db/00143/AddSpOrderPropertyCvAndCvterms.pm

   1 #!/usr/bin/env perl
   2
   3
   4 =head1 NAME
   5
   6  AddSpOrderPropertyCvAndCvterms
   7
   8 =head1 SYNOPSIS
   9
  10 mx-run AddSpOrderPropertyCvAndCvterms [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 sp_order_property cv and order_batch_json, order_progress_json cvterms
  17 This subclass uses L<Moose>. The parent class uses L<MooseX::Runnable>
  18
  19 =head1 AUTHOR
  20
  21 Titima Tantikanjana <tt15@cornell.edu>
  22
  23 =head1 COPYRIGHT & LICENSE
  24
  25 Copyright 2010 Boyce Thompson Institute for Plant Research
  26
  27 This program is free software; you can redistribute it and/or modify
  28 it under the same terms as Perl itself.
  29
  30 =cut
  31
  32
  33 package AddSpOrderPropertyCvAndCvterms;
  34
  35 use Moose;
  36 use Bio::Chado::Schema;
  37 use Try::Tiny;
  38 extends 'CXGN::Metadata::Dbpatch';
  39
  40
  41 has '+description' => ( default => <<'' );
  42 This patch adds the 'sp_order_property' cv and 'order_batch_json', 'order_progress_json' sp_order_property cvterms
  43
  44 has '+prereq' => (
  45         default => sub {
  46         [],
  47     },
  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     my $schema = Bio::Chado::Schema->connect( sub { $self->dbh->clone } );
  60     my $cv_rs = $schema->resultset("Cv::Cv");
  61     my $cvterm_rs = $schema->resultset("Cv::Cvterm");
  62
  63     print STDERR "CREATING CV...\n";
  64     my $cv = $cv_rs->find_or_create({ name => 'sp_order_property' });
  65
  66     print STDERR "ADDING CVTERMS...\n";
  67         my $terms = {
  68             'sp_order_property' => [
  69             'order_batch_json',
  70             'order_progress_json'],
  71         };
  72
  73         foreach my $t (keys %$terms){
  74                 foreach (@{$terms->{$t}}){
  75                         $schema->resultset("Cv::Cvterm")->create_with({
  76                                 name => $_,
  77                                 cv => $t
  78                         });
  79                 }
  80         }
  81
  82     print "You're done!\n";
  83 }
  84
  85
  86 ####
  87 1; #
  88 ####