Merge pull request #182 from CitrineInformatics/maintain/update-objec…

…t-model

Add central registry for classes; add metaclass for DictSerializable

gemd/builders/tests/test_builders.py

@@ -16,7 +16,7 @@
 from typing import Union
 
 
-class UnsupportedBounds(BaseBounds):
+class UnsupportedBounds(BaseBounds, typ="unsupported_bounds"):
     """Dummy object to test Bounds type checking."""
 
     def contains(self, bounds):  # pragma: no cover
@@ -32,15 +32,15 @@ def update(self, *others: Union["BaseBounds", "BaseValue"]):  # pragma: no cover
         pass
 
 
-class UnsupportedAttribute(BaseAttribute):
+class UnsupportedAttribute(BaseAttribute, typ="unsupported_attribute"):
     """Dummy object to test Attribute type checking."""
 
     def _template_type(self):  # pragma: no cover
         """Only here to satisfy abstract method."""
         return str
 
 
-class UnsupportedAttributeTemplate(AttributeTemplate):
+class UnsupportedAttributeTemplate(AttributeTemplate, typ="unsupported_template"):
     """Dummy object to test Attribute type checking."""
 
 

gemd/entity/attribute/condition.py

@@ -4,7 +4,7 @@
 from typing import Type
 
 
-class Condition(BaseAttribute):
+class Condition(BaseAttribute, typ="condition"):
     """
     Condition of a property, process, or measurement.
 
@@ -31,8 +31,6 @@ class Condition(BaseAttribute):
 
     """
 
-    typ = "condition"
-
     @staticmethod
     def _template_type() -> Type:
         return ConditionTemplate

gemd/entity/attribute/parameter.py

@@ -4,7 +4,7 @@
 from typing import Type
 
 
-class Parameter(BaseAttribute):
+class Parameter(BaseAttribute, typ="parameter"):
     """
     Parameter of a process or measurement.
 
@@ -32,8 +32,6 @@ class Parameter(BaseAttribute):
 
     """
 
-    typ = "parameter"
-
     @staticmethod
     def _template_type() -> Type:
         return ParameterTemplate

gemd/entity/attribute/property.py

@@ -4,7 +4,7 @@
 from typing import Type
 
 
-class Property(BaseAttribute):
+class Property(BaseAttribute, typ="property"):
     """
     Property of a material, measured in a MeasurementRun or specified in a MaterialSpec.
 
@@ -31,8 +31,6 @@ class Property(BaseAttribute):
 
     """
 
-    typ = "property"
-
     @staticmethod
     def _template_type() -> Type:
         return PropertyTemplate

gemd/entity/attribute/property_and_conditions.py

@@ -9,7 +9,7 @@
 from typing import Optional, Union, Iterable, List
 
 
-class PropertyAndConditions(DictSerializable):
+class PropertyAndConditions(DictSerializable, typ="property_and_conditions"):
     """
     A property and the conditions under which that property was determined.
 
@@ -24,8 +24,6 @@ class PropertyAndConditions(DictSerializable):
 
     """
 
-    typ = "property_and_conditions"
-
     def __init__(self,
                  property: Property = None,
                  conditions: Union[Iterable[Condition], Condition] = None):

gemd/entity/base_entity.py

@@ -24,8 +24,6 @@ class BaseEntity(DictSerializable):
 
     """
 
-    typ = "base"
-
     def __init__(self, uids: Mapping[str, str], tags: Iterable[str]):
         self._tags = None
         self.tags = tags

gemd/entity/bounds/categorical_bounds.py

@@ -5,7 +5,7 @@
 from typing import Union, Set, Optional, Iterable
 
 
-class CategoricalBounds(BaseBounds):
+class CategoricalBounds(BaseBounds, typ="categorical_bounds"):
     """
     Categorical bounds, parameterized by a set of string-valued category labels.
 
@@ -16,8 +16,6 @@ class CategoricalBounds(BaseBounds):
 
     """
 
-    typ = "categorical_bounds"
-
     def __init__(self, categories: Optional[Iterable[str]] = None):
         self._categories = None
         self.categories = categories

gemd/entity/bounds/composition_bounds.py

@@ -5,7 +5,7 @@
 from typing import Union
 
 
-class CompositionBounds(BaseBounds):
+class CompositionBounds(BaseBounds, typ="composition_bounds"):
     """
     Composition bounds, parameterized by a set of string-valued category labels.
 
