Basic setup and database to store patient data using Flask

.flaskenv

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+FLASK_APP=webscas.py
+FLASK_DEBUG=1

.gitignore

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+__pycache__
+migrations
+*.db
+venv
+whoosh

README.md

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 Web application for sepsis clinical assessment scores using batch ICU patient data
 Backend of the application will be in Flask and the project will be completely python based
 Frontend will be purely based on html, css and may be on javascript.
+
+# Run Web
+```shell
+To run the web Do:
+>>> pip install -r requirements.txt
+And run the flask server
+>>> flask run
+Open it on your localhost http://127.0.0.1:5000

app/__init__.py

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+from flask import Flask
+from config import Config
+from flask_sqlalchemy import SQLAlchemy
+from flask_migrate import Migrate
+
+app = Flask(__name__)
+app.config.from_object(Config)
+db = SQLAlchemy(app)
+migrate = Migrate(app, db)
+
+from app import routes, models

app/forms.py

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+from flask_wtf import FlaskForm
+from wtforms import StringField, PasswordField, BooleanField, SubmitField
+from wtforms.validators import DataRequired
+
+class PatientForm(FlaskForm):
+    patient_id = StringField('Patient Id', validators=[DataRequired()])
+    patient_name = StringField('Patient Name', validators=[DataRequired()])
+    patient_disease = StringField('Disease', validators=[DataRequired()])
+    submit = SubmitField('Submit')
+
+class SepsisForm(FlaskForm):
+    patient_id = StringField('Patient ID', validators=[DataRequired()])
+    fever = StringField('Fever(in degree celsius)', validators=[DataRequired()])
+    heart_rate = StringField('Heart Rate(in beats per minute)', validators=[DataRequired()])
+    respiratory_rate = StringField('Respiratory Rate(in breaths per minute)', validators=[DataRequired()])
+    abnormal_white_blood_cell_count = StringField('Abnormal White Blood Cell Count(/mm3)', validators=[DataRequired()])
+    paco2 = StringField('PaCO2(Partial pressure of carbon dioxide)')
+    submit = SubmitField('Submit')

app/models.py

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+from app import db, app
+import flask_whooshalchemy as wa
+
+class Patient(db.Model):
+    # id = db.Column(db.Integer, primary_key=1)
+    __searchable__ = ['patien_name', 'patient_disease']
+    patient_id = db.Column(db.Integer, primary_key=1)
+    patient_name = db.Column(db.String(64))
+    patient_disease = db.Column(db.String(128))
+    sepsis = db.relationship('Sepsis', backref='patient', lazy='dynamic')
+
+    def __repr__(self):
+        return '<Patient {}>'.format(self.patient_id)
+
+wa.whoosh_index(app, Patient)
+class Sepsis(db.Model):
+    s_id = db.Column(db.Integer, primary_key=1)
+    fever = db.Column(db.Integer)
+    heart_rate = db.Column(db.Integer)
+    respiratory_rate = db.Column(db.Integer)
+    abnormal_white_blood_cell_count = db.Column(db.Integer)
+    paco2 = db.Column(db.Integer)
+    patient_id = db.Column(db.Integer, db.ForeignKey('patient.patient_id'))
+
+# def load_user(id):
+#     return User.query.get(int(id))

