Phenotypes

Phenotypes

Bases: Endpoint

Queries phenotypes/ endpoints

Functions

get(**kwargs)

Queries phenotypes/, with optional query parameters

Other Parameters:

Name	Type	Description
search	string	Keyword search
collections	list	IDs of collections
tags	list	IDs of tags
datasources	list	IDs of datasources

Returns:

Name	Type	Description
Response	list	List of phenotypes matching query parameters

Examples:

>>> from pyconceptlibraryclient import Client
>>> client = Client(public=False)

>>> # Get all phenotypes
>>> client.phenotypes.get()

>>> # Search phenotypes
>>> client.phenotypes.get(search='asthma', collections=19)

get_versions(id)

Queries phenotypes/{id}/get-versions/

Parameters:

Name	Type	Description	Default
id	str	ID of entity to query, in format PH[\d+]	required

Returns:

Name	Type	Description
Response	list	Version list of queried phenotype

Examples:

>>> from pyconceptlibraryclient import Client
>>> client = Client(public=False)
>>> client.phenotypes.get_versions('PH1')

get_detail(id, version_id=None)

Queries phenotypes/{id}/detail/ or phenotypes/{id}/version/{version_id}/detail if version_id is supplied

Parameters:

Name	Type	Description	Default
id	str	ID of entity to query, in format PH[\d+]	required
version_id	int	version ID of entity	None

Returns:

Name	Type	Description
Response	list	Details of queried phenotype

Examples:

>>> from pyconceptlibraryclient import Client
>>> client = Client(public=False)

>>> # Get detail of phenotype, PH1
>>> client.phenotypes.get_detail('PH1')

>>> # Get detail of version 2 of phenotype, PH1
>>> client.phenotypes.get_detail('PH1', version_id=2)

get_codelist(id, version_id=None)

Queries phenotypes/{id}/export/codes/ or phenotypes/{id}/version/{version_id}/export/codes if version_id is supplied

Parameters:

Name	Type	Description	Default
id	str	ID of entity to query, in format PH[\d+]	required
version_id	int	version ID of entity	None

Returns:

Name	Type	Description
Response	list	Codelist of queried phenotype

Examples:

>>> from pyconceptlibraryclient import Client
>>> client = Client(public=False)

>>> # Get codelist of phenotype, PH1
>>> client.phenotypes.get_codelist('PH1')

>>> # Get codelist of version 2 of phenotype, PH1
>>> client.phenotypes.get_codelist('PH1', version_id=2)

save_definition_file(path, id, version_id=None)

Saves the YAML definition of the queried phenotype to file

Parameters:

Name	Type	Description	Default
path	str	Location to save the YAML file	required
id	str	ID of entity to query, in format PH[\d+]	required
version_id	int	version ID of entity	None

Examples:

>>> from pyconceptlibraryclient import Client
>>> client = Client(public=False)

>>> # Get codelist of phenotype, PH1
>>> client.phenotypes.save_definition_file('./path/to/file.yaml', 'PH1')

>>> # Get codelist of version 2 of phenotype, PH1
>>> client.phenotypes.save_definition_file('./path/to/file.yaml', 'PH1', version_id=2)

create(path)

Uploads the specified phenotype definition file to the ConceptLibrary and creates a new phenotype

Parameters:

Name	Type	Description	Default
path	str	Location where the definition file is saved on your local machine	required

Returns:

Name	Type	Description
Response	list	Details of the newly created phenotype

Examples:

>>> from pyconceptlibraryclient import Client
>>> client = Client(public=False)
>>> client.phenotypes.create('./path/to/file.yaml')

update(path)

Uses the specified phenotype definition file to update an already existing phenotype

Parameters:

Name	Type	Description	Default
path	str	Location where the definition file is saved on your local machine	required

Returns:

Name	Type	Description
Response	list	Details of the updated phenotype

Examples:

>>> from pyconceptlibraryclient import Client
>>> client = Client(public=False)
>>> client.phenotypes.create('./path/to/file.yaml')