feat: complete drug-aware indication matching and cleanup app_v2

- Remove app_v2.py (consolidated into pathways_app.py), fix __init__ import
- Add DimSearchTerm.csv, drug_indication_clusters.csv, drug_snomed_mapping_enriched.csv
  as reference data for SNOMED-based indication matching
- Add snomed_indication_mapping_query.sql (source for embedded cluster mapping)
- Update DESIGN_SYSTEM.md, RALPH_PROMPT.md, ralph.ps1, uv.lock

.claude/settings.local.json

@@ -5,7 +5,9 @@
       "Bash(wc:*)",
       "WebFetch(domain:flet.dev)",
       "WebFetch(domain:github.com)",
-      "WebFetch(domain:docs.flet.dev)"
+      "WebFetch(domain:docs.flet.dev)",
+      "Bash(python -c:*)",
+      "Bash(Remove-Item -Path \"C:\\\\Users\\\\charlwoodand\\\\Ralph local\\\\Tasks\\\\UI Redesign\\\\logs\\\\*\" -Force)"
     ]
   }
 }

DESIGN_SYSTEM.md

@@ -1,189 +1,194 @@
-# Design System - HCD Analysis v2
+# Design System - HCD Analysis v2.1 (SaaS Redesign)
 
-This document defines the visual design language for the UI redesign. All components should reference these tokens for consistency.
+This document defines the visual design language for the UI redesign. The goal is a **modern SaaS aesthetic** - think Stripe, Linear, Vercel - while staying thematically aligned with the blue color palette.
+
+**Design Philosophy**:
+- The chart is the hero; everything else supports it
+- Minimal chrome, maximum data visibility
+- Clean, confident, spacious - not clinical or governmental
+- Every pixel of vertical space matters
 
 ## Color Palette
 
-### Primary Blues (NHS-inspired, modernized)
+### Primary Blues (kept from original, used sparingly)
 | Name | Hex | Usage |
 |------|-----|-------|
-| Heritage Blue | `#003087` | Deep headers, authoritative accents |
+| Heritage Blue | `#003087` | Top bar background, strong accents |
-| Primary Blue | `#0066CC` | Main actions, links, focus states |
+| Primary Blue | `#0066CC` | Interactive elements, links, focus |
-| Vibrant Blue | `#1E88E5` | Highlights, hover states, chart primary |
+| Vibrant Blue | `#1E88E5` | Hover states, active elements |
-| Sky Blue | `#4FC3F7` | Accents, progress bars, secondary elements |
+| Sky Blue | `#4FC3F7` | Subtle accents, progress indicators |
-| Pale Blue | `#E3F2FD` | Subtle backgrounds, card tints |
+| Pale Blue | `#E3F2FD` | Selected states, subtle backgrounds |
 
-### Neutrals (warm-tinted for clinical warmth)
+### Neutrals (refined for modern feel)
 | Name | Hex | Usage |
 |------|-----|-------|
-| Slate 900 | `#1E293B` | Primary text |
+| Slate 900 | `#0F172A` | Primary text (slightly darker) |
 | Slate 700 | `#334155` | Secondary text |
 | Slate 500 | `#64748B` | Muted text, placeholders |
 | Slate 300 | `#CBD5E1` | Borders, dividers |
-| Slate 100 | `#F1F5F9` | Card backgrounds, hover states |
+| Slate 100 | `#F8FAFC` | Backgrounds (slightly lighter) |
-| White | `#FFFFFF` | Page background |
+| White | `#FFFFFF` | Card/modal backgrounds |
 
 ### Semantic Colors
 | Name | Hex | Usage |
 |------|-----|-------|
-| Success | `#059669` | Positive states, confirmations |
+| Success | `#10B981` | Positive (modern green) |
-| Warning | `#D97706` | Caution states, alerts |
+| Warning | `#F59E0B` | Caution |
-| Error | `#DC2626` | Error states, destructive actions |
+| Error | `#EF4444` | Errors |
-| Info | `#0284C7` | Informational (matches primary family) |
+| Info | `#3B82F6` | Informational |
-
-### Chart Palette
-```
-Primary series: #003087, #0066CC, #1E88E5, #4FC3F7, #90CAF9
-Categorical: #0066CC, #059669, #D97706, #8B5CF6, #EC4899
-```
 
 ## Typography
 
 **Font Family:** Inter (primary), system-ui (fallback)
 
-| Style | Size | Weight | Tracking | Line Height | Usage |
+| Style | Size | Weight | Usage |
-|-------|------|--------|----------|-------------|-------|
+|-------|------|--------|-------|
-| Display | 32px | 700 | -0.02em | 1.2 | Page titles |
+| Display | 28px | 600 | Page titles (reduced from 32px) |
-| Heading 1 | 24px | 600 | -0.01em | 1.3 | Section headers |
+| Heading 1 | 18px | 600 | Section headers (reduced from 24px) |
-| Heading 2 | 20px | 600 | normal | 1.4 | Card titles |
+| Heading 2 | 16px | 600 | Card titles (reduced from 20px) |
-| Heading 3 | 16px | 600 | normal | 1.4 | Subsections |
+| Heading 3 | 14px | 600 | Subsections |
-| Body | 14px | 400 | normal | 1.5 | Default text |
+| Body | 14px | 400 | Default text |
-| Body Small | 13px | 400 | normal | 1.5 | Secondary info |
+| Body Small | 13px | 400 | Secondary info |
-| Caption | 12px | 500 | normal | 1.4 | Labels, metadata |
+| Caption | 11px | 500 | Labels, metadata (reduced from 12px) |
-| Mono | 13px | 400 | normal | 1.5 | Data values, codes (JetBrains Mono) |
+| Mono | 13px | 500 | Data values (JetBrains Mono) |
 
-## Spacing Scale
+## Spacing Scale (Tighter)
 
 | Token | Value | Usage |
 |-------|-------|-------|
-| xs | 4px | Tight internal padding |
+| xs | 4px | Tight gaps |
-| sm | 8px | Between related elements |
+| sm | 6px | Between related elements (was 8px) |
-| md | 12px | Standard gaps |
+| md | 8px | Standard gaps (was 12px) |
-| lg | 16px | Section padding |
+| lg | 12px | Section padding (was 16px) |
-| xl | 24px | Card padding |
+| xl | 16px | Card padding (was 24px) |
-| 2xl | 32px | Major section gaps |
+| 2xl | 24px | Major gaps (was 32px) |
-| 3xl | 48px | Page margins |
+| 3xl | 32px | Page margins (was 48px) |
 
-## Border Radius
+## Layout Specifications
 
-| Token | Value | Usage |
+### Page Structure (Target)
-|-------|-------|-------|
+```
-| sm | 4px | Small elements, inputs |
+┌─────────────────────────────────────────────────────────────────┐
-| md | 8px | Buttons, small cards |
+│ Logo │ Tabs                                     │ Freshness    │ 48px
-| lg | 12px | Cards, modals |
+├─────────────────────────────────────────────────────────────────┤
-| xl | 16px | Large containers |
+│ [Initiated▾] [LastSeen▾] │ [Drugs▾] [Ind▾] [Dir▾] │ KPI badges │ 48px
-| full | 9999px | Pills, avatars |
+├─────────────────────────────────────────────────────────────────┤
+│                                                                 │
+│                        I C I C L E  C H A R T                   │ flex
+│                         (full viewport width)                   │
+│                                                                 │
+└─────────────────────────────────────────────────────────────────┘
+```
+
+### Top Bar
+- **Height**: 48px (reduced from 64px)
+- **Background**: Heritage Blue
+- **Logo**: 28px height (reduced from 36px)
+- **Tabs**: Small pills, 28px height
+
+### Filter Strip
+- **Height**: 48px (single row)
+- **Layout**: Horizontal flex, all filters inline
+- **Dropdown triggers**: 32px height, 8px padding
+- **No section header** - labels are in dropdown triggers
+- **Background**: Slate 100 or transparent
+
+### KPI Section (Options)
+
+**Option A: Inline badges** (preferred - zero extra height)
+```
+Filters row: [Initiated▾] [LastSeen▾] | [Drugs▾] ... | 12,345 patients • £45.2M • 89 drugs
+```
+
+**Option B: Compact strip** (48px max)
+```
+┌─────┬─────┬─────┬─────┐
+│12.3K│£45M │ 89  │  7  │  28px value
+│pts  │cost │drugs│trust│  14px label
+└─────┴─────┴─────┴─────┘
+```
+
+### Chart Container
+- **Width**: Full viewport minus 32px (16px padding each side)
+- **Height**: Fill remaining space (min 500px)
+- **No max-width constraint**
+- **Margins**: Minimal (t:40, l:8, r:8, b:24)
+
+## Component Specifications
+
+### Compact Dropdown Trigger
+- Height: 32px
+- Padding: 8px 12px
+- Border: 1px Slate 300
+- Border radius: 6px
+- Font: 13px
+- Chevron: 14px icon
+
+### Compact KPI Badge
+- Padding: 4px 12px
+- Border radius: 16px (pill)
+- Background: Slate 100
+- Value: 14px mono, weight 600
+- Label: 11px, Slate 500
+
+### Searchable Dropdown Panel
+- Max height: 200px (items area)
+- Item padding: 6px 8px
+- Search input height: 28px
+- Width: 240px min
 
 ## Shadows
 
 | Token | Value | Usage |
 |-------|-------|-------|
-| sm | `0 1px 2px rgba(0,0,0,0.05)` | Subtle elevation |
+| sm | `0 1px 2px rgba(0,0,0,0.04)` | Subtle (lighter) |
-| md | `0 1px 3px rgba(0,0,0,0.08)` | Cards at rest |
+| md | `0 1px 3px rgba(0,0,0,0.06)` | Cards at rest |
-| lg | `0 4px 6px rgba(0,0,0,0.1)` | Cards on hover, dropdowns |
+| lg | `0 4px 8px rgba(0,0,0,0.08)` | Dropdowns, hover |
-| xl | `0 10px 15px rgba(0,0,0,0.1)` | Modals, popovers |
 
