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: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);/*  w w w .j  a v a2s . c o 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:com.googlecode.fascinator.portal.services.cache.JythonCacheEntryFactory.java

/**
 * Creates a jython object instance for the script cache.
 * /*from   ww  w.j a v a2 s  .  c o m*/
 * @param key the path to the jython script
 * @return an instantiated jython object
 * @throws Exception if the jython object failed to be instantiated
 */
@Override
public Object createEntry(Object key) throws Exception {
    // log.debug("createEntry({})", key);
    String path = key.toString();
    int qmarkPos = path.lastIndexOf("?");
    if (qmarkPos != -1) {
        path = path.substring(0, qmarkPos);
    }
    int slashPos = path.indexOf("/");
    String portalId = path.substring(0, slashPos);
    PyObject scriptObject = null;
    InputStream in = velocityService.getResource(path);
    if (in == null) {
        log.debug("Failed to load script: '{}'", path);
    } else {
        // add current and default portal directories to python sys.path
        addSysPaths(portalId, Py.getSystemState());
        // setup the python interpreter
        PythonInterpreter python = PythonInterpreter.threadLocalStateInterpreter(null);
        // expose services for backward compatibility - deprecated
        python.set("Services", scriptingServices);
        // python.setLocals(scriptObject);
        JythonLogger jythonLogger = new JythonLogger(path);
        python.setOut(jythonLogger);
        python.setErr(jythonLogger);
        python.execfile(in, path);
        String scriptClassName = StringUtils.capitalize(FilenameUtils.getBaseName(path)) + "Data";
        PyObject scriptClass = python.get(scriptClassName);
        if (scriptClass != null) {
            scriptObject = scriptClass.__call__();
        } else {
            log.debug("Failed to find class '{}'", scriptClassName);
        }
        python.cleanup();
    }
    return scriptObject;
}

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

public void execute() throws IOException {
    final Slice slices[] = new Slice[numParts];
    File file = new File(input);
    if (!(file.isFile() && file.exists() && file.canRead())) {
        System.err.println("Input file cannot be read: " + input);
        System.exit(1);/*from  w w w .j a  v a 2s  .  c  om*/
    }
    int i = 0;
    for (final Slice slice : slices) {

        slices[i++] = new Slice();
    }
    final long fileLength = file.length();
    final long sliceLength = fileLength / numParts;
    long currentOffset = 0;

    for (final Slice slice : slices) {

        slice.startOffset = currentOffset;
        slice.endOffset = currentOffset + sliceLength;
        currentOffset = slice.endOffset;
    }

    final ObjectOpenHashSet<String> allOutputs = new ObjectOpenHashSet<String>();
    final ObjectOpenHashSet<String> allFastq = new ObjectOpenHashSet<String>();

    final DoInParallel loop = new DoInParallel(numParts) {
        IsDone done = new IsDone();

        @Override
        public void action(final DoInParallel forDataAccess, final String inputBasename, final int loopIndex) {
            try {

                CompactToFastaMode ctfm = new CompactToFastaMode();
                ctfm.setInputFilename(input);
                ctfm.setOutputFormat(CompactToFastaMode.OutputFormat.FASTQ);
                ctfm.setStartPosition(slices[loopIndex].startOffset);
                ctfm.setEndPosition(slices[loopIndex].endOffset);

                String s = FilenameUtils.getBaseName(FilenameUtils.removeExtension(input)) + "-"
                        + Integer.toString(loopIndex);
                String fastqFilename = s + "-input.fq";
                allFastq.add(fastqFilename);
                File tmp1 = new File(s + "-tmp");
                tmp1.deleteOnExit();
                File output = new File(s + "-out");
                output.deleteOnExit();
                ctfm.setOutputFilename(fastqFilename);
                LOG.info(String.format("Extracting FASTQ for slice [%d-%d] loopIndex=%d %n",
                        slices[loopIndex].startOffset, slices[loopIndex].endOffset, loopIndex));
                ctfm.execute();
                if (loopIndex > 0) {
                    while (!done.isDone()) {
                        // wait a bit to give the first thread the time to load the database and establish shared memory pool
                        //   System.out.println("sleep 5 thread "+loopIndex);
                        sleep(5);
                    }
                    System.out.println("Thread " + loopIndex + " can now start.");
                }
                final Map<String, String> replacements = new HashMap<String, String>();

