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NCBI C++ ToolKit: CPSGS_AsyncResolveBase Class Reference

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#include "async_resolve_base.hpp"
(Private to src/app/pubseq_gateway/server.)

CPSGS_AsyncResolveBase () CPSGS_AsyncResolveBase (shared_ptr< CPSGS_Request > request, shared_ptr< CPSGS_Reply > reply, TContinueResolveCB continue_resolve_cb, TSeqIdResolutionFinishedCB finished_cb, TSeqIdResolutionErrorCB error_cb, TSeqIdResolutionStartProcessingCB start_processing_cb) virtual ~CPSGS_AsyncResolveBase () void Process (int16_t effective_version, int16_t effective_seq_id_type, list< string > &&secondary_id_list, string &&primary_seq_id, bool composed_ok, bool seq_id_resolve, SBioseqResolution &&bioseq_resolution) void x_OnBioseqInfo (vector< CBioseqInfoRecord > &&records) void x_OnBioseqInfoWithoutSeqIdType (vector< CBioseqInfoRecord > &&records) void x_OnBioseqInfoError (CRequestStatus::ECode status, int code, EDiagSev severity, const string &message) void x_OnSi2csiRecord (vector< CSI2CSIRecord > &&records) void x_OnSi2csiError (CRequestStatus::ECode status, int code, EDiagSev severity, const string &message) CPSGS_CassProcessorBase () CPSGS_CassProcessorBase (shared_ptr< CPSGS_Request > request, shared_ptr< CPSGS_Reply > reply, TProcessorPriority priority) virtual ~CPSGS_CassProcessorBase () virtual void Cancel (void) override The infrastructure request to cancel processing. More...
void SignalFinishProcessing (void) void UnlockWaitingProcessor (void) void CallOnData (void) string GetVerboseFetches (void) const void EnforceWait (void) const IPSGS_Processor () virtual ~IPSGS_Processor () virtual bool CanProcess (shared_ptr< CPSGS_Request > request, shared_ptr< CPSGS_Reply > reply) const Tells if processor can process the given request. More...
virtual vector< string > WhatCanProcess (shared_ptr< CPSGS_Request > request, shared_ptr< CPSGS_Reply > reply) const Needs to be implemented only for the ID/get_na requests. More...
virtual IPSGS_Processor * CreateProcessor (shared_ptr< CPSGS_Request > request, shared_ptr< CPSGS_Reply > reply, TProcessorPriority priority) const =0 Create processor to fulfil PSG request using the data source. More...
virtual void Process (void)=0 Main processing function. More...
virtual string GetName (void) const =0 Tells the processor name (used in logging and tracing) More...
virtual string GetGroupName (void) const =0 Tells the processor group name. More...
virtual void ProcessEvent (void) Called when an event happened which may require to have some processing. More...
shared_ptr< CPSGS_Request > GetRequest (void) const Provides the user request. More...
shared_ptr< CPSGS_Reply > GetReply (void) const Provides the reply wrapper. More...
TProcessorPriority GetPriority (void) const Provides the processor priority. More...
void PostponeInvoke (CPSGS_UvLoopBinder::TProcessorCB cb, void *user_data) The provided callback will be called from the libuv loop assigned to the processor. More...
void SetSocketCallback (int fd, CPSGS_SocketIOCallback::EPSGS_Event event, uint64_t timeout_millisec, void *user_data, CPSGS_SocketIOCallback::TEventCB event_cb, CPSGS_SocketIOCallback::TTimeoutCB timeout_cb, CPSGS_SocketIOCallback::TErrorCB error_cb) The provided callbacks will be called from the libuv loop assigned to the processor when the corresponding event appeared on the provided socket. More...
void SetUVThreadId (uv_thread_t uv_thread_id) Saves the libuv worker thread id which runs the processor. More...
uv_thread_t GetUVThreadId (void) const Provides the libuv thread id which runs the processor. More...
bool IsUVThreadAssigned (void) const Tells if a libuv thread id has been assigned to the processor. More...
psg_time_point_t GetProcessInvokeTimestamp (bool &is_valid) const Provides the timestamp of when the Process() method was called. More...
psg_time_point_t GetSignalStartTimestamp (bool &is_valid) const Provides the timestamp of when the processor called SignalStartProcessing() method. More...
