Example usage for org.apache.commons.io FilenameUtils concat

List of usage examples for org.apache.commons.io FilenameUtils concat

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Introduction

In this page you can find the example usage for org.apache.commons.io FilenameUtils concat.

Prototype

public static String concat(String basePath, String fullFilenameToAdd)

Source Link

Document

Concatenates a filename to a base path using normal command line style rules.

Usage

From source file:com.iyonger.apm.web.service.PerfTestService.java

/**
 * Create {@link GrinderProperties} based on the passed {@link PerfTest}.
 *
 * @param perfTest      base data/*from  w  ww .  j a  v  a  2  s .c o  m*/
 * @param scriptHandler scriptHandler
 * @return created {@link GrinderProperties} instance
 */
public GrinderProperties getGrinderProperties(PerfTest perfTest, ScriptHandler scriptHandler) {
    try {
        // Use default properties first
        GrinderProperties grinderProperties = new GrinderProperties(
                config.getHome().getDefaultGrinderProperties());

        User user = perfTest.getCreatedUser();

        // Get all files in the script path
        String scriptName = perfTest.getScriptName();
        FileEntry userDefinedGrinderProperties = fileEntryService.getOne(user,
                FilenameUtils.concat(FilenameUtils.getPath(scriptName), DEFAULT_GRINDER_PROPERTIES), -1L);
        if (!config.isSecurityEnabled() && userDefinedGrinderProperties != null) {
            // Make the property overridden by user property.
            GrinderProperties userProperties = new GrinderProperties();
            userProperties.load(new StringReader(userDefinedGrinderProperties.getContent()));
            grinderProperties.putAll(userProperties);
        }
        grinderProperties.setAssociatedFile(new File(DEFAULT_GRINDER_PROPERTIES));
        grinderProperties.setProperty(GRINDER_PROP_SCRIPT, scriptHandler.getScriptExecutePath(scriptName));

        grinderProperties.setProperty(GRINDER_PROP_TEST_ID, "test_" + perfTest.getId());
        grinderProperties.setInt(GRINDER_PROP_AGENTS, getSafe(perfTest.getAgentCount()));
        grinderProperties.setInt(GRINDER_PROP_PROCESSES, getSafe(perfTest.getProcesses()));
        grinderProperties.setInt(GRINDER_PROP_THREAD, getSafe(perfTest.getThreads()));
        if (perfTest.isThresholdDuration()) {
            grinderProperties.setLong(GRINDER_PROP_DURATION, getSafe(perfTest.getDuration()));
            grinderProperties.setInt(GRINDER_PROP_RUNS, 0);
        } else {
            grinderProperties.setInt(GRINDER_PROP_RUNS, getSafe(perfTest.getRunCount()));
            if (grinderProperties.containsKey(GRINDER_PROP_DURATION)) {
                grinderProperties.remove(GRINDER_PROP_DURATION);
            }
        }
        grinderProperties.setProperty(GRINDER_PROP_ETC_HOSTS,
                StringUtils.defaultIfBlank(perfTest.getTargetHosts(), ""));
        grinderProperties.setBoolean(GRINDER_PROP_USE_CONSOLE, true);
        if (BooleanUtils.isTrue(perfTest.getUseRampUp())) {
            grinderProperties.setBoolean(GRINDER_PROP_THREAD_RAMPUP, perfTest.getRampUpType() == RampUp.THREAD);
            grinderProperties.setInt(GRINDER_PROP_PROCESS_INCREMENT, getSafe(perfTest.getRampUpStep()));
            grinderProperties.setInt(GRINDER_PROP_PROCESS_INCREMENT_INTERVAL,
                    getSafe(perfTest.getRampUpIncrementInterval()));
            if (perfTest.getRampUpType() == RampUp.PROCESS) {
                grinderProperties.setInt(GRINDER_PROP_INITIAL_SLEEP_TIME,
                        getSafe(perfTest.getRampUpInitSleepTime()));
            } else {
                grinderProperties.setInt(GRINDER_PROP_INITIAL_THREAD_SLEEP_TIME,
                        getSafe(perfTest.getRampUpInitSleepTime()));
            }
            grinderProperties.setInt(GRINDER_PROP_INITIAL_PROCESS, getSafe(perfTest.getRampUpInitCount()));
        } else {
            grinderProperties.setInt(GRINDER_PROP_PROCESS_INCREMENT, 0);
        }

