db/00087/UpdateNdExperimentProperty.pm

   1 #!/usr/bin/env perl
   2
   3
   4 =head1 NAME
   5
   6  UpdateNdExperimentProperty.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 updates the cvterm "crossing_metadata_json" by changing from  cv = "nd_experiment_property" to cv = "stock_property"  and removes unused cvterms related to crossing experiments.
  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 UpdateNdExperimentProperty;
  34
  35 use Moose;
  36 use Bio::Chado::Schema;
  37 use SGN::Model::Cvterm;
  38 use Try::Tiny;
  39 extends 'CXGN::Metadata::Dbpatch';
  40
  41
  42
  43 has '+description' => ( default => <<'' );
  44 This patch updates the cvterm "crossing_metadata_json" by changing from  cv = "nd_experiment_property" to cv = "stock_property"  and removes unused cvterms related to crossing experiments.
  45
  46 has '+prereq' => (
  47         default => sub {
  48         ['AddCrossingExperimentCvterms', 'AddNewCrossCvterms', 'AddSystemCvterms'],
  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     # update crossing_metadata_json cvterm
  64
  65     my $crossing_metadata_json_cvterm = $schema->resultset("Cv::Cvterm")->find(
  66         { name => 'crossing_metadata_json'});
  67
  68     my $stock_property_cv = $schema->resultset("Cv::Cv")->find(
  69         { name => 'stock_property'});
  70
  71     $crossing_metadata_json_cvterm->update({cv_id => $stock_property_cv->cv_id});
  72
  73     # delete unused cvterms related to crossing experiment
  74
  75     my $nd_experiment_property_id = $schema->resultset("Cv::Cv")->find(
  76         { name => 'nd_experiment_property'})->cv_id();
  77
  78     my $cvterm_rs = $schema->resultset("Cv::Cvterm")->search(
  79         { cv_id => $nd_experiment_property_id,
  80
  81           name => ['date_of_embryo_rescue',
  82                  'date_of_harvest',
  83                  'date_of_pollination',
  84                  'date_of_seed_extraction',
  85                  'days_from_extraction_to_embryo_rescue',
  86                  'days_from_harvest_to_extraction',
  87                  'days_to_maturity',
  88                  'number_of_embryos_contaminated',
  89                  'number_of_embryos_germinated',
  90                  'number_of_embryos_rescued',
  91                  'number_of_flowers',
  92                  'number_of_fruits',
  93                  'number_of_nonviable_seeds',
  94                  'number_of_seedlings_transplanted',
  95                  'number_of_seeds',
  96                  'number_of_seeds_extracted',
  97                  'number_of_seeds_germinated',
  98                  'number_of_seeds_planted',
  99                  'number_of_viable_seeds'],
 100         });
 101
 102     $cvterm_rs->delete_all;
 103
 104     print "You're done!\n";
 105 }
 106
 107
 108 ####
 109 1; #
 110 ####