diff --git a/progress.txt b/progress.txt index 70e34ba..032ac43 100644 --- a/progress.txt +++ b/progress.txt @@ -107,3 +107,44 @@ The previous `batch_lookup_indication_groups()` function in `diagnosis_lookup.py - The key integration point: extract unique PseudoNHSNoLinked values from HCD data, call this function, map results back to UPID for indication_df ### Blocked items: - None + +## Iteration 2 — 2026-02-05 +### Task: 1.2 Update Data Pipeline to Include Indications & 2.3 Update Refresh Command +### Why this task: +- Task 1.1 verification would naturally happen when running the full pipeline with real data +- Task 1.2 is the logical next step - integrates the new function into the CLI +- Task 2.3 overlaps with 1.2 - both involve updating refresh_pathways.py to use the new approach +- Combined these tasks since they're tightly coupled +### Status: COMPLETE +### What was done: +- Modified `cli/refresh_pathways.py` to use `get_patient_indication_groups()` instead of `batch_lookup_indication_groups()` +- Updated import statement to use the new function +- Replaced the indication chart processing section (lines 361-441) with new logic: + 1. Extracts unique PseudoNHSNoLinked values from df + 2. Calls `get_patient_indication_groups()` with patient list + 3. Builds indication_df mapping UPID → Indication_Group: + - For matched patients: Search_Term (from GP record) + - For unmatched patients: Directory + " (no GP dx)" + 4. Logs coverage statistics and top indications + 5. Passes indication_df to existing `process_indication_pathway_for_date_filter()` +### Validation results: +- Tier 1 (Code): ✅ `python -m py_compile cli/refresh_pathways.py` passed +- Tier 1 (Import): ✅ `from cli.refresh_pathways import refresh_pathways` works +- Tier 1 (Import): ✅ `from data_processing.diagnosis_lookup import get_patient_indication_groups` works +- Tier 2 (Data): Pending - needs live Snowflake test with `--chart-type indication` +- Tier 3 (Functional): Pending - needs full pipeline test +### Files changed: +- `cli/refresh_pathways.py` — replaced batch_lookup_indication_groups with get_patient_indication_groups integration +- `IMPLEMENTATION_PLAN.md` — marked Task 1.2 and 2.3 subtasks complete +### Committed: ad10b37 "feat: integrate Snowflake-direct indication lookup into CLI refresh (Task 1.2, 2.3)" +### Patterns discovered: +- The indication processing follows the same flow as before, just with different data source +- patient_lookup DataFrame helps map PseudoNHSNoLinked → UPID for the final indication_df +- match_lookup dict (PatientPseudonym → Search_Term) makes joining simple +### Next iteration should: +- Run a live test with `python -m cli.refresh_pathways --chart-type indication --dry-run` to verify the full pipeline +- This will test Task 1.1 verification (function returns expected Search_Terms) and Task 3.1 (full pipeline test) +- Alternatively, proceed to Phase 4 (Reflex UI) if confident +- Key verification points: coverage statistics logged, indication_df structure correct +### Blocked items: +- None