/**
 * UGENE - Integrated Bioinformatics Tools.
 * Copyright (C) 2008-2024 UniPro <ugene@unipro.ru>
 * http://ugene.net
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
 * as published by the Free Software Foundation; either version 2
 * of the License, or (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
 * MA 02110-1301, USA.
 */

#include "ExternalProcessWorker.h"

#include <QDateTime>
#include <QFile>
#include <QUuid>

#include <U2Core/AnnotationTableObject.h>
#include <U2Core/AppContext.h>
#include <U2Core/AppSettings.h>
#include <U2Core/CmdlineTaskRunner.h>
#include <U2Core/DNASequenceObject.h>
#include <U2Core/DocumentModel.h>
#include <U2Core/ExternalToolRegistry.h>
#include <U2Core/ExternalToolRunTask.h>
#include <U2Core/FailTask.h>
#include <U2Core/FileAndDirectoryUtils.h>
#include <U2Core/GObjectRelationRoles.h>
#include <U2Core/GUrlUtils.h>
#include <U2Core/IOAdapter.h>
#include <U2Core/MsaImportUtils.h>
#include <U2Core/MsaObject.h>
#include <U2Core/TextObject.h>
#include <U2Core/U2AlphabetUtils.h>
#include <U2Core/U2OpStatusUtils.h>
#include <U2Core/U2SequenceUtils.h>
#include <U2Core/UserApplicationsSettings.h>

#include <U2Designer/DelegateEditors.h>

#include <U2Lang/ActorPrototypeRegistry.h>
#include <U2Lang/BaseActorCategories.h>
#include <U2Lang/BaseSlots.h>
#include <U2Lang/BaseTypes.h>
#include <U2Lang/ExternalToolCfg.h>
#include <U2Lang/IncludedProtoFactory.h>
#include <U2Lang/WorkflowEnv.h>
#include <U2Lang/WorkflowMonitor.h>

#include "CustomExternalToolLogParser.h"
#include "CustomExternalToolRunTaskHelper.h"
#include "util/CustomWorkerUtils.h"

namespace U2 {
namespace LocalWorkflow {

const static QString INPUT_PORT_TYPE("input-for-");
const static QString OUTPUT_PORT_TYPE("output-for-");
static const QString OUT_PORT_ID("out");

bool ExternalProcessWorkerFactory::init(ExternalProcessConfig* cfg) {
    QScopedPointer<ActorPrototype> proto(IncludedProtoFactory::getExternalToolProto(cfg));
    const bool prototypeRegistered = WorkflowEnv::getProtoRegistry()->registerProto(BaseActorCategories::CATEGORY_EXTERNAL(), proto.data());
    CHECK(prototypeRegistered, false);
    proto.take();

    const bool factoryRegistered = IncludedProtoFactory::registerExternalToolWorker(cfg);
    CHECK_EXT(factoryRegistered, delete WorkflowEnv::getProtoRegistry()->unregisterProto(cfg->id), false);

    return true;
}

namespace {
static QString toStringValue(const QVariantMap& data, U2OpStatus& os) {
    QString slot = BaseSlots::TEXT_SLOT().getId();
    if (!data.contains(slot)) {
        os.setError(QObject::tr("Empty text slot"));
        return "";
    }
    return data[slot].value<QString>();
}

static U2SequenceObject* toSequence(const QVariantMap& data, WorkflowContext* context, U2OpStatus& os) {
    QString slot = BaseSlots::DNA_SEQUENCE_SLOT().getId();
    if (!data.contains(slot)) {
        os.setError(QObject::tr("Empty sequence slot"));
        return nullptr;
    }
    SharedDbiDataHandler seqId = data[slot].value<SharedDbiDataHandler>();
    U2SequenceObject* seqObj = StorageUtils::getSequenceObject(context->getDataStorage(), seqId);
    if (seqObj == nullptr) {
        os.setError(QObject::tr("Error with sequence object"));
    }
    return seqObj;
}

static AnnotationTableObject* toAnotations(const QVariantMap& data, WorkflowContext* context, U2OpStatus& os) {
    QString slot = BaseSlots::ANNOTATION_TABLE_SLOT().getId();
    if (!data.contains(slot)) {
        os.setError(QObject::tr("Empty annotations slot"));
        return nullptr;
    }
    const QVariant annotationsData = data[slot];
    const QList<SharedAnnotationData> annList = StorageUtils::getAnnotationTable(context->getDataStorage(), annotationsData);

