Example usage for java.io PrintWriter write

List of usage examples for java.io PrintWriter write

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Introduction

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

Prototype

public void write(String s)

Source Link

Document

Writes a string.

Usage

From source file:com.cloud.agent.api.storage.OVFHelper.java

public void rewriteOVFFile(final String origOvfFilePath, final String newOvfFilePath, final String diskName) {
    try {/*w  ww  .  j a v a 2s  .  c o m*/
        final Document doc = DocumentBuilderFactory.newInstance().newDocumentBuilder()
                .parse(new File(origOvfFilePath));
        NodeList disks = doc.getElementsByTagName("Disk");
        NodeList files = doc.getElementsByTagName("File");
        NodeList items = doc.getElementsByTagName("Item");
        String keepfile = null;
        List<Element> toremove = new ArrayList<Element>();
        for (int j = 0; j < files.getLength(); j++) {
            Element file = (Element) files.item(j);
            String href = file.getAttribute("ovf:href");
            if (diskName.equals(href)) {
                keepfile = file.getAttribute("ovf:id");
            } else {
                toremove.add(file);
            }
        }
        String keepdisk = null;
        for (int i = 0; i < disks.getLength(); i++) {
            Element disk = (Element) disks.item(i);
            String fileRef = disk.getAttribute("ovf:fileRef");
            if (keepfile == null) {
                s_logger.info("FATAL: OVA format error");
            } else if (keepfile.equals(fileRef)) {
                keepdisk = disk.getAttribute("ovf:diskId");
            } else {
                toremove.add(disk);
            }
        }
        for (int k = 0; k < items.getLength(); k++) {
            Element item = (Element) items.item(k);
            NodeList cn = item.getChildNodes();
            for (int l = 0; l < cn.getLength(); l++) {
                if (cn.item(l) instanceof Element) {
                    Element el = (Element) cn.item(l);
                    if ("rasd:HostResource".equals(el.getNodeName())
                            && !(el.getTextContent().contains("ovf:/file/" + keepdisk)
                                    || el.getTextContent().contains("ovf:/disk/" + keepdisk))) {
                        toremove.add(item);
                        break;
                    }
                }
            }
        }

        for (Element rme : toremove) {
            if (rme.getParentNode() != null) {
                rme.getParentNode().removeChild(rme);
            }
        }

        final StringWriter writer = new StringWriter();
        final StreamResult result = new StreamResult(writer);
        final TransformerFactory tf = TransformerFactory.newInstance();
        final Transformer transformer = tf.newTransformer();
        final DOMSource domSource = new DOMSource(doc);
        transformer.transform(domSource, result);
        PrintWriter outfile = new PrintWriter(newOvfFilePath);
        outfile.write(writer.toString());
        outfile.close();
    } catch (SAXException | IOException | ParserConfigurationException | TransformerException e) {
        s_logger.info("Unexpected exception caught while removing network elements from OVF:" + e.getMessage(),
                e);
        throw new CloudRuntimeException(e);
    }
}

From source file:io.github.egonw.base.CMLEnricher.java

/**
 * Writes current document to a CML file.
 * //from   w w w.  j a va2s  .  c  om
 * @param fileName
 * @param extension
 *
 * @throws IOException
 *             Problems with opening output file.
 * @throws CDKException
 *             Problems with writing the CML XOM.
 */
private void writeFile(String fileName, String extension) throws IOException, CDKException {
    String basename = FilenameUtils.getBaseName(fileName);
    OutputStream outFile = new BufferedOutputStream(new FileOutputStream(basename + "-" + extension + ".cml"));
    PrintWriter output = new PrintWriter(outFile);
    this.doc.getRootElement().addNamespaceDeclaration(SreNamespace.getInstance().prefix,
            SreNamespace.getInstance().uri);
    output.write(XOMUtil.toPrettyXML(this.doc));
    output.flush();
    output.close();
}

