lds.cpp

来自「ncbi源码」· C++ 代码 · 共 339 行

/*
 * ===========================================================================
 * PRODUCTION $Log: lds.cpp,v $
 * PRODUCTION Revision 1000.2  2004/06/01 19:45:47  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.17
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: lds.cpp,v 1000.2 2004/06/01 19:45:47 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 implementation.
 *
 */

#include <ncbi_pch.hpp>
#include <corelib/ncbifile.hpp>

#include <bdb/bdb_cursor.hpp>

#include <objtools/lds/lds.hpp>
#include <objtools/lds/admin/lds_object.hpp>
#include <objtools/lds/admin/lds_files.hpp>

BEGIN_NCBI_SCOPE
BEGIN_SCOPE(objects)


CLDS_Database::CLDS_Database(const string& db_dir_name, 
                             const string& db_name,
                             const string& alias)
: m_LDS_DirName(db_dir_name),
  m_LDS_DbName(db_name)
{
    if (alias.empty()) {
        m_Alias = db_dir_name;
    }
    else {
        m_Alias = alias;
    }
}

CLDS_Database::CLDS_Database(const string& db_dir_name,
                             const string& alias)
: m_LDS_DirName(db_dir_name)
{
    m_LDS_DbName = "lds.db";
    if (alias.empty()) {
        m_Alias = db_dir_name;
    }
    else {
        m_Alias = alias;
    }
}


CLDS_Database::~CLDS_Database()
{
    LOG_POST(Info << "Closing LDS database: " << m_LDS_DbName);
}

void CLDS_Database::Create()
{
    string fname;
    LOG_POST(Info << "Creating LDS database: " << m_LDS_DbName);

    {{
        m_LDS_DirName = CDirEntry::AddTrailingPathSeparator(m_LDS_DirName);

        // Conditionally add LDS subdirectory name 
        // TODO: make name check more robust
        if (m_LDS_DirName.find("LDS") == string::npos) {
            m_LDS_DirName = CDirEntry::AddTrailingPathSeparator(m_LDS_DirName);
            m_LDS_DirName += "LDS";
            m_LDS_DirName = CDirEntry::AddTrailingPathSeparator(m_LDS_DirName);
        }

        CDir  lds_dir(m_LDS_DirName);

        if (!lds_dir.Exists()) {
            if (!lds_dir.Create()) {
                LDS_THROW(eCannotCreateDir, 
                          "Cannot create directory:"+m_LDS_DirName);
            }
        }

    }}

    LOG_POST(Info << "Creating LDS table: " << "file");

    fname = m_LDS_DirName + "lds_file.db"; 
    m_db.file_db.Open(fname.c_str(),
                      "file",
                      CBDB_RawFile::eCreate);

    LOG_POST(Info << "Creating LDS table: " << "objecttype");

    fname = m_LDS_DirName + "lds_objecttype.db"; 
    m_db.object_type_db.Open(fname.c_str(),
                             "objecttype",
                             CBDB_RawFile::eCreate);
    LOG_POST(Info << "Creating LDS table: " << "object");

    fname = m_LDS_DirName + "lds_object.db"; 
    m_db.object_db.Open(fname.c_str(),
                    "object",
                    CBDB_RawFile::eCreate);
/*
    LOG_POST(Info << "Creating LDS table: " << "objectattr");
    fname = m_LDS_DirName + "lds_objectattr.db"; 
    m_db.object_attr_db.Open(fname.c_str(),
                             "objectattr",
                             CBDB_RawFile::eCreate);
*/
    LOG_POST(Info << "Creating LDS table: " << "annotation");
    fname = m_LDS_DirName + "lds_annotation.db"; 
    m_db.annot_db.Open(fname.c_str(),
                       "annotation",
                       CBDB_RawFile::eCreate);

    LOG_POST(Info << "Creating LDS table: " << "annot2obj");
    fname = m_LDS_DirName + "lds_annot2obj.db"; 
    m_db.annot2obj_db.Open(fname.c_str(),
                           "annot2obj",
                           CBDB_RawFile::eCreate);

    LOG_POST(Info << "Creating LDS table: " << "seq_id_list");
    fname = m_LDS_DirName + "lds_seq_id_list.db"; 
    m_db.seq_id_list.Open(fname.c_str(),
                          "seq_id_list",
                          CBDB_RawFile::eCreate);
}


void CLDS_Database::Sync()
{
    m_db.annot2obj_db.Sync();
    m_db.annot_db.Sync();
    m_db.file_db.Sync();
//    m_db.object_attr_db.Sync();
    m_db.object_db.Sync();
    m_db.object_type_db.Sync();
    m_db.seq_id_list.Sync();    
}


void CLDS_Database::Open()
{
    string fname;

    m_LDS_DirName = CDirEntry::AddTrailingPathSeparator(m_LDS_DirName);

    if (m_LDS_DirName.find("LDS") == string::npos) {
        m_LDS_DirName += "LDS";
        m_LDS_DirName = CDirEntry::AddTrailingPathSeparator(m_LDS_DirName);
    }

    fname = m_LDS_DirName + "lds_file.db"; 
    m_db.file_db.Open(fname.c_str(),
                      "file",
                      CBDB_RawFile::eReadWrite);

