db/AddStockGenotype.pm

   1 #!/usr/bin/env perl
   2
   3
   4 =head1 NAME
   5
   6  AddStockGenotype.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 patch for adding stock_id column to tables migrated to chado's stock schem (genotype)
  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 2011 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 AddStockGenotype;
  36
  37 use Try::Tiny;
  38 use Moose;
  39 extends 'CXGN::Metadata::Dbpatch';
  40
  41
  42 sub init_patch {
  43     my $self=shift;
  44     my $name = __PACKAGE__;
  45     print "dbpatch name is : '" .  $name . "'\n\n";
  46     my $description = 'Adding stock_id FK to phenome.genotype table';
  47     my @previous_requested_patches = ('AddStockLinks'); #ADD HERE
  48
  49     $self->name($name);
  50     $self->description($description);
  51     $self->prereq(\@previous_requested_patches);
  52
  53 }
  54
  55 sub patch {
  56     my $self=shift;
  57
  58     print STDOUT "Executing the patch:\n " .   $self->name . ".\n\nDescription:\n  ".  $self->description . ".\n\nExecuted by:\n " .  $self->username . " .";
  59
  60     print STDOUT "\nChecking if this db_patch was executed before or if previous db_patches have been executed.\n";
  61
  62     print STDOUT "\nExecuting the SQL commands.\n";
  63
  64
  65     $self->dbh->do(<<EOSQL);
  66
  67 SET SEARCH_PATH  TO phenome;
  68 --do your SQL here
  69
  70      ALTER TABLE phenome.genotype ADD COLUMN stock_id INTEGER;
  71
  72     UPDATE genotype SET stock_id  = individual.stock_id FROM individual WHERE genotype.individual_id = individual.individual_id ;
  73
  74
  75 EOSQL
  76
  77 print "You're done!\n";
  78 }
  79
  80
  81 return 1;