label int64 0 1 | func1 stringlengths 173 53.1k | func2 stringlengths 173 53.1k | id int64 0 901k |
|---|---|---|---|
1 | private void prepareQueryResultData(ZipEntryRef zer, String nodeDir, String reportDir, Set<ZipEntryRef> statusZers) throws Exception { String jobDir = nodeDir + File.separator + "job_" + zer.getUri(); if (!WorkDirectory.isWorkingDirectoryValid(jobDir)) { throw new Exception("Cannot acces to " + jobDir); } File f = new File(jobDir + File.separator + "result.xml"); if (!f.exists() || !f.isFile() || !f.canRead()) { throw new Exception("Cannot acces to result file " + f.getAbsolutePath()); } String fcopyName = reportDir + File.separator + zer.getName() + ".xml"; BufferedInputStream bis = new BufferedInputStream(new FileInputStream(f)); BufferedOutputStream bos = new BufferedOutputStream(new FileOutputStream(fcopyName)); IOUtils.copy(bis, bos); bis.close(); bos.close(); zer.setUri(fcopyName); f = new File(jobDir + File.separator + "status.xml"); if (!f.exists() || !f.isFile() || !f.canRead()) { throw new Exception("Cannot acces to status file " + f.getAbsolutePath()); } fcopyName = reportDir + File.separator + zer.getName() + "_status.xml"; bis = new BufferedInputStream(new FileInputStream(f)); bos = new BufferedOutputStream(new FileOutputStream(fcopyName)); IOUtils.copy(bis, bos); bis.close(); bos.close(); statusZers.add(new ZipEntryRef(ZipEntryRef.SINGLE_FILE, zer.getName(), fcopyName, ZipEntryRef.WITH_REL)); } | @Override public void fileUpload(UploadEvent uploadEvent) { FileOutputStream tmpOutStream = null; try { tmpUpload = File.createTempFile("projectImport", ".xml"); tmpOutStream = new FileOutputStream(tmpUpload); IOUtils.copy(uploadEvent.getInputStream(), tmpOutStream); panel.setGeneralMessage("Project file " + uploadEvent.getFileName() + " uploaded and ready for import."); } catch (Exception e) { panel.setGeneralMessage("Could not upload file: " + e); } finally { if (tmpOutStream != null) { IOUtils.closeQuietly(tmpOutStream); } } } | 15,000 |
1 | public static synchronized String toMD5(String str) { Nulls.failIfNull(str, "Cannot create an MD5 encryption form a NULL string"); String hashword = null; try { MessageDigest md5 = MessageDigest.getInstance(MD5); md5.update(str.getBytes()); BigInteger hash = new BigInteger(1, md5.digest()); hashword = hash.toString(16); return Strings.padLeft(hashword, 32, "0"); } catch (NoSuchAlgorithmException ex) { ex.printStackTrace(); } return hashword; } | public static String generate(String source) { byte[] SHA = new byte[20]; try { MessageDigest digest = MessageDigest.getInstance("SHA-1"); digest.update(source.getBytes()); SHA = digest.digest(); } catch (NoSuchAlgorithmException e) { System.out.println("NO SUCH ALGORITHM EXCEPTION: " + e.getMessage()); } CommunicationLogger.warning("SHA1 DIGEST: " + SHA); return SHA.toString(); } | 15,001 |
0 | public static InputStream getResourceRelativeAsStream(final String name, final Class context) { final URL url = getResourceRelative(name, context); if (url == null) { return null; } try { return url.openStream(); } catch (IOException e) { return null; } } | @Override public InputStream getInputStream() throws IOException { if (dfos == null) { int deferredOutputStreamThreshold = Config.getInstance().getDeferredOutputStreamThreshold(); dfos = new DeferredFileOutputStream(deferredOutputStreamThreshold, Definitions.PROJECT_NAME, "." + Definitions.TMP_EXTENSION); try { IOUtils.copy(is, dfos); } finally { dfos.close(); } } return dfos.getDeferredInputStream(); } | 15,002 |
0 | public void create_list() { try { String data = URLEncoder.encode("PHPSESSID", "UTF-8") + "=" + URLEncoder.encode(this.get_session(), "UTF-8"); URL url = new URL(URL_LOLA + FILE_CREATE_LIST); URLConnection conn = url.openConnection(); conn.setDoOutput(true); OutputStreamWriter wr = new OutputStreamWriter(conn.getOutputStream()); wr.write(data); wr.flush(); BufferedReader rd = new BufferedReader(new InputStreamReader(conn.getInputStream())); String line; line = rd.readLine(); wr.close(); rd.close(); System.out.println("Gene list saved in LOLA"); } catch (Exception e) { System.out.println("error in createList()"); e.printStackTrace(); } } | void loadPlaylist() { if (running_as_applet) { String s = null; for (int i = 0; i < 10; i++) { s = getParameter("jorbis.player.play." + i); if (s == null) break; playlist.addElement(s); } } if (playlistfile == null) { return; } try { InputStream is = null; try { URL url = null; if (running_as_applet) url = new URL(getCodeBase(), playlistfile); else url = new URL(playlistfile); URLConnection urlc = url.openConnection(); is = urlc.getInputStream(); } catch (Exception ee) { } if (is == null && !running_as_applet) { try { is = new FileInputStream(System.getProperty("user.dir") + System.getProperty("file.separator") + playlistfile); } catch (Exception ee) { } } if (is == null) return; while (true) { String line = readline(is); if (line == null) break; byte[] foo = line.getBytes(); for (int i = 0; i < foo.length; i++) { if (foo[i] == 0x0d) { line = new String(foo, 0, i); break; } } playlist.addElement(line); } } catch (Exception e) { System.out.println(e); } } | 15,003 |
1 | static void copy(String src, String dest) throws IOException { File ifp = new File(src); File ofp = new File(dest); if (ifp.exists() == false) { throw new IOException("file '" + src + "' does not exist"); } FileInputStream fis = new FileInputStream(ifp); FileOutputStream fos = new FileOutputStream(ofp); byte[] b = new byte[1024]; while (fis.read(b) > 0) fos.write(b); fis.close(); fos.close(); } | private DataFileType[] getDataFiles(Collection<ContentToSend> contentsToSend) { DataFileType[] files = new DataFileType[contentsToSend.size()]; int fileIndex = 0; for (ContentToSend contentToSend : contentsToSend) { DataFileType dataFile = DataFileType.Factory.newInstance(); dataFile.setFilename(contentToSend.getFileName()); dataFile.setId("D" + fileIndex); dataFile.setMimeType(contentToSend.getMimeType()); dataFile.setContentType(DataFileType.ContentType.EMBEDDED_BASE_64); final StringWriter stringWriter = new StringWriter(); final OutputStream encodeStream = Base64.newEncoder(stringWriter, 0, null); final InputStream is = contentToSend.getInputStream(); try { long sizeCopied = IOUtils.copyLarge(is, encodeStream); dataFile.setSize(BigDecimal.valueOf(sizeCopied)); } catch (IOException e) { throw new RuntimeException("Failed to get input to the file to be sent", e); } finally { IOUtils.closeQuietly(encodeStream); IOUtils.closeQuietly(is); } dataFile.setStringValue(stringWriter.toString()); files[fileIndex++] = dataFile; } return files; } | 15,004 |
1 | public static boolean copy(File source, File dest) { FileChannel in = null, out = null; try { in = new FileInputStream(source).getChannel(); out = new FileOutputStream(dest).getChannel(); long size = in.size(); MappedByteBuffer buf = in.map(FileChannel.MapMode.READ_ONLY, 0, size); out.write(buf); if (in != null) in.close(); if (out != null) out.close(); } catch (IOException e) { e.printStackTrace(); return false; } return true; } | public static void main(final String[] args) { final Runnable startDerby = new Runnable() { public void run() { try { final NetworkServerControl control = new NetworkServerControl(InetAddress.getByName("localhost"), 1527); control.start(new PrintWriter(System.out)); } catch (final Exception ex) { throw new RuntimeException(ex); } } }; new Thread(startDerby).start(); final Runnable startActiveMq = new Runnable() { public void run() { Main.main(new String[] { "start", "xbean:file:active-mq-config.xml" }); } }; new Thread(startActiveMq).start(); final Runnable startMailServer = new Runnable() { public void run() { final SimpleMessageListener listener = new SimpleMessageListener() { public final boolean accept(final String from, final String recipient) { return true; } public final void deliver(final String from, final String recipient, final InputStream data) throws TooMuchDataException, IOException { System.out.println("FROM: " + from); System.out.println("TO: " + recipient); final File tmpDir = new File(System.getProperty("java.io.tmpdir")); final File file = new File(tmpDir, recipient); final FileWriter fw = new FileWriter(file); try { IOUtils.copy(data, fw); } finally { fw.close(); } } }; final SMTPServer smtpServer = new SMTPServer(new SimpleMessageListenerAdapter(listener)); smtpServer.start(); System.out.println("Started SMTP Server"); } }; new Thread(startMailServer).start(); } | 15,005 |
0 | public void parse(Project project, Object source, RootHandler handler) { AntXMLContext context = (AntXMLContext) Reflect.getField(handler, "context"); File buildFile = null; URL url = null; String buildFileName = null; if (source instanceof File) { buildFile = (File) source; buildFile = fu.normalize(buildFile.getAbsolutePath()); context.setBuildFile(buildFile); buildFileName = buildFile.toString(); } else if (source instanceof URL) { url = (URL) source; buildFileName = url.toString(); } else { throw new BuildException("Source " + source.getClass().getName() + " not supported by this plugin"); } InputStream inputStream = null; InputSource inputSource = null; try { XMLReader parser = JAXPUtils.getNamespaceXMLReader(); String uri = null; if (buildFile != null) { uri = fu.toURI(buildFile.getAbsolutePath()); inputStream = new FileInputStream(buildFile); } else { inputStream = url.openStream(); uri = url.toString(); } inputSource = new InputSource(inputStream); if (uri != null) { inputSource.setSystemId(uri); } project.log("parsing buildfile " + buildFileName + " with URI = " + uri, Project.MSG_VERBOSE); DefaultHandler hb = handler; parser.setContentHandler(hb); parser.setEntityResolver(hb); parser.setErrorHandler(hb); parser.setDTDHandler(hb); parser.parse(inputSource); } catch (SAXParseException exc) { Location location = new Location(exc.getSystemId(), exc.getLineNumber(), exc.getColumnNumber()); Throwable t = exc.getException(); if (t instanceof BuildException) { BuildException be = (BuildException) t; if (be.getLocation() == Location.UNKNOWN_LOCATION) { be.setLocation(location); } throw be; } throw new BuildException(exc.getMessage(), t, location); } catch (SAXException exc) { Throwable t = exc.getException(); if (t instanceof BuildException) { throw (BuildException) t; } throw new BuildException(exc.getMessage(), t); } catch (FileNotFoundException exc) { throw new BuildException(exc); } catch (UnsupportedEncodingException exc) { throw new BuildException("Encoding of project file " + buildFileName + " is invalid.", exc); } catch (IOException exc) { throw new BuildException("Error reading project file " + buildFileName + ": " + exc.getMessage(), exc); } finally { if (inputStream != null) { try { inputStream.close(); } catch (IOException ioe) { } } } } | public void convert(File src, File dest) throws IOException { InputStream in = new BufferedInputStream(new FileInputStream(src)); DcmParser p = pfact.newDcmParser(in); Dataset ds = fact.newDataset(); p.setDcmHandler(ds.getDcmHandler()); try { FileFormat format = p.detectFileFormat(); if (format != FileFormat.ACRNEMA_STREAM) { System.out.println("\n" + src + ": not an ACRNEMA stream!"); return; } p.parseDcmFile(format, Tags.PixelData); if (ds.contains(Tags.StudyInstanceUID) || ds.contains(Tags.SeriesInstanceUID) || ds.contains(Tags.SOPInstanceUID) || ds.contains(Tags.SOPClassUID)) { System.out.println("\n" + src + ": contains UIDs!" + " => probable already DICOM - do not convert"); return; } boolean hasPixelData = p.getReadTag() == Tags.PixelData; boolean inflate = hasPixelData && ds.getInt(Tags.BitsAllocated, 0) == 12; int pxlen = p.getReadLength(); if (hasPixelData) { if (inflate) { ds.putUS(Tags.BitsAllocated, 16); pxlen = pxlen * 4 / 3; } if (pxlen != (ds.getInt(Tags.BitsAllocated, 0) >>> 3) * ds.getInt(Tags.Rows, 0) * ds.getInt(Tags.Columns, 0) * ds.getInt(Tags.NumberOfFrames, 1) * ds.getInt(Tags.NumberOfSamples, 1)) { System.out.println("\n" + src + ": mismatch pixel data length!" + " => do not convert"); return; } } ds.putUI(Tags.StudyInstanceUID, uid(studyUID)); ds.putUI(Tags.SeriesInstanceUID, uid(seriesUID)); ds.putUI(Tags.SOPInstanceUID, uid(instUID)); ds.putUI(Tags.SOPClassUID, classUID); if (!ds.contains(Tags.NumberOfSamples)) { ds.putUS(Tags.NumberOfSamples, 1); } if (!ds.contains(Tags.PhotometricInterpretation)) { ds.putCS(Tags.PhotometricInterpretation, "MONOCHROME2"); } if (fmi) { ds.setFileMetaInfo(fact.newFileMetaInfo(ds, UIDs.ImplicitVRLittleEndian)); } OutputStream out = new BufferedOutputStream(new FileOutputStream(dest)); try { } finally { ds.writeFile(out, encodeParam()); if (hasPixelData) { if (!skipGroupLen) { out.write(PXDATA_GROUPLEN); int grlen = pxlen + 8; out.write((byte) grlen); out.write((byte) (grlen >> 8)); out.write((byte) (grlen >> 16)); out.write((byte) (grlen >> 24)); } out.write(PXDATA_TAG); out.write((byte) pxlen); out.write((byte) (pxlen >> 8)); out.write((byte) (pxlen >> 16)); out.write((byte) (pxlen >> 24)); } if (inflate) { int b2, b3; for (; pxlen > 0; pxlen -= 3) { out.write(in.read()); b2 = in.read(); b3 = in.read(); out.write(b2 & 0x0f); out.write(b2 >> 4 | ((b3 & 0x0f) << 4)); out.write(b3 >> 4); } } else { for (; pxlen > 0; --pxlen) { out.write(in.read()); } } out.close(); } System.out.print('.'); } finally { in.close(); } } | 15,006 |
0 | private void getRandomGUID(boolean secure) { MessageDigest md5 = null; StringBuffer sbValueBeforeMD5 = new StringBuffer(); try { md5 = MessageDigest.getInstance("MD5"); } catch (NoSuchAlgorithmException e) { System.out.println("Error: " + e); } try { long time = System.currentTimeMillis(); long rand = 0; if (secure) { rand = mySecureRand.nextLong(); } else { rand = myRand.nextLong(); } sbValueBeforeMD5.append(s_id); sbValueBeforeMD5.append(":"); sbValueBeforeMD5.append(Long.toString(time)); sbValueBeforeMD5.append(":"); sbValueBeforeMD5.append(Long.toString(rand)); valueBeforeMD5 = sbValueBeforeMD5.toString(); md5.update(valueBeforeMD5.getBytes()); byte[] array = md5.digest(); StringBuffer sb = new StringBuffer(); for (int j = 0; j < array.length; ++j) { int b = array[j] & 0xFF; if (b < 0x10) sb.append('0'); sb.append(Integer.toHexString(b)); } valueAfterMD5 = sb.toString(); } catch (Exception e) { System.out.println("Error:" + e); } } | public static void zip(ZipOutputStream out, File f, String base) throws Exception { if (f.isDirectory()) { File[] fl = f.listFiles(); base = base.length() == 0 ? "" : base + File.separator; for (int i = 0; i < fl.length; i++) { zip(out, fl[i], base + fl[i].getName()); } } else { out.putNextEntry(new org.apache.tools.zip.ZipEntry(base)); FileInputStream in = new FileInputStream(f); IOUtils.copyStream(in, out); in.close(); } Thread.sleep(10); } | 15,007 |
1 | public File getFile(String file) { DirProperties dp; List files = new ArrayList(); for (int i = 0; i < locs.size(); i++) { dp = (DirProperties) locs.get(i); if (dp.isReadable()) { File g = new File(dp.getLocation() + slash() + file); if (g.exists()) files.add(g); } } if (files.size() == 0) { throw new UnsupportedOperationException("at least one DirProperty should get 'read=true'"); } else if (files.size() == 1) { return (File) files.get(0); } else { File fromFile = (File) files.get(files.size() - 2); File toFile = (File) files.get(files.size() - 1); byte reading[] = new byte[2024]; try { FileInputStream stream = new FileInputStream(fromFile); FileOutputStream outStr = new FileOutputStream(toFile); while (stream.read(reading) != -1) { outStr.write(reading); } } catch (FileNotFoundException ex) { getLogger().severe("FileNotFound: while copying from " + fromFile + " to " + toFile); } catch (IOException ex) { getLogger().severe("IOException: while copying from " + fromFile + " to " + toFile); } return toFile; } } | private static String readStreamToString(InputStream is, boolean passInVelocity, String tplName, Map<String, Object> templateVarsMap) throws IOException { StringWriter sw = new StringWriter(); IOUtils.copy(is, sw, "UTF-8"); if (passInVelocity) { return tpl.formatStr(sw.toString(), templateVarsMap, tplName); } return sw.toString(); } | 15,008 |
1 | public void testAutoCommit() throws Exception { Connection con = getConnectionOverrideProperties(new Properties()); try { Statement stmt = con.createStatement(); assertEquals(0, stmt.executeUpdate("create table #testAutoCommit (i int)")); con.setAutoCommit(false); assertEquals(1, stmt.executeUpdate("insert into #testAutoCommit (i) values (0)")); con.setAutoCommit(false); con.rollback(); assertEquals(1, stmt.executeUpdate("insert into #testAutoCommit (i) values (1)")); con.setAutoCommit(true); con.setAutoCommit(false); con.rollback(); con.setAutoCommit(true); ResultSet rs = stmt.executeQuery("select i from #testAutoCommit"); assertTrue(rs.next()); assertEquals(1, rs.getInt(1)); assertFalse(rs.next()); rs.close(); stmt.close(); } finally { con.close(); } } | public void removeStadium(String name, String city) throws StadiumException { Connection conn = ConnectionManager.getManager().getConnection(); int id = findStadiumBy_N_C(name, city); if (id == -1) throw new StadiumException("No such stadium"); try { conn.setAutoCommit(false); PreparedStatement stm = conn.prepareStatement(Statements.SELECT_STAD_TRIBUNE); stm.setInt(1, id); ResultSet rs = stm.executeQuery(); TribuneLogic logic = TribuneLogic.getInstance(); while (rs.next()) { logic.removeTribune(rs.getInt("tribuneID")); } stm = conn.prepareStatement(Statements.DELETE_STADIUM); stm.setInt(1, id); stm.executeUpdate(); } catch (SQLException e) { try { conn.rollback(); conn.setAutoCommit(true); } catch (SQLException e1) { e1.printStackTrace(); } throw new StadiumException("Removing stadium failed", e); } try { conn.commit(); conn.setAutoCommit(true); } catch (SQLException e) { e.printStackTrace(); } } | 15,009 |
0 | public void registerSchema(String newSchemaName, String objectControlller, long boui, String expression, String schema) throws SQLException { Connection cndef = null; PreparedStatement pstm = null; try { cndef = this.getRepositoryConnection(p_ctx.getApplication(), "default", 2); String friendlyName = "Schema created by object [" + objectControlller + "] with boui [" + boui + "]"; pstm = cndef.prepareStatement("DELETE FROM NGTDIC WHERE TABLENAME=? and objecttype='S'"); pstm.setString(1, newSchemaName); pstm.executeUpdate(); pstm.close(); pstm = cndef.prepareStatement("INSERT INTO NGTDIC (\"SCHEMA\",OBJECTNAME,OBJECTTYPE,TABLENAME, " + "FRIENDLYNAME, EXPRESSION) VALUES (" + "?,?,?,?,?,?)"); pstm.setString(1, schema); pstm.setString(2, newSchemaName); pstm.setString(3, "S"); pstm.setString(4, newSchemaName); pstm.setString(5, friendlyName); pstm.setString(6, expression); pstm.executeUpdate(); pstm.close(); cndef.commit(); } catch (Exception e) { cndef.rollback(); e.printStackTrace(); throw new SQLException(e.getMessage()); } finally { if (pstm != null) { try { pstm.close(); } catch (Exception e) { } } } } | public static void copyFile(File in, File out) throws IOException { FileChannel inChannel = new FileInputStream(in).getChannel(); FileChannel outChannel = new FileOutputStream(out).getChannel(); try { inChannel.transferTo(0, inChannel.size(), outChannel); } catch (IOException e) { throw e; } finally { if (inChannel != null) inChannel.close(); if (outChannel != null) outChannel.close(); } } | 15,010 |
0 | @Override protected IProject createProject(String projectName, IProgressMonitor monitor) throws CoreException { monitor.beginTask(CheatSheetsPlugin.INSTANCE.getString("_UI_CreateJavaProject_message", new String[] { projectName }), 5); IProject project = super.createProject(projectName, new SubProgressMonitor(monitor, 1)); if (project != null) { IProjectDescription description = project.getDescription(); if (!description.hasNature(JavaCore.NATURE_ID)) { IJavaProject javaProject = JavaCore.create(project); if (javaProject != null) { String[] natures = description.getNatureIds(); String[] javaNatures = new String[natures.length + 1]; System.arraycopy(natures, 0, javaNatures, 0, natures.length); javaNatures[natures.length] = JavaCore.NATURE_ID; description.setNatureIds(javaNatures); project.setDescription(description, new SubProgressMonitor(monitor, 1)); IFolder sourceFolder = project.getFolder(SOURCE_FOLDER); if (!sourceFolder.exists()) { sourceFolder.create(true, true, new SubProgressMonitor(monitor, 1)); } javaProject.setOutputLocation(project.getFolder(OUTPUT_FOLDER).getFullPath(), new SubProgressMonitor(monitor, 1)); IClasspathEntry[] entries = new IClasspathEntry[] { JavaCore.newSourceEntry(sourceFolder.getFullPath()), JavaCore.newContainerEntry(new Path("org.eclipse.jdt.launching.JRE_CONTAINER")) }; javaProject.setRawClasspath(entries, new SubProgressMonitor(monitor, 1)); } } } monitor.done(); return project; } | @SuppressWarnings("finally") private void compress(File src) throws IOException { if (this.switches.contains(Switch.test)) return; checkSourceFile(src); if (src.getPath().endsWith(".bz2")) { this.log.println("WARNING: skipping file because it already has .bz2 suffix:").println(src); return; } final File dst = new File(src.getPath() + ".bz2").getAbsoluteFile(); if (!checkDestFile(dst)) return; FileChannel inChannel = null; FileChannel outChannel = null; FileOutputStream fileOut = null; BZip2OutputStream bzOut = null; FileLock inLock = null; FileLock outLock = null; try { inChannel = new FileInputStream(src).getChannel(); final long inSize = inChannel.size(); inLock = inChannel.tryLock(0, inSize, true); if (inLock == null) throw error("source file locked by another process: " + src); fileOut = new FileOutputStream(dst); outChannel = fileOut.getChannel(); bzOut = new BZip2OutputStream( new BufferedXOutputStream(fileOut, 8192), Math.min( (this.blockSize == -1) ? BZip2OutputStream.MAX_BLOCK_SIZE : this.blockSize, BZip2OutputStream.chooseBlockSize(inSize) ) ); outLock = outChannel.tryLock(); if (outLock == null) throw error("destination file locked by another process: " + dst); final boolean showProgress = this.switches.contains(Switch.showProgress); long pos = 0; int progress = 0; if (showProgress || this.verbose) { this.log.print("source: " + src).print(": size=").println(inSize); this.log.println("target: " + dst); } while (true) { final long maxStep = showProgress ? Math.max(8192, (inSize - pos) / MAX_PROGRESS) : (inSize - pos); if (maxStep <= 0) { if (showProgress) { for (int i = progress; i < MAX_PROGRESS; i++) this.log.print('#'); this.log.println(" done"); } break; } else { final long step = inChannel.transferTo(pos, maxStep, bzOut); if ((step == 0) && (inChannel.size() != inSize)) throw error("file " + src + " has been modified concurrently by another process"); pos += step; if (showProgress) { final double p = (double) pos / (double) inSize; final int newProgress = (int) (MAX_PROGRESS * p); for (int i = progress; i < newProgress; i++) this.log.print('#'); progress = newProgress; } } } inLock.release(); inChannel.close(); bzOut.closeInstance(); final long outSize = outChannel.position(); outChannel.truncate(outSize); outLock.release(); fileOut.close(); if (this.verbose) { final double ratio = (inSize == 0) ? (outSize * 100) : ((double) outSize / (double) inSize); this.log.print("raw size: ").print(inSize) .print("; compressed size: ").print(outSize) .print("; compression ratio: ").print(ratio).println('%'); } if (!this.switches.contains(Switch.keep)) { if (!src.delete()) throw error("unable to delete sourcefile: " + src); } } catch (final IOException ex) { IO.tryClose(inChannel); IO.tryClose(bzOut); IO.tryClose(fileOut); IO.tryRelease(inLock); IO.tryRelease(outLock); try { this.log.println(); } finally { throw ex; } } } | 15,011 |
0 | @Override public void run(ProcedureRunner runner) throws Exception { if (url == null) { throw BuiltinExceptionFactory.createAttributeMissing(this, "url"); } if (inputPath == null) { throw BuiltinExceptionFactory.createAttributeMissing(this, "inputPath"); } CompositeMap context = runner.getContext(); Object inputObject = context.getObject(inputPath); if (inputObject == null) throw BuiltinExceptionFactory.createDataFromXPathIsNull(this, inputPath); if (!(inputObject instanceof CompositeMap)) throw BuiltinExceptionFactory.createInstanceTypeWrongException(inputPath, CompositeMap.class, inputObject.getClass()); URI uri = new URI(url); URL url = uri.toURL(); PrintWriter out = null; BufferedReader br = null; CompositeMap soapBody = createSOAPBody(); soapBody.addChild((CompositeMap) inputObject); String content = XMLOutputter.defaultInstance().toXML(soapBody.getRoot(), true); LoggingContext.getLogger(context, this.getClass().getCanonicalName()).config("request:\r\n" + content); HttpURLConnection httpUrlConnection = null; try { httpUrlConnection = (HttpURLConnection) url.openConnection(); httpUrlConnection.setDoInput(true); httpUrlConnection.setDoOutput(true); httpUrlConnection.setRequestMethod("POST"); httpUrlConnection.setRequestProperty("SOAPAction", "urn:anonOutInOp"); httpUrlConnection.setRequestProperty("Content-Type", "text/xml; charset=UTF-8"); httpUrlConnection.connect(); OutputStream os = httpUrlConnection.getOutputStream(); out = new PrintWriter(os); out.println("<?xml version='1.0' encoding='UTF-8'?>"); out.println(new String(content.getBytes("UTF-8"))); out.flush(); out.close(); String soapResponse = null; CompositeMap soap = null; CompositeLoader cl = new CompositeLoader(); if (HttpURLConnection.HTTP_OK == httpUrlConnection.getResponseCode()) { soap = cl.loadFromStream(httpUrlConnection.getInputStream()); soapResponse = soap.toXML(); LoggingContext.getLogger(context, this.getClass().getCanonicalName()).config("correct response:" + soapResponse); } else { soap = cl.loadFromStream(httpUrlConnection.getErrorStream()); soapResponse = soap.toXML(); LoggingContext.getLogger(context, this.getClass().getCanonicalName()).config("error response:" + soapResponse); if (raiseExceptionOnError) { throw new ConfigurationFileException(WS_INVOKER_ERROR_CODE, new Object[] { url, soapResponse }, this); } } httpUrlConnection.disconnect(); CompositeMap result = (CompositeMap) soap.getChild(SOAPServiceInterpreter.BODY.getLocalName()).getChilds().get(0); if (returnPath != null) runner.getContext().putObject(returnPath, result, true); } catch (Exception e) { LoggingContext.getLogger(context, this.getClass().getCanonicalName()).log(Level.SEVERE, "", e); throw new RuntimeException(e); } finally { if (out != null) { out.close(); } if (br != null) { br.close(); } if (httpUrlConnection != null) { httpUrlConnection.disconnect(); } } } | @Override public void create(DisciplinaDTO disciplina) { try { this.criaConexao(false); } catch (ClassNotFoundException ex) { java.util.logging.Logger.getLogger(PostgresqlDisciplinaDAO.class.getName()).log(Level.SEVERE, null, ex); } catch (SQLException ex) { java.util.logging.Logger.getLogger(PostgresqlDisciplinaDAO.class.getName()).log(Level.SEVERE, null, ex); } String sql = "insert into Disciplina select nextval('sq_Disciplina') as id, ? as nome"; PreparedStatement stmt = null; try { stmt = this.getConnection().prepareStatement(sql); stmt.setString(1, disciplina.getNome()); int retorno = stmt.executeUpdate(); if (retorno == 0) { this.getConnection().rollback(); throw new SQLException("Ocorreu um erro inesperado no momento de inserir dados de Disciplina no banco!"); } this.getConnection().commit(); } catch (SQLException e) { try { this.getConnection().rollback(); } catch (SQLException ex) { java.util.logging.Logger.getLogger(PostgresqlDisciplinaDAO.class.getName()).log(Level.SEVERE, null, ex); } try { throw e; } catch (SQLException ex) { java.util.logging.Logger.getLogger(PostgresqlDisciplinaDAO.class.getName()).log(Level.SEVERE, null, ex); } } finally { try { stmt.close(); this.fechaConexao(); } catch (SQLException e) { try { throw e; } catch (SQLException ex) { java.util.logging.Logger.getLogger(PostgresqlDisciplinaDAO.class.getName()).log(Level.SEVERE, null, ex); } } } } | 15,012 |
0 | private static void readAndRewrite(File inFile, File outFile) throws IOException { ImageInputStream iis = ImageIO.createImageInputStream(new BufferedInputStream(new FileInputStream(inFile))); DcmParser dcmParser = DcmParserFactory.getInstance().newDcmParser(iis); Dataset ds = DcmObjectFactory.getInstance().newDataset(); dcmParser.setDcmHandler(ds.getDcmHandler()); dcmParser.parseDcmFile(null, Tags.PixelData); PixelDataReader pdReader = pdFact.newReader(ds, iis, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); System.out.println("reading " + inFile + "..."); pdReader.readPixelData(false); ImageOutputStream out = ImageIO.createImageOutputStream(new BufferedOutputStream(new FileOutputStream(outFile))); DcmEncodeParam dcmEncParam = DcmEncodeParam.IVR_LE; ds.writeDataset(out, dcmEncParam); ds.writeHeader(out, dcmEncParam, Tags.PixelData, dcmParser.getReadVR(), dcmParser.getReadLength()); System.out.println("writing " + outFile + "..."); PixelDataWriter pdWriter = pdFact.newWriter(pdReader.getPixelDataArray(), false, ds, out, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); pdWriter.writePixelData(); out.flush(); out.close(); System.out.println("done!"); } | public static byte[] generateAuthId(String userName, String password) { byte[] ret = new byte[16]; try { MessageDigest messageDigest = MessageDigest.getInstance("MD5"); String str = userName + password; messageDigest.update(str.getBytes()); ret = messageDigest.digest(); } catch (NoSuchAlgorithmException ex) { ex.printStackTrace(); } return ret; } | 15,013 |
0 | public void execute(HttpResponse response) throws HttpException, IOException { StringBuffer content = new StringBuffer(); NodeSet allNodes = membershipRegistry.listAllMembers(); for (Node node : allNodes) { content.append(node.getId().toString()); content.append(SystemUtils.LINE_SEPARATOR); } StringEntity body = new StringEntity(content.toString()); body.setContentType(PLAIN_TEXT_RESPONSE_CONTENT_TYPE); response.setEntity(body); } | public static final String crypt(String password, String salt) throws NoSuchAlgorithmException { String magic = "$1$"; byte finalState[]; MessageDigest ctx, ctx1; long l; if (salt.startsWith(magic)) { salt = salt.substring(magic.length()); } if (salt.indexOf('$') != -1) { salt = salt.substring(0, salt.indexOf('$')); } if (salt.length() > 8) { salt = salt.substring(0, 8); } ctx = MessageDigest.getInstance("MD5"); ctx.update(password.getBytes()); ctx.update(magic.getBytes()); ctx.update(salt.getBytes()); ctx1 = MessageDigest.getInstance("MD5"); ctx1.update(password.getBytes()); ctx1.update(salt.getBytes()); ctx1.update(password.getBytes()); finalState = ctx1.digest(); for (int pl = password.length(); pl > 0; pl -= 16) { for (int i = 0; i < (pl > 16 ? 16 : pl); i++) ctx.update(finalState[i]); } clearbits(finalState); for (int i = password.length(); i != 0; i >>>= 1) { if ((i & 1) != 0) { ctx.update(finalState[0]); } else { ctx.update(password.getBytes()[0]); } } finalState = ctx.digest(); for (int i = 0; i < 1000; i++) { ctx1 = MessageDigest.getInstance("MD5"); if ((i & 1) != 0) { ctx1.update(password.getBytes()); } else { for (int c = 0; c < 16; c++) ctx1.update(finalState[c]); } if ((i % 3) != 0) { ctx1.update(salt.getBytes()); } if ((i % 7) != 0) { ctx1.update(password.getBytes()); } if ((i & 1) != 0) { for (int c = 0; c < 16; c++) ctx1.update(finalState[c]); } else { ctx1.update(password.getBytes()); } finalState = ctx1.digest(); } StringBuffer result = new StringBuffer(); result.append(magic); result.append(salt); result.append("$"); l = (bytes2u(finalState[0]) << 16) | (bytes2u(finalState[6]) << 8) | bytes2u(finalState[12]); result.append(to64(l, 4)); l = (bytes2u(finalState[1]) << 16) | (bytes2u(finalState[7]) << 8) | bytes2u(finalState[13]); result.append(to64(l, 4)); l = (bytes2u(finalState[2]) << 16) | (bytes2u(finalState[8]) << 8) | bytes2u(finalState[14]); result.append(to64(l, 4)); l = (bytes2u(finalState[3]) << 16) | (bytes2u(finalState[9]) << 8) | bytes2u(finalState[15]); result.append(to64(l, 4)); l = (bytes2u(finalState[4]) << 16) | (bytes2u(finalState[10]) << 8) | bytes2u(finalState[5]); result.append(to64(l, 4)); l = bytes2u(finalState[11]); result.append(to64(l, 2)); clearbits(finalState); return result.toString(); } | 15,014 |
