db/00066/AddNewCrossCvterms.pm

   1 #!/usr/bin/env perl
   2
   3 =head1 NAME
   4
   5 AddNewCrossCvterms.pm
   6
   7 =head1 SYNOPSIS
   8
   9 mx-run AddNewCrossCvterms [options] -H hostname -D dbname -u username [-F]
  10
  11 this is a subclass of L<CXGN::Metadata::Dbpatch>
  12 see the perldoc of parent class for more details.
  13
  14 =head1 DESCRIPTION
  15
  16 This patch adds new cross cvterms so that they can be stored in the nd_experimentprop table.
  17
  18 =head1 AUTHOR
  19
  20 Bryan Ellerbrock<bje24@cornell.edu>
  21
  22 =head1 COPYRIGHT & LICENSE
  23
  24 Copyright 2010 Boyce Thompson Institute for Plant Research
  25
  26 This program is free software; you can redistribute it and/or modify
  27 it under the same terms as Perl itself.
  28
  29 =cut
  30
  31
  32 package AddNewCrossCvterms;
  33
  34 use Moose;
  35 use Bio::Chado::Schema;
  36 use Try::Tiny;
  37 extends 'CXGN::Metadata::Dbpatch';
  38
  39
  40 has '+description' => ( default => <<'' );
  41 This patch adds new cross cvterms so that they can be stored in the nd_experimentprop table.
  42
  43
  44 sub patch {
  45   my $self=shift;
  46
  47   print STDOUT "Executing the patch:\n " .   $self->name . ".\n\nDescription:\n  ".  $self->description . ".\n\nExecuted by:\n " .  $self->username . " .";
  48
  49   print STDOUT "\nChecking if this db_patch was executed before or if previous db_patches have been executed.\n";
  50
  51   print STDOUT "\nExecuting the SQL commands.\n";
  52
  53   my $schema = Bio::Chado::Schema->connect( sub { $self->dbh->clone } );
  54
  55   my $coderef = sub {
  56
  57     my $date_of_pollination = $schema->resultset("Cv::Cvterm")->create_with({
  58         name => 'date_of_pollination',
  59         cv   => 'nd_experiment_property',
  60     });
  61
  62     my $date_of_harvest  = $schema->resultset("Cv::Cvterm")->create_with({
  63         name => 'date_of_harvest',
  64         cv   => 'nd_experiment_property',
  65     });
  66
  67     my $date_of_seed_extraction  = $schema->resultset("Cv::Cvterm")->create_with({
  68         name => 'date_of_seed_extraction',
  69         cv   => 'nd_experiment_property',
  70     });
  71
  72     my $number_of_seeds_extracted  = $schema->resultset("Cv::Cvterm")->create_with({
  73         name => 'number_of_seeds_extracted',
  74         cv   => 'nd_experiment_property',
  75     });
  76
  77     my $number_of_viable_seeds  = $schema->resultset("Cv::Cvterm")->create_with({
  78         name => 'number_of_viable_seeds',
  79         cv   => 'nd_experiment_property',
  80     });
  81
  82     my $number_of_nonviable_seeds = $schema->resultset("Cv::Cvterm")->create_with({
  83         name => 'number_of_nonviable_seeds',
  84         cv   => 'nd_experiment_property',
  85     });
  86
  87     my $date_of_embryo_rescue  = $schema->resultset("Cv::Cvterm")->create_with({
  88         name => 'date_of_embryo_rescue',
  89         cv   => 'nd_experiment_property',
  90     });
  91
  92     my $number_of_embryos_rescued  = $schema->resultset("Cv::Cvterm")->create_with({
  93         name => 'number_of_embryos_rescued',
  94         cv   => 'nd_experiment_property',
  95     });
  96
  97     my $number_of_embryos_germinated  = $schema->resultset("Cv::Cvterm")->create_with({
  98         name => 'number_of_embryos_germinated',
  99         cv   => 'nd_experiment_property',
 100     });
 101
 102     my $number_of_embryos_contaminated  = $schema->resultset("Cv::Cvterm")->create_with({
 103         name => 'number_of_embryos_contaminated',
 104         cv   => 'nd_experiment_property',
 105     });
 106
 107     my $number_of_seeds_planted  = $schema->resultset("Cv::Cvterm")->create_with({
 108         name => 'number_of_seeds_planted',
 109         cv   => 'nd_experiment_property',
 110     });
 111
 112     my $number_of_seeds_germinated  = $schema->resultset("Cv::Cvterm")->create_with({
 113         name => 'number_of_seeds_germinated',
 114         cv   => 'nd_experiment_property',
 115     });
 116
 117     my $days_to_maturity = $schema->resultset("Cv::Cvterm")->create_with({
 118         name => 'days_to_maturity',
 119         cv   => 'nd_experiment_property',
 120     });
 121
 122     my $days_from_harvest_to_extraction = $schema->resultset("Cv::Cvterm")->create_with({
 123         name => 'days_from_harvest_to_extraction',
 124         cv   => 'nd_experiment_property',
 125     });
 126
 127     my $days_from_extraction_to_embryo_rescue = $schema->resultset("Cv::Cvterm")->create_with({
 128         name => 'days_from_extraction_to_embryo_rescue',
 129         cv   => 'nd_experiment_property',
 130     });
 131
 132     my $number_of_progeny  = $schema->resultset("Cv::Cvterm")->create_with({
 133         name => 'number_of_progeny',
 134         cv   => 'nd_experiment_property',
 135     });
 136
 137   };
 138
 139   try {
 140     $schema->txn_do($coderef);
 141   } catch {
 142     die "Load failed! " . $_ .  "\n" ;
 143   };
 144
 145   print "You're done!\n";
 146
 147 }
 148
 149 ####
 150 1; #
 151 ####