reader_pubseq.cpp File Reference

#include <ncbi_pch.hpp>
#include <corelib/ncbi_param.hpp>
#include <objtools/data_loaders/genbank/pubseq/reader_pubseq.hpp>
#include <objtools/data_loaders/genbank/pubseq/reader_pubseq_entry.hpp>
#include <objtools/data_loaders/genbank/pubseq/reader_pubseq_params.h>
#include <objtools/data_loaders/genbank/readers.hpp>
#include <objtools/data_loaders/genbank/impl/request_result.hpp>
#include <objtools/data_loaders/genbank/impl/dispatcher.hpp>
#include <objtools/error_codes.hpp>
#include <objmgr/objmgr_exception.hpp>
#include <objmgr/impl/tse_info.hpp>
#include <objmgr/annot_selector.hpp>
#include <dbapi/driver/types.hpp>
#include <dbapi/driver/exception.hpp>
#include <dbapi/driver/driver_mgr.hpp>
#include <dbapi/driver/drivers.hpp>
#include <dbapi/driver/dbapi_svc_mapper.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <objects/seqset/Seq_entry.hpp>
#include <objects/seqsplit/ID2S_Seq_annot_Info.hpp>
#include <objects/seqsplit/ID2S_Feat_type_Info.hpp>
#include <corelib/ncbicntr.hpp>
#include <corelib/plugin_manager_impl.hpp>
#include <corelib/plugin_manager_store.hpp>
#include <corelib/rwstream.hpp>
#include <serial/objistrasnb.hpp>
#include <serial/objostrasn.hpp>
#include <serial/serial.hpp>
#include <util/compress/zlib.hpp>
#include <corelib/ncbi_cookies.hpp>

Include dependency graph for reader_pubseq.cpp:

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Classes
struct	SPubseqReaderReceiveData
class	CPubseqReaderCF
	Class factory for Pubseq reader. More...

Macros
#define	DEFAULT_DB_SERVER   "PUBSEQ_OS_PUBLIC_GI64"
#define	DEFAULT_DB_USER   "anyone"
#define	DEFAULT_DB_PASSWORD   "allowed"
#define	DEFAULT_DB_DRIVER   "ftds;ctlib"
#define	DEFAULT_NUM_CONN   2
#define	MAX_MT_CONN   5
#define	DEFAULT_ALLOW_GZIP   true
#define	DEFAULT_EXCL_WGS_MASTER   true
#define	NCBI_USE_ERRCODE_X   Objtools_Rd_Pubseq
#define	RPC_GET_ASN   "id_get_asn"
#define	RPC_GET_BLOB_INFO   "id_get_blob_prop"

Enumerations
enum	{ fZipType_gzipped = 2 }

Functions
	NCBI_PARAM_DECL (int, GENBANK, PUBSEQOS_DEBUG)
	NCBI_PARAM_DEF_EX (int, GENBANK, PUBSEQOS_DEBUG, 0, eParam_NoThread, GENBANK_PUBSEQOS_DEBUG)
static int	GetDebugLevel (void)
static void	sx_SetIntId (CDB_RPCCmd &cmd, const char *param, TIntId id)
static TIntId	sx_GetIntId (CDB_Result &dbr, int pos)
void	GenBankReaders_Register_Pubseq (void)
void	NCBI_EntryPoint_ReaderPubseqos (CPluginManager< objects::CReader >::TDriverInfoList &info_list, CPluginManager< objects::CReader >::EEntryPointRequest method)
void	NCBI_EntryPoint_xreader_pubseqos (CPluginManager< objects::CReader >::TDriverInfoList &info_list, CPluginManager< objects::CReader >::EEntryPointRequest method)

Macro Definition Documentation

DEFAULT_ALLOW_GZIP

#define DEFAULT_ALLOW_GZIP   true

Definition at line 74 of file reader_pubseq.cpp.

DEFAULT_DB_DRIVER

#define DEFAULT_DB_DRIVER   "ftds;ctlib"

Definition at line 71 of file reader_pubseq.cpp.

DEFAULT_DB_PASSWORD

#define DEFAULT_DB_PASSWORD   "allowed"

Definition at line 70 of file reader_pubseq.cpp.

