Cleanup & formatting

Author: jstone-dev

src/mavedb/lib/score_sets.py

@@ -619,26 +619,12 @@ def variant_to_csv_row(
         elif column_key == "post_mapped_hgvs_g":
             hgvs_str = get_hgvs_from_mapped_variant(mapping.post_mapped) if mapping and mapping.post_mapped else None
             if hgvs_str is not None and is_hgvs_g(hgvs_str):
-                # parsed_variant = hgvs_parser.parse(hgvs_str)
-                # if parsed_variant is None:
-                #     raise ValueError(f"Invalid HGVS notation in post-mapped variant: {hgvs_str}")
-                # elif parsed_variant.type == "g":
-                #     value = hgvs_str
-                # else:
-                #     value = ""
                 value = hgvs_str
             else:
                 value = ""
         elif column_key == "post_mapped_hgvs_p":
             hgvs_str = get_hgvs_from_mapped_variant(mapping.post_mapped) if mapping and mapping.post_mapped else None
             if hgvs_str is not None and is_hgvs_p(hgvs_str):
-                # parsed_variant = hgvs_parser.parse(hgvs_str)
-                # if parsed_variant is None:
-                #     raise ValueError(f"Invalid HGVS notation in post-mapped variant: {hgvs_str}")
-                # elif parsed_variant.type == "p":
-                #     value = hgvs_str
-                # else:
-                #     value = ""
                 value = hgvs_str
             else:
                 value = ""

tests/helpers/constants.py

@@ -1095,10 +1095,7 @@
 TEST_POST_MAPPED_VRS_WITH_HGVS_G_EXPRESSION = {
     "id": "ga4gh:VA.fRW7u-kBQnAKitu1PoDMLvlECWZTHCos",
     "type": "Allele",
-    "state": {
-        "type": "LiteralSequenceExpression",
-        "sequence": "G"
-    },
+    "state": {"type": "LiteralSequenceExpression", "sequence": "G"},
     "digest": "fRW7u-kBQnAKitu1PoDMLvlECWZTHCos",
     "location": {
         "id": "ga4gh:SL.99b3WBaSSmaSTs6YmJfIhl1ZDCV07VZY",
@@ -1109,48 +1106,28 @@
         "sequenceReference": {
             "type": "SequenceReference",
             "label": "NC_000018.10",
-            "refgetAccession": "SQ.vWwFhJ5lQDMhh-czg06YtlWqu0lvFAZV"
-        }
+            "refgetAccession": "SQ.vWwFhJ5lQDMhh-czg06YtlWqu0lvFAZV",
+        },
     },
-    "extensions": [{
-        "name": "vrs_ref_allele_seq",
-        "type": "Extension",
-        "value": "C"
-    }],
-    "expressions": [{
-        "value": "NC_000018.10:g.23536836C>G",
-        "syntax": "hgvs.g"
-    }]
+    "extensions": [{"name": "vrs_ref_allele_seq", "type": "Extension", "value": "C"}],
+    "expressions": [{"value": "NC_000018.10:g.23536836C>G", "syntax": "hgvs.g"}],
 }
 
 TEST_POST_MAPPED_VRS_WITH_HGVS_P_EXPRESSION = {
     "id": "ga4gh:VA.zkOAzZK5qG0D0mkJUfXlK1aS075OGSjh",
     "type": "Allele",
-    "state": {
-        "type": "LiteralSequenceExpression",
-        "sequence": "R"
-    },
+    "state": {"type": "LiteralSequenceExpression", "sequence": "R"},
     "digest": "zkOAzZK5qG0D0mkJUfXlK1aS075OGSjh",
     "location": {
         "id": "ga4gh:SL.uUyRpJbrPttRThL7A2zeWAnTcb_7f1R2",
         "end": 116,
         "type": "SequenceLocation",
         "start": 115,
         "digest": "uUyRpJbrPttRThL7A2zeWAnTcb_7f1R2",
-        "sequenceReference": {
-            "type": "SequenceReference",
-            "refgetAccession": "SQ.StlJo3M4b8cS253ufe9nPpWqQHBDOSPs"
-        }
+        "sequenceReference": {"type": "SequenceReference", "refgetAccession": "SQ.StlJo3M4b8cS253ufe9nPpWqQHBDOSPs"},
     },
-    "extensions": [{
-        "name": "vrs_ref_allele_seq",
-        "type": "Extension",
-        "value": "Q"
-    }],
-    "expressions": [{
-        "value": "NP_002746.1:p.Gln116Arg",
-        "syntax": "hgvs.p"
-    }]
+    "extensions": [{"name": "vrs_ref_allele_seq", "type": "Extension", "value": "Q"}],
+    "expressions": [{"value": "NP_002746.1:p.Gln116Arg", "syntax": "hgvs.p"}],
 }
 
 TEST_MAPPED_VARIANT_WITH_HGVS_G_EXPRESSION = {

tests/routers/test_score_set.py

@@ -2351,8 +2351,19 @@ def test_upload_a_non_utf8_file(session, client, setup_router_db, data_files):
 # Score set download files
 ########################################################################################################################
 
-@pytest.mark.parametrize("mapped_variant,has_hgvs_g,has_hgvs_p", [(None, False, False), (TEST_MAPPED_VARIANT_WITH_HGVS_G_EXPRESSION, True, False), (TEST_MAPPED_VARIANT_WITH_HGVS_P_EXPRESSION, False, True)], ids=["without_post_mapped_vrs", "with_post_mapped_hgvs_g", "with_post_mapped_hgvs_p"])
-def test_download_variants_data_file(session, data_provider, client, setup_router_db, data_files, mapped_variant, has_hgvs_g, has_hgvs_p):
+
+@pytest.mark.parametrize(
+    "mapped_variant,has_hgvs_g,has_hgvs_p",
+    [
+        (None, False, False),
+        (TEST_MAPPED_VARIANT_WITH_HGVS_G_EXPRESSION, True, False),
+        (TEST_MAPPED_VARIANT_WITH_HGVS_P_EXPRESSION, False, True),
+    ],
+    ids=["without_post_mapped_vrs", "with_post_mapped_hgvs_g", "with_post_mapped_hgvs_p"],
+)
+def test_download_variants_data_file(
+    session, data_provider, client, setup_router_db, data_files, mapped_variant, has_hgvs_g, has_hgvs_p
+):
     experiment = create_experiment(client)
     score_set = create_seq_score_set(client, experiment["urn"])
     score_set = mock_worker_variant_insertion(client, session, data_provider, score_set, data_files / "scores.csv")
@@ -2370,14 +2381,16 @@ def test_download_variants_data_file(session, data_provider, client, setup_route
     download_scores_csv = download_scores_csv_response.text
 
     reader = csv.DictReader(StringIO(download_scores_csv))
-    assert sorted(reader.fieldnames) == sorted([
-        "accession",
-        "hgvs_nt",
-        "hgvs_pro",
-        "post_mapped_hgvs_g",
-        "post_mapped_hgvs_p",
-        "score",
-    ])
+    assert sorted(reader.fieldnames) == sorted(
+        [
+            "accession",
+            "hgvs_nt",
+            "hgvs_pro",
+            "post_mapped_hgvs_g",
+            "post_mapped_hgvs_p",
+            "score",
+        ]
+    )
     rows = list(reader)
     for row in rows:
         if has_hgvs_g: