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:DataCrawler.OpenAIRE.XMLGenerator.java

public static void main(String[] args) {
    String text = "";

    try {//  w  ww  .  ja  va2 s . com
        if (args.length < 4) {
            System.out.println("<command> template_file csv_file output_dir log_file [start_id]");
        }

        // InputStream fis = new FileInputStream("E:/Downloads/result-r-00000");
        InputStream fis = new FileInputStream(args[1]);
        BufferedReader br = new BufferedReader(new InputStreamReader(fis, Charset.forName("UTF-8")));

        // String content = new String(Files.readAllBytes(Paths.get("publications_template.xml")));
        String content = new String(Files.readAllBytes(Paths.get(args[0])));
        Document doc = Jsoup.parse(content, "UTF-8", Parser.xmlParser());
        // String outputDirectory = "G:/";
        String outputDirectory = args[2];
        // PrintWriter logWriter = new PrintWriter(new FileOutputStream("publication.log",false));
        PrintWriter logWriter = new PrintWriter(new FileOutputStream(args[3], false));
        Element objectId = null, title = null, publisher = null, dateofacceptance = null, bestlicense = null,
                resulttype = null, originalId = null, originalId2 = null;
        boolean start = true;
        // String startID = "dedup_wf_001::207a098867b64f3b5af505fa3aeecd24";
        String startID = "";
        if (args.length >= 5) {
            start = false;
            startID = args[4];
        }
        String previousText = "";
        while ((text = br.readLine()) != null) {
            /*  For publications:
                0. dri:objIdentifier context
               9. title context
               12. publisher context
               18. dateofacceptance
               19. bestlicense @classname
               21. resulttype  @classname
               26. originalId context  
               (Notice that the prefix is null and will use space to separate two different "originalId")
            */

            if (!previousText.isEmpty()) {
                text = previousText + text;
                start = true;
                previousText = "";
            }

            String[] items = text.split("!");
            for (int i = 0; i < items.length; ++i) {
                items[i] = StringUtils.strip(items[i], "#");
            }
            if (objectId == null)
                objectId = doc.getElementsByTag("dri:objIdentifier").first();
            objectId.text(items[0]);

            if (!start && items[0].equals(startID)) {
                start = true;
            }

            if (title == null)
                title = doc.getElementsByTag("title").first();
            title.text(items[9]);

            if (publisher == null)
                publisher = doc.getElementsByTag("publisher").first();

            if (items.length < 12) {
                previousText = text;
                continue;
            }
            publisher.text(items[12]);

            if (dateofacceptance == null)
                dateofacceptance = doc.getElementsByTag("dateofacceptance").first();
            dateofacceptance.text(items[18]);

            if (bestlicense == null)
                bestlicense = doc.getElementsByTag("bestlicense").first();
            bestlicense.attr("classname", items[19]);

            if (resulttype == null)
                resulttype = doc.getElementsByTag("resulttype").first();
            resulttype.attr("classname", items[21]);

            if (originalId == null || originalId2 == null) {
                Elements elements = doc.getElementsByTag("originalId");
                String[] context = items[26].split(" ");
                if (elements.size() > 0) {
                    if (elements.size() >= 1) {
                        originalId = elements.get(0);
                        if (context.length >= 1) {
                            int indexOfnull = context[0].trim().indexOf("null");
                            String value = "";
                            if (indexOfnull != -1) {
                                if (context[0].trim().length() >= (indexOfnull + 5))
                                    value = context[0].trim().substring(indexOfnull + 5);

                            } else {
                                value = context[0].trim();
                            }
                            originalId.text(value);
                        }
                    }
                    if (elements.size() >= 2) {
                        originalId2 = elements.get(1);
                        if (context.length >= 2) {
                            int indexOfnull = context[1].trim().indexOf("null");
                            String value = "";
                            if (indexOfnull != -1) {
                                if (context[1].trim().length() >= (indexOfnull + 5))
                                    value = context[1].trim().substring(indexOfnull + 5);

                            } else {
                                value = context[1].trim();
                            }
                            originalId2.text(value);
                        }
                    }
                }
            } else {
                String[] context = items[26].split(" ");
                if (context.length >= 1) {
                    int indexOfnull = context[0].trim().indexOf("null");
                    String value = "";
                    if (indexOfnull != -1) {
                        if (context[0].trim().length() >= (indexOfnull + 5))
                            value = context[0].trim().substring(indexOfnull + 5);

