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NCBI C++ ToolKit: src/app/pubseq_gateway/server/get_processor.cpp Source File

std::placeholders;

shared_ptr<CPSGS_Reply> reply,

this, _1, _2, _3, _4),

this, _1, _2, _3, _4, _5),

this, _1, _2, _3, _4, _5))

shared_ptr<CPSGS_Reply> reply)

startup_data_state = app->GetStartupDataState();

(request->NeedTrace()) {

+

request->GetStartTimestamp());

shared_ptr<CPSGS_Reply> reply,

& message)

& bioseq_info_record = bioseq_resolution.GetBioseqInfo();

bioseq_info_record.GetAccession(),

bioseq_info_record.GetName(),

bioseq_info_record.GetVersion());

}

(

exception & exc) {

(

+

(exc.what()));

(

);

bioseq_resolution.GetBioseqInfo().GetSatKey(),

need_to_check_blob_exclude_cache =

(need_to_check_blob_exclude_cache) {

completed =

;

(app->GetExcludeBlobCache()->IsInCache(

completed, completed_time)) {

finish_processing =

;

sent_mks_ago < m_BlobRequest->m_ResendTimeoutMks) {

app->GetExcludeBlobCache()->Remove(

finish_processing =

;

(finish_processing) {

, _1, _2, _3, _4, _5));

(populate_result) {

shared_ptr<CCassConnection> cass_connection;

(!cass_connection) {

}

(

exception & exc) {

unique_ptr<CCassBlobFetch> fetch_details;

unique_ptr<CBlobRecord> blob_record(

);

blob_prop_cache_lookup_result =

std::move(blob_record),

fetch_details->SetLoader(load_task);

,

,

fetch_details->RemoveFromExcludeBlobCache();

fetch_details->SetLoader(load_task);

, _1, _2, _3, _4, _5),

fetch_details.get()));

+

& message)

* chunk_data,

data_size,

chunk_data, data_size, chunk_no);

(details->InPeek()) {

details->SetInPeek(

);

(details, need_wait);

details->SetInPeek(

);

details->SetExcludeBlobCacheCompleted();

(!fetch_details->GetLoader())

final_state =

;

(!fetch_details->ReadFinished()) {

final_state = fetch_details->GetLoader()->Wait();

fetch_details->SetReadFinished();

(fetch_details->GetLoader()->HasError() &&

= fetch_details->GetLoader()->LastError();

fetch_details->GetLoader()->ClearError();

fetch_details->SetReadFinished();

& message)

const string kCassandraProcessorGroupName

const string kCassandraProcessorEvent

void SetDataReadyCB(shared_ptr< CCassDataCallbackReceiver > callback)

void SetPropsCallback(TBlobPropsCallback callback)

void SetErrorCB(TDataErrorCallback error_cb)

EPSGS_CacheLookupResult LookupBlobProp(IPSGS_Processor *processor, int sat, int sat_key, int64_t &last_modified, CBlobRecord &blob_record)

EPSGS_AccessionAdjustmentResult AdjustBioseqAccession(SBioseqResolution &bioseq_resolution)

void OnGetBlobChunk(bool cancelled, CCassBlobFetch *fetch_details, const unsigned char *chunk_data, unsigned int data_size, int chunk_no)

void OnGetBlobProp(CCassBlobFetch *fetch_details, CBlobRecord const &blob, bool is_found)

void PrepareServerErrorMessage(CCassBlobFetch *fetch_details, int code, EDiagSev severity, const string &message)

void OnGetBlobError(CCassBlobFetch *fetch_details, CRequestStatus::ECode status, int code, EDiagSev severity, const string &message)

void ReportFailureToGetCassConnection(void)

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)

void UpdateOverallStatus(CRequestStatus::ECode status)

bool IsCassandraProcessorEnabled(shared_ptr< CPSGS_Request > request) const

SCass_BlobId TranslateSatToKeyspace(CBioseqInfoRecord::TSat sat, CBioseqInfoRecord::TSatKey sat_key, const string &seq_id)

EPSGS_MyNCBILookupResult PopulateMyNCBIUser(TMyNCBIDataCB data_cb, TMyNCBIErrorCB error_cb)

void ReportSecureSatUnauthorized(const string &user_name)

list< unique_ptr< CCassFetch > > m_FetchDetails

@ ePSGS_FoundInNotFoundCache

@ ePSGS_IncludeHUPSetToNo

@ ePSGS_FoundInErrorCache

bool AreAllFinishedRead(void) const

bool IsMyNCBIFinished(void) const

void UnlockWaitingProcessor(void)

void CleanupMyNCBICache(void)

