// ---------------------------------------------------------------------------
private void printDependencies() throws TablesawException {
m_printedDependencies = new HashSet<String>();
try {
PrintWriter pw = new PrintWriter(new FileWriter("dependency.txt"));
pw.println("Targets marked with a * have already been printed");
// Create a reduced set of stuff to print
Set<String> ruleNames = new HashSet<String>();
for (String name : m_nameRuleMap.keySet()) ruleNames.add(name);
for (String name : m_nameRuleMap.keySet()) {
Rule rule = m_nameRuleMap.get(name);
for (String dep : rule.getDependNames()) ruleNames.remove(dep);
for (Rule dep : rule.getDependRules()) {
if (dep.getName() != null) ruleNames.remove(dep.getName());
}
}
for (String name : ruleNames) {
if (!name.startsWith(NAMED_RULE_PREFIX)) printDependencies(name, pw, 0);
}
pw.close();
} catch (IOException ioe) {
throw new TablesawException("Cannot write to file dependency.txt", -1);
}
}
// FIXME: fails! needs MarcCombiningReader for mhld or at least a diff version of RawRecordReader
@Test
public void testMultMHLDsWithSameID() throws IOException {
// bib134, multMhlds1
String bibFilePath = testDataParentPath + File.separator + "mhldMergeBibs134.mrc";
String mhldFilePath = testDataParentPath + File.separator + "mhldMergeMhlds1Mult.mrc";
Map<String, Record> mergedRecs =
MergeSummaryHoldings.mergeMhldsIntoBibRecordsAsMap(bibFilePath, mhldFilePath);
Record mergedRec = mergedRecs.get("a1");
assertEquals("Expected three 852", 3, mergedRec.getVariableFields("852").size());
Set<String> expectedVals = new HashSet<String>();
expectedVals.add("Location1");
expectedVals.add("Location2");
RecordTestingUtils.assertSubfieldHasExpectedValues(mergedRec, "852", 'b', expectedVals);
expectedVals.clear();
expectedVals.add("(month)");
expectedVals.add("(season)");
RecordTestingUtils.assertSubfieldHasExpectedValues(mergedRec, "853", 'b', expectedVals);
assertEquals("Expected one 863", 2, mergedRec.getVariableFields("863").size());
assertEquals("Expected one 866", 1, mergedRec.getVariableFields("866").size());
// fail("Implement me");
System.out.println("Test testMultMHLDsWithSameID() successful");
}
public GeneOrthologyEntry(String line) {
String[] a = line.split("\\s");
geneName = a[0];
s288cCoords = parseCoordsString(a[1]);
sigmaCoords = parseCoordsString(a[2]);
try {
identity = Double.parseDouble(a[3]);
} catch (NumberFormatException e) {
identity = null;
}
flags = new HashSet<Flag>();
orfCoords = null;
if (a.length > 4) {
String[] fa = a[4].split(",");
for (int i = 0; i < fa.length; i++) {
try {
if (fa[i].length() > 0) {
flags.add(Flag.valueOf(fa[i]));
} else {
flags.add(Flag.UNKNOWN);
}
} catch (IllegalArgumentException e) {
System.err.println(String.format("Unknown FLAG: \"%s\"", fa[i]));
flags.add(Flag.UNKNOWN);
}
}
if (a.length > 5) {
orfCoords = parseCoordsString(a[5]);
}
}
}
public static void viewTagInfo(String inurl, String tag) throws Exception {
// pr = new PrintStream(new FileOutputStream("/semplest/lluis/keywordExp/urldata.txt"));
pr = System.out;
long start = System.currentTimeMillis();
pr.println(inurl + "****************************************************************");
printList(cleanUrlText(TextUtils.HTMLText(inurl, tag)));
String urls = TextUtils.HTMLLinkString(inurl, inurl);
String[] url = urls.split("\\s+");
Set<String> urlMap = new HashSet<String>(url.length);
urlMap.add(inurl);
for (String ur : url) {
if (!urlMap.contains(ur)) {
pr.println(ur + "***************************************************************");
try {
printList(cleanUrlText(TextUtils.HTMLText(ur, tag)));
} catch (Exception e) {
System.out.println("Error with url :" + ur);
e.printStackTrace();
logger.error("Problem", e);
}
urlMap.add(ur);
}
}
pr.println("Time elapsed" + (start - System.currentTimeMillis()));
}
/**
* Expands list of files to process into full list of all files that can be found by recursively
* descending directories.