From source file:net.sf.jasperreports.web.servlets.ReportServlet.java

protected void pageUpdate(HttpServletRequest request, HttpServletResponse response,
        WebReportContext webReportContext) throws JRException, IOException {
    JasperPrintAccessor jasperPrintAccessor = (JasperPrintAccessor) webReportContext
            .getParameterValue(WebReportContext.REPORT_CONTEXT_PARAMETER_JASPER_PRINT_ACCESSOR);
    if (jasperPrintAccessor == null) {
        throw new JRRuntimeException("Did not find the report on the session.");
    }// w ww .  j a v  a  2 s . c om

    String pageIdxParam = request.getParameter(WebUtil.REQUEST_PARAMETER_PAGE);
    Integer pageIndex = pageIdxParam == null ? null : Integer.valueOf(pageIdxParam);
    String pageTimestampParam = request.getParameter(WebUtil.REQUEST_PARAMETER_PAGE_TIMESTAMP);
    Long pageTimestamp = pageTimestampParam == null ? null : Long.valueOf(pageTimestampParam);

    if (log.isDebugEnabled()) {
        log.debug("report page update check for pageIndex: " + pageIndex + ", pageTimestamp: " + pageTimestamp);
    }

    LinkedHashMap<String, Object> result = new LinkedHashMap<String, Object>();
    putReportStatusResult(response, jasperPrintAccessor, result);

    if (pageIndex != null && pageTimestamp != null) {
        ReportPageStatus pageStatus = jasperPrintAccessor.pageStatus(pageIndex, pageTimestamp);
        boolean modified = pageStatus.hasModified();
        result.put("pageModified", modified);

        if (log.isDebugEnabled()) {
            log.debug("page " + pageIndex + " modified " + modified);
        }
    }

    String resultString = JacksonUtil.getInstance(getJasperReportsContext()).getJsonString(result);
    response.setContentType("application/json");
    PrintWriter out = response.getWriter();
    out.write(resultString);
    out.flush();
}

From source file:com.esri.gpt.control.arcims.ServletConnectorProxy.java

/**
 * Sends request to the opened HTTP connection.
 * //from  w  w w  .j  a v a 2s . c om
 * @param input
 *          data as stream
 * @param output
 *          output as stream
 * 
 * @throws java.io.IOException
 *           if sending data failed
 */
private void send(InputStream input, OutputStream output) throws IOException {

    PrintWriter outputWriter = null;
    try {
        outputWriter = new PrintWriter(output);
        outputWriter.write(readInputCharacters(input));
        outputWriter.flush();

    } catch (Exception e) {
        e.printStackTrace();
    } finally {
        if (outputWriter != null) {
            outputWriter.close();
        }
    }
}

From source file:co.cask.cdap.security.tools.AccessTokenClient.java

public String execute0(String[] args) {
    buildOptions();/*from   ww w .ja va  2  s .  c o m*/
    parseArguments(args);
    if (help) {
        return "";
    }

    String baseUrl;
    try {
        baseUrl = getAuthenticationServerAddress();
    } catch (IOException e) {
        errorDebugExit("Could not find Authentication service to connect to.", e);
        return null;
    }

    System.out.println(String.format("Authentication server address is: %s", baseUrl));
    System.out.println(String.format("Authenticating as: %s", username));

    HttpClient client = new DefaultHttpClient();
    if (useSsl && disableCertCheck) {
        try {
            client = getHTTPClient();
        } catch (Exception e) {
            errorDebugExit("Could not create HTTP Client with SSL enabled", e);
            return null;
        }
    }

    // construct the full URL and verify its well-formedness
    try {
        URI.create(baseUrl);
    } catch (IllegalArgumentException e) {
        System.err.println(
                "Invalid base URL '" + baseUrl + "'. Check the validity of --host or --port arguments.");
        return null;
    }

