test_validator.cpp

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    for ( CValidError_CI vit(*errors); vit; ++vit ) {
        if ( vit->GetSeverity() < show ) {
            continue;
        }
        PrintBatchItem(*vit, *os);
        ++reported;
    }

    return reported;
}


CRef<CSeq_entry> CTest_validatorApplication::ReadSeqEntry(void)
{
    CRef<CSeq_entry> se(new CSeq_entry);
    m_In->Read(ObjectInfo(*se), CObjectIStream::eNoFileHeader);

    return se;
}


CConstRef<CValidError> CTest_validatorApplication::ProcessSeqEntry(void)
{
    // Get seq-entry to validate
    CRef<CSeq_entry> se(ReadSeqEntry());

    // Validate Seq-entry
    CValidator validator(*m_ObjMgr);
    return validator.Validate(*se, 0, m_Options);
}


CConstRef<CValidError> CTest_validatorApplication::ProcessSeqSubmit(void)
{
    CRef<CSeq_submit> ss(new CSeq_submit);

    // Get seq-submit to validate
    m_In->Read(ObjectInfo(*ss), CObjectIStream::eNoFileHeader);

    // Validae Seq-submit
    CValidator validator(*m_ObjMgr);
    return validator.Validate(*ss, 0, m_Options);
}


CConstRef<CValidError> CTest_validatorApplication::ProcessSeqAnnot(void)
{
    CRef<CSeq_annot> sa(new CSeq_annot);

    // Get seq-annot to validate
    m_In->Read(ObjectInfo(*sa), CObjectIStream::eNoFileHeader);

    // Validae Seq-annot
    CValidator validator(*m_ObjMgr);
    return validator.Validate(*sa, 0, m_Options);
}


void CTest_validatorApplication::Setup(const CArgs& args)
{
    // Setup application registry and logs for CONNECT library
    CORE_SetLOG(LOG_cxx2c());
    CORE_SetREG(REG_cxx2c(&GetConfig(), false));
    // Setup MT-safety for CONNECT library
    // CORE_SetLOCK(MT_LOCK_cxx2c());

    // Create object manager
    m_ObjMgr.Reset(new CObjectManager);
    if ( args["g"] ) {
        // 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.
        m_ObjMgr->RegisterDataLoader(*new CGBDataLoader("ID"),
            CObjectManager::eDefault);
    }

    SetupValidatorOptions(args);
}


void CTest_validatorApplication::SetupValidatorOptions(const CArgs& args)
{
    // Set validator options
    m_Options = 0;

    m_Options |= args["nonascii"] ? CValidator::eVal_non_ascii    : 0;
    m_Options |= args["context"]  ? CValidator::eVal_no_context   : 0;
    m_Options |= args["align"]    ? CValidator::eVal_val_align    : 0;
    m_Options |= args["exon"]     ? CValidator::eVal_val_exons    : 0;
    m_Options |= args["splice"]   ? CValidator::eVal_splice_err   : 0;
    m_Options |= args["ovlpep"]   ? CValidator::eVal_ovl_pep_err  : 0;
    m_Options |= args["taxid"]    ? CValidator::eVal_need_taxid   : 0;
    m_Options |= args["isojta"]   ? CValidator::eVal_need_isojta  : 0;
    m_Options |= args["g"]        ? CValidator::eVal_remote_fetch : 0;

    // !!!  DEBUG {
    // For testing only. Should be removed in the future
    m_Options |= args["debug"].HasValue() ? CValidator::eVal_perf_bottlenecks : 0;
    // }
}


CObjectIStream* CTest_validatorApplication::OpenFile
(const CArgs& args)
{
    // file name
    string fname = args["i"].AsString();

    // file format 
    ESerialDataFormat format = eSerial_AsnText;
    if ( args["b"] ) {
        format = eSerial_AsnBinary;
    }

    return CObjectIStream::Open(fname, format);
}


SIZE_TYPE CTest_validatorApplication::PrintValidError
(CConstRef<CValidError> errors, 
 const CArgs& args)
{
    EDiagSev show = static_cast<EDiagSev>(args["q"].AsInteger());
    EDiagSev count = static_cast<EDiagSev>(args["r"].AsInteger());

    CNcbiOstream* os = args["x"] ? &(args["x"].AsOutputFile()) : &NcbiCout;

    if ( errors->TotalSize() == 0 ) {
        *os << "All entries are OK!" << endl;
        os->flush();
        return 0;
    }

    SIZE_TYPE result = 0;
    SIZE_TYPE reported = 0;

    for ( CValidError_CI vit(*errors); vit; ++vit) {
        if ( vit->GetSeverity() >= count ) {
            ++result;
        }
        if ( vit->GetSeverity() < show ) {
            continue;
        }
        PrintValidErrItem(*vit, *os);
        ++reported;
    }
    *os << reported << " messages reported" << endl;
    os->flush();

