db/00078/AddPlantListType.pm

   1 #!/usr/bin/env perl
   2
   3
   4 =head1 NAME
   5
   6  AddPlantListType.pm
   7
   8 =head1 SYNOPSIS
   9
  10 mx-run AddNewListTypes [options] -H hostname -D dbname -u username [-F]
  11
  12 Adds the list type "Plants" required for validation of list containing plants.
  13
  14 this is a subclass of L<CXGN::Metadata::Dbpatch>
  15 see the perldoc of parent class for more details.
  16
  17 =head1 DESCRIPTION
  18
  19 This is a test dummy patch.
  20 This subclass uses L<Moose>. The parent class uses L<MooseX::Runnable>
  21
  22 =head1 AUTHOR
  23
  24  Lukas Mueller <lam87@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 AddPlantListType;
  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 This patch will create the cvterm 'plant'.
  46
  47
  48 sub patch {
  49     my $self=shift;
  50
  51     print STDOUT "Executing the patch:\n " .   $self->name . ".\n\nDescription:\n  ".  $self->description . ".\n\nExecuted by:\n " .  $self->username . " .";
  52
  53     print STDOUT "\nChecking if this db_patch was executed before or if previous db_patches have been executed.\n";
  54
  55     print STDOUT "\nExecuting the SQL commands.\n";
  56
  57     my $schema = Bio::Chado::Schema->connect( sub { $self->dbh->clone } );
  58
  59     my $coderef = sub {
  60
  61   my $numbers_list_type_cvterm = $schema->resultset("Cv::Cvterm")->create_with({
  62       name => 'plants',
  63       definition => 'plants',
  64       cv   => 'list_types',
  65   });
  66
  67     };
  68
  69     try {
  70         $schema->txn_do($coderef);
  71
  72     } catch {
  73         die "Load failed! " . $_ .  "\n" ;
  74     };
  75
  76     print "You're done!\n";
  77 }
  78
  79
  80 ####
  81 1; #
  82 ####