Java Code Examples for org.apache.commons.io.FilenameUtils

The following are top voted examples for showing how to use org.apache.commons.io.FilenameUtils. These examples are extracted from open source projects. You can vote up the examples you like and your votes will be used in our system to generate more good examples.
Example 1
Project: DIA-Umpire-Maven   File: LCMSPeakBase.java   View source code 6 votes vote down vote up
private boolean FS_PeakClusterRead() {
    if (!new File(FilenameUtils.getFullPath(ParentmzXMLName) + FilenameUtils.getBaseName(ParentmzXMLName) + "_Peak/" + FilenameUtils.getBaseName(ScanCollectionName) + "_PeakCluster.serFS").exists()) {
        return false;
    }
    try {
        Logger.getRootLogger().info("Reading PeakCluster serialization from file:" + FilenameUtils.getBaseName(ScanCollectionName) + "_PeakCluster.serFS...");

        FileInputStream fileIn = new FileInputStream(FilenameUtils.getFullPath(ParentmzXMLName) + FilenameUtils.getBaseName(ParentmzXMLName) + "_Peak/" + FilenameUtils.getBaseName(ScanCollectionName) + "_PeakCluster.serFS");
        FSTObjectInput in = new FSTObjectInput(fileIn);
        PeakClusters = (ArrayList<PeakCluster>) in.readObject();
        in.close();
        fileIn.close();
    } catch (Exception ex) {
        Logger.getRootLogger().error(ExceptionUtils.getStackTrace(ex));
        if (FS_PeakClusterRead_Old()) {
            WritePeakClusterSerialization();
            return true;
        }
        Logger.getRootLogger().error(ExceptionUtils.getStackTrace(ex));
        return false;
    }
    return true;
}
 
Example 2
Project: DIA-Umpire-Maven   File: LCMSID.java   View source code 6 votes vote down vote up
private boolean FSWrite(String filepath, String tag) {
    try {
        if (!tag.equals("")) {
            tag = "_" + tag;
        }
        Logger.getRootLogger().info("Writing ID results to file:" + FilenameUtils.getFullPath(filepath) + FilenameUtils.getBaseName(filepath) + tag + "_LCMSID.serFS...");
        FileOutputStream fout = new FileOutputStream(FilenameUtils.getFullPath(filepath) + FilenameUtils.getBaseName(filepath) + tag + "_LCMSID.serFS", false);
        FSTObjectOutput out = new FSTObjectOutput(fout);
        ReduceMemoryUsage();
        out.writeObject(this, LCMSID.class);
        out.close();
        fout.close();
    } catch (Exception ex) {
        Logger.getRootLogger().error(ExceptionUtils.getStackTrace(ex));
        return false;
    }
    return true;
}
 
Example 3
Project: jhipster-microservices-example   File: WebConfigurerTest.java   View source code 6 votes vote down vote up
@Test
public void testCustomizeServletContainer() {
    env.setActiveProfiles(JHipsterConstants.SPRING_PROFILE_PRODUCTION);
    UndertowEmbeddedServletContainerFactory container = new UndertowEmbeddedServletContainerFactory();
    webConfigurer.customize(container);
    assertThat(container.getMimeMappings().get("abs")).isEqualTo("audio/x-mpeg");
    assertThat(container.getMimeMappings().get("html")).isEqualTo("text/html;charset=utf-8");
    assertThat(container.getMimeMappings().get("json")).isEqualTo("text/html;charset=utf-8");
    if (container.getDocumentRoot() != null) {
        assertThat(container.getDocumentRoot().getPath()).isEqualTo(FilenameUtils.separatorsToSystem("target/www"));
    }

    Builder builder = Undertow.builder();
    container.getBuilderCustomizers().forEach(c -> c.customize(builder));
    OptionMap.Builder serverOptions = (OptionMap.Builder) ReflectionTestUtils.getField(builder, "serverOptions");
    assertThat(serverOptions.getMap().get(UndertowOptions.ENABLE_HTTP2)).isNull();
}
 
Example 4
Project: SkyDocs   File: DocsPage.java   View source code 6 votes vote down vote up
/**
 * Creates a new DocsPage instance.
 * 
 * @param project The project this page belongs to.
 * @param title The title of this page.
 * @param language The language of this page.
 * @param file The file (HTML or MarkDown) that represents the content of this page.
 */

public DocsPage(final DocsProject project, final File file) {
	final Map<String, Object> header = Utils.decodeFileHeader(Utils.separateFileHeader(file)[0]);
	
	this.project = project;
	this.title = header != null && header.containsKey(Constants.KEY_HEADER_TITLE) ? header.get(Constants.KEY_HEADER_TITLE).toString() : StringUtils.capitalize(FilenameUtils.removeExtension(file.getName()));
	this.language = header != null && header.containsKey(Constants.KEY_HEADER_LANGUAGE) ? header.get(Constants.KEY_HEADER_LANGUAGE).toString() : project.getDefaultLanguage();
	this.absolutePath = file.getPath();
	this.path = absolutePath.replace(project.getContentDirectory().getPath(), "").replace(project.getBuildDirectory().getPath(), "");
	this.relativeURL = getBuildDestination().getPath().replace(project.getBuildDirectory().getPath(), "").replace(File.separator, "/");
	
	if(header != null) {
		if(header.containsKey(Constants.KEY_HEADER_PREVIOUS)) {
			this.previous = header.get(Constants.KEY_HEADER_PREVIOUS).toString();
		}
		if(header.containsKey(Constants.KEY_HEADER_NEXT)) {
			this.next = header.get(Constants.KEY_HEADER_NEXT).toString();
		}
		this.header.putAll(header);
	}
}
 
