Example usage for java.io BufferedWriter newLine

List of usage examples for java.io BufferedWriter newLine

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Introduction

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

Prototype

public void newLine() throws IOException

Source Link

Document

Writes a line separator.

Usage

From source file:me.ryanhamshire.griefprevention.DataStore.java

private void saveSoftMutes() {
    BufferedWriter outStream = null;

    try {//from ww w . j  a v  a  2s  . co  m
        // open the file and write the new value
        File softMuteFile = softMuteFilePath.toFile();
        softMuteFile.createNewFile();
        outStream = new BufferedWriter(new FileWriter(softMuteFile));

        for (Map.Entry<UUID, Boolean> entry : softMuteMap.entrySet()) {
            if (entry.getValue().booleanValue()) {
                outStream.write(entry.getKey().toString());
                outStream.newLine();
            }
        }

    }

    // if any problem, log it
    catch (Exception e) {
        GriefPreventionPlugin.addLogEntry("Unexpected exception saving soft mute data: " + e.getMessage());
        e.printStackTrace();
    }

    // close the file
    try {
        if (outStream != null) {
            outStream.close();
        }
    } catch (IOException exception) {
    }
}

From source file:de.dfki.km.perspecting.obie.experiments.PhraseExperiment.java

/**
 * Test method for/* ww w.  j a v  a 2s  .c  o m*/
 * {@link de.dfki.km.perspecting.obie.dixi.service.SimpleScobieService#extractInformationFromURL(java.lang.String, java.lang.String)}
 * .
 */
@Test
public void analyseTokenPhraseFrequencies() {
    final String template = "SELECT * WHERE {?s ?p ?o}";

    try {
        final BufferedWriter bw = new BufferedWriter(
                new FileWriter($SCOOBIE_HOME + "results/token_phrase_frequency_wikipedia.csv"));

        final String randomWikipediaPage = "http://en.wikipedia.org/wiki/Special:Random";

        bw.append("tok in doc\tnp in doc\ttok in nps\tdistinct tok in nps\tdistinct tok in doc");
        for (int i = 0; i < 100; i++) {

            Document document = pipeline.createDocument(FileUtils.toFile(new URL(randomWikipediaPage)),
                    new URI(randomWikipediaPage), MediaType.HTML, template, Language.EN);

            for (int step = 0; pipeline.hasNext(step) && step <= 5; step = pipeline.execute(step, document)) {
                System.out.println(step);
            }

            HashSet<String> wordsOfPhrases = new HashSet<String>();
            HashSet<String> wordsOfDocument = new HashSet<String>();

            for (Token token : document.getTokens()) {
                wordsOfDocument.add(token.toString());
            }

            int count = 0;
            for (TokenSequence<String> np : document.getNounPhrases()) {
                String[] words = np.toString().split("[\\s]+");
                count += words.length;
                wordsOfPhrases.addAll(Arrays.asList(words));
            }

            bw.append(document.getTokens().size() + "\t" + document.getNounPhrases().size() + "\t" + count
                    + "\t" + wordsOfPhrases.size() + "\t" + wordsOfDocument.size());
            bw.newLine();

        }
        bw.close();
    } catch (Exception e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }

    try {
        final BufferedWriter bw = new BufferedWriter(
                new FileWriter($SCOOBIE_HOME + "results/token_phrase_frequency_reuters.csv"));

        final TextCorpus corpus = new TextCorpus(new File("../corpora/reuters/reuters.zip"), MediaType.ZIP,
                MediaType.HTML, Language.EN);

        bw.append("tok in doc\tnp in doc\ttok in nps\tdistinct tok in nps\tdistinct tok in doc");

        corpus.forEach(new DocumentProcedure<URI>() {

            @Override
            public URI process(Reader reader, URI uri) throws Exception {

                Document document = pipeline.createDocument(reader, uri, corpus.getMediatype(), template,
                        corpus.getLanguage());

                for (int step = 0; pipeline.hasNext(step)
                        && step <= 5; step = pipeline.execute(step, document)) {
                    System.out.println(step);
                }

