Datasets:

google

/

code_x_glue_cc_clone_detection_big_clone_bench

like 9

public static void copyFile(File sourceFile, File destFile) { FileChannel source = null; FileChannel destination = null; try { if (!destFile.exists()) { destFile.createNewFile(); } source = new FileInputStream(sourceFile).getChannel(); destination = new FileOutputStream(destFile).getChannel(); destination.transferFrom(source, 0, source.size()); } catch (Exception e) { e.printStackTrace(); } finally { try { if (source != null) { source.close(); } if (destination != null) { destination.close(); } } catch (Exception e) { e.printStackTrace(); } } }

private synchronized Map load() { if (!mustReloadConfigurationFiles()) { return groups; } SAXParser saxParser = null; JSODefaultHandler saxHandler = new JSODefaultHandler(); try { final Collection resourcesByOrigin = getConfigResources(); final LinkedList resourcesList = new LinkedList(); Iterator iOrigin = resourcesByOrigin.iterator(); while (iOrigin.hasNext()) { Resource resource = (Resource) iOrigin.next(); String origin = resource.getSource(); if (origin.startsWith(LOCAL_CLASSPATH) || JarRestrictionManager.getInstance().isJarAllowed(origin)) { LOG.debug("Adding " + CONFIGURATION_FILE_NAME + " from " + origin + "."); resourcesList.addFirst(resource.getUrl()); } else { LOG.debug("Jar " + origin + " refused. See jso.allowedJar property in jso.properties file."); } } URL external = getExternalResource(); if (external != null) { resourcesList.addFirst(external); } saxParser = SAXParserFactory.newInstance().newSAXParser(); Iterator ite = resourcesList.iterator(); while (ite.hasNext()) { final URL url = (URL) ite.next(); LOG.debug("Parsing of file " + url.toString() + "."); InputStream input = null; try { input = url.openStream(); saxParser.parse(input, saxHandler); } catch (SAXException e) { LOG.error("Parsing of file " + url.toString() + " failed! Parsing still continues.", e); } catch (IOException e) { LOG.error("Reading of file " + url.toString() + " failed! Parsing still continues.", e); } finally { if (input != null) { try { input.close(); } catch (IOException e) { LOG.error("Closing inputstream of file " + url.toString() + " failed! Parsing still continues.", e); } } } } } catch (SAXException e) { throw new RuntimeException(e); } catch (IOException e) { throw new RuntimeException(e); } catch (ParserConfigurationException e) { throw new RuntimeException(e); } this.defaultLocation = (String) saxHandler.getDefaultValues().get("location"); this.defaultTimestampPolicy = (String) saxHandler.getDefaultValues().get("timeStampPolicy"); if (this.defaultTimestampPolicy == null) this.defaultTimestampPolicy = Group.TIMESTAMP_LOCAL; this.groups = saxHandler.getListGroups(); return this.groups; }

public void save(UploadedFile file, Long student, Long activity) { File destiny = new File(fileFolder, student + "_" + activity + "_" + file.getFileName()); try { IOUtils.copy(file.getFile(), new FileOutputStream(destiny)); } catch (IOException e) { throw new RuntimeException("Erro ao copiar o arquivo.", e); } }

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(); } }

private static boolean prepareProbeFile(String completePath, String outputFile) { try { File inFile = new File(completePath + fSep + "probe.txt"); FileChannel inC = new FileInputStream(inFile).getChannel(); BufferedReader br = new BufferedReader(new FileReader(inFile)); File outFile = new File(completePath + fSep + "SmartGRAPE" + fSep + outputFile); FileChannel outC = new FileOutputStream(outFile, true).getChannel(); boolean endOfFile = true; short movieName = 0; int customer = 0; while (endOfFile) { String line = br.readLine(); if (line != null) { if (line.indexOf(":") >= 0) { movieName = new Short(line.substring(0, line.length() - 1)).shortValue(); } else { customer = new Integer(line).intValue(); ByteBuffer outBuf = ByteBuffer.allocate(6); outBuf.putShort(movieName); outBuf.putInt(customer); outBuf.flip(); outC.write(outBuf); } } else endOfFile = false; } br.close(); outC.close(); return true; } catch (IOException e) { System.err.println(e); return false; } }

private void copy(File srouceFile, File destinationFile) throws IOException { FileChannel sourceChannel = new FileInputStream(srouceFile).getChannel(); FileChannel destinationChannel = new FileOutputStream(destinationFile).getChannel(); destinationChannel.transferFrom(sourceChannel, 0, sourceChannel.size()); sourceChannel.close(); destinationChannel.close(); }

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); } } }

public static void copyDirs(File sourceDir, File destDir) throws IOException { if (!destDir.exists()) destDir.mkdirs(); for (File file : sourceDir.listFiles()) { if (file.isDirectory()) { copyDirs(file, new File(destDir, file.getName())); } else { FileChannel srcChannel = new FileInputStream(file).getChannel(); File out = new File(destDir, file.getName()); out.createNewFile(); FileChannel dstChannel = new FileOutputStream(out).getChannel(); dstChannel.transferFrom(srcChannel, 0, srcChannel.size()); srcChannel.close(); dstChannel.close(); } } }

public void migrate(InputMetadata meta, InputStream input, OutputCreator outputCreator) throws IOException, ResourceMigrationException { RestartInputStream restartInput = new RestartInputStream(input); Match match = resourceIdentifier.identifyResource(meta, restartInput); restartInput.restart(); if (match != null) { reporter.reportNotification(notificationFactory.createLocalizedNotification(NotificationType.INFO, "migration-resource-migrating", new Object[] { meta.getURI(), match.getTypeName(), match.getVersionName() })); processMigrationSteps(match, restartInput, outputCreator); } else { reporter.reportNotification(notificationFactory.createLocalizedNotification(NotificationType.INFO, "migration-resource-copying", new Object[] { meta.getURI() })); IOUtils.copyAndClose(restartInput, outputCreator.createOutputStream()); } }

public static void downloadFile(HttpServletResponse response, String file) throws IOException { response.setContentType(FileUtils.getContentType(file)); response.setContentLength(FileUtils.getContentLength(file)); response.setHeader("Content-type", ResponseUtils.DOWNLOAD_CONTENT_TYPE); response.setHeader("Content-Disposition", "attachment; filename=\"" + FileUtils.getFileName(file) + "\""); response.setHeader("Content-Length", Integer.toString(FileUtils.getContentLength(file))); InputStream input = new FileInputStream(file); OutputStream output = response.getOutputStream(); IOUtils.copy(input, output, true); }

public static boolean copyDataToNewTable(EboContext p_eboctx, String srcTableName, String destTableName, String where, boolean log, int mode) throws boRuntimeException { srcTableName = srcTableName.toUpperCase(); destTableName = destTableName.toUpperCase(); Connection cn = null; Connection cndef = null; boolean ret = false; try { boolean srcexists = false; boolean destexists = false; final InitialContext ic = new InitialContext(); cn = p_eboctx.getConnectionData(); cndef = p_eboctx.getConnectionDef(); PreparedStatement pstm = cn.prepareStatement("SELECT TABLE_NAME FROM USER_TABLES WHERE TABLE_NAME=?"); pstm.setString(1, srcTableName); ResultSet rslt = pstm.executeQuery(); if (rslt.next()) { srcexists = true; } rslt.close(); pstm.setString(1, destTableName); rslt = pstm.executeQuery(); if (rslt.next()) { destexists = true; } if (!destexists) { rslt.close(); pstm.close(); pstm = cn.prepareStatement("SELECT VIEW_NAME FROM USER_VIEWS WHERE VIEW_NAME=?"); pstm.setString(1, destTableName); rslt = pstm.executeQuery(); if (rslt.next()) { CallableStatement cstm = cn.prepareCall("DROP VIEW " + destTableName); cstm.execute(); cstm.close(); } } rslt.close(); pstm.close(); if (srcexists && !destexists) { if (log) { logger.finest(LoggerMessageLocalizer.getMessage("CREATING_AND_COPY_DATA_FROM") + " [" + srcTableName + "] " + LoggerMessageLocalizer.getMessage("TO") + " [" + destTableName + "]"); } CallableStatement cstm = cn.prepareCall("CREATE TABLE " + destTableName + " AS SELECT * FROM " + srcTableName + " " + (((where != null) && (where.length() > 0)) ? (" WHERE " + where) : "")); cstm.execute(); cstm.close(); if (log) { logger.finest(LoggerMessageLocalizer.getMessage("UPDATING_NGTDIC")); } cn.commit(); ret = true; } else if (srcexists && destexists) { if (log) { logger.finest(LoggerMessageLocalizer.getMessage("COPY_DATA_FROM") + " [" + srcTableName + "] " + LoggerMessageLocalizer.getMessage("TO") + " [" + destTableName + "]"); } PreparedStatement pstm2 = cn.prepareStatement("SELECT COLUMN_NAME FROM USER_TAB_COLUMNS WHERE TABLE_NAME = ? "); pstm2.setString(1, destTableName); ResultSet rslt2 = pstm2.executeQuery(); StringBuffer fields = new StringBuffer(); PreparedStatement pstm3 = cn.prepareStatement("SELECT COLUMN_NAME FROM USER_TAB_COLUMNS WHERE TABLE_NAME = ? and COLUMN_NAME=?"); while (rslt2.next()) { pstm3.setString(1, srcTableName); pstm3.setString(2, rslt2.getString(1)); ResultSet rslt3 = pstm3.executeQuery(); if (rslt3.next()) { if (fields.length() > 0) { fields.append(','); } fields.append('"').append(rslt2.getString(1)).append('"'); } rslt3.close(); } pstm3.close(); rslt2.close(); pstm2.close(); CallableStatement cstm; int recs = 0; if ((mode == 0) || (mode == 1)) { cstm = cn.prepareCall("INSERT INTO " + destTableName + "( " + fields.toString() + " ) ( SELECT " + fields.toString() + " FROM " + srcTableName + " " + (((where != null) && (where.length() > 0)) ? (" WHERE " + where) : "") + ")"); recs = cstm.executeUpdate(); cstm.close(); if (log) { logger.finest(LoggerMessageLocalizer.getMessage("DONE") + " [" + recs + "] " + LoggerMessageLocalizer.getMessage("RECORDS_COPIED")); } } cn.commit(); ret = true; } } catch (Exception e) { try { cn.rollback(); } catch (Exception z) { throw new boRuntimeException("boBuildDB.moveTable", "BO-1304", z); } throw new boRuntimeException("boBuildDB.moveTable", "BO-1304", e); } finally { try { cn.close(); } catch (Exception e) { } try { cndef.close(); } catch (Exception e) { } } return ret; }

protected void init() throws MXQueryException { String add = getStringValueOrEmpty(subIters[0]); if (add == null) { currentToken = BooleanToken.FALSE_TOKEN; return; } URI uri; if (!TypeLexicalConstraints.isValidURI(add)) throw new DynamicException(ErrorCodes.F0017_INVALID_ARGUMENT_TO_FN_DOC, "Invalid URI given to fn:doc-available", loc); try { if (TypeLexicalConstraints.isAbsoluteURI(add)) { uri = new URI(add); } else { uri = new URI(IOLib.convertToAndroid(add)); } } catch (URISyntaxException se) { throw new DynamicException(ErrorCodes.F0017_INVALID_ARGUMENT_TO_FN_DOC, "Invalid URI given to fn:doc-available", loc); } if (add.startsWith("http://")) { URL url; try { url = uri.toURL(); } catch (MalformedURLException e) { throw new DynamicException(ErrorCodes.F0017_INVALID_ARGUMENT_TO_FN_DOC, "Invalid URI given to fn:doc-available", loc); } try { InputStream in = url.openStream(); in.close(); } catch (IOException e) { currentToken = BooleanToken.FALSE_TOKEN; return; } currentToken = BooleanToken.TRUE_TOKEN; } else { try { BufferedReader in = new BufferedReader(new InputStreamReader(MXQuery.getContext().openFileInput(uri.toString()))); currentToken = BooleanToken.TRUE_TOKEN; } catch (FileNotFoundException e) { currentToken = BooleanToken.FALSE_TOKEN; } catch (IOException e) { currentToken = BooleanToken.FALSE_TOKEN; } } }

private void chopFileDisk() throws IOException { File tempFile = new File("" + logFile + ".tmp"); BufferedInputStream bis = null; BufferedOutputStream bos = null; long startCopyPos; byte readBuffer[] = new byte[2048]; int readCount; long totalBytesRead = 0; if (reductionRatio > 0 && logFile.length() > 0) { startCopyPos = logFile.length() / reductionRatio; } else { startCopyPos = 0; } try { bis = new BufferedInputStream(new FileInputStream(logFile)); bos = new BufferedOutputStream(new FileOutputStream(tempFile)); do { readCount = bis.read(readBuffer, 0, readBuffer.length); if (readCount > 0) { totalBytesRead += readCount; if (totalBytesRead > startCopyPos) { bos.write(readBuffer, 0, readCount); } } } while (readCount > 0); } finally { if (bos != null) { try { bos.close(); } catch (IOException ex) { } } if (bis != null) { try { bis.close(); } catch (IOException ex) { } } } if (tempFile.isFile()) { if (!logFile.delete()) { throw new IOException("Error when attempting to delete the " + logFile + " file."); } if (!tempFile.renameTo(logFile)) { throw new IOException("Error when renaming the " + tempFile + " to " + logFile + "."); } } }

public void launchJob(final String workingDir, final AppConfigType appConfig) throws FaultType { logger.info("called for job: " + jobID); MessageContext mc = MessageContext.getCurrentContext(); HttpServletRequest req = (HttpServletRequest) mc.getProperty(HTTPConstants.MC_HTTP_SERVLETREQUEST); String clientDN = (String) req.getAttribute(GSIConstants.GSI_USER_DN); if (clientDN != null) { logger.info("Client's DN: " + clientDN); } else { clientDN = "Unknown client"; } String remoteIP = req.getRemoteAddr(); SOAPService service = mc.getService(); String serviceName = service.getName(); if (serviceName == null) { serviceName = "Unknown service"; } if (appConfig.isParallel()) { if (AppServiceImpl.drmaaInUse) { if (AppServiceImpl.drmaaPE == null) { logger.error("drmaa.pe property must be specified in opal.properties " + "for parallel execution using DRMAA"); throw new FaultType("drmaa.pe property must be specified in opal.properties " + "for parallel execution using DRMAA"); } if (AppServiceImpl.mpiRun == null) { logger.error("mpi.run property must be specified in opal.properties " + "for parallel execution using DRMAA"); throw new FaultType("mpi.run property must be specified in " + "opal.properties for parallel execution " + "using DRMAA"); } } else if (!AppServiceImpl.globusInUse) { if (AppServiceImpl.mpiRun == null) { logger.error("mpi.run property must be specified in opal.properties " + "for parallel execution without using Globus"); throw new FaultType("mpi.run property must be specified in " + "opal.properties for parallel execution " + "without using Globus"); } } if (jobIn.getNumProcs() == null) { logger.error("Number of processes unspecified for parallel job"); throw new FaultType("Number of processes unspecified for parallel job"); } else if (jobIn.getNumProcs().intValue() > AppServiceImpl.numProcs) { logger.error("Processors required - " + jobIn.getNumProcs() + ", available - " + AppServiceImpl.numProcs); throw new FaultType("Processors required - " + jobIn.getNumProcs() + ", available - " + AppServiceImpl.numProcs); } } try { status.setCode(GramJob.STATUS_PENDING); status.setMessage("Launching executable"); status.setBaseURL(new URI(AppServiceImpl.tomcatURL + jobID)); } catch (MalformedURIException mue) { logger.error("Cannot convert base_url string to URI - " + mue.getMessage()); throw new FaultType("Cannot convert base_url string to URI - " + mue.getMessage()); } if (!AppServiceImpl.dbInUse) { AppServiceImpl.statusTable.put(jobID, status); } else { Connection conn = null; try { conn = DriverManager.getConnection(AppServiceImpl.dbUrl, AppServiceImpl.dbUser, AppServiceImpl.dbPasswd); } catch (SQLException e) { logger.error("Cannot connect to database - " + e.getMessage()); throw new FaultType("Cannot connect to database - " + e.getMessage()); } String time = new SimpleDateFormat("MMM d, yyyy h:mm:ss a", Locale.US).format(new Date()); String sqlStmt = "insert into job_status(job_id, code, message, base_url, " + "client_dn, client_ip, service_name, start_time, last_update) " + "values ('" + jobID + "', " + status.getCode() + ", " + "'" + status.getMessage() + "', " + "'" + status.getBaseURL() + "', " + "'" + clientDN + "', " + "'" + remoteIP + "', " + "'" + serviceName + "', " + "'" + time + "', " + "'" + time + "');"; try { Statement stmt = conn.createStatement(); stmt.executeUpdate(sqlStmt); conn.close(); } catch (SQLException e) { logger.error("Cannot insert job status into database - " + e.getMessage()); throw new FaultType("Cannot insert job status into database - " + e.getMessage()); } } String args = appConfig.getDefaultArgs(); if (args == null) { args = jobIn.getArgList(); } else { String userArgs = jobIn.getArgList(); if (userArgs != null) args += " " + userArgs; } if (args != null) { args = args.trim(); } logger.debug("Argument list: " + args); if (AppServiceImpl.drmaaInUse) { String cmd = null; String[] argsArray = null; if (appConfig.isParallel()) { cmd = "/bin/sh"; String newArgs = AppServiceImpl.mpiRun + " -machinefile $TMPDIR/machines" + " -np " + jobIn.getNumProcs() + " " + appConfig.getBinaryLocation(); if (args != null) { args = newArgs + " " + args; } else { args = newArgs; } logger.debug("CMD: " + args); argsArray = new String[] { "-c", args }; } else { cmd = appConfig.getBinaryLocation(); if (args == null) args = ""; logger.debug("CMD: " + cmd + " " + args); argsArray = args.split(" "); } try { logger.debug("Working directory: " + workingDir); JobTemplate jt = session.createJobTemplate(); if (appConfig.isParallel()) jt.setNativeSpecification("-pe " + AppServiceImpl.drmaaPE + " " + jobIn.getNumProcs()); jt.setRemoteCommand(cmd); jt.setArgs(argsArray); jt.setJobName(jobID); jt.setWorkingDirectory(workingDir); jt.setErrorPath(":" + workingDir + "/stderr.txt"); jt.setOutputPath(":" + workingDir + "/stdout.txt"); drmaaJobID = session.runJob(jt); logger.info("DRMAA job has been submitted with id " + drmaaJobID); session.deleteJobTemplate(jt); } catch (Exception ex) { logger.error(ex); status.setCode(GramJob.STATUS_FAILED); status.setMessage("Error while running executable via DRMAA - " + ex.getMessage()); if (AppServiceImpl.dbInUse) { try { updateStatusInDatabase(jobID, status); } catch (SQLException e) { logger.error(e); throw new FaultType("Cannot update status into database - " + e.getMessage()); } } return; } status.setCode(GramJob.STATUS_ACTIVE); status.setMessage("Execution in progress"); if (AppServiceImpl.dbInUse) { try { updateStatusInDatabase(jobID, status); } catch (SQLException e) { logger.error(e); throw new FaultType("Cannot update status into database - " + e.getMessage()); } } } else if (AppServiceImpl.globusInUse) { String rsl = null; if (appConfig.isParallel()) { rsl = "&(directory=" + workingDir + ")" + "(executable=" + appConfig.getBinaryLocation() + ")" + "(count=" + jobIn.getNumProcs() + ")" + "(jobtype=mpi)" + "(stdout=stdout.txt)" + "(stderr=stderr.txt)"; } else { rsl = "&(directory=" + workingDir + ")" + "(executable=" + appConfig.getBinaryLocation() + ")" + "(stdout=stdout.txt)" + "(stderr=stderr.txt)"; } if (args != null) { args = "\"" + args + "\""; args = args.replaceAll("[\\s]+", "\" \""); rsl += "(arguments=" + args + ")"; } logger.debug("RSL: " + rsl); try { job = new GramJob(rsl); GlobusCredential globusCred = new GlobusCredential(AppServiceImpl.serviceCertPath, AppServiceImpl.serviceKeyPath); GSSCredential gssCred = new GlobusGSSCredentialImpl(globusCred, GSSCredential.INITIATE_AND_ACCEPT); job.setCredentials(gssCred); job.addListener(this); job.request(AppServiceImpl.gatekeeperContact); } catch (Exception ge) { logger.error(ge); status.setCode(GramJob.STATUS_FAILED); status.setMessage("Error while running executable via Globus - " + ge.getMessage()); if (AppServiceImpl.dbInUse) { try { updateStatusInDatabase(jobID, status); } catch (SQLException e) { logger.error(e); throw new FaultType("Cannot update status into database - " + e.getMessage()); } } return; } } else { String cmd = null; if (appConfig.isParallel()) { cmd = new String(AppServiceImpl.mpiRun + " " + "-np " + jobIn.getNumProcs() + " " + appConfig.getBinaryLocation()); } else { cmd = new String(appConfig.getBinaryLocation()); } if (args != null) { cmd += " " + args; } logger.debug("CMD: " + cmd); try { logger.debug("Working directory: " + workingDir); proc = Runtime.getRuntime().exec(cmd, null, new File(workingDir)); stdoutThread = writeStdOut(proc, workingDir); stderrThread = writeStdErr(proc, workingDir); } catch (IOException ioe) { logger.error(ioe); status.setCode(GramJob.STATUS_FAILED); status.setMessage("Error while running executable via fork - " + ioe.getMessage()); if (AppServiceImpl.dbInUse) { try { updateStatusInDatabase(jobID, status); } catch (SQLException e) { logger.error(e); throw new FaultType("Cannot update status into database - " + e.getMessage()); } } return; } status.setCode(GramJob.STATUS_ACTIVE); status.setMessage("Execution in progress"); if (AppServiceImpl.dbInUse) { try { updateStatusInDatabase(jobID, status); } catch (SQLException e) { logger.error(e); throw new FaultType("Cannot update status into database - " + e.getMessage()); } } } new Thread() { public void run() { try { waitForCompletion(); } catch (FaultType f) { logger.error(f); synchronized (status) { status.notifyAll(); } return; } if (AppServiceImpl.drmaaInUse || !AppServiceImpl.globusInUse) { done = true; status.setCode(GramJob.STATUS_STAGE_OUT); status.setMessage("Writing output metadata"); if (AppServiceImpl.dbInUse) { try { updateStatusInDatabase(jobID, status); } catch (SQLException e) { status.setCode(GramJob.STATUS_FAILED); status.setMessage("Cannot update status database after finish - " + e.getMessage()); logger.error(e); synchronized (status) { status.notifyAll(); } return; } } } try { if (!AppServiceImpl.drmaaInUse && !AppServiceImpl.globusInUse) { try { logger.debug("Waiting for all outputs to be written out"); stdoutThread.join(); stderrThread.join(); logger.debug("All outputs successfully written out"); } catch (InterruptedException ignore) { } } File stdOutFile = new File(workingDir + File.separator + "stdout.txt"); if (!stdOutFile.exists()) { throw new IOException("Standard output missing for execution"); } File stdErrFile = new File(workingDir + File.separator + "stderr.txt"); if (!stdErrFile.exists()) { throw new IOException("Standard error missing for execution"); } if (AppServiceImpl.archiveData) { logger.debug("Archiving output files"); File f = new File(workingDir); File[] outputFiles = f.listFiles(); ZipOutputStream out = new ZipOutputStream(new FileOutputStream(workingDir + File.separator + jobID + ".zip")); byte[] buf = new byte[1024]; try { for (int i = 0; i < outputFiles.length; i++) { FileInputStream in = new FileInputStream(outputFiles[i]); out.putNextEntry(new ZipEntry(outputFiles[i].getName())); int len; while ((len = in.read(buf)) > 0) { out.write(buf, 0, len); } out.closeEntry(); in.close(); } out.close(); } catch (IOException e) { logger.error(e); logger.error("Error not fatal - moving on"); } } File f = new File(workingDir); File[] outputFiles = f.listFiles(); OutputFileType[] outputFileObj = new OutputFileType[outputFiles.length - 2]; int j = 0; for (int i = 0; i < outputFiles.length; i++) { if (outputFiles[i].getName().equals("stdout.txt")) { outputs.setStdOut(new URI(AppServiceImpl.tomcatURL + jobID + "/stdout.txt")); } else if (outputFiles[i].getName().equals("stderr.txt")) { outputs.setStdErr(new URI(AppServiceImpl.tomcatURL + jobID + "/stderr.txt")); } else { OutputFileType next = new OutputFileType(); next.setName(outputFiles[i].getName()); next.setUrl(new URI(AppServiceImpl.tomcatURL + jobID + "/" + outputFiles[i].getName())); outputFileObj[j++] = next; } } outputs.setOutputFile(outputFileObj); } catch (IOException e) { status.setCode(GramJob.STATUS_FAILED); status.setMessage("Cannot retrieve outputs after finish - " + e.getMessage()); logger.error(e); if (AppServiceImpl.dbInUse) { try { updateStatusInDatabase(jobID, status); } catch (SQLException se) { logger.error(se); } } synchronized (status) { status.notifyAll(); } return; } if (!AppServiceImpl.dbInUse) { AppServiceImpl.outputTable.put(jobID, outputs); } else { Connection conn = null; try { conn = DriverManager.getConnection(AppServiceImpl.dbUrl, AppServiceImpl.dbUser, AppServiceImpl.dbPasswd); } catch (SQLException e) { status.setCode(GramJob.STATUS_FAILED); status.setMessage("Cannot connect to database after finish - " + e.getMessage()); logger.error(e); synchronized (status) { status.notifyAll(); } return; } String sqlStmt = "insert into job_output(job_id, std_out, std_err) " + "values ('" + jobID + "', " + "'" + outputs.getStdOut().toString() + "', " + "'" + outputs.getStdErr().toString() + "');"; Statement stmt = null; try { stmt = conn.createStatement(); stmt.executeUpdate(sqlStmt); } catch (SQLException e) { status.setCode(GramJob.STATUS_FAILED); status.setMessage("Cannot update job output database after finish - " + e.getMessage()); logger.error(e); try { updateStatusInDatabase(jobID, status); } catch (SQLException se) { logger.error(se); } synchronized (status) { status.notifyAll(); } return; } OutputFileType[] outputFile = outputs.getOutputFile(); for (int i = 0; i < outputFile.length; i++) { sqlStmt = "insert into output_file(job_id, name, url) " + "values ('" + jobID + "', " + "'" + outputFile[i].getName() + "', " + "'" + outputFile[i].getUrl().toString() + "');"; try { stmt = conn.createStatement(); stmt.executeUpdate(sqlStmt); } catch (SQLException e) { status.setCode(GramJob.STATUS_FAILED); status.setMessage("Cannot update output_file DB after finish - " + e.getMessage()); logger.error(e); try { updateStatusInDatabase(jobID, status); } catch (SQLException se) { logger.error(se); } synchronized (status) { status.notifyAll(); } return; } } } if (terminatedOK()) { status.setCode(GramJob.STATUS_DONE); status.setMessage("Execution complete - " + "check outputs to verify successful execution"); } else { status.setCode(GramJob.STATUS_FAILED); status.setMessage("Execution failed"); } if (AppServiceImpl.dbInUse) { try { updateStatusInDatabase(jobID, status); } catch (SQLException e) { status.setCode(GramJob.STATUS_FAILED); status.setMessage("Cannot update status database after finish - " + e.getMessage()); logger.error(e); synchronized (status) { status.notifyAll(); } return; } } AppServiceImpl.jobTable.remove(jobID); synchronized (status) { status.notifyAll(); } logger.info("Execution complete for job: " + jobID); } }.start(); }

