db/00139/CreateFeaturepropJSONTable.pm

   1 #!/usr/bin/env perl
   2
   3
   4 =head1 NAME
   5
   6     CreateFeaturepropJSONTable.pm
   7
   8 =head1 SYNOPSIS
   9
  10 mx-run CreateFeaturepropJSONTable [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 the featureprop_json table used for storing sequence metadata as JSON objects
  18 This subclass uses L<Moose>. The parent class uses L<MooseX::Runnable>
  19
  20 =head1 AUTHOR
  21
  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 CreateFeaturepropJSONTable;
  34
  35 use Moose;
  36
  37 extends 'CXGN::Metadata::Dbpatch';
  38
  39 has '+description' => ( default => <<'');
  40 This patch creates the featureprop_json table used for storing sequence metadata as JSON objects
  41
  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
  59
  60     $self->dbh->do(<<EOSQL);
  61
  62 -- table definition
  63 CREATE TABLE IF NOT EXISTS public.featureprop_json (
  64     "featureprop_json_id" SERIAL PRIMARY KEY,
  65     "feature_id" int8 REFERENCES feature,
  66     "type_id" int8 REFERENCES cvterm,
  67     "nd_protocol_id" int8 REFERENCES nd_protocol,
  68     "start_pos" int8,
  69     "end_pos" int8,
  70     "json" jsonb
  71 );
  72
  73 -- add indices
  74 CREATE INDEX feaureprop_json_idx1 ON featureprop_json(feature_id);
  75 CREATE INDEX feaureprop_json_idx2 ON featureprop_json(type_id);
  76 CREATE INDEX feaureprop_json_idx3 ON featureprop_json(nd_protocol_id);
  77 CREATE INDEX feaureprop_json_idx4 ON featureprop_json(start_pos);
  78 CREATE INDEX feaureprop_json_idx5 ON featureprop_json(end_pos);
  79
  80 -- grant usage to web_usr
  81 GRANT ALL on public.featureprop_json to web_usr;
  82 GRANT USAGE ON public.featureprop_json_featureprop_json_id_seq to web_usr;
  83
  84 EOSQL
  85
  86 print "You're done!\n";
  87 }
  88
  89
  90 ####
  91 1; #
  92 ####