label int64 0 1 | func1 stringlengths 173 53.1k | func2 stringlengths 173 53.1k | id int64 0 901k |
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0 | public Object run() { List correctUsers = (List) JsonPath.query("select * from ? where name=?", usersTable(), username); if (correctUsers.size() == 0) { return new LoginException("user " + username + " not found"); } Persistable userObject = (Persistable) correctUsers.get(0); boolean alreadyHashed = false; boolean passwordMatch = password.equals(userObject.get(PASSWORD_FIELD)); if (!passwordMatch) { try { MessageDigest md = MessageDigest.getInstance("SHA"); md.update(((String) userObject.get(PASSWORD_FIELD)).getBytes()); passwordMatch = password.equals(new String(new Base64().encode(md.digest()))); } catch (NoSuchAlgorithmException e) { throw new RuntimeException(e); } alreadyHashed = true; } if (passwordMatch) { Logger.getLogger(User.class.toString()).info("User " + username + " has been authenticated"); User user = (User) userObject; try { if (alreadyHashed) user.currentTicket = password; else { MessageDigest md = MessageDigest.getInstance("SHA"); md.update(password.getBytes()); user.currentTicket = new String(new Base64().encode(md.digest())); } } catch (NoSuchAlgorithmException e) { throw new RuntimeException(e); } return user; } else { Logger.getLogger(User.class.toString()).info("The password was incorrect for " + username); return new LoginException("The password was incorrect for user " + username + ". "); } } | public static Vector<String> readFileFromURL(URL url) { Vector<String> text = new Vector<String>(); try { BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream())); String line; while ((line = in.readLine()) != null) { text.add(line); } in.close(); } catch (Exception e) { return null; } return text; } | 17,000 |
0 | public void removerTopicos(Topicos topicos) throws ClassNotFoundException, SQLException { this.criaConexao(false); String sql = "DELETE FROM \"Topicos\" " + " WHERE \"id_Topicos\" = ?"; PreparedStatement stmt = null; try { stmt = connection.prepareStatement(sql); stmt.setString(1, topicos.getIdTopicos()); stmt.executeUpdate(); connection.commit(); } catch (SQLException e) { connection.rollback(); throw e; } finally { try { stmt.close(); this.fechaConexao(); } catch (SQLException e) { throw e; } } } | public ResourceMigrator createDefaultResourceMigrator(NotificationReporter reporter, boolean strictMode) throws ResourceMigrationException { return new ResourceMigrator() { public void migrate(InputMetadata meta, InputStream inputStream, OutputCreator outputCreator) throws IOException, ResourceMigrationException { OutputStream outputStream = outputCreator.createOutputStream(); IOUtils.copy(inputStream, outputStream); } }; } | 17,001 |
0 | private static void readAndRewrite(File inFile, File outFile) throws IOException { ImageInputStream iis = ImageIO.createImageInputStream(new BufferedInputStream(new FileInputStream(inFile))); DcmParser dcmParser = DcmParserFactory.getInstance().newDcmParser(iis); Dataset ds = DcmObjectFactory.getInstance().newDataset(); dcmParser.setDcmHandler(ds.getDcmHandler()); dcmParser.parseDcmFile(null, Tags.PixelData); PixelDataReader pdReader = pdFact.newReader(ds, iis, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); System.out.println("reading " + inFile + "..."); pdReader.readPixelData(false); ImageOutputStream out = ImageIO.createImageOutputStream(new BufferedOutputStream(new FileOutputStream(outFile))); DcmEncodeParam dcmEncParam = DcmEncodeParam.IVR_LE; ds.writeDataset(out, dcmEncParam); ds.writeHeader(out, dcmEncParam, Tags.PixelData, dcmParser.getReadVR(), dcmParser.getReadLength()); System.out.println("writing " + outFile + "..."); PixelDataWriter pdWriter = pdFact.newWriter(pdReader.getPixelDataArray(), false, ds, out, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); pdWriter.writePixelData(); out.flush(); out.close(); System.out.println("done!"); } | public void deleteInstance(int instanceId) throws FidoDatabaseException, ObjectNotFoundException { try { Connection conn = null; Statement stmt = null; try { conn = fido.util.FidoDataSource.getConnection(); conn.setAutoCommit(false); stmt = conn.createStatement(); if (contains(stmt, instanceId) == false) throw new ObjectNotFoundException(instanceId); ObjectLinkTable objectLinkList = new ObjectLinkTable(); ObjectAttributeTable objectAttributeList = new ObjectAttributeTable(); objectLinkList.deleteObject(stmt, instanceId); objectAttributeList.deleteObject(stmt, instanceId); stmt.executeUpdate("delete from Objects where ObjectId = " + instanceId); 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); } } | 17,002 |
1 | public boolean updateLOB(String sql, int displayType, Object value, String trxName, SecurityToken token) { validateSecurityToken(token); if (sql == null || value == null) { log.fine("No sql or data"); return false; } log.fine(sql); Trx trx = null; if (trxName != null && trxName.trim().length() > 0) { trx = Trx.get(trxName, false); if (trx == null) throw new RuntimeException("Transaction lost - " + trxName); } m_updateLOBCount++; boolean success = true; Connection con = trx != null ? trx.getConnection() : DB.createConnection(false, Connection.TRANSACTION_READ_COMMITTED); PreparedStatement pstmt = null; try { pstmt = con.prepareStatement(sql); if (displayType == DisplayType.TextLong) pstmt.setString(1, (String) value); else pstmt.setBytes(1, (byte[]) value); int no = pstmt.executeUpdate(); } catch (Exception e) { log.log(Level.FINE, sql, e); success = false; } finally { DB.close(pstmt); pstmt = null; } if (success && trx == null) { try { con.commit(); } catch (Exception e) { log.log(Level.SEVERE, "commit", e); success = false; } finally { try { con.close(); } catch (SQLException e) { } con = null; } } if (!success) { log.severe("rollback"); if (trx == null) { try { con.rollback(); } catch (Exception ee) { log.log(Level.SEVERE, "rollback", ee); } finally { try { con.close(); } catch (SQLException e) { } con = null; } } else { trx.rollback(); } } return success; } | 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); } } | 17,003 |
0 | public InputStream sendCommandRaw(String command, boolean usePost) throws IOException { try { String fullCommand = prefix + command + fixSuffix(command, suffix); long curGap = System.currentTimeMillis() - lastCommandTime; long delayTime = minimumCommandPeriod - curGap; delay(delayTime); URI uri = new URI(fullCommand); URL url = uri.toURL(); if (trace || traceSends) { System.out.println("Sending--> " + url); } if (logFile != null) { logFile.println("Sending--> " + url); } InputStream is = null; for (int i = 0; i < tryCount; i++) { try { URLConnection urc = url.openConnection(); if (usePost) { if (urc instanceof HttpURLConnection) { ((HttpURLConnection) urc).setRequestMethod("POST"); } } if (getTimeout() != -1) { urc.setReadTimeout(getTimeout()); urc.setConnectTimeout(getTimeout()); } is = new BufferedInputStream(urc.getInputStream()); break; } catch (FileNotFoundException e) { throw e; } catch (IOException e) { System.out.println(name + " Error: " + e + " cmd: " + command); } } lastCommandTime = System.currentTimeMillis(); if (is == null) { System.out.println(name + " retry failure cmd: " + url); throw new IOException("Can't send command"); } return is; } catch (URISyntaxException ex) { throw new IOException("bad uri " + ex); } } | public void deleteGroup(String groupID) throws XregistryException { try { Connection connection = context.createConnection(); connection.setAutoCommit(false); try { PreparedStatement statement1 = connection.prepareStatement(DELETE_GROUP_SQL_MAIN); statement1.setString(1, groupID); int updateCount = statement1.executeUpdate(); if (updateCount == 0) { throw new XregistryException("Database is not updated, Can not find such Group " + groupID); } if (cascadingDeletes) { PreparedStatement statement2 = connection.prepareStatement(DELETE_GROUP_SQL_DEPEND); statement2.setString(1, groupID); statement2.setString(2, groupID); statement2.executeUpdate(); } connection.commit(); groups.remove(groupID); log.info("Delete Group " + groupID + (cascadingDeletes ? " with cascading deletes " : "")); } catch (SQLException e) { connection.rollback(); throw new XregistryException(e); } finally { context.closeConnection(connection); } } catch (SQLException e) { throw new XregistryException(e); } } | 17,004 |
0 | private void bubbleSort(int values[]) { 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; } } } } | public void print(PrintWriter out) { out.println("<?xml version=\"1.0\"?>\n" + "<?xml-stylesheet type=\"text/xsl\" href=\"http://www.urbigene.com/foaf/foaf2html.xsl\" ?>\n" + "<rdf:RDF \n" + "xml:lang=\"en\" \n" + "xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" \n" + "xmlns:rdfs=\"http://www.w3.org/2000/01/rdf-schema#\" \n" + "xmlns=\"http://xmlns.com/foaf/0.1/\" \n" + "xmlns:foaf=\"http://xmlns.com/foaf/0.1/\" \n" + "xmlns:dc=\"http://purl.org/dc/elements/1.1/\">\n"); out.println("<!-- generated with SciFoaf http://www.urbigene.com/foaf -->"); if (this.mainAuthor == null && this.authors.getAuthorCount() > 0) { this.mainAuthor = this.authors.getAuthorAt(0); } if (this.mainAuthor != null) { out.println("<foaf:PersonalProfileDocument rdf:about=\"\">\n" + "\t<foaf:primaryTopic rdf:nodeID=\"" + this.mainAuthor.getID() + "\"/>\n" + "\t<foaf:maker rdf:resource=\"mailto:plindenbaum@yahoo.fr\"/>\n" + "\t<dc:title>FOAF for " + XMLUtilities.escape(this.mainAuthor.getName()) + "</dc:title>\n" + "\t<dc:description>\n" + "\tFriend-of-a-Friend description for " + XMLUtilities.escape(this.mainAuthor.getName()) + "\n" + "\t</dc:description>\n" + "</foaf:PersonalProfileDocument>\n\n"); } for (int i = 0; i < this.laboratories.size(); ++i) { Laboratory lab = this.laboratories.getLabAt(i); out.println("<foaf:Group rdf:ID=\"laboratory_ID" + i + "\" >"); out.println("\t<foaf:name>" + XMLUtilities.escape(lab.toString()) + "</foaf:name>"); for (int j = 0; j < lab.getAuthorCount(); ++j) { out.println("\t<foaf:member rdf:resource=\"#" + lab.getAuthorAt(j).getID() + "\" />"); } out.println("</foaf:Group>\n\n"); } for (int i = 0; i < this.authors.size(); ++i) { Author author = authors.getAuthorAt(i); out.println("<foaf:Person rdf:ID=\"" + xmlName(author.getID()) + "\" >"); out.println("\t<foaf:name>" + xmlName(author.getName()) + "</foaf:name>"); out.println("\t<foaf:title>Dr</foaf:title>"); out.println("\t<foaf:family_name>" + xmlName(author.getLastName()) + "</foaf:family_name>"); if (author.getForeName() != null && author.getForeName().length() > 2) { out.println("\t<foaf:firstName>" + xmlName(author.getForeName()) + "</foaf:firstName>"); } String prop = author.getProperty("foaf:mbox"); if (prop != null) { String tokens[] = prop.split("[\t ]+"); for (int j = 0; j < tokens.length; ++j) { if (tokens[j].trim().length() == 0) continue; if (tokens[j].equals("mailto:")) continue; if (!tokens[j].startsWith("mailto:")) tokens[j] = "mailto:" + tokens[j]; try { MessageDigest md = MessageDigest.getInstance("SHA"); md.update(tokens[j].getBytes()); byte[] digest = md.digest(); out.print("\t<foaf:mbox_sha1sum>"); for (int k = 0; k < digest.length; k++) { String hex = Integer.toHexString(digest[k]); if (hex.length() == 1) hex = "0" + hex; hex = hex.substring(hex.length() - 2); out.print(hex); } out.println("</foaf:mbox_sha1sum>"); } catch (Exception err) { out.println("\t<foaf:mbox rdf:resource=\"" + tokens[j] + "\" />"); } } } prop = author.getProperty("foaf:nick"); if (prop != null) { String tokens[] = prop.split("[\t ]+"); for (int j = 0; j < tokens.length; ++j) { if (tokens[j].trim().length() == 0) continue; out.println("\t<foaf:surname>" + XMLUtilities.escape(tokens[j]) + "</foaf:surname>"); } } prop = author.getProperty("foaf:homepage"); if (prop != null) { String tokens[] = prop.split("[\t ]+"); for (int j = 0; j < tokens.length; ++j) { if (!tokens[j].trim().startsWith("http://")) continue; if (tokens[j].trim().equals("http://")) continue; out.println("\t<foaf:homepage rdf:resource=\"" + XMLUtilities.escape(tokens[j].trim()) + "\"/>"); } } out.println("\t<foaf:publications rdf:resource=\"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Search&itool=pubmed_Abstract&term=" + author.getTerm() + "\"/>"); prop = author.getProperty("foaf:img"); if (prop != null) { String tokens[] = prop.split("[\t ]+"); for (int j = 0; j < tokens.length; ++j) { if (!tokens[j].trim().startsWith("http://")) continue; if (tokens[j].trim().equals("http://")) continue; out.println("\t<foaf:depiction rdf:resource=\"" + XMLUtilities.escape(tokens[j].trim()) + "\"/>"); } } AuthorList knows = this.whoknowwho.getKnown(author); for (int j = 0; j < knows.size(); ++j) { out.println("\t<foaf:knows rdf:resource=\"#" + xmlName(knows.getAuthorAt(j).getID()) + "\" />"); } Paper publications[] = this.papers.getAuthorPublications(author).toArray(); if (!(publications.length == 0)) { HashSet meshes = new HashSet(); for (int j = 0; j < publications.length; ++j) { meshes.addAll(publications[j].meshTerms); } for (Iterator itermesh = meshes.iterator(); itermesh.hasNext(); ) { MeshTerm meshterm = (MeshTerm) itermesh.next(); out.println("\t<foaf:interest>\n" + "\t\t<rdf:Description rdf:about=\"" + meshterm.getURL() + "\">\n" + "\t\t\t<dc:title>" + XMLUtilities.escape(meshterm.toString()) + "</dc:title>\n" + "\t\t</rdf:Description>\n" + "\t</foaf:interest>"); } } out.println("</foaf:Person>\n\n"); } Paper paperarray[] = this.papers.toArray(); for (int i = 0; i < paperarray.length; ++i) { out.println("<foaf:Document rdf:about=\"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=" + paperarray[i].getPMID() + "\">"); out.println("<dc:title>" + XMLUtilities.escape(paperarray[i].getTitle()) + "</dc:title>"); for (Iterator iter = paperarray[i].authors.iterator(); iter.hasNext(); ) { Author author = (Author) iter.next(); out.println("<dc:author rdf:resource=\"#" + XMLUtilities.escape(author.getID()) + "\"/>"); } out.println("</foaf:Document>"); } out.println("</rdf:RDF>"); } | 17,005 |
1 | @Override public void run() { long timeout = 10 * 1000L; long start = (new Date()).getTime(); try { InputStream is = socket.getInputStream(); boolean available = false; while (!available && !socket.isClosed()) { try { if (is.available() != 0) { available = true; } else { Thread.sleep(100); } } catch (Exception e) { LOG.error("Error checking socket", e); } long curr = (new Date()).getTime(); if ((curr - start) >= timeout) { break; } } if (socket.isClosed()) { } else { tmpFile = File.createTempFile("ftp", "dat", new File("./tmp")); BufferedOutputStream bos = new BufferedOutputStream(new FileOutputStream(tmpFile)); IOUtils.copy(is, bos); bos.flush(); bos.close(); } String msg = FtpResponse.ReadComplete.asString() + ClientCommand.SP + "Read Complete" + ClientCommand.CRLF; List<String> list = new ArrayList<String>(); list.add(msg); ClientResponse response = new ClientResponse(list); ftpClient.notifyListeners(response); } catch (Exception e) { LOG.error("Error reading server response", e); } } | 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; } | 17,006 |
0 | public static String hashPassword(String password) { try { MessageDigest md5 = MessageDigest.getInstance("MD5"); md5.update(password.getBytes()); byte result[] = md5.digest("InTeRlOgY".getBytes()); StringBuffer sb = new StringBuffer(); for (int i = 0; i < result.length; i++) { String s = Integer.toHexString(result[i]); int length = s.length(); if (length >= 2) { sb.append(s.substring(length - 2, length)); } else { sb.append("0"); sb.append(s); } } return "{md5}" + sb.toString(); } catch (NoSuchAlgorithmException e) { return password; } } | public int batchTransactionUpdate(List<String> queryStrLisyt, Connection con) throws Exception { int ret = 0; Statement stmt; if (con != null) { con.setAutoCommit(false); stmt = con.createStatement(); try { stmt.executeUpdate("START TRANSACTION;"); for (int i = 0; i < queryStrLisyt.size(); i++) { stmt.addBatch(queryStrLisyt.get(i)); } int[] updateCounts = stmt.executeBatch(); for (int i = 0; i < updateCounts.length; i++) { FileLogger.debug("batch update result:" + updateCounts[i] + ", Statement.SUCCESS_NO_INFO" + Statement.SUCCESS_NO_INFO); if (updateCounts[i] == Statement.SUCCESS_NO_INFO || updateCounts[i] > 0) { ret++; } else if (updateCounts[i] == Statement.EXECUTE_FAILED) ; { throw new Exception("query failed, while process batch update"); } } con.commit(); } catch (Exception e) { ret = 0; FileLogger.debug(e.getMessage()); con.rollback(); } finally { con.setAutoCommit(true); stmt.close(); } } return ret; } | 17,007 |
1 | @Override public String entryToObject(TupleInput input) { boolean zipped = input.readBoolean(); if (!zipped) { return input.readString(); } int len = input.readInt(); try { byte array[] = new byte[len]; input.read(array); GZIPInputStream in = new GZIPInputStream(new ByteArrayInputStream(array)); ByteArrayOutputStream out = new ByteArrayOutputStream(); IOUtils.copyTo(in, out); in.close(); out.close(); return new String(out.toByteArray()); } catch (IOException err) { throw new RuntimeException(err); } } | @Test public void testWriteAndReadFirstLevel() throws Exception { JCFSFileServer server = new JCFSFileServer(defaultTcpPort, defaultTcpAddress, defaultUdpPort, defaultUdpAddress, dir, 0, 0); JCFS.configureDiscovery(defaultUdpAddress, defaultUdpPort); try { server.start(); RFile directory1 = new RFile("directory1"); RFile file = new RFile(directory1, "testreadwrite1st.txt"); RFileOutputStream out = new RFileOutputStream(file); out.write("test".getBytes("utf-8")); out.close(); RFileInputStream in = new RFileInputStream(file); byte[] buffer = new byte[4]; int readCount = in.read(buffer); in.close(); assertEquals(4, readCount); String resultRead = new String(buffer, "utf-8"); assertEquals("test", resultRead); } finally { server.stop(); } } | 17,008 |
1 | static boolean writeProperties(Map<String, String> customProps, File destination) throws IOException { synchronized (PropertiesIO.class) { L.info(Msg.msg("PropertiesIO.writeProperties.start")); File tempFile = null; BufferedInputStream existingCfgInStream = null; FileInputStream in = null; FileOutputStream out = null; PrintStream ps = null; FileChannel fromChannel = null, toChannel = null; String line = null; try { existingCfgInStream = new BufferedInputStream(destination.exists() ? new FileInputStream(destination) : defaultPropertiesStream()); tempFile = File.createTempFile("properties-", ".tmp", null); ps = new PrintStream(tempFile); while ((line = Utils.readLine(existingCfgInStream)) != null) { String lineReady2write = setupLine(line, customProps); ps.println(lineReady2write); } destination.getParentFile().mkdirs(); in = new FileInputStream(tempFile); out = new FileOutputStream(destination, false); fromChannel = in.getChannel(); toChannel = out.getChannel(); fromChannel.transferTo(0, fromChannel.size(), toChannel); L.info(Msg.msg("PropertiesIO.writeProperties.done").replace("#file#", destination.getAbsolutePath())); return true; } finally { if (existingCfgInStream != null) existingCfgInStream.close(); if (ps != null) ps.close(); if (fromChannel != null) fromChannel.close(); if (toChannel != null) toChannel.close(); if (out != null) out.close(); if (in != null) in.close(); if (tempFile != null && tempFile.exists()) tempFile.delete(); } } } | private LinkedList<Datum> processDatum(Datum dataset) { ArrayList<Object[]> markerTestResults = new ArrayList<Object[]>(); ArrayList<Object[]> alleleEstimateResults = new ArrayList<Object[]>(); boolean hasAlleleNames = false; String blank = new String(""); MarkerPhenotypeAdapter theAdapter; if (dataset.getDataType().equals(MarkerPhenotype.class)) { theAdapter = new MarkerPhenotypeAdapter((MarkerPhenotype) dataset.getData()); } else theAdapter = new MarkerPhenotypeAdapter((Phenotype) dataset.getData()); int numberOfMarkers = theAdapter.getNumberOfMarkers(); if (numberOfMarkers == 0) { return calculateBLUEsFromPhenotypes(theAdapter, dataset.getName()); } int numberOfCovariates = theAdapter.getNumberOfCovariates(); int numberOfFactors = theAdapter.getNumberOfFactors(); int numberOfPhenotypes = theAdapter.getNumberOfPhenotypes(); int expectedIterations = numberOfPhenotypes * numberOfMarkers; int iterationsSofar = 0; int percentFinished = 0; File tempFile = null; File ftestFile = null; File blueFile = null; BufferedWriter ftestWriter = null; BufferedWriter BLUEWriter = null; String ftestHeader = "Trait\tMarker\tLocus\tLocus_pos\tChr\tChr_pos\tmarker_F\tmarker_p\tperm_p\tmarkerR2\tmarkerDF\tmarkerMS\terrorDF\terrorMS\tmodelDF\tmodelMS"; String BLUEHeader = "Trait\tMarker\tObs\tLocus\tLocus_pos\tChr\tChr_pos\tAllele\tEstimate"; if (writeOutputToFile) { String outputbase = outputName; if (outputbase.endsWith(".txt")) { int index = outputbase.lastIndexOf("."); outputbase = outputbase.substring(0, index); } String datasetNameNoSpace = dataset.getName().trim().replaceAll("\\ ", "_"); ftestFile = new File(outputbase + "_" + datasetNameNoSpace + "_ftest.txt"); int count = 0; while (ftestFile.exists()) { count++; ftestFile = new File(outputbase + "_" + datasetNameNoSpace + "_ftest" + count + ".txt"); } blueFile = new File(outputbase + "_" + datasetNameNoSpace + "_BLUEs.txt"); count = 0; while (blueFile.exists()) { count++; blueFile = new File(outputbase + "_" + datasetNameNoSpace + "_BLUEs" + count + ".txt"); } tempFile = new File(outputbase + "_" + datasetNameNoSpace + "_ftest.tmp"); try { if (permute) { ftestWriter = new BufferedWriter(new FileWriter(tempFile)); ftestWriter.write(ftestHeader); ftestWriter.newLine(); } else { ftestWriter = new BufferedWriter(new FileWriter(ftestFile)); ftestWriter.write(ftestHeader); ftestWriter.newLine(); } if (reportBLUEs) { BLUEWriter = new BufferedWriter(new FileWriter(blueFile)); BLUEWriter.write(BLUEHeader); BLUEWriter.newLine(); } } catch (IOException e) { myLogger.error("Failed to open file for output"); myLogger.error(e); return null; } } if (permute) { minP = new double[numberOfPhenotypes][numberOfPermutations]; for (int i = 0; i < numberOfPermutations; i++) { for (int j = 0; j < numberOfPhenotypes; j++) { minP[j][i] = 1; } } } for (int ph = 0; ph < numberOfPhenotypes; ph++) { double[] phenotypeData = theAdapter.getPhenotypeValues(ph); boolean[] missing = theAdapter.getMissingPhenotypes(ph); ArrayList<String[]> factorList = MarkerPhenotypeAdapterUtils.getFactorList(theAdapter, ph, missing); ArrayList<double[]> covariateList = MarkerPhenotypeAdapterUtils.getCovariateList(theAdapter, ph, missing); double[][] permutedData = null; if (permute) { permutedData = permuteData(phenotypeData, missing, factorList, covariateList, theAdapter); } for (int m = 0; m < numberOfMarkers; m++) { Object[] markerData = theAdapter.getMarkerValue(ph, m); boolean[] finalMissing = new boolean[missing.length]; System.arraycopy(missing, 0, finalMissing, 0, missing.length); MarkerPhenotypeAdapterUtils.updateMissing(finalMissing, theAdapter.getMissingMarkers(ph, m)); int[] nonmissingRows = MarkerPhenotypeAdapterUtils.getNonMissingIndex(finalMissing); int numberOfObs = nonmissingRows.length; double[] y = new double[numberOfObs]; for (int i = 0; i < numberOfObs; i++) y[i] = phenotypeData[nonmissingRows[i]]; int firstMarkerAlleleEstimate = 1; ArrayList<ModelEffect> modelEffects = new ArrayList<ModelEffect>(); FactorModelEffect meanEffect = new FactorModelEffect(new int[numberOfObs], false); meanEffect.setID("mean"); modelEffects.add(meanEffect); if (numberOfFactors > 0) { for (int f = 0; f < numberOfFactors; f++) { String[] afactor = factorList.get(f); String[] factorLabels = new String[numberOfObs]; for (int i = 0; i < numberOfObs; i++) factorLabels[i] = afactor[nonmissingRows[i]]; FactorModelEffect fme = new FactorModelEffect(ModelEffectUtils.getIntegerLevels(factorLabels), true, theAdapter.getFactorName(f)); modelEffects.add(fme); firstMarkerAlleleEstimate += fme.getNumberOfLevels() - 1; } } if (numberOfCovariates > 0) { for (int c = 0; c < numberOfCovariates; c++) { double[] covar = new double[numberOfObs]; double[] covariateData = covariateList.get(c); for (int i = 0; i < numberOfObs; i++) covar[i] = covariateData[nonmissingRows[i]]; modelEffects.add(new CovariateModelEffect(covar, theAdapter.getCovariateName(c))); firstMarkerAlleleEstimate++; } } ModelEffect markerEffect; boolean markerIsDiscrete = theAdapter.isMarkerDiscrete(m); ArrayList<Object> alleleNames = new ArrayList<Object>(); if (markerIsDiscrete) { Object[] markers = new Object[numberOfObs]; for (int i = 0; i < numberOfObs; i++) markers[i] = markerData[nonmissingRows[i]]; int[] markerLevels = ModelEffectUtils.getIntegerLevels(markers, alleleNames); markerEffect = new FactorModelEffect(markerLevels, true, theAdapter.getMarkerName(m)); hasAlleleNames = true; } else { double[] markerdbl = new double[numberOfObs]; for (int i = 0; i < numberOfObs; i++) markerdbl[i] = ((Double) markerData[nonmissingRows[i]]).doubleValue(); markerEffect = new CovariateModelEffect(markerdbl, theAdapter.getMarkerName(m)); } int[] alleleCounts = markerEffect.getLevelCounts(); modelEffects.add(markerEffect); int markerEffectNumber = modelEffects.size() - 1; Identifier[] taxaSublist = new Identifier[numberOfObs]; Identifier[] taxa = theAdapter.getTaxa(ph); for (int i = 0; i < numberOfObs; i++) taxaSublist[i] = taxa[nonmissingRows[i]]; boolean areTaxaReplicated = containsDuplicates(taxaSublist); double[] markerSSdf = null, errorSSdf = null, modelSSdf = null; double F, p; double[] beta = null; if (areTaxaReplicated && markerIsDiscrete) { ModelEffect taxaEffect = new FactorModelEffect(ModelEffectUtils.getIntegerLevels(taxaSublist), true); modelEffects.add(taxaEffect); SweepFastNestedModel sfnm = new SweepFastNestedModel(modelEffects, y); double[] taxaSSdf = sfnm.getTaxaInMarkerSSdf(); double[] residualSSdf = sfnm.getErrorSSdf(); markerSSdf = sfnm.getMarkerSSdf(); errorSSdf = sfnm.getErrorSSdf(); modelSSdf = sfnm.getModelcfmSSdf(); F = markerSSdf[0] / markerSSdf[1] / taxaSSdf[0] * taxaSSdf[1]; try { p = LinearModelUtils.Ftest(F, markerSSdf[1], taxaSSdf[1]); } catch (Exception e) { p = Double.NaN; } beta = sfnm.getBeta(); int markerdf = (int) markerSSdf[1]; if (permute && markerdf > 0) { updatePermutationPValues(ph, permutedData, nonMissingIndex(missing, finalMissing), getXfromModelEffects(modelEffects), sfnm.getInverseOfXtX(), markerdf); } } else { SweepFastLinearModel sflm = new SweepFastLinearModel(modelEffects, y); modelSSdf = sflm.getModelcfmSSdf(); markerSSdf = sflm.getMarginalSSdf(markerEffectNumber); errorSSdf = sflm.getResidualSSdf(); F = markerSSdf[0] / markerSSdf[1] / errorSSdf[0] * errorSSdf[1]; try { p = LinearModelUtils.Ftest(F, markerSSdf[1], errorSSdf[1]); } catch (Exception e) { p = Double.NaN; } beta = sflm.getBeta(); int markerdf = (int) markerSSdf[1]; if (permute && markerdf > 0) { updatePermutationPValues(ph, permutedData, nonMissingIndex(missing, finalMissing), getXfromModelEffects(modelEffects), sflm.getInverseOfXtX(), markerdf); } } if (!filterOutput || p < maxp) { String traitname = theAdapter.getPhenotypeName(ph); if (traitname == null) traitname = blank; String marker = theAdapter.getMarkerName(m); if (marker == null) marker = blank; String locus = theAdapter.getLocusName(m); Integer site = new Integer(theAdapter.getLocusPosition(m)); String chrname = ""; Double chrpos = Double.NaN; if (hasMap) { int ndx = -1; ndx = myMap.getMarkerIndex(marker); if (ndx > -1) { chrname = myMap.getChromosome(ndx); chrpos = myMap.getGeneticPosition(ndx); } } Object[] result = new Object[16]; int col = 0; result[col++] = traitname; result[col++] = marker; result[col++] = locus; result[col++] = site; result[col++] = chrname; result[col++] = chrpos; result[col++] = new Double(F); result[col++] = new Double(p); result[col++] = Double.NaN; result[col++] = new Double(markerSSdf[0] / (modelSSdf[0] + errorSSdf[0])); result[col++] = new Double(markerSSdf[1]); result[col++] = new Double(markerSSdf[0] / markerSSdf[1]); result[col++] = new Double(errorSSdf[1]); result[col++] = new Double(errorSSdf[0] / errorSSdf[1]); result[col++] = new Double(modelSSdf[1]); result[col++] = new Double(modelSSdf[0] / modelSSdf[1]); if (writeOutputToFile) { StringBuilder sb = new StringBuilder(); sb.append(result[0]); for (int i = 1; i < 16; i++) sb.append("\t").append(result[i]); try { ftestWriter.write(sb.toString()); ftestWriter.newLine(); } catch (IOException e) { myLogger.error("Failed to write output to ftest file. Ending prematurely"); try { ftestWriter.flush(); BLUEWriter.flush(); } catch (Exception e1) { } myLogger.error(e); return null; } } else { markerTestResults.add(result); } int numberOfMarkerAlleles = alleleNames.size(); if (numberOfMarkerAlleles == 0) numberOfMarkerAlleles++; for (int i = 0; i < numberOfMarkerAlleles; i++) { result = new Object[9]; result[0] = traitname; result[1] = marker; result[2] = new Integer(alleleCounts[i]); result[3] = locus; result[4] = site; result[5] = chrname; result[6] = chrpos; if (numberOfMarkerAlleles == 1) result[7] = ""; else result[7] = alleleNames.get(i); if (i == numberOfMarkerAlleles - 1) result[8] = 0.0; else result[8] = beta[firstMarkerAlleleEstimate + i]; if (writeOutputToFile) { StringBuilder sb = new StringBuilder(); sb.append(result[0]); for (int j = 1; j < 9; j++) sb.append("\t").append(result[j]); try { BLUEWriter.write(sb.toString()); BLUEWriter.newLine(); } catch (IOException e) { myLogger.error("Failed to write output to ftest file. Ending prematurely"); try { ftestWriter.flush(); BLUEWriter.flush(); } catch (Exception e1) { } myLogger.error(e); return null; } } else { alleleEstimateResults.add(result); } } } int tmpPercent = ++iterationsSofar * 100 / expectedIterations; if (tmpPercent > percentFinished) { percentFinished = tmpPercent; fireProgress(percentFinished); } } } fireProgress(0); if (writeOutputToFile) { try { ftestWriter.close(); BLUEWriter.close(); } catch (IOException e) { e.printStackTrace(); } } HashMap<String, Integer> traitnameMap = new HashMap<String, Integer>(); if (permute) { for (int ph = 0; ph < numberOfPhenotypes; ph++) { Arrays.sort(minP[ph]); traitnameMap.put(theAdapter.getPhenotypeName(ph), ph); } if (writeOutputToFile) { try { BufferedReader tempReader = new BufferedReader(new FileReader(tempFile)); ftestWriter = new BufferedWriter(new FileWriter(ftestFile)); ftestWriter.write(tempReader.readLine()); ftestWriter.newLine(); String input; String[] data; Pattern tab = Pattern.compile("\t"); while ((input = tempReader.readLine()) != null) { data = tab.split(input); String trait = data[0]; double pval = Double.parseDouble(data[7]); int ph = traitnameMap.get(trait); int ndx = Arrays.binarySearch(minP[ph], pval); if (ndx < 0) ndx = -ndx - 1; if (ndx == 0) ndx = 1; data[8] = Double.toString((double) ndx / (double) numberOfPermutations); ftestWriter.write(data[0]); for (int i = 1; i < data.length; i++) { ftestWriter.write("\t"); ftestWriter.write(data[i]); } ftestWriter.newLine(); } tempReader.close(); ftestWriter.close(); tempFile.delete(); } catch (IOException e) { myLogger.error(e); } } else { for (Object[] result : markerTestResults) { String trait = result[0].toString(); double pval = (Double) result[7]; int ph = traitnameMap.get(trait); int ndx = Arrays.binarySearch(minP[ph], pval); if (ndx < 0) ndx = -ndx - 1; if (ndx == 0) ndx = 1; result[8] = new Double((double) ndx / (double) numberOfPermutations); } } } String[] columnLabels = new String[] { "Trait", "Marker", "Locus", "Locus_pos", "Chr", "Chr_pos", "marker_F", "marker_p", "perm_p", "markerR2", "markerDF", "markerMS", "errorDF", "errorMS", "modelDF", "modelMS" }; boolean hasMarkerNames = theAdapter.hasMarkerNames(); LinkedList<Integer> outputList = new LinkedList<Integer>(); outputList.add(0); if (hasMarkerNames) outputList.add(1); outputList.add(2); outputList.add(3); if (hasMap) { outputList.add(4); outputList.add(5); } outputList.add(6); outputList.add(7); if (permute) outputList.add(8); for (int i = 9; i < 16; i++) outputList.add(i); LinkedList<Datum> resultset = new LinkedList<Datum>(); int nrows = markerTestResults.size(); Object[][] table = new Object[nrows][]; int numberOfColumns = outputList.size(); String[] colnames = new String[numberOfColumns]; int count = 0; for (Integer ndx : outputList) colnames[count++] = columnLabels[ndx]; for (int i = 0; i < nrows; i++) { table[i] = new Object[numberOfColumns]; Object[] result = markerTestResults.get(i); count = 0; for (Integer ndx : outputList) table[i][count++] = result[ndx]; } StringBuilder tableName = new StringBuilder("GLM_marker_test_"); tableName.append(dataset.getName()); StringBuilder comments = new StringBuilder("Tests of Marker-Phenotype Association"); comments.append("GLM: fixed effect linear model\n"); comments.append("Data set: ").append(dataset.getName()); comments.append("\nmodel: trait = mean"); for (int i = 0; i < theAdapter.getNumberOfFactors(); i++) { comments.append(" + "); comments.append(theAdapter.getFactorName(i)); } for (int i = 0; i < theAdapter.getNumberOfCovariates(); i++) { comments.append(" + "); comments.append(theAdapter.getCovariateName(i)); } comments.append(" + marker"); if (writeOutputToFile) { comments.append("\nOutput written to " + ftestFile.getPath()); } TableReport markerTestReport = new SimpleTableReport("Marker Test", colnames, table); resultset.add(new Datum(tableName.toString(), markerTestReport, comments.toString())); int[] outputIndex; columnLabels = new String[] { "Trait", "Marker", "Obs", "Locus", "Locus_pos", "Chr", "Chr_pos", "Allele", "Estimate" }; if (hasAlleleNames) { if (hasMarkerNames && hasMap) { outputIndex = new int[] { 0, 1, 2, 3, 4, 5, 6, 7, 8 }; } else if (hasMarkerNames) { outputIndex = new int[] { 0, 1, 2, 3, 4, 7, 8 }; } else if (hasMap) { outputIndex = new int[] { 0, 2, 3, 4, 5, 6, 7, 8 }; } else { outputIndex = new int[] { 0, 2, 3, 4, 7, 8 }; } } else { if (hasMarkerNames && hasMap) { outputIndex = new int[] { 0, 1, 2, 3, 4, 5, 6, 8 }; } else if (hasMarkerNames) { outputIndex = new int[] { 0, 1, 2, 3, 4, 8 }; } else if (hasMap) { outputIndex = new int[] { 0, 2, 3, 4, 5, 6, 8 }; } else { outputIndex = new int[] { 0, 2, 3, 4, 8 }; } } nrows = alleleEstimateResults.size(); table = new Object[nrows][]; numberOfColumns = outputIndex.length; colnames = new String[numberOfColumns]; for (int j = 0; j < numberOfColumns; j++) { colnames[j] = columnLabels[outputIndex[j]]; } for (int i = 0; i < nrows; i++) { table[i] = new Object[numberOfColumns]; Object[] result = alleleEstimateResults.get(i); for (int j = 0; j < numberOfColumns; j++) { table[i][j] = result[outputIndex[j]]; } } tableName = new StringBuilder("GLM allele estimates for "); tableName.append(dataset.getName()); comments = new StringBuilder("Marker allele effect estimates\n"); comments.append("GLM: fixed effect linear model\n"); comments.append("Data set: ").append(dataset.getName()); comments.append("\nmodel: trait = mean"); for (int i = 0; i < theAdapter.getNumberOfFactors(); i++) { comments.append(" + "); comments.append(theAdapter.getFactorName(i)); } for (int i = 0; i < theAdapter.getNumberOfCovariates(); i++) { comments.append(" + "); comments.append(theAdapter.getCovariateName(i)); } comments.append(" + marker"); if (writeOutputToFile) { comments.append("\nOutput written to " + blueFile.getPath()); } TableReport alleleEstimateReport = new SimpleTableReport("Allele Estimates", colnames, table); resultset.add(new Datum(tableName.toString(), alleleEstimateReport, comments.toString())); fireProgress(0); return resultset; } | 17,009 |
0 | public DataSet guessAtUnknowns(String filename) { TasselFileType guess = TasselFileType.Sequence; DataSet tds = null; try { BufferedReader br = null; if (filename.startsWith("http")) { URL url = new URL(filename); br = new BufferedReader(new InputStreamReader(url.openStream())); } else { br = new BufferedReader(new FileReader(filename)); } String line1 = br.readLine().trim(); String[] sval1 = line1.split("\\s"); String line2 = br.readLine().trim(); String[] sval2 = line2.split("\\s"); boolean lociMatchNumber = false; if (!sval1[0].startsWith("<") && (sval1.length == 2) && (line1.indexOf(':') < 0)) { int countLoci = Integer.parseInt(sval1[1]); if (countLoci == sval2.length) { lociMatchNumber = true; } } if (sval1[0].equalsIgnoreCase("<Annotated>")) { guess = TasselFileType.Annotated; } else if (line1.startsWith("<") || line1.startsWith("#")) { boolean isTrait = false; boolean isMarker = false; boolean isNumeric = false; boolean isMap = false; Pattern tagPattern = Pattern.compile("[<>\\s]+"); String[] info1 = tagPattern.split(line1); String[] info2 = tagPattern.split(line2); if (info1.length > 1) { if (info1[1].toUpperCase().startsWith("MARKER")) { isMarker = true; } else if (info1[1].toUpperCase().startsWith("TRAIT")) { isTrait = true; } else if (info1[1].toUpperCase().startsWith("NUMER")) { isNumeric = true; } else if (info1[1].toUpperCase().startsWith("MAP")) { isMap = true; } } if (info2.length > 1) { if (info2[1].toUpperCase().startsWith("MARKER")) { isMarker = true; } else if (info2[1].toUpperCase().startsWith("TRAIT")) { isTrait = true; } else if (info2[1].toUpperCase().startsWith("NUMER")) { isNumeric = true; } else if (info2[1].toUpperCase().startsWith("MAP")) { isMap = true; } } else { guess = null; String inline = br.readLine(); while (guess == null && inline != null && (inline.startsWith("#") || inline.startsWith("<"))) { if (inline.startsWith("<")) { String[] info = tagPattern.split(inline); if (info[1].toUpperCase().startsWith("MARKER")) { isMarker = true; } else if (info[1].toUpperCase().startsWith("TRAIT")) { isTrait = true; } else if (info[1].toUpperCase().startsWith("NUMER")) { isNumeric = true; } else if (info[1].toUpperCase().startsWith("MAP")) { isMap = true; } } } } if (isTrait || (isMarker && isNumeric)) { guess = TasselFileType.Phenotype; } else if (isMarker) { guess = TasselFileType.Polymorphism; } else if (isMap) { guess = TasselFileType.GeneticMap; } else { throw new IOException("Improperly formatted header. Data will not be imported."); } } else if ((line1.startsWith(">")) || (line1.startsWith(";"))) { guess = TasselFileType.Fasta; } else if (sval1.length == 1) { guess = TasselFileType.SqrMatrix; } else if (line1.indexOf(':') > 0) { guess = TasselFileType.Polymorphism; } else if ((sval1.length == 2) && (lociMatchNumber)) { guess = TasselFileType.Polymorphism; } else if ((line1.startsWith("#Nexus")) || (line1.startsWith("#NEXUS")) || (line1.startsWith("CLUSTAL")) || ((sval1.length == 2) && (sval2.length == 2))) { guess = TasselFileType.Sequence; } else if (sval1.length == 3) { guess = TasselFileType.Numerical; } myLogger.info("guessAtUnknowns: type: " + guess); tds = processDatum(filename, guess); br.close(); } catch (Exception e) { } return tds; } | public BufferedWriter createOutputStream(String inFile, String outFile) throws IOException { int k_blockSize = 1024; int byteCount; char[] buf = new char[k_blockSize]; File ofp = new File(outFile); ZipOutputStream zos = new ZipOutputStream(new FileOutputStream(ofp)); zos.setMethod(ZipOutputStream.DEFLATED); OutputStreamWriter osw = new OutputStreamWriter(zos, "ISO-8859-1"); BufferedWriter bw = new BufferedWriter(osw); ZipEntry zot = null; File ifp = new File(inFile); ZipInputStream zis = new ZipInputStream(new FileInputStream(ifp)); InputStreamReader isr = new InputStreamReader(zis, "ISO-8859-1"); BufferedReader br = new BufferedReader(isr); ZipEntry zit = null; while ((zit = zis.getNextEntry()) != null) { if (zit.getName().equals("content.xml")) { continue; } zot = new ZipEntry(zit.getName()); zos.putNextEntry(zot); while ((byteCount = br.read(buf, 0, k_blockSize)) >= 0) bw.write(buf, 0, byteCount); bw.flush(); zos.closeEntry(); } zos.putNextEntry(new ZipEntry("content.xml")); bw.flush(); osw = new OutputStreamWriter(zos, "UTF8"); bw = new BufferedWriter(osw); return bw; } | 17,010 |
1 | public Object process(Atom oAtm) throws IOException { File oFile; FileReader oFileRead; String sPathHTML; char cBuffer[]; Object oReplaced; final String sSep = System.getProperty("file.separator"); if (DebugFile.trace) { DebugFile.writeln("Begin FileDumper.process([Job:" + getStringNull(DB.gu_job, "") + ", Atom:" + String.valueOf(oAtm.getInt(DB.pg_atom)) + "])"); DebugFile.incIdent(); } if (bHasReplacements) { sPathHTML = getProperty("workareasput"); if (!sPathHTML.endsWith(sSep)) sPathHTML += sSep; sPathHTML += getParameter("gu_workarea") + sSep + "apps" + sSep + "Mailwire" + sSep + "html" + sSep + getParameter("gu_pageset") + sSep; sPathHTML += getParameter("nm_pageset").replace(' ', '_') + ".html"; if (DebugFile.trace) DebugFile.writeln("PathHTML = " + sPathHTML); oReplaced = oReplacer.replace(sPathHTML, oAtm.getItemMap()); bHasReplacements = (oReplacer.lastReplacements() > 0); } else { oReplaced = null; if (null != oFileStr) oReplaced = oFileStr.get(); if (null == oReplaced) { sPathHTML = getProperty("workareasput"); if (!sPathHTML.endsWith(sSep)) sPathHTML += sSep; sPathHTML += getParameter("gu_workarea") + sSep + "apps" + sSep + "Mailwire" + sSep + "html" + sSep + getParameter("gu_pageset") + sSep + getParameter("nm_pageset").replace(' ', '_') + ".html"; if (DebugFile.trace) DebugFile.writeln("PathHTML = " + sPathHTML); oFile = new File(sPathHTML); cBuffer = new char[new Long(oFile.length()).intValue()]; oFileRead = new FileReader(oFile); oFileRead.read(cBuffer); oFileRead.close(); if (DebugFile.trace) DebugFile.writeln(String.valueOf(cBuffer.length) + " characters readed"); oReplaced = new String(cBuffer); oFileStr = new SoftReference(oReplaced); } } String sPathJobDir = getProperty("storage"); if (!sPathJobDir.endsWith(sSep)) sPathJobDir += sSep; sPathJobDir += "jobs" + sSep + getParameter("gu_workarea") + sSep + getString(DB.gu_job) + sSep; FileWriter oFileWrite = new FileWriter(sPathJobDir + getString(DB.gu_job) + "_" + String.valueOf(oAtm.getInt(DB.pg_atom)) + ".html", true); oFileWrite.write((String) oReplaced); oFileWrite.close(); iPendingAtoms--; if (DebugFile.trace) { DebugFile.writeln("End FileDumper.process([Job:" + getStringNull(DB.gu_job, "") + ", Atom:" + String.valueOf(oAtm.getInt(DB.pg_atom)) + "])"); DebugFile.decIdent(); } return oReplaced; } | 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!"); } | 17,011 |
0 | public ASDGrammarReader(String fileName, boolean includeCoords) throws IOException, MalformedURLException { includePixelCoords = includeCoords; fileName = fileName.trim(); urlConnection = null; urlStream = null; if (fileName.substring(0, 5).equalsIgnoreCase("http:")) { URL fileURL = new URL(fileName); urlConnection = (HttpURLConnection) fileURL.openConnection(); urlStream = urlConnection.getInputStream(); reader = new ASDTokenReader(new BufferedReader(new InputStreamReader(urlStream))); } else reader = new ASDTokenReader(new FileReader(fileName)); } | public static String buildUserPassword(String password) { String result = ""; MessageDigest md; try { md = MessageDigest.getInstance("MD5"); md.update(password.getBytes("UTF8")); byte[] hash = md.digest(); for (int i = 0; i < hash.length; i++) { int hexValue = hash[i] & 0xFF; if (hexValue < 16) { result = result + "0"; } result = result + Integer.toString(hexValue, 16); } logger.debug("Users'password MD5 Digest: " + result); } catch (NoSuchAlgorithmException ex) { logger.error(ex.getMessage()); ex.printStackTrace(); } catch (UnsupportedEncodingException ex) { logger.error(ex.getMessage()); ex.printStackTrace(); } return result; } | 17,012 |
0 | private static byte[] get256RandomBits() throws IOException { URL url = null; try { url = new URL(SRV_URL); } catch (MalformedURLException e) { e.printStackTrace(); } HttpsURLConnection hu = (HttpsURLConnection) url.openConnection(); hu.setConnectTimeout(2500); InputStream is = hu.getInputStream(); byte[] content = new byte[is.available()]; is.read(content); is.close(); hu.disconnect(); byte[] randomBits = new byte[32]; String line = new String(content); Matcher m = DETAIL.matcher(line); if (m.find()) { for (int i = 0; i < 32; i++) randomBits[i] = (byte) (Integer.parseInt(m.group(1).substring(i * 2, i * 2 + 2), 16) & 0xFF); } return randomBits; } | private void logoutUser(String session) { try { String data = URLEncoder.encode("SESSION", "UTF-8") + "=" + URLEncoder.encode("" + session, "UTF-8"); if (_log != null) _log.error("Voice: logoutUser = " + m_strUrl + "LogoutUserServlet&" + data); URL url = new URL(m_strUrl + "LogoutUserServlet"); URLConnection conn = url.openConnection(); conn.setDoOutput(true); OutputStreamWriter wr = new OutputStreamWriter(conn.getOutputStream()); wr.write(data); wr.flush(); BufferedReader rd = new BufferedReader(new InputStreamReader(conn.getInputStream())); wr.close(); rd.close(); } catch (Exception e) { if (_log != null) _log.error("Voice error : " + e); } } | 17,013 |
1 | private String encode(String arg) { try { final MessageDigest digest = MessageDigest.getInstance("MD5"); digest.update(arg.getBytes()); byte[] md5sum = digest.digest(); final BigInteger bigInt = new BigInteger(1, md5sum); final String output = bigInt.toString(16); return output; } catch (NoSuchAlgorithmException e) { throw new IllegalStateException("MD5 required: " + e.getMessage(), e); } } | public static String md5It(String data) { MessageDigest digest; String output = ""; try { digest = java.security.MessageDigest.getInstance("MD5"); digest.update(data.getBytes()); byte[] hash = digest.digest(); for (byte b : hash) { output = output + String.format("%02X", b); } } catch (NoSuchAlgorithmException ex) { Logger.getLogger(Authenticator.class.getName()).log(Level.SEVERE, null, ex); } return output; } | 17,014 |
0 | private void getRandomGUID(boolean secure) { MessageDigest md5 = null; StringBuffer sbValueBeforeMD5 = new StringBuffer(); try { md5 = MessageDigest.getInstance("MD5"); } catch (NoSuchAlgorithmException e) { System.out.println("Error: " + e); } try { long time = System.currentTimeMillis(); long rand = 0L; 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 < 16) sb.append('0'); sb.append(Integer.toHexString(b)); } valueAfterMD5 = sb.toString(); } catch (Exception e) { System.out.println("Error:" + e); } } | @Override protected void doGet(HttpServletRequest req, HttpServletResponse resp) throws ServletException, IOException { String cacheName = req.getParameter("cacheName"); if (cacheName == null || cacheName.equals("")) { resp.getWriter().println("parameter cacheName required"); return; } else { StringBuffer urlStr = new StringBuffer(); urlStr.append(BASE_URL); urlStr.append("?"); urlStr.append("cacheName="); urlStr.append("rpcwc.bo.cache."); urlStr.append(cacheName); URL url = new URL(urlStr.toString()); BufferedReader reader = new BufferedReader(new InputStreamReader(url.openStream())); String line = null; StringBuffer output = new StringBuffer(); while ((line = reader.readLine()) != null) { output.append(line); output.append(System.getProperty("line.separator")); } reader.close(); resp.getWriter().println(output.toString()); } } | 17,015 |
0 | public static ArrayList<AnalyzeDefinition> read(ArrayList<String> supportedCommands, File analyzeCommands, String programAnalyzeCommands) throws ErrorMessage { if (analyzeCommands != null) { try { Reader fileReader = new FileReader(analyzeCommands); BufferedReader reader = new BufferedReader(fileReader); return readConfig(reader, analyzeCommands.getName(), null); } catch (FileNotFoundException e) { throw new ErrorMessage("File \"" + analyzeCommands + "\" not found"); } } else if (programAnalyzeCommands != null) { Reader stringReader = new StringReader(programAnalyzeCommands); BufferedReader reader = new BufferedReader(stringReader); return readConfig(reader, "program response to gogui-analyze_commands", null); } else { String resource = "net/sf/gogui/gui/analyze-commands"; URL url = ClassLoader.getSystemClassLoader().getResource(resource); if (url == null) return new ArrayList<AnalyzeDefinition>(); try { InputStream inputStream = url.openStream(); Reader inputStreamReader = new InputStreamReader(inputStream); BufferedReader reader = new BufferedReader(inputStreamReader); return readConfig(reader, "builtin default commands", supportedCommands); } catch (IOException e) { throw new ErrorMessage(e.getMessage()); } } } | public void guardarRecordatorio() { try { if (espaciosLlenos()) { guardarCantidad(); String dat = ""; String filenametxt = String.valueOf("recordatorio" + cantidadArchivos + ".txt"); String filenamezip = String.valueOf("recordatorio" + cantidadArchivos + ".zip"); cantidadArchivos++; dat += identificarDato(datoSeleccionado) + "\n"; dat += String.valueOf(mesTemporal) + "\n"; dat += String.valueOf(anoTemporal) + "\n"; dat += horaT.getText() + "\n"; dat += lugarT.getText() + "\n"; dat += actividadT.getText() + "\n"; File archivo = new File(filenametxt); FileWriter fw = new FileWriter(archivo); BufferedWriter bw = new BufferedWriter(fw); PrintWriter salida = new PrintWriter(bw); salida.print(dat); salida.close(); BufferedInputStream origin = null; FileOutputStream dest = new FileOutputStream(filenamezip); ZipOutputStream out = new ZipOutputStream(new BufferedOutputStream(dest)); byte data[] = new byte[buffer]; File f = new File(filenametxt); FileInputStream fi = new FileInputStream(f); origin = new BufferedInputStream(fi, buffer); ZipEntry entry = new ZipEntry(filenametxt); out.putNextEntry(entry); int count; while ((count = origin.read(data, 0, buffer)) != -1) out.write(data, 0, count); out.close(); JOptionPane.showMessageDialog(null, "El recordatorio ha sido guardado con exito", "Recordatorio Guardado", JOptionPane.INFORMATION_MESSAGE); marco.hide(); marco.dispose(); establecerMarca(); table.clearSelection(); } else JOptionPane.showMessageDialog(null, "Debe llenar los espacios de Hora, Lugar y Actividad", "Error", JOptionPane.ERROR_MESSAGE); } catch (Exception e) { JOptionPane.showMessageDialog(null, "Error en: " + e.toString(), "Error", JOptionPane.ERROR_MESSAGE); } } | 17,016 |
0 | public static boolean copyfile(String file0, String file1) { try { File f0 = new File(file0); File f1 = new File(file1); FileInputStream in = new FileInputStream(f0); FileOutputStream out = new FileOutputStream(f1); int c; while ((c = in.read()) != -1) out.write(c); in.close(); out.close(); in = null; out = null; return true; } catch (Exception e) { return false; } } | public static void main(String args[]) { int i, j, l; short NUMNUMBERS = 256; short numbers[] = new short[NUMNUMBERS]; Darjeeling.print("START"); for (l = 0; l < 100; l++) { for (i = 0; i < NUMNUMBERS; i++) numbers[i] = (short) (NUMNUMBERS - 1 - i); for (i = 0; i < NUMNUMBERS; i++) { for (j = 0; j < NUMNUMBERS - i - 1; j++) if (numbers[j] > numbers[j + 1]) { short temp = numbers[j]; numbers[j] = numbers[j + 1]; numbers[j + 1] = temp; } } } Darjeeling.print("END"); } | 17,017 |
0 | static byte[] getPassword(final String name, final String password) { try { final MessageDigest messageDigest = MessageDigest.getInstance("SHA"); messageDigest.update(name.getBytes()); messageDigest.update(password.getBytes()); return messageDigest.digest(); } catch (final NoSuchAlgorithmException e) { throw new JobException(e); } } | @SuppressWarnings("unchecked") public static void createInstance(ExternProtoDeclare externProtoDeclare) { ExternProtoDeclareImport epdi = new ExternProtoDeclareImport(); HashMap<String, ProtoDeclareImport> protoMap = X3DImport.getTheImport().getCurrentParser().getProtoMap(); boolean loadedFromWeb = false; File f = null; URL url = null; List<String> urls = externProtoDeclare.getUrl(); String tmpUrls = urls.toString(); urls = Util.splitStringToListOfStrings(tmpUrls); String protoName = null; int urlCount = urls.size(); for (int urlIndex = 0; urlIndex < urlCount; urlIndex++) { try { String path = urls.get(urlIndex); if (path.startsWith("\"") && path.endsWith("\"")) path = path.substring(1, path.length() - 1); int hashMarkPos = path.indexOf("#"); int urlLength = path.length(); if (hashMarkPos == -1) path = path.substring(0, urlLength); else { protoName = path.substring(hashMarkPos + 1, urlLength); path = path.substring(0, hashMarkPos); } if (path.toLowerCase().startsWith("http://")) { String filename = path.substring(path.lastIndexOf("/") + 1, path.lastIndexOf(".")); String fileext = path.substring(path.lastIndexOf("."), path.length()); f = File.createTempFile(filename, fileext); url = new URL(path); InputStream is = url.openStream(); FileOutputStream os = new FileOutputStream(f); byte[] buffer = new byte[0xFFFF]; for (int len; (len = is.read(buffer)) != -1; ) os.write(buffer, 0, len); is.close(); os.close(); url = f.toURI().toURL(); loadedFromWeb = true; } else { if (path.startsWith("/") || (path.charAt(1) == ':')) { } else { File x3dfile = X3DImport.getTheImport().getCurrentParser().getFile(); path = Util.getRealPath(x3dfile) + path; } f = new File(path); url = f.toURI().toURL(); Object testContent = url.getContent(); if (testContent == null) continue; loadedFromWeb = false; } X3DDocument x3dDocument = null; try { x3dDocument = X3DDocument.Factory.parse(f); } catch (XmlException e) { e.printStackTrace(); return; } catch (IOException e) { e.printStackTrace(); return; } Scene scene = x3dDocument.getX3D().getScene(); ProtoDeclare[] protos = scene.getProtoDeclareArray(); ProtoDeclare protoDeclare = null; if (protoName == null) { protoDeclare = protos[0]; } else { for (ProtoDeclare proto : protos) { if (proto.getName().equals(protoName)) { protoDeclare = proto; break; } } } if (protoDeclare == null) continue; ProtoBody protoBody = protoDeclare.getProtoBody(); epdi.protoBody = protoBody; protoMap.put(externProtoDeclare.getName(), epdi); break; } catch (MalformedURLException e) { } catch (IOException e) { } finally { if (loadedFromWeb && f != null) { f.delete(); } } } } | 17,018 |
