A Web Service

Routing HTTP requests to functions.
Separating routing from model.
Creating HTML pages from Jinja templates.
Serving static files (and what that means).
The difference between data as HTML and data for machine consumption.

Terms defined: controller (in model-view-controller), extend (a template), model (in model-view-controller), model-view-controller, route, view (in model-view-controller)

Getting Data

Assay database from Chapter 10
- staff
- experiment
- performed
- plate
- invalidated
Use sqlite3 module directly
- Exercise: convert to SQLModel
MVC design separates model, controller, and view
- Model is data storage
- Controller is the verbs
- View is the display
Model functions:
- get_all to get all records (but not 1-1 with database records)
- get_count to count records of a particular type
- get_plate_filename to turn a plate ID into an assay filename

def get_count(kind):
    """How many entries of the given kind?"""
    conn = sqlite3.connect(os.getenv('RSDX_DB_PATH'))
    if kind == 'staff':
        result = conn.execute('select count(*) from staff').fetchone()
    elif kind == 'experiments':
        result = conn.execute('select count(*) from experiment').fetchone()
    elif kind == 'plates':
        result = conn.execute('select count(*) from plate').fetchone()
    else:
        assert False, f'Unknown kind {kind}'
    conn.close()
    return result[0]

Controller

Use Flask
- Define a function to handle a request to a particular URL
- Use a decorator to route appropriate requests to it

app = Flask(__name__)


@app.route("/")
def index():
    """Display data server home page."""
    page_data = {
        "site_title": SITE_TITLE,
        "num_staff": model.get_count("staff"),
        "num_experiments": model.get_count("experiments"),
        "num_plates": model.get_count("plates"),
    }
    return render_template("index.html", **page_data)

Run from the command line

RSDX_DB_PATH=../../data/assays.db flask --app server run

 * Serving Flask app 'server'
 * Debug mode: off
WARNING: This is a development server. Do not use it in a production deployment.
Use a production WSGI server instead.
 * Running on http://127.0.0.1:5000
Press CTRL+C to quit

Go to port 5000 (Figure 13.1)

screenshot of data server home page — Figure 13.1: Home page of data server

Templates

render_template looks in the templates directory for index.html

{% extends "base.html" %}
{% block content %}
<table>
  <thead>
    <tr><th>What</th><th>How Many</th></tr>
  </thead>
  <tbody>
    <tr><td><a href="/staff">Staff:</a></td><td>{{ num_staff }}</td></tr>
    <tr><td><a href="/experiments">Experiments:</a></td><td>{{ num_experiments }}</td></tr>
    <tr><td><a href="/plates">Plates:</a></td><td>{{ num_plates }}</td></tr>
  </tbody>
</table>
{% endblock %}

This template extends base.html

<!DOCTYPE html>
<html lang="en">
  <head>
    <link rel="stylesheet" href="/static/style.css">
    <title>{{ site_title }}{% if page_title %}: {{ page_title }}{% endif %}</title>
  </head>
  <body>
    <h1>{{ site_title }}{% if page_title %}: {{ page_title }}{% endif %}</h1>
    {% block content %}
    {% endblock %}
  </body>
</html>