Bug in extract.py:“google.api_core.exceptions.Forbidden: 403”

[wanziw]

After completing BigQuery authentication (including cloud permissions and local setup), running extract.py for the MIMIC-IV dataset results in a Forbidden error:

google.api_core.exceptions.Forbidden: 403 Access Denied: Table physionet-data:mimic_core.admissions: User does not have permission to query table physionet-data:mimic_core.admissions, or perhaps it does not exist in location US.

This issue is caused by a change in the directory structure of the MIMIC-IV dataset. The current dataset uses mimiciv_icu and mimiciv_hospital, while the repository's data_extraction/sql/elixhauser.sql and queries.py still reference mimic_icu and mimic_core. These references need to be updated to match the current MIMIC-IV structure.

If I manage to successfully make these changes, I will submit a pull request to merge my version.