Try fixing tests

Author: calvinlu3

requirements/common.txt

@@ -1,2 +1,2 @@
-requests==2.34.0
+requests==2.32.4
 urllib3==2.2.3

test_Annotation.py

@@ -314,6 +314,10 @@ def test_fake_cna():
     fake_gene_one_query_suite(annotations, True)
 
 
+def assert_treatments_equal(actual, expected):
+    assert set(actual.split(',')) == set(expected.split(','))
+
+
 def check_brca2_s1882_without_cancertype(annotation, genomic_query=False):
     assert len(annotation) == NUMBER_OF_GC_ANNOTATION_COLUMNS if genomic_query else NUMBER_OF_ANNOTATION_COLUMNS
     assert annotation[(
@@ -322,12 +326,18 @@ def check_brca2_s1882_without_cancertype(annotation, genomic_query=False):
             NUMBER_OF_ONCOKB_ANNOTATION_GC_COLUMNS + ONCOGENIC_INDEX) if genomic_query else ONCOGENIC_INDEX] == 'Likely Oncogenic'
     assert annotation[(
             NUMBER_OF_ONCOKB_ANNOTATION_GC_COLUMNS + HIGHEST_LEVEL_INDEX) if genomic_query else HIGHEST_LEVEL_INDEX] == 'LEVEL_1'
-    assert annotation[(
-            NUMBER_OF_ONCOKB_ANNOTATION_GC_COLUMNS + LEVEL_1_INDEX) if genomic_query else LEVEL_1_INDEX] == 'Olaparib,Olaparib+Bevacizumab,Rucaparib,Olaparib+Abiraterone+Prednisone,Niraparib,Talazoparib+Enzalutamide,Niraparib+Abiraterone Acetate+Prednisone'
-    assert annotation[(
-            NUMBER_OF_ONCOKB_ANNOTATION_GC_COLUMNS + LEVEL_2_INDEX) if genomic_query else LEVEL_2_INDEX] == 'Olaparib,Rucaparib,Niraparib'
-    assert annotation[(
-            NUMBER_OF_ONCOKB_ANNOTATION_GC_COLUMNS + LEVEL_3A_INDEX) if genomic_query else LEVEL_3A_INDEX] == 'Olaparib,Talazoparib'
+    assert_treatments_equal(
+        annotation[(NUMBER_OF_ONCOKB_ANNOTATION_GC_COLUMNS + LEVEL_1_INDEX) if genomic_query else LEVEL_1_INDEX],
+        'Olaparib,Olaparib+Bevacizumab,Rucaparib,Olaparib+Abiraterone+Prednisone,Niraparib,Talazoparib+Enzalutamide,Niraparib+Abiraterone Acetate+Prednisone'
+    )
+    assert_treatments_equal(
+        annotation[(NUMBER_OF_ONCOKB_ANNOTATION_GC_COLUMNS + LEVEL_2_INDEX) if genomic_query else LEVEL_2_INDEX],
+        'Olaparib,Rucaparib,Niraparib'
+    )
+    assert_treatments_equal(
+        annotation[(NUMBER_OF_ONCOKB_ANNOTATION_GC_COLUMNS + LEVEL_3A_INDEX) if genomic_query else LEVEL_3A_INDEX],
+        'Olaparib,Talazoparib'
+    )
 
 
 @pytest.mark.skipif(ONCOKB_API_TOKEN in (None, ''), reason="oncokb api token required")

test_AnnotatorCore.py

@@ -183,9 +183,9 @@ def test_resolve_query_type_for_row():
 def test_combined_headers():
     headers = get_oncokb_annotation_column_headers(False, True, MutationStatus.SOMATIC, combined_mode=True)
     assert 'ONCOGENIC' in headers
-    assert 'PATHOGENIC' in headers
-    assert 'PENETRANCE' in headers
-    assert 'GENOMIC_INDICATOR' in headers
+    assert 'PATHOGENIC (Germline)' in headers
+    assert 'PENETRANCE (Germline)' in headers
+    assert 'GENOMIC_INDICATOR (Germline)' in headers
     assert 'ONCOKB_HUGO_SYMBOL' in headers
 
 
@@ -237,7 +237,7 @@ def fake_pull_hgvsc_info(queries, include_descriptions, annotate_hotspot, mutati
 
     annotated_index = header.index('ANNOTATED')
     oncogenic_index = header.index('ONCOGENIC')
-    pathogenic_index = header.index('PATHOGENIC')
+    pathogenic_index = header.index('PATHOGENIC (Germline)')
     assert rows[0][annotated_index] == 'True'
     assert rows[1][annotated_index] == 'True'
     assert rows[1][oncogenic_index] == ''