Command* Parser::nextCommand() throw(ParserException,
UnsafeInterruptException) {
Debug("parser") << "nextCommand()" << std::endl;
Command* cmd = NULL;
if (!d_commandQueue.empty()) {
cmd = d_commandQueue.front();
d_commandQueue.pop_front();
setDone(cmd == NULL);
} else {
try {
cmd = d_input->parseCommand();
d_commandQueue.push_back(cmd);
cmd = d_commandQueue.front();
d_commandQueue.pop_front();
setDone(cmd == NULL);
} catch (ParserException& e) {
setDone();
throw;
} catch (exception& e) {
setDone();
parseError(e.what());
}
}
Debug("parser") << "nextCommand() => " << cmd << std::endl;
if (cmd != NULL && dynamic_cast<SetOptionCommand*>(cmd) == NULL &&
dynamic_cast<QuitCommand*>(cmd) == NULL) {
// don't count set-option commands as to not get stuck in an infinite
// loop of resourcing out
const Options& options = d_exprManager->getOptions();
d_resourceManager->spendResource(options.getParseStep());
}
return cmd;
}
Command* Parser::nextCommand() throw(ParserException) {
Debug("parser") << "nextCommand()" << std::endl;
Command* cmd = NULL;
if(!d_commandQueue.empty()) {
cmd = d_commandQueue.front();
d_commandQueue.pop_front();
setDone(cmd == NULL);
} else {
try {
cmd = d_input->parseCommand();
d_commandQueue.push_back(cmd);
cmd = d_commandQueue.front();
d_commandQueue.pop_front();
setDone(cmd == NULL);
} catch(ParserException& e) {
setDone();
throw;
} catch(exception& e) {
setDone();
parseError(e.what());
}
}
Debug("parser") << "nextCommand() => " << cmd << std::endl;
return cmd;
}
int licensePage::setReady()
{
if (agreeCheckBox->isChecked())
{
setDone(true);
}
else
{
setDone(false);
}
return 0;
}
int configurationPage::confirmRootPassword()
{
QString icon;
if(rootPasswordLineEdit->text() == rootPasswordConfLineEdit->text())
{
icon = getApplicationFile("/Icons/right.png");
setDone(true);
}
else
{
icon = getApplicationFile("/Icons/wrong.png");
setDone(false);
}
rootPasswordConfLabel->setText("<img src=\""+icon+ "\" height=20 width=20 >");
return 0;
}
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;
}
void
GetUserTrackRequest::processPacket(PacketContainer* pack)
{
switch (m_state) {
case INIT:
mc2log << error << "GetUserTrackRequest: Got packet in INIT" << endl;
break;
case GET_USER_TRACK_PACKET : {
GetUserTrackReplyPacket* p =
static_cast<GetUserTrackReplyPacket*>(pack->getPacket());
if (p->getStatus() == StringTable::OK) {
p->getUserTrackElements(m_resultElements);
m_state = DONE;
setDone(true);
} else {
m_state = ERROR;
}
} break;
case DONE:
mc2log << error << "GetUserTrackRequest: Got packet in DONE" << endl;
break;
case ERROR:
mc2log << error << "GetUserTrackRequest: Got packet in ERROR" << endl;
break;
}
delete pack;
}
void AlarmSchedulerPrecise::processExpiredAlarms(
boost::optional<AlarmScheduler::AlarmExpireHook> hook) {
AlarmCount processed = 0;
auto now = clockSource()->now();
std::vector<Promise<void>> toExpire;
AlarmMapIt it;
stdx::unique_lock<stdx::mutex> lk(_mutex);
for (it = _alarms.begin(); it != _alarms.end();) {
if (hook && !(*hook)(processed + 1)) {
break;
}
if (it->first > now) {
break;
}
processed++;
toExpire.push_back(std::move(it->second.promise));
auto handle = it->second.handle.lock();
if (handle) {
handle->setDone();
}
it = _alarms.erase(it);
}
lk.unlock();
for (auto& promise : toExpire) {
promise.emplaceValue();
}
}
Task* PFMatrixBuildWorker::tick() {
if (input->hasMessage()) {
