added wsgi support and service documentation for the frontend

.gitignore

@@ -0,0 +1,33 @@
+# Python
+__pycache__/
+*.py[cod]
+*$py.class
+*.so
+.Python
+*.egg-info/
+dist/
+build/
+
+# Virtual environments
+venv/
+env/
+ENV/
+
+# IDE
+.vscode/
+.idea/
+*.swp
+*.swo
+
+# OS
+.DS_Store
+Thumbs.db
+
+# Logs
+*.log
+logs/
+
+# Model checkpoints and data (large files)
+*.ckpt
+*.pth
+*.pt

DEPLOYMENT.md

@@ -0,0 +1,245 @@
+# Deployment Guide - Text2Trait Frontend
+
+This guide explains how to deploy the Text2Trait frontend application using Gunicorn and the provided WSGI entry point.
+
+## Prerequisites
+
+1. Python 3.12 or higher
+2. Install dependencies from `text2trait_forntend_app/src/pyproject.toml`:
+   (Note: The directory name contains a typo 'forntend' - this is the actual name in the repository)
+   ```bash
+   cd text2trait_forntend_app/src
+   pip install -r pyproject.toml
+   # or with poetry:
+   poetry install
+   ```
+
+3. Install Gunicorn:
+   ```bash
+   pip install gunicorn
+   ```
+
+## WSGI Entry Point
+
+The `wsgi_t2tfe.py` file at the root of the repository provides a Gunicorn-compatible WSGI entry point for the Text2Trait frontend Dash application.
+
+## Usage
+
+### Local Development
+
+For local development and testing:
+
+```bash
+python wsgi_t2tfe.py
+```
+
+The application will be available at `http://localhost:8051/`
+
+### Production Deployment with Gunicorn
+
+For production deployment, use Gunicorn:
+
+```bash
+gunicorn wsgi_t2tfe:server --bind 0.0.0.0:8051 --workers 4
+```
+
+#### Recommended Gunicorn Configuration
+
+```bash
+gunicorn wsgi_t2tfe:server \
+    --bind 127.0.0.1:8051 \
+    --workers 4 \
+    --timeout 120 \
+    --access-logfile /var/log/text2trait/access.log \
+    --error-logfile /var/log/text2trait/error.log \
+    --log-level info
+```
+
+#### Configuration Options Explained
+
+- `--bind 127.0.0.1:8051` - Bind only to localhost on port 8051
+- `--workers 4` - Use 4 worker processes (adjust based on CPU cores: 2-4 × CPU cores)
+- `--timeout 120` - Worker timeout in seconds (adjust based on your needs)
+- `--access-logfile` - Path for access logs
+- `--error-logfile` - Path for error logs
+- `--log-level` - Logging level (debug, info, warning, error, critical)
+
+### Running as a Systemd Service
+
+Create a systemd service file `/etc/systemd/system/text2trait-frontend.service`:
+
+```ini
+[Unit]
+Description=Text2Trait Frontend Application
+After=network.target
+
+[Service]
+Type=simple
+User=harvest
+Group=harvest
+WorkingDirectory=/path/to/Text2Trait
+Environment="PATH=/path/to/venv/bin"
+ExecStart=/path/to/venv/bin/gunicorn wsgi_t2tfe:server \
+    --bind 127.0.0.1:8051 \
+    --workers 4 \
+    --timeout 120 \
+    --access-logfile /var/log/text2trait/access.log \
+    --error-logfile /var/log/text2trait/error.log
+ExecReload=/bin/kill -s HUP $MAINPID
+KillMode=mixed
+TimeoutStopSec=5
+PrivateTmp=true
+
+[Install]
+WantedBy=multi-user.target
+```
+
+Enable and start the service:
+
+```bash
+sudo systemctl daemon-reload
+sudo systemctl enable text2trait-frontend
+sudo systemctl start text2trait-frontend
+sudo systemctl status text2trait-frontend
+```
+
+### Using with Nginx (Reverse Proxy)
+
+Create an Nginx configuration `/etc/nginx/sites-available/text2trait`:
+
+```nginx
+server {
+    listen 80;
+    server_name your-domain.com;
+
+    location / {
+        proxy_pass http://127.0.0.1:8051;
+        proxy_set_header Host $host;
+        proxy_set_header X-Real-IP $remote_addr;
+        proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
+        proxy_set_header X-Forwarded-Proto $scheme;
+
+        # WebSocket support (if needed by Dash)
+        proxy_http_version 1.1;
+        proxy_set_header Upgrade $http_upgrade;
+        proxy_set_header Connection "upgrade";
+
+        # Increase timeouts for long-running requests
+        proxy_connect_timeout 120s;
+        proxy_send_timeout 120s;
+        proxy_read_timeout 120s;
+    }
+}
+```
+
+Enable the site:
+
+```bash
+sudo ln -s /etc/nginx/sites-available/text2trait /etc/nginx/sites-enabled/
+sudo nginx -t
+sudo systemctl reload nginx
+```
+
+## Environment Variables
+
+If your application requires environment variables, set them before running:
+
+```bash
+export DATA_PATH=/path/to/data
+export LOG_LEVEL=INFO
+gunicorn wsgi_t2tfe:server --bind 127.0.0.1:8051 --workers 4
+```
+
+## Monitoring and Logs
+
+Monitor the application:
+
+```bash
+# View logs
+tail -f /var/log/text2trait/access.log
+tail -f /var/log/text2trait/error.log
+
+# Check service status
+sudo systemctl status text2trait-frontend
+
+# View systemd logs
+sudo journalctl -u text2trait-frontend -f
+```
+
+## Performance Tuning
+
+### Worker Count
+
+The optimal number of workers depends on your server:
+
+- CPU-bound applications: `(2 × CPU cores) + 1`
+- I/O-bound applications: `(4 × CPU cores) + 1`
+
+For the Dash application (mostly I/O-bound):
+
+```bash
+# For a 4-core server:
+gunicorn wsgi_t2tfe:server --bind 127.0.0.1:8051 --workers 17
+```
+
+### Worker Class
+
+For better async support, use the gevent worker class:
+
+```bash
+pip install gevent
+gunicorn wsgi_t2tfe:server \
+    --bind 127.0.0.1:8051 \
+    --workers 4 \
+    --worker-class gevent \
+    --worker-connections 1000
+```
+
+## Troubleshooting
+
+### Application won't start
+
+1. Check Python path and dependencies:
+   ```bash
+   python -c "from wsgi_t2tfe import server; print('OK')"
+   ```
+
+2. Check Gunicorn syntax:
+   ```bash
+   gunicorn --check-config wsgi_t2tfe:server
+   ```
+
+3. Check logs for errors:
+   ```bash
+   tail -f /var/log/text2trait/error.log
+   ```
+
+### High memory usage
+
+Reduce the number of workers:
+
+```bash
+gunicorn wsgi_t2tfe:server --bind 127.0.0.1:8051 --workers 2
+```
+
+### Timeout errors
+
+Increase the timeout:
+
+```bash
+gunicorn wsgi_t2tfe:server --bind 127.0.0.1:8051 --timeout 300
+```
+
+## Security Considerations
+
+1. **Never expose Gunicorn directly to the internet** - Always use a reverse proxy like Nginx
+2. **Use HTTPS** - Configure SSL/TLS in Nginx
+3. **Firewall rules** - Restrict access to port 8051 to localhost only
+4. **Keep dependencies updated** - Regularly update Python packages
+5. **Use a dedicated user** - Don't run as root
+
+## Additional Resources
+
+- [Gunicorn Documentation](https://docs.gunicorn.org/)
+- [Dash Deployment Guide](https://dash.plotly.com/deployment)
+- [Nginx Documentation](https://nginx.org/en/docs/)