                    } else {
                        value = context[0].trim();
                    }
                    originalId.text(value);
                }
                if (context.length >= 2) {
                    int indexOfnull = context[1].trim().indexOf("null");
                    String value = "";
                    if (indexOfnull != -1) {
                        if (context[1].trim().length() >= (indexOfnull + 5))
                            value = context[1].trim().substring(indexOfnull + 5);

                    } else {
                        value = context[1].trim();
                    }
                    originalId2.text(value);
                }
            }
            if (start) {
                String filePath = outputDirectory + items[0].replace(":", "#") + ".xml";
                PrintWriter writer = new PrintWriter(new FileOutputStream(filePath, false));
                logWriter.write(filePath + " > Start" + System.lineSeparator());
                writer.write("<?xml version=\"1.0\" encoding=\"UTF-8\"?>" + System.lineSeparator());
                writer.write(doc.getElementsByTag("response").first().toString());
                writer.close();
                logWriter.write(filePath + " > OK" + System.lineSeparator());
                logWriter.flush();
            }

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

From source file:edu.msu.cme.rdp.multicompare.Main.java

public static void main(String[] args) throws Exception {
    PrintStream hier_out = null;//  w ww . j  a  v a  2s .  c o m
    PrintWriter assign_out = new PrintWriter(new NullWriter());
    PrintStream bootstrap_out = null;
    File hier_out_filename = null;
    String propFile = null;
    File biomFile = null;
    File metadataFile = null;
    PrintWriter shortseq_out = null;
    List<MCSample> samples = new ArrayList();
    ClassificationResultFormatter.FORMAT format = ClassificationResultFormatter.FORMAT.allRank;
    float conf = CmdOptions.DEFAULT_CONF;
    String gene = null;
    int min_bootstrap_words = Classifier.MIN_BOOTSTRSP_WORDS;

    try {
        CommandLine line = new PosixParser().parse(options, args);

        if (line.hasOption(CmdOptions.OUTFILE_SHORT_OPT)) {
            assign_out = new PrintWriter(line.getOptionValue(CmdOptions.OUTFILE_SHORT_OPT));
        } else {
            throw new IllegalArgumentException("Require the output file for classification assignment");
        }
        if (line.hasOption(CmdOptions.HIER_OUTFILE_SHORT_OPT)) {
            hier_out_filename = new File(line.getOptionValue(CmdOptions.HIER_OUTFILE_SHORT_OPT));
            hier_out = new PrintStream(hier_out_filename);
        }
        if (line.hasOption(CmdOptions.BIOMFILE_SHORT_OPT)) {
            biomFile = new File(line.getOptionValue(CmdOptions.BIOMFILE_SHORT_OPT));
        }
        if (line.hasOption(CmdOptions.METADATA_SHORT_OPT)) {
            metadataFile = new File(line.getOptionValue(CmdOptions.METADATA_SHORT_OPT));
        }

        if (line.hasOption(CmdOptions.TRAINPROPFILE_SHORT_OPT)) {
            if (gene != null) {
                throw new IllegalArgumentException(
                        "Already specified the gene from the default location. Can not specify train_propfile");
            } else {
                propFile = line.getOptionValue(CmdOptions.TRAINPROPFILE_SHORT_OPT);
            }
        }
        if (line.hasOption(CmdOptions.FORMAT_SHORT_OPT)) {
            String f = line.getOptionValue(CmdOptions.FORMAT_SHORT_OPT);
            if (f.equalsIgnoreCase("allrank")) {
                format = ClassificationResultFormatter.FORMAT.allRank;
            } else if (f.equalsIgnoreCase("fixrank")) {
                format = ClassificationResultFormatter.FORMAT.fixRank;
            } else if (f.equalsIgnoreCase("filterbyconf")) {
                format = ClassificationResultFormatter.FORMAT.filterbyconf;
            } else if (f.equalsIgnoreCase("db")) {
                format = ClassificationResultFormatter.FORMAT.dbformat;
            } else if (f.equalsIgnoreCase("biom")) {
                format = ClassificationResultFormatter.FORMAT.biom;
            } else {
                throw new IllegalArgumentException(
                        "Not an valid output format, only allrank, fixrank, biom, filterbyconf and db allowed");
            }
        }
        if (line.hasOption(CmdOptions.GENE_SHORT_OPT)) {
            if (propFile != null) {
                throw new IllegalArgumentException(
                        "Already specified train_propfile. Can not specify gene any more");
            }
            gene = line.getOptionValue(CmdOptions.GENE_SHORT_OPT).toLowerCase();

