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SynBioHub / synbiohub

Web application enabling users and software to browse, upload, and share synthetic biology designs
https://wiki.synbiohub.org
BSD 2-Clause "Simplified" License
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SynBioHub is down #1537

Closed jakebeal closed 3 months ago

jakebeal commented 5 months ago

synbiohub.org is down and has been for the last day or so, according to the failed regressions tests I'm seeing.

cjmyers commented 5 months ago

Should be back up now. It went down when I was traveling and did not have time till now to restart.

jakebeal commented 5 months ago

Did anything change between before and after the restart? pySBOL2 is now getting failures on certain SynBioHub search queries that were not failures before: https://github.com/SynBioDex/pySBOL2/actions/runs/8683864240/job/23821869774

cjmyers commented 5 months ago

Shouldn't have changed. I can check on this when I get a moment.

cjmyers commented 5 months ago

I'm really confused by this one. When I click on the part that it says it cannot find. It comes right up. Can you provide any more context about the error?

jakebeal commented 5 months ago

It's happening because the SynBioHub search API is not returning an object with the expected identity. I haven't dug farther in to see if it's not getting the object or if it's coming back with a different identity.

cjmyers commented 5 months ago

Can you point me to the test code where the error is happening? Nothing has changed with SBH1 in ages.

jakebeal commented 5 months ago

Here are the two places where failures are occurring:

cjmyers commented 5 months ago

I think I figured it out. I turned off SBOLExplorer, since it was using a lot of resources and seems to be one of the reasons for SBH going down. This would indeed change search results.

jakebeal commented 5 months ago

Is it OK for SBOLExplorer to be turned back on, or do you need to leave it off? My impression is that it does make a big difference for search results.

cjmyers commented 5 months ago

I would prefer to wait until we can figure out why it was using so much memory before turning it back on. It seems it was what was causing SBH to go down a lot, since it used up resources. The recent instances going down are unrelated to SBH. They were due to some issue with Caddy. I've updated the Caddyfile just now and hoping this will make things more stable. It would be good if your tests did not depend on SBOLExplorer, since we cannot guarantee that it will always be on. Make a search that is only going to return less than 50 results, and you should be good.

jakebeal commented 3 months ago

Well, things seem to have resolved on their own, which suggests something odd happened down in the external dependencies...

cjmyers commented 3 months ago

Hmm, that does not make sense. We still have SBOLExplorer off.

jakebeal commented 3 months ago

My guess is that it had nothing to do with SynBioHub, but something in the dependencies of pySBOL2. Something like this happened with the GitHub mac build environment for SBOL-utilities a little while back also

cjmyers commented 3 months ago

Interesting. Glad you don't have an SBOLExplorer dependency. Hope to get it running again at some point.