psg_time_point_t GetSignalFinishTimestamp (bool &is_valid) const Provides the timestamp of when the processor called SignalFinishProcessing() method. More...
void OnBeforeProcess (void) Called just before the virtual Process() method is called. More...
EPSGS_StartProcessing SignalStartProcessing (void) A processor should call the method when it decides that it successfully started processing the request. More...
void SignalFinishProcessing (void) A processor should call this method when it decides that there is nothing else to be done. More...
EPSGS_SeqIdParsingResult ParseInputSeqId (objects::CSeq_id &seq_id, const string &request_seq_id, int request_seq_id_type, string *err_msg=nullptr) Parse seq-id from a string and type representation. More...
int16_t GetEffectiveVersion (const CTextseq_id *text_seq_id) SPSGS_ResolveRequest::TPSGS_BioseqIncludeData GetBioseqInfoFields (void) bool NonKeyBioseqInfoFieldsRequested (void) bool CanSkipBioseqInfoRetrieval (const CBioseqInfoRecord &bioseq_info_record) SPSGS_RequestBase::EPSGS_AccSubstitutioOption GetAccessionSubstitutionOption (void) EPSGS_AccessionAdjustmentResult AdjustBioseqAccession (SBioseqResolution &bioseq_resolution) void SetupSeqIdToResolve (void) void SetupSeqIdToResolve (const string &seq_id, int16_t seq_id_type) string GetCouldNotResolveMessage (void) const psg_time_point_t GetAsyncResolutionStartTimestamp (void) const void SetAsyncResolutionStartTimestamp (const psg_time_point_t &ts) bool MoveToNextSeqId (void) bool GetSeqIdResolve (void) bool OptimizationPrecondition (const string &primary_id, int16_t effective_seq_id_type) const IPSGS_Processor::EPSGS_Status GetStatus (void) override Tells the processor status (if it has finished or in progress) More...
bool AreAllFinishedRead (void) const bool IsMyNCBIFinished (void) const void UpdateOverallStatus (CRequestStatus::ECode status) bool IsCassandraProcessorEnabled (shared_ptr< CPSGS_Request > request) const void CancelLoaders (void) SCass_BlobId TranslateSatToKeyspace (CBioseqInfoRecord::TSat sat, CBioseqInfoRecord::TSatKey sat_key, const string &seq_id) bool IsTimeoutError (const string &msg) const bool IsTimeoutError (int code) const bool IsError (EDiagSev severity) const CRequestStatus::ECode CountError (CCassFetch *fetch_details, CRequestStatus::ECode status, int code, EDiagSev severity, const string &message, EPSGS_LoggingFlag logging_flag, EPSGS_StatusUpdateFlag status_update_flag) EPSGS_MyNCBILookupResult PopulateMyNCBIUser (TMyNCBIDataCB data_cb, TMyNCBIErrorCB error_cb) void ReportNoWebCubbyUser (void) void ReportExplicitIncludeHUPSetToNo (void) void ReportMyNCBIError (CRequestStatus::ECode status, const string &my_ncbi_message) void ReportMyNCBINotFound (void) void ReportSecureSatUnauthorized (const string &user_name) void ReportFailureToGetCassConnection (const string &message) void ReportFailureToGetCassConnection (void) void CleanupMyNCBICache (void) bool GetEffectiveSeqIdType (const objects::CSeq_id &parsed_seq_id, int request_seq_id_type, int16_t &eff_seq_id_type, bool need_trace) enum EPSGS_Status {
  ePSGS_InProgress , ePSGS_Done , ePSGS_NotFound , ePSGS_Canceled ,
  ePSGS_Timeout , ePSGS_Error , ePSGS_Unauthorized
} The GetStatus() method returns a processor current status. More...
enum EPSGS_StartProcessing { ePSGS_Proceed , ePSGS_Cancel } Tells wether to continue or not after a processor called SignalStartProcessing() method. More...
static string StatusToString (EPSGS_Status status) Converts the processor status to a string for tracing and logging purposes. More...
static string StatusToProgressMessage (EPSGS_Status status) Converts the processor status to a string for protocol message. More...
enum EPSGS_MyNCBILookupResult {
  ePSGS_IncludeHUPSetToNo , ePSGS_FoundInOKCache , ePSGS_FoundInErrorCache , ePSGS_FoundInNotFoundCache ,
  ePSGS_CookieNotPresent , ePSGS_RequestInitiated , ePSGS_AddedToWaitlist
}