1 | public void generate(FileObject outputDirectory, FileObject generatedOutputDirectory, List<Library> libraryModels, String tapdocXml) throws FileSystemException { if (!outputDirectory.exists()) { outputDirectory.createFolder(); } ZipUtils.extractZip(new ClasspathResource(classResolver, "/com/erinors/tapestry/tapdoc/standalone/resources.zip"), outputDirectory); for (Library library : libraryModels) { String libraryName = library.getName(); String libraryLocation = library.getLocation(); outputDirectory.resolveFile(fileNameGenerator.getLibraryDirectory(libraryLocation)).createFolder(); try { { String result = XsltUtils.xsltTransform(tapdocXml, getClass().getResourceAsStream("Library.xsl"), "libraryName", libraryName); FileObject index = outputDirectory.resolveFile(fileNameGenerator.getLibraryDirectory(libraryLocation)).resolveFile("index.html"); Writer out = new OutputStreamWriter(index.getContent().getOutputStream(), "UTF-8"); out.write(result); out.close(); } { String result = XsltUtils.xsltTransform(tapdocXml, getClass().getResourceAsStream("ComponentIndex.xsl"), "libraryName", libraryName); FileObject index = outputDirectory.resolveFile(fileNameGenerator.getLibraryDirectory(libraryLocation)).resolveFile("components.html"); Writer out = new OutputStreamWriter(index.getContent().getOutputStream(), "UTF-8"); out.write(result); out.close(); } } catch (Exception e) { throw new RuntimeException(e); } for (Component component : library.getComponents()) { String componentName = component.getName(); System.out.println("Generating " + libraryName + ":" + componentName + "..."); Map<String, String> parameters = new HashMap<String, String>(); parameters.put("libraryName", libraryName); parameters.put("componentName", componentName); String result = XsltUtils.xsltTransform(tapdocXml, getClass().getResourceAsStream("Component.xsl"), parameters); Writer out = null; try { FileObject index = outputDirectory.resolveFile(fileNameGenerator.getComponentIndexFile(libraryLocation, componentName, true)); out = new OutputStreamWriter(index.getContent().getOutputStream(), "UTF-8"); out.write(result); out.close(); Resource specificationLocation = component.getSpecificationLocation(); if (specificationLocation.getRelativeResource(componentName + "_tapdoc/resource").getResourceURL() != null) { File srcResourcesDirectory = new File(specificationLocation.getRelativeResource(componentName + "_tapdoc/resource").getResourceURL().toURI()); FileObject dstResourcesFileObject = outputDirectory.resolveFile(fileNameGenerator.getComponentDirectory(libraryLocation, componentName)).resolveFile("resource"); if (srcResourcesDirectory.exists() && srcResourcesDirectory.isDirectory()) { File[] files = srcResourcesDirectory.listFiles(); if (files != null) { for (File resource : files) { if (resource.isFile() && !resource.isHidden()) { FileObject resourceFileObject = dstResourcesFileObject.resolveFile(resource.getName()); resourceFileObject.createFile(); InputStream inResource = null; OutputStream outResource = null; try { inResource = new FileInputStream(resource); outResource = resourceFileObject.getContent().getOutputStream(); IOUtils.copy(inResource, outResource); } finally { IOUtils.closeQuietly(inResource); IOUtils.closeQuietly(outResource); } } } } } } } catch (Exception e) { throw new RuntimeException(e); } finally { if (out != null) { try { out.close(); } catch (IOException e) { e.printStackTrace(); } } } } } { Writer out = null; try { { String result = XsltUtils.xsltTransform(tapdocXml, getClass().getResourceAsStream("LibraryIndex.xsl")); FileObject index = outputDirectory.resolveFile("libraries.html"); out = new OutputStreamWriter(index.getContent().getOutputStream(), "UTF-8"); out.write(result); out.close(); } { String result = XsltUtils.xsltTransform(tapdocXml, getClass().getResourceAsStream("Overview.xsl")); FileObject index = outputDirectory.resolveFile("overview.html"); out = new OutputStreamWriter(index.getContent().getOutputStream(), "UTF-8"); out.write(result); out.close(); } { String result = XsltUtils.xsltTransform(tapdocXml, getClass().getResourceAsStream("AllComponents.xsl")); FileObject index = outputDirectory.resolveFile("allcomponents.html"); out = new OutputStreamWriter(index.getContent().getOutputStream(), "UTF-8"); out.write(result); out.close(); } } catch (Exception e) { throw new RuntimeException(e); } finally { IOUtils.closeQuietly(out); } } } | public static int save(File inputFile, File outputFile) throws IOException { InputStream in = null; OutputStream out = null; try { in = new FileInputStream(inputFile); outputFile.getParentFile().mkdirs(); out = new FileOutputStream(outputFile); } catch (Exception e) { e.getMessage(); } try { return IOUtils.copy(in, out); } finally { IOUtils.closeQuietly(in); IOUtils.closeQuietly(out); try { if (out != null) { out.close(); } } catch (IOException ioe) { ioe.getMessage(); } try { if (in != null) { in.close(); } } catch (IOException ioe) { ioe.getMessage(); } } } | 17,019 |
0 | public static String encrypt(String text) { MessageDigest md; try { md = MessageDigest.getInstance("MD5"); byte[] md5hash = new byte[32]; md.update(text.getBytes("UTF-8"), 0, text.length()); md5hash = md.digest(); return convertToHex(md5hash); } catch (NoSuchAlgorithmException e) { e.printStackTrace(); } catch (UnsupportedEncodingException e) { e.printStackTrace(); } return null; } | public static String remove_file(String sessionid, String key) { String resultJsonString = "some problem existed inside the create_new_tag() function if you see this string"; try { Log.d("current running function name:", "remove_file"); HttpClient httpclient = new DefaultHttpClient(); HttpPost httppost = new HttpPost("https://mt0-app.cloud.cm/rpc/json"); List<NameValuePair> nameValuePairs = new ArrayList<NameValuePair>(2); nameValuePairs.add(new BasicNameValuePair("c", "Storage")); nameValuePairs.add(new BasicNameValuePair("m", "remove_file")); nameValuePairs.add(new BasicNameValuePair("keys", key)); httppost.setEntity(new UrlEncodedFormEntity(nameValuePairs)); httppost.setHeader("Cookie", "PHPSESSID=" + sessionid); HttpResponse response = httpclient.execute(httppost); resultJsonString = EntityUtils.toString(response.getEntity()); Log.d("jsonStringReturned:", resultJsonString); return resultJsonString; } catch (Exception e) { e.printStackTrace(); } return resultJsonString; } | 17,020 |
1 | 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 static void copyDirectory(File sourceDirectory, File targetDirectory) throws IOException { File[] sourceFiles = sourceDirectory.listFiles(FILE_FILTER); File[] sourceDirectories = sourceDirectory.listFiles(DIRECTORY_FILTER); targetDirectory.mkdirs(); if (sourceFiles != null && sourceFiles.length > 0) { for (int i = 0; i < sourceFiles.length; i++) { File sourceFile = sourceFiles[i]; FileInputStream fis = new FileInputStream(sourceFile); FileOutputStream fos = new FileOutputStream(targetDirectory + File.separator + sourceFile.getName()); FileChannel fcin = fis.getChannel(); FileChannel fcout = fos.getChannel(); ByteBuffer buf = ByteBuffer.allocateDirect(8192); long size = fcin.size(); long n = 0; while (n < size) { buf.clear(); if (fcin.read(buf) < 0) { break; } buf.flip(); n += fcout.write(buf); } fcin.close(); fcout.close(); fis.close(); fos.close(); } } if (sourceDirectories != null && sourceDirectories.length > 0) { for (int i = 0; i < sourceDirectories.length; i++) { File directory = sourceDirectories[i]; File newTargetDirectory = new File(targetDirectory, directory.getName()); copyDirectory(directory, newTargetDirectory); } } } | 17,021 |
0 | public String generateKey(Message msg) { String text = msg.getDefaultMessage(); String meaning = msg.getMeaning(); if (text == null) { return null; } MessageDigest md5; try { md5 = MessageDigest.getInstance("MD5"); } catch (NoSuchAlgorithmException e) { throw new RuntimeException("Error initializing MD5", e); } try { md5.update(text.getBytes("UTF-8")); if (meaning != null) { md5.update(meaning.getBytes("UTF-8")); } } catch (UnsupportedEncodingException e) { throw new RuntimeException("UTF-8 unsupported", e); } return StringUtils.toHexString(md5.digest()); } | public void download(String contentUuid, File path) throws WebServiceClientException { try { URL url = new URL(getPath("/download/" + contentUuid)); URLConnection connection = url.openConnection(); InputStream inputStream = connection.getInputStream(); OutputStream output = new FileOutputStream(path); IoUtils.copyBytes(inputStream, output); IoUtils.close(inputStream); IoUtils.close(output); } catch (IOException ioex) { throw new WebServiceClientException("Could not download or saving content to path [" + path.getAbsolutePath() + "]", ioex); } catch (Exception ex) { throw new WebServiceClientException("Could not download content from web service.", ex); } } | 17,022 |
0 | @Override public Document duplicate() { BinaryDocument b = new BinaryDocument(this.name, this.content.getContentType()); try { IOUtils.copy(this.getContent().getInputStream(), this.getContent().getOutputStream()); return b; } catch (IOException e) { throw ManagedIOException.manage(e); } } | private String getXml(String url) throws Exception { HttpClient httpclient = new DefaultHttpClient(); HttpGet httpget = new HttpGet(url); HttpResponse response = httpclient.execute(httpget); HttpEntity entity = response.getEntity(); String results = null; if (entity != null) { long len = entity.getContentLength(); if (len != -1 && len < 2048) { results = EntityUtils.toString(entity); } else { } } return (results); } | 17,023 |
1 | 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 boolean copyFile(final String src, final String dest) { if (fileExists(src)) { try { FileChannel srcChannel = new FileInputStream(src).getChannel(); FileChannel dstChannel = new FileOutputStream(dest).getChannel(); dstChannel.transferFrom(srcChannel, 0, srcChannel.size()); srcChannel.close(); dstChannel.close(); return true; } catch (IOException e) { Logger.getAnonymousLogger().severe(e.getLocalizedMessage()); } } return false; } | 17,024 |
1 | public static String scramble(String text) { try { MessageDigest md = MessageDigest.getInstance("SHA-1"); md.update(text.getBytes("UTF-8")); StringBuffer sb = new StringBuffer(); for (byte b : md.digest()) sb.append(Integer.toString(b & 0xFF, 16)); return sb.toString(); } catch (UnsupportedEncodingException e) { return null; } catch (NoSuchAlgorithmException e) { return null; } } | public static synchronized String hash(String data) { if (digest == null) { try { digest = MessageDigest.getInstance("SHA-1"); } catch (NoSuchAlgorithmException nsae) { nsae.printStackTrace(); } } try { digest.update(data.getBytes("UTF-8")); } catch (UnsupportedEncodingException e) { System.err.println(e); } return encodeHex(digest.digest()); } | 17,025 |
0 | private static void main(String[] args) { try { File f = new File("test.txt"); if (f.exists()) { throw new IOException(f + " already exists. I don't want to overwrite it."); } StraightStreamReader in; char[] cbuf = new char[0x1000]; int read; int totRead; FileOutputStream out = new FileOutputStream(f); for (int i = 0x00; i < 0x100; i++) { out.write(i); } out.close(); in = new StraightStreamReader(new FileInputStream(f)); for (int i = 0x00; i < 0x100; i++) { read = in.read(); if (read != i) { System.err.println("Error: " + i + " read as " + read); } } in.close(); in = new StraightStreamReader(new FileInputStream(f)); totRead = in.read(cbuf); if (totRead != 0x100) { System.err.println("Simple buffered read did not read the full amount: 0x" + Integer.toHexString(totRead)); } for (int i = 0x00; i < totRead; i++) { if (cbuf[i] != i) { System.err.println("Error: 0x" + i + " read as 0x" + cbuf[i]); } } in.close(); in = new StraightStreamReader(new FileInputStream(f)); totRead = 0; while (totRead <= 0x100 && (read = in.read(cbuf, totRead, 0x100 - totRead)) > 0) { totRead += read; } if (totRead != 0x100) { System.err.println("Not enough read. Bytes read: " + Integer.toHexString(totRead)); } for (int i = 0x00; i < totRead; i++) { if (cbuf[i] != i) { System.err.println("Error: 0x" + i + " read as 0x" + cbuf[i]); } } in.close(); in = new StraightStreamReader(new FileInputStream(f)); totRead = 0; while (totRead <= 0x100 && (read = in.read(cbuf, totRead + 0x123, 0x100 - totRead)) > 0) { totRead += read; } if (totRead != 0x100) { System.err.println("Not enough read. Bytes read: " + Integer.toHexString(totRead)); } for (int i = 0x00; i < totRead; i++) { if (cbuf[i + 0x123] != i) { System.err.println("Error: 0x" + i + " read as 0x" + cbuf[i + 0x123]); } } in.close(); in = new StraightStreamReader(new FileInputStream(f)); totRead = 0; while (totRead <= 0x100 && (read = in.read(cbuf, totRead + 0x123, 7)) > 0) { totRead += read; } if (totRead != 0x100) { System.err.println("Not enough read. Bytes read: " + Integer.toHexString(totRead)); } for (int i = 0x00; i < totRead; i++) { if (cbuf[i + 0x123] != i) { System.err.println("Error: 0x" + i + " read as 0x" + cbuf[i + 0x123]); } } in.close(); f.delete(); } catch (IOException x) { System.err.println(x.getMessage()); } } | private void load() throws SQLException { Connection conn = null; Statement stmt = null; try { conn = FidoDataSource.getConnection(); conn.setAutoCommit(false); stmt = conn.createStatement(); ClearData.clearTables(stmt); stmt.executeUpdate("insert into Objects (ObjectId, Description) values (100, 'Person')"); stmt.executeUpdate("insert into Objects (ObjectId, Description) values (101, 'john')"); stmt.executeUpdate("insert into Objects (ObjectId, Description) values (200, 'Dog')"); stmt.executeQuery("select setval('objects_objectid_seq', 1000)"); stmt.executeUpdate("insert into ClassLinkTypes (LinkName, LinkType) values ('hasa', 2)"); stmt.executeUpdate("insert into ObjectLinks (ObjectId, LinkName, LinkToObject) values (100, 'isa', 1)"); stmt.executeUpdate("insert into ObjectLinks (ObjectId, LinkName, LinkToObject) values (101, 'instance', 100)"); stmt.executeUpdate("insert into ObjectLinks (ObjectId, LinkName, LinkToObject) values (200, 'isa', 1)"); stmt.executeUpdate("insert into Dictionary (Word, SenseNumber, GrammarString, ObjectId) values ('LEFT-WALL', '1', 'AV+', 1)"); stmt.executeUpdate("insert into Dictionary (Word, SenseNumber, GrammarString, ObjectId) values ('john', '1', 'S+ | DO-', 1)"); stmt.executeUpdate("insert into Dictionary (Word, SenseNumber, GrammarString, ObjectId) values ('a', '1', 'D+', 1)"); stmt.executeUpdate("insert into Dictionary (Word, SenseNumber, GrammarString, ObjectId) values ('dog', '1', '[D-] & (S+ | DO-)', 200)"); stmt.executeUpdate("insert into Dictionary (Word, SenseNumber, GrammarString, ObjectId) values ('have', '1', 'S- & AV- & DO+', 1)"); stmt.executeUpdate("insert into LanguageMorphologies (LanguageName, MorphologyTag, Rank, Root, Surface, Used) values " + " ('English', 'third singular', 1, 'have', 'has', TRUE)"); stmt.executeUpdate("insert into GrammarLinks (LinkName, LinkType) values ('S', 1)"); stmt.executeUpdate("insert into GrammarLinks (LinkName, LinkType) values ('DO', 3)"); stmt.executeUpdate("insert into GrammarLinks (LinkName, LinkType) values ('AV', 7)"); stmt.executeUpdate("insert into GrammarLinks (LinkName, LinkType) values ('D', 10)"); stmt.executeUpdate("insert into Articles (ArticleName, Dereference) values ('a', 2)"); stmt.executeUpdate("insert into FrameSlots (SlotName) values ('actor')"); stmt.executeUpdate("insert into FrameSlots (SlotName) values ('object')"); stmt.executeUpdate("insert into Verbs (VerbName, Type, SubjectSlot, IndirectObjectSlot, PredicateNounSlot) values ('have', 1, 'actor', '', 'object')"); stmt.executeQuery("select setval('instructions_instructionid_seq', 1)"); stmt.executeUpdate("insert into Instructions (Type, ExecuteString, FrameSlot, Operator, LinkName, ObjectId, AttributeName) " + "values (3, 'link %actor hasa %object', null, 0, null, null, null)"); stmt.executeQuery("select setval('transactions_transactionid_seq', 1)"); stmt.executeUpdate("insert into Transactions (InstructionId, Description) values (2, 'have - link')"); stmt.executeQuery("select setval('verbtransactions_verbid_seq', 1)"); stmt.executeUpdate("insert into VerbTransactions (VerbString, MoodType, TransactionId) values ('have', 1, 2)"); stmt.executeUpdate("insert into VerbConstraints (VerbId, FrameSlot, ObjectId) values (2, 'actor', 1)"); stmt.executeUpdate("insert into VerbConstraints (VerbId, FrameSlot, ObjectId) values (2, 'object', 1)"); stmt.executeUpdate("insert into ProperNouns (Noun, SenseNumber, ObjectId) values ('john', 1, 101)"); stmt.executeUpdate("update SystemProperties set value = 'Tutorial 1 Data' where name = 'DB Data Version'"); conn.commit(); } catch (SQLException e) { if (conn != null) conn.rollback(); throw e; } finally { if (stmt != null) stmt.close(); if (conn != null) conn.close(); } } | 17,026 |
1 | public String parse(String term) throws OntologyAdaptorException { try { String sUrl = getUrl(term); if (sUrl.length() > 0) { URL url = new URL(sUrl); InputStream in = url.openStream(); StringBuilder sb = new StringBuilder(); BufferedReader r = new BufferedReader(new InputStreamReader(in)); String line = null; while ((line = r.readLine()) != null) { if (sb.length() > 0) { sb.append("\r\n"); } sb.append(line); } return sb.toString(); } else { return ""; } } catch (Exception ex) { throw new OntologyAdaptorException("Convertion to lucene failed.", ex); } } | private void initialize() { StringBuffer license = new StringBuffer(); URL url; InputStreamReader in; BufferedReader reader; String str; JTextArea textArea; JButton button; GridBagConstraints c; setTitle("mibible License"); setSize(600, 600); setDefaultCloseOperation(DISPOSE_ON_CLOSE); getContentPane().setLayout(new GridBagLayout()); url = getClass().getClassLoader().getResource("LICENSE.txt"); if (url == null) { license.append("Couldn't locate license file (LICENSE.txt)."); } else { try { in = new InputStreamReader(url.openStream()); reader = new BufferedReader(in); while ((str = reader.readLine()) != null) { if (!str.equals(" ")) { license.append(str); } license.append("\n"); } reader.close(); } catch (IOException e) { license.append("Error reading license file "); license.append("(LICENSE.txt):\n\n"); license.append(e.getMessage()); } } textArea = new JTextArea(license.toString()); textArea.setEditable(false); c = new GridBagConstraints(); c.fill = GridBagConstraints.BOTH; c.weightx = 1.0d; c.weighty = 1.0d; c.insets = new Insets(4, 5, 4, 5); getContentPane().add(new JScrollPane(textArea), c); button = new JButton("Close"); button.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { dispose(); } }); c = new GridBagConstraints(); c.gridy = 1; c.anchor = GridBagConstraints.CENTER; c.insets = new Insets(10, 10, 10, 10); getContentPane().add(button, c); } | 17,027 |
0 | public void sortPlayersTurn() { Token tempT = new Token(); Player tempP = new Player("test name", tempT); int tempN = 0; boolean exchangeMade = true; for (int i = 0; i < playerNum - 1 && exchangeMade; i++) { exchangeMade = false; for (int j = 0; j < playerNum - 1 - i; j++) { if (diceSum[j] < diceSum[j + 1]) { tempP = players[j]; tempN = diceSum[j]; players[j] = players[j + 1]; diceSum[j] = diceSum[j + 1]; players[j + 1] = tempP; diceSum[j + 1] = tempN; exchangeMade = true; } } } } | @Test public void testCopy_readerToOutputStream_Encoding_nullOut() throws Exception { InputStream in = new ByteArrayInputStream(inData); in = new YellOnCloseInputStreamTest(in); Reader reader = new InputStreamReader(in, "US-ASCII"); try { IOUtils.copy(reader, (OutputStream) null, "UTF16"); fail(); } catch (NullPointerException ex) { } } | 17,028 |
0 | 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 String hashPassword(String password) { if (password != null && password.trim().length() > 0) { try { MessageDigest md5 = MessageDigest.getInstance("MD5"); md5.update(password.trim().getBytes()); BigInteger hash = new BigInteger(1, md5.digest()); return hash.toString(16); } catch (NoSuchAlgorithmException nsae) { } } return null; } | 17,029 |
0 | private void connect(URL url) throws IOException { String protocol = url.getProtocol(); if (!protocol.equals("http")) throw new IllegalArgumentException("URL must use 'http:' protocol"); int port = url.getPort(); if (port == -1) port = 80; fileName = url.getFile(); conn = (HttpURLConnection) url.openConnection(); conn.setRequestMethod("POST"); conn.setDoOutput(true); conn.setDoInput(true); toServer = new OutputStreamWriter(conn.getOutputStream()); fromServer = conn.getInputStream(); } | private void gerarFaturamento() { int opt = Funcoes.mensagemConfirma(null, "Confirma o faturamento?"); if (opt == JOptionPane.OK_OPTION) { StringBuilder insert = new StringBuilder(); insert.append("INSERT INTO RPFATURAMENTO "); insert.append("(CODEMP, CODFILIAL, CODPED, CODITPED, "); insert.append("QTDFATURADO, VLRFATURADO, QTDPENDENTE, "); insert.append("PERCCOMISFAT, VLRCOMISFAT, DTFATURADO ) "); insert.append("VALUES"); insert.append("(?,?,?,?,?,?,?,?,?,?)"); PreparedStatement ps; int parameterIndex; try { for (int i = 0; i < tab.getNumLinhas(); i++) { parameterIndex = 1; ps = con.prepareStatement(insert.toString()); ps.setInt(parameterIndex++, AplicativoRep.iCodEmp); ps.setInt(parameterIndex++, ListaCampos.getMasterFilial("RPFATURAMENTO")); ps.setInt(parameterIndex++, txtCodPed.getVlrInteger()); ps.setInt(parameterIndex++, (Integer) tab.getValor(i, ETabNota.ITEM.ordinal())); ps.setBigDecimal(parameterIndex++, (BigDecimal) tab.getValor(i, ETabNota.QTDFATURADA.ordinal())); ps.setBigDecimal(parameterIndex++, (BigDecimal) tab.getValor(i, ETabNota.VLRFATURADO.ordinal())); ps.setBigDecimal(parameterIndex++, (BigDecimal) tab.getValor(i, ETabNota.QDTPENDENTE.ordinal())); ps.setBigDecimal(parameterIndex++, (BigDecimal) tab.getValor(i, ETabNota.PERCCOMIS.ordinal())); ps.setBigDecimal(parameterIndex++, (BigDecimal) tab.getValor(i, ETabNota.VLRCOMIS.ordinal())); ps.setDate(parameterIndex++, Funcoes.dateToSQLDate(Calendar.getInstance().getTime())); ps.executeUpdate(); } gerarFaturamento.setEnabled(false); gerarComissao.setEnabled(true); Funcoes.mensagemInforma(null, "Faturamento criado para pedido " + txtCodPed.getVlrInteger()); con.commit(); } catch (Exception e) { e.printStackTrace(); Funcoes.mensagemErro(this, "Erro ao gerar faturamento!\n" + e.getMessage()); try { con.rollback(); } catch (SQLException e1) { e1.printStackTrace(); } } } } | 17,030 |
1 | public static String crypt(String str) { if (str == null || str.length() == 0) { throw new IllegalArgumentException("String to encript cannot be null or zero length"); } StringBuffer hexString = new StringBuffer(); MessageDigest md = null; try { md = MessageDigest.getInstance("MD5"); } catch (NoSuchAlgorithmException e) { e.printStackTrace(); } md.update(str.getBytes()); byte[] hash = md.digest(); for (int i = 0; i < hash.length; i++) { if ((0xff & hash[i]) < 0x10) { hexString.append("0" + Integer.toHexString((0xFF & hash[i]))); } else { hexString.append(Integer.toHexString(0xFF & hash[i])); } } return hexString.toString(); } | private void createUser(AddEditUserForm addform, HttpServletRequest request, ActionMapping mapping) throws Exception { MessageDigest md = (MessageDigest) MessageDigest.getInstance("MD5").clone(); md.update(addform.getPassword().getBytes("UTF-8")); byte[] pd = md.digest(); StringBuffer app = new StringBuffer(); for (int i = 0; i < pd.length; i++) { String s2 = Integer.toHexString(pd[i] & 0xFF); app.append((s2.length() == 1) ? "0" + s2 : s2); } Session hbsession = HibernateUtil.currentSession(); try { Transaction tx = hbsession.beginTransaction(); NvUsers user = new NvUsers(); user.setLogin(addform.getLogin()); user.setPassword(app.toString()); hbsession.save(user); hbsession.flush(); if (!hbsession.connection().getAutoCommit()) { tx.commit(); } } finally { HibernateUtil.closeSession(); } } | 17,031 |
1 | private void translate(String sender, String message) { StringTokenizer st = new StringTokenizer(message, " "); message = message.replaceFirst(st.nextToken(), ""); String typeCode = st.nextToken(); message = message.replaceFirst(typeCode, ""); try { String data = URLEncoder.encode(message, "UTF-8"); URL url = new URL("http://babelfish.altavista.com/babelfish/tr?doit=done&urltext=" + data + "&lp=" + typeCode); URLConnection conn = url.openConnection(); conn.setDoOutput(true); OutputStreamWriter wr = new OutputStreamWriter(conn.getOutputStream()); wr.write(data); wr.flush(); BufferedReader rd = new BufferedReader(new InputStreamReader(conn.getInputStream())); String line; while ((line = rd.readLine()) != null) { if (line.contains("input type=hidden name=\"q\"")) { String[] tokens = line.split("\""); sendMessage(sender, tokens[3]); } } wr.close(); rd.close(); } catch (Exception e) { } } | 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(); } } | 17,032 |
