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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/resolve__base_8cpp_source.html below:

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

52 using namespace

std::placeholders;

60

shared_ptr<CPSGS_Reply> reply,

70

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

77

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

78

m_FinalFinishedCB(finished_cb),

79

m_FinalErrorCB(error_cb),

80

m_FinalStartProcessingCB(resolution_start_processing_cb),

81

m_AsyncStarted(

false

)

107 "Not handled request type "

108

to_string(

static_cast<int>

(

m_Request

->GetRequestType())));

114 int16_t

& effective_seq_id_type,

115

list<string> & secondary_id_list,

118 bool

need_trace =

m_Request

->NeedTrace();

122

effective_seq_id_type, need_trace)) {

124 m_Reply

->SendTrace(

"OSLT has not been tried due to mismatch " 125 "between the parsed CSeq_id seq_id_type and " 126 "the URL provided one"

133

primary_id = parsed_seq_id.

ComposeOSLT

(&secondary_id_list,

137 m_Reply

->SendTrace(

"OSLT call failure (exception)"

144 string

trace_msg(

"OSLT succeeded"

);

145

trace_msg +=

"\nOSLT primary id: "

+ primary_id;

147 if

(secondary_id_list.empty()) {

148

trace_msg +=

"\nOSLT secondary id list is empty"

;

150 for

(

const auto

& item : secondary_id_list) {

151

trace_msg +=

"\nOSLT secondary id: "

+ item;

163 const string

& primary_id,

170 if

(!primary_id.empty()) {

181 this

, bioseq_resolution);

187

bioseq_resolution.

Reset

();

189 return

bioseq_cache_lookup_result;

195 const string

& secondary_id,

206 auto

si2csi_cache_lookup_result =

213

bioseq_resolution.

Reset

();

230

upper_seq_id, seq_id_type,

234

bioseq_resolution.

Reset

();

239 return

cache_lookup_result;

248 const

list<string> & secondary_id_list,

249 const string

& primary_id,

254 bool

cache_failure =

false

;

256 if

(!primary_id.empty()) {

257 auto

cache_lookup_result =

259

effective_seq_id_type,

264

cache_failure =

true

;

267 for

(

const auto

& secondary_id : secondary_id_list) {

268 auto

cache_lookup_result =

270

effective_seq_id_type,

275

cache_failure =

true

;

289 if

(primary_id != upper_seq_id)

295

cache_failure =

true

;

297

bioseq_resolution.

Reset

();

330 string

parse_err_msg;

340 if

(seq_id_resolve ==

false

) {

346 "seq_id_resolve flag is set " 347 "to 'no' and there is a seq id parsing failure: "

355

list<string> secondary_id_list;

357 bool

composed_ok =

false

;

359

composed_ok =

x_ComposeOSLT

(oslt_seq_id, effective_seq_id_type,

360

secondary_id_list, primary_id);

364 if

(seq_id_resolve ==

false

) {

370 "seq_id_resolve flag is set to 'no' and " 371 "there is a failure to compose OSLT."

);

378 "seq_id_resolve flag is set " 379 "to 'no' and the seq id type ("

380

to_string(effective_seq_id_type) +

381 ") does not satisfy a condition for " 390 if

(seq_id_resolve) {

394

secondary_id_list, primary_id,

402

effective_seq_id_type,

406 if

(bioseq_resolution.

IsValid

()) {

408 bool

continue_with_cassandra =

false

;

415 auto

bioseq_cache_lookup_result =

420

continue_with_cassandra =

true

;

421

bioseq_resolution.

Reset

();

429

continue_with_cassandra =

true

;

430

bioseq_resolution.

Reset

();

440

continue_with_cassandra =

true

;

441

bioseq_resolution.

Reset

();

445 if

(!continue_with_cassandra) {

456 if

(! parse_err_msg.empty() &&

466

effective_seq_id_type,

467

std::move(secondary_id_list),

468

std::move(primary_id),

471

std::move(bioseq_resolution));

481

app->GetCounters().Increment(

this

487

}

else if

(!parse_err_msg.empty()) {

508 const string

& primary_id,

520

effective_seq_id_type, bioseq_resolution);

534

app->GetCounters().Increment(

this

564 string

parse_err_msg;

572

list<string> secondary_id_list;

574 bool

composed_ok =

false

;

576

composed_ok =

x_ComposeOSLT

(oslt_seq_id, effective_seq_id_type,

577

secondary_id_list, primary_id);

583

secondary_id_list, primary_id,

589 if

(!bioseq_resolution.

IsValid

()) {

591 if

(!parse_err_msg.empty()) {

597 return

bioseq_resolution;

606 const string

& message,

634 const string

& message,

637 if

(!message.empty()) {

669 auto

cache_lookup_result =

680 if

(bioseq_resolution.m_CassQueryCount == 0) {

687

std::move(bioseq_resolution));

692 "Data inconsistency: the bioseq key info was " 694 " but the bioseq info is not found"

function< void(SBioseqResolution &&async_bioseq_resolution)> TSeqIdResolutionFinishedCB

function< void(void)> TSeqIdResolutionStartProcessingCB

function< void(CRequestStatus::ECode status, int code, EDiagSev severity, const string &message, EPSGS_LoggingFlag logging_flag)> TSeqIdResolutionErrorCB

CBioseqInfoRecord & SetSeqIdType(TSeqIdType value)

CBioseqInfoRecord & SetVersion(TVersion value)

