add eval_r command

[bin.git] / pubmed_search

diff --git a/pubmed_search b/pubmed_search
index cc90661e363918f5a1e6cb3a5e8dffd78da9323e..778960a7f187db49f5eaa4c8d8934a6d8bcb1cec 100755 (executable)
--- a/pubmed_search
+++ b/pubmed_search
@@ -92,6 +92,9 @@ my $result = $fac->esearch(-email => 'don@donarmstrong.com',
                            -retmax => 1000,
                           )->run();
 my @ids = $result->ids;
+if (@ids > 0 and ref($ids[0])) {
+    @ids = @{$ids[0]};
+}
 if ($options{org_mode}) {
     print "* Pubmed search results for ".join(' ',@ARGV)." (".scalar(@ids).")\n";
     print "  + ";
@@ -107,11 +110,14 @@ my $raw_xml = $fac->efetch(-email => 'don@donarmstrong.com',
                           )->run(-raw_xml => 1);
 use XML::LibXML;
 my $xml = XML::LibXML->load_xml(string => $raw_xml);
-for my $article ($xml->findnodes('PubmedArticleSet/PubmedArticle/MedlineCitation')) {
-    # print $article->toString;
-    my ($pmid) = $article->findnodes('./PMID');
-    my ($title) = $article->findnodes('./Article/ArticleTitle');
-    my ($abstract) = $article->findnodes('./Article/Abstract');
+print STDERR $xml->toString if $DEBUG;
+for my $article ($xml->findnodes(q{//*[local-name()='MedlineCitation']})) {
+    print STDERR $article->toString if $DEBUG;
+    my ($pmid) = $article->findnodes(q{./*[local-name()='PMID']});
+    my ($title) = $article->findnodes(q{./*[local-name()='Article']}.
+                                      q{/*[local-name()='ArticleTitle']});
+    my ($abstract) = $article->findnodes(q{./*[local-name()='Article']}.
+                                         q{/*[local-name()='Abstract']});
     if ($options{org_mode}) {
         print "** PMID: ";
     }