db/00161/AddFacilityIdentifierCvterm.pm

   1 #!/usr/bin/env perl
   2
   3 =head1 NAME
   4
   5  AddFacilityIdentifierCvterm
   6
   7 =head1 SYNOPSIS
   8
   9 mx-run AddFacilityIdentifierCvterm [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 facility_identifier cvterm
  16 This subclass uses L<Moose>. The parent class uses L<MooseX::Runnable>
  17
  18 =head1 AUTHOR
  19
  20 Titima Tantikanjana <tt15@cornell.edu>
  21
  22 =head1 COPYRIGHT & LICENSE
  23
  24 Copyright 2010 Boyce Thompson Institute for Plant Research
  25
  26 This program is free software; you can redistribute it and/or modify
  27 it under the same terms as Perl itself.
  28
  29 =cut
  30
  31 package AddFacilityIdentifierCvterm;
  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 'facility_identifier stock_property cvterm
  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             'facility_identifier'],
  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 ####