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

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

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Introduction

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

Prototype

public static String getName(String filename)

Source Link

Document

Gets the name minus the path from a full filename.

Usage

From source file:massbank.svn.SVNOperation.java

public boolean addEntry(String[] srcFilePaths, String destSubDirName) {
    String destPath = workCopyPath + File.separator;
    if (!destSubDirName.equals("")) {
        destPath += destSubDirName + File.separator;
    }/* ww w  .  j  a v  a  2s.  co  m*/
    try {
        for (String path : srcFilePaths) {
            FileUtils.copyFileToDirectory(new File(path), new File(destPath));
            String name = FilenameUtils.getName(path);
            this.svnClient.add(destPath + name);
        }
    } catch (Exception e) {
        e.printStackTrace();
        return false;
    }
    return true;
}

From source file:ca.on.oicr.pde.workflows.GATKGenotypeGVCFsWorkflow.java

@Override
public Map<String, SqwFile> setupFiles() {

    List<String> inputFilesList = Arrays.asList(StringUtils.split(getProperty("input_files"), ","));
    Set<String> inputFilesSet = new HashSet<>(inputFilesList);

    if (inputFilesList.size() != inputFilesSet.size()) {
        throw new RuntimeException("Duplicate files detected in input_files");
    }/*ww w .j  ava  2  s  .  c o m*/

    if ((inputFilesSet.size() % 2) != 0) {
        throw new RuntimeException("Each GVCF should have a corresponding index");
    }

    Map<String, String> gvcfs = new HashMap<>();
    Map<String, String> gvcfIndexes = new HashMap<>();
    for (String f : inputFilesSet) {
        if (f == null || f.isEmpty()) {
        } else if (f.endsWith("g.vcf.gz")) {
            gvcfs.put(StringUtils.removeEnd(f, "g.vcf.gz"), f);
        } else if (f.endsWith("g.vcf.gz.tbi")) {
            gvcfIndexes.put(StringUtils.removeEnd(f, "g.vcf.gz.tbi"), f);
        } else {
            throw new RuntimeException("Unsupported input file: [" + f + "]");
        }
    }

    int id = 0;
    for (Entry<String, String> e : gvcfs.entrySet()) {
        String key = e.getKey();
        String gvcfFilePath = e.getValue();

        String gvcfIndexFilePath = gvcfIndexes.get(key);
        if (gvcfIndexFilePath == null) {
            throw new RuntimeException("Missing index for " + FilenameUtils.getName(gvcfFilePath));
        }

        SqwFile gvcf = this.createFile("file_in_" + id++);
        gvcf.setSourcePath(gvcfFilePath);
        gvcf.setType("application/g-vcf-gz");
        gvcf.setIsInput(true);

        SqwFile gvcfIndex = this.createFile("file_in_" + id++);
        gvcfIndex.setSourcePath(gvcfIndexFilePath);
        gvcfIndex.setType("application/tbi");
        gvcfIndex.setIsInput(true);

        //FIXME: this seems to work for now, it would be better to be able to set the provisionedPath as
        //bai.getProvisionedPath != bai.getOutputPath ...
        //at least with seqware 1.1.0, setting output path changes where the output file will be stored,
        //but the commonly used get provisioned path will return the incorrect path to the file
        gvcfIndex.setOutputPath(FilenameUtils.getPath(gvcf.getProvisionedPath()));

        inputFiles.add(gvcf.getProvisionedPath());
    }

    return this.getFiles();
}

From source file:com.atlassian.theplugin.util.CodeNavigationUtil.java

/**
 * Note: must be run from event dispatch thread or inside read-action only!
 *
 * @param project  project//from   w  w w .j  a va  2 s. c om
 * @param filePath filePath
 * @return collection of matching PsiFiles
 */
@Nullable
public static Collection<PsiFile> findPsiFiles(final Project project, final String filePath) {
    // find files (do not care about path - IDEA7 compatibility)
    final PsiFile[] psifiles = IdeaVersionFacade.getInstance().getFiles(FilenameUtils.getName(filePath),
            project);

    return CodeNavigationUtil.getMatchingFiles(filePath, psifiles);
}

From source file:io.github.retz.cli.CommandGetFile.java

@Override
public int handle(ClientCLIConfig fileConfig, boolean verbose) throws Throwable {
    LOG.debug("Configuration: {}", fileConfig.toString());

    try (Client webClient = Client.newBuilder(fileConfig.getUri())
            .setAuthenticator(fileConfig.getAuthenticator()).checkCert(!fileConfig.insecure())
            .setVerboseLog(verbose).build()) {

        if (verbose) {
            LOG.info("Getting file {} (offset={}, length={}) of a job(id={})", filename, offset, length, id);
        }/*from  ww  w  .  j  a v a2 s .  c o m*/

        if (isBinary) {
            if ("-".equals(resultDir)) {
                LOG.error("--binary must be with -R option, to download the file.");
                return -1;
            } else if (poll) {
                LOG.error("--binary cannot work with --poll");
                return -1;
            }

            String fullpath = FilenameUtils.concat(resultDir, FilenameUtils.getName(filename));
            LOG.info("Binary mode: ignoring offset and length but downloading while file to '{}/{}'.",
                    resultDir, filename);
            try (FileOutputStream out = new FileOutputStream(fullpath)) {
                ClientHelper.getWholeBinaryFile(webClient, id, filename, out);
                return 0;
            }
        }

        Date start = Calendar.getInstance().getTime();
        Callable<Boolean> timedout;
        if (timeout > 0) {
            timedout = () -> {
                Date now = Calendar.getInstance().getTime();
                long diff = now.getTime() - start.getTime();
                return diff / 60 > timeout * 60;
            };
        } else {
            timedout = () -> false;
        }

        OutputStream out = this.tentativeOutputStream(webClient, resultDir, filename);
        if (length < 0) {
            try {
                ClientHelper.getWholeFileWithTerminator(webClient, id, filename, poll, out, timedout);
            } catch (TimeoutException e) {
                webClient.kill(id);
                LOG.error("Job(id={}) has been killed due to timeout after {} minute(s)", id, timeout);
                return -1;
            }
            return 0;
        }

        Response res = webClient.getFile(id, filename, offset, length);

        if (res instanceof GetFileResponse) {
            GetFileResponse getFileResponse = (GetFileResponse) res;

            if (getFileResponse.job().isPresent()) {
                Job job = getFileResponse.job().get();

                if (getFileResponse.file().isPresent()) {
                    if (verbose) {
                        LOG.info("offset={}", getFileResponse.file().get().offset());
                    }
                    out.write(getFileResponse.file().get().data().getBytes(UTF_8));

                } else if (verbose) {
                    LOG.info("Job: {}", job);
                }

                if (out != null && "-".equals(resultDir)) {
                    out.close();
                }
                return 0;

            } else {
                LOG.error("No such job: id={}", id);
            }
        } else {
            ErrorResponse errorResponse = (ErrorResponse) res;
            LOG.error("Error: {}", errorResponse.status());
        }
    }
    return -1;
}

From source file:dynamicrefactoring.domain.TestExport.java

/**
 * Comprueba que el proceso de exportacin de la refactorizacin dinmica
 * Rename Class a un directorio temporal "./temp" se ha realizado
 * correctamente.//from   ww w  . j a v a  2  s .c  om
 * 
 * @throws XMLRefactoringReaderException
 *             XMLRefactoringReaderException.
 * @throws IOException
 *             IOException.
 */
@Test
public void testExportRefactoring() throws XMLRefactoringReaderException, IOException {

    // Primero exportamos la refactorizacin Rename Class a un directorio
    // temporal que luego eliminaremos
    ExportImportUtilities.exportRefactoring(TEMP_DIR, RENAME_CLASS_XML_FILE, false);

    JDOMXMLRefactoringReaderImp reader = new JDOMXMLRefactoringReaderImp();

    for (String element : RefactoringMechanismInstance.getMechanismListClassNames(
            reader.getDynamicRefactoringDefinition(new File(RENAME_CLASS_XML_FILE)).getAllMechanisms())) {

        String name = FilenameUtils.getName(PluginStringUtils.splitGetLast(element, "."));
        String namefolder = FilenameUtils.getName(new File(RENAME_CLASS_XML_FILE).getParent());

        File resultFile = new File(
                TEMP_DIR + File.separatorChar + namefolder + File.separatorChar + name + ".class");
        assertEquals(true, resultFile.exists());
    }

}

From source file:edu.wisc.doit.tcrypt.controller.EncryptController.java

@RequestMapping(value = "/encryptFile", method = RequestMethod.POST)
public ModelAndView encryptFile(@RequestParam("fileToEncrypt") MultipartFile file,
        @RequestParam("selectedServiceName") String serviceName, HttpServletResponse response)
        throws Exception {
    if (file.isEmpty()) {
        ModelAndView modelAndView = encryptTextInit();
        modelAndView.addObject("selectedServiceName", serviceName);
        return modelAndView;
    }//w  ww  . j  av  a  2 s . c  o m

    final FileEncrypter fileEncrypter = this.getFileEncrypter(serviceName);
    final String filename = FilenameUtils.getName(file.getOriginalFilename());

    response.setHeader("Content-Type", "application/x-tar");
    response.setHeader("Content-Disposition", "attachment; filename=\"" + filename + ".tar" + "\"");

    final long size = file.getSize();
    try (final InputStream inputStream = file.getInputStream();
            final ServletOutputStream outputStream = response.getOutputStream()) {

        fileEncrypter.encrypt(filename, (int) size, inputStream, outputStream);
    }

    return null;
}

From source file:ca.on.oicr.pde.workflows.GATKHaplotypeCallerWorkflow.java

@Override
public Map<String, SqwFile> setupFiles() {

    List<String> inputFilesList = Arrays.asList(StringUtils.split(getProperty("input_files"), ","));
    Set<String> inputFilesSet = new HashSet<>(inputFilesList);

    if (inputFilesList.size() != inputFilesSet.size()) {
        throw new RuntimeException("Duplicate files detected in input_files");
    }// w w  w .j  a  v a  2  s .co m

    if ((inputFilesSet.size() % 2) != 0) {
        throw new RuntimeException("Each bam should have a corresponding index");
    }