    AnnotationTableObject* annsObj = new AnnotationTableObject("Annotations", context->getDataStorage()->getDbiRef());
    annsObj->addAnnotations(annList);

    return annsObj;
}

static MsaObject* toAlignment(const QVariantMap& data, WorkflowContext* context, U2OpStatus& os) {
    QString slot = BaseSlots::MULTIPLE_ALIGNMENT_SLOT().getId();
    if (!data.contains(slot)) {
        os.setError(QObject::tr("Empty alignment slot"));
        return nullptr;
    }
    SharedDbiDataHandler msaId = data[slot].value<SharedDbiDataHandler>();
    MsaObject* msaObj = StorageUtils::getMsaObject(context->getDataStorage(), msaId);
    if (msaObj == nullptr) {
        os.setError(QObject::tr("Error with alignment object"));
    }
    return msaObj;
}

static TextObject* toText(const QVariantMap& data, WorkflowContext* context, U2OpStatus& os) {
    QString slot = BaseSlots::TEXT_SLOT().getId();
    if (!data.contains(slot)) {
        os.setError(QObject::tr("Empty text slot"));
        return nullptr;
    }
    QString text = data[slot].value<QString>();
    return TextObject::createInstance(text, "tmp_text_object", context->getDataStorage()->getDbiRef(), os);
}

static QString generateAndCreateURL(const QString& extention, const QString& name) {
    QString url;
    QString path = AppContext::getAppSettings()->getUserAppsSettings()->getCurrentProcessTemporaryDirPath("wd_external");
    QDir dir(path);
    if (!dir.exists()) {
        dir.mkpath(path);
    }
    url = path + "/tmp" + GUrlUtils::fixFileName(name + "_" + QUuid::createUuid().toString()) + "." + extention;
    return url;
}

static DocumentFormat* getFormat(const DataConfig& dataCfg, U2OpStatus& os) {
    DocumentFormat* f = AppContext::getDocumentFormatRegistry()->getFormatById(dataCfg.format);
    if (f == nullptr) {
        os.setError(QObject::tr("Unknown document format: %1").arg(dataCfg.format));
    }
    return f;
}

static Document* createDocument(const DataConfig& dataCfg, U2OpStatus& os) {
    DocumentFormat* f = getFormat(dataCfg, os);
    CHECK_OP(os, nullptr);

    IOAdapterFactory* iof = AppContext::getIOAdapterRegistry()->getIOAdapterFactoryById(BaseIOAdapters::LOCAL_FILE);
    QString url = generateAndCreateURL(f->getSupportedDocumentFileExtensions().first(), dataCfg.attrName);
    QScopedPointer<Document> d(f->createNewLoadedDocument(iof, url, os));
    CHECK_OP(os, nullptr);
    d->setDocumentOwnsDbiResources(false);
    return d.take();
}

static Document* loadDocument(const QString& url, const DataConfig& dataCfg, WorkflowContext* context, U2OpStatus& os) {
    DocumentFormat* f = getFormat(dataCfg, os);
    CHECK_OP(os, nullptr);

    IOAdapterFactory* iof = AppContext::getIOAdapterRegistry()->getIOAdapterFactoryById(BaseIOAdapters::LOCAL_FILE);
    QVariantMap hints;
    U2DbiRef dbiRef = context->getDataStorage()->getDbiRef();
    hints.insert(DocumentFormat::DBI_REF_HINT, qVariantFromValue(dbiRef));
    QScopedPointer<Document> d(f->loadDocument(iof, url, hints, os));
    CHECK_OP(os, nullptr);
    d->setDocumentOwnsDbiResources(false);
    return d.take();
}

static void addObjects(Document* d, WorkflowContext* context, const DataConfig& dataCfg, const QVariantMap& data, U2OpStatus& os) {
    if (dataCfg.isSequence()) {
        U2SequenceObject* seqObj = toSequence(data, context, os);
        CHECK_OP(os, );
        d->addObject(seqObj);
    } else if (dataCfg.isAnnotations()) {
        AnnotationTableObject* annsObj = toAnotations(data, context, os);
        CHECK_OP(os, );
        d->addObject(annsObj);
    } else if (dataCfg.isAlignment()) {
        MsaObject* msaObj = toAlignment(data, context, os);
        CHECK_OP(os, );
        d->addObject(msaObj);
    } else if (dataCfg.isAnnotatedSequence()) {
        U2SequenceObject* seqObj = toSequence(data, context, os);
        CHECK_OP(os, );
        d->addObject(seqObj);
        AnnotationTableObject* annsObj = toAnotations(data, context, os);
        CHECK_OP(os, );
        d->addObject(annsObj);

