QList<Task*> WorkflowRunFromCMDLineBase::onSubTaskFinished( Task* subTask ) {
assert( subTask != NULL );
QList<Task*> res;
propagateSubtaskError();
if( hasError() || isCanceled() ) {
return res;
}
assert( !hasError() ); // if error, we won't be here
if( loadTask == subTask ) {
Schema * schema = loadTask->getSchema();
assert( schema != NULL );
remapping = loadTask->getRemapping();
setSchemaCMDLineOptions( schema, optionsStartAt );
if( schema->getDomain().isEmpty() ) {
QList<QString> domainsId = WorkflowEnv::getDomainRegistry()->getAllIds();
assert(!domainsId.isEmpty());
if(!domainsId.isEmpty()) { schema->setDomain(domainsId.first()); }
}
QStringList l;
bool good = WorkflowUtils::validate(*schema, l);
if(!good) {
QString schemaHelpStr = QString("\n\nsee 'ugene --help=%1' for details").arg(schemaName);
setError("\n\n" + l.join("\n\n") + schemaHelpStr);
return res;
}
workflowRunTask = getWorkflowRunTask();
res << workflowRunTask;
}
return res;
}
Task::ReportResult GTest_uHMMERBuild::report() {
propagateSubtaskError();
if(buildTask->hasError()) {
stateInfo.setError( buildTask->getError() );
}
return ReportResult_Finished;
}
Task::ReportResult PairwiseAlignmentHirschbergTask::report() {
propagateSubtaskError();
CHECK_OP(stateInfo, ReportResult_Finished);
assert(kalignSubTask->inputMA.getNumRows() == kalignSubTask->resultMA.getNumRows());
return ReportResult_Finished;
}
QList<Task*> BAMImporterTask::onSubTaskFinished(Task* subTask) {
QList<Task*> res;
if (subTask->hasError()) {
propagateSubtaskError();
return res;
}
if (loadInfoTask == subTask) {
initPrepareToImportTask();
CHECK(NULL != prepareToImportTask, res);
res << prepareToImportTask;
}
else if (prepareToImportTask == subTask && prepareToImportTask->isNewURL()) {
initLoadBamInfoTask();
CHECK(NULL != loadBamInfoTask, res);
res << loadBamInfoTask;
}
else if (loadBamInfoTask == subTask || prepareToImportTask == subTask) {
initConvertToSqliteTask();
CHECK(NULL != convertTask, res);
res << convertTask;
}
else if (isSqliteDbTransit && convertTask == subTask) {
initCloneObjectTasks();
CHECK(!cloneTasks.isEmpty(), res);
res << cloneTasks;
}
else if (!isSqliteDbTransit && convertTask == subTask) {
initLoadDocumentTask();
CHECK(NULL != loadDocTask, res);
res << loadDocTask;
}
else if ((isSqliteDbTransit && cloneTasks.contains(subTask))) {
cloneTasks.removeOne(subTask);
CloneObjectTask *cloneTask = qobject_cast<CloneObjectTask *>(subTask);
SAFE_POINT_EXT(NULL != cloneTask, setError("Unexpected task type: CloneObjectTask expected"), res);
delete cloneTask->getSourceObject();
if (cloneTasks.isEmpty()) {
initLoadDocumentTask();
CHECK(NULL != loadDocTask, res);
res << loadDocTask;
}
}
else if (subTask == loadDocTask) {
resultDocument = loadDocTask->takeDocument();
}
return res;
}
QList<Task*> DNASequenceGeneratorTask::onSubTaskFinished(Task* subTask) {
QList<Task*> tasks;
if (hasError() || isCanceled() || subTask->isCanceled()) {
return tasks;
}
propagateSubtaskError();
if (subTask == loadRefTask) {
tasks << onLoadRefTaskFinished( );
} else if (subTask == evalTask) {
tasks << onEvalTaskFinished( );
} else if ( subTask == generateTask ) {
tasks << onGenerateTaskFinished( );
} else if (saveTask == subTask) {
tasks << onSaveTaskFinished( );
}
return tasks;
}
Task::ReportResult GTest_uHMMERCalibrate::report() {
propagateSubtaskError();
if (isCanceled() || hasError()) {
return ReportResult_Finished;
}
for(int i=0; i < nCalibrates; i++){
float new_mu = ((::plan7_s*)calibrateTask[i]->getHMM())->mu;
if (qAbs(new_mu - mu) > 0.1) {
stateInfo.setError( QString("mu value %1, expected %2").arg(new_mu).arg(mu) );
break;
}
float new_lambda = ((::plan7_s*)calibrateTask[i]->getHMM())->lambda;
if (qAbs(new_lambda - lambda) > 0.1){
stateInfo.setError( QString("lambda value %1, expected %2").arg(new_lambda).arg(lambda) );
break;
}
}
return ReportResult_Finished;
}
QList<Task *> SpideyAlignmentTask::onSubTaskFinished(Task *subTask) {
QList<Task *> res;
propagateSubtaskError();
if (hasError() || isCanceled()) {
return res;
}
if (subTask == prepareDataForSpideyTask) {
SAFE_POINT(!prepareDataForSpideyTask->getResultPath().isEmpty(), "Invalid result path!",
res);
tmpOutputUrl = prepareDataForSpideyTask->getResultPath();
const QStringList &arguments = prepareDataForSpideyTask->getArgumentsList();
spideyTask = new ExternalToolRunTask(ET_SPIDEY, arguments, new SpideyLogParser());
spideyTask->setSubtaskProgressWeight(95);
res.append(spideyTask);
} else if (subTask == spideyTask) {
if (!QFile::exists(tmpOutputUrl)) {
if (AppContext::getExternalToolRegistry()->getByName(ET_SPIDEY)->isValid()) {
stateInfo.setError(tr("Output file not found"));
} else {
ExternalTool *spideyTool = AppContext::getExternalToolRegistry()->getByName(ET_SPIDEY);
SAFE_POINT(NULL != spideyTool, "Invalid Spidey tool!", res);
stateInfo.setError(
tr("Output file not found. May be %1 tool path '%2' not valid?")
