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NCBI C++ ToolKit: src/sra/data_loaders/wgs/wgsloader_impl.cpp File Reference

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  NCBI_DEFINE_ERR_SUBCODE_X (23)     NCBI_PARAM_DECL (int, WGS_LOADER, DEBUG)     NCBI_PARAM_DEF_EX (int, WGS_LOADER, DEBUG, 0, eParam_NoThread, WGS_LOADER_DEBUG)   static int  GetDebugLevel (void)     NCBI_PARAM_DECL (bool, WGS_LOADER, MASTER_DESCR)     NCBI_PARAM_DEF (bool, WGS_LOADER, MASTER_DESCR, true)   static bool  GetMasterDescrParam (void)     NCBI_PARAM_DECL (size_t, WGS_LOADER, GC_SIZE)     NCBI_PARAM_DEF (size_t, WGS_LOADER, GC_SIZE, 100)   static size_t  GetGCSizeParam (void)     NCBI_PARAM_DECL (string, WGS_LOADER, VOL_PATH)     NCBI_PARAM_DEF (string, WGS_LOADER, VOL_PATH, "")   static string  GetWGSVolPath (void)     NCBI_PARAM_DECL (bool, WGS_LOADER, RESOLVE_GIS)     NCBI_PARAM_DEF (bool, WGS_LOADER, RESOLVE_GIS, true)   static bool  GetResolveGIsParam (void)     NCBI_PARAM_DECL (bool, WGS_LOADER, RESOLVE_PROT_ACCS)     NCBI_PARAM_DEF (bool, WGS_LOADER, RESOLVE_PROT_ACCS, true)   static bool  GetResolveProtAccsParam (void)     NCBI_PARAM_DECL (bool, WGS_LOADER, SPLIT_QUALITY_GRAPH)     NCBI_PARAM_DEF (bool, WGS_LOADER, SPLIT_QUALITY_GRAPH, true)   static bool  GetSplitQualityGraphParam (void)     NCBI_PARAM_DECL (bool, WGS_LOADER, SPLIT_SEQUENCE)     NCBI_PARAM_DEF (bool, WGS_LOADER, SPLIT_SEQUENCE, true)   static bool  GetSplitSequenceParam (void)     NCBI_PARAM_DECL (bool, WGS_LOADER, SPLIT_FEATURES)     NCBI_PARAM_DEF (bool, WGS_LOADER, SPLIT_FEATURES, true)   static bool  GetSplitFeaturesParam (void)     NCBI_PARAM_DECL (bool, WGS_LOADER, KEEP_REPLACED)     NCBI_PARAM_DEF (bool, WGS_LOADER, KEEP_REPLACED, true)     NCBI_PARAM_DECL (bool, WGS_LOADER, KEEP_MIGRATED)     NCBI_PARAM_DEF (bool, WGS_LOADER, KEEP_MIGRATED, false)   static bool  GetKeepReplacedParam (void)   static bool  GetKeepMigratedParam (void)     NCBI_PARAM_DECL (unsigned, WGS_LOADER, INDEX_UPDATE_TIME)     NCBI_PARAM_DEF (unsigned, WGS_LOADER, INDEX_UPDATE_TIME, 600)   static unsigned  GetIndexUpdateTimeParam (void)     NCBI_PARAM_DECL (unsigned, WGS_LOADER, RETRY_COUNT)     NCBI_PARAM_DEF (unsigned, WGS_LOADER, RETRY_COUNT, 3)   static unsigned  GetRetryCountParam (void)     NCBI_PARAM_DECL (unsigned, WGS_LOADER, FILE_REOPEN_TIME)     NCBI_PARAM_DEF (unsigned, WGS_LOADER, FILE_REOPEN_TIME, 60 *60)   static unsigned  GetFileReopenTimeParam (void)     NCBI_PARAM_DECL (unsigned, WGS_LOADER, FILE_RECHECK_TIME)     NCBI_PARAM_DEF (unsigned, WGS_LOADER, FILE_RECHECK_TIME, 5 *60)   static unsigned  GetFileRecheckTimeParam (void)   void  sx_Update (CWGSResolver &resolver)     NCBI_PARAM_DECL (bool, WGS, RESOLVER_GENBANK)     NCBI_PARAM_DEF (bool, WGS, RESOLVER_GENBANK, true)   static bool  s_ValidateAcc (const CConstRef< CSeq_id > &real_seq_id, const CTextseq_id &asked_text_id)   static CBioseq_Handle::TBioseqStateFlags  s_GBStateToOM (NCBI_gb_state gb_state)   ◆ NCBI_USE_ERRCODE_X ◆ GetDebugLevel()

Definition at line 94 of file wgsloader_impl.cpp.

