Exemplo n.º 1
0
 // topK sort,write the result to hdfs
 public void reduce(DoubleWritable key, Iterable<DataPair> values, Context context)
     throws IOException, InterruptedException {
   for (DataPair val : values) {
     if (count < k) {
       hf.createNewHDFSFile(val.getLigandPath(), val.getVinaResult());
       hf.createNewHDFSFile(val.getLogPath(), val.getVinaLog());
       int position = val.getLigandPath().lastIndexOf("/");
       String ligandName = val.getLigandPath().substring(position + 1);
       context.write(new DoubleWritable(val.getLigandDouble()), new Text(ligandName));
       /*  context.write(new DoubleWritable(val.getLigandDouble()),
       new Text(val.getLigandPath()));*/
       count++;
     } else {
       break;
     }
   }
 }
Exemplo n.º 2
0
    /*
     * (non-Javadoc)
     *
     * @see org.apache.hadoop.mapreduce.Mapper#map(KEYIN, VALUEIN,
     * org.apache.hadoop.mapreduce.Mapper.Context)
     */
    public void map(Object key, Text value, Context context)
        throws IOException, InterruptedException {
      String path = value.toString();
      String[] sub = value.toString().split("/");
      String ligandName = sub[sub.length - 1];
      String ligandLocal = "/home/hadoop/vinaJob/" + tmpPath + "/data/" + ligandName;
      hf.HadoopToLocal(path, ligandLocal);
      String out = "/home/hadoop/vinaJob/" + tmpPath + "/out/" + ligandName;
      fo.createDir("/home/hadoop/vinaJob/" + tmpPath + "/out/");
      String log = "/home/hadoop/vinaJob/" + tmpPath + "/out/" + ligandName + ".log";
      String exceptionPath =
          "/vinaResult/vinaJobID/" + vinaJobID + "/exception/" + ligandName + ".exception";
      String exceptionBackupPath =
          "/vinaResult/vinaJobID/" + vinaJobID + "/exceptionBackup/" + ligandName + ".exception";
      RunVina vinajob = new RunVina(conf2Local, ligandLocal, receptorLocal, seed, out, log, path);
      String flag = vinajob.runVina();
      if ("success".equals(flag)) {
        String logHdfsPath =
            "/vinaResult/vinaJobID/" + vinaJobID + "/result/" + ligandName + ".log";
        String outHdfsPath = "/vinaResult/vinaJobID/" + vinaJobID + "/result/" + ligandName;
        String result = fo.readFile(out);
        String logInfo = fo.readFile(log);
        try {
          DataPair data =
              new DataPair(
                  Double.parseDouble(result.split("\n")[1].split("    ")[1].trim()),
                  outHdfsPath,
                  result,
                  logHdfsPath,
                  logInfo);
          tree.add(data);
          if (tree.size() > k) {
            tree.pollLast();
          }
        } catch (Exception e) {
          hf.createNewHDFSFile(exceptionPath, path + " bad result");
        }

      } else {
        hf.createNewHDFSFile(exceptionPath, flag);
        hf.createNewHDFSFile(exceptionBackupPath, flag);
      }
    }