List of usage examples for java.io BufferedWriter flush
public void flush() throws IOException
From source file:Main.java
public static void main(String[] args) throws Exception { Socket socket = new Socket("localhost", 12900); System.out.println("Started client socket at " + socket.getLocalSocketAddress()); BufferedReader socketReader = new BufferedReader(new InputStreamReader(socket.getInputStream())); BufferedWriter socketWriter = new BufferedWriter(new OutputStreamWriter(socket.getOutputStream())); BufferedReader consoleReader = new BufferedReader(new InputStreamReader(System.in)); String promptMsg = "Please enter a message (Bye to quit):"; String outMsg = null;// www . jav a 2 s .c o m System.out.print(promptMsg); while ((outMsg = consoleReader.readLine()) != null) { if (outMsg.equalsIgnoreCase("bye")) { break; } // Add a new line to the message to the server, // because the server reads one line at a time. socketWriter.write(outMsg); socketWriter.write("\n"); socketWriter.flush(); // Read and display the message from the server String inMsg = socketReader.readLine(); System.out.println("Server: " + inMsg); System.out.println(); // Print a blank line System.out.print(promptMsg); } socket.close(); }
From source file:at.newmedialab.ldpath.template.LDTemplate.java
public static void main(String[] args) { Options options = buildOptions();//from w w w . j ava 2 s.c o m CommandLineParser parser = new PosixParser(); try { CommandLine cmd = parser.parse(options, args); Level logLevel = Level.WARN; if (cmd.hasOption("loglevel")) { String logLevelName = cmd.getOptionValue("loglevel"); if ("DEBUG".equals(logLevelName.toUpperCase())) { logLevel = Level.DEBUG; } else if ("INFO".equals(logLevelName.toUpperCase())) { logLevel = Level.INFO; } else if ("WARN".equals(logLevelName.toUpperCase())) { logLevel = Level.WARN; } else if ("ERROR".equals(logLevelName.toUpperCase())) { logLevel = Level.ERROR; } else { log.error("unsupported log level: {}", logLevelName); } } if (logLevel != null) { for (String logname : new String[] { "at", "org", "net", "com" }) { ch.qos.logback.classic.Logger logger = (ch.qos.logback.classic.Logger) LoggerFactory .getLogger(logname); logger.setLevel(logLevel); } } File template = null; if (cmd.hasOption("template")) { template = new File(cmd.getOptionValue("template")); } GenericSesameBackend backend; if (cmd.hasOption("store")) { backend = new LDPersistentBackend(new File(cmd.getOptionValue("store"))); } else { backend = new LDMemoryBackend(); } Resource context = null; if (cmd.hasOption("context")) { context = backend.getRepository().getValueFactory().createURI(cmd.getOptionValue("context")); } BufferedWriter out = null; if (cmd.hasOption("out")) { File of = new File(cmd.getOptionValue("out")); if (of.canWrite()) { out = new BufferedWriter(new FileWriter(of)); } else { log.error("cannot write to output file {}", of); System.exit(1); } } else { out = new BufferedWriter(new OutputStreamWriter(System.out)); } if (backend != null && context != null && template != null) { TemplateEngine<Value> engine = new TemplateEngine<Value>(backend); engine.setDirectoryForTemplateLoading(template.getParentFile()); engine.processFileTemplate(context, template.getName(), out); out.flush(); out.close(); } if (backend instanceof LDPersistentBackend) { ((LDPersistentBackend) backend).shutdown(); } } catch (ParseException e) { System.err.println("invalid arguments"); HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("LDQuery", options, true); } catch (FileNotFoundException e) { System.err.println("file or program could not be found"); HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("LDQuery", options, true); } catch (IOException e) { System.err.println("could not access file"); e.printStackTrace(System.err); } catch (TemplateException e) { System.err.println("error while processing template"); e.printStackTrace(System.err); } }
From source file:fr.eo.util.dumper.JSONDumper.java
/** * @param args main args//from w ww .j av a 2 s . com */ public static void main(String[] args) { String appName = args[0]; String jdbcConnectionType = args.length > 1 ? args[1] : "jtds"; System.out.println("Starting dumper ..."); try (Connection conn = getConnection(jdbcConnectionType)) { System.out.println("Getting database connection ..."); List<RequestDefinitionBean> requests = RequestDefinitionParser.getRequests(appName); baseFolder = RequestDefinitionParser.getAppBaseDir(appName) + "/"; System.out.println("Reading old table dumps..."); Map<String, JsonTableDump> oldTables = JSONDeltaDumper.readOldTables(baseFolder); List<JsonTableDump> newTables = new ArrayList<>(); for (RequestDefinitionBean request : requests) { try (Statement stmt = conn.createStatement()) { BufferedWriter bw = getWriter(request.name, baseFolder); if (!request.disabled) { System.out.println("Dumping " + request.name + "..."); ResultSet rs = stmt.executeQuery(request.sql); JsonTableWritable dump = new JsonTableWritable(); dump.name = request.table; while (rs.next()) { int pos = 0; for (String fieldName : request.fields) { Object obj = getFieldValue(request, pos, rs, fieldName); dump.addColumn(obj); pos++; } dump.commit(); } bw.append(dump.toJson()); newTables.add(dump); bw.flush(); bw.close(); } else { System.out.println("Skiping " + request.name + "..."); } } System.out.println("done."); } newTables.addAll(BlueprintDumper.dump(baseFolder)); newTables.addAll(TranslationsDumper.dump(baseFolder, jdbcConnectionType)); System.out.println("Computing delta..."); JSONDeltaDumper.computeDelta(oldTables, newTables, baseFolder); } catch (SQLException | ClassNotFoundException | IOException e) { e.printStackTrace(); } }
