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:edu.cornell.med.icb.goby.alignments.TestMerge.java

public void testIgnoreTooManyHits3() throws IOException {
    synchronized (this) {
        // make the too many hits info:
        final AlignmentTooManyHitsWriter tmhWriter = new AlignmentTooManyHitsWriter(
                FilenameUtils.concat(BASE_TEST_DIR, "align-103"), 10);

        // tmhWriter will only write entries if numHits > thresh
        tmhWriter.getNewAmbiguousLocation().setAtLeastNumberOfHits(2);
        tmhWriter.getNewAmbiguousLocation().setQueryIndex(0);
        tmhWriter.append();/*  ww  w .  jav  a 2  s.c om*/
        tmhWriter.getNewAmbiguousLocation().setAtLeastNumberOfHits(1);
        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-103")));
        inputFiles.add(new File(FilenameUtils.concat(BASE_TEST_DIR, "align-103")));

        outputFile = FilenameUtils.concat(BASE_TEST_DIR, "out-103-merged");
        merger.setK(3);
        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 - 1) * 2/* one query excluded because of too many hits with k=3 */);
    }
}

From source file:ffx.xray.RescoreAndCluster.java

private File rescoreSingle(File modelFile, RescoreStrategy rscType, DoubleIndexPair[] energies, int i) {
    Path filepath = generatePath(modelFile);
    if (filepath == null) {
        logger.warning(String.format(" Could not generate path to file %s", modelFile.toPath()));
        return null;
    }/*from   ww  w .  j a  v  a  2s.c  om*/
    String filename = pwdPath.relativize(filepath).toString();
    File retFile = modelFile;
    try {
        MolecularAssembly[] openedAssemblies = utils.open(filename);
        MolecularAssembly assembly = openedAssemblies[0];
        switch (rscType) {
        case NO_RESCORE:
            logger.warning(" Rescore is being called with rscType = NO_RESCORE");
            break;
        case ENERGY_EVAL:
            break;
        case MINIMIZE:
            logger.info(String.format("\n Running minimize on %s", filename));
            logger.info(String.format(" RMS gradient convergence criteria: %f", eps));
            utils.energy(assembly);
            utils.minimize(assembly, eps);

            String ext = FilenameUtils.getExtension(filename);
            ext = ".".concat(ext);

            if (resultDir != null) {
                filename = FilenameUtils.getBaseName(filename);
                filename = FilenameUtils.concat(resultPath.toString(), filename);
            } else {
                filename = FilenameUtils.removeExtension(filename);
            }
            filename = filename.concat(fileSuffix).concat(ext);
            retFile = new File(filename);
            if (ext.toUpperCase().contains("XYZ")) {
                utils.saveAsXYZ(assembly, retFile);
            } else {
                utils.saveAsPDB(assembly, retFile);
            }
            break;
        case XRAY_MIN:
            logger.info(String.format("\n Running x-ray minimize on %s", filename));

            DiffractionFile diffractionFile = null;
            if (diffractionFiles.isEmpty()) {
                diffractionFile = new DiffractionFile(assembly, 1.0, false);
                diffractionFiles.add(diffractionFile);
            }
            CompositeConfiguration properties = Keyword.loadProperties(modelFile);
            DiffractionData diffractionData = new DiffractionData(assembly, properties, SolventModel.POLYNOMIAL,
                    diffractionFiles.toArray(new DiffractionFile[diffractionFiles.size()]));

            diffractionData.scaleBulkFit();
            diffractionData.printStats();
            utils.energy(assembly);

