tests & fixes for hgvs parser

countess/plugins/hgvs_parser.py

@@ -2,6 +2,7 @@
 from typing import Optional
 
 import pandas as pd
+import numpy as np
 
 from countess import VERSION
 from countess.core.parameters import BooleanParam, ColumnChoiceParam, ColumnOrNoneChoiceParam, IntegerParam, StringParam
@@ -25,10 +26,10 @@ def process_dict(self, data: dict):
         try:
             value = data[str(self.column)]
         except KeyError:
-            return None
+            return {}
 
-        if value is None:
-            return None
+        if type(value) is not str:
+            return {}
 
         output = {}
 
@@ -56,7 +57,7 @@ def process_dict(self, data: dict):
         max_variations = int(self.max_var)
         variations = [v for v in variations if v not in guides]
         if len(variations) > max_variations:
-            return None
+            return {}
 
         output_vars: list[Optional[str]] = [None] * max_variations
         output_locs: list[Optional[str]] = [None] * max_variations

tests/plugins/test_hgvs_parser.py

@@ -1,8 +1,5 @@
-import sys
-from time import sleep
-
+import numpy as np
 import pandas as pd
-import pytest
 
 from countess.plugins.hgvs_parser import HgvsParserPlugin
 
@@ -76,3 +73,21 @@ def test_hgvs_parser_split_and_multi():
     assert df["var"].iloc[1] == "A>G"
     assert df["loc"].iloc[0] == "43124175"
     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]"}]
+)
+
+def test_hgvs_parser_bad():
+    plugin = HgvsParserPlugin()
+    plugin.set_parameter("column", "hgvs")
+
+    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])
+