db/00084/AddSubplotCvterms.pm

   1 #!/usr/bin/env perl
   2
   3
   4 =head1 NAME
   5
   6  AddSubplotCvterms.pm
   7
   8 =head1 SYNOPSIS
   9
  10 mx-run AddSubplotCvterms [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 brapi germplasm, programs, and studies.
  17 This subclass uses L<Moose>. The parent class uses L<MooseX::Runnable>
  18
  19 =head1 AUTHOR
  20
  21  Nick Morales
  22
  23 =head1 COPYRIGHT & LICENSE
  24
  25 Copyright 2010 Boyce Thompson Institute for Plant Research
  26
  27 This program is free software; you can redistribute it and/or modify
  28 it under the same terms as Perl itself.
  29
  30 =cut
  31
  32
  33 package AddSubplotCvterms;
  34
  35 use Moose;
  36 use Bio::Chado::Schema;
  37 use Try::Tiny;
  38 extends 'CXGN::Metadata::Dbpatch';
  39
  40
  41 has '+description' => ( default => <<'' );
  42 Adds subplot stock_type, subplot_index_number stockprop, and subplot_of stock_relationship cvterms.
  43
  44 has '+prereq' => (
  45         default => sub {
  46         [],
  47     },
  48
  49   );
  50
  51 sub patch {
  52     my $self=shift;
  53
  54     print STDOUT "Executing the patch:\n " .   $self->name . ".\n\nDescription:\n  ".  $self->description . ".\n\nExecuted by:\n " .  $self->username . " .";
  55
  56     print STDOUT "\nChecking if this db_patch was executed before or if previous db_patches have been executed.\n";
  57
  58     print STDOUT "\nExecuting the SQL commands.\n";
  59     my $schema = Bio::Chado::Schema->connect( sub { $self->dbh->clone } );
  60
  61
  62     print STDERR "INSERTING CV TERMS...\n";
  63
  64         my $terms = {
  65                 'stock_type' => [
  66                         'subplot',
  67                 ],
  68                 'stock_property' => [
  69                         'subplot_index_number',
  70                 ],
  71                 'stock_relationship' => [
  72                         'subplot_of',
  73                         'plant_of_subplot'
  74                 ],
  75                 'list_types' => [
  76                         'subplots'
  77                 ],
  78                 'project_property' => [
  79                         'project_has_subplot_entries'
  80                 ]
  81         };
  82
  83         foreach my $t (keys %$terms){
  84                 foreach (@{$terms->{$t}}){
  85                         $schema->resultset("Cv::Cvterm")->create_with({
  86                                 name => $_,
  87                                 cv => $t
  88                         });
  89                 }
  90         }
  91
  92
  93 print "You're done!\n";
  94 }
  95
  96
  97 ####
  98 1; #
  99 ####