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NCBI C++ ToolKit: src/objtools/data_loaders/genbank/psg_loader_impl.cpp Source File

,

,

m_CancelRequested(

),

m_QueueGuard(*loader.m_ThreadPool, *loader.m_Queue),

m_CancelRequested.store(

, memory_order_release);

m_CancelRequested.load(memory_order_acquire);

m_QueueGuard.CancelAll();

m_AddRequestSemaphore.Post();

m_ReadResultsThread.join();

( !IsCancelRequested() ) {

(

= m_QueueGuard.GetNextResult() ) {

(

<<

<< processor->m_CDDIds);

m_AddRequestSemaphore.Wait();

( IsCancelRequested() ) {

( m_Loader.m_Caches->m_NoCDDCache.Find(blob_id) ) {

cached = m_Loader.m_Caches->m_AnnotInfoCache.Find(make_pair(

, ids));

(

&

: ids) {

request = make_shared<CPSG_Request_NamedAnnotInfo>(std::move(bio_ids), annot_names);

m_Loader.m_Caches.get()));

m_QueueGuard.AddRequest(request, processor);

m_AddRequestSemaphore.Post();

<

TParamType>

= NStr::StringToNumeric<TParamType>(

);

<

TParamDescription>

TParam::TValueType

= TParam::GetDefault();

TParam::GetState(0, &

);

s_ConvertParamValue<typename TParam::TValueType>(

, node->GetValue().value);

unique_ptr<CPSGDataLoader::TParamTree> app_params;

(service_name.empty() && psg_params) {

(service_name.empty()) {

service_name = TPSG_ServiceName::GetDefault();

(!

.empty()) {

= (s_GetParamValue<X_NCBI_PARAM_DECLNAME(PSG_LOADER, WHOLE_TSE)>(psg_params)?

= (s_GetParamValue<X_NCBI_PARAM_DECLNAME(PSG_LOADER, WHOLE_TSE_BULK)>(psg_params)?

( !param.empty() ) {

<<param<<

);

(!

.empty()) {

cache_lifespan = NStr::StringToNumeric<int>(

);

(!

.empty()) {

no_data_cache_lifespan = NStr::StringToNumeric<int>(

);

(!

.empty()) {

cache_max_size = NStr::StringToNumeric<size_t>(

);

s_GetParamValue<X_NCBI_PARAM_DECLNAME(PSG_LOADER, RETRY_COUNT)>(psg_params);

s_GetParamValue<X_NCBI_PARAM_DECLNAME(PSG_LOADER, BULK_RETRY_COUNT)>(psg_params);

= make_unique<CPSGCaches>(cache_lifespan, cache_max_size,

no_data_cache_lifespan, cache_max_size);

(TPSG_PrefetchCDD::GetDefault()) {

s_PSGLoaderInstanceCounter = 0;

current_instance_number = ++s_PSGLoaderInstanceCounter;

( current_instance_number > 1 ) {

args.

(

, new_client_id);

(!args.

().empty()) {

<

Call>

( retry_count == 0 ) {

(

= 1;

< retry_count; ++

) {

(

<<

<<name<<

<<

<<

<<exc);

(

<<

<<name<<

<<

<<

<<exc);

( exception& exc ) {

(

<<

<<name<<

<<

<<

<<exc.

());

(

<<

<<name<<

<<

<<

);

(

<<

<<wait_sec<<

);

cref(idh), ref(ids)),

(!seq_info)

;

( seq_info->gi !=

) {

ret.

= seq_info->gi;

( seq_info->canonical.IsAccVer() ) {

ret.

= seq_info->canonical;

(

<<idh);

( seq_info->tax_id <= 0 ) {

(

<<idh<<

<<seq_info->tax_id);

<<

<<formatter.

<<

<<formatter.

;

cref(ids), ref(loaded), ref(ret)),

);

[ load_count1, failed_processor1 ] =

(ids, loaded, ret);

failed_processor = failed_processor1;

( load_count1 != ids.size() ) {

vector<shared_ptr<SPsgBioseqInfo>> infos;

infos.resize(ret.size());

(

= 0;

< infos.size(); ++

) {

(loaded[

] || !infos[

].get()) {

ret[

] = infos[

]->tax_id;

( !failed_processor1 ) {

failed_processor1 = failed_processor2;

( failed_processor ) {

);

( seq_info->hash ) {

ret.

= seq_info->hash;

ret.

= seq_info->molecule_type;

data_source, cref(idh)),

);

( !

.first ) {

(

.second.first ) {

|=

.second.first->blob_state_flags;

data_source, cref(idh), choice),

bioseq_info =

->m_BioseqInfoCache.Find(idh);

( bioseq_info && bioseq_info->KnowsBlobId() ) {

( !bioseq_info->HasBlobId() ) {

(

->m_NoBioseqInfoCache.Find(idh) ) {

request = make_shared<CPSG_Request_Biodata>(std::move(bio_id));

<<idh<<

<<

(

tse_lock = processor->GetTSE_Lock() ) {

( !processor->HasBlob_id() ) {

( processor->GotForbidden() ) {

+idh.

(),

processor->GetForbiddenBlobState());

(

bioseq_info =

->m_BioseqInfoCache.Find(idh) ) {

seq_info =

->m_BioseqInfoCache.Find(idh);

( seq_info && seq_info->KnowsBlobId() ) {

request = make_shared<CPSG_Request_Biodata>(std::move(bio_id));

(

<< idh);

<<idh<<

<<

(

<< idh);

<<

seq_info = processor->GetBioseqInfoResult();

( !seq_info->HasBlobId() ) {

seq_info->GetDLBlobId();

data_source, cref(blob_id)),

(

<<blob_id.

