Merge branch 'dev'

Vagrantfile

@@ -18,7 +18,8 @@ Vagrant.configure("2") do |config|
     apt-get clean
     rm -rf /var/lib/apt/lists/*
     apt-get update
-    apt-get install -y unzip apache2 python3 python3-pip mysql-server libmysqlclient-dev python3-dev libssl-dev python3-sphinx libpq-dev virtualenv
+    apt-get install -y unzip apache2 python3 python3-pip mysql-server libmysqlclient-dev \
+                       python3-dev libssl-dev python3-sphinx libpq-dev virtualenv
     apt-get upgrade -y
     pip3 install -r /home/vagrant/femr_onchain/requirements.txt
     curl -sL https://deb.nodesource.com/setup_14.x | bash -

femr_onchain/settings.py

@@ -50,7 +50,7 @@
     'session_security',
     'django_user_agents',
     'background_task',
-    'rest_framework_swagger',
+    'drf_yasg',
 ]
 
 AUTHENTICATION_BACKENDS = [

femr_onchain/urls.py

@@ -1,3 +1,6 @@
+"""
+Main URL configurations for fEMR-OnChain-Core. This redirects to the other apps in this project.
+"""
 from django.conf.urls import url
 from django.contrib import admin
 from django.contrib.auth import views as auth_views

main/admin.py

@@ -11,10 +11,16 @@
 
 
 class TreatmentAdmin(admin.ModelAdmin):
+    """
+    Register a TreatmentForm as accessible in the Admin site.
+    """
     form = TreatmentForm
 
 
 class PatientEncounterAdmin(admin.ModelAdmin):
+    """
+    Register a PatientEncounterForm as accessible in the Admin site.
+    """
     form = PatientEncounterForm
 
 

main/background_tasks.py

@@ -1,3 +1,6 @@
+"""
+Non-view functions used to carry out background processes.
+"""
 from datetime import timedelta
 
 from django.utils import timezone
@@ -26,7 +29,11 @@ def run_encounter_close():
                     e.save_no_timestamp()
 
 
-def reset_sessions():
+def reset_sessions() -> None:
+    """
+    Empty out sessions older than 1 minute.
+    :return:
+    """
     now = timezone.now()
     d = now - timedelta(minutes=1)
     for x in UserSession.objects.all():

main/csvio/added_inventory.py

@@ -1,3 +1,6 @@
+"""
+AddedInventoryHandler and required imports.
+"""
 import csv
 
 import requests
@@ -7,13 +10,28 @@
 
 
 class AddedInventoryHandler(CSVHandler):
+    """
+    Implements CSVHandler and adds inventory to supplies that already existed in the formulary.
+    """
     def __init__(self) -> None:
         super().__init__()
 
     def read(self, upload, campaign):
+        """
+        Given an upload file and a campaign to upload to, execute a CSV import.
+        :param upload:
+        :param campaign:
+        :return:
+        """
         return self.__import(upload, campaign)
 
     def write(self, response, formulary):
+        """
+        Given an HTTPResponse and a formulary object, write out the formulary as a CSV file.
+        :param response:
+        :param formulary:
+        :return:
+        """
         return self.__export(response, formulary)
 
     def __export(self, response, formulary):

main/delete_views.py

@@ -60,6 +60,14 @@ def patient_delete_view(request, id=None):
 
 
 def delete_chief_complaint(request, id=None, patient_id=None, encounter_id=None):
+    """
+    Delete a selected Chief Complaint and redirect back.
+    :param request:
+    :param id:
+    :param patient_id:
+    :param encounter_id:
+    :return:
+    """
     if request.user.is_authenticated:
         p = get_object_or_404(ChiefComplaint, pk=id)
         p.active = False

main/edit_views.py

@@ -602,6 +602,7 @@ def upload_photo_view(request, patient_id=None, encounter_id=None):
                 ph.save()
                 m.photos.add(ph)
                 m.save()
+                aux_form = PhotoForm()
                 DatabaseChangeLog.objects.create(action="Edit", model="PatientEncounter", instance=str(m),
                                                  ip=get_client_ip(request), username=request.user.username,
                                                  campaign=Campaign.objects.get(name=request.session['campaign']))

main/form_views.py

@@ -78,7 +78,7 @@ def patient_form_view(request):
                                                           'match_list': match,
                                                           'form': form,
                                                           'page_name': 'New Patient',
-                                                          'page_tip': "Complete form with patient demographics as instructed. Any box with an asterix (*) is required. Shared contact information would be if two patients have a household phone or email that they share, for example."})
+                                                          'page_tip': "Complete form with patient demographics as instructed. Any box with an asterisk (*) is required. Shared contact information would be if two patients have a household phone or email that they share, for example."})
     else:
         return redirect('/not_logged_in')
 
