Search Toolkit Book for CPSGS_AsyncResolveBase

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

Inheritance diagram for CPSGS_AsyncResolveBase:

Collaboration diagram for CPSGS_AsyncResolveBase:

Public Member Functions
	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, 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)

Public Member Functions inherited from CPSGS_CassProcessorBase
	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

Public Member Functions inherited from IPSGS_Processor
	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...

Protected Member Functions
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)

Protected Member Functions inherited from CPSGS_CassProcessorBase
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)

Protected Member Functions inherited from IPSGS_Processor
bool	GetEffectiveSeqIdType (const objects::CSeq_id &parsed_seq_id, int request_seq_id_type, int16_t &eff_seq_id_type, bool need_trace)

Protected Attributes
TContinueResolveCB	m_ContinueResolveCB

TSeqIdResolutionFinishedCB	m_FinishedCB

TSeqIdResolutionErrorCB	m_ErrorCB

TSeqIdResolutionStartProcessingCB	m_StartProcessingCB

EPSGS_ResolveStage	m_ResolveStage

bool	m_ComposedOk

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

Protected Attributes inherited from CPSGS_CassProcessorBase
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

Protected Attributes inherited from IPSGS_Processor
shared_ptr< CPSGS_Request >	m_Request

shared_ptr< CPSGS_Reply >	m_Reply

TProcessorPriority	m_Priority

bool	m_FinishSignalled

uv_thread_t	m_UVThreadId

Private Types
enum	EPSGS_ResolveStage { eInit , ePrimaryBioseq , eSecondarySi2csi , eSecondaryAsIs , eFinished , ePostSi2Csi }

Private Member Functions
void	x_Process (void)

string	x_GetRequestSeqId (void)

int16_t	x_GetRequestSeqIdType (void)

string	x_GetSeqIdsToResolveList (void) const

void	x_PreparePrimaryBioseqInfoQuery (const CBioseqInfoRecord::TAccession &seq_id, CBioseqInfoRecord::TVersion version, CBioseqInfoRecord::TSeqIdType seq_id_type, CBioseqInfoRecord::TGI gi, bool with_seq_id_type)

void	x_PrepareSecondarySi2csiQuery (void)

void	x_PrepareSecondaryAsIsSi2csiQuery (void)

void	x_PrepareSi2csiQuery (const string &secondary_id, int16_t effective_seq_id_type)

void	x_OnSeqIdAsyncResolutionFinished (SBioseqResolution &&async_bioseq_resolution)

void	x_SignalStartProcessing (void)

Additional Inherited Members
Public Types inherited from IPSGS_Processor
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 Public Member Functions inherited from IPSGS_Processor
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...

Protected Types inherited from CPSGS_CassProcessorBase
enum	EPSGS_MyNCBILookupResult { ePSGS_IncludeHUPSetToNo , ePSGS_FoundInOKCache , ePSGS_FoundInErrorCache , ePSGS_FoundInNotFoundCache , ePSGS_CookieNotPresent , ePSGS_RequestInitiated , ePSGS_AddedToWaitlist }

Detailed Description

Definition at line 87 of file async_resolve_base.hpp.

Member Enumeration Documentation

◆ EPSGS_ResolveStage

enum CPSGS_AsyncResolveBase::EPSGS_ResolveStage

private

Enumerator
eInit
ePrimaryBioseq
eSecondarySi2csi
eSecondaryAsIs
eFinished
ePostSi2Csi

Definition at line 110 of file async_resolve_base.hpp.

Constructor & Destructor Documentation

◆ CPSGS_AsyncResolveBase() [1/2]

CPSGS_AsyncResolveBase::CPSGS_AsyncResolveBase ( )

Definition at line 111 of file async_resolve_base.cpp.

◆ CPSGS_AsyncResolveBase() [2/2]

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
	)

Definition at line 115 of file async_resolve_base.cpp.

