db/00089/AddProjectTissueSampleCvterms.pm

   1 #!/usr/bin/env perl
   2
   3
   4 =head1 NAME
   5
   6  AddProjectTissueSampleCvterms
   7
   8 =head1 SYNOPSIS
   9
  10 mx-run AddProjectTissueSampleCvterms [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 phenotype_property cvterm for storing a suppressed plot phenotype.
  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 AddProjectTissueSampleCvterms;
  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 cvterms for saving tissue_sample stocks from plants in a trial.
  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         'project_property' => [
  64             'project_has_tissue_sample_entries',
  65         ],
  66         'stock_property' => [
  67             'tissue_sample_index_number',
  68         ]
  69     };
  70
  71         foreach my $t (keys %$terms){
  72                 foreach (@{$terms->{$t}}){
  73                         $schema->resultset("Cv::Cvterm")->create_with({
  74                                 name => $_,
  75                                 cv => $t
  76                         });
  77                 }
  78         }
  79
  80
  81 print "You're done!\n";
  82 }
  83
  84
  85 ####
  86 1; #
  87 ####