db/00129/FixPhenomeGenotypingTable.pm

   1 #!/usr/bin/env perl
   2
   3
   4 =head1 NAME
   5
   6  FixPhenomeGenotypingTable.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
  17 This is a test dummy patch.
  18 This subclass uses L<Moose>. The parent class uses L<MooseX::Runnable>
  19
  20 =head1 AUTHOR
  21
  22  Naama Menda<nm249@cornell.edu>
  23
  24 =head1 COPYRIGHT & LICENSE
  25
  26 Copyright 2010 Boyce Thompson Institute for Plant Research
  27
  28 This program is free software; you can redistribute it and/or modify
  29 it under the same terms as Perl itself.
  30
  31 =cut
  32
  33
  34 package FixPhenomeGenotypingTable;
  35
  36 use Moose;
  37 extends 'CXGN::Metadata::Dbpatch';
  38
  39
  40 has '+description' => ( default => <<'' );
  41 Rename phenome.genotype table to phenome.phenome_genotype along with all genotype_id fields in the phenome schema
  42
  43 has '+prereq' => (
  44     default => sub {
  45         [],
  46     },
  47   );
  48
  49 sub patch {
  50     my $self=shift;
  51
  52     print STDOUT "Executing the patch:\n " .   $self->name . ".\n\nDescription:\n  ".  $self->description . ".\n\nExecuted by:\n " .  $self->username . " .";
  53
  54     print STDOUT "\nChecking if this db_patch was executed before or if previous db_patches have been executed.\n";
  55
  56     print STDOUT "\nExecuting the SQL commands.\n";
  57
  58     $self->dbh->do(<<EOSQL);
  59
  60 ALTER TABLE phenome.genotype RENAME TO phenome_genotype;
  61 ALTER TABLE phenome.phenome_genotype RENAME COLUMN genotype_id TO phenome_genotype_id;
  62 ALTER TABLE phenome.genotype_region RENAME COLUMN genotype_id TO phenome_genotype_id;
  63 ALTER TABLE phenome.polymorphic_fragment RENAME COLUMN genotype_id TO phenome_genotype_id;
  64
  65 EOSQL
  66
  67
  68 print "You're done!\n";
  69 }
  70
  71
  72 ####
  73 1; #
  74 ####