Message inputMessage = getMessageAndSetupScriptValues(input);
if (inputMessage.isEmpty()) {
output->transit();
return NULL;
}
mtype = PFMatrixWorkerFactory::FREQUENCY_MATRIX_MODEL_TYPE();
QVariantMap data = inputMessage.getData().toMap();
cfg.type = actor->getParameter(TYPE_ATTR)->getAttributeValue<bool>(context) ? PM_DINUCLEOTIDE : PM_MONONUCLEOTIDE;
QVariantMap qm = inputMessage.getData().toMap();
SharedDbiDataHandler msaId = qm.value(BaseSlots::MULTIPLE_ALIGNMENT_SLOT().getId()).value<SharedDbiDataHandler>();
QScopedPointer<MAlignmentObject> msaObj(StorageUtils::getMsaObject(context->getDataStorage(), msaId));
SAFE_POINT(!msaObj.isNull(), "NULL MSA Object!", NULL);
const MAlignment &msa = msaObj->getMAlignment();
Task* t = new PFMatrixBuildTask(cfg, msa);
connect(t, SIGNAL(si_stateChanged()), SLOT(sl_taskFinished()));
return t;
} 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 * 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;
}
void doJob()
{
test("Nothing");
postBlinds.insert(HDValue(Hash("ARC1"), ""));
test("Single blind install");
postBlinds.insert(HDValue(Hash("ARC2"), "a"));
postBlinds.insert(HDValue(Hash("ARC3"), "b/"));
post["blah"] = Hash("blah");
test("Multi-blind install with paths");
postBlinds.insert(HDValue(Hash("ARC1"), ""));
pre["blah"] = Hash("blah");
test("Single install, with upgrade info present");
preBlinds.insert(HDValue(Hash("ARC1"), ""));
preBlinds.insert(HDValue(Hash("ARC2"), "a"));
postBlinds.insert(HDValue(Hash("ARC3"), "b/"));
postBlinds.insert(HDValue(Hash("ARC4"), ""));
test("Pre and post blinds");
preBlinds.insert(HDValue(Hash("ARC1"), ""));
preBlinds.insert(HDValue(Hash("ARC2"), "a"));
test("Just pre blinds");
assert(!checkStatus());
setDone();
}
Task * SortBamWorker::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());
BamSortSetting setting;
setting.outDir = outputDir;
setting.outName = getTargetName(url, outputDir);
setting.inputUrl = url;
setting.index = getValue<bool>(INDEX_ID);
Task *t = new SamtoolsSortTask(setting);
connect(new TaskSignalMapper(t), SIGNAL(si_taskFinished(Task*)), SLOT(sl_taskFinished(Task*)));
return t;
}
}
if (inputUrlPort->isEnded()) {
setDone();
outputUrlPort->setEnded();
}
return NULL;
}
void BrowseModelPrivate::onCallReady()
{
auto call = qobject_cast<ServiceProxyCall *>(sender());
if (call == 0) {
return;
}
if (call->cancelled()) {
return;
}
call->finalize(QStringList() << QLatin1String("Result")
<< QLatin1String("NumberReturned")
<< QLatin1String("TotalMatches"));
setBusy(false);
if (call->hasError()) {
Q_EMIT error(call->errorCode(), call->errorMessage());
return;
}
unsigned int numberReturned = call->get(QLatin1String("NumberReturned")).toUInt();
if (numberReturned == 0) {
setDone(true);
return;
}
auto objects = DIDLLiteParser().parse(call->get(QLatin1String("Result")).toString());
beginInsertRows(QModelIndex(),
m_data.count(),
m_data.count() + numberReturned - 1);
m_data << objects;
endInsertRows();
m_currentOffset += numberReturned;
unsigned int totalMatches = call->get(QLatin1String("TotalMatches")).toUInt();
if (totalMatches > 0 && m_currentOffset < totalMatches) {
m_call->setArg(QLatin1String("StartingIndex"), m_currentOffset);
m_call->run();
} else {
setDone(true);
}
}
/** Executes the request now, i.e. in the main thread and without involving
* the manager thread.. This calles prepareOperation, operation, and
* afterOperation.
