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Guard plot_cross_validation.save_outliers for institutionId and seriesId columns confirm with unit test #446

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merged 7 commits into from
Apr 29, 2021

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@dumbledad dumbledad commented Apr 27, 2021

Fixing Issue #423

Overview:

Guarding the call to create_portal_query_for_outliers so that the required columns are present, and providing unit test that confirms the change.

Detail:

The functions save_outliers and create_portal_query_for_outliers in InnerEye.ML.cisualizers.lot_cross_validation
fail if the columns institutionId and seriesId are missing from the data. This PR

  • Augments create_portal_query_for_outliers so that it checks for the required columns and raises an informative ValueError if they are missing. The function description is updated accordingly.
  • Changes save_outliers in two ways. If the columns are missing
    • they are not used in the groupby which gleans the stats, and
    • the portal query is omitted.
  • Test data is provided to check that the revised save_outliers produces expected data when the columns are missing
  • The unit tests test_save_outliers and test_create_portal_query_for_outliers in Tests.ML.visualizers.test_plot_cross_validation are extended to exercise the new code with columns missing.

Checklist:

  • Ensure that your PR is small, and implements one change.
  • Add unit tests for all functions that you introduced or modified.
  • Run PyCharm's code cleanup tools on your Python files. (I'm using VS Code and have not done this.)
  • Link the correct GitHub issue for tracking.
  • Update the Changelog file: Describe your change in terms of
    Added/Changed/Removed/... in the "Upcoming" section.
  • When merging your PR, replace the default merge message with a description of your PR,
    and if needed a motivation why that change was required.

@dumbledad dumbledad self-assigned this Apr 27, 2021
@dumbledad dumbledad force-pushed the timregan/423-save_outliers-fails branch 2 times, most recently from 36e27e5 to a1a1274 Compare April 28, 2021 11:44
Tim Regan added 6 commits April 28, 2021 13:39
@dumbledad dumbledad force-pushed the timregan/423-save_outliers-fails branch from a5e60c5 to 131f393 Compare April 28, 2021 12:41
@dumbledad dumbledad marked this pull request as ready for review April 28, 2021 12:41
@dumbledad dumbledad enabled auto-merge (squash) April 28, 2021 14:14
@dumbledad dumbledad merged commit 9a7ac87 into main Apr 29, 2021
@dumbledad dumbledad deleted the timregan/423-save_outliers-fails branch April 29, 2021 14:23
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save_outliers() fails if institutionId and seriesId undefined in dataset.csv
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