Cleaned up old reflex files/legacy code etc
This commit is contained in:
Andrew Charlwood
@@ -4,12 +4,13 @@ A web-based application for analyzing secondary care patient treatment pathways.
|
||||
|
||||
## Features
|
||||
|
||||
- **Desktop App**: Native window experience via pywebview (no browser needed)
|
||||
- **Interactive Visualization**: Plotly icicle charts showing patient treatment hierarchies with cost and frequency statistics
|
||||
- **Dual Chart Types**: Directory-based (Trust → Directorate → Drug → Pathway) and Indication-based (Trust → GP Diagnosis → Drug → Pathway) views
|
||||
- **Pre-computed Pathways**: Treatment pathways pre-processed and stored in SQLite for sub-50ms filter response times
|
||||
- **GP Diagnosis Matching**: Patient indications matched from GP records using SNOMED cluster codes (~93% match rate)
|
||||
- **Modern Web Interface**: Browser-based UI using Dash (Plotly) + Dash Mantine Components with NHS branding
|
||||
- **Drug Browser**: Drawer-based card browser organized by clinical directorate for drug/indication selection
|
||||
- **Trend Analysis**: Historical trend views showing how drug usage and costs change over time
|
||||
- **Modern Web Interface**: Dash (Plotly) + Dash Mantine Components with NHS branding
|
||||
- **Flexible Filtering**: Filter by date range, NHS trusts, drugs, and medical directories
|
||||
|
||||
## Requirements
|
||||
@@ -29,20 +30,21 @@ cd patient-pathway-analysis
|
||||
|
||||
# Install dependencies
|
||||
uv sync
|
||||
|
||||
# One-time dev setup: adds src/ to Python path via .pth file
|
||||
uv run python setup_dev.py
|
||||
```
|
||||
|
||||
## Quick Start
|
||||
|
||||
### Run the Web Application
|
||||
### Run the Application
|
||||
|
||||
```bash
|
||||
# Run as desktop app (recommended)
|
||||
python app_desktop.py
|
||||
|
||||
# Run in browser (development)
|
||||
python run_dash.py
|
||||
```
|
||||
|
||||
Open http://localhost:8050 in your browser.
|
||||
The desktop app opens automatically in a native window. For browser mode, open http://localhost:8050.
|
||||
|
||||
The application loads pre-computed pathway data from SQLite on startup. No additional configuration is needed for viewing existing data.
|
||||
|
||||
@@ -65,6 +67,19 @@ python -m cli.refresh_pathways --chart-type indication
|
||||
python -m cli.refresh_pathways --chart-type all --dry-run -v
|
||||
```
|
||||
|
||||
**Compute Trends (for Trends view):**
|
||||
|
||||
```bash
|
||||
# Compute historical trend snapshots
|
||||
python -m cli.compute_trends
|
||||
|
||||
# Custom date range
|
||||
python -m cli.compute_trends --start 2022-01-01 --end 2025-06-30
|
||||
|
||||
# Help
|
||||
python -m cli.compute_trends --help
|
||||
```
|
||||
|
||||
## Usage
|
||||
|
||||
### Interface Overview
|
||||
@@ -73,21 +88,28 @@ The application has a single-page layout with:
|
||||
|
||||
| Component | Purpose |
|
||||
|-----------|---------|
|
||||
| **Header** | NHS branding, data freshness indicator (patient count + relative time) |
|
||||
| **Sidebar** | Navigation items with drawer triggers for Drug Selection, Trust Selection, Indications |
|
||||
| **KPI Row** | 4 cards: Unique Patients, Drug Types, Total Cost, Indication Match Rate |
|
||||
| **Filter Bar** | Chart type toggle (By Directory / By Indication) + date filter dropdowns |
|
||||
| **Chart Card** | Interactive Plotly icicle chart with loading spinner |
|
||||
