private boolean runSecondPhaseEnrichmentJob(
AminoEnrichmentJob aej, Configuration conf, int jobType) throws Exception {
System.out.println("Running Amino Job");
final Job job = new Job(conf, aej.getJobName() + " phase 2");
job.setJarByClass(aej.getClass());
AminoDriverUtils.setAminoJob(job.getConfiguration(), aej.getClass());
if (jobType == JOB_TYPE_ENRICHMENT) {
job.getConfiguration().set(AminoDriverUtils.ENRICHMENT_OUTPUT, this.enrichmentOutput);
} else if (jobType == JOB_TYPE_REUSE_ENRICHMENT) {
String root = conf.get(AminoDriverUtils.ENRICHMENT_ROOT_OUTPUT);
String front = "";
if (!root.endsWith("/")) {
front = "/";
}
root += front;
final Iterable<String> inputs =
((AminoReuseEnrichmentJob) aej)
.getSecondPhaseEnrichmentInputDirectories(job.getConfiguration());
String inputStr = "";
System.out.println("Using enrichment input paths:");
for (String input : inputs) {
if (inputStr.length() > 0) {
inputStr += "," + PathUtils.getJobDataPath(root + input);
} else {
inputStr += PathUtils.getJobDataPath(root + input);
}
System.out.println(PathUtils.getJobDataPath(root + input));
}
job.getConfiguration().set(AminoDriverUtils.ENRICHMENT_OUTPUT, inputStr);
// Need to do this because the first phase data loader is sitting in this slot currently
AminoInputFormat.setDataLoader(
job.getConfiguration(), aej.getDataLoaderClass().newInstance());
}
int numReducers =
job.getConfiguration()
.getInt(
AMINO_NUM_REDUCERS_ENRICH_PHASE2,
job.getConfiguration().getInt(AMINO_NUM_REDUCERS, DEFAULT_NUM_REDUCERS));
job.setNumReduceTasks(numReducers);
job.setMapperClass(FrameworkMapper.class);
job.setReducerClass(FrameworkReducer.class);
job.setMapOutputKeyClass(BucketStripped.class);
job.setMapOutputValueClass(MapWritable.class);
job.setOutputKeyClass(BucketStripped.class);
job.setOutputValueClass(AminoWritable.class);
job.setInputFormatClass(AminoMultiInputFormat.class);
AminoMultiInputFormat.setDataLoader(
job.getConfiguration(), aej.getDataLoaderClass().newInstance());
// Call job configuration for special properties
jobConfiguration(job);
@SuppressWarnings("serial")
ArrayList<Class<? extends DataLoader>> joinSource =
new ArrayList<Class<? extends DataLoader>>() {
{
add(EnrichmentDataLoader.class);
}
};
AminoMultiInputFormat.setJoinDataLoaders(job.getConfiguration(), joinSource);
job.setOutputFormatClass(AminoOutputFormat.class);
AminoOutputFormat.setAminoConfigPath(
job, job.getConfiguration().get(AminoConfiguration.DEFAULT_CONFIGURATION_PATH_KEY));
String output = job.getConfiguration().get("amino.output");
System.out.println("Output will be written to: " + PathUtils.getJobDataPath(output));
AminoOutputFormat.setOutputPath(job, new Path(PathUtils.getJobDataPath(output)));
JobUtilities.deleteDirectory(job.getConfiguration(), output);
CacheBuilder.buildCaches(
AminoDataUtils.getDataLoader(job.getConfiguration()), aej, output, job.getConfiguration());
return job.waitForCompletion(true);
}
private int setJobParameters(Job job, AminoJob aj) throws Exception {
final Configuration conf = job.getConfiguration();
final Class<? extends DataLoader> dataLoaderClass = aj.getDataLoaderClass();
AminoInputFormat.setDataLoader(job.getConfiguration(), dataLoaderClass.newInstance());
if (aj instanceof AminoEnrichmentJob) {
String output = "";
int returnType = JOB_TYPE_ENRICHMENT;
if (aj instanceof AminoReuseEnrichmentJob) {
