From dd8ec1d4cecf282940831171ef0f796570d781fd Mon Sep 17 00:00:00 2001
From: Don Armstrong <don@donarmstrong.com>
Date: Tue, 28 Aug 2007 02:54:48 +0000
Subject: [PATCH] update everything again

git-svn-id: file:///srv/svn/function2gene/trunk@11 a0738b58-4706-0410-8799-fb830574a030
---
 bin/get_genecard_results    | 30 +++++++++++++++---------------
 bin/get_harvester_results   |  4 +++-
 bin/parse_genecard_results  |  2 +-
 bin/parse_harvester_results |  6 ++++--
 4 files changed, 23 insertions(+), 19 deletions(-)

diff --git a/bin/get_genecard_results b/bin/get_genecard_results
index 6345227..051e39d 100755
--- a/bin/get_genecard_results
+++ b/bin/get_genecard_results
@@ -68,8 +68,8 @@ BEGIN{
 }
 
 use IO::File;
-use URI::ParamMunge;
-use LWP::UserAgent;
+use URI;
+use WWW::Mechanize;
 
 # XXX parse config file
 
@@ -82,7 +82,7 @@ my %options = (debug    => 0,
 	       name     => '${search}_results_genecard',
 	       terms    => '-',
 	       genecard_site => 'http://bioinfo.weizmann.ac.il/cards-bin/',
-	       genecard_search_url  => 'cardsearch.pl?search_type=keyword%28s%29&search=complement',
+	       genecard_search_url  => 'cardsearch.pl?search_type=kwd&mini=no&speed=fast&matches=999999',
 	      );
 
 GetOptions(\%options,'format|f=s','database|b=s','name|n=s',
@@ -106,24 +106,24 @@ else {
      $terms = new IO::File $options{terms}, 'r' or die "Unable to open file $options{terms}: $!";
 }
 
-my $ua = new LWP::UserAgent(agent=>"DA_get_harvester_results/$REVISION");
-
 #For every term
 while (<$terms>) {
      # Get uids to retrieve
      chomp;
      my $search = $_;
-     my $url = uri_param_munge($options{genecard_site}.$options{genecard_search_url},
-			       {search => $search,
-			       },
-			      );
-     my $request = HTTP::Request->new('GET', $url);
-     my $response = $ua->request($request);
-     $response = $response->content;
-     my @result_urls = $response =~ m#<a\s+href=\"(carddisp?[^\"]+)\"\s*>\s+<b>Display</b>\s*<font size=-1>\s*<br>\s*the<b>\s*complete#sg;
-
+     my $uri = URI->new($options{genecard_site}.$options{genecard_search_url});
+     $uri->query_form($uri->query_form(),
+		      search => $search,
+		     );
+     my $url = $uri->as_string;
+     my $mech = WWW::Mechanize->new(agent=>"DA_get_harvester_results/$REVISION");
+     $mech->get($url);
+     my $response = $mech->content();
+     my @result_urls = $response =~ m#<a\s+target\=\'card\'\s+href=\"(carddisp\.pl\?[^\"]+)\"\s*>#sg;
      my $dir_name = eval qq("$options{name}") or die $@;
-     mkdir("$options{dir}/$dir_name") or die "Unable to make directory $options{dir}/$dir_name $!";
+     if (not -d "$options{dir}/$dir_name") {
+	  mkdir("$options{dir}/$dir_name") or die "Unable to make directory $options{dir}/$dir_name $!";
+     }
      # Get XML file
      my @current_urls;
      while (@current_urls = map{$options{genecard_site}.$_} splice(@result_urls,0,30)) {
diff --git a/bin/get_harvester_results b/bin/get_harvester_results
index 97734e9..7446e08 100755
--- a/bin/get_harvester_results
+++ b/bin/get_harvester_results
@@ -125,7 +125,9 @@ while (<$terms>) {
      my $url = $uri->as_string;
      my $queue = Thread::Queue->new();
      my $dir_name = eval qq("$options{name}") or die $@;
-     mkdir("$options{dir}/$dir_name") or die "Unable to make directory $options{dir}/$dir_name $!";
+     if (not -d "$options{dir}/$dir_name") {
+	mkdir("$options{dir}/$dir_name") or die "Unable to make directory $options{dir}/$dir_name $!";
+     }
      my $wget_thread = threads->new(\&get_url,"$options{dir}/$dir_name",$queue);
      push @threads,$wget_thread;
 
diff --git a/bin/parse_genecard_results b/bin/parse_genecard_results
index 6024d9b..a6718c5 100755
--- a/bin/parse_genecard_results
+++ b/bin/parse_genecard_results
@@ -104,7 +104,7 @@ if ($options{keywords}) {
      if (@ARGV != 1) {
 	  pod2usage("If the --keywords option is used, exactly one argument (the keyword) must be passed");
      }
-     $option{dir} = "$ARGV[0]_results_genecard";
+     $options{dir} = "$ARGV[0]_results_genecard";
 }
 
 if (not -d $options{dir}) {
diff --git a/bin/parse_harvester_results b/bin/parse_harvester_results
index a35c9b9..7a8cfd4 100755
--- a/bin/parse_harvester_results
+++ b/bin/parse_harvester_results
@@ -80,7 +80,9 @@ my %options = (debug    => 0,
 	       keywords => 0,
 	      );
 
-GetOptions(\%options,'keyword|k=s','dir|D=s','debug|d+','help|h|?','man|m');
+GetOptions(\%options,'keyword|k=s','dir|D=s','debug|d+','help|h|?','man|m',
+	   'keywords',
+	  );
 
 
 pod2usage() if $options{help};
@@ -104,7 +106,7 @@ if ($options{keywords}) {
      if (@ARGV != 1) {
 	  pod2usage("If the --keywords option is used, exactly one argument (the keyword) must be passed");
      }
-     $option{dir} = "$ARGV[0]_results_harvester";
+     $options{dir} = "$ARGV[0]_results_harvester";
 }
 
 
-- 
2.39.2