
TrainingSample<BxZoneLabel> sample = new TrainingSample<BxZoneLabel>(fv, label);
ret.add(sample);
}
br.close();
return ret;
}
#location 20
#vulnerability type RESOURCE_LEAK
|
#fixed code
public static List<TrainingSample<BxZoneLabel>> loadProblem(File file, FeatureVectorBuilder<BxZone, BxPage> fvb) throws IOException {
List<TrainingSample<BxZoneLabel>> ret = new ArrayList<TrainingSample<BxZoneLabel>>();
BufferedReader br = new BufferedReader(new InputStreamReader(new FileInputStream(file), "UTF-8"));
String line;
final Pattern partsPattern = Pattern.compile(" ");
final Pattern twopartPattern = Pattern.compile(":");
while ((line = br.readLine()) != null) {
String[] parts = partsPattern.split(line);
BxZoneLabel label = BxZoneLabel.values()[Integer.parseInt(parts[0])];
FeatureVector fv = new FeatureVector();
List<String> featureNames = fvb.getFeatureNames();
for (int partIdx = 1; partIdx < parts.length; ++partIdx) {
String[] subparts = twopartPattern.split(parts[partIdx]);
fv.addFeature(featureNames.get(partIdx - 1), Double.parseDouble(subparts[1]));
}
TrainingSample<BxZoneLabel> sample = new TrainingSample<BxZoneLabel>(fv, label);
ret.add(sample);
}
br.close();
return ret;
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
public void loadModelFromResources(String modelFilePath, String rangeFilePath) throws IOException {
InputStreamReader modelISR = new InputStreamReader(SVMClassifier.class.getResourceAsStream(modelFilePath));
BufferedReader modelFile = new BufferedReader(modelISR);
InputStreamReader rangeISR = new InputStreamReader(SVMClassifier.class.getResourceAsStream(rangeFilePath));
BufferedReader rangeFile = new BufferedReader(rangeISR);
loadModelFromFile(modelFile, rangeFile);
}
#location 7
#vulnerability type RESOURCE_LEAK
|
#fixed code
public void loadModelFromResources(String modelFilePath, String rangeFilePath) throws IOException {
InputStreamReader modelISR = new InputStreamReader(SVMClassifier.class.getResourceAsStream(modelFilePath), "UTF-8");
BufferedReader modelFile = new BufferedReader(modelISR);
InputStreamReader rangeISR = new InputStreamReader(SVMClassifier.class.getResourceAsStream(rangeFilePath), "UTF-8");
BufferedReader rangeFile = new BufferedReader(rangeISR);
loadModelFromFile(modelFile, rangeFile);
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
public static void main(String[] args) {
if (args.length != 1) {
System.err.println("Usage: <pubmed directory>");
System.exit(1);
}
File dir = new File(args[0]);
for (File pdfFile : FileUtils.listFiles(dir, new String[]{"pdf"}, true)) {
try {
String pdfPath = pdfFile.getPath();
String nxmlPath = StringTools.getNLMPath(pdfPath);
File xmlFile = new File(StringTools.getTrueVizPath(nxmlPath));
if (xmlFile.exists()) {
continue;
}
System.out.print(pdfPath+" ");
InputStream pdfStream = new FileInputStream(pdfPath);
InputStream nxmlStream = new FileInputStream(nxmlPath);
PubmedXMLGenerator datasetGenerator = new PubmedXMLGenerator();
datasetGenerator.setVerbose(false);
BxDocument bxDoc = datasetGenerator.generateTrueViz(pdfStream, nxmlStream);
FileWriter fstream = new FileWriter(StringTools.getTrueVizPath(nxmlPath));
BufferedWriter out = new BufferedWriter(fstream);
BxDocumentToTrueVizWriter writer = new BxDocumentToTrueVizWriter();
out.write(writer.write(bxDoc.getPages()));
out.close();
System.out.println("done");
} catch (Exception e) {
e.printStackTrace();
}
}
}
#location 34
#vulnerability type RESOURCE_LEAK
|
#fixed code
public static void main(String[] args) {
if (args.length != 1) {
System.err.println("Usage: <pubmed directory>");
System.exit(1);
}
File dir = new File(args[0]);
for (File pdfFile : FileUtils.listFiles(dir, new String[]{"pdf"}, true)) {
try {
String pdfPath = pdfFile.getPath();
String nxmlPath = StringTools.getNLMPath(pdfPath);
File xmlFile = new File(StringTools.getTrueVizPath(nxmlPath));
if (xmlFile.exists()) {
continue;
}
System.out.print(pdfPath+" ");
InputStream pdfStream = new FileInputStream(pdfPath);
InputStream nxmlStream = new FileInputStream(nxmlPath);
PubmedXMLGenerator datasetGenerator = new PubmedXMLGenerator();
datasetGenerator.setVerbose(false);
BxDocument bxDoc = datasetGenerator.generateTrueViz(pdfStream, nxmlStream);
int keys = 0;
Set<BxZoneLabel> set = EnumSet.noneOf(BxZoneLabel.class);
int total = 0;
int known = 0;
for (BxZone z: bxDoc.asZones()) {
total++;
if (z.getLabel() != null) {
known++;
if (z.getLabel().isOfCategoryOrGeneral(BxZoneLabelCategory.CAT_METADATA)) {
set.add(z.getLabel());
}
if (BxZoneLabel.REFERENCES.equals(z.getLabel())) {
keys = 1;
}
}
}
if (set.contains(BxZoneLabel.MET_AFFILIATION)) {
keys++;
}
if (set.contains(BxZoneLabel.MET_AUTHOR)) {
keys++;
}
if (set.contains(BxZoneLabel.MET_BIB_INFO)) {
keys++;
}
if (set.contains(BxZoneLabel.MET_TITLE)) {
keys++;
}
int coverage = 0;
if (total > 0) {
coverage = known*100/total;
}
System.out.print(coverage+" "+set.size()+" "+keys);
FileWriter fstream = new FileWriter(
StringTools.getTrueVizPath(nxmlPath).replace(".xml", "."+coverage+"."+set.size()+"."+keys+".cerm.xml"));
BufferedWriter out = new BufferedWriter(fstream);
BxDocumentToTrueVizWriter writer = new BxDocumentToTrueVizWriter();
out.write(writer.write(bxDoc.getPages()));
out.close();
System.out.println(" done");
} catch (Exception e) {
e.printStackTrace();
}
}
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
public void loadModelFromFile(String modelFilePath, String rangeFilePath) throws IOException {
BufferedReader modelFile = new BufferedReader(new InputStreamReader(new FileInputStream(modelFilePath)));
BufferedReader rangeFile = null;
if (rangeFilePath != null) {
rangeFile = new BufferedReader(new InputStreamReader(new FileInputStream(rangeFilePath)));
}
loadModelFromFile(modelFile, rangeFile);
}
#location 6
#vulnerability type RESOURCE_LEAK
|
#fixed code
public void loadModelFromFile(String modelFilePath, String rangeFilePath) throws IOException {
BufferedReader modelFile = new BufferedReader(new InputStreamReader(new FileInputStream(modelFilePath), "UTF-8"));
BufferedReader rangeFile = null;
if (rangeFilePath != null) {
rangeFile = new BufferedReader(new InputStreamReader(new FileInputStream(rangeFilePath), "UTF-8"));
}
loadModelFromFile(modelFile, rangeFile);
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
private BxDocument getDocumentFromZip(String filename) throws TransformationException, IOException {
TrueVizToBxDocumentReader tvReader = new TrueVizToBxDocumentReader();
Enumeration<? extends ZipEntry> entries = zipFile.entries();
while (entries.hasMoreElements()) {
ZipEntry zipEntry = (ZipEntry) entries.nextElement();
if (zipEntry.getName().equals(filename)) {
List<BxPage> pages = tvReader.read(new InputStreamReader(zipFile.getInputStream(zipEntry)));
BxDocument newDoc = new BxDocument();
for (BxPage page : pages) {
page.setParent(newDoc);
}
newDoc.setFilename(zipEntry.getName());
newDoc.setPages(pages);
return newDoc;
}
}
return null;
}
#location 7
#vulnerability type RESOURCE_LEAK
|
#fixed code
private BxDocument getDocumentFromZip(String filename) throws TransformationException, IOException {
TrueVizToBxDocumentReader tvReader = new TrueVizToBxDocumentReader();
Enumeration<? extends ZipEntry> entries = zipFile.entries();
while (entries.hasMoreElements()) {
ZipEntry zipEntry = (ZipEntry) entries.nextElement();
if (zipEntry.getName().equals(filename)) {
List<BxPage> pages = tvReader.read(new InputStreamReader(zipFile.getInputStream(zipEntry), "UTF-8"));
BxDocument newDoc = new BxDocument();
for (BxPage page : pages) {
page.setParent(newDoc);
}
newDoc.setFilename(zipEntry.getName());
newDoc.setPages(pages);
return newDoc;
}
}
return null;
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
public static void main(String[] args) throws AnalysisException, TransformationException, IOException {
// args[0] path to xml directory
if(args.length != 1) {
System.err.println("Source directory needed!");
System.exit(1);
}
InputStreamReader modelISR = new InputStreamReader(Thread.currentThread().getClass()
.getResourceAsStream("/pl/edu/icm/cermine/structure/svm_initial_classifier"));
BufferedReader modelFile = new BufferedReader(modelISR);
InputStreamReader rangeISR = new InputStreamReader(Thread.currentThread().getClass()
.getResourceAsStream("/pl/edu/icm/cermine/structure/svm_initial_classifier.range"));
BufferedReader rangeFile = new BufferedReader(rangeISR);
SVMZoneClassifier classifier = new SVMInitialZoneClassifier(modelFile, rangeFile);
ReadingOrderResolver ror = new HierarchicalReadingOrderResolver();
BxDocumentToTrueVizWriter tvw = new BxDocumentToTrueVizWriter();
List<BxDocument> docs = EvaluationUtils.getDocumentsFromPath(args[0]);
for(BxDocument doc: docs) {
System.out.println(">> " + doc.getFilename());
ror.resolve(doc);
classifier.classifyZones(doc);
BufferedWriter out = null;
try {
// Create file
FileWriter fstream = new FileWriter(doc.getFilename());
out = new BufferedWriter(fstream);
out.write(tvw.write(doc.getPages()));
out.close();
} catch (Exception e){//Catch exception if any
System.err.println("Error: " + e.getMessage());
} finally {
if(out != null) {
out.close();
}
}
}
}
#location 15
#vulnerability type RESOURCE_LEAK
|
#fixed code
public static void main(String[] args) throws AnalysisException, TransformationException, IOException {
// args[0] path to xml directory
if(args.length != 1) {
System.err.println("Source directory needed!");
System.exit(1);
}
SVMInitialZoneClassifier classifier = new SVMInitialZoneClassifier("/pl/edu/icm/cermine/structure/svm_initial_classifier",
"/pl/edu/icm/cermine/structure/svm_initial_classifier.range");
ReadingOrderResolver ror = new HierarchicalReadingOrderResolver();
BxDocumentToTrueVizWriter tvw = new BxDocumentToTrueVizWriter();
List<BxDocument> docs = EvaluationUtils.getDocumentsFromPath(args[0]);
for(BxDocument doc: docs) {
System.out.println(">> " + doc.getFilename());
ror.resolve(doc);
classifier.classifyZones(doc);
BufferedWriter out = null;
try {
// Create file
FileWriter fstream = new FileWriter(doc.getFilename());
out = new BufferedWriter(fstream);
out.write(tvw.write(doc.getPages()));
out.close();
} catch (Exception e){//Catch exception if any
System.err.println("Error: " + e.getMessage());
} finally {
if(out != null) {
out.close();
}
}
}
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
public static String getFileSha1(File file) {
if (!file.isFile()) {
return null;
}
MessageDigest digest = null;
FileInputStream in = null;
byte buffer[] = new byte[8192];
int len;
try {
digest = MessageDigest.getInstance("SHA-1");
in = new FileInputStream(file);
while ((len = in.read(buffer)) != -1) {
digest.update(buffer, 0, len);
}
BigInteger bigInt = new BigInteger(1, digest.digest());
return bigInt.toString(16);
} catch (Exception e) {
e.printStackTrace();
return null;
} finally {
try {
in.close();
} catch (Exception e) {
e.printStackTrace();
}
}
}
#location 22
#vulnerability type NULL_DEREFERENCE
|
#fixed code
public static String getFileSha1(File file) {
if (!file.isFile()) {
return null;
}
MessageDigest digest = null;
FileInputStream in = null;
byte[] buffer = new byte[8192];
int len;
try {
digest = MessageDigest.getInstance("SHA-1");
in = new FileInputStream(file);
while ((len = in.read(buffer)) != -1) {
digest.update(buffer, 0, len);
}
BigInteger bigInt = new BigInteger(1, digest.digest());
return bigInt.toString(16);
} catch (Exception e) {
e.printStackTrace();
return null;
} finally {
try {
if (in != null) {
in.close();
}
} catch (Exception e) {
e.printStackTrace();
}
}
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
public void writeToXml() throws Exception {
// 排版缩进的格式
OutputFormat format = OutputFormat.createPrettyPrint();
// 设置编码
format.setEncoding("UTF-8");
// 创建XMLWriter对象,指定了写出文件及编码格式
XMLWriter writer = null;
writer = new XMLWriter(
new OutputStreamWriter(new FileOutputStream(new File(ConstantsTools.PATH_CONFIG)), "UTF-8"), format);
// 写入
writer.write(document);
writer.flush();
writer.close();
}
#location 8
#vulnerability type RESOURCE_LEAK
|
#fixed code
public void writeToXml() throws Exception {
// 排版缩进的格式
OutputFormat format = OutputFormat.createPrettyPrint();
// 设置编码
format.setEncoding("UTF-8");
// 创建XMLWriter对象,指定了写出文件及编码格式
XMLWriter writer = null;
writer = new XMLWriter(
new OutputStreamWriter(new FileOutputStream(new File(ConstantsTools.PATH_CONFIG)), StandardCharsets.UTF_8), format);
// 写入
writer.write(document);
writer.flush();
writer.close();
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
public static void clearDirectiory(String dir) {
File dirFile = new File(dir);
for (File file : dirFile.listFiles()) {
file.delete();
}
}
#location 3
#vulnerability type NULL_DEREFERENCE
|
#fixed code
public static void clearDirectiory(String dir) {
File dirFile = new File(dir);
for (File file : Objects.requireNonNull(dirFile.listFiles())) {
file.delete();
}
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
public static String getFileMD5(File file) {
if (!file.isFile()) {
return null;
}
MessageDigest digest = null;
FileInputStream in = null;
byte buffer[] = new byte[8192];
int len;
try {
digest = MessageDigest.getInstance("MD5");
in = new FileInputStream(file);
while ((len = in.read(buffer)) != -1) {
digest.update(buffer, 0, len);
}
BigInteger bigInt = new BigInteger(1, digest.digest());
return bigInt.toString(16);
} catch (Exception e) {
e.printStackTrace();
return null;
} finally {
try {
in.close();
} catch (Exception e) {
e.printStackTrace();
}
}
}
#location 22
#vulnerability type NULL_DEREFERENCE
|
#fixed code
public static String getFileMD5(File file) {
if (!file.isFile()) {
return null;
}
MessageDigest digest = null;
FileInputStream in = null;
byte[] buffer = new byte[8192];
int len;
try {
digest = MessageDigest.getInstance("MD5");
in = new FileInputStream(file);
while ((len = in.read(buffer)) != -1) {
digest.update(buffer, 0, len);
}
BigInteger bigInt = new BigInteger(1, digest.digest());
return bigInt.toString(16);
} catch (Exception e) {
e.printStackTrace();
return null;
} finally {
try {
if (in != null) {
in.close();
}
} catch (Exception e) {
e.printStackTrace();
}
}
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
<T extends GHMetaExamples.GHMetaExample> GHMetaExamples.GHMetaExample getMetaExample(Class<T> clazz)
throws IOException {
return retrieve().to("/meta", clazz);
}
#location 3
#vulnerability type THREAD_SAFETY_VIOLATION
|
#fixed code
GitHub(String apiUrl, String login, String oauthAccessToken, String jwtToken, String password,
HttpConnector connector, RateLimitHandler rateLimitHandler, AbuseLimitHandler abuseLimitHandler)
throws IOException {
if (apiUrl.endsWith("/"))
apiUrl = apiUrl.substring(0, apiUrl.length() - 1); // normalize
this.apiUrl = apiUrl;
if (null != connector)
this.connector = connector;
if (oauthAccessToken != null) {
encodedAuthorization = "token " + oauthAccessToken;
} else {
if (jwtToken != null) {
encodedAuthorization = "Bearer " + jwtToken;
} else if (password != null) {
String authorization = (login + ':' + password);
String charsetName = Charsets.UTF_8.name();
encodedAuthorization = "Basic "
+ new String(Base64.encodeBase64(authorization.getBytes(charsetName)), charsetName);
} else {// anonymous access
encodedAuthorization = null;
}
}
users = new ConcurrentHashMap<String, GHUser>();
orgs = new ConcurrentHashMap<String, GHOrganization>();
this.rateLimitHandler = rateLimitHandler;
this.abuseLimitHandler = abuseLimitHandler;
if (login == null && encodedAuthorization != null && jwtToken == null)
login = getMyself().getLogin();
this.login = login;
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
@Override
protected String getApiRoute() {
if (owner == null) {
// Issues returned from search to do not have an owner. Attempt to use url.
return StringUtils.prependIfMissing(getUrl().toString().replace(root.getApiUrl(), ""), "/");
}
return "/repos/" + owner.getOwnerName() + "/" + owner.getName() + "/pulls/" + number;
}
#location 5
#vulnerability type NULL_DEREFERENCE
|
#fixed code
@Override
protected String getApiRoute() {
if (owner == null) {
// Issues returned from search to do not have an owner. Attempt to use url.
final URL url = Objects.requireNonNull(getUrl(), "Missing instance URL!");
return StringUtils.prependIfMissing(url.toString().replace(root.getApiUrl(), ""), "/");
}
return "/repos/" + owner.getOwnerName() + "/" + owner.getName() + "/pulls/" + number;
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
public <T> T to(URL url, Class<T> type) throws IOException {
HttpURLConnection uc = (HttpURLConnection) url.openConnection();
uc.setDoOutput(true);
uc.setRequestProperty("Content-type","application/x-www-form-urlencoded");
uc.setRequestMethod("POST");
StringBuilder body = new StringBuilder();
for (Entry<String, String> e : args.entrySet()) {
if (body.length()>0) body.append('&');
body.append(URLEncoder.encode(e.getKey(),"UTF-8"));
body.append('=');
body.append(URLEncoder.encode(e.getValue(),"UTF-8"));
}
OutputStreamWriter o = new OutputStreamWriter(uc.getOutputStream(), "UTF-8");
o.write(body.toString());
o.close();
try {
InputStreamReader r = new InputStreamReader(uc.getInputStream(), "UTF-8");
if (type==null) return null;
return MAPPER.readValue(r,type);
} catch (IOException e) {
throw (IOException)new IOException(IOUtils.toString(uc.getErrorStream(),"UTF-8")).initCause(e);
}
}
#location 24
#vulnerability type RESOURCE_LEAK
|
#fixed code
public <T> T to(URL url, Class<T> type) throws IOException {
HttpURLConnection uc = (HttpURLConnection) url.openConnection();
uc.setDoOutput(true);
uc.setRequestProperty("Content-type","application/x-www-form-urlencoded");
uc.setRequestMethod("POST");
StringBuilder body = new StringBuilder();
for (Entry<String, String> e : args.entrySet()) {
if (body.length()>0) body.append('&');
body.append(URLEncoder.encode(e.getKey(),"UTF-8"));
body.append('=');
body.append(URLEncoder.encode(e.getValue(),"UTF-8"));
}
OutputStreamWriter o = new OutputStreamWriter(uc.getOutputStream(), "UTF-8");
o.write(body.toString());
o.close();
try {
InputStreamReader r = new InputStreamReader(uc.getInputStream(), "UTF-8");
if (type==null) {
String data = IOUtils.toString(r);
return null;
}
return MAPPER.readValue(r,type);
} catch (IOException e) {
throw (IOException)new IOException(IOUtils.toString(uc.getErrorStream(),"UTF-8")).initCause(e);
}
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
protected String getIssuesApiRoute() {
if (owner == null) {
// Issues returned from search to do not have an owner. Attempt to use url.
return StringUtils.prependIfMissing(getUrl().toString().replace(root.getApiUrl(), ""), "/");
}
return "/repos/" + owner.getOwnerName() + "/" + owner.getName() + "/issues/" + number;
}
#location 4
#vulnerability type NULL_DEREFERENCE
|
#fixed code
protected String getIssuesApiRoute() {
if (owner == null) {
// Issues returned from search to do not have an owner. Attempt to use url.
final URL url = Objects.requireNonNull(getUrl(), "Missing instance URL!");
return StringUtils.prependIfMissing(url.toString().replace(root.getApiUrl(), ""), "/");
}
return "/repos/" + owner.getOwnerName() + "/" + owner.getName() + "/issues/" + number;
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
static PagedIterable<GHDiscussion> readAll(GHTeam team) throws IOException {
return team.root.createRequest()
.setRawUrlPath(team.getUrl().toString() + "/discussions")
.toIterable(GHDiscussion[].class, item -> item.wrapUp(team));
}
#location 3
#vulnerability type NULL_DEREFERENCE
|
#fixed code
static PagedIterable<GHDiscussion> readAll(GHTeam team) throws IOException {
return team.root.createRequest()
.setRawUrlPath(getRawUrlPath(team, null))
.toIterable(GHDiscussion[].class, item -> item.wrapUp(team));
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
static GHDiscussion read(GHTeam team, long discussionNumber) throws IOException {
return team.root.createRequest()
.setRawUrlPath(team.getUrl().toString() + "/discussions/" + discussionNumber)
.fetch(GHDiscussion.class)
.wrapUp(team);
}
#location 3
#vulnerability type NULL_DEREFERENCE
|
#fixed code
static GHDiscussion read(GHTeam team, long discussionNumber) throws IOException {
return team.root.createRequest()
.setRawUrlPath(getRawUrlPath(team, discussionNumber))
.fetch(GHDiscussion.class)
.wrapUp(team);
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
public void delete() throws IOException {
team.root.createRequest()
.method("DELETE")
.setRawUrlPath(team.getUrl().toString() + "/discussions/" + number)
.send();
}
#location 4
#vulnerability type NULL_DEREFERENCE
|
#fixed code
public void delete() throws IOException {
team.root.createRequest().method("DELETE").setRawUrlPath(getRawUrlPath(team, number)).send();
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
public <T> T to(URL url, Class<T> type) throws IOException {
HttpURLConnection uc = (HttpURLConnection) url.openConnection();
uc.setDoOutput(true);
uc.setRequestProperty("Content-type","application/x-www-form-urlencoded");
uc.setRequestMethod("POST");
StringBuilder body = new StringBuilder();
for (Entry<String, String> e : args.entrySet()) {
if (body.length()>0) body.append('&');
body.append(URLEncoder.encode(e.getKey(),"UTF-8"));
body.append('=');
body.append(URLEncoder.encode(e.getValue(),"UTF-8"));
}
OutputStreamWriter o = new OutputStreamWriter(uc.getOutputStream(), "UTF-8");
o.write(body.toString());
o.close();
try {
InputStreamReader r = new InputStreamReader(uc.getInputStream(), "UTF-8");
if (type==null) return null;
return MAPPER.readValue(r,type);
} catch (IOException e) {
throw (IOException)new IOException(IOUtils.toString(uc.getErrorStream(),"UTF-8")).initCause(e);
}
}
#location 24
#vulnerability type RESOURCE_LEAK
|
#fixed code
public <T> T to(URL url, Class<T> type) throws IOException {
HttpURLConnection uc = (HttpURLConnection) url.openConnection();
uc.setDoOutput(true);
uc.setRequestProperty("Content-type","application/x-www-form-urlencoded");
uc.setRequestMethod("POST");
StringBuilder body = new StringBuilder();
for (Entry<String, String> e : args.entrySet()) {
if (body.length()>0) body.append('&');
body.append(URLEncoder.encode(e.getKey(),"UTF-8"));
body.append('=');
body.append(URLEncoder.encode(e.getValue(),"UTF-8"));
}
OutputStreamWriter o = new OutputStreamWriter(uc.getOutputStream(), "UTF-8");
o.write(body.toString());
o.close();
try {
InputStreamReader r = new InputStreamReader(uc.getInputStream(), "UTF-8");
if (type==null) {
String data = IOUtils.toString(r);
return null;
}
return MAPPER.readValue(r,type);
} catch (IOException e) {
throw (IOException)new IOException(IOUtils.toString(uc.getErrorStream(),"UTF-8")).initCause(e);
}
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
@Test
public void testWindowPeer() throws Exception {
if (Platform.isMacOSX() ||
System.getProperty("java.version)").matches("1\\.6\\..*")) {
// Oracle Java and jawt: it's complicated.
// See http://forum.lwjgl.org/index.php?topic=4326.0
// OpenJDK 6 + Linux seem problematic too.
return;
}
assertEquals(6 * Pointer.SIZE, BridJ.sizeOf(JAWT_DrawingSurface.class));
assertEquals(4 * 4, BridJ.sizeOf(JAWT_Rectangle.class));
//assertEquals(4 + 5 * Pointer.SIZE, BridJ.sizeOf(JAWT.class));
//assertEquals(2 * 4 * 4 + 4 + Pointer.SIZE, BridJ.sizeOf(JAWT_DrawingSurfaceInfo.class));
Frame f = new Frame();
f.pack();
f.setVisible(true);
Thread.sleep(500);
long p = JAWTUtils.getNativePeerHandle(f);
assertTrue(p != 0);
f.setVisible(false);
}
#location 4
#vulnerability type NULL_DEREFERENCE
|
#fixed code
@Test
public void testWindowPeer() throws Exception {
if (Platform.isMacOSX() ||
System.getProperty("java.version").matches("1\\.6\\..*")) {
// Oracle Java and jawt: it's complicated.