◆ ~CPSGS_AsyncResolveBase()

CPSGS_AsyncResolveBase::~CPSGS_AsyncResolveBase ( )

virtual

Definition at line 134 of file async_resolve_base.cpp.

Member Function Documentation

◆ AdjustBioseqAccession()

EPSGS_AccessionAdjustmentResult CPSGS_AsyncResolveBase::AdjustBioseqAccession ( SBioseqResolution & bioseq_resolution )

protected

Definition at line 363 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()

bool CPSGS_AsyncResolveBase::CanSkipBioseqInfoRetrieval ( const CBioseqInfoRecord & bioseq_info_record )

protected

Definition at line 307 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()

SPSGS_RequestBase::EPSGS_AccSubstitutioOption CPSGS_AsyncResolveBase::GetAccessionSubstitutionOption ( void )

protected

Definition at line 339 of file async_resolve_base.cpp.

References CPSGS_Request::ePSGS_AccessionVersionHistoryRequest, CPSGS_Request::ePSGS_AnnotationRequest, CPSGS_Request::ePSGS_BlobBySeqIdRequest, SPSGS_RequestBase::ePSGS_DefaultAccSubstitution, CPSGS_Request::ePSGS_IPGResolveRequest, SPSGS_RequestBase::ePSGS_NeverAccSubstitute, CPSGS_Request::ePSGS_ResolveRequest, IPSGS_Processor::m_Request, and NCBI_THROW.

Referenced by AdjustBioseqAccession().

◆ GetAsyncResolutionStartTimestamp()

psg_time_point_t CPSGS_AsyncResolveBase::GetAsyncResolutionStartTimestamp ( void ) const

inlineprotected

Definition at line 137 of file async_resolve_base.hpp.

References m_AsyncCassResolutionStart.

Referenced by CPSGS_ResolveBase::x_OnSeqIdResolveError(), and CPSGS_ResolveBase::x_RegisterSuccessTiming().

◆ GetBioseqInfoFields()

SPSGS_ResolveRequest::TPSGS_BioseqIncludeData CPSGS_AsyncResolveBase::GetBioseqInfoFields ( void )

protected

Definition at line 286 of file async_resolve_base.cpp.

References CPSGS_Request::ePSGS_ResolveRequest, SPSGS_ResolveRequest::fPSGS_AllBioseqFields, and IPSGS_Processor::m_Request.

Referenced by NonKeyBioseqInfoFieldsRequested().

◆ GetCouldNotResolveMessage()

string CPSGS_AsyncResolveBase::GetCouldNotResolveMessage ( void ) const

protected

Definition at line 1053 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(), and CPSGS_ResolveBase::x_ResolveSeqId().

◆ GetEffectiveVersion()

int16_t CPSGS_AsyncResolveBase::GetEffectiveVersion ( const CTextseq_id * text_seq_id )

protected

Definition at line 163 of file async_resolve_base.cpp.

References CTextseq_id_Base::CanGetVersion(), and CTextseq_id_Base::GetVersion().

Referenced by CPSGS_ResolveBase::x_ResolveSeqId(), and CPSGS_ResolveBase::x_ResolveViaComposeOSLTInCache().

◆ MoveToNextSeqId()

bool CPSGS_AsyncResolveBase::MoveToNextSeqId ( void )

protected

Definition at line 1031 of file async_resolve_base.cpp.

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

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

◆ NonKeyBioseqInfoFieldsRequested()

bool CPSGS_AsyncResolveBase::NonKeyBioseqInfoFieldsRequested ( void )

protected

Definition at line 295 of file async_resolve_base.cpp.

References SPSGS_ResolveRequest::fPSGS_BioseqKeyFields, and GetBioseqInfoFields().

Referenced by CanSkipBioseqInfoRetrieval().

◆ Process()

void CPSGS_AsyncResolveBase::Process	(	int16_t	effective_version,
		int16_t	effective_seq_id_type,
		list< string > &&	secondary_id_list,
		string &&	primary_seq_id,
		bool	composed_ok,
		SBioseqResolution &&	bioseq_resolution
	)

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, and x_Process().