@@ -194,7 +194,7 @@ def patient_encounter_form_view(request, id=None):
                        'page_name': 'New Encounter for {} {} {}'.format(p.first_name, p.last_name, suffix),
                        'birth_sex': p.sex_assigned_at_birth, 'patient_id': id, 'units': units, 'telehealth': telehealth,
                        'encounter_open': encounter_open,
-                       'page_tip': "Complete form with patient vitals as instructed. Any box with an asterix (*) is required. For max efficiency, use 'tab' to navigate through this page."})
+                       'page_tip': "Complete form with patient vitals as instructed. Any box with an asterisk (*) is required. For max efficiency, use 'tab' to navigate through this page."})
     else:
         return redirect('/not_logged_in')
 

main/forms.py

@@ -304,7 +304,7 @@ def save(self, commit=True):
                 m.body_height_secondary = (
                                                   ((tmp * 12) + m.body_height_secondary) * 2.54) % 100
             if m.body_weight is not None:
-                m.body_weight = m.body_weight / 2.2046
+                m.body_weight /= 2.2046
         if commit:
             m.save()
         return m

main/formulary_management.py

@@ -1,4 +1,3 @@
-from main.csvio.added_inventory import AddedInventoryHandler
 from django.db.models.query_utils import Q
 from django.http.response import HttpResponse
 from django.shortcuts import redirect, render
@@ -55,9 +54,8 @@ def edit_add_supply_view(request, id=None):
             elif request.method == "POST":
                 form = AddSupplyForm(request.POST)
                 if form.is_valid():
-                    inventory_entry.initial_quantity = inventory_entry.initial_quantity + \
-                                                       int(request.POST['quantity'])
-                    inventory_entry.quantity = inventory_entry.quantity + int(request.POST['quantity'])
+                    inventory_entry.initial_quantity += int(request.POST['quantity'])
+                    inventory_entry.quantity += int(request.POST['quantity'])
                     inventory_entry.save()
                     return redirect('main:formulary_home_view')
                 else:
@@ -84,9 +82,8 @@ def edit_sub_supply_view(request, id=None):
                 if form.is_valid():
                     if inventory_entry.initial_quantity > int(
                             request.POST['quantity']) and inventory_entry.quantity > int(request.POST['quantity']):
-                        inventory_entry.initial_quantity = inventory_entry.initial_quantity - \
-                                                           int(request.POST['quantity'])
-                        inventory_entry.quantity = inventory_entry.quantity - int(request.POST['quantity'])
+                        inventory_entry.initial_quantity -= int(request.POST['quantity'])
+                        inventory_entry.quantity -= int(request.POST['quantity'])
                     else:
                         inventory_entry.initial_quantity = 0
                         inventory_entry.quantity = 0

main/list_views.py

@@ -70,7 +70,7 @@ def patient_csv_export_view(request):
                          'Body Temperature (F)', 'Height', 'Weight (lbs)', 'BMI', 'Oxygen Concentration',
                          'Glucose Level', 'History of Tobacco Use',
                          'History of Diabetes', 'History of Hypertension', 'History of High Cholesterol',
-                         'History of Alchol Abuse/Substance Abuse', 'Community Health Worker Notes',
+                         'History of Alcohol Abuse/Substance Abuse', 'Community Health Worker Notes',
                          'Procedure/Counseling', 'Pharmacy Notes',
                          'Medical/Surgical History', 'Social History', 'Current Medications', 'Family History']
         else:
@@ -80,9 +80,9 @@ def patient_csv_export_view(request):
                          'Glucose Level',
                          'History of Tobacco Use', 'History of Diabetes', 'History of Hypertension',
                          'History of High Cholesterol',
-                         'History of Alchol Abuse/Substance Abuse', 'Community Health Worker Notes',
+                         'History of Alcohol Abuse/Substance Abuse', 'Community Health Worker Notes',
                          'Procedure/Counseling', 'Pharmacy Notes',
-                         'Medical/Surgical History', 'Socil History', 'Current Medications', 'Family History']
+                         'Medical/Surgical History', 'Social History', 'Current Medications', 'Family History']
         try:
             data = Patient.objects.filter(
                 campaign=Campaign.objects.get(name=request.session['campaign'])).exclude(

main/middleware.py

@@ -1,8 +1,7 @@
 import pytz
 from django.contrib.auth import logout
 from django.contrib.auth.models import AnonymousUser
-from django.contrib.sessions.exceptions import SessionInterrupted
-from django.shortcuts import redirect, render
+from django.shortcuts import render
 from django.utils import timezone
 