From source file:fr.eo.util.dumper.Dumper.java
/** * @param args// w w w . ja v a 2s . c o m */ public static void main(String[] args) { String appName = args[0]; System.out.println("Starting dumper ..."); Statement stmt = null; try { System.out.println("Getting database connection ..."); Connection conn = getJtdsConnection(); List<RequestDefinitionBean> requests = RequestDefinitionParser.getRequests(appName); assetFolder = RequestDefinitionParser.getAppBaseDir(appName) + "assets/"; for (RequestDefinitionBean request : requests) { int currentFileSize = 0, cpt = 1; stmt = conn.createStatement(); System.out.println("Dumping " + request.name + "..."); ResultSet rs = stmt.executeQuery(request.sql); BufferedWriter bw = getWriter(request.name, cpt); bw.append(COPYRIGHTS); currentFileSize += COPYRIGHTS.length(); bw.append("--" + request.name + "\n"); while (rs.next()) { StringBuilder sb = new StringBuilder(); sb.append("INSERT INTO "); sb.append(request.table).append(" VALUES ("); int pos = 0; for (String fieldName : request.fields) { String str = getFieldValue(request, pos, rs, fieldName); sb.append(str); pos++; if (pos < request.fields.size()) { sb.append(","); } } sb.append(");\n"); currentFileSize += sb.length(); bw.append(sb.toString()); bw.flush(); if (currentFileSize > MAX_FILE_SIZE) { bw.close(); bw = getWriter(request.name, ++cpt); bw.append(COPYRIGHTS); bw.append("--" + request.name + "\n"); currentFileSize = COPYRIGHTS.length(); } } bw.flush(); bw.close(); } System.out.println("done."); } catch (SQLException e) { e.printStackTrace(); } catch (ClassNotFoundException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } finally { if (stmt != null) { try { stmt.close(); } catch (SQLException e) { e.printStackTrace(); } } } DumpFilesDescriptor descriptor = new DumpFilesDescriptor(); descriptor.lineNumbers = getDumpLinesNumber(); descriptor.dumpFileNames = dumpFileNames; writeDescriptorFile(descriptor); System.out.println("nb :" + descriptor.lineNumbers); }
From source file:di.uniba.it.tee2.wiki.Wikidump2Text.java
/** * @param args the command line arguments *//*from www.j a va 2s . c o m*/ public static void main(String[] args) { try { CommandLine cmd = cmdParser.parse(options, args); if (cmd.hasOption("l") && cmd.hasOption("d") && cmd.hasOption("o")) { encoding = cmd.getOptionValue("e", "UTF-8"); int counter = 0; try { BufferedWriter writer = new BufferedWriter(new OutputStreamWriter( new GZIPOutputStream(new FileOutputStream(cmd.getOptionValue("o"))), "UTF-8")); WikipediaDumpIterator it = new WikipediaDumpIterator(new File(cmd.getOptionValue("d")), encoding); PageCleaner cleaner = PageCleanerWrapper.getInstance(cmd.getOptionValue("l")); while (it.hasNext()) { WikiPage wikiPage = it.next(); ParsedPage parsedPage = wikiPage.getParsedPage(); if (parsedPage != null) { String title = wikiPage.getTitle(); if (!title.matches(notValidTitle)) { if (parsedPage.getText() != null) { writer.append(cleaner.clean(parsedPage.getText())); writer.newLine(); writer.newLine(); counter++; if (counter % 10000 == 0) { System.out.println(counter); writer.flush(); } } } } } writer.flush(); writer.close(); } catch (Exception ex) { Logger.getLogger(Wikidump2Text.class.getName()).log(Level.SEVERE, null, ex); } System.out.println("Indexed pages: " + counter); } else { HelpFormatter helpFormatter = new HelpFormatter(); helpFormatter.printHelp("Wikipedia dump to text", options, true); } } catch (ParseException ex) { Logger.getLogger(Wikidump2Text.class.getName()).log(Level.SEVERE, null, ex); } }
From source file:com.nextdoor.bender.S3SnsNotifier.java
