db/00144/FixFieldbookImageCvterm.pm

   1 #!/usr/bin/env perl
   2
   3
   4 =head1 NAME
   5
   6 FixFieldbookImageCvterm
   7
   8 =head1 SYNOPSIS
   9
  10 mx-run FixFieldbookImageCvterm [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 fixes the fieldbook_image cvterm from showing up in the trait search as an ontology. This term was missing the upper link to its ontology.
  17
  18 Since this cvterm needs to be linked to an internal ontology instead of a crop ontology it is now removed from the database
  19
  20 This subclass uses L<Moose>. The parent class uses L<MooseX::Runnable>
  21
  22 =head1 AUTHOR
  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 FixFieldbookImageCvterm;
  35
  36 use Moose;
  37 use Bio::Chado::Schema;
  38 use Try::Tiny;
  39 use SGN::Model::Cvterm;
  40 extends 'CXGN::Metadata::Dbpatch';
  41
  42
  43 has '+description' => ( default => <<'' );
  44 This patch used to fix the fieldbook_image cvterm from showing up in the trait search as an ontology. This term was missing the upper link to its ontology.
  45 Now it does nothing because it should not be linked to a crop ontology cv. A future patch will remove it from databases that ran the old version of this patch
  46 has '+prereq' => (
  47         default => sub {
  48         [],
  49     },
  50
  51
  52 sub patch {
  53     my $self=shift;
  54
  55     print STDOUT "Executing the patch:\n " .   $self->name . ".\n\nDescription:\n  ".  $self->description . ".\n\nExecuted by:\n " .  $self->username . " .";
  56
  57     print STDOUT "\nChecking if this db_patch was executed before or if previous db_patches have been executed.\n";
  58
  59     print STDOUT "\nExecuting the SQL commands.\n";
  60     my $schema = Bio::Chado::Schema->connect( sub { $self->dbh->clone } );
  61
  62     print STDERR "Doing nothing ...\n";
  63
  64
  65     print "You're done!\n";
  66 }
  67
  68
  69 ####
  70 1; #
  71 ####