System.out.println("Running REUSE Enrichment Join Job");
AminoReuseEnrichmentJob reuseJob = (AminoReuseEnrichmentJob) aj;
AminoInputFormat.setDataLoader(
job.getConfiguration(), reuseJob.getFirstPhaseDataLoaderClass().newInstance());
String root = conf.get(AminoDriverUtils.ENRICHMENT_ROOT_OUTPUT);
String front = "";
if (!root.endsWith("/")) front = "/";
root += front;
String dir = reuseJob.getOutputSubDirectory(conf);
output += root + dir;
returnType = JOB_TYPE_REUSE_ENRICHMENT;
} else {
System.out.println("Running Enrichment Join Job");
}
int numReducers =
conf.getInt(
AMINO_NUM_REDUCERS_ENRICH_PHASE1,
conf.getInt(AMINO_NUM_REDUCERS, DEFAULT_NUM_REDUCERS));
job.setNumReduceTasks(numReducers);
// Our Framework mapper and reducer
job.setMapperClass(FrameworkEnrichmentJoinMapper.class);
job.setCombinerClass(FrameworkEnrichmentJoinCombiner.class);
job.setReducerClass(FrameworkEnrichmentJoinReducer.class);
job.setMapOutputKeyClass(EnrichmentJoinKey.class); // Different
job.setMapOutputValueClass(MapWritable.class);
job.setOutputKeyClass(BucketStripped.class);
job.setOutputValueClass(MapWritable.class); // Different
job.setPartitionerClass(NaturalKeyPartitioner.class);
job.setGroupingComparatorClass(NaturalKeyGroupingComparator.class);
job.setSortComparatorClass(CompositeKeyComparator.class);
job.setInputFormatClass(AminoMultiInputFormat.class);
AminoEnrichmentJob aej = (AminoEnrichmentJob) aj;
// AminoMultiInputFormat.setJoinDataLoader(conf, aej.getEnrichmentDataLoader().newInstance());
AminoMultiInputFormat.setJoinDataLoaders(conf, aej.getEnrichmentDataLoaders());
AminoMultiInputFormat.setEnrichWorker(conf, aej.getEnrichWorker().newInstance());
job.setOutputFormatClass(SequenceFileOutputFormat.class);
// TODO If it already exists, and its age is less than job running frequency, just reuse it
// instead of doing the above job...
if (output.length() == 0) {
output = getEnrichmentOutputPath(aej, conf);
}
System.out.println("Output will be written to: " + PathUtils.getJobDataPath(output));
SequenceFileOutputFormat.setOutputPath(job, new Path(PathUtils.getJobDataPath(output)));
JobUtilities.deleteDirectory(conf, output);
CacheBuilder.buildCaches(AminoDataUtils.getDataLoader(conf), aj, output, conf);
return returnType;
} else {
System.out.println("\n==================== Running Amino Job =================\n");
// Our Framework mapper and reducer
job.setMapperClass(FrameworkMapper.class);
job.setReducerClass(FrameworkReducer.class);
job.setMapOutputKeyClass(BucketStripped.class);
job.setMapOutputValueClass(MapWritable.class);
job.setOutputKeyClass(BucketStripped.class);
job.setOutputValueClass(AminoWritable.class);
job.setInputFormatClass(AminoInputFormat.class);
job.setOutputFormatClass(AminoOutputFormat.class);
job.setNumReduceTasks(conf.getInt(AMINO_NUM_REDUCERS, DEFAULT_NUM_REDUCERS));
AminoOutputFormat.setAminoConfigPath(
job, job.getConfiguration().get(AminoConfiguration.DEFAULT_CONFIGURATION_PATH_KEY));
String output = conf.get("amino.output");
System.out.println("Output will be written to: " + PathUtils.getJobDataPath(output));
AminoOutputFormat.setOutputPath(job, new Path(PathUtils.getJobDataPath(output)));
JobUtilities.deleteDirectory(conf, output);
CacheBuilder.buildCaches(AminoDataUtils.getDataLoader(conf), aj, output, conf);
return JOB_TYPE_NORMAL;
}
}