/**
* Construct a frequency table from an InputStream. This will create a temporary file to copy the
* InputStream in.
*
* @param source the Input Stream
* @return an InputStream which is a copy of the source Stream, provided to re-Read the same Bytes
* for the actual compression process.
*/
public InputStream constructTable(InputStream source, boolean copy) {
freq = new int[TABLESIZE];
try {
File file = null;
FileOutputStream fos = null;
if (copy == true) {
file = File.createTempFile("huf", "tmp");
file.deleteOnExit();
fos = new FileOutputStream(file);
}
while (source.available() != 0) {
int c = source.read();
freq[c]++;
if (copy) fos.write(c);
}
source.close();
if (copy) {
fos.close();
return new FileInputStream(file);
}
return null;
} catch (Exception ex) {
ExHandler.handle(ex);
return null;
}
}
public Graph(WeightedBVGraph graph, String[] names) {
org.apache.log4j.Logger logger =
org.apache.log4j.Logger.getLogger("it.unimi.dsi.webgraph.ImmutableGraph");
logger.setLevel(org.apache.log4j.Level.FATAL);
if (names.length != graph.numNodes())
throw new Error("Problem with the list of names for the nodes in the graph.");
try {
File auxFile = File.createTempFile("graph-maps-" + System.currentTimeMillis(), "aux");
auxFile.deleteOnExit();
RecordManager recMan = RecordManagerFactory.createRecordManager(auxFile.getAbsolutePath());
nodes = recMan.hashMap("nodes");
nodesReverse = recMan.hashMap("nodesReverse");
} catch (IOException ex) {
throw new Error(ex);
}
nodes.clear();
nodesReverse.clear();
Constructor[] cons = WeightedArc.class.getDeclaredConstructors();
for (int i = 0; i < cons.length; i++) cons[i].setAccessible(true);
this.graph = graph;
WeightedArcSet list = new WeightedArcSet();
ArcLabelledNodeIterator it = graph.nodeIterator();
while (it.hasNext()) {
if (commit++ % COMMIT_SIZE == 0) {
commit();
list.commit();
}
Integer aux1 = it.nextInt();
Integer aux2 = null;
ArcLabelledNodeIterator.LabelledArcIterator suc = it.successors();
while ((aux2 = suc.nextInt()) != null && aux2 >= 0 && (aux2 < graph.numNodes()))
try {
WeightedArc arc = (WeightedArc) cons[0].newInstance(aux2, aux1, suc.label().getFloat());
list.add(arc);
this.nodes.put(aux1, names[aux1]);
this.nodes.put(aux2, names[aux2]);
this.nodesReverse.put(names[aux1], aux1);
this.nodesReverse.put(names[aux2], aux2);
} catch (Exception ex) {
throw new Error(ex);
}
}
reverse = new WeightedBVGraph(list.toArray(new WeightedArc[0]));
numArcs = list.size();
iterator = nodeIterator();
try {
File auxFile = File.createTempFile("graph" + System.currentTimeMillis(), "aux");
auxFile.deleteOnExit();
String basename = auxFile.getAbsolutePath();
store(basename);
} catch (IOException ex) {
throw new Error(ex);
}
commit();
}
private static File patchConfFile(File conf, String library) throws IOException {
File tmpConf = File.createTempFile("idea-", "-mvn.conf");
tmpConf.deleteOnExit();
patchConfFile(conf, tmpConf, library);
return tmpConf;
}
public static String createTempImageFile(String origFile, String prefix, String suffix)
throws Exception {
File outputFile = createTempFile(prefix, suffix);
outputFile.deleteOnExit();
copyFile(outputFile.getAbsolutePath(), origFile);
return outputFile.getAbsolutePath();
}
private static String getArtifactResolverJar(boolean isMaven3) throws IOException {
Class marker =
isMaven3 ? MavenArtifactResolvedM3RtMarker.class : MavenArtifactResolvedM2RtMarker.class;
File classDirOrJar = new File(PathUtil.getJarPathForClass(marker));
if (!classDirOrJar.isDirectory()) {
return classDirOrJar.getAbsolutePath(); // it's a jar in IDEA installation.
}
// it's a classes directory, we are in development mode.
