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NCBI C++ ToolKit: CPSGDataLoader_Impl Class Reference

Search Toolkit Book for CPSGDataLoader_Impl

#include <objtools/data_loaders/genbank/impl/psg_loader_impl.hpp>

Definition at line 65 of file psg_loader_impl.hpp.

◆ CPSGCaches ◆ CPSGL_Processor ◆ CPSGL_Queue ◆ CPSGL_QueueGuard ◆ CPSGL_ResultGuard ◆ SPsgBioseqInfo ◆ SPsgBlobInfo ◆ TBioseqAndBlobInfo ◆ TBioseqAndBlobInfos ◆ TBioseqInfos ◆ TBulkIds ◆ TCDD_Locks ◆ TGis ◆ THashKnown ◆ TIds ◆ TLabels ◆ TLoaded ◆ TLoadedSeqIds ◆ TSeqIdSets ◆ TSequenceHashes ◆ TSequenceLengths ◆ TSequenceStates ◆ TSequenceTypes ◆ TTaxIds ◆ TTSE_LockSets ◆ EProcessResult ◆ CPSGDataLoader_Impl()

Definition at line 307 of file psg_loader_impl.cpp.

◆ ~CPSGDataLoader_Impl() CPSGDataLoader_Impl::~CPSGDataLoader_Impl ( void ) override ◆ CallWithRetry()

template<class Call >

std::invoke_result< Call >::type CPSGDataLoader_Impl::CallWithRetry ( Call && call, const char * name, int retry_count = 0 )

Definition at line 490 of file psg_loader_impl.cpp.

References CLoaderException::eConnectionFailed, CLoaderException::eLoaderFailed, CException::GetErrCode(), CIncreasingTime::GetTime(), LOG_POST, m_RetryCount, m_WaitTime, SleepMilliSec(), t, Warning(), and CException::what().

Referenced by GetAccVer(), GetAccVers(), GetAnnotRecordsNA(), GetBlobById(), GetBlobId(), GetBlobs(), GetBulkIds(), GetCDDAnnots(), GetGi(), GetGis(), GetIds(), GetLabels(), GetRecords(), GetSequenceHash(), GetSequenceHashes(), GetSequenceLength(), GetSequenceLengths(), GetSequenceState(), GetSequenceStates(), GetSequenceType(), GetSequenceTypes(), GetTaxId(), GetTaxIds(), and LoadChunks().

◆ DropTSE() ◆ GetAccVer() ◆ GetAccVerOnce() ◆ GetAccVers() ◆ GetAccVersOnce() ◆ GetAnnotRecordsNA() ◆ GetAnnotRecordsNAOnce()

Definition at line 1672 of file psg_loader_impl.cpp.

References _TRACE, CPSGL_QueueGuard::AddRequest(), CThreadPool_Task::eCompleted, NStr::EqualNocase(), map_checker< Container >::erase(), CSeq_id::eSNPScaleLimit_Default, FormatError(), SAnnotSelector::GetNamedAnnotAccessions(), CPSGL_QueueGuard::GetNextResult(), CPSGDataLoader::GetSNP_Scale_Limit(), SAnnotSelector::GetSNPScaleLimit(), set< Key, Compare >::insert(), SAnnotSelector::IsIncludedAnyNamedAnnotAccession(), ITERATE, kCDDAnnotName, kCreateLocalCDDEntries, m_AddWGSMasterDescr, m_Caches, m_Queue, m_ThreadPool, m_TSERequestMode, NCBI_THROW_FMT, NStr::NumericToString(), r(), result, CDataLoader::SetProcessedNA(), x_CheckAnnotCache(), x_CreateLocalCDDEntry(), and x_GetCDDIds().

Referenced by GetAnnotRecordsNA().

◆ GetBlobById() ◆ GetBlobByIdOnce()

Definition at line 1041 of file psg_loader_impl.cpp.