    HttpGet get = new HttpGet(baseUrl);
    String auth = Base64.encodeBase64String(String.format("%s:%s", username, password).getBytes());
    auth = auth.replaceAll("(\r|\n)", "");
    get.addHeader("Authorization", String.format("Basic %s", auth));
    HttpResponse response;
    try {
        response = client.execute(get);
    } catch (IOException e) {
        errorDebugExit("Error sending HTTP request: " + e.getMessage(), e);
        return null;
    }
    if (response.getStatusLine().getStatusCode() != HttpStatus.SC_OK) {
        System.out.println(
                "Authentication failed. Please ensure that the username and password provided are correct.");
        return null;
    } else {
        try {
            ByteArrayOutputStream bos = new ByteArrayOutputStream();
            ByteStreams.copy(response.getEntity().getContent(), bos);
            String responseBody = bos.toString("UTF-8");
            bos.close();
            JsonParser parser = new JsonParser();
            JsonObject responseJson = (JsonObject) parser.parse(responseBody);
            String token = responseJson.get(ExternalAuthenticationServer.ResponseFields.ACCESS_TOKEN)
                    .getAsString();

            PrintWriter writer = new PrintWriter(filePath, "UTF-8");
            writer.write(token);
            writer.close();
            System.out.println("Your Access Token is:" + token);
            System.out.println("Access Token saved to file " + filePath);
        } catch (Exception e) {
            System.err.println("Could not parse response contents.");
            e.printStackTrace(System.err);
            return null;
        }
    }
    client.getConnectionManager().shutdown();
    return "OK.";
}

From source file:com.globalsight.everest.webapp.pagehandler.projects.workflows.JobControlInProgressHandler.java

/**
 * Invokes this EntryPageHandler object/*w ww.  j a va  2  s.  c  o m*/
 * <p>
 * 
 * @param p_ageDescriptor
 *            the description of the page to be produced.
 * @param p_request
 *            original request sent from the browser.
 * @param p_response
 *            original response object.
 * @param p_context
 *            the Servlet context.
 */
public void myInvokePageHandler(WebPageDescriptor p_thePageDescriptor, HttpServletRequest p_request,
        HttpServletResponse p_response, ServletContext p_context)
        throws ServletException, IOException, RemoteException, EnvoyServletException {
    HttpSession session = p_request.getSession(false);
    SessionManager sessionMgr = (SessionManager) session.getAttribute(SESSION_MANAGER);
    boolean stateMarch = false;
    if (Job.DISPATCHED.equals((String) sessionMgr.getMyjobsAttribute("lastState")))
        stateMarch = true;
    String action = p_request.getParameter(ACTION_STRING);
    if (StringUtil.isNotEmpty(action) && "removeJobFromGroup".equals(action)) {
        removeJobFromGroup(p_request);
    }
    setJobSearchFilters(sessionMgr, p_request, stateMarch);

    HashMap beanMap = invokeJobControlPage(p_thePageDescriptor, p_request, BASE_BEAN);
    p_request.setAttribute("searchType", p_request.getParameter("searchType"));

    // since an instance of a page handler is used by different clients,
    // this instance variable needs to be set only once. There's no need
    // to synchronize this section as the value of export url is always the
    // same.
    if (m_exportUrl == null) {
        m_exportUrl = ((NavigationBean) beanMap.get(EXPORT_BEAN)).getPageURL();
    }

