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NCBI C++ ToolKit: CPSGS_ResolveBase Class Reference
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#include "resolve_base.hpp"
(Private to src/app/pubseq_gateway/server.)
CPSGS_ResolveBase () CPSGS_ResolveBase (shared_ptr< CPSGS_Request > request, shared_ptr< CPSGS_Reply > reply, TSeqIdResolutionFinishedCB finished_cb, TSeqIdResolutionErrorCB error_cb, TSeqIdResolutionStartProcessingCB resolution_start_processing_cb) virtual ~CPSGS_ResolveBase () SBioseqResolution ResolveTestInputSeqId (void) 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...
CPSGS_AsyncBioseqInfoBase () CPSGS_AsyncBioseqInfoBase (shared_ptr< CPSGS_Request > request, shared_ptr< CPSGS_Reply > reply, TSeqIdResolutionFinishedCB finished_cb, TSeqIdResolutionErrorCB error_cb) virtual ~CPSGS_AsyncBioseqInfoBase () void ResolveInputSeqId (void) void ResolveInputSeqId (const string &seq_id, int16_t seq_id_type) 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) void MakeRequest (SBioseqResolution &&bioseq_resolution) SPSGS_RequestBase::EPSGS_CacheAndDbUse x_GetRequestUseCache (void) bool x_ComposeOSLT (CSeq_id &parsed_seq_id, int16_t &effective_seq_id_type, list< string > &secondary_id_list, string &primary_id) EPSGS_CacheLookupResult x_ResolvePrimaryOSLTInCache (const string &primary_id, int16_t effective_version, int16_t effective_seq_id_type, SBioseqResolution &bioseq_resolution) EPSGS_CacheLookupResult x_ResolveSecondaryOSLTInCache (const string &secondary_id, int16_t effective_seq_id_type, SBioseqResolution &bioseq_resolution) EPSGS_CacheLookupResult x_ResolveAsIsInCache (SBioseqResolution &bioseq_resolution) void x_OptimizedResolutionInCache (CSeq_id &parsed_seq_id, const string &primary_id, int16_t effective_seq_id_type, SBioseqResolution &bioseq_resolution) void x_ResolveViaComposeOSLTInCache (CSeq_id &parsed_seq_id, int16_t effective_seq_id_type, const list< string > &secondary_id_list, const string &primary_id, SBioseqResolution &bioseq_resolution) void x_ResolveSeqId (void) void x_OnResolutionGoodData (void) void x_OnSeqIdResolveError (CRequestStatus::ECode status, int code, EDiagSev severity, const string &message, EPSGS_LoggingFlag loging_flag=ePSGS_NeedLogging) void x_OnAsyncBioseqInfoResolveError (CRequestStatus::ECode status, int code, EDiagSev severity, const string &message, EPSGS_LoggingFlag loging_flag=ePSGS_NeedLogging) void x_OnSeqIdResolveFinished (SBioseqResolution &&bioseq_resolution) void x_RegisterSuccessTiming (const SBioseqResolution &bioseq_resolution) void x_OptimizedNotFound (const string &err_msg) 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
} TContinueResolveCB m_ContinueResolveCB TSeqIdResolutionFinishedCB m_FinishedCB TSeqIdResolutionErrorCB m_ErrorCB TSeqIdResolutionStartProcessingCB m_StartProcessingCB EPSGS_ResolveStage m_ResolveStage bool m_ComposedOk bool m_SeqIdResolve string m_PrimarySeqId int16_t m_EffectiveVersion int16_t m_EffectiveSeqIdType size_t m_SecondaryIndex list< string > m_SecondaryIdList SBioseqResolution m_BioseqResolution CCassFetch * m_CurrentFetch CCassFetch * m_NoSeqIdTypeFetch CBioseqInfoRecord::TAccession m_BioseqInfoRequestedAccession CBioseqInfoRecord::TVersion m_BioseqInfoRequestedVersion CBioseqInfoRecord::TSeqIdType m_BioseqInfoRequestedSeqIdType CBioseqInfoRecord::TGI m_BioseqInfoRequestedGI psg_time_point_t m_BioseqInfoStart psg_time_point_t m_Si2csiStart psg_time_point_t m_AsyncCassResolutionStart bool m_StartProcessingCalled list< SPSGSeqId > m_SeqIdsToResolve list< SPSGSeqId >::const_iterator m_CurrentSeqIdToResolve CPSGSResolveErrors m_ResolveErrors list< unique_ptr< CCassFetch > > m_FetchDetails bool m_Canceled bool m_Unlocked CRequestStatus::ECode m_Status optional< string > m_UserName shared_ptr< CPSG_MyNCBIRequest_WhoAmI > m_WhoAmIRequest optional< string > m_MyNCBICookie shared_ptr< CPSGS_Request > m_Request shared_ptr< CPSGS_Reply > m_Reply TProcessorPriority m_Priority bool m_FinishSignalled uv_thread_t m_UVThreadId
Definition at line 56 of file resolve_base.hpp.