 from clinic_messages.models import Message

main/static/main/js/bmi_calc.js

@@ -11,7 +11,7 @@ function get_input_and_calc() {
 }
 
 function set_final_value() {
-  console.log("Imperial BMI compuation.");
+  console.log("Imperial BMI computation.");
   $("#id_form-body_mass_index").val(get_input_and_calc);
 }
 

main/static/main/js/bmi_calc_metric.js

@@ -11,7 +11,7 @@ function get_input_and_calc() {
 }
 
 function set_final_value() {
-  console.log("Metric BMI compuation.");
+  console.log("Metric BMI computation.");
   $("#id_form-body_mass_index").val(get_input_and_calc);
 }
 

main/static/main/js/bmi_edit_calc.js

@@ -11,7 +11,7 @@ function get_input_and_calc() {
 }
 
 function set_final_value() {
-  console.log("Imperial BMI compuation.");
+  console.log("Imperial BMI computation.");
   $("#id_body_mass_index").val(get_input_and_calc);
 }
 

main/static/main/js/bmi_edit_calc_metric.js

@@ -11,7 +11,7 @@ function get_input_and_calc() {
 }
 
 function set_final_value() {
-  console.log("Metric BMI compuation.");
+  console.log("Metric BMI computation.");
   $("#id_form-body_mass_index").val(get_input_and_calc);
 }
 

main/templates/admin/home.html

@@ -6,8 +6,8 @@
         <h3>Campaign Management</h3>
         <div>
             <a href="{% url 'main:list_users_view' %}">User Management</a>
-            <a data-content="Click here to create new users or edit existing users." data-toggle="popover" data-trigger="hover"
-               href="#"><i
+            <a data-content="Click here to create new users or edit existing users."
+               data-toggle="popover" data-trigger="hover" href="#"><i
                     class="fa fa-question-circle"></i></a>
         </div>
         <!-- <div>
@@ -18,14 +18,14 @@ <h3>Campaign Management</h3>
         </div> -->
         <div>
             <a href="{% url 'main:get_audit_logs_view' %}">Access Audit Log Management</a>
-            <a data-content="Cick here to see who has logged in and out of fEMR On-Chain." data-toggle="popover" data-trigger="hover"
-               href="#"><i
+            <a data-content="Click here to see who has logged in and out of fEMR On-Chain." data-toggle="popover"
+               data-trigger="hover" href="#"><i
                     class="fa fa-question-circle"></i></a>
         </div>
         <div>
             <a href="{% url 'main:get_database_logs_view' %}">Database Access Log Management</a>
-            <a data-content="Click here to see who edited or accessed patient records." data-toggle="popover" data-trigger="hover"
-               href="#"><i
+            <a data-content="Click here to see who edited or accessed patient records." data-toggle="popover"
+               data-trigger="hover" href="#"><i
                     class="fa fa-question-circle"></i></a>
         </div>
         <div>

main/templates/data/base.html

@@ -8,8 +8,6 @@
     <meta content="width=device-width, initial-scale=1" name="viewport">
     <title>fEMR On-Chain</title>
     <script src="{% static 'admin/js/vendor/jquery/jquery.js' %}" type="text/javascript"></script>
-    <!-- <script crossorigin="anonymous" integrity="sha384-q8i/X+965DzO0rT7abK41JStQIAqVgRVzpbzo5smXKp4YfRvH+8abtTE1Pi6jizo"
-        src="https://code.jquery.com/jquery-3.3.1.slim.min.js"></script> -->
     <script crossorigin="anonymous" integrity="sha384-UO2eT0CpHqdSJQ6hJty5KVphtPhzWj9WO1clHTMGa3JDZwrnQq4sF86dIHNDz0W1"
             src="https://cdnjs.cloudflare.com/ajax/libs/popper.js/1.14.7/umd/popper.min.js"></script>
     <script src="{% static 'main/js/node_modules/inputmask/dist/jquery.inputmask.min.js' %}"></script>
@@ -35,7 +33,10 @@
         <img alt=""
              src="https://demo.teamfemr.org/assets/img/52749c927045848ae798e9df58dcc0dd-logo_color_sm.png" width="60">
     </a>
-    <a data-content="Make sure you are using Google Chrome. Make sure Campaign is set to the correct clinic location or program. It is easiest to tab through each screen. For help contact [email protected]." data-toggle="popover" data-trigger="hover" href="#"
+    <a data-content="Make sure you are using Google Chrome.
+    Make sure Campaign is set to the correct clinic location or program.
+    It is easiest to tab through each screen. For help contact [email protected]."
+       data-toggle="popover" data-trigger="hover" href="#"
        id="main_popover"><i
             class="fa fa-question-circle"></i></a>
 
