validator.cpp

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/* $Id: validator.cpp 101247 2023-11-20 15:20:49Z stakhovv $
 * ===========================================================================
 *
 *                            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.
 *
 * ===========================================================================
 *
 * Author:  Jonathan Kans, Clifford Clausen, Aaron Ucko.......
 *
 * File Description:
 *   Validates CSeq_entries and CSeq_submits
 *
 */
#include <ncbi_pch.hpp>
#include <corelib/ncbistd.hpp>
#include <serial/serialbase.hpp>
#include <objects/submit/Seq_submit.hpp>
#include <objects/seq/Bioseq.hpp>
#include <objects/seq/Seqdesc.hpp>
#include <objmgr/object_manager.hpp>
#include <objmgr/util/sequence.hpp>
#include <objtools/validator/validator.hpp>
#include <util/static_map.hpp>
#include <util/sgml_entity.hpp>
#include <objects/taxon3/itaxon3.hpp>
#include <objects/taxon3/taxon3.hpp>
#include <objects/taxon3/cached_taxon3.hpp>
 
#include <objtools/validator/validatorp.hpp>
#include <objtools/validator/validerror_format.hpp>
#include <objtools/validator/validerror_desc.hpp>
#include <objtools/validator/validator_context.hpp>
 
 
BEGIN_NCBI_SCOPE
BEGIN_SCOPE(objects)
BEGIN_SCOPE(validator)
USING_SCOPE(sequence);
 
 
// *********************** CValidator implementation *******************
//
CValidator::CValidator(CObjectManager& objmgr) :
    CValidator(objmgr, make_shared<SValidatorContext>())
{
    SetTaxon3(make_shared<CTaxon3>());
}
 
CValidator::CValidator(CObjectManager& objmgr,
        shared_ptr<SValidatorContext> pContext):
    m_ObjMgr{&objmgr},
    m_pContext{pContext}
{}
 
 
void CValidator::SetTaxon3(shared_ptr<ITaxon3> pTaxon)
{
    m_pOwnTaxon = pTaxon;
    if (m_pOwnTaxon)
        m_pContext->m_taxon_update = MakeTaxUpdateFunction(m_pOwnTaxon);
}
 
CValidator::~CValidator()
{}
 
taxupdate_func_t CValidator::MakeTaxUpdateFunction(shared_ptr<ITaxon3> taxon)
{
    taxon->Init();
    return [remote = taxon](const vector< CRef<COrg_ref> >& query) -> CRef<CTaxon3_reply>
        { // we need to make a copy of record to prevent changes put back to cache
            if (!query.empty() && remote) {
                CConstRef<CTaxon3_reply> res = remote->SendOrgRefList(query);
                CRef<CTaxon3_reply> copied (new CTaxon3_reply);
                copied->Assign(*res);
                return copied;
            } else {
                return {};
            }
        };
}
 
CRef<CValidError> CValidator::Validate(
    const CSeq_entry& se,
    CScope* scope,
    Uint4 options)
{
    CRef<CValidError> errors(new CValidError(&se));
    CValidErrorFormat::SetSuppressionRules(se, *errors);
    CValidError_imp imp(*m_ObjMgr, m_pContext, &(*errors), options);
    imp.SetProgressCallback(m_PrgCallback, m_UserData);
    if ( !imp.Validate(se, nullptr, scope) ) {
        errors.Reset();
    }
    x_SetEntryInfo(imp.GetEntryInfo());
    SValidatorContext& ctx = imp.SetContext();
    ctx.NumGenes += imp.GetGeneCount();
    ctx.NumGeneXrefs += imp.GetGeneXrefCount();
    return errors;
}
 
 
//LCOV_EXCL_START
// not used by asnvalidate, used by external programs
CRef<CValidError> CValidator::Validate(
    const CSeq_entry_Handle& seh,
    Uint4 options)
{
    CRef<CValidError> errors(new CValidError(&*seh.GetCompleteSeq_entry()));
    CValidErrorFormat::SetSuppressionRules(seh, *errors);
    CValidError_imp imp(*m_ObjMgr, m_pContext, &(*errors), options);
    imp.SetProgressCallback(m_PrgCallback, m_UserData);
    if ( !imp.Validate(seh) ) {
        errors.Reset();
    }
    x_SetEntryInfo(imp.GetEntryInfo());
    SValidatorContext& ctx = imp.SetContext();
    ctx.NumGenes += imp.GetGeneCount();
    ctx.NumGeneXrefs += imp.GetGeneXrefCount();
    return errors;
}
 
