db/00106/AddMissingProgramPropsToLocations.pm

   1 #!/usr/bin/env perl
   2
   3
   4 =head1 NAME
   5
   6  AddMissingProgramPropsToLocations.pm
   7
   8 =head1 SYNOPSIS
   9
  10 mx-run ThisPackageName [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 finds locations that are missing a program prop, and adds the correct program if it can be inferred based on the trials that have been held at the location.
  17 This subclass uses L<Moose>. The parent class uses L<MooseX::Runnable>
  18
  19 =head1 AUTHOR
  20
  21 Bryan Ellerbrock
  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  AddMissingProgramPropsToLocations;
  34
  35 use Moose;
  36 use Bio::Chado::Schema;
  37 use SGN::Model::Cvterm;
  38 use Try::Tiny;
  39 extends 'CXGN::Metadata::Dbpatch';
  40
  41
  42 has '+description' => ( default => <<'' );
  43 This patch finds locations that are missing a program prop, and adds the correct program if it can be inferred based on the trials that have been held at the location.
  44
  45 has '+prereq' => (
  46         default => sub {
  47         [],
  48     },
  49
  50   );
  51
  52 sub patch {
  53     my $self=shift;
  54
  55     print STDOUT "Executing the patch:\n " .   $self->name . ".\n\nDescription:\n  ".  $self->description . ".\n\nExecuted by:\n " .  $self->username . " .";
  56
  57     print STDOUT "\nChecking if this db_patch was executed before or if previous db_patches have been executed.\n";
  58
  59     print STDOUT "\nExecuting the SQL commands.\n";
  60
  61     my $schema = Bio::Chado::Schema->connect( sub { $self->dbh->clone } );
  62
  63     my $coderef = sub {
  64         print STDERR "Updating location breeding programs . . .\n";
  65
  66         my $query = "SELECT nd_geolocation.nd_geolocation_id, project.project_id, nd_geolocation.description, project.name
  67         FROM nd_geolocation
  68         JOIN nd_experiment using(nd_geolocation_id)
  69         JOIN nd_experiment_project using(nd_experiment_id)
  70         JOIN project_relationship on (nd_experiment_project.project_id = subject_project_id and project_relationship.type_id = (select cvterm_id from cvterm where name = 'breeding_program_trial_relationship'))
  71         JOIN project on (project_relationship.object_project_id = project.project_id)
  72         GROUP by 1,2,3,4";
  73
  74         my $h = $schema->storage->dbh->prepare($query);
  75         $h->execute();
  76
  77         my $breeding_program_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'breeding_program', 'project_property')->cvterm_id();
  78         my @locations;
  79         while (my ($location_id, $program_id, $location_name, $program_name) = $h->fetchrow_array()) {
  80             print STDERR "Trials from $program_name have been held at location $location_name. Checking to see if these are already linked through nd_geolocationprop\n";
  81             my $location = $schema->resultset("NaturalDiversity::NdGeolocation")->find( { nd_geolocation_id => $location_id });
  82             my $rs = $schema->resultset("NaturalDiversity::NdGeolocationprop")->search({ nd_geolocation_id=> $location_id, value => $program_id, type_id => $breeding_program_cvterm_id });
  83
  84             if($rs->next()) {
  85                 #skip, this program - location link is already stored in nd_geolocationprop
  86             } else {
  87                 print STDERR "No prop found, linking $program_name to $location_name in nd_geolocationprop\n";
  88                 my $count = $schema->resultset("NaturalDiversity::NdGeolocationprop")->search({ nd_geolocation_id=> $location_id, type_id => $breeding_program_cvterm_id })->count();
  89                 my $stored_location = $location->create_geolocationprops({ 'breeding_program' => $program_id }, {cv_name => 'project_property', rank => $count });
  90             }
  91         }
  92     };
  93
  94     try {
  95       $schema->txn_do($coderef);
  96     } catch {
  97       die " patch failed! " . $_ .  "\n" ;
  98     };
  99
 100     print "You're done!\n";
 101
 102   }
 103
 104
 105 ####
 106 1; #
 107 ####