0 | protected URLConnection openConnection(URL url) throws IOException { if (url == null) return null; if (!url.getProtocol().equals("nntp")) return null; if (m_connection != null) { if (m_connection.getURL().getHost().equals(url.getHost()) && (m_connection.getURL().getPort() == url.getPort()) && (m_connection.getURL().getUserInfo().equals(url.getUserInfo()))) { return m_connection; } } m_connection = new NNTPConnection(url); return m_connection; } | public static void test() { try { Pattern pattern = Pattern.compile("[0-9]{3}\\. <a href='(.*)\\.html'>(.*)</a><br />"); URL url = new URL("http://farmfive.com/"); BufferedReader br = new BufferedReader(new InputStreamReader(url.openStream())); String line; int count = 0; while ((line = br.readLine()) != null) { Matcher match = pattern.matcher(line); if (match.matches()) { System.out.println(match.group(1) + " " + match.group(2)); count++; } } System.out.println(count + " counted"); br.close(); } catch (Exception e) { e.printStackTrace(); } } | 15,015 |
0 | public void run() { long id = 0; try { URL url = new URL(httpRequest + blockSize); BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream())); try { String str = in.readLine(); if (str == null) { throw new IllegalStateException("Parsing error"); } if (str.matches(".*SUCCESS.*")) { str = in.readLine(); if (str.matches(".*Start:.*")) { str = in.readLine(); id = Long.parseLong(str); } else { throw new IllegalStateException("Invalid response for blocksize(" + blockSize + "):" + str); } } else { throw new IllegalStateException("Invalid response for blocksize(" + blockSize + "):" + str); } } finally { in.close(); } if (id <= 0) throw new IllegalStateException("Invalid GUID start value " + id); synchronized (ids) { boolean absent = ids.add(new Long(id)); if (!absent) { logErrorMessage(id + " already exists for thread " + Thread.currentThread().getName()); } } } catch (Exception e) { logErrorMessage("Unexpected IdGenerator thread failure" + e.getMessage()); e.printStackTrace(); } finally { synchronized (test) { test.liveThreads--; test.notify(); } } } | private void copy(File source, File destination) throws PackageException { try { FileInputStream in = new FileInputStream(source); FileOutputStream out = new FileOutputStream(destination); byte[] buff = new byte[1024]; int len; while ((len = in.read(buff)) > 0) out.write(buff, 0, len); in.close(); out.close(); } catch (IOException e) { throw new PackageException("Unable to copy " + source.getPath() + " to " + destination.getPath() + " :: " + e.toString()); } } | 15,016 |
1 | public void testQueryForBinary() throws InvalidNodeTypeDefException, ParseException, Exception { JCRNodeSource source = (JCRNodeSource) resolveSource(BASE_URL + "images/photo.png"); assertNotNull(source); assertEquals(false, source.exists()); OutputStream os = source.getOutputStream(); assertNotNull(os); String content = "foo is a bar"; os.write(content.getBytes()); os.flush(); os.close(); QueryResultSource qResult = (QueryResultSource) resolveSource(BASE_URL + "images?/*[contains(local-name(), 'photo.png')]"); assertNotNull(qResult); Collection results = qResult.getChildren(); assertEquals(1, results.size()); Iterator it = results.iterator(); JCRNodeSource rSrc = (JCRNodeSource) it.next(); InputStream rSrcIn = rSrc.getInputStream(); ByteArrayOutputStream actualOut = new ByteArrayOutputStream(); IOUtils.copy(rSrcIn, actualOut); rSrcIn.close(); assertEquals(content, actualOut.toString()); actualOut.close(); rSrc.delete(); } | public static File copyFile(File srcFile, File destFolder, FileCopyListener copyListener) { File dest = new File(destFolder, srcFile.getName()); try { FileInputStream in = new FileInputStream(srcFile); FileOutputStream out = new FileOutputStream(dest); byte[] readBuf = new byte[1024 * 512]; int readLength; long totalCopiedSize = 0; long totalSize = srcFile.length(); boolean canceled = false; if (copyListener == null) { while ((readLength = in.read(readBuf)) != -1) { out.write(readBuf, 0, readLength); } } else { while ((readLength = in.read(readBuf)) != -1) { out.write(readBuf, 0, readLength); if (!copyListener.updateCheck(readLength, totalSize)) { canceled = true; break; } } } in.close(); out.close(); if (canceled) { dest.delete(); } } catch (FileNotFoundException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } return dest; } | 15,017 |
1 | public void copy(final File source, final File target) throws FileSystemException { LogHelper.logMethod(log, toObjectString(), "copy(), source = " + source + ", target = " + target); FileChannel sourceChannel = null; FileChannel targetChannel = null; try { sourceChannel = new FileInputStream(source).getChannel(); targetChannel = new FileOutputStream(target).getChannel(); sourceChannel.transferTo(0L, sourceChannel.size(), targetChannel); log.info("Copied " + source + " to " + target); } catch (FileNotFoundException e) { throw new FileSystemException("Unexpected FileNotFoundException while copying a file", e); } catch (IOException e) { throw new FileSystemException("Unexpected IOException while copying a file", e); } finally { if (sourceChannel != null) { try { sourceChannel.close(); } catch (IOException e) { log.error("IOException during source channel close after copy", e); } } if (targetChannel != null) { try { targetChannel.close(); } catch (IOException e) { log.error("IOException during target channel close after copy", e); } } } } | @Test public void testStandardTee() throws Exception { final byte[] test = "test".getBytes(); final InputStream source = new ByteArrayInputStream(test); final ByteArrayOutputStream destination1 = new ByteArrayOutputStream(); final ByteArrayOutputStream destination2 = new ByteArrayOutputStream(); final TeeOutputStream tee = new TeeOutputStream(destination1, destination2); org.apache.commons.io.IOUtils.copy(source, tee); tee.close(); assertArrayEquals("the two arrays are equals", test, destination1.toByteArray()); assertArrayEquals("the two arrays are equals", test, destination2.toByteArray()); assertEquals("byte count", test.length, tee.getSize()); } | 15,018 |
1 | public static boolean decodeFileToFile(String infile, String outfile) { boolean success = false; java.io.InputStream in = null; java.io.OutputStream out = null; try { in = new Base64.InputStream(new java.io.BufferedInputStream(new java.io.FileInputStream(infile)), Base64.DECODE); out = new java.io.BufferedOutputStream(new java.io.FileOutputStream(outfile)); byte[] buffer = new byte[65536]; int read = -1; while ((read = in.read(buffer)) >= 0) { out.write(buffer, 0, read); } success = true; } catch (java.io.IOException exc) { logger.error(Logger.SECURITY_FAILURE, "Problem decoding file to file", exc); } finally { try { in.close(); } catch (Exception exc) { } try { out.close(); } catch (Exception exc) { } } return success; } | public static void copyFile(File sourceFile, File destFile) throws IOException { if (!sourceFile.exists()) { return; } if (!destFile.exists()) { destFile.createNewFile(); } FileChannel source = null; FileChannel destination = null; source = new FileInputStream(sourceFile).getChannel(); destination = new FileOutputStream(destFile).getChannel(); if (destination != null && source != null) { destination.transferFrom(source, 0, source.size()); } if (source != null) { source.close(); } if (destination != null) { destination.close(); } } | 15,019 |
0 | public String decrypt(String text, String passphrase, int keylen) { RC2ParameterSpec parm = new RC2ParameterSpec(keylen); MessageDigest md; try { md = MessageDigest.getInstance("MD5"); md.update(passphrase.getBytes(getCharset())); SecretKeySpec skeySpec = new SecretKeySpec(md.digest(), "RC2"); Cipher cipher = Cipher.getInstance("RC2/ECB/NOPADDING"); cipher.init(Cipher.DECRYPT_MODE, skeySpec, parm); byte[] dString = Base64.decode(text); byte[] d = cipher.doFinal(dString); String clearTextNew = decodeBytesNew(d); return clearTextNew; } catch (NoSuchAlgorithmException e) { e.printStackTrace(); } catch (NoSuchPaddingException e) { e.printStackTrace(); } catch (InvalidKeyException e) { e.printStackTrace(); } catch (InvalidAlgorithmParameterException e) { e.printStackTrace(); } catch (IllegalBlockSizeException e) { e.printStackTrace(); } catch (BadPaddingException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } return null; } | @Test public void GetBingSearchResult() throws UnsupportedEncodingException { String query = "Scanner Java example"; String request = "http://api.bing.net/xml.aspx?AppId=731DD1E61BE6DE4601A3008DC7A0EB379149EC29" + "&Version=2.2&Market=en-US&Query=" + URLEncoder.encode(query, "UTF-8") + "&Sources=web+spell&Web.Count=50"; try { URL url = new URL(request); System.out.println("Host : " + url.getHost()); BufferedReader reader = new BufferedReader(new InputStreamReader(url.openStream())); String inputLine; String finalContents = ""; while ((inputLine = reader.readLine()) != null) { finalContents += "\n" + inputLine; } Document doc = Jsoup.parse(finalContents); Elements eles = doc.getElementsByTag("web:Url"); for (Element ele : eles) { System.out.println(ele.text()); } } catch (Exception e) { e.printStackTrace(); } } | 15,020 |
1 | static ConversionMap create(String file) { ConversionMap out = new ConversionMap(); URL url = ConversionMap.class.getResource(file); try { BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream())); String line = in.readLine(); while (line != null) { if (line.length() > 0) { String[] arr = line.split("\t"); try { double value = Double.parseDouble(arr[1]); out.put(translate(lowercase(arr[0].getBytes())), value); out.defaultValue += value; out.length = arr[0].length(); } catch (NumberFormatException e) { throw new RuntimeException("Something is wrong with in conversion file: " + e); } } line = in.readLine(); } in.close(); out.defaultValue /= Math.pow(4, out.length); } catch (Exception e) { e.printStackTrace(); throw new RuntimeException("Their was an error while reading the conversion map: " + e); } return out; } | private static void loadQueryProcessorFactories() { qpFactoryMap = new HashMap<String, QueryProcessorFactoryIF>(); Enumeration<URL> resources = null; try { resources = QueryUtils.class.getClassLoader().getResources(RESOURCE_STRING); } catch (IOException e) { log.error("Error while trying to look for " + "QueryProcessorFactoryIF implementations.", e); } while (resources != null && resources.hasMoreElements()) { URL url = resources.nextElement(); InputStream is = null; try { is = url.openStream(); } catch (IOException e) { log.warn("Error opening stream to QueryProcessorFactoryIF service description.", e); } if (is != null) { BufferedReader rdr = new BufferedReader(new InputStreamReader(is)); String line; try { while ((line = rdr.readLine()) != null) { try { ClassLoader classLoader = Thread.currentThread().getContextClassLoader(); Class<?> c = Class.forName(line, true, classLoader); if (QueryProcessorFactoryIF.class.isAssignableFrom(c)) { QueryProcessorFactoryIF factory = (QueryProcessorFactoryIF) c.newInstance(); qpFactoryMap.put(factory.getQueryLanguage().toUpperCase(), factory); } else { log.warn("Wrong entry for QueryProcessorFactoryIF service " + "description, '" + line + "' is not implementing the " + "correct interface."); } } catch (Exception e) { log.warn("Could not create an instance for " + "QueryProcessorFactoryIF service '" + line + "'."); } } } catch (IOException e) { log.warn("Could not read from QueryProcessorFactoryIF " + "service descriptor.", e); } } } if (!qpFactoryMap.containsKey(DEFAULT_LANGUAGE)) { qpFactoryMap.put(DEFAULT_LANGUAGE, new TologQueryProcessorFactory()); } } | 15,021 |
1 | private void performDownload() { List<String> selected = filesPane.getSelectedValuesList(); if (selected == null || selected.isEmpty() || selected.size() != 1) { JOptionPane.showMessageDialog(this, "Please select one path"); return; } RFile file = new RFile(selected.get(0)); if (!file.isFile()) { JOptionPane.showMessageDialog(this, "file does not exist anymore"); return; } chooser.setSelectedFile(new File(chooser.getCurrentDirectory(), file.getName())); int ok = chooser.showSaveDialog(this); if (ok != JFileChooser.APPROVE_OPTION) { return; } FileOutputStream fout = null; RFileInputStream in = null; try { fout = new FileOutputStream(chooser.getSelectedFile()); in = new RFileInputStream(file); IOUtils.copy(in, fout); JOptionPane.showMessageDialog(this, "File downloaded to " + chooser.getSelectedFile(), "Download finished", JOptionPane.INFORMATION_MESSAGE); } catch (IOException iOException) { JOptionPane.showMessageDialog(this, "Error: " + iOException, "Error", JOptionPane.ERROR_MESSAGE); } finally { if (in != null) { try { in.close(); } catch (Throwable t) { } } if (fout != null) { try { fout.close(); } catch (Throwable t) { } } } } | private File uploadToTmp() { if (fileFileName == null) { return null; } File tmpFile = dataDir.tmpFile(shortname, fileFileName); log.debug("Uploading dwc archive file for new resource " + shortname + " to " + tmpFile.getAbsolutePath()); InputStream input = null; OutputStream output = null; try { input = new FileInputStream(file); output = new FileOutputStream(tmpFile); IOUtils.copy(input, output); output.flush(); log.debug("Uploaded file " + fileFileName + " with content-type " + fileContentType); } catch (IOException e) { log.error(e); return null; } finally { if (output != null) { IOUtils.closeQuietly(output); } if (input != null) { IOUtils.closeQuietly(input); } } return tmpFile; } | 15,022 |
1 | void IconmenuItem5_actionPerformed(ActionEvent e) { JFileChooser jFileChooser1 = new JFileChooser(); String separator = ""; if (getPath() != null && !getPath().equals("")) { jFileChooser1.setCurrentDirectory(new File(getPath())); jFileChooser1.setSelectedFile(new File(getPath())); } if (JFileChooser.APPROVE_OPTION == jFileChooser1.showOpenDialog(this.getFatherFrame())) { setPath(jFileChooser1.getSelectedFile().getPath()); separator = jFileChooser1.getSelectedFile().separator; File dirImg = new File("." + separator + "images"); if (!dirImg.exists()) { dirImg.mkdir(); } int index = getPath().lastIndexOf(separator); String imgName = getPath().substring(index); String newPath = dirImg + imgName; try { File inputFile = new File(getPath()); File outputFile = new File(newPath); if (!inputFile.getCanonicalPath().equals(outputFile.getCanonicalPath())) { FileInputStream in = new FileInputStream(inputFile); FileOutputStream out = new FileOutputStream(outputFile); int c; while ((c = in.read()) != -1) out.write(c); in.close(); out.close(); } } catch (Exception ex) { ex.printStackTrace(); LogHandler.log(ex.getMessage(), Level.INFO, "LOG_MSG", isLoggingEnabled()); JOptionPane.showMessageDialog(null, ex.getMessage().substring(0, Math.min(ex.getMessage().length(), getFatherPanel().MAX_DIALOG_MSG_SZ)) + "-" + getClass(), "", JOptionPane.ERROR_MESSAGE); } setPath(newPath); if (getDefaultPath() == null || getDefaultPath().equals("")) { String msgString = "E' stata selezionata un'immagine da associare all'IconShape, ma non e' " + "stata selezionata ancora nessun'immagine di default. Imposto quella scelta anche come " + "immagine di default?"; if (JOptionPane.showConfirmDialog(null, msgString.substring(0, Math.min(msgString.length(), getFatherPanel().MAX_DIALOG_MSG_SZ)), "choose one", JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION) { setDefaultPath(newPath); createDefaultImage(); } } createImage(); } } | public void writeOutput(String directory) throws IOException { File f = new File(directory); int i = 0; if (f.isDirectory()) { for (AppInventorScreen screen : screens.values()) { File screenFile = new File(getScreenFilePath(f.getAbsolutePath(), screen)); screenFile.getParentFile().mkdirs(); screenFile.createNewFile(); FileWriter out = new FileWriter(screenFile); String initial = files.get(i).toString(); Map<String, String> types = screen.getTypes(); String[] lines = initial.split("\n"); for (String key : types.keySet()) { if (!key.trim().equals(screen.getName().trim())) { String value = types.get(key); boolean varFound = false; boolean importFound = false; for (String line : lines) { if (line.matches("^\\s*(public|private)\\s+" + value + "\\s+" + key + "\\s*=.*;$")) varFound = true; if (line.matches("^\\s*(public|private)\\s+" + value + "\\s+" + key + "\\s*;$")) varFound = true; if (line.matches("^\\s*import\\s+.*" + value + "\\s*;$")) importFound = true; } if (!varFound) initial = initial.replaceFirst("(?s)(?<=\\{\n)", "\tprivate " + value + " " + key + ";\n"); if (!importFound) initial = initial.replaceFirst("(?=import)", "import com.google.devtools.simple.runtime.components.android." + value + ";\n"); } } out.write(initial); out.close(); i++; } File manifestFile = new File(getManifestFilePath(f.getAbsolutePath(), manifest)); manifestFile.getParentFile().mkdirs(); manifestFile.createNewFile(); FileWriter out = new FileWriter(manifestFile); out.write(manifest.toString()); out.close(); File projectFile = new File(getProjectFilePath(f.getAbsolutePath(), project)); projectFile.getParentFile().mkdirs(); projectFile.createNewFile(); out = new FileWriter(projectFile); out.write(project.toString()); out.close(); String[] copyResourceFilenames = { "proguard.cfg", "project.properties", "libSimpleAndroidRuntime.jar", "\\.classpath", "res/drawable/icon.png", "\\.settings/org.eclipse.jdt.core.prefs" }; for (String copyResourceFilename : copyResourceFilenames) { InputStream is = getClass().getResourceAsStream("/resources/" + copyResourceFilename.replace("\\.", "")); File outputFile = new File(f.getAbsoluteFile() + File.separator + copyResourceFilename.replace("\\.", ".")); outputFile.getParentFile().mkdirs(); OutputStream os = new FileOutputStream(outputFile); byte[] buf = new byte[1024]; int readBytes; if (is == null) System.out.println("/resources/" + copyResourceFilename.replace("\\.", "")); if (os == null) System.out.println(f.getAbsolutePath() + File.separator + copyResourceFilename.replace("\\.", ".")); while ((readBytes = is.read(buf)) > 0) { os.write(buf, 0, readBytes); } } for (String assetName : assets) { InputStream is = new FileInputStream(new File(assetsDir.getAbsolutePath() + File.separator + assetName)); File outputFile = new File(f.getAbsoluteFile() + File.separator + assetName); outputFile.getParentFile().mkdirs(); OutputStream os = new FileOutputStream(outputFile); byte[] buf = new byte[1024]; int readBytes; while ((readBytes = is.read(buf)) > 0) { os.write(buf, 0, readBytes); } } File assetsOutput = new File(getAssetsFilePath(f.getAbsolutePath())); new File(assetsDir.getAbsoluteFile() + File.separator + "assets").renameTo(assetsOutput); } } | 15,023 |
1 | public void xtest1() throws Exception { InputStream input = new FileInputStream("C:/Documentos/j931_01.pdf"); InputStream tmp = new ITextManager().cut(input, 3, 8); FileOutputStream output = new FileOutputStream("C:/temp/split.pdf"); IOUtils.copy(tmp, output); input.close(); tmp.close(); output.close(); } | private void publishCMap(LWMap map) throws IOException { try { File savedCMap = PublishUtil.createIMSCP(Publisher.resourceVector); InputStream istream = new BufferedInputStream(new FileInputStream(savedCMap)); OutputStream ostream = new BufferedOutputStream(new FileOutputStream(ActionUtil.selectFile("IMSCP", "zip"))); int fileLength = (int) savedCMap.length(); byte bytes[] = new byte[fileLength]; while (istream.read(bytes, 0, fileLength) != -1) ostream.write(bytes, 0, fileLength); istream.close(); ostream.close(); } catch (IOException ex) { throw ex; } catch (Exception ex) { System.out.println(ex); VueUtil.alert(VUE.getDialogParent(), VueResources.getString("dialog.export.message") + ex.getMessage(), VueResources.getString("dialog.export.title"), JOptionPane.ERROR_MESSAGE); } } | 15,024 |
0 | public static void copyFile(File sourceFile, File destFile, boolean overwrite) throws IOException, DirNotFoundException, FileNotFoundException, FileExistsAlreadyException { File destDir = new File(destFile.getParent()); if (!destDir.exists()) { throw new DirNotFoundException(destDir.getAbsolutePath()); } if (!sourceFile.exists()) { throw new FileNotFoundException(sourceFile.getAbsolutePath()); } if (!overwrite && destFile.exists()) { throw new FileExistsAlreadyException(destFile.getAbsolutePath()); } FileInputStream in = new FileInputStream(sourceFile); FileOutputStream out = new FileOutputStream(destFile); byte[] buffer = new byte[8 * 1024]; int count = 0; do { out.write(buffer, 0, count); count = in.read(buffer, 0, buffer.length); } while (count != -1); in.close(); out.close(); } | private Bitmap fetchImage(String urlstr) throws Exception { URL url; url = new URL(urlstr); HttpURLConnection c = (HttpURLConnection) url.openConnection(); c.setDoInput(true); c.setRequestProperty("User-Agent", "Agent"); c.connect(); InputStream is = c.getInputStream(); Bitmap img; img = BitmapFactory.decodeStream(is); return img; } | 15,025 |
1 | public static String SHA1(String password) throws BusinessException { try { MessageDigest digest = MessageDigest.getInstance("SHA-1"); digest.update(password.getBytes()); BigInteger hash = new BigInteger(1, digest.digest()); return hash.toString(16); } catch (java.security.NoSuchAlgorithmException e) { throw new BusinessException(); } } | public static String digestMd5(String str) { if (str == null || str.length() == 0) { throw new IllegalArgumentException("文字列がNull、または空です。"); } MessageDigest md5; byte[] enclyptedHash; try { md5 = MessageDigest.getInstance("MD5"); md5.update(str.getBytes()); enclyptedHash = md5.digest(); } catch (NoSuchAlgorithmException ex) { ex.printStackTrace(); return ""; } return bytesToHexString(enclyptedHash); } | 15,026 |
1 | @Override protected void loadInternals(final File internDir, final ExecutionMonitor exec) throws IOException, CanceledExecutionException { List<String> taxa = new Vector<String>(); String domain = m_domain.getStringValue(); String id = ""; if (domain.equalsIgnoreCase("Eukaryota")) id = "eukaryota"; try { URL url = new URL("http://www.ebi.ac.uk/genomes/" + id + ".details.txt"); BufferedReader reader = new BufferedReader(new InputStreamReader(url.openStream())); String link = ""; String key = ""; String name = ""; int counter = 0; String line = ""; while ((line = reader.readLine()) != null) { String[] st = line.split("\t"); ena_details ena = new ena_details(st[0], st[1], st[2], st[3], st[4]); ENADataHolder.instance().put(ena.desc, ena); taxa.add(ena.desc); } reader.close(); } catch (MalformedURLException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } } | public static String[] readStats() throws Exception { URL url = null; BufferedReader reader = null; StringBuilder stringBuilder; try { url = new URL("http://localhost:" + port + webctx + "/shared/js/libOO/health_check.sjs"); HttpURLConnection connection = (HttpURLConnection) url.openConnection(); connection.setRequestMethod("GET"); connection.setReadTimeout(10 * 1000); connection.connect(); reader = new BufferedReader(new InputStreamReader(connection.getInputStream())); stringBuilder = new StringBuilder(); String line = null; while ((line = reader.readLine()) != null) { stringBuilder.append(line); } return stringBuilder.toString().split(","); } catch (Exception e) { e.printStackTrace(); throw e; } finally { if (reader != null) { try { reader.close(); } catch (IOException ioe) { ioe.printStackTrace(); } } } } | 15,027 |
1 | private static void doCopyFile(File srcFile, File destFile, boolean preserveFileDate) throws IOException { if (destFile.exists() && destFile.isDirectory()) { throw new IOException("Destination '" + destFile + "' exists but is a directory"); } FileInputStream input = new FileInputStream(srcFile); try { FileOutputStream output = new FileOutputStream(destFile); try { IOUtils.copy(input, output); } finally { IOUtils.closeQuietly(output); } } finally { IOUtils.closeQuietly(input); } if (srcFile.length() != destFile.length()) { throw new IOException("Failed to copy full contents from '" + srcFile + "' to '" + destFile + "'"); } if (preserveFileDate) { destFile.setLastModified(srcFile.lastModified()); } } | private JButton getButtonSonido() { if (buttonSonido == null) { buttonSonido = new JButton(); buttonSonido.setText(Messages.getString("gui.AdministracionResorces.15")); buttonSonido.setIcon(new ImageIcon("data/icons/view_sidetree.png")); buttonSonido.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(java.awt.event.ActionEvent e) { JFileChooser fc = new JFileChooser(); fc.addChoosableFileFilter(new SoundFilter()); int returnVal = fc.showDialog(AdministracionResorces.this, Messages.getString("gui.AdministracionResorces.17")); if (returnVal == JFileChooser.APPROVE_OPTION) { File file = fc.getSelectedFile(); String rutaGlobal = System.getProperty("user.dir") + "/" + rutaDatos + "sonidos/" + file.getName(); String rutaRelativa = rutaDatos + "sonidos/" + file.getName(); try { FileInputStream fis = new FileInputStream(file); FileOutputStream fos = new FileOutputStream(rutaGlobal, true); FileChannel canalFuente = fis.getChannel(); FileChannel canalDestino = fos.getChannel(); canalFuente.transferTo(0, canalFuente.size(), canalDestino); fis.close(); fos.close(); imagen.setSonidoURL(rutaRelativa); System.out.println(rutaGlobal + " " + rutaRelativa); buttonSonido.setIcon(new ImageIcon("data/icons/view_sidetreeOK.png")); gui.getAudio().reproduceAudio(imagen); } catch (IOException ex) { ex.printStackTrace(); } } else { } } }); } return buttonSonido; } | 15,028 |
0 | public static void executa(String arquivo, String filial, String ip) { String drive = arquivo.substring(0, 2); if (drive.indexOf(":") == -1) drive = ""; Properties p = Util.lerPropriedades(arquivo); String servidor = p.getProperty("servidor"); String impressora = p.getProperty("fila"); String arqRel = new String(drive + p.getProperty("arquivo")); String copias = p.getProperty("copias"); if (filial.equalsIgnoreCase(servidor)) { Socket s = null; int tentativas = 0; boolean conectado = false; while (!conectado) { try { tentativas++; System.out.println("Tentando conectar " + ip + " (" + tentativas + ")"); s = new Socket(ip, 7000); conectado = s.isConnected(); } catch (ConnectException ce) { System.err.println(ce.getMessage()); System.err.println(ce.getCause()); } catch (UnknownHostException uhe) { System.err.println(uhe.getMessage()); } catch (IOException ioe) { System.err.println(ioe.getMessage()); } } FileInputStream in = null; BufferedOutputStream out = null; try { in = new FileInputStream(new File(arqRel)); out = new BufferedOutputStream(new GZIPOutputStream(s.getOutputStream())); } catch (FileNotFoundException e3) { e3.printStackTrace(); } catch (IOException e3) { e3.printStackTrace(); } String arqtr = arqRel.substring(2); System.out.println("Proximo arquivo: " + arqRel + " ->" + arqtr); while (arqtr.length() < 30) arqtr += " "; while (impressora.length() < 30) impressora += " "; byte aux[] = new byte[30]; byte cop[] = new byte[2]; try { aux = arqtr.getBytes("UTF8"); out.write(aux); aux = impressora.getBytes("UTF8"); out.write(aux); cop = copias.getBytes("UTF8"); out.write(cop); out.flush(); } catch (UnsupportedEncodingException e2) { e2.printStackTrace(); } catch (IOException e2) { e2.printStackTrace(); } byte b[] = new byte[1024]; int nBytes; try { while ((nBytes = in.read(b)) != -1) out.write(b, 0, nBytes); out.flush(); out.close(); in.close(); s.close(); } catch (IOException e1) { e1.printStackTrace(); } System.out.println("Arquivo " + arqRel + " foi transmitido. \n\n"); try { Thread.sleep(1000); } catch (InterruptedException e) { e.printStackTrace(); } SimpleDateFormat dfArq = new SimpleDateFormat("yyyy-MM-dd"); SimpleDateFormat dfLog = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss"); String arqLog = "log" + filial + dfArq.format(new Date()) + ".txt"; PrintWriter pw = null; try { pw = new PrintWriter(new FileWriter(arqLog, true)); } catch (IOException e) { e.printStackTrace(); } pw.println("Arquivo: " + arquivo + " " + dfLog.format(new Date())); pw.flush(); pw.close(); File f = new File(arquivo); while (!f.delete()) { System.out.println("Erro apagando " + arquivo); } } } | public boolean ponerRivalxRonda(int idJugadorDiv, int idRonda, int dato) { int intResult = 0; String sql = "UPDATE jugadorxdivxronda " + " SET idPareoRival = " + dato + " WHERE jugadorxDivision_idJugadorxDivision = " + idJugadorDiv + " AND ronda_numeroRonda = " + idRonda; try { connection = conexionBD.getConnection(); connection.setAutoCommit(false); ps = connection.prepareStatement(sql); intResult = ps.executeUpdate(); connection.commit(); } catch (SQLException ex) { ex.printStackTrace(); try { connection.rollback(); } catch (SQLException exe) { exe.printStackTrace(); } } finally { conexionBD.close(ps); conexionBD.close(connection); } return (intResult > 0); } | 15,029 |
