Comments (6)
Thanks @lpalbou! Yep, rather than the data required by the GO-CAM site, those cached JSON files currently contain the error message from the query timeout:
{"message": "Endpoint request timed out"}
I'm currently looking at re-triggering this lambda process to regenerate the JSON files for the current GO release.
BTW, noting here that @kltm attempted to bump from 30000 to 60000ms on internal and production RDF endpoints. Hopefully, once @lpalbou's PR to update the timeout on the GO-CAM API side the query problems will be solved.
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@kltm Thanks, I just dug deeper and noticed the terms api is not working and returning Internal Server Error
https://s3.amazonaws.com/geneontology-public/gocam/gocam-goterms.json
Tagging @dustine32 @sierra-moxon
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@tmushayahama Great--thank you for the detective work! It looks like that file literally cached the upstream server error.
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Hello everyone. https://s3.amazonaws.com/geneontology-public/gocam/gocam-goterms.json is a file caching the SPARQL queries after a new release. The file is generated from AWS (cloudwatch alarm serving as a CRON to detect a new release and trigger a lambda function that compute and store the results of queries in this file). @dustine32 may remember a bit more - I think there is a recording on the topic made 1st week of September -.
I saw in other threads that some queries experienced timeout, a possible reason could be a timeout on that lambda while doing the queries. Let me know if you need further info.
Otherwise, happy holiday season 🎄🎅
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You can use AWS/Cloud9 and this environment:
Then, selecting the lambda_function from the GoUpdateGoCams package, you can click run (top green button). Be sure on the drop down to the right to select lamba/remote:
That should run only the code for GO-CAMs cache. Btw, this code is also on GH in the go-stats repo, however you may want to push the code from Cloud9 to GH.. As there may have been some changes over time !
Hope that will work !
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This is now fixed--thank you everybody!
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Related Issues (20)
- GO-terms retrieved as values of enabled_by
- Redirects system via file HOT 6
- Choose representative GO-CAMs to show on the main page
- AWS SSL certificates migration HOT 2
- Gene product display on GO-CAM page not ideal ? HOT 5
- Technical planning: Handover of GO-CAM site HOT 8
- Handover of GO-CAM API HOT 7
- Different numbers of GO-CAMs between User Page & Browse Page with filter
- Display only causal models on GO-CAM site HOT 14
- View button in /go-cam for model should point to Alliance Pathway Viewer HOT 12
- External links should go to new AmiGO GO-CAM pages HOT 9
- Remove GO-CAM download card from /go-cam site HOT 7
- Browse Page - GO-CAM with same user using multiple providedBy duplicates user name
- Access to development models
- Search by Gene Product and PMID HOT 2
- Several Features & Improvements HOT 7
- SIF Archive Download HOT 2
- GO-CAM Documentation
- Feedback HOT 3
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