Example 5
Project: sctalk   File: ThumbUrlUtils.java   View source code 6 votes vote down vote up
/**
 * 缩略图文件URL/ID编辑 <br>
 * 取原图
 * 
 * @param thumbUrl 缩略图
 * @return 原图URL
 */
public static String getOrgiUrl(String thumbUrl) {

    if (thumbUrl == null) {
        return null;
    }

    String extension = FilenameUtils.getExtension(thumbUrl);
    if (extension == null) {
        return thumbUrl;
    }

    if ("jpg".equalsIgnoreCase(extension)) {
        // 缩略图
    } else if ("png".equalsIgnoreCase(extension)) {
        // 缩略图
    } else {
        return thumbUrl;
    }

    return thumbUrl.replaceAll("_\\d+x\\d+\\." + extension + "$", "." + extension);
}
 
Example 6
Project: DIA-Umpire-Maven   File: TargetMatchScoring.java   View source code 6 votes vote down vote up
public static TargetMatchScoring LibraryMatchRead(String Filename, String LibID) throws FileNotFoundException {

        if (!new File(FilenameUtils.getFullPath(Filename) + FilenameUtils.getBaseName(Filename) + "_" + LibID + "_LibMatch.serFS").exists()) {
            return null;
        }
        TargetMatchScoring match = null;
        try {
            Logger.getRootLogger().info("Loading Target library match results to file:" + FilenameUtils.getFullPath(Filename) + FilenameUtils.getBaseName(Filename) + "_" + LibID + "_LibMatch.serFS...");
            FileInputStream fileIn = new FileInputStream(FilenameUtils.getFullPath(Filename) + FilenameUtils.getBaseName(Filename) + "_" + LibID + "_LibMatch.serFS");
            FSTObjectInput in = new FSTObjectInput(fileIn);
            match = (TargetMatchScoring) in.readObject();
            in.close();
            fileIn.close();
        } catch (Exception ex) {
            Logger.getRootLogger().error(ExceptionUtils.getStackTrace(ex));
            return null;
        }
        return match;
    }
 
Example 7
Project: onprom   File: UMLDiagramPanel.java   View source code 6 votes vote down vote up
public void exportImage() {
  try {
    File file = IOUtility.selectFileToSave(FileType.IMAGE);
    if (file != null) {
      Rectangle drawingArea = getDrawingArea();
      String extension = FilenameUtils.getExtension(file.getName());
      if (extension.equals("svg")) {
        SVGGraphics2D svgGenerator = IOUtility.getSVGGraphics(drawingArea.getSize());
        paintDrawing(svgGenerator, drawingArea.x, drawingArea.y);
        svgGenerator.stream(new FileWriter(file));
        svgGenerator.dispose();
      } else {
        BufferedImage bi = new BufferedImage(drawingArea.width, drawingArea.height, BufferedImage.TYPE_INT_RGB);
        Graphics g = bi.createGraphics();
        paintDrawing(g, drawingArea.x, drawingArea.y);
        ImageIO.write(bi, extension, file);
        g.dispose();
      }
    }
  } catch (Exception e) {
    e.printStackTrace();
  }
}
 
Example 8
Project: buenojo   File: ImageResourceService.java   View source code 6 votes vote down vote up
public ImageResource createImageResource(MultipartFile loResImage, MultipartFile hiResImage, Boolean dryRun) throws IOException, BuenOjoFileException, BuenOjoInconsistencyException {
	ImageResource imageResource = new ImageResource();
	if (loResImage!=null) {
		if (imageResource.getName()==null)
			imageResource.setName(FilenameUtils.removeExtension(loResImage.getOriginalFilename()));
		imageResource.setLoResImage(loResImage.getBytes());
		imageResource.setLoResImageContentType(loResImage.getContentType());

	}
	if (hiResImage != null){
		if (imageResource.getName()==null)
			imageResource.setName(FilenameUtils.removeExtension(hiResImage.getOriginalFilename()));
		imageResource.setHiResImage(hiResImage.getBytes());
		imageResource.setHiResImageContentType(hiResImage.getContentType());

	}
	return createImageResource(imageResource,dryRun);
}
 
Example 9
Project: DIA-Umpire-Maven   File: PKLScanParser.java   View source code 6 votes vote down vote up
private void Parse() throws FileNotFoundException, IOException {
    //806.080993652344,8429.974609375,1
    //832.287536621094,7226.927734375,1
    //854.039978027344,6682.37646484375,1
    //861.061340332031,8370.4716796875,1
    BufferedReader reader = new BufferedReader(new FileReader(filename));
    String line = "";
    String[] Values = null;
    scan = new ScanData();
    scan.MGFTitle = FilenameUtils.getBaseName(filename);
    while ((line = reader.readLine()) != null) {
        if ((Values = line.split(",")).length == 3) {
            scan.AddPoint(Float.parseFloat(Values[0]), Float.parseFloat(Values[1]));
        }
    }
    reader.close();
}
 