 
CConstRef<CValidError> CValidator::GetTSANStretchErrors(const CSeq_entry_Handle& se)
{
    CRef<CValidError> errors(new CValidError(&*se.GetCompleteSeq_entry()));
    CValidErrorFormat::SetSuppressionRules(se, *errors);
    CValidError_imp imp(*m_ObjMgr, m_pContext, &(*errors), 0);
    imp.SetProgressCallback(m_PrgCallback, m_UserData);
    if ( !imp.GetTSANStretchErrors(se) ) {
        errors.Reset();
    }
    return errors;
}
 
 
CConstRef<CValidError> CValidator::GetTSACDSOnMinusStrandErrors (const CSeq_entry_Handle& se)
{
    CRef<CValidError> errors(new CValidError(&*se.GetCompleteSeq_entry()));
    CValidErrorFormat::SetSuppressionRules(se, *errors);
    CValidError_imp imp(*m_ObjMgr, m_pContext, &(*errors), 0);
    imp.SetProgressCallback(m_PrgCallback, m_UserData);
    if ( !imp.GetTSACDSOnMinusStrandErrors(se) ) {
        errors.Reset();
    }
    return errors;
}
 
 
CConstRef<CValidError> CValidator::GetTSAConflictingBiomolTechErrors (const CSeq_entry_Handle& se)
{
    CRef<CValidError> errors(new CValidError(&*se.GetCompleteSeq_entry()));
    CValidErrorFormat::SetSuppressionRules(se, *errors);
    CValidError_imp imp(*m_ObjMgr, m_pContext, &(*errors), 0);
    imp.SetProgressCallback(m_PrgCallback, m_UserData);
    if ( !imp.GetTSAConflictingBiomolTechErrors(se) ) {
        errors.Reset();
    }
    return errors;
}
 
 
CConstRef<CValidError> CValidator::GetTSANStretchErrors(const CBioseq& seq)
{
 
    CRef<CValidError> errors(new CValidError(&seq));
    CValidErrorFormat::SetSuppressionRules(seq, *errors);
    CValidError_imp imp(*m_ObjMgr, m_pContext, &(*errors), 0);
    imp.SetProgressCallback(m_PrgCallback, m_UserData);
    if ( !imp.GetTSANStretchErrors(seq) ) {
        errors.Reset();
    }
    return errors;
}
 
 
CConstRef<CValidError> CValidator::GetTSACDSOnMinusStrandErrors (const CSeq_feat& f, const CBioseq& seq)
{
    CRef<CValidError> errors(new CValidError(&f));
    CValidErrorFormat::SetSuppressionRules(seq, *errors);
    CValidError_imp imp(*m_ObjMgr, m_pContext, &(*errors), 0);
    imp.SetProgressCallback(m_PrgCallback, m_UserData);
    if ( !imp.GetTSACDSOnMinusStrandErrors(f, seq) ) {
        errors.Reset();
    }
    return errors;
}
 
 
CConstRef<CValidError> CValidator::GetTSAConflictingBiomolTechErrors (const CBioseq& seq)
{
    CRef<CValidError> errors(new CValidError(&seq));
    CValidErrorFormat::SetSuppressionRules(seq, *errors);
    CValidError_imp imp(*m_ObjMgr, m_pContext, &(*errors), 0);
    imp.SetProgressCallback(m_PrgCallback, m_UserData);
    if ( !imp.GetTSAConflictingBiomolTechErrors(seq) ) {
        errors.Reset();
    }
    return errors;
}
//LCOV_EXCL_STOP
 
 
CRef<CValidError> CValidator::Validate(
    const CSeq_submit& ss,
    CScope* scope,
    Uint4 options)
{
    options |= CValidator::eVal_seqsubmit_parent;
    CRef<CValidError> errors(new CValidError(&ss));
    CValidErrorFormat::SetSuppressionRules(ss, *errors);
    CValidError_imp imp(*m_ObjMgr, m_pContext, &(*errors), options);
    imp.Validate(ss, scope);
 
    x_SetEntryInfo(imp.GetEntryInfo());
 
    return errors;
}
 
 
CConstRef<CValidError> CValidator::Validate(
    const CSeq_annot_Handle& sah,
    Uint4 options)
{
    auto errors = Ref(new CValidError(&*(sah.GetCompleteSeq_annot())));
    Validate(sah, options, *errors);
    return errors;
}
 
 
void CValidator::Validate(
    const CSeq_annot_Handle& sah,
    Uint4 options,
    CValidError& errors)
{
    CValidError_imp imp(*m_ObjMgr, m_pContext, &errors, options);
    imp.Validate(sah);
}
 