*/
void expand(File dir, String[] files, boolean isUpdate) {
if (files == null) {
return;
}
for (int i = 0; i < files.length; i++) {
File f;
if (dir == null) {
f = new File(files[i]);
} else {
f = new File(dir, files[i]);
}
if (f.isFile()) {
if (entries.add(f)) {
if (isUpdate) entryMap.put(entryName(f.getPath()), f);
}
} else if (f.isDirectory()) {
if (entries.add(f)) {
if (isUpdate) {
String dirPath = f.getPath();
dirPath = (dirPath.endsWith(File.separator)) ? dirPath : (dirPath + File.separator);
entryMap.put(entryName(dirPath), f);
}
expand(f, f.list(), isUpdate);
}
} else {
error(formatMsg("error.nosuch.fileordir", String.valueOf(f)));
ok = false;
}
}
}
/**
* Compute the set of all IA32 opcodes that have emit methods in the Assembler. This method uses
* the stylized form of all emit method names in the Assembler to extract the opcode of each one.
* It returns a set of all such distinct names, as a set of Strings.
*
* @param emitters the set of all emit methods in the Assembler
* @return the set of all opcodes handled by the Assembler
*/
private static Set<String> getOpcodes(Method[] emitters) {
Set<String> s = new HashSet<String>();
for (int i = 0; i < emitters.length; i++) {
String name = emitters[i].getName();
if (DEBUG) System.err.println(name);
if (name.startsWith("emit")) {
int posOf_ = name.indexOf('_');
if (posOf_ != -1) {
String opcode = name.substring(4, posOf_);
if (!excludedOpcodes.contains(opcode)) {
s.add(opcode);
}
} else {
String opcode = name.substring(4);
// make sure it is an opcode
if (opcode.equals(opcode.toUpperCase(Locale.getDefault()))) {
if (!excludedOpcodes.contains(opcode)) {
s.add(opcode);
}
}
}
}
}
return s;
}
private void onFinishWebUITests(ITestContext testContext) {
// List of test results which we will delete later because of duplication or because the test
// eventually passed
List<ITestResult> testsToBeRemoved = new ArrayList<ITestResult>();
// collect all id's from passed test
Set<Integer> passedTestIds = new HashSet<Integer>();
for (ITestResult passedTest : testContext.getPassedTests().getAllResults()) {
passedTestIds.add(getTestId(passedTest));
}
Set<Integer> failedTestIds = new HashSet<Integer>();
for (ITestResult failedTest : testContext.getFailedTests().getAllResults()) {
int failedTestId = getTestId(failedTest);
// if this test failed before mark as to be deleted
// or delete this failed test if there is at least one passed version
if (failedTestIds.contains(failedTestId) || passedTestIds.contains(failedTestId)) {
testsToBeRemoved.add(failedTest);
} else {
failedTestIds.add(failedTestId);
}
}
// finally delete all tests that are marked
for (Iterator<ITestResult> iterator = testContext.getFailedTests().getAllResults().iterator();
iterator.hasNext(); ) {
ITestResult testResult = iterator.next();
if (testsToBeRemoved.contains(testResult)) {
iterator.remove();
}
}
}
static {
Set<EncodingRule> rules = new HashSet<EncodingRule>();
rules.add(new EncodingRule("*", "%2A"));
rules.add(new EncodingRule("+", "%20"));
rules.add(new EncodingRule("%7E", "~"));
ENCODING_RULES = Collections.unmodifiableSet(rules);
}
private static void check(String what, MBeanNotificationInfo[] mbnis) {
System.out.print(what + ": checking notification info: ");
if (mbnis.length == 0) {
System.out.println("NONE (suspicious)");
suspicious.add(what);
return;
}
// Each MBeanNotificationInfo.getName() should be an existent
// Java class that is Notification or a subclass of it
for (int j = 0; j < mbnis.length; j++) {
String notifClassName = mbnis[j].getName();
Class notifClass;
try {
notifClass = Class.forName(notifClassName);
} catch (Exception e) {
System.out.print("FAILED(" + notifClassName + ": " + e + ") ");
failed.add(what);
continue;
}
if (!Notification.class.isAssignableFrom(notifClass)) {
System.out.print("FAILED(" + notifClassName + ": not a Notification) ");
failed.add(what);
continue;
}
System.out.print("OK(" + notifClassName + ") ");
}
System.out.println();
}
private static List<String> calcVCFGenotypeKeys(VariantContext vc) {
Set<String> keys = new HashSet<String>();
boolean sawGoodGT = false;
boolean sawGoodQual = false;
boolean sawGenotypeFilter = false;
for (Genotype g : vc.getGenotypes().values()) {
keys.addAll(g.getAttributes().keySet());
if (g.isAvailable()) sawGoodGT = true;
if (g.hasNegLog10PError()) sawGoodQual = true;
if (g.isFiltered() && g.isCalled()) sawGenotypeFilter = true;
}
if (sawGoodQual) keys.add(VCFConstants.GENOTYPE_QUALITY_KEY);
if (sawGenotypeFilter) keys.add(VCFConstants.GENOTYPE_FILTER_KEY);
List<String> sortedList = ParsingUtils.sortList(new ArrayList<String>(keys));
// make sure the GT is first
if (sawGoodGT) {
List<String> newList = new ArrayList<String>(sortedList.size() + 1);
newList.add(VCFConstants.GENOTYPE_KEY);
newList.addAll(sortedList);
sortedList = newList;
}
return sortedList;
}
/**
* Return information about the objects in this Tree.
