Update tests to reflect multi-target mapper changes

Author: sallybg

tests/helpers/constants.py

@@ -832,17 +832,47 @@
     }
 }
 
-TEST_VARIANT_MAPPING_SCAFFOLD = {
+TEST_SEQ_SCORESET_VARIANT_MAPPING_SCAFFOLD = {
     "metadata": {},
-    "computed_genomic_reference_sequence": {
-        "sequence_type": "dna",
-        "sequence_id": "ga4gh:SQ.ref_test",
-        "sequence": "ACGTTT",
+    "reference_sequences": {
+        "TEST1": {
+            "g": {
+                "computed_reference_sequence": {
+                    "sequence_type": "dna",
+                    "sequence_id": "ga4gh:SQ.ref_test",
+                    "sequence": "ACGTTT",
+                },
+                "mapped_reference_sequence": {
+                    "sequence_type": "dna",
+                    "sequence_id": "ga4gh:SQ.map_test",
+                    "sequence_accessions": ["NC_000001.11"],
+                },
+            }
+        }
     },
-    "mapped_genomic_reference_sequence": {
-        "sequence_type": "dna",
-        "sequence_id": "ga4gh:SQ.map_test",
-        "sequence_accessions": ["NC_000001.11"],
+    "mapped_scores": [],
+    "vrs_version": "2.0",
+    "dcd_mapping_version": "pytest.0.0",
+    "mapped_date_utc": datetime.isoformat(datetime.now()),
+}
+
+TEST_ACC_SCORESET_VARIANT_MAPPING_SCAFFOLD = {
+    "metadata": {},
+    "reference_sequences": {
+        "TEST2": {
+            "g": {
+                "computed_reference_sequence": {
+                    "sequence_type": "dna",
+                    "sequence_id": "ga4gh:SQ.ref_test",
+                    "sequence": "ACGTTT",
+                },
+                "mapped_reference_sequence": {
+                    "sequence_type": "dna",
+                    "sequence_id": "ga4gh:SQ.map_test",
+                    "sequence_accessions": ["NC_000001.11"],
+                },
+            }
+        }
     },
     "mapped_scores": [],
     "vrs_version": "2.0",

tests/worker/test_jobs.py

@@ -40,6 +40,7 @@
 
 
 from tests.helpers.constants import (
+    TEST_ACC_SCORESET_VARIANT_MAPPING_SCAFFOLD,
     TEST_CLINGEN_SUBMISSION_RESPONSE,
     TEST_CLINGEN_SUBMISSION_BAD_RESQUEST_RESPONSE,
     TEST_CLINGEN_SUBMISSION_UNAUTHORIZED_RESPONSE,
@@ -48,7 +49,7 @@
     TEST_MINIMAL_ACC_SCORESET,
     TEST_MINIMAL_EXPERIMENT,
     TEST_MINIMAL_SEQ_SCORESET,
-    TEST_VARIANT_MAPPING_SCAFFOLD,
+    TEST_SEQ_SCORESET_VARIANT_MAPPING_SCAFFOLD,
     VALID_NT_ACCESSION,
     TEST_VALID_PRE_MAPPED_VRS_ALLELE_VRS1_X,
     TEST_VALID_PRE_MAPPED_VRS_ALLELE_VRS2_X,
@@ -150,10 +151,13 @@ async def sanitize_mapping_queue(standalone_worker_context, score_set):
     assert int(queued_job.decode("utf-8")) == score_set.id
 
 
-async def setup_mapping_output(async_client, session, score_set, empty=False):
+async def setup_mapping_output(async_client, session, score_set, score_set_is_seq_based=True, empty=False):
     score_set_response = await async_client.get(f"/api/v1/score-sets/{score_set.urn}")
 
-    mapping_output = deepcopy(TEST_VARIANT_MAPPING_SCAFFOLD)
+    if score_set_is_seq_based:
+        mapping_output = deepcopy(TEST_SEQ_SCORESET_VARIANT_MAPPING_SCAFFOLD)
+    else:
+        mapping_output = deepcopy(TEST_ACC_SCORESET_VARIANT_MAPPING_SCAFFOLD)
     mapping_output["metadata"] = score_set_response.json()
 
     if empty:
@@ -477,11 +481,12 @@ async def test_create_variants_for_score_set_enqueues_manager_and_successful_map
     arq_worker,
     arq_redis,
 ):
+    score_set_is_seq = all(["targetSequence" in target for target in input_score_set["targetGenes"]])
     score_set_urn, scores, counts = await setup_records_and_files(async_client, data_files, input_score_set)
     score_set = session.scalars(select(ScoreSetDbModel).where(ScoreSetDbModel.urn == score_set_urn)).one()
 
     async def dummy_mapping_job():
-        return await setup_mapping_output(async_client, session, score_set)
+        return await setup_mapping_output(async_client, session, score_set, score_set_is_seq)
 
     async def dummy_submission_job():
         return [TEST_CLINGEN_SUBMISSION_RESPONSE, None]
@@ -511,7 +516,7 @@ async def dummy_linking_job():
         await arq_worker.run_check()
 
         # Call data provider _get_transcript method if this is an accession based score set, otherwise do not.
-        if all(["targetSequence" in target for target in input_score_set["targetGenes"]]):
+        if score_set_is_seq:
             hdp.assert_not_called()
         else:
             hdp.assert_called_once()