#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/annot_selector.hpp>
#include <objmgr/impl/data_source.hpp>
#include <objmgr/impl/tse_loadlock.hpp>
#include <objmgr/impl/tse_split_info.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 <sra/readers/sra/graphread.hpp>
#include <sra/data_loaders/vdbgraph/vdbgraphloader.hpp>
#include <sra/data_loaders/vdbgraph/impl/vdbgraphloader_impl.hpp>
#include <sra/error_codes.hpp>

Include dependency graph for vdbgraphloader_impl.cpp:

Go to the SVN repository for this file.

Classes
class	CVDBGraphBlobId

Macros
#define	NCBI_USE_ERRCODE_X VDBGraphLoader

#define	OVERVIEW_NAME_SUFFIX "@@5000"

#define	MID_ZOOM_NAME_SUFFIX "@@100"

Functions
	NCBI_DEFINE_ERR_SUBCODE_X (8)

	NCBI_PARAM_DECL (int, VDBGRAPH_LOADER, DEBUG)

	NCBI_PARAM_DEF_EX (int, VDBGRAPH_LOADER, DEBUG, 0, eParam_NoThread, VDBGRAPH_LOADER_DEBUG)

static int	GetDebugLevel (void)

	NCBI_PARAM_DECL (size_t, VDBGRAPH_LOADER, GC_SIZE)

	NCBI_PARAM_DEF_EX (size_t, VDBGRAPH_LOADER, GC_SIZE, 10, eParam_NoThread, VDBGRAPH_LOADER_GC_SIZE)

static size_t	GetGCSize (void)

	NCBI_PARAM_DECL (size_t, VDBGRAPH_LOADER, MISSING_GC_SIZE)

	NCBI_PARAM_DEF_EX (size_t, VDBGRAPH_LOADER, MISSING_GC_SIZE, 10000, eParam_NoThread, VDBGRAPH_LOADER_MISSING_GC_SIZE)

static size_t	GetMissingGCSize (void)

	NCBI_PARAM_DECL (int, VDBGRAPH_LOADER, USE_TABLE)

	NCBI_PARAM_DEF_EX (int, VDBGRAPH_LOADER, USE_TABLE, 2, eParam_NoThread, VDBGRAPH_LOADER_USE_TABLE)

static int	GetUseTable (void)

	NCBI_PARAM_DECL (bool, VDBGRAPH_LOADER, DISABLE_ZOOM)

	NCBI_PARAM_DEF_EX (bool, VDBGRAPH_LOADER, DISABLE_ZOOM, false, eParam_NoThread, VDBGRAPH_LOADER_DISABLE_ZOOM)

static bool	GetDisabledZoom (void)

static bool	GetEnabledOverview (void)

static bool	GetEnabledMidZoom (void)

	NCBI_PARAM_DECL (int, VDBGRAPH_LOADER, LOOKUP_TYPE)

	NCBI_PARAM_DEF_EX (int, VDBGRAPH_LOADER, LOOKUP_TYPE, CVDBGraphDb_Impl::eLookupDefault, eParam_NoThread, VDBGRAPH_LOADER_LOOKUP_TYPE)

static CVDBGraphDb_Impl::ELookupType	GetLookupType (void)

	NCBI_PARAM_DECL (unsigned, VDBGRAPH_LOADER, RETRY_COUNT)

	NCBI_PARAM_DEF (unsigned, VDBGRAPH_LOADER, RETRY_COUNT, 3)

static unsigned	GetRetryCountParam (void)

static bool	sx_IsNA (const string &s)

Variables
static const TSeqPos	kOverviewChunkSize = 20000*5000

static const TSeqPos	kMidZoomChunkSize = 20000*100

static const TSeqPos	kMainChunkSize = 100000

static const size_t	kOverviewChunkIdAdd = 0

static const size_t	kMidZoomChunkIdAdd = 1

static const size_t	kMainGraphChunkIdAdd = 2

static const size_t	kMainTableChunkIdAdd = 3

static const size_t	kChunkIdMul = 4

static const int	kTSEId = 1

Macro Definition Documentation

◆ MID_ZOOM_NAME_SUFFIX

#define MID_ZOOM_NAME_SUFFIX "@@100"

Definition at line 67 of file vdbgraphloader_impl.cpp.