public static void main(String[] args) throws ParseException, InterruptedException, IOException { formatter = DateTimeFormat.forPattern("yyyy-MM-dd'T'HH:mm:ss.SSS'Z'").withZoneUTC(); /*//from w ww . j av a 2s . c om * Parse cli arguments */ Options options = new Options(); options.addOption(Option.builder().longOpt("bucket").hasArg().required() .desc("Name of S3 bucket to list s3 objects from").build()); options.addOption(Option.builder().longOpt("key-file").hasArg().required() .desc("Local file of S3 keys to process").build()); options.addOption( Option.builder().longOpt("sns-arn").hasArg().required().desc("SNS arn to publish to").build()); options.addOption(Option.builder().longOpt("throttle-ms").hasArg() .desc("Amount of ms to wait between publishing to SNS").build()); options.addOption(Option.builder().longOpt("processed-file").hasArg() .desc("Local file to use to store procssed S3 object names").build()); options.addOption(Option.builder().longOpt("skip-processed").hasArg(false) .desc("Whether to skip S3 objects that have been processed").build()); options.addOption( Option.builder().longOpt("dry-run").hasArg(false).desc("If set do not publish to SNS").build()); CommandLineParser parser = new DefaultParser(); CommandLine cmd = parser.parse(options, args); String bucket = cmd.getOptionValue("bucket"); String keyFile = cmd.getOptionValue("key-file"); String snsArn = cmd.getOptionValue("sns-arn"); String processedFile = cmd.getOptionValue("processed-file", null); boolean skipProcessed = cmd.hasOption("skip-processed"); dryRun = cmd.hasOption("dry-run"); long throttle = Long.parseLong(cmd.getOptionValue("throttle-ms", "-1")); if (processedFile != null) { File file = new File(processedFile); if (!file.exists()) { logger.debug("creating local file to store processed s3 object names: " + processedFile); file.createNewFile(); } } /* * Import S3 keys that have been processed */ if (skipProcessed && processedFile != null) { try (BufferedReader br = new BufferedReader(new FileReader(processedFile))) { String line; while ((line = br.readLine()) != null) { alreadyPublished.add(line.trim()); } } } /* * Setup writer for file containing processed S3 keys */ FileWriter fw = null; BufferedWriter bw = null; if (processedFile != null) { fw = new FileWriter(processedFile, true); bw = new BufferedWriter(fw); } /* * Create clients */ AmazonS3Client s3Client = new AmazonS3Client(); AmazonSNSClient snsClient = new AmazonSNSClient(); /* * Get S3 object list */ try (BufferedReader br = new BufferedReader(new FileReader(keyFile))) { String line; while ((line = br.readLine()) != null) { String key = line.trim(); if (alreadyPublished.contains(key)) { logger.info("skipping " + key); } ObjectMetadata om = s3Client.getObjectMetadata(bucket, key); S3EventNotification s3Notification = getS3Notification(key, bucket, om.getContentLength()); String json = s3Notification.toJson(); /* * Publish to SNS */ if (publish(snsArn, json, snsClient, key) && processedFile != null) { bw.write(key + "\n"); bw.flush(); } if (throttle != -1) { Thread.sleep(throttle); } } } if (processedFile != null) { bw.close(); fw.close(); } }
From source file:main.java.RMDupper.java
public static void main(String[] args) throws IOException { System.err.println("DeDup v" + VERSION); // the command line parameters Options helpOptions = new Options(); helpOptions.addOption("h", "help", false, "show this help page"); Options options = new Options(); options.addOption("h", "help", false, "show this help page"); options.addOption("i", "input", true, "the input file if this option is not specified,\nthe input is expected to be piped in"); options.addOption("o", "output", true, "the output folder. Has to be specified if input is set."); options.addOption("m", "merged", false, "the input only contains merged reads.\n If this option is specified read names are not examined for prefixes.\n Both the start and end of the aligment are considered for all reads."); options.addOption("v", "version", false, "the version of DeDup."); HelpFormatter helpformatter = new HelpFormatter(); CommandLineParser parser = new BasicParser(); try {/*from ww w. j a v a 2 s .c o m*/ CommandLine cmd = parser.parse(helpOptions, args); if (cmd.hasOption('h')) { helpformatter.printHelp(CLASS_NAME, options); System.exit(0); } } catch (ParseException e1) { } String input = ""; String outputpath = ""; Boolean merged = Boolean.FALSE; try { CommandLine cmd = parser.parse(options, args); if (cmd.hasOption('i')) { input = cmd.getOptionValue('i'); piped = false; } if (cmd.hasOption('o')) { outputpath = cmd.getOptionValue('o'); } if (cmd.hasOption('m')) { merged = Boolean.TRUE; } if (cmd.hasOption('v')) { System.out.println("DeDup v" + VERSION); System.exit(0); } } catch (ParseException e) { helpformatter.printHelp(CLASS_NAME, options); System.err.println(e.getMessage()); System.exit(0); } DecimalFormat df = new DecimalFormat("##.