Example 10
Project: buenojo   File: BuenOjoFileUtils.java   View source code 6 votes vote down vote up
public static Optional<String> contentType(Path path) {
	
	String extension = FilenameUtils.getExtension(path.getFileName().toString());
	
	switch (extension.toLowerCase()) {
	case "jpeg":
		return Optional.of("image/jpeg");
	case "jpg":
		return Optional.of("image/jpg");
	case "png":
		return Optional.of("image/png");
	case "gif":
		return Optional.of("image/gif");
	case "tif":
	case "tiff":
		return Optional.of("image/tiff");
	case "csv":
		return Optional.of("text/csv");
	default:			
		return Optional.empty();
	}
	
}
 
Example 11
Project: monarch   File: ClusterConfigurationService.java   View source code 6 votes vote down vote up
public ClusterConfigurationService(Cache cache) throws IOException {
  this.cache = (GemFireCacheImpl) cache;
  Properties properties = cache.getDistributedSystem().getProperties();
  // resolve the cluster config dir
  String clusterConfigRootDir = properties.getProperty(CLUSTER_CONFIGURATION_DIR);

  if (StringUtils.isBlank(clusterConfigRootDir)) {
    clusterConfigRootDir = System.getProperty("user.dir");
  } else {
    File diskDir = new File(clusterConfigRootDir);
    if (!diskDir.exists() && !diskDir.mkdirs()) {
      throw new IOException("Cannot create directory : " + clusterConfigRootDir);
    }
    clusterConfigRootDir = diskDir.getCanonicalPath();
  }

  // resolve the file paths
  String configDiskDirName =
      CLUSTER_CONFIG_DISK_DIR_PREFIX + cache.getDistributedSystem().getName();

  configDirPath = FilenameUtils.concat(clusterConfigRootDir, CLUSTER_CONFIG_ARTIFACTS_DIR_NAME);
  configDiskDirPath = FilenameUtils.concat(clusterConfigRootDir, configDiskDirName);
  sharedConfigLockingService = getSharedConfigLockService(cache.getDistributedSystem());
  status.set(SharedConfigurationStatus.NOT_STARTED);
}
 
Example 12
Project: coffee-gb   File: Cartridge.java   View source code 6 votes vote down vote up
private static int[] loadFile(File file) throws IOException {
    String ext = FilenameUtils.getExtension(file.getName());
    try (InputStream is = new FileInputStream(file)) {
        if ("zip".equalsIgnoreCase(ext)) {
            try (ZipInputStream zis = new ZipInputStream(is)) {
                ZipEntry entry;
                while ((entry = zis.getNextEntry()) != null) {
                    String name = entry.getName();
                    String entryExt = FilenameUtils.getExtension(name);
                    if (Stream.of("gb", "gbc", "rom").anyMatch(e -> e.equalsIgnoreCase(entryExt))) {
                        return load(zis, (int) entry.getSize());
                    }
                    zis.closeEntry();
                }
            }
            throw new IllegalArgumentException("Can't find ROM file inside the zip.");
        } else {
            return load(is, (int) file.length());
        }
    }
}
 
Example 13
Project: cloud-portal   File: MailTemplateService.java   View source code 6 votes vote down vote up
@PostConstruct
public void init() {
	
	try {
		
		File mailFolder = resourceService.getClasspathResource(TEMPLATE_FOLDER_NAME);
		if (!mailFolder.isFile()) {
			File[] mailFolderArray = mailFolder.listFiles();
			for (File mailTemplateFile : mailFolderArray) {
				String mailTemplateName = FilenameUtils.getBaseName(mailTemplateFile.getName());
				String mailTemplatePath = TEMPLATE_FOLDER_NAME + File.separator + mailTemplateFile.getName(); 
				mailTemplateMap.put(mailTemplateName, mailTemplatePath);
			}
		}
	}
	catch (Exception e) {
		LOG.error(e.getMessage(), e);
	}
}
 
Example 14
Project: CORNETTO   File: ExportImageController.java   View source code 6 votes vote down vote up
/**
 * Detects the filetype of the selected output file based on the file extension and selects radio buttons accordingly
 * @param fileName String with the filename of the selected output file
 * @return
 */
private String setFileType(String fileName) {
    String ext = FilenameUtils.getExtension(fileName);
    System.out.println("FT: " + ext);
    switch (ext) {
        case "png":
            imgRadioPng.setSelected(true);
            break;
        case "jpg":
            imgRadioJpg.setSelected(true);
            break;
        case "jpeg":
            imgRadioJpg.setSelected(true);
            break;
        case "gif":
            imgRadioGif.setSelected(true);
            break;
        default:
            System.out.println("No Correct File Ending");
            break;
    }
    return ext;
}
 
