db/00088/AddAccessionStockpropCvterms.pm

   1 #!/usr/bin/env perl
   2
   3
   4 =head1 NAME
   5
   6  AddAccessionStockpropCvterms
   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 cvterm for storing a cached trial layout in json
  17 This subclass uses L<Moose>. The parent class uses L<MooseX::Runnable>
  18
  19 =head1 AUTHOR
  20
  21 =head1 COPYRIGHT & LICENSE
  22
  23 Copyright 2010 Boyce Thompson Institute for Plant Research
  24
  25 This program is free software; you can redistribute it and/or modify
  26 it under the same terms as Perl itself.
  27
  28 =cut
  29
  30
  31 package AddAccessionStockpropCvterms;
  32
  33 use Moose;
  34 use Bio::Chado::Schema;
  35 use Try::Tiny;
  36 extends 'CXGN::Metadata::Dbpatch';
  37
  38
  39 has '+description' => ( default => <<'' );
  40 This patch adds the necessary cvterms for accession stockprops
  41
  42 has '+prereq' => (
  43         default => sub {
  44         [],
  45     },
  46
  47   );
  48
  49 sub patch {
  50     my $self=shift;
  51
  52     print STDOUT "Executing the patch:\n " .   $self->name . ".\n\nDescription:\n  ".  $self->description . ".\n\nExecuted by:\n " .  $self->username . " .";
  53
  54     print STDOUT "\nChecking if this db_patch was executed before or if previous db_patches have been executed.\n";
  55
  56     print STDOUT "\nExecuting the SQL commands.\n";
  57     my $schema = Bio::Chado::Schema->connect( sub { $self->dbh->clone } );
  58
  59
  60     print STDERR "INSERTING CV TERMS...\n";
  61
  62     my $terms = {
  63         'stock_property' => [
  64             'genome_structure',
  65             'ploidy_level',
  66             'introgression_parent',
  67             'introgression_backcross_parent',
  68             'introgression_map_version',
  69             'introgression_chromosome',
  70             'introgression_start_position_bp',
  71             'introgression_end_position_bp',
  72             'notes', #Found in editable_stock_props
  73             'variety', #Found in editable_stock_props
  74             'state', #Found in editable_stock_props
  75         ]
  76     };
  77
  78         foreach my $t (keys %$terms){
  79                 foreach (@{$terms->{$t}}){
  80                         $schema->resultset("Cv::Cvterm")->create_with({
  81                                 name => $_,
  82                                 cv => $t
  83                         });
  84                 }
  85         }
  86
  87
  88 print "You're done!\n";
  89 }
  90
  91
  92 ####
  93 1; #
  94 ####