db/00051/UpdateLocalCvterms.pm

   1 #!/usr/bin/env perl
   2
   3
   4 =head1 NAME
   5
   6  UpdateLocalCvterms
   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 changes the cv of local cvterms to the correct one
  18
  19 This subclass uses L<Moose>. The parent class uses L<MooseX::Runnable>
  20
  21 =head1 AUTHOR
  22
  23  Naama Menda<nm249@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 UpdateLocalCvterms;
  36
  37 use Moose;
  38 use Bio::Chado::Schema;
  39 use Try::Tiny;
  40
  41 extends 'CXGN::Metadata::Dbpatch';
  42
  43
  44 has '+description' => ( default => <<'' );
  45 This patch will update the cv id of the following cvterms that currently have a local cv name
  46 cross_type
  47 breeding_program
  48 breeding_program_trial_relationship
  49 harvest_date
  50 number_of_flowers
  51 number_of_seeds
  52 planting_date
  53 this is important for making CVterms uniform and having an explicit cv name that provides the right context
  54
  55 has '+prereq' => (
  56     default => sub {
  57         [],
  58     },
  59   );
  60
  61 sub patch {
  62     my $self=shift;
  63
  64     print STDOUT "Executing the patch:\n " .   $self->name . ".\n\nDescription:\n  ".  $self->description . ".\n\nExecuted by:\n " .  $self->username . " .";
  65
  66     print STDOUT "\nChecking if this db_patch was executed before or if previous db_patches have been executed.\n";
  67
  68     print STDOUT "\nExecuting the SQL commands.\n";
  69     my $schema = Bio::Chado::Schema->connect( sub { $self->dbh->clone } );
  70
  71     my $coderef = sub {
  72         my $cvterm_rs = $schema->resultset("Cv::Cvterm");
  73         my $cv_rs = $schema->resultset("Cv::Cv");
  74
  75         my $nd_experiment_property_cv = $cv_rs->find_or_create( { name => 'nd_experiment_property' });
  76
  77         my $cross_type_cvterm = $cvterm_rs->search(
  78             { name => 'cross_type', } );
  79
  80         if ( $cross_type_cvterm->count() == 0 ) {
  81             print "Creating new cvterm 'cross_type' cv = 'nd_experiment_property' \n";
  82             $cvterm_rs->create_with(
  83                 {
  84                     name => 'cross_type',
  85                     cv   => 'nd_experiment_property',
  86                 } );
  87         } else {
  88             print "Updating existing cvterm 'cross_type' cv = 'nd_experiment_property' \n";
  89             $cross_type_cvterm->first->update( { cv_id => $nd_experiment_property_cv->cv_id }, );
  90         }
  91         ####
  92         my $number_of_flowers_cvterm = $cvterm_rs->search(
  93             { name => 'number_of_flowers', } );
  94
  95         if ( $number_of_flowers_cvterm->count() == 0 ) {
  96             print "Creating new cvterm 'number_of_flowers' cv = 'nd_experiment_property' \n";
  97             $cvterm_rs->create_with(
  98                 {
  99                     name => 'number_of_flowers',
 100                     cv   => 'nd_experiment_property',
 101                 } );
 102         } else {
 103             print "Updating existing cvterm 'number_of_flowers' cv = 'nd_experiment_property' \n";
 104             $number_of_flowers_cvterm->first->update( { cv_id => $nd_experiment_property_cv->cv_id }, );
 105         }
 106         ##########
 107         my $number_of_seeds_cvterm = $cvterm_rs->search(
 108             { name => 'number_of_seeds', } );
 109
 110         if ( $number_of_seeds_cvterm->count() == 0 ) {
 111             print "Creating new cvterm 'number_of_seeds' cv = 'nd_experiment_property' \n";
 112             $cvterm_rs->create_with(
 113                 {
 114                     name => 'number_of_seeds',
 115                     cv   => 'nd_experiment_property',
 116                 } );
 117         } else {
 118             print "Updating existing cvterm 'number_of_seeds' cv = 'nd_experiment_property' \n";
 119             $number_of_seeds_cvterm->first->update( { cv_id => $nd_experiment_property_cv->cv_id }, );
 120
 121         }
 122 #####
 123
 124             my $project_property_cv = $cv_rs->find_or_create( { name => 'project_property' });
 125             my $breeding_program_cvterm = $cvterm_rs->search(
 126                 { name => 'breeding_program', } );
 127
 128             if ( $breeding_program_cvterm->count() == 0 ) {
 129             print "Creating new cvterm 'breeding_program' cv = 'project_property' \n";
 130             $cvterm_rs->create_with(
 131                 {
 132                     name => 'breeding_program',
 133                     cv   => 'project_property',
 134                 } );
 135         } else {
 136             print "Updating existing cvterm 'breeding_program' cv = 'project_property' \n";
 137             $breeding_program_cvterm->first->update( { cv_id => $project_property_cv->cv_id }, );
 138            }
 139             ##############
 140             my $harvest_date_cvterm = $cvterm_rs->search(
 141                 { name => 'harvest_date', } );
 142
 143             if ( $harvest_date_cvterm->count() == 0 ) {
 144             print "Creating new cvterm 'harvest_date' cv = 'project_property' \n";
 145             $cvterm_rs->create_with(
 146                 {
 147                     name => 'harvest_date',
 148                     cv   => 'project_property',
 149                 } );
 150         } else {
 151             print "Updating existing cvterm 'harvest_date' cv = 'project_property' \n";
 152             $harvest_date_cvterm->first->update( { cv_id => $project_property_cv->cv_id }, );
 153           }
 154             ####
 155             my $planting_date_cvterm = $cvterm_rs->search(
 156                 { name => 'planting_date', } );
 157
 158             if ( $planting_date_cvterm->count() == 0 ) {
 159             print "Creating new cvterm 'planting_date' cv = 'project_property' \n";
 160             $cvterm_rs->create_with(
 161                 {
 162                     name => 'planting_date',
 163                     cv   => 'project_property',
 164                 } );
 165         } else {
 166             print "Updating existing cvterm 'planting_date' cv = 'project_property' \n";
 167             $planting_date_cvterm->first->update( { cv_id => $project_property_cv->cv_id }, );
 168          }
 169             ###########
 170
 171             my $project_relationship_cv = $cv_rs->find_or_create( { name => 'project_relationship' });
 172             my $breeding_program_trial_cvterm = $cvterm_rs->search(
 173                 { name => 'breeding_program_trial_relationship', } );
 174
 175             if ( $breeding_program_trial_cvterm->count() == 0 ) {
 176             print "Creating new cvterm 'breeding_program_trial_relationship' cv = 'project_relationship' \n";
 177             $cvterm_rs->create_with(
 178                 {
 179                     name => 'breeding_program_trial_relationship',
 180                     cv   => 'project_relationship',
 181                 } );
 182         } else {
 183             print "Updating existing cvterm 'breeding_program_trial_relationship' cv = 'project_relationship' \n";
 184             $breeding_program_trial_cvterm->first->update( { cv_id => $project_relationship_cv->cv_id }, );
 185         }
 186
 187             ##############
 188
 189         if ($self->trial) {
 190             print "Trial mode! Rolling back transaction\n\n";
 191             $schema->txn_rollback;
 192             return 0;
 193         }
 194         return 1;
 195     };
 196
 197     try {
 198         $schema->txn_do($coderef);
 199
 200     } catch {
 201         die "Load failed! " . $_ .  "\n" ;
 202     };
 203
 204
 205     print "You're done!\n";
 206 }
 207
 208
 209 ####
 210 1; #
 211 ####