Definition at line 87 of file async_resolve_base.hpp.

◆ EPSGS_ResolveStage Enumerator eInit ePrimaryBioseq eSecondarySi2csi eSecondaryAsIs eFinished ePostSi2Csi

Definition at line 111 of file async_resolve_base.hpp.

◆ CPSGS_AsyncResolveBase() [1/2] ◆ CPSGS_AsyncResolveBase() [2/2] ◆ ~CPSGS_AsyncResolveBase() ◆ AdjustBioseqAccession()

Definition at line 434 of file async_resolve_base.cpp.

References SBioseqResolution::AdjustAccession(), CanSkipBioseqInfoRetrieval(), CSeq_id_Base::e_Gi, CSeq_id_Base::e_Pdb, CSeq_id_Base::e_Pir, CSeq_id_Base::e_Prf, ePSGS_BioseqCache, SPSGS_RequestBase::ePSGS_DefaultAccSubstitution, SPSGS_RequestBase::ePSGS_LimitedAccSubstitution, ePSGS_LogicError, SPSGS_RequestBase::ePSGS_NeverAccSubstitute, ePSGS_NotRequired, ePSGS_SeqIdsEmpty, GetAccessionSubstitutionOption(), SBioseqResolution::GetBioseqInfo(), CBioseqInfoRecord::GetSeqIdType(), CBioseqInfoRecord::GetVersion(), SBioseqResolution::m_AdjustmentError, IPSGS_Processor::m_Reply, IPSGS_Processor::m_Request, SBioseqResolution::m_ResolutionResult, PSG_WARNING, and dtl::version.

Referenced by x_OnBioseqInfo(), CPSGS_ResolveBase::x_ResolveSeqId(), CPSGS_AccessionVersionHistoryProcessor::x_SendBioseqInfo(), CPSGS_AnnotProcessor::x_SendBioseqInfo(), CPSGS_GetProcessor::x_SendBioseqInfo(), and CPSGS_ResolveProcessor::x_SendBioseqInfo().

◆ CanSkipBioseqInfoRetrieval()

Definition at line 378 of file async_resolve_base.cpp.

References CSeq_id_Base::e_Gi, SPSGS_RequestBase::ePSGS_LimitedAccSubstitution, SPSGS_RequestBase::ePSGS_NeverAccSubstitute, CPSGS_Request::ePSGS_ResolveRequest, SPSGS_ResolveRequest::fPSGS_Gi, CBioseqInfoRecord::GetSeqIdType(), CBioseqInfoRecord::GetVersion(), IPSGS_Processor::m_Request, and NonKeyBioseqInfoFieldsRequested().

Referenced by AdjustBioseqAccession(), CPSGS_ResolveBase::x_OnSeqIdResolveFinished(), x_OnSi2csiRecord(), and CPSGS_ResolveBase::x_ResolveSeqId().

◆ GetAccessionSubstitutionOption() ◆ GetAsyncResolutionStartTimestamp() psg_time_point_t CPSGS_AsyncResolveBase::GetAsyncResolutionStartTimestamp ( void ) const inlineprotected ◆ GetBioseqInfoFields() ◆ GetCouldNotResolveMessage() string CPSGS_AsyncResolveBase::GetCouldNotResolveMessage ( void ) const protected

Definition at line 1137 of file async_resolve_base.cpp.

References m_SeqIdsToResolve, msg(), and SanitizeInputValue().

