List of usage examples for java.util Arrays asList
@SafeVarargs @SuppressWarnings("varargs") public static <T> List<T> asList(T... a)
From source file:com.revo.deployr.client.example.data.io.auth.stateful.preload.EncodedDataInBinaryFileOut.java
public static void main(String args[]) throws Exception { RClient rClient = null;/*from w ww. ja v a2 s .com*/ RProject rProject = null; try { /* * Determine DeployR server endpoint. */ String endpoint = System.getProperty("endpoint"); log.info("[ CONFIGURATION ] Using endpoint=" + endpoint); /* * Establish RClient connection to DeployR server. * * An RClient connection is the mandatory starting * point for any application using the client library. */ rClient = RClientFactory.createClient(endpoint); log.info("[ CONNECTION ] Established anonymous " + "connection [ RClient ]."); /* * Build a basic authentication token. */ RAuthentication rAuth = new RBasicAuthentication(System.getProperty("username"), System.getProperty("password")); /* * Establish an authenticated handle with the DeployR * server, rUser. Following this call the rClient * connection is operating as an authenticated connection * and all calls on rClient inherit the access permissions * of the authenticated user, rUser. */ RUser rUser = rClient.login(rAuth); log.info("[ AUTHENTICATION ] Upgraded to authenticated " + "connection [ RUser ]."); /* * Create a ProjectCreationOptions instance * to specify data inputs that "pre-heat" the R session * workspace or working directory for your project. */ ProjectCreationOptions options = new ProjectCreationOptions(); /* * Simulate application generated data. This data * is first encoded using the RDataFactory before * being passed as an input on project initialization. * * This encoded R input is automatically converted * into a workspace object at project initialization. */ RData generatedData = simulateGeneratedData(); if (generatedData != null) { List<RData> rinputs = Arrays.asList(generatedData); options.rinputs = rinputs; } log.info("[ PRELOAD INPUT ] DeployR-encoded R input set on " + "project creation, [ ProjectCreationOptions.rinputs ]."); /* * Create a temporary project (R session) passing a * ProjectCreationOptions to "pre-heat" data into the * workspace and/or working directory. */ rProject = rUser.createProject(options); log.info("[ GO STATEFUL ] Created stateful temporary " + "R session [ RProject ]."); /* * Execute a public analytics Web service as an authenticated * user based on a repository-managed R script: * /testuser/example-data-io/dataIO.R */ RProjectExecution exec = rProject.executeScript("dataIO.R", "example-data-io", "testuser", null, null); log.info("[ EXECUTION ] Stateful R script " + "execution completed [ RProjectExecution ]."); /* * Retrieve the working directory file (artifact) called * hip.rData that was generated by the execution. * * Outputs generated by an execution can be used in any * number of ways by client applications, including: * * 1. Use output data to perform further calculations. * 2. Display output data to an end-user. * 3. Write output data to a database. * 4. Pass output data along to another Web service. * 5. etc. */ List<RProjectFile> wdFiles = exec.about().artifacts; for (RProjectFile wdFile : wdFiles) { if (wdFile.about().filename.equals("hip.rData")) { log.info("[ DATA OUTPUT ] Retrieved working directory " + "file output " + wdFile.about().filename + " [ RProjectFile ]."); InputStream fis = null; try { fis = wdFile.download(); } catch (Exception ex) { log.warn("Working directory binary file download " + ex); } finally { IOUtils.closeQuietly(fis); } } } } catch (Exception ex) { log.warn("Unexpected runtime exception=" + ex); } finally { try { if (rProject != null) { /* * Close rProject before application exits. */ rProject.close(); } } catch (Exception fex) { } try { if (rClient != null) { /* * Release rClient connection before application exits. */ rClient.release(); } } catch (Exception fex) { } } }
From source file:edu.scripps.fl.pubchem.app.ResultDownloader.java