            RefinementMinimize refinementMinimize = new RefinementMinimize(diffractionData, refinementMode);
            if (eps < 0.0) {
                eps = refinementMinimize.getEps();
            }
            logger.info(String.format("\n RMS gradient convergence criteria: %8.5f max number of iterations %d",
                    eps, maxiter));
            refinementMinimize.minimize(eps, maxiter);
            diffractionData.scaleBulkFit();
            diffractionData.printStats();

            ext = FilenameUtils.getExtension(filename);
            ext = ".".concat(ext);

            if (resultDir != null) {
                filename = FilenameUtils.getBaseName(filename);
                filename = FilenameUtils.concat(resultPath.toString(), filename);
            } else {
                filename = FilenameUtils.removeExtension(filename);
            }
            filename = filename.concat(fileSuffix);
            diffractionData.writeData(filename + ".mtz");
            filename = filename.concat(ext);
            diffractionData.writeModel(filename);

            retFile = new File(filename);
            if (diffractionFile != null) {
                try {
                    diffractionFiles.remove(diffractionFile);
                } catch (UnsupportedOperationException ex) {
                    // This should never occur, because diffractionFiles should be of a List type supporting remove(object).
                    diffractionFiles = new ArrayList<>();
                }
            }
            break;
        case RS_MIN:
            logger.info(String.format("\n Running real-space minimize on %s", filename));

            RealSpaceFile realspaceFile = null;
            if (mapFiles.isEmpty()) {
                realspaceFile = new RealSpaceFile(assembly);
                mapFiles.add(realspaceFile);
            }
            properties = Keyword.loadProperties(modelFile);
            RealSpaceData realspaceData = new RealSpaceData(assembly, properties,
                    mapFiles.toArray(new RealSpaceFile[mapFiles.size()]));
            utils.energy(assembly);

            refinementMinimize = new RefinementMinimize(realspaceData, refinementMode);
            if (eps < 0.0) {
                eps = 1.0;
            }
            logger.info(String.format("\n RMS gradient convergence criteria: %8.5f max number of iterations %d",
                    eps, maxiter));
            refinementMinimize.minimize(eps, maxiter);

            ext = FilenameUtils.getExtension(filename);
            ext = ".".concat(ext);
            if (resultDir != null) {
                filename = FilenameUtils.getBaseName(filename);
                filename = FilenameUtils.concat(resultPath.toString(), filename);
            } else {
                filename = FilenameUtils.removeExtension(filename);
            }
            filename = filename.concat(fileSuffix).concat(ext);
            retFile = new File(filename);
            if (ext.toUpperCase().contains("XYZ")) {
                utils.saveAsXYZ(assembly, retFile);
            } else {
                utils.saveAsPDB(assembly, retFile);
            }

            if (realspaceFile != null) {
                try {
                    mapFiles.remove(realspaceFile);
                } catch (UnsupportedOperationException ex) {
                    // This should never occur, because diffractionFiles should be of a List type supporting remove(object).
                    mapFiles = new ArrayList<>();
                }
            }
            break;
        default:
            logger.severe(" No valid rescore type: FFX will not continue.");
        }
        double e = utils.returnEnergy(assembly);
        energies[i] = new DoubleIndexPair(i, e);
        utils.closeAll(openedAssemblies);
    } catch (Exception ex) {
        logger.warning(String.format(" Exception rescoring on file %s", filename));
        logger.info(ex.toString());
    }
    return retFile;
}

From source file:com.xiaomi.linden.core.search.MultiLindenCoreImpl.java

private Response deleteIndex(LindenIndexRequest request) throws IOException {

    // Only INDEX_NAME division type supports index delete
    if (multiIndexStrategy instanceof TimeLimitMultiIndexStrategy
            || multiIndexStrategy instanceof DocNumLimitMultiIndexStrategy) {
        return ResponseUtils.buildFailedResponse("Index delete is not supported in current multi-index core");
    }/*from  w ww. jav  a  2  s  .co  m*/

    if (request.getIndexName() == null) {
        return ResponseUtils.buildFailedResponse("Index name is not set in index delete request.");
    }

