Example #1
0
  /*
   * Fetch a file that is in a Hadoop file system. Return a local File.
   * Interruptible.
   */
  private File hdfsFetch(Path fromPath, Reporter reporter)
      throws IOException, InterruptedException {
    UUID uniqueId = UUID.randomUUID();
    File toFile = new File(tempDir, uniqueId.toString() + "/" + fromPath.getName());
    File toDir = new File(toFile.getParent());
    if (toDir.exists()) {
      FileUtils.deleteDirectory(toDir);
    }
    toDir.mkdirs();
    Path toPath = new Path(toFile.getCanonicalPath());

    FileSystem fS = fromPath.getFileSystem(hadoopConf);
    FileSystem tofS = FileSystem.getLocal(hadoopConf);

    Throttler throttler = new Throttler((double) bytesPerSecThrottle);
    try {
      for (FileStatus fStatus : fS.globStatus(fromPath)) {
        log.info("Copying " + fStatus.getPath() + " to " + toPath);
        long bytesSoFar = 0;

        FSDataInputStream iS = fS.open(fStatus.getPath());
        FSDataOutputStream oS = tofS.create(toPath);

        byte[] buffer = new byte[downloadBufferSize];

        int nRead;
        while ((nRead = iS.read(buffer, 0, buffer.length)) != -1) {
          // Needed to being able to be interrupted at any moment.
          if (Thread.interrupted()) {
            iS.close();
            oS.close();
            cleanDirNoExceptions(toDir);
            throw new InterruptedException();
          }
          bytesSoFar += nRead;
          oS.write(buffer, 0, nRead);
          throttler.incrementAndThrottle(nRead);
          if (bytesSoFar >= bytesToReportProgress) {
            reporter.progress(bytesSoFar);
            bytesSoFar = 0l;
          }
        }

        if (reporter != null) {
          reporter.progress(bytesSoFar);
        }

        oS.close();
        iS.close();
      }

      return toDir;
    } catch (ClosedByInterruptException e) {
      // This can be thrown by the method read.
      cleanDirNoExceptions(toDir);
      throw new InterruptedIOException();
    }
  }
  public void map(
      LongWritable key, Point value, OutputCollector<LongWritable, Point> output, Reporter reporter)
      throws IOException {
    double min = value.sumOfSquares(centers.get(0));
    int best = 0;

    for (int index = 1; index < numberOfCenters; ++index) {
      double current = value.sumOfSquares(centers.get(index));

      if (current < min) {
        min = current;
        best = index;
      }
    }

    reporter.incrCounter("NUMBER", "NODES", 1);
    reporter.incrCounter("CENTER", "" + best, 1);

    output.collect(new LongWritable(best), value);
  }
Example #3
0
 /**
  * Map method. Copies one file from source file system to destination.
  *
  * @param key src len
  * @param value FilePair (FileStatus src, Path dst)
  * @param out Log of failed copies
  * @param reporter
  */
 public void map(
     LongWritable key,
     FilePair value,
     OutputCollector<WritableComparable<?>, Text> out,
     Reporter reporter)
     throws IOException {
   final FileStatus srcstat = value.input;
   final Path relativedst = new Path(value.output);
   try {
     copy(srcstat, relativedst, out, reporter);
   } catch (IOException e) {
     ++failcount;
     reporter.incrCounter(Counter.FAIL, 1);
     updateStatus(reporter);
     final String sfailure = "FAIL " + relativedst + " : " + StringUtils.stringifyException(e);
     out.collect(null, new Text(sfailure));
     LOG.info(sfailure);
     try {
       for (int i = 0; i < 3; ++i) {
         try {
           final Path tmp = new Path(job.get(TMP_DIR_LABEL), relativedst);
           if (destFileSys.delete(tmp, true)) break;
         } catch (Throwable ex) {
           // ignore, we are just cleaning up
           LOG.debug("Ignoring cleanup exception", ex);
         }
         // update status, so we don't get timed out
         updateStatus(reporter);
         Thread.sleep(3 * 1000);
       }
     } catch (InterruptedException inte) {
       throw (IOException) new IOException().initCause(inte);
     }
   } finally {
     updateStatus(reporter);
   }
 }
Example #4
0
    /**
     * Copy a file to a destination.
     *
     * @param srcstat src path and metadata
     * @param dstpath dst path
     * @param reporter
     */
    private void copy(
        FileStatus srcstat,
        Path relativedst,
        OutputCollector<WritableComparable<?>, Text> outc,
        Reporter reporter)
        throws IOException {
      Path absdst = new Path(destPath, relativedst);
      int totfiles = job.getInt(SRC_COUNT_LABEL, -1);
      assert totfiles >= 0 : "Invalid file count " + totfiles;