()<<

);

( load_lock && load_lock.

() ) {

(

<< blob_id.

());

request = make_shared<CPSG_Request_Blob>(bid);

<<blob_id.

()<<

<<

ret = processor->GetTSE_Lock();

( !ret && (processor->GotForbidden() || processor->GotUnauthorized()) ) {

( processor->GotUnauthorized() ) {

|= processor->GetBlobInfoState(blob_id.

());

+blob_id.

()+

);

data_source, ref(loaded), ref(tse_sets)),

make_optional<TResult>();

make_optional<TResult>({tse});

make_optional<TResult>({tse});

optional<CPSGDataLoader_Impl::CGetRequests::TResult>

( bioseq_info && bioseq_info->KnowsBlobId() ) {

( !bioseq_info->HasBlobId() ) {

& blob_id = bioseq_info->GetPSGBlobId();

( load_lock && load_lock.

() ) {

(

<< blob_id);

(idh, load_lock);

(

<< blob_id);

(

<<

<< blob_id<<

<<idh);

request = make_shared<CPSG_Request_Blob>(

(blob_id));

request = make_shared<CPSG_Request_Biodata>(std::move(bio_id));

optional<CPSGDataLoader_Impl::CGetRequests::TResult>

(

.GetIndex() == eRequestGet ) {

SaveFailure(processor);

(

tse_lock = processor->GetTSE_Lock() ) {

Ready(idh, tse_lock);

( !processor->HasBlob_id() ) {

(

<<

<< processor->GetPSGBlobId()<<

<<idh);

request = make_shared<CPSG_Request_Blob>(std::move(blob_id));

request->IncludeData(m_IncludeData);

m_Loader.m_Caches.get(),

m_Loader.m_AddWGSMasterDescr));

m_GetBlob2Reqs[processor2].push_back(idh);

AddRequest(request, processor2, eRequestGetBlob);

reqs = std::move(m_GetBlob2Reqs[processor]);

m_GetBlob2Reqs.erase(processor);

!processor->GetTSE_Lock() ) {

SaveFailure(processor);

tse_lock = processor->GetTSE_Lock();

Ready(std::move(reqs), tse_lock);

( !m_FirstFailedProcessor ) {

m_FirstFailedProcessor = processor;

( m_FailedCount ) {

( loaded.count(idh) ) {

tse_sets[idh] = std::move(*tse_set);

tse_sets[idh] = *tse_set;

data_source, id_sets, ref(loaded), ref(ret)),

chunks.push_back(

(&chunk_info));

(

<<blob_id.ToString());

(

<< blob_id.ToString());

(

&

: annot_ids ) {

data_source, cref(chunks)),

(chunks.empty())

;

(

& it : chunks) {

request = make_shared<CPSG_Request_NamedAnnotInfo>(bio_id,

);

ids.push_back(cdd_ids.gi);

( cdd_ids.acc_ver ) {

ids.push_back(cdd_ids.acc_ver);

queue.

(request, processor, eRequestCDD);

request = make_shared<CPSG_Request_Blob>(blob_id.

());

queue.

(request, processor, eRequestDelayedTSE);

queue.

(request, processor, eRequestChunk);

failed_count = 0;

(

<<

( !first_failed_processor ) {

first_failed_processor =

.GetProcessor();

(

<<

( failed_count ) {

pair<CRef<CTSE_Chunk_Info>,

>

pair<CRef<CTSE_Chunk_Info>,

> ret;

main_count = 0;

zoom_count = 0;

vector<SAnnotTypeSelector>

;

(

feat_type_info_iter : annot_info.

() ) {

feat_type = finfo.

();

( feat_type == 0 ) {

(

feat_subtype : finfo.

() ) {

(

.size() == 1 ) {

ret.second = *

.begin();

<<ret.second<<

<<main_count<<

<<zoom_count);

( !

.empty() ) {

data_source, cref(ids), sel, processed_nas),

);

& name,

cached =

->m_AnnotInfoCache.Find(make_pair(name, ids));

( !cached->infos.empty() ) {

(

&

: cached->infos ) {

blob_id->SetTSEName(name);

load_lock->

(cached->name);

locks.

(load_lock);

(

->m_NoAnnotInfoCache.Find(make_pair(name, ids)) ) {

( !data_source || ids.empty() ) {

snp_name =

;

(

&

: ids) {

name = it->first;

(name ==

) {

annot_names.push_back(it->first);

( !annot_names.empty() ) {

request = make_shared<CPSG_Request_NamedAnnotInfo>(std::move(bio_ids), annot_names);

request->SetSNPScaleLimit(snp_scale_limit);

queue.

(request, processor, eRequestNA);

vector<string> TRequests;

(

.GetIndex() == eRequestNA ) {

(

<<ids.front());

<<ids.front()<<

<<

(

&

: processor->GetResults() ) {

(

.m_TSE_Lock ) {

locks.

(

.m_TSE_Lock);

request = make_shared<CPSG_Request_Blob>(std::move(blob_id));

dl_blob_id->SetTSEName(

.m_NA);

getblob2reqs[processor2].push_back(

.m_NA);

queue.

(request, processor2, eRequestGetBlob);

TRequests reqs = std::move(getblob2reqs[processor]);

getblob2reqs.

(processor);

(

<<ids.front());

<<ids.front()<<

<<

(

& name : reqs ) {

locks.