Example 15
Project: DIA-Umpire-Maven   File: DIA_Umpire_ProtQuant.java   View source code 6 votes vote down vote up
private static void SaintOutput(LCMSID protID, LCMSID IDsummary, FragmentSelection fragselection, FileWriter interactionfile, String filename, String samplename, HashMap<String, String> PreyID, int quanttype) throws IOException {
    for (String key : protID.ProteinList.keySet()) {
        if (IDsummary.ProteinList.containsKey(key)) {
            ProtID protein = IDsummary.ProteinList.get(key);
            float abundance = 0f;

            if (quanttype == 1) {
                abundance = protein.GetAbundanceByMS1_IBAQ();
            } else if (quanttype == 2) {
                abundance = protein.GetAbundanceByTopCorrFragAcrossSample(fragselection.TopPeps.get(protein.getAccNo()), fragselection.TopFrags);
            }
            if (abundance > 0) {
                interactionfile.write(FilenameUtils.getBaseName(filename) + "\t" + samplename + "\t" + protein.getAccNo() + "\t" + abundance + "\n");
                if (!PreyID.containsKey(protein.getAccNo())) {
                    PreyID.put(protein.getAccNo(), /*protein.Sequence.length()+"\t"+*/ protein.GetGeneName());
                }
            }
        }
    }
}
 
Example 16
Project: sponge   File: DefaultKnowledgeBaseManager.java   View source code 6 votes vote down vote up
public KnowledgeBaseType inferKnowledgeBaseType(ScriptKnowledgeBase scriptKnowledgeBase) {
    List<KnowledgeBaseScript> scripts = scriptKnowledgeBase.getScripts();
    if (scripts.isEmpty()) {
        throw new SpongeException("Cannot infer knowledge base '" + scriptKnowledgeBase.getName() + "' type because it has no files");
    }

    String fileName = scripts.get(0).getFileName();
    String extension = FilenameUtils.getExtension(fileName);

    Optional<KnowledgeBaseType> typeO = knowledgeBaseInterpreterFactories.values().stream()
            .filter(factory -> StringUtils.equalsIgnoreCase(factory.getSupportedType().getFileExtension(), extension))
            .map(factory -> factory.getSupportedType()).findFirst();

    if (!typeO.isPresent()) {
        throw new SpongeException("Unsupported file extension '" + extension + "' for file '" + fileName + "' in knowledge base '"
                + scriptKnowledgeBase.getName() + "'");
    }

    return typeO.get();
}
 
Example 17
Project: gin   File: TestRunnerTest.java   View source code 6 votes vote down vote up
@Test
public void compile() {

    testRunner.ensureDirectory(testRunner.getTmpDir());
    testRunner.copySource(new SourceFile(exampleSourceFilename));
    testRunner.compile();

    // Should have created temp source file
    File origSource = new File(exampleSourceFilename);
    String tmpClassFilename = FilenameUtils.removeExtension(origSource.getName()) + ".class";
    String tmpTestClassFilename = FilenameUtils.removeExtension(origSource.getName()) + "Test.class";

    File tmpClassFile = new File(testRunner.getTmpDir(), tmpClassFilename);
    File tmpTestClassFile = new File(testRunner.getTmpDir(), tmpTestClassFilename);

    assertTrue(tmpClassFile.exists());
    assertTrue(tmpTestClassFile.exists());

}
 
Example 18
Project: cyberduck   File: RenameExistingFilter.java   View source code 6 votes vote down vote up
/**
 * Rename existing file on server if there is a conflict.
 */
@Override
public void apply(final Path file, final Local local, final TransferStatus status,
                  final ProgressListener listener) throws BackgroundException {
    // Rename existing file before putting new file in place
    if(status.isExists()) {
        Path rename;
        do {
            final String proposal = MessageFormat.format(PreferencesFactory.get().getProperty("queue.upload.file.rename.format"),
                    FilenameUtils.getBaseName(file.getName()),
                    UserDateFormatterFactory.get().getMediumFormat(System.currentTimeMillis(), false).replace(Path.DELIMITER, '-').replace(':', '-'),
                    StringUtils.isNotBlank(file.getExtension()) ? String.format(".%s", file.getExtension()) : StringUtils.EMPTY);
            rename = new Path(file.getParent(), proposal, file.getType());
        }
        while(find.find(rename));
        if(log.isInfoEnabled()) {
            log.info(String.format("Rename existing file %s to %s", file, rename));
        }
        move.move(file, rename, new TransferStatus().exists(false), new Delete.DisabledCallback(), new DisabledConnectionCallback());
        if(log.isDebugEnabled()) {
            log.debug(String.format("Clear exist flag for file %s", file));
        }
        status.setExists(false);
    }
    super.apply(file, local, status, listener);
}
 
Example 19
Project: Android-FileBrowser-FilePicker   File: FileNavigator.java   View source code 6 votes vote down vote up
public File [] getFilesInCurrentDirectory() {
   if(mAllowedFileExtensionFilter!=null) {
       FilenameFilter fileNameFilter = new FilenameFilter() {
           @Override
           public boolean accept(File dir, String name) {
               String fileExtension = FilenameUtils.getExtension(name);
               if(mAllowedFileExtensionFilter.contains(fileExtension) || fileExtension.isEmpty() )
                   return true;
               else
                   return false;
           }
       };
       return mCurrentNode.listFiles(fileNameFilter);
   }
   return mCurrentNode.listFiles();
}
 
