lib/CXGN/Transformation/AddTransformationIdentifier.pm

   1 =head1 NAME
   2
   3 CXGN::Transformation::AddTransformationIdentifier - a module for adding transformation identifier
   4
   5 =cut
   6
   7
   8 package CXGN::Transformation::AddTransformationIdentifier;
   9
  10 use Moose;
  11 use MooseX::FollowPBP;
  12 use Moose::Util::TypeConstraints;
  13 use Try::Tiny;
  14 use CXGN::Location::LocationLookup;
  15 use CXGN::Trial;
  16 use SGN::Model::Cvterm;
  17 use Data::Dumper;
  18
  19 has 'chado_schema' => (
  20     isa => 'DBIx::Class::Schema',
  21     is => 'rw',
  22     required => 1,
  23 );
  24
  25 has 'dbh' => (
  26     is  => 'rw',
  27     required => 1,
  28 );
  29
  30 has 'phenome_schema' => (
  31     is => 'rw',
  32     isa => 'DBIx::Class::Schema',
  33     predicate => 'has_phenome_schema',
  34     required => 1,
  35 );
  36
  37 has 'transformation_identifier' => (
  38     isa =>'Str',
  39     is => 'rw',
  40     required => 1,
  41 );
  42
  43 has 'plant_material' => (
  44     isa => 'Str',
  45     is => 'rw',
  46     required => 1,
  47 );
  48
  49 has 'vector_construct' => (
  50     isa => 'Str',
  51     is => 'rw',
  52     required => 1,
  53 );
  54
  55 has 'notes' => (
  56     isa => 'Str',
  57     is => 'rw',
  58 );
  59
  60 has 'owner_id' => (
  61     isa => 'Int',
  62     is => 'rw',
  63 );
  64
  65 has 'transformation_project_id' => (
  66     isa =>'Int',
  67     is => 'rw',
  68     required => 1,
  69 );
  70
  71
  72 sub add_transformation_identifier {
  73     my $self = shift;
  74     my $schema = $self->get_chado_schema();
  75     my $phenome_schema = $self->get_phenome_schema();
  76     my $transformation_identifier = $self->get_transformation_identifier();
  77     my $plant_material = $self->get_plant_material();
  78         my $vector_construct = $self->get_vector_construct();
  79         my $transformation_notes = $self->get_notes();
  80         my $transformation_project_id = $self->get_transformation_project_id();
  81         my $plant_material_stock_id;
  82         my $vector_construct_stock_id;
  83     my %return;
  84         my $transformation_stock_id;
  85
  86     my $owner_id = $self->get_owner_id();;
  87
  88     my $coderef = sub {
  89
  90         my $transformation_cvterm_id =  SGN::Model::Cvterm->get_cvterm_row($schema, 'transformation', 'stock_type')->cvterm_id();
  91         my $transformation_experiment_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'transformation_experiment', 'experiment_type')->cvterm_id();
  92         my $transformation_project_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'transformation_project', 'project_type')->cvterm_id();
  93         my $plant_material_of_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema,  'plant_material_of', 'stock_relationship')->cvterm_id();
  94         my $vector_construct_of_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema,  'vector_construct_of', 'stock_relationship')->cvterm_id();
  95 #        my $transformation_notes_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema,  'transformation_notes', 'stock_property')->cvterm_id();
  96                 my $accession_cvterm_id =  SGN::Model::Cvterm->get_cvterm_row($schema, 'accession', 'stock_type')->cvterm_id();
  97                 my $vector_construct_cvterm_id =  SGN::Model::Cvterm->get_cvterm_row($schema, 'vector_construct', 'stock_type')->cvterm_id();
  98
  99                 my $project_location_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'project location', 'project_property')->cvterm_id();
 100                 my $geolocation_rs = $schema->resultset("Project::Projectprop")->find({project_id => $transformation_project_id, type_id => $project_location_cvterm_id});
 101
 102                 my $plant_material_rs = $schema->resultset("Stock::Stock")->find({
 103                         uniquename => $plant_material,
 104                         type_id => $accession_cvterm_id,
 105                 });
 106
 107                 if ($plant_material_rs) {
 108             $plant_material_stock_id = $plant_material_rs->stock_id();
 109                 }
 110
 111                 my $vector_construct_rs = $schema->resultset("Stock::Stock")->find({
 112                         uniquename => $vector_construct,
 113                         type_id => $vector_construct_cvterm_id,
 114                 });
 115
 116                 if ($vector_construct_rs) {
 117             $vector_construct_stock_id = $vector_construct_rs->stock_id();
 118                 }
 119
 120                 my $experiment = $schema->resultset('NaturalDiversity::NdExperiment')->create({
 121                         nd_geolocation_id => $geolocation_rs->value,
 122                         type_id => $transformation_experiment_cvterm_id,
 123                 });
 124                 my $nd_experiment_id = $experiment->nd_experiment_id();
 125
 126                 my $transformation_identifier_stock = $schema->resultset("Stock::Stock")->find_or_create({
 127                         name => $transformation_identifier,
 128                         uniquename => $transformation_identifier,
 129                         type_id => $transformation_cvterm_id,
 130                 });
 131
 132                 $transformation_identifier_stock->find_or_create_related('stock_relationship_objects', {
 133                         type_id => $plant_material_of_cvterm_id,
 134                         object_id => $transformation_identifier_stock->stock_id(),
 135                         subject_id => $plant_material_stock_id,
 136                 });
 137
 138                 $transformation_identifier_stock->find_or_create_related('stock_relationship_objects', {
 139                         type_id => $vector_construct_of_cvterm_id,
 140                         object_id => $transformation_identifier_stock->stock_id(),
 141                         subject_id => $vector_construct_stock_id,
 142                 });
 143
 144                 $experiment->find_or_create_related('nd_experiment_stocks' , {
 145                           stock_id => $transformation_identifier_stock->stock_id(),
 146                           type_id  => $transformation_experiment_cvterm_id,
 147                         });
 148
 149                 $experiment->find_or_create_related('nd_experiment_projects', {
 150                         project_id => $transformation_project_id,
 151                 });
 152
 153         $transformation_stock_id = $transformation_identifier_stock->stock_id();
 154     };
 155     print STDERR "TRANSFORMATION STOCK ID =".Dumper($transformation_stock_id)."\n";
 156     my $transaction_error;
 157     try {
 158         $schema->txn_do($coderef);
 159     } catch {
 160         print STDERR "Transaction Error: $_\n";
 161         $transaction_error =  $_;
 162     };
 163
 164     if ($transaction_error){
 165         return { error=>$transaction_error };
 166     } else {
 167         $phenome_schema->resultset("StockOwner")->find_or_create({
 168             stock_id => $transformation_stock_id,
 169             sp_person_id =>  $owner_id,
 170         });
 171
 172         return { success=>1, transformation_id=>$transformation_stock_id };
 173     }
 174
 175 }
 176
 177
 178
 179 #########
 180 1;
 181 #########