psg_cdd.cpp File Reference

#include <ncbi_pch.hpp>
#include <objtools/data_loaders/genbank/impl/psg_cdd.hpp>
#include <objtools/data_loaders/genbank/psg_loader.hpp>
#include <objmgr/impl/data_source.hpp>
#include <objmgr/impl/tse_split_info.hpp>
#include <objmgr/impl/tse_chunk_info.hpp>
#include <objmgr/impl/tse_loadlock.hpp>
#include <serial/objistr.hpp>
#include <serial/serial.hpp>
#include <util/compress/compress.hpp>
#include <util/compress/stream.hpp>
#include <util/compress/zlib.hpp>

Include dependency graph for psg_cdd.cpp:

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Functions
	BEGIN_NAMESPACE (objects)
	BEGIN_NAMESPACE (psgl)
	NCBI_PARAM_DECL (unsigned, PSG_LOADER, DEBUG)
	NCBI_PARAM_DEF_EX (unsigned, PSG_LOADER, DEBUG, 1, eParam_NoThread, PSG_LOADER_DEBUG)
typedef	NCBI_PARAM_TYPE (PSG_LOADER, DEBUG) TPSG_Debug
unsigned	s_GetDebugLevel ()
CSeq_id_Handle	PsgIdToHandle (const CPSG_BioId &id)
void	UpdateOMBlobId (CTSE_LoadLock &load_lock, const CConstRef< CPsgBlobId > &dl_blob_id)
CObjectIStream *	GetBlobDataStream (const CPSG_BlobInfo &blob_info, const CPSG_BlobData &blob_data)
SCDDIds	x_GetCDDIds (const CDataLoader::TIds &ids)
string	x_MakeLocalCDDEntryId (const SCDDIds &cdd_ids)
bool	x_IsLocalCDDEntryId (const CPsgBlobId &blob_id)
SCDDIds	x_ParseLocalCDDEntryId (const CPsgBlobId &blob_id)
bool	x_ParseLocalCDDEntryId (const CPsgBlobId &blob_id, SCDDIds &cdd_ids)
CPSG_BioId	x_LocalCDDEntryIdToBioId (const SCDDIds &cdd_ids)
CPSG_BioId	x_LocalCDDEntryIdToBioId (const CPsgBlobId &blob_id)
CRef< CTSE_Chunk_Info >	x_CreateLocalCDDEntryChunk (const SCDDIds &cdd_ids)
CTSE_Lock	x_CreateLocalCDDEntry (CDataSource *data_source, const SCDDIds &cdd_ids)
void	x_CreateEmptyLocalCDDEntry (CDataSource *data_source, CTSE_Chunk_Info *chunk)
bool	x_IsEmptyCDD (const CTSE_Info &tse)
	END_NAMESPACE (psgl)
	END_NAMESPACE (objects)

Variables
	BEGIN_NCBI_NAMESPACE
bool	s_GetBlobByIdShouldFail = false
	END_NCBI_NAMESPACE

Function Documentation

BEGIN_NAMESPACE() [1/2]

BEGIN_NAMESPACE

(

objects

)

BEGIN_NAMESPACE() [2/2]

BEGIN_NAMESPACE

(

psgl

)

END_NAMESPACE() [1/2]

END_NAMESPACE

(

objects

)

END_NAMESPACE() [2/2]

END_NAMESPACE

(

psgl

)

GetBlobDataStream()

CObjectIStream* GetBlobDataStream	(	const CPSG_BlobInfo &	blob_info,
		const CPSG_BlobData &	blob_data
	)

Definition at line 123 of file psg_cdd.cpp.

References _ASSERT, _TRACE, eNoOwnership, eSerial_AsnBinary, eSerial_AsnText, eSerial_Json, eSerial_Xml, eTakeOwnership, CZipCompression::fGZip, CCompressionStream::fOwnProcessor, CPSG_BlobInfo::GetCompression(), CPSG_BlobInfo::GetFormat(), CPSG_BlobData::GetStream(), in(), CObjectIStream::Open(), and z_stream.

Referenced by CPSGL_Blob_Processor::ParseChunk(), CPSGL_Blob_Processor::ParseSplitInfo(), CPSGL_Blob_Processor::ParseTSE(), CPSGL_CDDAnnot_Processor::ProcessReplySlow(), and CPSGDataLoader_Impl::x_ReadCDDChunk().

NCBI_PARAM_DECL()

NCBI_PARAM_DECL	(	unsigned	,
		PSG_LOADER	,
		DEBUG
	)

NCBI_PARAM_DEF_EX()

NCBI_PARAM_DEF_EX	(	unsigned	,
		PSG_LOADER	,
		DEBUG	,
		1	,
		eParam_NoThread	,
		PSG_LOADER_DEBUG
	)

NCBI_PARAM_TYPE()

typedef NCBI_PARAM_TYPE	(	PSG_LOADER	,
		DEBUG
	)

PsgIdToHandle()

CSeq_id_Handle PsgIdToHandle

(

const CPSG_BioId &

id

)

Definition at line 73 of file psg_cdd.cpp.

