Java Code Examples for java.io.File#getName()

private static void zipDir(File dir, String relativePath, ZipOutputStream zos,
                           boolean start) throws IOException {
  String[] dirList = dir.list();
  for (String aDirList : dirList) {
    File f = new File(dir, aDirList);
    if (!f.isHidden()) {
      if (f.isDirectory()) {
        if (!start) {
          ZipEntry dirEntry = new ZipEntry(relativePath + f.getName() + "/");
          zos.putNextEntry(dirEntry);
          zos.closeEntry();
        }
        String filePath = f.getPath();
        File file = new File(filePath);
        zipDir(file, relativePath + f.getName() + "/", zos, false);
      }
      else {
        String path = relativePath + f.getName();
        if (!path.equals(JarFile.MANIFEST_NAME)) {
          ZipEntry anEntry = new ZipEntry(path);
          copyToZipStream(f, anEntry, zos);
        }
      }
    }
  }
}
 

private void fallbackToCopyFilesDirectly() {
	File[] files = new File(sSourceDir).listFiles();
	rdProUI.println(LogLevel.debug, "Fall back to copy files directly for dir:" + sSourceDir );
	if (files!=null) {
		for (File childFile : files) {

			if (RunTimeProperties.instance.isStopThreads()) {
				rdProUI.println("[PackageSmallFilesThread]\n" + Thread.currentThread().getName() + "is stopped.");
				return;
			}


			String newDestFile = sTargetDir + File.separator + childFile.getName();
			File targetFile = new File(newDestFile);
			if (!targetFile.exists() || FileUtils.overrideTargetFile(childFile, targetFile)) {
				CopyFileThread t = new CopyFileThread(rdProUI
						, childFile, targetFile, null, statistics);
				fileCopyWorkersPool.addTask(t);
			} else {
					rdProUI.println(LogLevel.debug, String.format("\tFile %s exists on the target dir, skipped. ", newDestFile));
			}
		}

	}

}
 

@Test
public void testSynchronizeAddSubFileFromBDeleteFromA() throws NoSessionException, NoPeerConnectionException,
		IOException, IllegalArgumentException, IllegalArgumentException, GetFailedException {
	logger.info("Upload a new file 'folder1/subfolder/file1FromB' from B.");
	File subFile1FromBAtB = FileTestUtil.createFileRandomContent("file1FromB", new Random().nextInt(MAX_NUM_CHUNKS) + 1,
			subFolderB);
	UseCaseTestUtil.uploadNewFile(nodeB, subFile1FromBAtB);

	logger.info("Wait till new file 'folder1/subfolder/file1FromB' gets synchronized with A.");
	File subFile1FromBAtA = new File(subFolderA, subFile1FromBAtB.getName());
	waitTillSynchronized(subFile1FromBAtA, true);
	compareFiles(subFile1FromBAtA, subFile1FromBAtB);
	checkIndex(subFile1FromBAtA, subFile1FromBAtB, false);

	logger.info("Delete file 'folder1/subfolder/file1FromB' from A.");
	UseCaseTestUtil.deleteFile(nodeA, subFile1FromBAtA);

	logger.info("Wait till deletion of file 'folder1/subfolder/file1FromB' gets synchronized with B.");
	waitTillSynchronized(subFile1FromBAtB, false);
	checkIndex(subFile1FromBAtA, subFile1FromBAtB, true);
}
 

@Test
public void testSynchronizeAddFolderFromBMoveToSubfolderAtB() throws NoSessionException, NoPeerConnectionException,
		IOException, IllegalArgumentException, IllegalArgumentException, GetFailedException {
	logger.info("Upload a new folder 'sharedfolder/subfolder2FromB' from B.");
	File folderFromBAtB = new File(sharedFolderB, "subfolder2FromB");
	folderFromBAtB.mkdir();
	UseCaseTestUtil.uploadNewFile(network.get(1), folderFromBAtB);

	logger.info("Wait till new folder 'sharedFolder/subfolder2FromB' gets synchronized with A.");
	File folderFromBAtA = new File(sharedFolderB, folderFromBAtB.getName());
	waitTillSynchronized(folderFromBAtA, true);

	logger.info("Move folder 'subfolder2FromB' at B into shared subfolder 'sharedfolder/subfolder1'.");
	File movedFolderFromBAtB = new File(subFolder1AtB, folderFromBAtB.getName());
	FileUtils.moveDirectory(folderFromBAtB, movedFolderFromBAtB);
	UseCaseTestUtil.moveFile(network.get(1), folderFromBAtB, movedFolderFromBAtB);

	logger.info("Wait till moved folder 'subfolderFromB' gets synchronized with A.");
	File movedFolderFromBAtA = new File(subFolder1AtA, folderFromBAtA.getName());
	waitTillSynchronized(movedFolderFromBAtA, true);
	compareFiles(movedFolderFromBAtA, movedFolderFromBAtB);
	checkIndex(folderFromBAtA, folderFromBAtB, movedFolderFromBAtA, movedFolderFromBAtB);
}
 

public static void writeCatch(final File file, final String content) {
    String name = file.getName();
    final Lock lock;