File tempFile = FileUtil.createTempFile("idea-", "-artifactResolver.jar");
tempFile.deleteOnExit();
ZipOutputStream zipOutput = new ZipOutputStream(new FileOutputStream(tempFile));
try {
ZipUtil.addDirToZipRecursively(zipOutput, null, classDirOrJar, "", null, null);
if (isMaven3) {
File m2Module = new File(PathUtil.getJarPathForClass(MavenModuleMap.class));
String commonClassesPath = MavenModuleMap.class.getPackage().getName().replace('.', '/');
ZipUtil.addDirToZipRecursively(
zipOutput, null, new File(m2Module, commonClassesPath), commonClassesPath, null, null);
}
} finally {
zipOutput.close();
}
return tempFile.getAbsolutePath();
}
void put(final URI uri, ArtifactData data) throws Exception {
reporter.trace("put %s %s", uri, data);
File tmp = createTempFile(repoDir, "mtp", ".whatever");
tmp.deleteOnExit();
try {
copy(uri.toURL(), tmp);
byte[] sha = SHA1.digest(tmp).digest();
reporter.trace("SHA %s %s", uri, Hex.toHexString(sha));
ArtifactData existing = get(sha);
if (existing != null) {
reporter.trace("existing");
xcopy(existing, data);
return;
}
File meta = new File(repoDir, Hex.toHexString(sha) + ".json");
File file = new File(repoDir, Hex.toHexString(sha));
rename(tmp, file);
reporter.trace("file %s", file);
data.file = file.getAbsolutePath();
data.sha = sha;
data.busy = false;
CommandData cmddata = parseCommandData(data);
if (cmddata.bsn != null) {
data.name = cmddata.bsn + "-" + cmddata.version;
} else data.name = Strings.display(cmddata.title, cmddata.bsn, cmddata.name, uri);
codec.enc().to(meta).put(data);
reporter.trace("TD = " + data);
} finally {
tmp.delete();
reporter.trace("puted %s %s", uri, data);
}
}
@Test
public void shouldHonorDiskStorageRootOverride() throws IOException, ClassNotFoundException {
File tmpDir = TestUtil.createTmpDir();
try {
String tmpDirPath = tmpDir.getAbsolutePath();
systemEnv.put(TlbConstants.Server.TLB_DATA_DIR.key, tmpDirPath);
initializer = new TlbServerInitializer(new SystemEnvironment(systemEnv));
EntryRepoFactory factory = initializer.repoFactory();
File file =
new File(
tmpDirPath,
new EntryRepoFactory.VersionedNamespace(LATEST_VERSION, SUBSET_SIZE)
.getIdUnder("quux"));
file.deleteOnExit();
writeEntriedTo(file);
SubsetSizeRepo repo = factory.createSubsetRepo("quux", LATEST_VERSION);
assertThat(
(List<SubsetSizeEntry>) repo.list(),
is(
Arrays.asList(
new SubsetSizeEntry(1), new SubsetSizeEntry(2), new SubsetSizeEntry(3))));
} finally {
FileUtils.deleteQuietly(tmpDir);
}
}
/**
* Take the name of a jar file and extract the plugin.xml file, if possible, to a temporary file.
*
* @param f The jar file to extract from.
* @return a temporary file to which the plugin.xml file has been copied.
*/
public static File unpackPluginXML(File f) {
InputStream in = null;
OutputStream out = null;
try {
JarFile jar = new JarFile(f);
ZipEntry entry = jar.getEntry(PLUGIN_XML_FILE);
if (entry == null) {
return null;
}
File dest = File.createTempFile("jabref_plugin", ".xml");
dest.deleteOnExit();
in = new BufferedInputStream(jar.getInputStream(entry));
out = new BufferedOutputStream(new FileOutputStream(dest));
byte[] buffer = new byte[2048];
for (; ; ) {
int nBytes = in.read(buffer);
if (nBytes <= 0) break;
out.write(buffer, 0, nBytes);
}
out.flush();
return dest;
} catch (IOException ex) {
ex.printStackTrace();
return null;
} finally {
try {
if (out != null) out.close();
if (in != null) in.close();
} catch (IOException ex) {
ex.printStackTrace();
}
}
}
/**
* Extract the dependent libs and return the extracted jar files
*
* @return the collection of extracted files
*/
private Collection<File> extractDependentLibs(final File cachedir) throws IOException {
final Attributes attributes = getMainAttributes();
if (null == attributes) {
debug("no manifest attributes");
return null;
}
final ArrayList<File> files = new ArrayList<File>();
final String libs = attributes.getValue(RUNDECK_PLUGIN_LIBS);
if (null != libs) {
debug("jar libs listed: " + libs + " for file: " + pluginJar);
if (!cachedir.isDirectory()) {
if (!cachedir.mkdirs()) {
debug("Failed to create cachedJar dir for dependent libs: " + cachedir);
}
}
final String[] libsarr = libs.split(" ");
extractJarContents(libsarr, cachedir);
for (final String s : libsarr) {
File libFile = new File(cachedir, s);
libFile.deleteOnExit();
files.add(libFile);
}
} else {
debug("no jar libs listed in manifest: " + pluginJar);
}
return files;
}
@Test
public void canFollowLogfile() throws IOException {
File tempFile =
File.createTempFile("commons-io", "", new File(System.getProperty("java.io.tmpdir")));
tempFile.deleteOnExit();
System.out.println("Temp file = " + tempFile.getAbsolutePath());
PrintStream log = new PrintStream(tempFile);
LogfileFollower follower = new LogfileFollower(tempFile);
List<String> lines;