◆ CPSGS_ResolveBase() [1/2] ◆ CPSGS_ResolveBase() [2/2] ◆ ~CPSGS_ResolveBase() CPSGS_ResolveBase::~CPSGS_ResolveBase ( ) virtual
Definition at line 85 of file resolve_base.cpp.
◆ ResolveInputSeqId() [1/2] ◆ ResolveInputSeqId() [2/2] void CPSGS_ResolveBase::ResolveInputSeqId ( void ) protected ◆ ResolveTestInputSeqId()
Definition at line 557 of file resolve_base.cpp.
References ePSGS_ParsedOK, SResolveInputSeqIdError::HasError(), SBioseqResolution::IsValid(), CPSGS_AsyncResolveBase::m_CurrentSeqIdToResolve, SBioseqResolution::m_Error, SResolveInputSeqIdError::m_ErrorMessage, IPSGS_Processor::ParseInputSeqId(), CPSGS_AsyncResolveBase::SetupSeqIdToResolve(), x_ComposeOSLT(), x_ResolveAsIsInCache(), and x_ResolveViaComposeOSLTInCache().
◆ x_ComposeOSLT() bool CPSGS_ResolveBase::x_ComposeOSLT ( CSeq_id & parsed_seq_id, int16_t & effective_seq_id_type, list< string > & secondary_id_list, string & primary_id ) private ◆ x_GetRequestUseCache() ◆ x_OnAsyncBioseqInfoResolveError() ◆ x_OnResolutionGoodData() void CPSGS_ResolveBase::x_OnResolutionGoodData ( void ) private ◆ x_OnSeqIdResolveError()
Definition at line 602 of file resolve_base.cpp.
References CRequestStatus::e404_NotFound, eOpStatusNotFound, eResolutionCass, eResolutionError, eResolutionLmdb, eResolutionNotFound, CPSGS_AsyncResolveBase::GetAsyncResolutionStartTimestamp(), CPubseqGatewayApp::GetInstance(), m_AsyncStarted, m_FinalErrorCB, and IPSGS_Processor::m_Request.
Referenced by x_OnAsyncBioseqInfoResolveError(), x_OnSeqIdResolveFinished(), x_OptimizedNotFound(), and x_ResolveSeqId().
◆ x_OnSeqIdResolveFinished() void CPSGS_ResolveBase::x_OnSeqIdResolveFinished ( SBioseqResolution && bioseq_resolution ) private
Definition at line 656 of file resolve_base.cpp.