    // Create lock for each file if there isn't already one.
    if (locks.containsKey(name)) {
        lock = locks.get(name);
    } else {
        ReadWriteLock rwl = new ReentrantReadWriteLock();
        lock = rwl.writeLock();
        locks.put(name, lock);
    }
    lock.lock();
    try {
        file.createNewFile();
        Files.write(content, file, StandardCharsets.UTF_8);
    } catch (IOException e) {
        IridiumSkyblock.getInstance().sendErrorMessage(e);
    } finally {
        lock.unlock();
    }
}
 

@Test
public void testSynchronizeAddSubFileAtAMoveToSubfolderAtA() throws NoSessionException, NoPeerConnectionException,
		IOException, IllegalArgumentException, IllegalArgumentException, GetFailedException {
	File fileFromAAtA = FileTestUtil.createFileRandomContent("subfile3FromA", new Random().nextInt(MAX_NUM_CHUNKS) + 1,
			subFolder1A);
	logger.info("Upload a new file '{}' at A.", fileFromAAtA.getName());
	UseCaseTestUtil.uploadNewFile(nodeA, fileFromAAtA);

	logger.info("Wait till new file '{}' gets synchronized with B.", fileFromAAtA.getName());
	File fileFromAAtB = new File(subFolder1B, fileFromAAtA.getName());
	waitTillSynchronized(fileFromAAtB, true);

	File movedFileFromAAtA = new File(subFolder2A, fileFromAAtA.getName());
	logger.info("Move file '{}' at A into shared subfolder '{}'.", fileFromAAtA.getName(), subFolder2A);
	FileUtils.moveFile(fileFromAAtA, movedFileFromAAtA);
	UseCaseTestUtil.moveFile(nodeA, fileFromAAtA, movedFileFromAAtA);

	logger.info("Wait till new moved file '{}' gets synchronized with B.", fileFromAAtA.getName());
	File movedFileFromAAtB = new File(subFolder2B, fileFromAAtA.getName());
	waitTillSynchronized(movedFileFromAAtB, true);
	compareFiles(movedFileFromAAtA, movedFileFromAAtB);
	checkIndexAfterMoving(fileFromAAtA, fileFromAAtB, movedFileFromAAtA, movedFileFromAAtB);
}
 

private void createJar(final File jarFile, final File[] files) throws IOException
{
	final Manifest manifest = new Manifest();
	final Attributes attributes = manifest.getMainAttributes();
	attributes.putValue("Manifest-Version", "1.0");
	attributes.putValue("Created-By", "RepoGen 1.0.0");
	final FileOutputStream fos = new FileOutputStream(jarFile);
	final JarOutputStream jos = new JarOutputStream(fos, manifest);
	for (final File file : files)
	{
		final ZipEntry entry = new ZipEntry(file.getName());
		jos.putNextEntry(entry);
		final FileInputStream fis = new FileInputStream(file);
		pipeStream(fis, jos);
		fis.close();
	}
	jos.close();
}
 

public static byte[] getBytesFromFile(String fileName) throws IOException {
  File file = new File(fileName);
  
  java.io.InputStream is = new FileInputStream(file);

   // Get the size of the file
   long length = file.length();

   // Create the byte array to hold the data
   byte[] bytes = new byte[(int)length];

   // Read in the bytes
   int offset = 0;
   int numRead = 0;
   while (offset < bytes.length
          && (numRead=is.read(bytes, offset, bytes.length-offset)) >= 0) {
       offset += numRead;
   }

   // Ensure all the bytes have been read in
   if (offset < bytes.length) {
       throw new IOException("Could not completely read file "+file.getName());
   }
  
   is.close();
   return bytes;
}
 

public WZFile(File wzfile, boolean provideImages) throws IOException {
    this.wzfile = wzfile;
    lea = new GenericLittleEndianAccessor(new InputStreamByteStream(new BufferedInputStream(new FileInputStream(wzfile))));
    RandomAccessFile raf = new RandomAccessFile(wzfile, "r");
    slea = new GenericSeekableLittleEndianAccessor(new RandomAccessByteStream(raf));
    root = new WZDirectoryEntry(wzfile.getName(), 0, 0, null);
    this.provideImages = provideImages;
    load();
}
 