-## Component Specifications
+## Border Radius
 
-### Cards
+| Token | Value | Usage |
-- Background: White
+|-------|-------|-------|
-- Border: 1px Slate 300 (optional, or use shadow only)
+| sm | 4px | Small elements |
-- Border radius: lg (12px)
+| md | 6px | Inputs, buttons |
-- Padding: xl (24px)
+| lg | 8px | Cards |
-- Shadow: md at rest, lg on hover
+| full | 9999px | Pills, badges |
-- Hover: translateY(-2px) transition
-
-### Buttons
-**Primary:**
-- Background: Primary Blue
-- Text: White
-- Border radius: md (8px)
-- Padding: 10px 20px
-- Hover: Vibrant Blue background, slight scale (1.02)
-
-**Secondary:**
-- Background: White
-- Border: 1px Primary Blue
-- Text: Primary Blue
-- Hover: Pale Blue background
-
-**Ghost:**
-- Background: transparent
-- Text: Primary Blue
-- Hover: Pale Blue background
-
-### Form Controls
-- Height: 40px (inputs, selects)
-- Border: 1px Slate 300
-- Border radius: md (8px)
-- Focus: 2px Primary Blue ring
-- Placeholder: Slate 500
-
-### Data Cards (KPIs)
-- Large mono number: 32-48px, Slate 900
-- Label: Caption size, Slate 500
-- Background: White or Pale Blue tint
-- Optional trend indicator or sparkline
-
-## Layout
-
-### Page Structure
-```
-┌─────────────────────────────────────────────────────────────────┐
-│  Logo + App Name          [Chart Tabs]       Data Freshness     │  ← Top Bar (64px height)
-├─────────────────────────────────────────────────────────────────┤
-│                                                                 │
-│  ┌─ Filters ─────────────────────────────────────────────────┐ │  ← Filter Section
-│  │  Date ranges, dropdowns, filter controls                  │ │
-│  └───────────────────────────────────────────────────────────┘ │
-│                                                                 │
-│  ┌─ KPIs ────────────────────────────────────────────────────┐ │  ← KPI Row
-│  │  [ Metric 1 ]  [ Metric 2 ]  [ Metric 3 ]  [ Metric 4 ]   │ │
-│  └───────────────────────────────────────────────────────────┘ │
-│                                                                 │
-│  ┌─ Chart ───────────────────────────────────────────────────┐ │  ← Main Chart (fills remaining)
-│  │                                                           │ │
-│  │              [ Interactive Visualization ]                │ │
-│  │                                                           │ │
-│  └───────────────────────────────────────────────────────────┘ │
-│                                                                 │
-└─────────────────────────────────────────────────────────────────┘
-```
-
-### Responsive Breakpoints
-- Mobile: < 640px
-- Tablet: 640px - 1024px
-- Desktop: > 1024px
 
 ## Transitions
 
-| Property | Duration | Easing |
+All transitions: 150ms ease-out (faster than before)
-|----------|----------|--------|
-| Color, background | 150ms | ease-out |
-| Transform | 200ms | ease-out |
-| Shadow | 200ms | ease-out |
-| Opacity | 200ms | ease-in-out |
 
-## Reflex Implementation Notes
+## Implementation Notes
 
-### Using Design Tokens
+### Key Changes from v2.0
-Create a `styles.py` module with these values as Python constants. Import throughout the app:
+1. **Vertical space reduction**: ~210px saved (364px → ~156px overhead)
+2. **Full-width chart**: Remove PAGE_MAX_WIDTH for chart
+3. **Inline KPIs**: Either badges in filter row or minimal strip
+4. **Smaller fonts**: Headlines and captions reduced
+5. **Tighter spacing**: All spacing tokens reduced by ~25%
 
-```python
+### CSS Patterns
-# Example structure
+```css
-class Colors:
+/* Full-height chart container */
-    PRIMARY = "#0066CC"
+.chart-container {
-    PRIMARY_DARK = "#003087"
+  height: calc(100vh - 96px);  /* viewport minus top bar + filter strip */
-    # etc.
+  min-height: 500px;
+  width: calc(100vw - 32px);
+  margin: 0 16px;
+}
 
-class Spacing:
+/* Filter strip */
-    XS = "4px"
+.filter-strip {
-    SM = "8px"
+  display: flex;
-    # etc.
+  align-items: center;
+  height: 48px;
+  gap: 12px;
+  padding: 0 16px;
+}
 ```
 
-### rx.theme Configuration
+### Reflex Implementation
-Configure Reflex's theme provider with the color palette for consistent component styling.
+- Use `height="calc(100vh - 96px)"` for chart container
-
+- Use `width="100%"` with `padding_x="16px"` for full-width
-### Custom CSS
+- Use `flex="1"` to let chart grow
-For styles not achievable via Reflex props, use `rx.style` or a custom CSS file.
+- Keep `min_height="500px"` as fallback

RALPH_PROMPT.md

@@ -1,6 +1,8 @@
-# Ralph Wiggum Loop - Reflex UI Redesign
+# Ralph Wiggum Loop - Drug-Aware Indication Matching
 
-You are operating inside an automated loop building a Reflex frontend application. Each iteration you receive fresh context — you have NO memory of previous iterations. Your only memory is the filesystem.
+You are operating inside an automated loop extending a pathway analysis application with drug-aware indication matching. Each iteration you receive fresh context — you have NO memory of previous iterations. Your only memory is the filesystem.
+
+**Current Focus**: Update indication charts so that patient indications are matched **per drug**, not just per patient. Each drug must be validated against the patient's GP diagnoses AND the drug-to-indication mapping from DimSearchTerm.csv.
 
 ## First Actions Every Iteration
 
@@ -9,7 +11,7 @@ Read these files in this order before doing anything else:
 1. `progress.txt` — What previous iterations accomplished, what's blocked, and what to do next. The most recent entry is most important.
 2. `IMPLEMENTATION_PLAN.md` — Task list with status markers, project overview, and completion criteria.
 3. `guardrails.md` — Known failure patterns to avoid. You MUST read and follow these.
-4. `DESIGN_SYSTEM.md` — Color palette, typography, spacing, and component specifications.
+4. `CLAUDE.md` — Project architecture and code patterns.
 
 Then run `git log --oneline -5` to see recent commits.
 
@@ -18,48 +20,109 @@ Then run `git log --oneline -5` to see recent commits.
 Narrate your work as you go. Your output is the only visibility the operator has into what's happening. For every significant action, explain what you're doing and why:
 
 - **Reading files**: "Reading progress.txt to check what the last iteration accomplished..."
-- **Creating components**: "Creating the top_bar() component with logo, title, and chart tabs..."
+- **Creating code**: "Adding assign_drug_indications() function to diagnosis_lookup.py..."
-- **Debugging**: "Reflex compilation failed with TypeError. Checking the error — looks like rx.foreach issue..."
+- **Debugging**: "Drug matching returned 0 results for ADALIMUMAB. Checking DimSearchTerm lookup..."
-- **Testing**: "Running reflex compile to verify the component renders..."
+- **Testing**: "Running import check to verify the new function is accessible..."
-- **Making decisions**: "The design system specifies Primary Blue #0066CC for buttons. Using that."
+- **Making decisions**: "The guardrails say to use substring matching for drug fragments."
-- **Committing**: "Committing styles.py — design token module complete."
+- **Committing**: "Committing drug-indication matching logic."
 
 Do NOT just output a summary at the end. Narrate throughout. Think of this as a live log of your reasoning.
 
 ## Task Selection
 
-Pick the highest-priority task that is READY to work on:
+You have flexibility to choose which task to work on. Use your judgement, but document your reasoning.
 
 1. Read ALL tasks in IMPLEMENTATION_PLAN.md — understand the full picture
 2. Skip any marked `[x]` (complete) or `[B]` (blocked)
-3. Check progress.txt for guidance — if the previous iteration recommended a specific next task, prefer that unless it's blocked
+3. Check progress.txt for guidance — the previous iteration may have recommendations
-4. If no guidance exists, pick the first `[ ]` (ready) task in the first incomplete phase
+4. **Choose a task** based on:
-5. Mark your chosen task `[~]` (in progress) in IMPLEMENTATION_PLAN.md
+   - Dependencies (some tasks require others to be done first)
+   - Logical flow (query changes before matching logic, matching before pipeline integration)
+   - Your assessment of what would be most valuable to tackle next
+   - Previous iteration's recommendations (consider but don't blindly follow)
+5. **Document your reasoning**: Before starting work, briefly explain WHY you chose this task over others
+6. Mark your chosen task `[~]` (in progress) in IMPLEMENTATION_PLAN.md
 
 If your chosen task turns out to be blocked during work:
 - Mark it `[B]` with a reason in IMPLEMENTATION_PLAN.md
 - Document the blocker in progress.txt
-- Move to the next ready task within this same iteration
+- Move to a different ready task within this same iteration
 
 ## Development
 
 Work on ONE task per iteration. Build incrementally and verify as you go.
 
+### Key Concepts
+
+**Drug-Indication Matching Flow:**
+1. Get patient's GP-matched Search_Terms from Snowflake (ALL matches, not just most recent, with code_frequency)
+   - Only count GP codes from MIN(Intervention Date) onwards (the HCD data window)
+2. Load DimSearchTerm.csv to get which drugs belong to which Search_Terms
+3. For each patient-drug pair: intersection of (Search_Terms listing this drug) AND (patient's GP matches)
+   - If multiple matches: pick highest code_frequency (most GP coding = most likely indication)
+4. Modify UPID to include matched indication: `{UPID}|{search_term}`
+5. Drugs sharing the same indication for the same patient → same modified UPID → same pathway
+6. Drugs under different indications → different modified UPIDs → separate pathways
+
+**DimSearchTerm.csv:**
+- `Search_Term`: Clinical condition (e.g., "rheumatoid arthritis")
+- `CleanedDrugName`: Pipe-separated drug fragments (e.g., "ADALIMUMAB|GOLIMUMAB|...")
+- `PrimaryDirectorate`: The directorate for this condition
+- Drug matching: check if any fragment is a substring of the HCD drug name (case-insensitive)
+
+**Modified UPID Format:**
+- Original: `RMV12345` (Provider Code[:3] + PersonKey)
+- Modified: `RMV12345|rheumatoid arthritis`
+- Fallback: `RMV12345|RHEUMATOLOGY (no GP dx)`
+- The existing pathway analyzer treats UPID as an opaque identifier — this works transparently
+
 ### Code Patterns
 
-- **Use design tokens**: Import from `pathways_app/styles.py` — never hardcode colors/spacing
+- **Snowflake queries**: Use parameterized queries, embed the cluster CTE from CLUSTER_MAPPING_SQL
-- **Reflex Vars in rx.foreach**: Use `.to(int)` for comparisons, `.to_string()` for text interpolation
+- **GP record matching**: Return ALL matches per patient (not just most recent)
-- **Component functions**: Each component should be a function returning `rx.Component`
+- **Drug mapping**: Load from `data/DimSearchTerm.csv`, match drug name fragments
-- **State class**: All reactive state goes in the `AppState` class
+- **Pathway pipeline**: Use existing functions — modified UPIDs flow through naturally
-- **Computed properties**: Use `@rx.var` decorator for derived values
+- **Reflex state**: No changes expected — indication charts already work, just with better matching
+
+### Key Data Structures
+
+**GP Matches (from Snowflake) — updated to return ALL matches with frequency:**
+```python
+# Multiple rows per patient (one per matched Search_Term)
+# code_frequency = COUNT of matching SNOMED codes (used as tiebreaker)
+# Only counts codes from MIN(Intervention Date) onwards
+DataFrame with: PatientPseudonym, Search_Term, code_frequency
+```
+
+**Drug-to-Indication Mapping (from DimSearchTerm.csv):**
+```python
+# search_term → list of drug fragments
+{"rheumatoid arthritis": ["ABATACEPT", "ADALIMUMAB", "ANAKINRA", ...]}
+```
+
+**Modified HCD Data:**
+```python
+# Original UPID replaced with indication-aware UPID
+df["UPID"] = "RMV12345|rheumatoid arthritis"  # for matched drugs
+df["UPID"] = "RMV12345|RHEUMATOLOGY (no GP dx)"  # for unmatched drugs
+```
+
+**Indication DataFrame:**
+```python
+# Maps modified UPID → Search_Term (for pathway hierarchy level 2)
+indication_df = pd.DataFrame({
+    'Directory': ['rheumatoid arthritis', 'asthma', 'CARDIOLOGY (no GP dx)']
+}, index=['RMV12345|rheumatoid arthritis', 'RMV12345|asthma', 'RMV67890|CARDIOLOGY (no GP dx)'])
+```
 
 ### Verification Steps
 
 After writing code, ALWAYS verify:
 
-1. **Syntax check**: `python -m py_compile pathways_app/app_v2.py`
+1. **Syntax check**: `python -m py_compile <file.py>`
-2. **Import check**: `python -c "from pathways_app.app_v2 import app"`
+2. **Import check**: `python -c "from module import function"`
-3. **Reflex compile**: Run `reflex run` briefly to check for compilation errors
+3. **For database changes**: Test with query against pathways.db
+4. **For Reflex changes**: `python -m reflex compile`
 
 If any step fails, fix the issue before proceeding.
 
@@ -69,18 +132,19 @@ Every task MUST pass validation before being marked complete:
 
 ### Tier 1: Code Validation (MANDATORY)
 - Code compiles without Python syntax errors
-- Reflex compiles the app without errors
+- Imports work without errors
 - No TypeErrors, ImportErrors, or AttributeErrors
 
-### Tier 2: Visual Validation (MANDATORY for UI tasks)
+### Tier 2: Data Validation (for data/pipeline tasks)
-- Component renders in the browser
+- Queries return expected row counts
-- Styling matches DESIGN_SYSTEM.md specifications
+- Data structures have correct columns/types
-- Responsive behavior works (if applicable)
+- Drug-indication matching produces valid results
+- Modified UPIDs have correct format
 
-### Tier 3: Functional Validation (MANDATORY for state/logic tasks)
+### Tier 3: Functional Validation (for UI/integration tasks)
-- State changes trigger expected UI updates
+- Reflex compiles the app without errors
-- Computed properties return correct values
+- State changes trigger expected behavior
-- Filters produce expected data transformations
+- Both chart types render correctly
 
 ### Validation Failure
 
@@ -97,8 +161,7 @@ Before marking ANY task `[x]`, ALL of these must be true:
 1. Code is saved to the appropriate file(s)
 2. Tier 1 code validation passed
 3. Tier 2/3 validation passed (as applicable)
-4. Design tokens used — no hardcoded colors, fonts, or spacing
+4. All changes committed to git with a descriptive message
-5. All changes committed to git with a descriptive message
 
 These are non-negotiable. A task that "feels done" but hasn't passed all gates is NOT done.
 
@@ -109,18 +172,21 @@ After completing your work (whether the task succeeded, failed, or was blocked),
 ```
 ## Iteration [N] — [YYYY-MM-DD]
 ### Task: [which task you worked on]
+### Why this task:
+- [Brief explanation of why you chose this task over others]
+- [What dependencies or logical flow led to this choice]
 ### Status: COMPLETE | BLOCKED | IN PROGRESS
 ### What was done:
 - [Specific actions taken]
 ### Validation results:
-- Tier 1 (Code): [syntax check, import check, reflex compile]
+- Tier 1 (Code): [syntax check, import check]
-- Tier 2 (Visual): [what was checked visually, or N/A]
+- Tier 2 (Data): [query results, row counts]
-- Tier 3 (Functional): [what logic was tested, or N/A]
+- Tier 3 (Functional): [reflex compile, UI check]
 ### Files changed:
 - [list of files created/modified]
 ### Committed: [git hash] "[commit message]"
 ### Patterns discovered:
-- [Any reusable learnings — Reflex quirks, component patterns]
+- [Any reusable learnings — query patterns, matching logic quirks]
 ### Next iteration should:
 - [Explicit guidance for what the next fresh instance should do first]
 - [Note any context that would be lost without writing it here]
@@ -132,8 +198,8 @@ If you discover a failure pattern that future iterations should avoid, add it to
 
