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NCBI C++ ToolKit: src/objtools/edit/remote_updater.cpp Source File

(

& pPub :

) {

pPub->GetPmid().Get();

s_IsConnectionFailure(

errorVal)

maxCount =

(1, maxAttempts);

isConnectionError = s_IsConnectionFailure(errorVal);

(isConnectionError &&

< maxCount - 1) {

std::ostringstream oss;

oss <<

(isConnectionError) {

oss <<

+ 1 <<

;

oss <<

<< errorVal;

= oss.str();

(pMessageListener) {

timeout = { seconds, 0 };

std::ostringstream os;

(reply.

()) {

reply =

->SetReply().front();

(reply->

() && f_logger) {

& error_message =

f_logger(error_message);

vector<string> keys(

);

vector<CRef<CT3Reply>*> cache_refs(

);

(

= 0;

<

; ++

) {

std::ostringstream os;

keys[

] = os.str();

cache_refs[

] = &reply;

to_ask[keys[

]] = make_pair(

[

], &reply);

( !to_ask.

() ) {

(

& it : to_ask ) {

to_ask_vec.push_back(it.second);

m = to_ask_vec.size();

& requests = whole_request.

();

(

& it : to_ask_vec ) {

rq->SetOrg(*it.first);

requests.push_back(rq);

& replies = whole_reply->SetReply();

( replies.size() != m ) {

& error_message =

logger(error_message);

(

& reply : replies ) {

& ask = to_ask_vec[

++];

(reply->IsError() && logger) {

& in_org = *ask.first;

& error_message =

reply->GetError().GetMessage();

logger(error_message);

}

(reply->IsData() && reply->SetData().IsSetOrg()) {

reply->SetData().SetOrg().ResetSyn();

(

= 0;

<

; ++

) {

->SetReply().push_back(*cache_refs[

]);

(

& it :

) {

(! (pub && pub->IsMedline())) {

(! pub->GetMedline().IsSetCit()) {

.push_back(new_pmid);

.push_back(new_pub);

copied->Assign(*res);

(cfg.

(

)) {

sect =

;

delay = cfg.

(sect,

, 20);

exponential = cfg.

(sect,

,

);

(cfg.

(

)) {

sect =

;

(cfg.

(sect,

)) {

(desc.

()) {

std::lock_guard<std::mutex> guard(

);

m_pMessageListener(pMessageListener)

= [

](

& error_message) {

m_pMessageListener(pMessageListener), m_pm_normalize(norm)

m_taxon(logger), m_pubmed(

, norm)

m_taxon(pMessageListener), m_pubmed(pMessageListener, norm)

std::lock_guard<std::mutex> guard(

);

std::lock_guard<std::mutex> guard(

);

(

& it : submit->

().SetEntrys()) {

(entry.

()) {

std::lock_guard<std::mutex> guard(

);

(

& pDesc : seq_descr.

()) {

(! pDesc->IsPub() || ! pDesc->GetPub().IsSetPub()) {

&

= pDesc->SetPub().SetPub().Set();

(

& pPub :

) {

(pPub->IsArticle()) {

_UpdateOrgFromTaxon(

& entry, TOrgMap& m)

(entry.

()) {

_UpdateOrgFromTaxon(*it, m);

(

& it : entry.

().Set()) {

(desc.

()) {

std::ostringstream os;

v.owner.insert(&owner);

xUpdate(TOwnerSet& owners,

& org_ref)

(

& owner_it : owners) {

((*owner_it)->IsOrg()) {

(*owner_it)->SetOrg(org_ref);

}

((*owner_it)->IsSource()) {

(*owner_it)->SetSource().SetOrg(org_ref);

TOrgMap org_to_update;

_UpdateOrgFromTaxon(entry, org_to_update);

(org_to_update.empty())

std::lock_guard<std::mutex> guard(

);

vector<CRef<COrg_ref>> reflist;

(

& it : org_to_update) {

reflist.push_back(it.second.org_ref);

(

& it : org_to_update) {

vector<CRef<COrg_ref>> reflist;

reflist.push_back(it.second.org_ref);

& reply_it = reply->SetReply().front();

(reply_it->IsData() && reply_it->SetData().IsSetOrg()) {

xUpdate(it.second.owner, reply_it->SetData().SetOrg());

list<CRef<CAuthor>> authors_with_affil;

(it->IsSetAffil()) {

authors_with_affil.push_back(it);

(authors_with_affil.size() == 1) {

(

<<

);

auth_list.

