From b47bdd6e2014b3959241a3c25a7e6282ff2f7335 Mon Sep 17 00:00:00 2001 From: Hongxin Date: Thu, 7 Apr 2022 21:56:04 -0500 Subject: [PATCH] Update tests based on v3.12 --- test_Annotation.py | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/test_Annotation.py b/test_Annotation.py index 21a4953..deda639 100644 --- a/test_Annotation.py +++ b/test_Annotation.py @@ -27,7 +27,7 @@ def fake_gene_one_query_suite(annotations): annotation = annotations[0] assert len(annotation) == NUMBER_OF_ANNOTATION_COLUMNS assert annotation[MUTATION_EFFECT_INDEX] == UNKNOWN - assert annotation[ONCOGENIC_INDEX] == '' + assert annotation[ONCOGENIC_INDEX] == UNKNOWN assert annotation[HIGHEST_LEVEL_INDEX] == '' @@ -282,13 +282,14 @@ def test_fake_cna(): annotations = pull_cna_info(queries) fake_gene_one_query_suite(annotations) -def check_brca2_n3214i_without_cancertype(annotation): +def check_brca2_s1882_without_cancertype(annotation): assert len(annotation) == NUMBER_OF_ANNOTATION_COLUMNS assert annotation[MUTATION_EFFECT_INDEX] == 'Likely Loss-of-function' assert annotation[ONCOGENIC_INDEX] == 'Likely Oncogenic' assert annotation[HIGHEST_LEVEL_INDEX] == 'LEVEL_1' assert annotation[LEVEL_1_INDEX] == 'Olaparib,Olaparib+Bevacizumab,Rucaparib,Niraparib' - assert annotation[LEVEL_3A_INDEX] == 'Rucaparib,Talazoparib,Olaparib' + assert annotation[LEVEL_2_INDEX] == 'Olaparib,Rucaparib,Niraparib' + assert annotation[LEVEL_3A_INDEX] == 'Olaparib,Talazoparib' @pytest.mark.skipif(ONCOKB_API_TOKEN in (None, ''), reason="oncokb api token required") def test_duplicated_treatments(): @@ -301,7 +302,7 @@ def test_duplicated_treatments(): annotations = pull_protein_change_info(queries, False) assert len(annotations) == 1 - check_brca2_n3214i_without_cancertype(annotations[0]) + check_brca2_s1882_without_cancertype(annotations[0]) # test genomic change query queries = [ @@ -310,4 +311,4 @@ def test_duplicated_treatments(): annotations = pull_genomic_change_info(queries, False) assert len(annotations) == 1 - check_brca2_n3214i_without_cancertype(annotations[0]) + check_brca2_s1882_without_cancertype(annotations[0])