(processor->GetTSE_Lock());

locks.

(tse_lock);

(id_sets.empty())

;

(id_sets.size() == loaded.size());

(id_sets.size() == ret.size());

vector<SCDDIds> cdd_ids(id_sets.size());

(

= 0;

< id_sets.size(); ++

) {

( loaded[

] ) {

& ids = id_sets[

];

( ids.empty() ) {

( !cdd_ids[

] ) {

loaded[

] =

;

loaded[

] =

;

(

&

: ids) {

(

& bid : blob_ids) {

loaded[

] =

;

loaded[

] =

;

(

&

: ids) {

request = make_shared<CPSG_Request_NamedAnnotInfo>(std::move(bio_ids), annot_names);

failed_count = 0;

=

.GetIndex();

(

< cdd_ids.size() && cdd_ids[

]);

(

<< cdd_ids[

]);

( !first_failed_processor ) {

first_failed_processor =

.GetProcessor();

ret[

] = processor->m_TSE_Lock;

loaded[

] =

;

( failed_count ) {

cref(ids), ref(loaded), ref(ret)),

vector<shared_ptr<SPsgBioseqInfo>> infos;

infos.resize(ret.size());

(

= 0;

< infos.size(); ++

) {

(loaded[

] || !infos[

].get())

;

ret[

].push_back(*it);

loaded[

] =

;

( failed_processor ) {

cref(ids), ref(loaded), ref(ret)),

vector<shared_ptr<SPsgBioseqInfo>> infos;

infos.resize(ret.size());

(

= 0;

< infos.size(); ++

) {

(loaded[

] || !infos[

].get())

;

loaded[

] =

;

( failed_processor ) {

cref(ids), ref(loaded), ref(ret)),

vector<shared_ptr<SPsgBioseqInfo>> infos;

infos.resize(ret.size());

(

= 0;

< infos.size(); ++

) {

(loaded[

] || !infos[

].get())

;

ret[

] = infos[

]->gi;

loaded[

] =

;

( failed_processor ) {

cref(ids), ref(loaded), ref(ret)),

vector<shared_ptr<SPsgBioseqInfo>> infos;

infos.resize(ret.size());

(

= 0;

< infos.size(); ++

) {

(loaded[

] || !infos[

].get())

;

(!ret[

].

()) loaded[

] =

;

( failed_processor ) {

cref(ids), ref(loaded), ref(ret)),

,

vector<shared_ptr<SPsgBioseqInfo>> infos;

infos.resize(ret.size());

(

= 0;

< infos.size(); ++

) {

(loaded[

] || !infos[

].get())

;

length = infos[

]->length;

loaded[

] =

;

( failed_processor ) {

cref(ids), ref(loaded), ref(ret)),

,

vector<shared_ptr<SPsgBioseqInfo>> infos;

infos.resize(ret.size());

(

= 0;

< infos.size(); ++

) {

(loaded[

] || !infos[

].get())

;

ret[

] = infos[

]->molecule_type;

loaded[

] =

;

( failed_processor ) {

data_source, cref(ids), ref(loaded), ref(ret)),

,

infos.resize(ret.size());

(

= 0;

< infos.size(); ++

) {

( loaded[

] || !infos[

].

) {

loaded[

] =

;

( failed_processor ) {

cref(ids), ref(loaded), ref(ret), ref(known)),

,

vector<shared_ptr<SPsgBioseqInfo>> infos;

infos.resize(ret.size());

(

= 0;

< infos.size(); ++

) {

(loaded[

] || !infos[

].get())

;

ret[

] = infos[

]->hash;

known[

] = infos[

]->hash != 0;

loaded[

] =

;

( failed_processor ) {

( shared_ptr<SPsgBioseqInfo> ret =

->m_BioseqInfoCache.Find(idh) ) {

( ret->tax_id <= 0 ) {

(

<<idh<<

<<ret->tax_id);

(

->m_NoBioseqInfoCache.Find(idh) ) {

shared_ptr<CPSG_Request_Resolve> request = make_shared<CPSG_Request_Resolve>(std::move(bio_id));

processor->m_BioseqInfoResult;

(!text_id)

;

((acc_info & kAccFlags) != kAccFlags) {

( !text_id->IsSetAccession() || !text_id->IsSetVersion() ) {

is_wp_acc =

;

shared_ptr<CPSG_Request_IpgResolve> request = make_shared<CPSG_Request_IpgResolve>(acc_ver);

(

<< idh);

+acc_ver);

processor->m_TaxId;

pair<size_t, CRef<CPSGL_Processor>>

make_pair(0,

);

load_count = 0;

(

= 0;

< ids.size(); ++

) {

loaded[

] =

;

is_wp_acc =

;

shared_ptr<CPSG_Request_IpgResolve> request = make_shared<CPSG_Request_IpgResolve>(acc_ver);

=

.GetIndex();

(

<< ids[

]);

( !failed_processor ) {

failed_processor =

.GetProcessor();

tax_id = processor->m_TaxId;

loaded[

] =

;

make_pair(load_count, failed_processor);

<<idh);

shared_ptr<SPsgBioseqInfo> bioseq_info =

->m_BioseqInfoCache.Find(idh);

shared_ptr<SPsgBlobInfo> blob_info;

( bioseq_info && bioseq_info->KnowsBlobId() ) {

ret.first = bioseq_info;

( !bioseq_info->HasBlobId() ) {

blob_info =

->m_BlobInfoCache.Find(bioseq_info->GetPSGBlobId());

ret.second.first = blob_info;

ret.second.second =

->m_NoBlobInfoCache.Find(bioseq_info->GetPSGBlobId());

shared_ptr<CPSG_Request_Blob> request = make_shared<CPSG_Request_Blob>(std::move(bid));

(

->m_NoBioseqInfoCache.Find(idh) ) {

blob_request = make_shared<CPSG_Request_Biodata>(std::move(bio_id));

queue.