(authors_with_affil.front()->SetAffil());

authors_with_affil.front()->ResetAffil();

(desc_it->IsPub()) {

(it->IsSetAuthors()) {

(

bioseq_it(obj); bioseq_it; ++bioseq_it) {

std::lock_guard<std::mutex> guard(

);

std::lock_guard<std::mutex> guard(

);

std::lock_guard<std::mutex> guard(

);

upd->ReportStats(os);

User-defined methods of the data storage class.

@Auth_list.hpp User-defined methods of the data storage class.

void ConvertMlToStd(bool normalize_suffix)

CRef< CTaxon3_reply > SendOrgRefList(const vector< CRef< COrg_ref >> &query, CTaxonomyUpdater::FLogger logger)

CRef< CT3Reply > GetOrgReply(const COrg_ref &in_org, CTaxonomyUpdater::FLogger f_logger)

map< string, CRef< CT3Reply > > CCachedReplyMap

unique_ptr< CTaxon3 > m_taxon

void InitWithTimeout(unsigned seconds, unsigned retries, bool exponential)

void ReportStats(std::ostream &str)

unique_ptr< CCachedReplyMap > m_cache

CRef< COrg_ref > GetOrg(const COrg_ref &org, CTaxonomyUpdater::FLogger f_logger)

virtual CRef< CPub > GetPubmedEntry(TEntrezId pmid, EPubmedError *=nullptr)

CAuth_list & SetAuthors(void)

bool IsSetAuthors(void) const

@Pubdesc.hpp User-defined methods of the data storage class.

IObjtoolsListener * m_pMessageListener

TPubInterceptor m_pm_interceptor

static void ConvertToStandardAuthors(CAuth_list &auth_list)

CPub::E_Choice m_pm_pub_type

CPubmedUpdater(IObjtoolsListener *, CEUtilsUpdater::ENormalize=CEUtilsUpdater::ENormalize::Off)

void ReportStats(std::ostream &str)

CEUtilsUpdater::ENormalize m_pm_normalize

void SetPubmedClient(CEUtilsUpdater *)

static void PostProcessPubs(CSeq_entry_EditHandle &obj)

void xUpdatePubReferences(CSeq_entry &entry)

bool xUpdatePubPMID(list< CRef< CPub >> &pubs, TEntrezId id)

void SetMaxMlaAttempts(int max)

unique_ptr< CEUtilsUpdater > m_pubmed

void UpdatePubReferences(CSerialObject &obj)

static CRemoteUpdater & GetInstance()

CRemoteUpdater(IObjtoolsListener *pMessageListener, CEUtilsUpdater::ENormalize=CEUtilsUpdater::ENormalize::Off)

@Seq_descr.hpp User-defined methods of the data storage class.

void SetDescr(CSeq_descr &value)

bool IsSetDescr(void) const

Base class for all serializable objects.

void SetTaxonTimeout(unsigned seconds=20, unsigned retries=5, bool exponential=false)

function< void(const string &)> FLogger

void xUpdateOrgTaxname(COrg_ref &org)

CTaxonomyUpdater(IObjtoolsListener *pMessageListener)

IObjtoolsListener * m_pMessageListener

void UpdateOrgFromTaxon(CSeq_entry &entry)

void ReportStats(std::ostream &)

unique_ptr< CCachedTaxon3_impl > m_taxClient

CConstRef< CTaxon3_reply > SendOrgRefList(const vector< CRef< COrg_ref >> &list)

taxupdate_func_t m_taxon_update

static vector< string > arr

@ cannot_connect_searchbackend_pmdb

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

SStrictId_Entrez::TId TEntrezId

TEntrezId type for entrez ids which require the same strictness as TGi.

const CNcbiRegistry & GetConfig(void) const

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

static CNcbiApplicationAPI * Instance(void)

Singleton method.

