test_objmgr_mt.cpp

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/*
 * ===========================================================================
 * PRODUCTION $Log: test_objmgr_mt.cpp,v $
 * PRODUCTION Revision 1000.3  2004/06/01 19:25:20  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.26
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: test_objmgr_mt.cpp,v 1000.3 2004/06/01 19:25:20 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:  Eugene Vasilchenko, Aleksey Grichenko, Denis Vakatov
*
* File Description:
*   Test the functionality of C++ object manager in MT mode
*
* ===========================================================================
*/

#include <ncbi_pch.hpp>
#include <corelib/ncbistd.hpp>
#include <corelib/ncbiapp.hpp>
#include <corelib/ncbienv.hpp>
#include <corelib/ncbiargs.hpp>
#include <corelib/ncbitime.hpp>
#include <corelib/ncbithr.hpp>
#include <corelib/test_mt.hpp>

#include <objects/seqloc/Seq_id.hpp>
#include <objects/seqset/Seq_entry.hpp>
#include <objects/seq/Seq_annot.hpp>

#include "test_helper.hpp"



BEGIN_NCBI_SCOPE
using namespace objects;


/////////////////////////////////////////////////////////////////////////////
//
//  Test application
//

class CTestObjectManager : public CThreadedApp
{
protected:
    virtual bool Thread_Run(int idx);
    virtual bool TestApp_Init(void);
    virtual bool TestApp_Exit(void);
    virtual bool TestApp_Args(CArgDescriptions& args);

    CRef<CObjectManager> m_ObjMgr;
    CRef<CScope> m_Scope;
};


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

bool CTestObjectManager::Thread_Run(int idx)
{
    ++idx;
    // Test global scope
    // read data from a scope, which is shared by all threads
    CTestHelper::TestDataRetrieval(*m_Scope, 0, 0);
    // add more data to the global scope
    CRef<CSeq_entry> entry1(&CDataGenerator::CreateTestEntry1(idx));
    CRef<CSeq_entry> entry2(&CDataGenerator::CreateTestEntry2(idx));
    m_Scope->AddTopLevelSeqEntry(*entry1);
    m_Scope->AddTopLevelSeqEntry(*entry2);
    CTestHelper::TestDataRetrieval(*m_Scope, idx, 0);

    // Test local scope
    // 1.2.5 add annotation to one sequence
    // verify that others did not change
    {
        CScope scope(*m_ObjMgr);
        // create new seq.entries - to be able to check unresolved lengths
        CRef<CSeq_entry> entry1(&CDataGenerator::CreateTestEntry1(idx));
        CRef<CSeq_entry> entry2(&CDataGenerator::CreateTestEntry2(idx));
        scope.AddTopLevelSeqEntry(*entry1);
        scope.AddTopLevelSeqEntry(*entry2);
        CRef<CSeq_annot> annot(&CDataGenerator::CreateAnnotation1(idx));
        scope.AttachAnnot(*entry1, *annot);
        CTestHelper::TestDataRetrieval(scope, idx, 1);

        // 1.2.6. Constructed bio sequences
        CSeq_id id;
        {{
            CRef<CSeq_entry> constr_entry
                (&CDataGenerator::CreateConstructedEntry( idx, 1));
            scope.AddTopLevelSeqEntry(*constr_entry);
            id.SetLocal().SetStr("constructed1");
            CTestHelper::ProcessBioseq(scope, id, 27,
                "GCGGTACAATAACCTCAGCAGCAACAA", "",
                0, 5, 0, 0, 0, 0, 0, 0, 0, 0);
        }}
        {{
            CRef<CSeq_entry> constr_entry
                (&CDataGenerator::CreateConstructedEntry( idx, 2));
            scope.AddTopLevelSeqEntry(*constr_entry);
            id.SetLocal().SetStr("constructed2");
            CTestHelper::ProcessBioseq(scope, id, 27,
                "TACCGCCAATAACCTCAGCAGCAACAA", "",
                0, 5, 0, 0, 0, 0, 0, 0, 0, 0);
        }}
    }