##"); if (piped) { RMDupper rmdup = new RMDupper(System.in, System.out, merged); rmdup.readSAMFile(); System.err.println("We are in piping mode!"); System.err.println("Total reads: " + rmdup.dupStats.total + "\n"); System.err.println("Reverse removed: " + rmdup.dupStats.removed_reverse + "\n"); System.err.println("Forward removed: " + rmdup.dupStats.removed_forward + "\n"); System.err.println("Merged removed: " + rmdup.dupStats.removed_merged + "\n"); System.err.println("Total removed: " + (rmdup.dupStats.removed_forward + rmdup.dupStats.removed_merged + rmdup.dupStats.removed_reverse) + "\n"); if (rmdup.dupStats.removed_merged + rmdup.dupStats.removed_forward + rmdup.dupStats.removed_reverse == 0) { System.err.println("Duplication Rate: " + df.format(0.00)); } else { System.err.println("Duplication Rate: " + df.format((double) (rmdup.dupStats.removed_merged + rmdup.dupStats.removed_reverse + rmdup.dupStats.removed_forward) / (double) rmdup.dupStats.total)); } } else { if (outputpath.length() == 0) { System.err.println("The output folder has to be specified"); helpformatter.printHelp(CLASS_NAME, options); System.exit(0); } //Check whether we have a directory as output path, else produce error message and quit! File f = new File(outputpath); if (!f.isDirectory()) { System.err.println("The output folder should be a folder and not a file!"); System.exit(0); } File inputFile = new File(input); File outputFile = new File( outputpath + "/" + Files.getNameWithoutExtension(inputFile.getAbsolutePath()) + "_rmdup.bam"); File outputlog = new File( outputpath + "/" + Files.getNameWithoutExtension(inputFile.getAbsolutePath()) + ".log"); File outputhist = new File( outputpath + "/" + Files.getNameWithoutExtension(inputFile.getAbsolutePath()) + ".hist"); try { FileWriter fw = new FileWriter(outputlog); FileWriter histfw = new FileWriter(outputhist); BufferedWriter bfw = new BufferedWriter(fw); BufferedWriter histbfw = new BufferedWriter(histfw); RMDupper rmdup = new RMDupper(inputFile, outputFile, merged); rmdup.readSAMFile(); rmdup.inputSam.close(); rmdup.outputSam.close(); bfw.write("Total reads: " + rmdup.dupStats.total + "\n"); bfw.write("Reverse removed: " + rmdup.dupStats.removed_reverse + "\n"); bfw.write("Forward removed: " + rmdup.dupStats.removed_forward + "\n"); bfw.write("Merged removed: " + rmdup.dupStats.removed_merged + "\n"); bfw.write("Total removed: " + (rmdup.dupStats.removed_forward + rmdup.dupStats.removed_merged + rmdup.dupStats.removed_reverse) + "\n"); bfw.write("Duplication Rate: " + df.format((double) (rmdup.dupStats.removed_merged + rmdup.dupStats.removed_reverse + rmdup.dupStats.removed_forward) / (double) rmdup.dupStats.total)); bfw.flush(); bfw.close(); histbfw.write(rmdup.oc.getHistogram()); histbfw.flush(); histbfw.close(); System.out.println("Total reads: " + rmdup.dupStats.total + "\n"); System.out.println("Unmerged removed: " + (rmdup.dupStats.removed_forward + rmdup.dupStats.removed_reverse) + "\n"); System.out.println("Merged removed: " + rmdup.dupStats.removed_merged + "\n"); System.out.println("Total removed: " + (rmdup.dupStats.removed_forward + rmdup.dupStats.removed_merged + rmdup.dupStats.removed_reverse) + "\n"); if (rmdup.dupStats.removed_merged + rmdup.dupStats.removed_forward + rmdup.dupStats.removed_reverse == 0) { System.out.println("Duplication Rate: " + df.format(0.00)); } else { System.out.println("Duplication Rate: " + df.format((double) (rmdup.dupStats.removed_merged + rmdup.dupStats.removed_reverse + rmdup.dupStats.removed_forward) / (double) rmdup.dupStats.total)); } } catch (IOException e) { e.printStackTrace(); } } }
From source file:com.twentyn.chemicalClassifier.Runner.java
public static void main(String[] args) throws Exception { BufferedReader reader = new BufferedReader(new FileReader(args[0])); BufferedWriter writer = new BufferedWriter(new FileWriter(args[1])); try {/*from w w w. j a v a 2 s.c om*/ Oscar oscar = new Oscar(); String line = null; /* NOTE: this is exactly the wrong way to write a TSV reader. Caveat emptor. * See http://tburette.github.io/blog/2014/05/25/so-you-want-to-write-your-own-CSV-code/ * and then use org.apache.commons.csv.CSVParser instead. */ while ((line = reader.readLine()) != null) { // TSV means split on tabs! Nothing else will do. List<String> fields = Arrays.asList(line.split("\t")); // Choke if our invariants aren't satisfied. We expect ever line to have a name and an InChI. if (fields.size() != 2) { throw new RuntimeException( String.format("Found malformed line (all lines must have two fields: %s", line)); } String name = fields.get(1); List<ResolvedNamedEntity> entities = oscar.findAndResolveNamedEntities(name); System.out.println("**********"); System.out.println("Name: " + name); List<String> outputFields = new ArrayList<>(fields.size() + 1); outputFields.addAll(fields); if (entities.size() == 0) { System.out.println("No match"); outputFields.add("noMatch"); } else if (entities.size() == 1) { ResolvedNamedEntity entity = entities.get(0); NamedEntity ne = entity.getNamedEntity(); if (ne.getStart() != 0 || ne.getEnd() != name.length()) { System.out.println("Partial match"); printEntity(entity); outputFields.add("partialMatch"); } else { System.out.println("Exact match"); printEntity(entity); outputFields.add("exactMatch"); List<ChemicalStructure> structures = entity.getChemicalStructures(FormatType.STD_INCHI); for (ChemicalStructure s : structures) { outputFields.add(s.getValue()); } } } else { // Multiple matches found! System.out.println("Multiple matches"); for (ResolvedNamedEntity e : entities) { printEntity(e); } outputFields.add("multipleMatches"); } writer.write(String.join("\t", outputFields)); writer.newLine(); } } finally { writer.flush(); writer.close(); } }