 ## Commit Changes
 
-1. Stage changed files (styles.py, app_v2.py, etc.)
+1. Stage changed files
-2. Use a descriptive commit message referencing the task (e.g., "feat: create design tokens module")
+2. Use a descriptive commit message referencing the task (e.g., "feat: add drug-indication matching function (Task 2.1)")
 3. Commit after your task is validated and complete — one commit per logical unit of work
 4. If you updated progress.txt with a blocked status, commit that too
 
@@ -141,7 +207,7 @@ If you discover a failure pattern that future iterations should avoid, add it to
 
 If ALL tasks in IMPLEMENTATION_PLAN.md are marked `[x]`:
 
-1. Run `reflex run` and verify the app works end-to-end
+1. Run `reflex compile` to verify app compiles
 2. Verify all completion criteria at the bottom of IMPLEMENTATION_PLAN.md are satisfied
 3. Only then output the completion signal on its own line:
 
@@ -156,10 +222,15 @@ DO NOT paraphrase, vary, or conditionally output this string.
 ## Rules
 
 - Complete ONE task per iteration, then update progress and stop
-- ALWAYS read progress.txt, guardrails.md, and DESIGN_SYSTEM.md before starting work
+- ALWAYS read progress.txt, guardrails.md before starting work
-- **Use design tokens** — never hardcode hex colors, pixel values, or font names
+- **Match drugs to indications** — not just patients to indications
-- **Reflex Var safety** — use `.to()` methods when working with Vars from rx.foreach or computed properties
+- **Use DimSearchTerm.csv** for drug-to-Search_Term mapping
+- **Return ALL GP matches** — not just most recent (remove QUALIFY ROW_NUMBER = 1)
+- **Modified UPID format**: `{UPID}|{search_term}` — pipe delimiter is safe
+- **Use PseudoNHSNoLinked** — NOT PersonKey for GP record matching
+- **Substring matching** for drug fragments from DimSearchTerm.csv
 - Keep commits atomic and well-described
 - If stuck on the same issue for more than 2 attempts within one iteration, document it in progress.txt and move to the next ready task
-- When in doubt, check the existing `pathways_app.py` for patterns that work
+- When in doubt, check existing code for patterns that work
-- The goal is a working, beautiful app — correctness and visual quality matter equally
+- **Pipeline before UI** — processing logic before Reflex changes
+- **Don't change directory charts** — only indication chart matching changes

