label int64 0 1 | func1 stringlengths 173 53.1k | func2 stringlengths 173 53.1k | id int64 0 901k |
|---|---|---|---|
0 | public static String hashStringMD5(String string) throws NoSuchAlgorithmException { MessageDigest md = MessageDigest.getInstance("MD5"); md.update(string.getBytes()); byte byteData[] = md.digest(); StringBuffer sb = new StringBuffer(); for (int i = 0; i < byteData.length; i++) { sb.append(Integer.toString((byteData[i] & 0xff) + 0x100, 16).substring(1)); } StringBuffer hexString = new StringBuffer(); for (int i = 0; i < byteData.length; i++) { String hex = Integer.toHexString(0xff & byteData[i]); if (hex.length() == 1) hexString.append('0'); hexString.append(hex); } return hexString.toString(); } | public void execute() { checkInput(); try { client = new FTPClient(); log("Connecting to " + ftpServer, Project.MSG_INFO); client.connect(ftpServer, ftpPort); checkFtpCode(client, "FTP server refused connection:"); log("Connected", Project.MSG_INFO); log("Logging in", Project.MSG_INFO); if (!client.login(username, password)) { log("Login failed: " + client.getReplyString(), Project.MSG_ERR); } log("Login successful", Project.MSG_INFO); client.enterLocalPassiveMode(); checkFtpCode(client, "Couldn't change connection type to passive: "); log("Changed to passive mode.", Project.MSG_VERBOSE); client.changeWorkingDirectory(remoteDir); checkFtpCode(client, "Can't change to directory: " + remoteDir); log("Listing FTP files", Project.MSG_INFO); for (int i = 0; i < remoteFileStrings.length; i++) { remoteFilePatterns = makePattern(remoteFileStrings[i]); numDir = remoteFilePatterns.length - 1; log("Setting number of directories to: " + numDir, Project.MSG_VERBOSE); FTPFile[] files = client.listFiles(remoteDir); files = followSymLink(client, files); log("# of files in " + remoteDir + " is " + files.length, Project.MSG_VERBOSE); scanDir(0, numDir, files, null); } bw.flush(); bw.close(); } catch (IOException ioe) { if (client.isConnected()) { try { client.disconnect(); } catch (IOException iof) { } } log("Could not connect to " + ftpServer + " " + ioe.getMessage(), Project.MSG_ERR); } } | 19,400 |
1 | private boolean copyFile(File file) throws Exception { destination = new File(ServiceLocator.getSqliteDir(), file.getName()); logger.debug("Writing to: " + destination); if (destination.exists()) { Frame.showMessage(ServiceLocator.getText("Error.file.exists") + file.getName(), null); logger.debug("File already exists: " + file); return false; } destination.createNewFile(); InputStream in = null; OutputStream out = null; try { in = new FileInputStream(file); out = new FileOutputStream(destination); int read = 0; byte[] buffer = new byte[2048]; while ((read = in.read(buffer)) > 0) { out.write(buffer, 0, read); } } finally { if (in != null) in.close(); if (out != null) out.close(); } return true; } | public void run() { try { FileChannel in = (new FileInputStream(file)).getChannel(); FileChannel out = (new FileOutputStream(updaterFile)).getChannel(); in.transferTo(0, file.length(), out); updater.setProgress(50); in.close(); out.close(); } catch (IOException e) { e.printStackTrace(); } startUpdater(); } | 19,401 |
0 | public int procesar() { int mas = 0; String uriOntologia = "", source = "", uri = ""; String fichOrigenHTML = "", fichOrigenLN = ""; String ficheroOutOWL = ""; md5 firma = null; StringTokenV2 entra = null, entra2 = null, entra3 = null; FileInputStream lengNat = null; BufferedInputStream lengNat2 = null; DataInputStream entradaLenguajeNatural = null; FileWriter salOWL = null; BufferedWriter salOWL2 = null; PrintWriter salidaOWL = null; String sujeto = "", verbo = "", CD = "", CI = "", fraseOrigen = ""; StringTokenV2 token2; boolean bandera = false; OntClass c = null; OntClass cBak = null; String claseTrabajo = ""; String nombreClase = "", nombrePropiedad = "", variasPalabras = ""; int incre = 0, emergencia = 0; String lineaSalida = ""; String[] ontologia = new String[5]; ontologia[0] = "http://www.criado.info/owl/vertebrados_es.owl#"; ontologia[1] = "http://www.w3.org/2001/sw/WebOnt/guide-src/wine#"; ontologia[2] = "http://www.co-ode.org/ontologies/pizza/2005/10/18/pizza.owl#"; ontologia[3] = "http://www.w3.org/2001/sw/WebOnt/guide-src/food#"; ontologia[4] = "http://www.daml.org/2001/01/gedcom/gedcom#"; String[] ontologiaSource = new String[5]; ontologiaSource[0] = this.directorioMapeo + "\\" + "mapeo_vertebrados_es.xml"; ontologiaSource[1] = this.directorioMapeo + "\\" + "mapeo_wine_es.xml"; ontologiaSource[2] = this.directorioMapeo + "\\" + "mapeo_pizza_es.xml"; ontologiaSource[3] = this.directorioMapeo + "\\" + "mapeo_food_es.xml"; ontologiaSource[4] = this.directorioMapeo + "\\" + "mapeo_parentesco_es.xml"; mapeoIdiomas clasesOntologias; try { if ((entrada = entradaFichero.readLine()) != null) { if (entrada.trim().length() > 10) { entrada2 = new StringTokenV2(entrada.trim(), "\""); if (entrada2.isIncluidaSubcadena("<fichero ontologia=")) { ontologiaOrigen = entrada2.getToken(2); fichOrigenHTML = entrada2.getToken(4); fichOrigenLN = entrada2.getToken(6); if (ontologiaOrigen.equals("VERTEBRADOS")) { source = ontologiaSource[0]; uriOntologia = ontologia[0]; } if (ontologiaOrigen.equals("WINE")) { source = ontologiaSource[1]; uriOntologia = ontologia[1]; } if (ontologiaOrigen.equals("PIZZA")) { source = ontologiaSource[2]; uriOntologia = ontologia[2]; } if (ontologiaOrigen.equals("FOOD")) { source = ontologiaSource[3]; uriOntologia = ontologia[3]; } if (ontologiaOrigen.equals("PARENTESCOS")) { source = ontologiaSource[4]; uriOntologia = ontologia[4]; } firma = new md5(uriOntologia, false); clasesOntologias = new mapeoIdiomas(source); uri = ""; ficheroOutOWL = ""; entra2 = new StringTokenV2(fichOrigenHTML, "\\"); int numToken = entra2.getNumeroTokenTotales(); entra = new StringTokenV2(fichOrigenHTML, " "); if (entra.isIncluidaSubcadena(directorioLocal)) { entra = new StringTokenV2(entra.getQuitar(directorioLocal) + "", " "); uri = entra.getCambiar("\\", "/"); uri = entra.getQuitar(entra2.getToken(numToken)) + ""; entra3 = new StringTokenV2(entra2.getToken(numToken), "."); ficheroOutOWL = entra3.getToken(1) + "_" + firma.toString() + ".owl"; uri = urlPatron + uri + ficheroOutOWL; } entra3 = new StringTokenV2(fichOrigenHTML, "."); ficheroOutOWL = entra3.getToken(1) + "_" + firma.toString() + ".owl"; lineaSalida = "<vistasemantica origen=\"" + fichOrigenLN + "\" destino=\"" + uri + "\" />"; lengNat = new FileInputStream(fichOrigenLN); lengNat2 = new BufferedInputStream(lengNat); entradaLenguajeNatural = new DataInputStream(lengNat2); salOWL = new FileWriter(ficheroOutOWL); salOWL2 = new BufferedWriter(salOWL); salidaOWL = new PrintWriter(salOWL2); while ((entradaInstancias = entradaLenguajeNatural.readLine()) != null) { sujeto = ""; verbo = ""; CD = ""; CI = ""; fraseOrigen = ""; if (entradaInstancias.trim().length() > 10) { entrada2 = new StringTokenV2(entradaInstancias.trim(), "\""); if (entrada2.isIncluidaSubcadena("<oracion sujeto=")) { sujeto = entrada2.getToken(2).trim(); verbo = entrada2.getToken(4).trim(); CD = entrada2.getToken(6).trim(); CI = entrada2.getToken(8).trim(); fraseOrigen = entrada2.getToken(10).trim(); if (sujeto.length() > 0 & verbo.length() > 0 & CD.length() > 0) { bandera = false; c = null; cBak = null; nombreClase = clasesOntologias.getClaseInstancia(CD); if (nombreClase.length() > 0) { bandera = true; } if (bandera) { if (incre == 0) { salidaOWL.write(" <rdf:RDF " + "\n"); salidaOWL.write(" xmlns:j.0=\"" + uriOntologia + "\"" + "\n"); salidaOWL.write(" xmlns:protege=\"http://protege.stanford.edu/plugins/owl/protege#\"" + "\n"); salidaOWL.write(" xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\"" + "\n"); salidaOWL.write(" xmlns:xsd=\"http://www.w3.org/2001/XMLSchema#\"" + "\n"); salidaOWL.write(" xmlns:rdfs=\"http://www.w3.org/2000/01/rdf-schema#\"" + "\n"); salidaOWL.write(" xmlns:owl=\"http://www.w3.org/2002/07/owl#\" " + "\n"); salidaOWL.write(" xmlns=\"" + uri + "#\"" + "\n"); salidaOWL.write(" xml:base=\"" + uri + "\">" + "\n"); salidaOWL.write(" <owl:Ontology rdf:about=\"\">" + "\n"); salidaOWL.write(" <owl:imports rdf:resource=\"" + uriOntologia + "\"/>" + "\n"); salidaOWL.write(" </owl:Ontology>" + "\n"); salidaOWL.flush(); salida.write(lineaSalida + "\n"); salida.flush(); incre = 1; } salidaOWL.write(" <j.0:" + nombreClase + " rdf:ID=\"" + sujeto.toUpperCase() + "\"/>" + "\n"); salidaOWL.write(" <owl:AllDifferent>" + "\n"); salidaOWL.write(" <owl:distinctMembers rdf:parseType=\"Collection\">" + "\n"); salidaOWL.write(" <" + nombreClase + " rdf:about=\"#" + sujeto.toUpperCase() + "\"/>" + "\n"); salidaOWL.write(" </owl:distinctMembers>" + "\n"); salidaOWL.write(" </owl:AllDifferent>" + "\n"); salidaOWL.flush(); bandera = false; } } } } } salidaOWL.write(" </rdf:RDF>" + "\n" + "\n"); salidaOWL.write("<!-- Creado por [html2ws] http://www.luis.criado.org -->" + "\n"); salidaOWL.flush(); } } mas = 1; } else { salida.write("</listaVistasSemanticas>\n"); salida.flush(); salida.close(); bw2.close(); fw2.close(); salidaOWL.close(); entradaFichero.close(); ent2.close(); ent1.close(); mas = -1; } } catch (Exception e) { mas = -2; salida.write("No se encuentra: " + fichOrigen + "\n"); salida.flush(); } return mas; } | public boolean getAuth(String content) throws IOException { String resp_remote; try { URL url = new URL(remoteurl); HttpURLConnection connection = (HttpURLConnection) url.openConnection(); connection.setDoOutput(true); connection.setDoInput(true); connection.setRequestMethod("POST"); OutputStreamWriter writer = new OutputStreamWriter(connection.getOutputStream()); writer.write("md5sum=" + content); writer.close(); if (connection.getResponseCode() == HttpURLConnection.HTTP_OK) { InputStream is = connection.getInputStream(); BufferedReader rd = new BufferedReader(new InputStreamReader(is)); String line; StringBuffer response = new StringBuffer(); while ((line = rd.readLine()) != null) { response.append(line); response.append('\r'); } rd.close(); resp_remote = response.toString(); wd.del(); wd.setKey(resp_remote); return true; } else { return false; } } catch (MalformedURLException e) { } catch (IOException e) { } return false; } | 19,402 |
0 | public static void entering(String[] args) throws IOException, CodeCheckException { ClassWriter writer = new ClassWriter(); writer.readClass(new BufferedInputStream(new FileInputStream(args[0]))); int constantIndex = writer.getStringConstantIndex("Entering "); int fieldRefIndex = writer.getReferenceIndex(ClassWriter.CONSTANT_Fieldref, "java/lang/System", "out", "Ljava/io/PrintStream;"); int printlnRefIndex = writer.getReferenceIndex(ClassWriter.CONSTANT_Methodref, "java/io/PrintStream", "println", "(Ljava/lang/String;)V"); int printRefIndex = writer.getReferenceIndex(ClassWriter.CONSTANT_Methodref, "java/io/PrintStream", "print", "(Ljava/lang/String;)V"); for (Iterator i = writer.getMethods().iterator(); i.hasNext(); ) { MethodInfo method = (MethodInfo) i.next(); if (method.getName().equals("readConstant")) continue; CodeAttribute attribute = method.getCodeAttribute(); ArrayList instructions = new ArrayList(10); byte[] operands; operands = new byte[2]; NetByte.intToPair(fieldRefIndex, operands, 0); instructions.add(new Instruction(OpCode.getOpCodeByMnemonic("getstatic"), 0, operands, false)); instructions.add(new Instruction(OpCode.getOpCodeByMnemonic("dup"), 0, null, false)); instructions.add(Instruction.appropriateLdc(constantIndex, false)); operands = new byte[2]; NetByte.intToPair(printRefIndex, operands, 0); instructions.add(new Instruction(OpCode.getOpCodeByMnemonic("invokevirtual"), 0, operands, false)); instructions.add(Instruction.appropriateLdc(writer.getStringConstantIndex(method.getName()), false)); operands = new byte[2]; NetByte.intToPair(printlnRefIndex, operands, 0); instructions.add(new Instruction(OpCode.getOpCodeByMnemonic("invokevirtual"), 0, operands, false)); attribute.insertInstructions(0, 0, instructions); attribute.codeCheck(); } BufferedOutputStream outStream = new BufferedOutputStream(new FileOutputStream(args[1])); writer.writeClass(outStream); outStream.close(); } | String readArticleFromFile(String urlStr) { String docbase = getDocumentBase().toString(); int pos = docbase.lastIndexOf('/'); if (pos > -1) { docbase = docbase.substring(0, pos + 1); } else { docbase = ""; } docbase = docbase + urlStr; String prog = ""; try { URL url = new URL(docbase); BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream())); if (in != null) { while (true) { try { String mark = in.readLine(); if (mark == null) break; prog = prog + mark + "\n"; } catch (Exception e) { } } in.close(); } } catch (Exception e) { } return prog; } | 19,403 |
0 | public Result request(URL url) { try { return xmlUtil.unmarshall(urlOpener.openStream(url)); } catch (FileNotFoundException e) { log.info("File not found: " + url); } catch (IOException e) { log.error("Failed to read from url: " + url + ". " + e.getMessage(), e); } return null; } | public static String MD5(String source) { logger.info(source); String result = null; try { MessageDigest digest = MessageDigest.getInstance("MD5"); digest.update(source.getBytes()); byte[] bytes = digest.digest(); result = EncodeUtils.hexEncode(bytes); } catch (NoSuchAlgorithmException e) { e.printStackTrace(); } logger.info(result); return result; } | 19,404 |
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 JavaCodeAnalyzer(String filenameIn, String filenameOut, String lineLength) { try { File tmp = File.createTempFile("JavaCodeAnalyzer", "tmp"); BufferedReader br = new BufferedReader(new FileReader(filenameIn)); BufferedWriter out = new BufferedWriter(new FileWriter(tmp)); while (br.ready()) { out.write(br.read()); } br.close(); out.close(); jco = new JavaCodeOutput(tmp, filenameOut, lineLength); SourceCodeParser p = new JavaCCParserFactory().createParser(new FileReader(tmp), null); List statements = p.parseCompilationUnit(); ListIterator it = statements.listIterator(); eh = new ExpressionHelper(this, jco); Node n; printLog("Parsed file " + filenameIn + "\n"); while (it.hasNext()) { n = (Node) it.next(); parseObject(n); } tmp.delete(); } catch (Exception e) { System.err.println(getClass() + ": " + e); } } | 19,405 |
0 | public GridDirectoryList(String gridSource) throws McIDASException { try { URL url = new URL(gridSource); urlc = (AddeURLConnection) url.openConnection(); inputStream = new DataInputStream(new BufferedInputStream(urlc.getInputStream())); } catch (IOException e) { throw new McIDASException("Error opening URL for grids:" + e); } readDirectory(); } | @Override public void start() throws Exception { initMetaData(); Map<String, Set<ONDEXConcept>> accessions = new HashMap<String, Set<ONDEXConcept>>(); for (ONDEXConcept c : graph.getConcepts()) { for (ConceptAccession ca : c.getConceptAccessions()) { if (ca.getElementOf().equals(dsCHEMBL) && !accessions.containsKey(ca.getAccession())) accessions.put(ca.getAccession(), new HashSet<ONDEXConcept>()); accessions.get(ca.getAccession()).add(c); } } System.out.println(accessions); int count = 0; for (String accession : accessions.keySet()) { URL url = new URL("https://www.ebi.ac.uk/chemblws/compounds/" + accession + "/bioactivities"); HttpURLConnection uc = (HttpURLConnection) url.openConnection(); int code = uc.getResponseCode(); if (code != 200) { String response = uc.getResponseMessage(); fireEventOccurred(new ParsingErrorEvent("HTTP/1.x " + code + " " + response, getCurrentMethodName())); } else { InputStream in = new BufferedInputStream(uc.getInputStream()); DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance(); DocumentBuilder dBuilder = dbFactory.newDocumentBuilder(); Document doc = dBuilder.parse(in); doc.getDocumentElement().normalize(); NodeList nList = doc.getElementsByTagName("bioactivity"); for (int temp = 0; temp < nList.getLength(); temp++) { Node nNode = nList.item(temp); if (nNode.getNodeType() == Node.ELEMENT_NODE) { Element eElement = (Element) nNode; ONDEXConcept activity = graph.getFactory().createConcept(getTagValue("assay__chemblid", eElement), getTagValue("assay__description", eElement), dsCHEMBL, ccActivity, evidencetype); activity.createConceptAccession(getTagValue("assay__chemblid", eElement), dsASSAY, false); activity.createAttribute(anRef, getTagValue("reference", eElement), true); activity.createAttribute(anOrg, getTagValue("organism", eElement), true); String type = getTagValue("bioactivity__type", eElement); type = type.replace(" ", "_"); if (!anTypes.containsKey(type)) { AttributeName an = graph.getMetaData().getFactory().createAttributeName(type, Double.class); String units = getTagValue("units", eElement); if (graph.getMetaData().getUnit(units) == null) graph.getMetaData().getFactory().createUnit(units); an.setUnit(graph.getMetaData().getUnit(units)); anTypes.put(type, an); } String value = getTagValue("value", eElement); try { Double d = Double.valueOf(value); activity.createAttribute(anTypes.get(type), d, false); } catch (NumberFormatException nfe) { } String comment = getTagValue("activity__comment", eElement); if (comment != null && comment.trim().length() > 0) { if (mapping.containsKey(comment)) comment = mapping.get(comment); activity.createAttribute(anComment, comment, true); } count++; Set<ONDEXConcept> compounds = accessions.get(accession); for (ONDEXConcept c : compounds) { graph.getFactory().createRelation(c, activity, rtActivity, evidencetype); } String key = getTagValue("target__chemblid", eElement); if (!targets.containsKey(key)) { ONDEXConcept c = graph.getFactory().createConcept(key, dsCHEMBL, ccTarget, evidencetype); c.createConceptName(getTagValue("target__name", eElement), true); c.createConceptAccession(key, dsTARGET, false); targets.put(key, c); } ONDEXConcept target = targets.get(key); ONDEXRelation r = graph.getFactory().createRelation(activity, target, rtOccin, evidencetype); r.createAttribute(anConf, Double.valueOf(getTagValue("target__confidence", eElement)), false); } } } } fireEventOccurred(new GeneralOutputEvent("Total assays parsed:" + count, getCurrentMethodName())); } | 19,406 |
0 | protected Properties loadFile(String fileName) { Properties prop = new Properties(); try { String packageName = getClass().getName(); packageName = packageName.substring(0, packageName.lastIndexOf(".")); String src = "src"; if (mavenBuild) { src = src + File.separator + "test" + File.separator + "resources"; } packageName = src + File.separator + packageName.replace('.', File.separatorChar); packageName += File.separator; packageName += fileName; URL url0 = new File(packageName).toURI().toURL(); final InputStream input = url0.openStream(); prop.load(input); } catch (FileNotFoundException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } return prop; } | public void testDecode1000BinaryStore() throws Exception { EXISchema corpus = EXISchemaFactoryTestUtil.getEXISchema("/DataStore/DataStore.xsd", getClass(), m_compilerErrors); Assert.assertEquals(0, m_compilerErrors.getTotalCount()); GrammarCache grammarCache = new GrammarCache(corpus, GrammarOptions.STRICT_OPTIONS); String[] base64Values100 = { "R0lGODdhWALCov////T09M7Ozqampn19fVZWVi0tLQUFBSxYAsJAA/8Iutz+MMpJq7046827/2Ao\n", "/9j/4BBKRklGAQEBASwBLP/hGlZFeGlmTU0qF5ZOSUtPTiBDT1JQT1JBVElPTk5J", "R0lGODlhHh73KSkpOTk5QkJCSkpKUlJSWlpaY2Nja2trc3Nze3t7hISEjIyMlJSUnJycpaWlra2t\n" + "tbW1vb29xsbGzs7O1tbW3t7e5+fn7+/v//////////8=", "/9j/4BBKRklGAQEBAf/bQwYEBQYFBAYGBQYHBwYIChAKCgkJChQODwwQFxQYGBc=", "R0lGODlhHh73M2aZzP8zMzNmM5kzzDP/M2YzZmZmmWbM", "/9j/4BBKRklGAQEBAf/bQwYEBQYFBAYGBQYHBwYIChAKCgkJChQODwwQFxQYGBcUFhYaHSUfGhsj\n" + "HBYWICwgIyYnKSopGR8tMC0oMCUoKSj/20M=", "R0lGODdhWAK+ov////j4+NTU1JOTk0tLSx8fHwkJCSxYAr5AA/8IMkzjrEEmahy23SpC", "R0lGODdh4QIpAncJIf4aU29mdHdhcmU6IE1pY3Jvc29mdCBPZmZpY2Us4QIpAof//////8z//5n/\n", "R0lGODdhWAK+ov////v7++fn58DAwI6Ojl5eXjExMQMDAyxYAr5AA/8Iutz+MMpJq7046827/2Ao\n" + "jmRpnmiqPsKxvg==", "R0lGODdh4QIpAncJIf4aU29mdHdhcmU6IE1pY3Jvc29mdCBPZmZpY2Us4QIpAob//////8z//5n/\nzP//zMw=" }; AlignmentType alignment = AlignmentType.bitPacked; Transmogrifier encoder = new Transmogrifier(); encoder.setEXISchema(grammarCache); encoder.setAlignmentType(alignment); ByteArrayOutputStream baos = new ByteArrayOutputStream(); encoder.setOutputStream(baos); URL url = resolveSystemIdAsURL("/DataStore/instance/1000BinaryStore.xml"); encoder.encode(new InputSource(url.openStream())); byte[] bts = baos.toByteArray(); Scanner scanner; int n_texts; EXIDecoder decoder = new EXIDecoder(999); decoder.setEXISchema(grammarCache); decoder.setAlignmentType(alignment); decoder.setInputStream(new ByteArrayInputStream(bts)); scanner = decoder.processHeader(); EXIEvent exiEvent; n_texts = 0; while ((exiEvent = scanner.nextEvent()) != null) { if (exiEvent.getEventVariety() == EXIEvent.EVENT_CH) { if (++n_texts % 100 == 0) { String expected = base64Values100[(n_texts / 100) - 1]; String val = exiEvent.getCharacters().makeString(); Assert.assertEquals(expected, val); } } } Assert.assertEquals(1000, n_texts); } | 19,407 |
0 | private void writeStatsToDatabase(long transferJobAIPCount, long reprocessingJobAIPCount, long transferJobAIPVolume, long reprocessingJobAIPVolume, long overallBinaryAIPCount, Map<String, AIPStatistics> mimeTypeRegister) throws SQLException { int nextAIPStatsID; long nextMimetypeStatsID; Statement select = dbConnection.createStatement(); String aipStatsQuery = "select max(aip_statistics_id) from aip_statistics"; ResultSet result = select.executeQuery(aipStatsQuery); if (result.next()) { nextAIPStatsID = result.getInt(1) + 1; } else { throw new SQLException("Problem getting maximum AIP Statistics ID"); } String mimetypeStatsQuery = "select max(mimetype_aip_statistics_id) from mimetype_aip_statistics"; result = select.executeQuery(mimetypeStatsQuery); if (result.next()) { nextMimetypeStatsID = result.getLong(1) + 1; } else { throw new SQLException("Problem getting maximum MIME type AIP Statistics ID"); } String insertAIPStatsEntryQuery = "insert into aip_statistics " + "(aip_statistics_id, tj_aip_count, tj_aip_volume, rj_aip_count, rj_aip_volume, " + "collation_date, binary_aip_count) " + "values (?, ?, ?, ?, ?, ?, ?)"; PreparedStatement insert = dbConnection.prepareStatement(insertAIPStatsEntryQuery); insert.setInt(1, nextAIPStatsID); insert.setLong(2, transferJobAIPCount); insert.setLong(3, transferJobAIPVolume); insert.setLong(4, reprocessingJobAIPCount); insert.setLong(5, reprocessingJobAIPVolume); insert.setDate(6, new java.sql.Date(System.currentTimeMillis())); insert.setLong(7, overallBinaryAIPCount); int rowsAdded = insert.executeUpdate(); if (rowsAdded != 1) { dbConnection.rollback(); throw new SQLException("Could not insert row into AIP statistics table"); } String insertMimeTypeStatsQuery = "insert into mimetype_aip_statistics " + "(mimetype_aip_statistics_id, aip_statistics_id, mimetype_aip_count, mimetype_aip_volume, mimetype) " + "values (?, ?, ?, ?, ?)"; insert = dbConnection.prepareStatement(insertMimeTypeStatsQuery); insert.setInt(2, nextAIPStatsID); for (String mimeType : mimeTypeRegister.keySet()) { AIPStatistics mimeTypeStats = mimeTypeRegister.get(mimeType); insert.setLong(1, nextMimetypeStatsID); insert.setLong(3, mimeTypeStats.aipCount); insert.setLong(4, mimeTypeStats.aipVolume); insert.setString(5, mimeType); nextMimetypeStatsID++; rowsAdded = insert.executeUpdate(); if (rowsAdded != 1) { dbConnection.rollback(); throw new SQLException("Could not insert row into MIME Type AIP statistics table"); } } dbConnection.commit(); } | public static void main(String[] args) { if (args.length < 1) { System.out.println("Parameters: method arg1 arg2 arg3 etc"); System.out.println(""); System.out.println("Methods:"); System.out.println(" reloadpolicies"); System.out.println(" migratedatastreamcontrolgroup"); System.exit(0); } String method = args[0].toLowerCase(); if (method.equals("reloadpolicies")) { if (args.length == 4) { try { reloadPolicies(args[1], args[2], args[3]); System.out.println("SUCCESS: Policies have been reloaded"); System.exit(0); } catch (Throwable th) { th.printStackTrace(); System.err.println("ERROR: Reloading policies failed; see above"); System.exit(1); } } else { System.err.println("ERROR: Three arguments required: " + "http|https username password"); System.exit(1); } } else if (method.equals("migratedatastreamcontrolgroup")) { if (args.length > 10) { System.err.println("ERROR: too many arguments provided"); System.exit(1); } if (args.length < 7) { System.err.println("ERROR: insufficient arguments provided. Arguments are: "); System.err.println(" protocol [http|https]"); System.err.println(" user"); System.err.println(" password"); System.err.println(" pid - either"); System.err.println(" a single pid, eg demo:object"); System.err.println(" list of pids separated by commas, eg demo:object1,demo:object2"); System.err.println(" name of file containing pids, eg file:///path/to/file"); System.err.println(" dsid - either"); System.err.println(" a single datastream id, eg DC"); System.err.println(" list of ids separated by commas, eg DC,RELS-EXT"); System.err.println(" controlGroup - target control group (note only M is implemented)"); System.err.println(" addXMLHeader - add an XML header to the datastream [true|false, default false]"); System.err.println(" reformat - reformat the XML [true|false, default false]"); System.err.println(" setMIMETypeCharset - add charset=UTF-8 to the MIMEType [true|false, default false]"); System.exit(1); } try { boolean addXMLHeader = getArgBoolean(args, 7, false); boolean reformat = getArgBoolean(args, 8, false); boolean setMIMETypeCharset = getArgBoolean(args, 9, false); ; InputStream is = modifyDatastreamControlGroup(args[1], args[2], args[3], args[4], args[5], args[6], addXMLHeader, reformat, setMIMETypeCharset); IOUtils.copy(is, System.out); is.close(); System.out.println("SUCCESS: Datastreams modified"); System.exit(0); } catch (Throwable th) { th.printStackTrace(); System.err.println("ERROR: migrating datastream control group failed; see above"); System.exit(1); } } else { System.err.println("ERROR: unrecognised method " + method); System.exit(1); } } | 19,408 |
0 | public static void copyFile(File file, String destDir) throws IOException { if (!isCanReadFile(file)) throw new RuntimeException("The File can't read:" + file.getPath()); if (!isCanWriteDirectory(destDir)) throw new RuntimeException("The Directory can't write:" + destDir); FileChannel srcChannel = null; FileChannel dstChannel = null; try { srcChannel = new FileInputStream(file).getChannel(); dstChannel = new FileOutputStream(destDir + "/" + file.getName()).getChannel(); dstChannel.transferFrom(srcChannel, 0, srcChannel.size()); } catch (IOException e) { throw e; } finally { if (srcChannel != null) try { srcChannel.close(); } catch (IOException e) { } if (dstChannel != null) try { dstChannel.close(); } catch (IOException e) { } } } | public static String toMd5(String s) { String res = ""; try { MessageDigest digest = java.security.MessageDigest.getInstance("MD5"); digest.update(s.getBytes()); byte messageDigest[] = digest.digest(); res = toHexString(messageDigest); } catch (NoSuchAlgorithmException e) { } return res; } | 19,409 |
1 | public MemoryTextBody(InputStream is, String mimeCharset) throws IOException { this.mimeCharset = mimeCharset; TempPath tempPath = TempStorage.getInstance().getRootTempPath(); ByteArrayOutputStream out = new ByteArrayOutputStream(); IOUtils.copy(is, out); out.close(); tempFile = out.toByteArray(); } | 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!"); } | 19,410 |
1 | public void fileCopy2(File inFile, File outFile) throws Exception { try { FileChannel srcChannel = new FileInputStream(inFile).getChannel(); FileChannel dstChannel = new FileOutputStream(outFile).getChannel(); dstChannel.transferFrom(srcChannel, 0, srcChannel.size()); srcChannel.close(); dstChannel.close(); } catch (IOException e) { throw new Exception("Could not copy file: " + inFile.getName()); } } | private MimeTypesProvider() { File mimeTypesFile = new File(XPontusConstantsIF.XPONTUS_HOME_DIR, "mimes.properties"); try { if (!mimeTypesFile.exists()) { OutputStream os = null; InputStream is = getClass().getResourceAsStream("/net/sf/xpontus/configuration/mimetypes.properties"); os = FileUtils.openOutputStream(mimeTypesFile); IOUtils.copy(is, os); IOUtils.closeQuietly(is); IOUtils.closeQuietly(os); } provider = new XPontusMimetypesFileTypeMap(mimeTypesFile.getAbsolutePath()); MimetypesFileTypeMap.setDefaultFileTypeMap(provider); } catch (Exception err) { err.printStackTrace(); } } | 19,411 |
1 | public static void main(String[] args) throws Exception { String uri = args[0]; Configuration conf = new Configuration(); FileSystem fs = FileSystem.get(URI.create(uri), conf); FSDataInputStream in = null; try { in = fs.open(new Path(uri)); IOUtils.copyBytes(in, System.out, 4096, false); in.seek(0); IOUtils.copyBytes(in, System.out, 4096, false); } finally { IOUtils.closeStream(in); } } | public static void copy(File from, File to) { if (from.getAbsolutePath().equals(to.getAbsolutePath())) { return; } FileInputStream is = null; FileOutputStream os = null; try { is = new FileInputStream(from); os = new FileOutputStream(to); int read = -1; byte[] buffer = new byte[10000]; while ((read = is.read(buffer)) > 0) { os.write(buffer, 0, read); } } catch (Exception e) { throw new RuntimeException(); } finally { try { is.close(); } catch (Exception e) { } try { os.close(); } catch (Exception e) { } } } | 19,412 |
