The test for the biomass SBO term on biomass reactions fails when the term is actually present because test_biomass_specific_sbo_presence in test_sbo.py is checking for presence of terms, but the search for specific SBO terms only returns an element if the element is missing the term.
Specifically, this line returns ids of elements that are missing the SBO term:
But the assert statement at the end of the test is expecting ann["data] to be of the same length as the number of biomass reactions; I think this should be 0 instead:
Problem description
The test for the biomass SBO term on biomass reactions fails when the term is actually present because
test_biomass_specific_sbo_presence
intest_sbo.py
is checking for presence of terms, but the search for specific SBO terms only returns an element if the element is missing the term.Specifically, this line returns ids of elements that are missing the SBO term:
ann["data"] = get_ids(sbo.check_component_for_specific_sbo_term( biomass, "SBO:0000629"))
But the assert statement at the end of the test is expecting
ann["data]
to be of the same length as the number of biomass reactions; I think this should be 0 instead:assert len(ann["data"]) == len(biomass), ann["message"]
I can create a PR for this and updated unit tests soon. The change is small, so might be worth doing before resolving #469