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Cleaned up old reflex files/legacy code etc

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Andrew Charlwood
2026-02-10 16:27:36 +00:00
parent a496c01eb4
commit b9fe89a4ee
10 changed files with 86 additions and 67 deletions
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README.md
+69 -37
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@@ -4,12 +4,13 @@ A web-based application for analyzing secondary care patient treatment pathways.
## Features ## 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 - **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 - **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 - **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) - **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 - **Trend Analysis**: Historical trend views showing how drug usage and costs change over time
- **Drug Browser**: Drawer-based card browser organized by clinical directorate for drug/indication selection - **Modern Web Interface**: Dash (Plotly) + Dash Mantine Components with NHS branding
- **Flexible Filtering**: Filter by date range, NHS trusts, drugs, and medical directories - **Flexible Filtering**: Filter by date range, NHS trusts, drugs, and medical directories
## Requirements ## Requirements
@@ -29,20 +30,21 @@ cd patient-pathway-analysis
# Install dependencies # Install dependencies
uv sync uv sync
# One-time dev setup: adds src/ to Python path via .pth file
uv run python setup_dev.py
``` ```
## Quick Start ## Quick Start
### Run the Web Application ### Run the Application
```bash ```bash
# Run as desktop app (recommended)
python app_desktop.py
# Run in browser (development)
python run_dash.py 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. 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 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 ## Usage
### Interface Overview ### Interface Overview
@@ -73,21 +88,28 @@ The application has a single-page layout with:
| Component | Purpose | | Component | Purpose |
|-----------|---------| |-----------|---------|
| **Header** | NHS branding, data freshness indicator (patient count + relative time) | | **Header** | NHS branding, fraction KPIs (patients, drugs, cost), data freshness indicator |
| **Sidebar** | Navigation items with drawer triggers for Drug Selection, Trust Selection, Indications | | **Sidebar** | Navigation: Patient Pathways, Trust Comparison, Trends |
| **KPI Row** | 4 cards: Unique Patients, Drug Types, Total Cost, Indication Match Rate | | **Sub-Header** | Chart type toggle (By Directory / By Indication) + date filter dropdowns |
| **Filter Bar** | Chart type toggle (By Directory / By Indication) + date filter dropdowns | | **Filter Bar** | Patient Pathways drug/trust/directorate filter buttons with modals |
| **Chart Card** | Interactive Plotly icicle chart with loading spinner | | **Chart Card** | 9-tab chart area (Icicle, Sankey, Heatmap, Funnel, Depth, Scatter, Network, Timeline, Doses) |
| **Drawer** | Right-side panel with drug chips, trust chips, and directorate card browser | | **Trust Comparison** | Per-directorate 6-chart dashboard comparing drugs across trusts |
| **Trends** | Historical trend analysis with directorate overview + drug drill-down |
### Filtering Data ### Filtering Data
1. **Chart Type**: Toggle between "By Directory" and "By Indication" views The application has three analytical views:
2. **Date Filters**: Select treatment initiation period and last-seen window
3. **Drug Selection**: Open the drawer to select specific drugs via chips 1. **Patient Pathways**: Icicle chart + 8 additional analytics tabs with drug/trust/directorate filtering
4. **Trust Selection**: Open the drawer to filter by NHS trusts 2. **Trust Comparison**: Per-directorate analysis comparing drugs across trusts
5. **Directorate Browser**: Navigate directorates → indications → drug fragments in the drawer 3. **Trends**: Historical trend analysis showing directorate and drug-level changes over time
6. **Clear Filters**: Reset all selections to show full dataset
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 ### Understanding the Pathway Chart
@@ -121,22 +143,23 @@ Root (Regional Total)
``` ```
. .
├── src/ # All application library code ├── core/ # Foundation: paths, models, logging
│ ├── core/ # Foundation: paths, models, logging ├── config/ # Snowflake connection settings
│ ├── config/ # Snowflake connection settings ├── data_processing/ # Data layer (SQLite, Snowflake, transforms)
│ ├── data_processing/ # Data layer (SQLite, Snowflake, transforms) ├── analysis/ # Analysis pipeline
│ ├── analysis/ # Analysis pipeline ├── visualization/ # Plotly chart generation
│ ├── visualization/ # Plotly chart generation ├── cli/ # CLI tools (refresh_pathways, compute_trends)
│ └── cli/ # CLI tools (refresh_pathways)
├── dash_app/ # Dash web application ├── dash_app/ # Dash web application
│ ├── app.py # App entry point, layout, stores │ ├── app.py # App entry point, layout, stores
│ ├── assets/nhs.css # NHS design system CSS │ ├── assets/nhs.css # NHS design system CSS
│ ├── data/ # Query wrappers + card browser data │ ├── data/ # Query wrappers + card browser data
│ ├── components/ # UI components (header, sidebar, etc.) │ ├── components/ # UI components (header, sidebar, chart_card, trends, etc.)
│ └── callbacks/ # Dash callbacks (filters, chart, KPI, drawer) │ └── callbacks/ # Dash callbacks (filters, chart, KPI, trends, etc.)
├── run_dash.py # Entry point: python run_dash.py ├── 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) ├── data/ # Reference data + SQLite DB (pathways.db)
├── tests/ # Test suite (113 tests) ├── tests/ # Test suite (114 tests)
├── docs/ # Documentation ├── docs/ # Documentation
└── archive/ # Historical/deprecated code └── archive/ # Historical/deprecated code
``` ```
@@ -149,7 +172,7 @@ See `CLAUDE.md` for detailed architecture documentation.
