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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/classCPSGS__CDDProcessor.html below:

NCBI C++ ToolKit: CPSGS_CDDProcessor Class Reference

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

CPSGS_CDDProcessor (void) ~CPSGS_CDDProcessor (void) override vector< string > WhatCanProcess (shared_ptr< CPSGS_Request > request, shared_ptr< CPSGS_Reply > reply) const override Needs to be implemented only for the ID/get_na requests. More...
bool CanProcess (shared_ptr< CPSGS_Request > request, shared_ptr< CPSGS_Reply > reply) const override Tells if processor can process the given request. More...
IPSGS_Processor * CreateProcessor (shared_ptr< CPSGS_Request > request, shared_ptr< CPSGS_Reply > reply, TProcessorPriority priority) const override Create processor to fulfil PSG request using the data source. More...
void Process (void) override Main processing function. More...
void Cancel (void) override The infrastructure request to cancel processing. More...
EPSGS_Status GetStatus (void) override Tells the processor status (if it has finished or in progress) More...
string GetName (void) const override Tells the processor name (used in logging and tracing) More...
string GetGroupName (void) const override Tells the processor group name. More...
void GetBlobId (void) void OnGotBlobId (void) void GetBlobBySeqId (void) void OnGotBlobBySeqId (void) void GetBlobByBlobId (void) void OnGotBlobByBlobId (void) IPSGS_Processor () virtual ~IPSGS_Processor () 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...
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...
bool GetEffectiveSeqIdType (const objects::CSeq_id &parsed_seq_id, int request_seq_id_type, int16_t &eff_seq_id_type, bool need_trace) 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 60 of file cdd_processor.hpp.

◆ CPSGS_CDDProcessor() [1/2] CPSGS_CDDProcessor::CPSGS_CDDProcessor ( void )

Definition at line 145 of file cdd_processor.cpp.

References CTimeout::eDefault, IRegistry::GetDouble(), CPubseqGatewayApp::GetInstance(), IRegistry::GetInt(), kCDDProcessorSection, kDefaultCDDBackendTimeout, kDefaultMaxConn, kMax_UInt, kParamCDDBackendTimeout, kParamMaxConn, m_ClientPool, m_ThreadPool, min(), and registry.

Referenced by CreateProcessor().

◆ ~CPSGS_CDDProcessor() CPSGS_CDDProcessor::~CPSGS_CDDProcessor ( void ) override ◆ CPSGS_CDDProcessor() [2/2] CPSGS_CDDProcessor::CPSGS_CDDProcessor ( shared_ptr< objects::CCDDClientPool > client_pool, shared_ptr< ncbi::CThreadPool > thread_pool, shared_ptr< CPSGS_Request > request, shared_ptr< CPSGS_Reply > reply, TProcessorPriority priority ) private ◆ Cancel() void CPSGS_CDDProcessor::Cancel ( void ) overridevirtual ◆ CanProcess() ◆ CreateProcessor() ◆ GetBlobByBlobId() void CPSGS_CDDProcessor::GetBlobByBlobId ( void )

Definition at line 509 of file cdd_processor.cpp.

References CCDDClientPool::BlobIdToString(), IPSGS_Processor::GetReply(), IPSGS_Processor::GetRequest(), kCDDProcessorName, m_BlobId, m_CDDBlob, m_ClientPool, m_Error, IPSGS_Processor::PostponeInvoke(), s_OnGotBlobByBlobId(), and string.

Referenced by CCDDThreadPoolTask_GetBlobByBlobId::Execute().

◆ GetBlobBySeqId() void CPSGS_CDDProcessor::GetBlobBySeqId ( void ) ◆ GetBlobId() void CPSGS_CDDProcessor::GetBlobId ( void ) ◆ GetGroupName() string CPSGS_CDDProcessor::GetGroupName ( void ) const overridevirtual

Tells the processor group name.

For example, all the processors which retrieve data from Cassandra should return the same name in response to this call. This name is used to control the total number of simultaneously working processors retrieving from the same backend.

Returns: the processor group name

Implements IPSGS_Processor.

Definition at line 316 of file cdd_processor.cpp.

References kCDDProcessorGroupName.

◆ GetName() string CPSGS_CDDProcessor::GetName ( void ) const overridevirtual ◆ GetStatus() ◆ OnGotBlobByBlobId() void CPSGS_CDDProcessor::OnGotBlobByBlobId ( void )

Definition at line 630 of file cdd_processor.cpp.

References eNARetrieve, IPSGS_Processor::ePSGS_Done, IPSGS_Processor::ePSGS_Error, IPSGS_Processor::ePSGS_NotFound, IPSGS_Processor::GetReply(), IPSGS_Processor::GetRequest(), kCDDProcessorName, m_BlobId, m_CDDBlob, m_Error, s_SimulateError(), string, x_Finish(), x_IsCanceled(), x_RegisterTimingNotFound(), x_SendAnnot(), x_SendError(), and x_SignalStartProcessing().

