Merge 732c133 into af6cd3b

elcid/api.py

@@ -1,20 +1,18 @@
 import datetime
+import re
 from operator import itemgetter
 from collections import defaultdict
 from django.conf import settings
 from django.utils.text import slugify
 from django.http import HttpResponseBadRequest
-from django.db.models import Q
 from intrahospital_api import loader
 from rest_framework import viewsets
 from opal.core.api import OPALRouter
 from opal.core.api import patient_from_pk, LoginRequiredViewset
 from opal.core.views import json_response
 from opal.core import serialization
 from elcid import models as emodels
-from lab import models as lmodels
 from elcid.utils import timing
-from opal import models as omodels
 
 
 _LAB_TEST_TAGS = {
@@ -67,16 +65,11 @@ def extract_observation_value(observation_value):
         if its >12 return >12
         else return None
     """
-    obs_result = observation_value.split("~")[0]
-    try:
-        # we return None if its not numeric
+    regex = r'^[0-9][0-9.]*$'
+    obs_result = observation_value.strip()
+    obs_result = obs_result.split("~")[0].strip("<").strip(">").strip()
+    if re.match(regex, obs_result):
         return float(obs_result)
-    except ValueError:
-        try:
-            float(obs_result.strip("<").strip(">").strip())
-            return obs_result
-        except ValueError:
-            return None
 
 
 def get_observation_value(observation):

elcid/models.py

@@ -5,7 +5,9 @@
 from django.db.models.signals import post_save
 from django.dispatch import receiver
 from django.db import models
+from django.conf import settings
 from django.contrib.contenttypes.models import ContentType
+from django.utils import timezone
 from lab import models as lmodels
 import opal.models as omodels
 
@@ -132,6 +134,22 @@ def update_from_dict(self, data, *args, **kwargs):
         """
         pass
 
+    def set_datetime_ordered(self, value, *args, **kwargs):
+        if value is None:
+            self.datetime_ordered = None
+        elif isinstance(value, datetime.datetime):
+            self.datetime_ordered = value
+        else:
+            input_format = settings.DATETIME_INPUT_FORMATS[0]
+
+            # never use DST, if we're an hour back, we're an hour back
+            with_tz = timezone.make_aware(
+                datetime.datetime.strptime(value, input_format),
+                timezone.get_current_timezone(),
+                is_dst=False
+            )
+            self.datetime_ordered = with_tz
+
     def update_from_api_dict(self, patient, data, user):
         """
             This is the updateFromDict of the the UpstreamLabTest
@@ -221,10 +239,10 @@ def get_relevant_tests(self, patient):
             "GENTAMICIN LEVEL",
             "CLOTTING SCREEN"
         ]
-        six_months_ago = datetime.date.today() - datetime.timedelta(6*30)
+        three_weeks_ago = timezone.now() - datetime.timedelta(3*7)
         qs = UpstreamLabTest.objects.filter(
             patient=patient,
-            datetime_ordered__gt=six_months_ago
+            datetime_ordered__gt=three_weeks_ago
         ).order_by("datetime_ordered")
         return [i for i in qs if i.extras.get("test_name") in relevent_tests]
 

elcid/templates/detail/inpatient.html

@@ -25,7 +25,7 @@
   </div>
 
   {% record_panel models.Line %}
-  {% record_panel models.Antimicrobial %}
+  {% include "partials/antimicrobial_panel.html" %}
   {% record_panel models.Imaging %}
   {% include "partials/blood_culture_result_display.html" %}
   {% if permissions.view_lab_test_trends %}

elcid/templates/partials/antimicrobial_panel.html

@@ -0,0 +1,31 @@
+{% with name=models.Antimicrobial.get_api_name %}
+  <div ng-repeat="parent in [episode]">
+    <div class="panel panel-default record-panel antimicrobial-panel">
+      <div class="panel-heading">
+        <h3>
+          <i class="{{ models.Antimicrobial.get_icon }}"></i> {{ models.Antimicrobial.get_display_name }}
+          <span>
+              <i class="fa fa-plus-circle edit pull-right pointer"
+                 ng-click="parent.recordEditor.newItem('{{ name }}')"></i>
+              <i ng-show="parent.{{ name }}.length" class="fa fa-clipboard edit pull-right pointer" clipboard data-clipboard-target=".antimicrobial-panel"></i>
+         </span>
+        </h3>
+      </div>
+      <ul class="list-group">
+        <li class="list-group-item" ng-repeat="item in parent.{{ name }}">
+          <div class="row">
+            <div class="col-md-9">
+              {% include models.Antimicrobial.get_display_template %}
+            </div>
+            <div class="col-md-3">
+              <span>
+                  <i class="fa fa-pencil edit pull-right pointer"
+                     ng-click="parent.recordEditor.editItem('{{ name }}', $index)"></i>
+              </span>
+            </div>
+          </div>
+        </li>
+      </ul>
+    </div>
+  </div>
+{% endwith %}

elcid/templates/partials/lab_test_sparklines.html

@@ -23,7 +23,7 @@ <h2 class="text-center no-results">No results found</h2>
             [[ date | shortDate ]]
           </th>
           <th class="text-center">
-            3 month trend
+            3 week trend
           </th>
         </tr>
       </thead>

elcid/test/test_api.py

@@ -7,9 +7,27 @@
     BloodCultureResultApi, UpstreamBloodCultureApi
 )
 from elcid import models as emodels
+from elcid import api
 from django.test import override_settings
 
