|
0
|
1 #!/usr/bin/env perl
|
|
|
2
|
|
|
3 use strict;
|
|
|
4 use warnings;
|
|
|
5
|
|
|
6 use LWP::UserAgent;
|
|
|
7 require HTTP::Cookies;
|
|
|
8
|
|
|
9 #######################################################
|
|
|
10 # ctd.pl
|
|
|
11 # Submit a batch query to CTD and fetch results into galaxy history
|
|
|
12 # usage: ctd.pl inFile idCol inputType resultType actionType outFile
|
|
|
13 #######################################################
|
|
|
14
|
|
|
15 if (!@ARGV or scalar @ARGV != 6) {
|
|
|
16 print "usage: ctd.pl inFile idCol inputType resultType actionType outFile\n";
|
|
|
17 exit;
|
|
|
18 }
|
|
|
19
|
|
|
20 my $in = shift @ARGV;
|
|
|
21 my $col = shift @ARGV;
|
|
|
22 if ($col < 1) {
|
|
|
23 print "The column number is with a 1 start\n";
|
|
|
24 exit 1;
|
|
|
25 }
|
|
|
26 my $type = shift @ARGV;
|
|
|
27 my $resType = shift @ARGV;
|
|
|
28 my $actType = shift @ARGV;
|
|
|
29 my $out = shift @ARGV;
|
|
|
30
|
|
|
31 my @data;
|
|
|
32 open(FH, $in) or die "Couldn't open $in, $!\n";
|
|
|
33 while (<FH>) {
|
|
|
34 chomp;
|
|
|
35 my @f = split(/\t/);
|
|
|
36 if (scalar @f < $col) {
|
|
|
37 print "ERROR the requested column is not in the file $col\n";
|
|
|
38 exit 1;
|
|
|
39 }
|
|
|
40 push(@data, $f[$col-1]);
|
|
|
41 }
|
|
|
42 close FH or die "Couldn't close $in, $!\n";
|
|
|
43
|
|
|
44 my $url = 'http://ctd.mdibl.org/tools/batchQuery.go';
|
|
|
45 #my $url = 'http://globin.bx.psu.edu/cgi-bin/print-query';
|
|
|
46 my $d = join("\n", @data);
|
|
|
47 #list maintains order, where hash doesn't
|
|
|
48 #order matters at ctd
|
|
|
49 #to use input file (gives error can't find file)
|
|
|
50 #my @form = ('inputType', $type, 'inputTerms', '', 'report', $resType,
|
|
|
51 #'queryFile', [$in, ''], 'queryFileColumn', $col, 'format', 'tsv', 'action', 'Submit');
|
|
|
52 my @form = ('inputType', $type, 'inputTerms', $d, 'report', $resType,
|
|
|
53 'queryFile', '', 'format', 'tsv', 'action', 'Submit');
|
|
|
54 if ($resType eq 'cgixns') { #only add if this type
|
|
|
55 push(@form, 'actionTypes', $actType);
|
|
|
56 }
|
|
|
57 my $ua = LWP::UserAgent->new;
|
|
|
58 $ua->cookie_jar(HTTP::Cookies->new( () ));
|
|
|
59 $ua->agent('Mozilla/5.0');
|
|
|
60 my $page = $ua->post($url, \@form, 'Content_Type'=>'form-data');
|
|
|
61 if ($page->is_success) {
|
|
|
62 open(FH, ">", $out) or die "Couldn't open $out, $!\n";
|
|
|
63 print FH "#";
|
|
|
64 print FH $page->content, "\n";
|
|
|
65 close FH or die "Couldn't close $out, $!\n";
|
|
|
66 }else {
|
|
|
67 print "ERROR failed to get page from CTD, ", $page->status_line, "\n";
|
|
|
68 print $page->content, "\n";
|
|
|
69 my $req = $page->request();
|
|
|
70 print "Requested \n";
|
|
|
71 foreach my $k(keys %$req) {
|
|
|
72 if ($k eq '_headers') {
|
|
|
73 my $t = $req->{$k};
|
|
|
74 foreach my $k2 (keys %$t) { print "$k2 => $t->{$k2}\n"; }
|
|
|
75 }else { print "$k => $req->{$k}\n"; }
|
|
|
76 }
|
|
|
77 exit 1;
|
|
|
78 }
|
|
|
79 exit;
|
|
|
80
|
