test_objmgr.cpp

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/*
 * ===========================================================================
 * PRODUCTION $Log: test_objmgr.cpp,v $
 * PRODUCTION Revision 1000.3  2004/06/01 19:25:14  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.41
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: test_objmgr.cpp,v 1000.3 2004/06/01 19:25:14 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 <objects/seqloc/Seq_id.hpp>
#include <objects/seqset/Seq_entry.hpp>
#include <objects/seq/Seq_annot.hpp>

#include "test_helper.hpp"

#include <objects/general/Date.hpp>

BEGIN_NCBI_SCOPE
using namespace objects;


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

class CTestApp : public CNcbiApplication
{
public:
    virtual void Init(void);
    virtual int  Run (void);
private:
    CRef<CObjectManager> m_ObjMgr;
};


void CTestApp::Init(void)
{
    // Prepare command line descriptions
    auto_ptr<CArgDescriptions> arg_desc(new CArgDescriptions);

    arg_desc->AddFlag("dump_entries", "print all generated seq entries");
    arg_desc->AddFlag("dump_features", "print all found features");

    string prog_description = "testobjmgr";
    arg_desc->SetUsageContext(GetArguments().GetProgramBasename(),
                              prog_description, false);

    SetupArgDescriptions(arg_desc.release());
}


int CTestApp::Run(void)
{
    SetDiagPostFlag(eDPF_All);
    NcbiCout << "Testing ObjectManager..." << NcbiEndl;
    CSeq_id id;
    int idx;

    const CArgs& args = GetArgs();
    CDataGenerator::sm_DumpEntries = args["dump_entries"];
    CTestHelper::sm_DumpFeatures = args["dump_features"];
    CTestHelper::sm_TestRemoveEntry = true;

    m_ObjMgr = new CObjectManager;

    // 1.2.3. Scope is an object on the stack
    for (idx = 0; idx <= 0; idx++) {
        CScope Scope1(*m_ObjMgr);
        CScope Scope2(*m_ObjMgr);
        CScope Scope(*m_ObjMgr);
        // populate
#if 1
        CRef<CSeq_entry> entry1(&CDataGenerator::CreateTestEntry1(idx));
        Scope1.AddTopLevelSeqEntry(*entry1);
        CRef<CSeq_entry> entry2(&CDataGenerator::CreateTestEntry2(idx));
        Scope2.AddTopLevelSeqEntry(*entry2);
        Scope.AddScope(Scope1);
        Scope.AddScope(Scope2);
#else
        CRef<CSeq_entry> entry1(&CDataGenerator::CreateTestEntry1(idx));
        Scope.AddTopLevelSeqEntry(*entry1);
        CRef<CSeq_entry> entry2(&CDataGenerator::CreateTestEntry2(idx));
        Scope.AddTopLevelSeqEntry(*entry2);
#endif
        // retrieve data
        CTestHelper::TestDataRetrieval( Scope, 0, 0);
    }

    // 1.2.3. The same scope twice with the same priority
    for (idx = 0; idx <= 0; idx++) {
        CScope Scope1(*m_ObjMgr);
        CScope Scope(*m_ObjMgr);
        // populate
        CRef<CSeq_entry> entry1(&CDataGenerator::CreateTestEntry1(idx));
        Scope1.AddTopLevelSeqEntry(*entry1);
        CRef<CSeq_entry> entry2(&CDataGenerator::CreateTestEntry2(idx));
        Scope1.AddTopLevelSeqEntry(*entry2);
        Scope.AddScope(Scope1);
        Scope.AddScope(Scope1);
        // retrieve data
        CTestHelper::TestDataRetrieval( Scope, 0, 0);
    }

    // 1.2.4. Scope is an object on the heap
    for (idx = 1; idx <= 1; idx++) {
        CRef<CScope> pScope(new CScope(*m_ObjMgr));
        // populate
        CRef<CSeq_entry> entry1(&CDataGenerator::CreateTestEntry1(idx));
        pScope->AddTopLevelSeqEntry(*entry1);
        CRef<CSeq_entry> entry2(&CDataGenerator::CreateTestEntry2(idx));
        pScope->AddTopLevelSeqEntry(*entry2);
        // retrieve data
        CTestHelper::TestDataRetrieval( *pScope, idx, 0);
    }

