List of usage examples for java.util ArrayList add
public boolean add(E e)
From source file:com.bright.json.JSonRequestor.java
public static void main(String[] args) { String fileBasename = null;//w w w .ja v a 2 s . c om String[] zipArgs = null; JFileChooser chooser = new JFileChooser("/Users/panos/STR_GRID"); try { chooser.setCurrentDirectory(new java.io.File(".")); chooser.setDialogTitle("Select the input directory"); chooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY); chooser.setAcceptAllFileFilterUsed(false); if (chooser.showOpenDialog(null) == JFileChooser.APPROVE_OPTION) { System.out.println("getCurrentDirectory(): " + chooser.getCurrentDirectory()); System.out.println("getSelectedFile() : " + chooser.getSelectedFile()); // String fileBasename = // chooser.getSelectedFile().toString().substring(chooser.getSelectedFile().toString().lastIndexOf(File.separator)+1,chooser.getSelectedFile().toString().lastIndexOf(".")); fileBasename = chooser.getSelectedFile().toString() .substring(chooser.getSelectedFile().toString().lastIndexOf(File.separator) + 1); System.out.println("Base name: " + fileBasename); zipArgs = new String[] { chooser.getSelectedFile().toString(), chooser.getCurrentDirectory().toString() + File.separator + fileBasename + ".zip" }; com.bright.utils.ZipFile.main(zipArgs); } else { System.out.println("No Selection "); } } catch (Exception e) { System.out.println(e.toString()); } JTextField uiHost = new JTextField("ucs-head.brightcomputing.com"); // TextPrompt puiHost = new // TextPrompt("hadoop.brightcomputing.com",uiHost); JTextField uiUser = new JTextField("nexus"); // TextPrompt puiUser = new TextPrompt("nexus", uiUser); JTextField uiPass = new JPasswordField("system"); // TextPrompt puiPass = new TextPrompt("", uiPass); JTextField uiWdir = new JTextField("/home/nexus/pp1234"); // TextPrompt puiWdir = new TextPrompt("/home/nexus/nexus_workdir", // uiWdir); JTextField uiOut = new JTextField("foo"); // TextPrompt puiOut = new TextPrompt("foobar123", uiOut); JPanel myPanel = new JPanel(new GridLayout(5, 1)); myPanel.add(new JLabel("Bright HeadNode hostname:")); myPanel.add(uiHost); // myPanel.add(Box.createHorizontalStrut(1)); // a spacer myPanel.add(new JLabel("Username:")); myPanel.add(uiUser); myPanel.add(new JLabel("Password:")); myPanel.add(uiPass); myPanel.add(new JLabel("Working Directory:")); myPanel.add(uiWdir); // myPanel.add(Box.createHorizontalStrut(1)); // a spacer myPanel.add(new JLabel("Output Study Name ( -s ):")); myPanel.add(uiOut); int result = JOptionPane.showConfirmDialog(null, myPanel, "Please fill in all the fields.", JOptionPane.OK_CANCEL_OPTION); if (result == JOptionPane.OK_OPTION) { System.out.println("Input received."); } String rfile = uiWdir.getText(); String rhost = uiHost.getText(); String ruser = uiUser.getText(); String rpass = uiPass.getText(); String nexusOut = uiOut.getText(); String[] myarg = new String[] { zipArgs[1], ruser + "@" + rhost + ":" + rfile, nexusOut, fileBasename }; com.bright.utils.ScpTo.main(myarg); String cmURL = "https://" + rhost + ":8081/json"; List<Cookie> cookies = doLogin(ruser, rpass, cmURL); chkVersion(cmURL, cookies); jobSubmit myjob = new jobSubmit(); jobSubmit.jobObject myjobObj = new jobSubmit.jobObject(); myjob.setService("cmjob"); myjob.setCall("submitJob"); myjobObj.setQueue("defq"); myjobObj.setJobname("myNexusJob"); myjobObj.setAccount(ruser); myjobObj.setRundirectory(rfile); myjobObj.setUsername(ruser); myjobObj.setGroupname("cmsupport"); myjobObj.setPriority("1"); myjobObj.setStdinfile(rfile + "/stdin-mpi"); myjobObj.setStdoutfile(rfile + "/stdout-mpi"); myjobObj.setStderrfile(rfile + "/stderr-mpi"); myjobObj.setResourceList(Arrays.asList("")); myjobObj.setDependencies(Arrays.asList("")); myjobObj.setMailNotify(false); myjobObj.setMailOptions("ALL"); myjobObj.setMaxWallClock("00:10:00"); myjobObj.setNumberOfProcesses(1); myjobObj.setNumberOfNodes(1); myjobObj.setNodes(Arrays.asList("")); myjobObj.setCommandLineInterpreter("/bin/bash"); myjobObj.setUserdefined(Arrays.asList("cd " + rfile, "date", "pwd")); myjobObj.setExecutable("mpirun"); myjobObj.setArguments("-env I_MPI_FABRICS shm:tcp " + Constants.NEXUSSIM_EXEC + " -mpi -c " + rfile + "/" + fileBasename + "/" + fileBasename + " -s " + rfile + "/" + fileBasename + "/" + nexusOut); myjobObj.setModules(Arrays.asList("shared", "nexus", "intel-mpi/64")); myjobObj.setDebug(false); myjobObj.setBaseType("Job"); myjobObj.setIsSlurm(true); myjobObj.setUniqueKey(0); myjobObj.setModified(false); myjobObj.setToBeRemoved(false); myjobObj.setChildType("SlurmJob"); myjobObj.setJobID("Nexus