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GLYCAM-Web / website

A bare-bones repo to contain public website stuff and issues related to the GLYCAM Web Django apps.
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Testrun with ~120 structures - all failed #134

Open ReneRanzinger opened 1 year ago

ReneRanzinger commented 1 year ago

Tool: GLYCAM glycan structure generation API

Bug Description: I did a testrun with ~120 glycan structures using the API to generate their PDB files. All of them are stuck in status "minimizing" even after 1 day. Except one that failed with #133.

To Reproduce: The spreadsheet contains the Glycam sequence, submission time, job ID: SubmissionResults.xlsx

Expected behavior They should finish after a few seconds. There are a few big ones but most of them are small.

Lachele commented 1 year ago

Thanks for letting us know!

Based on checking one of the the job IDs (thanks for including those), these seem to have been run on test.glycam.org (and not glycam.org). If you disagree, please say so.

The files appear to be there, so it appears that the builds happened. I'm going to add Dan. I would be surprised if they suddenly appear after a day, but it's not outside comprehension. Maybe some part of a request got confused. Maybe GEMS is returning the wrong path... could be lots of things.

danwentworthart commented 1 year ago

I have verified and examined your experience in the logs. I can also back up Lachele's observation: the structures were all built. I also replicated your experience, in that when I poll for the project status of any of those builds I see "minimizing" as the status, consistently. My initial observation is that polling for project status is the culprit here. When I looked at the state of test.glycam.org, it appears to have been spun up on 2023-03-27.

That was quite some time ago, and I did work to improve polling logic earlier this year, though I have yet to isolate exact dates. I believe this issue is going to resolve itself when test.glycam.org is updated next. I will coordinate with the team to see when it would be appropriate to update test.glycam.org, and then we will test that and get back to you with the results.

danwentworthart commented 1 year ago

I was wrong with my guessing. I know what is happening now. I did update polling logic earlier this year, to address changes on the server-side. However, it seems I forgot to update this specific url pattern:

/json/project_status/sequence// I can replicate the same errors in my dev env, so the issue definitely still exists, and I need to fix it.
ReneRanzinger commented 1 year ago

@danwentworthart OK, leave a comment in this ticket once its fixed and deploy to test. I will make a new attempt at this time and we will see how it goes.

danwentworthart commented 1 year ago

Will do. I have diagnosed and fixed this, as well as written a test to catch it in the future. It has not yet been deployed. We will need to update you when that happens.

danwentworthart commented 1 year ago

I believe this fix should be testable on test.glycam.org. Please let us know if the issue persists, or if it is resolved?