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:com.uwsoft.editor.data.manager.TextureManager.java

public void loadCurrentProjectSpineAnimations(String path, String curResolution) {
    spineAnimAtlases.clear();/*from  w w w . j  a v  a 2s.c  o m*/
    FileHandle sourceDir = new FileHandle(path + "orig/spine-animations");
    for (FileHandle entry : sourceDir.list()) {
        if (entry.file().isDirectory()) {
            String animName = FilenameUtils.removeExtension(entry.file().getName());
            TextureAtlas atlas = new TextureAtlas(Gdx.files.internal(path + curResolution + "/spine-animations/"
                    + File.separator + animName + File.separator + animName + ".atlas"));
            FileHandle animJsonFile = Gdx.files
                    .internal(entry.file().getAbsolutePath() + File.separator + animName + ".json");
            SpineAnimData data = new SpineAnimData();
            data.atlas = atlas;
            data.jsonFile = animJsonFile;
            data.animName = animName;
            spineAnimAtlases.put(animName, data);
        }
    }

}

From source file:com.liferay.sync.engine.SyncSystemTest.java

@Test
public void run() throws Exception {
    SyncEngine.start();//w w w  .  j  a  v  a2  s  .  c o  m

    _rootFilePathName = FileUtil.getFilePathName(System.getProperty("user.home"), "liferay-sync-test");

    _syncAccount = SyncAccountService.addSyncAccount(FileUtil.getFilePathName(_rootFilePathName, "test"),
            "test@liferay.com", Integer.MAX_VALUE, "test", "test", 5, null, false, "http://localhost:8080");

    SyncAccountService.update(_syncAccount);

    long guestGroupId = SyncSystemTestUtil.getGuestGroupId(_syncAccount.getSyncAccountId());

    _syncSiteIds.put("Guest", guestGroupId);

    BufferedReader bufferedReader = Files.newBufferedReader(_testFilePath, Charset.defaultCharset());

    ObjectMapper objectMapper = new ObjectMapper();

    JsonNode rootJsonNode = objectMapper.readTree(bufferedReader);

    executeSteps(_testFilePath, rootJsonNode);

    Path testFileNameFilePath = _testFilePath.getFileName();

    String testFileName = testFileNameFilePath.toString();

    _logger.info("Test {} passed.", FilenameUtils.removeExtension(testFileName));
}

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

private void removeDAFileFromDocument(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 {//  w ww .  j a v a 2  s .  c o  m
        logger.debug("Remove from document " + file);
        boolean removed = doc.removeDAFile(file);
        if (!removed)
            logger.warn("Remove from document not succesful for dafile " + file);
    }
}

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);// ww  w .  ja v  a 2s  . c  o  m
    }
    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:edu.cornell.med.icb.goby.alignments.AlignmentReaderImpl.java

/**
 * Returns true if filename belongs to an alignment basename that can be read.
 *
 * @param filename Filename of an alignment component.
 * @return True if the alignment can be read, false otherwise.
 *///from   ww w . j a v a2s. c  o m
public static boolean canRead(final String filename) {

    final String filenameNoExtension = FilenameUtils.removeExtension(filename);
    String fileExtension = FilenameUtils.getExtension(filename);

    if (!ArrayUtils.contains(AlignmentReaderImpl.COMPACT_ALIGNMENT_FILE_REQUIRED_EXTS, "." + fileExtension)
            && !ArrayUtils.contains(AlignmentReaderImpl.COMPACT_ALIGNMENT_FILE_POSSIBLE_EXTS,
                    "." + fileExtension)) {
        // the file does not contain any of the Goby required or possible extensions. It is not a supported file.
        return false;
    }
    // the file contains a Goby alignment extension, we further check that each needed extension exists:
    int count = 0;
    for (final String extension : AlignmentReaderImpl.COMPACT_ALIGNMENT_FILE_REQUIRED_EXTS) {

        if (RepositionableInputStream.resourceExist(filenameNoExtension + extension)) {
            // we can read this file.
            count++;
        }
    }
    return count == AlignmentReaderImpl.COMPACT_ALIGNMENT_FILE_REQUIRED_EXTS.length;
}

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

/**
 * Constructor./*from  w ww .j  a v a2  s  . com*/
 * @param ip IP Address of the provider.
 * @param port Port where the provider is listening.
 * @param topic 
 */
public DMasonWorker(String ip, String port, String topic) {
    DMasonWorker.ip = ip;
    DMasonWorker.port = port;
    if (!autoStart) {
        beaconListener = new BeaconMessageListener();
        beaconListener.addObserver(this);
        new Thread(beaconListener).start();

        while (!isReady) {
            lock.lock();
            {
                try {
                    readyCondition.await();
                } catch (InterruptedException e) {
                    // TODO Auto-generated catch block
                    e.printStackTrace();
                } //wait beacon
            }
            lock.unlock();
        }
        isReady = false;
    }

    connection = new ConnectionNFieldsWithActiveMQAPI();
    ipAddress = new Address(DMasonWorker.ip, DMasonWorker.port);

    myTopic = topic;