 
CConstRef<CValidError> CValidator::Validate(
    const CSeq_feat& feat,
    CScope* scope,
    Uint4 options)
{
    CRef<CValidError> errors(new CValidError(&feat));
    CValidError_imp imp(*m_ObjMgr, m_pContext, &(*errors), options);
    imp.Validate(feat, scope);
    return errors;
}
 
 
CConstRef<CValidError> CValidator::Validate(
    const CBioSource& src,
    CScope* scope,
    Uint4 options)
{
    CRef<CValidError> errors(new CValidError(&src));
    CValidError_imp imp(*m_ObjMgr, m_pContext, &(*errors), options);
    imp.Validate(src, scope);
    return errors;
}
 
CConstRef<CValidError> CValidator::Validate(
    const CPubdesc& pubdesc,
    CScope* scope,
    Uint4 options)
{
    CRef<CValidError> errors(new CValidError(&pubdesc));
    CValidError_imp imp(*m_ObjMgr, m_pContext, &(*errors), options);
    imp.Validate(pubdesc, scope);
    return errors;
}
 
CConstRef<CValidError> CValidator::Validate(
    const CSeqdesc& desc,
    const CSeq_entry& ctx,
    Uint4 options)
{
    CRef<CValidError> errors(new CValidError(&desc));
    CValidError_imp imp(*m_ObjMgr, m_pContext, &(*errors), options);
    imp.Validate(desc, ctx);
    return errors;
}
 
 
bool CValidator::IsValidStructuredComment(
    const CSeqdesc& desc) const
{
    if (!desc.IsUser()) {
        return false;
    }
 
    CValidError_imp imp(const_cast<CObjectManager&>(*m_ObjMgr), m_pContext, nullptr);
    return CValidError_desc(imp).IsValidStructuredComment(desc);
}
 
 
void CValidator::SetProgressCallback(TProgressCallback callback, void* user_data)
{
    m_PrgCallback = callback;
    m_UserData = user_data;
}
 
 
bool CValidator::BadCharsInAuthorName(const string& str, bool allowcomma, bool allowperiod, bool last)
{
    if (NStr::IsBlank(str)) {
        return false;
    }
 
 
    size_t stp = string::npos;
    if (last) {
        if (NStr::StartsWith(str, "St.")) {
            stp = 2;
        }
        else if (NStr::StartsWith(str, "de M.")) {
            stp = 4;
        }
    }
 
    size_t pos = 0;
    const char *ptr = str.c_str();
 
    while (*ptr != 0) {
        if (isalpha(*ptr)
            || *ptr == '-'
            || *ptr == '\''
            || *ptr == ' '
            || (*ptr == ',' && allowcomma)
            || (*ptr == '.' && (allowperiod || pos == stp))) {
            // all these are ok
            ptr++;
            pos++;
        } else {
            string tail = str.substr(pos);
            if (NStr::Equal(tail, "2nd") ||
                NStr::Equal(tail, "3rd") ||
                NStr::Equal(tail, "4th") ||
                NStr::Equal(tail, "5th") ||
                NStr::Equal(tail, "6th")) {
                return false;
            }
            return true;
        }
    }
    return false;
}
 
 
bool CValidator::BadCharsInAuthorLastName(const string& str)
{
    if (NStr::EqualNocase(str, "et al.")) {
        // this is ok
        return false;
    } else {
        return BadCharsInAuthorName(str, false, false, true);
    }
}
 
bool CValidator::BadCharsInAuthorFirstName(const string& str)
{
    return BadCharsInAuthorName(str, false, true, false);
}
 
 
bool CValidator::BadCharsInAuthorInitials(const string& str)
{
    return BadCharsInAuthorName(str, false, true, false);
}
 
 
bool CValidator::BadCharsInAuthorSuffix(const string& str)
{
    return BadCharsInAuthorName(str, false, true, false);
}
 
 
string CValidator::BadCharsInAuthor(const CName_std& author, bool& last_is_bad)
{
    string badauthor;
    last_is_bad = false;
 
    if (author.IsSetLast() && BadCharsInAuthorLastName(author.GetLast())) {
        last_is_bad = true;
        badauthor = author.GetLast();
    } else if (author.IsSetFirst() && BadCharsInAuthorFirstName(author.GetFirst())) {
        badauthor = author.GetFirst();
    }
    else if (author.IsSetInitials() && BadCharsInAuthorInitials(author.GetInitials())) {
        badauthor = author.GetInitials();
    } else if (author.IsSetSuffix() && BadCharsInAuthorSuffix(author.GetSuffix())) {
        badauthor = author.GetSuffix();
    }
    return badauthor;
}
 