    if (p_request.getParameter("checkIsUploadingForExport") != null) {
        long jobId = Long.parseLong(p_request.getParameter("jobId"));
        Job job = WorkflowHandlerHelper.getJobById(jobId);
        String result = "";
        for (Workflow workflow : job.getWorkflows()) {
            if (result.length() > 0)
                break;
            Hashtable<Long, Task> tasks = workflow.getTasks();
            for (Long taskKey : tasks.keySet()) {
                if (tasks.get(taskKey).getIsUploading() == 'Y') {
                    result = "uploading";
                    break;
                }
            }
        }
        PrintWriter out = p_response.getWriter();
        p_response.setContentType("text/html");
        out.write(result);
        out.close();
        return;
    } else if (p_request.getParameter("action") != null
            && "checkDownloadQAReport".equals(p_request.getParameter("action"))) {
        ServletOutputStream out = p_response.getOutputStream();
        String jobIds = p_request.getParameter("jobIds");
        boolean checkQA = checkQAReport(sessionMgr, jobIds);
        String download = "";
        if (checkQA) {
            download = "success";
        } else {
            download = "fail";
        }
        Map<String, Object> returnValue = new HashMap();
        returnValue.put("download", download);
        out.write((JsonUtil.toObjectJson(returnValue)).getBytes("UTF-8"));
        return;
    } else if (p_request.getParameter("action") != null
            && "downloadQAReport".equals(p_request.getParameter("action"))) {
        Set<Long> jobIdSet = (Set<Long>) sessionMgr.getAttribute("jobIdSet");
        Set<File> exportFilesSet = (Set<File>) sessionMgr.getAttribute("exportFilesSet");
        Set<String> localesSet = (Set<String>) sessionMgr.getAttribute("localesSet");
        long companyId = (Long) sessionMgr.getAttribute("companyId");
        WorkflowHandlerHelper.zippedFolder(p_request, p_response, companyId, jobIdSet, exportFilesSet,
                localesSet);
        sessionMgr.removeElement("jobIdSet");
        sessionMgr.removeElement("exportFilesSet");
        sessionMgr.removeElement("localesSet");
        return;
    }

    performAppropriateOperation(p_request);

    sessionMgr.setMyjobsAttribute("lastState", Job.DISPATCHED);
    JobVoInProgressSearcher searcher = new JobVoInProgressSearcher();
    searcher.setJobVos(p_request, true);
    p_request.setAttribute(EXPORT_URL_PARAM, m_exportUrl);
    p_request.setAttribute(JOB_ID, JOB_ID);
    p_request.setAttribute(JOB_LIST_START_PARAM, p_request.getParameter(JOB_LIST_START_PARAM));
    p_request.setAttribute(PAGING_SCRIPTLET,
            getPagingText(p_request, ((NavigationBean) beanMap.get(BASE_BEAN)).getPageURL(), Job.DISPATCHED));
    try {
        Company company = ServerProxy.getJobHandler()
                .getCompanyById(CompanyWrapper.getCurrentCompanyIdAsLong());
        p_request.setAttribute("company", company);
    } catch (Exception e) {
        e.printStackTrace();
    }

    // Set the EXPORT_INIT_PARAM in the sessionMgr so we can bring
    // the user back here after they Export
    sessionMgr.setAttribute(JobManagementHandler.EXPORT_INIT_PARAM, BASE_BEAN);
    sessionMgr.setAttribute("destinationPage", "inprogress");
    // clear the session for download job from joblist page
    sessionMgr.setAttribute(DownloadFileHandler.DOWNLOAD_JOB_LOCALES, null);
    sessionMgr.setAttribute(DownloadFileHandler.DESKTOP_FOLDER, null);
    setJobProjectsLocales(sessionMgr, session);

    // turn on cache. do both. "pragma" for the older browsers.
    p_response.setHeader("Pragma", "yes-cache"); // HTTP 1.0
    p_response.setHeader("Cache-Control", "yes-cache"); // HTTP 1.1
    p_response.addHeader("Cache-Control", "yes-store"); // tell proxy not to
                                                        // cache
                                                        // forward to the jsp page.
    RequestDispatcher dispatcher = p_context.getRequestDispatcher(p_thePageDescriptor.getJspURL());
    dispatcher.forward(p_request, p_response);
}

From source file:com.esri.gpt.control.arcims.ServletConnectorProxy.java

/**
 * Sends request to the opened HTTP connection.
 * /*from  w  w  w  . j av a  2s . c  o m*/
 * @param requestBody
 *          as string
 * @param output
 *          to stream the data
 * 
 * @throws java.io.IOException
 *           if sending data failed
 */
private void send(String requestBody, OutputStream output) throws IOException {

    PrintWriter outputWriter = null;
    try {
        outputWriter = new PrintWriter(output);
        outputWriter.write(requestBody);
        outputWriter.flush();

    } catch (Exception e) {
        e.printStackTrace();
    }

    finally {
        try {
            if (output != null) {
                output.close();
            }
        } catch (Exception ef) {
            ef.printStackTrace();
        }
    }
}

