update invalid tests for normalize + put in todo reminder

cancervariants · Aug 1, 2023 · ce7bbfb · ce7bbfb
1 parent 1bb95ae
commit ce7bbfb
Showing 1 changed file with 21 additions and 17 deletions.
diff --git a/tests/test_normalize.py b/tests/test_normalize.py
@@ -1022,6 +1022,9 @@ async def test_genomic_delins(
  "NC_000003.12:g.10149938delinsAA",
  )
 
+ # TODO: Add response
+ resp = await test_handler.normalize("BRAF g.140453135_140453136delinsAT")
+
 
 @pytest.mark.asyncio
 async def test_protein_delins(test_handler, protein_delins):
@@ -1305,24 +1308,24 @@ async def test_valid_queries(test_handler):
 async def test_no_matches(test_handler):
  """Test no matches work correctly."""
  queries = [
- "braf",
- "braf v600e",
- "braf v600000932092039e",
- "NP_000213.1:cp.Leu862=",
- "NP_000213.1:cp.Leu862",
- "BRAF V600E 33",
- "NP_004324.2:p.Glu600Val",
- "NP_004324.2:p.Glu600Gal",
- "NP_004324.2839:p.Glu600Val",
- "NP_004324.2:t.Glu600Val",
- "this:c.54G>H",
- "NC_000007.13:g.4T<A",
+ "braf", # no change
+ "braf v600e", # incorrect case
+ "braf v600000932092039e", # invalid pos
+ "NP_000213.1:cp.Leu862=", # cp is invalid
+ "NP_000213.1:cp.Leu862", # cp is invalid
+ "BRAF V600E 33", # not supported query type
+ "NP_004324.2:p.Glu600Val", # not valid ref
+ "NP_004324.2:p.Glu600Gal", # not valid ref
+ "NP_004324.2839:p.Glu600Val", # not valid accession
+ "NP_004324.2:t.Glu600Val", # t is invalid
+ "this:c.54G>H", # not a valid accession
+ "NC_000007.13:g.4T<A", # invalid hgvs format
  "test",
  "131",
- "braf z600e",
- "braf e600z",
- "Thr790Met",
- "p.Tyr365Ter",
+ "braf Z600E", # invalid ref
+ "braf E600Z", # invalid ref
+ "Thr790Met", # no gene/accession
+ "p.Tyr365Ter", # no accession
  "ERBB2 G776delinsVCZ",
  "NP005219.2:p.Glu746_Thr751delinsValAla",
  "NP_005219.2:p.Glu746Thr751delinsValAla",
@@ -1331,7 +1334,8 @@ async def test_no_matches(test_handler):
  "EGFR delins",
  "NM_004333.4:c.1799_1800delTGinsAT",
  "NM_173851.3(SLC30A8):c.973C>T%20(p.Arg325Trp)",
- "NG_008212.3:g.5426_5445del",
+ "NG_008212.3:g.5426_5445del", # NG accessions not supported
+ "NC_000010.11-87925523-C-G", # invalid format
  ]
  for q in queries:
  assert isinstance(q, str)