            if (!gene.equals(ClassifierFactory.RRNA_16S_GENE) && !gene.equals(ClassifierFactory.FUNGALLSU_GENE)
                    && !gene.equals(ClassifierFactory.FUNGALITS_warcup_GENE)
                    && !gene.equals(ClassifierFactory.FUNGALITS_unite_GENE)) {
                throw new IllegalArgumentException(gene + " not found, choose from"
                        + ClassifierFactory.RRNA_16S_GENE + ", " + ClassifierFactory.FUNGALLSU_GENE + ", "
                        + ClassifierFactory.FUNGALITS_warcup_GENE + ", "
                        + ClassifierFactory.FUNGALITS_unite_GENE);
            }
        }
        if (line.hasOption(CmdOptions.MIN_BOOTSTRAP_WORDS_SHORT_OPT)) {
            min_bootstrap_words = Integer
                    .parseInt(line.getOptionValue(CmdOptions.MIN_BOOTSTRAP_WORDS_SHORT_OPT));
            if (min_bootstrap_words < Classifier.MIN_BOOTSTRSP_WORDS) {
                throw new IllegalArgumentException(CmdOptions.MIN_BOOTSTRAP_WORDS_LONG_OPT
                        + " must be at least " + Classifier.MIN_BOOTSTRSP_WORDS);
            }
        }
        if (line.hasOption(CmdOptions.BOOTSTRAP_SHORT_OPT)) {
            String confString = line.getOptionValue(CmdOptions.BOOTSTRAP_SHORT_OPT);
            try {
                conf = Float.valueOf(confString);
            } catch (NumberFormatException e) {
                throw new IllegalArgumentException("Confidence must be a decimal number");
            }

            if (conf < 0 || conf > 1) {
                throw new IllegalArgumentException("Confidence must be in the range [0,1]");
            }
        }
        if (line.hasOption(CmdOptions.SHORTSEQ_OUTFILE_SHORT_OPT)) {
            shortseq_out = new PrintWriter(line.getOptionValue(CmdOptions.SHORTSEQ_OUTFILE_SHORT_OPT));
        }
        if (line.hasOption(CmdOptions.BOOTSTRAP_OUTFILE_SHORT_OPT)) {
            bootstrap_out = new PrintStream(line.getOptionValue(CmdOptions.BOOTSTRAP_OUTFILE_SHORT_OPT));
        }

        if (format.equals(ClassificationResultFormatter.FORMAT.biom) && biomFile == null) {
            throw new IllegalArgumentException("biom format requires an input biom file");
        }
        if (biomFile != null) { // if input biom file provided, use biom format
            format = ClassificationResultFormatter.FORMAT.biom;
        }

        args = line.getArgs();
        for (String arg : args) {
            String[] inFileNames = arg.split(",");
            File inputFile = new File(inFileNames[0]);
            File idmappingFile = null;
            if (!inputFile.exists()) {
                throw new IllegalArgumentException("Failed to find input file \"" + inFileNames[0] + "\"");
            }
            if (inFileNames.length == 2) {
                idmappingFile = new File(inFileNames[1]);
                if (!idmappingFile.exists()) {
                    throw new IllegalArgumentException("Failed to find input file \"" + inFileNames[1] + "\"");
                }
            }

            MCSample nextSample = new MCSample(inputFile, idmappingFile);
            samples.add(nextSample);
        }
        if (propFile == null && gene == null) {
            gene = CmdOptions.DEFAULT_GENE;
        }
        if (samples.size() < 1) {
            throw new IllegalArgumentException("Require at least one sample files");
        }
    } catch (Exception e) {
        System.out.println("Command Error: " + e.getMessage());
        new HelpFormatter().printHelp(80, " [options] <samplefile>[,idmappingfile] ...", "", options, "");
        return;
    }

    MultiClassifier multiClassifier = new MultiClassifier(propFile, gene, biomFile, metadataFile);
    MultiClassifierResult result = multiClassifier.multiCompare(samples, conf, assign_out, format,
            min_bootstrap_words);
    assign_out.close();
    if (hier_out != null) {
        DefaultPrintVisitor printVisitor = new DefaultPrintVisitor(hier_out, samples);
        result.getRoot().topDownVisit(printVisitor);
        hier_out.close();
        if (multiClassifier.hasCopyNumber()) {
            // print copy number corrected counts
            File cn_corrected_s = new File(hier_out_filename.getParentFile(),
                    "cnadjusted_" + hier_out_filename.getName());
            PrintStream cn_corrected_hier_out = new PrintStream(cn_corrected_s);
            printVisitor = new DefaultPrintVisitor(cn_corrected_hier_out, samples, true);
            result.getRoot().topDownVisit(printVisitor);
            cn_corrected_hier_out.close();
        }
    }

    if (bootstrap_out != null) {
        for (MCSample sample : samples) {
            MCSamplePrintUtil.printBootstrapCountTable(bootstrap_out, sample);
        }
        bootstrap_out.close();
    }

    if (shortseq_out != null) {
        for (String id : result.getBadSequences()) {
            shortseq_out.write(id + "\n");
        }
        shortseq_out.close();
    }

