db/00083/UpdateGeolocationCvName.pm

   1 #!/usr/bin/env perl
   2
   3
   4 =head1 NAME
   5
   6  UpdateGeolocationCvName.pm
   7
   8 =head1 SYNOPSIS
   9
  10 mx-run UpdateGeolocationCvName [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 geolocation property cvname to the chado default of 'geolocations_property'
  17 This subclass uses L<Moose>. The parent class uses L<MooseX::Runnable>
  18
  19 =head1 AUTHOR
  20
  21 Bryan Ellerbrock
  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 UpdateGeolocationCvName;
  34
  35 use Moose;
  36 use Bio::Chado::Schema;
  37 use Try::Tiny;
  38 extends 'CXGN::Metadata::Dbpatch';
  39
  40
  41 has '+description' => ( default => <<'' );
  42 Description of this patch goes here
  43
  44 has '+prereq' => (
  45         default => sub {
  46         [],
  47     },
  48
  49   );
  50
  51 sub patch {
  52     my $self=shift;
  53
  54     print STDOUT "Executing the patch:\n " .   $self->name . ".\n\nDescription:\n  ".  $self->description . ".\n\nExecuted by:\n " .  $self->username . " .";
  55
  56     print STDOUT "\nChecking if this db_patch was executed before or if previous db_patches have been executed.\n";
  57
  58     print STDOUT "\nExecuting the SQL commands.\n";
  59
  60     my $schema = Bio::Chado::Schema->connect( sub { $self->dbh->clone } );
  61
  62     my $plural_row = $schema->resultset("Cv::Cv")->find( { name => 'geolocations_property' } );
  63     my $singular_row = $schema->resultset("Cv::Cv")->find( { name => 'geolocation_property' } );
  64
  65     if (defined $plural_row && defined $singular_row) {
  66         my $old_id = $plural_row->cv_id();
  67         my $new_id = $singular_row->cv_id();
  68         my $rows_to_update = $schema->resultset("Cv::Cvterm")->search( { cv_id => $old_id } );
  69         foreach my $row ($rows_to_update->all()) {
  70             $row->cv_id($new_id);
  71             $row->update();
  72         }
  73         $plural_row->delete();
  74     }
  75     elsif (defined $plural_row) {
  76         print STDOUT "Fixing cv name...\n";
  77         $plural_row->name('geolocation_property');
  78         $plural_row->update();
  79     }
  80     elsif (defined $singular_row) {
  81         print STDOUT "Cv name is already correct, no changes necessary.\n";
  82     }
  83     else {
  84         print STDOUT "No geolocation property cv found. Run patch 00076/AddBrAPIPropertyCvterms.pm to add geolocation props.\n";
  85     }
  86
  87     print "You're done!\n";
  88 }
  89
  90
  91 ####
  92 1; #
  93 ####