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FIX: update how fetch-kaiju-db action discovers DB URLs #201

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merged 2 commits into from
Sep 2, 2024

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misialq
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@misialq misialq commented Aug 30, 2024

Closes #197.

To test, execute the action with a DB of choice (viruses, plasmids or fungi are some good, small DBs to try):

qiime moshpit fetch-kaiju-db \
  --p-database-type<db type> \
  --o-database db.qza \
  --verbose

@misialq misialq requested review from a team and ChristosMatzoros and removed request for a team August 30, 2024 13:15
@misialq misialq marked this pull request as ready for review August 30, 2024 13:15
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codecov bot commented Aug 30, 2024

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 98.00%. Comparing base (1bb3e46) to head (55716d8).

Additional details and impacted files
@@            Coverage Diff             @@
##             main     #201      +/-   ##
==========================================
- Coverage   98.56%   98.00%   -0.56%     
==========================================
  Files          85      155      +70     
  Lines        4882     9684    +4802     
  Branches        0      423     +423     
==========================================
+ Hits         4812     9491    +4679     
- Misses         70      140      +70     
- Partials        0       53      +53     

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@ChristosMatzoros ChristosMatzoros left a comment

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Hey @misialq,

I tested it with the options (viruses, plasmids, fungi), and everything's working great. The code looks good to me. Go ahead and merge when you're ready!

@misialq misialq merged commit 2562a9a into bokulich-lab:main Sep 2, 2024
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Successfully merging this pull request may close these issues.

BUG: fetch-kaiju-db action does not work after Kaiju server shutdown
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