Update output options for multilingual analysis

monarch-initiative / ontogpt

LLM-based ontological extraction tools, including SPIRES

https://monarch-initiative.github.io/ontogpt/

BSD 3-Clause "New" or "Revised" License

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Update output options for multilingual analysis #438

Closed caufieldjh closed 2 months ago

caufieldjh commented 2 months ago

The multilingual analysis function doesn't use the output exporters in the CLI. It should be able to use those options rather than opening its own output file - minimally, it should be able to append results to the same file rather than attempting to re-open the same file anew each time.

See https://github.com/monarch-initiative/ontogpt/blob/23399505db7052ea663d446d114cde16e4fb8c33/src/ontogpt/cli.py#L1504-L1519

leokim-l commented 2 months ago

Using ontogpt run-multilingual-analysis --output=some/path/filename.yaml ... on an existing some/path/filename.yaml overwrites the file. It would be nice if it could append results, especially for longer runs.