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NCBI C++ ToolKit: CWGSDataLoader_Impl Class Reference

Search Toolkit Book for CWGSDataLoader_Impl

#include <sra/data_loaders/wgs/impl/wgsloader_impl.hpp>

Definition at line 142 of file wgsloader_impl.hpp.

◆ SAccFileInfo ◆ SWGSFileInfoSlot ◆ TFixedFiles ◆ TFoundFiles ◆ TIds ◆ CWGSDataLoader_Impl()

Definition at line 415 of file wgsloader_impl.cpp.

References CVDBCacheWithExpiration::GetSlot(), GetWGSVolPath(), info, map_checker< Container >::insert(), ITERATE, m_FixedFiles, m_FoundFiles, CWGSDataLoader::SLoaderParams::m_WGSFiles, m_WGSVolPath, NCBI_THROW_FMT, and OpenWGSFile().

◆ ~CWGSDataLoader_Impl() CWGSDataLoader_Impl::~CWGSDataLoader_Impl ( void ) ◆ CallWithRetry()

template<class Call >

std::invoke_result< Call >::type CWGSDataLoader_Impl::CallWithRetry ( Call && call, const char * name, unsigned retry_count = 0 ) ◆ GetAccVer() ◆ GetAccVerOnce() ◆ GetAddWGSMasterDescr() bool CWGSDataLoader_Impl::GetAddWGSMasterDescr ( void ) const inline ◆ GetBlobById() ◆ GetBlobByIdOnce() ◆ GetBlobId() ◆ GetBlobIdOnce() ◆ GetChunk() ◆ GetChunkOnce() ◆ GetFileInfo() [1/2]

Definition at line 927 of file wgsloader_impl.cpp.

References CSeq_id_Base::e_General, CSeq_id_Base::e_Gi, CSeq_id_Base::e_Gibbmt, CSeq_id_Base::e_Gibbsq, CSeq_id_Base::e_Giim, CSeq_id_Base::e_Local, CSeq_id_Base::e_not_set, CSeq_id_Base::e_Patent, CSeq_id_Base::e_Pdb, GetFileInfoByAcc(), GetFileInfoByGeneral(), GetFileInfoByGi(), CSeq_id_Base::GetGeneral(), CSeq_id_Handle::GetGi(), CSeq_id_Handle::GetSeqId(), CSeq_id_Handle::IsGi(), CTextseq_id_Base::IsSetAccession(), m_ResolveGIs, and CSeq_id_Handle::Which().

◆ GetFileInfo() [2/2] ◆ GetFileInfoByAcc()

Definition at line 778 of file wgsloader_impl.cpp.

References CSeq_id::eAcc_division_mask, CSeq_id::eAcc_embl_prot, CSeq_id::eAcc_gb_prot, CSeq_id::eAcc_other, CSeq_id::eAcc_targeted, CSeq_id::eAcc_tsa, CSeq_id::eAcc_wgs, CSeq_id::eAcc_wgs_intermed, CSeq_id::fAcc_prot, NStr::fConvErr_NoThrow, CWGSFileInfo::SAccFileInfo::file, CTextseq_id_Base::GetAccession(), GetFileInfoByProtAcc(), GetWGSFile(), i, CSeq_id::IdentifyAccession(), info, isalpha(), isdigit(), kMaxWGSPrefixLetters, kMaxWGSProteinAccLen, kMinWGSPrefixLetters, kWGSPrefixDigits, m_ResolveProtAccs, CWGSFileInfo::SAccFileInfo::row_id, CWGSFileInfo::SAccFileInfo::seq_type, NStr::ToUpper(), and CWGSFileInfo::SAccFileInfo::ValidateAcc().

Referenced by GetFileInfo().

◆ GetFileInfoByGeneral()

Definition at line 866 of file wgsloader_impl.cpp.

References NStr::eNocase, CWGSFileInfo::SAccFileInfo::file, CWGSDb::GetContigNameRowId(), CDbtag_Base::GetDb(), CObject_id_Base::GetId(), CWGSDb::GetProteinNameRowId(), CWGSDb::GetScaffoldNameRowId(), CObject_id_Base::GetStr(), CDbtag_Base::GetTag(), GetWGSFile(), info, isalpha(), CObject_id_Base::IsStr(), NStr::NumericToString(), row, CWGSFileInfo::SAccFileInfo::row_id, CWGSFileInfo::SAccFileInfo::seq_type, NStr::StartsWith(), tag, and NStr::ToUpper().

Referenced by GetFileInfo().

◆ GetFileInfoByGi()

Definition at line 691 of file wgsloader_impl.cpp.

References map_checker< Container >::empty(), ERR_POST_X, CWGSFileInfo::SAccFileInfo::file, file, CWGSFileInfo::FindGi(), GetDebugLevel(), CWGSResolver::GetPrefixes(), GetResolver(), GetWGSFile(), CWGSFileInfo::GetWGSPrefix(), Info(), ITERATE, LOG_POST_X, m_FixedFiles, CWGSResolver::SetNonWGS(), CWGSResolver::SetWGSPrefix(), and x_GetFileInfo().

