db/00154/AddFamilyTypeCvterm.pm

   1 #!/usr/bin/env perl
   2
   3
   4 =head1 NAME
   5
   6  AddFamilyTypeCvterm
   7
   8 =head1 SYNOPSIS
   9
  10 mx-run AddFamilyTypeCvterm [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_type stock_property cvterm
  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 AddFamilyTypeCvterm;
  34
  35 use Moose;
  36 use Bio::Chado::Schema;
  37 use Try::Tiny;
  38 use SGN::Model::Cvterm;
  39
  40 extends 'CXGN::Metadata::Dbpatch';
  41
  42
  43 has '+description' => ( default => <<'' );
  44 This patch adds the 'family_type' stock_property cvterm
  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 CV TERMS...\n";
  65
  66     my $terms = {
  67         'stock_property' => [
  68             'family_type',
  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     #add missing family_type stockprop
  82     my $family_name_cvterm_id =  SGN::Model::Cvterm->get_cvterm_row($schema, 'family_name', 'stock_type')->cvterm_id();
  83     my $family_type_cvterm = SGN::Model::Cvterm->get_cvterm_row($schema,  'family_type', 'stock_property');
  84         my $family_name_rs = $schema->resultset("Stock::Stock")->search({type_id => $family_name_cvterm_id});
  85     if ($family_name_rs) {
  86         while(my $family = $family_name_rs->next()){
  87             my $family_id = $family->stock_id."\n";
  88             my $stored_family_type = $schema->resultset("Stock::Stockprop")->find({ stock_id => $family_id, type_id => $family_type_cvterm->cvterm_id()});
  89             if (!$stored_family_type) {
  90                 $family->create_stockprops({$family_type_cvterm->name() => 'same_parents'});
  91             }
  92         }
  93     }
  94
  95     print "You're done!\n";
  96 }
  97
  98
  99 ####
 100 1; #
 101 ####