From c960dcfdfae77ea2ff5d4f14575df0446a5a77be Mon Sep 17 00:00:00 2001
From: Nick Moore <nick@zoic.org>
Date: Fri, 5 Apr 2024 16:36:30 +1100
Subject: [PATCH] fix for saving & restoring ColumnOrStringParam value

---
 countess/core/parameters.py   | 18 ++++++------------
 countess/gui/config.py        |  1 +
 tests/plugins/test_variant.py | 22 +++++++++++++++++++++-
 3 files changed, 28 insertions(+), 13 deletions(-)

diff --git a/countess/core/parameters.py b/countess/core/parameters.py
index 11173e3..dcda12e 100644
--- a/countess/core/parameters.py
+++ b/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):
diff --git a/countess/gui/config.py b/countess/gui/config.py
index 0ac31bb..556ca0e 100644
--- a/countess/gui/config.py
+++ b/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):
diff --git a/tests/plugins/test_variant.py b/tests/plugins/test_variant.py
index 94be184..09bef85 100644
--- a/tests/plugins/test_variant.py
+++ b/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)