        QList<GObjectRelation> rel;
        rel << GObjectRelation(GObjectReference(seqObj), ObjectRole_Sequence);
        annsObj->setObjectRelations(rel);
    } else if (dataCfg.isText()) {
        TextObject* textObj = toText(data, context, os);
        CHECK_OP(os, );
        d->addObject(textObj);
    }
}
}  // namespace

ExternalProcessWorker::ExternalProcessWorker(Actor* a)
    : BaseWorker(a, false),
      output(nullptr) {
    ExternalToolCfgRegistry* reg = WorkflowEnv::getExternalCfgRegistry();
    cfg = reg->getConfigById(actor->getProto()->getId());
}

void ExternalProcessWorker::applySpecialInternalEnvvars(QString& execString,
                                                        ExternalProcessConfig* cfg) {
    CustomWorkerUtils::commandReplaceAllSpecialByUgenePath(execString, cfg);
}

void ExternalProcessWorker::applyAttributes(QString& execString) {
    QList<Attribute*> actorAttributes = actor->getAttributes();
    for (Attribute* a : qAsConst(actorAttributes)) {
        QString attrValue = a->getAttributePureValue().toString();
        DataTypePtr attrType = a->getAttributeType();
        if (attrType == BaseTypes::STRING_TYPE()) {
            attrValue = GUrlUtils::getQuotedString(attrValue);
        }
        bool wasReplaced = applyParamsToExecString(execString,
                                                   a->getId(),
                                                   attrValue);

        if (wasReplaced) {
            foreach (const AttributeConfig& attributeConfig, cfg->attrs) {
                if (attributeConfig.attributeId == a->getId() && attributeConfig.flags.testFlag(AttributeConfig::AddToDashboard)) {
                    urlsForDashboard.insert(attrValue,
                                            !attributeConfig.flags.testFlag(AttributeConfig::OpenWithUgene));
                    break;
                }
            }
        }
    }
}

bool ExternalProcessWorker::applyParamsToExecString(QString& execString, QString parName, QString parValue) {
    QRegularExpression regex = QRegularExpression(QString("((([^\\\\])|([^\\\\](\\\\\\\\)+)|(^))\\$)") + QString("(") + parName + QString(")") + (QString("(?=([^") + WorkflowEntityValidator::ID_ACCEPTABLE_SYMBOLS_TEMPLATE + QString("]|$))")));
    bool wasReplaced = false;

    // Replace the params one-by-one
    QRegularExpressionMatchIterator iter = regex.globalMatch(execString);
    while (iter.hasNext()) {
        QRegularExpressionMatch match = iter.next();
        if (match.hasMatch()) {
            QString m1 = match.captured(1);
            int start = match.capturedStart(0);
            int len = match.capturedLength();
            execString.replace(start + m1.length() - 1, len - m1.length() + 1, parValue);
            wasReplaced = true;

            // We need to re-iterate as the string was changed
            iter = regex.globalMatch(execString);
        }
    }

    return wasReplaced;
}

void ExternalProcessWorker::applyEscapedSymbols(QString& execString) {
    // Replace escaped symbols
    // Example:
    // "%USUPP_JAVA% \\%USUPP_JAVA% -version \\\$\%\\\\\%\\$"   ─┐
    // "/usr/bin/java \/usr/bin/java -version $%\\%\$"         <─┘
    execString.replace(QRegularExpression("\\\\([\\\\\\%\\$])"), "\\1");
}

QStringList ExternalProcessWorker::applyInputMessage(QString& execString, const DataConfig& dataCfg, const QVariantMap& data, U2OpStatus& os) {
    QStringList urls;
    QString paramValue;

    if (dataCfg.isStringValue()) {
        paramValue = GUrlUtils::getQuotedString(toStringValue(data, os));
        CHECK_OP(os, urls);
    } else {
        QScopedPointer<Document> d(createDocument(dataCfg, os));
        CHECK_OP(os, urls);
        addObjects(d.data(), context, dataCfg, data, os);
        CHECK_OP(os, urls);

        DocumentFormat* f = getFormat(dataCfg, os);
        CHECK_OP(os, urls);
        f->storeDocument(d.data(), os);
        CHECK_OP(os, urls);
        urls << d->getURLString();
        paramValue = GUrlUtils::getQuotedString(d->getURLString());
    }

    applyParamsToExecString(execString, dataCfg.attributeId, paramValue);
    return urls;
}

