sp_ref.cpp File Reference

#include <ncbi_pch.hpp>
#include "ftacpp.hpp"
#include <objects/biblio/Cit_pat.hpp>
#include <objects/biblio/Auth_list.hpp>
#include <objects/pub/Pub_equiv.hpp>
#include <objects/pub/Pub.hpp>
#include <objects/seq/Pubdesc.hpp>
#include <objects/biblio/Cit_gen.hpp>
#include <objects/biblio/Cit_book.hpp>
#include <objects/biblio/Imprint.hpp>
#include <objects/biblio/Cit_jour.hpp>
#include <objects/biblio/ArticleIdSet.hpp>
#include <objects/biblio/ArticleId.hpp>
#include <objects/biblio/Cit_art.hpp>
#include <objects/general/Dbtag.hpp>
#include <objects/general/Object_id.hpp>
#include <objects/biblio/Cit_sub.hpp>
#include <objects/biblio/Affil.hpp>
#include <objects/biblio/Cit_let.hpp>
#include "sprot.h"
#include <objtools/flatfile/flatdefn.h>
#include "ftaerr.hpp"
#include "ftablock.h"
#include "asci_blk.h"
#include "utilref.h"
#include "add.h"
#include "utilfun.h"
#include "ref.h"

Include dependency graph for sp_ref.cpp:

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Classes
struct	ParRefBlk

Macros
#define	THIS_FILE   "sp_ref.cpp"

Typedefs
using	ParRefBlkPtr = ParRefBlk *

Functions
	USING_SCOPE (objects)
static bool	NotName (const char *name)
static Int4	GetDataFromRN (DataBlkPtr dbp, Uint2 col_data)
static void	CkSPComTopics (ParserPtr pp, const char *str)
static string	ParseYear (const char *str)
static bool	ParseJourLine (ParserPtr pp, ParRefBlkPtr prbp, const char *str)
static void	ParseRLDataSP (ParserPtr pp, ParRefBlkPtr prbp, char *str)
static void	GetSprotIds (ParRefBlk *prbp, char *str)
static ParRefBlkPtr	SprotRefString (ParserPtr pp, DataBlkPtr dbp, Uint2 col_data)
static CRef< CDate >	get_s_date (const Char *str, bool bstring)
static void	SetCitTitle (CTitle &title, const string &title_str)
static bool	GetImprintPtr (ParRefBlkPtr prbp, CImprint &imp)
static bool	GetCitSubmit (ParRefBlkPtr prbp, CCit_sub &sub)
static bool	GetCitBookOld (ParRefBlkPtr prbp, CCit_art &article)
static bool	GetCitBook (ParRefBlkPtr prbp, CCit_art &article)
static bool	GetCitPatent (ParRefBlkPtr prbp, Parser::ESource source, CCit_pat &pat)
static bool	GetCitGen (ParRefBlkPtr prbp, CCit_gen &cit_gen)
static bool	GetCitLetThesis (ParRefBlkPtr prbp, CCit_let &cit_let)
static bool	GetCitArticle (ParRefBlkPtr prbp, CCit_art &article)
static void	FreeParRefBlkPtr (ParRefBlkPtr prbp)
static void	DisrootImprint (CCit_sub &sub)
static CRef< CPubdesc >	GetPubRef (ParRefBlkPtr prbp, Parser::ESource source)
CRef< CPubdesc >	sp_refs (ParserPtr pp, DataBlkPtr dbp, Uint2 col_data)

Variables
const char *	ParFlat_SPRefRcToken []

Macro Definition Documentation

THIS_FILE

#define THIS_FILE   "sp_ref.cpp"

Definition at line 71 of file sp_ref.cpp.

Typedef Documentation

ParRefBlkPtr

using ParRefBlkPtr = ParRefBlk*

Definition at line 105 of file sp_ref.cpp.

Function Documentation

CkSPComTopics()

static void CkSPComTopics ( ParserPtr  pp, const char *  str  )

static

Definition at line 189 of file sp_ref.cpp.

References ERR_REFERENCE_UnkRefRcToken, ErrPostEx, fta_StringMatch(), ParFlat_SPRefRcToken, SEV_WARNING, and str().

Referenced by SprotRefString().

DisrootImprint()

static void DisrootImprint ( CCit_sub &  sub )

static

Definition at line 1178 of file sp_ref.cpp.

