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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/wgs__processor_8cpp_source.html below:

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

*

=

*

(

);

error_rate =

(WGS_PROCESSOR, ERROR_RATE)::GetDefault();

( error_rate > 0 ) {

error_counter = 0;

( ++error_counter >= error_rate ) {

m_Status(ePSGS_NotFound),

shared_ptr<CWGSClient>&

,

shared_ptr<ncbi::CThreadPool> thread_pool,

shared_ptr<CPSGS_Request> request,

shared_ptr<CPSGS_Reply> reply,

m_Status(ePSGS_InProgress),

m_ThreadPool(thread_pool)

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

shared_ptr<CPSGS_Reply>

)

->CanProcessRequest(*request);

shared_ptr<CPSGS_Reply> reply,

( !

->CanProcessRequest(*request) )

;

req_type =

()->GetRequestType();

(exception& exc) {

(

, exc);

enabled = app->Settings().m_WGSProcessorsEnabled;

(

<< (err.empty() ? resolve_request.

: err));

+

+

->AsFastaString() +

,

(exception& exc) {

(exception& exc) {

(

<< (err.empty() ? get_request.

: err));

+

+

->AsFastaString() +

,

(exception& exc) {

(exception& exc) {

(

, exc);

(exception& exc) {

(exception& exc) {

(

, exc);

(exception& exc) {

(exception& exc) {

(

, exc);

(

.GetData_compression() ==

.eData_compression_gzip ) {

GetTiming().Register(

,

, status, start, blob_size);

blob_size = 0;

(

& chunk :

.GetData() ) {

blob_size += chunk->size();

item_id =

()->GetItemId();

()->PrepareBioseqData(item_id,

(), data_to_send, output_format);

item_id = reply.GetItemId();

reply.PrepareBlobPropData(item_id,

(), psg_blob_id, data_to_send);

reply.PrepareBlobPropCompletion(item_id,

(), 2);

item_id = reply.GetItemId();

reply.PrepareBlobMessage(item_id,

(),

,

reply.PrepareBlobCompletion(item_id,

(), 2);

item_id =

()->GetItemId();

(

& chunk :

.GetData() ) {

(

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

& id2_info,

item_id =

()->GetItemId();

()->PrepareTSEBlobPropData(item_id,

(), chunk_id, id2_info, data_to_send);

& id2_info,

item_id =

()->GetItemId();

(

& chunk :

.GetData() ) {

(

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

()->PrepareTSEBlobCompletion(item_id,

(), chunk_no+1);

split_version =

->m_SplitVersion;

id2_info =

(id2_blob_id, split_version);

main_blob_id =

->m_BlobId;

& psg_blob_id =

->m_BlobId;

(

->m_Data->GetMainObject().GetThisTypeInfo() == CID2S_Split_Info::GetTypeInfo() ) {

split_version =

->m_SplitVersion;

id2_info =

(id2_blob_id, split_version);

COSSWriter writer(

.SetData());

&

)

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

,

,

&

,

exception& exc)

s <<

<< blob_version <<

<< split_version;

cache_result = app->GetExcludeBlobCache()->AddBlobId(

completed, completed_time);

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

const string kCassandraProcessorEvent

virtual void Serialize(CObjectOStreamAsnBinary &out) const

CBlobRecord & SetNChunks(int32_t value)

CBlobRecord & SetId2Info(string const &value)

CBlobRecord & SetSuppress(bool value)

CBlobRecord & SetGzip(bool value)

CBlobRecord & SetWithdrawn(bool value)

CBlobRecord & SetDead(bool value)

CBlobRecord & SetModified(TTimestamp value)

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 –.

@ ePSGS_BlobBySatSatKeyRequest

@ ePSGS_BlobBySeqIdRequest

TRequest & GetRequest(void)

void x_SendResult(const string &data_to_send, EOutputFormat output_format)

void x_SendChunkBlobData(const string &id2_info, TID2ChunkId chunk_id, const objects::CID2_Reply_Data &data)

void x_ProcessBlobBySatSatKeyRequest(void)

void OnGotBlobBySeqId(void)

void GetBlobBySeqId(void)

void x_ProcessResolveRequest(void)

void x_InitClient(void) const

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

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

EPSGS_Status GetStatus(void) override

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

EOutputFormat x_GetOutputFormat(void)

string GetName(void) const override

Tells the processor name (used in logging and tracing)

void Process(void) override

Main processing function.

bool x_CheckExcludedCache(void)

void x_ProcessTSEChunkRequest(void)

void x_Finish(EPSGS_Status status)

string GetGroupName(void) const override

Tells the processor group name.

