db/00087/UpdateProjectTypes.pm

   1 #!/usr/bin/env perl
   2
   3
   4 =head1 NAME
   5
   6  UpdateProjectTypes.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 cvterms phenotypeing_trial and genotyping_trial with cv = project_type to be consistent with other projectprops in the database
  17 cvterm crossing_trial is redundant and is now deleted, as well as the cv.name trial_type. All trial types in the database should use the project_type cvterm since these are stored in the project table
  18
  19
  20 This subclass uses L<Moose>. The parent class uses L<MooseX::Runnable>
  21
  22 =head1 AUTHOR
  23
  24  Naama Menda<nm249@cornell.edu>
  25
  26 =head1 COPYRIGHT & LICENSE
  27
  28 Copyright 2010 Boyce Thompson Institute for Plant Research
  29
  30 This program is free software; you can redistribute it and/or modify
  31 it under the same terms as Perl itself.
  32
  33 =cut
  34
  35
  36 package UpdateProjectTypes;
  37
  38 use Moose;
  39 use Bio::Chado::Schema;
  40 use SGN::Model::Cvterm;
  41 use Try::Tiny;
  42 extends 'CXGN::Metadata::Dbpatch';
  43
  44
  45
  46 has '+description' => ( default => <<'' );
  47 This patch updates the cvterms phenotypeing_trial and genotyping_trial with cv = project_type to be consistent with other projectprops in the database
  48 cvterm crossing_trial is redundant and is now deleted, as well as the cv.name trial_type. All trial types in the database should use the project_type cvterm since these are stored in the project table
  49
  50 has '+prereq' => (
  51         default => sub {
  52         ['AddGraftingCvterms', 'AddTrialTypes'],
  53     },
  54
  55   );
  56
  57 sub patch {
  58     my $self=shift;
  59
  60     print STDOUT "Executing the patch:\n " .   $self->name . ".\n\nDescription:\n  ".  $self->description . ".\n\nExecuted by:\n " .  $self->username . " .";
  61
  62     print STDOUT "\nChecking if this db_patch was executed before or if previous db_patches have been executed.\n";
  63
  64     print STDOUT "\nExecuting the SQL commands.\n";
  65     my $schema = Bio::Chado::Schema->connect( sub { $self->dbh->clone } );
  66
  67
  68
  69     my $phenotyping_cvterm =  SGN::Model::Cvterm->get_cvterm_row($schema, 'phenotyping_trial', 'trial_type');
  70     my $genotyping_cvterm = SGN::Model::Cvterm->get_cvterm_row($schema, 'genotyping_trial' , 'trial_type' ) ;
  71     my $crossing_cvterm = SGN::Model::Cvterm->get_cvterm_row($schema, 'crossing_trial' , 'trial_type' ) ;
  72     my $trial_type_cv = $schema->resultset("Cv::Cv")->find(
  73         { name => 'trial_type' });
  74     my $project_type_cv = $schema->resultset("Cv::Cv")->find(
  75         { name => 'project_type' } );
  76
  77     $phenotyping_cvterm->update( { cv_id => $project_type_cv->cv_id  } );
  78     $genotyping_cvterm->update( { cv_id =>  $project_type_cv->cv_id } );
  79     $crossing_cvterm->delete;
  80     $trial_type_cv->delete;
  81
  82     print "You're done!\n";
  83 }
  84
  85
  86 ####
  87 1; #
  88 ####