Referenced by CPSGS_ResolveBase::x_OnAsyncBioseqInfoResolveError(), x_OnBioseqInfo(), x_OnBioseqInfoError(), x_OnBioseqInfoWithoutSeqIdType(), x_OnSeqIdAsyncResolutionFinished(), CPSGS_ResolveBase::x_OnSeqIdResolveFinished(), x_OnSi2csiError(), CPSGS_ResolveBase::x_OptimizedNotFound(), and CPSGS_ResolveBase::x_ResolveSeqId().

◆ GetEffectiveVersion() ◆ GetSeqIdResolve() bool CPSGS_AsyncResolveBase::GetSeqIdResolve ( void ) protected ◆ MoveToNextSeqId() bool CPSGS_AsyncResolveBase::MoveToNextSeqId ( void ) protected

Definition at line 1115 of file async_resolve_base.cpp.

References m_CurrentSeqIdToResolve, IPSGS_Processor::m_Reply, IPSGS_Processor::m_Request, and m_SeqIdsToResolve.

◆ NonKeyBioseqInfoFieldsRequested() bool CPSGS_AsyncResolveBase::NonKeyBioseqInfoFieldsRequested ( void ) protected ◆ OptimizationPrecondition() bool CPSGS_AsyncResolveBase::OptimizationPrecondition ( const string & primary_id, int16_t effective_seq_id_type ) const protected

Definition at line 330 of file async_resolve_base.cpp.

References CSeq_id_Base::e_Ddbj, CSeq_id_Base::e_Embl, CSeq_id_Base::e_Genbank, CSeq_id_Base::e_Gpipe, CSeq_id_Base::e_Other, CSeq_id_Base::e_Pdb, CSeq_id_Base::e_Pir, CSeq_id_Base::e_Prf, CSeq_id_Base::e_Swissprot, CSeq_id_Base::e_Tpd, CSeq_id_Base::e_Tpe, and CSeq_id_Base::e_Tpg.

Referenced by CPSGS_ResolveBase::x_OptimizedResolutionInCache(), x_Process(), and CPSGS_ResolveBase::x_ResolveSeqId().

◆ Process()

Definition at line 139 of file async_resolve_base.cpp.

References eInit, m_AsyncCassResolutionStart, m_BioseqResolution, m_ComposedOk, m_CurrentFetch, m_EffectiveSeqIdType, m_EffectiveVersion, m_NoSeqIdTypeFetch, m_PrimarySeqId, m_ResolveStage, m_SecondaryIdList, m_SeqIdResolve, and x_Process().

◆ SetAsyncResolutionStartTimestamp() ◆ SetupSeqIdToResolve() [1/2] void CPSGS_AsyncResolveBase::SetupSeqIdToResolve ( const string & seq_id, int16_t seq_id_type ) protected ◆ SetupSeqIdToResolve() [2/2] void CPSGS_AsyncResolveBase::SetupSeqIdToResolve ( void ) protected

Definition at line 192 of file async_resolve_base.cpp.

References CPSGS_Request::ePSGS_AnnotationRequest, m_CurrentSeqIdToResolve, IPSGS_Processor::m_Reply, IPSGS_Processor::m_Request, SPSGS_AnnotRequest::m_SeqIds, m_SeqIdsToResolve, PSGSortSeqIds(), x_GetRequestSeqId(), x_GetRequestSeqIdType(), and x_GetSeqIdsToResolveList().

Referenced by CPSGS_ResolveBase::ResolveInputSeqId(), and CPSGS_ResolveBase::ResolveTestInputSeqId().

◆ x_GetRequestSeqId() string CPSGS_AsyncResolveBase::x_GetRequestSeqId ( void ) private ◆ x_GetRequestSeqIdType() int16_t CPSGS_AsyncResolveBase::x_GetRequestSeqIdType ( void ) private ◆ x_GetSeqIdsToResolveList() string CPSGS_AsyncResolveBase::x_GetSeqIdsToResolveList ( void ) const private ◆ x_OnBioseqInfo() void CPSGS_AsyncResolveBase::x_OnBioseqInfo ( vector< CBioseqInfoRecord > && records )

Definition at line 732 of file async_resolve_base.cpp.

