From 6393dd536c70975fa68ab1f24099ec73cfddfc5b Mon Sep 17 00:00:00 2001 From: Anushya Muruganujan Date: Tue, 26 Mar 2024 10:23:32 -0700 Subject: [PATCH 1/2] For #2108 --- ontobio/io/qc.py | 2 +- tests/test_qc.py | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/ontobio/io/qc.py b/ontobio/io/qc.py index e826d654..dd89f745 100644 --- a/ontobio/io/qc.py +++ b/ontobio/io/qc.py @@ -913,7 +913,7 @@ def test(self, annotation: association.GoAssociation, config: assocparser.AssocP class GoRule63(GoRule): def __init__(self): - super().__init__("GORULE:0000063", "Annotations using ISS/ISA/ISO evidence should refer to a gene product (in the 'with' column)", FailMode.HARD) + super().__init__("GORULE:0000063", "Annotations using ISS/ISA/ISO evidence should refer to a gene product (in the 'with' column)", FailMode.SOFT) def test(self, annotation: association.GoAssociation, config: assocparser.AssocParserConfig, group=None) -> TestResult: evidence = str(annotation.evidence.type) diff --git a/tests/test_qc.py b/tests/test_qc.py index 35facea7..64514d4a 100644 --- a/tests/test_qc.py +++ b/tests/test_qc.py @@ -764,17 +764,17 @@ def test_go_rule_63(): # ISS with nothing in withfrom assoc = make_annotation(evidence="ISS", withfrom="").associations[0] test_result = qc.GoRule63().test(assoc, all_rules_config()) - assert test_result.result_type == qc.ResultType.ERROR + assert test_result.result_type == qc.ResultType.WARNING # ISA with with nothing in withfrom assoc = make_annotation(evidence="ISA", withfrom="").associations[0] test_result = qc.GoRule63().test(assoc, all_rules_config()) - assert test_result.result_type == qc.ResultType.ERROR + assert test_result.result_type == qc.ResultType.WARNING # ISO with with nothing in withfrom assoc = make_annotation(evidence="ISO", withfrom="").associations[0] test_result = qc.GoRule63().test(assoc, all_rules_config()) - assert test_result.result_type == qc.ResultType.ERROR + assert test_result.result_type == qc.ResultType.WARNING def test_all_rules(): # pass From b0e7bdd2719fba8f126a189eada5454fa0e5e8bb Mon Sep 17 00:00:00 2001 From: Anushya Muruganujan Date: Tue, 26 Mar 2024 16:11:00 -0700 Subject: [PATCH 2/2] For #2108 --- Makefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Makefile b/Makefile index fdb853e7..5ffb8954 100644 --- a/Makefile +++ b/Makefile @@ -29,7 +29,7 @@ travis_test: tests/test_validation_rules.py tests/unit/test_annotation_scorer.py \ tests/test_goassociation_model.py tests/test_relations.py \ tests/unit/test_golr_search_query.py tests/unit/test_owlsim2_api.py \ - tests/unit/test_clinical_mod.py tests/test_collections.py \ + tests/test_collections.py \ tests/test_gocamgen.py cleandist: