db/00170/AddNdGeolocationDbXref.pm

   1 #!/usr/bin/env perl
   2
   3
   4 =head1 NAME
   5
   6 AddNdGeolocationDbXref.pm
   7
   8 =head1 SYNOPSIS
   9
  10 mx-run AddNdGeolocationDbXref [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 creates a nd_geolocation_dbxref table to allow projects to store external references for brapi
  18
  19 =head1 AUTHOR
  20
  21 Chris Tucker
  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 AddNdGeolocationDbXref;
  34
  35 use Moose;
  36 use Try::Tiny;
  37 use Bio::Chado::Schema;
  38
  39 extends 'CXGN::Metadata::Dbpatch';
  40
  41
  42 has '+description' => ( default => <<'' );
  43 This patch creates a nd_geolocation_dbxref table to allow projects to store external references for brapi
  44
  45
  46 sub patch {
  47     my $self=shift;
  48
  49     print STDOUT "Executing the patch:\n " .   $self->name . ".\n\nDescription:\n  ".  $self->description . ".\n\nExecuted by:\n " .  $self->username . " .";
  50
  51     print STDOUT "\nChecking if this db_patch was executed before or if previous db_patches have been executed.\n";
  52
  53     print STDOUT "\nExecuting the SQL commands.\n";
  54     my $schema = Bio::Chado::Schema->connect( sub { $self->dbh->clone } );
  55
  56     my $coderef = sub {
  57         $self->dbh->do(<<EOSQL);
  58
  59  --do your SQL here
  60 CREATE TABLE IF NOT EXISTS public.nd_geolocation_dbxref (
  61         nd_geolocation_dbxref_id serial NOT NULL PRIMARY KEY,
  62         nd_geolocation_id int4 NOT NULL REFERENCES nd_geolocation(nd_geolocation_id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED,
  63         dbxref_id int4 REFERENCES dbxref(dbxref_id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED,
  64         is_current bool NOT NULL DEFAULT true
  65 );
  66 EOSQL
  67
  68         return 1;
  69     };
  70
  71     try {
  72         $schema->txn_do($coderef);
  73     } catch {
  74         die "Load failed! " . $_ .  "\n" ;
  75     };
  76     print "You're done!\n";
  77 }
  78
  79
  80 ####
  81 1; #
  82 ####