// Empty file:
lines = follower.newLines();
assertEquals(0, lines.size());
// Write two lines:
log.println("Line 1");
log.println("Line 2");
lines = follower.newLines();
assertEquals(2, lines.size());
assertEquals("Line 2", lines.get(1));
// Write one more line:
log.println("Line 3");
lines = follower.newLines();
assertEquals(1, lines.size());
assertEquals("Line 3", lines.get(0));
// Write one and a half line and finish later:
log.println("Line 4");
log.print("Line 5 begin");
lines = follower.newLines();
assertEquals(1, lines.size());
// End last line and start a new one:
log.println(" end");
log.print("Line 6 begin");
lines = follower.newLines();
assertEquals(1, lines.size());
assertEquals("Line 5 begin end", lines.get(0));
// End last line:
log.println(" end");
lines = follower.newLines();
assertEquals(1, lines.size());
assertEquals("Line 6 begin end", lines.get(0));
// A line only missing a newline:
log.print("Line 7");
lines = follower.newLines();
assertEquals(0, lines.size());
log.println();
lines = follower.newLines();
assertEquals(1, lines.size());
assertEquals("Line 7", lines.get(0));
// Delete:
log.close();
lines = follower.newLines();
assertEquals(0, lines.size());
}
protected File createTempFile(JarEntry je) throws IOException {
byte[] jeBytes = getJarEntryBytes(outerFile, je);
String tempName = je.getName().replace('/', '_') + ".";
File tempDir = new File("execwartmp");
if (tempDir.mkdir()) tempDir.deleteOnExit();
File file = File.createTempFile("moqui_temp", tempName, tempDir);
file.deleteOnExit();
BufferedOutputStream os = null;
try {
os = new BufferedOutputStream(new FileOutputStream(file));
os.write(jeBytes);
} finally {
if (os != null) os.close();
}
return file;
}
/**
* Creates a single cached version of the pluginJar located within pluginJarCacheDirectory
* deleting all existing versions of pluginJar
*
* @param jarName
*/
protected File createCachedJar(final File dir, final String jarName) throws PluginException {
File cachedJar;
try {
cachedJar = new File(dir, jarName);
cachedJar.deleteOnExit();
FileUtils.fileCopy(pluginJar, cachedJar, true);
} catch (IOException e) {
throw new PluginException(e);
}
return cachedJar;
}
/**
* Create a file that contains the specified message
*
* @param root a git repository root
* @param message a message to write
* @return a file reference
* @throws IOException if file cannot be created
*/
private File createMessageFile(VirtualFile root, final String message) throws IOException {
// filter comment lines
File file = FileUtil.createTempFile(GIT_COMMIT_MSG_FILE_PREFIX, GIT_COMMIT_MSG_FILE_EXT);
file.deleteOnExit();
@NonNls String encoding = GitConfigUtil.getCommitEncoding(myProject, root);
Writer out = new OutputStreamWriter(new FileOutputStream(file), encoding);
try {
out.write(message);
} finally {
out.close();
}
return file;
}
/**
* Creates a file on the local FS. Pass size as {@link LocalDirAllocator.SIZE_UNKNOWN} if not
* known apriori. We round-robin over the set of disks (via the configured dirs) and return a
* file on the first path which has enough space. The file is guaranteed to go away when the JVM
* exits.
*/
public File createTmpFileForWrite(String pathStr, long size, Configuration conf)
throws IOException {
// find an appropriate directory
Path path = getLocalPathForWrite(pathStr, size, conf, true);
File dir = new File(path.getParent().toUri().getPath());
String prefix = path.getName();
// create a temp file on this directory
File result = File.createTempFile(prefix, null, dir);
result.deleteOnExit();
return result;
}
private String createTemporaryPreinstallFile() {
try {
File tempFile = File.createTempFile("preinstall", null);
tempFile.deleteOnExit();
InstallUtil.copyResourceToFile("/gnu/io/installer/resources/macosx/preinstall", tempFile);
String absPath = tempFile.getAbsolutePath();
Process p = Runtime.getRuntime().exec(new String[] {"chmod", "a+x", absPath});
p.waitFor();
return absPath;
} catch (Throwable t) {
}
return null;
}
private void installAuthKit() {
boolean usingJWS = false;
final ClassLoader originalClassLoader = Thread.currentThread().getContextClassLoader();
if (originalClassLoader.toString().toLowerCase().indexOf("jnlp") != -1) usingJWS = true;
if (usingJWS) return;
try {
File tempFile = new File(jarFolder, "libAuthKit.jnilib");
tempFile.deleteOnExit();
InstallUtil.copyResourceToFile(
"/gnu/io/installer/resources/macosx/lib/libAuthKit.jnilib", tempFile);
} catch (Throwable t) {
System.out.println("installAuthKit Throwable " + t);
}
}
public void deployElement(Element e, String fileName, boolean encrypt, boolean isTransient)
throws ISOException, IOException, GeneralSecurityException {
e = ((Element) e.clone());
XMLOutputter out = new XMLOutputter(Format.getPrettyFormat());
Document doc = new Document();
