Task * CufflinksWorker::tick() {
if (false == settingsAreCorrect) {
return NULL;
}
if (input->hasMessage()) {
Message inputMessage = getMessageAndSetupScriptValues(input);
SAFE_POINT(!inputMessage.isEmpty(), "Internal error: message can't be NULL!", NULL);
QVariantMap data = inputMessage.getData().toMap();
if (settings.fromFile) {
settings.url = data[BaseSlots::URL_SLOT().getId()].toString();
} else {
settings.assemblyId = data[BaseSlots::ASSEMBLY_SLOT().getId()].value<SharedDbiDataHandler>();
}
// Create the task
CufflinksSupportTask* cufflinksSupportTask = new CufflinksSupportTask(settings);
cufflinksSupportTask->addListeners(createLogListeners());
connect(cufflinksSupportTask, SIGNAL(si_stateChanged()), SLOT(sl_cufflinksTaskFinished()));
return cufflinksSupportTask;
}
else if (input->isEnded()) {
setDone();
output->setEnded();
}
return NULL;
}
Task * MergeFastqWorker::tick() {
while (inputUrlPort->hasMessage()) {
const QString url = takeUrl();
CHECK(!url.isEmpty(), NULL);
inputUrls.append(url);
}
if (!inputUrlPort->isEnded()) {
return NULL;
}
if(!inputUrls.isEmpty()){
const QString outputDir = FileAndDirectoryUtils::createWorkingDir(inputUrls.first(), getValue<int>(OUT_MODE_ID), getValue<QString>(CUSTOM_DIR_ID), context->workingDir());
BaseNGSSetting setting;
setting.outDir = outputDir;
setting.outName = getTargetName(inputUrls.first(), outputDir);
setting.inputUrl = inputUrls.first();
setting.customParameters = getCustomParameters();
setting.listeners = createLogListeners();
Task *t = getTask(setting);
connect(new TaskSignalMapper(t), SIGNAL(si_taskFinished(Task*)), SLOT(sl_taskFinished(Task*)));
inputUrls.clear();;
return t;
}
if (inputUrlPort->isEnded()) {
setDone();
outputUrlPort->setEnded();
}
return NULL;
}
Task * CAP3Worker::runCap3() {
// Modify output file name, if required
QString fileName = getValue<QString>(OUTPUT_FILE);
const QString ext = ".ace";
if (datasetNumber > 0) {
bool appendExtToResult = false;
if (fileName.endsWith(ext)) {
int location = fileName.size() - ext.size();
fileName.truncate(location);
appendExtToResult = true;
}
fileName += "_" + QString::number(datasetNumber);
if (appendExtToResult) {
fileName += ext;
}
settings.outputFilePath = fileName;
}
// Run the task
CAP3SupportTask *capTask = new CAP3SupportTask(settings);
capTask->addListeners(createLogListeners());
connect(capTask, SIGNAL(si_stateChanged()), SLOT(sl_taskFinished()));
datasetNumber++;
settings.inputFiles.clear();
return capTask;
}
Task * RmdupBamWorker::tick() {
if (inputUrlPort->hasMessage()) {
const QString url = takeUrl();
CHECK(!url.isEmpty(), NULL);
const QString detectedFormat = FileAndDirectoryUtils::detectFormat(url);
if(detectedFormat.isEmpty()){
coreLog.info(tr("Unknown file format: ") + url);
return NULL;
}
if(detectedFormat == BaseDocumentFormats::BAM){
const QString outputDir = FileAndDirectoryUtils::createWorkingDir(url, getValue<int>(OUT_MODE_ID), getValue<QString>(CUSTOM_DIR_ID), context->workingDir());
BamRmdupSetting setting;
setting.outDir = outputDir;
setting.outName = getTargetName(url, outputDir);
setting.inputUrl = url;
setting.removeSingleEnd = getValue<bool>(REMOVE_SINGLE_END_ID);
setting.treatReads = getValue<bool>(TREAT_READS_ID);
SamtoolsRmdupTask *t = new SamtoolsRmdupTask(setting);
t->addListeners(createLogListeners());
connect(new TaskSignalMapper(t), SIGNAL(si_taskFinished(Task*)), SLOT(sl_taskFinished(Task*)));
return t;
}
}
if (inputUrlPort->isEnded()) {
setDone();
outputUrlPort->setEnded();
}
return NULL;
}
Task * CuffmergeWorker::createCuffmergeTask() {
CuffmergeSettings result = scanParameters();
result.storage = context->getDataStorage();
result.annotationTables = annTableHandlers;
CuffmergeSupportTask* supportTask = new CuffmergeSupportTask(result);
supportTask->addListeners(createLogListeners());
return supportTask;
}
Task* ClustalOWorker::tick() {
if (input->hasMessage()) {
Message inputMessage = getMessageAndSetupScriptValues(input);
if (inputMessage.isEmpty()) {
output->transit();
return NULL;
}