Example 20
Project: airsonic   File: CoverArtController.java   View source code 6 votes vote down vote up
/**
 * Returns an input stream to the image in the given file.  If the file is an audio file,
 * the embedded album art is returned. In addition returns the mime type
 */
private Pair<InputStream, String> getImageInputStreamWithType(File file) throws IOException {
    InputStream is;
    String mimeType;
    if (jaudiotaggerParser.isApplicable(file)) {
        LOG.trace("Using Jaudio Tagger for reading artwork from {}", file);
        MediaFile mediaFile = mediaFileService.getMediaFile(file);
        Artwork artwork;
        try {
            LOG.trace("Reading artwork from file {}", mediaFile);
            artwork = jaudiotaggerParser.getArtwork(mediaFile);
        } catch (Exception e) {
            LOG.debug("Could not read artwork from file {}", mediaFile);
            throw new RuntimeException(e);
        }
        is = new ByteArrayInputStream(artwork.getBinaryData());
        mimeType = artwork.getMimeType();
    } else {
        is =  new FileInputStream(file);
        mimeType = StringUtil.getMimeType(FilenameUtils.getExtension(file.getName()));
    }
    return Pair.of(is, mimeType);
}
 
Example 21
Project: DIA-Umpire-Maven   File: TargetMatchScoring.java   View source code 6 votes vote down vote up
public static TargetMatchScoring LibraryMatchReadJS(String Filename, String LibID) throws FileNotFoundException {

        if (!new File(FilenameUtils.getFullPath(Filename) + FilenameUtils.getBaseName(Filename) + "_" + LibID + "_LibMatch.serFS").exists()) {
            return null;
        }
        TargetMatchScoring match = null;
        try {
            Logger.getRootLogger().info("Loading Target library match results to file:" + FilenameUtils.getFullPath(Filename) + FilenameUtils.getBaseName(Filename) + "_" + LibID + "_LibMatch.ser...");
            FileInputStream fileIn = new FileInputStream(FilenameUtils.getFullPath(Filename) + FilenameUtils.getBaseName(Filename) + "_" + LibID + "_LibMatch.ser");
            ObjectInputStream in = new ObjectInputStream(fileIn);
            match = (TargetMatchScoring) in.readObject();
            in.close();
            fileIn.close();
        } catch (Exception ex) {
            Logger.getRootLogger().error(ExceptionUtils.getStackTrace(ex));
            return null;
        }
        return match;
    }
 
Example 22
Project: airsonic   File: JaudiotaggerParser.java   View source code 6 votes vote down vote up
/**
 * Returns whether this parser is applicable to the given file.
 *
 * @param file The music file in question.
 * @return Whether this parser is applicable to the given file.
 */
@Override
public boolean isApplicable(File file) {
    if (!file.isFile()) {
        return false;
    }

    String format = FilenameUtils.getExtension(file.getName()).toLowerCase();

    return format.equals("mp3") ||
            format.equals("m4a") ||
            format.equals("aac") ||
            format.equals("ogg") ||
            format.equals("flac") ||
            format.equals("wav") ||
            format.equals("mpc") ||
            format.equals("mp+") ||
            format.equals("ape") ||
            format.equals("wma");
}
 
Example 23
Project: java-natives   File: NativeLibrary.java   View source code 5 votes vote down vote up
private File extractNativeLibraries(final File nativesDirectory, final String libraryPath) {
  final URL libraryUrl = Thread.currentThread().getContextClassLoader().getResource(libraryPath);
  if (libraryUrl == null) {
    throw new IllegalArgumentException(
        String.format("Unable to find native binary %s for library %s", libraryPath, key));
  }
  final String libraryName;
  libraryName = FilenameUtils.getName(libraryPath);
  final File libraryFile = new File(nativesDirectory, libraryName);
  libraryFile.getParentFile().mkdirs();
  try {
    final URLConnection urlConnection = libraryUrl.openConnection();
    try (final InputStream inputStream = urlConnection.getInputStream()) {
      try (final OutputStream outputStream =
          new BufferedOutputStream(new FileOutputStream(libraryFile))) {
        IOUtils.copy(inputStream, outputStream);
      }
    }
  } catch (final Exception exception) {
    throw new RuntimeException(exception);
  }
  if (deleteOnExit) {
    libraryFile.deleteOnExit();
  }
  // TODO make accessible for linux and mac
  return libraryFile;
}
 
Example 24
Project: Reer   File: PCHUtils.java   View source code 5 votes vote down vote up
public static <T extends NativeCompileSpec> File generatePCHSourceFile(T original, File sourceFile) {
    File generatedSourceDir = new File(original.getTempDir(), "pchGenerated");
    generatedSourceDir.mkdirs();
    File generatedSource = new File(generatedSourceDir, FilenameUtils.removeExtension(sourceFile.getName()).concat(getSourceFileExtension(original.getClass())));
    File headerFileCopy = new File(generatedSourceDir, sourceFile.getName());
    try {
        FileUtils.copyFile(sourceFile, headerFileCopy);
        FileUtils.writeStringToFile(generatedSource, "#include \"".concat(headerFileCopy.getName()).concat("\""));
        return generatedSource;
    } catch (IOException e) {
        throw new UncheckedIOException(e);
    }
}
 