test"); // Map<String,jobSubmit.jobObject > mymap= new HashMap<String, // jobSubmit.jobObject>(); // mymap.put("Slurm",myjobObj); ArrayList<Object> mylist = new ArrayList<Object>(); mylist.add("slurm"); mylist.add(myjobObj); myjob.setArgs(mylist); GsonBuilder builder = new GsonBuilder(); builder.enableComplexMapKeySerialization(); // Gson g = new Gson(); Gson g = builder.create(); String json2 = g.toJson(myjob); // To be used from a real console and not Eclipse Delete.main(zipArgs[1]); String message = JSonRequestor.doRequest(json2, cmURL, cookies); @SuppressWarnings("resource") Scanner resInt = new Scanner(message).useDelimiter("[^0-9]+"); int jobID = resInt.nextInt(); System.out.println("Job ID: " + jobID); JOptionPane optionPane = new JOptionPane(message); JDialog myDialog = optionPane.createDialog(null, "CMDaemon response: "); myDialog.setModal(false); myDialog.setVisible(true); ArrayList<Object> mylist2 = new ArrayList<Object>(); mylist2.add("slurm"); String JobID = Integer.toString(jobID); mylist2.add(JobID); myjob.setArgs(mylist2); myjob.setService("cmjob"); myjob.setCall("getJob"); String json3 = g.toJson(myjob); System.out.println("JSON Request No. 4 " + json3); cmReadFile readfile = new cmReadFile(); readfile.setService("cmmain"); readfile.setCall("readFile"); readfile.setUserName(ruser); int fileByteIdx = 1; readfile.setPath(rfile + "/" + fileBasename + "/" + fileBasename + ".sum@+" + fileByteIdx); String json4 = g.toJson(readfile); String monFile = JSonRequestor.doRequest(json4, cmURL, cookies).replaceAll("^\"|\"$", ""); if (monFile.startsWith("Unable")) { monFile = ""; } else { fileByteIdx += countLines(monFile, "\\\\n"); System.out.println(""); } StringBuffer output = new StringBuffer(); // Get the correct Line Separator for the OS (CRLF or LF) String nl = System.getProperty("line.separator"); String filename = chooser.getCurrentDirectory().toString() + File.separator + fileBasename + ".sum.txt"; System.out.println("Local monitoring file: " + filename); output.append(monFile.replaceAll("\\\\n", System.getProperty("line.separator"))); String getJobJSON = JSonRequestor.doRequest(json3, cmURL, cookies); jobGet getJobObj = new Gson().fromJson(getJobJSON, jobGet.class); System.out.println("Job " + jobID + " status: " + getJobObj.getStatus().toString()); while (getJobObj.getStatus().toString().equals("RUNNING") || getJobObj.getStatus().toString().equals("COMPLETING")) { try { getJobJSON = JSonRequestor.doRequest(json3, cmURL, cookies); getJobObj = new Gson().fromJson(getJobJSON, jobGet.class); System.out.println("Job " + jobID + " status: " + getJobObj.getStatus().toString()); readfile.setPath(rfile + "/" + fileBasename + "/" + fileBasename + ".sum@+" + fileByteIdx); json4 = g.toJson(readfile); monFile = JSonRequestor.doRequest(json4, cmURL, cookies).replaceAll("^\"|\"$", ""); if (monFile.startsWith("Unable")) { monFile = ""; } else { output.append(monFile.replaceAll("\\\\n", System.getProperty("line.separator"))); System.out.println("FILE INDEX:" + fileByteIdx); fileByteIdx += countLines(monFile, "\\\\n"); } Thread.sleep(Constants.STATUS_CHECK_INTERVAL); } catch (InterruptedException ex) { Thread.currentThread().interrupt(); } } Gson gson_nice = new GsonBuilder().setPrettyPrinting().create(); String json_out = gson_nice.toJson(getJobJSON); System.out.println(json_out); System.out.println("JSON Request No. 5 " + json4); readfile.setPath(rfile + "/" + fileBasename + "/" + fileBasename + ".sum@+" + fileByteIdx); json4 = g.toJson(readfile); monFile = JSonRequestor.doRequest(json4, cmURL, cookies).replaceAll("^\"|\"$", ""); if (monFile.startsWith("Unable")) { monFile = ""; } else { output.append(monFile.replaceAll("\\\\n", System.getProperty("line.separator"))); fileByteIdx += countLines(monFile, "\\\\n"); } System.out.println("FILE INDEX:" + fileByteIdx); /* * System.out.print("Monitoring file: " + monFile.replaceAll("\\n", * System.getProperty("line.separator"))); try { * FileUtils.writeStringToFile( new * File(chooser.getCurrentDirectory().toString() + File.separator + * fileBasename + ".sum.txt"), monFile.replaceAll("\\n", * System.getProperty("line.separator"))); } catch (IOException e) { * * e.printStackTrace(); } */ if (getJobObj.getStatus().toString().equals("COMPLETED")) { String[] zipArgs_from = new String[] { chooser.getSelectedFile().toString(), chooser.getCurrentDirectory().toString() + File.separator + fileBasename + "_out.zip" }; String[] myarg_from = new String[] { ruser + "@" + rhost + ":" + rfile + "/" + fileBasename + "_out.zip", zipArgs_from[1], rfile, fileBasename }; com.bright.utils.ScpFrom.main(myarg_from); JOptionPane optionPaneS = new JOptionPane("Job execution completed without errors!"); JDialog myDialogS = optionPaneS.createDialog(null, "Job status: "); myDialogS.setModal(false); myDialogS.setVisible(true); } else { JOptionPane optionPaneF = new JOptionPane("Job execution FAILED!"); JDialog myDialogF = optionPaneF.createDialog(null, "Job status: "); myDialogF.setModal(false); myDialogF.setVisible(true); } try { System.out.println("Local monitoring file: " + filename); BufferedWriter out = new BufferedWriter(new FileWriter(filename)); String outText = output.toString(); String newString = outText.replace("\\\\n", nl); System.out.println("Text: " + outText); out.write(newString); out.close(); rmDuplicateLines.main(filename); } catch (IOException e) { e.printStackTrace(); } doLogout(cmURL, cookies); System.exit(0); }
From source file:com.hp.test.framework.Utlis.java
public static void main(String ar[]) throws IOException { ArrayList<String> runs_list = new ArrayList<String>(); String basepath = replacelogs(); String path = basepath + "ATU Reports\\Results"; File directory = new File(path); File[] subdirs = directory.listFiles((FileFilter) DirectoryFileFilter.DIRECTORY); for (File dir : subdirs) { log.info("Directory: " + dir.getName()); runs_list.add(dir.getName()); }// w w w. java 2s. co m Map<String, List<String>> runCounts = GetCountsrunsWise(runs_list, path); int success = replaceCounts(runCounts, path); if (success == 0) { File SourceFile = new File(path + "\\lineChart_temp.js"); File RenameFile = new File(path + "\\lineChart.js"); renameOriginalFile(SourceFile, RenameFile); File SourceFile1 = new File(path + "\\barChart_temp.js"); File RenameFile1 = new File(path + "\\barChart.js"); renameOriginalFile(SourceFile1, RenameFile1); String Reports_path = basepath + "ATU Reports\\"; int LatestRun = Utlis.getLastRun(Reports_path); Utlis.getpaths(Reports_path + "\\Results\\Run_" + String.valueOf(LatestRun)); try { Utlis.replaceMainTable(false, new File(Reports_path + "index.html")); Utlis.replaceMainTable(true, new File(Reports_path + "results\\" + "ConsolidatedPage.html")); Utlis.replaceMainTable(true, new File(Reports_path + "Results\\Run_" + String.valueOf(LatestRun) + "CurrentRun.html")); fileList.add( new File(Reports_path + "\\Results\\Run_" + String.valueOf(LatestRun) + "CurrentRun.html")); for (File f : fileList) { Utlis.replaceMainTable(true, f); } } catch (Exception ex) { log.error("Error in updating Report format" + ex.getMessage()); } } }
From source file:ProducerTool.java
public static void main(String[] args) { ArrayList<ProducerTool> threads = new ArrayList(); ProducerTool producerTool = new ProducerTool(); String[] unknown = CommandLineSupport.setOptions(producerTool, args); if (unknown.length > 0) { System.out.println("Unknown options: " + Arrays.toString(unknown)); System.exit(-1);/* w w w . j a va 2 s .c o m*/ } producerTool.showParameters(); for (int threadCount = 1; threadCount <= parallelThreads; threadCount++) { producerTool = new ProducerTool(); CommandLineSupport.setOptions(producerTool, args); producerTool.start(); threads.add(producerTool); } while (true) { Iterator<ProducerTool> itr = threads.iterator(); int running = 0; while (itr.hasNext()) { ProducerTool thread = itr.next(); if (thread.isAlive()) { running++; } } if (running <= 0) { System.out.println("All threads completed their work"); break; } try { Thread.sleep(1000); } catch (Exception e) { } } }
From source file:Anaphora_Resolution.ParseAllXMLDocuments.java
public static void main(String[] args) throws IOException, SAXException, ParserConfigurationException, TransformerException { // File dataFolder = new File("DataToPort"); // File[] documents; String grammar = "grammar/englishPCFG.ser.gz"; String[] options = { "-maxLength", "100", "-retainTmpSubcategories" }; //LexicalizedParser lp = new LexicalizedParser(grammar, options); LexicalizedParser lp = LexicalizedParser.loadModel("edu/stanford/nlp/models/lexparser/englishPCFG.ser.gz"); ////w w w.j a v a2 s .co m // if (dataFolder.isDirectory()) { // documents = dataFolder.listFiles(); // } else { // documents = new File[] {dataFolder}; // } // int currfile = 0; // int totfiles = documents.length; // for (File paper : documents) { // currfile++; // if (paper.getName().equals(".DS_Store")||paper.getName().equals(".xml")) { // currfile--; // totfiles--; // continue; // } // System.out.println("Working on "+paper.getName()+" (file "+currfile+" out of "+totfiles+")."); // // DocumentBuilderFactory docFactory = DocumentBuilderFactory.newInstance(); // This is for XML // DocumentBuilder docBuilder = docFactory.newDocumentBuilder(); // Document doc = docBuilder.parse(paper.getAbsolutePath()); // // NodeList textlist = doc.getElementsByTagName("text"); // for(int i=0; i < textlist.getLength(); i++) { // Node currentnode = textlist.item(i); // String wholetext = textlist.item(i).getTextContent(); String wholetext = "How about other changes for example the ways of doing the work and \n" + "\n" + "Iwould say security has , there 's more pressure put on people now than there used to be because obviously , especially after Locherbie , they tightened up on security and there 's a lot more pressure now especially from the ETR and stuff like that \n" + "People do n't feel valued any more , they feel I do n't know I think they feel that nobody cares about them really anyway \n"; //System.out.println(wholetext); //Iterable<List<? extends HasWord>> sentences; ArrayList<Tree> parseTrees = new ArrayList<Tree>(); String asd = ""; int j = 0; StringReader stringreader = new StringReader(wholetext); DocumentPreprocessor dp = new DocumentPreprocessor(stringreader); @SuppressWarnings("rawtypes") ArrayList<List> sentences = preprocess(dp); for (List sentence : sentences) { parseTrees.add(lp.apply(sentence)); // Parsing a new sentence and adding it to the parsed tree ArrayList<Tree> PronounsList = findPronouns(parseTrees.get(j)); // Locating all pronouns to resolve in the sentence Tree corefedTree; for (Tree pronounTree : PronounsList) { parseTrees.set(parseTrees.size() - 1, HobbsResolve(pronounTree, parseTrees)); // Resolving the coref and modifying the tree for each pronoun } StringWriter strwr = new StringWriter(); PrintWriter prwr = new PrintWriter(strwr); TreePrint tp = new TreePrint("penn"); tp.printTree(parseTrees.get(j), prwr); prwr.flush(); asd += strwr.toString(); j++; } String armando = ""; for (Tree sentence : parseTrees) { for (Tree leaf : Trees.leaves(sentence)) armando += leaf + " "; } System.out.println(wholetext); System.out.println(); System.out.println("......"); System.out.println(armando); System.out.println("All done."); // currentnode.setTextContent(asd); // } // TransformerFactory transformerFactory = TransformerFactory.newInstance(); // Transformer transformer = transformerFactory.newTransformer(); // DOMSource source = new DOMSource(doc); // StreamResult result = new StreamResult(paper); // transformer.transform(source, result); // // System.out.println("Done"); // } }
From source file:com.github.xbn.examples.regexutil.non_xbn.BetweenLineMarkersButSkipFirstXmpl.java
public static final void main(String[] as_1RqdTxtFilePath) { Iterator<String> lineItr = null; try {/*from w ww. j av a 2s .c o m*/ lineItr = FileUtils.lineIterator(new File(as_1RqdTxtFilePath[0])); //Throws npx if null } catch (IOException iox) { throw new RuntimeException("Attempting to open \"" + as_1RqdTxtFilePath[0] + "\"", iox); } catch (RuntimeException rx) { throw new RuntimeException("One required parameter: The path to the text file.", rx); } String LINE_SEP = System.getProperty("line.separator", "\n"); ArrayList<String> alsItems = new ArrayList<String>(); boolean bStartMark = false; boolean bLine1Skipped = false; StringBuilder sdCurrentItem = new StringBuilder(); while (lineItr.hasNext()) { String sLine = lineItr.next().trim(); if (!bStartMark) { if (sLine.startsWith(".START_SEQUENCE")) { bStartMark = true; continue; } throw new IllegalStateException("Start mark not found."); } if (!bLine1Skipped) { bLine1Skipped = true; continue; } else if (!sLine.equals(".END_SEQUENCE")) { sdCurrentItem.append(sLine).append(LINE_SEP); } else { alsItems.add(sdCurrentItem.toString()); sdCurrentItem.setLength(0); bStartMark = false; bLine1Skipped = false; continue; } } for (String s : alsItems) { System.out.println("----------"); System.out.print(s); } }
From source file:edu.harvard.i2b2.analysis.queryClient.CRCQueryClient.java
public static void main(String[] args) throws Exception { PDORequestMessageModel pdoFactory = new PDORequestMessageModel(); String conceptPath = new String( "\\RPDR\\Labtests\\LAB\\(LLB16) Chemistry\\(LLB21) General Chemistries\\CA"); ArrayList<String> paths = new ArrayList<String>(); // paths.add(conceptPath); conceptPath = new String("\\RPDR\\Labtests\\LAB\\(LLB16) Chemistry\\(LLB21) General Chemistries\\GGT"); paths.add(conceptPath); // conceptPath = new String( // "\\RPDR\\Labtests\\LAB\\(LLB16) Chemistry\\(LLB21) General Chemistries\\GGT" // );//from ww w. j a v a 2 s.c o m // paths.add(conceptPath); ArrayList<String> ppaths = new ArrayList<String>(); conceptPath = new String("\\Providers\\BWH"); // ppaths.add(conceptPath); String