Merge pull request #88 from apdavison/separate-reverse-properties

Separate forward and reverse properties into different attributes

Author: apdavison

builder/fairgraph_module_template.py.txt

@@ -32,6 +32,8 @@ class {{ class_name }}({{ base_class }}):
             {%- if prop.required %}required={{prop.required}},{% endif -%}
             doc="{{prop.doc}}"),
         {% endfor %}
+    ]
+    reverse_properties = [
         {% for prop in reverse_properties -%}
         Property(
             "{{prop.name}}", {{prop.type_str}},

fairgraph/base.py

@@ -19,7 +19,6 @@
 
 
 from __future__ import annotations
-
 from typing import TYPE_CHECKING, Optional, Dict, List, Union, Any
 from typing_extensions import TypeAlias
 from copy import copy
@@ -76,6 +75,7 @@ def resolve(
 
 class ContainsMetadata(Resolvable, metaclass=Registry):  # KGObject and EmbeddedMetadata
     properties: List[Property]
+    reverse_properties: List[Property]
     context: Dict[str, str]
     type_: List[str]
     scope: Optional[str]
@@ -86,7 +86,7 @@ class ContainsMetadata(Resolvable, metaclass=Registry):  # KGObject and Embedded
 
     def __init__(self, data: Optional[Dict] = None, **properties):
         properties_copy = copy(properties)
-        for prop in self.properties:
+        for prop in self.__class__.all_properties:
             try:
                 val = properties[prop.name]
             except KeyError:
@@ -169,7 +169,7 @@ def to_jsonld(
             data: JSONdict = {"@type": self.type_}
             if hasattr(self, "id") and self.id:
                 data["@id"] = self.id
-            for prop in self.properties:
+            for prop in self.__class__.all_properties:
                 if prop.intrinsic or include_reverse_properties:
                     expanded_path = prop.expanded_path
                     value = getattr(self, prop.name)
@@ -242,7 +242,7 @@ def set_error_handling(
                 else:
                     prop.error_handling = value
         else:
-            for prop in cls.properties:
+            for prop in cls.all_properties:
                 prop.error_handling = value
 
     @classmethod
@@ -267,7 +267,7 @@ def normalize_filter(cls, filter_dict: Dict[str, Any]) -> Dict[str, Any]:
             if name_ in filter_dict_copy:
                 filter_dict_copy[alias_] = filter_dict_copy.pop(name_)
 
-        for prop in cls.properties:
+        for prop in cls.all_properties:
             if prop.name in filter_dict_copy:
                 value = filter_dict_copy[prop.name]
                 if isinstance(value, dict):
@@ -289,7 +289,7 @@ def generate_query_properties(cls, follow_links: Optional[Dict[str, Any]] = None
         """
         properties = [QueryProperty("@type")]
         reverse_aliases = invert_dict(cls.aliases)
-        for prop in cls.properties:
+        for prop in cls.all_properties:
             if prop.is_link and follow_links:
                 if prop.name in follow_links:
                     properties.extend(prop.get_query_properties(follow_links[prop.name]))
@@ -314,7 +314,7 @@ def generate_query_filter_properties(
         if filters is None:
             filters = {}
         properties = []
-        for prop in cls.properties:
+        for prop in cls.all_properties:
             if prop.name in filters:
                 properties.append(prop.get_query_filter_property(filters[prop.name]))
         return properties
@@ -343,7 +343,7 @@ def _deserialize_data(cls, data: JSONdict, client: KGClient, include_id: bool =
             if otype not in D["@type"]:
                 raise TypeError("type mismatch {} - {}".format(otype, D["@type"]))
         deserialized_data = {}
-        for prop in cls.properties:
+        for prop in cls.all_properties:
             expanded_path = expand_uri(prop.path, cls.context)
             data_item = D.get(expanded_path)
             if data_item is not None and prop.reverse:
@@ -386,7 +386,7 @@ def resolve(
         use_scope = scope or self.scope or "released"
         if follow_links:
             reverse_aliases = invert_dict(self.__class__.aliases)
-            for prop in self.properties:
+            for prop in self.__class__.all_properties:
                 if prop.is_link:
                     follow_name = None
                     if prop.name in follow_links:
@@ -436,7 +436,7 @@ def _build_existence_query(self) -> Union[None, Dict[str, Any]]:
 