@@ -16,8 +16,6 @@ class CompositionBounds(BaseBounds):
 
     """
 
-    typ = "composition_bounds"
-
     def __init__(self, components=None):
         self._components = None
         self.components = components

gemd/entity/bounds/integer_bounds.py

@@ -4,7 +4,7 @@
 from typing import Union
 
 
-class IntegerBounds(BaseBounds):
+class IntegerBounds(BaseBounds, typ="integer_bounds"):
     """
     Bounded subset of the integers, parameterized by a lower and upper bound.
 
@@ -17,8 +17,6 @@ class IntegerBounds(BaseBounds):
 
     """
 
-    typ = "integer_bounds"
-
     def __init__(self, lower_bound=None, upper_bound=None):
         self.lower_bound = lower_bound
         self.upper_bound = upper_bound

gemd/entity/bounds/molecular_structure_bounds.py

@@ -8,14 +8,9 @@
 from typing import Union
 
 
-class MolecularStructureBounds(BaseBounds):
+class MolecularStructureBounds(BaseBounds, typ="molecular_structure_bounds"):
     """Molecular bounds, with no component or substructural restrictions (yet)."""
 
-    typ = "molecular_structure_bounds"
-
-    def __init__(self):
-        pass
-
     def contains(self, bounds: Union[BaseBounds, "BaseValue"]) -> bool:
         """
         Check if another bounds or value object is contained by this bounds.

gemd/entity/bounds/real_bounds.py

@@ -5,7 +5,7 @@
 from typing import Union
 
 
-class RealBounds(BaseBounds):
+class RealBounds(BaseBounds, typ="real_bounds"):
     """
     Bounded subset of the real numbers, parameterized by a lower and upper bound.
 
@@ -21,8 +21,6 @@ class RealBounds(BaseBounds):
 
     """
 
-    typ = "real_bounds"
-
     def __init__(self, lower_bound=None, upper_bound=None, default_units=None):
         self.lower_bound = lower_bound
         self.upper_bound = upper_bound

gemd/entity/dict_serializable.py

@@ -1,24 +1,61 @@
-from abc import ABC
+from abc import ABC, ABCMeta
 from logging import getLogger
 
 import json
 import inspect
 import functools
-from typing import Union, Iterable, List, Mapping, Dict, Any
+from typing import TypeVar, Union, Iterable, List, Mapping, Dict, Set, Any
 
 # There are some weird (probably resolvable) errors during object cloning if this is an
 # instance variable of DictSerializable.
 logger = getLogger(__name__)
 
+DictSerializableType = TypeVar("DictSerializableType", bound="DictSerializable")
 
-class DictSerializable(ABC):
-    """A base class for objects that can be represented as a dictionary and serialized."""
 
-    typ = NotImplemented
-    skip = set()
+class DictSerializableMeta(ABCMeta):
+    """Metaclass for tracking DictSerializable type string to class mappings."""
+
+    _class: Dict[str, type] = {}
+
+    def __new__(mcs, name, bases, *args,
+                typ: str = None, skip: Set[str] = frozenset(),
+                **kwargs):  # noqa: D102
+        return super().__new__(mcs, name, bases, *args, **kwargs)
+
+    def __init__(cls, name, bases, *args, typ: str = None, skip: Set[str] = frozenset(), **kwargs):
+        super().__init__(name, bases, *args, **kwargs)
+        if typ is not None:
+            if typ in cls._class and not issubclass(cls, cls._class.get(typ)):
+                raise ValueError(f"{cls} attempted to take typ {typ} from {cls._class.get(typ)}, "
+                                 f"which is not its ancestor.")
+            cls.typ = typ
+            cls._class[typ] = cls
+        elif not hasattr(cls, "typ"):
+            cls.typ = NotImplementedError
+        cls.skip = {x for b in bases for x in getattr(b, 'skip', {})} | skip
+
+    @property
+    def class_mapping(cls) -> Dict[str, type]:
+        """
+        Return class typ string -> class map for DictSerializable and its descendants.
+
+        Note that is actually returns a copy of the internal dict to avoid accidental breakage.
+
+        Returns
+        -------
+        Dict[str, type]
+            The mapping from typ string to class
+
+        """
+        return cls._class.copy()
+
+
+class DictSerializable(ABC, metaclass=DictSerializableMeta):
+    """A base class for objects that can be represented as a dictionary and serialized."""
 
