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

Introduction

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

Prototype

public static String removeExtension(String filename) 

Source Link

Document

Removes the extension from a filename.

Usage

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

/**
 * Actually perform the split of the compact reads file between
 * start and end position to the new compact reads file.
 *
 * @throws java.io.IOException/*from  ww  w.  j  ava2 s . c o m*/
 */
@Override
public void execute() throws IOException {
    if (inputFiles == null || inputFiles.size() == 0) {
        throw new IOException("--input not specified");
    }
    if (StringUtils.isBlank(outputFilename)) {
        throw new IOException("--output not specified");
    }

    if (quickConcat) {
        performQuickConcat();
    } else {

        final ReadsWriter writer = new ReadsWriterImpl(new FileOutputStream(outputFilename));
        writer.setNumEntriesPerChunk(sequencePerChunk);
        final MutableString sequence = new MutableString();

        ReadsReader readsReader = null;
        numberOfReads = 0;
        minReadLength = Integer.MAX_VALUE;
        maxReadLength = Integer.MIN_VALUE;
        int removedByFilterCount = 0;
        try {
            final ProgressLogger progress = new ProgressLogger();
            progress.start("concatenating files");
            progress.displayFreeMemory = true;
            progress.expectedUpdates = inputFiles.size();
            progress.start();
            for (final File inputFile : inputFiles) {

                readsReader = new ReadsReader(inputFile);
                String basename = FilenameUtils.removeExtension(inputFile.getPath());
                String filterFilename = basename + optionalFilterExtension;
                File filterFile = new File(filterFilename);
                ReadSet readIndexFilter = null;
                if (filterFile.exists() && filterFile.canRead()) {
                    readIndexFilter = new ReadSet();
                    readIndexFilter.load(filterFile);
                    LOG.info(String.format("Loaded optional filter %s with %d elements. ", filterFile,
                            readIndexFilter.size()));
                } else {
                    if (optionalFilterExtension != null) {
                        LOG.info("Could not locate filter for filename " + filterFilename);
                    }
                }

                for (final Reads.ReadEntry readEntry : readsReader) {
                    // only concatenate if (1) there is no filter or (2) the read index is in the filter.
                    if (readIndexFilter == null || readIndexFilter.contains(readEntry.getReadIndex())) {
                        final Reads.ReadEntry.Builder readEntryBuilder = Reads.ReadEntry.newBuilder(readEntry);
                        readEntryBuilder.setReadIndex(numberOfReads);
                        writer.appendEntry(readEntryBuilder);
                        minReadLength = Math.min(minReadLength, readEntry.getReadLength());
                        maxReadLength = Math.max(maxReadLength, readEntry.getReadLength());
                        numberOfReads++;
                    } else {
                        removedByFilterCount++;
                    }
                }
                readsReader.close();
                readsReader = null;
                progress.update();
            }
            progress.stop();
        } finally {
            writer.printStats(System.out);
            System.out.println("Number of reads=" + numberOfReads);
            System.out.println("Minimum Read Length=" + minReadLength);
            System.out.println("Maximum Read Length=" + maxReadLength);
            System.out.println("Reads removed by filter=" + removedByFilterCount);
            writer.close();
            if (readsReader != null) {
                readsReader.close();
            }
        }
    }
}

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From source file:de.uni.bremen.monty.moco.Main.java

private static void writeAssembly(String outputFileName, String inputFileName, String llvmCode)
        throws IOException {
    PrintStream assemblyStream = null;
    if (outputFileName != null) {
        assemblyStream = new PrintStream(outputFileName);
    } else if (inputFileName != null) {
        assemblyStream = new PrintStream(FilenameUtils.removeExtension(inputFileName) + ".ll");
    } else {/*from   w  w w . java  2  s  . c o  m*/
        assemblyStream = new PrintStream("output.ll");
    }
    assemblyStream.print(llvmCode);
    assemblyStream.close();
}

