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

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

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  6. 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:de.fhg.iais.asc.xslt.binaries.DownloadAndScale.java

private void addBinaryNodeWithPath(List<Node> result, Node inputNode, Object variant, String subPath,
        String mimeType) {/*from   ww  w .  jav a  2  s  .  c  om*/
    final Element binaryElement = this.targetDoc.createElement("binary");
    copyAttributes(inputNode, binaryElement, ATTRNAMES_COPY_TO_RESULT);

    if (variant instanceof URI) {
        binaryElement.setAttribute(ATTRNAME_PATH, variant.toString());
    } else {
        String resultPath = this.parameters.get(PARAMNAME_RESULT_PATH);
        if (StringUtils.isNotEmpty(resultPath)) {
            binaryElement.setAttribute(PARAMNAME_RESULT_PATH, resultPath);
        }

        binaryElement.setAttribute(ATTRNAME_LOCAL_PATHNAME, (String) variant);

        if (mimeType.startsWith("video/") || mimeType.startsWith("audio/")) { //  Todo Test anpassen
            binaryElement.setAttribute(ATTRNAME_CATEGORY, "full");
        }

        if (!mimeType.equals("video/vimeo")) {
            String prefix = FilenameUtils.removeExtension((String) variant)
                    .replace(FilenameUtils.removeExtension(subPath), "");
            binaryElement.setAttribute(ATTRNAME_PATH,
                    prefix + binaryElement.getAttribute(ATTRNAME_POSITION) + getExtension((String) variant));

            if (mimeType.startsWith("image/") || mimeType.equals("application/pdf")) { //  ToDo Test anpassen

                binaryElement.setAttribute(ATTRNAME_CATEGORY, prefix.replace("/", ""));
            }

        } else {
            binaryElement.setAttribute(ATTRNAME_PATH, (String) variant);
        }
    }

    binaryElement.setAttribute(ATTRNAME_MIMETYPE, mimeType);

    //  binaryElement.setAttribute(ATTRNAME_FULL, full);

    result.add(binaryElement);
}

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

private void importAiHints(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);
                    String script = String.join("\n", lines);
                    AiHint hint = new AiHint(id, script);
                    //datastore.createAiHint(hint);
                    aiHintCache.put(id, hint);
                    logger.info("Imported hint " + id);
                }//  w w w.  ja v  a2 s .c  o m
            } catch (Exception e) {
                throw new RuntimeException("Failed to parse " + filePath + ": " + e.getMessage());
            }
        }
    });
}

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

@Override
public void execute() throws IOException {
    // output file extension is based on the output format type
    final String outputExtension = "." + outputFormat.name().toLowerCase(Locale.getDefault());
    if (outputFilename == null) {
        outputFilename = FilenameUtils.removeExtension(inputFilename) + (hashOutputFilename ? hash() : "")
                + outputExtension;/*w w  w  . j  ava2 s .  c  om*/
    } else if (hashOutputFilename) {
        outputFilename = FilenameUtils.removeExtension(outputFilename) + (hashOutputFilename ? hash() : "")
                + outputExtension;
    }

    ReadSet readIndexFilter = new ReadSet();
    if (readIndexFilterFile == null) {
        readIndexFilter = null;
    } else {
        readIndexFilter.load(readIndexFilterFile);
    }

    final ProgressLogger progress = new ProgressLogger();
    progress.start();
    progress.displayFreeMemory = true;

    // Only sanger and illumina encoding are supported at this time
    if (qualityEncoding == QualityEncoding.SOLEXA) {
        throw new UnsupportedOperationException(
                "SOLEXA encoding is not supported " + "at this time for lack of clear documentation.");
    } else if (qualityEncoding != QualityEncoding.SANGER && qualityEncoding != QualityEncoding.ILLUMINA) {
        throw new UnsupportedOperationException("Unknown encoding: " + qualityEncoding);
    }