@@ -63,8 +64,8 @@
             </li>
             {% if request.message_number > 0 %}
             <li class="nav-item" style="background-color: red;">
-                <a class="nav-link" href="{% url 'clinic_messages:index' %}" style="color: black;">Messages ({{
-                    request.message_number }})</a>
+                <a class="nav-link" href="{% url 'clinic_messages:index' %}" style="color: black;">
+                    Messages ({{ request.message_number }})</a>
             </li>
             {% else %}
             <li class="nav-item">
@@ -142,7 +143,7 @@ <h1>{{ page_name }}</h1>
                 Find a bug or problem? <a href="{% url 'appMR:index' %}">Let us know.</a>
             </div>
             <div class="col-sm-12 col-md-4 text-center">
-                v1.4.2.10132021
+                v1.4.3.10142021
             </div>
             <div class="col-sm-12 col-md-4">
                 <a href="https://github.com/FEMR/fEMR-OnChain-Core/wiki" target="_blank">fEMR On-Chain Wiki</a>

main/templates/data/base_login.html

@@ -50,7 +50,7 @@
             <div class="col-sm-12 col-md-4">
             </div>
             <div class="col-sm-12 col-md-4 text-center">
-                v1.4.2.10132021
+                v1.4.3.10142021
             </div>
             <div class="col-sm-12 col-md-4">
             </div>

main/templates/data/home.html

@@ -9,7 +9,7 @@
 </div>
 {% endif %}
 <div>
-    Welcome to fEMR On-Chain v1.4.2.10132021, {{ user.first_name }} {{ user.last_name }}!
+    Welcome to fEMR On-Chain v1.4.3.10142021, {{ user.first_name }} {{ user.last_name }}!
 </div>
 <div>
     Please select a tab at the top, search below, or select a campaign below to get started!

main/templates/data/patient_deleted_success.html

@@ -1,6 +1,6 @@
 {% extends "data/base.html" %}
 {% block content %}
 <div>
-    <div>Paitent record successfully deleted.</div>
+    <div>Patient record successfully deleted.</div>
 </div>
 {% endblock %}

main/templates/forms/edit_encounter.html

@@ -301,7 +301,8 @@ <h3>Treatments</h3>
                 <div class="row">
                     <div class="form-group col-md-12">
                         {{ form.chief_complaint|as_crispy_field }}
-                        <a class="btn btn-primary" href="{% url 'main:chief_complaint_list_view' patient.id encounter_id %}"
+                        <a class="btn btn-primary"
+                           href="{% url 'main:chief_complaint_list_view' patient.id encounter_id %}"
                            target="_blank">Manage</a>
                     </div>
                 </div>

main/templates/forms/encounter.html

@@ -170,8 +170,9 @@ <h5 class="modal-title">Patient Already Has an Open Encounter</h5>
                 <div class="col-md-4">
                     <input class="btn btn-primary ml-auto" id="submit_refer" name="submit_refer" type="submit"
                            value="Save and Refer"/>
-                    <a data-content="Click this button if another campaign or location should have access to this patient record." data-toggle="popover" data-trigger="hover"
-                       href="#"><i
+                    <a data-content="Click this button if another campaign or
+                     location should have access to this patient record."
+                       data-toggle="popover" data-trigger="hover" href="#"><i
                             class="fa fa-question-circle"></i></a>
                 </div>
             </div>

main/templates/list/patient.html

@@ -76,7 +76,8 @@
     <tr>
         <td>{{ o.campaign_key }}</td>
         <td>{{ o|open_encounters }}</td>
-        <td><a href="{% url 'main:patient_edit_form_view' id=o.id %}">{{ o.first_name }} {{ o|has_middle_name }} {{ o.last_name }} {{ o|has_suffix }}</a></td>
+        <td><a href="{% url 'main:patient_edit_form_view' id=o.id %}">{{ o.first_name }}
+             {{ o|has_middle_name }} {{ o.last_name }} {{ o|has_suffix }}</a></td>
         <td>{{ o|last_timestamp }}</td>
         <td>{{ o|get_campaign_info }}</td>
         <td><a href="{% url 'main:patient_medical' id=o.id %}">Medical</a></td>

main/templatetags/campaign_tags.py

@@ -1,8 +1,19 @@
+"""
+TemplateTags used to carry out more complex display actions on Campaigns.
+"""
 from django import template
 
+from main.models import Campaign
+
 register = template.Library()
 
 
 @register.filter('is_selected')
-def is_selected(campaign, selected):
+def is_selected(campaign: Campaign, selected: str) -> bool:
+    """
+    Given a campaign and a campaign name, check if they match.
+    :param campaign:
+    :param selected:
+    :return:
+    """
     return True if campaign.name == selected else False