SStrictId_Tax::TId TTaxId

Taxon id type.

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

#define LOG_POST(message)

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

@ eDiag_Warning

Warning message.

void Error(CExceptionArgs_Base &args)

#define NCBI_THROW(exception_class, err_code, message)

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

void Info(CExceptionArgs_Base &args)

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Set object to copy of another one.

virtual const CTypeInfo * GetThisTypeInfo(void) const =0

#define MSerial_AsnText

I/O stream manipulators –.

bool NotNull(void) const THROWS_NONE

Check if pointer is not null – same effect as NotEmpty().

void Reset(void)

Reset reference object.

bool NotEmpty(void) const THROWS_NONE

Check if CRef is not empty – pointing to an object and has a non-null value.

bool Empty(void) const THROWS_NONE

Check if CRef is empty – not pointing to any object, which means having a null value.

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 bool HasEntry(const string &section, const string &name=kEmptyStr, TFlags flags=0) const

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

Get the parameter string value.

#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 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.

double Elapsed(void) const

Return time elapsed since first Start() or last Restart() call (in seconds).

@ eStart

Start timer immediately after creating.

virtual bool IsType(TTypeInfo type) const

bool IsSetAffil(void) const

author affiliation Check if a value has been assigned to Affil data member.

void SetAffil(TAffil &value)

Assign a value to Affil data member.

bool IsSetNames(void) const

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

void SetNames(TNames &value)

Assign a value to Names data member.

const TNames & GetNames(void) const

Get the Names member data.

bool IsStd(void) const

Check if variant Std is selected.

bool IsSetOrg(void) const

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

void SetOrg(TOrg &value)

Assign a value to Org data member.

const TTaxname & GetTaxname(void) const

Get the Taxname member data.

bool IsSetTaxname(void) const

preferred formal name Check if a value has been assigned to Taxname data member.

TPmid & SetPmid(void)

Select the variant.

TMedline & SetMedline(void)

Select the variant.

TArticle & SetArticle(void)

Select the variant.

TSet & SetSet(void)

Select the variant.

bool IsSeq(void) const

Check if variant Seq is selected.

bool IsSet(void) const

Check if variant Set is selected.

TSeq & SetSeq(void)

Select the variant.

TSeq_set & SetSeq_set(void)

Assign a value to Seq_set data member.

void SetPub(TPub &value)

Assign a value to Pub data member.

TOrg & SetOrg(void)

Select the variant.

bool IsOrg(void) const

Check if variant Org is selected.

const TSource & GetSource(void) const

Get the variant data.

bool IsSource(void) const

Check if variant Source is selected.

TSource & SetSource(void)

Select the variant.

void SetDescr(TDescr &value)

Assign a value to Descr data member.

bool IsSetPub(void) const

the citation(s) Check if a value has been assigned to Pub data member.

Tdata & Set(void)

Assign a value to data member.

@ e_Pub

a reference to the publication

void SetData(TData &value)

Assign a value to Data data member.

bool IsData(void) const

Check if variant Data is selected.

bool IsSetOrg(void) const

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

TRequest & SetRequest(void)

Assign a value to Request data member.

void SetOrg(TOrg &value)

Assign a value to Org data member.

bool IsError(void) const

Check if variant Error is selected.

const TError & GetError(void) const

Get the variant data.

const TMessage & GetMessage(void) const

Get the Message member data.

TData & SetData(void)

Select the variant.

static const bool kUseBulkTaxonQuery

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

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