References _ASSERT, _TRACE, CPSGL_QueueGuard::AddRequest(), CThreadPool_Task::eCompleted, FormatError(), CBioseq_Handle::fState_confidential, CBioseq_Handle::fState_no_data, CBioseq_Handle::fState_withdrawn, GetGetBlobByIdShouldFail(), CPSGL_QueueGuard::GetNextResult(), CDataSource::GetTSE_LoadLockIfLoaded(), Info(), CTSE_LoadLock::IsLoaded(), LOG_POST, m_AddWGSMasterDescr, m_Caches, m_Queue, m_ThreadPool, m_TSERequestMode, NCBI_THROW2, NCBI_THROW_FMT, result, s_GetDebugLevel(), CPsgBlobId::ToPsgId(), CPsgBlobId::ToString(), x_CreateLocalCDDEntry(), and x_ParseLocalCDDEntryId().

Referenced by GetBlobById(), and GetRecordsOnce().

◆ GetBlobId() ◆ GetBlobIdOnce()

Definition at line 969 of file psg_loader_impl.cpp.

References _ASSERT, _TRACE, CPSGL_QueueGuard::AddRequest(), CannotProcess(), CThreadPool_Task::eCompleted, eError, CPSG_Request_Biodata::eNoTSE, FormatError(), CPSGL_QueueGuard::GetNextResult(), m_AddWGSMasterDescr, m_Caches, m_Queue, m_ThreadPool, NCBI_THROW_FMT, and result.

Referenced by GetBlobId().

◆ GetBlobs() ◆ GetBlobsOnce() ◆ GetBulkIds() ◆ GetBulkIdsOnce() ◆ GetCDDAnnots() ◆ GetCDDAnnotsOnce()

Definition at line 1799 of file psg_loader_impl.cpp.

References _ASSERT, _TRACE, CPSGL_QueueGuard::AddRequest(), set< Key, Compare >::begin(), CThreadPool_Task::eCompleted, CPSG_Request_Biodata::eWholeTSE, CDataSource::fLoaded_bioseq_annots, FormatBulkError(), CDataSource::GetLoadedBlob_ids(), CPSGL_QueueGuard::GetNextResult(), CDataSource::GetTSE_LoadLockIfLoaded(), i, kCDDAnnotName, m_Caches, m_Queue, m_ThreadPool, NCBI_THROW_FMT, result, set< Key, Compare >::size(), x_CheckAnnotCache(), x_GetCDDIds(), x_IsEmptyCDD(), x_IsLocalCDDEntryId(), x_MakeLocalCDDEntryId(), and CTSE_Info::x_NeedsDelayedMainChunk().

Referenced by GetCDDAnnots().

◆ GetGetBlobByIdShouldFail() bool CPSGDataLoader_Impl::GetGetBlobByIdShouldFail ( ) static ◆ GetGi() ◆ GetGiOnce() ◆ GetGis() ◆ GetGisOnce() ◆ GetIds() ◆ GetIdsOnce() ◆ GetLabels() ◆ GetLabelsOnce() ◆ GetRecords() ◆ GetRecordsOnce()

Definition at line 867 of file psg_loader_impl.cpp.

References _ASSERT, CPSGL_QueueGuard::AddRequest(), CSeq_id_Handle::AsString(), CannotProcess(), CThreadPool_Task::eCompleted, CDataLoader::eOrphanAnnot, CDataSource::fKnown_bioseqs, FormatError(), GetBlobByIdOnce(), CDataSource::GetLoadedBlob_ids(), CPSGL_QueueGuard::GetNextResult(), set< Key, Compare >::insert(), ITERATE, m_AddWGSMasterDescr, m_Caches, m_CDDPrefetchTask, m_Queue, m_ThreadPool, m_TSERequestMode, NCBI_THROW2, NCBI_THROW_FMT, result, CPsgBlobId::ToPsgId(), x_GetCDDIds(), and x_MakeLocalCDDEntryId().

Referenced by GetRecords().