    ReadsReader reader = null;
    Writer writer = null;
    OutputStreamWriter pairWriter = null;
    final int newEntryCharacter;
    switch (outputFormat) {
    case FASTQ:
        newEntryCharacter = '@';
        break;
    case FASTA:
    default:
        newEntryCharacter = '>';
        break;
    }
    try {
        writer = new OutputStreamWriter(new FastBufferedOutputStream(new FileOutputStream(outputFilename)));
        pairWriter = processPairs
                ? new OutputStreamWriter(new FastBufferedOutputStream(new FileOutputStream(outputPairFilename)))
                : null;

        final MutableString colorSpaceBuffer = new MutableString();
        final MutableString sequence = new MutableString();
        final MutableString sequencePair = new MutableString();

        if (hasStartOrEndPosition) {
            reader = new ReadsReader(startPosition, endPosition, inputFilename);
        } else {
            reader = new ReadsReader(inputFilename);
        }

        for (final Reads.ReadEntry readEntry : reader) {
            if (readIndexFilter == null || readIndexFilter.contains(readEntry.getReadIndex())) {
                final String description;

                if (indexToHeader) {
                    description = Integer.toString(readEntry.getReadIndex());
                } else if (identifierToHeader && readEntry.hasReadIdentifier()) {
                    description = readEntry.getReadIdentifier();
                } else if (readEntry.hasDescription()) {
                    description = readEntry.getDescription();
                } else {
                    description = Integer.toString(readEntry.getReadIndex());
                }

                writer.write(newEntryCharacter);
                writer.write(description);
                writer.write('\n');
                final boolean processPairInThisRead = processPairs && readEntry.hasSequencePair();
                if (processPairInThisRead) {
                    pairWriter.write(newEntryCharacter);
                    pairWriter.write(description);
                    pairWriter.write('\n');
                }
                observeReadIndex(readEntry.getReadIndex());
                ReadsReader.decodeSequence(readEntry, sequence);

                if (processPairInThisRead) {
                    ReadsReader.decodeSequence(readEntry, sequencePair, true);
                }

                if (queryLengths != null) {
                    queryLengths.put(readEntry.getReadIndex(), sequence.length());
                }

                MutableString transformedSequence = sequence;
                MutableString transformedSequencePair = sequencePair;
                if (outputColorMode) {
                    ColorSpaceConverter.convert(transformedSequence, colorSpaceBuffer, referenceConversion);
                    transformedSequence = colorSpaceBuffer;
                    if (processPairInThisRead) {
                        ColorSpaceConverter.convert(transformedSequencePair, colorSpaceBuffer,
                                referenceConversion);
                        transformedSequencePair = colorSpaceBuffer;
                    }
                }
                if (outputFakeNtMode) {
                    for (int i = 0; i < transformedSequence.length(); i++) {
                        transformedSequence.charAt(i, getFakeNtCharacter(transformedSequence.charAt(i)));
                    }
                    if (processPairInThisRead) {
                        for (int i = 0; i < transformedSequencePair.length(); i++) {
                            transformedSequencePair.charAt(i,
                                    getFakeNtCharacter(transformedSequencePair.charAt(i)));
                        }
                    }
                }
                if (trimAdaptorLength > 0) {
                    transformedSequence = transformedSequence.substring(trimAdaptorLength);
                    if (processPairInThisRead) {
                        transformedSequencePair = transformedSequencePair.substring(trimAdaptorLength);
                    }
                }
                // filter unrecognized bases from output
                if (alphabet != null) {
                    for (int i = 0; i < transformedSequence.length(); i++) {
                        if (alphabet.indexOf(transformedSequence.charAt(i)) == -1) {
                            transformedSequence.charAt(i, 'N');
                        }
                    }
                }
                if (processPairInThisRead) {
                    if (alphabet != null) {

