#include <ncbi_pch.hpp>
#include "wgs_processor.hpp"
#include "pubseq_gateway.hpp"
#include "pubseq_gateway_convert_utils.hpp"
#include "pubseq_gateway_logging.hpp"
#include "id2info.hpp"
#include "cass_processor_base.hpp"
#include "psgs_thread_pool.hpp"
#include <sra/readers/sra/wgsread.hpp>
#include <sra/readers/sra/wgsresolver.hpp>
#include <corelib/rwstream.hpp>
#include <serial/serial.hpp>
#include <serial/objostrasnb.hpp>
#include <util/compress/zlib.hpp>
#include <util/thread_pool.hpp>
#include <objects/general/general__.hpp>
#include <objects/seqfeat/SeqFeatData.hpp>
#include <objects/seqset/seqset__.hpp>
#include <objects/id2/ID2_Blob_Id.hpp>
#include <objects/id2/ID2_Blob_State.hpp>
#include <objects/id2/ID2_Reply_Data.hpp>
#include <objtools/pubseq_gateway/impl/cassandra/bioseq_info/record.hpp>

Include dependency graph for wgs_processor.cpp:

Go to the SVN repository for this file.

Classes
class	COSSWriter

class	CWGSThreadPoolTask_ResolveSeqId

class	CWGSThreadPoolTask_GetBlobBySeqId

class	CWGSThreadPoolTask_GetBlobByBlobId

class	CWGSThreadPoolTask_GetChunk

Macros
#define	PARAM_VDB_CACHE_SIZE "vdb_cache_size"

#define	PARAM_INDEX_UPDATE_TIME "index_update_time"

#define	PARAM_FILE_REOPEN_TIME "file_reopen_time"

#define	PARAM_FILE_RECHECK_TIME "file_recheck_time"

#define	PARAM_COMPRESS_DATA "compress_data"

#define	DEFAULT_VDB_CACHE_SIZE 100

#define	DEFAULT_INDEX_UPDATE_TIME 600

#define	DEFAULT_FILE_REOPEN_TIME 3600

#define	DEFAULT_FILE_RECHECK_TIME 600

#define	DEFAULT_COMPRESS_DATA SWGSProcessor_Config::eCompressData_some

Functions
	BEGIN_NAMESPACE (psg)

	BEGIN_NAMESPACE (wgs)

	USING_SCOPE (objects)

	NCBI_PARAM_DECL (int, WGS_PROCESSOR, ERROR_RATE)

	NCBI_PARAM_DEF (int, WGS_PROCESSOR, ERROR_RATE, 0)

static bool	s_SimulateError ()

static void	s_FormatBlobId (ostream &s, const CID2_Blob_Id &blob_id)

static void	s_OnResolvedSeqId (void *data)

static void	s_OnGotBlobBySeqId (void *data)

static void	s_OnGotBlobByBlobId (void *data)

static void	s_OnGotChunk (void *data)

void	s_SetBlobVersion (CBlobRecord &blob_props, const CID2_Blob_Id &blob_id)

void	s_SetBlobState (CBlobRecord &blob_props, int id2_blob_state)

void	s_SetBlobDataProps (CBlobRecord &blob_props, const CID2_Reply_Data &data)

	END_NAMESPACE (wgs)

	END_NAMESPACE (psg)

Variables
	BEGIN_NCBI_NAMESPACE

static const string	kWGSProcessorName = "WGS"

static const string	kWGSProcessorGroupName = "WGS"

static const string	kWGSProcessorSection = "WGS_PROCESSOR"

static const string	kParamMaxConn = "maxconn"

static const int	kDefaultMaxConn = 64

	BEGIN_LOCAL_NAMESPACE

	END_LOCAL_NAMESPACE

static const char	kSubSatSeparator = '/'

	END_NCBI_NAMESPACE

Macro Definition Documentation

◆ DEFAULT_COMPRESS_DATA

#define DEFAULT_COMPRESS_DATA SWGSProcessor_Config::eCompressData_some

Definition at line 219 of file wgs_processor.cpp.

◆ DEFAULT_FILE_RECHECK_TIME

#define DEFAULT_FILE_RECHECK_TIME 600

Definition at line 218 of file wgs_processor.cpp.

◆ DEFAULT_FILE_REOPEN_TIME

#define DEFAULT_FILE_REOPEN_TIME 3600

Definition at line 217 of file wgs_processor.cpp.

◆ DEFAULT_INDEX_UPDATE_TIME

#define DEFAULT_INDEX_UPDATE_TIME 600

Definition at line 216 of file wgs_processor.cpp.

