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

*

=

;

=

;

=

;

=

;

=

;

=

;

(

(

) |

(

));

(!

.GetMl().empty()) {

.GetMl().front();

}

(

.IsStd()) {

(!

.GetStd().empty()) {

& first_author(*

.GetStd().front());

name(name_std.

());

(

.IsSetAuthors()) {

(

.IsSetFrom() &&

.GetFrom().IsJournal()) {

(

.IsSetTitle()) {

(

.IsSet() && !

.Get().empty()) {

(

.IsSetImp()) {

year =

.GetStd().GetYear();

this->

= to_string(year);

pos = this->

.find(

);

(pos != string::npos) {

this->

.resize(pos);

(

.IsSetTitle()) {

(

.IsSet() && !

.Get().empty()) {

NormalizeJournal(

& s)

(

& c : s) {

(

& c : s) {

((rule &

) && cm.

.empty()) {

((rule &

) && cm.

.empty()) {

((rule &

) && cm.

.empty()) {

((rule &

) && cm.

.empty()) {

((rule &

) && cm.

.empty()) {

((rule &

) && cm.

.empty()) {

v.push_back(

+

);

v.push_back(cm.

+

);

v.push_back(cm.

+

);

page = cm.

;

pos = page.find(

);

(pos != string::npos) {

v.push_back(page +

);

v.push_back(cm.

+

);

v.push_back(cm.

+

);

title = cm.

;

v.push_back(title +

);

args =

;

esearch::CESearchResult

;

(

.IsSetData()) {

(

.IsInfo() &&

.GetInfo().IsSetContent() &&

.GetInfo().GetContent().IsSetIdList()) {

& idList =

.GetInfo().GetContent().GetIdList();

(idList.IsSetId()) {

& ids = idList.GetId();

(ids.size() == 0) {

}

(ids.size() == 1) {

= ids.front();

CSearch_Request req(

);

& ruleset = cm.

? ruleset_in_press : ruleset_single;

= cm.

? 6 : 5;

(

= 0;

<

; ++

) {

(CSearch_Request::BuildSearchTerm(cm,

, term)) {

pmid = req.GetResponse(err, term);

(

.IsSetTitle() && !

.GetTitle().Get().empty()) {

& title =

.SetTitle().Set().front();

(title->IsName()) {

& name = title->SetName();

(! name.empty()) {

ch = name.back();

name.push_back(

);

(

.IsSetIds()) {

& ids =

.SetIds().Set();

& dbt =

->GetOther();

& dbn = dbt.

();

ids.remove_if(IsELocationID);

& dbtl =

->GetOther();

& dbtr =

->GetOther();

& dbnl = dbtl.

();

& dbnr = dbtr.

();

(

.IsSetFrom() &&

.GetFrom().IsBook()) {

book.

().ResetHistory();

GetURL()

s(

);

CFetch_Request req(

, pmid);

CPubOneRequest req(

, pmid);

eutils::CPubmedArticleSet pas;

(pas.IsSetPP() && pas.GetPP().IsSetPP()) {

& pp = pas.GetPP().GetPP();

& ppf = *pp.front();

(ppf.IsPubmedArticle()) {

eutils::CPubmedArticle& article = ppf.GetPubmedArticle();

article.ToPubmed_entry();

}

(ppf.IsPubmedBookArticle()) {

eutils::CPubmedBookArticle& article = ppf.GetPubmedBookArticle();

article.ToPubmed_entry();

eutils::CPubmedBookArticleSet pbas;

(pbas.IsSetPubmedBookArticle()) {

& articles = pbas.GetPubmedBookArticle();

(! articles.empty()) {

eutils::CPubmedBookArticle& article = *articles.front();

article.ToPubmed_entry();

(pme && pme->IsSetMedent()) {

(

& json, vector<TEntrezId>& pmids,

&

)

(dobj[

].GetValue().GetString() ==

);

(dobj[

].GetValue().GetString() ==

);

(! dobj[

].GetValue().GetBool()) {

&

= dobj.

(

);

(!

.IsObject()) {

=

;

& result_obj =

.GetObject();

&

= result_obj.at(

);

&

= result_obj.at(

);

(

.GetValue().GetString() ==

);

& uids = result_obj.at(

);

(! uids.IsArray()) {

=

;

& uids_array = uids.GetArray();

(

it = uids_array.begin(); it != uids_array.end(); ++it) {

(it->IsObject()) {

& uid_obj = it->GetObject();

it2 = uid_obj.find(

);

(it2 != uid_obj.end()) {

sPubmed = it2->value.GetValue().GetString();

pmid = NStr::StringToNumeric<TEntrezId>(sPubmed);

pmids.push_back(pmid);

hostname =

;

path =

;

args =

;

(

attempt = 1; attempt <= 5; ++attempt) {

(! http.fail()) {

http.read(

,

(

));

! pmids.empty();

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

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

This stream exchanges data with an HTTP server located at the URL: http[s]://host[:port]/path[?...

