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phyloref / jphyloref

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Document how we execute JPhyloRef on our backend server #59

Closed gaurav closed 5 years ago

gaurav commented 5 years ago

This PR documents how we execute JPhyloRef on our backend server by using the webhook tool to host a webserver that can accept jobs and submit them to a Slurm workload manager by using the srun command. I've tried to remove any internal details, but note that the X-Hub-Signature secret will always be disclosed in the HTML source of our one-page apps, unless we hide it behind a server somewhere.

I'm not completely convinced that we need to document this information on our Github page rather than just keeping the documentation on our backend server. If you think this is too much information to make public, feel free to delete this PR.

gaurav commented 5 years ago

Thanks for the suggestions, Hilmar! I've modified JPhyloRef so it either produces the complete JSON document for successful requests (including {"phylorefs": {...}}) or a JSON string that contains an error message when the --errors-as-json flag is used. In both cases it returns an exit code of zero, so Webhooks will return the JSON document to the browser using an HTTP 200 status code. I've filed an issue with the Authoring Tool to modify its behavior in line with this update (phyloref/curation-tool#162) and have resubmitted this PR to you for review.