text2trait_forntend_app/src/app.py

@@ -123,4 +123,4 @@
 # Application Entry Point
 # ───────────────────────────────
 if __name__ == "__main__":
-    app.run(host="0.0.0.0", port=8050, debug=False)
+    app.run(host="127.0.0.1", port=8051, debug=False)

text2trait_forntend_app/src/pages/home.py

@@ -1,8 +1,8 @@
 """
-Home Page – GWAS-P
-------------------
+Home Page – Text2Trait
+----------------------
 
-This is the landing page for the GWAS-P application.
+This is the landing page for the Text2Trait application.
 It provides:
     - An introductory description of the app.
     - Search inputs for traits and (optionally) specific genes.
@@ -22,7 +22,7 @@
     __name__,
     path="/",
     name="Home",
-    title="GWAS-P",
+    title="Text2Trait",
 )
 
 
@@ -38,7 +38,7 @@
             [
                 html.Img(
                     src=dash.get_asset_url("text2trait_logo.png"),
-                    alt="GWAS-P logo",
+                    alt="Text2Trait logo",
                     style={
                         "width": "200px",
                         "height": "200px",

text2trait_forntend_app/src/pages/index.py

@@ -1,6 +1,6 @@
 """
-Index Page – GWAS-P
--------------------
+Index Page – Text2Trait
+------------------------
 
 This page provides a browsable index of:
     - All traits in the knowledge graph.
@@ -186,7 +186,7 @@ def generate_trait_gene_tab() -> dash_table.DataTable:
 # Page Layout
 # ───────────────────────────────
 layout = dbc.Container([
-    html.H2("GWAS-P Knowledge Graph Explorer", className="my-4"),
+    html.H2("Text2Trait Knowledge Graph Explorer", className="my-4"),
     dbc.Row([
         dbc.Col([
             dbc.Tabs([

text2trait_forntend_app/src/pages/questions.py

@@ -1,9 +1,9 @@
 """
-Questions Page – GWAS-P
------------------------
+Questions Page – Text2Trait
+----------------------------
 
 This page contains an FAQ section for common user questions
-about the GWAS-P application.
+about the Text2Trait application.
 """
 
 import dash

text2trait_forntend_app/src/pages/results.py

@@ -1,8 +1,8 @@
 """
-Results Page – GWAS-P
-----------------------
+Results Page – Text2Trait
+--------------------------
 
-This page displays the GWAS-P results, including a trait-gene interaction 
+This page displays the Text2Trait results, including a trait-gene interaction 
 graph using Cytoscape, interactive tables for matched genes, and a side panel 
 for detailed gene information retrieved from NCBI.
 """
@@ -41,7 +41,7 @@
     __name__,
     path="/results",
     name="Results",
-    title="GWAS-P Results"
+    title="Text2Trait Results"
 )
 
 # ───────────────────────────────

text2trait_forntend_app/src/pyproject.toml

@@ -1,7 +1,7 @@
 [project]
-name = "gwas-frontend-project"
+name = "text2trait-frontend-project"
 version = "0.1.0"
-description = "Requirments for the frontend"
+description = "Requirements for the frontend"
 authors = [
 ]
 readme = "README.md"
@@ -21,3 +21,4 @@ dependencies = [
 [build-system]
 requires = ["poetry-core>=2.0.0,<3.0.0"]
 build-backend = "poetry.core.masonry.api"
+package-mode = false