    // 1.2.5 add annotation to one sequence
    // verify that others did not change
    for (idx = 1; idx <= 1; idx++) {
        CRef<CScope> pScope(new CScope(*m_ObjMgr));
        // populate
        CRef<CSeq_entry> entry1(&CDataGenerator::CreateTestEntry1(idx));
        pScope->AddTopLevelSeqEntry(*entry1);
        CRef<CSeq_entry> entry2(&CDataGenerator::CreateTestEntry2(idx));
        pScope->AddTopLevelSeqEntry(*entry2);
        CTestHelper::TestDataRetrieval( *pScope, idx, 0);
        // add annotation
        CRef<CSeq_annot> annot(&CDataGenerator::CreateAnnotation1(idx));
        pScope->AttachAnnot(*entry1, *annot);
        // retrieve data  (delta=1 - one more annotation)
        CTestHelper::TestDataRetrieval( *pScope, idx, 1);

        // Take the added annotation back
        pScope->RemoveAnnot(*entry1, *annot);
        CTestHelper::TestDataRetrieval( *pScope, idx, 0);
    }

    // 1.2.6. Constructed bio sequences
    for (idx = 1; idx <= 1; idx++) {
        CScope Scope(*m_ObjMgr);
        CRef<CSeq_entry> entry1(&CDataGenerator::CreateTestEntry1(idx));
        Scope.AddTopLevelSeqEntry(*entry1);
        {{
            CRef<CSeq_entry> constr_entry
                (&CDataGenerator::CreateConstructedEntry( idx, 1));
            Scope.AddTopLevelSeqEntry(*constr_entry);
            // test
            id.SetLocal().SetStr("constructed1");
            CTestHelper::ProcessBioseq(Scope, id, 27,
                "GCGGTACAATAACCTCAGCAGCAACAA", "",
                0, 3, 0, 0, 0, 0, 0, 0, 0, 0);
        }}
        {{
            CRef<CSeq_entry> constr_entry
                (&CDataGenerator::CreateConstructedEntry( idx, 2));
            Scope.AddTopLevelSeqEntry(*constr_entry);
            // test
            id.SetLocal().SetStr("constructed2");
            CTestHelper::ProcessBioseq(Scope, id, 27,
                "TACCGCCAATAACCTCAGCAGCAACAA", "",
                0, 3, 0, 0, 0, 0, 0, 0, 0, 0);
        }}
    }

    // 1.2.7. one entry in two scopes
    for (idx = 1; idx <= 1; idx++) {
        // populate 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
        id.SetGi(21+idx*1000);
        CTestHelper::ProcessBioseq(*pScope2, id, 22,
            "\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00"
            "\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00",
            "\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00"
            "\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00\\x00",
            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);
    }

    NcbiCout << " Passed" << NcbiEndl << NcbiEndl;

    return 0;
}


END_NCBI_SCOPE



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


USING_NCBI_SCOPE;