---

From source file:com.wx3.galacdecks.Bootstrap.java

private void importPlayValidators(GameDatastore datastore, String path) throws IOException {
    Files.walk(Paths.get(path)).forEach(filePath -> {
        if (Files.isRegularFile(filePath)) {
            try {
                if (FilenameUtils.getExtension(filePath.getFileName().toString()).toLowerCase().equals("js")) {
                    String id = FilenameUtils.removeExtension(filePath.getFileName().toString());
                    List<String> lines = Files.readAllLines(filePath);
                    if (lines.size() < 3) {
                        throw new RuntimeException(
                                "Script file should have at least 2 lines: description and code.");
                    }/*from  w  w w .j a  v  a 2s  .  c  om*/
                    String description = lines.get(0).substring(2).trim();
                    String script = String.join("\n", lines);
                    ValidatorScript validator = ValidatorScript.createValidator(id, script, description);
                    //datastore.createValidator(validator);
                    playValidatorCache.put(id, validator);
                    logger.info("Imported play validator " + id);
                }
            } catch (Exception e) {
                throw new RuntimeException("Failed to parse " + filePath + ": " + e.getMessage());
            }
        }
    });
}

---

From source file:com.nohowdezign.gcpmanager.Main.java

public static void dowloadFile(Job job) throws CloudPrintException {
    SimpleDateFormat sdf = new SimpleDateFormat("MM-dd-yyyy HH-mm-ss");

    File directory = new File(
            "./jobstorage/" + sdf.format(Long.parseLong(job.getCreateTime())) + "/" + job.getOwnerId() + "/");
    if (!directory.exists()) {
        directory.mkdirs();//from   w  w  w  . j av a  2  s  . co m
    }

    String fileName = FilenameUtils.removeExtension(job.getTitle()) + ".pdf";
    File outputFile = new File(directory, fileName);

    if (!outputFile.exists()) {
        cloudPrint.downloadFile(job.getFileUrl(), outputFile);
        logger.info("mod date: {}", sdf.format(outputFile.lastModified()));
        JobStorageManager manager = new JobStorageManager();
        manager.addJobFileDownloaded(outputFile);
    }
}

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From source file:ch.ifocusit.livingdoc.plugin.publish.HtmlPostProcessor.java

public String getPageTitle(Path path) {
    String pageContent = null;//from www  .j  a v a2 s. c o m
    try {
        pageContent = IOUtils.readFull(new FileInputStream(path.toFile()));
    } catch (FileNotFoundException e) {
        throw new IllegalStateException("Unable to read page title !", e);
    }
    try {
        if (isAdoc(path)) {
            return getTitle(asciidoctor, pageContent).orElseThrow(
                    () -> new IllegalStateException("top-level heading or title meta information must be set"));

        }
        // try to read h1 tag
        return tagText(pageContent, "h1");
    } catch (IllegalStateException e) {
        return FilenameUtils.removeExtension(path.getFileName().toString());
    }
}

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From source file:io.proleap.vb6.asg.runner.impl.VbParserRunnerImpl.java

protected String getModuleName(final File inputFile) {
    return StringUtils.capitalize(FilenameUtils.removeExtension(inputFile.getName()));
}

---

From source file:it.isislab.dmason.util.SystemManagement.Worker.thrower.DMasonWorkerWithGui.java

public DMasonWorkerWithGui(boolean start, boolean up, boolean batch, String topic, String ipCS, String portCS) {
    initComponents();/* w w  w . ja v a 2s.c  om*/

    beaconListener = new BeaconMessageListener();
    beaconListener.addObserver(this);

    new Thread(beaconListener).start();

    connection = new ConnectionNFieldsWithActiveMQAPI();

    connection.addObserver(this);

    setDefaultCloseOperation(EXIT_ON_CLOSE);
    setVisible(true);

    // Get the path from which worker was started
    String path;
    try {
        path = URLDecoder.decode(
                DMasonWorkerWithGui.class.getProtectionDomain().getCodeSource().getLocation().getFile(),
                "UTF-8");
    } catch (UnsupportedEncodingException e1) {
        // TODO Auto-generated catch block
        e1.printStackTrace();
        path = "";
    }
    logger.debug("Path: " + path);

    if (path.contains(".jar")) //from jar
    {

        File jarfile = new File(path);

