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Fix mitochondrial fraction value #201

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merged 1 commit into from
Apr 12, 2021

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cosa65
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@cosa65 cosa65 commented Apr 9, 2021

Background

Both the pipeline and the default value set in data ingest expect maxFraction to be a fraction while the UI should display a percentage instead.

As the ticket says, the permanent fix would entail modifying the maxFraction processingConfig property to be maxPercentage in all the relevant places, which includes: data ingest (default value), pipeline, api (validation), ui (because it now accounts for this disparity) and also all the processingConfigs in experiments in dynamodb.

Performing this right now is not ideal since we are now using many experiments across both staging and production, so we have decided to create a ticket to implement the permanent solution when we are able to create databases migrations automatically.

The ticket for this is here: https://biomage.atlassian.net/browse/BIOMAGE-797

Link to issue

https://biomage.atlassian.net/browse/BIOMAGE-776

Link to staging deployment URL

https://ui-martinfosco-ui201.scp-staging.biomage.net/

Links to any Pull Requests related to this

Anything else the reviewers should know about the changes here

Changes

Code changes

Definition of DONE

Your changes will be ready for merging after each of the steps below have been completed:

Testing

  • Unit tests written
  • Tested locally with Inframock
  • Deployed to staging

To set up easy local testing with inframock, follow the instructions here: https://github.com/biomage-ltd/inframock
To deploy to the staging environment, follow the instructions here: https://github.com/biomage-ltd/biomage-utils

Documentation updates

Is all relevant documentation updated to reflect the proposed changes in this PR?

  • Relevant Github READMEs updated
  • Relevant wiki pages created/updated

Approvers

  • Approved by a member of the core engineering team
  • (UX changes) Approved by vickymorrison (this is her username, tag her if you need approval)

Just before merging:

Optional

  • Photo of a cute animal attached to this PR

@@ -411,7 +411,7 @@ const mitochondrialFractionLogHistogram = {
marker: markerBaseState,
label: labelBaseState,
binStep: 0.05,
maxFraction: 3.5,
maxFraction: 0.2,
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Use the default value between 0 and 1 instead of 3.5 which breaks the plot.

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happy for getting it merged after changes in staging are working

@cosa65 cosa65 merged commit 509d6f9 into master Apr 12, 2021
@cosa65 cosa65 deleted the fix-mitochondrial-fraction-value-being-sent branch April 12, 2021 17:58
alexvpickering pushed a commit that referenced this pull request Mar 21, 2023
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2 participants