From fb6c876aa2b186d3dd67ab73c590688621644800 Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Thu, 6 Sep 2018 11:15:54 +0200
Subject: [PATCH] Use book publisher info in mmCIF reader
---
modules/io/src/mol/mmcif_reader.cc | 12 ++++++++++++
modules/io/src/mol/mmcif_reader.hh | 2 ++
modules/io/tests/test_mmcif_reader.cc | 10 ++++++++++
3 files changed, 24 insertions(+)
diff --git a/modules/io/src/mol/mmcif_reader.cc b/modules/io/src/mol/mmcif_reader.cc
index 1bd0011c8..213e6e922 100644
--- a/modules/io/src/mol/mmcif_reader.cc
+++ b/modules/io/src/mol/mmcif_reader.cc
@@ -191,6 +191,8 @@ bool MMCifReader::OnBeginLoop(const StarLoopDesc& header)
indices_[ABSTRACT_ID_CAS] = header.GetIndex("abstract_id_CAS");
indices_[BOOK_ID_ISBN] = header.GetIndex("book_id_ISBN");
indices_[BOOK_TITLE] = header.GetIndex("book_title");
+ indices_[BOOK_PUBLISHER] = header.GetIndex("book_publisher");
+ indices_[BOOK_PUBLISHER_CITY] = header.GetIndex("book_publisher_city");
indices_[JOURNAL_ABBREV] = header.GetIndex("journal_abbrev");
indices_[YEAR] = header.GetIndex("year");
indices_[TITLE] = header.GetIndex("title");
@@ -816,6 +818,16 @@ void MMCifReader::ParseCitation(const std::vector<StringRef>& columns)
// the journal_abbrev attribute.
cit.SetPublishedIn(columns[indices_[BOOK_TITLE]].str());
cit.SetCitationTypeBook();
+
+ // In theory, book_publisher and book_publisher_city are only set for
+ // books and book chapters, so we only try to fetch them if the citation
+ // type points to book.
+ if (indices_[BOOK_PUBLISHER] != -1) {
+ cit.SetBookPublisher(columns[indices_[BOOK_PUBLISHER]].str());
+ }
+ if (indices_[BOOK_PUBLISHER_CITY] != -1) {
+ cit.SetBookPublisherCity(columns[indices_[BOOK_PUBLISHER_CITY]].str());
+ }
}
}
if (indices_[JOURNAL_VOLUME] != -1) {
diff --git a/modules/io/src/mol/mmcif_reader.hh b/modules/io/src/mol/mmcif_reader.hh
index edd249f38..fa747a2ab 100644
--- a/modules/io/src/mol/mmcif_reader.hh
+++ b/modules/io/src/mol/mmcif_reader.hh
@@ -400,6 +400,8 @@ private:
ABSTRACT_ID_CAS, ///< CAS identifier
BOOK_ID_ISBN, ///< ISBN code assigned, if book cited
BOOK_TITLE, ///< title of book storing the citation
+ BOOK_PUBLISHER, ///< name of publisher f a book
+ BOOK_PUBLISHER_CITY, ///< location of a publisher of a book
JOURNAL_ABBREV, ///< abbreviated journal title for articles
JOURNAL_VOLUME, ///< volume of cited journal
PAGE_FIRST, ///< first page of citation
diff --git a/modules/io/tests/test_mmcif_reader.cc b/modules/io/tests/test_mmcif_reader.cc
index 233403c61..682e43c31 100644
--- a/modules/io/tests/test_mmcif_reader.cc
+++ b/modules/io/tests/test_mmcif_reader.cc
@@ -583,14 +583,18 @@ BOOST_AUTO_TEST_CASE(mmcif_citation_tests)
tmmcif_h.SetCategory(StringRef("citation", 8));
tmmcif_h.Add(StringRef("id", 2));
tmmcif_h.Add(StringRef("year", 4));
+ tmmcif_h.Add(StringRef("book_publisher_city", 19));
tmmcif_h.Add(StringRef("book_title", 10));
+ tmmcif_h.Add(StringRef("book_publisher", 14));
tmmcif_h.Add(StringRef("journal_abbrev", 14));
tmmcif_p.OnBeginLoop(tmmcif_h);
// ensure that we use book_title if no journal given (no RCSB use of this)
columns.push_back(StringRef("Foo", 3));
columns.push_back(StringRef("1979", 4));
+ columns.push_back(StringRef("The restaurant", 14));
columns.push_back(StringRef("The Guide", 9));
+ columns.push_back(StringRef("Doug", 4));
columns.push_back(StringRef(".", 1));
BOOST_CHECK_NO_THROW(tmmcif_p.ParseCitation(columns));
@@ -598,12 +602,16 @@ 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.GetBookPublisher(), String("Doug"));
+ BOOST_CHECK_EQUAL(cit.GetBookPublisherCity(), String("The restaurant"));
BOOST_CHECK_EQUAL(cit.IsCitationTypeBook(), true);
// ensure that we override book_title if not properly given
columns.pop_back();
columns.pop_back();
+ columns.pop_back();
columns.push_back(StringRef(".", 1));
+ columns.push_back(StringRef("Doug", 4));
columns.push_back(StringRef("Hitch", 5));
BOOST_CHECK_NO_THROW(tmmcif_p.ParseCitation(columns));
@@ -613,7 +621,9 @@ BOOST_AUTO_TEST_CASE(mmcif_citation_tests)
// ensure that we override journal if book_title given
columns.pop_back();
columns.pop_back();
+ columns.pop_back();
columns.push_back(StringRef("The Guide", 9));
+ columns.push_back(StringRef("Doug", 4));
columns.push_back(StringRef("Hitch", 5));
BOOST_CHECK_NO_THROW(tmmcif_p.ParseCitation(columns));
--
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