(blob_request, blob_processor,

(

<< processor->GetSeq_id());

ret.first = processor->m_BioseqInfoResult;

(

<< processor->GetSeq_id());

ret.second.first = processor->m_BlobInfoResult;

ret.second.second = processor->m_BlobInfoStatus;

( ret.second.first ) {

( ret.first->HasBlobId() &&

ret.second.second =

->m_NoBlobInfoCache.Find(ret.first->GetPSGBlobId());

shared_ptr<CPSG_Request_Blob> request = make_shared<CPSG_Request_Blob>(std::move(bid));

(

<< processor->GetSeq_id());

ret.second.first = processor->m_BlobInfoResult;

ret.second.second = processor->m_BlobInfoStatus;

( ret.second.first ) {

(

<< processor->GetSeq_id());

& blob_id)

( shared_ptr<SPsgBlobInfo> ret =

->m_BlobInfoCache.Find(blob_id) ) {

( data_source ) {

( load_lock && load_lock.IsLoaded() ) {

blob_info = make_shared<SPsgBlobInfo>(*load_lock);

->m_BlobInfoCache.Add(blob_id, blob_info);

shared_ptr<CPSG_Request_Blob> request = make_shared<CPSG_Request_Blob>(std::move(bid));

(

<< blob_id);

( !processor->m_BlobInfo ) {

(

<< blob_id);

blob_info = make_shared<SPsgBlobInfo>(*processor->m_BlobInfo);

->m_BlobInfoCache.Add(blob_id, blob_info);

seq_state =

.first->GetBioseqStateFlags();

chain_state =

.first->GetChainStateFlags();

pair<size_t, CRef<CPSGL_Processor>>

load_count = 0;

(

= 0;

< ids.size(); ++

) {

( loaded[

] ) {

ret[

] =

->m_BioseqInfoCache.Find(ids[

]);

(

->m_NoBioseqInfoCache.Find(ids[

]) ) {

shared_ptr<CPSG_Request_Resolve> request = make_shared<CPSG_Request_Resolve>(std::move(bio_id));

=

.GetIndex();

(

<< ids[

]);

( !failed_processor ) {

failed_processor = processor;

ret[

] = processor->m_BioseqInfoResult;

make_pair(load_count, failed_processor);

pair<size_t, CRef<CPSGL_Processor>>

load_count = 0;

vector<bool> errors(ids.size());

(

= 0;

< ids.size(); ++

) {

( !failed_processor ) {

failed_processor =

.GetProcessor();

make_pair(load_count, failed_processor);

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 & GetName(void) const

Blob state exceptions, used by GenBank loader.

CTSE_LoadLock GetTSE_LoadLock(const TBlobId &blob_id)

CTSE_LoadLock GetTSE_LoadLockIfLoaded(const TBlobId &blob_id)

CDataLoader * GetDataLoader(void) const

vector< TBlobId > TLoadedBlob_ids

void GetLoadedBlob_ids(const CSeq_id_Handle &idh, TLoadedTypes types, TLoadedBlob_ids &blob_ids) const

static TParamTree * GetParamsSubnode(TParamTree *params, const string &subnode_name)

static string GetParam(const TParamTree *params, const string &param_name)

bool GetPSGNoSplit(void) const

const string & GetPSGServiceName(void) const

bool IsSetEnableCDD(void) const

const TParamTree * GetParamTree(void) const

bool IsSetEnableSNP(void) const

const string & GetWebCookie(void) const

bool GetEnableWGS(void) const

bool HasHUPIncluded(void) const

bool GetEnableCDD(void) const

bool GetEnableSNP(void) const

bool IsSetEnableWGS(void) const

CID2S_Feat_type_Info –.

CID2S_Seq_annot_Info –.

double GetTime(int step) const

void Init(CConfig &conf, const string &driver_name, const SAllParams &params)

Data loader exceptions, used by GenBank loader.

optional< TResult > CreateGetRequests(const CSeq_id_Handle &idh)

CPSGDataLoader_Impl & m_Loader

CGetRequests(CPSGDataLoader_Impl &loader, CDataSource *data_source, CPSG_Request_Biodata::EIncludeData include_data)

optional< TResult > ProcessResult(const CPSGL_ResultGuard &result)

vector< CSeq_id_Handle > TRequests

optional< TResult > NotReady()

CDataLoader::TTSE_LockSet TResult

void SaveFailure(const CRef< CPSGL_Processor > &processor)

CRef< CPSGL_Processor > m_FirstFailedProcessor

optional< TResult > Ready(const CSeq_id_Handle &request, const CTSE_Lock &tse)

const TRequests & GetReadyRequests() const

TRequests m_ReadyRequests

optional< TResult > Empty(const CSeq_id_Handle &request)

CPSG_Request_Biodata::EIncludeData m_IncludeData

CDataSource * m_DataSource

map< CRef< CPSGL_GetBlob_Processor >, TRequests > m_GetBlob2Reqs

optional< TResult > Ready(TRequests &&requests, const CTSE_Lock &tse)

void AddRequest(const CDataLoader::TIds &ids)

CPSG_PrefetchCDD_Task(CPSGDataLoader_Impl &loader)

