Merge 542c1fa into 57c276a

elcid/api.py

@@ -605,6 +605,21 @@ def create(self, request):
             status_code=status.HTTP_201_CREATED
         )
 
+    @item_from_pk
+    def destroy(self, request, item):
+        """
+        Delete a blood culture isolate.
+        Update the updated* and previous_mrn fields of the parent
+        blood culture set.
+        """
+        blood_culture_set = item.blood_culture_set
+        blood_culture_set.set_updated_by_id(None, request.user)
+        blood_culture_set.set_updated(None, request.user)
+        if blood_culture_set.previous_mrn:
+            blood_culture_set.previous_mrn = None
+        blood_culture_set.save()
+        return super().destroy(request, item.id)
+
 
 class AddToServiceViewSet(LoginRequiredViewset):
     basename = 'add_to_service'

elcid/assets/js/elcid/controllers/blood_culture_panel.js

@@ -37,10 +37,15 @@ angular.module('opal.controllers').controller('BloodCulturePanelCtrl', function(
     var deferred = $q.defer();
     $http.get("/api/v0.1/blood_culture_set/" + bcs.id + "/").then(function(result){
       var bcs_idx = _.findIndex($scope.patient.blood_culture_set, {id: bcs.id})
+      // when we update isolates we update the fields the previous_mrn, updated*
+      // fields on the set.
       $scope.patient.blood_culture_set[bcs_idx].isolates = result.data.isolates;
+      $scope.patient.blood_culture_set[bcs_idx].previous_mrn = result.data.previous_mrn;
+      $scope.patient.blood_culture_set[bcs_idx].updated = result.data.updated;
+      $scope.patient.blood_culture_set[bcs_idx].updated_by_id = result.data.updated_by_id;
       deferred.resolve();
     })
 
     return deferred.promise;
   };
-});
+});

elcid/assets/js/elcid/services/blood_culture_isolate.js

@@ -23,11 +23,20 @@ angular.module('opal.services').service(
       this.isolateUrl = baseUrl;
       this.editing = {
         consistency_token: "",
-        blood_culture_set_id: blood_culture_set.id
+        blood_culture_set_id: blood_culture_set.id,
       }
       this.isNew = true;
     }
 
+    // we consider an isolate and a set to be one thing
+    // for the purposes of created*/updated*/previous_mrn
+    // even if when we are creating a new isolate.
+    this.editing.created = blood_culture_set.created;
+    this.editing.created_by_id = blood_culture_set.created_by_id;
+    this.editing.updated = blood_culture_set.updated;
+    this.editing.updated_by_id = blood_culture_set.updated_by_id;
+    this.editing.previous_mrn = blood_culture_set.previous_mrn;
+
     var isolate = this;
 
     Referencedata.load().then(function(referenceData){
@@ -101,4 +110,4 @@ recently changed it - refresh the page and try again');
   }
 
   return BloodCultureIsolate;
-});
+});

elcid/migrations/0069_blood_culture_updated_created.py

@@ -0,0 +1,56 @@
+"""
+BloodCultureIsolate will no longer have created*/updated* attributes
+and instead we will use the BloodCultureSet created*/updated*
+
+If the isolate has been updated more recently than the set, make
+sure the set has the most recent data.
+"""
+# Generated by Django 2.2.16 on 2023-05-10 07:39
+
+from django.db import migrations
+
+def forwards(apps, schema_editor):
+    """
+    If the isolate has been updated more recently than the blood culture set
+    copy the isolates updated/updated_by onto the set.
+    """
+    BloodCultureIsolate = apps.get_model('elcid', 'BloodCultureIsolate')
+    isolates = BloodCultureIsolate.objects.exclude(updated=None).select_related('blood_culture_set')
+    for isolate in isolates:
+        if isolate.blood_culture_set.updated is None:
+            bcs = isolate.blood_culture_set
+            bcs.updated = isolate.updated
+            bcs.updated_by = isolate.updated_by
+            bcs.save()
+        elif isolate.updated > isolate.blood_culture_set.updated:
+            bcs = isolate.blood_culture_set
+            bcs.updated = isolate.updated
+            bcs.updated_by = isolate.updated_by
+            bcs.save()
+
+def backwards(apps, schema_editor):
+    """
+    As defaults copy the created*/updated* fields back onto the blood culture
+    set.
+    """
+    BloodCultureSet = apps.get_model('elcid', 'BloodCultureSet')
+    for bcs in BloodCultureSet.objects.all():
+        bcs.isolates.update(
+            created=bcs.created,
+            created_by=bcs.created_by,
+            updated=bcs.updated,
+            updated_by=bcs.updated_by,
+        )
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('elcid', '0068_remove_mergedmrn_upstream_merge_datetime'),
+    ]
+
+    operations = [
+        migrations.RunPython(
+            forwards, backwards
+        )
+    ]