References CCit_sub_Base::GetAuthors(), CCit_sub_Base::GetImp(), CAuth_list_Base::IsSetAffil(), CCit_sub_Base::IsSetAuthors(), CCit_sub_Base::IsSetDate(), CImprint_Base::IsSetDate(), CCit_sub_Base::IsSetImp(), CImprint_Base::IsSetPub(), CCit_sub_Base::ResetImp(), CCit_sub_Base::SetAuthors(), CCit_sub_Base::SetDate(), and CCit_sub_Base::SetImp().

Referenced by GetPubRef().

FreeParRefBlkPtr()

static void FreeParRefBlkPtr ( ParRefBlkPtr  prbp )

static

Definition at line 1172 of file sp_ref.cpp.

Referenced by sp_refs().

get_s_date()

static CRef<CDate> get_s_date ( const Char *  str, bool  bstring  )

static

Definition at line 525 of file sp_ref.cpp.

References CTime::eCurrent, ERR_REFERENCE_IllegalDate, ErrPostEx, NStr::fAllowTrailingSymbols, CDate_std_Base::GetYear(), months, CRef< C, Locker >::Reset(), CDate_std_Base::SetMonth(), CDate_Base::SetStd(), CDate_Base::SetStr(), CDate_std_Base::SetYear(), SEV_WARNING, str(), StringEquNI(), and NStr::StringToInt().

Referenced by GetCitSubmit().

GetCitArticle()

static bool GetCitArticle ( ParRefBlkPtr  prbp, CCit_art &  article  )

static

Definition at line 1128 of file sp_ref.cpp.

References ParRefBlk::agricola, ParRefBlk::authors, ParRefBlk::doi, GetImprintPtr(), journal(), ParRefBlk::journal, CRef< C, Locker >::NotEmpty(), CCit_art_Base::SetAuthors(), SetCitTitle(), CCit_art_Base::SetFrom(), CCit_art_Base::SetIds(), CCit_art_Base::SetTitle(), and ParRefBlk::title.

Referenced by GetPubRef().

GetCitBook()

static bool GetCitBook ( ParRefBlkPtr  prbp, CCit_art &  article  )

static

Definition at line 819 of file sp_ref.cpp.

References ParRefBlk::authors, CRef< C, Locker >::Empty(), NStr::eNocase, NStr::fAllowTrailingSymbols, NStr::Find(), get_auth(), GetCitBookOld(), ParRefBlk::journal, MemFree(), CRef< C, Locker >::NotEmpty(), NPOS, CCit_art_Base::SetAuthors(), CCit_book_Base::SetAuthors(), SetCitTitle(), CImprint_Base::SetDate(), CCit_art_Base::SetFrom(), CCit_book_Base::SetImp(), CImprint_Base::SetPages(), CImprint_Base::SetPub(), CCit_art_Base::SetTitle(), CCit_book_Base::SetTitle(), CImprint_Base::SetVolume(), SP_REF, string, StringChr, StringIStr(), StringSave, NStr::StringToInt(), and ParRefBlk::title.

Referenced by GetPubRef().

GetCitBookOld()

static bool GetCitBookOld ( ParRefBlkPtr  prbp, CCit_art &  article  )

static

Definition at line 666 of file sp_ref.cpp.

References ParRefBlk::authors, buf, ValNode::data, CRef< C, Locker >::Empty(), NStr::eNocase, NStr::Find(), NStr::FindNoCase(), get_auth_from_toks(), get_date(), get_tokens(), isdigit(), isspace(), ParRefBlk::journal, len, ValNode::next, CRef< C, Locker >::NotEmpty(), NotName(), NPOS, NStr::Sanitize(), CCit_art_Base::SetAuthors(), CCit_book_Base::SetAuthors(), SetCitTitle(), CCit_art_Base::SetFrom(), CCit_book_Base::SetImp(), CCit_art_Base::SetTitle(), CCit_book_Base::SetTitle(), SP_REF, StringIStr(), StringLen(), and ParRefBlk::title.

Referenced by GetCitBook().

GetCitGen()

static bool GetCitGen ( ParRefBlkPtr  prbp, CCit_gen &  cit_gen  )

static

Definition at line 1066 of file sp_ref.cpp.

References ParRefBlk::authors, ParRefBlk::cit, ParRefBlk::journal, CRef< C, Locker >::NotEmpty(), CCit_gen_Base::SetAuthors(), CCit_gen_Base::SetCit(), CCit_gen_Base::SetTitle(), and ParRefBlk::title.

Referenced by GetPubRef().

GetCitLetThesis()

static bool GetCitLetThesis ( ParRefBlkPtr  prbp, CCit_let &  cit_let  )

static

Definition at line 1100 of file sp_ref.cpp.