CPSGDataLoader_Impl & m_Loader

CSemaphore m_AddRequestSemaphore

atomic< bool > m_CancelRequested

CPSGL_QueueGuard m_QueueGuard

thread m_ReadResultsThread

unique_ptr< CThreadPool > m_ThreadPool

CDataLoader::TSequenceStates TSequenceStates

pair< shared_ptr< SPsgBioseqInfo >, pair< shared_ptr< SPsgBlobInfo >, EPSG_Status > > TBioseqAndBlobInfo

void GetBulkIds(const TIds &ids, TLoaded &loaded, TBulkIds &ret)

void GetCDDAnnotsOnce(CDataSource *data_source, const TSeqIdSets &id_sets, TLoaded &loaded, TCDD_Locks &ret)

void GetBlobsOnce(CDataSource *data_source, TLoadedSeqIds &loaded, TTSE_LockSets &tse_sets)

shared_ptr< SPsgBlobInfo > x_GetBlobInfo(CDataSource *data_source, const string &blob_id)

void GetSequenceStatesOnce(CDataSource *data_source, const TIds &ids, TLoaded &loaded, TSequenceStates &ret)

CConstRef< CPsgBlobId > GetBlobIdOnce(const CSeq_id_Handle &idh)

void GetSequenceTypesOnce(const TIds &ids, TLoaded &loaded, TSequenceTypes &ret)

void GetAccVers(const TIds &ids, TLoaded &loaded, TIds &ret)

static void SetGetBlobByIdShouldFail(bool value)

CRef< CRequestContext > m_RequestContext

int x_MakeSequenceState(const TBioseqAndBlobInfo &info)

void GetTaxIdsOnce(const TIds &ids, TLoaded &loaded, TTaxIds &ret)

CDataLoader::TBulkIds TBulkIds

void GetIds(const CSeq_id_Handle &idh, TIds &ids)

CDataLoader::SGiFound GetGi(const CSeq_id_Handle &idh)

void DropTSE(const CPsgBlobId &blob_id)

void LoadChunk(CDataSource *data_source, CTSE_Chunk_Info &chunk_info)

bool x_ReadCDDChunk(CDataSource *data_source, CDataLoader::TChunk chunk, const CPSG_BlobInfo &blob_info, const CPSG_BlobData &blob_data)

CTSE_Lock GetBlobById(CDataSource *data_source, const CPsgBlobId &blob_id)

pair< size_t, CRef< CPSGL_Processor > > x_GetBulkBioseqInfo(const TIds &ids, const TLoaded &loaded, TBioseqInfos &ret)

void LoadChunks(CDataSource *data_source, const CDataLoader::TChunkSet &chunks)

int GetSequenceState(CDataSource *data_source, const CSeq_id_Handle &idh)

shared_ptr< SPsgBioseqInfo > x_GetBioseqInfo(const CSeq_id_Handle &idh)

void GetSequenceStates(CDataSource *data_source, const TIds &ids, TLoaded &loaded, TSequenceStates &ret)

void GetBulkIdsOnce(const TIds &ids, TLoaded &loaded, TBulkIds &ret)

CDataLoader::TSequenceHashes TSequenceHashes

CDataLoader::TTSE_LockSet GetRecordsOnce(CDataSource *data_source, const CSeq_id_Handle &idh, CDataLoader::EChoice choice)

CDataLoader::TSeqIdSets TSeqIdSets

TTaxId GetTaxId(const CSeq_id_Handle &idh)

void GetGisOnce(const TIds &ids, TLoaded &loaded, TGis &ret)

CDataLoader::TTSE_LockSet GetRecords(CDataSource *data_source, const CSeq_id_Handle &idh, CDataLoader::EChoice choice)

void GetSequenceHashes(const TIds &ids, TLoaded &loaded, TSequenceHashes &ret, THashKnown &known)

vector< shared_ptr< SPsgBioseqInfo > > TBioseqInfos

CDataLoader::TSequenceLengths TSequenceLengths

CDataLoader::STypeFound GetSequenceType(const CSeq_id_Handle &idh)

void GetGis(const TIds &ids, TLoaded &loaded, TGis &ret)

void GetSequenceHashesOnce(const TIds &ids, TLoaded &loaded, TSequenceHashes &ret, THashKnown &known)

CPSG_Request_Biodata::EIncludeData m_TSERequestMode

CPSG_Request_Biodata::EIncludeData m_TSERequestModeBulk

EProcessResult x_ProcessBioseqAndBlobInfoResult(CPSGL_QueueGuard &queue, const CSeq_id_Handle &idh, TBioseqAndBlobInfo &ret, const CPSGL_ResultGuard &result)

CRef< CPSG_PrefetchCDD_Task > m_CDDPrefetchTask

void GetLabels(const TIds &ids, TLoaded &loaded, TLabels &ret)

CDataLoader::SHashFound GetSequenceHashOnce(const CSeq_id_Handle &idh)

unique_ptr< CPSGCaches > m_Caches

void x_AdjustBlobState(TBioseqAndBlobInfo &info)

CTSE_Lock GetBlobByIdOnce(CDataSource *data_source, const CPsgBlobId &blob_id)

CDataLoader::STypeFound GetSequenceTypeOnce(const CSeq_id_Handle &idh)

vector< TBioseqAndBlobInfo > TBioseqAndBlobInfos

CConstRef< CPsgBlobId > GetBlobId(const CSeq_id_Handle &idh)

void GetSequenceTypes(const TIds &ids, TLoaded &loaded, TSequenceTypes &ret)

