db/00069/AddNdExperimentProperty.pm

   1 #!/usr/bin/env perl
   2
   3
   4 =head1 NAME
   5
   6  AddNdExperimentProperty
   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 additional properties to the nd_experiment_property cvterm in the cxgn database
  18
  19 This subclass uses L<Moose>. The parent class uses L<MooseX::Runnable>
  20
  21 =head1 AUTHOR
  22
  23  Alex Ogbonna<aco46@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 AddNdExperimentProperty;
  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 number_of_fruits, number_of_seeds_planted and number_of_seedlings_transplanted cvterms to the nd_experiment_property cv.
  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
  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
  62
  63       my %cvterms =
  64       (
  65
  66         'nd_experiment_property' => [ 'number_of_fruits',
  67                                       'number_of_seeds_planted',
  68                                       'number_of_seedlings_transplanted' ]
  69
  70         );
  71
  72
  73         my $schema = Bio::Chado::Schema->connect( sub { $self->dbh->clone } );
  74
  75
  76         my $coderef = sub {
  77
  78
  79             foreach my $cv_name ( keys  %cvterms  ) {
  80             print "\nKEY = $cv_name \n\n";
  81             my @cvterm_names = @{$cvterms{ $cv_name } }  ;
  82
  83             foreach  my $cvterm_name ( @cvterm_names ) {
  84                 print "cvterm= $cvterm_name \n";
  85                 my $new_cvterm = $schema->resultset("Cv::Cvterm")->create_with(
  86                     {
  87                         name => $cvterm_name,
  88                         cv   => $cv_name,
  89                     });
  90             }
  91         }
  92         };
  93
  94         try {
  95             $schema->txn_do($coderef);
  96
  97         } catch {
  98             die "Load failed! " . $_ .  "\n" ;
  99         };
 100
 101     print "You're done!\n";
 102     }
 103
 104
 105     ####
 106     1; #
 107     ####