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

Introduction

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

Prototype

public static String getExtension(String filename) 

Source Link

Document

Gets the extension of a filename.

Usage

From source file:com.pentaho.repository.importexport.PdiContentProvider.java

private NamedParams getMeta(RepositoryFile file) throws KettleException {

    NamedParams meta = null;/*from w  ww  . j ava  2s  .c om*/

    if (file != null) {

        String extension = FilenameUtils.getExtension(file.getName());
        Repository repo = PDIImportUtil.connectToRepository(null);

        if ("ktr".equalsIgnoreCase(extension)) {

            meta = new TransMeta(convertTransformation(file.getId()), repo, true, null, null);

        } else if ("kjb".equalsIgnoreCase(extension)) {

            meta = new JobMeta(convertJob(file.getId()), repo, null);

        }
    }

    return meta;
}

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From source file:ca.on.oicr.pde.workflows.GATK3Workflow.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  2s.  c  om*/

    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":
                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();
}

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From source file:mj.ocraptor.extraction.tika.parser.epub.EpubParser.java

public void parse(InputStream stream, ContentHandler handler, Metadata metadata, ParseContext context)
        throws IOException, SAXException, TikaException {
    // Because an EPub file is often made up of multiple XHTML files,
    // we need explicit control over the start and end of the document
    XHTMLContentHandler xhtml = new XHTMLContentHandler(handler, metadata);
    xhtml.startDocument();/*from   www.j  a v  a2  s.c om*/
    ContentHandler childHandler = new EmbeddedContentHandler(new BodyContentHandler(xhtml));

    ZipInputStream zip = new ZipInputStream(stream);
    ZipEntry entry = zip.getNextEntry();

    TikaImageHelper helper = new TikaImageHelper(metadata);
    try {
        while (entry != null) {
            // TODO: images
            String entryExtension = null;
            try {
                entryExtension = FilenameUtils.getExtension(new File(entry.getName()).getName());
            } catch (Exception e) {
                e.printStackTrace();
            }
            if (entryExtension != null && FileType.isValidImageFileExtension(entryExtension)
                    && Config.inst().getProp(ConfigBool.ENABLE_IMAGE_OCR)) {
                File imageFile = null;
                try {
                    imageFile = TikaImageHelper.saveZipEntryToTemp(zip, entry);
                    helper.addImage(imageFile);
                } catch (Exception e) {
                    e.printStackTrace();
                } finally {
                    if (imageFile != null) {
                        imageFile.delete();
                    }
                }
            } else if (entry.getName().equals("mimetype")) {
                String type = IOUtils.toString(zip, "UTF-8");
                metadata.set(Metadata.CONTENT_TYPE, type);
            } else if (entry.getName().equals("metadata.xml")) {
                meta.parse(zip, new DefaultHandler(), metadata, context);
            } else if (entry.getName().endsWith(".opf")) {
                meta.parse(zip, new DefaultHandler(), metadata, context);
            } else if (entry.getName().endsWith(".html") || entry.getName().endsWith(".xhtml")) {
                content.parse(zip, childHandler, metadata, context);
            }
            entry = zip.getNextEntry();
        }
        helper.addTextToHandler(xhtml);
    } catch (Exception e) {
        e.printStackTrace();
    } finally {
        if (helper != null) {
            helper.close();
        }
    }

    // Finish everything
    xhtml.endDocument();
}

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From source file:com.github.cbismuth.fdupes.io.PathOrganizer.java

private void onNoTimestampPath(final Path destination, final PathElement pathElement,
        final AtomicInteger counter) {
    final Path path = pathElement.getPath();

    final String baseName = FilenameUtils.getBaseName(path.toString());
    final int count = counter.getAndIncrement();
    final String extension = FilenameUtils.getExtension(path.toString());

    final String newName = String.format("%s-%d.%s", baseName, count, extension);

    final Path sibling = path.resolveSibling(newName);

    try {//w w  w  .  j  av  a  2s . co  m
        FileUtils.moveFile(path.toFile(), sibling.toFile());

