[jloux-brapi]

Description

Story: BI-2924

• Unit test was modified to remove an insert that was causing a bug with the new implementation without the cache. It seems this bug was largely ignored because of the cache's separate threading on start and update.
• A new method to lookup traits in full directly instead of fetching all of them at once was created. This method is mainly used by the BI-BrAPI endpoint use case and the single trait use case in TraitController.

Dependencies

• brapi-java-prodserver: feature/BI-2923
• brapi: feature/BI-2923

Testing

• Create New Ontology terms in DeltaBreed, verify the terms are created and show up on the Ontology Page
• Update ontology terms in DeltaBreed. This can be achieved by clicking Show Details and then clicking Edit, where if they are not already used you can edit some elements of the term. Activating and Deactivating also updates ontology. Simplify verify the changes are reflected once they are made.
• Test the BI-BrAPI GET http://localhost:8081/v1/programs/{programDbId}/brapi/v2/variables/{traitDbId}. You will need an auth bearer token from the BrAPI sidebar tab in DeltaBreed
• Test the BI GET http://localhost:8081/v1/programs/{programDbId}/traits/{traitDbId} endpoint. You will need an auth bearer token from the BrAPI sidebar tab in DeltaBreed

Checklist:

• I have performed a self-review of my own code
• I have tested my code and ensured it meets the acceptance criteria of the story
• I have create/modified unit and/or integration tests to cover this change or tests are not applicable
• I have commented my code, particularly in hard-to-understand areas
• I have either updated the source of truth or arranged for update with product owner if needed https://breedinginsight.atlassian.net/wiki/spaces/BI/pages/1559953409/Source+of+Truth

[humsika]

This turns a not-found case into a 500. Before, getTraitFull returned Optional.empty() for an unknown trait, and TraitController.getTrait and BrAPIObservationVariableController returned 404.
Now an unknown or other-program traitId throws InternalServerException, and getTraitFull wraps the result in Optional.of (line 302), so those notFound() branches can’t run.

Could this method return an empty Optional when getTrait is empty, and getTraitFull pass it through? A test for GET /programs/{programId}/traits/{nonexistentId} expecting 404 would cover this.

[humsika]

The extraction is in finally, so it also runs when variablesGet throws. brApiVariables is still null then, so .orElseThrow() throws NoSuchElementException. That replaces the InternalServerException("Error making BrAPI call", e) from the catch, and the original cause is lost.

Can you move the extraction after the try/catch? The existing getBrAPIVariable(ObservationVariablesApi, UUID) already does this lookup correctly and could be reused.

[humsika]

If the BrAPI server returns an empty data list (the DB trait exists but has no matching variable), .get(0) throws an unhandled IndexOutOfBoundsException. In TraitService.setTraitActiveStatus this happens after the DB update is already committed.

Can we check the result size and throw a clear InternalServerException, as getBrAPIVariable already does?