Java Code Examples for au.com.bytecode.opencsv.CSVWriter#NO_QUOTE_CHARACTER

/**
 * Reads a very basic tsv (numbers separated by tabs) into a RealMatrix.
 * <p>Very little error checking happens in this method</p>
 *
 * @param inputFile readable file.  Not {@code null}
 * @return never {@code null}
 */
public static RealMatrix readTsvIntoMatrix(final File inputFile) {
    IOUtils.canReadFile(inputFile);
    final List<double []> allData = new ArrayList<>();
    int ctr = 0;
    try {

        final CSVReader reader = new CSVReader(new FileReader(inputFile), '\t', CSVWriter.NO_QUOTE_CHARACTER);
        String[] nextLine;
        while ((nextLine = reader.readNext()) != null) {
            ctr++;
            allData.add(Arrays.stream(nextLine).filter(s -> StringUtils.trim(s).length() > 0).map(s -> Double.parseDouble(StringUtils.trim(s))).mapToDouble(d -> d).toArray());
        }
    } catch (final IOException ioe) {
        Assert.fail("Could not open test file: " + inputFile, ioe);
    }
    final RealMatrix result = new Array2DRowRealMatrix(allData.size(), allData.get(0).length);
    for (int i = 0; i < result.getRowDimension(); i++) {
        result.setRow(i, allData.get(i));
    }
    return result;
}
 

private Path createTempHdfsFileForInsertion(FixTable fixTable, TestRun testRun) throws Exception {

        Path pathToParent = new Path(testRun.getHdfsPrefix(), ".hive");
        Path pathTo = new Path(pathToParent, UUID.randomUUID().toString());
        FileSystem fileSystem = testRun.getCiContext().getFileSystem();
        fileSystem.mkdirs(pathTo.getParent());
        FSDataOutputStream outputStream = fileSystem.create(pathTo);

        CSVWriter writer = new CSVWriter(new OutputStreamWriter(outputStream), '\t', CSVWriter.NO_QUOTE_CHARACTER);

        for (FixTable.FixRow fixRow : fixTable.getRows()) {
            List<String> rowData = Lists.newArrayList();
            for (String colName : fixTable.getColumnNames()) {
                rowData.add(fixRow.getCells().get(colName));
            }
            String[] dataArray = rowData.toArray(new String[rowData.size()]);
            writer.writeNext(dataArray);
        }

        writer.close();

        fileSystem.setPermission(pathToParent, new FsPermission(FsAction.ALL, FsAction.ALL, FsAction.ALL));
        fileSystem.setPermission(pathTo, new FsPermission(FsAction.ALL, FsAction.ALL, FsAction.ALL));
        return pathTo;
    }
 

public CsvPrinter(List<String> fieldNames, Writer writer, CsvOutputFormat csvOutputFormat)
{
    requireNonNull(fieldNames, "fieldNames is null");
    requireNonNull(writer, "writer is null");
    this.fieldNames = ImmutableList.copyOf(fieldNames);
    this.writer = csvOutputFormat.isQuoted() ? new CSVWriter(writer) : new CSVWriter(writer, CSVWriter.DEFAULT_SEPARATOR, CSVWriter.NO_QUOTE_CHARACTER);
    this.needHeader = csvOutputFormat.showHeader();
}
 

private void writeMatrix(final RealMatrix m, final File outputFilename) throws IOException {
    final List<String []> textTable = new ArrayList<>();
    for (int i = 0; i < m.getRowDimension(); i ++){
        textTable.add(Arrays.stream(m.getRow(i)).mapToObj(Double::toString).toArray(String[]::new));
    }
    final FileWriter fw = new FileWriter(outputFilename);
    CSVWriter csvWriter = new CSVWriter(fw, '\t', CSVWriter.NO_QUOTE_CHARACTER);
    csvWriter.writeAll(textTable);
    csvWriter.flush();
    csvWriter.close();
}
 

public SkippedInteractionWriter(File skippedInteractionsFile) throws IOException {
	writer = new CSVWriter(new FileWriter(skippedInteractionsFile), '\t', CSVWriter.NO_QUOTE_CHARACTER);
	
	c = 0;
	row[c++] = "Covariate";
	row[c++] = "CountSingular";
	row[c++] = "CountSharedQtl";
	row[c++] = "SingularQtls";
	row[c++] = "SharedQtls";
	
	writer.writeNext(row);
}
 

private long readEndTime( File file ) throws Exception {
    CSVReader reader = new CSVReader( new FileReader( file ), SEPARATOR, CSVWriter.NO_QUOTE_CHARACTER, '\'' );
    try {
        String[] firstLine = reader.readNext();
        if ( "start".equals( firstLine[0] ) && "end".equals( firstLine[2] ) ) {
            return Long.parseLong( firstLine[3] );
        }
    }
    finally {
        reader.close();
    }
    return 0;
}
 

public static void main(String[] args) throws Exception {

		File oldResultsFile = new File(args[0]);
		File newResultsFile = new File(args[1]);
		int threads = Integer.parseInt(args[2]);