    // 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;
    }
}

From source file:com.opendoorlogistics.core.geometry.ImportShapefile.java

/**
 * Import the shapefile. All geometry is transformed into WGS84.
 * /*from   w w w .  j  av a2s. c o m*/
 * @param file
 * @param ds
 */
@SuppressWarnings("deprecation")
public static HashMap<ShapefileLink, ODLGeom> importShapefile(File file, boolean isLinkedGeometry,
        ODLDatastoreAlterable<? extends ODLTableAlterable> ds, boolean returnGeometry) {
    Spatial.initSpatial();

    file = RelativeFiles.validateRelativeFiles(file.getPath(), AppConstants.SHAPEFILES_DIRECTORY);
    if (file == null) {
        return new HashMap<>();
    }

    // check if we're actually opening a render optimised geometry file... do something if we are? 
    String ext = FilenameUtils.getExtension(file.getAbsolutePath());
    boolean isRog = Strings.equalsStd(ext, RogReaderUtils.RENDER_GEOMETRY_FILE_EXT);
    File originalFile = file;
    List<ODLRenderOptimisedGeom> rogs = null;
    if (isRog) {
        rogs = new LargeList<>();
        RogSingleton.singleton().createLoader(file, rogs);

        // get the shapefile from the main one
        String shpFile = FilenameUtils.removeExtension(file.getPath()) + ".shp";
        file = new File(shpFile);
    }

    SimpleFeatureIterator it = null;
    DataStore shapefile = null;

    // create return object
    HashMap<ShapefileLink, ODLGeom> ret = null;
    if (returnGeometry) {
        ret = new HashMap<>();
    }

    try {
        shapefile = openDataStore(file);
        if (shapefile == null) {
            throw new RuntimeException("Could not open shapefile: " + file);
        }

        // get the linkfile using the *original file*, not the potentially redirected file
        String linkFile = RelativeFiles.getFilenameToSaveInLink(originalFile,
                AppConstants.SHAPEFILES_DIRECTORY);

        for (String type : shapefile.getTypeNames()) {

            // make table
            ODLTableAlterable table = null;
            if (ds != null) {
                String tableName = type;
                if (TableUtils.findTable(ds, tableName) != null) {
                    tableName = TableUtils.getUniqueNumberedTableName(type, ds);
                }
                table = ds.createTable(type, -1);
            }

            // add columns for each usable feature
            SimpleFeatureType schema = shapefile.getSchema(type);
            int nAttrib = schema.getAttributeCount();
            int[] mapped = new int[nAttrib];
            Arrays.fill(mapped, -1);
            if (ds != null) {
                for (int i = 0; i < nAttrib; i++) {
                    AttributeType attributeType = schema.getType(i);
                    Class<?> binding = attributeType.getBinding();
                    ODLColumnType colType = BeanTypeConversion.getInternalType(binding);
                    if (colType != null) {
                        String attributeName = schema.getDescriptor(i).getLocalName();
                        if (table.addColumn(i, attributeName, colType, 0) != -1) {
                            mapped[i] = table.getColumnCount() - 1;
                            if (colType == ODLColumnType.GEOM) {
                                table.setColumnTags(mapped[i], Strings.toTreeSet(PredefinedTags.GEOMETRY));
                            }
                        }
                    }
                }
            }

            // get coord transform to turn into wgs84 long-lat
            MathTransform toWGS84 = getTransformToWGS84(shapefile, type);

            SimpleFeatureSource source = shapefile.getFeatureSource(type);
            SimpleFeatureCollection collection = source.getFeatures();

            // parse all features recording all attributes, including geometry
            it = collection.features();
            int objectIndex = 0;
            while (it.hasNext()) {
                SimpleFeature feature = it.next();

                //System.out.println(feature.getID());

                if (SimpleFeature.class.isInstance(feature)) {
                    SimpleFeature sf = (SimpleFeature) feature;

                    // create row if we're outputting to a datastore
                    int row = -1;
                    if (ds != null) {
                        row = table.createEmptyRow(-1);
                    }

                    for (int i = 0; i < nAttrib; i++) {
                        Object value = sf.getAttribute(i);

                        // process geometry
                        ShapefileLink link = null;
                        if (value != null && Geometry.class.isInstance(value)) {

                            if (!isLinkedGeometry || ret != null) {
                                if (rogs != null) {
                                    value = rogs.get(objectIndex);
                                } else {
                                    // Transform the geometry to wgs84 if we need it 
                                    value = JTS.transform((Geometry) value, toWGS84);
                                    value = new ODLLoadedGeometry((Geometry) value);
                                }
                            } else {
                                // Geometry not needed
                                value = null;
                            }

                            // Create geometry link
                            link = new ShapefileLink(linkFile, type, sf.getID());

