Make Worker Variants Fully Qualified for Accession Tests

Author: bencap

tests/worker/data/counts_acc.csv

@@ -1,4 +1,4 @@
 hgvs_nt,c_0,c_1
-c.1G>C,10,20
-c.2A>G,8,8
-c.6C>A,90,2
+NM_001637.3:c.1G>C,10,20
+NM_001637.3:c.2A>G,8,8
+NM_001637.3:c.6C>A,90,2

tests/worker/data/scores_acc.csv

@@ -1,4 +1,4 @@
 hgvs_nt,score
-c.1G>C,0.3
-c.2A>G,0.0
-c.6C>A,-1.65
+NM_001637.3:c.1G>C,0.3
+NM_001637.3:c.2A>G,0.0
+NM_001637.3:c.6C>A,-1.65

tests/worker/test_jobs.py

@@ -35,6 +35,7 @@
     TEST_MINIMAL_EXPERIMENT,
     TEST_MINIMAL_SEQ_SCORESET,
     TEST_VARIANT_MAPPING_SCAFFOLD,
+    VALID_ACCESSION,
 )
 
 
@@ -130,8 +131,10 @@ async def test_create_variants_for_score_set_with_validation_error(
 ):
     score_set_urn, scores, counts = await setup_records_and_files(async_client, data_files, input_score_set)
 
-    # This is invalid for both data sets.
-    scores.loc[:, HGVS_NT_COLUMN].iloc[0] = "c.1T>A"
+    if input_score_set == TEST_MINIMAL_SEQ_SCORESET:
+        scores.loc[:, HGVS_NT_COLUMN].iloc[0] = "c.1T>A"
+    else:
+        scores.loc[:, HGVS_NT_COLUMN].iloc[0] = f"{VALID_ACCESSION}:c.1T>A"
 
     with (
         patch.object(