References AdjustBioseqAccession(), CPSGSResolveErrors::AppendError(), CCassBlobWaiter::ClearError(), CRequestStatus::e502_BadGateway, eDiag_Error, eLookupCassBioseqInfo, eOpStatusFound, eOpStatusNotFound, ePostSi2Csi, ePSGS_BioseqDB, ePSGS_BioseqInfoAccessionAdjustmentError, CPSGSCounters::ePSGS_BioseqInfoFoundMany, CPSGSCounters::ePSGS_BioseqInfoFoundOne, CPSGSCounters::ePSGS_BioseqInfoNotFound, ePSGS_LogicError, ePSGS_NeedLogging, ePSGS_NoBioseqInfoForGiError, ePSGS_SeqIdsEmpty, SPSGS_ResolveRequest::fPSGS_AllBioseqFields, CBioseqInfoRecord::GetAccession(), SBioseqResolution::GetBioseqInfo(), CPSGSResolveErrors::GetCombinedErrorCode(), CPSGSResolveErrors::GetCombinedErrorMessage(), GetCouldNotResolveMessage(), CPubseqGatewayApp::GetInstance(), CCassFetch::GetLoader(), IsINSDCSeqIdType(), SBioseqResolution::m_AdjustmentError, m_BioseqInfoRequestedAccession, m_BioseqInfoRequestedGI, m_BioseqInfoRequestedSeqIdType, m_BioseqInfoRequestedVersion, m_BioseqInfoStart, m_BioseqResolution, m_ContinueResolveCB, m_CurrentFetch, m_ErrorCB, IPSGS_Processor::m_Reply, IPSGS_Processor::m_Request, SBioseqResolution::m_ResolutionResult, m_ResolveErrors, m_ResolveStage, m_SeqIdsToResolve, MoveToNextSeqId(), msg(), SelectBioseqInfoRecord(), SBioseqResolution::SetBioseqInfo(), CCassFetch::SetReadFinished(), ToJsonString(), x_OnSeqIdAsyncResolutionFinished(), x_PreparePrimaryBioseqInfoQuery(), x_Process(), and x_SignalStartProcessing().

Referenced by x_PreparePrimaryBioseqInfoQuery().

◆ x_OnBioseqInfoError()

Definition at line 990 of file async_resolve_base.cpp.

References CPSGSResolveErrors::AppendError(), CCassBlobWaiter::ClearError(), CPSGSCounters::ePSGS_BioseqInfoError, ePSGS_NeedLogging, CPSGSResolveErrors::GetCombinedErrorCode(), CPSGSResolveErrors::GetCombinedErrorMessage(), GetCouldNotResolveMessage(), CPubseqGatewayApp::GetCounters(), CPubseqGatewayApp::GetInstance(), CCassFetch::GetLoader(), CPSGSCounters::Increment(), CPSGS_CassProcessorBase::IsTimeoutError(), m_ContinueResolveCB, m_CurrentFetch, m_ErrorCB, m_NoSeqIdTypeFetch, m_ResolveErrors, m_SeqIdsToResolve, MoveToNextSeqId(), and CCassFetch::SetReadFinished().

Referenced by x_PreparePrimaryBioseqInfoQuery().

◆ x_OnBioseqInfoWithoutSeqIdType() void CPSGS_AsyncResolveBase::x_OnBioseqInfoWithoutSeqIdType ( vector< CBioseqInfoRecord > && records )

Definition at line 873 of file async_resolve_base.cpp.