*/
void Request::executeNow()
{
assert(isPreparing());
setBusy();
execute();
callback();
setDone();
} // executeNow
int languagesPage::initAll()
{
pageBase::initAll();
initLanguages();
connect(okPushButton, SIGNAL(clicked()), this, SLOT(applyLanguage()));
setDone(true);
return 0;
}
Expr Parser::nextExpression() throw(ParserException) {
Debug("parser") << "nextExpression()" << std::endl;
Expr result;
if(!done()) {
try {
result = d_input->parseExpr();
setDone(result.isNull());
} catch(ParserException& e) {
setDone();
throw;
} catch(exception& e) {
setDone();
parseError(e.what());
}
}
Debug("parser") << "nextExpression() => " << result << std::endl;
return result;
}
MainMenu::MainMenu( World * worldObject )
{
cout << "Main Menu instansiated . . .\n\n";
setNextState (Screen_GAME);
setDone(true);
//object setup
this->worldObject = worldObject; // world object
}
virtual MoveInfo getMove(Creature* c) override {
if (!c->hasSkill(Skill::get(SkillId::CONSTRUCTION)))
return NoMove;
Vec2 dir = getPosition() - c->getPosition();
if (dir.length8() == 1) {
if (c->canConstruct(dir, type))
return {1.0, [this, c, dir] {
c->construct(dir, type);
if (!c->canConstruct(dir, type)) {
setDone();
getCollective()->onConstructed(getPosition(), type);
}
}};
else {
setDone();
return NoMove;
}
} else
return getMoveToPosition(c);
}
Expr Parser::nextExpression() throw(ParserException, UnsafeInterruptException) {
Debug("parser") << "nextExpression()" << std::endl;
const Options& options = d_exprManager->getOptions();
d_resourceManager->spendResource(options.getParseStep());
Expr result;
if (!done()) {
try {
result = d_input->parseExpr();
setDone(result.isNull());
} catch (ParserException& e) {
setDone();
throw;
} catch (exception& e) {
setDone();
parseError(e.what());
}
}
Debug("parser") << "nextExpression() => " << result << std::endl;
return result;
}
void
ExpandRouteRequest::processPacket( PacketContainer* cont ) {
m_expander->packetReceived( cont );
if (m_expander->getDone()) {
// We're done, create answer. Answer can be null,
// then something went wrong.
m_answer = m_expander->createAnswer();
setDone( true );
}
delete cont;
}
void BrowseModelPrivate::refresh() {
beginResetModel();
setDone(false);
setBusy(true);
m_currentOffset = 0;
m_data.clear();
qDebug () << "Starting to browse" << m_call->arg(QLatin1String("ObjectID"));
m_call->setArg(QLatin1String("StartingIndex"), m_currentOffset);
m_call->run();
endResetModel();
}
void ConservationPlotWorker::sl_taskFinished() {
ConservationPlotTask *t = dynamic_cast<ConservationPlotTask*>(sender());
if (!t->isFinished() || t->hasError() || t->isCanceled()) {
return;
}
context->getMonitor()->addOutputFile(t->getSettings().outFile, getActor()->getId(), true);
if (inChannel->isEnded() && !inChannel->hasMessage()) {
setDone();
}
}
int KernelRenderThread::cancel()
{
if (isRunning())
{
setDone(true);
while (isRunning())
{
OpenThreads::Thread::YieldCurrentThread();
}
}
return 0;
}
Task* SiteconReader::tick() {
if (urls.isEmpty() && tasks.isEmpty()) {
setDone();
output->setEnded();
} else {
Task* t = new SiteconReadTask(urls.takeFirst());
connect(t, SIGNAL(si_stateChanged()), SLOT(sl_taskFinished()));
tasks.append(t);
return t;
}
return NULL;
}
virtual MoveInfo getMove(Creature* c) override {
CHECK(!pickedUp);
if (!itemsExist(c->getLevel()->getSquare(position))) {
callback->onCantPickItem(items);
setDone();
return NoMove;
}
if (c->getPosition() == position) {
vector<Item*> hereItems;
for (Item* it : c->getPickUpOptions())
if (items.contains(it)) {
hereItems.push_back(it);
items.erase(it);
}
callback->onCantPickItem(items);
if (hereItems.empty()) {
setDone();
return NoMove;
}
