Troubleshooting

Report Not Found

  • Run biofilter report list.

  • Use --report-name with one of the listed names.

Input Conflict in report run

If you pass --input/--input-file, do not also pass input keys through params (input_data, items, input_path).

Explain Page Not Found

  • Check if guide exists at biofilter/modules/report/reports_explain/report_<module>.md.

  • If missing, Biofilter will fall back to class explain().

PostgreSQL-only Reports

db_pg_table_stats and db_pg_index_stats require PostgreSQL.

Migration/Upgrade Issues

Use:

biofilter db migrate --status
biofilter db migrate --target head
biofilter db upgrade

ETL Batch Resume

If etl update-all was interrupted, run it again. Successful data sources are skipped.

Report Output Not Found (Docker)

If you run BF4 in a container and export with --output, mount a host volume and write to that mounted path.

Example:

docker run --rm \
  -e DATABASE_URL="postgresql+psycopg2://user:pass@host:5432/db" \
  -v "$(pwd)/outputs:/workspace/outputs" \
  biofilter:bf4 \
  biofilter report run --report-name etl_status --output /workspace/outputs/etl_status.csv