Example #1
0
    public void initialize(InputSplit genericSplit, TaskAttemptContext context) throws IOException {
      FileSplit split = (FileSplit) genericSplit;
      Configuration job = context.getConfiguration();
      m_Sb.setLength(0);
      m_Start = split.getStart();
      m_End = m_Start + split.getLength();
      final Path file = split.getPath();
      compressionCodecs = new CompressionCodecFactory(job);
      final CompressionCodec codec = compressionCodecs.getCodec(file);

      // open the file and seek to the m_Start of the split
      FileSystem fs = file.getFileSystem(job);
      //  getFileStatus fileStatus = fs.getFileStatus(split.getPath());
      //noinspection deprecation
      @SuppressWarnings(value = "deprecated")
      long length = fs.getLength(file);
      FSDataInputStream fileIn = fs.open(split.getPath());
      if (m_Start > 0) fileIn.seek(m_Start);
      if (codec != null) {
        CompressionInputStream inputStream = codec.createInputStream(fileIn);
        m_Input = new BufferedReader(new InputStreamReader(inputStream));
        m_End = length;
      } else {
        m_Input = new BufferedReader(new InputStreamReader(fileIn));
      }
      m_Current = m_Start;
      m_Key = split.getPath().getName();
    }
Example #2
0
  /**
   * Create a map-only Hadoop Job out of the passed in parameters.  Does not set the
   * Job name.
   *
   * @see #getCustomJobName(String, org.apache.hadoop.mapreduce.JobContext, Class, Class)
   */
  @SuppressWarnings("rawtypes")
	public static Job prepareJob(Path inputPath,
                                 Path outputPath,
                                 Class<? extends InputFormat> inputFormat,
                                 Class<? extends Mapper> mapper,
                                 Class<? extends Writable> mapperKey,
                                 Class<? extends Writable> mapperValue,
                                 Class<? extends OutputFormat> outputFormat, Configuration conf) throws IOException {

    //Job job = new Job(new Configuration(conf));
  	Job job = Job.getInstance(conf);
    Configuration jobConf = job.getConfiguration();

    if (mapper.equals(Mapper.class)) {
        throw new IllegalStateException("Can't figure out the user class jar file from mapper/reducer");
    }
    job.setJarByClass(mapper);

    job.setInputFormatClass(inputFormat);
    jobConf.set("mapred.input.dir", inputPath.toString());

    job.setMapperClass(mapper);
    job.setMapOutputKeyClass(mapperKey);
    job.setMapOutputValueClass(mapperValue);
    job.setOutputKeyClass(mapperKey);
    job.setOutputValueClass(mapperValue);
    jobConf.setBoolean("mapred.compress.map.output", true);
    job.setNumReduceTasks(0);

    job.setOutputFormatClass(outputFormat);
    jobConf.set("mapred.output.dir", outputPath.toString());

    return job;
  }
Example #3
0
  /**
   * Generate the list of files and make them into FileSplits. This needs to be copied to insert a
   * filter on acceptable data
   */
  @Override
  public List<InputSplit> getSplits(JobContext job) throws IOException {
    long minSize = Math.max(getFormatMinSplitSize(), getMinSplitSize(job));
    long maxSize = getMaxSplitSize(job);
    long desiredMappers =
        job.getConfiguration().getLong("org.systemsbiology.jxtandem.DesiredXMLInputMappers", 0);

    // generate splits
    List<InputSplit> splits = new ArrayList<InputSplit>();
    List<FileStatus> fileStatuses = listStatus(job);
    boolean forceNumberMappers = fileStatuses.size() == 1;
    for (FileStatus file : fileStatuses) {
      Path path = file.getPath();
      if (!isPathAcceptable(path)) // filter acceptable data
      continue;
      FileSystem fs = path.getFileSystem(job.getConfiguration());
      long length = file.getLen();
      BlockLocation[] blkLocations = fs.getFileBlockLocations(file, 0, length);
      if ((length != 0) && isSplitable(job, path)) {
        long blockSize = file.getBlockSize();
        // use desired mappers to force more splits
        if (forceNumberMappers && desiredMappers > 0)
          maxSize = Math.min(maxSize, (length / desiredMappers));

        long splitSize = computeSplitSize(blockSize, minSize, maxSize);