                        for (int i = 0; i < transformedSequencePair.length(); i++) {
                            if (alphabet.indexOf(transformedSequencePair.charAt(i)) == -1) {
                                transformedSequencePair.charAt(i, 'N');
                            }
                        }
                    }
                }
                writeSequence(writer, transformedSequence, fastaLineLength);
                if (processPairInThisRead) {
                    writeSequence(pairWriter, transformedSequencePair, fastaLineLength);
                }
                if (outputFormat == OutputFormat.FASTQ) {
                    final int readLength = transformedSequence.length();
                    final byte[] qualityScores = readEntry.getQualityScores().toByteArray();
                    final boolean hasQualityScores = readEntry.hasQualityScores()
                            && !ArrayUtils.isEmpty(qualityScores);
                    writeQualityScores(writer, hasQualityScores, qualityScores, outputFakeQualityMode,
                            readLength);

                    if (processPairInThisRead) {
                        final int readLengthPair = transformedSequencePair.length();
                        final byte[] qualityScoresPair = readEntry.getQualityScoresPair().toByteArray();
                        final boolean hasPairQualityScores = readEntry.hasQualityScoresPair()
                                && !ArrayUtils.isEmpty(qualityScoresPair);
                        writeQualityScores(pairWriter, hasPairQualityScores, qualityScoresPair,
                                outputFakeQualityMode, readLengthPair);

                    }
                }
                ++numberOfFilteredSequences;

                progress.lightUpdate();
                ++numberOfSequences;
            }

        }
    } finally {
        IOUtils.closeQuietly(writer);
        if (processPairs) {
            IOUtils.closeQuietly(pairWriter);
        }
        if (reader != null) {
            try {
                reader.close();
            } catch (IOException e) { // NOPMD
                // silently ignore
            }
        }
    }

    progress.stop();
}

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

/**
 * @return/* w w w . j  ava 2  s . c  o  m*/
 */
private Map<String, List<File>> generateDocumentsToFilesMap() {

    Map<String, List<File>> documentsToFiles = new HashMap<String, List<File>>();

    Collection<File> files = FileUtils.listFiles(wa.dataPath().toFile(), TrueFileFilter.INSTANCE,
            TrueFileFilter.INSTANCE);
    for (File file : files) {
        String document = file.getAbsolutePath().replace(wa.dataPath().toFile().getAbsolutePath(), "");
        document = document.substring(1);
        document = FilenameUtils.removeExtension(document);

        if (!documentsToFiles.keySet().contains(document)) {

            List<File> filesList = new ArrayList<File>();
            filesList.add(file);
            documentsToFiles.put(document, filesList);
        } else {
            documentsToFiles.get(document).add(file);
        }
    }

    return documentsToFiles;
}

From source file:de.mprengemann.intellij.plugin.androidicons.settings.PluginSettings.java

private void scanForMaterialIconsAssets() {
    int categoriesCount = 0;
    int assetCount = 0;
    if (this.selectedMaterialIconsFile != null && this.selectedMaterialIconsFile.getCanonicalPath() != null) {
        File assetRoot = new File(this.selectedMaterialIconsFile.getCanonicalPath());
        final FilenameFilter drawableFileNameFiler = new FilenameFilter() {
            @Override//from  w  w  w . ja va2 s  . c o  m
            public boolean accept(File file, String s) {
                if (!FilenameUtils.isExtension(s, "png")) {
                    return false;
                }
                String filename = FilenameUtils.removeExtension(s);
                return filename.startsWith("ic_") && filename.endsWith("_black_48dp");
            }
        };
        final FilenameFilter folderFileNameFiler = new FilenameFilter() {
            @Override
            public boolean accept(File file, String s) {
                return !s.startsWith(".") && new File(file, s).isDirectory()
                        && !BLACKLISTED_MATERIAL_ICONS_FOLDER.contains(FilenameUtils.removeExtension(s));
            }
        };
        File[] categories = assetRoot.listFiles(folderFileNameFiler);
        if (categories != null) {
            categoriesCount = categories.length;
            if (categories.length >= 1) {
                for (File category : categories) {
                    File[] densities = category.listFiles(folderFileNameFiler);
                    if (densities != null && densities.length >= 1) {
                        File exDensity = densities[0];
                        File[] assets = exDensity.listFiles(drawableFileNameFiler);
                        assetCount += assets != null ? assets.length : 0;
                    }
                }
            }
        }
    }
    materialIconsFoundCategories.setText(categoriesCount + " categories");
    materialIconsFoundDrawables.setText(assetCount + " drawables");
}

