fix for saving & restoring ColumnOrStringParam value

countess/core/parameters.py

@@ -417,21 +417,15 @@ def get_column_name(self):
 
  def get_value(self, data: dict):
  if self.value.startswith(self.PREFIX):
- return data[self.value[len(self.PREFIX):]]
+ return data[self.value[len(self.PREFIX) :]]
  else:
  return self.value
 
-
-class ColumnOrIntegerParam(ColumnOrStringParam):
- def clean_value(self, value):
- if isinstance(value, str):
- return int("".join(re.split(r"\D+", value)))
- else:
- return int(value)
-
-
-class MultipleChoiceParam(ChoiceParam):
- pass
+ def set_choices(self, choices: Iterable[str]):
+ self.choices = list(choices)
+ if self._value is not None and self._value.startswith(self.PREFIX) and self._value not in self.choices:
+ self._value = self.DEFAULT_VALUE
+ self._choice = None
 
 
 class ArrayParam(BaseParam):

countess/gui/config.py

@@ -198,6 +198,7 @@ def update(self):
  elif isinstance(self.parameter, ChoiceParam):
  choices = self.parameter.choices or [""]
  self.entry["values"] = choices
+ self.var.set(self.parameter.value)
  elif isinstance(self.parameter, BooleanParam):
  self.set_checkbox_value()
  elif isinstance(self.parameter, TextParam):

tests/plugins/test_variant.py

@@ -6,6 +6,26 @@
 
 logger = MultiprocessLogger()
 
+def test_variant_ref_value():
+ input_df = pd.DataFrame(
+ [{"seq": "TGAAGTAGAGG"}, {"seq": "AGAAGTTGTGG"}, {"seq": "ATAAGAAGAGG"}]
+ )
+ plugin = VariantPlugin()
+ plugin.set_parameter("column", "seq")
+ plugin.set_parameter("reference", "AGAAGTAGAGG")
+ plugin.set_parameter("output", "out")
+
+ plugin.prepare(["test"], None)
+
+ output_df = plugin.process_dataframe(input_df, logger)
+
+ output = output_df.to_records()
+
+ assert output[0]["out"] == "g.1A>T"
+ assert output[1]["out"] == "g.[7A>T;9A>T]"
+ assert output[2]["out"] == "g.[2G>T;6T>A]"
+
+
 
 def test_variant_ref_column():
  input_df = pd.DataFrame(
@@ -14,7 +34,7 @@ def test_variant_ref_column():
 
  plugin = VariantPlugin()
  plugin.set_parameter("column", "seq")
- plugin.set_parameter("reference", "ref")
+ plugin.set_parameter("reference", "— ref")
  plugin.set_parameter("output", "out")
 
  plugin.prepare(["test"], None)