Terra API workaround?

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Laura Gauthier

• October 16, 2020 13:05

I have a workflow I'm running on a set of ~1500 samples.  The workflow failed, but Job Manager won't give me any information.  I get a 500 error.  From the Swagger API page, the metadata is too big to return (>150MB).  I'm only asking for includeKey=executionStatus, but apparently it's still too big. Am I using that endpoint wrong?  How can I get the smallest metadata possible?  Even just to know which tasks failed would be helpful.  Crawling through the execution directory in my bucket, everything that I've seen has succeeded.  It looks like most if not all of the subworkflows succeeded.  Is there a way to get the outputs of the subworkflows?  If so, I can manually stitch them together.

The weird thing is that this workflow has succeeded before on these samples, so I know it's not the number of samples or the inputs that's causing the problem.

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  Samantha (she/her)

  • October 16, 2020 14:01

  Hi Laura Gauthier,

   

  Thanks for reaching out. Can you share the workspace where you are seeing this issue with GROUP_FireCloud-Support@firecloud.org by clicking the Share button in your workspace? The Share option is in the three-dots menu at the top-right.

  1. Add GROUP_FireCloud-Support@firecloud.org to the User email field and press enter on your keyboard.
  2. Click Save.

   

  Let us know the workspace name, as well as the relevant submission and workflow IDs. We’ll be happy to take a closer look as soon as we can.

   

  Best,

  Samantha

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  Laura Gauthier

  • October 16, 2020 15:44

  I've shared the workspace.

  The workflow I can't view in Job Manager is 3fb30759-583c-493f-88fb-4273b487a4a4.  After crawling the outputs folders, it looked like two tasks failed for no reason, so I relaunched the workflow.

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