Example 25
Project: Cognizant-Intelligent-Test-Scripter   File: MIME.java   View source code 5 votes vote down vote up
public static String getType(String fileName) {
    try {
        return getTypeFor(FilenameUtils.getExtension(fileName));
    } catch (Exception ex) {
        LOG.log(Level.SEVERE, ex.getMessage(), ex);
    }
    return null;
}
 
Example 26
Project: DIA-Umpire-Maven   File: RTMappingExtLib.java   View source code 5 votes vote down vote up
public void GenerateModel() throws IOException {

        XYPointCollection points = new XYPointCollection();
        XYSeries series = new XYSeries("Peptide ions");
        XYSeriesCollection xySeriesCollection = new XYSeriesCollection();

        FileWriter writer = new FileWriter(FilenameUtils.getFullPath(TargetLCMS.mzXMLFileName) + "/" + FilenameUtils.getBaseName(TargetLCMS.mzXMLFileName) + "_" + libManager.LibID + "_RTMapPoints.txt");

        for (String pepkey : libManager.PeptideFragmentLib.keySet()) {
            if (TargetLCMS.GetPepIonList().containsKey(pepkey)) {
                PepFragmentLib peplib = libManager.GetFragmentLib(pepkey);
                for (float rt : peplib.RetentionTime) {
                    float y = TargetLCMS.GetPepIonList().get(pepkey).GetRT();
                    points.AddPoint(rt, y);
                    series.add(new XYDataItem(rt, y));
                    writer.write(rt + "\t" + y + "\n");
                }
            }
        }
        writer.close();
        regression = new PiecewiseRegression(parameter.MaxCurveRTRange, parameter.MaxCurveRTRange);
        regression.SetData(points);
        float R2 = regression.GetR2();
        Logger.getRootLogger().info("Retention time prediction model:(" + FilenameUtils.getBaseName(TargetLCMS.mzXMLFileName) + "..R2=" + R2 + "(No. of commonly identified peptide ions=" + points.PointCount() + ")");

        GenerateRTMapPNG(xySeriesCollection, series, R2);
    }
 
Example 27
Project: GitHub   File: Jsonschema2Pojo.java   View source code 5 votes vote down vote up
private static String getNodeName(URL file, GenerationConfig config) {
    try {
        String fileName = FilenameUtils.getName(URLDecoder.decode(file.toString(), "UTF-8"));
        String[] extensions = config.getFileExtensions();
        boolean extensionRemoved = false;
        for (int i = 0; i < extensions.length; i++) {
            String extension = extensions[i];
            if (extension.length() == 0) {
                continue;
            }
            if (!extension.startsWith(".")) {
                extension = "." + extension;
            }
            if (fileName.endsWith(extension)) {
                fileName = removeEnd(fileName, extension);
                extensionRemoved = true;
                break;
            }
        }
        if (!extensionRemoved) {
            fileName = FilenameUtils.getBaseName(fileName);
        }
        return fileName;
    } catch (UnsupportedEncodingException e) {
        throw new IllegalArgumentException(String.format("Unable to generate node name from URL: %s", file.toString()), e);
    }

}
 
Example 28
Project: incubator-servicecomb-java-chassis   File: SchemaLoader.java   View source code 5 votes vote down vote up
/**
 * resource的路径格式,至少是以这个形式结尾:schemaId.yaml
 */
public SchemaMeta registerSchema(String microserviceName, Resource resource) {
  try {
    String schemaId = FilenameUtils.getBaseName(resource.getFilename());

    String swaggerContent = IOUtils.toString(resource.getURL());
    SchemaMeta schemaMeta = registerSchema(microserviceName, schemaId, swaggerContent);

    return schemaMeta;
  } catch (Throwable e) {
    throw new Error(e);
  }
}
 
Example 29
Project: DIA-Umpire-Maven   File: TargetMatchScoring.java   View source code 5 votes vote down vote up
public boolean LibraryMatchWrite() throws FileNotFoundException {
    try {
        Logger.getRootLogger().info("Writing Target match results to file:" + FilenameUtils.getFullPath(Filename) + FilenameUtils.getBaseName(Filename) + "_" + LibID + "_LibMatch.serFS...");
        FileOutputStream fout = new FileOutputStream(FilenameUtils.getFullPath(Filename) + FilenameUtils.getBaseName(Filename) + "_" + LibID + "_LibMatch.serFS", false);
        FSTObjectOutput out = new FSTObjectOutput(fout);
        out.writeObject(this);
        out.close();
        fout.close();
    } catch (Exception ex) {
        Logger.getRootLogger().error(ExceptionUtils.getStackTrace(ex));
        return false;
    }
    return true;
}
 