public static void main(String[] args) throws Exception { CommandLineHandler clh = new CommandLineHandler() { public void configureOptions(Options options) { options.addOption(OptionBuilder.withLongOpt("data_url").withType("").withValueSeparator('=') .hasArg().create()); }/*from w w w .ja v a 2s. co m*/ }; args = clh.handle(args); String data_url = clh.getCommandLine().getOptionValue("data_url"); ResultDownloader rd = new ResultDownloader(); if (data_url != null) rd.setDataUrl(new URL(data_url)); else rd.setDataUrl(new URL("ftp://ftp.ncbi.nlm.nih.gov/pubchem/Bioassay/CSV/")); if (args.length == 0) rd.process(); else { Integer[] list = (Integer[]) ConvertUtils.convert(args, Integer[].class); rd.process(((List<Integer>) Arrays.asList(list)).iterator()); } }
From source file:com.revo.deployr.client.example.data.io.auth.stateful.preload.ExternalDataInDataFileOut.java
public static void main(String args[]) throws Exception { RClient rClient = null;//from www .j av a 2 s . c o m RProject rProject = null; try { /* * Determine DeployR server endpoint. */ String endpoint = System.getProperty("endpoint"); log.info("[ CONFIGURATION ] Using endpoint=" + endpoint); /* * Establish RClient connection to DeployR server. * * An RClient connection is the mandatory starting * point for any application using the client library. */ rClient = RClientFactory.createClient(endpoint); log.info("[ CONNECTION ] Established anonymous " + "connection [ RClient ]."); /* * Build a basic authentication token. */ RAuthentication rAuth = new RBasicAuthentication(System.getProperty("username"), System.getProperty("password")); /* * Establish an authenticated handle with the DeployR * server, rUser. Following this call the rClient * connection is operating as an authenticated connection * and all calls on rClient inherit the access permissions * of the authenticated user, rUser. */ RUser rUser = rClient.login(rAuth); log.info("[ AUTHENTICATION ] Upgraded to authenticated " + "connection [ RUser ]."); /* * Create a ProjectCreationOptions instance * to specify data inputs that "pre-heat" the R session * workspace or working directory for your project. */ ProjectCreationOptions options = new ProjectCreationOptions(); /* * Load an R object literal "hipStarUrl" into the * workspace on project initialization. * * The R script execution that follows will check for * the existence of "hipStarUrl" in the workspace and if * present uses the URL path to load the Hipparcos star * dataset from the DAT file at that location. */ RData hipStarUrl = RDataFactory.createString("hipStarUrl", HIP_DAT_URL); List<RData> rinputs = Arrays.asList(hipStarUrl); options.rinputs = rinputs; log.info("[ PRELOAD INPUT ] External data source input " + "set on project creation, [ ProjectCreationOptions.rinputs ]."); /* * Create a temporary project (R session) passing a * ProjectCreationOptions to "pre-heat" data into the * workspace and/or working directory. */ rProject = rUser.createProject(options); log.info("[ GO STATEFUL ] Created stateful temporary " + "R session [ RProject ]."); /* * Execute a public analytics Web service as an authenticated * user based on a repository-managed R script: * /testuser/example-data-io/dataIO.R */ RProjectExecution exec = rProject.executeScript("dataIO.R", "example-data-io", "testuser", null, null); log.info("[ EXECUTION ] Stateful R script " + "execution completed [ RProjectExecution ]."); /* * Retrieve the working directory file (artifact) called * hip.csv that was generated by the execution. * * Outputs generated by an execution can be used in any * number of ways by client applications, including: * * 1. Use output data to perform further calculations. * 2. Display output data to an end-user. * 3. Write output data to a database. * 4. Pass output data along to another Web service. * 5. etc. */ List<RProjectFile> wdFiles = exec.about().artifacts; for (RProjectFile wdFile : wdFiles) { if (wdFile.about().filename.equals("hip.csv")) { log.info("[ DATA OUTPUT ] Retrieved working directory " + "file output " + wdFile.about().filename + " [ RProjectFile ]."); InputStream fis = null; try { fis = wdFile.download(); } catch (Exception ex) { log.warn("Working directory data file download " + ex); } finally { IOUtils.closeQuietly(fis); } } } } catch (Exception ex) { log.warn("Unexpected runtime exception=" + ex); } finally { try { if (rProject != null) { /* * Close rProject before application exits. */ rProject.close(); } } catch (Exception fex) { } try { if (rClient != null) { /* * Release rClient connection before application exits. */ rClient.release(); } } catch (Exception fex) { } } }