◆ DEFAULT_VDB_CACHE_SIZE

#define DEFAULT_VDB_CACHE_SIZE 100

Definition at line 215 of file wgs_processor.cpp.

◆ PARAM_COMPRESS_DATA

#define PARAM_COMPRESS_DATA "compress_data"

Definition at line 213 of file wgs_processor.cpp.

◆ PARAM_FILE_RECHECK_TIME

#define PARAM_FILE_RECHECK_TIME "file_recheck_time"

Definition at line 212 of file wgs_processor.cpp.

◆ PARAM_FILE_REOPEN_TIME

#define PARAM_FILE_REOPEN_TIME "file_reopen_time"

Definition at line 211 of file wgs_processor.cpp.

◆ PARAM_INDEX_UPDATE_TIME

#define PARAM_INDEX_UPDATE_TIME "index_update_time"

Definition at line 210 of file wgs_processor.cpp.

◆ PARAM_VDB_CACHE_SIZE

#define PARAM_VDB_CACHE_SIZE "vdb_cache_size"

Definition at line 209 of file wgs_processor.cpp.

Function Documentation

◆ BEGIN_NAMESPACE() [1/2]

BEGIN_NAMESPACE ( psg )

◆ BEGIN_NAMESPACE() [2/2]

BEGIN_NAMESPACE ( wgs )

◆ END_NAMESPACE() [1/2]

END_NAMESPACE ( psg )

◆ END_NAMESPACE() [2/2]

END_NAMESPACE ( wgs )

◆ NCBI_PARAM_DECL()

NCBI_PARAM_DECL	(	int	,
		WGS_PROCESSOR	,
		ERROR_RATE
	)

◆ NCBI_PARAM_DEF()

NCBI_PARAM_DEF	(	int	,
		WGS_PROCESSOR	,
		ERROR_RATE	,
		0
	)

◆ s_FormatBlobId()

static void s_FormatBlobId	(	ostream &	s,
		const CID2_Blob_Id &	blob_id
	)

static

Definition at line 196 of file wgs_processor.cpp.

References CID2_Blob_Id_Base::GetSat(), CID2_Blob_Id_Base::GetSat_key(), CID2_Blob_Id_Base::GetSub_sat(), and kSubSatSeparator.

Referenced by CPSGS_WGSProcessor::GetPSGId2Info().

◆ s_OnGotBlobByBlobId()

static void s_OnGotBlobByBlobId ( void * data )

static

Definition at line 602 of file wgs_processor.cpp.

References data.

Referenced by CPSGS_WGSProcessor::GetBlobByBlobId().

◆ s_OnGotBlobBySeqId()

static void s_OnGotBlobBySeqId ( void * data )

static

Definition at line 486 of file wgs_processor.cpp.

References data.

Referenced by CPSGS_WGSProcessor::GetBlobBySeqId().

◆ s_OnGotChunk()

static void s_OnGotChunk ( void * data )

static

Definition at line 689 of file wgs_processor.cpp.

References data.

Referenced by CPSGS_WGSProcessor::GetChunk().

◆ s_OnResolvedSeqId()

static void s_OnResolvedSeqId ( void * data )

static

Definition at line 392 of file wgs_processor.cpp.

References data.

Referenced by CPSGS_WGSProcessor::ResolveSeqId().

◆ s_SetBlobDataProps()

void s_SetBlobDataProps	(	CBlobRecord &	blob_props,
		const CID2_Reply_Data &	data
	)

Definition at line 819 of file wgs_processor.cpp.

References data, CBlobRecord::SetGzip(), and CBlobRecord::SetNChunks().

Referenced by CPSGS_WGSProcessor::x_SendChunk(), CPSGS_WGSProcessor::x_SendMainEntry(), and CPSGS_WGSProcessor::x_SendSplitInfo().

◆ s_SetBlobState()

void s_SetBlobState	(	CBlobRecord &	blob_props,
		int	id2_blob_state
	)

Definition at line 804 of file wgs_processor.cpp.

References eID2_Blob_State_dead, eID2_Blob_State_suppressed, eID2_Blob_State_suppressed_temp, eID2_Blob_State_withdrawn, CBlobRecord::SetDead(), CBlobRecord::SetSuppress(), and CBlobRecord::SetWithdrawn().

Referenced by CPSGS_WGSProcessor::x_SendForbidden(), CPSGS_WGSProcessor::x_SendMainEntry(), and CPSGS_WGSProcessor::x_SendSplitInfo().