1 | private static void readAndRewrite(File inFile, File outFile) throws IOException { ImageInputStream iis = ImageIO.createImageInputStream(new BufferedInputStream(new FileInputStream(inFile))); DcmParser dcmParser = DcmParserFactory.getInstance().newDcmParser(iis); Dataset ds = DcmObjectFactory.getInstance().newDataset(); dcmParser.setDcmHandler(ds.getDcmHandler()); dcmParser.parseDcmFile(null, Tags.PixelData); PixelDataReader pdReader = pdFact.newReader(ds, iis, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); System.out.println("reading " + inFile + "..."); pdReader.readPixelData(false); ImageOutputStream out = ImageIO.createImageOutputStream(new BufferedOutputStream(new FileOutputStream(outFile))); DcmEncodeParam dcmEncParam = DcmEncodeParam.IVR_LE; ds.writeDataset(out, dcmEncParam); ds.writeHeader(out, dcmEncParam, Tags.PixelData, dcmParser.getReadVR(), dcmParser.getReadLength()); System.out.println("writing " + outFile + "..."); PixelDataWriter pdWriter = pdFact.newWriter(pdReader.getPixelDataArray(), false, ds, out, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); pdWriter.writePixelData(); out.flush(); out.close(); System.out.println("done!"); } | public void writeConfigurationFile() throws IOException, ComponentException { SystemConfig config = parent.getParentSystem().getConfiguration(); File original = config.getLocation(); File backup = new File(original.getParentFile(), original.getName() + "." + System.currentTimeMillis()); FileInputStream in = new FileInputStream(original); FileOutputStream out = new FileOutputStream(backup); byte[] buffer = new byte[2048]; try { int bytesread = 0; while ((bytesread = in.read(buffer)) > 0) { out.write(buffer, 0, bytesread); } } catch (IOException e) { logger.warn("Failed to copy backup of configuration file"); throw e; } finally { in.close(); out.close(); } FileWriter replace = new FileWriter(original); replace.write(config.toFileFormat()); replace.close(); logger.info("Re-wrote configuration file " + original.getPath()); } | 15,030 |
0 | public static void main(String[] args) { FTPClient client = new FTPClient(); FileInputStream fis = null; try { client.connect("192.168.1.10"); client.login("a", "123456"); String filename = "D:\\DHTH5CLT\\HK3\\Ung dung phan tan\\FTP_JAVA\\FTP_DETAI\\FTP\\src\\DemoFTP\\filename\\5s.txt"; fis = new FileInputStream(filename); client.storeFile(filename, fis); client.logout(); } catch (IOException e) { e.printStackTrace(); } finally { try { if (fis != null) { fis.close(); } client.disconnect(); } catch (IOException e) { e.printStackTrace(); } } } | private void getXMLData() { String result = null; URL url = null; URLConnection conn = null; BufferedReader rd = null; StringBuffer sb = new StringBuffer(); String line; try { url = new URL(this.url); conn = url.openConnection(); rd = new BufferedReader(new InputStreamReader(conn.getInputStream())); while ((line = rd.readLine()) != null) { sb.append(line + "\n"); } rd.close(); result = sb.toString(); } catch (MalformedURLException e) { log.error("URL was malformed: {}", url, e); } catch (IOException e) { log.error("IOException thrown: {}", url, e); } this.xmlString = result; } | 15,031 |
1 | public void copyFile(String source_name, String dest_name) throws IOException { File source_file = new File(source_name); File destination_file = new File(dest_name); FileInputStream source = null; FileOutputStream destination = null; byte[] buffer; int bytes_read; try { if (!source_file.exists() || !source_file.isFile()) throw new FileCopyException(QZ.PHRASES.getPhrase("25") + " " + source_name); if (!source_file.canRead()) throw new FileCopyException(QZ.PHRASES.getPhrase("26") + " " + QZ.PHRASES.getPhrase("27") + ": " + source_name); if (destination_file.exists()) { if (destination_file.isFile()) { DataInputStream in = new DataInputStream(System.in); String response; if (!destination_file.canWrite()) throw new FileCopyException(QZ.PHRASES.getPhrase("28") + " " + QZ.PHRASES.getPhrase("29") + ": " + dest_name); System.out.print(QZ.PHRASES.getPhrase("19") + dest_name + QZ.PHRASES.getPhrase("30") + ": "); System.out.flush(); response = in.readLine(); if (!response.equals("Y") && !response.equals("y")) throw new FileCopyException(QZ.PHRASES.getPhrase("31")); } else throw new FileCopyException(QZ.PHRASES.getPhrase("28") + " " + QZ.PHRASES.getPhrase("32") + ": " + dest_name); } else { File parentdir = parent(destination_file); if (!parentdir.exists()) throw new FileCopyException(QZ.PHRASES.getPhrase("28") + " " + QZ.PHRASES.getPhrase("33") + ": " + dest_name); if (!parentdir.canWrite()) throw new FileCopyException(QZ.PHRASES.getPhrase("28") + " " + QZ.PHRASES.getPhrase("34") + ": " + dest_name); } source = new FileInputStream(source_file); destination = new FileOutputStream(destination_file); buffer = new byte[1024]; while (true) { bytes_read = source.read(buffer); if (bytes_read == -1) break; destination.write(buffer, 0, bytes_read); } } finally { if (source != null) try { source.close(); } catch (IOException e) { ; } if (destination != null) try { destination.close(); } catch (IOException e) { ; } } } | private static void readAndRewrite(File inFile, File outFile) throws IOException { ImageInputStream iis = ImageIO.createImageInputStream(new BufferedInputStream(new FileInputStream(inFile))); DcmParser dcmParser = DcmParserFactory.getInstance().newDcmParser(iis); Dataset ds = DcmObjectFactory.getInstance().newDataset(); dcmParser.setDcmHandler(ds.getDcmHandler()); dcmParser.parseDcmFile(null, Tags.PixelData); PixelDataReader pdReader = pdFact.newReader(ds, iis, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); System.out.println("reading " + inFile + "..."); pdReader.readPixelData(false); ImageOutputStream out = ImageIO.createImageOutputStream(new BufferedOutputStream(new FileOutputStream(outFile))); DcmEncodeParam dcmEncParam = DcmEncodeParam.IVR_LE; ds.writeDataset(out, dcmEncParam); ds.writeHeader(out, dcmEncParam, Tags.PixelData, dcmParser.getReadVR(), dcmParser.getReadLength()); System.out.println("writing " + outFile + "..."); PixelDataWriter pdWriter = pdFact.newWriter(pdReader.getPixelDataArray(), false, ds, out, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); pdWriter.writePixelData(); out.flush(); out.close(); System.out.println("done!"); } | 15,032 |
0 | public static void logout4www() throws NetworkException { HttpClient client = HttpUtil.newInstance(); HttpGet get = new HttpGet(HttpUtil.KAIXIN_WWW_LOGOUT_URL); HttpUtil.setHeader(get); try { HttpResponse response = client.execute(get); if (response != null && response.getEntity() != null) { HTTPUtil.consume(response.getEntity()); } } catch (Exception e) { e.printStackTrace(); throw new NetworkException(e); } } | public String getNextObjectId() throws SQLException { long nextserial = 1; String s0 = "lock table serials in exclusive mode"; String s1 = "SELECT nextserial FROM serials WHERE tablename = 'SERVER_OIDS'"; String s2; try { Statement stmt = dbconnect.connection.createStatement(); stmt.executeUpdate(s0); ResultSet rs = stmt.executeQuery(s1); if (!rs.next()) { s2 = "insert into serials (tablename,nextserial) values ('SERVER_OIDS', " + (nextserial) + ")"; } else { nextserial = rs.getLong(1) + 1; s2 = "update serials set nextserial=" + (nextserial) + " where tablename='SERVER_OIDS'"; } stmt.executeUpdate(s2); dbconnect.connection.commit(); rs.close(); stmt.close(); return "" + nextserial; } catch (SQLException e) { dbconnect.connection.rollback(); throw e; } } | 15,033 |
1 | public static void copyFile(File sourceFile, File targetFile) throws IOException { if (sourceFile == null || targetFile == null) { throw new NullPointerException("Source file and target file must not be null"); } File directory = targetFile.getParentFile(); if (!directory.exists() && !directory.mkdirs()) { throw new IOException("Could not create directory '" + directory + "'"); } InputStream inputStream = null; OutputStream outputStream = null; try { inputStream = new BufferedInputStream(new FileInputStream(sourceFile)); outputStream = new BufferedOutputStream(new FileOutputStream(targetFile)); try { byte[] buffer = new byte[32768]; for (int readBytes = inputStream.read(buffer); readBytes > 0; readBytes = inputStream.read(buffer)) { outputStream.write(buffer, 0, readBytes); } } catch (IOException ex) { targetFile.delete(); throw ex; } } finally { if (inputStream != null) { try { inputStream.close(); } catch (IOException ex) { } } if (outputStream != null) { try { outputStream.close(); } catch (IOException ex) { } } } } | public void convert(File src, File dest) throws IOException { InputStream in = new BufferedInputStream(new FileInputStream(src)); DcmParser p = pfact.newDcmParser(in); Dataset ds = fact.newDataset(); p.setDcmHandler(ds.getDcmHandler()); try { FileFormat format = p.detectFileFormat(); if (format != FileFormat.ACRNEMA_STREAM) { System.out.println("\n" + src + ": not an ACRNEMA stream!"); return; } p.parseDcmFile(format, Tags.PixelData); if (ds.contains(Tags.StudyInstanceUID) || ds.contains(Tags.SeriesInstanceUID) || ds.contains(Tags.SOPInstanceUID) || ds.contains(Tags.SOPClassUID)) { System.out.println("\n" + src + ": contains UIDs!" + " => probable already DICOM - do not convert"); return; } boolean hasPixelData = p.getReadTag() == Tags.PixelData; boolean inflate = hasPixelData && ds.getInt(Tags.BitsAllocated, 0) == 12; int pxlen = p.getReadLength(); if (hasPixelData) { if (inflate) { ds.putUS(Tags.BitsAllocated, 16); pxlen = pxlen * 4 / 3; } if (pxlen != (ds.getInt(Tags.BitsAllocated, 0) >>> 3) * ds.getInt(Tags.Rows, 0) * ds.getInt(Tags.Columns, 0) * ds.getInt(Tags.NumberOfFrames, 1) * ds.getInt(Tags.NumberOfSamples, 1)) { System.out.println("\n" + src + ": mismatch pixel data length!" + " => do not convert"); return; } } ds.putUI(Tags.StudyInstanceUID, uid(studyUID)); ds.putUI(Tags.SeriesInstanceUID, uid(seriesUID)); ds.putUI(Tags.SOPInstanceUID, uid(instUID)); ds.putUI(Tags.SOPClassUID, classUID); if (!ds.contains(Tags.NumberOfSamples)) { ds.putUS(Tags.NumberOfSamples, 1); } if (!ds.contains(Tags.PhotometricInterpretation)) { ds.putCS(Tags.PhotometricInterpretation, "MONOCHROME2"); } if (fmi) { ds.setFileMetaInfo(fact.newFileMetaInfo(ds, UIDs.ImplicitVRLittleEndian)); } OutputStream out = new BufferedOutputStream(new FileOutputStream(dest)); try { } finally { ds.writeFile(out, encodeParam()); if (hasPixelData) { if (!skipGroupLen) { out.write(PXDATA_GROUPLEN); int grlen = pxlen + 8; out.write((byte) grlen); out.write((byte) (grlen >> 8)); out.write((byte) (grlen >> 16)); out.write((byte) (grlen >> 24)); } out.write(PXDATA_TAG); out.write((byte) pxlen); out.write((byte) (pxlen >> 8)); out.write((byte) (pxlen >> 16)); out.write((byte) (pxlen >> 24)); } if (inflate) { int b2, b3; for (; pxlen > 0; pxlen -= 3) { out.write(in.read()); b2 = in.read(); b3 = in.read(); out.write(b2 & 0x0f); out.write(b2 >> 4 | ((b3 & 0x0f) << 4)); out.write(b3 >> 4); } } else { for (; pxlen > 0; --pxlen) { out.write(in.read()); } } out.close(); } System.out.print('.'); } finally { in.close(); } } | 15,034 |
0 | public static void main(final String[] args) { final Runnable startDerby = new Runnable() { public void run() { try { final NetworkServerControl control = new NetworkServerControl(InetAddress.getByName("localhost"), 1527); control.start(new PrintWriter(System.out)); } catch (final Exception ex) { throw new RuntimeException(ex); } } }; new Thread(startDerby).start(); final Runnable startActiveMq = new Runnable() { public void run() { Main.main(new String[] { "start", "xbean:file:active-mq-config.xml" }); } }; new Thread(startActiveMq).start(); final Runnable startMailServer = new Runnable() { public void run() { final SimpleMessageListener listener = new SimpleMessageListener() { public final boolean accept(final String from, final String recipient) { return true; } public final void deliver(final String from, final String recipient, final InputStream data) throws TooMuchDataException, IOException { System.out.println("FROM: " + from); System.out.println("TO: " + recipient); final File tmpDir = new File(System.getProperty("java.io.tmpdir")); final File file = new File(tmpDir, recipient); final FileWriter fw = new FileWriter(file); try { IOUtils.copy(data, fw); } finally { fw.close(); } } }; final SMTPServer smtpServer = new SMTPServer(new SimpleMessageListenerAdapter(listener)); smtpServer.start(); System.out.println("Started SMTP Server"); } }; new Thread(startMailServer).start(); } | private URLConnection openGetConnection(StringBuffer sb) throws IOException, IOException, MalformedURLException { URL url = new URL(m_gatewayAddress + "?" + sb.toString()); URLConnection connection = url.openConnection(); connection.setUseCaches(false); return connection; } | 15,035 |
0 | public void importarHistoricoDoPIB(Andamento pAndamento) throws FileNotFoundException, SQLException, Exception { pAndamento.delimitarIntervaloDeVariacao(0, 49); PIB[] valoresPendentesDoPIB = obterValoresPendentesDoPIB(pAndamento); pAndamento.delimitarIntervaloDeVariacao(50, 100); if (valoresPendentesDoPIB != null && valoresPendentesDoPIB.length > 0) { String sql = "INSERT INTO tmp_TB_PIB(ULTIMO_DIA_DO_MES, PIB_ACUM_12MESES_REAL, PIB_ACUM_12MESES_DOLAR) VALUES(:ULTIMO_DIA_DO_MES, :PIB_ACUM_12MESES_REAL, :PIB_ACUM_12MESES_DOLAR)"; OraclePreparedStatement stmtDestino = (OraclePreparedStatement) conDestino.prepareStatement(sql); stmtDestino.setExecuteBatch(COMANDOS_POR_LOTE); int quantidadeDeRegistrosASeremImportados = valoresPendentesDoPIB.length; try { int quantidadeDeRegistrosImportados = 0; int numeroDoRegistro = 0; final BigDecimal MILHAO = new BigDecimal("1000000"); for (PIB valorPendenteDoPIB : valoresPendentesDoPIB) { ++numeroDoRegistro; stmtDestino.clearParameters(); java.sql.Date vULTIMO_DIA_DO_MES = new java.sql.Date(obterUltimoDiaDoMes(valorPendenteDoPIB.mesEAno).getTime()); BigDecimal vPIB_ACUM_12MESES_REAL = valorPendenteDoPIB.valorDoPIBEmReais.multiply(MILHAO).setScale(0, RoundingMode.DOWN); BigDecimal vPIB_ACUM_12MESES_DOLAR = valorPendenteDoPIB.valorDoPIBEmDolares.multiply(MILHAO).setScale(0, RoundingMode.DOWN); stmtDestino.setDateAtName("ULTIMO_DIA_DO_MES", vULTIMO_DIA_DO_MES); stmtDestino.setBigDecimalAtName("PIB_ACUM_12MESES_REAL", vPIB_ACUM_12MESES_REAL); stmtDestino.setBigDecimalAtName("PIB_ACUM_12MESES_DOLAR", vPIB_ACUM_12MESES_DOLAR); int contagemDasInsercoes = stmtDestino.executeUpdate(); quantidadeDeRegistrosImportados++; double percentualCompleto = (double) quantidadeDeRegistrosImportados / quantidadeDeRegistrosASeremImportados * 100; pAndamento.setPercentualCompleto((int) percentualCompleto); } conDestino.commit(); } catch (Exception ex) { conDestino.rollback(); throw ex; } finally { if (stmtDestino != null && (!stmtDestino.isClosed())) { stmtDestino.close(); } } } pAndamento.setPercentualCompleto(100); } | private void doDissemTest(String what, boolean redirectOK) throws Exception { final int num = 30; System.out.println("Getting " + what + " " + num + " times..."); int i = 0; try { URL url = new URL(BASE_URL + "/get/" + what); for (i = 0; i < num; i++) { HttpURLConnection conn = (HttpURLConnection) url.openConnection(); InputStream in = conn.getInputStream(); in.read(); in.close(); conn.disconnect(); } } catch (Exception e) { fail("Dissemination of " + what + " failed on iter " + i + ": " + e.getMessage()); } } | 15,036 |
1 | private static void loadEmoticons() { emoticons = new Hashtable(); URL url = ChatPanel.class.getResource("/resources/text/emoticon.properties"); BufferedReader br = null; try { br = new BufferedReader(new InputStreamReader(url.openStream())); String line = null; while ((line = br.readLine()) != null) { if (line.trim().length() == 0 || line.charAt(0) == '#') continue; int i0 = line.indexOf('='); if (i0 != -1) { String key = line.substring(0, i0).trim(); String value = line.substring(i0 + 1).trim(); value = StringUtil.replaceString(value, "\\n", "\n"); URL eUrl = ChatPanel.class.getResource("/resources/emoticon/" + value); if (eUrl != null) emoticons.put(key, new ImageIcon(eUrl)); } } } catch (Exception e) { e.printStackTrace(); } finally { if (br != null) { try { br.close(); } catch (Exception e) { } } } } | public static String readURL(String urlStr, boolean debug) { if (debug) System.out.print(" trying: " + urlStr + "\n"); URL url = null; try { url = new URL(urlStr); } catch (java.net.MalformedURLException e) { System.out.print("test failed: using URL: "); System.out.print(e.getMessage()); System.out.print('\n'); return null; } HttpURLConnection huc = null; try { huc = (HttpURLConnection) url.openConnection(); } catch (IOException e) { System.out.print("test failed: using URL: "); System.out.print(e.getMessage()); System.out.print('\n'); return null; } String contentType = huc.getContentType(); if (contentType == null || contentType.indexOf("text/xml") < 0) { System.out.print("*** Warning *** Content-Type not set to text/xml"); System.out.print('\n'); System.out.print(" Content-type: "); System.out.print(contentType); System.out.print('\n'); } InputStream urlStream = null; try { urlStream = huc.getInputStream(); } catch (java.io.IOException e) { System.out.print("test failed: opening URL: "); System.out.print(e.getMessage()); System.out.print('\n'); return null; } BufferedReader in = new BufferedReader(new InputStreamReader(urlStream)); boolean xml = true; String href = null, inputLine = null; StringBuffer content = new StringBuffer(), stylesheet = null; Transformer transformer = null; try { inputLine = in.readLine(); } catch (java.io.IOException e) { System.out.print("test failed: reading first line of response: "); System.out.print(e.getMessage()); System.out.print('\n'); return null; } if (inputLine == null) { System.out.print("test failed: No input read from URL"); System.out.print('\n'); return null; } if (!inputLine.startsWith("<?xml ")) { xml = false; content.append(inputLine); } if (xml) { int offset = inputLine.indexOf('>'); if (offset + 2 < inputLine.length()) { inputLine = inputLine.substring(offset + 1); offset = inputLine.indexOf('<'); if (offset > 0) inputLine = inputLine.substring(offset); } else try { inputLine = in.readLine(); } catch (java.io.IOException e) { System.out.print("test failed: reading response: "); System.out.print(e.getMessage()); System.out.print('\n'); return null; } content.append(inputLine); } try { while ((inputLine = in.readLine()) != null) content.append(inputLine); } catch (java.io.IOException e) { System.out.print("test failed: reading response: "); System.out.print(e.getMessage()); System.out.print('\n'); return null; } String contentStr = content.toString(); if (transformer != null) { StreamSource streamXMLRecord = new StreamSource(new StringReader(contentStr)); StringWriter xmlRecordWriter = new StringWriter(); try { transformer.transform(streamXMLRecord, new StreamResult(xmlRecordWriter)); System.out.print(" successfully applied stylesheet '"); System.out.print(href); System.out.print("'"); System.out.print('\n'); } catch (javax.xml.transform.TransformerException e) { System.out.print("unable to apply stylesheet '"); System.out.print(href); System.out.print("'to response: "); System.out.print(e.getMessage()); System.out.print('\n'); e.printStackTrace(); } } return contentStr; } | 15,037 |
0 | public static void copyFile(File src, File dst) throws IOException { FileChannel sourceChannel = new FileInputStream(src).getChannel(); FileChannel destinationChannel = new FileOutputStream(dst).getChannel(); sourceChannel.transferTo(0, sourceChannel.size(), destinationChannel); sourceChannel.close(); destinationChannel.close(); } | public String report() { if (true) return "-"; StringBuffer parameter = new StringBuffer("?"); if (getRecord_ID() == 0) return "ID=0"; if (getRecord_ID() == 1) { parameter.append("ISSUE="); HashMap htOut = get_HashMap(); try { ByteArrayOutputStream bOut = new ByteArrayOutputStream(); ObjectOutput oOut = new ObjectOutputStream(bOut); oOut.writeObject(htOut); oOut.flush(); String hexString = Secure.convertToHexString(bOut.toByteArray()); parameter.append(hexString); } catch (Exception e) { log.severe(e.getLocalizedMessage()); return "New-" + e.getLocalizedMessage(); } } else { try { parameter.append("RECORDID=").append(getRecord_ID()); parameter.append("&DBADDRESS=").append(URLEncoder.encode(getDBAddress(), "UTF-8")); parameter.append("&COMMENTS=").append(URLEncoder.encode(getComments(), "UTF-8")); } catch (Exception e) { log.severe(e.getLocalizedMessage()); return "Update-" + e.getLocalizedMessage(); } } InputStreamReader in = null; String target = "http://dev1/wstore/issueReportServlet"; try { StringBuffer urlString = new StringBuffer(target).append(parameter); URL url = new URL(urlString.toString()); URLConnection uc = url.openConnection(); in = new InputStreamReader(uc.getInputStream()); } catch (Exception e) { String msg = "Cannot connect to http://" + target; if (e instanceof FileNotFoundException || e instanceof ConnectException) msg += "\nServer temporarily down - Please try again later"; else { msg += "\nCheck connection - " + e.getLocalizedMessage(); log.log(Level.FINE, msg); } return msg; } return readResponse(in); } | 15,038 |
1 | public static void copyAFile(final String entree, final String sortie) { FileChannel in = null; FileChannel out = null; try { in = new FileInputStream(entree).getChannel(); out = new FileOutputStream(sortie).getChannel(); in.transferTo(0, in.size(), out); } catch (Exception e) { e.printStackTrace(); } finally { if (in != null) { try { in.close(); } catch (IOException e) { e.printStackTrace(); } } if (out != null) { try { out.close(); } catch (IOException e) { e.printStackTrace(); } } } } | @Override public void sendContent(OutputStream out, Range range, Map<String, String> params, String contentType) throws IOException, NotAuthorizedException, BadRequestException, NotFoundException { try { resolveFileAttachment(); } catch (NoFileByTheIdException e) { throw new NotFoundException(e.getLocalizedMessage()); } DefinableEntity owningEntity = fa.getOwner().getEntity(); InputStream in = getFileModule().readFile(owningEntity.getParentBinder(), owningEntity, fa); try { if (range != null) { if (logger.isDebugEnabled()) logger.debug("sendContent: ranged content: " + toString(fa)); PartialGetHelper.writeRange(in, range, out); } else { if (logger.isDebugEnabled()) logger.debug("sendContent: send whole file " + toString(fa)); IOUtils.copy(in, out); } out.flush(); } catch (ReadingException e) { throw new IOException(e); } catch (WritingException e) { throw new IOException(e); } finally { IOUtils.closeQuietly(in); } } | 15,039 |
0 | public static Reader createReader(TreeLogger logger, URL url) throws UnableToCompleteException { try { return new InputStreamReader(url.openStream()); } catch (IOException e) { logger.log(TreeLogger.ERROR, "Unable to open resource: " + url, e); throw new UnableToCompleteException(); } } | public void createZip(String baseDir, String objFileName) throws Exception { logger.info("createZip: [ " + baseDir + "] [" + objFileName + "]"); baseDir = baseDir + "/" + timesmpt; File folderObject = new File(baseDir); if (folderObject.exists()) { List<?> fileList = getSubFiles(new File(baseDir)); ZipOutputStream zos = new ZipOutputStream(new FileOutputStream(objFileName)); ZipEntry ze = null; byte[] buf = new byte[1024]; int readLen = 0; for (int i = 0; i < fileList.size(); i++) { File f = (File) fileList.get(i); ze = new ZipEntry(getAbsFileName(baseDir, f)); ze.setSize(f.length()); ze.setTime(f.lastModified()); zos.putNextEntry(ze); InputStream is = new BufferedInputStream(new FileInputStream(f)); while ((readLen = is.read(buf, 0, 1024)) != -1) { zos.write(buf, 0, readLen); } is.close(); } zos.close(); } else { throw new Exception("this folder isnot exist!"); } } | 15,040 |
0 | public void salva(UploadedFile imagem, Usuario usuario) { File destino; if (usuario.getId() == null) { destino = new File(pastaImagens, usuario.hashCode() + ".jpg"); } else { destino = new File(pastaImagens, usuario.getId() + ".jpg"); } try { IOUtils.copyLarge(imagem.getFile(), new FileOutputStream(destino)); } catch (Exception e) { throw new RuntimeException("Erro ao copiar imagem", e); } redimensionar(destino.getPath(), destino.getPath(), "jpg", 110, 110); } | @TestTargetNew(level = TestLevel.COMPLETE, notes = "", method = "getJarFileURL", args = { }) public void test_getJarFileURL() throws Exception { URL u = createContent("lf.jar", "plus.bmp"); URL fileURL = new URL(u.getPath().substring(0, u.getPath().indexOf("!"))); juc = (JarURLConnection) u.openConnection(); assertTrue("Returned incorrect file URL", juc.getJarFileURL().equals(fileURL)); URL url = new URL("jar:file:///bar.jar!/foo.jar!/Bugs/HelloWorld.class"); assertEquals("file:/bar.jar", ((JarURLConnection) url.openConnection()).getJarFileURL().toString()); } | 15,041 |
0 | @Test public void shouldSetAlias() throws Exception { HttpResponse response = executePost("/yum/alias/snapshots/testAlias", new StringEntity(VERSION_1)); assertEquals(VERSION_1, EntityUtils.toString(response.getEntity())); assertEquals(VERSION_1, executeGet("/yum/alias/snapshots/testAlias")); response = executePost("/yum/alias/snapshots/testAlias", new StringEntity(VERSION_2)); assertEquals(VERSION_2, EntityUtils.toString(response.getEntity())); assertEquals(VERSION_2, executeGet("/yum/alias/snapshots/testAlias")); } | public Login authenticateClient() { Object o; String user, password; Vector<Login> clientLogins = ClientLoginsTableModel.getClientLogins(); Login login = null; try { socket.setSoTimeout(25000); objectOut.writeObject("JFRITZ SERVER 1.1"); objectOut.flush(); o = objectIn.readObject(); if (o instanceof String) { user = (String) o; objectOut.flush(); for (Login l : clientLogins) { if (l.getUser().equals(user)) { login = l; break; } } if (login != null) { MessageDigest md = MessageDigest.getInstance("MD5"); md.update(login.getPassword().getBytes()); DESKeySpec desKeySpec = new DESKeySpec(md.digest()); SecretKeyFactory keyFactory = SecretKeyFactory.getInstance("DES"); SecretKey secretKey = keyFactory.generateSecret(desKeySpec); Cipher desCipher = Cipher.getInstance("DES/ECB/PKCS5Padding"); desCipher.init(Cipher.ENCRYPT_MODE, secretKey); byte[] dataKeySeed = new byte[32]; Random random = new Random(); random.nextBytes(dataKeySeed); md.reset(); md.update(dataKeySeed); dataKeySeed = md.digest(); SealedObject dataKeySeedSealed; dataKeySeedSealed = new SealedObject(dataKeySeed, desCipher); objectOut.writeObject(dataKeySeedSealed); objectOut.flush(); desKeySpec = new DESKeySpec(dataKeySeed); secretKey = keyFactory.generateSecret(desKeySpec); inCipher = Cipher.getInstance("DES/ECB/PKCS5Padding"); outCipher = Cipher.getInstance("DES/ECB/PKCS5Padding"); inCipher.init(Cipher.DECRYPT_MODE, secretKey); outCipher.init(Cipher.ENCRYPT_MODE, secretKey); SealedObject sealedObject = (SealedObject) objectIn.readObject(); o = sealedObject.getObject(inCipher); if (o instanceof String) { String response = (String) o; if (response.equals("OK")) { SealedObject ok_sealed = new SealedObject("OK", outCipher); objectOut.writeObject(ok_sealed); return login; } else { Debug.netMsg("Client sent false response to challenge!"); } } else { Debug.netMsg("Client sent false object as response to challenge!"); } } else { Debug.netMsg("client sent unkown username: " + user); } } } catch (IllegalBlockSizeException e) { Debug.netMsg("Wrong blocksize for sealed object!"); Debug.error(e.toString()); e.printStackTrace(); } catch (ClassNotFoundException e) { Debug.netMsg("received unrecognized object from client!"); Debug.error(e.toString()); e.printStackTrace(); } catch (NoSuchAlgorithmException e) { Debug.netMsg("MD5 Algorithm not present in this JVM!"); Debug.error(e.toString()); e.printStackTrace(); } catch (InvalidKeySpecException e) { Debug.netMsg("Error generating cipher, problems with key spec?"); Debug.error(e.toString()); e.printStackTrace(); } catch (InvalidKeyException e) { Debug.netMsg("Error genertating cipher, problems with key?"); Debug.error(e.toString()); e.printStackTrace(); } catch (NoSuchPaddingException e) { Debug.netMsg("Error generating cipher, problems with padding?"); Debug.error(e.toString()); e.printStackTrace(); } catch (IOException e) { Debug.netMsg("Error authenticating client!"); Debug.error(e.toString()); e.printStackTrace(); } catch (BadPaddingException e) { Debug.netMsg("Bad padding exception!"); Debug.error(e.toString()); e.printStackTrace(); } return null; } | 15,042 |
1 | public static void copyFile(File sourceFile, File destFile) throws IOException { if (!destFile.exists()) { destFile.createNewFile(); } FileChannel source = null; FileChannel destination = null; try { source = new FileInputStream(sourceFile).getChannel(); destination = new FileOutputStream(destFile).getChannel(); destination.transferFrom(source, 0, source.size()); } finally { if (source != null) { source.close(); } if (destination != null) { destination.close(); } } } | public static void rewrite(String[] args) throws IOException, CodeCheckException { ClassWriter writer = new ClassWriter(); writer.readClass(new FileInputStream(args[0])); for (Iterator i = writer.getMethods().iterator(); i.hasNext(); ) { MethodInfo method = (MethodInfo) i.next(); CodeAttribute attribute = method.getCodeAttribute(); int origStack = attribute.getMaxStack(); System.out.print(method.getName()); attribute.codeCheck(); System.out.println(" " + origStack + " " + attribute.getMaxStack()); } BufferedOutputStream outStream = new BufferedOutputStream(new FileOutputStream(args[1])); writer.writeClass(outStream); outStream.close(); } | 15,043 |
0 | void extractEnsemblCoords(String geneviewLink) { try { URL connectURL = new URL(geneviewLink); InputStream urlStream = connectURL.openStream(); BufferedReader reader = new BufferedReader(new InputStreamReader(urlStream)); String line; while ((line = reader.readLine()) != null) { if (line.indexOf("View gene in genomic location") != -1) { line = line.substring(line.indexOf("contigview?")); String chr, start, stop; chr = line.substring(line.indexOf("chr=") + 4); chr = chr.substring(0, chr.indexOf("&")); start = line.substring(line.indexOf("vc_start=") + 9); start = start.substring(0, start.indexOf("&")); stop = line.substring(line.indexOf("vc_end=") + 7); stop = stop.substring(0, stop.indexOf("\"")); String selString; for (int s = 0; s < selPanel.chrField.getModel().getSize(); s++) { if (chr.equals(selPanel.chrField.getModel().getElementAt(s))) { selPanel.chrField.setSelectedIndex(s); break; } } selPanel.setStart(Integer.parseInt(start)); selPanel.setStop(Integer.parseInt(stop)); selPanel.refreshButton.doClick(); break; } } } catch (Exception e) { System.out.println("Problems retrieving Geneview from Ensembl"); e.printStackTrace(); } } | public Boolean compress(String sSourceDir, ArrayList<String> aFiles, String sDestinationFilename) { logger.debug("compress(%s, %s, %s)", sSourceDir, aFiles, sDestinationFilename); BufferedInputStream oOrigin = null; FileOutputStream oDestination; ZipOutputStream oOutput = null; Iterator<String> oIterator; byte[] aData; try { oDestination = new FileOutputStream(sDestinationFilename); oOutput = new ZipOutputStream(new BufferedOutputStream(oDestination)); aData = new byte[BUFFER_SIZE]; oIterator = aFiles.iterator(); while (oIterator.hasNext()) { try { String sFilename = (String) oIterator.next(); FileInputStream fisInput = new FileInputStream(sSourceDir + File.separator + sFilename); oOrigin = new BufferedInputStream(fisInput, BUFFER_SIZE); ZipEntry oEntry = new ZipEntry(sFilename.replace('\\', '/')); oOutput.putNextEntry(oEntry); int iCount; while ((iCount = oOrigin.read(aData, 0, BUFFER_SIZE)) != -1) oOutput.write(aData, 0, iCount); } finally { StreamHelper.close(oOrigin); } } } catch (Exception oException) { logger.error(oException.getMessage(), oException); return false; } finally { StreamHelper.close(oOutput); } return true; } | 15,044 |
