add reset usb bus command

[bin.git] / pubmed_search

diff --git a/pubmed_search b/pubmed_search
index cc90661e363918f5a1e6cb3a5e8dffd78da9323e..acd327d594710f5d04876de5aba39213a55a379a 100755 (executable)
--- a/pubmed_search
+++ b/pubmed_search
@@ -1,9 +1,9 @@
 #! /usr/bin/perl
-# , and is released
+# pubmed_search searches for articles on pubmed, and is released
 # under the terms of the GPL version 2, or any later version, at your
 # option. See the file README and COPYING for more information.
-# Copyright 2011 by Don Armstrong <don@donarmstrong.com>.
-# $Id: perl_script 1825 2011-01-02 01:53:43Z don $
+# Copyright 2011,2017 by Don Armstrong <don@donarmstrong.com>.
+
 
 
 use warnings;
@@ -12,7 +12,7 @@ use strict;
 use Getopt::Long;
 use Pod::Usage;
 
-use Bio::DB::SoapEUtilities;
+use Bio::DB::EUtilities;
 
 use Encode qw(encode_utf8);
 use Term::ANSIColor qw(:constants);
@@ -59,16 +59,18 @@ Display this manual.
 use vars qw($DEBUG);
 
 my %options = (debug           => 0,
-              help            => 0,
-              man             => 0,
-              color           => 1,
-              org_mode        => 0,
-              );
+               help            => 0,
+               man             => 0,
+               color           => 1,
+               org_mode        => 0,
+               abstract        => 1,
+              );
 
 GetOptions(\%options,
            'color|c!',
            'org_mode|org-mode',
            'pmid_only|pmid-only',
+           'abstract|abstracts|a!',
            'debug|d+','help|h|?','man|m');
 
 pod2usage() if $options{help};
@@ -84,14 +86,26 @@ if (not @ARGV) {
 pod2usage(join("\n",@USAGE_ERRORS)) if @USAGE_ERRORS;
 
 
-my $fac = Bio::DB::SoapEUtilities->new();
-
-my $result = $fac->esearch(-email => 'don@donarmstrong.com',
-                           -db    => 'pubmed',
-                           -term => join(' ',@ARGV),
-                           -retmax => 1000,
-                          )->run();
-my @ids = $result->ids;
+my $result =
+    Bio::DB::EUtilities->new(-email => 'don@donarmstrong.com',
+                             -db    => 'pubmed',
+                             -term => join(' ',@ARGV),
+                             -retmax => 1000,
+                             -eutil  => 'esearch',
+                            );
+my @ids;
+eval {
+    # this warns for everything, so hide the warning.
+    local $SIG{__WARN__} = sub {};
+    @ids = $result->get_ids('pubmed')
+};
+if (not @ids) {
+    print "No results\n";
+    exit;
+}
+if (@ids > 0 and ref($ids[0])) {
+    @ids = @{$ids[0]};
+}
 if ($options{org_mode}) {
     print "* Pubmed search results for ".join(' ',@ARGV)." (".scalar(@ids).")\n";
     print "  + ";
@@ -101,17 +115,21 @@ if ($options{org_mode}) {
 }
 print scalar(@ids)." results:\n";
 exit 0 unless @ids;
-my $raw_xml = $fac->efetch(-email => 'don@donarmstrong.com',
-                           -db    => 'pubmed',
-                           -id  => \@ids
-                          )->run(-raw_xml => 1);
+my $raw_xml = Bio::DB::EUtilities->new(-email => 'don@donarmstrong.com',
+                                       -db    => 'pubmed',
+                                       -id  => \@ids,
+                                       -eutil => 'efetch',
+                                      );
 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');
+my $xml = XML::LibXML->load_xml(string => $raw_xml->get_Response->content);
+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: ";
     }
@@ -122,8 +140,8 @@ for my $article ($xml->findnodes('PubmedArticleSet/PubmedArticle/MedlineCitation
     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 (defined $abstract and $options{abstract}) {
+        print BOLD MAGENTA if $options{color};
         if ($options{org_mode}) {
             print "*** Abstract\n";
         }