diff ctd.pl @ 0:72ce01e2dad9 draft default tip

Uploaded tool tarball.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ctd.pl	Tue Aug 20 09:36:33 2013 -0400
@@ -0,0 +1,80 @@
+#!/usr/bin/perl -w
+use strict;
+use LWP::UserAgent;
+require HTTP::Cookies;
+
+#######################################################
+# ctd.pl 
+# Submit a batch query to CTD and fetch results into galaxy history
+# usage: ctd.pl inFile idCol inputType resultType actionType outFile
+#######################################################
+
+if (!@ARGV or scalar @ARGV != 6) {
+   print "usage: ctd.pl inFile idCol inputType resultType actionType outFile\n";
+   exit;
+}
+
+my $in = shift @ARGV;
+my $col = shift @ARGV;
+if ($col < 1) {
+   print "The column number is with a 1 start\n";
+   exit 1;
+}
+my $type = shift @ARGV;
+my $resType = shift @ARGV;
+my $actType = shift @ARGV;
+my $out = shift @ARGV;
+
+my @data;
+open(FH, $in) or die "Couldn't open $in, $!\n";
+while (<FH>) {
+   chomp;
+   my @f = split(/\t/);
+   if (scalar @f < $col) { 
+      print "ERROR the requested column is not in the file $col\n";
+      exit 1;
+   }
+   push(@data, $f[$col-1]);
+}
+close FH or die "Couldn't close $in, $!\n";
+
+my $url = 'http://ctdbase.org/tools/batchQuery.go';
+#my $url = 'http://ctd.mdibl.org/tools/batchQuery.go';
+my $d = join("\n", @data);
+#list maintains order, where hash doesn't
+#order matters at ctd
+#to use input file (gives error can't find file)
+#my @form = ('inputType', $type, 'inputTerms', '', 'report', $resType, 
+   #'queryFile', [$in, ''], 'queryFileColumn', $col, 'format', 'tsv', 'action', 'Submit');
+my @form = ('inputType', $type, 'inputTerms', $d, 'report', $resType,
+  'queryFile', '', 'format', 'tsv', 'action', 'Submit');
+if ($resType eq 'cgixns') { #only add if this type
+   push(@form, 'actionTypes', $actType);
+}
+if ($resType eq 'go' or $resType eq 'go_enriched') {
+   push(@form, 'ontology', 'go_bp', 'ontology', 'go_mf', 'ontology', 'go_cc');
+}
+my $ua = LWP::UserAgent->new;
+$ua->cookie_jar(HTTP::Cookies->new( () ));
+$ua->agent('Mozilla/5.0');
+my $page = $ua->post($url, \@form, 'Content_Type'=>'form-data');
+if ($page->is_success) {
+   open(FH, ">", $out) or die "Couldn't open $out, $!\n";
+   print FH "#";
+   print FH $page->content, "\n";
+   close FH or die "Couldn't close $out, $!\n";
+}else {
+   print "ERROR failed to get page from CTD, ", $page->status_line, "\n";
+   print $page->content, "\n";
+   my $req = $page->request();
+   print "Requested \n";
+   foreach my $k(keys %$req) { 
+      if ($k eq '_headers') {
+         my $t = $req->{$k};
+         foreach my $k2 (keys %$t) { print "$k2 => $t->{$k2}\n"; }
+      }else { print "$k => $req->{$k}\n"; }
+   }
+   exit 1;
+}
+exit;
+