lds_dataloader.cpp

来自「ncbi源码」· C++ 代码 · 共 363 行

/*
 * ===========================================================================
 * PRODUCTION $Log: lds_dataloader.cpp,v $
 * PRODUCTION Revision 1000.3  2004/06/01 19:42:43  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.15
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: lds_dataloader.cpp,v 1000.3 2004/06/01 19:42:43 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: Anatoliy Kuznetsov
 *
 * File Description:  LDS dataloader. Implementations.
 *
 */


#include <ncbi_pch.hpp>
#include <objtools/data_loaders/lds/lds_dataloader.hpp>
#include <objtools/lds/lds_reader.hpp>
#include <objtools/lds/lds_util.hpp>

#include <objects/general/Object_id.hpp>

#include <bdb/bdb_util.hpp>
#include <objtools/lds/lds.hpp>
#include <objmgr/impl/handle_range_map.hpp>
#include <objmgr/impl/tse_info.hpp>
#include <objmgr/impl/data_source.hpp>
#include <corelib/plugin_manager.hpp>
#include <corelib/plugin_manager_impl.hpp>

BEGIN_NCBI_SCOPE

NCBI_DECLARE_INTERFACE_VERSION(objects::CDataLoader,  "omdataloader", 1, 1, 0);

BEGIN_SCOPE(objects)


class CLDS_BlobId : public CObject
{
public:
    CLDS_BlobId(int rec_id)
    : m_RecId(rec_id)
    {}
    int GetRecId() const { return m_RecId; }
private:
    int    m_RecId;
};


class CLDS_FindSeqIdFunc
{
public:
    CLDS_FindSeqIdFunc(SLDS_TablesCollection& db,
                       const CHandleRangeMap&  hrmap)
    : m_HrMap(hrmap),
      m_db(db)
    {}

    void operator()(SLDS_ObjectDB& dbf)
    {
        if (dbf.primary_seqid.IsNull())
            return;
        int object_id = dbf.object_id;
        int tse_id = dbf.TSE_object_id;

        string seq_id_str = (const char*)dbf.primary_seqid;
        if (seq_id_str.empty())
            return;
        {{
            CSeq_id seq_id_db(seq_id_str);
            if (seq_id_db.Which() == CSeq_id::e_not_set) {
                seq_id_db.SetLocal().SetStr(seq_id_str);
                if (seq_id_db.Which() == CSeq_id::e_not_set) {
                    return;
                }
            }

            ITERATE (CHandleRangeMap, it, m_HrMap) {
                CSeq_id_Handle seq_id_hnd = it->first;
                CConstRef<CSeq_id> seq_id = seq_id_hnd.GetSeqId();
                if (seq_id->Match(seq_id_db)) {
                    m_ids.insert(tse_id ? tse_id : object_id);
                    return;
                }
            } // ITERATE
        }}

        // Primaty seq_id scan gave no results
        // Trying supplemental aliases
/*
        m_db.object_attr_db.object_attr_id = object_id;
        if (m_db.object_attr_db.Fetch() != eBDB_Ok) {
            return;
        }

        if (m_db.object_attr_db.seq_ids.IsNull() || 
            m_db.object_attr_db.seq_ids.IsEmpty()) {
            return;
        }
*/
        if (dbf.seq_ids.IsNull() || 
            dbf.seq_ids.IsEmpty()) {
            return;
        }
        string attr_seq_ids((const char*)dbf.seq_ids);
        vector<string> seq_id_arr;
        
        NStr::Tokenize(attr_seq_ids, " ", seq_id_arr, NStr::eMergeDelims);

        ITERATE (vector<string>, it, seq_id_arr) {
            CSeq_id seq_id_db(*it);

            if (seq_id_db.Which() == CSeq_id::e_not_set) {
                seq_id_db.SetLocal().SetStr(*it);
                if (seq_id_db.Which() == CSeq_id::e_not_set) {
                    continue;
                }
            }

            {{
            
            ITERATE (CHandleRangeMap, it2, m_HrMap) {
                CSeq_id_Handle seq_id_hnd = it2->first;
                CConstRef<CSeq_id> seq_id = seq_id_hnd.GetSeqId();

                if (seq_id->Match(seq_id_db)) {
                    m_ids.insert(tse_id ? tse_id : object_id);
                    return;
                }
            } // ITERATE
            
            }}

        } // ITERATE
    }

    CLDS_Set& GetIds() { return m_ids; }

private:
    const CHandleRangeMap&  m_HrMap;  // Range map of seq ids to search
    SLDS_TablesCollection&  m_db;     // The LDS database
    CLDS_Set                m_ids;    // TSE results, found
};



CLDS_DataLoader::CLDS_DataLoader()
: m_LDS_db(0)
{}



CLDS_DataLoader::CLDS_DataLoader(CLDS_Database& lds_db,
                                 const string& dl_name)
 : CDataLoader(dl_name),
   m_LDS_db(&lds_db),
   m_OwnDatabase(false)
{
}


CLDS_DataLoader::CLDS_DataLoader(const string& db_path,
                                 const string& dl_name)
 : CDataLoader(dl_name),
   m_LDS_db(new CLDS_Database(db_path, kEmptyStr)),
   m_OwnDatabase(true)
{
    try {
        m_LDS_db->Open();
    } 
    catch(...)
    {
        delete m_LDS_db;
        throw;
    }
}