app/routes.py

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+from flask import render_template, redirect, url_for, flash, request
+from app.forms import PatientForm, SepsisForm
+from app.models import Patient, Sepsis
+from app import app, db
+import flask_whooshalchemy as wa
+
+@app.route('/')
+@app.route('/index')
+def index():
+    patients = Patient.query.all()
+    for patient in patients:
+        print(patient.patient_name)
+    return render_template("index.html", title="webscas", patients=patients)
+
+@app.route('/add_patient', methods=['GET', 'POST'])
+def add_patient():
+    form = PatientForm()
+    if request.method == 'GET':
+        return render_template('add_patient.html', title='Add Patient', form=form)
+    elif form.validate_on_submit():
+        patient_id = Patient.query.filter_by(patient_id=form.patient_id.data).first()
+        print(type(patient_id))
+        if patient_id is not None:
+            flash('Patient with id {} already exist'.format(form.patient_id.data), 'info')
+            return redirect(url_for('add_patient'))
+        else:
+            patient = Patient(patient_name=form.patient_name.data, patient_id=form.patient_id.data, patient_disease=form.patient_disease.data)
+            db.session.add(patient)
+            db.session.commit()
+            flash('Your data has been saved successfully', 'success')
+            return redirect(url_for('index'))
+    return render_template('add_patient.html',title='Add Patient', form=form)
+
+@app.route('/patient_details', methods=['GET', 'POST'])
+def patient_details():
+    form = SepsisForm()
+    if request.method == 'GET':
+        return render_template('patient_details.html', title='Patient Details', form=form)
+    elif form.validate_on_submit():
+        patient_id = Patient.query.filter_by(patient_id=form.patient_id.data).first()
+        if patient_id: 
+            s_id = Sepsis.query.filter_by(patient_id=form.patient_id.data).first()
+            if not s_id:
+                details = Sepsis(fever=form.fever.data, heart_rate=form.heart_rate.data, respiratory_rate=form.respiratory_rate.data, abnormal_white_blood_cell_count=form.abnormal_white_blood_cell_count.data, paco2=form.paco2.data, patient_id=form.patient_id.data)
+                db.session.add(details)
+                db.session.commit()
+                flash('Details has been saved', 'success')
+            else:
+                s_id.fever=form.fever.data
+                s_id.heart_rate=form.heart_rate.data
+                s_id.respiratory_rate=form.respiratory_rate.data
+                s_id.abnormal_white_blood_cell_count=form.abnormal_white_blood_cell_count.data
+                s_id.paco2=form.paco2.data
+                db.session.commit()
+                flash("Details has been updated", 'success')
+        else:
+            flash('No Patient exist with Patient ID {}'.format(form.patient_id.data), 'warning')
+    return render_template('patient_details.html', title='Patient Details', form=form)
+
+# @app.route('/search')
+# def search():
+#     data = request.args.get('query')
+#     # print(data)
+#     patients = Patient.query.whoosh_search(data).all()
+#     print(type(patients))
+#     return render_template('index.html', patients=patients)
+#     # return 'hi'

app/templates/add_patient.html

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+{% extends 'base.html' %}
+
+{% block content %}
+    <style >
+        h3 {margin-top: 5%;margin-bottom: 5%;}
+    </style>
+    <center>
+        <h3>Add Patient</h3>
+        <form action="" method="POST" novalidate>
+            {{ form.hidden_tag() }}
+            <p>
+                {{ form.patient_name.label }} <br>
+                {{ form.patient_name(size=32) }} <br>
+                {% for error in form.patient_name.errors %}
+                <span style="color: red;">[{{ error }}]</span>
+                {% endfor %}                
+            </p>
+            <p>
+                {{ form.patient_id.label }} <br>
+                {{ form.patient_id(size=32) }} <br>
+                {% for error in form.patient_id.errors %}
+                <span style="color: red;">[{{ error }}]</span>
+                {% endfor %}                
+            </p>
+            <p>
+                {{ form.patient_disease.label }} <br>
+                {{ form.patient_disease(size=32) }} <br>
+                {% for error in form.patient_disease.errors %}
+                <span style="color: red;">[{{ error }}]</span>
+                {% endfor %}                
+            </p>
+            <p>
+                {{ form.submit() }}
+            </p>
+        </form>
+    </center>
+{% endblock %}

app/templates/base.html

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+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <meta http-equiv="X-UA-Compatible" content="ie=edge">
+    <script src="https://code.jquery.com/jquery-3.3.1.slim.min.js" integrity="sha384-q8i/X+965DzO0rT7abK41JStQIAqVgRVzpbzo5smXKp4YfRvH+8abtTE1Pi6jizo" crossorigin="anonymous"></script>
+    <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/4.3.1/css/bootstrap.min.css">
+    <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css">    
+    <title>{{ title }}</title>
+</head>
+<body>
+    <nav class="navbar navbar-expand-lg navbar-light bg-dark fixed-top">
+        <!-- <a class="navbar-brand text-light col-sm-4" href="#">
+          <img src="/docs/4.1/assets/brand/bootstrap-solid.svg" width="30" height="30" class="d-inline-block align-top" alt="">
+          Builder
+        </a> -->
+        <button type="button" class="navbar-toggler bg-light float-right" data-toggle="collapse" data-target="#navbarCollapse">
+            <span class="navbar-toggler-icon"></span>
+        </button>
+        <div class="collapse navbar-collapse" id="navbarCollapse">
+            <ul class="navbar-nav mr-auto col-sm-12">
+                <li class="nav-item active" style="margin-right: 2%;margin-left: 5%;">
+                    <a class="nav-link text-light" href="{{ url_for('index') }}">Web Scas <span class="sr-only">(current)</span></a>
+                </li>
+                <li class="nav-item"><a href="{{ url_for('add_patient') }}" class="nav-link text-light">&nbsp;<i class="fa fa-user-plus" aria-hidden="true"></i>&nbsp;Add Patient</a></li>
+                <li class="nav-item">
+                    <a href="{{ url_for('patient_details') }}" class="nav-link text-light">&nbsp;
+                    <i class="fa fa-user-plus" aria-hidden="true"></i>&nbsp;Add Patient Detail</a>
+                </li>
+            </ul>
+        </div>
+    </nav>    
+    <div class="container message" style="margin-top: 5%;">
+        {% with messages = get_flashed_messages(with_categories=true) %}
+        <!-- Categories: success (green), info (blue), warning (yellow), danger (red) -->
+        {% if messages %}
+        {% for category, message in messages %}
+        <div class="alert alert-{{ category }} alert-dismissible" role="alert">
+          <button type="button" class="close" data-dismiss="alert" aria-label="Close"><span
+              aria-hidden="true">&times;</span></button>
+          {{ message }}
+        </div>
+        {% endfor %}
+        {% endif %}
+        {% endwith %}
+    </div>    
+    {% block content %} {% endblock %}
+    <script>
+        setTimeout(function() {
+            $('.alert-dismissible').remove();
+        }, 2000); 
+
+        $(".custom-file-input").on("change", function() {
+        var fileName = $(this).val().split("\\").pop();
+        $(this).siblings(".custom-file-label").addClass("selected").html(fileName);
+        });
+    </script>    
+</body>
+</html>