doc.setRootElement(e);
File qbean = new File(deployDir, fileName);
if (isTransient) {
e.setAttribute("instance", getInstanceId().toString());
qbean.deleteOnExit();
}
FileWriter writer = new FileWriter(qbean);
if (encrypt) doc = encrypt(doc);
out.output(doc, writer);
writer.close();
}
private boolean tryToWriteTestFile() {
boolean testFileWrite = false;
File testFile = new File(configDirectory, "tmp" + System.currentTimeMillis());
try {
boolean success = testFile.createNewFile();
if (success) {
boolean deleted = testFile.delete();
if (!deleted) {
testFile.deleteOnExit();
} else {
testFileWrite = true;
}
}
} catch (IOException e) {
ConfigLogImplementation.logMethods.warn(
"Test file write to config directory failed at " + configDirectory);
}
return testFileWrite;
}
public void run() {
try {
URL url = new URL(protocol + "://localhost:" + port + "/test1/" + f);
HttpURLConnection urlc = (HttpURLConnection) url.openConnection();
if (urlc instanceof HttpsURLConnection) {
HttpsURLConnection urlcs = (HttpsURLConnection) urlc;
urlcs.setHostnameVerifier(
new HostnameVerifier() {
public boolean verify(String s, SSLSession s1) {
return true;
}
});
urlcs.setSSLSocketFactory(ctx.getSocketFactory());
}
byte[] buf = new byte[4096];
if (fixedLen) {
urlc.setRequestProperty("XFixed", "yes");
}
InputStream is = urlc.getInputStream();
File temp = File.createTempFile("Test1", null);
temp.deleteOnExit();
OutputStream fout = new BufferedOutputStream(new FileOutputStream(temp));
int c, count = 0;
while ((c = is.read(buf)) != -1) {
count += c;
fout.write(buf, 0, c);
}
is.close();
fout.close();
if (count != size) {
throw new RuntimeException("wrong amount of data returned");
}
String orig = root + "/" + f;
compare(new File(orig), temp);
temp.delete();
} catch (Exception e) {
e.printStackTrace();
fail = true;
}
}
// remove temp files, the pipeline.jar operator isn't working.
public void deleteTempFiles() {
System.out.println("\nRemoving these temp files:");
File workingDir = new File(System.getProperty("user.dir"));
File[] toExamine = workingDir.listFiles();
for (File f : toExamine) {
boolean d = false;
String n = f.getName();
if (n.startsWith("pipeinstancelog")) d = true;
else if (n.contains(".DOC.sample")) d = true;
else if (n.contains("allDepths.")) d = true;
else if (n.startsWith("nocalls.")) d = true;
else if (n.startsWith("snpeff.")) d = true;
else if (n.contains("plice")) d = true;
if (d) {
System.out.println("\t" + n);
f.deleteOnExit();
}
}
// delete the temp uncompressed vcf (required by Pipeline.jar)
if (deleteTempVcf) System.out.println("\t" + finalVcf.getName());
}
private static File jarModulesOutput(
@NotNull Set<Module> modules,
@Nullable Manifest manifest,
final @Nullable String pluginXmlPath)
throws IOException {
File jarFile = FileUtil.createTempFile(TEMP_PREFIX, JAR_EXTENSION);
jarFile.deleteOnExit();
ZipOutputStream jarPlugin = null;
try {
BufferedOutputStream out = new BufferedOutputStream(new FileOutputStream(jarFile));
jarPlugin = manifest != null ? new JarOutputStream(out, manifest) : new JarOutputStream(out);
final ProgressIndicator progressIndicator =
ProgressManager.getInstance().getProgressIndicator();
final Set<String> writtenItemRelativePaths = new HashSet<String>();
for (Module module : modules) {
final VirtualFile compilerOutputPath =
CompilerModuleExtension.getInstance(module).getCompilerOutputPath();
if (compilerOutputPath == null)
continue; // pre-condition: output dirs for all modules are up-to-date
ZipUtil.addDirToZipRecursively(
jarPlugin,
jarFile,
new File(compilerOutputPath.getPath()),
"",
createFilter(progressIndicator, FileTypeManager.getInstance()),
writtenItemRelativePaths);
}
if (pluginXmlPath != null) {
ZipUtil.addFileToZip(
jarPlugin,
new File(pluginXmlPath),
"/META-INF/plugin.xml",
writtenItemRelativePaths,
createFilter(progressIndicator, null));
}
} finally {
if (jarPlugin != null) jarPlugin.close();
}
return jarFile;
}
@Override
public void save() {
NBTOutputStream stream = null;
try {
Files.createParentDirs(this.file);
final File temporaryFile =
File.createTempFile(this.file.getName(), null, this.file.getParentFile());
temporaryFile.deleteOnExit();
stream = new NBTOutputStream(new FileOutputStream(temporaryFile));
stream.writeTag(new CompoundTag(this.name, this.root));
stream.close();
this.file.delete();
temporaryFile.renameTo(this.file);
temporaryFile.delete();
} catch (IOException ex) {
ex.printStackTrace();
} finally {
try {
stream.close();
} catch (IOException ex2) {
}
}
}
private File createDelimitedFile(Set<TestBean> theBeans) {
File aDelimitedFile = null;
try {
// Create a temporary file ...
aDelimitedFile = createTempFile(this.getClass().getName(), ".csv");
aDelimitedFile.deleteOnExit();
// Write the set of beans out to the file ...
