monarch-initiative / automaxo Goto Github PK

A minimal click CLI would make it much easier to run project scripts and specify parameters.

I think that .openai_cache.db just has my local key, so probably it should not be in the repository.

git pull
Updating f65d6cf..089ee6f
error: Your local changes to the following files would be overwritten by merge:
	.openai_cache.db
Please commit your changes or stash them before you merge.
Aborting

OntoGPT processing could be handled through this project, too - just add it to the dependencies and import:

from ontogpt.engines.spires_engine import SPIRESEngine

A more hard-coded version of the extract command used in the OntoGPT CLI would get it done and would allow any project-specific preprocessing to be easily added to this project.

In the document retrieval functions:

The search_term is hardcoded to search on title or abstract, which is great if you're looking for specific disease names.
If you are trying to retrieve a specific document or set of documents, this doesn't work as well since the PMID is found elsewhere in the document metadata.

One solution would be to have the function default to adding [Title/Abstract] to the search string like it currently does,
but provide an additional argument like raw to allow passing a search string without that filter.