◆ SetAsyncResolutionStartTimestamp()

void CPSGS_AsyncResolveBase::SetAsyncResolutionStartTimestamp ( const psg_time_point_t & ts )

inlineprotected

Definition at line 142 of file async_resolve_base.hpp.

References m_AsyncCassResolutionStart.

Referenced by CPSGS_ResolveBase::x_OnSeqIdResolveFinished().

◆ SetupSeqIdToResolve() [1/2]

void CPSGS_AsyncResolveBase::SetupSeqIdToResolve	(	const string &	seq_id,
		int16_t	seq_id_type
	)

protected

Definition at line 234 of file async_resolve_base.cpp.

References m_CurrentSeqIdToResolve, and m_SeqIdsToResolve.

◆ SetupSeqIdToResolve() [2/2]

void CPSGS_AsyncResolveBase::SetupSeqIdToResolve ( void )

protected

Definition at line 190 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

Definition at line 244 of file async_resolve_base.cpp.

References CPSGS_Request::ePSGS_AccessionVersionHistoryRequest, CPSGS_Request::ePSGS_AnnotationRequest, CPSGS_Request::ePSGS_BlobBySeqIdRequest, CPSGS_Request::ePSGS_ResolveRequest, IPSGS_Processor::m_Request, NCBI_THROW, and CPSGS_Request::TypeToString().

Referenced by SetupSeqIdToResolve().

◆ x_GetRequestSeqIdType()

int16_t CPSGS_AsyncResolveBase::x_GetRequestSeqIdType ( void )

private

Definition at line 265 of file async_resolve_base.cpp.

References CPSGS_Request::ePSGS_AccessionVersionHistoryRequest, CPSGS_Request::ePSGS_AnnotationRequest, CPSGS_Request::ePSGS_BlobBySeqIdRequest, CPSGS_Request::ePSGS_ResolveRequest, IPSGS_Processor::m_Request, NCBI_THROW, and CPSGS_Request::TypeToString().

Referenced by SetupSeqIdToResolve().

◆ x_GetSeqIdsToResolveList()

string CPSGS_AsyncResolveBase::x_GetSeqIdsToResolveList ( void ) const

private

Definition at line 176 of file async_resolve_base.cpp.

References m_SeqIdsToResolve.

Referenced by SetupSeqIdToResolve().

◆ x_OnBioseqInfo()

void CPSGS_AsyncResolveBase::x_OnBioseqInfo ( vector< CBioseqInfoRecord > && records )

Definition at line 646 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()

void CPSGS_AsyncResolveBase::x_OnBioseqInfoError	(	CRequestStatus::ECode	status,
		int	code,
		EDiagSev	severity,
		const string &	message
	)

◆ x_OnBioseqInfoWithoutSeqIdType()

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

Definition at line 789 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

◆ x_OnSi2csiError()

void CPSGS_AsyncResolveBase::x_OnSi2csiError	(	CRequestStatus::ECode	status,
		int	code,
		EDiagSev	severity,
		const string &	message
	)

◆ x_OnSi2csiRecord()

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

Definition at line 939 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()

void CPSGS_AsyncResolveBase::x_PreparePrimaryBioseqInfoQuery	(	const CBioseqInfoRecord::TAccession &	seq_id,
		CBioseqInfoRecord::TVersion	version,
		CBioseqInfoRecord::TSeqIdType	seq_id_type,
		CBioseqInfoRecord::TGI	gi,
		bool	with_seq_id_type
	)

private

Definition at line 504 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

Definition at line 626 of file async_resolve_base.cpp.

References m_CurrentSeqIdToResolve, m_EffectiveSeqIdType, m_PrimarySeqId, NStr::ToUpper(), x_PrepareSi2csiQuery(), and x_Process().

Referenced by x_Process().

◆ x_PrepareSecondarySi2csiQuery()

void CPSGS_AsyncResolveBase::x_PrepareSecondarySi2csiQuery ( void )

private

Definition at line 617 of file async_resolve_base.cpp.

