db/00032/AddTrialTypes.pm

   1 #!/usr/bin/env perl
   2
   3
   4 =head1 NAME
   5
   6  AddTrialTypes.pm
   7
   8 =head1 SYNOPSIS
   9
  10 mx-run AddTrialTypes [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 patch adds a cv for trial types.
  18 This subclass uses L<Moose>. The parent class uses L<MooseX::Runnable>
  19
  20 =head1 AUTHOR
  21
  22   Jeremy D. Edwards <jde22@cornell.edu>
  23   Naama Menda <nm249@cornell.edu>
  24
  25 =head1 COPYRIGHT & LICENSE
  26
  27 Copyright 2010 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 AddTrialTypes;
  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         [ ],
  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 --do your SQL here
  61 --
  62
  63 INSERT INTO cv (name, definition) VALUES ('trial type', '');
  64
  65 EOSQL
  66
  67     print STDERR "INSERTING CV TERMS...\n";
  68
  69     my @terms = qw | phenotyping_trial genotyping_trial crossing_trial  | ;
  70
  71     foreach my $t (@terms) {
  72
  73         $self->dbh->do(<<EOSQL);
  74 INSERT INTO dbxref (db_id, accession) VALUES ((SELECT db_id FROM db WHERE name='local'), '$t');
  75
  76 INSERT INTO cvterm (cv_id, name, definition, dbxref_id) VALUES ( (SELECT cv_id FROM cv where name='trial type' ), '$t', '$t', (SELECT dbxref_id FROM dbxref WHERE accession='$t'));
  77
  78
  79 EOSQL
  80
  81 }
  82
  83 print "Done!\n";
  84
  85 }
  86
  87 ####
  88 1; #
  89 ####