app, prokit

README.md

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+Clinic PGHD Requester App
+===========================
+
+
+A [SMART on FHIR][sf] app to dispatch patient generated health data (PGHD) requests to the `patient`. An array of [instruments][ilist] is compiled from FHIR `ValueSets` stored in the clinic's FHIR server. 
+
+This is a companion app for the [SMART Markers][sm] framework and its apps. As the FHIR `ServiceRequest` is generated, the downstream SMART Markers apps can fulfill those requests by generated or aggregating data and submitting back to the health system's FHIR server.
+
+This app is fully SMART on FHIR compliant and represents the concept of sending PGHD requests with emphasis on interoperability. 
+
+
+Installation
+-----------
+
+1. Clone this repository: 
+2. Install modules 
+3. Edit `app.py` with the settings for the SMART on FHIR endpoints and SMART credentails 
+4. run app.py
+
+
+```bash
+$ git clone https://github.com/SMARTMarkers/practitioner-ehr-app.git
+$ cd practitioner-ehr-app
+$ pip3 install fhirclient
+$ chmod +x app.py
+
+//Edit app.py with settings for the SMART on FHIR endpoints
+$ ./app.py
+```
+
+Notice
+----------
+This work is under further development and eventually will become a framework to support multiple SMART EHR apps.
+
+[sf]: https://docs.smarthealthit.org
+[ilist]: https://github.com/SMARTMarkers/smartmarkers-ios/tree/master/Sources/Instruments
+[sm]: https://github.com/SMARTMarkers/smartmarkers-ios
+
+
+
+

__init__.py

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+import sys
+import os.path
+abspath = os.path.abspath(os.path.dirname(__file__))
+if abspath not in sys.path:
+    sys.path.insert(0, abspath)

app.py

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+#!/usr/bin/env python3
+
+import jwt
+import logging
+from prokit import smartclient
+from flask import Flask, redirect, session, request, render_template, jsonify
+from fhirclient import client
+from fhirclient.models import practitioner
+
+
+app = Flask(__name__, template_folder='app/templates')
+app_secret = "applicaitonsecret123"
+app.secret_key = app_secret
+app.debug = True
+app.user_practitioner = None
+
+
+smart_settings = {
+        'app_id'        :       'pro_app2',
+        'redirect_uri'  :       'http://127.0.0.1:8000/callback',
+        'scope'         :       'openid fhirUser launch launch/patient',
+        'app_secret'    :        app_secret,
+        'patient_id'    :       '39234650-0229-4aee-975b-c8ee68bab40b'
+        }
+
+
+
+def _save_state(state):
+    session['state'] = state 
+    session.modified = True
+
+def _smart_client(): 
+
+    state = session.get('state')
+    if state:
+        return smartclient.PROClient(state=state, save_func=_save_state)
+    else:
+        return smartclient.PROClient(settings=smart_settings, save_func=_save_state)
+
+@app.route('/launch.html')
+def app_launch(): 
+    smart_settings.update({'api_base': request.args.get('iss', '')}) 
+    smart = _smart_client()
+    if smart.ready and smart.patient is not None:
+        return redirect('/index.html')
+    else:
+        auth_url = smart.authorize_url
+        if auth_url:
+            return redirect(auth_url) 
+        else:
+            return msg('error authorizing')
+
+
+@app.route('/requests/new') 
+def request_pgd(): 
+    smart = _smart_client()
+
+    instrument_type = request.args.get('instrumenttype')
+    instrument_id   = request.args.get('instrumentid')
+    if instrument_id is None or instrument_type is None:
+        return msg('No')
+
+    instr = None
+    if instrument_type == 'webrepository':
+        instr = [instr for instr in smart.instrumentlist_devices if instr.identifier == instrument_id][0]
+    elif instrument_type == 'activity':
+        instr = [instr for instr in smart.instrumentList_activity if instr.identifier == instrument_id][0]
+    elif instrument_type == 'survey':
+        instr = [instr for instr in smart.instrumentlist_questionnaires if instr.identifier == instrument_id][0]
+    elif instrument_type == 'activetask':
+        instr = [instr for instr in smart.instrumentlist_activetasks if instr.identifier == instrument_id][0]
+
+    print(f'selected instrument is {instr.identifier}')
+
+    if instr is None:
+        return msg('No')
+
+    success = smart.dispatchRequest(selected_instrument=instr, practitioner_resource=app.user_practitioner, selected_schedule=None)
+    print(success)
+    if success:
+        return jsonify(result={'result':'success', 'request_id': success.identifier, 'request_title': success.title})
+    else:
+        return jsonify(result={'result': 'fail'})
+
+@app.route('/index.html')
+def app_main():
+
+    smart = _smart_client() 
+    print(session['state'])
+    if app.user_practitioner is None:
+        idtoken = session['state']['launch_context']['id_token']
+        if idtoken is None: 
+            return msg('id-token not found')
+        jwtDecoded = jwt.decode(idtoken, verify=False)
+        practitioner_id = jwtDecoded['fhirUser'].split('/')[1]
+        app.user_practitioner = smart.user_practitioner(practitioner_id)
+
+    return render_template('index.html', 
+            page='request', 
+            proclient=smart, 
+            observations=smart.getobservations(),
+            requests=smart.getrequests(),
+            questionnaires=smart.instrumentlist_questionnaires,
+            promis=smart.instrumentlist_promis, 
+            activetasks=smart.instrumentlist_activetasks,
+            activityInstruments=smart.instrumentList_activity,
+            healthkit=smart.instrumentlist_healthkit,
+            devices=smart.instrumentlist_devices
+            )
+
+@app.route('/reset')
+def reset():
+    _reset()
+    return msg('Deleted session')
+
+
+def _reset():
+    if 'state' in session:
+        del session['state']
+
+
+
+@app.route('/callback')
+def auth_callback():
+    smart = _smart_client()
+    try:
+        smart.handle_callback(request.url)
+    except Exception as e:
+        return """<h1>Authorization Error</h1>{0}""".format(e)
+    return redirect('/index.html')
+
+
+def msg(test):
+    return f'{test}'
+
+def log(msg):
+    logging.debug(msg)
+
+
+
+
+
+
+if '__main__' == __name__:
+    logging.basicConfig(level=logging.DEBUG)
+    app.run(debug=True, port=8000)

