void countSample(BioSample s) {
stat.incUniqSampleCounter();
if (AbstractXMLFormatter.isSamplePublic(s, stat.getNowDate()))
stat.incSamplePublicUniqCounter();
if (hasSourcesByName || hasSourcesByAcc) {
for (MSI gmsi : s.getMSIs()) {
for (DatabaseRecordRef db : gmsi.getDatabaseRecordRefs()) {
if (hasSourcesByAcc) {
String scrNm = db.getAcc();
if (scrNm != null) {
scrNm = scrNm.trim();
if (scrNm.length() != 0) stat.addToSourceByAcc(scrNm, 1);
}
}
if (hasSourcesByName) {
String scrNm = db.getDbName();
if (scrNm != null) {
scrNm = scrNm.trim();
if (scrNm.length() != 0) stat.addToSourceByAcc(scrNm, 1);
}
}
}
}
}
}
@Override
public void run() {
procThread = Thread.currentThread();
procThread.setName(procThread.getName() + "-ExporterTask-gen" + (++genNo) + "-lane" + laneNo);
AuxInfo auxInf = null;
if (myEqFactory != null) auxInf = new AuxInfoImpl(myEqFactory);
int objCount = 0;
try {
StringBuilder sb = new StringBuilder();
while (true) {
if (needGroupLoop) {
Collection<BioSampleGroup> grps = null;
int restart = 0;
while (true) {
try {
grps = sgQM.getGroups();
break;
} catch (PersistenceException e) {
sgQM.close();
restart++;
stat.incRecoverAttempt();
if (restart > MaxErrorRecoverAttempts) throw e;
}
}
if (grps.size() == 0) {
log.debug("({}) No more groups to process", Thread.currentThread().getName());
needGroupLoop = false;
}
for (BioSampleGroup grp : grps) {
if (stopFlag.get()) {
log.debug(
"({}) Stop flag set. Sending FINISH message", Thread.currentThread().getName());
putIntoQueue(controlQueue, new ControlMessage(Type.PROCESS_FINISH, this));
return;
}
if (!stat.addGroup(grp.getId())) continue;
objCount++;
// System.out.printf("=MSI (L%d-G%d-N%d) %s Processing group %s %n"
// ,laneNo,genNo,msiCount,msi.getAcc(), g.getAcc());
stat.incGroupCounter();
boolean grpPub = AbstractXMLFormatter.isGroupPublic(grp, stat.getNowDate());
if (grpPub) stat.incGroupPublicCounter();
for (FormattingTask ft : tasks) {
if (ft.getGroupQueue() == null) continue;
if (!ft.confirmOutput()) continue;
restart = 0;
while (true) {
try {
sb.setLength(0);
ft.getFormatter().exportGroup(grp, auxInf, sb, false);
break;
} catch (PersistenceException e) {
restart++;
stat.incRecoverAttempt();
if (restart > MaxErrorRecoverAttempts) throw e;
}
}
putIntoQueue(ft.getGroupQueue(), sb.toString());
}
if (hasGroupedSmp
|| maxObjsPerThr <= 0
|| maxObjsPerThr - objCount > sgQM.getChunkSize()) {
for (BioSample s : grp.getSamples()) {
if (!hasGroupedSmp
&& maxObjsPerThr > 0
&& maxObjsPerThr - objCount <= sgQM.getChunkSize()) break;
if (!stat.addSample(s.getId())) continue;
objCount++;
countSample(s);
for (FormattingTask ft : tasks) {
if (ft.getSampleQueue() == null) continue;
if (!ft.confirmOutput()) continue;
restart = 0;
while (true) {
try {
sb.setLength(0);
ft.getFormatter().exportSample(s, auxInf, sb, false);
break;
} catch (PersistenceException e) {
restart++;
stat.incRecoverAttempt();
if (restart > MaxErrorRecoverAttempts) throw e;
}
}
putIntoQueue(ft.getSampleQueue(), sb.toString());
}
}
}
if (stopFlag.get()) {
log.debug(
"({}) Stop flag set. Sending FINISH message", Thread.currentThread().getName());
putIntoQueue(controlQueue, new ControlMessage(Type.PROCESS_FINISH, this));
return;
}
}
}
if (hasUngroupedSmp) {
Collection<BioSample> smpls = null;
int restart = 0;
while (true) {
try {
smpls = sgQM.getSamples();
break;
} catch (PersistenceException e) {
sgQM.close();
restart++;
stat.incRecoverAttempt();
if (restart > MaxErrorRecoverAttempts) throw e;
}
}
if (smpls.size() == 0 && !needGroupLoop) {
log.debug("({}) No more data to process", Thread.currentThread().getName());
break;
}
for (BioSample s : smpls) {
if (!stat.addSample(s.getId())) continue;
objCount++;
if (stopFlag.get()) {
log.debug(
"({}) Stop flag set. Sending FINISH message", Thread.currentThread().getName());
putIntoQueue(controlQueue, new ControlMessage(Type.PROCESS_FINISH, this));
return;
}
countSample(s);
for (FormattingTask ft : tasks) {
if (ft.getSampleQueue() == null || ft.isGroupedSamplesOnly()) continue;
if (!ft.confirmOutput()) continue;
restart = 0;
while (true) {
try {
sb.setLength(0);
ft.getFormatter().exportSample(s, auxInf, sb, false);
break;
} catch (PersistenceException e) {
restart++;
stat.incRecoverAttempt();
if (restart > MaxErrorRecoverAttempts) throw e;
}
}
putIntoQueue(ft.getSampleQueue(), sb.toString());
}
}
} else if (!needGroupLoop) {
log.debug("({}) No more data to process", Thread.currentThread().getName());
break;
}
boolean needMoreData = false;
for (FormattingTask ft : tasks) {
if (ft.confirmOutput()) {
needMoreData = true;
break;
}
}
if (!needMoreData) {
log.debug(
"({}) Output tasks don't need more data. Breaking loop",
Thread.currentThread().getName());
break;
}
if (maxObjsPerThr > 0 && objCount >= maxObjsPerThr) {
log.debug(
"({}) Thread TTL expared. Processed {} objects. Sending TTL message",
Thread.currentThread().getName(),
objCount);
if (auxInf != null) auxInf.destroy();
auxInf = null;
sgQM.close();
putIntoQueue(controlQueue, new ControlMessage(Type.PROCESS_TTL, this));
return;
}
if (auxInf != null) auxInf.clear();
}
log.debug(
"({}) Thread terminating. Sending FINISH message", Thread.currentThread().getName());
putIntoQueue(controlQueue, new ControlMessage(Type.PROCESS_FINISH, this));
} catch (Throwable e) {
e.printStackTrace();
putIntoQueue(controlQueue, new ControlMessage(Type.PROCESS_ERROR, this, e));
} finally {
if (auxInf != null) auxInf.destroy();
sgQM.close();
}
}
