/**
 * 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 "DbiDocumentFormat.h"

#include <U2Core/AppContext.h>
#include <U2Core/AssemblyObject.h>
#include <U2Core/DNASequenceObject.h>
#include <U2Core/GObjectUtils.h>
#include <U2Core/IOAdapter.h>
#include <U2Core/U2DbiUtils.h>
#include <U2Core/U2ObjectDbi.h>
#include <U2Core/U2ObjectRelationsDbi.h>
#include <U2Core/U2OpStatusUtils.h>
#include <U2Core/U2SafePoints.h>

namespace U2 {

DbiDocumentFormat::DbiDocumentFormat(const U2DbiFactoryId& _id, const DocumentFormatId& _formatId, const QString& _formatName, const QStringList& exts, DocumentFormatFlags flags, QObject* p)
    : DocumentFormat(p, _formatId, flags, exts) {
    id = _id;
    formatName = _formatName;
    formatDescription = tr("ugenedb is a internal UGENE database file format");
    supportedObjectTypes += GObjectTypes::ASSEMBLY;
    supportedObjectTypes += GObjectTypes::MULTIPLE_CHROMATOGRAM_ALIGNMENT;
    supportedObjectTypes += GObjectTypes::SEQUENCE;
    supportedObjectTypes += GObjectTypes::ANNOTATION_TABLE;
    formatFlags |= DocumentFormatFlag_NoPack;
    formatFlags |= DocumentFormatFlag_NoFullMemoryLoad;
    formatFlags |= DocumentFormatFlag_DirectWriteOperations;
}

static void renameObjectsIfNamesEqual(QList<GObject*>& objs) {
    for (int i = 0; i < objs.size(); ++i) {
        int howManyEquals = 0;
        for (int j = i + 1; j < objs.size(); ++j) {
            if (objs[i]->getGObjectName() == objs[j]->getGObjectName()) {
                objs[j]->setGObjectName(QString("%1 %2").arg(objs[j]->getGObjectName()).arg(++howManyEquals));
            }
        }
    }
}

Document* DbiDocumentFormat::loadDocument(IOAdapter* io, const U2DbiRef& dstDbiRef, const QVariantMap& fs, U2OpStatus& os) {
    // 1. open db
    // 2. read all objects
    // 3. if there is a DEEP_COPY_OBJECT hint, all objects are cloned to the db defined by dstDbiRef
    // 3. close db
    QString url = io->getURL().getURLString();
    U2DbiRef srcDbiRef(id, url);
    DbiConnection handle(srcDbiRef, true, os);
    CHECK_OP(os, nullptr);

    U2ObjectDbi* odbi = handle.dbi->getObjectDbi();
    QList<U2DataId> objectIds = odbi->getObjects(U2ObjectDbi::ROOT_FOLDER, 0, U2DbiOptions::U2_DBI_NO_LIMIT, os);
    CHECK_OP(os, nullptr);

    QList<GObject*> objects = prepareObjects(handle, objectIds);
    if (fs.value(DEEP_COPY_OBJECT, false).toBool()) {
        QList<GObject*> clonedObjects = cloneObjects(objects, dstDbiRef, fs, os);
        qDeleteAll(objects);
        CHECK_OP_EXT(os, qDeleteAll(clonedObjects), nullptr);
        objects = clonedObjects;
    } else {
        renameObjectsIfNamesEqual(objects);
    }

    QString lockReason = handle.dbi->isReadOnly() ? "The database is read-only" : "";
    Document* d = new Document(this, io->getFactory(), io->getURL(), dstDbiRef, objects, fs, lockReason);
    d->setDocumentOwnsDbiResources(false);
    d->setModificationTrack(false);

    return d;
}

QList<GObject*> DbiDocumentFormat::prepareObjects(DbiConnection& handle, const QList<U2DataId>& objectIds) {
    QList<GObject*> objects;
    U2EntityRef ref;
    ref.dbiRef = handle.dbi->getDbiRef();

    QMap<U2DataId, GObject*> match;

    for (const U2DataId& dataId : qAsConst(objectIds)) {
        U2OpStatus2Log status;
        ref.entityId = dataId;

        U2Object object;
        handle.dbi->getObjectDbi()->getObject(object, dataId, status);
        CHECK_CONTINUE(!status.isCoR());

        if (object.visualName.isEmpty()) {
            object.visualName = "Unnamed object";
        }