      // if a directory, ensure created even if empty
      if (srcstat.isDir()) {
        if (destFileSys.exists(absdst)) {
          if (!destFileSys.getFileStatus(absdst).isDir()) {
            throw new IOException("Failed to mkdirs: " + absdst + " is a file.");
          }
        } else if (!destFileSys.mkdirs(absdst)) {
          throw new IOException("Failed to mkdirs " + absdst);
        }
        // TODO: when modification times can be set, directories should be
        // emitted to reducers so they might be preserved. Also, mkdirs does
        // not currently return an error when the directory already exists;
        // if this changes, all directory work might as well be done in reduce
        return;
      }

      if (destFileSys.exists(absdst) && !overwrite && !needsUpdate(srcstat, destFileSys, absdst)) {
        outc.collect(null, new Text("SKIP: " + srcstat.getPath()));
        ++skipcount;
        reporter.incrCounter(Counter.SKIP, 1);
        updateStatus(reporter);
        return;
      }

      Path tmpfile = new Path(job.get(TMP_DIR_LABEL), relativedst);
      long cbcopied = 0L;
      FSDataInputStream in = null;
      FSDataOutputStream out = null;
      try {
        // open src file
        try {
          in = srcstat.getPath().getFileSystem(job).open(srcstat.getPath());
        } catch (IOException e) {
          LOG.error("Failed to open src file " + srcstat.getPath() + ", ignore and return");
          in = null;
          return;
        }
        reporter.incrCounter(Counter.BYTESEXPECTED, srcstat.getLen());
        // open tmp file
        out = create(tmpfile, reporter, srcstat);
        // copy file
        for (int cbread; (cbread = in.read(buffer)) >= 0; ) {
          out.write(buffer, 0, cbread);
          cbcopied += cbread;
          reporter.setStatus(
              String.format("%.2f ", cbcopied * 100.0 / srcstat.getLen())
                  + absdst
                  + " [ "
                  + StringUtils.humanReadableInt(cbcopied)
                  + " / "
                  + StringUtils.humanReadableInt(srcstat.getLen())
                  + " ]");
        }
      } finally {
        checkAndClose(in);
        checkAndClose(out);
      }

      if (cbcopied != srcstat.getLen()) {
        if (srcstat.getLen() == 0 && cbcopied > 0) {
          LOG.info("most likely see a WAL file corruption: " + srcstat.getPath());
        } else {
          throw new IOException(
              "File size not matched: copied "
                  + bytesString(cbcopied)
                  + " to tmpfile (="
                  + tmpfile
                  + ") but expected "
                  + bytesString(srcstat.getLen())
                  + " from "
                  + srcstat.getPath());
        }
      } else {
        if (totfiles == 1) {
          // Copying a single file; use dst path provided by user as destination
          // rather than destination directory, if a file
          Path dstparent = absdst.getParent();
          if (!(destFileSys.exists(dstparent) && destFileSys.getFileStatus(dstparent).isDir())) {
            absdst = dstparent;
          }
        }
        if (destFileSys.exists(absdst) && destFileSys.getFileStatus(absdst).isDir()) {
          throw new IOException(absdst + " is a directory");
        }
        if (!destFileSys.mkdirs(absdst.getParent())) {
          throw new IOException("Failed to craete parent dir: " + absdst.getParent());
        }
        rename(tmpfile, absdst);

        FileStatus dststat = destFileSys.getFileStatus(absdst);
        if (dststat.getLen() != srcstat.getLen()) {
          destFileSys.delete(absdst, false);
          throw new IOException(
              "File size not matched: copied "
                  + bytesString(dststat.getLen())
                  + " to dst (="
                  + absdst
                  + ") but expected "
                  + bytesString(srcstat.getLen())
                  + " from "
                  + srcstat.getPath());
        }
        updatePermissions(srcstat, dststat);
      }

