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NCBI C++ ToolKit: CPSGS_SNPProcessor Class Reference

Search Toolkit Book for CPSGS_SNPProcessor

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

  CPSGS_SNPProcessor (void)     ~CPSGS_SNPProcessor (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  GetAnnotation (void)   void  OnGotAnnotation (void)   void  GetBlobByBlobId (void)   void  OnGotBlobByBlobId (void)   void  GetChunk (void)   void  OnGotChunk (void)   void  ProcessEvent (void) override   Called when an event happened which may require to have some processing. More...
    CPSGS_CassProcessorBase ()     CPSGS_CassProcessorBase (shared_ptr< CPSGS_Request > request, shared_ptr< CPSGS_Reply > reply, TProcessorPriority priority)   virtual  ~CPSGS_CassProcessorBase ()   void  SignalFinishProcessing (void)   void  UnlockWaitingProcessor (void)   void  CallOnData (void)   string  GetVerboseFetches (void) const   void  EnforceWait (void) const     IPSGS_Processor ()   virtual  ~IPSGS_Processor ()   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_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_AsyncBioseqInfoBase ()     CPSGS_AsyncBioseqInfoBase (shared_ptr< CPSGS_Request > request, shared_ptr< CPSGS_Reply > reply, TSeqIdResolutionFinishedCB finished_cb, TSeqIdResolutionErrorCB error_cb)   virtual  ~CPSGS_AsyncBioseqInfoBase ()     CPSGS_SNPProcessor (const CPSGS_SNPProcessor &parent, shared_ptr< CPSGS_Request > request, shared_ptr< CPSGS_Reply > reply, TProcessorPriority priority)   void  x_LoadConfig (void)   bool  x_IsEnabled (CPSGS_Request &request) const   void  x_InitClient (void) const   void  x_ProcessAnnotationRequest (void)   void  x_ProcessBlobBySatSatKeyRequest (void)   void  x_ProcessTSEChunkRequest (void)   void  x_OnSeqIdResolveFinished (SBioseqResolution &&bioseq_resolution)   void  x_OnSeqIdResolveError (CRequestStatus::ECode status, int code, EDiagSev severity, const string &message)   void  x_OnResolutionGoodData (void)   void  x_Peek (bool need_wait)   bool  x_Peek (unique_ptr< CCassFetch > &fetch_details, bool need_wait)   void  x_RegisterTiming (psg_time_point_t start, EPSGOperation operation, EPSGOperationStatus status, size_t size)   void  x_RegisterTimingFound (psg_time_point_t start, EPSGOperation operation, const objects::CID2_Reply_Data &data)   void  x_RegisterTimingNotFound (EPSGOperation operation)   void  x_WriteData (objects::CID2_Reply_Data &data, const CSerialObject &obj) const   void  x_SendAnnotInfo (const SSNPData &data)   void  x_SendAnnotInfo (void)   void  x_SendBlob (void)   void  x_SendChunk (void)   void  x_SendSplitInfo (const SSNPData &data)   void  x_SendMainEntry (const SSNPData &data)   void  x_SendBlobProps (const string &psg_blob_id, CBlobRecord &blob_props)   void  x_SendBlobData (const string &psg_blob_id, const objects::CID2_Reply_Data &data)   void  x_SendChunkBlobProps (const string &id2_info, int chunk_id, CBlobRecord &blob_props)   void  x_SendChunkBlobData (const string &id2_info, int chunk_id, const objects::CID2_Reply_Data &data)   void  x_SendError (const string &msg)   void  x_SendError (const string &msg, const exception &exc)   void  x_ReportResultStatusForAllNA (SPSGS_AnnotRequest::EPSGS_ResultStatus status)   void  x_UnlockRequest (void)   void  x_Finish (EPSGS_Status status)   bool  x_IsCanceled ()   bool  x_SignalStartProcessing ()   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
}   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  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   void  MakeRequest (SBioseqResolution &&bioseq_resolution)   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   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  

Definition at line 62 of file snp_processor.hpp.