        if (BooleanUtils.isTrue(perfTest.getUseFixedRateRPS())) {
            grinderProperties.setDouble(GRINDER_PROP_FIXED_RPS_RATE, perfTest.getRps());
        }
        grinderProperties.setInt(GRINDER_PROP_REPORT_TO_CONSOLE, 500);
        grinderProperties.setProperty(GRINDER_PROP_USER, perfTest.getCreatedUser().getUserId());
        grinderProperties.setProperty(GRINDER_PROP_JVM_CLASSPATH, getCustomClassPath(perfTest));
        grinderProperties.setInt(GRINDER_PROP_IGNORE_SAMPLE_COUNT, getSafe(perfTest.getIgnoreSampleCount()));
        grinderProperties.setBoolean(GRINDER_PROP_SECURITY, config.isSecurityEnabled());
        // For backward agent compatibility.
        // If the security is not enabled, pass it as jvm argument.
        // If enabled, pass it to grinder.param. In this case, I drop the
        // compatibility.
        if (StringUtils.isNotBlank(perfTest.getParam())) {
            String param = perfTest.getParam().replace("'", "\\'").replace(" ", "");
            if (config.isSecurityEnabled()) {
                grinderProperties.setProperty(GRINDER_PROP_PARAM, StringUtils.trimToEmpty(param));
            } else {
                String property = grinderProperties.getProperty(GRINDER_PROP_JVM_ARGUMENTS, "");
                property = property + " -Dparam=" + param + " ";
                grinderProperties.setProperty(GRINDER_PROP_JVM_ARGUMENTS, property);
            }
        }
        LOGGER.info("Grinder Properties : {} ", grinderProperties);
        return grinderProperties;
    } catch (Exception e) {
        throw processException("error while prepare grinder property for " + perfTest.getTestName(), e);
    }
}

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

@Test
// To test import of soft clips:
public void testSamToCompactTrickCase13NoGenomeSoftClips() throws IOException {

    SAMToCompactMode importer = new SAMToCompactMode();
    importer.setInputFile("test-data/splicedsamhelper/tricky-spliced-13.sam");
    final String outputFilename = FilenameUtils.concat(BASE_TEST_DIR, "spliced-output-alignment-13");
    importer.setOutputFile(outputFilename);
    importer.setPreserveSoftClips(true);
    importer.execute();//from   w w  w . j a v a2  s.c  o m

    AlignmentReader reader = new AlignmentReaderImpl(outputFilename);
    assertTrue(reader.hasNext());
    Alignments.AlignmentEntry first = reader.next();
    assertTrue(reader.hasNext());
    Alignments.AlignmentEntry second = reader.next();

    assertEquals(15013, first.getPosition());
    assertEquals(3, first.getQueryPosition());
    assertEquals("AAT", first.getSoftClippedBasesLeft());
    assertEquals("", first.getSoftClippedBasesRight());
    assertEquals(25, first.getQueryAlignedLength());

    assertEquals(15795, second.getPosition());
    assertEquals(28, second.getQueryPosition());
    assertEquals(1, second.getFragmentIndex());
    assertEquals(5, second.getQueryAlignedLength());
    assertEquals("", second.getSoftClippedBasesLeft());
    assertEquals("TC", second.getSoftClippedBasesRight());
}

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

@Test
// To test import of soft clips:
public void testSamToCompactTrickCase13SoftClipsWithGenome() throws IOException {

    SAMToCompactMode importer = new SAMToCompactMode();
    importer.setInputFile("test-data/splicedsamhelper/tricky-spliced-14.sam");
    final String outputFilename = FilenameUtils.concat(BASE_TEST_DIR, "spliced-output-alignment-14");

    MutableString seq = new MutableString();

    seq.append("NCAGTGCCCACCTTGGCTCGTGGCTCTCANNNNNNNNNNCTTGCCTNNN");
    String[] refs = { seq.toString() };

