psg_loader.cpp

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/*  $Id: psg_loader.cpp 101837 2024-02-20 19:11:32Z vasilche $
 * ===========================================================================
 *
 *                            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: Eugene Vasilchenko, Aleksey Grichenko
 *
 * File Description: PSG data loader
 *
 * ===========================================================================
 */
 
#include <ncbi_pch.hpp>
#include <corelib/ncbistd.hpp>
 
#include <objects/general/general__.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <objects/seq/seq__.hpp>
#include <objects/seqres/seqres__.hpp>
 
#include <objmgr/impl/data_source.hpp>
#include <objmgr/impl/tse_loadlock.hpp>
#include <objmgr/impl/tse_chunk_info.hpp>
#include <objmgr/data_loader_factory.hpp>
#include <corelib/plugin_manager_impl.hpp>
#include <corelib/plugin_manager_store.hpp>
 
#include <objtools/data_loaders/genbank/psg_loader.hpp>
#include <objtools/data_loaders/genbank/impl/psg_loader_impl.hpp>
 
#if defined(HAVE_PSG_LOADER)
 
BEGIN_NCBI_SCOPE
 
NCBI_PARAM_ENUM_ARRAY(objects::CSeq_id::ESNPScaleLimit, PSG_LOADER, SNP_SCALE_LIMIT) {
    {"", objects::CSeq_id::eSNPScaleLimit_Default},
    {"Unit", objects::CSeq_id::eSNPScaleLimit_Unit},
    {"Contig", objects::CSeq_id::eSNPScaleLimit_Contig},
    {"Supercontig", objects::CSeq_id::eSNPScaleLimit_Supercontig},
    {"Chromosome", objects::CSeq_id::eSNPScaleLimit_Chromosome},
};
NCBI_PARAM_ENUM_DECL(objects::CSeq_id::ESNPScaleLimit, PSG_LOADER, SNP_SCALE_LIMIT);
NCBI_PARAM_ENUM_DEF_EX(objects::CSeq_id::ESNPScaleLimit, PSG_LOADER, SNP_SCALE_LIMIT,
                       objects::CSeq_id::eSNPScaleLimit_Default,
                       eParam_NoThread, PSG_LOADER_SNP_SCALE_LIMIT);
typedef NCBI_PARAM_TYPE(PSG_LOADER, SNP_SCALE_LIMIT) TSNP_Scale_Limit;
 
BEGIN_SCOPE(objects)
 
/////////////////////////////////////////////////////////////////////////////
// CPsgBlobId
/////////////////////////////////////////////////////////////////////////////
 
 
CPsgBlobId::CPsgBlobId(const string& id)
    : m_Id(id)
{
}
 
 
CPsgBlobId::CPsgBlobId(const string& id, const string& id2_info)
    : m_Id(id),
      m_Id2Info(id2_info)
{
}
 
 
CPsgBlobId::~CPsgBlobId()
{
}
 
 
string CPsgBlobId::ToString(void) const
{
    return m_Id;
}
 
 
bool CPsgBlobId::operator==(const CBlobId& id_ref) const
{
    const CPsgBlobId* id = dynamic_cast<const CPsgBlobId*>(&id_ref);
    return id && m_Id == id->m_Id;
}
 
 
bool CPsgBlobId::operator<(const CBlobId& id_ref) const
{
    const CPsgBlobId* id = dynamic_cast<const CPsgBlobId*>(&id_ref);
    if ( !id ) {
        return LessByTypeId(id_ref);
    }
    return m_Id < id->m_Id;
}
 
 
bool CPsgBlobId::GetSatSatkey(int& sat, int& satkey) const
{
    string ssat, ssatkey;
    NStr::SplitInTwo(m_Id, ".", ssat, ssatkey);
    if (ssat.empty() || ssatkey.empty()) return false;
    try {
        sat = NStr::StringToNumeric<int>(ssat);
        satkey = NStr::StringToNumeric<int>(ssatkey);
    }
    catch (CStringException&) {
        return false;
    }
    return true;
}
 
 
CConstRef<CPsgBlobId> CPsgBlobId::GetPsgBlobId(const CBlobId& blob_id)
{
    if ( auto psg_blob_id = dynamic_cast<const CPsgBlobId*>(&blob_id) ) {
        return ConstRef(psg_blob_id);
    }
    const CBlob_id* gb_blob_id = dynamic_cast<const CBlob_id*>(&blob_id);
    if (!gb_blob_id) {
        NCBI_THROW(CLoaderException, eOtherError, "Incompatible blob-id: " + blob_id.ToString());
    }
    return ConstRef(new CPsgBlobId(
                        NStr::NumericToString(gb_blob_id->GetSat()) +
                        '.' +
                        NStr::NumericToString(gb_blob_id->GetSatKey())));
}
 