Referenced by GetFileInfo().

◆ GetFileInfoByProtAcc()

Definition at line 734 of file wgsloader_impl.cpp.

References map_checker< Container >::empty(), ERR_POST_X, CWGSFileInfo::SAccFileInfo::file, file, CWGSFileInfo::FindProtAcc(), CTextseq_id_Base::GetAccession(), GetDebugLevel(), CWGSResolver::GetPrefixes(), GetResolver(), GetWGSFile(), CWGSFileInfo::GetWGSPrefix(), Info(), ITERATE, LOG_POST_X, m_FixedFiles, CWGSResolver::SetNonWGS(), CWGSResolver::SetWGSPrefix(), and x_GetFileInfo().

Referenced by GetFileInfoByAcc().

◆ GetGi() ◆ GetGiOnce() ◆ GetIds() ◆ GetIdsOnce() ◆ GetRecords() ◆ GetRecordsOnce()

Definition at line 1125 of file wgsloader_impl.cpp.

References CSeq_id_Handle::AsString(), CDataLoader::eExtAlign, CDataLoader::eExtAnnot, CDataLoader::eExtFeatures, CDataLoader::eExtGraph, CDataLoader::eOrphanAnnot, CBioseq_Handle::fState_no_data, CTSE_Info::GetBlobState(), set< Key, Compare >::insert(), and NCBI_THROW2.

Referenced by GetRecords().

◆ GetResolver()

Definition at line 586 of file wgsloader_impl.cpp.

References CWGSResolver::CreateResolver(), CWGSResolver_DL::CreateResolver(), m_IndexUpdateDelay, m_IndexUpdateThread, m_Mgr, m_Resolver, m_ResolverCreated, m_ResolverMutex, CThread::Run(), and sx_Update().

Referenced by GetFileInfoByGi(), and GetFileInfoByProtAcc().

◆ GetSequenceHash() ◆ GetSequenceHashOnce() ◆ GetSequenceLength() ◆ GetSequenceLengthOnce() ◆ GetSequenceType() ◆ GetSequenceTypeOnce() ◆ GetTaxId() ◆ GetTaxIdOnce() ◆ GetWGSFile()

Definition at line 620 of file wgsloader_impl.cpp.

References map_checker< Container >::empty(), map_checker< Container >::end(), ERR_POST_X, map_checker< Container >::find(), GetDebugLevel(), GetKeepReplacedParam(), CVDBCacheWithExpiration::GetSlot(), info, m_FixedFiles, m_FoundFiles, and x_GetFileInfo().

Referenced by GetFileInfo(), GetFileInfoByAcc(), GetFileInfoByGeneral(), GetFileInfoByGi(), and GetFileInfoByProtAcc().

◆ LoadBlob() ◆ OpenWGSFile() ◆ OpenWGSFileOnce() ◆ SetAddWGSMasterDescr() void CWGSDataLoader_Impl::SetAddWGSMasterDescr ( bool flag ) inline ◆ x_GetFileInfo()

Definition at line 653 of file wgsloader_impl.cpp.

References CSraException::eNotFoundDb, CSraException::eProtectedDb, GetDebugLevel(), CSraException::GetErrCode(), CVDBCacheWithExpiration::CSlot::GetObject(), CVDBCacheWithExpiration::CSlot::GetSlotMutex(), Info(), info, CVDBCacheWithExpiration::CSlot::IsExpired(), LOG_POST_X, m_FoundFiles, OpenWGSFileOnce(), CVDBCacheWithExpiration::CSlot::ResetObject(), and CRef< C, Locker >::Swap().

Referenced by GetFileInfoByGi(), GetFileInfoByProtAcc(), and GetWGSFile().

◆ CWGSFileInfo ◆ m_AddWGSMasterDescr bool CWGSDataLoader_Impl::m_AddWGSMasterDescr private ◆ m_FileRecheckTime unsigned CWGSDataLoader_Impl::m_FileRecheckTime private

Definition at line 239 of file wgsloader_impl.hpp.

◆ m_FileReopenTime unsigned CWGSDataLoader_Impl::m_FileReopenTime private

Definition at line 238 of file wgsloader_impl.hpp.

◆ m_FixedFiles ◆ m_FoundFiles ◆ m_IndexUpdateDelay unsigned CWGSDataLoader_Impl::m_IndexUpdateDelay private ◆ m_IndexUpdateThread ◆ m_Mgr ◆ m_ResolveGIs bool CWGSDataLoader_Impl::m_ResolveGIs private ◆ m_ResolveProtAccs bool CWGSDataLoader_Impl::m_ResolveProtAccs private ◆ m_Resolver ◆ m_ResolverCreated atomic<bool> CWGSDataLoader_Impl::m_ResolverCreated private ◆ m_ResolverMutex ◆ m_RetryCount unsigned CWGSDataLoader_Impl::m_RetryCount private ◆ m_WGSVolPath string CWGSDataLoader_Impl::m_WGSVolPath private

The documentation for this class was generated from the following files:

include/sra/data_loaders/wgs/impl/wgsloader_impl.hpp
src/sra/data_loaders/wgs/wgsloader_impl.cpp

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