Change the type_ attribute to be a string (as in openMINDS Python), rather than a single-element list containing that string (as in the KG). (#89)

Author: apdavison

builder/fairgraph_module_template.py.txt

@@ -17,7 +17,7 @@ class {{ class_name }}({{ base_class }}):
     {%- if default_space %}
     default_space = "{{ default_space }}"
     {%- endif %}
-    type_ = ["{{ openminds_type }}"]
+    type_ = "{{ openminds_type }}"
     context = {
         "schema": "http://schema.org/",
         "kg": "https://kg.ebrains.eu/api/instances/",

fairgraph/base.py

@@ -77,7 +77,7 @@ class ContainsMetadata(Resolvable, metaclass=Registry):  # KGObject and Embedded
     properties: List[Property]
     reverse_properties: List[Property]
     context: Dict[str, str]
-    type_: List[str]
+    type_: str
     scope: Optional[str]
     space: Union[str, None]
     default_space: Union[str, None]
@@ -166,7 +166,7 @@ def to_jsonld(
 
         """
         if self.properties:
-            data: JSONdict = {"@type": self.type_}
+            data: JSONdict = {"@type": [self.type_]}
             if hasattr(self, "id") and self.id:
                 data["@id"] = self.id
             for prop in self.__class__.all_properties:
@@ -339,9 +339,16 @@ def _deserialize_data(cls, data: JSONdict, client: KGClient, include_id: bool =
             elif key[0] != "@":
                 normalised_key = expand_uri(key, cls.context)
                 D[normalised_key] = value
-        for otype in expand_uri(as_list(cls.type_), cls.context):
-            if otype not in D["@type"]:
-                raise TypeError("type mismatch {} - {}".format(otype, D["@type"]))
+        if cls.type_ not in D["@type"]:
+            raise TypeError("type mismatch {} - {}".format(cls.type_, D["@type"]))
+
+        def _get_type_from_data(data_item):
+            type_ = data_item.get("@type", None)
+            if type_:
+                return type_[0]
+            else:
+                return None
+
         deserialized_data = {}
         for prop in cls.all_properties:
             expanded_path = expand_uri(prop.path, cls.context)
@@ -352,7 +359,7 @@ def _deserialize_data(cls, data: JSONdict, client: KGClient, include_id: bool =
                 try:
                     data_item = [
                         part for part in as_list(data_item)
-                        if part.get("@type", None) in [t.type_ for t in prop.types]
+                        if _get_type_from_data(part) in [t.type_ for t in prop.types]
                     ]
                 except AttributeError:
                     # problem when a forward and reverse path both given the same expanded path

fairgraph/client.py

@@ -576,7 +576,7 @@ def configure_space(self, space_name: Optional[str] = None, types: Optional[List
         if result:  # error
             raise Exception(f"Unable to configure KG space for space '{space_name}': {result}")
         for cls in types:
-            result = self._kg_admin_client.assign_type_to_space(space=space_name, target_type=cls.type_[0])
+            result = self._kg_admin_client.assign_type_to_space(space=space_name, target_type=cls.type_)
             if result:  # error
                 raise Exception(f"Unable to assign {cls.__name__} to space {space_name}: {result}")
         return space_name

fairgraph/kgobject.py

@@ -229,7 +229,7 @@ def from_id(
             if follow_links is not None:
                 raise NotImplementedError
             data = client.instance_from_full_uri(uri, use_cache=use_cache, scope=scope)
-            cls_from_data = lookup_type(data["@type"])
+            cls_from_data = lookup_type(data["@type"][0])
             return cls_from_data.from_kg_instance(data, client, scope=scope)
 
     @classmethod
@@ -760,7 +760,7 @@ def show(self, max_width: Optional[int] = None, include_empty_properties=False):
         data = [
             ("id", str(self.id)),
             ("space", str(self.space)),
-            ("type", self.type_[0]),
+            ("type", self.type_),
         ]
         for prop in self.__class__.all_properties:
             value = getattr(self, prop.name, None)
@@ -813,7 +813,7 @@ def generate_query(
             normalized_filters = None
         # first pass, we build the basic structure
         query = Query(
-            node_type=cls.type_[0],
+            node_type=cls.type_,
             label=label,
             space=real_space,
             properties=cls.generate_query_properties(follow_links),

fairgraph/openminds/chemicals/amount_of_chemical.py

@@ -13,7 +13,7 @@ class AmountOfChemical(EmbeddedMetadata):
     Structured information about the amount of a given chemical that was used.
     """
 
-    type_ = ["https://openminds.ebrains.eu/chemicals/AmountOfChemical"]
+    type_ = "https://openminds.ebrains.eu/chemicals/AmountOfChemical"
     context = {
         "schema": "http://schema.org/",
         "kg": "https://kg.ebrains.eu/api/instances/",

fairgraph/openminds/chemicals/chemical_mixture.py

@@ -14,7 +14,7 @@ class ChemicalMixture(KGObject):
     """
 
     default_space = "in-depth"
-    type_ = ["https://openminds.ebrains.eu/chemicals/ChemicalMixture"]
+    type_ = "https://openminds.ebrains.eu/chemicals/ChemicalMixture"
     context = {
         "schema": "http://schema.org/",
         "kg": "https://kg.ebrains.eu/api/instances/",

fairgraph/openminds/chemicals/chemical_substance.py

@@ -14,7 +14,7 @@ class ChemicalSubstance(KGObject):
     """
 
     default_space = "in-depth"
-    type_ = ["https://openminds.ebrains.eu/chemicals/ChemicalSubstance"]
+    type_ = "https://openminds.ebrains.eu/chemicals/ChemicalSubstance"
     context = {
         "schema": "http://schema.org/",
         "kg": "https://kg.ebrains.eu/api/instances/",

fairgraph/openminds/chemicals/product_source.py

@@ -14,7 +14,7 @@ class ProductSource(KGObject):
     """
 
     default_space = "in-depth"
-    type_ = ["https://openminds.ebrains.eu/chemicals/ProductSource"]
+    type_ = "https://openminds.ebrains.eu/chemicals/ProductSource"
     context = {
         "schema": "http://schema.org/",
         "kg": "https://kg.ebrains.eu/api/instances/",

fairgraph/openminds/computation/data_analysis.py

@@ -17,7 +17,7 @@ class DataAnalysis(KGObject):
     """
 
     default_space = "computation"
-    type_ = ["https://openminds.ebrains.eu/computation/DataAnalysis"]
+    type_ = "https://openminds.ebrains.eu/computation/DataAnalysis"
     context = {
         "schema": "http://schema.org/",
         "kg": "https://kg.ebrains.eu/api/instances/",

fairgraph/openminds/computation/data_copy.py

@@ -17,7 +17,7 @@ class DataCopy(KGObject):
     """
 
     default_space = "computation"
-    type_ = ["https://openminds.ebrains.eu/computation/DataCopy"]
+    type_ = "https://openminds.ebrains.eu/computation/DataCopy"
     context = {
         "schema": "http://schema.org/",
         "kg": "https://kg.ebrains.eu/api/instances/",