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1 #!/usr/bin/perl -w
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2 use strict;
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3 use LWP::UserAgent;
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4 require HTTP::Cookies;
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5
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6 #######################################################
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7 # ctd.pl
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8 # Submit a batch query to CTD and fetch results into galaxy history
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9 # usage: ctd.pl inFile idCol inputType resultType actionType outFile
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10 #######################################################
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11
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12 if (!@ARGV or scalar @ARGV != 6) {
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13 print "usage: ctd.pl inFile idCol inputType resultType actionType outFile\n";
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14 exit;
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15 }
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16
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17 my $in = shift @ARGV;
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18 my $col = shift @ARGV;
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19 if ($col < 1) {
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20 print "The column number is with a 1 start\n";
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21 exit 1;
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22 }
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23 my $type = shift @ARGV;
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24 my $resType = shift @ARGV;
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25 my $actType = shift @ARGV;
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26 my $out = shift @ARGV;
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27
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28 my @data;
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29 open(FH, $in) or die "Couldn't open $in, $!\n";
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30 while (<FH>) {
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31 chomp;
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32 my @f = split(/\t/);
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33 if (scalar @f < $col) {
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34 print "ERROR the requested column is not in the file $col\n";
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35 exit 1;
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36 }
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37 push(@data, $f[$col-1]);
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38 }
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39 close FH or die "Couldn't close $in, $!\n";
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40
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41 my $url = 'http://ctdbase.org/tools/batchQuery.go';
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42 #my $url = 'http://ctd.mdibl.org/tools/batchQuery.go';
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43 my $d = join("\n", @data);
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44 #list maintains order, where hash doesn't
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45 #order matters at ctd
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46 #to use input file (gives error can't find file)
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47 #my @form = ('inputType', $type, 'inputTerms', '', 'report', $resType,
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48 #'queryFile', [$in, ''], 'queryFileColumn', $col, 'format', 'tsv', 'action', 'Submit');
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49 my @form = ('inputType', $type, 'inputTerms', $d, 'report', $resType,
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50 'queryFile', '', 'format', 'tsv', 'action', 'Submit');
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51 if ($resType eq 'cgixns') { #only add if this type
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52 push(@form, 'actionTypes', $actType);
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53 }
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54 if ($resType eq 'go' or $resType eq 'go_enriched') {
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55 push(@form, 'ontology', 'go_bp', 'ontology', 'go_mf', 'ontology', 'go_cc');
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56 }
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57 my $ua = LWP::UserAgent->new;
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58 $ua->cookie_jar(HTTP::Cookies->new( () ));
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59 $ua->agent('Mozilla/5.0');
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60 my $page = $ua->post($url, \@form, 'Content_Type'=>'form-data');
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61 if ($page->is_success) {
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62 open(FH, ">", $out) or die "Couldn't open $out, $!\n";
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63 print FH "#";
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64 print FH $page->content, "\n";
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65 close FH or die "Couldn't close $out, $!\n";
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66 }else {
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67 print "ERROR failed to get page from CTD, ", $page->status_line, "\n";
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68 print $page->content, "\n";
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69 my $req = $page->request();
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70 print "Requested \n";
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71 foreach my $k(keys %$req) {
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72 if ($k eq '_headers') {
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73 my $t = $req->{$k};
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74 foreach my $k2 (keys %$t) { print "$k2 => $t->{$k2}\n"; }
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75 }else { print "$k => $req->{$k}\n"; }
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76 }
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77 exit 1;
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78 }
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79 exit;
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80
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