diff --git a/CLAUDE.md b/CLAUDE.md index 95ca207..fdaf953 100644 --- a/CLAUDE.md +++ b/CLAUDE.md @@ -11,7 +11,7 @@ NHS High-Cost Drug Patient Pathway Analysis Tool - a web-based application that - **Pre-computed pathway architecture**: Treatment pathways pre-processed and stored in SQLite for instant filtering - **GP diagnosis matching**: Patient indications matched from GP records using SNOMED cluster codes queried directly from Snowflake (~93% match rate) - Data pipeline: Snowflake → pre-computed SQLite pathway nodes (CSV/Parquet file loading retained for legacy compatibility) -- Interactive browser-based UI using Reflex framework +- Interactive browser-based UI using Dash (Plotly) + Dash Mantine Components - 6 pre-defined date filter combinations × 2 chart types = 12 pre-computed datasets with sub-50ms response times ## Running the Application @@ -29,11 +29,11 @@ python -m data_processing.migrate # Refresh pathway data from Snowflake (requires SSO auth) python -m cli.refresh_pathways -# Run the Reflex web application -reflex run +# Run the Dash web application +python run_dash.py ``` -The application requires Python 3.10+ and runs on http://localhost:3000 by default. +The application requires Python 3.10+ and runs on http://localhost:8050 by default. ### CLI Commands @@ -68,7 +68,7 @@ The refresh command: 2. Applies UPID, drug name, and directory transformations (~6 minutes) 3. For indication charts: queries GP records via SNOMED clusters (~9 minutes for 37K patients) 4. Processes 6 date filter combinations × selected chart types -5. Inserts pathway nodes to SQLite for fast Reflex filtering +5. Inserts pathway nodes to SQLite for fast Dash filtering ## Architecture @@ -103,20 +103,41 @@ The refresh command: │ │ └── statistics.py # Statistical calculation functions │ │ │ ├── visualization/ # Chart generation -│ │ └── plotly_generator.py # create_icicle_figure, save_figure_html +│ │ └── plotly_generator.py # create_icicle_figure, create_icicle_from_nodes │ │ │ └── cli/ # CLI tools │ └── refresh_pathways.py # Data refresh command │ -├── pathways_app/ # Reflex web app (stays at root — framework requirement) -│ ├── pathways_app.py # AppState + page components -│ └── components/ # Layout and navigation components +├── dash_app/ # Dash web application +│ ├── app.py # Dash app, layout root, dcc.Store, register_callbacks +│ ├── assets/ +│ │ └── nhs.css # NHS design system CSS (from 01_nhs_classic.html) +│ ├── data/ +│ │ ├── queries.py # Thin wrapper calling src/data_processing/pathway_queries.py +│ │ └── card_browser.py # DimSearchTerm.csv → directorate tree for drawer +│ ├── components/ +│ │ ├── header.py # Top header bar with data freshness indicator +│ │ ├── sidebar.py # Left navigation with drawer triggers +│ │ ├── kpi_row.py # 4 KPI cards (patients, drugs, cost, match rate) +│ │ ├── filter_bar.py # Chart type toggle pills + date filter dropdowns +│ │ ├── chart_card.py # Chart area with tabs + dcc.Graph + loading spinner +│ │ ├── drawer.py # dmc.Drawer with drug/trust chips + directorate cards +│ │ └── footer.py # Page footer +│ ├── callbacks/ +│ │ ├── __init__.py # register_callbacks(app) +│ │ ├── filters.py # Reference data loading + filter state management +│ │ ├── chart.py # Pathway data loading + icicle chart rendering +│ │ ├── drawer.py # Drawer open/close + drug/trust selection +│ │ └── kpi.py # KPI card value updates +│ └── utils/ +│ └── __init__.py │ +├── run_dash.py # Entry point: python run_dash.py ├── tests/ # Test suite (113 tests) ├── data/ # Reference data + SQLite DB ├── docs/ # Documentation ├── assets/ # Static assets (logo, favicon) -├── archive/ # Historical/deprecated +├── archive/ # Historical/deprecated (includes old Reflex app) └── logs/ # Runtime logs ``` @@ -127,11 +148,11 @@ All imports use package names directly: `from core import ...