| **Drawer** | Right-side panel with drug chips, trust chips, and directorate card browser |
|
||||
| **Header** | NHS branding, fraction KPIs (patients, drugs, cost), data freshness indicator |
|
||||
| **Sidebar** | Navigation: Patient Pathways, Trust Comparison, Trends |
|
||||
| **Sub-Header** | Chart type toggle (By Directory / By Indication) + date filter dropdowns |
|
||||
| **Filter Bar** | Patient Pathways drug/trust/directorate filter buttons with modals |
|
||||
| **Chart Card** | 9-tab chart area (Icicle, Sankey, Heatmap, Funnel, Depth, Scatter, Network, Timeline, Doses) |
|
||||
| **Trust Comparison** | Per-directorate 6-chart dashboard comparing drugs across trusts |
|
||||
| **Trends** | Historical trend analysis with directorate overview + drug drill-down |
|
||||
|
||||
### Filtering Data
|
||||
|
||||
1. **Chart Type**: Toggle between "By Directory" and "By Indication" views
|
||||
2. **Date Filters**: Select treatment initiation period and last-seen window
|
||||
3. **Drug Selection**: Open the drawer to select specific drugs via chips
|
||||
4. **Trust Selection**: Open the drawer to filter by NHS trusts
|
||||
5. **Directorate Browser**: Navigate directorates → indications → drug fragments in the drawer
|
||||
6. **Clear Filters**: Reset all selections to show full dataset
|
||||
The application has three analytical views:
|
||||
|
||||
1. **Patient Pathways**: Icicle chart + 8 additional analytics tabs with drug/trust/directorate filtering
|
||||
2. **Trust Comparison**: Per-directorate analysis comparing drugs across trusts
|
||||
3. **Trends**: Historical trend analysis showing directorate and drug-level changes over time
|
||||
|
||||
Common controls across all views:
|
||||
|
||||
- **Chart Type**: Toggle between "By Directory" and "By Indication" views
|
||||
- **Date Filters**: Select treatment initiation period and last-seen window
|
||||
- **Drug/Trust/Directorate Selection**: Open modals to filter by specific drugs, trusts, or directorates (Patient Pathways)
|
||||
- **Clear Filters**: Reset all selections to show full dataset
|
||||
|
||||
### Understanding the Pathway Chart
|
||||
|
||||
@@ -121,22 +143,23 @@ Root (Regional Total)
|
||||
|
||||
```
|
||||
.
|
||||
├── src/ # All application library code
|
||||
│ ├── core/ # Foundation: paths, models, logging
|
||||
│ ├── config/ # Snowflake connection settings
|
||||
│ ├── data_processing/ # Data layer (SQLite, Snowflake, transforms)
|
||||
│ ├── analysis/ # Analysis pipeline
|
||||
│ ├── visualization/ # Plotly chart generation
|
||||
│ └── cli/ # CLI tools (refresh_pathways)
|
||||
├── core/ # Foundation: paths, models, logging
|
||||
├── config/ # Snowflake connection settings
|
||||
├── data_processing/ # Data layer (SQLite, Snowflake, transforms)
|
||||
├── analysis/ # Analysis pipeline
|
||||
├── visualization/ # Plotly chart generation
|
||||
├── cli/ # CLI tools (refresh_pathways, compute_trends)
|
||||
├── dash_app/ # Dash web application
|
||||
│ ├── app.py # App entry point, layout, stores
|
||||
│ ├── assets/nhs.css # NHS design system CSS
|
||||
│ ├── data/ # Query wrappers + card browser data
|
||||
│ ├── components/ # UI components (header, sidebar, etc.)
|
||||
│ └── callbacks/ # Dash callbacks (filters, chart, KPI, drawer)
|
||||
├── run_dash.py # Entry point: python run_dash.py
|
||||
│ ├── components/ # UI components (header, sidebar, chart_card, trends, etc.)
|
||||
│ └── callbacks/ # Dash callbacks (filters, chart, KPI, trends, etc.)