    fname = m_LDS_DirName + "lds_objecttype.db"; 
    m_db.object_type_db.Open(fname.c_str(),
                             "objecttype",
                             CBDB_RawFile::eReadWrite);
    LoadTypeMap();

    fname = m_LDS_DirName + "lds_object.db"; 
    m_db.object_db.Open(fname.c_str(),
                        "object",
                        CBDB_RawFile::eReadWrite);
/*
    fname = m_LDS_DirName + "lds_objectattr.db"; 
    m_db.object_attr_db.Open(fname.c_str(),
                            "objectattr",
                            CBDB_RawFile::eReadWrite);
*/
    fname = m_LDS_DirName + "lds_annotation.db"; 
    m_db.annot_db.Open(fname.c_str(),
                       "annotation",
                       CBDB_RawFile::eReadWrite);

    fname = m_LDS_DirName + "lds_annot2obj.db"; 
    m_db.annot2obj_db.Open(fname.c_str(),
                           "annot2obj",
                           CBDB_RawFile::eReadWrite);

    fname = m_LDS_DirName + "lds_seq_id_list.db"; 
    m_db.seq_id_list.Open(fname.c_str(),
                          "seq_id_list",
                           CBDB_RawFile::eReadWrite);
}

void CLDS_Database::LoadTypeMap()
{
    CBDB_FileCursor cur(m_db.object_type_db); 
    cur.SetCondition(CBDB_FileCursor::eFirst); 
    while (cur.Fetch() == eBDB_Ok) { 
        m_ObjTypeMap.insert(pair<string, int>(string(m_db.object_type_db.type_name), 
                                              m_db.object_type_db.object_type)
                           );
    }
}


CLDS_DatabaseHolder::CLDS_DatabaseHolder(CLDS_Database* db) 
{
    if (db) {
        m_DataBases.push_back(db);
    }
}


CLDS_DatabaseHolder::~CLDS_DatabaseHolder() 
{ 
    ITERATE(vector<CLDS_Database*>, it, m_DataBases) {
        CLDS_Database* db = *it;
        delete db;
    }   
}

CLDS_Database* CLDS_DatabaseHolder::GetDatabase(const string& alias)
{
    ITERATE(vector<CLDS_Database*>, it, m_DataBases) {
        CLDS_Database* db = *it;
        const string& db_alias = db->GetAlias();
        if (db_alias == alias) {
            return db;
        }
    }
    return 0;
    
}

void CLDS_DatabaseHolder::EnumerateAliases(vector<string>* aliases)
{
    ITERATE(vector<CLDS_Database*>, it, m_DataBases) {
        CLDS_Database* db = *it;
        const string& db_alias = db->GetAlias();
        aliases->push_back(db_alias);
    }
}


END_SCOPE(objects)
END_NCBI_SCOPE

/*
 * ===========================================================================
 * $Log: lds.cpp,v $
 * Revision 1000.2  2004/06/01 19:45:47  gouriano
 * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.17
 *
 * Revision 1.17  2004/05/21 21:42:54  gorelenk
 * Added PCH ncbi_pch.hpp
 *
 * Revision 1.16  2004/03/09 17:16:59  kuznets
 * Merge object attributes with objects
 *
 * Revision 1.15  2003/10/29 16:23:31  kuznets
 * Implemented CLDS_DatabaseHolder::EnumerateAliases
 *
 * Revision 1.14  2003/10/27 20:16:57  kuznets
 * +CLDS_DatabaseHolder::GetDatabase
 *
 * Revision 1.13  2003/10/27 19:18:59  kuznets
 * Added NULL database protection into CLDS_DatabaseHolder::CLDS_DatabaseHolder
 *
 * Revision 1.12  2003/10/09 18:12:26  kuznets
 * Some functionality of lds migrated into lds_admin
 *
 * Revision 1.11  2003/10/09 16:48:33  kuznets
 * Sync() implemented
 *
 * Revision 1.10  2003/10/08 18:19:52  kuznets
 * Changes to support multi instance databases
 *
 * Revision 1.9  2003/08/12 14:12:05  kuznets
 * All database files now created in separate LDS subdirectory.
 *
 * Revision 1.8  2003/08/11 20:01:00  kuznets
 * Reworked lds database and file open procedure.
 * Now all db tables are created in separate OS files, not colocate in one
 * lds.db (looks like BerkeleyDB is not really supporting multiple tables in one file)
 *
 * Revision 1.7  2003/08/05 14:32:01  kuznets
 * Reflecting changes in obj_sniff.hpp
 *
 * Revision 1.6  2003/07/09 19:33:40  kuznets
 * Modified databse Open/Create procedures. (Reflecting new sequence id list table)
 *
 * Revision 1.5  2003/06/25 18:30:11  kuznets
 * Fixed bug with creation of object attributes table
 *
 * Revision 1.4  2003/06/16 16:24:43  kuznets
 * Fixed #include paths (lds <-> lds_admin separation)
 *
 * Revision 1.3  2003/06/16 15:39:18  kuznets
 * Removing dead code
 *
 * Revision 1.2  2003/06/16 14:55:00  kuznets
 * lds splitted into "lds" and "lds_admin"
 *
 * Revision 1.1  2003/06/03 14:13:25  kuznets
 * Initial revision
 *
 *
 * ===========================================================================
 */