db/00141/AddVcfType.pm

   1 #!/usr/bin/env perl
   2
   3
   4 =head1 NAME
   5
   6  AddVcfType.pm
   7
   8 =head1 SYNOPSIS
   9
  10 mx-run ThisPackageName [options] -H hostname -D dbname -u username [-F]
  11
  12 This patch add new cvterm vcf_snp_dbxref to nd_protocol
  13
  14 =head1 DESCRIPTION
  15
  16 This dbpatch adds vcf_snp_dbxref to nd_protocol and nd_protocolprop to provide external links to marker_names
  17
  18
  19 =head1 AUTHOR
  20
  21  Clay Birkett<clb343@cornell.edu>
  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 AddVcfType;
  34
  35 use Moose;
  36 use Bio::Chado::Schema;
  37 use Try::Tiny;
  38 extends 'CXGN::Metadata::Dbpatch';
  39
  40 has '+description' => ( default => <<'' );
  41 This patch add new cvterm vcf_snp_dbxref to nd_protocol
  42
  43 has '+prereq' => (
  44     default => sub {
  45         [],
  46     },
  47   );
  48
  49 sub patch {
  50     my $self=shift;
  51
  52     print STDOUT "Executing the patch:\n " .   $self->name . ".\n\nDescription:\n  ".  $self->description . ".\n\nExecuted by:\n " .  $self->username . " .";
  53
  54     print STDOUT "\nChecking if this db_patch was executed before or if previous db_patches have been executed.\n";
  55
  56     print STDOUT "\nExecuting the SQL commands.\n";
  57
  58     my $schema = Bio::Chado::Schema->connect( sub { $self->dbh->clone } );
  59
  60         my $term = 'vcf_snp_dbxref';
  61
  62         $schema->resultset("Cv::Cvterm")->create_with( {
  63                 name => $term,
  64                 cv => 'protocol_property', }
  65                 );
  66
  67
  68 print "You're done!\n";
  69 }
  70
  71
  72 ####
  73 1; #
  74 ####