0 | public int[] sort() { boolean t = true; int temp = 0; int[] mas = new int[N]; Random rand = new Random(); for (int i = 0; i < N; i++) { mas[i] = rand.nextInt(10) + 1; } while (t) { t = false; for (int i = 0; i < mas.length - 1; i++) { if (mas[i] > mas[i + 1]) { temp = mas[i]; mas[i] = mas[i + 1]; mas[i + 1] = temp; t = true; } } } return mas; } | public static boolean encodeFileToFile(String infile, String outfile) { boolean success = false; java.io.InputStream in = null; java.io.OutputStream out = null; try { in = new Base64.InputStream(new java.io.BufferedInputStream(new java.io.FileInputStream(infile)), Base64.ENCODE); out = new java.io.BufferedOutputStream(new java.io.FileOutputStream(outfile)); byte[] buffer = new byte[65536]; int read = -1; while ((read = in.read(buffer)) >= 0) { out.write(buffer, 0, read); } success = true; } catch (java.io.IOException exc) { exc.printStackTrace(); } finally { try { in.close(); } catch (Exception exc) { } try { out.close(); } catch (Exception exc) { } } return success; } | 15,045 |
0 | public static void get_PK_data() { try { FileWriter file_writer = new FileWriter("xml_data/PK_data_dump.xml"); BufferedWriter file_buffered_writer = new BufferedWriter(file_writer); URL fdt = new URL("http://opendata.5t.torino.it/get_pk"); URLConnection url_connection = fdt.openConnection(); BufferedReader in = new BufferedReader(new InputStreamReader(url_connection.getInputStream())); String input_line; int num_lines = 0; while ((input_line = in.readLine()) != null) { file_buffered_writer.write(input_line + "\n"); num_lines++; } System.out.println("Parking :: Writed " + num_lines + " lines."); in.close(); } catch (Exception e) { System.err.println("Error: " + e.getMessage()); } } | private void copyFileToDir(MyFile file, MyFile to, wlPanel panel) throws IOException { Utilities.print("started copying " + file.getAbsolutePath() + "\n"); FileOutputStream fos = new FileOutputStream(new File(to.getAbsolutePath())); FileChannel foc = fos.getChannel(); FileInputStream fis = new FileInputStream(new File(file.getAbsolutePath())); FileChannel fic = fis.getChannel(); Date d1 = new Date(); long amount = foc.transferFrom(fic, rest, fic.size() - rest); fic.close(); foc.force(false); foc.close(); Date d2 = new Date(); long time = d2.getTime() - d1.getTime(); double secs = time / 1000.0; double rate = amount / secs; frame.getStatusArea().append(secs + "s " + "amount: " + Utilities.humanReadable(amount) + " rate: " + Utilities.humanReadable(rate) + "/s\n", "black"); panel.updateView(); } | 15,046 |
0 | private void fetchAvailable(ProgressObserver po) { if (po == null) throw new IllegalArgumentException("the progress observer can't be null"); if (availables == null) availables = new ArrayList<Dictionary>(); else availables.clear(); if (installed == null) initInstalled(); File home = SpellCheckPlugin.getHomeDir(jEdit.getActiveView()); File target = new File(home, "available.lst"); try { boolean skipDownload = false; if (target.exists()) { long modifiedDate = target.lastModified(); Calendar c = Calendar.getInstance(); c.setTimeInMillis(modifiedDate); Calendar yesterday = Calendar.getInstance(); yesterday.add(Calendar.HOUR, -1); skipDownload = yesterday.before(c); } String enc = null; if (!skipDownload) { URL available_url = new URL(jEdit.getProperty(OOO_DICTS_PROP) + "available.lst"); URLConnection connect = available_url.openConnection(); connect.connect(); InputStream is = connect.getInputStream(); po.setMaximum(connect.getContentLength()); OutputStream os = new FileOutputStream(target); boolean copied = IOUtilities.copyStream(po, is, os, true); if (!copied) { Log.log(Log.ERROR, HunspellDictsManager.class, "Unable to download " + available_url.toString()); GUIUtilities.error(null, "spell-check-hunspell-error-fetch", new String[] { "Unable to download file " + available_url.toString() }); availables = null; if (target.exists()) target.delete(); return; } IOUtilities.closeQuietly(os); enc = connect.getContentEncoding(); } FileInputStream fis = new FileInputStream(target); Reader r; if (enc != null) { try { r = new InputStreamReader(fis, enc); } catch (UnsupportedEncodingException uee) { r = new InputStreamReader(fis, "UTF-8"); } } else { r = new InputStreamReader(fis, "UTF-8"); } BufferedReader br = new BufferedReader(r); for (String line = br.readLine(); line != null; line = br.readLine()) { Dictionary d = parseLine(line); if (d != null) { int ind = installed.indexOf(d); if (ind == -1) { d.installed = false; availables.add(d); } else { Dictionary id = installed.get(ind); if (!skipDownload) { Date lmd = fetchLastModifiedDate(id.archiveName); if (lmd != null) { id.lastModified = lmd; } } } } } IOUtilities.closeQuietly(fis); } catch (IOException ioe) { if (ioe instanceof UnknownHostException) { GUIUtilities.error(null, "spell-check-hunspell-error-unknownhost", new String[] { ioe.getMessage() }); } else { GUIUtilities.error(null, "spell-check-hunspell-error-fetch", new String[] { ioe.getMessage() }); } ioe.printStackTrace(); if (target.exists()) target.delete(); } } | public static boolean copyFile(final File src, final File dst) throws FileNotFoundException { if (src == null || dst == null || src.equals(dst)) { return false; } boolean result = false; if (src.exists()) { if (dst.exists() && !dst.canWrite()) { return false; } final FileInputStream srcStream = new FileInputStream(src); final FileOutputStream dstStream = new FileOutputStream(dst); final FileChannel srcChannel = srcStream.getChannel(); final FileChannel dstChannel = dstStream.getChannel(); FileLock dstLock = null; FileLock srcLock = null; try { srcLock = srcChannel.tryLock(0, Long.MAX_VALUE, true); dstLock = dstChannel.tryLock(); if (srcLock != null && dstLock != null) { int maxCount = 64 * 1024 * 1024 - 32 * 1024; long size = srcChannel.size(); long position = 0; while (position < size) { position += srcChannel.transferTo(position, maxCount, dstChannel); } } } catch (IOException ex) { Logger.getLogger(FileUtils.class.getName()).log(Level.SEVERE, null, ex); } finally { if (srcChannel != null) { try { if (srcLock != null) { srcLock.release(); } srcChannel.close(); srcStream.close(); } catch (IOException ex) { Logger.getLogger(FileUtils.class.getName()).log(Level.SEVERE, null, ex); } } if (dstChannel != null) { try { if (dstLock != null) { dstLock.release(); } dstChannel.close(); dstStream.close(); result = true; } catch (IOException ex) { Logger.getLogger(FileUtils.class.getName()).log(Level.SEVERE, null, ex); } } } } return result; } | 15,047 |
0 | public static boolean predictDataSet(String completePath, String Type, String predictionOutputFileName, String slopeOneDataFolderName) { try { if (Type.equalsIgnoreCase("Qualifying")) { File inputFile = new File(completePath + fSep + "SmartGRAPE" + fSep + "CompleteQualifyingDataInByteFormat.txt"); FileChannel inC = new FileInputStream(inputFile).getChannel(); int filesize = (int) inC.size(); TShortObjectHashMap qualMap = new TShortObjectHashMap(17770, 1); ByteBuffer qualmappedfile = inC.map(FileChannel.MapMode.READ_ONLY, 0, filesize); while (qualmappedfile.hasRemaining()) { short movie = qualmappedfile.getShort(); int customer = qualmappedfile.getInt(); if (qualMap.containsKey(movie)) { TIntArrayList arr = (TIntArrayList) qualMap.get(movie); arr.add(customer); qualMap.put(movie, arr); } else { TIntArrayList arr = new TIntArrayList(); arr.add(customer); qualMap.put(movie, arr); } } System.out.println("Populated qualifying hashmap"); File outFile = new File(completePath + fSep + "SmartGRAPE" + fSep + predictionOutputFileName); FileChannel outC = new FileOutputStream(outFile).getChannel(); ByteBuffer buf; TShortObjectHashMap movieDiffStats; double finalPrediction; short[] movies = qualMap.keys(); Arrays.sort(movies); for (int i = 0; i < movies.length; i++) { short movieToProcess = movies[i]; movieDiffStats = loadMovieDiffStats(completePath, movieToProcess, slopeOneDataFolderName); System.out.println(movieDiffStats.size()); TIntArrayList customersToProcess = (TIntArrayList) qualMap.get(movieToProcess); for (int j = 0; j < customersToProcess.size(); j++) { int customerToProcess = customersToProcess.getQuick(j); finalPrediction = predictSlopeOneRating(customerToProcess, movieDiffStats); if (finalPrediction == finalPrediction) { if (finalPrediction < 1.0) finalPrediction = 1.0; else if (finalPrediction > 5.0) finalPrediction = 5.0; } else finalPrediction = GetAveragePrediction(movieToProcess); buf = ByteBuffer.allocate(10); buf.putShort(movieToProcess); buf.putInt(customerToProcess); buf.putFloat(new Double(finalPrediction).floatValue()); buf.flip(); outC.write(buf); } } outC.close(); return true; } else if (Type.equalsIgnoreCase("Probe")) { File inputFile = new File(completePath + fSep + "SmartGRAPE" + fSep + "CompleteProbeDataInByteFormat.txt"); FileChannel inC = new FileInputStream(inputFile).getChannel(); int filesize = (int) inC.size(); TShortObjectHashMap probeMap = new TShortObjectHashMap(17770, 1); ByteBuffer probemappedfile = inC.map(FileChannel.MapMode.READ_ONLY, 0, filesize); while (probemappedfile.hasRemaining()) { short movie = probemappedfile.getShort(); int customer = probemappedfile.getInt(); byte rating = probemappedfile.get(); if (probeMap.containsKey(movie)) { TIntByteHashMap actualRatings = (TIntByteHashMap) probeMap.get(movie); actualRatings.put(customer, rating); probeMap.put(movie, actualRatings); } else { TIntByteHashMap actualRatings = new TIntByteHashMap(); actualRatings.put(customer, rating); probeMap.put(movie, actualRatings); } } System.out.println("Populated probe hashmap"); File outFile = new File(completePath + fSep + "SmartGRAPE" + fSep + predictionOutputFileName); FileChannel outC = new FileOutputStream(outFile).getChannel(); ByteBuffer buf; double finalPrediction; TShortObjectHashMap movieDiffStats; short[] movies = probeMap.keys(); Arrays.sort(movies); for (int i = 0; i < movies.length; i++) { short movieToProcess = movies[i]; movieDiffStats = loadMovieDiffStats(completePath, movieToProcess, slopeOneDataFolderName); TIntByteHashMap custRatingsToProcess = (TIntByteHashMap) probeMap.get(movieToProcess); TIntArrayList customersToProcess = new TIntArrayList(custRatingsToProcess.keys()); for (int j = 0; j < customersToProcess.size(); j++) { int customerToProcess = customersToProcess.getQuick(j); byte rating = custRatingsToProcess.get(customerToProcess); finalPrediction = predictSlopeOneRating(customerToProcess, movieDiffStats); if (finalPrediction == finalPrediction) { if (finalPrediction < 1.0) finalPrediction = 1.0; else if (finalPrediction > 5.0) finalPrediction = 5.0; } else finalPrediction = GetAveragePrediction(movieToProcess); buf = ByteBuffer.allocate(11); buf.putShort(movieToProcess); buf.putInt(customerToProcess); buf.put(rating); buf.putFloat(new Double(finalPrediction).floatValue()); buf.flip(); outC.write(buf); } } outC.close(); return true; } else return false; } catch (Exception e) { e.printStackTrace(); return false; } } | public Service findServiceFor(final int serviceID) throws JAXBException, IOException, BadResponseException { final String USER_AGENT = "SBSIVisual (CSBE, University of Edinburgh)"; String urlToConnectTo = "http://www.biocatalogue.org/services/" + serviceID; URL url = new URL(urlToConnectTo); HttpURLConnection conn = (HttpURLConnection) url.openConnection(); conn.setRequestProperty("User-Agent", USER_AGENT); conn.setRequestProperty("Accept", "application/xml"); int iResponseCode = conn.getResponseCode(); InputStream serverResponse = null; switch(iResponseCode) { case HttpURLConnection.HTTP_OK: serverResponse = conn.getInputStream(); break; case HttpURLConnection.HTTP_BAD_REQUEST: throw new BadResponseException("Received BadResponse from server:" + HttpURLConnection.HTTP_BAD_REQUEST); } Service service = new ResponseParser<Service>().getObjectFor(serverResponse, Service.class); return service; } | 15,048 |
0 | @RequestMapping(value = "/verdocumentoFisico.html", method = RequestMethod.GET) public String editFile(ModelMap model, @RequestParam("id") int idAnexo) { Anexo anexo = anexoService.selectById(idAnexo); model.addAttribute("path", anexo.getAnexoCaminho()); try { InputStream is = new FileInputStream(new File(config.baseDir + "/arquivos_upload_direto/" + anexo.getAnexoCaminho())); FileOutputStream fos = new FileOutputStream(new File(config.baseDir + "/temp/" + anexo.getAnexoCaminho())); IOUtils.copy(is, fos); Runtime.getRuntime().exec("chmod 777 " + config.tempDir + anexo.getAnexoCaminho()); } catch (FileNotFoundException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } return "verdocumentoFisico"; } | public HashMap parseFile(File newfile) throws IOException { String s; String[] tokens; int nvalues = 0; double num1, num2, num3; boolean baddata = false; URL url = newfile.toURL(); InputStream is = url.openStream(); InputStreamReader isr = new InputStreamReader(is); BufferedReader br = new BufferedReader(isr); HashMap data = new HashMap(); while ((s = br.readLine()) != null) { tokens = s.split("\\s+"); nvalues = tokens.length; if (nvalues == 2) { data.put(new String(tokens[0]), new Double(Double.parseDouble(tokens[1]))); } else { System.out.println("Sorry, trouble reading reference file."); } } return data; } | 15,049 |
0 | protected int authenticate(long companyId, String login, String password, String authType, Map headerMap, Map parameterMap) throws PortalException, SystemException { login = login.trim().toLowerCase(); long userId = GetterUtil.getLong(login); if (authType.equals(CompanyImpl.AUTH_TYPE_EA)) { if (!Validator.isEmailAddress(login)) { throw new UserEmailAddressException(); } } else if (authType.equals(CompanyImpl.AUTH_TYPE_SN)) { if (Validator.isNull(login)) { throw new UserScreenNameException(); } } else if (authType.equals(CompanyImpl.AUTH_TYPE_ID)) { if (Validator.isNull(login)) { throw new UserIdException(); } } if (Validator.isNull(password)) { throw new UserPasswordException(UserPasswordException.PASSWORD_INVALID); } int authResult = Authenticator.FAILURE; String[] authPipelinePre = PropsUtil.getArray(PropsUtil.AUTH_PIPELINE_PRE); if (authType.equals(CompanyImpl.AUTH_TYPE_EA)) { authResult = AuthPipeline.authenticateByEmailAddress(authPipelinePre, companyId, login, password, headerMap, parameterMap); } else if (authType.equals(CompanyImpl.AUTH_TYPE_SN)) { authResult = AuthPipeline.authenticateByScreenName(authPipelinePre, companyId, login, password, headerMap, parameterMap); } else if (authType.equals(CompanyImpl.AUTH_TYPE_ID)) { authResult = AuthPipeline.authenticateByUserId(authPipelinePre, companyId, userId, password, headerMap, parameterMap); } User user = null; try { if (authType.equals(CompanyImpl.AUTH_TYPE_EA)) { user = UserUtil.findByC_EA(companyId, login); } else if (authType.equals(CompanyImpl.AUTH_TYPE_SN)) { user = UserUtil.findByC_SN(companyId, login); } else if (authType.equals(CompanyImpl.AUTH_TYPE_ID)) { user = UserUtil.findByC_U(companyId, GetterUtil.getLong(login)); } } catch (NoSuchUserException nsue) { return Authenticator.DNE; } if (user.isDefaultUser()) { _log.error("The default user should never be allowed to authenticate"); return Authenticator.DNE; } if (!user.isPasswordEncrypted()) { user.setPassword(PwdEncryptor.encrypt(user.getPassword())); user.setPasswordEncrypted(true); UserUtil.update(user); } checkLockout(user); checkPasswordExpired(user); if (authResult == Authenticator.SUCCESS) { if (GetterUtil.getBoolean(PropsUtil.get(PropsUtil.AUTH_PIPELINE_ENABLE_LIFERAY_CHECK))) { String encPwd = PwdEncryptor.encrypt(password, user.getPassword()); if (user.getPassword().equals(encPwd)) { authResult = Authenticator.SUCCESS; } else if (GetterUtil.getBoolean(PropsUtil.get(PropsUtil.AUTH_MAC_ALLOW))) { try { MessageDigest digester = MessageDigest.getInstance(PropsUtil.get(PropsUtil.AUTH_MAC_ALGORITHM)); digester.update(login.getBytes("UTF8")); String shardKey = PropsUtil.get(PropsUtil.AUTH_MAC_SHARED_KEY); encPwd = Base64.encode(digester.digest(shardKey.getBytes("UTF8"))); if (password.equals(encPwd)) { authResult = Authenticator.SUCCESS; } else { authResult = Authenticator.FAILURE; } } catch (NoSuchAlgorithmException nsae) { throw new SystemException(nsae); } catch (UnsupportedEncodingException uee) { throw new SystemException(uee); } } else { authResult = Authenticator.FAILURE; } } } if (authResult == Authenticator.SUCCESS) { String[] authPipelinePost = PropsUtil.getArray(PropsUtil.AUTH_PIPELINE_POST); if (authType.equals(CompanyImpl.AUTH_TYPE_EA)) { authResult = AuthPipeline.authenticateByEmailAddress(authPipelinePost, companyId, login, password, headerMap, parameterMap); } else if (authType.equals(CompanyImpl.AUTH_TYPE_SN)) { authResult = AuthPipeline.authenticateByScreenName(authPipelinePost, companyId, login, password, headerMap, parameterMap); } else if (authType.equals(CompanyImpl.AUTH_TYPE_ID)) { authResult = AuthPipeline.authenticateByUserId(authPipelinePost, companyId, userId, password, headerMap, parameterMap); } } if (authResult == Authenticator.FAILURE) { try { String[] authFailure = PropsUtil.getArray(PropsUtil.AUTH_FAILURE); if (authType.equals(CompanyImpl.AUTH_TYPE_EA)) { AuthPipeline.onFailureByEmailAddress(authFailure, companyId, login, headerMap, parameterMap); } else if (authType.equals(CompanyImpl.AUTH_TYPE_SN)) { AuthPipeline.onFailureByScreenName(authFailure, companyId, login, headerMap, parameterMap); } else if (authType.equals(CompanyImpl.AUTH_TYPE_ID)) { AuthPipeline.onFailureByUserId(authFailure, companyId, userId, headerMap, parameterMap); } if (!PortalLDAPUtil.isPasswordPolicyEnabled(user.getCompanyId())) { PasswordPolicy passwordPolicy = user.getPasswordPolicy(); int failedLoginAttempts = user.getFailedLoginAttempts(); int maxFailures = passwordPolicy.getMaxFailure(); if ((failedLoginAttempts >= maxFailures) && (maxFailures != 0)) { String[] authMaxFailures = PropsUtil.getArray(PropsUtil.AUTH_MAX_FAILURES); if (authType.equals(CompanyImpl.AUTH_TYPE_EA)) { AuthPipeline.onMaxFailuresByEmailAddress(authMaxFailures, companyId, login, headerMap, parameterMap); } else if (authType.equals(CompanyImpl.AUTH_TYPE_SN)) { AuthPipeline.onMaxFailuresByScreenName(authMaxFailures, companyId, login, headerMap, parameterMap); } else if (authType.equals(CompanyImpl.AUTH_TYPE_ID)) { AuthPipeline.onMaxFailuresByUserId(authMaxFailures, companyId, userId, headerMap, parameterMap); } } } } catch (Exception e) { _log.error(e, e); } } return authResult; } | public void setPilot(PilotData pilotData) throws UsernameNotValidException { try { if (pilotData.username.trim().equals("") || pilotData.password.trim().equals("")) throw new UsernameNotValidException(1, "Username or password missing"); PreparedStatement psta; if (pilotData.id == 0) { psta = jdbc.prepareStatement("INSERT INTO pilot " + "(name, address1, address2, zip, city, state, country, birthdate, " + "pft_theory, pft, medical, passenger, instructor, loc_language, " + "loc_country, loc_variant, username, password, id) " + "VALUES (?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,nextval('pilot_id_seq'))"); } else { psta = jdbc.prepareStatement("UPDATE pilot SET " + "name = ?, address1 = ?, address2 = ?, " + "zip = ?, city = ?, state = ?, country = ?, birthdate = ?, pft_theory = ?," + "pft = ?, medical = ?, passenger = ?, instructor = ?, loc_language = ?, " + "loc_country = ?, loc_variant = ?, username = ?, password = ? " + "WHERE id = ?"); } psta.setString(1, pilotData.name); psta.setString(2, pilotData.address1); psta.setString(3, pilotData.address2); psta.setString(4, pilotData.zip); psta.setString(5, pilotData.city); psta.setString(6, pilotData.state); psta.setString(7, pilotData.country); if (pilotData.birthdate != null) psta.setLong(8, pilotData.birthdate.getTime()); else psta.setNull(8, java.sql.Types.INTEGER); if (pilotData.pft_theory != null) psta.setLong(9, pilotData.pft_theory.getTime()); else psta.setNull(9, java.sql.Types.INTEGER); if (pilotData.pft != null) psta.setLong(10, pilotData.pft.getTime()); else psta.setNull(10, java.sql.Types.INTEGER); if (pilotData.medical != null) psta.setLong(11, pilotData.medical.getTime()); else psta.setNull(11, java.sql.Types.INTEGER); if (pilotData.passenger) psta.setString(12, "Y"); else psta.setString(12, "N"); if (pilotData.instructor) psta.setString(13, "Y"); else psta.setString(13, "N"); psta.setString(14, pilotData.loc_language); psta.setString(15, pilotData.loc_country); psta.setString(16, pilotData.loc_variant); psta.setString(17, pilotData.username); psta.setString(18, pilotData.password); if (pilotData.id != 0) { psta.setInt(19, pilotData.id); } psta.executeUpdate(); jdbc.commit(); } catch (SQLException sql) { jdbc.rollback(); sql.printStackTrace(); throw new UsernameNotValidException(2, "Username allready exist"); } } | 15,050 |
1 | public JTree createTree() { DefaultMutableTreeNode top = new DefaultMutableTreeNode("Contents"); DefaultMutableTreeNode[] nodeLevels = new DefaultMutableTreeNode[0]; URL url = ResourceManager.getResource("tree.txt"); try { InputStream is = url.openStream(); InputStreamReader isr = new InputStreamReader(is); BufferedReader reader = new BufferedReader(isr); String line = reader.readLine(); int numLevels = 0; if (line != null) { while (line.startsWith("#")) line = reader.readLine(); numLevels = Integer.parseInt(line); line = reader.readLine(); nodeLevels = new DefaultMutableTreeNode[numLevels + 1]; nodeLevels[0] = top; } while (line != null) { if (!line.startsWith("#")) { int level = Integer.parseInt(line.substring(0, 1)); line = line.substring(line.indexOf(",") + 1); String nodeDescription = line.substring(0, line.indexOf(",")); String nodeURL = line.substring(line.indexOf(",") + 1, line.length()); nodeLevels[level] = new DefaultMutableTreeNode(new HelpTopic(nodeDescription, nodeURL)); nodeLevels[level - 1].add(nodeLevels[level]); } line = reader.readLine(); } } catch (IOException e) { showErrorDialog("Unable to read resource tree.txt", true); } catch (NumberFormatException nfe) { showErrorDialog("Invalid format tree.txt", true); } return new JTree(top) { public java.awt.Insets getInsets() { return new java.awt.Insets(5, 5, 5, 5); } }; } | public byte[] downloadAttachmentContent(Attachment issueAttachment) throws IOException { byte[] result = null; URL url = new URL(issueAttachment.getContentURL()); BufferedReader inputReader = null; try { inputReader = new BufferedReader(new InputStreamReader(url.openStream())); StringBuilder contentBuilder = new StringBuilder(); String line; while ((line = inputReader.readLine()) != null) { contentBuilder.append(line); } result = contentBuilder.toString().getBytes(); } finally { if (inputReader != null) { inputReader.close(); } } return result; } | 15,051 |
1 | private void displayDiffResults() throws IOException { File outFile = File.createTempFile("diff", ".htm"); outFile.deleteOnExit(); FileOutputStream outStream = new FileOutputStream(outFile); BufferedWriter out = new BufferedWriter(new OutputStreamWriter(outStream)); out.write("<html><head><title>LOC Differences</title>\n" + SCRIPT + "</head>\n" + "<body bgcolor='#ffffff'>\n" + "<div onMouseOver=\"window.defaultStatus='Metrics'\">\n"); if (addedTable.length() > 0) { out.write("<table border><tr><th>Files Added:</th>" + "<th>Add</th><th>Type</th></tr>"); out.write(addedTable.toString()); out.write("</table><br><br>"); } if (modifiedTable.length() > 0) { out.write("<table border><tr><th>Files Modified:</th>" + "<th>Base</th><th>Del</th><th>Mod</th><th>Add</th>" + "<th>Total</th><th>Type</th></tr>"); out.write(modifiedTable.toString()); out.write("</table><br><br>"); } if (deletedTable.length() > 0) { out.write("<table border><tr><th>Files Deleted:</th>" + "<th>Del</th><th>Type</th></tr>"); out.write(deletedTable.toString()); out.write("</table><br><br>"); } out.write("<table name=METRICS BORDER>\n"); if (modifiedTable.length() > 0 || deletedTable.length() > 0) { out.write("<tr><td>Base: </td><td>"); out.write(Long.toString(base)); out.write("</td></tr>\n<tr><td>Deleted: </td><td>"); out.write(Long.toString(deleted)); out.write("</td></tr>\n<tr><td>Modified: </td><td>"); out.write(Long.toString(modified)); out.write("</td></tr>\n<tr><td>Added: </td><td>"); out.write(Long.toString(added)); out.write("</td></tr>\n<tr><td>New & Changed: </td><td>"); out.write(Long.toString(added + modified)); out.write("</td></tr>\n"); } out.write("<tr><td>Total: </td><td>"); out.write(Long.toString(total)); out.write("</td></tr>\n</table></div>"); redlinesOut.close(); out.flush(); InputStream redlines = new FileInputStream(redlinesTempFile); byte[] buffer = new byte[4096]; int bytesRead; while ((bytesRead = redlines.read(buffer)) != -1) outStream.write(buffer, 0, bytesRead); outStream.write("</BODY></HTML>".getBytes()); outStream.close(); Browser.launch(outFile.toURL().toString()); } | public static void concatFiles(List<File> sourceFiles, File destFile) throws IOException { FileOutputStream outFile = new FileOutputStream(destFile); FileChannel outChannel = outFile.getChannel(); for (File f : sourceFiles) { FileInputStream fis = new FileInputStream(f); FileChannel channel = fis.getChannel(); channel.transferTo(0, channel.size(), outChannel); channel.close(); fis.close(); } outChannel.close(); } | 15,052 |
0 | public RobotList<Location> sort_incr_Location(RobotList<Location> list, String field) { int length = list.size(); Index_value[] enemy_dist = new Index_value[length]; Location cur_loc = this.getLocation(); for (int i = 0; i < length; i++) { enemy_dist[i] = new Index_value(i, distance(cur_loc, list.get(i))); } boolean permut; do { permut = false; for (int i = 0; i < length - 1; i++) { if (enemy_dist[i].value > enemy_dist[i + 1].value) { Index_value a = enemy_dist[i]; enemy_dist[i] = enemy_dist[i + 1]; enemy_dist[i + 1] = a; permut = true; } } } while (permut); RobotList<Location> new_location_list = new RobotList<Location>(Location.class); for (int i = 0; i < length; i++) { new_location_list.addLast(list.get(enemy_dist[i].index)); } return new_location_list; } | public void encryptFile(String originalFile, String encryptedFile, String password) throws Exception { CipherOutputStream out; InputStream in; Cipher cipher; SecretKey key; byte[] byteBuffer; cipher = Cipher.getInstance("DES"); key = new SecretKeySpec(password.getBytes(), "DES"); cipher.init(Cipher.ENCRYPT_MODE, key); in = new FileInputStream(originalFile); out = new CipherOutputStream(new FileOutputStream(encryptedFile), cipher); byteBuffer = new byte[1024]; for (int n; (n = in.read(byteBuffer)) != -1; out.write(byteBuffer, 0, n)) ; in.close(); out.close(); } | 15,053 |
0 | @Override protected boolean sendBytes(byte[] data, int offset, int length) { try { String hex = toHex(data, offset, length); URL url = new URL(this.endpoint, "?raw=" + hex); System.out.println("Connecting to " + url); URLConnection conn = url.openConnection(); conn.connect(); Object content = conn.getContent(); return true; } catch (IOException ex) { LOGGER.warning(ex.getMessage()); return false; } } | private String doMessageDigestAndBase64Encoding(String sequence) throws SeguidException { if (sequence == null) { throw new NullPointerException("You must give a non null sequence"); } try { MessageDigest messageDigest = MessageDigest.getInstance("SHA"); sequence = sequence.trim().toUpperCase(); messageDigest.update(sequence.getBytes()); byte[] digest = messageDigest.digest(); String seguid = Base64.encodeBytes(digest); seguid = seguid.replace("=", ""); if (log.isTraceEnabled()) { log.trace("SEGUID " + seguid); } return seguid; } catch (NoSuchAlgorithmException e) { throw new SeguidException("Exception thrown when calculating Seguid for " + sequence, e.getCause()); } } | 15,054 |
1 | public File getFile(String file) { DirProperties dp; List files = new ArrayList(); for (int i = 0; i < locs.size(); i++) { dp = (DirProperties) locs.get(i); if (dp.isReadable()) { File g = new File(dp.getLocation() + slash() + file); if (g.exists()) files.add(g); } } if (files.size() == 0) { throw new UnsupportedOperationException("at least one DirProperty should get 'read=true'"); } else if (files.size() == 1) { return (File) files.get(0); } else { File fromFile = (File) files.get(files.size() - 2); File toFile = (File) files.get(files.size() - 1); byte reading[] = new byte[2024]; try { FileInputStream stream = new FileInputStream(fromFile); FileOutputStream outStr = new FileOutputStream(toFile); while (stream.read(reading) != -1) { outStr.write(reading); } } catch (FileNotFoundException ex) { getLogger().severe("FileNotFound: while copying from " + fromFile + " to " + toFile); } catch (IOException ex) { getLogger().severe("IOException: while copying from " + fromFile + " to " + toFile); } return toFile; } } | public static ByteBuffer join(ByteBuffer buffer1, ByteBuffer buffer2) { if (buffer2 == null || buffer2.remaining() == 0) return NIOUtils.copy(buffer1); if (buffer1 == null || buffer1.remaining() == 0) return NIOUtils.copy(buffer2); ByteBuffer buffer = ByteBuffer.allocate(buffer1.remaining() + buffer2.remaining()); buffer.put(buffer1); buffer.put(buffer2); buffer.flip(); return buffer; } | 15,055 |
1 | public void testQueryForBinary() throws InvalidNodeTypeDefException, ParseException, Exception { JCRNodeSource source = (JCRNodeSource) resolveSource(BASE_URL + "images/photo.png"); assertNotNull(source); assertEquals(false, source.exists()); OutputStream os = source.getOutputStream(); assertNotNull(os); String content = "foo is a bar"; os.write(content.getBytes()); os.flush(); os.close(); QueryResultSource qResult = (QueryResultSource) resolveSource(BASE_URL + "images?/*[contains(local-name(), 'photo.png')]"); assertNotNull(qResult); Collection results = qResult.getChildren(); assertEquals(1, results.size()); Iterator it = results.iterator(); JCRNodeSource rSrc = (JCRNodeSource) it.next(); InputStream rSrcIn = rSrc.getInputStream(); ByteArrayOutputStream actualOut = new ByteArrayOutputStream(); IOUtils.copy(rSrcIn, actualOut); rSrcIn.close(); assertEquals(content, actualOut.toString()); actualOut.close(); rSrc.delete(); } | private void copyFile(File sourceFile, File destFile) throws IOException { if (!sourceFile.exists()) { return; } if (!destFile.exists()) { destFile.createNewFile(); } FileChannel source = null; FileChannel destination = null; source = new FileInputStream(sourceFile).getChannel(); destination = new FileOutputStream(destFile).getChannel(); if (destination != null && source != null) { destination.transferFrom(source, 0, source.size()); } if (source != null) { source.close(); } if (destination != null) { destination.close(); } } | 15,056 |