1 | public static boolean copyDataToNewTable(EboContext p_eboctx, String srcTableName, String destTableName, String where, boolean log, int mode) throws boRuntimeException { srcTableName = srcTableName.toUpperCase(); destTableName = destTableName.toUpperCase(); Connection cn = null; Connection cndef = null; boolean ret = false; try { boolean srcexists = false; boolean destexists = false; final InitialContext ic = new InitialContext(); cn = p_eboctx.getConnectionData(); cndef = p_eboctx.getConnectionDef(); PreparedStatement pstm = cn.prepareStatement("SELECT TABLE_NAME FROM USER_TABLES WHERE TABLE_NAME=?"); pstm.setString(1, srcTableName); ResultSet rslt = pstm.executeQuery(); if (rslt.next()) { srcexists = true; } rslt.close(); pstm.setString(1, destTableName); rslt = pstm.executeQuery(); if (rslt.next()) { destexists = true; } if (!destexists) { rslt.close(); pstm.close(); pstm = cn.prepareStatement("SELECT VIEW_NAME FROM USER_VIEWS WHERE VIEW_NAME=?"); pstm.setString(1, destTableName); rslt = pstm.executeQuery(); if (rslt.next()) { CallableStatement cstm = cn.prepareCall("DROP VIEW " + destTableName); cstm.execute(); cstm.close(); } } rslt.close(); pstm.close(); if (srcexists && !destexists) { if (log) { logger.finest(LoggerMessageLocalizer.getMessage("CREATING_AND_COPY_DATA_FROM") + " [" + srcTableName + "] " + LoggerMessageLocalizer.getMessage("TO") + " [" + destTableName + "]"); } CallableStatement cstm = cn.prepareCall("CREATE TABLE " + destTableName + " AS SELECT * FROM " + srcTableName + " " + (((where != null) && (where.length() > 0)) ? (" WHERE " + where) : "")); cstm.execute(); cstm.close(); if (log) { logger.finest(LoggerMessageLocalizer.getMessage("UPDATING_NGTDIC")); } cn.commit(); ret = true; } else if (srcexists && destexists) { if (log) { logger.finest(LoggerMessageLocalizer.getMessage("COPY_DATA_FROM") + " [" + srcTableName + "] " + LoggerMessageLocalizer.getMessage("TO") + " [" + destTableName + "]"); } PreparedStatement pstm2 = cn.prepareStatement("SELECT COLUMN_NAME FROM USER_TAB_COLUMNS WHERE TABLE_NAME = ? "); pstm2.setString(1, destTableName); ResultSet rslt2 = pstm2.executeQuery(); StringBuffer fields = new StringBuffer(); PreparedStatement pstm3 = cn.prepareStatement("SELECT COLUMN_NAME FROM USER_TAB_COLUMNS WHERE TABLE_NAME = ? and COLUMN_NAME=?"); while (rslt2.next()) { pstm3.setString(1, srcTableName); pstm3.setString(2, rslt2.getString(1)); ResultSet rslt3 = pstm3.executeQuery(); if (rslt3.next()) { if (fields.length() > 0) { fields.append(','); } fields.append('"').append(rslt2.getString(1)).append('"'); } rslt3.close(); } pstm3.close(); rslt2.close(); pstm2.close(); CallableStatement cstm; int recs = 0; if ((mode == 0) || (mode == 1)) { cstm = cn.prepareCall("INSERT INTO " + destTableName + "( " + fields.toString() + " ) ( SELECT " + fields.toString() + " FROM " + srcTableName + " " + (((where != null) && (where.length() > 0)) ? (" WHERE " + where) : "") + ")"); recs = cstm.executeUpdate(); cstm.close(); if (log) { logger.finest(LoggerMessageLocalizer.getMessage("DONE") + " [" + recs + "] " + LoggerMessageLocalizer.getMessage("RECORDS_COPIED")); } } cn.commit(); ret = true; } } catch (Exception e) { try { cn.rollback(); } catch (Exception z) { throw new boRuntimeException("boBuildDB.moveTable", "BO-1304", z); } throw new boRuntimeException("boBuildDB.moveTable", "BO-1304", e); } finally { try { cn.close(); } catch (Exception e) { } try { cndef.close(); } catch (Exception e) { } } return ret; } | public ProjectDeploymentConfiguration deleteProjectDeploymentConfig(int id) throws AdaptationException { ProjectDeploymentConfiguration config = null; Connection connection = null; Statement statement = null; ResultSet resultSet = null; try { String query = "SELECT * FROM ProjectDeploymentConfigurations " + "WHERE id = " + id; connection = DriverManager.getConnection(CONN_STR); statement = connection.createStatement(); resultSet = statement.executeQuery(query); if (!resultSet.next()) { connection.rollback(); String msg = "Attempt to delete project deployment " + "configuration failed."; log.error(msg); throw new AdaptationException(msg); } config = getProjectDeploymentConfiguration(resultSet); query = "DELETE FROM ProjectDeploymentConfigurations " + "WHERE id = " + id; statement.executeUpdate(query); connection.commit(); } catch (SQLException ex) { try { connection.rollback(); } catch (Exception e) { } String msg = "SQLException in deleteProjectDeploymentConfig"; log.error(msg, ex); throw new AdaptationException(msg, ex); } finally { try { resultSet.close(); } catch (Exception ex) { } try { statement.close(); } catch (Exception ex) { } try { connection.close(); } catch (Exception ex) { } } return config; } | 19,413 |
1 | public void testCopyFolderContents() throws IOException { log.info("Running: testCopyFolderContents()"); IOUtils.copyFolderContents(srcFolderName, destFolderName); Assert.assertTrue(destFile1.exists() && destFile1.isFile()); Assert.assertTrue(destFile2.exists() && destFile2.isFile()); Assert.assertTrue(destFile3.exists() && destFile3.isFile()); } | private void putAlgosFromJar(File jarfile, AlgoDir dir, Model model) throws FileNotFoundException, IOException { URLClassLoader urlLoader = new URLClassLoader(new URL[] { jarfile.toURI().toURL() }); JarInputStream jis = new JarInputStream(new FileInputStream(jarfile)); JarEntry entry = jis.getNextJarEntry(); String name = null; String tmpdir = System.getProperty("user.dir") + File.separator + Application.getProperty("dir.tmp") + File.separator; byte[] buffer = new byte[1000]; while (entry != null) { name = entry.getName(); if (name.endsWith(".class")) { name = name.substring(0, name.length() - 6); name = name.replace('/', '.'); try { Class<?> cls = urlLoader.loadClass(name); if (IAlgorithm.class.isAssignableFrom(cls) && !cls.isInterface() && ((cls.getModifiers() & Modifier.ABSTRACT) == 0)) { dir.addAlgorithm(cls); model.putClass(cls.getName(), cls); } else if (ISerializable.class.isAssignableFrom(cls)) { model.putClass(cls.getName(), cls); } } catch (ClassNotFoundException e) { e.printStackTrace(); } } else if (Constants.isAllowedImageType(name)) { int lastSep = name.lastIndexOf("/"); if (lastSep != -1) { String dirs = tmpdir + name.substring(0, lastSep); File d = new File(dirs); if (!d.exists()) d.mkdirs(); } String filename = tmpdir + name; File f = new File(filename); if (!f.exists()) { f.createNewFile(); FileOutputStream fos = new FileOutputStream(f); int read = -1; while ((read = jis.read(buffer)) != -1) { fos.write(buffer, 0, read); } fos.close(); } } entry = jis.getNextJarEntry(); } } | 19,414 |
1 | @Override public void save(String arxivId, InputStream inputStream, String encoding) { String filename = StringUtil.arxivid2filename(arxivId, "tex"); try { Writer writer = new OutputStreamWriter(new FileOutputStream(String.format("%s/%s", LATEX_DOCUMENT_DIR, filename)), encoding); IOUtils.copy(inputStream, writer, encoding); writer.flush(); writer.close(); inputStream.close(); } catch (IOException e) { logger.error("Failed to save the Latex source with id='{}'", arxivId, e); throw new RuntimeException(e); } } | private static boolean computeCustomerAverages(String completePath, String CustomerAveragesOutputFileName, String CustIndexFileName) { try { File inputFile = new File(completePath + fSep + "SmartGRAPE" + fSep + CustIndexFileName); FileChannel inC = new FileInputStream(inputFile).getChannel(); int filesize = (int) inC.size(); ByteBuffer mappedfile = inC.map(FileChannel.MapMode.READ_ONLY, 0, filesize); TIntObjectHashMap CustomerLimitsTHash = new TIntObjectHashMap(480189, 1); int startIndex, endIndex; TIntArrayList a; int custid; while (mappedfile.hasRemaining()) { custid = mappedfile.getInt(); startIndex = mappedfile.getInt(); endIndex = mappedfile.getInt(); a = new TIntArrayList(2); a.add(startIndex); a.add(endIndex); CustomerLimitsTHash.put(custid, a); } inC.close(); mappedfile = null; System.out.println("Loaded customer index hash"); File outFile = new File(completePath + fSep + "SmartGRAPE" + fSep + CustomerAveragesOutputFileName); FileChannel outC = new FileOutputStream(outFile, true).getChannel(); int totalCusts = CustomerLimitsTHash.size(); File movieMMAPDATAFile = new File(completePath + fSep + "SmartGRAPE" + fSep + "MovieRatingBinaryFile.txt"); inC = new FileInputStream(movieMMAPDATAFile).getChannel(); int[] itr = CustomerLimitsTHash.keys(); startIndex = 0; endIndex = 0; a = null; ByteBuffer buf; for (int i = 0; i < totalCusts; i++) { int currentCust = itr[i]; a = (TIntArrayList) CustomerLimitsTHash.get(currentCust); startIndex = a.get(0); endIndex = a.get(1); if (endIndex > startIndex) { buf = ByteBuffer.allocate((endIndex - startIndex + 1) * 3); inC.read(buf, (startIndex - 1) * 3); } else { buf = ByteBuffer.allocate(3); inC.read(buf, (startIndex - 1) * 3); } buf.flip(); int bufsize = buf.capacity() / 3; float sum = 0; for (int q = 0; q < bufsize; q++) { buf.getShort(); sum += buf.get(); } ByteBuffer outbuf = ByteBuffer.allocate(8); outbuf.putInt(currentCust); outbuf.putFloat(sum / bufsize); outbuf.flip(); outC.write(outbuf); buf.clear(); buf = null; a.clear(); a = null; } inC.close(); outC.close(); return true; } catch (Exception e) { e.printStackTrace(); return false; } } | 19,415 |
0 | private static URL getURL(String name) throws EfreetException { URL url = ClassLoader.getSystemResource(name + ".xml"); try { if (url == null) { try { Context initContext = new InitialContext(); Context envContext = (Context) initContext.lookup("java:/comp/env"); String xmlFileDir = (String) envContext.lookup("xml/efreet"); url = new URL("file:" + xmlFileDir + "/" + name + ".xml"); } catch (NameNotFoundException nnfe) { logger.warn("Name not found on context "); } catch (NamingException e) { logger.error("Error retrieving Context : ", e); } } try { if (url != null) { url.openConnection(); } } catch (FileNotFoundException fnfe) { url = null; } if (url == null) { url = Thread.currentThread().getContextClassLoader().getResource(name + ".xml"); } } catch (IOException ioe) { logger.error("Error reading XML file", ioe); throw new EfreetException(ioe.getMessage()); } return url; } | private static ImageIcon tryLoadImageIconFromResource(String filename, String path, int width, int height) { ImageIcon icon = null; try { URL url = cl.getResource(path + pathSeparator + fixFilename(filename)); if (url != null && url.openStream() != null) { icon = new ImageIcon(url); } } catch (Exception e) { } if (icon == null) { return null; } if ((icon.getIconWidth() == width) && (icon.getIconHeight() == height)) { return icon; } else { return new ImageIcon(icon.getImage().getScaledInstance(width, height, java.awt.Image.SCALE_SMOOTH)); } } | 19,416 |
1 | private String MD5(String s) { Log.d("MD5", "Hashing '" + s + "'"); String hash = ""; try { MessageDigest m = MessageDigest.getInstance("MD5"); m.update(s.getBytes(), 0, s.length()); hash = new BigInteger(1, m.digest()).toString(16); Log.d("MD5", "Hash: " + hash); } catch (Exception e) { Log.e("MD5", e.getMessage()); } return hash; } | public String generateMappackMD5(File mapPackFile) throws IOException, NoSuchAlgorithmException { ZipFile zip = new ZipFile(mapPackFile); try { Enumeration<? extends ZipEntry> entries = zip.entries(); MessageDigest md5Total = MessageDigest.getInstance("MD5"); MessageDigest md5 = MessageDigest.getInstance("MD5"); while (entries.hasMoreElements()) { ZipEntry entry = entries.nextElement(); if (entry.isDirectory()) continue; String name = entry.getName(); if (name.toUpperCase().startsWith("META-INF")) continue; md5.reset(); InputStream in = zip.getInputStream(entry); byte[] data = Utilities.getInputBytes(in); in.close(); byte[] digest = md5.digest(data); log.trace("Hashsum " + Hex.encodeHexString(digest) + " includes \"" + name + "\""); md5Total.update(digest); md5Total.update(name.getBytes()); } String md5sum = Hex.encodeHexString(md5Total.digest()); log.trace("md5sum of " + mapPackFile.getName() + ": " + md5sum); return md5sum; } finally { zip.close(); } } | 19,417 |
0 | 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 batchInsertOrder(Order o) throws AppException { Connection conn = DBUtils.getDataConnection(); PreparedStatement pstmt = null; ResultSet rs = null; String sqlOrder = null; String sqlDetail = null; try { conn.setAutoCommit(false); sqlOrder = "insert into SO_SOMain (ID,cSOCode,dDate," + "cBusType,cCusCode,cCusName," + "cDepCode,cSTCode," + "iVTid,cMaker,cMemo) values (?,?,?,?,?,?,?,?,?,?,?)"; sqlDetail = "insert into SO_SODetails (ID,cSOCode,cInvCode,cInvName," + "iNum,iQuantity,iTaxUnitPrice,iSum,dPreDate,iSOsID,cFree1,cUnitID) values(?,?,?,?,?,?,?,?,?,?,?,?)"; pstmt = conn.prepareStatement(sqlOrder); long maxId = getMaxID(conn, pstmt, rs); maxId++; pstmt.setLong(1, maxId); Long l = maxId; o.setId(l.intValue()); String code = o.getCode(); long maxCSOCode = getMaxCSOCode(code, conn, pstmt, rs); String csOCode = getCSOCode(code, maxCSOCode); o.setCode(csOCode); pstmt.setString(2, csOCode); pstmt.setDate(3, DateUtil.getSqlDateFormUtilDate(o.getOrderDate())); pstmt.setString(4, o.getBusinessType()); pstmt.setString(5, o.getC().getId()); pstmt.setString(6, o.getC().getName()); pstmt.setString(7, o.getP().getDept().getId()); pstmt.setString(8, o.getSaleType().getId()); pstmt.setInt(9, o.getiVtid()); pstmt.setString(10, o.getP().getName()); pstmt.setString(11, o.getRemark()); pstmt.executeUpdate(); pstmt.clearParameters(); pstmt = conn.prepareStatement(sqlDetail); ArrayList<OrderDetail> ods = o.getOds(); long iSOsID = getiSOsID(conn, pstmt, rs); for (OrderDetail od : ods) { pstmt.setLong(1, maxId); pstmt.setString(2, csOCode); pstmt.setString(3, od.getInventory().getId()); pstmt.setString(4, od.getInventory().getName()); pstmt.setInt(5, od.getPiece()); pstmt.setBigDecimal(6, od.getCount()); pstmt.setBigDecimal(7, od.getPrice()); pstmt.setBigDecimal(8, od.getSum()); pstmt.setDate(9, DateUtil.getSqlDateFormUtilDate(od.getSendDate())); pstmt.setLong(10, ++iSOsID); pstmt.setString(11, od.getPacking().getcValue()); pstmt.setString(12, od.getInventory().getSAComUnitCode()); pstmt.executeUpdate(); pstmt.clearParameters(); } conn.commit(); } catch (SQLException sqle) { try { conn.rollback(); throw new AppException(sqle.getMessage()); } catch (SQLException ex) { Logger.getLogger(OrderDAO.class.getName()).log(Level.SEVERE, null, ex); throw new AppException(ex.getMessage()); } } finally { DBUtils.closeAll(rs, pstmt, conn); } } | 19,418 |
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(); } } | public static String encrypt(String message) { try { MessageDigest digest = MessageDigest.getInstance("MD5"); digest.update(message.getBytes()); BASE64Encoder encoder = new BASE64Encoder(); return encoder.encode(digest.digest()); } catch (NoSuchAlgorithmException ex) { ex.printStackTrace(); return null; } } | 19,419 |
0 | @Override public void run() { URL url = null; FileOutputStream fos = null; FTPClient ftp = null; try { url = new URL(super.getAddress()); String host = url.getHost(); String folder = StringUtils.substringBeforeLast(url.getPath(), "/"); String fileName = StringUtils.substringAfterLast(url.getPath(), "/"); ftp = new FTPClient(host, 21); if (!ftp.connected()) { ftp.connect(); } ftp.login("anonymous", "me@mymail.com"); logger.info("Connected to " + host + "."); logger.info(ftp.getLastValidReply().getReplyText()); logger.debug("changing dir to " + folder); ftp.chdir(folder); fos = new FileOutputStream(localFileName); logger.info("Downloading file " + fileName + "..."); ftp.setType(FTPTransferType.BINARY); ftp.get(fos, fileName); logger.info("Done."); } catch (Exception e) { logger.error(e.getMessage()); logger.debug(e.getStackTrace()); } finally { try { ftp.quit(); fos.close(); } catch (Exception e) { } } } | public static String SHA1(String text) throws NoSuchAlgorithmException, UnsupportedEncodingException { MessageDigest md; md = MessageDigest.getInstance("SHA-1"); byte[] sha1hash = new byte[40]; md.update(text.getBytes("iso-8859-1"), 0, text.length()); sha1hash = md.digest(); return convertToHex(sha1hash); } | 19,420 |
0 | public static boolean isAnimated(Icon icon) { if (icon instanceof ImageIcon) { Image image = ((ImageIcon) icon).getImage(); if (image != null) { Object comment = image.getProperty("comment", null); if (String.valueOf(comment).startsWith("GifBuilder")) return true; if (decoded.containsKey(image)) { return Boolean.TRUE.equals(decoded.get(image)); } InputStream is = null; try { URL url = new URL(icon.toString()); is = url.openConnection().getInputStream(); } catch (Exception e) { e.printStackTrace(); } if (is == null) { try { ImageProducer p = image.getSource(); if (p instanceof InputStreamImageSource) { Method m = InputStreamImageSource.class.getDeclaredMethod("getDecoder", null); m.setAccessible(true); ImageDecoder d = (ImageDecoder) m.invoke(p, null); if (d instanceof GifImageDecoder) { GifImageDecoder gd = (GifImageDecoder) d; Field input = ImageDecoder.class.getDeclaredField("input"); input.setAccessible(true); is = (InputStream) input.get(gd); } } } catch (Exception e) { e.printStackTrace(); } } if (is != null) { GifDecoder decoder = new GifDecoder(); decoder.read(is); boolean animated = decoder.getFrameCount() > 1; decoded.put(image, Boolean.valueOf(animated)); return animated; } } return false; } return icon instanceof AnimatedIcon; } | public void write(File file) throws Exception { if (medooFile != null) { if (!medooFile.renameTo(file)) { BufferedInputStream in = null; BufferedOutputStream out = null; try { in = new BufferedInputStream(new FileInputStream(medooFile)); out = new BufferedOutputStream(new FileOutputStream(file)); IOUtils.copy(in, out); } finally { if (in != null) { try { in.close(); } catch (IOException e) { } } if (out != null) { try { out.close(); } catch (IOException e) { } } } } } else { throw new FileUploadException("Cannot write uploaded file to disk!"); } } | 19,421 |
0 | private boolean subtitleDownload(Movie movie, File movieFile, File subtitleFile) { try { String ret; String xml; String moviehash = getHash(movieFile); String moviebytesize = String.valueOf(movieFile.length()); xml = generateXMLRPCSS(moviehash, moviebytesize); ret = sendRPC(xml); String subDownloadLink = getValue("SubDownloadLink", ret); if (subDownloadLink.equals("")) { String moviefilename = movieFile.getName(); if (!(moviefilename.toUpperCase().endsWith(".M2TS") && moviefilename.startsWith("0"))) { String subfilename = subtitleFile.getName(); int index = subfilename.lastIndexOf("."); String query = subfilename.substring(0, index); xml = generateXMLRPCSS(query); ret = sendRPC(xml); subDownloadLink = getValue("SubDownloadLink", ret); } } if (subDownloadLink.equals("")) { logger.finer("OpenSubtitles Plugin: Subtitle not found for " + movie.getBaseName()); return false; } logger.finer("OpenSubtitles Plugin: Download subtitle for " + movie.getBaseName()); URL url = new URL(subDownloadLink); HttpURLConnection connection = (HttpURLConnection) (url.openConnection()); connection.setRequestProperty("Connection", "Close"); InputStream inputStream = connection.getInputStream(); int code = connection.getResponseCode(); if (code != HttpURLConnection.HTTP_OK) { logger.severe("OpenSubtitles Plugin: Download Failed"); return false; } GZIPInputStream a = new GZIPInputStream(inputStream); OutputStream out = new FileOutputStream(subtitleFile); byte buf[] = new byte[1024]; int len; while ((len = a.read(buf)) > 0) { out.write(buf, 0, len); } out.close(); movie.setSubtitles(true); return true; } catch (Exception e) { logger.severe("OpenSubtitles Plugin: Download Exception (Movie Not Found)"); return false; } } | public static final int executeSql(final Connection conn, final String sql, final boolean rollback) throws SQLException { if (null == sql) return 0; Statement stmt = null; try { stmt = conn.createStatement(); final int updated = stmt.executeUpdate(sql); return updated; } catch (final SQLException e) { if (rollback) conn.rollback(); throw e; } finally { closeAll(null, stmt, null); } } | 19,422 |
0 | 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(); } } | public Constructor run() throws Exception { String path = "META-INF/services/" + ComponentApplicationContext.class.getName(); ClassLoader loader = Thread.currentThread().getContextClassLoader(); final Enumeration<URL> urls; if (loader == null) { urls = ComponentApplicationContext.class.getClassLoader().getResources(path); } else { urls = loader.getResources(path); } while (urls.hasMoreElements()) { URL url = urls.nextElement(); BufferedReader reader = new BufferedReader(new InputStreamReader(url.openStream())); try { String className = null; while ((className = reader.readLine()) != null) { final String name = className.trim(); if (!name.startsWith("#") && !name.startsWith(";") && !name.startsWith("//")) { final Class<?> cls; if (loader == null) { cls = Class.forName(name); } else { cls = Class.forName(name, true, loader); } int m = cls.getModifiers(); if (ComponentApplicationContext.class.isAssignableFrom(cls) && !Modifier.isAbstract(m) && !Modifier.isInterface(m)) { Constructor constructor = cls.getDeclaredConstructor(); if (!Modifier.isPublic(constructor.getModifiers())) { constructor.setAccessible(true); } return constructor; } else { throw new ClassCastException(cls.getName()); } } } } finally { reader.close(); } } throw new ComponentApplicationException("No " + "ComponentApplicationContext implementation " + "found."); } | 19,423 |
1 | @Test public void testCopy_readerToOutputStream_Encoding_nullEncoding() throws Exception { InputStream in = new ByteArrayInputStream(inData); in = new YellOnCloseInputStreamTest(in); Reader reader = new InputStreamReader(in, "US-ASCII"); ByteArrayOutputStream baout = new ByteArrayOutputStream(); OutputStream out = new YellOnFlushAndCloseOutputStreamTest(baout, false, true); IOUtils.copy(reader, out, null); assertEquals("Sizes differ", inData.length, baout.size()); assertTrue("Content differs", Arrays.equals(inData, baout.toByteArray())); } | private Tuple execute(final HttpMethodBase method, int numTries) throws IOException { final Timer timer = Metric.newTimer("RestClientImpl.execute"); try { final int sc = httpClient.executeMethod(method); if (sc < OK_MIN || sc > OK_MAX) { throw new RestException("Unexpected status code: " + sc + ": " + method.getStatusText() + " -- " + method, sc); } final InputStream in = method.getResponseBodyAsStream(); try { final StringWriter writer = new StringWriter(2048); IOUtils.copy(in, writer, method.getResponseCharSet()); return new Tuple(sc, writer.toString()); } finally { in.close(); } } catch (NullPointerException e) { if (numTries < 3) { try { Thread.sleep(200); } catch (InterruptedException ie) { Thread.interrupted(); } return execute(method, numTries + 1); } throw new IOException("Failed to connet to " + url + " [" + method + "]", e); } catch (SocketException e) { if (numTries < 3) { try { Thread.sleep(200); } catch (InterruptedException ie) { Thread.interrupted(); } return execute(method, numTries + 1); } throw new IOException("Failed to connet to " + url + " [" + method + "]", e); } catch (IOException e) { if (numTries < 3) { try { Thread.sleep(200); } catch (InterruptedException ie) { Thread.interrupted(); } return execute(method, numTries + 1); } throw e; } finally { method.releaseConnection(); timer.stop(); } } | 19,424 |
0 | private void loadProperties() { if (properties == null) { properties = new Properties(); try { URL url = getClass().getResource(propsFile); if (url != null) properties.load(url.openStream()); } catch (IOException ioe) { ioe.printStackTrace(); } } } | public void copyFile(File s, File t) { try { FileChannel in = (new FileInputStream(s)).getChannel(); FileChannel out = (new FileOutputStream(t)).getChannel(); in.transferTo(0, s.length(), out); in.close(); out.close(); } catch (Exception e) { System.out.println(e); } } | 19,425 |
0 | private String MD5Sum(String input) { String hashtext = null; try { MessageDigest md = MessageDigest.getInstance("MD5"); md.reset(); md.update(input.getBytes()); byte[] digest = md.digest(); BigInteger bigInt = new BigInteger(1, digest); hashtext = bigInt.toString(16); while (hashtext.length() < 32) { hashtext = "0" + hashtext; } } catch (NoSuchAlgorithmException e) { e.printStackTrace(); } return hashtext; } | private CExtractHelper getData(String p_url) { CExtractHelper l_extractHelper = new CExtractHelper(); URL l_url; HttpURLConnection l_connection; try { System.out.println("Getting [" + p_url + "]"); l_url = new URL(p_url); try { URLConnection l_uconn = l_url.openConnection(); l_connection = (HttpURLConnection) l_uconn; l_connection.setConnectTimeout(2000); l_connection.setReadTimeout(2000); l_connection.setRequestProperty("User-Agent", "Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.8.1.1) Gecko/20061204 Firefox/2.0.0.1"); l_connection.connect(); int l_responseCode = l_connection.getResponseCode(); String response = l_connection.getResponseMessage(); System.out.println("HTTP/1.x " + l_responseCode + " " + response); for (int j = 1; ; j++) { String l_header = l_connection.getHeaderField(j); String l_key = l_connection.getHeaderFieldKey(j); if (l_header == null || l_key == null) { break; } } InputStream l_inputStream = new BufferedInputStream(l_connection.getInputStream()); CRemoteXML l_parser = new CRemoteXML(); try { Document l_document = l_parser.parse(l_inputStream); PrintWriter l_writerOut = new PrintWriter(new OutputStreamWriter(System.out, charsetName), true); OutputFormat l_format = OutputFormat.createPrettyPrint(); XMLWriter l_xmlWriter = new XMLWriter(l_writerOut, l_format); l_xmlWriter.write(l_document); l_xmlWriter.flush(); l_connection.disconnect(); l_extractHelper.m_document = l_document; return l_extractHelper; } catch (DocumentException e) { e.printStackTrace(); l_connection.disconnect(); System.out.println("XML parsing issue"); l_extractHelper.m_generalFailure = true; } } catch (SocketTimeoutException e) { l_extractHelper.m_timeoutFailure = true; System.out.println("Timed out"); } catch (IOException e) { e.printStackTrace(); l_extractHelper.m_generalFailure = true; } } catch (MalformedURLException e) { e.printStackTrace(); l_extractHelper.m_generalFailure = true; } return l_extractHelper; } | 19,426 |