From source file:de.mprengemann.intellij.plugin.androidicons.dialogs.AndroidBatchScaleImporter.java

private void initRenderers() {
    final DefaultTableCellRenderer fileCellRenderer = new DefaultTableCellRenderer() {
        @Override//from   w  w  w .  j ava  2 s  .c o  m
        protected void setValue(Object o) {
            File file = (File) o;
            if (file == null) {
                setText("");
                return;
            }
            if (file.isDirectory()) {
                setText(file.getAbsolutePath());
            } else {
                setText(FilenameUtils.removeExtension(file.getName()));
            }
        }
    };
    fileCellRenderer.setHorizontalTextPosition(DefaultTableCellRenderer.TRAILING);
    table.setDefaultRenderer(File.class, fileCellRenderer);
    table.setDefaultRenderer(ArrayList.class, new DefaultTableCellRenderer() {
        @Override
        protected void setValue(Object o) {
            if (o == null) {
                setText("");
            } else {
                ArrayList list = (ArrayList) o;
                Collections.sort(list);
                StringBuilder buffer = new StringBuilder();
                Iterator iterator = list.iterator();
                while (iterator.hasNext()) {
                    Object val = iterator.next();
                    buffer.append(val.toString());
                    if (iterator.hasNext()) {
                        buffer.append(", ");
                    }
                }
                setText(buffer.toString());
            }
        }
    });
}

From source file:eu.edisonproject.training.execute.Main.java

private static void calculateTFIDF(String in, String out) throws IOException {
    File tmpFolder = null;//  ww  w  .  jav a2  s.  c  om
    try {
        String contextName = FilenameUtils.removeExtension(in.substring(in.lastIndexOf(File.separator) + 1));
        ITFIDFDriver tfidfDriver = new TFIDFDriverImpl(contextName);
        File inFile = new File(in);

        String workingFolder = System.getProperty("working.folder");
        if (workingFolder == null) {
            workingFolder = prop.getProperty("working.folder", System.getProperty("java.io.tmpdir"));
        }

        tmpFolder = new File(workingFolder + File.separator + System.currentTimeMillis());

        tmpFolder.mkdir();
        tmpFolder.deleteOnExit();

        setTFIDFDriverImplPaths(inFile, tmpFolder);

        tfidfDriver.executeTFIDF(tmpFolder.getAbsolutePath());
        tfidfDriver.driveProcessResizeVector();
        File ctxPath = new File(TFIDFDriverImpl.CONTEXT_PATH);
        for (File f : ctxPath.listFiles()) {
            if (FilenameUtils.getExtension(f.getName()).endsWith("csv")) {
                FileUtils.moveFile(f, new File(out + File.separator + f.getName()));
            }
        }
    } finally {
        if (tmpFolder != null && tmpFolder.exists()) {
            tmpFolder.delete();
            FileUtils.forceDelete(tmpFolder);
        }
    }
}

From source file:de.fhg.iais.asc.sipmaker.impl.DefaultSipMaker.java

private void addPostprocessingScripts(String scriptsFolder, File sipMakerBaseDir,
        TransformerListBuilder builder) {

    File postprocessingFolder = new File(getTransformersDir(sipMakerBaseDir), scriptsFolder);
    if (!postprocessingFolder.exists()) {
        throw new AscConfigFailureException("Loading postprocessing scripts failed: Folder '"
                + postprocessingFolder.getAbsolutePath() + "' does not exist!");
    }/*from w w  w. j  a v a2  s  . c om*/

    Collection<File> postprocessingScripts = FileUtils.listFiles(postprocessingFolder, new String[] { "xsl" },
            true);
    Iterator<File> scriptIter = postprocessingScripts.iterator();
    while (scriptIter.hasNext()) {
        AbstractTransformer preprocessTransformer = new AscTransformXSLResolver(postprocessingFolder)
                .createPostprocessingTransformer(FilenameUtils.removeExtension(scriptIter.next().getName()));
        builder.addTransformer(preprocessTransformer);
    }

}

From source file:com.vvote.verifier.component.votePacking.VotePackingDataStore.java