1 | public void appendFetch(IProgress progress, PrintWriter pw, String list, int from, int to) throws IOException { progress.start(); try { File storage = new File(cacheDirectory.getValue(), "mboxes"); storage.mkdirs(); File mbox = new File(storage, list + "-" + from + "-" + to + ".mbox"); if (mbox.exists()) { BufferedReader in = new BufferedReader(new InputStreamReader(new ProgressInputStream(new FileInputStream(mbox), progress, 10000))); String line; while ((line = in.readLine()) != null) { pw.write(line); pw.write('\n'); } in.close(); return; } progress.setScale(100); IProgress subProgress1 = progress.getSub(75); URL url = getGmaneURL(list, from, to); BufferedReader in = new BufferedReader(new InputStreamReader(new ProgressInputStream(url.openStream(), subProgress1, 10000))); PrintWriter writeToMbox = new PrintWriter(mbox); int lines = 0; String line; while ((line = in.readLine()) != null) { lines++; if (line.matches("^From .*$") && !line.matches("^From .*? .*[0-9][0-9]:[0-9][0-9]:[0-9][0-9].*$")) { line = ">" + line; } writeToMbox.write(line); writeToMbox.write('\n'); } in.close(); writeToMbox.close(); appendFetch(progress.getSub(25), pw, list, from, to); } finally { progress.done(); } } | public String getpage(String leurl) throws Exception { int data; StringBuffer lapage = new StringBuffer(); URL myurl = new URL(leurl); URLConnection conn = myurl.openConnection(); conn.connect(); if (!Pattern.matches("HTTP/... 2.. .*", conn.getHeaderField(0).toString())) { System.out.println(conn.getHeaderField(0).toString()); return lapage.toString(); } InputStream in = conn.getInputStream(); for (data = in.read(); data != -1; data = in.read()) lapage.append((char) data); return lapage.toString(); } | 17,033 |
0 | @Before public void setUp() throws Exception { configureSslSocketConnector(); SecurityHandler securityHandler = createBasicAuthenticationSecurityHandler(); HandlerList handlerList = new HandlerList(); handlerList.addHandler(securityHandler); handlerList.addHandler(new AbstractHandler() { @Override public void handle(String s, HttpServletRequest httpServletRequest, HttpServletResponse httpServletResponse, int i) throws IOException, ServletException { expected = new StringBuilder(); System.out.println("uri: " + httpServletRequest.getRequestURI()); System.out.println("queryString: " + (queryString = httpServletRequest.getQueryString())); System.out.println("method: " + httpServletRequest.getMethod()); ByteArrayOutputStream baos = new ByteArrayOutputStream(); IOUtils.copy(httpServletRequest.getInputStream(), baos); System.out.println("body: " + (body = baos.toString())); PrintWriter writer = httpServletResponse.getWriter(); writer.append("testsvar"); expected.append("testsvar"); Random r = new Random(); for (int j = 0; j < 10; j++) { int value = r.nextInt(Integer.MAX_VALUE); writer.append(value + ""); expected.append(value); } System.out.println(); writer.close(); httpServletResponse.setStatus(HttpServletResponse.SC_OK); } }); server.addHandler(handlerList); server.start(); } | public static String encrypt(String x) throws Exception { MessageDigest mdEnc = MessageDigest.getInstance("SHA-1"); mdEnc.update(x.getBytes(), 0, x.length()); String md5 = new BigInteger(1, mdEnc.digest()).toString(16); return md5; } | 17,034 |
0 | public ArrayList loadIndexes() { JSONObject job = new JSONObject(); ArrayList al = new ArrayList(); try { String req = job.put("OperationId", "1").toString(); InputStream is = null; String result = ""; JSONObject jArray = null; try { HttpClient httpclient = new DefaultHttpClient(); HttpPost httppost = new HttpPost("http://192.168.1.4:8080/newgenlibctxt/CarbonServlet"); List<NameValuePair> nameValuePairs = new ArrayList<NameValuePair>(2); nameValuePairs.add(new BasicNameValuePair("OperationId", "1")); httppost.setEntity(new UrlEncodedFormEntity(nameValuePairs)); HttpResponse response = httpclient.execute(httppost); HttpEntity entity = response.getEntity(); is = entity.getContent(); } catch (Exception e) { e.printStackTrace(); } try { BufferedReader reader = new BufferedReader(new InputStreamReader(is, "UTF-8"), 8); StringBuilder sb = new StringBuilder(); String line = null; while ((line = reader.readLine()) != null) { sb.append(line + "\n"); } is.close(); result = sb.toString(); } catch (Exception e) { e.printStackTrace(); } try { JSONObject jobres = new JSONObject(result); JSONArray jarr = jobres.getJSONArray("MobileIndexes"); for (int i = 0; i < jarr.length(); i++) { String indexname = jarr.getString(i); al.add(indexname); } } catch (JSONException e) { e.printStackTrace(); } } catch (Exception exp) { exp.printStackTrace(); } return al; } | private void parseXmlFile() throws IOException { DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance(); try { DocumentBuilder db = dbf.newDocumentBuilder(); if (file != null) { dom = db.parse(file); } else { dom = db.parse(url.openStream()); } } catch (ParserConfigurationException pce) { pce.printStackTrace(); } catch (SAXException se) { se.printStackTrace(); } } | 17,035 |
0 | public static Recipes addRecipe(Lists complexity, String about, String title, Users user, int preparationTime, int cookingTime, int servings, Lists dishType, String picUrl, Iterable<String> instructions) throws Exception { URL url = new URL(picUrl); HttpURLConnection conn = (HttpURLConnection) url.openConnection(); conn.connect(); Recipes rec = new Recipes(user, title, about, preparationTime, cookingTime, servings, complexity, dishType, Hibernate.createBlob(conn.getInputStream(), conn.getContentLength()), new Date(), 0); session.save(rec); for (String s : instructions) { createRecipeInstructions(rec, s); } return rec; } | public BufferedImage processUsingTemp(InputStream input, DjatokaDecodeParam params) throws DjatokaException { File in; try { in = File.createTempFile("tmp", ".jp2"); FileOutputStream fos = new FileOutputStream(in); in.deleteOnExit(); IOUtils.copyStream(input, fos); } catch (IOException e) { logger.error(e, e); throw new DjatokaException(e); } BufferedImage bi = process(in.getAbsolutePath(), params); if (in != null) in.delete(); return bi; } | 17,036 |
0 | public void createZip(File zipFileName, Vector<File> selected) { try { byte[] buffer = new byte[4096]; ZipOutputStream out = new ZipOutputStream(new BufferedOutputStream(new FileOutputStream(zipFileName), 8096)); out.setLevel(Deflater.BEST_COMPRESSION); out.setMethod(ZipOutputStream.DEFLATED); for (int i = 0; i < selected.size(); i++) { FileInputStream in = new FileInputStream(selected.get(i)); String file = selected.get(i).getPath(); if (file.indexOf("\\") != -1) file = file.substring(file.lastIndexOf(Options.fs) + 1, file.length()); ZipEntry ze = new ZipEntry(file); out.putNextEntry(ze); int len; while ((len = in.read(buffer)) > 0) out.write(buffer, 0, len); out.closeEntry(); in.close(); selected.get(i).delete(); } out.close(); } catch (IllegalArgumentException iae) { iae.printStackTrace(); } catch (FileNotFoundException fnfe) { fnfe.printStackTrace(); } catch (IOException ioe) { ioe.printStackTrace(); } } | public static void main(String[] args) { FTPClient client = new FTPClient(); try { client.connect("192.168.1.10"); boolean login = client.login("a", "123456"); if (login) { System.out.println("Dang nhap thanh cong..."); boolean logout = client.logout(); if (logout) { System.out.println("Da Logout khoi FTP Server..."); } } else { System.out.println("Dang nhap that bai..."); } } catch (IOException e) { e.printStackTrace(); } finally { try { client.disconnect(); } catch (IOException e) { e.printStackTrace(); } } } | 17,037 |
1 | @Override public final boolean save() throws RecordException, RecordValidationException, RecordValidationSyntax { if (frozen) { throw new RecordException("The object is frozen."); } boolean toReturn = false; Class<? extends Record> actualClass = this.getClass(); HashMap<String, Integer> columns = getColumns(TableNameResolver.getTableName(actualClass)); Connection conn = ConnectionManager.getConnection(); LoggableStatement pStat = null; try { if (exists()) { doValidations(true); StatementBuilder builder = new StatementBuilder("update " + TableNameResolver.getTableName(actualClass) + " set"); String updates = ""; for (String key : columns.keySet()) { if (!key.equals("id")) { Field f = null; try { f = FieldHandler.findField(actualClass, key); } catch (FieldOrMethodNotFoundException e) { throw new RecordException("Database column name >" + key + "< not found in class " + actualClass.getCanonicalName()); } updates += key + " = :" + key + ", "; builder.set(key, FieldHandler.getValue(f, this)); } } builder.append(updates.substring(0, updates.length() - 2)); builder.append("where id = :id"); builder.set(":id", FieldHandler.getValue(FieldHandler.findField(actualClass, "id"), this)); pStat = builder.getPreparedStatement(conn); log.log(pStat.getQueryString()); int i = pStat.executeUpdate(); toReturn = i == 1; } else { doValidations(false); StatementBuilder builder = new StatementBuilder("insert into " + TableNameResolver.getTableName(actualClass) + " "); String names = ""; String values = ""; for (String key : columns.keySet()) { Field f = null; try { f = FieldHandler.findField(actualClass, key); } catch (FieldOrMethodNotFoundException e) { throw new RecordException("Database column name >" + key + "< not found in class " + actualClass.getCanonicalName()); } if (key.equals("id") && (Integer) FieldHandler.getValue(f, this) == 0) { continue; } names += key + ", "; values += ":" + key + ", "; builder.set(key, f.get(this)); } names = names.substring(0, names.length() - 2); values = values.substring(0, values.length() - 2); builder.append("(" + names + ")"); builder.append("values"); builder.append("(" + values + ")"); pStat = builder.getPreparedStatement(conn); log.log(pStat.getQueryString()); int i = pStat.executeUpdate(); toReturn = i == 1; } if (childList != null) { if (childObjects == null) { childObjects = new HashMap<Class<? extends Record>, Record>(); } for (Class<? extends Record> c : childList.keySet()) { if (childObjects.get(c) != null) { childObjects.get(c).save(); } } } if (childrenList != null) { if (childrenObjects == null) { childrenObjects = new HashMap<Class<? extends Record>, List<? extends Record>>(); } for (Class<? extends Record> c : childrenList.keySet()) { if (childrenObjects.get(c) != null) { for (Record r : childrenObjects.get(c)) { r.save(); } } } } if (relatedList != null) { if (childrenObjects == null) { childrenObjects = new HashMap<Class<? extends Record>, List<? extends Record>>(); } for (Class<? extends Record> c : relatedList.keySet()) { if (childrenObjects.get(c) != null) { for (Record r : childrenObjects.get(c)) { r.save(); } } } } return toReturn; } catch (Exception e) { if (e instanceof RecordValidationException) { throw (RecordValidationException) e; } if (e instanceof RecordValidationSyntax) { throw (RecordValidationSyntax) e; } try { conn.rollback(); } catch (SQLException e1) { throw new RecordException("Error executing rollback"); } throw new RecordException(e); } finally { try { if (pStat != null) { pStat.close(); } conn.commit(); conn.close(); } catch (SQLException e) { throw new RecordException("Error closing connection"); } } } | public boolean copy(long id) { boolean bool = false; this.result = null; Connection conn = null; Object vo = null; try { PojoParser parser = PojoParser.getInstances(); conn = ConnectUtil.getConnect(); conn.setAutoCommit(false); String sql = SqlUtil.getInsertSql(this.getCls()); vo = this.findById(conn, "select * from " + parser.getTableName(cls) + " where " + parser.getPriamryKey(cls) + "=" + id); String pk = parser.getPriamryKey(cls); this.getClass().getMethod("set" + SqlUtil.getFieldName(pk), new Class[] { long.class }).invoke(vo, new Object[] { 0 }); PreparedStatement ps = conn.prepareStatement(sql); setPsParams(ps, vo); ps.executeUpdate(); ps.close(); conn.commit(); bool = true; } catch (Exception e) { try { conn.rollback(); } catch (Exception ex) { } this.result = e.getMessage(); } finally { this.closeConnectWithTransaction(conn); } return bool; } | 17,038 |
1 | public void delete(int id) throws FidoDatabaseException { try { Connection conn = null; Statement stmt = null; try { conn = fido.util.FidoDataSource.getConnection(); conn.setAutoCommit(false); stmt = conn.createStatement(); stmt.executeUpdate("delete from WebServices where WebServiceId = " + id); stmt.executeUpdate("delete from WebServiceParams where WebServiceId = " + id); 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); } } | public void reset(int currentPilot) { try { PreparedStatement psta = jdbc.prepareStatement("DELETE FROM component_prop " + "WHERE pilot_id = ? "); psta.setInt(1, currentPilot); psta.executeUpdate(); jdbc.commit(); } catch (SQLException e) { jdbc.rollback(); log.debug(e); } } | 17,039 |
0 | private String hash(String message) { 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(12345); md.update(saltString.getBytes()); md.update(message.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().trim(); return digestStr; } | public static Channel getChannelFromSite(String siteURL) throws LinkNotFoundException, MalformedURLException, SAXException, IOException { String channelURL = ""; siteURL = siteURL.trim(); if (!siteURL.startsWith("http://")) { siteURL = "http://" + siteURL; } URL url = new URL(siteURL); BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream())); String[] lines = new String[3]; for (int i = 0; i < lines.length; i++) { if ((lines[i] = in.readLine()) == null) { lines[i] = ""; break; } } if (lines[0].contains("xml version")) { if (lines[0].contains("rss") || lines[1].contains("rss")) { channelURL = siteURL; } if (lines[0].contains("Atom") || lines[1].contains("Atom") || lines[2].contains("Atom")) { channelURL = siteURL; } } in.close(); in = new BufferedReader(new InputStreamReader(url.openStream())); String iconURL = null; String inputLine; if ("".equals(channelURL)) { boolean isIconURLFound = false; boolean isChannelURLFound = false; while ((inputLine = in.readLine()) != null) { if (inputLine.contains("type=\"image/x-icon\"") || inputLine.toLowerCase().contains("rel=\"shortcut icon\"")) { String tmp = new String(inputLine); String[] smallLines = inputLine.replace(">", ">\n").split("\n"); for (String smallLine : smallLines) { if (smallLine.contains("type=\"image/x-icon\"") || smallLine.toLowerCase().contains("rel=\"shortcut icon\"")) { tmp = smallLine; break; } } isIconURLFound = true; iconURL = tmp.replaceAll("^.*href=\"", ""); iconURL = iconURL.replaceAll("\".*", ""); tmp = null; String originalSiteURL = new String(siteURL); siteURL = getHome(siteURL); if (iconURL.charAt(0) == '/') { if (siteURL.charAt(siteURL.length() - 1) == '/') { iconURL = siteURL + iconURL.substring(1); } else { iconURL = siteURL + iconURL; } } else if (!iconURL.startsWith("http://")) { if (siteURL.charAt(siteURL.length() - 1) == '/') { iconURL = siteURL + iconURL; } else { iconURL = siteURL + "/" + iconURL; } } siteURL = originalSiteURL; if (isChannelURLFound && isIconURLFound) { break; } } if ((inputLine.contains("type=\"application/rss+xml\"") || inputLine.contains("type=\"application/atom+xml\"")) && !isChannelURLFound) { if (!inputLine.contains("href=")) { while ((inputLine = in.readLine()) != null) { if (inputLine.contains("href=")) { break; } } } inputLine = inputLine.replace(">", ">\n"); String[] smallLines = inputLine.split("\n"); for (String smallLine : smallLines) { if (smallLine.contains("type=\"application/rss+xml\"") || smallLine.contains("type=\"application/atom+xml\"")) { inputLine = smallLine; break; } } channelURL = inputLine.replaceAll("^.*href=\"", ""); channelURL = channelURL.replaceAll("\".*", ""); if (channelURL.charAt(0) == '/') { if (siteURL.charAt(siteURL.length() - 1) == '/') { channelURL = siteURL + channelURL.substring(1); } else { channelURL = siteURL + channelURL; } } else if (!channelURL.startsWith("http://")) { if (siteURL.charAt(siteURL.length() - 1) == '/') { channelURL = siteURL + channelURL; } else { channelURL = siteURL + "/" + channelURL; } } isChannelURLFound = true; if (isChannelURLFound && isIconURLFound) { break; } } if (inputLine.contains("</head>".toLowerCase())) { break; } } in.close(); if ("".equals(channelURL)) { throw new LinkNotFoundException(); } } channel = getChannelFromXML(channelURL.trim()); if (iconURL == null || "".equals(iconURL.trim())) { iconURL = "favicon.ico"; if (siteURL.equalsIgnoreCase(channel.getChannelURL())) { siteURL = channel.getLink(); } siteURL = getHome(siteURL); if (siteURL.charAt(siteURL.length() - 1) == '/') { iconURL = siteURL + iconURL; } else { iconURL = siteURL + "/" + iconURL; } } try { String iconFileName = getHome(channel.getLink()); if (iconFileName.startsWith("http://")) { iconFileName = iconFileName.substring(7); } iconFileName = iconFileName.replaceAll("\\W", " ").trim().replace(" ", "_").concat(".ico"); String iconPath = JReader.getConfig().getShortcutIconsDir() + File.separator + iconFileName; InputStream inIcon = new URL(iconURL).openStream(); OutputStream outIcon = new FileOutputStream(iconPath); byte[] buf = new byte[1024]; int len; while ((len = inIcon.read(buf)) > 0) { outIcon.write(buf, 0, len); } inIcon.close(); outIcon.close(); channel.setIconPath(iconPath); } catch (Exception e) { } return channel; } | 17,040 |
1 | protected void setUp() throws Exception { this.testOutputDirectory = new File(getClass().getResource("/").getPath()); this.pluginFile = new File(this.testOutputDirectory, "/plugin.zip"); ZipOutputStream zos = new ZipOutputStream(new FileOutputStream(pluginFile)); zos.putNextEntry(new ZipEntry("WEB-INF/")); zos.putNextEntry(new ZipEntry("WEB-INF/classes/")); zos.putNextEntry(new ZipEntry("WEB-INF/classes/system.properties")); System.getProperties().store(zos, null); zos.closeEntry(); zos.putNextEntry(new ZipEntry("WEB-INF/lib/")); zos.putNextEntry(new ZipEntry("WEB-INF/lib/plugin.jar")); File jarFile = new File(this.testOutputDirectory.getPath() + "/plugin.jar"); JarOutputStream jos = new JarOutputStream(new FileOutputStream(jarFile)); jos.putNextEntry(new ZipEntry("vqwiki/")); jos.putNextEntry(new ZipEntry("vqwiki/plugins/")); jos.putNextEntry(new ZipEntry("vqwiki/plugins/system.properties")); System.getProperties().store(jos, null); jos.closeEntry(); jos.close(); IOUtils.copy(new FileInputStream(jarFile), zos); zos.closeEntry(); zos.close(); jarFile.delete(); pcl = new PluginClassLoader(new File(testOutputDirectory, "/work")); pcl.addPlugin(pluginFile); } | public static String stringOfUrl(String addr) throws IOException { ByteArrayOutputStream output = new ByteArrayOutputStream(); System.out.println("test"); URL url = new URL(addr); System.out.println("test2"); IOUtils.copy(url.openStream(), output); return output.toString(); } | 17,041 |
1 | public void writeToFile(File out) throws IOException, DocumentException { FileChannel inChannel = new FileInputStream(pdf_file).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(); } } | public static void copyFile4(File srcFile, File destFile) throws IOException { InputStream in = new FileInputStream(srcFile); OutputStream out = new FileOutputStream(destFile); IOUtils.copy(in, out); in.close(); out.close(); } | 17,042 |
0 | public boolean copy(String file, String path) { try { File file_in = new File(file); String tmp1, tmp2; tmp1 = file; tmp2 = path; while (tmp2.contains("\\")) { tmp2 = tmp2.substring(tmp2.indexOf("\\") + 1); tmp1 = tmp1.substring(tmp1.indexOf("\\") + 1); } tmp1 = file.substring(0, file.length() - tmp1.length()) + tmp2 + tmp1.substring(tmp1.indexOf("\\")); File file_out = new File(tmp1); File parent = file_out.getParentFile(); parent.mkdirs(); FileInputStream in1 = new FileInputStream(file_in); FileOutputStream out1 = new FileOutputStream(file_out); byte[] bytes = new byte[1024]; int c; while ((c = in1.read(bytes)) != -1) out1.write(bytes, 0, c); in1.close(); out1.close(); return true; } catch (Exception e) { e.printStackTrace(); System.out.println("Error!"); return false; } } | public void run() { iStream = null; try { tryProxy = false; URLConnection connection = url.openConnection(); if (connection instanceof HttpURLConnection) { HttpURLConnection htc = (HttpURLConnection) connection; contentLength = htc.getContentLength(); } InputStream i = connection.getInputStream(); iStream = new LoggedInputStream(i, wa); } catch (ConnectException x) { tryProxy = true; exception = x; } catch (Exception x) { exception = x; } finally { if (dialog != null) { Thread.yield(); dialog.setVisible(false); } } } | 17,043 |
1 | public static void main(String[] args) { JFileChooser askDir = new JFileChooser(); askDir.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY); askDir.setMultiSelectionEnabled(false); int returnVal = askDir.showOpenDialog(null); if (returnVal == JFileChooser.CANCEL_OPTION) { System.exit(returnVal); } File startDir = askDir.getSelectedFile(); ArrayList<File> files = new ArrayList<File>(); goThrough(startDir, files); SearchClient client = new SearchClient("VZFo5W5i"); MyID3 singleton = new MyID3(); for (File song : files) { try { MusicMetadataSet set = singleton.read(song); IMusicMetadata meta = set.getSimplified(); String qu = song.getName(); if (meta.getAlbum() != null) { qu = meta.getAlbum(); } else if (meta.getArtist() != null) { qu = meta.getArtist(); } if (qu.length() > 2) { ImageSearchRequest req = new ImageSearchRequest(qu); ImageSearchResults res = client.imageSearch(req); if (res.getTotalResultsAvailable().doubleValue() > 1) { System.out.println("Downloading " + res.listResults()[0].getUrl()); URL url = new URL(res.listResults()[0].getUrl()); URLConnection con = url.openConnection(); con.setConnectTimeout(10000); int realSize = con.getContentLength(); if (realSize > 0) { String mime = con.getContentType(); InputStream stream = con.getInputStream(); byte[] realData = new byte[realSize]; for (int i = 0; i < realSize; i++) { stream.read(realData, i, 1); } stream.close(); ImageData imgData = new ImageData(realData, mime, qu, 0); meta.addPicture(imgData); File temp = File.createTempFile("tempsong", "mp3"); singleton.write(song, temp, set, meta); FileChannel inChannel = new FileInputStream(temp).getChannel(); FileChannel outChannel = new FileOutputStream(song).getChannel(); try { inChannel.transferTo(0, inChannel.size(), outChannel); } catch (IOException e) { throw e; } finally { if (inChannel != null) inChannel.close(); if (outChannel != null) outChannel.close(); } temp.delete(); } } } } catch (ID3ReadException e) { } catch (MalformedURLException e) { } catch (UnsupportedEncodingException e) { } catch (ID3WriteException e) { } catch (IOException e) { } catch (SearchException e) { } } } | public static void copyFile(File src, File dest) throws IOException { FileInputStream fIn; FileOutputStream fOut; FileChannel fIChan, fOChan; long fSize; MappedByteBuffer mBuf; fIn = new FileInputStream(src); fOut = new FileOutputStream(dest); fIChan = fIn.getChannel(); fOChan = fOut.getChannel(); fSize = fIChan.size(); mBuf = fIChan.map(FileChannel.MapMode.READ_ONLY, 0, fSize); fOChan.write(mBuf); fIChan.close(); fIn.close(); fOChan.close(); fOut.close(); } | 17,044 |
1 | public static String convertStringToMD5(String toEnc) { try { MessageDigest mdEnc = MessageDigest.getInstance("MD5"); mdEnc.update(toEnc.getBytes(), 0, toEnc.length()); return new BigInteger(1, mdEnc.digest()).toString(16); } catch (Exception e) { return null; } } | public void calculate() throws FormatException, java.io.IOException { if (input == null) throw new IllegalStateException("FastaChecksummer input not set"); contigHashes = new HashMap<String, ChecksumEntry>(); String currentContig = null; java.security.MessageDigest hasher = null; try { hasher = java.security.MessageDigest.getInstance(checksumAlgorithm); } catch (java.security.NoSuchAlgorithmException e) { throw new RuntimeException("Unexpected NoSuchAlgorithmException when asking for " + checksumAlgorithm + " algorithm"); } String line = input.readLine(); if (line == null) throw new FormatException("empty Fasta"); try { while (line != null) { if (line.startsWith(">")) { if (currentContig != null) { String cs = new String(Hex.encodeHex(hasher.digest())); contigHashes.put(currentContig, new ChecksumEntry(currentContig, cs)); } Matcher m = ContigNamePattern.matcher(line); if (m.matches()) { currentContig = m.group(1); hasher.reset(); } else throw new FormatException("Unexpected contig name format: " + line); } else { if (currentContig == null) throw new FormatException("Sequence outside any fasta record (header is missing). Line: " + line); else hasher.update(line.getBytes("US-ASCII")); } line = input.readLine(); } if (currentContig != null) { String cs = new String(Hex.encodeHex(hasher.digest())); contigHashes.put(currentContig, new ChecksumEntry(currentContig, cs)); } } catch (java.io.UnsupportedEncodingException e) { throw new RuntimeException("Unexpected UnsupportedEncodingException! Line: " + line); } } | 17,045 |
0 | public void write(HttpServletRequest req, HttpServletResponse res, Object bean) throws IntrospectionException, IllegalAccessException, NoSuchMethodException, InvocationTargetException, IOException { res.setContentType(contentType); final Object r; if (HttpRpcServer.HttpRpcOutput.class.isAssignableFrom(bean.getClass())) { HttpRpcServer.HttpRpcOutput output = (HttpRpcServer.HttpRpcOutput) bean; r = output.getResult(); } else r = bean; if (r != null) { if (File.class.isAssignableFrom(r.getClass())) { File file = (File) r; InputStream in = null; try { in = new FileInputStream(file); IOUtils.copy(in, res.getOutputStream()); } finally { if (in != null) in.close(); } } else if (InputStream.class.isAssignableFrom(r.getClass())) { InputStream in = null; try { in = (InputStream) r; IOUtils.copy(in, res.getOutputStream()); } finally { if (in != null) in.close(); } } else if (XFile.class.isAssignableFrom(r.getClass())) { XFile file = (XFile) r; InputStream in = null; try { in = new XFileInputStream(file); IOUtils.copy(in, res.getOutputStream()); } finally { if (in != null) in.close(); } } res.getOutputStream().flush(); } } | public static float medianElement(float[] array, int size) { float[] tmpArray = new float[size]; System.arraycopy(array, 0, tmpArray, 0, size); boolean changed = true; while (changed) { changed = false; for (int i = 0; i < size - 1; i++) { if (tmpArray[i] > tmpArray[i + 1]) { changed = true; float tmp = tmpArray[i]; tmpArray[i] = tmpArray[i + 1]; tmpArray[i + 1] = tmp; } } } return tmpArray[size / 2]; } | 17,046 |
1 | public static void copyFile(File from, File to) throws Exception { if (!from.exists()) return; FileInputStream in = new FileInputStream(from); FileOutputStream out = new FileOutputStream(to); byte[] buffer = new byte[BUFFER_SIZE]; int bytes_read; while (true) { bytes_read = in.read(buffer); if (bytes_read == -1) break; out.write(buffer, 0, bytes_read); } out.flush(); out.close(); in.close(); } | public RepeatStatus execute(StepContribution contribution, ChunkContext chunkContext) throws Exception { ZipInputStream zis = new ZipInputStream(new BufferedInputStream(inputResource.getInputStream())); File targetDirectoryAsFile = new File(targetDirectory); if (!targetDirectoryAsFile.exists()) { FileUtils.forceMkdir(targetDirectoryAsFile); } File target = new File(targetDirectory, targetFile); BufferedOutputStream dest = null; while (zis.getNextEntry() != null) { if (!target.exists()) { target.createNewFile(); } FileOutputStream fos = new FileOutputStream(target); dest = new BufferedOutputStream(fos); IOUtils.copy(zis, dest); dest.flush(); dest.close(); } zis.close(); if (!target.exists()) { throw new IllegalStateException("Could not decompress anything from the archive!"); } return RepeatStatus.FINISHED; } | 17,047 |
