// 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));
}
// 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#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);
}
protected void setup(Context context) throws IOException, InterruptedException {
Configuration conf = context.getConfiguration();
hf = new HadoopFile();
k = conf.getInt("k", 1000);
}