◆ NCBI_USE_ERRCODE_X

#define NCBI_USE_ERRCODE_X VDBGraphLoader

Definition at line 57 of file vdbgraphloader_impl.cpp.

◆ OVERVIEW_NAME_SUFFIX

#define OVERVIEW_NAME_SUFFIX "@@5000"

Definition at line 66 of file vdbgraphloader_impl.cpp.

Function Documentation

◆ GetDebugLevel()

static int GetDebugLevel ( void )

static

Definition at line 85 of file vdbgraphloader_impl.cpp.

References DEBUG, NCBI_PARAM_TYPE, and ncbi::grid::netcache::search::s_Value().

Referenced by CVDBGraphDataLoader_Impl::CVDBGraphDataLoader_Impl(), CVDBGraphDataLoader_Impl::GetChunkOnce(), CVDBGraphDataLoader_Impl::LoadFullEntry(), CVDBGraphDataLoader_Impl::LoadSplitEntry(), and CVDBGraphDataLoader_Impl::x_GetNAFileInfo().

◆ GetDisabledZoom()

static bool GetDisabledZoom ( void )

static

Definition at line 129 of file vdbgraphloader_impl.cpp.

References NCBI_PARAM_TYPE, and ncbi::grid::netcache::search::s_Value().

Referenced by GetEnabledMidZoom(), and GetEnabledOverview().

◆ GetEnabledMidZoom()

static bool GetEnabledMidZoom ( void )

static

Definition at line 142 of file vdbgraphloader_impl.cpp.

References GetDisabledZoom().

Referenced by CVDBGraphDataLoader_Impl::LoadFullEntry(), and CVDBGraphDataLoader_Impl::LoadSplitEntry().

◆ GetEnabledOverview()

static bool GetEnabledOverview ( void )

static

Definition at line 136 of file vdbgraphloader_impl.cpp.

References GetDisabledZoom().

Referenced by CVDBGraphDataLoader_Impl::LoadFullEntry(), and CVDBGraphDataLoader_Impl::LoadSplitEntry().

◆ GetGCSize()

static size_t GetGCSize ( void )

static

Definition at line 96 of file vdbgraphloader_impl.cpp.

References NCBI_PARAM_TYPE, and ncbi::grid::netcache::search::s_Value().

Referenced by CVDBGraphDataLoader_Impl::GetOrphanAnnotRecordsOnce().

◆ GetLookupType()

static CVDBGraphDb_Impl::ELookupType GetLookupType ( void )

static

Definition at line 152 of file vdbgraphloader_impl.cpp.

References NCBI_PARAM_TYPE.

Referenced by CVDBGraphDataLoader_Impl::OpenVDBGraphFileOnce(), and CVDBGraphDataLoader_Impl::x_GetNAFileInfo().

◆ GetMissingGCSize()

static size_t GetMissingGCSize ( void )

static

Definition at line 107 of file vdbgraphloader_impl.cpp.

References NCBI_PARAM_TYPE, and ncbi::grid::netcache::search::s_Value().

Referenced by CVDBGraphDataLoader_Impl::GetOrphanAnnotRecordsOnce().

◆ GetRetryCountParam()

static unsigned GetRetryCountParam ( void )

static

Definition at line 162 of file vdbgraphloader_impl.cpp.

References NCBI_PARAM_TYPE, and rapidjson::value.

◆ GetUseTable()

static int GetUseTable ( void )

static

Definition at line 118 of file vdbgraphloader_impl.cpp.

References NCBI_PARAM_TYPE, and ncbi::grid::netcache::search::s_Value().

Referenced by CVDBGraphDataLoader_Impl::LoadFullEntry(), and CVDBGraphDataLoader_Impl::LoadSplitEntry().