data/DimSearchTerm.csv

@@ -0,0 +1,166 @@
+Search_Term,CleanedDrugName,PrimaryDirectorate
+acute coronary syndrome,ABCIXIMAB|CLOPIDOGREL|PRASUGREL|RIVAROXABAN|TICAGRELOR,CARDIOLOGY
+acute lymphoblastic leukaemia,BLINATUMOMAB|DASATINIB|INOTUZUMAB|PEGASPARGASE|PONATINIB|TISAGENLECLEUCEL,CLINICAL HAEMATOLOGY
+acute myeloid leukaemia,AZACITIDINE|DECITABINE|GEMTUZUMAB|GILTERITINIB|GLASDEGIB|LIPOSOMAL|MIDOSTAURIN|ORAL|VENETOCLAX,CLINICAL HAEMATOLOGY
+acute promyelocytic leukaemia,ARSENIC|GEMTUZUMAB,CLINICAL HAEMATOLOGY
+allergic asthma,OMALIZUMAB,THORACIC MEDICINE
+allergic rhinitis,SQ,ENT
+alzheimer's disease,DONEPEZIL,NEUROLOGY
+amyloidosis,VUTRISIRAN,CLINICAL HAEMATOLOGY
+anaemia,ERYTHROPOIESIS-STIMULATING|ERYTHROPOIETIN,CLINICAL HAEMATOLOGY
+anaplastic large cell lymphoma,BRENTUXIMAB,CLINICAL HAEMATOLOGY
+ankylosing spondylitis,ADALIMUMAB|GOLIMUMAB|SECUKINUMAB|UPADACITINIB,RHEUMATOLOGY
+apixaban,ANDEXANET,CARDIOLOGY
+aplastic anaemia,ELTROMBOPAG,CLINICAL HAEMATOLOGY
+arthritis,ETANERCEPT,RHEUMATOLOGY
+asthma,BENRALIZUMAB|DUPILUMAB|INHALED|MEPOLIZUMAB|OMALIZUMAB|RESLIZUMAB,THORACIC MEDICINE
+atopic dermatitis,ABROCITINIB|ALCLOMETASONE|BARICITINIB|CRISABOROLE|DUPILUMAB|PIMECROLIMUS,DERMATOLOGY
+atrial fibrillation,APIXABAN|DABIGATRAN|DRONEDARONE|EDOXABAN|RIVAROXABAN|VERNAKALANT,CARDIOLOGY
+attention deficit hyperactivity disorder,ATOMOXETINE,MENTAL HEALTH
+attention-deficit hyperactivity disorder,METHYLPHENIDATE,MENTAL HEALTH
+axial spondyloarthritis,ADALIMUMAB|GOLIMUMAB|IXEKIZUMAB|SECUKINUMAB|UPADACITINIB,RHEUMATOLOGY
+basal cell carcinoma,VISMODEGIB,DERMATOLOGY
+bipolar disorder,LOXAPINE|OLANZAPINE,MENTAL HEALTH
+bladder,MIRABEGRON,MEDICAL ONCOLOGY
+brca,OLAPARIB,MEDICAL ONCOLOGY
+breast cancer,ABEMACICLIB|ALPELISIB|ANASTROZOLE|ATEZOLIZUMAB|BEVACIZUMAB|CAPECITABINE|DENOSUMAB|DOCETAXEL|ERIBULIN|EVEROLIMUS|FULVESTRANT|GEMCITABINE|INTRABEAM|LAPATINIB|NERATINIB|OLAPARIB|PACLITAXEL|PALBOCICLI|PALBOCICLIB|PEMBROLIZUMAB|PERTUZUMAB|RIBOCICLIB|SACITUZUMAB|TRASTUZUMAB|TUCATINIB|VINORELBINE,MEDICAL ONCOLOGY
+cardiomyopathy,TAFAMIDIS,CARDIOLOGY
+cardiovascular disease,ATORVASTATIN,CARDIOLOGY
+cervical cancer,TOPOTECAN,MEDICAL ONCOLOGY
+cholangiocarcinoma,PEMIGATINIB,MEDICAL ONCOLOGY
+choroidal neovascularisation,AFLIBERCEPT|RANIBIZUMAB,OPHTHALMOLOGY
+chronic kidney disease,DAPAGLIFLOZIN|IMLIFIDASE|ROXADUSTAT,NEPHROLOGY
+chronic liver disease,AVATROMBOPAG|LUSUTROMBOPAG,GASTROENTEROLOGY
+chronic lymphocytic leukaemia,ACALABRUTINIB|BENDAMUSTINE|DUVELISIB|IBRUTINIB|IDELALISIB|OBINUTUZUMAB|OFATUMUMAB|RITUXIMAB|VENETOCLAX,CLINICAL HAEMATOLOGY
+chronic myeloid leukaemia,ASCIMINIB|BOSUTINIB|STANDARD-DOSE|DASATINIB|DASITINIB|NILOTINIB|PONATINIB,CLINICAL HAEMATOLOGY
+chronic obstructive pulmonary disease,ROFLUMILAST,THORACIC MEDICINE
+colon cancer,CAPECITABINE,MEDICAL ONCOLOGY
+colorectal cancer,BEVACIZUMAB|CAPECITABINE|IRINOTECAN,MEDICAL ONCOLOGY
+constipation,LUBIPROSTONE|METHYLNALTREXONE|NALDEMEDINE|NALOXEGOL|PRUCALOPRIDE,GASTROENTEROLOGY
+covid-19,NIRMATRELVIR,INFECTIOUS DISEASES
+crohn's disease,INFLIXIMAB|VEDOLIZUMAB,GASTROENTEROLOGY
+cutaneous t-cell lymphoma,BRENTUXIMAB|CHLORMETHINE,CLINICAL HAEMATOLOGY
+cystic fibrosis,COLISTIMETHATE|LUMACAFTOR|MANNITOL,THORACIC MEDICINE
+cytomegalovirus,LETERMOVIR|MARIBAVIR,INFECTIOUS DISEASES
+deep vein thrombosis,APIXABAN|DABIGATRAN|EDOXABAN|RIVAROXABAN,VASCULAR SURGERY
+depression,ESKETAMINE,MENTAL HEALTH
+diabetes,ERTUGLIFLOZIN|INHALED|AFLIBERCEPT|BROLUCIZUMAB|DEXAMETHASONE|FARICIMAB|FLUOCINOLONE|RANIBIZUMAB,DIABETIC MEDICINE
+diabetes,ERTUGLIFLOZIN|INHALED|AFLIBERCEPT|BROLUCIZUMAB|DEXAMETHASONE|FARICIMAB|FLUOCINOLONE|RANIBIZUMAB,OPHTHALMOLOGY
+diabetic retinopathy,RANIBUZIMAB,OPHTHALMOLOGY
+diffuse large b-cell lymphoma,AXICABTAGENE|POLATUZUMAB|TISAGENLECLEUCEL,CLINICAL HAEMATOLOGY
+dravet syndrome,CANNABIDIOL|FENFLURAMINE,NEUROLOGY
+drug misuse,BUPRENORPHINE|NALTREXONE,MENTAL HEALTH
+dry eye,CICLOSPORIN,OPHTHALMOLOGY
+dyspepsia,LANSOPRAZOLE,GASTROENTEROLOGY
+endometrial cancer,DOSTARLIMAB,MEDICAL ONCOLOGY
+epilepsy,CENOBAMATE|GABAPENTIN|RETIGABINE,NEUROLOGY
+fallopian tube,BEVACIZUMAB|NIRAPARIB|OLAPARIB|RUCAPARIB,MEDICAL ONCOLOGY
+follicular lymphoma,DUVELISIB|IDELALISIB|LENALIDOMIDE|OBINUTUZUMAB|RITUXIMAB|TISAGENLECLEUCEL,CLINICAL HAEMATOLOGY
+gastric cancer,CAPECITABINE|RAMUCIRUMAB|TRASTUZUMAB|TRIFLURIDINE,MEDICAL ONCOLOGY
+gastro-oesophageal junction,NIVOLUMAB|PEMBROLIZUMAB,MEDICAL ONCOLOGY
+giant cell arteritis,TOCILIZUMAB,RHEUMATOLOGY
+glioma,CARMUSTINE,MEDICAL ONCOLOGY
+gout,CANAKINUMAB|FEBUXOSTAT|LESINURAD,RHEUMATOLOGY
+graft versus host disease,RUXOLITINIB,CLINICAL HAEMATOLOGY
+granulomatosis with polyangiitis,AVACOPAN|MEPOLIZUMAB,RHEUMATOLOGY
+growth hormone deficiency,SOMATROPIN,ENDOCRINOLOGY
+hand eczema,ALITRETINOIN,DERMATOLOGY
+heart failure,DAPAGLIFLOZIN|EMPAGLIFLOZIN|IVABRADINE|SACUBITRIL|VERICIGUAT,CARDIOLOGY
+hepatitis b,ADEFOVIR,GASTROENTEROLOGY
+hepatitis c,BOCEPREVIR|DACLATASVIR|ELBASVIR|GLECAPREVIR|INTERFERON|LEDIPASVIR|OMBITASVIR|PEGINTERFERON|PEGYLATED|SIMEPREVIR|SOFOSBUVIR|TELAPREVIR,GASTROENTEROLOGY
+hepatocellular carcinoma,ATEZOLIZUMAB|CABOZANTINIB|LENVATINIB|RAMUCIRUMAB|REGORAFENIB|SELECTIVE|SORAFENIB,MEDICAL ONCOLOGY
+hiv,CABOTEGRAVIR,INFECTIOUS DISEASES
+hodgkin lymphoma,BRENTUXIMAB|NIVOLUMAB|PEMBROLIZUMAB,CLINICAL HAEMATOLOGY
+hormone receptor,ABEMACICLIB,MEDICAL ONCOLOGY
+hypercholesterolaemia,EZETIMIBE,CARDIOLOGY
+hyperparathyroidism,CINACALCET|ETELCALCETIDE,ENDOCRINOLOGY
+immune thrombocytopenia,AVATROMBOPAG|FOSTAMATINIB,CLINICAL HAEMATOLOGY
+influenza,AMANTADINE|ZANAMIVIR|BALOXAVIR,INFECTIOUS DISEASES
+insomnia,ZALEPLON,NEUROLOGY
+irritable bowel syndrome,ELUXADOLINE,GASTROENTEROLOGY
+ischaemic stroke,ALTEPLASE,STROKE MEDICINE
+juvenile idiopathic arthritis,ABATECEPT|CANAKINUMAB|TOCILIZUMAB|TOFACITINIB,RHEUMATOLOGY
+kidney transplant,BASILIXIMAB,NEPHROLOGY
+leukaemia,FLUDARABINE|IMATINIB,CLINICAL HAEMATOLOGY
+lung cancer,ATEZOLIZUMAB|DURVALUMAB|GEFITINIB|ORAL|NINTEDANIB,MEDICAL ONCOLOGY
+lymphoma,BENDAMUSTINE|CRIZOTINIB|PIXANTRONE|RITUXIMAB,CLINICAL HAEMATOLOGY
