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chore!: update vrs/gks-common submodules (#424)
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* Removes Information Entity, Activity, Contribution, Agent, Document,
Method, + Record Metadata pydantic models
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@korikuzma
korikuzma committed Jul 10, 2024
1 parent a2477e1 commit ae49021
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143 changes: 3 additions & 140 deletions src/ga4gh/core/_internal/models.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,25 +10,18 @@
* `import ga4gh.core`, and refer to models using the fully-qualified
module name, e.g., `ga4gh.core.common_models.Gene`
"""
from __future__ import annotations
import datetime
from typing import Any, Dict, Literal, Annotated, Optional, Union, List
from enum import Enum

from pydantic import BaseModel, Field, RootModel, StringConstraints, constr, field_validator, model_serializer, model_validator
from pydantic import BaseModel, Field, RootModel, StringConstraints, model_serializer

from ga4gh.core import GA4GH_IR_REGEXP


#########################################
# GKS Common Abstract Entity & Utility Class Definitions
# GKS Common Utility Class Definitions
#########################################

class AgentSubtype(str, Enum):
"""Define constraints for agent subtype"""

PERSON = "person"
ORGANIZATION = "organization"
COMPUTER = "computer"

class Relation(str, Enum):
"""A mapping relation between concepts as defined by the Simple Knowledge
Expand Down Expand Up @@ -102,18 +95,6 @@ def ga4gh_serialize(self):
)


class RecordMetadata(BaseModel):
"""A reusable structure that encapsulates provenance metadata about a serialized
data record or object in a particular dataset (as opposed to provenance about the
real world entity this record or object represents).
"""

recordIdentifier: Optional[str] = Field(None, description="The identifier of the data record or object described in this RecordMetadata object.")
recordVersion: Optional[str] = Field(None, description="The version number of the record-level artifact the object describes.")
derivedFrom: Optional[str] = Field(None, description="Another data record from which the record described here was derived, through a data ingest and/or transformation process. Value should be a string representing the identifier of the source record.")
dateRecordCreated: Optional[str] = Field(None, description="The date the record was initially created.")
contributions: Optional[List[Contribution]] = Field(None, description="Describes specific contributions made by an human or software agent to the creation, modification, or administrative management of a data record or object.")


class Coding(BaseModel):
"""A structured representation of a code for a defined concept in a terminology or
Expand Down Expand Up @@ -176,15 +157,6 @@ class Expression(BaseModel):
#########################################


class CommonEntityType(str, Enum):
"""Define GKS Common Entity types"""

AGENT = "Agent"
CONTRIBUTION = "Contribution"
DOCUMENT = "Document"
METHOD = "Method"


class _Entity(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,
Expand Down Expand Up @@ -219,115 +191,6 @@ 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.")


class Agent(_Entity):
"""An autonomous actor (person, organization, or computational agent) that bears
some form of responsibility for an activity taking place, for the existence of an
entity, or for another agent's activity.
"""

type: Literal[CommonEntityType.AGENT] = Field(CommonEntityType.AGENT, description=f"MUST be '{CommonEntityType.AGENT.value}'.")
name: Optional[str] = Field(None, description="The descriptive name of the agent.")
subtype: Optional[AgentSubtype] = Field(None, description="A more specific type of agent the agent represents.")


class Activity(_Entity):
"""An action or set of actions performed by an agent, that occurs over a period of
time. Activities may use, generate, modify, move, or destroy one or more entities.
"""

subtype: Optional[Coding] = Field(None, description="A more specific type of activity that an Activity object may represent.")
date: Optional[str] = Field(None, description="The date that the Activity was completed. The date SHOULD be formatted as a date string in ISO format 'YYYY-MM-DD'.")
performedBy: Optional[List[Agent]] = Field(None, description="An Agent who contributed to executing the Activity.")
specifiedBy: Optional[List[Method]] = Field(None, description="A method that was followed in performing an Activity, that describes how it was executed.")