From source file:edu.msu.cme.rdp.graph.sandbox.KmerStartsFromKnown.java
public static void main(String[] args) throws Exception { final KmerStartsWriter out; final boolean translQuery; final int wordSize; final int translTable; try {/*from www . j av a 2 s. c o m*/ CommandLine cmdLine = new PosixParser().parse(options, args); args = cmdLine.getArgs(); if (args.length < 2) { throw new Exception("Unexpected number of arguments"); } if (cmdLine.hasOption("out")) { out = new KmerStartsWriter(cmdLine.getOptionValue("out")); } else { out = new KmerStartsWriter(System.out); } if (cmdLine.hasOption("transl-table")) { translTable = Integer.valueOf(cmdLine.getOptionValue("transl-table")); } else { translTable = 11; } translQuery = cmdLine.hasOption("transl-kmer"); wordSize = Integer.valueOf(args[0]); } catch (Exception e) { new HelpFormatter().printHelp("KmerStartsFromKnown <word_size> [name=]<ref_file> ...", options); System.err.println(e.getMessage()); System.exit(1); throw new RuntimeException("Stupid jvm"); //While this will never get thrown it is required to make sure javac doesn't get confused about uninitialized variables } long startTime = System.currentTimeMillis(); /* * if (args.length == 4) { maxThreads = Integer.valueOf(args[3]); } else * { */ //} System.err.println("Starting kmer mapping at " + new Date()); System.err.println("* References: " + Arrays.asList(args)); System.err.println("* Kmer length: " + wordSize); for (int index = 1; index < args.length; index++) { String refName; String refFileName = args[index]; if (refFileName.contains("=")) { String[] lexemes = refFileName.split("="); refName = lexemes[0]; refFileName = lexemes[1]; } else { String tmpName = new File(refFileName).getName(); if (tmpName.contains(".")) { refName = tmpName.substring(0, tmpName.lastIndexOf(".")); } else { refName = tmpName; } } File refFile = new File(refFileName); if (SeqUtils.guessSequenceType(refFile) != SequenceType.Nucleotide) { throw new Exception("Reference file " + refFile + " contains " + SeqUtils.guessFileFormat(refFile) + " sequences but expected nucleotide sequences"); } SequenceReader seqReader = new SequenceReader(refFile); Sequence seq; while ((seq = seqReader.readNextSequence()) != null) { if (seq.getSeqName().startsWith("#")) { continue; } ModelPositionKmerGenerator kmers = new ModelPositionKmerGenerator(seq.getSeqString(), wordSize, SequenceType.Nucleotide); for (char[] charmer : kmers) { int pos = kmers.getModelPosition() - 1; if (translQuery) { if (pos % 3 != 0) { continue; } else { pos /= 3; } } String kmer = new String(charmer); out.write(new KmerStart(refName, seq.getSeqName(), seq.getSeqName(), kmer, 1, pos, translQuery, (translQuery ? ProteinUtils.getInstance().translateToProtein(kmer, true, translTable) : null))); } } seqReader.close(); } out.close(); }
From source file:com.eternitywall.ots.OtsCli.java
public static void main(String[] args) { // Create the Options Options options = new Options(); options.addOption("c", "calendar", true, "Create timestamp with the aid of a remote calendar. May be specified multiple times."); options.addOption("k", "key", true, "Signature key file of private remote calendars."); options.addOption("d", "digest", true, "Verify a (hex-encoded) digest rather than a file."); options.addOption("a", "algorithm", true, "Pass the hashing algorithm of the document to timestamp: SHA256(default), SHA1, RIPEMD160."); options.addOption("m", "", true, "Commitments are sent to remote calendars in the event of timeout the timestamp is considered done if at least M calendars replied."); options.addOption("s", "shrink", false, "Shrink upgraded timestamp."); options.addOption("V", "version", false, "Print " + title + " version."); options.addOption("v", "verbose", false, "Be more verbose.."); options.addOption("f", "file", true, "Specify target file explicitly (default: original file present in the same directory without .ots)"); options.addOption("h", "help", false, "print this help."); // Parse the args to retrieve options & command CommandLineParser parser = new BasicParser(); try {// w w w . j a v a 2 s . co m CommandLine line = parser.parse(options, args); // args are the arguments passed to the the application via the main method if (line.hasOption("c")) { String[] cals = line.getOptionValues("c"); calendarsUrl.addAll(Arrays.asList(cals)); } if (line.hasOption("m")) { m = Integer.valueOf(line.getOptionValue("m")); } if (line.hasOption("k")) { signatureFile = line.getOptionValue("k"); calendarsUrl.clear(); } if (line.hasOption("s")) { shrink = true; } if (line.hasOption("v")) { verbose = true; } if (line.hasOption("V")) { System.out.println("Version: " + title + " v." + version + '\n'); return; } if (line.hasOption("h")) { showHelp(); return; } if (line.hasOption("d")) { shasum = Utils.hexToBytes(line.getOptionValue("d")); } if (line.hasOption("f")) { verifyFile = line.getOptionValue("f"); } if (line.hasOption("a")) { algorithm = line.getOptionValue("a"); if (!Arrays.asList(algorithms).contains(algorithm.toUpperCase())) { System.out.println("Algorithm: " + algorithm + " not supported\n"); return; } } if (line.getArgList().isEmpty()) { showHelp(); return; } cmd = line.getArgList().get(0); files = line.getArgList().subList(1, line.getArgList().size()); } catch (Exception e) { System.out.println(title + ": invalid parameters "); return; } // Parse the command switch (cmd) { case "info": case "i": if (files.isEmpty()) { System.out.println("Show information on a timestamp given as argument.\n"); System.out.println(title + " info: bad options "); break; } info(files.get(0), verbose); break; case "stamp": case "s": if (!files.isEmpty()) { multistamp(files, calendarsUrl, m, signatureFile, algorithm); } else if (shasum != null) { Hash hash = new Hash(shasum, algorithm); stamp(hash, calendarsUrl, m, signatureFile); } else { System.out.println("Create timestamp with the aid of a remote calendar.\n"); System.out.println(title + ": bad options number "); } break; case "verify": case "v": if (!files.isEmpty()) { Hash hash = null; if (shasum != null) { hash = new Hash(shasum, algorithm); } if (verifyFile == null) { verifyFile = files.get(0).replace(".ots", ""); } verify(files.get(0), hash, verifyFile); } else { System.out.println("Verify the timestamp attestations given as argument.\n"); System.out.println(title + ": bad options number "); } break; case "upgrade": case "u": if (files.isEmpty()) { System.out.println("Upgrade remote calendar timestamps to be locally verifiable.\n"); System.out.println(title + ": bad options number "); break; } upgrade(files.get(0), shrink); break; default: System.out.println(title + ": bad option: " + cmd); } }
From source file:TwitterClustering.java
public static void main(String[] args) throws FileNotFoundException, IOException { // TODO code application logic here File outFile = new File(args[3]); Scanner s = new Scanner(new File(args[1])).useDelimiter(","); JSONParser parser = new JSONParser(); Set<Cluster> clusterSet = new HashSet<Cluster>(); HashMap<String, Tweet> tweets = new HashMap(); FileWriter fw = new FileWriter(outFile.getAbsoluteFile()); BufferedWriter bw = new BufferedWriter(fw); // init/* w w w. j av a 2 s .c o m*/ try { Object obj = parser.parse(new FileReader(args[2])); JSONArray jsonArray = (JSONArray) obj; for (int i = 0; i < jsonArray.size(); i++) { Tweet twt = new Tweet(); JSONObject jObj = (JSONObject) jsonArray.get(i); String text = jObj.get("text").toString(); long sum = 0; for (int y = 0; y < text.toCharArray().length; y++) { sum += (int) text.toCharArray()[y]; } String[] token = text.split(" "); String tID = jObj.get("id").toString(); Set<String> mySet = new HashSet<String>(Arrays.asList(token)); twt.setAttributeValue(sum); twt.setText(mySet); twt.setTweetID(tID); tweets.put(tID, twt); } // preparing initial clusters int i = 0; while (s.hasNext()) { String