                            // Save the transformed geometry if flagged
                            if (ret != null) {
                                ret.put(link, (ODLGeom) value);
                            }

                            // If we're using linked geometry the value for the table is the link
                            if (isLinkedGeometry) {
                                value = new ODLShapefileLinkGeom(link);
                            }
                        }

                        // save to table if mapped
                        int col = mapped[i];
                        if (col != -1) {
                            ODLColumnType odlType = table.getColumnType(col);
                            value = ColumnValueProcessor.convertToMe(odlType, value);
                            table.setValueAt(value, row, col);
                        }
                    }

                    objectIndex++;

                } else {
                    throw new RuntimeException();
                }

            }

        }

    } catch (Throwable e) {
        throw new RuntimeException(e);
    } finally {
        if (it != null) {
            it.close();
        }
        if (shapefile != null) {
            shapefile.dispose();
        }
    }

    return ret;
}

From source file:de.uzk.hki.da.core.RegisterObjectService.java

/**
 * Compares the csn/origName pair of a SIP which identifies an object uniquely against the database.
 * If there is a match, the SIP is considered a delta. If not is considered a primary import.
 * <br><br>/*www  .j a v  a2s . c o  m*/
 * If the SIP is a delta, a new package gets created and attached to the object (which gets fetched from db).
 * If it is a primary import, a new object gets created. In this case a new technical identifier gets created, which
 * is base on the nodes urn index and the preservation systems urnNameSpace. The nodes urn index gets incremented when
 * generating the identifier. The database record gets updated. For security reasons the the object database gets checked of
 * the identifier does not already exist.
 *
 * @param containerName the file name of the SIP container
 * @param contractor the contractor who owns the container
 * 
 * @throws UserException when trying to register a delta record for an object which is not archived (<50) yet
 * @throws IllegalStateException if the system tries to generate an identifier for which an object already exists. 
 * 
 * @return the object.
 */
public Object registerObject(String containerName, User contractor) {
    if (!initialized)
        throw new IllegalStateException("call init first");
    if (contractor == null)
        throw new IllegalArgumentException("contractor is null");
    if (contractor.getShort_name() == null || contractor.getShort_name().isEmpty())
        throw new IllegalArgumentException("contractor short name not set");

    String origName = convertMaskedSlashes(FilenameUtils.removeExtension(containerName));

    Object obj;
    if ((obj = (new ObjectNamedQueryDAO().getUniqueObject(origName, contractor.getShort_name()))) != null) { // is delta then

        logger.info("Package is a delta record for Object with identifier: " + obj.getIdentifier());
        updateExistingObject(obj, containerName);
    } else {
        final String technicalIdentifier = convertURNtoTechnicalIdentifier(generateURNForNode(localNodeId));

        // check identifier
        if (getUniqueObject(technicalIdentifier) != null)
            throw new IllegalStateException("CRITICAL SYSTEM ERROR: DUPLICATE IDENTIFIER");

        logger.info("Creating new Object with identifier " + technicalIdentifier);
        obj = createNewObject(containerName, origName, contractor);
        obj.setIdentifier(technicalIdentifier);
    }
    return obj;
}

From source file:com.doplgangr.secrecy.filesystem.encryption.AES_ECB_Crypter.java

@Override
public void renameFile(File file, String newName) throws SecrecyCipherStreamException, FileNotFoundException {

    File parent = file.getParentFile();
    newName = FilenameUtils.removeExtension(newName);
    newName = Base64Coder.encodeString(newName);
    newName += "." + FilenameUtils.getExtension(file.getName());
    file.renameTo(new File(parent, newName));
}

From source file:com.ibm.bluemix.samples.PostgreSQLReportedErrors.java

/**
 * Retrieve the file information/*from  ww w  . j  a  va  2s .  co  m*/
 * 
 * @return JSON object with file information
 * @throws Exception TODO describe exception
 */
public JSONObject getFileInfo(String entryId) throws Exception {
    String sql = "SELECT * FROM reportedErrors WHERE entry_id = " + entryId;
    Connection connection = null;
    PreparedStatement statement = null;
    ResultSet results = null;

    try {
        connection = getConnection();
        statement = connection.prepareStatement(sql);
        results = statement.executeQuery();
        results.next();
        JSONObject infoObject = new JSONObject();
        infoObject.put("entry_id", Integer.toString(results.getInt("entry_id")));
        infoObject.put("file_name", results.getString("file_name"));
        infoObject.put("s_language", results.getString("s_language"));
        infoObject.put("nlp_parser", results.getString("nlp_parser"));
        infoObject.put("upload_date", results.getDate("upload_date").toString());
        infoObject.put("output_name", FilenameUtils.removeExtension(results.getString("file_name")) + ".xml");

        return infoObject;
    } finally {
        if (results != null) {
            results.close();
        }

        if (statement != null) {
            statement.close();
        }

        if (connection != null) {
            connection.close();
        }
    }
}