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

error_rate =

(CDD_PROCESSOR, ERROR_RATE)::GetDefault();

( error_rate > 0 ) {

error_counter = 0;

( ++error_counter >= error_rate ) {

m_Status(ePSGS_NotFound),

(3u, max_conn), max_conn)));

shared_ptr<CCDDClientPool> client_pool,

shared_ptr<CThreadPool> thread_pool,

shared_ptr<CPSGS_Request> request,

shared_ptr<CPSGS_Reply> reply,

: m_ClientPool(client_pool),

m_Status(ePSGS_InProgress),

m_ThreadPool(thread_pool)

shared_ptr<CPSGS_Reply> reply)

vector<string> can_process;

(

& name : annot_request.

) {

can_process.push_back(name);

( exception& exc ) {

(reply,

, exc);

shared_ptr<CPSGS_Reply> reply)

req_type = request->GetRequestType();

( exception& exc ) {

(reply,

, exc);

shared_ptr<CPSGS_Reply> reply,

req_type = request->GetRequestType();

( exception& exc ) {

(reply,

, exc);

&

,

exception& exc)

req_type =

()->GetRequestType();

(exception& exc) {

(

, exc);

(

&

: annot_request.

) {

(annot_request.

== SPSGS_BlobRequestBase::EPSGS_TSEOption::ePSGS_SmartTSE ||

annot_request.

== SPSGS_BlobRequestBase::EPSGS_TSEOption::ePSGS_WholeTSE ||

annot_request.

== SPSGS_BlobRequestBase::EPSGS_TSEOption::ePSGS_OrigTSE) {

+

+

.AsString(),

(exception& exc) {

+

+ exc.what(),

=

+

(exc.what());

(exception& exc) {

+

+ exc.what(),

=

+

(exc.what());

(exception& exc) {

+

+ exc.what(),

=

+

(exc.what());

=

;

(exception& exc) {

=

+

(exc.what());

=

;

(exception& exc) {

=

+

(exc.what());

=

;

(exception& exc) {

=

+

(exc.what());

+

,

annot_info->SetFeat().push_back(feat_info);

annot_info->SetFeat().push_back(feat_info);

( annot_id.

() ) {

annot_info->SetSeq_loc().SetWhole_gi(annot_id.

());

annot_info->SetSeq_loc().SetWhole_seq_id().Assign(annot_id);

ostringstream annot_str;

entry->

().push_back(annot);

ostringstream blob_str;

blob_data = blob_str.str();

item_id =

()->GetItemId();

(

*)blob_data.data(), blob_data.size(), 0);

+

,

(!

.IsGi() && !

.GetTextseq_Id())

;

(exception& e) {

(

&

: annot_request.

) {

blob_id && blob_id->GetSat() ==

;

(

& name :

) {

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

static bool s_SimulateError()

static void s_OnGotBlobBySeqId(void *data)

static void s_OnGotBlobId(void *data)

static const string kCDDProcessorSection

static const string kCDDProcessorName

NCBI_PARAM_DEF(int, CDD_PROCESSOR, ERROR_RATE, 0)

NCBI_PARAM_DECL(int, CDD_PROCESSOR, ERROR_RATE)

static const string kCDDAnnotName

const CID2_Blob_Id::TSat kCDDSat

static const string kParamMaxConn

static const int kDefaultMaxConn

static void s_OnGotBlobByBlobId(void *data)

static const string kCDDProcessorGroupName

static const double kDefaultCDDBackendTimeout

static const string kParamCDDBackendTimeout

const string kCDDProcessorEvent

CBlobRecord & SetNChunks(int32_t value)

CBlobRecord & SetModified(TTimestamp value)

static CRef< TBlobId > StringToBlobId(const string &s)

static string BlobIdToString(const TBlobId &blob_id)

CCDDThreadPoolTask_GetBlobByBlobId(CPSGS_CDDProcessor &processor)

virtual EStatus Execute(void) override

Do the actual job.

CPSGS_CDDProcessor & m_Processor

CPSGS_CDDProcessor & m_Processor

virtual EStatus Execute(void) override

Do the actual job.

CCDDThreadPoolTask_GetBlobBySeqId(CPSGS_CDDProcessor &processor)

virtual EStatus Execute(void) override

Do the actual job.

CCDDThreadPoolTask_GetBlobId(CPSGS_CDDProcessor &processor)

CPSGS_CDDProcessor & m_Processor

CCDD_Reply_Get_Blob_Id –.

CID2S_Feat_type_Info –.

CID2S_Seq_annot_Info –.

string Repr(TReprFlags flags=0) const

Return a string representation of this node.

void SetString(const string &key, const string &value)

Set a JSON object element to the specified string value.

void SetInteger(const string &key, Int8 value)

Set a JSON object element to the specified integer value.

static CJsonNode NewObjectNode()

Create a new JSON object node.

void x_UnlockRequest(void)

void x_SendAnnotInfo(const objects::CCDD_Reply_Get_Blob_Id &blob_info)

vector< objects::CSeq_id_Handle > m_SeqIds

void x_SendAnnot(const objects::CID2_Blob_Id &id2_blob_id, CRef< objects::CSeq_annot > &annot)

bool x_CanProcessAnnotRequestIds(SPSGS_AnnotRequest &annot_request) const

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.

bool x_SignalStartProcessing()

void GetBlobByBlobId(void)

void OnGotBlobByBlobId(void)

void x_Finish(EPSGS_Status status)

objects::CCDDClientPool::SCDDBlob m_CDDBlob

void x_ProcessGetBlobRequest(void)

string GetGroupName(void) const override

Tells the processor group name.

bool x_CanProcessSeq_id(const string &psg_id) const

void x_RegisterTimingNotFound(EPSGOperation operation)

void Process(void) override

Main processing function.