.arg(spideyTool->getName()).arg(spideyTool->getPath()));
}
return res;
}
// parse result
QFile resultFile(tmpOutputUrl);
if (!resultFile.open(QFile::ReadOnly)) {
setError(tr("Failed to open result file %1").arg(tmpOutputUrl));
return res;
}
QTextStream inStream(&resultFile);
bool strandDirect = true;
U2Location location;
location->op = U2LocationOperator_Join;
while (!inStream.atEnd()) {
QByteArray buf = inStream.readLine().toLatin1();
if (buf.startsWith("Strand")) {
strandDirect = buf.contains("plus");
}
if (buf.startsWith("Exon")) {
// TODO: better to use reg exp here
int startPos = buf.indexOf(":") + 1;
int endPos = buf.indexOf("(gen)");
if (startPos == -1 || endPos == -1) {
continue;
}
QByteArray loc = buf.mid(startPos, endPos - startPos).trimmed();
QList<QByteArray> loci = loc.split('-');
if (loci.size() < 2) {
continue;
}
int start = QString(loci.at(0)).toInt();
int finish = QString(loci.at(1)).toInt();
if (start == finish) {
continue;
}
location->regions.append(U2Region(start - 1, finish - start + 1));
}
}
if (!location->isEmpty()) {
SharedAnnotationData data(new AnnotationData);
data->location = location;
data->setStrand(U2Strand(strandDirect ? U2Strand::Direct : U2Strand::Complementary));
data->type = U2FeatureTypes::Exon;
data->name = "exon";
U1AnnotationUtils::addDescriptionQualifier(data, annDescription);
resultAnnotations.append(data);
}
}
return res;
}
QList<Task*> MafftAddToAlignmentTask::onSubTaskFinished(Task* subTask) {
QList<Task*> subTasks;
propagateSubtaskError();
if(subTask->isCanceled() || isCanceled() || hasError()) {
return subTasks;
}
if((subTask == saveAlignmentDocumentTask || subTask == saveSequencesDocumentTask) && saveAlignmentDocumentTask->isFinished()
&& saveSequencesDocumentTask->isFinished()) {
resultFilePath = settings.resultFileName.isEmpty() ? tmpDirUrl + QDir::separator() + "result_aln.fa" : settings.resultFileName.getURLString();
QStringList arguments;
if(settings.addAsFragments) {
arguments << "--addfragments";
} else {
arguments << "--add";
}
arguments << saveSequencesDocumentTask->getURL().getURLString();
const DNAAlphabet* alphabet = U2AlphabetUtils::getById(settings.alphabet);
SAFE_POINT_EXT(alphabet != NULL, setError("Albhabet is invalid."), subTasks);
if(alphabet->isRaw()) {
arguments << "--anysymbol";
}
if(useMemsaveOption()) {
arguments << "--memsave";
}
if(settings.reorderSequences) {
arguments << "--reorder";
}
arguments << saveAlignmentDocumentTask->getDocument()->getURLString();
QString outputUrl = resultFilePath + ".out.fa";
logParser = new MAFFTLogParser(inputMsa->getNumRows(), 1, outputUrl);
mafftTask = new ExternalToolRunTask(ET_MAFFT, arguments, logParser);
mafftTask->setStandartOutputFile(resultFilePath);
mafftTask->setSubtaskProgressWeight(65);
subTasks.append(mafftTask);
} else if (subTask == mafftTask) {
SAFE_POINT(logParser != NULL, "logParser is null", subTasks);
logParser->cleanup();
if (!QFileInfo(resultFilePath).exists()) {
if (AppContext::getExternalToolRegistry()->getByName(ET_MAFFT)->isValid()){
stateInfo.setError(tr("Output file '%1' not found").arg(resultFilePath));
} else {
stateInfo.setError(tr("Output file '%3' not found. May be %1 tool path '%2' not valid?")
.arg(AppContext::getExternalToolRegistry()->getByName(ET_MAFFT)->getName())
.arg(AppContext::getExternalToolRegistry()->getByName(ET_MAFFT)->getPath())
.arg(resultFilePath));
}
return subTasks;
}
ioLog.details(tr("Loading output file '%1'").arg(resultFilePath));
IOAdapterFactory* iof = AppContext::getIOAdapterRegistry()->getIOAdapterFactoryById(BaseIOAdapters::LOCAL_FILE);
loadTmpDocumentTask = new LoadDocumentTask(BaseDocumentFormats::FASTA, resultFilePath, iof);
loadTmpDocumentTask->setSubtaskProgressWeight(5);
subTasks.append(loadTmpDocumentTask);
} else if(subTask == loadTmpDocumentTask) {
modStep = new U2UseCommonUserModStep(settings.msaRef, stateInfo);
}
return subTasks;
}