xmlStr = pdoFactory.requestXmlMessage(null, "1545", new Integer(1), new Integer(20), false); String result = sendPDOQueryRequestREST(xmlStr); // FileWriter fwr = new FileWriter("c:\\testdir\\response.txt"); // fwr.write(result); log.debug(result); PDOItem set = new PDOItem(); set.fullPath = "\\RPDR\\Labtests\\LAB\\(LLB16) Chemistry\\(LLB21) General Chemistries\\CA"; set.hasValueDisplayProperty = true; PDOValueData valdp = new PDOValueData(); valdp.left = 0.0; valdp.right = 8.4; valdp.color = "red"; valdp.height = "Very Low"; set.valDisplayProperties.add(valdp); valdp = new PDOValueData(); valdp.left = 8.4; valdp.right = 8.9; valdp.color = "gold"; valdp.height = "Low"; set.valDisplayProperties.add(valdp); valdp = new PDOValueData(); valdp.left = 8.9; valdp.right = 10.0; valdp.color = "green"; valdp.height = "Medium"; set.valDisplayProperties.add(valdp); valdp = new PDOValueData(); valdp.left = 10.0; valdp.right = 10.6; valdp.color = "gold"; valdp.height = "Tall"; set.valDisplayProperties.add(valdp); valdp = new PDOValueData(); valdp.left = 10.6; valdp.right = Integer.MAX_VALUE; valdp.color = "red"; valdp.height = "Very Tall"; set.valDisplayProperties.add(valdp); set.tableType = "fact"; TimelineRow row = new TimelineRow(); row.pdoItems.add(set); row.displayName = "Calcium (Group:CA)"; ArrayList<TimelineRow> rows = new ArrayList<TimelineRow>(); rows.add(row); set = new PDOItem(); set.fullPath = "\\RPDR\\Labtests\\LAB\\(LLB16) Chemistry\\(LLB21) General Chemistries\\GGT"; set.hasValueDisplayProperty = true; valdp = new PDOValueData(); valdp.left = 0.0; valdp.right = 1.0; valdp.color = "red"; valdp.height = "Very Low"; set.valDisplayProperties.add(valdp); valdp = new PDOValueData(); valdp.left = 1.0; valdp.right = 19.0; valdp.color = "gold"; valdp.height = "Low"; set.valDisplayProperties.add(valdp); valdp = new PDOValueData(); valdp.left = 19.0; valdp.right = 34.0; valdp.color = "green"; valdp.height = "Medium"; set.valDisplayProperties.add(valdp); valdp = new PDOValueData(); valdp.left = 34.0; valdp.right = 82.0; valdp.color = "gold"; valdp.height = "Tall"; set.valDisplayProperties.add(valdp); valdp = new PDOValueData(); valdp.left = 82.0; valdp.right = Integer.MAX_VALUE; valdp.color = "red"; valdp.height = "Very Tall"; set.valDisplayProperties.add(valdp); set.tableType = "fact"; row = new TimelineRow(); row.pdoItems.add(set); row.displayName = "Gamma Glutamyltrans (Group:GGT)"; rows.add(row); // testWritelld(result, rows, true); testWriteTableFile(result); }
From source file:it.unimi.di.big.mg4j.tool.URLMPHVirtualDocumentResolver.java
public static void main(final String[] arg) throws JSAPException, IOException { final SimpleJSAP jsap = new SimpleJSAP(URLMPHVirtualDocumentResolver.class.getName(), "Builds a URL document resolver from a sequence of URIs, extracted typically using ScanMetadata, using a suitable function. You can specify that the list is sorted, in which case it is possible to generate a resolver that occupies less space.", new Parameter[] { new Switch("sorted", 's', "sorted", "URIs are sorted: use a monotone minimal perfect hash function."), new Switch("iso", 'i', "iso", "Use ISO-8859-1 coding internally (i.e., just use the lower eight bits of each character)."), new FlaggedOption("bufferSize", JSAP.INTSIZE_PARSER, "64Ki", JSAP.NOT_REQUIRED, 'b', "buffer-size", "The size of the I/O buffer used to read terms."), new FlaggedOption("class", MG4JClassParser.getParser(), JSAP.NO_DEFAULT, JSAP.NOT_REQUIRED, 'c', "class", "A class used to create the function from URIs to their ranks; defaults to it.unimi.dsi.sux4j.mph.MHWCFunction for non-sorted inputs, and to it.unimi.dsi.sux4j.mph.TwoStepsLcpMonotoneMinimalPerfectHashFunction for sorted inputs."), new FlaggedOption("width", JSAP.INTEGER_PARSER, Integer.toString(Long.SIZE), JSAP.NOT_REQUIRED, 'w', "width", "The width, in bits, of the signatures used to sign the function from URIs to their rank."), new FlaggedOption("termFile", JSAP.STRING_PARSER, JSAP.NO_DEFAULT, JSAP.NOT_REQUIRED, 'o', "offline", "Read terms from this file (without loading them into core memory) instead of standard input."), new FlaggedOption("uniqueUris", JSAP.INTSIZE_PARSER, JSAP.NO_DEFAULT, JSAP.NOT_REQUIRED, 'U', "unique-uris", "Force URIs to be unique by adding random garbage at the end of duplicates; the argument is an upper bound for the number of URIs that will be read, and will be used to create a Bloom filter."), new UnflaggedOption("resolver", JSAP.STRING_PARSER, JSAP.NO_DEFAULT, JSAP.REQUIRED, JSAP.NOT_GREEDY, "The filename for the resolver.") }); JSAPResult jsapResult = jsap.parse(arg); if (jsap.messagePrinted()) return;//from w w w . j av a 2 s.c om final int bufferSize = jsapResult.getInt("bufferSize"); final String resolverName = jsapResult.getString("resolver"); //final Class<?