References CPSGSResolveErrors::AppendError(), CCassBlobWaiter::ClearError(), DecideINSDC(), CRequestStatus::e200_Ok, CRequestStatus::e404_NotFound, CRequestStatus::e500_InternalServerError, CRequestStatus::e502_BadGateway, eDiag_Error, eLookupCassBioseqInfo, eOpStatusFound, eOpStatusNotFound, ePostSi2Csi, ePSGS_BioseqDB, CPSGSCounters::ePSGS_BioseqInfoFoundMany, CPSGSCounters::ePSGS_BioseqInfoFoundOne, CPSGSCounters::ePSGS_BioseqInfoNotFound, ePSGS_NeedLogging, ePSGS_NoBioseqInfoForGiError, ePSGS_ServerLogicError, SPSGS_ResolveRequest::fPSGS_AllBioseqFields, CBioseqInfoRecord::GetAccession(), SBioseqResolution::GetBioseqInfo(), CPSGSResolveErrors::GetCombinedErrorCode(), CPSGSResolveErrors::GetCombinedErrorMessage(), GetCouldNotResolveMessage(), CPubseqGatewayApp::GetInstance(), CCassFetch::GetLoader(), m_BioseqInfoRequestedVersion, m_BioseqInfoStart, m_BioseqResolution, m_ContinueResolveCB, m_ErrorCB, m_NoSeqIdTypeFetch, IPSGS_Processor::m_Reply, IPSGS_Processor::m_Request, SBioseqResolution::m_ResolutionResult, m_ResolveErrors, m_ResolveStage, m_SeqIdsToResolve, MoveToNextSeqId(), msg(), SBioseqResolution::SetBioseqInfo(), CCassFetch::SetReadFinished(), ToJsonString(), x_OnSeqIdAsyncResolutionFinished(), x_Process(), and x_SignalStartProcessing().

Referenced by x_PreparePrimaryBioseqInfoQuery().

◆ x_OnSeqIdAsyncResolutionFinished() void CPSGS_AsyncResolveBase::x_OnSeqIdAsyncResolutionFinished ( SBioseqResolution && async_bioseq_resolution ) private

Definition at line 1159 of file async_resolve_base.cpp.

References CPSGSResolveErrors::AppendError(), CRequestStatus::e404_NotFound, eDiag_Error, CPSGSCounters::ePSGS_InputSeqIdNotResolved, ePSGS_SkipLogging, ePSGS_UnresolvedSeqId, CPSGSResolveErrors::GetCombinedErrorMessage(), GetCouldNotResolveMessage(), CPubseqGatewayApp::GetInstance(), CPSGSResolveErrors::HasErrors(), m_ContinueResolveCB, m_ErrorCB, m_FinishedCB, m_ResolveErrors, m_SeqIdsToResolve, MoveToNextSeqId(), msg(), and x_SignalStartProcessing().

Referenced by x_OnBioseqInfo(), x_OnBioseqInfoWithoutSeqIdType(), x_OnSi2csiRecord(), and x_Process().

◆ x_OnSi2csiError()

Definition at line 1088 of file async_resolve_base.cpp.

References CPSGSResolveErrors::AppendError(), CCassBlobWaiter::ClearError(), ePSGS_NeedLogging, CPSGSCounters::ePSGS_Si2csiError, CPSGSResolveErrors::GetCombinedErrorCode(), CPSGSResolveErrors::GetCombinedErrorMessage(), GetCouldNotResolveMessage(), CPubseqGatewayApp::GetCounters(), CPubseqGatewayApp::GetInstance(), CCassFetch::GetLoader(), CPSGSCounters::Increment(), CPSGS_CassProcessorBase::IsTimeoutError(), m_ContinueResolveCB, m_CurrentFetch, m_ErrorCB, m_ResolveErrors, m_SeqIdsToResolve, MoveToNextSeqId(), and CCassFetch::SetReadFinished().

Referenced by x_PrepareSi2csiQuery().

◆ x_OnSi2csiRecord() void CPSGS_AsyncResolveBase::x_OnSi2csiRecord ( vector< CSI2CSIRecord > && records )

Definition at line 1023 of file async_resolve_base.cpp.