    // 1.2.7. one entry in two scopes
    {
        CScope Scope1(*m_ObjMgr);
        CRef<CScope> pScope2(new CScope(*m_ObjMgr));
        CRef<CSeq_entry> entry1(&CDataGenerator::CreateTestEntry1(idx));
        CRef<CSeq_entry> entry2(&CDataGenerator::CreateTestEntry2(idx));
        Scope1.AddTopLevelSeqEntry(*entry1);
        Scope1.AddTopLevelSeqEntry(*entry2);
        pScope2->AddTopLevelSeqEntry(*entry2);
        // Test with unresolvable references
        CSeq_id id;
        id.SetGi(21+idx*1000);
        CTestHelper::ProcessBioseq(*pScope2, id, 22,
          "\\0\\0\\0\\0\\0\\0\\0\\0\\0\\0\\0\\0\\0\\0\\0\\0\\0\\0\\0\\0\\0\\0",
          "\\0\\0\\0\\0\\0\\0\\0\\0\\0\\0\\0\\0\\0\\0\\0\\0\\0\\0\\0\\0\\0\\0",
          1, -1, 1, 1, 0, 0, 1, 1, 0, 0, false, true);

        // add more data to the scope - to make references resolvable
        CRef<CSeq_entry> entry1a(&CDataGenerator::CreateTestEntry1a(idx));
        pScope2->AddTopLevelSeqEntry(*entry1a);
        // Test with resolvable references
        id.SetGi(21+idx*1000);
        CTestHelper::ProcessBioseq(*pScope2, id, 62,
            "AAAAATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTAAAAATTTTTTTTTTTT",
            "TTTTTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATTTTTAAAAAAAAAAAA",
            1, 2, 2, 1, 0, 0, 1, 1, 0, 0);

        // 1.2.8. Test scope history
        CRef<CSeq_entry> entry1b(&CDataGenerator::CreateTestEntry1(idx));
        pScope2->AddTopLevelSeqEntry(*entry1b);
        id.SetLocal().SetStr("seq"+NStr::IntToString(11+idx*1000));
        // gi|11 from entry1a must be selected
        CTestHelper::ProcessBioseq(*pScope2, id, 40,
            "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA",
            "TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT",
            0, 2, 2, 1, 0, 0, 1, 1, 0, 0);
    }
    return true;
}

bool CTestObjectManager::TestApp_Init(void)
{
    const CArgs& args = GetArgs();
    CDataGenerator::sm_DumpEntries = args["dump_entries"];
    CTestHelper::sm_DumpFeatures = args["dump_features"];

    NcbiCout << "Testing ObjectManager (" << s_NumThreads << " threads)..." << NcbiEndl;

    m_ObjMgr = new CObjectManager;
    // Scope shared by all threads
    m_Scope = new CScope(*m_ObjMgr);
    CRef<CSeq_entry> entry1(&CDataGenerator::CreateTestEntry1(0));
    CRef<CSeq_entry> entry2(&CDataGenerator::CreateTestEntry2(0));
    m_Scope->AddTopLevelSeqEntry(*entry1);
    m_Scope->AddTopLevelSeqEntry(*entry2);
    return true;
}

bool CTestObjectManager::TestApp_Exit(void)
{
    NcbiCout << " Passed" << NcbiEndl << NcbiEndl;
    return true;
}

bool CTestObjectManager::TestApp_Args(CArgDescriptions& args)
{
    // Prepare command line descriptions
    args.AddFlag("dump_entries", "print all generated seq entries");
    args.AddFlag("dump_features", "print all found features");
    return true;
}

END_NCBI_SCOPE


/////////////////////////////////////////////////////////////////////////////
//  MAIN

USING_NCBI_SCOPE;

int main(int argc, const char* argv[])
{
    return CTestObjectManager().AppMain(argc, argv, 0, eDS_Default, 0);
}

