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

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

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Introduction

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

Prototype

public static String getBaseName(String filename)

Source Link

Document

Gets the base name, minus the full path and extension, from a full filename.

Usage

From source file:com.salsaw.msalsa.clustal.ClustalOmegaManager.java

@Override
public void callClustal(String clustalPath, ClustalFileMapper clustalFileMapper)
        throws IOException, InterruptedException, SALSAException {
    // Get program path to execute
    List<String> clustalProcessCommands = new ArrayList<String>();
    clustalProcessCommands.add(clustalPath);

    // Create the name of output files
    String inputFileName = FilenameUtils.getBaseName(clustalFileMapper.getInputFilePath());
    String inputFileFolderPath = FilenameUtils.getFullPath(clustalFileMapper.getInputFilePath());
    Path alignmentFilePath = Paths.get(inputFileFolderPath, inputFileName + "-aln.fasta");
    Path guideTreeFilePath = Paths.get(inputFileFolderPath, inputFileName + "-tree.dnd");

    // Set inside file mapper
    clustalFileMapper.setAlignmentFilePath(alignmentFilePath.toString());
    clustalFileMapper.setGuideTreeFilePath(guideTreeFilePath.toString());
    setClustalFileMapper(clustalFileMapper);

    // Create clustal omega data
    generateClustalArguments(clustalProcessCommands);

    // http://www.rgagnon.com/javadetails/java-0014.html
    ProcessBuilder builder = new ProcessBuilder(clustalProcessCommands);
    builder.redirectErrorStream(true);//w  ww  .  j  a  va  2  s.  c o m
    System.out.println(builder.command());
    final Process process = builder.start();
    InputStream is = process.getInputStream();
    InputStreamReader isr = new InputStreamReader(is);
    BufferedReader br = new BufferedReader(isr);

    String line;
    while ((line = br.readLine()) != null) {
        System.out.println(line);
    }
    process.waitFor();

    if (process.exitValue() != 0) {
        throw new SALSAException("Failed clustal omega call");
    }
}

From source file:de.mpg.imeji.presentation.beans.PropertyBean.java

/**
 * @return the internalStorageBase//from w w w  . jav a  2  s. c  o m
 * @throws URISyntaxException
 * @throws IOException
 */
public String getInternalStorageBase() throws IOException, URISyntaxException {
    this.internalStorageBase = FilenameUtils.getBaseName(
            FilenameUtils.normalizeNoEndSeparator(PropertyReader.getProperty("imeji.storage.path")));
    return internalStorageBase;
}

From source file:eu.uqasar.web.upload.FileUploadUtil.java

Path getNewFileName(FileUpload file, User user, boolean overwrite) throws IOException {
    Path target;// w  w w  .  j a v  a2s  .c  o m
    String uploadedFileFileName = file.getClientFileName();
    if (overwrite) {
        target = FileSystems.getDefault().getPath(getUserUploadFolder(user).toString(), uploadedFileFileName);
    } else {
        final String extensionPart = FilenameUtils.getExtension(uploadedFileFileName);
        final String extension = StringUtils.isEmpty(extensionPart) ? "" : "." + extensionPart;
        // we add a dot (".") before the UUID, so +1
        final int UUID_LENGTH = 1 + 36;
        // extension length is given out of extension length + the dot (".txt" == 4, no extension == 0)
        final int EXTENSION_LENGTH = extension.length();
        // MAX file name length is 255 - UUID part - Extension part
        final int MAX_BASE_FILENAME_LENGTH = 255 - UUID_LENGTH - EXTENSION_LENGTH;
        // shorten file name to no longer than max length, calculated above
        final String fileNameWithoutExtension = StringUtils
                .left(FilenameUtils.getBaseName(uploadedFileFileName), MAX_BASE_FILENAME_LENGTH);
        // generate new file name out of shortened base name + "." + UUID + any extension (including ".")
        final String targetFileName = String.format("%s.%s%s", fileNameWithoutExtension,
                UUID.randomUUID().toString(), extension);
        target = FileSystems.getDefault().getPath(getUserUploadFolder(user).toString(), targetFileName);
    }
    return target;
}

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

/**
 *///  w  w  w .j  av  a2  s .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:br.com.pontocontrol.controleponto.controller.impl.ArquivoController.java

