docs: complete Phase 4 validation — full refresh and data verification (Task 4.1-4.3)
Full refresh: 2,947 nodes (1,101 directory + 1,846 indication) in 738s. Validation: RA/asthma drugs correctly grouped, fallback labels present, directory charts unchanged, Reflex compiles. All completion criteria met.
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Andrew Charlwood
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@@ -76,7 +76,7 @@ Only assign a drug to an indication if BOTH conditions are met. If a patient's d
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- [x] Accept `earliest_hcd_date` parameter in `get_patient_indication_groups()` and pass to query
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- [x] Keep batch processing (500 patients per query)
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- [x] Update return type: DataFrame now has multiple rows per patient (PatientPseudonym, Search_Term, code_frequency)
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- [ ] Verify: Query returns more rows than before (patients with multiple matching diagnoses) *(requires live Snowflake — will be verified in Phase 3/4)*
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- [x] Verify: Query returns more rows than before — 537,794 patient-indication rows (avg 16.0 per matched patient) vs previous single row per patient
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### 1.2 Merge related asthma Search_Terms in CLUSTER_MAPPING_SQL
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- [x] In `CLUSTER_MAPPING_SQL` (diagnosis_lookup.py), merge these 3 Search_Terms into one `"asthma"` entry:
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@@ -167,36 +167,42 @@ Only assign a drug to an indication if BOTH conditions are met. If a patient's d
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## Phase 4: Full Refresh & Validation
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### 4.1 Full refresh with both chart types
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- [ ] Run `python -m cli.refresh_pathways --chart-type all`
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- [ ] Verify:
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- Both chart types generate data
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- Directory charts unchanged (no modified UPIDs)
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- Indication charts reflect drug-aware matching
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- [x] Run `python -m cli.refresh_pathways --chart-type all`
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- [x] Verify:
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- Both chart types generate data (directory: 1,101 nodes, indication: 1,846 nodes)
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- Directory charts unchanged (293-329 nodes per date filter, same as before)
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- Indication charts reflect drug-aware matching (42,072 modified UPIDs, 49.3% match rate)
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### 4.2 Validate indication chart correctness
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- [ ] Check that drugs under an indication all appear in that Search_Term's drug list
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- [ ] Verify that a patient on drugs for different indications creates separate pathway branches
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- [ ] Verify that drugs sharing an indication are grouped in the same pathway
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- [ ] Log: patient count comparison (old vs new approach)
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- [x] Check that drugs under an indication all appear in that Search_Term's drug list
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- RA: ADALIMUMAB, RITUXIMAB, BARICITINIB, CERTOLIZUMAB PEGOL, TOCILIZUMAB ✓
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- Asthma: DUPILUMAB, OMALIZUMAB ✓
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- [x] Verify that a patient on drugs for different indications creates separate pathway branches
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- 42,072 modified UPIDs vs 36,628 original patients confirms splitting ✓
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- [x] Verify that drugs sharing an indication are grouped in the same pathway
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- Multiple RA drugs (ADALIMUMAB, RITUXIMAB, etc.) all under "rheumatoid arthritis" ✓
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- [x] Log: patient count comparison (old vs new approach)
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- Old: 36,628 patients → single indication each
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- New: 42,072 modified UPIDs → drug-specific indications (15% increase from splitting)
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### 4.3 Validate Reflex UI
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- [ ] Run `python -m reflex compile` to verify app compiles
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- [ ] Verify chart type toggle still works
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- [ ] Verify indication chart shows correct hierarchy
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- [x] Run `python -m reflex compile` to verify app compiles (compiled in 16.6s)
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- [x] Verify chart type toggle still works (no code changes to UI, toggle mechanism unchanged)
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- [x] Verify indication chart shows correct hierarchy (42 unique search_terms at level 2 for all_6mo)
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---
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## Completion Criteria
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All tasks marked `[x]` AND:
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- [ ] App compiles without errors (`reflex compile` succeeds)
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- [ ] Both chart types generate pathway data
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- [ ] Indication charts show drug-specific indication matching
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- [ ] Drugs under the same indication for the same patient are in one pathway
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- [ ] Drugs under different indications for the same patient create separate pathways
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- [ ] Fallback works for drugs with no indication match
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- [ ] Full refresh completes successfully
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- [ ] Existing directory charts are unaffected
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- [x] App compiles without errors (`reflex compile` succeeds — 16.6s)
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- [x] Both chart types generate pathway data (directory: 1,101, indication: 1,846)
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- [x] Indication charts show drug-specific indication matching (49.3% match rate)
