Structural variants API endpoint

[Bekir Ergüner]

Hi,

We are running an internal cBioPortal instance (v5.4.7) and trying to query for structural variants via the web API. The structural variant profile IDs appear in the "/molecular-profiles" endpoint but we are getting "Not Found (HTTP 404)" error when we query the "/molecular-profiles/{molecularProfileId}/molecular-data". I saw that there were a dedicated endpoint for structural variants but I don't see it in the API docs anymore. Has it been deprecated, is there an alternative?

Best wishes,

Bekir 

[Benjamin Gross]

Hi Bekir.  There is a dedicated endpoint and it has not been deprecated.  We have updated our public instance to v6.0.2, but the SV support did not change.  Do you have access to the following swagger doc on your internal instance (of course update URL with your internal hostname):

https://www.cbioportal.org/api/swagger-ui/index.html#/Structural%20Variants/fetchStructuralVariantsUsingPOST

Best,

-Benjamin

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[Bekir Ergüner]

Sorry, forgot to include the cbioportal group address in my replies.

---------- Forwarded message ---------
From: Bekir Ergüner <berg...@exscientia.co.uk>
Date: Wed, 28 Feb 2024 at 07:32
Subject: Re: [cbioportal] Structural variants API endpoint
To: Benjamin Gross <benjami...@gmail.com>

Yes, I see the swagger page but it is quite different compared to the cbiportal.org , please have a look at the attached image.

I tried upgrading to v6.0.2 but the cbioportal container didn't work with the existing docker compose recipe. The current Docker compose repo supports v5.4.10, do you know the reason why they are so far behind?

Best,

Bekir

On Tue, 27 Feb 2024 at 17:15, Benjamin Gross <benjami...@gmail.com> wrote:

This is strange.  Are you able to access the swagger page at all?

You may as well update to the the latest release.  Seems like it would be time better spent than trying to track down the cause of the missing endpoint.

Best,

Benjamin

On Feb 27, 2024, at 1:40 AM, Bekir Ergüner <berg...@exscientia.co.uk> wrote:

Hi Benjamin,

Thanks for looking into this. I tried that URL and didn't get anything on our instance. We are using the latest version supported by the Docker compose repository. Do you think I should try updating to a more recent version independently?

Best,

Bekir

[Benjamin Gross]

The drop down on the top right of the swagger page (Select a definition), what other choices do you have?

To view this discussion on the web visit https://groups.google.com/d/msgid/cbioportal/CALt5mU_A45%3D%3DQuk5AdjeGXmygtjSqRxJ_fMYOECo-WFi9Tz8DQ%40mail.gmail.com.
<Screenshot 2024-02-28 at 07.23.30.png>

[Bekir Ergüner]

"default" and "internal". I can see the "/structural-vatiant/fetch" endpoint when internal is selected but can I access that from outside?

[Benjamin Gross]

Bekir,

I think its safe to use the endpoint found in the internal definition.  Internal is meant for web site usage, but this endpoint should be propagated to the public definition.

Best,

-Benjamin

<Screenshot 2024-03-01 at 09.43.13.png>