/**
 * Returns the path at which to output map file(s) based on the path at which
 * the JS binary will be placed.
 *
 * @return The path in which to place the generated map file(s).
 */
private String getMapPath(String outputFile) {
  String basePath = "";

  if (outputFile.equals("")) {
    // If we have a js_module_binary rule, output the maps
    // at modulename_props_map.out, etc.
    if (!config.moduleOutputPathPrefix.equals("")) {
      basePath = config.moduleOutputPathPrefix;
    } else {
      basePath = "jscompiler";
    }
  } else {
    // Get the path of the output file.
    File file = new File(outputFile);

    String outputFileName = file.getName();

    // Strip the .js from the name.
    if (outputFileName.endsWith(".js")) {
      outputFileName =
          outputFileName.substring(0, outputFileName.length() - 3);
    }

    basePath = file.getParent() + File.separatorChar + outputFileName;
  }

  return basePath;
}
 

/**
 * Adds a upload file section to the request
 *
 * @param fieldName name attribute in <input type="file" name="..." />
 * @param uploadFile a File to be uploaded
 * @throws IOException
 */
public void addFilePart(String fieldName, File uploadFile)
        throws IOException {
    String fileName = uploadFile.getName();
    writer.append("--" + boundary).append(LINE_FEED);
    writer.append(
            "Content-Disposition: form-data; name=\"" + fieldName
            + "\"; filename=\"" + fileName + "\"")
            .append(LINE_FEED);
    writer.append(
            "Content-Type: "
            + URLConnection.guessContentTypeFromName(fileName))
            .append(LINE_FEED);
    writer.append("Content-Transfer-Encoding: binary").append(LINE_FEED);
    writer.append(LINE_FEED);
    writer.flush();

    FileInputStream inputStream = new FileInputStream(uploadFile);
    byte[] buffer = new byte[4096];
    int bytesRead = -1;
    while ((bytesRead = inputStream.read(buffer)) != -1) {
        outputStream.write(buffer, 0, bytesRead);
    }
    outputStream.flush();
    inputStream.close();

    writer.append(LINE_FEED);
    writer.flush();
}
 

/**
 * Submit feature-based molecular networking (FBMN) job to GNPS
 * 
 * @param file
 * @param param
 * @return
 */
public static String submitFbmnJob(File file, GnpsFbmnSubmitParameters param) throws IOException {
  // optional
  boolean useMeta = param.getParameter(GnpsFbmnSubmitParameters.META_FILE).getValue();
  boolean openWebsite = param.getParameter(GnpsFbmnSubmitParameters.OPEN_WEBSITE).getValue();
  String presets = param.getParameter(GnpsFbmnSubmitParameters.PRESETS).getValue().toString();
  String title = param.getParameter(GnpsFbmnSubmitParameters.JOB_TITLE).getValue();
  String email = param.getParameter(GnpsFbmnSubmitParameters.EMAIL).getValue();
  String username = param.getParameter(GnpsFbmnSubmitParameters.USER).getValue();
  String password = param.getParameter(GnpsFbmnSubmitParameters.PASSWORD).getValue();
  //
  File folder = file.getParentFile();
  String name = file.getName();
  // all file paths
  File mgf = FileAndPathUtil.getRealFilePath(folder, name, "mgf");
  File quan = FileAndPathUtil.getRealFilePath(folder, name + "_quant", "csv");

  // NEEDED files
  if (mgf.exists() && quan.exists()) {
    File meta = !useMeta ? null
        : param.getParameter(GnpsFbmnSubmitParameters.META_FILE).getEmbeddedParameter()
            .getValue();

    return submitFbmnJob(mgf, quan, meta, null, title, email, username, password, presets,
        openWebsite);
  } else
    return "";
}
 

/**
 * Process in a custom way when there is only one file result
 * 
 * @param d the parent payload
 * @param theData the bytes to process
 * @param f the file the data comes from
 * @return 0 when it works
 */
protected int processSingleChild(IBaseDataObject d, byte[] theData, File f) {
    String filename = f.getName();
    d.setData(theData);
    if (setTitleToFile) {
        d.putParameter("DocumentTitle", filename);
    }
    List<String> tmpForms = getFormsFromFile(f);
    for (int i = 0; i < tmpForms.size(); i++) {
        d.pushCurrentForm(tmpForms.get(i));
    }
    d.setFileType(SINGLE_CHILD_FILETYPE);
    return (0);
}
 

@Override
public void
refresh(
	TableCell 	cell,
	boolean 	sortOnlyRefresh)
{
	DownloadStubFile fileInfo = (DownloadStubFile) cell.getDataSource();

