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

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

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Introduction

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

Prototype

public static String getFullPath(String filename)

Source Link

Document

Gets the full path from a full filename, which is the prefix + path.

Usage

From source file:it.drwolf.ridire.session.async.WordCounter.java

@Asynchronous
public void countWords(Integer jobId) {
    try {/*from  w  w w  .  ja va  2s. c o m*/
        this.userTx = (UserTransaction) org.jboss.seam.Component
                .getInstance("org.jboss.seam.transaction.transaction");
        String resourcesDir = null;
        if (!this.userTx.isActive()) {
            this.userTx.begin();
        }
        this.entityManager.joinTransaction();
        String dir = this.entityManager.find(Parameter.class, Parameter.JOBS_DIR.getKey()).getValue();
        Job curJ = this.entityManager.find(Job.class, jobId);
        if (curJ.getChildJobName() != null && !curJ.isMappedResources()) {
            resourcesDir = dir + JobMapperMonitor.FILE_SEPARATOR + curJ.getChildJobName()
                    + JobMapperMonitor.FILE_SEPARATOR + "arcs" + JobMapperMonitor.FILE_SEPARATOR
                    + JobMapperMonitor.RESOURCESDIR;
        } else {
            resourcesDir = dir + JobMapperMonitor.FILE_SEPARATOR + curJ.getName()
                    + JobMapperMonitor.FILE_SEPARATOR + "arcs" + JobMapperMonitor.FILE_SEPARATOR
                    + JobMapperMonitor.RESOURCESDIR;
        }

        // back compatibility with Heritrix 2
        File resourcesDirFile = new File(resourcesDir);
        if (resourcesDirFile == null || !resourcesDirFile.isDirectory()) {
            resourcesDir = "completed-" + resourcesDir;
        }
        this.entityManager.flush();
        this.userTx.commit();
        Integer jobWords = 0;
        for (CrawledResource cr : curJ.getCrawledResources()) {
            if (!this.userTx.isActive()) {
                this.userTx.begin();
            }
            this.entityManager.joinTransaction();
            this.entityManager.refresh(cr);
            String digest = cr.getDigest();
            if (digest != null) {
                File posFile = new File(resourcesDir + JobMapperMonitor.FILE_SEPARATOR + digest + ".txt.pos");
                if (posFile != null && posFile.exists() && posFile.canRead()) {
                    try {
                        Integer countWordsFromPoSTagResource = this.countWordsFromPoSTagResource(posFile);
                        jobWords += countWordsFromPoSTagResource;
                        cr.setWordsNumber(countWordsFromPoSTagResource);
                        File f = new File(FilenameUtils.getFullPath(cr.getArcFile())
                                + JobMapperMonitor.RESOURCESDIR + cr.getDigest() + ".txt");
                        if (f.exists() && f.canRead()) {
                            cr.setExtractedTextHash(MD5DigestCreator.getMD5Digest(f));
                        }
                        this.entityManager.merge(cr);
                    } catch (IOException e) {
                        // TODO Auto-generated catch block
                        e.printStackTrace();
                    } catch (NoSuchAlgorithmException e) {
                        // TODO Auto-generated catch block
                        e.printStackTrace();
                    }
                }
            }
            this.entityManager.flush();
            this.userTx.commit();
        }
        if (!this.userTx.isActive()) {
            this.userTx.begin();
        }
        this.entityManager.joinTransaction();
        Job j = this.entityManager.find(Job.class, jobId);
        j.setWordsNumber(jobWords);
        this.entityManager.persist(j);
        this.entityManager.flush();
        this.userTx.commit();
    } catch (NotSupportedException e1) {
        // TODO Auto-generated catch block
        e1.printStackTrace();
    } catch (SystemException e1) {
        // TODO Auto-generated catch block
        e1.printStackTrace();
    } catch (SecurityException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    } catch (IllegalStateException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    } catch (RollbackException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    } catch (HeuristicMixedException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    } catch (HeuristicRollbackException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
}

