db/00084/AddTreatmentCvterms.pm

   1 #!/usr/bin/env perl
   2
   3
   4 =head1 NAME
   5
   6  AddTreatmentCvterms.pm
   7
   8 =head1 SYNOPSIS
   9
  10 mx-run ThisPackageName [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 the necessary cvterms that are used for storing grafted stocks,
  17 rootstock-scion stock_relationship, grafting_experiment ,and missing project types
  18
  19
  20 This subclass uses L<Moose>. The parent class uses L<MooseX::Runnable>
  21
  22 =head1 AUTHOR
  23
  24  <nm529@cornell.edu>
  25
  26 =head1 COPYRIGHT & LICENSE
  27
  28 Copyright 2010 Boyce Thompson Institute for Plant Research
  29
  30 This program is free software; you can redistribute it and/or modify
  31 it under the same terms as Perl itself.
  32
  33 =cut
  34
  35
  36 package AddTreatmentCvterms;
  37
  38 use Moose;
  39 use Bio::Chado::Schema;
  40 use Try::Tiny;
  41 extends 'CXGN::Metadata::Dbpatch';
  42
  43
  44 has '+description' => ( default => <<'' );
  45 Add missing cvterms for storing grafted stocks, and grafting experiments or projects
  46
  47 has '+prereq' => (
  48         default => sub {
  49         [],
  50     },
  51
  52   );
  53
  54 sub patch {
  55     my $self=shift;
  56
  57     print STDOUT "Executing the patch:\n " .   $self->name . ".\n\nDescription:\n  ".  $self->description . ".\n\nExecuted by:\n " .  $self->username . " .";
  58
  59     print STDOUT "\nChecking if this db_patch was executed before or if previous db_patches have been executed.\n";
  60
  61     print STDOUT "\nExecuting the SQL commands.\n";
  62     my $schema = Bio::Chado::Schema->connect( sub { $self->dbh->clone } );
  63
  64
  65     print STDERR "INSERTING CVTERMS...\n";
  66
  67     my $terms = {
  68         'experiment_type' => [
  69             'treatment_experiment',
  70         ],
  71         'project_relationship' => [
  72             'trial_treatment_relationship'
  73         ]
  74     };
  75
  76     foreach my $t (keys %$terms){
  77         foreach (@{$terms->{$t}}){
  78             $schema->resultset("Cv::Cvterm")->create_with({
  79                 name => $_,
  80                 cv => $t
  81             });
  82         }
  83     }
  84
  85
  86     print "You're done!\n";
  87 }
  88
  89
  90 ####
  91 1; #
  92 ####