Merge pull request #870 from openhealthcare/v0.29

V0.29

deployment_tests/fabric_tests.py

@@ -491,9 +491,11 @@ def test_services_symlink_upstart_if_exists(
         )
 
     @mock.patch('fabfile.local')
+    @mock.patch('fabfile.generate_secret_key')
     def test_sevices_create_local_settings(
-        self, local, print_function
+        self, generate_secret_key, local, print_function
     ):
+        generate_secret_key.return_value = "blah"
         some_dir = tempfile.mkdtemp()
         project_dir = "{}/elcid".format(some_dir)
         os.mkdir(project_dir)
@@ -514,6 +516,7 @@ def test_sevices_create_local_settings(
 
         self.assertIn("Some = 'settings'", output_file)
         self.assertIn("'NAME': 'elcidrfh_some_branch'", output_file)
+        self.assertIn('SECRET_KEY = "blah"', output_file)
 
         local.assert_called_once_with(
             "rm -f {}".format(local_settings_file)
@@ -1405,6 +1408,12 @@ def test_error_not_raised(
         clean_old_backups.assert_called_once_with()
 
 
+class GenerateSecretKeyTestCase(FabfileTestCase):
+    def test_generate_secret_key(self):
+        result = fabfile.generate_secret_key()
+        self.assertEqual(len(result), 50)
+
+
 @mock.patch("fabfile.is_load_running")
 @mock.patch("fabfile.local")
 @mock.patch("fabfile.time")

elcid/api.py

@@ -269,6 +269,42 @@ class InfectionServiceTestSummaryApi(LoginRequiredViewset):
 
     NUM_RESULTS = 5
 
+    def get_ticker_observations(self, patient):
+        """
+        Some results are displayed as a ticker in chronological
+        order.
+        """
+        ticker = []
+        tests = lab_test_models.LabTest.objects.filter(
+            test_name='2019 NOVEL CORONAVIRUS',
+            patient=patient
+        ).order_by('-datetime_ordered')
+        for test in tests:
+            if len(ticker) < 3:
+                observations = {
+                    t.observation_name: t for t in test.observation_set.all()
+                }
+                value = observations['2019 nCoV'].observation_value
+                if value == 'Pending':
+                    continue
+
+                specimen = observations.get('2019 nCoV Specimen Type', None)
+                timestamp = test.datetime_ordered.strftime('%d/%m/%Y %H:%M')
+                result_string = "{}".format(value)
+
+                if specimen:
+                    result_string += " ({})".format(specimen.observation_value)
+
+                ticker.append(
+                    {
+                        'timestamp': timestamp,
+                        'name': '2019 nCoV',
+                        'value': result_string
+                    }
+                )
+
+        return ticker
+
     def get_recent_dates_to_observations(self, qs):
         """
         We are looking for the last 5 dates
@@ -339,13 +375,15 @@ def serialise_lab_tests(self, patient):
         # the patient does not have a lot of results
         while len(recent_dates) < self.NUM_RESULTS:
             recent_dates.append(None)
+
         obs_values = []
 
         for obs_set in obs:
             obs_values.append(self.serialize_observations(obs_set))
         return dict(
             obs_values=obs_values,
-            recent_dates=recent_dates
+            recent_dates=recent_dates,
+            ticker=self.get_ticker_observations(patient)
         )
 
     @patient_from_pk

elcid/migrations/0035_auto_20200326_1517.py

@@ -0,0 +1,18 @@
+# Generated by Django 2.0.9 on 2020-03-26 15:17
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('elcid', '0034_auto_20200323_1813'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='icuadmission',
+            name='outcome',
+            field=models.CharField(blank=True, choices=[('Survived', 'Survived'), ('Covid-19 Atributable Death', 'Covid-19 Atributable Death'), ('Covid-19 Non-attributable Death', 'Covid-19 Non-attributable Death')], max_length=200, null=True),
+        ),
+    ]

elcid/models.py

@@ -780,7 +780,7 @@ def record_positive_blood_culture(sender, instance, **kwargs):
 class ICUAdmission(EpisodeSubrecord):
     _icon = 'fa fa-heartbeat'
 
