Example usage for java.io PrintStream PrintStream

Introduction

In this page you can find the example usage for java.io PrintStream PrintStream.

Prototype

public PrintStream(File file) throws FileNotFoundException

Source Link

Document

Creates a new print stream, without automatic line flushing, with the specified file.

Usage

From source file:edu.dfci.cccb.mev.stats.domain.cli.CliRWilcoxonBuilder.java

@Override
public Wilcoxon build() throws DatasetException {
    try (TemporaryFile sample1 = new TemporaryFile();
            TemporaryFile sample2 = new TemporaryFile();
            TemporaryFile wilcoxon = new TemporaryFile();
            ByteArrayOutputStream script = new ByteArrayOutputStream();
            PrintStream s = new PrintStream(script)) {

        try (PrintStream s1 = new PrintStream(new FileOutputStream(sample1));
                PrintStream s2 = new PrintStream(new FileOutputStream(sample2))) {
            s1.println(Lambda.join(column(first()), "\t"));
            if (second() != null)
                s2.println(Lambda.join(column(second()), "\t"));
        }/* ww w.j  av  a2s .c om*/

        s.println("SAMPLE1_FILE=\"" + sample1.getAbsolutePath() + "\"");
        s.println("SAMPLE2_FILE=" + (second() == null ? "NULL" : ("\"" + sample2.getAbsolutePath() + "\"")));
        s.println("ALT_HYPOTHESIS=\"" + hypothesis() + "\"");
        s.println("IS_PAIRED=" + valueOf(pair()).toString().toUpperCase());
        s.println("IS_CONF_INT=" + valueOf(confidentInterval()).toString().toUpperCase());
        s.println("WILCOX_OUT=\"" + wilcoxon.getAbsolutePath() + "\"");

        copy(getClass().getResourceAsStream("/wilcoxon.r"), s);

        r.eval(script.toString());

        try (BufferedReader reader = new BufferedReader(new FileReader(wilcoxon))) {
            reader.readLine();
            final double wStat = Double.parseDouble(reader.readLine().split("\t")[1]);
            final double pValue = Double.parseDouble(reader.readLine().split("\t")[1]);

            return new PojoWilcoxon(wStat, pValue).name(this.name()).type(type());
        }
    } catch (IOException | ScriptException e) {
        throw new DatasetException(e);
    }
}

From source file:mx.itesm.imb.handlers.RooHandler.java

@SuppressWarnings("unchecked")
public Object execute(final ExecutionEvent event) throws ExecutionException {
    File rooFile;// w  ww.j  av a 2s  . com
    File ecoreFile;
    IProject project;
    File installRooFile;
    Map<String, File> rooFiles;
    List<File> installRooFiles;
    List<EPackage> ecorePackages;
    MessageConsoleStream consoleStream;

    consoleStream = this.getConsoleStream();
    ecorePackages = (List<EPackage>) Util.getSelectedItems(event);

    // Generate the IMB artifacts for the selected Ecore packages
    this.clearConsole();
    for (EPackage ecorePackage : ecorePackages) {
        try {
            ecoreFile = Util.getEcoreFile(ecorePackage);

            // Roo and Bus scripts
            consoleStream.println("Generating roo scripts for package: " + ecorePackage.getName() + "...");
            rooFiles = Util.executeAtlQueries(this, ecoreFile, consoleStream);

            // Generate a new project for each roo script
            installRooFiles = new ArrayList<File>(rooFiles.size());
            for (String script : rooFiles.keySet()) {
                rooFile = rooFiles.get(script);
                project = Util.createProject(ecoreFile.getName().replace(".ecore", "." + script));
                installRooFile = new File(project.getLocation().toFile(), rooFile.getName());

                installRooFiles.add(installRooFile);
                FileUtils.copyFile(rooFile, installRooFile);
                rooFile.delete();
            }
        } catch (Exception e) {
            consoleStream
                    .println("The Ecore package could not be successfully transformed to a Spring Roo script");
            e.printStackTrace(new PrintStream(consoleStream));
        }
    }

