db/00030/AddListTypes.pm

   1 #!/usr/bin/env perl
   2
   3
   4 =head1 NAME
   5
   6  AddListTypes.pm
   7
   8 =head1 SYNOPSIS
   9
  10 mx-run AddListTypes [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 patch adds a type_id field to the list table (sgn_people.list).
  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 AddListTypes;
  35
  36 use Moose;
  37 extends 'CXGN::Metadata::Dbpatch';
  38
  39
  40 has '+description' => ( default => <<'' );
  41 Description of this patch goes here
  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 --do your SQL here
  60 --
  61
  62 ALTER TABLE sgn_people.list ADD COLUMN type_id bigint REFERENCES cvterm;
  63
  64 INSERT INTO cv (name, definition) VALUES ('list_types', '');
  65
  66 EOSQL
  67
  68     print STDERR "INSERTING CV TERMS...\n";
  69
  70     my @terms = qw | plots accessions locations trials years traits unigene_ids locus_ids | ;
  71
  72     foreach my $t (@terms) {
  73
  74         $self->dbh->do(<<EOSQL);
  75 INSERT INTO dbxref (db_id, accession) VALUES ((SELECT db_id FROM db WHERE name='local'), '$t');
  76
  77 INSERT INTO cvterm (cv_id, name, definition, dbxref_id) VALUES ( (SELECT currval('cv_cv_id_seq')), '$t', '$t', (SELECT dbxref_id FROM dbxref WHERE accession='$t'));
  78
  79
  80 EOSQL
  81
  82 }
  83
  84 print "Done!\n";
  85
  86 }
  87
  88 ####
  89 1; #
  90 ####