1 | public static boolean decodeFileToFile(String infile, String outfile) { boolean success = false; java.io.InputStream in = null; java.io.OutputStream out = null; try { in = new Base64.InputStream(new java.io.BufferedInputStream(new java.io.FileInputStream(infile)), Base64.DECODE); out = new java.io.BufferedOutputStream(new java.io.FileOutputStream(outfile)); byte[] buffer = new byte[65536]; int read = -1; while ((read = in.read(buffer)) >= 0) { out.write(buffer, 0, read); } success = true; } catch (java.io.IOException exc) { exc.printStackTrace(); } finally { try { in.close(); } catch (Exception exc) { } try { out.close(); } catch (Exception exc) { } } return success; } | public static void CreateBackupOfDataFile(String _src, String _dest) { try { File src = new File(_src); File dest = new File(_dest); if (new File(_src).exists()) { BufferedOutputStream out = new BufferedOutputStream(new FileOutputStream(dest)); BufferedInputStream in = new BufferedInputStream(new FileInputStream(src)); byte[] read = new byte[128]; int len = 128; while ((len = in.read(read)) > 0) out.write(read, 0, len); out.flush(); out.close(); in.close(); } } catch (IOException e) { e.printStackTrace(); } } | 15,057 |
0 | private long getNextHighValue() throws Exception { Connection con = null; PreparedStatement psGetHighValue = null; PreparedStatement psUpdateHighValue = null; ResultSet rs = null; long high = -1L; int isolation = -1; DBOperation dbo = factory.createDBOperation(POOL_NAME); try { con = dbo.getConnection(); psGetHighValue = con.prepareStatement(strGetHighValue); psGetHighValue.setString(1, this.name); for (rs = psGetHighValue.executeQuery(); rs.next(); ) { high = rs.getLong("high"); } psUpdateHighValue = con.prepareStatement(strUpdateHighValue); psUpdateHighValue.setLong(1, high + 1L); psUpdateHighValue.setString(2, this.name); psUpdateHighValue.executeUpdate(); } catch (SQLException e) { if (con != null) { con.rollback(); } throw e; } finally { if (psUpdateHighValue != null) { psUpdateHighValue.close(); } close(dbo, psGetHighValue, rs); } return high; } | private void createWikiPages(WikiContext context) throws PluginException { OntologyWikiPageName owpn = new OntologyWikiPageName(omemo.getFormDataAlias().toUpperCase(), omemo.getFormDataVersionDate()); String wikiPageFullFileName = WikiPageName2FullFileName(context, owpn.toString()); String rdfFileNameWithPath = getWorkDir(context) + File.separator + owpn.toFileName(); FileOutputStream fos = null; FileInputStream fis = null; try { fos = new FileOutputStream(wikiPageFullFileName); fis = new FileInputStream(rdfFileNameWithPath); InfoExtractor infoe = new InfoExtractor(fis, omemo.getFormDataNS(), omemo.getFormDataOntLang()); infoe.writePage(getWorkDir(context), owpn, Omemo.checksWikiPageName); fis.close(); fos.close(); } catch (Exception e) { log.error("Can not read local rdf file or can not write wiki page"); throw new PluginException("Error creating wiki pages. See logs"); } } | 15,058 |
1 | public List<SuspectFileProcessingStatus> retrieve() throws Exception { BufferedOutputStream bos = null; try { String listFilePath = GeneralUtils.generateAbsolutePath(getDownloadDirectoryPath(), getListName(), "/"); listFilePath = listFilePath.concat(".xml"); if (!new File(getDownloadDirectoryPath()).exists()) { FileUtils.forceMkdir(new File(getDownloadDirectoryPath())); } FileOutputStream listFileOutputStream = new FileOutputStream(listFilePath); bos = new BufferedOutputStream(listFileOutputStream); InputStream is = null; if (getUseProxy()) { is = URLUtils.getResponse(getUrl(), getUserName(), getPassword(), URLUtils.HTTP_GET_METHOD, getProxyHost(), getProxyPort()); IOUtils.copyLarge(is, bos); } else { URLUtils.getResponse(getUrl(), getUserName(), getPassword(), bos, null); } bos.flush(); bos.close(); File listFile = new File(listFilePath); if (!listFile.exists()) { throw new IllegalStateException("The list file did not get created"); } if (isLoggingInfo()) { logInfo("Downloaded list file : " + listFile); } List<SuspectFileProcessingStatus> sfpsList = new ArrayList<SuspectFileProcessingStatus>(); String loadType = GeneralConstants.LOAD_TYPE_FULL; String feedType = GeneralConstants.EMPTY_TOKEN; String listName = getListName(); String errorCode = ""; String description = ""; SuspectFileProcessingStatus sfps = getSuspectsLoaderService().storeFileIntoListIncomingDir(listFile, loadType, feedType, listName, errorCode, description); sfpsList.add(sfps); if (isLoggingInfo()) { logInfo("Retrieved list file with SuspectFileProcessingStatus: " + sfps); } return sfpsList; } finally { if (null != bos) { bos.close(); } } } | public static File getClassLoaderFile(String filename) throws IOException { Resource resource = new ClassPathResource(filename); try { return resource.getFile(); } catch (IOException e) { } InputStream is = null; FileOutputStream os = null; try { String tempFilename = RandomStringUtils.randomAlphanumeric(20); File file = File.createTempFile(tempFilename, null); is = resource.getInputStream(); os = new FileOutputStream(file); IOUtils.copy(is, os); return file; } finally { IOUtils.closeQuietly(is); IOUtils.closeQuietly(os); } } | 15,059 |
0 | private void updateSystem() throws IOException { String stringUrl="http://code.google.com/p/senai-pe-cronos/downloads/list"; try { url = new URL(stringUrl); } catch (MalformedURLException ex) { ex.printStackTrace(); } InputStream is = url.openStream(); InputStreamReader isr = new InputStreamReader(is); BufferedReader br = new BufferedReader(isr); String linha = br.readLine(); while (linha != null) { linha = br.readLine(); if(linha.contains("/files/updateCronos-0-")){ String[] s=linha.split("-"); String[] v=s[4].split(".exe"); versao=v[0]; println("----"+versao); break; } } stringUrl="http://senai-pe-cronos.googlecode.com/files/updateCronos-0-"+versao+".exe"; UpdateCronos update=new UpdateCronos(); try { url = new URL(stringUrl); } catch (MalformedURLException ex) { ex.printStackTrace(); } System.out.println("versão:"+versao); if(Integer.parseInt(versao)>version){ File f = update.gravaArquivoDeURL(url,System.getProperty("user.dir"),String.valueOf(version),versao); if(update.isS()) { Runtime.getRuntime().exec(location+"\\update.exe"); System.exit(0); } } } | public void test_UseCache_HttpURLConnection_NoCached_GetOutputStream() throws Exception { ResponseCache.setDefault(new MockNonCachedResponseCache()); uc = (HttpURLConnection) url.openConnection(); uc.setChunkedStreamingMode(10); uc.setDoOutput(true); uc.getOutputStream(); assertTrue(isGetCalled); assertFalse(isPutCalled); assertFalse(isAbortCalled); uc.disconnect(); } | 15,060 |
1 | protected void assignListeners() { groupsList.addListSelectionListener(new ListSelectionListener() { @Override public void valueChanged(ListSelectionEvent event) { refreshInfo(); } }); saveButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent event) { JFileChooser fileDialog = new JFileChooser("."); fileDialog.setFileFilter(ReaderData.mkExtensionFileFilter(".grp", "Group Files")); int outcome = fileDialog.showSaveDialog((Frame) null); if (outcome == JFileChooser.APPROVE_OPTION) { assert (fileDialog.getCurrentDirectory() != null); assert (fileDialog.getSelectedFile() != null); String fileName = fileDialog.getCurrentDirectory().toString() + File.separator + fileDialog.getSelectedFile().getName(); try { PrintWriter out = new PrintWriter(new BufferedWriter(new FileWriter(fileName))); ReaderWriterGroup.write(out, writer); System.err.println("Wrote groups informations to output '" + fileName + "'."); out.close(); } catch (IOException e) { System.err.println("error while writing (GroupManager.saveClt):"); e.printStackTrace(); } } else if (outcome == JFileChooser.CANCEL_OPTION) { } } }); loadButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent evt) { JFileChooser fileDialog = new JFileChooser("."); fileDialog.setFileFilter(ReaderData.mkExtensionFileFilter(".grp", "Group Files")); int outcome = fileDialog.showOpenDialog((Frame) null); if (outcome == JFileChooser.APPROVE_OPTION) { assert (fileDialog.getCurrentDirectory() != null); assert (fileDialog.getSelectedFile() != null); String fileName = fileDialog.getCurrentDirectory().toString() + File.separator + fileDialog.getSelectedFile().getName(); BufferedReader fileReader = null; try { fileReader = new BufferedReader(new FileReader(fileName)); ReaderWriterGroup.read(fileReader, writer); fileReader.close(); } catch (Exception e) { System.err.println("Exception while reading from file '" + fileName + "'."); System.err.println(e); } } else if (outcome == JFileChooser.CANCEL_OPTION) { } } }); ItemListener propItemListener = new ItemListener() { @Override public void itemStateChanged(ItemEvent event) { int[] indices = groupsList.getSelectedIndices(); for (int index : indices) { Group group = getGroupFromListIndex(index); if (group != null) { if (event.getSource() instanceof JComboBox) { JComboBox eventSource = (JComboBox) event.getSource(); if (eventSource == colorComboBox) { Color color = colorComboBox.getSelectedColor(); assert (color != null); group.setColor(color); shapeComboBox.setColor(color); } else if (eventSource == shapeComboBox) { Shape shape = shapeComboBox.getSelectedShape(); assert (shape != null); group.setShape(shape); } } else if (event.getSource() instanceof JCheckBox) { JCheckBox eventSource = (JCheckBox) event.getSource(); if (eventSource == showGroupCheckBox) { group.visible = showGroupCheckBox.isSelected(); } else if (eventSource == showGraphicInfoCheckBox) { group.info = showGraphicInfoCheckBox.isSelected(); } } } } graph.notifyAboutGroupsChange(null); } }; colorComboBox.addItemListener(propItemListener); shapeComboBox.addItemListener(propItemListener); showGroupCheckBox.addItemListener(propItemListener); showGraphicInfoCheckBox.addItemListener(propItemListener); showGroupfreeNodesCheckBox.addItemListener(new ItemListener() { @Override public void itemStateChanged(ItemEvent event) { graph.getGroup(0).visible = showGroupfreeNodesCheckBox.isSelected(); graph.notifyAboutGroupsChange(null); } }); ActionListener propActionListener = new ActionListener() { @Override public void actionPerformed(ActionEvent event) { JButton botton = (JButton) event.getSource(); Group group = getGroupFromListIndex(groupsList.getSelectedIndex()); if (group != null) { for (GraphVertex graphVertex : group) { if (botton == showLabelsButton) { graphVertex.setShowName(NameVisibility.Priority.GROUPS, true); } else if (botton == hideLabelsButton) { graphVertex.setShowName(NameVisibility.Priority.GROUPS, false); } } graph.notifyAboutGroupsChange(null); } } }; showLabelsButton.addActionListener(propActionListener); hideLabelsButton.addActionListener(propActionListener); newButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent event) { String newGroupName = JOptionPane.showInputDialog(null, "Enter a name", "Name of the new group", JOptionPane.QUESTION_MESSAGE); if (newGroupName != null) { if (graph.getGroup(newGroupName) == null) { graph.addGroup(new Group(newGroupName, graph)); } } } }); editButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent event) { Group group = getGroupFromListIndex(groupsList.getSelectedIndex()); if (group != null) { DialogEditGroup dialog = new DialogEditGroup(graph, group); dialog.setModal(true); dialog.setVisible(true); } } }); deleteButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent event) { int index = groupsList.getSelectedIndex(); if (index > 0 && index < graph.getNumberOfGroups() - 1) { graph.removeGroup(index); } } }); upButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent event) { int index = groupsList.getSelectedIndex(); if (index < graph.getNumberOfGroups() - 1) { graph.moveGroupUp(index); groupsList.setSelectedIndex(index - 1); } } }); downButton.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent event) { int index = groupsList.getSelectedIndex(); if (index < graph.getNumberOfGroups() - 1) { graph.moveGroupDown(index); groupsList.setSelectedIndex(index + 1); } } }); } | private void handleSSI(HttpData data) throws HttpError, IOException { File tempFile = TempFileHandler.getTempFile(); FileOutputStream out = new FileOutputStream(tempFile); BufferedReader in = new BufferedReader(new FileReader(data.realPath)); String[] env = getEnvironmentVariables(data); if (ssi == null) { ssi = new BSssi(); } ssi.addEnvironment(env); if (data.resp == null) { SimpleResponse resp = new SimpleResponse(); resp.setHeader("Content-Type", "text/html"); moreHeaders(resp); resp.setHeader("Connection", "close"); data.resp = resp; resp.write(data.out); } String t; int start; Enumeration en; boolean anIfCondition = true; while ((t = in.readLine()) != null) { if ((start = t.indexOf("<!--#")) > -1) { if (anIfCondition) out.write(t.substring(0, start).getBytes()); try { en = ssi.parse(t.substring(start)).elements(); SSICommand command; while (en.hasMoreElements()) { command = (SSICommand) en.nextElement(); logger.fine("Command=" + command); switch(command.getCommand()) { case BSssi.CMD_IF_TRUE: anIfCondition = true; break; case BSssi.CMD_IF_FALSE: anIfCondition = false; break; case BSssi.CMD_CGI: out.flush(); if (command.getFileType() != null && command.getFileType().startsWith("shtm")) { HttpData d = newHttpData(data); d.out = out; d.realPath = HttpThread.getMappedFilename(command.getMessage(), data.req.getUrl()); new SsiHandler(d, ssi).perform(); } else { String application = getExtension(command.getFileType()); if (application == null) { writePaused(new FileInputStream(HttpThread.getMappedFilename(command.getMessage(), data.req.getUrl())), out, pause); } else { String parameter = ""; if (command.getMessage().indexOf("php") >= 0) { parameter = "-f "; } Process p = Runtime.getRuntime().exec(application + " " + parameter + HttpThread.getMappedFilename(command.getMessage(), data.req.getUrl())); BufferedReader pIn = new BufferedReader(new InputStreamReader(p.getInputStream())); String aLine; while ((aLine = pIn.readLine()) != null) out.write((aLine + "\n").getBytes()); pIn.close(); } } break; case BSssi.CMD_EXEC: Process p = Runtime.getRuntime().exec(command.getMessage()); BufferedReader pIn = new BufferedReader(new InputStreamReader(p.getInputStream())); String aLine; while ((aLine = pIn.readLine()) != null) out.write((aLine + "\n").getBytes()); BufferedReader pErr = new BufferedReader(new InputStreamReader(p.getErrorStream())); while ((aLine = pErr.readLine()) != null) out.write((aLine + "\n").getBytes()); pIn.close(); pErr.close(); p.destroy(); break; case BSssi.CMD_INCLUDE: File incFile = HttpThread.getMappedFilename(command.getMessage()); if (incFile.exists() && incFile.canRead()) { writePaused(new FileInputStream(incFile), out, pause); } break; case BSssi.CMD_FILESIZE: long sizeBytes = HttpThread.getMappedFilename(command.getMessage(), data.req.getUrl()).length(); double smartSize; String unit = "bytes"; if (command.getFileType().trim().equals("abbrev")) { if (sizeBytes > 1000000) { smartSize = sizeBytes / 1024000.0; unit = "M"; } else if (sizeBytes > 1000) { smartSize = sizeBytes / 1024.0; unit = "K"; } else { smartSize = sizeBytes; unit = "bytes"; } NumberFormat numberFormat = new DecimalFormat("#,##0", new DecimalFormatSymbols(Locale.ENGLISH)); out.write((numberFormat.format(smartSize) + "" + unit).getBytes()); } else { NumberFormat numberFormat = new DecimalFormat("#,###,##0", new DecimalFormatSymbols(Locale.ENGLISH)); out.write((numberFormat.format(sizeBytes) + " " + unit).getBytes()); } break; case BSssi.CMD_FLASTMOD: out.write(ssi.format(new Date(HttpThread.getMappedFilename(command.getMessage(), data.req.getUrl()).lastModified()), TimeZone.getTimeZone("GMT")).getBytes()); break; case BSssi.CMD_NOECHO: break; case BSssi.CMD_ECHO: default: out.write(command.getMessage().getBytes()); break; } } } catch (Exception e) { e.printStackTrace(); out.write((ssi.getErrorMessage() + " " + e.getMessage()).getBytes()); } if (anIfCondition) out.write("\n".getBytes()); } else { if (anIfCondition) out.write((t + "\n").getBytes()); } out.flush(); } in.close(); out.close(); data.fileData.setContentType("text/html"); data.fileData.setFile(tempFile); writePaused(new FileInputStream(tempFile), data.out, pause); logger.fine("HandleSSI done for " + data.resp); } | 15,061 |
1 | public static String md5It(String data) { MessageDigest digest; String output = ""; try { digest = java.security.MessageDigest.getInstance("MD5"); digest.update(data.getBytes()); byte[] hash = digest.digest(); for (byte b : hash) { output = output + String.format("%02X", b); } } catch (NoSuchAlgorithmException ex) { Logger.getLogger(Authenticator.class.getName()).log(Level.SEVERE, null, ex); } return output; } | @SmallTest public void testSha1() throws Exception { MessageDigest digest = MessageDigest.getInstance("SHA-1"); int numTests = mTestData.length; for (int i = 0; i < numTests; i++) { digest.update(mTestData[i].input.getBytes()); byte[] hash = digest.digest(); String encodedHash = encodeHex(hash); assertEquals(encodedHash, mTestData[i].result); } } | 15,062 |
1 | @SuppressWarnings("unchecked") public static void main(String[] args) { System.out.println("Starting encoding test...."); Properties p = new Properties(); try { InputStream pStream = ClassLoader.getSystemResourceAsStream("sample_weather.properties"); p.load(pStream); } catch (Exception e) { System.err.println("Could not load properties file."); System.err.println(e.getMessage()); e.printStackTrace(); return; } if (WeatherUpdater.DEBUG) { System.out.println("hostname: " + p.getProperty("weather.hostname")); } if (WeatherUpdater.DEBUG) { System.out.println("database: " + p.getProperty("weather.database")); } if (WeatherUpdater.DEBUG) { System.out.println("username: " + p.getProperty("weather.username")); } if (WeatherUpdater.DEBUG) { System.out.println("password: " + p.getProperty("weather.password")); } SqlAccount sqlAccount = new SqlAccount(p.getProperty("weather.hostname"), p.getProperty("weather.database"), p.getProperty("weather.username"), p.getProperty("weather.password")); DatabaseInterface dbi = null; try { dbi = new DatabaseInterface(sqlAccount); } catch (Exception e) { System.err.println(e.getMessage()); e.printStackTrace(); return; } System.out.println("Established connection to database."); String query = "SELECT * FROM Current_Weather WHERE ZipCode = '99702'"; ResultTable results; System.out.println("Executing query: " + query); try { results = dbi.executeQuery(query); } catch (Exception e) { System.err.println(e.getMessage()); e.printStackTrace(); return; } System.out.println("Got results from query."); System.out.println("Converted results into the following table:"); System.out.println(results); System.out.println(); Class<? extends ResultEncoder> encoder_class; Class<? extends ResultDecoder> decoder_class; try { encoder_class = (Class<? extends ResultEncoder>) Class.forName(p.getProperty("mysms.coding.resultEncoder")); decoder_class = (Class<? extends ResultDecoder>) Class.forName(p.getProperty("mysms.coding.resultDecoder")); } catch (Exception e) { System.err.println("Could not find specified encoder: " + p.getProperty("result.encoder")); System.err.println(e.getMessage()); e.printStackTrace(); return; } System.out.println("Found class of encoder: " + encoder_class); System.out.println("Found class of decoder: " + decoder_class); ResultEncoder encoder; ResultDecoder decoder; try { encoder = encoder_class.newInstance(); if (encoder_class.equals(decoder_class) && decoder_class.isInstance(encoder)) { decoder = (ResultDecoder) encoder; } else { decoder = decoder_class.newInstance(); } } catch (Exception e) { System.err.println("Could not create instances of encoder and decoder."); System.err.println(e.getMessage()); e.printStackTrace(); return; } System.out.println("Created instances of encoder and decoder."); if (decoder.equals(encoder)) { System.out.println("Decoder and encoder are same object."); } ByteBuffer buffer; try { buffer = encoder.encode(null, results); } catch (Exception e) { System.err.println("Could not encode results."); System.err.println(e.getMessage()); e.printStackTrace(); return; } System.out.println("Encoded results to ByteBuffer with size: " + buffer.capacity()); File temp; try { temp = File.createTempFile("encoding_test", ".results"); temp.deleteOnExit(); FileChannel out = new FileOutputStream(temp).getChannel(); out.write(buffer); out.close(); } catch (Exception e) { System.err.println("Could not write buffer to file."); System.err.println(e.getMessage()); e.printStackTrace(); return; } System.out.println("Wrote buffer to file: \"" + temp.getName() + "\" with length: " + temp.length()); ByteBuffer re_buffer; try { FileInputStream in = new FileInputStream(temp.getAbsolutePath()); byte[] temp_buffer = new byte[(int) temp.length()]; int totalRead = 0; int numRead = 0; while (totalRead < temp_buffer.length) { numRead = in.read(temp_buffer, totalRead, temp_buffer.length - totalRead); if (numRead < 0) { break; } else { totalRead += numRead; } } re_buffer = ByteBuffer.wrap(temp_buffer); in.close(); } catch (Exception e) { System.err.println("Could not read from temporary file into buffer."); System.err.println(e.getMessage()); e.printStackTrace(); return; } System.out.println("Read file back into buffer with length: " + re_buffer.capacity()); ResultTable re_results; try { re_results = decoder.decode(null, re_buffer); } catch (Exception e) { System.err.println("Could not decode buffer into a ResultTable."); System.err.println(e.getMessage()); e.printStackTrace(); return; } System.out.println("Decoded buffer back into the following table:"); System.out.println(re_results); System.out.println(); System.out.println("... encoding test complete."); } | public static void unzip(File sourceZipFile, File unzipDestinationDirectory, FileFilter filter) throws IOException { unzipDestinationDirectory.mkdirs(); if (!unzipDestinationDirectory.exists()) { throw new IOException("Unable to create destination directory: " + unzipDestinationDirectory); } ZipFile zipFile; zipFile = new ZipFile(sourceZipFile, ZipFile.OPEN_READ); Enumeration<? extends ZipEntry> zipFileEntries = zipFile.entries(); while (zipFileEntries.hasMoreElements()) { ZipEntry entry = (ZipEntry) zipFileEntries.nextElement(); if (!entry.isDirectory()) { String currentEntry = entry.getName(); File destFile = new File(unzipDestinationDirectory, currentEntry); if (filter == null || filter.accept(destFile)) { File destinationParent = destFile.getParentFile(); destinationParent.mkdirs(); BufferedInputStream is = new BufferedInputStream(zipFile.getInputStream(entry)); FileOutputStream fos = new FileOutputStream(destFile); IOUtils.copyLarge(is, fos); fos.flush(); IOUtils.closeQuietly(fos); } } } zipFile.close(); } | 15,063 |
1 | public boolean validateLogin(String username, String password) { boolean user_exists = false; try { MessageDigest md5 = MessageDigest.getInstance("MD5"); md5.update(password.getBytes()); BigInteger hash = new BigInteger(1, md5.digest()); String password_hash = hash.toString(16); statement = connect.prepareStatement("SELECT id from toepen.users WHERE username = ? AND password = ?"); statement.setString(1, username); statement.setString(2, password_hash); resultSet = statement.executeQuery(); while (resultSet.next()) { user_exists = true; } } catch (Exception ex) { System.out.println(ex); } finally { close(); return user_exists; } } | Object onSuccess() { this.mErrorExist = true; this.mErrorMdp = true; if (!mClientManager.exists(this.mNewMail)) { this.mErrorExist = false; if (mNewMdp.equals(mNewMdpConfirm)) { this.mErrorMdp = false; MessageDigest sha1Instance; try { sha1Instance = MessageDigest.getInstance("SHA1"); sha1Instance.reset(); sha1Instance.update(this.mNewMdp.getBytes()); byte[] digest = sha1Instance.digest(); BigInteger bigInt = new BigInteger(1, digest); String vHashPassword = bigInt.toString(16); Client vClient = new Client(this.mNewNom, (this.mNewPrenom != null ? this.mNewPrenom : ""), this.mNewMail, vHashPassword, this.mNewAdresse, 1); mClientManager.save(vClient); mComponentResources.discardPersistentFieldChanges(); return "Client/List"; } catch (NoSuchAlgorithmException e) { mLogger.error(e.getMessage(), e); } } } return errorZone.getBody(); } | 15,064 |
1 | public void copieFichier(String fileIn, String fileOut) { FileChannel in = null; FileChannel out = null; try { in = new FileInputStream(fileIn).getChannel(); out = new FileOutputStream(fileOut).getChannel(); in.transferTo(0, in.size(), out); } catch (Exception e) { e.printStackTrace(); } finally { if (in != null) { try { in.close(); } catch (IOException e) { } } if (out != null) { try { out.close(); } catch (IOException e) { } } } } | public void init(String[] arguments) { if (arguments.length < 1) { printHelp(); return; } String[] valid_args = new String[] { "device*", "d*", "help", "h", "speed#", "s#", "file*", "f*", "gpsd*", "nmea", "n", "garmin", "g", "sirf", "i", "rawdata", "downloadtracks", "downloadwaypoints", "downloadroutes", "deviceinfo", "printposonce", "printpos", "p", "printalt", "printspeed", "printheading", "printsat", "template*", "outfile*", "screenshot*", "printdefaulttemplate", "helptemplate", "nmealogfile*", "l", "uploadtracks", "uploadroutes", "uploadwaypoints", "infile*" }; CommandArguments args = null; try { args = new CommandArguments(arguments, valid_args); } catch (CommandArgumentException cae) { System.err.println("Invalid arguments: " + cae.getMessage()); printHelp(); return; } String filename = null; String serial_port_name = null; boolean gpsd = false; String gpsd_host = "localhost"; int gpsd_port = 2947; int serial_port_speed = -1; GPSDataProcessor gps_data_processor; String nmea_log_file = null; if (args.isSet("help") || (args.isSet("h"))) { printHelp(); return; } if (args.isSet("helptemplate")) { printHelpTemplate(); } if (args.isSet("printdefaulttemplate")) { System.out.println(DEFAULT_TEMPLATE); } if (args.isSet("device")) { serial_port_name = (String) args.getValue("device"); } else if (args.isSet("d")) { serial_port_name = (String) args.getValue("d"); } if (args.isSet("speed")) { serial_port_speed = ((Integer) args.getValue("speed")).intValue(); } else if (args.isSet("s")) { serial_port_speed = ((Integer) args.getValue("s")).intValue(); } if (args.isSet("file")) { filename = (String) args.getValue("file"); } else if (args.isSet("f")) { filename = (String) args.getValue("f"); } if (args.isSet("gpsd")) { gpsd = true; String gpsd_host_port = (String) args.getValue("gpsd"); if (gpsd_host_port != null && gpsd_host_port.length() > 0) { String[] params = gpsd_host_port.split(":"); gpsd_host = params[0]; if (params.length > 0) { gpsd_port = Integer.parseInt(params[1]); } } } if (args.isSet("garmin") || args.isSet("g")) { gps_data_processor = new GPSGarminDataProcessor(); serial_port_speed = 9600; if (filename != null) { System.err.println("ERROR: Cannot read garmin data from file, only serial port supported!"); return; } } else if (args.isSet("sirf") || args.isSet("i")) { gps_data_processor = new GPSSirfDataProcessor(); serial_port_speed = 19200; if (filename != null) { System.err.println("ERROR: Cannot read sirf data from file, only serial port supported!"); return; } } else { gps_data_processor = new GPSNmeaDataProcessor(); serial_port_speed = 4800; } if (args.isSet("nmealogfile") || (args.isSet("l"))) { if (args.isSet("nmealogfile")) nmea_log_file = args.getStringValue("nmealogfile"); else nmea_log_file = args.getStringValue("l"); } if (args.isSet("rawdata")) { gps_data_processor.addGPSRawDataListener(new GPSRawDataListener() { public void gpsRawDataReceived(char[] data, int offset, int length) { System.out.println("RAWLOG: " + new String(data, offset, length)); } }); } GPSDevice gps_device; Hashtable environment = new Hashtable(); if (filename != null) { environment.put(GPSFileDevice.PATH_NAME_KEY, filename); gps_device = new GPSFileDevice(); } else if (gpsd) { environment.put(GPSNetworkGpsdDevice.GPSD_HOST_KEY, gpsd_host); environment.put(GPSNetworkGpsdDevice.GPSD_PORT_KEY, new Integer(gpsd_port)); gps_device = new GPSNetworkGpsdDevice(); } else { if (serial_port_name != null) environment.put(GPSSerialDevice.PORT_NAME_KEY, serial_port_name); if (serial_port_speed > -1) environment.put(GPSSerialDevice.PORT_SPEED_KEY, new Integer(serial_port_speed)); gps_device = new GPSSerialDevice(); } try { gps_device.init(environment); gps_data_processor.setGPSDevice(gps_device); gps_data_processor.open(); gps_data_processor.addProgressListener(this); if ((nmea_log_file != null) && (nmea_log_file.length() > 0)) { gps_data_processor.addGPSRawDataListener(new GPSRawDataFileLogger(nmea_log_file)); } if (args.isSet("deviceinfo")) { System.out.println("GPSInfo:"); String[] infos = gps_data_processor.getGPSInfo(); for (int index = 0; index < infos.length; index++) { System.out.println(infos[index]); } } if (args.isSet("screenshot")) { FileOutputStream out = new FileOutputStream((String) args.getValue("screenshot")); BufferedImage image = gps_data_processor.getScreenShot(); ImageIO.write(image, "PNG", out); } boolean print_waypoints = args.isSet("downloadwaypoints"); boolean print_routes = args.isSet("downloadroutes"); boolean print_tracks = args.isSet("downloadtracks"); if (print_waypoints || print_routes || print_tracks) { VelocityContext context = new VelocityContext(); if (print_waypoints) { List waypoints = gps_data_processor.getWaypoints(); if (waypoints != null) context.put("waypoints", waypoints); else print_waypoints = false; } if (print_tracks) { List tracks = gps_data_processor.getTracks(); if (tracks != null) context.put("tracks", tracks); else print_tracks = false; } if (print_routes) { List routes = gps_data_processor.getRoutes(); if (routes != null) context.put("routes", routes); else print_routes = false; } context.put("printwaypoints", new Boolean(print_waypoints)); context.put("printtracks", new Boolean(print_tracks)); context.put("printroutes", new Boolean(print_routes)); Writer writer; Reader reader; if (args.isSet("template")) { String template_file = (String) args.getValue("template"); reader = new FileReader(template_file); } else { reader = new StringReader(DEFAULT_TEMPLATE); } if (args.isSet("outfile")) writer = new FileWriter((String) args.getValue("outfile")); else writer = new OutputStreamWriter(System.out); addDefaultValuesToContext(context); boolean result = printTemplate(context, reader, writer); } boolean read_waypoints = (args.isSet("uploadwaypoints") && args.isSet("infile")); boolean read_routes = (args.isSet("uploadroutes") && args.isSet("infile")); boolean read_tracks = (args.isSet("uploadtracks") && args.isSet("infile")); if (read_waypoints || read_routes || read_tracks) { ReadGPX reader = new ReadGPX(); String in_file = (String) args.getValue("infile"); reader.parseFile(in_file); if (read_waypoints) gps_data_processor.setWaypoints(reader.getWaypoints()); if (read_routes) gps_data_processor.setRoutes(reader.getRoutes()); if (read_tracks) gps_data_processor.setTracks(reader.getTracks()); } if (args.isSet("printposonce")) { GPSPosition pos = gps_data_processor.getGPSPosition(); System.out.println("Current Position: " + pos); } if (args.isSet("printpos") || args.isSet("p")) { gps_data_processor.addGPSDataChangeListener(GPSDataProcessor.LOCATION, this); } if (args.isSet("printalt")) { gps_data_processor.addGPSDataChangeListener(GPSDataProcessor.ALTITUDE, this); } if (args.isSet("printspeed")) { gps_data_processor.addGPSDataChangeListener(GPSDataProcessor.SPEED, this); } if (args.isSet("printheading")) { gps_data_processor.addGPSDataChangeListener(GPSDataProcessor.HEADING, this); } if (args.isSet("printsat")) { gps_data_processor.addGPSDataChangeListener(GPSDataProcessor.NUMBER_SATELLITES, this); gps_data_processor.addGPSDataChangeListener(GPSDataProcessor.SATELLITE_INFO, this); } if (args.isSet("printpos") || args.isSet("p") || args.isSet("printalt") || args.isSet("printsat") || args.isSet("printspeed") || args.isSet("printheading")) { gps_data_processor.startSendPositionPeriodically(1000L); try { System.in.read(); } catch (IOException ignore) { } } gps_data_processor.close(); } catch (GPSException e) { e.printStackTrace(); } catch (FileNotFoundException fnfe) { System.err.println("ERROR: File not found: " + fnfe.getMessage()); } catch (IOException ioe) { System.err.println("ERROR: I/O Error: " + ioe.getMessage()); } } | 15,065 |
