db/00155/FixOutOfSyncNdGeolocations.pm

   1 #!/usr/bin/env perl
   2
   3
   4 =head1 NAME
   5
   6 FixOutOfSyncNdGeolocations
   7
   8 =head1 SYNOPSIS
   9
  10 mx-run FixOutOfSyncNdGeolocations [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 This patch updates nd_experiment.nd_geolocation_ids that are out of sync with the location specified in linked projectprop.values
  17 This subclass uses L<Moose>. The parent class uses L<MooseX::Runnable>
  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 FixOutOfSyncNdGeolocations;
  34
  35 use Moose;
  36 use Bio::Chado::Schema;
  37 use Try::Tiny;
  38 use SGN::Model::Cvterm;
  39 use JSON;
  40 use Data::Dumper;
  41
  42 extends 'CXGN::Metadata::Dbpatch';
  43
  44
  45 has '+description' => ( default => <<'' );
  46 This patch updates nd_experiment.nd_geolocation_ids that are out of sync with the location specified in linked projectprop.values
  47
  48 has '+prereq' => (
  49         default => sub {
  50         [],
  51     },
  52
  53   );
  54
  55 sub patch {
  56     my $self=shift;
  57
  58     print STDOUT "Executing the patch:\n " .   $self->name . ".\n\nDescription:\n  ".  $self->description . ".\n\nExecuted by:\n " .  $self->username . " .";
  59
  60     print STDOUT "\nChecking if this db_patch was executed before or if previous db_patches have been executed.\n";
  61
  62     print STDOUT "\nExecuting the SQL commands.\n";
  63
  64     my $schema = Bio::Chado::Schema->connect( sub { $self->dbh->clone } );
  65     my $project_location_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'project location', 'project_property')->cvterm_id();
  66
  67     my $query = "UPDATE nd_experiment
  68         SET nd_geolocation_id = projectprop.value::int
  69         FROM nd_experiment_project
  70         JOIN projectprop ON(
  71             nd_experiment_project.project_id = projectprop.project_id AND
  72             projectprop.type_id = ?
  73         )
  74         WHERE nd_experiment_project.nd_experiment_id = nd_experiment.nd_experiment_id
  75         AND nd_experiment_project.nd_experiment_id IN (
  76             SELECT ne.nd_experiment_id
  77             FROM nd_experiment_project nep
  78             JOIN nd_experiment ne USING(nd_experiment_id)
  79             EXCEPT
  80             SELECT ne.nd_experiment_id
  81             FROM project p
  82             JOIN projectprop pp ON(
  83                 p.project_id=pp.project_id AND
  84                 pp.type_id = (
  85                     SELECT cvterm_id FROM cvterm WHERE name = 'project location'
  86                 )
  87             )
  88             JOIN nd_experiment_project nep ON(p.project_id = nep.project_id)
  89             JOIN nd_experiment ne ON(
  90                 nep.nd_experiment_id = ne.nd_experiment_id AND
  91                 ne.nd_geolocation_id = pp.value::int
  92             )
  93             JOIN cvterm c ON(ne.type_id=c.cvterm_id)
  94         );";
  95
  96     # print STDERR Dumper $q;
  97     my $h = $schema->storage->dbh()->prepare($query);
  98     $h->execute($project_location_id);
  99
 100     print "You're done!\n";
 101 }
 102
 103
 104 ####
 105 1; #
 106 ####