pub_report Namespace Reference

Classes
class	CBaseReport
class	CSkipPubJournalHook
class	CJournalReport
class	CPubReportApp
class	CSkipSeqEntryHook
class	CSkipSeqIdHook
class	CSkipPubUnpublishedHook
class	CPubData
class	CUnpublishedReport

Enumerations
enum	AuthorNameMatch {   eNoMatch , eLastNameMatch , eOneInitialMatch , eTwoInitialsMatch ,   eNoHyphenMatch , eFullMatch , eLastValue }

Functions
static bool	IsJournal (const CPub &pub)
static CConstRef< CSeq_id >	GetBestId (const CBioseq::TId &ids)
static bool	IsGenUnpublished (const CCit_gen &cit)
static bool	IsArtUnpublished (const CCit_art &cit)
static bool	IsUnpublished (const CPub &pub)
static void	ProcessInitials (string &initials)
static void	GetAuthorsFromList (list< string > &authors, const CAuth_list &auth_list)
static void	CollectDataGen (const CCit_gen &cit, CPubData &data)
static void	CollectDataArt (const CCit_art &cit, CPubData &data)
static void	CollectData (const CPub &pub, CPubData &data)
static AuthorNameMatch	CompareAuthorNames (string first, string second)
static AuthorNameMatch	CompareAuthors (const list< string > &first, const list< string > &second)
static void	GetOneInitialAuthorName (const string &author, string &name)
static void	GetNameFromStdName (const CPerson_id &person, string &name)
static bool	FirstOrLastAuthorMatches (const list< string > &authors, const CAuth_list::C_Names &pubmed_authors)
static bool	CheckRefs (const CMedline_entry &medline_entry, const CPubData::TSeqIds &seq_ids)
static bool	CheckDate (int year, int month, int max_date_check, const CCit_jour &juornal)
static TEntrezId	DoHydraSearch (const CPubData &data)
static TEntrezId	ConvertPMCtoPMID (TEntrezId pmc)
static void	NormalizeTitle (string &s)
static TEntrezId	DoEUtilsSearch (CEutilsClient &eutils, const string &database, const string &term)
static AuthorNameMatch	IsAuthorInList (const list< string > &auths, const string &author)
static void	ReportSeqIds (CNcbiOstream &out, const CPubData::TSeqIds &ids)
static string	GetAuthorsCmpResultStr (AuthorNameMatch res)
static bool	ReportAuthorDiff (CNcbiOstream &out, const list< string > &pubmed_auths, const list< string > &auths)
static bool	ReportTitleDiff (CNcbiOstream &out, const list< string > &pubmed_title_words, const list< string > &title_words)
static void	ReportAuththors (CNcbiOstream &out, const char *prefix, const list< string > &auths)
static void	ReportTitle (CNcbiOstream &out, const char *prefix, const CPubData &data)
static void	ReportJournal (CNcbiOstream &out, const char *prefix, const CPubData &data)
static void	ReportOnePub (CNcbiOstream &out, const CCit_art &pubmed_cit_art, const CPubData &data, TEntrezId pmid)
string	GetBestTitle (const CTitle &titles)
	USING_SCOPE (objects)

Variables
	USING_NCBI_SCOPE
static string	authors_cmp_result_label []

Enumeration Type Documentation

AuthorNameMatch

enum pub_report::AuthorNameMatch

Enumerator
eNoMatch
eLastNameMatch
eOneInitialMatch
eTwoInitialsMatch
eNoHyphenMatch
eFullMatch
eLastValue

Definition at line 395 of file unpub_report.cpp.

Function Documentation

CheckDate()

static bool pub_report::CheckDate ( int  year, int  month, int  max_date_check, const CCit_jour &  juornal  )

static

Definition at line 616 of file unpub_report.cpp.

References CDate_std::Compare(), CDate::eCompare_after, CDate::eCompare_before, CDate::eCompare_same, CImprint_Base::GetDate(), CCit_jour_Base::GetImp(), CDate_Base::GetStd(), CImprint_Base::IsSetDate(), CCit_jour_Base::IsSetImp(), CDate_std_Base::IsSetYear(), CDate_Base::IsStd(), CDate_std_Base::SetMonth(), and CDate_std_Base::SetYear().

Referenced by pub_report::CUnpublishedReport::FetchPub().

CheckRefs()

static bool pub_report::CheckRefs ( const CMedline_entry &  medline_entry, const CPubData::TSeqIds &  seq_ids  )

static

Definition at line 598 of file unpub_report.cpp.