1 | public static void main(String[] args) { File directory = new File(args[0]); File[] files = directory.listFiles(); try { PrintWriter writer = new PrintWriter(new BufferedWriter(new FileWriter(args[1]))); for (int i = 0; i < files.length; i++) { BufferedReader reader = new BufferedReader(new FileReader(files[i])); while (reader.ready()) writer.println(reader.readLine()); reader.close(); } writer.flush(); writer.close(); } catch (FileNotFoundException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } } | public static String CreateZip(String[] filesToZip, String zipFileName) { byte[] buffer = new byte[18024]; try { ZipOutputStream out = new ZipOutputStream(new FileOutputStream(zipFileName)); out.setLevel(Deflater.BEST_COMPRESSION); for (int i = 0; i < filesToZip.length; i++) { FileInputStream in = new FileInputStream(filesToZip[i]); String fileName = null; for (int X = filesToZip[i].length() - 1; X >= 0; X--) { if (filesToZip[i].charAt(X) == '\\' || filesToZip[i].charAt(X) == '/') { fileName = filesToZip[i].substring(X + 1); break; } else if (X == 0) fileName = filesToZip[i]; } out.putNextEntry(new ZipEntry(fileName)); int len; while ((len = in.read(buffer)) > 0) out.write(buffer, 0, len); out.closeEntry(); in.close(); } out.close(); } catch (IllegalArgumentException e) { return "Failed to create zip: " + e.toString(); } catch (FileNotFoundException e) { return "Failed to create zip: " + e.toString(); } catch (IOException e) { return "Failed to create zip: " + e.toString(); } return "Success"; } | 15,066 |
1 | public static void convertEncoding(File infile, File outfile, String from, String to) throws IOException, UnsupportedEncodingException { InputStream in; if (infile != null) in = new FileInputStream(infile); else in = System.in; OutputStream out; outfile.createNewFile(); if (outfile != null) out = new FileOutputStream(outfile); else out = System.out; if (from == null) from = System.getProperty("file.encoding"); if (to == null) to = "Unicode"; Reader r = new BufferedReader(new InputStreamReader(in, from)); Writer w = new BufferedWriter(new OutputStreamWriter(out, to)); char[] buffer = new char[4096]; int len; while ((len = r.read(buffer)) != -1) w.write(buffer, 0, len); r.close(); w.close(); } | private void initialize() { if (!initialized) { if (context.getJavadocLinks() != null) { for (String url : context.getJavadocLinks()) { if (!url.endsWith("/")) { url += "/"; } StringWriter writer = new StringWriter(); try { IOUtils.copy(new URL(url + "package-list").openStream(), writer); } catch (Exception e) { e.printStackTrace(); continue; } StringTokenizer tokenizer2 = new StringTokenizer(writer.toString()); while (tokenizer2.hasMoreTokens()) { javadocByPackage.put(tokenizer2.nextToken(), url); } } } initialized = true; } } | 15,067 |
0 | public void testSimpleHttpPostsChunked() throws Exception { int reqNo = 20; Random rnd = new Random(); List testData = new ArrayList(reqNo); for (int i = 0; i < reqNo; i++) { int size = rnd.nextInt(20000); byte[] data = new byte[size]; rnd.nextBytes(data); testData.add(data); } this.server.registerHandler("*", new HttpRequestHandler() { public void handle(final HttpRequest request, final HttpResponse response, final HttpContext context) throws HttpException, IOException { if (request instanceof HttpEntityEnclosingRequest) { HttpEntity incoming = ((HttpEntityEnclosingRequest) request).getEntity(); byte[] data = EntityUtils.toByteArray(incoming); ByteArrayEntity outgoing = new ByteArrayEntity(data); outgoing.setChunked(true); response.setEntity(outgoing); } else { StringEntity outgoing = new StringEntity("No content"); response.setEntity(outgoing); } } }); this.server.start(); DefaultHttpClientConnection conn = new DefaultHttpClientConnection(); HttpHost host = new HttpHost("localhost", this.server.getPort()); try { for (int r = 0; r < reqNo; r++) { if (!conn.isOpen()) { Socket socket = new Socket(host.getHostName(), host.getPort()); conn.bind(socket, this.client.getParams()); } BasicHttpEntityEnclosingRequest post = new BasicHttpEntityEnclosingRequest("POST", "/"); byte[] data = (byte[]) testData.get(r); ByteArrayEntity outgoing = new ByteArrayEntity(data); outgoing.setChunked(true); post.setEntity(outgoing); HttpResponse response = this.client.execute(post, host, conn); byte[] received = EntityUtils.toByteArray(response.getEntity()); byte[] expected = (byte[]) testData.get(r); assertEquals(expected.length, received.length); for (int i = 0; i < expected.length; i++) { assertEquals(expected[i], received[i]); } if (!this.client.keepAlive(response)) { conn.close(); } } HttpConnectionMetrics cm = conn.getMetrics(); assertEquals(reqNo, cm.getRequestCount()); assertEquals(reqNo, cm.getResponseCount()); } finally { conn.close(); this.server.shutdown(); } } | public static String getURLContent(String urlPath, String charset) { BufferedReader reader = null; HttpURLConnection conn = null; StringBuffer buffer = new StringBuffer(); try { URL url = new URL(urlPath); HttpURLConnection.setFollowRedirects(false); conn = (HttpURLConnection) url.openConnection(); conn.setRequestMethod("GET"); conn.setDoOutput(true); conn.setUseCaches(false); conn.setDefaultUseCaches(false); conn.setConnectTimeout(10000); conn.setReadTimeout(60000); conn.connect(); int repCode = conn.getResponseCode(); if (repCode == 200) { int count = 0; char[] chBuffer = new char[1024]; BufferedReader input = new BufferedReader(new InputStreamReader(conn.getInputStream(), charset)); while ((count = input.read(chBuffer)) != -1) { buffer.append(chBuffer, 0, count); } } } catch (Exception ex) { logger.error("", ex); } finally { try { if (reader != null) { reader.close(); } if (conn != null) { conn.disconnect(); } } catch (Exception ex) { } } return buffer.toString(); } | 15,068 |
1 | private static void readAndRewrite(File inFile, File outFile) throws IOException { ImageInputStream iis = ImageIO.createImageInputStream(new BufferedInputStream(new FileInputStream(inFile))); DcmParser dcmParser = DcmParserFactory.getInstance().newDcmParser(iis); Dataset ds = DcmObjectFactory.getInstance().newDataset(); dcmParser.setDcmHandler(ds.getDcmHandler()); dcmParser.parseDcmFile(null, Tags.PixelData); PixelDataReader pdReader = pdFact.newReader(ds, iis, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); System.out.println("reading " + inFile + "..."); pdReader.readPixelData(false); ImageOutputStream out = ImageIO.createImageOutputStream(new BufferedOutputStream(new FileOutputStream(outFile))); DcmEncodeParam dcmEncParam = DcmEncodeParam.IVR_LE; ds.writeDataset(out, dcmEncParam); ds.writeHeader(out, dcmEncParam, Tags.PixelData, dcmParser.getReadVR(), dcmParser.getReadLength()); System.out.println("writing " + outFile + "..."); PixelDataWriter pdWriter = pdFact.newWriter(pdReader.getPixelDataArray(), false, ds, out, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); pdWriter.writePixelData(); out.flush(); out.close(); System.out.println("done!"); } | public static void extractFile(String jarArchive, String fileToExtract, String destination) { FileWriter writer = null; ZipInputStream zipStream = null; try { FileInputStream inputStream = new FileInputStream(jarArchive); BufferedInputStream bufferedStream = new BufferedInputStream(inputStream); zipStream = new ZipInputStream(bufferedStream); writer = new FileWriter(new File(destination)); ZipEntry zipEntry = null; while ((zipEntry = zipStream.getNextEntry()) != null) { if (zipEntry.getName().equals(fileToExtract)) { int size = (int) zipEntry.getSize(); for (int i = 0; i < size; i++) { writer.write(zipStream.read()); } } } } catch (IOException e) { e.printStackTrace(); } finally { if (zipStream != null) try { zipStream.close(); } catch (IOException e) { e.printStackTrace(); } if (writer != null) try { writer.close(); } catch (IOException e) { e.printStackTrace(); } } } | 15,069 |
0 | public String[] retrieveFasta(String id) throws Exception { URL url = new URL("http://www.ebi.ac.uk/ena/data/view/" + id + "&display=fasta"); BufferedReader reader = new BufferedReader(new InputStreamReader(url.openStream())); String header = reader.readLine(); StringBuffer seq = new StringBuffer(); String line = ""; while ((line = reader.readLine()) != null) { seq.append(line); } reader.close(); return new String[] { header, seq.toString() }; } | private final void copyTargetFileToSourceFile(File sourceFile, File targetFile) throws MJProcessorException { if (!targetFile.exists()) { targetFile.getParentFile().mkdirs(); try { if (!targetFile.exists()) { targetFile.createNewFile(); } } catch (IOException e) { throw new MJProcessorException(e.getMessage(), e); } } FileChannel in = null, out = null; try { in = new FileInputStream(sourceFile).getChannel(); out = new FileOutputStream(targetFile).getChannel(); long size = in.size(); MappedByteBuffer buf = in.map(FileChannel.MapMode.READ_ONLY, 0, size); out.write(buf); } catch (IOException e) { log.error(e); } finally { if (in != null) try { in.close(); } catch (IOException e) { log.error(e); } if (out != null) try { out.close(); } catch (IOException e) { log.error(e); } } } | 15,070 |
1 | private void handleUpload(CommonsMultipartFile file, String newFileName, String uploadDir) throws IOException, FileNotFoundException { File dirPath = new File(uploadDir); if (!dirPath.exists()) { dirPath.mkdirs(); } InputStream stream = file.getInputStream(); OutputStream bos = new FileOutputStream(uploadDir + newFileName); IOUtils.copy(stream, bos); } | @Override protected void copyContent(String filename) throws IOException { InputStream in = null; try { String resourceDir = System.getProperty("resourceDir"); File resource = new File(resourceDir, filename); ByteArrayOutputStream out = new ByteArrayOutputStream(); if (resource.exists()) { in = new FileInputStream(resource); } else { in = LOADER.getResourceAsStream(RES_PKG + filename); } IOUtils.copy(in, out); setResponseData(out.toByteArray()); } finally { if (in != null) { in.close(); } } } | 15,071 |
1 | static byte[] getSystemEntropy() { byte[] ba; final MessageDigest md; try { md = MessageDigest.getInstance("SHA"); } catch (NoSuchAlgorithmException nsae) { throw new InternalError("internal error: SHA-1 not available."); } byte b = (byte) System.currentTimeMillis(); md.update(b); java.security.AccessController.doPrivileged(new java.security.PrivilegedAction() { public Object run() { try { String s; Properties p = System.getProperties(); Enumeration e = p.propertyNames(); while (e.hasMoreElements()) { s = (String) e.nextElement(); md.update(s.getBytes()); md.update(p.getProperty(s).getBytes()); } md.update(InetAddress.getLocalHost().toString().getBytes()); File f = new File(p.getProperty("java.io.tmpdir")); String[] sa = f.list(); for (int i = 0; i < sa.length; i++) md.update(sa[i].getBytes()); } catch (Exception ex) { md.update((byte) ex.hashCode()); } Runtime rt = Runtime.getRuntime(); byte[] memBytes = longToByteArray(rt.totalMemory()); md.update(memBytes, 0, memBytes.length); memBytes = longToByteArray(rt.freeMemory()); md.update(memBytes, 0, memBytes.length); return null; } }); return md.digest(); } | public boolean isPasswordCorrect(String attempt) { try { MessageDigest digest = MessageDigest.getInstance(attempt); digest.update(salt); digest.update(attempt.getBytes("UTF-8")); byte[] attemptHash = digest.digest(); return attemptHash.equals(hash); } catch (UnsupportedEncodingException ex) { Logger.getLogger(UserRecord.class.getName()).log(Level.SEVERE, null, ex); return false; } catch (NoSuchAlgorithmException ex) { Logger.getLogger(UserRecord.class.getName()).log(Level.SEVERE, null, ex); return false; } } | 15,072 |
0 | public Login authenticateClient() { Object o; String user, password; Vector<Login> clientLogins = ClientLoginsTableModel.getClientLogins(); Login login = null; try { socket.setSoTimeout(25000); objectOut.writeObject("JFRITZ SERVER 1.1"); objectOut.flush(); o = objectIn.readObject(); if (o instanceof String) { user = (String) o; objectOut.flush(); for (Login l : clientLogins) { if (l.getUser().equals(user)) { login = l; break; } } if (login != null) { MessageDigest md = MessageDigest.getInstance("MD5"); md.update(login.getPassword().getBytes()); DESKeySpec desKeySpec = new DESKeySpec(md.digest()); SecretKeyFactory keyFactory = SecretKeyFactory.getInstance("DES"); SecretKey secretKey = keyFactory.generateSecret(desKeySpec); Cipher desCipher = Cipher.getInstance("DES/ECB/PKCS5Padding"); desCipher.init(Cipher.ENCRYPT_MODE, secretKey); byte[] dataKeySeed = new byte[32]; Random random = new Random(); random.nextBytes(dataKeySeed); md.reset(); md.update(dataKeySeed); dataKeySeed = md.digest(); SealedObject dataKeySeedSealed; dataKeySeedSealed = new SealedObject(dataKeySeed, desCipher); objectOut.writeObject(dataKeySeedSealed); objectOut.flush(); desKeySpec = new DESKeySpec(dataKeySeed); secretKey = keyFactory.generateSecret(desKeySpec); inCipher = Cipher.getInstance("DES/ECB/PKCS5Padding"); outCipher = Cipher.getInstance("DES/ECB/PKCS5Padding"); inCipher.init(Cipher.DECRYPT_MODE, secretKey); outCipher.init(Cipher.ENCRYPT_MODE, secretKey); SealedObject sealedObject = (SealedObject) objectIn.readObject(); o = sealedObject.getObject(inCipher); if (o instanceof String) { String response = (String) o; if (response.equals("OK")) { SealedObject ok_sealed = new SealedObject("OK", outCipher); objectOut.writeObject(ok_sealed); return login; } else { Debug.netMsg("Client sent false response to challenge!"); } } else { Debug.netMsg("Client sent false object as response to challenge!"); } } else { Debug.netMsg("client sent unkown username: " + user); } } } catch (IllegalBlockSizeException e) { Debug.netMsg("Wrong blocksize for sealed object!"); Debug.error(e.toString()); e.printStackTrace(); } catch (ClassNotFoundException e) { Debug.netMsg("received unrecognized object from client!"); Debug.error(e.toString()); e.printStackTrace(); } catch (NoSuchAlgorithmException e) { Debug.netMsg("MD5 Algorithm not present in this JVM!"); Debug.error(e.toString()); e.printStackTrace(); } catch (InvalidKeySpecException e) { Debug.netMsg("Error generating cipher, problems with key spec?"); Debug.error(e.toString()); e.printStackTrace(); } catch (InvalidKeyException e) { Debug.netMsg("Error genertating cipher, problems with key?"); Debug.error(e.toString()); e.printStackTrace(); } catch (NoSuchPaddingException e) { Debug.netMsg("Error generating cipher, problems with padding?"); Debug.error(e.toString()); e.printStackTrace(); } catch (IOException e) { Debug.netMsg("Error authenticating client!"); Debug.error(e.toString()); e.printStackTrace(); } catch (BadPaddingException e) { Debug.netMsg("Bad padding exception!"); Debug.error(e.toString()); e.printStackTrace(); } return null; } | public static void extractFile(String jarArchive, String fileToExtract, String destination) { FileWriter writer = null; ZipInputStream zipStream = null; try { FileInputStream inputStream = new FileInputStream(jarArchive); BufferedInputStream bufferedStream = new BufferedInputStream(inputStream); zipStream = new ZipInputStream(bufferedStream); writer = new FileWriter(new File(destination)); ZipEntry zipEntry = null; while ((zipEntry = zipStream.getNextEntry()) != null) { if (zipEntry.getName().equals(fileToExtract)) { int size = (int) zipEntry.getSize(); for (int i = 0; i < size; i++) { writer.write(zipStream.read()); } } } } catch (IOException e) { e.printStackTrace(); } finally { if (zipStream != null) try { zipStream.close(); } catch (IOException e) { e.printStackTrace(); } if (writer != null) try { writer.close(); } catch (IOException e) { e.printStackTrace(); } } } | 15,073 |
0 | private static List<CountryEntry> retrieveCountries() throws IOException { URL url = new URL("http://" + ISO_3166_HOST + ISO_3166_TXT_FILE_PATH); BufferedReader input = new BufferedReader(new InputStreamReader(url.openStream())); List<CountryEntry> countries = new LinkedList<CountryEntry>(); boolean parsing = false; int trCount = 0; int tdCount = 0; CountryEntry current = new CountryEntry(); String nextLine = input.readLine(); while (nextLine != null) { if (nextLine.startsWith("<table")) { parsing = true; } if (nextLine.startsWith("</table>")) { break; } if (parsing) { if (nextLine.startsWith("<tr")) { trCount++; } else { if ((trCount > 1 && nextLine.startsWith("<td"))) { tdCount++; String data = pullData(nextLine); switch(tdCount) { case 1: current.setName(getCountryName(data)); break; case 2: current.setNumber(data); break; case 3: current.setAlpha3(data); break; case 4: current.setAlpha2(data); break; case 5: countries.add(current); current = new CountryEntry(); tdCount = 0; break; default: String msg = "Parsing error. Unexpected column: [" + data + "]"; throw new IllegalStateException(msg); } } } } nextLine = input.readLine(); } input.close(); return countries; } | public String doAdd(ActionMapping mapping, ActionForm form, HttpServletRequest request, HttpServletResponse response) throws Exception { UploadFileForm vo = (UploadFileForm) form; String review = request.getParameter("review"); String realpath = getServlet().getServletContext().getRealPath("/"); realpath = realpath.replaceAll("\\\\", "/"); String inforId = request.getParameter("inforId"); request.setAttribute("id", inforId); String str_postFIX = ""; int i_p = 0; if (null == review) { FormFile file = vo.getFile(); if (file != null) { String rootFilePath = getServlet().getServletContext().getRealPath(request.getContextPath()); rootFilePath = (new StringBuilder(String.valueOf(rootFilePath))).append(UploadFileOne.strPath).toString(); String strAppend = (new StringBuilder(String.valueOf(UUIDGenerator.nextHex()))).append(UploadFileOne.getFileType(file)).toString(); if (file.getFileSize() != 0) { file.getInputStream(); String name = file.getFileName(); i_p = file.getFileName().lastIndexOf("."); str_postFIX = file.getFileName().substring(i_p, file.getFileName().length()); String fullPath = realpath + "attach/" + strAppend + str_postFIX; t_attach attach = new t_attach(); attach.setAttach_fullname(fullPath); attach.setAttach_name(name); attach.setInfor_id(Integer.parseInt(inforId)); attach.setInsert_day(new Date()); attach.setUpdate_day(new Date()); t_attach_EditMap attachEdit = new t_attach_EditMap(); attachEdit.add(attach); File sysfile = new File(fullPath); if (!sysfile.exists()) { sysfile.createNewFile(); } java.io.OutputStream out = new FileOutputStream(sysfile); org.apache.commons.io.IOUtils.copy(file.getInputStream(), out); out.close(); } } request.setAttribute("operating-status", "�����ɹ�! ��ӭ����ʹ�á�"); return "editsave"; } else { String rootFilePath = getServlet().getServletContext().getRealPath(request.getContextPath()); rootFilePath = (new StringBuilder(String.valueOf(rootFilePath))).append(UploadFileOne.strPath).toString(); FormFile file = vo.getFile(); FormFile file2 = vo.getFile2(); FormFile file3 = vo.getFile3(); t_infor_review newreview = new t_infor_review(); String content = request.getParameter("content"); newreview.setContent(content); if (null != inforId) newreview.setInfor_id(Integer.parseInt(inforId)); newreview.setInsert_day(new Date()); UserDetails user = LoginUtils.getLoginUser(request); newreview.setCreate_name(user.getUsercode()); if (null != file.getFileName() && !"".equals(file.getFileName())) { newreview.setAttachname1(file.getFileName()); String strAppend1 = (new StringBuilder(String.valueOf(UUIDGenerator.nextHex()))).append(UploadFileOne.getFileType(file)).toString(); i_p = file.getFileName().lastIndexOf("."); str_postFIX = file.getFileName().substring(i_p, file.getFileName().length()); newreview.setAttachfullname1(realpath + "attach/" + strAppend1 + str_postFIX); saveFile(file.getInputStream(), realpath + "attach/" + strAppend1 + str_postFIX); } if (null != file2.getFileName() && !"".equals(file2.getFileName())) { newreview.setAttachname2(file2.getFileName()); String strAppend2 = (new StringBuilder(String.valueOf(UUIDGenerator.nextHex()))).append(UploadFileOne.getFileType(file)).toString(); i_p = file2.getFileName().lastIndexOf("."); str_postFIX = file2.getFileName().substring(i_p, file2.getFileName().length()); newreview.setAttachfullname2(realpath + "attach/" + strAppend2 + str_postFIX); saveFile(file2.getInputStream(), realpath + "attach/" + strAppend2 + str_postFIX); } if (null != file3.getFileName() && !"".equals(file3.getFileName())) { newreview.setAttachname3(file3.getFileName()); String strAppend3 = (new StringBuilder(String.valueOf(UUIDGenerator.nextHex()))).append(UploadFileOne.getFileType(file)).toString(); i_p = file3.getFileName().lastIndexOf("."); str_postFIX = file3.getFileName().substring(i_p, file3.getFileName().length()); newreview.setAttachfullname3(realpath + "attach/" + strAppend3 + str_postFIX); saveFile(file3.getInputStream(), realpath + "attach/" + strAppend3 + str_postFIX); } t_infor_review_EditMap reviewEdit = new t_infor_review_EditMap(); reviewEdit.add(newreview); request.setAttribute("review", "1"); return "aftersave"; } } | 15,074 |
1 | public void copyFile(File s, File t) { try { FileChannel in = (new FileInputStream(s)).getChannel(); FileChannel out = (new FileOutputStream(t)).getChannel(); in.transferTo(0, s.length(), out); in.close(); out.close(); } catch (Exception e) { System.out.println(e); } } | public void testStorageByteArray() throws Exception { TranslationResponseInMemory r = new TranslationResponseInMemory(2048, "UTF-8"); { OutputStream output = r.getOutputStream(); output.write("This is an example".getBytes("UTF-8")); output.write(" and another one.".getBytes("UTF-8")); assertEquals("This is an example and another one.", r.getText()); } { InputStream input = r.getInputStream(); StringWriter writer = new StringWriter(); try { IOUtils.copy(input, writer, "UTF-8"); } finally { input.close(); writer.close(); } assertEquals("This is an example and another one.", writer.toString()); } { OutputStream output = r.getOutputStream(); output.write(" and another line".getBytes("UTF-8")); assertEquals("This is an example and another one. and another line", r.getText()); } { Writer output = r.getWriter(); output.write(" and write some more"); assertEquals("This is an example and another one. and another line and write some more", r.getText()); } { r.addText(" and even more."); assertEquals("This is an example and another one. and another line and write some more and even more.", r.getText()); } assertFalse(r.hasEnded()); r.setEndState(ResponseStateOk.getInstance()); assertTrue(r.hasEnded()); try { r.getOutputStream(); fail("Previous line should throw IOException as result closed."); } catch (IOException e) { } try { r.getWriter(); fail("Previous line should throw IOException as result closed."); } catch (IOException e) { } } | 15,075 |
0 | private static void readAndRewrite(File inFile, File outFile) throws IOException { ImageInputStream iis = ImageIO.createImageInputStream(new BufferedInputStream(new FileInputStream(inFile))); DcmParser dcmParser = DcmParserFactory.getInstance().newDcmParser(iis); Dataset ds = DcmObjectFactory.getInstance().newDataset(); dcmParser.setDcmHandler(ds.getDcmHandler()); dcmParser.parseDcmFile(null, Tags.PixelData); PixelDataReader pdReader = pdFact.newReader(ds, iis, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); System.out.println("reading " + inFile + "..."); pdReader.readPixelData(false); ImageOutputStream out = ImageIO.createImageOutputStream(new BufferedOutputStream(new FileOutputStream(outFile))); DcmEncodeParam dcmEncParam = DcmEncodeParam.IVR_LE; ds.writeDataset(out, dcmEncParam); ds.writeHeader(out, dcmEncParam, Tags.PixelData, dcmParser.getReadVR(), dcmParser.getReadLength()); System.out.println("writing " + outFile + "..."); PixelDataWriter pdWriter = pdFact.newWriter(pdReader.getPixelDataArray(), false, ds, out, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); pdWriter.writePixelData(); out.flush(); out.close(); System.out.println("done!"); } | public InputStream resolve(String uri) throws SAJException { try { URI url = new URI(uri); InputStream stream = url.toURL().openStream(); if (stream == null) throw new SAJException("URI " + uri + " can't be resolved"); return stream; } catch (SAJException e) { throw e; } catch (Exception e) { throw new SAJException("Invalid uri to resolve " + uri, e); } } | 15,076 |
0 | void loadPlaylist() { if (running_as_applet) { String s = null; for (int i = 0; i < 10; i++) { s = getParameter("jorbis.player.play." + i); if (s == null) break; playlist.addElement(s); } } if (playlistfile == null) { return; } try { InputStream is = null; try { URL url = null; if (running_as_applet) url = new URL(getCodeBase(), playlistfile); else url = new URL(playlistfile); URLConnection urlc = url.openConnection(); is = urlc.getInputStream(); } catch (Exception ee) { } if (is == null && !running_as_applet) { try { is = new FileInputStream(System.getProperty("user.dir") + System.getProperty("file.separator") + playlistfile); } catch (Exception ee) { } } if (is == null) return; while (true) { String line = readline(is); if (line == null) break; byte[] foo = line.getBytes(); for (int i = 0; i < foo.length; i++) { if (foo[i] == 0x0d) { line = new String(foo, 0, i); break; } } playlist.addElement(line); } } catch (Exception e) { System.out.println(e); } } | public String sruRead(String initialURL) { out('\n'); out(" trying: "); out(initialURL); out('\n'); numTests++; URL url = null; try { url = new URL(initialURL); } catch (java.net.MalformedURLException e) { out("</pre><pre class='red'>"); out("test failed: using URL: "); out(e.getMessage()); out('\n'); out("</pre><pre>"); return null; } HttpURLConnection huc = null; try { huc = (HttpURLConnection) url.openConnection(); } catch (IOException e) { out("</pre><pre class='red'>"); out("test failed: using URL: "); out(e.getMessage()); out('\n'); out("</pre><pre>"); return null; } String contentType = huc.getContentType(); if (contentType == null || (contentType.indexOf("text/xml") < 0 && contentType.indexOf("application/xml") < 0)) { out(" ** Warning: Content-Type not set to text/xml or application/xml"); out('\n'); out(" Content-type: "); out(contentType); out('\n'); numWarns++; } InputStream urlStream = null; try { urlStream = huc.getInputStream(); } catch (java.io.IOException e) { out("</pre><pre class='red'>"); out("test failed: opening URL: "); out(e.getMessage()); out('\n'); out("</pre><pre>"); return null; } BufferedReader in = new BufferedReader(new InputStreamReader(urlStream)); boolean xml = true; String href = null, inputLine = null; StringBuffer content = new StringBuffer(), stylesheet = null; Transformer transformer = null; try { inputLine = in.readLine(); } catch (java.io.IOException e) { out("</pre><pre class='red'>"); out("test failed: reading first line of response: "); out(e.getMessage()); out('\n'); out("</pre><pre>"); return null; } if (inputLine == null) { out("</pre><pre class='red'>"); out("test failed: No input read from URL"); out('\n'); out("</pre><pre>"); return null; } if (!inputLine.startsWith("<?xml ")) { xml = false; content.append(inputLine); } if (xml) { int offset = inputLine.indexOf('>'); if (offset + 2 < inputLine.length()) { inputLine = inputLine.substring(offset + 1); offset = inputLine.indexOf('<'); if (offset > 0) inputLine = inputLine.substring(offset); } else try { inputLine = in.readLine(); while (inputLine.length() == 0) inputLine = in.readLine(); } catch (java.io.IOException e) { out("</pre><pre class='red'>"); out("test failed: reading response: "); out(e.getMessage()); out('\n'); out("</pre><pre>"); return null; } if (inputLine.startsWith("<?xml-stylesheet ")) { offset = inputLine.indexOf("href="); href = (inputLine.substring(inputLine.indexOf("href=") + 6)); href = href.substring(0, href.indexOf('"')); transformer = (Transformer) transformers.get(href); if (stylesheets.get(href) == null) try { out(" reading stylesheet: "); out(href); out('\n'); out(" from source: "); out(url.toString()); out('\n'); StreamSource source = new StreamSource(url.toString()); TransformerFactory tFactory = TransformerFactory.newInstance(); Source stylesht = tFactory.getAssociatedStylesheet(source, null, null, null); transformer = tFactory.newTransformer(stylesht); transformers.put(href, transformer); } catch (Exception e) { e.printStackTrace(); out("</pre><pre class='red'>"); out("unable to load stylesheet: "); out(e.getMessage()); out('\n'); out("</pre><pre>"); } stylesheets.put(href, href); } else content.append(inputLine); } try { while ((inputLine = in.readLine()) != null) content.append(inputLine); } catch (java.io.IOException e) { out("</pre><pre class='red'>"); out("test failed: reading response: "); out(e.getMessage()); out('\n'); out("</pre><pre>"); return null; } String contentStr = content.toString(); if (transformer != null) { StreamSource streamXMLRecord = new StreamSource(new StringReader(contentStr)); StringWriter xmlRecordWriter = new StringWriter(); try { transformer.transform(streamXMLRecord, new StreamResult(xmlRecordWriter)); out(" successfully applied stylesheet '"); out(href); out("'"); out('\n'); } catch (javax.xml.transform.TransformerException e) { out("</pre><pre class='red'>"); out("unable to apply stylesheet '"); out(href); out("'to response: "); out(e.getMessage()); out('\n'); out("</pre><pre>"); e.printStackTrace(); } } return contentStr; } | 15,077 |
