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nlpsandbox / support

Where NLP Sandbox users can request submission logs, share ideas and report issues.
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Submission `9712751` #1

Closed tschaffter closed 3 years ago

tschaffter commented 3 years ago

Tool type: Location Annotator Submission ID: 9712751 Submission Status: ACCEPTED Submission MCW Status: INVALID Synapse user: tschaffter

tschaffter commented 3 years ago

Hi @gkowalski, the above submission failed on MCW PHI dataset. Could you share by email with me the log that you have? Thanks!

gkowalski commented 3 years ago

How do I obtain these again ?

thomasyu888 commented 3 years ago

@gkowalski Here are the steps:

  1. Go to this view and search for 9712751. You will find that it has submission id: 9712756.
  2. Scroll to the right in that view and look for the orgSagebionetworksSynapseWorkflowOrchestratorSubmissionFolder column and download the submission logs in that folder.
  3. Go to the MCW ELK stack and export logs.
  4. upload logs and provide access to @tschaffter

In this scenario after doing step 2, I found that it was an issue with the pipeline not being able to find the container, so this submission needs to be resubmitted. Can you resubmit @tschaffter ?

gkowalski commented 3 years ago

Is exporting all ELT stack logs the norm, or just logs from the date that the submission was made on more appropriate ? Also I could limit the export to docker.image:sagebionetworks/synapse-workflow-orchestrator . Last time I shared these to Conner from a folder in https://www.synapse.org/ . I'll do that going forward.

I see the first time for conner I only exported the ELK logs. I've not shared the logs from synapse . I'll add the ELK logs today.

gkowalski commented 3 years ago

Then what does step 2 above for ?

thomasyu888 commented 3 years ago

I think just exporting the ELK stack logs for that particular submission is appropriate. The ELK logs will have to be scrubbed just in case if contains any trace of MCW data. I think the first step is to look at the sagebionetworks/synapse-workflow-orchestrator logs then determine whether or not ELK logs need to be uploaded. Sharing them to a folder on Synapse is perfect.

tschaffter commented 3 years ago

@thomasyu888 In my mind the only meaning full logs for the user are the ELK logs. Is that correct? If yes, no need to share the workflow logs, which may be confusing.

tschaffter commented 3 years ago

I like the idea of sharing the log with Synapse rather than email for audit purpose.

gkowalski commented 3 years ago

done