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

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:au.org.ala.delta.io.OutputFileManager.java

protected File createFile(String fileName) {

    File parent = null;//from   w  ww  . ja v  a  2s  .c  o  m

    if (_context.getFile() != null) {
        parent = _context.getFile().getParentFile();
    }

    if (parent == null) {
        parent = new File(System.getProperty("user.dir"));
    }

    File file = new File(fileName);
    if (!file.isAbsolute()) {
        file = new File(FilenameUtils.concat(parent.getAbsolutePath(), fileName));
    }
    return file;
}

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From source file:io.wcm.devops.conga.generator.EnvironmentGenerator.java

private void generateFile(RoleFile roleFile, String dir, String fileName, Map<String, Object> config,
        File nodeDir, Template template, String roleName, String roleVariantName, String templateName) {
    File file = new File(nodeDir, dir != null ? FilenameUtils.concat(dir, fileName) : fileName);
    boolean duplicateFile = generatedFilePaths.contains(FileUtil.getCanonicalPath(file));
    if (file.exists()) {
        file.delete();//from   www  .  j  a v  a 2 s.co  m
    }

    // skip file if condition does not evaluate to a non-empty string or is "false"
    if (StringUtils.isNotEmpty(roleFile.getCondition())) {
        String condition = VariableStringResolver.resolve(roleFile.getCondition(), config);
        if (StringUtils.isBlank(condition) || StringUtils.equalsIgnoreCase(condition, "false")) {
            return;
        }
    }

    FileGenerator fileGenerator = new FileGenerator(environmentName, roleName, roleVariantName, templateName,
            nodeDir, file, roleFile, config, template, pluginManager, version, dependencyVersions, log);
    try {
        fileGenerator.generate();
        generatedFilePaths.add(FileUtil.getCanonicalPath(file));
        if (duplicateFile) {
            log.warn("File was generated already, check for file name clashes: "
                    + FileUtil.getCanonicalPath(file));
        }
    } catch (ValidationException ex) {
        throw new GeneratorException(
                "File validation failed " + FileUtil.getCanonicalPath(file) + " - " + ex.getMessage());
    } catch (Throwable ex) {
        throw new GeneratorException(
                "Unable to generate file: " + FileUtil.getCanonicalPath(file) + "\n" + ex.getMessage(), ex);
    }
}

---

From source file:es.urjc.mctwp.image.impl.collection.fs.ImageContentCollectionFSImpl.java

/**
 * It resolves properly collection file directory.
 * /*from  ww  w.  ja  va2  s . c  om*/
 * @param colName
 * @param temporal
 * @return
 */
private File getProperCollection(String colName, boolean temporal) {
    String basePath = temporal ? tmpcoll.getAbsolutePath() : basedir.getAbsolutePath();
    return new File(FilenameUtils.concat(basePath, colName));
}

---

From source file:edu.cornell.med.icb.goby.alignments.TestSkipTo.java

@Test
public void testEmptyAlignment() throws IOException {
    final String basename = "align-skip-to-3";
    final AlignmentWriterImpl writer = new AlignmentWriterImpl(FilenameUtils.concat(BASE_TEST_DIR, basename));
    writer.setNumAlignmentEntriesPerChunk(numEntriesPerChunk);

    final int numTargets = 3;
    final int[] targetLengths = new int[numTargets];

    for (int referenceIndex = 0; referenceIndex < numTargets; referenceIndex++) {
        targetLengths[referenceIndex] = 1000;
    }/* w  ww  .j  a v  a2  s. com*/
    writer.setTargetLengths(targetLengths);
    // we write this alignment sorted:

    writer.setSorted(true);

    writer.close();
    writer.printStats(System.out);

    final AlignmentReader reader = new AlignmentReaderImpl(FilenameUtils.concat(BASE_TEST_DIR, basename));

    final Alignments.AlignmentEntry c = reader.skipTo(2, 0);
    assertNull(c);

    assertFalse(reader.hasNext());

}

---

From source file:com.abiquo.api.services.stub.TarantinoJobCreator.java

/**
 * Add the secondary hard disks./*  www .  j  ava 2 s  .  co m*/
 * 
 * @param virtualMachine virtual machine object.
 * @param vmDesc definition to send.
 */
@Transactional(readOnly = true, propagation = Propagation.REQUIRED)
private void secondaryHardDisksDefinition(final VirtualMachine virtualMachine,
        final VirtualMachineDescriptionBuilder vmDesc) {

    List<DiskManagement> hardDisks = virtualMachine.getDisks();

