Troubleshooting

Encountering an error, mystery, or other unexplained oddity? Open a ticket on the GitHub repository: https://github.com/monarch-initiative/ontogpt/issues

I get an error like TypeError: ConfiguredBaseModel.__init_subclass__() takes no keyword arguments

This can happen if you have installed a version of the Pydantic package older than version 2 and/or if you're using a schema generated for Pydantic v1. Versions of OntoGPT of v0.3.3 and above should prevent this from happening, but if you're still seeing the error, then running make again may fix it.

I get an error like urllib.error.HTTPError: HTTP Error 404: Not Found

There are a variety of reasons why this may happen, but one cause is if your schema specifies an annotator which does not exist. If the stack trace of the error includes the get_adapter method from oaklib, then this is a likely cause, and you may want to verify that all annotators are accessible to OAK.

I get a lot of warnings like WARNING:root:Could not find any mappings for ... and I don't get the expected identifiers in my extracted object

Verify that the id_prefixes you specify in your schema correspond to those provided by the annotator. If your annotator is sqlite:obo:hp, for example, the prefix will be HP rather than HPO.

I need to store the annotator files OntoGPT downloads somewhere other than ~/.data/oaklib

OntoGPT uses oaklib to handle the ontologies it uses as annotators, and oaklib uses the pystow package to determine where downloads should go.

To change the download location, set the PYSTOW_HOME variable in your environment to your preferred path.

For example, to save downloads to /tmp/oaklib, set the varible like this:

export PYSTOW_HOME='/tmp/'

You may then reset that variable with this command:

unset PYSTOW_HOME

Or make the change more permanent by adding it to your .bashrc file and then run

source ~/.bashrc