@Override
public List<Integer> getAvalableFileMonths(int ano) {
    File dir = new File(getYearPath(ano));
    List<Integer> saida = new ArrayList<Integer>();
    if (dir.exists()) {
        File[] listFiles = dir.listFiles();
        for (File file : listFiles) {
            final String ext = FilenameUtils.getExtension(file.getName());
            final String nomeArquivo = FilenameUtils.getBaseName(file.getName());
            final String[] nomeArquivoSplit = nomeArquivo.split("_");
            if (file.isFile() && EXTENSAO_ARQUIVOS.equalsIgnoreCase(ext)
                    && PREFIXO_ARQUIVOS.equalsIgnoreCase(nomeArquivoSplit[0])) {
                String mesStr = nomeArquivoSplit[1];
                try {
                    Date date = new SimpleDateFormat(SUFIXO_ARQUIVOS_PARSER).parse(mesStr);
                    Calendar calendar = Calendar.getInstance();
                    calendar.setTime(date);
                    saida.add(calendar.get(Calendar.MONTH));
                } catch (ParseException ex) {
                    LOG.log(Level.SEVERE, format(
                            "Erro ao executar parse de data da entrada \"%s\" atravs do padro \"MMM\" o arquivo ser descartado.",
                            mesStr), ex);
                }/*from   w ww .  j a v a  2 s.  c  om*/
            }
        }
    }
    return saida;
}

From source file:integr.org.pgptool.gui.encryption.EncryptionDecryptionTests.java

@Test
public void testWeCanDecryptTheProductOfEncryption() throws Exception {
    String targetFilename = tempDirPath + File.separator + FilenameUtils.getBaseName(testSubjectFilename)
            + ".pgp";
    encryptionService.encrypt(testSubjectFilename, targetFilename, keys.values(), null, null, null);

    PasswordDeterminedForKey keyAndPassword = buildPasswordDeterminedForKey(targetFilename, "Alice.asc",
            "pass");

    encryptionService.decrypt(targetFilename, targetFilename + ".test", keyAndPassword, null, null);
    String result = TextFile.read(targetFilename + ".test");
    assertEquals(testSubjectContents, result);
}

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

@Override
public void execute() throws IOException {
    final PrintWriter out = outputFilename == null ? new PrintWriter(System.out)
            : new PrintWriter(outputFilename);
    try {//  ww w. j a  v a 2  s .  c om
        int index = 0;
        out.print("trackName\t");
        for (String attributeName : attributeNames) {
            if (!"ignore".equals(attributeName)) {
                out.print(attributeName);

                if (index != attributeNames.length) {
                    out.print('\t');
                }
            }
            index++;
        }
        out.println();
        for (String file : filenames) {
            final String file1 = file;
            String name = FilenameUtils.getName(file1);
            String filename = FilenameUtils.getBaseName(name);
            String[] tokens = filename.split(delimiter);
            out.printf("%s\t", adjustSuffix(name));
            for (int i = 0; i < attributeNames.length; i++) {
                if (!"ignore".equals(attributeNames[i])) {
                    if (tokens.length <= i) {
                        continue;
                    }
                    out.print(tokens[i]);
                    if (i != attributeNames.length) {
                        out.print('\t');
                    }
                }

            }
            out.println();
        }
        out.flush();
    } finally {
        out.close();

    }
}

From source file:controller.servlet.ImportAmenities.java

/**
 * Handles the HTTP <code>POST</code> method.
 *
 * @param request servlet request/*from w  w  w .j av a 2s  .  com*/
 * @param response servlet response
 * @throws ServletException if a servlet-specific error occurs
 * @throws IOException if an I/O error occurs
 */
@Override
protected void doPost(HttpServletRequest request, HttpServletResponse response)
        throws ServletException, IOException {

    // Obtencin de la regin
    String regionName = request.getParameter("regionname");

    boolean isXML = false;
    // Procesado del fichero para subirlo al servidor.
    for (Part part : request.getParts()) {
        if (part.getName().equals("file")) {
            try (InputStream is = request.getPart(part.getName()).getInputStream()) {
                int i = is.available();
                byte[] b = new byte[i];

                if (b.length == 0) {
                    break;
                }

                is.read(b);
                String fileName = obtenerNombreFichero(part);
                String extension = FilenameUtils.getExtension(fileName);
                String path = this.getServletContext().getRealPath("");
                String ruta = path + File.separator + Path.POIS_FOLDER + File.separator + fileName;
                File directory = new File(path + File.separator + Path.POIS_FOLDER);
                fileName = FilenameUtils.getBaseName(fileName);

                if (!directory.exists()) {
                    directory.mkdirs();
                }

                try (FileOutputStream os = new FileOutputStream(ruta)) {
                    os.write(b);
                }