    *os << "Total number of errors: " << errors->TotalSize() << endl
        << "Info: "     << errors->InfoSize()     << endl
        << "Warning: "  << errors->WarningSize()  << endl
        << "Error: "    << errors->ErrorSize()    << endl
        << "Critical: " << errors->CriticalSize() << endl
        << "Fatal: "    << errors->FatalSize()    << endl;

    return result;
}


void CTest_validatorApplication::PrintValidErrItem
(const CValidErrItem& item,
 CNcbiOstream& os)
{
    os << item.GetSevAsStr() << ":       " << item.GetErrCode() << endl << endl
       << "Message: " << item.GetMsg() << endl << endl;
     //<< "Verbose: " << item.GetVerbose() << endl << endl;
}



void CTest_validatorApplication::PrintBatchItem
(const CValidErrItem& item,
 CNcbiOstream&os)
{
    os << item.GetSevAsStr() << ": [" << item.GetErrCode() <<"] ["
       << item.GetMsg() << "]" << endl;
}


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


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




/*
 * ===========================================================================
 *
 * $Log: test_validator.cpp,v $
 * Revision 1000.2  2004/06/01 19:48:09  gouriano
 * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.27
 *
 * Revision 1.27  2004/05/21 21:42:56  gorelenk
 * Added PCH ncbi_pch.hpp
 *
 * Revision 1.26  2004/02/09 19:18:58  grichenk
 * Renamed CDesc_CI to CSeq_descr_CI. Redesigned CSeq_descr_CI
 * and CSeqdesc_CI to avoid using data directly.
 *
 * Revision 1.25  2004/01/07 17:37:39  vasilche
 * Fixed include path to genbank loader.
 * Moved split_cache application.
 *
 * Revision 1.24  2003/08/06 15:07:22  shomrat
 * Added fix for batch processing
 *
 * Revision 1.23  2003/06/02 16:06:43  dicuccio
 * Rearranged src/objects/ subtree.  This includes the following shifts:
 *     - src/objects/asn2asn --> arc/app/asn2asn
 *     - src/objects/testmedline --> src/objects/ncbimime/test
 *     - src/objects/objmgr --> src/objmgr
 *     - src/objects/util --> src/objmgr/util
 *     - src/objects/alnmgr --> src/objtools/alnmgr
 *     - src/objects/flat --> src/objtools/flat
 *     - src/objects/validator --> src/objtools/validator
 *     - src/objects/cddalignview --> src/objtools/cddalignview
 * In addition, libseq now includes six of the objects/seq... libs, and libmmdb
 * replaces the three libmmdb? libs.
 *
 * Revision 1.22  2003/05/28 16:39:19  shomrat
 * Indentation corrections
 *
 * Revision 1.21  2003/05/15 02:10:05  ucko
 * Be consistent about SIZE_TYPE vs. unsigned int in PrintValidError.
 *
 * Revision 1.20  2003/05/14 21:16:48  shomrat
 * Using CRef instead of auto_ptr; changed to output format
 *
 * Revision 1.19  2003/04/24 16:16:00  vasilche
 * Added missing includes and forward class declarations.
 *
 * Revision 1.18  2003/04/15 14:56:52  shomrat
 * cout -> NcbiCout; test before derefernce
 *
 * Revision 1.17  2003/04/15 14:22:42  vasilche
 * Added missing includes.
 *
 * Revision 1.16  2003/04/04 18:44:42  shomrat
 * Added remote fetch flag
 *
 * Revision 1.15  2003/03/20 18:58:22  shomrat
 * Added support for validation of standalone Seq-annot files
 *
 * Revision 1.14  2003/03/10 18:13:14  shomrat
 * Print extended statistics
 *
 * Revision 1.13  2003/03/06 19:41:15  shomrat
 * Changed eval from auto_ptr to CRef
 *
 * Revision 1.12  2003/02/24 20:36:15  shomrat
 * Added several application flags, including batch processing
 *
 * Revision 1.11  2003/02/14 21:55:13  shomrat
 * Output the severity of an error
 *
 * Revision 1.10  2003/02/07 21:26:01  shomrat
 * More detailed error report
 *
 * Revision 1.9  2003/02/05 00:28:07  ucko
 * +<serial/objistr.hpp> (formerly pulled in via reader_id1.hpp)
 *
 * Revision 1.8  2003/02/03 20:22:25  shomrat
 * Added flag to supress performance bottlenecks
 *
 * Revision 1.7  2003/02/03 17:51:06  shomrat
 * Bug fix - Trailing comma in a parameter list
 *
 * Revision 1.6  2003/02/03 17:06:48  shomrat
 * Changed parameters to CGBDataLoader
 *
 * Revision 1.5  2003/01/28 16:01:22  shomrat
 * Bug fixes
 *
 * Revision 1.4  2003/01/24 22:04:33  shomrat
 * Added flags to specify input format (Seq-entry or Seq-submit)
 *
 * Revision 1.3  2003/01/07 20:04:26  shomrat
 * GetMessage changed to GetMsg
 *
 * Revision 1.2  2003/01/07 17:57:05  ucko
 * Use the new path to the validator's public header.
 *
 * Revision 1.1  2002/12/23 21:11:59  shomrat
 * Moved from objects/objmgr/test
 *
 * Revision 1.3  2002/11/04 21:29:14  grichenk
 * Fixed usage of const CRef<> and CRef<> constructor
 *
 * Revision 1.2  2002/10/08 13:40:38  clausen
 * Changed current.asn to current.prt
 *
 * Revision 1.1  2002/10/03 18:34:13  clausen
 * Initial version
 *
 *
 * ===========================================================================
 */