From source file:com.notesrender.templatej.TemplateProcessor.java

public void process(String filePath) {
    try {/*ww w.jav  a  2 s . c  o  m*/
        XMLReader rd = XMLReaderFactory.createXMLReader();
        rd.setContentHandler(this);
        rd.parse(new InputSource(new FileInputStream(filePath)));

        String fullFilePath = new File(filePath).getAbsolutePath();
        String dir = FilenameUtils.getFullPath(fullFilePath);
        String tplFullFilePath = new File(dir, _ref).getAbsolutePath();
        String outFullFilePath = new File(dir, _out).getAbsolutePath();

        _writer = new PrintWriter(new BufferedWriter(new FileWriter(outFullFilePath)));
        rd.parse(new InputSource(new FileInputStream(tplFullFilePath)));
        _writer.close();
    } catch (SAXException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    } catch (FileNotFoundException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    } catch (IOException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
}

From source file:de.uzk.hki.da.convert.TiffConversionStrategy.java

@Override
public List<Event> convertFile(WorkArea wa, ConversionInstruction ci) {

    List<Event> resultEvents = new ArrayList<Event>();

    String input = wa.toFile(ci.getSource_file()).getAbsolutePath();
    String[] commandAsArray;//from  w w w.  j  av a2 s.c  o  m
    String prunedError = "";
    FormatCmdLineExecutor cle = new FormatCmdLineExecutor(cliConnector, knownErrors);
    try {
        // Codec identification is done by subformatidentification
        ImageMagickSubformatIdentifier imsf = new ImageMagickSubformatIdentifier();
        imsf.setKnownFormatCommandLineErrors(knownErrors);
        imsf.setCliConnector(cliConnector);

        if (imsf.identify(new File(input), prune).indexOf("None") >= 0)
            return resultEvents;

        // create subfolder if necessary
        Path.make(wa.dataPath(), object.getNameOfLatestBRep(), ci.getTarget_folder()).toFile().mkdirs();

        commandAsArray = new String[] { "convert", "+compress", input, generateTargetFilePath(wa, ci) };

        logger.debug("Try to Execute conversion command: " + StringUtils.join(commandAsArray, ","));

        cle.setPruneExceptions(prune);
        try {
            cle.execute(commandAsArray);
        } catch (UserFileFormatException ufe) {
            if (!ufe.isWasPruned())
                throw ufe;
            prunedError = " " + ufe.getKnownError().getError_name() + " ISSUED WAS PRUNED BY USER!";
        }
    } catch (IOException e1) {
        throw new RuntimeException(e1);
    }

    File result = new File(generateTargetFilePath(wa, ci));

    String baseName = FilenameUtils.getBaseName(result.getAbsolutePath());
    String extension = FilenameUtils.getExtension(result.getAbsolutePath());
    logger.info("Finding files matching wildcard expression \"" + baseName + "*." + extension
            + "\" in order to check them and test if conversion was successful");
    List<File> results = findFilesWithWildcard(new File(FilenameUtils.getFullPath(result.getAbsolutePath())),
            baseName + "*." + extension);

    for (File f : results) {
        DAFile daf = new DAFile(object.getNameOfLatestBRep(),
                StringUtilities.slashize(ci.getTarget_folder()) + f.getName());
        logger.debug("new dafile:" + daf);

        Event e = new Event();
        e.setType("CONVERT");

        e.setDetail(StringUtilities.createString(commandAsArray) + prunedError);
        e.setSource_file(ci.getSource_file());
        e.setTarget_file(daf);
        e.setDate(new Date());

        resultEvents.add(e);
    }

    return resultEvents;
}

From source file:eu.esdihumboldt.hale.io.html.HtmlMappingExporter.java

@Override
protected IOReport execute(ProgressIndicator progress, IOReporter reporter)
        throws IOProviderConfigurationException, IOException {
    this.reporter = reporter;

    context = new VelocityContext();
    cellIds = new Identifiers<Cell>(Cell.class, false);

