db/00060/AddPlantOfCvterm.pm

   1 #!/usr/bin/env perl
   2
   3
   4 =head1 NAME
   5
   6  AddPlantOfCvterm.pm
   7
   8 =head1 SYNOPSIS
   9
  10 mx-run AddPlantOfCvterm [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
  17 This patch adds the cvterm plant_of into the stock_relationship cv. plant_of is similar to plot_of, and is used to describe plant entities which are plants of accessions.
  18 This subclass uses L<Moose>. The parent class uses L<MooseX::Runnable>
  19
  20 =head1 AUTHOR
  21
  22  Nicolas Morales <nm529@cornell.edu>
  23
  24 =head1 COPYRIGHT & LICENSE
  25
  26 Copyright 2010 Boyce Thompson Institute for Plant Research
  27
  28 This program is free software; you can redistribute it and/or modify
  29 it under the same terms as Perl itself.
  30
  31 =cut
  32
  33
  34 package AddPlantOfCvterm;
  35
  36 use Moose;
  37 use Bio::Chado::Schema;
  38 use Try::Tiny;
  39 extends 'CXGN::Metadata::Dbpatch';
  40
  41
  42 has '+description' => ( default => <<'' );
  43 This patch will find_or_create a cvterm name of vector, which is a new stock type
  44
  45 has '+prereq' => (
  46     default => sub {
  47         ['AddVectorStockType'],
  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
  60     my $schema = Bio::Chado::Schema->connect( sub { $self->dbh->clone } );
  61
  62     my $coderef = sub {
  63
  64         my $cvterm = $schema->resultset("Cv::Cvterm")->create_with({
  65             name => 'plant_of',
  66             cv   => 'stock_relationship',
  67         });
  68
  69     };
  70
  71     try {
  72         $schema->txn_do($coderef);
  73
  74     } catch {
  75         die "Load failed! " . $_ .  "\n" ;
  76     };
  77
  78     print "You're done!\n";
  79 }
  80
  81
  82 ####
  83 1; #
  84 ####
  85