phenopacket_mapper.api_requests package

This module is intended to provide a set of functions that will be used to make requests to the APIs of various code systems.

class phenopacket_mapper.api_requests.APIRequestSuperClass[source]

Bases: ABC

Super class for API requests to get details abput concepts from code systems

A class should implement this super class to provide a method to get details about a concept from one specific code system. An example of this can be seen in orpha_api_request.py where the Orphanet API is used to get details about a concept from the Orphanet code system.

abstract get(concept_id) → Coding[source]

phenopacket_mapper.api_requests.get(url: str, params: Dict = None, json=False)[source]

class phenopacket_mapper.api_requests.OrphaAPIRequest(orpha_code_system: ~phenopacket_mapper.data_standards.code_system.CodeSystem = CodeSystem(name=Orphanet Rare Disease Ontology, name space prefix=ORPHA, version=0.0.0))[source]

Bases: APIRequestSuperClass

A class to request data from the Orphanet API.

api_base_url = 'https://www.orpha.net/en/disease/detail/'

get(concept_id: str | int) → Coding[source]: Get details about a concept from the Orphanet API.

class phenopacket_mapper.api_requests.HPOAPIRequest(hpo_code_system: ~phenopacket_mapper.data_standards.code_system.CodeSystem = CodeSystem(name=Human Phenotype Ontology, name space prefix=HP, version=0.0.0))[source]

Bases: APIRequestSuperClass

A class to request data from the HPO API.

api_base_url = 'https://ontology.jax.org/api/hp/terms/HP:'

get(concept_id: str | int) → Coding[source]: Get details about a concept from the Orphanet API.

phenopacket_mapper.api_requests package

Submodules