public BufferedImage extract() throws DjatokaException { boolean useRegion = false; int left = 0; int top = 0; int width = 50; int height = 50; boolean useleftDouble = false; Double leftDouble = 0.0; boolean usetopDouble = false; Double topDouble = 0.0; boolean usewidthDouble = false; Double widthDouble = 0.0; boolean useheightDouble = false; Double heightDouble = 0.0; if (params.getRegion() != null) { StringTokenizer st = new StringTokenizer(params.getRegion(), "{},"); String token; if ((token = st.nextToken()).contains(".")) { topDouble = Double.parseDouble(token); usetopDouble = true; } else top = Integer.parseInt(token); if ((token = st.nextToken()).contains(".")) { leftDouble = Double.parseDouble(token); useleftDouble = true; } else left = Integer.parseInt(token); if ((token = st.nextToken()).contains(".")) { heightDouble = Double.parseDouble(token); useheightDouble = true; } else height = Integer.parseInt(token); if ((token = st.nextToken()).contains(".")) { widthDouble = Double.parseDouble(token); usewidthDouble = true; } else width = Integer.parseInt(token); useRegion = true; } try { if (is != null) { File f = File.createTempFile("tmp", ".jp2"); f.deleteOnExit(); FileOutputStream fos = new FileOutputStream(f); sourceFile = f.getAbsolutePath(); IOUtils.copyStream(is, fos); is.close(); fos.close(); } } catch (IOException e) { throw new DjatokaException(e); } try { Jp2_source inputSource = new Jp2_source(); Kdu_compressed_source input = null; Jp2_family_src jp2_family_in = new Jp2_family_src(); Jp2_locator loc = new Jp2_locator(); jp2_family_in.Open(sourceFile, true); inputSource.Open(jp2_family_in, loc); inputSource.Read_header(); input = inputSource; Kdu_codestream codestream = new Kdu_codestream(); codestream.Create(input); Kdu_channel_mapping channels = new Kdu_channel_mapping(); if (inputSource.Exists()) channels.Configure(inputSource, false); else channels.Configure(codestream); int ref_component = channels.Get_source_component(0); Kdu_coords ref_expansion = getReferenceExpansion(ref_component, channels, codestream); Kdu_dims image_dims = new Kdu_dims(); codestream.Get_dims(ref_component, image_dims); Kdu_coords imageSize = image_dims.Access_size(); Kdu_coords imagePosition = image_dims.Access_pos(); if (useleftDouble) left = imagePosition.Get_x() + (int) Math.round(leftDouble * imageSize.Get_x()); if (usetopDouble) top = imagePosition.Get_y() + (int) Math.round(topDouble * imageSize.Get_y()); if (useheightDouble) height = (int) Math.round(heightDouble * imageSize.Get_y()); if (usewidthDouble) width = (int) Math.round(widthDouble * imageSize.Get_x()); if (useRegion) { imageSize.Set_x(width); imageSize.Set_y(height); imagePosition.Set_x(left); imagePosition.Set_y(top); } int reduce = 1 << params.getLevelReductionFactor(); imageSize.Set_x(imageSize.Get_x() * ref_expansion.Get_x()); imageSize.Set_y(imageSize.Get_y() * ref_expansion.Get_y()); imagePosition.Set_x(imagePosition.Get_x() * ref_expansion.Get_x() / reduce - ((ref_expansion.Get_x() / reduce - 1) / 2)); imagePosition.Set_y(imagePosition.Get_y() * ref_expansion.Get_y() / reduce - ((ref_expansion.Get_y() / reduce - 1) / 2)); Kdu_dims view_dims = new Kdu_dims(); view_dims.Assign(image_dims); view_dims.Access_size().Set_x(imageSize.Get_x()); view_dims.Access_size().Set_y(imageSize.Get_y()); int region_buf_size = imageSize.Get_x() * imageSize.Get_y(); int[] region_buf = new int[region_buf_size]; Kdu_region_decompressor decompressor = new Kdu_region_decompressor(); decompressor.Start(codestream, channels, -1, params.getLevelReductionFactor(), 16384, image_dims, ref_expansion, new Kdu_coords(1, 1), false, Kdu_global.KDU_WANT_OUTPUT_COMPONENTS); Kdu_dims new_region = new Kdu_dims(); Kdu_dims incomplete_region = new Kdu_dims(); Kdu_coords viewSize = view_dims.Access_size(); incomplete_region.Assign(image_dims); int[] imgBuffer = new int[viewSize.Get_x() * viewSize.Get_y()]; int[] kduBuffer = null; while (decompressor.Process(region_buf, image_dims.Access_pos(), 0, 0, region_buf_size, incomplete_region, new_region)) { Kdu_coords newOffset = new_region.Access_pos(); Kdu_coords newSize = new_region.Access_size(); newOffset.Subtract(view_dims.Access_pos()); kduBuffer = region_buf; int imgBuffereIdx = newOffset.Get_x() + newOffset.Get_y() * viewSize.Get_x(); int kduBufferIdx = 0; int xDiff = viewSize.Get_x() - newSize.Get_x(); for (int j = 0; j < newSize.Get_y(); j++, imgBuffereIdx += xDiff) { for (int i = 0; i < newSize.Get_x(); i++) { imgBuffer[imgBuffereIdx++] = kduBuffer[kduBufferIdx++]; } } } BufferedImage image = new BufferedImage(imageSize.Get_x(), imageSize.Get_y(), BufferedImage.TYPE_INT_RGB); image.setRGB(0, 0, viewSize.Get_x(), viewSize.Get_y(), imgBuffer, 0, viewSize.Get_x()); if (params.getRotationDegree() > 0) { image = ImageProcessingUtils.rotate(image, params.getRotationDegree()); } decompressor.Native_destroy(); channels.Native_destroy(); if (codestream.Exists()) codestream.Destroy(); inputSource.Native_destroy(); input.Native_destroy(); jp2_family_in.Native_destroy(); return image; } catch (KduException e) { e.printStackTrace(); throw new DjatokaException(e); } catch (Exception e) { e.printStackTrace(); throw new DjatokaException(e); } }

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); } }

public static InputStream sendReq(String url, String content, ConnectData data) { try { URLConnection con = new URL(url).openConnection(); con.setConnectTimeout(TIMEOUT); con.setReadTimeout(TIMEOUT); con.setUseCaches(false); setUA(con); con.setRequestProperty("Accept-Charset", "utf-8"); con.setDoOutput(true); con.setRequestProperty("Content-Type", "application/x-www-form-urlencoded"); if (data.cookie != null) con.setRequestProperty("Cookie", data.cookie); HttpURLConnection httpurl = (HttpURLConnection) con; httpurl.setRequestMethod("POST"); Writer wr = new OutputStreamWriter(con.getOutputStream()); wr.write(content); wr.flush(); con.connect(); InputStream is = con.getInputStream(); is = new BufferedInputStream(is); wr.close(); parseCookie(con, data); return is; } catch (IOException ioe) { Log.except("failed to send request " + url, ioe); } return null; }

private static String webService(String strUrl) { StringBuffer buffer = new StringBuffer(); try { URL url = new URL(strUrl); InputStream input = url.openStream(); String sCurrentLine = ""; InputStreamReader read = new InputStreamReader(input, "utf-8"); BufferedReader l_reader = new java.io.BufferedReader(read); while ((sCurrentLine = l_reader.readLine()) != null) { buffer.append(sCurrentLine); } return buffer.toString(); } catch (Exception e) { e.printStackTrace(); return null; } }

public static byte[] ComputeForBinary(String ThisString) throws Exception { byte[] Result; MessageDigest MD5Hasher; MD5Hasher = MessageDigest.getInstance("MD5"); MD5Hasher.update(ThisString.getBytes("iso-8859-1")); Result = MD5Hasher.digest(); return Result; }

private static String GetSHA1(String text) throws NoSuchAlgorithmException, UnsupportedEncodingException { MessageDigest md; md = MessageDigest.getInstance("SHA-1"); byte[] sha1hash = new byte[40]; md.update(text.getBytes("iso-8859-1"), 0, text.length()); sha1hash = md.digest(); return LoginHttpPostProcessor.ConvertToHex(sha1hash); }

@Override public InputSource resolveEntity(String publicId, String systemId) throws SAXException, IOException { URL url = new URL(System.getenv("plugg_home") + "/" + systemId); System.out.println("SystemId = " + systemId); return new InputSource(url.openStream()); }

public static void copyFile(String file1, String file2) { File filedata1 = new java.io.File(file1); if (filedata1.exists()) { try { BufferedOutputStream out = new BufferedOutputStream(new FileOutputStream(file2)); BufferedInputStream in = new BufferedInputStream(new FileInputStream(file1)); try { int read; while ((read = in.read()) != -1) { out.write(read); } out.flush(); } catch (IOException ex1) { ex1.printStackTrace(); } finally { out.close(); in.close(); } } catch (Exception ex) { ex.printStackTrace(); } } }

public static String getUserToken(String userName) { if (userName != null && userName.trim().length() > 0) try { MessageDigest md = MessageDigest.getInstance("MD5"); md.update((userName + seed).getBytes("ISO-8859-1")); return BaseController.bytesToHex(md.digest()); } catch (NullPointerException npe) { } catch (NoSuchAlgorithmException e) { } catch (UnsupportedEncodingException e) { } return null; }

static JSONObject executeMethod(HttpClient httpClient, HttpMethod method, int timeout) throws HttpRequestFailureException, HttpException, IOException, HttpRequestTimeoutException { try { method.getParams().setSoTimeout(timeout * 1000); int status = -1; JSONObject result = null; for (int i = 0; i < RETRY; i++) { System.out.println("Execute method[" + method.getURI() + "](try " + (i + 1) + ")"); status = httpClient.executeMethod(method); if (status == HttpStatus.SC_OK) { InputStream inputStream = method.getResponseBodyAsStream(); ByteArrayOutputStream baos = new ByteArrayOutputStream(); IOUtils.copy(inputStream, baos); String response = new String(baos.toByteArray(), "UTF-8"); System.out.println(response); result = JSONObject.fromString(response); if (result.has("status")) { String lingrStatus = result.getString("status"); if ("ok".equals(lingrStatus)) { break; } else { try { Thread.sleep(1000); } catch (InterruptedException e) { } } } } else { throw new HttpRequestFailureException(status); } } return result; } catch (SocketTimeoutException e) { throw new HttpRequestTimeoutException(e); } finally { method.releaseConnection(); } }

public static void copyFile(File src, File dest, boolean force) throws IOException { if (dest.exists()) { if (force) { dest.delete(); } else { throw new IOException("Cannot overwrite existing file: " + dest); } } byte[] buffer = new byte[1]; int read = 0; InputStream in = null; OutputStream out = null; try { in = new FileInputStream(src); out = new FileOutputStream(dest); while (true) { read = in.read(buffer); if (read == -1) { break; } out.write(buffer, 0, read); } } finally { if (in != null) { try { in.close(); } finally { if (out != null) { out.close(); } } } } }

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!"); }

private synchronized void awaitResponse() throws BOSHException { HttpEntity entity = null; try { HttpResponse httpResp = client.execute(post, context); entity = httpResp.getEntity(); byte[] data = EntityUtils.toByteArray(entity); String encoding = entity.getContentEncoding() != null ? entity.getContentEncoding().getValue() : null; if (ZLIBCodec.getID().equalsIgnoreCase(encoding)) { data = ZLIBCodec.decode(data); } else if (GZIPCodec.getID().equalsIgnoreCase(encoding)) { data = GZIPCodec.decode(data); } body = StaticBody.fromString(new String(data, CHARSET)); statusCode = httpResp.getStatusLine().getStatusCode(); sent = true; } catch (IOException iox) { abort(); toThrow = new BOSHException("Could not obtain response", iox); throw (toThrow); } catch (RuntimeException ex) { abort(); throw (ex); } }

public void unpack(File destDirectory, boolean delete) { if (delete) delete(destDirectory); if (destDirectory.exists()) throw new ContentPackageException("Destination directory already exists."); this.destDirectory = destDirectory; this.manifestFile = new File(destDirectory, MANIFEST_FILE_NAME); try { if (zipInputStream == null) zipInputStream = new ZipInputStream(new FileInputStream(zipFile)); ZipEntry zipEntry; while ((zipEntry = zipInputStream.getNextEntry()) != null) { File destFile = new File(destDirectory, zipEntry.getName()); destFile.getParentFile().mkdirs(); if (!zipEntry.isDirectory()) { BufferedOutputStream output = new BufferedOutputStream(new FileOutputStream(destFile), BUFFER_SIZE); byte[] buffer = new byte[BUFFER_SIZE]; int length; while ((length = zipInputStream.read(buffer, 0, BUFFER_SIZE)) != -1) output.write(buffer, 0, length); output.close(); zipInputStream.closeEntry(); } } zipInputStream.close(); } catch (IOException ex) { throw new ContentPackageException(ex); } }

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; } }

public static String readFromUrl(String url) { URL url_ = null; URLConnection uc = null; BufferedReader in = null; StringBuilder str = new StringBuilder(); try { url_ = new URL(url); uc = url_.openConnection(); in = new BufferedReader(new InputStreamReader(uc.getInputStream())); String inputLine; while ((inputLine = in.readLine()) != null) str.append(inputLine); in.close(); } catch (IOException e) { e.printStackTrace(); } return str.toString(); }

protected static void copyOrMove(File sourceLocation, File targetLocation, boolean move) throws IOException { String[] children; int i; InputStream in; OutputStream out; byte[] buf; int len; if (sourceLocation.isDirectory()) { if (!targetLocation.exists()) targetLocation.mkdir(); children = sourceLocation.list(); for (i = 0; i < children.length; i++) { copyOrMove(new File(sourceLocation, children[i]), new File(targetLocation, children[i]), move); } if (move) sourceLocation.delete(); } else { in = new FileInputStream(sourceLocation); if (targetLocation.isDirectory()) out = new FileOutputStream(targetLocation.getAbsolutePath() + File.separator + sourceLocation.getName()); else out = new FileOutputStream(targetLocation); buf = new byte[1024]; while ((len = in.read(buf)) > 0) out.write(buf, 0, len); in.close(); out.close(); if (move) sourceLocation.delete(); } }

public void run(IAction action) { Shell shell = new Shell(); GraphicalViewer viewer = new ScrollingGraphicalViewer(); viewer.createControl(shell); viewer.setEditDomain(new DefaultEditDomain(null)); viewer.setRootEditPart(new ScalableFreeformRootEditPart()); viewer.setEditPartFactory(new GraphicalPartFactory()); viewer.setContents(getContents()); viewer.flush(); int printMode = new PrintModeDialog(shell).open(); if (printMode == -1) return; PrintDialog dialog = new PrintDialog(shell, SWT.NULL); PrinterData data = dialog.open(); if (data != null) { PrintGraphicalViewerOperation op = new PrintGraphicalViewerOperation(new Printer(data), viewer); op.setPrintMode(printMode); op.run(selectedFile.getName()); } }

public static String md5(String input) { String res = ""; try { MessageDigest algorithm = MessageDigest.getInstance("MD5"); algorithm.reset(); algorithm.update(input.getBytes()); byte[] md5 = algorithm.digest(); String tmp = ""; for (int i = 0; i < md5.length; i++) { tmp = (Integer.toHexString(0xFF & md5[i])); if (tmp.length() == 1) res += "0" + tmp; else res += tmp; } } catch (NoSuchAlgorithmException ex) { } return res; }

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(); } }

public static String getHashedStringMD5(String value) throws java.security.NoSuchAlgorithmException { java.security.MessageDigest d = java.security.MessageDigest.getInstance("MD5"); d.reset(); d.update(value.getBytes()); byte[] buf = d.digest(); return new String(buf); }

public static final synchronized String md5(final String data) { try { final MessageDigest md = MessageDigest.getInstance("MD5"); md.update(data.getBytes()); final byte[] b = md.digest(); return toHexString(b); } catch (final Exception e) { } return ""; }

@Override public void start() { try { ftp = new FTPClient(); ftp.connect(this.url.getHost(), this.url.getPort() == -1 ? this.url.getDefaultPort() : this.url.getPort()); String username = "anonymous"; String password = ""; if (this.url.getUserInfo() != null) { username = this.url.getUserInfo().split(":")[0]; password = this.url.getUserInfo().split(":")[1]; } ftp.login(username, password); long startPos = 0; if (getFile().exists()) startPos = getFile().length(); else getFile().createNewFile(); ftp.download(this.url.getPath(), getFile(), startPos, new FTPDTImpl()); ftp.disconnect(true); } catch (Exception ex) { ex.printStackTrace(); speedTimer.cancel(); } }

public void logout(String cookieString) throws NetworkException { HttpClient client = HttpConfig.newInstance(); HttpGet get = new HttpGet(HttpConfig.bbsURL() + HttpConfig.BBS_LOGOUT); if (cookieString != null && cookieString.length() != 0) get.setHeader("Cookie", cookieString); 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 static int sendButton(String url, String id, String command) throws ClientProtocolException, IOException { String connectString = url + "/rest/button/" + id + "/" + command; HttpClient client = new DefaultHttpClient(); HttpPost post = new HttpPost(connectString); HttpResponse response = client.execute(post); int code = response.getStatusLine().getStatusCode(); return code; }

private ResponseStatus performHandshake(String url) throws IOException { HttpURLConnection connection = Caller.getInstance().openConnection(url); InputStream is = connection.getInputStream(); BufferedReader r = new BufferedReader(new InputStreamReader(is)); String status = r.readLine(); int statusCode = ResponseStatus.codeForStatus(status); ResponseStatus responseStatus; if (statusCode == ResponseStatus.OK) { this.sessionId = r.readLine(); this.nowPlayingUrl = r.readLine(); this.submissionUrl = r.readLine(); responseStatus = new ResponseStatus(statusCode); } else if (statusCode == ResponseStatus.FAILED) { responseStatus = new ResponseStatus(statusCode, status.substring(status.indexOf(' ') + 1)); } else { return new ResponseStatus(statusCode); } r.close(); return responseStatus; }

private byte[] hash(String toHash) { try { MessageDigest md5 = MessageDigest.getInstance("MD5", "BC"); md5.update(toHash.getBytes("ISO-8859-1")); return md5.digest(); } catch (Exception ex) { ex.printStackTrace(); return null; } }

private void processar() { boolean bOK = false; String sSQL = "DELETE FROM FNSALDOLANCA WHERE CODEMP=? AND CODFILIAL=?"; try { state("Excluindo base atual de saldos..."); PreparedStatement ps = con.prepareStatement(sSQL); ps.setInt(1, Aplicativo.iCodEmp); ps.setInt(2, ListaCampos.getMasterFilial("FNSALDOLANCA")); ps.executeUpdate(); ps.close(); state("Base excluida..."); bOK = true; } catch (SQLException err) { Funcoes.mensagemErro(this, "Erro ao excluir os saldos!\n" + err.getMessage(), true, con, err); err.printStackTrace(); } if (bOK) { bOK = false; sSQL = "SELECT CODPLAN,DATASUBLANCA,SUM(VLRSUBLANCA) VLRSUBLANCA FROM " + "FNSUBLANCA WHERE CODEMP=? AND CODFILIAL=? GROUP BY CODPLAN,DATASUBLANCA " + "ORDER BY CODPLAN,DATASUBLANCA"; try { state("Iniciando reconstru��o..."); PreparedStatement ps = con.prepareStatement(sSQL); ps.setInt(1, Aplicativo.iCodEmp); ps.setInt(2, ListaCampos.getMasterFilial("FNLANCA")); ResultSet rs = ps.executeQuery(); String sPlanAnt = ""; double dSaldo = 0; bOK = true; int iFilialPlan = ListaCampos.getMasterFilial("FNPLANEJAMENTO"); int iFilialSaldo = ListaCampos.getMasterFilial("FNSALDOLANCA"); while (rs.next() && bOK) { if ("1010100000004".equals(rs.getString("CodPlan"))) { System.out.println("Debug"); } if (sPlanAnt.equals(rs.getString("CodPlan"))) { dSaldo += rs.getDouble("VLRSUBLANCA"); } else dSaldo = rs.getDouble("VLRSUBLANCA"); bOK = insereSaldo(iFilialSaldo, iFilialPlan, rs.getString("CodPlan"), rs.getDate("DataSubLanca"), dSaldo); sPlanAnt = rs.getString("CodPlan"); if ("1010100000004".equals(sPlanAnt)) { System.out.println("Debug"); } } ps.close(); state("Aguardando grava��o final..."); } catch (SQLException err) { bOK = false; Funcoes.mensagemErro(this, "Erro ao excluir os lan�amentos!\n" + err.getMessage(), true, con, err); err.printStackTrace(); } } try { if (bOK) { con.commit(); state("Registros processados com sucesso!"); } else { state("Registros antigos restaurados!"); con.rollback(); } } catch (SQLException err) { Funcoes.mensagemErro(this, "Erro ao relizar precedimento!\n" + err.getMessage(), true, con, err); err.printStackTrace(); } bRunProcesso = false; btProcessar.setEnabled(true); }

public static void main(String[] args) { FTPClient client = new FTPClient(); String sFTP = "ftp.servidor.com"; String sUser = "usuario"; String sPassword = "pasword"; try { System.out.println("Conectandose a " + sFTP); client.connect(sFTP); client.login(sUser, sPassword); System.out.println(client.printWorkingDirectory()); client.changeWorkingDirectory("\\httpdocs"); System.out.println(client.printWorkingDirectory()); System.out.println("Desconectando."); client.logout(); client.disconnect(); } catch (IOException ioe) { ioe.printStackTrace(); } }

private void generateArchetype(final IProject project, final IDataModel model, final IProgressMonitor monitor, final boolean offline) throws CoreException, InterruptedException, IOException { if (getArchetypeArtifactId(model) != null) { final Properties properties = new Properties(); properties.put("archetypeArtifactId", getArchetypeArtifactId(model)); properties.put("archetypeGroupId", getArchetypeGroupId(model)); properties.put("archetypeVersion", getArchetypeVersion(model)); String artifact = (String) model.getProperty(IMavenFacetInstallDataModelProperties.PROJECT_ARTIFACT_ID); if (artifact == null || artifact.trim().length() == 0) { artifact = project.getName(); } properties.put("artifactId", artifact); String group = (String) model.getProperty(IMavenFacetInstallDataModelProperties.PROJECT_GROUP_ID); if (group == null || group.trim().length() == 0) { group = project.getName(); } properties.put("groupId", group); properties.put("version", model.getProperty(IMavenFacetInstallDataModelProperties.PROJECT_VERSION)); final StringBuffer sb = new StringBuffer(System.getProperty("user.home")).append(File.separator); sb.append(".m2").append(File.separator).append("repository"); final String local = sb.toString(); Logger.getLog().debug("Local Maven2 repository :: " + local); properties.put("localRepository", local); if (!offline) { final String sbRepos = getRepositories(); properties.put("remoteRepositories", sbRepos); } final ILaunchManager launchManager = DebugPlugin.getDefault().getLaunchManager(); final ILaunchConfigurationType launchConfigurationType = launchManager.getLaunchConfigurationType(LAUNCH_CONFIGURATION_TYPE_ID); final ILaunchConfigurationWorkingCopy workingCopy = launchConfigurationType.newInstance(null, "Creating project using Apache Maven archetype"); File archetypePomDirectory = getDefaultArchetypePomDirectory(); try { String dfPom = getPomFile(group, artifact); ByteArrayInputStream bais = new ByteArrayInputStream(dfPom.getBytes()); File f = new File(archetypePomDirectory, "pom.xml"); OutputStream fous = null; try { fous = new FileOutputStream(f); IOUtils.copy(bais, fous); } finally { try { if (fous != null) { fous.close(); } if (bais != null) { bais.close(); } } catch (IOException e) { } } if (SiteManager.isHttpProxyEnable()) { addProxySettings(properties); } workingCopy.setAttribute(ATTR_POM_DIR, archetypePomDirectory.getAbsolutePath()); workingCopy.setAttribute(ATTR_PROPERTIES, convertPropertiesToList(properties)); String goalName = "archetype:create"; if (offline) { goalName = new StringBuffer(goalName).append(" -o").toString(); } goalName = updateGoal(goalName); workingCopy.setAttribute(ATTR_GOALS, goalName); final long timeout = org.maven.ide.eclipse.ext.Maven2Plugin.getTimeout(); TimeoutLaunchConfiguration.launchWithTimeout(monitor, workingCopy, project, timeout); monitor.setTaskName("Moving to workspace"); FileUtils.copyDirectoryStructure(new File(archetypePomDirectory, project.getName()), ArchetypePOMHelper.getProjectDirectory(project)); monitor.worked(1); performMavenInstall(monitor, project, offline); project.refreshLocal(2, monitor); } catch (final IOException ioe) { Logger.log(Logger.ERROR, "I/O exception. One probably solution is absence " + "of mvn2 archetypes or not the correct version, " + "in your local repository. Please, check existence " + "of this archetype."); Logger.getLog().error("I/O Exception arised creating mvn2 archetype", ioe); throw ioe; } finally { FileUtils.deleteDirectory(archetypePomDirectory); Logger.log(Logger.INFO, "Invoked removing of archetype POM directory"); } } monitor.worked(1); }