1 | public static void unzipFile(File zipFile, File destFile, boolean removeSrcFile) throws Exception { ZipInputStream zipinputstream = new ZipInputStream(new FileInputStream(zipFile)); ZipEntry zipentry = zipinputstream.getNextEntry(); int BUFFER_SIZE = 4096; while (zipentry != null) { String entryName = zipentry.getName(); log.info("<<<<<< ZipUtility.unzipFile - Extracting: " + zipentry.getName()); File newFile = null; if (destFile.isDirectory()) newFile = new File(destFile, entryName); else newFile = destFile; if (zipentry.isDirectory() || entryName.endsWith(File.separator + ".")) { newFile.mkdirs(); } else { ByteBuffer buffer = ByteBuffer.allocate(BUFFER_SIZE); byte[] bufferArray = buffer.array(); FileUtilities.createDirectory(newFile.getParentFile()); FileChannel destinationChannel = new FileOutputStream(newFile).getChannel(); while (true) { buffer.clear(); int lim = zipinputstream.read(bufferArray); if (lim == -1) break; buffer.flip(); buffer.limit(lim); destinationChannel.write(buffer); } destinationChannel.close(); zipinputstream.closeEntry(); } zipentry = zipinputstream.getNextEntry(); } zipinputstream.close(); if (removeSrcFile) { if (zipFile.exists()) zipFile.delete(); } } | public void transport(File file) throws TransportException { if (file.exists()) { if (file.isDirectory()) { File[] files = file.listFiles(); for (int i = 0; i < files.length; i++) { transport(file); } } else if (file.isFile()) { try { FileChannel inChannel = new FileInputStream(file).getChannel(); FileChannel outChannel = new FileOutputStream(getOption("destination")).getChannel(); inChannel.transferTo(0, inChannel.size(), outChannel); } catch (IOException e) { log.error("File transfer failed", e); } } } } | 17,048 |
0 | 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 String fetchContent() throws IOException { BufferedReader reader = new BufferedReader(new InputStreamReader(url.openStream())); StringBuffer buf = new StringBuffer(); String str; while ((str = reader.readLine()) != null) { buf.append(str); } return buf.toString(); } | 17,049 |
0 | public boolean import_status(String filename) { int pieceId; int i, j, col, row; int rotation; int number; boolean byurl = false; e2piece temppiece; String lineread; StringTokenizer tok; BufferedReader entree; try { if (byurl == true) { URL url = new URL(baseURL, filename); InputStream in = url.openStream(); entree = new BufferedReader(new InputStreamReader(in)); } else { entree = new BufferedReader(new FileReader(filename)); } pieceId = 0; for (i = 0; i < board.colnb; i++) { for (j = 0; j < board.rownb; j++) { unplace_piece_at(i, j); } } while (true) { lineread = entree.readLine(); if (lineread == null) { break; } tok = new StringTokenizer(lineread, " "); pieceId = Integer.parseInt(tok.nextToken()); col = Integer.parseInt(tok.nextToken()) - 1; row = Integer.parseInt(tok.nextToken()) - 1; rotation = Integer.parseInt(tok.nextToken()); place_piece_at(pieceId, col, row, 0); temppiece = board.get_piece_at(col, row); temppiece.reset_rotation(); temppiece.rotate(rotation); } return true; } catch (IOException err) { return false; } } | public final void propertyChange(final PropertyChangeEvent event) { if (fChecker != null && event.getProperty().equals(ISpellCheckPreferenceKeys.SPELLING_USER_DICTIONARY)) { if (fUserDictionary != null) { fChecker.removeDictionary(fUserDictionary); fUserDictionary = null; } final String file = (String) event.getNewValue(); if (file.length() > 0) { try { final URL url = new URL("file", null, file); InputStream stream = url.openStream(); if (stream != null) { try { fUserDictionary = new PersistentSpellDictionary(url); fChecker.addDictionary(fUserDictionary); } finally { stream.close(); } } } catch (MalformedURLException exception) { } catch (IOException exception) { } } } } | 17,050 |
0 | public boolean authenticate() { if (empresaFeta == null) empresaFeta = new AltaEmpresaBean(); log.info("authenticating {0}", credentials.getUsername()); boolean bo; try { String passwordEncriptat = credentials.getPassword(); MessageDigest m = MessageDigest.getInstance("MD5"); m.update(passwordEncriptat.getBytes(), 0, passwordEncriptat.length()); passwordEncriptat = new BigInteger(1, m.digest()).toString(16); Query q = entityManager.createQuery("select usuari from Usuaris usuari where usuari.login=? and usuari.password=?"); q.setParameter(1, credentials.getUsername()); q.setParameter(2, passwordEncriptat); Usuaris usuari = (Usuaris) q.getSingleResult(); bo = (usuari != null); if (bo) { if (usuari.isEsAdministrador()) { identity.addRole("admin"); } else { carregaDadesEmpresa(); log.info("nom de l'empresa: " + empresaFeta.getInstance().getNom()); } } } catch (Throwable t) { log.error(t); bo = false; } log.info("L'usuari {0} s'ha identificat bé? : {1} ", credentials.getUsername(), bo ? "si" : "no"); return bo; } | private File download(String filename, URL url) { int size = -1; int received = 0; try { fireDownloadStarted(filename); File file = createFile(filename); BufferedOutputStream bos = new BufferedOutputStream(new FileOutputStream(file)); System.out.println("下载资源：" + filename + ", url=" + url); // BufferedInputStream bis = new // BufferedInputStream(url.openStream()); InputStream bis = url.openStream(); byte[] buf = new byte[1024]; int count = 0; long lastUpdate = 0; size = bis.available(); while ((count = bis.read(buf)) != -1) { bos.write(buf, 0, count); received += count; long now = System.currentTimeMillis(); if (now - lastUpdate > 500) { fireDownloadUpdate(filename, size, received); lastUpdate = now; } } bos.close(); System.out.println("资源下载完毕：" + filename); fireDownloadCompleted(filename); return file; } catch (IOException e) { System.out.println("下载资源失败：" + filename + ", error=" + e.getMessage()); fireDownloadInterrupted(filename); if (!(e instanceof FileNotFoundException)) { e.printStackTrace(); } } return null; } | 17,051 |
1 | private String unJar(String jarPath, String jarEntry) { String path; if (jarPath.lastIndexOf("lib/") >= 0) path = jarPath.substring(0, jarPath.lastIndexOf("lib/")); else path = jarPath.substring(0, jarPath.lastIndexOf("/")); String relPath = jarEntry.substring(0, jarEntry.lastIndexOf("/")); try { new File(path + "/" + relPath).mkdirs(); JarFile jar = new JarFile(jarPath); ZipEntry ze = jar.getEntry(jarEntry); File bin = new File(path + "/" + jarEntry); IOUtils.copy(jar.getInputStream(ze), new FileOutputStream(bin)); } catch (Exception e) { e.printStackTrace(); } return path + "/" + jarEntry; } | public void run() { Vector<Update> updates = new Vector<Update>(); if (dic != null) updates.add(dic); if (gen != null) updates.add(gen); if (res != null) updates.add(res); if (help != null) updates.add(help); for (Iterator iterator = updates.iterator(); iterator.hasNext(); ) { Update update = (Update) iterator.next(); try { File temp = File.createTempFile("fm_" + update.getType(), ".jar"); temp.deleteOnExit(); FileOutputStream out = new FileOutputStream(temp); URL url = new URL(update.getAction()); URLConnection conn = url.openConnection(); com.diccionarioderimas.Utils.setupProxy(conn); InputStream in = conn.getInputStream(); byte[] buffer = new byte[1024]; int read = 0; int total = 0; while ((read = in.read(buffer)) != -1) { out.write(buffer, 0, read); total += read; if (total > 10000) { progressBar.setValue(progressBar.getValue() + total); total = 0; } } out.close(); in.close(); String fileTo = basePath + "diccionariorimas.jar"; if (update.getType() == Update.GENERATOR) fileTo = basePath + "generador.jar"; else if (update.getType() == Update.RESBC) fileTo = basePath + "resbc.me"; else if (update.getType() == Update.HELP) fileTo = basePath + "help.html"; if (update.getType() == Update.RESBC) { Utils.unzip(temp, new File(fileTo)); } else { Utils.copyFile(new FileInputStream(temp), new File(fileTo)); } } catch (Exception e) { e.printStackTrace(); } } setVisible(false); if (gen != null || res != null) { try { new Main(null, basePath, false); } catch (Exception e) { new ErrorDialog(frame, e); } } String restart = ""; if (dic != null) restart += "\nAlgunas de ellas s�lo estar�n disponibles despu�s de reiniciar el diccionario."; JOptionPane.showMessageDialog(frame, "Se han terminado de realizar las actualizaciones." + restart, "Actualizaciones", JOptionPane.INFORMATION_MESSAGE); } | 17,052 |
1 | public static void copy(File in, File out) throws IOException { FileChannel ic = new FileInputStream(in).getChannel(); FileChannel oc = new FileOutputStream(out).getChannel(); ic.transferTo(0, ic.size(), oc); ic.close(); oc.close(); } | public void setBckImg(String newPath) { try { File inputFile = new File(getPath()); File outputFile = new File(newPath); if (!inputFile.getCanonicalPath().equals(outputFile.getCanonicalPath())) { FileInputStream in = new FileInputStream(inputFile); FileOutputStream out = null; try { out = new FileOutputStream(outputFile); } catch (FileNotFoundException ex1) { ex1.printStackTrace(); JOptionPane.showMessageDialog(null, ex1.getMessage().substring(0, Math.min(ex1.getMessage().length(), drawPanel.MAX_DIALOG_MSG_SZ)) + "-" + getClass(), "Set Bck Img", JOptionPane.ERROR_MESSAGE); } int c; if (out != null) { while ((c = in.read()) != -1) out.write(c); out.close(); } in.close(); } } catch (Exception ex) { ex.printStackTrace(); LogHandler.log(ex.getMessage(), Level.INFO, "LOG_MSG", isLoggingEnabled()); JOptionPane.showMessageDialog(null, ex.getMessage().substring(0, Math.min(ex.getMessage().length(), drawPanel.MAX_DIALOG_MSG_SZ)) + "-" + getClass(), "Set Bck Img", JOptionPane.ERROR_MESSAGE); } setPath(newPath); bckImg = new ImageIcon(getPath()); } | 17,053 |
1 | public static void transfer(FileInputStream fileInStream, FileOutputStream fileOutStream) throws IOException { FileChannel fileInChannel = fileInStream.getChannel(); FileChannel fileOutChannel = fileOutStream.getChannel(); long fileInSize = fileInChannel.size(); try { long transferred = fileInChannel.transferTo(0, fileInSize, fileOutChannel); if (transferred != fileInSize) { throw new IOException("transfer() did not complete"); } } finally { ensureClose(fileInChannel, fileOutChannel); } } | private static void main(String[] args) { try { File f = new File("test.txt"); if (f.exists()) { throw new IOException(f + " already exists. I don't want to overwrite it."); } StraightStreamReader in; char[] cbuf = new char[0x1000]; int read; int totRead; FileOutputStream out = new FileOutputStream(f); for (int i = 0x00; i < 0x100; i++) { out.write(i); } out.close(); in = new StraightStreamReader(new FileInputStream(f)); for (int i = 0x00; i < 0x100; i++) { read = in.read(); if (read != i) { System.err.println("Error: " + i + " read as " + read); } } in.close(); in = new StraightStreamReader(new FileInputStream(f)); totRead = in.read(cbuf); if (totRead != 0x100) { System.err.println("Simple buffered read did not read the full amount: 0x" + Integer.toHexString(totRead)); } for (int i = 0x00; i < totRead; i++) { if (cbuf[i] != i) { System.err.println("Error: 0x" + i + " read as 0x" + cbuf[i]); } } in.close(); in = new StraightStreamReader(new FileInputStream(f)); totRead = 0; while (totRead <= 0x100 && (read = in.read(cbuf, totRead, 0x100 - totRead)) > 0) { totRead += read; } if (totRead != 0x100) { System.err.println("Not enough read. Bytes read: " + Integer.toHexString(totRead)); } for (int i = 0x00; i < totRead; i++) { if (cbuf[i] != i) { System.err.println("Error: 0x" + i + " read as 0x" + cbuf[i]); } } in.close(); in = new StraightStreamReader(new FileInputStream(f)); totRead = 0; while (totRead <= 0x100 && (read = in.read(cbuf, totRead + 0x123, 0x100 - totRead)) > 0) { totRead += read; } if (totRead != 0x100) { System.err.println("Not enough read. Bytes read: " + Integer.toHexString(totRead)); } for (int i = 0x00; i < totRead; i++) { if (cbuf[i + 0x123] != i) { System.err.println("Error: 0x" + i + " read as 0x" + cbuf[i + 0x123]); } } in.close(); in = new StraightStreamReader(new FileInputStream(f)); totRead = 0; while (totRead <= 0x100 && (read = in.read(cbuf, totRead + 0x123, 7)) > 0) { totRead += read; } if (totRead != 0x100) { System.err.println("Not enough read. Bytes read: " + Integer.toHexString(totRead)); } for (int i = 0x00; i < totRead; i++) { if (cbuf[i + 0x123] != i) { System.err.println("Error: 0x" + i + " read as 0x" + cbuf[i + 0x123]); } } in.close(); f.delete(); } catch (IOException x) { System.err.println(x.getMessage()); } } | 17,054 |
0 | protected static void copyFile(File in, File out) throws IOException { java.io.FileWriter filewriter = null; java.io.FileReader filereader = null; try { filewriter = new java.io.FileWriter(out); filereader = new java.io.FileReader(in); char[] buf = new char[4096]; int nread = filereader.read(buf, 0, 4096); while (nread >= 0) { filewriter.write(buf, 0, nread); nread = filereader.read(buf, 0, 4096); } buf = null; } finally { try { filereader.close(); } catch (Throwable t) { } try { filewriter.close(); } catch (Throwable t) { } } } | public RespID(PublicKey key) throws OCSPException { try { MessageDigest digest = MessageDigest.getInstance("SHA1"); ASN1InputStream aIn = new ASN1InputStream(key.getEncoded()); SubjectPublicKeyInfo info = SubjectPublicKeyInfo.getInstance(aIn.readObject()); digest.update(info.getPublicKeyData().getBytes()); ASN1OctetString keyHash = new DEROctetString(digest.digest()); this.id = new ResponderID(keyHash); } catch (Exception e) { throw new OCSPException("problem creating ID: " + e, e); } } | 17,055 |
1 | public void doPost(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException { try { String act = request.getParameter("act"); if (null == act) { } else if ("down".equalsIgnoreCase(act)) { String vest = request.getParameter("vest"); String id = request.getParameter("id"); if (null == vest) { t_attach_Form attach = null; t_attach_QueryMap query = new t_attach_QueryMap(); attach = query.getByID(id); if (null != attach) { String filename = attach.getAttach_name(); String fullname = attach.getAttach_fullname(); response.addHeader("Content-Disposition", "attachment;filename=" + filename + ""); File file = new File(fullname); if (file.exists()) { java.io.FileInputStream in = new FileInputStream(file); org.apache.commons.io.IOUtils.copy(in, response.getOutputStream()); } } } else if ("review".equalsIgnoreCase(vest)) { t_infor_review_QueryMap reviewQuery = new t_infor_review_QueryMap(); t_infor_review_Form review = reviewQuery.getByID(id); String seq = request.getParameter("seq"); String name = null, fullname = null; if ("1".equals(seq)) { name = review.getAttachname1(); fullname = review.getAttachfullname1(); } else if ("2".equals(seq)) { name = review.getAttachname2(); fullname = review.getAttachfullname2(); } else if ("3".equals(seq)) { name = review.getAttachname3(); fullname = review.getAttachfullname3(); } String downTypeStr = DownType.getInst().getDownTypeByFileName(name); logger.debug("filename=" + name + " downtype=" + downTypeStr); response.setContentType(downTypeStr); response.addHeader("Content-Disposition", "attachment;filename=" + name + ""); File file = new File(fullname); if (file.exists()) { java.io.FileInputStream in = new FileInputStream(file); org.apache.commons.io.IOUtils.copy(in, response.getOutputStream()); in.close(); } } } else if ("upload".equalsIgnoreCase(act)) { String infoId = request.getParameter("inforId"); logger.debug("infoId=" + infoId); } } catch (Exception e) { } } | 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; } | 17,056 |
0 | public void doGet(OutputStream os) throws IOException { try { uc = (HttpURLConnection) url.openConnection(); uc.setRequestProperty("User-Agent", USER_AGENT); uc.setReadTimeout(READ_TIMEOUT); logger.debug("Connect timeout=" + uc.getConnectTimeout() + " read timeout=" + uc.getReadTimeout() + " u=" + url); InputStream buffer = new BufferedInputStream(uc.getInputStream()); int c; while ((c = buffer.read()) != -1) { os.write(c); } headers = uc.getHeaderFields(); status = uc.getResponseCode(); responseMessage = uc.getResponseMessage(); } catch (Exception e) { throw new IOException(e.getMessage()); } finally { if (status != 200) logger.error("Download failed status: " + status + " " + responseMessage + " for " + url); else logger.debug("HTTP status=" + status + " " + uc.getResponseMessage()); os.close(); uc.disconnect(); } } | public void read(Model model, String url) { try { URLConnection conn = new URL(url).openConnection(); String encoding = conn.getContentEncoding(); if (encoding == null) { read(model, conn.getInputStream(), url); } else { read(model, new InputStreamReader(conn.getInputStream(), encoding), url); } } catch (IOException e) { throw new JenaException(e); } } | 17,057 |
1 | public static void zipFile(String file, String entry) throws IOException { FileInputStream in = new FileInputStream(file); ZipOutputStream out = new ZipOutputStream(new FileOutputStream(file + ".zip")); out.putNextEntry(new ZipEntry(entry)); byte[] buffer = new byte[4096]; int bytes_read; while ((bytes_read = in.read(buffer)) != -1) out.write(buffer, 0, bytes_read); in.close(); out.closeEntry(); out.close(); File fin = new File(file); fin.delete(); } | 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(); } } | 17,058 |
1 | public static void unzip(File sourceZipFile, File unzipDestinationDirectory, FileFilter filter) throws IOException { unzipDestinationDirectory.mkdirs(); if (!unzipDestinationDirectory.exists()) { throw new IOException("Unable to create destination directory: " + unzipDestinationDirectory); } ZipFile zipFile; zipFile = new ZipFile(sourceZipFile, ZipFile.OPEN_READ); Enumeration<? extends ZipEntry> zipFileEntries = zipFile.entries(); while (zipFileEntries.hasMoreElements()) { ZipEntry entry = (ZipEntry) zipFileEntries.nextElement(); if (!entry.isDirectory()) { String currentEntry = entry.getName(); File destFile = new File(unzipDestinationDirectory, currentEntry); if (filter == null || filter.accept(destFile)) { File destinationParent = destFile.getParentFile(); destinationParent.mkdirs(); BufferedInputStream is = new BufferedInputStream(zipFile.getInputStream(entry)); FileOutputStream fos = new FileOutputStream(destFile); IOUtils.copyLarge(is, fos); fos.flush(); IOUtils.closeQuietly(fos); } } } zipFile.close(); } | public static void extract(final File destDir, final Collection<ZipEntryInfo> entryInfos) throws IOException { if (destDir == null || CollectionUtils.isEmpty(entryInfos)) throw new IllegalArgumentException("One or parameter is null or empty!"); if (!destDir.exists()) destDir.mkdirs(); for (ZipEntryInfo entryInfo : entryInfos) { ZipEntry entry = entryInfo.getZipEntry(); InputStream in = entryInfo.getInputStream(); File entryDest = new File(destDir, entry.getName()); entryDest.getParentFile().mkdirs(); if (!entry.isDirectory()) { OutputStream out = new FileOutputStream(new File(destDir, entry.getName())); try { IOUtils.copy(in, out); out.flush(); } finally { IOUtils.closeQuietly(in); IOUtils.closeQuietly(out); } } } } | 17,059 |
1 | protected String readFileUsingHttp(String fileUrlName) { String response = ""; try { URL url = new URL(fileUrlName); URLConnection connection = url.openConnection(); HttpURLConnection httpConn = (HttpURLConnection) connection; httpConn.setRequestProperty("Content-Type", "text/html"); httpConn.setRequestProperty("Content-Length", "0"); httpConn.setRequestMethod("GET"); httpConn.setDoOutput(true); httpConn.setDoInput(true); httpConn.setAllowUserInteraction(false); InputStreamReader isr = new InputStreamReader(httpConn.getInputStream()); BufferedReader in = new BufferedReader(isr); String inputLine = ""; while ((inputLine = in.readLine()) != null) { response += inputLine + "\n"; } if (response.endsWith("\n")) { response = response.substring(0, response.length() - 1); } in.close(); } catch (Exception x) { x.printStackTrace(); } return response; } | 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(); } } | 17,060 |
1 | public static String MD5(String text) throws NoSuchAlgorithmException, UnsupportedEncodingException { MessageDigest md; md = MessageDigest.getInstance("MD5"); byte[] md5hash = new byte[32]; md.update(text.getBytes("iso-8859-1"), 0, text.length()); md5hash = md.digest(); return convertToHex(md5hash); } | private void getRandomGUID(boolean secure) { MessageDigest md5 = null; StringBuffer sbValueBeforeMD5 = new StringBuffer(); try { md5 = MessageDigest.getInstance("MD5"); } catch (NoSuchAlgorithmException e) { } try { long time = System.currentTimeMillis(); long rand = 0; if (secure) { rand = mySecureRand.nextLong(); } else { rand = random.nextLong(); } sbValueBeforeMD5.append(sid); 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) { } } | 17,061 |
1 | public final void deliver(final String from, final String recipient, final InputStream data) throws TooMuchDataException, IOException { System.out.println("FROM: " + from); System.out.println("TO: " + recipient); final File tmpDir = new File(System.getProperty("java.io.tmpdir")); final File file = new File(tmpDir, recipient); final FileWriter fw = new FileWriter(file); try { IOUtils.copy(data, fw); } finally { fw.close(); } } | private void show(String fileName, HttpServletResponse response) throws IOException { TelnetInputStream ftpIn = ftpClient_sun.get(fileName); OutputStream out = null; try { out = response.getOutputStream(); IOUtils.copy(ftpIn, out); } finally { if (ftpIn != null) { ftpIn.close(); } } } | 17,062 |
1 | 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 void doCompress(File[] files, File out, List<String> excludedKeys) { Map<String, File> map = new HashMap<String, File>(); String parent = FilenameUtils.getBaseName(out.getName()); for (File f : files) { CompressionUtil.list(f, parent, map, excludedKeys); } if (!map.isEmpty()) { FileOutputStream fos = null; ArchiveOutputStream aos = null; InputStream is = null; try { fos = new FileOutputStream(out); aos = getArchiveOutputStream(fos); for (Map.Entry<String, File> entry : map.entrySet()) { File file = entry.getValue(); ArchiveEntry ae = getArchiveEntry(file, entry.getKey()); aos.putArchiveEntry(ae); if (file.isFile()) { IOUtils.copy(is = new FileInputStream(file), aos); IOUtils.closeQuietly(is); is = null; } aos.closeArchiveEntry(); } aos.finish(); } catch (IOException ex) { ex.printStackTrace(); } finally { IOUtils.closeQuietly(is); IOUtils.closeQuietly(aos); IOUtils.closeQuietly(fos); } } } | 17,063 |
1 | public void generate(FileObject outputDirectory, FileObject generatedOutputDirectory, List<Library> libraryModels, String tapdocXml) throws FileSystemException { if (!generatedOutputDirectory.exists()) { generatedOutputDirectory.createFolder(); } if (outputDirectory.exists()) { outputDirectory.createFolder(); } ZipUtils.extractZip(new ClasspathResource(classResolver, "/com/erinors/tapestry/tapdoc/service/xdoc/resources.zip"), outputDirectory); for (Library library : libraryModels) { String libraryName = library.getName(); String libraryLocation = library.getLocation(); generatedOutputDirectory.resolveFile(fileNameGenerator.getLibraryDirectory(libraryLocation)).createFolder(); try { String result = XsltUtils.xsltTransform(tapdocXml, getClass().getResourceAsStream("Library.xsl"), "libraryName", libraryName); FileObject index = generatedOutputDirectory.resolveFile(fileNameGenerator.getLibraryDirectory(libraryLocation)).resolveFile("index.xml"); Writer out = new OutputStreamWriter(index.getContent().getOutputStream(), "UTF-8"); out.write(result); out.close(); } catch (Exception e) { throw new RuntimeException(e); } for (Component component : library.getComponents()) { String componentName = component.getName(); System.out.println("Generating " + libraryName + ":" + componentName + "..."); Map<String, String> parameters = new HashMap<String, String>(); parameters.put("libraryName", libraryName); parameters.put("componentName", componentName); String result = XsltUtils.xsltTransform(tapdocXml, getClass().getResourceAsStream("Component.xsl"), parameters); Writer out = null; try { FileObject index = generatedOutputDirectory.resolveFile(fileNameGenerator.getComponentIndexFile(libraryLocation, componentName, true)); out = new OutputStreamWriter(index.getContent().getOutputStream(), "UTF-8"); out.write(result); out.close(); Resource specificationLocation = component.getSpecificationLocation(); if (specificationLocation.getRelativeResource(componentName + "_tapdoc/resource").getResourceURL() != null) { File srcResourcesDirectory = new File(specificationLocation.getRelativeResource(componentName + "_tapdoc/resource").getResourceURL().toURI()); FileObject dstResourcesFileObject = outputDirectory.resolveFile(fileNameGenerator.getComponentDirectory(libraryLocation, componentName)).resolveFile("resource"); if (srcResourcesDirectory.exists() && srcResourcesDirectory.isDirectory()) { File[] files = srcResourcesDirectory.listFiles(); if (files != null) { for (File resource : files) { if (resource.isFile() && !resource.isHidden()) { FileObject resourceFileObject = dstResourcesFileObject.resolveFile(resource.getName()); resourceFileObject.createFile(); InputStream inResource = null; OutputStream outResource = null; try { inResource = new FileInputStream(resource); outResource = resourceFileObject.getContent().getOutputStream(); IOUtils.copy(inResource, outResource); } finally { IOUtils.closeQuietly(inResource); IOUtils.closeQuietly(outResource); } } } } } } } catch (Exception e) { throw new RuntimeException(e); } finally { IOUtils.closeQuietly(out); } } } { Writer out = null; try { String result = XsltUtils.xsltTransform(tapdocXml, getClass().getResourceAsStream("Overview.xsl")); FileObject index = generatedOutputDirectory.resolveFile("index.xml"); out = new OutputStreamWriter(index.getContent().getOutputStream(), "UTF-8"); out.write(result); out.close(); } catch (Exception e) { throw new RuntimeException(e); } finally { IOUtils.closeQuietly(out); } } } | public void importCertFile(File file) throws IOException { File kd; File cd; synchronized (this) { kd = keysDir; cd = certsDir; } if (!cd.isDirectory()) { kd.mkdirs(); cd.mkdirs(); } String newName = file.getName(); File dest = new File(cd, newName); FileChannel sourceChannel = null; FileChannel destinationChannel = null; try { sourceChannel = new FileInputStream(file).getChannel(); destinationChannel = new FileOutputStream(dest).getChannel(); sourceChannel.transferTo(0, sourceChannel.size(), destinationChannel); } finally { if (sourceChannel != null) { try { sourceChannel.close(); } catch (IOException e) { } } if (destinationChannel != null) { try { destinationChannel.close(); } catch (IOException e) { } } } } | 17,064 |
