Update tests due to data change

oncokb · Jun 23, 2021 · 8e0d7ad · 8e0d7ad
1 parent 08ac330
commit 8e0d7ad
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Showing 2 changed files with 5 additions and 4 deletions.
diff --git a/AnnotatorCore.py b/AnnotatorCore.py
@@ -557,6 +557,7 @@ def process_genomic_change(maffilereader, outf, maf_headers, ncols, nannotationc
         queries.append(query)
         rows.append(row)
 
+        if len(queries) == POST_QUERIES_THRESHOLD_GC_HGVSG:
             annotations = pull_genomic_change_info(queries,annotatehotspots)
             append_annotation_to_file(outf, ncols+nannotationcols, rows, annotations)
             queries = []

diff --git a/test_Annotation.py b/test_Annotation.py
@@ -139,13 +139,13 @@ def test_check_hgvsg():
     assert len(annotation) == 22
     assert annotation[MUTATION_EFFECT_INDEX] == 'Gain-of-function'
     assert annotation[ONCOGENIC_INDEX] == 'Oncogenic'
-    assert annotation[HIGHEST_LEVEL_INDEX] == 'LEVEL_3A'
+    assert annotation[HIGHEST_LEVEL_INDEX] == 'LEVEL_1'
 
     annotation = annotations[1]
     assert len(annotation) == 22
     assert annotation[MUTATION_EFFECT_INDEX] == 'Gain-of-function'
     assert annotation[ONCOGENIC_INDEX] == 'Oncogenic'
-    assert annotation[HIGHEST_LEVEL_INDEX] == 'LEVEL_3A'
+    assert annotation[HIGHEST_LEVEL_INDEX] == 'LEVEL_1'
 
     annotation = annotations[2]
     assert len(annotation) == 22
@@ -168,13 +168,13 @@ def test_check_genomic_change():
     assert len(annotation) == 22
     assert annotation[MUTATION_EFFECT_INDEX] == 'Gain-of-function'
     assert annotation[ONCOGENIC_INDEX] == 'Oncogenic'
-    assert annotation[HIGHEST_LEVEL_INDEX] == 'LEVEL_3A'
+    assert annotation[HIGHEST_LEVEL_INDEX] == 'LEVEL_1'
 
     annotation = annotations[1]
     assert len(annotation) == 22
     assert annotation[MUTATION_EFFECT_INDEX] == 'Gain-of-function'
     assert annotation[ONCOGENIC_INDEX] == 'Oncogenic'
-    assert annotation[HIGHEST_LEVEL_INDEX] == 'LEVEL_3A'
+    assert annotation[HIGHEST_LEVEL_INDEX] == 'LEVEL_1'
 
     annotation = annotations[2]
     assert len(annotation) == 22