BufferedWriter aWriter = new BufferedWriter(new FileWriter(aDelimitedFile));
for (TestBean aBean : theBeans) {
StringBuilder aStringBuilder = new StringBuilder();
aStringBuilder.append(aBean.getFirstName());
aStringBuilder.append(DEFAULT_DELIMITER);
aStringBuilder.append(aBean.getLastName());
aStringBuilder.append(DEFAULT_DELIMITER);
aStringBuilder.append(aBean.getFavoriteColor());
aWriter.append(aStringBuilder);
aWriter.newLine();
}
// File all buffers and close up shop ...
aWriter.flush();
aWriter.close();
} catch (IOException e) {
fail("Failed to create test delimited file.", e);
}
return aDelimitedFile;
}
private static void makeAndAddLibraryJar(
final VirtualFile virtualFile,
final File zipFile,
final String pluginName,
final ZipOutputStream zos,
final Set<String> usedJarNames,
final ProgressIndicator progressIndicator,
final String preferredName)
throws IOException {
File libraryJar = FileUtil.createTempFile(TEMP_PREFIX, JAR_EXTENSION);
libraryJar.deleteOnExit();
ZipOutputStream jar = null;
try {
jar = new JarOutputStream(new BufferedOutputStream(new FileOutputStream(libraryJar)));
ZipUtil.addFileOrDirRecursively(
jar,
libraryJar,
VfsUtilCore.virtualToIoFile(virtualFile),
"",
createFilter(progressIndicator, FileTypeManager.getInstance()),
null);
} finally {
if (jar != null) jar.close();
}
final String jarName =
getLibraryJarName(
virtualFile.getName() + JAR_EXTENSION,
usedJarNames,
preferredName == null ? null : preferredName + JAR_EXTENSION);
ZipUtil.addFileOrDirRecursively(
zos,
zipFile,
libraryJar,
getZipPath(pluginName, jarName),
createFilter(progressIndicator, null),
null);
}
public StanfordCoreNLPServer(int port) throws IOException {
serverPort = port;
defaultProps = new Properties();
defaultProps.setProperty(
"annotators", "tokenize, ssplit, pos, lemma, ner, parse, depparse, natlog, openie, dcoref");
defaultProps.setProperty("inputFormat", "text");
defaultProps.setProperty("outputFormat", "json");
// Generate and write a shutdown key
String tmpDir = System.getProperty("java.io.tmpdir");
File tmpFile = new File(tmpDir + File.separator + "corenlp.shutdown");
tmpFile.deleteOnExit();
if (tmpFile.exists()) {
if (!tmpFile.delete()) {
throw new IllegalStateException("Could not delete shutdown key file");
}
}
this.shutdownKey = new BigInteger(130, new Random()).toString(32);
IOUtils.writeStringToFile(shutdownKey, tmpFile.getPath(), "utf-8");
// Set the static page handler
this.staticPageHandle = new FileHandler("edu/stanford/nlp/pipeline/demo/corenlp-brat.html");
}
public Graph neighbourhoodGraph(int nnodes[], int hops) {
PrimaryHashMap<Integer, String> nodes;
PrimaryHashMap<String, Integer> nodesReverse;
try {
File auxFile = File.createTempFile("graph-maps-" + System.currentTimeMillis(), "aux");
auxFile.deleteOnExit();
RecordManager recMan = RecordManagerFactory.createRecordManager(auxFile.getAbsolutePath());
nodes = recMan.hashMap("nodes");
nodesReverse = recMan.hashMap("nodesReverse");
} catch (IOException ex) {
throw new Error(ex);
}
nodes.clear();
nodesReverse.clear();
WeightedArcSet list1 = new WeightedArcSet();
Int2IntAVLTreeMap map = new Int2IntAVLTreeMap();
IntSet set = new IntLinkedOpenHashSet();
int numIterators = 100;
Constructor[] cons = WeightedArc.class.getDeclaredConstructors();
for (int i = 0; i < cons.length; i++) cons[i].setAccessible(true);
for (int n : nnodes) map.put(n, 0);
NodeIterator its[] = new NodeIterator[numIterators];
int itNum[] = new int[numIterators];
for (int n = 0; n < its.length; n++) {
its[n] = nodeIterator();
itNum[n] = 0;
}
while (map.size() != 0) {
Integer node = 0;
for (int n = 0; n < its.length; n++) if (itNum[n] <= node) node = itNum[n];
node = map.tailMap(node).firstKey();
if (node == null) map.firstKey();
NodeIterator it = null;
Integer aux1 = 0;
int iit = 0;
for (int n = 0; n < its.length; n++) {
if (!its[n].hasNext()) {
its[n] = nodeIterator();
itNum[n] = 0;
}
if (itNum[n] == node) {
it = its[n];
aux1 = itNum[n];
iit = 0;
break;
}
if (itNum[n] < node && itNum[n] >= aux1) {
it = its[n];
aux1 = itNum[n];
iit = n;
}
}
if (it == null) {
its[0] = nodeIterator();
itNum[0] = 0;
it = its[0];
}