        FileUtils.moveFileToDirectory(sibling.toFile(), Paths.get(destination.toString(), "misc").toFile(),
                true);
    } catch (final IOException e) {
        LOGGER.error(e.getMessage());
    }
}

---

From source file:com.iyonger.apm.web.model.FileEntry.java

/**
 * Get file type. If fileType is set, it returns the set fileType.
 * Otherwise, it tries to detect the file type by the extension.
 *
 * @return file type./*  w  w  w  .  j a  va  2  s . c o m*/
 */
public FileType getFileType() {
    if (fileType == null) {
        fileType = FileType.getFileTypeByExtension(FilenameUtils.getExtension(getPath()));
    }
    return fileType;
}

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From source file:com.ostrichemulators.jfxhacc.engine.impl.RdfDataEngine.java

/**
 * Dumps the data to the given file. If the file is null, dumps it in NTriples
 * format to stdout. If the file isn't null, the extension is used to
 * determine the format (either nt, ttl, or rdf). If the extension parsing
 * fails for whatever reason, the dump will be in NTriples format
 *
 * @param de/*  ww  w.ja v  a2  s  . c om*/
 * @param out
 * @throws IOException
 */
public void dump(File out) throws RepositoryException, IOException {
    String ext = (null == out ? "nt" : FilenameUtils.getExtension(out.getName()).toLowerCase());
    Map<String, RDFFormat> map = new HashMap<>();
    map.put("ttl", RDFFormat.TURTLE);
    map.put("rdf", RDFFormat.RDFXML);

    RDFFormat fmt = map.getOrDefault(ext, NTRIPLES);
    try (Writer w = (null == out ? new PrintWriter(System.out) : new FileWriter(out))) {
        RDFHandler handler = null;
        if (RDFFormat.RDFXML == fmt) {
            handler = new RDFXMLWriter(w);
        } else if (RDFFormat.TURTLE == fmt) {
            handler = new TurtleWriter(w);
        } else {
            handler = new NTriplesWriter(w);
        }

        try {
            rc.export(handler);
        } catch (RDFHandlerException re) {
            log.error(re, re);
        }
    }
}

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From source file:net.morphbank.mbsvc3.mapsheet.MapSpreadsheetToXml.java

public Request createRequestFromFile(String fileName, Credentials submitter, Credentials owner,
        PrintWriter report, int numLines, int firstLine) {
    String extension = FilenameUtils.getExtension(fileName);
    if ("xls".equals(extension)) {
        XlsFieldMapper xlsFieldMapper = new XlsFieldMapper(fileName);
        getCredentials(xlsFieldMapper);/*from   w  w w .  ja v  a  2  s. c  o  m*/
        this.submitter = getSubmitter(submitter);
        this.contributor = getContributor(owner);
        fieldMapper = xlsFieldMapper;
        fields = new SpreadsheetFields();
    } else if ("csv".equals(extension)) {
        fieldMapper = new TextFieldMapper(fileName);
    } else { // dwc-Archive folder. filename is the actual folder, not the
             // zipped archive
             // MapDwcaToXml mapDwca = new MapDwcaToXml();
             // return mapDwca.createRequestFromFile(fileName, null, null, null);
    }
    fieldMapper.moveToLine(firstLine - 1);
    request = new Request();
    request.setSubmitter(this.submitter);
    Insert insert = new Insert();
    insert.setSubmitter(this.submitter);
    request.getInsert().add(insert);
    Set<String> specimenIds = new HashSet<String>();// keep track of
    // specimen ids
    int lineNumber = 0;
    while (fieldMapper.hasNext()) {
        int spreadSheetLineNumber = firstLine + lineNumber + 1;
        fieldMapper.getNextLine();
        String origFileName = fieldMapper.getValue("Original File Name");
        if (origFileName.length() > 0) {
            if (fieldMapper.getValue(VIEW_MORPHBANK_ID_FIELD).equalsIgnoreCase("")) {
                XmlBaseObject xmlView;
                if (fieldMapper instanceof XlsFieldMapper)
                    xmlView = createXmlView(spreadSheetLineNumber);
                else
                    xmlView = createXmlViewFromDwca(spreadSheetLineNumber);
                if (xmlView != null) {
                    xmlView.setOwner(this.contributor);
                    insert.getXmlObjectList().add(xmlView);
                }
            }
            // switched image and specimen order
            XmlBaseObject xmlImage;
            if (fieldMapper instanceof XlsFieldMapper) {
                xmlImage = createXmlImage(spreadSheetLineNumber);
            } else {
                xmlImage = createXmlImageFromDwca(spreadSheetLineNumber);
            }
            xmlImage.setOwner(this.contributor);
            insert.getXmlObjectList().add(xmlImage);
            XmlBaseObject xmlSpecimen;
            if (fieldMapper instanceof XlsFieldMapper) {
                xmlSpecimen = createXmlSpecimen(spreadSheetLineNumber);
            } else {
                xmlSpecimen = createXmlSpecimenFromDwca(spreadSheetLineNumber);
            }
            xmlSpecimen.setOwner(this.contributor);
            insert.getXmlObjectList().add(xmlSpecimen);

