db/00052/AddSystemCvterms.pm

   1 #!/usr/bin/env perl
   2
   3
   4 =head1 NAME
   5
   6  AddSystemCvterms
   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 creates the system cvterms that are needed for the cxgn databases.
  18 Without these many pages and functions would not work since we are not using anymore the create_with BCS function for auto-creating new cvterms.
  19 Instead all the needed cvterms need to be predefined in the databases.
  20 This is important for the functionality and integrity of the databases, and for preventing overloading with redundant or obscure cvterms.
  21
  22 This subclass uses L<Moose>. The parent class uses L<MooseX::Runnable>
  23
  24 =head1 AUTHOR
  25
  26  Naama Menda<nm249@cornell.edu>
  27
  28 =head1 COPYRIGHT & LICENSE
  29
  30 Copyright 2010 Boyce Thompson Institute for Plant Research
  31
  32 This program is free software; you can redistribute it and/or modify
  33 it under the same terms as Perl itself.
  34
  35 =cut
  36
  37
  38 package AddSystemCvterms;
  39
  40 use Moose;
  41 use Try::Tiny;
  42 use Bio::Chado::Schema;
  43
  44 extends 'CXGN::Metadata::Dbpatch';
  45
  46
  47 has '+description' => ( default => <<'' );
  48 This patch will add system cvterms required for the functionality of the cxgn databases
  49
  50 has '+prereq' => (
  51     default => sub {
  52         [],
  53     },
  54   );
  55
  56 sub patch {
  57     my $self=shift;
  58
  59     print STDOUT "Executing the patch:\n " .   $self->name . ".\n\nDescription:\n  ".  $self->description . ".\n\nExecuted by:\n " .  $self->username . " .";
  60
  61     print STDOUT "\nChecking if this db_patch was executed before or if previous db_patches have been executed.\n";
  62
  63     print STDOUT "\nExecuting the SQL commands.\n";
  64
  65
  66     my %cvterms =
  67     (
  68         'calendar' => ['Planning Event',
  69                        'Fertilizer Event',
  70                        'Genotyping Event',
  71                        'Harvest Event',
  72                        'Meeting Event',
  73                        'Phenotyping Event',
  74                        'Planting Event',
  75                        'Presentation Event' ],
  76
  77         'experiment_type' => [ 'cross_experiment',
  78                                'field_layout',
  79                                'genotyping_experiment',
  80                                'genotyping_layout',
  81                                'phenotyping_experiment' ],
  82         'genotype_property' => ['igd number',
  83                                 'snp genotyping' ],
  84
  85         'local' => ['sp_person_id',
  86                     'visible_to_role' ],
  87
  88         'nd_experiment_property' => [ 'cross_name',
  89                                       'cross_type',
  90                                       'genotyping_project_name',
  91                                       'genotyping_user_id',
  92                                       'number_of_flowers',
  93                                       'number_of_seeds' ],
  94
  95         'organism_property' => [ 'organism_synonym' ],
  96
  97         'project_property'  => [ 'breeding_program',
  98                                  'harvest_date',
  99                                  'planting_date',
 100                                  'trial_folder' ],
 101
 102         'project_relationship' => [ 'breeding_program_trial_relationship' ] ,
 103
 104         'project_type'         => ['Advance Yield Trial',
 105                                    'Preliminary Yield Trial',
 106                                    'Uniform Yield Trial' ],
 107
 108         'stock_property'      => ['block',
 109                                   'col_number',
 110                                   'igd_synonym',
 111                                   'is a control',
 112                                   'location_code',
 113                                   'organization',
 114                                   'plot number',
 115                                   'range',
 116                                   'replicate',
 117                                   'row_number',
 118                                   'stock_synonym',
 119                                   'T1',
 120                                   'T2',
 121                                   'transgenic' ],
 122
 123      'stock_relationship'  =>   [ 'cross_relationship',
 124                                   'female_parent',
 125                                   'male_parent',
 126                                   'member_of',
 127                                   'offspring_of',
 128                                   'plant_of',
 129                                   'plot_of',
 130                                   'tissue_sample_of' ],
 131
 132      'stock_type'    =>  ['accession',
 133                           'backcross population',
 134                           'cross',
 135                           'f2 population',
 136                           'mutant population',
 137                           'plant',
 138                           'plot',
 139                           'population',
 140                           'tissue_sample',
 141                           'training population',
 142                           'vector_construct'  ],
 143
 144      'trait_property' => [ 'trait_categories',
 145                            'trait_default_value',
 146                            'trait_details',
 147                            'trait_format',
 148                            'trait_maximum',
 149                            'trait_minimum' ]
 150
 151     );
 152
 153
 154     my $schema = Bio::Chado::Schema->connect( sub { $self->dbh->clone } );
 155
 156
 157     my $coderef = sub {
 158
 159
 160         foreach my $cv_name ( keys  %cvterms  ) {
 161             print "\nKEY = $cv_name \n\n";
 162             my @cvterm_names = @{$cvterms{ $cv_name } }  ;
 163
 164             foreach  my $cvterm_name ( @cvterm_names ) {
 165                 print "cvterm= $cvterm_name \n";
 166                 my $new_cvterm = $schema->resultset("Cv::Cvterm")->create_with(
 167                     {
 168                         name => $cvterm_name,
 169                         cv   => $cv_name,
 170                     });
 171             }
 172         }
 173     };
 174
 175     try {
 176         $schema->txn_do($coderef);
 177
 178     } catch {
 179         die "Load failed! " . $_ .  "\n" ;
 180     };
 181
 182 print "You're done!\n";
 183 }
 184
 185
 186 ####
 187 1; #
 188 ####