    Map<String, String> bams = new HashMap<>();
    Map<String, String> bais = new HashMap<>();
    for (String f : inputFilesSet) {
        String fileExtension = FilenameUtils.getExtension(f);
        String fileKey = FilenameUtils.removeExtension(f);
        if (null != fileExtension) {
            switch (fileExtension) {
            case "bam":
                bams.put(fileKey, f);
                break;
            case "bai":
                if (fileKey.endsWith(".bam")) {
                    fileKey = FilenameUtils.removeExtension(fileKey);
                }
                bais.put(fileKey, f);
                break;
            default:
                throw new RuntimeException("Unsupported input file type");
            }
        }
    }

    int id = 0;
    for (Entry<String, String> e : bams.entrySet()) {
        String key = e.getKey();
        String bamFilePath = e.getValue();

        String baiFilePath = bais.get(key);
        if (baiFilePath == null) {
            throw new RuntimeException("Missing index for " + FilenameUtils.getName(bamFilePath));
        }

        SqwFile bam = this.createFile("file_in_" + id++);
        bam.setSourcePath(bamFilePath);
        bam.setType("application/bam");
        bam.setIsInput(true);

        SqwFile bai = this.createFile("file_in_" + id++);
        bai.setSourcePath(baiFilePath);
        bai.setType("application/bam-index");
        bai.setIsInput(true);

        //FIXME: this seems to work for now, it would be better to be able to set the provisionedPath as
        //bai.getProvisionedPath != bai.getOutputPath ...
        //at least with seqware 1.1.0, setting output path changes where the output file will be stored,
        //but the commonly used get provisioned path will return the incorrect path to the file
        bai.setOutputPath(FilenameUtils.getPath(bam.getProvisionedPath()));

        inputBamFiles.add(bam.getProvisionedPath());
    }

    return this.getFiles();
}

From source file:ddf.catalog.source.solr.ConfigurationFileProxy.java

/**
 * Writes the solr configuration files out of the bundle onto the disk. This method requires
 * that the dataDirectoryPath has been set. If the code is run in an OSGi container, it will
 * automatically have a default dataDirectory location set and will not require setting
 * dataDirectory ahead of time.//from w w  w.  j  a v a 2s. com
 */
public void writeBundleFilesTo(File configDir) {
    if (bundleContext != null && configDir != null) {

        boolean directoriesMade = configDir.mkdirs();

        LOGGER.info("Solr Config directories made?  " + directoriesMade);

        @SuppressWarnings("rawtypes")
        Enumeration entries = bundleContext.getBundle().findEntries(SOLR_CONFIG_LOCATION_IN_BUNDLE, "*.*",
                false);

        while (entries.hasMoreElements()) {
            URL resourceURL = (URL) (entries.nextElement());
            LOGGER.debug("Found " + resourceURL);

            InputStream inputStream = null;
            try {
                inputStream = resourceURL.openStream();

                String fileName = FilenameUtils.getName(resourceURL.getPath());

                File currentFile = new File(configDir, fileName);

                if (!currentFile.exists()) {
                    FileOutputStream outputStream = null;

                    try {
                        outputStream = new FileOutputStream(currentFile);

                        long byteCount = IOUtils.copyLarge(inputStream, outputStream);

                        LOGGER.debug("Wrote out " + byteCount + " bytes.");

                    } finally {
                        IOUtils.closeQuietly(outputStream);
                    }
                }

            } catch (IOException e) {
                LOGGER.warn(e);
            } finally {
                IOUtils.closeQuietly(inputStream);
            }

        }
    }
}

From source file:de.mpg.imeji.logic.item.ItemController.java

@Override
public List<Item> updateBatch(List<Item> l, User user) throws ImejiException {
    if (l != null && !l.isEmpty()) {
        for (final Item item : l) {
            prepareUpdate(item, user);/*from   www.j  a va2 s  .c o  m*/
            item.setFilename(FilenameUtils.getName(item.getFilename()));
        }
        cleanItem(l);
        createMissingStatement(l);
        validateMetadata(l, Method.UPDATE);
        WRITER.update(J2JHelper.cast2ObjectList(l), user, true);
    }
    return l;
}

From source file:com.epam.ngb.cli.TestHttpServer.java

/**
 * Enables file registration on the server
 *//*from   w w w  .j  a v  a 2s  .co  m*/
public void addFileRegistration(Long refId, String path, String index, String name, Long fileId, Long fileBioId,
        BiologicalDataItemFormat format) {
    onRequest().havingMethodEqualTo(HTTP_POST)
            .havingPathEqualTo(String.format(REGISTRATION_URL, format.name().toLowerCase()))
            .havingBodyEqualTo(TestDataProvider.getRegistrationJson(refId, path, name, index, null)).respond()
            .withBody(TestDataProvider.getFilePayloadJson(fileId, fileBioId, format, path,
                    name == null ? FilenameUtils.getName(path) : name))
            .withStatus(HTTP_STATUS_OK);
}