    RandomAccessSequenceTestSupport genomeTestSupport = new RandomAccessSequenceTestSupport(refs);
    importer.setGenome(genomeTestSupport);
    importer.setOutputFile(outputFilename);
    importer.setPreserveSoftClips(true);
    importer.execute();/*ww  w.j a  v  a  2  s . co  m*/

    AlignmentReader reader = new AlignmentReaderImpl(outputFilename);
    assertTrue(reader.hasNext());
    Alignments.AlignmentEntry first = reader.next();
    assertTrue(reader.hasNext());
    Alignments.AlignmentEntry second = reader.next();

    assertEquals(4, first.getPosition());
    assertEquals(3, first.getQueryPosition());
    assertEquals("A=T", first.getSoftClippedBasesLeft());
    assertEquals("", first.getSoftClippedBasesRight());
    assertEquals(25, first.getQueryAlignedLength());

    assertEquals(40 - 1, second.getPosition());
    assertEquals(28, second.getQueryPosition());
    assertEquals(1, second.getFragmentIndex());
    assertEquals(5, second.getQueryAlignedLength());
    assertEquals("TC", second.getSoftClippedBasesRight());
    assertEquals("", second.getSoftClippedBasesLeft());

}

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

@Test
// To test import of three splice with initial 2-clip.
public void testSamToCompactTrickCase15NoGenomeThreeSplice() throws IOException {

    SAMToCompactMode importer = new SAMToCompactMode();
    importer.setInputFile("test-data/splicedsamhelper/tricky-spliced-15.sam");
    final String outputFilename = FilenameUtils.concat(BASE_TEST_DIR, "spliced-output-alignment-15");
    importer.setOutputFile(outputFilename);
    importer.setPreserveSoftClips(true);
    //  importer.setPropagateTargetIds(true);
    importer.execute();//  w  ww. j  av a 2s .  co m

    AlignmentReader reader = new AlignmentReaderImpl(outputFilename);
    assertTrue(reader.hasNext());
    Alignments.AlignmentEntry first = reader.next();
    assertTrue(reader.hasNext());
    Alignments.AlignmentEntry second = reader.next();
    assertTrue(reader.hasNext());
    Alignments.AlignmentEntry third = reader.next();

    assertEquals(32485524 - 1, first.getPosition());
    assertEquals(2, first.getQueryPosition());
    assertEquals("CG", first.getSoftClippedBasesLeft());
    assertEquals("", first.getSoftClippedBasesRight());
    assertEquals(6, first.getQueryAlignedLength());

    assertEquals(32485524 + 6 + 301 - 1, second.getPosition());
    assertEquals(8, second.getQueryPosition());
    assertEquals("", second.getSoftClippedBasesLeft());
    assertEquals("", second.getSoftClippedBasesRight());
    assertEquals(24, second.getQueryAlignedLength());

    assertEquals(32485524 + 6 + 301 + 24 + 478 - 1, third.getPosition());
    assertEquals(32, third.getQueryPosition());
    assertEquals("", third.getSoftClippedBasesLeft());
    assertEquals("", third.getSoftClippedBasesRight());
    assertEquals(3, third.getQueryAlignedLength());
}

From source file:edu.cornell.med.icb.goby.stats.TestAnnotationAveragingWriter.java

private String makeDensityEstimator() throws IOException {
    int fixedValue = 40;
    EstimatedDistribution estimator = new EstimatedDistribution(1,
            new PassThroughStatisticAdaptor(100, fixedValue));
    estimator.setBinningStrategy(new FastSmallAndLog10BinningStrategy());
    int[] delta = { 0000, 001, 002, 003, 004, 5 };
    int[] frequencies = { 1000, 900, 800, 700, 600, 1 };
    for (int index = 0; index < delta.length; index++) {

        for (int i = 0; i < frequencies[index]; i++) {
            estimator.observe(0, fixedValue, delta[index]);
        }//from  w  ww.j a  v a 2s  . co  m
    }
    String filename = FilenameUtils.concat(BASE_TEST_DIR, "density.bin");
    EstimatedDistribution.store(estimator, filename);
    return filename;
}

