org.seqdoop.hadoop_bam.util.NIOFileUtil Maven / Gradle / Ivy

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A Java library for the manipulation of files in common bioinformatics formats using the Hadoop MapReduce framework.
There is a newer version: 7.10.0
package org.seqdoop.hadoop_bam.util;

import java.io.IOException;
import java.io.OutputStream;
import java.net.URI;
import java.nio.file.FileSystemNotFoundException;
import java.nio.file.FileSystems;
import java.nio.file.FileVisitResult;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.PathMatcher;
import java.nio.file.Paths;
import java.nio.file.SimpleFileVisitor;
import java.nio.file.attribute.BasicFileAttributes;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.stream.Collectors;

public class NIOFileUtil {
  private NIOFileUtil() {
  }

  static final String PARTS_GLOB = "glob:**/part-[mr]-[0-9][0-9][0-9][0-9][0-9]*";

  /**
   * Convert the given path {@link URI} to a {@link Path} object.
   * @param uri the path to convert
   * @return a {@link Path} object
   */
  public static Path asPath(URI uri) {
    try {
      return Paths.get(uri);
    } catch (FileSystemNotFoundException e) {
      ClassLoader cl = Thread.currentThread().getContextClassLoader();
      if (cl == null) {
        throw e;
      }
      try {
        return FileSystems.newFileSystem(uri, new HashMap<>(), cl).provider().getPath(uri);
      } catch (IOException ex) {
        throw new RuntimeException("Cannot create filesystem for " + uri, ex);
      }
    }
  }

  /**
   * Convert the given path string to a {@link Path} object.
   * @param path the path to convert
   * @return a {@link Path} object
   */
  public static Path asPath(String path) {
    URI uri = URI.create(path);
    return uri.getScheme() == null ? Paths.get(path) : asPath(uri);
  }

  /**
   * Delete the given directory and all of its contents if non-empty.
   * @param directory the directory to delete
   * @throws IOException
   */
  static void deleteRecursive(Path directory) throws IOException {
    Files.walkFileTree(directory, new SimpleFileVisitor() {
      @Override
      public FileVisitResult visitFile(Path file, BasicFileAttributes attrs) throws IOException {
        Files.delete(file);
        return FileVisitResult.CONTINUE;
      }
      @Override
      public FileVisitResult postVisitDirectory(Path dir, IOException exc) throws IOException {
        Files.deleteIfExists(dir);
        return FileVisitResult.CONTINUE;
      }
    });
  }

  /**
   * Returns all the files in a directory that match the given pattern, and that don't
   * have the given extension.
   * @param directory the directory to look for files in, subdirectories are not
   *                  considered
   * @param syntaxAndPattern the syntax and pattern to use for matching (see
   * {@link java.nio.file.FileSystem#getPathMatcher}
   * @param excludesExt the extension to exclude, or null to exclude nothing
   * @return a list of files, sorted by name
   * @throws IOException
   */
  static List getFilesMatching(Path directory,
      String syntaxAndPattern, String excludesExt) throws IOException {
    PathMatcher matcher = directory.getFileSystem().getPathMatcher(syntaxAndPattern);
    List parts = Files.walk(directory)
        .filter(matcher::matches)
        .filter(path -> excludesExt == null || !path.toString().endsWith(excludesExt))
        .collect(Collectors.toList());
    Collections.sort(parts);
    return parts;
  }

  /**
   * Merge the given part files in order into an output stream.
   * @param parts the part files to merge
   * @param out the stream to write each file into, in order
   * @throws IOException
   */
  static void mergeInto(List parts, OutputStream out)
      throws IOException {
    for (final Path part : parts) {
      Files.copy(part, out);
    }
    for (final Path part : parts) {
      Files.delete(part);
    }
  }
}