@Override public ResourceBundle newBundle(String baseName, Locale locale, String format, ClassLoader loader, boolean reload) throws IllegalAccessException, InstantiationException, IOException { if ((baseName == null) || (locale == null) || (format == null) || (loader == null)) { throw new NullPointerException(); } ResourceBundle bundle = null; if (format.equals(XML)) { String bundleName = toBundleName(baseName, locale); String resourceName = toResourceName(bundleName, format); URL url = loader.getResource(resourceName); if (url != null) { URLConnection connection = url.openConnection(); if (connection != null) { if (reload) { connection.setUseCaches(false); } InputStream stream = connection.getInputStream(); if (stream != null) { BufferedInputStream bis = new BufferedInputStream(stream); bundle = new XMLResourceBundle(bis); bis.close(); } } } } return bundle; }

public static String[] getURLListFromResource(String resourceName, String regExFilter, boolean firstNoEmptyMatched) { String[] urlArray; Vector<String> urlVector = new Vector<String>(); try { ClassLoader classLoader = MqatMain.class.getClassLoader(); URLClassLoader urlClassLoader = (URLClassLoader) classLoader; Enumeration e = urlClassLoader.findResources(resourceName); for (; e.hasMoreElements(); ) { URL url = (URL) e.nextElement(); if ("file".equals(url.getProtocol())) { File file = new File(url.getPath()); File[] fileList = file.listFiles(); if (fileList != null) { for (int i = 0; i < fileList.length; i++) { String urlStr = fileList[i].toURL().toString(); if (urlStr.matches(regExFilter)) { urlVector.add(urlStr); } } } } else if ("jar".equals(url.getProtocol())) { JarURLConnection jarConnection = (JarURLConnection) url.openConnection(); JarFile jarFile = jarConnection.getJarFile(); Enumeration jarEntries = jarFile.entries(); for (; jarEntries.hasMoreElements(); ) { JarEntry jarEntry = (JarEntry) jarEntries.nextElement(); if (!jarEntry.isDirectory()) { String urlStr = url.toString().substring(0, url.toString().lastIndexOf('!') + 1); urlStr += "/" + jarEntry; if (urlStr.matches(regExFilter)) { urlVector.add(urlStr); } } } } if (!urlVector.isEmpty() && firstNoEmptyMatched) { break; } } } catch (Exception ex) { ExceptionHandler.handle(ex, ExceptionHandler.NO_VISUAL); } urlArray = urlVector.toArray(new String[urlVector.size()]); return urlArray; }

public static void s_copy(FileInputStream fis, FileOutputStream fos) throws Exception { FileChannel in = fis.getChannel(); FileChannel out = fos.getChannel(); in.transferTo(0, in.size(), out); if (in != null) in.close(); if (out != null) out.close(); }

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 void writeValue(Value v) throws IOException, SQLException { int type = v.getType(); writeInt(type); switch(type) { case Value.NULL: break; case Value.BYTES: case Value.JAVA_OBJECT: writeBytes(v.getBytesNoCopy()); break; case Value.UUID: { ValueUuid uuid = (ValueUuid) v; writeLong(uuid.getHigh()); writeLong(uuid.getLow()); break; } case Value.BOOLEAN: writeBoolean(v.getBoolean().booleanValue()); break; case Value.BYTE: writeByte(v.getByte()); break; case Value.TIME: writeLong(v.getTimeNoCopy().getTime()); break; case Value.DATE: writeLong(v.getDateNoCopy().getTime()); break; case Value.TIMESTAMP: { Timestamp ts = v.getTimestampNoCopy(); writeLong(ts.getTime()); writeInt(ts.getNanos()); break; } case Value.DECIMAL: writeString(v.getString()); break; case Value.DOUBLE: writeDouble(v.getDouble()); break; case Value.FLOAT: writeFloat(v.getFloat()); break; case Value.INT: writeInt(v.getInt()); break; case Value.LONG: writeLong(v.getLong()); break; case Value.SHORT: writeInt(v.getShort()); break; case Value.STRING: case Value.STRING_IGNORECASE: case Value.STRING_FIXED: writeString(v.getString()); break; case Value.BLOB: { long length = v.getPrecision(); if (SysProperties.CHECK && length < 0) { Message.throwInternalError("length: " + length); } writeLong(length); InputStream in = v.getInputStream(); long written = IOUtils.copyAndCloseInput(in, out); if (SysProperties.CHECK && written != length) { Message.throwInternalError("length:" + length + " written:" + written); } writeInt(LOB_MAGIC); break; } case Value.CLOB: { long length = v.getPrecision(); if (SysProperties.CHECK && length < 0) { Message.throwInternalError("length: " + length); } writeLong(length); Reader reader = v.getReader(); java.io.OutputStream out2 = new java.io.FilterOutputStream(out) { public void flush() { } }; Writer writer = new BufferedWriter(new OutputStreamWriter(out2, Constants.UTF8)); long written = IOUtils.copyAndCloseInput(reader, writer); if (SysProperties.CHECK && written != length) { Message.throwInternalError("length:" + length + " written:" + written); } writer.flush(); writeInt(LOB_MAGIC); break; } case Value.ARRAY: { Value[] list = ((ValueArray) v).getList(); writeInt(list.length); for (Value value : list) { writeValue(value); } break; } case Value.RESULT_SET: { ResultSet rs = ((ValueResultSet) v).getResultSet(); rs.beforeFirst(); ResultSetMetaData meta = rs.getMetaData(); int columnCount = meta.getColumnCount(); writeInt(columnCount); for (int i = 0; i < columnCount; i++) { writeString(meta.getColumnName(i + 1)); writeInt(meta.getColumnType(i + 1)); writeInt(meta.getPrecision(i + 1)); writeInt(meta.getScale(i + 1)); } while (rs.next()) { writeBoolean(true); for (int i = 0; i < columnCount; i++) { int t = DataType.convertSQLTypeToValueType(meta.getColumnType(i + 1)); Value val = DataType.readValue(session, rs, i + 1, t); writeValue(val); } } writeBoolean(false); rs.beforeFirst(); break; } default: Message.throwInternalError("type=" + type); } }

public static void copyFile(File source, File dest) throws IOException { FileChannel in = null, out = null; try { in = new FileInputStream(source).getChannel(); out = new FileOutputStream(dest).getChannel(); in.transferTo(0, in.size(), out); } catch (FileNotFoundException fnfe) { Log.debug(fnfe); } finally { if (in != null) in.close(); if (out != null) out.close(); } }

private void createHomeTab() { Tabpanel homeTab = new Tabpanel(); windowContainer.addWindow(homeTab, Msg.getMsg(EnvWeb.getCtx(), "Home").replaceAll("&", ""), false); Portallayout portalLayout = new Portallayout(); portalLayout.setWidth("100%"); portalLayout.setHeight("100%"); portalLayout.setStyle("position: absolute; overflow: auto"); homeTab.appendChild(portalLayout); Portalchildren portalchildren = null; int currentColumnNo = 0; String sql = "SELECT COUNT(DISTINCT COLUMNNO) " + "FROM PA_DASHBOARDCONTENT " + "WHERE (AD_CLIENT_ID=0 OR AD_CLIENT_ID=?) AND ISACTIVE='Y'"; int noOfCols = DB.getSQLValue(null, sql, EnvWeb.getCtx().getAD_Client_ID()); int width = noOfCols <= 0 ? 100 : 100 / noOfCols; sql = "SELECT x.*, m.AD_MENU_ID " + "FROM PA_DASHBOARDCONTENT x " + "LEFT OUTER JOIN AD_MENU m ON x.AD_WINDOW_ID=m.AD_WINDOW_ID " + "WHERE (x.AD_CLIENT_ID=0 OR x.AD_CLIENT_ID=?) AND x.ISACTIVE='Y' " + "AND x.zulfilepath not in (?, ?, ?) " + "ORDER BY x.COLUMNNO, x.AD_CLIENT_ID, x.LINE "; PreparedStatement pstmt = null; ResultSet rs = null; try { pstmt = DB.prepareStatement(sql, null); pstmt.setInt(1, EnvWeb.getCtx().getAD_Client_ID()); pstmt.setString(2, ACTIVITIES_PATH); pstmt.setString(3, FAVOURITES_PATH); pstmt.setString(4, VIEWS_PATH); rs = pstmt.executeQuery(); while (rs.next()) { int columnNo = rs.getInt("ColumnNo"); if (portalchildren == null || currentColumnNo != columnNo) { portalchildren = new Portalchildren(); portalLayout.appendChild(portalchildren); portalchildren.setWidth(width + "%"); portalchildren.setStyle("padding: 5px"); currentColumnNo = columnNo; } Panel panel = new Panel(); panel.setStyle("margin-bottom:10px"); panel.setTitle(rs.getString("Name")); String description = rs.getString("Description"); if (description != null) panel.setTooltiptext(description); String collapsible = rs.getString("IsCollapsible"); panel.setCollapsible(collapsible.equals("Y")); panel.setBorder("normal"); portalchildren.appendChild(panel); Panelchildren content = new Panelchildren(); panel.appendChild(content); boolean panelEmpty = true; String htmlContent = rs.getString("HTML"); if (htmlContent != null) { StringBuffer result = new StringBuffer("<html><head>"); URL url = getClass().getClassLoader().getResource("org/compiere/images/PAPanel.css"); InputStreamReader ins; try { ins = new InputStreamReader(url.openStream()); BufferedReader bufferedReader = new BufferedReader(ins); String cssLine; while ((cssLine = bufferedReader.readLine()) != null) result.append(cssLine + "\n"); } catch (IOException e1) { logger.log(Level.SEVERE, e1.getLocalizedMessage(), e1); } result.append("</head><body><div class=\"content\">\n"); result.append(stripHtml(htmlContent, false) + "<br>\n"); result.append("</div>\n</body>\n</html>\n</html>"); Html html = new Html(); html.setContent(result.toString()); content.appendChild(html); panelEmpty = false; } int AD_Window_ID = rs.getInt("AD_Window_ID"); if (AD_Window_ID > 0) { int AD_Menu_ID = rs.getInt("AD_Menu_ID"); ToolBarButton btn = new ToolBarButton(String.valueOf(AD_Menu_ID)); MMenu menu = new MMenu(EnvWeb.getCtx(), AD_Menu_ID, null); btn.setLabel(menu.getName()); btn.addEventListener(Events.ON_CLICK, this); content.appendChild(btn); panelEmpty = false; } int PA_Goal_ID = rs.getInt("PA_Goal_ID"); if (PA_Goal_ID > 0) { StringBuffer result = new StringBuffer("<html><head>"); URL url = getClass().getClassLoader().getResource("org/compiere/images/PAPanel.css"); InputStreamReader ins; try { ins = new InputStreamReader(url.openStream()); BufferedReader bufferedReader = new BufferedReader(ins); String cssLine; while ((cssLine = bufferedReader.readLine()) != null) result.append(cssLine + "\n"); } catch (IOException e1) { logger.log(Level.SEVERE, e1.getLocalizedMessage(), e1); } result.append("</head><body><div class=\"content\">\n"); result.append(renderGoals(PA_Goal_ID, content)); result.append("</div>\n</body>\n</html>\n</html>"); Html html = new Html(); html.setContent(result.toString()); content.appendChild(html); panelEmpty = false; } String url = rs.getString("ZulFilePath"); if (url != null) { try { Component component = Executions.createComponents(url, content, null); if (component != null) { if (component instanceof DashboardPanel) { DashboardPanel dashboardPanel = (DashboardPanel) component; if (!dashboardPanel.getChildren().isEmpty()) { content.appendChild(dashboardPanel); dashboardRunnable.add(dashboardPanel); panelEmpty = false; } } else { content.appendChild(component); panelEmpty = false; } } } catch (Exception e) { logger.log(Level.WARNING, "Failed to create components. zul=" + url, e); } } if (panelEmpty) panel.detach(); } } catch (Exception e) { logger.log(Level.WARNING, "Failed to create dashboard content", e); } finally { Util.closeCursor(pstmt, rs); } registerWindow(homeTab); if (!portalLayout.getDesktop().isServerPushEnabled()) portalLayout.getDesktop().enableServerPush(true); dashboardRunnable.refreshDashboard(); dashboardThread = new Thread(dashboardRunnable, "UpdateInfo"); dashboardThread.setDaemon(true); dashboardThread.start(); }

public String htmlContentSimple(String urlStr, String charset) { StringBuffer html = new StringBuffer(); URL url = null; BufferedReader reader = null; try { url = new URL(urlStr); reader = new BufferedReader(new InputStreamReader(url.openStream(), charset)); String line; while ((line = reader.readLine()) != null) { html.append(line).append("\r\n"); } } catch (MalformedURLException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } finally { if (reader != null) try { reader.close(); } catch (IOException e) { e.printStackTrace(); } } return html.toString(); }

public static String SHA256(String source) { logger.info(source); String result = null; try { MessageDigest digest = MessageDigest.getInstance("SHA-256"); digest.update(source.getBytes()); byte[] bytes = digest.digest(); result = EncodeUtils.hexEncode(bytes); } catch (NoSuchAlgorithmException e) { e.printStackTrace(); } logger.info(result); return result; }

public Psrxml getPsrxmlForCandidateList(CandidateList clist) throws BookKeeprCommunicationException { try { synchronized (httpClient) { long psrxmlid = clist.getPsrxmlId(); HttpGet req = new HttpGet(remoteHost.getUrl() + "/id/" + StringConvertable.ID.toString(psrxmlid)); HttpResponse resp = httpClient.execute(req); if (resp.getStatusLine().getStatusCode() == HttpStatus.SC_OK) { try { InputStream in = resp.getEntity().getContent(); XMLAble xmlable = XMLReader.read(in); in.close(); if (xmlable instanceof Psrxml) { Psrxml psrxml = (Psrxml) xmlable; return psrxml; } else { throw new BookKeeprCommunicationException("BookKeepr returned the wrong thing for psrxml id " + psrxmlid); } } catch (SAXException ex) { Logger.getLogger(BookKeeprConnection.class.getName()).log(Level.WARNING, "Got a malformed message from the bookkeepr", ex); throw new BookKeeprCommunicationException(ex); } } else { resp.getEntity().consumeContent(); throw new BookKeeprCommunicationException("Got a " + resp.getStatusLine().getStatusCode() + " from the BookKeepr (" + remoteHost.getUrl() + "/id/" + StringConvertable.ID + ")"); } } } catch (HttpException ex) { throw new BookKeeprCommunicationException(ex); } catch (IOException ex) { throw new BookKeeprCommunicationException(ex); } catch (URISyntaxException ex) { throw new BookKeeprCommunicationException(ex); } }

private static void backupFile(File file) { FileChannel in = null, out = null; try { if (!file.getName().endsWith(".bak")) { in = new FileInputStream(file).getChannel(); out = new FileOutputStream(new File(file.toString() + ".bak")).getChannel(); long size = in.size(); MappedByteBuffer buf = in.map(FileChannel.MapMode.READ_ONLY, 0, size); out.write(buf); } } catch (Exception e) { e.getMessage(); } finally { try { System.gc(); if (in != null) in.close(); if (out != null) out.close(); } catch (Exception e) { e.getMessage(); } } }

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 Channel getChannelFromXML(String channelURL) throws SAXException, IOException { channel = new Channel(channelURL); downloadedItems = new LinkedList<Item>(); URL url = new URL(channelURL); XMLReader xr = XMLReaderFactory.createXMLReader(); ChannelFactory handler = new ChannelFactory(); xr.setContentHandler(handler); xr.setErrorHandler(handler); xr.parse(new InputSource(url.openStream())); channel.setUnreadItemsCount(downloadedItems.size()); return channel; }

public static FTPClient getFtpClient(TopAnalysisConfig topAnalyzerConfig) throws SocketException, IOException { FTPClient ftp = new FTPClient(); ftp.addProtocolCommandListener(new PrintCommandListener(new PrintWriter(System.out))); ftp.connect(topAnalyzerConfig.getFtpServer()); int reply = ftp.getReplyCode(); if (!FTPReply.isPositiveCompletion(reply)) { ftp.disconnect(); throw new java.lang.RuntimeException("PullFileJobWorker connect ftp error!"); } if (!ftp.login(topAnalyzerConfig.getFtpUserName(), topAnalyzerConfig.getFtpPassWord())) { ftp.logout(); throw new java.lang.RuntimeException("PullFileJobWorker login ftp error!"); } logger.info("Remote system is " + ftp.getSystemName()); ftp.setFileType(FTP.BINARY_FILE_TYPE); if (topAnalyzerConfig.isLocalPassiveMode()) ftp.enterLocalPassiveMode(); return ftp; }

public long copyDirAllFilesToDirectoryRecursive(String baseDirStr, String destDirStr, boolean copyOutputsRtIDsDirs) throws Exception { long plussQuotaSize = 0; if (baseDirStr.endsWith(sep)) { baseDirStr = baseDirStr.substring(0, baseDirStr.length() - 1); } if (destDirStr.endsWith(sep)) { destDirStr = destDirStr.substring(0, destDirStr.length() - 1); } FileUtils.getInstance().createDirectory(destDirStr); BufferedInputStream in = null; BufferedOutputStream out = null; byte dataBuff[] = new byte[bufferSize]; File baseDir = new File(baseDirStr); baseDir.mkdirs(); if (!baseDir.exists()) { createDirectory(baseDirStr); } if ((baseDir.exists()) && (baseDir.isDirectory())) { String[] entryList = baseDir.list(); if (entryList.length > 0) { for (int pos = 0; pos < entryList.length; pos++) { String entryName = entryList[pos]; String oldPathFileName = baseDirStr + sep + entryName; File entryFile = new File(oldPathFileName); if (entryFile.isFile()) { String newPathFileName = destDirStr + sep + entryName; File newFile = new File(newPathFileName); if (newFile.exists()) { plussQuotaSize -= newFile.length(); newFile.delete(); } in = new BufferedInputStream(new FileInputStream(oldPathFileName), bufferSize); out = new BufferedOutputStream(new FileOutputStream(newPathFileName), bufferSize); int readLen; while ((readLen = in.read(dataBuff)) > 0) { out.write(dataBuff, 0, readLen); plussQuotaSize += readLen; } out.flush(); in.close(); out.close(); } if (entryFile.isDirectory()) { boolean enableCopyDir = false; if (copyOutputsRtIDsDirs) { enableCopyDir = true; } else { if (entryFile.getParentFile().getName().equals("outputs")) { enableCopyDir = false; } else { enableCopyDir = true; } } if (enableCopyDir) { plussQuotaSize += this.copyDirAllFilesToDirectoryRecursive(baseDirStr + sep + entryName, destDirStr + sep + entryName, copyOutputsRtIDsDirs); } } } } } else { throw new Exception("Base dir not exist ! baseDirStr = (" + baseDirStr + ")"); } return plussQuotaSize; }

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; }

public void onUploadClicked(Event event) { Media[] medias = null; try { medias = Fileupload.get("Select one or more files to upload to " + "the current directory.", "Upload Files", 5); } catch (Exception e) { log.error("An exception occurred when displaying the file " + "upload dialog", e); } if (medias == null) { return; } for (Media media : medias) { String name = media.getName(); CSPath potentialFile = model.getPathForFile(name); if (media.isBinary()) { CSPathOutputStream writer = null; try { potentialFile.createNewFile(); if (potentialFile.exists()) { writer = new CSPathOutputStream(potentialFile); IOUtils.copy(media.getStreamData(), writer); } } catch (IOException e) { displayError("An error occurred when uploading the file " + name + ": " + e.getMessage()); } finally { if (writer != null) { try { writer.close(); } catch (IOException e) { } } } } else { CSPathWriter writer = null; try { potentialFile.createNewFile(); if (potentialFile.exists()) { writer = new CSPathWriter(potentialFile); IOUtils.write(media.getStringData(), writer); } } catch (IOException e) { displayError("An error occurred when uploading the file " + name + ": " + e.getMessage()); } finally { if (writer != null) { try { writer.close(); } catch (IOException e) { } } } } model.fileCleanup(potentialFile); updateFileGrid(); } }

public static void main(String[] args) { File file = null; try { file = File.createTempFile("TestFileChannel", ".dat"); final ByteBuffer buffer = ByteBuffer.allocateDirect(4); final ByteChannel output = new FileOutputStream(file).getChannel(); buffer.putInt(MAGIC_INT); buffer.flip(); output.write(buffer); output.close(); final ByteChannel input = new FileInputStream(file).getChannel(); buffer.clear(); while (buffer.hasRemaining()) { input.read(buffer); } input.close(); buffer.flip(); final int file_int = buffer.getInt(); if (file_int != MAGIC_INT) { System.out.println("TestFileChannel FAILURE"); System.out.println("Wrote " + Integer.toHexString(MAGIC_INT) + " but read " + Integer.toHexString(file_int)); } else { System.out.println("TestFileChannel SUCCESS"); } } catch (Exception e) { System.out.println("TestFileChannel FAILURE"); e.printStackTrace(System.out); } finally { if (null != file) { file.delete(); } } }

private void pack() { String szImageDir = m_szBasePath + "Images"; File fImageDir = new File(szImageDir); fImageDir.mkdirs(); String ljIcon = System.getProperty("user.home"); ljIcon += System.getProperty("file.separator") + "MochaJournal" + System.getProperty("file.separator") + m_szUsername + System.getProperty("file.separator") + "Cache"; File fUserDir = new File(ljIcon); File[] fIcons = fUserDir.listFiles(); int iSize = fIcons.length; for (int i = 0; i < iSize; i++) { try { File fOutput = new File(fImageDir, fIcons[i].getName()); if (!fOutput.exists()) { fOutput.createNewFile(); FileOutputStream fOut = new FileOutputStream(fOutput); FileInputStream fIn = new FileInputStream(fIcons[i]); while (fIn.available() > 0) fOut.write(fIn.read()); } } catch (IOException e) { System.err.println(e); } } try { FileOutputStream fOut; InputStream fLJIcon = getClass().getResourceAsStream("/org/homedns/krolain/MochaJournal/Images/userinfo.gif"); File fLJOut = new File(fImageDir, "user.gif"); if (!fLJOut.exists()) { fOut = new FileOutputStream(fLJOut); while (fLJIcon.available() > 0) fOut.write(fLJIcon.read()); } fLJIcon = getClass().getResourceAsStream("/org/homedns/krolain/MochaJournal/Images/communitynfo.gif"); fLJOut = new File(fImageDir, "comm.gif"); if (!fLJOut.exists()) { fOut = new FileOutputStream(fLJOut); while (fLJIcon.available() > 0) fOut.write(fLJIcon.read()); } fLJIcon = getClass().getResourceAsStream("/org/homedns/krolain/MochaJournal/Images/icon_private.gif"); fLJOut = new File(fImageDir, "icon_private.gif"); if (!fLJOut.exists()) { fOut = new FileOutputStream(fLJOut); while (fLJIcon.available() > 0) fOut.write(fLJIcon.read()); } fLJIcon = getClass().getResourceAsStream("/org/homedns/krolain/MochaJournal/Images/icon_protected.gif"); fLJOut = new File(fImageDir, "icon_protected.gif"); if (!fLJOut.exists()) { fOut = new FileOutputStream(fLJOut); while (fLJIcon.available() > 0) fOut.write(fLJIcon.read()); } } catch (IOException e) { System.err.println(e); } }