~CPSGS_CDDProcessor(void) override

void GetBlobBySeqId(void)

bool x_NameIncluded(const vector< string > &names) const

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.

bool x_IsEnabled(CPSGS_Request &request) const

void Cancel(void) override

The infrastructure request to cancel processing.

bool x_CanProcessAnnotRequest(SPSGS_AnnotRequest &annot_request, TProcessorPriority priority) const

void x_ReportResultStatus(SPSGS_AnnotRequest::EPSGS_ResultStatus status)

void OnGotBlobBySeqId(void)

string GetName(void) const override

Tells the processor name (used in logging and tracing)

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

Tells if processor can process the given request.

EPSGS_Status GetStatus(void) override

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

shared_ptr< ncbi::CThreadPool > m_ThreadPool

CRef< objects::CCDDClientPool::TBlobId > m_BlobId

static void x_SendError(shared_ptr< CPSGS_Reply > reply, const string &msg)

void x_RegisterTiming(EPSGOperation operation, EPSGOperationStatus status, size_t size)

bool x_CanProcessBlobRequest(SPSGS_BlobBySatSatKeyRequest &blob_request) const

shared_ptr< objects::CCDDClientPool > m_ClientPool

void x_ProcessResolveRequest(void)

@ ePSGS_AnnotationRequest

@ ePSGS_BlobBySatSatKeyRequest

TRequest & GetRequest(void)

static CPubseqGatewayApp * GetInstance(void)

const SPubseqGatewaySettings & Settings(void) const

Abstract class for representing single task executing in pool of threads To use this class in applica...

Main class implementing functionality of pool of threads.

CTimeout – Timeout interval.

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

shared_ptr< CPSGS_Reply > GetReply(void) const

Provides the reply wrapper.

shared_ptr< CPSGS_Request > GetRequest(void) const

Provides the user request.

bool IsUVThreadAssigned(void) const

Tells if a libuv thread id has been assigned to the processor.

shared_ptr< CPSGS_Reply > m_Reply

TProcessorPriority GetPriority(void) const

Provides the processor priority.

EPSGS_Status

The GetStatus() method returns a processor current status.

void PostponeInvoke(CPSGS_UvLoopBinder::TProcessorCB cb, void *user_data)

The provided callback will be called from the libuv loop assigned to the processor.

void SignalFinishProcessing(void)

A processor should call this method when it decides that there is nothing else to be done.

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

TProcessorPriority m_Priority

static const struct name_t names[]

@ eDiag_Error

Error message.

@ e500_InternalServerError

#define MSerial_AsnBinary

static CSeq_id_Handle GetHandle(const CSeq_id &id)

Normal way of getting a handle, works for any seq-id.

void Reset(void)

Reset reference object.

#define NCBI_PARAM_TYPE(section, name)

Generate typename for a parameter from its {section, name} attributes.

virtual int GetInt(const string &section, const string &name, int default_value, TFlags flags=0, EErrAction err_action=eThrow) const

Get integer value of specified parameter name.

virtual double GetDouble(const string &section, const string &name, double default_value, TFlags flags=0, EErrAction err_action=eThrow) const

Get double value of specified parameter name.

static string Base64Encode(const CTempString str, size_t line_len=0)

Base64-encode string.

static bool EqualNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive equality of a substring with another string.

EStatus

Status of the task.

@ eCompleted

executed successfully

@ eDefault

Default timeout (to be interpreted by the client code)

operation

Bit operations.

const TBlob_id & GetBlob_id(void) const

Get the Blob_id member data.

const TSeq_id & GetSeq_id(void) const

Get the Seq_id member data.

TVersion GetVersion(void) const

Get the Version member data.

bool IsSetVersion(void) const

version of blob, optional in some requests Check if a value has been assigned to Version data member.

@ e_Region

named region (globin locus)

TGi GetGi(void) const

Get the variant data.

bool IsGi(void) const

Check if variant Gi is selected.

TSet & SetSet(void)

Select the variant.

TSeq_set & SetSeq_set(void)

Assign a value to Seq_set data member.

Pool of generic task-executing threads.

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

chrono::steady_clock psg_clock_t

static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

TProcessorPriority RegisterProcessedName(TProcessorPriority priority, const string &name)

vector< string > GetNotProcessedName(TProcessorPriority priority)

vector< string > m_SeqIds

void ReportResultStatus(const string &annot_name, EPSGS_ResultStatus rs)

EPSGS_TSEOption m_TSEOption

vector< string > m_DisabledProcessors

vector< string > m_EnabledProcessors

bool m_CDDProcessorsEnabled

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