// See http://forum.lwjgl.org/index.php?topic=4326.0
// OpenJDK 6 + Linux seem problematic too.
return;
}
assertEquals(6 * Pointer.SIZE, BridJ.sizeOf(JAWT_DrawingSurface.class));
assertEquals(4 * 4, BridJ.sizeOf(JAWT_Rectangle.class));
//assertEquals(4 + 5 * Pointer.SIZE, BridJ.sizeOf(JAWT.class));
//assertEquals(2 * 4 * 4 + 4 + Pointer.SIZE, BridJ.sizeOf(JAWT_DrawingSurfaceInfo.class));
Frame f = new Frame();
f.pack();
f.setVisible(true);
Thread.sleep(500);
long p = JAWTUtils.getNativePeerHandle(f);
assertTrue(p != 0);
f.setVisible(false);
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
private HttpClient getHttpClient(PrintStream logger) {
HttpClient client = null;
boolean ignoreUnverifiedSSL = ignoreUnverifiedSSLPeer;
String url = stashServerBaseUrl;
DescriptorImpl descriptor = getDescriptor();
if ("".equals(url) || url == null) {
url = descriptor.getStashRootUrl();
}
if (!ignoreUnverifiedSSL) {
ignoreUnverifiedSSL = descriptor.isIgnoreUnverifiedSsl();
}
if (url.startsWith("https")
&& ignoreUnverifiedSSL) {
// add unsafe trust manager to avoid thrown
// SSLPeerUnverifiedException
try {
HttpClientBuilder builder = HttpClientBuilder.create();
TrustStrategy easyStrategy = new TrustStrategy() {
public boolean isTrusted(X509Certificate[] chain, String authType)
throws CertificateException {
return true;
}
};
SSLContext sslContext = SSLContexts.custom()
.loadTrustMaterial(null, easyStrategy)
.useTLS().build();
SSLConnectionSocketFactory sslConnSocketFactory
= new SSLConnectionSocketFactory(sslContext,
SSLConnectionSocketFactory.ALLOW_ALL_HOSTNAME_VERIFIER);
builder.setSSLSocketFactory(sslConnSocketFactory);
Registry<ConnectionSocketFactory> registry
= RegistryBuilder.<ConnectionSocketFactory>create()
.register("https", sslConnSocketFactory)
.build();
HttpClientConnectionManager ccm
= new BasicHttpClientConnectionManager(registry);
builder.setConnectionManager(ccm);
client = builder.build();
} catch (NoSuchAlgorithmException nsae) {
logger.println("Couldn't establish SSL context:");
nsae.printStackTrace(logger);
} catch (KeyManagementException kme) {
logger.println("Couldn't initialize SSL context:");
kme.printStackTrace(logger);
} catch (KeyStoreException kse) {
logger.println("Couldn't initialize SSL context:");
kse.printStackTrace(logger);
} finally {
if (client == null) {
logger.println("Trying with safe trust manager, instead!");
client = HttpClientBuilder.create().build();
}
}
} else {
client = HttpClientBuilder.create().build();
}
ProxyConfiguration proxy = Jenkins.getInstance().proxy;
if(proxy != null && !proxy.name.isEmpty() && !proxy.name.startsWith("http") && !isHostOnNoProxyList(proxy)){
SchemeRegistry schemeRegistry = client.getConnectionManager().getSchemeRegistry();
schemeRegistry.register(new Scheme("http", proxy.port, new PlainSocketFactory()));
client.getParams().setParameter(ConnRoutePNames.DEFAULT_PROXY, new HttpHost(proxy.name, proxy.port));
}
return client;
}
#location 12
#vulnerability type NULL_DEREFERENCE
|
#fixed code
private HttpClient getHttpClient(PrintStream logger) throws Exception {
boolean ignoreUnverifiedSSL = ignoreUnverifiedSSLPeer;
String stashServer = stashServerBaseUrl;
DescriptorImpl descriptor = getDescriptor();
if ("".equals(stashServer) || stashServer == null) {
stashServer = descriptor.getStashRootUrl();
}
if (!ignoreUnverifiedSSL) {
ignoreUnverifiedSSL = descriptor.isIgnoreUnverifiedSsl();
}
URL url = new URL(stashServer);
HttpClientBuilder builder = HttpClientBuilder.create();
if (url.getProtocol().equals("https")
&& ignoreUnverifiedSSL) {
// add unsafe trust manager to avoid thrown
// SSLPeerUnverifiedException
try {
TrustStrategy easyStrategy = new TrustStrategy() {
public boolean isTrusted(X509Certificate[] chain, String authType)
throws CertificateException {
return true;
}
};
SSLContext sslContext = SSLContexts.custom()
.loadTrustMaterial(null, easyStrategy)
.useTLS().build();
SSLConnectionSocketFactory sslConnSocketFactory
= new SSLConnectionSocketFactory(sslContext,
SSLConnectionSocketFactory.ALLOW_ALL_HOSTNAME_VERIFIER);
builder.setSSLSocketFactory(sslConnSocketFactory);
Registry<ConnectionSocketFactory> registry
= RegistryBuilder.<ConnectionSocketFactory>create()
.register("https", sslConnSocketFactory)
.build();
HttpClientConnectionManager ccm
= new BasicHttpClientConnectionManager(registry);
builder.setConnectionManager(ccm);
} catch (NoSuchAlgorithmException nsae) {
logger.println("Couldn't establish SSL context:");
nsae.printStackTrace(logger);
} catch (KeyManagementException kme) {
logger.println("Couldn't initialize SSL context:");
kme.printStackTrace(logger);
} catch (KeyStoreException kse) {
logger.println("Couldn't initialize SSL context:");
kse.printStackTrace(logger);
}
}
// Configure the proxy, if needed
// Using the Jenkins methods handles the noProxyHost settings
ProxyConfiguration proxyConfig = Jenkins.getInstance().proxy;
if (proxyConfig != null) {
Proxy proxy = proxyConfig.createProxy(url.getHost());
if (proxy != null && proxy.type() == Proxy.Type.HTTP) {
SocketAddress addr = proxy.address();
if (addr != null && addr instanceof InetSocketAddress) {
InetSocketAddress proxyAddr = (InetSocketAddress) addr;
HttpHost proxyHost = new HttpHost(proxyAddr.getAddress().getHostAddress(), proxyAddr.getPort());
builder = builder.setProxy(proxyHost);
String proxyUser = proxyConfig.getUserName();
if (proxyUser != null) {
String proxyPass = proxyConfig.getPassword();
CredentialsProvider cred = new BasicCredentialsProvider();
cred.setCredentials(new AuthScope(proxyHost),
new UsernamePasswordCredentials(proxyUser, proxyPass));
builder = builder
.setDefaultCredentialsProvider(cred)
.setProxyAuthenticationStrategy(new ProxyAuthenticationStrategy());
}
}
}
}
return builder.build();
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
public static void main(String[] args) {
AppUtil appUtil = new AppUtil();
AService service = (AService) appUtil.getComponentInstance("aService");
AggregateRootA aggregateRootA = service.getAggregateRootA("11");
DomainMessage res = service.commandA("11", aggregateRootA, 100);
long start = System.currentTimeMillis();
int result = 0;
DomainMessage res1 = (DomainMessage) res.getBlockEventResult();
if (res1.getBlockEventResult() != null)
result = (Integer) res1.getBlockEventResult();
long stop = System.currentTimeMillis();
Assert.assertEquals(result, 400);
System.out.print("\n ok \n" + result + (stop - start));
}
#location 10
#vulnerability type NULL_DEREFERENCE
|
#fixed code
public static void main(String[] args) {
AppUtil appUtil = new AppUtil();
AService service = (AService) appUtil.getComponentInstance("aService");
AggregateRootA aggregateRootA = service.getAggregateRootA("11");
DomainMessage res = service.commandA("11", aggregateRootA, 100);
long start = System.currentTimeMillis();
int result = 0;
DomainMessage res1 = (DomainMessage) res.getBlockEventResult();
if (res1 != null && res1.getBlockEventResult() != null)
result = (Integer) res1.getBlockEventResult();
long stop = System.currentTimeMillis();
Assert.assertEquals(result, 400);
System.out.print("\n ok \n" + result + " time:" + (stop - start));
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
public boolean doExists(String name, Locale locale, String path) throws Exception {
return file != null && file.exists() && new ZipFile(file).getEntry(name) != null;
}
#location 2
#vulnerability type RESOURCE_LEAK
|
#fixed code
public boolean doExists(String name, Locale locale, String path) throws Exception {
if (file != null && file.exists()) {
ZipFile zipFile = new ZipFile(file);
try {
return zipFile.getEntry(name) != null;
} finally {
zipFile.close();
}
}
return false;
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
public long getLastModified() {
try {
JarFile zipFile = new JarFile(file);
return zipFile.getEntry(getName()).getTime();
} catch (Throwable e) {
return super.getLastModified();
}
}
#location 4
#vulnerability type RESOURCE_LEAK
|
#fixed code
public long getLastModified() {
try {
JarFile jarFile = new JarFile(file);
return jarFile.getEntry(getName()).getTime();
} catch (Throwable e) {
return super.getLastModified();
}
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
public Template extend(String name, Locale locale, String encoding) throws IOException, ParseException {
if (name == null || name.length() == 0) {
throw new IllegalArgumentException("include template name == null");
}
String macro = null;
int i = name.indexOf('#');
if (i > 0) {
macro = name.substring(i + 1);
name = name.substring(0, i);
}
Template template = Context.getContext().getTemplate();
if (template != null) {
if (encoding == null || encoding.length() == 0) {
encoding = template.getEncoding();
}
name = UrlUtils.relativeUrl(name, template.getName());
if (locale == null) {
locale = template.getLocale();
}
}
Template extend = engine.getTemplate(name);
if (macro != null && macro.length() > 0) {
extend = extend.getMacros().get(macro);
}
if (template != null && template == extend) {
throw new IllegalStateException("The template " + template.getName() + " can not be recursive extending the self template.");
}
Context.getContext().putAll(template.getMacros());
return extend;
}
#location 28
#vulnerability type NULL_DEREFERENCE
|
#fixed code
public Template extend(String name, Locale locale, String encoding) throws IOException, ParseException {
if (name == null || name.length() == 0) {
throw new IllegalArgumentException("include template name == null");
}
String macro = null;
int i = name.indexOf('#');
if (i > 0) {
macro = name.substring(i + 1);
name = name.substring(0, i);
}
Template template = Context.getContext().getTemplate();
if (template != null) {
if (encoding == null || encoding.length() == 0) {
encoding = template.getEncoding();
}
name = UrlUtils.relativeUrl(name, template.getName());
if (locale == null) {
locale = template.getLocale();
}
}
Template extend = engine.getTemplate(name);
if (macro != null && macro.length() > 0) {
extend = extend.getMacros().get(macro);
}
if (template != null) {
if (template == extend) {
throw new IllegalStateException("The template " + template.getName() + " can not be recursive extending the self template.");
}
Context.getContext().putAll(template.getMacros());
}
return extend;
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
public Template parse(String name, String encoding) throws IOException, ParseException {
if (name == null || name.length() == 0) {
throw new IllegalArgumentException("include template name == null");
}
String macro = null;
int i = name.indexOf('#');
if (i > 0) {
macro = name.substring(i + 1);
name = name.substring(0, i);
}
Template template = Context.getContext().getTemplate();
if (template != null) {
if (encoding == null || encoding.length() == 0) {
encoding = template.getEncoding();
}
name = UrlUtils.relativeUrl(name, template.getName());
}
name = UrlUtils.cleanUrl(name.trim());
template = engine.getTemplate(name, encoding);
if (macro != null && macro.length() > 0) {
return template.getMacros().get(macro);
}
return template;
}
#location 18
#vulnerability type NULL_DEREFERENCE
|
#fixed code
public Template parse(String name, String encoding) throws IOException, ParseException {
if (name == null || name.length() == 0) {
throw new IllegalArgumentException("include template name == null");
}
String macro = null;
int i = name.indexOf('#');
if (i > 0) {
macro = name.substring(i + 1);
name = name.substring(0, i);
}
Template template = Context.getContext().getTemplate();
if (template != null) {
if (encoding == null || encoding.length() == 0) {
encoding = template.getEncoding();
}
name = UrlUtils.relativeUrl(name, template.getName());
}
template = engine.getTemplate(name, encoding);
if (macro != null && macro.length() > 0) {
return template.getMacros().get(macro);
}
return template;
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
public boolean doExists(String name, Locale locale, String path) throws Exception {
return file != null && file.exists() && new JarFile(file).getEntry(name) != null;
}
#location 2
#vulnerability type RESOURCE_LEAK
|
#fixed code
public boolean doExists(String name, Locale locale, String path) throws Exception {
if (file != null && file.exists()) {
JarFile jarFile = new JarFile(file);
try {
return jarFile.getEntry(name) != null;
} finally {
jarFile.close();
}
}
return false;
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
public Template include(String name, Locale locale, String encoding) throws IOException, ParseException {
if (name == null || name.length() == 0) {
throw new IllegalArgumentException("include template name == null");
}
String macro = null;
int i = name.indexOf('#');
if (i > 0) {
macro = name.substring(i + 1);
name = name.substring(0, i);
}
Template template = Context.getContext().getTemplate();
if (template != null) {
if (encoding == null || encoding.length() == 0) {
encoding = template.getEncoding();
}
name = UrlUtils.relativeUrl(name, template.getName());
if (locale == null) {
locale = template.getLocale();
}
}
Template include = engine.getTemplate(name, locale, encoding);
if (macro != null && macro.length() > 0) {
include = include.getMacros().get(macro);
}
if (include == template) {
throw new IllegalStateException("The template " + template.getName() + " can not be recursive including the self template.");
}
return include;
}
#location 26
#vulnerability type NULL_DEREFERENCE
|
#fixed code
public Template include(String name, Locale locale, String encoding) throws IOException, ParseException {
if (name == null || name.length() == 0) {
throw new IllegalArgumentException("include template name == null");
}
String macro = null;
int i = name.indexOf('#');
if (i > 0) {
macro = name.substring(i + 1);
name = name.substring(0, i);
}
Template template = Context.getContext().getTemplate();
if (template != null) {
if (encoding == null || encoding.length() == 0) {
encoding = template.getEncoding();
}
name = UrlUtils.relativeUrl(name, template.getName());
if (locale == null) {
locale = template.getLocale();
}
}
Template include = engine.getTemplate(name, locale, encoding);
if (macro != null && macro.length() > 0) {
include = include.getMacros().get(macro);
}
if (template != null && template == include) {
throw new IllegalStateException("The template " + template.getName() + " can not be recursive including the self template.");
}
return include;
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
public static Object decodeToObject(
String encodedObject, int options, final ClassLoader loader )
throws java.io.IOException, java.lang.ClassNotFoundException {
// Decode and gunzip if necessary
byte[] objBytes = decode( encodedObject, options );
java.io.ByteArrayInputStream bais = null;
java.io.ObjectInputStream ois = null;
Object obj = null;
try {
bais = new java.io.ByteArrayInputStream( objBytes );
// If no custom class loader is provided, use Java's builtin OIS.
if( loader == null ){
ois = new java.io.ObjectInputStream( bais );
} // end if: no loader provided
// Else make a customized object input stream that uses
// the provided class loader.
else {
ois = new java.io.ObjectInputStream(bais){
@Override
public Class<?> resolveClass(java.io.ObjectStreamClass streamClass)
throws java.io.IOException, ClassNotFoundException {
Class<?> c = Class.forName(streamClass.getName(), false, loader);
if( c == null ){
return super.resolveClass(streamClass);
} else {
return c; // Class loader knows of this class.
} // end else: not null
} // end resolveClass
}; // end ois
} // end else: no custom class loader
obj = ois.readObject();
} // end try
catch( java.io.IOException e ) {
throw e; // Catch and throw in order to execute finally{}
} // end catch
catch( java.lang.ClassNotFoundException e ) {
throw e; // Catch and throw in order to execute finally{}
} // end catch
finally {
try{ bais.close(); } catch( Exception e ){}
try{ ois.close(); } catch( Exception e ){}
} // end finally
return obj;
}
#location 47
#vulnerability type NULL_DEREFERENCE
|
#fixed code
public static Object decodeToObject(
String encodedObject, int options, final ClassLoader loader )
throws java.io.IOException, java.lang.ClassNotFoundException {
// Decode and gunzip if necessary
byte[] objBytes = decode( encodedObject, options );
java.io.ByteArrayInputStream bais = null;
java.io.ObjectInputStream ois = null;
Object obj = null;
try {
bais = new java.io.ByteArrayInputStream( objBytes );
// If no custom class loader is provided, use Java's builtin OIS.
if( loader == null ){
ois = new java.io.ObjectInputStream( bais );
} // end if: no loader provided
// Else make a customized object input stream that uses
// the provided class loader.
else {
ois = new java.io.ObjectInputStream(bais){
@Override
public Class<?> resolveClass(java.io.ObjectStreamClass streamClass)
throws java.io.IOException, ClassNotFoundException {
Class<?> c = Class.forName(streamClass.getName(), false, loader);
if( c == null ){
return super.resolveClass(streamClass);
} else {
return c; // Class loader knows of this class.
} // end else: not null
} // end resolveClass
}; // end ois
} // end else: no custom class loader
obj = ois.readObject();
} // end try
catch( java.io.IOException e ) {
throw e; // Catch and throw in order to execute finally{}
} // end catch
catch( java.lang.ClassNotFoundException e ) {
throw e; // Catch and throw in order to execute finally{}
} // end catch
finally {
try {
if (bais != null) bais.close();
} finally {
if (ois != null) ois.close();
}
} // end finally
return obj;
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
@Test
public void testException() throws Exception {
boolean profile = "true".equals(System.getProperty("profile"));
if (! profile)
System.out.println("========httl-exception.properties========");
Engine engine = Engine.getEngine("httl-exception.properties");
String dir = engine.getProperty("template.directory", "");
if (dir.length() > 0 && dir.startsWith("/")) {
dir = dir.substring(1);
}
if (dir.length() > 0 && ! dir.endsWith("/")) {
dir += "/";
}
File directory = new File(this.getClass().getClassLoader().getResource(dir + "templates/").getFile());
assertTrue(directory.isDirectory());
File[] files = directory.listFiles();
for (int i = 0, n = files.length; i < n; i ++) {
File file = files[i];
System.out.println(file.getName());
URL url = this.getClass().getClassLoader().getResource(dir + "results/" + file.getName() + ".txt");
if (url == null) {
throw new FileNotFoundException("Not found file: " + dir + "results/" + file.getName() + ".txt");
}
File result = new File(url.getFile());
if (! result.exists()) {
throw new FileNotFoundException("Not found file: " + result.getAbsolutePath());
}
try {
engine.getTemplate("/templates/" + file.getName());
fail(file.getName());
} catch (ParseException e) {
if (! profile) {
String message = e.getMessage();
assertTrue(StringUtils.isNotEmpty(message));
List<String> expected = IOUtils.readLines(new FileReader(result));
assertTrue(expected != null && expected.size() > 0);
for (String part : expected) {
assertTrue(StringUtils.isNotEmpty(part));
part = StringUtils.unescapeString(part).trim();
assertTrue(file.getName() + ", exception message: \"" + message + "\" not contains: \"" + part + "\"", message.contains(part));
}
}
}
}
}
#location 17
#vulnerability type NULL_DEREFERENCE
|
#fixed code
@Test
public void testException() throws Exception {
boolean profile = "true".equals(System.getProperty("profile"));
Engine engine = Engine.getEngine("httl-exception.properties");
String dir = engine.getProperty("template.directory", "");
if (dir.length() > 0 && dir.startsWith("/")) {
dir = dir.substring(1);
}
if (dir.length() > 0 && ! dir.endsWith("/")) {
dir += "/";
}
URL url = this.getClass().getClassLoader().getResource(dir + "results/" + templateName + ".txt");
if (url == null) {
throw new FileNotFoundException("Not found file: " + dir + "results/" + templateName + ".txt");
}
File result = new File(url.getFile());
if (! result.exists()) {
throw new FileNotFoundException("Not found file: " + result.getAbsolutePath());
}
try {
engine.getTemplate("/templates/" + templateName);
fail(templateName);
} catch (ParseException e) {
if (! profile) {
String message = e.getMessage();
assertTrue(StringUtils.isNotEmpty(message));
List<String> expected = IOUtils.readLines(new FileReader(result));
assertTrue(expected != null && expected.size() > 0);
for (String part : expected) {
assertTrue(StringUtils.isNotEmpty(part));
part = StringUtils.unescapeString(part).trim();
assertTrue(templateName + ", exception message: \"" + message + "\" not contains: \"" + part + "\"", message.contains(part));
}
}
}
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
public long getLength() {
try {
JarFile jarFile = new JarFile(file);
return jarFile.getEntry(getName()).getSize();
} catch (IOException e) {
return super.getLength();
}
}
#location 4
#vulnerability type RESOURCE_LEAK
|
#fixed code
public long getLength() {
try {
JarFile jarFile = new JarFile(file);
try {
return jarFile.getEntry(getName()).getSize();
} finally {
jarFile.close();
}
} catch (IOException e) {
return super.getLength();
}
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
public static void setServletContext(ServletContext servletContext) {
if (servletContext == null) {
return;
}
if (ServletLoader.getServletContext() == null) {
ServletLoader.setServletContext(servletContext);
}
if (ENGINE == null) {
synchronized (WebEngine.class) {
if (ENGINE == null) { // double check
Properties properties = new Properties();
String config = servletContext.getInitParameter(CONFIG_KEY);
if (config == null || config.length() == 0) {
config = WEBINF_CONFIG;
}
if (config.startsWith("/")) {
InputStream in = servletContext.getResourceAsStream(config);
if (in != null) {
try {
properties.load(in);
} catch (IOException e) {
throw new IllegalStateException("Failed to load httl config " + config + " in wepapp. cause: " + e.getMessage(), e);
}
} else if (servletContext.getInitParameter(CONFIG_KEY) != null) { // 用户主动配置错误提醒
throw new IllegalStateException("Not found httl config " + config + " in wepapp.");
} else {
config = null;
}
}
ENGINE = Engine.getEngine(config, addProperties(properties));
logConfigPath(ENGINE, servletContext, config);
}
}
}
}
#location 5
#vulnerability type THREAD_SAFETY_VIOLATION
|
#fixed code
public static void setServletContext(ServletContext servletContext) {
if (servletContext == null) {
return;
}
if (ServletLoader.getServletContext() == null) {
ServletLoader.setServletContext(servletContext);
}
if (ENGINE == null) {
synchronized (WebEngine.class) {
if (ENGINE == null) { // double check
Properties properties = new Properties();
String config = servletContext.getInitParameter(CONFIG_KEY);
if (StringUtils.isEmpty(config)) {
config = WEBINF_CONFIG;
}
if (config.startsWith("/")) {
InputStream in = servletContext.getResourceAsStream(config);
if (in != null) {
try {
properties.load(in);
} catch (IOException e) {
throw new IllegalStateException("Failed to load httl config " + config + " in wepapp. cause: " + e.getMessage(), e);
}
} else if (servletContext.getInitParameter(CONFIG_KEY) != null) { // 用户主动配置错误提醒
throw new IllegalStateException("Not found httl config " + config + " in wepapp.");
} else {
config = null;
}
}
ENGINE = Engine.getEngine(config, addProperties(properties));
logConfigPath(ENGINE, servletContext, config);
}
}
}
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
public static String encodeObject( java.io.Serializable serializableObject, int options )
throws java.io.IOException {
if( serializableObject == null ){
throw new NullPointerException( "Cannot serialize a null object." );
} // end if: null
// Streams
java.io.ByteArrayOutputStream baos = null;
java.io.OutputStream b64os = null;
java.util.zip.GZIPOutputStream gzos = null;
java.io.ObjectOutputStream oos = null;
try {
// ObjectOutputStream -> (GZIP) -> Base64 -> ByteArrayOutputStream
baos = new java.io.ByteArrayOutputStream();
b64os = new Base64.OutputStream( baos, ENCODE | options );
if( (options & GZIP) != 0 ){
// Gzip
gzos = new java.util.zip.GZIPOutputStream(b64os);
oos = new java.io.ObjectOutputStream( gzos );
} else {
// Not gzipped
oos = new java.io.ObjectOutputStream( b64os );
}
oos.writeObject( serializableObject );
} // end try
catch( java.io.IOException e ) {
// Catch it and then throw it immediately so that
// the finally{} block is called for cleanup.
throw e;
} // end catch
finally {
try{ oos.close(); } catch( Exception e ){}
try{ gzos.close(); } catch( Exception e ){}
try{ b64os.close(); } catch( Exception e ){}
try{ baos.close(); } catch( Exception e ){}
} // end finally
// Return value according to relevant encoding.
try {
return new String( baos.toByteArray(), PREFERRED_ENCODING );
} // end try
catch (java.io.UnsupportedEncodingException uue){
// Fall back to some Java default
return new String( baos.toByteArray() );
} // end catch
}
#location 35
#vulnerability type NULL_DEREFERENCE
|
#fixed code
public static String encodeObject( java.io.Serializable serializableObject, int options )
throws java.io.IOException {
if( serializableObject == null ){
throw new NullPointerException( "Cannot serialize a null object." );
} // end if: null
// Streams
java.io.ByteArrayOutputStream baos = null;
java.io.OutputStream b64os = null;
java.util.zip.GZIPOutputStream gzos = null;
java.io.ObjectOutputStream oos = null;
try {
// ObjectOutputStream -> (GZIP) -> Base64 -> ByteArrayOutputStream
baos = new java.io.ByteArrayOutputStream();
b64os = new Base64.OutputStream( baos, ENCODE | options );
if( (options & GZIP) != 0 ){
// Gzip
gzos = new java.util.zip.GZIPOutputStream(b64os);
oos = new java.io.ObjectOutputStream( gzos );
} else {
// Not gzipped
oos = new java.io.ObjectOutputStream( b64os );
}
oos.writeObject( serializableObject );
} // end try
catch( java.io.IOException e ) {
// Catch it and then throw it immediately so that
// the finally{} block is called for cleanup.
throw e;
} // end catch
finally {
try {
if (oos != null) oos.close();
} finally {
try {
if (gzos != null) gzos.close();
} finally {
try {
if (b64os != null) b64os.close();
} finally {
if (baos != null) baos.close();
}
}
}
} // end finally
// Return value according to relevant encoding.