-    OUTCOMES = enum('Survived', 'Atributable Death', 'Non-attributable Death')
+    OUTCOMES = enum('Survived', 'Covid-19 Atributable Death', 'Covid-19 Non-attributable Death')
 
     admission_date = models.DateField(blank=True, null=True)
     discharge_date = models.DateField(blank=True, null=True)

elcid/templates/partials/lab_test_sparklines.html

@@ -11,9 +11,18 @@ <h2 class="text-center no-results">Unable to get lab tests for this patient</h2>
     <h2 class="text-center no-results">Failed To load lab tests for this patient</h2>
   </div>
   <div ng-show="patientLoadStatus.isLoaded()">
-    <div ng-hide="data.obs_values.length">
+    <div ng-hide="data.obs_values.length || data.ticker.length">
       <h2 class="text-center no-results">No results found</h2>
     </div>
+
+    <div class="content-offset-below-20" ng-show="data.ticker.length">
+      <div class="row" ng-repeat="test in data.ticker">
+        <div class="col-md-4">[[ test.timestamp ]]</div>
+        <div class="col-md-4">[[ test.name ]]</div>
+        <div class="col-md-4">[[ test.value ]]</div>
+      </div>
+    </div>
+
     <table ng-show="data.obs_values.length" class="col-md-12 table">
       <thead>
         <tr>
@@ -23,9 +32,9 @@ <h2 class="text-center no-results">No results found</h2>
             [[ date | displayDate ]]
           </th>
           {% comment %}
-          <th class="text-center">
-            3 week trend
-          </th>
+            <th class="text-center">
+              3 week trend
+            </th>
           {% endcomment %}
         </tr>
       </thead>
@@ -37,9 +46,9 @@ <h2 class="text-center no-results">No results found</h2>
             [[ item.latest_results[date] ]]
           </td>
           {% comment %}
-          <td class="text-center">
-            <div spark-line="item.graph_values"></div>
-          </td>
+            <td class="text-center">
+              <div spark-line="item.graph_values"></div>
+            </td>
           {% endcomment %}
         </tr>
       </tbody>

elcid/test/test_api.py

@@ -966,6 +966,7 @@ def test_vanilla_check(self):
 
         result = self.client.get(self.url)
         expected = {
+            'ticker': [],
             'obs_values': [
                 {
                     'latest_results': {'04/06/2019': 1.8, '05/06/2019': 1.8},
@@ -1020,6 +1021,7 @@ def test_multiple_results_on_the_same_day(self):
         })
         result = self.client.get(self.url)
         expected = {
+            'ticker': [],
             'obs_values': [
                 {
                     'latest_results': {'04/06/2019': 1.3},
@@ -1061,6 +1063,7 @@ def test_results_date_crunching(self):
             dt_4: "1.4", dt_5: "1.5", dt_6: "1.6", dt_7: "1.7", dt_8: "1.8"
         })
         expected = {
+            'ticker': [],
             'obs_values':
                 [
                     {
@@ -1109,6 +1112,7 @@ def test_ignores_strings(self):
         })
         result = self.client.get(self.url)
         expected = {
+            'ticker': [],
              'obs_values': [],
              'recent_dates': [None, None, None, None, None]
         }
@@ -1124,6 +1128,7 @@ def test_ignore_strings_same_date(self):
     def test_handles_no_tests(self):
         result = self.client.get(self.url)
         expected = {
+            'ticker': [],
              'obs_values': [],
              'recent_dates': [None, None, None, None, None]
         }

etc/conf_templates/local_settings.py.jinja2

@@ -9,6 +9,8 @@ DATABASES = {
     }
 }
 
+SECRET_KEY = "{{ secret_key }}"
+
 DEBUG = False
 
 {% for k, v in additional_settings.items() %}

fabfile.py

@@ -44,6 +44,7 @@
 import json
 import copy
 import time
+import random
 from jinja2 import Environment, FileSystemLoader
 
 from fabric.api import local, env
@@ -326,12 +327,18 @@ def services_symlink_upstart(new_env):
         symlink_name
     ))
 
+def generate_secret_key():
+    chars = 'abcdefghijklmnopqrstuvwxyz0123456789!@#$%^&*(-_=+)'
+    return ''.join([
+        random.SystemRandom().choice(chars) for i in range(50)
+    ])
 
 def services_create_local_settings(new_env, additional_settings):
     print("Creating local settings")
     new_settings = copy.copy(additional_settings)
     new_settings["db_name"] = new_env.database_name
     new_settings["db_user"] = DB_USER
+    new_settings["secret_key"] = generate_secret_key()
     template = jinja_env.get_template(
         'etc/conf_templates/local_settings.py.jinja2'
     )