db/00076/AddBrAPIPropertyCvterms.pm

   1 #!/usr/bin/env perl
   2
   3
   4 =head1 NAME
   5
   6  AddBrAPIPropertyCvterms.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 This patch adds the necessary cvterms that are used for brapi germplasm, programs, and studies.
  17 This subclass uses L<Moose>. The parent class uses L<MooseX::Runnable>
  18
  19 =head1 AUTHOR
  20
  21  Nick Morales
  22
  23 =head1 COPYRIGHT & LICENSE
  24
  25 Copyright 2010 Boyce Thompson Institute for Plant Research
  26
  27 This program is free software; you can redistribute it and/or modify
  28 it under the same terms as Perl itself.
  29
  30 =cut
  31
  32
  33 package AddBrAPIPropertyCvterms;
  34
  35 use Moose;
  36 use Bio::Chado::Schema;
  37 use Try::Tiny;
  38 extends 'CXGN::Metadata::Dbpatch';
  39
  40
  41 has '+description' => ( default => <<'' );
  42 Description of this patch goes here
  43
  44 has '+prereq' => (
  45         default => sub {
  46         [],
  47     },
  48
  49   );
  50
  51 sub patch {
  52     my $self=shift;
  53
  54     print STDOUT "Executing the patch:\n " .   $self->name . ".\n\nDescription:\n  ".  $self->description . ".\n\nExecuted by:\n " .  $self->username . " .";
  55
  56     print STDOUT "\nChecking if this db_patch was executed before or if previous db_patches have been executed.\n";
  57
  58     print STDOUT "\nExecuting the SQL commands.\n";
  59     my $schema = Bio::Chado::Schema->connect( sub { $self->dbh->clone } );
  60
  61
  62     print STDERR "INSERTING CV TERMS...\n";
  63
  64     my $terms = {
  65                 'stock_property' => [
  66                         'accession number',
  67                         'PUI',
  68                         'donor',
  69                         'donor institute',
  70                         'donor PUI',
  71                         'seed source',
  72                         'institute code',
  73                         'institute name',
  74                         'biological status of accession code',
  75                         'country of origin',
  76                         'type of germplasm storage code',
  77                         'entry number',
  78                         'acquisition date'
  79                 ],
  80                 'project_property' => [
  81                         'active',
  82                         'breeding_program_abbreviation'
  83                 ],
  84                 'cvterm_property' => [
  85                         'uri',
  86                         #'date determined',
  87                         'datatype',
  88                         'code'
  89                 ],
  90                 'geolocation_property' => [
  91                         'country_name',
  92                         'country_code',
  93                         'abbreviation',
  94                         'location_type',
  95                         'annual_total_precipitation',
  96                         'continent',
  97                         'annual_mean_temperature',
  98                         'adm1',
  99                         'adm2',
 100                         'adm3',
 101                         'local_name',
 102                         'region',
 103                         'alternative_name'
 104                 ],
 105                 'organism_property' => [
 106                         'species authority',
 107                         'subtaxa',
 108                         'subtaxa authority',
 109                 ],
 110                 'protocol_property' => [
 111                         'published date',
 112                         'protocol type',
 113                         'protocol unit',
 114                         'protocol comment'
 115                 ]
 116         };
 117
 118         foreach my $t (keys %$terms){
 119                 foreach (@{$terms->{$t}}){
 120                         $schema->resultset("Cv::Cvterm")->create_with({
 121                                 name => $_,
 122                                 cv => $t
 123                         });
 124                 }
 125         }
 126
 127
 128 print "You're done!\n";
 129 }
 130
 131
 132 ####
 133 1; #
 134 ####