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@alimourey alimourey commented Nov 7, 2025

PLEASE NOTE: This is ready to review but should NOT be merged with master until after 25q4. It also is dependent on the completion of the pipeline changes in this related draft PR (not ready to review. Alison and I will be teaming up to finish it on Monday): #451

These changes update Context Explorer to:

  1. Use Compounds instead of Compound Experiments.
  2. Use collapsed compound datasets and their associated given ids instead of the older non-collapsed legacy compound datasets.
  3. Changes in variable names to be more consistent with Breadbox terminology (e.g. entity --> feature).
  4. Removes the Context Explorer dependency on the old DependencyDataset and Entity tables.
  5. Removes old Enriched Lineages tile code and tests (The tests broke due to the Context Explorer changes. Upon investigation, I realized these tests were for code that is no longer needed/used anymore as of the 25q3 release, so I deleted the tests and associated code).
  6. More dose curves code is shared between Context Explorer and the new dose curves tab than before.

@alimourey alimourey force-pushed the ce-use-compound-datasets branch from 5c5f1cc to 07340e7 Compare November 7, 2025 21:14
@alimourey alimourey marked this pull request as ready for review November 7, 2025 21:29
@alimourey alimourey requested a review from snwessel November 7, 2025 21:29
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2 participants