From 378e71de8e4cfeaf9196d8cf68ac3ef192a2ac1b Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Wed, 5 Sep 2018 15:51:24 +0200
Subject: [PATCH] Used new cytation type handling in mmCIF reader
---
modules/io/src/mol/mmcif_reader.cc | 30 +++++++++++----------------
modules/io/tests/test_mmcif_reader.cc | 6 +++---
2 files changed, 15 insertions(+), 21 deletions(-)
diff --git a/modules/io/src/mol/mmcif_reader.cc b/modules/io/src/mol/mmcif_reader.cc
index 2df3966fa..1bd0011c8 100644
--- a/modules/io/src/mol/mmcif_reader.cc
+++ b/modules/io/src/mol/mmcif_reader.cc
@@ -797,31 +797,25 @@ void MMCifReader::ParseCitation(const std::vector<StringRef>& columns)
cit.SetISBN(columns[indices_[BOOK_ID_ISBN]].str());
}
}
+ if (indices_[JOURNAL_ABBREV] != -1) {
+ if ((columns[indices_[JOURNAL_ABBREV]] != StringRef(".", 1)) &&
+ (columns[indices_[JOURNAL_ABBREV]][0] != '?')) {
+ cit.SetPublishedIn(columns[indices_[JOURNAL_ABBREV]].str());
+ cit.SetCitationTypeJournal();
+ }
+ }
if (indices_[BOOK_TITLE] != -1) {
// this is only set in few PDB entries and RCSB overrides it with
// the journal_abbrev for their citations
// -> as of August 1, 2017, 5 entries known: 5b1j, 5b1k, 5fax, 5fbz, 5ffn
// -> all those have journal_abbrev set
if ((columns[indices_[BOOK_TITLE]] != StringRef(".", 1)) &&
- (columns[indices_[BOOK_TITLE]][0]!='?')) {
+ (columns[indices_[BOOK_TITLE]][0] != '?')) {
+ // This will override published_in if already set by journal_abbrev. We
+ // consider this OK for now since usually the book title is copied to
+ // the journal_abbrev attribute.
cit.SetPublishedIn(columns[indices_[BOOK_TITLE]].str());
- }
- }
- if (indices_[JOURNAL_ABBREV] != -1) {
- if (columns[indices_[JOURNAL_ABBREV]] != StringRef(".", 1)) {
- const String journal_abbrev = columns[indices_[JOURNAL_ABBREV]].str();
- const String published_in = cit.GetPublishedIn();
- if (published_in.length() > 0 && published_in != journal_abbrev) {
- LOG_WARNING(this->FormatDiagnostic(STAR_DIAG_WARNING,
- "The 'published_in' field was "
- "already set by citation.book_title "
- "'" + published_in + "'! "
- "This will be overwritten by "
- "citation.journal_abbrev '" +
- journal_abbrev + "'.",
- this->GetCurrentLinenum()));
- }
- cit.SetPublishedIn(journal_abbrev);
+ cit.SetCitationTypeBook();
}
}
if (indices_[JOURNAL_VOLUME] != -1) {
diff --git a/modules/io/tests/test_mmcif_reader.cc b/modules/io/tests/test_mmcif_reader.cc
index 69210a1b9..233403c61 100644
--- a/modules/io/tests/test_mmcif_reader.cc
+++ b/modules/io/tests/test_mmcif_reader.cc
@@ -598,6 +598,7 @@ BOOST_AUTO_TEST_CASE(mmcif_citation_tests)
BOOST_CHECK_EQUAL(cit.GetID(), String("Foo"));
BOOST_CHECK_EQUAL(cit.GetYear(), 1979);
BOOST_CHECK_EQUAL(cit.GetPublishedIn(), String("The Guide"));
+ BOOST_CHECK_EQUAL(cit.IsCitationTypeBook(), true);
// ensure that we override book_title if not properly given
columns.pop_back();
@@ -609,8 +610,7 @@ BOOST_AUTO_TEST_CASE(mmcif_citation_tests)
BOOST_CHECK_EQUAL(tmmcif_p.GetInfo().GetCitations().back().GetPublishedIn(),
String("Hitch"));
- // ensure that we override book_title if journal given
- // (def. behavior on RCSB webpage)
+ // ensure that we override journal if book_title given
columns.pop_back();
columns.pop_back();
columns.push_back(StringRef("The Guide", 9));
@@ -618,7 +618,7 @@ BOOST_AUTO_TEST_CASE(mmcif_citation_tests)
BOOST_CHECK_NO_THROW(tmmcif_p.ParseCitation(columns));
BOOST_CHECK_EQUAL(tmmcif_p.GetInfo().GetCitations().back().GetPublishedIn(),
- String("Hitch"));
+ String("The Guide"));
BOOST_TEST_MESSAGE(" done.");
}
--
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