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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/snp__processor_8cpp_source.html below:

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

*

=

*

(

);

(

.GetData_compression() ==

.eData_compression_gzip ) {

error_rate =

(SNP_PROCESSOR, ERROR_RATE)::GetDefault();

( error_rate > 0 ) {

error_counter = 0;

( ++error_counter >= error_rate ) {

m_PreResolving(

),

m_ScaleLimit(

::eSNPScaleLimit_Default)

shared_ptr<CPSGS_Request> request,

shared_ptr<CPSGS_Reply> reply,

this, placeholders::_1),

this, placeholders::_1, placeholders::_2, placeholders::_3, placeholders::_4),

m_Config(parent.m_Config),

m_Client(parent.m_Client),

m_ThreadPool(parent.m_ThreadPool),

m_Status(ePSGS_InProgress),

m_PreResolving(

),

m_ScaleLimit(

::eSNPScaleLimit_Default)

(

);

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

enabled = app->Settings().m_SNPProcessorsEnabled;

shared_ptr<CPSGS_Reply> reply)

(!

(*request))

vector<string>();

( exception& exc ) {

(reply,

, exc);

shared_ptr<CPSGS_Reply> reply)

(!

->CanProcessRequest(*request, 0))

;

( exception& exc ) {

(reply,

, exc);

shared_ptr<CPSGS_Request> request,

shared_ptr<CPSGS_Reply> reply,

( exception& exc ) {

(reply,

, exc);

reply->PrepareProcessorMessage(reply->GetItemId(),

,

,

&

,

exception& exc)

req_type =

()->GetRequestType();

(exception& exc) {

(

, exc);

(!annot_request.

.empty()) {

(exception& e) {

(

&

: annot_request.

) {

(exception& e) {

need_resolve =

;

need_resolve =

;

(!

->m_AllowNonRefSeq) {

(!

->IsValidSeqId(

))

;

(exception& exc) {

.m_Error =

+

(exc.what());

s.m_Error =

;

( !

.m_Error.empty() ) {

(exception& exc) {

( has_error.count(name) ) {

( !has_data.count(name) ) {

GetTiming().Register(

,

, status, start, blob_size);

blob_size = 0;

(

& chunk :

.GetData() ) {

blob_size += chunk->size();

COSSWriter writer(

.SetData());

+

,

ostringstream annot_str;

(

& it :

.m_AnnotInfo) {

item_id = reply.GetItemId();

reply.PrepareBlobPropData(item_id,

(), psg_blob_id, data_to_send);

reply.PrepareBlobPropCompletion(item_id,

(), 2);

item_id =

()->GetItemId();

(

& chunk :

.GetData() ) {

(

*)chunk->data(), chunk->size(), chunk_no++);

item_id =

()->GetItemId();

()->PrepareTSEBlobPropData(item_id,

(), chunk_id, id2_info, data_to_send);

item_id =

()->GetItemId();

(

& chunk :

.GetData() ) {

(

*)chunk->data(), chunk->size(), chunk_no++,

()->PrepareTSEBlobCompletion(item_id,

(), chunk_no+1);

&

= bioseq_resolution.GetBioseqInfo();

(

->IsValidSeqId(

.GetAccession(),

.GetSeqIdType(),

.GetVersion())) {

(

& it :

.GetSeqIds()) {

(!

->IsValidSeqId(get<1>(it), get<0>(it)))

;

(

<< (err.empty() ? get<1>(it) : err));

& message)

(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();

(final_state) fetch_details->SetReadFinished();

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

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

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

fetch_details->SetReadFinished();

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

CBlobRecord & SetNChunks(int32_t value)

CBlobRecord & SetId2Info(string const &value)

CBlobRecord & SetGzip(bool value)

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.

static CJsonNode NewObjectNode()

Create a new JSON object node.

list< TOctetString * > TOctetStringSequence

virtual ERW_Result Flush(void)

Flush pending data (if any) down to the output device.

COSSWriter(TOctetStringSequence &out)

TOctetStringSequence & m_Output

vector< char > TOctetString

virtual ERW_Result Write(const void *buffer, size_t count, size_t *written)

Write up to "count" bytes from the buffer pointed to by the "buf" argument onto the output device.

CObjectOStreamAsnBinary –.

void UpdateOverallStatus(CRequestStatus::ECode status)

list< unique_ptr< CCassFetch > > m_FetchDetails

bool AreAllFinishedRead(void) const

void SignalFinishProcessing(void)

virtual void Cancel(void) override

The infrastructure request to cancel processing.

@ ePSGS_AnnotationRequest

@ ePSGS_BlobBySatSatKeyRequest

TRequest & GetRequest(void)

void ResolveInputSeqId(void)

void x_ProcessAnnotationRequest(void)

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.

shared_ptr< CSNPClient > m_Client

void x_UnlockRequest(void)

void x_RegisterTimingFound(psg_time_point_t start, EPSGOperation operation, const objects::CID2_Reply_Data &data)

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

void x_SendAnnotInfo(void)

void x_WriteData(objects::CID2_Reply_Data &data, const CSerialObject &obj) const

string GetName(void) const override

Tells the processor name (used in logging and tracing)

bool x_IsEnabled(CPSGS_Request &request) const

void x_Finish(EPSGS_Status status)

void x_Peek(bool need_wait)

void x_RegisterTimingNotFound(EPSGOperation operation)

void x_SendChunkBlobProps(const string &id2_info, int chunk_id, CBlobRecord &blob_props)

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

Tells if processor can process the given request.