id = s.next();// id Tweet t = tweets.get(id.trim()); clusterSet.add(new Cluster(i + 1, t, new LinkedList())); i++; } Iterator it = tweets.entrySet().iterator(); for (int l = 0; l < 2; l++) { // limit to 25 iterations while (it.hasNext()) { Map.Entry me = (Map.Entry) it.next(); // calculate distance to each centroid Tweet p = (Tweet) me.getValue(); HashMap<Cluster, Float> distMap = new HashMap(); for (Cluster clust : clusterSet) { distMap.put(clust, jaccardDistance(p.getText(), clust.getCentroid().getText())); } HashMap<Cluster, Float> sorted = (HashMap<Cluster, Float>) sortByValue(distMap); sorted.keySet().iterator().next().getMembers().add(p); } // calculate new centroid and update Clusterset for (Cluster clust : clusterSet) { TreeMap<String, Long> tDistMap = new TreeMap(); Tweet newCentroid = null; Long avgSumDist = new Long(0); for (int j = 0; j < clust.getMembers().size(); j++) { avgSumDist += clust.getMembers().get(j).getAttributeValue(); tDistMap.put(clust.getMembers().get(j).getTweetID(), clust.getMembers().get(j).getAttributeValue()); } if (clust.getMembers().size() != 0) { avgSumDist /= (clust.getMembers().size()); } ArrayList<Long> listValues = new ArrayList<Long>(tDistMap.values()); if (tDistMap.containsValue(findClosestNumber(listValues, avgSumDist))) { // found closest newCentroid = tweets .get(getKeyByValue(tDistMap, findClosestNumber(listValues, avgSumDist))); clust.setCentroid(newCentroid); } } } // create an iterator Iterator iterator = clusterSet.iterator(); // check values while (iterator.hasNext()) { Cluster c = (Cluster) iterator.next(); bw.write(c.getId() + "\t"); System.out.print(c.getId() + "\t"); for (Tweet t : c.getMembers()) { bw.write(t.getTweetID() + ", "); System.out.print(t.getTweetID() + ","); } bw.write("\n"); System.out.println(""); } System.out.println(""); System.out.println("SSE " + sumSquaredErrror(clusterSet)); } catch (Exception e) { e.printStackTrace(); } finally { bw.close(); fw.close(); } }
From source file:com.edduarte.protbox.Protbox.java
public static void main(String... args) { // activate debug / verbose mode if (args.length != 0) { List<String> argsList = Arrays.asList(args); if (argsList.contains("-v")) { Constants.verbose = true;//from w w w . j av a 2 s. c o m } } // use System's look and feel try { UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName()); } catch (Exception ex) { // If the System's look and feel is not obtainable, continue execution with JRE look and feel } // check this is a single instance try { new ServerSocket(1882); } catch (IOException ex) { JOptionPane.showMessageDialog(null, "Another instance of Protbox is already running.\n" + "Please close the other instance first.", "Protbox already running", JOptionPane.ERROR_MESSAGE); System.exit(1); } // check if System Tray is supported by this operative system if (!SystemTray.isSupported()) { JOptionPane.showMessageDialog(null, "Your operative system does not support system tray functionality.\n" + "Please try running Protbox on another operative system.", "System tray not supported", JOptionPane.ERROR_MESSAGE); System.exit(1); } // add PKCS11 providers FileFilter fileFilter = new AndFileFilter(new WildcardFileFilter(Lists.newArrayList("*.config")), HiddenFileFilter.VISIBLE); File[] providersConfigFiles = new File(Constants.PROVIDERS_DIR).listFiles(fileFilter); if (providersConfigFiles != null) { for (File f : providersConfigFiles) { try { List<String> lines = FileUtils.readLines(f); String aliasLine = lines.stream().filter(line -> line.contains("alias")).findFirst().get(); lines.remove(aliasLine); String alias = aliasLine.split("=")[1].trim(); StringBuilder sb = new StringBuilder(); for (String s : lines) { sb.append(s); sb.append("\n"); } Provider p = new SunPKCS11(new ReaderInputStream(new StringReader(sb.toString()))); Security.addProvider(p); pkcs11Providers.put(p.getName(), alias); } catch (IOException | ProviderException ex) { if (ex.getMessage().equals("Initialization failed")) { ex.printStackTrace(); String s = "The following error occurred:\n" + ex.getCause().getMessage() + "\n\nIn addition, make sure you have " + "an available smart card reader connected before opening the application."; JTextArea textArea = new JTextArea(s); textArea.setColumns(60); textArea.setLineWrap(true); textArea.setWrapStyleWord(true); textArea.setSize(textArea.getPreferredSize().width, 1); JOptionPane.showMessageDialog(null, textArea, "Error loading PKCS11 provider", JOptionPane.ERROR_MESSAGE); System.exit(1); } else { ex.printStackTrace(); JOptionPane.showMessageDialog(null, "Error while setting up PKCS11 provider from configuration file " + f.getName() + ".