From source file:edu.cornell.med.icb.goby.modes.CountsArchiveToWiggleMode.java

/**
 * Run the map2text mode./*w w w  .  j  a  v a2s  . c  om*/
 *
 * @throws java.io.IOException error reading / writing
 */
@Override
public void execute() throws IOException {
    PrintWriter writer = null;
    try {
        writer = new PrintWriter(
                new GZIPOutputStream(new FastBufferedOutputStream(new FileOutputStream(outputFile + ".gz"))));
        writer.write("track type=wiggle_0 name=" + label + " visibility=full viewLimits=1:200\n");
        final AlignmentReaderImpl alignment = new AlignmentReaderImpl(inputBasename);
        alignment.readHeader();
        alignment.close();
        final IndexedIdentifier referenceIds = alignment.getTargetIdentifiers();
        final DoubleIndexedIdentifier backwards = new DoubleIndexedIdentifier(referenceIds);
        final CountsArchiveReader reader = new CountsArchiveReader(inputBasename,
                alternativeCountArchiveExtension);
        final WiggleWindow wiggleWindow = new WiggleWindow(writer, resolution, 0);

        for (int referenceIndex = 0; referenceIndex < reader.getNumberOfIndices(); referenceIndex++) {
            String referenceId = backwards.getId(referenceIndex).toString();
            boolean processThisSequence = true;
            // prepare reference ID for UCSC genome browser.
            if ("MT".equalsIgnoreCase(referenceId)) {
                // patch chromosome name for UCSC genome browser:
                referenceId = "M";
            }

            // ignore c22_H2, c5_H2, and other contigs but not things like chr1 (mm9)
            if (referenceId.startsWith("c") && !referenceId.startsWith("chr")) {
                processThisSequence = false;
            }

            // ignore NT_*
            if (referenceId.startsWith("NT_")) {
                processThisSequence = false;
            }

            if (filterByReferenceNames && !includeReferenceNames.contains(referenceId)) {
                processThisSequence = false;
            }

            if (processThisSequence) {
                // prepend the reference id with "chr" if it doesn't use that already
                final String chromosome;
                if (referenceId.startsWith("chr")) {
                    chromosome = referenceId;
                } else {
                    chromosome = "chr" + referenceId;
                }

                long sumCount = 0;
                int numCounts = 0;

                CountsReader counts = reader.getCountReader(referenceIndex);
                int lastLength = 0;
                int lastPosition = 0;
                while (counts.hasNextTransition()) {
                    counts.nextTransition();
                    lastPosition = counts.getPosition();
                    lastLength = counts.getLength();
                }
                final int maxWritePosition = (lastPosition + lastLength - 1);
                wiggleWindow.reset();
                wiggleWindow.setMaxDataSize(maxWritePosition);

                writer.printf("variableStep chrom=%s span=%d\n", chromosome, resolution);
                counts = reader.getCountReader(referenceIndex);

                while (counts.hasNextTransition()) {
                    counts.nextTransition();
                    final int length = counts.getLength();

                    final int count = counts.getCount();
                    final int position = counts.getPosition();

                    wiggleWindow.addData(position, length, count);

                    sumCount += count;
                    numCounts++;
                }
                wiggleWindow.finish();
                final double averageCount = sumCount / (double) numCounts;
                System.out.println("average count for sequence " + referenceId + " " + averageCount);
            }
        }
    } finally {
        IOUtils.closeQuietly(writer);
    }
}

From source file:com.imagelake.android.settings.Servlet_UserSetting.java

protected void doGet(HttpServletRequest request, HttpServletResponse response)
        throws IOException, ServletException {
    PrintWriter out = response.getWriter();
    try {/*from   w  w w. ja  va  2 s  . c  om*/

        String type = request.getParameter("type");

        if (type.equals("all")) {
            //ja = new JSONArray();
            String chart = udi.getSubadminList();
            System.out.println(chart);
            out.write(chart);
        } else if (type.equals("user_type_all")) {
            String list = udi.getJSONAllUserTypeList();
            out.write("json=" + list);
        } else if (type.equals("update")) {
            String adtype = request.getParameter("admintype");
            String state = request.getParameter("state");
            String id = request.getParameter("id");

