[BUG] Pipeline catalog is now inside the container but still not found by the CLI

[michellewang]

Is there an existing issue for this?

• I have searched the existing issues

Expected Behavior

No response

Current Behavior

• Inside the container, the pipeline catalog is in /app/src/pipeline-catalog, thanks to [FIX] Make pipeline-catalog submodule available to built Docker image #373
• This does not match the value in bagel.mappings.PROCESSING_PIPELINE_PATH, which points to /usr/local/lib/python3.10/site-packages/pipeline-catalog/processing
• This is because PROCESSING_PIPELINE_PATH is built from the file at /usr/local/lib/python3.10/site-packages/bagel/mappings.py, which is part of the installed Python package, not the source code
• So I think this is more of a packaging problem, not a Docker-building problem. A solution would be to move the pipeline-catalog submodule inside the bagel directory. Or there could be a script that generates a static JSON file from the pipeline catalog and stores it inside the bagel directory, then at runtime that JSON file could be loaded into KNOWN_PIPELINE_URIS directly. A third possible solution would be to configure pyproject.toml to somehow include the pipeline catalog, but I'm not sure how to do that and also that might not guarantee that PROCESSING_PIPELINE_PATH will still point to the correct directory.

Error message

No response

Environment

bagelcli v0.3.2

How to reproduce

No response

Anything else?

No response

[neurobagel-bot]

🚀 Issue was released in v0.3.3 🚀