\n" + ex.getMessage(), "Error loading PKCS11 provider", JOptionPane.ERROR_MESSAGE); } } } } // adds a shutdown hook to save instantiated directories into files when the application is being closed Runtime.getRuntime().addShutdownHook(new Thread(Protbox::exit)); // get system tray and run tray applet tray = SystemTray.getSystemTray(); SwingUtilities.invokeLater(() -> { if (Constants.verbose) { logger.info("Starting application"); } //Start a new TrayApplet object trayApplet = TrayApplet.getInstance(); }); // prompts the user to choose which provider to use ProviderListWindow.showWindow(Protbox.pkcs11Providers.keySet(), providerName -> { // loads eID token eIDTokenLoadingWindow.showPrompt(providerName, (returnedUser, returnedCertificateData) -> { user = returnedUser; certificateData = returnedCertificateData; // gets a password to use on the saved registry files (for loading and saving) final AtomicReference<Consumer<SecretKey>> consumerHolder = new AtomicReference<>(null); consumerHolder.set(password -> { registriesPasswordKey = password; try { // if there are serialized files, load them if they can be decoded by this user's private key final List<SavedRegistry> serializedDirectories = new ArrayList<>(); if (Constants.verbose) { logger.info("Reading serialized registry files..."); } File[] registryFileList = new File(Constants.REGISTRIES_DIR).listFiles(); if (registryFileList != null) { for (File f : registryFileList) { if (f.isFile()) { byte[] data = FileUtils.readFileToByteArray(f); try { Cipher cipher = Cipher.getInstance("AES"); cipher.init(Cipher.DECRYPT_MODE, registriesPasswordKey); byte[] registryDecryptedData = cipher.doFinal(data); serializedDirectories.add(new SavedRegistry(f, registryDecryptedData)); } catch (GeneralSecurityException ex) { if (Constants.verbose) { logger.info("Inserted Password does not correspond to " + f.getName()); } } } } } // if there were no serialized directories, show NewDirectory window to configure the first folder if (serializedDirectories.isEmpty() || registryFileList == null) { if (Constants.verbose) { logger.info("No registry files were found: running app as first time!"); } NewRegistryWindow.start(true); } else { // there were serialized directories loadRegistry(serializedDirectories); trayApplet.repaint(); showTrayApplet(); } } catch (AWTException | IOException | GeneralSecurityException | ReflectiveOperationException | ProtboxException ex) { JOptionPane.showMessageDialog(null, "The inserted password was invalid! Please try another one!", "Invalid password!", JOptionPane.ERROR_MESSAGE); insertPassword(consumerHolder.get()); } }); insertPassword(consumerHolder.get()); }); }); }
From source file:com.eviware.loadui.launcher.LoadUILauncher.java
public static void main(String[] args) { for (String arg : args) { System.out.println("LoadUILauncher arg: " + arg); if (arg.contains("cmd")) { List<String> argList = new ArrayList<>(Arrays.asList(args)); argList.remove(arg);/* w w w . j a v a 2 s.c om*/ String[] newArgs = argList.toArray(new String[argList.size()]); Application.launch(CommandApplication.class, newArgs); return; } } Application.launch(FXApplication.class, args); // Is the below just old legacy code from JavaFX 1? // System.setSecurityManager( null ); // // LoadUILauncher launcher = new LoadUILauncher( args ); // launcher.init(); // launcher.start(); // // new Thread( new LauncherWatchdog( launcher.framework, 20000 ), "loadUI Launcher Watchdog" ).start(); }
From source file:com.revo.deployr.client.example.data.io.auth.discrete.exec.EncodedDataInBinaryFileOut.java
