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smith-chem-wisc / MetaNetwork

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Issues connecting to g:Profiler via the gprofiler2 package api #36

Open avc1551 opened 2 years ago

avc1551 commented 2 years ago

User currently experiencing a series of errors.

  1. Error 500 from the g:Profiler server. I sent in a support ticket, and the issue was fixed on the g:Profiler server.
  2. Warning: Error in : Empty reply from server. Support ticket submitted.
  3. Error 400 from the server.

The issue is entirely on the g:Profiler side of the server, which points to the larger issue of relying on a large chunk of code for the gene ontology enrichment analysis portion of MetaNetwork's workflow that we don't maintain ourselves. There's no way that we can port a version of g:Profiler into the MetaNetwork Docker container.

avc1551 commented 2 years ago

I think the best course of action would be to submit a small list of genes to g:Profiler when MetaNetwork is initializing, then awaiting a response. If it goes through, then MetaNetwork functions normally. Otherwise, MetaNetwork should disable the functional annotation enrichment portions and display an error message without killing the program.

In the meantime, I'm going to create a docker container without the functional annotation enrichment and that should serve as a stop-gap until I'm done working with the g:Profiler people.