db/00020/CreatePhenProp.pm

   1 #!/usr/bin/env perl
   2
   3
   4 =head1 NAME
   5
   6 CreatePhenProp.pm
   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 Create new phenotypeprop table nad grant web_usr permission
  18 This subclass uses L<Moose>. The parent class uses L<MooseX::Runnable>
  19
  20 =head1 AUTHOR
  21
  22  Naama Menda<nm249@cornell.edu>
  23
  24 =head1 COPYRIGHT & LICENSE
  25
  26 Copyright 2011 Boyce Thompson Institute for Plant Research
  27
  28 This program is free software; you can redistribute it and/or modify
  29 it under the same terms as Perl itself.
  30
  31 =cut
  32
  33
  34 package CreatePhenProp;
  35
  36 use Moose;
  37 extends 'CXGN::Metadata::Dbpatch';
  38
  39
  40 has '+description' => ( default => <<'' );
  41 Create new phenotypeprop table nad grant web_usr permission
  42
  43
  44 sub patch {
  45     my $self=shift;
  46
  47     print STDOUT "Executing the patch:\n " .   $self->name . ".\n\nDescription:\n  ".  $self->description . ".\n\nExecuted by:\n " .  $self->username . " .";
  48
  49     print STDOUT "\nChecking if this db_patch was executed before or if previous db_patches have been executed.\n";
  50
  51     print STDOUT "\nExecuting the SQL commands.\n";
  52
  53     $self->dbh->do(<<EOSQL);
  54
  55     set search_path to public;
  56 create table phenotypeprop (
  57        phenotypeprop_id serial not null,
  58        primary key (phenotypeprop_id),
  59        phenotype_id int not null,
  60        foreign key (phenotype_id) references phenotype (phenotype_id) on delete cascade INITIALLY DEFERRED,
  61        type_id int not null,
  62        foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED,
  63        value text null,
  64        rank int not null default 0,
  65        constraint phenotypeprop_c1 unique (phenotype_id,type_id,rank)
  66 );
  67 create index phenotypeprop_idx1 on phenotypeprop (phenotype_id);
  68 create index phenotypeprop_idx2 on phenotypeprop (type_id);
  69
  70 COMMENT ON TABLE phenotypeprop IS 'A phenotype can have any number of
  71 slot-value property tags attached to it. This is an alternative to
  72 hardcoding a list of columns in the relational schema, and is
  73 completely extensible. There is a unique constraint, phenotypeprop_c1, for
  74 the combination of phenotype_id, rank, and type_id. Multivalued property-value pairs must be differentiated by rank.';
  75
  76
  77 GRANT all ON phenotypeprop TO web_usr;
  78 GRANT usage ON phenotypeprop_phenotypeprop_id_seq TO web_usr;
  79
  80 EOSQL
  81
  82 print "You're done!\n";
  83 }
  84
  85
  86 ####
  87 1; #
  88 ####