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Merged
merged 23 commits into from
Mar 20, 2025
Merged

Integrate uniprot #78

merged 23 commits into from
Mar 20, 2025

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GFJHogue
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@GFJHogue GFJHogue commented Mar 11, 2025

This PR adds @heliamoh's Reactome-Uniprot Cross-DB prototype as a usable chat profile (leveraging the code reorg work done in #77).

To enable the cross-db profile, add the following entry to config.yml:

profiles:
  - React-to-Me
  - Cross-Database Prototype

If you don't yet have config.yml, create it by duplicating config_default.yml.

Code improvements tacked on after #77:

  • Improved usage of TypedDict's to enable the type-checker to better enforce valid state keys (to avoid KeyErrors at runtime).
  • Split out BaseState into InputState and OutputState to use as a type-checked interface for graph input/output from the Chainlit layer.
  • CompletenessGrader moved out of /tools/external_search to its own task (in /agent/tasks/).
  • Current hybrid ChromaDB (vector db) & BM25 (csv) retrieval method abstracted out to retrievers/csv_chroma.py for code consistency.
  • Added progress bars to embeddings generation.
  • (The functionality of the React-to-Me profile remains identical.)

heliamoh and others added 22 commits February 10, 2025 19:51
@GFJHogue GFJHogue mentioned this pull request Mar 12, 2025
@GFJHogue GFJHogue marked this pull request as ready for review March 19, 2025 17:35
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@adamjohnwright adamjohnwright left a comment

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I looked at it. I think it goes with the design principles that you discussed with me a couple weeks ago. I don't think I will fully understand it till I start using it but it looks good to me!!! Lots of work :)

@adamjohnwright adamjohnwright merged commit bf34543 into main Mar 20, 2025
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@adamjohnwright adamjohnwright deleted the integrate-uniprot branch March 20, 2025 16:01
GFJHogue pushed a commit that referenced this pull request Apr 17, 2025
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3 participants