    String fullIndexName = MultiIndexStrategy.MULTI_INDEX_PREFIX_NAME + request.getIndexName();
    if (lindenCoreMap.containsKey(fullIndexName)) {
        LindenCore core = lindenCoreMap.remove(fullIndexName);
        if (core != null) {
            core.close();
        }

        if (config.getIndexType() != LindenConfig.IndexType.RAM) {
            String dir = FilenameUtils.concat(baseIndexDir, fullIndexName);
            String destDir = FilenameUtils.concat(baseIndexDir, "delete_" + fullIndexName);
            if (new File(dir).exists()) {
                FileUtils.moveDirectory(new File(dir), new File(destDir));
            }
        }
        return ResponseUtils.SUCCESS;
    }
    return ResponseUtils.buildFailedResponse("Index " + request.getIndexName() + " is not found.");
}

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

private File getWorkDir() {
    File f = new File(FilenameUtils.concat(node.getTmpDirectory(), "" + this.ji.getId()));
    if (!f.isDirectory()) {
        try {//from w  w  w  .  ja  v  a 2s  . c o m
            FileUtils.forceMkdir(f);
        } catch (Exception e) {
            throw new JqmRuntimeException("Could not create work directory", e);
        }
    }
    return f;
}

From source file:com.turn.griffin.GriffinLibCacheUtil.java

private String getMetadataFilePath(String parentDir) {
    return FilenameUtils.concat(parentDir, METADATA_FILE);
}

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

public void testSamToCompactTrickCase4() throws IOException {

    SAMToCompactMode importer = new SAMToCompactMode();
    importer.setInputFile("test-data/splicedsamhelper/tricky-spliced-4.sam");
    final String outputFilename = FilenameUtils.concat(BASE_TEST_DIR, "spliced-output-alignment-4");
    importer.setOutputFile(outputFilename);
    importer.execute();/*from  w  w w. j  a v  a2 s . c om*/

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

    assertEquals(0, first.getQueryIndex());
    assertEquals(0, first.getFragmentIndex());
    assertEquals(188966 - 1, first.getPosition());
    assertFalse(first.hasPairAlignmentLink());
    assertFalse(first.hasSplicedForwardAlignmentLink());
    assertFalse(first.hasSplicedBackwardAlignmentLink());

}

From source file:com.mosso.client.cloudfiles.sample.FilesCopy.java

public static File zipFile(File f) throws IOException {
    byte[] buf = new byte[1024];
    int len;/*from ww  w .  j  a va  2s .  c o m*/

    // Create the ZIP file
    String filenameWithZipExt = f.getName() + ZIPEXTENSION;
    File zippedFile = new File(FilenameUtils.concat(SYSTEM_TMP.getAbsolutePath(), filenameWithZipExt));

    ZipOutputStream out = new ZipOutputStream(new FileOutputStream(zippedFile));
    FileInputStream in = new FileInputStream(f);

    // Add ZIP entry to output stream.
    out.putNextEntry(new ZipEntry(f.getName()));

    // Transfer bytes from the file to the ZIP file
    while ((len = in.read(buf)) > 0) {
        out.write(buf, 0, len);
    }

    // Complete the entry
    out.closeEntry();
    out.flush();

    in.close();
    out.close();

    return zippedFile;
}

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

/**
 * In community there are no statful template. If some {@link VirtualImageConversion} attached
 * use his properties when defining the {@link PrimaryDisk}, else use the
 * {@link VirtualMachineTemplate}/*w ww.j  av  a2 s.  c o m*/
 * 
 * @param virtualMachine
 * @param vmDesc
 * @param idDatacenter void
 */
@Transactional(readOnly = true, propagation = Propagation.REQUIRED)
protected void primaryDiskDefinitionConfiguration(final VirtualMachine virtualMachine,
        final VirtualMachineDescriptionBuilder vmDesc, final Integer idDatacenter) {
    String datastore = "";
    if (virtualMachine.getDatastore() != null) {
        if (virtualMachine.getDatastore().getDirectory() != null
                && !StringUtils.isEmpty(virtualMachine.getDatastore().getDirectory())) {
            datastore = FilenameUtils.concat(virtualMachine.getDatastore().getRootPath(),
                    virtualMachine.getDatastore().getDirectory());
        } else {
            datastore = virtualMachine.getDatastore().getRootPath();
        }
    }