|
||||
├── app_desktop.py # Desktop entry point (pywebview native window)
|
||||
├── run_dash.py # Browser entry point
|
||||
├── app.spec # PyInstaller packaging spec
|
||||
├── data/ # Reference data + SQLite DB (pathways.db)
|
||||
├── tests/ # Test suite (113 tests)
|
||||
├── tests/ # Test suite (114 tests)
|
||||
├── docs/ # Documentation
|
||||
└── archive/ # Historical/deprecated code
|
||||
```
|
||||
@@ -149,7 +172,7 @@ See `CLAUDE.md` for detailed architecture documentation.
|
||||
# Run all tests
|
||||
python -m pytest tests/ -v
|
||||
|
||||
# Run with coverage
|
||||
# Run with coverage (114 tests)
|
||||
python -m pytest tests/ -v --cov=core --cov=data_processing --cov=analysis
|
||||
|
||||
# Run only fast tests
|
||||
@@ -158,7 +181,16 @@ python -m pytest tests/ -v -m "not slow"
|
||||
|
||||
## Configuration
|
||||
|
||||
### Snowflake Connection (`src/config/snowflake.toml`)
|
||||
### Desktop Packaging
|
||||
|
||||
```bash
|
||||
# Build standalone executable (Windows)
|
||||
pyinstaller app.spec
|
||||
|
||||
# Output: dist/NHS_Pathway_Analysis/NHS_Pathway_Analysis.exe
|
||||
```
|
||||
|
||||
### Snowflake Connection (`config/snowflake.toml`)
|
||||
|
||||
```toml
|
||||
[snowflake]
|
||||
@@ -177,11 +209,11 @@ authenticator = "externalbrowser" # Required for NHS SSO
|
||||
# Ensure dependencies are installed
|
||||
uv sync
|
||||
|
||||
# Ensure src/ is on Python path
|
||||
uv run python setup_dev.py
|
||||
# Try desktop mode
|
||||
python app_desktop.py
|
||||
|
||||
# Try running with uv
|
||||
uv run python run_dash.py
|
||||
# Or browser mode
|
||||
python run_dash.py
|
||||
```
|
||||
|
||||
### Database not found
|
||||
@@ -193,7 +225,7 @@ python -m data_processing.migrate
|
||||
|
||||
### Snowflake connection issues
|
||||
|
||||
1. Ensure `src/config/snowflake.toml` has the correct account identifier
|
||||
1. Ensure `config/snowflake.toml` has the correct account identifier
|
||||
2. A browser window will open for SSO authentication
|
||||
3. Verify your network allows Snowflake connections
|
||||
|
||||
|
||||
@@ -10,7 +10,7 @@ ROOT = os.path.abspath(os.path.dirname(SPECPATH)) if 'SPECPATH' in dir() else os
|
||||
|
||||
a = Analysis(
|
||||
['app_desktop.py'],
|
||||
pathex=[os.path.join(ROOT, 'src')],
|
||||
pathex=[ROOT],
|
||||
binaries=[],
|
||||
datas=[
|
||||
('data/pathways.db', 'data'),
|
||||
@@ -39,7 +39,7 @@ a = Analysis(
|
||||
'pandas._libs.tslibs',
|
||||
'numpy',
|
||||
'sqlite3',
|
||||
# App packages (src/ on pathex)
|
||||
# App packages (project root on pathex)
|
||||
'core',
|
||||
'core.config',
|
||||
'core.models',
|
||||
|
||||
+4
-4
@@ -6,10 +6,10 @@ import threading
|
||||
import time
|
||||
from pathlib import Path
|
||||
|
||||
# Ensure src/ is on sys.path so that core/, data_processing/, etc. are importable
|
||||
_src_dir = str(Path(__file__).resolve().parent / "src")
|
||||
if _src_dir not in sys.path:
|
||||
sys.path.insert(0, _src_dir)
|
||||
# Ensure project root is on sys.path so that core/, data_processing/, etc. are importable
|
||||
_project_root = str(Path(__file__).resolve().parent)
|
||||
if _project_root not in sys.path:
|
||||
sys.path.insert(0, _project_root)
|
||||
|
||||
import webview
|
||||
from dash_app.app import app
|
||||
|
||||
@@ -26,7 +26,7 @@ from datetime import date, timedelta
|
||||
from pathlib import Path
|
||||
from typing import Optional
|
||||
|
||||
# Ensure src/ is on sys.path when run as `python -m cli.compute_trends`
|
||||
# Ensure project root is on sys.path when run as `python -m cli.compute_trends`
|
||||
_src_dir = str(Path(__file__).resolve().parent.parent)
|
||||
if _src_dir not in sys.path:
|
||||
sys.path.insert(0, _src_dir)
|
||||
|
||||
@@ -28,7 +28,7 @@ from datetime import datetime
|
||||
from pathlib import Path
|
||||
from typing import Optional
|
||||
|
||||
# Ensure src/ is on sys.path when run as `python -m cli.refresh_pathways`
|
||||
# Ensure project root is on sys.path when run as `python -m cli.refresh_pathways`
|
||||
_src_dir = str(Path(__file__).resolve().parent.parent)
|
||||
if _src_dir not in sys.path:
|
||||
sys.path.insert(0, _src_dir)
|
||||
|
||||
@@ -8,11 +8,11 @@ def get_resource_path(relative_path: str) -> Path:
|
||||
"""Return absolute path to a bundled resource.