 
string CValidator::BadCharsInAuthor(const CAuthor& author, bool& last_is_bad)
{
    last_is_bad = false;
    if (author.IsSetName() && author.GetName().IsName()) {
        return BadCharsInAuthor(author.GetName().GetName(), last_is_bad);
    } else {
        return kEmptyStr;
    }
}
 
 
typedef bool(*CompareConsecutiveIntervalProc) (const CSeq_interval& int1, const CSeq_interval& int2, CScope *scope);
 
bool x_CompareConsecutiveIntervals(
    const CPacked_seqint& packed_int,
    CConstRef<CSeq_interval>& int_cur,
    CConstRef<CSeq_interval>& int_prv,
    CScope* scope,
    CompareConsecutiveIntervalProc compar)
{
    bool ok = true;
    ITERATE(CPacked_seqint::Tdata, it, packed_int.Get()) {
        int_cur = (*it);
        if (int_prv && !compar(*int_cur, *int_prv, scope)) {
            ok = false;
            break;
        }
 
        int_prv = int_cur;
    }
    return ok;
}
 
 
bool CheckConsecutiveIntervals(const CSeq_loc& loc, CScope& scope, CompareConsecutiveIntervalProc compar)
{
    bool ok = true;
    const CSeq_interval *int_cur = nullptr, *int_prv = nullptr;
 
    CTypeConstIterator<CSeq_loc> lit = ConstBegin(loc);
    for (; lit && ok; ++lit) {
        CSeq_loc::E_Choice loc_choice = lit->Which();
        switch (loc_choice) {
        case CSeq_loc::e_Int: {
            int_cur = &lit->GetInt();
            if (int_prv) {
                ok = compar(*int_cur, *int_prv, &scope);
            }
            int_prv = int_cur;
        } break;
        case CSeq_loc::e_Pnt:
            int_prv = nullptr;
            break;
        case CSeq_loc::e_Packed_pnt:
            int_prv = nullptr;
            break;
        case CSeq_loc::e_Packed_int: {
            CConstRef<CSeq_interval> this_int_cur(int_cur);
            CConstRef<CSeq_interval> this_int_prv(int_prv);
            ok = x_CompareConsecutiveIntervals
                (lit->GetPacked_int(), this_int_cur, this_int_prv, &scope, compar);
        } break;
        case CSeq_loc::e_Null:
            break;
        default:
            int_prv = nullptr;
            break;
        }
    }
    return ok;
}
 
 
bool x_IsCorrectlyOrdered(
    const CSeq_interval& int_cur,
    const CSeq_interval& int_prv,
    CScope* scope)
{
    ENa_strand strand_cur = int_cur.IsSetStrand() ?
        int_cur.GetStrand() : eNa_strand_unknown;
 
    if (IsSameBioseq(int_prv.GetId(), int_cur.GetId(), scope)) {
        if (strand_cur == eNa_strand_minus) {
            if (int_prv.GetTo() < int_cur.GetTo()) {
                return false;
            }
        }
        else {
            if (int_prv.GetTo() > int_cur.GetTo()) {
                return false;
            }
        }
    }
    return true;
}
 
 
bool CValidator::IsSeqLocCorrectlyOrdered(const CSeq_loc& loc, CScope& scope)
{
    CBioseq_Handle seq;
    try {
        CBioseq_Handle seq = scope.GetBioseqHandle(loc);
    } catch (CObjMgrException& ) {
        // no way to tell
        return true;
    } catch (const exception& ) {
        // no way to tell
        return true;
    }
    if (seq  &&  seq.GetInst_Topology() == CSeq_inst::eTopology_circular) {
        // no way to check if topology is circular
        return true;
    }
 
    return CheckConsecutiveIntervals(loc, scope, x_IsCorrectlyOrdered);
}
 
 
bool x_IsNotAdjacent(
    const CSeq_interval& int_cur,
    const CSeq_interval& int_prv,
    CScope* scope)
{
    ENa_strand strand_cur = int_cur.IsSetStrand() ?
        int_cur.GetStrand() : eNa_strand_unknown;
 
    bool ok = true;
    if (IsSameBioseq(int_prv.GetId(), int_cur.GetId(), scope)) {
        if (strand_cur == eNa_strand_minus) {
            if (int_cur.GetTo() + 1 == int_prv.GetFrom()) {
                ok = false;
            }
        }
        else {
            if (int_prv.GetTo() + 1 == int_cur.GetFrom()) {
                ok = false;
            }
        }
    }
    return ok;
}
 
 
bool CValidator::DoesSeqLocContainAdjacentIntervals
(const CSeq_loc& loc, CScope &scope)
{
    return !CheckConsecutiveIntervals(loc, scope, x_IsNotAdjacent);
}
 