try {
return new String( baos.toByteArray(), PREFERRED_ENCODING );
} // end try
catch (java.io.UnsupportedEncodingException uue){
// Fall back to some Java default
return new String( baos.toByteArray() );
} // end catch
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
private static String getRefValue(Properties result, String v) {
if (v != null) {
while (v.startsWith(REF)) {
String ref = v.substring(1);
v = result.getProperty(ref);
if (v == null) {
v = System.getProperty(ref);
}
}
}
return v == null ? "" : v;
}
#location 3
#vulnerability type NULL_DEREFERENCE
|
#fixed code
private static String getRefValue(Properties result, String v) {
while (v != null && v.startsWith(REF)) {
String ref = v.substring(1);
v = result.getProperty(ref);
if (v == null) {
v = System.getProperty(ref);
}
}
return v == null ? "" : v;
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
public long getLength() {
try {
ZipFile zipFile = new ZipFile(file);
return zipFile.getEntry(getName()).getSize();
} catch (IOException e) {
return super.getLength();
}
}
#location 4
#vulnerability type RESOURCE_LEAK
|
#fixed code
public long getLength() {
try {
ZipFile zipFile = new ZipFile(file);
try {
return zipFile.getEntry(getName()).getSize();
} finally {
zipFile.close();
}
} catch (IOException e) {
return super.getLength();
}
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
public static void setServletContext(ServletContext servletContext) {
if (servletContext == null) {
return;
}
if (ServletLoader.getServletContext() == null) {
ServletLoader.setServletContext(servletContext);
}
if (ENGINE == null) {
synchronized (WebEngine.class) {
if (ENGINE == null) { // double check
Properties properties = new Properties();
String config = servletContext.getInitParameter(CONFIG_KEY);
if (config == null || config.length() == 0) {
config = WEBINF_CONFIG;
}
if (config.startsWith("/")) {
InputStream in = servletContext.getResourceAsStream(config);
if (in != null) {
try {
properties.load(in);
} catch (IOException e) {
throw new IllegalStateException("Failed to load httl config " + config + " in wepapp. cause: " + e.getMessage(), e);
}
} else if (servletContext.getInitParameter(CONFIG_KEY) != null) { // 用户主动配置错误提醒
throw new IllegalStateException("Not found httl config " + config + " in wepapp.");
} else {
config = null;
}
}
ENGINE = Engine.getEngine(config, addProperties(properties));
logConfigPath(ENGINE, servletContext, config);
}
}
}
}
#location 6
#vulnerability type THREAD_SAFETY_VIOLATION
|
#fixed code
public static void setServletContext(ServletContext servletContext) {
if (servletContext == null) {
return;
}
if (ServletLoader.getServletContext() == null) {
ServletLoader.setServletContext(servletContext);
}
if (ENGINE == null) {
synchronized (WebEngine.class) {
if (ENGINE == null) { // double check
Properties properties = new Properties();
String config = servletContext.getInitParameter(CONFIG_KEY);
if (StringUtils.isEmpty(config)) {
config = WEBINF_CONFIG;
}
if (config.startsWith("/")) {
InputStream in = servletContext.getResourceAsStream(config);
if (in != null) {
try {
properties.load(in);
} catch (IOException e) {
throw new IllegalStateException("Failed to load httl config " + config + " in wepapp. cause: " + e.getMessage(), e);
}
} else if (servletContext.getInitParameter(CONFIG_KEY) != null) { // 用户主动配置错误提醒
throw new IllegalStateException("Not found httl config " + config + " in wepapp.");
} else {
config = null;
}
}
ENGINE = Engine.getEngine(config, addProperties(properties));
logConfigPath(ENGINE, servletContext, config);
}
}
}
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
public static byte[] decode( String s, int options ) throws java.io.IOException {
if( s == null ){
throw new NullPointerException( "Input string was null." );
} // end if
byte[] bytes;
try {
bytes = s.getBytes( PREFERRED_ENCODING );
} // end try
catch( java.io.UnsupportedEncodingException uee ) {
bytes = s.getBytes();
} // end catch
//</change>
// Decode
bytes = decode( bytes, 0, bytes.length, options );
// Check to see if it's gzip-compressed
// GZIP Magic Two-Byte Number: 0x8b1f (35615)
boolean dontGunzip = (options & DONT_GUNZIP) != 0;
if( (bytes != null) && (bytes.length >= 4) && (!dontGunzip) ) {
int head = ((int)bytes[0] & 0xff) | ((bytes[1] << 8) & 0xff00);
if( java.util.zip.GZIPInputStream.GZIP_MAGIC == head ) {
java.io.ByteArrayInputStream bais = null;
java.util.zip.GZIPInputStream gzis = null;
java.io.ByteArrayOutputStream baos = null;
byte[] buffer = new byte[2048];
int length = 0;
try {
baos = new java.io.ByteArrayOutputStream();
bais = new java.io.ByteArrayInputStream( bytes );
gzis = new java.util.zip.GZIPInputStream( bais );
while( ( length = gzis.read( buffer ) ) >= 0 ) {
baos.write(buffer,0,length);
} // end while: reading input
// No error? Get new bytes.
bytes = baos.toByteArray();
} // end try
catch( java.io.IOException e ) {
// Just return originally-decoded bytes
} // end catch
finally {
try{ baos.close(); } catch( Exception e ){}
try{ gzis.close(); } catch( Exception e ){}
try{ bais.close(); } catch( Exception e ){}
} // end finally
} // end if: gzipped
} // end if: bytes.length >= 2
return bytes;
}
#location 50
#vulnerability type NULL_DEREFERENCE
|
#fixed code
public static byte[] decode( String s, int options ) throws java.io.IOException {
if( s == null ){
throw new NullPointerException( "Input string was null." );
} // end if
byte[] bytes;
try {
bytes = s.getBytes( PREFERRED_ENCODING );
} // end try
catch( java.io.UnsupportedEncodingException uee ) {
bytes = s.getBytes();
} // end catch
//</change>
// Decode
bytes = decode( bytes, 0, bytes.length, options );
// Check to see if it's gzip-compressed
// GZIP Magic Two-Byte Number: 0x8b1f (35615)
boolean dontGunzip = (options & DONT_GUNZIP) != 0;
if( (bytes != null) && (bytes.length >= 4) && (!dontGunzip) ) {
int head = ((int)bytes[0] & 0xff) | ((bytes[1] << 8) & 0xff00);
if( java.util.zip.GZIPInputStream.GZIP_MAGIC == head ) {
java.io.ByteArrayInputStream bais = null;
java.util.zip.GZIPInputStream gzis = null;
java.io.ByteArrayOutputStream baos = null;
byte[] buffer = new byte[2048];
int length = 0;
try {
baos = new java.io.ByteArrayOutputStream();
bais = new java.io.ByteArrayInputStream( bytes );
gzis = new java.util.zip.GZIPInputStream( bais );
while( ( length = gzis.read( buffer ) ) >= 0 ) {
baos.write(buffer,0,length);
} // end while: reading input
// No error? Get new bytes.
bytes = baos.toByteArray();
} // end try
catch( java.io.IOException e ) {
// Just return originally-decoded bytes
} // end catch
finally {
try {
if (baos != null) baos.close();
} finally {
try {
if (gzis != null) gzis.close();
} finally {
if (bais != null) bais.close();
}
}
} // end finally
} // end if: gzipped
} // end if: bytes.length >= 2
return bytes;
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
public boolean doExists(String name, Locale locale, String path) throws Exception {
InputStream in = new URL(path).openStream();
try {
return in != null;
} finally {
in.close();
}
}
#location 6
#vulnerability type NULL_DEREFERENCE
|
#fixed code
public boolean doExists(String name, Locale locale, String path) throws Exception {
InputStream in = new URL(path).openStream();
try {
return in != null;
} finally {
if (in != null)
in.close();
}
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
public void init() {
defaultFilterVariable = "$" + filterVariable;
defaultFormatterVariable = "$" + formatterVariable;
if (importVariables != null && importVariables.length > 0) {
this.importTypes = new HashMap<String, Class<?>>();
for (String var : importVariables) {
int i = var.lastIndexOf(' ');
if (i < 0) {
throw new IllegalArgumentException("Illegal config import.setVariables");
}
this.importTypes.put(var.substring(i + 1), ClassUtils.forName(importPackages, var.substring(0, i)));
}
}
if (importMethods != null && importMethods.length > 0) {
for (String method : importMethods) {
Class<?> cls = ClassUtils.forName(importPackages, method);
Object ins;
try {
ins = cls.newInstance();
} catch (Exception e) {
ins = cls;
}
this.functions.put(cls, ins);
}
}
}
#location 19
#vulnerability type NULL_DEREFERENCE
|
#fixed code
public void init() {
defaultFilterVariable = "$" + filterVariable;
defaultFormatterVariable = "$" + formatterVariable;
if (importVariables != null && importVariables.length > 0) {
this.importTypes = new HashMap<String, Class<?>>();
for (String var : importVariables) {
int i = var.lastIndexOf(' ');
if (i < 0) {
throw new IllegalArgumentException("Illegal config import.setVariables");
}
this.importTypes.put(var.substring(i + 1), ClassUtils.forName(importPackages, var.substring(0, i)));
}
}
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
public static Object parseXbean(String xml) {
if (xml == null) {
return null;
}
ByteArrayInputStream bi = new ByteArrayInputStream(xml.getBytes());
XMLDecoder xd = new XMLDecoder(bi);
return xd.readObject();
}
#location 7
#vulnerability type RESOURCE_LEAK
|
#fixed code
public static Object parseXbean(String xml) {
if (xml == null) {
return null;
}
ByteArrayInputStream bi = new ByteArrayInputStream(xml.getBytes());
XMLDecoder xd = new XMLDecoder(bi);
try {
return xd.readObject();
} finally {
xd.close();
}
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
public static byte[] encodeBytesToBytes( byte[] source, int off, int len, int options ) throws java.io.IOException {
if( source == null ){
throw new NullPointerException( "Cannot serialize a null array." );
} // end if: null
if( off < 0 ){
throw new IllegalArgumentException( "Cannot have negative offset: " + off );
} // end if: off < 0
if( len < 0 ){
throw new IllegalArgumentException( "Cannot have length offset: " + len );
} // end if: len < 0
if( off + len > source.length ){
throw new IllegalArgumentException(
String.format( "Cannot have offset of %d and length of %d with array of length %d", off,len,source.length));
} // end if: off < 0
// Compress?
if( (options & GZIP) != 0 ) {
java.io.ByteArrayOutputStream baos = null;
java.util.zip.GZIPOutputStream gzos = null;
Base64.OutputStream b64os = null;
try {
// GZip -> Base64 -> ByteArray
baos = new java.io.ByteArrayOutputStream();
b64os = new Base64.OutputStream( baos, ENCODE | options );
gzos = new java.util.zip.GZIPOutputStream( b64os );
gzos.write( source, off, len );
gzos.close();
} // end try
catch( java.io.IOException e ) {
// Catch it and then throw it immediately so that
// the finally{} block is called for cleanup.
throw e;
} // end catch
finally {
try{ gzos.close(); } catch( Exception e ){}
try{ b64os.close(); } catch( Exception e ){}
try{ baos.close(); } catch( Exception e ){}
} // end finally
return baos.toByteArray();
} // end if: compress
// Else, don't compress. Better not to use streams at all then.
else {
boolean breakLines = (options & DO_BREAK_LINES) != 0;
//int len43 = len * 4 / 3;
//byte[] outBuff = new byte[ ( len43 ) // Main 4:3
// + ( (len % 3) > 0 ? 4 : 0 ) // Account for padding
// + (breakLines ? ( len43 / MAX_LINE_LENGTH ) : 0) ]; // New lines
// Try to determine more precisely how big the array needs to be.
// If we get it right, we don't have to do an array copy, and
// we save a bunch of memory.
int encLen = ( len / 3 ) * 4 + ( len % 3 > 0 ? 4 : 0 ); // Bytes needed for actual encoding
if( breakLines ){
encLen += encLen / MAX_LINE_LENGTH; // Plus extra newline characters
}
byte[] outBuff = new byte[ encLen ];
int d = 0;
int e = 0;
int len2 = len - 2;
int lineLength = 0;
for( ; d < len2; d+=3, e+=4 ) {
encode3to4( source, d+off, 3, outBuff, e, options );
lineLength += 4;
if( breakLines && lineLength >= MAX_LINE_LENGTH )
{
outBuff[e+4] = NEW_LINE;
e++;
lineLength = 0;
} // end if: end of line
} // en dfor: each piece of array
if( d < len ) {
encode3to4( source, d+off, len - d, outBuff, e, options );
e += 4;
} // end if: some padding needed
// Only resize array if we didn't guess it right.
if( e <= outBuff.length - 1 ){
// If breaking lines and the last byte falls right at
// the line length (76 bytes per line), there will be
// one extra byte, and the array will need to be resized.
// Not too bad of an estimate on array size, I'd say.
byte[] finalOut = new byte[e];
System.arraycopy(outBuff,0, finalOut,0,e);
//System.err.println("Having to resize array from " + outBuff.length + " to " + e );
return finalOut;
} else {
//System.err.println("No need to resize array.");
return outBuff;
}
} // end else: don't compress
}
#location 43
#vulnerability type NULL_DEREFERENCE
|
#fixed code
public static byte[] encodeBytesToBytes( byte[] source, int off, int len, int options ) throws java.io.IOException {
if( source == null ){
throw new NullPointerException( "Cannot serialize a null array." );
} // end if: null
if( off < 0 ){
throw new IllegalArgumentException( "Cannot have negative offset: " + off );
} // end if: off < 0
if( len < 0 ){
throw new IllegalArgumentException( "Cannot have length offset: " + len );
} // end if: len < 0
if( off + len > source.length ){
throw new IllegalArgumentException(
String.format( "Cannot have offset of %d and length of %d with array of length %d", off,len,source.length));
} // end if: off < 0
// Compress?
if( (options & GZIP) != 0 ) {
java.io.ByteArrayOutputStream baos = null;
java.util.zip.GZIPOutputStream gzos = null;
Base64.OutputStream b64os = null;
try {
// GZip -> Base64 -> ByteArray
baos = new java.io.ByteArrayOutputStream();
b64os = new Base64.OutputStream( baos, ENCODE | options );
gzos = new java.util.zip.GZIPOutputStream( b64os );
gzos.write( source, off, len );
gzos.close();
} // end try
catch( java.io.IOException e ) {
// Catch it and then throw it immediately so that
// the finally{} block is called for cleanup.
throw e;
} // end catch
finally {
try {
if (gzos != null) gzos.close();
} finally {
try {
if (b64os != null) b64os.close();
} finally {
if (baos != null) baos.close();
}
}
} // end finally
return baos.toByteArray();
} // end if: compress
// Else, don't compress. Better not to use streams at all then.
else {
boolean breakLines = (options & DO_BREAK_LINES) != 0;
//int len43 = len * 4 / 3;
//byte[] outBuff = new byte[ ( len43 ) // Main 4:3
// + ( (len % 3) > 0 ? 4 : 0 ) // Account for padding
// + (breakLines ? ( len43 / MAX_LINE_LENGTH ) : 0) ]; // New lines
// Try to determine more precisely how big the array needs to be.
// If we get it right, we don't have to do an array copy, and
// we save a bunch of memory.
int encLen = ( len / 3 ) * 4 + ( len % 3 > 0 ? 4 : 0 ); // Bytes needed for actual encoding
if( breakLines ){
encLen += encLen / MAX_LINE_LENGTH; // Plus extra newline characters
}
byte[] outBuff = new byte[ encLen ];
int d = 0;
int e = 0;
int len2 = len - 2;
int lineLength = 0;
for( ; d < len2; d+=3, e+=4 ) {
encode3to4( source, d+off, 3, outBuff, e, options );
lineLength += 4;
if( breakLines && lineLength >= MAX_LINE_LENGTH )
{
outBuff[e+4] = NEW_LINE;
e++;
lineLength = 0;
} // end if: end of line
} // en dfor: each piece of array
if( d < len ) {
encode3to4( source, d+off, len - d, outBuff, e, options );
e += 4;
} // end if: some padding needed
// Only resize array if we didn't guess it right.
if( e <= outBuff.length - 1 ){
// If breaking lines and the last byte falls right at
// the line length (76 bytes per line), there will be
// one extra byte, and the array will need to be resized.
// Not too bad of an estimate on array size, I'd say.
byte[] finalOut = new byte[e];
System.arraycopy(outBuff,0, finalOut,0,e);
//System.err.println("Having to resize array from " + outBuff.length + " to " + e );
return finalOut;
} else {
//System.err.println("No need to resize array.");
return outBuff;
}
} // end else: don't compress
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
public void init() {
if (importVariables != null && importVariables.length > 0) {
this.importTypes = new HashMap<String, Class<?>>();
for (String var : importVariables) {
int i = var.lastIndexOf(' ');
if (i < 0) {
throw new IllegalArgumentException("Illegal config import.setVariables");
}
this.importTypes.put(var.substring(i + 1), ClassUtils.forName(importPackages, var.substring(0, i)));
}
}
if (importMethods != null && importMethods.length > 0) {
for (String method : importMethods) {
Class<?> cls = ClassUtils.forName(importPackages, method);
Object ins;
try {
ins = cls.newInstance();
} catch (Exception e) {
ins = cls;
}
this.functions.put(cls, ins);
}
}
}
#location 17
#vulnerability type NULL_DEREFERENCE
|
#fixed code
public void init() {
if (importVariables != null && importVariables.length > 0) {
this.importTypes = new HashMap<String, Class<?>>();
for (String var : importVariables) {
int i = var.lastIndexOf(' ');
if (i < 0) {
throw new IllegalArgumentException("Illegal config import.setVariables");
}
this.importTypes.put(var.substring(i + 1), ClassUtils.forName(importPackages, var.substring(0, i)));
}
}
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
public InputStream getInputStream() throws IOException {
// 注：JarFile与File的设计是不一样的，File相当于C#的FileInfo，只持有信息，
// 而JarFile构造时即打开流，所以每次读取数据时，重新new新的实例，而不作为属性字段持有。
JarFile zipFile = new JarFile(file);
return zipFile.getInputStream(zipFile.getEntry(getName()));
}
#location 5
#vulnerability type RESOURCE_LEAK
|
#fixed code
public InputStream getInputStream() throws IOException {
// 注：JarFile与File的设计是不一样的，File相当于C#的FileInfo，只持有信息，
// 而JarFile构造时即打开流，所以每次读取数据时，重新new新的实例，而不作为属性字段持有。
JarFile jarFile = new JarFile(file);
return jarFile.getInputStream(jarFile.getEntry(getName()));
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
@Test
public void testNoProcessorWroManagerFactory() throws IOException {
final WroManagerFactory factory = new ServletContextAwareWroManagerFactory();
manager = factory.getInstance();
manager.setModelFactory(getValidModelFactory());
final HttpServletRequest request = Mockito.mock(HttpServletRequest.class);
final OutputStream os = System.out;
final HttpServletResponse response = Context.get().getResponse();
final InputStream actualStream = WroTestUtils.convertToInputStream(os);
Mockito.when(response.getOutputStream()).thenReturn(new DelegatingServletOutputStream(os));
Mockito.when(request.getRequestURI()).thenReturn("/app/g1.css");
manager.process(request, response);
WroTestUtils.compare(getInputStream("classpath:ro/isdc/wro/manager/noProcessorsResult.css"), actualStream);
}
#location 11
#vulnerability type RESOURCE_LEAK
|
#fixed code
@Test
public void testNoProcessorWroManagerFactory() throws IOException {
final WroManagerFactory factory = new ServletContextAwareWroManagerFactory();
manager = factory.getInstance();
manager.setModelFactory(getValidModelFactory());
final HttpServletRequest request = Mockito.mock(HttpServletRequest.class);
final HttpServletResponse response = Context.get().getResponse();
final ByteArrayOutputStream out = new ByteArrayOutputStream();
Mockito.when(response.getOutputStream()).thenReturn(new DelegatingServletOutputStream(out));
Mockito.when(request.getRequestURI()).thenReturn("/app/g1.css");
manager.process(request, response);
//compare written bytes to output stream with the content from specified css.
WroTestUtils.compare(getInputStream("classpath:ro/isdc/wro/manager/noProcessorsResult.css"), new ByteArrayInputStream(out.toByteArray()));
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
public void process(final Resource resource, final Reader reader, final Writer writer)
throws IOException {
try {
System.out.println("BOM:");
// using ReaderInputStream instead of ByteArrayInputStream, cause processing to freeze
final InputStream is = new BomStripperInputStream(new ByteArrayInputStream(IOUtils.toByteArray(reader)));
IOUtils.copy(is, writer, Context.get().getConfig().getEncoding());
System.out.println("END BOM");
} finally {
reader.close();
writer.close();
}
}
#location 10
#vulnerability type RESOURCE_LEAK
|
#fixed code
public void process(final Resource resource, final Reader reader, final Writer writer)
throws IOException {
try {
// using ReaderInputStream instead of ByteArrayInputStream, cause processing to freeze
final String encoding = Context.get().getConfig().getEncoding();
final InputStream is = new BomStripperInputStream(new ByteArrayInputStream(IOUtils.toByteArray(reader, encoding)));
IOUtils.copy(is, writer, encoding);
} finally {
reader.close();
writer.close();
}
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
public void destroy() {
//kill running threads
executorService.shutdownNow();
}
#location 3
#vulnerability type THREAD_SAFETY_VIOLATION
|
#fixed code
public void destroy() {
//kill running threads
scheduler.shutdownNow();
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
public void doFilter(final ServletRequest req, final ServletResponse res, final FilterChain chain)
throws IOException, ServletException {
final HttpServletRequest request = (HttpServletRequest) req;
final HttpServletResponse response = (HttpServletResponse) res;
try {
// add request, response & servletContext to thread local
Context.set(Context.webContext(request, response, filterConfig));
final ByteArrayOutputStream os = new ByteArrayOutputStream();
HttpServletResponse wrappedResponse = new RedirectedStreamServletResponseWrapper(os, response);
chain.doFilter(req, wrappedResponse);
final Reader reader = new StringReader(new String(os.toByteArray(), Context.get().getConfig().getEncoding()));
doProcess(reader, response.getWriter());
response.flushBuffer();
} catch (final RuntimeException e) {
onRuntimeException(e, response, chain);
} finally {
Context.unset();
}
}
#location 11
#vulnerability type RESOURCE_LEAK
|
#fixed code
public void doFilter(final ServletRequest req, final ServletResponse res, final FilterChain chain)
throws IOException, ServletException {
final HttpServletRequest request = (HttpServletRequest) req;
final HttpServletResponse response = (HttpServletResponse) res;
try {
// add request, response & servletContext to thread local
Context.set(Context.webContext(request, response, filterConfig));
IOUtils.write("\nBefore chain!\n", response.getOutputStream());
final ByteArrayOutputStream os = new ByteArrayOutputStream();
System.out.println(response.getOutputStream());
final HttpServletResponse wrappedResponse = new RedirectedStreamServletResponseWrapper(os, response);
chain.doFilter(request, wrappedResponse);
final Reader reader = new StringReader(new String(os.toByteArray(), Context.get().getConfig().getEncoding()));
doProcess(reader, new OutputStreamWriter(os));
IOUtils.write(os.toByteArray(), response.getOutputStream());
response.flushBuffer();
response.getOutputStream().close();
} catch (final RuntimeException e) {
onRuntimeException(e, response, chain);
} finally {
Context.unset();
}
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
@Test
public void testNoProcessorWroManagerFactory() throws IOException {
final WroManagerFactory factory = new ServletContextAwareWroManagerFactory();
manager = factory.getInstance();
manager.setModelFactory(getValidModelFactory());
final HttpServletRequest request = Mockito.mock(HttpServletRequest.class);
final OutputStream os = System.out;
final HttpServletResponse response = Context.get().getResponse();
final InputStream actualStream = WroTestUtils.convertToInputStream(os);
Mockito.when(response.getOutputStream()).thenReturn(new DelegatingServletOutputStream(os));
Mockito.when(request.getRequestURI()).thenReturn("/app/g1.css");
manager.process(request, response);
WroTestUtils.compare(getInputStream("classpath:ro/isdc/wro/manager/noProcessorsResult.css"), actualStream);
}
#location 15
#vulnerability type RESOURCE_LEAK
|
#fixed code
@Test
public void testNoProcessorWroManagerFactory() throws IOException {
final WroManagerFactory factory = new ServletContextAwareWroManagerFactory();
manager = factory.getInstance();
manager.setModelFactory(getValidModelFactory());
final HttpServletRequest request = Mockito.mock(HttpServletRequest.class);
final HttpServletResponse response = Context.get().getResponse();
final ByteArrayOutputStream out = new ByteArrayOutputStream();
Mockito.when(response.getOutputStream()).thenReturn(new DelegatingServletOutputStream(out));
Mockito.when(request.getRequestURI()).thenReturn("/app/g1.css");
manager.process(request, response);
//compare written bytes to output stream with the content from specified css.
