db/00063/RenameObsoleteStocks.pm

   1 #!/usr/bin/env perl
   2
   3 =head1 NAME
   4
   5 RenameObsoleteStocks.pm
   6
   7 =head1 SYNOPSIS
   8
   9 mx-run RenameObsoleteStocks [options] -H hostname -D dbname -u username [-F]
  10
  11 this is a subclass of L<CXGN::Metadata::Dbpatch>
  12 see the perldoc of parent class for more details.
  13
  14 =head1 DESCRIPTION
  15
  16 This patch renames obsolete stocks by adding _OBSOLETED and a timestamp to the end of the uniquename and name. This then allows new stocks to be added with the same name as the obsoleted stock.
  17
  18 =head1 AUTHOR
  19
  20 Bryan Ellerbrock<bje24@cornell.edu>
  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 RenameObsoleteStocks;
  33
  34 use Moose;
  35 use Bio::Chado::Schema;
  36 use Try::Tiny;
  37 extends 'CXGN::Metadata::Dbpatch';
  38
  39
  40 has '+description' => ( default => <<'' );
  41 This patch renames obsolete stocks by adding _OBSOLETED and a timestamp to the end of the uniquename and name. This then allows new stocks to be added with the same name as the obsoleted stock.
  42
  43
  44 sub patch {
  45   my $self=shift;
  46
  47   print STDOUT "Executing the patch:\n " .   $self->name . ".\n\nDescription:\n  ".  $self->description . ".\n\nExecuted by:\n " .  $self->username . " .";
  48
  49   print STDOUT "\nChecking if this db_patch was executed before or if previous db_patches have been executed.\n";
  50
  51   print STDOUT "\nExecuting the SQL commands.\n";
  52
  53   my $schema = Bio::Chado::Schema->connect( sub { $self->dbh->clone } );
  54
  55   my $coderef = sub {
  56       print STDERR "Updating names of obsolete stocks . . .\n";
  57
  58       my $obsolete_stocks = $schema->resultset("Stock::Stock")->search({is_obsolete => 't'});
  59
  60       while (my $stock = $obsolete_stocks->next) {
  61         my $obsolete_string = '_OBSOLETED_' . localtime();
  62         my $name = $stock->name();
  63         my $uniquename = $stock->uniquename();
  64
  65         unless ($name =~ /OBSOLETE/ || $uniquename =~ /OBSOLETE/) { # skip if already renamed
  66           $stock->update( { name => $name . $obsolete_string, uniquename => $uniquename . $obsolete_string }, );
  67           print STDERR "Set stock $name name to $name$obsolete_string and uniquename to $uniquename$obsolete_string . . .\n";
  68         }
  69
  70       }
  71   };
  72
  73   try {
  74     $schema->txn_do($coderef);
  75   } catch {
  76     die "RenameObsoleteStocks patch failed! " . $_ .  "\n" ;
  77   };
  78
  79   print "You're done!\n";
  80
  81 }
  82
  83 ####
  84 1; #
  85 ####