t/controller_Clone_Genomic.t

   1 use Data::Dumper;
   2 use File::Temp;
   3
   4 use Test::More tests => 2;
   5
   6 use Path::Class;
   7
   8 use CXGN::Genomic::Clone;
   9 use CXGN::PotatoGenome::FileRepository;
  10 use CXGN::Publish;
  11
  12 use_ok('SGN::Controller::Clone::Genomic');
  13
  14 my $tempdir  = File::Temp->newdir;
  15 my $tempfile = File::Temp->new;
  16 file($tempfile->filename)->openw->print(">RH123D21\nACTGACTGACTAGATGATCATCGATCGAGAGCG\n");
  17
  18 my $repos = CXGN::PotatoGenome::FileRepository->new( "$tempdir" );
  19
  20 my $ctl = SGN::Controller::Clone::Genomic->new;
  21 my $clone = CXGN::Genomic::Clone->retrieve_from_clone_name( 'RH123D21' );
  22
  23 SKIP: {
  24     my $test_vf;
  25     eval {
  26         $test_vf = $repos->get_vf( class => 'SingleCloneSequence',
  27                         sequence_name => $clone->latest_sequence_name,
  28                         format => 'fasta',
  29                         project => $clone->seqprops->{project_country} );
  30     };
  31     skip 'could not retrieve clone, cannot test _potato_seq_files', 1 unless $test_vf;
  32
  33     $repos->publish( $test_vf->publish_new_version( $tempfile->filename ) );
  34
  35     skip 'could not retrieve clone, cannot test _potato_seq_files', 1 unless $clone;
  36
  37     my %files = $ctl->_potato_seq_files( undef, $clone, $tempdir );
  38     ok( -f $files{seq}, 'got a potato seq file' )
  39     or diag Dumper { files =>  \%files, find => scalar(`find $tempdir`) };
  40 }
  41