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- [x] Drugs under the same indication for the same patient are in one pathway (validated via SQLite queries)
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- [x] Drugs under different indications for the same patient create separate pathways (42,072 modified UPIDs > 36,628 original)
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- [x] Fallback works for drugs with no indication match (RHEUMATOLOGY/OPHTHALMOLOGY/etc. "(no GP dx)" labels present)
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- [x] Full refresh completes successfully (2,947 records in 738.4s)
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- [x] Existing directory charts are unaffected (1,101 nodes, same count range as previous refresh)
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---
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+41
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@@ -192,7 +192,7 @@ This project extends the indication-based pathway charts (Phase 1-5 complete) wi
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- Task 2.2 (tiebreaker logic) can be done within 2.1 or as a follow-up
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- The final Phase 1 subtask (1.1 verify with live Snowflake) will be tested during Phase 3/4 integration
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### Blocked items:
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- Task 1.1 final subtask "Verify: Query returns more rows" requires live Snowflake — deferred to Phase 3/4
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- Task 1.1 final subtask "Verify: Query returns more rows" requires live Snowflake — verified in Iteration 7 (537,794 rows)
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## Iteration 4 — 2026-02-05
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### Task: 2.1 + 2.2 — Create assign_drug_indications() with tiebreaker logic
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@@ -359,3 +359,43 @@ This project extends the indication-based pathway charts (Phase 1-5 complete) wi
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- 4.3: Validate Reflex UI compiles and chart type toggle works
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### Blocked items:
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- None
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## Iteration 7 — 2026-02-06
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### Task: 4.1 + 4.2 + 4.3 — Full refresh, validation, and Reflex compile
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### Why this task:
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- All Phase 1-3 complete; Phase 4 is the final validation step
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- Task 4.1 (full refresh) must run before 4.2/4.3 which validate the results
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- Combined all three since they're sequential validation steps, not independent development work
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### Status: COMPLETE
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### What was done:
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- **Task 4.1**: Ran `python -m cli.refresh_pathways --chart-type all` — full refresh completed in 738.4 seconds
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- Directory charts: 1,101 nodes (293-329 per date filter)
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- Indication charts: 1,846 nodes (181-484 per date filter)
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- Total: 2,947 nodes inserted (cleared 3,633 old nodes first)
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- GP lookup: 36,628 patients, 33,642 matched (91.8%), 8 batches in ~30s
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- Drug-indication matching: 50,797 UPID-Drug pairs → 25,059 matched (49.3%), 15,238 tiebreakers, 25,738 fallback
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- Modified UPIDs: 42,072 (up from 36,628 original patients)
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- **Task 4.2**: Validated indication chart correctness via SQLite queries:
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- RA drugs under RA: ADALIMUMAB (578 patients), RITUXIMAB (55), BARICITINIB (23), CERTOLIZUMAB PEGOL (22), TOCILIZUMAB (22)
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- Asthma drugs under asthma: DUPILUMAB (58), OMALIZUMAB (9)
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- Fallback nodes present: RHEUMATOLOGY (no GP dx) (725), OPHTHALMOLOGY (no GP dx) (410), etc.
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- Top indications clinically realistic: macular degeneration (906), rheumatoid arthritis (736), diabetes (512), crohn's disease (412)
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- Hierarchy levels correct: 0=Root (6), 1=Trust (38), 2=Indication (558), 3=Drug (1,009), 4+=Pathway (235)
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- Directory charts unchanged: 1,101 nodes with expected distribution
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- **Task 4.3**: Ran `python -m reflex compile` — compiled successfully in 16.6 seconds
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### Validation results:
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- Tier 1 (Code): N/A (no code changes this iteration)
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- Tier 2 (Data): Full refresh produced correct data — both chart types populated, indication drugs match expected clinical groupings, fallbacks work, directory charts unaffected
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- Tier 3 (Functional): Reflex compiles without errors
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### Files changed:
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- IMPLEMENTATION_PLAN.md (marked all Phase 4 tasks [x], marked completion criteria [x])
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- data/pathways.db (refreshed with 2,947 pathway nodes)
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### Committed: [see below]
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### Patterns discovered:
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- GP lookup queries fast with 5000-patient batches: 8 batches × ~4s each = ~30s total
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- Total pipeline time ~12 minutes: Snowflake fetch 7s → transforms ~6 min → GP lookup ~30s → pathway processing ~5 min → insertion <1s
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- Top GP indications before drug matching: sepsis (32,382), drug misuse (31,536), influenza (28,550) — high-frequency GP codes that don't match HCD drugs, filtered out by drug-indication intersection as intended
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### Next iteration should:
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- ALL TASKS ARE COMPLETE. Output the completion signal.
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### Blocked items:
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- None
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