*
* @param t The tree to examine.
* @return A human-readable String
*/
public static String toDebugStructureString(Tree t) {
StringBuilder sb = new StringBuilder();
String tCl = StringUtils.getShortClassName(t);
String tfCl = StringUtils.getShortClassName(t.treeFactory());
String lCl = StringUtils.getShortClassName(t.label());
String lfCl = StringUtils.getShortClassName(t.label().labelFactory());
Set<String> otherClasses = new HashSet<String>();
for (Tree st : t) {
String stCl = StringUtils.getShortClassName(st);
String stfCl = StringUtils.getShortClassName(st.treeFactory());
String slCl = StringUtils.getShortClassName(st.label());
String slfCl = StringUtils.getShortClassName(st.label().labelFactory());
if (!tCl.equals(stCl)) {
otherClasses.add(stCl);
}
if (!tfCl.equals(stfCl)) {
otherClasses.add(stfCl);
}
if (!lCl.equals(slCl)) {
otherClasses.add(slCl);
}
if (!lfCl.equals(slfCl)) {
otherClasses.add(slfCl);
}
}
sb.append("Tree with root of class ").append(tCl).append(" and factory ").append(tfCl);
sb.append(" with label class ").append(lCl).append(" and factory ").append(lfCl);
if (!otherClasses.isEmpty()) {
sb.append(" with the following classes also found within the tree: ").append(otherClasses);
}
return sb.toString();
}
/** Extracts specified entries from JAR file. */
void extract(InputStream in, String files[]) throws IOException {
ZipInputStream zis = new ZipInputStream(in);
ZipEntry e;
// Set of all directory entries specified in archive. Disallows
// null entries. Disallows all entries if using pre-6.0 behavior.
Set<ZipEntry> dirs = newDirSet();
while ((e = zis.getNextEntry()) != null) {
if (files == null) {
dirs.add(extractFile(zis, e));
} else {
String name = e.getName();
for (String file : files) {
if (name.startsWith(file)) {
dirs.add(extractFile(zis, e));
break;
}
}
}
}
// Update timestamps of directories specified in archive with their
// timestamps as given in the archive. We do this after extraction,
// instead of during, because creating a file in a directory changes
// that directory's timestamp.
updateLastModifiedTime(dirs);
}
private void readOldState(DataInputStream dis) throws IOException, TeamException {
int repoSize = dis.readInt();
boolean version1 = false;
if (repoSize == STATE_FILE_VERSION_1) {
version1 = true;
repoSize = dis.readInt();
}
for (int i = 0; i < repoSize; i++) {
ICVSRepositoryLocation root = KnownRepositories.getInstance().getRepository(dis.readUTF());
RepositoryRoot repoRoot = getRepositoryRootFor(root);
// read branch tags associated with this root
int tagsSize = dis.readInt();
CVSTag[] branchTags = new CVSTag[tagsSize];
for (int j = 0; j < tagsSize; j++) {
String tagName = dis.readUTF();
int tagType = dis.readInt();
branchTags[j] = new CVSTag(tagName, tagType);
}
// Ignore the branch tags since they are handled differently now
// addBranchTags(root, branchTags);
// read the number of projects for this root that have version tags
int projSize = dis.readInt();
if (projSize > 0) {
for (int j = 0; j < projSize; j++) {
String name = dis.readUTF();
Set tagSet = new HashSet();
int numTags = dis.readInt();
for (int k = 0; k < numTags; k++) {
tagSet.add(new CVSTag(dis.readUTF(), CVSTag.VERSION));
}
CVSTag[] tags = (CVSTag[]) tagSet.toArray(new CVSTag[tagSet.size()]);
repoRoot.addTags(name, tags);
}
}
// read the auto refresh filenames for this project
if (version1) {
try {
projSize = dis.readInt();
if (projSize > 0) {
for (int j = 0; j < projSize; j++) {
String name = dis.readUTF();
Set filenames = new HashSet();
int numFilenames = dis.readInt();
for (int k = 0; k < numFilenames; k++) {
filenames.add(name + "/" + dis.readUTF()); // $NON-NLS-1$
}
repoRoot.setAutoRefreshFiles(
name, (String[]) filenames.toArray(new String[filenames.size()]));
}
}
} catch (EOFException e) {
// auto refresh files are not persisted, continue and save them next time.
