db/00111/UpdateFamilyNameCvterm.pm

   1 #!/usr/bin/env perl
   2
   3
   4 =head1 NAME
   5
   6  UpdateFamilyNameCvterm.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 cvterm family_name by changing from cv = stock_property to cv = stock_type.
  17 This subclass uses L<Moose>. The parent class uses L<MooseX::Runnable>
  18
  19 =head1 AUTHOR
  20
  21  Titima Tantikanjana<tt15@cornell.edu>
  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 UpdateFamilyNameCvterm;
  34
  35 use Moose;
  36 use Bio::Chado::Schema;
  37 use SGN::Model::Cvterm;
  38 use Try::Tiny;
  39 extends 'CXGN::Metadata::Dbpatch';
  40
  41
  42
  43 has '+description' => ( default => <<'' );
  44 This patch updates the cvterm family_name by changing from cv = stock_property to cv = stock_type.
  45
  46 has '+prereq' => (
  47         default => sub {
  48         ['AddFamilyNameCvterm'],
  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
  65     my $family_name_cvterm =  SGN::Model::Cvterm->get_cvterm_row($schema, 'family_name', 'stock_property');
  66     my $stock_type_cv = $schema->resultset("Cv::Cv")->find({ name => 'stock_type' });
  67
  68     $family_name_cvterm->update( { cv_id => $stock_type_cv->cv_id  } );
  69
  70     print "You're done!\n";
  71 }
  72
  73
  74 ####
  75 1; #
  76 ####