◆ CPSGS_SNPProcessor() [1/2] CPSGS_SNPProcessor::CPSGS_SNPProcessor ( void  ) ◆ ~CPSGS_SNPProcessor() CPSGS_SNPProcessor::~CPSGS_SNPProcessor ( void  ) override ◆ CPSGS_SNPProcessor() [2/2] ◆ Cancel() void CPSGS_SNPProcessor::Cancel ( void  ) overridevirtual ◆ CanProcess() ◆ CreateProcessor() ◆ GetAnnotation() void CPSGS_SNPProcessor::GetAnnotation ( void  )

Definition at line 536 of file snp_processor.cpp.

References data, IPSGS_Processor::GetReply(), IPSGS_Processor::GetRequest(), kSNPProcessorName, m_Canceled, m_Client, m_ProcessNAs, m_ScaleLimit, m_SeqIds, m_SNPData, IPSGS_Processor::PostponeInvoke(), s_OnGotAnnotation(), and string.

Referenced by CSNPThreadPoolTask_GetAnnotation::Execute().

◆ GetBlobByBlobId() void CPSGS_SNPProcessor::GetBlobByBlobId ( void  ) ◆ GetChunk() void CPSGS_SNPProcessor::GetChunk ( void  )

Definition at line 736 of file snp_processor.cpp.

References data, IPSGS_Processor::GetReply(), IPSGS_Processor::GetRequest(), kSNPProcessorName, m_ChunkId, m_Client, m_Id2Info, m_SNPData, NStr::NumericToString(), IPSGS_Processor::PostponeInvoke(), and s_OnGotChunk().

Referenced by CSNPThreadPoolTask_GetChunk::Execute().

◆ GetGroupName() string CPSGS_SNPProcessor::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 383 of file snp_processor.cpp.

References kSNPProcessorGroupName.

◆ GetName() string CPSGS_SNPProcessor::GetName ( void  ) const overridevirtual ◆ GetStatus() ◆ OnGotAnnotation() void CPSGS_SNPProcessor::OnGotAnnotation ( void  )

Definition at line 568 of file snp_processor.cpp.

References data, set< Key, Compare >::empty(), 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(), set< Key, Compare >::insert(), kSNPProcessorName, m_ProcessNAs, m_SNPData, m_SNPDataError, SPSGS_AnnotRequest::ReportResultStatus(), s_SimulateError(), string, x_Finish(), x_IsCanceled(), x_RegisterTimingNotFound(), x_ReportResultStatusForAllNA(), x_SendAnnotInfo(), x_SendError(), and x_SignalStartProcessing().

◆ OnGotBlobByBlobId() void CPSGS_SNPProcessor::OnGotBlobByBlobId ( void  )

Definition at line 679 of file snp_processor.cpp.

References eNARetrieve, IPSGS_Processor::ePSGS_Done, IPSGS_Processor::ePSGS_Error, IPSGS_Processor::ePSGS_NotFound, IPSGS_Processor::GetReply(), IPSGS_Processor::GetRequest(), kSNPProcessorName, m_PSGBlobId, m_SNPData, m_SNPDataError, s_SimulateError(), x_Finish(), x_IsCanceled(), x_RegisterTimingNotFound(), x_SendBlob(), x_SendError(), and x_SignalStartProcessing().

◆ OnGotChunk() void CPSGS_SNPProcessor::OnGotChunk ( void  )

Definition at line 756 of file snp_processor.cpp.

References IPSGS_Processor::ePSGS_Done, IPSGS_Processor::ePSGS_Error, IPSGS_Processor::ePSGS_NotFound, eTseChunkRetrieve, IPSGS_Processor::GetReply(), IPSGS_Processor::GetRequest(), kSNPProcessorName, m_ChunkId, m_Id2Info, m_SNPData, m_SNPDataError, NStr::NumericToString(), s_SimulateError(), x_Finish(), x_IsCanceled(), x_RegisterTimingNotFound(), x_SendChunk(), x_SendError(), and x_SignalStartProcessing().

