From d854925a60b80c6866f148dd70e717da6186ce32 Mon Sep 17 00:00:00 2001
From: Don Armstrong <don@donarmstrong.com>
Date: Wed, 10 Oct 2012 21:33:42 +0000
Subject: [PATCH] output org mode

---
 pubmed_search | 43 ++++++++++++++++++++++++++++++-------------
 1 file changed, 30 insertions(+), 13 deletions(-)

diff --git a/pubmed_search b/pubmed_search
index b5272e3..b3367d9 100755
--- a/pubmed_search
+++ b/pubmed_search
@@ -61,9 +61,13 @@ use vars qw($DEBUG);
 my %options = (debug           => 0,
 	       help            => 0,
 	       man             => 0,
+	       color           => 1,
+	       org_mode        => 0,
 	       );
 
 GetOptions(\%options,
+	   'color|c!',
+	   'org_mode|org-mode',
 	   'debug|d+','help|h|?','man|m');
 
 pod2usage() if $options{help};
@@ -86,7 +90,12 @@ my $search = Bio::DB::EUtilities->new(-eutil => 'esearch',
 				       -retmax => 1000,
 				      );
 my @ids = $search->get_ids();
+if ($options{org_mode}) {
+    print "* Pubmed search results for ".join(' ',@ARGV)." (".scalar(@ids).")\n";
+    print "  + ";
+}
 print scalar(@ids)." results:\n";
+exit 0 unless @ids;
 my $esummary = Bio::DB::EUtilities->new(-eutil => 'efetch',
 					-email => 'don@donarmstrong.com',
 					-db    => 'pubmed',
@@ -99,21 +108,29 @@ for my $article ($xml->findnodes('PubmedArticleSet/PubmedArticle/MedlineCitation
     my ($pmid) = $article->findnodes('./PMID');
     my ($title) = $article->findnodes('./Article/ArticleTitle');
     my ($abstract) = $article->findnodes('./Article/Abstract');
-    print BOLD GREEN;
+    if ($options{org_mode}) {
+	print "** PMID: ";
+    }
+    print BOLD GREEN if $options{color};
     print $pmid->textContent();
     print ": ";
-    print RESET;
-    print BOLD CYAN;
-    print $title->textContent()."\n";
-    print RESET;
-    print BOLD MAGENTA;
-    $abstract = $abstract->textContent();
-    $abstract =~ s/^\s*//mg;
-    $abstract =~ s/(.{,80})\s/$1\n/g;
-    $abstract = encode_utf8($abstract);
-    print wrap('','',$abstract);
-    print "\n\n";
-    print RESET;
+    print RESET if $options{color};
+    print BOLD CYAN if $options{color};
+    print encode_utf8($title->textContent())."\n";
+    print RESET if $options{color};
+    print BOLD MAGENTA if $options{color};
+    if (defined $abstract) {
+	if ($options{org_mode}) {
+	    print "*** Abstract\n";
+	}
+	$abstract = $abstract->textContent();
+	$abstract =~ s/^\s*//mg;
+	$abstract =~ s/(.{,80})\s/$1\n/g;
+	$abstract = encode_utf8($abstract);
+	print wrap('','',$abstract);
+	print "\n\n";
+	print RESET if $options{color};
+    }
 }
 
 __END__
-- 
2.39.5