db/00151/RemoveFieldbookImageCvterm.pm

   1 #!/usr/bin/env perl
   2
   3
   4 =head1 NAME
   5
   6 RemoveFieldbookImageCvterm
   7
   8 =head1 SYNOPSIS
   9
  10 mx-run RemoveFieldbookImageCvterm [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 removes the fieldbook_image cvterm from the cassavs_trait ontology. This term is not used by the Fieldbook App, and if it is needed in the future should be linked to stock_prop or a "local" cv.
  17 This subclass uses L<Moose>. The parent class uses L<MooseX::Runnable>
  18
  19 =head1 AUTHOR
  20
  21 =head1 COPYRIGHT & LICENSE
  22
  23 Copyright 2010 Boyce Thompson Institute for Plant Research
  24
  25 This program is free software; you can redistribute it and/or modify
  26 it under the same terms as Perl itself.
  27
  28 =cut
  29
  30
  31 package RemoveFieldbookImageCvterm;
  32
  33 use Moose;
  34 use Bio::Chado::Schema;
  35 use Try::Tiny;
  36 use SGN::Model::Cvterm;
  37 extends 'CXGN::Metadata::Dbpatch';
  38
  39
  40 has '+description' => ( default => <<'' );
  41 This patch removes the fieldbook_image cvterm from the ontology.
  42
  43 has '+prereq' => (
  44         default => sub {
  45         [],
  46     },
  47
  48 );
  49
  50 sub patch {
  51     my $self=shift;
  52
  53     print STDOUT "Executing the patch:\n " .   $self->name . ".\n\nDescription:\n  ".  $self->description . ".\n\nExecuted by:\n " .  $self->username . " .";
  54
  55     print STDOUT "\nChecking if this db_patch was executed before or if previous db_patches have been executed.\n";
  56
  57     print STDOUT "\nExecuting the SQL commands.\n";
  58     my $schema = Bio::Chado::Schema->connect( sub { $self->dbh->clone } );
  59
  60     print STDERR "Removing CVTERM fieldbook_image...\n";
  61
  62     my $coderef = sub {
  63
  64
  65         my $subject_id;
  66         my $subject = SGN::Model::Cvterm->get_cvterm_row($schema, 'fieldbook_image', 'cassava_trait');
  67         if ($subject) {
  68             $subject_id = $subject->cvterm_id ;
  69         } else {
  70             print STDERR "Cvterm fieldbook_image does not exist in the database. Exiting\n";
  71             return 0;
  72         }
  73
  74          #my $object_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'CGIAR cassava trait ontology', 'cassava_trait')->cvterm_id();
  75         my $cvterm_relationship_rs = $schema->resultset("Cv::CvtermRelationship")->search( { subject_id => $subject_id });
  76         $cvterm_relationship_rs->delete();
  77
  78         my $cvterm = $schema->resultset( "Cv::Cvterm" )->find({ cvterm_id  => $subject_id  });
  79         $cvterm->delete();
  80
  81     };
  82
  83     try {
  84         $schema->txn_do($coderef);
  85     } catch {
  86         die "Load failed! " . $_ .  "\n" ;
  87     };
  88
  89     print "You're done!\n";
  90 }
  91
  92
  93 ####
  94 1; #
  95 ####