mkt.databases.cbioportal.ClinicalSample

class mkt.databases.cbioportal.ClinicalSample(bool_prefix: bool = True, list_col_explode: list[str] | None = None, pathfile: str | None = None, *, study_id: str)[source]

Bases: Clinical

Class to get sample-level clinical information from a cBioPortal study.

__init__(bool_prefix: bool = True, list_col_explode: list[str] | None = None, pathfile: str | None = None, *, study_id: str) → None

Methods

`__eq__`(other)	Return self==value.
`__init__`([bool_prefix, list_col_explode, ...])
`__post_init__`()	Post-initialization to get clinical info from cBioPortal.
`_stamp_from_response`(res)	Record query datetime + cache provenance from a requests-cache response.
`_stamp_now`()	Record current UTC datetime; cache provenance unknown.
`check_entity_id`()	Check if the study ID is valid.
`check_response`(res)	Check the response status code for errors.
`convert_api_query_to_dataframe`()	Convert API to query to a dataframe.
`get_cbioportal`()	Get cBioPortal API object.
`get_data`()	Get cBioPortal data.
`get_df`()	Get DataFrame of cBioPortal data in dataframe.
`get_entity_id`()	Get cBioPortal study ID.
`get_instance`()	Get cBioPortal instance.
`get_url`()	Get cBioPortal API URL.
`load_from_csv`([str_path])	Load DataFrame from CSV file.
`maybe_get_token`()	Get API token, if available.
`query_api`()	Query a Swagger API and return result.
`query_sub_api`()	Get clinical info cBioPortal data.
`regenerate_dataframe`()	Regenerate DataFrame from API query.
`return_adjusted_colname`(colname[, prefix])	Return adjusted column name based on bool_prefix.
`set_api_key`()	Set API key for cBioPortal API.

Attributes

`__dataclass_fields__`
`__dataclass_params__`
`__match_args__`
`_cbioportal`	cBioPortal API object (post-init).
`_data`	List of cBioPortal sub-API queries; None if ID not found (post-init).
`_df`	DataFrame of cBioPortal data; None if DataFrame could not be created (post-init).
`bool_prefix`	Add prefix to ABC column names if True; default is True.
`bool_sample`	If True, return sample-level clinical data; if False, return patient-level clinical data
`from_cache`	Whether the most recent response was served from requests-cache.
`instance`	cBioPortal instance.
`list_col_explode`	List of columns to explode in convert_api_query_to_dataframe; None if no columns to explode (post-init).
`pathfile`	Path to load dataframe from CSV file; if None, regenerate (post-init).
`query_datetime`	UTC datetime the underlying network query was made (cache creation time if served from cache).
`url`	cBioPortal API URL.
`study_id`	cBioPortal study ID.

__init__(bool_prefix: bool = True, list_col_explode: list[str] | None = None, pathfile: str | None = None, *, study_id: str) → None

bool_sample: bool = True: If True, return sample-level clinical data; if False, return patient-level clinical data

study_id: str: cBioPortal study ID.