reader_id1_cache.hpp

ncbi源码

/*
 * ===========================================================================
 * PRODUCTION $Log: reader_id1_cache.hpp,v $
 * PRODUCTION Revision 1000.2  2004/06/01 19:38:22  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.16
 * PRODUCTION
 * ===========================================================================
 */

#ifndef READER_ID1_CACHE__HPP_INCLUDED
#define READER_ID1_CACHE__HPP_INCLUDED

/*  $Id: reader_id1_cache.hpp,v 1000.2 2004/06/01 19:38:22 gouriano Exp $
* ===========================================================================
*                            PUBLIC DOMAIN NOTICE
*               National Center for Biotechnology Information
*
*  This software/database is a "United States Government Work" under the
*  terms of the United States Copyright Act.  It was written as part of
*  the author's official duties as a United States Government employee and
*  thus cannot be copyrighted.  This software/database is freely available
*  to the public for use. The National Library of Medicine and the U.S.
*  Government have not placed any restriction on its use or reproduction.
*
*  Although all reasonable efforts have been taken to ensure the accuracy
*  and reliability of the software and data, the NLM and the U.S.
*  Government do not and cannot warrant the performance or results that
*  may be obtained by using this software or data. The NLM and the U.S.
*  Government disclaim all warranties, express or implied, including
*  warranties of performance, merchantability or fitness for any particular
*  purpose.
*
*  Please cite the author in any work or product based on this material.
* ===========================================================================
*
*  Author:  Eugene Vasilchenko, Anatoliy Kuznetsov
*
*  File Description: Cached extension of data reader from ID1
*
*/

#include <objtools/data_loaders/genbank/readers/id1/reader_id1.hpp>

#include <vector>

BEGIN_NCBI_SCOPE

class IBLOB_Cache;
class IIntCache;
class ICache;
class IReader;
class IWriter;

BEGIN_SCOPE(objects)

class CID2_Reply_Data;

/// ID1 reader with caching capabilities
///
class NCBI_XREADER_ID1_EXPORT CCachedId1Reader : public CId1Reader
{
public:
    CCachedId1Reader(TConn noConn = 5,
                     ICache* blob_cache = 0,
                     ICache* id_cache = 0);
    CCachedId1Reader(TConn noConn, 
                     IBLOB_Cache* blob_cache,
                     IIntCache* id_cache = 0);
    ~CCachedId1Reader();

    void SetBlobCache(ICache* blob_cache);
    void SetIdCache(ICache* id_cache);

    void SetBlobCache(IBLOB_Cache* blob_cache);
    void SetIdCache(IIntCache* id_cache);

    int ResolveSeq_id_to_gi(const CSeq_id& id, TConn conn);
    void RetrieveSeqrefs(TSeqrefs& sr, int gi, TConn conn);
    void PurgeSeqrefs(const TSeqrefs& srs, const CSeq_id& id);

    /// Return BLOB cache key string based on CSeqref Sat() and SatKey()
    /// @sa CSeqref::Sat(), CSeqref::SatKey()
    string GetBlobKey(const CSeqref& seqref) const;
    /// BLOB cache subkeys:
    const char* GetSeqEntrySubkey(void) const;
    const char* GetSNPTableSubkey(void) const;
    const char* GetSkeletonSubkey(void) const;
    const char* GetSplitInfoSubkey(void) const;
    string GetChunkSubkey(int chunk_id) const;

    /// Return Id cache key string based on CSeq_id of gi
    string GetIdKey(const CSeq_id& id) const;
    string GetIdKey(int gi) const;

    /// Id cache subkeys:
    const char* GetSeqrefsSubkey(void) const; //Seq-id/gi -> seqrefs (5*N ints)
    const char* GetGiSubkey(void) const;      //Seq-id -> gi (1 int)

    // seqref -> blob version (1 int)
    const char* GetBlobVersionSubkey(void) const;

    int GetBlobVersion(const CSeqref& seqref);

    void GetTSEChunk(const CSeqref& seqref, CTSE_Chunk_Info& chunk_info,
                     TConn conn);

protected:
    
    void PrintStatistics(void) const;

    bool x_GetIdCache(const string& key,
                      const string& subkey,
                      vector<int>& ints);
    bool x_GetIdCache(const string& key,
                      const string& subkey,
                      int& value);
    void x_StoreIdCache(const string& key,
                        const string& subkey,
                        const vector<int>& ints);
    void x_StoreIdCache(const string& key,
                        const string& subkey,
                        const int& value);
    
    int x_GetVersion(const CSeqref& seqref, TConn conn);

    void x_GetTSEBlob(CID1server_back& id1_reply,
                      CRef<CID2S_Split_Info>& split_info,
                      const CSeqref& seqref,
                      TConn conn);
    void x_GetSNPAnnot(CSeq_annot_SNP_Info& snp_info,
                       const CSeqref& seqref,
                       TConn conn);

    void x_ReadTSEBlob(CID1server_back& id1_reply,
                       const CSeqref&   seqref,
                       CNcbiIstream&    stream);