}
}
broadcastRepositoryChange(repoRoot);
}
}
static {
_reachableStoppers.add(HttpServer.class);
_reachableStoppers.add(AppServer.class);
_reachableStoppers.add(DBTCP.class);
_reachableStoppers.add(Mongo.class);
_reachableStoppers.add(WeakBag.class);
_reachableStoppers.add(WeakValueMap.class);
}
/**
* Reads query file and parses the queries.
*
* @requires querystream, outstream, are successfully initialized
* @requires g to be already generated
* @param queryStream file input stream of query file
* @param outStream file output stream of output file
* @param g
* @effects writes results to output file
*/
private static void parseQuery(FileInputStream queryStream, FileOutputStream outStream, Graph g) {
try {
BufferedWriter output = new BufferedWriter(new OutputStreamWriter(outStream));
BufferedReader queryReader = new BufferedReader(new InputStreamReader(queryStream));
final int COMMAND_INDEX = 0;
final int U1_INDEX = 1;
final int U2_INDEX = 2;
final String QUERY_ENDING = " ?";
Set<Set<String>> queries = new LinkedHashSet<Set<String>>();
String line;
while ((line = queryReader.readLine()) != null) {
// each query set contains two user id strings and a command
// this also handles duplicate user ids with different commands
Set<String> query = new LinkedHashSet<String>();
// a bit overkill, but eliminate any unnecessary whitespace if needed and replaces with
// single space
String[] columns = line.trim().replaceAll("\\s+", " ").split(" ");
// first column is query
// second column is user 1
// third column is user 2
String command = columns[COMMAND_INDEX];
String id1 = columns[U1_INDEX];
String id2 = columns[U2_INDEX];
query.add(id1);
query.add(id2);
query.add(command);
// check if query ends with question mark (with leading space) and query is unique
if (line.endsWith(QUERY_ENDING) && !queries.contains(query)) {
queries.add(query);
Vertex u1 = new Vertex(id1);
Vertex u2 = new Vertex(id2);
printResults(output, g, u1, u2, command);
}
}
queryReader.close();
output.close();
// return new LinkedHashMap<List<Vertex>, String>(queries);
} catch (Exception e) { // if something goes wrong
throw new RuntimeException(e);
}
}
private void computeMatchSet() {
for (Vertex v : LV) {
for (Vertex neighb : v.getNeighbors()) {
if (neighb.getId() != SOURCE_ID && getFlow(v, neighb) > 0) {
matches.add(v);
matches.add(neighb);
}
}
}
}
private static void processLibrariesAndJpsPlugins(
final File jarFile,
final File zipFile,
final String pluginName,
final Set<Library> libs,
Map<Module, String> jpsModules,
final ProgressIndicator progressIndicator)
throws IOException {
if (FileUtil.ensureCanCreateFile(zipFile)) {
ZipOutputStream zos = null;
try {
zos = new ZipOutputStream(new BufferedOutputStream(new FileOutputStream(zipFile)));
addStructure(pluginName, zos);
addStructure(pluginName + "/" + MIDDLE_LIB_DIR, zos);
final String entryName = pluginName + JAR_EXTENSION;
ZipUtil.addFileToZip(
zos,
jarFile,
getZipPath(pluginName, entryName),
new HashSet<String>(),
createFilter(progressIndicator, FileTypeManager.getInstance()));
for (Map.Entry<Module, String> entry : jpsModules.entrySet()) {
File jpsPluginJar = jarModulesOutput(Collections.singleton(entry.getKey()), null, null);
ZipUtil.addFileToZip(
zos, jpsPluginJar, getZipPath(pluginName, entry.getValue()), null, null);
}
Set<String> usedJarNames = new HashSet<String>();
usedJarNames.add(entryName);
Set<VirtualFile> jarredVirtualFiles = new HashSet<VirtualFile>();
for (Library library : libs) {
final VirtualFile[] files = library.getFiles(OrderRootType.CLASSES);
for (VirtualFile virtualFile : files) {
