db/00079/AddGraftingCvterms.pm

   1 #!/usr/bin/env perl
   2
   3
   4 =head1 NAME
   5
   6  AddGraftingCvterms.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  Naama Menda<nm249@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 AddGraftingCvterms;
  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         'stock_type' => [
  69             'grafted_accession',
  70             ],
  71             'stock_relationship'  => [
  72                 'rootstock_of',
  73                 'scion_of',
  74             ],
  75             'experiment_type'  => [
  76                 'grafting_experiment',
  77             ],
  78             'project_type'     => [
  79                 'crossing_trial',
  80                 'grafting_trial',
  81                 'pollinating_trial'
  82             ],
  83         };
  84
  85     foreach my $t (keys %$terms){
  86         foreach (@{$terms->{$t}}){
  87             $schema->resultset("Cv::Cvterm")->create_with({
  88                 name => $_,
  89                 cv => $t
  90                                                           });
  91         }
  92     }
  93
  94
  95     print "You're done!\n";
  96 }
  97
  98
  99 ####
 100 1; #
 101 ####