        Digester dg = new Digester(DigestAlgorithm.MD5);

        try {
            InputStream in = new FileInputStream(path);

            digest = dg.getDigest(in);

            String fileName = FilenameUtils.removeExtension(jarfile.getName());
            //save properties to project root folder
            dg.storeToPropFile(fileName + ".hash");

        } catch (IOException ex) {
            ex.printStackTrace();
        } catch (NoDigestFoundException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        }

    } else { // not from jar
        digest = null;
    }

    autoStart = start;
    updated = up;
    myTopic = topic;
    isBatch = batch;
    ip = ipCS;
    port = portCS;

    if (autoStart)
        connect();

    //initSchedule();
}

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From source file:de.uzk.hki.da.cb.ConvertAction.java

private void addDAFileToDocument(Object o, DAFile file) {
    Document doc = o.getDocument(FilenameUtils.removeExtension(file.getRelative_path()));
    if (doc == null) {
        throw new IllegalStateException("Cannot add new dafile to document "
                + FilenameUtils.removeExtension(file.getRelative_path()) + ".");
    } else {//from  w  w w .  j a va 2s  . c  o m
        doc.addDAFile(file);
    }
}

---

From source file:jease.cms.service.Imports.java

private static Image newImage(String filename, InputStream inputStream) throws IOException {
    Image image = new Image();
    image.setId(Filenames.asId(filename));
    image.setTitle(FilenameUtils.removeExtension(filename));
    image.setLastModified(new Date());
    image.setContentType(MimeTypes.guessContentTypeFromName(filename));
    copyStreamToFile(inputStream, image.getFile());
    return image;
}

---

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

/**
 * Tokenizes commandLine and replaces certain strings.
 * "input" and "output" get replaced by paths of source and destination file.
 * strings beginning with "{" and ending with "}" get replaced by the contents of additionalParams of the ConversionInstruction.
 * Each of the {}-surrounded string gets replaced by exactly one token of additional params.
 *
 * @param ci the ci//from   ww w .  j ava 2  s . c om
 * @param repName the rep name
 * @return The processed command as list of tokens. The tokenized string has the right format
 * for a call in Runtime.getRuntime().exec(commandToExecute). This holds especially true
 * for filenames (which replace the input/output parameters) that are separated by
 * whitespaces. "file 2.jpg" is represented as one token only.
 */
protected String[] assemble(ConversionInstruction ci, String repName) {

    String commandLine_ = commandLine;

    // replace additional params
    List<String> ap = tokenize(ci.getAdditional_params(), ",");
    for (String s : ap) {

        Pattern pattern = Pattern.compile("\\{.*?\\}");
        Matcher matcher = pattern.matcher(commandLine_);
        commandLine_ = matcher.replaceFirst(s);
    }

    // tokenize before replacement to group original tokens together
    // (to prevent wrong tokenization like two tokens for "file" "2.jpg"
    //  which can result from replacement)
    String[] tokenizedCmd = tokenize(commandLine_);

    String targetSuffix = ci.getConversion_routine().getTarget_suffix();
    if (targetSuffix.equals("*"))
        targetSuffix = FilenameUtils.getExtension(ci.getSource_file().toRegularFile().getAbsolutePath());
    Utilities.replace(tokenizedCmd, "input", ci.getSource_file().toRegularFile().getAbsolutePath());
    Utilities.replace(tokenizedCmd, "output",
            object.getDataPath() + "/" + repName + "/" + Utilities.slashize(ci.getTarget_folder())
                    + FilenameUtils.removeExtension(Matcher.quoteReplacement(
                            FilenameUtils.getName(ci.getSource_file().toRegularFile().getAbsolutePath())))
                    + "." + targetSuffix);

    return tokenizedCmd;
}

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