lib/CXGN/TrackingActivity/AddTrackingIdentifier.pm

   1 package CXGN::TrackingActivity::AddTrackingIdentifier;
   2
   3 =head1 NAME
   4
   5 CXGN::TrackingActivity::AddTrackingIdentifier - a module to add tracking identifier.
   6
   7 =head1 USAGE
   8
   9
  10 =head1 DESCRIPTION
  11
  12 =head1 AUTHORS
  13
  14 Titima Tantikanjana (tt15@cornell.edu)
  15
  16 =cut
  17
  18 use Moose;
  19 use MooseX::FollowPBP;
  20 use Moose::Util::TypeConstraints;
  21 use Try::Tiny;
  22 use SGN::Model::Cvterm;
  23 use Data::Dumper;
  24
  25 has 'schema' => (
  26     is => 'rw',
  27     isa => 'DBIx::Class::Schema',
  28     required => 1,
  29 );
  30
  31 has 'phenome_schema' => (
  32     is => 'rw',
  33     isa => 'DBIx::Class::Schema',
  34     required => 1,
  35 );
  36
  37 has 'tracking_identifier' => (
  38     isa => 'Str',
  39     is => 'rw',
  40     required => 1,
  41 );
  42
  43 has 'material' => (
  44     isa =>'Str',
  45     is => 'rw',
  46     required => 1,
  47 );
  48
  49 has 'project_id' => (
  50     isa => 'Int',
  51     is => 'rw',
  52     required => 1,
  53 );
  54
  55 has 'user_id' => (
  56     isa => 'Int',
  57     is => 'rw',
  58     required => 1,
  59 );
  60
  61 sub store {
  62     my $self = shift;
  63     my $schema = $self->get_schema();
  64     my $phenome_schema = $self->get_phenome_schema();
  65     my $tracking_identifier = $self->get_tracking_identifier();
  66     my $material_name = $self->get_material();
  67     my $project_id = $self->get_project_id();
  68     my $user_id = $self->get_user_id();
  69     my $error;
  70
  71     my $tracking_identifier_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'tracking_identifier', 'stock_type')->cvterm_id();
  72     my $material_of_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'material_of', 'stock_relationship')->cvterm_id();
  73     my $experiment_type_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'tracking_activity', 'experiment_type')->cvterm_id();
  74     my $project_location_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'project location', 'project_property')->cvterm_id();
  75     my $geolocation_rs = $schema->resultset("Project::Projectprop")->find({project_id => $project_id, type_id => $project_location_cvterm_id});
  76
  77     my $tracking_id;
  78
  79     my $check_id_rs = $schema->resultset("Stock::Stock")->search({
  80         uniquename => $tracking_identifier,
  81     });
  82     if ($check_id_rs->count() > 0){
  83         return { error => "$tracking_identifier already used in the database! " };
  84     }
  85
  86     my $coderef = sub {
  87         my $tracking_id_rs = $schema->resultset("Stock::Stock")->create({
  88             name => $tracking_identifier,
  89             uniquename => $tracking_identifier,
  90             type_id => $tracking_identifier_cvterm_id,
  91         });
  92         $tracking_id = $tracking_id_rs->stock_id();
  93
  94         my $material_rs = $schema->resultset("Stock::Stock")->find({ uniquename => $material_name});
  95         my $tracking_material = $schema->resultset("Stock::StockRelationship")->find_or_create({
  96             subject_id => $material_rs->stock_id,
  97             object_id => $tracking_id,
  98             type_id => $material_of_cvterm_id,
  99         });
 100
 101         my $experiment = $schema->resultset('NaturalDiversity::NdExperiment')->create({
 102             nd_geolocation_id => $geolocation_rs->value,
 103             type_id => $experiment_type_cvterm_id,
 104         });
 105
 106         $experiment->find_or_create_related('nd_experiment_stocks' , {
 107             stock_id => $tracking_id,
 108             type_id  => $experiment_type_cvterm_id,
 109         });
 110
 111         $experiment->find_or_create_related('nd_experiment_projects', {
 112             project_id => $project_id,
 113         });
 114
 115     };
 116
 117     my $error;
 118     try {
 119         $schema->txn_do($coderef);
 120     } catch {
 121         $error =  $_;
 122     };
 123
 124     if ($error) {
 125         return { error => "Error creating a tracking identifier: $error\n" };
 126     }
 127
 128     $phenome_schema->resultset("StockOwner")->find_or_create({
 129         stock_id => $tracking_id,
 130         sp_person_id => $user_id,
 131     });
 132
 133     return {tracking_id => $tracking_id};
 134
 135 }
 136
 137
 138
 139 #######
 140 1;
 141 #######