initial commit

Author: mounika

.env

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+FHIR_USERNAME=
+FHIR_PASSWORD=
+FHIR_PORT=5000

.gitignore

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+venv

README.md

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+# fhir-condition-finder
+
+This is a FHIR web application written in Python and using Flask as the backend. It can only be used for synthea datasets.
+
+Following are the server port number and their respective datasets
+
+```
+9090 -> synthea10 (demo dataset)
+9091 -> synthea_ri_adult
+9092 -> synthea_ri_peds
+```
+
+## 1. Dependencies
+This app depends on Python 3 and a few Python packages outlined in the `requirements.txt` file. 
+
+## 2. Before running the app
+
+Change these parameters in the .env file
+
+```
+FHIR_USERNAME = ???
+FHIR_PASSWORD = ???
+FHIR_PORT=5000
+```
+
+and change the port number according to the dataset in the app.py file 
+FHIR_SERVER_BASE_URL= "http://pwebmedcit.services.brown.edu:????/fhir"
+
+## 3. Running the App
+
+We begin by creating a Python virtual environment using the `venv` module. This is done by running the command below from the "root" of this repo. 
+
+```
+python3 -m venv venv                 # create a virtual environment called venv
+
+source venv/bin/activate             # activate our virtual environment
+
+pip3 install -r requirements.txt     # install all our dependencies into the virtual environment
+```
+
+
+After the above steps, we should be able to launch our app using the following command.
+
+```
+python3 src/app.py
+```
+
+
+This will start the app on port 5000. You can open your preferred browser and see the app running on `http://localhost:5000`
+
+

requirements.txt

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+blinker==1.6.2
+certifi==2023.7.22
+charset-normalizer==3.2.0
+click==8.1.7
+Flask==2.3.3
+idna==3.4
+importlib-metadata==6.8.0
+itsdangerous==2.1.2
+Jinja2==3.1.2
+MarkupSafe==2.1.3
+python-dotenv==1.0.0
+requests==2.31.0
+urllib3==2.0.5
+Werkzeug==2.3.7
+zipp==3.17.0

src/app.py

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+import requests
+import os
+from flask import Flask, request, render_template
+from dotenv import load_dotenv
+
+
+app = Flask(__name__)
+
+FHIR_SERVER_BASE_URL="http://pwebmedcit.services.brown.edu:9091/fhir"
+
+load_dotenv()
+
+username = os.getenv("FHIR_USERNAME")
+password = os.getenv("FHIR_PASSWORD")
+
+
+def request_patient(patient_id, credentials):
+
+    req = requests.get(FHIR_SERVER_BASE_URL + "/Patient/" + str(patient_id), auth = credentials)
+
+    print(f"Requests status: {req.status_code}")
+
+    response = req.json()
+    print(response.keys())
+
+    return response
+
+def search_patients_by_condition(condition_id, credentials):
+    # Search for patients with a specific condition
+    search_url = f"{FHIR_SERVER_BASE_URL}/Condition?code={condition_id}"
+    req = requests.get(search_url, auth=credentials)
+
+    if req.status_code == 200:
+        conditions = req.json()['entry']
+        patient_ids = [entry['resource']['subject']['reference'].split('/')[-1] for entry in conditions]
+        patients = [request_patient(patient_id, credentials) for patient_id in patient_ids]
+         # Convert patient details into set of tuples to ensure uniqueness
+        unique_patients = set((patient['id'], patient['name'][0]['given'][0], patient['name'][0]['family'], patient['gender'], patient['birthDate']) for patient in patients)
+
+        total_patients = len(unique_patients)
+        return {'unique_patients': unique_patients, 'total_patients': total_patients}
+    else:
+        return None
+
+
+
+
+
+@app.route('/', methods=['GET', 'POST'])
+def index():
+    result = None
+    credentials = (username, password)
+
+    if request.method == 'POST':
+        try:
+            condition_id = request.form['condition_id']
+            result = search_patients_by_condition(condition_id, credentials)
+        except ValueError:
+            result = 'Invalid input. Please enter a valid condition ID.'
+
+    return render_template('index.html', result=result)
+
+
+if __name__ == '__main__':
+    port_str = os.environ['FHIR_PORT']
+    port_int = int(port_str)
+    app.run(debug=True, port=port_int)

src/templates/index.html

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+<!DOCTYPE html>
+
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <title>Patient Finder for a given condition_id</title>
+</head>
+<body>
+    <div class=container>
+    <h1>Patient Finder for a given condition_id</h1>
+
+    <form method="post">
+        <label for="condition_id">Enter a condition ID:</label>
+        <input type="text" name="condition_id" id="condition_id">
+        <input type="submit" value="Search">
+    </form>
+   
+    {% if result %}
+    <h3>Total Patients: {{ result['total_patients'] }}</h3>
+    <h3>Results:</h3>
+    <ul>
+        {% for patient in result['unique_patients'] %}
+            <li>
+                <p>Patient ID: {{ patient[0] }}</p>
+                <p>First Name: {{ patient[1] }}</p>
+                <p>Last Name: {{ patient[2] }}</p>
+                <p>Gender: {{ patient[3] }}</p>
+                <p>Birth Date: {{ patient[4] }}</p>
+            </li>
+        {% endfor %}
+    </ul>
+{% endif %}
+
+
+    </div>
+</body>
+</html>
+
+
+<style>
+    .container {
+        display: grid;
+        place-items: center;
+    }
+</style>