DEFAULT_DB_SERVER

#define DEFAULT_DB_SERVER   "PUBSEQ_OS_PUBLIC_GI64"

Definition at line 68 of file reader_pubseq.cpp.

DEFAULT_DB_USER

#define DEFAULT_DB_USER   "anyone"

Definition at line 69 of file reader_pubseq.cpp.

DEFAULT_EXCL_WGS_MASTER

#define DEFAULT_EXCL_WGS_MASTER   true

Definition at line 75 of file reader_pubseq.cpp.

DEFAULT_NUM_CONN

#define DEFAULT_NUM_CONN   2

Definition at line 72 of file reader_pubseq.cpp.

MAX_MT_CONN

#define MAX_MT_CONN   5

Definition at line 73 of file reader_pubseq.cpp.

NCBI_USE_ERRCODE_X

#define NCBI_USE_ERRCODE_X   Objtools_Rd_Pubseq

Definition at line 77 of file reader_pubseq.cpp.

RPC_GET_ASN

#define RPC_GET_ASN   "id_get_asn"

Definition at line 92 of file reader_pubseq.cpp.

RPC_GET_BLOB_INFO

#define RPC_GET_BLOB_INFO   "id_get_blob_prop"

Definition at line 93 of file reader_pubseq.cpp.

Enumeration Type Documentation

anonymous enum

anonymous enum

Enumerator
fZipType_gzipped

Definition at line 95 of file reader_pubseq.cpp.

Function Documentation

GenBankReaders_Register_Pubseq()

void GenBankReaders_Register_Pubseq

(

void

)

Definition at line 1326 of file reader_pubseq.cpp.

References NCBI_EntryPoint_ReaderPubseqos().

Referenced by CDemoApp::Run(), and CDataLoadersUtil::x_SetupGenbankDataLoader().

GetDebugLevel()

static int GetDebugLevel ( void  )

static

Definition at line 86 of file reader_pubseq.cpp.

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

Referenced by CPubseqReader::LoadSeq_idInfo(), and CPubseqReader::x_ConnectAtSlot().

NCBI_EntryPoint_ReaderPubseqos()

void NCBI_EntryPoint_ReaderPubseqos	(	CPluginManager< objects::CReader >::TDriverInfoList &	info_list,
		CPluginManager< objects::CReader >::EEntryPointRequest	method
	)

Definition at line 1368 of file reader_pubseq.cpp.

References CHostEntryPointImpl< TClassFactory >::NCBI_EntryPointImpl().

Referenced by GenBankReaders_Register_Pubseq(), and NCBI_EntryPoint_xreader_pubseqos().

NCBI_EntryPoint_xreader_pubseqos()

void NCBI_EntryPoint_xreader_pubseqos	(	CPluginManager< objects::CReader >::TDriverInfoList &	info_list,
		CPluginManager< objects::CReader >::EEntryPointRequest	method
	)

Definition at line 1377 of file reader_pubseq.cpp.

References NCBI_EntryPoint_ReaderPubseqos().

NCBI_PARAM_DECL()

NCBI_PARAM_DECL	(	int	,
		GENBANK	,
		PUBSEQOS_DEBUG
	)

NCBI_PARAM_DEF_EX()

NCBI_PARAM_DEF_EX	(	int	,
		GENBANK	,
		PUBSEQOS_DEBUG	,
		0	,
		eParam_NoThread	,
		GENBANK_PUBSEQOS_DEBUG
	)

sx_GetIntId()

static TIntId sx_GetIntId ( CDB_Result &  dbr, int  pos  )

static

Definition at line 115 of file reader_pubseq.cpp.

References CDB_Result::GetItem(), CDB_Result::ItemName(), NCBI_THROW_FMT, and CDB_BigInt::Value().

Referenced by CPubseqReader::LoadSeq_idInfo().

sx_SetIntId()

static void sx_SetIntId ( CDB_RPCCmd &  cmd, const char *  param, TIntId  id  )

static

Definition at line 100 of file reader_pubseq.cpp.

References cmd.

Referenced by CPubseqReader::LoadGiHash(), CPubseqReader::LoadGiSeq_ids(), CPubseqReader::LoadSeq_idAccVer(), and CPubseqReader::LoadSeq_idInfo().