      // report at least once for each file
      ++copycount;
      reporter.incrCounter(Counter.BYTESCOPIED, cbcopied);
      reporter.incrCounter(Counter.COPY, 1);
      updateStatus(reporter);
    }
Example #5
0
 private void updateStatus(Reporter reporter) {
   reporter.setStatus(getCountString());
 }
Example #6
0
  /** In case of interrupted, written file is not deleted. */
  private void copyFile(File sourceFile, File destFile, Reporter reporter)
      throws IOException, InterruptedException {
    if (!destFile.exists()) {
      destFile.createNewFile();
    }
    FileChannel source = null;
    FileChannel destination = null;

    Throttler throttler = new Throttler((double) bytesPerSecThrottle);

    FileInputStream iS = null;
    FileOutputStream oS = null;

    try {
      iS = new FileInputStream(sourceFile);
      oS = new FileOutputStream(destFile);
      source = iS.getChannel();
      destination = oS.getChannel();
      long bytesSoFar = 0;
      long reportingBytesSoFar = 0;
      long size = source.size();

      int transferred = 0;

      while (bytesSoFar < size) {
        // Needed to being able to be interrupted at any moment.
        if (Thread.interrupted()) {
          throw new InterruptedException();
        }

        // Casting to int here is safe since we will transfer at most "downloadBufferSize" bytes.
        // This is done on purpose for being able to implement Throttling.
        transferred = (int) destination.transferFrom(source, bytesSoFar, downloadBufferSize);
        bytesSoFar += transferred;
        reportingBytesSoFar += transferred;
        throttler.incrementAndThrottle(transferred);
        if (reportingBytesSoFar >= bytesToReportProgress) {
          reporter.progress(reportingBytesSoFar);
          reportingBytesSoFar = 0l;
        }
      }

      if (reporter != null) {
        reporter.progress(reportingBytesSoFar);
      }

    } catch (InterruptedException e) {
      e.printStackTrace();
    } finally {
      if (iS != null) {
        iS.close();
      }
      if (oS != null) {
        oS.close();
      }
      if (source != null) {
        source.close();
      }
      if (destination != null) {
        destination.close();
      }
    }
  }
Example #7
0
  /*
   * Fetch a file that is in a S3 file system. Return a local File. It accepts "s3://" and "s3n://" prefixes.
   * Interruptible.
   */
  private File s3Fetch(URI uri, Reporter reporter) throws IOException, InterruptedException {
    String bucketName = uri.getHost();
    String path = uri.getPath();
    UUID uniqueId = UUID.randomUUID();
    File destFolder = new File(tempDir, uniqueId.toString() + "/" + path);
    if (destFolder.exists()) {
      FileUtils.deleteDirectory(destFolder);
    }
    destFolder.mkdirs();

    Throttler throttler = new Throttler((double) bytesPerSecThrottle);

    boolean done = false;
    try {
      s3Service = new RestS3Service(getCredentials());
      if (s3Service.checkBucketStatus(bucketName) != RestS3Service.BUCKET_STATUS__MY_BUCKET) {
        throw new IOException("Bucket doesn't exist or is already claimed: " + bucketName);
      }

      if (path.startsWith("/")) {
        path = path.substring(1, path.length());
      }

      for (S3Object object : s3Service.listObjects(new S3Bucket(bucketName), path, "")) {
        long bytesSoFar = 0;

        String fileName = path;
        if (path.contains("/")) {
          fileName = path.substring(path.lastIndexOf("/") + 1, path.length());
        }
        File fileDest = new File(destFolder, fileName);
        log.info("Downloading " + object.getKey() + " to " + fileDest + " ...");

        if (fileDest.exists()) {
          fileDest.delete();
        }

        object = s3Service.getObject(new S3Bucket(bucketName), object.getKey());
        InputStream iS = object.getDataInputStream();
        FileOutputStream writer = new FileOutputStream(fileDest);
        byte[] buffer = new byte[downloadBufferSize];

        int nRead;
        while ((nRead = iS.read(buffer, 0, buffer.length)) != -1) {
          // Needed to being able to be interrupted at any moment.
          if (Thread.interrupted()) {
            iS.close();
            writer.close();
            cleanDirNoExceptions(destFolder);
            throw new InterruptedException();
          }

