# Progress Log - Pathway Data Architecture

## Project Context

This project extends the existing Reflex UI redesign (`pathways_app/app_v2.py`) with pre-computed pathway data from Snowflake. The current app uses a simplified `prepare_chart_data()` that only does Trust → Directory → Drug aggregation. The goal is to support full sequential patient treatment pathways with treatment statistics.

## Key Files Reference

**Existing (reuse these):**
- `analysis/pathway_analyzer.py` - Has `prepare_data()`, `calculate_statistics()`, `build_hierarchy()`, `generate_icicle_chart()`
- `visualization/plotly_generator.py` - Has chart generation with full customdata structure
- `data_processing/snowflake_connector.py` - Snowflake connection with SSO auth
- `tools/data.py` - `patient_id()`, `drug_names()`, `department_identification()`
- `data_processing/schema.py` - Existing SQLite schema

**To create:**
- `data_processing/pathway_pipeline.py` - New pathway processing pipeline
- `cli/refresh_pathways.py` - CLI command for data refresh

## Known Patterns

### Pathway ids format
The `ids` column in ice_df contains hierarchical paths like:
- "Norfolk & Waveney ICS" (root)
- "Norfolk & Waveney ICS|NNUH" (trust)
- "Norfolk & Waveney ICS|NNUH|OPHTHALMOLOGY" (directory)
- "Norfolk & Waveney ICS|NNUH|OPHTHALMOLOGY|RANIBIZUMAB" (drug)
- "Norfolk & Waveney ICS|NNUH|OPHTHALMOLOGY|RANIBIZUMAB|AFLIBERCEPT" (pathway)

### Date filter combinations
6 pre-defined combinations stored in `pathway_date_filters` table:
- all_6mo (default), all_12mo, 1yr_6mo, 1yr_12mo, 2yr_6mo, 2yr_12mo

### Expected data volumes
- ~440K intervention records
- ~35K patients
- ~6-12 minutes for full refresh (6 date combinations)

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## Iteration Log

## Iteration 1 — 2026-02-04
### Task: 1.1 Extend Database Schema
### Why this task:
- Foundation task with no dependencies — everything else needs the schema first
- Task 1.2 (Pipeline Module) and 1.3 (Migration Script) both depend on having schema constants defined
- Logical starting point for a new project
### Status: COMPLETE
### What was done:
- Added `PATHWAY_DATE_FILTERS_SCHEMA` with 6 pre-defined date combinations (all_6mo, all_12mo, 1yr_6mo, 1yr_12mo, 2yr_6mo, 2yr_12mo)
- Added `PATHWAY_NODES_SCHEMA` with all required columns:
  - Hierarchy: parents, ids, labels, level
  - Counts: value (patient count)
  - Costs: cost, costpp, cost_pp_pa
  - Dates: first_seen, last_seen, first_seen_parent, last_seen_parent
  - Statistics: average_spacing, average_administered, avg_days
  - Denormalized filters: trust_name, directory, drug_sequence
  - Metadata: date_filter_id (FK), created_at, data_refresh_id
- Added `PATHWAY_REFRESH_LOG_SCHEMA` for tracking refresh status
- Created 8 indexes for efficient filtering
- Added helper functions:
  - `create_pathway_tables()` / `drop_pathway_tables()`
  - `get_pathway_table_counts()` / `verify_pathway_tables_exist()`
  - `clear_pathway_nodes(date_filter_id=None)` — selective or full clearing
  - `get_pathway_refresh_status()` — returns latest refresh status
- Updated `ALL_TABLES_SCHEMA` and combined helpers to include pathway tables
### Validation results:
- Tier 1 (Code): ✅ python -m py_compile passed, all imports successful
- Tier 2 (Visual): N/A (schema work, no UI)
- Tier 3 (Functional): ✅ Created test database, verified all 6 date filters populated, all 8 indexes created, all helper functions work correctly
### Files changed:
- `data_processing/schema.py` — added ~300 lines (3 new schema constants, 6 new helper functions)
- `IMPLEMENTATION_PLAN.md` — marked Task 1.1 subtasks complete
### Committed: 34396fe "feat: add pathway data architecture schema (Task 1.1)"
### Patterns discovered:
- The INSERT OR REPLACE pattern works well for pre-populating date filters
- Using tempfile.TemporaryDirectory() for test databases avoids polluting the workspace
### Next iteration should:
- Start Task 1.2: Create Pathway Pipeline Module (`data_processing/pathway_pipeline.py`)
- Reference `analysis/pathway_analyzer.py` for existing pathway logic to reuse
- The pipeline needs to: fetch_and_transform_data(), process_pathway_for_date_filter(), extract_denormalized_fields(), convert_to_records()
### Blocked items:
- None