CLI Package

Command-line interface for pathway data refresh operations.

refresh_pathways.py

Main CLI module for refreshing pre-computed pathway data from Snowflake to SQLite.

Key Functions:

refresh_pathways() — Orchestrates full pipeline: fetch from Snowflake, transform via tools/data.py, generate pathway charts, insert to SQLite
insert_pathway_records() — Bulk inserts using parameterized queries with INSERT OR REPLACE (handles overwrites via UNIQUE constraint)
log_refresh_start(), log_refresh_complete(), log_refresh_failed() — Tracks refresh status in pathway_refresh_log table
get_default_filters() — Loads available trusts, drugs, directories from CSV files

CLI Arguments:

--chart-type [all|directory|indication] — Which pathway types to refresh (default: all)
--dry-run — Test without database changes
--minimum-patients N — Pathway nodes with <N patients filtered out (default: 5)
-v, --verbose — Enable debug logging

Usage:

python -m cli.refresh_pathways --chart-type all
python -m cli.refresh_pathways --chart-type indication --dry-run -v

Note: Module uses sys.path bootstrap at top to enable python -m cli.refresh_pathways from project root.