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

Yes. The corresponding tests have been updated.

If so, do the tests pass/fail?

Tests pass with release/93 branch code.

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 exist.

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;
 }
 

[Marek Szuba]

Created by: nerdstrike

On balance, perhaps _include_ontology() should not have an underscore prefix if it was intended to be called from outside the object. I won't ask you to change it here, but it is unconventional

[Marek Szuba]

Created by: ima23

Thanks for checking @nerdstrike. Yes, well spotted and totally agree. Will sort this out in one of the future releases, as it involves deeper look into the API.