0 | public HttpURLConnection execute(S3Bucket pBucket, S3Object pObject, S3OperationParameters pOpParams) throws S3Exception { S3OperationParameters opParams = pOpParams; if (opParams == null) opParams = new S3OperationParameters(); HttpURLConnection result = null; URL url = getURL(pBucket, pObject, opParams.getQueryParameters()); mLogger.log(Level.FINEST, "URL: " + url.toString()); opParams.addDateHeader(); switch(mStyle) { case Path: opParams.addHostHeader(BASE_DOMAIN); break; case Subdomain: if (pBucket == null) opParams.addHostHeader(BASE_DOMAIN); else opParams.addHostHeader(pBucket.getName() + "." + BASE_DOMAIN); break; case VirtualHost: if (pBucket == null) opParams.addHostHeader(BASE_DOMAIN); else opParams.addHostHeader(pBucket.getName()); break; } if (opParams.isSign()) { StringBuilder sb = new StringBuilder(); sb.append(opParams.getVerb().toString()); sb.append(NEWLINE); sb.append(posHeader(MD5, opParams.getRequestHeaders())); sb.append(posHeader(TYPE, opParams.getRequestHeaders())); if (opParams.getQueryParameters().has(EXPIRES)) { sb.append(opParams.getQueryParameters().get(EXPIRES).getValue()); sb.append(NEWLINE); } else { sb.append(posHeader(DATE, opParams.getRequestHeaders())); } sb.append(canonicalizeAmazonHeaders(opParams.getRequestHeaders())); try { sb.append("/"); if (pBucket != null) { sb.append(URLEncoder.encode(pBucket.getName(), URL_ENCODING)); sb.append("/"); if (pObject != null) { sb.append(URLEncoder.encode(pObject.getKey(), URL_ENCODING)); } } sb.append(opParams.getQueryParameters().getAmazonSubresources().toQueryString()); String signThis = sb.toString(); mLogger.log(Level.FINEST, "String being signed: " + signThis); String sig = encode(mCredential.getMSecretAccessKey(), signThis, false); sb = new StringBuilder(); sb.append("AWS "); sb.append(mCredential.getMAccessKeyID()); sb.append(":"); sb.append(sig); opParams.addAuthorizationHeader(sb.toString()); } catch (UnsupportedEncodingException e) { throw new S3Exception("URL encoding not supported: " + URL_ENCODING, e); } } try { killHostVerifier(); URLConnection urlConn = url.openConnection(); if (!(urlConn instanceof HttpURLConnection)) throw new S3Exception("URLConnection is not instance of HttpURLConnection!"); result = (HttpURLConnection) urlConn; result.setRequestMethod(opParams.getVerb().toString()); mLogger.log(Level.FINEST, "HTTP Operation: " + opParams.getVerb().toString()); if (opParams.getVerb() == HttpVerb.PUT) { result.setDoOutput(true); } result.setRequestProperty(TYPE, ""); for (AWSParameter param : opParams.getRequestHeaders()) { result.setRequestProperty(param.getName(), param.getValue()); mLogger.log(Level.FINEST, "Header " + param.getName() + ": " + param.getValue()); } } catch (IOException e) { throw new S3Exception("Problem opening connection to URL: " + url.toString(), e); } return result; } | public String parse() { try { URL url = new URL(mUrl); HttpURLConnection connection = (HttpURLConnection) url.openConnection(); connection.setRequestMethod("GET"); connection.setDoOutput(true); connection.connect(); BufferedReader reader = new BufferedReader(new InputStreamReader(connection.getInputStream())); String line; boolean flag1 = false; while ((line = reader.readLine()) != null) { line = line.trim(); if (!flag1 && line.contains("</center>")) flag1 = true; if (flag1 && line.contains("<br><center>")) break; if (flag1) { mText.append(line); } } } catch (MalformedURLException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } return mText.toString(); } | 17,065 |
0 | private String sha1(String s) { String encrypt = s; try { MessageDigest sha = MessageDigest.getInstance("SHA-1"); sha.update(s.getBytes()); byte[] digest = sha.digest(); final StringBuffer buffer = new StringBuffer(); for (int i = 0; i < digest.length; ++i) { final byte b = digest[i]; final int value = (b & 0x7F) + (b < 0 ? 128 : 0); buffer.append(value < 16 ? "0" : ""); buffer.append(Integer.toHexString(value)); } encrypt = buffer.toString(); } catch (NoSuchAlgorithmException e) { e.printStackTrace(); } return encrypt; } | public static void copyFile(File src, File dest) throws IOException { log.debug("Copying file: '" + src + "' to '" + dest + "'"); FileChannel srcChannel = new FileInputStream(src).getChannel(); FileChannel dstChannel = new FileOutputStream(dest).getChannel(); dstChannel.transferFrom(srcChannel, 0, srcChannel.size()); srcChannel.close(); dstChannel.close(); } | 17,066 |
0 | private static FTPClient getFtpClient(String ftpHost, String ftpUsername, String ftpPassword) throws SocketException, IOException { FTPClient ftp = new FTPClient(); ftp.connect(ftpHost); int reply = ftp.getReplyCode(); if (!FTPReply.isPositiveCompletion(reply)) { ftp.disconnect(); return null; } if (!ftp.login(ftpUsername, ftpPassword)) { return null; } ftp.setFileType(FTP.BINARY_FILE_TYPE); ftp.enterLocalPassiveMode(); return ftp; } | public HttpResponse execute(final HttpRequest request, final HttpClientConnection conn, final HttpContext context) throws IOException, HttpException { if (request == null) { throw new IllegalArgumentException("HTTP request may not be null"); } if (conn == null) { throw new IllegalArgumentException("Client connection may not be null"); } if (context == null) { throw new IllegalArgumentException("HTTP context may not be null"); } try { HttpResponse response = doSendRequest(request, conn, context); if (response == null) { response = doReceiveResponse(request, conn, context); } return response; } catch (IOException ex) { conn.close(); throw ex; } catch (HttpException ex) { conn.close(); throw ex; } catch (RuntimeException ex) { conn.close(); throw ex; } } | 17,067 |
0 | public void excluir(Cliente cliente) throws Exception { Connection connection = criaConexao(false); String sql = "delete from cliente where cod_cliente = ?"; PreparedStatement stmt = null; try { stmt = connection.prepareStatement(sql); stmt.setLong(1, cliente.getId()); int retorno = stmt.executeUpdate(); if (retorno == 0) { connection.rollback(); throw new SQLException("Ocorreu um erro inesperado no momento de remover dados de cliente no banco!"); } connection.commit(); } catch (SQLException e) { connection.rollback(); throw e; } finally { try { stmt.close(); this.fechaConexao(); } catch (SQLException e) { throw e; } } } | public void initGet() throws Exception { cl = new FTPClient(); cl.connect(getHostName()); Authentication auth = AuthManager.getAuth(getSite()); if (auth == null) auth = new FTPAuthentication(getSite()); while (!cl.login(auth.getUser(), auth.getPassword())) { ap.setSite(getSite()); auth = ap.promptAuthentication(); if (auth == null) throw new Exception("User Cancelled Auth Operation"); } cl.connect(getHostName()); cl.login(auth.getUser(), auth.getPassword()); cl.enterLocalPassiveMode(); cl.setFileType(FTP.BINARY_FILE_TYPE); cl.setRestartOffset(getPosition()); setInputStream(cl.retrieveFileStream(new URL(getURL()).getFile())); } | 17,068 |
0 | private void loadRDFURL(URL url) throws RDFParseException, RepositoryException { URI urlContext = valueFactory.createURI(url.toString()); try { URLConnection urlConn = url.openConnection(); urlConn.setRequestProperty("Accept", "application/rdf+xml"); InputStream is = urlConn.getInputStream(); repoConn.add(is, url.toString(), RDFFormat.RDFXML, urlContext); is.close(); repoConn.commit(); } catch (IOException e) { e.printStackTrace(); } } | public static ArrayList search(String query) throws Exception { ArrayList list = new ArrayList(); String url = "http://hypem.com/playlist/search/" + query + "/xml/1/list.xspf"; HttpURLConnection conn = (HttpURLConnection) (new URL(url)).openConnection(); conn.setRequestProperty("User-Agent", "Mozilla/4.0 (compatible; MSIE 6.0; Windows NT 5.1; SV1; .NET CLR 1.1.4322; .NET CLR 2.0.50727)"); XmlNode node = XmlLoader.load(conn.getInputStream()); XmlNode tracks[] = node.getFirstChild("trackList").getChild("track"); for (int i = 0; i < tracks.length; i++) { String location = decrypt(tracks[i].getFirstChild("location").getText()); String annotation = tracks[i].getFirstChild("annotation").getText().replaceAll("[\r\n]", ""); list.add(location); System.out.print("found in Hypem: "); System.out.print(annotation); System.out.print(", "); System.out.println(location); } return list; } | 17,069 |
0 | public static String md5Encode16(String s) { try { MessageDigest md = MessageDigest.getInstance("MD5"); md.update(s.getBytes("utf-8")); byte b[] = md.digest(); int i; StringBuilder buf = new StringBuilder(""); for (int offset = 0; offset < b.length; offset++) { i = b[offset]; if (i < 0) i += 256; if (i < 16) buf.append("0"); buf.append(Integer.toHexString(i)); } return buf.toString().substring(8, 24); } catch (NoSuchAlgorithmException e) { throw new IllegalArgumentException(e); } catch (UnsupportedEncodingException e) { throw new IllegalArgumentException(e); } } | private void getViolationsReportByProductOfferIdYearMonthDay() throws IOException { String xmlFile9Send = System.getenv("SLASOI_HOME") + System.getProperty("file.separator") + "Integration" + System.getProperty("file.separator") + "soap" + System.getProperty("file.separator") + "getViolationsReportByProductOfferIdYearMonthDay.xml"; URL url9; url9 = new URL(bmReportingWSUrl); URLConnection connection9 = url9.openConnection(); HttpURLConnection httpConn9 = (HttpURLConnection) connection9; FileInputStream fin9 = new FileInputStream(xmlFile9Send); ByteArrayOutputStream bout9 = new ByteArrayOutputStream(); SOAPClient4XG.copy(fin9, bout9); fin9.close(); byte[] b9 = bout9.toByteArray(); httpConn9.setRequestProperty("Content-Length", String.valueOf(b9.length)); httpConn9.setRequestProperty("Content-Type", "application/soap+xml; charset=UTF-8"); httpConn9.setRequestProperty("SOAPAction", soapAction); httpConn9.setRequestMethod("POST"); httpConn9.setDoOutput(true); httpConn9.setDoInput(true); OutputStream out9 = httpConn9.getOutputStream(); out9.write(b9); out9.close(); InputStreamReader isr9 = new InputStreamReader(httpConn9.getInputStream()); BufferedReader in9 = new BufferedReader(isr9); String inputLine9; StringBuffer response9 = new StringBuffer(); while ((inputLine9 = in9.readLine()) != null) { response9.append(inputLine9); } in9.close(); System.out.println("\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n" + "####################################################" + "#################################################\n" + "####################################################" + "#################################################\n" + "Component Name: Business Manager\n" + "Interface Name: getReport\n" + "Operation Name: " + "getViolationsReportByProductOfferIdYearMonthDay\n" + "Input" + "ProductOfferID-1\n" + "PartyID-1\n" + "\n" + "####################################################" + "#################################################\n" + "####################################################" + "#################################################\n" + "######################################## RESPONSE" + "############################################\n\n"); System.out.println("--------------------------------"); System.out.println("Response\n" + response9.toString()); } | 17,070 |
1 | public static void messageDigestTest() { try { MessageDigest md = MessageDigest.getInstance("MD5"); md.update("computer".getBytes()); md.update("networks".getBytes()); System.out.println(new String(md.digest())); System.out.println(new String(md.digest("computernetworks".getBytes()))); } catch (Exception e) { e.printStackTrace(); } } | public void test_digest() throws UnsupportedEncodingException { MessageDigest sha = null; try { sha = MessageDigest.getInstance("SHA"); assertNotNull(sha); } catch (NoSuchAlgorithmException e) { fail("getInstance did not find algorithm"); } sha.update(MESSAGE.getBytes("UTF-8")); byte[] digest = sha.digest(); assertTrue("bug in SHA", MessageDigest.isEqual(digest, MESSAGE_DIGEST)); sha.reset(); for (int i = 0; i < 63; i++) { sha.update((byte) 'a'); } digest = sha.digest(); assertTrue("bug in SHA", MessageDigest.isEqual(digest, MESSAGE_DIGEST_63_As)); sha.reset(); for (int i = 0; i < 64; i++) { sha.update((byte) 'a'); } digest = sha.digest(); assertTrue("bug in SHA", MessageDigest.isEqual(digest, MESSAGE_DIGEST_64_As)); sha.reset(); for (int i = 0; i < 65; i++) { sha.update((byte) 'a'); } digest = sha.digest(); assertTrue("bug in SHA", MessageDigest.isEqual(digest, MESSAGE_DIGEST_65_As)); testSerializationSHA_DATA_1(sha); testSerializationSHA_DATA_2(sha); } | 17,071 |
0 | public static String encryptPassword(String password) { try { MessageDigest md = MessageDigest.getInstance("SHA"); md.update(password.getBytes()); byte[] hash = md.digest(); StringBuffer hashStringBuf = new StringBuffer(); String byteString; int byteLength; for (int index = 0; index < hash.length; index++) { byteString = String.valueOf(hash[index] + 128); byteLength = byteString.length(); switch(byteLength) { case 1: byteString = "00" + byteString; break; case 2: byteString = "0" + byteString; break; } hashStringBuf.append(byteString); } return hashStringBuf.toString(); } catch (NoSuchAlgorithmException nsae) { log.error("Error getting password hash - " + nsae.getMessage()); return null; } } | private void gerarComissao() { int opt = Funcoes.mensagemConfirma(null, "Confirma gerar comiss�es para o vendedor " + txtNomeVend.getVlrString().trim() + "?"); if (opt == JOptionPane.OK_OPTION) { StringBuilder insert = new StringBuilder(); insert.append("INSERT INTO RPCOMISSAO "); insert.append("(CODEMP, CODFILIAL, CODPED, CODITPED, "); insert.append("CODEMPVD, CODFILIALVD, CODVEND, VLRCOMISS ) "); insert.append("VALUES "); insert.append("(?,?,?,?,?,?,?,?)"); PreparedStatement ps; int parameterIndex; boolean gerou = false; try { for (int i = 0; i < tab.getNumLinhas(); i++) { if (((BigDecimal) tab.getValor(i, 8)).floatValue() > 0) { parameterIndex = 1; ps = con.prepareStatement(insert.toString()); ps.setInt(parameterIndex++, AplicativoRep.iCodEmp); ps.setInt(parameterIndex++, ListaCampos.getMasterFilial("RPCOMISSAO")); ps.setInt(parameterIndex++, txtCodPed.getVlrInteger()); ps.setInt(parameterIndex++, (Integer) tab.getValor(i, ETabNota.ITEM.ordinal())); ps.setInt(parameterIndex++, AplicativoRep.iCodEmp); ps.setInt(parameterIndex++, ListaCampos.getMasterFilial("RPVENDEDOR")); ps.setInt(parameterIndex++, txtCodVend.getVlrInteger()); ps.setBigDecimal(parameterIndex++, (BigDecimal) tab.getValor(i, ETabNota.VLRCOMIS.ordinal())); ps.executeUpdate(); gerou = true; } } if (gerou) { Funcoes.mensagemInforma(null, "Comiss�o gerada para " + txtNomeVend.getVlrString().trim()); txtCodPed.setText("0"); lcPedido.carregaDados(); carregaTabela(); con.commit(); } else { Funcoes.mensagemInforma(null, "N�o foi possiv�l gerar comiss�o!\nVerifique os valores das comiss�es dos itens."); } } catch (Exception e) { e.printStackTrace(); Funcoes.mensagemErro(this, "Erro ao gerar comiss�o!\n" + e.getMessage()); try { con.rollback(); } catch (SQLException e1) { e1.printStackTrace(); } } } } | 17,072 |
1 | public File addFile(File file, String suffix) throws IOException { if (file.exists() && file.isFile()) { File nf = File.createTempFile(prefix, "." + suffix, workdir); nf.delete(); if (!file.renameTo(nf)) { IOUtils.copy(file, nf); } synchronized (fileList) { fileList.add(nf); } if (log.isDebugEnabled()) { log.debug("Add file [" + file.getPath() + "] -> [" + nf.getPath() + "]"); } return nf; } return file; } | 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(); } } | 17,073 |
1 | public static Checksum checksum(File file, Checksum checksum) throws IOException { if (file.isDirectory()) { throw new IllegalArgumentException("Checksums can't be computed on directories"); } InputStream in = null; try { in = new CheckedInputStream(new FileInputStream(file), checksum); IOUtils.copy(in, new OutputStream() { @Override public void write(byte[] b, int off, int len) { } @Override public void write(int b) { } @Override public void write(byte[] b) throws IOException { } }); } finally { IOUtils.closeQuietly(in); } return checksum; } | private static void copyFile(File source, File dest, boolean visibleFilesOnly) throws IOException { if (visibleFilesOnly && isHiddenOrDotFile(source)) { return; } if (dest.exists()) { System.err.println("Destination File Already Exists: " + dest); } FileChannel in = null, out = null; try { in = new FileInputStream(source).getChannel(); out = new FileOutputStream(dest).getChannel(); in.transferTo(0, in.size(), out); } finally { if (in != null) { in.close(); } if (out != null) { out.close(); } } } | 17,074 |
1 | public static Document validateXml(File messageFile, URL inputUrl, String[] catalogs) throws IOException, ParserConfigurationException, Exception, SAXException, FileNotFoundException { InputSource source = new InputSource(inputUrl.openStream()); Document logDoc = DomUtil.getNewDom(); XMLReader reader = SaxUtil.getXMLFormatLoggingXMLReader(log, logDoc, true, catalogs); reader.parse(source); InputStream logStream = DomUtil.serializeToInputStream(logDoc, "utf-8"); System.out.println("Creating message file \"" + messageFile.getAbsolutePath() + "\"..."); OutputStream fos = new FileOutputStream(messageFile); IOUtils.copy(logStream, fos); return logDoc; } | public String doAdd(ActionMapping mapping, ActionForm form, HttpServletRequest request, HttpServletResponse response) throws Exception { UploadFileForm vo = (UploadFileForm) form; String review = request.getParameter("review"); String realpath = getServlet().getServletContext().getRealPath("/"); realpath = realpath.replaceAll("\\\\", "/"); String inforId = request.getParameter("inforId"); request.setAttribute("id", inforId); String str_postFIX = ""; int i_p = 0; if (null == review) { FormFile file = vo.getFile(); if (file != null) { String rootFilePath = getServlet().getServletContext().getRealPath(request.getContextPath()); rootFilePath = (new StringBuilder(String.valueOf(rootFilePath))).append(UploadFileOne.strPath).toString(); String strAppend = (new StringBuilder(String.valueOf(UUIDGenerator.nextHex()))).append(UploadFileOne.getFileType(file)).toString(); if (file.getFileSize() != 0) { file.getInputStream(); String name = file.getFileName(); i_p = file.getFileName().lastIndexOf("."); str_postFIX = file.getFileName().substring(i_p, file.getFileName().length()); String fullPath = realpath + "attach/" + strAppend + str_postFIX; t_attach attach = new t_attach(); attach.setAttach_fullname(fullPath); attach.setAttach_name(name); attach.setInfor_id(Integer.parseInt(inforId)); attach.setInsert_day(new Date()); attach.setUpdate_day(new Date()); t_attach_EditMap attachEdit = new t_attach_EditMap(); attachEdit.add(attach); File sysfile = new File(fullPath); if (!sysfile.exists()) { sysfile.createNewFile(); } java.io.OutputStream out = new FileOutputStream(sysfile); org.apache.commons.io.IOUtils.copy(file.getInputStream(), out); out.close(); } } request.setAttribute("operating-status", "�����ɹ�! ��ӭ����ʹ�á�"); return "editsave"; } else { String rootFilePath = getServlet().getServletContext().getRealPath(request.getContextPath()); rootFilePath = (new StringBuilder(String.valueOf(rootFilePath))).append(UploadFileOne.strPath).toString(); FormFile file = vo.getFile(); FormFile file2 = vo.getFile2(); FormFile file3 = vo.getFile3(); t_infor_review newreview = new t_infor_review(); String content = request.getParameter("content"); newreview.setContent(content); if (null != inforId) newreview.setInfor_id(Integer.parseInt(inforId)); newreview.setInsert_day(new Date()); UserDetails user = LoginUtils.getLoginUser(request); newreview.setCreate_name(user.getUsercode()); if (null != file.getFileName() && !"".equals(file.getFileName())) { newreview.setAttachname1(file.getFileName()); String strAppend1 = (new StringBuilder(String.valueOf(UUIDGenerator.nextHex()))).append(UploadFileOne.getFileType(file)).toString(); i_p = file.getFileName().lastIndexOf("."); str_postFIX = file.getFileName().substring(i_p, file.getFileName().length()); newreview.setAttachfullname1(realpath + "attach/" + strAppend1 + str_postFIX); saveFile(file.getInputStream(), realpath + "attach/" + strAppend1 + str_postFIX); } if (null != file2.getFileName() && !"".equals(file2.getFileName())) { newreview.setAttachname2(file2.getFileName()); String strAppend2 = (new StringBuilder(String.valueOf(UUIDGenerator.nextHex()))).append(UploadFileOne.getFileType(file)).toString(); i_p = file2.getFileName().lastIndexOf("."); str_postFIX = file2.getFileName().substring(i_p, file2.getFileName().length()); newreview.setAttachfullname2(realpath + "attach/" + strAppend2 + str_postFIX); saveFile(file2.getInputStream(), realpath + "attach/" + strAppend2 + str_postFIX); } if (null != file3.getFileName() && !"".equals(file3.getFileName())) { newreview.setAttachname3(file3.getFileName()); String strAppend3 = (new StringBuilder(String.valueOf(UUIDGenerator.nextHex()))).append(UploadFileOne.getFileType(file)).toString(); i_p = file3.getFileName().lastIndexOf("."); str_postFIX = file3.getFileName().substring(i_p, file3.getFileName().length()); newreview.setAttachfullname3(realpath + "attach/" + strAppend3 + str_postFIX); saveFile(file3.getInputStream(), realpath + "attach/" + strAppend3 + str_postFIX); } t_infor_review_EditMap reviewEdit = new t_infor_review_EditMap(); reviewEdit.add(newreview); request.setAttribute("review", "1"); return "aftersave"; } } | 17,075 |
1 | public static void copy(FileInputStream source, FileOutputStream target) throws IOException { FileChannel sourceChannel = source.getChannel(); FileChannel targetChannel = target.getChannel(); sourceChannel.transferTo(0, sourceChannel.size(), targetChannel); sourceChannel.close(); targetChannel.close(); } | public Void doInBackground() { setProgress(0); for (int i = 0; i < uploadFiles.size(); i++) { String filePath = uploadFiles.elementAt(i).getFilePath(); String fileName = uploadFiles.elementAt(i).getFileName(); String fileMsg = "Uploading file " + (i + 1) + "/" + uploadFiles.size() + "\n"; this.publish(fileMsg); try { File inFile = new File(filePath); FileInputStream in = new FileInputStream(inFile); byte[] inBytes = new byte[(int) chunkSize]; int count = 1; int maxCount = (int) (inFile.length() / chunkSize); if (inFile.length() % chunkSize > 0) { maxCount++; } int readCount = 0; readCount = in.read(inBytes); while (readCount > 0) { File splitFile = File.createTempFile("upl", null, null); String splitName = splitFile.getPath(); FileOutputStream out = new FileOutputStream(splitFile); out.write(inBytes, 0, readCount); out.close(); boolean chunkFinal = (count == maxCount); fileMsg = " - Sending chunk " + count + "/" + maxCount + ": "; this.publish(fileMsg); boolean uploadSuccess = false; int uploadTries = 0; while (!uploadSuccess && uploadTries <= 5) { uploadTries++; boolean uploadStatus = upload(splitName, fileName, count, chunkFinal); if (uploadStatus) { fileMsg = "OK\n"; this.publish(fileMsg); uploadSuccess = true; } else { fileMsg = "ERROR\n"; this.publish(fileMsg); uploadSuccess = false; } } if (!uploadSuccess) { fileMsg = "There was an error uploading your files. Please let the pipeline administrator know about this problem. Cut and paste the messages in this box, and supply them.\n"; this.publish(fileMsg); errorFlag = true; return null; } float thisProgress = (count * 100) / (maxCount); float completeProgress = (i * (100 / uploadFiles.size())); float totalProgress = completeProgress + (thisProgress / uploadFiles.size()); setProgress((int) totalProgress); splitFile.delete(); readCount = in.read(inBytes); count++; } } catch (Exception e) { this.publish(e.toString()); } } return null; } | 17,076 |
0 | public static void copyFile(File file, File dest_file) throws FileNotFoundException, IOException { DataInputStream in = new DataInputStream(new BufferedInputStream(new FileInputStream(file))); DataOutputStream out = new DataOutputStream(new BufferedOutputStream(new FileOutputStream(dest_file))); byte[] buffer = new byte[1024]; int read; while ((read = in.read(buffer)) > 0) { out.write(buffer, 0, read); } in.close(); out.close(); } | public static ArrayList<FriendInfo> downloadFriendsList(String username) { try { URL url; url = new URL(WS_URL + "/user/" + URLEncoder.encode(username, "UTF-8") + "/friends.xml"); HttpURLConnection conn = (HttpURLConnection) url.openConnection(); conn.connect(); InputStream is = conn.getInputStream(); DocumentBuilderFactory dbFac = DocumentBuilderFactory.newInstance(); DocumentBuilder db = dbFac.newDocumentBuilder(); Document doc = db.parse(is); NodeList friends = doc.getElementsByTagName("user"); ArrayList<FriendInfo> result = new ArrayList<FriendInfo>(); for (int i = 0; i < friends.getLength(); i++) try { result.add(new FriendInfo((Element) friends.item(i))); } catch (Utils.ParseException e) { Log.e(TAG, "in downloadFriendsList", e); return null; } return result; } catch (Exception e) { Log.e(TAG, "in downloadFriendsList", e); return null; } } | 17,077 |
0 | public String fetchDataDailyByStockId(String StockId, String market) throws IOException { URL url = new URL(urlDailyStockPrice.replace("{0}", StockId + "." + market)); URLConnection con = url.openConnection(); con.setConnectTimeout(20000); InputStream is = con.getInputStream(); byte[] bs = new byte[1024]; int len; OutputStream os = new FileOutputStream(dailyStockPriceList, true); while ((len = is.read(bs)) != -1) { os.write(bs, 0, len); } os.flush(); os.close(); is.close(); con = null; url = null; return null; } | public static Image load(final InputStream input, String format, Point dimension) throws CoreException { MultiStatus status = new MultiStatus(GraphVizActivator.ID, 0, "Errors occurred while running Graphviz", null); File dotInput = null, dotOutput = null; ByteArrayOutputStream dotContents = new ByteArrayOutputStream(); try { dotInput = File.createTempFile(TMP_FILE_PREFIX, DOT_EXTENSION); dotOutput = File.createTempFile(TMP_FILE_PREFIX, "." + format); dotOutput.delete(); FileOutputStream tmpDotOutputStream = null; try { IOUtils.copy(input, dotContents); tmpDotOutputStream = new FileOutputStream(dotInput); IOUtils.copy(new ByteArrayInputStream(dotContents.toByteArray()), tmpDotOutputStream); } finally { IOUtils.closeQuietly(tmpDotOutputStream); } IStatus result = runDot(format, dimension, dotInput, dotOutput); status.add(result); status.add(logInput(dotContents)); if (dotOutput.isFile()) { if (!result.isOK() && Platform.inDebugMode()) LogUtils.log(status); ImageLoader loader = new ImageLoader(); ImageData[] imageData = loader.load(dotOutput.getAbsolutePath()); return new Image(Display.getDefault(), imageData[0]); } } catch (SWTException e) { status.add(new Status(IStatus.ERROR, GraphVizActivator.ID, "", e)); } catch (IOException e) { status.add(new Status(IStatus.ERROR, GraphVizActivator.ID, "", e)); } finally { dotInput.delete(); dotOutput.delete(); IOUtils.closeQuietly(input); } throw new CoreException(status); } | 17,078 |