References m_EffectiveSeqIdType, m_SecondaryIdList, m_SecondaryIndex, next(), and x_PrepareSi2csiQuery().

Referenced by x_Process().

◆ x_PrepareSi2csiQuery()

void CPSGS_AsyncResolveBase::x_PrepareSi2csiQuery	(	const string &	secondary_id,
		int16_t	effective_seq_id_type
	)

private

◆ x_Process()

void CPSGS_AsyncResolveBase::x_Process ( void )

private

◆ x_SignalStartProcessing()

void CPSGS_AsyncResolveBase::x_SignalStartProcessing ( void )

private

Definition at line 1114 of file async_resolve_base.cpp.

References m_StartProcessingCalled, and m_StartProcessingCB.

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

Member Data Documentation

◆ m_AsyncCassResolutionStart

psg_time_point_t CPSGS_AsyncResolveBase::m_AsyncCassResolutionStart

protected

Definition at line 207 of file async_resolve_base.hpp.

Referenced by GetAsyncResolutionStartTimestamp(), Process(), and SetAsyncResolutionStartTimestamp().

◆ m_BioseqInfoRequestedAccession

CBioseqInfoRecord::TAccession CPSGS_AsyncResolveBase::m_BioseqInfoRequestedAccession

protected

Definition at line 200 of file async_resolve_base.hpp.

Referenced by x_OnBioseqInfo(), and x_PreparePrimaryBioseqInfoQuery().

◆ m_BioseqInfoRequestedGI

CBioseqInfoRecord::TGI CPSGS_AsyncResolveBase::m_BioseqInfoRequestedGI

protected

Definition at line 203 of file async_resolve_base.hpp.

Referenced by x_OnBioseqInfo(), and x_PreparePrimaryBioseqInfoQuery().

◆ m_BioseqInfoRequestedSeqIdType

CBioseqInfoRecord::TSeqIdType CPSGS_AsyncResolveBase::m_BioseqInfoRequestedSeqIdType

protected

Definition at line 202 of file async_resolve_base.hpp.

Referenced by x_OnBioseqInfo(), and x_PreparePrimaryBioseqInfoQuery().

◆ m_BioseqInfoRequestedVersion

CBioseqInfoRecord::TVersion CPSGS_AsyncResolveBase::m_BioseqInfoRequestedVersion

protected

Definition at line 201 of file async_resolve_base.hpp.

Referenced by x_OnBioseqInfo(), x_OnBioseqInfoWithoutSeqIdType(), and x_PreparePrimaryBioseqInfoQuery().

◆ m_BioseqInfoStart

psg_time_point_t CPSGS_AsyncResolveBase::m_BioseqInfoStart

protected

Definition at line 205 of file async_resolve_base.hpp.

Referenced by x_OnBioseqInfo(), x_OnBioseqInfoWithoutSeqIdType(), and x_PreparePrimaryBioseqInfoQuery().

◆ m_BioseqResolution

SBioseqResolution CPSGS_AsyncResolveBase::m_BioseqResolution

protected

Definition at line 195 of file async_resolve_base.hpp.

Referenced by Process(), x_OnBioseqInfo(), x_OnBioseqInfoWithoutSeqIdType(), x_OnSi2csiRecord(), x_PreparePrimaryBioseqInfoQuery(), x_PrepareSi2csiQuery(), and x_Process().

◆ m_ComposedOk

bool CPSGS_AsyncResolveBase::m_ComposedOk

protected

Definition at line 189 of file async_resolve_base.hpp.

Referenced by Process(), and x_Process().

◆ m_ContinueResolveCB

TContinueResolveCB CPSGS_AsyncResolveBase::m_ContinueResolveCB

protected

Definition at line 183 of file async_resolve_base.hpp.

