export phenotype ontology accessions

Created by: ima23

Description

The phenotype REST endpoint retrieves the existing phenotypes but currently does not report the associated ontology accession terms. This is now being updated.

Use case

The endpoint functionality stays the same.

Benefits

The result of the endpoint will now also contain ontology accessions.

Possible Drawbacks

None.

Testing

Have you added/modified unit tests to test the changes?

Yes. The corresponding tests have been updated.

If so, do the tests pass/fail?

Tests pass.

Have you run the entire test suite and no regression was detected?

Yes.

Changelog

Are you changing the functionality of an endpoint? If so, please give a one line summary for the public facing changelog.

The endpoint functions as before, just the output is enriched with accession terms if they are present.

lib/EnsEMBL/REST/Model/Phenotype.pm

@@ -221,6 +221,7 @@ sub fetch_features_by_gene {
   unless (defined $gene_ad ) {Catalyst::Exception->throw("Species $species not found.");}
 
   my $phenfeat_ad = $c->model('Registry')->get_adaptor($species,'variation', 'phenotypefeature');
+  $phenfeat_ad->_include_ontology(1);
   my $slice_ad = $c->model('Registry')->get_adaptor($species, "core", "slice");
 
   my $include_assoc = $c->request->parameters->{include_associated};
@@ -269,6 +270,7 @@ sub fetch_features_by_gene {
       push @phenotype_features, $record;
     }
   }
+  $phenfeat_ad->_include_ontology(0);
   return \@phenotype_features;
 }