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biosimulations / biosim-client

library for accessing biosimulations APIs.
MIT License
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🐛: if a sim fails during /verify/omex, BiosimClient hangs #33

Open jcschaff opened 3 days ago

jcschaff commented 3 days ago

Contact Details

schaff@uchc.edu

Location

Other (please describe below)

Version

Production (Deployed on a .org domain)

What browsers are you seeing the problem on?

No response

What happened?

a /verify/omex call hung and eventually timed out after 10 minutes, when the simulation failed. After looking at the logs, the simulation (and the workflow) failed in 26 seconds. So the client should have returned a failure quickly.

What made it happen?

submit

run = (BiosimClient().compare_omex(r'/Users/jimschaff/Documents/workspace/biosim-client/notebooks/BIOMD0000000001.omex', simulators=["copasi", "tellurium:2.2.1", "tellurium:2.2.10"]))

Relevant log output

Code of Conduct

jcschaff commented 3 days ago

@luciansmith I've recorded the bug - now to find the time to fix it.

jcschaff commented 3 days ago

Note that this version of BIOMD0000000001.omex had a new Kisao term which was not understood by the legacy simulator (Tellurium 2.2.1).

jcschaff commented 3 days ago

The problem may be server-side, (see bsvs-server repo)

luciansmith commented 3 days ago

It would also be nice if failures were reported just like all the other results. The figure would have a [failed] image or something; the heat maps would have inf's. That way I could fire off a verification experiment for (say) five simulators and still get useful results even if one of them failed.

luciansmith commented 3 days ago

Ideally the actual error message would also be available.