        }
        lineNumber++;
        if (numLines >= 1 && lineNumber >= numLines)
            break;
    }
    if (0 == lineNumber) {
        // no lines!
        return null;
    }
    System.out.println("Lines: " + firstLine + " to line " + (firstLine + lineNumber - 1) + " processed");
    return request;
}

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From source file:com.googlesource.gerrit.plugins.xdocs.formatter.Formatters.java

public FormatterProvider get(ProjectState project, String fileName) {
    XDocGlobalConfig globalCfg = new XDocGlobalConfig(pluginCfgFactory.getGlobalPluginConfig(pluginName));
    MimeType mimeType = fileTypeRegistry.getMimeType(fileName, null);
    mimeType = new MimeType(
            FileContentUtil.resolveContentType(project, fileName, FileMode.FILE, mimeType.toString()));
    String extension = FilenameUtils.getExtension(fileName);
    FormatterProvider formatter = null;// ww  w. j av a  2s  . com
    int formatterPrio = 0;
    for (String pluginName : formatters.plugins()) {
        for (Entry<String, Provider<Formatter>> e : formatters.byPlugin(pluginName).entrySet()) {
            if (!globalCfg.getFormatterConfig(e.getKey()).getBoolean(KEY_ENABLED, true)) {
                continue;
            }
            ConfigSection formatterCfg = getFormatterConfig(e.getKey(), project);
            String[] prefixes = formatterCfg.getStringList(KEY_PREFIX);
            if (prefixes.length > 0) {
                boolean match = false;
                for (String prefix : prefixes) {
                    if (fileName.startsWith(prefix)) {
                        match = true;
                        break;
                    }
                }
                if (!match) {
                    continue;
                }
            }
            for (String mt : formatterCfg.getStringList(KEY_MIME_TYPE)) {
                MimeType configuredMimeType = new MimeType(mt);
                if (mimeType.equals(configuredMimeType) || ("*".equals(configuredMimeType.getSubType())
                        && mimeType.getMediaType().equals(configuredMimeType.getMediaType()))) {
                    int prio = formatterCfg.getInt(KEY_PRIO, 0);
                    if (formatter == null || prio > formatterPrio) {
                        formatter = new FormatterProvider(e.getKey(), e.getValue());
                        formatterPrio = prio;
                    }
                }
            }
            for (String ext : formatterCfg.getStringList(KEY_EXT)) {
                if (extension.equals(ext) || "*".equals(ext)) {
                    int prio = formatterCfg.getInt(KEY_PRIO, 0);
                    if (formatter == null || prio > formatterPrio) {
                        formatter = new FormatterProvider(e.getKey(), e.getValue());
                        formatterPrio = prio;
                    }
                }
            }
        }
    }
    return formatter;
}