if (jarredVirtualFiles.add(virtualFile)) {
if (virtualFile.getFileSystem() instanceof JarFileSystem) {
addLibraryJar(
virtualFile, zipFile, pluginName, zos, usedJarNames, progressIndicator);
} else {
makeAndAddLibraryJar(
virtualFile,
zipFile,
pluginName,
zos,
usedJarNames,
progressIndicator,
library.getName());
}
}
}
}
} finally {
if (zos != null) zos.close();
}
}
}
@Ignore
@Test
/**
* Tests ConflictTreeSimulatedSession with unsolvable ontologies, target diagnoses are calculated
*/
public void doUnsolvableOAEIConferenceTest()
throws SolverException, InconsistentTheoryException, OWLOntologyCreationException {
logger.info("doUnsolveableTest_with_2015_ontologies");
String matchingsDir = "oaei11conference/matchings/";
String ontologyDir = "oaei11conference/ontology";
File[] f = getMappingFiles(matchingsDir, "incoherent", "incoherent_2015.txt");
File[] f2 = getMappingFiles(matchingsDir, "inconsistent", "inconsistent_2015.txt");
Set<File> files = new LinkedHashSet<File>();
Map<File, String> map = new HashMap<File, String>();
for (File file : f) {
files.add(file);
map.put(file, "incoherent");
}
for (File file : f2) {
files.add(file);
map.put(file, "inconsistent");
}
runOaeiConferenceTests(matchingsDir, ontologyDir, files, map);
/*
result: 2015-02-26-T-10-58-50
junit.framework.AssertionFailedError
at at.ainf.owlapi3.performance.ConflictTreeTest.computeHSShortLog(ConflictTreeTest.java:562)
at at.ainf.owlapi3.performance.ConflictTreeSession.search(ConflictTreeSession.java:109)
at at.ainf.owlapi3.performance.ConflictTreeSession.search(ConflictTreeSession.java:69)
at at.ainf.owlapi3.performance.ConflictTreeTest.runOaeiConferenceTests(ConflictTreeTest.java:315)
at at.ainf.owlapi3.performance.ConflictTreeTest.doUnsolvableOAEIConferenceTest(ConflictTreeTest.java:174)
and
result: 2015-02-26-T-12-13-55
at.ainf.diagnosis.model.InconsistentTheoryException: Background theory or test cases are inconsistent! Finding conflicts is impossible!
at at.ainf.diagnosis.quickxplain.BaseQuickXplain.verifyKnowledgeBase(BaseQuickXplain.java:173)
at at.ainf.diagnosis.quickxplain.MultiQuickXplain.search(MultiQuickXplain.java:107)
at at.ainf.diagnosis.quickxplain.BaseQuickXplain.search(BaseQuickXplain.java:116)
at at.ainf.owlapi3.performance.ConflictTreeSession.computeNConflictsAtTime(ConflictTreeSession.java:193)
at at.ainf.owlapi3.performance.ConflictTreeSession.search(ConflictTreeSession.java:83)
at at.ainf.owlapi3.performance.ConflictTreeSession.search(ConflictTreeSession.java:69)
at at.ainf.owlapi3.performance.ConflictTreeTest.runOaeiConferenceTests(ConflictTreeTest.java:353)
at at.ainf.owlapi3.performance.ConflictTreeTest.doUnsolvableOAEIConferenceTest(ConflictTreeTest.java:219)
*/
}
@Ignore
@Test
/**
* Tests ConflictTreeSimulatedSession with solvable ontologies from OAEI11 Conference, target
* diagnoses are calculated
*/
public void doOAEIConferenceTest()
throws SolverException, InconsistentTheoryException, OWLOntologyCreationException {
logger.info("doOAEIConferenceTest");
String matchingsDir = "oaei11conference/matchings/";
String ontologyDir = "oaei11conference/ontology";
File[] f = getMappingFiles(matchingsDir, "incoherent", "includedIncoher.txt");
File[] f2 = getMappingFiles(matchingsDir, "inconsistent", "included.txt");
Set<File> files = new LinkedHashSet<File>();
Map<File, String> map = new HashMap<File, String>();
for (File file : f) {
files.add(file);
map.put(file, "incoherent");
}
for (File file : f2) {
files.add(file);
map.put(file, "inconsistent");
}
runOaeiConferenceTests(matchingsDir, ontologyDir, files, map);
/*
result: 2015-02-26-T-09-29-38