From source file:com.era7.bioinfo.annotation.AutomaticQualityControl.java
public static void main(String[] args) { if (args.length != 4) { System.out.println("This program expects four parameters: \n" + "1. Gene annotation XML filename \n" + "2. Reference protein set (.fasta)\n" + "3. Output TXT filename\n" + "4. Initial Blast XML results filename (the one used at the very beginning of the semiautomatic annotation process)\n"); } else {// ww w .j a v a 2 s . co m BufferedWriter outBuff = null; try { File inFile = new File(args[0]); File fastaFile = new File(args[1]); File outFile = new File(args[2]); File blastFile = new File(args[3]); //Primero cargo todos los datos del archivo xml del blast BufferedReader buffReader = new BufferedReader(new FileReader(blastFile)); StringBuilder stBuilder = new StringBuilder(); String line = null; while ((line = buffReader.readLine()) != null) { stBuilder.append(line); } buffReader.close(); System.out.println("Creating blastoutput..."); BlastOutput blastOutput = new BlastOutput(stBuilder.toString()); System.out.println("BlastOutput created! :)"); stBuilder.delete(0, stBuilder.length()); HashMap<String, String> blastProteinsMap = new HashMap<String, String>(); ArrayList<Iteration> iterations = blastOutput.getBlastOutputIterations(); for (Iteration iteration : iterations) { blastProteinsMap.put(iteration.getQueryDef().split("\\|")[1].trim(), iteration.toString()); } //freeing some memory blastOutput = null; //------------------------------------------------------------------------ //Initializing writer for output file outBuff = new BufferedWriter(new FileWriter(outFile)); //reading gene annotation xml file..... buffReader = new BufferedReader(new FileReader(inFile)); stBuilder = new StringBuilder(); line = null; while ((line = buffReader.readLine()) != null) { stBuilder.append(line); } buffReader.close(); XMLElement genesXML = new XMLElement(stBuilder.toString()); //freeing some memory I don't need anymore stBuilder.delete(0, stBuilder.length()); //reading file with the reference proteins set ArrayList<String> proteinsReferenceSet = new ArrayList<String>(); buffReader = new BufferedReader(new FileReader(fastaFile)); while ((line = buffReader.readLine()) != null) { if (line.charAt(0) == '>') { proteinsReferenceSet.add(line.split("\\|")[1]); } } buffReader.close(); Element pGenes = genesXML.asJDomElement().getChild(PredictedGenes.TAG_NAME); List<Element> contigs = pGenes.getChildren(ContigXML.TAG_NAME); System.out.println("There are " + contigs.size() + " contigs to be checked... "); outBuff.write("There are " + contigs.size() + " contigs to be checked... \n"); outBuff.write("Proteins reference set: \n"); for (String st : proteinsReferenceSet) { outBuff.write(st + ","); } outBuff.write("\n"); for (Element elem : contigs) { ContigXML contig = new ContigXML(elem); //escribo el id del contig en el que estoy outBuff.write("Checking contig: " + contig.getId() + "\n"); outBuff.flush(); List<XMLElement> geneList = contig.getChildrenWith(PredictedGene.TAG_NAME); System.out.println("geneList.size() = " + geneList.size()); int numeroDeGenesParaAnalizar = geneList.size() / FACTOR; if (numeroDeGenesParaAnalizar == 0) { numeroDeGenesParaAnalizar++; } ArrayList<Integer> indicesUtilizados = new ArrayList<Integer>(); outBuff.write("\nThe contig has " + geneList.size() + " predicted genes, let's analyze: " + numeroDeGenesParaAnalizar + "\n"); for (int j = 0; j < numeroDeGenesParaAnalizar; j++) { int geneIndex; boolean geneIsDismissed = false; do { geneIsDismissed = false; geneIndex = (int) Math.round(Math.floor(Math.random() * geneList.size())); PredictedGene tempGene = new PredictedGene(geneList.get(geneIndex).asJDomElement()); if (tempGene.getStatus().equals(PredictedGene.STATUS_DISMISSED)) { geneIsDismissed = true; } } while (indicesUtilizados.contains(new Integer(geneIndex)) && geneIsDismissed); indicesUtilizados.add(geneIndex); System.out.println("geneIndex = " + geneIndex); //Ahora hay que sacar el gen correspondiente al indice y hacer el control de calidad PredictedGene gene = new PredictedGene(geneList.get(geneIndex).asJDomElement()); outBuff.write("\nAnalyzing gene with id: " + gene.getId() + " , annotation uniprot id: " + gene.getAnnotationUniprotId() + "\n"); outBuff.write("eValue: " + gene.getEvalue() + "\n"); //--------------PETICION POST HTTP BLAST---------------------- PostMethod post = new PostMethod(BLAST_URL); post.addParameter("program", "blastx"); post.addParameter("sequence", gene.getSequence()); post.addParameter("database", "uniprotkb"); post.addParameter("email", "ppareja@era7.com"); post.addParameter("exp", "1e-10"); post.addParameter("stype", "dna"); // execute the POST HttpClient client = new HttpClient(); int status = client.executeMethod(post); System.out.println("status post = " + status); InputStream inStream = post.getResponseBodyAsStream(); String fileName = "jobid.txt"; FileOutputStream outStream = new FileOutputStream(new File(fileName)); byte[] buffer = new byte[1024]; int len; while ((len = inStream.read(buffer)) != -1) { outStream.write(buffer, 0, len); } outStream.close(); //Once the file is created I just have to read one line in order to extract the job id buffReader = new BufferedReader(new FileReader(new File(fileName))); String jobId = buffReader.readLine(); buffReader.close(); System.out.println("jobId = " + jobId); //--------------HTTP CHECK JOB STATUS REQUEST---------------------- GetMethod get = new GetMethod(CHECK_JOB_STATUS_URL + jobId); String jobStatus = ""; do { try { Thread.sleep(1000);//sleep for 1000 ms } catch (InterruptedException ie) { //If this thread was intrrupted by nother thread } status = client.executeMethod(get); //System.out.println("status get = " + status); inStream = get.getResponseBodyAsStream(); fileName = "jobStatus.txt"; outStream = new FileOutputStream(new File(fileName)); while ((len = inStream.read(buffer)) != -1) { outStream.write(buffer, 0, len); } outStream.close(); //Once the file is created I just have to read one line in order to extract the job id buffReader = new BufferedReader(new FileReader(new File(fileName))); jobStatus = buffReader.readLine(); //System.out.println("jobStatus = " + jobStatus); buffReader.close(); } while (!jobStatus.equals(FINISHED_JOB_STATUS)); //Once I'm here the blast should've already finished //--------------JOB RESULTS HTTP REQUEST---------------------- get = new GetMethod(JOB_RESULT_URL + jobId + "/out"); status = client.executeMethod(get); System.out.println("status get = " + status); inStream = get.getResponseBodyAsStream(); fileName = "jobResults.txt"; outStream = new FileOutputStream(new File(fileName)); while ((len = inStream.read(buffer)) != -1) { outStream.write(buffer, 0, len); } outStream.close(); //--------parsing the blast results file----- TreeSet<GeneEValuePair> featuresBlast = new TreeSet<GeneEValuePair>(); buffReader = new BufferedReader(new FileReader(new File(fileName))); while ((line = buffReader.readLine()) != null) { if (line.length() > 3) { String prefix = line.substring(0, 3); if (prefix.equals("TR:") || prefix.equals("SP:")) { String[] columns = line.split(" "); String id = columns[1]; //System.out.println("id = " + id); String e = ""; String[] arraySt = line.split("\\.\\.\\."); if (arraySt.length > 1) { arraySt = arraySt[1].trim().split(" "); int contador = 0; for (int k = 0; k < arraySt.length && contador <= 2; k++) { String string = arraySt[k]; if (!string.equals("")) { contador++; if (contador == 2) { e = string; } } } } else { //Number before e- String[] arr = arraySt[0].split("e-")[0].split(" "); String numeroAntesE = arr[arr.length - 1]; String numeroDespuesE = arraySt[0].split("e-")[1].split(" ")[0]; e = numeroAntesE + "e-" + numeroDespuesE; } double eValue = Double.parseDouble(e); //System.out.println("eValue = " + eValue); GeneEValuePair g = new GeneEValuePair(id, eValue); featuresBlast.add(g); } } } GeneEValuePair currentGeneEValuePair = new GeneEValuePair(gene.getAnnotationUniprotId(), gene.getEvalue()); System.out.println("currentGeneEValuePair.id = " + currentGeneEValuePair.id); System.out.println("currentGeneEValuePair.eValue = " + currentGeneEValuePair.eValue); boolean blastContainsGene = false; for (GeneEValuePair geneEValuePair : featuresBlast) { if (geneEValuePair.id.equals(currentGeneEValuePair.id)) { blastContainsGene = true; //le pongo la e que tiene en el wu-blast para poder comparar currentGeneEValuePair.eValue = geneEValuePair.eValue; break; } } if (blastContainsGene) { outBuff.write("The protein was found in the WU-BLAST result.. \n"); //Una vez que se que esta en el blast tengo que ver que sea la mejor GeneEValuePair first = featuresBlast.first(); outBuff.write("Protein with best eValue according to the WU-BLAST result: " + first.id + " , " + first.eValue + "\n"); if (first.id.equals(currentGeneEValuePair.id)) { outBuff.write("Proteins with best eValue match up \n"); } else { if (first.eValue == currentGeneEValuePair.eValue) { outBuff.write( "The one with best eValue is not the same protein but has the same eValue \n"); } else if (first.eValue > currentGeneEValuePair.eValue) { outBuff.write( "The one with best eValue is not the same protein but has a worse eValue :) \n"); } else { outBuff.write( "The best protein from BLAST has an eValue smaller than ours, checking if it's part of the reference set...\n"); //System.exit(-1); if (proteinsReferenceSet.contains(first.id)) { //The protein is in the reference set and that shouldn't happen outBuff.write( "The protein was found on the reference set, checking if it belongs to the same contig...\n"); String iterationSt = blastProteinsMap.get(gene.getAnnotationUniprotId()); if (iterationSt != null) { outBuff.write( "The protein was found in the BLAST used at the beginning of the annotation process.