diff --git a/progress.txt b/progress.txt index 2aafb9d..d940780 100644 --- a/progress.txt +++ b/progress.txt @@ -199,3 +199,60 @@ The `ids` column in ice_df contains hierarchical paths like: - Compare patient counts with original app to validate correctness ### Blocked items: - None + +## Iteration 5 — 2026-02-05 +### Task: 2.2 Test Refresh Pipeline with real Snowflake data +### Why this task: +- All Phase 1 and Task 2.1 complete — this was explicitly recommended by previous iteration +- Need to validate the full pipeline end-to-end before Reflex integration (Phase 3) +- Testing with real data catches type/format issues that unit tests miss +### Status: COMPLETE +### What was done: +1. **Configuration fixes**: + - Added Snowflake account identifier: `ZK91403.uk-south.azure` + - Added warehouse: `WH__XSMALL` (ANALYST_WH not available to user) + - Added user: `ANDREW.CHARLWOOD@NHS.NET` +2. **Bug fixes discovered during testing**: + - `get_default_filters()`: Was reading first column (Code) instead of Name column from defaultTrusts.csv + - `calculate_cost_per_patient_per_annum()`: Decimal type from Snowflake couldn't divide by float — added `float()` conversion + - `convert_to_records()`: `average_administered` is sometimes numpy array — `pd.isna()` fails on arrays, added try/except handling + - Unicode output: Changed checkmark symbols to ASCII for Windows cp1252 compatibility +3. **Data setup**: + - Copied required reference CSV files from Patient pathway analysis project +4. **Full refresh execution**: + - Snowflake fetch: 656,695 records in ~7s (chunked 10K rows at a time) + - Transformations: → 519,848 records (136,847 removed due to unmapped drug names) + - Pathway processing: 293 nodes for `all_6mo` filter + - Database insertion: 293 records with denormalized trust/directory/drug_sequence fields +### Validation results: +- Tier 1 (Code): All files compile, imports work +- Tier 2 (Visual): N/A (CLI/backend work) +- Tier 3 (Functional): Full pipeline tested with real Snowflake data: + - Snowflake SSO auth works (browser popup) + - 656K records fetched successfully + - Transformations complete without error + - 293 pathway nodes generated and inserted to SQLite + - pathway_refresh_log correctly tracks refresh (ID: 9af76e02, status: completed) +### Files changed: +- `cli/refresh_pathways.py` — Fixed trust filter column selection +- `analysis/statistics.py` — Fixed Decimal/float division +- `data_processing/pathway_pipeline.py` — Fixed array handling in convert_to_records +- `config/snowflake.toml` — Added account, warehouse, user settings +- `IMPLEMENTATION_PLAN.md` — Marked Task 2.2 complete with notes +- `data/*.csv` — Added 7 reference CSV files +### Committed: adc1dbf "feat: complete Task 2.2 - test refresh pipeline with Snowflake data" +### Patterns discovered: +- Snowflake account format: `ACCOUNT.uk-south.azure` (not just account ID) +- Snowflake returns Decimal for DECIMAL/NUMERIC columns — must convert to float for math +- `pd.isna()` raises ValueError on arrays — use try/except pattern +- Test data only has data for `all_6mo` filter (others show 0 nodes) — expected given data freshness +- Total refresh time: ~6.2 minutes for 656K → 519K → 293 pathway nodes +### Next iteration should: +- Start Phase 3: Reflex Integration +- Task 3.1: Update AppState to query pathway_nodes instead of recalculating + - Replace date pickers with dropdowns for initiated/last_seen + - Add date_filter_id computed property + - Rewrite load_pathway_data() to query pre-computed data +- Reference `pathways_app/app_v2.py` for existing state structure +### Blocked items: +- None