References ERR_POST, and CSeq_id_Handle::GetHandle().

Referenced by SPsgBioseqInfo::Update().

s_GetDebugLevel()

unsigned s_GetDebugLevel

(

void

)

Definition at line 66 of file psg_cdd.cpp.

References rapidjson::value.

Referenced by CPSGDataLoader_Impl::GetBlobByIdOnce(), CPSGDataLoader_Impl::GetBlobsOnce(), CPSGL_Blob_Processor::ObtainSkippedTSE_Lock(), s_CreateNAChunk(), CPSGL_Blob_Processor::TSE_ToOM(), x_CreateEmptyLocalCDDEntry(), x_CreateLocalCDDEntryChunk(), and CPSGDataLoader_Impl::x_ReadCDDChunk().

UpdateOMBlobId()

void UpdateOMBlobId	(	CTSE_LoadLock &	load_lock,
		const CConstRef< CPsgBlobId > &	dl_blob_id
	)

Definition at line 87 of file psg_cdd.cpp.

References _ASSERT, CPsgBlobId::BioseqIsDead(), CBioseq_Handle::fState_dead, CTSE_Info::GetBlobId(), CPsgBlobId::GetTSEName(), CPsgBlobId::HasBioseqIsDead(), CPsgBlobId::HasTSEName(), CTSE_Info::SetBlobState(), and CTSE_Info::SetName().

Referenced by CPSGL_NA_Processor::ProcessItemSlow(), CPSGL_CDDAnnot_Processor::ProcessReplySlow(), CPSGL_Blob_Processor::TSE_ToOM(), and x_CreateLocalCDDEntry().

x_CreateEmptyLocalCDDEntry()

void x_CreateEmptyLocalCDDEntry	(	CDataSource *	data_source,
		CTSE_Chunk_Info *	chunk
	)

Definition at line 329 of file psg_cdd.cpp.

References _ASSERT, CTSE_Chunk_Info::GetBlobId(), CTSE_Info::GetBlobId(), CDataSource::GetTSE_LoadLock(), CSeq_entry_Info::HasNoSeq_entry(), Info(), CTSE_LoadLock::IsLoaded(), LOG_POST, s_GetDebugLevel(), CTSE_Chunk_Info::SetLoaded(), CTSE_Info::SetSeq_entry(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), and CBlobIdKey::ToString().

Referenced by CPSGDataLoader_Impl::LoadChunksOnce(), and CPSGL_LocalCDDBlob_Processor::ProcessReplySlow().

x_CreateLocalCDDEntry()

CTSE_Lock x_CreateLocalCDDEntry	(	CDataSource *	data_source,
		const SCDDIds &	cdd_ids
	)

Definition at line 305 of file psg_cdd.cpp.

References _ASSERT, CTSE_Split_Info::AddChunk(), CTSE_Info::GetSplitInfo(), CDataSource::GetTSE_LoadLock(), CTSE_LoadLock::IsLoaded(), kCDDAnnotName, s_GetBlobByIdShouldFail, CTSE_LoadLock::SetLoaded(), UpdateOMBlobId(), x_CreateLocalCDDEntryChunk(), x_MakeLocalCDDEntryId(), and CTSE_Info::x_NeedsDelayedMainChunk().

Referenced by CPSGDataLoader_Impl::GetAnnotRecordsNAOnce(), CPSGDataLoader_Impl::GetBlobByIdOnce(), and CPSGL_CDDAnnot_Processor::ProcessReplySlow().

x_CreateLocalCDDEntryChunk()

CRef<CTSE_Chunk_Info> x_CreateLocalCDDEntryChunk

(

const SCDDIds &

cdd_ids

)

Definition at line 269 of file psg_cdd.cpp.

References SCDDIds::acc_ver, CSeqFeatData::eSubtype_region, CSeqFeatData::eSubtype_site, GetSeqId(), COpenRange< Position >::GetWhole(), SCDDIds::gi, i, Info(), set< Key, Compare >::insert(), kCDDAnnotName, kDelayedMain_ChunkId, LOG_POST, MSerial_AsnText, compile_time_bits::range(), s_GetDebugLevel(), type, and CTSE_Chunk_Info::x_AddAnnotType().

Referenced by x_CreateLocalCDDEntry().

x_GetCDDIds()

SCDDIds x_GetCDDIds

(

const CDataLoader::TIds &

ids

)

Definition at line 170 of file psg_cdd.cpp.

References SCDDIds::acc_ver, CSeq_id_Base::e_Pdb, CSeq_id::fAcc_nuc, CSeq_id::fAcc_prot, CSeq_id_Handle::GetHandle(), CSeq_id_Handle::GetSeqId(), SCDDIds::gi, CSeq_id::IdentifyAccession(), NStr::NumericToString(), and CSeq_id_Handle::Reset().