Referenced by x_OnBioseqInfo(), x_OnBioseqInfoError(), x_OnBioseqInfoWithoutSeqIdType(), x_OnSeqIdAsyncResolutionFinished(), and x_OnSi2csiError().

◆ m_CurrentFetch

CCassFetch* CPSGS_AsyncResolveBase::m_CurrentFetch

protected

Definition at line 197 of file async_resolve_base.hpp.

Referenced by Process(), x_OnBioseqInfo(), x_OnBioseqInfoError(), x_OnSi2csiError(), x_OnSi2csiRecord(), x_PreparePrimaryBioseqInfoQuery(), and x_PrepareSi2csiQuery().

◆ m_CurrentSeqIdToResolve

list<SPSGSeqId>::const_iterator CPSGS_AsyncResolveBase::m_CurrentSeqIdToResolve

protected

Definition at line 216 of file async_resolve_base.hpp.

Referenced by MoveToNextSeqId(), CPSGS_ResolveBase::ResolveTestInputSeqId(), SetupSeqIdToResolve(), CPSGS_ResolveBase::x_ComposeOSLT(), CPSGS_ResolveBase::x_OnSeqIdResolveFinished(), x_PrepareSecondaryAsIsSi2csiQuery(), CPSGS_ResolveBase::x_ResolveAsIsInCache(), CPSGS_ResolveBase::x_ResolveSeqId(), and CPSGS_ResolveBase::x_ResolveViaComposeOSLTInCache().

◆ m_EffectiveSeqIdType

int16_t CPSGS_AsyncResolveBase::m_EffectiveSeqIdType

protected

Definition at line 192 of file async_resolve_base.hpp.

Referenced by Process(), x_PrepareSecondaryAsIsSi2csiQuery(), x_PrepareSecondarySi2csiQuery(), and x_Process().

◆ m_EffectiveVersion

int16_t CPSGS_AsyncResolveBase::m_EffectiveVersion

protected

Definition at line 191 of file async_resolve_base.hpp.

Referenced by Process(), and x_Process().

◆ m_ErrorCB

TSeqIdResolutionErrorCB CPSGS_AsyncResolveBase::m_ErrorCB

protected

Definition at line 185 of file async_resolve_base.hpp.

Referenced by x_OnBioseqInfo(), x_OnBioseqInfoError(), x_OnBioseqInfoWithoutSeqIdType(), x_OnSeqIdAsyncResolutionFinished(), and x_OnSi2csiError().

◆ m_FinishedCB

TSeqIdResolutionFinishedCB CPSGS_AsyncResolveBase::m_FinishedCB

protected

Definition at line 184 of file async_resolve_base.hpp.

Referenced by x_OnSeqIdAsyncResolutionFinished().

◆ m_NoSeqIdTypeFetch

CCassFetch* CPSGS_AsyncResolveBase::m_NoSeqIdTypeFetch

protected

Definition at line 198 of file async_resolve_base.hpp.

Referenced by Process(), x_OnBioseqInfoError(), x_OnBioseqInfoWithoutSeqIdType(), and x_PreparePrimaryBioseqInfoQuery().

◆ m_PrimarySeqId

string CPSGS_AsyncResolveBase::m_PrimarySeqId

protected

Definition at line 190 of file async_resolve_base.hpp.

Referenced by Process(), x_PrepareSecondaryAsIsSi2csiQuery(), and x_Process().

◆ m_ResolveErrors

CPSGSResolveErrors CPSGS_AsyncResolveBase::m_ResolveErrors

protected

Definition at line 217 of file async_resolve_base.hpp.

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

◆ m_ResolveStage

EPSGS_ResolveStage CPSGS_AsyncResolveBase::m_ResolveStage

protected

Definition at line 188 of file async_resolve_base.hpp.

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

◆ m_SecondaryIdList

list<string> CPSGS_AsyncResolveBase::m_SecondaryIdList

protected

Definition at line 194 of file async_resolve_base.hpp.

Referenced by Process(), x_PrepareSecondarySi2csiQuery(), and x_Process().