`, `from data_proce The application uses a pre-computed pathway architecture for performance: -**Architecture:** `Snowflake → Pathway Processing → SQLite (pre-computed) → Reflex (filter & view)` +**Architecture:** `Snowflake → Pathway Processing → SQLite (pre-computed) → Dash (filter & view)` **Key Benefits:** - **Performance**: Pathway calculation done once during data refresh, not on every filter change -- **Simplicity**: Reflex filters pre-computed data with simple SQL WHERE clauses +- **Simplicity**: Dash callbacks filter pre-computed data with simple SQL WHERE clauses - **Full Pathways**: Sequential treatment pathways (drug_0 → drug_1 → drug_2...) with statistics **Chart Types:** @@ -203,7 +224,7 @@ Each node in `pathway_nodes` contains: - `process_all_date_filters()` - Convenience function to process all 6 filters **Data Loaders:** -- `FileDataLoader` - Loads from CSV/Parquet files (used by legacy pipeline, not by Reflex app) +- `FileDataLoader` - Loads from CSV/Parquet files (used by legacy pipeline, not by Dash app) - Factory function `get_loader()` creates a `FileDataLoader` **Snowflake Integration:** @@ -233,25 +254,51 @@ Refactored from the original 267-line `generate_graph()` function: ### Visualization Module (`visualization/`) -- **create_icicle_figure()** - Generate Plotly icicle chart figure +- **create_icicle_figure(ice_df)** - Generate Plotly icicle chart from DataFrame (legacy/pipeline use) +- **create_icicle_from_nodes(nodes, title)** - Generate icicle chart from list-of-dicts (Dash use). Accepts JSON-serializable node dicts from `dcc.Store`. Uses NHS blue gradient colorscale, 10-field customdata, Source Sans 3 font. - **save_figure_html()** - Save interactive HTML file - **open_figure_in_browser()** - Open chart in default browser -### Reflex Application (`pathways_app/`) +### Shared Data Queries (`data_processing/pathway_queries.py`) -The `AppState` class manages all application state: -- **Chart type**: `selected_chart_type` ("directory" or "indication"), toggled via `set_chart_type()` -- **Computed vars**: `chart_hierarchy_label` (dynamic "Trust → Directorate → ..." or "Trust → Indication → ..."), `chart_type_label` -- Filter variables: dates, drugs, trusts, directories -- Reference data: available options loaded from pathway_nodes and CSV files -- Analysis state: running flag, status messages, chart data -- `load_data()` sources available drugs/directorates from `pathway_nodes` and `total_records` from `pathway_refresh_log.source_row_count` +Shared query functions used by both the Dash app and potentially other consumers: +- **load_initial_data(db_path)** - Returns available drugs (42), directorates (14), indications (32), trusts (7), total_patients, last_updated +- **load_pathway_nodes(db_path, filter_id, chart_type, selected_drugs, selected_directorates, selected_trusts)** - Returns pathway nodes, unique_patients, total_drugs, total_cost, last_updated. Parameterized SQL with optional drug/directorate/trust filters. -**Chart Type Toggle** (`chart_type_toggle()` component): -- Segmented control with "By Directory" and "By Indication" pill buttons -- Placed first in the filter strip before date filters -- Switching reloads pathway data from SQLite filtered by `chart_type` -- Note: Directory filter only applies to directory charts (indication charts store Search_Terms in the directory column) +### Dash Application (`dash_app/`) + +**State Management** via 3 `dcc.Store` components: +- **app-state** (session): `chart_type`, `initiated`, `last_seen`, `date_filter_id`, `selected_drugs`, `selected_directorates`, `selected_trusts` +- **chart-data** (memory): `nodes[]`, `unique_patients`, `total_drugs`, `total_cost`, `last_updated` +- **reference-data** (session): `available_drugs`, `available_directorates`, `available_indications`, `available_trusts`, `total_patients`, `last_updated` + +**Callback Chain** (unidirectional): +``` +Page Load → load_reference_data → reference-data store + header indicators + → update_app_state → app-state store (default filters) + → load_pathway_data → chart-data store + ├→ update_kpis → KPI cards + └→ update_chart → dcc.Graph + +Filter change → update_app_state → app-state → load_pathway_data → (chain above) +Drawer selection → all-drugs-chips/trust-chips → update_app_state → (chain above) +``` + +**Key Components:** +- **Header** (`header.py`): NHS branding, data freshness indicator (patient count + relative time) +- **Sidebar** (`sidebar.py`): Navigation items with drawer trigger IDs for Drug Selection, Trust Selection, Indications +- **Filter Bar** (`filter_bar.py`): Chart type toggle pills (By Directory / By Indication) + date filter dropdowns +- **KPI Row** (`kpi_row.py`): 4 cards — Unique Patients, Drug Types, Total Cost, Indication Match Rate (~93%) +- **Chart Card** (`chart_card.py`): Icicle chart with `dcc.Loading` spinner, dynamic subtitle, tab row +- **Drawer** (`drawer.py`): `dmc.Drawer` with drug chips (`dmc.ChipGroup`), trust chips, directorate accordion with indication sub-items and drug fragment badges +- **Footer** (`footer.py`): NHS Norfolk and Waveney ICB branding + +**Drawer Drug Browser:** +- "All Drugs" section: flat `dmc.ChipGroup` with 42 drugs from pathway_nodes level 3 +- "Trusts" section: `dmc.ChipGroup` with 7 trusts +- "By Directorate" section: nested `dmc.Accordion` — 19 directorates → indications → drug fragment `dmc.Badge` items +- Clicking a drug fragment badge selects all full drug names containing that fragment (substring match) +- "Clear All Filters" button resets drug and trust selections ### Data Transformations (`data_processing/transforms.py`) @@ -317,38 +364,33 @@ Core data transformation functions used by the pipeline: └──────────────────────────────────────────┘ -[Reflex App: reflex run] +[Dash App: python run_dash.py] ┌──────────────────────────────────────────┐ - │ Chart Type Toggle (segmented control) │ - │ → "By Directory" | "By Indication" │ - │ → Triggers set_chart_type() handler │ + │ Filter Bar + Drawer (toggle pills, │ + │ date dropdowns, drug/trust chips) │ + │ → Triggers update_app_state callback │ └──────────────────────────────────────────┘ │ ▼ ┌──────────────────────────────────────────┐ - │ AppState.load_pathway_data() │ - │ → Query pathway_nodes WHERE │ - │ date_filter AND chart_type │ - │ → Apply drug/directory filters │ - │ → recalculate_parent_totals() │ + │ load_pathway_data callback │ + │ → Input: app-state dcc.Store │ + │ → Calls pathway_queries.load_pathway_ │ + │ nodes() with filters │ + │ → Output: chart-data dcc.Store │ └──────────────────────────────────────────┘ │ - ▼ - ┌──────────────────────────────────────────┐ - │ AppState.icicle_figure │ - │ → Plotly icicle chart │ - │ → 10-field customdata structure │ - │ → Full hover/text templates │ - └──────────────────────────────────────────┘ - │ - ▼ - ┌──────────────────────────────────────────┐ - │ Reflex UI (rx.plotly component) │ - │ → <50ms filter response time │ - │ → Treatment statistics in tooltips │ - │ → Dynamic hierarchy label updates │ - └──────────────────────────────────────────┘ + ├──────────────────────────────┐ + ▼ ▼ + ┌────────────────────┐ ┌──────────────────────┐ + │ update_kpis │ │ update_chart │ + │ → 4 KPI cards │ │ → create_icicle_ │ + │ → formatted │ │ from_nodes() │ + │ counts/costs │ │ → 10-field custom- │ + └────────────────────┘ │ data + NHS blue │ + │ → dcc.Graph figure │ + └──────────────────────┘ ``` ### Reference Data Files (`data/`) @@ -386,7 +428,7 @@ The `department_identification()` function has 5 levels of fallback: 3. Build `indication_df` mapping UPID → Search_Term (matched) or Directorate + " (no GP dx)" (unmatched) 4. Pass to `generate_icicle_chart_indication()` for pathway hierarchy building -**Data Source Fallback Chain** (for raw data loading, not used by Reflex app): +**Data Source Fallback Chain** (for raw data loading, not used by Dash app): 1. Query cache for recent results 2. Attempt Snowflake connection 3. Fall back to CSV/Parquet files @@ -491,26 +533,19 @@ The pre-computed pathway architecture introduces these changes: - **Impact**: Data is as fresh as the last `python -m cli.refresh_pathways` run - **Benefit**: Sub-50ms filter response time vs multi-minute calculations -### State Variables -- **Removed**: `start_date`, `end_date`, `set_start_date()`, `set_end_date()` -- **Added**: `selected_initiated`, `selected_last_seen`, `date_filter_id` -- **Added**: `selected_chart_type` ("directory" or "indication"), `chart_type_options` -- **Added**: `set_chart_type()` - switches chart type and reloads data -- **Added**: `chart_hierarchy_label`, `chart_type_label` - computed vars for dynamic UI text -- **Added**: `load_pathway_data()` - queries pre-computed `pathway_nodes` filtered by `date_filter_id` AND `chart_type` -- **Added**: `recalculate_parent_totals()` - adjusts hierarchy after filtering - -### Chart Type Toggle -- **New**: Segmented control ("By Directory" | "By Indication") in filter strip -- **Added**: `selected_chart_type` state variable, `set_chart_type()` handler -- **Added**: Dynamic hierarchy label ("Trust → Directorate → ..." or "Trust → Indication → ...") -- **Note**: Directory filter only applies to directory charts; for indication charts the `directory` column stores Search_Terms +### State Management (Dash) +- State lives in 3 `dcc.Store` components: `app-state`, `chart-data`, `reference-data` +- Filter state: `chart_type`, `initiated`, `last_seen`, `date_filter_id`, `selected_drugs`, `selected_directorates`, `selected_trusts` +- Chart type toggle: "By Directory" / "By Indication" pills in filter bar +- Dynamic subtitle: "Trust → Directorate → Drug → Pathway" or "Trust → Indication → Drug → Pathway" +- Drug/trust selection via `dmc.ChipGroup` in right-side drawer ### Icicle Chart -- **Enhanced**: Now includes full 10-field customdata structure -- **Added**: Treatment statistics (average_spacing, cost_pp_pa) in hover tooltips -- **Added**: First/last seen dates for drug nodes -- **Added**: Indication chart uses `generate_icicle_chart_indication()` with Search_Term hierarchy +- Full 10-field customdata structure (value, colour, cost, costpp, first_seen, last_seen, first_seen_parent, last_seen_parent, average_spacing, cost_pp_pa) +- NHS blue gradient colorscale: Heritage Blue #003087 → Pale Blue #E3F2FD +- Treatment statistics (average_spacing, cost_pp_pa) in hover tooltips +- First/last seen dates for drug nodes +- `create_icicle_from_nodes()` in `src/visualization/plotly_generator.py` — shared function accepting list-of-dicts ## Development diff --git a/IMPLEMENTATION_PLAN.md b/IMPLEMENTATION_PLAN.md index c93c564..d9c48b5 100644 --- a/IMPLEMENTATION_PLAN.md +++ b/IMPLEMENTATION_PLAN.md @@ -248,12 +248,12 @@ Drawer selection → update_drug_selection → app-state store → load_pathway_ - **Checkpoint**: Header shows correct data freshness ### 5.4 Remove Reflex + final validation -- [ ] Remove `reflex` from `pyproject.toml` dependencies -- [ ] Delete or archive `pathways_app/` directory (move to `archive/`) -- [ ] Delete `pathways_app/styles.py` and any Reflex-specific files -- [ ] Update