QString ExternalProcessWorker::prepareOutput(QString& execString, const DataConfig& dataCfg, U2OpStatus& os) {
    QString extension;

    if (dataCfg.isFileUrl()) {
        extension = "tmp";
    } else {
        DocumentFormat* f = getFormat(dataCfg, os);
        CHECK_OP(os, "")
        extension = f->getSupportedDocumentFileExtensions().first();
    }
    QString url = generateAndCreateURL(extension, dataCfg.attrName);
    bool replaced = applyParamsToExecString(execString, dataCfg.attributeId, GUrlUtils::getQuotedString(url));
    CHECK(replaced, "")

    return url;
}

Task* ExternalProcessWorker::tick() {
    QString error;
    if (!inputs.isEmpty() && finishWorkIfInputEnded(error)) {
        if (!error.isEmpty()) {
            return new FailTask(error);
        } else {
            return nullptr;
        }
    }

    QString execString = commandLine;

    int i = 0;
    foreach (const DataConfig& dataCfg, cfg->inputs) {  // write all input data to files
        Message inputMessage = getMessageAndSetupScriptValues(inputs[i]);
        i++;
        QVariantMap data = inputMessage.getData().toMap();
        U2OpStatusImpl os;
        inputUrls << applyInputMessage(execString, dataCfg, data, os);
        CHECK_OP(os, new FailTask(os.getError()));
    }

    QMap<QString, DataConfig> outputUrls;
    foreach (const DataConfig& dataCfg, cfg->outputs) {
        U2OpStatusImpl os;
        QString url = prepareOutput(execString, dataCfg, os);
        CHECK_OP(os, new FailTask(os.getError()));
        if (!url.isEmpty()) {
            outputUrls[url] = dataCfg;
        }
    }

    // The following call must be last call in the preparing execString chain
    // So, this is a very last step for execString:
    //     1) function init(): the first one is substitution of the internal vars (like '%...%')
    //     2) function init(): the second is applying attributes (something like '$...')
    //     3) this function: apply substitutions for Input/Output
    //     4) this function: this call replaces escaped symbols: '\$', '\%', '\\' by the '$', '%', '\'
    applyEscapedSymbols(execString);

    const QString workingDirectory = FileAndDirectoryUtils::createWorkingDir(context->workingDir(), FileAndDirectoryUtils::WORKFLOW_INTERNAL, "", context->workingDir());
    QString externalProcessFolder = GUrlUtils::fixFileName(cfg->name).replace(' ', '_');
    U2OpStatusImpl os;
    const QString externalProcessWorkingDir = GUrlUtils::createDirectory(workingDirectory + externalProcessFolder, "_", os);
    CHECK_OP(os, new FailTask(os.getError()));

    LaunchExternalToolTask* task = new LaunchExternalToolTask(execString, externalProcessWorkingDir, outputUrls);
    QList<ExternalToolListener*> listeners(createLogListeners());
    task->addListeners(listeners);
    connect(task, SIGNAL(si_stateChanged()), SLOT(sl_onTaskFinishied()));
    if (listeners[0] != nullptr) {
        listeners[0]->setToolName(cfg->name);
    }
    return task;
}

bool ExternalProcessWorker::finishWorkIfInputEnded(QString& error) {
    error.clear();
    const InputsCheckResult checkResult = checkInputBusState();
    switch (checkResult) {
        case ALL_INPUTS_FINISH:
            finish();
            return true;
        case SOME_INPUTS_FINISH:
            error = tr("Some inputs are finished while other still have not processed messages");
            finish();
            return true;
        case ALL_INPUTS_HAVE_MESSAGE:
            return false;
        case INTERNAL_ERROR:
            error = tr("An internal error has been spotted");
            finish();
            return true;
        case NOT_ALL_INPUTS_HAVE_MESSAGE:
            return false;
        default:
            error = tr("Unexpected result");
            finish();
            return true;
    }
}

void ExternalProcessWorker::finish() {
    setDone();
    if (output != nullptr) {
        output->setEnded();
    }
}

namespace {
static GObject* getObject(Document* d, GObjectType t, U2OpStatus& os) {
    QList<GObject*> objs = d->findGObjectByType(t, UOF_LoadedAndUnloaded);
    if (objs.isEmpty()) {
        os.setError(QObject::tr("No target objects in the file: %1").arg(d->getURLString()));
        return nullptr;
    }
    return objs.first();
}

static SharedDbiDataHandler getAlignment(Document* d, WorkflowContext* context, U2OpStatus& os) {
    GObject* obj = getObject(d, GObjectTypes::MULTIPLE_SEQUENCE_ALIGNMENT, os);
    CHECK_OP(os, SharedDbiDataHandler());