    String datastore;
    if (virtualMachine.getDatastore().getDirectory() != null
            && !StringUtils.isEmpty(virtualMachine.getDatastore().getDirectory())) {
        datastore = FilenameUtils.concat(virtualMachine.getDatastore().getRootPath(),
                virtualMachine.getDatastore().getDirectory());
    } else {
        datastore = virtualMachine.getDatastore().getRootPath();
    }

    DiskControllerType cntrlType = getDiskController(virtualMachine.getHypervisor().getType(), false, false);

    for (DiskManagement imHard : hardDisks) {
        vmDesc.addSecondaryHardDisk(imHard.getSizeInMb() * 1048576, imHard.getSequence(), datastore, cntrlType);
    }
}

---

From source file:es.urjc.mctwp.image.impl.collection.fs.ImageContentCollectionFSImpl.java

/**
 * It stores properly a single file.//from w  w w. j  av  a  2 s . c  o  m
 * 
 * @param collection
 * @param file
 * @throws ImageCollectionException
 * @throws IOException
 */
private void storeFile(File collection, File file) throws ImageCollectionException, IOException {
    File dest = new File(FilenameUtils.concat(collection.getAbsolutePath(), file.getName()));
    FileUtils.copyFile(file, dest);
}

---

From source file:edu.cornell.med.icb.goby.alignments.TestReadWriteAlignments.java

/**
 * Validate that the the alignment header constant query length
 * ({@link edu.cornell.med.icb.goby.alignments.Alignments.AlignmentHeader#hasConstantQueryLength()})
 * is set to false when queries of the same length get appended.
 * @throws IOException if there is a problem reading or writing the alignment
 *///w  w  w.j a  va 2s  . co  m
@Test
public void nonConstantQueryLengths() throws IOException {
    final int[] queryLengths = { 11, 21, 12, 42 };
    final AlignmentWriter writer = new AlignmentWriterImpl(
            FilenameUtils.concat(BASE_TEST_DIR, "non-constant-query-lengths"));

    int queryIndex = 0;
    for (final int queryLength : queryLengths) {
        final Alignments.AlignmentEntry.Builder builder = Alignments.AlignmentEntry.newBuilder();
        builder.setQueryLength(queryLength);
        builder.setQueryIndex(queryIndex++);
        builder.setTargetIndex(42);
        builder.setPosition(0);
        builder.setMatchingReverseStrand(true);
        final Alignments.AlignmentEntry entry = builder.build();
        writer.appendEntry(entry);
    }
    writer.close();

    final AlignmentReaderImpl reader = new AlignmentReaderImpl(
            FilenameUtils.concat(BASE_TEST_DIR, "non-constant-query-lengths"));
    for (final Alignments.AlignmentEntry entry : reader) {
        assertEquals(queryLengths[entry.getQueryIndex()], entry.getQueryLength());
    }
    reader.readHeader();
    assertFalse("query length must not be constant", reader.isConstantQueryLengths());
    assertEquals("Number of queries do not match", 4, reader.getNumberOfQueries());

}

---

From source file:com.enioka.jqm.tools.Loader.java

private void endOfRun() {
    // Register end date as soon as possible to be as exact as possible (sending mails may take time for example)
    endDate = GregorianCalendar.getInstance(Locale.getDefault());

    // This block is needed for external payloads, as the single runner may forcefully call endOfRun.
    synchronized (this) {
        if (!isDone) {
            isDone = true;/*w  w  w  . java2  s .co m*/
        } else {
            return;
        }
    }

    // Release the slot so as to allow other job instances to run (first op!)
    if (p != null) {
        p.decreaseNbThread(this.job.getId());
    }

    // Send e-mail before releasing the slot - it may be long
    if (job.getEmail() != null) {
        try {
            Helpers.sendEndMessage(job);
        } catch (Exception e) {
            jqmlogger.warn("An e-mail could not be sent. No impact on the engine.", e);
        }
    }

    // Clean class loader
    ClassLoaderLeakCleaner.clean(Thread.currentThread().getContextClassLoader());

    // Clean JDBC connections
    ClassLoaderLeakCleaner.cleanJdbc(Thread.currentThread());

    // Restore class loader
    if (this.classLoaderToRestoreAtEnd != null) {
        Thread.currentThread().setContextClassLoader(classLoaderToRestoreAtEnd);
        jqmlogger.trace("Class Loader was correctly restored");
    }