public static void main(String args[]) throws Exception { RClient rClient = null;//from w w w. ja v a 2 s.com try { /* * Determine DeployR server endpoint. */ String endpoint = System.getProperty("endpoint"); log.info("[ CONFIGURATION ] Using endpoint=" + endpoint); /* * Establish RClient connection to DeployR server. * * An RClient connection is the mandatory starting * point for any application using the client library. */ rClient = RClientFactory.createClient(endpoint); log.info("[ CONNECTION ] Established anonymous " + "connection [ RClient ]."); /* * Build a basic authentication token. */ RAuthentication rAuth = new RBasicAuthentication(System.getProperty("username"), System.getProperty("password")); /* * Establish an authenticated handle with the DeployR * server, rUser. Following this call the rClient * connection is operating as an authenticated connection * and all calls on rClient inherit the access permissions * of the authenticated user, rUser. */ RUser rUser = rClient.login(rAuth); log.info("[ AUTHENTICATION ] Upgraded to authenticated " + "connection [ RUser ]."); /* * Create the AnonymousProjectExecutionOptions object * to specify data inputs and output to the script. * * This options object can be used to pass standard * execution model parameters on execution calls. All * fields are optional. * * See the Standard Execution Model chapter in the * Client Library Tutorial on the DeployR website for * further details. */ AnonymousProjectExecutionOptions options = new AnonymousProjectExecutionOptions(); /* * Simulate application generated data. This data * is first encoded using the RDataFactory before * being passed as an input on the execution. * * This encoded R input is automatically converted * into a workspace object before script execution. */ RData generatedData = simulateGeneratedData(); if (generatedData != null) { List<RData> rinputs = Arrays.asList(generatedData); options.rinputs = rinputs; } log.info("[ DATA INPUT ] DeployR-encoded R input " + "set on execution, [ ProjectExecutionOptions.rinputs ]."); /* * Execute an analytics Web service as an authenticated * user based on a repository-managed R script: * /testuser/example-data-io/dataIO.R */ RScriptExecution exec = rClient.executeScript("dataIO.R", "example-data-io", "testuser", null, options); log.info("[ EXECUTION ] Discrete R script " + "execution completed [ RScriptExecution ]."); /* * Retrieve the working directory file (artifact) called * hip.rData that was generated by the execution. * * Outputs generated by an execution can be used in any * number of ways by client applications, including: * * 1. Use output data to perform further calculations. * 2. Display output data to an end-user. * 3. Write output data to a database. * 4. Pass output data along to another Web service. * 5. etc. */ List<RProjectFile> wdFiles = exec.about().artifacts; for (RProjectFile wdFile : wdFiles) { if (wdFile.about().filename.equals("hip.rData")) { log.info("[ DATA OUTPUT ] Retrieved working directory " + "file output " + wdFile.about().filename + " [ RProjectFile ]."); InputStream fis = null; try { fis = wdFile.download(); } catch (Exception ex) { log.warn("Working directory binary file " + ex); } finally { IOUtils.closeQuietly(fis); } } } } catch (Exception ex) { log.warn("Unexpected runtime exception=" + ex); } finally { try { if (rClient != null) { /* * Release rClient connection before application exits. */ rClient.release(); } } catch (Exception fex) { } } }
From source file:gov.nih.nci.cacis.mirth.XSLForMirthFormatter.java
/** * @param args - main method args// w w w .j a v a 2 s.c o m * @throws IOException - error thrown, if any * @throws URISyntaxException - error thrown, if any */ public static void main(String[] args) throws IOException, URISyntaxException { if (args.length < 2) { LOG.error("Usage: XSLForMirthFormatter <formatted-file-output-dir> <xsl-file-1> <xsl-file-2> ..."); System.exit(1); } final List<String> lst = new ArrayList<String>(Arrays.asList(args)); lst.remove(0); final XSLForMirthFormatter frmtr = new XSLForMirthFormatter(); frmtr.formatXSL(args[0], (String[]) lst.toArray(new String[lst.size()])); }