NCBI C++ ToolKit
Classes | Functions | Variables
PubmedArticle.cpp File Reference
#include <ncbi_pch.hpp>
#include <codecvt>
#include <numeric>
#include <regex>
#include <unordered_map>
#include <objects/pubmed/Pubmed_entry.hpp>
#include <objects/medline/Medline_entry.hpp>
#include <objects/general/Date.hpp>
#include <objects/general/Date_std.hpp>
#include <objects/biblio/biblio__.hpp>
#include <objects/general/Dbtag.hpp>
#include <objects/general/Object_id.hpp>
#include <objects/general/Person_id.hpp>
#include <objects/medline/medline__.hpp>
#include <objtools/eutils/efetch/efetch__.hpp>
#include <util/unicode.hpp>
#include <objtools/eutils/efetch/PubmedArticle.hpp>
+ Include dependency graph for PubmedArticle.cpp:
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Classes

struct  pubmed_date_t
 

Functions

 USING_SCOPE (objects)
 
template<typename StringT >
void s_ToLower (StringT &str)
 
template<typename StringT >
void s_ToUpper (StringT &str)
 
static bool s_StringToInt (const string &str, int &i)
 
static int s_TranslateMonth (const string &month_str)
 
template<class container_type , class check_type , class proc_type >
void s_ForeachToken (container_type &container, check_type f, proc_type proc)
 
static string utf8_to_string (const string &str)
 
template<class TE >
string s_Utf8TextListToString (const list< CRef< TE >> &text_list)
 
static string s_GetInitialsFromForeName (string fore_name)
 
static pubmed_date_t s_GetPubmedDate (const CPubDate &pub_date)
 
static CRef< CDates_GetDateFromArticleDate (const CArticleDate &adate)
 
static CRef< CTitles_GetJournalTitle (const CPubmedArticle &pubmed_article)
 
static bool s_SetCommentCorrection (CRef< CImprint > &imprint, const CCommentsCorrectionsList &comments_corrections, CCitRetract::EType type, const string &ref_type)
 
static EPubStatus s_GetPublicationStatusId (const string &publication_status)
 
static CRef< CImprints_GetImprint (const CPubmedArticle &pubmed_article)
 
static CRef< CCit_jours_GetJournalCitation (const CPubmedArticle &pubmed_article)
 
bool s_IsValidYN (const CAuthor &auth)
 
static CRef< CAuth_lists_GetAuthorList (const CArticle &article)
 
static objects::CArticleId::E_Choice s_GetArticleIdTypeId (const CArticleId &article_id)
 
static CRef< CCit_arts_GetCitation (const CPubmedArticle &pubmed_article)
 
static void s_FillMesh (CMedline_entry::TMesh &mesh, const CMeshHeadingList &mesh_heading_list)
 
static void s_FillChem (CMedline_entry::TSubstance &chems, const CChemicalList &chemical_list)
 
static int s_GetDatabankTypeId (const string &databank_name)
 
static void s_FillXref (CMedline_entry::TXref &refs, const CDataBankList &databank_list)
 
static void s_FillGenes (CMedline_entry::TGene &mgenes, const CGeneSymbolList &gene_symbol_list)
 
static void s_FillPubtypeList (CMedline_entry::TPub_type &pub_types, const CPublicationTypeList &publication_type_list)
 
static CRef< CPubMedPubDates_FindPubDateStatus (const list< CRef< CPubMedPubDate >> &pubmed_pubdates, CPubMedPubDate::C_Attlist::EAttlist_PubStatus status)
 
static string s_GetAbstractText (const CAbstract &abstr)
 
static CRef< CMedline_entrys_GetMedlineEntry (const CPubmedArticle &pubmed_article)
 
string s_CleanupText (string str)
 
CRef< CDates_GetDateFromPubDate (const CPubDate &pub_date)
 
CRef< CDates_GetDateFromPubMedPubDate (const CPubMedPubDate &pdate)
 
string s_GetArticleTitleStr (const CArticleTitle &article_title)
 
string s_GetVernacularTitleStr (const CVernacularTitle &vernacular_title)
 
CRef< CTitles_MakeTitle (const string &title_str, const string &vernacular_title_str)
 
string s_GetAuthorMedlineName (const CAuthor &author)
 
string s_GetPagination (const CPagination &pagination)
 
CRef< CArticleIdSets_GetArticleIdSet (const CArticleIdList &article_id_list, const CArticle *article)
 
void s_FillGrants (list< string > &id_nums, const CGrantList &grant_list)
 

Variables

BEGIN_eutils_SCOPE NCBI_USING_NAMESPACE_STD
 
 USING_NCBI_SCOPE
 
 BEGIN_LOCAL_NAMESPACE
 
 END_LOCAL_NAMESPACE
 

Function Documentation

◆ s_CleanupText()

string s_CleanupText ( string  str)

Definition at line 743 of file PubmedArticle.cpp.

References str(), and utf8_to_string().

Referenced by s_GetMedlineEntry().