                final String outputFilename = output.getName();

                replacements.put("%read.fastq%", fastqFilename);
                replacements.put("%tmp1%", tmp1.getName());
                replacements.put("%output%", outputFilename);
                final String transformedCommand = transform(processPartCommand, replacements);
                final DefaultExecutor executor = new DefaultExecutor();
                OutputStream logStream = null;
                try {
                    logStream = new LoggingOutputStream(getClass(), Level.INFO, "");
                    executor.setStreamHandler(
                            new PumpStreamHandler(new StreamSignal(done, "scanning", logStream)));

                    final CommandLine parse = CommandLine.parse(transformedCommand, replacements);
                    LOG.info("About to execute: " + parse);
                    final int exitValue = executor.execute(parse);
                    LOG.info("Exit value = " + exitValue);
                    if (new File(outputFilename + ".header").exists()) {
                        // found output alignment:
                        System.out.println("found output file: " + outputFilename);
                        allOutputs.add(outputFilename + ".header");
                    } else {
                        System.out.println("Warning: did not find output alignment: " + outputFilename);
                    }
                } finally {
                    IOUtils.closeQuietly(logStream);
                    // remove the fastq file
                    new File(fastqFilename).delete();
                }

            } catch (IOException e) {
                LOG.error("Error processing index " + loopIndex + ", " + inputBasename, e);
            }
        }
    };
    String[] parts = new String[numParts];

    for (int j = 0; j < numParts; j++) {
        parts[j] = Integer.toString(j);
    }
    try {
        loop.execute(true, parts);
    } catch (Exception e) {
        System.err.println("An error occurred executing a parallel command: ");
        e.printStackTrace();
    }

    System.out.printf("Preparing to concatenate %d outputs..%n", allOutputs.size());
    final ConcatenateAlignmentMode concat = new ConcatenateAlignmentMode();
    concat.setInputFileNames(allOutputs.toArray(new String[allOutputs.size()]));
    concat.setOutputFilename(output);
    concat.setAdjustQueryIndices(false);
    concat.setAdjustSampleIndices(false);
    concat.execute();

}

From source file:gov.nih.nci.caarray.plugins.agilent.AgilentXmlDesignFileHandler.java

/**
 * {@inheritDoc}//  w  ww  . jav  a  2  s.c o m
 */
@Override
public void load(ArrayDesign arrayDesign) throws PlatformFileReadException {
    try {
        arrayDesign.setName(FilenameUtils.getBaseName(this.designFile.getName()));
        arrayDesign.setLsidForEntity(
                String.format("%s:%s:%s", LSID_AUTHORITY, LSID_NAMESPACE, arrayDesign.getName()));
        getArrayDao().save(arrayDesign);
    } catch (final Exception e) {
        throw new PlatformFileReadException(this.fileOnDisk,
                "Unexpected error while loading " + this.designFile.getName(), e);
    }
}

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

/**
 * Remove the files created by imagemagick.
 * // w  ww  .  j  a  va 2  s  . co m
 * @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:dialog.DialogFunctionUser.java