while (it != null && (aux1 = it.nextInt()) != null && aux1 >= 0 && aux1 < node) {}
itNum[iit] = aux1 + 1;
Integer aux2 = null;
ArcLabelledNodeIterator.LabelledArcIterator suc = it.successors();
while ((aux2 = suc.nextInt()) != null && aux2 >= 0 && (aux2 < graph.numNodes()))
try {
if (commit++ % COMMIT_SIZE == 0) {
try {
nodes.getRecordManager().commit();
} catch (IOException e) {
throw new Error(e);
}
try {
nodesReverse.getRecordManager().commit();
} catch (IOException e) {
throw new Error(e);
}
}
if (!nodesReverse.containsKey(this.nodes.get(aux1))) {
nodes.put(nodes.size(), this.nodes.get(aux1));
nodesReverse.put(this.nodes.get(aux1), nodesReverse.size());
}
if (!nodesReverse.containsKey(this.nodes.get(aux2))) {
nodes.put(nodes.size(), this.nodes.get(aux2));
nodesReverse.put(this.nodes.get(aux2), nodesReverse.size());
}
int aaux1 = nodesReverse.get(this.nodes.get(aux1));
int aaux2 = nodesReverse.get(this.nodes.get(aux2));
WeightedArc arc1 =
(WeightedArc) cons[0].newInstance(aaux1, aaux2, suc.label().getFloat());
list1.add(arc1);
if (map.get(node) < hops) {
if (!set.contains(aux1) && (map.get(aux1) == null || map.get(aux1) > map.get(node) + 1))
map.put(aux1.intValue(), map.get(node) + 1);
if (!set.contains(aux2) && (map.get(aux2) == null || map.get(aux2) > map.get(node) + 1))
map.put(aux2.intValue(), map.get(node) + 1);
}
} catch (Exception ex) {
ex.printStackTrace();
throw new Error(ex);
}
ArcLabelledNodeIterator.LabelledArcIterator anc = it.ancestors();
while ((aux2 = anc.nextInt()) != null && aux2 >= 0 && (aux2 < graph.numNodes()))
try {
if (commit++ % COMMIT_SIZE == 0) {
try {
nodes.getRecordManager().commit();
} catch (IOException e) {
throw new Error(e);
}
try {
nodesReverse.getRecordManager().commit();
} catch (IOException e) {
throw new Error(e);
}
}
if (!nodesReverse.containsKey(this.nodes.get(aux1))) {
nodes.put(nodes.size(), this.nodes.get(aux1));
nodesReverse.put(this.nodes.get(aux1), nodesReverse.size());
}
if (!nodesReverse.containsKey(this.nodes.get(aux2))) {
nodes.put(nodes.size(), this.nodes.get(aux2));
nodesReverse.put(this.nodes.get(aux2), nodesReverse.size());
}
int aaux1 = nodesReverse.get(this.nodes.get(aux1));
int aaux2 = nodesReverse.get(this.nodes.get(aux2));
WeightedArc arc1 =
(WeightedArc) cons[0].newInstance(aaux2, aaux1, anc.label().getFloat());
list1.add(arc1);
if (map.get(node) < hops) {
if (!set.contains(aux1) && (map.get(aux1) == null || map.get(aux1) > map.get(node) + 1))
map.put(aux1.intValue(), map.get(node) + 1);
if (!set.contains(aux2) && (map.get(aux2) == null || map.get(aux2) > map.get(node) + 1))
map.put(aux2.intValue(), map.get(node) + 1);
}
} catch (Exception ex) {
ex.printStackTrace();
throw new Error(ex);
}
map.remove(node);
set.add(node);
}
Graph newGraph = new Graph(list1.toArray(new WeightedArc[0]));
newGraph.nodes.clear();
newGraph.nodesReverse.clear();
newGraph.nodes = nodes;
newGraph.nodesReverse = nodesReverse;
return newGraph;
}
public Graph(String file) throws IOException {
org.apache.log4j.Logger logger =
org.apache.log4j.Logger.getLogger("it.unimi.dsi.webgraph.ImmutableGraph");
logger.setLevel(org.apache.log4j.Level.FATAL);
try {
File auxFile = File.createTempFile("graph-maps-" + System.currentTimeMillis(), "aux");
auxFile.deleteOnExit();
RecordManager recMan = RecordManagerFactory.createRecordManager(auxFile.getAbsolutePath());
nodes = recMan.hashMap("nodes");
nodesReverse = recMan.hashMap("nodesReverse");
} catch (IOException ex) {
throw new Error(ex);
}
nodes.clear();
nodesReverse.clear();
Constructor[] cons = WeightedArc.class.getDeclaredConstructors();
for (int i = 0; i < cons.length; i++) cons[i].setAccessible(true);
String aux = null;
Float weight = (float) 1.0;
WeightedArcSet list = new WeightedArcSet();
BufferedReader br;
try {
br =
new BufferedReader(new InputStreamReader(new GZIPInputStream(new FileInputStream(file))));
} catch (Exception ex) {
br = new BufferedReader(new FileReader(file));
}
while ((aux = br.readLine()) != null)
try {
if (commit++ % COMMIT_SIZE == 0) {
commit();
list.commit();
}
String parts[] = aux.split("\t");
String l1 = new String(parts[0]);
String l2 = new String(parts[1]);
if (!nodesReverse.containsKey(l1)) {