References CPSGSResolveErrors::AppendError(), CPSGS_AsyncResolveBase::CanSkipBioseqInfoRetrieval(), CRequestStatus::e502_BadGateway, eDiag_Error, ePSGS_BioseqCache, ePSGS_CacheHit, SPSGS_RequestBase::ePSGS_CacheOnly, ePSGS_NoBioseqInfo, ePSGS_Si2csiCache, ePSGS_Si2csiDB, CPSGSResolveErrors::GetCombinedErrorCode(), CPSGSResolveErrors::GetCombinedErrorMessage(), CPSGS_AsyncResolveBase::GetCouldNotResolveMessage(), CPSGCache::LookupBioseqInfo(), m_AsyncStarted, CPSGS_AsyncResolveBase::m_CurrentSeqIdToResolve, m_FinalFinishedCB, IPSGS_Processor::m_Reply, IPSGS_Processor::m_Request, CPSGS_AsyncResolveBase::m_ResolveErrors, CPSGS_AsyncResolveBase::m_SeqIdsToResolve, CPSGS_AsyncBioseqInfoBase::MakeRequest(), CPSGS_AsyncResolveBase::MoveToNextSeqId(), CPSGS_AsyncResolveBase::SetAsyncResolutionStartTimestamp(), x_GetRequestUseCache(), x_OnResolutionGoodData(), x_OnSeqIdResolveError(), x_RegisterSuccessTiming(), and x_ResolveSeqId().
Referenced by x_ResolveSeqId().
◆ x_OptimizedNotFound() void CPSGS_ResolveBase::x_OptimizedNotFound ( const string & err_msg ) private
Definition at line 530 of file resolve_base.cpp.
References CPSGSResolveErrors::AppendError(), CRequestStatus::e404_NotFound, eDiag_Error, CPSGSCounters::ePSGS_InputSeqIdNotResolved, ePSGS_SkipLogging, ePSGS_UnresolvedSeqId, CPSGSResolveErrors::GetCombinedErrorCode(), CPSGSResolveErrors::GetCombinedErrorMessage(), CPSGS_AsyncResolveBase::GetCouldNotResolveMessage(), CPubseqGatewayApp::GetInstance(), IPSGS_Processor::m_Reply, IPSGS_Processor::m_Request, CPSGS_AsyncResolveBase::m_ResolveErrors, CPSGS_AsyncResolveBase::m_SeqIdsToResolve, and x_OnSeqIdResolveError().
Referenced by x_ResolveSeqId().
◆ x_OptimizedResolutionInCache() ◆ x_RegisterSuccessTiming() ◆ x_ResolveAsIsInCache()
Definition at line 222 of file resolve_base.cpp.
References CRequestStatus::e500_InternalServerError, ePSGS_CacheFailure, CPSGS_AsyncResolveBase::m_CurrentSeqIdToResolve, SBioseqResolution::m_Error, SResolveInputSeqIdError::m_ErrorCode, SResolveInputSeqIdError::m_ErrorMessage, SBioseqResolution::Reset(), NStr::ToUpper(), and x_ResolveSecondaryOSLTInCache().
Referenced by ResolveTestInputSeqId(), x_ResolveSeqId(), and x_ResolveViaComposeOSLTInCache().
◆ x_ResolvePrimaryOSLTInCache()
Definition at line 162 of file resolve_base.cpp.
References ePSGS_BioseqCache, ePSGS_CacheHit, ePSGS_CacheNotHit, CPSGCache::LookupBioseqInfo(), IPSGS_Processor::m_Reply, IPSGS_Processor::m_Request, SBioseqResolution::m_ResolutionResult, SBioseqResolution::Reset(), CBioseqInfoRecord::SetAccession(), SBioseqResolution::SetBioseqInfo(), CBioseqInfoRecord::SetSeqIdType(), and CBioseqInfoRecord::SetVersion().
Referenced by x_OptimizedResolutionInCache(), and x_ResolveViaComposeOSLTInCache().
◆ x_ResolveSecondaryOSLTInCache()
Definition at line 194 of file resolve_base.cpp.
References ePSGS_CacheFailure, ePSGS_CacheHit, ePSGS_CacheNotHit, ePSGS_Si2csiCache, CPSGCache::LookupSi2csi(), IPSGS_Processor::m_Reply, IPSGS_Processor::m_Request, SBioseqResolution::m_ResolutionResult, SBioseqResolution::Reset(), CBioseqInfoRecord::SetAccession(), SBioseqResolution::SetBioseqInfo(), and CBioseqInfoRecord::SetSeqIdType().
