mkt.databases.cbioportal.cBioPortalQuery

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

Bases: cBioPortal

Class to get data from a cBioPortal instance.

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

Methods

`__eq__`(other)	Return self==value.
`__init__`([bool_prefix, list_col_explode, ...])
`__post_init__`()	Post-initialization to check study ID in instance and query API data.
`_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 entity 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 the entity ID (study_id or panel_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`()	Query a sub-API of cBioPortal and return result.
`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.

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

bool_prefix: bool = True: Add prefix to ABC column names if True; default is True.

abstract check_entity_id() → bool[source]

Check if the entity ID is valid.

Returns:: True if the entity ID is valid, False otherwise
Return type:: bool

convert_api_query_to_dataframe() → DataFrame | None[source]

Convert API to query to a dataframe.

Returns:: DataFrame of API query if successful, otherwise None
Return type:: pd.DataFrame | None

get_data()[source]: Get cBioPortal data.

get_df()[source]: Get DataFrame of cBioPortal data in dataframe.

abstract get_entity_id()[source]

Get the entity ID (study_id or panel_id).

Returns:: Entity ID
Return type:: str

list_col_explode: list[str] | None = None: List of columns to explode in convert_api_query_to_dataframe; None if no columns to explode (post-init).

load_from_csv(str_path: str | None = None) → DataFrame | None[source]

Load DataFrame from CSV file.

Parameters:: str_path (str | None) – Path to CSV file; if None, use self.pathfile
Returns:: DataFrame loaded from CSV file if successful, otherwise None
Return type:: pd.DataFrame | None

pathfile: str | None = None: Path to load dataframe from CSV file; if None, regenerate (post-init).

abstract query_sub_api()[source]

Query a sub-API of cBioPortal and return result.

Returns:: API response
Return type:: SwaggerClient

regenerate_dataframe() → DataFrame | None[source]

Regenerate DataFrame from API query.

Returns:: DataFrame of API query if successful, otherwise None
Return type:: pd.DataFrame | None

return_adjusted_colname(colname: str, prefix: str = 'gene') → str[source]

Return adjusted column name based on bool_prefix.

Parameters:

colname (str) – Column name to adjust
prefix (str) – Prefix to add to the column name if bool_prefix is True; default is “gene”

Returns:

Adjusted column name

Return type:

str