IPSGS_Processor::EPSGS_Status GetStatus(void) override

Tells the processor status (if it has finished or in progress)

void ReportMyNCBINotFound(void)

void ReportMyNCBIError(CRequestStatus::ECode status, const string &my_ncbi_message)

void SignalFinishProcessing(void)

optional< string > m_UserName

void x_OnMyNCBIData(const string &cookie, CPSG_MyNCBIRequest_WhoAmI::SUserInfo user_info)

void x_GetBlobFinalStage(void)

void OnGetBlobError(CCassBlobFetch *fetch_details, CRequestStatus::ECode status, int code, EDiagSev severity, const string &message)

virtual EPSGS_Status GetStatus(void)

Tells the processor status (if it has finished or in progress)

virtual string GetName(void) const

Tells the processor name (used in logging and tracing)

void x_Peek(bool need_wait)

virtual bool CanProcess(shared_ptr< CPSGS_Request > request, shared_ptr< CPSGS_Reply > reply) const

Tells if processor can process the given request.

void x_OnResolutionGoodData(void)

virtual ~CPSGS_GetProcessor()

void OnGetBlobProp(CCassBlobFetch *fetch_details, CBlobRecord const &blob, bool is_found)

virtual void Process(void)

Main processing function.

void x_SendBioseqInfo(SBioseqResolution &bioseq_resolution)

void OnGetBlobChunk(CCassBlobFetch *fetch_details, CBlobRecord const &blob, const unsigned char *chunk_data, unsigned int data_size, int chunk_no)

virtual void ProcessEvent(void)

Called when an event happened which may require to have some processing.

bool x_IsExcludedBlob(void) const

virtual IPSGS_Processor * CreateProcessor(shared_ptr< CPSGS_Request > request, shared_ptr< CPSGS_Reply > reply, TProcessorPriority priority) const

Create processor to fulfil PSG request using the data source.

void x_OnSeqIdResolveFinished(SBioseqResolution &&bioseq_resolution)

vector< SCass_BlobId > m_ExcludeBlobs

virtual string GetGroupName(void) const

Tells the processor group name.

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

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

SPSGS_BlobBySeqIdRequest * m_BlobRequest

@ ePSGS_BlobBySeqIdRequest

void ResolveInputSeqId(void)

static CPubseqGatewayApp * GetInstance(void)

Interface class (and self-factory) for request processor objects that can retrieve data from a given ...

shared_ptr< CPSGS_Reply > m_Reply

EPSGS_Status

The GetStatus() method returns a processor current status.

EPSGS_StartProcessing SignalStartProcessing(void)

A processor should call the method when it decides that it successfully started processing the reques...

shared_ptr< CPSGS_Request > m_Request

static const string kGetProcessorName

EDiagSev

Severity level for the posted diagnostics.

@ eDiag_Error

Error message.

@ e500_InternalServerError

CSeq_id & Set(const CTempString &the_id, TParseFlags flags=fParse_AnyRaw)

Reassign based on flat specifications; arguments interpreted as with constructors.

E_Choice

Choice variants.

string ToJsonString(const CBioseqInfoRecord &bioseq_info, SPSGS_ResolveRequest::TPSGS_BioseqIncludeData include_data_flags, const string &custom_blob_id)

#define PSG_ERROR(message)

#define PSG_WARNING(message)

psg_clock_t::time_point psg_time_point_t

unsigned long GetTimespanToNowMks(const psg_time_point_t &t_point)

string GetCassStartupDataStateMessage(EPSGS_StartupDataState state)

EPSGS_ResolutionResult m_ResolutionResult

CBioseqInfoRecord & GetBioseqInfo(void)

bool AdjustName(shared_ptr< CPSGS_Request > request, shared_ptr< CPSGS_Reply > reply)

string ToString(void) const

CBioseqInfoRecord::TSat m_Sat

optional< SSatInfoEntry > m_Keyspace

optional< bool > m_IsSecureKeyspace

CBioseqInfoRecord::TSatKey m_SatKey

vector< string > m_ExcludeBlobs

unsigned long m_ResendTimeoutMks

EPSGS_CacheAndDbUse m_UseCache

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