CRef< CPSGL_Queue > m_Queue

psgl::CPSGL_Queue CPSGL_Queue

CDataLoader::TLabels TLabels

CDataLoader::TSequenceTypes TSequenceTypes

int GetSequenceStateOnce(CDataSource *data_source, const CSeq_id_Handle &idh)

unsigned int m_RetryCount

TSeqPos GetSequenceLength(const CSeq_id_Handle &idh)

void GetSequenceLengths(const TIds &ids, TLoaded &loaded, TSequenceLengths &ret)

unsigned int m_BulkRetryCount

CDataLoader::TLoaded TLoaded

void GetLabelsOnce(const TIds &ids, TLoaded &loaded, TLabels &ret)

CDataLoader::SAccVerFound GetAccVerOnce(const CSeq_id_Handle &idh)

void LoadChunksOnce(CDataSource *data_source, const CDataLoader::TChunkSet &chunks)

bool x_CheckAnnotCache(const string &name, const TIds &ids, CDataSource *data_source, CDataLoader::TProcessedNAs *processed_nas, CDataLoader::TTSE_LockSet &locks)

CDataLoader::TTaxIds TTaxIds

~CPSGDataLoader_Impl(void) override

TTaxId GetTaxIdOnce(const CSeq_id_Handle &idh)

CDataLoader::SHashFound GetSequenceHash(const CSeq_id_Handle &idh)

void GetSequenceLengthsOnce(const TIds &ids, TLoaded &loaded, TSequenceLengths &ret)

CDataLoader::TTSE_LockSet GetAnnotRecordsNAOnce(CDataSource *data_source, const TIds &ids, const SAnnotSelector *sel, CDataLoader::TProcessedNAs *processed_nas)

std::invoke_result< Call >::type CallWithRetry(Call &&call, const char *name, int retry_count=0)

CDataLoader::THashKnown THashKnown

CIncreasingTime m_WaitTime

void GetBlobs(CDataSource *data_source, TTSE_LockSets &tse_sets)

TSeqPos GetSequenceLengthOnce(const CSeq_id_Handle &idh)

void GetCDDAnnots(CDataSource *data_source, const TSeqIdSets &id_sets, TLoaded &loaded, TCDD_Locks &ret)

static bool GetGetBlobByIdShouldFail()

CDataLoader::TTSE_LockSet GetAnnotRecordsNA(CDataSource *data_source, const TIds &ids, const SAnnotSelector *sel, CDataLoader::TProcessedNAs *processed_nas)

void GetIdsOnce(const CSeq_id_Handle &idh, TIds &ids)

CDataLoader::TCDD_Locks TCDD_Locks

EProcessResult x_CreateBioseqAndBlobInfoRequests(CPSGL_QueueGuard &queue, const CSeq_id_Handle &idh, TBioseqAndBlobInfo &ret, size_t id_index=0)

TTaxId x_GetIpgTaxId(const CSeq_id_Handle &idh)

void GetTaxIds(const TIds &ids, TLoaded &loaded, TTaxIds &ret)

pair< size_t, CRef< CPSGL_Processor > > x_GetIpgTaxIds(const TIds &ids, TLoaded &loaded, TTaxIds &ret)

void GetAccVersOnce(const TIds &ids, TLoaded &loaded, TIds &ret)

CDataLoader::SAccVerFound GetAccVer(const CSeq_id_Handle &idh)

TBioseqAndBlobInfo x_GetBioseqAndBlobInfo(CDataSource *data_source, const CSeq_id_Handle &idh)

pair< size_t, CRef< CPSGL_Processor > > x_GetBulkBioseqAndBlobInfo(CDataSource *data_source, const TIds &ids, const TLoaded &loaded, TBioseqAndBlobInfos &ret)

CPSGDataLoader_Impl(const CGBLoaderParams &params)

CDataLoader::SGiFound GetGiOnce(const CSeq_id_Handle &idh)

static CSeq_id::ESNPScaleLimit GetSNP_Scale_Limit(void)

void SetLockedDelayedChunkInfo(const string &psg_blob_id, CTSE_Chunk_Info &locked_chunk_info)

vector< CSeq_id_Handle > TSeq_ids

SProcessorDescrPrinter Descr() const

const vector< string > & GetErrors() const

CRef< CPSGL_Queue > m_Queue

void AddRequest(const shared_ptr< CPSG_Request > &request, const CRef< CPSGL_Processor > &processor, size_t index=0)

CThreadPool & m_ThreadPool

CPSGL_ResultGuard GetNextResult()

void SetRequestContext(const CRef< CRequestContext > &context)

CPSG_EventLoop & GetPSG_Queue()

Bio-id (such as accession)

const string & GetId() const

Get ID.

const string & GetId() const

Get ID.

Blob data meta information.

Named Annotations (NAs) metainfo – reply to CPSG_Request_NamedAnnotInfo.

CPSG_BlobId GetBlobId() const

Coordinates of the blob that contains the NA data.

TId2AnnotInfoList GetId2AnnotInfoList() const

void SetUserArgs(SPSG_UserArgs user_args)

Set arbitrary URL arguments to add to every request.

void SetRequestFlags(CPSG_Request::TFlags request_flags)

Set request flags.

EIncludeData

Specify which info and data is needed.

@ eSmartTSE

If ID2 split is available, return split info blob only.

@ eWholeTSE

If ID2 split is available, return all split blobs.