public void readMESHDescriptorFileIntoFiles(String outfiledir) { String inputLine, ins; String filename = getMESHdescriptorfilename(); String uid = ""; String name = ""; String description = ""; String element_of = ""; Vector treenr = new Vector(); Vector related = new Vector(); Vector synonyms = new Vector(); Vector actions = new Vector(); Vector chemicals = new Vector(); Vector allCASchemicals = new Vector(); Set CAS = new TreeSet(); Map treenr2uid = new TreeMap(); Map uid2name = new TreeMap(); String cut1, cut2; try { BufferedReader in = new BufferedReader(new FileReader(filename)); String outfile = outfiledir + "\\mesh"; BufferedWriter out_concept = new BufferedWriter(new FileWriter(outfile + "_concept.txt")); BufferedWriter out_concept_name = new BufferedWriter(new FileWriter(outfile + "_concept_name.txt")); BufferedWriter out_relation = new BufferedWriter(new FileWriter(outfile + "_relation.txt")); BufferedWriter cas_mapping = new BufferedWriter(new FileWriter(outfile + "to_cas_mapping.txt")); BufferedWriter ec_mapping = new BufferedWriter(new FileWriter(outfile + "to_ec_mapping.txt")); Connection db = tools.openDB("kb"); String query = "SELECT hierarchy_complete,uid FROM mesh_tree, mesh_graph_uid_name WHERE term=name"; ResultSet rs = tools.executeQuery(db, query); while (rs.next()) { String db_treenr = rs.getString("hierarchy_complete"); String db_uid = rs.getString("uid"); treenr2uid.put(db_treenr, db_uid); } db.close(); System.out.println("Reading in the DUIDs ..."); BufferedReader in_for_mapping = new BufferedReader(new FileReader(filename)); inputLine = getNextLine(in_for_mapping); boolean leave = false; while ((in_for_mapping != null) && (inputLine != null)) { if (inputLine.startsWith("<DescriptorRecord DescriptorClass")) { inputLine = getNextLine(in_for_mapping); cut1 = "<DescriptorUI>"; cut2 = "</DescriptorUI>"; String mesh_uid = inputLine.substring(cut1.length(), inputLine.indexOf(cut2)); if (mesh_uid.compareTo("D041441") == 0) leave = true; inputLine = getNextLine(in_for_mapping); inputLine = getNextLine(in_for_mapping); cut1 = "<String>"; cut2 = "</String>"; String mesh_name = inputLine.substring(cut1.length(), inputLine.indexOf(cut2)); uid2name.put(mesh_uid, mesh_name); } inputLine = getNextLine(in_for_mapping); } in_for_mapping.close(); BufferedReader in_ec_numbers = new BufferedReader(new FileReader("e:\\projects\\ondex\\ec_concept_acc.txt")); Set ec_numbers = new TreeSet(); String ec_line = in_ec_numbers.readLine(); while (in_ec_numbers.ready()) { StringTokenizer st = new StringTokenizer(ec_line); st.nextToken(); ec_numbers.add(st.nextToken()); ec_line = in_ec_numbers.readLine(); } in_ec_numbers.close(); tools.printDate(); inputLine = getNextLine(in); while (inputLine != null) { if (inputLine.startsWith("<DescriptorRecord DescriptorClass")) { treenr.clear(); related.clear(); synonyms.clear(); actions.clear(); chemicals.clear(); boolean id_ready = false; boolean line_read = false; while ((inputLine != null) && (!inputLine.startsWith("</DescriptorRecord>"))) { line_read = false; if ((inputLine.startsWith("<DescriptorUI>")) && (!id_ready)) { cut1 = "<DescriptorUI>"; cut2 = "</DescriptorUI>"; uid = inputLine.substring(cut1.length(), inputLine.indexOf(cut2)); inputLine = getNextLine(in); inputLine = getNextLine(in); cut1 = "<String>"; cut2 = "</String>"; name = inputLine.substring(cut1.length(), inputLine.indexOf(cut2)); id_ready = true; } if (inputLine.compareTo("<SeeRelatedList>") == 0) { while ((inputLine != null) && (inputLine.indexOf("</SeeRelatedList>") == -1)) { if (inputLine.startsWith("<DescriptorUI>")) { cut1 = "<DescriptorUI>"; cut2 = "</DescriptorUI>"; String id = inputLine.substring(cut1.length(), inputLine.indexOf(cut2)); related.add(id); } inputLine = getNextLine(in); line_read = true; } } if (inputLine.compareTo("<TreeNumberList>") == 0) { while ((inputLine != null) && (inputLine.indexOf("</TreeNumberList>") == -1)) { if (inputLine.startsWith("<TreeNumber>")) { cut1 = "<TreeNumber>"; cut2 = "</TreeNumber>"; String id = inputLine.substring(cut1.length(), inputLine.indexOf(cut2)); treenr.add(id); } inputLine = getNextLine(in); line_read = true; } } if (inputLine.startsWith("<Concept PreferredConceptYN")) { boolean prefConcept = false; if (inputLine.compareTo("<Concept PreferredConceptYN=\"Y\">") == 0) prefConcept = true; while ((inputLine != null) && (inputLine.indexOf("</Concept>") == -1)) { if (inputLine.startsWith("<CASN1Name>") && prefConcept) { cut1 = "<CASN1Name>"; cut2 = "</CASN1Name>"; String casn1 = inputLine.substring(cut1.length(), inputLine.indexOf(cut2)); String chem_name = casn1; String chem_description = ""; if (casn1.length() > chem_name.length() + 2) chem_description = casn1.substring(chem_name.length() + 2, casn1.length()); String reg_number = ""; inputLine = getNextLine(in); if (inputLine.startsWith("<RegistryNumber>")) { cut1 = "<RegistryNumber>"; cut2 = "</RegistryNumber>"; reg_number = inputLine.substring(cut1.length(), inputLine.indexOf(cut2)); } Vector chemical = new Vector(); String type = ""; if (reg_number.startsWith("EC")) { type = "EC"; reg_number = reg_number.substring(3, reg_number.length()); } else { type = "CAS"; } chemical.add(type); chemical.add(reg_number); chemical.add(chem_name); chemical.add(chem_description); chemicals.add(chemical); if (type.compareTo("CAS") == 0) { if (!CAS.contains(reg_number)) { CAS.add(reg_number); allCASchemicals.add(chemical); } } } if (inputLine.startsWith("<ScopeNote>") && prefConcept) { cut1 = "<ScopeNote>"; description = inputLine.substring(cut1.length(), inputLine.length()); } if (inputLine.startsWith("<TermUI>")) { inputLine = getNextLine(in); cut1 = "<String>"; cut2 = "</String>"; String syn = inputLine.substring(cut1.length(), inputLine.indexOf(cut2)); if (syn.indexOf("&amp;") != -1) { String syn1 = syn.substring(0, syn.indexOf("&amp;")); String syn2 = syn.substring(syn.indexOf("amp;") + 4, syn.length()); syn = syn1 + " & " + syn2; } if (name.compareTo(syn) != 0) synonyms.add(syn); } if (inputLine.startsWith("<PharmacologicalAction>")) { inputLine = getNextLine(in); inputLine = getNextLine(in); cut1 = "<DescriptorUI>"; cut2 = "</DescriptorUI>"; String act_ui = inputLine.substring(cut1.length(), inputLine.indexOf(cut2)); actions.add(act_ui); } inputLine = getNextLine(in); line_read = true; } } if (!line_read) inputLine = getNextLine(in); } String pos_tag = ""; element_of = "MESHD"; String is_primary = "0"; out_concept.write(uid + "\t" + pos_tag + "\t" + description + "\t" + element_of + "\t"); out_concept.write(is_primary + "\n"); String name_stemmed = ""; String name_tagged = ""; element_of = "MESHD"; String is_unique = "0"; int is_preferred = 1; String original_name = name; String is_not_substring = "0"; out_concept_name.write(uid + "\t" + name + "\t" + name_stemmed + "\t"); out_concept_name.write(name_tagged + "\t" + element_of + "\t"); out_concept_name.write(is_unique + "\t" + is_preferred + "\t"); out_concept_name.write(original_name + "\t" + is_not_substring + "\n"); is_preferred = 0; for (int i = 0; i < synonyms.size(); i++) { name = (String) synonyms.get(i); original_name = name; out_concept_name.write(uid + "\t" + name + "\t" + name_stemmed + "\t"); out_concept_name.write(name_tagged + "\t" + element_of + "\t"); out_concept_name.write(is_unique + "\t" + is_preferred + "\t"); out_concept_name.write(original_name + "\t" + is_not_substring + "\n"); } String rel_type = "is_r"; element_of = "MESHD"; String from_name = name; for (int i = 0; i < related.size(); i++) { String to_uid = (String) related.get(i); String to_name = (String) uid2name.get(to_uid); out_relation.write(uid + "\t" + to_uid + "\t"); out_relation.write(rel_type + "\t" + element_of + "\t"); out_relation.write(from_name + "\t" + to_name + "\n"); } rel_type = "is_a"; element_of = "MESHD"; related.clear(); for (int i = 0; i < treenr.size(); i++) { String tnr = (String) treenr.get(i); if (tnr.length() > 3) tnr = tnr.substring(0, tnr.lastIndexOf(".")); String rel_uid = (String) treenr2uid.get(tnr); if (rel_uid != null) related.add(rel_uid); else System.out.println(uid + ": No DUI found for " + tnr); } for (int i = 0; i < related.size(); i++) { String to_uid = (String) related.get(i); String to_name = (String) uid2name.get(to_uid); out_relation.write(uid + "\t" + to_uid + "\t"); out_relation.write(rel_type + "\t" + element_of + "\t"); out_relation.write(from_name + "\t" + to_name + "\n"); } if (related.size() == 0) System.out.println(uid + ": No is_a relations"); rel_type = "act"; element_of = "MESHD"; for (int i = 0; i < actions.size(); i++) { String to_uid = (String) actions.get(i); String to_name = (String) uid2name.get(to_uid); out_relation.write(uid + "\t" + to_uid + "\t"); out_relation.write(rel_type + "\t" + element_of + "\t"); out_relation.write(from_name + "\t" + to_name + "\n"); } String method = "IMPM"; String score = "1.0"; for (int i = 0; i < chemicals.size(); i++) { Vector chemical = (Vector) chemicals.get(i); String type = (String) chemical.get(0); String chem = (String) chemical.get(1); if (!ec_numbers.contains(chem) && (type.compareTo("EC") == 0)) { if (chem.compareTo("1.14.-") == 0) chem = "1.14.-.-"; else System.out.println("MISSING EC: " + chem); } String id = type + ":" + chem; String entry = uid + "\t" + id + "\t" + method + "\t" + score + "\n"; if (type.compareTo("CAS") == 0) cas_mapping.write(entry); else ec_mapping.write(entry); } } else inputLine = getNextLine(in); } System.out.println("End import descriptors"); tools.printDate(); in.close(); out_concept.close(); out_concept_name.close(); out_relation.close(); cas_mapping.close(); ec_mapping.close(); outfile = outfiledir + "\\cas"; out_concept = new BufferedWriter(new FileWriter(outfile + "_concept.txt")); out_concept_name = new BufferedWriter(new FileWriter(outfile + "_concept_name.txt")); BufferedWriter out_concept_acc = new BufferedWriter(new FileWriter(outfile + "_concept_acc.txt")); for (int i = 0; i < allCASchemicals.size(); i++) { Vector chemical = (Vector) allCASchemicals.get(i); String cas_id = "CAS:" + (String) chemical.get(1); String cas_name = (String) chemical.get(2); String cas_pos_tag = ""; String cas_description = (String) chemical.get(3); String cas_element_of = "CAS"; String cas_is_primary = "0"; out_concept.write(cas_id + "\t" + cas_pos_tag + "\t" + cas_description + "\t"); out_concept.write(cas_element_of + "\t" + cas_is_primary + "\n"); String cas_name_stemmed = ""; String cas_name_tagged = ""; String cas_is_unique = "0"; String cas_is_preferred = "0"; String cas_original_name = cas_name; String cas_is_not_substring = "0"; out_concept_name.write(cas_id + "\t" + cas_name + "\t" + cas_name_stemmed + "\t"); out_concept_name.write(cas_name_tagged + "\t" + cas_element_of + "\t"); out_concept_name.write(cas_is_unique + "\t" + cas_is_preferred + "\t"); out_concept_name.write(cas_original_name + "\t" + cas_is_not_substring + "\n"); out_concept_acc.write(cas_id + "\t" + (String) chemical.get(1) + "\t"); out_concept_acc.write(cas_element_of + "\n"); } out_concept.close(); out_concept_name.close(); out_concept_acc.close(); } catch (Exception e) { settings.writeLog("Error while reading MESH descriptor file: " + e.getMessage()); } }

private static void copyImage(String srcImg, String destImg) { try { FileChannel srcChannel = new FileInputStream(srcImg).getChannel(); FileChannel dstChannel = new FileOutputStream(destImg).getChannel(); dstChannel.transferFrom(srcChannel, 0, srcChannel.size()); srcChannel.close(); dstChannel.close(); } catch (Exception e) { e.printStackTrace(); } }

protected static URL[] createUrls(URL jarUrls[]) { ArrayList<URL> additionalUrls = new ArrayList<URL>(Arrays.asList(jarUrls)); for (URL ju : jarUrls) { try { JarFile jar = new JarFile(ju.getFile()); Enumeration<JarEntry> entries = jar.entries(); while (entries.hasMoreElements()) { JarEntry j = entries.nextElement(); if (j.isDirectory()) continue; if (j.getName().startsWith("lib/") && j.getName().endsWith(".jar")) { URL url = new URL("jar:" + ju.getProtocol() + ":" + ju.getFile() + "!/" + j.getName()); InputStream is = url.openStream(); File tmpFile = File.createTempFile("SCDeploy", ".jar"); FileOutputStream fos = new FileOutputStream(tmpFile); IOUtils.copy(is, fos); is.close(); fos.close(); additionalUrls.add(new URL("file://" + tmpFile.getAbsolutePath())); } } } catch (IOException e) { } } return additionalUrls.toArray(new URL[] {}); }

public static void parseSohuStock(ArrayList<String> dataSource, final ArrayList<SohuStockBean> sohuStockBeanList) throws IOReactorException, InterruptedException { HttpAsyncClient httpclient = new DefaultHttpAsyncClient(); httpclient.start(); if (dataSource != null && dataSource.size() > 0) { final CountDownLatch latch = new CountDownLatch(dataSource.size()); for (int i = 0; i < dataSource.size(); i++) { final HttpGet request = new HttpGet(dataSource.get(i)); httpclient.execute(request, new FutureCallback<HttpResponse>() { public void completed(final HttpResponse response) { System.out.println(" Request completed " + count + " " + request.getRequestLine() + " " + response.getStatusLine()); try { HttpEntity he = response.getEntity(); try { String resp = EntityUtils.toString(he, "gb2312"); if (resp != null && resp.length() > 0) { SohuStockBean shstBean = SohuStockPostProcess.postSohuStockBeanProcess(resp); sohuStockBeanList.add(shstBean); } count++; } catch (ParseException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } latch.countDown(); } catch (RuntimeException re) { latch.countDown(); } } public void failed(final Exception ex) { latch.countDown(); } public void cancelled() { latch.countDown(); } }); } latch.await(); System.out.println("done"); } if (httpclient != null) { httpclient.shutdown(); } System.out.println(sohuStockBeanList.size()); }

public static boolean matchPassword(String prevPassStr, String newPassword) throws NoSuchAlgorithmException, java.io.IOException, java.io.UnsupportedEncodingException { MessageDigest md = MessageDigest.getInstance("MD5"); byte[] seed = new byte[12]; byte[] prevPass = new sun.misc.BASE64Decoder().decodeBuffer(prevPassStr); System.arraycopy(prevPass, 0, seed, 0, 12); md.update(seed); md.update(newPassword.getBytes("UTF8")); byte[] digestNewPassword = md.digest(); byte[] choppedPrevPassword = new byte[prevPass.length - 12]; System.arraycopy(prevPass, 12, choppedPrevPassword, 0, prevPass.length - 12); boolean isMatching = Arrays.equals(digestNewPassword, choppedPrevPassword); return isMatching; }

public void save(InputStream is) throws IOException { File dest = Config.getDataFile(getInternalDate(), getPhysMessageID()); OutputStream os = null; try { os = new FileOutputStream(dest); IOUtils.copyLarge(is, os); } finally { IOUtils.closeQuietly(os); IOUtils.closeQuietly(is); } }

@Override public String resolveItem(String oldJpgFsPath) throws DatabaseException { if (oldJpgFsPath == null || "".equals(oldJpgFsPath)) throw new NullPointerException("oldJpgFsPath"); try { getConnection().setAutoCommit(false); } catch (SQLException e) { LOGGER.warn("Unable to set autocommit off", e); } PreparedStatement statement = null; String ret = null; try { statement = getConnection().prepareStatement(SELECT_ITEM_STATEMENT); statement.setString(1, oldJpgFsPath); ResultSet rs = statement.executeQuery(); int i = 0; int id = -1; int rowsAffected = 0; while (rs.next()) { id = rs.getInt("id"); ret = rs.getString("imageFile"); i++; } if (id != -1 && new File(ret).exists()) { statement = getConnection().prepareStatement(UPDATE_ITEM_STATEMENT); statement.setInt(1, id); rowsAffected = statement.executeUpdate(); } else { return null; } if (rowsAffected == 1) { getConnection().commit(); LOGGER.debug("DB has been updated."); } else { getConnection().rollback(); LOGGER.error("DB has not been updated -> rollback!"); } } catch (SQLException e) { LOGGER.error(e); } finally { closeConnection(); } return ret; }

@Override public byte[] read(String path) throws PersistenceException { path = fmtPath(path); try { S3Object fileObj = s3Service.getObject(bucketObj, path); ByteArrayOutputStream out = new ByteArrayOutputStream(); IOUtils.copy(fileObj.getDataInputStream(), out); return out.toByteArray(); } catch (Exception e) { throw new PersistenceException("fail to read s3 file - " + path, e); } }

public String downloadToSdCard(String localFileName, String suffixFromHeader, String extension) { InputStream in = null; FileOutputStream fos = null; String absolutePath = null; try { Log.i(TAG, "Opening URL: " + url); StreamAndHeader inAndHeader = HTTPUtils.openWithHeader(url, suffixFromHeader); if (inAndHeader == null || inAndHeader.mStream == null) { return null; } in = inAndHeader.mStream; String sdcardpath = android.os.Environment.getExternalStorageDirectory().getAbsolutePath(); String headerValue = suffixFromHeader == null || inAndHeader.mHeaderValue == null ? "" : inAndHeader.mHeaderValue; headerValue = headerValue.replaceAll("[-:]*\\s*", ""); String filename = sdcardpath + "/" + localFileName + headerValue + (extension == null ? "" : extension); mSize = in.available(); Log.i(TAG, "Downloading " + filename + ", size: " + mSize); fos = new FileOutputStream(new File(filename)); int buffersize = 1024; byte[] buffer = new byte[buffersize]; int readsize = buffersize; mCount = 0; while (readsize != -1) { readsize = in.read(buffer, 0, buffersize); if (readsize > 0) { Log.i(TAG, "Read " + readsize + " bytes..."); fos.write(buffer, 0, readsize); mCount += readsize; } } fos.flush(); fos.close(); FileInputStream controlIn = new FileInputStream(filename); mSavedSize = controlIn.available(); Log.v(TAG, "saved size: " + mSavedSize); mAbsolutePath = filename; done(); } catch (Exception e) { Log.e(TAG, "LoadingWorker.run", e); } finally { HTTPUtils.close(in); } return mAbsolutePath; }

public static String readUrlText(String urlString) throws IOException { URL url = new URL(urlString); InputStream stream = url.openStream(); StringBuilder buf = new StringBuilder(); BufferedReader in = null; try { in = new BufferedReader(new InputStreamReader(stream)); String str; while ((str = in.readLine()) != null) { buf.append(str); buf.append(System.getProperty("line.separator")); } } catch (IOException e) { System.out.println("Error reading text from URL [" + url + "]: " + e.toString()); throw e; } finally { if (in != null) { try { in.close(); } catch (IOException e) { System.out.println("Error closing after reading text from URL [" + url + "]: " + e.toString()); } } } return buf.toString(); }

public int subclass(int objectId, String description) throws FidoDatabaseException, ObjectNotFoundException { try { Connection conn = null; Statement stmt = null; ResultSet rs = null; try { String sql = "insert into Objects (Description) " + "values ('" + description + "')"; conn = fido.util.FidoDataSource.getConnection(); conn.setAutoCommit(false); stmt = conn.createStatement(); if (contains(stmt, objectId) == false) throw new ObjectNotFoundException(objectId); stmt.executeUpdate(sql); int id; sql = "select currval('objects_objectid_seq')"; rs = stmt.executeQuery(sql); if (rs.next() == false) throw new SQLException("No rows returned from select currval() query"); else id = rs.getInt(1); ObjectLinkTable objectLinkList = new ObjectLinkTable(); objectLinkList.linkObjects(stmt, id, "isa", objectId); conn.commit(); return id; } catch (SQLException e) { if (conn != null) conn.rollback(); throw e; } finally { if (rs != null) rs.close(); if (stmt != null) stmt.close(); if (conn != null) conn.close(); } } catch (SQLException e) { throw new FidoDatabaseException(e); } }

public void moveRuleDown(String language, String tag, int row) throws FidoDatabaseException { try { Connection conn = null; Statement stmt = null; try { conn = fido.util.FidoDataSource.getConnection(); conn.setAutoCommit(false); stmt = conn.createStatement(); int max = findMaxRank(stmt, language, tag); if ((row < 1) || (row > (max - 1))) throw new IllegalArgumentException("Row number (" + row + ") was not between 1 and " + (max - 1)); stmt.executeUpdate("update LanguageMorphologies set Rank = -1 " + "where Rank = " + row + " and MorphologyTag = '" + tag + "' and " + " LanguageName = '" + language + "'"); stmt.executeUpdate("update LanguageMorphologies set Rank = " + row + "where Rank = " + (row + 1) + " and MorphologyTag = '" + tag + "' and " + " LanguageName = '" + language + "'"); stmt.executeUpdate("update LanguageMorphologies set Rank = " + (row + 1) + "where Rank = -1 and MorphologyTag = '" + tag + "' and " + " LanguageName = '" + language + "'"); conn.commit(); } catch (SQLException e) { if (conn != null) conn.rollback(); throw e; } finally { if (stmt != null) stmt.close(); if (conn != null) conn.close(); } } catch (SQLException e) { throw new FidoDatabaseException(e); } }

private void getServiceReponse(String service, NameSpaceDefinition nsDefinition) throws Exception { Pattern pattern = Pattern.compile("(?i)(?:.*(xmlns(?:\\:\\w+)?=\\\"http\\:\\/\\/www\\.ivoa\\.net\\/.*" + service + "[^\\\"]*\\\").*)"); pattern = Pattern.compile(".*xmlns(?::\\w+)?=(\"[^\"]*(?i)(?:" + service + ")[^\"]*\").*"); logger.debug("read " + this.url + service); BufferedReader in = new BufferedReader(new InputStreamReader((new URL(this.url + service)).openStream())); String inputLine; BufferedWriter bfw = new BufferedWriter(new FileWriter(this.baseDirectory + service + ".xml")); boolean found = false; while ((inputLine = in.readLine()) != null) { if (!found) { Matcher m = pattern.matcher(inputLine); if (m.matches()) { nsDefinition.init("xmlns:vosi=" + m.group(1)); found = true; } } bfw.write(inputLine + "\n"); } in.close(); bfw.close(); }

public FTPClient sample2(String server, String username, String password) throws IllegalStateException, IOException, FTPIllegalReplyException, FTPException { FTPClient ftpClient = new FTPClient(); ftpClient.connect(server); ftpClient.login(username, password); return ftpClient; }

