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Integrate uniprot #78
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…for specified database
…on of multiple databases
… return only the retriever
…iple database LLMs
…iple database LLMs
…iple database LLMs
Merged
adamjohnwright
approved these changes
Mar 20, 2025
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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 :)
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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
:If you don't yet have
config.yml
, create it by duplicatingconfig_default.yml
.Code improvements tacked on after #77:
TypedDict
's to enable the type-checker to better enforce valid state keys (to avoid KeyErrors at runtime).BaseState
intoInputState
andOutputState
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/
).retrievers/csv_chroma.py
for code consistency.React-to-Me
profile remains identical.)