    auto msaObj = static_cast<MsaObject*>(obj);
    if (msaObj == nullptr) {
        os.setError(QObject::tr("Error with alignment object"));
        return SharedDbiDataHandler();
    }
    return context->getDataStorage()->getDataHandler(msaObj->getEntityRef());
}

static SharedDbiDataHandler getAnnotations(Document* d, WorkflowContext* context, U2OpStatus& os) {
    GObject* obj = getObject(d, GObjectTypes::ANNOTATION_TABLE, os);
    CHECK_OP(os, SharedDbiDataHandler());

    auto annsObj = static_cast<AnnotationTableObject*>(obj);
    if (annsObj == nullptr) {
        os.setError(QObject::tr("Error with annotations object"));
        return SharedDbiDataHandler();
    }
    return context->getDataStorage()->getDataHandler(annsObj->getEntityRef());
}

}  // namespace

void ExternalProcessWorker::sl_onTaskFinishied() {
    auto t = qobject_cast<LaunchExternalToolTask*>(sender());
    CHECK(t->isFinished(), );

    if (inputs.isEmpty()) {
        finish();
    }

    CHECK(!t->hasError(), );

    foreach (const QString& url, urlsForDashboard.keys()) {
        QFileInfo fileInfo(url);
        if (fileInfo.exists()) {
            if (fileInfo.isFile()) {
                monitor()->addOutputFile(url, getActorId(), urlsForDashboard.value(url));
            } else if (fileInfo.isDir()) {
                monitor()->addOutputFolder(url, getActorId());
            }
        }
    }

    CHECK(output != nullptr, );

    /* This variable and corresponded code parts with it
     * are temporary created for merging sequences.
     * When standard multiplexing/merging tools will be created
     * then the variable and code parts must be deleted.
     */
    QMap<QString, QList<U2EntityRef>> seqsForMergingBySlotId;
    QMap<QString, DataConfig> outputUrls = t->takeOutputUrls();
    QMap<QString, DataConfig>::iterator i = outputUrls.begin();
    QVariantMap v;

    for (; i != outputUrls.end(); i++) {
        DataConfig cfg = i.value();
        QString url = i.key();

        if (cfg.isFileUrl()) {
            if (QFile::exists(url)) {
                DataTypePtr dataType = WorkflowEnv::getDataTypeRegistry()->getById(cfg.type);
                v[WorkflowUtils::getSlotDescOfDatatype(dataType).getId()] = url;
                context->addExternalProcessFile(url);
            } else {
                reportError(tr("%1 file was not created").arg(url));
            }
        } else {
            U2OpStatusImpl os;
            QScopedPointer<Document> d(loadDocument(url, cfg, context, os));
            CHECK_OP_EXT(os, reportError(os.getError()), );
            d->setDocumentOwnsDbiResources(false);