◆ NCBI_DEFINE_ERR_SUBCODE_X()

NCBI_DEFINE_ERR_SUBCODE_X ( 8 )

◆ NCBI_PARAM_DECL() [1/7]

NCBI_PARAM_DECL	(	bool	,
		VDBGRAPH_LOADER	,
		DISABLE_ZOOM
	)

◆ NCBI_PARAM_DECL() [2/7]

NCBI_PARAM_DECL	(	int	,
		VDBGRAPH_LOADER	,
		DEBUG
	)

◆ NCBI_PARAM_DECL() [3/7]

NCBI_PARAM_DECL	(	int	,
		VDBGRAPH_LOADER	,
		LOOKUP_TYPE
	)

◆ NCBI_PARAM_DECL() [4/7]

NCBI_PARAM_DECL	(	int	,
		VDBGRAPH_LOADER	,
		USE_TABLE
	)

◆ NCBI_PARAM_DECL() [5/7]

NCBI_PARAM_DECL	(	size_t	,
		VDBGRAPH_LOADER	,
		GC_SIZE
	)

◆ NCBI_PARAM_DECL() [6/7]

NCBI_PARAM_DECL	(	size_t	,
		VDBGRAPH_LOADER	,
		MISSING_GC_SIZE
	)

◆ NCBI_PARAM_DECL() [7/7]

NCBI_PARAM_DECL	(	unsigned	,
		VDBGRAPH_LOADER	,
		RETRY_COUNT
	)

◆ NCBI_PARAM_DEF()

NCBI_PARAM_DEF	(	unsigned	,
		VDBGRAPH_LOADER	,
		RETRY_COUNT	,
		3
	)

◆ NCBI_PARAM_DEF_EX() [1/6]

NCBI_PARAM_DEF_EX	(	bool	,
		VDBGRAPH_LOADER	,
		DISABLE_ZOOM	,
		false	,
		eParam_NoThread	,
		VDBGRAPH_LOADER_DISABLE_ZOOM
	)

◆ NCBI_PARAM_DEF_EX() [2/6]

NCBI_PARAM_DEF_EX	(	int	,
		VDBGRAPH_LOADER	,
		DEBUG	,
		0	,
		eParam_NoThread	,
		VDBGRAPH_LOADER_DEBUG
	)

◆ NCBI_PARAM_DEF_EX() [3/6]

NCBI_PARAM_DEF_EX	(	int	,
		VDBGRAPH_LOADER	,
		LOOKUP_TYPE	,
		CVDBGraphDb_Impl::eLookupDefault	,
		eParam_NoThread	,
		VDBGRAPH_LOADER_LOOKUP_TYPE
	)

◆ NCBI_PARAM_DEF_EX() [4/6]

NCBI_PARAM_DEF_EX	(	int	,
		VDBGRAPH_LOADER	,
		USE_TABLE	,
		2	,
		eParam_NoThread	,
		VDBGRAPH_LOADER_USE_TABLE
	)

◆ NCBI_PARAM_DEF_EX() [5/6]

NCBI_PARAM_DEF_EX	(	size_t	,
		VDBGRAPH_LOADER	,
		GC_SIZE	,
		10	,
		eParam_NoThread	,
		VDBGRAPH_LOADER_GC_SIZE
	)

◆ NCBI_PARAM_DEF_EX() [6/6]

NCBI_PARAM_DEF_EX	(	size_t	,
		VDBGRAPH_LOADER	,
		MISSING_GC_SIZE	,
		10000	,
		eParam_NoThread	,
		VDBGRAPH_LOADER_MISSING_GC_SIZE
	)

◆ sx_IsNA()

static bool sx_IsNA ( const string & s )

static

Definition at line 662 of file vdbgraphloader_impl.cpp.

References i, isdigit(), and NStr::StringToNonNegativeInt().

Referenced by CVDBGraphDataLoader_Impl::x_GetNAFileInfo().

Variable Documentation

◆ kChunkIdMul

const size_t kChunkIdMul = 4

static

Definition at line 77 of file vdbgraphloader_impl.cpp.

Referenced by CVDBGraphDataLoader_Impl::GetChunkOnce(), and CVDBGraphDataLoader_Impl::LoadSplitEntry().

