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fix: remove domain models from entity models #426

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Jul 11, 2024
Merged

fix: remove domain models from entity models #426

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131 changes: 1 addition & 130 deletions src/ga4gh/core/entity_models.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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}".'
)
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