mkt.databases.oncokb.OncoKBCancerGeneList

class mkt.databases.oncokb.OncoKBCancerGeneList(url: str = 'https://www.oncokb.org/api/v1/utils/cancerGeneList')[source]

Bases: RESTAPIClient

Client for the OncoKB cancer gene list endpoint.

Fetches the full OncoKB cancer gene list (/utils/cancerGeneList) in a single network call, exposing the raw JSON in _json and a tidy table in _df. The endpoint is public (no token required), so this subclasses the plain RESTAPIClient rather than the token-bearing OncoKB hierarchy used for therapeutic-level/variant annotations. Mirrors the cancerhotspots client: query once, filter client-side via get_gene(), and round-trip to CSV via to_csv() / from_csv().

__init__(url: str = 'https://www.oncokb.org/api/v1/utils/cancerGeneList') → None

Methods

`__eq__`(other)	Return self==value.
`__init__`([url])
`__post_init__`()
`_stamp_from_response`(res)	Record query datetime + cache provenance from a requests-cache response.
`_stamp_now`()	Record current UTC datetime; cache provenance unknown.
`check_response`(res)	Check the response status code for errors.
`from_csv`(path)	Build a client from a CSV written by `to_csv()`, without querying.
`from_dataframe`(df)	Build a client from an existing table without querying the API.
`get_gene`(hugo_symbol)	Return the cancer gene list record(s) for a single gene.
`query_api`()	Query the OncoKB cancer gene list endpoint and populate `_json` and `_df`.
`read_csv`(path)	Read a cancer gene list written by `to_csv()` back into a DataFrame.
`to_csv`(path)	Write the cancer gene list to CSV, json-encoding list-valued columns.

Attributes

`__dataclass_fields__`
`__dataclass_params__`
`__match_args__`
`_df`
`_json`
`df`	Cancer gene list as a DataFrame (one row per gene).
`from_cache`	Whether the most recent response was served from requests-cache.
`query_datetime`	UTC datetime the underlying network query was made (cache creation time if served from cache).
`url`	URL for the OncoKB cancer gene list endpoint.

__init__(url: str = 'https://www.oncokb.org/api/v1/utils/cancerGeneList') → None

property df: DataFrame | None: Cancer gene list as a DataFrame (one row per gene).

classmethod from_csv(path: str) → OncoKBCancerGeneList[source]

Build a client from a CSV written by to_csv(), without querying.

Parameters:: path (str) – Path to a CSV previously written by to_csv().
Returns:: Instance backed by the cached table.
Return type:: OncoKBCancerGeneList

classmethod from_dataframe(df: DataFrame) → OncoKBCancerGeneList[source]

Build a client from an existing table without querying the API.

Bypasses __post_init__ (which would issue the network query) via object.__new__ and sets _df directly, so cached data can be reloaded offline. _json is left None.

Parameters:: df (pd.DataFrame) – Cancer gene list table (e.g. from read_csv() or df).
Returns:: Instance backed by df; get_gene() works as usual.
Return type:: OncoKBCancerGeneList

get_gene(hugo_symbol: str) → DataFrame[source]

Return the cancer gene list record(s) for a single gene.

Parameters:: hugo_symbol (str) – HGNC gene symbol to filter on (e.g. "BRAF").
Returns:: Rows of df whose hugoSymbol matches; empty if none.
Return type:: pd.DataFrame

query_api() → None[source]: Query the OncoKB cancer gene list endpoint and populate _json and _df.

static read_csv(path: str) → DataFrame[source]

Read a cancer gene list written by to_csv() back into a DataFrame.

Inverts to_csv(): json-decodes the list-valued columns.

Parameters:: path (str) – Path to a CSV previously written by to_csv().
Returns:: Cancer gene list equivalent to df.
Return type:: pd.DataFrame

to_csv(path: str) → None[source]

Write the cancer gene list to CSV, json-encoding list-valued columns.

Parameters:: path (str) – Output CSV path.

url: str = 'https://www.oncokb.org/api/v1/utils/cancerGeneList': URL for the OncoKB cancer gene list endpoint.