◆ m_SecondaryIndex

size_t CPSGS_AsyncResolveBase::m_SecondaryIndex

protected

Definition at line 193 of file async_resolve_base.hpp.

Referenced by x_PrepareSecondarySi2csiQuery(), and x_Process().

◆ m_SeqIdsToResolve

list<SPSGSeqId> CPSGS_AsyncResolveBase::m_SeqIdsToResolve

protected

Definition at line 215 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(), and CPSGS_ResolveBase::x_ResolveSeqId().

◆ m_Si2csiStart

psg_time_point_t CPSGS_AsyncResolveBase::m_Si2csiStart

protected

Definition at line 206 of file async_resolve_base.hpp.

Referenced by x_OnSi2csiRecord(), and x_PrepareSi2csiQuery().

◆ m_StartProcessingCalled

bool CPSGS_AsyncResolveBase::m_StartProcessingCalled

protected

Definition at line 209 of file async_resolve_base.hpp.

Referenced by x_SignalStartProcessing().

◆ m_StartProcessingCB

TSeqIdResolutionStartProcessingCB CPSGS_AsyncResolveBase::m_StartProcessingCB

protected

Definition at line 186 of file async_resolve_base.hpp.

Referenced by x_SignalStartProcessing().

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

Public Member Functions

Protected Member Functions

Protected Attributes

Private Types

Private Member Functions

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

◆ EPSGS_ResolveStage

Constructor & Destructor Documentation

◆ CPSGS_AsyncResolveBase() [1/2]

◆ CPSGS_AsyncResolveBase() [2/2]

◆ ~CPSGS_AsyncResolveBase()

Member Function Documentation

◆ AdjustBioseqAccession()

◆ CanSkipBioseqInfoRetrieval()

◆ GetAccessionSubstitutionOption()

◆ GetAsyncResolutionStartTimestamp()

◆ GetBioseqInfoFields()

◆ GetCouldNotResolveMessage()

◆ GetEffectiveVersion()

◆ MoveToNextSeqId()

◆ NonKeyBioseqInfoFieldsRequested()

◆ Process()

◆ SetAsyncResolutionStartTimestamp()

◆ SetupSeqIdToResolve() [1/2]

◆ SetupSeqIdToResolve() [2/2]

◆ x_GetRequestSeqId()

◆ x_GetRequestSeqIdType()

◆ x_GetSeqIdsToResolveList()

◆ x_OnBioseqInfo()

◆ x_OnBioseqInfoError()

◆ x_OnBioseqInfoWithoutSeqIdType()

◆ x_OnSeqIdAsyncResolutionFinished()

◆ x_OnSi2csiError()

◆ x_OnSi2csiRecord()

◆ x_PreparePrimaryBioseqInfoQuery()

◆ x_PrepareSecondaryAsIsSi2csiQuery()

◆ x_PrepareSecondarySi2csiQuery()

◆ x_PrepareSi2csiQuery()

◆ x_Process()

◆ x_SignalStartProcessing()

Member Data Documentation

◆ m_AsyncCassResolutionStart

◆ m_BioseqInfoRequestedAccession

◆ m_BioseqInfoRequestedGI

◆ m_BioseqInfoRequestedSeqIdType

◆ m_BioseqInfoRequestedVersion

◆ m_BioseqInfoStart

◆ m_BioseqResolution

◆ m_ComposedOk

◆ m_ContinueResolveCB

◆ m_CurrentFetch

◆ m_CurrentSeqIdToResolve

◆ m_EffectiveSeqIdType

◆ m_EffectiveVersion

◆ m_ErrorCB

◆ m_FinishedCB

◆ m_NoSeqIdTypeFetch

◆ m_PrimarySeqId

◆ m_ResolveErrors

◆ m_ResolveStage

◆ m_SecondaryIdList

◆ m_SecondaryIndex

◆ m_SeqIdsToResolve

◆ m_Si2csiStart

◆ m_StartProcessingCalled

◆ m_StartProcessingCB