            if (cfg.isSequence()) {
                QList<GObject*> seqObjects = d->findGObjectByType(GObjectTypes::SEQUENCE, UOF_LoadedAndUnloaded);
                DataTypePtr dataType = WorkflowEnv::getDataTypeRegistry()->getById(cfg.type);
                QString slotId = WorkflowUtils::getSlotDescOfDatatype(dataType).getId();
                if (seqObjects.size() == 1) {
                    GObject* obj = seqObjects.first();
                    Workflow::SharedDbiDataHandler id = context->getDataStorage()->getDataHandler(obj->getEntityRef());
                    v[slotId] = qVariantFromValue<SharedDbiDataHandler>(id);
                } else if (1 < seqObjects.size()) {
                    QList<U2EntityRef> refs;
                    foreach (GObject* obj, seqObjects) {
                        refs << obj->getEntityRef();
                    }
                    seqsForMergingBySlotId.insert(slotId, refs);
                }
            } else if (cfg.isAlignment()) {
                SharedDbiDataHandler msaId = getAlignment(d.data(), context, os);
                CHECK_OP_EXT(os, reportError(os.getError()), );
                DataTypePtr dataType = WorkflowEnv::getDataTypeRegistry()->getById(cfg.type);
                v[WorkflowUtils::getSlotDescOfDatatype(dataType).getId()] = qVariantFromValue<SharedDbiDataHandler>(msaId);
            } else if (cfg.isAnnotations()) {
                const SharedDbiDataHandler annTableId = getAnnotations(d.data(), context, os);
                CHECK_OP_EXT(os, reportError(os.getError()), );
                DataTypePtr dataType = WorkflowEnv::getDataTypeRegistry()->getById(cfg.type);
                v[WorkflowUtils::getSlotDescOfDatatype(dataType).getId()] = qVariantFromValue<SharedDbiDataHandler>(annTableId);
            } else if (cfg.isAnnotatedSequence()) {
                if (!d->findGObjectByType(GObjectTypes::SEQUENCE, UOF_LoadedAndUnloaded).isEmpty()) {
                    auto seqObj = static_cast<U2SequenceObject*>(d->findGObjectByType(GObjectTypes::SEQUENCE, UOF_LoadedAndUnloaded).first());
                    DNASequence seq = seqObj->getWholeSequence(os);
                    CHECK_OP_EXT(os, reportError(os.getError()), );
                    seq.alphabet = U2AlphabetUtils::getById(BaseDNAAlphabetIds::RAW());
                    SharedDbiDataHandler seqId = context->getDataStorage()->putSequence(seq);
                    v[BaseSlots::DNA_SEQUENCE_SLOT().getId()] = qVariantFromValue<SharedDbiDataHandler>(seqId);
                }
                const SharedDbiDataHandler annTableId = getAnnotations(d.data(), context, os);
                if (!os.hasError()) {
                    DataTypePtr dataType = WorkflowEnv::getDataTypeRegistry()->getById(cfg.type);
                    v[BaseSlots::ANNOTATION_TABLE_SLOT().getId()] = qVariantFromValue<SharedDbiDataHandler>(annTableId);
                }
            } else if (cfg.isText()) {
                if (!d->findGObjectByType(GObjectTypes::TEXT, UOF_LoadedAndUnloaded).isEmpty()) {
                    auto obj = static_cast<TextObject*>(d->findGObjectByType(GObjectTypes::TEXT, UOF_LoadedAndUnloaded).first());
                    DataTypePtr dataType = WorkflowEnv::getDataTypeRegistry()->getById(cfg.type);
                    v[WorkflowUtils::getSlotDescOfDatatype(dataType).getId()] = qVariantFromValue<QString>(obj->getText());
                }
            }

            QFile::remove(url);
        }
    }

    DataTypePtr dataType = WorkflowEnv::getDataTypeRegistry()->getById(OUTPUT_PORT_TYPE + cfg->id);

    if (seqsForMergingBySlotId.isEmpty()) {
        output->put(Message(dataType, v));
    } else if (seqsForMergingBySlotId.size() == 1) {
        // create a message for every sequence
        QString slotId = seqsForMergingBySlotId.keys().first();
        const QList<U2EntityRef>& refs = seqsForMergingBySlotId.value(slotId);
        foreach (const U2EntityRef& eRef, refs) {
            SharedDbiDataHandler id = context->getDataStorage()->getDataHandler(eRef);
            v[slotId] = qVariantFromValue<SharedDbiDataHandler>(id);
            output->put(Message(dataType, v));
        }
    } else {
        // merge every sequence group and send one message
        U2SequenceImporter seqImporter = U2SequenceImporter(QVariantMap());
        U2OpStatus2Log os;

        foreach (const QString& slotId, seqsForMergingBySlotId.keys()) {
            QList<U2EntityRef> refs = seqsForMergingBySlotId.value(slotId);
            bool first = true;
            for (const U2EntityRef& eRef : qAsConst(refs)) {
                QScopedPointer<U2SequenceObject> obj(new U2SequenceObject("tmp_name", eRef));
                if (first) {
                    seqImporter.startSequence(os, context->getDataStorage()->getDbiRef(), U2ObjectDbi::ROOT_FOLDER, slotId, false);
                    first = false;
                }
                U2Region wholeSeq(0, obj->getSequenceLength());
                seqImporter.addSequenceBlock(eRef, wholeSeq, os);
            }
            U2Sequence seq = seqImporter.finalizeSequenceAndValidate(os);
            U2EntityRef eRef(context->getDataStorage()->getDbiRef(), seq.id);
            SharedDbiDataHandler id = context->getDataStorage()->getDataHandler(eRef);
            v[slotId] = qVariantFromValue<SharedDbiDataHandler>(id);
        }
        CHECK_OP(os, );
        output->put(Message(dataType, v));
    }
}

void ExternalProcessWorker::init() {
    commandLine = cfg->cmdLine;
    applySpecialInternalEnvvars(commandLine, cfg);
    applyAttributes(commandLine);

    output = ports.value(OUT_PORT_ID);

    foreach (const DataConfig& input, cfg->inputs) {
        IntegralBus* inBus = ports.value(input.attributeId);
        inputs << inBus;

