fix_orgmod_institution.cpp

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/*  $Id: fix_orgmod_institution.cpp 42189 2019-01-09 22:13:08Z asztalos $
 * ===========================================================================
 *
 *                            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:  Igor Filippov
 */
 
#include <ncbi_pch.hpp>
#include <objects/misc/sequence_macros.hpp>
#include <gui/packages/pkg_sequence_edit/fix_orgmod_institution.hpp>
 
BEGIN_NCBI_SCOPE
USING_SCOPE(objects);
 
 
CRef<CCmdComposite> CFixOrgModInst::GetCommand(CSeq_entry_Handle tse)
{
    return x_GetCommand(tse, "Fix OrgMod Institution");
}
 
bool CFixOrgModInst::x_ApplyToBioSource (CBioSource& biosource)
{
    bool modified = false;
 
    EDIT_EACH_ORGMOD_ON_BIOSOURCE(orgmod, biosource) {
        if ((*orgmod)->IsSetSubtype() && (*orgmod)->IsSetSubname() &&
            ((*orgmod)->GetSubtype() == COrgMod::eSubtype_specimen_voucher || 
            (*orgmod)->GetSubtype() == COrgMod::eSubtype_culture_collection || 
                (*orgmod)->GetSubtype() == COrgMod::eSubtype_bio_material))
        {
            string inst_code, coll_code, id, inst_coll;      // See CValidError_imp::ValidateOrgModVoucher
            if (!COrgMod::ParseStructuredVoucher((*orgmod)->GetSubname(), inst_code, coll_code, id)) continue;
            if (NStr::IsBlank(coll_code))   inst_coll = inst_code;
            else inst_coll = inst_code + ":" + coll_code;
            string voucher_type;
            bool is_miscapitalized;
            bool needs_country;
            bool erroneous_country;
            string correct_cap;
            if (COrgMod::IsInstitutionCodeValid(inst_coll, voucher_type, is_miscapitalized, correct_cap, needs_country, erroneous_country)) continue; // Returns true if invalid, actually
            if (NStr::StartsWith(inst_coll, "personal", NStr::eNocase)) continue;
            if (COrgMod::IsInstitutionCodeValid(inst_code, voucher_type, is_miscapitalized, correct_cap, needs_country, erroneous_country) && NStr::Equal(coll_code, "DNA")) continue;
            string abbr = COrgMod::GetInstitutionShortName(inst_code);
            if (!NStr::IsBlank(abbr))
            {
                if (NStr::IsBlank(id))
                    (*orgmod)->SetSubname(abbr);
                else
                    (*orgmod)->SetSubname(abbr + ":" + id);
                modified = true;
            }
        }
    }
    return modified;
}
 
END_NCBI_SCOPE