◆ Process() void CPSGS_SNPProcessor::Process ( void  ) overridevirtual

Main processing function.

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

Implements IPSGS_Processor.

Definition at line 418 of file snp_processor.cpp.

References CPSGS_Request::ePSGS_AnnotationRequest, CPSGS_Request::ePSGS_BlobBySatSatKeyRequest, IPSGS_Processor::ePSGS_Error, CPSGS_Request::ePSGS_TSEChunkRequest, IPSGS_Processor::GetRequest(), kSNPProcessorEvent, m_Mutex, m_Unlocked, x_Finish(), x_ProcessAnnotationRequest(), x_ProcessBlobBySatSatKeyRequest(), x_ProcessTSEChunkRequest(), and x_SendError().

◆ ProcessEvent() void CPSGS_SNPProcessor::ProcessEvent ( void  ) overridevirtual ◆ WhatCanProcess()

Needs to be implemented only for the ID/get_na requests.

It returns a list of named annotations which a processor recognizes as suitable for processing.

Parameters
request PSG request to retrieve the data for. It is guaranteed to be not null. reply The way to send reply chunks to the client. It is guaranteed to be not null.
Returns
a list of annotations which can be processed

Reimplemented from IPSGS_Processor.

Definition at line 325 of file snp_processor.cpp.

References _ASSERT, m_Client, x_InitClient(), x_IsEnabled(), and x_SendError().

◆ x_Finish()

Definition at line 1026 of file snp_processor.cpp.

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

Referenced by Cancel(), OnGotAnnotation(), OnGotBlobByBlobId(), OnGotChunk(), Process(), x_IsCanceled(), x_OnSeqIdResolveError(), x_OnSeqIdResolveFinished(), x_Peek(), x_ProcessAnnotationRequest(), and x_SignalStartProcessing().

◆ x_InitClient() void CPSGS_SNPProcessor::x_InitClient ( void  ) const inlineprivate ◆ x_IsCanceled() bool CPSGS_SNPProcessor::x_IsCanceled ( ) private ◆ x_IsEnabled() ◆ x_LoadConfig() void CPSGS_SNPProcessor::x_LoadConfig ( void  ) private

Definition at line 261 of file snp_processor.cpp.

References DEFAULT_ADD_PTIS, DEFAULT_ALLOW_NON_REFSEQ, DEFAULT_ANNOT_NAME, DEFAULT_FILE_OPEN_RETRY, DEFAULT_FILE_RECHECK_TIME, DEFAULT_FILE_REOPEN_TIME, DEFAULT_GC_CACHE_SIZE, DEFAULT_MISSING_GC_SIZE, DEFAULT_SNP_SCALE_LIMIT, DEFAULT_SPLIT, IRegistry::GetBool(), CPubseqGatewayApp::GetInstance(), IRegistry::GetInt(), CSeq_id::GetSNPScaleLimit_Value(), IRegistry::GetString(), CSnpPtisClient::IsEnabled(), kDefaultMaxConn, kMax_UInt, kParamMaxConn, kSNPProcessorSection, m_Config, m_ThreadPool, min(), PARAM_ADD_PTIS, PARAM_ALLOW_NON_REFSEQ, PARAM_ANNOT_NAME, PARAM_FILE_OPEN_RETRY, PARAM_FILE_RECHECK_TIME, PARAM_FILE_REOPEN_TIME, PARAM_GC_CACHE_SIZE, PARAM_MISSING_GC_SIZE, PARAM_SNP_SCALE_LIMIT, PARAM_SPLIT, PSG_ERROR, and registry.

Referenced by CPSGS_SNPProcessor().