app/app.py

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+#!/usr/bin/env python3 
+
+
+from prokit import request

app/templates/about.html

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+<h1>About</h1>
+
+<p>Patient-Reported Outcomes</p>
+

app/templates/footer.html

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+<footer class="footer fixed-bottom bg-dark">
+    <div class="footer-copyright text-center py-3 text-light"> 
+            <span class="small" >© 2019 <a class="text-light" target="_blank" href="http://chip.org">Computational Health Informatics Program</a><br> Boston Children's Hospital</span>
+          </div>
+</footer>

app/templates/index.html

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+<!DOCTYPE html>
+<html lang="en">
+<head>
+	<meta charset="utf-8">
+	<meta http-equiv="X-UA-Compatible" content="IE=edge">
+	<meta name="viewport" content="width=device-width, initial-scale=1">
+
+
+	<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/4.4.1/css/bootstrap.min.css">
+
+	<!-- jQuery library -->
+	<script src="https://ajax.googleapis.com/ajax/libs/jquery/3.4.1/jquery.min.js"></script>
+
+	<!-- Popper JS -->
+	<script src="https://cdnjs.cloudflare.com/ajax/libs/popper.js/1.16.0/umd/popper.min.js"></script>
+
+	<!-- Latest compiled JavaScript -->
+	<script src="https://maxcdn.bootstrapcdn.com/bootstrap/4.4.1/js/bootstrap.min.js"></script>
+
+	<script type=text/javascript>
+	$SCRIPT_ROOT = {{ request.script_root|tojson|safe }};
+ 	</script>
+	<title>Patient Generated Data</title>
+
+</head>
+<body>
+	{% include 'navbar.html' %}
+		<div class="container" id="content" style="margin-top:30px">
+            {% if page == 'main' %}
+            {% include 'observations.html' %}
+            {% else %} 
+            {% include 'request.html' %}
+            {% endif %}
+
+    	</div>
+	{% include 'footer.html' %}
+
+
+
+
+</body>
+
+</html>

app/templates/navbar.html

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+<nav class="navbar navbar-expand-lg navbar-dark bg-dark">
+	<span class="navbar-brand mb-0 h1">SMARTMarkers: Patient Data Request</span>
+	<button class="navbar-toggler" type="button" data-toggle="collapse" data-target="#navbarSupportedContent"
+	 aria-controls="navbarSupportedContent" aria-expanded="false" aria-label="Toggle navigation">
+		<span class="navbar-toggler-icon"></span>
+	</button>
+
+<!-- 	
+	<div class="collapse navbar-collapse" id="navbarSupportedContent">
+		<ul class="navbar-nav mr-auto">
+			<li class="nav-item active">
+				<a class="nav-link" href="/">PROMIS<span class="sr-only">(current)</span></a>
+			</li>
+			<li class="nav-item active">
+				<a class="nav-link" href="/requests">Requests</a>
+			</li>
+
+			<li class="nav-item">
+				<a class="nav-link disabled" href="#">Disabled</a>
+			</li>
+		</ul>
+	</div> -->
+</nav>

app/templates/observations.html

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+    <div id="observations-page">
+	<div class="row">
+		{% for result in observations  %}
+        <div class="col-sm-6">
+            <div class="card">
+                <div class="card-header">
+                    <b class="card-title">{{result.identifier}} <span class="badge badge-secondary">3</span>
+                    </b>
+                    <br>
+                    <span class="badge badge-primary">Active</span><span class="text-muted small">Code: {{result.code}}
+                        <br>Recent:</span>
+                    <br>
+                </div>
+                <div class="card-body">
+                    <div class="container">
+                        <div id="identifier-chart"></div>
+                    </div>
+                </div>
+
+            </div>
+        </div>
+        {% endfor %}
+    </div> 
+
+</div>