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ncbo / ncbo_annotator

To automatically process a piece of data text to annotate it with relevant ontology concepts and return the annotations.
http://bioportal.bioontology.org/annotator
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Unit tests encounter errors when retrieving metrics, but overall tests still pass. #32

Open alexskr opened 1 month ago

alexskr commented 1 month ago

Unit tests encounter errors when retrieving metrics, but they still pass, which raises questions about the validity of those tests.

TestRecommender#test_recommend = E, [2024-07-04T00:18:44.738241 #8] ERROR -- : Unable to retrieve metrics for latest submission of http://data.bioontology.org/ontologies/BROTEST-0 in Recommender.
E, [2024-07-04T00:18:44.776653 #8] ERROR -- : Unable to retrieve metrics for latest submission of http://data.bioontology.org/ontologies/ONTOMATEST-0 in Recommender.
E, [2024-07-04T00:18:44.815828 #8] ERROR -- : Unable to retrieve metrics for latest submission of http://data.bioontology.org/ontologies/MCCLTEST-0 in Recommender.
0.15 s = .
TestRecommender#test_recommend_with_classes = E, [2024-07-04T00:18:44.884464 #8] ERROR -- : Unable to retrieve metrics for latest submission of http://data.bioontology.org/ontologies/BROTEST-0 in Recommender.
E, [2024-07-04T00:18:44.923456 #8] ERROR -- : Unable to retrieve metrics for latest submission of http://data.bioontology.org/ontologies/ONTOMATEST-0 in Recommender.
E, [2024-07-04T00:18:44.961876 #8] ERROR -- : Unable to retrieve metrics for latest submission of http://data.bioontology.org/ontologies/MCCLTEST-0 in Recommender.
0.15 s = .
TestRecommender#test_recommend_with_ontologies = E, [2024-07-04T00:18:45.029686 #8] ERROR -- : Unable to retrieve metrics for latest submission of http://data.bioontology.org/ontologies/BROTEST-0 in Recommender.
E, [2024-07-04T00:18:45.068835 #8] ERROR -- : Unable to retrieve metrics for latest submission of http://data.bioontology.org/ontologies/MCCLTEST-0 in Recommender.
0.11 s = .

Finished tests in 24.179108s, 0.6204 tests/s, 535.8758 assertions/s.

15 tests, 12957 assertions, 0 failures, 0 errors, 1 skips

I think its because we are rescuing error here https://github.com/ncbo/ncbo_annotator/blob/63c986880aa88c9384043e6611a682434a14aba7/lib/ncbo_recommender.rb#L74-L82