From 8e1fe04cb712a2231b9a7112b7a701a67f9ddd31 Mon Sep 17 00:00:00 2001
From: Don Armstrong <don@donarmstrong.com>
Date: Tue, 28 Aug 2007 01:00:57 +0000
Subject: [PATCH]  * Update ncbi results to handle the new ncbi output format

git-svn-id: file:///srv/svn/function2gene/trunk@7 a0738b58-4706-0410-8799-fb830574a030
---
 bin/get_ncbi_results | 60 ++++++++++++++++++++++++++------------------
 1 file changed, 35 insertions(+), 25 deletions(-)

diff --git a/bin/get_ncbi_results b/bin/get_ncbi_results
index c104356..7a86901 100755
--- a/bin/get_ncbi_results
+++ b/bin/get_ncbi_results
@@ -73,8 +73,8 @@ BEGIN{
 }
 
 use IO::File;
-use URI::ParamMunge;
-use LWP::UserAgent;
+use URI;
+use WWW::Mechanize;
 
 # XXX parse config file
 
@@ -86,9 +86,10 @@ my %options = (debug    => 0,
 	       dir      => '.',
 	       name     => 'ncbi_${search}_results.$format',
 	       terms    => '-',
+	       orgn     => 'homo',
 	       pubmed_site => 'http://www.ncbi.nlm.nih.gov',
-	       pubmed_search_url  => '/entrez/query.fcgi?db=gene&cmd=search&term=12q24*+AND+homo[Orgn]&doptcmdl=Brief&dispmax=1000',
-	       pubmed_get_url     => '/entrez/query.fcgi?db=gene&cmd=Text&dopt=XML',
+	       pubmed_search_url  => '/entrez/query.fcgi?cmd=search&doptcmdl=Brief&dispmax=1000',
+	       pubmed_get_url     => '/entrez/query.fcgi?cmd=Text',
 	      );
 
 GetOptions(\%options,'format|f=s','database|b=s','name|n=s',
@@ -120,30 +121,39 @@ while (<$terms>) {
      chomp;
      my $search = $_;
      my $format = $options{format};
-     my $url = uri_param_munge($options{pubmed_site}.$options{pubmed_search_url},
-			       {term => $search,
-				db   => $options{database},
-			       },
-			      );
-     my $request = HTTP::Request->new('GET', $url);
-     my $response = $ua->request($request);
-     $response = $response->content;
-     my @gene_ids = $response =~ m/\[GeneID\:\s+(\d+)\]/g;
-
+     my $uri = URI->new($options{pubmed_site}.$options{pubmed_search_url});
+     $uri->query_form($uri->query_form(),
+		      term => $search.' AND '.$options{orgn}.'[Orgn]',
+		      db   => $options{database},
+		     );
+     my $url = $uri->as_string;
+     my $mech = WWW::Mechanize->new(agent => "DA_get_ncbi_results/$REVISION");
+     $mech->get($url);
+     my @gene_ids;
+     {
+	  do {
+	       my $response = $mech->content();
+	       push @gene_ids , $response =~ m{\[GeneID\:\s+(\d+)\s*\]\s*</td>}mg;
+	       last unless $mech->find_link(text => 'Next');
+	       $mech->follow_link(text => 'Next');
+	  } while (1);
+     }
      my $file_name = eval qq("$options{name}") or die $@;
      my $xml_file = new IO::File "$options{dir}/$file_name", 'w' or die "Unable to open $options{dir}/$file_name: $!";
 
      # Get XML file
      my @current_ids;
-     while (@current_ids = splice(@gene_ids,0,20)) {
-	  $url = uri_param_munge($options{pubmed_site}.$options{pubmed_get_url},
-				 {dopt => uc($options{format}),
-				  db   => $options{database},
-				 },
-				) .'&' . join('&',map {qq(uid=$_)} @current_ids);
-	  $request = HTTP::Request->new('GET', $url);
-	  $response = $ua->request($request);
-	  $response = $response->content;
+     while (@current_ids = splice(@gene_ids,0,5)) {
+	  $uri = URI->new($options{pubmed_site}.$options{pubmed_get_url});
+	  $uri->query_form($uri->query_form(),
+			   dopt => uc($options{format}),
+			   db   => $options{database},
+			   map {('uid',$_)} @current_ids,
+			  );
+	  $url = $uri->as_string;
+	  print STDERR "url: $url\n";
+	  $mech->get($url);
+	  my $response = $mech->content;
 	  # For some dumb reason, they send us xml with html
 	  # entities. Ditch them.
 	  #$response = decode_entities($response);
@@ -152,11 +162,11 @@ while (<$terms>) {
 	  $response =~ s/&quot;/"/gso;
 
 	  # They also affix a <pre> and suffix a </pre> ditch them.
+	  $response =~ s#<\?xml[^>]+>##gso;
+	  $response =~ s#<!DOCTYPE[^>]+>##gso;
 	  $response =~ s/^\s*<pre>//gso;
 	  $response =~ s#</pre>\s*$##gso;
 
-	  $response =~ s#<\?xml[^>]+>##gso;
-	  $response =~ s#<!DOCTYPE[^>]+>##gso;
 
 	  print {$xml_file} $response;
 	  sleep 10;
-- 
2.39.2