/**
 * UGENE - Integrated Bioinformatics Tools.
 * Copyright (C) 2008-2023 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.
 */

#pragma once

#include <U2Core/DNASequence.h>
#include <U2Core/DNASequenceObject.h>
#include <U2Core/DocumentModel.h>
#include <U2Core/Msa.h>

#include <U2Lang/LocalDomain.h>

namespace U2 {

class DatasetFilesIterator;

namespace LocalWorkflow {

class GenericDocReader : public BaseWorker {
    Q_OBJECT
public:
    GenericDocReader(Actor* a);
    ~GenericDocReader() override;

    void init() override;
    Task* tick() override;
    bool isDone() const override;
    void cleanup() override;

protected slots:
    virtual void sl_datasetEnded();

protected:
    virtual void onTaskFinished(Task* task) = 0;
    virtual Task* createReadTask(const QString& url, const QString& datasetName);
    // The method is to be overridden in subclasses capable of reading from shared DBs.
    // Returns a name of data for metadata.
    virtual QString addReadDbObjectToData(const QString& objUrl, QVariantMap& data);

    SharedDbiDataHandler getDbObjectHandlerByUrl(const QString& url) const;
    QString getObjectName(const SharedDbiDataHandler& handler, const U2DataType& type) const;

    CommunicationChannel* ch = nullptr;
    QList<Message> cache;
    DataTypePtr mtype;
    DatasetFilesIterator* files = nullptr;

private:
    void readObjectFromDb(const QString& url, const QString& datasetName);

private slots:
    void sl_taskFinished();
};

/************************************************************************/
/* Inherited classes */
/************************************************************************/
class DNASelector {
public:
    bool matches(const DNASequence&);
    bool objectMatches(const U2SequenceObject*);
    QString accExpr;
};

class LoadSeqTask : public Task {
    Q_OBJECT
public:
    LoadSeqTask(QString url, const QVariantMap& cfg, DNASelector* sel, DbiDataStorage* storage)
        : Task(tr("Read sequences from %1").arg(url), TaskFlag_None),
          url(url), selector(sel), cfg(cfg), storage(storage), format(nullptr) {
    }
    virtual void prepare();
    virtual void run();

    QString url;
    DNASelector* selector;
    QVariantMap cfg;
    QList<QVariantMap> results;
    DbiDataStorage* storage;
    DocumentFormat* format;
};

class LoadMSATask : public Task {
    Q_OBJECT
public:
    LoadMSATask(const QString& url, const QString& datasetName, DbiDataStorage* storage);
    virtual void prepare();
    virtual void run();

    QString url;
    QString datasetName;
    QVariantMap cfg;
    QList<QVariant> results;
    DbiDataStorage* storage;
};

class GenericMSAReader : public GenericDocReader {
    Q_OBJECT
public:
    GenericMSAReader(Actor* a)
        : GenericDocReader(a) {
    }
    virtual void init();
    virtual void cleanup() {
    }

protected:
    virtual void onTaskFinished(Task* task);
    virtual QString addReadDbObjectToData(const QString& objUrl, QVariantMap& data);

protected:
    virtual Task* createReadTask(const QString& url, const QString& datasetName) {
        return new LoadMSATask(url, datasetName, context->getDataStorage());
    }
};

class GenericSeqReader : public GenericDocReader {
    Q_OBJECT
public:
    GenericSeqReader(Actor* a)
        : GenericDocReader(a) {
    }
    virtual void init();

protected:
    virtual void onTaskFinished(Task* task);
    virtual QString addReadDbObjectToData(const QString& objUrl, QVariantMap& data);

protected:
    virtual Task* createReadTask(const QString& url, const QString& datasetName);
    QVariantMap cfg;
    DNASelector selector;
};

}  // namespace LocalWorkflow
}  // namespace U2
