snploader_impl.cpp File Reference

#include <ncbi_pch.hpp>
#include <corelib/ncbistd.hpp>
#include <objects/general/general__.hpp>
#include <objects/seqloc/seqloc__.hpp>
#include <objects/seq/seq__.hpp>
#include <objects/seqres/seqres__.hpp>
#include <objects/seqsplit/ID2S_Split_Info.hpp>
#include <objects/seqsplit/ID2S_Chunk.hpp>
#include <objmgr/annot_selector.hpp>
#include <objmgr/impl/data_source.hpp>
#include <objmgr/impl/tse_loadlock.hpp>
#include <objmgr/impl/tse_chunk_info.hpp>
#include <objmgr/impl/tse_split_info.hpp>
#include <objmgr/impl/split_parser.hpp>
#include <objmgr/data_loader_factory.hpp>
#include <corelib/plugin_manager_impl.hpp>
#include <corelib/plugin_manager_store.hpp>
#include <serial/objistr.hpp>
#include <serial/serial.hpp>
#include <sra/error_codes.hpp>
#include <sra/readers/ncbi_traces_path.hpp>
#include <sra/data_loaders/snp/snploader.hpp>
#include <sra/data_loaders/snp/impl/snploader_impl.hpp>
#include <util/sequtil/sequtil_manip.hpp>
#include <objects/dbsnp/primary_track/snpptis.hpp>
#include <algorithm>
#include <cmath>

Include dependency graph for snploader_impl.cpp:

Go to the source code of this file.

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Macros
#define	NCBI_USE_ERRCODE_X   SNPLoader

Enumerations
enum	{   eDebug_open = 1 , eDebug_open_time = 2 , eDebug_load = 3 , eDebug_load_time = 4 ,   eDebug_resolve = 5 , eDebug_data = 9 }

Functions
	NCBI_DEFINE_ERR_SUBCODE_X (16)
	NCBI_PARAM_DECL (int, SNP_LOADER, DEBUG)
	NCBI_PARAM_DEF_EX (int, SNP_LOADER, DEBUG, 0, eParam_NoThread, SNP_LOADER_DEBUG)
static int	GetDebugLevel (void)
	NCBI_PARAM_DECL (size_t, SNP_LOADER, GC_SIZE)
	NCBI_PARAM_DEF_EX (size_t, SNP_LOADER, GC_SIZE, 10, eParam_NoThread, SNP_LOADER_GC_SIZE)
static size_t	GetGCSize (void)
	NCBI_PARAM_DECL (unsigned, SNP_LOADER, RETRY_COUNT)
	NCBI_PARAM_DEF (unsigned, SNP_LOADER, RETRY_COUNT, 3)
static unsigned	GetRetryCountParam (void)
	NCBI_PARAM_DECL (unsigned, SNP_LOADER, FILE_REOPEN_TIME)
	NCBI_PARAM_DEF (unsigned, SNP_LOADER, FILE_REOPEN_TIME, 60 *60)
static unsigned	GetFileReopenTimeParam (void)
	NCBI_PARAM_DECL (unsigned, SNP_LOADER, FILE_RECHECK_TIME)
	NCBI_PARAM_DEF (unsigned, SNP_LOADER, FILE_RECHECK_TIME, 5 *60)
static unsigned	GetFileRecheckTimeParam (void)
	NCBI_PARAM_DECL (bool, SNP_LOADER, SPLIT)
	NCBI_PARAM_DEF_EX (bool, SNP_LOADER, SPLIT, true, eParam_NoThread, SNP_LOADER_SPLIT)
static bool	IsSplitEnabled (void)
static size_t	sx_ExtractFilterIndex (string &s)
static string	sx_AddFilterIndex (const string &s, size_t filter_index)
static string	s_GetAccVer (const CSeq_id_Handle &id)

Variables
const int	kSNPSatBase = 2000
const int	kSNPSatPrimary = 3000
const int	kSNPSubSatGraph = 1000000000
const int	kNAVersionMin = 1
const int	kNAVersionMax = 99
const int	kSeqIndexCount = 1000000
const int	kFilterIndexCount = 2000
const int	kFilterIndexMaxLength = 4
static const char	kFileEnd [] = "|||"
static const char	kFilterPrefixChar = '#'

Macro Definition Documentation

NCBI_USE_ERRCODE_X

#define NCBI_USE_ERRCODE_X   SNPLoader

Definition at line 69 of file snploader_impl.cpp.

Enumeration Type Documentation

anonymous enum

anonymous enum

Enumerator
eDebug_open
eDebug_open_time
eDebug_load
eDebug_load_time
eDebug_resolve
eDebug_data

Definition at line 80 of file snploader_impl.cpp.

Function Documentation

GetDebugLevel()

static int GetDebugLevel ( void  )

static

Definition at line 89 of file snploader_impl.cpp.

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

Referenced by CSNPDataLoader_Impl::GetChunkOnce(), CSNPDataLoader_Impl::GetOrphanAnnotRecordsOnce(), CSNPFileInfo::InitializeDb(), CSNPSeqInfo::LoadAnnotBlob(), CSNPSeqInfo::LoadAnnotChunk(), CSNPDataLoader_Impl::LoadBlob(), and CSNPDataLoader_Impl::x_GetFileInfo().

GetFileRecheckTimeParam()

static unsigned GetFileRecheckTimeParam ( void  )

static

Definition at line 133 of file snploader_impl.cpp.

References NCBI_PARAM_TYPE, and rapidjson::value.

GetFileReopenTimeParam()

static unsigned GetFileReopenTimeParam ( void  )

static

Definition at line 121 of file snploader_impl.cpp.

