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Refactor analysis module #177

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merged 195 commits into from
Sep 30, 2024
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prasham21
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@prasham21 prasham21 commented Jul 16, 2024

This pr refactors the gene_blueprints and metabolite_blueprints to separate web dependency code from analysis code.

TODO:

  • FIx Docstrings
  • Use new analysis code in the WebAPI
  • write unit tests for the new code.

kkaris

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@prasham21 prasham21 force-pushed the refactor-analysis-module branch 2 times, most recently from d4d69d6 to e2b3cf1 Compare August 2, 2024 22:16
kkaris

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@kkaris kkaris self-requested a review September 17, 2024 22:05
kkaris

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@kkaris kkaris self-requested a review September 20, 2024 04:48
@kkaris kkaris force-pushed the refactor-analysis-module branch from 720f166 to 135b89f Compare September 20, 2024 19:37
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@kkaris kkaris force-pushed the refactor-analysis-module branch from eef6e15 to 394cd0a Compare September 24, 2024 16:34
@bgyori bgyori marked this pull request as ready for review September 24, 2024 21:55
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kkaris commented Sep 25, 2024

I tried to add the neo4j url as an explicit environment variable, but the NEO4J client still can't find the URL in the test runs.

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kkaris commented Sep 26, 2024

The new tests I added are now all failing with this error (they are passing locally for me):

neo4j.exceptions.AuthError: {code: Neo.ClientError.Security.Unauthorized} {message: Unsupported authentication token, missing key `scheme`}

I'm not sure what to make of that, since all I can find on searching this is that there could be typos in the credentials. I've checked the URL and it corresponds to what I have locally, where things work.

@bgyori bgyori force-pushed the refactor-analysis-module branch from 788eb7f to acfe2b7 Compare September 27, 2024 20:40
@kkaris kkaris force-pushed the refactor-analysis-module branch from acfe2b7 to 473a85a Compare September 30, 2024 18:24
@kkaris kkaris merged commit be84293 into gyorilab:main Sep 30, 2024
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4 participants