Bacpop-194 All Beebop changes for multi-db #81
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Remove the unused import in CreateProjectButton.vue to improve code cleanliness and maintainability.
The README.md file was updated to provide clearer instructions for adding new species to the project. The step to add a new database to [mrcdata](https://mrcdata.dide.ic.ac.uk/beebop) was removed, as it is now handled by the `download_db` script in *beebop_py*. The step to add a new species to `args.json` in *beebop_py* remains unchanged.
…into bacpop-194-popunk-run
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## bacpop-188-mutli-db #81 +/- ##
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+ Coverage 98.69% 98.72% +0.03%
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Files 33 34 +1
Lines 1914 1966 +52
Branches 242 246 +4
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+ Hits 1889 1941 +52
Misses 24 24
Partials 1 1 ☔ View full report in Codecov by Sentry. |
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Code looks good to me.
AMR for strep samples always shows as "unknown" - is that expected? This is on running this branch with the run_test script.
One thing I forgot to ask in the last PR - will the code be backward compatible with old projects stored without a "species" field. Looks like it probably default to undefined, but should default to pneumo: https://github.com/bacpop/beebop/pull/80/files#diff-6b11b12f8cdd9323969a2b053f174be528aebc9603ca7ef6c174af538c441534R104
| @@ -109,5 +107,14 @@ export default (config) => { | |||
| handleAPIError(request, response, error); | |||
| }); | |||
| }, | |||
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| async getSketchKmerArguments(request, response) { | |||
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Might be less confusing to call this getSpeciesConfig - that seems to be the terminology elsewhere in the chain, and other config might get added in future.
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good catch i missed this in renaming haha
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- Added the --pull always flag to the docker run command in the run_dependencies script. This ensures that the latest version of the mrcide/beebop-py image is always pulled before running the script. Refactor: Update test file errors.test.ts - Reordered the import statements in the errors.test.ts file to match the specified order. - Updated the newProject function to include the species parameter when creating a new project. - Updated the projectData variable in the test function to include the species parameter when calling the testSample function.
This PR covers all changes that will be needed for multi-db.When the beebop_py portion of work is done, this can be then merged and tested with that branch. Currently I ve tested with beebop_py poc. Feel free to look for context and play around (API branch is pointing to that poc branch).
The following is done in this PR