private void actionEditUserNoController() {
    if (!isValidData()) {
        return;// ww w. j av a  2 s .  c  om
    }
    tfUsername.setEditable(false);
    String username = tfUsername.getText();
    String fullname = tfFullname.getText();
    String password = mUser.getPassword();
    if (tfPassword.getPassword().length == 0) {
        password = new String(tfPassword.getPassword());
        password = LibraryString.md5(password);
    }
    int role = cbRole.getSelectedIndex();
    User objUser;
    if (mAvatar != null) {
        objUser = new User(mUser.getIdUser(), username, password, fullname, role,
                new Date(System.currentTimeMillis()), mAvatar.getPath());
        if ((new ModelUser()).editItem(objUser)) {
            String fileName = FilenameUtils.getBaseName(mAvatar.getName()) + "-" + System.nanoTime() + "."
                    + FilenameUtils.getExtension(mAvatar.getName());
            Path source = Paths.get(mAvatar.toURI());
            Path destination = Paths.get("files/" + fileName);
            Path pathOldAvatar = Paths.get(mUser.getAvatar());
            try {
                Files.copy(source, destination, StandardCopyOption.REPLACE_EXISTING);
                Files.deleteIfExists(pathOldAvatar);
            } catch (IOException ex) {
                Logger.getLogger(DialogFunctionRoom.class.getName()).log(Level.SEVERE, null, ex);
            }
            ImageIcon icon = new ImageIcon(getClass().getResource("/images/ic_success.png"));
            JOptionPane.showMessageDialog(this.getParent(), "Sa thnh cng", "Success",
                    JOptionPane.INFORMATION_MESSAGE, icon);
        } else {
            JOptionPane.showMessageDialog(this.getParent(), "Sa tht bi", "Fail",
                    JOptionPane.ERROR_MESSAGE);
        }
    } else {
        objUser = new User(mUser.getIdUser(), username, password, fullname, role,
                new Date(System.currentTimeMillis()), mUser.getAvatar());
        if (mControllerUser.editItem(objUser, mRow)) {
            ImageIcon icon = new ImageIcon(getClass().getResource("/images/ic_success.png"));
            JOptionPane.showMessageDialog(this.getParent(), "Sa thnh cng", "Success",
                    JOptionPane.INFORMATION_MESSAGE, icon);
        } else {
            JOptionPane.showMessageDialog(this.getParent(), "Sa tht bi", "Fail",
                    JOptionPane.ERROR_MESSAGE);
        }
    }
    mUser = objUser;
    this.dispose();
}

From source file:com.consol.citrus.admin.service.TestCaseService.java

/**
 * Finds all tests case declarations in given source files. Method is loading tests by their annotation presence of @CitrusTest or @CitrusXmlTest.
 * @param project/*  w ww. j  a v  a 2 s  . c  om*/
 * @param sourceFiles
 */
private List<Test> findTests(Project project, List<File> sourceFiles) {
    List<Test> tests = new ArrayList<>();
    for (File sourceFile : sourceFiles) {
        String className = FilenameUtils.getBaseName(sourceFile.getName());
        String testPackageName = sourceFile.getPath()
                .substring(project.getJavaDirectory().length(),
                        sourceFile.getPath().length() - sourceFile.getName().length())
                .replace(File.separatorChar, '.');

        if (testPackageName.endsWith(".")) {
            testPackageName = testPackageName.substring(0, testPackageName.length() - 1);
        }

        tests.addAll(findTests(sourceFile, testPackageName, className));
    }

    return tests;
}

From source file:it.geosolutions.geobatch.actions.ds2ds.Ds2dsAction.java

/**
* Imports data from the source DataStore to the output one
* transforming the data as configured.//from  w  w  w  .  j  ava  2  s.  co  m
 */
@Override
public Queue<EventObject> execute(Queue<EventObject> events) throws ActionException {

    // return object
    final Queue<EventObject> outputEvents = new LinkedList<EventObject>();

    while (events.size() > 0) {
        final EventObject ev;
        try {
            if ((ev = events.remove()) != null) {
                listenerForwarder.started();

                updateTask("Working on incoming event: " + ev.getSource());

                Queue<FileSystemEvent> acceptableFiles = acceptableFiles(unpackCompressedFiles(ev));
                if (ev instanceof FileSystemEvent
                        && ((FileSystemEvent) ev).getEventType().equals(FileSystemEventType.POLLING_EVENT)) {
                    String fileType = getFileType((FileSystemEvent) ev);
                    EventObject output = null;
                    if ("feature".equalsIgnoreCase(fileType)) {
                        configuration.getOutputFeature().setTypeName(
                                FilenameUtils.getBaseName(((FileSystemEvent) ev).getSource().getName()));
                        output = buildOutputEvent();
                        updateImportProgress(1, 1, "Completed");
                    } else {
                        output = importFile((FileSystemEvent) ev);
                    }