References CanSkipBioseqInfoRetrieval(), CCassBlobWaiter::ClearError(), eLookupCassSi2csi, eOpStatusFound, eOpStatusNotFound, ePostSi2Csi, ePSGS_Si2csiDB, CPSGSCounters::ePSGS_Si2csiFoundMany, CPSGSCounters::ePSGS_Si2csiFoundOne, CPSGSCounters::ePSGS_Si2csiNotFound, GetAccession(), SBioseqResolution::GetBioseqInfo(), CPubseqGatewayApp::GetInstance(), CCassFetch::GetLoader(), m_BioseqResolution, m_CurrentFetch, IPSGS_Processor::m_Reply, IPSGS_Processor::m_Request, SBioseqResolution::m_ResolutionResult, m_ResolveStage, m_Si2csiStart, msg(), CBioseqInfoRecord::SetAccession(), SBioseqResolution::SetBioseqInfo(), CBioseqInfoRecord::SetGI(), CCassFetch::SetReadFinished(), CBioseqInfoRecord::SetSeqIdType(), CBioseqInfoRecord::SetVersion(), ToJsonString(), x_OnSeqIdAsyncResolutionFinished(), x_Process(), and x_SignalStartProcessing().

Referenced by x_PrepareSi2csiQuery().

◆ x_PreparePrimaryBioseqInfoQuery()

Definition at line 590 of file async_resolve_base.cpp.

References CPubseqGatewayApp::GetBioseqKeyspace(), CPubseqGatewayApp::GetInstance(), m_BioseqInfoRequestedAccession, m_BioseqInfoRequestedGI, m_BioseqInfoRequestedSeqIdType, m_BioseqInfoRequestedVersion, m_BioseqInfoStart, m_BioseqResolution, SBioseqResolution::m_CassQueryCount, m_CurrentFetch, CPSGS_CassProcessorBase::m_FetchDetails, m_NoSeqIdTypeFetch, IPSGS_Processor::m_Reply, IPSGS_Processor::m_Request, CBioseqInfoFetchRequest::SetAccession(), CCassBioseqInfoTaskFetch::SetConsumeCallback(), CCassBioseqInfoTaskFetch::SetDataReadyCB(), CCassBlobWaiter::SetErrorCB(), CBioseqInfoFetchRequest::SetGI(), CBioseqInfoFetchRequest::SetSeqIdType(), CBioseqInfoFetchRequest::SetVersion(), StripTrailingVerticalBars(), ToJsonString(), dtl::version, CCassBlobWaiter::Wait(), x_OnBioseqInfo(), x_OnBioseqInfoError(), and x_OnBioseqInfoWithoutSeqIdType().

Referenced by x_OnBioseqInfo(), and x_Process().

◆ x_PrepareSecondaryAsIsSi2csiQuery() void CPSGS_AsyncResolveBase::x_PrepareSecondaryAsIsSi2csiQuery ( void ) private ◆ x_PrepareSecondarySi2csiQuery() void CPSGS_AsyncResolveBase::x_PrepareSecondarySi2csiQuery ( void ) private ◆ x_PrepareSi2csiQuery() void CPSGS_AsyncResolveBase::x_PrepareSi2csiQuery ( const string & secondary_id, int16_t effective_seq_id_type ) private

Definition at line 662 of file async_resolve_base.cpp.

References CPubseqGatewayApp::GetBioseqKeyspace(), CPubseqGatewayApp::GetInstance(), m_BioseqResolution, SBioseqResolution::m_CassQueryCount, m_CurrentFetch, CPSGS_CassProcessorBase::m_FetchDetails, IPSGS_Processor::m_Reply, IPSGS_Processor::m_Request, m_Si2csiStart, CCassSI2CSITaskFetch::SetConsumeCallback(), CCassSI2CSITaskFetch::SetDataReadyCB(), CCassBlobWaiter::SetErrorCB(), CSi2CsiFetchRequest::SetSecSeqId(), CSi2CsiFetchRequest::SetSecSeqIdType(), StripTrailingVerticalBars(), ToJsonString(), CCassBlobWaiter::Wait(), x_OnSi2csiError(), and x_OnSi2csiRecord().

Referenced by x_PrepareSecondaryAsIsSi2csiQuery(), and x_PrepareSecondarySi2csiQuery().

◆ x_Process() void CPSGS_AsyncResolveBase::x_Process ( void ) private

Definition at line 506 of file async_resolve_base.cpp.

