C++ (Cpp) takeUrl Examples

Example #1

File: FASTQWorkersLibrary.cpp Project: ugeneunipro/ugene-old

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;
}

Example #2

File: SortBamWorker.cpp Project: ggrekhov/ugene

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;
}

Example #3

File: RmdupBamWorker.cpp Project: ugeneunipro/ugene

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;
}

Example #4

File: SnpEffWorker.cpp Project: ugeneunipro/ugene-old

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;
}