db/00184/AddTransformationRelatedCvterms.pm

   1 #!/usr/bin/env perl
   2
   3 =head1 NAME
   4
   5 AddTransformationRelatedCvterms.pm
   6
   7 =head1 SYNOPSIS
   8
   9 mx-run ThisPackageName [options] -H hostname -D dbname -u username [-F]
  10
  11 this is a subclass of L<CXGN::Metadata::Dbpatch>
  12 see the perldoc of parent class for more details.
  13
  14 =head1 DESCRIPTION
  15 This patch adds transformation_project project_type, transformation_experiment experiment_type, folder_for_transformations project_property, transformation stock_type, plant_material_of, vector_construct_of, transformant_of stock_relationship cvterms.
  16 This subclass uses L<Moose>. The parent class uses L<MooseX::Runnable>
  17
  18 =head1 AUTHOR
  19
  20 Titima Tantikanjana<tt15@cornell.edu>
  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 AddTransformationRelatedCvterms;
  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 Description of this patch goes here
  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         'project_type' => [
  65             'transformation_project'
  66         ],
  67         'project_property' => [
  68             'folder_for_transformations'
  69         ],
  70         'experiment_type' => [
  71             'transformation_experiment'
  72         ],
  73         'stock_type' => [
  74             'transformation'
  75         ],
  76         'stock_relationship' => [
  77             'plant_material_of',
  78             'vector_construct_of',
  79             'transformant_of'
  80         ],
  81         'stock_property' => [
  82             'transformation_notes',
  83         ],
  84     };
  85
  86     foreach my $t (keys %$terms){
  87         foreach (@{$terms->{$t}}){
  88             $schema->resultset("Cv::Cvterm")->create_with({
  89                 name => $_,
  90                 cv => $t
  91             });
  92         }
  93     }
  94
  95     print "You're done!\n";
  96
  97 }
  98
  99
 100 ####
 101 1; #
 102 ####