> tableClass = jsapResult.getClass( "class" ); final boolean iso = jsapResult.getBoolean("iso"); String termFile = jsapResult.getString("termFile"); BloomFilter<Void> filter = null; final boolean uniqueURIs = jsapResult.userSpecified("uniqueUris"); if (uniqueURIs) filter = BloomFilter.create(jsapResult.getInt("uniqueUris")); final Collection<? extends CharSequence> collection; if (termFile == null) { ArrayList<MutableString> termList = new ArrayList<MutableString>(); final ProgressLogger pl = new ProgressLogger(); pl.itemsName = "URIs"; final LineIterator termIterator = new LineIterator( new FastBufferedReader(new InputStreamReader(System.in, "UTF-8"), bufferSize), pl); pl.start("Reading URIs..."); MutableString uri; while (termIterator.hasNext()) { uri = termIterator.next(); if (uniqueURIs) makeUnique(filter, uri); termList.add(uri.copy()); } pl.done(); collection = termList; } else { if (uniqueURIs) { // Create temporary file with unique URIs final ProgressLogger pl = new ProgressLogger(); pl.itemsName = "URIs"; pl.start("Copying URIs..."); final LineIterator termIterator = new LineIterator( new FastBufferedReader(new InputStreamReader(new FileInputStream(termFile)), bufferSize), pl); File temp = File.createTempFile(URLMPHVirtualDocumentResolver.class.getName(), ".uniqueuris"); temp.deleteOnExit(); termFile = temp.toString(); final FastBufferedOutputStream outputStream = new FastBufferedOutputStream( new FileOutputStream(termFile), bufferSize); MutableString uri; while (termIterator.hasNext()) { uri = termIterator.next(); makeUnique(filter, uri); uri.writeUTF8(outputStream); outputStream.write('\n'); } pl.done(); outputStream.close(); } collection = new FileLinesCollection(termFile, "UTF-8"); } LOGGER.debug("Building function..."); final int width = jsapResult.getInt("width"); if (jsapResult.getBoolean("sorted")) BinIO.storeObject( new URLMPHVirtualDocumentResolver( new ShiftAddXorSignedStringMap(collection.iterator(), new TwoStepsLcpMonotoneMinimalPerfectHashFunction<CharSequence>(collection, iso ? TransformationStrategies.prefixFreeIso() : TransformationStrategies.prefixFreeUtf16()), width)), resolverName); else BinIO.storeObject( new URLMPHVirtualDocumentResolver(new ShiftAddXorSignedStringMap(collection.iterator(), new MWHCFunction<CharSequence>(collection, iso ? TransformationStrategies.iso() : TransformationStrategies.utf16()), width)), resolverName); LOGGER.debug(" done."); }
From source file:mmllabvsdextractfeature.MMllabVSDExtractFeature.java
/** * @param args the command line arguments *//*from w ww.j a v a2 s. co m*/ public static void main(String[] args) throws IOException { // TODO code application logic here MMllabVSDExtractFeature hello = new MMllabVSDExtractFeature(); FileStructer metdata = new FileStructer(); //Utility utilityClassIni = new Utility(); FrameStructer frameStructer = new FrameStructer(); /* Flow : 1. Read metdata file 2. Untar folder: -1 Shot content 25 frame -1 folder 50 shot Process with 1 shot: - Resize All image 1 shot --> delete orginal. - Extract feature 25 frame - Pooling Max and aveg. - Delete Image, feature - zip file Feature 3. Delete File. */ // Load metadata File String dir = "/media/data1"; String metadataFileDir = "/media/data1/metdata/devel2011-new.lst"; ArrayList<FileStructer> listFileFromMetadata = metdata.readMetadata(metadataFileDir); // String test = utilityClass.readTextFile("C:\\Users\\tiendv\\Downloads\\VSD_devel2011_1.shot_1.RKF_1.Frame_1.txt"); // ArrayList <String> testFeatureSave = utilityClass.SplitUsingTokenizerWithLineArrayList(test, " "); // utilityClass.writeToFile("C:\\Users\\tiendv\\Downloads\\VSD_devel2011_1.shot_1.txt", testFeatureSave); // System.out.println(test); for (int i = 0; i < listFileFromMetadata.size(); i++) { Utility utilityClass = new Utility(); //Un zip file String folderName = listFileFromMetadata.get(i).getWholeFolderName(); String nameZipFile = dir + "/" + folderName + "/" + listFileFromMetadata.get(i).getNameZipFileName() + ".tar"; nameZipFile = nameZipFile.replaceAll("\\s", ""); String outPutFolder = dir + "/" + folderName + "/" + listFileFromMetadata.get(i).getNameZipFileName(); outPutFolder = outPutFolder.replaceAll("\\s", ""); utilityClass.unTarFolder(UNTARSHFILE, nameZipFile, outPutFolder + "_"); // Resize all image in folder has been unzip utilityClass.createFolder(CREADFOLDER, outPutFolder); utilityClass.resizeWholeFolder(outPutFolder + "_", outPutFolder, resizeWidth, resizeHeight); utilityClass.deleteWholeFolder(DELETEFOLDER, outPutFolder + "_"); // Read all file from Folder has been unzip ArrayList<FrameStructer> allFrameInZipFolder = new ArrayList<>(); allFrameInZipFolder = frameStructer.getListFileInZipFolder(outPutFolder); System.out.println(allFrameInZipFolder.size()); // sort with shot ID Collections.sort(allFrameInZipFolder, FrameStructer.frameIDNo); // Loop with 1 shot int indexFrame = 0; for (int n = 0; n < allFrameInZipFolder.size() / 25; n++) { // Process with 1 ArrayList<String> nameAllFrameOneShot = new ArrayList<>(); String shotAndFolderName = new String(); for (; indexFrame < Math.min((n + 1) * 25, allFrameInZipFolder.size()); indexFrame++) { String imageForExtract = outPutFolder + "/" + allFrameInZipFolder.get(indexFrame).toFullName() + ".jpg"; shotAndFolderName = allFrameInZipFolder.get(indexFrame).shotName(); String resultNameAfterExtract = outPutFolder + "/" + allFrameInZipFolder.get(indexFrame).toFullName() + ".txt"; nameAllFrameOneShot.add(resultNameAfterExtract); // extract and Delete image file --> ouput image'feature utilityClass.excuteFeatureExtractionAnImage(EXTRACTFEATUREANDDELETESOURCEIMAGESHFILE, "0", CUDAOVERFEATPATH, imageForExtract, resultNameAfterExtract); } // Pooling // DenseMatrix64F resultMaTrixFeatureOneShot = utilityClass.buidEJMLMatrixFeatureOneShot(nameAllFrameOneShot); // utilityClass.savePoolingFeatureOneShotWithEJMLFromMatrix(resultMaTrixFeatureOneShot,outPutFolder,shotAndFolderName); utilityClass.buidPoolingFileWithOutMatrixFeatureOneShot(nameAllFrameOneShot, outPutFolder, shotAndFolderName); // Save A file for (int frameCount = 0; frameCount < nameAllFrameOneShot.size(); frameCount++) { // Delete feature extract file utilityClass.deletefile(DELETEFILE, nameAllFrameOneShot.get(frameCount)); } // Release one shot data nameAllFrameOneShot.clear(); System.out.print("The end of one's shot" + "\n" + n); } // Delete zip file utilityClass.deletefile(DELETEFILE, nameZipFile); // Zip Whole Folder /** * Extract 1 shot * Resize 25 frame with the same shotid --> delete orgra. * Extract 25 frame --> feature file --->delete * */ } }
From source file:org.apache.s4.client.Adapter.java
@SuppressWarnings("static-access") public static void main(String args[]) throws IOException, InterruptedException { Options options = new Options(); options.addOption(OptionBuilder.withArgName("corehome").hasArg().withDescription("core home").create("c")); options.addOption(/*www.ja v a2 s . c om*/ OptionBuilder.withArgName("instanceid").hasArg().withDescription("instance id").create("i")); options.addOption( OptionBuilder.withArgName("configtype").hasArg().withDescription("configuration type").create("t")); options.addOption(OptionBuilder.withArgName("userconfig").hasArg() .withDescription("user-defined legacy data adapter configuration file").create("d")); CommandLineParser parser = new GnuParser(); CommandLine commandLine = null; try { commandLine = parser.parse(options, args); } catch (ParseException pe) { System.err.println(pe.getLocalizedMessage()); System.exit(1); } int instanceId = -1; if (commandLine.hasOption("i")) { String instanceIdStr = commandLine.getOptionValue("i"); try { instanceId = Integer.parseInt(instanceIdStr); } catch (NumberFormatException nfe) { System.err.println("Bad instance id: %s" + instanceIdStr); System.exit(1); } } if (commandLine.hasOption("c")) { coreHome = commandLine.getOptionValue("c"); } String configType = "typical"; if (commandLine.hasOption("t")) { configType = commandLine.getOptionValue("t"); } String userConfigFilename = null; if (commandLine.hasOption("d")) { userConfigFilename = commandLine.getOptionValue("d"); } File userConfigFile = new File(userConfigFilename); if (!userConfigFile.isFile()) { System.err.println("Bad user configuration file: " + userConfigFilename); System.exit(1); } File coreHomeFile = new File(coreHome); if (!coreHomeFile.isDirectory()) { System.err.println("Bad core home: " + coreHome); System.exit(1); } if (instanceId > -1) { System.setProperty("instanceId", "" + instanceId); } else { System.setProperty("instanceId", "" + S4Util.getPID()); } String configBase = coreHome + File.separatorChar + "conf" + File.separatorChar + configType; String configPath = configBase + File.separatorChar + "client-adapter-conf.xml"; File configFile = new File(configPath); if (!configFile.exists()) { System.err.printf("adapter config file %s does not exist\n", configPath); System.exit(1); } // load adapter config xml ApplicationContext coreContext; coreContext = new FileSystemXmlApplicationContext("file:" + configPath); ApplicationContext context = coreContext; Adapter adapter = (Adapter) context.getBean("client_adapter"); ApplicationContext appContext = new FileSystemXmlApplicationContext( new String[] { "file:" + userConfigFilename }, context); Map<?, ?