Example 30
Project: onprom   File: OnpromToolkit.java   View source code 5 votes vote down vote up
private Void saveAll() {
  File selectedFile = IOUtility.selectFileToSave(FileType.ONTOLOGY);
  if (selectedFile != null) {
    String fileName = FilenameUtils.removeExtension(selectedFile.getAbsolutePath());
    for (int i = 0; i < objects.getCount(); i++) {
      TreeNode node = objects.getNode(i);
      saveObject(fileName, node.getType(), node.getUserObject());
    }
  }
  return null;
}
 
Example 31
Project: DIA-Umpire-Maven   File: InstrumentParameter.java   View source code 5 votes vote down vote up
public void WriteParamSerialization(String mzXMLFileName) {
    try {
        Logger.getRootLogger().info("Writing parameter to file:" + FilenameUtils.getFullPath(mzXMLFileName) + FilenameUtils.getBaseName(mzXMLFileName) + "_params.ser...");
        FileOutputStream fout = new FileOutputStream(FilenameUtils.getFullPath(mzXMLFileName) + FilenameUtils.getBaseName(mzXMLFileName) + "_params.ser", false);
        ObjectOutputStream oos = new ObjectOutputStream(fout);
        oos.writeObject(this);
        oos.close();
        fout.close();
    } catch (Exception ex) {
        Logger.getRootLogger().error(ExceptionUtils.getStackTrace(ex));
    }
}
 
Example 32
Project: DIA-Umpire-Maven   File: LCMSPeakMS1.java   View source code 5 votes vote down vote up
public void AssignMappedPepQuant() throws SQLException, IOException {
    if (IDsummary == null || IDsummary.GetMappedPepIonList().isEmpty()) {
        return;
    }
    if (!FilenameUtils.getBaseName(IDsummary.mzXMLFileName).equals(FilenameUtils.getBaseName(ScanCollectionName))) {
        return;
    }
    Logger.getRootLogger().info("Assigning peak cluster to mapped peptide IDs......");
    for (PepIonID pepIonID : IDsummary.GetMappedPepIonList().values()) {
        pepIonID.CreateQuantInstance(MaxNoPeakCluster);

        ArrayList<PeakCluster> clusterList = FindAllPeakClustersForMappedPep(pepIonID);

        if (!clusterList.isEmpty()) {
            PeakCluster targetCluster = null;
            float Score = 0f;

            for (int i = 0; i < clusterList.size(); i++) {
                PeakCluster cluster = clusterList.get(i);
                if ("".equals(cluster.AssignedPepIon)) {
                    Score = cluster.PeakHeight[0] * cluster.MS1Score;
                    if (targetCluster == null || clusterList.get(i).MS1Score > Score) {
                        targetCluster = cluster;
                        Score = cluster.MS1Score;
                    }
                }
            }
            if (targetCluster != null) {
                pepIonID.PeakArea = targetCluster.PeakArea;
                pepIonID.PeakHeight = targetCluster.PeakHeight;
                pepIonID.MS1PeakClusters.add(targetCluster);
                pepIonID.PeakClusterScore = targetCluster.MS1Score;
                pepIonID.PeakRT = targetCluster.PeakHeightRT[0];
                pepIonID.ObservedMz = targetCluster.mz[0];
                targetCluster.AssignedPepIon = pepIonID.GetKey();
            }
        }
    }
}
 
Example 33
Project: ZooKeeper   File: QuorumKerberosHostBasedAuthTest.java   View source code 5 votes vote down vote up
private static void setupJaasConfigEntries(String hostServerPrincipal,
        String hostLearnerPrincipal, String hostNamedLearnerPrincipal) {
    String keytabFilePath = FilenameUtils.normalize(KerberosTestUtils.getKeytabFile(), true);
    String jaasEntries = new String(""
            + "QuorumServer {\n"
            + "       com.sun.security.auth.module.Krb5LoginModule required\n"
            + "       useKeyTab=true\n"
            + "       keyTab=\"" + keytabFilePath + "\"\n"
            + "       storeKey=true\n"
            + "       useTicketCache=false\n"
            + "       debug=true\n"
            + "       doNotPrompt=true\n"
            + "       refreshKrb5Config=true\n"
            + "       principal=\"" + KerberosTestUtils.replaceHostPattern(hostServerPrincipal) + "\";\n" + "};\n"
            + "QuorumLearner {\n"
            + "       com.sun.security.auth.module.Krb5LoginModule required\n"
            + "       useKeyTab=true\n"
            + "       keyTab=\"" + keytabFilePath + "\"\n"
            + "       storeKey=true\n"
            + "       useTicketCache=false\n"
            + "       debug=true\n"
            + "       doNotPrompt=true\n"
            + "       refreshKrb5Config=true\n"
            + "       isInitiator=true\n"
            + "       principal=\"" + KerberosTestUtils.replaceHostPattern(hostLearnerPrincipal) + "\";\n" + "};\n"
            + "QuorumLearnerMyHost {\n"
            + "       com.sun.security.auth.module.Krb5LoginModule required\n"
            + "       useKeyTab=true\n"
            + "       keyTab=\"" + keytabFilePath + "\"\n"
            + "       storeKey=true\n"
            + "       useTicketCache=false\n"
            + "       debug=true\n"
            + "       doNotPrompt=true\n"
            + "       refreshKrb5Config=true\n"
            + "       isInitiator=true\n"
            + "       principal=\"" + hostNamedLearnerPrincipal + "\";\n" + "};\n");
    setupJaasConfig(jaasEntries);
}
 