    return null;
}

From source file:com.xqdev.jam.MLJAM.java

private static Interpreter getInterpreter(String contextId) throws EvalError {
    // Get the appropriate interpreter
    Interpreter i = null;// ww  w  .  ja  va2 s. com
    boolean createdInterp = false;
    synchronized (interpreters) { // serialize two gets of the same name
        i = interpreters.get(contextId);
        if (i == null) {
            i = new Interpreter();
            interpreters.put(contextId, i);
            createdInterp = true;
        }
    }
    if (createdInterp) {
        Log.log("Created context: " + contextId + " (" + i + ")");

        // Now configure stdin and stdout to capture 10k of content
        // Store references to the circular buffers within the interpreter itself.
        // This provides a nice place to store them plus theoretically allows
        // advanced use from within the bsh environment.
        // On Windows print() outputs \r\n but in XQuery that's normalized to \n
        // so the 10k of Java buffer may produce less than 10k of content in XQuery!
        OutputStream circularOutput = new CircularByteArrayOutputStream(10240);
        PrintStream printOutput = new PrintStream(circularOutput);
        i.setOut(printOutput);
        i.set("mljamout", circularOutput);

        OutputStream circularError = new CircularByteArrayOutputStream(10240);
        PrintStream printError = new PrintStream(circularError);
        i.setErr(printError);
        i.set("mljamerr", circularError);

        // Capture the built-in System.out and System.err also.
        // (Commented out since System appears global, can't do per interpreter.)
        //i.set("mljamprintout", printOutput);
        //i.set("mljamprinterr", printError);
        //i.eval("System.setOut(mljamprintout);");
        //i.eval("System.setErr(mljamprinterr);");

        // Need to expose hexdecode() and base64decode() built-in functions
        i.eval("hexdecode(String s) { return com.xqdev.jam.MLJAM.hexDecode(s); }");
        i.eval("base64decode(String s) { return com.xqdev.jam.MLJAM.base64Decode(s); }");

        // Let's tell the context what its id is
        i.set("mljamid", contextId);
    }

    // Update the last accessed time, used for cleaning
    i.set("mljamlast", System.currentTimeMillis());

    // If it's been long enough, go snooping for stale contexts
    if (System.currentTimeMillis() > lastClean + CLEAN_INTERVAL) {
        Log.log("Initiated periodic scan for stale context objects");
        lastClean = System.currentTimeMillis();
        Iterator<Interpreter> itr = interpreters.values().iterator();
        while (itr.hasNext()) {
            Interpreter interp = itr.next();
            Long last = (Long) interp.get("mljamlast");
            if (System.currentTimeMillis() > last + STALE_TIMEOUT) {
                itr.remove();
                Log.log("Staled context: " + interp.get("mljamid") + " (" + interp + ")");
            } else if ((System.currentTimeMillis() > last + TEMP_STALE_TIMEOUT)
                    && ("" + interp.get("mljamid")).startsWith("temp:")) {
                itr.remove();
                Log.log("Staled temp context: " + interp.get("mljamid") + " (" + interp + ")");
            }
        }
    }

    return i;
}

From source file:edu.msu.cme.rdp.alignment.errorcheck.CompareErrorType.java

public CompareErrorType(File mismatch_out, File indel_out, File qualOutFile) throws IOException {
    misMatch_writer = new PrintStream(mismatch_out);
    indel_writer = new PrintStream(indel_out);

    if (qualOutFile != null) {
        qualOut = new PrintStream(qualOutFile);
    }//from w w  w .j  a  v  a 2s.  com

}

From source file:S3DataManagerTest.java

@Before
public void setUp() throws FileNotFoundException {
    //set the CodeBuilder instance to write its messages to the log here so
    //we can read what it prints.
    log = new ByteArrayOutputStream();
    PrintStream p = new PrintStream(log);
    when(listener.getLogger()).thenReturn(p);
}