bool x_SignalStartProcessing()

void ProcessEvent(void) override

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

~CPSGS_SNPProcessor(void) override

shared_ptr< ncbi::CThreadPool > m_ThreadPool

void x_InitClient(void) const

void x_ReportResultStatusForAllNA(SPSGS_AnnotRequest::EPSGS_ResultStatus status)

shared_ptr< SSNPProcessor_Config > m_Config

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

void x_SendBlobData(const string &psg_blob_id, const objects::CID2_Reply_Data &data)

void x_SendChunkBlobData(const string &id2_info, int chunk_id, const objects::CID2_Reply_Data &data)

vector< SSNPData > m_SNPData

void x_OnSeqIdResolveFinished(SBioseqResolution &&bioseq_resolution)

EPSGS_Status GetStatus(void) override

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

string GetGroupName(void) const override

Tells the processor group name.

void x_ProcessBlobBySatSatKeyRequest(void)

vector< CSeq_id_Handle > m_SeqIds

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.

void OnGotBlobByBlobId(void)

void x_SendBlobProps(const string &psg_blob_id, CBlobRecord &blob_props)

void OnGotAnnotation(void)

void Cancel(void) override

The infrastructure request to cancel processing.

void x_ProcessTSEChunkRequest(void)

vector< string > m_ProcessNAs

void Process(void) override

Main processing function.

void GetBlobByBlobId(void)

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

void x_SendMainEntry(const SSNPData &data)

void x_SendSplitInfo(const SSNPData &data)

objects::CSeq_id::ESNPScaleLimit m_ScaleLimit

void x_OnResolutionGoodData(void)

static CPubseqGatewayApp * GetInstance(void)

virtual EStatus Execute(void) override

Do the actual job.

CSNPThreadPoolTask_GetAnnotation(CPSGS_SNPProcessor &processor)

CPSGS_SNPProcessor & m_Processor

virtual EStatus Execute(void) override

Do the actual job.

CSNPThreadPoolTask_GetBlobByBlobId(CPSGS_SNPProcessor &processor)

CPSGS_SNPProcessor & m_Processor

virtual EStatus Execute(void) override

Do the actual job.

CPSGS_SNPProcessor & m_Processor

CSNPThreadPoolTask_GetChunk(CPSGS_SNPProcessor &processor)

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.

Writer-based output stream.

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.

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

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.

TProcessorPriority m_Priority

A very basic data-write interface.

iterator_bool insert(const value_type &val)

std::ofstream out("events_result.xml")

main entry point for tests

void swap(NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair1, NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair2)

EDiagSev

Severity level for the posted diagnostics.

@ eDiag_Error

Error message.

@ e500_InternalServerError

#define MSerial_AsnBinary

static ESNPScaleLimit GetSNPScaleLimit_Value(const string &name)

static CSeq_id_Handle GetHandle(const CSeq_id &id)

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

#define NCBI_PARAM_TYPE(section, name)

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

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

Get boolean value of specified parameter name.

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 string GetString(const string &section, const string &name, const string &default_value, TFlags flags=0) const

Get the parameter string value.

ERW_Result

Result codes for I/O operations.

@ eRW_Success

Everything is okay, I/O completed.

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.

static enable_if< is_arithmetic< TNumeric >::value||is_convertible< TNumeric, Int8 >::value, string >::type NumericToString(TNumeric value, TNumToStringFlags flags=0, int base=10)

Convert numeric value to string.

EStatus

Status of the task.

@ eCompleted

executed successfully

#define DEFINE_STATIC_FAST_MUTEX(id)

Define static fast mutex and initialize it.

operation

Bit operations.

@ eData_format_asn_binary

E_Choice

Choice variants.

const int64_t kSplitInfoChunk

Pool of generic task-executing threads.

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

#define PSG_ERROR(message)

chrono::steady_clock psg_clock_t

psg_clock_t::time_point psg_time_point_t

Reader-writer based streams.

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

NCBI_PARAM_DEF(int, SNP_PROCESSOR, ERROR_RATE, 0)

#define DEFAULT_FILE_REOPEN_TIME

static bool s_SimulateError()

#define PARAM_FILE_RECHECK_TIME

static void s_OnGotAnnotation(void *data)

#define DEFAULT_SNP_SCALE_LIMIT

#define PARAM_ALLOW_NON_REFSEQ

#define DEFAULT_FILE_RECHECK_TIME

NCBI_PARAM_DECL(int, SNP_PROCESSOR, ERROR_RATE)

#define DEFAULT_GC_CACHE_SIZE

static const string kSNPProcessorGroupName

#define PARAM_GC_CACHE_SIZE

#define PARAM_FILE_REOPEN_TIME

#define PARAM_MISSING_GC_SIZE

#define PARAM_FILE_OPEN_RETRY

#define DEFAULT_ANNOT_NAME

#define DEFAULT_FILE_OPEN_RETRY

static const string kParamMaxConn

#define DEFAULT_MISSING_GC_SIZE

#define PARAM_SNP_SCALE_LIMIT

#define DEFAULT_ALLOW_NON_REFSEQ

static const string kSNPProcessorSection

static const int kDefaultMaxConn

static const string kSNPProcessorName

static void s_OnGotBlobByBlobId(void *data)

static void s_OnGotChunk(void *data)

void s_SetBlobDataProps(CBlobRecord &blob_props, const CID2_Reply_Data &data)

const string kSNPProcessorEvent

TProcessorPriority RegisterProcessedName(TProcessorPriority priority, const string &name)

optional< CSeq_id::ESNPScaleLimit > m_SNPScaleLimit

vector< string > m_SeqIds

void ReportResultStatus(const string &annot_name, EPSGS_ResultStatus rs)

vector< string > m_DisabledProcessors

vector< string > m_EnabledProcessors

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