 
+class ExtractObservationValueTestCase(OpalTestCase):
+    def test_extract_observation_value(self):
+        inputs_to_expected_results = (
+            ("<1", float(1),),
+            ("1>", float(1),),
+            (" 1 ", float(1),),
+            ("< 1", float(1),),
+            (" < 1", float(1),),
+            (".1 ", None),
+            ("0.1 ", 0.1),
+            ("1E", None),
+            ("'1'", None),
+        )
+        for input, expected in inputs_to_expected_results:
+            self.assertEqual(api.extract_observation_value(input), expected)
+
+
 class UpstreamBloodCultureApiTestCase(OpalTestCase):
     def setUp(self):
         self.api = UpstreamBloodCultureApi()

elcid/test/test_models.py

@@ -1,7 +1,9 @@
 import datetime
-
 from django.test import TestCase
+from django.utils import timezone
 from django.contrib.contenttypes.models import ContentType
+from django.utils import timezone
+from django.conf import settings
 
 from opal.core import exceptions
 from opal.core.test import OpalTestCase
@@ -325,6 +327,42 @@ def test_update_from_api_dict_repeated(self):
             found_hl7_result.status, emodels.UpstreamLabTest.COMPLETE
         )
 
+    def test_set_datetime_ordered_none(self):
+        lab_test = emodels.UpstreamLabTest(patient=self.patient)
+        lab_test.datetime_ordered = timezone.now()
+        lab_test.set_datetime_ordered(None)
+        self.assertIsNone(lab_test.datetime_ordered)
+
+    def test_set_datetime_ordered_datetime(self):
+        lab_test = emodels.UpstreamLabTest(patient=self.patient)
+        now = timezone.now()
+        lab_test.set_datetime_ordered(now)
+        self.assertEqual(
+            lab_test.datetime_ordered, now
+        )
+
+    def test_set_datetime_ordered_string(self):
+        lab_test = emodels.UpstreamLabTest(patient=self.patient)
+        date_str = "29/10/2017 10:00:00"
+        lab_test.set_datetime_ordered(date_str)
+        dt = datetime.datetime(2017, 10, 29, 10, 0)
+        dt = timezone.make_aware(dt)
+        self.assertEqual(
+            lab_test.datetime_ordered,
+            dt
+        )
+
+    def test_set_datetime_ordered_dst(self):
+        lab_test = emodels.UpstreamLabTest(patient=self.patient)
+        date_str = "29/10/2017 1:00:00"
+        lab_test.set_datetime_ordered(date_str)
+        as_str = lab_test.datetime_ordered.strftime(
+            settings.DATETIME_INPUT_FORMATS[0]
+        )
+        self.assertEqual(
+            as_str, "29/10/2017 01:00:00"
+        )
+
     def test_update_from_api_dict_first_time(self):
         update_dict = dict(
             external_identifier="1",
@@ -364,6 +402,57 @@ def test_update_from_dict(self):
         # validate that is hasn't been saved
         self.assertIsNone(hl7_result.id)
 
+    def test_get_relevant_tests(self):
+        patient, _ = self.new_patient_and_episode_please()
+        upstream_lab_test = emodels.UpstreamLabTest(patient=patient)
+        yesterday = timezone.now() - datetime.timedelta(
+            1
+        )
+        upstream_lab_test.datetime_ordered = yesterday
+        upstream_lab_test.extras = dict(test_name="C REACTIVE PROTEIN")
+        upstream_lab_test.save()
+
+        relevant = emodels.UpstreamLabTest.get_relevant_tests(patient)
+        self.assertEqual(
+            len(relevant), 1
+        )
+        self.assertEqual(
+            relevant[0].datetime_ordered, yesterday
+        )
+        self.assertEqual(
+            relevant[0].extras["test_name"], "C REACTIVE PROTEIN"
+        )
+
+    def test_get_relevant_tests_over_three_weeks(self):
+        patient, _ = self.new_patient_and_episode_please()
+        upstream_lab_test = emodels.UpstreamLabTest(patient=patient)
+        four_weeks_ago = timezone.now() - datetime.timedelta(
+            4 * 7
+        )
+        upstream_lab_test.datetime_ordered = four_weeks_ago
+        upstream_lab_test.extras = dict(test_name="C REACTIVE PROTEIN")
+        upstream_lab_test.save()
+
+        relevant = emodels.UpstreamLabTest.get_relevant_tests(patient)
+        self.assertEqual(
+            len(relevant), 0
+        )
+
+    def test_get_not_relevant_tests(self):
+        patient, _ = self.new_patient_and_episode_please()
+        upstream_lab_test = emodels.UpstreamLabTest(patient=patient)
+        yesterday = timezone.now() - datetime.timedelta(
+            1
+        )
+        upstream_lab_test.datetime_ordered = yesterday
+        upstream_lab_test.extras = dict(test_name="SOME OTHER TEST")
+        upstream_lab_test.save()
+
+        relevant = emodels.UpstreamLabTest.get_relevant_tests(patient)
+        self.assertEqual(
+            len(relevant), 0
+        )
+
 