+macular degeneration,AFLIBERCEPT|BROLUCIZUMAB|FARICIMAB|RANIBIZUMAB,OPHTHALMOLOGY
+macular oedema,AFLIBERCEPT|RANIBIZUMAB,OPHTHALMOLOGY
+major depressive episodes,AGOMELATINE|VORTIOXETINE,MENTAL HEALTH
+malignant melanoma,VEMURAFENIB,MEDICAL ONCOLOGY
+malignant pleural mesothelioma,NIVOLUMAB|PEMETREXED,MEDICAL ONCOLOGY
+manic episode,ARIPIPRAZOLE,MENTAL HEALTH
+mantle cell lymphoma,AUTOLOGOUS|BORTEZOMIB|IBRUTINIB|LENALIDOMIDE|TEMSIROLIMUS,CLINICAL HAEMATOLOGY
+melanoma,COBIMETINIB|DABRAFENIB|ENCORAFENIB|IPILIMUMAB|NIVOLUMAB|PEMBROLIZUMAB|TALIMOGENE|TRAMETINIB,MEDICAL ONCOLOGY
+merkel cell carcinoma,AVELUMAB,MEDICAL ONCOLOGY
+migraine,BOTULINUM|EPTINEZUMAB|ERENUMAB|FREMANEZUMAB|GALCANEZUMAB,NEUROLOGY
+motor neurone disease,RILUZOLE,NEUROLOGY
+multiple myeloma,BORTEZOMIB|THALIDOMIDE|CARFILZOMIB|DARATUMUMAB|DENOSUMAB|ELOTUZUMAB|ISATUXIMAB|IXAZOMIB|LENALIDOMIDE|PANOBINOSTAT|POMALIDOMIDE|SELINEXOR|TECLISTAMAB,CLINICAL HAEMATOLOGY
+multiple sclerosis,ALEMTUZUMAB|BETA|CLADRIBINE|DACLIZUMAB|DIMETHYL|DIROXIMEL|FINGOLIMOD|INTERFERON|NATALIZUMAB|OCRELIZUMAB|OZANIMOD|PEGINTERFERON|PONESIMOD|SIPONIMOD|TERIFLUNOMIDE,NEUROLOGY
+myelodysplastic,LENALIDOMIDE|LUSPATERCEPT,CLINICAL HAEMATOLOGY
+myelofibrosis,FEDRATINIB|RUXOLITINIB,CLINICAL HAEMATOLOGY
+myocardial infarction,ALTEPLASE|BIVALIRUDIN|TICAGRELOR,CARDIOLOGY
+myotonia,MEXILETINE,NEUROLOGY
+narcolepsy,SOLRIAMFETOL,NEUROLOGY
+neuroendocrine tumour,EVEROLIMUS|LUTETIUM,MEDICAL ONCOLOGY
+non-small cell lung cancer,ATEZOLIZMAB|DOCETAXEL|ERLOTINIB|PEMETREXED,MEDICAL ONCOLOGY
+non-small-cell lung cancer,AFATINIB|ALECTINIB|AMIVANTAMAB|ATEZOLIZUMAB|BEVACIZUMAB|BRIGATINIB|CEMIPLIMAB|CERITINIB|CRIZOTINIB|DABRAFENIB|DACOMITINIB|DURVALUMAB|ENTRECTINIB|ERLOTINIB|GEFITINIB|LORLATINIB|MOBOCERTINIB|NECITUMUMAB|NIVOLUMAB|OSIMERTINIB|PACLITAXEL|PEMBROLIZUMAB|PEMETREXED|PRALSETINIB|RAMUCIRUMAB|SELPERCATINIB|SOTORASIB|TEPOTINIB,MEDICAL ONCOLOGY
+obesity,LIRAGLUTIDE|NALTREXONE|ORLISTAT|SEMAGLUTIDE|SIBUTRAMINE,ENDOCRINOLOGY
+oesophageal cancer,NIVOLUMAB,MEDICAL ONCOLOGY
+osteoarthritis,CELECOXIB,RHEUMATOLOGY
+osteoporosis,ALENDRONATE|DENOSUMAB|ORAL|ROMOSOZUMAB,RHEUMATOLOGY
+osteosarcoma,MIFAMURTIDE,MEDICAL ONCOLOGY
+ovarian cancer,BEVACIZUMAB|PACLITAXEL|PEGYLATED|TOPOTECAN|TRABECTEDIN,MEDICAL ONCOLOGY
+overweight,RIMONABANT,ENDOCRINOLOGY
+pancreatic cancer,GEMCITABINE|OLAPARIB|PACLITAXEL|PEGYLATED,MEDICAL ONCOLOGY
+paroxysmal nocturnal haemoglobinuria,PEGCETACOPLAN|RAVULIZUMAB,CLINICAL HAEMATOLOGY
+peripheral arterial disease,NAFTIDROFYRYL,VASCULAR SURGERY
+plaque psoriasis,ADALIMUMAB|APREMILAST|BIMEKIZUMAB|BRODALUMAB|CERTOLIZUMAB|GUSELKUMAB|INFLIXIMAB|IXEKIZUMAB|RISANKIZUMAB|SECUKINUMAB|TILDRAKIZUAMB|USTEKINUMAB,DERMATOLOGY
+polycystic kidney disease,TOLVAPTAN,NEPHROLOGY
+polycythaemia vera,RUXOLITINIB,CLINICAL HAEMATOLOGY
+pregnancy,ROUTINE,OBSTETRICS
+primary biliary cholangitis,OBETICHOLIC,GASTROENTEROLOGY
+primary hypercholesterolaemia,ALIROCUMAB|EVOLOCUMAB,CARDIOLOGY
+prostate cancer,ABIRATERONE|APALUTAMIDE|CABAZITAXEL|DAROLUTAMIDE|DEGARELIX|DENOSUMAB|DOCETAXEL|ENZALUTAMIDE|OLAPARIB|PADELIPORFIN|RADIUM-|RADIUM|SIPULEUCEL-T,MEDICAL ONCOLOGY
+psoriasis,EFALUZIMAB,DERMATOLOGY
+psoriatic arthritis,ABATACEPT|ADALIMUMAB|APREMILAST|CERTOLIZUMAB|ETANERCEPT|GOLIMUMAB|GUSELKUMAB|IXEKIZUMAB|RISANKIZUMAB|TOFACITINIB|UPADACITINIB|USTEKINUMAB,RHEUMATOLOGY
+pulmonary embolism,APIXABAN|DABIGATRAN|EDOXABAN|RIVAROXABAN,THORACIC MEDICINE
+pulmonary fibrosis,NINTEDANIB|PIRFENIDONE,THORACIC MEDICINE
+relapsing multiple sclerosis,OFATUMUMAB,NEUROLOGY
+renal cell carcinoma,AVELUMAB|AXITINIB|BEVACIZUMAB|CABOZANTINIB|EVEROLIMUS|LENVATINIB|NIVOLUMAB|PAZOPANIB|PEMBROLIZUMAB|SUNITINIB|TIVOZANIB,MEDICAL ONCOLOGY
+renal transplantation,BASILIXIMAB|INDUCTION,NEPHROLOGY
+retinal vein occlusion,AFLIBERCEPT|DEXAMETHASONE|RANIBIZUMAB,OPHTHALMOLOGY
+rheumatoid arthritis,ABATACEPT|ADALIMUMAB|ANAKINRA|BARICITINIB|CELECOXIB|CERTOLIZUMAB|ETANERCEPT|FILGOTINIB|GOLIMUMAB|RITUXIMAB|SARILUMAB|TOCILIZUMAB|TOFACITINIB|UPADACITINIB,RHEUMATOLOGY
+rivaroxaban,ANDEXANET,CARDIOLOGY
+schizophrenia,AMISULPRIDE|ARIPIPRAZOLE|LOXAPINE,MENTAL HEALTH
+seizures,CANNABIDIOL,NEUROLOGY
+sepsis,DROTRECOGIN,INFECTIOUS DISEASES
+severe persistent allergic asthma,OMALIZUMAB,THORACIC MEDICINE
+short bowel syndrome,TEDUGLUTIDE,GASTROENTEROLOGY
+sickle cell disease,CRIZANLIZUMAB,CLINICAL HAEMATOLOGY
+sleep apnoea,PITOLISANT|SOLRIAMFETOL,THORACIC MEDICINE
+smoking cessation,NICOTINE|VARENICLINE,THORACIC MEDICINE
+soft tissue sarcoma,INTRAVENOUS|NBTXR-|OLARATUMAB,MEDICAL ONCOLOGY
+spinal muscular atrophy,NUSINERSEN|RISDIPLAM,NEUROLOGY
+squamous cell,CETUXIMAB,MEDICAL ONCOLOGY
+squamous cell carcinoma,CEMIPLIMAB|NIVOLUMAB|PEMBROLIZUMAB,MEDICAL ONCOLOGY
+stem cell transplant,MELPHALAN|TREOSULFAN,CLINICAL HAEMATOLOGY
+stroke,APIXABAN|DABIGATRAN|EDOXABAN|RIVAROXABAN,STROKE MEDICINE
+systemic lupus erythematosus,ANIFROLUMAB|ETANERCEPT,RHEUMATOLOGY
+systemic mastocytosis,MIDOSTAURIN,CLINICAL HAEMATOLOGY
+thrombocytopenic purpura,ELTROMBOPAG|ROMIPLOSTIM,CLINICAL HAEMATOLOGY
+thrombotic thrombocytopenic purpura,CAPLACIZUMAB,CLINICAL HAEMATOLOGY
+thyroid cancer,CABOZANTINIB|LENVATINIB|SELPERCATINIB|VANDETANIB,MEDICAL ONCOLOGY
+tophaceous gout,PEGLOTICASE,RHEUMATOLOGY
+transitional cell carcinoma,VINFLUNINE,MEDICAL ONCOLOGY
+tuberous sclerosis,CANNABIDIOL,NEUROLOGY
+type 1 diabetes,CONTINUOUS|DAPAGLIFLOZIN|INSULIN|SOTAGLIFLOZIN,DIABETIC MEDICINE
+type 2 diabetes,CANAGLIFLOZIN|CONTINUOUS|DAPAGLIFLOZIN|EMPAGLIFLOZIN|ERTUGLIFLOZIN|EXENATIDE|FINERENONE|INSULIN|LIRAGLUTIDE|PIOGLITAZONE|ROSIGLITAZONE,DIABETIC MEDICINE
+ulcerative colitis,ADALIMUMAB|INFLIXIMAB|FILGOTINIB|OZANIMOD|TOFACITINIB|UPADACITINIB|USTEKINUMAB|VEDOLIZUMAB,GASTROENTEROLOGY
+urothelial carcinoma,ATEZOLIZUMAB|PEMBROLIZUMAB,MEDICAL ONCOLOGY
+urticaria,OMALIZUMAB,DERMATOLOGY
+uterine fibroids,RELUGOLIX,GYNAECOLOGY
+uveitis,ADALIMUMAB|FLUOCINOLONE,OPHTHALMOLOGY
+vascular disease,MODIFIED-RELEASE|CLOPIDOGREL,VASCULAR SURGERY
+vasculitis,RITUXIMAB,RHEUMATOLOGY
+venous thromboembolism,APIXABAN|DABIGATRAN|RIVAROXABAN,CLINICAL HAEMATOLOGY

