db/00085/AddSeedlotCurrentCountCvterm.pm

   1 #!/usr/bin/env perl
   2
   3
   4 =head1 NAME
   5
   6  AddSeedlotCurrentCountCvterm.pm
   7
   8 =head1 SYNOPSIS
   9
  10 mx-run AddSeedlotCurrentCountCvterm [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 the necessary cvterms that are used for brapi germplasm, programs, and studies.
  17 This subclass uses L<Moose>. The parent class uses L<MooseX::Runnable>
  18
  19 =head1 AUTHOR
  20
  21  Nick Morales
  22
  23 =head1 COPYRIGHT & LICENSE
  24
  25 Copyright 2010 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 AddSeedlotCurrentCountCvterm;
  34
  35 use Moose;
  36 use Bio::Chado::Schema;
  37 use Try::Tiny;
  38 use CXGN::Stock::Seedlot;
  39 use SGN::Model::Cvterm;
  40 extends 'CXGN::Metadata::Dbpatch';
  41
  42
  43 has '+description' => ( default => <<'' );
  44 Adds current_count stock_property cvterm which acts as a store for the current count of a seedlot
  45
  46 has '+prereq' => (
  47         default => sub {
  48         [],
  49     },
  50
  51   );
  52
  53 sub patch {
  54     my $self=shift;
  55
  56     print STDOUT "Executing the patch:\n " .   $self->name . ".\n\nDescription:\n  ".  $self->description . ".\n\nExecuted by:\n " .  $self->username . " .";
  57
  58     print STDOUT "\nChecking if this db_patch was executed before or if previous db_patches have been executed.\n";
  59
  60     print STDOUT "\nExecuting the SQL commands.\n";
  61     my $schema = Bio::Chado::Schema->connect( sub { $self->dbh->clone } );
  62
  63
  64     print STDERR "INSERTING CV TERMS...\n";
  65
  66         my $terms = {
  67                 'stock_property' => [
  68                         'current_count',
  69                 ],
  70         };
  71
  72         foreach my $t (keys %$terms){
  73                 foreach (@{$terms->{$t}}){
  74                         $schema->resultset("Cv::Cvterm")->create_with({
  75                                 name => $_,
  76                                 cv => $t
  77                         });
  78                 }
  79         }
  80
  81         # Applies current_count to all existing seedlots in database
  82         my $seedlot_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'seedlot', 'stock_type')->cvterm_id();
  83         my $seedlot_rs = $schema->resultset("Stock::Stock")->search({
  84                 type_id=>$seedlot_type_id
  85         });
  86         while(my $r=$seedlot_rs->next){
  87                 my $sl = CXGN::Stock::Seedlot->new(schema => $schema, seedlot_id=>$r->stock_id);
  88                 $sl->set_current_count_property();
  89         }
  90
  91 print "You're done!\n";
  92 }
  93
  94
  95 ####
  96 1; #
  97 ####