◆ OnGotBlobBySeqId() void CPSGS_CDDProcessor::OnGotBlobBySeqId ( void )

Definition at line 582 of file cdd_processor.cpp.

References eNAResolve, IPSGS_Processor::ePSGS_Done, IPSGS_Processor::ePSGS_Error, IPSGS_Processor::ePSGS_NotFound, SPSGS_AnnotRequest::ePSGS_RS_Error, SPSGS_AnnotRequest::ePSGS_RS_NotFound, IPSGS_Processor::GetReply(), IPSGS_Processor::GetRequest(), kCDDProcessorName, m_CDDBlob, m_Error, s_SimulateError(), string, x_Finish(), x_IsCanceled(), x_RegisterTimingNotFound(), x_ReportResultStatus(), x_SendAnnot(), x_SendAnnotInfo(), x_SendError(), and x_SignalStartProcessing().

◆ OnGotBlobId() void CPSGS_CDDProcessor::OnGotBlobId ( void )

Definition at line 535 of file cdd_processor.cpp.

References eNAResolve, IPSGS_Processor::ePSGS_Done, IPSGS_Processor::ePSGS_Error, IPSGS_Processor::ePSGS_NotFound, SPSGS_AnnotRequest::ePSGS_RS_Error, SPSGS_AnnotRequest::ePSGS_RS_NotFound, IPSGS_Processor::GetReply(), IPSGS_Processor::GetRequest(), kCDDProcessorName, m_CDDBlob, m_Error, s_SimulateError(), string, x_Finish(), x_IsCanceled(), x_RegisterTimingNotFound(), x_ReportResultStatus(), x_SendAnnotInfo(), x_SendError(), and x_SignalStartProcessing().

◆ Process() void CPSGS_CDDProcessor::Process ( void ) overridevirtual

Main processing function.

It should avoid throwing exceptions. In case of errors it must make sure that:

the consequent GetStatus() calls return appropriate status
call SignalFinishProcessing() if there in no more processor activity If an exception is generated it is still a must for a processor to fulfill the obligations above. The dispatching code will log the message (and possibly trace) and continue in this case.

Implements IPSGS_Processor.

Definition at line 358 of file cdd_processor.cpp.

References _ASSERT, CPSGS_Request::ePSGS_AnnotationRequest, CPSGS_Request::ePSGS_BlobBySatSatKeyRequest, IPSGS_Processor::ePSGS_Error, IPSGS_Processor::GetRequest(), kCDDProcessorEvent, m_Mutex, m_Unlocked, x_Finish(), x_ProcessGetBlobRequest(), x_ProcessResolveRequest(), and x_SendError().

◆ WhatCanProcess() ◆ x_CanProcessAnnotRequest() ◆ x_CanProcessAnnotRequestIds() ◆ x_CanProcessBlobRequest() ◆ x_CanProcessSeq_id() bool CPSGS_CDDProcessor::x_CanProcessSeq_id ( const string & psg_id ) const private ◆ x_Finish()

Definition at line 894 of file cdd_processor.cpp.

References _ASSERT, IPSGS_Processor::ePSGS_InProgress, m_Status, IPSGS_Processor::SignalFinishProcessing(), and x_UnlockRequest().

Referenced by Cancel(), OnGotBlobByBlobId(), OnGotBlobBySeqId(), OnGotBlobId(), Process(), x_IsCanceled(), x_ProcessGetBlobRequest(), x_ProcessResolveRequest(), x_SendAnnotInfo(), and x_SignalStartProcessing().

◆ x_IsCanceled() bool CPSGS_CDDProcessor::x_IsCanceled ( ) private ◆ x_IsEnabled() ◆ x_NameIncluded() bool CPSGS_CDDProcessor::x_NameIncluded ( const vector< string > & names ) const private ◆ x_ProcessGetBlobRequest() void CPSGS_CDDProcessor::x_ProcessGetBlobRequest ( void ) private ◆ x_ProcessResolveRequest() void CPSGS_CDDProcessor::x_ProcessResolveRequest ( void ) private

Definition at line 402 of file cdd_processor.cpp.

References IPSGS_Processor::ePSGS_NotFound, SPSGS_AnnotRequest::ePSGS_RS_NotFound, CSeq_id_Handle::GetHandle(), SPSGS_AnnotRequest::GetNotProcessedName(), IPSGS_Processor::GetRequest(), IPSGS_Processor::m_Priority, SPSGS_AnnotRequest::m_SeqId, m_SeqIds, SPSGS_AnnotRequest::m_SeqIds, m_ThreadPool, SPSGS_BlobRequestBase::m_TSEOption, x_CanProcessSeq_id(), x_Finish(), x_NameIncluded(), and x_ReportResultStatus().

Referenced by Process().

