/**
 * 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 "bowtieTests.h"

#include <QDir>
#include <QRegExp>

#include <U2Core/AppContext.h>
#include <U2Core/BaseDocumentFormats.h>
#include <U2Core/DNASequenceObject.h>
#include <U2Core/DNATranslation.h>
#include <U2Core/DocumentModel.h>
#include <U2Core/GObjectTypes.h>
#include <U2Core/IOAdapter.h>
#include <U2Core/IOAdapterUtils.h>
#include <U2Core/Log.h>
#include <U2Core/MsaObject.h>
#include <U2Core/SaveDocumentTask.h>
#include <U2Core/TextObject.h>
#include <U2Core/TextUtils.h>
#include <U2Core/U2AlphabetUtils.h>
#include <U2Core/U2OpStatusUtils.h>
#include <U2Core/U2SafePoints.h>

#include <U2Formats/BAMUtils.h>
#include <U2Formats/SAMFormat.h>

#include <U2View/DnaAssemblyUtils.h>

/* TRANSLATOR U2::GTest*/

namespace U2 {

#define READS_FILE_NAME_ATTR "reads"
#define INDEX_ATTR "index"
#define PATTERN_FILE_NAME_ATTR "pattern"
#define PATTERN_FILE_FORMAT_ATTR "pat_format"
#define BUILD_INDEX_ATTR "build"
#define NEGATIVE_ATTR "negative"
#define N_MODE_ATTR "n"
#define V_MODE_ATTR "v"
#define MAQERR_ATTR "maqerr"
#define SEEDLEN_ATTR "seedlen"
#define MAXBTS_ATTR "maxbts"
#define SEED_ATTR "seed"
#define NOMAQROUND_ATTR "nomaqround"
#define NOFW_ATTR "nofw"
#define NORC_ATTR "norc"
#define TRYHARD_ATTR "tryhard"
#define FORMAT_ATTR "format"
#define BEST_ATTR "best"
#define ALL_ATTR "all"

void GTest_Bowtie::init(XMLTestFormat*, const QDomElement& el) {
    bowtieTask = nullptr;
    indexName = "";
    readsFileName = "";
    patternFileName = "";
    negativeError = "";
    usePrebuildIndex = true;
    subTaskFailed = false;
    indexName = el.attribute(INDEX_ATTR);
    format = BaseDocumentFormats::FASTA;
    patternFormat = BaseDocumentFormats::PLAIN_TEXT;
    if (indexName.isEmpty()) {
        failMissingValue(INDEX_ATTR);
        return;
    }
    QString buildStr = el.attribute(BUILD_INDEX_ATTR);
    if (!buildStr.isEmpty()) {
        bool ok = false;
        usePrebuildIndex = !buildStr.toInt(&ok);
        if (!ok) {
            failMissingValue(BUILD_INDEX_ATTR);
            return;
        }
    }
    readsFileName = el.attribute(READS_FILE_NAME_ATTR);
    if (readsFileName.isEmpty()) {
        failMissingValue(READS_FILE_NAME_ATTR);
        return;
    }
    patternFileName = el.attribute(PATTERN_FILE_NAME_ATTR);
    if (patternFileName.isEmpty()) {
        failMissingValue(PATTERN_FILE_NAME_ATTR);
        return;
    }
    negativeError = el.attribute(NEGATIVE_ATTR);
    QString formatStr = el.attribute(FORMAT_ATTR);
    if (!formatStr.isEmpty()) {
        if (formatStr == "fasta")
            format = BaseDocumentFormats::FASTA;
        else if (formatStr == "fastq")
            format = BaseDocumentFormats::FASTQ;
        else {
            failMissingValue(FORMAT_ATTR);
            return;
        }
    }
    QString patternFormatStr = el.attribute(PATTERN_FILE_FORMAT_ATTR);
    if (!patternFormatStr.isEmpty()) {
        if (patternFormatStr == "sam")
            patternFormat = BaseDocumentFormats::SAM;
        else if (patternFormatStr == "map")
            patternFormat = BaseDocumentFormats::PLAIN_TEXT;
        else {
            failMissingValue(PATTERN_FILE_FORMAT_ATTR);
            return;
        }
    }

    bool ok = false;
    {
        const QString attr = N_MODE_ATTR;

        if (!el.attribute(attr).isEmpty()) {
            config.setCustomValue(BowtieTask::OPTION_N_MISMATCHES, el.attribute(attr).toInt(&ok));
            if (!ok)
                failMissingValue(attr);
        }
    }
    {
        const QString attr = V_MODE_ATTR;
        if (!el.attribute(attr).isEmpty()) {
            config.setCustomValue(BowtieTask::OPTION_V_MISMATCHES, el.attribute(attr).toInt(&ok));
            if (!ok)
                failMissingValue(attr);
        }
    }
    {
        const QString attr = MAQERR_ATTR;
        if (!el.attribute(attr).isEmpty()) {
            config.setCustomValue(BowtieTask::OPTION_MAQERR, el.attribute(attr).toInt(&ok));
            if (!ok)
                failMissingValue(attr);
        }
    }
    {
        const QString attr = SEEDLEN_ATTR;
        if (!el.attribute(attr).isEmpty()) {
            config.setCustomValue(BowtieTask::OPTION_SEED_LEN, el.attribute(attr).toInt(&ok));
            if (!ok)
                failMissingValue(attr);
        }
    }
    {
        const QString attr = SEED_ATTR;
        if (!el.attribute(attr).isEmpty()) {
            config.setCustomValue(BowtieTask::OPTION_SEED, el.attribute(attr).toInt(&ok));
            if (!ok)
                failMissingValue(attr);
        }
    }
    {
        const QString attr = MAXBTS_ATTR;
        if (!el.attribute(attr).isEmpty()) {
            config.setCustomValue(BowtieTask::OPTION_MAXBTS, el.attribute(attr).toInt(&ok));
            if (!ok)
                failMissingValue(attr);
        }
    }
    {
        const QString attr = NOMAQROUND_ATTR;
        if (!el.attribute(attr).isEmpty()) {
            config.setCustomValue(BowtieTask::OPTION_NOMAQROUND, true);
        }
    }
    {
        const QString attr = NOFW_ATTR;
        if (!el.attribute(attr).isEmpty()) {
            config.setCustomValue(BowtieTask::OPTION_NOFW, true);
        }
    }
    {
        const QString attr = NORC_ATTR;
        if (!el.attribute(attr).isEmpty()) {
            config.setCustomValue(BowtieTask::OPTION_NORC, true);
        }
    }
    {
        const QString attr = TRYHARD_ATTR;
        if (!el.attribute(attr).isEmpty()) {
            config.setCustomValue(BowtieTask::OPTION_TRYHARD, true);
        }
    }
}