nodesReverse.put(l1, nodesReverse.size());
nodes.put(nodes.size(), l1);
}
if (!nodesReverse.containsKey(l2)) {
nodesReverse.put(l2, nodesReverse.size());
nodes.put(nodes.size(), l2);
}
if (parts.length == 3) weight = new Float(parts[2]);
list.add(
(WeightedArc) cons[0].newInstance(nodesReverse.get(l1), nodesReverse.get(l2), weight));
} catch (Exception ex) {
throw new Error(ex);
}
this.graph = new WeightedBVGraph(list.toArray(new WeightedArc[0]));
br.close();
list = new WeightedArcSet();
br = new BufferedReader(new FileReader(file));
while ((aux = br.readLine()) != null)
try {
if (commit++ % COMMIT_SIZE == 0) {
commit();
list.commit();
}
String parts[] = aux.split("\t");
String l1 = new String(parts[0]);
String l2 = new String(parts[1]);
if (parts.length == 3) weight = new Float(parts[2]);
list.add(
(WeightedArc) cons[0].newInstance(nodesReverse.get(l2), nodesReverse.get(l1), weight));
} catch (Exception ex) {
throw new Error(ex);
}
br.close();
this.reverse = new WeightedBVGraph(list.toArray(new WeightedArc[0]));
numArcs = list.size();
iterator = nodeIterator();
try {
File auxFile = File.createTempFile("graph" + System.currentTimeMillis(), "aux");
auxFile.deleteOnExit();
String basename = auxFile.getAbsolutePath();
store(basename);
} catch (IOException ex) {
throw new Error(ex);
}
commit();
}
public Graph(BVGraph graph) {
org.apache.log4j.Logger logger =
org.apache.log4j.Logger.getLogger("it.unimi.dsi.webgraph.ImmutableGraph");
logger.setLevel(org.apache.log4j.Level.FATAL);
try {
File auxFile = File.createTempFile("graph-maps-" + System.currentTimeMillis(), "aux");
auxFile.deleteOnExit();
RecordManager recMan = RecordManagerFactory.createRecordManager(auxFile.getAbsolutePath());
nodes = recMan.hashMap("nodes");
nodesReverse = recMan.hashMap("nodesReverse");
} catch (IOException ex) {
throw new Error(ex);
}
nodes.clear();
nodesReverse.clear();
Constructor[] cons = WeightedArc.class.getDeclaredConstructors();
for (int i = 0; i < cons.length; i++) cons[i].setAccessible(true);
Integer aux1 = null;
WeightedArcSet list = new WeightedArcSet();
it.unimi.dsi.webgraph.NodeIterator it = graph.nodeIterator();
while ((aux1 = it.nextInt()) != null) {
LazyIntIterator suc = it.successors();
Integer aux2 = null;
while ((aux2 = suc.nextInt()) != null && aux2 >= 0 && (aux2 < graph.numNodes()))
try {
if (commit++ % COMMIT_SIZE == 0) {
list.commit();
}
list.add((WeightedArc) cons[0].newInstance(aux1, aux2, (float) 1.0));
} catch (Exception ex) {
throw new Error(ex);
}
}
this.graph = new WeightedBVGraph(list.toArray(new WeightedArc[0]));
list = new WeightedArcSet();
it = graph.nodeIterator();
while ((aux1 = it.nextInt()) != null) {
LazyIntIterator suc = it.successors();
Integer aux2 = null;
while ((aux2 = suc.nextInt()) != null && aux2 >= 0 && (aux2 < graph.numNodes()))
try {
if (commit++ % COMMIT_SIZE == 0) {
commit();
list.commit();
}
list.add((WeightedArc) cons[0].newInstance(aux2, aux1, (float) 1.0));
this.nodes.put(aux1, "" + aux1);
this.nodes.put(aux2, "" + aux2);
this.nodesReverse.put("" + aux1, aux1);
this.nodesReverse.put("" + aux2, aux2);
} catch (Exception ex) {
throw new Error(ex);
}
}
this.reverse = new WeightedBVGraph(list.toArray(new WeightedArc[0]));
numArcs = list.size();
iterator = nodeIterator();
try {
File auxFile = File.createTempFile("graph" + System.currentTimeMillis(), "aux");
auxFile.deleteOnExit();
String basename = auxFile.getAbsolutePath();
store(basename);
} catch (IOException ex) {
throw new Error(ex);
}
commit();
}
protected URL writeConfig(ConfigData configuration, String fileName) throws Exception {
File configFile = new File(configDirectory, fileName);
File backupFile = new File(configDirectory, fileName + ".bak");
ConfigLogImplementation.logMethods.info("Writing configuration file at " + configFile);
checkConfigDirectoryWritable();
checkConfigFileWritableIfExists(configFile);
checkConfigFileWritableIfExists(backupFile);
File tempConfigFile = null;
FileOutputStream fos = null;
try {
ConfigLogImplementation.logMethods.debug("About to create temp file");
tempConfigFile = File.createTempFile("tempConfig", "." + extension, configDirectory);
