db/00073/AddComposedTraitCv.pm

   1 #!/usr/bin/env perl
   2
   3
   4 =head1 NAME
   5
   6 AddComposedTraitCv
   7
   8 =head1 SYNOPSIS
   9
  10 mx-run AddComposedTraitCv [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 Adds a composed trait cv with namespace COMP to allow composition of traits
  18 This subclass uses L<Moose>. The parent class uses L<MooseX::Runnable>
  19
  20 =head1 AUTHOR
  21
  22 Bryan Ellerbrock<bje24@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 AddComposedTraitCv;
  35
  36 use Moose;
  37 extends 'CXGN::Metadata::Dbpatch';
  38
  39
  40 has '+description' => ( default => <<'' );
  41 Adds a composed trait cv with namespace COMP to allow composition of traits
  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 --do your SQL here
  55
  56
  57 -- add cv and db for composed traits
  58
  59 INSERT into db (name) values ('COMP');
  60 CREATE SEQUENCE composed_trait_ids;
  61 ALTER SEQUENCE composed_trait_ids OWNER TO web_usr;
  62 GRANT ALL ON cvterm_relationship to web_usr;
  63 GRANT ALL ON cvterm_relationship_cvterm_relationship_id_seq to web_usr;
  64 GRANT ALL ON cvtermsynonym to web_usr;
  65 GRANT ALL ON cvtermsynonym_cvtermsynonym_id_seq to web_usr;
  66 INSERT into cv (name) values ('composed_trait');
  67 INSERT into dbxref (db_id, accession) select db_id, nextval('composed_trait_ids') from db where name = 'COMP';
  68 INSERT into cvterm (cv_id,name,dbxref_id) select cv_id, 'Composed traits', dbxref_id from cv join db on true AND db.name = 'COMP' join dbxref using(db_id) where cv.name = 'composed_trait';
  69
  70 EOSQL
  71
  72 print "You're done!\n";
  73 }
  74
  75
  76 ####
  77 1; #
  78 ####