 
bool x_SameStrand(const CSeq_interval& int1, const CSeq_interval& int2)
{
    ENa_strand strand1 = int1.IsSetStrand() ?
        int1.GetStrand() : eNa_strand_unknown;
    ENa_strand strand2 = int2.IsSetStrand() ?
        int2.GetStrand() : eNa_strand_unknown;
    return (strand1 == strand2);
}
 
 
bool IsNotDuplicateInterval(const CSeq_interval& int1, const CSeq_interval& int2, CScope* scope)
{
    if (IsSameBioseq(int1.GetId(), int2.GetId(), scope) &&
        x_SameStrand(int1, int2) &&
        int1.GetFrom() == int2.GetFrom() &&
        int1.GetTo() == int2.GetTo()) {
        return false;
    }
    return true;
}
 
bool CValidator::DoesSeqLocContainDuplicateIntervals(const CSeq_loc& loc, CScope& scope)
{
    return !CheckConsecutiveIntervals(loc, scope, IsNotDuplicateInterval);
}
 
 
EErrType CValidator::ConvertCode(CSubSource::ELatLonCountryErr errcode)
{
    EErrType rval = eErr_UNKNOWN;
    switch (errcode) {
    case CSubSource::eLatLonCountryErr_Country:
        rval = eErr_SEQ_DESCR_LatLonCountry;
        break;
    case CSubSource::eLatLonCountryErr_State:
        rval = eErr_SEQ_DESCR_LatLonState;
        break;
    case CSubSource::eLatLonCountryErr_Water:
        rval = eErr_SEQ_DESCR_LatLonWater;
        break;
    case CSubSource::eLatLonCountryErr_Value:
        rval = eErr_SEQ_DESCR_LatLonValue;
        break;
    default:
        break;
    }
    return rval;
}
 
 
CValidator::TDbxrefValidFlags CValidator::IsValidDbxref(const CDbtag& xref, bool is_biosource, bool is_refseq_or_gps)
{
    TDbxrefValidFlags flags = eValid;
 
    if (xref.IsSetTag() && xref.GetTag().IsStr()) {
        if (ContainsSgml(xref.GetTag().GetStr())) {
            flags |= eTagHasSgml;
        }
 
        if (xref.GetTag().GetStr().find(' ') != string::npos) {
            flags |= eContainsSpace;
        }
    }
 
    if (!xref.IsSetDb()) {
        return flags;
    }
    const string& db = xref.GetDb();
    string dbv;
    if (xref.IsSetTag() && xref.GetTag().IsStr()) {
        dbv = xref.GetTag().GetStr();
    }
    else if (xref.IsSetTag() && xref.GetTag().IsId()) {
        dbv = NStr::NumericToString(xref.GetTag().GetId());
    }
 
    if (ContainsSgml(db)) {
        flags |= eDbHasSgml;
    }
 
    bool src_db = false;
    bool refseq_db = false;
    string correct_caps;
 
    if (xref.GetDBFlags(refseq_db, src_db, correct_caps)) {
        if (!NStr::EqualCase(correct_caps, db)) {
            // capitalization is bad
            flags |= eBadCapitalization;
        }
 
        if (is_biosource && !src_db) {
            flags |= eNotForSource;
            if (refseq_db && is_refseq_or_gps) {
                flags |= eRefSeqNotForSource;
            }
        } else if (!is_biosource && src_db && NStr::EqualNocase(db, "taxon")) {
            flags |= eOnlyForSource;
        }
        if (refseq_db && !is_refseq_or_gps) {
            flags |= eOnlyForRefSeq;
        }
    } else {
        flags |= eUnrecognized;
    }
    return flags;
}
 
void CValidator::x_SetEntryInfo(const CValidator::TEntryInfo& info)
{
    m_pEntryInfo.reset(new TEntryInfo(info));
}
 
 
bool CValidator::IsSetEntryInfo() const
{
    return m_pEntryInfo.get() != nullptr;
}
 
 
const CValidator::TEntryInfo& CValidator::GetEntryInfo() const
{
    return *m_pEntryInfo;
}
 
 
//LCOV_EXCL_START
//code is not used
CCache::CCache()
{
    m_impl = new CCacheImpl;
}
 
CCache::~CCache()
{
    delete m_impl;
}
 
CRef<CCache>
CValidator::MakeEmptyCache()
{
    return Ref(new CCache);
}
//LCOV_EXCL_STOP
 
END_SCOPE(validator)
END_SCOPE(objects)
END_NCBI_SCOPE