---

From source file:com.maskyn.fileeditorpro.adapter.AdapterDetailedList.java

private void setIcon(final ViewHolder viewHolder, final FileDetail fileDetail) {
    final String fileName = fileDetail.getName();
    final String ext = FilenameUtils.getExtension(fileName);
    if (fileDetail.isFolder()) {
        viewHolder.icon.setImageResource(R.color.file_folder);
    } else if (Arrays.asList(MimeTypes.MIME_HTML).contains(ext) || ext.endsWith("html")) {
        viewHolder.icon.setImageResource(R.color.file_html);
    } else if (Arrays.asList(MimeTypes.MIME_CODE).contains(ext) || fileName.endsWith("css")
            || fileName.endsWith("js")) {
        viewHolder.icon.setImageResource(R.color.file_code);
    } else if (Arrays.asList(MimeTypes.MIME_ARCHIVE).contains(ext)) {
        viewHolder.icon.setImageResource(R.color.file_archive);
    } else if (Arrays.asList(MimeTypes.MIME_MUSIC).contains(ext)) {
        viewHolder.icon.setImageResource(R.color.file_media_music);
    } else if (Arrays.asList(MimeTypes.MIME_PICTURE).contains(ext)) {
        viewHolder.icon.setImageResource(R.color.file_media_picture);
    } else if (Arrays.asList(MimeTypes.MIME_VIDEO).contains(ext)) {
        viewHolder.icon.setImageResource(R.color.file_media_video);
    } else {/*from  www.  j  ava 2s .com*/
        viewHolder.icon.setImageResource(R.color.file_text);
    }
}

---

From source file:com.s2g.pst.resume.importer.PSTFileHelper.java

/**
 * */* w  w  w.  j a  va 2s .  co  m*/
 *
 * @param email
 * @throws FileNotFoundException
 * @throws PSTException
 * @throws IOException
 */
public void saveAttachmentFromEmail(PSTMessage email, FilterInfo filterInfo)
        throws FileNotFoundException, PSTException, IOException, Exception {

    FileOutputStream out = null;
    this.uniqueFileName = null;
    int numberOfAttachments = email.getNumberOfAttachments();
    for (int x = 0; x < numberOfAttachments; x++) {

        PSTAttachment attach = email.getAttachment(x);
        //System.out.println("file size : " + attach.getAttachSize());
        //check file size
        if ((filterInfo.emailAttachFileSizeFrom == 0
                || filterInfo.emailAttachFileSizeFrom <= attach.getAttachSize())
                && (filterInfo.emailAttachFileSizeTo == 0
                        || attach.getAttachSize() <= filterInfo.emailAttachFileSizeTo)) {
            InputStream attachmentStream = attach.getFileInputStream();
            // both long and short filenames can be used for attachments
            String filename = attach.getLongFilename();
            if (filename.isEmpty()) {
                filename = attach.getFilename();
            }
            FileHelper fileHelper = new FileHelper();
            filename = fileHelper.getUniqueFileName(this.emailAttachmentSavePath, filename);
            String fullFileName = this.emailAttachmentSavePath + filename;

            out = new FileOutputStream(fullFileName);
            // 8176 is the block size used internally and should give the best performance
            int bufferSize = 8176;
            byte[] buffer = new byte[bufferSize];
            int count = attachmentStream.read(buffer);
            while (count == bufferSize) {
                out.write(buffer);
                count = attachmentStream.read(buffer);
            }
            byte[] endBuffer = new byte[count];
            System.arraycopy(buffer, 0, endBuffer, 0, count);
            out.write(endBuffer);
            out.close();
            //System.out.println("saved fullFileName : " + fullFileName);
            attachmentStream.close();
            //extract if zip file
            if ("zip".equals(FilenameUtils.getExtension(filename))) {
                UnZipHelper unZipHelper = new UnZipHelper();
                unZipHelper.unZipFolder(fullFileName, this.emailAttachmentSavePath);

            }
        }
    }
}

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