cfg.numIterations=actor->getParameter(NUM_ITERATIONS)->getAttributeValue<int>(context);
cfg.maxGuidetreeIterations=actor->getParameter(MAX_GT_ITERATIONS)->getAttributeValue<int>(context);
cfg.maxHMMIterations=actor->getParameter(MAX_HMM_ITERATIONS)->getAttributeValue<int>(context);
cfg.setAutoOptions=actor->getParameter(SET_AUTO)->getAttributeValue<bool>(context);
cfg.numberOfProcessors=AppContext::getAppSettings()->getAppResourcePool()->getIdealThreadCount();
QString path=actor->getParameter(EXT_TOOL_PATH)->getAttributeValue<QString>(context);
if(QString::compare(path, "default", Qt::CaseInsensitive) != 0){
AppContext::getExternalToolRegistry()->getByName(ET_CLUSTALO)->setPath(path);
}
path=actor->getParameter(TMP_DIR_PATH)->getAttributeValue<QString>(context);
if(QString::compare(path, "default", Qt::CaseInsensitive) != 0){
AppContext::getAppSettings()->getUserAppsSettings()->setUserTemporaryDirPath(path);
}
QVariantMap qm = inputMessage.getData().toMap();
SharedDbiDataHandler msaId = qm.value(BaseSlots::MULTIPLE_ALIGNMENT_SLOT().getId()).value<SharedDbiDataHandler>();
QScopedPointer<MultipleSequenceAlignmentObject> msaObj(StorageUtils::getMsaObject(context->getDataStorage(), msaId));
SAFE_POINT(!msaObj.isNull(), "NULL MSA Object!", NULL);
const MultipleSequenceAlignment msa = msaObj->getMultipleAlignment();
if (msa->isEmpty()) {
algoLog.error(tr("An empty MSA '%1' has been supplied to ClustalO.").arg(msa->getName()));
return NULL;
}
ClustalOSupportTask* supportTask = new ClustalOSupportTask(msa, GObjectReference(), cfg);
supportTask->addListeners(createLogListeners());
Task *t = new NoFailTaskWrapper(supportTask);
connect(t, SIGNAL(si_stateChanged()), SLOT(sl_taskFinished()));
return t;
} else if (input->isEnded()) {
setDone();
output->setEnded();
}
return NULL;
}
Task* CallVariantsWorker::tick() {
U2OpStatus2Log os;
//put variant tracks
while (!cache.isEmpty()) {
output->put(cache.takeFirst());
}
checkState(os);
CHECK_OP_EXT(os, setDone(), NULL);
//take assemblies from one dataset
if (assemblyPort->hasMessage() && settings.assemblyUrls.isEmpty()) {
takeAssembly(os);
CHECK_OP_EXT(os, processError(os), NULL);
} else if (settings.assemblyUrls.isEmpty() && !assemblyUrls.isEmpty()) {
settings.assemblyUrls = assemblyUrls;
assemblyUrls.clear();
}
//take reference sequence
if (refSeqPort->hasMessage() && settings.refSeqUrl.isEmpty()) {
takeReference(os);
CHECK_OP_EXT(os, processError(os), NULL);
}
//do
if (cache.isEmpty() && !settings.refSeqUrl.isEmpty() && !settings.assemblyUrls.isEmpty()) {
settings.variationsUrl = GUrlUtils::rollFileName(getValue<QString>(OUT_URL), "_", QSet<QString>());
CallVariantsTask* t = new CallVariantsTask(settings, context->getDataStorage());
t->addListeners(createLogListeners(3));
connect(t, SIGNAL(si_stateChanged()), SLOT(sl_taskFinished()));
settings.assemblyUrls.clear();
settings.refSeqUrl.clear();
return t;
}
return NULL;
}
Task * SnpEffWorker::tick() {
if (inputUrlPort->hasMessage()) {
const QString url = takeUrl();
CHECK(!url.isEmpty(), NULL);
QString outputDir = FileAndDirectoryUtils::createWorkingDir(url, getValue<int>(OUT_MODE_ID), getValue<QString>(CUSTOM_DIR_ID), context->workingDir());
U2OpStatusImpl os;
outputDir = GUrlUtils::createDirectory(outputDir + SnpEffWorker::BASE_SNPEFF_SUBDIR, "_", os);
SnpEffSetting setting;
setting.inputUrl = url;
setting.outDir = outputDir;
setting.inFormat = getValue<QString>(INPUT_FORMAT);
setting.outFormat = getValue<QString>(OUTPUT_FORMAT);
setting.genome = getValue<QString>(GENOME);
setting.updownLength = getValue<QString>(UPDOWN_LENGTH);
setting.canon = getValue<bool>(CANON);
setting.hgvs = getValue<bool>(HGVS);
setting.lof = getValue<bool>(LOF);
setting.motif = getValue<bool>(MOTIF);
SnpEffTask *t = new SnpEffTask (setting);
connect(new TaskSignalMapper(t), SIGNAL(si_taskFinished(Task*)), SLOT(sl_taskFinished(Task*)));
QList<ExternalToolListener *> listeners = createLogListeners();
listeners[0]->setLogProcessor(new SnpEffLogProcessor(monitor(), getActorId()));
t->addListeners(listeners);
return t;
}