|
||||
|
||||
In frozen mode (PyInstaller), resolves from sys._MEIPASS.
|
||||
In dev mode, resolves from the project root (3 parents up from this file:
|
||||
src/core/resource_path.py → src/core → src → project root).
|
||||
In dev mode, resolves from the project root (2 parents up from this file:
|
||||
core/resource_path.py → core → project root).
|
||||
"""
|
||||
if getattr(sys, "frozen", False):
|
||||
base = Path(sys._MEIPASS)
|
||||
else:
|
||||
base = Path(__file__).resolve().parents[2]
|
||||
base = Path(__file__).resolve().parents[1]
|
||||
return base / relative_path
|
||||
|
||||
+2
-2
@@ -26,7 +26,7 @@ test = [
|
||||
]
|
||||
|
||||
[tool.pytest.ini_options]
|
||||
pythonpath = ["src"]
|
||||
pythonpath = ["."]
|
||||
testpaths = ["tests"]
|
||||
python_files = ["test_*.py"]
|
||||
python_classes = ["Test*"]
|
||||
@@ -43,7 +43,7 @@ markers = [
|
||||
]
|
||||
|
||||
[tool.coverage.run]
|
||||
source = ["src/core", "src/data_processing", "src/analysis", "src/visualization"]
|
||||
source = ["core", "data_processing", "analysis", "visualization"]
|
||||
branch = true
|
||||
omit = [
|
||||
"*/tests/*",
|
||||
|
||||
Binary file not shown.
+4
-4
@@ -2,10 +2,10 @@
|
||||
import sys
|
||||
from pathlib import Path
|
||||
|
||||
# Ensure src/ is on sys.path so that core/, data_processing/, etc. are importable
|
||||
_src_dir = str(Path(__file__).resolve().parent / "src")
|
||||
if _src_dir not in sys.path:
|
||||
sys.path.insert(0, _src_dir)
|
||||
# Ensure project root is on sys.path so that core/, data_processing/, etc. are importable
|
||||
_project_root = str(Path(__file__).resolve().parent)
|
||||
if _project_root not in sys.path:
|
||||
sys.path.insert(0, _project_root)
|
||||
|
||||
from dash_app.app import app
|
||||
|
||||
|
||||
@@ -1,13 +0,0 @@
|
||||
"""One-time dev setup: adds src/ to the venv's Python path via a .pth file."""
|
||||
|
||||
import site
|
||||
import sys
|
||||
from pathlib import Path
|
||||
|
||||
src_dir = Path(__file__).resolve().parent / "src"
|
||||
site_packages = Path(site.getsitepackages()[-1])
|
||||
pth_file = site_packages / "patient_pathways.pth"
|
||||
|
||||
pth_file.write_text(str(src_dir) + "\n")
|
||||
print(f"Created {pth_file}")
|
||||
print(f" -> {src_dir}")
|
||||
Reference in New Issue
Block a user