db/00111/AddFamilyNamesListTypesCvterm.pm

   1 #!/usr/bin/env perl
   2
   3
   4 =head1 NAME
   5
   6  AddFamilyNamesListTypesCvterm.pm
   7
   8 =head1 SYNOPSIS
   9
  10 mx-run ThisPackageName [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 family_names as list_types cvterm
  17
  18
  19 This subclass uses L<Moose>. The parent class uses L<MooseX::Runnable>
  20
  21 =head1 AUTHOR
  22
  23  Titima Tantikanjana<tt15@cornell.edu>
  24
  25 =head1 COPYRIGHT & LICENSE
  26
  27 Copyright 2010 Boyce Thompson Institute for Plant Research
  28
  29 This program is free software; you can redistribute it and/or modify
  30 it under the same terms as Perl itself.
  31
  32 =cut
  33
  34
  35 package AddFamilyNamesListTypesCvterm;
  36
  37 use Moose;
  38 use Bio::Chado::Schema;
  39 use Try::Tiny;
  40 extends 'CXGN::Metadata::Dbpatch';
  41
  42
  43 has '+description' => ( default => <<'' );
  44 Add cvterm for family_names list types
  45
  46 has '+prereq' => (
  47         default => sub {
  48         [],
  49     },
  50
  51   );
  52
  53 sub patch {
  54     my $self=shift;
  55
  56     print STDOUT "Executing the patch:\n " .   $self->name . ".\n\nDescription:\n  ".  $self->description . ".\n\nExecuted by:\n " .  $self->username . " .";
  57
  58     print STDOUT "\nChecking if this db_patch was executed before or if previous db_patches have been executed.\n";
  59
  60     print STDOUT "\nExecuting the SQL commands.\n";
  61     my $schema = Bio::Chado::Schema->connect( sub { $self->dbh->clone } );
  62
  63
  64     print STDERR "INSERTING CVTERMS...\n";
  65
  66     my $terms = {
  67         'list_types' => [
  68             'family_names',
  69         ],
  70     };
  71
  72     foreach my $t (keys %$terms){
  73         foreach (@{$terms->{$t}}){
  74             $schema->resultset("Cv::Cvterm")->create_with({
  75                 name => $_,
  76                 cv => $t
  77             });
  78         }
  79     }
  80
  81
  82     print "You're done!\n";
  83 }
  84
  85
  86 ####
  87 1; #
  88 ####