/*
* ---------------------------------------------------------------------------
* $Log: test_objmgr_mt.cpp,v $
* Revision 1000.3  2004/06/01 19:25:20  gouriano
* PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.26
*
* Revision 1.26  2004/05/21 21:42:14  gorelenk
* Added PCH ncbi_pch.hpp
*
* Revision 1.25  2004/04/01 20:18:12  grichenk
* Added initialization of m_MultiId member.
*
* Revision 1.24  2004/03/31 22:35:17  grichenk
* Fixed number of features found
*
* Revision 1.23  2003/11/04 16:21:37  grichenk
* Updated CAnnotTypes_CI to map whole features instead of splitting
* them by sequence segments.
*
* Revision 1.22  2003/05/09 20:28:03  grichenk
* Changed warnings to info
*
* Revision 1.21  2003/04/24 16:12:39  vasilche
* Object manager internal structures are splitted more straightforward.
* Removed excessive header dependencies.
*
* Revision 1.20  2003/03/04 16:43:53  grichenk
* +Test CFeat_CI with eResolve_All flag
*
* Revision 1.19  2002/12/26 16:39:24  vasilche
* Object manager class CSeqMap rewritten.
*
* Revision 1.18  2002/11/04 21:29:14  grichenk
* Fixed usage of const CRef<> and CRef<> constructor
*
* Revision 1.17  2002/07/12 18:34:56  grichenk
* m_ObjMgr member should live longer than m_Scope - fixed
*
* Revision 1.16  2002/05/09 14:21:50  grichenk
* Turned GetTitle() test on, removed unresolved seq-map test
*
* Revision 1.15  2002/04/25 18:15:26  grichenk
* Adjusted tests to work with the updated CSeqVector
*
* Revision 1.14  2002/04/23 15:26:47  gouriano
* use test_mt library
*
* Revision 1.13  2002/04/22 20:07:45  grichenk
* Commented calls to CBioseq::ConstructExcludedSequence()
*
* Revision 1.12  2002/04/21 05:16:59  vakatov
* Decreased the # of threads from 40 to 34 to avoid triggering guard-bomb
* on SCHROEDER
*
* Revision 1.11  2002/03/18 21:47:16  grichenk
* Moved most includes to test_helper.cpp
* Added test for CBioseq::ConstructExcludedSequence()
*
* Revision 1.10  2002/03/13 18:06:31  gouriano
* restructured MT test. Put common functions into a separate file
*
* Revision 1.9  2002/03/07 21:42:06  grichenk
* +Test for GetSeq_annot()
*
* Revision 1.8  2002/03/05 16:08:16  grichenk
* Moved TSE-restriction to new constructors
*
* Revision 1.7  2002/03/04 17:07:19  grichenk
* +Testing feature iterators with single TSE restriction
*
* Revision 1.6  2002/02/25 21:05:31  grichenk
* Removed seq-data references caching. Increased MT-safety. Fixed typos.
*
* Revision 1.5  2002/02/07 21:27:36  grichenk
* Redesigned CDataSource indexing: seq-id handle -> TSE -> seq/annot
*
* Revision 1.4  2002/01/23 21:59:34  grichenk
* Redesigned seq-id handles and mapper
*
* Revision 1.3  2002/01/16 18:56:30  grichenk
* Removed CRef<> argument from choice variant setter, updated sources to
* use references instead of CRef<>s
*
* Revision 1.2  2002/01/16 16:28:47  gouriano
* restructured objmgr
*
* Revision 1.1  2002/01/11 19:06:29  gouriano
* restructured objmgr
*
* Revision 1.4  2001/12/20 20:00:30  grichenk
* CObjectManager::ConstructBioseq(CSeq_loc) -> CBioseq::CBioseq(CSeq_loc ...)
*
* Revision 1.3  2001/12/12 22:39:12  grichenk
* Added test for minus-strand intervals in constructed bioseqs
*
* Revision 1.2  2001/12/12 17:48:45  grichenk
* Fixed code using generated classes to work with the updated datatool
*
* Revision 1.1  2001/12/07 19:08:58  grichenk
* Initial revision
*
*
* ===========================================================================
*/