@Override public void run() { try { IOUtils.copy(getSource(), processStdIn); System.err.println("Copy done."); close(); } catch (IOException e) { e.printStackTrace(); IOUtils.closeQuietly(ExternalDecoder.this); } }

public byte[] read(IFile input) { InputStream contents = null; try { ByteArrayOutputStream baos = new ByteArrayOutputStream(); contents = input.getContents(); IOUtils.copy(contents, baos); return baos.toByteArray(); } catch (IOException e) { Activator.logUnexpected(null, e); } catch (CoreException e) { Activator.logUnexpected(null, e); } finally { IOUtils.closeQuietly(contents); } return null; }

public List<String> generate(String geronimoVersion, String geronimoHome, String instanceNumber) { geronimoRepository = geronimoHome + "/repository"; Debug.logInfo("The WASCE or Geronimo Repository is " + geronimoRepository, module); Classpath classPath = new Classpath(System.getProperty("java.class.path")); List<File> elements = classPath.getElements(); List<String> jar_version = new ArrayList<String>(); String jarPath = null; String jarName = null; String newJarName = null; String jarNameSimple = null; String jarVersion = "1.0"; int lastDash = -1; for (File f : elements) { if (f.exists()) { if (f.isFile()) { jarPath = f.getAbsolutePath(); jarName = f.getName(); String jarNameWithoutExt = (String) jarName.subSequence(0, jarName.length() - 4); lastDash = jarNameWithoutExt.lastIndexOf("-"); if (lastDash > -1) { jarVersion = jarNameWithoutExt.substring(lastDash + 1, jarNameWithoutExt.length()); jarNameSimple = jarNameWithoutExt.substring(0, lastDash); boolean alreadyVersioned = 0 < StringUtil.removeRegex(jarVersion, "[^.0123456789]").length(); if (!alreadyVersioned) { jarVersion = "1.0"; jarNameSimple = jarNameWithoutExt; newJarName = jarNameWithoutExt + "-" + jarVersion + ".jar"; } else { newJarName = jarName; } } else { jarVersion = "1.0"; jarNameSimple = jarNameWithoutExt; newJarName = jarNameWithoutExt + "-" + jarVersion + ".jar"; } jar_version.add(jarNameSimple + "#" + jarVersion); String targetDirectory = geronimoRepository + "/org/ofbiz/" + jarNameSimple + "/" + jarVersion; File targetDir = new File(targetDirectory); if (!targetDir.exists()) { boolean created = targetDir.mkdirs(); if (!created) { Debug.logFatal("Unable to create target directory - " + targetDirectory, module); return null; } } if (!targetDirectory.endsWith("/")) { targetDirectory = targetDirectory + "/"; } String newCompleteJarName = targetDirectory + newJarName; File newJarFile = new File(newCompleteJarName); try { FileChannel srcChannel = new FileInputStream(jarPath).getChannel(); FileChannel dstChannel = new FileOutputStream(newCompleteJarName).getChannel(); dstChannel.transferFrom(srcChannel, 0, srcChannel.size()); Debug.log("Created jar file : " + newJarName + " in WASCE or Geronimo repository", module); srcChannel.close(); dstChannel.close(); } catch (IOException e) { Debug.logFatal("Unable to create jar file - " + newJarName + " in WASCE or Geronimo repository (certainly already exists)", module); return null; } } } } List<ComponentConfig.WebappInfo> webApps = ComponentConfig.getAllWebappResourceInfos(); File geronimoWebXml = new File(System.getProperty("ofbiz.home") + "/framework/appserver/templates/" + geronimoVersion + "/geronimo-web.xml"); for (ComponentConfig.WebappInfo webApp : webApps) { if (null != webApp) { parseTemplate(geronimoWebXml, webApp); } } return jar_version; }

public void connect(final URLConnectAdapter urlAdapter) { if (this.connectSettings == null) { throw new IllegalStateException("Invalid Connect Settings (is null)"); } final HttpURLConnection httpConnection = (HttpURLConnection) urlAdapter.openConnection(); BufferedReader in; try { in = new BufferedReader(new InputStreamReader(httpConnection.getInputStream())); final StringBuilder buf = new StringBuilder(200); String str; while ((str = in.readLine()) != null) { buf.append(str); buf.append('\n'); } final ConnectResult result = new ConnectResult(httpConnection.getResponseCode(), buf.toString()); final Map<String, List<String>> headerFields = httpConnection.getHeaderFields(); for (Map.Entry<String, List<String>> entry : headerFields.entrySet()) { final String key = entry.getKey(); final List<String> val = entry.getValue(); if ((val != null) && (val.size() > 1)) { System.out.println("WARN: Invalid header value : " + key + " url=" + this.connectSettings.getUrl()); } if (key != null) { result.addHeader(key, val.get(0), val); } else { result.addHeader("Status", val.get(0), val); } } this.lastResult = result; } catch (IOException e) { throw new ConnectException(e); } }

public void readFully(String urlS) throws Exception { URL url = new URL(urlS); URLConnection conn = url.openConnection(); InputStream is = conn.getInputStream(); byte[] data = new byte[10240]; int b = is.read(data); while (b > 0) { size += b; b = is.read(data); } is.close(); }

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; } }

private static String getBase64(String text, String algorithm) throws NoSuchAlgorithmException { AssertUtility.notNull(text); AssertUtility.notNullAndNotSpace(algorithm); String base64; MessageDigest md = MessageDigest.getInstance(algorithm); md.update(text.getBytes()); base64 = new BASE64Encoder().encode(md.digest()); return base64; }

public static void copy(File sourceFile, File destinationFile) throws IOException { FileChannel sourceChannel = new FileInputStream(sourceFile).getChannel(); FileChannel destinationChannel = new FileOutputStream(destinationFile).getChannel(); destinationChannel.transferFrom(sourceChannel, 0, sourceChannel.size()); sourceChannel.close(); destinationChannel.close(); }

public InputStream getResource(FCValue name) throws FCException { Element el = _factory.getElementWithID(name.getAsString()); if (el == null) { throw new FCException("Could not find resource \"" + name + "\""); } String urlString = el.getTextTrim(); if (!urlString.startsWith("http")) { try { log.debug("Get resource: " + urlString); URL url; if (urlString.startsWith("file:")) { url = new URL(urlString); } else { url = getClass().getResource(urlString); } return url.openStream(); } catch (Exception e) { throw new FCException("Failed to load resource.", e); } } else { try { FCService http = getRuntime().getServiceFor(FCService.HTTP_DOWNLOAD); return http.perform(new FCValue[] { name }).getAsInputStream(); } catch (Exception e) { throw new FCException("Failed to load resource.", e); } } }

public static void main(String[] args) { try { FileReader reader = new FileReader(args[0]); FileWriter writer = new FileWriter(args[1]); html2xhtml(reader, writer); writer.close(); reader.close(); } catch (Exception e) { freemind.main.Resources.getInstance().logException(e); } }

public void copy(String original, String copy) throws SQLException { try { OutputStream out = openFileOutputStream(copy, false); InputStream in = openFileInputStream(original); IOUtils.copyAndClose(in, out); } catch (IOException e) { throw Message.convertIOException(e, "Can not copy " + original + " to " + copy); } }

public static String md5(String str) { try { MessageDigest digest = java.security.MessageDigest.getInstance("MD5"); digest.update(str.getBytes()); byte messageDigest[] = digest.digest(); StringBuffer hexString = new StringBuffer(); for (int i = 0; i < messageDigest.length; i++) hexString.append(Integer.toHexString(0xFF & messageDigest[i])); String md5 = hexString.toString(); Log.v(FileUtil.class.getName(), md5); return md5; } catch (NoSuchAlgorithmException e) { e.printStackTrace(); } return ""; }

private String hash(String clearPassword) { if (salt == 0) return null; MessageDigest md = null; try { md = MessageDigest.getInstance("SHA1"); } catch (NoSuchAlgorithmException e) { throw new AssertionError("Can't find the SHA1 algorithm in the java.security package"); } String saltString = String.valueOf(salt); md.update(saltString.getBytes()); md.update(clearPassword.getBytes()); byte[] digestBytes = md.digest(); StringBuffer digestSB = new StringBuffer(); for (int i = 0; i < digestBytes.length; i++) { int lowNibble = digestBytes[i] & 0x0f; int highNibble = (digestBytes[i] >> 4) & 0x0f; digestSB.append(Integer.toHexString(highNibble)); digestSB.append(Integer.toHexString(lowNibble)); } String digestStr = digestSB.toString(); return digestStr; }

public static boolean filecopy(final File source, final File target) { boolean out = false; if (source.isDirectory() || !source.exists() || target.isDirectory() || source.equals(target)) return false; try { target.getParentFile().mkdirs(); target.createNewFile(); FileChannel sourceChannel = new FileInputStream(source).getChannel(); try { FileChannel targetChannel = new FileOutputStream(target).getChannel(); try { targetChannel.transferFrom(sourceChannel, 0, sourceChannel.size()); out = true; } finally { targetChannel.close(); } } finally { sourceChannel.close(); } } catch (IOException e) { out = false; } return out; }

public static void copyFile(File file, String pathExport) throws IOException { File out = new File(pathExport); FileChannel sourceChannel = new FileInputStream(file).getChannel(); FileChannel destinationChannel = new FileOutputStream(out).getChannel(); sourceChannel.transferTo(0, sourceChannel.size(), destinationChannel); sourceChannel.close(); destinationChannel.close(); }

public void testGetOldVersion() throws ServiceException, IOException, SAXException, ParserConfigurationException { JCRNodeSource emptySource = loadTestSource(); for (int i = 0; i < 3; i++) { OutputStream sourceOut = emptySource.getOutputStream(); InputStream contentIn = getClass().getResourceAsStream(CONTENT_FILE); try { IOUtils.copy(contentIn, sourceOut); sourceOut.flush(); } finally { sourceOut.close(); contentIn.close(); } } String testSourceUri = BASE_URL + "users/lars.trieloff?revision=1.1"; JCRNodeSource secondSource = (JCRNodeSource) resolveSource(testSourceUri); System.out.println("Read again at:" + secondSource.getSourceRevision()); InputStream expected = emptySource.getInputStream(); InputStream actual = secondSource.getInputStream(); assertTrue(isXmlEqual(expected, actual)); }

@Override public User createUser(User bean) throws SitoolsException { checkUser(); if (!User.isValid(bean)) { throw new SitoolsException("CREATE_USER_MALFORMED"); } Connection cx = null; try { cx = ds.getConnection(); cx.setAutoCommit(false); PreparedStatement st = cx.prepareStatement(jdbcStoreResource.CREATE_USER); int i = 1; st.setString(i++, bean.getIdentifier()); st.setString(i++, bean.getFirstName()); st.setString(i++, bean.getLastName()); st.setString(i++, bean.getSecret()); st.setString(i++, bean.getEmail()); st.executeUpdate(); st.close(); createProperties(bean, cx); if (!cx.getAutoCommit()) { cx.commit(); } } catch (SQLException e) { try { cx.rollback(); } catch (SQLException e1) { e1.printStackTrace(); throw new SitoolsException("CREATE_USER ROLLBACK" + e1.getMessage(), e1); } e.printStackTrace(); throw new SitoolsException("CREATE_USER " + e.getMessage(), e); } finally { closeConnection(cx); } return getUserById(bean.getIdentifier()); }

private static String getDocumentAt(String urlString) { StringBuffer html_text = new StringBuffer(); try { URL url = new URL(urlString); URLConnection conn = url.openConnection(); BufferedReader reader = new BufferedReader(new InputStreamReader(conn.getInputStream())); String line = null; while ((line = reader.readLine()) != null) html_text.append(line + "\n"); reader.close(); } catch (MalformedURLException e) { System.out.println("����URL: " + urlString); } catch (IOException e) { e.printStackTrace(); } return html_text.toString(); }

public boolean load() { if (getFilename() != null && getFilename().length() > 0) { try { File file = new File(PreferencesManager.loadDirectoryLocation("macros") + File.separator + getFilename()); URL url = file.toURL(); InputStreamReader isr = new InputStreamReader(url.openStream()); BufferedReader br = new BufferedReader(isr); String line = br.readLine(); String macro_text = ""; while (line != null) { macro_text = macro_text.concat(line); line = br.readLine(); if (line != null) { macro_text = macro_text.concat(System.getProperty("line.separator")); } } code = macro_text; } catch (Exception e) { System.err.println("Exception at StoredMacro.load(): " + e.toString()); return false; } } return true; }

public byte[] getCoded(String name, String pass) { byte[] digest = null; if (pass != null && 0 < pass.length()) { try { MessageDigest md = MessageDigest.getInstance("SHA-1"); md.update(name.getBytes()); md.update(pass.getBytes()); digest = md.digest(); } catch (Exception e) { e.printStackTrace(); digest = null; } } return digest; }

private Metadata readMetadataIndexFileFromNetwork(String mediaMetadataURI) throws IOException { Metadata tempMetadata = new Metadata(); URL url = new URL(mediaMetadataURI); BufferedReader input = new BufferedReader(new InputStreamReader(url.openStream())); String tempLine = null; while ((tempLine = input.readLine()) != null) { Property tempProperty = PropertyList.splitStringIntoKeyAndValue(tempLine); if (tempProperty != null) { tempMetadata.addIfNotNull(tempProperty.getKey(), tempProperty.getValue()); } } input.close(); return tempMetadata; }

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.B64InputStream(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 void writeBack(File destinationFile, boolean makeCopy) throws IOException { if (makeCopy) { FileChannel sourceChannel = new java.io.FileInputStream(getFile()).getChannel(); FileChannel destinationChannel = new java.io.FileOutputStream(destinationFile).getChannel(); sourceChannel.transferTo(0, sourceChannel.size(), destinationChannel); sourceChannel.close(); destinationChannel.close(); } else { getFile().renameTo(destinationFile); } if (getExifTime() != null && getOriginalTime() != null && !getExifTime().equals(getOriginalTime())) { String adjustArgument = "-ts" + m_dfJhead.format(getExifTime()); ProcessBuilder pb = new ProcessBuilder(m_tm.getJheadCommand(), adjustArgument, destinationFile.getAbsolutePath()); pb.directory(destinationFile.getParentFile()); System.out.println(pb.command().get(0) + " " + pb.command().get(1) + " " + pb.command().get(2)); final Process p = pb.start(); try { p.waitFor(); } catch (InterruptedException e) { e.printStackTrace(); } } }

public static String getEncryptedPwd(String password) throws NoSuchAlgorithmException, UnsupportedEncodingException { byte[] pwd = null; SecureRandom random = new SecureRandom(); byte[] salt = new byte[SALT_LENGTH]; random.nextBytes(salt); MessageDigest md = null; md = MessageDigest.getInstance("MD5"); md.update(salt); md.update(password.getBytes("UTF-8")); byte[] digest = md.digest(); pwd = new byte[digest.length + SALT_LENGTH]; System.arraycopy(salt, 0, pwd, 0, SALT_LENGTH); System.arraycopy(digest, 0, pwd, SALT_LENGTH, digest.length); return byteToHexString(pwd); }

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; }

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(getClass().getResource("/es/unizar/cps/tecnoDiscap/data/icons/view_sidetreeOK.png"))); gui.getAudio().reproduceAudio(imagen); } catch (IOException ex) { ex.printStackTrace(); } } else { } }

public String getText() throws IOException { InputStreamReader r = new InputStreamReader(getInputStream(), encoding); StringWriter w = new StringWriter(256 * 128); try { IOUtils.copy(r, w); } finally { IOUtils.closeQuietly(w); IOUtils.closeQuietly(r); } return w.toString(); }

public void GetList() throws Exception { Authenticator.setDefault(new MyAuth(this._user, this._pwd)); URL url = new URL(MyFanfou.PublicTimeLine); InputStream ins = url.openConnection().getInputStream(); BufferedReader reader = new BufferedReader(new InputStreamReader(ins)); String json = ""; String line; while ((line = reader.readLine()) != null) json += line; JSONArray array = new JSONArray(json); for (int i = 0; i < array.length(); i++) { JSONObject object = array.getJSONObject(i); String users = object.getString("user"); JSONObject user = new JSONObject(users); System.out.println(object.getString("id") + ":" + user.getString("birthday")); } }

private void backupFile(ZipOutputStream out, String base, String fn) throws IOException { String f = FileUtils.getAbsolutePath(fn); base = FileUtils.getAbsolutePath(base); if (!f.startsWith(base)) { Message.throwInternalError(f + " does not start with " + base); } f = f.substring(base.length()); f = correctFileName(f); out.putNextEntry(new ZipEntry(f)); InputStream in = FileUtils.openFileInputStream(fn); IOUtils.copyAndCloseInput(in, out); out.closeEntry(); }

public void compressImage(InputStream input, OutputStream output, DjatokaEncodeParam params) throws DjatokaException { if (params == null) params = new DjatokaEncodeParam(); File inputFile = null; try { inputFile = File.createTempFile("tmp", ".tif"); IOUtils.copyStream(input, new FileOutputStream(inputFile)); if (params.getLevels() == 0) { ImageRecord dim = ImageRecordUtils.getImageDimensions(inputFile.getAbsolutePath()); params.setLevels(ImageProcessingUtils.getLevelCount(dim.getWidth(), dim.getHeight())); dim = null; } } catch (IOException e1) { logger.error("Unexpected file format; expecting uncompressed TIFF", e1); throw new DjatokaException("Unexpected file format; expecting uncompressed TIFF"); } String out = STDOUT; File winOut = null; if (isWindows) { try { winOut = File.createTempFile("pipe_", ".jp2"); } catch (IOException e) { logger.error(e, e); throw new DjatokaException(e); } out = winOut.getAbsolutePath(); } String command = getKduCompressCommand(inputFile.getAbsolutePath(), out, params); logger.debug("compressCommand: " + command); Runtime rt = Runtime.getRuntime(); try { final Process process = rt.exec(command, envParams, new File(env)); if (out.equals(STDOUT)) { IOUtils.copyStream(process.getInputStream(), output); } else if (isWindows) { FileInputStream fis = new FileInputStream(out); IOUtils.copyStream(fis, output); fis.close(); } process.waitFor(); if (process != null) { String errorCheck = null; try { errorCheck = new String(IOUtils.getByteArray(process.getErrorStream())); } catch (Exception e1) { logger.error(e1, e1); } process.getInputStream().close(); process.getOutputStream().close(); process.getErrorStream().close(); process.destroy(); if (errorCheck != null) throw new DjatokaException(errorCheck); } } catch (IOException e) { logger.error(e, e); throw new DjatokaException(e); } catch (InterruptedException e) { logger.error(e, e); throw new DjatokaException(e); } if (inputFile != null) inputFile.delete(); if (winOut != null) winOut.delete(); }

private void invokeTest(String queryfile, String target) { try { String query = IOUtils.toString(XPathMarkBenchmarkTest.class.getResourceAsStream(queryfile)).trim(); String args = EXEC_CMD + " \"" + query + "\" \"" + target + '"'; System.out.println("Invoke command: \n " + args); Process proc = Runtime.getRuntime().exec(args, null, benchmarkDir); InputStream is = proc.getInputStream(); File outFile = new File(outDir, queryfile + ".result"); IOUtils.copy(is, new FileOutputStream(outFile)); is.close(); int ret = proc.waitFor(); if (ret != 0) { System.out.println("process exited with value : " + ret); } } catch (IOException ioe) { throw new IllegalStateException(ioe); } catch (InterruptedException irre) { throw new IllegalStateException(irre); } }

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!"); }

void shutdown(final boolean unexpected) { if (unexpected) { log.warn("S H U T D O W N --- received unexpected shutdown request."); } else { log.info("S H U T D O W N --- start regular shutdown."); } if (this.uncaughtException != null) { log.warn("Shutdown probably caused by the following Exception.", this.uncaughtException); } log.error("check if we need the controler listener infrastructure"); if (this.dumpDataAtEnd) { new PopulationWriter(this.population, this.network).write(this.controlerIO.getOutputFilename(FILENAME_POPULATION)); new NetworkWriter(this.network).write(this.controlerIO.getOutputFilename(FILENAME_NETWORK)); new ConfigWriter(this.config).write(this.controlerIO.getOutputFilename(FILENAME_CONFIG)); if (!unexpected && this.getConfig().vspExperimental().isWritingOutputEvents()) { File toFile = new File(this.controlerIO.getOutputFilename("output_events.xml.gz")); File fromFile = new File(this.controlerIO.getIterationFilename(this.getLastIteration(), "events.xml.gz")); IOUtils.copyFile(fromFile, toFile); } } if (unexpected) { log.info("S H U T D O W N --- unexpected shutdown request completed."); } else { log.info("S H U T D O W N --- regular shutdown completed."); } try { Runtime.getRuntime().removeShutdownHook(this.shutdownHook); } catch (IllegalStateException e) { log.info("Cannot remove shutdown hook. " + e.getMessage()); } this.shutdownHook = null; this.collectLogMessagesAppender = null; IOUtils.closeOutputDirLogging(); }

private String determineGuardedHtml() { StringBuffer buf = new StringBuffer(); if (m_guardedButtonPresent) { buf.append("\n<span id='" + getHtmlIdPrefix() + PUSH_PAGE_SUFFIX + "' style='display:none'>\n"); String location = m_guardedHtmlLocation != null ? m_guardedHtmlLocation : (String) Config.getProperty(Config.PROP_PRESENTATION_DEFAULT_GUARDED_HTML_LOCATION); String html = (String) c_guardedHtmlCache.get(location); if (html == null) { if (log.isDebugEnabled()) log.debug(this.NAME + ".determineGuardedHtml: Reading the Guarded Html Fragment: " + location); URL url = getUrl(location); if (url != null) { BufferedReader in = null; try { in = new BufferedReader(new InputStreamReader(url.openStream())); StringBuffer buf1 = new StringBuffer(); String line = null; while ((line = in.readLine()) != null) { buf1.append(line); buf1.append('\n'); } html = buf1.toString(); } catch (IOException e) { log.warn(this.NAME + ".determineGuardedHtml: Failed to read the Guarded Html Fragment: " + location, e); } finally { try { if (in != null) in.close(); } catch (IOException ex) { log.warn(this.NAME + ".determineGuardedHtml: Failed to close the Guarded Html Fragment: " + location, ex); } } } else { log.warn("Failed to read the Guarded Html Fragment: " + location); } if (html == null) html = "Transaction in Progress"; c_guardedHtmlCache.put(location, html); } buf.append(html); buf.append("\n</span>\n"); } return buf.toString(); }

private static String sendGetRequest(String endpoint, String requestParameters) throws Exception { String result = null; if (endpoint.startsWith("http://")) { StringBuffer data = new StringBuffer(); String urlStr = prepareUrl(endpoint, requestParameters); URL url = new URL(urlStr); URLConnection conn = url.openConnection(); BufferedReader rd = new BufferedReader(new InputStreamReader(conn.getInputStream())); StringBuffer sb = new StringBuffer(); String line; while ((line = rd.readLine()) != null) { sb.append(line); } rd.close(); result = sb.toString(); } return result; }

public XmldbURI createFile(String newName, InputStream is, Long length, String contentType) throws IOException, PermissionDeniedException, CollectionDoesNotExistException { if (LOG.isDebugEnabled()) LOG.debug("Create '" + newName + "' in '" + xmldbUri + "'"); XmldbURI newNameUri = XmldbURI.create(newName); MimeType mime = MimeTable.getInstance().getContentTypeFor(newName); if (mime == null) { mime = MimeType.BINARY_TYPE; } DBBroker broker = null; Collection collection = null; BufferedInputStream bis = new BufferedInputStream(is); VirtualTempFile vtf = new VirtualTempFile(); BufferedOutputStream bos = new BufferedOutputStream(vtf); IOUtils.copy(bis, bos); bis.close(); bos.close(); vtf.close(); if (mime.isXMLType() && vtf.length() == 0L) { if (LOG.isDebugEnabled()) LOG.debug("Creating dummy XML file for null resource lock '" + newNameUri + "'"); vtf = new VirtualTempFile(); IOUtils.write("<null_resource/>", vtf); vtf.close(); } TransactionManager transact = brokerPool.getTransactionManager(); Txn txn = transact.beginTransaction(); try { broker = brokerPool.get(subject); collection = broker.openCollection(xmldbUri, Lock.WRITE_LOCK); if (collection == null) { LOG.debug("Collection " + xmldbUri + " does not exist"); transact.abort(txn); throw new CollectionDoesNotExistException(xmldbUri + ""); } if (mime.isXMLType()) { if (LOG.isDebugEnabled()) LOG.debug("Inserting XML document '" + mime.getName() + "'"); VirtualTempFileInputSource vtfis = new VirtualTempFileInputSource(vtf); IndexInfo info = collection.validateXMLResource(txn, broker, newNameUri, vtfis); DocumentImpl doc = info.getDocument(); doc.getMetadata().setMimeType(mime.getName()); collection.store(txn, broker, info, vtfis, false); } else { if (LOG.isDebugEnabled()) LOG.debug("Inserting BINARY document '" + mime.getName() + "'"); InputStream fis = vtf.getByteStream(); bis = new BufferedInputStream(fis); DocumentImpl doc = collection.addBinaryResource(txn, broker, newNameUri, bis, mime.getName(), length.longValue()); bis.close(); } transact.commit(txn); if (LOG.isDebugEnabled()) LOG.debug("Document created sucessfully"); } catch (EXistException e) { LOG.error(e); transact.abort(txn); throw new IOException(e); } catch (TriggerException e) { LOG.error(e); transact.abort(txn); throw new IOException(e); } catch (SAXException e) { LOG.error(e); transact.abort(txn); throw new IOException(e); } catch (LockException e) { LOG.error(e); transact.abort(txn); throw new PermissionDeniedException(xmldbUri + ""); } catch (IOException e) { LOG.error(e); transact.abort(txn); throw e; } catch (PermissionDeniedException e) { LOG.error(e); transact.abort(txn); throw e; } finally { if (vtf != null) { vtf.delete(); } if (collection != null) { collection.release(Lock.WRITE_LOCK); } brokerPool.release(broker); if (LOG.isDebugEnabled()) LOG.debug("Finished creation"); } XmldbURI newResource = xmldbUri.append(newName); return newResource; }