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

Referenced by CWGSDataLoader_Impl::GetFileInfoByGi(), CWGSDataLoader_Impl::GetFileInfoByProtAcc(), CWGSDataLoader_Impl::GetWGSFile(), CWGSFileInfo::LoadBlob(), CWGSFileInfo::LoadChunk(), CWGSFileInfo::Open(), sx_Update(), CWGSFileInfo::SAccFileInfo::ValidateAcc(), CWGSFileInfo::SAccFileInfo::ValidateGi(), CWGSDataLoader_Impl::x_GetFileInfo(), and CWGSFileInfo::x_Initialize().

◆ GetFileRecheckTimeParam() static unsigned GetFileRecheckTimeParam ( void  ) static ◆ GetFileReopenTimeParam() static unsigned GetFileReopenTimeParam ( void  ) static ◆ GetGCSizeParam() static size_t GetGCSizeParam ( void  ) static ◆ GetIndexUpdateTimeParam() static unsigned GetIndexUpdateTimeParam ( void  ) static ◆ GetKeepMigratedParam() ◆ GetKeepReplacedParam() ◆ GetMasterDescrParam() ◆ GetResolveGIsParam() ◆ GetResolveProtAccsParam() ◆ GetRetryCountParam() static unsigned GetRetryCountParam ( void  ) static ◆ GetSplitFeaturesParam() ◆ GetSplitQualityGraphParam() ◆ GetSplitSequenceParam() ◆ GetWGSVolPath() ◆ NCBI_DEFINE_ERR_SUBCODE_X() NCBI_DEFINE_ERR_SUBCODE_X ( 23  ) ◆ NCBI_PARAM_DECL() [1/16] NCBI_PARAM_DECL ( bool  , WGS  , RESOLVER_GENBANK    ) ◆ NCBI_PARAM_DECL() [2/16] NCBI_PARAM_DECL ( bool  , WGS_LOADER  , KEEP_MIGRATED    ) ◆ NCBI_PARAM_DECL() [3/16] NCBI_PARAM_DECL ( bool  , WGS_LOADER  , KEEP_REPLACED    ) ◆ NCBI_PARAM_DECL() [4/16] NCBI_PARAM_DECL ( bool  , WGS_LOADER  , MASTER_DESCR    ) ◆ NCBI_PARAM_DECL() [5/16] NCBI_PARAM_DECL ( bool  , WGS_LOADER  , RESOLVE_GIS    ) ◆ NCBI_PARAM_DECL() [6/16] NCBI_PARAM_DECL ( bool  , WGS_LOADER  , RESOLVE_PROT_ACCS    ) ◆ NCBI_PARAM_DECL() [7/16] NCBI_PARAM_DECL ( bool  , WGS_LOADER  , SPLIT_FEATURES    ) ◆ NCBI_PARAM_DECL() [8/16] NCBI_PARAM_DECL ( bool  , WGS_LOADER  , SPLIT_QUALITY_GRAPH    ) ◆ NCBI_PARAM_DECL() [9/16] NCBI_PARAM_DECL ( bool  , WGS_LOADER  , SPLIT_SEQUENCE    ) ◆ NCBI_PARAM_DECL() [10/16] NCBI_PARAM_DECL ( int  , WGS_LOADER  , DEBUG    ) ◆ NCBI_PARAM_DECL() [11/16] NCBI_PARAM_DECL ( size_t  , WGS_LOADER  , GC_SIZE    ) ◆ NCBI_PARAM_DECL() [12/16] NCBI_PARAM_DECL ( string  , WGS_LOADER  , VOL_PATH    ) ◆ NCBI_PARAM_DECL() [13/16] NCBI_PARAM_DECL ( unsigned  , WGS_LOADER  , FILE_RECHECK_TIME    ) ◆ NCBI_PARAM_DECL() [14/16] NCBI_PARAM_DECL ( unsigned  , WGS_LOADER  , FILE_REOPEN_TIME    ) ◆ NCBI_PARAM_DECL() [15/16] NCBI_PARAM_DECL ( unsigned  , WGS_LOADER  , INDEX_UPDATE_TIME    ) ◆ NCBI_PARAM_DECL() [16/16] NCBI_PARAM_DECL ( unsigned  , WGS_LOADER  , RETRY_COUNT    ) ◆ NCBI_PARAM_DEF() [1/15] NCBI_PARAM_DEF ( bool  , WGS  , RESOLVER_GENBANK  , true    ) ◆ NCBI_PARAM_DEF() [2/15] NCBI_PARAM_DEF ( bool  , WGS_LOADER  , KEEP_MIGRATED  , false    ) ◆ NCBI_PARAM_DEF() [3/15] NCBI_PARAM_DEF ( bool  , WGS_LOADER  , KEEP_REPLACED  , true    ) ◆ NCBI_PARAM_DEF() [4/15] NCBI_PARAM_DEF ( bool  , WGS_LOADER  , MASTER_DESCR  , true    ) ◆ NCBI_PARAM_DEF() [5/15] NCBI_PARAM_DEF ( bool  , WGS_LOADER  , RESOLVE_GIS  , true    ) ◆ NCBI_PARAM_DEF() [6/15] NCBI_PARAM_DEF ( bool  , WGS_LOADER  , RESOLVE_PROT_ACCS  , true    ) ◆ NCBI_PARAM_DEF() [7/15] NCBI_PARAM_DEF ( bool  , WGS_LOADER  , SPLIT_FEATURES  , true    ) ◆ NCBI_PARAM_DEF() [8/15] NCBI_PARAM_DEF ( bool  , WGS_LOADER  , SPLIT_QUALITY_GRAPH  , true    ) ◆ NCBI_PARAM_DEF() [9/15] NCBI_PARAM_DEF ( bool  , WGS_LOADER  , SPLIT_SEQUENCE  , true    ) ◆ NCBI_PARAM_DEF() [10/15] NCBI_PARAM_DEF ( size_t  , WGS_LOADER  , GC_SIZE  , 100    ) ◆ NCBI_PARAM_DEF() [11/15] NCBI_PARAM_DEF ( string  , WGS_LOADER  , VOL_PATH  , ""    ) ◆ NCBI_PARAM_DEF() [12/15] NCBI_PARAM_DEF ( unsigned  , WGS_LOADER  , FILE_RECHECK_TIME  , 5 *  60  ) ◆ NCBI_PARAM_DEF() [13/15] NCBI_PARAM_DEF ( unsigned  , WGS_LOADER  , FILE_REOPEN_TIME  , 60 *  60  ) ◆ NCBI_PARAM_DEF() [14/15] NCBI_PARAM_DEF ( unsigned  , WGS_LOADER  , INDEX_UPDATE_TIME  , 600    ) ◆ NCBI_PARAM_DEF() [15/15] NCBI_PARAM_DEF ( unsigned  , WGS_LOADER  , RETRY_COUNT  , 3    ) ◆ NCBI_PARAM_DEF_EX() ◆ s_GBStateToOM() ◆ s_ValidateAcc() ◆ sx_Update() ◆ BEGIN_LOCAL_NAMESPACE ◆ END_LOCAL_NAMESPACE ◆ kMaxWGSPrefixLetters const size_t kMaxWGSPrefixLetters = 6 static ◆ kMaxWGSProteinAccLen const size_t kMaxWGSProteinAccLen = 3+7 static ◆ kMinWGSPrefixLetters const size_t kMinWGSPrefixLetters = 4 static ◆ kWGSPrefixDigits const size_t kWGSPrefixDigits = 2 static

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