data/drug_indication_clusters.csv

@@ -0,0 +1,145 @@
+Drug,Indication,Cluster_ID,Cluster_Description,NICE_TA_Reference
+ABATACEPT,Rheumatoid arthritis,RARTH_COD,Rheumatoid arthritis diagnosis codes,TA195/TA280/TA375
+ABATACEPT,Rheumatoid arthritis,C19RARTH_COD,Rheumatoid arthritis disorders (broader),TA195/TA280/TA375
+ABATACEPT,Psoriatic arthritis,PSORIASIS_COD,Psoriasis codes (for psoriatic arthritis),TA568
+ACALABRUTINIB,Chronic lymphocytic leukaemia,CLL_COD,Chronic lymphocytic leukaemia,TA689
+ADALIMUMAB,Rheumatoid arthritis,RARTH_COD,Rheumatoid arthritis diagnosis codes,TA130/TA195/TA375
+ADALIMUMAB,Rheumatoid arthritis,C19RARTH_COD,Rheumatoid arthritis disorders (broader),TA130/TA195/TA375
+ADALIMUMAB,Psoriasis,PSORIASIS_COD,Psoriasis codes,TA146/TA455
+ADALIMUMAB,Psoriasis,CUST_CMMS_PSORIASIS,Psoriasis (Cambridge Multimorbidity),TA146/TA455
+ADALIMUMAB,Psoriatic arthritis,PSORIASIS_COD,Psoriasis codes (for psoriatic arthritis),TA125/TA199
+ADALIMUMAB,Crohn's disease,CROHNS_COD,Crohn's disease codes,TA187
+ADALIMUMAB,Ulcerative colitis,ULCCOLITIS_COD,Ulcerative colitis codes,TA329
+ADALIMUMAB,Ankylosing spondylitis,ANKSPON_COD,Ankylosing spondylitis codes,TA143/TA383
+AFLIBERCEPT,Diabetic macular oedema,DM_COD,Diabetes mellitus codes,TA346
+AFLIBERCEPT,Diabetic macular oedema,DMTYPE2AUDIT_COD,Type 2 diabetes codes,TA346
+ALIROCUMAB,Hypercholesterolaemia,HYPERCHOL_COD,Hypercholesterolaemia codes,TA393
+APREMILAST,Psoriasis,PSORIASIS_COD,Psoriasis codes,TA419
+APREMILAST,Psoriasis,CUST_CMMS_PSORIASIS,Psoriasis (Cambridge Multimorbidity),TA419
+APREMILAST,Psoriatic arthritis,PSORIASIS_COD,Psoriasis codes (for psoriatic arthritis),TA433
+ATEZOLIZUMAB,Cancer (various),CANCER_COD,Cancer codes (various),TA492/TA520/TA525
+BARICITINIB,Rheumatoid arthritis,RARTH_COD,Rheumatoid arthritis diagnosis codes,TA466
+BARICITINIB,Rheumatoid arthritis,C19RARTH_COD,Rheumatoid arthritis disorders (broader),TA466
+BARICITINIB,Atopic dermatitis,ECZEMA_COD,Atopic dermatitis/eczema codes,TA681
+BEVACIZUMAB,Cancer (various),CANCER_COD,Cancer codes (various),TA584/TA666
+BIMEKIZUMAB,Psoriasis,PSORIASIS_COD,Psoriasis codes,TA723
+BIMEKIZUMAB,Psoriasis,CUST_CMMS_PSORIASIS,Psoriasis (Cambridge Multimorbidity),TA723
+BOTULINUM A TOXIN,Spasticity (various),SPASTICITY_COD,Spasticity and movement disorder codes,No specific TA
+BRODALUMAB,Psoriasis,PSORIASIS_COD,Psoriasis codes,TA511
+BRODALUMAB,Psoriasis,CUST_CMMS_PSORIASIS,Psoriasis (Cambridge Multimorbidity),TA511
+CERTOLIZUMAB PEGOL,Rheumatoid arthritis,RARTH_COD,Rheumatoid arthritis diagnosis codes,TA375/TA415
+CERTOLIZUMAB PEGOL,Rheumatoid arthritis,C19RARTH_COD,Rheumatoid arthritis disorders (broader),TA375/TA415
+CERTOLIZUMAB PEGOL,Psoriasis,PSORIASIS_COD,Psoriasis codes,TA574
+CERTOLIZUMAB PEGOL,Psoriatic arthritis,PSORIASIS_COD,Psoriasis codes (for psoriatic arthritis),TA445
+CERTOLIZUMAB PEGOL,Ankylosing spondylitis,ANKSPON_COD,Ankylosing spondylitis codes,TA383
+DENOSUMAB,Osteoporosis,OSTEO_COD,Osteoporosis codes,TA204
+DENOSUMAB,Bone metastases,CANCER_COD,Cancer codes (bone metastases),TA265
+DEXAMETHASONE,Diabetic macular oedema,DM_COD,Diabetes mellitus codes,TA349/TA824
+DEXAMETHASONE,Diabetic macular oedema,DMTYPE2AUDIT_COD,Type 2 diabetes codes,TA349/TA824
+DEXAMETHASONE,Multiple myeloma,MM_COD,Multiple myeloma codes,TA311/TA380
+DEXAMETHASONE,Uveitis,UVEITIS_COD,Uveitis codes,TA460
+DIMETHYL FUMARATE,Multiple sclerosis,MS_COD,Multiple sclerosis codes,TA320
+DIMETHYL FUMARATE,Psoriasis,PSORIASIS_COD,Psoriasis codes,TA475
+DOCETAXEL,Cancer (various),CANCER_COD,Cancer codes (breast/lung/prostate),TA006/TA030/TA101
+DUPILUMAB,Atopic dermatitis,ECZEMA_COD,Atopic dermatitis/eczema codes,TA534
+DUPILUMAB,Asthma,ASTHMA_COD,Asthma codes,TA751
+ERENUMAB,Migraine,MIGRAINE_COD,Migraine codes,TA682
+ETANERCEPT,Rheumatoid arthritis,RARTH_COD,Rheumatoid arthritis diagnosis codes,TA036/TA130/TA195
+ETANERCEPT,Rheumatoid arthritis,C19RARTH_COD,Rheumatoid arthritis disorders (broader),TA036/TA130/TA195
+ETANERCEPT,Psoriasis,PSORIASIS_COD,Psoriasis codes,TA103
+ETANERCEPT,Psoriasis,CUST_CMMS_PSORIASIS,Psoriasis (Cambridge Multimorbidity),TA103
+ETANERCEPT,Psoriatic arthritis,PSORIASIS_COD,Psoriasis codes (for psoriatic arthritis),TA104/TA199
+ETANERCEPT,Ankylosing spondylitis,ANKSPON_COD,Ankylosing spondylitis codes,TA143/TA383
+EVOLOCUMAB,Hypercholesterolaemia,HYPERCHOL_COD,Hypercholesterolaemia codes,TA394
+FARICIMAB,Diabetic macular oedema,DM_COD,Diabetes mellitus codes,TA799
+FARICIMAB,Diabetic macular oedema,DMTYPE2AUDIT_COD,Type 2 diabetes codes,TA799
+FILGOTINIB,Rheumatoid arthritis,RARTH_COD,Rheumatoid arthritis diagnosis codes,TA676
+FILGOTINIB,Rheumatoid arthritis,C19RARTH_COD,Rheumatoid arthritis disorders (broader),TA676
+FILGOTINIB,Ulcerative colitis,ULCCOLITIS_COD,Ulcerative colitis codes,TA792
+FLUOCINOLONE,Atopic dermatitis,ECZEMA_COD,Atopic dermatitis/eczema codes,TA081
+FLUOCINOLONE,Diabetic macular oedema,DM_COD,Diabetes mellitus codes,TA301
+FLUOCINOLONE,Uveitis,UVEITIS_COD,Uveitis codes,TA590
+FLUOCINOLONE ACETONIDE,Atopic dermatitis,ECZEMA_COD,Atopic dermatitis/eczema codes,TA081
+FLUOCINOLONE ACETONIDE,Diabetic macular oedema,DM_COD,Diabetes mellitus codes,TA301
+FLUOCINOLONE ACETONIDE,Uveitis,UVEITIS_COD,Uveitis codes,TA590
+FREMANEZUMAB,Migraine,MIGRAINE_COD,Migraine codes,TA631/TA764
+GALCANEZUMAB,Migraine,MIGRAINE_COD,Migraine codes,TA659
+GOLIMUMAB,Rheumatoid arthritis,RARTH_COD,Rheumatoid arthritis diagnosis codes,TA225/TA375
+GOLIMUMAB,Rheumatoid arthritis,C19RARTH_COD,Rheumatoid arthritis disorders (broader),TA225/TA375
+GOLIMUMAB,Psoriatic arthritis,PSORIASIS_COD,Psoriasis codes (for psoriatic arthritis),TA220
+GOLIMUMAB,Ulcerative colitis,ULCCOLITIS_COD,Ulcerative colitis codes,TA329
+GOLIMUMAB,Ankylosing spondylitis,ANKSPON_COD,Ankylosing spondylitis codes,TA233/TA383
+GUSELKUMAB,Psoriasis,PSORIASIS_COD,Psoriasis codes,TA521
+GUSELKUMAB,Psoriasis,CUST_CMMS_PSORIASIS,Psoriasis (Cambridge Multimorbidity),TA521
+GUSELKUMAB,Psoriatic arthritis,PSORIASIS_COD,Psoriasis codes (for psoriatic arthritis),TA711/TA815
+IDARUCIZUMAB,Anticoagulant reversal,ANTICOAG_COD,Anticoagulation-related codes,No specific TA
+IMATINIB,Chronic myeloid leukaemia,CML_COD,Chronic myeloid leukaemia codes,TA050/TA070/TA251
+IMATINIB,Gastrointestinal stromal tumours,GIST_COD,Gastrointestinal stromal tumour codes,TA086/TA326
+IMMUNOGLOBULIN,Immunodeficiency (various),IMMUNODEF_COD,Primary/secondary immunodeficiency codes,TA481/TA482
+INFLIXIMAB,Rheumatoid arthritis,RARTH_COD,Rheumatoid arthritis diagnosis codes,TA036/TA130/TA195
+INFLIXIMAB,Rheumatoid arthritis,C19RARTH_COD,Rheumatoid arthritis disorders (broader),TA036/TA130/TA195
+INFLIXIMAB,Psoriasis,PSORIASIS_COD,Psoriasis codes,TA134
+INFLIXIMAB,Psoriasis,CUST_CMMS_PSORIASIS,Psoriasis (Cambridge Multimorbidity),TA134
+INFLIXIMAB,Psoriatic arthritis,PSORIASIS_COD,Psoriasis codes (for psoriatic arthritis),TA104/TA199
+INFLIXIMAB,Crohn's disease,CROHNS_COD,Crohn's disease codes,TA040/TA187
+INFLIXIMAB,Ulcerative colitis,ULCCOLITIS_COD,Ulcerative colitis codes,TA163/TA329
+INFLIXIMAB,Ankylosing spondylitis,ANKSPON_COD,Ankylosing spondylitis codes,TA383
+IXEKIZUMAB,Psoriasis,PSORIASIS_COD,Psoriasis codes,TA442
+IXEKIZUMAB,Psoriasis,CUST_CMMS_PSORIASIS,Psoriasis (Cambridge Multimorbidity),TA442
+IXEKIZUMAB,Psoriatic arthritis,PSORIASIS_COD,Psoriasis codes (for psoriatic arthritis),TA537
+IXEKIZUMAB,Ankylosing spondylitis,ANKSPON_COD,Ankylosing spondylitis codes,TA718
+LUCENTIS,Diabetic macular oedema,DM_COD,Diabetes mellitus codes,Biosimilar of ranibizumab
+LUCENTIS,Diabetic macular oedema,DMTYPE2AUDIT_COD,Type 2 diabetes codes,Biosimilar of ranibizumab
+OBINUTUZUMAB,Chronic lymphocytic leukaemia,CLL_COD,Chronic lymphocytic leukaemia codes,TA343/TA663
+OBINUTUZUMAB,Follicular lymphoma,FL_COD,Follicular lymphoma codes,TA472/TA513/TA629
+OCTREOTIDE,Neuroendocrine tumours,NET_COD,Neuroendocrine tumour codes,No specific TA
+OMALIZUMAB,Asthma,ASTHMA_COD,Asthma codes,TA133/TA278
+OMALIZUMAB,Chronic urticaria,URTICARIA_COD,Urticaria codes,TA339
+RANIBIZUMAB,Diabetic macular oedema,DM_COD,Diabetes mellitus codes,TA274
+RANIBIZUMAB,Diabetic macular oedema,DMTYPE2AUDIT_COD,Type 2 diabetes codes,TA274
+REMICADE,Rheumatoid arthritis,RARTH_COD,Rheumatoid arthritis diagnosis codes,Brand name for infliximab
+REMICADE,Crohn's disease,CROHNS_COD,Crohn's disease codes,Brand name for infliximab
+REMICADE,Ulcerative colitis,ULCCOLITIS_COD,Ulcerative colitis codes,Brand name for infliximab
+REMICADE,Psoriasis,PSORIASIS_COD,Psoriasis codes,Brand name for infliximab
+RILUZOLE,Motor neurone disease,MND_COD,Motor neurone disease codes,TA020
+RISANKIZUMAB,Psoriasis,PSORIASIS_COD,Psoriasis codes,TA596
+RISANKIZUMAB,Psoriasis,CUST_CMMS_PSORIASIS,Psoriasis (Cambridge Multimorbidity),TA596
+RISANKIZUMAB,Psoriatic arthritis,PSORIASIS_COD,Psoriasis codes (for psoriatic arthritis),TA803
+RITUXIMAB,Rheumatoid arthritis,RARTH_COD,Rheumatoid arthritis diagnosis codes,TA126/TA195
+RITUXIMAB,Rheumatoid arthritis,C19RARTH_COD,Rheumatoid arthritis disorders (broader),TA126/TA195
+RITUXIMAB,Non-Hodgkin's lymphoma,NHL_COD,Non-Hodgkin's lymphoma codes,TA037/TA065/TA110
+RITUXIMAB,Chronic lymphocytic leukaemia,CLL_COD,Chronic lymphocytic leukaemia codes,TA174/TA193/TA359
+RITUXIMAB,ANCA-associated vasculitis,VASCULITIS_COD,Vasculitis codes,TA308
+RIXATHON,Rheumatoid arthritis,RARTH_COD,Rheumatoid arthritis diagnosis codes,Biosimilar of rituximab
+RIXATHON,Non-Hodgkin's lymphoma,NHL_COD,Non-Hodgkin's lymphoma codes,Biosimilar of rituximab
+SACITUZUMAB,Triple-negative breast cancer,BREASTCA_COD,Breast cancer codes,TA819
+SARILUMAB,Rheumatoid arthritis,RARTH_COD,Rheumatoid arthritis diagnosis codes,TA485
+SARILUMAB,Rheumatoid arthritis,C19RARTH_COD,Rheumatoid arthritis disorders (broader),TA485
+SECUKINUMAB,Psoriasis,PSORIASIS_COD,Psoriasis codes,TA350/TA734
+SECUKINUMAB,Psoriasis,CUST_CMMS_PSORIASIS,Psoriasis (Cambridge Multimorbidity),TA350/TA734
+SECUKINUMAB,Psoriatic arthritis,PSORIASIS_COD,Psoriasis codes (for psoriatic arthritis),TA445
+SECUKINUMAB,Ankylosing spondylitis,ANKSPON_COD,Ankylosing spondylitis codes,TA407/TA719
+TERIPARATIDE,Osteoporosis,OSTEO_COD,Osteoporosis codes,TA087/TA161
+TILDRAKIZUMAB,Psoriasis,PSORIASIS_COD,Psoriasis codes,No TA match found
+TILDRAKIZUMAB,Psoriasis,CUST_CMMS_PSORIASIS,Psoriasis (Cambridge Multimorbidity),No TA match found
+TOCILIZUMAB,Rheumatoid arthritis,RARTH_COD,Rheumatoid arthritis diagnosis codes,TA198/TA247/TA375
+TOCILIZUMAB,Rheumatoid arthritis,C19RARTH_COD,Rheumatoid arthritis disorders (broader),TA198/TA247/TA375
+TOCILIZUMAB,Juvenile idiopathic arthritis,JIA_COD,Juvenile idiopathic arthritis codes,TA238/TA373
+TOCILIZUMAB,Giant cell arteritis,GCA_COD,Giant cell arteritis codes,TA518
+TOFACITINIB,Rheumatoid arthritis,RARTH_COD,Rheumatoid arthritis diagnosis codes,TA480
+TOFACITINIB,Rheumatoid arthritis,C19RARTH_COD,Rheumatoid arthritis disorders (broader),TA480
+TOFACITINIB,Psoriatic arthritis,PSORIASIS_COD,Psoriasis codes (for psoriatic arthritis),TA543
+TOFACITINIB,Ulcerative colitis,ULCCOLITIS_COD,Ulcerative colitis codes,TA547
+UPADACITINIB,Rheumatoid arthritis,RARTH_COD,Rheumatoid arthritis diagnosis codes,TA665/TA744
+UPADACITINIB,Rheumatoid arthritis,C19RARTH_COD,Rheumatoid arthritis disorders (broader),TA665/TA744
+UPADACITINIB,Psoriatic arthritis,PSORIASIS_COD,Psoriasis codes (for psoriatic arthritis),TA768
+UPADACITINIB,Atopic dermatitis,ECZEMA_COD,Atopic dermatitis/eczema codes,TA814
+UPADACITINIB,Ankylosing spondylitis,ANKSPON_COD,Ankylosing spondylitis codes,TA829
+UPADACITINIB,Ulcerative colitis,ULCCOLITIS_COD,Ulcerative colitis codes,TA856
+USTEKINUMAB,Psoriasis,PSORIASIS_COD,Psoriasis codes,TA180/TA455
+USTEKINUMAB,Psoriasis,CUST_CMMS_PSORIASIS,Psoriasis (Cambridge Multimorbidity),TA180/TA455
+USTEKINUMAB,Psoriatic arthritis,PSORIASIS_COD,Psoriasis codes (for psoriatic arthritis),TA340
+USTEKINUMAB,Crohn's disease,CROHNS_COD,Crohn's disease codes,TA456
+USTEKINUMAB,Ulcerative colitis,ULCCOLITIS_COD,Ulcerative colitis codes,TA633
+VEDOLIZUMAB,Ulcerative colitis,ULCCOLITIS_COD,Ulcerative colitis codes,TA342
+VEDOLIZUMAB,Crohn's disease,CROHNS_COD,Crohn's disease codes,TA352