                // Comprobacin de que sea un fichero xml.
                if (extension.equals("xml")) {
                    isXML = true;
                } else {
                    break;
                }

                if (isXML) {
                    // Crear entrada en la tabla de ficheros de PDIs.
                    UploadedPoiFileDaoImpl uPFDao = new UploadedPoiFileDaoImpl();
                    UploadedFile uFile = new UploadedFile();
                    uFile.setName(fileName);
                    uFile.setProcessedDate(new java.sql.Date(new java.util.Date().getTime()));
                    uPFDao.createFile(uFile);

                    // Almacenado de los datos en la Base de Datos.
                    NotifyingThread nT = new AmenityProcessing(ruta, regionName);
                    nT.addListener(this);
                    nT.setName(ThreadName.AMENITIES_THREAD_NAME);
                    nT.start();
                }
            }
        }
    }

    HttpSession session = request.getSession(true);
    session.setAttribute("isXML", isXML);

    if (!isXML) {
        session.setAttribute("error", true);
        String page = "/pages/amenitiesmanage.jsp";
        RequestDispatcher requestDispatcher = getServletContext().getRequestDispatcher(page);
        requestDispatcher.forward(request, response);
    } else {
        session.setAttribute("error", false);
        processRequest(request, response);
    }

}

From source file:MSUmpire.LCMSPeakStructure.LCMSPeakDIAMS2.java

public LCMSPeakDIAMS2(String Filename, DIAPack parentDIA, InstrumentParameter parameter, XYData WindowMZ,
        XYData LastWindowMZ, SpectrumParserBase spectrumparser, int NoCPUs) {
    this.DIA_MZ_Range = WindowMZ;
    this.Last_MZ_Range = LastWindowMZ;
    this.WindowID = (int) Math.floor(WindowMZ.getX()) + "_" + (int) Math.floor(WindowMZ.getY());
    this.SpectrumParser = spectrumparser;
    this.ScanCollectionName = FilenameUtils.getFullPath(Filename) + "/" + FilenameUtils.getBaseName(Filename)
            + "_" + (int) Math.floor(WindowMZ.getX()) + "_" + (int) Math.floor(WindowMZ.getY());
    this.ParentmzXMLName = FilenameUtils.getFullPath(Filename) + "/" + FilenameUtils.getBaseName(Filename);
    this.parentDIA = parentDIA;
    this.parameter = parameter;
    this.MaxNoPeakCluster = parameter.MaxMS2NoPeakCluster;
    this.MinNoPeakCluster = parameter.MinMS2NoPeakCluster;
    this.StartCharge = parameter.MS2StartCharge;
    this.EndCharge = parameter.MS2EndCharge;
    this.MiniIntensity = parameter.MinMSMSIntensity;
    this.SNR = parameter.MS2SNThreshold;
    this.NoCPUs = NoCPUs;
}

From source file:ee.ria.DigiDoc.activity.OpenExternalFileActivity.java

private ContainerFacade createContainer(List<Uri> uris) {
    if (!uris.isEmpty()) {
        List<Uri> containers = searchForContainers(uris);
        if (!containers.isEmpty()) {
            Uri containerUri = containers.get(0);
            uris.remove(containerUri);/*from w w  w . j a  v  a2  s.  c  o  m*/
            try {
                return ContainerBuilder.aContainer(this).fromExternalContainer(containerUri).withDataFiles(uris)
                        .build();
            } catch (ContainerBuilder.ExternalContainerSaveException e) {
                Timber.e(e, "Failed to create container");
                return null;
            }
        }

        String fileName = FileUtils.resolveFileName(uris.get(0), getContentResolver());
        return ContainerBuilder.aContainer(this).withDataFiles(uris)
                .withContainerName(FilenameUtils.getBaseName(fileName) + "." + getContainerFormat()).build();
    }
    return null;
}