WroTestUtils.compare(getInputStream("classpath:ro/isdc/wro/manager/noProcessorsResult.css"), new ByteArrayInputStream(out.toByteArray()));
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
protected void onRuntimeException(final RuntimeException e, final HttpServletResponse response,
final FilterChain chain) {
LOG.debug("RuntimeException occured", e);
try {
LOG.debug("Cannot process. Proceeding with chain execution.");
final OutputStream os = new ByteArrayOutputStream();
HttpServletResponse wrappedResponse = new RedirectedStreamServletResponseWrapper(os, response);
chain.doFilter(Context.get().getRequest(), wrappedResponse);
} catch (final Exception ex) {
// should never happen
LOG.error("Error while chaining the request: " + HttpServletResponse.SC_NOT_FOUND);
}
}
#location 9
#vulnerability type RESOURCE_LEAK
|
#fixed code
protected void onRuntimeException(final RuntimeException e, final HttpServletResponse response,
final FilterChain chain) {
LOG.debug("RuntimeException occured", e);
try {
LOG.debug("Cannot process. Proceeding with chain execution.");
chain.doFilter(Context.get().getRequest(), response);
} catch (final Exception ex) {
// should never happen
LOG.error("Error while chaining the request: " + HttpServletResponse.SC_NOT_FOUND);
}
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
private InputStream locateStreamFromJar(final String uri, final File jarPath)
throws IOException {
LOG.debug("\t\tLocating stream from jar");
String classPath = FilenameUtils.getPath(uri);
final String wildcard = FilenameUtils.getName(uri);
if (classPath.startsWith(ClasspathUriLocator.PREFIX)) {
classPath = StringUtils.substringAfter(classPath, ClasspathUriLocator.PREFIX);
}
final JarFile file = open(jarPath);
List<JarEntry> jarEntryList = Collections.list(file.entries());
final ByteArrayOutputStream out = new ByteArrayOutputStream();
for (JarEntry entry : jarEntryList) {
if (entry.getName().startsWith(classPath) && accept(entry, wildcard)) {
final InputStream is = file.getInputStream(entry);
IOUtils.copy(is, out);
is.close();
}
}
return new BufferedInputStream(new ByteArrayInputStream(out.toByteArray()));
}
#location 23
#vulnerability type RESOURCE_LEAK
|
#fixed code
private InputStream locateStreamFromJar(final String uri, final File jarPath)
throws IOException {
LOG.debug("\t\tLocating stream from jar");
String classPath = FilenameUtils.getPath(uri);
final String wildcard = FilenameUtils.getName(uri);
if (classPath.startsWith(ClasspathUriLocator.PREFIX)) {
classPath = StringUtils.substringAfter(classPath, ClasspathUriLocator.PREFIX);
}
final JarFile file = open(jarPath);
final List<JarEntry> jarEntryList = Collections.list(file.entries());
final List<JarEntry> filteredJarEntryList = new ArrayList<JarEntry>();
for (final JarEntry entry : jarEntryList) {
final boolean isSupportedEntry = entry.getName().startsWith(classPath) && accept(entry, wildcard);
if (isSupportedEntry) {
filteredJarEntryList.add(entry);
}
}
final ByteArrayOutputStream out = new ByteArrayOutputStream();
for (final JarEntry entry : filteredJarEntryList) {
final InputStream is = file.getInputStream(entry);
IOUtils.copy(is, out);
is.close();
}
return new BufferedInputStream(new ByteArrayInputStream(out.toByteArray()));
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
protected void onRuntimeException(final RuntimeException e, final HttpServletResponse response,
final FilterChain chain) {
LOG.debug("RuntimeException occured", e);
try {
LOG.debug("Cannot process. Proceeding with chain execution.");
final OutputStream os = new ByteArrayOutputStream();
HttpServletResponse wrappedResponse = new RedirectedStreamServletResponseWrapper(os, response);
chain.doFilter(Context.get().getRequest(), wrappedResponse);
} catch (final Exception ex) {
// should never happen
LOG.error("Error while chaining the request: " + HttpServletResponse.SC_NOT_FOUND);
}
}
#location 8
#vulnerability type RESOURCE_LEAK
|
#fixed code
protected void onRuntimeException(final RuntimeException e, final HttpServletResponse response,
final FilterChain chain) {
LOG.debug("RuntimeException occured", e);
try {
LOG.debug("Cannot process. Proceeding with chain execution.");
chain.doFilter(Context.get().getRequest(), response);
} catch (final Exception ex) {
// should never happen
LOG.error("Error while chaining the request: " + HttpServletResponse.SC_NOT_FOUND);
}
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
public void process(final Reader reader, final Writer writer)
throws IOException {
final StopWatch watch = new StopWatch();
watch.start("pack");
final InputStream is = new ByteArrayInputStream(IOUtils.toByteArray(reader));
try {
final JavaScriptCompressor compressor = new JavaScriptCompressor(new InputStreamReader(is), new YUIErrorReporter());
compressor.compress(writer, linebreakpos, munge, verbose, preserveAllSemiColons, disableOptimizations);
} catch (final RuntimeException e) {
LOG.error("Problem while applying YUI compressor", e);
//keep js unchanged if it contains errors -> this should be configurable
LOG.debug("Leave resource unchanged...");
is.reset();
IOUtils.copy(is, writer);
//throw new WroRuntimeException("Problem while applying YUI compressor", e);
} finally {
is.close();
reader.close();
writer.close();
watch.stop();
LOG.debug(watch.prettyPrint());
}
}
#location 7
#vulnerability type RESOURCE_LEAK
|
#fixed code
public void process(final Reader reader, final Writer writer)
throws IOException {
final StopWatch watch = new StopWatch();
watch.start("pack");
final String content = IOUtils.toString(reader);
try {
final JavaScriptCompressor compressor = new JavaScriptCompressor(new StringReader(content), new YUIErrorReporter());
compressor.compress(writer, linebreakpos, munge, verbose, preserveAllSemiColons, disableOptimizations);
} catch (final RuntimeException e) {
LOG.error("Problem while applying YUI compressor", e);
//keep js unchanged if it contains errors -> this should be configurable
LOG.debug("Leave resource unchanged...");
IOUtils.copy(new StringReader(content), writer);
//throw new WroRuntimeException("Problem while applying YUI compressor", e);
} finally {
reader.close();
writer.close();
watch.stop();
LOG.debug(watch.prettyPrint());
}
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
public InputStream getInputStream(final HttpServletRequest request, final HttpServletResponse response,
final String location)
throws IOException {
Validate.notNull(request);
Validate.notNull(response);
// where to write the bytes of the stream
final ByteArrayOutputStream os = new ByteArrayOutputStream();
boolean warnOnEmptyStream = false;
// preserve context, in case it is unset during dispatching
final Context originalContext = Context.get();
try {
final RequestDispatcher dispatcher = request.getRequestDispatcher(location);
if (dispatcher == null) {
// happens when dynamic servlet context relative resources are included outside of the request cycle (inside
// the thread responsible for refreshing resources)
// Returns the part URL from the protocol name up to the query string and contextPath.
final String servletContextPath = request.getRequestURL().toString().replace(request.getServletPath(), "");
final String absolutePath = servletContextPath + location;
return getLocationStream(absolutePath);
}
// Wrap request
final ServletRequest wrappedRequest = getWrappedServletRequest(request, location);
// Wrap response
final ServletResponse wrappedResponse = getWrappedServletResponse(response, os);
LOG.debug("dispatching request to location: " + location);
// use dispatcher
dispatcher.include(wrappedRequest, wrappedResponse);
warnOnEmptyStream = true;
// force flushing - the content will be written to
// BytArrayOutputStream. Otherwise exactly 32K of data will be
// written.
wrappedResponse.getWriter().flush();
os.close();
} catch (final Exception e) {
// Not only servletException can be thrown, also dispatch.include can throw NPE when the scheduler runs outside
// of the request cycle, thus connection is unavailable. This is caused mostly when invalid resources are
// included.
LOG.debug("[FAIL] Error while dispatching the request for location {}", location);
throw new IOException("Error while dispatching the request for location " + location);
} finally {
if (warnOnEmptyStream && os.size() == 0) {
LOG.warn("Wrong or empty resource with location: {}", location);
}
// Put the context back
if (!Context.isContextSet()) {
Context.set(originalContext);
}
}
return new ByteArrayInputStream(os.toByteArray());
}
#location 34
#vulnerability type RESOURCE_LEAK
|
#fixed code
public InputStream getInputStream(final HttpServletRequest request, final HttpServletResponse response,
final String location)
throws IOException {
Validate.notNull(request);
Validate.notNull(response);
// where to write the bytes of the stream
final ByteArrayOutputStream os = new ByteArrayOutputStream();
boolean warnOnEmptyStream = false;
// preserve context, in case it is unset during dispatching
final Context originalContext = Context.get();
try {
final RequestDispatcher dispatcher = request.getRequestDispatcher(location);
if (dispatcher == null) {
// happens when dynamic servlet context relative resources are included outside of the request cycle (inside
// the thread responsible for refreshing resources)
// Returns the part URL from the protocol name up to the query string and contextPath.
final String servletContextPath = request.getRequestURL().toString().replace(request.getServletPath(), "");
final String absolutePath = servletContextPath + location;
return externalResourceLocator.locate(absolutePath);
}
// Wrap request
final ServletRequest servletRequest = getWrappedServletRequest(request, location);
// Wrap response
final ServletResponse servletResponse = new RedirectedStreamServletResponseWrapper(os, response);
LOG.debug("dispatching request to location: " + location);
// use dispatcher
dispatcher.include(servletRequest, servletResponse);
warnOnEmptyStream = true;
// force flushing - the content will be written to
// BytArrayOutputStream. Otherwise exactly 32K of data will be
// written.
servletResponse.getWriter().flush();
os.close();
} catch (final Exception e) {
// Not only servletException can be thrown, also dispatch.include can throw NPE when the scheduler runs outside
// of the request cycle, thus connection is unavailable. This is caused mostly when invalid resources are
// included.
LOG.debug("[FAIL] Error while dispatching the request for location {}", location);
throw new IOException("Error while dispatching the request for location " + location);
} finally {
if (warnOnEmptyStream && os.size() == 0) {
LOG.warn("Wrong or empty resource with location: {}", location);
}
// Put the context back
if (!Context.isContextSet()) {
Context.set(originalContext);
}
}
return new ByteArrayInputStream(os.toByteArray());
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
public void onModelPeriodChanged() {
//force scheduler to reload
initScheduler();
}
#location 3
#vulnerability type THREAD_SAFETY_VIOLATION
|
#fixed code
public void onModelPeriodChanged() {
//force scheduler to reload
model = null;
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
public String getScalarValue(String key) throws ConfiguratorException {
return get(key).asScalar().getValue();
}
#location 2
#vulnerability type NULL_DEREFERENCE
|
#fixed code
public String getScalarValue(String key) throws ConfiguratorException {
return remove(key).asScalar().getValue();
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
@Override
public Object configure(Object c) throws Exception {
final ExtensionList list = Jenkins.getInstance().getExtensionList(target);
if (list.size() != 1) {
throw new IllegalStateException();
}
final Object o = list.get(0);
if (c instanceof Map) {
Map config = (Map) c;
final Set<Attribute> attributes = describe();
for (Attribute attribute : attributes) {
final String name = attribute.getName();
if (config.containsKey(name)) {
final Object value = Configurator.lookup(attribute.getType()).configure(config.get(name));
attribute.setValue(o, value);
}
}
}
return o;
}
#location 15
#vulnerability type NULL_DEREFERENCE
|
#fixed code
@Override
public Object configure(Object c) throws Exception {
final ExtensionList list = Jenkins.getInstance().getExtensionList(target);
if (list.size() != 1) {
throw new IllegalStateException();
}
final Object o = list.get(0);
if (c instanceof Map) {
Map config = (Map) c;
final Set<Attribute> attributes = describe();
for (Attribute attribute : attributes) {
final String name = attribute.getName();
if (config.containsKey(name)) {
final Class k = attribute.getType();
final Configurator configurator = Configurator.lookup(k);
if (configurator == null) throw new IllegalStateException("No configurator implementation to manage "+ k);
final Object value = configurator.configure(config.get(name));
attribute.setValue(o, value);
}
}
}
return o;
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
@Override
public Object configure(Object c) throws Exception {
Map config = c instanceof Map ? (Map) c : Collections.EMPTY_MAP;
final Constructor constructor = getDataBoundConstructor(target);
if (constructor == null) {
throw new IllegalStateException(target.getName() + " is missing a @DataBoundConstructor");
}
final Parameter[] parameters = constructor.getParameters();
final String[] names = ClassDescriptor.loadParameterNames(constructor);
Object[] args = new Object[names.length];
if (parameters.length > 0) {
// Many jenkins components haven't been migrated to @DataBoundSetter vs @NotNull constructor parameters
// as a result it might be valid to reference a describable without parameters
for (int i = 0; i < names.length; i++) {
final Object value = config.remove(names[i]);
if (value == null && parameters[i].getAnnotation(Nonnull.class) != null) {
throw new IllegalArgumentException(names[i] + " is required to configure " + target);
}
final Class t = parameters[i].getType();
if (value != null) {
if (Collection.class.isAssignableFrom(t)) {
if (!(value instanceof List)) {
throw new IllegalArgumentException(names[i] + " should be a list");
}
final Type pt = parameters[i].getParameterizedType();
final Configurator lookup = Configurator.lookup(pt);
final ArrayList<Object> list = new ArrayList<>();
for (Object o : (List) value) {
list.add(lookup.configure(o));
}
args[i] = list;
} else {
final Type pt = parameters[i].getParameterizedType();
final Type k = pt != null ? pt : t;
final Configurator configurator = Configurator.lookup(k);
if (configurator == null) throw new IllegalStateException("No configurator implementation to manage "+k);
args[i] = configurator.configure(value);
}
System.out.println("Setting " + target + "." + names[i] + " = " + value);
} else if (t.isPrimitive()) {
args[i] = Defaults.defaultValue(t);
}
}
}
final Object object;
try {
object = constructor.newInstance(args);
} catch (IllegalArgumentException ex) {
List<String> argumentTypes = new ArrayList<>(args.length);
for (Object arg : args) {
argumentTypes.add(arg != null ? arg.getClass().getName() : "null");
}
throw new IOException("Failed to construct instance of " + target +
". Constructor: " + constructor.toString() +
". Arguments: " + argumentTypes, ex);
}
final Set<Attribute> attributes = describe();
for (Attribute attribute : attributes) {
final String name = attribute.getName();
final Configurator lookup = Configurator.lookup(attribute.getType());
if (config.containsKey(name)) {
final Object yaml = config.get(name);
Object value;
if (attribute.isMultiple()) {
List l = new ArrayList<>();
for (Object o : (List) yaml) {
l.add(lookup.configure(o));
}
value = l;
} else {
value = lookup.configure(config.get(name));
}
attribute.setValue(object, value);
}
}
return object;
}
#location 81
#vulnerability type NULL_DEREFERENCE
|
#fixed code
@Override
public Object configure(Object c) throws Exception {
Map config = c instanceof Map ? (Map) c : Collections.EMPTY_MAP;
final Constructor constructor = getDataBoundConstructor(target);
if (constructor == null) {
throw new IllegalStateException(target.getName() + " is missing a @DataBoundConstructor");
}
final Parameter[] parameters = constructor.getParameters();
final String[] names = ClassDescriptor.loadParameterNames(constructor);
Object[] args = new Object[names.length];
if (parameters.length > 0) {
// Many jenkins components haven't been migrated to @DataBoundSetter vs @NotNull constructor parameters
// as a result it might be valid to reference a describable without parameters
for (int i = 0; i < names.length; i++) {
final Object value = config.remove(names[i]);
if (value == null && parameters[i].getAnnotation(Nonnull.class) != null) {
throw new IllegalArgumentException(names[i] + " is required to configure " + target);
}
final Class t = parameters[i].getType();
if (value != null) {
if (Collection.class.isAssignableFrom(t)) {
if (!(value instanceof List)) {
throw new IllegalArgumentException(names[i] + " should be a list");
}
final Type pt = parameters[i].getParameterizedType();
final Configurator lookup = Configurator.lookup(pt);
final ArrayList<Object> list = new ArrayList<>();
for (Object o : (List) value) {
list.add(lookup.configure(o));
}
args[i] = list;
} else {
final Type pt = parameters[i].getParameterizedType();
final Type k = pt != null ? pt : t;
final Configurator configurator = Configurator.lookup(k);
if (configurator == null) throw new IllegalStateException("No configurator implementation to manage "+k);
args[i] = configurator.configure(value);
}
System.out.println("Setting " + target + "." + names[i] + " = " + value);
} else if (t.isPrimitive()) {
args[i] = Defaults.defaultValue(t);
}
}
}
final Object object;
try {
object = constructor.newInstance(args);
} catch (IllegalArgumentException ex) {
List<String> argumentTypes = new ArrayList<>(args.length);
for (Object arg : args) {
argumentTypes.add(arg != null ? arg.getClass().getName() : "null");
}
throw new IOException("Failed to construct instance of " + target +
". Constructor: " + constructor.toString() +
". Arguments: " + argumentTypes, ex);
}
final Set<Attribute> attributes = describe();
for (Attribute attribute : attributes) {
final String name = attribute.getName();
final Configurator lookup = Configurator.lookup(attribute.getType());
if (config.containsKey(name)) {
final Object yaml = config.get(name);
Object value;
if (attribute.isMultiple()) {
List l = new ArrayList<>();
for (Object o : (List) yaml) {
l.add(lookup.configure(o));
}
value = l;
} else {
value = lookup.configure(config.get(name));
}
attribute.setValue(object, value);
}
}
for (Method method : target.getMethods()) {
if (method.getParameterCount() == 0 && method.getAnnotation(PostConstruct.class) != null) {
method.invoke(object, null);
}
}
return object;
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
protected void configure(Map config, T instance) throws Exception {
final Set<Attribute> attributes = describe();
for (Attribute attribute : attributes) {
final String name = attribute.getName();
final Object sub = removeIgnoreCase(config, name);
if (sub != null) {
if (attribute.isMultiple()) {
List values = new ArrayList<>();
for (Object o : (List) sub) {
Object value = Configurator.lookup(attribute.getType()).configure(o);
values.add(value);
}
attribute.setValue(instance, values);
} else {
Object value = Configurator.lookup(attribute.getType()).configure(sub);
attribute.setValue(instance, value);
}
}
}
if (!config.isEmpty()) {
final String invalid = StringUtils.join(config.keySet(), ',');
throw new IllegalArgumentException("Invalid configuration elements for type " + instance.getClass() + " : " + invalid);
}
}
#location 11
#vulnerability type NULL_DEREFERENCE
|
#fixed code
protected void configure(Map config, T instance) throws Exception {
final Set<Attribute> attributes = describe();
for (Attribute attribute : attributes) {
final String name = attribute.getName();
final Object sub = removeIgnoreCase(config, name);
if (sub != null) {
final Class k = attribute.getType();
final Configurator configurator = Configurator.lookup(k);
if (configurator == null) throw new IllegalStateException("No configurator implementation to manage "+k);
if (attribute.isMultiple()) {
List values = new ArrayList<>();
for (Object o : (List) sub) {
Object value = configurator.configure(o);
values.add(value);
}
attribute.setValue(instance, values);
} else {
Object value = configurator.configure(sub);
attribute.setValue(instance, value);
}
}
}
if (!config.isEmpty()) {
final String invalid = StringUtils.join(config.keySet(), ',');
throw new IllegalArgumentException("Invalid configuration elements for type " + instance.getClass() + " : " + invalid);
}
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
@Nonnull
private static RoleMap retrieveRoleMap(@Nonnull CNode config, @Nonnull String name, Configurator<RoleDefinition> configurator) throws ConfiguratorException {
Mapping map = config.asMapping();
final Sequence c = map.get(name).asSequence();
TreeMap<Role, Set<String>> resMap = new TreeMap<>();
if (c == null) {
// we cannot return emptyMap here due to the Role Strategy code
return new RoleMap(resMap);
}
for (CNode entry : c) {
RoleDefinition definition = configurator.configure(entry);
resMap.put(definition.getRole(), definition.getAssignments());
}
return new RoleMap(resMap);
}
#location 4
#vulnerability type NULL_DEREFERENCE
|
#fixed code
@Nonnull
private static RoleMap retrieveRoleMap(@Nonnull CNode config, @Nonnull String name, Configurator<RoleDefinition> configurator) throws ConfiguratorException {
Mapping map = config.asMapping();
final CNode c = map.get(name);
TreeMap<Role, Set<String>> resMap = new TreeMap<>();
if (c == null || c.asSequence() == null) {
// we cannot return emptyMap here due to the Role Strategy code
return new RoleMap(resMap);
}
for (CNode entry : c.asSequence()) {
RoleDefinition definition = configurator.configure(entry);
resMap.put(definition.getRole(), definition.getAssignments());
}
return new RoleMap(resMap);
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
@Override
public Describable configure(Object config) throws Exception {
String shortname;
Object subconfig = null;
if (config instanceof String) {
shortname = (String) config;
} else if (config instanceof Map) {
Map<String, ?> map = (Map) config;
if (map.size() != 1) {
throw new IllegalArgumentException("single entry map expected to configure a "+target.getName());
}
final Map.Entry<String, ?> next = map.entrySet().iterator().next();
shortname = next.getKey();
subconfig = next.getValue();
} else {
throw new IllegalArgumentException("Unexpected configuration type "+config);
}
final List<Descriptor> candidates = Jenkins.getInstance().getDescriptorList(target);
Class<? extends Describable> k = findDescribableBySymbol(shortname, candidates);
return (Describable) Configurator.lookup(k).configure(subconfig);
}
#location 22
#vulnerability type NULL_DEREFERENCE
|
#fixed code
@Override
public Describable configure(Object config) throws Exception {
String shortname;
Object subconfig = null;
if (config instanceof String) {
shortname = (String) config;
} else if (config instanceof Map) {
Map<String, ?> map = (Map) config;
if (map.size() != 1) {
throw new IllegalArgumentException("single entry map expected to configure a "+target.getName());
}
final Map.Entry<String, ?> next = map.entrySet().iterator().next();
shortname = next.getKey();
subconfig = next.getValue();
} else {
throw new IllegalArgumentException("Unexpected configuration type "+config);
}
final List<Descriptor> candidates = Jenkins.getInstance().getDescriptorList(target);
Class<? extends Describable> k = findDescribableBySymbol(shortname, candidates);
final Configurator configurator = Configurator.lookup(k);
if (configurator == null) throw new IllegalStateException("No configurator implementation to manage "+k);
return (Describable) configurator.configure(subconfig);
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
@CheckForNull
@Override
public CNode describe(T instance) throws Exception {
// Here we assume a correctly designed DataBound Object will have required attributes set by DataBoundConstructor
// and all others using DataBoundSetters. So constructor parameters for sure are part of the description, others
// need to be compared with default values.
// Build same object with only constructor parameters
final Constructor constructor = getDataBoundConstructor(target);
final Parameter[] parameters = constructor.getParameters();
final String[] names = ClassDescriptor.loadParameterNames(constructor);
final Attribute[] attributes = new Attribute[parameters.length];
final Object[] args = new Object[parameters.length];
for (int i = 0; i < parameters.length; i++) {
final Parameter p = parameters[i];
final Attribute a = detectActualType(names[i], p.getParameterizedType());
args[i] = a.getValue(instance);
attributes[i] = a;
}
T ref = (T) constructor.newInstance(args);
// compare instance with this "default" object
Mapping mapping = compare(instance, ref);
// add constructor parameters
for (int i = 0; i < parameters.length; i++) {
final Configurator c = Configurator.lookup(attributes[i].getType());
if (args[i] == null) continue;
mapping.put(names[i], attributes[i].describe(args[i]));
}
return mapping;
}
#location 12
#vulnerability type NULL_DEREFERENCE
|
#fixed code
@CheckForNull
@Override
public CNode describe(T instance) throws Exception {
// Here we assume a correctly designed DataBound Object will have required attributes set by DataBoundConstructor
// and all others using DataBoundSetters. So constructor parameters for sure are part of the description, others
// need to be compared with default values.
// Build same object with only constructor parameters
final Constructor constructor = getDataBoundConstructor();
final Parameter[] parameters = constructor.getParameters();
final String[] names = ClassDescriptor.loadParameterNames(constructor);
final Attribute[] attributes = new Attribute[parameters.length];
final Object[] args = new Object[parameters.length];
for (int i = 0; i < parameters.length; i++) {
final Parameter p = parameters[i];
final Attribute a = detectActualType(names[i], p.getParameterizedType());
args[i] = a.getValue(instance);
attributes[i] = a;
}
T ref = (T) constructor.newInstance(args);
// compare instance with this "default" object
Mapping mapping = compare(instance, ref);
// add constructor parameters
for (int i = 0; i < parameters.length; i++) {
final Configurator c = Configurator.lookup(attributes[i].getType());
if (args[i] == null) continue;
mapping.put(names[i], attributes[i].describe(args[i]));
}
return mapping;
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
@Nonnull
@Override
public T configure(CNode c, ConfigurationContext context) throws ConfiguratorException {
final Mapping mapping = (c != null ? c.asMapping() : Mapping.EMPTY);
final T instance = instance(mapping, context);
if (instance instanceof Saveable) {
BulkChange bc = new BulkChange((Saveable) instance);
configure(mapping, instance, false, context);
try {
bc.commit();
} catch (IOException e) {
throw new ConfiguratorException("Failed to save "+instance, e);
}
} else {
configure(mapping, instance, false, context);
}
return instance;
}
#location 10
#vulnerability type RESOURCE_LEAK
|
#fixed code
@Nonnull
@Override
public T configure(CNode c, ConfigurationContext context) throws ConfiguratorException {
final Mapping mapping = (c != null ? c.asMapping() : Mapping.EMPTY);
final T instance = instance(mapping, context);
if (instance instanceof Saveable) {
try (BulkChange bc = new BulkChange((Saveable) instance) ){
configure(mapping, instance, false, context);
bc.commit();
} catch (IOException e) {
throw new ConfiguratorException("Failed to save "+instance, e);
}
} else {
configure(mapping, instance, false, context);
}
return instance;
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
@Override
public ProjectMatrixAuthorizationStrategy configure(Object config) throws Exception {
Map map = (Map) config;
Collection o = (Collection<?>)map.get("grantedPermissions");
Configurator<GroupPermissionDefinition> permissionConfigurator = Configurator.lookup(GroupPermissionDefinition.class);
Map<Permission,Set<String>> grantedPermissions = new HashMap<>();
for(Object entry : o) {
GroupPermissionDefinition gpd = permissionConfigurator.configure(entry);
//We transform the linear list to a matrix (Where permission is the key instead)
gpd.grantPermission(grantedPermissions);
}
ProjectMatrixAuthorizationStrategy gms = new ProjectMatrixAuthorizationStrategy();
for(Map.Entry<Permission,Set<String>> permission : grantedPermissions.entrySet()) {
for(String sid : permission.getValue()) {
gms.add(permission.getKey(), sid);
}
}
return gms;
}
#location 8
#vulnerability type NULL_DEREFERENCE
|
#fixed code
@Override
public ProjectMatrixAuthorizationStrategy configure(Object config) throws ConfiguratorException {
Map map = (Map) config;
Collection o = (Collection<?>)map.get("grantedPermissions");
Configurator<GroupPermissionDefinition> permissionConfigurator = Configurator.lookupOrFail(GroupPermissionDefinition.class);
Map<Permission,Set<String>> grantedPermissions = new HashMap<>();
for(Object entry : o) {
GroupPermissionDefinition gpd = permissionConfigurator.configureNonNull(entry);
//We transform the linear list to a matrix (Where permission is the key instead)
gpd.grantPermission(grantedPermissions);
}
ProjectMatrixAuthorizationStrategy gms = new ProjectMatrixAuthorizationStrategy();
for(Map.Entry<Permission,Set<String>> permission : grantedPermissions.entrySet()) {
for(String sid : permission.getValue()) {
gms.add(permission.getKey(), sid);
}
}
return gms;
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
@POST
public FormValidation doCheckNewSource(@QueryParameter String newSource) {
Jenkins.getInstance().checkPermission(Jenkins.ADMINISTER);
String normalizedSource = Util.fixEmptyAndTrim(newSource);
File file = new File(Util.fixNull(normalizedSource));
if (normalizedSource == null) {
return FormValidation.ok(); // empty, do nothing
}
if (!file.exists() && !ConfigurationAsCode.isSupportedURI(normalizedSource)) {
return FormValidation.error("Configuration cannot be applied. File or URL cannot be parsed or do not exist.");
}
try {
final Map<Source, String> issues = collectIssues(normalizedSource);
final JSONArray errors = collectProblems(issues, "error");
if (!errors.isEmpty()) {
return FormValidation.error(errors.toString());
}
final JSONArray warnings = collectProblems(issues, "warning");
if (!warnings.isEmpty()) {
return FormValidation.warning(warnings.toString());
}
return FormValidation.okWithMarkup("The configuration can be applied");
} catch (ConfiguratorException | IllegalArgumentException e) {
return FormValidation.error(e, e.getCause() == null ? e.getMessage() : e.getCause().getMessage());
}
}
#location 14
#vulnerability type NULL_DEREFERENCE
|
#fixed code
@POST
public FormValidation doCheckNewSource(@QueryParameter String newSource) {
Jenkins.getInstance().checkPermission(Jenkins.ADMINISTER);
String normalizedSource = Util.fixEmptyAndTrim(newSource);
File file = new File(Util.fixNull(normalizedSource));
if (normalizedSource == null) {
return FormValidation.ok(); // empty, do nothing
}
if (!file.exists() && !ConfigurationAsCode.isSupportedURI(normalizedSource)) {
return FormValidation.error("Configuration cannot be applied. File or URL cannot be parsed or do not exist.");
}
List<YamlSource> yamlSources = Collections.emptyList();
try {
List<String> sources = Collections.singletonList(normalizedSource);
yamlSources = getConfigFromSources(sources);
final Map<Source, String> issues = checkWith(yamlSources);
final JSONArray errors = collectProblems(issues, "error");
if (!errors.isEmpty()) {
return FormValidation.error(errors.toString());
}
final JSONArray warnings = collectProblems(issues, "warning");
if (!warnings.isEmpty()) {
return FormValidation.warning(warnings.toString());
}
return FormValidation.okWithMarkup("The configuration can be applied");
} catch (ConfiguratorException | IllegalArgumentException e) {
return FormValidation.error(e, e.getCause() == null ? e.getMessage() : e.getCause().getMessage());
} finally {
closeSources(yamlSources);
}
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
public boolean equals(O o1, O o2) throws Exception {
final Object v1 = getValue(o1);
final Object v2 = getValue(o2);
if (v1 == null && v2 == null) return true;
return (v1.equals(v2));
}
#location 5
#vulnerability type NULL_DEREFERENCE
|
#fixed code
public boolean equals(O o1, O o2) throws Exception {
final Object v1 = getValue(o1);
final Object v2 = getValue(o2);
if (v1 == null && v2 == null) return true;
return (v1 != null && v1.equals(v2));
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
@Override
public GlobalMatrixAuthorizationStrategy configure(Object config) throws Exception {
Map map = (Map) config;
Collection o = (Collection<?>)map.get("grantedPermissions");
Configurator<GroupPermissionDefinition> permissionConfigurator = Configurator.lookup(GroupPermissionDefinition.class);
Map<Permission,Set<String>> grantedPermissions = new HashMap<>();
for(Object entry : o) {
GroupPermissionDefinition gpd = permissionConfigurator.configure(entry);
//We transform the linear list to a matrix (Where permission is the key instead)
gpd.grantPermission(grantedPermissions);
}
//TODO: Once change is in place for GlobalMatrixAuthentication. Switch away from reflection
GlobalMatrixAuthorizationStrategy gms = new GlobalMatrixAuthorizationStrategy();
Field f = gms.getClass().getDeclaredField("grantedPermissions");
f.setAccessible(true);
f.set(gms, grantedPermissions);
return gms;
}
#location 8
#vulnerability type NULL_DEREFERENCE
|
#fixed code
@Override
public GlobalMatrixAuthorizationStrategy configure(Object config) throws ConfiguratorException {
Map map = (Map) config;
Collection o = (Collection<?>)map.get("grantedPermissions");
Configurator<GroupPermissionDefinition> permissionConfigurator = Configurator.lookupOrFail(GroupPermissionDefinition.class);
Map<Permission,Set<String>> grantedPermissions = new HashMap<>();
for(Object entry : o) {
GroupPermissionDefinition gpd = permissionConfigurator.configureNonNull(entry);
//We transform the linear list to a matrix (Where permission is the key instead)
gpd.grantPermission(grantedPermissions);
}
//TODO: Once change is in place for GlobalMatrixAuthentication. Switch away from reflection
GlobalMatrixAuthorizationStrategy gms = new GlobalMatrixAuthorizationStrategy();
try {
Field f = gms.getClass().getDeclaredField("grantedPermissions");
f.setAccessible(true);
f.set(gms, grantedPermissions);
} catch (NoSuchFieldException | IllegalAccessException ex) {
throw new ConfiguratorException(this, "Cannot set GlobalMatrixAuthorizationStrategy#grantedPermissions via reflection", ex);
}
return gms;
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
@CheckForNull
@Override
public CNode describe(T instance) throws Exception {
// Here we assume a correctly designed DataBound Object will have required attributes set by DataBoundConstructor
// and all others using DataBoundSetters. So constructor parameters for sure are part of the description, others
// need to be compared with default values.
