db/00061/RedefineTraitsView.pm

   1 #!/usr/bin/env perl
   2
   3
   4 =head1 NAME
   5
   6 RedefineTraitsView.pm
   7
   8 =head1 SYNOPSIS
   9
  10 mx-run RedefineTraitsView [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 updates the materialized view that stores traits
  18
  19 =head1 AUTHOR
  20
  21 Bryan Ellerbrock<bje24@cornell.edu>
  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 RedefineTraitsView;
  34
  35 use Moose;
  36 extends 'CXGN::Metadata::Dbpatch';
  37
  38
  39 has '+description' => ( default => <<'' );
  40 This patch updates the materialized view that stores traits
  41
  42 sub patch {
  43     my $self=shift;
  44
  45     print STDOUT "Executing the patch:\n " .   $self->name . ".\n\nDescription:\n  ".  $self->description . ".\n\nExecuted by:\n " .  $self->username . " .";
  46
  47     print STDOUT "\nChecking if this db_patch was executed before or if previous db_patches have been executed.\n";
  48
  49     print STDOUT "\nExecuting the SQL commands.\n";
  50
  51     $self->dbh->do(<<EOSQL);
  52 --do your SQL here
  53
  54 DROP MATERIALIZED VIEW public.traits;
  55
  56 CREATE MATERIALIZED VIEW public.traits AS
  57 SELECT   cvterm.cvterm_id AS trait_id,
  58   (((cvterm.name::text || '|'::text) || db.name::text) || ':'::text) || dbxref.accession::text AS trait_name
  59   FROM cvterm
  60   JOIN dbxref ON cvterm.dbxref_id = dbxref.dbxref_id
  61   JOIN db ON dbxref.db_id = db.db_id
  62   WHERE cvterm.cvterm_id IN (SELECT cvterm_relationship.subject_id FROM cvterm_relationship JOIN cvterm on (cvterm_relationship.subject_id = cvterm.cvterm_id) where cvterm_relationship.type_id = (SELECT cvterm_id from cvterm where name = 'VARIABLE_OF') GROUP BY 1)
  63   AND db.db_id =
  64 (SELECT dbxref.db_id
  65    FROM stock
  66    JOIN nd_experiment_stock USING(stock_id)
  67    JOIN nd_experiment_phenotype USING(nd_experiment_id)
  68    JOIN phenotype USING(phenotype_id)
  69    JOIN cvterm ON phenotype.cvalue_id = cvterm.cvterm_id
  70    JOIN dbxref ON cvterm.dbxref_id = dbxref.dbxref_id LIMIT 1)
  71    GROUP BY public.cvterm.cvterm_id, trait_name
  72 WITH DATA;
  73 CREATE UNIQUE INDEX traits_idx ON public.traits(trait_id) WITH (fillfactor=100);
  74 ALTER MATERIALIZED VIEW traits OWNER TO web_usr;
  75
  76 --
  77
  78 EOSQL
  79
  80 print "You're done!\n";
  81 }
  82
  83
  84 ####
  85 1; #
  86 ####