NCBI C++ ToolKit
Classes | Macros | Functions | Variables
wgs_processor.cpp File Reference
#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 source code of this file.

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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  ,
 
)

◆ s_FormatBlobId()

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

◆ 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 
)

◆ s_SetBlobState()

void s_SetBlobState ( CBlobRecord blob_props,
int  id2_blob_state 
)

◆ s_SetBlobVersion()

void s_SetBlobVersion ( CBlobRecord blob_props,
const CID2_Blob_Id blob_id 
)

◆ s_SimulateError()

static bool s_SimulateError ( )
static

◆ 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

◆ kWGSProcessorSection

const string kWGSProcessorSection = "WGS_PROCESSOR"
static

Definition at line 66 of file wgs_processor.cpp.

Referenced by CPSGS_WGSProcessor::x_LoadConfig().

Modified on Sun Jul 21 04:16:13 2024 by modify_doxy.py rev. 669887