db/00091/AddTissueSampleListCvterm.pm

   1 #!/usr/bin/env perl
   2
   3
   4 =head1 NAME
   5
   6  AddTissueSampleListCvterm
   7
   8 =head1 SYNOPSIS
   9
  10 mx-run AddTissueSampleListCvterm [options] -H hostname -D dbname -u username [-F]
  11
  12 this is a subclass of L<CXGN::Metadata::Dbpatch>
  13 see the perldoc of parent class for more details.
  14
  15 =head1 DESCRIPTION
  16 This patch adds stock)type cvterm for tissue sample.
  17 This subclass uses L<Moose>. The parent class uses L<MooseX::Runnable>
  18
  19 =head1 AUTHOR
  20
  21
  22 =head1 COPYRIGHT & LICENSE
  23
  24 Copyright 2010 Boyce Thompson Institute for Plant Research
  25
  26 This program is free software; you can redistribute it and/or modify
  27 it under the same terms as Perl itself.
  28
  29 =cut
  30
  31
  32 package AddTissueSampleListCvterm;
  33
  34 use Moose;
  35 use Bio::Chado::Schema;
  36 use Try::Tiny;
  37 extends 'CXGN::Metadata::Dbpatch';
  38
  39
  40 has '+description' => ( default => <<'' );
  41 This patch adds list type for tissue_samples.
  42
  43 has '+prereq' => (
  44         default => sub {
  45         [],
  46     },
  47
  48   );
  49
  50 sub patch {
  51     my $self=shift;
  52
  53     print STDOUT "Executing the patch:\n " .   $self->name . ".\n\nDescription:\n  ".  $self->description . ".\n\nExecuted by:\n " .  $self->username . " .";
  54
  55     print STDOUT "\nChecking if this db_patch was executed before or if previous db_patches have been executed.\n";
  56
  57     print STDOUT "\nExecuting the SQL commands.\n";
  58     my $schema = Bio::Chado::Schema->connect( sub { $self->dbh->clone } );
  59
  60
  61     print STDERR "INSERTING CV TERMS...\n";
  62
  63     my $terms = {
  64         'list_types' => [
  65             'tissue_samples',
  66         ]
  67     };
  68
  69         foreach my $t (keys %$terms){
  70                 foreach (@{$terms->{$t}}){
  71                         $schema->resultset("Cv::Cvterm")->create_with({
  72                                 name => $_,
  73                                 cv => $t
  74                         });
  75                 }
  76         }
  77
  78
  79 print "You're done!\n";
  80 }
  81
  82
  83 ####
  84 1; #
  85 ####