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

@Test
// Failed on server when converting back to BAM because seqVar.position would be set to zero:

public void testSamToCompactTrickCase19() throws IOException {

    SAMToCompactMode importer = new SAMToCompactMode();
    importer.setInputFile("test-data/splicedsamhelper/tricky-spliced-19.sam");
    final String outputFilename = FilenameUtils.concat(BASE_TEST_DIR, "spliced-output-alignment-19");
    importer.setOutputFile(outputFilename);
    importer.setPreserveSoftClips(true);
    //  importer.setPropagateTargetIds(true);
    importer.execute();//w  w w  . jav a2  s. c o  m
    AlignmentReader reader = new AlignmentReaderImpl(outputFilename);
    assertTrue(reader.hasNext());
    Alignments.AlignmentEntry first = reader.next();
    assertFalse(reader.hasNext());
    assertEquals("seqVar.position must be zero", 0, first.getSequenceVariations(0).getPosition());
}

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

@Test
// Failed on server when converting back to BAM because seqVar.position would be set to zero:

public void testSamToCompactTrickCase20() throws IOException {

    SAMToCompactMode importer = new SAMToCompactMode();
    importer.setInputFile("test-data/sam/test.sam");
    final String outputFilename = FilenameUtils.concat(BASE_TEST_DIR, "test-sam-1");
    importer.setOutputFile(outputFilename);

    importer.setPreserveAllTags(true);// w w w . ja  v  a2 s  .com
    importer.setPreserveReadName(true);
    //  importer.setPropagateTargetIds(true);
    importer.execute();
    AlignmentReader reader = new AlignmentReaderImpl(outputFilename);
    assertTrue(reader.hasNext());
    Alignments.AlignmentEntry first = reader.next();

    CompactToSAMMode exporter = new CompactToSAMMode();
    final String samOutputFilename = FilenameUtils.concat(BASE_TEST_DIR, "test-sam-out.sam");

    exporter.setInputBasename(outputFilename);
    exporter.setOutput(samOutputFilename);
    exporter.setGenome("test-data/sam/test.fa");
    exporter.execute();
    FileAssert.assertEquals(new File("test-data/sam/test.sam"), new File(samOutputFilename));
}

From source file:net.sf.jvifm.ui.FileLister.java

private void updateEditItem(Text textEditor, String itemType) {
    if (!textEditor.getText().trim().equals("")) {
        TableItem item = table.getItem(currentRow);
        File currentFile = new File(FilenameUtils.concat(pwd, textEditor.getText()));
        boolean isSuccess = false;
        if (itemType.equals("file")) {
            isSuccess = true;/*  ww w.  j av a2s.c o m*/
            if (!currentFile.exists()) {
                try {
                    currentFile.createNewFile();
                } catch (IOException e) {
                    isSuccess = false;
                }
            } else {
                currentFile.setLastModified(System.currentTimeMillis());
            }

        } else if (itemType.equals("folder")) {
            isSuccess = fileModelManager.mkdir(currentFile.getPath());

        } else if (itemType.equals("rename")) {
            isSuccess = currentFile.renameTo(new File(FilenameUtils.concat(pwd, textEditor.getText().trim())));
        }

        if (isSuccess) {
            fileManager.setStatusInfo("command successed."); //$NON-NLS-1$
        } else {
            fileManager.setStatusInfo("command failed."); //$NON-NLS-1$
        }

        item.setText(0, textEditor.getText().trim());
        textEditor.dispose();
        editor.dispose();
    }
    updateStatusText();
}

From source file:com.daphne.es.showcase.excel.service.ExcelDataService.java

private String generateFilename(final User user, final String contextRootPath, Integer index,
        final String extension) {
    String path = FilenameUtils.concat(contextRootPath, storePath);
    path = FilenameUtils.concat(path, user.getUsername());
    path = FilenameUtils.concat(path,//from  ww w  .  j  av  a 2s .c o m
            EXPORT_FILENAME_PREFIX + "_" + DateFormatUtils.format(new Date(), "yyyyMMddHHmmssSSS")
                    + (index != null ? ("_" + index) : "") + "." + extension);