// Build same object with only constructor parameters
final Constructor constructor = getDataBoundConstructor(target);
final Parameter[] parameters = constructor.getParameters();
final String[] names = ClassDescriptor.loadParameterNames(constructor);
final Attribute[] attributes = new Attribute[parameters.length];
final Object[] args = new Object[parameters.length];
for (int i = 0; i < parameters.length; i++) {
final Parameter p = parameters[i];
final Attribute a = detectActualType(names[i], p.getParameterizedType());
args[i] = a.getValue(instance);
attributes[i] = a;
}
T ref = (T) constructor.newInstance(args);
// compare instance with this "default" object
Mapping mapping = compare(instance, ref);
// add constructor parameters
for (int i = 0; i < parameters.length; i++) {
final Configurator c = Configurator.lookup(attributes[i].getType());
mapping.put(names[i], c.describe(args[i]));
}
return mapping;
}
#location 31
#vulnerability type NULL_DEREFERENCE
|
#fixed code
@CheckForNull
@Override
public CNode describe(T instance) throws Exception {
// Here we assume a correctly designed DataBound Object will have required attributes set by DataBoundConstructor
// and all others using DataBoundSetters. So constructor parameters for sure are part of the description, others
// need to be compared with default values.
// Build same object with only constructor parameters
final Constructor constructor = getDataBoundConstructor(target);
final Parameter[] parameters = constructor.getParameters();
final String[] names = ClassDescriptor.loadParameterNames(constructor);
final Attribute[] attributes = new Attribute[parameters.length];
final Object[] args = new Object[parameters.length];
for (int i = 0; i < parameters.length; i++) {
final Parameter p = parameters[i];
final Attribute a = detectActualType(names[i], p.getParameterizedType());
args[i] = a.getValue(instance);
attributes[i] = a;
}
T ref = (T) constructor.newInstance(args);
// compare instance with this "default" object
Mapping mapping = compare(instance, ref);
// add constructor parameters
for (int i = 0; i < parameters.length; i++) {
final Configurator c = Configurator.lookup(attributes[i].getType());
if (args[i] == null) continue;
mapping.put(names[i], attributes[i].describe(args[i]));
}
return mapping;
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
protected void configure(Map config, T instance) throws Exception {
final Set<Attribute> attributes = describe();
for (Attribute attribute : attributes) {
final String name = attribute.getName();
final Object sub = removeIgnoreCase(config, name);
if (sub != null) {
if (attribute.isMultiple()) {
List values = new ArrayList<>();
for (Object o : (List) sub) {
Object value = Configurator.lookup(attribute.getType()).configure(o);
values.add(value);
}
attribute.setValue(instance, values);
} else {
Object value = Configurator.lookup(attribute.getType()).configure(sub);
attribute.setValue(instance, value);
}
}
}
if (!config.isEmpty()) {
final String invalid = StringUtils.join(config.keySet(), ',');
throw new IllegalArgumentException("Invalid configuration elements for type " + instance.getClass() + " : " + invalid);
}
}
#location 16
#vulnerability type NULL_DEREFERENCE
|
#fixed code
protected void configure(Map config, T instance) throws Exception {
final Set<Attribute> attributes = describe();
for (Attribute attribute : attributes) {
final String name = attribute.getName();
final Object sub = removeIgnoreCase(config, name);
if (sub != null) {
final Class k = attribute.getType();
final Configurator configurator = Configurator.lookup(k);
if (configurator == null) throw new IllegalStateException("No configurator implementation to manage "+k);
if (attribute.isMultiple()) {
List values = new ArrayList<>();
for (Object o : (List) sub) {
Object value = configurator.configure(o);
values.add(value);
}
attribute.setValue(instance, values);
} else {
Object value = configurator.configure(sub);
attribute.setValue(instance, value);
}
}
}
if (!config.isEmpty()) {
final String invalid = StringUtils.join(config.keySet(), ',');
throw new IllegalArgumentException("Invalid configuration elements for type " + instance.getClass() + " : " + invalid);
}
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
@Override
public DLegerEntry get(Long index) {
PreConditions.check(index <= legerEndIndex, DLegerException.Code.INDEX_OUT_OF_RANGE, String.format("%d should < %d", index, legerEndIndex), memberState.getLeaderId());
SelectMmapBufferResult indexSbr = indexFileQueue.getData(index * INDEX_NUIT_SIZE, INDEX_NUIT_SIZE);
PreConditions.check(indexSbr.getByteBuffer() != null, DLegerException.Code.DISK_ERROR, null);
indexSbr.getByteBuffer().getInt(); //magic
long pos = indexSbr.getByteBuffer().getLong();
int size = indexSbr.getByteBuffer().getInt();
indexSbr.release();
SelectMmapBufferResult dataSbr = dataFileQueue.getData(pos, size);
PreConditions.check(dataSbr.getByteBuffer() != null, DLegerException.Code.DISK_ERROR, null);
DLegerEntry dLegerEntry = DLegerEntryCoder.decode(dataSbr.getByteBuffer());
dataSbr.release();
return dLegerEntry;
}
#location 3
#vulnerability type THREAD_SAFETY_VIOLATION
|
#fixed code
@Override
public DLegerEntry get(Long index) {
PreConditions.check(index <= legerEndIndex && index >= legerBeginIndex, DLegerException.Code.INDEX_OUT_OF_RANGE, String.format("%d should between %d-%d", index, legerBeginIndex, legerEndIndex), memberState.getLeaderId());
SelectMmapBufferResult indexSbr = indexFileQueue.getData(index * INDEX_NUIT_SIZE, INDEX_NUIT_SIZE);
PreConditions.check(indexSbr.getByteBuffer() != null, DLegerException.Code.DISK_ERROR, null);
indexSbr.getByteBuffer().getInt(); //magic
long pos = indexSbr.getByteBuffer().getLong();
int size = indexSbr.getByteBuffer().getInt();
indexSbr.release();
SelectMmapBufferResult dataSbr = dataFileQueue.getData(pos, size);
PreConditions.check(dataSbr.getByteBuffer() != null, DLegerException.Code.DISK_ERROR, null);
DLegerEntry dLegerEntry = DLegerEntryCoder.decode(dataSbr.getByteBuffer());
dataSbr.release();
return dLegerEntry;
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
public void recover() {
final List<MmapFile> mappedFiles = this.dataFileQueue.getMappedFiles();
if (mappedFiles.isEmpty()) {
this.indexFileQueue.updateWherePosition(0);
this.indexFileQueue.truncateDirtyFiles(0);
return;
}
int index = mappedFiles.size() - 3;
if (index < 0) {
index = 0;
}
long firstEntryIndex = -1;
for (int i = index; i >= 0; i--) {
index = i;
MmapFile mappedFile = mappedFiles.get(index);
ByteBuffer byteBuffer = mappedFile.sliceByteBuffer();
try {
int magic = byteBuffer.getInt();
int size = byteBuffer.getInt();
long entryIndex = byteBuffer.getLong();
long entryTerm = byteBuffer.get();
PreConditions.check(magic != MmapFileQueue.BLANK_MAGIC_CODE && magic >= MAGIC_1 && MAGIC_1 <= CURRENT_MAGIC, DLegerException.Code.DISK_ERROR, "unknown magic is " + magic);
PreConditions.check(size > DLegerEntry.HEADER_SIZE, DLegerException.Code.DISK_ERROR, String.format("Size %d should greater than %d", size, DLegerEntry.HEADER_SIZE) );
SelectMmapBufferResult indexSbr = indexFileQueue.getData(entryIndex * INDEX_NUIT_SIZE);
PreConditions.check(indexSbr != null, DLegerException.Code.DISK_ERROR, String.format("index: %d pos: %d", entryIndex, entryIndex * INDEX_NUIT_SIZE));
indexSbr.release();
ByteBuffer indexByteBuffer = indexSbr.getByteBuffer();
int magicFromIndex = indexByteBuffer.getInt();
long posFromIndex = indexByteBuffer.getLong();
int sizeFromIndex = indexByteBuffer.getInt();
long indexFromIndex = indexByteBuffer.getLong();
long termFromIndex = indexByteBuffer.get();
PreConditions.check(magic == magicFromIndex, DLegerException.Code.DISK_ERROR, String.format("magic %d != %d", magic, magicFromIndex));
PreConditions.check(size == sizeFromIndex, DLegerException.Code.DISK_ERROR, String.format("size %d != %d", size, sizeFromIndex));
PreConditions.check(entryIndex == indexFromIndex, DLegerException.Code.DISK_ERROR, String.format("index %d != %d", entryIndex, indexFromIndex));
PreConditions.check(entryTerm == termFromIndex, DLegerException.Code.DISK_ERROR, String.format("term %d != %d", entryTerm, termFromIndex));
PreConditions.check(posFromIndex == mappedFile.getFileFromOffset(), DLegerException.Code.DISK_ERROR, String.format("pos %d != %d", mappedFile.getFileFromOffset(), posFromIndex));
firstEntryIndex = entryIndex;
break;
} catch (Throwable t) {
logger.warn("Pre check data and index failed {}", mappedFile.getFileName(), t);
}
}
MmapFile mappedFile = mappedFiles.get(index);
ByteBuffer byteBuffer = mappedFile.sliceByteBuffer();
logger.info("Begin to recover data from entryIndex: {} fileIndex: {} fileSize: {} fileName:{} ", firstEntryIndex, index, mappedFiles.size(), mappedFile.getFileName());
long lastEntryIndex = -1;
long lastEntryTerm = -1;
long processOffset = mappedFile.getFileFromOffset();
boolean needWriteIndex = false;
while (true) {
try {
int relativePos = byteBuffer.position();
long absolutePos = mappedFile.getFileFromOffset() + relativePos;
int magic = byteBuffer.getInt();
if (magic == MmapFileQueue.BLANK_MAGIC_CODE) {
processOffset = mappedFile.getFileFromOffset() + mappedFile.getFileSize();
index++;
if (index >= mappedFiles.size()) {
logger.info("Recover data file over, the last file {}", mappedFile.getFileName());
break;
} else {
mappedFile = mappedFiles.get(index);
byteBuffer = mappedFile.sliceByteBuffer();
processOffset = mappedFile.getFileFromOffset();
logger.info("Trying to recover index file {}", mappedFile.getFileName());
continue;
}
}
int size = byteBuffer.getInt();
long entryIndex = byteBuffer.getLong();
long entryTerm = byteBuffer.get();
byteBuffer.position(relativePos + size);
String message = String.format("pos: %d size: %d magic:%d index:%d term:%d", absolutePos, size, magic, entryIndex, entryTerm);
PreConditions.check(magic <= CURRENT_MAGIC && magic >= MAGIC_1, DLegerException.Code.DISK_ERROR, String.format("%s currMagic: %d", message, CURRENT_MAGIC));
if (lastEntryIndex != -1) {
PreConditions.check(entryIndex == lastEntryIndex + 1, DLegerException.Code.DISK_ERROR, String.format("%s lastEntryIndex: %d", message, lastEntryIndex));
}
PreConditions.check(entryTerm >= lastEntryTerm, DLegerException.Code.DISK_ERROR, String.format("%s lastEntryTerm: ", message, lastEntryTerm));
PreConditions.check(size > DLegerEntry.HEADER_SIZE, DLegerException.Code.DISK_ERROR, String.format("Size %d should greater than %d", size, DLegerEntry.HEADER_SIZE) );
if (!needWriteIndex) {
try {
SelectMmapBufferResult indexSbr = indexFileQueue.getData(entryIndex * INDEX_NUIT_SIZE);
PreConditions.check(indexSbr != null, DLegerException.Code.DISK_ERROR, String.format("index: %d pos: %d", entryIndex, entryIndex * INDEX_NUIT_SIZE));
indexSbr.release();
ByteBuffer indexByteBuffer = indexSbr.getByteBuffer();
int magicFromIndex = indexByteBuffer.getInt();
long posFromIndex = indexByteBuffer.getLong();
int sizeFromIndex = indexByteBuffer.getInt();
long indexFromIndex = indexByteBuffer.getLong();
long termFromIndex = indexByteBuffer.get();
PreConditions.check(magic == magicFromIndex, DLegerException.Code.DISK_ERROR, String.format("magic %d != %d", magic, magicFromIndex));
PreConditions.check(size == sizeFromIndex, DLegerException.Code.DISK_ERROR, String.format("size %d != %d", size, sizeFromIndex));
PreConditions.check(entryIndex == indexFromIndex, DLegerException.Code.DISK_ERROR, String.format("index %d != %d", entryIndex, indexFromIndex));
PreConditions.check(entryTerm == termFromIndex, DLegerException.Code.DISK_ERROR, String.format("term %d != %d", entryTerm, termFromIndex));
PreConditions.check(absolutePos == posFromIndex, DLegerException.Code.DISK_ERROR, String.format("pos %d != %d", mappedFile.getFileFromOffset(), posFromIndex));
} catch (Exception e) {
logger.warn("Compare data to index failed {}", mappedFile.getFileName());
indexFileQueue.truncateDirtyFiles(entryIndex * INDEX_NUIT_SIZE);
if (indexFileQueue.getMaxWrotePosition() != entryIndex * INDEX_NUIT_SIZE) {
logger.warn("Unexpected wrote position in index file {} != {}", indexFileQueue.getMaxWrotePosition(), entryIndex * INDEX_NUIT_SIZE);
indexFileQueue.truncateDirtyFiles(0);
}
if (indexFileQueue.getMappedFiles().isEmpty()) {
indexFileQueue.getLastMappedFile(entryIndex * INDEX_NUIT_SIZE);
}
needWriteIndex = true;
}
}
if (needWriteIndex) {
ByteBuffer indexBuffer = localIndexBuffer.get();
DLegerEntryCoder.encodeIndex(absolutePos, size, magic, entryIndex, entryTerm, indexBuffer);
long indexPos = indexFileQueue.append(indexBuffer.array(), 0, indexBuffer.remaining());
PreConditions.check(indexPos == entryIndex * INDEX_NUIT_SIZE, DLegerException.Code.DISK_ERROR, String.format("Write index failed index: %d", entryIndex));
}
lastEntryIndex = entryIndex;
lastEntryTerm = entryTerm;
processOffset += size;
} catch (Throwable t) {
logger.info("Recover data file to the end of {} ", mappedFile.getFileName(), t);
break;
}
}
logger.info("Recover data to the end entryIndex:{} processOffset:{}", lastEntryIndex, processOffset);
legerEndIndex = lastEntryIndex;
legerEndTerm = lastEntryTerm;
if (lastEntryIndex != -1) {
DLegerEntry entry = get(lastEntryIndex);
PreConditions.check(entry != null, DLegerException.Code.DISK_ERROR, "recheck get null entry");
PreConditions.check(entry.getIndex() == lastEntryIndex, DLegerException.Code.DISK_ERROR, String.format("recheck index %d != %d", entry.getIndex(), lastEntryIndex));
//get leger begin index
ByteBuffer tmpBuffer = dataFileQueue.getFirstMappedFile().sliceByteBuffer();
tmpBuffer.getInt(); //magic
tmpBuffer.getInt(); //size
legerBeginIndex = byteBuffer.getLong();
} else {
processOffset = 0;
}
this.dataFileQueue.updateWherePosition(processOffset);
this.dataFileQueue.truncateDirtyFiles(processOffset);
long indexProcessOffset = (lastEntryIndex + 1) * INDEX_NUIT_SIZE;
this.indexFileQueue.updateWherePosition(indexProcessOffset);
this.indexFileQueue.truncateDirtyFiles(indexProcessOffset);
return;
}
#location 140
#vulnerability type THREAD_SAFETY_VIOLATION
|
#fixed code
public void recover() {
final List<MmapFile> mappedFiles = this.dataFileQueue.getMappedFiles();
if (mappedFiles.isEmpty()) {
this.indexFileQueue.updateWherePosition(0);
this.indexFileQueue.truncateDirtyFiles(0);
return;
}
int index = mappedFiles.size() - 3;
if (index < 0) {
index = 0;
}
long firstEntryIndex = -1;
for (int i = index; i >= 0; i--) {
index = i;
MmapFile mappedFile = mappedFiles.get(index);
ByteBuffer byteBuffer = mappedFile.sliceByteBuffer();
try {
int magic = byteBuffer.getInt();
int size = byteBuffer.getInt();
long entryIndex = byteBuffer.getLong();
long entryTerm = byteBuffer.get();
PreConditions.check(magic != MmapFileQueue.BLANK_MAGIC_CODE && magic >= MAGIC_1 && MAGIC_1 <= CURRENT_MAGIC, DLegerException.Code.DISK_ERROR, "unknown magic is " + magic);
PreConditions.check(size > DLegerEntry.HEADER_SIZE, DLegerException.Code.DISK_ERROR, String.format("Size %d should greater than %d", size, DLegerEntry.HEADER_SIZE) );
SelectMmapBufferResult indexSbr = indexFileQueue.getData(entryIndex * INDEX_NUIT_SIZE);
PreConditions.check(indexSbr != null, DLegerException.Code.DISK_ERROR, String.format("index: %d pos: %d", entryIndex, entryIndex * INDEX_NUIT_SIZE));
indexSbr.release();
ByteBuffer indexByteBuffer = indexSbr.getByteBuffer();
int magicFromIndex = indexByteBuffer.getInt();
long posFromIndex = indexByteBuffer.getLong();
int sizeFromIndex = indexByteBuffer.getInt();
long indexFromIndex = indexByteBuffer.getLong();
long termFromIndex = indexByteBuffer.get();
PreConditions.check(magic == magicFromIndex, DLegerException.Code.DISK_ERROR, String.format("magic %d != %d", magic, magicFromIndex));
PreConditions.check(size == sizeFromIndex, DLegerException.Code.DISK_ERROR, String.format("size %d != %d", size, sizeFromIndex));
PreConditions.check(entryIndex == indexFromIndex, DLegerException.Code.DISK_ERROR, String.format("index %d != %d", entryIndex, indexFromIndex));
PreConditions.check(entryTerm == termFromIndex, DLegerException.Code.DISK_ERROR, String.format("term %d != %d", entryTerm, termFromIndex));
PreConditions.check(posFromIndex == mappedFile.getFileFromOffset(), DLegerException.Code.DISK_ERROR, String.format("pos %d != %d", mappedFile.getFileFromOffset(), posFromIndex));
firstEntryIndex = entryIndex;
break;
} catch (Throwable t) {
logger.warn("Pre check data and index failed {}", mappedFile.getFileName(), t);
}
}
MmapFile mappedFile = mappedFiles.get(index);
ByteBuffer byteBuffer = mappedFile.sliceByteBuffer();
logger.info("Begin to recover data from entryIndex: {} fileIndex: {} fileSize: {} fileName:{} ", firstEntryIndex, index, mappedFiles.size(), mappedFile.getFileName());
long lastEntryIndex = -1;
long lastEntryTerm = -1;
long processOffset = mappedFile.getFileFromOffset();
boolean needWriteIndex = false;
while (true) {
try {
int relativePos = byteBuffer.position();
long absolutePos = mappedFile.getFileFromOffset() + relativePos;
int magic = byteBuffer.getInt();
if (magic == MmapFileQueue.BLANK_MAGIC_CODE) {
processOffset = mappedFile.getFileFromOffset() + mappedFile.getFileSize();
index++;
if (index >= mappedFiles.size()) {
logger.info("Recover data file over, the last file {}", mappedFile.getFileName());
break;
} else {
mappedFile = mappedFiles.get(index);
byteBuffer = mappedFile.sliceByteBuffer();
processOffset = mappedFile.getFileFromOffset();
logger.info("Trying to recover index file {}", mappedFile.getFileName());
continue;
}
}
int size = byteBuffer.getInt();
long entryIndex = byteBuffer.getLong();
long entryTerm = byteBuffer.get();
byteBuffer.position(relativePos + size);
String message = String.format("pos: %d size: %d magic:%d index:%d term:%d", absolutePos, size, magic, entryIndex, entryTerm);
PreConditions.check(magic <= CURRENT_MAGIC && magic >= MAGIC_1, DLegerException.Code.DISK_ERROR, String.format("%s currMagic: %d", message, CURRENT_MAGIC));
if (lastEntryIndex != -1) {
PreConditions.check(entryIndex == lastEntryIndex + 1, DLegerException.Code.DISK_ERROR, String.format("%s lastEntryIndex: %d", message, lastEntryIndex));
}
PreConditions.check(entryTerm >= lastEntryTerm, DLegerException.Code.DISK_ERROR, String.format("%s lastEntryTerm: ", message, lastEntryTerm));
PreConditions.check(size > DLegerEntry.HEADER_SIZE, DLegerException.Code.DISK_ERROR, String.format("Size %d should greater than %d", size, DLegerEntry.HEADER_SIZE) );
if (!needWriteIndex) {
try {
SelectMmapBufferResult indexSbr = indexFileQueue.getData(entryIndex * INDEX_NUIT_SIZE);
PreConditions.check(indexSbr != null, DLegerException.Code.DISK_ERROR, String.format("index: %d pos: %d", entryIndex, entryIndex * INDEX_NUIT_SIZE));
indexSbr.release();
ByteBuffer indexByteBuffer = indexSbr.getByteBuffer();
int magicFromIndex = indexByteBuffer.getInt();
long posFromIndex = indexByteBuffer.getLong();
int sizeFromIndex = indexByteBuffer.getInt();
long indexFromIndex = indexByteBuffer.getLong();
long termFromIndex = indexByteBuffer.get();
PreConditions.check(magic == magicFromIndex, DLegerException.Code.DISK_ERROR, String.format("magic %d != %d", magic, magicFromIndex));
PreConditions.check(size == sizeFromIndex, DLegerException.Code.DISK_ERROR, String.format("size %d != %d", size, sizeFromIndex));
PreConditions.check(entryIndex == indexFromIndex, DLegerException.Code.DISK_ERROR, String.format("index %d != %d", entryIndex, indexFromIndex));
PreConditions.check(entryTerm == termFromIndex, DLegerException.Code.DISK_ERROR, String.format("term %d != %d", entryTerm, termFromIndex));
PreConditions.check(absolutePos == posFromIndex, DLegerException.Code.DISK_ERROR, String.format("pos %d != %d", mappedFile.getFileFromOffset(), posFromIndex));
} catch (Exception e) {
logger.warn("Compare data to index failed {}", mappedFile.getFileName());
indexFileQueue.truncateDirtyFiles(entryIndex * INDEX_NUIT_SIZE);
if (indexFileQueue.getMaxWrotePosition() != entryIndex * INDEX_NUIT_SIZE) {
logger.warn("Unexpected wrote position in index file {} != {}", indexFileQueue.getMaxWrotePosition(), entryIndex * INDEX_NUIT_SIZE);
indexFileQueue.truncateDirtyFiles(0);
}
if (indexFileQueue.getMappedFiles().isEmpty()) {
indexFileQueue.getLastMappedFile(entryIndex * INDEX_NUIT_SIZE);
}
needWriteIndex = true;
}
}
if (needWriteIndex) {
ByteBuffer indexBuffer = localIndexBuffer.get();
DLegerEntryCoder.encodeIndex(absolutePos, size, magic, entryIndex, entryTerm, indexBuffer);
long indexPos = indexFileQueue.append(indexBuffer.array(), 0, indexBuffer.remaining());
PreConditions.check(indexPos == entryIndex * INDEX_NUIT_SIZE, DLegerException.Code.DISK_ERROR, String.format("Write index failed index: %d", entryIndex));
}
lastEntryIndex = entryIndex;
lastEntryTerm = entryTerm;
processOffset += size;
} catch (Throwable t) {
logger.info("Recover data file to the end of {} ", mappedFile.getFileName(), t);
break;
}
}
logger.info("Recover data to the end entryIndex:{} processOffset:{}", lastEntryIndex, processOffset);
legerEndIndex = lastEntryIndex;
legerEndTerm = lastEntryTerm;
if (lastEntryIndex != -1) {
DLegerEntry entry = get(lastEntryIndex);
PreConditions.check(entry != null, DLegerException.Code.DISK_ERROR, "recheck get null entry");
PreConditions.check(entry.getIndex() == lastEntryIndex, DLegerException.Code.DISK_ERROR, String.format("recheck index %d != %d", entry.getIndex(), lastEntryIndex));
reviseLegerBeginIndex();
} else {
processOffset = 0;
}
this.dataFileQueue.updateWherePosition(processOffset);
this.dataFileQueue.truncateDirtyFiles(processOffset);
long indexProcessOffset = (lastEntryIndex + 1) * INDEX_NUIT_SIZE;
this.indexFileQueue.updateWherePosition(indexProcessOffset);
this.indexFileQueue.truncateDirtyFiles(indexProcessOffset);
return;
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
public void changeRoleToCandidate(long term) {
logger.info("[{}][ChangeRoleToCandidate] from term: {} and currterm: {}", memberState.getSelfId(), term, memberState.currTerm());
memberState.changeToCandidate(term);
nextTimeToRequestVote = -1;
}
#location 4
#vulnerability type THREAD_SAFETY_VIOLATION
|
#fixed code
public void changeRoleToCandidate(long term) {
logger.info("[{}][ChangeRoleToCandidate] from term: {} and currterm: {}", memberState.getSelfId(), term, memberState.currTerm());
memberState.changeToCandidate(term);
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
public void recover() {
