// delete random directory
protected void cleanup(Context context) throws IOException, InterruptedException {
Iterator<DataPair> it = tree.iterator();
while (it.hasNext()) {
DataPair dp = it.next();
context.write(new DoubleWritable(dp.getLigandDouble()), dp);
}
fo.deleteDir(new File("/home/hadoop/vinaJob/" + tmpPath));
}
/*
* (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);
}
}
/*
* (non-Javadoc)
*
* @see org.apache.hadoop.mapreduce.Mapper#setup(org.apache.hadoop.mapreduce.Mapper.Context)
*/
public void setup(Context context) throws IOException, InterruptedException {
conf = context.getConfiguration();
conf2HDFS = conf.get("conf2HDFS");
receptorHDFS = conf.get("receptorHDFS");
seed = conf.get("seed");
vinaJobID = conf.get("vinaJobID");
k = conf.getInt("k", 1000);
hf = new HadoopFile();
fo = new FileOperation();
tmpPath = fo.randomString();
conf2Local =
"/home/hadoop/vinaJob/"
+ tmpPath
+ "/"
+ conf2HDFS.substring(conf2HDFS.lastIndexOf("/") + 1);
receptorLocal =
"/home/hadoop/vinaJob/"
+ tmpPath
+ "/"
+ receptorHDFS.substring(receptorHDFS.lastIndexOf("/") + 1);
hf.HadoopToLocal(conf2HDFS, conf2Local);
hf.HadoopToLocal(receptorHDFS, receptorLocal);
}