        long bytesRemaining = length;
        while (withinSlop(splitSize, bytesRemaining)) {
          int blkIndex = getBlockIndex(blkLocations, length - bytesRemaining);
          splits.add(
              new FileSplit(
                  path, length - bytesRemaining, splitSize, blkLocations[blkIndex].getHosts()));
          bytesRemaining -= splitSize;
        }

        if (bytesRemaining != 0) {
          splits.add(
              new FileSplit(
                  path,
                  length - bytesRemaining,
                  bytesRemaining,
                  blkLocations[blkLocations.length - 1].getHosts()));
        }
      } else if (length != 0) {
        splits.add(new FileSplit(path, 0, length, blkLocations[0].getHosts()));
      } else {
        // Create empty hosts array for zero length files
        splits.add(new FileSplit(path, 0, length, new String[0]));
      }
    }
    System.out.println("Total # of splits: " + splits.size());
    //     LOG.debug("Total # of splits: " + splits.size());
    return splits;
  }
Example #4
0
 public static void delete(Configuration conf, Iterable<Path> paths) throws IOException {
   if (conf == null) {
     conf = new Configuration();
   }
   for (Path path : paths) {
     FileSystem fs = path.getFileSystem(conf);
     if (fs.exists(path)) {
       log.info("Deleting {}", path);
       fs.delete(path, true);
     }
   }
 }
Example #5
0
 @Override
 protected boolean isSplitable(JobContext context, Path file) {
   String fname = file.getName().toLowerCase();
   //noinspection SimplifiableIfStatementf,RedundantIfStatement
   if (fname.endsWith(".gz")) return false;
   return true;
 }
Example #6
0
 public static void writeInt(int value, Path path, Configuration conf) throws IOException {
   FileSystem fs = FileSystem.get(path.toUri(), conf);
   FSDataOutputStream out = fs.create(path);
   try {
     out.writeInt(value);
   } finally {
     out.close();
   }
 }
Example #7
0
 public static int readInt(Path path, Configuration conf) throws IOException {
   FileSystem fs = FileSystem.get(path.toUri(), conf);
   //FileSystem fs = path.getFileSystem(conf);
   FSDataInputStream in = fs.open(path);
   try {
     return in.readInt();
   } finally {
     in.close();
   }
 }
Example #8
0
 protected boolean isPathAcceptable(final Path pPath1) {
   String path = pPath1.toString().toLowerCase();
   if (path.startsWith("part-r-")) return true;
   String extension = getExtension();
   if (extension != null && path.endsWith(extension.toLowerCase())) return true;
   if (extension != null && path.endsWith(extension.toLowerCase() + ".gz")) return true;
   //noinspection SimplifiableIfStatement,RedundantIfStatement
   if (extension == null) return true;
   return false;
 }
Example #9
0
 private static boolean writeChecksum(Path localPath, String checksum) {
   try {
     java.io.BufferedWriter writer =
         Files.newBufferedWriter(
             java.nio.file.Paths.get(localPath.toString() + ".crc"), Charset.forName("UTF-8"));
     writer.write(checksum);
     writer.flush();
     writer.close();
     return true;
   } catch (Exception e) {
     logger.warn("Unable to write CRC file!");
     return false;
   }
 }
 public static void recursePath(Configuration conf, Path path, Job job) {
   try {
     FileSystem fs = path.getFileSystem(conf);
     FileStatus[] fstats = fs.listStatus(path);
     if (fstats != null) {
       for (FileStatus f : fstats) {
         Path p = f.getPath();
         ;
         if (fs.isFile(p)) {
           // connection times out otherwise
           System.err.println("file:" + p.toString());
           FileInputFormat.addInputPath(job, p);
         } else {
           System.err.println("dir:" + p.toString());
           recursePath(conf, p, job);
         }
       }
     }
   } catch (IOException e) {
     // shouldn't be here
     throw new RuntimeException(e);
   }
 }
Example #11
0
 private static boolean checksumLocalTest(Path localPath, String checksum) {
   String crcPath = localPath.toString() + ".crc";
   if (Files.isReadable(java.nio.file.Paths.get(crcPath))) {
     try {
       List<String> lines =
           Files.readAllLines(java.nio.file.Paths.get(crcPath), Charset.forName("UTF-8"));
       for (String line : lines) {
         if (line.equals(checksum)) {
           return true;
         }
       }
     } catch (Exception e) {
       return false;
     }
   }
   return false;
 }
Example #12
0
 public static void cacheFiles(Path fileToCache, Configuration conf) {
   DistributedCache.setCacheFiles(new URI[]{fileToCache.toUri()}, conf);
 }
Example #13
0
 public static InputStream openStream(Path path, Configuration conf) throws IOException {
   FileSystem fs = FileSystem.get(path.toUri(), conf);
   return fs.open(path.makeQualified(fs));
 }
Example #14
0
  public int run(String[] args) throws Exception {
    // printUsage();
    /*
     * SETUP
     */
    Configuration argConf = getConf();
    Hashtable<String, String> confArg = new Hashtable<String, String>();
    setup(confArg, argConf);
    Date currentTime = new Date();
    Date endDate = new Date(new Long(confArg.get("timestamp_stop")));
    Boolean full_run = confArg.get("intermediate").matches("(?i).*true.*");
    Boolean quick_add = confArg.get("quick_add").matches("(?i).*true.*");
    logger.info("Running GeStore");