Referenced by CPSGDataLoader_Impl::CPSG_PrefetchCDD_Task::AddRequest(), CPSGDataLoader_Impl::GetAnnotRecordsNAOnce(), CPSGDataLoader_Impl::GetCDDAnnotsOnce(), and CPSGDataLoader_Impl::GetRecordsOnce().

x_IsEmptyCDD()

bool x_IsEmptyCDD

(

const CTSE_Info &

tse

)

Definition at line 346 of file psg_cdd.cpp.

References CBioseq_set_Base::GetSeq_set(), CSeq_entry_Base::GetSet(), and CTSE_Info::GetTSECore().

Referenced by CPSGDataLoader_Impl::GetCDDAnnotsOnce(), and CPSGL_CDDAnnot_Processor::ProcessReplySlow().

x_IsLocalCDDEntryId()

bool x_IsLocalCDDEntryId

(

const CPsgBlobId &

blob_id

)

Definition at line 220 of file psg_cdd.cpp.

References kLocalCDDEntryIdPrefix, NStr::StartsWith(), and CPsgBlobId::ToPsgId().

Referenced by CPSGDataLoader_Impl::GetCDDAnnotsOnce(), x_ParseLocalCDDEntryId(), and CPSGDataLoader_Impl::x_ReadCDDChunk().

x_LocalCDDEntryIdToBioId() [1/2]

CPSG_BioId x_LocalCDDEntryIdToBioId

(

const CPsgBlobId &

blob_id

)

Definition at line 260 of file psg_cdd.cpp.

References CSeq_id_Base::e_Gi, kLocalCDDEntryIdPrefix, kLocalCDDEntryIdSeparator, str(), and CPsgBlobId::ToPsgId().

x_LocalCDDEntryIdToBioId() [2/2]

CPSG_BioId x_LocalCDDEntryIdToBioId

(

const SCDDIds &

cdd_ids

)

Definition at line 254 of file psg_cdd.cpp.

References CSeq_id_Base::e_Gi, CSeq_id_Handle::GetGi(), SCDDIds::gi, and NStr::NumericToString().

Referenced by CPSGDataLoader_Impl::LoadChunksOnce().

x_MakeLocalCDDEntryId()

string x_MakeLocalCDDEntryId

(

const SCDDIds &

cdd_ids

)

Definition at line 208 of file psg_cdd.cpp.

References _ASSERT, SCDDIds::acc_ver, CSeq_id_Handle::GetGi(), SCDDIds::gi, CSeq_id_Handle::IsGi(), kLocalCDDEntryIdPrefix, kLocalCDDEntryIdSeparator, and str().

Referenced by CPSGDataLoader_Impl::CPSG_PrefetchCDD_Task::AddRequest(), CPSGDataLoader_Impl::GetCDDAnnotsOnce(), CPSGDataLoader_Impl::GetRecordsOnce(), CPSGL_CDDAnnot_Processor::ProcessReplyFast(), CPSGL_CDDAnnot_Processor::ProcessReplySlow(), and x_CreateLocalCDDEntry().

x_ParseLocalCDDEntryId() [1/2]

SCDDIds x_ParseLocalCDDEntryId

(

const CPsgBlobId &

blob_id

)

Definition at line 226 of file psg_cdd.cpp.

References CSeq_id_Handle::GetGiHandle(), CSeq_id_Handle::GetHandle(), GI_FROM, kLocalCDDEntryIdPrefix, kLocalCDDEntryIdSeparator, str(), CPsgBlobId::ToPsgId(), and x_IsLocalCDDEntryId().

Referenced by CPSGDataLoader_Impl::GetBlobByIdOnce(), CPSGDataLoader_Impl::LoadChunksOnce(), and x_ParseLocalCDDEntryId().

x_ParseLocalCDDEntryId() [2/2]

bool x_ParseLocalCDDEntryId	(	const CPsgBlobId &	blob_id,
		SCDDIds &	cdd_ids
	)

Definition at line 248 of file psg_cdd.cpp.

References x_ParseLocalCDDEntryId().

Variable Documentation

BEGIN_NCBI_NAMESPACE

BEGIN_NCBI_NAMESPACE

Definition at line 48 of file psg_cdd.cpp.

END_NCBI_NAMESPACE

END_NCBI_NAMESPACE

Definition at line 361 of file psg_cdd.cpp.

s_GetBlobByIdShouldFail

bool s_GetBlobByIdShouldFail = false

Definition at line 58 of file psg_cdd.cpp.

Referenced by CPSGDataLoader_Impl::GetGetBlobByIdShouldFail(), CPSGDataLoader_Impl::SetGetBlobByIdShouldFail(), and x_CreateLocalCDDEntry().