public int run(String[] args) throws Exception {
ServiceLoader<? extends AminoJob> jobs = ServiceLoader.load(AminoJob.class);
if (!jobs.iterator().hasNext()) {
jobs = ServiceLoader.load(AminoEnrichmentJob.class);
}
if (!jobs.iterator().hasNext()) {
jobs = ServiceLoader.load(AminoReuseEnrichmentJob.class);
}
Configuration conf = getConf();
// AminoConfiguration.loadDefault(conf, "AminoDefaults", true);
// boolean complete = createTables(conf);
boolean complete = true;
updateStatus(JobStatus.RUNNING);
// boolean complete = true;
for (AminoJob aj : jobs) {
aj.setConfig(conf);
logger.info("Running Job -> " + aj.getJobName());
if (complete) {
Job job = new Job(conf, aj.getJobName());
job.setJarByClass(aj.getClass());
// Add the class to the conf it can be grabbed in the Reduce phase
AminoDriverUtils.setAminoJob(job.getConfiguration(), aj.getClass());
int jobType = setJobParameters(job, aj);
// Call job configuration for special properties
jobConfiguration(job);
complete = job.waitForCompletion(true);
if (jobType == JOB_TYPE_ENRICHMENT || jobType == JOB_TYPE_REUSE_ENRICHMENT) {
if (!stopOnFirstPhase) {
stopOnFirstPhase = conf.getBoolean("stop.on.first.phase", stopOnFirstPhase);
}
if (complete && !stopOnFirstPhase) {
complete = runSecondPhaseEnrichmentJob((AminoEnrichmentJob) aj, conf, jobType);
if (jobType == JOB_TYPE_REUSE_ENRICHMENT)
((AminoReuseEnrichmentJob) aj).directoryCleanup(conf);
} else if (!complete) {
System.err.println("Job failed, unable to run second enrichment step");
}
}
}
}
updateStatus(complete ? JobStatus.COMPLETE : JobStatus.FAILED);
return complete ? 0 : 1;
}
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);
}
