db/00174/AddListDbXref.pm

   1 #!/usr/bin/env perl
   2
   3
   4 =head1 NAME
   5
   6 AddListDbXref.pm
   7
   8 =head1 SYNOPSIS
   9
  10 mx-run AddListDbXref [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 list_dbxref table to allow lists 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 AddListDbXref;
  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 list_dbxref table to allow lists 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 alter table sgn_people.list add constraint list_id_unique unique(list_id);
  61 CREATE TABLE sgn_people.list_dbxref (
  62         list_dbxref_id serial4 NOT null PRIMARY KEY,
  63         list_id int4 NOT NULL REFERENCES sgn_people.list(list_id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED,
  64         dbxref_id int4 NOT NULL REFERENCES public.dbxref(dbxref_id) ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED,
  65         is_current bool NOT NULL DEFAULT true,
  66         CONSTRAINT list_dbxref_c1 UNIQUE (list_id, dbxref_id)
  67 );
  68 CREATE INDEX IF NOT EXISTS list_dbxref_idx1 ON sgn_people.list_dbxref USING btree (list_id);
  69 CREATE INDEX IF NOT EXISTS list_dbxref_idx2 ON sgn_people.list_dbxref USING btree (dbxref_id);
  70 EOSQL
  71
  72         return 1;
  73     };
  74
  75     try {
  76         $schema->txn_do($coderef);
  77     } catch {
  78         die "Load failed! " . $_ .  "\n" ;
  79     };
  80     print "You're done!\n";
  81 }
  82
  83
  84 ####
  85 1; #
  86 ####