void GTest_Bowtie::prepare() {
    if (!usePrebuildIndex) {
        QFileInfo refFile(env->getVar("COMMON_DATA_DIR") + "/" + indexName);
        if (!refFile.exists()) {
            stateInfo.setError(QString("file not exist %1").arg(refFile.absoluteFilePath()));
            return;
        }
    }
    QFileInfo readsFile(env->getVar("COMMON_DATA_DIR") + "/" + readsFileName);
    if (!readsFile.exists()) {
        stateInfo.setError(QString("file not exist %1").arg(readsFile.absoluteFilePath()));
        return;
    }

    readsFileUrl = readsFile.absoluteFilePath();

    QFileInfo patternFile(env->getVar("COMMON_DATA_DIR") + "/" + patternFileName);
    if (!patternFile.exists()) {
        stateInfo.setError(QString("file not exist %1").arg(patternFile.absoluteFilePath()));
        return;
    }

    QString tmpDataDir = getTempDataDir();
    if (tmpDataDir.isEmpty()) {
        setError("Can't create tmp data dir!");
        return;
    }

    config.shortReadSets.append(readsFileUrl);
    config.refSeqUrl = GUrl(env->getVar("COMMON_DATA_DIR") + "/" + indexName);
    config.prebuiltIndex = usePrebuildIndex;
    config.resultFileName = GUrl(tmpDataDir + "/" + QString::number(getTaskId()));
    config.algName = BowtieTask::taskName;
    config.openView = false;
    bowtieTask = new BowtieTask(config);

    addSubTask(bowtieTask);
}

QList<Task*> GTest_Bowtie::onSubTaskFinished(Task* subTask) {
    Q_UNUSED(subTask);
    QList<Task*> res;
    if (hasError() || subTask->hasError() || isCanceled()) {
        subTaskFailed = true;
        return res;
    }

    if (subTask == bowtieTask) {
        if (bowtieTask->hasError()) {
            subTaskFailed = true;
            return res;
        }
        if (!bowtieTask->hasResult()) {
            subTaskFailed = true;
            bowtieTask->setError("Reference assembly failed - no possible alignment found");
            return res;
        }
    }
    return res;
}

void GTest_Bowtie::run() {
    if (subTaskFailed) {
        return;
    }
    QFileInfo patternFile(env->getVar("COMMON_DATA_DIR") + "/" + patternFileName);
    BAMUtils::isEqualByLength(config.resultFileName.getURLString(), patternFile.absoluteFilePath(), stateInfo);
}

Task::ReportResult GTest_Bowtie::report() {
    if (!negativeError.isEmpty()) {
        if (hasSubtasksWithErrors()) {
            return ReportResult_Finished;
        } else {
            setError(QString("Negative test failed: error string is empty, expected error \"%1\"").arg(negativeError));
        }
    } else {
        propagateSubtaskError();
    }
    return ReportResult_Finished;
}

void GTest_Bowtie::cleanup() {
    // delete index
    if (!hasError() && !usePrebuildIndex) {
        QString prefix = env->getVar("TEMP_DATA_DIR") + "/" + QString::number(getTaskId());
        QStringList files(QStringList() << prefix + ".1.ebwt" << prefix + ".2.ebwt"
                                        << prefix + ".3.ebwt" << prefix + ".4.ebwt" << prefix + ".rev.1.ebwt" << prefix + ".rev.2.ebwt");
        foreach (QString file, files) {
            QFileInfo tmpFile(file);
            if (tmpFile.exists()) {
                ioLog.trace(QString("Deleting index file \"%1\"").arg(tmpFile.absoluteFilePath()));
                QFile::remove(tmpFile.absoluteFilePath());
            }
        }
    }
    // delete tmp result
    QFileInfo tmpResult(config.resultFileName.getURLString());
    if (!hasError() && tmpResult.exists()) {
        ioLog.trace(QString("Deleting tmp result file :%1").arg(tmpResult.absoluteFilePath()));
        QFile::remove(tmpResult.absoluteFilePath());
    }

    XmlTest::cleanup();
}

QString GTest_Bowtie::getTempDataDir() {
    QString dir(env->getVar("TEMP_DATA_DIR"));
    if (!QDir(dir).exists()) {
        bool ok = QDir::root().mkpath(dir);
        if (!ok) {
            return QString();
        }
    }
    return dir;
}

QList<XMLTestFactory*> BowtieTests::createTestFactories() {
    QList<XMLTestFactory*> res;
    res.append(GTest_Bowtie::createFactory());
    return res;
}
}  // namespace U2