                HashSet<String> wordsOfPhrases = new HashSet<String>();
                HashSet<String> wordsOfDocument = new HashSet<String>();

                for (Token token : document.getTokens()) {
                    wordsOfDocument.add(token.toString());
                }

                int count = 0;
                for (TokenSequence<String> np : document.getNounPhrases()) {
                    String[] words = np.toString().split("[\\s]+");
                    count += words.length;
                    wordsOfPhrases.addAll(Arrays.asList(words));
                }

                bw.append(document.getTokens().size() + "\t" + document.getNounPhrases().size() + "\t" + count
                        + "\t" + wordsOfPhrases.size() + "\t" + wordsOfDocument.size());
                bw.newLine();
                return uri;
            }
        });

        bw.close();
    } catch (Exception e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }

}

From source file:gdsc.smlm.ij.plugins.TraceDiffusion.java

private void saveStatistics(StoredDataStatistics stats, String title, String label, boolean rounded) {
    if (!directoryChosen)
        rawDataDirectory = Utils.getDirectory("Data_directory", rawDataDirectory);
    directoryChosen = true;/*from  w w  w . ja v a  2  s .  c om*/
    if (rawDataDirectory == null)
        return;
    String filename = rawDataDirectory + title.replace("/", " per ").replace("*", "star") + ".txt";

    BufferedWriter out = null;
    try {
        FileOutputStream fos = new FileOutputStream(filename);
        out = new BufferedWriter(new OutputStreamWriter(fos, "UTF-8"));
        out.write(label);
        out.newLine();
        double[] data = stats.getValues();
        Arrays.sort(data);
        if (rounded) {
            for (double d : data) {
                out.write(Utils.rounded(d, 4));
                out.newLine();
            }
        } else {
            for (double d : data) {
                out.write(Double.toString(d));
                out.newLine();
            }
        }
    } catch (Exception e) {
    } finally {
        if (out != null) {
            try {
                out.close();
            } catch (IOException e) {
            }
        }
    }
}

From source file:analytics.storage.store2csv.java

@Override
public void storeElementData(HashMap<String, Double> data, String metricName, String dataProvider,
        String analysisType, String headerColumn, Boolean fed) {
    // TODO Auto-generated method stub

    String sFileName = dataProvider + analysisType + ".csv";

    Properties props = new Properties();
    try {//from w ww.jav  a 2 s.  c  om
        props.load(new FileInputStream("configure.properties"));
    } catch (FileNotFoundException e1) {
        // TODO Auto-generated catch block
        e1.printStackTrace();
        System.exit(-1);
    } catch (IOException e1) {
        // TODO Auto-generated catch block
        e1.printStackTrace();
        System.exit(-1);
    }

    File anls = new File(props.getProperty(AnalyticsConstants.resultsPath) + "Analysis_Results");

    if (!anls.exists())
        anls.mkdir();

    File dir = new File(anls, dataProvider);
    if (!dir.exists())
        dir.mkdir();

    File file = new File(dir, sFileName);

    this.setElementDataFilePath(file.getAbsolutePath());
    FileWriter writer = null;
    BufferedWriter bw = null;

    BufferedReader reader = null;
    try {

        if (file.exists() && isAppendData() == false) {

            if (fed == false)
                file.delete();
            setAppend(true);
        } else if (!file.exists() && isAppendData() == false)
            setAppend(true);

        if (!file.exists() && isAppendData() == true) {
            writer = new FileWriter(file);
            bw = new BufferedWriter(writer);
            createHeaders(bw, metricName, headerColumn);

            Set<String> keySet = data.keySet();
            Iterator<String> iterator = keySet.iterator();

            StringBuffer key = new StringBuffer();
            while (iterator.hasNext()) {
                // String key = iterator.next();
                key.append(iterator.next());
                // System.out.println(key);
                bw.append(key.toString());
                bw.append(',');
                Double value = data.get(key.toString());
                bw.append(String.valueOf(value));
                bw.newLine();
                key.delete(0, key.length());
            }

            bw.close();
            writer.close();
        } else if (file.exists() && isAppendData() == true) {

            reader = new BufferedReader(new FileReader(file));

            File temp = new File(dir, "temp.csv");

            writer = new FileWriter(temp);
            bw = new BufferedWriter(writer);

            String line;
            int counter = 0;

            // Set<String> keySet = data.keySet();
            // Iterator<String> iterator = keySet.iterator();

            StringBuffer key = new StringBuffer();
            while ((line = reader.readLine()) != null) {

                String[] split = line.split(",");