    alignment = getAlignment();/*from   w  w  w  .ja  v  a  2s  .c  o m*/

    URL headlinePath = this.getClass().getResource("bg-headline.png"); //$NON-NLS-1$
    URL cssPath = this.getClass().getResource("style.css"); //$NON-NLS-1$
    URL linkPath = this.getClass().getResource("int_link.png"); //$NON-NLS-1$
    URL tooltipIcon = this.getClass().getResource("tooltip.gif"); //$NON-NLS-1$
    final String filesSubDir = FilenameUtils
            .removeExtension(FilenameUtils.getName(getTarget().getLocation().getPath())) + "_files"; //$NON-NLS-1$
    final File filesDir = new File(FilenameUtils.getFullPath(getTarget().getLocation().getPath()), filesSubDir);

    filesDir.mkdirs();
    context.put(FILE_DIRECTORY, filesSubDir);

    try {
        init();
    } catch (Exception e) {
        return reportError(reporter, "Initializing error", e);
    }
    File cssOutputFile = new File(filesDir, "style.css");
    FileUtils.copyFile(getInputFile(cssPath), cssOutputFile);

    // create headline picture
    File headlineOutputFile = new File(filesDir, "bg-headline.png"); //$NON-NLS-1$
    FileUtils.copyFile(getInputFile(headlinePath), headlineOutputFile);

    File linkOutputFile = new File(filesDir, "int_link.png"); //$NON-NLS-1$
    FileUtils.copyFile(getInputFile(linkPath), linkOutputFile);

    File tooltipIconFile = new File(filesDir, "tooltip.png"); //$NON-NLS-1$
    FileUtils.copyFile(getInputFile(tooltipIcon), tooltipIconFile);

    File htmlExportFile = new File(getTarget().getLocation().getPath());
    if (projectInfo != null) {
        Date date = new Date();
        DateFormat dfm = DateFormat.getDateTimeInstance(DateFormat.MEDIUM, DateFormat.SHORT);

        // associate variables with information data
        String exportDate = dfm.format(date);
        context.put(EXPORT_DATE, exportDate);

        if (projectInfo.getCreated() != null) {
            String created = dfm.format(projectInfo.getCreated());
            context.put(CREATED_DATE, created);
        }

        context.put(PROJECT_INFO, projectInfo);
    }

    if (alignment != null) {
        Collection<TypeCellInfo> typeCellInfos = new ArrayList<TypeCellInfo>();
        Collection<? extends Cell> cells = alignment.getTypeCells();
        Iterator<? extends Cell> it = cells.iterator();
        while (it.hasNext()) {
            final Cell cell = it.next();
            // this is the collection of type cell info
            TypeCellInfo typeCellInfo = new TypeCellInfo(cell, alignment, cellIds, filesSubDir);
            typeCellInfos.add(typeCellInfo);
        }
        // put the full collection of type cell info to the context (for the
        // template)
        context.put(TYPE_CELL_INFOS, typeCellInfos);
        createImages(filesDir);
    }

    context.put(TOOLTIP, getParameter(TOOLTIP).as(boolean.class));

    Template template;
    try {
        template = velocityEngine.getTemplate(templateFile.getName(), "UTF-8");
    } catch (Exception e) {
        return reportError(reporter, "Could not load template", e);
    }

    FileWriter fileWriter = new FileWriter(htmlExportFile);
    template.merge(context, fileWriter);
    fileWriter.close();

    reporter.setSuccess(true);
    return reporter;
}

From source file:ch.unibas.charmmtools.gui.step1.mdAssistant.CHARMM_GUI_InputAssistant.java

private File convertWithBabel(File xyz) {
    String parent = FilenameUtils.getFullPath(xyz.getAbsolutePath());
    String basename = FilenameUtils.getBaseName(xyz.getAbsolutePath());

    File pdbOut = new File(parent + basename + ".pdb");