◆ x_OnResolutionGoodData() void CPSGS_SNPProcessor::x_OnResolutionGoodData ( void  ) private ◆ x_OnSeqIdResolveError()

Definition at line 1074 of file snp_processor.cpp.

References CRequestStatus::e404_NotFound, IPSGS_Processor::ePSGS_Error, IPSGS_Processor::ePSGS_NotFound, SPSGS_AnnotRequest::ePSGS_RS_Error, SPSGS_AnnotRequest::ePSGS_RS_NotFound, IPSGS_Processor::GetReply(), IPSGS_Processor::GetRequest(), kSNPProcessorName, m_PreResolving, x_Finish(), x_IsCanceled(), and x_ReportResultStatusForAllNA().

◆ x_OnSeqIdResolveFinished() void CPSGS_SNPProcessor::x_OnSeqIdResolveFinished ( SBioseqResolution &&  bioseq_resolution ) private

Definition at line 1035 of file snp_processor.cpp.

References IPSGS_Processor::ePSGS_Error, ePSGS_ParsedOK, CSeq_id_Handle::GetHandle(), IPSGS_Processor::GetReply(), IPSGS_Processor::GetRequest(), info, kSNPProcessorName, m_Client, m_PreResolving, m_SeqIds, m_ThreadPool, IPSGS_Processor::ParseInputSeqId(), PSG_ERROR, x_Finish(), and x_IsCanceled().

◆ x_Peek() [1/2] void CPSGS_SNPProcessor::x_Peek ( bool  need_wait ) private ◆ x_Peek() [2/2] bool CPSGS_SNPProcessor::x_Peek ( unique_ptr< CCassFetch > &  fetch_details, bool  need_wait  ) private ◆ x_ProcessAnnotationRequest() void CPSGS_SNPProcessor::x_ProcessAnnotationRequest ( void  ) private

Definition at line 468 of file snp_processor.cpp.

References IPSGS_Processor::ePSGS_NotFound, SPSGS_AnnotRequest::ePSGS_RS_NotFound, CSeq_id::eSNPScaleLimit_Default, CSeq_id_Handle::GetHandle(), IPSGS_Processor::GetReply(), IPSGS_Processor::GetRequest(), i, kSNPProcessorName, m_Client, m_Config, m_PreResolving, m_ScaleLimit, SPSGS_AnnotRequest::m_SeqId, SPSGS_AnnotRequest::m_SeqIdResolve, SPSGS_AnnotRequest::m_SeqIds, m_SeqIds, SPSGS_AnnotRequest::m_SNPScaleLimit, m_ThreadPool, CPSGS_ResolveBase::ResolveInputSeqId(), swap(), x_Finish(), and x_ReportResultStatusForAllNA().

Referenced by Process().

◆ x_ProcessBlobBySatSatKeyRequest() void CPSGS_SNPProcessor::x_ProcessBlobBySatSatKeyRequest ( void  ) private ◆ x_ProcessTSEChunkRequest() void CPSGS_SNPProcessor::x_ProcessTSEChunkRequest ( void  ) private ◆ x_RegisterTiming() ◆ x_RegisterTimingFound() ◆ x_RegisterTimingNotFound() void CPSGS_SNPProcessor::x_RegisterTimingNotFound ( EPSGOperation  operation ) private ◆ x_ReportResultStatusForAllNA() ◆ x_SendAnnotInfo() [1/2] void CPSGS_SNPProcessor::x_SendAnnotInfo ( const SSNPData &  data ) private

Definition at line 837 of file snp_processor.cpp.

References NStr::Base64Encode(), data, eNAResolve, eOpStatusFound, CJsonNode::fStandardJson, IPSGS_Processor::GetPriority(), IPSGS_Processor::GetReply(), IPSGS_Processor::GetRequest(), kSNPProcessorName, MSerial_AsnBinary, CJsonNode::NewObjectNode(), SPSGS_AnnotRequest::RegisterProcessedName(), CJsonNode::Repr(), CJsonNode::SetString(), and x_RegisterTiming().