From source file:br.com.ingenieux.mojo.beanstalk.env.DumpInstancesMojo.java

@Override
protected Object executeInternal() throws Exception {
    AmazonEC2 ec2 = clientFactory.getService(AmazonEC2Client.class);

    DescribeEnvironmentResourcesResult envResources = getService().describeEnvironmentResources(
            new DescribeEnvironmentResourcesRequest().withEnvironmentId(curEnv.getEnvironmentId())
                    .withEnvironmentName(curEnv.getEnvironmentName()));
    List<String> instanceIds = new ArrayList<String>();

    for (Instance i : envResources.getEnvironmentResources().getInstances()) {
        instanceIds.add(i.getId());//  w  w w. j a v a  2  s . c  om
    }

    DescribeInstancesResult ec2Instances = ec2
            .describeInstances(new DescribeInstancesRequest().withInstanceIds(instanceIds));

    PrintStream printStream = null;

    if (null != outputFile) {
        printStream = new PrintStream(outputFile);
    }

    for (Reservation r : ec2Instances.getReservations()) {
        for (com.amazonaws.services.ec2.model.Instance i : r.getInstances()) {
            String ipAddress = dumpPrivateAddresses ? i.getPrivateIpAddress()
                    : StringUtils.defaultString(i.getPublicIpAddress(), i.getPrivateDnsName());
            String instanceId = i.getInstanceId();

            if (null != printStream) {
                printStream.println(ipAddress + " # " + instanceId);
            } else {
                getLog().info(" * " + instanceId + ": " + ipAddress);
            }
        }
    }

    if (null != printStream) {
        printStream.close();
    }

    return null;
}

From source file:com.dragome.compiler.parser.Parser.java

public static void main(String[] args) throws Exception {
    String className = args[0];//from   ww  w. j a va2  s  .c o m
    DragomeJsCompiler.compiler = new DragomeJsCompiler(CompilerType.Standard);

    Project.createSingleton(null);
    ClassUnit classUnit = new ClassUnit(Project.singleton, Project.singleton.getSignature(className));
    classUnit.setClassFile(new FileObject(new File(args[1])));
    Parser parser = new Parser(classUnit);
    TypeDeclaration typeDecl = parser.parse();
    DragomeJavaScriptGenerator dragomeJavaScriptGenerator = new DragomeJavaScriptGenerator(Project.singleton);
    dragomeJavaScriptGenerator
            .setOutputStream(new PrintStream(new FileOutputStream(new File("/tmp/webapp.js"))));
    dragomeJavaScriptGenerator.visit(typeDecl);

    FileInputStream fis = new FileInputStream(new File("/tmp/webapp.js"));
    String md5 = org.apache.commons.codec.digest.DigestUtils.md5Hex(fis);
    System.out.println(md5);
}

From source file:uk.org.openeyes.oink.itest.karaf.OinkCommandIT.java

@Test
public void testOinkEnableCommandIsAvailableOnShellOnAFreshCopyOfCustomDistro() throws Exception {
    ByteArrayOutputStream out = new ByteArrayOutputStream();
    ByteArrayOutputStream err = new ByteArrayOutputStream();
    PrintStream psout = new PrintStream(out);
    PrintStream pser = new PrintStream(err);
    CommandSession cs = commandProcessor.createSession(System.in, psout, pser);
    cs.execute("help oink:enable");
    cs.close();/*w w w.  j  a va  2  s  .c  o m*/
    psout.close();
    pser.close();
    assertTrue(err.toString().isEmpty());
    assertFalse(out.toString().contains("COMMANDS"));
}

From source file:io.hightide.handlers.ErrorHandler.java

@Override
public void handleRequest(HttpServerExchange exchange) throws Exception {
    exchange.addDefaultResponseListener(new DefaultResponseListener() {
        @Override/*w  w w  . jav a2  s  . c  o  m*/
        public boolean handleDefaultResponse(final HttpServerExchange exchange) {
            if (!exchange.isResponseChannelAvailable()) {
                return false;
            }
            if (exchange.getResponseCode() >= 400) {
                Throwable t = exchange.getAttachment(HightideHandler.EXCEPTION_ATTACHMENT);
                String exceptionString;
                String message = exchange.getResponseCode() == 404 ? "Wrong address, no one lives here!"
                        : "Server's on fire, run for your life!";

