lds_loader.cpp

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/*
 * ===========================================================================
 * PRODUCTION $Log: lds_loader.cpp,v $
 * PRODUCTION Revision 1000.5  2004/06/01 20:58:08  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.31
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: lds_loader.cpp,v 1000.5 2004/06/01 20:58:08 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.
 *
 * ===========================================================================
 *
 * Authors:  Anatoliy Kuznetsov
 *
 * File Description:
 *    CDataPlugin_LDSLoader - load sequence information from the local data storage(LDS).
 */

#include <ncbi_pch.hpp>
#include <corelib/ncbiapp.hpp>
#include <corelib/ncbireg.hpp>
#include <corelib/ncbitime.hpp>

#include <gui/plugin/PluginInfo.hpp>
#include <gui/core/version.hpp>
#include <gui/core/doc_exception.hpp>
#include <gui/core/doc_manager.hpp>
#include <gui/core/idocument.hpp>
#include <gui/core/plugin_utils.hpp>
#include <gui/core/data_store.hpp>
#include <gui/objutils/utils.hpp>
#include <gui/plugin/PluginValue.hpp>
#include <gui/plugin/PluginCommandSet.hpp>
#include <gui/utils/message_box.hpp>
#include <objmgr/scope.hpp>

#include "lds_loader.hpp"
#include "loader_utils.hpp"

#include <objtools/lds/lds.hpp>
#include <objtools/lds/lds_util.hpp>
#include <objtools/lds/lds_reader.hpp>
#include <objtools/lds/admin/lds_admin.hpp>

#include "lds_search_dlg.hpp"

BEGIN_NCBI_SCOPE
USING_SCOPE(objects);


//////////////////////////////////////////////////////////////////
//
// class CDataPlugin_LDSLoaderException defines some internal exception types used in
// processing files.
//
// This class is used internally to avoid an ad-hoc exception mechanism;
//
class CDataPlugin_LDSLoaderException : EXCEPTION_VIRTUAL_BASE public CException
{
public:
    // Enumerated list of exception types
    enum EErrCode {
        eInvalidId
    };

    // Convert an enumerated exception to a human-readable string representation
    // of this exception.
    virtual const char* GetErrCodeString(void) const
    {
        switch (GetErrCode()) {
        case eInvalidId:        return "eInvalidId";
        default:                return CException::GetErrCodeString();
        }
    }

    // constructor boilerplate
    NCBI_EXCEPTION_DEFAULT(CDataPlugin_LDSLoaderException, CException);
};


//////////////////////////////////////////////////////////////////

void CDataPlugin_LDSLoader::GetInfo(CPluginInfo& info)
{
    info.Reset();

    // version info macro
    info.SetInfo(CPluginVersion::eMajor, CPluginVersion::eMinor, 0,
                 string(__DATE__) + " " + string(__TIME__),
                 "CDataPlugin_LDSLoader", "Local sequence",
                 "Open a molecule by sequence Id", "");

    // command info
    CPluginCommandSet& cmds    = info.SetCommands();
    
    CPluginCommand& load_args  = cmds.AddDataCommand(eDataCommand_load);

    load_args.AddArgument("acc", "Local sequence to load",
                          CPluginArg::eString,
                          CPluginArg::TData::e_Array);

    load_args.AddArgument("search_all", "Search all references",
                          CPluginArg::eBoolean,
                          CPluginArg::TData::e_Single);

    CPluginCommand& search_args = cmds.AddDataCommand(eDataCommand_search);
    {{
        CPluginArg& arg = 
            search_args.AddArgument("query", "Search string",
                                    CPluginArg::eString);
        arg.SetHidden(true);
    }}

}


CDataPlugin_LDSLoader::CDataPlugin_LDSLoader()
 : m_DbHolder(0)
{
    if (CDataStore::HasObject("LDS_Database")) {
        CObject& obj = CDataStore::GetObject("LDS_Database");
        m_DbHolder = dynamic_cast<CLDS_DatabaseHolder*>(&obj);
//        if (dbh)
//            m_db = dbh->GetDefaultDatabase();
    }
}

