Merge branch 'main' into cleanup

src/ga4gh/core/domain_models.py

@@ -15,7 +15,7 @@
 
 from pydantic import Field, RootModel
 
-from ga4gh.core.entity_models import _DomainEntity
+from ga4gh.core.entity_models import DomainEntity
 
 
 class CommonDomainType(str, Enum):
@@ -30,7 +30,7 @@ class CommonDomainType(str, Enum):
     TR_COMB = "CombinationTherapy"
     GENE = "Gene"
 
-class Phenotype(_DomainEntity):
+class Phenotype(DomainEntity):
     """An observable characteristic or trait of an organism."""
 
     type: Literal[CommonDomainType.PHENOTYPE] = Field(
@@ -39,7 +39,7 @@ class Phenotype(_DomainEntity):
     )
 
 
-class Disease(_DomainEntity):
+class Disease(DomainEntity):
     """A particular abnormal condition that negatively affects the structure or function
     of all or part of an organism and is not immediately due to any external injury.
     """
@@ -50,7 +50,7 @@ class Disease(_DomainEntity):
     )
 
 
-class TraitSet(_DomainEntity):
+class TraitSet(DomainEntity):
     """A set of phenotype and/or disease concepts that together constitute a condition."""
 
     type: Literal[CommonDomainType.TRAIT_SET] = Field(
@@ -73,7 +73,7 @@ class Condition(RootModel):
     )
 
 
-class TherapeuticAction(_DomainEntity):
+class TherapeuticAction(DomainEntity):
     """A therapeutic action taken that is intended to alter or stop a pathologic process."""
 
     type: Literal[CommonDomainType.TR_ACTION] = Field(
@@ -82,7 +82,7 @@ class TherapeuticAction(_DomainEntity):
     )
 
 
-class TherapeuticAgent(_DomainEntity):
+class TherapeuticAgent(DomainEntity):
     """An administered therapeutic agent that is intended to alter or stop a pathologic process."""
 
     type: Literal[CommonDomainType.TR_AGENT] = Field(
@@ -91,7 +91,7 @@ class TherapeuticAgent(_DomainEntity):
     )
 
 
-class TherapeuticSubstituteGroup(_DomainEntity):
+class TherapeuticSubstituteGroup(DomainEntity):
     """A group of therapeutic procedures that may be treated as substitutes for one another."""
 
     type: Literal[CommonDomainType.TR_SUB] = Field(
@@ -105,7 +105,7 @@ class TherapeuticSubstituteGroup(_DomainEntity):
     )
 
 
-class CombinationTherapy(_DomainEntity):
+class CombinationTherapy(DomainEntity):
     """A therapeutic procedure that involves multiple different therapeutic procedures
     performed in combination.
     """
@@ -133,7 +133,7 @@ class TherapeuticProcedure(RootModel):
     )
 
 
-class Gene(_DomainEntity):
+class Gene(DomainEntity):
     """A basic physical and functional unit of heredity."""
 
     type: Literal[CommonDomainType.GENE] = Field(

src/ga4gh/core/entity_models.py

@@ -10,6 +10,7 @@
   * `import ga4gh.core`, and refer to models using the fully-qualified
     module name, e.g., `ga4gh.core.entity_models.Coding`
 """
+from abc import ABC
 from typing import Any, Dict, Annotated, Optional, Union, List
 from enum import Enum
 
@@ -153,7 +154,7 @@ class Expression(BaseModel):
 #########################################
 
 
-class _Entity(BaseModel):
+class Entity(ABC, BaseModel):
     """Entity is the root class of the 'gks-common' core information model classes -
     those that have identifiers and other general metadata like labels, xrefs, urls,
     descriptions, etc. All common classes descend from and inherit its attributes.
@@ -176,7 +177,7 @@ class _Entity(BaseModel):
     extensions: Optional[List[Extension]] = Field(None, description="A list of extensions to the entity. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems.")
 
 
-class _DomainEntity(_Entity):
+class DomainEntity(Entity, ABC):
     """An Entity that is specific to a particular biomedical domain such as disease,
     therapeutics, or genes. Domain Entities are considered as 'concept-level' entities,
     as opposed to particular instances. e.g. 'Lung Cancer', not 'patient123's lung

src/ga4gh/vrs/models.py

@@ -10,6 +10,7 @@
   * `import ga4gh.vrs`, and refer to models using the fully-qualified
     module name, e.g., `ga4gh.vrs.models.Allele`
 """
+from abc import ABC
 from typing import List, Literal, Optional, Union, Dict, Annotated
 from collections import OrderedDict
 from enum import Enum
@@ -30,7 +31,7 @@
 from ga4gh.core.pydantic import (
     getattr_in
 )
-from ga4gh.core.entity_models import IRI, Expression, _DomainEntity
+from ga4gh.core.entity_models import IRI, Expression, DomainEntity
 
 
 def flatten(vals):
@@ -186,7 +187,7 @@ def _recurse_ga4gh_serialize(obj):
         return obj
 
 
-class _ValueObject(_DomainEntity):
+class _ValueObject(DomainEntity, ABC):
     """A contextual value whose equality is based on value, not identity.
     See https://en.wikipedia.org/wiki/Value_object for more on Value Objects.
     """
@@ -210,7 +211,7 @@ def is_ga4gh_identifiable():
         return False
 
 
-class _Ga4ghIdentifiableObject(_ValueObject):
+class _Ga4ghIdentifiableObject(_ValueObject, ABC):
     """A contextual value object for which a GA4GH computed identifier can be created.
     All GA4GH Identifiable Objects may have computed digests from the VRS Computed
     Identifier algorithm.
@@ -513,7 +514,7 @@ class ga4gh(_Ga4ghIdentifiableObject.ga4gh):
 #########################################
 
 
-class _VariationBase(_Ga4ghIdentifiableObject):
+class _VariationBase(_Ga4ghIdentifiableObject, ABC):
     """Base class for variation"""
 
     expressions: Optional[List[Expression]] = None
@@ -666,7 +667,7 @@ class ga4gh(_Ga4ghIdentifiableObject.ga4gh):
 #########################################
 
 
-class _CopyNumber(_VariationBase):
+class _CopyNumber(_VariationBase, ABC):
     """A measure of the copies of a `Location` within a system (e.g. genome, cell, etc.)"""
 
     location: Union[IRI, SequenceLocation] = Field(