From 448538c99017a139fc973be757ee3d45f1ff5215 Mon Sep 17 00:00:00 2001
From: Kori Kuzma <korikuzma@gmail.com>
Date: Thu, 11 Jul 2024 12:45:59 -0400
Subject: [PATCH] fix: remove domain models from entity models (#426)

* Forgot to remove in #422
---
 src/ga4gh/core/entity_models.py | 131 +-------------------------------
 1 file changed, 1 insertion(+), 130 deletions(-)

diff --git a/src/ga4gh/core/entity_models.py b/src/ga4gh/core/entity_models.py
index ea575bf2..bf91f597 100644
--- a/src/ga4gh/core/entity_models.py
+++ b/src/ga4gh/core/entity_models.py
@@ -10,7 +10,7 @@
   * `import ga4gh.core`, and refer to models using the fully-qualified
     module name, e.g., `ga4gh.core.entity_models.Coding`
 """
-from typing import Any, Dict, Literal, Annotated, Optional, Union, List
+from typing import Any, Dict, Annotated, Optional, Union, List
 from enum import Enum
 
 from pydantic import BaseModel, Field, RootModel, StringConstraints, model_serializer
@@ -185,132 +185,3 @@ class _DomainEntity(_Entity):
     """
 
     mappings: Optional[List[ConceptMapping]] = Field(None, description="A list of mappings to concepts in terminologies or code systems. Each mapping should include a coding and a relation.")
-
-
-#########################################
-# GKS Common Domain Entities
-#########################################
-
-
-class CommonDomainType(str, Enum):
-    """Define GKS Common Domain Entity types"""
-
-    PHENOTYPE = "Phenotype"
-    DISEASE = "Disease"
-    TRAIT_SET = "TraitSet"
-    TR_ACTION = "TherapeuticAction"
-    TR_AGENT = "TherapeuticAgent"
-    TR_SUB = "TherapeuticSubstituteGroup"
-    TR_COMB = "CombinationTherapy"
-    GENE = "Gene"
-
-class Phenotype(_DomainEntity):
-    """An observable characteristic or trait of an organism."""
-
-    type: Literal[CommonDomainType.PHENOTYPE] = Field(
-        CommonDomainType.PHENOTYPE,
-        description=f'MUST be "{CommonDomainType.PHENOTYPE.value}".'
-    )
-
-
-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.
-    """
-
-    type: Literal[CommonDomainType.DISEASE] = Field(
-        CommonDomainType.DISEASE,
-        description=f'MUST be "{CommonDomainType.DISEASE.value}".'
-    )
-
-
-class TraitSet(_DomainEntity):
-    """A set of phenotype and/or disease concepts that together constitute a condition."""
-
-    type: Literal[CommonDomainType.TRAIT_SET] = Field(
-        CommonDomainType.TRAIT_SET,
-        description=f'MUST be "{CommonDomainType.TRAIT_SET.value}".'
-    )
-    traits: List[Union[Disease, Phenotype]] = Field(
-        ...,
-        min_length=2
-    )
-
-
-class Condition(RootModel):
-    """A disease or other medical disorder."""
-
-    root: Union[TraitSet, Disease, Phenotype] = Field(
-        ...,
-        json_schema_extra={'description': 'A disease or other medical disorder.'},
-        discriminator='type',
-    )
-
-
-class TherapeuticAction(_DomainEntity):
-    """A therapeutic action taken that is intended to alter or stop a pathologic process."""
-
-    type: Literal[CommonDomainType.TR_ACTION] = Field(
-        CommonDomainType.TR_ACTION,
-        description=f'MUST be "{CommonDomainType.TR_ACTION.value}".'
-    )
-
-
-class TherapeuticAgent(_DomainEntity):
-    """An administered therapeutic agent that is intended to alter or stop a pathologic process."""
-
-    type: Literal[CommonDomainType.TR_AGENT] = Field(
-        CommonDomainType.TR_AGENT,
-        description=f'MUST be "{CommonDomainType.TR_AGENT.value}".'
-    )
-
-
-class TherapeuticSubstituteGroup(_DomainEntity):
-    """A group of therapeutic procedures that may be treated as substitutes for one another."""
-
-    type: Literal[CommonDomainType.TR_SUB] = Field(
-        CommonDomainType.TR_SUB,
-        description=f'MUST be "{CommonDomainType.TR_SUB.value}".'
-    )
-    substitutes: List[Union[TherapeuticAction, TherapeuticAgent]] = Field(
-        ...,
-        description='The individual therapeutic procedures that may be treated as substitutes.',
-        min_length=2
-    )
-
-
-class CombinationTherapy(_DomainEntity):
-    """A therapeutic procedure that involves multiple different therapeutic procedures
-    performed in combination.
-    """
-
-    type: Literal[CommonDomainType.TR_COMB] = Field(
-        CommonDomainType.TR_COMB,
-        description=f'MUST be "{CommonDomainType.TR_COMB.value}".'
-    )
-    components: List[Union[TherapeuticSubstituteGroup, TherapeuticAction, TherapeuticAgent]] = Field(
-        ...,
-        description='The individual therapeutic procedure components that constitute the combination therapy.',
-        min_length=2
-    )
-
-
-class TherapeuticProcedure(RootModel):
-    """An action or administration of therapeutic agents to produce an effect  that is
-    intended to alter or stop a pathologic process.
-    """
-
-    root: Union[CombinationTherapy, TherapeuticSubstituteGroup, TherapeuticAction, TherapeuticAgent] = Field(
-        ...,
-        json_schema_extra={'description': 'An action or administration of therapeutic agents to produce an effect that is intended to alter or stop a pathologic process.'},
-        discriminator='type',
-    )
-
-
-class Gene(_DomainEntity):
-    """A basic physical and functional unit of heredity."""
-
-    type: Literal[CommonDomainType.GENE] = Field(
-        CommonDomainType.GENE,
-        description=f'MUST be "{CommonDomainType.GENE.value}".'
-    )