References set< Key, Compare >::end(), set< Key, Compare >::find(), CMedline_entry_Base::GetXref(), and CMedline_entry_Base::IsSetXref().

Referenced by pub_report::CUnpublishedReport::FetchPub().

CollectData()

static void pub_report::CollectData ( const CPub &  pub, CPubData &  data  )

static

Definition at line 382 of file unpub_report.cpp.

References CollectDataArt(), CollectDataGen(), data, IAbstractCitation::fLabel_Unique, CPub_Base::GetArticle(), CPub_Base::GetGen(), CPub::GetLabel(), CPub_Base::IsArticle(), CPub_Base::IsGen(), and label.

Referenced by pub_report::CUnpublishedReport::ReportUnpublished().

CollectDataArt()

static void pub_report::CollectDataArt ( const CCit_art &  cit, CPubData &  data  )

static

Definition at line 344 of file unpub_report.cpp.

References data, CTitle_Base::Get(), CCit_art_Base::GetAuthors(), GetBestTitle(), CImprint_Base::GetDate(), CCit_art_Base::GetFrom(), CCit_jour_Base::GetImp(), CCit_art_Base::C_From::GetJournal(), CImprint_Base::GetPages(), CDate_Base::GetStd(), CCit_art_Base::GetTitle(), CCit_jour_Base::GetTitle(), CImprint_Base::GetVolume(), CCit_art_Base::C_From::IsJournal(), CTitle_Base::IsSet(), CCit_art_Base::IsSetAuthors(), CImprint_Base::IsSetDate(), CCit_art_Base::IsSetFrom(), CCit_jour_Base::IsSetImp(), CImprint_Base::IsSetPages(), CCit_art_Base::IsSetTitle(), CCit_jour_Base::IsSetTitle(), CImprint_Base::IsSetVolume(), CDate_Base::IsStd(), and NCBI_ASSERT.

Referenced by CollectData(), and ReportOnePub().

CollectDataGen()

static void pub_report::CollectDataGen ( const CCit_gen &  cit, CPubData &  data  )

static

Definition at line 325 of file unpub_report.cpp.

References data, CCit_gen_Base::GetAuthors(), GetBestTitle(), CCit_gen_Base::GetDate(), CCit_gen_Base::GetJournal(), CDate_Base::GetStd(), CCit_gen_Base::GetTitle(), CCit_gen_Base::IsSetAuthors(), CCit_gen_Base::IsSetDate(), CCit_gen_Base::IsSetJournal(), CCit_gen_Base::IsSetTitle(), and CDate_Base::IsStd().

Referenced by CollectData().

CompareAuthorNames()

static AuthorNameMatch pub_report::CompareAuthorNames ( string  first, string  second  )

static

Definition at line 405 of file unpub_report.cpp.

References eFullMatch, eLastNameMatch, eNoHyphenMatch, eNoMatch, eOneInitialMatch, NStr::EqualNocase(), eTwoInitialsMatch, first(), and remove_if().

Referenced by CompareAuthors(), and IsAuthorInList().

CompareAuthors()

static AuthorNameMatch pub_report::CompareAuthors ( const list< string > &  first, const list< string > &  second  )

static

Definition at line 458 of file unpub_report.cpp.

References CompareAuthorNames(), eFullMatch, eNoMatch, and first().

Referenced by ReportOnePub(), and pub_report::CUnpublishedReport::ReportUnpublished().

ConvertPMCtoPMID()

static TEntrezId pub_report::ConvertPMCtoPMID ( TEntrezId  pmc )

static

Definition at line 685 of file unpub_report.cpp.

References buf, ENTREZ_ID_FROM, ENTREZ_ID_TO, ERR_POST, NStr::fAllowTrailingSymbols, NStr::IntToString(), result, NStr::StartsWith(), NStr::StringToInt(), Warning(), and ZERO_ENTREZ_ID.

Referenced by pub_report::CUnpublishedReport::RetrievePMid().

DoEUtilsSearch()

static TEntrezId pub_report::DoEUtilsSearch ( CEutilsClient &  eutils, const string &  database, const string &  term  )

static

Definition at line 749 of file unpub_report.cpp.

References database, CEutilsClient::Search(), and ZERO_ENTREZ_ID.

Referenced by pub_report::CUnpublishedReport::RetrievePMid().

DoHydraSearch()

static TEntrezId pub_report::DoHydraSearch ( const CPubData &  data )

static

Definition at line 651 of file unpub_report.cpp.

References data, ERR_POST, NStr::fSplit_MergeDelimiters, NStr::fSplit_Truncate, names, query, NStr::Split(), Warning(), and ZERO_ENTREZ_ID.

