db/00011/AddMarkerExpAccession.pm

   1 #!/usr/bin/env perl
   2
   3
   4 =head1 NAME
   5
   6  SampleDbpatchMoose.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 AddMarkerExpAccession;
  35
  36 use Moose;
  37 extends 'CXGN::Metadata::Dbpatch';
  38
  39
  40 sub init_patch {
  41     my $self=shift;
  42     my $name = __PACKAGE__;
  43     print "dbpatch name is ':" .  $name . "\n\n";
  44     my $description = 'Adds a stock_id column to pcr_exp_accession and populates it.';
  45     my @previous_requested_patches = (); #ADD HERE
  46
  47     $self->name($name);
  48     $self->description($description);
  49     $self->prereq(\@previous_requested_patches);
  50
  51 }
  52
  53 sub patch {
  54     my $self=shift;
  55
  56
  57     print STDOUT "Executing the patch:\n " .   $self->name . ".\n\nDescription:\n  ".  $self->description . ".\n\nExecuted by:\n " .  $self->username . " .";
  58
  59     print STDOUT "\nChecking if this db_patch was executed before or if previous db_patches have been executed.\n";
  60
  61
  62
  63     print STDOUT "\nExecuting the SQL commands.\n";
  64
  65     $self->dbh->do(<<EOSQL);
  66 --do your SQL here
  67 --
  68 -- add a stock_id column to pcr_exp_accession
  69
  70 set search_path=public,sgn;
  71
  72 alter table sgn.pcr_exp_accession add column stock_id bigint references public.stock;
  73
  74 -- copy the stock to accession mapping from sgn.accession
  75 --
  76 update sgn.pcr_exp_accession set stock_id=sgn.accession.stock_id FROM sgn.accession where sgn.accession.accession_id=pcr_exp_accession.accession_id;
  77
  78 alter table sgn.map add column parent1_stock_id bigint references public.stock;
  79
  80 alter table sgn.map add column parent2_stock_id bigint references public.stock;
  81
  82 alter table sgn.map add column population_stock_id bigint references public.stock;
  83
  84     update sgn.map set parent1_stock_id=accession.stock_id FROM sgn.accession where sgn.accession.accession_id=map.parent_1;
  85
  86     update sgn.map set parent2_stock_id=accession.stock_id FROM sgn.accession where sgn.accession.accession_id=map.parent_2;
  87
  88 update sgn.map set population_stock_id=phenome.population.stock_id FROM phenome.population WHERE sgn.map.population_id=phenome.population.population_id;
  89
  90 -- remove trigger
  91     drop trigger pcr_accession_check_trigger on sgn.pcr_exp_accession;;
  92
  93 alter table sgn.pcr_exp_accession drop constraint accession_id_check;
  94
  95 EOSQL
  96
  97 print "You're done!\n";
  98
  99 }
 100
 101
 102 ####
 103 1; #
 104 ####