Possible change in cBioPortal API - intentional?

[Matteo Tiberti]

Dear all,

We've been using the cBioPortal API to retrieve data in the context of the Cancermuts Python package.

Recently (probably within a week's time), the data returned by the cBioPortal API has been in a different format than our package normally expects. We've been doing this to retrieve cancer studies:

            ...

            result = self._client.Studies.getAllStudiesUsingGET().result()

            ...

            df = pandas.DataFrame(dict([ (attr, [ getattr(entry, attr) for entry in result ]) for attr in dir(result[0]) ]))

      

basically, we flatten the resulting data to a dataframe, which until last week seemed to be working fine. Now, It looks like the returned data structure has changed, specifically in the cancerType column. Our cancerType column now looks something like:

TypeOfCancer(cancerTypeId=None, dedicatedColor='HotPink', id='acbc', name='Adenoid Cystic Breast Cancer', parent='brca', shortName='ACBC')

while it used to be a simple string with the cancer type name, for what I can tell.

I can easily change the parsing so that we get the right data structure and extract what we need, but I would first like to know if the change I see is intentional and there to stay for the foreseeable future, so that I can rely on it moving forward, or it's due to a mistake which is bound to be corrected eventually.

Thank you and kind regards,

____________________________

Matteo Tiberti, PhD

Staff Scientist at the Cancer Structural Biology group
Danish Cancer Society Research Center

Strandboulevarden 49

2100, Copenhagen, Denmark

[Gaofei Zhao]

Hi Matteo,

Sorry for the inconvenience. We recently did some refactoring work around our API endpoints, and this endpoint unexpectedly started returning a different result format.
We’ve just updated the portal and restored the original response format. Would you mind trying again and letting us know if things are working as expected now?
Thanks for reporting this.

Best,
Gaofei

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[Matteo Tiberti]

Hi Gaofei,

thank you for your answer and the quick fix, I just tested it and it works as it previously did, so that's great

more in general, are changes in the API advertised or tracked somewhere I can follow? Mostly, it would be useful to understand if we need to make changes to our code

Thank you again, 

_____________________________

Matteo Tiberti, PhD

Staff Scientist at the Cancer Structural Biology group
Danish Cancer Society Research Center

Strandboulevarden 49

2100, Copenhagen, Denmark

[Gaofei Zhao]

Hi Matteo,

That’s a great question. We do weekly releases, and API-related changes are typically documented in our Release Note, for example: "⚙️ REST API Changes" indicate updates to the API in that release.

That said, we currently don’t explicitly distinguish between backward-compatible and breaking API changes, so that’s probably something we should improve to make it easier for downstream users to assess whether code changes may be needed.

Best,

Gaofei