/**
 * Load the mixnet output data/*ww w  . jav  a 2s  .c o m*/
 * 
 * @throws JSONException
 * @throws MixDataException
 * @throws ASN1Exception
 * @throws JSONIOException
 */
private void loadMixOutputData() throws JSONException, MixDataException, ASN1Exception, JSONIOException {
    this.mixOutput = new HashMap<RaceIdentifier, List<List<ECPoint>>>();

    final File mixOutputDirectory = new File(this.mixOutputPath);

    logger.debug("Loading in the mix output data from the folder: {}", mixOutputDirectory);

    // check whether the provided directory is valid
    if (!mixOutputDirectory.isDirectory()) {
        logger.error("The mix output folder must be a directory: {}", mixOutputDirectory);
        throw new MixDataException("The mix output folder must be a directory: " + mixOutputDirectory);
    }

    String jsonFile = null;

    RaceIdentifier currentIdentifier = null;

    JSONArray mixOutputArray = null;

    JSONArray plaintexts = null;

    List<ECPoint> currentIds = null;

    List<List<ECPoint>> currentFileIds = null;

    // loop over each file in the directory
    for (File file : mixOutputDirectory.listFiles()) {

        logger.debug("Current file in mix output directory: {}", file.getName());

        if (IOUtils.checkExtension(FileType.MIX_OUTPUT, file.getName())) {

            // get equivalent json filename
            jsonFile = IOUtils.addExtension(FilenameUtils.removeExtension(file.getPath()), FileType.JSON);

            // convert from asn.1 to json format
            ASN1ToJSONConverter.asn1ToJSON(file.getPath(), jsonFile, FileType.MIX_OUTPUT);

            // get current identifier
            currentIdentifier = Utils.getRaceIdentifierFromFileName(jsonFile, this.hasRaceMap);

            mixOutputArray = IOUtils.readJSONArrayFromFile(jsonFile);

            currentFileIds = new ArrayList<List<ECPoint>>();

            // loop over each ballot
            for (int i = 0; i < mixOutputArray.length(); i++) {

                currentIds = new ArrayList<ECPoint>();

                plaintexts = mixOutputArray.getJSONArray(i);

                // loop over each plaintext
                for (int j = 0; j < plaintexts.length(); j++) {
                    currentIds.add(ECUtils.constructECPointFromJSON(plaintexts.getJSONObject(j)));
                }

                currentFileIds.add(currentIds);
            }

            this.mixOutput.put(currentIdentifier, currentFileIds);
        }
    }

    logger.debug("Successfully loaded mixnet output data");
}

From source file:de.mprengemann.intellij.plugin.androidicons.forms.MaterialIconsImporter.java

private void fillSizes() {
    final String lastSelectedSize = this.lastSelectedSize;
    sizeSpinner.removeAllItems();//w  w w .  j  av  a2 s .co m
    if (this.assetRoot.getCanonicalPath() == null) {
        return;
    }
    File assetRoot = new File(this.assetRoot.getCanonicalPath());
    assetRoot = new File(assetRoot, (String) categorySpinner.getSelectedItem());
    assetRoot = new File(assetRoot, DEFAULT_RESOLUTION);
    final String assetName = (String) assetSpinner.getSelectedItem();
    final FilenameFilter drawableFileNameFiler = new FilenameFilter() {
        @Override
        public boolean accept(File file, String s) {
            if (!FilenameUtils.isExtension(s, "png")) {
                return false;
            }
            String filename = FilenameUtils.removeExtension(s);
            return filename.startsWith("ic_" + assetName + "_");
        }
    };
    File[] assets = assetRoot.listFiles(drawableFileNameFiler);
    Set<String> sizes = new HashSet<String>();
    for (File asset : assets) {
        String drawableName = FilenameUtils.removeExtension(asset.getName());
        String[] numbers = drawableName.replaceAll("[^-?0-9]+", " ").trim().split(" ");
        drawableName = numbers[numbers.length - 1].trim() + "dp";
        sizes.add(drawableName);
    }
    List<String> list = new ArrayList<String>();
    list.addAll(sizes);
    Collections.sort(list);
    for (String size : list) {
        sizeSpinner.addItem(size);
    }
    if (list.contains(lastSelectedSize)) {
        sizeSpinner.setSelectedIndex(list.indexOf(lastSelectedSize));
    }
}