◆ kMainChunkSize

const TSeqPos kMainChunkSize = 100000

static

Definition at line 71 of file vdbgraphloader_impl.cpp.

Referenced by CVDBGraphDataLoader_Impl::GetChunkOnce(), and CVDBGraphDataLoader_Impl::LoadSplitEntry().

◆ kMainGraphChunkIdAdd

const size_t kMainGraphChunkIdAdd = 2

static

Definition at line 75 of file vdbgraphloader_impl.cpp.

Referenced by CVDBGraphDataLoader_Impl::LoadSplitEntry().

◆ kMainTableChunkIdAdd

const size_t kMainTableChunkIdAdd = 3

static

Definition at line 76 of file vdbgraphloader_impl.cpp.

Referenced by CVDBGraphDataLoader_Impl::LoadSplitEntry().

◆ kMidZoomChunkIdAdd

const size_t kMidZoomChunkIdAdd = 1

static

Definition at line 74 of file vdbgraphloader_impl.cpp.

Referenced by CVDBGraphDataLoader_Impl::LoadSplitEntry().

◆ kMidZoomChunkSize

const TSeqPos kMidZoomChunkSize = 20000*100

static

Definition at line 70 of file vdbgraphloader_impl.cpp.

Referenced by CVDBGraphDataLoader_Impl::GetChunkOnce(), and CVDBGraphDataLoader_Impl::LoadSplitEntry().

◆ kOverviewChunkIdAdd

const size_t kOverviewChunkIdAdd = 0

static

Definition at line 73 of file vdbgraphloader_impl.cpp.

Referenced by CVDBGraphDataLoader_Impl::LoadSplitEntry().

◆ kOverviewChunkSize

const TSeqPos kOverviewChunkSize = 20000*5000

static

Definition at line 69 of file vdbgraphloader_impl.cpp.

Referenced by CVDBGraphDataLoader_Impl::GetChunkOnce(), and CVDBGraphDataLoader_Impl::LoadSplitEntry().

◆ kTSEId

const int kTSEId = 1

static

Definition at line 79 of file vdbgraphloader_impl.cpp.

Referenced by CVDBGraphDataLoader_Impl::GetChunkOnce(), and CVDBGraphDataLoader_Impl::LoadSplitEntry().

Classes

Macros

Functions

Variables

Macro Definition Documentation

◆ MID_ZOOM_NAME_SUFFIX

◆ NCBI_USE_ERRCODE_X

◆ OVERVIEW_NAME_SUFFIX

Function Documentation

◆ GetDebugLevel()

◆ GetDisabledZoom()

◆ GetEnabledMidZoom()

◆ GetEnabledOverview()

◆ GetGCSize()

◆ GetLookupType()

◆ GetMissingGCSize()

◆ GetRetryCountParam()

◆ GetUseTable()

◆ NCBI_DEFINE_ERR_SUBCODE_X()

◆ NCBI_PARAM_DECL() [1/7]

◆ NCBI_PARAM_DECL() [2/7]

◆ NCBI_PARAM_DECL() [3/7]

◆ NCBI_PARAM_DECL() [4/7]

◆ NCBI_PARAM_DECL() [5/7]

◆ NCBI_PARAM_DECL() [6/7]

◆ NCBI_PARAM_DECL() [7/7]

◆ NCBI_PARAM_DEF()

◆ NCBI_PARAM_DEF_EX() [1/6]

◆ NCBI_PARAM_DEF_EX() [2/6]

◆ NCBI_PARAM_DEF_EX() [3/6]

◆ NCBI_PARAM_DEF_EX() [4/6]

◆ NCBI_PARAM_DEF_EX() [5/6]

◆ NCBI_PARAM_DEF_EX() [6/6]

◆ sx_IsNA()

Variable Documentation

◆ kChunkIdMul

◆ kMainChunkSize

◆ kMainGraphChunkIdAdd

◆ kMainTableChunkIdAdd

◆ kMidZoomChunkIdAdd

◆ kMidZoomChunkSize

◆ kOverviewChunkIdAdd

◆ kOverviewChunkSize

◆ kTSEId