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.
Merge request reports
Activity
Created by: lairdm
Failed tests: archive - due to branching and master now being release/94, will be fixed with my travis pull branch change gene_tree, genomic_alignment - Compara have been made aware of the test breaking bcause of changes in their repos, they're investigating. Not relevant to this pull request. ratelimit - the usual, timing issue
221 221 unless (defined $gene_ad ) {Catalyst::Exception->throw("Species $species not found.");} 222 222 223 223 my $phenfeat_ad = $c->model('Registry')->get_adaptor($species,'variation', 'phenotypefeature'); 224 $phenfeat_ad->_include_ontology(1); 221 221 unless (defined $gene_ad ) {Catalyst::Exception->throw("Species $species not found.");} 222 222 223 223 my $phenfeat_ad = $c->model('Registry')->get_adaptor($species,'variation', 'phenotypefeature'); 224 $phenfeat_ad->_include_ontology(1);