elcid/migrations/0070_auto_20230510_0750.py

@@ -0,0 +1,29 @@
+# Generated by Django 2.2.16 on 2023-05-10 07:50
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('elcid', '0069_blood_culture_updated_created'),
+    ]
+
+    operations = [
+        migrations.RemoveField(
+            model_name='bloodcultureisolate',
+            name='created',
+        ),
+        migrations.RemoveField(
+            model_name='bloodcultureisolate',
+            name='created_by',
+        ),
+        migrations.RemoveField(
+            model_name='bloodcultureisolate',
+            name='updated',
+        ),
+        migrations.RemoveField(
+            model_name='bloodcultureisolate',
+            name='updated_by',
+        ),
+    ]

elcid/models.py

@@ -620,7 +620,6 @@ class Meta:
 class BloodCultureIsolate(
     omodels.UpdatesFromDictMixin,
     omodels.ToDictMixin,
-    omodels.TrackedModel,
     models.Model
 ):
     AEROBIC = "Aerobic"
@@ -663,6 +662,36 @@ class BloodCultureIsolate(
     )
     notes = models.TextField(blank=True)
 
+    def update_from_dict(self, data, user, *args, **kwargs):
+        """
+        Changes updated*/previousMRN on the related
+        BloodCultureSet when the isolate is updated.
+        """
+        # created*/updated*/previous_mrn are hoisted onto
+        # the blood culture isolate from the blood culture set
+        # by the blood_culture_isolate.js, they are not fields
+        # on the isolate so need to be removed.
+        blood_culture_set_fields = [
+            "previous_mrn", "created", "created_by_id", "updated", "updated_by_id"
+        ]
+        for field in blood_culture_set_fields:
+            if field in data:
+                data.pop(field)
+
+        blood_culture_set_id = data.get('blood_culture_set_id')
+        blood_culture_set = BloodCultureSet.objects.get(
+            id=blood_culture_set_id
+        )
+        # data is ignored by the below for functions
+        blood_culture_set.set_updated_by_id(data, user)
+        blood_culture_set.set_updated(data, user)
+        blood_culture_set.save()
+
+        if blood_culture_set.previous_mrn:
+            blood_culture_set.previous_mrn = None
+            blood_culture_set.save()
+        return super().update_from_dict(data, user, *args, **kwargs)
+
     @classmethod
     def get_api_name(cls):
         return camelcase_to_underscore(cls._meta.object_name)

elcid/test/test_api.py

@@ -9,6 +9,8 @@
 from django.utils import timezone
 from django.test import override_settings
 from rest_framework.reverse import reverse
+from django.contrib.auth.models import User
+from django.conf import settings
 
 from elcid import models as emodels
 from elcid import patient_lists
@@ -600,8 +602,6 @@ def test_retrieve_with_isolates(self):
                 'date_positive': datetime.date(2019, 5, 9),
                 'blood_culture_set_id': 1,
                 'consistency_token': '111',
-                'created': None,
-                'created_by_id': None,
                 'gpc_staph': '',
                 'gpc_strep': '',
                 'gram_stain': 'Gram -ve Rods',
@@ -612,8 +612,6 @@ def test_retrieve_with_isolates(self):
                 'sepsityper_organism': '',
                 'resistance': [],
                 'sensitivities': [],
-                'updated': None,
-                'updated_by_id': None
             }],
             'lab_number': '111',
             'patient_id': 1,
@@ -746,10 +744,10 @@ def test_update_with_empty_isolates(self):
 class BloodCultureIsolateTestCase(OpalTestCase):
     def setUp(self):
         positive = datetime.date(2019, 5, 8)
-        yesterday = positive - datetime.timedelta(1)
+        self.yesterday = positive - datetime.timedelta(1)
         patient, _ = self.new_patient_and_episode_please()
         self.bcs = emodels.BloodCultureSet.objects.create(
-            date_ordered=yesterday,
+            date_ordered=self.yesterday,
             source="Hickman",
             lab_number="111",
             patient=patient
@@ -790,17 +788,13 @@ def test_retrieve(self):
             'resistance': [],
             'sepsityper_organism': '',
             'gpc_strep': '',
-            'created_by_id': None,
-            'updated': None,
             'id': self.isolate.id,
             'gram_stain': 'Gram -ve Rods',
             'date_positive': datetime.date(2019, 5, 8),
             'sensitivities': [],
-            'updated_by_id': None,
             'quick_fish': 'Negative',
             'blood_culture_set_id': 1,
             'gpc_staph': '',
-            'created': None,
             'organism': '',
             'consistency_token': '111',
             'aerobic_or_anaerobic': 'Aerobic'
@@ -819,17 +813,13 @@ def test_list(self):
             'resistance': [],
             'date_positive': datetime.date(2019, 5, 8),
             'gpc_strep': '',
-            'created_by_id': None,
-            'updated': None,
             'id': self.isolate.id,
             'gram_stain': 'Gram -ve Rods',
             'sensitivities': [],
             'sepsityper_organism': '',
-            'updated_by_id': None,
             'quick_fish': 'Negative',
             'blood_culture_set_id': 1,
             'gpc_staph': '',
-            'created': None,
             'organism': '',
             'consistency_token': '111',
             'aerobic_or_anaerobic': 'Aerobic'
@@ -874,6 +864,9 @@ def test_create(self):
         )
 