◆ x_SendAnnotInfo() [2/2] void CPSGS_SNPProcessor::x_SendAnnotInfo ( void  ) private ◆ x_SendBlob() void CPSGS_SNPProcessor::x_SendBlob ( void  ) private ◆ x_SendBlobData() void CPSGS_SNPProcessor::x_SendBlobData ( const string &  psg_blob_id, const objects::CID2_Reply_Data &  data  ) private ◆ x_SendBlobProps() ◆ x_SendChunk() void CPSGS_SNPProcessor::x_SendChunk ( void  ) private ◆ x_SendChunkBlobData() void CPSGS_SNPProcessor::x_SendChunkBlobData ( const string &  id2_info, int  chunk_id, const objects::CID2_Reply_Data &  data  ) private ◆ x_SendChunkBlobProps() ◆ x_SendError() [1/4] void CPSGS_SNPProcessor::x_SendError ( const string &  msg ) private ◆ x_SendError() [2/4] void CPSGS_SNPProcessor::x_SendError ( const string &  msg, const exception &  exc  ) private ◆ x_SendError() [3/4]

Definition at line 389 of file snp_processor.cpp.

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

Referenced by CanProcess(), CreateProcessor(), OnGotAnnotation(), OnGotBlobByBlobId(), OnGotChunk(), Process(), WhatCanProcess(), and x_SendError().

◆ x_SendError() [4/4] ◆ x_SendMainEntry() void CPSGS_SNPProcessor::x_SendMainEntry ( const SSNPData &  data ) private ◆ x_SendSplitInfo() void CPSGS_SNPProcessor::x_SendSplitInfo ( const SSNPData &  data ) private

Definition at line 892 of file snp_processor.cpp.

References data, eNARetrieve, info, kSplitInfoChunk, m_PSGBlobId, NStr::NumericToString(), s_SetBlobDataProps(), CBlobRecord::SetId2Info(), x_RegisterTimingFound(), x_SendBlobProps(), x_SendChunkBlobData(), x_SendChunkBlobProps(), and x_WriteData().

Referenced by x_SendBlob().

◆ x_SignalStartProcessing() bool CPSGS_SNPProcessor::x_SignalStartProcessing ( void  ) private ◆ x_UnlockRequest() void CPSGS_SNPProcessor::x_UnlockRequest ( void  ) private ◆ x_WriteData() void CPSGS_SNPProcessor::x_WriteData ( objects::CID2_Reply_Data &  data, const CSerialObject &  obj  ) const private ◆ m_Canceled ◆ m_ChunkId int CPSGS_SNPProcessor::m_ChunkId private ◆ m_Client shared_ptr<CSNPClient> CPSGS_SNPProcessor::m_Client mutableprivate ◆ m_Config ◆ m_Id2Info string CPSGS_SNPProcessor::m_Id2Info private ◆ m_Mutex ◆ m_PreResolving bool CPSGS_SNPProcessor::m_PreResolving private ◆ m_ProcessNAs vector<string> CPSGS_SNPProcessor::m_ProcessNAs private ◆ m_PSGBlobId string CPSGS_SNPProcessor::m_PSGBlobId private ◆ m_ScaleLimit objects::CSeq_id::ESNPScaleLimit CPSGS_SNPProcessor::m_ScaleLimit private ◆ m_SeqIds ◆ m_SNPData vector<SSNPData> CPSGS_SNPProcessor::m_SNPData private ◆ m_SNPDataError string CPSGS_SNPProcessor::m_SNPDataError private ◆ m_Start ◆ m_Status ◆ m_ThreadPool shared_ptr<ncbi::CThreadPool> CPSGS_SNPProcessor::m_ThreadPool private ◆ m_Unlocked bool CPSGS_SNPProcessor::m_Unlocked private

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

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