/**
 * UGENE - Integrated Bioinformatics Tools.
 * Copyright (C) 2008-2021 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.
 */

#ifndef _U2_SQLITE_DBI_H_
#define _U2_SQLITE_DBI_H_

#include <QStack>

#include <U2Core/U2AbstractDbi.h>
#include <U2Core/U2DbiRegistry.h>
#include <U2Core/U2SqlHelpers.h>

struct sqlite3;

namespace U2 {

class DbRef;
class SQLiteAssemblyDbi;
class SQLiteAttributeDbi;
class SQLiteCrossDatabaseReferenceDbi;
class SQLiteFeatureDbi;
class SQLiteModDbi;
class SQLiteMsaDbi;
class SQLiteObjectDbi;
class SQLiteObjectRelationsDbi;
class SQLiteSequenceDbi;
class SQLiteUdrDbi;
class SQLiteVariantDbi;

/** Name of the init property used to indicate assembly reads storage method for all new assemblies */
#define SQLITE_DBI_ASSEMBLY_READ_ELEN_METHOD_KEY "sqlite-assembly-reads-elen-method"
/** Stores all reads in a single table. Not optimal if read effective length varies */
#define SQLITE_DBI_ASSEMBLY_READ_ELEN_METHOD_SINGLE_TABLE "single-table"
/** Store all reads in N tables sorted by effective read length */
#define SQLITE_DBI_ASSEMBLY_READ_ELEN_METHOD_MULTITABLE_V1 "multi-table-v1"
/** Uses RTree index to store reads. This method is simple but not very efficient in terms of space/insert time */
#define SQLITE_DBI_ASSEMBLY_READ_ELEN_METHOD_RTREE "rtree2d"

/** Name of the property used to indicate compression algorithm for reads data */
#define SQLITE_DBI_ASSEMBLY_READ_COMPRESSION_METHOD_KEY "sqlite-assembly-reads-compression-method"
/** No compression is applied. Best for manual DB browsing  (default)*/
#define SQLITE_DBI_ASSEMBLY_READ_COMPRESSION_METHOD_NO_COMPRESSION "no-compression"
/** CIGAR and sequence are packed using bits compression and stored as a single BLOB */
#define SQLITE_DBI_ASSEMBLY_READ_COMPRESSION_METHOD_BITS_1 "compress-bits-1"

// Values of SQLiteDbi flags
#define SQLITE_DBI_VALUE_MEMORY_DB_URL ":memory:"

class U2FORMATS_EXPORT SQLiteDbi : public U2AbstractDbi {
public:
    SQLiteDbi();
    ~SQLiteDbi();

    /**
    Boots the database up to functional state.
    Can be called again after successful shutdown, to re-load the database.
    special flags
    "assembly-reads-compression=1" - enables reads compression for assembly. Affects new DB only
    */
    virtual void init(const QHash<QString, QString> &properties, const QVariantMap &persistentData, U2OpStatus &os);

    /** Stops the database and frees up used resources. */
    virtual QVariantMap shutdown(U2OpStatus &os);

    /**
    Ensures that dbi state is synchronized with storage
    Return 'true' of operation is successful
    */
    virtual bool flush(U2OpStatus &os);

    /** Unique database id. Used for cross-database references. */
    virtual QString getDbiId() const;

    virtual bool isInitialized(U2OpStatus &os);

    virtual void populateDefaultSchema(U2OpStatus &os);

    /** Returns database meta-info. Any set of properties to be shown to user */
    virtual QHash<QString, QString> getDbiMetaInfo(U2OpStatus &os);

    /** Returns type of the entity referenced by the given ID */
    virtual U2DataType getEntityTypeById(const U2DataId &id) const;

    virtual U2ObjectDbi *getObjectDbi();

    virtual U2ObjectRelationsDbi *getObjectRelationsDbi();

    virtual U2SequenceDbi *getSequenceDbi();

    virtual U2MsaDbi *getMsaDbi();

    virtual U2AssemblyDbi *getAssemblyDbi();

    virtual U2CrossDatabaseReferenceDbi *getCrossDatabaseReferenceDbi();

    virtual U2AttributeDbi *getAttributeDbi();

    virtual U2VariantDbi *getVariantDbi();

    virtual U2FeatureDbi *getFeatureDbi();

    virtual U2ModDbi *getModDbi();

    virtual UdrDbi *getUdrDbi();

