OncoKB API connection issue with Terra

Post author
Sara Balch

Hi Terra team,

About a year ago I wrote a a public Terra method that launches OncoKB's maf annotator to ingest mafs in the data model and output new annotations. This method worked as of a couple of months ago but recently (unsure of the exact time frame when it stopped working as I haven't used the method since the summer) it is reporting SSL errors when trying to connect with OncoKB's API. This failure occurs independent of the maf annotator version (v.3.0.0 or v3.1.1) or different users OncoKB API keys. I haven't changed the contents of the WDL or the python script. When I run OncoKB's maf annotator locally (independent of Firecloud) it works. Have there been any recent changes to Firecloud that are preventing the connection? I've add  GROUP_FireCloud-Support@firecloud.org to the workspace (called "er_loss").

Thanks,

Sara

Comments

3 comments

  • Comment author
    Samantha (she/her)

    Hi Sara Balch,

     

    Thanks for writing in. I am not able to find a workspace by the name "er_loss." Can you confirm that it has been successfully shared with us? When adding our support email GROUP_FireCloud-Support@firecloud.org to the User email field, be sure to press enter on your keyboard and then click Save. 

    Please provide us with

    1. A link to your workspace
    2. The relevant submission ID
    3. The relevant workflow ID

    We’ll be happy to take a closer look as soon as we can!

     

    Kind regards,

    Samantha​ 

    0
  • Comment author
    Sara Balch

    Hi Samantha,

    The workspace is called waglelab-billing/sbalch_er_loss. The relevant submission ID is 3af9b8e1-81db-473c-b62c-6c7681f475ce and the relevant workflow ID is oncokb_maf_annotator. You'll notice that the workflow successfully runs but when you click on the backend log, there are SSL certificate errors when trying to run OncoKB's maf annotator python package.

    Thanks in advance for all your help!

    Sara

    0
  • Comment author
    Samantha (she/her)

    Hi Sara Balch,

    Sorry for the delayed response. I brought this to our engineers to look into and they noticed that oncokb.org uses a LetsEncrypt certification so if things stopped working between September 14 (the last time your workflow was successful) and now, the issue could be due to the following: https://letsencrypt.org/docs/dst-root-ca-x3-expiration-september-2021/.

    Best,

    Samantha

    0

Please sign in to leave a comment.