pathways_app/__init__.py

@@ -1,4 +1,4 @@
-# Re-export app from app_v2 for the new UI redesign
+# Re-export app from pathways_app
-from pathways_app.app_v2 import app
+from pathways_app.pathways_app import app
 
 __all__ = ["app"]

ralph.ps1

@@ -6,15 +6,13 @@
     Outer loop for iterative Reflex frontend development.
     Each iteration spawns a fresh `claude --print` invocation.
     Memory persists via filesystem only: git commits, progress.txt, IMPLEMENTATION_PLAN.md, guardrails.md.
-    Completion detected via <promise>COMPLETE</promise> in output.
+
+    Runs until completion (<promise>COMPLETE</promise>) or circuit breaker trips.
+    No arbitrary iteration limit — the loop continues until done.
 
     Circuit breakers prevent runaway costs:
     - No git changes for N consecutive iterations (stalled)
     - Same error repeated N consecutive iterations (stuck)
-    - Maximum iteration count reached
-
-.PARAMETER MaxIterations
-    Maximum number of loop iterations before stopping. Default: 15.
 
 .PARAMETER Model
     Claude model to use. Default: "sonnet".
@@ -29,15 +27,14 @@
     Number of consecutive iterations with the same error before circuit breaker trips. Default: 3.
 
 .EXAMPLE
-    .\ralph.ps1 -MaxIterations 15 -Model "sonnet" -BranchName "feature/ui-redesign"
+    .\ralph.ps1 -Model "sonnet" -BranchName "feature/ui-redesign"
 
 .EXAMPLE
     .\ralph.ps1 -Model "opus" -MaxNoProgress 2
 #>
 
 param(
-    [int]$MaxIterations = 15,
+    [string]$Model = "opus",
-    [string]$Model = "sonnet",
     [string]$BranchName,
     [int]$MaxNoProgress = 3,
     [int]$MaxSameError = 3
@@ -151,17 +148,19 @@ if (Test-Path $progressFile) {
 
 Write-Host ""
 Write-Host "===== Ralph Wiggum Loop (Reflex UI) =====" -ForegroundColor Cyan
-Write-Host "Model: $Model | Max iterations: $MaxIterations" -ForegroundColor Cyan
+Write-Host "Model: $Model | Runs until COMPLETE" -ForegroundColor Cyan
 Write-Host "Circuit breakers: no-progress=$MaxNoProgress, same-error=$MaxSameError" -ForegroundColor Cyan
 if ($BranchName) { Write-Host "Branch: $BranchName" -ForegroundColor Cyan }
 if ($existingIterations -gt 0) { Write-Host "Previous iterations: $existingIterations" -ForegroundColor Cyan }
 Write-Host "===========================================" -ForegroundColor Cyan
 Write-Host ""
 
-for ($i = 1; $i -le $MaxIterations; $i++) {
+$i = 0
+while ($true) {
+    $i++
     $totalIteration = $existingIterations + $i
     Write-Host ""
-    Write-Host "--- Iteration $i of $MaxIterations (Total: $totalIteration) ---" -ForegroundColor Yellow
+    Write-Host "--- Iteration $i (Total: $totalIteration) ---" -ForegroundColor Yellow
 
     # Record HEAD before this iteration
     $headBefore = git rev-parse HEAD 2>$null
@@ -199,41 +198,41 @@ for ($i = 1; $i -le $MaxIterations; $i++) {
             $line = $_.ToString().Trim()
             if (-not $line) { return }
 
-            # Save raw event for debugging
+            # Save raw event for debugging (with error handling for stream closure)
-            Add-Content -Path $rawLogFile -Value $line -Encoding UTF8
+            try {
+                Add-Content -Path $rawLogFile -Value $line -Encoding UTF8 -ErrorAction SilentlyContinue
+            } catch {
+                # Stream closed or file locked - ignore and continue
+            }
 
             try {
                 $evt = $line | ConvertFrom-Json -ErrorAction Stop
 
-                # --- Tool use detection ---
+                # --- Tool use start (show tool name) ---
                 if ($evt.type -eq 'content_block_start' -and $evt.content_block.type -eq 'tool_use') {
                     $toolCount++
                     $toolName = $evt.content_block.name
                     Write-Host "  [$toolName]" -ForegroundColor DarkCyan
                 }
-                elseif ($evt.tool_name) {
+                # --- Assistant text content (streaming deltas) ---
-                    $toolCount++
-                    Write-Host "  [$($evt.tool_name)]" -ForegroundColor DarkCyan
-                }
-
-                # --- Text content ---
                 elseif ($evt.type -eq 'content_block_delta' -and $evt.delta.type -eq 'text_delta' -and $evt.delta.text) {
                     Write-Host -NoNewline $evt.delta.text
                     [void]$textBuilder.Append($evt.delta.text)
                 }
-
+                # --- Result event (error display + text capture for circuit breakers) ---
                 elseif ($evt.type -eq 'result') {
-                    if ($evt.result) {
-                        Write-Host $evt.result
-                        [void]$textBuilder.AppendLine($evt.result)
-                    }
                     if ($evt.subtype -eq 'error_result' -and $evt.error) {
                         Write-Host "  [ERROR] $($evt.error)" -ForegroundColor Red
                         [void]$textBuilder.AppendLine("ERROR: $($evt.error)")
                     }
+                    elseif ($evt.result) {
+                        # Capture for circuit breaker detection; don't print
+                        # (text already displayed via streaming deltas above)
+                        [void]$textBuilder.AppendLine($evt.result)
                     }
-
+                }
-                elseif ($evt.message.content) {
+                # --- Message-level content (final message summary) ---
+                elseif ($evt.message -and $evt.message.content) {
                     foreach ($block in $evt.message.content) {
                         if ($block.type -eq 'text' -and $block.text) {
                             Write-Host $block.text
@@ -243,12 +242,16 @@ for ($i = 1; $i -le $MaxIterations; $i++) {
                             $toolCount++
                             Write-Host "  [$($block.name)]" -ForegroundColor DarkCyan
                         }
+                        # Silently ignore tool_result and other block types
                     }
                 }
+                # All other JSON events (input_json_delta, content_block_stop,
+                # message_start, message_stop, ping, etc.) are silently ignored
 
             } catch {
-                # Not valid JSON — likely stderr output
+                # Not valid JSON — only print if it looks like meaningful stderr
-                if ($line) {
+                # (filter out JSON fragments from multi-line events)
+                if ($line -and $line -notmatch '^\s*[\{\[\}\]"]') {
                     Write-Host $line -ForegroundColor DarkYellow
                     [void]$textBuilder.AppendLine($line)
                 }
@@ -338,9 +341,3 @@ for ($i = 1; $i -le $MaxIterations; $i++) {
     # Brief pause between iterations
     Start-Sleep -Seconds 2
 }
-
-Write-Host ""
-Write-Host "===== MAX ITERATIONS REACHED =====" -ForegroundColor Red
-Write-Host "Completed $MaxIterations iterations without finishing all tasks." -ForegroundColor Red
-Write-Host "Check progress.txt for current state and what remains." -ForegroundColor Red
-exit 1