                String errorPage;
                try {
                    Map<String, Object> errorMap = new HashMap<>();
                    errorMap.put("message", message);
                    errorMap.put("responseCode", exchange.getResponseCode());
                    errorMap.put("reason", StatusCodes.getReason(exchange.getResponseCode()));
                    ByteArrayOutputStream baos = new ByteArrayOutputStream();
                    t.printStackTrace(new PrintStream(baos));
                    exceptionString = baos.toString();
                    errorMap.put("exception", exceptionString);
                    errorMap.put("exceptionMsg", t.getMessage());
                    errorPage = new RythmHtmlRenderer().render("errors/default.html.rythm", errorMap);
                } catch (Exception e) {
                    exceptionString = printException(t);
                    errorPage = "<html><head><title>Error</title></head><body>" + "<h1>" + message + "</h1>"
                            + exchange.getResponseCode() + " - "
                            + StatusCodes.getReason(exchange.getResponseCode()) + exceptionString
                            + "</body></html>";
                }
                exchange.getResponseHeaders().put(Headers.CONTENT_LENGTH, "" + errorPage.length());
                exchange.getResponseHeaders().put(Headers.CONTENT_TYPE, "text/html");
                Sender sender = exchange.getResponseSender();
                sender.send(errorPage);
                return true;
            }
            return false;
        }
    });
    next.handleRequest(exchange);
}

From source file:com.collabnet.ccf.core.hospital.Ambulance.java

public Object[] process(Object data) {
    log.warn("Artifact reached ambulance");
    if (data instanceof MessageException) {
        MessageException exception = (MessageException) data;
        Object dataObj = exception.getData();
        String source = exception.getOriginatingModule();
        Exception rootCause = exception.getException();
        Document doc = createXMLDocument("UTF-8");
        Element failure = doc.addElement("Failure");
        Element failureSource = failure.addElement("Source");
        if (source != null)
            failureSource.setText(source);
        Element exceptionDetail = failure.addElement("Exception");
        ByteArrayOutputStream bos = new ByteArrayOutputStream();
        PrintStream st = new PrintStream(bos);
        rootCause.printStackTrace(st);/* w w w  .ja va 2 s  . co  m*/
        exceptionDetail.setText(new String(bos.toByteArray()));
        Element dataElement = failure.addElement("Data");
        if (dataObj instanceof Document) {
            Document dataDoc = (Document) dataObj;
            String artifactFileName = null;
            try {
                artifactFileName = CCFUtils.getTempFileName(dataDoc);
            } catch (GenericArtifactParsingException e) {
                log.warn("The data that reached the hospital is not a Generic Artifact");
            }
            if (artifactFileName == null) {
                artifactFileName = "sync-info";
            }
            String tempFilePath = null;
            FileOutputStream fos = null;
            try {
                File tempFile = File.createTempFile(artifactFileName, ".xml", artifactsDirectoryFile);
                fos = new FileOutputStream(tempFile);
                String dataXML = dataDoc.asXML();
                fos.write(dataXML.getBytes());
                fos.flush();
                fos.close();
                tempFilePath = tempFile.getAbsolutePath();
            } catch (IOException e) {
                log.error("Could not create temporary File", e);
            } finally {
                if (fos != null) {
                    try {
                        fos.close();
                    } catch (IOException e) {
                        log.warn("Could not close temp file stream", e);
                    }
                }
            }
            dataElement.setText(tempFilePath);
        }
        String writeData = failure.asXML();
        try {
            fos.write(writeData.getBytes());
            fos.write(System.getProperty("line.separator").getBytes());
            fos.flush();
        } catch (IOException e) {
            log.error("An IO-Exception occured in the hospital: " + e.getMessage());
            return null;
        }
    }
    return new Object[0];
}