0 | public static void initialize(Monitor monitor, final JETEmitter jetEmitter) throws JETException { IProgressMonitor progressMonitor = BasicMonitor.toIProgressMonitor(monitor); progressMonitor.beginTask("", 10); progressMonitor.subTask(CodeGenPlugin.getPlugin().getString("_UI_GeneratingJETEmitterFor_message", new Object[] { jetEmitter.templateURI })); final IWorkspace workspace = ResourcesPlugin.getWorkspace(); IJavaModel javaModel = JavaCore.create(ResourcesPlugin.getWorkspace().getRoot()); try { final JETCompiler jetCompiler = jetEmitter.templateURIPath == null ? new MyBaseJETCompiler(jetEmitter.templateURI, jetEmitter.encoding, jetEmitter.classLoader) : new MyBaseJETCompiler(jetEmitter.templateURIPath, jetEmitter.templateURI, jetEmitter.encoding, jetEmitter.classLoader); progressMonitor.subTask(CodeGenPlugin.getPlugin().getString("_UI_JETParsing_message", new Object[] { jetCompiler.getResolvedTemplateURI() })); jetCompiler.parse(); progressMonitor.worked(1); String packageName = jetCompiler.getSkeleton().getPackageName(); if (jetEmitter.templateURIPath != null) { URI templateURI = URI.createURI(jetEmitter.templateURIPath[0]); URLClassLoader theClassLoader = null; if (templateURI.isPlatformResource()) { IProject project = workspace.getRoot().getProject(templateURI.segment(1)); if (JETNature.getRuntime(project) != null) { List<URL> urls = new ArrayList<URL>(); IJavaProject javaProject = JavaCore.create(project); urls.add(new File(project.getLocation() + "/" + javaProject.getOutputLocation().removeFirstSegments(1) + "/").toURL()); for (IClasspathEntry classpathEntry : javaProject.getResolvedClasspath(true)) { if (classpathEntry.getEntryKind() == IClasspathEntry.CPE_PROJECT) { IPath projectPath = classpathEntry.getPath(); IProject otherProject = workspace.getRoot().getProject(projectPath.segment(0)); IJavaProject otherJavaProject = JavaCore.create(otherProject); urls.add(new File(otherProject.getLocation() + "/" + otherJavaProject.getOutputLocation().removeFirstSegments(1) + "/").toURL()); } } theClassLoader = new URLClassLoader(urls.toArray(new URL[0])) { @Override public Class<?> loadClass(String className) throws ClassNotFoundException { try { return super.loadClass(className); } catch (ClassNotFoundException classNotFoundException) { return jetEmitter.classLoader.loadClass(className); } } }; } } else if (templateURI.isPlatformPlugin()) { final Bundle bundle = Platform.getBundle(templateURI.segment(1)); if (bundle != null) { theClassLoader = new URLClassLoader(new URL[0], jetEmitter.classLoader) { @Override public Class<?> loadClass(String className) throws ClassNotFoundException { try { return bundle.loadClass(className); } catch (ClassNotFoundException classNotFoundException) { return super.loadClass(className); } } }; } } if (theClassLoader != null) { String className = (packageName.length() == 0 ? "" : packageName + ".") + jetCompiler.getSkeleton().getClassName(); if (className.endsWith("_")) { className = className.substring(0, className.length() - 1); } try { Class<?> theClass = theClassLoader.loadClass(className); Class<?> theOtherClass = null; try { theOtherClass = jetEmitter.classLoader.loadClass(className); } catch (ClassNotFoundException exception) { } if (theClass != theOtherClass) { String methodName = jetCompiler.getSkeleton().getMethodName(); Method[] methods = theClass.getDeclaredMethods(); for (int i = 0; i < methods.length; ++i) { if (methods[i].getName().equals(methodName)) { jetEmitter.setMethod(methods[i]); break; } } return; } } catch (ClassNotFoundException exception) { } } } ByteArrayOutputStream outputStream = new ByteArrayOutputStream(); jetCompiler.generate(outputStream); final InputStream contents = new ByteArrayInputStream(outputStream.toByteArray()); if (!javaModel.isOpen()) { javaModel.open(new SubProgressMonitor(progressMonitor, 1)); } else { progressMonitor.worked(1); } final IProject project = workspace.getRoot().getProject(jetEmitter.getProjectName()); progressMonitor.subTask(CodeGenPlugin.getPlugin().getString("_UI_JETPreparingProject_message", new Object[] { project.getName() })); IJavaProject javaProject; if (!project.exists()) { progressMonitor.subTask("JET creating project " + project.getName()); project.create(new SubProgressMonitor(progressMonitor, 1)); progressMonitor.subTask(CodeGenPlugin.getPlugin().getString("_UI_JETCreatingProject_message", new Object[] { project.getName() })); IProjectDescription description = workspace.newProjectDescription(project.getName()); description.setNatureIds(new String[] { JavaCore.NATURE_ID }); description.setLocation(null); project.open(new SubProgressMonitor(progressMonitor, 1)); project.setDescription(description, new SubProgressMonitor(progressMonitor, 1)); javaProject = JavaCore.create(project); for (Map.Entry<String, String> option : jetEmitter.getJavaOptions().entrySet()) { javaProject.setOption(option.getKey(), option.getValue()); } } else { project.open(new SubProgressMonitor(progressMonitor, 5)); IProjectDescription description = project.getDescription(); description.setNatureIds(new String[] { JavaCore.NATURE_ID }); project.setDescription(description, new SubProgressMonitor(progressMonitor, 1)); javaProject = JavaCore.create(project); } List<IClasspathEntry> classpath = new UniqueEList<IClasspathEntry>(Arrays.asList(javaProject.getRawClasspath())); for (int i = 0, len = classpath.size(); i < len; i++) { IClasspathEntry entry = classpath.get(i); if (entry.getEntryKind() == IClasspathEntry.CPE_SOURCE && ("/" + project.getName()).equals(entry.getPath().toString())) { classpath.remove(i); } } progressMonitor.subTask(CodeGenPlugin.getPlugin().getString("_UI_JETInitializingProject_message", new Object[] { project.getName() })); IClasspathEntry classpathEntry = JavaCore.newSourceEntry(new Path("/" + project.getName() + "/src")); IClasspathEntry jreClasspathEntry = JavaCore.newContainerEntry(new Path("org.eclipse.jdt.launching.JRE_CONTAINER")); classpath.add(classpathEntry); classpath.add(jreClasspathEntry); classpath.addAll(jetEmitter.classpathEntries); IFolder sourceFolder = project.getFolder(new Path("src")); if (!sourceFolder.exists()) { sourceFolder.create(false, true, new SubProgressMonitor(progressMonitor, 1)); } IFolder runtimeFolder = project.getFolder(new Path("bin")); if (!runtimeFolder.exists()) { runtimeFolder.create(false, true, new SubProgressMonitor(progressMonitor, 1)); } javaProject.setRawClasspath(classpath.toArray(new IClasspathEntry[classpath.size()]), new SubProgressMonitor(progressMonitor, 1)); javaProject.setOutputLocation(new Path("/" + project.getName() + "/bin"), new SubProgressMonitor(progressMonitor, 1)); javaProject.close(); progressMonitor.subTask(CodeGenPlugin.getPlugin().getString("_UI_JETOpeningJavaProject_message", new Object[] { project.getName() })); javaProject.open(new SubProgressMonitor(progressMonitor, 1)); IPackageFragmentRoot[] packageFragmentRoots = javaProject.getPackageFragmentRoots(); IPackageFragmentRoot sourcePackageFragmentRoot = null; for (int j = 0; j < packageFragmentRoots.length; ++j) { IPackageFragmentRoot packageFragmentRoot = packageFragmentRoots[j]; if (packageFragmentRoot.getKind() == IPackageFragmentRoot.K_SOURCE) { sourcePackageFragmentRoot = packageFragmentRoot; break; } } StringTokenizer stringTokenizer = new StringTokenizer(packageName, "."); IProgressMonitor subProgressMonitor = new SubProgressMonitor(progressMonitor, 1); subProgressMonitor.beginTask("", stringTokenizer.countTokens() + 4); subProgressMonitor.subTask(CodeGenPlugin.getPlugin().getString("_UI_CreateTargetFile_message")); IContainer sourceContainer = sourcePackageFragmentRoot == null ? project : (IContainer) sourcePackageFragmentRoot.getCorrespondingResource(); while (stringTokenizer.hasMoreElements()) { String folderName = stringTokenizer.nextToken(); sourceContainer = sourceContainer.getFolder(new Path(folderName)); if (!sourceContainer.exists()) { ((IFolder) sourceContainer).create(false, true, new SubProgressMonitor(subProgressMonitor, 1)); } } IFile targetFile = sourceContainer.getFile(new Path(jetCompiler.getSkeleton().getClassName() + ".java")); if (!targetFile.exists()) { subProgressMonitor.subTask(CodeGenPlugin.getPlugin().getString("_UI_JETCreating_message", new Object[] { targetFile.getFullPath() })); targetFile.create(contents, true, new SubProgressMonitor(subProgressMonitor, 1)); } else { subProgressMonitor.subTask(CodeGenPlugin.getPlugin().getString("_UI_JETUpdating_message", new Object[] { targetFile.getFullPath() })); targetFile.setContents(contents, true, true, new SubProgressMonitor(subProgressMonitor, 1)); } subProgressMonitor.subTask(CodeGenPlugin.getPlugin().getString("_UI_JETBuilding_message", new Object[] { project.getName() })); project.build(IncrementalProjectBuilder.INCREMENTAL_BUILD, new SubProgressMonitor(subProgressMonitor, 1)); IMarker[] markers = targetFile.findMarkers(IMarker.PROBLEM, true, IResource.DEPTH_INFINITE); boolean errors = false; for (int i = 0; i < markers.length; ++i) { IMarker marker = markers[i]; if (marker.getAttribute(IMarker.SEVERITY, IMarker.SEVERITY_INFO) == IMarker.SEVERITY_ERROR) { errors = true; subProgressMonitor.subTask(marker.getAttribute(IMarker.MESSAGE) + " : " + (CodeGenPlugin.getPlugin().getString("jet.mark.file.line", new Object[] { targetFile.getLocation(), marker.getAttribute(IMarker.LINE_NUMBER) }))); } } if (!errors) { subProgressMonitor.subTask(CodeGenPlugin.getPlugin().getString("_UI_JETLoadingClass_message", new Object[] { jetCompiler.getSkeleton().getClassName() + ".class" })); List<URL> urls = new ArrayList<URL>(); urls.add(new File(project.getLocation() + "/" + javaProject.getOutputLocation().removeFirstSegments(1) + "/").toURL()); final Set<Bundle> bundles = new HashSet<Bundle>(); LOOP: for (IClasspathEntry jetEmitterClasspathEntry : jetEmitter.getClasspathEntries()) { IClasspathAttribute[] classpathAttributes = jetEmitterClasspathEntry.getExtraAttributes(); if (classpathAttributes != null) { for (IClasspathAttribute classpathAttribute : classpathAttributes) { if (classpathAttribute.getName().equals(CodeGenUtil.EclipseUtil.PLUGIN_ID_CLASSPATH_ATTRIBUTE_NAME)) { Bundle bundle = Platform.getBundle(classpathAttribute.getValue()); if (bundle != null) { bundles.add(bundle); continue LOOP; } } } } urls.add(new URL("platform:/resource" + jetEmitterClasspathEntry.getPath() + "/")); } URLClassLoader theClassLoader = new URLClassLoader(urls.toArray(new URL[0]), jetEmitter.classLoader) { @Override public Class<?> loadClass(String className) throws ClassNotFoundException { try { return super.loadClass(className); } catch (ClassNotFoundException exception) { for (Bundle bundle : bundles) { try { return bundle.loadClass(className); } catch (ClassNotFoundException exception2) { } } throw exception; } } }; Class<?> theClass = theClassLoader.loadClass((packageName.length() == 0 ? "" : packageName + ".") + jetCompiler.getSkeleton().getClassName()); String methodName = jetCompiler.getSkeleton().getMethodName(); Method[] methods = theClass.getDeclaredMethods(); for (int i = 0; i < methods.length; ++i) { if (methods[i].getName().equals(methodName)) { jetEmitter.setMethod(methods[i]); break; } } } subProgressMonitor.done(); } catch (CoreException exception) { throw new JETException(exception); } catch (Exception exception) { throw new JETException(exception); } finally { progressMonitor.done(); } } | public void imagesParserAssesmentItem(int file, int currentquestion, Resource resTemp) { NodeList nl = null; Node n = null; NamedNodeMap nnp = null; Node nsrc = null; URL url = null; String sFilename = ""; String sNewPath = ""; int index; String sOldPath = ""; try { if (file == 1) { nl = doc.getElementsByTagName("img"); } else { nl = doc_[currentquestion].getElementsByTagName("img"); } for (int i = 0; i < nl.getLength(); i++) { n = nl.item(i); nnp = n.getAttributes(); nsrc = nnp.getNamedItem("src"); String sTemp = nsrc.getTextContent(); url = new URL("file", "localhost", sTemp); sOldPath = url.getPath(); sOldPath = sOldPath.replace('/', File.separatorChar); int indexFirstSlash = sOldPath.indexOf(File.separatorChar); String sSourcePath = sOldPath.substring(indexFirstSlash + 1); index = sOldPath.lastIndexOf(File.separatorChar); sFilename = sOldPath.substring(index + 1); sNewPath = this.sTempLocation + sFilename; FileChannel in = null; FileChannel out = null; try { in = new FileInputStream(sSourcePath).getChannel(); out = new FileOutputStream(sNewPath).getChannel(); long size = in.size(); MappedByteBuffer buf = in.map(FileChannel.MapMode.READ_ONLY, 0, size); out.write(buf); } finally { if (in != null) in.close(); if (out != null) out.close(); } if (file == 1) { sXml = sXml.replace(nsrc.getTextContent(), sFilename); } else { sXml_[currentquestion] = sXml_[currentquestion].replace(nsrc.getTextContent(), sFilename); } lsImages.add(sFilename); resTemp.addFile(sFilename); } } catch (MalformedURLException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } } | 19,427 |
0 | private static boolean prepareQualifyingFile(String completePath, String outputFile) { try { File inFile = new File(completePath + fSep + "qualifying.txt"); FileChannel inC = new FileInputStream(inFile).getChannel(); BufferedReader br = new BufferedReader(new FileReader(inFile)); File outFile = new File(completePath + fSep + "SmartGRAPE" + fSep + outputFile); FileChannel outC = new FileOutputStream(outFile, true).getChannel(); boolean endOfFile = true; short movieName = 0; int customer = 0; while (endOfFile) { String line = br.readLine(); if (line != null) { if (line.indexOf(":") >= 0) { movieName = new Short(line.substring(0, line.length() - 1)).shortValue(); } else { customer = new Integer(line.substring(0, line.indexOf(","))).intValue(); ByteBuffer outBuf = ByteBuffer.allocate(6); outBuf.putShort(movieName); outBuf.putInt(customer); outBuf.flip(); outC.write(outBuf); } } else endOfFile = false; } br.close(); outC.close(); return true; } catch (IOException e) { System.err.println(e); return false; } } | public void load(URL urlin) throws IOException { index = hs.getDoIndex(); loaded = false; url = urlin; int c, i; htmlDocLength = 0; HtmlReader in = new HtmlReader(new InputStreamReader(url.openStream(), charset)); try { if (debug >= 2) System.out.print("Loading " + urlin.toString() + " ... "); while ((c = in.read()) >= 0) { htmlDoc[htmlDocLength++] = (char) (c); if (htmlDocLength == htmlDocMaxLength) { char[] newHtmlDoc = new char[2 * htmlDocMaxLength]; System.arraycopy(htmlDoc, 0, newHtmlDoc, 0, htmlDocMaxLength); htmlDocMaxLength = 2 * htmlDocMaxLength; htmlDoc = newHtmlDoc; } } if (debug >= 2) System.out.println("done."); } catch (ArrayIndexOutOfBoundsException aioobe) { if (debug >= 1) System.out.println("Error, reading file into memory (too big) - skipping " + urlin.toString()); loaded = false; return; } in.close(); fetchURLpos = 0; dumpPos = 0; dumpLastChar = SPACE; loaded = true; frameset = false; titledone = false; headdone = false; checkhead = false; checkbody = false; } | 19,428 |
1 | public static String validateSession(String sessionid, String servicekey, HttpServletRequest request) { if (sessionid == null) { return "error"; } String loginapp = SSOFilter.getLoginapp(); String u = SSOUtil.addParameter(loginapp + "/api/validatesessionid", "sessionid", sessionid); u = SSOUtil.addParameter(u, "servicekey", servicekey); u = SSOUtil.addParameter(u, "ip", request.getRemoteHost()); u = SSOUtil.addParameter(u, "url", encodeUrl(request.getRequestURI())); u = SSOUtil.addParameter(u, "useragent", request.getHeader("User-Agent")); String response = "error"; try { URL url = new URL(u); BufferedReader reader = new BufferedReader(new InputStreamReader(url.openStream())); String line; while ((line = reader.readLine()) != null) { response = line.trim(); } reader.close(); } catch (MalformedURLException e) { } catch (IOException e) { } if ("error".equals(response)) { return "error"; } else { return response; } } | @Override public void exec() { BufferedReader in = null; try { URL url = new URL(getUrl()); in = new BufferedReader(new InputStreamReader(url.openStream())); StringBuffer result = new StringBuffer(); String str; while ((str = in.readLine()) != null) { result.append(str); } logger.info("received message: " + result); } catch (Exception e) { logger.error("HttpGetEvent could not execute", e); } finally { if (in != null) { try { in.close(); } catch (IOException e) { logger.error("BufferedReader could not be closed", e); } } } } | 19,429 |
0 | public static String[] parsePLS(String strURL, Context c) { URL url; URLConnection urlConn = null; String TAG = "parsePLS"; Vector<String> radio = new Vector<String>(); final String filetoken = "file"; final String SPLITTER = "="; try { url = new URL(strURL); urlConn = url.openConnection(); Log.d(TAG, "Got data"); } catch (IOException ioe) { Log.e(TAG, "Could not connect to " + strURL); } try { DataInputStream in = new DataInputStream(urlConn.getInputStream()); BufferedReader br = new BufferedReader(new InputStreamReader(in)); String strLine; while ((strLine = br.readLine()) != null) { String temp = strLine.toLowerCase(); Log.d(TAG, strLine); if (temp.startsWith(filetoken)) { String[] s = Pattern.compile(SPLITTER).split(temp); radio.add(s[1]); Log.d(TAG, "Found audio " + s[1]); } } br.close(); in.close(); } catch (Exception e) { Log.e(TAG, "Trouble reading file: " + e.getMessage()); } String[] t = new String[0]; String[] r = null; if (radio.size() != 0) { r = (String[]) radio.toArray(t); Log.d(TAG, "Found total: " + String.valueOf(r.length)); } return r; } | public static void main(String[] args) { try { String user = "techbeherca"; String targetUrl = "http://api.fanfou.com/statuses/user_timeline.xml?id=" + user; URL url = new URL(targetUrl); InputStream in = url.openStream(); ArrayList<MessageObj> list; if (in != null) { MessageListDOMParser parser = new MessageListDOMParser(); list = (ArrayList<MessageObj>) parser.parseXML(in); TransactionDAO dao = new TransactionDAO(); dao.insert(list); } } catch (Exception e) { e.printStackTrace(); } } | 19,430 |
1 | private static byte[] Md5f(String plainText) { byte[] ab = new byte[16]; try { MessageDigest md = MessageDigest.getInstance("MD5"); md.update(plainText.getBytes()); byte b[] = md.digest(); ab = b; } catch (NoSuchAlgorithmException e) { e.printStackTrace(); } return ab; } | public static void main(String[] args) throws NoSuchAlgorithmException { String password = "root"; MessageDigest messageDigest = MessageDigest.getInstance("MD5"); messageDigest.update(password.getBytes()); final byte[] digest = messageDigest.digest(); final StringBuilder buf = new StringBuilder(digest.length * 2); for (int j = 0; j < digest.length; j++) { buf.append(HEX_DIGITS[(digest[j] >> 4) & 0x0f]); buf.append(HEX_DIGITS[digest[j] & 0x0f]); } String pwd = buf.toString(); System.out.println(pwd); } | 19,431 |
1 | @Override public void execute() throws ProcessorExecutionException { try { if (getSource().getPaths() == null || getSource().getPaths().size() == 0 || getDestination().getPaths() == null || getDestination().getPaths().size() == 0) { throw new ProcessorExecutionException("No input and/or output paths specified."); } String temp_dir_prefix = getDestination().getPath().getParent().toString() + "/bcc_" + getDestination().getPath().getName() + "_"; SequenceTempDirMgr dirMgr = new SequenceTempDirMgr(temp_dir_prefix, context); dirMgr.setSeqNum(0); Path tmpDir; System.out.println("++++++>" + dirMgr.getSeqNum() + ": Transform input to AdjSetVertex"); Transformer transformer = new OutAdjVertex2AdjSetVertexTransformer(); transformer.setConf(context); transformer.setSrcPath(getSource().getPath()); tmpDir = dirMgr.getTempDir(); transformer.setDestPath(tmpDir); transformer.setMapperNum(getMapperNum()); transformer.setReducerNum(getReducerNum()); transformer.execute(); System.out.println("++++++>" + dirMgr.getSeqNum() + ": Transform input to LabeledAdjSetVertex"); Vertex2LabeledTransformer l_transformer = new Vertex2LabeledTransformer(); l_transformer.setConf(context); l_transformer.setSrcPath(tmpDir); tmpDir = dirMgr.getTempDir(); l_transformer.setDestPath(tmpDir); l_transformer.setMapperNum(getMapperNum()); l_transformer.setReducerNum(getReducerNum()); l_transformer.setOutputValueClass(LabeledAdjSetVertex.class); l_transformer.execute(); Graph src; Graph dest; Path path_to_remember = tmpDir; System.out.println("++++++>" + dirMgr.getSeqNum() + ": SpanningTreeRootChoose"); src = new Graph(Graph.defaultGraph()); src.setPath(tmpDir); dest = new Graph(Graph.defaultGraph()); tmpDir = dirMgr.getTempDir(); dest.setPath(tmpDir); GraphAlgorithm choose_root = new SpanningTreeRootChoose(); choose_root.setConf(context); choose_root.setSource(src); choose_root.setDestination(dest); choose_root.setMapperNum(getMapperNum()); choose_root.setReducerNum(getReducerNum()); choose_root.execute(); Path the_file = new Path(tmpDir.toString() + "/part-00000"); FileSystem client = FileSystem.get(context); if (!client.exists(the_file)) { throw new ProcessorExecutionException("Did not find the chosen vertex in " + the_file.toString()); } FSDataInputStream input_stream = client.open(the_file); ByteArrayOutputStream output_stream = new ByteArrayOutputStream(); IOUtils.copyBytes(input_stream, output_stream, context, false); String the_line = output_stream.toString(); String root_vertex_id = the_line.substring(SpanningTreeRootChoose.SPANNING_TREE_ROOT.length()).trim(); input_stream.close(); output_stream.close(); System.out.println("++++++> Chosen the root of spanning tree = " + root_vertex_id); while (true) { System.out.println("++++++>" + dirMgr.getSeqNum() + " Generate the spanning tree rooted at : (" + root_vertex_id + ") from " + tmpDir); src = new Graph(Graph.defaultGraph()); src.setPath(path_to_remember); tmpDir = dirMgr.getTempDir(); dest = new Graph(Graph.defaultGraph()); dest.setPath(tmpDir); path_to_remember = tmpDir; GraphAlgorithm spanning = new SpanningTreeGenerate(); spanning.setConf(context); spanning.setSource(src); spanning.setDestination(dest); spanning.setMapperNum(getMapperNum()); spanning.setReducerNum(getReducerNum()); spanning.setParameter(ConstantLabels.ROOT_ID, root_vertex_id); spanning.execute(); System.out.println("++++++>" + dirMgr.getSeqNum() + " Test spanning convergence"); src = new Graph(Graph.defaultGraph()); src.setPath(tmpDir); tmpDir = dirMgr.getTempDir(); dest = new Graph(Graph.defaultGraph()); dest.setPath(tmpDir); GraphAlgorithm conv_tester = new SpanningConvergenceTest(); conv_tester.setConf(context); conv_tester.setSource(src); conv_tester.setDestination(dest); conv_tester.setMapperNum(getMapperNum()); conv_tester.setReducerNum(getReducerNum()); conv_tester.execute(); long vertexes_out_of_tree = MRConsoleReader.getMapOutputRecordNum(conv_tester.getFinalStatus()); System.out.println("++++++> number of vertexes out of the spanning tree = " + vertexes_out_of_tree); if (vertexes_out_of_tree == 0) { break; } } System.out.println("++++++> From spanning tree to sets of edges"); src = new Graph(Graph.defaultGraph()); src.setPath(path_to_remember); tmpDir = dirMgr.getTempDir(); dest = new Graph(Graph.defaultGraph()); dest.setPath(tmpDir); GraphAlgorithm tree2set = new Tree2EdgeSet(); tree2set.setConf(context); tree2set.setSource(src); tree2set.setDestination(dest); tree2set.setMapperNum(getMapperNum()); tree2set.setReducerNum(getReducerNum()); tree2set.execute(); long map_input_records_num = -1; long map_output_records_num = -2; Stack<Path> expanding_stack = new Stack<Path>(); do { System.out.println("++++++>" + dirMgr.getSeqNum() + ": EdgeSetMinorJoin"); GraphAlgorithm minorjoin = new EdgeSetMinorJoin(); minorjoin.setConf(context); src = new Graph(Graph.defaultGraph()); src.setPath(tmpDir); dest = new Graph(Graph.defaultGraph()); tmpDir = dirMgr.getTempDir(); dest.setPath(tmpDir); minorjoin.setSource(src); minorjoin.setDestination(dest); minorjoin.setMapperNum(getMapperNum()); minorjoin.setReducerNum(getReducerNum()); minorjoin.execute(); expanding_stack.push(tmpDir); System.out.println("++++++>" + dirMgr.getSeqNum() + ": EdgeSetJoin"); GraphAlgorithm join = new EdgeSetJoin(); join.setConf(context); src = new Graph(Graph.defaultGraph()); src.setPath(tmpDir); dest = new Graph(Graph.defaultGraph()); tmpDir = dirMgr.getTempDir(); dest.setPath(tmpDir); join.setSource(src); join.setDestination(dest); join.setMapperNum(getMapperNum()); join.setReducerNum(getReducerNum()); join.execute(); map_input_records_num = MRConsoleReader.getMapInputRecordNum(join.getFinalStatus()); map_output_records_num = MRConsoleReader.getMapOutputRecordNum(join.getFinalStatus()); System.out.println("++++++> map in/out : " + map_input_records_num + "/" + map_output_records_num); } while (map_input_records_num != map_output_records_num); while (expanding_stack.size() > 0) { System.out.println("++++++>" + dirMgr.getSeqNum() + ": EdgeSetExpand"); GraphAlgorithm expand = new EdgeSetExpand(); expand.setConf(context); src = new Graph(Graph.defaultGraph()); src.addPath(expanding_stack.pop()); src.addPath(tmpDir); dest = new Graph(Graph.defaultGraph()); tmpDir = dirMgr.getTempDir(); dest.setPath(tmpDir); expand.setSource(src); expand.setDestination(dest); expand.setMapperNum(getMapperNum()); expand.setReducerNum(getReducerNum()); expand.execute(); System.out.println("++++++>" + dirMgr.getSeqNum() + ": EdgeSetMinorExpand"); GraphAlgorithm minorexpand = new EdgeSetMinorExpand(); minorexpand.setConf(context); src = new Graph(Graph.defaultGraph()); src.setPath(tmpDir); dest = new Graph(Graph.defaultGraph()); tmpDir = dirMgr.getTempDir(); dest.setPath(tmpDir); minorexpand.setSource(src); minorexpand.setDestination(dest); minorexpand.setMapperNum(getMapperNum()); minorexpand.setReducerNum(getReducerNum()); minorexpand.execute(); } System.out.println("++++++>" + dirMgr.getSeqNum() + ": EdgeSetSummarize"); GraphAlgorithm summarize = new EdgeSetSummarize(); summarize.setConf(context); src = new Graph(Graph.defaultGraph()); src.setPath(tmpDir); dest = new Graph(Graph.defaultGraph()); dest.setPath(getDestination().getPath()); summarize.setSource(src); summarize.setDestination(dest); summarize.setMapperNum(getMapperNum()); summarize.setReducerNum(getReducerNum()); summarize.execute(); dirMgr.deleteAll(); } catch (IOException e) { throw new ProcessorExecutionException(e); } catch (IllegalAccessException e) { throw new ProcessorExecutionException(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; } | 19,432 |
0 | public static InputStream getInputStream(String fileName) throws IOException { InputStream input; if (fileName.startsWith("http:")) { URL url = new URL(fileName); URLConnection connection = url.openConnection(); input = connection.getInputStream(); } else { input = new FileInputStream(fileName); } return input; } | void loadSVG(String svgFileURL) { try { URL url = new URL(svgFileURL); URLConnection c = url.openConnection(); c.setRequestProperty("Accept-Encoding", "gzip"); InputStream is = c.getInputStream(); String encoding = c.getContentEncoding(); if ("gzip".equals(encoding) || "x-gzip".equals(encoding) || svgFileURL.toLowerCase().endsWith(".svgz")) { is = new GZIPInputStream(is); } is = new BufferedInputStream(is); Document svgDoc = AppletUtils.parse(is, false); if (svgDoc != null) { if (grMngr.mainView.isBlank() == null) { grMngr.mainView.setBlank(cfgMngr.backgroundColor); } SVGReader.load(svgDoc, grMngr.mSpace, true, svgFileURL); grMngr.seekBoundingBox(); grMngr.buildLogicalStructure(); ConfigManager.defaultFont = VText.getMainFont(); grMngr.reveal(); if (grMngr.previousLocations.size() == 1) { grMngr.previousLocations.removeElementAt(0); } if (grMngr.rView != null) { grMngr.rView.getGlobalView(grMngr.mSpace.getCamera(1), 100); } grMngr.cameraMoved(null, null, 0); } else { System.err.println("An error occured while loading file " + svgFileURL); } } catch (Exception ex) { grMngr.reveal(); ex.printStackTrace(); } } | 19,433 |
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!"); } | private MimeTypesProvider() { File mimeTypesFile = new File(XPontusConstantsIF.XPONTUS_HOME_DIR, "mimes.properties"); try { if (!mimeTypesFile.exists()) { OutputStream os = null; InputStream is = getClass().getResourceAsStream("/net/sf/xpontus/configuration/mimetypes.properties"); os = FileUtils.openOutputStream(mimeTypesFile); IOUtils.copy(is, os); IOUtils.closeQuietly(is); IOUtils.closeQuietly(os); } provider = new XPontusMimetypesFileTypeMap(mimeTypesFile.getAbsolutePath()); MimetypesFileTypeMap.setDefaultFileTypeMap(provider); } catch (Exception err) { err.printStackTrace(); } } | 19,434 |
0 | private static void unzipEntry(ZipFile zipfile, ZipEntry entry, File outputDir) throws IOException { if (entry.isDirectory()) { createDir(new File(outputDir, entry.getName())); return; } File outputFile = new File(outputDir, entry.getName()); if (!outputFile.getParentFile().exists()) { createDir(outputFile.getParentFile()); } BufferedInputStream inputStream = new BufferedInputStream(zipfile.getInputStream(entry)); BufferedOutputStream outputStream = new BufferedOutputStream(new FileOutputStream(outputFile)); try { IOUtils.copy(inputStream, outputStream); } finally { outputStream.close(); inputStream.close(); } } | public ProjectDeploymentConfiguration deleteProjectDeploymentConfig(int id) throws AdaptationException { ProjectDeploymentConfiguration config = null; Connection connection = null; Statement statement = null; ResultSet resultSet = null; try { String query = "SELECT * FROM ProjectDeploymentConfigurations " + "WHERE id = " + id; connection = DriverManager.getConnection(CONN_STR); statement = connection.createStatement(); resultSet = statement.executeQuery(query); if (!resultSet.next()) { connection.rollback(); String msg = "Attempt to delete project deployment " + "configuration failed."; log.error(msg); throw new AdaptationException(msg); } config = getProjectDeploymentConfiguration(resultSet); query = "DELETE FROM ProjectDeploymentConfigurations " + "WHERE id = " + id; statement.executeUpdate(query); connection.commit(); } catch (SQLException ex) { try { connection.rollback(); } catch (Exception e) { } String msg = "SQLException in deleteProjectDeploymentConfig"; log.error(msg, ex); throw new AdaptationException(msg, ex); } finally { try { resultSet.close(); } catch (Exception ex) { } try { statement.close(); } catch (Exception ex) { } try { connection.close(); } catch (Exception ex) { } } return config; } | 19,435 |
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 ActualTask(TEditor editor, TIGDataBase dataBase, String directoryPath, Vector images) { int i; lengthOfTask = images.size(); Element dataBaseXML = new Element("dataBase"); for (i = 0; ((i < images.size()) && !stop && !cancel); i++) { Vector imagen = new Vector(2); imagen = (Vector) images.elementAt(i); String element = (String) imagen.elementAt(0); current = i; String pathSrc = System.getProperty("user.dir") + File.separator + "images" + File.separator + element.substring(0, 1).toUpperCase() + File.separator + element; String name = pathSrc.substring(pathSrc.lastIndexOf(File.separator) + 1, pathSrc.length()); String pathDst = directoryPath + name; try { FileChannel srcChannel = new FileInputStream(pathSrc).getChannel(); FileChannel dstChannel = new FileOutputStream(pathDst).getChannel(); dstChannel.transferFrom(srcChannel, 0, srcChannel.size()); srcChannel.close(); dstChannel.close(); } catch (IOException exc) { System.out.println(exc.getMessage()); System.out.println(exc.toString()); } Vector<String> keyWords = new Vector<String>(); keyWords = TIGDataBase.asociatedConceptSearch(element); Element image = new Element("image"); image.setAttribute("name", name); if (keyWords.size() != 0) { for (int k = 0; k < keyWords.size(); k++) { Element category = new Element("category"); category.setText(keyWords.get(k).trim()); image.addContent(category); } } dataBaseXML.addContent(image); } Document doc = new Document(dataBaseXML); try { XMLOutputter out = new XMLOutputter(); FileOutputStream f = new FileOutputStream(directoryPath + "images.xml"); out.output(doc, f); f.flush(); f.close(); } catch (Exception e) { e.printStackTrace(); } current = lengthOfTask; } | 19,436 |
1 | private static void userAuth(String challenge) throws IOException { try { MessageDigest md = MessageDigest.getInstance("BrokenMD4"); String passwd = null; if (System.getProperty("jarsync.password.gui") != null) { JPasswordField pass = new JPasswordField(); JPanel panel = new JPanel(new GridLayout(2, 1)); panel.add(new JLabel("Password:")); panel.add(pass); JOptionPane.showMessageDialog(null, panel, remoteUser + '@' + remoteHost + "'s Password", JOptionPane.QUESTION_MESSAGE); passwd = new String(pass.getPassword()); } else { System.out.print(remoteUser + '@' + remoteHost + "'s password: "); passwd = Util.readLine(System.in); System.out.println(); } md.update(new byte[4]); md.update(passwd.getBytes("US-ASCII")); md.update(challenge.getBytes("US-ASCII")); byte[] response = md.digest(); Util.writeASCII(out, remoteUser + " " + Util.base64(response) + '\n'); out.flush(); } catch (NoSuchAlgorithmException nsae) { throw new IOException("could not create message digest."); } } | public static String getEncryptedPwd(String password) throws NoSuchAlgorithmException, UnsupportedEncodingException { byte[] pwd = null; SecureRandom random = new SecureRandom(); byte[] salt = new byte[SALT_LENGTH]; random.nextBytes(salt); MessageDigest md = null; md = MessageDigest.getInstance("MD5"); md.update(salt); md.update(password.getBytes("UTF-8")); byte[] digest = md.digest(); pwd = new byte[digest.length + SALT_LENGTH]; System.arraycopy(salt, 0, pwd, 0, SALT_LENGTH); System.arraycopy(digest, 0, pwd, SALT_LENGTH, digest.length); return byteToHexString(pwd); } | 19,437 |