app/templates/index.html

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+{% extends 'base.html' %}
+
+{% block content %}
+    <center>
+        <!-- <h4>Search</h4>
+        <form action="search" method="GET">
+            <label for="query">Name</label>
+            <input type="text" name="query" id="query">
+            <button class="btn btn-primary">Search</button>
+        </form> -->
+    {% for patient in patients %}
+        <h6>{{ patient.patient_id }}</h6>
+        <h6>{{ patient.patient_name }}</h6>
+        <h6>{{ patient.patient_disease }}</h6>
+        <br>
+    {% endfor %}
+    </center>
+{% endblock %}

app/templates/patient_details.html

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+{% extends 'base.html' %}
+
+{% block content %}
+    <style>
+        h4 {margin-top: 5%; margin-bottom: 1%;}
+    </style>
+    <center>
+        <h4>Add Patient Details</h4>
+        <form action="" method="POST" novalidate>
+            {{ form.hidden_tag() }}
+            <p>
+                {{ form.patient_id.label }} <br>
+                {{ form.patient_id(size=32) }} <br>
+                {% for error in form.patient_id.errors %}
+                <span style="color: red;">[{{ error }}]</span>
+                {% endfor %}
+            </p>
+            <p>
+                {{ form.fever.label }} <br>
+                {{ form.fever(size=32) }} <br>
+                {% for error in form.fever.errors %}
+                <span style="color: red;">[{{ error }}]</span>
+                {% endfor %}
+            </p>
+            <p>
+                {{ form.heart_rate.label }} <br>
+                {{ form.heart_rate(size=32) }} <br>
+                {% for error in form.heart_rate.errors %}
+                <span style="color: red;">[{{ error }}]</span>
+                {% endfor %}
+            </p>
+            <p>
+                {{ form.respiratory_rate.label }} <br>
+                {{ form.respiratory_rate(size=32) }} <br>
+                {% for error in form.respiratory_rate.errors %}
+                <span style="color: red;">[{{ error }}]</span>
+                {% endfor %}
+            </p>
+            <p>
+                {{ form.abnormal_white_blood_cell_count.label }} <br>
+                {{ form.abnormal_white_blood_cell_count(size=32) }} <br>
+                {% for error in form.abnormal_white_blood_cell_count.errors %}
+                <span style="color: red;">[{{ error }}]</span>
+                {% endfor %}
+            </p>
+            <p>
+                {{ form.paco2.label }} <br>
+                {{ form.paco2(size=32) }} <br>
+                {% for error in form.paco2.errors %}
+                <span style="color: red;">[{{ error }}]</span>
+                {% endfor %}
+            </p>
+            <p>{{ form.submit() }}</p>
+        </form>
+    </center>
+{% endblock %}

config.py

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+import os
+basedir = os.path.abspath(os.path.dirname(__file__))
+
+class Config(object):
+    SECRET_KEY = os.environ.get('SECRET_KEY') or 'thisissecretkey'
+    SQLALCHEMY_DATABASE_URI = os.environ.get('DATABASE_URL') or \
+        'sqlite:///' + os.path.join(basedir, 'app.db')
+    SQLALCHEMY_TRACK_MODIFICATIONS = False    

webscas.py

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+from app import app, db
+from app.models import Patient
+
+@app.shell_context_processor
+def make_shell_context():
+    return {'db': db, 'Patient': Patient}