items = hereItems;
if (auto action = c->pickUp(hereItems))
return {1.0, action.append([=] {
pickedUp = true;
onPickedUp();
callback->onPickedUp(position, hereItems);
})};
else {
callback->onCantPickItem(items);
setDone();
return NoMove;
}
}
if (auto action = c->moveTowards(position, true))
return action;
else if (--tries == 0) {
callback->onCantPickItem(items);
setDone();
}
return NoMove;
}
virtual MoveInfo getMove(Creature* c) override {
CHECK(!pickedUp);
if (c->getPosition() == getPosition()) {
vector<Item*> hereItems;
for (Item* it : c->getPickUpOptions())
if (items.contains(it)) {
hereItems.push_back(it);
items.erase(it);
}
getCollective()->onCantPickItem(items);
if (hereItems.empty()) {
setDone();
return NoMove;
}
items = hereItems;
if (c->canPickUp(hereItems))
return {1.0, [=] {
for (auto elem : Item::stackItems(hereItems))
c->globalMessage(c->getTheName() + " picks up " + elem.first, "");
c->pickUp(hereItems);
pickedUp = true;
onPickedUp();
getCollective()->onPickedUp(getPosition(), hereItems);
}};
else {
getCollective()->onCantPickItem(items);
setDone();
return NoMove;
}
}
if (MoveInfo move = getMoveToPosition(c, true))
return move;
else if (--tries == 0) {
getCollective()->onCantPickItem(items);
setDone();
}
return NoMove;
}
void FindPrimerPairsWorker::sl_onTaskFinished(Task* t) {
QString reportFileUrl = getValue<QString>(FindPrimerPairsWorkerFactory::OUT_FILE);
FindPrimersTask* findTask = qobject_cast<FindPrimersTask*>(t);
if(!findTask->hasError() && !findTask->isCanceled()) {
if(!findTask->getReport().isEmpty()) {
context->getMonitor()->addOutputFile(reportFileUrl, getActor()->getId(), true);
} else {
context->getMonitor()->addError(tr("No correct primers pairs found"), getActor()->getId(), WorkflowNotification::U2_WARNING);
}
}
setDone();
}
void StartStage_AutoPatch::beginDownload()
{
if (!m_pkCurrentDownloadTask && m_kDownloadList.size())
{
m_pkCurrentDownloadTask = m_kDownloadList.at(0);
m_kDownloadList.erase(m_kDownloadList.begin());
m_pkCurrentDownloadTask->Download();
}
else if (0 == m_kDownloadList.size())
{
setDone();
m_pkStageUI->showDone();
}
}
void doJob()
{
test("Empty");
a("file1", Hash("FILE1"));
a("file2", Hash("FILE2"));
d("file3", Hash("FILE3"));
d("file4", Hash("FILE4"));
test("Non-matching entries");
a("file1", Hash("FILE1"));
a("file2", Hash("FILE2"));
d("file3", Hash("FILE2"));
d("file4", Hash("FILE4"));
test("One matching entry");
d("file1", Hash("FILE1"));
d("file2", Hash("FILE1"));
d("file3", Hash("FILE2"));
d("file4", Hash("FILE2"));
a("file5", Hash("FILE1"));
a("file6", Hash("FILE2"));
a("file7", Hash("FILE1"));
test("Multiple options");
d("file1", Hash("FILE1"));
d("file2", Hash("FILE2"));
d("file3", Hash("FILE3"));
d("file4", Hash("FILE4"));
a("file5", Hash("FILE3"));
a("file6", Hash("FILE1"));
a("file7", Hash("FILE4"));
a("file8", Hash("FILE2"));
test("All entries matching");
// This would give undefined results in the real world
d("file1", Hash("FILE1"));
d("file2", Hash("FILE2"));
d("file3", Hash("FILE3"));
d("file4", Hash("FILE4"));
a("file1", Hash("FILE3"));
a("file2", Hash("FILE1"));
a("file3", Hash("FILE4"));
a("file4", Hash("FILE2"));
test("Pandemonium!");
setDone();
}
Task * GetFileListWorker::tick() {
if (files->hasNext()) {
QVariantMap m;
QString url = files->getNextFile();
QString datasetName = files->getLastDatasetName();
m[BaseSlots::URL_SLOT().getId()] = url;
m[BaseSlots::DATASET_SLOT().getId()] = datasetName;
MessageMetadata metadata(url, datasetName);
context->getMetadataStorage().put(metadata);
outChannel->put(Message(outChannel->getBusType(), m, metadata.getId()));
} else {
setDone();
outChannel->setEnded();
}
return NULL;
}