            System.out.println("admin type:" + adtype);
            System.out.println("state:" + state);
            System.out.println("id:" + id);

            boolean A = udi.updateUserState(Integer.parseInt(id), Integer.parseInt(state));
            boolean B = udi.updateUserType(Integer.parseInt(id), Integer.parseInt(adtype));
            System.out.println(A + "|" + B);
            if (A && B) {
                out.write("msg=Us_Successful...");
            } else {
                out.write("msg=Unable to complete the action.");
            }

        } else if (type.equals("addnewsub")) {
            InterfaceDAOImp idi = new InterfaceDAOImp();
            Interfaces in = new Interfaces();
            in.setState(1);
            in.setUrl("RegAdmin.jsp");
            boolean o = idi.updateInteface(in);
            if (o) {
                out.write("msg=addnewsub_Successful...");
            } else {
                out.write("msg=Unable to complete the action.");
            }
        } else if (type.equals("closenewsub")) {
            InterfaceDAOImp idi = new InterfaceDAOImp();
            Interfaces in = new Interfaces();
            in.setState(2);
            in.setUrl("RegAdmin.jsp");
            boolean o = idi.updateInteface(in);
            if (o) {
                out.write("msg=closenewsub_Successful...");
            } else {
                out.write("msg=Unable to complete the action.");
            }
        } else if (type.equals("editsub")) {
            InterfaceDAOImp idi = new InterfaceDAOImp();
            Interfaces in = new Interfaces();
            in.setState(1);
            in.setUrl("UpdateAdmin.jsp");
            boolean o = idi.updateInteface(in);
            if (o) {
                out.write("msg=editsub_Successful...");
            } else {
                out.write("msg=Unable to complete the action.");
            }
        } else if (type.equals("closeeditsub")) {
            InterfaceDAOImp idi = new InterfaceDAOImp();
            Interfaces in = new Interfaces();
            in.setState(2);
            in.setUrl("UpdateAdmin.jsp");
            boolean o = idi.updateInteface(in);
            if (o) {
                out.write("msg=closeeditsub_Successful...");
            } else {
                out.write("msg=Unable to complete the action.");
            }
        }

    } catch (Exception e) {
        e.printStackTrace();
        out.write("msg=Internal server error,Please try again later.");
    }

}

From source file:edu.cornell.med.icb.goby.methylation.MethylSimilarityScan.java

private void process(String[] args) throws IOException {
    String inputFilename = CLI.getOption(args, "-i", "/data/lister/mc_h1.tsv");
    this.windowWidths = CLI.getOption(args, "-w", "10");
    this.maxBestHits = CLI.getIntOption(args, "-h", 100);
    String outputFilename = CLI.getOption(args, "-o", "out.tsv");
    final MethylationData data = load(inputFilename);
    File outputFile = new File(outputFilename);
    boolean outputFileExists = outputFile.exists();
    // append://from w w w  . j  a  v  a2 s . co  m
    PrintWriter output = new PrintWriter(new FileWriter(outputFilename, true));

    if (!outputFileExists) {
        output.write(
                "windowSize\tlocation\tchromosome\tforward strand start\tforward strand end\treverse strand start\treverse strand end\teffective window size\tstatistic\n");
    }
    for (String windowWidthString : windowWidths.split("[,]")) {
        final int windowWidth = Integer.parseInt(windowWidthString);
        System.out.println("Processing window size=" + windowWidth);
        final HitBoundedPriorityQueue hits = new HitBoundedPriorityQueue(maxBestHits);
        DoInParallel scan = new DoInParallel() {
            @Override
            public void action(DoInParallel forDataAccess, String chromosome, int loopIndex) {
                compareStrands(hits, data, windowWidth, new MutableString(chromosome));
            }
        };

        try {
            scan.execute(true, data.getChromosomeStrings());
        } catch (Exception e) {
            e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
        }

        printResults(hits, windowWidth, data, output);
    }
    output.close();
}