tests for hgvs parsed plugin

countess/plugins/hgvs_parser.py

@@ -38,8 +38,8 @@ def process_dict(self, data: dict):
  if self.guides_str:
  guides += self.guides_str.value.split(";")
 
- if m := re.match(r"([\w.]+):([ncg].)(.*)", value):
- output["reference"] = m.group(1)
+ if m := re.match(r"(?:([\w.]+):)?([ncg]\.)(.*)", value):
+ output["reference"] = m.group(1) or ''
  output["prefix"] = m.group(2)
  value = m.group(3)
 

tests/plugins/test_hgvs_parser.py

@@ -75,7 +75,7 @@ def test_hgvs_parser_split_and_multi():
  assert df["loc"].iloc[1] == "43124111"
 
 
-df2 = pd.DataFrame([{"fnords": "whatever"}, {"hgvs": None}, {"hgvs": "g.="}, {"hgvs": "g.[1A>T;2G>C;3C>T;4A>T;5A>T]"}])
+df2 = pd.DataFrame([{"fnords": "whatever"}, {"hgvs": None}, {"hgvs": "g.[1A>T;2G>C;3C>T;4A>T;5A>T]"}])
 
 
 def test_hgvs_parser_bad():
@@ -85,7 +85,17 @@ def test_hgvs_parser_bad():
  df = plugin.process_dataframe(df2)
 
  print(df)
- assert np.isnan(df["var_1"].iloc[0])
- assert np.isnan(df["var_1"].iloc[1])
- assert df["var_1"].iloc[2] == "g.="
- assert np.isnan(df["var_1"].iloc[3])
+ assert all(np.isnan(df["var_1"]))
+ #assert np.isnan(df["var_1"].iloc[0])
+ #assert np.isnan(df["var_1"].iloc[1])
+ #assert np.isnan(df["var_1"].iloc[2])
+
+
+def test_hgvs_parser_very_bad():
+ plugin = HgvsParserPlugin()
+ plugin.set_parameter("column", "hgvs")
+
+ dfi = pd.DataFrame([{'a': 1}])
+ dfo = plugin.process_dataframe(dfi)
+
+ assert all(dfo == dfi)