    BabelConverterAPI babelc = new BabelConverterAPI("xyz", "pdb");
    babelc.convert(xyz, pdbOut);//from w ww.  j av a2s. co  m

    if (pdbOut.exists()) {
        try {
            logger.info("Content of pdb file obtained from babel : \n"
                    + Files.readAllBytes(Paths.get(pdbOut.getAbsolutePath())));
        } catch (IOException ex) {
        }
    }

    return pdbOut;
}

From source file:de.uzk.hki.da.format.PublishImageConversionStrategy.java

/**
 *//*from ww  w .jav  a2s  .c o m*/
@Override
public List<Event> convertFile(ConversionInstruction ci) throws FileNotFoundException {
    if (cliConnector == null)
        throw new IllegalStateException("cliConnector not set");
    if (ci.getConversion_routine() == null)
        throw new IllegalStateException("conversionRoutine not set");
    if (ci.getConversion_routine().getTarget_suffix() == null
            || ci.getConversion_routine().getTarget_suffix().isEmpty())
        throw new IllegalStateException("target suffix in conversionRoutine not set");

    List<Event> results = new ArrayList<Event>();

    // connect dafile to package

    String input = ci.getSource_file().toRegularFile().getAbsolutePath();

    // Convert 
    ArrayList<String> commandAsList = null;
    for (String audience : audiences) {

        Path.makeFile(object.getDataPath(), pips, audience.toLowerCase(), ci.getTarget_folder()).mkdirs();

        commandAsList = new ArrayList<String>();
        commandAsList.add("convert");
        commandAsList.add(ci.getSource_file().toRegularFile().getAbsolutePath());
        logger.debug(commandAsList.toString());
        commandAsList = assembleResizeDimensionsCommand(commandAsList, audience);
        commandAsList = assembleWatermarkCommand(commandAsList, audience);
        commandAsList = assembleFooterTextCommand(commandAsList, audience,
                ci.getSource_file().toRegularFile().getAbsolutePath());

        DAFile target = new DAFile(pkg, pips + "/" + audience.toLowerCase(),
                Utilities.slashize(ci.getTarget_folder()) + FilenameUtils.getBaseName(input) + "."
                        + ci.getConversion_routine().getTarget_suffix());
        commandAsList.add(target.toRegularFile().getAbsolutePath());

        logger.debug(commandAsList.toString());
        String[] commandAsArray = new String[commandAsList.size()];
        commandAsArray = commandAsList.toArray(commandAsArray);
        if (!cliConnector.execute(commandAsArray))
            throw new RuntimeException("convert did not succeed: " + Arrays.toString(commandAsArray));

        // In order to support multipage tiffs, we check for files by wildcard expression
        String extension = FilenameUtils.getExtension(target.toRegularFile().getAbsolutePath());
        List<File> wild = findFilesWithRegex(
                new File(FilenameUtils.getFullPath(target.toRegularFile().getAbsolutePath())),
                Pattern.quote(FilenameUtils.getBaseName(target.getRelative_path())) + "-\\d+\\." + extension);
        if (!target.toRegularFile().exists() && !wild.isEmpty()) {
            for (File f : wild) {
                DAFile multipageTarget = new DAFile(pkg, pips + "/" + audience.toLowerCase(),
                        Utilities.slashize(ci.getTarget_folder()) + f.getName());

                Event e = new Event();
                e.setDetail(Utilities.createString(commandAsList));
                e.setSource_file(ci.getSource_file());
                e.setTarget_file(multipageTarget);
                e.setType("CONVERT");
                e.setDate(new Date());
                results.add(e);
            }
        } else {
            Event e = new Event();
            e.setDetail(Utilities.createString(commandAsList));
            e.setSource_file(ci.getSource_file());
            e.setTarget_file(target);
            e.setType("CONVERT");
            e.setDate(new Date());
            results.add(e);
        }
    }

    return results;
}

From source file:de.mpg.imeji.logic.storage.util.MediaUtils.java

/**
 * Remove the files created by imagemagick.
 * //from w  ww  .j  a  v  a 2  s  .c  om
 * @param path
 */
private static void removeFilesCreatedByImageMagick(String path) {
    int count = 0;
    String dir = FilenameUtils.getFullPath(path);
    String pathBase = FilenameUtils.getBaseName(path);
    File f = new File(dir + pathBase + "-" + count + ".jpg");
    while (f.exists()) {
        String newPath = f.getAbsolutePath().replace("-" + count, "-" + Integer.valueOf(count + 1));
        f.delete();
        f = new File(newPath);
        count++;
    }
}