java.lang.OutOfMemoryError: GC overhead limit exceeded
at java.util.TreeMap.keyIterator(TreeMap.java:1106)
at java.util.TreeMap$KeySet.iterator(TreeMap.java:1119)
at java.util.TreeSet.iterator(TreeSet.java:181)
at java.util.Collections$UnmodifiableCollection$1.<init>(Collections.java:1039)
at java.util.Collections$UnmodifiableCollection.iterator(Collections.java:1038)
at at.ainf.diagnosis.storage.FormulaSetImpl.iterator(FormulaSetImpl.java:123)
at at.ainf.diagnosis.tree.AbstractTreeSearch.intersectsWith(AbstractTreeSearch.java:712)
at at.ainf.diagnosis.tree.AbstractTreeSearch.canReuseConflict(AbstractTreeSearch.java:697)
at at.ainf.diagnosis.tree.AbstractTreeSearch.processNode(AbstractTreeSearch.java:363)
at at.ainf.diagnosis.tree.AbstractTreeSearch.processOpenNodes(AbstractTreeSearch.java:311)
at at.ainf.diagnosis.tree.AbstractTreeSearch.searchDiagnoses(AbstractTreeSearch.java:268)
at at.ainf.diagnosis.tree.AbstractTreeSearch.start(AbstractTreeSearch.java:202)
at at.ainf.owlapi3.base.OAEI11ConferenceSession.getRandomDiagSet(OAEI11ConferenceSession.java:151)
at at.ainf.owlapi3.performance.OAEI11ConferenceTests.runOaeiConferenceTests(OAEI11ConferenceTests.java:151)
at at.ainf.owlapi3.performance.OAEI11ConferenceTests.doTestsOAEIConference(OAEI11ConferenceTests.java:131)
*/
}
/** Scans the directory for new files. */
protected void scanDirectory() {
if (System.currentTimeMillis() - scanIntervalMillis >= lastScanMillis) {
Set<Path> newPaths = scanner.scan(fs, filePath, processedFiles);
for (Path newPath : newPaths) {
String newPathString = newPath.toString();
pendingFiles.add(newPathString);
processedFiles.add(newPathString);
localProcessedFileCount.increment();
}
lastScanMillis = System.currentTimeMillis();
}
}
/**
* Enumerates the resouces in a give package name. This works even if the resources are loaded
* from a jar file!
*
* <p>Adapted from code by mikewse on the java.sun.com message boards.
* http://forum.java.sun.com/thread.jsp?forum=22&thread=30984
*
* @param packageName The package to enumerate
* @return A Set of Strings for each resouce in the package.
*/
public static Set getResoucesInPackage(String packageName) throws IOException {
String localPackageName;
if (packageName.endsWith("/")) {
localPackageName = packageName;
} else {
localPackageName = packageName + '/';
}
Enumeration dirEnum = ClassLoader.getSystemResources(localPackageName);
Set names = new HashSet();
// Loop CLASSPATH directories
while (dirEnum.hasMoreElements()) {
URL resUrl = (URL) dirEnum.nextElement();
// Pointing to filesystem directory
if (resUrl.getProtocol().equals("file")) {
File dir = new File(resUrl.getFile());
File[] files = dir.listFiles();
if (files != null) {
for (int i = 0; i < files.length; i++) {
File file = files[i];
if (file.isDirectory()) continue;
names.add(localPackageName + file.getName());
}
}
// Pointing to Jar file
} else if (resUrl.getProtocol().equals("jar")) {
JarURLConnection jconn = (JarURLConnection) resUrl.openConnection();
JarFile jfile = jconn.getJarFile();
Enumeration entryEnum = jfile.entries();
while (entryEnum.hasMoreElements()) {
JarEntry entry = (JarEntry) entryEnum.nextElement();
String entryName = entry.getName();
// Exclude our own directory
if (entryName.equals(localPackageName)) continue;
String parentDirName = entryName.substring(0, entryName.lastIndexOf('/') + 1);
if (!parentDirName.equals(localPackageName)) continue;
names.add(entryName);
}
} else {
// Invalid classpath entry
}
}
return names;
}
public void run() {
super.run();
// save the last set of active JVMs
Set lastActiveVms = activeVms;