        inBus->addComplement(output);
    }
}

ExternalProcessWorker::InputsCheckResult ExternalProcessWorker::checkInputBusState() const {
    const int inputsCount = inputs.count();
    CHECK(0 < inputsCount, ALL_INPUTS_FINISH);

    int inputsWithMessagesCount = 0;
    int finishedInputs = 0;
    foreach (const CommunicationChannel* ch, inputs) {
        SAFE_POINT(ch != nullptr, "Input is nullptr", INTERNAL_ERROR);
        if (0 != ch->hasMessage()) {
            ++inputsWithMessagesCount;
        }
        if (ch->isEnded()) {
            ++finishedInputs;
        }
    }

    if (inputsCount == inputsWithMessagesCount) {
        return ALL_INPUTS_HAVE_MESSAGE;
    } else if (inputsCount == finishedInputs) {
        return ALL_INPUTS_FINISH;
    } else if (0 < finishedInputs && 0 < inputsWithMessagesCount) {
        return SOME_INPUTS_FINISH;
    } else {
        return NOT_ALL_INPUTS_HAVE_MESSAGE;
    }
}

bool ExternalProcessWorker::isReady() const {
    CHECK(!isDone(), false);
    if (inputs.isEmpty()) {
        return true;
    } else {
        const InputsCheckResult checkResult = checkInputBusState();
        switch (checkResult) {
            case ALL_INPUTS_FINISH:
            case SOME_INPUTS_FINISH:
            case ALL_INPUTS_HAVE_MESSAGE:
            case INTERNAL_ERROR:
                return true;  // the worker will be marked as 'done' in the 'tick' method
            case NOT_ALL_INPUTS_HAVE_MESSAGE:
                return false;
        }
    }
    return false;
}

void ExternalProcessWorker::cleanup() {
    foreach (const QString& url, inputUrls) {
        if (QFile::exists(url)) {
            QFile::remove(url);
        }
    }
}

/************************************************************************/
/* LaunchExternalToolTask */
/************************************************************************/
LaunchExternalToolTask::LaunchExternalToolTask(const QString& _execString, const QString& _workingDir, const QMap<QString, DataConfig>& _outputUrls)
    : Task(tr("Launch external process task"), TaskFlag_None), outputUrls(_outputUrls), execString(_execString), workingDir(_workingDir) {
}

LaunchExternalToolTask::~LaunchExternalToolTask() {
    foreach (const QString& url, outputUrls.keys()) {
        if (QFile::exists(url)) {
            QFile::remove(url);
        }
    }
}

#define WIN_LAUNCH_CMD_COMMAND "cmd /C "
#define START_WAIT_MSEC 3000

void LaunchExternalToolTask::run() {
    GCOUNTER(cvar, "A task for an element with external tool is launched");
    QProcess* externalProcess = new QProcess();
    externalProcess->setWorkingDirectory(workingDir);
    if (execString.contains(">")) {
        QString output = execString.split(">").last();
        output = output.trimmed();
        if (output.startsWith('\"')) {
            output = output.mid(1, output.length() - 2);
        }
        execString = execString.split(">").first();
        externalProcess->setStandardOutputFile(output);
    }
    QScopedPointer<CustomExternalToolLogParser> logParser(new CustomExternalToolLogParser());
    QScopedPointer<ExternalToolRunTaskHelper> helper(new CustomExternalToolRunTaskHelper(externalProcess, logParser.data(), stateInfo));
    CHECK(listeners.size() > 0, );
    helper->addOutputListener(listeners[0]);
    QStringList execStringArgs = ExternalToolSupportUtils::splitCmdLineArguments(execString);
    QString execStringProg = execStringArgs.takeAt(0);

    QProcessEnvironment env = QProcessEnvironment::systemEnvironment();
    externalProcess->setProcessEnvironment(env);
    taskLog.details(tr("Running external process: %1").arg(execString));
    bool startOk = WorkflowUtils::startExternalProcess(externalProcess, execStringProg, execStringArgs);

    if (!startOk) {
        stateInfo.setError(tr("Can't launch %1").arg(execString));
        return;
    }
    listeners[0]->addNewLogMessage(execString, ExternalToolListener::PROGRAM_WITH_ARGUMENTS);
    while (!externalProcess->waitForFinished(1000)) {
        if (isCanceled()) {
            CmdlineTaskRunner::killProcessTree(externalProcess);
        }
    }

