SVS files are unavailable through the APi

Posted in API by Maor Maor Tue Jun 05 2018 09:27:21 GMT+0000 (Coordinated Universal Time)·6·Viewed 515 times

SVS files are availble through the website: They are also available on the data portal as of May 21 2018: (same page, click on Files, it leads to data portal. You can see svs files for this case) However issue an API call to: No svs files are available.
Natasa Bezmarevic
June 6, 2018

Hello Maor,

I am Natasa from Seven Bridges Genomics Support team.

As part of our ongoing relationship with the National Cancer Institute, which provides funding to support researcher access to TCGA data through our platform, and in keeping with our commitment to make the most up-to-date data available to our platform users, we are in the process of updating the TCGA dataset we host on the CGC to align with the latest data release available from the GDC (Data Release 11.0).

The SVS files you asked about were made available via the GDC Portal as part of Data Release 11.0, so these files will be available through the CGC and our API once we complete our update. We expect that to occur later this month and will be notifying all CGC users about this soon.

If you have any additional questions, I am at your disposal.

Best regards,

Maor Maor
July 15, 2018

Thank you , it is indeed updated in the new API (v2):

However, the v0 api is now broken:
GET API call to :

Returns http 404

Similary GET API call to the case metadata:

returns http 404, whereas beforehand, it worked. I verified the CASE ID from the still working POST api call:

with payload:
data = {
"hasID": ["TCGA-CN-A63T"]

Maor Maor
July 15, 2018

correction: case ["TCGA-CJ-4902"]

Natasa Bezmarevic
July 18, 2018

Hi Maor,

I have checked with our team and it appears that GDC changed the way how they store IDs so before it was all in upper case like in the example you have shown (9FE336A8-08A7-4FE7-BF45-AFD6A8EB9C75) but GDC has changed and now they store all in lower case (9fe336a8-08a7-4fe7-bf45-afd6a8eb9c75). Mentioned changes is also reflected on our API too.

As a solution, we suggest that you lower the case for case ids ( and everything should work as before.

Hope this information helps if you need anything else let us know.

Best regards

Maor Maor
July 18, 2018

Thank you very much.
I could have sworn I tried smaller case :) However it works now. All is well.

Natasa Bezmarevic
July 18, 2018

You're welcome!
If you need anything else, we are happy to help.


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