 
/////////////////////////////////////////////////////////////////////////////
// CPSGDataLoader
/////////////////////////////////////////////////////////////////////////////
 
 
#define PSGLOADER_NAME "GBLOADER"
 
const char kDataLoader_PSG_DriverName[] = "psg";
 
 
CSeq_id::ESNPScaleLimit CPSGDataLoader::GetSNP_Scale_Limit(void)
{
    return TSNP_Scale_Limit::GetDefault();
}
 
 
void CPSGDataLoader::SetSNP_Scale_Limit(CSeq_id::ESNPScaleLimit value)
{
    TSNP_Scale_Limit::SetDefault(value);
}
 
 
CPSGDataLoader::TRegisterLoaderInfo CPSGDataLoader::RegisterInObjectManager(
    CObjectManager& om,
    CObjectManager::EIsDefault is_default,
    CObjectManager::TPriority priority)
{
    return RegisterInObjectManager(om, CGBLoaderParams(), is_default, priority);
}
 
 
CPSGDataLoader::TRegisterLoaderInfo CPSGDataLoader::RegisterInObjectManager(
    CObjectManager& om,
    const CGBLoaderParams& params,
    CObjectManager::EIsDefault is_default,
    CObjectManager::TPriority priority)
{
    CGBLoaderMaker<CPSGDataLoader> maker(params);
    CDataLoader::RegisterInObjectManager(om, maker, is_default, priority);
    return maker.GetRegisterInfo();
}
 
 
CPSGDataLoader::CPSGDataLoader(const string& loader_name,
                               const CGBLoaderParams& params)
    : CGBDataLoader(loader_name, params)
{
    m_Impl.Reset(new CPSGDataLoader_Impl(params));
}
 
 
CPSGDataLoader::~CPSGDataLoader(void)
{
}
 
 
CDataLoader::TBlobId CPSGDataLoader::GetBlobId(const CSeq_id_Handle& idh)
{
    return TBlobId(m_Impl->GetBlobId(idh).GetPointerOrNull());
}
 
 
CDataLoader::TBlobId
CPSGDataLoader::GetBlobIdFromString(const string& str) const
{
    return TBlobId(new CPsgBlobId(str));
}
 
 
bool CPSGDataLoader::CanGetBlobById(void) const
{
    return true;
}
 
 
CDataLoader::TTSE_LockSet
CPSGDataLoader::GetRecords(const CSeq_id_Handle& idh,
                           EChoice choice)
{
    return m_Impl->GetRecords(GetDataSource(), idh, choice);
}
 
 
CPSGDataLoader::TTSE_LockSet CPSGDataLoader::GetOrphanAnnotRecordsNA(const CSeq_id_Handle& idh,
    const SAnnotSelector* sel,
    TProcessedNAs* processed_nas)
{
    return CDataLoader::TTSE_LockSet();
}
 
 
namespace {
    struct SBetterId
    {
        int GetScore(const CSeq_id_Handle& id1) const
            {
                if ( id1.IsGi() ) {
                    return 100;
                }
                if ( !id1 ) {
                    return -1;
                }
                CConstRef<CSeq_id> seq_id = id1.GetSeqId();
                const CTextseq_id* text_id = seq_id->GetTextseq_Id();
                if ( text_id ) {
                    int score;
                    if ( text_id->IsSetAccession() ) {
                        if ( text_id->IsSetVersion() ) {
                            score = 99;
                        }
                        else {
                            score = 50;
                        }
                    }
                    else {
                        score = 0;
                    }
                    return score;
                }
                if ( seq_id->IsGeneral() ) {
                    return 10;
                }
                if ( seq_id->IsLocal() ) {
                    return 0;
                }
                return 1;
            }
        bool operator()(const CSeq_id_Handle& id1,
                        const CSeq_id_Handle& id2) const
            {
                int score1 = GetScore(id1);
                int score2 = GetScore(id2);
                if ( score1 != score2 ) {
                    return score1 > score2;
                }
                return id1 < id2;
            }
    };
}
 
 
CPSGDataLoader::TTSE_LockSet CPSGDataLoader::GetExternalAnnotRecordsNA(const CBioseq_Info& bioseq,
    const SAnnotSelector* sel,
    TProcessedNAs* processed_nas)
{
    TIds ids = bioseq.GetId();
    sort(ids.begin(), ids.end(), SBetterId());
    return m_Impl->GetAnnotRecordsNA(GetDataSource(), ids, sel, processed_nas);
}
 
 
void CPSGDataLoader::GetChunk(TChunk chunk)
{
    m_Impl->LoadChunk(GetDataSource(), *chunk);
}
 
 
void CPSGDataLoader::GetChunks(const TChunkSet& chunks)
{
    m_Impl->LoadChunks(GetDataSource(), chunks);
}
 
 
void CPSGDataLoader::GetBlobs(TTSE_LockSets& tse_sets)
{
    m_Impl->GetBlobs(GetDataSource(), tse_sets);
}
 
 
void CPSGDataLoader::GetCDDAnnots(const TSeqIdSets& id_sets, TLoaded& loaded, TCDD_Locks& ret)
{
    m_Impl->GetCDDAnnots(GetDataSource(), id_sets, loaded, ret);
}
 
