db/00104/UpdateProgenyOffspringOfRelationship.pm

   1 #!/usr/bin/env perl
   2
   3
   4 =head1 NAME
   5
   6  UpdateProgenyOffspringOfRelationship
   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 update relationship or cross stock to its progeny from member_of, which is used for populations, to offspring_of
  18
  19 This subclass uses L<Moose>. The parent class uses L<MooseX::Runnable>
  20
  21 =head1 AUTHOR
  22
  23  Naama Menda<nm249@cornell.edu>
  24
  25 =head1 COPYRIGHT & LICENSE
  26
  27 Copyright 2018 Boyce Thompson Institute for Plant Research
  28
  29 This program is free software; you can redistribute it and/or modify
  30 it under the same terms as Perl itself.
  31
  32 =cut
  33
  34
  35 package UpdateProgenyOffspringOfRelationship;
  36
  37 use Moose;
  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         ['AddSystemCvterms'],
  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
  59     $self->dbh->do(<<EOSQL);
  60
  61 UPDATE stock_relationship
  62 SET type_id = (SELECT cvterm_id FROM cvterm where cvterm.name = 'offspring_of' AND cv_id = (SELECT cv_id FROM cv WHERE name = 'stock_relationship'))
  63 WHERE object_id IN (SELECT stock_id FROM stock WHERE type_id = (SELECT cvterm_id FROM cvterm WHERE name = 'cross' AND cv_id = (SELECT cv_id FROM cv WHERE name = 'stock_type')))
  64 AND type_id = (SELECT cvterm_id FROM cvterm WHERE name = 'member_of' AND cv_id = (SELECT cv_id FROM cv WHERE name = 'stock_relationship'));
  65
  66 EOSQL
  67
  68 print "You're done!\n";
  69 }
  70
  71
  72 ####
  73 1; #
  74 ####