References NCBI_PARAM_TYPE, and rapidjson::value.

GetGCSize()

static size_t GetGCSize ( void  )

static

Definition at line 100 of file snploader_impl.cpp.

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

Referenced by CSNPDataLoader_Impl::GetOrphanAnnotRecordsOnce().

GetRetryCountParam()

static unsigned GetRetryCountParam ( void  )

static

Definition at line 110 of file snploader_impl.cpp.

References NCBI_PARAM_TYPE, and rapidjson::value.

IsSplitEnabled()

static bool IsSplitEnabled ( void  )

static

Definition at line 158 of file snploader_impl.cpp.

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

Referenced by CSNPSeqInfo::LoadAnnotBlob().

NCBI_DEFINE_ERR_SUBCODE_X()

NCBI_DEFINE_ERR_SUBCODE_X

(

16

)

NCBI_PARAM_DECL() [1/6]

NCBI_PARAM_DECL	(	bool	,
		SNP_LOADER	,
		SPLIT
	)

NCBI_PARAM_DECL() [2/6]

NCBI_PARAM_DECL	(	int	,
		SNP_LOADER	,
		DEBUG
	)

NCBI_PARAM_DECL() [3/6]

NCBI_PARAM_DECL	(	size_t	,
		SNP_LOADER	,
		GC_SIZE
	)

NCBI_PARAM_DECL() [4/6]

NCBI_PARAM_DECL	(	unsigned	,
		SNP_LOADER	,
		FILE_RECHECK_TIME
	)

NCBI_PARAM_DECL() [5/6]

NCBI_PARAM_DECL	(	unsigned	,
		SNP_LOADER	,
		FILE_REOPEN_TIME
	)

NCBI_PARAM_DECL() [6/6]

NCBI_PARAM_DECL	(	unsigned	,
		SNP_LOADER	,
		RETRY_COUNT
	)

NCBI_PARAM_DEF() [1/3]

NCBI_PARAM_DEF	(	unsigned	,
		SNP_LOADER	,
		FILE_RECHECK_TIME	,
		5 *	60
	)

NCBI_PARAM_DEF() [2/3]

NCBI_PARAM_DEF	(	unsigned	,
		SNP_LOADER	,
		FILE_REOPEN_TIME	,
		60 *	60
	)

NCBI_PARAM_DEF() [3/3]

NCBI_PARAM_DEF	(	unsigned	,
		SNP_LOADER	,
		RETRY_COUNT	,
		3
	)

NCBI_PARAM_DEF_EX() [1/3]

NCBI_PARAM_DEF_EX	(	bool	,
		SNP_LOADER	,
		SPLIT	,
		true	,
		eParam_NoThread	,
		SNP_LOADER_SPLIT
	)

NCBI_PARAM_DEF_EX() [2/3]

NCBI_PARAM_DEF_EX	(	int	,
		SNP_LOADER	,
		DEBUG	,
		0	,
		eParam_NoThread	,
		SNP_LOADER_DEBUG
	)

NCBI_PARAM_DEF_EX() [3/3]

NCBI_PARAM_DEF_EX	(	size_t	,
		SNP_LOADER	,
		GC_SIZE	,
		10	,
		eParam_NoThread	,
		SNP_LOADER_GC_SIZE
	)

s_GetAccVer()

static string s_GetAccVer ( const CSeq_id_Handle &  id )

static

Definition at line 825 of file snploader_impl.cpp.

References GetSeqId(), NStr::NumericToString(), and string.

Referenced by CSNPDataLoader_Impl::GetOrphanAnnotRecordsOnce().

sx_AddFilterIndex()

static string sx_AddFilterIndex ( const string &  s, size_t  filter_index  )

static

Definition at line 456 of file snploader_impl.cpp.

References kFilterPrefixChar, and str().

sx_ExtractFilterIndex()

static size_t sx_ExtractFilterIndex ( string &  s )

static

Definition at line 431 of file snploader_impl.cpp.

References isdigit(), CSNPBlobId::IsValidFilterIndex(), kFilterIndexMaxLength, kFilterPrefixChar, and ncbi::grid::netcache::search::fields::size.

Referenced by CSNPDataLoader_Impl::AddFixedFileOnce(), CSNPDataLoader_Impl::GetOrphanAnnotRecordsOnce(), and CSNPFileInfo::x_Initialize().

Variable Documentation

kFileEnd

const char kFileEnd[] = "|||"

static

Definition at line 426 of file snploader_impl.cpp.

kFilterIndexCount

const int kFilterIndexCount = 2000

Definition at line 185 of file snploader_impl.cpp.

kFilterIndexMaxLength

const int kFilterIndexMaxLength = 4

Definition at line 186 of file snploader_impl.cpp.

Referenced by sx_ExtractFilterIndex().

kFilterPrefixChar

const char kFilterPrefixChar = '#'

static

Definition at line 427 of file snploader_impl.cpp.

Referenced by sx_AddFilterIndex(), and sx_ExtractFilterIndex().

kNAVersionMax

const int kNAVersionMax = 99

Definition at line 183 of file snploader_impl.cpp.

kNAVersionMin

const int kNAVersionMin = 1

Definition at line 182 of file snploader_impl.cpp.

kSeqIndexCount

const int kSeqIndexCount = 1000000

Definition at line 184 of file snploader_impl.cpp.

kSNPSatBase

const int kSNPSatBase = 2000

Definition at line 179 of file snploader_impl.cpp.

kSNPSatPrimary

const int kSNPSatPrimary = 3000

Definition at line 180 of file snploader_impl.cpp.

kSNPSubSatGraph

const int kSNPSubSatGraph = 1000000000

Definition at line 181 of file snploader_impl.cpp.