// 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;
}
}
}
/*
* (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);
}
}