/**
 * UGENE - Integrated Bioinformatics Tools.
 * Copyright (C) 2008-2025 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 "ExportQualityScoresWorker.h"

#include <U2Core/DNASequenceObject.h>
#include <U2Core/FileFilters.h>
#include <U2Core/GUrl.h>
#include <U2Core/Log.h>
#include <U2Core/MultiTask.h>

#include <U2Designer/DelegateEditors.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/CoreLibConstants.h>
#include <U2Lang/IntegralBusModel.h>
#include <U2Lang/WorkflowEnv.h>

namespace U2 {
namespace LocalWorkflow {

/*************************************
 * ExportPhredQualityWorkerFactory
 *************************************/
const QString ExportPhredQualityWorkerFactory::ACTOR_ID("export-phred-qualities");
// const QString QUALITY_TYPE_ATTR("quality-format");

void ExportPhredQualityWorkerFactory::init() {
    QList<PortDescriptor*> portDescriptors;

    {
        Descriptor ind(BasePorts::IN_SEQ_PORT_ID(), ExportPhredQualityWorker::tr("DNA sequences"), ExportPhredQualityWorker::tr("The PHRED scores from these sequences will be exported"));
        QMap<Descriptor, DataTypePtr> inM;
        inM[BaseSlots::DNA_SEQUENCE_SLOT()] = BaseTypes::DNA_SEQUENCE_TYPE();
        portDescriptors << new PortDescriptor(ind, DataTypePtr(new MapDataType("Export.qual.in", inM)), true /*input*/);
    }

    QList<Attribute*> attributes;
    {
        Descriptor qualUrl(BaseAttributes::URL_OUT_ATTRIBUTE().getId(), ExportPhredQualityWorker::tr("PHRED output"), ExportPhredQualityWorker::tr("Path to file with PHRED quality scores."));
        attributes << new Attribute(qualUrl, BaseTypes::STRING_TYPE(), true /*required*/, QString());
    }

    QMap<QString, PropertyDelegate*> delegates;
    {
        delegates[BaseAttributes::URL_OUT_ATTRIBUTE().getId()] = new URLDelegate(FileFilters::createAllSupportedFormatsFileFilter(), "", false, false);
    }

    Descriptor actorDesc(ACTOR_ID, ExportPhredQualityWorker::tr("Export PHRED Qualities"), ExportPhredQualityWorker::tr("Export corresponding PHRED quality scores from input sequences."));

    ActorPrototype* proto = new IntegralBusActorPrototype(actorDesc, portDescriptors, attributes);
    proto->setEditor(new DelegateEditor(delegates));
    proto->setPrompter(new ExportPhredQualityPrompter());
    WorkflowEnv::getProtoRegistry()->registerProto(BaseActorCategories::CATEGORY_BASIC(), proto);

    DomainFactory* localDomain = WorkflowEnv::getDomainRegistry()->getById(LocalDomainFactory::ID);
    localDomain->registerEntry(new ExportPhredQualityWorkerFactory());
}

Worker* ExportPhredQualityWorkerFactory::createWorker(Actor* a) {
    return new ExportPhredQualityWorker(a);
}

/*************************************
 * ExportPhredQualityPrompter
 *************************************/
QString ExportPhredQualityPrompter::composeRichDoc() {
    IntegralBusPort* input = qobject_cast<IntegralBusPort*>(target->getPort(BasePorts::IN_SEQ_PORT_ID()));
    Actor* producer = input->getProducer(BasePorts::IN_SEQ_PORT_ID());
    QString producerName = producer ? tr(" from <u>%1</u>").arg(producer->getLabel()) : "";
    QString qualUrl = getParameter(BaseAttributes::URL_OUT_ATTRIBUTE().getId()).toString();
    QString qualSeq = qualUrl.isEmpty() ? "<font color='red'>" + tr("unset") + "</font>" : getHyperlink(BaseAttributes::URL_OUT_ATTRIBUTE().getId(), GUrl(qualUrl).fileName());

    QString doc = tr("Export PHRED quality scores%1 to %2.")
                      .arg(producerName)
                      .arg(qualSeq);

    return doc;
}

/*************************************
 * ExportPhredQualityWorker
 *************************************/
ExportPhredQualityWorker::ExportPhredQualityWorker(Actor* a)
    : BaseWorker(a), input(nullptr), currentTask(nullptr) {
}

void ExportPhredQualityWorker::init() {
    input = ports.value(BasePorts::IN_SEQ_PORT_ID());
    fileName = getValue<QString>(BaseAttributes::URL_OUT_ATTRIBUTE().getId());
}

Task* ExportPhredQualityWorker::tick() {
    if (currentTask != nullptr && currentTask->getState() != Task::State_Finished) {
        return nullptr;
    }

    if (input->hasMessage()) {
        Message inputMessage = getMessageAndSetupScriptValues(input);
        SharedDbiDataHandler seqId = inputMessage.getData().toMap().value(BaseSlots::DNA_SEQUENCE_SLOT().getId()).value<SharedDbiDataHandler>();
        U2SequenceObject* seqObj = StorageUtils::getSequenceObject(context->getDataStorage(), seqId);
        if (seqObj == nullptr) {
            return nullptr;
        }

        // Optimize clean up
        seqObjList.append(seqObj);

        ExportQualityScoresConfig cfg;
        cfg.dstFilePath = fileName;
        if (currentTask == nullptr) {
            cfg.appendData = false;
        }

        currentTask = new ExportPhredQualityScoresTask(seqObj, cfg);
        return currentTask;
    }

    setDone();
    return nullptr;
}

void ExportPhredQualityWorker::cleanup() {
    qDeleteAll(seqObjList);
}

}  // namespace LocalWorkflow
}  // namespace U2