    // ZooKeeper setup
    Configuration config = HBaseConfiguration.create();
    zkWatcher = new ZooKeeperWatcher(config, "Testing", new HBaseAdmin(config));
    zkInstance =
        new ZooKeeper(
            ZKConfig.getZKQuorumServersString(config),
            config.getInt("zookeeper.session.timeout", -1),
            zkWatcher);

    if (!confArg.get("task_id").isEmpty()) {
      confArg.put("temp_path", confArg.get("temp_path") + confArg.get("task_id"));
    }

    String lockRequest = confArg.get("file_id");
    if (!confArg.get("run_id").isEmpty())
      lockRequest = lockRequest + "_" + confArg.get("run_id") + "_";
    if (!confArg.get("task_id").isEmpty())
      lockRequest = lockRequest + "_" + confArg.get("task_id") + "_";

    // Get type of movement
    toFrom type_move = checkArgs(confArg);
    if (type_move == toFrom.LOCAL2REMOTE && !confArg.get("format").equals("unknown")) {
      List<String> arguments = new ArrayList<String>();
      arguments.add("-Dinput=" + confArg.get("local_path"));
      arguments.add("-Dtable=" + confArg.get("file_id"));
      arguments.add("-Dtimestamp=" + confArg.get("timestamp_stop"));
      arguments.add("-Dtype=" + confArg.get("format"));
      arguments.add("-Dtarget_dir=" + confArg.get("base_path") + "_" + confArg.get("file_id"));
      arguments.add("-Dtemp_hdfs_path=" + confArg.get("temp_path"));
      arguments.add("-Drun_id=" + confArg.get("run_id"));
      if (!confArg.get("run_id").isEmpty()) arguments.add("-Drun_id=" + confArg.get("run_id"));
      if (!confArg.get("task_id").isEmpty()) arguments.add("-Dtask_id=" + confArg.get("task_id"));
      if (quick_add) arguments.add("-Dquick_add=" + confArg.get("quick_add"));
      String lockName = lock(lockRequest);
      String[] argumentString = arguments.toArray(new String[arguments.size()]);
      adddb.main(argumentString);
      unlock(lockName);
      System.exit(0);
    }

    // Database registration

    dbutil db_util = new dbutil(config);
    db_util.register_database(confArg.get("db_name_files"), true);
    db_util.register_database(confArg.get("db_name_runs"), true);
    db_util.register_database(confArg.get("db_name_updates"), true);
    FileSystem hdfs = FileSystem.get(config);
    FileSystem localFS = FileSystem.getLocal(config);

    // Get source type
    confArg.put("source", getSource(db_util, confArg.get("db_name_files"), confArg.get("file_id")));
    confArg.put(
        "database", isDatabase(db_util, confArg.get("db_name_files"), confArg.get("file_id")));
    if (!confArg.get("source").equals("local")
        && type_move == toFrom.REMOTE2LOCAL
        && !confArg.get("timestamp_stop").equals(Integer.toString(Integer.MAX_VALUE))) {
      confArg.put("timestamp_stop", Long.toString(latestVersion(confArg, db_util)));
    }