@field_validator("date")
@classmethod
def date_format(cls, v: Optional[str]) -> Optional[str]:
"""Check that date is YYYY-MM-DD format"""
if v:
valid_format = "%Y-%m-%d"

try:
datetime.datetime.strptime(v, valid_format).replace(
tzinfo=datetime.timezone.utc
).strftime(valid_format)
except ValueError as e:
msg = "`date` must use YYYY-MM-DD format"
raise ValueError(msg) from e
return v


class Contribution(Activity):
"""An action taken by an agent in contributing to the creation, modification,
assessment, or deprecation of a particular entity (e.g. a Statement, EvidenceLine,
DataItem, Publication, etc.)
"""

type: Literal[CommonEntityType.CONTRIBUTION] = CommonEntityType.CONTRIBUTION
contributor: Optional[Agent] = Field(None, description="The agent that made the contribution.")
contributionMadeTo: Optional[_InformationEntity] = Field(None, description="The artifact toward which the contribution was made.") # noqa: N815
activityType: Optional[Coding] = Field(None, description="SHOULD describe a concept descending from the Contributor Role Ontology.")

@model_validator(mode="before")
def handle_extends_prop(cls, values: Dict[str, Any]) -> Dict[str, Any]:
"""Handle extends properties by renaming fields
:param values: Input values to process
:return: Processed values with extended properties renamed
"""
if "performedBy" in values:
values["contributor"] = values.pop("performedBy")
return values


class _InformationEntity(_Entity):
"""Information Entities are abstract (non-physical) entities that are about
something (i.e. they carry information about things in the real world).
"""

id: str
specifiedBy: Optional[Union[Method, IRI]] = Field(None, description="A `Method` that describes all or part of the process through which the information was generated.")
contributions: Optional[List[Contribution]] = Field(None, description="A list of `Contribution` objects that describe the activities performed by agents upon this entity.")
isReportedIn: Optional[List[Union[Document, IRI]]] = Field(None, description="A document in which the information content is expressed.")
dateAuthored: Optional[str] = Field(None, description="Indicates when the information content expressed in the Information Entity was generated.")
derivedFrom: Optional[List[_InformationEntity]] = Field(None, description="Another Information Entity from which this Information Entity is derived, in whole or in part.")
recordMetadata: Optional[RecordMetadata] = Field(None, description="Metadata that applies to a specific concrete record of information as encoded in a particular system.")

class Document(_InformationEntity):
"""a representation of a physical or digital document"""

type: Literal[CommonEntityType.DOCUMENT] = CommonEntityType.DOCUMENT
subtype: Optional[Coding] = Field(
None, description="A more specific type for the document (e.g. a publication, patent, pathology report)"
)
title: Optional[str] = Field(None, description="The title of the Document")
url: Optional[constr(pattern="^(https?|s?ftp)://")] = Field(
None, description="A URL at which the document may be retrieved."
)
doi: Optional[constr(pattern="^10.(\\d+)(\\.\\d+)*\\/[\\w\\-\\.]+")] = Field(
None,
description="A `Digital Object Identifier <https://www.doi.org/the-identifier/what-is-a-doi/>_` for the document.",
)
pmid: Optional[int] = Field(
None,
description="A `PubMed unique identifier <https://en.wikipedia.org/wiki/PubMed#PubMed_identifier>`_.",
)


class Method(_InformationEntity):
"""A set of instructions that specify how to achieve some objective (e.g.
experimental protocols, curation guidelines, rule sets, etc.)
"""

type: Literal[CommonEntityType.METHOD] = Field(CommonEntityType.METHOD, description=f"MUST be '{CommonEntityType.METHOD.value}'.")
isReportedIn: Optional[Union[Document, IRI]] = None # noqa: N815
subtype: Optional[Coding] = Field(
None,
description="A more specific type of entity the method represents (e.g. Variant Interpretation Guideline, Experimental Protocol)",
)
license: Optional[str] = Field(None, description="A particular license that dictates legal permissions for how a published method (e.g. an experimental protocol, workflow specification, curation guideline) can be used.")


#########################################
# GKS Common Domain Entities
#########################################
Expand Down
2 changes: 1 addition & 1 deletion submodules/vrs
Submodule vrs updated 2 files
+4 −0 schema/vrs/Makefile
+1 −1 submodules/gks-common

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