		System.out.println("Old: " + oldResultsFile.getAbsolutePath());
		System.out.println("New: " + newResultsFile.getAbsolutePath());
		System.out.println("Threads: " + threads);

		BufferedReader aseReader = new BufferedReader(new FileReader(oldResultsFile));

		ArrayList<AseVariantBean> inputAse = new ArrayList<AseVariantBean>();

		String line;
		String[] elements;
		//Header
		aseReader.readLine();
		while ((line = aseReader.readLine()) != null) {
			elements = TAB_PATTERN.split(line);
			inputAse.add(new AseVariantBean(elements));
		}
		aseReader.close();

		AseVariantRecalculate[] aseVariants = new AseVariantRecalculate[inputAse.size()];
		{
			int i = 0;
			for (AseVariantBean aseVariant : inputAse) {
				aseVariants[i] = new AseVariantRecalculate(aseVariant);
				++i;
			}
		}

		AseCalculator.startAseCalculators(aseVariants, threads);

		System.out.println("Completed ASE calculations");

		CSVWriter mappingReportWriter = new CSVWriter(new FileWriter(newResultsFile), '\t', CSVWriter.NO_QUOTE_CHARACTER);

		final String[] newResults = new String[17];
		int c = 0;
		newResults[c++] = "OldPvalue";
		newResults[c++] = "OldRatioD";
		newResults[c++] = "OldP";
		newResults[c++] = "NewPvalue";
		newResults[c++] = "NewRatioD";
		newResults[c++] = "NewP";
		newResults[c++] = "NewTheta";
		newResults[c++] = "SampleCount";
		newResults[c++] = "Chr";
		newResults[c++] = "Pos";
		newResults[c++] = "Id";
		newResults[c++] = "Ref_Allele";
		newResults[c++] = "Alt_Allele";
		newResults[c++] = "Id";
		newResults[c++] = "Genes";
		newResults[c++] = "Ref_Counts";
		newResults[c++] = "Alt_Counts";
		mappingReportWriter.writeNext(newResults);

		for (AseVariantRecalculate ase : aseVariants) {

			c = 0;
			newResults[c++] = String.valueOf(ase.getOriginalLikelihoodRatioP());
			newResults[c++] = String.valueOf(ase.getOriginalLikelihoodRatioD());
			newResults[c++] = String.valueOf(ase.getOriginalEffect());
			newResults[c++] = String.valueOf(ase.getLikelihoodRatioP());
			newResults[c++] = String.valueOf(ase.getLikelihoodRatioD());
			newResults[c++] = String.valueOf(ase.getEffect());
			newResults[c++] = String.valueOf(ase.getMle().getMaxLogLikelihoodTheta());
			newResults[c++] = String.valueOf(ase.getSampleCount());
			newResults[c++] = ase.getChr();
			newResults[c++] = String.valueOf(ase.getPos());
			newResults[c++] = ase.getId().getPrimairyId();
			newResults[c++] = ase.getA1().getAlleleAsString();
			newResults[c++] = ase.getA2().getAlleleAsString();
			newResults[c++] = String.valueOf(ase.getPos());
			newResults[c++] = ase.getGenes();
			newResults[c++] = createCountString(ase.getA1Counts());
			newResults[c++] = createCountString(ase.getA2Counts());
			mappingReportWriter.writeNext(newResults);


		}

		mappingReportWriter.close();


	}
 

@Override
public void runTool( CommandLine line ) throws Exception {

    // keep it light and fast
    System.setProperty( "cassandra.readcl", "ONE" );

    startSpring();
    setVerbose( line );

    applyOrgId( line );
    prepareBaseOutputFileName( line );
    outputDir = createOutputParentDir();
    logger.info( "Export directory: {}", outputDir.getAbsolutePath() );

    // create writer
    applyStartTime( line );
    applyEndTime( line );
    logger.error( "startTime: {}, endTime: {}", startTime, endTime );
    if ( startTime.getTime() >= endTime.getTime() ) {
        logger.error( "startTime must be before endTime. exiting." );
        System.exit( 1 );
    }

    // create "modified" query to select data
    StringBuilder builder = new StringBuilder();
    builder.append( "modified >= " ).append( startTime.getTime() ).append( " and " );
    builder.append( "modified <= " ).append( endTime.getTime() );
    String queryString = builder.toString();

    // create writer
    String dateString = DATE_FORMAT.format( new Date() );
    String fileName = outputDir.getAbsolutePath() + "/" + dateString + ".csv";
    FileWriter fw = new FileWriter( fileName );
    writer = new CSVWriter( fw, SEPARATOR, CSVWriter.NO_QUOTE_CHARACTER, '\'' );

    try {
        writeMetadata();
        writeHeaders();

        // Loop through the organizations
        Map<UUID, String> organizations = getOrganizations();
        for ( Entry<UUID, String> orgIdAndName : organizations.entrySet() ) {
            exportApplicationsForOrg( orgIdAndName, queryString );
        }
    }
    finally {
        writer.close();
    }

    // now that file is written, copy it to S3
    if ( line.hasOption( "upload" ) ) {
        logger.info( "Copy to S3" );
        copyToS3( fileName );
    }
}