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

CRef< objects::CSeq_id > m_SeqId

unsigned long m_ResendTimeoutMks

void x_WriteData(objects::CID2_Reply_Data &data, const objects::CAsnBinData &obj, bool compress) const

void OnGotBlobByBlobId(void)

void x_UnlockRequest(void)

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

Tells if processor can process the given request.

shared_ptr< CWGSClient > m_Client

void x_RegisterTimingNotFound(EPSGOperation operation)

shared_ptr< ncbi::CThreadPool > m_ThreadPool

void OnResolvedSeqId(void)

static string GetPSGId2Info(const CID2_Blob_Id &tse_id, CWGSClient::TID2SplitVersion split_version)

shared_ptr< SWGSData > m_WGSData

void GetBlobByBlobId(void)

void x_ProcessBlobBySeqIdRequest(void)

void x_SendSplitInfo(void)

unsigned long m_SentMksAgo

void x_SendForbidden(void)

~CPSGS_WGSProcessor(void) override

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.

void x_SendBlobForbidden(const string &psg_blob_id)

void Cancel(void) override

The infrastructure request to cancel processing.

void x_SetExcludedCacheCompleted(void)

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

void x_WaitForOtherProcessors(void)

void x_RemoveFromExcludedCache(void)

bool m_AddedToExcludedCache

bool x_SignalStartProcessing()

void x_SendChunkBlobProps(const string &id2_info, TID2ChunkId chunk_id, CBlobRecord &blob_props)

void x_SendMainEntry(void)

void x_SendBioseqInfo(void)

shared_ptr< SWGSProcessor_Config > m_Config

EOutputFormat m_OutputFormat

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

bool x_IsEnabled(CPSGS_Request &request) const

static CPubseqGatewayApp * GetInstance(void)

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.

static bool IsOSGBlob(const CID2_Blob_Id &blob_id)

virtual EStatus Execute(void) override

Do the actual job.

CPSGS_WGSProcessor & m_Processor

CWGSThreadPoolTask_GetBlobByBlobId(CPSGS_WGSProcessor &processor)

CWGSThreadPoolTask_GetBlobBySeqId(CPSGS_WGSProcessor &processor)

CPSGS_WGSProcessor & m_Processor

virtual EStatus Execute(void) override

Do the actual job.

CWGSThreadPoolTask_GetChunk(CPSGS_WGSProcessor &processor)

CPSGS_WGSProcessor & m_Processor

virtual EStatus Execute(void) override

Do the actual job.

CWGSThreadPoolTask_ResolveSeqId(CPSGS_WGSProcessor &processor)

CPSGS_WGSProcessor & m_Processor

virtual EStatus Execute(void) override

Do the actual job.

Writer-based output stream.

CZipStreamCompressor – zlib based compression stream processor.

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

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

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.

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

main entry point for tests

static const char * str(char *buf, int n)

@ eNoOwnership

No ownership is assumed.

@ eDiag_Error

Error message.

@ e500_InternalServerError

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.

ERW_Result

Result codes for I/O operations.

@ eRW_Success

Everything is okay, I/O completed.

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.

TVersion GetVersion(void) const

Get the Version member data.

TSat_key GetSat_key(void) const

Get the Sat_key member data.

bool IsSetVersion(void) const

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

TSub_sat GetSub_sat(void) const

Get the Sub_sat member data.

TSat GetSat(void) const

Get the Sat member data.

@ eData_format_asn_binary

@ eID2_Blob_State_suppressed

@ eID2_Blob_State_suppressed_temp

@ eID2_Blob_State_withdrawn

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)

string ToBioseqProtobuf(const CBioseqInfoRecord &bioseq_info)

#define PSG_ERROR(message)

chrono::steady_clock psg_clock_t

@ ePSGS_BlobRetrievalIsNotAuthorized

psg_clock_t::time_point psg_time_point_t

unsigned long GetTimespanToNowMks(const psg_time_point_t &t_point)

Reader-writer based streams.

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

static CNamedPipeClient * client

vector< string > m_ExcludeBlobs

unsigned long m_ResendTimeoutMks

EPSGS_TSEOption m_TSEOption

vector< string > m_DisabledProcessors

vector< string > m_EnabledProcessors

EPSGS_OutputFormat m_OutputFormat

#define DEFAULT_INDEX_UPDATE_TIME

#define DEFAULT_COMPRESS_DATA

#define DEFAULT_FILE_REOPEN_TIME

static bool s_SimulateError()

void s_SetBlobState(CBlobRecord &blob_props, int id2_blob_state)

#define PARAM_FILE_RECHECK_TIME

static void s_OnGotBlobBySeqId(void *data)

NCBI_PARAM_DEF(int, WGS_PROCESSOR, ERROR_RATE, 0)

#define DEFAULT_VDB_CACHE_SIZE

static const string kWGSProcessorSection

#define DEFAULT_FILE_RECHECK_TIME

#define PARAM_COMPRESS_DATA

#define PARAM_FILE_REOPEN_TIME

NCBI_PARAM_DECL(int, WGS_PROCESSOR, ERROR_RATE)

static void s_OnResolvedSeqId(void *data)

static const string kParamMaxConn

static const string kWGSProcessorGroupName

static const string kWGSProcessorName

static const int kDefaultMaxConn

#define PARAM_INDEX_UPDATE_TIME

static const char kSubSatSeparator

static void s_OnGotBlobByBlobId(void *data)

static void s_OnGotChunk(void *data)

#define PARAM_VDB_CACHE_SIZE

void s_SetBlobVersion(CBlobRecord &blob_props, const CID2_Blob_Id &blob_id)

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

static void s_FormatBlobId(ostream &s, const CID2_Blob_Id &blob_id)

const string kWGSProcessorEvent

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