          bytesSoFar += nRead;
          writer.write(buffer, 0, nRead);
          throttler.incrementAndThrottle(nRead);
          if (bytesSoFar >= bytesToReportProgress) {
            reporter.progress(bytesSoFar);
            bytesSoFar = 0l;
          }
        }

        if (reporter != null) {
          reporter.progress(bytesSoFar);
        }

        writer.close();
        iS.close();
        done = true;
      }

      if (!done) {
        throw new IOException("Bucket is empty! " + bucketName + " path: " + path);
      }
    } catch (S3ServiceException e) {
      throw new IOException(e);
    }

    return destFolder;
  }
Example #8
0
    public void map(
        WritableComparable<?> key,
        Text value,
        OutputCollector<Text, CrawlDatum> output,
        Reporter reporter)
        throws IOException {
      String url = value.toString(); // value is line of text

      if (url != null && url.trim().startsWith("#")) {
        /* Ignore line that start with # */
        return;
      }

      // if tabs : metadata that could be stored
      // must be name=value and separated by \t
      float customScore = -1f;
      int customInterval = interval;
      int fixedInterval = -1;
      Map<String, String> metadata = new TreeMap<String, String>();
      if (url.indexOf("\t") != -1) {
        String[] splits = url.split("\t");
        url = splits[0];
        for (int s = 1; s < splits.length; s++) {
          // find separation between name and value
          int indexEquals = splits[s].indexOf("=");
          if (indexEquals == -1) {
            // skip anything without a =
            continue;
          }
          String metaname = splits[s].substring(0, indexEquals);
          String metavalue = splits[s].substring(indexEquals + 1);
          if (metaname.equals(nutchScoreMDName)) {
            try {
              customScore = Float.parseFloat(metavalue);
            } catch (NumberFormatException nfe) {
            }
          } else if (metaname.equals(nutchFetchIntervalMDName)) {
            try {
              customInterval = Integer.parseInt(metavalue);
            } catch (NumberFormatException nfe) {
            }
          } else if (metaname.equals(nutchFixedFetchIntervalMDName)) {
            try {
              fixedInterval = Integer.parseInt(metavalue);
            } catch (NumberFormatException nfe) {
            }
          } else metadata.put(metaname, metavalue);
        }
      }
      try {
        url = urlNormalizers.normalize(url, URLNormalizers.SCOPE_INJECT);
        url = filters.filter(url); // filter the url
      } catch (Exception e) {
        if (LOG.isWarnEnabled()) {
          LOG.warn("Skipping " + url + ":" + e);
        }
        url = null;
      }
      if (url == null) {
        reporter.getCounter("injector", "urls_filtered").increment(1);
      } else { // if it passes
        value.set(url); // collect it
        CrawlDatum datum = new CrawlDatum();
        datum.setStatus(CrawlDatum.STATUS_INJECTED);

        // Is interval custom? Then set as meta data
        if (fixedInterval > -1) {
          // Set writable using float. Flaot is used by AdaptiveFetchSchedule
          datum
              .getMetaData()
              .put(Nutch.WRITABLE_FIXED_INTERVAL_KEY, new FloatWritable(fixedInterval));
          datum.setFetchInterval(fixedInterval);
        } else {
          datum.setFetchInterval(customInterval);
        }

        datum.setFetchTime(curTime);
        // now add the metadata
        Iterator<String> keysIter = metadata.keySet().iterator();
        while (keysIter.hasNext()) {
          String keymd = keysIter.next();
          String valuemd = metadata.get(keymd);
          datum.getMetaData().put(new Text(keymd), new Text(valuemd));
        }
        if (customScore != -1) datum.setScore(customScore);
        else datum.setScore(scoreInjected);
        try {
          scfilters.injectedScore(value, datum);
        } catch (ScoringFilterException e) {
          if (LOG.isWarnEnabled()) {
            LOG.warn(
                "Cannot filter injected score for url "
                    + url
                    + ", using default ("
                    + e.getMessage()
                    + ")");
          }
        }
        reporter.getCounter("injector", "urls_injected").increment(1);
        output.collect(value, datum);
      }
    }