1 | private void loadMap() { final String wordList = "vietwordlist.txt"; try { File dataFile = new File(supportDir, wordList); if (!dataFile.exists()) { final ReadableByteChannel input = Channels.newChannel(ClassLoader.getSystemResourceAsStream("dict/" + dataFile.getName())); final FileChannel output = new FileOutputStream(dataFile).getChannel(); output.transferFrom(input, 0, 1000000L); input.close(); output.close(); } long fileLastModified = dataFile.lastModified(); if (map == null) { map = new HashMap<String, String>(); } else { if (fileLastModified <= mapLastModified) { return; } map.clear(); } mapLastModified = fileLastModified; BufferedReader bs = new BufferedReader(new InputStreamReader(new FileInputStream(dataFile), "UTF-8")); String accented; while ((accented = bs.readLine()) != null) { String plain = VietUtilities.stripDiacritics(accented); map.put(plain.toLowerCase(), accented); } bs.close(); } catch (IOException e) { map = null; e.printStackTrace(); JOptionPane.showMessageDialog(this, myResources.getString("Cannot_find_\"") + wordList + myResources.getString("\"_in\n") + supportDir.toString(), VietPad.APP_NAME, JOptionPane.ERROR_MESSAGE); } } | public static void main(String[] args) { String inFile = "test_data/blobs.png"; String outFile = "ReadWriteTest.png"; itkImageFileReaderUC2_Pointer reader = itkImageFileReaderUC2.itkImageFileReaderUC2_New(); itkImageFileWriterUC2_Pointer writer = itkImageFileWriterUC2.itkImageFileWriterUC2_New(); reader.SetFileName(inFile); writer.SetFileName(outFile); writer.SetInput(reader.GetOutput()); writer.Update(); } | 15,078 |
0 | public void service(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException { ServletContext context = getServletContext(); String forw = null; try { int maxUploadSize = 50000000; MultipartRequest multi = new MultipartRequest(request, ".", maxUploadSize); String descrizione = multi.getParameter("text"); File myFile = multi.getFile("uploadfile"); String filePath = multi.getOriginalFileName("uploadfile"); String path = "C:\\files\\"; try { FileInputStream inStream = new FileInputStream(myFile); FileOutputStream outStream = new FileOutputStream(path + myFile.getName()); while (inStream.available() > 0) { outStream.write(inStream.read()); } inStream.close(); outStream.close(); } catch (FileNotFoundException fnfe) { fnfe.printStackTrace(); } catch (IOException ioe) { ioe.printStackTrace(); } forw = "../sendDoc.jsp"; request.setAttribute("contentType", context.getMimeType(path + myFile.getName())); request.setAttribute("text", descrizione); request.setAttribute("path", path + myFile.getName()); request.setAttribute("size", Long.toString(myFile.length()) + " Bytes"); RequestDispatcher rd = request.getRequestDispatcher(forw); rd.forward(request, response); } catch (Exception e) { e.printStackTrace(); } } | public static String getHash(String text) { if (text == null) return null; try { MessageDigest md = MessageDigest.getInstance("MD5"); md.update(text.getBytes()); byte[] hashedTextBytes = md.digest(); BigInteger hashedTextBigInteger = new BigInteger(1, hashedTextBytes); String hashedTextString = hashedTextBigInteger.toString(16); return hashedTextString; } catch (NoSuchAlgorithmException e) { LOG.warning(e.toString()); return null; } } | 15,079 |
1 | private boolean doStudentCreditUpdate(Double dblCAmnt, String stuID) throws Exception { Connection conn = null; Statement stmt = null; ResultSet rs = null; Boolean blOk = false; String strMessage = ""; try { conn = dbMan.getPOSConnection(); conn.setAutoCommit(false); stmt = conn.createStatement(); String host = getHostName(); String stuId = student.getStudentNumber(); String building = settings.get(DBSettings.MAIN_BUILDING); String cashier = dbMan.getPOSUser(); if (hasStudentCredit()) { stmt = conn.createStatement(); if (stmt.executeUpdate("UPDATE " + strPOSPrefix + "studentcredit set credit_amount = credit_amount + " + round2Places(dblCAmnt) + " WHERE credit_active = '1' and credit_studentid = '" + stuId + "'") == 1) { stmt.close(); stmt = conn.createStatement(); if (stmt.executeUpdate("UPDATE " + strPOSPrefix + "studentcredit set credit_lastused = NOW() where credit_active = '1' and credit_studentid = '" + stuId + "'") == 1) { stmt.close(); stmt = conn.createStatement(); if (stmt.executeUpdate("INSERT into " + strPOSPrefix + "studentcredit_log ( scl_studentid, scl_action, scl_datetime ) values( '" + stuId + "', '" + round2Places(dblCAmnt) + "', NOW() )") == 1) { stmt.close(); blOk = true; } else { strMessage = "Unable to update student credit log."; blOk = false; } } else { strMessage = "Unable to update student credit account."; blOk = false; } } else { strMessage = "Unable to update student credit account."; blOk = false; } } else { stmt = conn.createStatement(); if (stmt.executeUpdate("insert into " + strPOSPrefix + "studentcredit (credit_amount,credit_active,credit_studentid,credit_lastused) values('" + round2Places(dblCAmnt) + "','1','" + stuId + "', NOW())") == 1) { stmt.close(); stmt = conn.createStatement(); if (stmt.executeUpdate("insert into " + strPOSPrefix + "studentcredit_log ( scl_studentid, scl_action, scl_datetime ) values( '" + stuId + "', '" + round2Places(dblCAmnt) + "', NOW() )") == 1) { stmt.close(); blOk = true; } else { strMessage = "Unable to update student credit log."; blOk = false; } } else { strMessage = "Unable to create new student credit account."; blOk = false; } } if (blOk) { stmt = conn.createStatement(); if (stmt.executeUpdate("insert into " + strPOSPrefix + "creditTrans ( ctStudentNumber, ctCreditAction, ctBuilding, ctRegister, ctUser, ctDateTime ) values( '" + stuId + "', '" + round2Places(dblCAmnt) + "', '" + building + "', '" + host + "', '" + cashier + "', NOW() )") == 1) { stmt.close(); blOk = true; } else blOk = false; } if (blOk) { conn.commit(); return true; } else { conn.rollback(); throw new Exception("Error detected during credit adjustment! " + strMessage); } } catch (Exception exp) { try { conn.rollback(); } catch (SQLException sqlEx2) { System.err.println("Rollback failed: " + sqlEx2.getMessage()); return false; } finally { if (rs != null) { try { rs.close(); } catch (SQLException sqlEx) { rs = null; } if (stmt != null) { try { stmt.close(); } catch (SQLException sqlEx) { stmt = null; } catch (Exception e) { System.err.println("Exception: " + e.getMessage()); System.err.println(e); } } } } exp.printStackTrace(); throw new Exception("Error detected during credit adjustment: " + exp.getMessage()); } } | public boolean update(int idTorneo, torneo torneoModificado) { int intResult = 0; String sql = "UPDATE torneo " + "SET nombreTorneo = ?, ciudad = ?, fechaInicio = ?, fechaFinal = ?, " + " organizador = ? " + " WHERE idTorneo = " + idTorneo; try { connection = conexionBD.getConnection(); connection.setAutoCommit(false); ps = connection.prepareStatement(sql); populatePreparedStatement2(torneoModificado); intResult = ps.executeUpdate(); connection.commit(); } catch (SQLException ex) { ex.printStackTrace(); try { connection.rollback(); } catch (SQLException exe) { exe.printStackTrace(); } } finally { conexionBD.close(ps); conexionBD.close(connection); } return (intResult > 0); } | 15,080 |
1 | private synchronized void ensureParsed() throws IOException, BadIMSCPException { if (cp != null) return; if (on_disk == null) { on_disk = createTemporaryFile(); OutputStream to_disk = new FileOutputStream(on_disk); IOUtils.copy(in.getInputStream(), to_disk); to_disk.close(); } try { ZipFilePackageParser parser = utils.getIMSCPParserFactory().createParser(); parser.parse(on_disk); cp = parser.getPackage(); } catch (BadParseException x) { throw new BadIMSCPException("Cannot parse content package", x); } } | private LinkedList<Datum> processDatum(Datum dataset) { ArrayList<Object[]> markerTestResults = new ArrayList<Object[]>(); ArrayList<Object[]> alleleEstimateResults = new ArrayList<Object[]>(); boolean hasAlleleNames = false; String blank = new String(""); MarkerPhenotypeAdapter theAdapter; if (dataset.getDataType().equals(MarkerPhenotype.class)) { theAdapter = new MarkerPhenotypeAdapter((MarkerPhenotype) dataset.getData()); } else theAdapter = new MarkerPhenotypeAdapter((Phenotype) dataset.getData()); int numberOfMarkers = theAdapter.getNumberOfMarkers(); if (numberOfMarkers == 0) { return calculateBLUEsFromPhenotypes(theAdapter, dataset.getName()); } int numberOfCovariates = theAdapter.getNumberOfCovariates(); int numberOfFactors = theAdapter.getNumberOfFactors(); int numberOfPhenotypes = theAdapter.getNumberOfPhenotypes(); int expectedIterations = numberOfPhenotypes * numberOfMarkers; int iterationsSofar = 0; int percentFinished = 0; File tempFile = null; File ftestFile = null; File blueFile = null; BufferedWriter ftestWriter = null; BufferedWriter BLUEWriter = null; String ftestHeader = "Trait\tMarker\tLocus\tLocus_pos\tChr\tChr_pos\tmarker_F\tmarker_p\tperm_p\tmarkerR2\tmarkerDF\tmarkerMS\terrorDF\terrorMS\tmodelDF\tmodelMS"; String BLUEHeader = "Trait\tMarker\tObs\tLocus\tLocus_pos\tChr\tChr_pos\tAllele\tEstimate"; if (writeOutputToFile) { String outputbase = outputName; if (outputbase.endsWith(".txt")) { int index = outputbase.lastIndexOf("."); outputbase = outputbase.substring(0, index); } String datasetNameNoSpace = dataset.getName().trim().replaceAll("\\ ", "_"); ftestFile = new File(outputbase + "_" + datasetNameNoSpace + "_ftest.txt"); int count = 0; while (ftestFile.exists()) { count++; ftestFile = new File(outputbase + "_" + datasetNameNoSpace + "_ftest" + count + ".txt"); } blueFile = new File(outputbase + "_" + datasetNameNoSpace + "_BLUEs.txt"); count = 0; while (blueFile.exists()) { count++; blueFile = new File(outputbase + "_" + datasetNameNoSpace + "_BLUEs" + count + ".txt"); } tempFile = new File(outputbase + "_" + datasetNameNoSpace + "_ftest.tmp"); try { if (permute) { ftestWriter = new BufferedWriter(new FileWriter(tempFile)); ftestWriter.write(ftestHeader); ftestWriter.newLine(); } else { ftestWriter = new BufferedWriter(new FileWriter(ftestFile)); ftestWriter.write(ftestHeader); ftestWriter.newLine(); } if (reportBLUEs) { BLUEWriter = new BufferedWriter(new FileWriter(blueFile)); BLUEWriter.write(BLUEHeader); BLUEWriter.newLine(); } } catch (IOException e) { myLogger.error("Failed to open file for output"); myLogger.error(e); return null; } } if (permute) { minP = new double[numberOfPhenotypes][numberOfPermutations]; for (int i = 0; i < numberOfPermutations; i++) { for (int j = 0; j < numberOfPhenotypes; j++) { minP[j][i] = 1; } } } for (int ph = 0; ph < numberOfPhenotypes; ph++) { double[] phenotypeData = theAdapter.getPhenotypeValues(ph); boolean[] missing = theAdapter.getMissingPhenotypes(ph); ArrayList<String[]> factorList = MarkerPhenotypeAdapterUtils.getFactorList(theAdapter, ph, missing); ArrayList<double[]> covariateList = MarkerPhenotypeAdapterUtils.getCovariateList(theAdapter, ph, missing); double[][] permutedData = null; if (permute) { permutedData = permuteData(phenotypeData, missing, factorList, covariateList, theAdapter); } for (int m = 0; m < numberOfMarkers; m++) { Object[] markerData = theAdapter.getMarkerValue(ph, m); boolean[] finalMissing = new boolean[missing.length]; System.arraycopy(missing, 0, finalMissing, 0, missing.length); MarkerPhenotypeAdapterUtils.updateMissing(finalMissing, theAdapter.getMissingMarkers(ph, m)); int[] nonmissingRows = MarkerPhenotypeAdapterUtils.getNonMissingIndex(finalMissing); int numberOfObs = nonmissingRows.length; double[] y = new double[numberOfObs]; for (int i = 0; i < numberOfObs; i++) y[i] = phenotypeData[nonmissingRows[i]]; int firstMarkerAlleleEstimate = 1; ArrayList<ModelEffect> modelEffects = new ArrayList<ModelEffect>(); FactorModelEffect meanEffect = new FactorModelEffect(new int[numberOfObs], false); meanEffect.setID("mean"); modelEffects.add(meanEffect); if (numberOfFactors > 0) { for (int f = 0; f < numberOfFactors; f++) { String[] afactor = factorList.get(f); String[] factorLabels = new String[numberOfObs]; for (int i = 0; i < numberOfObs; i++) factorLabels[i] = afactor[nonmissingRows[i]]; FactorModelEffect fme = new FactorModelEffect(ModelEffectUtils.getIntegerLevels(factorLabels), true, theAdapter.getFactorName(f)); modelEffects.add(fme); firstMarkerAlleleEstimate += fme.getNumberOfLevels() - 1; } } if (numberOfCovariates > 0) { for (int c = 0; c < numberOfCovariates; c++) { double[] covar = new double[numberOfObs]; double[] covariateData = covariateList.get(c); for (int i = 0; i < numberOfObs; i++) covar[i] = covariateData[nonmissingRows[i]]; modelEffects.add(new CovariateModelEffect(covar, theAdapter.getCovariateName(c))); firstMarkerAlleleEstimate++; } } ModelEffect markerEffect; boolean markerIsDiscrete = theAdapter.isMarkerDiscrete(m); ArrayList<Object> alleleNames = new ArrayList<Object>(); if (markerIsDiscrete) { Object[] markers = new Object[numberOfObs]; for (int i = 0; i < numberOfObs; i++) markers[i] = markerData[nonmissingRows[i]]; int[] markerLevels = ModelEffectUtils.getIntegerLevels(markers, alleleNames); markerEffect = new FactorModelEffect(markerLevels, true, theAdapter.getMarkerName(m)); hasAlleleNames = true; } else { double[] markerdbl = new double[numberOfObs]; for (int i = 0; i < numberOfObs; i++) markerdbl[i] = ((Double) markerData[nonmissingRows[i]]).doubleValue(); markerEffect = new CovariateModelEffect(markerdbl, theAdapter.getMarkerName(m)); } int[] alleleCounts = markerEffect.getLevelCounts(); modelEffects.add(markerEffect); int markerEffectNumber = modelEffects.size() - 1; Identifier[] taxaSublist = new Identifier[numberOfObs]; Identifier[] taxa = theAdapter.getTaxa(ph); for (int i = 0; i < numberOfObs; i++) taxaSublist[i] = taxa[nonmissingRows[i]]; boolean areTaxaReplicated = containsDuplicates(taxaSublist); double[] markerSSdf = null, errorSSdf = null, modelSSdf = null; double F, p; double[] beta = null; if (areTaxaReplicated && markerIsDiscrete) { ModelEffect taxaEffect = new FactorModelEffect(ModelEffectUtils.getIntegerLevels(taxaSublist), true); modelEffects.add(taxaEffect); SweepFastNestedModel sfnm = new SweepFastNestedModel(modelEffects, y); double[] taxaSSdf = sfnm.getTaxaInMarkerSSdf(); double[] residualSSdf = sfnm.getErrorSSdf(); markerSSdf = sfnm.getMarkerSSdf(); errorSSdf = sfnm.getErrorSSdf(); modelSSdf = sfnm.getModelcfmSSdf(); F = markerSSdf[0] / markerSSdf[1] / taxaSSdf[0] * taxaSSdf[1]; try { p = LinearModelUtils.Ftest(F, markerSSdf[1], taxaSSdf[1]); } catch (Exception e) { p = Double.NaN; } beta = sfnm.getBeta(); int markerdf = (int) markerSSdf[1]; if (permute && markerdf > 0) { updatePermutationPValues(ph, permutedData, nonMissingIndex(missing, finalMissing), getXfromModelEffects(modelEffects), sfnm.getInverseOfXtX(), markerdf); } } else { SweepFastLinearModel sflm = new SweepFastLinearModel(modelEffects, y); modelSSdf = sflm.getModelcfmSSdf(); markerSSdf = sflm.getMarginalSSdf(markerEffectNumber); errorSSdf = sflm.getResidualSSdf(); F = markerSSdf[0] / markerSSdf[1] / errorSSdf[0] * errorSSdf[1]; try { p = LinearModelUtils.Ftest(F, markerSSdf[1], errorSSdf[1]); } catch (Exception e) { p = Double.NaN; } beta = sflm.getBeta(); int markerdf = (int) markerSSdf[1]; if (permute && markerdf > 0) { updatePermutationPValues(ph, permutedData, nonMissingIndex(missing, finalMissing), getXfromModelEffects(modelEffects), sflm.getInverseOfXtX(), markerdf); } } if (!filterOutput || p < maxp) { String traitname = theAdapter.getPhenotypeName(ph); if (traitname == null) traitname = blank; String marker = theAdapter.getMarkerName(m); if (marker == null) marker = blank; String locus = theAdapter.getLocusName(m); Integer site = new Integer(theAdapter.getLocusPosition(m)); String chrname = ""; Double chrpos = Double.NaN; if (hasMap) { int ndx = -1; ndx = myMap.getMarkerIndex(marker); if (ndx > -1) { chrname = myMap.getChromosome(ndx); chrpos = myMap.getGeneticPosition(ndx); } } Object[] result = new Object[16]; int col = 0; result[col++] = traitname; result[col++] = marker; result[col++] = locus; result[col++] = site; result[col++] = chrname; result[col++] = chrpos; result[col++] = new Double(F); result[col++] = new Double(p); result[col++] = Double.NaN; result[col++] = new Double(markerSSdf[0] / (modelSSdf[0] + errorSSdf[0])); result[col++] = new Double(markerSSdf[1]); result[col++] = new Double(markerSSdf[0] / markerSSdf[1]); result[col++] = new Double(errorSSdf[1]); result[col++] = new Double(errorSSdf[0] / errorSSdf[1]); result[col++] = new Double(modelSSdf[1]); result[col++] = new Double(modelSSdf[0] / modelSSdf[1]); if (writeOutputToFile) { StringBuilder sb = new StringBuilder(); sb.append(result[0]); for (int i = 1; i < 16; i++) sb.append("\t").append(result[i]); try { ftestWriter.write(sb.toString()); ftestWriter.newLine(); } catch (IOException e) { myLogger.error("Failed to write output to ftest file. Ending prematurely"); try { ftestWriter.flush(); BLUEWriter.flush(); } catch (Exception e1) { } myLogger.error(e); return null; } } else { markerTestResults.add(result); } int numberOfMarkerAlleles = alleleNames.size(); if (numberOfMarkerAlleles == 0) numberOfMarkerAlleles++; for (int i = 0; i < numberOfMarkerAlleles; i++) { result = new Object[9]; result[0] = traitname; result[1] = marker; result[2] = new Integer(alleleCounts[i]); result[3] = locus; result[4] = site; result[5] = chrname; result[6] = chrpos; if (numberOfMarkerAlleles == 1) result[7] = ""; else result[7] = alleleNames.get(i); if (i == numberOfMarkerAlleles - 1) result[8] = 0.0; else result[8] = beta[firstMarkerAlleleEstimate + i]; if (writeOutputToFile) { StringBuilder sb = new StringBuilder(); sb.append(result[0]); for (int j = 1; j < 9; j++) sb.append("\t").append(result[j]); try { BLUEWriter.write(sb.toString()); BLUEWriter.newLine(); } catch (IOException e) { myLogger.error("Failed to write output to ftest file. Ending prematurely"); try { ftestWriter.flush(); BLUEWriter.flush(); } catch (Exception e1) { } myLogger.error(e); return null; } } else { alleleEstimateResults.add(result); } } } int tmpPercent = ++iterationsSofar * 100 / expectedIterations; if (tmpPercent > percentFinished) { percentFinished = tmpPercent; fireProgress(percentFinished); } } } fireProgress(0); if (writeOutputToFile) { try { ftestWriter.close(); BLUEWriter.close(); } catch (IOException e) { e.printStackTrace(); } } HashMap<String, Integer> traitnameMap = new HashMap<String, Integer>(); if (permute) { for (int ph = 0; ph < numberOfPhenotypes; ph++) { Arrays.sort(minP[ph]); traitnameMap.put(theAdapter.getPhenotypeName(ph), ph); } if (writeOutputToFile) { try { BufferedReader tempReader = new BufferedReader(new FileReader(tempFile)); ftestWriter = new BufferedWriter(new FileWriter(ftestFile)); ftestWriter.write(tempReader.readLine()); ftestWriter.newLine(); String input; String[] data; Pattern tab = Pattern.compile("\t"); while ((input = tempReader.readLine()) != null) { data = tab.split(input); String trait = data[0]; double pval = Double.parseDouble(data[7]); int ph = traitnameMap.get(trait); int ndx = Arrays.binarySearch(minP[ph], pval); if (ndx < 0) ndx = -ndx - 1; if (ndx == 0) ndx = 1; data[8] = Double.toString((double) ndx / (double) numberOfPermutations); ftestWriter.write(data[0]); for (int i = 1; i < data.length; i++) { ftestWriter.write("\t"); ftestWriter.write(data[i]); } ftestWriter.newLine(); } tempReader.close(); ftestWriter.close(); tempFile.delete(); } catch (IOException e) { myLogger.error(e); } } else { for (Object[] result : markerTestResults) { String trait = result[0].toString(); double pval = (Double) result[7]; int ph = traitnameMap.get(trait); int ndx = Arrays.binarySearch(minP[ph], pval); if (ndx < 0) ndx = -ndx - 1; if (ndx == 0) ndx = 1; result[8] = new Double((double) ndx / (double) numberOfPermutations); } } } String[] columnLabels = new String[] { "Trait", "Marker", "Locus", "Locus_pos", "Chr", "Chr_pos", "marker_F", "marker_p", "perm_p", "markerR2", "markerDF", "markerMS", "errorDF", "errorMS", "modelDF", "modelMS" }; boolean hasMarkerNames = theAdapter.hasMarkerNames(); LinkedList<Integer> outputList = new LinkedList<Integer>(); outputList.add(0); if (hasMarkerNames) outputList.add(1); outputList.add(2); outputList.add(3); if (hasMap) { outputList.add(4); outputList.add(5); } outputList.add(6); outputList.add(7); if (permute) outputList.add(8); for (int i = 9; i < 16; i++) outputList.add(i); LinkedList<Datum> resultset = new LinkedList<Datum>(); int nrows = markerTestResults.size(); Object[][] table = new Object[nrows][]; int numberOfColumns = outputList.size(); String[] colnames = new String[numberOfColumns]; int count = 0; for (Integer ndx : outputList) colnames[count++] = columnLabels[ndx]; for (int i = 0; i < nrows; i++) { table[i] = new Object[numberOfColumns]; Object[] result = markerTestResults.get(i); count = 0; for (Integer ndx : outputList) table[i][count++] = result[ndx]; } StringBuilder tableName = new StringBuilder("GLM_marker_test_"); tableName.append(dataset.getName()); StringBuilder comments = new StringBuilder("Tests of Marker-Phenotype Association"); comments.append("GLM: fixed effect linear model\n"); comments.append("Data set: ").append(dataset.getName()); comments.append("\nmodel: trait = mean"); for (int i = 0; i < theAdapter.getNumberOfFactors(); i++) { comments.append(" + "); comments.append(theAdapter.getFactorName(i)); } for (int i = 0; i < theAdapter.getNumberOfCovariates(); i++) { comments.append(" + "); comments.append(theAdapter.getCovariateName(i)); } comments.append(" + marker"); if (writeOutputToFile) { comments.append("\nOutput written to " + ftestFile.getPath()); } TableReport markerTestReport = new SimpleTableReport("Marker Test", colnames, table); resultset.add(new Datum(tableName.toString(), markerTestReport, comments.toString())); int[] outputIndex; columnLabels = new String[] { "Trait", "Marker", "Obs", "Locus", "Locus_pos", "Chr", "Chr_pos", "Allele", "Estimate" }; if (hasAlleleNames) { if (hasMarkerNames && hasMap) { outputIndex = new int[] { 0, 1, 2, 3, 4, 5, 6, 7, 8 }; } else if (hasMarkerNames) { outputIndex = new int[] { 0, 1, 2, 3, 4, 7, 8 }; } else if (hasMap) { outputIndex = new int[] { 0, 2, 3, 4, 5, 6, 7, 8 }; } else { outputIndex = new int[] { 0, 2, 3, 4, 7, 8 }; } } else { if (hasMarkerNames && hasMap) { outputIndex = new int[] { 0, 1, 2, 3, 4, 5, 6, 8 }; } else if (hasMarkerNames) { outputIndex = new int[] { 0, 1, 2, 3, 4, 8 }; } else if (hasMap) { outputIndex = new int[] { 0, 2, 3, 4, 5, 6, 8 }; } else { outputIndex = new int[] { 0, 2, 3, 4, 8 }; } } nrows = alleleEstimateResults.size(); table = new Object[nrows][]; numberOfColumns = outputIndex.length; colnames = new String[numberOfColumns]; for (int j = 0; j < numberOfColumns; j++) { colnames[j] = columnLabels[outputIndex[j]]; } for (int i = 0; i < nrows; i++) { table[i] = new Object[numberOfColumns]; Object[] result = alleleEstimateResults.get(i); for (int j = 0; j < numberOfColumns; j++) { table[i][j] = result[outputIndex[j]]; } } tableName = new StringBuilder("GLM allele estimates for "); tableName.append(dataset.getName()); comments = new StringBuilder("Marker allele effect estimates\n"); comments.append("GLM: fixed effect linear model\n"); comments.append("Data set: ").append(dataset.getName()); comments.append("\nmodel: trait = mean"); for (int i = 0; i < theAdapter.getNumberOfFactors(); i++) { comments.append(" + "); comments.append(theAdapter.getFactorName(i)); } for (int i = 0; i < theAdapter.getNumberOfCovariates(); i++) { comments.append(" + "); comments.append(theAdapter.getCovariateName(i)); } comments.append(" + marker"); if (writeOutputToFile) { comments.append("\nOutput written to " + blueFile.getPath()); } TableReport alleleEstimateReport = new SimpleTableReport("Allele Estimates", colnames, table); resultset.add(new Datum(tableName.toString(), alleleEstimateReport, comments.toString())); fireProgress(0); return resultset; } | 15,081 |
1 | private void gzip(FileHolder fileHolder) { byte[] buffer = new byte[BUFFER_SIZE]; int bytes_read; if (fileHolder.selectedFileList.size() == 0) { return; } File destFile = new File(fileHolder.destFiles[0]); try { OutputStream outStream = new FileOutputStream(destFile); outStream = new GZIPOutputStream(outStream); File selectedFile = fileHolder.selectedFileList.get(0); super.currentObjBeingProcessed = selectedFile; this.inStream = new FileInputStream(selectedFile); while ((bytes_read = this.inStream.read(buffer)) != -1) { outStream.write(buffer, 0, bytes_read); } outStream.close(); this.inStream.close(); } catch (IOException e) { errEntry.setThrowable(e); errEntry.setAppContext("gzip()"); errEntry.setAppMessage("Error gzip'ing: " + destFile); logger.logError(errEntry); } } | public static boolean encodeFileToFile(String infile, String outfile) { boolean success = false; java.io.InputStream in = null; java.io.OutputStream out = null; try { in = new Base64.InputStream(new java.io.BufferedInputStream(new java.io.FileInputStream(infile)), Base64.ENCODE); out = new java.io.BufferedOutputStream(new java.io.FileOutputStream(outfile)); byte[] buffer = new byte[65536]; int read = -1; while ((read = in.read(buffer)) >= 0) { out.write(buffer, 0, read); } success = true; } catch (java.io.IOException exc) { exc.printStackTrace(); } finally { try { in.close(); } catch (Exception exc) { } try { out.close(); } catch (Exception exc) { } } return success; } | 15,082 |
0 | public static Model loadPrecomputedModel(URL url) { ArrayList<Geometry[]> frames = new ArrayList<Geometry[]>(); if (url.toExternalForm().endsWith(".amo")) { try { BufferedReader reader = new BufferedReader(new InputStreamReader(url.openStream())); String objFileName = reader.readLine(); objFileName = url.toExternalForm().substring(0, url.toExternalForm().lastIndexOf("/")) + "/" + objFileName; Model baseModel = loadOBJFrames(ModelLoader.getInstance(), objFileName, frames); ArrayList<ModelAnimation> anims = new ArrayList<ModelAnimation>(); String line; while ((line = reader.readLine()) != null) { StringTokenizer tokenizer = new StringTokenizer(line); String animName = tokenizer.nextToken(); int from = Integer.valueOf(tokenizer.nextToken()); int to = Integer.valueOf(tokenizer.nextToken()); tokenizer.nextToken(); int numFrames = to - from + 1; PrecomputedAnimationKeyFrameController[] controllers = new PrecomputedAnimationKeyFrameController[baseModel.getShapesCount()]; for (int i = 0; i < baseModel.getShapesCount(); i++) { Shape3D shape = baseModel.getShape(i); PrecomputedAnimationKeyFrame[] keyFrames = new PrecomputedAnimationKeyFrame[numFrames]; int k = 0; for (int j = from; j <= to; j++) { keyFrames[k++] = new PrecomputedAnimationKeyFrame(frames.get(j)[i]); } controllers[i] = new PrecomputedAnimationKeyFrameController(keyFrames, shape); } anims.add(new ModelAnimation(animName, numFrames, 25f, controllers)); } baseModel.setAnimations(anims.toArray(new ModelAnimation[anims.size()])); return (baseModel); } catch (FileNotFoundException e) { e.printStackTrace(); return (null); } catch (IOException e) { e.printStackTrace(); return (null); } } { Model baseModel = loadOBJFrames(ModelLoader.getInstance(), url.toExternalForm(), frames); PrecomputedAnimationKeyFrameController[] controllers = new PrecomputedAnimationKeyFrameController[baseModel.getShapesCount()]; for (int i = 0; i < baseModel.getShapesCount(); i++) { Shape3D shape = baseModel.getShape(i); PrecomputedAnimationKeyFrame[] keyFrames = new PrecomputedAnimationKeyFrame[frames.size()]; for (int j = 0; j < frames.size(); j++) { keyFrames[j] = new PrecomputedAnimationKeyFrame(frames.get(j)[i]); } controllers[i] = new PrecomputedAnimationKeyFrameController(keyFrames, shape); } ModelAnimation[] anims = new ModelAnimation[] { new ModelAnimation("default", frames.size(), 25f, controllers) }; baseModel.setAnimations(anims); return (baseModel); } } | public static String CreateHash(String s) { String str = s.toString(); if (str == null || str.length() == 0) { throw new IllegalArgumentException("String cannot be null or empty"); } StringBuffer hexString = new StringBuffer(); try { MessageDigest md = MessageDigest.getInstance("MD5"); md.update(str.getBytes()); byte[] hash = md.digest(); for (int i = 0; i < hash.length; i++) { if ((0xff & hash[i]) < 0x10) { hexString.append("0" + Integer.toHexString((0xFF & hash[i]))); } else { hexString.append(Integer.toHexString(0xFF & hash[i])); } } } catch (NoSuchAlgorithmException e) { e.printStackTrace(); } return (hexString.toString()); } | 15,083 |
1 | public void insertJobLog(String userId, String[] checkId, String checkType, String objType) throws Exception { DBOperation dbo = null; Connection connection = null; PreparedStatement preStm = null; String sql = "insert into COFFICE_JOBLOG_CHECKAUTH (USER_ID,CHECK_ID,CHECK_TYPE,OBJ_TYPE) values (?,?,?,?)"; String cleanSql = "delete from COFFICE_JOBLOG_CHECKAUTH where " + "user_id = '" + userId + "' and check_type = '" + checkType + "' and obj_type = '" + objType + "'"; try { dbo = createDBOperation(); connection = dbo.getConnection(); connection.setAutoCommit(false); preStm = connection.prepareStatement(cleanSql); int dCount = preStm.executeUpdate(); preStm = connection.prepareStatement(sql); String sHaveIns = ","; for (int j = 0; j < checkId.length; j++) { if (sHaveIns.indexOf("," + checkId[j] + ",") < 0) { preStm.setInt(1, Integer.parseInt(userId)); preStm.setInt(2, Integer.parseInt(checkId[j])); preStm.setInt(3, Integer.parseInt(checkType)); preStm.setInt(4, Integer.parseInt(objType)); preStm.executeUpdate(); sHaveIns += checkId[j] + ","; } } connection.commit(); } catch (Exception ex) { log.debug((new Date().toString()) + " ������Ȩ��ʧ��! "); try { connection.rollback(); } catch (SQLException e) { throw e; } throw ex; } finally { close(null, null, preStm, connection, dbo); } } | public void addGames(List<Game> games) throws StadiumException, SQLException { Connection conn = ConnectionManager.getManager().getConnection(); conn.setAutoCommit(false); PreparedStatement stm = null; ResultSet rs = null; try { for (Game game : games) { stm = conn.prepareStatement(Statements.SELECT_STADIUM); stm.setString(1, game.getStadiumName()); stm.setString(2, game.getStadiumCity()); rs = stm.executeQuery(); int stadiumId = -1; while (rs.next()) { stadiumId = rs.getInt("stadiumID"); } if (stadiumId == -1) throw new StadiumException("No such stadium"); stm = conn.prepareStatement(Statements.INSERT_GAME); stm.setInt(1, stadiumId); stm.setDate(2, game.getGameDate()); stm.setTime(3, game.getGameTime()); stm.setString(4, game.getTeamA()); stm.setString(5, game.getTeamB()); stm.executeUpdate(); int gameId = getMaxId(); List<SectorPrice> sectorPrices = game.getSectorPrices(); for (SectorPrice price : sectorPrices) { stm = conn.prepareStatement(Statements.INSERT_TICKET_PRICE); stm.setInt(1, gameId); stm.setInt(2, price.getSectorId()); stm.setInt(3, price.getPrice()); stm.executeUpdate(); } } } catch (SQLException e) { conn.rollback(); throw e; } finally { rs.close(); stm.close(); } conn.commit(); conn.setAutoCommit(true); } | 15,084 |