1 | public static void decryptFile(String input, String output, String pwd) throws Exception { CipherInputStream in; OutputStream out; Cipher cipher; SecretKey key; byte[] byteBuffer; cipher = Cipher.getInstance("DES"); key = new SecretKeySpec(pwd.getBytes(), "DES"); cipher.init(Cipher.DECRYPT_MODE, key); in = new CipherInputStream(new FileInputStream(input), cipher); out = new FileOutputStream(output); byteBuffer = new byte[1024]; for (int n; (n = in.read(byteBuffer)) != -1; out.write(byteBuffer, 0, n)) ; in.close(); out.close(); } | private static void readAndRewrite(File inFile, File outFile) throws IOException { ImageInputStream iis = ImageIO.createImageInputStream(new BufferedInputStream(new FileInputStream(inFile))); DcmParser dcmParser = DcmParserFactory.getInstance().newDcmParser(iis); Dataset ds = DcmObjectFactory.getInstance().newDataset(); dcmParser.setDcmHandler(ds.getDcmHandler()); dcmParser.parseDcmFile(null, Tags.PixelData); PixelDataReader pdReader = pdFact.newReader(ds, iis, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); System.out.println("reading " + inFile + "..."); pdReader.readPixelData(false); ImageOutputStream out = ImageIO.createImageOutputStream(new BufferedOutputStream(new FileOutputStream(outFile))); DcmEncodeParam dcmEncParam = DcmEncodeParam.IVR_LE; ds.writeDataset(out, dcmEncParam); ds.writeHeader(out, dcmEncParam, Tags.PixelData, dcmParser.getReadVR(), dcmParser.getReadLength()); System.out.println("writing " + outFile + "..."); PixelDataWriter pdWriter = pdFact.newWriter(pdReader.getPixelDataArray(), false, ds, out, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); pdWriter.writePixelData(); out.flush(); out.close(); System.out.println("done!"); } | 19,438 |
0 | private void getRandomGUID(boolean secure) { MessageDigest md5 = null; StringBuffer sbValueBeforeMD5 = new StringBuffer(); try { md5 = MessageDigest.getInstance("MD5"); } catch (NoSuchAlgorithmException e) { System.out.println("Error: " + e); } try { long time = System.currentTimeMillis(); long rand = 0; if (secure) { rand = mySecureRand.nextLong(); } else { rand = myRand.nextLong(); } sbValueBeforeMD5.append(s_id); sbValueBeforeMD5.append(":"); sbValueBeforeMD5.append(Long.toString(time)); sbValueBeforeMD5.append(":"); sbValueBeforeMD5.append(Long.toString(rand)); valueBeforeMD5 = sbValueBeforeMD5.toString(); md5.update(valueBeforeMD5.getBytes()); byte[] array = md5.digest(); StringBuffer sb = new StringBuffer(); for (int j = 0; j < array.length; ++j) { int b = array[j] & 0xFF; if (b < 0x10) sb.append('0'); sb.append(Integer.toHexString(b)); } valueAfterMD5 = sb.toString(); } catch (Exception e) { System.out.println("Error:" + e); } } | private void chopFileDisk() throws IOException { File tempFile = new File("" + logFile + ".tmp"); BufferedInputStream bis = null; BufferedOutputStream bos = null; long startCopyPos; byte readBuffer[] = new byte[2048]; int readCount; long totalBytesRead = 0; if (reductionRatio > 0 && logFile.length() > 0) { startCopyPos = logFile.length() / reductionRatio; } else { startCopyPos = 0; } try { bis = new BufferedInputStream(new FileInputStream(logFile)); bos = new BufferedOutputStream(new FileOutputStream(tempFile)); do { readCount = bis.read(readBuffer, 0, readBuffer.length); if (readCount > 0) { totalBytesRead += readCount; if (totalBytesRead > startCopyPos) { bos.write(readBuffer, 0, readCount); } } } while (readCount > 0); } finally { if (bos != null) { try { bos.close(); } catch (IOException ex) { } } if (bis != null) { try { bis.close(); } catch (IOException ex) { } } } if (tempFile.isFile()) { if (!logFile.delete()) { throw new IOException("Error when attempting to delete the " + logFile + " file."); } if (!tempFile.renameTo(logFile)) { throw new IOException("Error when renaming the " + tempFile + " to " + logFile + "."); } } } | 19,439 |
1 | public void testMemberSeek() throws IOException { GZIPMembersInputStream gzin = new GZIPMembersInputStream(new ByteArrayInputStream(allfour_gz)); gzin.setEofEachMember(true); gzin.compressedSeek(noise1k_gz.length + noise32k_gz.length); int count2 = IOUtils.copy(gzin, new NullOutputStream()); assertEquals("wrong 1-byte member count", 1, count2); assertEquals("wrong Member2 start", noise1k_gz.length + noise32k_gz.length, gzin.getCurrentMemberStart()); assertEquals("wrong Member2 end", noise1k_gz.length + noise32k_gz.length + a_gz.length, gzin.getCurrentMemberEnd()); gzin.nextMember(); int count3 = IOUtils.copy(gzin, new NullOutputStream()); assertEquals("wrong 5-byte member count", 5, count3); assertEquals("wrong Member3 start", noise1k_gz.length + noise32k_gz.length + a_gz.length, gzin.getCurrentMemberStart()); assertEquals("wrong Member3 end", noise1k_gz.length + noise32k_gz.length + a_gz.length + hello_gz.length, gzin.getCurrentMemberEnd()); gzin.nextMember(); int countEnd = IOUtils.copy(gzin, new NullOutputStream()); assertEquals("wrong eof count", 0, countEnd); } | public static void copyFile(File source, File dest) throws IOException { log.debug("Copy from {} to {}", source.getAbsoluteFile(), dest.getAbsoluteFile()); FileInputStream fi = new FileInputStream(source); FileChannel fic = fi.getChannel(); MappedByteBuffer mbuf = fic.map(FileChannel.MapMode.READ_ONLY, 0, source.length()); fic.close(); fi.close(); fi = null; if (!dest.exists()) { String destPath = dest.getPath(); log.debug("Destination path: {}", destPath); String destDir = destPath.substring(0, destPath.lastIndexOf(File.separatorChar)); log.debug("Destination dir: {}", destDir); File dir = new File(destDir); if (!dir.exists()) { if (dir.mkdirs()) { log.debug("Directory created"); } else { log.warn("Directory not created"); } } dir = null; } FileOutputStream fo = new FileOutputStream(dest); FileChannel foc = fo.getChannel(); foc.write(mbuf); foc.close(); fo.close(); fo = null; mbuf.clear(); mbuf = null; } | 19,440 |
1 | public static boolean decodeFileToFile(String infile, String outfile) { boolean success = false; java.io.InputStream in = null; java.io.OutputStream out = null; try { in = new Base64.InputStream(new java.io.BufferedInputStream(new java.io.FileInputStream(infile)), Base64.DECODE); out = new java.io.BufferedOutputStream(new java.io.FileOutputStream(outfile)); byte[] buffer = new byte[65536]; int read = -1; while ((read = in.read(buffer)) >= 0) { out.write(buffer, 0, read); } success = true; } catch (java.io.IOException exc) { exc.printStackTrace(); } finally { try { in.close(); } catch (Exception exc) { } try { out.close(); } catch (Exception exc) { } } return success; } | public static void copyFile(File src, File dst) throws IOException { if (T.t) T.info("Copying " + src + " -> " + dst + "..."); FileInputStream in = new FileInputStream(src); FileOutputStream out = new FileOutputStream(dst); byte buf[] = new byte[40 * KB]; int read; while ((read = in.read(buf)) != -1) { out.write(buf, 0, read); } out.flush(); out.close(); in.close(); if (T.t) T.info("File copied."); } | 19,441 |
1 | private void writeToFile(Body b, File mime4jFile) throws FileNotFoundException, IOException { if (b instanceof TextBody) { String charset = CharsetUtil.toJavaCharset(b.getParent().getCharset()); if (charset == null) { charset = "ISO8859-1"; } OutputStream out = new FileOutputStream(mime4jFile); IOUtils.copy(((TextBody) b).getReader(), out, charset); } else { OutputStream out = new FileOutputStream(mime4jFile); IOUtils.copy(((BinaryBody) b).getInputStream(), out); } } | private void copyResources(File oggDecDir, String[] resources, String resPrefix) throws FileNotFoundException, IOException { for (int i = 0; i < resources.length; i++) { String res = resPrefix + resources[i]; InputStream is = this.getClass().getResourceAsStream(res); if (is == null) throw new IllegalArgumentException("cannot find resource '" + res + "'"); File file = new File(oggDecDir, resources[i]); if (!file.exists() || file.length() == 0) { FileOutputStream fos = new FileOutputStream(file); try { IOUtils.copyStreams(is, fos); } finally { fos.close(); } } } } | 19,442 |
1 | private final void copyTargetFileToSourceFile(File sourceFile, File targetFile) throws MJProcessorException { if (!targetFile.exists()) { targetFile.getParentFile().mkdirs(); try { if (!targetFile.exists()) { targetFile.createNewFile(); } } catch (IOException e) { throw new MJProcessorException(e.getMessage(), e); } } FileChannel in = null, out = null; try { in = new FileInputStream(sourceFile).getChannel(); out = new FileOutputStream(targetFile).getChannel(); long size = in.size(); MappedByteBuffer buf = in.map(FileChannel.MapMode.READ_ONLY, 0, size); out.write(buf); } catch (IOException e) { log.error(e); } finally { if (in != null) try { in.close(); } catch (IOException e) { log.error(e); } if (out != null) try { out.close(); } catch (IOException e) { log.error(e); } } } | public Object read(InputStream inputStream, Map metadata) throws IOException, ClassNotFoundException { if (log.isTraceEnabled()) log.trace("Read input stream with metadata=" + metadata); Integer resCode = (Integer) metadata.get(HTTPMetadataConstants.RESPONSE_CODE); String resMessage = (String) metadata.get(HTTPMetadataConstants.RESPONSE_CODE_MESSAGE); if (resCode != null && validResponseCodes.contains(resCode) == false) throw new RuntimeException("Invalid HTTP server response [" + resCode + "] - " + resMessage); ByteArrayOutputStream baos = new ByteArrayOutputStream(1024); IOUtils.copyStream(baos, inputStream); String soapMessage = new String(baos.toByteArray(), charsetEncoding); if (isTraceEnabled) { String prettySoapMessage = DOMWriter.printNode(DOMUtils.parse(soapMessage), true); log.trace("Incoming Response SOAPMessage\n" + prettySoapMessage); } return soapMessage; } | 19,443 |
0 | public static List<String> getServers() throws Exception { List<String> servers = new ArrayList<String>(); URL url = new URL("http://tfast.org/en/servers.php"); BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream())); String line = null; while ((line = in.readLine()) != null) { if (line.contains("serv=")) { int i = line.indexOf("serv="); servers.add(line.substring(i + 5, line.indexOf("\"", i))); } } in.close(); return servers; } | public static URL toFileUrl(URL location) throws IOException { String protocol = location.getProtocol().intern(); if (protocol != "jar") throw new IOException("cannot explode " + location); JarURLConnection juc = (JarURLConnection) location.openConnection(); String path = juc.getEntryName(); String parentPath = parentPathOf(path); File tempDir = createTempDir("jartemp"); JarFile jarFile = juc.getJarFile(); for (Enumeration<JarEntry> en = jarFile.entries(); en.hasMoreElements(); ) { ZipEntry entry = en.nextElement(); if (entry.isDirectory()) continue; String entryPath = entry.getName(); if (entryPath.startsWith(parentPath)) { File dest = new File(tempDir, entryPath); dest.getParentFile().mkdirs(); InputStream in = jarFile.getInputStream(entry); OutputStream out = new FileOutputStream(dest); IOUtils.copy(in, out); dest.deleteOnExit(); } } File realFile = new File(tempDir, path); return realFile.toURL(); } | 19,444 |
1 | public static boolean decodeFileToFile(String infile, String outfile) { boolean success = false; java.io.InputStream in = null; java.io.OutputStream out = null; try { in = new Base64.InputStream(new java.io.BufferedInputStream(new java.io.FileInputStream(infile)), Base64.DECODE); out = new java.io.BufferedOutputStream(new java.io.FileOutputStream(outfile)); byte[] buffer = new byte[65536]; int read = -1; while ((read = in.read(buffer)) >= 0) { out.write(buffer, 0, read); } success = true; } catch (java.io.IOException exc) { exc.printStackTrace(); } finally { closeQuietly(in); closeQuietly(out); } return success; } | private void trainSRLParser(byte flag, JarArchiveOutputStream zout) throws Exception { AbstractSRLParser labeler = null; AbstractDecoder[] decoder = null; if (flag == SRLParser.FLAG_TRAIN_LEXICON) { System.out.println("\n* Save lexica"); labeler = new SRLParser(flag, s_featureXml); } else if (flag == SRLParser.FLAG_TRAIN_INSTANCE) { System.out.println("\n* Print training instances"); System.out.println("- loading lexica"); labeler = new SRLParser(flag, t_xml, s_lexiconFiles); } else if (flag == SRLParser.FLAG_TRAIN_BOOST) { System.out.println("\n* Train boost"); decoder = new AbstractDecoder[m_model.length]; for (int i = 0; i < decoder.length; i++) decoder[i] = new OneVsAllDecoder((OneVsAllModel) m_model[i]); labeler = new SRLParser(flag, t_xml, t_map, decoder); } AbstractReader<DepNode, DepTree> reader = new SRLReader(s_trainFile, true); DepTree tree; int n; labeler.setLanguage(s_language); reader.setLanguage(s_language); for (n = 0; (tree = reader.nextTree()) != null; n++) { labeler.parse(tree); if (n % 1000 == 0) System.out.printf("\r- parsing: %dK", n / 1000); } System.out.println("\r- labeling: " + n); if (flag == SRLParser.FLAG_TRAIN_LEXICON) { System.out.println("- labeling"); labeler.saveTags(s_lexiconFiles); t_xml = labeler.getSRLFtrXml(); } else if (flag == SRLParser.FLAG_TRAIN_INSTANCE || flag == SRLParser.FLAG_TRAIN_BOOST) { a_yx = labeler.a_trans; zout.putArchiveEntry(new JarArchiveEntry(ENTRY_FEATURE)); IOUtils.copy(new FileInputStream(s_featureXml), zout); zout.closeArchiveEntry(); for (String lexicaFile : s_lexiconFiles) { zout.putArchiveEntry(new JarArchiveEntry(lexicaFile)); IOUtils.copy(new FileInputStream(lexicaFile), zout); zout.closeArchiveEntry(); } if (flag == SRLParser.FLAG_TRAIN_INSTANCE) t_map = labeler.getSRLFtrMap(); } } | 19,445 |
1 | public void echo(HttpRequest request, HttpResponse response) throws IOException { InputStream in = request.getInputStream(); if ("gzip".equals(request.getField("Content-Encoding"))) { in = new GZIPInputStream(in); } IOUtils.copy(in, response.getOutputStream()); } | public static void copyFile(File src, File dst) throws IOException { LOGGER.info("Copying file '" + src.getAbsolutePath() + "' to '" + dst.getAbsolutePath() + "'"); FileChannel in = null; FileChannel out = null; try { FileInputStream fis = new FileInputStream(src); in = fis.getChannel(); FileOutputStream fos = new FileOutputStream(dst); out = fos.getChannel(); out.transferFrom(in, 0, in.size()); } finally { try { if (in != null) in.close(); } catch (IOException e) { LOGGER.log(Level.SEVERE, e.getMessage(), e); } if (out != null) { try { out.close(); } catch (IOException e) { LOGGER.log(Level.SEVERE, e.getMessage(), e); } } } } | 19,446 |
0 | @Override public void handlePeerEvent(PeerEvent event) { if (event.geteventInfo() instanceof EventServiceInfo) { EventServiceInfo info = (EventServiceInfo) event.geteventInfo(); if (info.getServiceState() != ServiceState.Deployed) return; long bid = info.getBundleId(); Bundle bundle = context.getBundle(bid); Enumeration entries = bundle.findEntries("OSGI-INF/PrivacyPolicy/", "*.xml", true); if (entries != null) { if (entries.hasMoreElements()) { try { URL url = (URL) entries.nextElement(); BufferedInputStream in = new BufferedInputStream(url.openStream()); XMLPolicyReader reader = new XMLPolicyReader(this.context); RequestPolicy policy = reader.readPolicyFromFile(in); if (policy != null) { this.policyMgr.addPrivacyPolicyForService(info.getServiceID(), policy); } } catch (IOException ioe) { } } } } } | public Resource readResource(URL url, ResourceManager resourceManager) throws NAFException { XMLResource resource = new XMLResource(resourceManager, url); InputStream in = null; try { in = url.openStream(); ArrayList<Transformer> trList = null; Document doc = docbuilder.parse(in); for (Node n = doc.getFirstChild(); n != null; n = n.getNextSibling()) { if (n.getNodeType() == Node.PROCESSING_INSTRUCTION_NODE && "xml-stylesheet".equals(n.getNodeName())) { ProcessingInstruction pi = (ProcessingInstruction) n; Map<String, String> attrs = DOMUtil.parseProcessingInstructionAttributes(pi); if ("text/xsl".equals(attrs.get("type"))) { String href = attrs.get("href"); if (href == null) throw new NAFException("Style sheet processing instructions must have an \"href\" attribute"); try { Transformer t = styleManager.createTransformer(new URL(url, href)); if (trList == null) trList = new ArrayList<Transformer>(); trList.add(t); } catch (Exception ex) { throw new NAFException("Error reading style sheet resource \"" + href + "\""); } } } } if (trList != null) { for (Transformer t : trList) { doc = (Document) styleManager.transform(t, doc); if (LOGGER_DUMP.isDebugEnabled()) { StringWriter swr = new StringWriter(); DOMUtil.dumpNode(doc, swr); LOGGER_DUMP.debug("Transformed instance:\n" + swr + "\n"); } } } Element rootE = doc.getDocumentElement(); if (!NAF_NAMESPACE_URI.equals(rootE.getNamespaceURI())) throw new NAFException("Root element does not use the NAF namespace"); Object comp = createComponent(rootE, resource, null); resource.setRootObject(comp); return resource; } catch (Exception ex) { throw new NAFException("Error reading NAF resource \"" + url.toExternalForm() + "\"", ex); } finally { if (in != null) try { in.close(); } catch (Exception ignored) { } } } | 19,447 |
0 | @Override public void checkConnection(byte[] options) throws Throwable { Properties opts = PropertiesUtils.deserializeProperties(options); String server = opts.getProperty(TRANSFER_OPTION_SERVER); String username = opts.getProperty(TRANSFER_OPTION_USERNAME); String password = opts.getProperty(TRANSFER_OPTION_PASSWORD); String filePath = opts.getProperty(TRANSFER_OPTION_FILEPATH); URL url = new URL(PROTOCOL_PREFIX + username + ":" + password + "@" + server + filePath + ";type=i"); URLConnection urlc = url.openConnection(BackEnd.getProxy(Proxy.Type.SOCKS)); urlc.setConnectTimeout(Preferences.getInstance().preferredTimeOut * 1000); urlc.setReadTimeout(Preferences.getInstance().preferredTimeOut * 1000); urlc.connect(); } | public void createNewFile(String filePath, InputStream in) throws IOException { FileOutputStream out = null; try { File file = newFileRef(filePath); FileHelper.createNewFile(file, true); out = new FileOutputStream(file); IOUtils.copy(in, out); } finally { IOUtils.closeQuietly(in); IOUtils.closeQuietly(out); } } | 19,448 |
1 | public static String encryptPassword(String password) throws PasswordException { String hash = null; if (password != null && !password.equals("")) { try { MessageDigest md = MessageDigest.getInstance("SHA"); md.update(password.getBytes("UTF-8")); byte raw[] = md.digest(); hash = (new BASE64Encoder()).encode(raw); } catch (NoSuchAlgorithmException nsae) { throw new PasswordException(PasswordException.SYSTEM_ERROR); } catch (UnsupportedEncodingException uee) { throw new PasswordException(PasswordException.SYSTEM_ERROR); } } return hash; } | private void createPropertyName(String objectID, String value, String propertyName, Long userID) throws JspTagException { rObject object = new rObject(new Long(objectID), userID); ClassProperty classProperty = new ClassProperty(propertyName, object.getClassName()); String newValue = value; if (classProperty.getName().equals("Password")) { try { MessageDigest crypt = MessageDigest.getInstance("MD5"); crypt.update(value.getBytes()); byte digest[] = crypt.digest(); StringBuffer hexString = new StringBuffer(); for (int i = 0; i < digest.length; i++) { hexString.append(hexDigit(digest[i])); } newValue = hexString.toString(); crypt.reset(); } catch (NoSuchAlgorithmException e) { System.err.println("jspShop: Could not get instance of MD5 algorithm. Please fix this!" + e.getMessage()); e.printStackTrace(); throw new JspTagException("Error crypting password!: " + e.getMessage()); } } Properties properties = new Properties(new Long(objectID), userID); try { Property property = properties.create(classProperty.getID(), newValue); pageContext.setAttribute(getId(), property); } catch (CreateException e) { throw new JspTagException("Could not create PropertyValue, CreateException: " + e.getMessage()); } } | 19,449 |
0 | private void copyFile(File sourceFile, File destFile) throws IOException { if (log.isDebugEnabled()) { log.debug("CopyFile : Source[" + sourceFile.getAbsolutePath() + "] Dest[" + destFile.getAbsolutePath() + "]"); } if (!destFile.exists()) { destFile.createNewFile(); } FileChannel source = null; FileChannel destination = null; try { source = new FileInputStream(sourceFile).getChannel(); destination = new FileOutputStream(destFile).getChannel(); destination.transferFrom(source, 0, source.size()); } finally { if (source != null) { source.close(); } if (destination != null) { destination.close(); } } } | public static int ToGSML(GeoSciML_Mapping mapping, String strTemplate, String strRequest, PrintWriter sortie, String requestedSRS) throws Exception { String level = "info."; if (ConnectorServlet.debug) level = "debug."; Log log = LogFactory.getLog(level + "fr.brgm.exows.gml2gsml.Gml2Gsml"); log.debug(strRequest); String tagFeature = "FIELDS"; URL url2Request = new URL(strRequest); URLConnection conn = url2Request.openConnection(); Date dDebut = new Date(); BufferedReader buffin = new BufferedReader(new InputStreamReader(conn.getInputStream())); String strLine = null; int nbFeatures = 0; Template template = VelocityCreator.createTemplate("/fr/brgm/exows/gml2gsml/templates/" + strTemplate); while ((strLine = buffin.readLine()) != null) { if (strLine.indexOf(tagFeature) != -1) { nbFeatures++; GSMLFeatureGeneric feature = createGSMLFeatureFromGMLFeatureString(mapping, strLine); VelocityContext context = new VelocityContext(); context.put("feature", feature); String outputFeatureMember = VelocityCreator.createXMLbyContext(context, template); sortie.println(outputFeatureMember); } } buffin.close(); Date dFin = new Date(); String output = "GEOSCIML : " + nbFeatures + " features handled - time : " + (dFin.getTime() - dDebut.getTime()) / 1000 + " [" + dDebut + " // " + dFin + "]"; log.trace(output); return nbFeatures; } | 19,450 |
1 | @Test public void testCopy_inputStreamToWriter_Encoding() throws Exception { InputStream in = new ByteArrayInputStream(inData); in = new YellOnCloseInputStreamTest(in); ByteArrayOutputStream baout = new ByteArrayOutputStream(); YellOnFlushAndCloseOutputStreamTest out = new YellOnFlushAndCloseOutputStreamTest(baout, true, true); Writer writer = new OutputStreamWriter(baout, "US-ASCII"); IOUtils.copy(in, writer, "UTF8"); out.off(); writer.flush(); assertTrue("Not all bytes were read", in.available() == 0); byte[] bytes = baout.toByteArray(); bytes = new String(bytes, "UTF8").getBytes("US-ASCII"); assertTrue("Content differs", Arrays.equals(inData, bytes)); } | private void copyImage(ProjectElement e) throws Exception { String fn = e.getName(); if (!fn.toLowerCase().endsWith(".png")) { if (fn.contains(".")) { fn = fn.substring(0, fn.lastIndexOf('.')) + ".png"; } else { fn += ".png"; } } File img = new File(resFolder, fn); File imgz = new File(resoutFolder.getAbsolutePath(), fn + ".zlib"); boolean copy = true; if (img.exists() && config.containsKey(img.getName())) { long modified = Long.parseLong(config.get(img.getName())); if (modified >= img.lastModified()) { copy = false; } } if (copy) { convertImage(e.getFile(), img); config.put(img.getName(), String.valueOf(img.lastModified())); } DeflaterOutputStream out = new DeflaterOutputStream(new BufferedOutputStream(new FileOutputStream(imgz))); BufferedInputStream in = new BufferedInputStream(new FileInputStream(img)); int read; while ((read = in.read()) != -1) { out.write(read); } out.close(); in.close(); imageFiles.add(imgz); imageNames.put(imgz, e.getName()); } | 19,451 |
0 | public static String translate(String s) { try { String result = null; URL url = new URL("http://translate.google.com/translate_t"); URLConnection connection = url.openConnection(); connection.setRequestProperty("User-Agent", "Mozilla/4.0 (compatible; MSIE 6.0; Windows NT 5.1)"); connection.setDoOutput(true); PrintWriter out = new PrintWriter(connection.getOutputStream()); out.print("text=" + URLEncoder.encode(s, "UTF-8") + "&langpair="); if (s.matches("[\\u0000-\\u00ff]+")) { out.print("en|ja"); } else { out.print("ja|en"); } out.print("&hl=en&ie=UTF-8&oe=UTF-8"); out.close(); BufferedReader in = new BufferedReader(new InputStreamReader(connection.getInputStream(), "UTF-8")); String inputLine; while ((inputLine = in.readLine()) != null) { int textPos = inputLine.indexOf("id=result_box"); if (textPos >= 0) { int ltrPos = inputLine.indexOf("dir=ltr", textPos + 9); if (ltrPos >= 0) { int closePos = inputLine.indexOf("<", ltrPos + 8); if (closePos >= 0) { result = inputLine.substring(ltrPos + 8, closePos); } } } } in.close(); return result; } catch (Exception e) { e.printStackTrace(); } return null; } | public void writeTo(OutputStream out) throws IOException { if (!closed) { throw new IOException("Stream not closed"); } if (isInMemory()) { memoryOutputStream.writeTo(out); } else { FileInputStream fis = new FileInputStream(outputFile); try { IOUtils.copy(fis, out); } finally { IOUtils.closeQuietly(fis); } } } | 19,452 |
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 static SubstanceSkin.ColorSchemes getColorSchemes(URL url) { List<SubstanceColorScheme> schemes = new ArrayList<SubstanceColorScheme>(); BufferedReader reader = null; Color ultraLight = null; Color extraLight = null; Color light = null; Color mid = null; Color dark = null; Color ultraDark = null; Color foreground = null; String name = null; ColorSchemeKind kind = null; boolean inColorSchemeBlock = false; try { reader = new BufferedReader(new InputStreamReader(url.openStream())); while (true) { String line = reader.readLine(); if (line == null) break; line = line.trim(); if (line.length() == 0) continue; if (line.startsWith("#")) { continue; } if (line.indexOf("{") >= 0) { if (inColorSchemeBlock) { throw new IllegalArgumentException("Already in color scheme definition"); } inColorSchemeBlock = true; name = line.substring(0, line.indexOf("{")).trim(); continue; } if (line.indexOf("}") >= 0) { if (!inColorSchemeBlock) { throw new IllegalArgumentException("Not in color scheme definition"); } inColorSchemeBlock = false; if ((name == null) || (kind == null) || (ultraLight == null) || (extraLight == null) || (light == null) || (mid == null) || (dark == null) || (ultraDark == null) || (foreground == null)) { throw new IllegalArgumentException("Incomplete specification"); } Color[] colors = new Color[] { ultraLight, extraLight, light, mid, dark, ultraDark, foreground }; if (kind == ColorSchemeKind.LIGHT) { schemes.add(getLightColorScheme(name, colors)); } else { schemes.add(getDarkColorScheme(name, colors)); } name = null; kind = null; ultraLight = null; extraLight = null; light = null; mid = null; dark = null; ultraDark = null; foreground = null; continue; } String[] split = line.split("="); if (split.length != 2) { throw new IllegalArgumentException("Unsupported format in line " + line); } String key = split[0].trim(); String value = split[1].trim(); if ("kind".equals(key)) { if (kind == null) { if ("Light".equals(value)) { kind = ColorSchemeKind.LIGHT; continue; } if ("Dark".equals(value)) { kind = ColorSchemeKind.DARK; continue; } throw new IllegalArgumentException("Unsupported format in line " + line); } throw new IllegalArgumentException("'kind' should only be defined once"); } if ("colorUltraLight".equals(key)) { if (ultraLight == null) { ultraLight = Color.decode(value); continue; } throw new IllegalArgumentException("'ultraLight' should only be defined once"); } if ("colorExtraLight".equals(key)) { if (extraLight == null) { extraLight = Color.decode(value); continue; } throw new IllegalArgumentException("'extraLight' should only be defined once"); } if ("colorLight".equals(key)) { if (light == null) { light = Color.decode(value); continue; } throw new IllegalArgumentException("'light' should only be defined once"); } if ("colorMid".equals(key)) { if (mid == null) { mid = Color.decode(value); continue; } throw new IllegalArgumentException("'mid' should only be defined once"); } if ("colorDark".equals(key)) { if (dark == null) { dark = Color.decode(value); continue; } throw new IllegalArgumentException("'dark' should only be defined once"); } if ("colorUltraDark".equals(key)) { if (ultraDark == null) { ultraDark = Color.decode(value); continue; } throw new IllegalArgumentException("'ultraDark' should only be defined once"); } if ("colorForeground".equals(key)) { if (foreground == null) { foreground = Color.decode(value); continue; } throw new IllegalArgumentException("'foreground' should only be defined once"); } throw new IllegalArgumentException("Unsupported format in line " + line); } ; } catch (IOException ioe) { throw new IllegalArgumentException(ioe); } finally { if (reader != null) { try { reader.close(); } catch (IOException ioe) { } } } return new SubstanceSkin.ColorSchemes(schemes); } | 19,453 |
1 | public synchronized String encrypt(String plaintext) { MessageDigest md = null; try { md = MessageDigest.getInstance("SHA"); md.update(plaintext.getBytes("UTF-8")); } catch (NoSuchAlgorithmException e) { log().error("failed to encrypt the password.", e); throw new RuntimeException("failed to encrypt the password.", e); } catch (UnsupportedEncodingException e) { log().error("failed to encrypt the password.", e); throw new RuntimeException("failed to encrypt the password.", e); } byte raw[] = md.digest(); String hash = (new BASE64Encoder()).encode(raw); return hash; } | public static String cryptoSHA(String _strSrc) { try { BASE64Encoder encoder = new BASE64Encoder(); MessageDigest sha = MessageDigest.getInstance("SHA"); sha.update(_strSrc.getBytes()); byte[] buffer = sha.digest(); return encoder.encode(buffer); } catch (Exception err) { System.out.println(err); } return ""; } | 19,454 |
