normalize_data no longer suppresses keys with value None. Fixes #101

Author: apdavison

fairgraph/kgobject.py

@@ -95,7 +95,7 @@ def __init__(
             self._raw_remote_data = data  # for debugging
             if data:
                 self.remote_data = normalize_data(
-                    self.to_jsonld(include_empty_properties=True, embed_linked_nodes=False),
+                    self.to_jsonld(include_empty_properties=False, embed_linked_nodes=False),
                     data.get("@context", self.context)
                 )
 
@@ -737,7 +737,10 @@ def save(
                     activity_log.update(item=self, delta=None, space=space, entry_type="no-op")
             else:
                 # update
-                local_data = normalize_data(self.to_jsonld(embed_linked_nodes=False), self.context)
+                local_data = normalize_data(
+                    self.to_jsonld(include_empty_properties=False, embed_linked_nodes=False),
+                    self.context
+                )
                 if replace:
                     logger.info(f"  - replacing - {self.__class__.__name__}(id={self.id})")
                     if activity_log:
@@ -793,7 +796,10 @@ def save(
                             activity_log.update(item=self, delta=None, space=space, entry_type="no-op")
         else:
             # create new
-            local_data = normalize_data(self.to_jsonld(embed_linked_nodes=False), self.context)
+            local_data = normalize_data(
+                self.to_jsonld(include_empty_properties=False, embed_linked_nodes=False),
+                self.context
+            )
             logger.info("  - creating instance with data {}".format(local_data))
             if self.id and self.id.startswith("http"):
                 instance_id = self.uuid

fairgraph/utility.py

@@ -218,8 +218,6 @@ def normalize_data(data: Union[None, JSONdict], context: Dict[str, Any]) -> Unio
 
         if hasattr(value, "__len__") and len(value) == 0:
             pass
-        elif value is None:
-            pass
         elif expanded_key == "@id":
             if value.startswith("http"):
                 # do not take local ids, e.g., those starting with "_"

test/test_base.py

@@ -485,18 +485,24 @@ def test_modified_data(self):
             self._construct_embedded_object_required_properties(-18),
             self._construct_embedded_object_required_properties(19),
         ]
+        obj.an_optional_list_of_linked_objects = None
         expected = {
             "https://openminds.ebrains.eu/vocab/aRequiredString": "pomme",
             "https://openminds.ebrains.eu/vocab/anOptionalListOfEmbeddedObjects": [
                 {
                     "@type": "https://openminds.ebrains.eu/mock/MockEmbeddedObject",
+                    "https://openminds.ebrains.eu/vocab/aDate": None,
                     "https://openminds.ebrains.eu/vocab/aNumber": -18,
+                    "https://openminds.ebrains.eu/vocab/aString": None,
                 },
                 {
                     "@type": "https://openminds.ebrains.eu/mock/MockEmbeddedObject",
+                    "https://openminds.ebrains.eu/vocab/aDate": None,
                     "https://openminds.ebrains.eu/vocab/aNumber": 19,
+                    "https://openminds.ebrains.eu/vocab/aString": None,
                 },
             ],
+            "https://openminds.ebrains.eu/vocab/anOptionalListOfLinkedObjects": None
         }
         assert obj.modified_data() == expected
 
@@ -594,7 +600,7 @@ def instance_from_full_uri(self, id, use_cache=True, release_status="in progress
                 # not just those that have changed
                 "https://openminds.ebrains.eu/vocab/aNumber": 41,
                 "https://openminds.ebrains.eu/vocab/aString": "forty one",
-                # "https://openminds.ebrains.eu/vocab/aDate": None,
+                "https://openminds.ebrains.eu/vocab/aDate": None,
             },
         }
         assert new_obj.modified_data() == expected

test/test_utility.py

@@ -82,6 +82,7 @@ def test_normalize_data():
         },
         "familyName": "Oakenshield",
         "givenName": "Thorin",
+        "alternateName": None
     }
     context = {"@vocab": "https://openminds.ebrains.eu/vocab/"}
     expected = {
@@ -96,6 +97,7 @@ def test_normalize_data():
         },
         "https://openminds.ebrains.eu/vocab/familyName": "Oakenshield",
         "https://openminds.ebrains.eu/vocab/givenName": "Thorin",
+        "https://openminds.ebrains.eu/vocab/alternateName": None
     }
     assert normalize_data(data, context) == expected