        GObject* gobject = GObjectUtils::createObject(ref.dbiRef, dataId, object.visualName);
        CHECK_CONTINUE(gobject != nullptr);

        match[dataId] = gobject;
        objects << gobject;
    }

    if (handle.dbi->getObjectRelationsDbi() != nullptr) {
        const QList<U2DataId> matchKeys = match.keys();
        for (const U2DataId& dataId : qAsConst(matchKeys)) {
            U2OpStatus2Log status;
            GObject* srcObj = match.value(dataId, nullptr);
            SAFE_POINT(srcObj != nullptr, "Source object is NULL", QList<GObject*>());
            QList<GObjectRelation> gRelations;
            QList<U2ObjectRelation> relations = handle.dbi->getObjectRelationsDbi()->getObjectRelations(dataId, status);
            foreach (const U2ObjectRelation& r, relations) {
                GObject* relatedObject = match[r.referencedObject];
                if (relatedObject == nullptr) {
                    continue;
                }
                // SANGER_TODO: dbiId - url, should not be left like this
                GObjectReference relatedRef(handle.dbi->getDbiId(), relatedObject->getGObjectName(), relatedObject->getGObjectType(), relatedObject->getEntityRef());
                GObjectRelation gRelation(relatedRef, r.relationRole);
                gRelations << gRelation;
            }
            srcObj->setObjectRelations(gRelations);
        }
    }

    return objects;
}
QList<GObject*> DbiDocumentFormat::cloneObjects(const QList<GObject*>& srcObjects, const U2DbiRef& dstDbiRef, const QVariantMap& hints, U2OpStatus& os) {
    QList<GObject*> clonedObjects;
    CHECK_EXT(dstDbiRef.isValid(), os.setError(tr("Invalid destination database reference")), clonedObjects);

    int number = 0;
    int total = srcObjects.size();
    foreach (GObject* srcObject, srcObjects) {
        U2OpStatusMapping mapping(number, (number + 1) / total);
        U2OpStatusChildImpl childOs(&os, mapping);
        GObject* clonedObject = srcObject->clone(dstDbiRef, childOs, hints);
        CHECK_OP(os, clonedObjects);
        clonedObjects << clonedObject;
        number++;
    }

    return clonedObjects;
}

void DbiDocumentFormat::storeDocument(Document* d, IOAdapter* ioAdapter, U2OpStatus& os) {
    const QString url = ioAdapter->getURL().getURLString();

    const U2DbiRef dstDbiRef(id, url);
    DbiConnection dstCon(dstDbiRef, true, os);
    CHECK_OP(os, );
    Q_UNUSED(dstCon);

    // The relations should be saved
    QMap<GObject*, GObject*> clonedObjects;
    QMap<GObjectReference, GObjectReference> match;

    foreach (GObject* object, d->getObjects()) {
        if (!supportedObjectTypes.contains(object->getGObjectType())) {
            continue;
        }

        U2DbiRef srcDbiRef = object->getEntityRef().dbiRef;
        if (srcDbiRef == dstDbiRef) {
            // do not need to import
            continue;
        }

        GObject* resultObject = object->clone(dstDbiRef, os);
        CHECK_OP(os, );

        clonedObjects[object] = resultObject;
        match[GObjectReference(object, false)] = GObjectReference(url, resultObject->getGObjectName(), resultObject->getGObjectType(), resultObject->getEntityRef());
    }

    foreach (GObject* initialObj, clonedObjects.keys()) {
        GObject* cloned = clonedObjects[initialObj];
        QList<GObjectRelation> relations;
        QList<GObjectRelation> initialRelations = initialObj->getObjectRelations();
        for (const GObjectRelation& r : qAsConst(initialRelations)) {
            if (match.contains(r.ref)) {
                relations << GObjectRelation(match[r.ref], r.role);
            }
        }
        cloned->setObjectRelations(relations);
    }

    qDeleteAll(clonedObjects);
    clonedObjects.clear();
}

FormatCheckResult DbiDocumentFormat::checkRawData(const QByteArray& rawData, const GUrl& url) const {
    U2DbiFactory* f = AppContext::getDbiRegistry()->getDbiFactoryById(id);
    if (f != nullptr) {
        QHash<QString, QString> props;
        props[U2DbiOptions::U2_DBI_OPTION_URL] = url.getURLString();
        U2OpStatusImpl os;
        FormatCheckResult r = f->isValidDbi(props, rawData, os);
        if (!os.hasError()) {
            return r;
        }
    }
    return FormatDetection_NotMatched;
}

}  // namespace U2
