Skip to content

add new options to phenotype endpoints and report MIM ids by default

Marek Szuba requested to merge github/fork/ima23/feature/rest_pheno into master

Created by: ima23

Description

The default result reporting for phenotype endpoints (gene, region, accession, term) has been changed to report MIM ids if present. New optional parameters (include_review_status, include_pubmed_id and include_submitter) have been added. All three parameters are available for gene and region endpoints, while the accession and term endpoints will have all but the include_submitter option. Additional code changes where performed to reflect the latest perl API methods.

Use case

The MIM id has been requested and the new options allow for more details to be retrieved.

Benefits

The update allows retrieval of MIM ids, PubMed ids, review status and submitter names.

Possible Drawbacks

None.

Testing

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

Yes. The corresponding tests have been updated and new ones added.

If so, do the tests pass/fail?

Tests pass.

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

Yes.

Changelog

The four phenotype endpoints will report by default MIM ids if they are present. [/phenotype/accession/:species/:accession] Added optional parameters include_review_status and include_pubmed_id [/phenotype/accession/:species/:term] Added optional parameters include_review_status and include_pubmed_id [/phenotype/gene/:species/:gene] Added optional parameters include_submitter, include_review_status and include_pubmed_id [/phenotype/gene/:species/:region] Added optional parameters include_submitter, include_review_status and include_pubmed_id

Merge request reports