plugin_init.cpp

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/*
 * ===========================================================================
 * PRODUCTION $Log: plugin_init.cpp,v $
 * PRODUCTION Revision 1000.5  2004/06/01 20:56:32  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.42
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: plugin_init.cpp,v 1000.5 2004/06/01 20:56:32 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:  Mike DiCuccio
 *           Anatoliy Kuznetsov
 *
 * File Description:
 *    CGBenchPluginInit -- single standard autoloading plugin for Genome
 *                         Workbench
 */


#include <ncbi_pch.hpp>
#include "plugin_init.hpp"

#include <bdb/bdb_blobcache.hpp>
#include <corelib/ncbiapp.hpp>
#include <corelib/ncbireg.hpp>
#include <corelib/ncbitime.hpp> 
#include <corelib/ncbi_process.hpp>

#include <gui/core/data_store.hpp>
#include <gui/core/doc_manager.hpp>
#include <gui/core/plugin_exception.hpp>
#include <gui/core/plugin_handle.hpp>
#include <gui/core/plugin_registry.hpp>
#include <gui/utils/system_path.hpp>
#include <gui/core/version.hpp>
#include <gui/plugin/PluginCommand.hpp>
#include <gui/plugin/PluginCommandSet.hpp>
#include <gui/plugin/PluginInfo.hpp>
#include <gui/plugin/PluginValueConstraint.hpp>
#include <gui/utils/message_box.hpp>

#include <objmgr/object_manager.hpp>
#include <objtools/data_loaders/lds/lds_dataloader.hpp>
#include <objtools/data_loaders/genbank/gbloader.hpp>
#include <objtools/data_loaders/genbank/readers/id1/reader_id1_cache.hpp>
#include <objtools/lds/admin/lds_admin.hpp>
#include <objtools/lds/lds.hpp>
#include <objtools/lds/lds_reader.hpp>


BEGIN_NCBI_SCOPE
USING_SCOPE(objects);


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

    // version info macro
    info.SetInfo(CPluginVersion::eMajor, CPluginVersion::eMinor, 0,
                 string(__DATE__) + " " + string(__TIME__),
                 "CGBenchPluginInit", "", "", "");

    // command info
    info.SetCommands().AddAlgoCommand(eAlgoCommand_run);
    info.SetAutorun(true);
}





void CGBenchPluginInit::RunCommand(CPluginMessage& msg)
{
    CPluginReply& reply = msg.SetReply();

    //
    // first, set up our stock data loaders
    // these must be present for sequence ID resolution to work correctly
    //

    // Create GenBank data loader and register it with the OM.
    // The last argument "eDefault" informs the OM that the loader must
    // be included in scopes during the CScope::AddDefaults() call.
    try {
        x_InitGenBank();
    }
    catch (CException& e) {
        LOG_POST(Error << "error creating GenBank data loader: " << e.what());
        string msg("Error connecting to GenBank:\n");
        msg += e.GetMsg();
        msg += "\nGenBank will not be available.";
        NcbiMessageBox(msg);
    }
#ifndef _DEBUG
    catch (...) {
        LOG_POST(Error << "unknown error creating GenBank data loader");
        NcbiMessageBox("An unknown error has occurred while trying to "
                       "connect to GenBank");
    }
#endif

    //
    // initialize the local data storage
    //
    try {
        x_InitLDS();
    }
    catch(CException& e) {
        LOG_POST(Error << "error initializing local data storage: "
                 << e.what());
        string msg("Error initializing local data storage:\n");
        msg += e.GetMsg();
        msg += "\nLDS will not be available.";
        NcbiMessageBox(msg);
    }
#ifndef _DEBUG
    catch (...) {
        LOG_POST(Error << "unknown error creating GenBank data loader");
        NcbiMessageBox("An unknown error has occurred while trying to "
                       "initialize the local data stores.");
    }
#endif


    //
    // PLANNED:
    //
    // - establish named pipe for gbench-agent (our mime droid)
    // - check NCBI to see if there are any gbench updates
    // - evaluate history to see what the user has looked at recently and see
    //   if there are any recent changes in those sequences / organisms
    // - check the user's cubby at NCBI to see if there are any updates in any
    //   watched files
    //

    reply.SetStatus(eMessageStatus_success);
}


//
// Create our GenBank connection
//

void CGBenchPluginInit::x_InitGenBank()
{
    CNcbiApplication* app = CNcbiApplication::Instance();
    _ASSERT(app);
    CNcbiRegistry& reg = app->GetConfig();