final List<MmapFile> mappedFiles = this.dataFileQueue.getMappedFiles();
if (mappedFiles.isEmpty()) {
this.indexFileQueue.updateWherePosition(0);
this.indexFileQueue.truncateDirtyFiles(0);
return;
}
int index = mappedFiles.size() - 3;
if (index < 0) {
index = 0;
}
long firstEntryIndex = -1;
for (int i = index; i >= 0; i--) {
index = i;
MmapFile mappedFile = mappedFiles.get(index);
ByteBuffer byteBuffer = mappedFile.sliceByteBuffer();
try {
int magic = byteBuffer.getInt();
int size = byteBuffer.getInt();
long entryIndex = byteBuffer.getLong();
long entryTerm = byteBuffer.get();
PreConditions.check(magic != MmapFileQueue.BLANK_MAGIC_CODE && magic >= MAGIC_1 && MAGIC_1 <= CURRENT_MAGIC, DLegerException.Code.DISK_ERROR, "unknown magic is " + magic);
PreConditions.check(size > DLegerEntry.HEADER_SIZE, DLegerException.Code.DISK_ERROR, String.format("Size %d should greater than %d", size, DLegerEntry.HEADER_SIZE) );
SelectMmapBufferResult indexSbr = indexFileQueue.getData(entryIndex * INDEX_NUIT_SIZE);
PreConditions.check(indexSbr != null, DLegerException.Code.DISK_ERROR, String.format("index: %d pos: %d", entryIndex, entryIndex * INDEX_NUIT_SIZE));
indexSbr.release();
ByteBuffer indexByteBuffer = indexSbr.getByteBuffer();
int magicFromIndex = indexByteBuffer.getInt();
long posFromIndex = indexByteBuffer.getLong();
int sizeFromIndex = indexByteBuffer.getInt();
long indexFromIndex = indexByteBuffer.getLong();
long termFromIndex = indexByteBuffer.get();
PreConditions.check(magic == magicFromIndex, DLegerException.Code.DISK_ERROR, String.format("magic %d != %d", magic, magicFromIndex));
PreConditions.check(size == sizeFromIndex, DLegerException.Code.DISK_ERROR, String.format("size %d != %d", size, sizeFromIndex));
PreConditions.check(entryIndex == indexFromIndex, DLegerException.Code.DISK_ERROR, String.format("index %d != %d", entryIndex, indexFromIndex));
PreConditions.check(entryTerm == termFromIndex, DLegerException.Code.DISK_ERROR, String.format("term %d != %d", entryTerm, termFromIndex));
PreConditions.check(posFromIndex == mappedFile.getFileFromOffset(), DLegerException.Code.DISK_ERROR, String.format("pos %d != %d", mappedFile.getFileFromOffset(), posFromIndex));
firstEntryIndex = entryIndex;
break;
} catch (Throwable t) {
logger.warn("Pre check data and index failed {}", mappedFile.getFileName(), t);
}
}
MmapFile mappedFile = mappedFiles.get(index);
ByteBuffer byteBuffer = mappedFile.sliceByteBuffer();
logger.info("Begin to recover data from entryIndex: {} fileIndex: {} fileSize: {} fileName:{} ", firstEntryIndex, index, mappedFiles.size(), mappedFile.getFileName());
long lastEntryIndex = -1;
long lastEntryTerm = -1;
long processOffset = mappedFile.getFileFromOffset();
boolean needWriteIndex = false;
while (true) {
try {
int relativePos = byteBuffer.position();
long absolutePos = mappedFile.getFileFromOffset() + relativePos;
int magic = byteBuffer.getInt();
if (magic == MmapFileQueue.BLANK_MAGIC_CODE) {
processOffset = mappedFile.getFileFromOffset() + mappedFile.getFileSize();
index++;
if (index >= mappedFiles.size()) {
logger.info("Recover data file over, the last file {}", mappedFile.getFileName());
break;
} else {
mappedFile = mappedFiles.get(index);
byteBuffer = mappedFile.sliceByteBuffer();
processOffset = mappedFile.getFileFromOffset();
logger.info("Trying to recover index file {}", mappedFile.getFileName());
continue;
}
}
int size = byteBuffer.getInt();
long entryIndex = byteBuffer.getLong();
long entryTerm = byteBuffer.get();
byteBuffer.position(relativePos + size);
String message = String.format("pos: %d size: %d magic:%d index:%d term:%d", absolutePos, size, magic, entryIndex, entryTerm);
PreConditions.check(magic <= CURRENT_MAGIC && magic >= MAGIC_1, DLegerException.Code.DISK_ERROR, String.format("%s currMagic: %d", message, CURRENT_MAGIC));
if (lastEntryIndex != -1) {
PreConditions.check(entryIndex == lastEntryIndex + 1, DLegerException.Code.DISK_ERROR, String.format("%s lastEntryIndex: %d", message, lastEntryIndex));
}
PreConditions.check(entryTerm >= lastEntryTerm, DLegerException.Code.DISK_ERROR, String.format("%s lastEntryTerm: ", message, lastEntryTerm));
PreConditions.check(size > DLegerEntry.HEADER_SIZE, DLegerException.Code.DISK_ERROR, String.format("Size %d should greater than %d", size, DLegerEntry.HEADER_SIZE) );
if (!needWriteIndex) {
try {
SelectMmapBufferResult indexSbr = indexFileQueue.getData(entryIndex * INDEX_NUIT_SIZE);
PreConditions.check(indexSbr != null, DLegerException.Code.DISK_ERROR, String.format("index: %d pos: %d", entryIndex, entryIndex * INDEX_NUIT_SIZE));
indexSbr.release();
ByteBuffer indexByteBuffer = indexSbr.getByteBuffer();
int magicFromIndex = indexByteBuffer.getInt();
long posFromIndex = indexByteBuffer.getLong();
int sizeFromIndex = indexByteBuffer.getInt();
long indexFromIndex = indexByteBuffer.getLong();
long termFromIndex = indexByteBuffer.get();
PreConditions.check(magic == magicFromIndex, DLegerException.Code.DISK_ERROR, String.format("magic %d != %d", magic, magicFromIndex));
PreConditions.check(size == sizeFromIndex, DLegerException.Code.DISK_ERROR, String.format("size %d != %d", size, sizeFromIndex));
PreConditions.check(entryIndex == indexFromIndex, DLegerException.Code.DISK_ERROR, String.format("index %d != %d", entryIndex, indexFromIndex));
PreConditions.check(entryTerm == termFromIndex, DLegerException.Code.DISK_ERROR, String.format("term %d != %d", entryTerm, termFromIndex));
PreConditions.check(absolutePos == posFromIndex, DLegerException.Code.DISK_ERROR, String.format("pos %d != %d", mappedFile.getFileFromOffset(), posFromIndex));
} catch (Exception e) {
logger.warn("Compare data to index failed {}", mappedFile.getFileName());
indexFileQueue.truncateDirtyFiles(entryIndex * INDEX_NUIT_SIZE);
if (indexFileQueue.getMaxWrotePosition() != entryIndex * INDEX_NUIT_SIZE) {
logger.warn("Unexpected wrote position in index file {} != {}", indexFileQueue.getMaxWrotePosition(), entryIndex * INDEX_NUIT_SIZE);
indexFileQueue.truncateDirtyFiles(0);
}
if (indexFileQueue.getMappedFiles().isEmpty()) {
indexFileQueue.getLastMappedFile(entryIndex * INDEX_NUIT_SIZE);
}
needWriteIndex = true;
}
}
if (needWriteIndex) {
ByteBuffer indexBuffer = localIndexBuffer.get();
DLegerEntryCoder.encodeIndex(absolutePos, size, magic, entryIndex, entryTerm, indexBuffer);
long indexPos = indexFileQueue.append(indexBuffer.array(), 0, indexBuffer.remaining());
PreConditions.check(indexPos == entryIndex * INDEX_NUIT_SIZE, DLegerException.Code.DISK_ERROR, String.format("Write index failed index: %d", entryIndex));
}
lastEntryIndex = entryIndex;
lastEntryTerm = entryTerm;
processOffset += size;
} catch (Throwable t) {
logger.info("Recover data file to the end of {} ", mappedFile.getFileName(), t);
break;
}
}
logger.info("Recover data to the end entryIndex:{} processOffset:{}", lastEntryIndex, processOffset);
legerEndIndex = lastEntryIndex;
legerEndTerm = lastEntryTerm;
if (lastEntryIndex != -1) {
DLegerEntry entry = get(lastEntryIndex);
PreConditions.check(entry != null, DLegerException.Code.DISK_ERROR, "recheck get null entry");
PreConditions.check(entry.getIndex() == lastEntryIndex, DLegerException.Code.DISK_ERROR, String.format("recheck index %d != %d", entry.getIndex(), lastEntryIndex));
//get leger begin index
ByteBuffer tmpBuffer = dataFileQueue.getFirstMappedFile().sliceByteBuffer();
tmpBuffer.getInt(); //magic
tmpBuffer.getInt(); //size
legerBeginIndex = byteBuffer.getLong();
} else {
processOffset = 0;
}
this.dataFileQueue.updateWherePosition(processOffset);
this.dataFileQueue.truncateDirtyFiles(processOffset);
long indexProcessOffset = (lastEntryIndex + 1) * INDEX_NUIT_SIZE;
this.indexFileQueue.updateWherePosition(indexProcessOffset);
this.indexFileQueue.truncateDirtyFiles(indexProcessOffset);
return;
}
#location 133
#vulnerability type THREAD_SAFETY_VIOLATION
|
#fixed code
public void recover() {
final List<MmapFile> mappedFiles = this.dataFileQueue.getMappedFiles();
if (mappedFiles.isEmpty()) {
this.indexFileQueue.updateWherePosition(0);
this.indexFileQueue.truncateDirtyFiles(0);
return;
}
int index = mappedFiles.size() - 3;
if (index < 0) {
index = 0;
}
long firstEntryIndex = -1;
for (int i = index; i >= 0; i--) {
index = i;
MmapFile mappedFile = mappedFiles.get(index);
ByteBuffer byteBuffer = mappedFile.sliceByteBuffer();
try {
int magic = byteBuffer.getInt();
int size = byteBuffer.getInt();
long entryIndex = byteBuffer.getLong();
long entryTerm = byteBuffer.get();
PreConditions.check(magic != MmapFileQueue.BLANK_MAGIC_CODE && magic >= MAGIC_1 && MAGIC_1 <= CURRENT_MAGIC, DLegerException.Code.DISK_ERROR, "unknown magic is " + magic);
PreConditions.check(size > DLegerEntry.HEADER_SIZE, DLegerException.Code.DISK_ERROR, String.format("Size %d should greater than %d", size, DLegerEntry.HEADER_SIZE) );
SelectMmapBufferResult indexSbr = indexFileQueue.getData(entryIndex * INDEX_NUIT_SIZE);
PreConditions.check(indexSbr != null, DLegerException.Code.DISK_ERROR, String.format("index: %d pos: %d", entryIndex, entryIndex * INDEX_NUIT_SIZE));
indexSbr.release();
ByteBuffer indexByteBuffer = indexSbr.getByteBuffer();
int magicFromIndex = indexByteBuffer.getInt();
long posFromIndex = indexByteBuffer.getLong();
int sizeFromIndex = indexByteBuffer.getInt();
long indexFromIndex = indexByteBuffer.getLong();
long termFromIndex = indexByteBuffer.get();
PreConditions.check(magic == magicFromIndex, DLegerException.Code.DISK_ERROR, String.format("magic %d != %d", magic, magicFromIndex));
PreConditions.check(size == sizeFromIndex, DLegerException.Code.DISK_ERROR, String.format("size %d != %d", size, sizeFromIndex));
PreConditions.check(entryIndex == indexFromIndex, DLegerException.Code.DISK_ERROR, String.format("index %d != %d", entryIndex, indexFromIndex));
PreConditions.check(entryTerm == termFromIndex, DLegerException.Code.DISK_ERROR, String.format("term %d != %d", entryTerm, termFromIndex));
PreConditions.check(posFromIndex == mappedFile.getFileFromOffset(), DLegerException.Code.DISK_ERROR, String.format("pos %d != %d", mappedFile.getFileFromOffset(), posFromIndex));
firstEntryIndex = entryIndex;
break;
} catch (Throwable t) {
logger.warn("Pre check data and index failed {}", mappedFile.getFileName(), t);
}
}
MmapFile mappedFile = mappedFiles.get(index);
ByteBuffer byteBuffer = mappedFile.sliceByteBuffer();
logger.info("Begin to recover data from entryIndex: {} fileIndex: {} fileSize: {} fileName:{} ", firstEntryIndex, index, mappedFiles.size(), mappedFile.getFileName());
long lastEntryIndex = -1;
long lastEntryTerm = -1;
long processOffset = mappedFile.getFileFromOffset();
boolean needWriteIndex = false;
while (true) {
try {
int relativePos = byteBuffer.position();
long absolutePos = mappedFile.getFileFromOffset() + relativePos;
int magic = byteBuffer.getInt();
if (magic == MmapFileQueue.BLANK_MAGIC_CODE) {
processOffset = mappedFile.getFileFromOffset() + mappedFile.getFileSize();
index++;
if (index >= mappedFiles.size()) {
logger.info("Recover data file over, the last file {}", mappedFile.getFileName());
break;
} else {
mappedFile = mappedFiles.get(index);
byteBuffer = mappedFile.sliceByteBuffer();
processOffset = mappedFile.getFileFromOffset();
logger.info("Trying to recover index file {}", mappedFile.getFileName());
continue;
}
}
int size = byteBuffer.getInt();
long entryIndex = byteBuffer.getLong();
long entryTerm = byteBuffer.get();
byteBuffer.position(relativePos + size);
String message = String.format("pos: %d size: %d magic:%d index:%d term:%d", absolutePos, size, magic, entryIndex, entryTerm);
PreConditions.check(magic <= CURRENT_MAGIC && magic >= MAGIC_1, DLegerException.Code.DISK_ERROR, String.format("%s currMagic: %d", message, CURRENT_MAGIC));
if (lastEntryIndex != -1) {
PreConditions.check(entryIndex == lastEntryIndex + 1, DLegerException.Code.DISK_ERROR, String.format("%s lastEntryIndex: %d", message, lastEntryIndex));
}
PreConditions.check(entryTerm >= lastEntryTerm, DLegerException.Code.DISK_ERROR, String.format("%s lastEntryTerm: ", message, lastEntryTerm));
PreConditions.check(size > DLegerEntry.HEADER_SIZE, DLegerException.Code.DISK_ERROR, String.format("Size %d should greater than %d", size, DLegerEntry.HEADER_SIZE) );
if (!needWriteIndex) {
try {
SelectMmapBufferResult indexSbr = indexFileQueue.getData(entryIndex * INDEX_NUIT_SIZE);
PreConditions.check(indexSbr != null, DLegerException.Code.DISK_ERROR, String.format("index: %d pos: %d", entryIndex, entryIndex * INDEX_NUIT_SIZE));
indexSbr.release();
ByteBuffer indexByteBuffer = indexSbr.getByteBuffer();
int magicFromIndex = indexByteBuffer.getInt();
long posFromIndex = indexByteBuffer.getLong();
int sizeFromIndex = indexByteBuffer.getInt();
long indexFromIndex = indexByteBuffer.getLong();
long termFromIndex = indexByteBuffer.get();
PreConditions.check(magic == magicFromIndex, DLegerException.Code.DISK_ERROR, String.format("magic %d != %d", magic, magicFromIndex));
PreConditions.check(size == sizeFromIndex, DLegerException.Code.DISK_ERROR, String.format("size %d != %d", size, sizeFromIndex));
PreConditions.check(entryIndex == indexFromIndex, DLegerException.Code.DISK_ERROR, String.format("index %d != %d", entryIndex, indexFromIndex));
PreConditions.check(entryTerm == termFromIndex, DLegerException.Code.DISK_ERROR, String.format("term %d != %d", entryTerm, termFromIndex));
PreConditions.check(absolutePos == posFromIndex, DLegerException.Code.DISK_ERROR, String.format("pos %d != %d", mappedFile.getFileFromOffset(), posFromIndex));
} catch (Exception e) {
logger.warn("Compare data to index failed {}", mappedFile.getFileName());
indexFileQueue.truncateDirtyFiles(entryIndex * INDEX_NUIT_SIZE);
if (indexFileQueue.getMaxWrotePosition() != entryIndex * INDEX_NUIT_SIZE) {
logger.warn("Unexpected wrote position in index file {} != {}", indexFileQueue.getMaxWrotePosition(), entryIndex * INDEX_NUIT_SIZE);
indexFileQueue.truncateDirtyFiles(0);
}
if (indexFileQueue.getMappedFiles().isEmpty()) {
indexFileQueue.getLastMappedFile(entryIndex * INDEX_NUIT_SIZE);
}
needWriteIndex = true;
}
}
if (needWriteIndex) {
ByteBuffer indexBuffer = localIndexBuffer.get();
DLegerEntryCoder.encodeIndex(absolutePos, size, magic, entryIndex, entryTerm, indexBuffer);
long indexPos = indexFileQueue.append(indexBuffer.array(), 0, indexBuffer.remaining());
PreConditions.check(indexPos == entryIndex * INDEX_NUIT_SIZE, DLegerException.Code.DISK_ERROR, String.format("Write index failed index: %d", entryIndex));
}
lastEntryIndex = entryIndex;
lastEntryTerm = entryTerm;
processOffset += size;
} catch (Throwable t) {
logger.info("Recover data file to the end of {} ", mappedFile.getFileName(), t);
break;
}
}
logger.info("Recover data to the end entryIndex:{} processOffset:{}", lastEntryIndex, processOffset);
legerEndIndex = lastEntryIndex;
legerEndTerm = lastEntryTerm;
if (lastEntryIndex != -1) {
DLegerEntry entry = get(lastEntryIndex);
PreConditions.check(entry != null, DLegerException.Code.DISK_ERROR, "recheck get null entry");
PreConditions.check(entry.getIndex() == lastEntryIndex, DLegerException.Code.DISK_ERROR, String.format("recheck index %d != %d", entry.getIndex(), lastEntryIndex));
reviseLegerBeginIndex();
} else {
processOffset = 0;
}
this.dataFileQueue.updateWherePosition(processOffset);
this.dataFileQueue.truncateDirtyFiles(processOffset);
long indexProcessOffset = (lastEntryIndex + 1) * INDEX_NUIT_SIZE;
this.indexFileQueue.updateWherePosition(indexProcessOffset);
this.indexFileQueue.truncateDirtyFiles(indexProcessOffset);
return;
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
public long append(byte[] data, int pos, int len, boolean useBlank) {
MmapFile mappedFile = getLastMappedFile();
if (null == mappedFile || mappedFile.isFull()) {
mappedFile = getLastMappedFile(0);
}
if (null == mappedFile) {
logger.error("Create mapped file for {}", storePath);
return -1;
}
int blank = useBlank ? MIN_BLANK_LEN : 0;
if (len + blank > mappedFile.getFileSize() - mappedFile.getWrotePosition()) {
if (blank < MIN_BLANK_LEN) {
logger.error("Blank {} should ge {}", blank, MIN_BLANK_LEN);
return -1;
} else {
ByteBuffer byteBuffer = ByteBuffer.allocate(mappedFile.getFileSize() - mappedFile.getWrotePosition());
byteBuffer.putInt(BLANK_MAGIC_CODE);
byteBuffer.putInt(mappedFile.getFileSize() - mappedFile.getWrotePosition());
if (mappedFile.appendMessage(byteBuffer.array())) {
//need to set the wrote position
mappedFile.setWrotePosition(mappedFile.getFileSize());
} else {
logger.error("Append blank error for {}", storePath);
return -1;
}
mappedFile = getLastMappedFile(0);
if (null == mappedFile) {
logger.error("Create mapped file for {}", storePath);
return -1;
}
}
}
long currPosition = mappedFile.getFileFromOffset() + mappedFile.getWrotePosition();
if (!mappedFile.appendMessage(data, pos, len)) {
logger.error("Append error for {}", storePath);
return -1;
}
return currPosition;
}
#location 34
#vulnerability type RESOURCE_LEAK
|
#fixed code
public long append(byte[] data, int pos, int len, boolean useBlank) {
if (preAppend(len, useBlank) == -1) {
return -1;
}
MmapFile mappedFile = getLastMappedFile();
long currPosition = mappedFile.getFileFromOffset() + mappedFile.getWrotePosition();
if (!mappedFile.appendMessage(data, pos, len)) {
logger.error("Append error for {}", storePath);
return -1;
}
return currPosition;
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
public CompletableFuture<HeartBeatResponse> handleHeartBeat(HeartBeatRequest request) throws Exception {
if (request.getTerm() < memberState.currTerm()) {
return CompletableFuture.completedFuture((HeartBeatResponse) new HeartBeatResponse().term(memberState.currTerm()).code(DLegerResponseCode.EXPIRED_TERM.getCode()));
} else if (request.getTerm() == memberState.currTerm()) {
if (request.getLeaderId().equals(memberState.getLeaderId())) {
lastLeaderHeartBeatTime = System.currentTimeMillis();
return CompletableFuture.completedFuture(new HeartBeatResponse());
}
}
//abnormal case
//hold the lock to get the latest term and leaderId
synchronized (memberState) {
if (request.getTerm() < memberState.currTerm()) {
return CompletableFuture.completedFuture((HeartBeatResponse) new HeartBeatResponse().term(memberState.currTerm()).code(DLegerResponseCode.EXPIRED_TERM.getCode()));
} else if (request.getTerm() == memberState.currTerm()) {
if (memberState.getLeaderId() == null) {
changeRoleToFollower(request.getTerm(), request.getLeaderId());
return CompletableFuture.completedFuture(new HeartBeatResponse());
} else if (request.getLeaderId().equals(memberState.getLeaderId())) {
lastLeaderHeartBeatTime = System.currentTimeMillis();
return CompletableFuture.completedFuture(new HeartBeatResponse());
} else {
//this should not happen, but if happened
logger.error("[{}][BUG] currterm {} has leader {}, but received leader {}", memberState.getSelfId(), memberState.currTerm(), memberState.getLeaderId(), request.getLeaderId());
return CompletableFuture.completedFuture((HeartBeatResponse) new HeartBeatResponse().code(DLegerResponseCode.INTERNAL_ERROR.getCode()));
}
} else {
//To make it simple, for larger term, do not change to follower immediately
//first change to candidate, and notify the state-maintainer thread
changeRoleToCandidate(request.getTerm());
//TOOD notify
return CompletableFuture.completedFuture(new HeartBeatResponse());
}
}
}
#location 5
#vulnerability type THREAD_SAFETY_VIOLATION
|
#fixed code
public CompletableFuture<HeartBeatResponse> handleHeartBeat(HeartBeatRequest request) throws Exception {
if (request.getTerm() < memberState.currTerm()) {
return CompletableFuture.completedFuture((HeartBeatResponse) new HeartBeatResponse().term(memberState.currTerm()).code(DLegerResponseCode.EXPIRED_TERM.getCode()));
} else if (request.getTerm() == memberState.currTerm()) {
if (request.getLeaderId().equals(memberState.getLeaderId())) {
lastLeaderHeartBeatTime = System.currentTimeMillis();
return CompletableFuture.completedFuture(new HeartBeatResponse());
}
}
//abnormal case
//hold the lock to get the latest term and leaderId
synchronized (memberState) {
if (request.getTerm() < memberState.currTerm()) {
return CompletableFuture.completedFuture((HeartBeatResponse) new HeartBeatResponse().term(memberState.currTerm()).code(DLegerResponseCode.EXPIRED_TERM.getCode()));
} else if (request.getTerm() == memberState.currTerm()) {
if (memberState.getLeaderId() == null) {
changeRoleToFollower(request.getTerm(), request.getLeaderId());
return CompletableFuture.completedFuture(new HeartBeatResponse());
} else if (request.getLeaderId().equals(memberState.getLeaderId())) {
lastLeaderHeartBeatTime = System.currentTimeMillis();
return CompletableFuture.completedFuture(new HeartBeatResponse());
} else {
//this should not happen, but if happened
logger.error("[{}][BUG] currterm {} has leader {}, but received leader {}", memberState.getSelfId(), memberState.currTerm(), memberState.getLeaderId(), request.getLeaderId());
return CompletableFuture.completedFuture((HeartBeatResponse) new HeartBeatResponse().code(DLegerResponseCode.INCONSISTENT_LEADER.getCode()));
}
} else {
//To make it simple, for larger term, do not change to follower immediately
//first change to candidate, and notify the state-maintainer thread
changeRoleToCandidate(request.getTerm());
//TOOD notify
return CompletableFuture.completedFuture(new HeartBeatResponse());
}
}
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
public long append(byte[] data, int pos, int len, boolean useBlank) {
MmapFile mappedFile = getLastMappedFile();
if (null == mappedFile || mappedFile.isFull()) {
mappedFile = getLastMappedFile(0);
}
if (null == mappedFile) {
logger.error("Create mapped file for {}", storePath);
return -1;
}
int blank = useBlank ? MIN_BLANK_LEN : 0;
if (len + blank > mappedFile.getFileSize() - mappedFile.getWrotePosition()) {
if (blank < MIN_BLANK_LEN) {
logger.error("Blank {} should ge {}", blank, MIN_BLANK_LEN);
return -1;
} else {
ByteBuffer byteBuffer = ByteBuffer.allocate(mappedFile.getFileSize() - mappedFile.getWrotePosition());
byteBuffer.putInt(BLANK_MAGIC_CODE);
byteBuffer.putInt(mappedFile.getFileSize() - mappedFile.getWrotePosition());
if (mappedFile.appendMessage(byteBuffer.array())) {
//need to set the wrote position
mappedFile.setWrotePosition(mappedFile.getFileSize());
} else {
logger.error("Append blank error for {}", storePath);
return -1;
}
mappedFile = getLastMappedFile(0);