}

From source file:Main.java

private static void writeFile(String filePath, String content) throws IOException {
    FileWriter fw = new FileWriter(filePath);
    PrintWriter out = new PrintWriter(fw);
    out.write(content);
    out.println();//from  ww  w .  j a  v  a 2s.c  om
    fw.close();
    out.close();
}

From source file:de.tudarmstadt.ukp.dkpro.c4corpus.boilerplate.standalone.HTMLBoilerplateRemoval.java

public static void processHtmlFile(File input, File outFile, boolean keepMinimalHtml) throws IOException {
    // read the html file
    String html = FileUtils.readFileToString(input, "utf-8");

    // boilerplate removal
    String cleanText;//from   ww  w.ja v  a 2  s . co  m
    if (keepMinimalHtml) {
        cleanText = boilerPlateRemoval.getMinimalHtml(html, null);
    } else {
        cleanText = boilerPlateRemoval.getPlainText(html, null);
    }

    // write to the output file
    PrintWriter writer = new PrintWriter(outFile, "utf-8");
    writer.write(cleanText);

    writer.close();
}

From source file:de.tudarmstadt.ukp.dkpro.c4corpus.hadoop.statistics.StatisticsTableCreator.java

public static void saveTableToCsv(Table<String, String, Long> table, OutputStream outputStream) {
    PrintWriter pw = new PrintWriter(outputStream);
    pw.write(";");
    for (String columnKey : table.columnKeySet()) {
        pw.printf("%s;", columnKey);
    }//from w w  w.j  av  a2 s.c o  m
    pw.println();

    for (String rowKey : table.rowKeySet()) {
        pw.printf("%s;", rowKey);
        for (String columnKey : table.columnKeySet()) {
            Long value = table.get(rowKey, columnKey);
            pw.printf("%d;", value != null ? value : 0);
        }
        pw.println();
    }

    IOUtils.closeQuietly(pw);
}

From source file:com.yolodata.tbana.testutils.FileTestUtils.java

public static boolean createFileWithContent(String filepath, String content) throws IOException {
    File f = new File(filepath);
    if (!f.createNewFile())
        return false;

    PrintWriter pw = new PrintWriter(f);
    pw.write(content);
    pw.close();/*  www  . j  av a 2 s .  co m*/

    return true;
}

From source file:com.arsdigita.util.parameter.ParameterPrinter.java

private static void writeRecord(final ParameterContext record, final PrintWriter out) {
    out.write("<record>");

    final Parameter[] params = record.getParameters();

    for (int i = 0; i < params.length; i++) {
        writeParameter(params[i], out);/*from  w w w.ja  v a2  s . c  om*/
    }

    out.write("</record>");
}

From source file:com.arsdigita.util.parameter.ParameterPrinter.java

private static void writeXML(final PrintWriter out) {
    out.write("<?xml version=\"1.0\"?>");
    out.write("<records>");

    final Iterator records = s_records.iterator();

    while (records.hasNext()) {
        writeRecord(((ParameterContext) records.next()), out);
    }// w w w  .  ja  v  a 2 s.  c  om

    out.write("</records>");
    out.close();
}

From source file:com.arsdigita.util.parameter.ParameterPrinter.java

private static void writeParameter(final Parameter param, final PrintWriter out) {
    out.write("<parameter>");

    field(out, "name", param.getName());

    if (param.isRequired()) {
        out.write("<required/>");
    }/*from   w  w  w  .  ja v a 2 s. c o m*/

    final ParameterInfo info = param.getInfo();

    if (info != null) {
        field(out, "title", info.getTitle());
        field(out, "purpose", info.getPurpose());
        field(out, "example", info.getExample());
        field(out, "format", info.getFormat());
    }

    out.write("</parameter>");
}

From source file:de.ocarthon.core.utility.GzipCompression.java

public static void compress(String input, OutputStream os) throws IOException {
    GZIPOutputStream gos = null;/*from ww w.  ja va2s  .  com*/
    PrintWriter pw = null;

    try {
        gos = new GZIPOutputStream(os);
        pw = new PrintWriter(gos);
        pw.write(input);
    } finally {
        IOUtils.closeQuietly(pw);
        IOUtils.closeQuietly(gos);
    }
}