db/00115/UpdateStoredNdProtocolpropGenotypeStorageCvterms.pm

   1 #!/usr/bin/env perl
   2
   3
   4 =head1 NAME
   5
   6  UpdateStoredNdProtocolpropGenotypeStorageCvterms
   7
   8 =head1 SYNOPSIS
   9
  10 mx-run UpdateStoredNdProtocolpropGenotypeStorageCvterms [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 converts the old single nd_protocolprop storage into the new three value nd_protocolprop genotype storage: one for each of the cvterms: vcf_map_details, vcf_map_details_markers, vcf_map_details_markers_array
  17 This subclass uses L<Moose>. The parent class uses L<MooseX::Runnable>
  18
  19 =head1 AUTHOR
  20
  21
  22 =head1 COPYRIGHT & LICENSE
  23
  24 Copyright 2010 Boyce Thompson Institute for Plant Research
  25
  26 This program is free software; you can redistribute it and/or modify
  27 it under the same terms as Perl itself.
  28
  29 =cut
  30
  31
  32 package UpdateStoredNdProtocolpropGenotypeStorageCvterms;
  33
  34 use Moose;
  35 use Bio::Chado::Schema;
  36 use Try::Tiny;
  37 use SGN::Model::Cvterm;
  38 use JSON;
  39 use Data::Dumper;
  40 extends 'CXGN::Metadata::Dbpatch';
  41
  42
  43 has '+description' => ( default => <<'' );
  44 This patch converts the old single nd_protocolprop storage into the new three value nd_protocolprop genotype storage: one for each of the cvterms: vcf_map_details, vcf_map_details_markers, vcf_map_details_markers_array
  45
  46 has '+prereq' => (
  47         default => sub {
  48         ['AddNdProtocolpropGenotypeStorageCvterms'],
  49     },
  50
  51 );
  52
  53 sub patch {
  54     my $self=shift;
  55
  56     print STDOUT "Executing the patch:\n " .   $self->name . ".\n\nDescription:\n  ".  $self->description . ".\n\nExecuted by:\n " .  $self->username . " .";
  57
  58     print STDOUT "\nChecking if this db_patch was executed before or if previous db_patches have been executed.\n";
  59
  60     print STDOUT "\nExecuting the SQL commands.\n";
  61     my $schema = Bio::Chado::Schema->connect( sub { $self->dbh->clone } );
  62
  63     my $vcf_map_details_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'vcf_map_details', 'protocol_property')->cvterm_id();
  64     my $vcf_map_details_markers_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'vcf_map_details_markers', 'protocol_property')->cvterm_id();
  65     my $vcf_map_details_markers_array_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'vcf_map_details_markers_array', 'protocol_property')->cvterm_id();
  66
  67     my $q = "SELECT nd_protocolprop_id, nd_protocol_id, value FROM nd_protocolprop WHERE type_id = $vcf_map_details_cvterm_id;";
  68     my $h = $schema->storage->dbh()->prepare($q);
  69
  70     my $update_protocolprop_sql = "UPDATE nd_protocolprop SET value = ? WHERE nd_protocolprop_id = ?;";
  71     my $new_protocolprop_sql = "INSERT INTO nd_protocolprop (nd_protocol_id, type_id, value) VALUES (?, ?, ?);";
  72     my $h_protocolprop_update = $schema->storage->dbh()->prepare($update_protocolprop_sql);
  73     my $h_protocolprop = $schema->storage->dbh()->prepare($new_protocolprop_sql);
  74
  75     $h->execute();
  76     while (my ($nd_protocolprop_id, $nd_protocol_id, $old_value) = $h->fetchrow_array()) {
  77         my $old_value = decode_json $old_value;
  78         print STDERR Dumper $old_value;
  79         my $new_vcf_map_details_markers = $old_value->{markers};
  80         my $new_vcf_map_details_markers_array = $old_value->{markers_array};
  81
  82         if ($new_vcf_map_details_markers) {
  83             my $nd_protocolprop_markers_json_string = encode_json $new_vcf_map_details_markers;
  84             $h_protocolprop->execute($nd_protocol_id, $vcf_map_details_markers_cvterm_id, $nd_protocolprop_markers_json_string);
  85         }
  86         if ($new_vcf_map_details_markers_array) {
  87             my $nd_protocolprop_markers_array_json_string = encode_json $new_vcf_map_details_markers_array;
  88             $h_protocolprop->execute($nd_protocol_id, $vcf_map_details_markers_array_cvterm_id, $nd_protocolprop_markers_array_json_string);
  89         }
  90
  91         delete($old_value->{markers});
  92         delete($old_value->{markers_array});
  93
  94         my $nd_protocol_json_string = encode_json $old_value;
  95         $h_protocolprop_update->execute($nd_protocol_json_string, $nd_protocolprop_id);
  96     }
  97
  98     print "You're done!\n";
  99 }
 100
 101
 102 ####
 103 1; #
 104 ####