     def test_update(self):
+        # created should be updated on the blood culture set
+        # make sure we start with None
+        self.assertIsNone(self.bcs.created)
         data = {
             'id': self.isolate.id,
             'notes': '',
@@ -905,6 +898,23 @@ def test_update(self):
         self.assertEqual(
             reloaded_isolate.aerobic_or_anaerobic, 'Anerobic'
         )
+        # created should be updated on the blood culture set
+        self.bcs.created = self.user
+
+    def test_delete(self):
+        self.bcs.updated = self.yesterday
+        other_user = User.objects.create(username="other user")
+        self.bcs.updated_by = other_user
+        self.bcs.save()
+        self.client.delete(self.detail_url)
+        self.bcs.refresh_from_db()
+        # it should be approximately now
+        self.assertTrue(
+            self.bcs.updated > timezone.now() - datetime.timedelta(minutes=1)
+        )
+        self.assertEqual(self.bcs.updated_by, self.user)
+
+
 
 @override_settings(NEW_LAB_TEST_SUMMARY_DISPLAY=True)
 class LabTestSummaryTestCase(OpalTestCase):

elcid/test/test_models.py

@@ -1,8 +1,11 @@
 import datetime
 from unittest import mock
+from django.urls import reverse
 from django.test import TestCase
 from django.utils import timezone
 from django.contrib.contenttypes.models import ContentType
+from django.contrib.auth.models import User
+from django.conf import settings
 from elcid import episode_categories
 
 from opal.core import exceptions
@@ -766,3 +769,46 @@ def test_only_one_instance_created(self):
         self.episode.set_tag_names(["bacteraemia"], self.user)
         self.episode.set_tag_names(["bacteraemia"], self.user)
         self.assertEqual(self.patient.positivebloodculturehistory_set.count(), 1)
+
+
+class BloodCultureIsolateTestCase(OpalTestCase):
+    def setUp(self):
+        self.patient, _ = self.new_patient_and_episode_please()
+        self.now = timezone.now()
+        self.yesterday = self.now - datetime.timedelta(1)
+        self.bcs = self.patient.bloodcultureset_set.create(
+            date_ordered=self.yesterday,
+            source="Hickman",
+            lab_number="111",
+            patient=self.patient,
+            created=self.yesterday,
+            created_by=self.user,
+            previous_mrn="123"
+        )
+        self.other_user = User.objects.create(
+            username="other_user"
+        )
+
+    def test_update_from_dict(self):
+        update_dict = {
+            "organism": "Aspergillus",
+            "blood_culture_set_id": self.bcs.id,
+            "created": self.yesterday,
+            "created_by_id": self.user.id,
+            "updated": self.now,
+            "updated_by_id": self.other_user.id
+        }
+        isolate = emodels.BloodCultureIsolate()
+        isolate.update_from_dict(update_dict, self.other_user)
+        self.bcs.refresh_from_db()
+        self.assertEqual(
+            self.bcs.created.strftime(settings.DATETIME_INPUT_FORMATS[0]),
+            self.yesterday.strftime(settings.DATETIME_INPUT_FORMATS[0])
+        )
+        self.assertEqual(self.bcs.created_by, self.user)
+        self.assertEqual(
+            self.bcs.updated.strftime(settings.DATETIME_INPUT_FORMATS[0]),
+            self.now.strftime(settings.DATETIME_INPUT_FORMATS[0])
+        )
+        self.assertEqual(self.bcs.updated_by, self.other_user)
+        self.assertIsNone(self.bcs.previous_mrn)