public void download(String ftpServer, String user, String password, String fileName, File destination) throws MalformedURLException, IOException { if (ftpServer != null && fileName != null && destination != null) { StringBuffer sb = new StringBuffer("ftp://"); if (user != null && password != null) { sb.append(user); sb.append(':'); sb.append(password); sb.append('@'); } sb.append(ftpServer); sb.append('/'); sb.append(fileName); sb.append(";type=i"); BufferedInputStream bis = null; BufferedOutputStream bos = null; try { URL url = new URL(sb.toString()); URLConnection urlc = url.openConnection(); bis = new BufferedInputStream(urlc.getInputStream()); bos = new BufferedOutputStream(new FileOutputStream(destination)); int i; while ((i = bis.read()) != -1) { bos.write(i); } } finally { if (bis != null) try { bis.close(); } catch (IOException ioe) { ioe.printStackTrace(); } if (bos != null) try { bos.close(); } catch (IOException ioe) { ioe.printStackTrace(); } } } else { System.out.println("Input not available"); } }

public void decryptFile(String encryptedFile, String decryptedFile, String password) throws Exception { CipherInputStream in; OutputStream out; Cipher cipher; SecretKey key; byte[] byteBuffer; cipher = Cipher.getInstance("DES"); key = new SecretKeySpec(password.getBytes(), "DES"); cipher.init(Cipher.DECRYPT_MODE, key); in = new CipherInputStream(new FileInputStream(encryptedFile), cipher); out = new FileOutputStream(decryptedFile); byteBuffer = new byte[1024]; for (int n; (n = in.read(byteBuffer)) != -1; out.write(byteBuffer, 0, n)) ; in.close(); out.close(); }

public static final String enCode(String algorithm, String string) { MessageDigest md; String result = ""; try { md = MessageDigest.getInstance(algorithm); md.update(string.getBytes()); result = binaryToString(md.digest()); } catch (NoSuchAlgorithmException e) { e.printStackTrace(); } return result; }

public static String getSignature(String s) { try { final AsciiEncoder coder = new AsciiEncoder(); final MessageDigest msgDigest = MessageDigest.getInstance("MD5"); msgDigest.update(s.getBytes("UTF-8")); final byte[] digest = msgDigest.digest(); return coder.encode(digest); } catch (NoSuchAlgorithmException e) { e.printStackTrace(); throw new IllegalStateException(); } catch (UnsupportedEncodingException e) { e.printStackTrace(); throw new IllegalStateException(); } }

public static String hash(String plaintext) { if (plaintext == null) { return ""; } MessageDigest md = null; try { md = MessageDigest.getInstance("SHA1"); md.update(plaintext.getBytes("UTF-8")); } catch (Exception e) { } return new String(Base64.encodeBase64(md.digest())); }

public static void copyFile(File file, String pathExport) throws IOException { File out = new File(pathExport); FileChannel sourceChannel = new FileInputStream(file).getChannel(); FileChannel destinationChannel = new FileOutputStream(out).getChannel(); sourceChannel.transferTo(0, sourceChannel.size(), destinationChannel); sourceChannel.close(); destinationChannel.close(); }

public static void ExtraeArchivoJAR(String Archivo, String DirJAR, String DirDestino) { FileInputStream entrada = null; FileOutputStream salida = null; try { File f = new File(DirDestino + separador + Archivo); try { f.createNewFile(); } catch (Exception sad) { sad.printStackTrace(); } InputStream source = OP_Proced.class.getResourceAsStream(DirJAR + "/" + Archivo); BufferedInputStream in = new BufferedInputStream(source); FileOutputStream out = new FileOutputStream(f); int ch; while ((ch = in.read()) != -1) out.write(ch); in.close(); out.close(); } catch (IOException ex) { System.out.println(ex); } finally { if (entrada != null) { try { entrada.close(); } catch (IOException ex) { ex.printStackTrace(); } } if (salida != null) { try { salida.close(); } catch (IOException ex) { ex.printStackTrace(); } } } }

@Test public void testTrainingDefault() throws IOException { File temp = File.createTempFile("fannj_", ".tmp"); temp.deleteOnExit(); IOUtils.copy(this.getClass().getResourceAsStream("xor.data"), new FileOutputStream(temp)); List<Layer> layers = new ArrayList<Layer>(); layers.add(Layer.create(2)); layers.add(Layer.create(3, ActivationFunction.FANN_SIGMOID_SYMMETRIC)); layers.add(Layer.create(1, ActivationFunction.FANN_SIGMOID_SYMMETRIC)); Fann fann = new Fann(layers); Trainer trainer = new Trainer(fann); float desiredError = .001f; float mse = trainer.train(temp.getPath(), 500000, 1000, desiredError); assertTrue("" + mse, mse <= desiredError); }

@Override protected void doPost(HttpServletRequest req, HttpServletResponse resp) throws ServletException, IOException { String uuid = req.getParameterValues(Constants.PARAM_UUID)[0]; String datastream = null; if (req.getRequestURI().contains(Constants.SERVLET_DOWNLOAD_FOXML_PREFIX)) { resp.addHeader("Content-Disposition", "attachment; ContentType = \"text/xml\"; filename=\"" + uuid + "_local_version.foxml\""); } else { datastream = req.getParameterValues(Constants.PARAM_DATASTREAM)[0]; resp.addHeader("Content-Disposition", "attachment; ContentType = \"text/xml\"; filename=\"" + uuid + "_local_version_" + datastream + ".xml\""); } String xmlContent = URLDecoder.decode(req.getParameterValues(Constants.PARAM_CONTENT)[0], "UTF-8"); InputStream is = new ByteArrayInputStream(xmlContent.getBytes("UTF-8")); ServletOutputStream os = resp.getOutputStream(); IOUtils.copyStreams(is, os); os.flush(); }

public void go() throws FBConnectionException, FBErrorException, IOException { clearError(); if (rg == null) { error = true; errorcode = -102; errortext = "No RootGalleryTree was defined"; return; } URL url = new URL(getHost() + getPath()); HttpURLConnection conn = (HttpURLConnection) url.openConnection(); conn.setRequestProperty("X-FB-User", getUser()); conn.setRequestProperty("X-FB-Auth", makeResponse()); conn.setRequestProperty("X-FB-Mode", "GetGals"); conn.connect(); Element fbresponse; try { fbresponse = readXML(conn); } catch (FBConnectionException fbce) { throw fbce; } catch (FBErrorException fbee) { throw fbee; } catch (Exception e) { FBConnectionException fbce = new FBConnectionException("XML parsing failed"); fbce.attachSubException(e); throw fbce; } NodeList gals = fbresponse.getElementsByTagName("Gal"); for (int i = 0; i < gals.getLength(); i++) { Gallery g; Element curelement = (Element) gals.item(i); try { if (DOMUtil.getSimpleElementText(curelement, "Name").startsWith("Tag: ")) { g = new Tag(rg, DOMUtil.getSimpleElementText(curelement, "Name").substring(5), Integer.parseInt(DOMUtil.getSimpleAttributeText(curelement, "id"))); } else { g = rg.createGallery(Integer.parseInt(DOMUtil.getSimpleAttributeText(curelement, "id")), DOMUtil.getSimpleElementText(curelement, "Name")); } } catch (Exception e) { complain("HEY! Gallery " + DOMUtil.getSimpleAttributeText(curelement, "id") + " failed to parse!"); continue; } try { g.setURL(DOMUtil.getSimpleElementText(curelement, "URL")); g.setSecurity(Integer.parseInt(DOMUtil.getSimpleElementText(curelement, "Sec"))); } catch (Exception e) { complain("HEY! Metadata failed on " + (g instanceof Tag ? "tag" : "gallery") + " " + DOMUtil.getSimpleAttributeText(curelement, "id") + "!"); complain(e.toString()); } try { g.setDate(DOMUtil.getSimpleElementText(curelement, "Date")); } catch (Exception e) { } } for (int i = 0; i < gals.getLength(); i++) { int current; Element curelement = (Element) gals.item(i); try { current = Integer.parseInt(DOMUtil.getSimpleAttributeText(curelement, "id")); } catch (Exception e) { complain("HEY! Gallery " + DOMUtil.getSimpleAttributeText(curelement, "id") + " failed to parse!"); continue; } Gallery g = rg.getNode(current); NodeList parents; try { parents = DOMUtil.getFirstElement(curelement, "ParentGals").getElementsByTagName("ParentGal"); } catch (Exception e) { complain("HEY! Parsing failed on gallery " + current + ", so I'm assuming it's unparented!"); continue; } for (int j = 0; j < parents.getLength(); j++) { try { g.addParent(rg.getNode(Integer.parseInt(DOMUtil.getSimpleAttributeText((Element) parents.item(j), "id")))); } catch (Exception e) { complain("HEY! Adding parent to gallery " + current + " failed!"); continue; } } } return; }

public static String md5(String input) throws NoSuchAlgorithmException, UnsupportedEncodingException { StringBuffer result = new StringBuffer(); MessageDigest md = MessageDigest.getInstance("MD5"); md.update(input.getBytes("utf-8")); byte[] digest = md.digest(); for (byte b : digest) { result.append(String.format("%02X ", b & 0xff)); } return result.toString(); }

public CopyAllDataToOtherFolderResponse CopyAllDataToOtherFolder(DPWSContext context, CopyAllDataToOtherFolder CopyAllDataInps) throws DPWSException { CopyAllDataToOtherFolderResponse cpyRp = new CopyAllDataToOtherFolderResponseImpl(); int hany = 0; String errorMsg = null; try { if ((rootDir == null) || (rootDir.length() == (-1))) { errorMsg = LocalStorVerify.ISNT_ROOTFLD; } else { String sourceN = CopyAllDataInps.getSourceName(); String targetN = CopyAllDataInps.getTargetName(); if (LocalStorVerify.isValid(sourceN) && LocalStorVerify.isValid(targetN)) { String srcDir = rootDir + File.separator + sourceN; String trgDir = rootDir + File.separator + targetN; if (LocalStorVerify.isLength(srcDir) && LocalStorVerify.isLength(trgDir)) { for (File fs : new File(srcDir).listFiles()) { File ft = new File(trgDir + '\\' + fs.getName()); FileChannel in = null, out = null; try { in = new FileInputStream(fs).getChannel(); out = new FileOutputStream(ft).getChannel(); long size = in.size(); MappedByteBuffer buf = in.map(FileChannel.MapMode.READ_ONLY, 0, size); out.write(buf); } finally { if (in != null) in.close(); if (out != null) out.close(); hany++; } } } else { errorMsg = LocalStorVerify.FLD_TOOLNG; } } else { errorMsg = LocalStorVerify.ISNT_VALID; } } } catch (Throwable tr) { tr.printStackTrace(); errorMsg = tr.getMessage(); hany = (-1); } if (errorMsg != null) { } cpyRp.setNum(hany); return cpyRp; }

private static void copyFile(File sourceFile, File destFile) { try { 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(); } } } catch (Exception e) { throw new RuntimeException(e); } }

public void covertFile(File file) throws IOException { if (!file.isFile()) { return; } Reader reader = null; OutputStream os = null; File newfile = null; String filename = file.getName(); boolean succeed = false; try { newfile = new File(file.getParentFile(), filename + ".bak"); reader = new InputStreamReader(new FileInputStream(file), fromEncoding); os = new FileOutputStream(newfile); IOUtils.copy(reader, os, toEncoding); } catch (Exception e) { e.printStackTrace(); throw new IOException("Encoding error for file [" + file.getAbsolutePath() + "]"); } finally { if (reader != null) { try { reader.close(); } catch (Exception e) { e.printStackTrace(); } } if (os != null) { try { os.close(); } catch (Exception e) { e.printStackTrace(); } } } try { file.delete(); succeed = newfile.renameTo(file); } catch (Exception e) { throw new IOException("Clear bak error for file [" + file.getAbsolutePath() + "]"); } if (succeed) { System.out.println("Changed encoding for file [" + file.getAbsolutePath() + "]"); } }

public static String encriptaSenha(String string) throws ApplicationException { try { MessageDigest digest = MessageDigest.getInstance("MD5"); digest.update(string.getBytes()); BASE64Encoder encoder = new BASE64Encoder(); return encoder.encode(digest.digest()); } catch (NoSuchAlgorithmException ns) { ns.printStackTrace(); throw new ApplicationException("Erro ao Encriptar Senha"); } }

public static void copyFile(File src, File dest) { try { FileInputStream in = new FileInputStream(src); FileOutputStream out = new FileOutputStream(dest); int c; while ((c = in.read()) != -1) out.write(c); in.close(); out.close(); } catch (IOException ioe) { System.err.println(ioe); } }

public static final void copyFile(File source, File destination) throws IOException { FileChannel sourceChannel = new FileInputStream(source).getChannel(); FileChannel targetChannel = new FileOutputStream(destination).getChannel(); sourceChannel.transferTo(0, sourceChannel.size(), targetChannel); sourceChannel.close(); targetChannel.close(); }

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 String digest(String algorithm, String text) { MessageDigest mDigest = null; try { mDigest = MessageDigest.getInstance(algorithm); mDigest.update(text.getBytes(ENCODING)); } catch (NoSuchAlgorithmException nsae) { _log.error(nsae, nsae); } catch (UnsupportedEncodingException uee) { _log.error(uee, uee); } byte[] raw = mDigest.digest(); BASE64Encoder encoder = new BASE64Encoder(); return encoder.encode(raw); }

private void sortWhats(String[] labels, int[] whats, String simplifyString) { int n = whats.length; boolean swapped; do { swapped = false; for (int i = 0; i < n - 1; i++) { int i0_pos = simplifyString.indexOf(labels[whats[i]]); int i1_pos = simplifyString.indexOf(labels[whats[i + 1]]); if (i0_pos > i1_pos) { int temp = whats[i]; whats[i] = whats[i + 1]; whats[i + 1] = temp; swapped = true; } } } while (swapped); }

protected InputStream makeSignedRequestAndGetJSONData(String url) { try { if (consumer == null) loginOAuth(); } catch (Exception e) { consumer = null; e.printStackTrace(); } DefaultHttpClient httpClient = new DefaultHttpClient(); URI uri; InputStream data = null; try { uri = new URI(url); HttpGet method = new HttpGet(uri); consumer.sign(method); HttpResponse response = httpClient.execute(method); data = response.getEntity().getContent(); } catch (Exception e) { e.printStackTrace(); } return data; }

public void copyFile(String source_file_path, String destination_file_path) { FileWriter fw = null; FileReader fr = null; BufferedReader br = null; BufferedWriter bw = null; File source = null; try { fr = new FileReader(source_file_path); fw = new FileWriter(destination_file_path); br = new BufferedReader(fr); bw = new BufferedWriter(fw); source = new File(source_file_path); int fileLength = (int) source.length(); char charBuff[] = new char[fileLength]; while (br.read(charBuff, 0, fileLength) != -1) bw.write(charBuff, 0, fileLength); } catch (FileNotFoundException fnfe) { System.out.println(source_file_path + " does not exist!"); } catch (IOException ioe) { System.out.println("Error reading/writing files!"); } finally { try { if (br != null) br.close(); if (bw != null) bw.close(); } catch (IOException ioe) { } } }

public void fileCopy(File inFile, File outFile) { try { FileInputStream in = new FileInputStream(inFile); FileOutputStream out = new FileOutputStream(outFile); int c; while ((c = in.read()) != -1) out.write(c); in.close(); out.close(); } catch (IOException e) { System.err.println("Hubo un error de entrada/salida!!!"); } }

@Override public DataUpdateResult<Record> archiveRecord(String authToken, Record record, Filter filter, Field sourceField, InputModel inputmodel) throws DataOperationException { validateUserIsSignedOn(authToken); validateUserHasAdminRights(authToken); DataUpdateResult<Record> recordUpdateResult = new DataUpdateResult<Record>(); if (record != null) { Connection connection = null; boolean archived = false; try { long userId = getSignedOnUser(authToken).getUserId(); connection = DatabaseConnector.getConnection(); connection.setAutoCommit(false); recordUpdateResult.setMessage(messages.server_record_delete_success("")); recordUpdateResult.setSuccessful(true); String sql = "update tms.records set archivedtimestamp = now() where recordid = ?"; PreparedStatement updateRecord = connection.prepareStatement(sql); updateRecord.setLong(1, record.getRecordid()); int recordArchived = 0; recordArchived = updateRecord.executeUpdate(); if (recordArchived > 0) AuditTrailManager.updateAuditTrail(connection, AuditTrailManager.createAuditTrailEvent(record, userId, AuditableEvent.EVENTYPE_DELETE), authToken, getSession()); TopicUpdateServiceImpl.archiveRecordTopics(connection, record.getTopics(), record.getRecordid()); ArrayList<RecordAttribute> recordAttributes = record.getRecordattributes(); if (recordAttributes != null && recordAttributes.size() > 0) { Iterator<RecordAttribute> rItr = recordAttributes.iterator(); while (rItr.hasNext()) { RecordAttribute r = rItr.next(); String rAtSql = "update tms.recordattributes set archivedtimestamp = now() where recordattributeid = ?"; PreparedStatement updateRecordAttribute = connection.prepareStatement(rAtSql); updateRecordAttribute.setLong(1, r.getRecordattributeid()); int recordAttribArchived = 0; recordAttribArchived = updateRecordAttribute.executeUpdate(); if (recordAttribArchived > 0) AuditTrailManager.updateAuditTrail(connection, AuditTrailManager.createAuditTrailEvent(r, userId, AuditableEvent.EVENTYPE_DELETE), authToken, getSession()); } } ArrayList<Term> terms = record.getTerms(); Iterator<Term> termsItr = terms.iterator(); while (termsItr.hasNext()) { Term term = termsItr.next(); TermUpdater.archiveTerm(connection, term, userId, authToken, getSession()); } connection.commit(); archived = true; if (filter != null) RecordIdTracker.refreshRecordIdsInSessionByFilter(this.getThreadLocalRequest().getSession(), connection, true, filter, sourceField, authToken); else RecordIdTracker.refreshRecordIdsInSession(this.getThreadLocalRequest().getSession(), connection, false, authToken); RecordRetrievalServiceImpl retriever = new RecordRetrievalServiceImpl(); RecordIdTracker.refreshRecordIdsInSession(this.getThreadLocalRequest().getSession(), connection, false, authToken); Record updatedRecord = retriever.retrieveRecordByRecordId(initSignedOnUser(authToken), record.getRecordid(), this.getThreadLocalRequest().getSession(), false, inputmodel, authToken); recordUpdateResult.setResult(updatedRecord); } catch (Exception e) { if (!archived && connection != null) { try { connection.rollback(); } catch (SQLException e1) { LogUtility.log(Level.SEVERE, getSession(), messages.log_db_rollback(""), e1, authToken); e1.printStackTrace(); } } recordUpdateResult.setFailed(true); if (archived) { recordUpdateResult.setMessage(messages.server_record_delete_retrieve("")); recordUpdateResult.setException(e); LogUtility.log(Level.SEVERE, getSession(), messages.server_record_delete_retrieve(""), e, authToken); } else { recordUpdateResult.setMessage(messages.server_record_delete_fail("")); recordUpdateResult.setException(new PersistenceException(e)); LogUtility.log(Level.SEVERE, getSession(), messages.server_record_delete_fail(""), e, authToken); } GWT.log(recordUpdateResult.getMessage(), e); } finally { try { if (connection != null) { connection.setAutoCommit(true); connection.close(); } } catch (Exception e) { LogUtility.log(Level.SEVERE, getSession(), messages.log_db_close(""), e, authToken); } } } return recordUpdateResult; }

public static final void newRead() { HTMLDocument html = new HTMLDocument(); html.putProperty("IgnoreCharsetDirective", new Boolean(true)); try { HTMLEditorKit kit = new HTMLEditorKit(); URL url = new URL("http://omega.rtu.lv/en/index.html"); kit.read(new BufferedReader(new InputStreamReader(url.openStream())), html, 0); Reader reader = new FileReader(html.getText(0, html.getLength())); List<String> links = HTMLUtils.extractLinks(reader); } catch (Exception e) { e.printStackTrace(); } }

private void deleteProject(String uid, String home, HttpServletRequest request, HttpServletResponse response) throws Exception { String project = request.getParameter("project"); String line; response.setContentType("text/html"); PrintWriter out = response.getWriter(); htmlHeader(out, "Project Status", ""); try { synchronized (Class.forName("com.sun.gep.SunTCP")) { Vector list = new Vector(); String directory = home; Runtime.getRuntime().exec("/usr/bin/rm -rf " + directory + project); FilePermission perm = new FilePermission(directory + SUNTCP_LIST, "read,write,execute"); File listfile = new File(directory + SUNTCP_LIST); BufferedReader read = new BufferedReader(new FileReader(listfile)); while ((line = read.readLine()) != null) { if (!((new StringTokenizer(line, "\t")).nextToken().equals(project))) { list.addElement(line); } } read.close(); if (list.size() > 0) { PrintWriter write = new PrintWriter(new BufferedWriter(new FileWriter(listfile))); for (int i = 0; i < list.size(); i++) { write.println((String) list.get(i)); } write.close(); } else { listfile.delete(); } out.println("The project was successfully deleted."); } } catch (Exception e) { out.println("Error accessing this project."); } out.println("<center><form><input type=button value=Continue onClick=\"opener.location.reload(); window.close()\"></form></center>"); htmlFooter(out); }

private void createWar() throws IOException, XMLStreamException { String appName = this.fileout.getName(); int i = appName.indexOf("."); if (i != -1) appName = appName.substring(0, i); ZipOutputStream zout = new ZipOutputStream(new FileOutputStream(this.fileout)); { ZipEntry entry = new ZipEntry("WEB-INF/web.xml"); zout.putNextEntry(entry); XMLOutputFactory factory = XMLOutputFactory.newInstance(); XMLStreamWriter w = factory.createXMLStreamWriter(zout, "ASCII"); w.writeStartDocument("ASCII", "1.0"); w.writeStartElement("web-app"); w.writeAttribute("xsi", XSI, "schemaLocation", "http://java.sun.com/xml/ns/javaee http://java.sun.com/xml /ns/javaee/web-app_2_5.xsd"); w.writeAttribute("version", "2.5"); w.writeAttribute("xmlns", J2EE); w.writeAttribute("xmlns:xsi", XSI); w.writeStartElement("description"); w.writeCharacters("Site maintenance for " + appName); w.writeEndElement(); w.writeStartElement("display-name"); w.writeCharacters(appName); w.writeEndElement(); w.writeStartElement("servlet"); w.writeStartElement("servlet-name"); w.writeCharacters("down"); w.writeEndElement(); w.writeStartElement("jsp-file"); w.writeCharacters("/WEB-INF/jsp/down.jsp"); w.writeEndElement(); w.writeEndElement(); w.writeStartElement("servlet-mapping"); w.writeStartElement("servlet-name"); w.writeCharacters("down"); w.writeEndElement(); w.writeStartElement("url-pattern"); w.writeCharacters("/*"); w.writeEndElement(); w.writeEndElement(); w.writeEndElement(); w.writeEndDocument(); w.flush(); zout.closeEntry(); } { ZipEntry entry = new ZipEntry("WEB-INF/jsp/down.jsp"); zout.putNextEntry(entry); PrintWriter w = new PrintWriter(zout); if (this.messageFile != null) { IOUtils.copyTo(new FileReader(this.messageFile), w); } else if (this.messageString != null) { w.print("<html><body>" + this.messageString + "</body></html>"); } else { w.print("<html><body><div style='text-align:center;font-size:500%;'>Oh No !<br/><b>" + appName + "</b><br/>is down for maintenance!</div></body></html>"); } w.flush(); zout.closeEntry(); } zout.finish(); zout.flush(); zout.close(); }

public void upload(String ftpServer, String user, String password, String fileName, File source) throws MalformedURLException, IOException { if (ftpServer != null && fileName != null && source != null) { StringBuffer sb = new StringBuffer("ftp://"); if (user != null && password != null) { sb.append(user); sb.append(':'); sb.append(password); sb.append('@'); } sb.append(ftpServer); sb.append('/'); sb.append(fileName); sb.append(";type=i"); BufferedInputStream bis = null; BufferedOutputStream bos = null; try { URL url = new URL(sb.toString()); URLConnection urlc = url.openConnection(); bos = new BufferedOutputStream(urlc.getOutputStream()); bis = new BufferedInputStream(new FileInputStream(source)); int i; while ((i = bis.read()) != -1) { bos.write(i); } } finally { if (bis != null) try { bis.close(); } catch (IOException ioe) { ioe.printStackTrace(); } if (bos != null) try { bos.close(); } catch (IOException ioe) { ioe.printStackTrace(); } } } else { System.out.println("Input not available."); } }

public String encrypt(String pwd) { MessageDigest md5 = null; try { md5 = MessageDigest.getInstance("MD5"); } catch (NoSuchAlgorithmException e) { e.printStackTrace(); System.out.println("Error"); } try { md5.update(pwd.getBytes("UTF-8")); } catch (UnsupportedEncodingException e) { e.printStackTrace(); JOptionPane.showMessageDialog(null, "That is not a valid encrpytion type"); } byte raw[] = md5.digest(); String empty = ""; String hash = ""; for (byte b : raw) { String tmp = empty + Integer.toHexString(b & 0xff); if (tmp.length() == 1) { tmp = 0 + tmp; } hash += tmp; } return hash; }