Referenced by pub_report::CUnpublishedReport::RetrievePMid().

FirstOrLastAuthorMatches()

static bool pub_report::FirstOrLastAuthorMatches ( const list< string > &  authors, const CAuth_list::C_Names &  pubmed_authors  )

static

Definition at line 556 of file unpub_report.cpp.

References NStr::EqualNocase(), CAuth_list_Base::C_Names::GetMl(), GetNameFromStdName(), GetOneInitialAuthorName(), CAuth_list_Base::C_Names::GetStd(), CAuth_list_Base::C_Names::GetStr(), CAuth_list_Base::C_Names::IsMl(), CAuth_list_Base::C_Names::IsStd(), and names.

Referenced by pub_report::CUnpublishedReport::FetchPub().

GetAuthorsCmpResultStr()

static string pub_report::GetAuthorsCmpResultStr ( AuthorNameMatch  res )

static

Definition at line 872 of file unpub_report.cpp.

References authors_cmp_result_label, eLastValue, and NCBI_ASSERT.

Referenced by ReportAuthorDiff(), and ReportOnePub().

GetAuthorsFromList()

static void pub_report::GetAuthorsFromList ( list< string > &  authors, const CAuth_list &  auth_list  )

static

Definition at line 90 of file unpub_report.cpp.

References CName_std_Base::GetInitials(), CName_std_Base::GetLast(), CPerson_id_Base::GetMl(), CPerson_id_Base::GetName(), CAuth_list_Base::GetNames(), CPerson_id_Base::GetStr(), CPerson_id_Base::IsMl(), CPerson_id_Base::IsName(), CName_std_Base::IsSetInitials(), CName_std_Base::IsSetLast(), CAuth_list_Base::IsSetNames(), CPerson_id_Base::IsStr(), names, and ProcessInitials().

Referenced by pub_report::CPubData::SetAuthors().

GetBestId()

static CConstRef<CSeq_id> pub_report::GetBestId ( const CBioseq::TId &  ids )

static

Definition at line 45 of file seqid_hook.cpp.

References CSeq_id::BaseBestRankScore(), and CSeq_id_Base::e_Genbank.

Referenced by pub_report::CSkipSeqIdHook::SkipClassMember().

GetBestTitle()

std::string pub_report::GetBestTitle

(

const CTitle &

titles

)

Definition at line 44 of file utils.cpp.

References CTitle_Base::Get(), and CTitle_Base::IsSet().

Referenced by CollectDataArt(), CollectDataGen(), and pub_report::CSkipPubJournalHook::ProcessJournal().

GetNameFromStdName()

static void pub_report::GetNameFromStdName ( const CPerson_id &  person, string &  name  )

static

Definition at line 539 of file unpub_report.cpp.

References CName_std_Base::GetInitials(), CName_std_Base::GetLast(), CPerson_id_Base::GetMl(), CPerson_id_Base::GetName(), CPerson_id_Base::GetStr(), CPerson_id_Base::IsMl(), CPerson_id_Base::IsName(), CName_std_Base::IsSetInitials(), CName_std_Base::IsSetLast(), and CPerson_id_Base::IsStr().

Referenced by FirstOrLastAuthorMatches().

GetOneInitialAuthorName()

static void pub_report::GetOneInitialAuthorName ( const string &  author, string &  name  )

static

Definition at line 526 of file unpub_report.cpp.

Referenced by FirstOrLastAuthorMatches().

IsArtUnpublished()

static bool pub_report::IsArtUnpublished ( const CCit_art &  cit )

static

Definition at line 65 of file unpub_hook.cpp.

References CImprint_Base::ePrepub_in_press, ePubStatus_aheadofprint, CCit_art_Base::GetFrom(), CCit_art_Base::C_From::GetJournal(), CImprint_Base::GetPrepub(), CImprint_Base::GetPubstatus(), CCit_art_Base::C_From::IsJournal(), CCit_art_Base::IsSetFrom(), CImprint_Base::IsSetPrepub(), CImprint_Base::IsSetPubstatus(), and journal().

Referenced by IsUnpublished().

IsAuthorInList()

static AuthorNameMatch pub_report::IsAuthorInList ( const list< string > &  auths, const string &  author  )

static

Definition at line 841 of file unpub_report.cpp.

References CompareAuthorNames(), eFullMatch, and eNoMatch.

Referenced by ReportAuthorDiff().

IsGenUnpublished()

static bool pub_report::IsGenUnpublished ( const CCit_gen &  cit )

static

Definition at line 58 of file unpub_hook.cpp.