if (null == mappedFile) {
logger.error("Create mapped file for {}", storePath);
return -1;
}
}
}
long currPosition = mappedFile.getFileFromOffset() + mappedFile.getWrotePosition();
if (!mappedFile.appendMessage(data, pos, len)) {
logger.error("Append error for {}", storePath);
return -1;
}
return currPosition;
}
#location 13
#vulnerability type RESOURCE_LEAK
|
#fixed code
public long append(byte[] data, int pos, int len, boolean useBlank) {
if (preAppend(len, useBlank) == -1) {
return -1;
}
MmapFile mappedFile = getLastMappedFile();
long currPosition = mappedFile.getFileFromOffset() + mappedFile.getWrotePosition();
if (!mappedFile.appendMessage(data, pos, len)) {
logger.error("Append error for {}", storePath);
return -1;
}
return currPosition;
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
@Override
public DLegerEntry get(Long index) {
PreConditions.check(index <= legerEndIndex && index >= legerBeginIndex, DLegerException.Code.INDEX_OUT_OF_RANGE, String.format("%d should between %d-%d", index, legerBeginIndex, legerEndIndex), memberState.getLeaderId());
SelectMmapBufferResult indexSbr = indexFileQueue.getData(index * INDEX_NUIT_SIZE, INDEX_NUIT_SIZE);
PreConditions.check(indexSbr.getByteBuffer() != null, DLegerException.Code.DISK_ERROR, null);
indexSbr.getByteBuffer().getInt(); //magic
long pos = indexSbr.getByteBuffer().getLong();
int size = indexSbr.getByteBuffer().getInt();
indexSbr.release();
SelectMmapBufferResult dataSbr = dataFileQueue.getData(pos, size);
PreConditions.check(dataSbr.getByteBuffer() != null, DLegerException.Code.DISK_ERROR, null);
DLegerEntry dLegerEntry = DLegerEntryCoder.decode(dataSbr.getByteBuffer());
dataSbr.release();
return dLegerEntry;
}
#location 3
#vulnerability type THREAD_SAFETY_VIOLATION
|
#fixed code
@Override
public DLegerEntry get(Long index) {
PreConditions.check(index <= legerEndIndex && index >= legerBeginIndex, DLegerException.Code.INDEX_OUT_OF_RANGE, String.format("%d should between %d-%d", index, legerBeginIndex, legerEndIndex), memberState.getLeaderId());
SelectMmapBufferResult indexSbr = indexFileQueue.getData(index * INDEX_NUIT_SIZE, INDEX_NUIT_SIZE);
PreConditions.check(indexSbr.getByteBuffer() != null, DLegerException.Code.DISK_ERROR, null);
indexSbr.getByteBuffer().getInt(); //magic
long pos = indexSbr.getByteBuffer().getLong();
int size = indexSbr.getByteBuffer().getInt();
indexSbr.release();
SelectMmapBufferResult dataSbr = dataFileQueue.getData(pos, size);
PreConditions.check(dataSbr.getByteBuffer() != null, DLegerException.Code.DISK_ERROR, null);
DLegerEntry dLegerEntry = DLegerEntryCoder.decode(dataSbr.getByteBuffer());
dLegerEntry.setPos(pos);
dataSbr.release();
return dLegerEntry;
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
@Test
public void testThressServer() throws Exception {
String group = UUID.randomUUID().toString();
String peers = "n0-localhost:10012;n1-localhost:10013;n2-localhost:10014";
List<DLegerServer> servers = new ArrayList<>();
servers.add(launchServer(group, peers, "n0"));
servers.add(launchServer(group, peers, "n1"));
servers.add(launchServer(group, peers, "n2"));
Thread.sleep(1000);
AtomicInteger leaderNum = new AtomicInteger(0);
AtomicInteger followerNum = new AtomicInteger(0);
DLegerServer leaderServer = parseServers(servers, leaderNum, followerNum);
Assert.assertEquals(1, leaderNum.get());
Assert.assertEquals(2, followerNum.get());
Assert.assertNotNull(leaderServer);
for (int i = 0; i < 10; i++) {
long maxTerm = servers.stream().max((o1, o2) -> {
if (o1.getMemberState().currTerm() < o2.getMemberState().currTerm()) {
return -1;
} else if (o1.getMemberState().currTerm() > o2.getMemberState().currTerm()) {
return 1;
} else {
return 0;
}
}).get().getMemberState().currTerm();
DLegerServer candidate = servers.get( i % servers.size());
candidate.getdLegerLeaderElector().revote(maxTerm + 1);
Thread.sleep(100);
leaderNum.set(0);
followerNum.set(0);
leaderServer = parseServers(servers, leaderNum, followerNum);
Assert.assertEquals(1, leaderNum.get());
Assert.assertEquals(2, followerNum.get());
Assert.assertNotNull(leaderServer);
Assert.assertTrue(candidate == leaderServer);
}
//write some data
for (int i = 0; i < 5; i++) {
AppendEntryRequest appendEntryRequest = new AppendEntryRequest();
appendEntryRequest.setRemoteId(leaderServer.getMemberState().getSelfId());
appendEntryRequest.setBody("Hello Three Server".getBytes());
AppendEntryResponse appendEntryResponse = leaderServer.getdLegerRpcService().append(appendEntryRequest).get();
Assert.assertEquals(DLegerResponseCode.SUCCESS.getCode(), appendEntryResponse.getCode());
}
}
#location 41
#vulnerability type NULL_DEREFERENCE
|
#fixed code
@Test
public void testThressServer() throws Exception {
String group = UUID.randomUUID().toString();
String peers = "n0-localhost:10012;n1-localhost:10013;n2-localhost:10014";
List<DLegerServer> servers = new ArrayList<>();
servers.add(launchServer(group, peers, "n0"));
servers.add(launchServer(group, peers, "n1"));
servers.add(launchServer(group, peers, "n2"));
Thread.sleep(1000);
AtomicInteger leaderNum = new AtomicInteger(0);
AtomicInteger followerNum = new AtomicInteger(0);
DLegerServer leaderServer = parseServers(servers, leaderNum, followerNum);
Assert.assertEquals(1, leaderNum.get());
Assert.assertEquals(2, followerNum.get());
Assert.assertNotNull(leaderServer);
for (int i = 0; i < 10; i++) {
long maxTerm = servers.stream().max((o1, o2) -> {
if (o1.getMemberState().currTerm() < o2.getMemberState().currTerm()) {
return -1;
} else if (o1.getMemberState().currTerm() > o2.getMemberState().currTerm()) {
return 1;
} else {
return 0;
}
}).get().getMemberState().currTerm();
DLegerServer candidate = servers.get( i % servers.size());
candidate.getdLegerLeaderElector().testRevote(maxTerm + 1);
Thread.sleep(100);
leaderNum.set(0);
followerNum.set(0);
leaderServer = parseServers(servers, leaderNum, followerNum);
Assert.assertEquals(1, leaderNum.get());
Assert.assertEquals(2, followerNum.get());
Assert.assertNotNull(leaderServer);
Assert.assertTrue(candidate == leaderServer);
}
//write some data
for (int i = 0; i < 5; i++) {
AppendEntryRequest appendEntryRequest = new AppendEntryRequest();
appendEntryRequest.setRemoteId(leaderServer.getMemberState().getSelfId());
appendEntryRequest.setBody("Hello Three Server".getBytes());
AppendEntryResponse appendEntryResponse = leaderServer.getdLegerRpcService().append(appendEntryRequest).get();
Assert.assertEquals(DLegerResponseCode.SUCCESS.getCode(), appendEntryResponse.getCode());
}
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
public void recover() {
final List<MmapFile> mappedFiles = this.dataFileQueue.getMappedFiles();
if (mappedFiles.isEmpty()) {
this.indexFileQueue.updateWherePosition(0);
this.indexFileQueue.truncateDirtyFiles(0);
return;
}
int index = mappedFiles.size() - 3;
if (index < 0) {
index = 0;
}
long firstEntryIndex = -1;
for (int i = index; i >= 0; i--) {
index = i;
MmapFile mappedFile = mappedFiles.get(index);
ByteBuffer byteBuffer = mappedFile.sliceByteBuffer();
try {
int magic = byteBuffer.getInt();
int size = byteBuffer.getInt();
long entryIndex = byteBuffer.getLong();
long entryTerm = byteBuffer.get();
PreConditions.check(magic != MmapFileQueue.BLANK_MAGIC_CODE && magic >= MAGIC_1 && MAGIC_1 <= CURRENT_MAGIC, DLegerException.Code.DISK_ERROR, "unknown magic is " + magic);
PreConditions.check(size > DLegerEntry.HEADER_SIZE, DLegerException.Code.DISK_ERROR, String.format("Size %d should greater than %d", size, DLegerEntry.HEADER_SIZE) );
SelectMmapBufferResult indexSbr = indexFileQueue.getData(entryIndex * INDEX_NUIT_SIZE);
PreConditions.check(indexSbr != null, DLegerException.Code.DISK_ERROR, String.format("index: %d pos: %d", entryIndex, entryIndex * INDEX_NUIT_SIZE));
indexSbr.release();
ByteBuffer indexByteBuffer = indexSbr.getByteBuffer();
int magicFromIndex = indexByteBuffer.getInt();
long posFromIndex = indexByteBuffer.getLong();
int sizeFromIndex = indexByteBuffer.getInt();
long indexFromIndex = indexByteBuffer.getLong();
long termFromIndex = indexByteBuffer.get();
PreConditions.check(magic == magicFromIndex, DLegerException.Code.DISK_ERROR, String.format("magic %d != %d", magic, magicFromIndex));
PreConditions.check(size == sizeFromIndex, DLegerException.Code.DISK_ERROR, String.format("size %d != %d", size, sizeFromIndex));
PreConditions.check(entryIndex == indexFromIndex, DLegerException.Code.DISK_ERROR, String.format("index %d != %d", entryIndex, indexFromIndex));
PreConditions.check(entryTerm == termFromIndex, DLegerException.Code.DISK_ERROR, String.format("term %d != %d", entryTerm, termFromIndex));
PreConditions.check(posFromIndex == mappedFile.getFileFromOffset(), DLegerException.Code.DISK_ERROR, String.format("pos %d != %d", mappedFile.getFileFromOffset(), posFromIndex));
firstEntryIndex = entryIndex;
break;
} catch (Throwable t) {
logger.warn("Pre check data and index failed {}", mappedFile.getFileName(), t);
}
}
MmapFile mappedFile = mappedFiles.get(index);
ByteBuffer byteBuffer = mappedFile.sliceByteBuffer();
logger.info("Begin to recover data from entryIndex: {} fileIndex: {} fileSize: {} fileName:{} ", firstEntryIndex, index, mappedFiles.size(), mappedFile.getFileName());
long lastEntryIndex = -1;
long lastEntryTerm = -1;
long processOffset = mappedFile.getFileFromOffset();
boolean needWriteIndex = false;
while (true) {
try {
int relativePos = byteBuffer.position();
long absolutePos = mappedFile.getFileFromOffset() + relativePos;
int magic = byteBuffer.getInt();
if (magic == MmapFileQueue.BLANK_MAGIC_CODE) {
processOffset = mappedFile.getFileFromOffset() + mappedFile.getFileSize();
index++;
if (index >= mappedFiles.size()) {
logger.info("Recover data file over, the last file {}", mappedFile.getFileName());
break;
} else {
mappedFile = mappedFiles.get(index);
byteBuffer = mappedFile.sliceByteBuffer();
processOffset = mappedFile.getFileFromOffset();
logger.info("Trying to recover index file {}", mappedFile.getFileName());
continue;
}
}
int size = byteBuffer.getInt();
long entryIndex = byteBuffer.getLong();
long entryTerm = byteBuffer.get();
byteBuffer.position(relativePos + size);
String message = String.format("pos: %d size: %d magic:%d index:%d term:%d", absolutePos, size, magic, entryIndex, entryTerm);
PreConditions.check(magic <= CURRENT_MAGIC && magic >= MAGIC_1, DLegerException.Code.DISK_ERROR, String.format("%s currMagic: %d", message, CURRENT_MAGIC));
if (lastEntryIndex != -1) {
PreConditions.check(entryIndex == lastEntryIndex + 1, DLegerException.Code.DISK_ERROR, String.format("%s lastEntryIndex: %d", message, lastEntryIndex));
}
PreConditions.check(entryTerm >= lastEntryTerm, DLegerException.Code.DISK_ERROR, String.format("%s lastEntryTerm: ", message, lastEntryTerm));
PreConditions.check(size > DLegerEntry.HEADER_SIZE, DLegerException.Code.DISK_ERROR, String.format("Size %d should greater than %d", size, DLegerEntry.HEADER_SIZE) );
if (!needWriteIndex) {
try {
SelectMmapBufferResult indexSbr = indexFileQueue.getData(entryIndex * INDEX_NUIT_SIZE);
PreConditions.check(indexSbr != null, DLegerException.Code.DISK_ERROR, String.format("index: %d pos: %d", entryIndex, entryIndex * INDEX_NUIT_SIZE));
indexSbr.release();
ByteBuffer indexByteBuffer = indexSbr.getByteBuffer();
int magicFromIndex = indexByteBuffer.getInt();
long posFromIndex = indexByteBuffer.getLong();
int sizeFromIndex = indexByteBuffer.getInt();
long indexFromIndex = indexByteBuffer.getLong();
long termFromIndex = indexByteBuffer.get();
PreConditions.check(magic == magicFromIndex, DLegerException.Code.DISK_ERROR, String.format("magic %d != %d", magic, magicFromIndex));
PreConditions.check(size == sizeFromIndex, DLegerException.Code.DISK_ERROR, String.format("size %d != %d", size, sizeFromIndex));
PreConditions.check(entryIndex == indexFromIndex, DLegerException.Code.DISK_ERROR, String.format("index %d != %d", entryIndex, indexFromIndex));
PreConditions.check(entryTerm == termFromIndex, DLegerException.Code.DISK_ERROR, String.format("term %d != %d", entryTerm, termFromIndex));
PreConditions.check(absolutePos == posFromIndex, DLegerException.Code.DISK_ERROR, String.format("pos %d != %d", mappedFile.getFileFromOffset(), posFromIndex));
} catch (Exception e) {
logger.warn("Compare data to index failed {}", mappedFile.getFileName());
indexFileQueue.truncateDirtyFiles(entryIndex * INDEX_NUIT_SIZE);
if (indexFileQueue.getMaxWrotePosition() != entryIndex * INDEX_NUIT_SIZE) {
logger.warn("Unexpected wrote position in index file {} != {}", indexFileQueue.getMaxWrotePosition(), entryIndex * INDEX_NUIT_SIZE);
indexFileQueue.truncateDirtyFiles(0);
}
if (indexFileQueue.getMappedFiles().isEmpty()) {
indexFileQueue.getLastMappedFile(entryIndex * INDEX_NUIT_SIZE);
}
needWriteIndex = true;
}
}
if (needWriteIndex) {
ByteBuffer indexBuffer = localIndexBuffer.get();
DLegerEntryCoder.encodeIndex(absolutePos, size, magic, entryIndex, entryTerm, indexBuffer);
long indexPos = indexFileQueue.append(indexBuffer.array(), 0, indexBuffer.remaining());
PreConditions.check(indexPos == entryIndex * INDEX_NUIT_SIZE, DLegerException.Code.DISK_ERROR, String.format("Write index failed index: %d", entryIndex));
}
lastEntryIndex = entryIndex;
lastEntryTerm = entryTerm;
processOffset += size;
} catch (Throwable t) {
logger.info("Recover data file to the end of {} ", mappedFile.getFileName(), t);
break;
}
}
logger.info("Recover data to the end entryIndex:{} processOffset:{}", lastEntryIndex, processOffset);
legerEndIndex = lastEntryIndex;
legerEndTerm = lastEntryTerm;
if (lastEntryIndex != -1) {
DLegerEntry entry = get(lastEntryIndex);
PreConditions.check(entry != null, DLegerException.Code.DISK_ERROR, "recheck get null entry");
PreConditions.check(entry.getIndex() == lastEntryIndex, DLegerException.Code.DISK_ERROR, String.format("recheck index %d != %d", entry.getIndex(), lastEntryIndex));
} else {
processOffset = 0;
}
this.dataFileQueue.updateWherePosition(processOffset);
this.dataFileQueue.truncateDirtyFiles(processOffset);
long indexProcessOffset = (lastEntryIndex + 1) * INDEX_NUIT_SIZE;
this.indexFileQueue.updateWherePosition(indexProcessOffset);
this.indexFileQueue.truncateDirtyFiles(indexProcessOffset);
return;
}
#location 133
#vulnerability type THREAD_SAFETY_VIOLATION
|
#fixed code
public void recover() {
final List<MmapFile> mappedFiles = this.dataFileQueue.getMappedFiles();
if (mappedFiles.isEmpty()) {
this.indexFileQueue.updateWherePosition(0);
this.indexFileQueue.truncateDirtyFiles(0);
return;
}
int index = mappedFiles.size() - 3;
if (index < 0) {
index = 0;
}
long firstEntryIndex = -1;
for (int i = index; i >= 0; i--) {
index = i;
MmapFile mappedFile = mappedFiles.get(index);
ByteBuffer byteBuffer = mappedFile.sliceByteBuffer();
try {
int magic = byteBuffer.getInt();
int size = byteBuffer.getInt();
long entryIndex = byteBuffer.getLong();
long entryTerm = byteBuffer.get();
PreConditions.check(magic != MmapFileQueue.BLANK_MAGIC_CODE && magic >= MAGIC_1 && MAGIC_1 <= CURRENT_MAGIC, DLegerException.Code.DISK_ERROR, "unknown magic is " + magic);
PreConditions.check(size > DLegerEntry.HEADER_SIZE, DLegerException.Code.DISK_ERROR, String.format("Size %d should greater than %d", size, DLegerEntry.HEADER_SIZE) );
SelectMmapBufferResult indexSbr = indexFileQueue.getData(entryIndex * INDEX_NUIT_SIZE);
PreConditions.check(indexSbr != null, DLegerException.Code.DISK_ERROR, String.format("index: %d pos: %d", entryIndex, entryIndex * INDEX_NUIT_SIZE));
indexSbr.release();
ByteBuffer indexByteBuffer = indexSbr.getByteBuffer();
int magicFromIndex = indexByteBuffer.getInt();
long posFromIndex = indexByteBuffer.getLong();
int sizeFromIndex = indexByteBuffer.getInt();
long indexFromIndex = indexByteBuffer.getLong();
long termFromIndex = indexByteBuffer.get();
PreConditions.check(magic == magicFromIndex, DLegerException.Code.DISK_ERROR, String.format("magic %d != %d", magic, magicFromIndex));
PreConditions.check(size == sizeFromIndex, DLegerException.Code.DISK_ERROR, String.format("size %d != %d", size, sizeFromIndex));
PreConditions.check(entryIndex == indexFromIndex, DLegerException.Code.DISK_ERROR, String.format("index %d != %d", entryIndex, indexFromIndex));
PreConditions.check(entryTerm == termFromIndex, DLegerException.Code.DISK_ERROR, String.format("term %d != %d", entryTerm, termFromIndex));
PreConditions.check(posFromIndex == mappedFile.getFileFromOffset(), DLegerException.Code.DISK_ERROR, String.format("pos %d != %d", mappedFile.getFileFromOffset(), posFromIndex));
firstEntryIndex = entryIndex;
break;
} catch (Throwable t) {
logger.warn("Pre check data and index failed {}", mappedFile.getFileName(), t);
}
}
MmapFile mappedFile = mappedFiles.get(index);
ByteBuffer byteBuffer = mappedFile.sliceByteBuffer();
logger.info("Begin to recover data from entryIndex: {} fileIndex: {} fileSize: {} fileName:{} ", firstEntryIndex, index, mappedFiles.size(), mappedFile.getFileName());
long lastEntryIndex = -1;
long lastEntryTerm = -1;
long processOffset = mappedFile.getFileFromOffset();
boolean needWriteIndex = false;
while (true) {
try {
int relativePos = byteBuffer.position();
long absolutePos = mappedFile.getFileFromOffset() + relativePos;
int magic = byteBuffer.getInt();
if (magic == MmapFileQueue.BLANK_MAGIC_CODE) {
processOffset = mappedFile.getFileFromOffset() + mappedFile.getFileSize();
index++;
if (index >= mappedFiles.size()) {
logger.info("Recover data file over, the last file {}", mappedFile.getFileName());
break;
} else {
mappedFile = mappedFiles.get(index);
byteBuffer = mappedFile.sliceByteBuffer();
processOffset = mappedFile.getFileFromOffset();
logger.info("Trying to recover index file {}", mappedFile.getFileName());
continue;
}
}
int size = byteBuffer.getInt();
long entryIndex = byteBuffer.getLong();
long entryTerm = byteBuffer.get();
byteBuffer.position(relativePos + size);
String message = String.format("pos: %d size: %d magic:%d index:%d term:%d", absolutePos, size, magic, entryIndex, entryTerm);
PreConditions.check(magic <= CURRENT_MAGIC && magic >= MAGIC_1, DLegerException.Code.DISK_ERROR, String.format("%s currMagic: %d", message, CURRENT_MAGIC));
if (lastEntryIndex != -1) {
PreConditions.check(entryIndex == lastEntryIndex + 1, DLegerException.Code.DISK_ERROR, String.format("%s lastEntryIndex: %d", message, lastEntryIndex));
}
PreConditions.check(entryTerm >= lastEntryTerm, DLegerException.Code.DISK_ERROR, String.format("%s lastEntryTerm: ", message, lastEntryTerm));
PreConditions.check(size > DLegerEntry.HEADER_SIZE, DLegerException.Code.DISK_ERROR, String.format("Size %d should greater than %d", size, DLegerEntry.HEADER_SIZE) );
if (!needWriteIndex) {
try {
SelectMmapBufferResult indexSbr = indexFileQueue.getData(entryIndex * INDEX_NUIT_SIZE);
PreConditions.check(indexSbr != null, DLegerException.Code.DISK_ERROR, String.format("index: %d pos: %d", entryIndex, entryIndex * INDEX_NUIT_SIZE));
indexSbr.release();
ByteBuffer indexByteBuffer = indexSbr.getByteBuffer();
int magicFromIndex = indexByteBuffer.getInt();
long posFromIndex = indexByteBuffer.getLong();
int sizeFromIndex = indexByteBuffer.getInt();
long indexFromIndex = indexByteBuffer.getLong();
long termFromIndex = indexByteBuffer.get();
PreConditions.check(magic == magicFromIndex, DLegerException.Code.DISK_ERROR, String.format("magic %d != %d", magic, magicFromIndex));
PreConditions.check(size == sizeFromIndex, DLegerException.Code.DISK_ERROR, String.format("size %d != %d", size, sizeFromIndex));
PreConditions.check(entryIndex == indexFromIndex, DLegerException.Code.DISK_ERROR, String.format("index %d != %d", entryIndex, indexFromIndex));
PreConditions.check(entryTerm == termFromIndex, DLegerException.Code.DISK_ERROR, String.format("term %d != %d", entryTerm, termFromIndex));
PreConditions.check(absolutePos == posFromIndex, DLegerException.Code.DISK_ERROR, String.format("pos %d != %d", mappedFile.getFileFromOffset(), posFromIndex));
} catch (Exception e) {
logger.warn("Compare data to index failed {}", mappedFile.getFileName());
indexFileQueue.truncateDirtyFiles(entryIndex * INDEX_NUIT_SIZE);
if (indexFileQueue.getMaxWrotePosition() != entryIndex * INDEX_NUIT_SIZE) {
logger.warn("Unexpected wrote position in index file {} != {}", indexFileQueue.getMaxWrotePosition(), entryIndex * INDEX_NUIT_SIZE);
indexFileQueue.truncateDirtyFiles(0);
}
if (indexFileQueue.getMappedFiles().isEmpty()) {
indexFileQueue.getLastMappedFile(entryIndex * INDEX_NUIT_SIZE);
}
needWriteIndex = true;
}
}
if (needWriteIndex) {
ByteBuffer indexBuffer = localIndexBuffer.get();
DLegerEntryCoder.encodeIndex(absolutePos, size, magic, entryIndex, entryTerm, indexBuffer);
long indexPos = indexFileQueue.append(indexBuffer.array(), 0, indexBuffer.remaining());
PreConditions.check(indexPos == entryIndex * INDEX_NUIT_SIZE, DLegerException.Code.DISK_ERROR, String.format("Write index failed index: %d", entryIndex));
}
lastEntryIndex = entryIndex;
lastEntryTerm = entryTerm;
processOffset += size;
} catch (Throwable t) {
logger.info("Recover data file to the end of {} ", mappedFile.getFileName(), t);
break;
}
}
logger.info("Recover data to the end entryIndex:{} processOffset:{}", lastEntryIndex, processOffset);
legerEndIndex = lastEntryIndex;
legerEndTerm = lastEntryTerm;
if (lastEntryIndex != -1) {
DLegerEntry entry = get(lastEntryIndex);
PreConditions.check(entry != null, DLegerException.Code.DISK_ERROR, "recheck get null entry");
PreConditions.check(entry.getIndex() == lastEntryIndex, DLegerException.Code.DISK_ERROR, String.format("recheck index %d != %d", entry.getIndex(), lastEntryIndex));
//get leger begin index
ByteBuffer tmpBuffer = dataFileQueue.getFirstMappedFile().sliceByteBuffer();
tmpBuffer.getInt(); //magic
tmpBuffer.getInt(); //size
legerBeginIndex = byteBuffer.getLong();
} else {
processOffset = 0;
}
this.dataFileQueue.updateWherePosition(processOffset);
this.dataFileQueue.truncateDirtyFiles(processOffset);
long indexProcessOffset = (lastEntryIndex + 1) * INDEX_NUIT_SIZE;
this.indexFileQueue.updateWherePosition(indexProcessOffset);
this.indexFileQueue.truncateDirtyFiles(indexProcessOffset);
return;
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
private InputStream buildWrappedInputStream(InputStream downloadInputStream)
throws TransformerException, IOException {
// Pass the download input stream through a transformer that removes the XML
// declaration.