         query_properties = []
         for property_name in self.existence_query_properties:
-            for property in self.properties:
+            for property in self.__class__.all_properties:
                 if property.name == property_name:
                     query_properties.append(property)
                     break

fairgraph/kgobject.py

@@ -77,8 +77,8 @@ def __init__(
         self.scope = scope
         self.allow_update = True
         super().__init__(data=data, **properties)
-        for prop in self.properties:
-            if prop.reverse and not hasattr(self, prop.name):
+        for prop in self.reverse_properties:
+            if not hasattr(self, prop.name):
                 query = KGQuery(
                     prop.types, {prop.reverse: self.id}, callback=lambda value: setattr(self, prop.name, value)
                 )
@@ -87,7 +87,7 @@ def __init__(
     def __repr__(self):
         template_parts = (
             "{}={{self.{}!r}}".format(prop.name, prop.name)
-            for prop in self.properties
+            for prop in self.__class__.all_properties
             if getattr(self, prop.name) is not None
         )
         template = "{self.__class__.__name__}(" + ", ".join(template_parts) + ", space={self.space}, id={self.id})"
@@ -424,7 +424,7 @@ def _update_empty_properties(self, data: JSONdict, client: KGClient):
         """Replace any empty properties (value None) with the supplied data"""
         cls = self.__class__
         deserialized_data = cls._deserialize_data(data, client, include_id=True)
-        for prop in cls.properties:
+        for prop in cls.all_properties:
             current_value = getattr(self, prop.name, None)
             if current_value is None:
                 value = deserialized_data[prop.name]
@@ -445,11 +445,11 @@ def __ne__(self, other):
         if self.id and other.id and self.id != other.id:
             return True
         for prop in self.properties:
-            if prop.intrinsic:
-                val_self = getattr(self, prop.name)
-                val_other = getattr(other, prop.name)
-                if val_self != val_other:
-                    return True
+            assert prop.intrinsic
+            val_self = getattr(self, prop.name)
+            val_other = getattr(other, prop.name)
+            if val_self != val_other:
+                return True
         return False
 
     def diff(self, other):
@@ -463,11 +463,11 @@ def diff(self, other):
             if self.id != other.id:
                 differences["id"] = (self.id, other.id)
             for prop in self.properties:
-                if prop.intrinsic:
-                    val_self = getattr(self, prop.name)
-                    val_other = getattr(other, prop.name)
-                    if val_self != val_other:
-                        differences["properties"][prop.name] = (val_self, val_other)
+                assert prop.intrinsic
+                val_self = getattr(self, prop.name)
+                val_other = getattr(other, prop.name)
+                if val_self != val_other:
+                    differences["properties"][prop.name] = (val_self, val_other)
         return differences
 