@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 main(String[] args) { if (args.length < 2) { System.out.println(" *** DDL (creates) and DML (inserts) script importer from DB ***"); System.out.println(" You must specify name of the file with script importing data"); System.out.println(" Fisrt rows of this file must be:"); System.out.println(" 1) JDBC driver class for your DBMS"); System.out.println(" 2) URL for your database instance"); System.out.println(" 3) user in that database (with sufficient priviliges)"); System.out.println(" 4) password of that user"); System.out.println(" Next rows can have:"); System.out.println(" '}' before table to create,"); System.out.println(" '{' before schema to create tables in,"); System.out.println(" ')' before table to insert into,"); System.out.println(" '(' before schema to insert into tables in."); System.out.println(" '!' before row means that it is a comment."); System.out.println(" If some exception is occured, all script is rolled back."); System.out.println(" 2nd command line argument is name of output file;"); System.out.println(" if its extension is *.sql, its format is standard SQL"); System.out.println(" otherwize format is short one, understanded by SQLScript tool"); System.out.println(" Connection information remains unchanged in the last format"); System.out.println(" but in the first one it takes form 'connect user/password@URL'"); System.out.println(" where URL can be formed with different rools for different DBMSs"); System.out.println(" If file (with short format header) already exists and you specify"); System.out.println(" 3rd command line argument -db, we generate objects in the database"); System.out.println(" (known from the file header; must differ from 1st DB) but not in file"); System.out.println(" Note: when importing to a file of short format, line separators"); System.out.println(" in VARCHARS will be lost; LOBs will be empty for any file"); System.exit(0); } try { String[] info = new String[4]; BufferedReader reader = new BufferedReader(new FileReader(new File(args[0]))); Writer writer = null; Connection outConnection = null; try { for (int i = 0; i < info.length; i++) info[i] = reader.readLine(); try { Class.forName(info[0]); Connection connection = DriverManager.getConnection(info[1], info[2], info[3]); int format = args[1].toLowerCase().endsWith("sql") ? SQL_FORMAT : SHORT_FORMAT; File file = new File(args[1]); if (format == SHORT_FORMAT) { if (file.exists() && args.length > 2 && args[2].equalsIgnoreCase("-db")) { String[] outInfo = new String[info.length]; BufferedReader outReader = new BufferedReader(new FileReader(file)); for (int i = 0; i < outInfo.length; i++) outInfo[i] = reader.readLine(); outReader.close(); if (!(outInfo[1].equals(info[1]) && outInfo[2].equals(info[2]))) { Class.forName(info[0]); outConnection = DriverManager.getConnection(outInfo[1], outInfo[2], outInfo[3]); format = SQL_FORMAT; } } } if (outConnection == null) writer = new BufferedWriter(new FileWriter(file)); SQLImporter script = new SQLImporter(outConnection, connection); script.setFormat(format); if (format == SQL_FORMAT) { writer.write("connect " + info[2] + "/" + info[3] + "@" + script.getDatabaseURL(info[1]) + script.statementTerminator); } else { for (int i = 0; i < info.length; i++) writer.write(info[i] + lineSep); writer.write(lineSep); } try { System.out.println(script.executeScript(reader, writer) + " operations with tables has been generated during import"); } catch (SQLException e4) { reader.close(); if (writer != null) writer.close(); else outConnection.close(); System.out.println(" Script generation error: " + e4); } connection.close(); } catch (Exception e3) { reader.close(); if (writer != null) writer.close(); System.out.println(" Connection error: " + e3); } } catch (IOException e2) { System.out.println("Error in file " + args[0]); } } catch (FileNotFoundException e1) { System.out.println("File " + args[0] + " not found"); } }

public void render(Map map, HttpServletRequest httpServletRequest, HttpServletResponse httpServletResponse) throws Exception { ByteArrayOutputStream baos = new ByteArrayOutputStream(OUTPUT_BYTE_ARRAY_INITIAL_SIZE); File file = (File) map.get("targetFile"); IOUtils.copy(new FileInputStream(file), baos); httpServletResponse.setContentType(getContentType()); httpServletResponse.setContentLength(baos.size()); httpServletResponse.addHeader("Content-disposition", "attachment; filename=" + file.getName()); ServletOutputStream out = httpServletResponse.getOutputStream(); baos.writeTo(out); out.flush(); }

public void readFully(String urlS) throws Exception { URL url = new URL(urlS); URLConnection conn = url.openConnection(); InputStream is = conn.getInputStream(); byte[] data = new byte[10240]; int b = is.read(data); while (b > 0) { size += b; b = is.read(data); } is.close(); }

public static String encrypt(String plaintext) throws Exception { String algorithm = XML.get("security.algorithm"); if (algorithm == null) algorithm = "SHA-1"; MessageDigest md = MessageDigest.getInstance(algorithm); md.update(plaintext.getBytes("UTF-8")); return new BASE64Encoder().encode(md.digest()); }

private String createHash() { String hash = ""; try { final java.util.Calendar c = java.util.Calendar.getInstance(); String day = "" + c.get(java.util.Calendar.DATE); day = (day.length() == 1) ? '0' + day : day; String month = "" + (c.get(java.util.Calendar.MONTH) + 1); month = (month.length() == 1) ? '0' + month : month; final String hashString = getStringProperty("hashkey") + day + "." + month + "." + c.get(java.util.Calendar.YEAR); final MessageDigest md = MessageDigest.getInstance("MD5"); md.update(hashString.getBytes()); final byte digest[] = md.digest(); hash = ""; for (int i = 0; i < digest.length; i++) { final String s = Integer.toHexString(digest[i] & 0xFF); hash += ((s.length() == 1) ? "0" + s : s); } } catch (final NoSuchAlgorithmException e) { bot.getLogger().log(e); } return hash; }

public void login(String UID, String PWD, int CTY) throws Exception { sSideURL = sSideURLCollection[CTY]; sUID = UID; sPWD = PWD; iCTY = CTY; sLoginLabel = getLoginLabel(sSideURL); String sParams = getLoginParams(); CookieHandler.setDefault(new ListCookieHandler()); URL url = new URL(sSideURL + sLoginURL); URLConnection conn = url.openConnection(); setRequestProperties(conn); conn.setDoInput(true); conn.setDoOutput(true); OutputStreamWriter wr = new OutputStreamWriter(conn.getOutputStream()); wr.write(sParams); wr.flush(); BufferedReader rd = new BufferedReader(new InputStreamReader(conn.getInputStream())); StringBuilder sb = new StringBuilder(); String line = rd.readLine(); while (line != null) { sb.append(line + "\n"); line = rd.readLine(); } wr.close(); rd.close(); String sPage = sb.toString(); Pattern p = Pattern.compile(">Dein Penner<"); Matcher matcher = p.matcher(sPage); LogedIn = matcher.find(); }

public static String hashClientPassword(String algorithm, String password, String salt) throws IllegalArgumentException, DruidSafeRuntimeException { if (algorithm == null) { throw new IllegalArgumentException("THE ALGORITHM MUST NOT BE NULL"); } if (password == null) { throw new IllegalArgumentException("THE PASSWORD MUST NOT BE NULL"); } if (salt == null) { salt = ""; } String result = null; try { MessageDigest md = MessageDigest.getInstance(algorithm); md.update(password.getBytes()); md.update(salt.getBytes()); result = SecurityHelper.byteArrayToHexString(md.digest()); } catch (NoSuchAlgorithmException e) { throw new DruidSafeRuntimeException(e); } return result; }

public static String SHA1(String text) throws NoSuchAlgorithmException, UnsupportedEncodingException { MessageDigest md; md = MessageDigest.getInstance("SHA-1"); byte[] sha1hash = new byte[40]; md.update(text.getBytes("iso-8859-1"), 0, text.length()); sha1hash = md.digest(); return convertToHex(sha1hash); }

public void run() { isRunning = true; try { URL url = new URL("http://dcg.ethz.ch/projects/sinalgo/version"); URLConnection con = url.openConnection(); con.setDoOutput(true); con.setDoInput(true); con.connect(); PrintStream ps = new PrintStream(con.getOutputStream()); ps.println("GET index.html HTTP/1.1"); ps.flush(); BufferedReader in = new BufferedReader(new InputStreamReader(con.getInputStream())); String line = in.readLine(); if (line != null) { if (line.equals(Configuration.versionString)) { if (displayIfOK) { Main.info("You are using the most recent version of Sinalgo."); } } else { String msg = "\n" + "+----------------------------------------------------------------------\n" + "| You are currently running Sinalgo " + Configuration.versionString + ".\n" + "| A more recent version of Sinalgo is available (" + line + ")\n" + "+---------------------------------------------------------------------\n" + "| To download the latest version, please visit\n" + "| http://sourceforge.net/projects/sinalgo/\n" + "+---------------------------------------------------------------------\n" + "| You may turn off these version checks through the 'Settings' dialog.\n" + "| Note: Sinalgo automatically tests for updates at most once\n" + "| every 24 hours.\n" + "+---------------------------------------------------------------------\n"; Main.warning(msg); } } } catch (Exception e) { String msg = "\n" + ">----------------------------------------------------------------------\n" + "> Unable to test for updates of Sinalgo. The installed version\n" + "> is " + Configuration.versionString + "\n" + ">---------------------------------------------------------------------\n" + "> To check for more recent versions, please visit\n" + "> http://sourceforge.net/projects/sinalgo/\n" + ">---------------------------------------------------------------------\n" + "> You may turn off these version checks through the 'Settings' dialog.\n" + "| Note: Sinalgo automatically tests for updates at most once\n" + "| every 24 hours.\n" + ">---------------------------------------------------------------------\n"; Main.warning(msg); } finally { isRunning = false; AppConfig.getAppConfig().timeStampOfLastUpdateCheck = System.currentTimeMillis(); } }

private void onDhReply(final SshDhReply msg) throws GeneralSecurityException, IOException { if ((this.keyPair == null) || this.connection.isServer()) throw new SshException("%s: unexpected %s", this.connection.uri, msg.getType()); final BigInteger k; { final DHPublicKeySpec remoteKeySpec = new DHPublicKeySpec(new BigInteger(msg.f), P1, G); final KeyFactory dhKeyFact = KeyFactory.getInstance("DH"); final DHPublicKey remotePubKey = (DHPublicKey) dhKeyFact.generatePublic(remoteKeySpec); final KeyAgreement dhKex = KeyAgreement.getInstance("DH"); dhKex.init(this.keyPair.getPrivate()); dhKex.doPhase(remotePubKey, true); k = new BigInteger(dhKex.generateSecret()); } final MessageDigest md = createMessageDigest(); final byte[] h; { updateByteArray(md, SshVersion.LOCAL.toString().getBytes()); updateByteArray(md, this.connection.getRemoteSshVersion().toString().getBytes()); updateByteArray(md, this.keyExchangeInitLocal.getPayload()); updateByteArray(md, this.keyExchangeInitRemote.getPayload()); updateByteArray(md, msg.hostKey); updateByteArray(md, ((DHPublicKey) this.keyPair.getPublic()).getY().toByteArray()); updateByteArray(md, msg.f); updateBigInt(md, k); h = md.digest(); } if (this.sessionId == null) this.sessionId = h; this.keyExchangeInitLocal = null; this.keyExchangeInitRemote = null; this.h = h; this.k = k; this.connection.send(new SshKeyExchangeNewKeys()); }

public static String encryptPassword(String password) { MessageDigest md = null; try { md = MessageDigest.getInstance("SHA-1"); } catch (NoSuchAlgorithmException e) { LOG.error(e); } try { md.update(password.getBytes("UTF-8")); } catch (UnsupportedEncodingException e) { LOG.error(e); } return (new BASE64Encoder()).encode(md.digest()); }

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(); } }

protected String getPostRequestContent(String urlText, String postParam) throws Exception { URL url = new URL(urlText); HttpURLConnection urlcon = (HttpURLConnection) url.openConnection(); urlcon.setRequestMethod("POST"); urlcon.setUseCaches(false); urlcon.setDoOutput(true); PrintStream ps = new PrintStream(urlcon.getOutputStream()); ps.print(postParam); ps.close(); urlcon.connect(); BufferedReader reader = new BufferedReader(new InputStreamReader(urlcon.getInputStream())); String line = reader.readLine(); reader.close(); urlcon.disconnect(); return line; }

private boolean saveDocumentXml(String repository, String tempRepo) { boolean result = true; try { XPath xpath = XPathFactory.newInstance().newXPath(); String expression = "documents/document"; InputSource insource = new InputSource(new FileInputStream(tempRepo + File.separator + AppConstants.DMS_XML)); NodeList nodeList = (NodeList) xpath.evaluate(expression, insource, XPathConstants.NODESET); for (int i = 0; i < nodeList.getLength(); i++) { Node node = nodeList.item(i); System.out.println(node.getNodeName()); DocumentModel document = new DocumentModel(); NodeList childs = node.getChildNodes(); for (int j = 0; j < childs.getLength(); j++) { Node child = childs.item(j); if (child.getNodeType() == Node.ELEMENT_NODE) { if (child.getNodeName() != null && child.getFirstChild() != null && child.getFirstChild().getNodeValue() != null) { System.out.println(child.getNodeName() + "::" + child.getFirstChild().getNodeValue()); } if (Document.FLD_ID.equals(child.getNodeName())) { if (child.getFirstChild() != null) { String szId = child.getFirstChild().getNodeValue(); if (szId != null && szId.length() > 0) { try { document.setId(new Long(szId)); } catch (Exception e) { e.printStackTrace(); } } } } else if (document.FLD_NAME.equals(child.getNodeName())) { document.setName(child.getFirstChild().getNodeValue()); document.setTitle(document.getName()); document.setDescr(document.getName()); document.setExt(getExtension(document.getName())); } else if (document.FLD_LOCATION.equals(child.getNodeName())) { document.setLocation(child.getFirstChild().getNodeValue()); } else if (document.FLD_OWNER.equals(child.getNodeName())) { Long id = new Long(child.getFirstChild().getNodeValue()); User user = new UserModel(); user.setId(id); user = (User) userService.find(user); if (user != null && user.getId() != null) { document.setOwner(user); } } } } boolean isSave = docService.save(document); if (isSave) { String repo = preference.getRepository(); Calendar calendar = Calendar.getInstance(); StringBuffer sbRepo = new StringBuffer(repo); sbRepo.append(File.separator); StringBuffer sbFolder = new StringBuffer(sdf.format(calendar.getTime())); sbFolder.append(File.separator).append(calendar.get(Calendar.HOUR_OF_DAY)); File fileFolder = new File(sbRepo.append(sbFolder).toString()); if (!fileFolder.exists()) { fileFolder.mkdirs(); } FileChannel fcSource = null, fcDest = null; try { StringBuffer sbFile = new StringBuffer(fileFolder.getAbsolutePath()); StringBuffer fname = new StringBuffer(document.getId().toString()); fname.append(".").append(document.getExt()); sbFile.append(File.separator).append(fname); fcSource = new FileInputStream(tempRepo + File.separator + document.getName()).getChannel(); fcDest = new FileOutputStream(sbFile.toString()).getChannel(); fcDest.transferFrom(fcSource, 0, fcSource.size()); document.setLocation(sbFolder.toString()); document.setSize(fcSource.size()); log.info("Batch upload file " + document.getName() + " into [" + document.getLocation() + "] as " + document.getName() + "." + document.getExt()); folder.setId(DEFAULT_FOLDER); folder = (Folder) folderService.find(folder); if (folder != null && folder.getId() != null) { document.setFolder(folder); } workspace.setId(DEFAULT_WORKSPACE); workspace = (Workspace) workspaceService.find(workspace); if (workspace != null && workspace.getId() != null) { document.setWorkspace(workspace); } user.setId(DEFAULT_USER); user = (User) userService.find(user); if (user != null && user.getId() != null) { document.setCrtby(user.getId()); } document.setCrtdate(new Date()); document = (DocumentModel) docService.resetDuplicateDocName(document); docService.save(document); DocumentIndexer.indexDocument(preference, document); } catch (FileNotFoundException notFoundEx) { log.error("saveFile file not found: " + document.getName(), notFoundEx); } catch (IOException ioEx) { log.error("saveFile IOException: " + document.getName(), ioEx); } finally { try { if (fcSource != null) { fcSource.close(); } if (fcDest != null) { fcDest.close(); } } catch (Exception e) { log.error(e.getMessage(), e); } } } } } catch (Exception e) { result = false; e.printStackTrace(); } return result; }

private String processFileUploadOperation(boolean isH264File) { String fileType = this.uploadFileFileName.substring(this.uploadFileFileName.lastIndexOf('.')); int uniqueHashCode = UUID.randomUUID().toString().hashCode(); if (uniqueHashCode < 0) { uniqueHashCode *= -1; } String randomFileName = uniqueHashCode + fileType; String fileName = (isH264File) ? getproperty("videoDraftPath") : getproperty("videoDraftPathForNonH264") + randomFileName; File targetVideoPath = new File(fileName + randomFileName); System.out.println("Path: " + targetVideoPath.getAbsolutePath()); try { targetVideoPath.createNewFile(); FileChannel outStreamChannel = new FileOutputStream(targetVideoPath).getChannel(); FileChannel inStreamChannel = new FileInputStream(this.uploadFile).getChannel(); inStreamChannel.transferTo(0, inStreamChannel.size(), outStreamChannel); outStreamChannel.close(); inStreamChannel.close(); return randomFileName; } catch (FileNotFoundException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } return null; }

public static void sendPostRequest() { String data = "text=Eschirichia coli"; try { URL url = new URL("http://taxonfinder.ubio.org/analyze?"); URLConnection conn = url.openConnection(); conn.setDoOutput(true); OutputStreamWriter writer = new OutputStreamWriter(conn.getOutputStream()); writer.write(data); writer.flush(); StringBuffer answer = new StringBuffer(); BufferedReader reader = new BufferedReader(new InputStreamReader(conn.getInputStream())); String line; while ((line = reader.readLine()) != null) { answer.append(line); } writer.close(); reader.close(); System.out.println(answer.toString()); } catch (MalformedURLException ex) { ex.printStackTrace(); } catch (IOException ex) { ex.printStackTrace(); } }

public static int UsePassword(String username, String password, String new_password) { try { URL url = new URL("http://eiffel.itba.edu.ar/hci/service/Security.groovy?method=ChangePassword&username=" + username + "&password=" + password + "&new_password=" + new_password); URLConnection urlc = url.openConnection(); urlc.setDoOutput(false); urlc.setAllowUserInteraction(false); BufferedReader br = new BufferedReader(new InputStreamReader(urlc.getInputStream())); String str; StringBuffer sb = new StringBuffer(); while ((str = br.readLine()) != null) { sb.append(str); sb.append("\n"); } br.close(); String response = sb.toString(); if (response == null) { return -1; } DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance(); DocumentBuilder db = dbf.newDocumentBuilder(); InputSource is = new InputSource(); is.setCharacterStream(new StringReader(response)); Document dom = db.parse(is); NodeList nl = dom.getElementsByTagName("response"); String status = ((Element) nl.item(0)).getAttributes().item(0).getTextContent(); if (status.toString().equals("fail")) { return -1; } return 0; } catch (Exception e) { e.printStackTrace(); } return -1; }

public static String contents(URL url) throws IOException { InputStream is = url.openStream(); ByteArrayOutputStream baos = new ByteArrayOutputStream(); byte[] buf = new byte[1024]; while (true) { int len = is.read(buf); if (len < 0) { break; } baos.write(buf, 0, len); } is.close(); String contents = new String(baos.toByteArray(), "iso8859_1"); baos.close(); return contents; }

public boolean openConnection(String url, Properties props) throws SQLException { try { Class.forName(RunConfig.getInstance().getDriverNameJDBC()); if (url == null) url = RunConfig.getInstance().getConnectionUrlJDBC(); connection = DriverManager.getConnection(url, props); if (statementTable == null) statementTable = new Hashtable<String, PreparedStatement>(); if (resultTable == null) resultTable = new Hashtable<String, ResultSet>(); clearStatus(); return true; } catch (Exception e) { setStatus(e); return false; } }

public static final int executeSql(final Connection conn, final String sql, final boolean rollback) throws SQLException { if (null == sql) return 0; Statement stmt = null; try { stmt = conn.createStatement(); final int updated = stmt.executeUpdate(sql); return updated; } catch (final SQLException e) { if (rollback) conn.rollback(); throw e; } finally { closeAll(null, stmt, null); } }

public void setDefaultDomain(final int domainId) { try { connection.setAutoCommit(false); new ProcessEnvelope().executeNull(new ExecuteProcessAbstractImpl(connection, false, false, true, true) { @Override public void executeProcessReturnNull() throws SQLException { psImpl = connImpl.prepareStatement(sqlCommands.getProperty("domain.setDefaultDomainId")); psImpl.setInt(1, domainId); psImpl.executeUpdate(); } }); connection.commit(); cm.updateDefaultDomain(); } catch (SQLException sqle) { log.error(sqle); if (connection != null) { try { connection.rollback(); } catch (SQLException ex) { } } } finally { if (connection != null) { try { connection.setAutoCommit(true); } catch (SQLException ex) { } } } }

public static void run(File targetFolder, URL url) throws UpdateException { try { run(targetFolder, new ZipInputStream(url.openStream())); } catch (Exception e) { if (e instanceof UpdateException) throw (UpdateException) e; else throw new UpdateException(e); } }

public void loginOAuth() throws OAuthMessageSignerException, OAuthExpectationFailedException, OAuthCommunicationException, ClientProtocolException, IOException, IllegalStateException, SAXException, ParserConfigurationException, FactoryConfigurationError, AndroidException { String url = getAuthentificationURL(); HttpGet reqLogin = new HttpGet(url); consumer = new CommonsHttpOAuthConsumer(getConsumerKey(), getConsumerSecret()); consumer.sign(reqLogin); HttpClient httpClient = new DefaultHttpClient(); HttpResponse resLogin = httpClient.execute(reqLogin); if (resLogin.getEntity() == null) { throw new AuthRemoteException(); } Document document = DocumentBuilderFactory.newInstance().newDocumentBuilder().parse(resLogin.getEntity().getContent()); Element eOAuthToken = (Element) document.getElementsByTagName("oauth_token").item(0); if (eOAuthToken == null) { throw new AuthRemoteException(); } Node e = eOAuthToken.getFirstChild(); String sOAuthToken = e.getNodeValue(); System.out.println("token: " + sOAuthToken); Element eOAuthTokenSecret = (Element) document.getElementsByTagName("oauth_token_secret").item(0); if (eOAuthTokenSecret == null) { throw new AuthRemoteException(); } e = eOAuthTokenSecret.getFirstChild(); String sOAuthTokenSecret = e.getNodeValue(); System.out.println("Secret: " + sOAuthTokenSecret); consumer.setTokenWithSecret(sOAuthToken, sOAuthTokenSecret); }

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(); } }

public static boolean cpy(File a, File b) { try { FileInputStream astream = null; FileOutputStream bstream = null; try { astream = new FileInputStream(a); bstream = new FileOutputStream(b); long flength = a.length(); int bufsize = (int) Math.min(flength, 1024); byte buf[] = new byte[bufsize]; long n = 0; while (n < flength) { int naread = astream.read(buf); bstream.write(buf, 0, naread); n += naread; } } finally { if (astream != null) astream.close(); if (bstream != null) bstream.close(); } } catch (IOException e) { e.printStackTrace(); return false; } return true; }