 
CDataLoader::TTSE_Lock
CPSGDataLoader::GetBlobById(const TBlobId& blob_id)
{
    return m_Impl->GetBlobById(GetDataSource(),
                               *CPsgBlobId::GetPsgBlobId(*blob_id));
}
 
 
void CPSGDataLoader::GetIds(const CSeq_id_Handle& idh, TIds& ids)
{
    m_Impl->GetIds(idh, ids);
}
 
 
CDataLoader::SGiFound
CPSGDataLoader::GetGiFound(const CSeq_id_Handle& idh)
{
    return m_Impl->GetGi(idh);
}
 
 
CDataLoader::SAccVerFound
CPSGDataLoader::GetAccVerFound(const CSeq_id_Handle& idh)
{
    return m_Impl->GetAccVer(idh);
}
 
 
TTaxId CPSGDataLoader::GetTaxId(const CSeq_id_Handle& idh)
{
    auto taxid = m_Impl->GetTaxId(idh);
    return taxid != INVALID_TAX_ID ? taxid : CDataLoader::GetTaxId(idh);
}
 
 
void CPSGDataLoader::GetTaxIds(const TIds& ids, TLoaded& loaded, TTaxIds& ret)
{
    m_Impl->GetTaxIds(ids, loaded, ret);
}
 
 
TSeqPos CPSGDataLoader::GetSequenceLength(const CSeq_id_Handle& idh)
{
    return m_Impl->GetSequenceLength(idh);
}
 
 
CDataLoader::SHashFound
CPSGDataLoader::GetSequenceHashFound(const CSeq_id_Handle& idh)
{
    return m_Impl->GetSequenceHash(idh);
}
 
 
CDataLoader::STypeFound
CPSGDataLoader::GetSequenceTypeFound(const CSeq_id_Handle& idh)
{
    return m_Impl->GetSequenceType(idh);
}
 
 
int CPSGDataLoader::GetSequenceState(const CSeq_id_Handle& idh)
{
    return m_Impl->GetSequenceState(GetDataSource(), idh);
}
 
 
void CPSGDataLoader::DropTSE(CRef<CTSE_Info> tse_info)
{
    m_Impl->DropTSE(dynamic_cast<const CPsgBlobId&>(*tse_info->GetBlobId()));
}
 
 
void CPSGDataLoader::GetBulkIds(const TIds& ids, TLoaded& loaded, TBulkIds& ret)
{
    m_Impl->GetBulkIds(ids, loaded, ret);
}
 
 
void CPSGDataLoader::GetAccVers(const TIds& ids, TLoaded& loaded, TIds& ret)
{
    m_Impl->GetAccVers(ids, loaded, ret);
}
 
 
void CPSGDataLoader::GetGis(const TIds& ids, TLoaded& loaded, TGis& ret)
{
    m_Impl->GetGis(ids, loaded, ret);
}
 
 
void CPSGDataLoader::GetLabels(const TIds& ids, TLoaded& loaded, TLabels& ret)
{
    m_Impl->GetLabels(ids, loaded, ret);
}
 
 
void CPSGDataLoader::GetSequenceLengths(const TIds& ids, TLoaded& loaded, TSequenceLengths& ret)
{
    m_Impl->GetSequenceLengths(ids, loaded, ret);
}
 
 
void CPSGDataLoader::GetSequenceTypes(const TIds& ids, TLoaded& loaded, TSequenceTypes& ret)
{
    m_Impl->GetSequenceTypes(ids, loaded, ret);
}
 
 
void CPSGDataLoader::GetSequenceStates(const TIds& ids, TLoaded& loaded, TSequenceStates& ret)
{
    m_Impl->GetSequenceStates(GetDataSource(), ids, loaded, ret);
}
 
 
void CPSGDataLoader::GetSequenceHashes(const TIds& ids, TLoaded& loaded, TSequenceHashes& ret, THashKnown& known)
{
    m_Impl->GetSequenceHashes(ids, loaded, ret, known);
}
 
 
CGBDataLoader::TNamedAnnotNames
CPSGDataLoader::GetNamedAnnotAccessions(const CSeq_id_Handle& sih)
{
    TNamedAnnotNames names;
 
    /*
    CGBReaderRequestResult result(this, sih);
    SAnnotSelector sel;
    sel.IncludeNamedAnnotAccession("NA*");
    CLoadLockBlobIds blobs(result, sih, &sel);
    m_Dispatcher->LoadSeq_idBlob_ids(result, sih, &sel);
    _ASSERT(blobs.IsLoaded());
 