1 | public static byte[] decrypt(byte[] ciphertext, byte[] key) throws IOException { CryptInputStream in = new CryptInputStream(new ByteArrayInputStream(ciphertext), new SerpentEngine(), key); ByteArrayOutputStream bout = new ByteArrayOutputStream(); IOUtils.copy(in, bout); return bout.toByteArray(); } | private void execute(File file) throws IOException { if (file == null) throw new RuntimeException("undefined file"); if (!file.exists()) throw new RuntimeException("file not found :" + file); if (!file.isFile()) throw new RuntimeException("not a file :" + file); String login = cfg.getProperty(GC_USERNAME); String password = null; if (cfg.containsKey(GC_PASSWORD)) { password = cfg.getProperty(GC_PASSWORD); } else { password = new String(Base64.decode(cfg.getProperty(GC_PASSWORD64))); } PostMethod post = null; try { HttpClient client = new HttpClient(); post = new PostMethod("https://" + projectName + ".googlecode.com/files"); post.addRequestHeader("User-Agent", getClass().getName()); post.addRequestHeader("Authorization", "Basic " + Base64.encode(login + ":" + password)); List<Part> parts = new ArrayList<Part>(); String s = this.summary; if (StringUtils.isBlank(s)) { s = file.getName() + " (" + TimeUtils.toYYYYMMDD() + ")"; } parts.add(new StringPart("summary", s)); for (String lbl : this.labels) { if (StringUtils.isBlank(lbl)) continue; parts.add(new StringPart("label", lbl.trim())); } parts.add(new FilePart("filename", file)); MultipartRequestEntity requestEntity = new MultipartRequestEntity(parts.toArray(new Part[parts.size()]), post.getParams()); post.setRequestEntity(requestEntity); int status = client.executeMethod(post); if (status != 201) { throw new IOException("http status !=201 : " + post.getResponseBodyAsString()); } else { IOUtils.copyTo(post.getResponseBodyAsStream(), new NullOutputStream()); } } finally { if (post != null) post.releaseConnection(); } } | 17,079 |
1 | 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 void verRecordatorio() { try { cantidadArchivos = obtenerCantidad() + 1; boolean existe = false; String filenametxt = ""; String filenamezip = ""; String hora = ""; String lugar = ""; String actividad = ""; String linea = ""; int dia = 0; int mes = 0; int ano = 0; for (int i = 1; i < cantidadArchivos; i++) { filenamezip = "recordatorio" + i + ".zip"; filenametxt = "recordatorio" + i + ".txt"; BufferedOutputStream dest = null; BufferedInputStream is = null; ZipEntry entry; ZipFile zipfile = new ZipFile(filenamezip); Enumeration e = zipfile.entries(); while (e.hasMoreElements()) { entry = (ZipEntry) e.nextElement(); is = new BufferedInputStream(zipfile.getInputStream(entry)); int count; byte data[] = new byte[buffer]; FileOutputStream fos = new FileOutputStream(entry.getName()); dest = new BufferedOutputStream(fos, buffer); while ((count = is.read(data, 0, buffer)) != -1) dest.write(data, 0, count); dest.flush(); dest.close(); is.close(); } DataInputStream input = new DataInputStream(new FileInputStream(filenametxt)); dia = Integer.parseInt(input.readLine()); mes = Integer.parseInt(input.readLine()); ano = Integer.parseInt(input.readLine()); if (dia == Integer.parseInt(identificarDato(datoSeleccionado))) { existe = true; hora = input.readLine(); lugar = input.readLine(); while ((linea = input.readLine()) != null) actividad += linea + "\n"; verRecordatorioInterfaz(hora, lugar, actividad); hora = ""; lugar = ""; actividad = ""; } input.close(); } if (!existe) JOptionPane.showMessageDialog(null, "No existe un recordatorio guardado\n" + "para el " + identificarDato(datoSeleccionado) + " de " + meses[mesTemporal].toLowerCase() + " del a�o " + anoTemporal, "No existe", JOptionPane.INFORMATION_MESSAGE); table.clearSelection(); } catch (Exception e) { JOptionPane.showMessageDialog(null, "Error en: " + e.toString(), "Error", JOptionPane.ERROR_MESSAGE); } } | 17,080 |
0 | public Document getKmlStream(String streetname, String number, String neighbourhood, String city, String state) throws RotaException { StringBuffer urlsb = new StringBuffer(resourceBundle.getString(Constants.URL_SEARCH)); DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance(); InputStream in = null; HttpURLConnection httpConnection = null; Document doc = null; dbf.setValidating(false); String proxy = resourceBundle.getString(Constants.PROXY_HOST); String port = resourceBundle.getString(Constants.PROXY_PORT); try { String address = String.format("%s+%s+%s+%s+%s", URLEncoder.encode(streetname.trim(), Constants.URL_ENCODING), URLEncoder.encode(number.trim(), Constants.URL_ENCODING), URLEncoder.encode(neighbourhood.trim(), Constants.URL_ENCODING), URLEncoder.encode(city.trim(), Constants.URL_ENCODING), URLEncoder.encode(state.trim(), Constants.URL_ENCODING)); DocumentBuilder df = dbf.newDocumentBuilder(); urlsb.append(address); urlsb.append(resourceBundle.getString(Constants.GOOGLE_TYPE_OUTPUT)); urlsb.append(resourceBundle.getString(Constants.SENSOR)); urlsb.append(resourceBundle.getString(Constants.GOOGLE_KEY)); urlsb.append(resourceBundle.getString(Constants.GOOGLE_KEY_VALUE)); String addressUTF8 = urlsb.toString(); URL url = new URL(addressUTF8); Properties systemproperties = System.getProperties(); if (proxy != null && !proxy.equals("")) { systemproperties.setProperty("http.proxyHost", proxy); systemproperties.setProperty("http.proxyPort", port); } httpConnection = (HttpURLConnection) url.openConnection(); httpConnection.connect(); in = httpConnection.getInputStream(); doc = df.parse(in); in.close(); httpConnection.disconnect(); if (doc == null || !verificaStatusRequisicao(doc)) { throw new RotaException("N�o foi poss�vel realizar a geodecodifica��o com o endere�o informado!"); } return doc; } catch (UnsupportedEncodingException ue) { logger.error(ue); throw new RotaException("Encoding n�o suportado : " + ue.getMessage()); } catch (MalformedURLException ma) { logger.error(ma); throw new RotaException("Erro na URL : " + ma.getMessage()); } catch (ParserConfigurationException pe) { logger.error(pe); throw new RotaException("Erro ao realizar o parser da configura��o : " + pe.getMessage()); } catch (SAXException sa) { logger.error(sa); throw new RotaException("Erro de SAX : " + sa.getMessage()); } catch (ConnectException co) { logger.error(co); throw new RotaException("N�o foi poss�vel estabelecer a conex�o http : " + co.getMessage()); } catch (IOException io) { logger.error(io); throw new RotaException("Erro de io : ", io); } catch (Exception ex) { throw new RotaException("N�o foi poss�vel gerar a rota : " + ex.getMessage()); } finally { if (in != null) { try { in.close(); } catch (Exception ex) { throw new RotaException("N�o foi poss�vel fechar o stream de dados ! : " + ex.getMessage()); } } if (httpConnection != null) { httpConnection.disconnect(); } } } | private void doLogin() { try { println("Logging in as '" + username.getText() + "'"); URL url = new URL("http://" + hostname + "/migrate"); URLConnection conn = url.openConnection(); conn.setDoOutput(true); OutputStreamWriter wr = new OutputStreamWriter(conn.getOutputStream()); wr.write(URLEncoder.encode("login", "UTF-8") + "=" + encodeCredentials()); wr.flush(); BufferedInputStream in = new BufferedInputStream(conn.getInputStream()); DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance(); dbf.setNamespaceAware(true); DocumentBuilder db = dbf.newDocumentBuilder(); Document doc = db.parse(in); Element root = doc.getDocumentElement(); in.close(); if (root.getAttribute("success").equals("false")) { println("Login Failed: " + getTextContent(root)); JOptionPane.showMessageDialog(this, "Login Failed: " + getTextContent(root), "Login Failed", JOptionPane.ERROR_MESSAGE); } else { token = root.hasAttribute("token") ? root.getAttribute("token") : null; if (token != null) { startImport(); } } } catch (Exception e) { ErrorReporter.showError(e, this); println(e.toString()); } } | 17,081 |
1 | public String getResource(String resourceName) throws IOException { InputStream resourceStream = resourceClass.getResourceAsStream(resourceName); ByteArrayOutputStream baos = new ByteArrayOutputStream(2048); IOUtils.copyAndClose(resourceStream, baos); String expected = new String(baos.toByteArray()); return expected; } | public static DownloadedContent downloadContent(final InputStream is) throws IOException { if (is == null) { return new DownloadedContent.InMemory(new byte[] {}); } final ByteArrayOutputStream bos = new ByteArrayOutputStream(); final byte[] buffer = new byte[1024]; int nbRead; try { while ((nbRead = is.read(buffer)) != -1) { bos.write(buffer, 0, nbRead); if (bos.size() > MAX_IN_MEMORY) { final File file = File.createTempFile("htmlunit", ".tmp"); file.deleteOnExit(); final FileOutputStream fos = new FileOutputStream(file); bos.writeTo(fos); IOUtils.copyLarge(is, fos); fos.close(); return new DownloadedContent.OnFile(file); } } } finally { IOUtils.closeQuietly(is); } return new DownloadedContent.InMemory(bos.toByteArray()); } | 17,082 |
1 | private static void doCopyFile(File srcFile, File destFile, boolean preserveFileDate) throws IOException { if (destFile.exists() && destFile.isDirectory()) { throw new IOException("Destination '" + destFile + "' exists but is a directory"); } FileInputStream input = new FileInputStream(srcFile); try { FileOutputStream output = new FileOutputStream(destFile); try { IOUtils.copy(input, output); } finally { IOUtils.closeQuietly(output); } } finally { IOUtils.closeQuietly(input); } if (srcFile.length() != destFile.length()) { throw new IOException("Failed to copy full contents from '" + srcFile + "' to '" + destFile + "'"); } if (preserveFileDate) { destFile.setLastModified(srcFile.lastModified()); } } | public static boolean predictDataSet(String completePath, String Type, String predictionOutputFileName, String slopeOneDataFolderName) { try { if (Type.equalsIgnoreCase("Qualifying")) { File inputFile = new File(completePath + fSep + "SmartGRAPE" + fSep + "CompleteQualifyingDataInByteFormat.txt"); FileChannel inC = new FileInputStream(inputFile).getChannel(); int filesize = (int) inC.size(); TShortObjectHashMap qualMap = new TShortObjectHashMap(17770, 1); ByteBuffer qualmappedfile = inC.map(FileChannel.MapMode.READ_ONLY, 0, filesize); while (qualmappedfile.hasRemaining()) { short movie = qualmappedfile.getShort(); int customer = qualmappedfile.getInt(); if (qualMap.containsKey(movie)) { TIntArrayList arr = (TIntArrayList) qualMap.get(movie); arr.add(customer); qualMap.put(movie, arr); } else { TIntArrayList arr = new TIntArrayList(); arr.add(customer); qualMap.put(movie, arr); } } System.out.println("Populated qualifying hashmap"); File outFile = new File(completePath + fSep + "SmartGRAPE" + fSep + predictionOutputFileName); FileChannel outC = new FileOutputStream(outFile).getChannel(); ByteBuffer buf; TShortObjectHashMap movieDiffStats; double finalPrediction; short[] movies = qualMap.keys(); Arrays.sort(movies); for (int i = 0; i < movies.length; i++) { short movieToProcess = movies[i]; movieDiffStats = loadMovieDiffStats(completePath, movieToProcess, slopeOneDataFolderName); System.out.println(movieDiffStats.size()); TIntArrayList customersToProcess = (TIntArrayList) qualMap.get(movieToProcess); for (int j = 0; j < customersToProcess.size(); j++) { int customerToProcess = customersToProcess.getQuick(j); finalPrediction = predictSlopeOneRating(customerToProcess, movieDiffStats); if (finalPrediction == finalPrediction) { if (finalPrediction < 1.0) finalPrediction = 1.0; else if (finalPrediction > 5.0) finalPrediction = 5.0; } else finalPrediction = GetAveragePrediction(movieToProcess); buf = ByteBuffer.allocate(10); buf.putShort(movieToProcess); buf.putInt(customerToProcess); buf.putFloat(new Double(finalPrediction).floatValue()); buf.flip(); outC.write(buf); } } outC.close(); return true; } else if (Type.equalsIgnoreCase("Probe")) { File inputFile = new File(completePath + fSep + "SmartGRAPE" + fSep + "CompleteProbeDataInByteFormat.txt"); FileChannel inC = new FileInputStream(inputFile).getChannel(); int filesize = (int) inC.size(); TShortObjectHashMap probeMap = new TShortObjectHashMap(17770, 1); ByteBuffer probemappedfile = inC.map(FileChannel.MapMode.READ_ONLY, 0, filesize); while (probemappedfile.hasRemaining()) { short movie = probemappedfile.getShort(); int customer = probemappedfile.getInt(); byte rating = probemappedfile.get(); if (probeMap.containsKey(movie)) { TIntByteHashMap actualRatings = (TIntByteHashMap) probeMap.get(movie); actualRatings.put(customer, rating); probeMap.put(movie, actualRatings); } else { TIntByteHashMap actualRatings = new TIntByteHashMap(); actualRatings.put(customer, rating); probeMap.put(movie, actualRatings); } } System.out.println("Populated probe hashmap"); File outFile = new File(completePath + fSep + "SmartGRAPE" + fSep + predictionOutputFileName); FileChannel outC = new FileOutputStream(outFile).getChannel(); ByteBuffer buf; double finalPrediction; TShortObjectHashMap movieDiffStats; short[] movies = probeMap.keys(); Arrays.sort(movies); for (int i = 0; i < movies.length; i++) { short movieToProcess = movies[i]; movieDiffStats = loadMovieDiffStats(completePath, movieToProcess, slopeOneDataFolderName); TIntByteHashMap custRatingsToProcess = (TIntByteHashMap) probeMap.get(movieToProcess); TIntArrayList customersToProcess = new TIntArrayList(custRatingsToProcess.keys()); for (int j = 0; j < customersToProcess.size(); j++) { int customerToProcess = customersToProcess.getQuick(j); byte rating = custRatingsToProcess.get(customerToProcess); finalPrediction = predictSlopeOneRating(customerToProcess, movieDiffStats); if (finalPrediction == finalPrediction) { if (finalPrediction < 1.0) finalPrediction = 1.0; else if (finalPrediction > 5.0) finalPrediction = 5.0; } else finalPrediction = GetAveragePrediction(movieToProcess); buf = ByteBuffer.allocate(11); buf.putShort(movieToProcess); buf.putInt(customerToProcess); buf.put(rating); buf.putFloat(new Double(finalPrediction).floatValue()); buf.flip(); outC.write(buf); } } outC.close(); return true; } else return false; } catch (Exception e) { e.printStackTrace(); return false; } } | 17,083 |
0 | @Test public void testCopy_readerToOutputStream_Encoding_nullOut() throws Exception { InputStream in = new ByteArrayInputStream(inData); in = new YellOnCloseInputStreamTest(in); Reader reader = new InputStreamReader(in, "US-ASCII"); try { IOUtils.copy(reader, (OutputStream) null, "UTF16"); fail(); } catch (NullPointerException ex) { } } | private static void addFromResource(String resource, OutputStream out) { URL url = OpenOfficeDocumentCreator.class.getResource(resource); try { InputStream in = url.openStream(); byte[] buffer = new byte[256]; synchronized (in) { synchronized (out) { while (true) { int bytesRead = in.read(buffer); if (bytesRead == -1) break; out.write(buffer, 0, bytesRead); } } } } catch (IOException e) { e.printStackTrace(); } } | 17,084 |
1 | public static synchronized String encrypt(String plaintext) throws NoSuchAlgorithmException, UnsupportedEncodingException { MessageDigest md = null; md = MessageDigest.getInstance("SHA"); md.update(plaintext.getBytes("UTF-8")); byte raw[] = md.digest(); String hash = (new BASE64Encoder()).encode(raw); return hash; } | public static String encryptString(String str) { StringBuffer sb = new StringBuffer(); int i; try { MessageDigest md5 = MessageDigest.getInstance("MD5"); md5.update(str.getBytes()); byte[] md5Bytes = md5.digest(); for (i = 0; i < md5Bytes.length; i++) { sb.append(md5Bytes[i]); } } catch (Exception e) { } return sb.toString(); } | 17,085 |
0 | private FTPClient getClient() throws SocketException, IOException { FTPClient ftp = new FTPClient(); ftp.addProtocolCommandListener(new PrintCommandListener(new PrintWriter(System.out))); ftp.setDefaultPort(getPort()); ftp.connect(getIp()); int reply = ftp.getReplyCode(); if (!FTPReply.isPositiveCompletion(reply)) { log.warn("FTP server refused connection: {}", getIp()); ftp.disconnect(); return null; } if (!ftp.login(getUsername(), getPassword())) { log.warn("FTP server refused login: {}, user: {}", getIp(), getUsername()); ftp.logout(); ftp.disconnect(); return null; } ftp.setControlEncoding(getEncoding()); ftp.setFileType(FTP.BINARY_FILE_TYPE); ftp.enterLocalPassiveMode(); return ftp; } | 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; } | 17,086 |
1 | private void initLogging() { File logging = new File(App.getHome(), "logging.properties"); if (!logging.exists()) { InputStream input = getClass().getResourceAsStream("logging.properties-setup"); OutputStream output = null; try { output = new FileOutputStream(logging); IOUtils.copy(input, output); } catch (Exception ex) { } finally { IOUtils.closeQuietly(input); IOUtils.closeQuietly(output); } } FileInputStream input = null; try { input = new FileInputStream(logging); LogManager.getLogManager().readConfiguration(input); } catch (Exception ex) { } finally { IOUtils.closeQuietly(input); } } | public static void copy(String source, String destination) { FileReader in = null; FileWriter out = null; try { File inputFile = new File(source); File outputFile = new File(destination); in = new FileReader(inputFile); out = new FileWriter(outputFile); int c; while ((c = in.read()) != -1) out.write(c); } catch (IOException e) { e.printStackTrace(); } finally { if (in != null) try { in.close(); } catch (IOException e) { e.printStackTrace(); } if (out != null) try { out.close(); } catch (IOException e) { e.printStackTrace(); } } } | 17,087 |
1 | protected static String getFileContentAsString(URL url, String encoding) throws IOException { InputStream input = null; StringWriter sw = new StringWriter(); try { System.out.println("Free mem :" + Runtime.getRuntime().freeMemory()); input = url.openStream(); IOUtils.copy(input, sw, encoding); System.out.println("Free mem :" + Runtime.getRuntime().freeMemory()); } finally { if (input != null) { input.close(); System.gc(); input = null; System.out.println("Free mem :" + Runtime.getRuntime().freeMemory()); } } return sw.toString(); } | public static void translateTableMetaData(String baseDir, String tableName, NameSpaceDefinition nsDefinition) throws Exception { setVosiNS(baseDir, "table", nsDefinition); String filename = baseDir + "table.xsl"; Scanner s = new Scanner(new File(filename)); PrintWriter fw = new PrintWriter(new File(baseDir + tableName + ".xsl")); while (s.hasNextLine()) { fw.println(s.nextLine().replaceAll("TABLENAME", tableName)); } s.close(); fw.close(); applyStyle(baseDir + "tables.xml", baseDir + tableName + ".json", baseDir + tableName + ".xsl"); } | 17,088 |
1 | @SuppressWarnings("unchecked") private void doService(final HttpServletRequest request, final HttpServletResponse response) throws Exception { final String url = request.getRequestURL().toString(); if (url.endsWith("/favicon.ico")) { response.setStatus(HttpServletResponse.SC_NOT_FOUND); return; } if (url.contains("/delay")) { final String delay = StringUtils.substringBetween(url, "/delay", "/"); final int ms = Integer.parseInt(delay); if (LOG.isDebugEnabled()) { LOG.debug("Sleeping for " + ms + " before to deliver " + url); } Thread.sleep(ms); } final URL requestedUrl = new URL(url); final WebRequest webRequest = new WebRequest(requestedUrl); webRequest.setHttpMethod(HttpMethod.valueOf(request.getMethod())); for (final Enumeration<String> en = request.getHeaderNames(); en.hasMoreElements(); ) { final String headerName = en.nextElement(); final String headerValue = request.getHeader(headerName); webRequest.setAdditionalHeader(headerName, headerValue); } final List<NameValuePair> requestParameters = new ArrayList<NameValuePair>(); for (final Enumeration<String> paramNames = request.getParameterNames(); paramNames.hasMoreElements(); ) { final String name = paramNames.nextElement(); final String[] values = request.getParameterValues(name); for (final String value : values) { requestParameters.add(new NameValuePair(name, value)); } } if ("PUT".equals(request.getMethod()) && request.getContentLength() > 0) { final byte[] buffer = new byte[request.getContentLength()]; request.getInputStream().readLine(buffer, 0, buffer.length); webRequest.setRequestBody(new String(buffer)); } else { webRequest.setRequestParameters(requestParameters); } final WebResponse resp = MockConnection_.getResponse(webRequest); response.setStatus(resp.getStatusCode()); for (final NameValuePair responseHeader : resp.getResponseHeaders()) { response.addHeader(responseHeader.getName(), responseHeader.getValue()); } if (WriteContentAsBytes_) { IOUtils.copy(resp.getContentAsStream(), response.getOutputStream()); } else { final String newContent = getModifiedContent(resp.getContentAsString()); final String contentCharset = resp.getContentCharset(); response.setCharacterEncoding(contentCharset); response.getWriter().print(newContent); } response.flushBuffer(); } | public static void copy(Context cx, Scriptable thisObj, Object[] args, Function funObj) throws IOException { InputStream input = (InputStream) ((NativeJavaObject) args[0]).unwrap(); OutputStream output = (OutputStream) ((NativeJavaObject) args[1]).unwrap(); IOUtils.copy(input, output); } | 17,089 |
1 | public static void compress(final File zip, final Map<InputStream, String> entries, final IProgressMonitor monitor) throws IOException { if (zip == null || entries == null || CollectionUtils.isEmpty(entries.keySet())) throw new IllegalArgumentException("One ore more parameters are empty!"); if (zip.exists()) zip.delete(); else if (!zip.getParentFile().exists()) zip.getParentFile().mkdirs(); ZipOutputStream out = new ZipOutputStream(new BufferedOutputStream(new FileOutputStream(zip))); out.setLevel(Deflater.BEST_COMPRESSION); try { for (InputStream inputStream : entries.keySet()) { ZipEntry zipEntry = new ZipEntry(skipBeginningSlash(entries.get(inputStream))); out.putNextEntry(zipEntry); IOUtils.copy(inputStream, out); out.closeEntry(); inputStream.close(); if (monitor != null) monitor.worked(1); } } finally { IOUtils.closeQuietly(out); } } | public void writeData(String name, int items, int mznum, int mzscale, long tstart, long tdelta, int[] peaks) { PrintWriter file = getWriter(name + ".txt"); file.println("999 9999"); file.println("Doe, John"); file.println("TEST Lab"); if (mzscale == 1) file.println("PALMS Positive Ion Data"); else if (mzscale == -1) file.println("PALMS Negative Ion Data"); else file.println("PALMS GJIFJIGJ Ion Data"); file.println("TEST Mission"); file.println("1 1"); file.println("1970 01 01 2008 07 09"); file.println("0"); file.println("TIME (UT SECONDS)"); file.println(mznum + 4); for (int i = 0; i < mznum + 4; i++) file.println("1.0"); for (int i = 0; i < mznum + 4; i++) file.println("9.9E29"); file.println("TOTION total MCP signal (electron units)"); file.println("HMASS high mass integral (fraction)"); file.println("UNLIST (unlisted low mass peaks (fraction)"); file.println("UFO unidentified peaks (fraction)"); for (int i = 1; i <= mznum; i++) file.println("MS" + i + " (fraction)"); int header2length = 13; file.println(header2length); for (int i = 0; i < header2length; i++) file.println("1.0"); for (int i = 0; i < header2length; i++) file.println("9.9E29"); file.println("AirCraftTime aircraft time (s)"); file.println("INDEX index ()"); file.println("SCAT scatter (V)"); file.println("JMETER joule meter ()"); file.println("ND neutral density (fraction)"); file.println("SCALEA Mass scale intercept (us)"); file.println("SCALEB mass scale slope (us)"); file.println("NUMPKS number of peaks ()"); file.println("CONF confidence (coded)"); file.println("CAT preliminary category ()"); file.println("AeroDiam aerodynamic diameter (um)"); file.println("AeroDiam1p7 aero diam if density=1.7 (um)"); file.println("TOTBACK total background subtracted (electron units)"); file.println("0"); file.println("0"); String nothing = "0.000000"; for (int i = 0; i < items; i++) { file.println(tstart + (tdelta * i)); file.println(tstart + (tdelta * i) - 3); file.println(i + 1); for (int j = 0; j < 15; j++) file.println(Math.random()); boolean peaked = false; for (int k = 1; k <= mznum; k++) { for (int j = 0; j < peaks.length && !peaked; j++) if (k == peaks[j]) { double randData = (int) (1000000 * (j + 1)); file.println(randData / 1000000); peaked = true; } if (!peaked) file.println(nothing); peaked = false; } } try { Scanner test = new Scanner(f); while (test.hasNext()) { System.out.println(test.nextLine()); } System.out.println("test"); } catch (Exception e) { } file.close(); } | 17,090 |
1 | public void copieFichier(String fileIn, String fileOut) { FileChannel in = null; FileChannel out = null; try { in = new FileInputStream(fileIn).getChannel(); out = new FileOutputStream(fileOut).getChannel(); in.transferTo(0, in.size(), out); } catch (Exception e) { e.printStackTrace(); } finally { if (in != null) { try { in.close(); } catch (IOException e) { } } if (out != null) { try { out.close(); } catch (IOException e) { } } } } | public void getZipFiles(String filename) { try { String destinationname = "c:\\mods\\peu\\"; byte[] buf = new byte[1024]; ZipInputStream zipinputstream = null; ZipEntry zipentry; zipinputstream = new ZipInputStream(new FileInputStream(filename)); zipentry = zipinputstream.getNextEntry(); while (zipentry != null) { String entryName = zipentry.getName(); System.out.println("entryname " + entryName); int n; FileOutputStream fileoutputstream; File newFile = new File(entryName); String directory = newFile.getParent(); if (directory == null) { if (newFile.isDirectory()) break; } fileoutputstream = new FileOutputStream(destinationname + entryName); while ((n = zipinputstream.read(buf, 0, 1024)) > -1) fileoutputstream.write(buf, 0, n); fileoutputstream.close(); zipinputstream.closeEntry(); zipentry = zipinputstream.getNextEntry(); } zipinputstream.close(); } catch (Exception e) { e.printStackTrace(); } } | 17,091 |
