Dry run test revealed GP lookup queries timing out at 30s (connection_timeout
in snowflake.toml). Increased to 600s. Also increased batch_size from 500 to
5000 — query time is ~40s regardless of batch size (CTE compilation overhead),
so larger batches reduce total time from ~50min to ~6min for 36K patients.
Dry run results: 91.8% GP match rate, 49.3% drug-indication match rate,
42,072 modified UPIDs, 1,846 pathway nodes across 6 date filters.
Tested full refresh pipeline end-to-end with real Snowflake data:
- Fixed trust filter to read Name column from defaultTrusts.csv
- Fixed Decimal type handling in calculate_cost_per_patient_per_annum
- Fixed array handling in convert_to_records for average_administered
- Added required reference CSV files to data/ directory
- Configured Snowflake connection (account, warehouse, user)
Results:
- Snowflake fetch: 656,695 records in ~7s
- Transformations: 519,848 records after UPID/drug/directory
- Pathway nodes: 293 for all_6mo (8 trusts, 14 directories)
- Total processing time: ~6.2 minutes
admin
Andrew Charlwood