◆ s_FillChem()

static void s_FillChem ( CMedline_entry::TSubstance chems,
const CChemicalList chemical_list 
)
static

Definition at line 582 of file PubmedArticle.cpp.

References CChemicalList_Base::GetChemical(), and toupper().

Referenced by s_GetMedlineEntry().

◆ s_FillGenes()

static void s_FillGenes ( CMedline_entry::TGene mgenes,
const CGeneSymbolList gene_symbol_list 
)
static

Definition at line 652 of file PubmedArticle.cpp.

References CGeneSymbolList_Base::GetGeneSymbol().

Referenced by s_GetMedlineEntry().

◆ s_FillGrants()

void s_FillGrants ( list< string > &  id_nums,
const CGrantList grant_list 
)

Definition at line 989 of file PubmedArticle.cpp.

References CGrantList_Base::GetGrant(), and utf8_to_string().

Referenced by s_GetMedlineEntry().

◆ s_FillMesh()

static void s_FillMesh ( CMedline_entry::TMesh mesh,
const CMeshHeadingList mesh_heading_list 
)
static

◆ s_FillPubtypeList()

static void s_FillPubtypeList ( CMedline_entry::TPub_type pub_types,
const CPublicationTypeList publication_type_list 
)
static

Definition at line 660 of file PubmedArticle.cpp.

References CPublicationTypeList_Base::GetPublicationType().

Referenced by s_GetMedlineEntry().

◆ s_FillXref()

static void s_FillXref ( CMedline_entry::TXref refs,
const CDataBankList databank_list 
)
static

◆ s_FindPubDateStatus()

static CRef<CPubMedPubDate> s_FindPubDateStatus ( const list< CRef< CPubMedPubDate >> &  pubmed_pubdates,
CPubMedPubDate::C_Attlist::EAttlist_PubStatus  status 
)
static

Definition at line 670 of file PubmedArticle.cpp.

Referenced by s_GetMedlineEntry().

◆ s_ForeachToken()

template<class container_type , class check_type , class proc_type >
void s_ForeachToken ( container_type &  container,
check_type  f,
proc_type  proc 
)

Definition at line 135 of file PubmedArticle.cpp.

References f(), first(), and proc.

Referenced by s_GetInitialsFromForeName(), s_GetPagination(), and s_GetPubmedDate().

◆ s_GetAbstractText()

static string s_GetAbstractText ( const CAbstract abstr)
static

Definition at line 683 of file PubmedArticle.cpp.

References CAbstract_Base::GetAbstractText(), label, and s_TextListToString().

Referenced by s_GetMedlineEntry().

◆ s_GetArticleIdSet()

CRef<CArticleIdSet> s_GetArticleIdSet ( const CArticleIdList article_id_list,
const CArticle article 
)

◆ s_GetArticleIdTypeId()

static objects::CArticleId::E_Choice s_GetArticleIdTypeId ( const CArticleId article_id)
static

◆ s_GetArticleTitleStr()

string s_GetArticleTitleStr ( const CArticleTitle article_title)

◆ s_GetAuthorList()

static CRef<CAuth_list> s_GetAuthorList ( const CArticle article)
static

◆ s_GetAuthorMedlineName()

string s_GetAuthorMedlineName ( const CAuthor author)

◆ s_GetCitation()

static CRef<CCit_art> s_GetCitation ( const CPubmedArticle pubmed_article)
static

◆ s_GetDatabankTypeId()

static int s_GetDatabankTypeId ( const string databank_name)
static

◆ s_GetDateFromArticleDate()

static CRef<CDate> s_GetDateFromArticleDate ( const CArticleDate adate)
static

◆ s_GetDateFromPubDate()

CRef<CDate> s_GetDateFromPubDate ( const CPubDate pub_date)

◆ s_GetDateFromPubMedPubDate()

CRef<CDate> s_GetDateFromPubMedPubDate ( const CPubMedPubDate pdate)

◆ s_GetImprint()

static CRef<CImprint> s_GetImprint ( const CPubmedArticle pubmed_article)
static

Definition at line 370 of file PubmedArticle.cpp.

References CArticleDate_Base::C_Attlist::eAttlist_DateType_Electronic, ePubStatus_other, CCitRetract_Base::eType_erratum, CCitRetract_Base::eType_in_error, CCitRetract_Base::eType_notice, CCitRetract_Base::eType_retracted, CIssue_Base::Get(), CVolume_Base::Get(), CMedlineCitation_Base::GetArticle(), CArticle_Base::GetArticleDate(), CArticle_Base::GetAttlist(), CMedlineCitation_Base::GetCommentsCorrectionsList(), CPubmedData_Base::GetHistory(), CJournalIssue_Base::GetIssue(), CArticle_Base::GetJournal(), CArticle_Base::GetLanguage(), CPubmedArticle_Base::GetMedlineCitation(), CArticle_Base::C_PE_2::C_PE::GetPagination(), CArticle_Base::C_PE_2::GetPE(), CArticle_Base::GetPE_2(), CJournalIssue_Base::GetPubDate(), CPubmedData_Base::GetPublicationStatus(), CPubmedArticle_Base::GetPubmedData(), CHistory_Base::GetPubMedPubDate(), CArticle_Base::C_Attlist::GetPubModel(), CJournalIssue_Base::GetVolume(), CArticle_Base::C_PE_2::IsPE(), CMedlineCitation_Base::IsSetCommentsCorrectionsList(), CPubmedData_Base::IsSetHistory(), CJournalIssue_Base::IsSetIssue(), CJournalIssue_Base::IsSetVolume(), journal(), next(), s_GetDateFromArticleDate(), s_GetDateFromPubDate(), s_GetDateFromPubMedPubDate(), s_GetPagination(), s_GetPublicationStatusId(), s_SetCommentCorrection(), CPubStatusDateSet_Base::Set(), CImprint_Base::SetDate(), CImprint_Base::SetHistory(), CImprint_Base::SetIssue(), CImprint_Base::SetLanguage(), CImprint_Base::SetPages(), CImprint_Base::SetPubstatus(), and CImprint_Base::SetVolume().

