db/00169/AddTraitCvterms.pm

   1 #!/usr/bin/env perl
   2
   3
   4 =head1 NAME
   5
   6  AddTraitCvterms
   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
  17 This patch adds system cvterms that are needed for cvtermprops to store BrAPI variable data.
  18
  19 This subclass uses L<Moose>. The parent class uses L<MooseX::Runnable>
  20
  21 =head1 AUTHOR
  22
  23  Nick Palladino<np398@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 AddTraitCvterms;
  36
  37 use Moose;
  38 use Try::Tiny;
  39 use Bio::Chado::Schema;
  40
  41 extends 'CXGN::Metadata::Dbpatch';
  42
  43
  44 has '+description' => ( default => <<'' );
  45 This patch will add system cvterms required for storing BrAPI variable data
  46
  47 has '+prereq' => (
  48     default => sub {
  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     print STDOUT "\nChecking if this db_patch was executed before or if previous db_patches have been executed.\n";
  58     print STDOUT "\nExecuting the SQL commands.\n";
  59
  60     my %cvterms =
  61         (
  62             'trait_property' =>
  63                 [
  64                     'trait_method_name',
  65                     'trait_method_description',
  66                     'trait_method_class',
  67                     'trait_method_formula',
  68                     'trait_decimal_places',
  69                     'trait_categories_label',
  70                     'trait_categories_value'
  71                 ]
  72         );
  73
  74     my $schema = Bio::Chado::Schema->connect( sub { $self->dbh->clone } );
  75
  76     my $coderef = sub {
  77
  78         foreach my $cv_name ( keys  %cvterms  ) {
  79             print "\nKEY = $cv_name \n\n";
  80             my @cvterm_names = @{$cvterms{ $cv_name } }  ;
  81
  82             foreach  my $cvterm_name ( @cvterm_names ) {
  83                 print "cvterm= $cvterm_name \n";
  84                 my $new_cvterm = $schema->resultset("Cv::Cvterm")->create_with(
  85                     {
  86                         name => $cvterm_name,
  87                         cv   => $cv_name,
  88                     });
  89             }
  90         }
  91     };
  92
  93     try {
  94         $schema->txn_do($coderef);
  95
  96     } catch {
  97         die "Load failed! " . $_ .  "\n" ;
  98     };
  99
 100     print "You're done!\n";
 101 }
 102
 103 ####
 104 1; #
 105 ####