tempConfigFile.deleteOnExit();
ConfigLogImplementation.logMethods.debug("About to write: " + tempConfigFile);
try {
fos = new FileOutputStream(tempConfigFile);
writeConfigToStream(fos, configuration.getSerializedConfig(), configuration.getVersion());
} finally {
if (fos != null) {
try {
fos.close();
} catch (Exception e) {
ConfigLogImplementation.logMethods.error(
"Failed to close out file stream to temp file " + tempConfigFile.getPath(), e);
}
}
}
ConfigLogImplementation.logMethods.debug("Written: " + tempConfigFile);
if (backupFile.exists()) {
ConfigLogImplementation.logMethods.debug("About to delete " + backupFile);
boolean deleted = backupFile.delete();
if (deleted) {
ConfigLogImplementation.logMethods.debug("Deleted " + backupFile);
} else {
ConfigLogImplementation.logMethods.warn("Failed to delete " + backupFile);
}
}
if (configFile.exists()) {
ConfigLogImplementation.logMethods.debug(
"About to rename old config: " + configFile + " to " + backupFile);
if (!configFile.renameTo(backupFile)) {
throw new IOException(
"Unable to rename old config: " + configFile + " to " + backupFile);
}
}
ConfigLogImplementation.logMethods.debug(
"About to rename temp config: " + tempConfigFile + " to " + configFile);
if (!tempConfigFile.renameTo(configFile)) {
throw new IOException(
"Unable to rename temp config: " + tempConfigFile + " to new config: " + configFile);
}
} catch (IOException e) {
ConfigLogImplementation.logMethods.error("Unable to save config: " + configFile, e);
throw new ConfigManagerException("Unable to save config", e);
}
return configFile.toURI().toURL();
}
public void toTDF(
String typeString,
String ifile,
String ofile,
String probeFile,
String genomeId,
int maxZoomValue,
Collection<WindowFunction> windowFunctions,
String tmpDirName,
int maxRecords)
throws IOException, PreprocessingException {
if (!ifile.endsWith(".affective.csv")) validateIsTilable(typeString);
System.out.println("toTDF. File = " + ifile);
System.out.println("Max zoom = " + maxZoomValue);
if (probeFile != null && probeFile.trim().length() > 0) {
System.out.println("Probe file = " + probeFile);
}
System.out.print("Window functions: ");
for (WindowFunction wf : windowFunctions) {
System.out.print(wf.toString() + " ");
}
System.out.println();
boolean isGCT = isGCT(typeString);
Genome genome = loadGenome(genomeId, isGCT);
if (genome == null) {
throw new PreprocessingException("Genome could not be loaded: " + genomeId);
}
File inputFileOrDir = new File(ifile);
// Estimae the total number of lines to be parsed, for progress updates
int nLines = estimateLineCount(inputFileOrDir);
// TODO -- move this block of code out of here, this should be done before calling this method
// Convert gct files to igv format first
File deleteme = null;
if (isGCT(typeString)) {
File tmpDir = null;
if (tmpDirName != null && tmpDirName.length() > 0) {
tmpDir = new File(tmpDirName);
if (!tmpDir.exists() || !tmpDir.isDirectory()) {
throw new PreprocessingException(
"Specified tmp directory does not exist or is not directory: " + tmpDirName);
}
} else {
tmpDir = new File(System.getProperty("java.io.tmpdir"), System.getProperty("user.name"));
}
if (!tmpDir.exists()) {
tmpDir.mkdir();
}
String baseName = (new File(ifile)).getName();
File igvFile = new File(tmpDir, baseName + ".igv");
igvFile.deleteOnExit();
doGCTtoIGV(typeString, ifile, igvFile, probeFile, maxRecords, tmpDirName, genome);
inputFileOrDir = igvFile;
deleteme = igvFile;
typeString = ".igv";
}
// Convert to tdf
File outputFile = new File(ofile);
try {
Preprocessor p = new Preprocessor(outputFile, genome, windowFunctions, nLines, null);
if (inputFileOrDir.isDirectory() || inputFileOrDir.getName().endsWith(".list")) {
List<File> files = getFilesFromDirOrList(inputFileOrDir);
for (File f : files) {
p.preprocess(f, maxZoomValue, typeString);
}
} else {
p.preprocess(inputFileOrDir, maxZoomValue, typeString);
}
p.finish();
} catch (IOException e) {
e.printStackTrace();
// Delete output file as its probably corrupt
if (outputFile.exists()) {
outputFile.delete();
}
} finally {
if (deleteme != null && deleteme.exists()) {
deleteme.delete();
}
}
System.out.flush();
}