if (inputUrlPort->isEnded()) {
setDone();
outputUrlPort->setEnded();
}
return NULL;
}
Task *ConservationPlotWorker::tick() {
U2OpStatus2Log os;
while (inChannel->hasMessage()) {
Message m = getMessageAndSetupScriptValues(inChannel);
QVariantMap data = m.getData().toMap();
if (!data.contains(ANNOT_SLOT_ID)) {
os.setError("Annotations slot is empty");
return new FailTask(os.getError());
}
plotData = StorageUtils::getAnnotationTableHandlers(data[ANNOT_SLOT_ID]);
}
if (!inChannel->isEnded()) {
return NULL;
}
ConservationPlotSettings settings = createConservationPlotSettings(os);
if (os.hasError()) {
return new FailTask(os.getError());
}
ConservationPlotTask* t = new ConservationPlotTask(settings, context->getDataStorage(), plotData);
t->addListeners(createLogListeners());
connect(t, SIGNAL(si_stateChanged()), SLOT(sl_taskFinished()));
return t;
if (inChannel->isEnded()) {
setDone();
}
return NULL;
}
Task* ClustalWWorker::tick() {
if (input->hasMessage()) {
Message inputMessage = getMessageAndSetupScriptValues(input);
if (inputMessage.isEmpty()) {
output->transit();
return NULL;
}
cfg.gapOpenPenalty=actor->getParameter(GAP_OPEN_PENALTY)->getAttributeValue<float>(context);
cfg.gapExtenstionPenalty=actor->getParameter(GAP_EXT_PENALTY)->getAttributeValue<float>(context);
cfg.gapDist=actor->getParameter(GAP_DIST)->getAttributeValue<float>(context);
cfg.endGaps=actor->getParameter(END_GAPS)->getAttributeValue<bool>(context);
cfg.noHGaps=actor->getParameter(NO_HGAPS)->getAttributeValue<bool>(context);
cfg.noPGaps=actor->getParameter(NO_PGAPS)->getAttributeValue<bool>(context);
if(actor->getParameter(ITERATION)->getAttributeValue<int>(context) != 0){
if(actor->getParameter(ITERATION)->getAttributeValue<int>(context) == 1){
cfg.iterationType="TREE";
}else if(actor->getParameter(ITERATION)->getAttributeValue<int>(context) == 2){
cfg.iterationType="ALIGNMENT";
}
if(actor->getParameter(NUM_ITERATIONS)->getAttributeValue<int>(context) != 3){
cfg.numIterations=actor->getParameter(NUM_ITERATIONS)->getAttributeValue<int>(context);
}
}
if(actor->getParameter(MATRIX)->getAttributeValue<int>(context) == -1){
if(actor->getParameter(MATRIX)->getAttributeValue<int>(context) == 0){
cfg.matrix="IUB";
}else if(actor->getParameter(MATRIX)->getAttributeValue<int>(context) == 1){
cfg.matrix="CLUSTALW";
}else if(actor->getParameter(MATRIX)->getAttributeValue<int>(context) == 2){
cfg.matrix="BLOSUM";
}else if(actor->getParameter(MATRIX)->getAttributeValue<int>(context) == 3){
cfg.matrix="PAM";
}else if(actor->getParameter(MATRIX)->getAttributeValue<int>(context) == 4){
cfg.matrix="GONNET";
}else if(actor->getParameter(MATRIX)->getAttributeValue<int>(context) == 5){
cfg.matrix="ID";
}
}
QString path=actor->getParameter(EXT_TOOL_PATH)->getAttributeValue<QString>(context);
if(QString::compare(path, "default", Qt::CaseInsensitive) != 0){
AppContext::getExternalToolRegistry()->getByName(ET_CLUSTAL)->setPath(path);
}
path=actor->getParameter(TMP_DIR_PATH)->getAttributeValue<QString>(context);
if(QString::compare(path, "default", Qt::CaseInsensitive) != 0){
AppContext::getAppSettings()->getUserAppsSettings()->setUserTemporaryDirPath(path);
}
QVariantMap qm = inputMessage.getData().toMap();
SharedDbiDataHandler msaId = qm.value(BaseSlots::MULTIPLE_ALIGNMENT_SLOT().getId()).value<SharedDbiDataHandler>();
QScopedPointer<MultipleSequenceAlignmentObject> msaObj(StorageUtils::getMsaObject(context->getDataStorage(), msaId));
SAFE_POINT(!msaObj.isNull(), "NULL MSA Object!", NULL);
const MultipleSequenceAlignment msa = msaObj->getMultipleAlignment();
if (msa->isEmpty()) {
algoLog.error(tr("An empty MSA '%1' has been supplied to ClustalW.").arg(msa->getName()));
return NULL;
}
ClustalWSupportTask* supportTask = new ClustalWSupportTask(msa, GObjectReference(), cfg);
supportTask->addListeners(createLogListeners());
Task *t = new NoFailTaskWrapper(supportTask);
connect(t, SIGNAL(si_stateChanged()), SLOT(sl_taskFinished()));
return t;
} else if (input->isEnded()) {
setDone();
output->setEnded();
}
return NULL;
}