     def exists(self, client: KGClient) -> bool:
@@ -568,39 +568,39 @@ def save(
         """
         if recursive:
             for prop in self.properties:
-                if prop.intrinsic:
-                    # we do not save reverse properties, those objects must be saved separately
-                    # this could be revisited, but we'll have to be careful about loops
-                    # if saving recursively
-                    values = getattr(self, prop.name)
-                    for value in as_list(values):
-                        if isinstance(value, ContainsMetadata):
-                            target_space: Optional[str]
-                            if value.space:
-                                target_space = value.space
-                            elif (
-                                isinstance(value, KGObject)
-                                and value.__class__.default_space == "controlled"
-                                and value.exists(client)
-                                and value.space == "controlled"
-                            ):
+                assert prop.intrinsic
+                # we do not save reverse properties, those objects must be saved separately
+                # this could be revisited, but we'll have to be careful about loops
+                # if saving recursively
+                values = getattr(self, prop.name)
+                for value in as_list(values):
+                    if isinstance(value, ContainsMetadata):
+                        target_space: Optional[str]
+                        if value.space:
+                            target_space = value.space
+                        elif (
+                            isinstance(value, KGObject)
+                            and value.__class__.default_space == "controlled"
+                            and value.exists(client)
+                            and value.space == "controlled"
+                        ):
+                            continue
+                        elif space is None and self.space is not None:
+                            target_space = self.space
+                        else:
+                            target_space = space
+                        if target_space == "controlled":
+                            assert isinstance(value, KGObject)  # for type checking
+                            if value.exists(client) and value.space == "controlled":
                                 continue
-                            elif space is None and self.space is not None:
-                                target_space = self.space
                             else:
-                                target_space = space
-                            if target_space == "controlled":
-                                assert isinstance(value, KGObject)  # for type checking
-                                if value.exists(client) and value.space == "controlled":
-                                    continue
-                                else:
-                                    raise AuthorizationError("Cannot write to controlled space")
-                            value.save(
-                                client,
-                                space=target_space,
-                                recursive=True,
-                                activity_log=activity_log,
-                            )
+                                raise AuthorizationError("Cannot write to controlled space")
+                        value.save(
+                            client,
+                            space=target_space,
+                            recursive=True,
+                            activity_log=activity_log,
+                        )
         if space is None:
             if self.space is None:
                 space = self.__class__.default_space
@@ -762,7 +762,7 @@ def show(self, max_width: Optional[int] = None, include_empty_properties=False):
             ("space", str(self.space)),
             ("type", self.type_[0]),
         ]
-        for prop in self.properties:
+        for prop in self.__class__.all_properties:
             value = getattr(self, prop.name, None)
             if include_empty_properties or not isinstance(value, (type(None), KGQuery)):
                 data.append((prop.name, str(value)))
@@ -836,7 +836,8 @@ def children(
             self.resolve(client, follow_links=follow_links)
         all_children = []
         for prop in self.properties:
-            if prop.intrinsic and prop.is_link:
+            assert prop.intrinsic
+            if prop.is_link:
                 children = as_list(getattr(self, prop.name))
                 all_children.extend(children)
                 if follow_links:

fairgraph/openminds/chemicals/amount_of_chemical.py

@@ -35,7 +35,7 @@ class AmountOfChemical(EmbeddedMetadata):
             doc="no description available",
         ),
     ]
-    existence_query_properties = ("chemical_product", "amount")
+    reverse_properties = []
 
     def __init__(self, amount=None, chemical_product=None, id=None, data=None, space=None, scope=None):
         return super().__init__(data=data, amount=amount, chemical_product=chemical_product)

fairgraph/openminds/chemicals/chemical_mixture.py

@@ -56,6 +56,8 @@ class ChemicalMixture(KGObject):
             required=True,
             doc="Distinct class to which a group of entities or concepts with similar characteristics or attributes belong to.",
         ),
+    ]
+    reverse_properties = [
         Property(
             "composes",
             ["openminds.ephys.Electrode", "openminds.ephys.ElectrodeArray", "openminds.ephys.Pipette"],

fairgraph/openminds/chemicals/chemical_substance.py

@@ -49,6 +49,8 @@ class ChemicalSubstance(KGObject):
             "vocab:purity",
             doc="no description available",
         ),
+    ]
+    reverse_properties = [
         Property(
             "composes",
             ["openminds.ephys.Electrode", "openminds.ephys.ElectrodeArray", "openminds.ephys.Pipette"],

fairgraph/openminds/chemicals/product_source.py

@@ -44,6 +44,8 @@ class ProductSource(KGObject):
             "vocab:purity",
             doc="no description available",
         ),
+    ]
+    reverse_properties = [
         Property(
             "is_source_of",
             ["openminds.chemicals.ChemicalMixture", "openminds.chemicals.ChemicalSubstance"],

fairgraph/openminds/computation/data_analysis.py

@@ -167,6 +167,8 @@ class DataAnalysis(KGObject):
             "vocab:wasInformedBy",
             doc="no description available",
         ),
+    ]
+    reverse_properties = [
         Property(
             "informed",
             [

fairgraph/openminds/computation/data_copy.py

@@ -163,6 +163,8 @@ class DataCopy(KGObject):
             "vocab:wasInformedBy",
             doc="no description available",
         ),
+    ]
+    reverse_properties = [
         Property(
             "informed",
             [

fairgraph/openminds/computation/environment.py

@@ -53,6 +53,8 @@ class Environment(KGObject):
             multiple=True,
             doc="no description available",
         ),
+    ]
+    reverse_properties = [
         Property(
             "used_for",
             [