0 | public static Document getDocument(String string, String defaultCharset) { DOMParser parser = new DOMParser(); try { URL url = new URL(string); HttpURLConnection con = (HttpURLConnection) url.openConnection(); con.setConnectTimeout(10000); con.setUseCaches(false); con.addRequestProperty("_", UUID.randomUUID().toString()); String contentType = con.getContentType(); if (contentType == null) { return null; } String charsetSearch = contentType.replaceFirst("(?i).*charset=(.*)", "$1"); String contentTypeCharset = con.getContentEncoding(); BufferedReader reader = null; if (!contentType.equals(charsetSearch)) { contentTypeCharset = charsetSearch; } if (contentTypeCharset == null) { reader = new BufferedReader(new InputStreamReader(con.getInputStream(), defaultCharset)); } else { reader = new BufferedReader(new InputStreamReader(con.getInputStream(), contentTypeCharset)); } InputSource source = new InputSource(reader); parser.setFeature("http://xml.org/sax/features/namespaces", false); parser.parse(source); Document document = parser.getDocument(); String metaTagCharset = getMetaTagCharset(document); if (metaTagCharset != null && !metaTagCharset.equals(contentTypeCharset)) { HttpURLConnection reconnection = (HttpURLConnection) url.openConnection(); reconnection.setConnectTimeout(10000); reconnection.setUseCaches(false); reconnection.addRequestProperty("_", UUID.randomUUID().toString()); reader = new BufferedReader(new InputStreamReader(reconnection.getInputStream(), metaTagCharset)); source = new InputSource(reader); parser.setFeature("http://xml.org/sax/features/namespaces", false); parser.parse(source); document = parser.getDocument(); } reader.close(); return document; } catch (DOMException e) { if (!"UTF-8".equals(defaultCharset)) { return getDocument(string, "UTF-8"); } return null; } catch (Exception ex) { return null; } } | private boolean get(String surl, File dst, Get get) throws IOException { boolean ret = false; InputStream is = null; OutputStream os = null; try { try { if (surl.startsWith("file://")) { is = new FileInputStream(surl.substring(7)); } else { URL url = new URL(surl); is = url.openStream(); } if (is != null) { os = new FileOutputStream(dst); int read; byte[] buffer = new byte[4096]; while ((read = is.read(buffer)) > 0) { os.write(buffer, 0, read); } ret = true; } } catch (ConnectException ex) { log("Connect exception " + ex.getMessage(), ex, 3); if (dst.exists()) dst.delete(); } catch (UnknownHostException ex) { log("Unknown host " + ex.getMessage(), ex, 3); } catch (FileNotFoundException ex) { log("File not found: " + ex.getMessage(), 3); } } finally { if (is != null) is.close(); if (os != null) os.close(); is = null; os = null; } if (ret) { try { is = new FileInputStream(dst); os = new FileOutputStream(getCachedFile(get)); int read; byte[] buffer = new byte[4096]; while ((read = is.read(buffer)) > 0) { os.write(buffer, 0, read); } } finally { if (is != null) is.close(); if (os != null) os.close(); is = null; os = null; } } return ret; } | 19,455 |
0 | public RobotList<Percentage> sort_incr_Percentage(RobotList<Percentage> list, String field) { int length = list.size(); Index_value[] distri = new Index_value[length]; for (int i = 0; i < length; i++) { distri[i] = new Index_value(i, list.get(i).percent); } boolean permut; do { permut = false; for (int i = 0; i < length - 1; i++) { if (distri[i].value > distri[i + 1].value) { Index_value a = distri[i]; distri[i] = distri[i + 1]; distri[i + 1] = a; permut = true; } } } while (permut); RobotList<Percentage> sol = new RobotList<Percentage>(Percentage.class); for (int i = 0; i < length; i++) { sol.addLast(new Percentage(distri[i].value)); } return sol; } | public CmsSetupTestResult execute(CmsSetupBean setupBean) { CmsSetupTestResult testResult = new CmsSetupTestResult(this); String basePath = setupBean.getWebAppRfsPath(); if (!basePath.endsWith(File.separator)) { basePath += File.separator; } File file1; Random rnd = new Random(); do { file1 = new File(basePath + "test" + rnd.nextInt(1000)); } while (file1.exists()); boolean success = false; try { file1.createNewFile(); FileWriter fw = new FileWriter(file1); fw.write("aA1"); fw.close(); success = true; FileReader fr = new FileReader(file1); success = success && (fr.read() == 'a'); success = success && (fr.read() == 'A'); success = success && (fr.read() == '1'); success = success && (fr.read() == -1); fr.close(); success = file1.delete(); success = !file1.exists(); } catch (Exception e) { success = false; } if (!success) { testResult.setRed(); testResult.setInfo("OpenCms cannot be installed without read and write privileges for path " + basePath + "! Please check you are running your servlet container with the right user and privileges."); testResult.setHelp("Not enough permissions to create/read/write a file"); testResult.setResult(RESULT_FAILED); } else { testResult.setGreen(); testResult.setResult(RESULT_PASSED); } return testResult; } | 19,456 |
0 | private void sendToFtp(String outputText) { String uid = this.properties.get(PROPERTY_OUTPUT_FTP_USERNAME); String pwd = this.properties.get(PROPERTY_OUTPUT_FTP_PASSWORD); String address = this.properties.get(PROPERTY_OUTPUT_FTP_ADDRESS); int port = 21; try { port = Integer.valueOf(this.properties.get(PROPERTY_OUTPUT_FTP_PORT)); } catch (Exception ex) { LOG.log(Level.WARNING, "Could not read FTP port from properties. Using port 21"); } String location = this.properties.get(PROPERTY_OUTPUT_FTP_LOCATION); String filename = this.properties.get(PROPERTY_OUTPUT_FTP_FILENAME); LOG.log(Level.INFO, "Uploading text output to {0}:{1}/{2}/{3}", new Object[] { address, port, location, filename }); FTPClient ftpClient = new FTPClient(); try { ftpClient.connect(address, port); int reply = ftpClient.getReplyCode(); if (!FTPReply.isPositiveCompletion(reply)) { ftpClient.disconnect(); LOG.log(Level.SEVERE, "Could not connect to FTP server: {0}", reply); return; } if (!ftpClient.login(uid, pwd)) { LOG.log(Level.SEVERE, "Could not login to FTP server ({0}) with given credentials.", address); return; } ftpClient.setFileType(FTP.BINARY_FILE_TYPE); ftpClient.enterLocalPassiveMode(); if (ftpClient.storeFile(location + "/" + filename, new ByteArrayInputStream(outputText.getBytes()))) { LOG.log(Level.INFO, "Transfer complete"); } else { LOG.log(Level.WARNING, "Transfer incomplete"); } } catch (SocketException ex) { LOG.log(Level.SEVERE, "Could not transfer file.", ex.getMessage()); LOG.log(Level.FINE, "", ex); } catch (IOException ex) { LOG.log(Level.SEVERE, "Could not transfer file.", ex.getMessage()); LOG.log(Level.FINE, "", ex); } if (ftpClient.isConnected()) { try { ftpClient.disconnect(); } catch (IOException ex) { LOG.log(Level.SEVERE, "Could not disconnect from FTP.", ex.getMessage()); LOG.log(Level.FINE, "", ex); } } } | public static String encryptPassword(String password) { String hash = null; try { MessageDigest md = null; md = MessageDigest.getInstance("SHA"); md.update(password.getBytes("UTF-8")); byte raw[] = md.digest(); hash = Base64.encode(raw, false); } catch (Exception e) { } return hash; } | 19,457 |
1 | private static void copy(File source, File dest) throws FileNotFoundException, IOException { FileInputStream input = new FileInputStream(source); FileOutputStream output = new FileOutputStream(dest); System.out.println("Copying " + source + " to " + dest); IOUtils.copy(input, output); output.close(); input.close(); dest.setLastModified(source.lastModified()); } | private static void copy(File in, File out) throws IOException { if (!out.getParentFile().isDirectory()) out.getParentFile().mkdirs(); FileChannel ic = new FileInputStream(in).getChannel(); FileChannel oc = new FileOutputStream(out).getChannel(); ic.transferTo(0, ic.size(), oc); ic.close(); oc.close(); } | 19,458 |
0 | private static int get(URL url, byte[] content) throws IOException { int len = -1; InputStream in = null; try { in = new BufferedInputStream(url.openStream()); String type = URLConnection.guessContentTypeFromStream(in); if (type == null || type.compareTo("text/html") != 0) { return -1; } len = read(in, content); } catch (IOException e) { throw e; } finally { close(in); } return len; } | public static void readAsFile(String fileName, String url) { BufferedInputStream in = null; BufferedOutputStream out = null; URLConnection conn = null; try { conn = new URL(url).openConnection(); conn.setDoInput(true); in = new BufferedInputStream(conn.getInputStream()); out = new BufferedOutputStream(new FileOutputStream(fileName)); int b; while ((b = in.read()) != -1) { out.write(b); } } catch (Exception ex) { log.error(ex.getMessage(), ex); } finally { if (null != in) { try { in.close(); } catch (IOException e) { } } if (null != out) { try { out.flush(); out.close(); } catch (IOException e) { } } } } | 19,459 |
0 | public static void copy(String a, String b) throws IOException { File inputFile = new File(a); File outputFile = new File(b); FileReader in = new FileReader(inputFile); FileWriter out = new FileWriter(outputFile); int c; while ((c = in.read()) != -1) out.write(c); in.close(); out.close(); } | private synchronized void executePrebuildCache() { isPrebuilding = true; String pathStr = ""; String[] paths = null; XMLCacheBuilder cacheBuilder = null; if (this.getConfigPath() != null) { cacheBuilder = CompositePageUtil.getCacheBuilder(); if (cacheBuilder == null) return; try { File file = new File(this.getConfigPath()); FileInputStream is = new FileInputStream(file); OutputStream os = new ByteArrayOutputStream(); int length = 0; if (is != null) { byte[] buf = new byte[8192]; while (((length = is.read(buf)) != -1)) { os.write(buf, 0, length); } is.close(); os.flush(); os.close(); is.close(); } String filesStr = os.toString(); if (filesStr == null) return; paths = filesStr.split("\n"); } catch (FileNotFoundException e) { logger.error(e); } catch (IOException e) { logger.error(e); } } else { XMLRoot root = ConfigureDigester.getXmlRoot(); cacheBuilder = root.getCacheBuilder(); if (cacheBuilder == null) return; pathStr = cacheBuilder.getPath(); if (pathStr == null) return; paths = pathStr.split("\n"); } logger.warn("[prebuildCache start:" + new java.util.Date() + "]"); for (int i = 0; i < paths.length; i++) { try { String path = paths[i]; logger.info("preBuildCache path:" + path); URL url = new URL(path); HttpURLConnection huc = (HttpURLConnection) url.openConnection(); huc.setDoInput(true); huc.setDoOutput(true); huc.setUseCaches(false); huc.setRequestProperty("Content-Type", "text/html"); DataOutputStream dos = new DataOutputStream(huc.getOutputStream()); dos.flush(); dos.close(); BufferedReader bufferedReader = new BufferedReader(new InputStreamReader(huc.getInputStream())); StringBuffer result = new StringBuffer(); String line; while (null != (line = bufferedReader.readLine())) result.append(line); bufferedReader.close(); huc.disconnect(); } catch (MalformedURLException e) { logger.warn("prebuildCache: MalformedURLException"); } catch (IOException e) { logger.warn("prebuildCache: IOException"); logger.warn("Is CACHE_SERVER dead? escape prebuild cache!"); logger.error("[****Prebuild cache interrupted! Please check the CACHE_SERVER's status.****]"); } catch (Exception e) { logger.warn("prebuildCache: Exception"); } } logger.warn("[prebuildCache end:" + new java.util.Date() + "]"); logger.info("[Time to migrate cache]"); if (CacheManager.getPreCacheMap() == null || CacheManager.getPreCacheMap().size() == 0) { logger.warn("[****Something wrong in prebuild cache process is CACHE_SERVER dead? escape sending cache to CLIENT****]"); return; } else { CacheManager.migrateCache(); } logger.info("[Cache migration finish!]"); if (cacheBuilder.getPoint() != null && cacheBuilder.getPoint().equals("SERVER")) { logger.info("Sending cache to CLIENT"); if (cuttleManagerList != null) { for (int i = 0; i < cuttleManagerList.size(); i++) { try { CuttleManager cuttleManager = (CuttleManager) cuttleManagerList.get(i); cuttleManager.migrateCache(CacheManager.getCacheTimeoutMap(), CacheManager.getCacheMap()); } catch (Exception e) { e.printStackTrace(); logger.error(e); logger.error("Sending cache to CLIENT:" + (i + 1) + " failed!"); } } } logger.info("Cache migrate to CLIENT finished!"); } try { logger.info("Time to sleep for sending cache to CLIENT: 1 minute"); Thread.sleep(60000); logger.info("Wake up for next prebuild cache!"); } catch (Exception e) { logger.warn("thread sleep interrupt!"); } isPrebuilding = false; } | 19,460 |
0 | public String SHA1(String text) { try { MessageDigest md = MessageDigest.getInstance("SHA-1"); byte[] sha1hash = new byte[40]; md.update(text.getBytes("iso-8859-1"), 0, text.length()); sha1hash = md.digest(); return convToHex(sha1hash); } catch (NoSuchAlgorithmException ex) { Logger.getLogger(CMessageDigestFile.class.getName()).log(Level.SEVERE, null, ex); } catch (UnsupportedEncodingException ex) { Logger.getLogger(CMessageDigestFile.class.getName()).log(Level.SEVERE, null, ex); } return ""; } | @Test public void testCopy_inputStreamToWriter_nullIn() throws Exception { ByteArrayOutputStream baout = new ByteArrayOutputStream(); OutputStream out = new YellOnFlushAndCloseOutputStreamTest(baout, true, true); Writer writer = new OutputStreamWriter(baout, "US-ASCII"); try { IOUtils.copy((InputStream) null, writer); fail(); } catch (NullPointerException ex) { } } | 19,461 |
1 | private Datastream addManagedDatastreamVersion(Entry entry) throws StreamIOException, ObjectIntegrityException { Datastream ds = new DatastreamManagedContent(); setDSCommonProperties(ds, entry); ds.DSLocationType = "INTERNAL_ID"; ds.DSMIME = getDSMimeType(entry); IRI contentLocation = entry.getContentSrc(); if (contentLocation != null) { if (m_obj.isNew()) { ValidationUtility.validateURL(contentLocation.toString(), ds.DSControlGrp); } if (m_format.equals(ATOM_ZIP1_1)) { if (!contentLocation.isAbsolute() && !contentLocation.isPathAbsolute()) { File f = getContentSrcAsFile(contentLocation); contentLocation = new IRI(DatastreamManagedContent.TEMP_SCHEME + f.getAbsolutePath()); } } ds.DSLocation = contentLocation.toString(); ds.DSLocation = (DOTranslationUtility.normalizeDSLocationURLs(m_obj.getPid(), ds, m_transContext)).DSLocation; return ds; } try { File temp = File.createTempFile("binary-datastream", null); OutputStream out = new FileOutputStream(temp); if (MimeTypeHelper.isText(ds.DSMIME) || MimeTypeHelper.isXml(ds.DSMIME)) { IOUtils.copy(new StringReader(entry.getContent()), out, m_encoding); } else { IOUtils.copy(entry.getContentStream(), out); } ds.DSLocation = DatastreamManagedContent.TEMP_SCHEME + temp.getAbsolutePath(); } catch (IOException e) { throw new StreamIOException(e.getMessage(), e); } return ds; } | public StringBuffer render(RenderEngine c) { String logTime = null; if (c.getWorkerContext() != null) { logTime = c.getWorkerContext().getWorkerStart(); } if (c.isBreakState() || !c.canRender("u")) { return new StringBuffer(); } StringBuffer buffer = new StringBuffer(); varname = TagInspector.processElement(varname, c); action = TagInspector.processElement(action, c); filemode = TagInspector.processElement(filemode, c); xmlparse = TagInspector.processElement(xmlparse, c); encoding = TagInspector.processElement(encoding, c); decoding = TagInspector.processElement(decoding, c); filter = TagInspector.processElement(filter, c); sort = TagInspector.processElement(sort, c); useDocroot = TagInspector.processElement(useDocroot, c); useFilename = TagInspector.processElement(useFilename, c); useDest = TagInspector.processElement(useDest, c); xmlOutput = TagInspector.processElement(xmlOutput, c); renderOutput = TagInspector.processElement(renderOutput, c); callProc = TagInspector.processElement(callProc, c); vartype = TagInspector.processElement(vartype, c); if (sort == null || sort.equals("")) { sort = "asc"; } if (useFilename.equals("") && !action.equalsIgnoreCase("listing")) { return new StringBuffer(); } boolean isRooted = true; if (useDocroot.equalsIgnoreCase("true")) { if (c.getVendContext().getVend().getIgnorableDocroot(c.getClientContext().getMatchedHost())) { isRooted = false; } } if (isRooted && (useFilename.indexOf("/") == -1 || useFilename.startsWith("./"))) { if (c.getWorkerContext() != null && useFilename.startsWith("./")) { useFilename = c.getWorkerContext().getClientContext().getPostVariable("current_path") + useFilename.substring(2); Debug.inform("CWD path specified in filename, rewritten to '" + useFilename + "'"); } else if (c.getWorkerContext() != null && useFilename.indexOf("/") == -1) { useFilename = c.getWorkerContext().getClientContext().getPostVariable("current_path") + useFilename; Debug.inform("No path specified in filename, rewritten to '" + useFilename + "'"); } else { Debug.inform("No path specified in filename, no worker context, not rewriting filename."); } } StringBuffer filenameData = null; StringBuffer contentsData = null; StringBuffer fileDestData = null; contentsData = TagInspector.processBody(this, c); filenameData = new StringBuffer(useFilename); fileDestData = new StringBuffer(useDest); String currentDocroot = null; if (c.getWorkerContext() == null) { if (c.getRenderContext().getCurrentDocroot() == null) { currentDocroot = "."; } else { currentDocroot = c.getRenderContext().getCurrentDocroot(); } } else { currentDocroot = c.getWorkerContext().getDocRoot(); } if (!isRooted) { currentDocroot = ""; } if (useDocroot.equalsIgnoreCase("true")) { if (c.getVendContext().getVend().getIgnorableDocroot(c.getClientContext().getMatchedHost())) { isRooted = false; currentDocroot = ""; } } if (!currentDocroot.endsWith("/")) { if (!currentDocroot.equals("") && currentDocroot.length() > 0) { currentDocroot += "/"; } } if (filenameData != null) { filenameData = new StringBuffer(filenameData.toString().replaceAll("\\.\\.", "")); } if (fileDestData != null) { fileDestData = new StringBuffer(fileDestData.toString().replaceAll("\\.\\.", "")); } if (action.equalsIgnoreCase("read")) { java.io.File file = new java.io.File(currentDocroot + filenameData.toString()); FileInputStream is = null; ByteArrayOutputStream bos = new ByteArrayOutputStream(); byte data[] = null; boolean vfsLoaded = false; try { data = c.getVendContext().getFileAccess().getFile(c.getWorkerContext(), filenameData.toString().replaceAll("\\.\\.", ""), c.getClientContext().getMatchedHost(), c.getVendContext().getVend().getRenderExtension(c.getClientContext().getMatchedHost()), null); bos.write(data, 0, data.length); vfsLoaded = true; } catch (Exception e) { Debug.user(logTime, "Included file attempt with VFS of file '" + filenameData + "' failed: " + e); } if (data == null) { try { is = new FileInputStream(file); } catch (Exception e) { Debug.user(logTime, "Unable to render: Filename '" + currentDocroot + filenameData + "' does not exist."); return new StringBuffer(); } } if (xmlparse == null || xmlparse.equals("")) { if (data == null) { Debug.user(logTime, "Opening filename '" + currentDocroot + filenameData + "' for reading into buffer '" + varname + "'"); data = new byte[32768]; int totalBytesRead = 0; while (true) { int bytesRead; try { bytesRead = is.read(data); bos.write(data, 0, bytesRead); } catch (Exception e) { break; } if (bytesRead <= 0) { break; } totalBytesRead += bytesRead; } } byte docOutput[] = bos.toByteArray(); if (renderOutput != null && renderOutput.equalsIgnoreCase("ssp")) { String outputData = "<?xml version=\"1.0\" encoding=\"utf-8\"?>\n\n" + new String(FileAccess.getDefault().processServerPageData(c.getWorkerContext(), docOutput)); docOutput = outputData.getBytes(); } Debug.user(logTime, "File read complete: " + docOutput.length + " byte(s)"); if (is != null) { try { is.close(); } catch (Exception e) { } } is = null; if (encoding != null && encoding.equalsIgnoreCase("url")) { if (!varname.equals("")) { if (c.isProtectedVariable(varname)) { c.setExceptionState(true, "Attempted to modify a read-only variable '" + varname + "'"); return new StringBuffer(); } c.getVariableContainer().setVariable(varname, Encoder.URLEncode(new String(docOutput))); } else { if (callProc != null && !callProc.equals("")) { Call call = new Call(); call.callProcedure(c, null, null, callProc, null); } return new StringBuffer(Encoder.URLEncode(new String(docOutput))); } } else if (encoding != null && encoding.equalsIgnoreCase("xml")) { if (!varname.equals("")) { if (c.isProtectedVariable(varname)) { c.setExceptionState(true, "Attempted to modify a read-only variable '" + varname + "'"); return new StringBuffer(); } c.getVariableContainer().setVariable(varname, Encoder.XMLEncode(new String(docOutput))); } else { if (callProc != null && !callProc.equals("")) { Call call = new Call(); call.callProcedure(c, null, null, callProc, null); } return new StringBuffer(Encoder.XMLEncode(new String(docOutput))); } } else if (encoding != null && encoding.equalsIgnoreCase("base64")) { if (!varname.equals("")) { if (c.isProtectedVariable(varname)) { c.setExceptionState(true, "Attempted to modify a read-only variable '" + varname + "'"); return new StringBuffer(); } c.getVariableContainer().setVariable(varname, Base64.encode(docOutput)); } else { if (callProc != null && !callProc.equals("")) { Call call = new Call(); call.callProcedure(c, null, null, callProc, null); } return new StringBuffer(Base64.encode(docOutput)); } } else if (encoding != null && (encoding.equalsIgnoreCase("javascript") || encoding.equalsIgnoreCase("js"))) { if (!varname.equals("")) { if (c.isProtectedVariable(varname)) { c.setExceptionState(true, "Attempted to modify a read-only variable '" + varname + "'"); return new StringBuffer(); } c.getVariableContainer().setVariable(varname, Encoder.JavascriptEncode(new String(docOutput))); } else { if (callProc != null && !callProc.equals("")) { Call call = new Call(); call.callProcedure(c, null, null, callProc, null); } return new StringBuffer(Encoder.JavascriptEncode(new String(docOutput))); } } else { if (!varname.equals("")) { if (c.isProtectedVariable(varname)) { c.setExceptionState(true, "Attempted to modify a read-only variable '" + varname + "'"); return new StringBuffer(); } c.getVariableContainer().setVariable(varname, new String(docOutput)); } else { if (callProc != null && !callProc.equals("")) { Call call = new Call(); call.callProcedure(c, null, null, callProc, null); } return new StringBuffer(new String(docOutput)); } } } else { RenderEngine engine = new RenderEngine(null); DocumentEngine docEngine = null; try { if (vfsLoaded) { ByteArrayInputStream bais = new ByteArrayInputStream(data); docEngine = new DocumentEngine(bais); } else { docEngine = new DocumentEngine(is); } } catch (Exception e) { c.setExceptionState(true, "XML parse of data read from file failed: " + e.getMessage()); } engine.setDocumentEngine(docEngine); c.addNodeSet(varname, docEngine.rootTag.thisNode); } if (is != null) { try { is.close(); } catch (Exception e) { } } is = null; if (callProc != null && !callProc.equals("")) { Call call = new Call(); call.callProcedure(c, null, null, callProc, null); } return new StringBuffer(); } else if (action.equalsIgnoreCase("write")) { try { String rootDir = filenameData.toString(); if (rootDir.lastIndexOf("/") != -1 && rootDir.lastIndexOf("/") != 0) { rootDir = rootDir.substring(0, rootDir.lastIndexOf("/")); java.io.File mkdirFile = new java.io.File(currentDocroot + rootDir); if (!mkdirFile.mkdirs()) { Debug.inform("Unable to create directory '" + currentDocroot + rootDir + "'"); } else { Debug.inform("Created directory '" + currentDocroot + rootDir + "'"); } } java.io.File file = new java.io.File(currentDocroot + filenameData.toString()); FileOutputStream fos = null; if (file == null) { c.setExceptionState(true, "Unable to write to file '" + filenameData + "': Cannot write to location specified"); return new StringBuffer(); } else if (file.isDirectory()) { c.setExceptionState(true, "Unable to write to file '" + filenameData + "': Is a directory."); return new StringBuffer(); } if (filemode.equalsIgnoreCase("append")) { fos = new FileOutputStream(file, true); } else { fos = new FileOutputStream(file, false); } if (decoding != null && !decoding.equals("")) { if (decoding.equalsIgnoreCase("base64")) { try { byte contentsDecoded[] = Base64.decode(contentsData.toString().getBytes()); fos.write(contentsDecoded); } catch (Exception e) { c.setExceptionState(true, "Encoded data in <content> element does not contain valid Base64-" + "encoded data."); } } else { fos.write(contentsData.toString().getBytes()); } } else { fos.write(contentsData.toString().getBytes()); } try { fos.flush(); } catch (IOException e) { Debug.inform("Unable to flush output data: " + e.getMessage()); } fos.close(); Debug.user(logTime, "Wrote contents to filename '" + currentDocroot + filenameData + "' (length=" + contentsData.length() + ")"); } catch (IOException e) { c.setExceptionState(true, "Unable to write to filename '" + filenameData + "': " + e.getMessage()); } catch (Exception e) { c.setExceptionState(true, "Unable to write to filename '" + filenameData + "': " + e.getMessage()); } } else if (action.equalsIgnoreCase("listing")) { String filenameDataString = filenameData.toString(); if (filenameDataString.equals("")) { filenameDataString = c.getClientContext().getPostVariable("current_path"); } if (filenameDataString == null) { c.setExceptionState(true, "Filename cannot be blank when listing."); return new StringBuffer(); } while (filenameDataString.endsWith("/")) { filenameDataString = filenameDataString.substring(0, filenameDataString.length() - 1); } Vector fileList = new Vector(); java.io.File file = new java.io.File(currentDocroot + filenameData.toString()); String curDirname = filenameData.toString(); String parentDirectory = null; String[] dirEntries = curDirname.split("/"); int numSlashes = 0; for (int i = 0; i < curDirname.length(); i++) { if (curDirname.toString().charAt(i) == '/') { numSlashes++; } } parentDirectory = "/"; if (numSlashes > 1) { for (int i = 0; i < (dirEntries.length - 1); i++) { if (dirEntries[i] != null && !dirEntries[i].equals("")) { parentDirectory += dirEntries[i] + "/"; } } } if (parentDirectory.length() > 1 && parentDirectory.endsWith("/")) { parentDirectory = parentDirectory.substring(0, parentDirectory.length() - 1); } if (c.getVendContext() != null && c.getVendContext().getFileAccess() != null && c.getVendContext().getFileAccess().getVFSType(filenameData.toString(), c.getClientContext().getMatchedHost()) == FileAccess.TYPE_JAR) { Vector listFiles = c.getVendContext().getFileAccess().listFiles(filenameData.toString(), c.getClientContext().getMatchedHost()); Object[] list = listFiles.toArray(); int depth = 0; for (int i = 0; i < filenameData.toString().length(); i++) { if (filenameData.toString().charAt(i) == '/') { depth++; } } buffer = new StringBuffer(); buffer.append("<listing filter=\""); buffer.append(filter); buffer.append("\" path=\""); buffer.append(filenameData); if (parentDirectory != null) { buffer.append("\" parent=\""); buffer.append(parentDirectory); } buffer.append("\">\n"); c.getVariableContainer().setVariable(c, varname + "(fileinfo)(filter)", false, filter); c.getVariableContainer().setVariable(c, varname + "(fileinfo)(path)", false, filenameData); if (parentDirectory != null) { c.getVariableContainer().setVariable(c, varname + "(fileinfo)(parent)", false, parentDirectory); } else { c.getVariableContainer().setVariable(c, varname + "(fileinfo)(parent)", false, "/"); } if (sort.equalsIgnoreCase("asc")) { Arrays.sort(list, new ZipSorterAscending()); } else { Arrays.sort(list, new ZipSorterDescending()); } for (int i = 0; i < list.length; i++) { ZipEntry zEntry = (ZipEntry) list[i]; String zipFile = filenameData.toString() + "/" + zEntry.getName(); String displayFilename = zipFile.replaceFirst(filenameData.toString(), ""); int curDepth = 0; if (zipFile.equalsIgnoreCase(".acl") || zipFile.equalsIgnoreCase("access.list") || zipFile.equalsIgnoreCase("application.inc") || zipFile.equalsIgnoreCase("global.inc") || zipFile.indexOf("/.proc") != -1 || zipFile.indexOf("/procedures") != -1) { continue; } for (int x = 0; x < displayFilename.length(); x++) { if (displayFilename.charAt(x) == '/') { curDepth++; } } if (zipFile.startsWith(filenameData.toString())) { String fileLength = "" + zEntry.getSize(); String fileType = "file"; if (curDepth == depth) { if (zEntry.isDirectory()) { fileType = "directory"; } else { fileType = "file"; } String fileMode = "read-only"; String fileTime = Long.toString(zEntry.getTime()); buffer.append(" <file name=\""); buffer.append(displayFilename); buffer.append("\" length=\""); buffer.append(fileLength); buffer.append("\" type=\""); buffer.append(fileType); buffer.append("\" mode=\""); buffer.append(fileMode); buffer.append("\" modtime=\""); buffer.append(fileTime); buffer.append("\"/>\n"); c.getVariableContainer().setVariable(c, varname + "(" + displayFilename + ")(length)", false, "" + fileLength); c.getVariableContainer().setVariable(c, varname + "(" + displayFilename + ")(type)", false, fileType); c.getVariableContainer().setVariable(c, varname + "(" + displayFilename + ")(mode)", false, fileMode); c.getVariableContainer().setVariable(c, varname + "(" + displayFilename + ")(time)", false, fileTime); } } else { if (curDepth == depth) { fileList.add(zipFile); } } } buffer.append("</listing>"); if (xmlOutput.equalsIgnoreCase("true")) { if (c.isProtectedVariable(varname)) { c.setExceptionState(true, "Attempted to modify a read-only variable '" + varname + "'"); return new StringBuffer(); } c.getVariableContainer().setVariable(varname, buffer.toString()); return new StringBuffer(); } c.getVariableContainer().setVector(varname, fileList); } else if (c.getVendContext() != null && c.getVendContext().getFileAccess() != null && c.getVendContext().getFileAccess().getVFSType(filenameData.toString(), c.getClientContext().getMatchedHost()) == FileAccess.TYPE_FS) { Vector listFiles = c.getVendContext().getFileAccess().listFiles(filenameData.toString(), c.getClientContext().getMatchedHost()); Object[] list = listFiles.toArray(); java.io.File[] filesorted = new java.io.File[list.length]; for (int i = 0; i < list.length; i++) { filesorted[i] = (java.io.File) list[i]; } if (sort.equalsIgnoreCase("asc")) { Arrays.sort(filesorted, new FileSorterAscending()); } else { Arrays.sort(filesorted, new FileSorterDescending()); } buffer = new StringBuffer(); buffer.append("<listing filter=\""); buffer.append(filter); buffer.append("\" path=\""); buffer.append(filenameData); if (parentDirectory != null) { buffer.append("\" parent=\""); buffer.append(parentDirectory); } buffer.append("\">\n"); c.getVariableContainer().setVariable(c, varname + "(fileinfo)(filter)", false, filter); c.getVariableContainer().setVariable(c, varname + "(fileinfo)(path)", false, filenameData); if (parentDirectory != null) { c.getVariableContainer().setVariable(c, varname + "(fileinfo)(parent)", false, parentDirectory); } else { c.getVariableContainer().setVariable(c, varname + "(fileinfo)(parent)", false, "/"); } for (int i = 0; i < filesorted.length; i++) { java.io.File zEntry = filesorted[i]; String filename = filenameData.toString() + "/" + zEntry.getName(); if (filename.equalsIgnoreCase(".acl") || filename.equalsIgnoreCase("access.list") || filename.equalsIgnoreCase("application.inc") || filename.equalsIgnoreCase("global.inc") || filename.indexOf("/.proc") != -1 || filename.indexOf("/procedures") != -1) { continue; } String displayFilename = filename.replaceFirst(filenameData.toString(), ""); String fileLength = "" + zEntry.length(); String fileType = "file"; if (zEntry.isDirectory()) { fileType = "directory"; } else if (zEntry.isFile()) { fileType = "file"; } else if (zEntry.isHidden()) { fileType = "hidden"; } else if (zEntry.isAbsolute()) { fileType = "absolute"; } String fileMode = "read-only"; if (zEntry.canRead() && !zEntry.canWrite()) { fileMode = "read-only"; } else if (!zEntry.canRead() && zEntry.canWrite()) { fileMode = "write-only"; } else if (zEntry.canRead() && zEntry.canWrite()) { fileMode = "read/write"; } String fileTime = Long.toString(zEntry.lastModified()); if (xmlOutput.equalsIgnoreCase("true")) { buffer.append(" <file name=\""); buffer.append(filename); buffer.append("\" length=\""); buffer.append(fileLength); buffer.append("\" type=\""); buffer.append(fileType); buffer.append("\" mode=\""); buffer.append(fileMode); buffer.append("\" modtime=\""); buffer.append(fileTime); buffer.append("\"/>\n"); } else { fileList.add(zEntry); } c.getVariableContainer().setVariable(c, varname + "(" + filename + ")(length)", false, "" + fileLength); c.getVariableContainer().setVariable(c, varname + "(" + filename + ")(type)", false, fileType); c.getVariableContainer().setVariable(c, varname + "(" + filename + ")(mode)", false, fileMode); c.getVariableContainer().setVariable(c, varname + "(" + filename + ")(time)", false, fileTime); } buffer.append("</listing>"); if (xmlOutput.equalsIgnoreCase("true")) { if (c.isProtectedVariable(varname)) { c.setExceptionState(true, "Attempted to modify a read-only variable '" + varname + "'"); return new StringBuffer(); } c.getVariableContainer().setVariable(varname, buffer.toString()); return new StringBuffer(); } c.getVariableContainer().setVector(varname, fileList); } else { String[] fileStringList = null; if (!filter.equals("")) { fileStringList = file.list(new ListFilter(filter)); } else { fileStringList = file.list(); } if (sort.equalsIgnoreCase("asc")) { Arrays.sort(fileStringList, new StringSorterAscending()); } else { Arrays.sort(fileStringList, new StringSorterDescending()); } if (fileStringList == null) { buffer.append("<listing filter=\""); buffer.append(filter); buffer.append("\" path=\""); buffer.append(filenameData); if (parentDirectory != null) { buffer.append("\" parent=\""); buffer.append(parentDirectory); } buffer.append("\"/>\n"); c.getVariableContainer().setVariable(c, varname + "(fileinfo)(filter)", false, filter); c.getVariableContainer().setVariable(c, varname + "(fileinfo)(path)", false, filenameData); if (parentDirectory != null) { c.getVariableContainer().setVariable(c, varname + "(fileinfo)(parent)", false, parentDirectory); } else { c.getVariableContainer().setVariable(c, varname + "(fileinfo)(parent)", false, "/"); } if (xmlOutput.equalsIgnoreCase("true")) { if (c.isProtectedVariable(varname)) { c.setExceptionState(true, "Attempted to modify a read-only variable '" + varname + "'"); return new StringBuffer(); } c.getVariableContainer().setVariable(varname, buffer.toString()); } else { c.getVariableContainer().setVector(varname, fileList); } return new StringBuffer(); } else { Debug.user(logTime, "Directory '" + currentDocroot + filenameData + "' returns " + fileStringList.length + " entry(ies)"); } buffer = new StringBuffer(); buffer.append("<listing filter=\""); buffer.append(filter); buffer.append("\" path=\""); buffer.append(filenameData); if (parentDirectory != null) { buffer.append("\" parent=\""); buffer.append(parentDirectory); } buffer.append("\">\n"); c.getVariableContainer().setVariable(c, varname + "(fileinfo)(filter)", false, filter); c.getVariableContainer().setVariable(c, varname + "(fileinfo)(path)", false, filenameData); if (parentDirectory != null) { c.getVariableContainer().setVariable(c, varname + "(fileinfo)(parent)", false, parentDirectory); } else { c.getVariableContainer().setVariable(c, varname + "(fileinfo)(parent)", false, "/"); } for (int i = 0; i < fileStringList.length; i++) { file = new java.io.File(currentDocroot + filenameData.toString() + "/" + fileStringList[i]); String fileLength = Long.toString(file.length()); String fileType = "file"; if (file.isDirectory()) { fileType = "directory"; } else if (file.isFile()) { fileType = "file"; } else if (file.isHidden()) { fileType = "hidden"; } else if (file.isAbsolute()) { fileType = "absolute"; } String fileMode = "read-only"; if (file.canRead() && !file.canWrite()) { fileMode = "read-only"; } else if (!file.canRead() && file.canWrite()) { fileMode = "write-only"; } else if (file.canRead() && file.canWrite()) { fileMode = "read/write"; } String fileTime = Long.toString(file.lastModified()); if (xmlOutput.equalsIgnoreCase("true")) { buffer.append(" <file name=\""); buffer.append(fileStringList[i]); buffer.append("\" length=\""); buffer.append(fileLength); buffer.append("\" type=\""); buffer.append(fileType); buffer.append("\" mode=\""); buffer.append(fileMode); buffer.append("\" modtime=\""); buffer.append(fileTime); buffer.append("\"/>\n"); } else { fileList.add(fileStringList[i]); } c.getVariableContainer().setVariable(c, varname + "(" + fileStringList[i] + ")(length)", false, "" + fileLength); c.getVariableContainer().setVariable(c, varname + "(" + fileStringList[i] + ")(type)", false, fileType); c.getVariableContainer().setVariable(c, varname + "(" + fileStringList[i] + ")(mode)", false, fileMode); c.getVariableContainer().setVariable(c, varname + "(" + fileStringList[i] + ")(time)", false, fileTime); } buffer.append("</listing>"); if (xmlOutput.equalsIgnoreCase("true")) { if (c.isProtectedVariable(varname)) { c.setExceptionState(true, "Attempted to modify a read-only variable '" + varname + "'"); return new StringBuffer(); } c.getVariableContainer().setVariable(varname, buffer.toString()); return new StringBuffer(); } c.getVariableContainer().setVector(varname, fileList); } } else if (action.equalsIgnoreCase("delete")) { java.io.File file = new java.io.File(currentDocroot + filenameData.toString()); if (file.isDirectory()) { boolean success = deleteDir(new java.io.File(currentDocroot + filenameData.toString())); if (!success) { c.setExceptionState(true, "Unable to delete '" + currentDocroot + filenameData + "'"); } } else { String filenamePattern = null; if (filenameData.toString().indexOf("/") != -1) { filenamePattern = filenameData.toString().substring(filenameData.toString().lastIndexOf("/") + 1); } String filenameDirectory = currentDocroot; if (filenameData.toString().indexOf("/") != -1) { filenameDirectory += filenameData.substring(0, filenameData.toString().lastIndexOf("/")); } String[] fileStringList = null; file = new java.io.File(filenameDirectory); fileStringList = file.list(new ListFilter(filenamePattern)); for (int i = 0; i < fileStringList.length; i++) { (new java.io.File(filenameDirectory + "/" + fileStringList[i])).delete(); } } } else if (action.equalsIgnoreCase("rename") || action.equalsIgnoreCase("move")) { if (fileDestData.equals("")) { c.getVariableContainer().setVariable(varname + "-result", filenameData + ": File operation failed: No destination filename given."); return new StringBuffer(); } java.io.File file = new java.io.File(currentDocroot + filenameData.toString()); boolean success = file.renameTo(new java.io.File(currentDocroot + fileDestData.toString(), file.getName())); if (!success) { c.setExceptionState(true, "Unable to rename '" + currentDocroot + filenameData + "' to '" + currentDocroot + fileDestData + "'"); } } else if (action.equalsIgnoreCase("copy")) { if (fileDestData.equals("")) { c.setExceptionState(true, "File copy operation failed for file '" + filenameData + "': No destination file specified."); return new StringBuffer(); } FileChannel srcChannel; FileChannel destChannel; String filename = null; filename = currentDocroot + filenameData.toString(); if (vartype != null && vartype.equalsIgnoreCase("file")) { if (useFilename.indexOf("/") != -1) { useFilename = useFilename.substring(useFilename.lastIndexOf("/") + 1); } filename = c.getVariableContainer().getFileVariable(useFilename); } try { Debug.debug("Copying from file '" + filename + "' to '" + fileDestData.toString() + "'"); srcChannel = new FileInputStream(filename).getChannel(); } catch (IOException e) { c.setExceptionState(true, "Filecopy from '" + filenameData + "' failed to read: " + e.getMessage()); return new StringBuffer(); } try { destChannel = new FileOutputStream(currentDocroot + fileDestData.toString()).getChannel(); } catch (IOException e) { c.setExceptionState(true, "Filecopy to '" + fileDestData + "' failed to write: " + e.getMessage()); return new StringBuffer(); } try { destChannel.transferFrom(srcChannel, 0, srcChannel.size()); srcChannel.close(); destChannel.close(); if (varname != null) { c.getVariableContainer().setVariable(varname + "-result", filenameData + " copy to " + fileDestData + ": File copy succeeded."); } else { return new StringBuffer("true"); } } catch (IOException e) { c.setExceptionState(true, "Filecopy from '" + filenameData + "' to '" + fileDestData + "' failed: " + e.getMessage()); } } else if (action.equalsIgnoreCase("exists")) { java.io.File file = new java.io.File(currentDocroot + filenameData.toString()); if (file.exists()) { if (varname != null) { if (c.isProtectedVariable(varname)) { c.setExceptionState(true, "Attempted to modify a read-only variable '" + varname + "'"); return new StringBuffer(); } c.getVariableContainer().setVariable(varname, "true"); } else { return new StringBuffer("true"); } } else { if (varname != null) { if (c.isProtectedVariable(varname)) { c.setExceptionState(true, "Attempted to modify a read-only variable '" + varname + "'"); return new StringBuffer(); } c.getVariableContainer().setVariable(varname, "false"); } else { return new StringBuffer("false"); } } } else if (action.equalsIgnoreCase("mkdir")) { java.io.File file = new java.io.File(currentDocroot + filenameData.toString()); if (file.mkdirs()) { if (varname != null) { c.getVariableContainer().setVariable(varname + "-result", "created"); } else { return new StringBuffer("true"); } } else { c.setExceptionState(true, "Unable to create directory '" + filenameData + "'"); } } else if (action.equalsIgnoreCase("info")) { java.io.File file = new java.io.File(currentDocroot + filenameData.toString()); String fileLength = Long.toString(file.length()); String fileType = "file"; if (file.isAbsolute()) { fileType = "absolute"; } else if (file.isDirectory()) { fileType = "directory"; } else if (file.isFile()) { fileType = "file"; } else if (file.isHidden()) { fileType = "hidden"; } String fileMode = "read-only"; if (file.canRead() && !file.canWrite()) { fileMode = "read-only"; } else if (!file.canRead() && file.canWrite()) { fileMode = "write-only"; } else if (file.canRead() && file.canWrite()) { fileMode = "read/write"; } String fileTime = Long.toString(file.lastModified()); if (varname != null && !varname.equals("")) { c.getVariableContainer().setVariable(varname + ".length", fileLength); c.getVariableContainer().setVariable(varname + ".type", fileType); c.getVariableContainer().setVariable(varname + ".mode", fileMode); c.getVariableContainer().setVariable(varname + ".modtime", fileTime); } else { buffer = new StringBuffer(); buffer.append("<file name=\""); buffer.append(filenameData); buffer.append("\" length=\""); buffer.append(fileLength); buffer.append("\" type=\""); buffer.append(fileType); buffer.append("\" mode=\""); buffer.append(fileMode); buffer.append("\" modtime=\""); buffer.append(fileTime); buffer.append("\"/>\n"); return buffer; } } if (callProc != null && !callProc.equals("")) { Call call = new Call(); call.callProcedure(c, null, null, callProc, null); } return new StringBuffer(); } | 19,462 |
0 | public void sendMessage(Message m) throws IOException { URL url = new URL(strURL); urlcon = (HttpURLConnection) url.openConnection(); urlcon.setUseCaches(false); urlcon.setDefaultUseCaches(false); urlcon.setDoOutput(true); urlcon.setDoInput(true); urlcon.setRequestProperty("Content-type", "application/octet-stream"); urlcon.setAllowUserInteraction(false); HttpURLConnection.setDefaultAllowUserInteraction(false); urlcon.setRequestMethod("POST"); ObjectOutputStream oos = new ObjectOutputStream(urlcon.getOutputStream()); oos.writeObject(m); oos.flush(); oos.close(); } | public osid.shared.Id ingest(String fileName, String templateFileName, String fileType, File file, Properties properties) throws osid.dr.DigitalRepositoryException, java.net.SocketException, java.io.IOException, osid.shared.SharedException, javax.xml.rpc.ServiceException { long sTime = System.currentTimeMillis(); if (DEBUG) System.out.println("INGESTING FILE TO FEDORA:fileName =" + fileName + "fileType =" + fileType + "t = 0"); String host = FedoraUtils.getFedoraProperty(this, "admin.ftp.address"); String url = FedoraUtils.getFedoraProperty(this, "admin.ftp.url"); int port = Integer.parseInt(FedoraUtils.getFedoraProperty(this, "admin.ftp.port")); String userName = FedoraUtils.getFedoraProperty(this, "admin.ftp.username"); String password = FedoraUtils.getFedoraProperty(this, "admin.ftp.password"); String directory = FedoraUtils.getFedoraProperty(this, "admin.ftp.directory"); FTPClient client = new FTPClient(); client.connect(host, port); client.login(userName, password); client.changeWorkingDirectory(directory); client.setFileType(FTP.BINARY_FILE_TYPE); client.storeFile(fileName, new FileInputStream(file.getAbsolutePath().replaceAll("%20", " "))); client.logout(); client.disconnect(); if (DEBUG) System.out.println("INGESTING FILE TO FEDORA: Writting to FTP Server:" + (System.currentTimeMillis() - sTime)); fileName = url + fileName; int BUFFER_SIZE = 10240; StringBuffer sb = new StringBuffer(); String s = new String(); BufferedInputStream fis = new BufferedInputStream(new FileInputStream(new File(getResource(templateFileName).getFile().replaceAll("%20", " ")))); byte[] buf = new byte[BUFFER_SIZE]; int ch; int len; while ((len = fis.read(buf)) > 0) { s = s + new String(buf); } fis.close(); if (DEBUG) System.out.println("INGESTING FILE TO FEDORA: Read Mets File:" + (System.currentTimeMillis() - sTime)); String r = updateMetadata(s, fileName, file.getName(), fileType, properties); if (DEBUG) System.out.println("INGESTING FILE TO FEDORA: Resplaced Metadata:" + (System.currentTimeMillis() - sTime)); File METSfile = File.createTempFile("vueMETSMap", ".xml"); FileOutputStream fos = new FileOutputStream(METSfile); fos.write(r.getBytes()); fos.close(); if (DEBUG) System.out.println("INGESTING FILE TO FEDORA: Ingest complete:" + (System.currentTimeMillis() - sTime)); String pid = "Method Not Supported any more"; System.out.println(" METSfile= " + METSfile.getPath() + " PID = " + pid); return new PID(pid); } | 19,463 |
0 | public JSONObject getSourceGraph(HttpSession session, JSONObject json) throws JSONException { StringBuffer out = new StringBuffer(); Graph src = null; MappingManager manager = (MappingManager) session.getAttribute(RuncibleConstants.MAPPING_MANAGER.key()); try { src = manager.getSourceGraph(); if (src != null) { FlexGraphViewFactory factory = new FlexGraphViewFactory(); factory.setColorScheme(ColorSchemes.BLUES); factory.visit(src); GraphView view = factory.getGraphView(); GraphViewRenderer renderer = new FlexGraphViewRenderer(); renderer.setGraphView(view); InputStream xmlStream = renderer.renderGraphView(); StringWriter writer = new StringWriter(); IOUtils.copy(xmlStream, writer); writer.close(); System.out.println(writer.toString()); out.append(writer.toString()); } else { out.append("No source graph loaded."); } } catch (Exception e) { e.printStackTrace(); return JSONUtils.SimpleJSONError("Cannot load source graph: " + e.getMessage()); } return JSONUtils.SimpleJSONResponse(out.toString()); } | public static String getPasswordHash(String password) { try { MessageDigest md = MessageDigest.getInstance("SHA-256"); md.update(password.getBytes()); byte[] byteData = md.digest(); StringBuilder sb = new StringBuilder(); for (int i = 0; i < byteData.length; i++) { sb.append(Integer.toString((byteData[i] & 0xff) + 0x100, 16).substring(1)); } return sb.toString(); } catch (NoSuchAlgorithmException e) { logger.log(Level.SEVERE, "Unknow error in hashing password", e); return "Unknow error, check system log"; } } | 19,464 |
1 | public static void compressFile(File orig) throws IOException { File file = new File(INPUT + orig.toString()); File target = new File(OUTPUT + orig.toString().replaceAll(".xml", ".xml.gz")); System.out.println(" Compressing \"" + file.getName() + "\" into \"" + target + "\""); long l = file.length(); FileInputStream fileinputstream = new FileInputStream(file); GZIPOutputStream gzipoutputstream = new GZIPOutputStream(new FileOutputStream(target)); byte abyte0[] = new byte[1024]; int i; while ((i = fileinputstream.read(abyte0)) != -1) gzipoutputstream.write(abyte0, 0, i); fileinputstream.close(); gzipoutputstream.close(); long l1 = target.length(); System.out.println(" Initial size: " + l + "; Compressed size: " + l1 + "."); System.out.println(" Done."); System.out.println(); } | @Override protected int run(CmdLineParser parser) { final List<String> args = parser.getRemainingArgs(); if (args.isEmpty()) { System.err.println("sort :: WORKDIR not given."); return 3; } if (args.size() == 1) { System.err.println("sort :: INPATH not given."); return 3; } final String wrkDir = args.get(0), out = (String) parser.getOptionValue(outputFileOpt); final List<String> strInputs = args.subList(1, args.size()); final List<Path> inputs = new ArrayList<Path>(strInputs.size()); for (final String in : strInputs) inputs.add(new Path(in)); final boolean verbose = parser.getBoolean(verboseOpt); final String intermediateOutName = out == null ? inputs.get(0).getName() : out; final Configuration conf = getConf(); conf.setStrings(INPUT_PATHS_PROP, strInputs.toArray(new String[0])); conf.set(SortOutputFormat.OUTPUT_NAME_PROP, intermediateOutName); final Path wrkDirPath = new Path(wrkDir); final Timer t = new Timer(); try { for (final Path in : inputs) Utils.configureSampling(in, conf); @SuppressWarnings("deprecation") final int maxReduceTasks = new JobClient(new JobConf(conf)).getClusterStatus().getMaxReduceTasks(); conf.setInt("mapred.reduce.tasks", Math.max(1, maxReduceTasks * 9 / 10)); final Job job = new Job(conf); job.setJarByClass(Sort.class); job.setMapperClass(Mapper.class); job.setReducerClass(SortReducer.class); job.setMapOutputKeyClass(LongWritable.class); job.setOutputKeyClass(NullWritable.class); job.setOutputValueClass(SAMRecordWritable.class); job.setInputFormatClass(BAMInputFormat.class); job.setOutputFormatClass(SortOutputFormat.class); for (final Path in : inputs) FileInputFormat.addInputPath(job, in); FileOutputFormat.setOutputPath(job, wrkDirPath); job.setPartitionerClass(TotalOrderPartitioner.class); System.out.println("sort :: Sampling..."); t.start(); InputSampler.<LongWritable, SAMRecordWritable>writePartitionFile(job, new InputSampler.IntervalSampler<LongWritable, SAMRecordWritable>(0.01, 100)); System.out.printf("sort :: Sampling complete in %d.%03d s.\n", t.stopS(), t.fms()); job.submit(); System.out.println("sort :: Waiting for job completion..."); t.start(); if (!job.waitForCompletion(verbose)) { System.err.println("sort :: Job failed."); return 4; } System.out.printf("sort :: Job complete in %d.%03d s.\n", t.stopS(), t.fms()); } catch (IOException e) { System.err.printf("sort :: Hadoop error: %s\n", e); return 4; } catch (ClassNotFoundException e) { throw new RuntimeException(e); } catch (InterruptedException e) { throw new RuntimeException(e); } if (out != null) try { System.out.println("sort :: Merging output..."); t.start(); final Path outPath = new Path(out); final FileSystem srcFS = wrkDirPath.getFileSystem(conf); FileSystem dstFS = outPath.getFileSystem(conf); if (dstFS instanceof LocalFileSystem && dstFS instanceof ChecksumFileSystem) dstFS = ((LocalFileSystem) dstFS).getRaw(); final BAMFileWriter w = new BAMFileWriter(dstFS.create(outPath), new File("")); w.setSortOrder(SAMFileHeader.SortOrder.coordinate, true); w.setHeader(getHeaderMerger(conf).getMergedHeader()); w.close(); final OutputStream outs = dstFS.append(outPath); final FileStatus[] parts = srcFS.globStatus(new Path(wrkDir, conf.get(SortOutputFormat.OUTPUT_NAME_PROP) + "-[0-9][0-9][0-9][0-9][0-9][0-9]*")); { int i = 0; final Timer t2 = new Timer(); for (final FileStatus part : parts) { t2.start(); final InputStream ins = srcFS.open(part.getPath()); IOUtils.copyBytes(ins, outs, conf, false); ins.close(); System.out.printf("sort :: Merged part %d in %d.%03d s.\n", ++i, t2.stopS(), t2.fms()); } } for (final FileStatus part : parts) srcFS.delete(part.getPath(), false); outs.write(BlockCompressedStreamConstants.EMPTY_GZIP_BLOCK); outs.close(); System.out.printf("sort :: Merging complete in %d.%03d s.\n", t.stopS(), t.fms()); } catch (IOException e) { System.err.printf("sort :: Output merging failed: %s\n", e); return 5; } return 0; } | 19,465 |
0 | public void moveMessage(DBMimeMessage oSrcMsg) throws MessagingException { if (DebugFile.trace) { DebugFile.writeln("Begin DBFolder.moveMessage()"); DebugFile.incIdent(); } JDCConnection oConn = null; PreparedStatement oStmt = null; ResultSet oRSet = null; BigDecimal oPg = null; BigDecimal oPos = null; int iLen = 0; try { oConn = ((DBStore) getStore()).getConnection(); oStmt = oConn.prepareStatement("SELECT " + DB.pg_message + "," + DB.nu_position + "," + DB.len_mimemsg + " FROM " + DB.k_mime_msgs + " WHERE " + DB.gu_mimemsg + "=?"); oStmt.setString(1, oSrcMsg.getMessageGuid()); oRSet = oStmt.executeQuery(); if (oRSet.next()) { oPg = oRSet.getBigDecimal(1); oPos = oRSet.getBigDecimal(2); iLen = oRSet.getInt(3); } oRSet.close(); oRSet = null; oStmt.close(); oStmt = null; oConn.setAutoCommit(false); oStmt = oConn.prepareStatement("UPDATE " + DB.k_categories + " SET " + DB.len_size + "=" + DB.len_size + "-" + String.valueOf(iLen) + " WHERE " + DB.gu_category + "=?"); oStmt.setString(1, ((DBFolder) (oSrcMsg.getFolder())).getCategory().getString(DB.gu_category)); oStmt.executeUpdate(); oStmt.close(); oStmt = null; oStmt = oConn.prepareStatement("UPDATE " + DB.k_categories + " SET " + DB.len_size + "=" + DB.len_size + "+" + String.valueOf(iLen) + " WHERE " + DB.gu_category + "=?"); oStmt.setString(1, getCategory().getString(DB.gu_category)); oStmt.executeUpdate(); oStmt.close(); oStmt = null; oConn.commit(); } catch (SQLException sqle) { if (null != oRSet) { try { oRSet.close(); } catch (Exception ignore) { } } if (null != oStmt) { try { oStmt.close(); } catch (Exception ignore) { } } if (null != oConn) { try { oConn.rollback(); } catch (Exception ignore) { } } throw new MessagingException(sqle.getMessage(), sqle); } if (null == oPg) throw new MessagingException("Source message not found"); if (null == oPos) throw new MessagingException("Source message position is not valid"); DBFolder oSrcFldr = (DBFolder) oSrcMsg.getFolder(); MboxFile oMboxSrc = null, oMboxThis = null; try { oMboxSrc = new MboxFile(oSrcFldr.getFile(), MboxFile.READ_WRITE); oMboxThis = new MboxFile(oSrcFldr.getFile(), MboxFile.READ_WRITE); oMboxThis.appendMessage(oMboxSrc, oPos.longValue(), iLen); oMboxThis.close(); oMboxThis = null; oMboxSrc.purge(new int[] { oPg.intValue() }); oMboxSrc.close(); oMboxSrc = null; } catch (Exception e) { if (oMboxThis != null) { try { oMboxThis.close(); } catch (Exception ignore) { } } if (oMboxSrc != null) { try { oMboxSrc.close(); } catch (Exception ignore) { } } throw new MessagingException(e.getMessage(), e); } try { oConn = ((DBStore) getStore()).getConnection(); BigDecimal dNext = getNextMessage(); String sCatGuid = getCategory().getString(DB.gu_category); oStmt = oConn.prepareStatement("UPDATE " + DB.k_mime_msgs + " SET " + DB.gu_category + "=?," + DB.pg_message + "=? WHERE " + DB.gu_mimemsg + "=?"); oStmt.setString(1, sCatGuid); oStmt.setBigDecimal(2, dNext); oStmt.setString(3, oSrcMsg.getMessageGuid()); oStmt.executeUpdate(); oStmt.close(); oStmt = null; oConn.commit(); } catch (SQLException sqle) { if (null != oStmt) { try { oStmt.close(); } catch (Exception ignore) { } } if (null != oConn) { try { oConn.rollback(); } catch (Exception ignore) { } } throw new MessagingException(sqle.getMessage(), sqle); } if (DebugFile.trace) { DebugFile.decIdent(); DebugFile.writeln("End DBFolder.moveMessage()"); } } | public static void copy_file(String fromFileName, String toFileName) throws IOException { File fromFile = new File(fromFileName); File toFile = new File(toFileName); if (!fromFile.exists()) throw new IOException("FileCopy: " + "no such source file: " + fromFileName); if (!fromFile.isFile()) throw new IOException("FileCopy: " + "can't copy directory: " + fromFileName); if (!fromFile.canRead()) throw new IOException("FileCopy: " + "source file is unreadable: " + fromFileName); if (toFile.isDirectory()) toFile = new File(toFile, fromFile.getName()); if (toFile.exists()) { if (!toFile.canWrite()) throw new IOException("FileCopy: " + "destination file is unwriteable: " + toFileName); System.out.print("Overwrite existing file " + toFile.getName() + "? (Y/N): "); System.out.flush(); BufferedReader in = new BufferedReader(new InputStreamReader(System.in)); String response = in.readLine(); if (!response.equals("Y") && !response.equals("y")) throw new IOException("FileCopy: " + "existing file was not overwritten."); } else { String parent = toFile.getParent(); if (parent == null) parent = System.getProperty("user.dir"); File dir = new File(parent); if (!dir.exists()) throw new IOException("FileCopy: " + "destination directory doesn't exist: " + parent); if (dir.isFile()) throw new IOException("FileCopy: " + "destination is not a directory: " + parent); if (!dir.canWrite()) throw new IOException("FileCopy: " + "destination directory is unwriteable: " + parent); } FileInputStream from = null; FileOutputStream to = null; try { from = new FileInputStream(fromFile); to = new FileOutputStream(toFile); byte[] buffer = new byte[4096]; int bytesRead; while ((bytesRead = from.read(buffer)) != -1) to.write(buffer, 0, bytesRead); } finally { if (from != null) try { from.close(); } catch (IOException e) { ; } if (to != null) try { to.close(); } catch (IOException e) { ; } } } | 19,466 |
1 | public static void copyFile(final File sourceFile, final File destFile) throws IOException { if (destFile.getParentFile() != null && !destFile.getParentFile().mkdirs()) { LOG.error("GeneralHelper.copyFile(): Cannot create parent directories from " + destFile); } FileInputStream fIn = null; FileOutputStream fOut = null; FileChannel source = null; FileChannel destination = null; try { fIn = new FileInputStream(sourceFile); source = fIn.getChannel(); fOut = new FileOutputStream(destFile); destination = fOut.getChannel(); long transfered = 0; final long bytes = source.size(); while (transfered < bytes) { transfered += destination.transferFrom(source, 0, source.size()); destination.position(transfered); } } finally { if (source != null) { source.close(); } else if (fIn != null) { fIn.close(); } if (destination != null) { destination.close(); } else if (fOut != null) { fOut.close(); } } } | private void javaToHtml(File source, File destination) throws IOException { Reader reader = new FileReader(source); Writer writer = new FileWriter(destination); JavaUtils.writeJava(reader, writer); writer.flush(); writer.close(); } | 19,467 |