◆ GetSequenceHash() ◆ GetSequenceHashes() ◆ GetSequenceHashesOnce() ◆ GetSequenceHashOnce() ◆ GetSequenceLength() ◆ GetSequenceLengthOnce() ◆ GetSequenceLengths() ◆ GetSequenceLengthsOnce() ◆ GetSequenceState() ◆ GetSequenceStateOnce() ◆ GetSequenceStates() ◆ GetSequenceStatesOnce() ◆ GetSequenceType() ◆ GetSequenceTypeOnce() ◆ GetSequenceTypes() ◆ GetSequenceTypesOnce() ◆ GetTaxId() ◆ GetTaxIdOnce() ◆ GetTaxIds() ◆ GetTaxIdsOnce() ◆ LoadChunk() ◆ LoadChunks() ◆ LoadChunksOnce()

Definition at line 1446 of file psg_loader_impl.cpp.

References _ASSERT, _TRACE, CPSGL_QueueGuard::AddRequest(), CPSGL_Processor::Descr(), CThreadPool_Task::eCompleted, FormatBulkError(), CTSE_Chunk_Info::GetBlobId(), CTSE_Chunk_Info::GetChunkId(), CDataSource::GetDataLoader(), CPSG_BioId::GetId(), CPsgBlobId::GetId2Info(), CPSGL_QueueGuard::GetNextResult(), CTSE_Chunk_Info::IsLoaded(), ITERATE, kCDDAnnotName, kDelayedMain_ChunkId, kMasterWGS_ChunkId, CWGSMasterSupport::LoadWGSMaster(), m_AddWGSMasterDescr, m_Caches, m_Queue, m_ThreadPool, m_TSERequestMode, names, NCBI_THROW_FMT, NPOS, result, CPSGL_Blob_Processor::SetLockedDelayedChunkInfo(), CPsgBlobId::ToPsgId(), CBlobId::ToString(), x_CreateEmptyLocalCDDEntry(), x_LocalCDDEntryIdToBioId(), and x_ParseLocalCDDEntryId().

Referenced by LoadChunks().

◆ SetGetBlobByIdShouldFail() void CPSGDataLoader_Impl::SetGetBlobByIdShouldFail ( bool value ) static ◆ x_AdjustBlobState() ◆ x_CheckAnnotCache()

Definition at line 1635 of file psg_loader_impl.cpp.

References _ASSERT, CTSE_Split_Info::AddChunk(), CTSE_Info::GetSplitInfo(), CDataSource::GetTSE_LoadLock(), info, set< Key, Compare >::insert(), CTSE_LoadLock::IsLoaded(), m_Caches, s_CreateNAChunk(), CTSE_LoadLock::SetLoaded(), CTSE_Info::SetName(), CDataLoader::SetProcessedNA(), and CTSE_Info::x_NeedsDelayedMainChunk().

Referenced by GetAnnotRecordsNAOnce(), and GetCDDAnnotsOnce().

◆ x_CreateBioseqAndBlobInfoRequests()

Definition at line 2364 of file psg_loader_impl.cpp.

References CPSGL_QueueGuard::AddRequest(), eCompleted, CPSG_Request_Biodata::eNoTSE, eQueued, eSuccess, kProcessorIndex_BlobInfo, kProcessorIndex_count, kProcessorIndex_Info, m_Caches, and x_AdjustBlobState().

Referenced by x_GetBioseqAndBlobInfo(), and x_GetBulkBioseqAndBlobInfo().

◆ x_GetBioseqAndBlobInfo() ◆ x_GetBioseqInfo()

Definition at line 2172 of file psg_loader_impl.cpp.

References _ASSERT, _TRACE, CPSGL_QueueGuard::AddRequest(), CThreadPool_Task::eCompleted, CPSG_Request_Resolve::fAllInfo, CPSGL_QueueGuard::GetNextResult(), m_Caches, m_Queue, m_ThreadPool, NCBI_THROW_FMT, and result.