Example 34
Project: WurmMapGen   File: FileGen.java   View source code 5 votes vote down vote up
/**
 * Generates the file
 */
public void generateFile() throws IOException {
	// Generate data
	String data = generateData();
	if (data == null) return;
	
	// Write data to file
	Logger.details("Writing " + filePath);
	FileWriter writer = new FileWriter(filePath, false);
	writer.write(data);
	writer.close();
	
	Logger.ok("Created " + FilenameUtils.getName(filePath));
}
 
Example 35
Project: couchmove   File: FileUtils.java   View source code 5 votes vote down vote up
/**
 * Get a path Stream to iterate over all regular files matching extensions in the directory
 *
 * @param directoryPath the path to the directory
 * @param extensions    The extensions of the files to iterate over
 * @return a new Stream object
 */
private static Stream<Path> directoryStream(@NotNull Path directoryPath, String... extensions) {
    try {
        return StreamSupport.stream(Files.newDirectoryStream(directoryPath).spliterator(), false)
                .filter(Files::isRegularFile)
                .filter(path -> Arrays.stream(extensions)
                        .anyMatch(extension -> FilenameUtils
                                .getExtension(path.getFileName().toString()).toLowerCase()
                                .equals(extension.toLowerCase())));
    } catch (IOException e) {
        throw new CouchmoveException("Unable to read directory '" + directoryPath + "'", e);
    }
}
 
Example 36
Project: Open_Source_ECOA_Toolset_AS5   File: NodePropertySource.java   View source code 5 votes vote down vote up
private String[] getComponentImpl() {
	ArrayList<String> ret = new ArrayList<String>();
	ret.add("");
	ArrayList<String> cDef = new PluginUtil().getResourcesWithExtension("cimpl", node.getContainerName());
	for (String str : cDef) {
		String name = FilenameUtils.getBaseName(str);
		ret.add(name);
	}
	return ret.toArray(new String[0]);
}
 
Example 37
Project: cloud-language-servers-container   File: WSSynchronization.java   View source code 5 votes vote down vote up
/**
 * @see HttpServlet#doPut(HttpServletRequest request, HttpServletResponse response)
 */
protected void doPost(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException {
	// Check if it is LSP registration
	String lspReg = request.getHeader("Register-lsp");
	if ( lspReg != null ) {
		handleLSPDest(Boolean.parseBoolean(lspReg), request.getReader());
		return;
	}

	// Otherwise process data passed from DI
	if( !checkSync() ) {
		response.setStatus(HttpServletResponse.SC_NO_CONTENT);
		return;
	}
	String artifactRelPath = request.getRequestURI().substring(request.getServletPath().length() + 1);
	String artifactPath = this.saveDir + artifactRelPath;

	File destination = new File(FilenameUtils.normalize(artifactPath));
	// Expected: one part containing zip
	try{
		Part part = request.getParts().iterator().next();

		WSChangeObserver changeObserver = new WSChangeObserver(ChangeType.CHANGE_UPDATED, lspDestPath);
		if (destination.exists() && !destination.isDirectory() && extract(part.getInputStream(), changeObserver)) {
			changeObserver.notifyLSP();
			response.setContentType("application/json");
			response.getWriter().append(String.format("{ \"updated\": \"%s\"}", artifactRelPath));
			response.setStatus(HttpServletResponse.SC_OK);
		} else {
			response.setStatus(HttpServletResponse.SC_INTERNAL_SERVER_ERROR);
		}
	} catch (NoSuchElementException ePart) {
		response.setStatus(HttpServletResponse.SC_NOT_MODIFIED);
	}
}
 
Example 38
Project: JAddOn   File: JUtils.java   View source code 5 votes vote down vote up
public static String[] getNamesWithOutExtensionOufOfFiles(File[] files) {
    String[] ausgabe = new String[files.length];
    int i = 0;
    for(File f : files) {
        ausgabe[i] = FilenameUtils.getBaseName(f.getName());
        i++;
    }
    return ausgabe;
}
 
Example 39
Project: cyberduck   File: QloudsonicVoucherFinder.java   View source code 5 votes vote down vote up
public QloudsonicVoucherFinder() {
    super(LocalFactory.get(
            PreferencesFactory.get().getProperty("application.support.path")), new Filter<Local>() {
        @Override
        public boolean accept(final Local file) {
            return "qloudsonicvoucher".equals(FilenameUtils.getExtension(file.getName()));
        }

        @Override
        public Pattern toPattern() {
            return Pattern.compile("qloudsonicvoucher");
        }
    });
}
 
Example 40
Project: course-examples   File: Photo.java   View source code 5 votes vote down vote up
/**
 * Constructor
 *
 * @param photoURI the URI of the photo file.
 */
public Photo(URI photoURI) throws FileNotFoundException {
    file = new File(photoURI);
    String filePath = file.getAbsolutePath();
    Image img = buildImage();

    baseName = FilenameUtils.getBaseName(filePath);
    format = FilenameUtils.getExtension(filePath);
    height = img.getHeight();
    width = img.getWidth();
}