From source file:com.seagate.kinetic.KineticTestSimulator.java

/**
 *
 * Create test simulator.// ww w  . ja  va 2s.  co m
 *
 * @param clearExistingDatabase
 *            If clear existing data, set true, if not, set false.
 * @param serverConfiguration
 *            Using different configuration to generate different simulator.
 *
 * @throws KineticException
 *             if any internal error occurred.
 * @throws IOException
 *             if any IO error occurred
 * @throws InterruptedException
 *             if any Interrupt error occurred
 *
 * @see SimulatorConfiguration
 */
public KineticTestSimulator(boolean clearExistingDatabase, SimulatorConfiguration serverConfiguration)
        throws IOException, InterruptedException, KineticException {
    javaServerConfiguration = serverConfiguration;

    String kineticPath = System.getProperty("KINETIC_PATH");
    String kineticHost = System.getProperty("KINETIC_HOST");

    int requestedPort = Integer.parseInt(System.getProperty("KINETIC_PORT", "8123"));

    if (!Boolean.parseBoolean(System.getProperty("RUN_AGAINST_EXTERNAL"))) {
        port = 8123;
        LOG.fine("Starting java simulator on port " + port);
        host = "localhost";
        serverConfiguration.setPort(port);

        if (clearExistingDatabase) {
            deleteJavaServerAuxilaryData();

            String defaultHome = System.getProperty("user.home") + File.separator + "leafcutter";

            String leafcutterHome = serverConfiguration.getProperty(SimulatorConfiguration.KINETIC_HOME,
                    defaultHome);

            FileUtils.deleteQuietly(new File(leafcutterHome));
        }

        // set nio services thread pool size
        serverConfiguration.setNioServiceBossThreads(1);
        serverConfiguration.setNioServiceWorkerThreads(1);

        kineticServer = new KineticSimulator(serverConfiguration);
        externalKineticServer = null;
    } else if (kineticPath != null) {
        port = requestedPort;
        LOG.fine("Running tests against external simulator at " + kineticPath + " using port " + port);
        host = "localhost";
        kineticServer = null;

        FinalizedProcessBuilder finalizedProcessBuilder = new FinalizedProcessBuilder("killall", "-9",
                "kineticd");
        finalizedProcessBuilder.start().waitFor(10 * 1000);
        Thread.sleep(500);

        // Since the cluster version is checked before performing an ISE we
        // need to manually remove
        // the file used to store the cluster version
        if (clearExistingDatabase) {
            final String workingDirectory = FilenameUtils.getFullPath(kineticPath);
            final String clusterStorePath = FilenameUtils.concat(workingDirectory, "cluster_version");
            FileUtils.deleteQuietly(new File(clusterStorePath));
        }

        finalizedProcessBuilder = new FinalizedProcessBuilder(kineticPath);
        finalizedProcessBuilder.directory(new File("."));
        finalizedProcessBuilder.gobbleStreamsWithLogging(true);

        externalKineticServer = finalizedProcessBuilder.start();
        waitForServerReady();
    } else {
        host = kineticHost;
        port = requestedPort;
        LOG.fine("Running tests against " + host + ":" + port);

        kineticServer = null;
        externalKineticServer = null;
    }

    if (clearExistingDatabase) {

        KineticClient kineticClient = buildClient();

        KineticMessage km = MessageFactory.createKineticMessageWithBuilder();
        Command.Builder commandBuillder = (Command.Builder) km.getCommand();

        commandBuillder.getBodyBuilder().getSetupBuilder();