1 | public static void copyFile(File file, String pathExport) throws IOException { File out = new File(pathExport); FileChannel sourceChannel = new FileInputStream(file).getChannel(); FileChannel destinationChannel = new FileOutputStream(out).getChannel(); sourceChannel.transferTo(0, sourceChannel.size(), destinationChannel); sourceChannel.close(); destinationChannel.close(); } | public static void getResponseAsStream(String _url, Object _stringOrStream, OutputStream _stream, Map<String, String> _headers, Map<String, String> _params, String _contentType, int _timeout) throws IOException { if (_url == null || _url.length() <= 0) throw new IllegalArgumentException("Url can not be null."); String temp = _url.toLowerCase(); if (!temp.startsWith("http://") && !temp.startsWith("https://")) _url = "http://" + _url; _url = encodeURL(_url); HttpMethod method = null; if (_stringOrStream == null && (_params == null || _params.size() <= 0)) method = new GetMethod(_url); else method = new PostMethod(_url); HttpMethodParams methodParams = ((HttpMethodBase) method).getParams(); if (methodParams == null) { methodParams = new HttpMethodParams(); ((HttpMethodBase) method).setParams(methodParams); } if (_timeout < 0) methodParams.setSoTimeout(0); else methodParams.setSoTimeout(_timeout); if (_contentType != null && _contentType.length() > 0) { if (_headers == null) _headers = new HashMap<String, String>(); _headers.put("Content-Type", _contentType); } if (_headers == null || !_headers.containsKey("User-Agent")) { if (_headers == null) _headers = new HashMap<String, String>(); _headers.put("User-Agent", DEFAULT_USERAGENT); } if (_headers != null) { Iterator<Map.Entry<String, String>> iter = _headers.entrySet().iterator(); while (iter.hasNext()) { Map.Entry<String, String> entry = iter.next(); method.setRequestHeader((String) entry.getKey(), (String) entry.getValue()); } } if (method instanceof PostMethod && (_params != null && _params.size() > 0)) { Iterator<Map.Entry<String, String>> iter = _params.entrySet().iterator(); while (iter.hasNext()) { Map.Entry<String, String> entry = iter.next(); ((PostMethod) method).addParameter((String) entry.getKey(), (String) entry.getValue()); } } if (method instanceof EntityEnclosingMethod && _stringOrStream != null) { if (_stringOrStream instanceof InputStream) { RequestEntity entity = new InputStreamRequestEntity((InputStream) _stringOrStream); ((EntityEnclosingMethod) method).setRequestEntity(entity); } else { RequestEntity entity = new StringRequestEntity(_stringOrStream.toString(), _contentType, null); ((EntityEnclosingMethod) method).setRequestEntity(entity); } } HttpClient httpClient = new HttpClient(new org.apache.commons.httpclient.SimpleHttpConnectionManager()); httpClient.getParams().setBooleanParameter(HttpClientParams.ALLOW_CIRCULAR_REDIRECTS, true); InputStream instream = null; try { int status = httpClient.executeMethod(method); if (status != HttpStatus.SC_OK) { LOG.warn("Http Satus:" + status + ",Url:" + _url); if (status >= 500 && status < 600) throw new IOException("Remote service<" + _url + "> respose a error, status:" + status); } instream = method.getResponseBodyAsStream(); IOUtils.copy(instream, _stream); } catch (IOException err) { LOG.error("Failed to access " + _url, err); throw err; } finally { IOUtils.closeQuietly(instream); if (method != null) method.releaseConnection(); } } | 19,468 |
0 | public InputStream getInputStream(long offset) throws IOException { if (is != null && raf == null) { try { is.close(); } catch (Throwable th) { } finally { is = null; } } if (is == null && getUrl() != null && getFile() == null) { is = url.openStream(); } if (is == null) { if (getFile() != null) { raf = null; try { raf = new RandomAccessFile(getFile(), "r"); } catch (Exception ex) { } is = (raf != null) ? new RAFInputStream(raf, 0) : new BufferedInputStream(new FileInputStream(getFile()), 1024 * 30); } } if (is instanceof RAFInputStream) { RAFInputStream ris = (RAFInputStream) is; ris.seek(offset); } else { is.skip(offset); } return is; } | 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; } | 19,469 |
1 | protected byte[] computeHash() { try { final MessageDigest inputHash = MessageDigest.getInstance("SHA"); inputHash.update(bufferFileData().getBytes()); return inputHash.digest(); } catch (final NoSuchAlgorithmException nsae) { lastException = nsae; return new byte[0]; } catch (final IOException ioe) { lastException = ioe; return new byte[0]; } } | @Override protected AuthenticationHandlerResponse authenticateInternal(final Connection c, final AuthenticationCriteria criteria) throws LdapException { byte[] hash; try { final MessageDigest md = MessageDigest.getInstance(passwordScheme); md.update(criteria.getCredential().getBytes()); hash = md.digest(); } catch (NoSuchAlgorithmException e) { throw new LdapException(e); } final LdapAttribute la = new LdapAttribute("userPassword", String.format("{%s}%s", passwordScheme, LdapUtils.base64Encode(hash)).getBytes()); final CompareOperation compare = new CompareOperation(c); final CompareRequest request = new CompareRequest(criteria.getDn(), la); request.setControls(getAuthenticationControls()); final Response<Boolean> compareResponse = compare.execute(request); return new AuthenticationHandlerResponse(compareResponse.getResult(), compareResponse.getResultCode(), c, compareResponse.getMessage(), compareResponse.getControls()); } | 19,470 |
1 | private void appendArchive() throws Exception { String cmd; if (profile == CompilationProfile.UNIX_GCC) { cmd = "cat"; } else if (profile == CompilationProfile.MINGW_WINDOWS) { cmd = "type"; } else { throw new Exception("Unknown cat equivalent for profile " + profile); } compFrame.writeLine("<span style='color: green;'>" + cmd + " \"" + imageArchive.getAbsolutePath() + "\" >> \"" + outputFile.getAbsolutePath() + "\"</span>"); BufferedOutputStream out = new BufferedOutputStream(new FileOutputStream(outputFile, true)); BufferedInputStream in = new BufferedInputStream(new FileInputStream(imageArchive)); int read; while ((read = in.read()) != -1) { out.write(read); } in.close(); out.close(); } | protected void writeToResponse(InputStream stream, HttpServletResponse response) throws IOException { OutputStream output = response.getOutputStream(); try { IOUtils.copy(stream, output); } finally { try { stream.close(); } finally { output.close(); } } } | 19,471 |
1 | public static void testclass(String[] args) throws IOException, CodeCheckException { ClassWriter writer = new ClassWriter(); writer.emptyClass(ClassWriter.ACC_PUBLIC, "TestClass", "java/lang/Object"); MethodInfo newMethod = writer.addMethod(ClassWriter.ACC_PUBLIC | ClassWriter.ACC_STATIC, "main", "([Ljava/lang/String;)V"); CodeAttribute attribute = newMethod.getCodeAttribute(); int constantIndex = writer.getStringConstantIndex("It's alive! It's alive!!"); int fieldRefIndex = writer.getReferenceIndex(ClassWriter.CONSTANT_Fieldref, "java/lang/System", "out", "Ljava/io/PrintStream;"); int methodRefIndex = writer.getReferenceIndex(ClassWriter.CONSTANT_Methodref, "java/io/PrintStream", "println", "(Ljava/lang/String;)V"); ArrayList instructions = new ArrayList(); byte[] operands; operands = new byte[2]; NetByte.intToPair(fieldRefIndex, operands, 0); instructions.add(new Instruction(OpCode.getOpCodeByMnemonic("getstatic"), 0, operands, false)); operands = new byte[1]; operands[0] = (byte) constantIndex; instructions.add(new Instruction(OpCode.getOpCodeByMnemonic("ldc"), 0, operands, false)); operands = new byte[2]; NetByte.intToPair(methodRefIndex, operands, 0); instructions.add(new Instruction(OpCode.getOpCodeByMnemonic("invokevirtual"), 0, operands, false)); instructions.add(new Instruction(OpCode.getOpCodeByMnemonic("return"), 0, null, false)); attribute.insertInstructions(0, 0, instructions); attribute.setMaxLocals(1); attribute.codeCheck(); System.out.println("constantIndex=" + constantIndex + " fieldRef=" + fieldRefIndex + " methodRef=" + methodRefIndex); writer.writeClass(new FileOutputStream("c:/cygnus/home/javaodb/classes/TestClass.class")); writer.readClass(new FileInputStream("c:/cygnus/home/javaodb/classes/TestClass.class")); } | public void actionPerformed(ActionEvent e) { final File inputFile = KeyboardHero.midiFile(); try { if (inputFile == null) return; final File dir = (new File(Util.DATA_FOLDER + MidiSong.MIDI_FILES_DIR)); if (dir.exists()) { if (!dir.isDirectory()) { Util.error(Util.getMsg("Err_MidiFilesDirNotDirectory"), dir.getParent()); return; } } else if (!dir.mkdirs()) { Util.error(Util.getMsg("Err_CouldntMkDir"), dir.getParent()); return; } File outputFile = new File(dir.getPath() + File.separator + inputFile.getName()); if (!outputFile.exists() || KeyboardHero.confirm("Que_FileExistsOverwrite")) { final FileChannel inChannel = new FileInputStream(inputFile).getChannel(); inChannel.transferTo(0, inChannel.size(), new FileOutputStream(outputFile).getChannel()); } } catch (Exception ex) { Util.getMsg(Util.getMsg("Err_CouldntImportSong"), ex.toString()); } SongSelector.refresh(); } | 19,472 |
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.close(output); } } finally { IOUtils.close(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 void main(String[] argz) { int X, Y, Z; X = 256; Y = 256; Z = 256; try { String work_folder = "C:\\Documents and Settings\\Entheogen\\My Documents\\school\\jung\\vol_data\\CT_HEAD3"; FileOutputStream out_stream = new FileOutputStream(new File(work_folder + "\\converted.dat")); FileChannel out = out_stream.getChannel(); String f_name = "head256.raw"; File file = new File(work_folder + "\\" + f_name); FileChannel in = new FileInputStream(file).getChannel(); ByteBuffer buffa = BufferUtil.newByteBuffer((int) file.length()); in.read(buffa); in.close(); int N = 256; FloatBuffer output_data = BufferUtil.newFloatBuffer(N * N * N); float min = Float.MAX_VALUE; for (int i = 0, j = 0; i < buffa.capacity(); i++, j++) { byte c = buffa.get(i); min = Math.min(min, (float) (c)); output_data.put((float) (c)); } for (int i = 0; i < Y - X; ++i) { for (int j = 0; j < Y; ++j) { for (int k = 0; k < Z; ++k) { output_data.put(min); } } } output_data.rewind(); System.out.println("size of output_data = " + Integer.toString(output_data.capacity())); out.write(BufferUtil.copyFloatBufferAsByteBuffer(output_data)); ByteBuffer buffa2 = BufferUtil.newByteBuffer(2); buffa2.put((byte) '.'); out.close(); } catch (Exception exc) { exc.printStackTrace(); } } | 19,473 |
0 | public static void copyFile(File from, File to) throws IOException { FileInputStream in = new FileInputStream(from); FileOutputStream out = new FileOutputStream(to); int c; while ((c = in.read()) != -1) out.write(c); in.close(); out.close(); } | private void request() { try { connection = (HttpURLConnection) new URL(url).openConnection(); if (isCometConnection) { connection.setReadTimeout(0); } else { connection.setReadTimeout(30000); } connection.setInstanceFollowRedirects(false); connection.setDoInput(true); connection.setRequestMethod(method); connection.setRequestProperty("User-Agent", "Mozilla/5.0 (Windows; U; Windows NT 6.0; en-US; rv:1.9.1.5) Gecko/20091102 Firefox/3.5.5 GTB5"); if ("post".equalsIgnoreCase(method)) { connection.setDoOutput(true); connection.setRequestProperty("Content-Type", "application/x-www-form-urlencoded"); } if (user != null) { String auth = user + ":" + (password != null ? password : ""); String base64Auth = HttpRequest.Base64.byteArrayToBase64(auth.getBytes()); connection.setRequestProperty("Authorization", "Basic " + base64Auth); } for (Iterator<String> iter = headers.keySet().iterator(); iter.hasNext(); ) { String key = (String) iter.next(); connection.setRequestProperty(key, (String) headers.get(key)); } connection.setUseCaches(false); if (checkAbort()) return; if ("post".equalsIgnoreCase(method)) { DataOutputStream dos = new DataOutputStream(connection.getOutputStream()); activeOS = dos; if (content != null) { dos.writeBytes(content); } if (checkAbort()) return; dos.flush(); dos.close(); activeOS = null; } if (checkAbort()) return; InputStream is = null; try { is = connection.getInputStream(); } catch (IOException e) { if (checkAbort()) return; readyState = 4; if (onreadystatechange != null) { onreadystatechange.onLoaded(); } connection = null; readyState = 0; return; } activeIS = is; if (readyState < 2) { readyState = 2; status = connection.getResponseCode(); statusText = connection.getResponseMessage(); if (onreadystatechange != null) { onreadystatechange.onSent(); } } receiving = initializeReceivingMonitor(); ByteArrayOutputStream baos = new ByteArrayOutputStream(10240); byte[] buffer = new byte[10240]; int read; while (!toAbort && (read = is.read(buffer)) != -1) { if (checkAbort()) return; if (readyState != 3) { readyState = 3; if (onreadystatechange != null) { onreadystatechange.onReceiving(); } } boolean received = false; if (receiving != null) { received = receiving.receiving(baos, buffer, 0, read); } if (!received) { baos.write(buffer, 0, read); } } if (checkAbort()) return; is.close(); activeIS = null; responseText = null; String type = connection.getHeaderField("Content-Type"); if (type != null) { String charset = null; String lowerType = type.toLowerCase(); int idx = lowerType.indexOf("charset="); if (idx != -1) { charset = type.substring(idx + 8); } else { idx = lowerType.indexOf("/xml"); if (idx != -1) { String tmp = baos.toString(); Matcher matcher = Pattern.compile("<\\?.*encoding\\s*=\\s*[\'\"]([^'\"]*)[\'\"].*\\?>", Pattern.MULTILINE).matcher(tmp); if (matcher.find()) { charset = matcher.group(1); } else { responseText = tmp; } } else { idx = lowerType.indexOf("html"); if (idx != -1) { String tmp = baos.toString(); Matcher matcher = Pattern.compile("<meta.*content\\s*=\\s*[\'\"][^'\"]*charset\\s*=\\s*([^'\"]*)\\s*[\'\"].*>", Pattern.MULTILINE | Pattern.CASE_INSENSITIVE).matcher(tmp); if (matcher.find()) { charset = matcher.group(1); } else { responseText = tmp; } } } } if (charset != null) { try { responseText = baos.toString(charset); } catch (UnsupportedEncodingException e) { } } } if (responseText == null) { try { responseText = baos.toString("iso-8859-1"); } catch (UnsupportedEncodingException e) { responseText = baos.toString(); } } readyState = 4; if (onreadystatechange != null) { onreadystatechange.onLoaded(); } connection.disconnect(); readyState = 0; } catch (Exception e) { if (checkAbort()) return; e.printStackTrace(); readyState = 4; if (onreadystatechange != null) { onreadystatechange.onLoaded(); } connection = null; readyState = 0; } } | 19,474 |
0 | public static int ToGSML(GeoSciML_Mapping mapping, String strTemplate, String strRequest, PrintWriter sortie, String requestedSRS) throws Exception { String level = "info."; if (ConnectorServlet.debug) level = "debug."; Log log = LogFactory.getLog(level + "fr.brgm.exows.gml2gsml.Gml2Gsml"); log.debug(strRequest); String tagFeature = "FIELDS"; URL url2Request = new URL(strRequest); URLConnection conn = url2Request.openConnection(); Date dDebut = new Date(); BufferedReader buffin = new BufferedReader(new InputStreamReader(conn.getInputStream())); String strLine = null; int nbFeatures = 0; Template template = VelocityCreator.createTemplate("/fr/brgm/exows/gml2gsml/templates/" + strTemplate); while ((strLine = buffin.readLine()) != null) { if (strLine.indexOf(tagFeature) != -1) { nbFeatures++; GSMLFeatureGeneric feature = createGSMLFeatureFromGMLFeatureString(mapping, strLine); VelocityContext context = new VelocityContext(); context.put("feature", feature); String outputFeatureMember = VelocityCreator.createXMLbyContext(context, template); sortie.println(outputFeatureMember); } } buffin.close(); Date dFin = new Date(); String output = "GEOSCIML : " + nbFeatures + " features handled - time : " + (dFin.getTime() - dDebut.getTime()) / 1000 + " [" + dDebut + " // " + dFin + "]"; log.trace(output); return nbFeatures; } | private byte[] getMergedContent(List names, ServletContext servletContext) throws IOException { ByteArrayOutputStream baos = new ByteArrayOutputStream(); for (Iterator iterator = names.iterator(); iterator.hasNext(); ) { String path = (String) iterator.next(); if (!path.startsWith("/")) path = "/" + path; URL url = servletContext.getResource(path); if (url == null) url = getClass().getResource(path); if (url == null) throw new IOException("The resources '" + path + "' could not be found neither in the webapp folder nor in a jar"); log.debug("Merging content of group : " + getName()); InputStream inputStream = url.openStream(); InputStreamReader r = new InputStreamReader(inputStream); IOUtils.copy(r, baos, "ASCII"); baos.write((byte) '\n'); inputStream.close(); } baos.close(); return baos.toByteArray(); } | 19,475 |
1 | public static void main(String[] args) { FileInputStream in; DeflaterOutputStream out; FileOutputStream fos; FileDialog fd; fd = new FileDialog(new Frame(), "Find a file to deflate", FileDialog.LOAD); fd.show(); if (fd.getFile() != null) { try { in = new FileInputStream(new File(fd.getDirectory(), fd.getFile())); fos = new FileOutputStream(new File("Deflated.out")); out = new DeflaterOutputStream(fos, new Deflater(Deflater.DEFLATED, true)); int bytes_read = 0; byte[] buffer = new byte[1024]; while ((bytes_read = in.read(buffer)) != -1) { out.write(buffer, 0, bytes_read); } fos.flush(); fos.close(); out.flush(); out.close(); in.close(); } catch (Exception e) { e.printStackTrace(); } System.out.println("Done"); } } | 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; } | 19,476 |
1 | protected void saveSelectedFiles() { if (dataList.getSelectedRowCount() == 0) { return; } if (dataList.getSelectedRowCount() == 1) { Object obj = model.getItemAtRow(sorter.convertRowIndexToModel(dataList.getSelectedRow())); AttachFile entry = (AttachFile) obj; JFileChooser fc = new JFileChooser(); fc.setSelectedFile(new File(fc.getCurrentDirectory(), entry.getCurrentPath().getName())); if (fc.showSaveDialog(this) == JFileChooser.APPROVE_OPTION) { File current = entry.getCurrentPath(); File dest = fc.getSelectedFile(); try { FileInputStream in = new FileInputStream(current); FileOutputStream out = new FileOutputStream(dest); byte[] readBuf = new byte[1024 * 512]; int readLength; while ((readLength = in.read(readBuf)) != -1) { out.write(readBuf, 0, readLength); } in.close(); out.close(); } catch (FileNotFoundException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } } return; } else { JFileChooser fc = new JFileChooser(); fc.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY); if (fc.showSaveDialog(this) == JFileChooser.APPROVE_OPTION) { for (Integer idx : dataList.getSelectedRows()) { Object obj = model.getItemAtRow(sorter.convertRowIndexToModel(idx)); AttachFile entry = (AttachFile) obj; File current = entry.getCurrentPath(); File dest = new File(fc.getSelectedFile(), entry.getName()); try { FileInputStream in = new FileInputStream(current); FileOutputStream out = new FileOutputStream(dest); byte[] readBuf = new byte[1024 * 512]; int readLength; while ((readLength = in.read(readBuf)) != -1) { out.write(readBuf, 0, readLength); } in.close(); out.close(); } catch (FileNotFoundException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } } } return; } } | 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(); } } | 19,477 |
0 | public static final int executeSql(final Connection conn, final String sql, final boolean rollback) throws SQLException { if (null == sql) return 0; Statement stmt = null; try { stmt = conn.createStatement(); final int updated = stmt.executeUpdate(sql); return updated; } catch (final SQLException e) { if (rollback) conn.rollback(); throw e; } finally { closeAll(null, stmt, null); } } | public void testGetResource_FileOutsideOfClasspath() throws Exception { File temp = File.createTempFile("dozerfiletest", ".txt"); temp.deleteOnExit(); String resourceName = "file:" + temp.getAbsolutePath(); URL url = loader.getResource(resourceName); assertNotNull("URL should not be null", url); InputStream is = url.openStream(); assertNotNull("input stream should not be null", is); } | 19,478 |
1 | private static void copyFile(File inputFile, File outputFile) throws IOException { FileReader in = new FileReader(inputFile); FileWriter out = new FileWriter(outputFile); int c; while ((c = in.read()) != -1) out.write(c); in.close(); out.close(); } | @Override protected void doPost(HttpServletRequest request, HttpServletResponse response) throws ServletException { PrintWriter writer = null; InputStream is = null; FileOutputStream fos = null; try { writer = response.getWriter(); } catch (IOException ex) { log(OctetStreamReader.class.getName() + "has thrown an exception: " + ex.getMessage()); } String filename = request.getHeader("X-File-Name"); try { is = request.getInputStream(); fos = new FileOutputStream(new File(realPath + filename)); IOUtils.copy(is, fos); response.setStatus(response.SC_OK); writer.print("{success: true}"); } catch (FileNotFoundException ex) { response.setStatus(response.SC_INTERNAL_SERVER_ERROR); writer.print("{success: false}"); log(OctetStreamReader.class.getName() + "has thrown an exception: " + ex.getMessage()); } catch (IOException ex) { response.setStatus(response.SC_INTERNAL_SERVER_ERROR); writer.print("{success: false}"); log(OctetStreamReader.class.getName() + "has thrown an exception: " + ex.getMessage()); } finally { try { fos.close(); is.close(); } catch (IOException ignored) { } } writer.flush(); writer.close(); } | 19,479 |
1 | public static void main(String[] args) { paraProc(args); CanonicalGFF cgff = new CanonicalGFF(gffFilename); CanonicalGFF geneModel = new CanonicalGFF(modelFilename); CanonicalGFF transcriptGff = new CanonicalGFF(transcriptFilename); TreeMap ksTable1 = getKsTable(ksTable1Filename); TreeMap ksTable2 = getKsTable(ksTable2Filename); Map intronReadCntMap = new TreeMap(); Map intronSplicingPosMap = new TreeMap(); try { BufferedReader fr = new BufferedReader(new FileReader(inFilename)); while (fr.ready()) { String line = fr.readLine(); if (line.startsWith("#")) continue; String tokens[] = line.split("\t"); String chr = tokens[0]; int start = Integer.parseInt(tokens[1]); int stop = Integer.parseInt(tokens[2]); GenomeInterval intron = new GenomeInterval(chr, start, stop); int readCnt = Integer.parseInt(tokens[3]); intronReadCntMap.put(intron, readCnt); String splicingMapStr = tokens[4]; Map splicingMap = getSplicingMap(splicingMapStr); intronSplicingPosMap.put(intron, splicingMap); } fr.close(); } catch (IOException ex) { ex.printStackTrace(); System.exit(1); } double[] hdCDF = getHdCdf(readLength, minimumOverlap); try { FileWriter fw = new FileWriter(outFilename); for (Iterator intronIterator = intronReadCntMap.keySet().iterator(); intronIterator.hasNext(); ) { GenomeInterval intron = (GenomeInterval) intronIterator.next(); int readCnt = ((Integer) intronReadCntMap.get(intron)).intValue(); TreeMap splicingMap = (TreeMap) intronSplicingPosMap.get(intron); Object ksInfoArray[] = distributionAccepter((TreeMap) splicingMap.clone(), readCnt, hdCDF, ksTable1, ksTable2); boolean ksAccepted = (Boolean) ksInfoArray[0]; double testK = (Double) ksInfoArray[1]; double standardK1 = (Double) ksInfoArray[2]; double standardK2 = (Double) ksInfoArray[3]; int positionCnt = splicingMap.size(); Object modelInfoArray[] = getModelAgreedSiteCnt(intron, cgff, geneModel, transcriptGff); int modelAgreedSiteCnt = (Integer) modelInfoArray[0]; int maxAgreedTransSiteCnt = (Integer) modelInfoArray[1]; boolean containedBySomeGene = (Boolean) modelInfoArray[2]; int numIntersectingGenes = (Integer) modelInfoArray[3]; int distance = intron.getStop() - intron.getStart(); fw.write(intron.getChr() + ":" + intron.getStart() + ".." + intron.getStop() + "\t" + distance + "\t" + readCnt + "\t" + splicingMap + "\t" + probabilityEvaluation(readLength, distance, readCnt, splicingMap, positionCnt) + "\t" + ksAccepted + "\t" + testK + "\t" + standardK1 + "\t" + standardK2 + "\t" + positionCnt + "\t" + modelAgreedSiteCnt + "\t" + maxAgreedTransSiteCnt + "\t" + containedBySomeGene + "\t" + numIntersectingGenes + "\n"); } fw.close(); } catch (IOException ex) { ex.printStackTrace(); System.exit(1); } } | public void notifyTerminated(Writer r) { all_writers.remove(r); if (all_writers.isEmpty()) { all_terminated = true; Iterator iterator = open_files.iterator(); while (iterator.hasNext()) { FileWriter.FileChunk fc = (FileWriter.FileChunk) iterator.next(); do { try { fc.stream.flush(); fc.stream.close(); } catch (IOException e) { } fc = fc.next; } while (fc != null); } iterator = open_files.iterator(); boolean all_ok = true; while (iterator.hasNext()) { FileWriter.FileChunk fc = (FileWriter.FileChunk) iterator.next(); logger.logComment("File chunk <" + fc.name + "> " + fc.start_byte + " " + fc.position + " " + fc.actual_file); boolean ok = true; while (fc.next != null) { ok = ok && (fc.start_byte + fc.actual_file.length()) == fc.next.start_byte; fc = fc.next; } if (ok) { logger.logComment("Received file <" + fc.name + "> is contiguous (and hopefully complete)"); } else { logger.logError("Received file <" + fc.name + "> is NOT contiguous"); all_ok = false; } } if (all_ok) { byte[] buffer = new byte[16384]; iterator = open_files.iterator(); while (iterator.hasNext()) { FileWriter.FileChunk fc = (FileWriter.FileChunk) iterator.next(); try { if (fc.next != null) { FileOutputStream fos = new FileOutputStream(fc.actual_file, true); fc = fc.next; while (fc != null) { FileInputStream fis = new FileInputStream(fc.actual_file); int actually_read = fis.read(buffer); while (actually_read != -1) { fos.write(buffer, 0, actually_read); actually_read = fis.read(buffer); } fc.actual_file.delete(); fc = fc.next; } } } catch (FileNotFoundException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } } } fte.allWritersTerminated(); fte = null; } } | 19,480 |
1 | public static String SHA1(String text) throws NoSuchAlgorithmException, UnsupportedEncodingException { MessageDigest md; md = MessageDigest.getInstance("SHA-1"); byte[] sha1hash = new byte[40]; md.update(text.getBytes("iso-8859-1"), 0, text.length()); sha1hash = md.digest(); return convertToHex(sha1hash); } | private void SaveLoginInfo() { int iSize; try { if (m_bSavePwd) { byte[] MD5PWD = new byte[80]; java.security.MessageDigest md = java.security.MessageDigest.getInstance("SHA-1"); String szPath = System.getProperty("user.home"); szPath += System.getProperty("file.separator") + "MochaJournal"; java.io.File file = new java.io.File(szPath); if (!file.exists()) file.mkdirs(); file = new java.io.File(file, "user.dat"); if (!file.exists()) file.createNewFile(); java.io.FileOutputStream pw = new java.io.FileOutputStream(file); iSize = m_PwdList.size(); for (int iIndex = 0; iIndex < iSize; iIndex++) { md.reset(); md.update(((String) m_UsrList.get(iIndex)).getBytes()); byte[] DESUSR = md.digest(); byte alpha = 0; for (int i = 0; i < DESUSR.length; i++) alpha += DESUSR[i]; String pwd = (String) m_PwdList.get(iIndex); if (pwd.length() > 0) { java.util.Arrays.fill(MD5PWD, (byte) 0); int iLen = pwd.length(); pw.write(iLen); for (int i = 0; i < iLen; i++) { int iDiff = (int) pwd.charAt(i) + (int) alpha; int c = iDiff % 256; MD5PWD[i] = (byte) c; pw.write((byte) c); } } else pw.write(0); } pw.flush(); } } catch (java.security.NoSuchAlgorithmException e) { System.err.println(e); } catch (java.io.IOException e3) { System.err.println(e3); } } | 19,481 |
1 | public static void copyFile(File source, File dest) throws IOException { FileChannel in = null, out = null; try { in = new FileInputStream(source).getChannel(); out = new FileOutputStream(dest).getChannel(); long size = in.size(); MappedByteBuffer buf = in.map(FileChannel.MapMode.READ_ONLY, 0, size); out.write(buf); } finally { if (in != null) in.close(); if (out != null) out.close(); } } | public void copy(File src, File dest) throws FileNotFoundException, IOException { FileInputStream srcStream = new FileInputStream(src); FileOutputStream destStream = new FileOutputStream(dest); FileChannel srcChannel = srcStream.getChannel(); FileChannel destChannel = destStream.getChannel(); srcChannel.transferTo(0, srcChannel.size(), destChannel); destChannel.close(); srcChannel.close(); destStream.close(); srcStream.close(); } | 19,482 |
0 | public String getContent(URL url) { Logger.getLogger(this.getClass().getName()).log(Level.INFO, "getting content from " + url.toString()); String content = ""; try { URLConnection httpc; httpc = url.openConnection(); httpc.setDoInput(true); httpc.connect(); BufferedReader in = new BufferedReader(new InputStreamReader(httpc.getInputStream())); String line = ""; while ((line = in.readLine()) != null) { content = content + line; } in.close(); } catch (IOException e) { Logger.getLogger(this.getClass().getName()).log(Level.SEVERE, "Problem writing to " + url, e); } return content; } | 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(); } } | 19,483 |
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 main(String[] args) { try { int encodeFlag = 0; if (args[0].equals("-e")) { encodeFlag = Base64.ENCODE; } else if (args[0].equals("-d")) { encodeFlag = Base64.DECODE; } String infile = args[1]; String outfile = args[2]; File fin = new File(infile); FileInputStream fis = new FileInputStream(fin); BufferedInputStream bis = new BufferedInputStream(fis); Base64.InputStream b64in = new Base64.InputStream(bis, encodeFlag | Base64.DO_BREAK_LINES); File fout = new File(outfile); FileOutputStream fos = new FileOutputStream(fout); BufferedOutputStream bos = new BufferedOutputStream(fos); byte[] buff = new byte[1024]; int read = -1; while ((read = b64in.read(buff)) >= 0) { bos.write(buff, 0, read); } bos.close(); b64in.close(); } catch (Exception e) { e.printStackTrace(); } } | 19,484 |
1 | public static void copy(final File src, final File dest) throws IOException { OutputStream stream = new FileOutputStream(dest); FileInputStream fis = new FileInputStream(src); byte[] buffer = new byte[16384]; while (fis.available() != 0) { int read = fis.read(buffer); stream.write(buffer, 0, read); } stream.flush(); } | @BeforeClass public static void setUpOnce() throws OWLOntologyCreationException { dbManager = (OWLDBOntologyManager) OWLDBManager.createOWLOntologyManager(OWLDataFactoryImpl.getInstance()); dbIRI = IRI.create(ontoUri); System.out.println("copying ontology to work folder..."); try { final File directory = new File("./resources/LUBM10-DB-forUpdate/"); final File[] filesToDelete = directory.listFiles(); if (filesToDelete != null && filesToDelete.length > 0) { for (final File file : filesToDelete) { if (!file.getName().endsWith(".svn")) Assert.assertTrue(file.delete()); } } final File original = new File("./resources/LUBM10-DB/LUBM10.h2.db"); final File copy = new File("./resources/LUBM10-DB-forUpdate/LUBM10.h2.db"); final FileChannel inChannel = new FileInputStream(original).getChannel(); final FileChannel outChannel = new FileOutputStream(copy).getChannel(); inChannel.transferTo(0, inChannel.size(), outChannel); } catch (final IOException ioe) { System.err.println(ioe.getMessage()); Assert.fail(); } onto = (OWLMutableOntology) dbManager.loadOntology(dbIRI); factory = dbManager.getOWLDataFactory(); } | 19,485 |