References NStr::EqualNocase(), CCit_gen_Base::GetCit(), CCit_gen_Base::GetTitle(), CCit_gen_Base::IsSetCit(), and CCit_gen_Base::IsSetTitle().

Referenced by IsUnpublished().

IsJournal()

static bool pub_report::IsJournal ( const CPub &  pub )

static

Definition at line 54 of file journal_hook.cpp.

References CPub_Base::GetArticle(), CCit_art_Base::GetFrom(), CPub_Base::IsArticle(), CCit_art_Base::C_From::IsJournal(), and CCit_art_Base::IsSetFrom().

Referenced by pub_report::CSkipPubJournalHook::SkipObject().

IsUnpublished()

static bool pub_report::IsUnpublished ( const CPub &  pub )

static

Definition at line 81 of file unpub_hook.cpp.

References CPub_Base::GetArticle(), CPub_Base::GetGen(), CPub_Base::IsArticle(), IsArtUnpublished(), CPub_Base::IsGen(), and IsGenUnpublished().

Referenced by pub_report::CSkipPubUnpublishedHook::SkipObject().

NormalizeTitle()

static void pub_report::NormalizeTitle ( string &  s )

static

Definition at line 727 of file unpub_report.cpp.

References isupper(), and tolower().

Referenced by pub_report::CUnpublishedReport::RetrievePMid().

ProcessInitials()

static void pub_report::ProcessInitials ( string &  initials )

static

Definition at line 77 of file unpub_report.cpp.

Referenced by GetAuthorsFromList().

ReportAuthorDiff()

static bool pub_report::ReportAuthorDiff ( CNcbiOstream &  out, const list< string > &  pubmed_auths, const list< string > &  auths  )

static

Definition at line 878 of file unpub_report.cpp.

References eFullMatch, eNoMatch, GetAuthorsCmpResultStr(), IsAuthorInList(), and out().

Referenced by ReportOnePub().

ReportAuththors()

static void pub_report::ReportAuththors ( CNcbiOstream &  out, const char *  prefix, const list< string > &  auths  )

static

Definition at line 949 of file unpub_report.cpp.

References out().

Referenced by ReportOnePub().

ReportJournal()

static void pub_report::ReportJournal ( CNcbiOstream &  out, const char *  prefix, const CPubData &  data  )

static

Definition at line 981 of file unpub_report.cpp.

References data, and out().

Referenced by ReportOnePub().

ReportOnePub()

static void pub_report::ReportOnePub ( CNcbiOstream &  out, const CCit_art &  pubmed_cit_art, const CPubData &  data, TEntrezId  pmid  )

static

Definition at line 1009 of file unpub_report.cpp.

References CollectDataArt(), CompareAuthors(), data, eNoMatch, ENTREZ_ID_TO, NStr::EqualNocase(), pub_report::CPubData::GetAuthors(), GetAuthorsCmpResultStr(), pub_report::CPubData::GetFullTitle(), pub_report::CPubData::GetTitleWords(), out(), ReportAuthorDiff(), ReportAuththors(), ReportJournal(), ReportSeqIds(), ReportTitle(), and ReportTitleDiff().

Referenced by pub_report::CUnpublishedReport::CompleteReport().

ReportSeqIds()

static void pub_report::ReportSeqIds ( CNcbiOstream &  out, const CPubData::TSeqIds &  ids  )

static

Definition at line 861 of file unpub_report.cpp.

References out().

Referenced by ReportOnePub().

ReportTitle()

static void pub_report::ReportTitle ( CNcbiOstream &  out, const char *  prefix, const CPubData &  data  )

static

Definition at line 962 of file unpub_report.cpp.

References data, and out().

Referenced by ReportOnePub().

ReportTitleDiff()

static bool pub_report::ReportTitleDiff ( CNcbiOstream &  out, const list< string > &  pubmed_title_words, const list< string > &  title_words  )

static

Definition at line 918 of file unpub_report.cpp.

References NStr::EqualNocase(), NStr::FindNoCase(), and out().

Referenced by ReportOnePub().

USING_SCOPE()

pub_report::USING_SCOPE

(

objects

)

Variable Documentation

authors_cmp_result_label

string pub_report::authors_cmp_result_label[]

static

Initial value:

= {
    "AUTH_MISMATCH", "LAST_NAMES", "ONE_INIT", "TWO_INITS", "NO_HYPHENS", "FULL_NAMES"
}

Definition at line 868 of file unpub_report.cpp.

Referenced by GetAuthorsCmpResultStr().

USING_NCBI_SCOPE

pub_report::USING_NCBI_SCOPE

Definition at line 48 of file journal_report.cpp.