◆ x_RegisterTiming() ◆ x_RegisterTimingNotFound() void CPSGS_CDDProcessor::x_RegisterTimingNotFound ( EPSGOperation operation ) private ◆ x_ReportResultStatus() ◆ x_SendAnnot() void CPSGS_CDDProcessor::x_SendAnnot ( const objects::CID2_Blob_Id & id2_blob_id, CRef< objects::CSeq_annot > & annot ) private

Definition at line 740 of file cdd_processor.cpp.

References CCDDClientPool::BlobIdToString(), eNARetrieve, eOpStatusFound, IPSGS_Processor::GetReply(), CID2_Blob_Id_Base::GetVersion(), CID2_Blob_Id_Base::IsSetVersion(), kCDDProcessorName, MSerial_AsnBinary, CSeq_entry::SetAnnot(), CBlobRecord::SetModified(), CBlobRecord::SetNChunks(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), ToJsonString(), and x_RegisterTiming().

Referenced by OnGotBlobByBlobId(), and OnGotBlobBySeqId().

◆ x_SendAnnotInfo() void CPSGS_CDDProcessor::x_SendAnnotInfo ( const objects::CCDD_Reply_Get_Blob_Id & blob_info ) private

Definition at line 689 of file cdd_processor.cpp.

References NStr::Base64Encode(), CCDDClientPool::BlobIdToString(), CSeqFeatData_Base::e_Region, CSeqFeatData_Base::e_Site, eNAResolve, eOpStatusFound, IPSGS_Processor::ePSGS_Canceled, CSeqFeatData::eSubtype_region, CSeqFeatData::eSubtype_site, CJsonNode::fStandardJson, CCDD_Reply_Get_Blob_Id_Base::GetBlob_id(), CSeq_id_Base::GetGi(), IPSGS_Processor::GetPriority(), IPSGS_Processor::GetReply(), IPSGS_Processor::GetRequest(), CCDD_Reply_Get_Blob_Id_Base::GetSeq_id(), CID2_Blob_Id_Base::GetVersion(), CSeq_id_Base::IsGi(), CID2_Blob_Id_Base::IsSetVersion(), kCDDAnnotName, kCDDProcessorName, MSerial_AsnBinary, CJsonNode::NewObjectNode(), SPSGS_AnnotRequest::RegisterProcessedName(), CJsonNode::Repr(), CRef< C, Locker >::Reset(), CJsonNode::SetInteger(), CJsonNode::SetString(), x_Finish(), and x_RegisterTiming().

Referenced by OnGotBlobBySeqId(), and OnGotBlobId().

◆ x_SendError() [1/4] void CPSGS_CDDProcessor::x_SendError ( const string & msg ) private ◆ x_SendError() [2/4] void CPSGS_CDDProcessor::x_SendError ( const string & msg, const exception & exc ) private ◆ x_SendError() [3/4]

Definition at line 322 of file cdd_processor.cpp.

References CRequestStatus::e500_InternalServerError, eDiag_Error, ePSGS_UnknownError, kCDDProcessorName, and msg().

Referenced by CanProcess(), CreateProcessor(), OnGotBlobByBlobId(), OnGotBlobBySeqId(), OnGotBlobId(), Process(), WhatCanProcess(), and x_SendError().

◆ x_SendError() [4/4] ◆ x_SignalStartProcessing() bool CPSGS_CDDProcessor::x_SignalStartProcessing ( void ) private

Definition at line 815 of file cdd_processor.cpp.

References CPSGS_Request::ePSGS_AnnotationRequest, IPSGS_Processor::ePSGS_Cancel, IPSGS_Processor::ePSGS_Canceled, IPSGS_Processor::GetPriority(), IPSGS_Processor::GetReply(), IPSGS_Processor::GetRequest(), kCDDAnnotName, kCDDProcessorName, SPSGS_AnnotRequest::RegisterProcessedName(), IPSGS_Processor::SignalStartProcessing(), and x_Finish().

Referenced by OnGotBlobByBlobId(), OnGotBlobBySeqId(), and OnGotBlobId().

◆ x_UnlockRequest() void CPSGS_CDDProcessor::x_UnlockRequest ( void ) private ◆ m_BlobId CRef<objects::CCDDClientPool::TBlobId> CPSGS_CDDProcessor::m_BlobId private ◆ m_Canceled bool CPSGS_CDDProcessor::m_Canceled private ◆ m_CDDBlob objects::CCDDClientPool::SCDDBlob CPSGS_CDDProcessor::m_CDDBlob private ◆ m_ClientPool shared_ptr<objects::CCDDClientPool> CPSGS_CDDProcessor::m_ClientPool private ◆ m_Error string CPSGS_CDDProcessor::m_Error private ◆ m_Mutex ◆ m_SeqIds vector<objects::CSeq_id_Handle> CPSGS_CDDProcessor::m_SeqIds private ◆ m_Start ◆ m_Status ◆ m_ThreadPool shared_ptr<ncbi::CThreadPool> CPSGS_CDDProcessor::m_ThreadPool private ◆ m_Unlocked bool CPSGS_CDDProcessor::m_Unlocked private

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

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

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