CU-8692uznvd: Allow empty-dict config.linking.filters.cuis and convert to set in memory

medcat/config.py

@@ -1,5 +1,5 @@
 from datetime import datetime
-from pydantic import BaseModel, Extra, ValidationError
+from pydantic import BaseModel, Extra, ValidationError, validator
 from pydantic.dataclasses import Any, Callable, Dict, Optional, Union
 from pydantic.fields import ModelField
 from typing import List, Set, Tuple, cast
@@ -433,6 +433,19 @@ class LinkingFilters(MixingConfig, BaseModel):
     cuis: Set[str] = set()
     cuis_exclude: Set[str] = set()
 
+    @validator("cuis", pre=True, always=True)
+    def convert_empty_dict_to_set(cls, value):
+        if isinstance(value, dict) and not value:
+            # is empty dict
+            logger.warning("Loading an old model where "
+                           "config.linking.filters.cuis has been "
+                           "dict to an empty dict instead of an empty "
+                           "set. Converting the dict to a set in memory "
+                           "as that is what is expected. Please consider "
+                           "saving the model again.")
+            return set()
+        return value
+
     def check_filters(self, cui: str) -> bool:
         """Checks is a CUI in the filters
 

tests/test_config.py

@@ -1,7 +1,7 @@
 import unittest
 import pickle
 import tempfile
-from medcat.config import Config, MixingConfig, VersionInfo, General
+from medcat.config import Config, MixingConfig, VersionInfo, General, LinkingFilters
 from pydantic import ValidationError
 import os
 
@@ -180,5 +180,24 @@ def test_from_dict(self):
         self.assertEqual("value", config.key)
 
 
+class ConfigLinkingFiltersTests(unittest.TestCase):
+
+    def test_allows_empty_dict_for_cuis(self):
+        lf = LinkingFilters(cuis={})
+        self.assertIsNotNone(lf)
+
+    def test_empty_dict_converted_to_empty_set(self):
+        lf = LinkingFilters(cuis={})
+        self.assertEqual(lf.cuis, set())
+
+    def test_not_allow_nonempty_dict_for_cuis(self):
+        with self.assertRaises(ValidationError):
+            LinkingFilters(cuis={"KEY": "VALUE"})
+
+    def test_not_allow_empty_dict_for_cuis_exclude(self):
+        with self.assertRaises(ValidationError):
+            LinkingFilters(cuis_exclude={})
+
+
 if __name__ == '__main__':
     unittest.main()