bug(medcat): CU-869b9dx49 Fix pydantic model serialisation (#242)

* CU-869b9dx49: Add test for config serialisation

* CU-869b9dx49: Fix issue with pydantic model serialisation when there are extra attributes

* CU-869b9dx49: Fix typing issue

Author: mart-r

medcat-v2/medcat/storage/serialisables.py

@@ -1,6 +1,8 @@
 from typing import Any, Union, Protocol, runtime_checkable, Iterable
 from enum import Enum, auto
 
+from pydantic import BaseModel
+
 
 class SerialisingStrategy(Enum):
     """Describes the strategy for serialising."""
@@ -50,6 +52,10 @@ def _iter_obj_items(self, obj: 'Serialisable'
                 # ignore privates
                 continue
             yield attr_name, attr
+        # deal with extras in pydantic models
+        if isinstance(obj, BaseModel) and obj.__pydantic_extra__:
+            for attr_name, attr in obj.__pydantic_extra__.items():
+                yield attr_name, attr
 
     def _iter_obj_values(self, obj: 'Serialisable') -> Iterable[Any]:
         for _, val in self._iter_obj_items(obj):

medcat-v2/tests/config/test_config_serialisation.py

@@ -0,0 +1,47 @@
+from medcat.config import Ner
+from medcat.storage.serialisers import serialise, deserialise
+from medcat.storage.serialisers import AvailableSerialisers
+
+import os
+import tempfile
+
+import unittest
+
+
+class SaveWithExtraTests(unittest.TestCase):
+    EXTRA_KEY = "some_extra_key"
+    EXTRA_VAL = {"val": 1, "f": ''}
+
+    def setUp(self):
+        self.base = Ner()
+        self.base.some_extra_key = self.EXTRA_VAL
+        self.temp_dir = tempfile.TemporaryDirectory()
+
+    def do_save(self) -> tuple[str, str]:
+        """Do the save and return folder path and raw dict path.
+
+        Returns:
+            tuple[str, str]: The folder and the path to raw dict.
+        """
+        serialise(AvailableSerialisers.dill, self.base, self.temp_dir.name)
+        return self.temp_dir.name, os.path.join(self.temp_dir.name,
+                                                "raw_dict.dat")
+
+    def tearDown(self):
+        self.temp_dir.cleanup()
+
+    def test_value_is_set(self):
+        self.assertTrue(hasattr(self.base, self.EXTRA_KEY))
+        self.assertIs(getattr(self.base, self.EXTRA_KEY), self.EXTRA_VAL)
+
+    def test_can_save_and_load_obj(self):
+        folder, _ = self.do_save()
+        other = deserialise(folder)
+        self.assertIsInstance(other, type(self.base))
+        self.assertEqual(other, self.base)
+
+    def test_loaded_has_extra_key(self):
+        folder, _ = self.do_save()
+        other = deserialise(folder)
+        self.assertTrue(hasattr(other, self.EXTRA_KEY))
+        self.assertEqual(getattr(other, self.EXTRA_KEY), self.EXTRA_VAL)