CDataPlugin_LDSLoader::~CDataPlugin_LDSLoader()
{
}


//
// load a record from Genbank into a fully-prepared document
//
void CDataPlugin_LDSLoader::Load(CPluginMessage& msg)
{
    const CPluginCommand& args = msg.GetRequest().GetCommand();
    CPluginReply& reply = msg.SetReply();
    reply.SetStatus(eMessageStatus_failed);

    bool request_success = false;

    if (!m_DbHolder) {
        reply.SetStatus(eMessageStatus_ignored);
        LOG_POST(Error << "Local data storage is not open.");
        return;
    }

    vector<string> str_vec = CPluginUtils::ArgToStringVec(args["acc"]);

    CLoaderStrFormatter::PrepareSearchVector(str_vec);

    if (str_vec.empty()) {
        reply.SetStatus(eMessageStatus_ignored);
        return;
    }

    bool search_all = args["search_all"].AsBoolean();
    string alias    = args["alias"].AsString();
    LOG_POST(Info << "loading from " << alias);

    string lds_alias = args["alias"].AsString();

    CLDS_Database* db = m_DbHolder->GetDatabase(lds_alias);

    if (!db) {
        reply.SetStatus(eMessageStatus_ignored);
        LOG_POST(Error << "LDS alias " << lds_alias << " not found.");
        return;
    }


    CStopWatch stw;
    stw.Start();

    SLDS_TablesCollection& tables = db->GetTables();

    CLDS_Set obj_search_results;
    CLDS_Query query(tables);
    query.FindSequences(str_vec, &obj_search_results);

    double elapsed = stw.Elapsed();

    LOG_POST(Info << "LDS sequence search time = " << elapsed);

    unsigned int obj_found = 0; // Number of objects found

    CLDS_Set obj_read; // list of objects already loaded

    obj_found += obj_search_results.size();

    if (obj_search_results.size() == 0) {
        LOG_POST(Info
                 << "Failed to find local sequence(s).");
    }
    else {
        ITERATE (CLDS_Set, rsit, obj_search_results) {
            try {
                int object_id = *rsit;
                if (!x_LoadLDS_BioTSE(object_id, db, &obj_read, reply)) {
                    continue;
                }
                request_success = true;
            } 
            catch (CLDS_Exception& _DEBUG_ARG(ex))
            {
                _TRACE("failed to read LDS file: " << ex.what());            
            }

        } // ITERATE
    }
    if (search_all) {

        CLDS_Set slist_search_results;

        query.FindSeqIdList(str_vec, &slist_search_results);
        obj_found += slist_search_results.size();

        ITERATE (CLDS_Set, it, slist_search_results) {
            try {
                int id = *it;

                CLDS_Query::SObjectDescr descr = 
                  query.GetObjectDescr(db->GetObjTypeMap(), id, true);

                if (LDS_SetTest(obj_read, descr.id)) {
                    continue;
                }

                if (x_Load(descr, db, &obj_read, reply)) {
                    request_success = true;                    
                }

            
            }
            catch (CLDS_Exception& _DEBUG_ARG(ex))
            {
                _TRACE("failed to read object: " << ex.what());            
            }
        } // ITERATE
    }

    if (obj_found == 0) {
        NcbiMessageBox("Failed to find local sequence(s).",  
                       eDialog_Ok,
                       eIcon_Stop,
                       "Error");
    }

    // set our status code
    // we don't set a default action - the documents are merely posted for
    // notification in case a user has called this plugin and expects
    // to receive the results in a return value
    if (request_success) {
        reply.SetStatus(eMessageStatus_success);
    }
}


void CDataPlugin_LDSLoader::Search(CPluginMessage& msg)
{