	String name;

	if ( fileInfo == null ){

		name = "";

	}else{

		File f = fileInfo.getFile();

		if ( show_full_path ){

			name = f.getAbsolutePath();
		}else{

			name = f.getName();
		}
	}

	cell.setText(name);
}
 

public static List<String> getSourcePaths(Context context) throws PackageManager.NameNotFoundException, IOException {
    ApplicationInfo applicationInfo = context.getPackageManager().getApplicationInfo(context.getPackageName(), 0);
    File sourceApk = new File(applicationInfo.sourceDir);
    File dexDir = new File(applicationInfo.dataDir, SECONDARY_FOLDER_NAME);

    List<String> sourcePaths = new ArrayList<String>();
    //default apk path
    sourcePaths.add(applicationInfo.sourceDir);

    String extractedFilePrefix = sourceApk.getName() + EXTRACTED_NAME_EXT;

    //get the dex number
    int totalDexNumber = getMultiDexPreferences(context).getInt(KEY_DEX_NUMBER, 1);

    //get other dexes
    for (int i = 2; i <= totalDexNumber; i++) {
        String fileName = extractedFilePrefix + i + EXTRACTED_SUFFIX;
        File extractedFile = new File(dexDir, fileName);
        if (extractedFile.isFile()) {
            sourcePaths.add(extractedFile.getAbsolutePath());
        } else {
            throw new IOException("Missing extracted secondary dex file '" +
                    extractedFile.getPath() + "'");
        }
    }

    return sourcePaths;
}
 

public static String getFileExtension( File file )
{
  String name = file.getName();
  return getFileExtension( name );
}
 

@Nonnull
public static String makeBackupFileName(@Nonnull final File orig, final int index) {
  final String name = orig.getName();
  return String.format(".%s.%d.abk", name, index);
}
 

public static File getExternalFilesBackupDir(File backupDir) {
    File attachmentsDir = FileHelper.getAttachmentDir(PalmApp.getContext());
    return new File(backupDir, attachmentsDir.getName());
}
 

/**
 * Constructor
 * @param pdvMainClass Parent class
 * @param proBAMFile ProBAM file
 * @param spectrumFileName Spectrum file name
 * @param spectrumFactory Spectrum factory
 * @param progressDialog Progress dialog
 * @throws SQLException
 * @throws ClassNotFoundException
 */
public ProBamFileImport(PDVMainClass pdvMainClass, File proBAMFile, String spectrumFileName, String spectrumFileType, SpectrumFactory spectrumFactory, ProgressDialogX progressDialog) throws SQLException, ClassNotFoundException {
    this.pdvMainClass = pdvMainClass;
    this.proBAMFile = proBAMFile;
    this.spectrumFactory = spectrumFactory;
    this.progressDialog = progressDialog;
    this.spectrumFileType = spectrumFileType;
    this.spectrumFileName = spectrumFileName;

    scoreName.add("Score");
    scoreName.add("FDR");
    scoreName.add("isAnnotated");
    scoreName.add("followingAA");
    scoreName.add("precedingAA");
    scoreName.add("enzyme");
    scoreName.add("peptideType");
    scoreName.add("geneMapNum");
    scoreName.add("peptideInt");
    scoreName.add("peptideMapNum");
    scoreName.add("missedCNum");
    scoreName.add("uniqueType");
    scoreName.add("originalSeq");
    scoreName.add("enzymeInSearch");
    scoreName.add("URI");

    String dbName = proBAMFile.getParentFile().getAbsolutePath()+"/"+ proBAMFile.getName()+".db";

    File dbFile = new File(dbName);
    File dbJournalFile = new File(dbName + "-journal");
    if (dbFile.isFile() && dbFile.exists()) {
        dbFile.delete();
    }
    if (dbJournalFile.isFile() && dbJournalFile.exists()) {
        dbJournalFile.delete();
    }

    sqLiteConnection = new SQLiteConnection(dbName);

    sqLiteConnection.setScoreNum(15);

    new Thread("DisplayThread") {
        @Override
        public void run() {
            try {
                parseProBAM();

                pdvMainClass.searchButton.setEnabled(true);
            } catch (Exception e) {
                progressDialog.setRunFinished();
                JOptionPane.showMessageDialog(
                        null, "Failed to parse proBAM file, please check your file.",
                        "Error Parsing File", JOptionPane.ERROR_MESSAGE);
                e.printStackTrace();
            }
        }
    }.start();
}
 

private static String extractFrameworkNameFrom(final File file) {
    final String fileName = file.getName();
    return fileName.substring(0, fileName.lastIndexOf(BRIDGESUPPORT_FILE_EXTENSION));
}