    bool GetSeqrefs(int gi, TSeqrefs& srs);
    void StoreSeqrefs(int gi, const TSeqrefs& srs);

    bool GetSeqrefs(const CSeq_id& id, TSeqrefs& srs);
    void StoreSeqrefs(const CSeq_id& id, const TSeqrefs& srs);

    bool GetSeqrefs(const string& key, TSeqrefs& srs);
    void StoreSeqrefs(const string& key, const TSeqrefs& srs);

    void StoreBlobVersion(const CSeqref& seqref, int version);

    bool LoadBlob(CID1server_back& id1_reply,
                  CRef<CID2S_Split_Info>& split_info,
                  const CSeqref& seqref);
    bool LoadWholeBlob(CID1server_back& id1_reply,
                       const CSeqref& seqref);
    bool LoadSplitBlob(CID1server_back& id1_reply,
                       CRef<CID2S_Split_Info>& split_info,
                       const CSeqref& seqref);

    bool LoadSNPTable(CSeq_annot_SNP_Info& snp_info,
                      const CSeqref& seqref);
    void StoreSNPTable(const CSeq_annot_SNP_Info& snp_info,
                       const CSeqref& seqref);

    bool LoadData(const string& key, int version, const char* suffix,
                  CID2_Reply_Data& data);
    bool LoadData(const string& key, const char* suffix,
                  int version, CID2_Reply_Data& data);

    enum ECompression
    {
        eCompression_none,
        eCompression_nlm_zip,
        eCompression_gzip
    };

    enum EDataType
    {
        eDataType_MainBlob = 0,
        eDataType_SplitInfo = 1,
        eDataType_Chunk = 2
    };

    CRef<CByteSourceReader> GetReader(CID2_Reply_Data& data,
                                      EDataType data_type);
    AutoPtr<CObjectIStream> OpenData(CID2_Reply_Data& data,
                                     CByteSourceReader& reader);

private:

    CCachedId1Reader(const CCachedId1Reader& );
    CCachedId1Reader& operator=(const CCachedId1Reader&);

private:
    ICache*   m_BlobCache;
    ICache*   m_IdCache;
    IBLOB_Cache*   m_OldBlobCache;
    IIntCache*     m_OldIdCache;
};


END_SCOPE(objects)
END_NCBI_SCOPE


/*
* $Log: reader_id1_cache.hpp,v $
* Revision 1000.2  2004/06/01 19:38:22  gouriano
* PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.16
*
* Revision 1.16  2004/04/28 17:06:25  vasilche
* Load split blobs from new ICache.
*
* Revision 1.15  2004/01/20 16:56:04  vasilche
* Allow storing version of any blob (not only SNP).
*
* Revision 1.14  2004/01/13 21:58:42  vasilche
* Requrrected new version
*
* Revision 1.4  2003/12/30 22:14:40  vasilche
* Updated genbank loader and readers plugins.
*
* Revision 1.12  2003/12/30 16:00:06  vasilche
* Added support for new ICache (CBDB_Cache) interface.
*
* Revision 1.11  2003/11/26 18:59:46  ucko
* Remove stray semicolon after BEGIN_SCOPE(objects) to fix the WorkShop build.
*
* Revision 1.10  2003/11/26 17:55:53  vasilche
* Implemented ID2 split in ID1 cache.
* Fixed loading of splitted annotations.
*
* Revision 1.9  2003/10/27 15:05:41  vasilche
* Added correct recovery of cached ID1 loader if gi->sat/satkey cache is invalid.
* Added recognition of ID1 error codes: private, etc.
* Some formatting of old code.
*
* Revision 1.8  2003/10/21 16:32:50  vasilche
* Cleaned ID1 statistics messages.
* Now by setting GENBANK_ID1_STATS=1 CId1Reader collects and displays stats.
* And by setting GENBANK_ID1_STATS=2 CId1Reader logs all activities.
*
* Revision 1.7  2003/10/21 14:27:34  vasilche
* Added caching of gi -> sat,satkey,version resolution.
* SNP blobs are stored in cache in preprocessed format (platform dependent).
* Limit number of connections to GenBank servers.
* Added collection of ID1 loader statistics.
*
* Revision 1.6  2003/10/14 18:31:53  vasilche
* Added caching support for SNP blobs.
* Added statistics collection of ID1 connection.
*
* Revision 1.5  2003/10/08 18:57:49  kuznets
* Implemeneted correct ID1 BLOB versions.
*
* Revision 1.4  2003/10/03 17:41:33  kuznets
* Added an option, that cache is owned by the ID1 reader.
* Cache destroyed with the reader.
*
* Revision 1.3  2003/10/02 19:28:34  kuznets
* First working revision
*
* Revision 1.2  2003/10/01 19:32:01  kuznets
* Work in progress
*
* Revision 1.1  2003/09/30 19:38:26  vasilche
* Added support for cached id1 reader.
*
*/

#endif // READER_ID1_CACHE__HPP_INCLUDED