    /*
     * Get previous timestamp
     */
    Get run_id_get = new Get(confArg.get("run_id").getBytes());
    Result run_get = db_util.doGet(confArg.get("db_name_runs"), run_id_get);
    KeyValue run_file_prev =
        run_get.getColumnLatest(
            "d".getBytes(), (confArg.get("file_id") + "_db_timestamp").getBytes());
    String last_timestamp = new String("0");
    if (null != run_file_prev && !confArg.get("source").equals("local")) {
      long last_timestamp_real = run_file_prev.getTimestamp();
      Long current_timestamp = new Long(confArg.get("timestamp_real"));
      if ((current_timestamp - last_timestamp_real) > 36000) {
        last_timestamp = new String(run_file_prev.getValue());
        Integer lastTimestamp = new Integer(last_timestamp);
        lastTimestamp += 1;
        last_timestamp = lastTimestamp.toString();
        logger.info("Last timestamp: " + last_timestamp + " End data: " + endDate);
        Date last_run = new Date(run_file_prev.getTimestamp());
        if (last_run.before(endDate) && !full_run) {
          confArg.put("timestamp_start", last_timestamp);
        }
      }
    }

    Integer tse = new Integer(confArg.get("timestamp_stop"));
    Integer tss = new Integer(confArg.get("timestamp_start"));
    if (tss > tse) {
      logger.info("No new version of requested file.");
      return 0;
    }

    /*
     * Generate file
     */

    String lockName = lock(lockRequest);

    Get file_id_get = new Get(confArg.get("file_id").getBytes());
    Result file_get = db_util.doGet(confArg.get("db_name_files"), file_id_get);
    if (!file_get.isEmpty()) {
      boolean found =
          hasFile(
              db_util,
              hdfs,
              confArg.get("db_name_files"),
              confArg.get("file_id"),
              getFullPath(confArg));
      if (confArg.get("source").equals("fullfile")) {
        found = false;
      }
      String filenames_put =
          getFileNames(
              db_util, confArg.get("db_name_files"), confArg.get("file_id"), getFullPath(confArg));
      // Filename not found in file database
      if (!found && type_move == toFrom.REMOTE2LOCAL) {
        if (!confArg.get("source").equals("local")) {
          // Generate intermediate file
          if (getFile(hdfs, confArg, db_util) == null) {
            unlock(lockName);
            return 1;
          }
          // Put generated file into file database
          if (!confArg.get("format").equals("fullfile")) {
            putFileEntry(
                db_util,
                hdfs,
                confArg.get("db_name_files"),
                confArg.get("file_id"),
                confArg.get("full_file_name"),
                confArg.get("source"));
          }
        } else {
          logger.warn("Remote file not found, and cannot be generated! File: " + confArg);
          unlock(lockName);
          return 1;
        }
      }
    } else {
      if (type_move == toFrom.REMOTE2LOCAL) {
        logger.warn("Remote file not found, and cannot be generated.");
        unlock(lockName);
        return 1;
      }
    }