CLDS_DataLoader::~CLDS_DataLoader()
{
    if (m_OwnDatabase)
        delete m_LDS_db;
}


void CLDS_DataLoader::SetDatabase(CLDS_Database& lds_db,
                                  const string&  dl_name)
{
    if (m_LDS_db && m_OwnDatabase)
        delete m_LDS_db;
    m_LDS_db = &lds_db;
    SetName(dl_name);
}


void CLDS_DataLoader::GetRecords(const CSeq_id_Handle& idh,
                                 EChoice choice)
{
    CHandleRangeMap hrmap;
    hrmap.AddRange(idh, CRange<TSeqPos>::GetWhole(), eNa_strand_unknown);
    CLDS_FindSeqIdFunc search_func(m_LDS_db->GetTables(), hrmap);
    
    SLDS_TablesCollection& db = m_LDS_db->GetTables();

    BDB_iterate_file(db.object_db, search_func);

    const CLDS_Set& ids = search_func.GetIds();

    CDataSource* data_source = GetDataSource();
    _ASSERT(data_source);

    CLDS_Set::const_iterator it;
    for (it = ids.begin(); it != ids.end(); ++it) {
        int object_id = *it;

        if (LDS_SetTest(m_LoadedObjects, object_id)) {
            // Object has already been loaded. Ignore.
            continue;
        }

        CRef<CSeq_entry> seq_entry = 
            LDS_LoadTSE(db, m_LDS_db->GetObjTypeMap(), object_id);

        if (seq_entry) {
            CRef<CTSE_Info> tse_info = 
                data_source->AddTSE(*seq_entry,
                                    false,
                                    new CLDS_BlobId(object_id));
            m_LoadedObjects.insert(object_id);
        }
    }
}

void CLDS_DataLoader::DropTSE(const CTSE_Info& tse_info)
{
    const CConstRef<CObject>& cobj_ref = tse_info.GetBlobId();
    const CObject* obj_ptr = cobj_ref.GetPointerOrNull();
    _ASSERT(obj_ptr);

    const CLDS_BlobId* blob_id = 
        dynamic_cast<const CLDS_BlobId*>(obj_ptr);
    _ASSERT(blob_id);
    
    int object_id = blob_id->GetRecId();
    m_LoadedObjects.erase(object_id);
}


END_SCOPE(objects)

// ===========================================================================

USING_SCOPE(objects);

class CLDS_DataLoaderCF : 
  public CSimpleClassFactoryImpl<objects::CDataLoader, objects::CLDS_DataLoader>
{
public:
    typedef CSimpleClassFactoryImpl<objects::CDataLoader, 
                                    objects::CLDS_DataLoader>    TParent;

    CLDS_DataLoaderCF() : TParent("CLDS_DataLoader")
    {}
};


extern "C"
{

void NCBI_XLOADER_LDS_EXPORT 
NCBI_EntryPoint_DataLoader_LDS(CPluginManager<CDataLoader>::TDriverInfoList&   info_list,
                               CPluginManager<CDataLoader>::EEntryPointRequest method)
{
    CHostEntryPointImpl<CLDS_DataLoaderCF>::NCBI_EntryPointImpl(info_list, method);
}


}


END_NCBI_SCOPE

/*
 * ===========================================================================
 * $Log: lds_dataloader.cpp,v $
 * Revision 1000.3  2004/06/01 19:42:43  gouriano
 * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.15
 *
 * Revision 1.15  2004/05/21 21:42:52  gorelenk
 * Added PCH ncbi_pch.hpp
 *
 * Revision 1.14  2004/03/09 17:17:20  kuznets
 * Merge object attributes with objects
 *
 * Revision 1.13  2003/12/16 20:49:18  vasilche
 * Fixed compile errors - added missing includes and declarations.
 *
 * Revision 1.12  2003/12/16 17:55:22  kuznets
 * Added plugin entry point
 *
 * Revision 1.11  2003/11/28 13:41:10  dicuccio
 * Fixed to match new API in CDataLoader
 *
 * Revision 1.10  2003/10/28 14:01:20  kuznets
 * Added constructor parameter name of the dataloader
 *
 * Revision 1.9  2003/10/08 19:40:55  kuznets
 * kEmptyStr instead database path as default alias
 *
 * Revision 1.8  2003/10/08 19:29:08  ucko
 * Adapt to new (multi-DB-capable) LDS API.
 *
 * Revision 1.7  2003/09/30 16:36:37  vasilche
 * Updated CDataLoader interface.
 *
 * Revision 1.6  2003/08/19 14:21:24  kuznets
 * +name("LDS_dataloader") for the dataloader class
 *
 * Revision 1.5  2003/07/30 19:52:15  kuznets
 * Cleaned compilation warnings
 *
 * Revision 1.4  2003/07/30 19:46:54  kuznets
 * Implemented alias search mode
 *
 * Revision 1.3  2003/07/30 18:36:38  kuznets
 * Minor syntactic fix
 *
 * Revision 1.2  2003/06/18 18:49:01  kuznets
 * Implemented new constructor.
 *
 * Revision 1.1  2003/06/16 15:48:28  kuznets
 * Initial revision.
 *
 *
 * ===========================================================================
 */