                // String key = split[0];
                key.append(split[0]);

                if (counter == 0) {
                    line = line + "," + metricName;
                    bw.append(line);
                    bw.newLine();

                } else {

                    Double value = data.get(key.toString());
                    // System.out.println("Appending key:" + key +
                    // " value:"
                    // + value);
                    line = line + "," + value;
                    // /System.out.println("Appending line:" + line);
                    bw.append(line);
                    bw.newLine();
                }

                counter += 1;
                key.delete(0, key.length());

            }
            bw.close();
            writer.close();

            FileUtils.copyFile(temp, file);
            temp.delete();
            reader.close();

        }

    } catch (IOException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    } finally {
        try {
            if (bw != null)
                bw.close();
            if (reader != null)
                reader.close();
            if (writer != null)
                writer.close();
        } catch (IOException ex) {
            ex.printStackTrace();
        }
    }
}

From source file:com.github.seqware.queryengine.system.exporters.VCFDumper.java

/**
 * <p>dumpVCFFromFeatureSetID.</p>
 *
 * @param fSet a {@link com.github.seqware.queryengine.model.FeatureSet} object.
 * @param file a {@link java.lang.String} object.
 *///  www.  j  a  va  2s  .c  o  m
public static void dumpVCFFromFeatureSetID(FeatureSet fSet, String file) {
    BufferedWriter outputStream = null;

    try {
        if (file != null) {
            outputStream = new BufferedWriter(new FileWriter(file));
        } else {
            outputStream = new BufferedWriter(new OutputStreamWriter(System.out));
        }
        outputStream.append("#CHROM   POS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\n");
    } catch (IOException e) {
        Logger.getLogger(VCFDumper.class.getName()).fatal("Exception thrown starting export to file:", e);
        System.exit(-1);
    }

    boolean caughtNonVCF = false;
    boolean mrSuccess = false;
    if (SWQEFactory.getQueryInterface() instanceof MRHBasePersistentBackEnd) {
        // hack to use VCF MR
        if (SWQEFactory.getModelManager() instanceof MRHBaseModelManager) {
            try {
                // pretend that the included com.github.seqware.queryengine.plugins.hbasemr.MRFeaturesByAttributesPlugin is an external plug-in
                Class<? extends PluginInterface> arbitraryPlugin;
                arbitraryPlugin = VCFDumperPlugin.class;
                // get a FeatureSet from the back-end
                QueryFuture<File> future = SWQEFactory.getQueryInterface().getFeaturesByPlugin(0,
                        arbitraryPlugin, fSet);
                File get = future.get();
                BufferedReader in = new BufferedReader(new FileReader(get));
                IOUtils.copy(in, outputStream);
                in.close();
                get.deleteOnExit();
                outputStream.flush();
                outputStream.close();
                mrSuccess = true;
            } catch (IOException e) {
                // fail out on IO error
                Logger.getLogger(VCFDumper.class.getName()).fatal("Exception thrown exporting to file:", e);
                System.exit(-1);
            } catch (Exception e) {
                Logger.getLogger(VCFDumper.class.getName())
                        .info("MapReduce exporting failed, falling-through to normal exporting to file");
                // fall-through and do normal exporting if Map Reduce exporting fails
            }
        } // TODO: clearly this should be expanded to include closing database etc 
    }
    if (mrSuccess) {
        return;
    }
    // fall-through if plugin-fails
    try {
        for (Feature feature : fSet) {
            StringBuffer buffer = new StringBuffer();
            boolean caught = outputFeatureInVCF(buffer, feature);
            if (caught) {
                caughtNonVCF = true;
            }
            outputStream.append(buffer);
            outputStream.newLine();
        }
        outputStream.flush();
    } catch (IOException e) {
        Logger.getLogger(VCFDumper.class.getName()).fatal("Exception thrown exporting to file:", e);
        System.exit(-1);
    } finally {
        IOUtils.closeQuietly(outputStream);
    }
}

From source file:gdsc.smlm.ij.plugins.TraceDiffusion.java

private void saveMSD(double[] x, double[] y, double[] se) {
    if (!directoryChosen)
        rawDataDirectory = Utils.getDirectory("Data_directory", rawDataDirectory);
    directoryChosen = true;/*  ww w .  ja v  a2s . c  o m*/
    if (rawDataDirectory == null)
        return;
    String filename = rawDataDirectory + "MSD.txt";

