db/00119/AddAnalysisAndMixedModelCvterms.pm

   1 #!/usr/bin/env perl
   2
   3
   4 =head1 NAME
   5
   6  AddAnalysisAndMixedModelCvterms
   7
   8 =head1 SYNOPSIS
   9
  10 mx-run  AddAnalysisAndMixedModelCvterms [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 dbpatch adds cvterms required for mixed models and analysis features.
  18
  19 =head1 AUTHOR
  20
  21   Lukas Mueller <lam87@cornell.edu>
  22
  23 =head1 COPYRIGHT & LICENSE
  24
  25 Copyright 2019 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 AddAnalysisAndMixedModelCvterms;
  34
  35 use Moose;
  36 use Bio::Chado::Schema;
  37 extends 'CXGN::Metadata::Dbpatch';
  38
  39
  40 has '+description' => ( default => <<'' );
  41 Adds cvterms required for mixed models and analysis features
  42
  43 has '+prereq' => (
  44     default => sub {
  45         [],
  46     },
  47   );
  48
  49 sub patch {
  50     my $self=shift;
  51
  52     print STDERR "Executing the patch:\n " .   $self->name . ".\n\nDescription:\n  ".  $self->description . ".\n\nExecuted by:\n " .  $self->username . " .";
  53
  54     print STDERR "\nChecking if this db_patch was executed before or if previous db_patches have been executed.\n";
  55
  56     print STDERR "\nExecuting the SQL commands.\n";
  57
  58     my $schema = Bio::Chado::Schema->connect( sub { $self->dbh->clone } );
  59
  60
  61
  62     print STDERR "INSERTING CV TERMS...\n";
  63
  64     $self->dbh->do("INSERT INTO nd_geolocation (description) values ('[Computation]')");
  65
  66     my $terms = {
  67         project_property =>
  68             [
  69              "analysis_project",
  70              "project_sp_person_id",
  71              "analysis_metadata_json",
  72             ],
  73
  74             stock_type =>
  75             [
  76              "analysis_instance",
  77             ],
  78             experiment_type =>
  79             [
  80              "analysis_experiment",
  81             ],
  82             stock_relationship =>
  83             [
  84              "analysis_of",
  85             ],
  86     };
  87
  88
  89
  90     foreach my $t (sort keys %$terms){
  91         foreach (@{$terms->{$t}}){
  92             $schema->resultset("Cv::Cvterm")->create_with(
  93                 {
  94                     name => $_,
  95                     cv => $t
  96                 });
  97         }
  98     }
  99     print STDERR "Patch complete\n";
 100 }
 101
 102
 103 ####
 104 1; #
 105 ####