    // Repository Manager address
    List<RemoteService> services = infRep.findRemoteServiceWithTypeInDatacenter(infRep.findById(idDatacenter),
            RemoteServiceType.APPLIANCE_MANAGER);
    RemoteService repositoryManager = null;
    if (!services.isEmpty()) {
        // Only one remote service of each type by datacenter.
        repositoryManager = services.get(0);
    } else {
        addNotFoundErrors(APIError.NON_EXISTENT_REMOTE_SERVICE_TYPE);
        flushErrors();
    }

    final VirtualMachineTemplate vmtemplate = virtualMachine.getVirtualMachineTemplate();
    final HypervisorType htype = virtualMachine.getHypervisor().getType();

    final VirtualImageConversion conversion = virtualMachine.getVirtualImageConversion();

    final DiskFormatType format = conversion != null ? conversion.getTargetType()
            : vmtemplate.getDiskFormatType();
    final Long size = conversion != null ? conversion.getSize() : vmtemplate.getDiskFileSize();
    final String path = conversion != null ? conversion.getTargetPath() : vmtemplate.getPath();
    final DiskControllerType cntrlType = getDiskController(htype, true, false);

    String url = "";
    if (virtualMachine.getVirtualMachineTemplate().getRepository() != null) // repo null when
                                                                            // imported.
    {
        url = virtualMachine.getVirtualMachineTemplate().getRepository().getUrl();
    }
    vmDesc.primaryDisk(DiskDescription.DiskFormatType.valueOf(format.name()), size, url, path, datastore,
            repositoryManager.getUri(), cntrlType);
}

From source file:de.sub.goobi.forms.ProzessverwaltungForm.java

/**
 * Save.//from  w w w  .j a  v a2s . com
 *
 * @return page or empty String
 */
public String Speichern() {
    /*
     * wenn der Vorgangstitel gendert wurde, wird dieser geprft und bei
     * erfolgreicher Prfung an allen relevanten Stellen mitgendert
     */
    if (this.myProzess != null && this.myProzess.getTitle() != null) {
        if (!this.myProzess.getTitle().equals(this.myNewProcessTitle)) {
            String validateRegEx = ConfigCore.getParameter("validateProzessTitelRegex", "[\\w-]*");
            if (!this.myNewProcessTitle.matches(validateRegEx)) {
                this.modusBearbeiten = "prozess";
                Helper.setFehlerMeldung(Helper.getTranslation("UngueltigerTitelFuerVorgang"));
                return "";
            } else {
                /* Prozesseigenschaften */
                for (org.kitodo.data.database.beans.ProcessProperty pe : this.myProzess.getProperties()) {
                    if (pe != null && pe.getValue() != null) {
                        if (pe.getValue().contains(this.myProzess.getTitle())) {
                            pe.setValue(pe.getValue().replaceAll(this.myProzess.getTitle(),
                                    this.myNewProcessTitle));
                        }
                    }
                }
                /* Scanvorlageneigenschaften */
                for (Template vl : this.myProzess.getTemplates()) {
                    for (TemplateProperty ve : vl.getProperties()) {
                        if (ve.getValue().contains(this.myProzess.getTitle())) {
                            ve.setValue(ve.getValue().replaceAll(this.myProzess.getTitle(),
                                    this.myNewProcessTitle));
                        }
                    }
                }
                /* Werkstckeigenschaften */
                for (Workpiece w : this.myProzess.getWorkpieces()) {
                    for (WorkpieceProperty we : w.getProperties()) {
                        if (we.getValue().contains(this.myProzess.getTitle())) {
                            we.setValue(we.getValue().replaceAll(this.myProzess.getTitle(),
                                    this.myNewProcessTitle));
                        }
                    }
                }