@ eOrigTSE

Return all Cassandra data chunks of the blob itself.

vector< string > TAnnotNames

Names of the named annotations.

const string & GetId2Info() const

virtual string ToString(void) const override

Get string representation of blob id.

const string & ToPsgId() const

static void x_ParseLocation(TLocationSet &vec, const CID2S_Seq_loc &loc)

TBlobId GetBlobId(void) const

void SetLoaded(CObject *obj=0)

vector< TLocation > TLocationSet

TChunkId GetChunkId(void) const

void x_AddAnnotType(const CAnnotName &annot_name, const SAnnotTypeSelector &annot_type, const TLocationId &location_id)

bool IsLoaded(void) const

void SetName(const CAnnotName &name)

const TBlobId & GetBlobId(void) const

CTSE_Split_Info & GetSplitInfo(void)

bool x_NeedsDelayedMainChunk(void) const

void SetSeq_entry(CSeq_entry &entry, CTSE_SetObjectInfo *set_info=0)

bool IsLoaded(void) const

void AddChunk(CTSE_Chunk_Info &chunk_info)

Main class implementing functionality of pool of threads.

definition of a Culling tree

Template class for iteration on objects of class C (non-medifiable version)

static void LoadWGSMaster(CDataLoader *loader, CRef< CTSE_Chunk_Info > chunk)

iterator_bool insert(const value_type &val)

const_iterator begin() const

Include a standard set of the NCBI C++ Toolkit most basic headers.

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

main entry point for tests

bool Empty(const CNcbiOstrstream &src)

static const struct name_t names[]

static DLIST_TYPE *DLIST_NAME() first(DLIST_LIST_TYPE *list)

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

static const struct type types[]

#define NCBI_GBLOADER_PARAM_ID_GC_SIZE

#define NCBI_GBLOADER_PARAM_ID_EXPIRATION_TIMEOUT

#define NCBI_GBLOADER_PARAM_NO_ID_EXPIRATION_TIMEOUT

static CNcbiApplicationGuard InstanceGuard(void)

Singleton method.

const CNcbiRegistry & GetConfig(void) const

Get the application's cached configuration parameters (read-only).

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

SStrictId_Tax::TId TTaxId

Taxon id type.

const TSeqPos kInvalidSeqPos

Define special value for invalid sequence position.

string GetStringUID(TUID uid=0) const

Return string representation of UID.

CDiagContext & GetDiagContext(void)

Get diag context instance.

void SetProperty(const string &name, const string &value)

Add/change property.

#define LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

#define NCBI_RETHROW_FMT(prev_exception, exception_class, err_code, message)

The same as NCBI_RETHROW but with message processed as output to ostream.

TErrCode GetErrCode(void) const

Get error code.

#define NCBI_THROW(exception_class, err_code, message)

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

void Warning(CExceptionArgs_Base &args)

#define NCBI_THROW2(exception_class, err_code, message, extra)

Throw exception with extra parameter.

#define NCBI_THROW_FMT(exception_class, err_code, message)

The same as NCBI_THROW but with message processed as output to ostream.

virtual const char * what(void) const noexcept

Standard report (includes full backlog).

void Info(CExceptionArgs_Base &args)

#define MSerial_AsnText

I/O stream manipulators –.

static TParamTree * ConvertRegToTree(const IRegistry &reg, NStr::ECase use_case=NStr::eNocase)

Reconstruct param tree from the application registry.

CConstRef< CSeq_id > GetSeqId(void) const

EAccessionInfo

For IdentifyAccession (below)

CSeq_id::EAccessionInfo IdentifyAccession(void) const

bool IsAccVer(void) const

static CSeq_id_Handle GetHandle(const CSeq_id &id)

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

string AsString(void) const

CSeq_id::E_Choice Which(void) const

string GetLabel(const CSeq_id &id)

const CTextseq_id * GetTextseq_Id(void) const

Return embedded CTextseq_id, if any.

@ eAcc_refseq_unique_prot

CConstBeginInfo ConstBegin(const C &obj)

Get starting point of non-modifiable object hierarchy.

string ToString(void) const

vector< CSeq_id_Handle > TIds

static void SetProcessedNA(const string &na, TProcessedNAs *processed_nas)

virtual string ToString(void) const =0

Get string representation of blob id.

EChoice

main blob is blob with sequence all other blobs are external and contain external annotations

vector< TChunk > TChunkSet

@ eOrphanAnnot

all external annotations if no Bioseq exists

bool IsIncludedAnyNamedAnnotAccession(void) const

check if any named annot accession is included in the search

TSNPScaleLimit GetSNPScaleLimit(void) const

bool ExtractZoomLevel(const string &full_name, string *acc_ptr, int *zoom_level_ptr)

Extract optional zoom level suffix from named annotation string.

const TNamedAnnotAccessions & GetNamedAnnotAccessions(void) const

CRef< C > Ref(C *object)

Helper functions to get CRef<> and CConstRef<> objects.

EParamSource

Source of the value returned by CParam::GetDefault().

@ eParam_NoThread

Do not use per-thread values.

@ eSource_Config

The app. config file.

@ eSource_NotSet

Not fully initialized.

@ eSource_Default

Hardcoded default.

uint32_t Uint4

4-byte (32-bit) unsigned integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

static bool StringToBool(const CTempString str)

Convert string to bool.

static bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

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.

@ eNocase

Case insensitive compare.