References ParRefBlk::authors, CCit_let_Base::eType_thesis, GetImprintPtr(), CRef< C, Locker >::NotEmpty(), CCit_book_Base::SetAuthors(), CCit_let_Base::SetCit(), SetCitTitle(), CCit_book_Base::SetImp(), CCit_book_Base::SetTitle(), CCit_let_Base::SetType(), and ParRefBlk::title.

Referenced by GetPubRef().

GetCitPatent()

static bool GetCitPatent ( ParRefBlkPtr  prbp, Parser::ESource  source, CCit_pat &  pat  )

static

Definition at line 981 of file sp_ref.cpp.

References ParRefBlk::authors, CRef< C, Locker >::Empty(), ERR_REFERENCE_Patent, ErrPostEx, get_full_date(), isdigit(), ParRefBlk::journal, CRef< C, Locker >::NotEmpty(), CCit_pat_Base::SetAuthors(), CCit_pat_Base::SetCountry(), CCit_pat_Base::SetDate_issue(), CCit_pat_Base::SetDoc_type(), CCit_pat_Base::SetNumber(), CCit_pat_Base::SetTitle(), SEV_ERROR, SEV_WARNING, rapidjson::source, StringLen(), and ParRefBlk::title.

Referenced by GetPubRef().

GetCitSubmit()

static bool GetCitSubmit ( ParRefBlkPtr  prbp, CCit_sub &  sub  )

static

Definition at line 621 of file sp_ref.cpp.

References ParRefBlk::authors, CCit_sub_Base::eMedium_other, CRef< C, Locker >::Empty(), NStr::Equal(), ERR_REFERENCE_IllegalDate, ErrPostStr, get_s_date(), ParRefBlk::journal, CRef< C, Locker >::NotEmpty(), NStr::Sanitize(), CCit_sub_Base::SetAuthors(), CCit_sub_Base::SetImp(), CCit_sub_Base::SetMedium(), SEV_WARNING, StringEquN(), and NStr::TrimSuffixInPlace().

Referenced by GetPubRef().

GetDataFromRN()

static Int4 GetDataFromRN ( DataBlkPtr  dbp, Uint2  col_data  )

static

Definition at line 162 of file sp_ref.cpp.

References NStr::fAllowTrailingSymbols, isdigit(), DataBlk::len, DataBlk::mOffset, str(), and NStr::StringToInt().

Referenced by SprotRefString().

GetImprintPtr()

static bool GetImprintPtr ( ParRefBlkPtr  prbp, CImprint &  imp  )

static

Definition at line 591 of file sp_ref.cpp.

References CImprint_Base::ePrepub_in_press, NStr::fAllowTrailingSymbols, ParRefBlk::pages, CImprint_Base::SetDate(), CImprint_Base::SetPages(), CImprint_Base::SetPrepub(), CImprint_Base::SetVolume(), NStr::StringToInt(), ParRefBlk::vol, and ParRefBlk::year.

Referenced by GetCitArticle(), and GetCitLetThesis().

GetPubRef()

static CRef<CPubdesc> GetPubRef ( ParRefBlkPtr  prbp, Parser::ESource  source  )

static

Definition at line 1201 of file sp_ref.cpp.

References ParRefBlk::comment, DisrootImprint(), ENTREZ_ID_FROM, ERR_REFERENCE_Fail_to_parse, ErrPostEx, GetCitArticle(), GetCitBook(), GetCitGen(), GetCitLetThesis(), GetCitPatent(), GetCitSubmit(), ParRefBlk::journal, msg(), ParRefBlk::muid, ParFlat_ReftypeArticle, ParFlat_ReftypeBook, ParFlat_ReftypeIgnore, ParFlat_ReftypeNoParse, ParFlat_ReftypePatent, ParFlat_ReftypeSubmit, ParFlat_ReftypeThesis, ParFlat_ReftypeUnpub, ParRefBlk::pmid, ParRefBlk::refnum, ParRefBlk::reftype, CRef< C, Locker >::Reset(), CAliasBase< TPrim >::Set(), CPub_Base::SetArticle(), CPub_Base::SetGen(), CPub_Base::SetMan(), CPub_Base::SetMuid(), CPub_Base::SetPatent(), CPub_Base::SetPmid(), CCit_gen_Base::SetSerial_number(), CPub_Base::SetSub(), SEV_ERROR, rapidjson::source, and ZERO_ENTREZ_ID.

Referenced by sp_refs().

GetSprotIds()

static void GetSprotIds ( ParRefBlk *  prbp, char *  str  )

static

Definition at line 361 of file sp_ref.cpp.