Referenced by s_GetJournalCitation().

◆ s_GetInitialsFromForeName()

static string s_GetInitialsFromForeName ( string  fore_name)
static

Definition at line 171 of file PubmedArticle.cpp.

References isspace(), s_ForeachToken(), s_ToUpper(), and string.

Referenced by s_GetAuthorMedlineName().

◆ s_GetJournalCitation()

static CRef<CCit_jour> s_GetJournalCitation ( const CPubmedArticle pubmed_article)
static

Definition at line 443 of file PubmedArticle.cpp.

References s_GetImprint(), and s_GetJournalTitle().

Referenced by s_GetCitation().

◆ s_GetJournalTitle()

static CRef<CTitle> s_GetJournalTitle ( const CPubmedArticle pubmed_article)
static

◆ s_GetMedlineEntry()

static CRef<CMedline_entry> s_GetMedlineEntry ( const CPubmedArticle pubmed_article)
static

◆ s_GetPagination()

string s_GetPagination ( const CPagination pagination)

◆ s_GetPublicationStatusId()

static EPubStatus s_GetPublicationStatusId ( const string publication_status)
static

◆ s_GetPubmedDate()

static pubmed_date_t s_GetPubmedDate ( const CPubDate pub_date)
static

◆ s_GetVernacularTitleStr()

string s_GetVernacularTitleStr ( const CVernacularTitle vernacular_title)

Definition at line 818 of file PubmedArticle.cpp.

References CVernacularTitle_Base::Get(), and s_Utf8TextListToString().

Referenced by s_GetTitle().

◆ s_IsValidYN()

bool s_IsValidYN ( const CAuthor auth)
inline

◆ s_MakeTitle()

CRef<CTitle> s_MakeTitle ( const string title_str,
const string vernacular_title_str 
)

Definition at line 824 of file PubmedArticle.cpp.

References CRef< C, Locker >::Reset(), and CTitle_Base::Set().

◆ s_SetCommentCorrection()

static bool s_SetCommentCorrection ( CRef< CImprint > &  imprint,
const CCommentsCorrectionsList comments_corrections,
CCitRetract::EType  type,
const string ref_type 
)
static

◆ s_StringToInt()

static bool s_StringToInt ( const string str,
int i 
)
static

Definition at line 93 of file PubmedArticle.cpp.

References i, and str().

Referenced by s_GetPubmedDate(), and s_TranslateMonth().

◆ s_ToLower()

template<typename StringT >
void s_ToLower ( StringT &  str)

Definition at line 76 of file PubmedArticle.cpp.

References locale, and str().

Referenced by s_FillXref().

◆ s_ToUpper()

template<typename StringT >
void s_ToUpper ( StringT &  str)

Definition at line 85 of file PubmedArticle.cpp.

References locale, and str().

Referenced by s_GetInitialsFromForeName().

◆ s_TranslateMonth()

static int s_TranslateMonth ( const string month_str)
static

Definition at line 107 of file PubmedArticle.cpp.

References s_StringToInt().

Referenced by s_GetPubmedDate().

◆ s_Utf8TextListToString()

template<class TE >
string s_Utf8TextListToString ( const list< CRef< TE >> &  text_list)

◆ USING_SCOPE()

USING_SCOPE ( objects  )

◆ utf8_to_string()

static string utf8_to_string ( const string str)
static

Variable Documentation

◆ BEGIN_LOCAL_NAMESPACE

BEGIN_LOCAL_NAMESPACE

Definition at line 73 of file PubmedArticle.cpp.

◆ END_LOCAL_NAMESPACE

END_LOCAL_NAMESPACE

Definition at line 740 of file PubmedArticle.cpp.

◆ NCBI_USING_NAMESPACE_STD

BEGIN_eutils_SCOPE NCBI_USING_NAMESPACE_STD

Definition at line 63 of file PubmedArticle.cpp.

◆ USING_NCBI_SCOPE

USING_NCBI_SCOPE

Definition at line 64 of file PubmedArticle.cpp.

Modified on Thu Jun 13 17:25:29 2024 by modify_doxy.py rev. 669887