References eFinished, eInit, ePostSi2Csi, ePrimaryBioseq, ePSGS_NotResolved, eSecondaryAsIs, eSecondarySi2csi, CBioseqInfoRecord::GetAccession(), SBioseqResolution::GetBioseqInfo(), CBioseqInfoRecord::GetGI(), CBioseqInfoRecord::GetSeqIdType(), CBioseqInfoRecord::GetVersion(), m_BioseqResolution, m_ComposedOk, m_EffectiveSeqIdType, m_EffectiveVersion, m_PrimarySeqId, SBioseqResolution::m_ResolutionResult, m_ResolveStage, m_SecondaryIdList, m_SecondaryIndex, m_SeqIdResolve, OptimizationPrecondition(), CBioseqInfoRecord::Reset(), x_OnSeqIdAsyncResolutionFinished(), x_PreparePrimaryBioseqInfoQuery(), x_PrepareSecondaryAsIsSi2csiQuery(), and x_PrepareSecondarySi2csiQuery().

Referenced by Process(), x_OnBioseqInfo(), x_OnBioseqInfoWithoutSeqIdType(), x_OnSi2csiRecord(), and x_PrepareSecondaryAsIsSi2csiQuery().

◆ x_SignalStartProcessing() void CPSGS_AsyncResolveBase::x_SignalStartProcessing ( void ) private ◆ m_AsyncCassResolutionStart ◆ m_BioseqInfoRequestedAccession ◆ m_BioseqInfoRequestedGI ◆ m_BioseqInfoRequestedSeqIdType ◆ m_BioseqInfoRequestedVersion ◆ m_BioseqInfoStart ◆ m_BioseqResolution ◆ m_ComposedOk bool CPSGS_AsyncResolveBase::m_ComposedOk protected ◆ m_ContinueResolveCB ◆ m_CurrentFetch CCassFetch* CPSGS_AsyncResolveBase::m_CurrentFetch protected ◆ m_CurrentSeqIdToResolve list<SPSGSeqId>::const_iterator CPSGS_AsyncResolveBase::m_CurrentSeqIdToResolve protected ◆ m_EffectiveSeqIdType int16_t CPSGS_AsyncResolveBase::m_EffectiveSeqIdType protected ◆ m_EffectiveVersion int16_t CPSGS_AsyncResolveBase::m_EffectiveVersion protected ◆ m_ErrorCB ◆ m_FinishedCB ◆ m_NoSeqIdTypeFetch CCassFetch* CPSGS_AsyncResolveBase::m_NoSeqIdTypeFetch protected ◆ m_PrimarySeqId string CPSGS_AsyncResolveBase::m_PrimarySeqId protected ◆ m_ResolveErrors ◆ m_ResolveStage ◆ m_SecondaryIdList list<string> CPSGS_AsyncResolveBase::m_SecondaryIdList protected ◆ m_SecondaryIndex size_t CPSGS_AsyncResolveBase::m_SecondaryIndex protected ◆ m_SeqIdResolve bool CPSGS_AsyncResolveBase::m_SeqIdResolve protected ◆ m_SeqIdsToResolve list<SPSGSeqId> CPSGS_AsyncResolveBase::m_SeqIdsToResolve protected

Definition at line 220 of file async_resolve_base.hpp.

Referenced by GetCouldNotResolveMessage(), MoveToNextSeqId(), SetupSeqIdToResolve(), x_GetSeqIdsToResolveList(), CPSGS_ResolveBase::x_OnAsyncBioseqInfoResolveError(), x_OnBioseqInfo(), x_OnBioseqInfoError(), x_OnBioseqInfoWithoutSeqIdType(), x_OnSeqIdAsyncResolutionFinished(), CPSGS_ResolveBase::x_OnSeqIdResolveFinished(), x_OnSi2csiError(), CPSGS_ResolveBase::x_OptimizedNotFound(), and CPSGS_ResolveBase::x_ResolveSeqId().

◆ m_Si2csiStart ◆ m_StartProcessingCalled bool CPSGS_AsyncResolveBase::m_StartProcessingCalled protected ◆ m_StartProcessingCB

The documentation for this class was generated from the following files:

src/app/pubseq_gateway/server/async_resolve_base.hpp
src/app/pubseq_gateway/server/async_resolve_base.cpp

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