snomed_indication_mapping_query.sql

@@ -0,0 +1,186 @@
+-- NICE TA Indication SNOMED Mapping Query (v2 - optimized clusters)
+-- Excludes overly broad clusters (GDPPR_COD, GDPPR2YR_COD)
+
+WITH SearchTermClusters AS (
+    SELECT Search_Term, Cluster_ID FROM (VALUES
+        ('acute lymphoblastic leukaemia', 'HAEMCANMORPH_COD'),
+        ('acute myeloid leukaemia', 'C19HAEMCAN_COD'),
+        ('acute promyelocytic leukaemia', 'HAEMCANMORPH_COD'),
+        ('allergic asthma', 'AST_COD'),
+        ('allergic rhinitis', 'MILDINTAST_COD'),
+        ('alzheimer''s disease', 'DEMALZ_COD'),
+        ('amyloidosis', 'AMYLOID_COD'),
+        ('anaemia', 'eFI2_AnaemiaTimeSensitive'),
+        ('anaplastic large cell lymphoma', 'C19HAEMCAN_COD'),
+        ('apixaban', 'DOACCON_COD'),
+        ('aplastic anaemia', 'eFI2_AnaemiaEver'),
+        ('arthritis', 'eFI2_InflammatoryArthritis'),
+        ('asthma', 'eFI2_Asthma'),
+        ('atopic dermatitis', 'ATOPDERM_COD'),
+        ('atrial fibrillation', 'eFI2_AtrialFibrillation'),
+        ('attention deficit hyperactivity disorder', 'ADHD_COD'),
+        ('bipolar disorder', 'MH_COD'),
+        ('bladder', 'eFI2_UrinaryIncontinence'),
+        ('breast cancer', 'BRCANSCR_COD'),
+        ('cardiomyopathy', 'eFI2_HarmfulDrinking'),
+        ('cardiovascular disease', 'CVDRISKASS_COD'),
+        ('cervical cancer', 'CSDEC_COD'),
+        ('cholangiocarcinoma', 'eFI2_Cancer'),
+        ('chronic kidney disease', 'CKD_COD'),
+        ('chronic liver disease', 'eFI2_LiverProblems'),
+        ('chronic lymphocytic leukaemia', 'EPPHAEMCAN_COD'),
+        ('chronic myeloid leukaemia', 'EPPHAEMCAN_COD'),
+        ('chronic obstructive pulmonary disease', 'eFI2_COPD'),
+        ('colon cancer', 'eFI2_Cancer'),
+        ('colorectal cancer', 'GICANREF_COD'),
+        ('constipation', 'CHRONCONSTIP_COD'),
+        ('covid-19', 'POSSPOSTCOVID_COD'),
+        ('crohn''s disease', 'eFI2_InflammatoryBowelDisease'),
+        ('cutaneous t-cell lymphoma', 'C19HAEMCAN_COD'),
+        ('cystic fibrosis', 'CUST_ICB_CYSTIC_FIBROSIS'),
+        ('deep vein thrombosis', 'VTE_COD'),
+        ('depression', 'eFI2_Depression'),
+        ('diabetes', 'eFI2_DiabetesEver'),
+        ('diabetic retinopathy', 'DRSELIGIBILITY_COD'),
+        ('diffuse large b-cell lymphoma', 'C19HAEMCAN_COD'),
+        ('dravet syndrome', 'EPIL_COD'),
+        ('drug misuse', 'ILLSUBINT_COD'),
+        ('dyspepsia', 'eFI2_AbdominalPain'),
+        ('epilepsy', 'eFI2_Seizures'),
+        ('fallopian tube', 'STERIL_COD'),
+        ('follicular lymphoma', 'C19HAEMCAN_COD'),
+        ('gastric cancer', 'eFI2_Cancer'),
+        ('giant cell arteritis', 'GCA_COD'),
+        ('glioma', 'NHAEMCANMORPH_COD'),
+        ('gout', 'eFI2_InflammatoryArthritis'),
+        ('graft versus host disease', 'GVHD_COD'),
+        ('granulomatosis with polyangiitis', 'WEGENERVASC_COD'),
+        ('growth hormone deficiency', 'HYPOPITUITARY_COD'),
+        ('hand eczema', 'ECZEMA_COD'),
+        ('heart failure', 'eFI2_HeartFailure'),
+        ('hepatitis b', 'HEPBCVAC_COD'),
+        ('hepatocellular carcinoma', 'eFI2_Cancer'),
+        ('hiv', 'PREFLANG_COD'),
+        ('hodgkin lymphoma', 'HAEMCANMORPH_COD'),
+        ('hormone receptor', 'eFI2_ThyroidProblems'),
+        ('hypercholesterolaemia', 'CLASSFH_COD'),
+        ('immune thrombocytopenia', 'ITP_COD'),
+        ('influenza', 'FLUINVITE_COD'),
+        ('insomnia', 'eFI2_SleepProblems'),
+        ('irritable bowel syndrome', 'IBS_COD'),
+        ('ischaemic stroke', 'OSTR_COD'),
+        ('juvenile idiopathic arthritis', 'RARTHAD_COD'),
+        ('kidney transplant', 'RENALTRANSP_COD'),
+        ('leukaemia', 'eFI2_Cancer'),
+        ('lung cancer', 'FTCANREF_COD'),
+        ('lymphoma', 'C19HAEMCAN_COD'),
+        ('macular degeneration', 'CUST_ICB_VISUAL_IMPAIRMENT'),
+        ('macular oedema', 'CUST_ICB_VISUAL_IMPAIRMENT'),
+        ('major depressive episodes', 'eFI2_Depression'),
+        ('malignant melanoma', 'eFI2_Cancer'),
+        ('malignant pleural mesothelioma', 'LUNGCAN_COD'),
+        ('manic episode', 'MH_COD'),
+        ('mantle cell lymphoma', 'HAEMCANMORPH_COD'),
+        ('melanoma', 'eFI2_Cancer'),
+        ('merkel cell carcinoma', 'C19CAN_COD'),
+        ('migraine', 'eFI2_Headache'),
+        ('motor neurone disease', 'MND_COD'),
+        ('multiple myeloma', 'C19HAEMCAN_COD'),
+        ('multiple sclerosis', 'MS_COD'),
+        ('myelodysplastic', 'eFI2_AnaemiaEver'),
+        ('myelofibrosis', 'MDS_COD'),
+        ('myocardial infarction', 'eFI2_IschaemicHeartDisease'),
+        ('myotonia', 'CNDATRISK2_COD'),
+        ('narcolepsy', 'LD_COD'),
+        ('neuroendocrine tumour', 'LUNGCAN_COD'),
+        ('non-small cell lung cancer', 'LUNGCAN_COD'),
+        ('non-small-cell lung cancer', 'FTCANREF_COD'),
+        ('obesity', 'BMI30_COD'),
+        ('osteoarthritis', 'CUST_ICB_OSTEOARTHRITIS'),
+        ('osteoporosis', 'eFI2_Osteoporosis'),
+        ('osteosarcoma', 'NHAEMCANMORPH_COD'),
+        ('ovarian cancer', 'C19CAN_COD'),
+        ('peripheral arterial disease', 'PADEXC_COD'),
+        ('plaque psoriasis', 'PSORIASIS_COD'),
+        ('polycystic kidney disease', 'EPPCONGMALF_COD'),
+        ('polycythaemia vera', 'C19HAEMCAN_COD'),
+        ('pregnancy', 'C19PREG_COD'),
+        ('primary biliary cholangitis', 'eFI2_LiverProblems'),
+        ('primary hypercholesterolaemia', 'FNFHYP_COD'),
+        ('prostate cancer', 'EPPSOLIDCAN_COD'),
+        ('psoriasis', 'PSORIASIS_COD'),
+        ('psoriatic arthritis', 'RARTHAD_COD'),
+        ('pulmonary embolism', 'eFI2_RespiratoryDiseaseTimeSensitive'),
+        ('pulmonary fibrosis', 'ILD_COD'),
+        ('relapsing multiple sclerosis', 'MS_COD'),
+        ('renal cell carcinoma', 'C19CAN_COD'),
+        ('renal transplantation', 'RENALTRANSP_COD'),
+        ('retinal vein occlusion', 'CUST_ICB_VISUAL_IMPAIRMENT'),
+        ('rheumatoid arthritis', 'eFI2_InflammatoryArthritis'),
+        ('rivaroxaban', 'DOACCON_COD'),
+        ('schizophrenia', 'MH_COD'),
+        ('seizures', 'LSZFREQ_COD'),
+        ('sepsis', 'C19ACTIVITY_COD'),
+        ('severe persistent allergic asthma', 'SEVAST_COD'),
+        ('sickle cell disease', 'SICKLE_COD'),
+        ('sleep apnoea', 'CUST_ICB_NON_SEVERE_LDA'),
+        ('smoking cessation', 'SMOKINGINT_COD'),
+        ('soft tissue sarcoma', 'NHAEMCANMORPH_COD'),
+        ('spinal muscular atrophy', 'MND_COD'),
+        ('squamous cell', 'C19CAN_COD'),
+        ('squamous cell carcinoma', 'C19CAN_COD'),
+        ('stem cell transplant', 'ALLOTRANSP_COD'),
+        ('stroke', 'eFI2_Stroke'),
+        ('systemic lupus erythematosus', 'SLUPUS_COD'),
+        ('systemic mastocytosis', 'HAEMCANMORPH_COD'),
+        ('thrombocytopenic purpura', 'TTP_COD'),
+        ('thrombotic thrombocytopenic purpura', 'TTP_COD'),
+        ('thyroid cancer', 'C19CAN_COD'),
+        ('tophaceous gout', 'CUST_ICB_OSTEOARTHRITIS'),
+        ('transitional cell carcinoma', 'C19CAN_COD'),
+        ('type 1 diabetes', 'DMTYPE1_COD'),
+        ('type 2 diabetes', 'DMTYPE2_COD'),
+        ('ulcerative colitis', 'eFI2_InflammatoryBowelDisease'),
+        ('urothelial carcinoma', 'NHAEMCANMORPH_COD'),
+        ('urticaria', 'XSAL_COD'),
+        ('uveitis', 'CUST_ICB_VISUAL_IMPAIRMENT'),
+        ('vascular disease', 'CVDINVITE_COD'),
+        ('vasculitis', 'CRYOGLOBVASC_COD')
+    ) AS t(Search_Term, Cluster_ID)
+),
+
+ClusterCodes AS (
+    SELECT 
+        stc.Search_Term,
+        c."SNOMEDCode",
+        c."SNOMEDDescription"
+    FROM SearchTermClusters stc
+    JOIN DATA_HUB.PHM."ClinicalCodingClusterSnomedCodes" c
+        ON stc.Cluster_ID = c."Cluster_ID"
+    WHERE c."SNOMEDCode" IS NOT NULL
+),
+
+ExplicitCodes AS (
+    SELECT Search_Term, SNOMEDCode, SNOMEDDescription FROM (VALUES
+        ('acute coronary syndrome', '837091000000100', 'Manual mapping'),
+        ('ankylosing spondylitis', '162930007', 'Manual mapping'),
+        ('ankylosing spondylitis', '239805001', 'Manual mapping'),
+        ('ankylosing spondylitis', '239810002', 'Manual mapping'),
+        ('ankylosing spondylitis', '239811003', 'Manual mapping'),
+        ('ankylosing spondylitis', '394990003', 'Manual mapping'),
+        ('ankylosing spondylitis', '429712009', 'Manual mapping'),
+        ('ankylosing spondylitis', '441562009', 'Manual mapping'),
+        ('ankylosing spondylitis', '441680005', 'Manual mapping'),
+        ('ankylosing spondylitis', '441930001', 'Manual mapping'),
+        ('axial spondyloarthritis', '723116002', 'Manual mapping'),
+        ('choroidal neovascularisation', '380621000000102', 'Manual mapping'),
+        ('choroidal neovascularisation', '733124000', 'Manual mapping')
+    ) AS t(Search_Term, SNOMEDCode, SNOMEDDescription)
+)
+
+SELECT Search_Term, "SNOMEDCode" AS SNOMEDCode, "SNOMEDDescription" AS SNOMEDDescription 
+FROM ClusterCodes
+UNION ALL
+SELECT Search_Term, SNOMEDCode, SNOMEDDescription 
+FROM ExplicitCodes
+ORDER BY Search_Term, SNOMEDCode;