    BufferedWriter out = null;
    try {
        FileOutputStream fos = new FileOutputStream(filename);
        out = new BufferedWriter(new OutputStreamWriter(fos, "UTF-8"));
        out.write("Time (s)\tDistance (um^2)\tS.E.");
        out.newLine();
        for (int i = 0; i < x.length; i++) {
            out.write(Utils.rounded(x[i]));
            out.write('\t');
            out.write(Double.toString(y[i]));
            out.write('\t');
            out.write(Double.toString(se[i]));
            out.newLine();
        }
    } catch (Exception e) {
    } finally {
        if (out != null) {
            try {
                out.close();
            } catch (IOException e) {
            }
        }
    }
}

From source file:ffx.ui.KeywordPanel.java

/**
 * <p>/*from  ww w . j  a va 2 s . c  om*/
 * saveKeywords</p>
 *
 * @param keyFile a {@link java.io.File} object.
 * @param keywordHashMap a {@link java.util.LinkedHashMap} object.
 * @param comments a {@link java.lang.StringBuilder} object.
 * @return a boolean.
 */
public boolean saveKeywords(File keyFile, LinkedHashMap<String, KeywordComponent> keywordHashMap,
        StringBuilder comments) {
    synchronized (this) {
        FileWriter fw = null;
        BufferedWriter bw = null;
        try {
            fw = new FileWriter(keyFile);
            bw = new BufferedWriter(fw);
            boolean writegroup = false;
            String pgroup = null;
            // Write out keywords in groups
            for (KeywordComponent keyword : keywordHashMap.values()) {
                String group = keyword.getKeywordGroup();
                if (pgroup == null || !group.equalsIgnoreCase(pgroup)) {
                    writegroup = true;
                    pgroup = group;
                }
                String line = keyword.toString();
                if (line != null) {
                    if (writegroup == true) {
                        bw.newLine();
                        bw.write("# " + group);
                        bw.newLine();
                        writegroup = false;
                    }
                    bw.write(line);
                    bw.newLine();
                }
            }
            bw.newLine();
            String s = comments.toString();
            if (s != null && !s.trim().equals("")) {
                bw.write(s.trim());
            }
            bw.newLine();
            bw.flush();
            KeywordComponent.setKeywordModified(false);
        } catch (FileNotFoundException e) {
            logger.warning(e.toString());
            return false;
        } catch (IOException e) {
            logger.warning(e.toString());
            return false;
        } finally {
            try {
                if (bw != null) {
                    bw.close();
                }
                if (fw != null) {
                    fw.close();
                }
            } catch (Exception e) {
                logger.warning(e.toString());
            }
        }
        return true;
    }
}

From source file:com.thalesgroup.hudson.plugins.klocwork.util.KloXMLGenerator.java

public static String GenerateXMLFromIssues(String a_host, String a_port, boolean useSSL, String a_projectname,
        String a_filename, BuildListener listener, String a_query, String a_user) {
    String kwurl = "";
    if (useSSL) {
        kwurl = "https://" + a_host + ":" + a_port;
    } else {//from w  ww  . j  a  va 2s  . c  om
        kwurl = "http://" + a_host + ":" + a_port;
    }
    listener.getLogger().println("Connecting to Klocwork Web API service... " + kwurl);
    KWApi KWservice = new KWApi(kwurl);