    // general genbank loader options
    int gc_size   = reg.GetInt("GBLOADER", "GcSize", 10000,
                               CNcbiRegistry::eErrPost);
    int priority  = reg.GetInt("GBLOADER", "Priority", 99,
                               CNcbiRegistry::eErrPost);

    // caching options
    string cache_path = CSystemPath::ResolvePath("<home>", "cache");
    cache_path    = reg.GetString("GBLOADER", "CachePath", cache_path,
                                  CNcbiRegistry::eErrPost);
    int cache_age = reg.GetInt("GBLOADER", "CacheAge", 5,
                               CNcbiRegistry::eErrPost);

    if (cache_age == 0) {
        cache_age = 5;   // keep objects for 5 days (default)
    }


    // ID resolution time in hours
    int id_resolution_time = reg.GetInt("GBLOADER",
                                        "IdResolutionTime", 24,
                                        CNcbiRegistry::eErrPost);

    if (id_resolution_time > 24 * 3) 
        id_resolution_time = 24 * 3; //  correct the unreasonable value

    bool disable_cache = reg.GetBool("GBLOADER", "DisableCache", false,
                                     CNcbiRegistry::eErrPost);


    auto_ptr<CCachedId1Reader> id1_reader;

    if (!cache_path.empty()  &&  !disable_cache) {
        try {
            auto_ptr<CBDB_Cache> bc(new CBDB_Cache());

            try {
                ICache::TTimeStampFlags flags =
                    ICache::fTimeStampOnRead |
                    ICache::fExpireLeastFrequentlyUsed |
                    ICache::fPurgeOnStartup;
                bc->SetTimeStampPolicy(flags, cache_age*24*60*60);

                bc->Open(cache_path.c_str(), "blobs", CBDB_Cache::ePidLock);

                // Cache cleaning
                // Objects age should be assigned in days, negative value
                // means cleaning is disabled

                if (cache_age > 0) {
                    CTime time_stamp(CTime::eCurrent);
                    time_t age = time_stamp.GetTimeT();

                    age -= 60 * 60 * 24 * cache_age;

                    bc->Purge(age);
                }


            } catch (CPIDGuardException& ex) {
                switch (ex.GetErrCode())
                {
                case CPIDGuardException::eStillRunning:
                    // We probably(!) have another program competing for cache,
                    // So this copy is not getting access
                    LOG_POST(Error << "GenBank Cache is in use by another process");
                    LOG_POST(Error << "Local caching will be disabled.");
                    throw;
                default:
                    throw;
                } // switch
            }

            auto_ptr<CBDB_Cache> idc(new CBDB_Cache());

            try {
                ICache::TTimeStampFlags flags =
                    ICache::fTimeStampOnCreate|
                    ICache::fCheckExpirationAlways;
                idc->SetTimeStampPolicy(flags, id_resolution_time * 60 * 60);

                idc->Open(cache_path.c_str(), "idc", CBDB_Cache::ePidLock);

            } catch (CPIDGuardException& ex) {
                switch (ex.GetErrCode())
                {
                case CPIDGuardException::eStillRunning:
                    // We probably(!) have another program competing for cache,
                    // So this copy is not getting access
                    LOG_POST(Error << "GenBank Cache is in use by another process");
                    LOG_POST(Error << "Local caching will be disabled.");
                    throw;
                default:
                    throw;
                } // switch
            }


            CRef<CBDB_CacheHolder> 
                       cache_holder(new CBDB_CacheHolder(bc.release(),
                                                         idc.release()));

            CDataStore::PutObject("BDB_Cache", *cache_holder);

            id1_reader.reset(new CCachedId1Reader(5, 
                                                  cache_holder->GetBlobCache(), 
                                                  cache_holder->GetIdCache()));


            LOG_POST(Info << "ID1 cache enabled at " << cache_path);
        }
        catch(CException& e) {
            LOG_POST(Error << "ID1 cache initialization failed in "
                     << cache_path << ": "
                     << e.what());
        }
#ifndef _DEBUG
        catch(...) {
            LOG_POST(Error << "ID1 cache initialization failed in "
                     << cache_path);
        }
#endif
    } else {
        LOG_POST(Info << "ID1 cache disabled.");
    }

    CRef<CGBDataLoader> loader
        (new CGBDataLoader("GenBank", id1_reader.release(), gc_size));
    if ( !loader  ) {
        NCBI_THROW(CPluginException, eUnknownError,
                   "CGBenchPluginInit(): "
                   "can't create GenBank data loader");
    }
    CDocManager::GetObjectManager()
        .RegisterDataLoader(*(loader.Release()),
                            CObjectManager::eDefault, priority);

    LOG_POST(Info << "registered GenBank data loader");
}