@Override
public void run() {
try {
StopWatch stp2 = new StopWatch();
stp2.start();
JSONObject json = new JSONObject();
job.setStatus("running");
if (job.progress() == 100.0) {
finalizeJob(job);
return;
}
Vector<String> ids = new Vector<String>();
Vector<String> original_names = new Vector<String>();
String data = job.getNextDataBatch();
if (data == null || data.equals("")) return;
String[] lines = data.split("\n");
if (job.containsId()) {
for (int i = 0; i < lines.length; i++) {
if (lines[i].trim().equals("")) continue;
ids.add(NameUtil.getNameId(lines[i]));
}
}
for (int i = 0; i < lines.length; i++) {
original_names.add(NameUtil.processName(lines[i], job.containsId()));
}
String names = NameUtil.CleanNames(lines, job);
if (names.equals("")) return;
if (job.getType() == TnrsJob.NAME_MATCH_JOB) {
TaxamatchInterface taxa_match = new TaxamatchInterface(tnrsBaseUrl);
String result = taxa_match.queryTaxamatch(names, job);
json = (JSONObject) JSONSerializer.toJSON(result);
} else if (job.getType() == TnrsJob.PARSING_JOB) {
json = gni_interface.parseNames(names);
}
if (job.outstandingNames() == 0) {
JobHelper.persistJobInfo(baseFolder, job);
}
saveResults(job, json, ids, original_names, "");
job.setStatus("idle");
stp2.stop();
log.info("overall :" + stp2.toString());
} catch (Exception ex) {
log.error(ExceptionUtils.getFullStackTrace(ex));
job.setStatus("failed");
ex.printStackTrace();
}
}
public void finalizeJob(TnrsJob job) throws Exception {
synchronized (jobs) {
jobs.remove(job);
}
job.setStatus("complete");
if (job.email() && !job.getRequest().getEmail().trim().equals("*****@*****.**")) {
job.setFinishedAt(new Date().toString());
job_ids.remove(job.getRequest().getId());
sendNormalCompletionEmail(job);
}
}
/**
* This main loop iterates over the submitted jobs and creates the corresponding threads that will
* carry the execution of each job segment.
*/
@Override
public void run() {
try {
int jobno = 0;
while (true) {
sleep(20);
synchronized (jobs) {
if (jobs.size() == 0) {
continue;
}
}
TnrsJob job = jobs.get(jobno % jobs.size());
if (job.status().equalsIgnoreCase("idle")) {
ExecutionThread thread = new ExecutionThread(job);
threads.add(thread);
thread.start();
} else if (job.status().equalsIgnoreCase("stopped")) {
jobs.remove(job);
JobHelper.cleanJobData(baseFolder, job);
jobno = 0;
continue;
} else if (job.status().equals("failed")) {
sendFailedJobEmail(job);
job.setStatus("error");
}
jobno++;
if (jobs.size() == 200) {
for (int i = 0; i < threads.size(); i++) {
threads.elementAt(i).join();
}
jobno = 0;
threads.clear();
}
sleep(10);
}
} catch (Exception e) {
log.error(ExceptionUtils.getFullStackTrace(e));
e.printStackTrace();
}
}
public TnrsJob submitJob(String jsons) throws Exception {
JSONObject json = (JSONObject) JSONSerializer.toJSON(jsons);
boolean emailr = false;
TnrsJobRequest request =
new TnrsJobRequest(
json.getString("email"),
json.getString("file_name"),
json.getString("original"),
emailr);
TnrsJob job = new TnrsJob(request, new Date().toString(), json.getString("type"));
job.setSensitivity(Double.parseDouble(json.getString("sensitivity").toLowerCase().trim()));
job.setTnrs_version(properties.getProperty("org.iplantc.tnrs.version"));
synchronized (jobs) {
jobs.add(job);
}
job_ids.put(request.getId(), job);
job.setContainsId(json.getBoolean("has_id"));
job.setStatus("idle");
job.getRequest().setId(json.getString("id"));
return job;
}