Transformer omitXmlDeclarationTransformer = getTransformer();
ByteArrayOutputStream outputStream = new ByteArrayOutputStream();
StreamResult streamResult = new StreamResult(outputStream);
Source xmlSource = new StreamSource(downloadInputStream);
omitXmlDeclarationTransformer.transform(xmlSource, streamResult);
return ByteSource.concat(
ByteSource.wrap(SOAP_START_BODY.getBytes()),
ByteSource.wrap(outputStream.toByteArray()),
ByteSource.wrap(SOAP_END_BODY.getBytes())).openStream();
}
#location 10
#vulnerability type NULL_DEREFERENCE
|
#fixed code
private InputStream buildWrappedInputStream(InputStream downloadInputStream)
throws TransformerException, IOException {
// Pass the download input stream through a Transformer that removes the XML
// declaration. Create a new TransformerFactory and Transformer on each invocation
// since these objects are <em>not</em> thread safe.
Transformer omitXmlDeclarationTransformer = TransformerFactory.newInstance().newTransformer();
omitXmlDeclarationTransformer.setOutputProperty(OutputKeys.INDENT, "yes");
omitXmlDeclarationTransformer.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
omitXmlDeclarationTransformer.setOutputProperty(
"{http://xml.apache.org/xslt}indent-amount", INDENT_AMOUNT);
ByteArrayOutputStream outputStream = new ByteArrayOutputStream();
StreamResult streamResult = new StreamResult(outputStream);
Source xmlSource = new StreamSource(downloadInputStream);
omitXmlDeclarationTransformer.transform(xmlSource, streamResult);
return ByteSource.concat(
ByteSource.wrap(SOAP_START_BODY.getBytes()),
ByteSource.wrap(outputStream.toByteArray()),
ByteSource.wrap(SOAP_END_BODY.getBytes())).openStream();
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
@Test
public void testMarkNotSupported() throws Exception {
byte[] plaintext = getRandomBytes(1);
final String password = "Testing1234";
JNCryptor cryptor = new AES256JNCryptor();
byte[] data = cryptor.encryptData(plaintext, password.toCharArray());
InputStream in = new AES256JNCryptorInputStream(new ByteArrayInputStream(
data), password.toCharArray());
assertFalse(in.markSupported());
}
#location 13
#vulnerability type RESOURCE_LEAK
|
#fixed code
@Test
public void testMarkNotSupported() throws Exception {
byte[] plaintext = getRandomBytes(1);
final String password = "Testing1234";
JNCryptor cryptor = new AES256JNCryptor();
byte[] data = cryptor.encryptData(plaintext, password.toCharArray());
InputStream in = new AES256JNCryptorInputStream(new ByteArrayInputStream(
data), password.toCharArray());
assertFalse(in.markSupported());
in.close();
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
private static String getLine(File file, int line) throws IOException {
BufferedReader reader = new BufferedReader(new FileReader(file));
String msg = "";
for (int i = 0; i <= line; i++) msg = reader.readLine();
reader.close();
return msg;
}
#location 10
#vulnerability type RESOURCE_LEAK
|
#fixed code
private static String getLine(File file, int line) throws IOException {
BufferedReader reader = Files.newBufferedReader(file.toPath(), Options.encoding);
String msg = "";
for (int i = 0; i <= line; i++) msg = reader.readLine();
reader.close();
return msg;
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
protected static ClassInfo guessPackageAndClass(File lexFile)
throws FileNotFoundException, IOException {
assert lexFile.isAbsolute() : lexFile;
LineNumberReader reader = new LineNumberReader(new FileReader(lexFile));
ClassInfo classInfo = new ClassInfo();
while (classInfo.className == null || classInfo.packageName == null) {
String line = reader.readLine();
if (line == null)
break;
if (classInfo.packageName == null) {
int index = line.indexOf("package");
if (index >= 0) {
index += 7;
int end = line.indexOf(';', index);
if (end >= index) {
classInfo.packageName = line.substring(index, end);
classInfo.packageName = classInfo.packageName.trim();
}
}
}
if (classInfo.className == null) {
int index = line.indexOf("%class");
if (index >= 0) {
index += 6;
classInfo.className = line.substring(index);
classInfo.className = classInfo.className.trim();
}
}
}
if (classInfo.className == null) {
classInfo.className = DEFAULT_NAME;
}
return classInfo;
}
#location 38
#vulnerability type RESOURCE_LEAK
|
#fixed code
protected static ClassInfo guessPackageAndClass(File lexFile) throws FileNotFoundException,
IOException {
assert lexFile.isAbsolute() : lexFile;
LineNumberReader reader = new LineNumberReader(new FileReader(lexFile));
try {
ClassInfo classInfo = new ClassInfo();
while (classInfo.className == null || classInfo.packageName == null) {
String line = reader.readLine();
if (line == null)
break;
if (classInfo.packageName == null) {
int index = line.indexOf("package");
if (index >= 0) {
index += 7;
int end = line.indexOf(';', index);
if (end >= index) {
classInfo.packageName = line.substring(index, end);
classInfo.packageName = classInfo.packageName.trim();
}
}
}
if (classInfo.className == null) {
int index = line.indexOf("%class");
if (index >= 0) {
index += 6;
classInfo.className = line.substring(index);
classInfo.className = classInfo.className.trim();
}
}
}
if (classInfo.className == null) {
classInfo.className = DEFAULT_NAME;
}
return classInfo;
} finally {
reader.close();
}
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
private String getPageContent(URL url) throws IOException {
InputStreamReader reader = new InputStreamReader(url.openStream(), "UTF-8");
StringBuilder builder = new StringBuilder();
char[] buf = new char[BUF_SIZE];
int charsRead;
while ((charsRead = reader.read(buf)) > 0) {
builder.append(buf, 0, charsRead);
}
return builder.toString();
}
#location 9
#vulnerability type RESOURCE_LEAK
|
#fixed code
private String getPageContent(URL url) throws IOException {
try(InputStreamReader reader = new InputStreamReader(url.openStream(), "UTF-8")) {
StringBuilder builder = new StringBuilder();
char[] buf = new char[BUF_SIZE];
int charsRead;
while ((charsRead = reader.read(buf)) > 0) {
builder.append(buf, 0, charsRead);
}
return builder.toString();
}
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
public void runNext() throws TestFailException {
// Get first file and remove it from vector
InputOutput current = inputOutput.remove(0);
// Create List with only first input in
List<String> param = new ArrayList<String>();
param.add(current.getName() + ".input");
// Excute Main on that input
classExecResult = Exec.execClass
(className, testPath.toString(), new ArrayList<String>(), param,
Main.jflexTestVersion);
if (Main.verbose) {
System.out.println("Running scanner on [" + current.getName() + "]");
}
// check for output conformance
File expected = new File(current.getName() + ".output");
if (expected.exists()) {
DiffStream check = new DiffStream();
String diff;
try {
diff = check.diff(jflexDiff, new StringReader(classExecResult.getOutput()),
new FileReader(expected));
}
catch (FileNotFoundException e) {
System.out.println("Error opening file " + expected);
throw new TestFailException();
}
if (diff != null) {
System.out.println("Test failed, unexpected output: " + diff);
System.out.println("Test output: " + classExecResult.getOutput());
throw new TestFailException();
}
}
else {
System.out.println("Warning: no file for expected output [" + expected + "]");
}
// System.out.println(classExecResult);
}
#location 23
#vulnerability type RESOURCE_LEAK
|
#fixed code
public void runNext() throws TestFailException, UnsupportedEncodingException {
// Get first file and remove it from vector
InputOutput current = inputOutput.remove(0);
// Create List with only first input in
List<String> param = new ArrayList<String>();
param.add(current.getName() + ".input");
// Excute Main on that input
classExecResult = Exec.execClass
(className, testPath.toString(), new ArrayList<String>(), param,
Main.jflexTestVersion, outputFileEncoding);
if (Main.verbose) {
System.out.println("Running scanner on [" + current.getName() + "]");
}
// check for output conformance
File expected = new File(current.getName() + ".output");
if (expected.exists()) {
DiffStream check = new DiffStream();
String diff;
try {
diff = check.diff(jflexDiff, new StringReader(classExecResult.getOutput()),
new InputStreamReader(new FileInputStream(expected),
outputFileEncoding));
}
catch (FileNotFoundException e) {
System.out.println("Error opening file " + expected);
throw new TestFailException();
} catch (UnsupportedEncodingException e) {
System.out.println("Unsupported encoding '" + outputFileEncoding + "'");
throw new TestFailException();
}
if (diff != null) {
System.out.println("Test failed, unexpected output: " + diff);
System.out.println("Test output: " + classExecResult.getOutput());
throw new TestFailException();
}
}
else {
System.out.println("Warning: no file for expected output [" + expected + "]");
}
// System.out.println(classExecResult);
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
private byte[] loadJarData(String path, String fileName) {
ZipFile zipFile;
ZipEntry entry;
int size;
try {
zipFile = new ZipFile(new File(path));
entry = zipFile.getEntry(fileName);
if (entry == null) return null;
size = (int) entry.getSize();
} catch (IOException io) {
return null;
}
InputStream stream = null;
try {
stream = zipFile.getInputStream(entry);
if (stream == null) return null;
byte[] data = new byte[size];
int pos = 0;
while (pos < size) {
int n = stream.read(data, pos, data.length - pos);
pos += n;
}
zipFile.close();
return data;
} catch (IOException e) {
} finally {
try {
if (stream != null) stream.close();
} catch (IOException e) {
}
}
return null;
}
#location 19
#vulnerability type RESOURCE_LEAK
|
#fixed code
private byte[] loadJarData(String path, String fileName) {
ZipFile zipFile;
ZipEntry entry;
int size;
try {
zipFile = new ZipFile(new File(path));
entry = zipFile.getEntry(fileName);
if (entry == null) {
zipFile.close();
return null;
}
size = (int) entry.getSize();
} catch (IOException io) {
return null;
}
InputStream stream = null;
try {
stream = zipFile.getInputStream(entry);
if (stream == null) {
zipFile.close();
return null;
}
byte[] data = new byte[size];
int pos = 0;
while (pos < size) {
int n = stream.read(data, pos, data.length - pos);
pos += n;
}
zipFile.close();
return data;
} catch (IOException e) {
} finally {
try {
if (stream != null) stream.close();
} catch (IOException e) {
}
}
return null;
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
public void findPackageAndClass() throws IOException {
// find name of the package and class in jflex source file
packageName = null;
className = null;
LineNumberReader reader = new LineNumberReader(new FileReader(inputFile));
while (className == null || packageName == null) {
String line = reader.readLine();
if (line == null) break;
if (packageName == null) {
Matcher matcher = PACKAGE_PATTERN.matcher(line);
if (matcher.find()) {
packageName = matcher.group(1);
}
}
if (className == null) {
Matcher matcher = CLASS_PATTERN.matcher(line);
if (matcher.find()) {
className = matcher.group(1);
}
}
}
// package name may be null, but class name not
if (className == null) className = "Yylex";
}
#location 28
#vulnerability type RESOURCE_LEAK
|
#fixed code
public void findPackageAndClass() throws IOException {
// find name of the package and class in jflex source file
packageName = null;
className = null;
LineNumberReader reader = new LineNumberReader(new FileReader(inputFile));
try {
while (className == null || packageName == null) {
String line = reader.readLine();
if (line == null)
break;
if (packageName == null) {
Matcher matcher = PACKAGE_PATTERN.matcher(line);
if (matcher.find()) {
packageName = matcher.group(1);
}
}
if (className == null) {
Matcher matcher = CLASS_PATTERN.matcher(line);
if (matcher.find()) {
className = matcher.group(1);
}
}
}
// package name may be null, but class name not
if (className == null) {
className = "Yylex";
}
} finally {
reader.close();
}
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
private byte[] loadJarData(String path, String fileName) {
ZipFile zipFile;
ZipEntry entry;
int size;
try {
zipFile = new ZipFile(new File(path));
entry = zipFile.getEntry(fileName);
if (entry == null) return null;
size = (int) entry.getSize();
} catch (IOException io) {
return null;
}
InputStream stream = null;
try {
stream = zipFile.getInputStream(entry);
if (stream == null) return null;
byte[] data = new byte[size];
int pos = 0;
while (pos < size) {
int n = stream.read(data, pos, data.length - pos);
pos += n;
}
zipFile.close();
return data;
} catch (IOException e) {
} finally {
try {
if (stream != null) stream.close();
} catch (IOException e) {
}
}
return null;
}
#location 10
#vulnerability type RESOURCE_LEAK
|
#fixed code
private byte[] loadJarData(String path, String fileName) {
ZipFile zipFile;
ZipEntry entry;
int size;
try {
zipFile = new ZipFile(new File(path));
entry = zipFile.getEntry(fileName);
if (entry == null) {
zipFile.close();
return null;
}
size = (int) entry.getSize();
} catch (IOException io) {
return null;
}
InputStream stream = null;
try {
stream = zipFile.getInputStream(entry);
if (stream == null) {
zipFile.close();
return null;
}
byte[] data = new byte[size];
int pos = 0;
while (pos < size) {
int n = stream.read(data, pos, data.length - pos);
pos += n;
}
zipFile.close();
return data;
} catch (IOException e) {
} finally {
try {
if (stream != null) stream.close();
} catch (IOException e) {
}
}
return null;
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
public void read(String skeletonFilename) throws Exception {
ClassLoader loader = UnicodePropertiesSkeleton.class.getClassLoader();
URL url = loader.getResource(skeletonFilename);
if (null == url) {
throw new Exception("Cannot locate '" + skeletonFilename
+ "' - aborting.");
}
String line;
StringBuilder section = new StringBuilder();
BufferedReader reader = new BufferedReader
(new InputStreamReader(url.openStream(), "UTF-8"));
while (null != (line = reader.readLine())) {
if (line.startsWith("---")) {
sections.add(section.toString());
section.setLength(0);
} else {
section.append(line);
section.append(NL);
}
}
if (section.length() > 0) {
sections.add(section.toString());
}
if (sections.size() != size) {
throw new Exception("Skeleton file '" + skeletonFilename + "' has "
+ sections.size() + " static sections, but " + size
+ " were expected.");
}
}
#location 9
#vulnerability type RESOURCE_LEAK
|
#fixed code
public void read(String skeletonFilename) throws Exception {
ClassLoader loader = UnicodePropertiesSkeleton.class.getClassLoader();
URL url = loader.getResource(skeletonFilename);
if (null == url) {
throw new Exception("Cannot locate '" + skeletonFilename
+ "' - aborting.");
}
String line;
StringBuilder section = new StringBuilder();
try (BufferedReader reader = new BufferedReader
(new InputStreamReader(url.openStream(), "UTF-8"))) {
while (null != (line = reader.readLine())) {
if (line.startsWith("---")) {
sections.add(section.toString());
section.setLength(0);
} else {
section.append(line);
section.append(NL);
}
}
if (section.length() > 0) {
sections.add(section.toString());
}
if (sections.size() != size) {
throw new Exception("Skeleton file '" + skeletonFilename + "' has "
+ sections.size() + " static sections, but " + size
+ " were expected.");
}
}
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
private InputStream getZipEntryStream(String file, String entryName) {
try {
ZipFile zip = new ZipFile(new File(file));
ZipEntry entry = zip.getEntry(entryName);
if (entry == null) return null;
return zip.getInputStream(entry);
}
catch (IOException e) {
return null;
}
}
#location 8
#vulnerability type RESOURCE_LEAK
|
#fixed code
private InputStream getZipEntryStream(String file, String entryName) {
try (ZipFile zip = new ZipFile(new File(file))) {
ZipEntry entry = zip.getEntry(entryName);
if (entry == null) return null;
return zip.getInputStream(entry);
}
catch (IOException e) {
return null;
}
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
private String getPageContent(URL url) throws IOException {
InputStreamReader reader = new InputStreamReader(url.openStream(), "UTF-8");
StringBuilder builder = new StringBuilder();
char[] buf = new char[BUF_SIZE];
int charsRead;
while ((charsRead = reader.read(buf)) > 0) {
builder.append(buf, 0, charsRead);
}
return builder.toString();
}
#location 9
#vulnerability type RESOURCE_LEAK
|
#fixed code
private String getPageContent(URL url) throws IOException {
try(InputStreamReader reader = new InputStreamReader(url.openStream(), "UTF-8")) {
StringBuilder builder = new StringBuilder();
char[] buf = new char[BUF_SIZE];
int charsRead;
while ((charsRead = reader.read(buf)) > 0) {
builder.append(buf, 0, charsRead);
}
return builder.toString();
}
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
private InputStream getZipEntryStream(String file, String entryName) {
try {
ZipFile zip = new ZipFile(new File(file));
ZipEntry entry = zip.getEntry(entryName);
if (entry == null) return null;
return zip.getInputStream(entry);
}
catch (IOException e) {
return null;
}
}
#location 6
#vulnerability type RESOURCE_LEAK
|
#fixed code
private InputStream getZipEntryStream(String file, String entryName) {
try (ZipFile zip = new ZipFile(new File(file))) {
ZipEntry entry = zip.getEntry(entryName);
if (entry == null) return null;
return zip.getInputStream(entry);
}
catch (IOException e) {
return null;
}
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
protected static ClassInfo guessPackageAndClass(File lexFile)
throws FileNotFoundException, IOException {
assert lexFile.isAbsolute() : lexFile;
LineNumberReader reader = new LineNumberReader(new FileReader(lexFile));
ClassInfo classInfo = new ClassInfo();
while (classInfo.className == null || classInfo.packageName == null) {
String line = reader.readLine();
if (line == null)
break;
if (classInfo.packageName == null) {
int index = line.indexOf("package");
if (index >= 0) {
index += 7;
int end = line.indexOf(';', index);
if (end >= index) {
classInfo.packageName = line.substring(index, end);
classInfo.packageName = classInfo.packageName.trim();
}
}
}
if (classInfo.className == null) {
int index = line.indexOf("%class");
if (index >= 0) {
index += 6;
classInfo.className = line.substring(index);
classInfo.className = classInfo.className.trim();
}
}
}
if (classInfo.className == null) {
classInfo.className = DEFAULT_NAME;
}
return classInfo;
}
#location 26
#vulnerability type RESOURCE_LEAK
|
#fixed code
protected static ClassInfo guessPackageAndClass(File lexFile) throws FileNotFoundException,
IOException {
assert lexFile.isAbsolute() : lexFile;
LineNumberReader reader = new LineNumberReader(new FileReader(lexFile));
try {
ClassInfo classInfo = new ClassInfo();
while (classInfo.className == null || classInfo.packageName == null) {
String line = reader.readLine();
if (line == null)
break;
if (classInfo.packageName == null) {
int index = line.indexOf("package");
if (index >= 0) {
index += 7;
int end = line.indexOf(';', index);
if (end >= index) {
classInfo.packageName = line.substring(index, end);
classInfo.packageName = classInfo.packageName.trim();
}
}
}
if (classInfo.className == null) {
int index = line.indexOf("%class");
if (index >= 0) {
index += 6;
classInfo.className = line.substring(index);
classInfo.className = classInfo.className.trim();
}
}
}
if (classInfo.className == null) {
classInfo.className = DEFAULT_NAME;
}
return classInfo;
} finally {
reader.close();
}
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
@Override
public void copyTo(Wire wire) {
while (bytes.remaining() > 0) {
int code = bytes.readUnsignedByte();
switch (code >> 4) {
case NUM0:
case NUM1:
case NUM2:
case NUM3:
case NUM4:
case NUM5:
case NUM6:
case NUM7:
writeValue.uint8(code);
break;
case CONTROL:
break;
case FLOAT:
double d = readFloat(code);
writeValue.float64(d);
break;
case INT:
long l = readInt(code);
writeValue.int64(l);
break;
case SPECIAL:
copySpecial(code);
break;
case FIELD0:
case FIELD1:
StringBuilder fsb = readField(code, Wires.acquireStringBuilder());
writeField(fsb);
break;
case STR0:
case STR1:
StringBuilder sb = readText(code, Wires.acquireStringBuilder());
writeValue.text(sb);
break;
}
}
}
#location 37
#vulnerability type NULL_DEREFERENCE
|
#fixed code
@Override
public void copyTo(Wire wire) {
while (bytes.remaining() > 0) {
int code = bytes.readUnsignedByte();
switch (code >> 4) {
case NUM0:
case NUM1:
case NUM2:
case NUM3:
case NUM4:
case NUM5:
case NUM6:
case NUM7:
wire.writeValue().uint8(code);
break;
case CONTROL:
break;
case FLOAT:
double d = readFloat(code);
wire.writeValue().float64(d);
break;
case INT:
long l = readInt(code);
wire.writeValue().int64(l);
break;
case SPECIAL:
copySpecial(wire, code);
break;
case FIELD0:
case FIELD1:
bytes.skip(-1);
StringBuilder fsb = readField(code, Wires.acquireStringBuilder());
wire.write(fsb, null);
break;
case STR0:
case STR1:
bytes.skip(-1);
StringBuilder sb = readText(code, Wires.acquireStringBuilder());
wire.writeValue().text(sb);
break;
}
}
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
public boolean readOne() {
for (; ; ) {
try (DocumentContext context = in.readingDocument()) {
if (!context.isPresent())
return false;
if (context.isMetaData()) {
StringBuilder sb = Wires.acquireStringBuilder();
long r = context.wire().bytes().readPosition();
try {
context.wire().readEventName(sb);
for (String s : metaIgnoreList) {
// we wish to ignore our system meta data field
if (s.contentEquals(sb))
return false;
}
} finally {
// roll back position to where is was before we read the SB
context.wire().bytes().readPosition(r);
}
wireParser.accept(context.wire());
return true;
}
if (!context.isData())
continue;
MessageHistory history = messageHistory;
history.reset(context.sourceId(), context.index());
wireParser.accept(context.wire());
}
return true;
}
}
#location 10
#vulnerability type NULL_DEREFERENCE
|
#fixed code
public boolean readOne() {
try (DocumentContext context = in.readingDocument()) {
if (!context.isPresent())
return false;
if (context.isMetaData())
return readOneMetaData(context);
assert context.isData();
messageHistory.reset(context.sourceId(), context.index());
wireParser.accept(context.wire());
}
return true;
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
private void setupOrTeardown(DbUnitTestContext testContext, boolean isSetup,
Collection<AnnotationAttributes> annotations) throws Exception {
IDatabaseConnection connection = testContext.getConnection();
DatabaseOperation lastOperation = null;
for (AnnotationAttributes annotation : annotations) {
for (String dataSetLocation : annotation.getValue()) {
DatabaseOperation operation = annotation.getType();
org.dbunit.operation.DatabaseOperation dbUnitDatabaseOperation = getDbUnitDatabaseOperation(
testContext, operation, lastOperation);
IDataSet dataSet = loadDataset(testContext, dataSetLocation);
if (dataSet != null) {
if (logger.isDebugEnabled()) {
logger.debug("Executing " + (isSetup ? "Setup" : "Teardown") + " of @DatabaseTest using "
+ operation + " on " + dataSetLocation);
}
dbUnitDatabaseOperation.execute(connection, dataSet);
lastOperation = operation;
}
}
}
}
#location 16
#vulnerability type NULL_DEREFERENCE
|
#fixed code
private void setupOrTeardown(DbUnitTestContext testContext, boolean isSetup,
Collection<AnnotationAttributes> annotations) throws Exception {
IDatabaseConnection connection = testContext.getConnection();
for (AnnotationAttributes annotation : annotations) {
List<IDataSet> datasets = loadDataSets(testContext, annotation);
DatabaseOperation operation = annotation.getType();
org.dbunit.operation.DatabaseOperation dbUnitOperation = getDbUnitDatabaseOperation(testContext, operation);
if (!datasets.isEmpty()) {
if (logger.isDebugEnabled()) {
logger.debug("Executing " + (isSetup ? "Setup" : "Teardown") + " of @DatabaseTest using "
+ operation + " on " + datasets.toString());
}
IDataSet dataSet = new CompositeDataSet(datasets.toArray(new IDataSet[datasets.size()]));
dbUnitOperation.execute(connection, dataSet);
}
}
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
#vulnerable code
@Override
public ListenableFuture<IBigQueue> queueReadyForDequeue() {
futureLock.lock();
if (dequeueFuture == null || dequeueFuture.isDone() || dequeueFuture.isCancelled()) {
dequeueFuture = SettableFuture.create();
}
futureLock.unlock();
return dequeueFuture;
}
#location 8
#vulnerability type THREAD_SAFETY_VIOLATION
|
#fixed code
@Override
public ListenableFuture<IBigQueue> queueReadyForDequeue() {
initializeFutureIfNecessary();
return dequeueFuture;
}
|
Below is the vulnerable code, please generate the patch based on the following information.
|
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