t/legacy/integration/feature_gene_group.t

   1 use strict;
   2 use warnings;
   3
   4 use Test::More;
   5
   6 use lib 't/lib';
   7 use SGN::Test::WWW::Mechanize skip_cgi => 1;
   8 use SGN::Test::Data qw/create_test/;
   9
  10 # set up test gene groups
  11 my $group = create_test('Sequence::Feature');
  12 my @orgs = map create_test('Organism::Organism'), 0..2;
  13 my $schema = $group->result_source->schema;
  14 for ( [ $orgs[0], 4 ], [ $orgs[1], 2 ], [ $orgs[2], 5 ] ) {
  15     my ( $org, $count ) = @$_;
  16     for( 1..$count ) {
  17         my $gene = create_test('Sequence::Feature',{
  18             type     => $schema->get_cvterm_or_die('sequence:gene'),
  19             organism => $org,
  20         });
  21         add_relationship( $gene, 'sequence:member_of', $group );
  22
  23         my $mrna = create_test('Sequence::Feature', {
  24             type => $schema->get_cvterm_or_die('sequence:mRNA'),
  25             organism => $org,
  26             residues => 'CATCATCATCAT',
  27         });
  28         add_relationship( $mrna, 'relationship:part_of', $gene );
  29
  30         my $poly = create_test('Sequence::Feature', {
  31             type => $schema->get_cvterm_or_die('sequence:polypeptide'),
  32             organism => $org,
  33             residues => 'MMMMMMMMMMMMMM',
  34         });
  35         add_relationship( $poly, 'relationship:derives_from', $mrna );
  36     }
  37 }
  38
  39 my $mech = SGN::Test::WWW::Mechanize->new;
  40 $mech->get_ok('/feature/'.$group->name.'/details');
  41 $mech->get_ok('/feature/'.$group->name.'/gene_group_protein_fasta');
  42 $mech->content_contains('>feature_');
  43 $mech->content_contains('MMMMMMMMMM');
  44 #diag $mech->content;
  45
  46 done_testing;
  47
  48 exit;
  49
  50 #####################################################
  51
  52 sub add_relationship {
  53     my ( $subject, $relationship, $object ) = @_;
  54
  55     $subject->add_to_feature_relationship_subjects(
  56         { type   => $schema->get_cvterm_or_die( $relationship ),
  57           object => $object,
  58         },
  59     );
  60
  61 }