References ParRefBlk::agricola, ParRefBlk::doi, ENTREZ_ID_FROM, ERR_REFERENCE_MultipleIdentifiers, ErrPostStr, ParRefBlk::muid, ParRefBlk::pmid, SEV_ERROR, str(), StringChr, StringEquNI(), and ZERO_ENTREZ_ID.

Referenced by SprotRefString().

NotName()

static bool NotName ( const char *  name )

static

Definition at line 120 of file sp_ref.cpp.

References ValNode::data, get_tokens(), i, isalpha(), MemFree(), ValNode::next, StringChr, StringLen(), StringSave, and tmp.

Referenced by GetCitBookOld().

ParseJourLine()

static bool ParseJourLine ( ParserPtr  pp, ParRefBlkPtr  prbp, const char *  str  )

static

Definition at line 242 of file sp_ref.cpp.

References NStr::eTrunc_End, ParRefBlk::journal, ParRefBlk::pages, ParseYear(), str(), StringChr, NStr::TruncateSpaces(), valid_pages_range(), ParRefBlk::vol, and ParRefBlk::year.

Referenced by ParseRLDataSP().

ParseRLDataSP()

static void ParseRLDataSP ( ParserPtr  pp, ParRefBlkPtr  prbp, char *  str  )

static

Definition at line 296 of file sp_ref.cpp.

References ParRefBlk::affil, ParRefBlk::cit, CleanTailNoneAlphaCharInString(), ParRefBlk::country, ERR_REFERENCE_IllegalFormat, ERR_REFERENCE_YearEquZero, ErrPostEx, GetTheCurrentToken(), ParRefBlk::journal, MemFree(), ParFlat_ReftypeArticle, ParFlat_ReftypeBook, ParFlat_ReftypeIgnore, ParFlat_ReftypePatent, ParFlat_ReftypeSubmit, ParFlat_ReftypeThesis, ParFlat_ReftypeUnpub, ParseJourLine(), ParseYear(), PointToNextToken(), ParRefBlk::refnum, ParRefBlk::reftype, SEV_WARNING, str(), StringChr, StringEquNI(), and ParRefBlk::year.

Referenced by SprotRefString().

ParseYear()

static string ParseYear ( const char *  str )

static

Definition at line 215 of file sp_ref.cpp.

References i, isdigit(), and str().

Referenced by ParseJourLine(), and ParseRLDataSP().

SetCitTitle()

static void SetCitTitle ( CTitle &  title, const string &  title_str  )

static

Definition at line 577 of file sp_ref.cpp.

References CTitle_Base::Set().

Referenced by GetCitArticle(), GetCitBook(), GetCitBookOld(), and GetCitLetThesis().

sp_refs()

CRef<CPubdesc> sp_refs	(	ParserPtr	pp,
		DataBlkPtr	dbp,
		Uint2	col_data
	)

Definition at line 1279 of file sp_ref.cpp.

References FreeParRefBlkPtr(), GetPubRef(), Parser::source, SprotRefString(), and ParRefBlk::title.

Referenced by DescrRefs().

SprotRefString()

static ParRefBlkPtr SprotRefString ( ParserPtr  pp, DataBlkPtr  dbp, Uint2  col_data  )

static

Definition at line 436 of file sp_ref.cpp.

References ParRefBlk::authors, CkSPComTopics(), ParRefBlk::comment, ERR_REFERENCE_UnkRefSubType, ErrPostEx, get_auth(), get_auth_consortium(), GetBlkDataReplaceNewLine(), GetDataFromRN(), GetSprotIds(), len, DataBlk::len, MemFree(), DataBlk::mOffset, DataBlk::mpData, DataBlk::mpNext, DataBlk::mType, ParRefBlk::muid, ParFlatSP_RA, ParFlatSP_RC, ParFlatSP_RG, ParFlatSP_RL, ParFlatSP_RM, ParFlatSP_RP, ParFlatSP_RT, ParFlatSP_RX, ParseRLDataSP(), ParRefBlk::refnum, NStr::Sanitize(), SEV_WARNING, SP_REF, str(), StringEquNI(), StringLen(), StringSave, and ParRefBlk::title.

Referenced by sp_refs().

USING_SCOPE()

USING_SCOPE

(

objects

)

Variable Documentation

ParFlat_SPRefRcToken

const char* ParFlat_SPRefRcToken[]

Initial value:

= {
    "MEDLINE", "PLASMID", "SPECIES", "STRAIN", "TISSUE", "TRANSPOSON", nullptr
}

Definition at line 107 of file sp_ref.cpp.

Referenced by CkSPComTopics().