Referenced by GetAccVerOnce(), GetGiOnce(), GetIdsOnce(), GetSequenceHashOnce(), GetSequenceLengthOnce(), GetSequenceTypeOnce(), and GetTaxIdOnce().

◆ x_GetBlobInfo()

Definition at line 2498 of file psg_loader_impl.cpp.

References _ASSERT, _TRACE, CPSGL_QueueGuard::AddRequest(), CThreadPool_Task::eCompleted, eError, CPSG_Request_Biodata::eNoTSE, CPSGL_QueueGuard::GetNextResult(), CDataSource::GetTSE_LoadLockIfLoaded(), m_Caches, m_Queue, m_ThreadPool, NCBI_THROW_FMT, and result.

◆ x_GetBulkBioseqAndBlobInfo()

Definition at line 2626 of file psg_loader_impl.cpp.

References _ASSERT, CannotProcess(), eCompleted, eFailed, CPSGL_QueueGuard::GetNextResult(), i, kProcessorIndex_count, m_Queue, m_ThreadPool, result, x_CreateBioseqAndBlobInfoRequests(), and x_ProcessBioseqAndBlobInfoResult().

Referenced by GetSequenceStatesOnce().

◆ x_GetBulkBioseqInfo()

Definition at line 2569 of file psg_loader_impl.cpp.

References _ASSERT, _TRACE, CPSGL_QueueGuard::AddRequest(), CannotProcess(), CThreadPool_Task::eCompleted, CPSG_Request_Resolve::fAllInfo, CPSGL_QueueGuard::GetNextResult(), i, m_Caches, m_Queue, m_ThreadPool, and result.

Referenced by GetAccVersOnce(), GetBulkIdsOnce(), GetGisOnce(), GetLabelsOnce(), GetSequenceHashesOnce(), GetSequenceLengthsOnce(), GetSequenceTypesOnce(), and GetTaxIdsOnce().

◆ x_GetIpgTaxId()

Definition at line 2229 of file psg_loader_impl.cpp.

References _ASSERT, _TRACE, CPSGL_QueueGuard::AddRequest(), CThreadPool_Task::eCompleted, CPSGL_QueueGuard::GetNextResult(), INVALID_TAX_ID, m_Caches, m_IpgTaxIdEnabled, m_Queue, m_ThreadPool, NCBI_THROW, result, and s_IsIpgAccession().

Referenced by GetTaxIdOnce().

◆ x_GetIpgTaxIds()

Definition at line 2268 of file psg_loader_impl.cpp.

References _ASSERT, _TRACE, CPSGL_QueueGuard::AddRequest(), CThreadPool_Task::eCompleted, CPSGL_QueueGuard::GetNextResult(), i, INVALID_TAX_ID, m_Caches, m_IpgTaxIdEnabled, m_Queue, m_ThreadPool, result, and s_IsIpgAccession().

Referenced by GetTaxIdsOnce().

◆ x_MakeSequenceState() ◆ x_ProcessBioseqAndBlobInfoResult()

Definition at line 2424 of file psg_loader_impl.cpp.

References _ASSERT, _TRACE, CPSGL_QueueGuard::AddRequest(), eCompleted, CThreadPool_Task::eCompleted, eFailed, eForbidden, CPSG_Request_Biodata::eNoTSE, eQueued, kProcessorIndex_BlobInfo, kProcessorIndex_count, kProcessorIndex_Info, m_Caches, result, and x_AdjustBlobState().

Referenced by x_GetBioseqAndBlobInfo(), and x_GetBulkBioseqAndBlobInfo().

◆ x_ReadCDDChunk()

Definition at line 1392 of file psg_loader_impl.cpp.

