Phenotypes

`Phenotypes`

Bases: Endpoint

Queries phenotypes/ endpoints

Functions

`get(**kwargs)`

Queries phenotypes/, with optional query parameters

NOTE

See the following URL for more information on query parameters: https://conceptlibrary.saildatabank.com/api/v1/#operations-tag-phenotypes

Other Parameters:

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

Response (dict|list): - If paginated: a dict of phenotypes matching query parameters - If unpaginated: a list of phenotypes matching query parameters

Examples:

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

>>> # Get all phenotypes (defaults to paginated)
>>> client.phenotypes.get()

>>> # [NOTE: not recommended!] Get unpaginated list of phenotypes
>>> client.phenotypes.get(no_pagination=True)

>>> # 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')