    /*
     * Copy file
     * Update tables
     */

    if (type_move == toFrom.LOCAL2REMOTE) {
      if (!confArg.get("format").equals("fullfile")) {
        putFileEntry(
            db_util,
            hdfs,
            confArg.get("db_name_files"),
            confArg.get("file_id"),
            getFullPath(confArg),
            confArg.get("source"));
      }
      putRunEntry(
          db_util,
          confArg.get("db_name_runs"),
          confArg.get("run_id"),
          confArg.get("file_id"),
          confArg.get("type"),
          confArg.get("timestamp_real"),
          confArg.get("timestamp_stop"),
          getFullPath(confArg),
          confArg.get("delimiter"));
      hdfs.copyFromLocalFile(new Path(confArg.get("local_path")), new Path(getFullPath(confArg)));
    } else if (type_move == toFrom.REMOTE2LOCAL) {
      FileStatus[] files = hdfs.globStatus(new Path(getFullPath(confArg) + "*"));
      putRunEntry(
          db_util,
          confArg.get("db_name_runs"),
          confArg.get("run_id"),
          confArg.get("file_id"),
          confArg.get("type"),
          confArg.get("timestamp_real"),
          confArg.get("timestamp_stop"),
          getFullPath(confArg),
          confArg.get("delimiter"));
      unlock(lockName);
      for (FileStatus file : files) {
        Path cur_file = file.getPath();
        Path cur_local_path =
            new Path(new String(confArg.get("local_path") + confArg.get("file_id")));
        String suffix = getSuffix(getFileName(confArg), cur_file.getName());
        if (suffix.length() > 0) {
          cur_local_path = cur_local_path.suffix(new String("." + suffix));
        }
        if (confArg.get("copy").equals("true")) {
          String crc = hdfs.getFileChecksum(cur_file).toString();
          if (checksumLocalTest(cur_local_path, crc)) {
            continue;
          } else {
            hdfs.copyToLocalFile(cur_file, cur_local_path);
            writeChecksum(cur_local_path, crc);
          }
        } else {
          System.out.println(cur_local_path + "\t" + cur_file);
        }
      }
    }
    unlock(lockName);
    return 0;
  }
Example #15
0
  // Information needed to get a single file:
  // BASE_PATH, FILE_ID, TIMESTAMP_START, TIMESTAMP_STOP, SOURCE, FILESYSTEM
  private static Vector<Path> getFile(
      FileSystem fs, Hashtable<String, String> config, dbutil db_util) throws Exception {
    Long latestVersion = latestVersion(config, db_util);

    try {
      config.put("timestamp_start", config.get("timestamp_start"));
      config.put("timestamp_real", latestVersion.toString());
      config.put("timestamp_stop", latestVersion.toString());
    } catch (Exception E) {
      logger.error("Tryign to get file that is impossible to generate: " + getFullPath(config));
      return null;
    }
    if (Integer.parseInt(config.get("timestamp_start"))
        > Integer.parseInt(config.get("timestamp_stop"))) {
      return null;
    }
    logger.debug(
        "Getting DB for timestamp "
            + config.get("timestamp_start")
            + " to "
            + config.get("timestamp_stop"));

    String final_result = getFullPath(config);

    String temp_path_base =
        config.get("local_temp_path")
            + "_"
            + config.get("task_id")
            + "_"
            + config.get("run_id")
            + "/";
    Path newPath = new Path(final_result + "*");
    Vector<Path> ret_path = new Vector<Path>();
    String lockName = lock(final_result.replaceAll("/", "_"));
    if (fs.globStatus(newPath).length != 0) {
      ret_path.add(newPath);
      unlock(lockName);
      config.put("full_file_name", final_result);
      return ret_path;
    } else {
      if (!config.get("source").equals("local")) {
        config.put("temp_path_base", temp_path_base);

        config.put("timestamp_start", config.get("timestamp_start"));
        config.put("timestamp_real", latestVersion.toString());
        config.put("timestamp_stop", latestVersion.toString());

        Class<?> sourceClass =
            Class.forName("org.gestore.plugin.source." + config.get("source") + "Source");
        Method process_data = sourceClass.getMethod("process", Hashtable.class, FileSystem.class);
        Object processor = sourceClass.newInstance();
        Object retVal;
        try {
          retVal = process_data.invoke(processor, config, fs);
        } catch (InvocationTargetException E) {
          Throwable exception = E.getTargetException();
          logger.error("Unable to call method in child class: " + exception.toString());
          exception.printStackTrace(System.out);
          unlock(lockName);
          return null;
        }
        FileStatus[] files = (FileStatus[]) retVal;
        if (files == null) {
          logger.error("Error getting files, no files returned");
          return null;
        }

        for (FileStatus file : files) {
          Path cur_file = file.getPath();
          Path cur_local_path = new Path(temp_path_base + config.get("file_id"));
          String suffix = getSuffix(config.get("file_id"), cur_file.getName());
          cur_local_path = cur_local_path.suffix(suffix);
          Path res_path = new Path(new String(final_result + suffix));
          logger.debug("Moving file" + cur_file.toString() + " to " + res_path.toString());
          if (config.get("copy").equals("true")) {
            fs.moveFromLocalFile(cur_file, res_path);
          } else {
            fs.rename(cur_file, res_path);
          }
        }

        config.put("full_file_name", final_result);
      }
    }
    unlock(lockName);
    return ret_path;
  }