Referenced by x_ResolveAsIsInCache(), and x_ResolveViaComposeOSLTInCache().
◆ x_ResolveSeqId() void CPSGS_ResolveBase::x_ResolveSeqId ( void ) private
Definition at line 326 of file resolve_base.cpp.
References CPSGS_AsyncResolveBase::AdjustBioseqAccession(), CPSGSResolveErrors::AppendError(), CPSGS_AsyncResolveBase::CanSkipBioseqInfoRetrieval(), CRequestStatus::e404_NotFound, eDiag_Error, ePSGS_BioseqCache, ePSGS_CacheHit, SPSGS_RequestBase::ePSGS_CacheOnly, SPSGS_RequestBase::ePSGS_DbOnly, CPSGSCounters::ePSGS_InputSeqIdNotResolved, ePSGS_LogicError, ePSGS_ParsedOK, ePSGS_ParseFailed, ePSGS_SeqIdsEmpty, ePSGS_Si2csiCache, ePSGS_SkipLogging, ePSGS_UnresolvedSeqId, SBioseqResolution::GetBioseqInfo(), CPSGSResolveErrors::GetCombinedErrorCode(), CPSGSResolveErrors::GetCombinedErrorMessage(), CPSGS_AsyncResolveBase::GetCouldNotResolveMessage(), CPSGS_AsyncResolveBase::GetEffectiveVersion(), CPubseqGatewayApp::GetInstance(), CPSGS_AsyncResolveBase::GetSeqIdResolve(), CSeq_id::GetTextseq_Id(), SResolveInputSeqIdError::HasError(), SBioseqResolution::IsValid(), CPSGCache::LookupBioseqInfo(), m_AsyncStarted, CPSGS_AsyncResolveBase::m_CurrentSeqIdToResolve, SBioseqResolution::m_Error, SResolveInputSeqIdError::m_ErrorCode, SResolveInputSeqIdError::m_ErrorMessage, IPSGS_Processor::m_Reply, IPSGS_Processor::m_Request, SBioseqResolution::m_ResolutionResult, CPSGS_AsyncResolveBase::m_ResolveErrors, CPSGS_AsyncResolveBase::m_SeqIdsToResolve, CPSGS_AsyncResolveBase::MoveToNextSeqId(), CPSGS_AsyncResolveBase::OptimizationPrecondition(), IPSGS_Processor::ParseInputSeqId(), IPSGS_Processor::Process(), SBioseqResolution::Reset(), x_ComposeOSLT(), x_GetRequestUseCache(), x_OnSeqIdResolveError(), x_OnSeqIdResolveFinished(), x_OptimizedNotFound(), x_OptimizedResolutionInCache(), x_ResolveAsIsInCache(), and x_ResolveViaComposeOSLTInCache().
Referenced by ResolveInputSeqId(), x_OnAsyncBioseqInfoResolveError(), and x_OnSeqIdResolveFinished().
◆ x_ResolveViaComposeOSLTInCache()
Definition at line 245 of file resolve_base.cpp.
References CRequestStatus::e500_InternalServerError, ePSGS_CacheFailure, ePSGS_CacheHit, ePSGS_CacheNotHit, CPSGS_AsyncResolveBase::GetEffectiveVersion(), CSeq_id::GetTextseq_Id(), CPSGS_AsyncResolveBase::m_CurrentSeqIdToResolve, SBioseqResolution::m_Error, SResolveInputSeqIdError::m_ErrorCode, SResolveInputSeqIdError::m_ErrorMessage, SBioseqResolution::Reset(), NStr::ToUpper(), x_ResolveAsIsInCache(), x_ResolvePrimaryOSLTInCache(), and x_ResolveSecondaryOSLTInCache().
Referenced by ResolveTestInputSeqId(), and x_ResolveSeqId().
◆ m_AsyncStarted bool CPSGS_ResolveBase::m_AsyncStarted private ◆ m_FinalErrorCB ◆ m_FinalFinishedCB ◆ m_FinalStartProcessingCB
The documentation for this class was generated from the following files:
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