    CFixedBlob_ids blob_ids = blobs.GetBlob_ids();
    if ((blob_ids.GetState() & CBioseq_Handle::fState_no_data) != 0) {
        if (blob_ids.GetState() == CBioseq_Handle::fState_no_data) {
            // default state - return empty name set
            return names;
        }
        NCBI_THROW2(CBlobStateException, eBlobStateError,
            "blob state error for " + sih.AsString(),
            blob_ids.GetState());
    }
 
    ITERATE(CFixedBlob_ids, it, blob_ids) {
        const CBlob_Info& info = *it;
        if (!info.IsSetAnnotInfo()) {
            continue;
        }
        CConstRef<CBlob_Annot_Info> annot_info = info.GetAnnotInfo();
        ITERATE(CBlob_Annot_Info::TNamedAnnotNames, jt,
            annot_info->GetNamedAnnotNames()) {
            names.insert(*jt);
        }
    }
    */
 
    return names;
}
 
 
CGBDataLoader::TNamedAnnotNames
CPSGDataLoader::GetNamedAnnotAccessions(const CSeq_id_Handle& sih,
    const string& named_acc)
{
    TNamedAnnotNames names;
 
    /*
    CGBReaderRequestResult result(this, sih);
    SAnnotSelector sel;
    if (!ExtractZoomLevel(named_acc, 0, 0)) {
        sel.IncludeNamedAnnotAccession(CombineWithZoomLevel(named_acc, -1));
    }
    else {
        sel.IncludeNamedAnnotAccession(named_acc);
    }
    CLoadLockBlobIds blobs(result, sih, &sel);
    m_Dispatcher->LoadSeq_idBlob_ids(result, sih, &sel);
    _ASSERT(blobs.IsLoaded());
 
    CFixedBlob_ids blob_ids = blobs.GetBlob_ids();
    if ((blob_ids.GetState() & CBioseq_Handle::fState_no_data) != 0) {
        if (blob_ids.GetState() == CBioseq_Handle::fState_no_data) {
            // default state - return empty name set
            return names;
        }
        NCBI_THROW2(CBlobStateException, eBlobStateError,
            "blob state error for " + sih.AsString(),
            blob_ids.GetState());
    }
 
    ITERATE(CFixedBlob_ids, it, blob_ids) {
        const CBlob_Info& info = *it;
        if (!info.IsSetAnnotInfo()) {
            continue;
        }
        CConstRef<CBlob_Annot_Info> annot_info = info.GetAnnotInfo();
        ITERATE(CBlob_Annot_Info::TNamedAnnotNames, jt,
            annot_info->GetNamedAnnotNames()) {
            names.insert(*jt);
        }
    }
    */
 
    return names;
}
 
 
CGBDataLoader::TRealBlobId
CPSGDataLoader::x_GetRealBlobId(const TBlobId& blob_id) const
{
    const CPsgBlobId* psg_blob_id = dynamic_cast<const CPsgBlobId*>(&*blob_id);
    if (psg_blob_id) {
        int sat, satkey;
        if (psg_blob_id->GetSatSatkey(sat, satkey)) {
            CBlob_id gb_blob_id;
            gb_blob_id.SetSat(sat);
            gb_blob_id.SetSatKey(satkey);
            return gb_blob_id;
        }
    }
    const CBlob_id* gb_blob_id = dynamic_cast<const CBlob_id*>(&*blob_id);
    if (gb_blob_id) return *gb_blob_id;
    return CBlob_id();
}
 
 
END_SCOPE(objects)
 
// ===========================================================================
 
USING_SCOPE(objects);
 
class CPSG_DataLoaderCF : public CDataLoaderFactory
{
public:
    CPSG_DataLoaderCF(void)
        : CDataLoaderFactory(objects::kDataLoader_PSG_DriverName) {}
    virtual ~CPSG_DataLoaderCF(void) {}
 
protected:
    virtual CDataLoader* CreateAndRegister(
        CObjectManager& om,
        const TPluginManagerParamTree* params) const;
};
 
 
CDataLoader* CPSG_DataLoaderCF::CreateAndRegister(
    CObjectManager& om,
    const TPluginManagerParamTree* params) const
{
    if ( !ValidParams(params) ) {
        // Use constructor without arguments
        return CPSGDataLoader::RegisterInObjectManager(om).GetLoader();
    }
    // IsDefault and Priority arguments may be specified
    return CPSGDataLoader::RegisterInObjectManager(
        om,
        GetIsDefault(params),
        GetPriority(params)).GetLoader();
}
 
END_NCBI_SCOPE
 
#endif // HAVE_PSG_LOADER