    // Clean temp dir (if it exists)
    File tmpDir = new File(FilenameUtils.concat(node.getTmpDirectory(), "" + job.getId()));
    if (tmpDir.isDirectory()) {
        try {
            if (FileUtils.deleteQuietly(tmpDir)) {
                jqmlogger.trace("temp directory was removed");
            } else {
                jqmlogger.warn("Could not remove temp directory " + tmpDir.getAbsolutePath()
                        + "for this job instance. There may be open handlers remaining open.");
            }
        } catch (Exception e) {
            jqmlogger.warn("Could not remove temp directory for unusual reasons", e);
        }
    }

    // Unregister MBean
    if (p != null && this.p.getEngine().loadJmxBeans) {
        try {
            MBeanServer mbs = ManagementFactory.getPlatformMBeanServer();
            mbs.unregisterMBean(name);
        } catch (Exception e) {
            jqmlogger.error("Could not unregister JobInstance JMX bean", e);
        }
    }

    // Unregister logger
    unregisterLogger();

    // Part needing DB connection with specific failure handling code.
    endOfRunDb();
}

---

From source file:edu.scripps.fl.pubchem.xmltool.gui.PubChemXMLCreatorGUI.java

public void mouseClicked(MouseEvent e) {
    try {//from w ww  . j  a  v a2  s. c om
        if (e.getClickCount() > 0) {
            setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR));
            if (e.getSource() == jtpExample) {
                URL url = getClass().getClassLoader().getResource("ExampleExcel.xlsx");
                File tmpFile = File.createTempFile("example", ".xlsx");
                FileUtils.copyURLToFile(url, tmpFile);
                tmpFile.deleteOnExit();
                Desktop.getDesktop().open(tmpFile);
            } else if (e.getSource() == jtpExcelTemplate) {
                File saveFile = gc.fileChooser(jtfFileExcel, ".xlsx", "save");
                if (saveFile != null) {
                    URL url = getClass().getClassLoader().getResource("ExcelTemplate_withBAO.xlsx");
                    OutputStream out = new FileOutputStream(saveFile, true);
                    IOUtils.copy(url.openStream(), out);
                    String output = FilenameUtils.concat(FilenameUtils.getFullPath(saveFile.toString()),
                            FilenameUtils.getBaseName(saveFile.toString()));
                    Desktop.getDesktop().open(new File(saveFile.toString()));
                }
            } else if (e.getSource() == jtfFileTemplate && jtfFileTemplate.getText().equals(template)) {
                jtfFileTemplate.setText("");
            } else if (e.getSource() == this) {
                if (jtfFileTemplate.getText().equals("")) {
                    jtfFileTemplate.setText(template);
                }
            }
        }
        setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR));
    } catch (Throwable throwable) {
        SwingGUI.handleError(this, throwable);
    }
}

---

From source file:edu.cornell.med.icb.goby.alignments.TestMerge.java

@Test
public void testIgnoreTooManyHits2() throws IOException {
    synchronized (this) {
        // make the too many hits info:
        final AlignmentTooManyHitsWriter tmhWriter = new AlignmentTooManyHitsWriter(
                FilenameUtils.concat(BASE_TEST_DIR, "align-102"), 4);

        // tmhWriter will only write entries if numHits > thresh
        tmhWriter.getNewAmbiguousLocation().setAtLeastNumberOfHits(5);
        tmhWriter.getNewAmbiguousLocation().setQueryIndex(0);
        tmhWriter.append();/*from   ww w .  ja  va  2  s .  c  o  m*/
        tmhWriter.getNewAmbiguousLocation().setAtLeastNumberOfHits(15);
        tmhWriter.getNewAmbiguousLocation().setQueryIndex(1);
        tmhWriter.append();
        tmhWriter.close();

        final Merge merger = new Merge(3);

        final List<File> inputFiles;
        final String outputFile;
        final String basename;
        final int count;
        inputFiles = new ArrayList<File>();
        inputFiles.add(new File(FilenameUtils.concat(BASE_TEST_DIR, "align-102")));
        inputFiles.add(new File(FilenameUtils.concat(BASE_TEST_DIR, "align-102")));

        outputFile = FilenameUtils.concat(BASE_TEST_DIR, "out-103-merged");
        merger.setK(30);
        merger.merge(inputFiles, outputFile);

        // With k=3 and twice the same input file, the merge should keep twice the queries with best score:
        basename = outputFile;
        count = countAlignmentEntries(basename);
        assertEquals(count, (numQueries102 - 2)
                * 2/* two queries excluded because of too many hits with k=30 > alignerThreshold */);
    }
}

---

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