References _ASSERT, _DEBUG_ARG, _TRACE, ConstBegin(), GetBlobDataStream(), CTSE_Chunk_Info::GetBlobId(), CTSE_Info::GetBlobId(), CTSE_Chunk_Info::GetChunkId(), CSeq_id_Handle::GetHandle(), GetSeqId(), CDataSource::GetTSE_LoadLock(), in(), Info(), set< Key, Compare >::insert(), CTSE_Chunk_Info::IsLoaded(), CTSE_LoadLock::IsLoaded(), kDelayedMain_ChunkId, LOG_POST, MSerial_AsnText, s_GetDebugLevel(), CTSE_Chunk_Info::SetLoaded(), CTSE_Info::SetSeq_entry(), CBlobIdKey::ToString(), x_IsLocalCDDEntryId(), and CTSE_Info::x_NeedsDelayedMainChunk().

◆ m_AddWGSMasterDescr bool CPSGDataLoader_Impl::m_AddWGSMasterDescr = true private ◆ m_BulkRetryCount unsigned int CPSGDataLoader_Impl::m_BulkRetryCount private

Definition at line 254 of file psg_loader_impl.hpp.

Referenced by CPSGDataLoader_Impl(), GetAccVers(), GetBlobs(), GetBulkIds(), GetCDDAnnots(), GetGis(), GetLabels(), GetSequenceHashes(), GetSequenceLengths(), GetSequenceStates(), and GetSequenceTypes().

◆ m_Caches unique_ptr<CPSGCaches> CPSGDataLoader_Impl::m_Caches private

Definition at line 248 of file psg_loader_impl.hpp.

Referenced by CPSGDataLoader_Impl(), CPSGDataLoader_Impl::CGetRequests::CreateGetRequests(), GetAnnotRecordsNAOnce(), GetBlobByIdOnce(), GetBlobIdOnce(), GetCDDAnnotsOnce(), GetRecordsOnce(), LoadChunksOnce(), x_CheckAnnotCache(), x_CreateBioseqAndBlobInfoRequests(), x_GetBioseqInfo(), x_GetBlobInfo(), x_GetBulkBioseqInfo(), x_GetIpgTaxId(), x_GetIpgTaxIds(), and x_ProcessBioseqAndBlobInfoResult().

◆ m_CDDPrefetchTask ◆ m_IpgTaxIdEnabled bool CPSGDataLoader_Impl::m_IpgTaxIdEnabled private ◆ m_Queue

Definition at line 246 of file psg_loader_impl.hpp.

Referenced by CPSGDataLoader_Impl(), GetAnnotRecordsNAOnce(), GetBlobByIdOnce(), GetBlobIdOnce(), GetCDDAnnotsOnce(), GetRecordsOnce(), LoadChunksOnce(), x_GetBioseqAndBlobInfo(), x_GetBioseqInfo(), x_GetBlobInfo(), x_GetBulkBioseqAndBlobInfo(), x_GetBulkBioseqInfo(), x_GetIpgTaxId(), and x_GetIpgTaxIds().

◆ m_RequestContext ◆ m_RetryCount unsigned int CPSGDataLoader_Impl::m_RetryCount private ◆ m_ThreadPool unique_ptr<CThreadPool> CPSGDataLoader_Impl::m_ThreadPool private

Definition at line 249 of file psg_loader_impl.hpp.

Referenced by GetAnnotRecordsNAOnce(), GetBlobByIdOnce(), GetBlobIdOnce(), GetCDDAnnotsOnce(), GetRecordsOnce(), LoadChunksOnce(), x_GetBioseqAndBlobInfo(), x_GetBioseqInfo(), x_GetBlobInfo(), x_GetBulkBioseqAndBlobInfo(), x_GetBulkBioseqInfo(), x_GetIpgTaxId(), x_GetIpgTaxIds(), and ~CPSGDataLoader_Impl().

◆ m_TSERequestMode ◆ m_TSERequestModeBulk ◆ m_WaitTime

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

include/objtools/data_loaders/genbank/impl/psg_loader_impl.hpp
src/objtools/data_loaders/genbank/psg_loader_impl.cpp

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