\n"); Iteration iteration = new Iteration(iterationSt); ArrayList<Hit> hits = iteration.getIterationHits(); boolean contigFound = false; Hit errorHit = null; for (Hit hit : hits) { if (hit.getHitDef().indexOf(contig.getId()) >= 0) { contigFound = true; errorHit = hit; break; } } if (contigFound) { outBuff.write( "ERROR: A hit from the same contig was find in the Blast file: \n" + errorHit.toString() + "\n"); } else { outBuff.write("There is no hit with the same contig! :)\n"); } } else { outBuff.write( "The protein is NOT in the BLAST used at the beginning of the annotation process.\n"); } } else { //The protein was not found on the reference set so everything's ok outBuff.write( "The protein was not found on the reference, everything's ok :)\n"); } } } } else { outBuff.write("The protein was NOT found on the WU-BLAST !! :( \n"); //System.exit(-1); } } } } catch (Exception ex) { ex.printStackTrace(); } finally { try { //closing outputfile outBuff.close(); } catch (IOException ex) { Logger.getLogger(AutomaticQualityControl.class.getName()).log(Level.SEVERE, null, ex); } } } }
From source file:com.cws.esolutions.security.main.PasswordUtility.java
public static void main(final String[] args) { final String methodName = PasswordUtility.CNAME + "#main(final String[] args)"; if (DEBUG) {//from w ww . ja v a2 s . c om DEBUGGER.debug("Value: {}", methodName); } if (args.length == 0) { HelpFormatter usage = new HelpFormatter(); usage.printHelp(PasswordUtility.CNAME, options, true); System.exit(1); } BufferedReader bReader = null; BufferedWriter bWriter = null; try { // load service config first !! SecurityServiceInitializer.initializeService(PasswordUtility.SEC_CONFIG, PasswordUtility.LOG_CONFIG, false); if (DEBUG) { DEBUGGER.debug("Options options: {}", options); for (String arg : args) { DEBUGGER.debug("Value: {}", arg); } } CommandLineParser parser = new PosixParser(); CommandLine commandLine = parser.parse(options, args); if (DEBUG) { DEBUGGER.debug("CommandLineParser parser: {}", parser); DEBUGGER.debug("CommandLine commandLine: {}", commandLine); DEBUGGER.debug("CommandLine commandLine.getOptions(): {}", (Object[]) commandLine.getOptions()); DEBUGGER.debug("CommandLine commandLine.getArgList(): {}", commandLine.getArgList()); } final SecurityConfigurationData secConfigData = PasswordUtility.svcBean.getConfigData(); final SecurityConfig secConfig = secConfigData.getSecurityConfig(); final PasswordRepositoryConfig repoConfig = secConfigData.getPasswordRepo(); final SystemConfig systemConfig = secConfigData.getSystemConfig(); if (DEBUG) { DEBUGGER.debug("SecurityConfigurationData secConfig: {}", secConfigData); DEBUGGER.debug("SecurityConfig secConfig: {}", secConfig); DEBUGGER.debug("RepositoryConfig secConfig: {}", repoConfig); DEBUGGER.debug("SystemConfig systemConfig: {}", systemConfig); } if (commandLine.hasOption("encrypt")) { if ((StringUtils.isBlank(repoConfig.getPasswordFile())) || (StringUtils.isBlank(repoConfig.getSaltFile()))) { System.err.println("The password/salt files are not configured. Entries will not be stored!"); } File passwordFile = FileUtils.getFile(repoConfig.getPasswordFile()); File saltFile = FileUtils.getFile(repoConfig.getSaltFile()); if (DEBUG) { DEBUGGER.debug("File passwordFile: {}", passwordFile); DEBUGGER.debug("File saltFile: {}", saltFile); } final String entryName = commandLine.getOptionValue("entry"); final String username = commandLine.getOptionValue("username"); final String password = commandLine.getOptionValue("password"); final String salt = RandomStringUtils.randomAlphanumeric(secConfig.getSaltLength()); if (DEBUG) { DEBUGGER.debug("String entryName: {}", entryName); DEBUGGER.debug("String username: {}", username); DEBUGGER.debug("String password: {}", password); DEBUGGER.debug("String salt: {}", salt); } final String encodedSalt = PasswordUtils.base64Encode(salt); final String encodedUserName = PasswordUtils.base64Encode(username); final String encryptedPassword = PasswordUtils.encryptText(password, salt, secConfig.getSecretAlgorithm(), secConfig.getIterations(), secConfig.getKeyBits(), secConfig.getEncryptionAlgorithm(), secConfig.getEncryptionInstance(), systemConfig.getEncoding()); final String encodedPassword = PasswordUtils.base64Encode(encryptedPassword); if (DEBUG) { DEBUGGER.debug("String encodedSalt: {}", encodedSalt); DEBUGGER.debug("String encodedUserName: {}", encodedUserName); DEBUGGER.debug("String encodedPassword: {}", encodedPassword); } if (commandLine.hasOption("store")) { try { new File(passwordFile.getParent()).mkdirs(); new File(saltFile.getParent()).mkdirs(); boolean saltFileExists = (saltFile.exists()) ? true : saltFile.createNewFile(); if (DEBUG) { DEBUGGER.debug("saltFileExists: {}", saltFileExists); } // write the salt out first if (!