                    outputEvents.add(output);
                } else {
                    if (acceptableFiles.size() == 0) {
                        failAction("No file to process");
                    } else {
                        List<ActionException> exceptions = new ArrayList<ActionException>();
                        for (FileSystemEvent fileEvent : acceptableFiles) {
                            try {
                                String fileType = getFileType(fileEvent);
                                EventObject output = null;
                                if ("feature".equalsIgnoreCase(fileType)) {
                                    configuration.getOutputFeature().setTypeName(FilenameUtils
                                            .getBaseName(((FileSystemEvent) ev).getSource().getName()));
                                    output = buildOutputEvent();
                                    updateImportProgress(1, 1, "Completed");
                                } else {
                                    output = importFile(fileEvent);
                                }
                                if (output != null) {
                                    // add the event to the return
                                    outputEvents.add(output);
                                } else {
                                    if (LOGGER.isWarnEnabled()) {
                                        LOGGER.warn("No output produced");
                                    }
                                }
                            } catch (ActionException e) {
                                exceptions.add(e);
                            }

                        }
                        if (acceptableFiles.size() == exceptions.size()) {
                            throw new ActionException(this, exceptions.get(0).getMessage());
                        } else if (exceptions.size() > 0) {
                            if (LOGGER.isWarnEnabled()) {
                                for (ActionException ex : exceptions) {
                                    LOGGER.warn("Error in action: " + ex.getMessage());
                                }
                            }
                        }
                    }
                }

            } else {
                if (LOGGER.isErrorEnabled()) {
                    LOGGER.error("Encountered a NULL event: SKIPPING...");
                }
                continue;
            }
        } catch (ActionException ioe) {
            failAction("Unable to produce the output, " + ioe.getLocalizedMessage(), ioe);
        } catch (Exception ioe) {
            failAction("Unable to produce the output: " + ioe.getLocalizedMessage(), ioe);
        }
    }
    return outputEvents;
}

From source file:com.vectorcast.plugins.vectorcastexecution.job.BaseJob.java

/**
 * Constructor//from   w  w w .ja  v  a 2  s.  co  m
 * @param request request object
 * @param response response object
 * @param useSavedData use saved data true/false
 * @throws ServletException exception
 * @throws IOException exception
 */
protected BaseJob(final StaplerRequest request, final StaplerResponse response, boolean useSavedData)
        throws ServletException, IOException {
    instance = Jenkins.getInstance();
    this.request = request;
    this.response = response;
    JSONObject json = request.getSubmittedForm();

    manageProjectName = json.optString("manageProjectName");
    if (!manageProjectName.isEmpty()) {
        // Force unix style path to avoid problems later
        manageProjectName = manageProjectName.replace('\\', '/');
    }
    baseName = FilenameUtils.getBaseName(manageProjectName);

    this.useSavedData = useSavedData;
    if (useSavedData) {
        // Data will be set later
    } else {
        this.usingSCM = false;

        environmentSetupWin = json.optString("environmentSetupWin");
        executePreambleWin = json.optString("executePreambleWin");
        environmentTeardownWin = json.optString("environmentTeardownWin");

        environmentSetupUnix = json.optString("environmentSetupUnix");
        executePreambleUnix = json.optString("executePreambleUnix");
        environmentTeardownUnix = json.optString("environmentTeardownUnix");

        optionUseReporting = json.optBoolean("optionUseReporting", true);
        optionErrorLevel = json.optString("optionErrorLevel", "Unstable");
        optionHtmlBuildDesc = json.optString("optionHtmlBuildDesc", "HTML");
        optionExecutionReport = json.optBoolean("optionExecutionReport", true);
        optionClean = json.optBoolean("optionClean", false);

        waitTime = json.optLong("waitTime", 5);
        waitLoops = json.optLong("waitLoops", 2);

        jobName = json.optString("jobName", null);
        nodeLabel = json.optString("nodeLabel", "");
    }
}

From source file:com.frostwire.transfers.YouTubeDownload.java

private static File buildTempFile(FileSystem fs, String filename, String ext) {
    String name = FilenameUtils.getBaseName(filename);
    return buildFile(fs, Platforms.temp(), name + "." + ext);
}