project `CLAUDE.md` to document Dash app structure, new run command, callback architecture -- [ ] Verify: `python run_dash.py` starts cleanly, full end-to-end workflow works -- [ ] Verify: No Reflex imports anywhere in `dash_app/` +- [x] Remove `reflex` from `pyproject.toml` dependencies +- [x] Delete or archive `pathways_app/` directory (move to `archive/`) +- [x] Delete `pathways_app/styles.py` and any Reflex-specific files +- [x] Update project `CLAUDE.md` to document Dash app structure, new run command, callback architecture +- [x] Verify: `python run_dash.py` starts cleanly, full end-to-end workflow works +- [x] Verify: No Reflex imports anywhere in `dash_app/` - **Checkpoint**: Full application works, no Reflex remnants, CLAUDE.md updated --- @@ -261,16 +261,16 @@ Drawer selection → update_drug_selection → app-state store → load_pathway_ ## Completion Criteria All tasks marked `[x]` AND: -- [ ] `python run_dash.py` starts cleanly at localhost:8050 -- [ ] Layout matches 01_nhs_classic.html (header, sidebar, KPIs, filter bar, chart card, footer) -- [ ] Icicle chart renders with real SQLite data (pathway_nodes) -- [ ] Date filters + chart type toggle update chart correctly -- [ ] dmc.Drawer opens, shows directorate cards with indications/drugs -- [ ] Selecting a drug from drawer filters the chart -- [ ] "All Drugs" card allows selecting any drug across all contexts -- [ ] "Clear Filters" resets all selections -- [ ] KPIs update dynamically (patients, drugs, cost) -- [ ] No Reflex imports in `dash_app/` +- [x] `python run_dash.py` starts cleanly at localhost:8050 +- [x] Layout matches 01_nhs_classic.html (header, sidebar, KPIs, filter bar, chart card, footer) +- [x] Icicle chart renders with real SQLite data (pathway_nodes) +- [x] Date filters + chart type toggle update chart correctly +- [x] dmc.Drawer opens, shows directorate cards with indications/drugs +- [x] Selecting a drug from drawer filters the chart +- [x] "All Drugs" card allows selecting any drug across all contexts +- [x] "Clear Filters" resets all selections +- [x] KPIs update dynamically (patients, drugs, cost) +- [x] No Reflex imports in `dash_app/` --- diff --git a/pathways_app/__init__.py b/archive/pathways_app/__init__.py similarity index 100% rename from pathways_app/__init__.py rename to archive/pathways_app/__init__.py diff --git a/pathways_app/components/__init__.py b/archive/pathways_app/components/__init__.py similarity index 100% rename from pathways_app/components/__init__.py rename to archive/pathways_app/components/__init__.py diff --git a/pathways_app/components/layout.py b/archive/pathways_app/components/layout.py similarity index 100% rename from pathways_app/components/layout.py rename to archive/pathways_app/components/layout.py diff --git a/pathways_app/components/navigation.py b/archive/pathways_app/components/navigation.py similarity index 100% rename from pathways_app/components/navigation.py rename to archive/pathways_app/components/navigation.py diff --git a/pathways_app/pathways_app.py b/archive/pathways_app/pathways_app.py similarity index 100% rename from pathways_app/pathways_app.py rename to archive/pathways_app/pathways_app.py diff --git a/pathways_app/styles.py b/archive/pathways_app/styles.py similarity index 100% rename from pathways_app/styles.py rename to archive/pathways_app/styles.py diff --git a/rxconfig.py b/archive/rxconfig.py similarity index 100% rename from rxconfig.py rename to archive/rxconfig.py diff --git a/pyproject.toml b/pyproject.toml index 9a9419e..d233c11 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -13,7 +13,6 @@ dependencies = [ "pillow>=10.0.0", "plotly>=5.15.0", "pyarrow>=20.0.0", - 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