1 | protected void truncate(File file) { LogLog.debug("Compression of file: " + file.getAbsolutePath() + " started."); if (FileUtils.isFileOlder(file, ManagementFactory.getRuntimeMXBean().getStartTime())) { File backupRoot = new File(getBackupDir()); if (!backupRoot.exists() && !backupRoot.mkdirs()) { throw new AppenderInitializationError("Can't create backup dir for backup storage"); } SimpleDateFormat df; try { df = new SimpleDateFormat(getBackupDateFormat()); } catch (Exception e) { throw new AppenderInitializationError("Invalid date formate for backup files: " + getBackupDateFormat(), e); } String date = df.format(new Date(file.lastModified())); File zipFile = new File(backupRoot, file.getName() + "." + date + ".zip"); ZipOutputStream zos = null; FileInputStream fis = null; try { zos = new ZipOutputStream(new FileOutputStream(zipFile)); ZipEntry entry = new ZipEntry(file.getName()); entry.setMethod(ZipEntry.DEFLATED); entry.setCrc(FileUtils.checksumCRC32(file)); zos.putNextEntry(entry); fis = FileUtils.openInputStream(file); byte[] buffer = new byte[1024]; int readed; while ((readed = fis.read(buffer)) != -1) { zos.write(buffer, 0, readed); } } catch (Exception e) { throw new AppenderInitializationError("Can't create zip file", e); } finally { if (zos != null) { try { zos.close(); } catch (IOException e) { LogLog.warn("Can't close zip file", e); } } if (fis != null) { try { fis.close(); } catch (IOException e) { LogLog.warn("Can't close zipped file", e); } } } if (!file.delete()) { throw new AppenderInitializationError("Can't delete old log file " + file.getAbsolutePath()); } } } | 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(); } } | 19,486 |
1 | private static void backupFile(File file) { FileChannel in = null, out = null; try { if (!file.getName().endsWith(".bak")) { in = new FileInputStream(file).getChannel(); out = new FileOutputStream(new File(file.toString() + ".bak")).getChannel(); long size = in.size(); MappedByteBuffer buf = in.map(FileChannel.MapMode.READ_ONLY, 0, size); out.write(buf); } } catch (Exception e) { e.getMessage(); } finally { try { System.gc(); if (in != null) in.close(); if (out != null) out.close(); } catch (Exception e) { e.getMessage(); } } } | private void copyFile(File s, File d) throws IOException { d.getParentFile().mkdirs(); FileChannel inChannel = new FileInputStream(s).getChannel(); FileChannel outChannel = new FileOutputStream(d).getChannel(); int maxCount = (64 * 1024 * 1024) - (32 * 1024); long size = inChannel.size(); long position = 0; while (position < size) { position += inChannel.transferTo(position, maxCount, outChannel); } inChannel.close(); outChannel.close(); d.setLastModified(s.lastModified()); } | 19,487 |
0 | private void Download(String uri) throws MalformedURLException { URL url = new URL(uri); try { bm = BitmapFactory.decodeStream(url.openConnection().getInputStream()); } catch (IOException ex) { bm = getError(); } } | public static void loadMemcachedConfigFromURL(URL url, XMLInputFactory factory, List<MemcachedClientConfig> memcachedClientconfigs, List<MemcachedClientSocketPoolConfig> memcachedClientSocketPoolConfigs, List<MemcachedClientClusterConfig> memcachedClientClusterConfig) { MemcachedClientConfig node = null; MemcachedClientSocketPoolConfig socketnode = null; MemcachedClientClusterConfig clusternode = null; InputStream in = null; XMLEventReader r = null; try { in = url.openStream(); r = factory.createXMLEventReader(in); String servers = null; String weights = null; while (r.hasNext()) { XMLEvent event = r.nextEvent(); if (event.isStartElement()) { StartElement start = event.asStartElement(); String tag = start.getName().getLocalPart(); if (tag.equalsIgnoreCase("client")) { node = new MemcachedClientConfig(); if (start.getAttributeByName(new QName("", "name")) != null) node.setName(start.getAttributeByName(new QName("", "name")).getValue()); else throw new RuntimeException("memcached client name can't not be null!"); if (start.getAttributeByName(new QName("", "socketpool")) != null) node.setSocketPool(start.getAttributeByName(new QName("", "socketpool")).getValue()); else throw new RuntimeException("memcached client socketpool can't not be null!"); if (start.getAttributeByName(new QName("", "compressEnable")) != null) node.setCompressEnable(Boolean.parseBoolean(start.getAttributeByName(new QName("", "compressEnable")).getValue())); else node.setCompressEnable(true); if (start.getAttributeByName(new QName("", "defaultEncoding")) != null) node.setDefaultEncoding(start.getAttributeByName(new QName("", "defaultEncoding")).getValue()); else node.setDefaultEncoding("UTF-8"); continue; } if (tag.equalsIgnoreCase("errorHandler") && node != null) { event = r.peek(); if (event.isCharacters()) { node.setErrorHandler(event.asCharacters().getData()); r.nextEvent(); } continue; } if (tag.equalsIgnoreCase("socketpool")) { socketnode = new MemcachedClientSocketPoolConfig(); servers = null; weights = null; if (start.getAttributeByName(new QName("", "name")) != null) socketnode.setName(start.getAttributeByName(new QName("", "name")).getValue()); else throw new RuntimeException("memcached client socketpool name can't not be null!"); if (start.getAttributeByName(new QName("", "failover")) != null) socketnode.setFailover(Boolean.parseBoolean(start.getAttributeByName(new QName("", "failover")).getValue())); if (start.getAttributeByName(new QName("", "initConn")) != null) socketnode.setInitConn(Integer.parseInt(start.getAttributeByName(new QName("", "initConn")).getValue())); if (start.getAttributeByName(new QName("", "minConn")) != null) socketnode.setMinConn(Integer.parseInt(start.getAttributeByName(new QName("", "minConn")).getValue())); if (start.getAttributeByName(new QName("", "maxConn")) != null) socketnode.setMaxConn(Integer.parseInt(start.getAttributeByName(new QName("", "maxConn")).getValue())); if (start.getAttributeByName(new QName("", "maintSleep")) != null) socketnode.setMaintSleep(Integer.parseInt(start.getAttributeByName(new QName("", "maintSleep")).getValue())); if (start.getAttributeByName(new QName("", "nagle")) != null) socketnode.setNagle(Boolean.parseBoolean(start.getAttributeByName(new QName("", "nagle")).getValue())); if (start.getAttributeByName(new QName("", "socketTO")) != null) socketnode.setSocketTo(Integer.parseInt(start.getAttributeByName(new QName("", "socketTO")).getValue())); if (start.getAttributeByName(new QName("", "maxIdle")) != null) socketnode.setMaxIdle(Integer.parseInt(start.getAttributeByName(new QName("", "maxIdle")).getValue())); if (start.getAttributeByName(new QName("", "aliveCheck")) != null) socketnode.setAliveCheck(Boolean.parseBoolean(start.getAttributeByName(new QName("", "aliveCheck")).getValue())); continue; } if (tag.equalsIgnoreCase("servers") && socketnode != null) { event = r.peek(); if (event.isCharacters()) { servers = event.asCharacters().getData(); socketnode.setServers(servers); r.nextEvent(); } continue; } if (tag.equalsIgnoreCase("weights") && socketnode != null) { event = r.peek(); if (event.isCharacters()) { weights = event.asCharacters().getData(); socketnode.setWeights(weights); r.nextEvent(); } continue; } if (tag.equalsIgnoreCase("cluster")) { clusternode = new MemcachedClientClusterConfig(); if (start.getAttributeByName(new QName("", "name")) != null) clusternode.setName(start.getAttributeByName(new QName("", "name")).getValue()); else throw new RuntimeException("memcached cluster name can't not be null!"); if (start.getAttributeByName(new QName("", "mode")) != null) clusternode.setMode(start.getAttributeByName(new QName("", "mode")).getValue()); continue; } if (tag.equalsIgnoreCase("memCachedClients") && clusternode != null) { event = r.peek(); if (event.isCharacters()) { String clients = event.asCharacters().getData(); if (clients != null && !clients.equals("")) { clusternode.setMemCachedClients(clients.split(",")); } r.nextEvent(); } continue; } } if (event.isEndElement()) { EndElement end = event.asEndElement(); if (node != null && end.getName().getLocalPart().equalsIgnoreCase("client")) { memcachedClientconfigs.add(node); Logger.info(new StringBuilder().append(" add memcachedClient config :").append(node.getName())); continue; } if (socketnode != null && end.getName().getLocalPart().equalsIgnoreCase("socketpool")) { memcachedClientSocketPoolConfigs.add(socketnode); Logger.info(new StringBuilder().append(" add socketpool config :").append(socketnode.getName())); continue; } if (clusternode != null && end.getName().getLocalPart().equalsIgnoreCase("cluster")) { memcachedClientClusterConfig.add(clusternode); Logger.info(new StringBuilder().append(" add cluster config :").append(clusternode.getName())); continue; } } } } catch (Exception e) { Logger.error(new StringBuilder("MemcachedManager loadConfig error !").append(" config url :").append(url.getFile()).toString()); node = null; } finally { try { if (r != null) r.close(); if (in != null) in.close(); r = null; in = null; } catch (Exception ex) { throw new RuntimeException("processConfigURL error !", ex); } } } | 19,488 |
1 | private void copyLocalFile(File sourceFile, File destFile) throws IOException { if (!destFile.exists()) { destFile.createNewFile(); } FileChannel source = null; FileChannel destination = null; try { source = new FileInputStream(sourceFile).getChannel(); destination = new FileOutputStream(destFile).getChannel(); destination.transferFrom(source, 0, source.size()); } finally { if (source != null) { source.close(); } if (destination != null) { destination.close(); } } } | public void write(File file) throws Exception { if (medooFile != null) { if (!medooFile.renameTo(file)) { BufferedInputStream in = null; BufferedOutputStream out = null; try { in = new BufferedInputStream(new FileInputStream(medooFile)); out = new BufferedOutputStream(new FileOutputStream(file)); IOUtils.copy(in, out); } finally { if (in != null) { try { in.close(); } catch (IOException e) { } } if (out != null) { try { out.close(); } catch (IOException e) { } } } } } else { throw new FileUploadException("Cannot write uploaded file to disk!"); } } | 19,489 |
1 | public static String encryptSHA(String pwd) throws NoSuchAlgorithmException { MessageDigest d = java.security.MessageDigest.getInstance("SHA-1"); d.reset(); d.update(pwd.getBytes()); BASE64Encoder encoder = new BASE64Encoder(); return encoder.encode(d.digest()); } | private void getRandomGUID(boolean secure) { MessageDigest md5 = null; final StringBuilder sbValueBeforeMD5 = new StringBuilder(); try { md5 = MessageDigest.getInstance("MD5"); } catch (NoSuchAlgorithmException e) { logger.fatal("", e); return; } try { final long time = System.currentTimeMillis(); long rand = 0; if (secure) { rand = mySecureRand.nextLong(); } else { rand = myRand.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()); final byte[] array = md5.digest(); final StringBuilder sb = new StringBuilder(); for (int j = 0; j < array.length; ++j) { final int b = array[j] & 0xFF; if (b < 0x10) { sb.append('0'); } sb.append(Integer.toHexString(b)); } valueAfterMD5 = sb.toString(); } catch (Exception e) { logger.fatal("", e); } } | 19,490 |
0 | private long getLastModification() { try { if (connection == null) connection = url.openConnection(); return connection.getLastModified(); } catch (IOException e) { LOG.warn("URL could not be opened: " + e.getMessage(), e); return 0; } } | public static int[] sortAscending(double input[]) { int[] order = new int[input.length]; for (int i = 0; i < order.length; i++) order[i] = i; for (int i = input.length; --i >= 0; ) { for (int j = 0; j < i; j++) { if (input[j] > input[j + 1]) { double mem = input[j]; input[j] = input[j + 1]; input[j + 1] = mem; int id = order[j]; order[j] = order[j + 1]; order[j + 1] = id; } } } return order; } | 19,491 |
1 | private void updateUser(AddEditUserForm addform, HttpServletRequest request) throws Exception { Session hbsession = HibernateUtil.currentSession(); try { Transaction tx = hbsession.beginTransaction(); NvUsers user = (NvUsers) hbsession.load(NvUsers.class, addform.getLogin()); if (!addform.getPassword().equalsIgnoreCase("")) { 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); } user.setPassword(app.toString()); } ActionErrors errors = new ActionErrors(); HashMap cAttrs = addform.getCustomAttrs(); Query q1 = hbsession.createQuery("from org.nodevision.portal.hibernate.om.NvCustomAttrs as a"); Iterator attrs = q1.iterate(); HashMap attrInfos = new HashMap(); while (attrs.hasNext()) { NvCustomAttrs element = (NvCustomAttrs) attrs.next(); attrInfos.put(element.getAttrName(), element.getAttrType()); NvCustomValuesId id = new NvCustomValuesId(); id.setNvUsers(user); NvCustomValues value = new NvCustomValues(); id.setNvCustomAttrs(element); value.setId(id); if (element.getAttrType().equalsIgnoreCase("String")) { ByteArrayOutputStream bout = new ByteArrayOutputStream(); ObjectOutputStream serializer = new ObjectOutputStream(bout); serializer.writeObject(cAttrs.get(element.getAttrName()).toString()); value.setAttrValue(Hibernate.createBlob(bout.toByteArray())); } else if (element.getAttrType().equalsIgnoreCase("Boolean")) { Boolean valueBoolean = Boolean.FALSE; if (cAttrs.get(element.getAttrName()) != null) { valueBoolean = Boolean.TRUE; } ByteArrayOutputStream bout = new ByteArrayOutputStream(); ObjectOutputStream serializer = new ObjectOutputStream(bout); serializer.writeObject(valueBoolean); value.setAttrValue(Hibernate.createBlob(bout.toByteArray())); } else if (element.getAttrType().equalsIgnoreCase("Date")) { Date date = new Date(0); if (!cAttrs.get(element.getAttrName()).toString().equalsIgnoreCase("")) { String bdate = cAttrs.get(element.getAttrName()).toString(); SimpleDateFormat df = new SimpleDateFormat("dd-MM-yyyy"); date = df.parse(bdate); } ByteArrayOutputStream bout = new ByteArrayOutputStream(); ObjectOutputStream serializer = new ObjectOutputStream(bout); serializer.writeObject(date); value.setAttrValue(Hibernate.createBlob(bout.toByteArray())); } hbsession.saveOrUpdate(value); hbsession.flush(); } String bdate = addform.getUser_bdate(); SimpleDateFormat df = new SimpleDateFormat("dd-MM-yyyy"); Date parsedDate = df.parse(bdate); user.setTimezone(addform.getTimezone()); user.setLocale(addform.getLocale()); user.setBdate(new BigDecimal(parsedDate.getTime())); user.setGender(addform.getUser_gender()); user.setEmployer(addform.getEmployer()); user.setDepartment(addform.getDepartment()); user.setJobtitle(addform.getJobtitle()); user.setNamePrefix(addform.getName_prefix()); user.setNameGiven(addform.getName_given()); user.setNameFamily(addform.getName_famliy()); user.setNameMiddle(addform.getName_middle()); user.setNameSuffix(addform.getName_suffix()); user.setHomeName(addform.getHome_name()); user.setHomeStreet(addform.getHome_street()); user.setHomeStateprov(addform.getHome_stateprov()); user.setHomePostalcode(addform.getHome_postalcode().equalsIgnoreCase("") ? new Integer(0) : new Integer(addform.getHome_postalcode())); user.setHomeOrganization(addform.getHome_organization_name()); user.setHomeCountry(addform.getHome_country()); user.setHomeCity(addform.getHome_city()); user.setHomePhoneIntcode((addform.getHome_phone_intcode().equalsIgnoreCase("")) ? new Integer(0) : Integer.valueOf(addform.getHome_phone_intcode())); user.setHomePhoneLoccode((addform.getHome_phone_loccode().equalsIgnoreCase("")) ? new Integer(0) : Integer.valueOf(addform.getHome_phone_loccode())); user.setHomePhoneNumber((addform.getHome_phone_number().equalsIgnoreCase("")) ? new Integer(0) : Integer.valueOf(addform.getHome_phone_number())); user.setHomePhoneExt((addform.getHome_phone_ext().equalsIgnoreCase("")) ? new Integer(0) : Integer.valueOf(addform.getHome_phone_ext())); user.setHomePhoneComment(addform.getHome_phone_commment()); user.setHomeFaxIntcode((addform.getHome_fax_intcode().equalsIgnoreCase("")) ? new Integer(0) : Integer.valueOf(addform.getHome_fax_intcode())); user.setHomeFaxLoccode((addform.getHome_fax_loccode().equalsIgnoreCase("")) ? new Integer(0) : Integer.valueOf(addform.getHome_fax_loccode())); user.setHomeFaxNumber((addform.getHome_fax_number().equalsIgnoreCase("")) ? new Integer(0) : Integer.valueOf(addform.getHome_fax_number())); user.setHomeFaxExt((addform.getHome_fax_ext().equalsIgnoreCase("")) ? new Integer(0) : Integer.valueOf(addform.getHome_fax_ext())); user.setHomeFaxComment(addform.getHome_fax_commment()); user.setHomeMobileIntcode((addform.getHome_mobile_intcode().equalsIgnoreCase("")) ? new Integer(0) : Integer.valueOf(addform.getHome_mobile_intcode())); user.setHomeMobileLoccode((addform.getHome_mobile_loccode().equalsIgnoreCase("")) ? new Integer(0) : Integer.valueOf(addform.getHome_mobile_loccode())); user.setHomeMobileNumber((addform.getHome_mobile_number().equalsIgnoreCase("")) ? new Integer(0) : Integer.valueOf(addform.getHome_mobile_number())); user.setHomeMobileExt((addform.getHome_mobile_ext().equalsIgnoreCase("")) ? new Integer(0) : Integer.valueOf(addform.getHome_mobile_ext())); user.setHomeMobileComment(addform.getHome_mobile_commment()); user.setHomePagerIntcode((addform.getHome_pager_intcode().equalsIgnoreCase("")) ? new Integer(0) : Integer.valueOf(addform.getHome_pager_intcode())); user.setHomePagerLoccode((addform.getHome_pager_loccode().equalsIgnoreCase("")) ? new Integer(0) : Integer.valueOf(addform.getHome_pager_loccode())); user.setHomePagerNumber((addform.getHome_pager_number().equalsIgnoreCase("")) ? new Integer(0) : Integer.valueOf(addform.getHome_pager_number())); user.setHomePagerExt((addform.getHome_pager_ext().equalsIgnoreCase("")) ? new Integer(0) : Integer.valueOf(addform.getHome_pager_ext())); user.setHomePagerComment(addform.getHome_pager_commment()); user.setHomeUri(addform.getHome_uri()); user.setHomeEmail(addform.getHome_email()); user.setBusinessName(addform.getBusiness_name()); user.setBusinessStreet(addform.getBusiness_street()); user.setBusinessStateprov(addform.getBusiness_stateprov()); user.setBusinessPostalcode((addform.getBusiness_postalcode().equalsIgnoreCase("")) ? new Integer(0) : Integer.valueOf(addform.getBusiness_postalcode())); user.setBusinessOrganization(addform.getBusiness_organization_name()); user.setBusinessCountry(addform.getBusiness_country()); user.setBusinessCity(addform.getBusiness_city()); user.setBusinessPhoneIntcode((addform.getBusiness_phone_intcode().equalsIgnoreCase("")) ? new Integer(0) : Integer.valueOf(addform.getBusiness_phone_intcode())); user.setBusinessPhoneLoccode((addform.getBusiness_phone_loccode().equalsIgnoreCase("")) ? new Integer(0) : Integer.valueOf(addform.getBusiness_phone_loccode())); user.setBusinessPhoneNumber((addform.getBusiness_phone_number().equalsIgnoreCase("")) ? new Integer(0) : Integer.valueOf(addform.getBusiness_phone_number())); user.setBusinessPhoneExt((addform.getBusiness_phone_ext().equalsIgnoreCase("")) ? new Integer(0) : Integer.valueOf(addform.getBusiness_phone_ext())); user.setBusinessPhoneComment(addform.getBusiness_phone_commment()); user.setBusinessFaxIntcode((addform.getBusiness_fax_intcode().equalsIgnoreCase("")) ? new Integer(0) : Integer.valueOf(addform.getBusiness_fax_intcode())); user.setBusinessFaxLoccode((addform.getBusiness_fax_loccode().equalsIgnoreCase("")) ? new Integer(0) : Integer.valueOf(addform.getBusiness_fax_loccode())); user.setBusinessFaxNumber((addform.getBusiness_fax_number().equalsIgnoreCase("")) ? new Integer(0) : Integer.valueOf(addform.getBusiness_fax_number())); user.setBusinessFaxExt((addform.getBusiness_fax_ext().equalsIgnoreCase("")) ? new Integer(0) : Integer.valueOf(addform.getBusiness_fax_ext())); user.setBusinessFaxComment(addform.getBusiness_fax_commment()); user.setBusinessMobileIntcode((addform.getBusiness_mobile_intcode().equalsIgnoreCase("")) ? new Integer(0) : Integer.valueOf(addform.getBusiness_mobile_intcode())); user.setBusinessMobileLoccode((addform.getBusiness_mobile_loccode().equalsIgnoreCase("")) ? new Integer(0) : Integer.valueOf(addform.getBusiness_mobile_loccode())); user.setBusinessMobileNumber((addform.getBusiness_mobile_number().equalsIgnoreCase("")) ? new Integer(0) : Integer.valueOf(addform.getBusiness_mobile_number())); user.setBusinessMobileExt((addform.getBusiness_mobile_ext().equalsIgnoreCase("")) ? new Integer(0) : Integer.valueOf(addform.getBusiness_mobile_ext())); user.setBusinessMobileComment(addform.getBusiness_mobile_commment()); user.setBusinessPagerIntcode((addform.getBusiness_pager_intcode().equalsIgnoreCase("")) ? new Integer(0) : Integer.valueOf(addform.getBusiness_pager_intcode())); user.setBusinessPagerLoccode((addform.getBusiness_pager_loccode().equalsIgnoreCase("")) ? new Integer(0) : Integer.valueOf(addform.getBusiness_pager_loccode())); user.setBusinessPagerNumber((addform.getBusiness_pager_number().equalsIgnoreCase("")) ? new Integer(0) : Integer.valueOf(addform.getBusiness_pager_number())); user.setBusinessPagerExt((addform.getBusiness_pager_ext().equalsIgnoreCase("")) ? new Integer(0) : Integer.valueOf(addform.getBusiness_pager_ext())); user.setBusinessPagerComment(addform.getBusiness_pager_commment()); user.setBusinessUri(addform.getBusiness_uri()); user.setBusinessEmail(addform.getBusiness_email()); String hqlDelete = "delete org.nodevision.portal.hibernate.om.NvUserRoles where login = :login"; int deletedEntities = hbsession.createQuery(hqlDelete).setString("login", user.getLogin()).executeUpdate(); String[] selectedGroups = addform.getSelectedGroups(); Set newGroups = new HashSet(); for (int i = 0; i < selectedGroups.length; i++) { NvUserRolesId userroles = new NvUserRolesId(); userroles.setNvUsers(user); userroles.setNvRoles((NvRoles) hbsession.load(NvRoles.class, selectedGroups[i])); NvUserRoles newRole = new NvUserRoles(); newRole.setId(userroles); newGroups.add(newRole); } user.setSetOfNvUserRoles(newGroups); hbsession.update(user); hbsession.flush(); if (!hbsession.connection().getAutoCommit()) { tx.commit(); } } finally { HibernateUtil.closeSession(); } } | public static String createMD5(String str) { String sig = null; String strSalt = str + StaticBox.getsSalt(); try { MessageDigest md5 = MessageDigest.getInstance("MD5"); md5.update(strSalt.getBytes(), 0, strSalt.length()); byte byteData[] = md5.digest(); StringBuffer sb = new StringBuffer(); for (int i = 0; i < byteData.length; i++) { sb.append(Integer.toString((byteData[i] & 0xff) + 0x100, 16).substring(1)); } sig = sb.toString(); } catch (NoSuchAlgorithmException e) { System.err.println("Can not use md5 algorithm"); } return sig; } | 19,492 |
0 | public void beforeMethod(TestBase testBase) throws IOException { TFileFactory fileFactory = new TFileFactory(new InMemoryFileSystem()); ftpServer.cleanFileSystem(fileFactory); TDirectory rootDir = fileFactory.dir("/"); testBase.inject(rootDir); FTPClient ftpClient = new FTPClient(); ftpClient.connect("localhost", 8021); ftpClient.login("anonymous", "test@test.com"); testBase.inject(ftpClient); } | public Graph getGraph(URL urlFilename) throws MraldException { try { System.out.print("DBGraphReader: gettingGraph using url"); InputStream inUrl = urlFilename.openStream(); XMLGraphReader gr = new XMLGraphReader(); gr.setNodeType(DefaultTreeNode.class); Graph graph = gr.loadGraph(inUrl); return graph; } catch (java.io.FileNotFoundException e) { throw new MraldException(e.getMessage()); } catch (java.io.IOException e) { throw new MraldException(e.getMessage()); } } | 19,493 |
0 | private String getMd5(String base64image) { String token = null; try { MessageDigest md5 = MessageDigest.getInstance("MD5"); md5.update(base64image.getBytes()); BigInteger hash = new BigInteger(1, md5.digest()); token = hash.toString(16); } catch (NoSuchAlgorithmException nsae) { } return token; } | public static void copyFile(String fromFilePath, String toFilePath, boolean overwrite) throws IOException { File fromFile = new File(fromFilePath); File toFile = new File(toFilePath); if (!fromFile.exists()) throw new IOException("FileCopy: " + "no such source file: " + fromFilePath); if (!fromFile.isFile()) throw new IOException("FileCopy: " + "can't copy directory: " + fromFilePath); if (!fromFile.canRead()) throw new IOException("FileCopy: " + "source file is unreadable: " + fromFilePath); if (toFile.isDirectory()) toFile = new File(toFile, fromFile.getName()); if (toFile.exists()) { if (!overwrite) { throw new IOException(toFilePath + " already exists!"); } if (!toFile.canWrite()) { throw new IOException("FileCopy: destination file is unwriteable: " + toFilePath); } String parent = toFile.getParent(); if (parent == null) { parent = System.getProperty("user.dir"); } File dir = new File(parent); if (!dir.exists()) { throw new IOException("FileCopy: destination directory doesn't exist: " + parent); } if (dir.isFile()) { throw new IOException("FileCopy: destination is not a directory: " + parent); } if (!dir.canWrite()) { throw new IOException("FileCopy: destination directory is unwriteable: " + parent); } } FileInputStream from = null; FileOutputStream to = null; try { from = new FileInputStream(fromFile); to = new FileOutputStream(toFile); byte[] buffer = new byte[4096]; int bytesRead; while ((bytesRead = from.read(buffer)) != -1) to.write(buffer, 0, bytesRead); } finally { long lastModified = fromFile.lastModified(); toFile.setLastModified(lastModified); if (from != null) { try { from.close(); } catch (IOException e) { } } if (to != null) { try { to.close(); } catch (IOException e) { } } } } | 19,494 |
0 | public Configuration load(URL url) throws ConfigurationException { LOG.info("Configuring from url : " + url.toString()); try { return load(url.openStream(), url.toString()); } catch (IOException ioe) { throw new ConfigurationException("Could not configure from URL : " + url, ioe); } } | public void trimAndWriteNewSff(OutputStream out) throws IOException { TrimParser trimmer = new TrimParser(); SffParser.parseSFF(untrimmedSffFile, trimmer); tempOut.close(); headerBuilder.withNoIndex().numberOfReads(numberOfTrimmedReads); SffWriter.writeCommonHeader(headerBuilder.build(), out); InputStream in = null; try { in = new FileInputStream(tempReadDataFile); IOUtils.copyLarge(in, out); } finally { IOUtil.closeAndIgnoreErrors(in); } } | 19,495 |
1 | public static void copyFile(File sourceFile, File destFile) throws IOException { if (!destFile.exists()) { destFile.createNewFile(); } FileChannel source = null; FileChannel destination = null; try { source = new FileInputStream(sourceFile).getChannel(); destination = new FileOutputStream(destFile).getChannel(); destination.transferFrom(source, 0, source.size()); } finally { if (source != null) { source.close(); } if (destination != null) { destination.close(); } } } | public static void copy(String inputFile, String outputFile) throws Exception { try { FileReader in = new FileReader(inputFile); FileWriter out = new FileWriter(outputFile); int c; while ((c = in.read()) != -1) out.write(c); in.close(); out.close(); } catch (Exception e) { throw new Exception("Could not copy " + inputFile + " into " + outputFile + " because:\n" + e.getMessage()); } } | 19,496 |
1 | private void copyPhoto(final IPhoto photo, final Map.Entry<String, Integer> size) { final File fileIn = new File(storageService.getPhotoPath(photo, storageService.getOriginalDir())); final File fileOut = new File(storageService.getPhotoPath(photo, size.getKey())); InputStream fileInputStream; OutputStream fileOutputStream; try { fileInputStream = new FileInputStream(fileIn); fileOutputStream = new FileOutputStream(fileOut); IOUtils.copy(fileInputStream, fileOutputStream); fileInputStream.close(); fileOutputStream.close(); } catch (final IOException e) { log.error("file io exception", e); return; } } | public static void copyFile(File file, String pathExport) throws IOException { File out = new File(pathExport); FileChannel sourceChannel = new FileInputStream(file).getChannel(); FileChannel destinationChannel = new FileOutputStream(out).getChannel(); sourceChannel.transferTo(0, sourceChannel.size(), destinationChannel); sourceChannel.close(); destinationChannel.close(); } | 19,497 |
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, NULL_OUTPUT_STREAM); } finally { IOUtils.close(in); } return checksum; } | private static void copyFile(File sourceFile, File targetFile) throws FileSaveException { try { FileInputStream inputStream = new FileInputStream(sourceFile); FileOutputStream outputStream = new FileOutputStream(targetFile); FileChannel readableChannel = inputStream.getChannel(); FileChannel writableChannel = outputStream.getChannel(); writableChannel.truncate(0); writableChannel.transferFrom(readableChannel, 0, readableChannel.size()); inputStream.close(); outputStream.close(); } catch (IOException ioException) { String exceptionMessage = "An error occurred when copying from the file \"" + sourceFile.getAbsolutePath() + "\" to the file \"" + targetFile.getAbsolutePath() + "\"."; throw new FileSaveException(exceptionMessage, ioException); } } | 19,498 |
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 static boolean cpy(File a, File b) { try { FileInputStream astream = null; FileOutputStream bstream = null; try { astream = new FileInputStream(a); bstream = new FileOutputStream(b); long flength = a.length(); int bufsize = (int) Math.min(flength, 1024); byte buf[] = new byte[bufsize]; long n = 0; while (n < flength) { int naread = astream.read(buf); bstream.write(buf, 0, naread); n += naread; } } finally { if (astream != null) astream.close(); if (bstream != null) bstream.close(); } } catch (IOException e) { e.printStackTrace(); return false; } return true; } | 19,499 |
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