    try {
        listener.getLogger().println("creating XML document");
        File outputFile = new File(a_filename);
        if (outputFile.exists()) {
            outputFile.delete();
        }
        BufferedWriter bw = null;
        try {
            bw = new BufferedWriter(new FileWriter(outputFile));
            if (outputFile.canWrite()) {
                //Get issues
                listener.getLogger().println("Retrieving Klocwork issues using kwjlib...");
                listener.getLogger()
                        .println("Sending request for project: " + a_projectname + " with query: " + a_query);
                ArrayList<JSONObject> issues = KWservice.search(a_projectname, a_query, null, null, null);
                if (issues != null) {
                    listener.getLogger().println("Number of issues returned: " + issues.size());
                    bw.write(
                            "<?xml version=\"1.0\" encoding=\"UTF-8\" ?><errorList xmlns=\"http://www.klocwork.com/inForce/report/1.0\">");
                    //Iterate through issues
                    for (JSONObject issue : issues) {
                        if (issue != null) {
                            try {
                                if (issue.has("id") && issue.optString("id").length() > 0) {
                                    String id = StringEscapeUtils.escapeXml(issue.optString("id"));
                                    String file = StringEscapeUtils.escapeXml(issue.optString("file"));
                                    String method = StringEscapeUtils.escapeXml(issue.optString("method"));
                                    String code = StringEscapeUtils.escapeXml(issue.optString("code"));
                                    String message = StringEscapeUtils.escapeXml(issue.optString("message"));
                                    String status = StringEscapeUtils.escapeXml(issue.optString("status"));
                                    String state = StringEscapeUtils.escapeXml(issue.optString("state"));
                                    String owner = StringEscapeUtils.escapeXml(issue.optString("owner"));
                                    String severity = StringEscapeUtils.escapeXml(issue.optString("severity"));
                                    String severityCode = StringEscapeUtils
                                            .escapeXml(issue.optString("severityCode"));
                                    String taxonomyName = StringEscapeUtils
                                            .escapeXml(issue.optString("taxonomyName"));
                                    String url = StringEscapeUtils.escapeXml(issue.optString("url"));
                                    bw.write("<problem>");
                                    bw.newLine();
                                    bw.write("<problemID>" + id + "</problemID>");
                                    bw.newLine();
                                    bw.write("<file>" + file + "</file>");
                                    bw.newLine();
                                    bw.write("<method>" + method + "</method>");
                                    bw.newLine();
                                    bw.write("<code>" + code + "</code>");
                                    bw.newLine();
                                    bw.write("<message>" + message + "</message>");
                                    bw.newLine();
                                    bw.write("<citingStatus>" + status + "</citingStatus>");
                                    bw.newLine();
                                    bw.write("<state>" + state + "</state>");
                                    bw.newLine();
                                    bw.write("<owner>" + owner + "</owner>");
                                    bw.newLine();
                                    bw.write("<severity>" + severity + "</severity>");
                                    bw.newLine();
                                    bw.write("<severitylevel>" + severityCode + "</severitylevel>");
                                    bw.newLine();
                                    bw.write("<displayAs>" + severity + "</displayAs>");
                                    bw.newLine();
                                    bw.write("<taxonomies>");
                                    bw.newLine();
                                    bw.write("<taxonomy name=\"" + taxonomyName + "\" metaInf=\"\" />");
                                    bw.newLine();
                                    bw.write("</taxonomies>");
                                    bw.newLine();
                                    bw.write("<url>" + url + "</url>");
                                    bw.newLine();
                                    bw.write("</problem>");
                                    bw.newLine();
                                }
                            } catch (Exception e) {
                                listener.getLogger().println("[ERROR]: " + e.getMessage());
                                listener.getLogger().println("\tissue: " + issue.toString());
                                e.printStackTrace();
                            }
                        }
                    }
                    bw.write("</errorList>");
                } else {
                    listener.getLogger().println("ERROR: Unable to get issues from Klocwork server");
                    if (!KWservice.errorMessage.isEmpty()) {
                        for (JSONObject message : KWservice.errorMessage) {
                            listener.getLogger().println("\t" + message.toString());
                        }
                        KWservice.errorMessage.clear();
                    }
                    return "1";
                }
            } else {
                listener.getLogger()
                        .println("ERROR while generating XML. Could not open file for writing: " + a_filename);
            }
        } finally {
            if (bw != null) {
                bw.close();
            }
        }
    } catch (IOException ioe) {
        listener.getLogger().println("ERROR while generating XML - IOException:" + ioe.getMessage());
        return "1";
    }
    File outputFile = new File(a_filename);
    if (outputFile.exists() && outputFile.length() > 0) {
        listener.getLogger().println("Creation of XML file complete. Closing connection to Web API.");
    } else {
        listener.getLogger().println(
                "Creation of XML file failed. You may have to run the kwauth command on your machine.");
    }
    return "0";
}

From source file:json_csv.JSON2CSV.java

public void printIngredientToCSV(Recipe recipe, BufferedWriter ibw) {

    Recipe newRecipe = recipe;//  w  ww  .  j a  va  2 s.  co m
    Ingredient ingredient = null;
    StringBuffer oneLine = null;
    BufferedWriter newIbw = ibw;

