/**
 * 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 "MarkSequenceWorker.h"

#include <QScopedPointer>

#include <U2Core/AnnotationTableObject.h>
#include <U2Core/DNASequence.h>
#include <U2Core/FailTask.h>
#include <U2Core/Log.h>
#include <U2Core/QVariantUtils.h>
#include <U2Core/U2OpStatusUtils.h>

#include <U2Designer/DelegateEditors.h>
#include <U2Designer/MarkerEditor.h>

#include <U2Lang/ActorPrototypeRegistry.h>
#include <U2Lang/BaseActorCategories.h>
#include <U2Lang/BaseAttributes.h>
#include <U2Lang/BasePorts.h>
#include <U2Lang/BaseSlots.h>
#include <U2Lang/BaseTypes.h>
#include <U2Lang/Marker.h>
#include <U2Lang/MarkerAttribute.h>
#include <U2Lang/WorkflowEnv.h>

namespace U2 {
namespace LocalWorkflow {

const QString MarkSequenceWorkerFactory::ACTOR_ID("mark-sequence");
namespace {
const QString SEQ_TYPESET_ID("seq.content");
const QString MARKED_SEQ_TYPESET_ID("marker.seq.content");
const QString MARKER_ATTR_ID("marker");
}  // namespace

/*******************************
 * MarkSequenceWorker
 *******************************/
MarkSequenceWorker::MarkSequenceWorker(Actor* p)
    : BaseWorker(p), inChannel(nullptr), outChannel(nullptr) {
}

void MarkSequenceWorker::init() {
    inChannel = ports.value(BasePorts::IN_SEQ_PORT_ID());
    outChannel = ports.value(MarkerPorts::OUT_MARKER_SEQ_PORT());
    mtype = ports.value(MarkerPorts::OUT_MARKER_SEQ_PORT())->getBusType();
}

Task* MarkSequenceWorker::tick() {
    while (inChannel->hasMessage()) {
        Message inputMessage = getMessageAndSetupScriptValues(inChannel);
        if (inputMessage.isEmpty()) {
            outChannel->transit();
            continue;
        }
        QVariantMap data = inputMessage.getData().toMap();
        SharedDbiDataHandler seqId = data.value(BaseSlots::DNA_SEQUENCE_SLOT().getId()).value<SharedDbiDataHandler>();
        QScopedPointer<U2SequenceObject> seqObj(StorageUtils::getSequenceObject(context->getDataStorage(), seqId));
        if (seqObj.data() == nullptr) {
            return nullptr;
        }
        U2OpStatusImpl os;
        DNASequence seq = seqObj->getWholeSequence(os);
        CHECK_OP(os, new FailTask(os.getError()));

        const QList<SharedAnnotationData> inputAnns = StorageUtils::getAnnotationTable(context->getDataStorage(),
                                                                                       data[BaseSlots::ANNOTATION_TABLE_SLOT().getId()]);

        QVariantList anns;
        foreach (const SharedAnnotationData& ad, inputAnns) {
            anns << QVariant::fromValue(ad);
        }

        auto attr = dynamic_cast<MarkerAttribute*>(actor->getParameter(MARKER_ATTR_ID));
        QVariantMap m;
        foreach (Marker* marker, attr->getMarkers()) {
            QString res;
            if (SEQUENCE == marker->getGroup()) {
                res = marker->getMarkingResult(qVariantFromValue<DNASequence>(seq));
            } else if (QUALIFIER == marker->getGroup() || ANNOTATION == marker->getGroup()) {
                res = marker->getMarkingResult(QVariant(anns));
            } else if (TEXT == marker->getGroup()) {
                res = marker->getMarkingResult(data.value(BaseSlots::URL_SLOT().getId()));
            }
            m.insert(marker->getName(), QVariant(res));
        }
        Message mes(mtype, m);
        outChannel->put(mes);
    }
    if (inChannel->isEnded()) {
        setDone();
        outChannel->setEnded();
    }
    return nullptr;
}

/*******************************
 * MarkSequenceWorkerFactory
 *******************************/
void MarkSequenceWorkerFactory::init() {
    QList<PortDescriptor*> portDescs;
    QList<Attribute*> attrs;

    // input port
    QMap<Descriptor, DataTypePtr> inTypeMap;
    Descriptor urlD(BaseSlots::URL_SLOT().getId(), MarkSequenceWorker::tr("Location"), MarkSequenceWorker::tr("Location of sequence"));
    inTypeMap[urlD] = BaseTypes::STRING_TYPE();
    inTypeMap[BaseSlots::DNA_SEQUENCE_SLOT()] = BaseTypes::DNA_SEQUENCE_TYPE();
    inTypeMap[BaseSlots::ANNOTATION_TABLE_SLOT()] = BaseTypes::ANNOTATION_TABLE_LIST_TYPE();
    DataTypePtr inTypeSet(new MapDataType(Descriptor(SEQ_TYPESET_ID), inTypeMap));

    Descriptor inPd(BasePorts::IN_SEQ_PORT_ID(), MarkSequenceWorker::tr("Sequence"), MarkSequenceWorker::tr("Sequence"));
    portDescs << new PortDescriptor(inPd, inTypeSet, true);

    // output port
    QMap<Descriptor, DataTypePtr> outTypeMap;
    DataTypePtr outTypeSet(new MapDataType(Descriptor(MARKED_SEQ_TYPESET_ID), outTypeMap));

    Descriptor outPd(MarkerPorts::OUT_MARKER_SEQ_PORT(), MarkSequenceWorker::tr("Marked sequence"), MarkSequenceWorker::tr("Marked sequence"));
    portDescs << new PortDescriptor(outPd, outTypeSet, false, true);

    Descriptor protoDesc(MarkSequenceWorkerFactory::ACTOR_ID,
                         MarkSequenceWorker::tr("Sequence Marker"),
                         MarkSequenceWorker::tr("Adds one or several marks to the input sequence depending on the sequence properties. "
                                                "Use this element, for example, in conjunction with the Filter element."));
    Descriptor markerDesc(MARKER_ATTR_ID, MarkSequenceWorker::tr("Markers"), MarkSequenceWorker::tr("Markers."));
    attrs << new MarkerAttribute(markerDesc, BaseTypes::STRING_TYPE(), false);

    ActorPrototype* proto = new IntegralBusActorPrototype(protoDesc, portDescs, attrs);

    proto->setEditor(new MarkerEditor());
    proto->setPrompter(new MarkSequencePrompter());
    proto->setPortValidator(inPd.getId(), new ScreenedSlotValidator(BaseSlots::URL_SLOT().getId()));

    WorkflowEnv::getProtoRegistry()->registerProto(BaseActorCategories::CATEGORY_DATAFLOW(), proto);
    WorkflowEnv::getDomainRegistry()->getById(LocalDomainFactory::ID)->registerEntry(new MarkSequenceWorkerFactory());
}

Worker* MarkSequenceWorkerFactory::createWorker(Actor* a) {
    return new MarkSequenceWorker(a);
}

/*******************************
 * MarkSequencePrompter
 *******************************/
QString MarkSequencePrompter::composeRichDoc() {
    return tr("Adds one or several marks to the input sequence.");
}

}  // namespace LocalWorkflow
}  // namespace U2