# Run all tests # Run all tests
python -m pytest tests/ -v 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 python -m pytest tests/ -v --cov=core --cov=data_processing --cov=analysis
# Run only fast tests # Run only fast tests
@@ -158,7 +181,16 @@ python -m pytest tests/ -v -m "not slow"
## Configuration ## 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 ```toml
[snowflake] [snowflake]
@@ -177,11 +209,11 @@ authenticator = "externalbrowser" # Required for NHS SSO
# Ensure dependencies are installed # Ensure dependencies are installed
uv sync uv sync
# Ensure src/ is on Python path # Try desktop mode
uv run python setup_dev.py python app_desktop.py
# Try running with uv # Or browser mode
uv run python run_dash.py python run_dash.py
``` ```
### Database not found ### Database not found
@@ -193,7 +225,7 @@ python -m data_processing.migrate
### Snowflake connection issues ### 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 2. A browser window will open for SSO authentication
3. Verify your network allows Snowflake connections 3. Verify your network allows Snowflake connections
app.spec
+2 -2
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@@ -10,7 +10,7 @@ ROOT = os.path.abspath(os.path.dirname(SPECPATH)) if 'SPECPATH' in dir() else os
a = Analysis( a = Analysis(
['app_desktop.py'], ['app_desktop.py'],
pathex=[os.path.join(ROOT, 'src')], pathex=[ROOT],
binaries=[], binaries=[],
datas=[ datas=[
('data/pathways.db', 'data'), ('data/pathways.db', 'data'),
@@ -39,7 +39,7 @@ a = Analysis(
'pandas._libs.tslibs', 'pandas._libs.tslibs',
'numpy', 'numpy',
'sqlite3', 'sqlite3',
# App packages (src/ on pathex) # App packages (project root on pathex)
'core', 'core',
'core.config', 'core.config',
'core.models', 'core.models',
app_desktop.py
+4 -4
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@@ -6,10 +6,10 @@ import threading
import time import time
from pathlib import Path from pathlib import Path
# Ensure src/ is on sys.path so that core/, data_processing/, etc. are importable # Ensure project root is on sys.path so that core/, data_processing/, etc. are importable
_src_dir = str(Path(__file__).resolve().parent / "src") _project_root = str(Path(__file__).resolve().parent)
if _src_dir not in sys.path: if _project_root not in sys.path:
sys.path.insert(0, _src_dir) sys.path.insert(0, _project_root)
import webview import webview
from dash_app.app import app from dash_app.app import app
cli/compute_trends.py
+1 -1
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@@ -26,7 +26,7 @@ from datetime import date, timedelta
from pathlib import Path from pathlib import Path
from typing import Optional 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) _src_dir = str(Path(__file__).resolve().parent.parent)
if _src_dir not in sys.path: if _src_dir not in sys.path:
sys.path.insert(0, _src_dir) sys.path.insert(0, _src_dir)
cli/refresh_pathways.py
+1 -1
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@@ -28,7 +28,7 @@ from datetime import datetime
from pathlib import Path from pathlib import Path
from typing import Optional 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) _src_dir = str(Path(__file__).resolve().parent.parent)
if _src_dir not in sys.path: if _src_dir not in sys.path:
sys.path.insert(0, _src_dir) sys.path.insert(0, _src_dir)
core/resource_path.py
+3 -3
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@@ -8,11 +8,11 @@ def get_resource_path(relative_path: str) -> Path:
"""Return absolute path to a bundled resource. """Return absolute path to a bundled resource.
In frozen mode (PyInstaller), resolves from sys._MEIPASS. In frozen mode (PyInstaller), resolves from sys._MEIPASS.
In dev mode, resolves from the project root (3 parents up from this file: In dev mode, resolves from the project root (2 parents up from this file:
src/core/resource_path.py → src/core → src → project root). core/resource_path.py → core → project root).
""" """
if getattr(sys, "frozen", False): if getattr(sys, "frozen", False):
base = Path(sys._MEIPASS) base = Path(sys._MEIPASS)
else: else:
base = Path(__file__).resolve().parents[2] base = Path(__file__).resolve().parents[1]
return base / relative_path return base / relative_path
pyproject.toml
+2 -2
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@@ -26,7 +26,7 @@ test = [
] ]
[tool.pytest.ini_options] [tool.pytest.ini_options]
pythonpath = ["src"] pythonpath = ["."]
testpaths = ["tests"] testpaths = ["tests"]
python_files = ["test_*.py"] python_files = ["test_*.py"]
python_classes = ["Test*"] python_classes = ["Test*"]
@@ -43,7 +43,7 @@ markers = [
] ]
[tool.coverage.run] [tool.coverage.run]
source = ["src/core", "src/data_processing", "src/analysis", "src/visualization"] source = ["core", "data_processing", "analysis", "visualization"]
branch = true branch = true
omit = [ omit = [
"*/tests/*", "*/tests/*",
requirements.txt
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run_dash.py
+4 -4
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@@ -2,10 +2,10 @@
import sys import sys
from pathlib import Path from pathlib import Path
# Ensure src/ is on sys.path so that core/, data_processing/, etc. are importable # Ensure project root is on sys.path so that core/, data_processing/, etc. are importable
_src_dir = str(Path(__file__).resolve().parent / "src") _project_root = str(Path(__file__).resolve().parent)
if _src_dir not in sys.path: if _project_root not in sys.path:
sys.path.insert(0, _src_dir) sys.path.insert(0, _project_root)
from dash_app.app import app from dash_app.app import app
setup_dev.py
-13
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@@ -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}")