db/00083/UpdateCoPrefix.pm

   1 #!/usr/bin/env perl
   2
   3
   4 =head1 NAME
   5
   6  UpdateCoPrefix.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 updates the cassava_trait db name from the generic CO prefix to the crop ontology CO_334 prefix
  17
  18
  19 This subclass uses L<Moose>. The parent class uses L<MooseX::Runnable>
  20
  21 =head1 AUTHOR
  22
  23  Naama Menda<nm249@cornell.edu>
  24
  25 =head1 COPYRIGHT & LICENSE
  26
  27 Copyright 2010 Boyce Thompson Institute for Plant Research
  28
  29 This program is free software; you can redistribute it and/or modify
  30 it under the same terms as Perl itself.
  31
  32 =cut
  33
  34
  35 package UpdateCoPrefix;
  36
  37 use Moose;
  38 use Bio::Chado::Schema;
  39 use Try::Tiny;
  40 extends 'CXGN::Metadata::Dbpatch';
  41
  42
  43 has '+description' => ( default => <<'' );
  44 Update cassava_trait db prefix
  45
  46 has '+prereq' => (
  47         default => sub {
  48         [],
  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 $db_rs = $schema->resultset("General::Db")->search(
  64         {
  65             'cv.name' => "cassava_trait" ,
  66         },
  67         { join => { 'dbxrefs' => { 'cvterm' => 'cv' } }},
  68         );
  69     if ($db_rs) {
  70         my $db = $db_rs->first;
  71         my $db_name = $db->name;
  72         print STDERR "db name = $db_name \n";
  73         if ($db_name eq "CO") {
  74             $db->name("CO_334");
  75             $db->update();
  76             print STDERR "db name is now " . $db->name() . "\n";
  77         }
  78     }
  79     print "You're done!\n";
  80 }
  81
  82
  83 ####
  84 1; #
  85 ####