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

void ReportStats(std::ostream &)

map< TEntrezId, CConstRef< CPub > > m_cache

EPubmedSource m_pubmed_src

CRef< CEUtils_ConnContext > m_Ctx

static bool DoPubSearch(const std::vector< string > &query, std::vector< TEntrezId > &pmids)

TPubInterceptor m_pub_interceptor

CEUtilsUpdater(ENormalize=ENormalize::Off, EPubmedSource=EPubmedSource::EUtils)

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

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

CRef< CPub > x_GetPub(TEntrezId pmid, EPubmedError *)

virtual TEntrezId CitMatch(const CPub &, EPubmedError *=nullptr)

CRef< CPubmed_entry > x_GetPubmedEntry(TEntrezId pmid, EPubmedError *)

CJson_Object SetObject(void)

Get JSON object contents of the node.

CJson_Node at(const CJson_Node::TKeyType &name)

Access an element with a given name.

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

Root class for all serialization exceptions.

const string & GetTitle(C_E::E_Choice type=C_E::e_not_set) const

If the internal list contains a title (of the specified type, if given), returns the corresponding st...

const_iterator end() const

const_iterator find(const key_type &key) const

User-defined methods of the data storage class.

static bool ParseJson(const string &json, vector< TEntrezId > &pmids, string &msg)

constexpr eCitMatchFlags operator|(eCitMatchFlags a, eCitMatchFlags b)

static void Normalize(CPub &pub)

static string GetFirstAuthor(const CAuth_list &authors)

@ cannot_connect_searchbackend_pmdb

SStrictId_Entrez::TId TEntrezId

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

#define ENTREZ_ID_FROM(T, value)

string GetQueryString(EAmpEncoding amp_enc, EUrlEncode encode) const

#define ERR_POST(message)

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

static void SetBaseURL(const string &url)

Set new base url for all e-utils requests.

void Warning(CExceptionArgs_Base &args)

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

Set object to copy of another one.

ESerialDataFormat

Data file format.

#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.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

static int CompareNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive compare of a substring with another string.

static TNumeric StringToNumeric(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to a numeric value.

static string Join(const TContainer &arr, const CTempString &delim)

Join strings using the specified delimiter.

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

Check if a string starts with a specified prefix value.

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.

static string URLEncode(const CTempString str, EUrlEncode flag=eUrlEnc_SkipMarkChars)

URL-encode string.

@ fConvErr_NoThrow

Do not throw an exception on error.

@ eUrlEnc_ProcessMarkChars

Convert all non-alphanumeric chars, spaces are converted to '+'.

@ eNocase

Case insensitive compare.

bool IsSetVolume(void) const

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

const TVolume & GetVolume(void) const

Get the Volume member data.

const TPages & GetPages(void) const

Get the Pages member data.

bool IsSetPrepub(void) const

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

bool IsSetHistory(void) const

dates for this record Check if a value has been assigned to History data member.

const TIssue & GetIssue(void) const

Get the Issue member data.

E_Choice

Choice variants.

TPrepub GetPrepub(void) const

Get the Prepub member data.

const TName & GetName(void) const

Get the Name member data.

void SetImp(TImp &value)

Assign a value to Imp data member.

bool IsSetNames(void) const

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

bool IsSetIssue(void) const

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

bool IsSetDate(void) const

date of publication Check if a value has been assigned to Date data member.

bool IsSetName(void) const

Author, Primary or Secondary Check if a value has been assigned to Name data member.

const TNames & GetNames(void) const

Get the Names member data.

const TDate & GetDate(void) const

Get the Date member data.

const TAuthors & GetAuthors(void) const

Get the Authors member data.

const TImp & GetImp(void) const

Get the Imp member data.

bool IsSetPages(void) const

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

bool IsSetImp(void) const

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

@ e_Other

generic catch all

@ ePrepub_in_press

accepted, not published

bool CanGetDb(void) const

Check if it is safe to call GetDb method.

const TInitials & GetInitials(void) const

Get the Initials member data.

bool IsName(void) const

Check if variant Name is selected.

const TDb & GetDb(void) const

Get the Db member data.

bool IsSetInitials(void) const

first + middle initials Check if a value has been assigned to Initials data member.

bool IsSetLast(void) const

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

const TLast & GetLast(void) const

Get the Last member data.

const TName & GetName(void) const

Get the variant data.

void SetCit(TCit &value)

Assign a value to Cit data member.

bool IsSetCit(void) const

article citation Check if a value has been assigned to Cit data member.

const TCit & GetCit(void) const

Get the Cit member data.

bool IsMedline(void) const

Check if variant Medline is selected.

const TMedline & GetMedline(void) const

Get the variant data.

const TArticle & GetArticle(void) const

Get the variant data.

TMedline & SetMedline(void)

Select the variant.

bool IsArticle(void) const

Check if variant Article is selected.

TArticle & SetArticle(void)

Select the variant.

static void NormalizeTitle(string &s)

void SleepSec(unsigned long sec, EInterruptOnSignal onsignal=eRestartOnSignal)

Sleep.

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

User-defined methods of the data storage class.

CRef< CPub > journal(ParserPtr pp, char *bptr, char *eptr, CRef< CAuth_list > &auth_list, CRef< CTitle::C_E > &title, bool has_muid, CRef< CCit_art > &cit_art, Int4 er)

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

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

void FillFromArticle(const CCit_art &)

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