     @classmethod
-    def from_dict(cls, d: Mapping[str, Any]) -> "DictSerializable":
+    def from_dict(cls, d: Mapping[str, Any]) -> DictSerializableType:
         """
         Reconstitute the object from a dictionary.
 
@@ -111,13 +148,14 @@ def build(d: Mapping[str, Any]) -> "DictSerializable":
     def __repr__(self) -> str:
         object_dict = self.as_dict()
         # as_dict() skips over keys in `skip`, but they should be in the representation.
-        skipped_keys = {x.lstrip('_') for x in vars(self) if x in self.skip}
+        skipped_keys = {x.lstrip('_') for x in self.skip}
         for key in skipped_keys:
             skipped_field = getattr(self, key, None)
             object_dict[key] = self._name_repr(skipped_field)
         return str(object_dict)
 
-    def _name_repr(self, entity: Union[Iterable["DictSerializable"], "DictSerializable"]) -> str:
+    def _name_repr(self,
+                   entity: Union[Iterable[DictSerializableType], DictSerializableType]) -> str:
         """
         A representation of an object or a list of objects that uses the name and type.
 

gemd/entity/file_link.py

@@ -2,7 +2,7 @@
 from gemd.entity.dict_serializable import DictSerializable
 
 
-class FileLink(DictSerializable):
+class FileLink(DictSerializable, typ="file_link"):
     """
     FileLink stores a name and link to an external resource.
 
@@ -21,8 +21,6 @@ class FileLink(DictSerializable):
 
     """
 
-    typ = "file_link"
-
     def __init__(self, filename, url):
         DictSerializable.__init__(self)
         self.filename = filename

gemd/entity/link_by_uid.py

@@ -5,7 +5,7 @@
 from gemd.entity.dict_serializable import DictSerializable
 
 
-class LinkByUID(DictSerializable):
+class LinkByUID(DictSerializable, typ="link_by_uid"):
     """
     Link object, which replaces pointers to other entities before serialization and writing.
 
@@ -18,8 +18,6 @@ class LinkByUID(DictSerializable):
 
     """
 
-    typ = "link_by_uid"
-
     def __init__(self, scope, id):
         # TODO: parse to make sure it's valid
         self.scope = scope

gemd/entity/object/ingredient_run.py

@@ -15,7 +15,9 @@
 from typing import Optional, Union, Iterable, List, Mapping, Type, Any
 
 
-class IngredientRun(BaseObject, HasQuantities, HasSpec, HasMaterial, HasProcess):
+class IngredientRun(BaseObject,
+                    HasQuantities, HasSpec, HasMaterial, HasProcess,
+                    typ="ingredient_run"):
     """
     An ingredient run.
 
@@ -56,8 +58,6 @@ class IngredientRun(BaseObject, HasQuantities, HasSpec, HasMaterial, HasProcess)
 
     """
 
-    typ = "ingredient_run"
-
     def __init__(self,
                  *,
                  material: Union[MaterialRun, LinkByUID] = None,

gemd/entity/object/ingredient_spec.py

@@ -13,7 +13,9 @@
 from typing import Optional, Union, Iterable, List, Mapping, Type
 
 
-class IngredientSpec(BaseObject, HasQuantities, HasTemplate, HasMaterial, HasProcess):
+class IngredientSpec(BaseObject,
+                     HasQuantities, HasTemplate, HasMaterial, HasProcess,
+                     typ="ingredient_spec"):
     """
     An ingredient specification.
 
@@ -56,8 +58,6 @@ class IngredientSpec(BaseObject, HasQuantities, HasTemplate, HasMaterial, HasPro
 
     """
 
-    typ = "ingredient_spec"
-
     def __init__(self,
                  name: str,
                  *,

gemd/entity/object/material_run.py

@@ -11,7 +11,7 @@
 from typing import Optional, Union, Iterable, List, Mapping, Type, Any
 
 
-class MaterialRun(BaseObject, HasSpec, HasProcess):
+class MaterialRun(BaseObject, HasSpec, HasProcess, typ="material_run", skip={"_measurements"}):
     """
     A material run.
 
@@ -50,10 +50,6 @@ class MaterialRun(BaseObject, HasSpec, HasProcess):
 
     """
 
-    typ = "material_run"
-
-    skip = {"_measurements"}
-
     def __init__(self,
                  name: str,
                  *,