db/00051/UnderlineExpCvterms.pm

   1 #!/usr/bin/env perl
   2
   3
   4 =head1 NAME
   5
   6  UnderlineExpCvterms.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
  17 This path adds underline to breeder toolbox cv names that are used with a space in their name instead of an underline. This patch goes along with code updates since some cv names are (were)  hardcoded
  18 This subclass uses L<Moose>. The parent class uses L<MooseX::Runnable>
  19
  20 =head1 AUTHOR
  21
  22  Naama Menda<nm249@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 UnderlineExpCvterms;
  35
  36 use Moose;
  37 extends 'CXGN::Metadata::Dbpatch';
  38
  39
  40 has '+description' => ( default => <<'' );
  41 This patch will add underline to the cvterm names with experiment_type cv
  42 field_layout
  43 phenotyping_experiment
  44 genotyping_layout
  45 genotyping_experiment
  46 this is important for making CVterms uniform and less room for errors when using these
  47
  48 has '+prereq' => (
  49     default => sub {
  50         [],
  51     },
  52   );
  53
  54 sub patch {
  55     my $self=shift;
  56
  57     print STDOUT "Executing the patch:\n " .   $self->name . ".\n\nDescription:\n  ".  $self->description . ".\n\nExecuted by:\n " .  $self->username . " .";
  58
  59     print STDOUT "\nChecking if this db_patch was executed before or if previous db_patches have been executed.\n";
  60
  61     print STDOUT "\nExecuting the SQL commands.\n";
  62
  63     $self->dbh->do(<<EOSQL);
  64 --do your SQL here
  65 --
  66 UPDATE cvterm SET name = 'field_layout' WHERE name = 'field layout';
  67 UPDATE cvterm SET name = 'genotyping_experiment' WHERE name = 'genotyping experiment';
  68 UPDATE cvterm SET name = 'genotyping_layout' WHERE name = 'genotyping layout';
  69 UPDATE cvterm SET name = 'phenotyping_experiment' WHERE name = 'phenotyping experiment';
  70
  71 EOSQL
  72
  73 print "You're done!\n";
  74 }
  75
  76
  77 ####
  78 1; #
  79 ####