@Override public void send() { BufferedReader in = null; StringBuffer result = new StringBuffer(); try { URL url = new URL(getUrl()); in = new BufferedReader(new InputStreamReader(url.openStream())); String str; while ((str = in.readLine()) != null) { result.append(str); } } catch (ConnectException ce) { logger.error("MockupExecutableCommand excute fail: " + ce.getMessage()); } catch (Exception e) { logger.error("MockupExecutableCommand excute fail: " + e.getMessage()); } finally { if (in != null) { try { in.close(); } catch (IOException e) { logger.error("BufferedReader could not be closed", e); } } } }

private boolean performModuleInstallation(Model m) { String seldir = directoryHandler.getSelectedDirectory(); if (seldir == null) { MessageBox box = new MessageBox(shell, SWT.ICON_WARNING | SWT.OK); box.setText("Cannot install"); box.setMessage("A target directory must be selected."); box.open(); return false; } String sjar = pathText.getText(); File fjar = new File(sjar); if (!fjar.exists()) { MessageBox box = new MessageBox(shell, SWT.ICON_WARNING | SWT.OK); box.setText("Cannot install"); box.setMessage("A non-existing jar file has been selected."); box.open(); return false; } int count = 0; try { URLClassLoader loader = new URLClassLoader(new URL[] { fjar.toURI().toURL() }); JarInputStream jis = new JarInputStream(new FileInputStream(fjar)); JarEntry entry = jis.getNextJarEntry(); while (entry != null) { String name = entry.getName(); if (name.endsWith(".class")) { name = name.substring(0, name.length() - 6); name = name.replace('/', '.'); Class<?> cls = loader.loadClass(name); if (IAlgorithm.class.isAssignableFrom(cls) && !cls.isInterface() && (cls.getModifiers() & Modifier.ABSTRACT) == 0) { if (!testAlgorithm(cls, m)) return false; count++; } } entry = jis.getNextJarEntry(); } } catch (Exception e1) { Application.logexcept("Could not load classes from jar file.", e1); return false; } if (count == 0) { MessageBox box = new MessageBox(shell, SWT.ICON_WARNING | SWT.OK); box.setText("Cannot install"); box.setMessage("There don't seem to be any algorithms in the specified module."); box.open(); return false; } try { FileChannel ic = new FileInputStream(sjar).getChannel(); FileChannel oc = new FileOutputStream(seldir + File.separator + fjar.getName()).getChannel(); ic.transferTo(0, ic.size(), oc); ic.close(); oc.close(); } catch (Exception e) { Application.logexcept("Could not install module", e); return false; } result = new Object(); return true; }

private Datastream addManagedDatastreamVersion(Entry entry) throws StreamIOException, ObjectIntegrityException { Datastream ds = new DatastreamManagedContent(); setDSCommonProperties(ds, entry); ds.DSLocationType = "INTERNAL_ID"; ds.DSMIME = getDSMimeType(entry); IRI contentLocation = entry.getContentSrc(); if (contentLocation != null) { if (m_obj.isNew()) { ValidationUtility.validateURL(contentLocation.toString(), ds.DSControlGrp); } if (m_format.equals(ATOM_ZIP1_1)) { if (!contentLocation.isAbsolute() && !contentLocation.isPathAbsolute()) { File f = getContentSrcAsFile(contentLocation); contentLocation = new IRI(DatastreamManagedContent.TEMP_SCHEME + f.getAbsolutePath()); } } ds.DSLocation = contentLocation.toString(); ds.DSLocation = (DOTranslationUtility.normalizeDSLocationURLs(m_obj.getPid(), ds, m_transContext)).DSLocation; return ds; } try { File temp = File.createTempFile("binary-datastream", null); OutputStream out = new FileOutputStream(temp); if (MimeTypeHelper.isText(ds.DSMIME) || MimeTypeHelper.isXml(ds.DSMIME)) { IOUtils.copy(new StringReader(entry.getContent()), out, m_encoding); } else { IOUtils.copy(entry.getContentStream(), out); } ds.DSLocation = DatastreamManagedContent.TEMP_SCHEME + temp.getAbsolutePath(); } catch (IOException e) { throw new StreamIOException(e.getMessage(), e); } return ds; }

public static HttpURLConnection create(URL url, String id, String action, HTTPRequestInfo info) throws IOException { HttpURLConnection connection = (HttpURLConnection) url.openConnection(); connection.setRequestMethod("POST"); if (id != null) { connection.setRequestProperty("id", id); } connection.setRequestProperty("action", action); connection.setUseCaches(false); if (info.getProxyUser() != null && info.getProxyPassword() != null) { String pwd = info.getProxyUser() + ":" + info.getProxyPassword(); String encoded = new String(Base64.encodeBase64(pwd.getBytes())); connection.setRequestProperty("Proxy-Authorization", "Basic " + encoded); } return connection; }

public InputStream getResourceAsStream(String name) { if (debug >= 2) log("getResourceAsStream(" + name + ")"); InputStream stream = null; stream = findLoadedResource(name); if (stream != null) { if (debug >= 2) log(" --> Returning stream from cache"); return (stream); } if (delegate) { if (debug >= 3) log(" Delegating to parent classloader"); ClassLoader loader = parent; if (loader == null) loader = system; stream = loader.getResourceAsStream(name); if (stream != null) { if (debug >= 2) log(" --> Returning stream from parent"); return (stream); } } if (debug >= 3) log(" Searching local repositories"); URL url = findResource(name); if (url != null) { if (debug >= 2) log(" --> Returning stream from local"); try { return (url.openStream()); } catch (IOException e) { log("url.openStream(" + url.toString() + ")", e); return (null); } } if (!delegate) { if (debug >= 3) log(" Delegating to parent classloader"); ClassLoader loader = parent; if (loader == null) loader = system; stream = loader.getResourceAsStream(name); if (stream != null) { if (debug >= 2) log(" --> Returning stream from parent"); return (stream); } } if (debug >= 2) log(" --> Resource not found, returning null"); return (null); }

private String read(URL url) throws IOException { BufferedReader in = null; try { in = new BufferedReader(new InputStreamReader(url.openStream())); StringBuffer text = new StringBuffer(); String line; while ((line = in.readLine()) != null) { text.append(line); } return text.toString(); } finally { in.close(); } }

public static String hashMD5(String baseString) { MessageDigest digest = null; StringBuffer hexString = new StringBuffer(); try { digest = java.security.MessageDigest.getInstance("MD5"); digest.update(baseString.getBytes()); byte[] hash = digest.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 ex) { Logger.getLogger(Password.class.getName()).log(Level.SEVERE, null, ex); } return hexString.toString(); }

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(); } }

private File prepareFileForUpload(File source, String s3key) throws IOException { File tmp = File.createTempFile("dirsync", ".tmp"); tmp.deleteOnExit(); InputStream in = null; OutputStream out = null; try { in = new FileInputStream(source); out = new DeflaterOutputStream(new CryptOutputStream(new FileOutputStream(tmp), cipher, getDataEncryptionKey())); IOUtils.copy(in, out); in.close(); out.close(); return tmp; } finally { IOUtils.closeQuietly(in); IOUtils.closeQuietly(out); } }

public static boolean writeFile(HttpServletResponse resp, File reqFile) { boolean retVal = false; InputStream in = null; try { in = new BufferedInputStream(new FileInputStream(reqFile)); IOUtils.copy(in, resp.getOutputStream()); logger.debug("File successful written to servlet response: " + reqFile.getAbsolutePath()); } catch (FileNotFoundException e) { logger.error("Resource not found: " + reqFile.getAbsolutePath()); } catch (IOException e) { logger.error(String.format("Error while rendering [%s]: %s", reqFile.getAbsolutePath(), e.getMessage()), e); } finally { IOUtils.closeQuietly(in); } return retVal; }

public static void sendPostRequest() { String data = "text=Eschirichia coli"; try { URL url = new URL("http://taxonfinder.ubio.org/analyze?"); URLConnection conn = url.openConnection(); conn.setDoOutput(true); OutputStreamWriter writer = new OutputStreamWriter(conn.getOutputStream()); writer.write(data); writer.flush(); StringBuffer answer = new StringBuffer(); BufferedReader reader = new BufferedReader(new InputStreamReader(conn.getInputStream())); String line; while ((line = reader.readLine()) != null) { answer.append(line); } writer.close(); reader.close(); System.out.println(answer.toString()); } catch (MalformedURLException ex) { ex.printStackTrace(); } catch (IOException ex) { ex.printStackTrace(); } }

protected BufferedReader getDataReader() { BufferedReader in = null; PrintWriter out = null; try { String line; URL url = new URL(this.catalog.getCatalogURL()); Debug.output("Catalog URL:" + url.toString()); in = new BufferedReader(new InputStreamReader(url.openStream())); File dir = (File) SessionHandler.getServletContext().getAttribute("javax.servlet.context.tempdir"); File temp = new File(dir, TEMP); Debug.output("Temp file:" + temp.toString()); out = new PrintWriter(new BufferedWriter(new FileWriter(temp))); while ((line = in.readLine()) != null) { out.println(line); } Debug.output("Temp file size:" + temp.length()); return new BufferedReader(new FileReader(temp)); } catch (IOException e) { throw new SeismoException(e); } finally { Util.close(in); Util.close(out); } }

public static GCalendar getNewestCalendar(Calendar startDate) throws IOException { GCalendar hoge = null; try { HttpClient httpclient = new DefaultHttpClient(); HttpClient http = new DefaultHttpClient(); HttpGet method = new HttpGet("http://localhost:8080/GoogleCalendar/select"); HttpResponse response = http.execute(method); String jsonstr = response.getEntity().toString(); System.out.println("jsonstr = " + jsonstr); hoge = JSON.decode(jsonstr, GCalendar.class); } catch (Exception ex) { ex.printStackTrace(); } return hoge; }

public static void copyFile(File source, File target) throws Exception { if (source == null || target == null) { throw new IllegalArgumentException("The arguments may not be null."); } try { FileChannel srcChannel = new FileInputStream(source).getChannel(); FileChannel dtnChannel = new FileOutputStream(target).getChannel(); srcChannel.transferTo(0, srcChannel.size(), dtnChannel); srcChannel.close(); dtnChannel.close(); } catch (Exception e) { String message = "Unable to copy file '" + source.getName() + "' to '" + target.getName() + "'."; logger.error(message, e); throw new Exception(message, e); } }

public static void saveDigraph(mainFrame parentFrame, DigraphView digraphView, File tobeSaved) { DigraphFile digraphFile = new DigraphFile(); DigraphTextFile digraphTextFile = new DigraphTextFile(); try { if (!DigraphFile.DIGRAPH_FILE_EXTENSION.equals(getExtension(tobeSaved))) { tobeSaved = new File(tobeSaved.getPath() + "." + DigraphFile.DIGRAPH_FILE_EXTENSION); } File dtdFile = new File(tobeSaved.getParent() + "/" + DigraphFile.DTD_FILE); if (!dtdFile.exists()) { File baseDigraphDtdFile = parentFrame.getDigraphDtdFile(); if (baseDigraphDtdFile != null && baseDigraphDtdFile.exists()) { try { BufferedOutputStream bos = new BufferedOutputStream(new FileOutputStream(dtdFile)); BufferedInputStream bis = new BufferedInputStream(new FileInputStream(baseDigraphDtdFile)); while (bis.available() > 1) { bos.write(bis.read()); } bis.close(); bos.close(); } catch (IOException ex) { System.out.println("Unable to Write Digraph DTD File: " + ex.getMessage()); } } else { System.out.println("Unable to Find Base Digraph DTD File: "); } } Digraph digraph = digraphView.getDigraph(); digraphFile.saveDigraph(tobeSaved, digraph); String fileName = tobeSaved.getName(); int extensionIndex = fileName.lastIndexOf("."); if (extensionIndex > 0) { fileName = fileName.substring(0, extensionIndex + 1) + "txt"; } else { fileName = fileName + ".txt"; } File textFile = new File(tobeSaved.getParent() + "/" + fileName); digraphTextFile.saveDigraph(textFile, digraph); digraphView.setDigraphDirty(false); parentFrame.setFilePath(tobeSaved.getPath()); parentFrame.setSavedOnce(true); } catch (DigraphFileException exep) { JOptionPane.showMessageDialog(parentFrame, "Error Saving File:\n" + exep.getMessage(), "Save Error", JOptionPane.ERROR_MESSAGE); } catch (DigraphException exep) { JOptionPane.showMessageDialog(parentFrame, "Error Retrieving Digraph from View:\n" + exep.getMessage(), "Save Error", JOptionPane.ERROR_MESSAGE); } }

private JButton getButtonImagen() { if (buttonImagen == null) { buttonImagen = new JButton(); buttonImagen.setText("Cargar Imagen"); buttonImagen.setIcon(new ImageIcon(getClass().getResource("/data/icons/view_sidetree.png"))); buttonImagen.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(java.awt.event.ActionEvent e) { JFileChooser fc = new JFileChooser(); fc.addChoosableFileFilter(new ImageFilter()); fc.setFileView(new ImageFileView()); fc.setAccessory(new ImagePreview(fc)); int returnVal = fc.showDialog(Resorces.this, "Seleccione una imagen"); if (returnVal == JFileChooser.APPROVE_OPTION) { File file = fc.getSelectedFile(); String rutaGlobal = System.getProperty("user.dir") + file.separator + "data" + file.separator + "imagenes" + file.separator + file.getName(); String rutaRelativa = "data" + file.separator + "imagenes" + file.separator + 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(); } catch (IOException ex) { ex.printStackTrace(); } imagen.setImagenURL(rutaRelativa); System.out.println(rutaGlobal + " " + rutaRelativa); buttonImagen.setIcon(new ImageIcon(getClass().getResource("/data/icons/view_sidetreeOK.png"))); labelImagenPreview.setIcon(gui.procesadorDatos.escalaImageIcon(imagen.getImagenURL())); } else { } } }); } return buttonImagen; }

public String get(String question) { try { System.out.println(url + question); URL urlonlineserver = new URL(url + question); BufferedReader in = new BufferedReader(new InputStreamReader(urlonlineserver.openStream())); String inputLine; String returnstring = ""; while ((inputLine = in.readLine()) != null) returnstring += inputLine; in.close(); return returnstring; } catch (IOException e) { return ""; } }

public static String loadWebsiteHtmlCode(String url, String useragent) { HttpClient httpClient = new DefaultHttpClient(); HttpGet getMethod = new HttpGet(url); String htmlCode = ""; if (useragent != null) { getMethod.setHeader("user-agent", useragent); } try { HttpResponse resp = httpClient.execute(getMethod); int statusCode = resp.getStatusLine().getStatusCode(); if (statusCode != HttpStatus.SC_OK) { logger.debug("Method failed!" + statusCode); } htmlCode = EntityUtils.toString(resp.getEntity()); } catch (Exception e) { logger.debug("Fatal protocol violation: " + e.getMessage()); logger.trace(e); } return htmlCode; }

private void bubbleSort(int values[]) { PerfMonTimer timerOuter = PerfMonTimer.start("SortingTest.bubbleSort"); try { int len = values.length - 1; for (int i = 0; i < len; i++) { for (int j = 0; j < len - i; j++) { if (values[j] > values[j + 1]) { int tmp = values[j]; values[j] = values[j + 1]; values[j + 1] = tmp; } } } } finally { PerfMonTimer.stop(timerOuter); } }

public int NthLowestSkill(int n) { int[] skillIds = new int[] { 0, 1, 2, 3 }; for (int j = 0; j < 3; j++) { for (int i = 0; i < 3 - j; i++) { if (Skills()[skillIds[i]] > Skills()[skillIds[i + 1]]) { int temp = skillIds[i]; skillIds[i] = skillIds[i + 1]; skillIds[i + 1] = temp; } } } return skillIds[n - 1]; }

private void serializeWithClass(Class theClass, int count, String comment) { for (int c = 0; c < 10; c++) { if (c == 9) { beginAction(1, "persistence write/read", count, comment); } String tempFile = ".tmp.archive"; SerializeClassInterface theInstance = null; try { theInstance = (SerializeClassInterface) theClass.newInstance(); } catch (Exception e) { e.printStackTrace(); } if (theInstance == null) { System.err.println("error: Couldn't initialize class to " + "be serialized!"); return; } reset(); for (int i = 0; i < count; i++) { try { FileOutputStream fout = new FileOutputStream(tempFile); BufferedOutputStream bout = new BufferedOutputStream(fout); ObjectOutputStream oout = new ObjectOutputStream(bout); oout.writeObject(theInstance); oout.flush(); oout.close(); } catch (IOException ioe) { System.err.println("serializing: " + tempFile + ":" + ioe.toString()); } try { FileInputStream fin = new FileInputStream(tempFile); BufferedInputStream bin = new BufferedInputStream(fin); ObjectInputStream oin = new ObjectInputStream(bin); theInstance = (SerializeClassInterface) oin.readObject(); oin.close(); } catch (Exception e) { System.err.println("deserializing: " + tempFile + ":" + e.toString()); break; } proceed(); } reset(); if (c == 9) { endAction(); } } }

private void processData(InputStream raw) { String fileName = remoteName; if (localName != null) { fileName = localName; } try { FileOutputStream fos = new FileOutputStream(new File(fileName), true); IOUtils.copy(raw, fos); LOG.info("ok"); } catch (IOException e) { LOG.error("error writing file", e); } }

public static InputStream call(String serviceUrl, Map parameters) throws IOException, RestException { StringBuffer urlString = new StringBuffer(serviceUrl); String query = RestClient.buildQueryString(parameters); HttpURLConnection conn; if ((urlString.length() + query.length() + 1) > MAX_URI_LENGTH_FOR_GET) { URL url = new URL(urlString.toString()); conn = (HttpURLConnection) url.openConnection(); conn.setRequestProperty("User-Agent", USER_AGENT_STRING); conn.setRequestMethod("POST"); conn.setRequestProperty("Content-Type", "application/x-www-form-urlencoded"); conn.setDoOutput(true); conn.getOutputStream().write(query.getBytes()); } else { if (query.length() > 0) { urlString.append("?").append(query); } URL url = new URL(urlString.toString()); conn = (HttpURLConnection) url.openConnection(); conn.setRequestProperty("User-Agent", USER_AGENT_STRING); conn.setRequestMethod("GET"); } int responseCode = conn.getResponseCode(); if (HttpURLConnection.HTTP_OK != responseCode) { ByteArrayOutputStream errorBuffer = new ByteArrayOutputStream(); int read; byte[] readBuffer = new byte[ERROR_READ_BUFFER_SIZE]; InputStream errorStream = conn.getErrorStream(); while (-1 != (read = errorStream.read(readBuffer))) { errorBuffer.write(readBuffer, 0, read); } throw new RestException("Request failed, HTTP " + responseCode + ": " + conn.getResponseMessage(), errorBuffer.toByteArray()); } return conn.getInputStream(); }

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(); } }

private void writeResponse(final Collection<? extends Resource> resources, final HttpServletResponse response) throws IOException { for (final Resource resource : resources) { InputStream in = null; try { in = resource.getInputStream(); final OutputStream out = response.getOutputStream(); final long bytesCopied = IOUtils.copyLarge(in, out); if (bytesCopied < 0L) throw new StreamCorruptedException("Bad number of copied bytes (" + bytesCopied + ") for resource=" + resource.getFilename()); if (logger.isDebugEnabled()) logger.debug("writeResponse(" + resource.getFile() + ") copied " + bytesCopied + " bytes"); } finally { if (in != null) in.close(); } } }

public static boolean writeFile(HttpServletResponse resp, File reqFile) { boolean retVal = false; InputStream in = null; try { in = new BufferedInputStream(new FileInputStream(reqFile)); IOUtils.copy(in, resp.getOutputStream()); logger.debug("File successful written to servlet response: " + reqFile.getAbsolutePath()); } catch (FileNotFoundException e) { logger.error("Resource not found: " + reqFile.getAbsolutePath()); } catch (IOException e) { logger.error(String.format("Error while rendering [%s]: %s", reqFile.getAbsolutePath(), e.getMessage()), e); } finally { IOUtils.closeQuietly(in); } return retVal; }

public OutputStream getAsOutputStream() throws IOException { OutputStream out; if (contentStream != null) { File tmp = File.createTempFile(getId(), null); out = new FileOutputStream(tmp); IOUtils.copy(contentStream, out); } else { out = new ByteArrayOutputStream(); out.write(getContent()); } return out; }

public static boolean joinFiles(File dest, Collection<File> sources) { FileInputStream fis = null; FileOutputStream fos = null; boolean rv = false; byte[] buf = new byte[1000000]; int bytesRead = 0; if (!dest.getParentFile().exists()) dest.getParentFile().mkdirs(); try { fos = new FileOutputStream(dest); for (File source : sources) { fis = new FileInputStream(source); while ((bytesRead = fis.read(buf)) > 0) fos.write(buf, 0, bytesRead); fis.close(); fis = null; } fos.close(); fos = null; rv = true; } catch (Throwable t) { throw new ApplicationException("error joining files to " + dest.getAbsolutePath(), t); } finally { if (fis != null) { try { fis.close(); } catch (Exception e) { } fis = null; } if (fos != null) { try { fos.close(); } catch (Exception e) { } fos = null; } } return rv; }

private void copyFileToPhotoFolder(File photo, String personId) { try { FileChannel in = new FileInputStream(photo).getChannel(); File dirServer = new File(Constants.PHOTO_DIR); if (!dirServer.exists()) { dirServer.mkdirs(); } File fileServer = new File(Constants.PHOTO_DIR + personId + ".jpg"); if (!fileServer.exists()) { fileServer.createNewFile(); } in.transferTo(0, in.size(), new FileOutputStream(fileServer).getChannel()); } catch (FileNotFoundException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } }

public static void upload(FTPDetails ftpDetails) { FTPClient ftp = new FTPClient(); try { String host = ftpDetails.getHost(); logger.info("Connecting to ftp host: " + host); ftp.connect(host); logger.info("Received reply from ftp :" + ftp.getReplyString()); ftp.login(ftpDetails.getUserName(), ftpDetails.getPassword()); ftp.setFileType(FTP.BINARY_FILE_TYPE); ftp.makeDirectory(ftpDetails.getRemoterDirectory()); logger.info("Created directory :" + ftpDetails.getRemoterDirectory()); ftp.changeWorkingDirectory(ftpDetails.getRemoterDirectory()); BufferedInputStream ftpInput = new BufferedInputStream(new FileInputStream(new File(ftpDetails.getLocalFilePath()))); OutputStream storeFileStream = ftp.storeFileStream(ftpDetails.getRemoteFileName()); IOUtils.copy(ftpInput, storeFileStream); logger.info("Copied file : " + ftpDetails.getLocalFilePath() + " >>> " + host + ":/" + ftpDetails.getRemoterDirectory() + "/" + ftpDetails.getRemoteFileName()); ftpInput.close(); storeFileStream.close(); ftp.logout(); ftp.disconnect(); logger.info("Logged out. "); } catch (Exception e) { throw new RuntimeException(e); } }

private void simulate() throws Exception { BufferedWriter out = null; out = new BufferedWriter(new FileWriter(outFile)); out.write("#Thread\tReputation\tAction\n"); out.flush(); System.out.println("Simulate..."); File file = new File(trsDemoSimulationfile); ObtainUserReputation obtainUserReputationRequest = new ObtainUserReputation(); ObtainUserReputationResponse obtainUserReputationResponse; RateUser rateUserRequest; RateUserResponse rateUserResponse; FileInputStream fis = new FileInputStream(file); BufferedReader br = new BufferedReader(new InputStreamReader(fis)); String call = br.readLine(); while (call != null) { rateUserRequest = generateRateUserRequest(call); try { rateUserResponse = trsPort.rateUser(rateUserRequest); System.out.println("----------------R A T I N G-------------------"); System.out.println("VBE: " + rateUserRequest.getVbeId()); System.out.println("VO: " + rateUserRequest.getVoId()); System.out.println("USER: " + rateUserRequest.getUserId()); System.out.println("SERVICE: " + rateUserRequest.getServiceId()); System.out.println("ACTION: " + rateUserRequest.getActionId()); System.out.println("OUTCOME: " + rateUserResponse.isOutcome()); System.out.println("----------------------------------------------"); assertEquals("The outcome field of the rateUser should be true: MESSAGE=" + rateUserResponse.getMessage(), true, rateUserResponse.isOutcome()); } catch (RemoteException e) { fail(e.getMessage()); } obtainUserReputationRequest.setIoi(null); obtainUserReputationRequest.setServiceId(null); obtainUserReputationRequest.setUserId(rateUserRequest.getUserId()); obtainUserReputationRequest.setVbeId(rateUserRequest.getVbeId()); obtainUserReputationRequest.setVoId(null); try { obtainUserReputationResponse = trsPort.obtainUserReputation(obtainUserReputationRequest); System.out.println("-----------R E P U T A T I O N----------------"); System.out.println("VBE: " + obtainUserReputationRequest.getVbeId()); System.out.println("VO: " + obtainUserReputationRequest.getVoId()); System.out.println("USER: " + obtainUserReputationRequest.getUserId()); System.out.println("SERVICE: " + obtainUserReputationRequest.getServiceId()); System.out.println("IOI: " + obtainUserReputationRequest.getIoi()); System.out.println("REPUTATION: " + obtainUserReputationResponse.getReputation()); System.out.println("----------------------------------------------"); assertEquals("The outcome field of the obtainUserReputation should be true: MESSAGE=" + obtainUserReputationResponse.getMessage(), true, obtainUserReputationResponse.isOutcome()); assertEquals(0.0, obtainUserReputationResponse.getReputation(), 1.0); } catch (RemoteException e) { fail(e.getMessage()); } obtainUserReputationRequest.setIoi(null); obtainUserReputationRequest.setServiceId(null); obtainUserReputationRequest.setUserId(rateUserRequest.getUserId()); obtainUserReputationRequest.setVbeId(rateUserRequest.getVbeId()); obtainUserReputationRequest.setVoId(rateUserRequest.getVoId()); try { obtainUserReputationResponse = trsPort.obtainUserReputation(obtainUserReputationRequest); System.out.println("-----------R E P U T A T I O N----------------"); System.out.println("VBE: " + obtainUserReputationRequest.getVbeId()); System.out.println("VO: " + obtainUserReputationRequest.getVoId()); System.out.println("USER: " + obtainUserReputationRequest.getUserId()); System.out.println("SERVICE: " + obtainUserReputationRequest.getServiceId()); System.out.println("IOI: " + obtainUserReputationRequest.getIoi()); System.out.println("REPUTATION: " + obtainUserReputationResponse.getReputation()); System.out.println("----------------------------------------------"); assertEquals("The outcome field of the obtainUserReputation should be true: MESSAGE=" + obtainUserReputationResponse.getMessage(), true, obtainUserReputationResponse.isOutcome()); assertEquals(0.0, obtainUserReputationResponse.getReputation(), 1.0); } catch (RemoteException e) { fail(e.getMessage()); } call = br.readLine(); } fis.close(); br.close(); out.flush(); out.close(); }

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; }