> inputStubBeanMap = appContext.getBeansOfType(InputStub.class); Map<?, ?> outputStubBeanMap = appContext.getBeansOfType(OutputStub.class); if (inputStubBeanMap.size() == 0 && outputStubBeanMap.size() == 0) { System.err.println("No user-defined input/output stub beans"); System.exit(1); } ArrayList<InputStub> inputStubs = new ArrayList<InputStub>(inputStubBeanMap.size()); ArrayList<OutputStub> outputStubs = new ArrayList<OutputStub>(outputStubBeanMap.size()); // add all input stubs for (Map.Entry<?, ?> e : inputStubBeanMap.entrySet()) { String beanName = (String) e.getKey(); System.out.println("Adding InputStub " + beanName); inputStubs.add((InputStub) e.getValue()); } // add all output stubs for (Map.Entry<?, ?> e : outputStubBeanMap.entrySet()) { String beanName = (String) e.getKey(); System.out.println("Adding OutputStub " + beanName); outputStubs.add((OutputStub) e.getValue()); } adapter.setInputStubs(inputStubs); adapter.setOutputStubs(outputStubs); }
From source file:edu.harvard.i2b2.explorer.serviceClient.PDOQueryClient.java
public static void main(String[] args) throws Exception { PDORequestMessageModel pdoFactory = new PDORequestMessageModel(); String conceptPath = new String( "\\RPDR\\Labtests\\LAB\\(LLB16) Chemistry\\(LLB21) General Chemistries\\CA"); ArrayList<String> paths = new ArrayList<String>(); // paths.add(conceptPath); conceptPath = new String("\\RPDR\\Labtests\\LAB\\(LLB16) Chemistry\\(LLB21) General Chemistries\\GGT"); paths.add(conceptPath); // conceptPath = new // String("\\RPDR\\Labtests\\LAB\\(LLB16) Chemistry\\(LLB21) General Chemistries\\GGT"); // paths.add(conceptPath); ArrayList<String> ppaths = new ArrayList<String>(); conceptPath = new String("\\Providers\\BWH"); // ppaths.add(conceptPath); String xmlStr = pdoFactory.requestXmlMessage(null, "1545", new Integer(1), new Integer(20), false, ""); String result = sendPDOQueryRequestREST(xmlStr); // FileWriter fwr = new FileWriter("c:\\testdir\\response.txt"); // fwr.write(result); log.debug(result);/* ww w . j a va 2s.c o m*/ PDOItem set = new PDOItem(); set.fullPath = "\\RPDR\\Labtests\\LAB\\(LLB16) Chemistry\\(LLB21) General Chemistries\\CA"; set.hasValueDisplayProperty = true; PDOValueModel valdp = new PDOValueModel(); valdp.left = 0.0; valdp.right = 8.4; valdp.color = "red"; valdp.height = "Very Low"; set.valDisplayProperties.add(valdp); valdp = new PDOValueModel(); valdp.left = 8.4; valdp.right = 8.9; valdp.color = "gold"; valdp.height = "Low"; set.valDisplayProperties.add(valdp); valdp = new PDOValueModel(); valdp.left = 8.9; valdp.right = 10.0; valdp.color = "green"; valdp.height = "Medium"; set.valDisplayProperties.add(valdp); valdp = new PDOValueModel(); valdp.left = 10.0; valdp.right = 10.6; valdp.color = "gold"; valdp.height = "Tall"; set.valDisplayProperties.add(valdp); valdp = new PDOValueModel(); valdp.left = 10.6; valdp.right = Integer.MAX_VALUE; valdp.color = "red"; valdp.height = "Very Tall"; set.valDisplayProperties.add(valdp); set.tableType = "fact"; TimelineRow row = new TimelineRow(); row.pdoItems.add(set); row.displayName = "Calcium (Group:CA)"; ArrayList<TimelineRow> rows = new ArrayList<TimelineRow>(); rows.add(row); set = new PDOItem(); set.fullPath = "\\RPDR\\Labtests\\LAB\\(LLB16) Chemistry\\(LLB21) General Chemistries\\GGT"; set.hasValueDisplayProperty = true; valdp = new PDOValueModel(); valdp.left = 0.0; valdp.right = 1.0; valdp.color = "red"; valdp.height = "Very Low"; set.valDisplayProperties.add(valdp); valdp = new PDOValueModel(); valdp.left = 1.0; valdp.right = 19.0; valdp.color = "gold"; valdp.height = "Low"; set.valDisplayProperties.add(valdp); valdp = new PDOValueModel(); valdp.left = 19.0; valdp.right = 34.0; valdp.color = "green"; valdp.height = "Medium"; set.valDisplayProperties.add(valdp); valdp = new PDOValueModel(); valdp.left = 34.0; valdp.right = 82.0; valdp.color = "gold"; valdp.height = "Tall"; set.valDisplayProperties.add(valdp); valdp = new PDOValueModel(); valdp.left = 82.0; valdp.right = Integer.MAX_VALUE; valdp.color = "red"; valdp.height = "Very Tall"; set.valDisplayProperties.add(valdp); set.tableType = "fact"; row = new TimelineRow(); row.pdoItems.add(set); row.displayName = "Gamma Glutamyltrans (Group:GGT)"; rows.add(row); // testWritelld(result, rows, true); testWriteTableFile(result); }