From 439df49d60fbad54b9970f03ab4eb5e24551b1c2 Mon Sep 17 00:00:00 2001
From: Don Armstrong <don@donarmstrong.com>
Date: Wed, 22 Jul 2015 17:03:11 -0500
Subject: [PATCH] handle journal database not being there

---
 lib/Reference/Retrieve/PubMed.pm | 66 ++++++++++----------------------
 1 file changed, 21 insertions(+), 45 deletions(-)

diff --git a/lib/Reference/Retrieve/PubMed.pm b/lib/Reference/Retrieve/PubMed.pm
index 1fc4dff..0ecc842 100644
--- a/lib/Reference/Retrieve/PubMed.pm
+++ b/lib/Reference/Retrieve/PubMed.pm
@@ -336,43 +336,20 @@ sub _fix_medline_journal($$$;){
      if (ref $ISSN) {
 	  $ISSN = $ISSN->{content};
      }
-     my $url = qq(http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=journals&term=$ISSN);
+     my $url = qq(http://www.ncbi.nlm.nih.gov/nlmcatalog/?term=${ISSN}[ISSN]&format=text&report=xml);
      print STDERR "url: $url" if $DEBUG;
      my $request = HTTP::Request->new('GET', $url);
      my $response = $ua->request($request);
      $response = $response->content;
-     print STDERR "response: $response" if $DEBUG;
+     $response =~ s/\&gt;/>/gso;
+     $response =~ s/\&lt;/</gso;
+     $response =~ s/^<\/?pre>//;
 
-     my ($journal_id) = $response =~ m#<Id>\s*(\d+)\s*</Id>#i;
-
-     # http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=journals&id=4559
-     #      <?xml version="1.0"?>
-     # <!DOCTYPE eSummaryResult PUBLIC "-//NLM//DTD eSummaryResult, 11 May 2002//EN" "http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eSummary_020511.dtd">
-     # <eSummaryResult>
-     # <DocSum>
-     # 	<Id>4559</Id>
-     # 	<Item Name="Title" Type="String">The Journal of biological chemistry.</Item>
-     # 	<Item Name="MedAbbr" Type="String">J Biol Chem</Item>
-     # 	<Item Name="IsoAbbr" Type="String">J. Biol. Chem.</Item>
-     # 	<Item Name="NlmId" Type="String">2985121R</Item>
-     #
-     # 	<Item Name="pISSN" Type="String">0021-9258</Item>
-     # 	<Item Name="eISSN" Type="String">1083-351X</Item>
-     # 	<Item Name="PublicationStartYear" Type="String">1905</Item>
-     # 	<Item Name="PublicationEndYear" Type="String"></Item>
-     # 	<Item Name="Publisher" Type="String">American Society for Biochemistry and Molecular Biology</Item>
-     # 	<Item Name="Language" Type="String">eng</Item>
-     #
-     # 	<Item Name="Country" Type="String">United States</Item>
-     # </DocSum>
-     #
-     # </eSummaryResult>
-     $url = qq(http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=journals&id=$journal_id);
-     print STDERR "url: $url" if $DEBUG;
-     $request = HTTP::Request->new('GET', $url);
-     $response = $ua->request($request);
-     $response = $response->content;
      print STDERR "response: $response" if $DEBUG;
+     my $xa = new XML::Simple;
+     my $ref_struct = $xa->XMLin($response,ForceArray=>['NCBICatalogRecord'],KeyAttr=>[]);
+     my $ref = $ref_struct->{NCBICatalogRecord}[0];
+     print STDERR Dumper($ref) if $DEBUG;
 
      my %journal;
      while ($response =~ m{^\s*(?:(?:<id>\s*(\d+)</id>)| # Match ids
@@ -384,20 +361,19 @@ sub _fix_medline_journal($$$;){
 	  else {
 	       $journal{lc($2)} = $3;
 	  }
-     }
-     my %journal_mapping = (title       => q(title),
-			    medlineabbr => q(medabbr),
-			    isoabbr     => q(isoabbr),
-			    nlmid       => q(nlmid),
-			    issn        => q(pissn),
-			    eissn       => q(eissn),
-			    publisher   => q(publisher),
-			    pmid    => q(id)
-			   );
-     my @journal_entry;
-     foreach my $key (keys %journal_mapping) {
-	  push @journal_entry,($key=>$journal{$journal_mapping{$key}});
-     }
+  }
+     my $print_issn = $ref->{JrXml}{Serial}{ISSN}[0]{IssnType} eq 'Print' ? 0 : 1;
+     my @journal_entry =
+         (title       => $ref->{JrXml}{Serial}{Title},
+          medlineabbr => $ref->{JrXml}{Serial}{MedlineTA},
+          isoabbr     => $ref->{JrXml}{Serial}{ISOAbbreviation},
+          nlmid       => $ref->{JrXml}{Serial}{NlmUniqueID},
+          issn        => $ref->{JrXml}{Serial}{ISSN}[$print_issn]{ISSN},
+          eissn       => $ref->{JrXml}{Serial}{ISSN}[1-$print_issn]{ISSN},
+          publisher   => $ref->{JrXml}{Serial}{publicationInfo}{Publisher},
+          pmid        => $ref->{JrXml}{id},
+         );
+     print STDERR Dumper(\@journal_entry) if $DEBUG;
      return @journal_entry;
 }
 
-- 
2.39.2