                try {
                    {
                        // renaming image directories
                        String imageDirectory = serviceManager.getProcessService()
                                .getImagesDirectory(myProzess);
                        SafeFile dir = new SafeFile(imageDirectory);
                        if (dir.isDirectory()) {
                            SafeFile[] subdirs = dir.listFiles();
                            for (SafeFile imagedir : subdirs) {
                                if (imagedir.isDirectory()) {
                                    imagedir.renameTo(new SafeFile(imagedir.getAbsolutePath()
                                            .replace(myProzess.getTitle(), myNewProcessTitle)));
                                }
                            }
                        }
                    }
                    {
                        // renaming ocr directories
                        String ocrDirectory = serviceManager.getProcessService().getOcrDirectory(myProzess);
                        SafeFile dir = new SafeFile(ocrDirectory);
                        if (dir.isDirectory()) {
                            SafeFile[] subdirs = dir.listFiles();
                            for (SafeFile imagedir : subdirs) {
                                if (imagedir.isDirectory()) {
                                    imagedir.renameTo(new SafeFile(imagedir.getAbsolutePath()
                                            .replace(myProzess.getTitle(), myNewProcessTitle)));
                                }
                            }
                        }
                    }
                    {
                        // renaming defined direcories
                        String[] processDirs = ConfigCore.getStringArrayParameter("processDirs");
                        for (String processDir : processDirs) {

                            String processDirAbsolut = FilenameUtils.concat(
                                    serviceManager.getProcessService().getProcessDataDirectory(myProzess),
                                    processDir.replace("(processtitle)", myProzess.getTitle()));

                            SafeFile dir = new SafeFile(processDirAbsolut);
                            if (dir.isDirectory()) {
                                dir.renameTo(new SafeFile(dir.getAbsolutePath().replace(myProzess.getTitle(),
                                        myNewProcessTitle)));
                            }
                        }
                    }
                } catch (Exception e) {
                    logger.warn("could not rename folder", e);
                }

                /* Vorgangstitel */
                this.myProzess.setTitle(this.myNewProcessTitle);

                if (!this.myProzess.isTemplate()) {
                    /* Tiffwriter-Datei lschen */
                    GoobiScript gs = new GoobiScript();
                    ArrayList<Process> pro = new ArrayList<Process>();
                    pro.add(this.myProzess);
                    gs.deleteTiffHeaderFile(pro);
                    gs.updateImagePath(pro);
                }
            }

        }

        try {
            serviceManager.getProcessService().save(this.myProzess);
        } catch (DAOException e) {
            Helper.setFehlerMeldung("fehlerNichtSpeicherbar", e.getMessage());
        } catch (IOException | ResponseException e) {
            Helper.setFehlerMeldung("errorElasticSearch", e.getMessage());
        }
    } else {
        Helper.setFehlerMeldung("titleEmpty");
    }
    return "";
}

From source file:com.enderville.enderinstaller.ui.Installer.java

private JComboBox getPresetDropdown() {
    if (presetDropdown == null) {
        presetDropdown = new JComboBox();
        presetDropdown.addItem(PRESET_NONE);
        presetDropdown.addItem(PRESET_ALL);
        presetDropdown.addItem(PRESET_CUSTOM);
        presetDropdown.addActionListener(this);
        File presetDir = new File(FilenameUtils.concat(InstallerConfig.getInstallerDir(), "config/presets"));
        if (!presetDir.exists() || !presetDir.isDirectory()) {
            LOGGER.warn("presets does not exist or is not a directory");
        } else {//w  w  w .  j  a va 2  s  . c o  m
            presetMap = new HashMap<String, List<String>>();
            File[] children = presetDir.listFiles();
            for (File child : children) {
                if (!child.isFile()) {
                    continue;
                }
                String name = FilenameUtils.getBaseName(child.getName());
                try {
                    BufferedReader r = new BufferedReader(new FileReader(child));
                    String l = null;
                    List<String> mods = new ArrayList<String>();
                    while ((l = r.readLine()) != null) {
                        mods.add(l);
                    }
                    presetMap.put(name, mods);
                    presetDropdown.addItem(name);
                } catch (IOException e) {
                    LOGGER.warn("Error reading " + child.getName(), e);
                }
            }
        }
    }
    return presetDropdown;
}