    DbRef *getDbRef() const {
        return db;
    }

    SQLiteObjectDbi *getSQLiteObjectDbi() const;

    SQLiteObjectRelationsDbi *getSQLiteObjectRelationsDbi() const;

    SQLiteMsaDbi *getSQLiteMsaDbi() const;

    SQLiteSequenceDbi *getSQLiteSequenceDbi() const;

    SQLiteModDbi *getSQLiteModDbi() const;

    SQLiteUdrDbi *getSQLiteUdrDbi() const;

    SQLiteFeatureDbi *getSQLiteFeatureDbi() const;

    /** Returns properties used to initialized the database */
    virtual QHash<QString, QString> getInitProperties() const {
        return initProperties;
    }

    virtual QString getProperty(const QString &name, const QString &defaultValue, U2OpStatus &os);

    virtual void setProperty(const QString &name, const QString &value, U2OpStatus &os);

    virtual void startOperationsBlock(U2OpStatus &os);

    virtual void stopOperationBlock(U2OpStatus &os);

    QMutex *getDbMutex() const;

    virtual bool isReadOnly() const;

    bool isTransactionActive() const;

    static const int BIND_PARAMETERS_LIMIT;

private:
    QString getLastErrorMessage(int rc);

    void setState(U2DbiState state);

    void internalInit(const QHash<QString, QString> &props, U2OpStatus &os);

    QString url;
    DbRef *db;

    SQLiteObjectDbi *objectDbi;
    SQLiteObjectRelationsDbi *objectRelationsDbi;
    SQLiteSequenceDbi *sequenceDbi;
    SQLiteMsaDbi *msaDbi;
    SQLiteAssemblyDbi *assemblyDbi;
    SQLiteCrossDatabaseReferenceDbi *crossDbi;
    SQLiteAttributeDbi *attributeDbi;
    SQLiteVariantDbi *variantDbi;
    SQLiteFeatureDbi *featureDbi;
    SQLiteModDbi *modDbi;
    SQLiteUdrDbi *udrDbi;

    QStack<SQLiteTransaction *> operationsBlockTransactions;

    friend class SQLiteObjectDbi;
    friend class SQLiteCrossDatabaseReferenceDbi;
    friend class SQLiteSequenceDbi;
    friend class SQLiteAssemblyDbi;
    friend class SQLiteMsaDbi;
    friend class SQLiteAttributeDbi;
};

class U2FORMATS_EXPORT SQLiteDbiFactory : public U2DbiFactory {
public:
    SQLiteDbiFactory();

    /** Creates new DBI instance */
    virtual U2Dbi *createDbi();

    /** Returns DBI type ID */
    virtual U2DbiFactoryId getId() const;

    /** Checks that data pointed by properties is a valid DBI resource */
    virtual FormatCheckResult isValidDbi(const QHash<QString, QString> &properties, const QByteArray &rawData, U2OpStatus &os) const;

    virtual GUrl id2Url(const U2DbiId &id) const {
        return GUrl(id, GUrl_File);
    }

    virtual bool isDbiExists(const U2DbiId &id) const;

public:
    static const U2DbiFactoryId ID;
};

/** helper class, used as a base for all SQLite<child>Dbis */
class SQLiteChildDBICommon {
public:
    SQLiteChildDBICommon(SQLiteDbi *dbi)
        : dbi(dbi), db(dbi->getDbRef()) {
    }
    virtual ~SQLiteChildDBICommon() {
    }

    virtual void initSqlSchema(U2OpStatus &os) = 0;
    virtual void shutdown(U2OpStatus &) {
    }

protected:
    SQLiteDbi *dbi;
    DbRef *db;
};

}    // namespace U2

#endif