CBioseqInfoRecord & SetAccession(const TAccession &value)

EPSGS_CacheLookupResult LookupBioseqInfo(IPSGS_Processor *processor, SBioseqResolution &bioseq_resolution)

EPSGS_CacheLookupResult LookupSi2csi(IPSGS_Processor *processor, SBioseqResolution &bioseq_resolution)

@ ePSGS_InputSeqIdNotResolved

CRequestStatus::ECode GetCombinedErrorCode(void) const

void AppendError(const string &msg, CRequestStatus::ECode code)

string GetCombinedErrorMessage(const list< SPSGSeqId > &seq_id_to_resolve) const

void MakeRequest(SBioseqResolution &&bioseq_resolution)

string GetCouldNotResolveMessage(void) const

bool MoveToNextSeqId(void)

list< SPSGSeqId > m_SeqIdsToResolve

psg_time_point_t GetAsyncResolutionStartTimestamp(void) const

void SetAsyncResolutionStartTimestamp(const psg_time_point_t &ts)

bool GetSeqIdResolve(void)

void SetupSeqIdToResolve(void)

bool CanSkipBioseqInfoRetrieval(const CBioseqInfoRecord &bioseq_info_record)

CPSGSResolveErrors m_ResolveErrors

bool OptimizationPrecondition(const string &primary_id, int16_t effective_seq_id_type) const

list< SPSGSeqId >::const_iterator m_CurrentSeqIdToResolve

EPSGS_AccessionAdjustmentResult AdjustBioseqAccession(SBioseqResolution &bioseq_resolution)

int16_t GetEffectiveVersion(const CTextseq_id *text_seq_id)

@ ePSGS_AnnotationRequest

@ ePSGS_IPGResolveRequest

@ ePSGS_AccessionVersionHistoryRequest

@ ePSGS_BlobBySeqIdRequest

void x_OptimizedResolutionInCache(CSeq_id &parsed_seq_id, const string &primary_id, int16_t effective_seq_id_type, SBioseqResolution &bioseq_resolution)

void x_ResolveViaComposeOSLTInCache(CSeq_id &parsed_seq_id, int16_t effective_seq_id_type, const list< string > &secondary_id_list, const string &primary_id, SBioseqResolution &bioseq_resolution)

void x_ResolveSeqId(void)

void x_OnAsyncBioseqInfoResolveError(CRequestStatus::ECode status, int code, EDiagSev severity, const string &message, EPSGS_LoggingFlag loging_flag=ePSGS_NeedLogging)

void x_OnResolutionGoodData(void)

virtual ~CPSGS_ResolveBase()

EPSGS_CacheLookupResult x_ResolveSecondaryOSLTInCache(const string &secondary_id, int16_t effective_seq_id_type, SBioseqResolution &bioseq_resolution)

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

SBioseqResolution ResolveTestInputSeqId(void)

void ResolveInputSeqId(void)

TSeqIdResolutionErrorCB m_FinalErrorCB

EPSGS_CacheLookupResult x_ResolvePrimaryOSLTInCache(const string &primary_id, int16_t effective_version, int16_t effective_seq_id_type, SBioseqResolution &bioseq_resolution)

EPSGS_CacheLookupResult x_ResolveAsIsInCache(SBioseqResolution &bioseq_resolution)

void x_OptimizedNotFound(const string &err_msg)

TSeqIdResolutionFinishedCB m_FinalFinishedCB

bool x_ComposeOSLT(CSeq_id &parsed_seq_id, int16_t &effective_seq_id_type, list< string > &secondary_id_list, string &primary_id)

void x_OnSeqIdResolveFinished(SBioseqResolution &&bioseq_resolution)

TSeqIdResolutionStartProcessingCB m_FinalStartProcessingCB

void x_RegisterSuccessTiming(const SBioseqResolution &bioseq_resolution)

SPSGS_RequestBase::EPSGS_CacheAndDbUse x_GetRequestUseCache(void)

static CPubseqGatewayApp * GetInstance(void)

virtual void Process(void)=0

Main processing function.

shared_ptr< CPSGS_Reply > m_Reply

bool GetEffectiveSeqIdType(const objects::CSeq_id &parsed_seq_id, int request_seq_id_type, int16_t &eff_seq_id_type, bool need_trace)

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.

EDiagSev

Severity level for the posted diagnostics.

@ eDiag_Error

Error message.

@ e500_InternalServerError

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

string ComposeOSLT(list< string > *secondary_ids=nullptr, TComposeOSLTFlags parse_flags=0) const

JIRA ID-5188 : Compose OSLT string for the primary id, as well as OSLT strings for the secondary ids,...

const CTextseq_id * GetTextseq_Id(void) const

Return embedded CTextseq_id, if any.

@ fGpipeAddSecondary

Add "ACC.VER(=1)" for a 2ndary id.

static string & ToUpper(string &str)

Convert string to upper case â string& version.

Defines NCBI C++ diagnostic APIs, classes, and macros.

Defines CRequestStatus class for NCBI C++ diagnostic API.

EPSGS_ResolutionResult m_ResolutionResult

CBioseqInfoRecord & GetBioseqInfo(void)

void SetBioseqInfo(const CBioseqInfoRecord &record)

SResolveInputSeqIdError m_Error

CRequestStatus::ECode m_ErrorCode

bool HasError(void) const

@ eResolutionFoundInCassandra

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