try {
// get the current set of active JVMs
activeVms = (HashSet) vmManager.activeVms();
} catch (MonitorException e) {
// XXX: use logging api
System.err.println("MonitoredHostProvider: polling task " + "caught MonitorException:");
e.printStackTrace();
// mark the HostManager as errored and notify listeners
setLastException(e);
fireDisconnectedEvents();
}
if (activeVms.isEmpty()) {
return;
}
Set startedVms = new HashSet();
Set terminatedVms = new HashSet();
for (Iterator i = activeVms.iterator(); i.hasNext(); /* empty */ ) {
Integer vmid = (Integer) i.next();
if (!lastActiveVms.contains(vmid)) {
// a new file has been detected, add to set
startedVms.add(vmid);
}
}
for (Iterator i = lastActiveVms.iterator(); i.hasNext();
/* empty */ ) {
Object o = i.next();
if (!activeVms.contains(o)) {
// JVM has terminated, remove it from the active list
terminatedVms.add(o);
}
}
if (!startedVms.isEmpty() || !terminatedVms.isEmpty()) {
fireVmStatusChangedEvents(activeVms, startedVms, terminatedVms);
}
}
@RequestMapping(value = CLIENT_CONNECT_PATH, method = RequestMethod.POST)
public @ResponseBody int connectClient(@RequestBody String allVid) {
try {
int reply = FAILED;
String[] videos = allVid.split(",");
String uName = videos[0].trim();
videos = java.util.Arrays.copyOfRange(videos, 1, videos.length);
// System.out.println("Client connect"+hostAdder+" "+uName+" "+ Arrays.asList(videos));
int ans = masterService.psConnectClient(hostAdder, uName, videos);
// System.out.println("ans =" +ans +" "+FAILED);
while (ans == PS_NOT_CONNECTED) {
reconnectToMS();
ans = masterService.psConnectClient(hostAdder, uName, videos);
}
if (ans == FAILED) return FAILED;
// System.out.println("Clinet "+ uName + " connected");
if (user_vidNameMap.containsKey(uName)) {
reply = CLIENT_ALREADY_CONNECTED;
} else {
reply = CLIENT_CONNECTED;
user_vidNameMap.put(uName, new HashSet<String>());
}
// System.out.println("Clinet "+ uName + " connected");
Set<String> vidSet = user_vidNameMap.get(uName);
for (int i = 0; i < videos.length; i++) {
String temp = videos[i].trim();
// System.out.println("add video");
if (!temp.equals("")) {
vidSet.add(temp);
addTovidName_UserMap(uName, temp);
}
}
// System.out.println("Clinet "+ uName + " connected");
userAliveMap.put(uName, new Long(System.currentTimeMillis() + TTL));
// System.out.println("Clinet "+ uName + " connected");
activeUsers.add(uName);
System.out.println("Clinet " + uName + " connected");
return reply;
} catch (Exception e) {
System.out.println("Error: " + e.getMessage());
return FAILED;
}
}
private static PencilPosition findShortestRoute(int[][] maze) {
// all found solutions to the maze
PriorityQueue<PencilPosition> solutions =
new PriorityQueue<PencilPosition>(5, new PencilPositionComparator());
// bread-first search queue
Queue<PencilPosition> routes = new LinkedList<PencilPosition>();
// set of already visited positions
Set<PencilPosition> visitedPositions = new HashSet<PencilPosition>();
// add the starting positions, which is always (0,0)
routes.add(new PencilPosition(0, 0, false, null));
while (!routes.isEmpty()) {
PencilPosition position = routes.poll();
// if this is the destinations position then we've found a solution
if (0 == maze[position.row][position.column]) {
solutions.add(position);
continue;
}
// if we haven't already visited this position
if (!visitedPositions.contains(position)) {
routes.addAll(findPossibleRoutes(position, maze));
visitedPositions.add(position);
}
}
return solutions.poll();
}
/**
* Get the list of ids of sequences in this sequence database
*
* @return the list of sequence ids.