    //String[] header = {"INGREDIENT_ID", "AISLE", "NAME", "AMOUNT", "ORIGINAL_STRING", "IMAGE", "UNIT", "UNIT_SHORT",
    //        "UNIT_LONG", "RECIPE_ID"};

    try {
        System.out.println(newRecipe.getExtendedIngredients().size());

        for (int i = 0; i < newRecipe.getExtendedIngredients().size(); i++) {

            ingredient = newRecipe.getExtendedIngredients().get(i);
            oneLine = new StringBuffer();

            oneLine.append(ingredient.getIngredientID());
            oneLine.append(CSV_SEPARATOR);
            oneLine.append(ingredient.getAisle().replace(",", ";"));
            oneLine.append(CSV_SEPARATOR);
            oneLine.append(ingredient.getName());
            oneLine.append(CSV_SEPARATOR);
            oneLine.append(ingredient.getAmount());
            oneLine.append(CSV_SEPARATOR);
            oneLine.append((ingredient.getOriginalString().replace(",", " ")));
            oneLine.append(CSV_SEPARATOR);
            oneLine.append(ingredient.getImage());
            oneLine.append(CSV_SEPARATOR);
            oneLine.append(ingredient.getUnit());
            oneLine.append(CSV_SEPARATOR);
            oneLine.append(ingredient.getUnitShort());
            oneLine.append(CSV_SEPARATOR);
            oneLine.append(ingredient.getUnitLong());
            oneLine.append(CSV_SEPARATOR);
            oneLine.append(recipe.getId());

            ibw.write(oneLine.toString());
            ibw.newLine();

        }
    } catch (UnsupportedEncodingException e) {
    } catch (FileNotFoundException e) {
    } catch (IOException e) {
    }

}

From source file:gov.nih.nci.ncicb.tcga.dcc.qclive.common.util.DownloadNCBITraceXML.java

public void saveFullXMLFiles(int p) {

    BufferedReader br = null;/*from   ww w.j  a  va  2s .c o  m*/
    BufferedWriter bw = null;

    try {
        String pagesquery = "http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?&cmd=retrieve&val=PROJECT_NAME%3D%22TCGA%22%20and%20LOAD_DATE%3E%3D%22"
                + latestLoaddate + "%22&size=" + querysize + "&dopt=xml_info&dispmax=" + pagesize + "&page="
                + p;
        //String pagesquery = "http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?&cmd=retrieve&val=project_name%3D%22TCGA%22%20and%20load_date%3E%3D%2204%2F09%2F2008%22&dopt=info&size=490552&dispmax=5&page=4&next=%3E%3E
        URL url = new URL(pagesquery);
        HttpURLConnection connection = (HttpURLConnection) url.openConnection();
        //System.out.println( "url = " + url );
        is = connection.getInputStream();
        //noinspection IOResourceOpenedButNotSafelyClosed
        br = new BufferedReader(new InputStreamReader(is));
        String line;
        fw = new FileWriter(downloaddir + File.separator + xmlfiles + "." + p + ".xml");
        //fw= new FileWriter("C:\\larry\\WorkingDoc\\"+ latestLoaddate + "\\" + xmlfiles + "." + p + ".xml");
        //noinspection IOResourceOpenedButNotSafelyClosed
        bw = new BufferedWriter(fw);
        bw.write("<traces>");
        while ((line = br.readLine()) != null) {
            for (int i = 0; i < allFieldsWeCare.length; i++) {
                if (line.contains(allFieldsWeCare[i])) {
                    if (line.contains("<pre><trace>")) {
                        line = "<trace>";
                        //System.out.println(line);
                        bw.write(line);
                        bw.newLine();
                    } else {
                        //System.out.println(line);
                        bw.write(line);
                        bw.newLine();
                    }
                }
            }
        }
        bw.write("</traces>");
        is.close();
        connection.disconnect();
    } catch (MalformedURLException e) {
        getLogger().logToLogger(Level.ERROR,
                "DownloadNCBITraceXML saveXMLFiles MalformedURLException " + e.toString());
    } catch (IOException e) {
        getLogger().logToLogger(Level.ERROR, "DownloadNCBITraceXML saveXMLFiles IOException " + e.toString());
    } finally {
        IOUtils.closeQuietly(br);
        IOUtils.closeQuietly(bw);
    }
}