(saltFileExists)) { throw new IOException("Unable to create salt file"); } boolean passwordFileExists = (passwordFile.exists()) ? true : passwordFile.createNewFile(); if (!(passwordFileExists)) { throw new IOException("Unable to create password file"); } if (commandLine.hasOption("replace")) { File[] files = new File[] { saltFile, passwordFile }; if (DEBUG) { DEBUGGER.debug("File[] files: {}", (Object) files); } for (File file : files) { if (DEBUG) { DEBUGGER.debug("File: {}", file); } String currentLine = null; File tmpFile = new File(FileUtils.getTempDirectory() + "/" + "tmpFile"); if (DEBUG) { DEBUGGER.debug("File tmpFile: {}", tmpFile); } bReader = new BufferedReader(new FileReader(file)); bWriter = new BufferedWriter(new FileWriter(tmpFile)); while ((currentLine = bReader.readLine()) != null) { if (!(StringUtils.equals(currentLine.trim().split(",")[0], entryName))) { bWriter.write(currentLine + System.getProperty("line.separator")); bWriter.flush(); } } bWriter.close(); FileUtils.deleteQuietly(file); FileUtils.copyFile(tmpFile, file); FileUtils.deleteQuietly(tmpFile); } } FileUtils.writeStringToFile(saltFile, entryName + "," + encodedUserName + "," + encodedSalt + System.getProperty("line.separator"), true); FileUtils.writeStringToFile(passwordFile, entryName + "," + encodedUserName + "," + encodedPassword + System.getProperty("line.separator"), true); } catch (IOException iox) { ERROR_RECORDER.error(iox.getMessage(), iox); } } System.out.println("Entry Name " + entryName + " stored."); } if (commandLine.hasOption("decrypt")) { String saltEntryName = null; String saltEntryValue = null; String decryptedPassword = null; String passwordEntryName = null; if ((StringUtils.isEmpty(commandLine.getOptionValue("entry")) && (StringUtils.isEmpty(commandLine.getOptionValue("username"))))) { throw new ParseException("No entry or username was provided to decrypt."); } if (StringUtils.isEmpty(commandLine.getOptionValue("username"))) { throw new ParseException("no entry provided to decrypt"); } String entryName = commandLine.getOptionValue("entry"); String username = commandLine.getOptionValue("username"); if (DEBUG) { DEBUGGER.debug("String entryName: {}", entryName); DEBUGGER.debug("String username: {}", username); } File passwordFile = FileUtils.getFile(repoConfig.getPasswordFile()); File saltFile = FileUtils.getFile(repoConfig.getSaltFile()); if (DEBUG) { DEBUGGER.debug("File passwordFile: {}", passwordFile); DEBUGGER.debug("File saltFile: {}", saltFile); } if ((!(saltFile.canRead())) || (!(passwordFile.canRead()))) { throw new IOException( "Unable to read configured password/salt file. Please check configuration and/or permissions."); } for (String lineEntry : FileUtils.readLines(saltFile, systemConfig.getEncoding())) { saltEntryName = lineEntry.split(",")[0]; if (DEBUG) { DEBUGGER.debug("String saltEntryName: {}", saltEntryName); } if (StringUtils.equals(saltEntryName, entryName)) { saltEntryValue = PasswordUtils.base64Decode(lineEntry.split(",")[2]); break; } } if (StringUtils.isEmpty(saltEntryValue)) { throw new SecurityException("No entries were found that matched the provided information"); } for (String lineEntry : FileUtils.readLines(passwordFile, systemConfig.getEncoding())) { passwordEntryName = lineEntry.split(",")[0]; if (DEBUG) { DEBUGGER.debug("String passwordEntryName: {}", passwordEntryName); } if (StringUtils.equals(passwordEntryName, saltEntryName)) { String decodedPassword = PasswordUtils.base64Decode(lineEntry.split(",")[2]); decryptedPassword = PasswordUtils.decryptText(decodedPassword, saltEntryValue, secConfig.getSecretAlgorithm(), secConfig.getIterations(), secConfig.getKeyBits(), secConfig.getEncryptionAlgorithm(), secConfig.getEncryptionInstance(), systemConfig.getEncoding()); break; } } if (StringUtils.isEmpty(decryptedPassword)) { throw new SecurityException("No entries were found that matched the provided information"); } System.out.println(decryptedPassword); } else if (commandLine.hasOption("encode")) { System.out.println(PasswordUtils.base64Encode((String) commandLine.getArgList().get(0))); } else if (commandLine.hasOption("decode")) { System.out.println(PasswordUtils.base64Decode((String) commandLine.getArgList().get(0))); } } catch (IOException iox) { ERROR_RECORDER.error(iox.getMessage(), iox); System.err.println("An error occurred during processing: " + iox.getMessage()); System.exit(1); } catch (ParseException px) { ERROR_RECORDER.error(px.getMessage(), px); System.err.println("An error occurred during processing: " + px.getMessage()); System.exit(1); } catch (SecurityException sx) { ERROR_RECORDER.error(sx.getMessage(), sx); System.err.println("An error occurred during processing: " + sx.getMessage()); System.exit(1); } catch (SecurityServiceException ssx) { ERROR_RECORDER.error(ssx.getMessage(), ssx); System.exit(1); } finally { try { if (bReader != null) { bReader.close(); } if (bWriter != null) { bReader.close(); } } catch (IOException iox) { } } System.exit(0); }