mkt.databases.cbioportal.Clinical

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

Bases: StudyData

Class to get 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, bool_sample: bool) → 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.
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.
bool_sample	If True, return sample-level clinical data; if False, return patient-level clinical data.
study_id	cBioPortal study ID.

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

bool_sample: bool

If True, return sample-level clinical data; if False, return patient-level clinical data.

query_sub_api() → list | None

Get clinical info cBioPortal data.

Returns:

• list | None –

  cBioPortal data as list of Abstract Base Classes

  objects if successful, otherwise None.

• bool_sample (bool) – If True, return sample-level clinical data; if False, return patient-level clinical data

study_id: str

cBioPortal study ID.