    QProcess::ExitStatus status = externalProcess->exitStatus();
    int exitCode = externalProcess->exitCode();
    if (status == QProcess::CrashExit && !hasError()) {
        setError(tr("External process %1 exited with the following error: %2 (Code: %3)")
                     .arg(execString)
                     .arg(externalProcess->errorString())
                     .arg(exitCode));
    } else if (status == QProcess::NormalExit && exitCode != EXIT_SUCCESS && !hasError()) {
        setError(tr("External process %1 exited with code %2").arg(execString).arg(exitCode));
    } else if (status == QProcess::NormalExit && exitCode == EXIT_SUCCESS && !hasError()) {
        algoLog.details(tr("External process \"%1\" finished successfully").arg(execString));
    }
}

QMap<QString, DataConfig> LaunchExternalToolTask::takeOutputUrls() {
    QMap<QString, DataConfig> result = outputUrls;
    outputUrls.clear();
    return result;
}

void LaunchExternalToolTask::addListeners(const QList<ExternalToolListener*>& listenersToAdd) {
    listeners.append(listenersToAdd);
}

/************************************************************************/
/* ExternalProcessWorkerPrompter */
/************************************************************************/
QString ExternalProcessWorkerPrompter::composeRichDoc() {
    ExternalProcessConfig* cfg = WorkflowEnv::getExternalCfgRegistry()->getConfigById(target->getProto()->getId());
    assert(cfg);
    QString doc(cfg->templateDescription);
    doc.replace("\n", "<br>");

    foreach (const DataConfig& dataCfg, cfg->inputs) {
        QRegExp param(QString("\\$%1[^%2]|$").arg(dataCfg.attributeId).arg(WorkflowEntityValidator::ID_ACCEPTABLE_SYMBOLS_TEMPLATE));
        if (doc.contains(param)) {
            auto input = qobject_cast<IntegralBusPort*>(target->getPort(dataCfg.attributeId));
            DataTypePtr dataType = WorkflowEnv::getDataTypeRegistry()->getById(dataCfg.type);
            if (dataCfg.type == SEQ_WITH_ANNS) {
                dataType = BaseTypes::DNA_SEQUENCE_TYPE();
            }
            Actor* producer = input->getProducer(WorkflowUtils::getSlotDescOfDatatype(dataType).getId());
            QString unsetStr = "<font color='red'>" + tr("unset") + "</font>";
            QString producerName = tr("<u>%1</u>").arg(producer ? producer->getLabel() : unsetStr);
            doc.replace("$" + dataCfg.attributeId, producerName);
        }
    }

    foreach (const DataConfig& dataCfg, cfg->outputs) {
        QRegExp param(QString("\\$%1[^%2]|$").arg(dataCfg.attributeId).arg(WorkflowEntityValidator::ID_ACCEPTABLE_SYMBOLS_TEMPLATE));
        if (doc.contains(param)) {
            auto output = qobject_cast<IntegralBusPort*>(target->getPort(OUT_PORT_ID));
            DataTypePtr dataType = WorkflowEnv::getDataTypeRegistry()->getById(dataCfg.type);
            if (dataCfg.type == SEQ_WITH_ANNS) {
                dataType = BaseTypes::DNA_SEQUENCE_TYPE();
            }
            QString destinations;
            QString unsetStr = "<font color='red'>" + tr("unset") + "</font>";
            if (!output->getLinks().isEmpty()) {
                QList<Port*> ports = output->getLinks().keys();
                for (Port* p : qAsConst(ports)) {
                    auto ibp = qobject_cast<IntegralBusPort*>(p);
                    Actor* dest = ibp->owner();
                    destinations += tr("<u>%1</u>").arg(dest ? dest->getLabel() : unsetStr) + ",";
                }
            }
            if (destinations.isEmpty()) {
                destinations = tr("<u>%1</u>").arg(unsetStr);
            } else {
                destinations.resize(destinations.size() - 1);  // remove last semicolon
            }
            doc.replace("$" + dataCfg.attributeId, destinations);
        }
    }

    foreach (const AttributeConfig& attrCfg, cfg->attrs) {
        QRegExp param(QString("\\$%1([^%2]|$)").arg(attrCfg.attributeId).arg(WorkflowEntityValidator::ID_ACCEPTABLE_SYMBOLS_TEMPLATE));
        if (doc.contains(param)) {
            QString prm = getRequiredParam(attrCfg.attributeId);
            doc.replace("$" + attrCfg.attributeId, getHyperlink(attrCfg.attrName, prm));
        }
    }

    return doc;
}

}  // namespace LocalWorkflow
}  // namespace U2