*/
public Set<Integer> getSequenceIDs() {
Set<Integer> set = new HashSet<Integer>();
for (Sequence sequence : getSequences()) {
set.add(sequence.getId());
}
return set;
}
private void findParents(JavaClass jclass, Set<JavaClass> changedParents) {
for (JavaClass parent : getParents(jclass)) {
if (changedParents.add(parent)) {
findParents(parent, changedParents);
}
}
}
private static boolean checkDependants(
final IdeaPluginDescriptor pluginDescriptor,
final Function<PluginId, IdeaPluginDescriptor> pluginId2Descriptor,
final Condition<PluginId> check,
final Set<PluginId> processed) {
processed.add(pluginDescriptor.getPluginId());
final PluginId[] dependentPluginIds = pluginDescriptor.getDependentPluginIds();
final Set<PluginId> optionalDependencies =
new HashSet<PluginId>(Arrays.asList(pluginDescriptor.getOptionalDependentPluginIds()));
for (final PluginId dependentPluginId : dependentPluginIds) {
if (processed.contains(dependentPluginId)) continue;
// TODO[yole] should this condition be a parameter?
if (isModuleDependency(dependentPluginId)
&& (ourAvailableModules.isEmpty()
|| ourAvailableModules.contains(dependentPluginId.getIdString()))) {
continue;
}
if (!optionalDependencies.contains(dependentPluginId)) {
if (!check.value(dependentPluginId)) {
return false;
}
final IdeaPluginDescriptor dependantPluginDescriptor =
pluginId2Descriptor.fun(dependentPluginId);
if (dependantPluginDescriptor != null
&& !checkDependants(dependantPluginDescriptor, pluginId2Descriptor, check, processed)) {
return false;
}
}
}
return true;
}
// ---------------------------------------------------------------------------
public Rule findTargetRule(String target) throws TablesawException {
Rule rule = null;
if (m_resolved) {
ArrayList<String> posTargets;
String posTarget = target;
if (m_noRulesList.contains(target)) return (null);
if ((rule = m_locatedRules.get(target)) != null) return (rule);
// First look in name map
rule = m_nameRuleMap.get(target);
if (rule == null) { // Now look for targets
rule = m_targetRuleMap.get(posTarget);
if (rule == null) {
posTargets = m_fileManager.getPossibleFiles(posTarget);
for (String t : posTargets) {
rule = m_targetRuleMap.get(t);
if (rule != null) break;
}
}
}
Debug.print("Rule for " + target + " is " + rule);
if (rule != null) {
m_locatedRules.put(target, rule);
} else m_noRulesList.add(target);
}
return (rule);
}
/**
* Creates an NL fragment project along with the locale specific properties files.
*
* @throws CoreException
* @throws IOException
* @throws InvocationTargetException
* @throws InterruptedException
*/
private void internationalizePlugins(List plugins, List locales, Map overwrites)
throws CoreException, IOException, InvocationTargetException, InterruptedException {
Set created = new HashSet();
for (Iterator it = plugins.iterator(); it.hasNext(); ) {
IPluginModelBase plugin = (IPluginModelBase) it.next();
for (Iterator iter = locales.iterator(); iter.hasNext(); ) {
Locale locale = (Locale) iter.next();
IProject project = getNLProject(plugin, locale);
if (created.contains(project)
|| overwriteWithoutAsking
|| !project.exists()
|| OVERWRITE == overwrites.get(project.getName())) {
if (!created.contains(project) && project.exists()) {
project.delete(true, getProgressMonitor());
}
if (!created.contains(project)) {
createNLFragment(plugin, project, locale);
created.add(project);
project.getFolder(RESOURCE_FOLDER_PARENT).create(false, true, getProgressMonitor());
}
project
.getFolder(RESOURCE_FOLDER_PARENT)
.getFolder(locale.toString())
.create(true, true, getProgressMonitor());
createLocaleSpecificPropertiesFile(project, plugin, locale);
}
}
}
}
// ---------------------------------------------------------------------------
private void printDependencies(String target, PrintWriter pw, int spacing)
throws TablesawException {
Rule tr = findTargetRule(target);
String[] pre;
for (int I = 0; I < spacing; I++) pw.print("\t");
List<String> targetList = new ArrayList<String>();
if (tr != null) {
for (String name : tr.getDependNames()) {
targetList.add(name);
}
for (Rule r : tr.getDependRules()) {
if ((r.getName() != null) && (!r.getName().startsWith(NAMED_RULE_PREFIX))) {
targetList.add(r.getName());
} else {
for (String t : r.getTargets()) {
targetList.add(t);
}
}
}
}
if (!m_printedDependencies.add(target) && (targetList.size() != 0)) {
pw.println(target + "*");
return;
}
pw.println(target);
for (String t : targetList) printDependencies(t, pw, spacing + 1);
}