t/data/fixture/patches/00144/00001/FixComposedTraitRelationships.pm

   1 #!/usr/bin/env perl
   2
   3
   4 =head1 NAME
   5
   6 FixComposedTraitRelationships.pm
   7
   8 =head1 SYNOPSIS
   9
  10 mx-run FixComposedTraitRelationships [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 patch updates cvterm_relationships for composed traits to include VARIABLE_OF relationships
  18 This subclass uses L<Moose>. The parent class uses L<MooseX::Runnable>
  19
  20 =head1 AUTHOR
  21
  22 Bryan Ellerbrock <bje24@cornell.edu>
  23
  24 =head1 COPYRIGHT & LICENSE
  25
  26 Copyright 2010 Boyce Thompson Institute for Plant Research
  27
  28 This program is free software; you can redistribute it and/or modify
  29 it under the same terms as Perl itself.
  30
  31 =cut
  32
  33
  34 package FixComposedTraitRelationships;
  35
  36 use Moose;
  37 extends 'CXGN::Metadata::Dbpatch';
  38
  39
  40 has '+description' => ( default => <<'' );
  41 This patch updates cvterm_relationships for composed traits to include VARIABLE_OF relationships
  42
  43 sub patch {
  44     my $self=shift;
  45
  46     print STDOUT "Executing the patch:\n " .   $self->name . ".\n\nDescription:\n  ".  $self->description . ".\n\nExecuted by:\n " .  $self->username . " .";
  47
  48     print STDOUT "\nChecking if this db_patch was executed before or if previous db_patches have been executed.\n";
  49
  50     print STDOUT "\nExecuting the SQL commands.\n";
  51
  52     $self->dbh->do(<<EOSQL);
  53
  54     UPDATE cvterm_relationship
  55     SET type_id = (SELECT cvterm_id FROM cvterm WHERE name = 'VARIABLE_OF')
  56     WHERE subject_id IN (SELECT cvterm_id FROM cvterm WHERE name LIKE '%|%');
  57
  58 EOSQL
  59
  60 print "You're done!\n";``
  61 }
  62
  63
  64 ####
  65 1; #
  66 ####