db/00166/AddPhenotypeExternalReferencesCvterm.pm

   1 #!/usr/bin/env perl
   2
   3
   4 =head1 NAME
   5
   6  AddPhenotypeExternalReferencesCvterm.pm
   7
   8 =head1 SYNOPSIS
   9
  10 mx-run AddPhenotypeExternalReferencesCvterm.pm [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 Mirella Flores<mrf252@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 AddPhenotypeExternalReferencesCvterm;
  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 phenotype_property cvterm for storing external references data for phenotype.
  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
  61
  62     print STDERR "INSERTING CV TERMS...\n";
  63
  64     my $terms = {
  65         'phenotype_property' => [
  66             'phenotype_external_references',
  67         ]
  68     };
  69
  70         foreach my $t (keys %$terms){
  71                 foreach (@{$terms->{$t}}){
  72                         $schema->resultset("Cv::Cvterm")->create_with({
  73                                 name => $_,
  74                                 cv => $t
  75                         });
  76                 }
  77         }
  78
  79
  80 print "You're done!\n";
  81 }
  82
  83
  84 ####
  85 1; #
  86 ####