@ eCompleted

executed successfully

const TTreeType * FindSubNode(const TKeyType &key) const

Non recursive linear scan of all subnodes, with key comparison.

void AddValue(const string &name, const string &value)

Add new value even if an argument with the same name already exists.

const TArgs & GetArgs(void) const

Get the const list of arguments.

const TDb & GetDb(void) const

Get the Db member data.

const TSubtypes & GetSubtypes(void) const

Get the Subtypes member data.

const TSeq_loc & GetSeq_loc(void) const

Get the Seq_loc member data.

bool IsSetGraph(void) const

Check if a value has been assigned to Graph data member.

bool IsSetAlign(void) const

Check if a value has been assigned to Align data member.

bool IsSetSubtypes(void) const

Check if a value has been assigned to Subtypes data member.

const TName & GetName(void) const

Get the Name member data.

const TFeat & GetFeat(void) const

Get the Feat member data.

bool IsSetFeat(void) const

Check if a value has been assigned to Feat data member.

TType GetType(void) const

Get the Type member data.

E_Choice

Choice variants.

const TGeneral & GetGeneral(void) const

Get the variant data.

@ e_General

for other databases

@ eMol_not_set

> cdna = rna

Pool of generic task-executing threads.

constexpr bool empty(list< Ts... >) noexcept

const GenericPointer< typename T::ValueType > T2 value

const CharType(& source)[N]

void SleepMilliSec(unsigned long ml_sec, EInterruptOnSignal onsignal=eRestartOnSignal)

Multi-threading – classes, functions, and features.

std::istream & in(std::istream &in_, double &x_)

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

SCDDIds x_ParseLocalCDDEntryId(const CPsgBlobId &blob_id)

CTSE_Lock x_CreateLocalCDDEntry(CDataSource *data_source, const SCDDIds &ids)

const char kCDDAnnotName[]

SCDDIds x_GetCDDIds(const vector< CSeq_id_Handle > &ids)

bool x_IsLocalCDDEntryId(const CPsgBlobId &blob_id)

unsigned s_GetDebugLevel()

bool s_GetBlobByIdShouldFail

CObjectIStream * GetBlobDataStream(const CPSG_BlobInfo &blob_info, const CPSG_BlobData &blob_data)

const bool kCreateLocalCDDEntries

CPSG_BioId x_LocalCDDEntryIdToBioId(const SCDDIds &cdd_ids)

string x_MakeLocalCDDEntryId(const SCDDIds &cdd_ids)

void x_CreateEmptyLocalCDDEntry(CDataSource *data_source, CTSE_Chunk_Info *chunk)

bool x_IsEmptyCDD(const CTSE_Info &tse)

EPSG_Status

Retrieval result.

@ eSuccess

Successfully retrieved.

@ eForbidden

User is not authorized for the retrieval.

@ eError

An error was encountered while trying to send request or to read and to process the reply.

vector< CPSG_BioId > CPSG_BioIds

static const TPluginManagerParamTree * s_FindSubNode(const TPluginManagerParamTree *params, const string &name)

#define NCBI_PSGLOADER_SERVICE_NAME

typedef NCBI_PARAM_TYPE(PSG_LOADER, SERVICE_NAME) TPSG_ServiceName

static pair< CRef< CTSE_Chunk_Info >, string > s_CreateNAChunk(const CPSG_NamedAnnotInfo &psg_annot_info)

const int kDefaultNoDataCacheLifespanSeconds

static TParamDescription::TValueType s_GetParamValue(const TPluginManagerParamTree *config)

static auto FormatError(const CPSGL_Processor *processor)

#define DEFAULT_WAIT_TIME_MAX

NCBI_PARAM_DEF_EX(string, PSG_LOADER, SERVICE_NAME, "PSG2", eParam_NoThread, PSG_LOADER_SERVICE_NAME)

static bool s_IsIpgAccession(const CSeq_id_Handle &idh, string &acc_ver, bool &is_wp_acc)

static CIncreasingTime::SAllParams s_WaitTimeParams

const size_t kDefaultMaxCacheSize

@ kProcessorIndex_BlobInfo

#define NCBI_PSGLOADER_NAME

#define NCBI_PSGLOADER_NOSPLIT

NCBI_PARAM_DECL(string, PSG_LOADER, SERVICE_NAME)

static auto FormatBulkError(const char *type, const CPSGL_Processor *processor)

const unsigned int kDefaultRetryCount

#define DEFAULT_WAIT_TIME_MULTIPLIER

static ostream & operator<<(ostream &out, SErrorFormatter formatter)

#define DEFAULT_WAIT_TIME_INCREMENT

static bool CannotProcess(const CSeq_id_Handle &sih)

void s_ConvertParamValue< bool >(bool &value, const string &str)

static void s_ConvertParamValue(TParamType &value, const string &str)

#define NCBI_PSGLOADER_ADD_WGS_MASTER

const unsigned int kDefaultBulkRetryCount

const int kDefaultCacheLifespanSeconds

#define DEFAULT_WAIT_TIME

static bool GetSeqId(const T &d, set< string > &labels, const string name="", bool detect=false, bool found=false)

Better replacement of GetAccVer(), this method should be defined in data loaders, GetAccVer() is left...

Better replacement of GetGi(), this method should be defined in data loaders, GetGi() is left for com...

Better replacement of GetSequenceHash(), this method should be defined in data loaders,...

Better replacement of GetSequenceType(), this method should be defined in data loaders,...

SErrorFormatter processor

SBulkErrorFormatter(const char *type, const CPSGL_Processor *processor)

const CPSGL_Processor * processor

SErrorFormatter(const CPSGL_Processor *processor)

Arbitrary request URL arguments.

vector< CSeq_id_Handle > TIds

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