db/00185/AddTrackingActivityRelatedCvterms.pm

   1 #!/usr/bin/env perl
   2
   3 =head1 NAME
   4
   5 AddTrackingActivityRelatedCvterms.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 activity_record project_type cvterm, tracking_activity experiment_type cvterm, tracking_identifier stock_type cvterm, material_of stock_relationship cvterm, tracking_tissue_culture_json stock_property cvterm and tracking_identifiers list_type cvterm.
  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 AddTrackingActivityRelatedCvterms;
  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             'activity_record'
  66         ],
  67         'project_property' => [
  68             'activity_type',
  69             'project_vendor',
  70             'folder_for_tracking_activities'
  71         ],
  72         'experiment_type' => [
  73             'tracking_activity'
  74         ],
  75         'stock_type' => [
  76             'tracking_identifier'
  77         ],
  78         'stock_relationship' => [
  79             'material_of'
  80         ],
  81         'stock_property' => [
  82             'tracking_tissue_culture_json',
  83             'terminated_metadata',
  84         ],
  85         'list_types' => [
  86             'tracking_identifiers'
  87         ],
  88         'sp_order_property' => [
  89             'order_tracking_identifiers'
  90         ],
  91     };
  92
  93     foreach my $t (keys %$terms){
  94         foreach (@{$terms->{$t}}){
  95             $schema->resultset("Cv::Cvterm")->create_with({
  96                 name => $_,
  97                 cv => $t
  98             });
  99         }
 100     }
 101
 102     print "You're done!\n";
 103
 104 }
 105
 106
 107 ####
 108 1; #
 109 ####