0 | public ResponseStatus nowPlaying(String artist, String track, String album, int length, int tracknumber) throws IOException { if (sessionId == null) throw new IllegalStateException("Perform successful handshake first."); String b = album != null ? encode(album) : ""; String l = length == -1 ? "" : String.valueOf(length); String n = tracknumber == -1 ? "" : String.valueOf(tracknumber); String body = String.format("s=%s&a=%s&t=%s&b=%s&l=%s&n=%s&m=", sessionId, encode(artist), encode(track), b, l, n); if (Caller.getInstance().isDebugMode()) System.out.println("now playing: " + body); Proxy proxy = Caller.getInstance().getProxy(); HttpURLConnection urlConnection = Caller.getInstance().openConnection(nowPlayingUrl); urlConnection.setRequestMethod("POST"); urlConnection.setDoOutput(true); OutputStream outputStream = urlConnection.getOutputStream(); BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(outputStream)); writer.write(body); writer.close(); InputStream is = urlConnection.getInputStream(); BufferedReader r = new BufferedReader(new InputStreamReader(is)); String status = r.readLine(); r.close(); return new ResponseStatus(ResponseStatus.codeForStatus(status)); } | @Test public void test_baseMaterialsForTypeID() throws Exception { URL url = new URL(baseUrl + "/baseMaterialsForTypeID/587"); HttpURLConnection connection = (HttpURLConnection) url.openConnection(); connection.setRequestMethod("GET"); connection.setRequestProperty("Accept", "application/json"); assertThat(connection.getResponseCode(), equalTo(200)); assertThat(getResponse(connection), equalTo("[{\"materialTypeID\":34,\"materialTypeName\":\"Tritanium\",\"materialTypeCategoryID\":4,\"materialTypeIcon\":\"06_14\",\"materialVolume\":\"0.01\",\"quantity\":20524},{\"materialTypeID\":35,\"materialTypeName\":\"Pyerite\",\"materialTypeCategoryID\":4,\"materialTypeIcon\":\"06_15\",\"materialVolume\":\"0.01\",\"quantity\":5529},{\"materialTypeID\":36,\"materialTypeName\":\"Mexallon\",\"materialTypeCategoryID\":4,\"materialTypeIcon\":\"06_12\",\"materialVolume\":\"0.01\",\"quantity\":1841},{\"materialTypeID\":37,\"materialTypeName\":\"Isogen\",\"materialTypeCategoryID\":4,\"materialTypeIcon\":\"06_16\",\"materialVolume\":\"0.01\",\"quantity\":317},{\"materialTypeID\":38,\"materialTypeName\":\"Nocxium\",\"materialTypeCategoryID\":4,\"materialTypeIcon\":\"11_09\",\"materialVolume\":\"0.01\",\"quantity\":118},{\"materialTypeID\":39,\"materialTypeName\":\"Zydrine\",\"materialTypeCategoryID\":4,\"materialTypeIcon\":\"11_11\",\"materialVolume\":\"0.01\",\"quantity\":13},{\"materialTypeID\":40,\"materialTypeName\":\"Megacyte\",\"materialTypeCategoryID\":4,\"materialTypeIcon\":\"11_10\",\"materialVolume\":\"0.01\",\"quantity\":1}]")); assertThat(connection.getHeaderField("Content-Type"), equalTo("application/json; charset=utf-8")); connection = (HttpURLConnection) url.openConnection(); connection.setRequestMethod("GET"); connection.setRequestProperty("Accept", "application/xml"); assertThat(connection.getResponseCode(), equalTo(200)); assertThat(getResponse(connection), equalTo("<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"yes\"?><rowset><row xsi:type=\"invTypeMaterialDto\" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\"><materialTypeCategoryID>4</materialTypeCategoryID><materialTypeID>34</materialTypeID><materialTypeIcon>06_14</materialTypeIcon><materialTypeName>Tritanium</materialTypeName><materialVolume>0.01</materialVolume><quantity>20524</quantity></row><row xsi:type=\"invTypeMaterialDto\" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\"><materialTypeCategoryID>4</materialTypeCategoryID><materialTypeID>35</materialTypeID><materialTypeIcon>06_15</materialTypeIcon><materialTypeName>Pyerite</materialTypeName><materialVolume>0.01</materialVolume><quantity>5529</quantity></row><row xsi:type=\"invTypeMaterialDto\" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\"><materialTypeCategoryID>4</materialTypeCategoryID><materialTypeID>36</materialTypeID><materialTypeIcon>06_12</materialTypeIcon><materialTypeName>Mexallon</materialTypeName><materialVolume>0.01</materialVolume><quantity>1841</quantity></row><row xsi:type=\"invTypeMaterialDto\" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\"><materialTypeCategoryID>4</materialTypeCategoryID><materialTypeID>37</materialTypeID><materialTypeIcon>06_16</materialTypeIcon><materialTypeName>Isogen</materialTypeName><materialVolume>0.01</materialVolume><quantity>317</quantity></row><row xsi:type=\"invTypeMaterialDto\" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\"><materialTypeCategoryID>4</materialTypeCategoryID><materialTypeID>38</materialTypeID><materialTypeIcon>11_09</materialTypeIcon><materialTypeName>Nocxium</materialTypeName><materialVolume>0.01</materialVolume><quantity>118</quantity></row><row xsi:type=\"invTypeMaterialDto\" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\"><materialTypeCategoryID>4</materialTypeCategoryID><materialTypeID>39</materialTypeID><materialTypeIcon>11_11</materialTypeIcon><materialTypeName>Zydrine</materialTypeName><materialVolume>0.01</materialVolume><quantity>13</quantity></row><row xsi:type=\"invTypeMaterialDto\" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\"><materialTypeCategoryID>4</materialTypeCategoryID><materialTypeID>40</materialTypeID><materialTypeIcon>11_10</materialTypeIcon><materialTypeName>Megacyte</materialTypeName><materialVolume>0.01</materialVolume><quantity>1</quantity></row></rowset>")); assertThat(connection.getHeaderField("Content-Type"), equalTo("application/xml; charset=utf-8")); } | 15,085 |
0 | public static void getCoverFromUrl(URL url, String directory) { try { url.openConnection(); InputStream is = url.openStream(); System.out.flush(); FileOutputStream fos = null; fos = new FileOutputStream(directory); int oneChar, count = 0; while ((oneChar = is.read()) != -1) { fos.write(oneChar); count++; } is.close(); fos.close(); } catch (MalformedURLException e) { System.err.println(" getCoverFromUrl " + e.toString()); e.printStackTrace(); } catch (IOException e) { System.err.println(" getCoverFromUrl " + e.toString()); e.printStackTrace(); } } | private Document post(String location, String content) throws ApplicationException { Document doc = null; try { URL url = new URL(location); HttpURLConnection uc = (HttpURLConnection) url.openConnection(); uc.setRequestMethod("POST"); uc.setRequestProperty("Content-Type", "application/xml"); uc.setRequestProperty("X-POST_DATA_FORMAT", "xml"); uc.setDoOutput(true); OutputStreamWriter out = new OutputStreamWriter(uc.getOutputStream()); out.write("<request>"); out.write("<token>" + configuration.getBackpackPassword() + "</token>"); if (content != null) { out.write("<item><content>" + content + "</content></item>"); } out.write("</request>"); out.close(); doc = XmlUtils.readDocumentFromInputStream(uc.getInputStream()); System.out.println(XmlUtils.toString(doc)); } catch (IOException e) { e.printStackTrace(); throw new ApplicationException(e); } return doc; } | 15,086 |
0 | protected static File UrlToFile(String urlSt) throws CaughtException { try { logger.info("copy from url: " + urlSt); URL url = new URL(urlSt); InputStream input = url.openStream(); File dir = tempDir; File tempFile = new File(tempDir + File.separator + fileName(url)); logger.info("created: " + tempFile.getAbsolutePath()); copyFile(tempFile, input); return tempFile; } catch (IOException e) { throw new CaughtException(e, logger); } } | public static boolean validPassword(String password, String passwordInDb) throws NoSuchAlgorithmException, UnsupportedEncodingException { byte[] pwdInDb = hexStringToByte(passwordInDb); byte[] salt = new byte[SALT_LENGTH]; System.arraycopy(pwdInDb, 0, salt, 0, SALT_LENGTH); MessageDigest md = MessageDigest.getInstance("MD5"); md.update(salt); md.update(password.getBytes("UTF-8")); byte[] digest = md.digest(); byte[] digestInDb = new byte[pwdInDb.length - SALT_LENGTH]; System.arraycopy(pwdInDb, SALT_LENGTH, digestInDb, 0, digestInDb.length); if (Arrays.equals(digest, digestInDb)) { return true; } else { return false; } } | 15,087 |
0 | public void myCheckCredHandler(View v) { Log.d("login_section", "entered handler"); EditText Username = (EditText) findViewById(R.id.Username); EditText Password = (EditText) findViewById(R.id.user_pass); String username_S = Username.getText().toString(); String pass_S = Password.getText().toString(); TextView ltv = (TextView) findViewById(R.id.LoginPagetv); HttpClient httpclient = createHttpClient(); HttpPost httppost = new HttpPost(authenticationURL); try { List<NameValuePair> nameValuePairs = new ArrayList<NameValuePair>(2); nameValuePairs.add(new BasicNameValuePair("login", username_S)); nameValuePairs.add(new BasicNameValuePair("password", pass_S)); httppost.setEntity(new UrlEncodedFormEntity(nameValuePairs)); HttpResponse response = httpclient.execute(httppost); int status = response.getStatusLine().getStatusCode(); String responseBody = EntityUtils.toString(response.getEntity()); Log.d("login_section", responseBody); JSONObject jsonObject = new JSONObject(responseBody); if (status == this.statusOK && jsonObject.getBoolean("logged_in")) { ltv.setText("You have been logged in. :D"); etracks.setLogged(true); etracks.setUserToken(jsonObject.getString("user_token")); Intent it = new Intent(Intent.ACTION_VIEW); it.setClassName(this, etracks.class.getName()); this.finish(); startActivity(it); } else if (status == this.statusUnprocessable && !jsonObject.getBoolean("logged_in")) { if (!jsonObject.isNull("errors")) ltv.setText(jsonObject.getString("errors")); else ltv.setText("login unsuccessful"); } else Log.d("login_section", "what just happened?"); } catch (ClientProtocolException e) { } catch (IOException e) { } catch (JSONException e) { e.printStackTrace(); } } | public static File enregistrerFichier(String fileName, File file, String path, String fileMime) throws Exception { if (file != null) { try { HttpServletRequest request = ServletActionContext.getRequest(); HttpSession session = request.getSession(); String pathFile = session.getServletContext().getRealPath(path) + File.separator + fileName; File outfile = new File(pathFile); String[] nomPhotoTab = fileName.split("\\."); String extension = nomPhotoTab[nomPhotoTab.length - 1]; StringBuffer pathResBuff = new StringBuffer(nomPhotoTab[0]); for (int i = 1; i < nomPhotoTab.length - 1; i++) { pathResBuff.append(".").append(nomPhotoTab[i]); } String pathRes = pathResBuff.toString(); String nomPhoto = fileName; for (int i = 0; !outfile.createNewFile(); i++) { nomPhoto = pathRes + "_" + +i + "." + extension; pathFile = session.getServletContext().getRealPath(path) + File.separator + nomPhoto; outfile = new File(pathFile); } logger.debug(" enregistrerFichier - Enregistrement du fichier : " + pathFile); FileChannel in = null; FileChannel out = null; try { in = new FileInputStream(file).getChannel(); out = new FileOutputStream(outfile).getChannel(); in.transferTo(0, in.size(), out); } catch (Exception e) { e.printStackTrace(); } finally { if (in != null) { try { in.close(); } catch (IOException e) { } } if (out != null) { try { out.close(); } catch (IOException e) { } } } return outfile; } catch (IOException e) { logger.error("Erreur lors de l'enregistrement de l'image ", e); throw new Exception("Erreur lors de l'enregistrement de l'image "); } } return null; } | 15,088 |
1 | public void salva(UploadedFile imagem, Usuario usuario) { File destino; if (usuario.getId() == null) { destino = new File(pastaImagens, usuario.hashCode() + ".jpg"); } else { destino = new File(pastaImagens, usuario.getId() + ".jpg"); } try { IOUtils.copyLarge(imagem.getFile(), new FileOutputStream(destino)); } catch (Exception e) { throw new RuntimeException("Erro ao copiar imagem", e); } redimensionar(destino.getPath(), destino.getPath(), "jpg", 110, 110); } | public static File copy(String inFileName, String outFileName) throws IOException { File inputFile = new File(inFileName); File outputFile = new File(outFileName); FileReader in = new FileReader(inputFile); FileWriter out = new FileWriter(outputFile); int c; while ((c = in.read()) != -1) out.write(c); in.close(); out.close(); return outputFile; } | 15,089 |
1 | public void movePrior(String[] showOrder, String[] orgID, String targetShowOrder, String targetOrgID) throws Exception { Connection con = null; PreparedStatement ps = null; ResultSet result = null; int moveCount = showOrder.length; DBOperation dbo = factory.createDBOperation(POOL_NAME); String strQuery = "select show_order from " + Common.ORGANIZE_TABLE + " where show_order=" + showOrder[moveCount - 1] + " and organize_id= '" + orgID[moveCount - 1] + "'"; try { con = dbo.getConnection(); con.setAutoCommit(false); ps = con.prepareStatement(strQuery); result = ps.executeQuery(); int maxOrderNo = 0; if (result.next()) { maxOrderNo = result.getInt(1); } String[] sqls = new String[moveCount + 1]; sqls[0] = "update " + Common.ORGANIZE_TABLE + " set show_order=" + maxOrderNo + " where show_order=" + targetShowOrder + " and organize_id= '" + targetOrgID + "'"; for (int i = 0; i < showOrder.length; i++) { sqls[i + 1] = "update " + Common.ORGANIZE_TABLE + " set show_order=show_order-1" + " where show_order=" + showOrder[i] + " and organize_id= '" + orgID[i] + "'"; } for (int j = 0; j < sqls.length; j++) { ps = con.prepareStatement(sqls[j]); int resultCount = ps.executeUpdate(); if (resultCount != 1) { throw new CesSystemException("Organize.movePrior(): ERROR Inserting data " + "in T_SYS_ORGANIZE update !! resultCount = " + resultCount); } } con.commit(); } catch (SQLException se) { if (con != null) { con.rollback(); } throw new CesSystemException("Organize.movePrior(): SQLException while mov organize order " + " :\n\t" + se); } finally { con.setAutoCommit(true); close(dbo, ps, result); } } | private void runUpdate(String sql, boolean transactional) { log().info("Vacuumd executing statement: " + sql); Connection dbConn = null; boolean commitRequired = false; boolean autoCommitFlag = !transactional; try { dbConn = getDataSourceFactory().getConnection(); dbConn.setAutoCommit(autoCommitFlag); PreparedStatement stmt = dbConn.prepareStatement(sql); int count = stmt.executeUpdate(); stmt.close(); if (log().isDebugEnabled()) { log().debug("Vacuumd: Ran update " + sql + ": this affected " + count + " rows"); } commitRequired = transactional; } catch (SQLException ex) { log().error("Vacuumd: Database error execuating statement " + sql, ex); } finally { if (dbConn != null) { try { if (commitRequired) { dbConn.commit(); } else if (transactional) { dbConn.rollback(); } } catch (SQLException ex) { } finally { if (dbConn != null) { try { dbConn.close(); } catch (Exception e) { } } } } } } | 15,090 |
1 | @org.junit.Test public void simpleRead() throws Exception { final InputStream istream = StatsInputStreamTest.class.getResourceAsStream("/testFile.txt"); final StatsInputStream ris = new StatsInputStream(istream); assertEquals("read size", 0, ris.getSize()); IOUtils.copy(ris, new NullOutputStream()); assertEquals("in the end", 30, ris.getSize()); } | public static void copyFile(File source, File destination) { if (!source.exists()) { return; } if ((destination.getParentFile() != null) && (!destination.getParentFile().exists())) { destination.getParentFile().mkdirs(); } try { FileChannel srcChannel = new FileInputStream(source).getChannel(); FileChannel dstChannel = new FileOutputStream(destination).getChannel(); dstChannel.transferFrom(srcChannel, 0, srcChannel.size()); srcChannel.close(); dstChannel.close(); } catch (IOException ioe) { ioe.printStackTrace(); } } | 15,091 |
1 | private static void readAndRewrite(File inFile, File outFile) throws IOException { ImageInputStream iis = ImageIO.createImageInputStream(new BufferedInputStream(new FileInputStream(inFile))); DcmParser dcmParser = DcmParserFactory.getInstance().newDcmParser(iis); Dataset ds = DcmObjectFactory.getInstance().newDataset(); dcmParser.setDcmHandler(ds.getDcmHandler()); dcmParser.parseDcmFile(null, Tags.PixelData); PixelDataReader pdReader = pdFact.newReader(ds, iis, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); System.out.println("reading " + inFile + "..."); pdReader.readPixelData(false); ImageOutputStream out = ImageIO.createImageOutputStream(new BufferedOutputStream(new FileOutputStream(outFile))); DcmEncodeParam dcmEncParam = DcmEncodeParam.IVR_LE; ds.writeDataset(out, dcmEncParam); ds.writeHeader(out, dcmEncParam, Tags.PixelData, dcmParser.getReadVR(), dcmParser.getReadLength()); System.out.println("writing " + outFile + "..."); PixelDataWriter pdWriter = pdFact.newWriter(pdReader.getPixelDataArray(), false, ds, out, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); pdWriter.writePixelData(); out.flush(); out.close(); System.out.println("done!"); } | @Override public void handle(HttpExchange http) throws IOException { Headers reqHeaders = http.getRequestHeaders(); Headers respHeader = http.getResponseHeaders(); respHeader.add("Content-Type", "text/plain"); http.sendResponseHeaders(200, 0); PrintWriter console = new PrintWriter(System.err); PrintWriter web = new PrintWriter(http.getResponseBody()); PrintWriter out = new PrintWriter(new YWriter(web, console)); out.println("### " + new Date() + " ###"); out.println("Method: " + http.getRequestMethod()); out.println("Protocol: " + http.getProtocol()); out.println("RemoteAddress.HostName: " + http.getRemoteAddress().getHostName()); for (String key : reqHeaders.keySet()) { out.println("* \"" + key + "\""); for (String v : reqHeaders.get(key)) { out.println("\t" + v); } } InputStream in = http.getRequestBody(); if (in != null) { out.println(); IOUtils.copyTo(new InputStreamReader(in), out); in.close(); } out.flush(); out.close(); } | 15,092 |
1 | public static void main(final String[] args) { final Runnable startDerby = new Runnable() { public void run() { try { final NetworkServerControl control = new NetworkServerControl(InetAddress.getByName("localhost"), 1527); control.start(new PrintWriter(System.out)); } catch (final Exception ex) { throw new RuntimeException(ex); } } }; new Thread(startDerby).start(); final Runnable startActiveMq = new Runnable() { public void run() { Main.main(new String[] { "start", "xbean:file:active-mq-config.xml" }); } }; new Thread(startActiveMq).start(); final Runnable startMailServer = new Runnable() { public void run() { final SimpleMessageListener listener = new SimpleMessageListener() { public final boolean accept(final String from, final String recipient) { return true; } public final void deliver(final String from, final String recipient, final InputStream data) throws TooMuchDataException, IOException { System.out.println("FROM: " + from); System.out.println("TO: " + recipient); final File tmpDir = new File(System.getProperty("java.io.tmpdir")); final File file = new File(tmpDir, recipient); final FileWriter fw = new FileWriter(file); try { IOUtils.copy(data, fw); } finally { fw.close(); } } }; final SMTPServer smtpServer = new SMTPServer(new SimpleMessageListenerAdapter(listener)); smtpServer.start(); System.out.println("Started SMTP Server"); } }; new Thread(startMailServer).start(); } | public static void createModelZip(String filename, String tempdir, boolean overwrite) throws Exception { FileTools.checkOutput(filename, overwrite); BufferedInputStream origin = null; FileOutputStream dest = new FileOutputStream(filename); ZipOutputStream out = new ZipOutputStream(new BufferedOutputStream(dest)); int BUFFER = 2048; byte data[] = new byte[BUFFER]; File f = new File(tempdir); for (File fs : f.listFiles()) { FileInputStream fi = new FileInputStream(fs.getAbsolutePath()); origin = new BufferedInputStream(fi, BUFFER); ZipEntry entry = new ZipEntry(fs.getName()); out.putNextEntry(entry); int count; while ((count = origin.read(data, 0, BUFFER)) != -1) out.write(data, 0, count); out.closeEntry(); origin.close(); } out.close(); } | 15,093 |
1 | @RequestMapping(value = "/image/{fileName}", method = RequestMethod.GET) public void getImage(@PathVariable String fileName, HttpServletRequest req, HttpServletResponse res) throws Exception { File file = new File(STORAGE_PATH + fileName + ".jpg"); res.setHeader("Cache-Control", "no-store"); res.setHeader("Pragma", "no-cache"); res.setDateHeader("Expires", 0); res.setContentType("image/jpg"); ServletOutputStream ostream = res.getOutputStream(); IOUtils.copy(new FileInputStream(file), ostream); ostream.flush(); ostream.close(); } | public void doFilter(ServletRequest request, ServletResponse response, FilterChain chain) throws IOException, ServletException { if (!(request instanceof HttpServletRequest)) { log.fatal("not a http request"); return; } HttpServletRequest httpRequest = (HttpServletRequest) request; String uri = httpRequest.getRequestURI(); int pathStartIdx = 0; String resourceName = null; pathStartIdx = uri.indexOf(path); if (pathStartIdx <= -1) { log.fatal("the url pattern must match: " + path + " found uri: " + uri); return; } resourceName = uri.substring(pathStartIdx + path.length()); int suffixIdx = uri.lastIndexOf('.'); if (suffixIdx <= -1) { log.fatal("no file suffix found for resource: " + uri); return; } String suffix = uri.substring(suffixIdx + 1).toLowerCase(); String mimeType = (String) mimeTypes.get(suffix); if (mimeType == null) { log.fatal("no mimeType found for resource: " + uri); log.fatal("valid mimeTypes are: " + mimeTypes.keySet()); return; } String themeName = getThemeName(); if (themeName == null) { themeName = this.themeName; } if (!themeName.startsWith("/")) { themeName = "/" + themeName; } InputStream is = null; is = ResourceFilter.class.getResourceAsStream(themeName + resourceName); if (is != null) { IOUtils.copy(is, response.getOutputStream()); response.setContentType(mimeType); response.flushBuffer(); IOUtils.closeQuietly(response.getOutputStream()); IOUtils.closeQuietly(is); } else { log.fatal("error loading resource: " + resourceName); } } | 15,094 |
1 | public boolean renameTo(File dest) throws IOException { if (dest == null) { throw new NullPointerException("dest"); } if (!file.renameTo(dest)) { FileInputStream inputStream = new FileInputStream(file); FileOutputStream outputStream = new FileOutputStream(dest); FileChannel in = inputStream.getChannel(); FileChannel out = outputStream.getChannel(); long destsize = in.transferTo(0, size, out); in.close(); out.close(); if (destsize == size) { file.delete(); file = dest; isRenamed = true; return true; } else { dest.delete(); return false; } } file = dest; isRenamed = true; return true; } | private void mergeOne(String level, char strand, String filename, Path outPath, FileSystem srcFS, FileSystem dstFS, Timer to) throws IOException { to.start(); final OutputStream outs = dstFS.create(new Path(outPath, filename)); final FileStatus[] parts = srcFS.globStatus(new Path(sorted ? getSortOutputDir(level, strand) : wrkDir, filename + "-[0-9][0-9][0-9][0-9][0-9][0-9]")); for (final FileStatus part : parts) { final InputStream ins = srcFS.open(part.getPath()); IOUtils.copyBytes(ins, outs, getConf(), false); ins.close(); } for (final FileStatus part : parts) srcFS.delete(part.getPath(), false); outs.write(BlockCompressedStreamConstants.EMPTY_GZIP_BLOCK); outs.close(); System.out.printf("summarize :: Merged %s%c in %d.%03d s.\n", level, strand, to.stopS(), to.fms()); } | 15,095 |
0 | private String hashSong(Song s) { if (s == null) return null; try { MessageDigest digest = MessageDigest.getInstance("SHA-256"); digest.update(s.getTitle().getBytes()); digest.update(s.getAllLyrics().getBytes()); String hash = Base64.encodeBytes(digest.digest()); return hash; } catch (NoSuchAlgorithmException e) { e.printStackTrace(); return null; } } | protected boolean writeFile(Interest outstandingInterest) throws IOException { File fileToWrite = ccnNameToFilePath(outstandingInterest.name()); Log.info("CCNFileProxy: extracted request for file: " + fileToWrite.getAbsolutePath() + " exists? ", fileToWrite.exists()); if (!fileToWrite.exists()) { Log.warning("File {0} does not exist. Ignoring request.", fileToWrite.getAbsoluteFile()); return false; } FileInputStream fis = null; try { fis = new FileInputStream(fileToWrite); } catch (FileNotFoundException fnf) { Log.warning("Unexpected: file we expected to exist doesn't exist: {0}!", fileToWrite.getAbsolutePath()); return false; } CCNTime modificationTime = new CCNTime(fileToWrite.lastModified()); ContentName versionedName = VersioningProfile.addVersion(new ContentName(_prefix, outstandingInterest.name().postfix(_prefix).components()), modificationTime); CCNFileOutputStream ccnout = new CCNFileOutputStream(versionedName, _handle); ccnout.addOutstandingInterest(outstandingInterest); byte[] buffer = new byte[BUF_SIZE]; int read = fis.read(buffer); while (read >= 0) { ccnout.write(buffer, 0, read); read = fis.read(buffer); } fis.close(); ccnout.close(); return true; } | 15,096 |
0 | public static String exchangeForSessionToken(String protocol, String domain, String onetimeUseToken, PrivateKey key) throws IOException, GeneralSecurityException, AuthenticationException { String sessionUrl = getSessionTokenUrl(protocol, domain); URL url = new URL(sessionUrl); HttpURLConnection httpConn = (HttpURLConnection) url.openConnection(); String header = formAuthorizationHeader(onetimeUseToken, key, url, "GET"); httpConn.setRequestProperty("Authorization", header); if (httpConn.getResponseCode() != HttpURLConnection.HTTP_OK) { throw new AuthenticationException(httpConn.getResponseCode() + ": " + httpConn.getResponseMessage()); } String body = IOUtils.toString(httpConn.getInputStream()); Map parsedTokens = StringUtils.string2Map(body, "\n", "=", true); parsedTokens = StringUtils.lowercaseKeys(parsedTokens); return (String) parsedTokens.get("token"); } | @Override @RemoteMethod public boolean encrypt(int idAnexo) { try { Anexo anexo = anexoService.selectById(idAnexo); aes.init(Cipher.ENCRYPT_MODE, aeskeySpec); FileInputStream fis = new FileInputStream(config.baseDir + "/arquivos_upload_direto/" + anexo.getAnexoCaminho()); CipherOutputStream cos = new CipherOutputStream(new FileOutputStream(config.baseDir + "/arquivos_upload_direto/encrypt/" + anexo.getAnexoCaminho()), aes); IOUtils.copy(fis, cos); cos.close(); fis.close(); } catch (Exception e) { e.printStackTrace(); return false; } return true; } | 15,097 |
0 | public void testAutoCommit() throws Exception { Connection con = getConnectionOverrideProperties(new Properties()); try { Statement stmt = con.createStatement(); assertEquals(0, stmt.executeUpdate("create table #testAutoCommit (i int)")); con.setAutoCommit(false); assertEquals(1, stmt.executeUpdate("insert into #testAutoCommit (i) values (0)")); con.setAutoCommit(false); con.rollback(); assertEquals(1, stmt.executeUpdate("insert into #testAutoCommit (i) values (1)")); con.setAutoCommit(true); con.setAutoCommit(false); con.rollback(); con.setAutoCommit(true); ResultSet rs = stmt.executeQuery("select i from #testAutoCommit"); assertTrue(rs.next()); assertEquals(1, rs.getInt(1)); assertFalse(rs.next()); rs.close(); stmt.close(); } finally { con.close(); } } | public String doAction(Action commandAction) throws Exception { Map<String, String> args = commandAction.getArgs(); EnumCommandActionType actionType = commandAction.getType(); String actionResult = ""; switch(actionType) { case SEND: String method = getMethod(); String contentType = getContentType(); String url = "http://" + getHost() + ":" + getPort() + "/"; String pathUrl = ""; String data = ""; if (args.containsKey("method")) { method = args.get("method").toUpperCase(); } else if (args.containsKey("contenttype")) { contentType = args.get("contenttype").toLowerCase(); } else if (args.containsKey("postdata")) { contentType = args.get("postdata").toLowerCase(); } if (!allowedHttpMethods.contains(method.toUpperCase())) { throw new GatewayException("Invalid HTTP method specified for command Action."); } String commandStr = Pattern.compile("^/").matcher(args.get("command")).replaceAll(""); if ("GET".equals(method)) { pathUrl = commandStr; } else { String[] argStr = args.get("command").split("\\?"); pathUrl = argStr[0]; data = argStr[1]; } url += pathUrl; URL urlObj = new URL(url); HttpURLConnection conn = (HttpURLConnection) urlObj.openConnection(); conn.setUseCaches(false); conn.setRequestMethod(method); conn.setConnectTimeout(getConnectTimeout()); if ("POST".equals(method)) { conn.setDoOutput(true); conn.setDoInput(true); conn.setRequestProperty("Content-Type", contentType); conn.setRequestProperty("Content-Length", Integer.toString(data.length())); OutputStream outputStream = conn.getOutputStream(); outputStream.write(data.getBytes()); outputStream.flush(); } InputStream inputStream = conn.getInputStream(); if (conn.getResponseCode() != 200) { Integer responseCode = conn.getResponseCode(); conn.disconnect(); throw new GatewayException("Invalid response from server, expecting status code 200 but received " + responseCode.toString()); } Calendar endTime = Calendar.getInstance(); endTime.add(Calendar.MILLISECOND, getReadTimeout()); while (Calendar.getInstance().before(endTime) && inputStream.available() == 0) { try { Thread.sleep(50); } catch (Exception e) { } } while (inputStream.available() > 0) { actionResult += (char) inputStream.read(); } if (actionResult.length() > 0) { responseBuffer = actionResult; actionResult = ""; break; } conn.disconnect(); break; case READ: actionResult = responseBuffer; responseBuffer = ""; break; } return actionResult; } | 15,098 |
0 | public InputStream getConfResourceAsInputStream(String name) { try { URL url = getResource(name); if (url == null) { LOG.info(name + " not found"); return null; } else { LOG.info("found resource " + name + " at " + url); } return url.openStream(); } catch (Exception e) { return null; } } | public String getInternetData() throws Exception { BufferedReader in = null; String data = null; try { HttpClient client = new DefaultHttpClient(); URI website = new URI("http://code.google.com/p/gadi-works"); HttpGet request = new HttpGet(); request.setURI(website); HttpResponse response = client.execute(request); in = new BufferedReader(new InputStreamReader(response.getEntity().getContent())); StringBuffer sb = new StringBuffer(""); String l = ""; String nl = System.getProperty("line.separator"); while ((l = in.readLine()) != null) { sb.append(l + nl); } in.close(); data = sb.toString(); return data; } finally { if (in != null) { try { in.close(); return data; } catch (Exception e) { e.printStackTrace(); } } } } | 15,099 |
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