        /**
         * XXX protocol-3.0.0
         */

        //com.seagate.kinetic.proto.Kinetic.Message.Builder builder = com.seagate.kinetic.proto.Kinetic.Message
        //      .newBuilder();
        //builder.getCommandBuilder().getBodyBuilder().getSetupBuilder()
        //.setInstantSecureErase(true);

        commandBuillder.getHeaderBuilder()
                .setMessageType(com.seagate.kinetic.proto.Kinetic.Command.MessageType.SETUP);

        kineticClient.request(km);
        kineticClient.close();
    }
}

From source file:MSUmpire.LCMSPeakStructure.LCMSPeakMS1.java

public String GetDefaultPepXML() {
    return FilenameUtils.separatorsToUnix(FilenameUtils.getFullPath(ScanCollectionName) + "interact-"
            + FilenameUtils.getBaseName(ScanCollectionName) + ".pep.xml");
}

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

/**
 * Split a fasta / fastq file by (a) readlength and (b) the maximum number of
 * entries per file. This will output the files that are written to stdout
 * @throws IOException error reading / writing files.
 *///from ww w.  j a  v  a2s . c om
@Override
public void execute() throws IOException {
    final FastXReader reader = new FastXReader(inputFile);
    final Int2ObjectMap<PrintStream> outputMap = new Int2ObjectOpenHashMap<PrintStream>();
    final Int2IntMap entriesPerReadLen = new Int2IntOpenHashMap();
    final Int2IntMap filesPerReadLen = new Int2IntOpenHashMap();
    final List<String> removeExt = Arrays.asList("gz", "fa", "mpfa", "fna", "fsa", "fas", "fasta", "fq", "mpfq",
            "fnq", "fsq", "fas", "fastq");
    String inputName = FilenameUtils.getName(inputFile);
    while (true) {
        // Remove the unwanted extensions from the file name
        final String ext = FilenameUtils.getExtension(inputName);
        if (!removeExt.contains(ext)) {
            break;
        }
        inputName = FilenameUtils.getBaseName(inputName);
    }
    final String outputFilenameTemplate = FilenameUtils.getFullPath(inputFile) + inputName
            + "._READLENGTH_._PART_." + reader.getFileType();
    final NumberFormat nf3 = NumberFormat.getInstance();
    nf3.setMinimumIntegerDigits(3);
    final NumberFormat nf2 = NumberFormat.getInstance();
    nf2.setMinimumIntegerDigits(2);
    for (final FastXEntry entry : reader) {
        final int readLen = Math.min(fastxSplitMaxLength, roundReadLen(entry.getReadLength(), splitReadsMod));
        PrintStream out = outputMap.get(readLen);
        if (out == null) {
            filesPerReadLen.put(readLen, 1);
            entriesPerReadLen.put(readLen, 0);
            String outputFilename = outputFilenameTemplate.replaceAll("_READLENGTH_", nf3.format(readLen));
            outputFilename = outputFilename.replaceAll("_PART_", nf2.format(1));
            System.out.println(outputFilename);
            out = new PrintStream(new BufferedOutputStream(new FileOutputStream(outputFilename)));
            outputMap.put(readLen, out);
        }
        int numEntries = entriesPerReadLen.get(readLen);
        if (numEntries == maxReadsPerFile) {
            out.close();
            numEntries = 0;
            int numFiles = filesPerReadLen.get(readLen);
            numFiles++;
            filesPerReadLen.put(readLen, numFiles);
            String outputFilename = outputFilenameTemplate.replaceAll("_READLENGTH_", nf3.format(readLen));
            outputFilename = outputFilename.replaceAll("_PART_", nf2.format(numFiles));
            System.out.println(outputFilename);
            out = new PrintStream(new BufferedOutputStream(new FileOutputStream(outputFilename)));
            outputMap.put(readLen, out);
        }
        out.println(entry.getEntry());
        entriesPerReadLen.put(readLen, numEntries + 1);
    }
    for (final PrintStream out : outputMap.values()) {
        out.close();
    }
    outputMap.clear();
    reader.close();
}