1 | private static void readAndRewrite(File inFile, File outFile) throws IOException { ImageInputStream iis = ImageIO.createImageInputStream(new BufferedInputStream(new FileInputStream(inFile))); DcmParser dcmParser = DcmParserFactory.getInstance().newDcmParser(iis); Dataset ds = DcmObjectFactory.getInstance().newDataset(); dcmParser.setDcmHandler(ds.getDcmHandler()); dcmParser.parseDcmFile(null, Tags.PixelData); PixelDataReader pdReader = pdFact.newReader(ds, iis, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); System.out.println("reading " + inFile + "..."); pdReader.readPixelData(false); ImageOutputStream out = ImageIO.createImageOutputStream(new BufferedOutputStream(new FileOutputStream(outFile))); DcmEncodeParam dcmEncParam = DcmEncodeParam.IVR_LE; ds.writeDataset(out, dcmEncParam); ds.writeHeader(out, dcmEncParam, Tags.PixelData, dcmParser.getReadVR(), dcmParser.getReadLength()); System.out.println("writing " + outFile + "..."); PixelDataWriter pdWriter = pdFact.newWriter(pdReader.getPixelDataArray(), false, ds, out, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); pdWriter.writePixelData(); out.flush(); out.close(); System.out.println("done!"); } | public static void copyFileTo(String destFileName, String resourceFileName) { if (destFileName == null || resourceFileName == null) throw new IllegalArgumentException("Argument cannot be null."); try { FileInputStream in = null; FileOutputStream out = null; File resourceFile = new File(resourceFileName); if (!resourceFile.isFile()) { System.out.println(resourceFileName + " cannot be opened."); return; } in = new FileInputStream(resourceFile); out = new FileOutputStream(new File(destFileName)); int c; while ((c = in.read()) != -1) out.write(c); in.close(); out.close(); } catch (IOException ex) { ex.printStackTrace(); } } | 17,092 |
0 | public APIResponse update(Transaction transaction) throws Exception { APIResponse response = new APIResponse(); connection = (HttpURLConnection) new URL(url + "/api/transaction/update").openConnection(); connection.setDoOutput(true); connection.setRequestMethod("PUT"); connection.setRequestProperty("Content-Type", "application/json; charset=utf-8"); connection.setUseCaches(false); connection.setConnectTimeout(TIMEOUT); connection.connect(); marshaller.marshal(transaction, new MappedXMLStreamWriter(new MappedNamespaceConvention(new Configuration()), new OutputStreamWriter(connection.getOutputStream(), "utf-8"))); connection.getOutputStream().flush(); connection.getOutputStream().close(); if (connection.getResponseCode() == HttpURLConnection.HTTP_OK) { JSONObject obj = new JSONObject(new String(new BufferedReader(new InputStreamReader(connection.getInputStream(), "utf-8")).readLine())); response.setDone(true); response.setMessage(unmarshaller.unmarshal(new MappedXMLStreamReader(obj, new MappedNamespaceConvention(new Configuration())))); connection.getInputStream().close(); } else { response.setDone(false); response.setMessage("Update Transaction Error Code: Http (" + connection.getResponseCode() + ")"); } connection.disconnect(); return response; } | private void work(String[] args) throws Exception { String dictLocation = CONTENT_URL; String cpeContentDirName = CONTENT_DIR; String fn = dictLocation.substring(dictLocation.lastIndexOf("/") + 1); File destFile = new File(cpeContentDirName + File.separator + fn); URL url = new URL(dictLocation); URLConnection conn = url.openConnection(); conn.connect(); long lmodifiedRemote = conn.getLastModified(); boolean needToDownload = false; if (destFile.exists()) { System.out.println(destFile.getAbsolutePath() + " exists, check modification time"); long lmodifiedLocal = destFile.lastModified(); if (lmodifiedRemote > lmodifiedLocal) { System.out.println("Server file is newer, need to download"); needToDownload = true; } else { System.out.println("Local version is newer, no need to download"); } } else { System.out.println("Local version doesn't exist, need to download"); needToDownload = true; } if (needToDownload) { InputStream is = conn.getInputStream(); FileOutputStream fos = new FileOutputStream(destFile); byte[] buff = new byte[8192]; int read = 0; while ((read = is.read(buff)) > 0) { fos.write(buff, 0, read); } fos.flush(); fos.close(); is.close(); } } | 17,093 |
1 | public void processExplicitSchemaAndWSDL(HttpServletRequest req, HttpServletResponse res) throws IOException, ServletException { HashMap services = configContext.getAxisConfiguration().getServices(); String filePart = req.getRequestURL().toString(); String schema = filePart.substring(filePart.lastIndexOf("/") + 1, filePart.length()); if ((services != null) && !services.isEmpty()) { Iterator i = services.values().iterator(); while (i.hasNext()) { AxisService service = (AxisService) i.next(); InputStream stream = service.getClassLoader().getResourceAsStream("META-INF/" + schema); if (stream != null) { OutputStream out = res.getOutputStream(); res.setContentType("text/xml"); IOUtils.copy(stream, out, true); return; } } } } | public RawTableData(int selectedId) { selectedProjectId = selectedId; String urlString = dms_url + "/servlet/com.ufnasoft.dms.server.ServerGetProjectDocuments"; String rvalue = ""; String filename = dms_home + FS + "temp" + FS + username + "documents.xml"; try { String urldata = urlString + "?username=" + URLEncoder.encode(username, "UTF-8") + "&key=" + URLEncoder.encode(key, "UTF-8") + "&projectid=" + selectedProjectId + "&filename=" + URLEncoder.encode(username, "UTF-8") + "documents.xml"; ; DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); DocumentBuilder parser = factory.newDocumentBuilder(); URL u = new URL(urldata); DataInputStream is = new DataInputStream(u.openStream()); FileOutputStream os = new FileOutputStream(filename); int iBufSize = is.available(); byte inBuf[] = new byte[20000 * 1024]; int iNumRead; while ((iNumRead = is.read(inBuf, 0, iBufSize)) > 0) os.write(inBuf, 0, iNumRead); os.close(); is.close(); File f = new File(filename); InputStream inputstream = new FileInputStream(f); Document document = parser.parse(inputstream); NodeList nodelist = document.getElementsByTagName("doc"); int num = nodelist.getLength(); rawTableData = new String[num][11]; imageNames = new String[num]; for (int i = 0; i < num; i++) { rawTableData[i][0] = new String(DOMUtil.getSimpleElementText((Element) nodelist.item(i), "did")); rawTableData[i][1] = new String(DOMUtil.getSimpleElementText((Element) nodelist.item(i), "t")); rawTableData[i][2] = new String(DOMUtil.getSimpleElementText((Element) nodelist.item(i), "f")); rawTableData[i][3] = new String(DOMUtil.getSimpleElementText((Element) nodelist.item(i), "d")); rawTableData[i][4] = new String(DOMUtil.getSimpleElementText((Element) nodelist.item(i), "l")); String firstname = new String(DOMUtil.getSimpleElementText((Element) nodelist.item(i), "fn")); String lastname = new String(DOMUtil.getSimpleElementText((Element) nodelist.item(i), "ln")); rawTableData[i][5] = firstname + " " + lastname; rawTableData[i][6] = new String(DOMUtil.getSimpleElementText((Element) nodelist.item(i), "dln")); rawTableData[i][7] = new String(DOMUtil.getSimpleElementText((Element) nodelist.item(i), "rsid")); rawTableData[i][8] = new String(DOMUtil.getSimpleElementText((Element) nodelist.item(i), "img")); imageNames[i] = new String(DOMUtil.getSimpleElementText((Element) nodelist.item(i), "img")); rawTableData[i][9] = new String(DOMUtil.getSimpleElementText((Element) nodelist.item(i), "ucin")); rawTableData[i][10] = new String(DOMUtil.getSimpleElementText((Element) nodelist.item(i), "dtid")); } } catch (MalformedURLException ex) { System.out.println(ex); } catch (ParserConfigurationException ex) { System.out.println(ex); } catch (NullPointerException e) { } catch (Exception ex) { System.out.println(ex); } } | 17,094 |
1 | 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); } } | private final long test(final boolean applyFilter, final int executionCount) throws NoSuchAlgorithmException, NoSuchPaddingException, FileNotFoundException, IOException, RuleLoadingException { final boolean stripHtmlEnabled = true; final boolean injectSecretTokensEnabled = true; final boolean encryptQueryStringsEnabled = true; final boolean protectParamsAndFormsEnabled = true; final boolean applyExtraProtectionForDisabledFormFields = true; final boolean applyExtraProtectionForReadonlyFormFields = false; final boolean applyExtraProtectionForRequestParamValueCount = false; final ContentInjectionHelper helper = new ContentInjectionHelper(); final RuleFileLoader ruleFileLoaderModificationExcludes = new ClasspathZipRuleFileLoader(); ruleFileLoaderModificationExcludes.setPath(WebCastellumFilter.MODIFICATION_EXCLUDES_DEFAULT); final ContentModificationExcludeDefinitionContainer containerModExcludes = new ContentModificationExcludeDefinitionContainer(ruleFileLoaderModificationExcludes); containerModExcludes.parseDefinitions(); helper.setContentModificationExcludeDefinitions(containerModExcludes); final AttackHandler attackHandler = new AttackHandler(null, 123, 600000, 100000, 300000, 300000, null, "MOCK", false, false, 0, false, false, Pattern.compile("sjghggfakgfjagfgajgfjasgfs"), Pattern.compile("sjghggfakgfjagfgajgfjasgfs"), true); final SessionCreationTracker sessionCreationTracker = new SessionCreationTracker(attackHandler, 0, 600000, 300000, 0, "", "", "", ""); final RequestWrapper request = new RequestWrapper(new RequestMock(), helper, sessionCreationTracker, "123.456.789.000", false, true, true); final RuleFileLoader ruleFileLoaderResponseModifications = new ClasspathZipRuleFileLoader(); ruleFileLoaderResponseModifications.setPath(WebCastellumFilter.RESPONSE_MODIFICATIONS_DEFAULT); final ResponseModificationDefinitionContainer container = new ResponseModificationDefinitionContainer(ruleFileLoaderResponseModifications); container.parseDefinitions(); final ResponseModificationDefinition[] responseModificationDefinitions = downCast(container.getAllEnabledRequestDefinitions()); final List tmpPatternsToExcludeCompleteTag = new ArrayList(responseModificationDefinitions.length); final List tmpPatternsToExcludeCompleteScript = new ArrayList(responseModificationDefinitions.length); final List tmpPatternsToExcludeLinksWithinScripts = new ArrayList(responseModificationDefinitions.length); final List tmpPatternsToExcludeLinksWithinTags = new ArrayList(responseModificationDefinitions.length); final List tmpPatternsToCaptureLinksWithinScripts = new ArrayList(responseModificationDefinitions.length); final List tmpPatternsToCaptureLinksWithinTags = new ArrayList(responseModificationDefinitions.length); final List tmpPrefiltersToExcludeCompleteTag = new ArrayList(responseModificationDefinitions.length); final List tmpPrefiltersToExcludeCompleteScript = new ArrayList(responseModificationDefinitions.length); final List tmpPrefiltersToExcludeLinksWithinScripts = new ArrayList(responseModificationDefinitions.length); final List tmpPrefiltersToExcludeLinksWithinTags = new ArrayList(responseModificationDefinitions.length); final List tmpPrefiltersToCaptureLinksWithinScripts = new ArrayList(responseModificationDefinitions.length); final List tmpPrefiltersToCaptureLinksWithinTags = new ArrayList(responseModificationDefinitions.length); final List tmpGroupNumbersToCaptureLinksWithinScripts = new ArrayList(responseModificationDefinitions.length); final List tmpGroupNumbersToCaptureLinksWithinTags = new ArrayList(responseModificationDefinitions.length); for (int i = 0; i < responseModificationDefinitions.length; i++) { final ResponseModificationDefinition responseModificationDefinition = responseModificationDefinitions[i]; if (responseModificationDefinition.isMatchesScripts()) { tmpPatternsToExcludeCompleteScript.add(responseModificationDefinition.getScriptExclusionPattern()); tmpPrefiltersToExcludeCompleteScript.add(responseModificationDefinition.getScriptExclusionPrefilter()); tmpPatternsToExcludeLinksWithinScripts.add(responseModificationDefinition.getUrlExclusionPattern()); tmpPrefiltersToExcludeLinksWithinScripts.add(responseModificationDefinition.getUrlExclusionPrefilter()); tmpPatternsToCaptureLinksWithinScripts.add(responseModificationDefinition.getUrlCapturingPattern()); tmpPrefiltersToCaptureLinksWithinScripts.add(responseModificationDefinition.getUrlCapturingPrefilter()); tmpGroupNumbersToCaptureLinksWithinScripts.add(ServerUtils.convertSimpleToObjectArray(responseModificationDefinition.getCapturingGroupNumbers())); } if (responseModificationDefinition.isMatchesTags()) { tmpPatternsToExcludeCompleteTag.add(responseModificationDefinition.getTagExclusionPattern()); tmpPrefiltersToExcludeCompleteTag.add(responseModificationDefinition.getTagExclusionPrefilter()); tmpPatternsToExcludeLinksWithinTags.add(responseModificationDefinition.getUrlExclusionPattern()); tmpPrefiltersToExcludeLinksWithinTags.add(responseModificationDefinition.getUrlExclusionPrefilter()); tmpPatternsToCaptureLinksWithinTags.add(responseModificationDefinition.getUrlCapturingPattern()); tmpPrefiltersToCaptureLinksWithinTags.add(responseModificationDefinition.getUrlCapturingPrefilter()); tmpGroupNumbersToCaptureLinksWithinTags.add(ServerUtils.convertSimpleToObjectArray(responseModificationDefinition.getCapturingGroupNumbers())); } } final Matcher[] matchersToExcludeCompleteTag = ServerUtils.convertListOfPatternToArrayOfMatcher(tmpPatternsToExcludeCompleteTag); final Matcher[] matchersToExcludeCompleteScript = ServerUtils.convertListOfPatternToArrayOfMatcher(tmpPatternsToExcludeCompleteScript); final Matcher[] matchersToExcludeLinksWithinScripts = ServerUtils.convertListOfPatternToArrayOfMatcher(tmpPatternsToExcludeLinksWithinScripts); final Matcher[] matchersToExcludeLinksWithinTags = ServerUtils.convertListOfPatternToArrayOfMatcher(tmpPatternsToExcludeLinksWithinTags); final Matcher[] matchersToCaptureLinksWithinScripts = ServerUtils.convertListOfPatternToArrayOfMatcher(tmpPatternsToCaptureLinksWithinScripts); final Matcher[] matchersToCaptureLinksWithinTags = ServerUtils.convertListOfPatternToArrayOfMatcher(tmpPatternsToCaptureLinksWithinTags); final WordDictionary[] prefiltersToExcludeCompleteTag = (WordDictionary[]) tmpPrefiltersToExcludeCompleteTag.toArray(new WordDictionary[0]); final WordDictionary[] prefiltersToExcludeCompleteScript = (WordDictionary[]) tmpPrefiltersToExcludeCompleteScript.toArray(new WordDictionary[0]); final WordDictionary[] prefiltersToExcludeLinksWithinScripts = (WordDictionary[]) tmpPrefiltersToExcludeLinksWithinScripts.toArray(new WordDictionary[0]); final WordDictionary[] prefiltersToExcludeLinksWithinTags = (WordDictionary[]) tmpPrefiltersToExcludeLinksWithinTags.toArray(new WordDictionary[0]); final WordDictionary[] prefiltersToCaptureLinksWithinScripts = (WordDictionary[]) tmpPrefiltersToCaptureLinksWithinScripts.toArray(new WordDictionary[0]); final WordDictionary[] prefiltersToCaptureLinksWithinTags = (WordDictionary[]) tmpPrefiltersToCaptureLinksWithinTags.toArray(new WordDictionary[0]); final int[][] groupNumbersToCaptureLinksWithinScripts = ServerUtils.convertArrayIntegerListTo2DimIntArray(tmpGroupNumbersToCaptureLinksWithinScripts); final int[][] groupNumbersToCaptureLinksWithinTags = ServerUtils.convertArrayIntegerListTo2DimIntArray(tmpGroupNumbersToCaptureLinksWithinTags); final Cipher cipher = CryptoUtils.getCipher(); final CryptoKeyAndSalt key = CryptoUtils.generateRandomCryptoKeyAndSalt(false); Cipher.getInstance("AES"); MessageDigest.getInstance("SHA-1"); final ResponseWrapper response = new ResponseWrapper(new ResponseMock(), request, attackHandler, helper, false, "___ENCRYPTED___", cipher, key, "___SEC-KEY___", "___SEC-VALUE___", "___PROT-KEY___", false, false, false, false, "123.456.789.000", new HashSet(), prefiltersToExcludeCompleteScript, matchersToExcludeCompleteScript, prefiltersToExcludeCompleteTag, matchersToExcludeCompleteTag, prefiltersToExcludeLinksWithinScripts, matchersToExcludeLinksWithinScripts, prefiltersToExcludeLinksWithinTags, matchersToExcludeLinksWithinTags, prefiltersToCaptureLinksWithinScripts, matchersToCaptureLinksWithinScripts, prefiltersToCaptureLinksWithinTags, matchersToCaptureLinksWithinTags, groupNumbersToCaptureLinksWithinScripts, groupNumbersToCaptureLinksWithinTags, true, false, true, true, true, true, true, true, true, true, true, false, false, true, "", "", (short) 3, true, false, false); final List durations = new ArrayList(); for (int i = 0; i < executionCount; i++) { final long start = System.currentTimeMillis(); Reader reader = null; Writer writer = null; try { reader = new BufferedReader(new FileReader(this.htmlFile)); writer = new FileWriter(this.outputFile); if (applyFilter) { writer = new ResponseFilterWriter(writer, true, "http://127.0.0.1/test/sample", "/test", "/test", "___SEC-KEY___", "___SEC-VALUE___", "___PROT-KEY___", cipher, key, helper, "___ENCRYPTED___", request, response, stripHtmlEnabled, injectSecretTokensEnabled, protectParamsAndFormsEnabled, encryptQueryStringsEnabled, applyExtraProtectionForDisabledFormFields, applyExtraProtectionForReadonlyFormFields, applyExtraProtectionForRequestParamValueCount, prefiltersToExcludeCompleteScript, matchersToExcludeCompleteScript, prefiltersToExcludeCompleteTag, matchersToExcludeCompleteTag, prefiltersToExcludeLinksWithinScripts, matchersToExcludeLinksWithinScripts, prefiltersToExcludeLinksWithinTags, matchersToExcludeLinksWithinTags, prefiltersToCaptureLinksWithinScripts, matchersToCaptureLinksWithinScripts, prefiltersToCaptureLinksWithinTags, matchersToCaptureLinksWithinTags, groupNumbersToCaptureLinksWithinScripts, groupNumbersToCaptureLinksWithinTags, true, true, false, true, true, true, true, true, true, true, true, false, false, true, "", "", (short) 3, true, false); writer = new BufferedWriter(writer); } char[] chars = new char[16 * 1024]; int read; while ((read = reader.read(chars)) != -1) { if (read > 0) { writer.write(chars, 0, read); } } durations.add(new Long(System.currentTimeMillis() - start)); } finally { if (reader != null) { try { reader.close(); } catch (IOException ignored) { } } if (writer != null) { try { writer.close(); } catch (IOException ignored) { } } } } long sum = 0; for (final Iterator iter = durations.iterator(); iter.hasNext(); ) { Long value = (Long) iter.next(); sum += value.longValue(); } return sum / durations.size(); } | 17,095 |
0 | private List<String> createProjectInfoFile() throws SocketException, IOException { FTPClient client = new FTPClient(); Set<String> projects = new HashSet<String>(); client.connect("ftp.drupal.org"); System.out.println("Connected to ftp.drupal.org"); System.out.println(client.getReplyString()); boolean loggedIn = client.login("anonymous", "info@regilo.org"); if (loggedIn) { FTPFile[] files = client.listFiles("pub/drupal/files/projects"); for (FTPFile file : files) { String name = file.getName(); Pattern p = Pattern.compile("([a-zAZ_]*)-(\\d.x)-(.*)"); Matcher m = p.matcher(name); if (m.matches()) { String projectName = m.group(1); String version = m.group(2); if (version.equals("6.x")) { projects.add(projectName); } } } } List<String> projectList = new ArrayList<String>(); for (String project : projects) { projectList.add(project); } Collections.sort(projectList); return projectList; } | public XMLResourceBundle() throws MissingResourceException { String systemId = getShortName() + ".xml"; URL url; if ((url = getClass().getResource(systemId)) != null) { InputStream is = null; try { is = url.openStream(); SAXParserFactory factory = SAXParserFactory.newInstance(); factory.setNamespaceAware(false); factory.setValidating(false); XMLReader xmlReader = factory.newSAXParser().getXMLReader(); xmlReader.setContentHandler(new MessageContentHandler()); xmlReader.parse(new InputSource(is)); } catch (IOException ioe) { System.err.println(ioe.getMessage()); ioe.printStackTrace(); } catch (SAXException se) { System.err.println(se.getMessage()); se.printStackTrace(); } catch (ParserConfigurationException pce) { System.err.println(pce.getMessage()); pce.printStackTrace(); } finally { try { if (is != null) is.close(); } catch (IOException ioe) { System.err.println(ioe.getMessage()); ioe.printStackTrace(); } } } else { throw new MissingResourceException("Resource file '" + systemId + "' could not be found.", systemId, null); } } | 17,096 |
1 | public void migrateTo(String newExt) throws IOException { DigitalObject input = new DigitalObject.Builder(Content.byReference(new File(AllJavaSEServiceTestsuite.TEST_FILE_LOCATION + "PlanetsLogo.png").toURI().toURL())).build(); System.out.println("Input: " + input); FormatRegistry format = FormatRegistryFactory.getFormatRegistry(); MigrateResult mr = dom.migrate(input, format.createExtensionUri("png"), format.createExtensionUri(newExt), null); ServiceReport sr = mr.getReport(); System.out.println("Got Report: " + sr); DigitalObject doOut = mr.getDigitalObject(); assertTrue("Resulting digital object is null.", doOut != null); System.out.println("Output: " + doOut); System.out.println("Output.content: " + doOut.getContent()); File out = new File("services/java-se/test/results/test." + newExt); FileOutputStream fo = new FileOutputStream(out); IOUtils.copyLarge(doOut.getContent().getInputStream(), fo); fo.close(); System.out.println("Recieved service report: " + mr.getReport()); System.out.println("Recieved service properties: "); ServiceProperties.printProperties(System.out, mr.getReport().getProperties()); } | public static void copyFile(File src, File dest) throws IOException { FileInputStream fis = new FileInputStream(src); FileOutputStream fos = new FileOutputStream(dest); java.nio.channels.FileChannel channelSrc = fis.getChannel(); java.nio.channels.FileChannel channelDest = fos.getChannel(); channelSrc.transferTo(0, channelSrc.size(), channelDest); fis.close(); fos.close(); } | 17,097 |
0 | 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(); } | private ArrayList<String> getYearsAndMonths() { String info = ""; ArrayList<String> items = new ArrayList<String>(); try { obtainServerFilesView.setLblProcessText(java.util.ResourceBundle.getBundle("bgpanalyzer/resources/Bundle").getString("ObtainServerFilesView.Label.Progress.Obtaining_Data")); URL url = new URL(URL_ROUTE_VIEWS); URLConnection conn = url.openConnection(); conn.setDoOutput(false); BufferedReader rd = new BufferedReader(new InputStreamReader(conn.getInputStream())); String line; while ((line = rd.readLine()) != null) { if (!line.equals("")) info += line + "%"; } obtainServerFilesView.setLblProcessText(java.util.ResourceBundle.getBundle("bgpanalyzer/resources/Bundle").getString("ObtainServerFilesView.Label.Progress.Processing_Data")); info = Patterns.removeTags(info); StringTokenizer st = new StringTokenizer(info, "%"); info = ""; boolean alternador = false; int index = 1; while (st.hasMoreTokens()) { String token = st.nextToken(); if (!token.trim().equals("")) { int pos = token.indexOf("/"); if (pos != -1) { token = token.substring(1, pos); if (Patterns.hasFormatYYYYdotMM(token)) { items.add(token); } } } } rd.close(); } catch (Exception e) { e.printStackTrace(); } return items; } | 17,098 |
0 | protected void createValueListAnnotation(IProgressMonitor monitor, IPackageFragment pack, Map model) throws CoreException { IProject pj = pack.getJavaProject().getProject(); QualifiedName qn = new QualifiedName(JstActivator.PLUGIN_ID, JstActivator.PACKAGE_INFO_LOCATION); String location = pj.getPersistentProperty(qn); if (location != null) { IFolder javaFolder = pj.getFolder(new Path(NexOpenFacetInstallDataModelProvider.WEB_SRC_MAIN_JAVA)); IFolder packageInfo = javaFolder.getFolder(location); if (!packageInfo.exists()) { Logger.log(Logger.INFO, "package-info package [" + location + "] does not exists."); Logger.log(Logger.INFO, "ValueList annotation will not be added by this wizard. " + "You must add manually in your package-info class if exist " + "or create a new one at location " + location); return; } IFile pkginfo = packageInfo.getFile("package-info.java"); if (!pkginfo.exists()) { Logger.log(Logger.INFO, "package-info class at location [" + location + "] does not exists."); return; } InputStream in = pkginfo.getContents(); ByteArrayOutputStream baos = new ByteArrayOutputStream(); try { IOUtils.copy(in, baos); String content = new String(baos.toByteArray()); VelocityEngine engine = VelocityEngineHolder.getEngine(); model.put("adapterType", getAdapterType()); model.put("packageInfo", location.replace('/', '.')); model.put("defaultNumberPerPage", "5"); model.put("defaultSortDirection", "asc"); if (isFacadeAdapter()) { model.put("facadeType", "true"); } if (content.indexOf("@ValueLists({})") > -1) { appendValueList(monitor, model, pkginfo, content, engine, true); return; } else if (content.indexOf("@ValueLists") > -1) { appendValueList(monitor, model, pkginfo, content, engine, false); return; } String vl = VelocityEngineUtils.mergeTemplateIntoString(engine, "ValueList.vm", model); ByteArrayInputStream bais = new ByteArrayInputStream(vl.getBytes()); try { pkginfo.setContents(bais, true, false, monitor); } finally { bais.close(); } return; } catch (IOException e) { IStatus status = new Status(IStatus.ERROR, JeeServiceComponentUIPlugin.PLUGIN_ID, IStatus.OK, "I/O exception", e); throw new CoreException(status); } catch (VelocityException e) { IStatus status = new Status(IStatus.ERROR, JeeServiceComponentUIPlugin.PLUGIN_ID, IStatus.OK, "Velocity exception", e); throw new CoreException(status); } finally { try { baos.close(); in.close(); } catch (IOException e) { } } } Logger.log(Logger.INFO, "package-info location property does not exists."); } | private String calculateHash(String s) { if (s == null) { return null; } MessageDigest messageDigest; try { messageDigest = MessageDigest.getInstance("SHA"); } catch (NoSuchAlgorithmException e) { logger.error("Could not find a message digest algorithm."); return null; } messageDigest.update(s.getBytes()); byte[] hash = messageDigest.digest(); StringBuilder sb = new StringBuilder(); for (byte b : hash) { sb.append(String.format("%02x", b)); } return sb.toString(); } | 17,099 |
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