    File file = new File(path);
    if (!file.exists()) {
        File parentFile = file.getParentFile();
        if (!parentFile.exists()) {
            parentFile.mkdirs();
        }
        return path;
    }
    return generateFilename(user, contextRootPath, extension);
}

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

@Test
// Failed on server when converting back to BAM because query_aligned_length and target_aligned_length differ
// without an apparent indel
public void testSamToCompactTrickCase16() throws IOException {

    SAMToCompactMode importer = new SAMToCompactMode();
    importer.setInputFile("test-data/splicedsamhelper/tricky-spliced-16.sam");
    final String outputFilename = FilenameUtils.concat(BASE_TEST_DIR, "spliced-output-alignment-16");
    importer.setOutputFile(outputFilename);
    importer.setPreserveSoftClips(true);
    //  importer.setPropagateTargetIds(true);
    importer.execute();//from   w  w  w.j a  v a2 s . c  om
    // cigar is  13S21M1I29M4S   13 21 -1 29 4
    AlignmentReader reader = new AlignmentReaderImpl(outputFilename);
    assertTrue(reader.hasNext());
    Alignments.AlignmentEntry first = reader.next();
    assertTrue(reader.hasNext());
    Alignments.AlignmentEntry second = reader.next();
    assertFalse(reader.hasNext());

    assertEquals(190077 - 1, first.getPosition());
    assertEquals(13, first.getQueryPosition());
    assertEquals("AGTGGCAGCACGA", first.getSoftClippedBasesLeft());
    assertEquals("TGCT", first.getSoftClippedBasesRight());
    assertEquals(51, first.getQueryAlignedLength());
    assertEquals(50, first.getTargetAlignedLength());

    assertEquals(5, first.getSequenceVariationsCount());

    Alignments.SequenceVariation seqvar = first.getSequenceVariations(0);
    assertEquals("T", seqvar.getFrom());
    assertEquals("C", seqvar.getTo());
    assertEquals(22, seqvar.getReadIndex());
    assertEquals(9, seqvar.getPosition());
    assertArrayEquals(byteArray(3), seqvar.getToQuality().toByteArray());

    seqvar = first.getSequenceVariations(1);
    assertEquals("T", seqvar.getFrom());
    assertEquals("G", seqvar.getTo());
    assertEquals(26, seqvar.getReadIndex());
    assertEquals(13, seqvar.getPosition());
    assertArrayEquals(byteArray(34), seqvar.getToQuality().toByteArray());

    seqvar = first.getSequenceVariations(2);
    assertEquals("C", seqvar.getFrom());
    assertEquals("A", seqvar.getTo());
    assertEquals(33, seqvar.getReadIndex());
    assertEquals(20, seqvar.getPosition());
    assertArrayEquals(byteArray(28), seqvar.getToQuality().toByteArray());

    seqvar = first.getSequenceVariations(3);
    assertEquals("-", seqvar.getFrom());
    assertEquals("C", seqvar.getTo());
    assertEquals(35, seqvar.getReadIndex());
    assertEquals(21, seqvar.getPosition());
    assertArrayEquals(byteArray(27), seqvar.getToQuality().toByteArray());

    seqvar = first.getSequenceVariations(4);
    assertEquals("T", seqvar.getFrom());
    assertEquals("A", seqvar.getTo());
    assertEquals(36, seqvar.getReadIndex());
    assertEquals(22, seqvar.getPosition());
    assertArrayEquals(byteArray(35), seqvar.getToQuality().toByteArray());

    //second's CIGAR is 20S48M
    assertEquals(190246 - 1, second.getPosition());
    assertEquals(20, second.getQueryPosition());
    assertEquals("CAGTGTCGTGGCTGCACGCC", second.getSoftClippedBasesLeft());
    assertEquals("", second.getSoftClippedBasesRight());
    assertEquals(48, second.getQueryAlignedLength());
    assertEquals(48, second.getTargetAlignedLength());

}