◆ s_SetBlobVersion()

void s_SetBlobVersion	(	CBlobRecord &	blob_props,
		const CID2_Blob_Id &	blob_id
	)

Definition at line 796 of file wgs_processor.cpp.

References CID2_Blob_Id_Base::GetVersion(), CID2_Blob_Id_Base::IsSetVersion(), and CBlobRecord::SetModified().

Referenced by CPSGS_WGSProcessor::x_SendForbidden(), CPSGS_WGSProcessor::x_SendMainEntry(), and CPSGS_WGSProcessor::x_SendSplitInfo().

◆ s_SimulateError()

static bool s_SimulateError ( )

static

Definition at line 180 of file wgs_processor.cpp.

References NCBI_PARAM_TYPE.

Referenced by CPSGS_WGSProcessor::OnGotBlobByBlobId(), CPSGS_WGSProcessor::OnGotBlobBySeqId(), CPSGS_WGSProcessor::OnGotChunk(), and CPSGS_WGSProcessor::OnResolvedSeqId().

◆ USING_SCOPE()

USING_SCOPE ( objects )

Variable Documentation

◆ BEGIN_LOCAL_NAMESPACE

BEGIN_LOCAL_NAMESPACE

Definition at line 76 of file wgs_processor.cpp.

◆ BEGIN_NCBI_NAMESPACE

BEGIN_NCBI_NAMESPACE

Definition at line 58 of file wgs_processor.cpp.

◆ END_LOCAL_NAMESPACE

END_LOCAL_NAMESPACE

Definition at line 174 of file wgs_processor.cpp.

◆ END_NCBI_NAMESPACE

END_NCBI_NAMESPACE

Definition at line 1240 of file wgs_processor.cpp.

◆ kDefaultMaxConn

const int kDefaultMaxConn = 64

static

Definition at line 69 of file wgs_processor.cpp.

Referenced by CPSGS_WGSProcessor::x_LoadConfig().

◆ kParamMaxConn

const string kParamMaxConn = "maxconn"

static

Definition at line 68 of file wgs_processor.cpp.

Referenced by CPSGS_WGSProcessor::x_LoadConfig().

◆ kSubSatSeparator

const char kSubSatSeparator = '/'

static

Definition at line 194 of file wgs_processor.cpp.

Referenced by s_FormatBlobId().

◆ kWGSProcessorGroupName

const string kWGSProcessorGroupName = "WGS"

static

Definition at line 65 of file wgs_processor.cpp.

Referenced by CPSGS_WGSProcessor::GetGroupName().

◆ kWGSProcessorName

const string kWGSProcessorName = "WGS"

static

Definition at line 64 of file wgs_processor.cpp.

◆ kWGSProcessorSection

const string kWGSProcessorSection = "WGS_PROCESSOR"

static

Definition at line 66 of file wgs_processor.cpp.

Referenced by CPSGS_WGSProcessor::x_LoadConfig().

Classes

Macros

Functions

Variables

Macro Definition Documentation

◆ DEFAULT_COMPRESS_DATA

◆ DEFAULT_FILE_RECHECK_TIME

◆ DEFAULT_FILE_REOPEN_TIME

◆ DEFAULT_INDEX_UPDATE_TIME

◆ DEFAULT_VDB_CACHE_SIZE

◆ PARAM_COMPRESS_DATA

◆ PARAM_FILE_RECHECK_TIME

◆ PARAM_FILE_REOPEN_TIME

◆ PARAM_INDEX_UPDATE_TIME

◆ PARAM_VDB_CACHE_SIZE

Function Documentation

◆ BEGIN_NAMESPACE() [1/2]

◆ BEGIN_NAMESPACE() [2/2]

◆ END_NAMESPACE() [1/2]

◆ END_NAMESPACE() [2/2]

◆ NCBI_PARAM_DECL()

◆ NCBI_PARAM_DEF()

◆ s_FormatBlobId()

◆ s_OnGotBlobByBlobId()

◆ s_OnGotBlobBySeqId()

◆ s_OnGotChunk()

◆ s_OnResolvedSeqId()

◆ s_SetBlobDataProps()

◆ s_SetBlobState()

◆ s_SetBlobVersion()

◆ s_SimulateError()

◆ USING_SCOPE()

Variable Documentation

◆ BEGIN_LOCAL_NAMESPACE

◆ BEGIN_NCBI_NAMESPACE

◆ END_LOCAL_NAMESPACE

◆ END_NCBI_NAMESPACE

◆ kDefaultMaxConn

◆ kParamMaxConn

◆ kSubSatSeparator

◆ kWGSProcessorGroupName

◆ kWGSProcessorName

◆ kWGSProcessorSection