db/00164/AddGenotypingProjectRelatedCvterms.pm

   1 #!/usr/bin/env perl
   2
   3 =head1 NAME
   4
   5  AddGenotypingProjectRelatedCvterms
   6
   7 =head1 SYNOPSIS
   8
   9 mx-run AddGenotypingProjectRelatedCvterms [options] -H hostname -D dbname -u username [-F]
  10
  11 this is a subclass of L<CXGN::Metadata::Dbpatch>
  12 see the perldoc of parent class for more details.
  13
  14 =head1 DESCRIPTION
  15 This patch adds cvterms for differentiating folder for genotyping projects and genotyping_project_type
  16 This subclass uses L<Moose>. The parent class uses L<MooseX::Runnable>
  17
  18 =head1 AUTHOR
  19
  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 AddGenotypingProjectRelatedCvterms;
  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 'folder_for_genotyping_projects' and 'genotyping_project_type' projectprop cvterms
  41
  42 has '+prereq' => (
  43     default => sub {
  44         [],
  45     },
  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     my $schema = Bio::Chado::Schema->connect( sub { $self->dbh->clone } );
  57
  58     print STDERR "INSERTING CV TERMS...\n";
  59
  60     my $terms = {
  61         'project_property' => [
  62             'folder_for_genotyping_projects',
  63             'genotyping_project_type',
  64         ]
  65     };
  66
  67     foreach my $t (keys %$terms){
  68         foreach (@{$terms->{$t}}){
  69             $schema->resultset("Cv::Cvterm")->create_with({
  70                 name => $_,
  71                 cv => $t
  72             });
  73         }
  74     }
  75
  76     print "You're done!\n";
  77 }
  78
  79
  80 ####
  81 1; #
  82 ####