db/00065/RedefineStockViews.pm

   1 #!/usr/bin/env perl
   2
   3
   4 =head1 NAME
   5
   6 RedefineStockViews.pm
   7
   8 =head1 SYNOPSIS
   9
  10 mx-run RedefineStockViews [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 views that store stocks (accessions, plots, plants) to exclude obsolete stocks
  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 RedefineStockViews;
  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.accessions;
  55
  56 CREATE MATERIALIZED VIEW public.accessions AS
  57   SELECT stock.stock_id AS accession_id,
  58   stock.uniquename AS accession_name
  59   FROM stock
  60   WHERE stock.type_id = (SELECT cvterm_id from cvterm where cvterm.name = 'accession') AND is_obsolete = 'f'
  61   GROUP BY stock.stock_id, stock.uniquename
  62   WITH DATA;
  63 CREATE UNIQUE INDEX accessions_idx ON public.accessions(accession_id) WITH (fillfactor=100);
  64 ALTER MATERIALIZED VIEW accessions OWNER TO web_usr;
  65
  66 DROP MATERIALIZED VIEW public.plots;
  67
  68 CREATE MATERIALIZED VIEW public.plots AS
  69 SELECT stock.stock_id AS plot_id,
  70     stock.uniquename AS plot_name
  71    FROM stock
  72    WHERE stock.type_id = (SELECT cvterm_id from cvterm where cvterm.name = 'plot') AND is_obsolete = 'f'
  73   GROUP BY public.stock.stock_id, public.stock.uniquename
  74 WITH DATA;
  75 CREATE UNIQUE INDEX plots_idx ON public.plots(plot_id) WITH (fillfactor=100);
  76 ALTER MATERIALIZED VIEW plots OWNER TO web_usr;
  77
  78 DROP MATERIALIZED VIEW public.plants;
  79
  80 CREATE MATERIALIZED VIEW public.plants AS
  81 SELECT stock.stock_id AS plant_id,
  82     stock.uniquename AS plant_name
  83    FROM stock
  84    WHERE stock.type_id = (SELECT cvterm_id from cvterm where cvterm.name = 'plant') AND is_obsolete = 'f'
  85   GROUP BY public.stock.stock_id, public.stock.uniquename
  86 WITH DATA;
  87 CREATE UNIQUE INDEX plants_idx ON public.plants(plant_id) WITH (fillfactor=100);
  88 ALTER MATERIALIZED VIEW plants OWNER TO web_usr;
  89
  90 --
  91
  92 EOSQL
  93
  94 print "You're done!\n";
  95 }
  96
  97
  98 ####
  99 1; #
 100 ####