 class DiagnosisTest(OpalTestCase, AbstractEpisodeTestCase):
 

etc/nginx.conf

@@ -9,7 +9,11 @@ server {
     server_name elcid-rfh-test.openhealthcare.org.uk;
     access_log /usr/lib/ohc/log/nginx.log timed_combined;
 
-   location /static {
+    location /himunin {
+        alias /var/cache/munin/www;
+    }
+
+    location /static {
         alias /var/www/media/static;
     }
 

intrahospital_api/api.py

@@ -6,6 +6,7 @@
 from opal.core import subrecords
 from lab import models as lmodels
 from elcid.episode_serialization import serialize
+from intrahospital_api import get_api
 
 
 def patient_to_dict(patient, user):
@@ -49,6 +50,19 @@ def patient_to_dict(patient, user):
     return d
 
 
+class UpstreamDataViewset(viewsets.ViewSet):
+    base_name = 'upstream'
+    permission_classes = (IsAuthenticated,)
+
+    def retrieve(self, request, pk=None):
+        patient = get_object_or_404(
+            omodels.Patient.objects.all(), pk=pk
+        )
+        api = get_api()
+        hospital_number = patient.demographics_set.first().hospital_number
+        return json_response(api.results_for_hospital_number(hospital_number))
+
+
 class PatientViewSet(viewsets.ViewSet):
     base_name = 'patient'
     permission_classes = (IsAuthenticated,)

intrahospital_api/management/commands/load_tests_from_json.py

@@ -4,24 +4,20 @@
 """
 import json
 from django.core.management.base import BaseCommand
-from django.contrib.auth.models import User
+from django.db import transaction
 from opal import models
 from elcid import models as emodels
 from lab import models as lmodels
-from intrahospital_api import loader
+from intrahospital_api import update_lab_tests
 
 
 class Command(BaseCommand):
     def add_arguments(self, parser):
         parser.add_argument('patient_id', type=int)
         parser.add_argument('file_name', type=str)
 
-    def handle(self, patient_id, file_name, *args, **options):
-        # we assume that there is a user called super
-        # which there won't be on prod, but we shouldn't
-        # be running this on prod
-        user = User.objects.get(username="super")
-        patient = models.Patient.objects.get(id=patient_id)
+    @transaction.atomic
+    def process(self, patient, results):
         lmodels.LabTest.objects.filter(
             patient=patient
         ).filter(
@@ -30,7 +26,14 @@ def handle(self, patient_id, file_name, *args, **options):
                 emodels.UpstreamBloodCulture.get_display_name(),
             ]
         ).delete()
+        update_lab_tests.update_tests(patient, results)
+
+    def handle(self, patient_id, file_name, *args, **options):
+        # we assume that there is a user called super
+        # which there won't be on prod, but we shouldn't
+        # be running this on prod
         with open(file_name) as f:
             results = json.load(f)
-            loader.save_lab_tests(patient, results, user)
+        patient = models.Patient.objects.get(id=patient_id)
+        self.process(patient, results)
         print "success"

intrahospital_api/models.py

@@ -76,7 +76,7 @@ class Meta:
 
 
 class InitialPatientLoad(PatientLoad, PatientSubrecord):
-    """ this model is the initial load of a patient
+    """ This model is the initial load of a patient
         future loads are done by the cron batch load
     """
 
@@ -96,6 +96,11 @@ def __unicode__(self):
                 self.started
             )
 
+    def update_from_dict(self, data, *args, **kwargs):
+        """ For the purposes of the front end this model is read only.
+        """
+        pass
+
 
 class BatchPatientLoad(PatientLoad):
     """ This is the batch load of all reconciled patients

intrahospital_api/plugin.py

@@ -20,4 +20,7 @@ class IntraHospitalApiPlugin(plugins.OpalPlugin):
             'js/intrahospital_api/services/initial_patient_lab_load_status.js'
         ]
     }
-    apis = [("patient", api.PatientViewSet,)]
+    apis = [
+        ("patient", api.PatientViewSet,),
+        ("upstream", api.UpstreamDataViewset,)
+    ]