db/00132/AddHighDimPhenotypeProtocolCvterms.pm

   1 #!/usr/bin/env perl
   2
   3
   4 =head1 NAME
   5
   6 AddHighDimPhenotypeProtocolCvterms
   7
   8 =head1 SYNOPSIS
   9
  10 mx-run AddProductProfileCvterm [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 adds cvterms for high dimensional phenotype protocols e.g. nirs, metabolite, transcriptomics
  17 This subclass uses L<Moose>. The parent class uses L<MooseX::Runnable>
  18
  19 =head1 AUTHOR
  20
  21 =head1 COPYRIGHT & LICENSE
  22
  23 Copyright 2010 Boyce Thompson Institute for Plant Research
  24
  25 This program is free software; you can redistribute it and/or modify
  26 it under the same terms as Perl itself.
  27
  28 =cut
  29
  30
  31 package AddHighDimPhenotypeProtocolCvterms;
  32
  33 use Moose;
  34 use Bio::Chado::Schema;
  35 use Try::Tiny;
  36 extends 'CXGN::Metadata::Dbpatch';
  37
  38
  39 has '+description' => ( default => <<'' );
  40 This patch adds cvterms for high dimensional phenotype protocols e.g. nirs, metabolite, transcriptomics
  41
  42 has '+prereq' => (
  43         default => sub {
  44         [],
  45     },
  46
  47 );
  48
  49 sub patch {
  50     my $self=shift;
  51
  52     print STDOUT "Executing the patch:\n " .   $self->name . ".\n\nDescription:\n  ".  $self->description . ".\n\nExecuted by:\n " .  $self->username . " .";
  53
  54     print STDOUT "\nChecking if this db_patch was executed before or if previous db_patches have been executed.\n";
  55
  56     print STDOUT "\nExecuting the SQL commands.\n";
  57     my $schema = Bio::Chado::Schema->connect( sub { $self->dbh->clone } );
  58
  59     print STDERR "INSERTING CV TERMS...\n";
  60
  61     my $terms = {
  62         'experiment_type' => [
  63             'sampling_layout'
  64         ],
  65         'project_property' => [
  66             'sampling_facility',
  67             'sampling_trial_sample_type'
  68         ],
  69         'project_relationship' => [
  70             'sampling_trial_from_field_trial'
  71         ],
  72         'protocol_type' => [
  73             'high_dimensional_phenotype_nirs_protocol',
  74             'high_dimensional_phenotype_transcriptomics_protocol',
  75             'high_dimensional_phenotype_metabolomics_protocol',
  76         ],
  77         'protocol_property' => [
  78             'high_dimensional_phenotype_protocol_properties'
  79         ]
  80     };
  81
  82     foreach my $t (keys %$terms){
  83         foreach (@{$terms->{$t}}){
  84             $schema->resultset("Cv::Cvterm")->create_with({
  85                 name => $_,
  86                 cv => $t
  87             });
  88         }
  89     }
  90
  91     print "You're done!\n";
  92 }
  93
  94
  95 ####
  96 1; #
  97 ####