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


/*
* ---------------------------------------------------------------------------
* $Log: test_objmgr.cpp,v $
* Revision 1000.3  2004/06/01 19:25:14  gouriano
* PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.41
*
* Revision 1.41  2004/05/21 21:42:14  gorelenk
* Added PCH ncbi_pch.hpp
*
* Revision 1.40  2004/04/01 20:18:12  grichenk
* Added initialization of m_MultiId member.
*
* Revision 1.39  2004/03/31 22:35:17  grichenk
* Fixed number of features found
*
* Revision 1.38  2004/02/03 17:58:51  vasilche
* Always test CScope::RemoveEntry() in single thread.
*
* Revision 1.37  2003/11/04 16:21:37  grichenk
* Updated CAnnotTypes_CI to map whole features instead of splitting
* them by sequence segments.
*
* Revision 1.36  2003/10/09 14:00:56  vasilche
* Added test for multiple instances of datasource.
*
* Revision 1.35  2003/09/30 20:40:48  vasilche
* Added test for CScope::AddScope().
*
* Revision 1.34  2003/09/30 18:04:13  vasilche
* Temporarily avoid failed assertion.
*
* Revision 1.33  2003/09/30 16:22:05  vasilche
* Updated internal object manager classes to be able to load ID2 data.
* SNP blobs are loaded as ID2 split blobs - readers convert them automatically.
* Scope caches results of requests for data to data loaders.
* Optimized CSeq_id_Handle for gis.
* Optimized bioseq lookup in scope.
* Reduced object allocations in annotation iterators.
* CScope is allowed to be destroyed before other objects using this scope are
* deleted (feature iterators, bioseq handles etc).
* Optimized lookup for matching Seq-ids in CSeq_id_Mapper.
* Added 'adaptive' option to objmgr_demo application.
*
* Revision 1.32  2003/08/29 13:34:48  vasilche
* Rewrote CSeqVector/CSeqVector_CI code to allow better inlining.
* CSeqVector::operator[] made significantly faster.
* Added possibility to have platform dependent byte unpacking functions.
*
* Revision 1.31  2003/04/24 16:12:39  vasilche
* Object manager internal structures are splitted more straightforward.
* Removed excessive header dependencies.
*
* Revision 1.30  2003/03/27 21:54:58  grichenk
* Renamed test applications and makefiles, updated references
*
* Revision 1.29  2003/03/26 14:30:23  lavr
* Conform to modified representation of NUL char in NStr::PrintableString()
*
* Revision 1.28  2003/03/04 16:43:53  grichenk
* +Test CFeat_CI with eResolve_All flag
*
* Revision 1.27  2003/02/28 16:37:47  vasilche
* Fixed expected feature count.
* Added optional flags to testobjmgr to dump generated data and found features.
*
* Revision 1.26  2002/12/26 16:39:24  vasilche
* Object manager class CSeqMap rewritten.
*
* Revision 1.25  2002/11/08 22:15:53  grichenk
* Added methods for removing/replacing annotations
*
* Revision 1.24  2002/11/04 21:29:14  grichenk
* Fixed usage of const CRef<> and CRef<> constructor
*
* Revision 1.23  2002/05/09 14:21:50  grichenk
* Turned GetTitle() test on, removed unresolved seq-map test
*
* Revision 1.22  2002/04/25 18:15:25  grichenk
* Adjusted tests to work with the updated CSeqVector
*
* Revision 1.21  2002/04/22 20:07:45  grichenk
* Commented calls to CBioseq::ConstructExcludedSequence()
*
* Revision 1.20  2002/03/18 21:47:16  grichenk
* Moved most includes to test_helper.cpp
* Added test for CBioseq::ConstructExcludedSequence()
*
* Revision 1.19  2002/03/13 18:06:31  gouriano
* restructured MT test. Put common functions into a separate file
*
* Revision 1.18  2002/03/08 21:23:50  gouriano
* reorganized and classified tests
*
* Revision 1.16  2002/03/05 16:08:16  grichenk
* Moved TSE-restriction to new constructors
*
* Revision 1.15  2002/03/04 17:07:18  grichenk
* +Testing feature iterators with single TSE restriction
*
* Revision 1.14  2002/02/25 21:05:31  grichenk
* Removed seq-data references caching. Increased MT-safety. Fixed typos.
*
* Revision 1.13  2002/02/21 19:27:09  grichenk
* Rearranged includes. Added scope history. Added searching for the
* best seq-id match in data sources and scopes. Updated tests.
*
* Revision 1.12  2002/02/07 21:27:36  grichenk
* Redesigned CDataSource indexing: seq-id handle -> TSE -> seq/annot
*
* Revision 1.11  2002/02/06 21:46:11  gouriano
* *** empty log message ***
*
* Revision 1.10  2002/02/05 21:46:28  gouriano
* added FindSeqid function, minor tuneup in CSeq_id_mapper
*
* Revision 1.9  2002/02/04 21:16:27  gouriano
* minor changes to make it run correctly on Solaris
*
* Revision 1.8  2002/01/30 22:09:28  gouriano
* changed CSeqMap interface
*
* Revision 1.7  2002/01/29 17:47:33  grichenk
* Removed commented part
*
* Revision 1.6  2002/01/28 19:44:50  gouriano
* changed the interface of BioseqHandle: two functions moved from Scope
*
* Revision 1.5  2002/01/23 21:59:34  grichenk
* Redesigned seq-id handles and mapper
*
* Revision 1.4  2002/01/18 17:06:30  gouriano
* renamed CScope::GetSequence to CScope::GetSeqVector
*
* 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 16:28:46  gouriano
* restructured objmgr
*
* Revision 1.1  2002/01/11 19:06:28  gouriano
* restructured objmgr
*
* Revision 1.31  2001/12/20 20:00:30  grichenk
* CObjectManager::ConstructBioseq(CSeq_loc) -> CBioseq::CBioseq(CSeq_loc ...)
*
* Revision 1.30  2001/12/12 22:39:11  grichenk
* Added test for minus-strand intervals in constructed bioseqs
*
* Revision 1.29  2001/12/12 17:48:45  grichenk
* Fixed code using generated classes to work with the updated datatool
*
* Revision 1.28  2001/12/07 19:08:44  grichenk
* Updated Object manager test
*
*
* ===========================================================================
*/