Adds a management command to sync the blood cultures with the new blo…

…od cultures

elcid/management/commands/sync_blood_cultures.py

@@ -1,76 +1,86 @@
-from collections import defaultdict
 from django.core.management.base import BaseCommand
 from django.db import transaction
 from opal.models import Patient
+from opal.core.serialization import deserialize_datetime
 from elcid import models
 
 
 def get_key(lab_test):
-    keys = ["aerobic", "lab_number", "source", "isolate"]
+    keys = ["lab_number", "source", "datetime_ordered"]
     extras = lab_test.extras
     return tuple([extras.get(i) for i in keys])
 
 
-def save_blood_culture_isolate(patient, lab_tests):
-    blood_culture_isolate = models.BloodCultureIsolate(patient=patient)
-    # we have to save for the many to many fields
-    blood_culture_isolate.save()
+def get_or_create_blood_culture_set(patient, old_lab_test):
+    extras = old_lab_test.extras
+    bcs_attrs = {"lab_number": extras.get("lab_number")}
+    bcs_datetime_ordered = extras.get("datetime_ordered")
+    if bcs_datetime_ordered:
+        bcs_attrs["date_ordered"] = deserialize_datetime(bcs_datetime_ordered)
+    source = extras.get("source")
+    if source:
+        source_model = models.BloodCultureSource.objects.first(name=source)
+        if source_model:
+            bcs_attrs["source_fk_id"] = source_model.id
+        else:
+            bcs_attrs["source_ft"] = source
+
+    bcs, created = patient.bloodcultureset_set.get_or_create(
+        **bcs_attrs
+    )
+
+    bcs.created = bcs.created or old_lab_test.created
+    bcs.created_by = bcs.created_by or old_lab_test.created_by
+    bcs.updated = bcs.updated or old_lab_test.updated
+    bcs.updated_by = bcs.updated_by or old_lab_test.updated_by
+
+
+def save_blood_culture_isolates(patient, old_lab_test):
+    bcs, _ = get_or_create_blood_culture_set(patient, old_lab_test)
 
-    lab_test_type_to_field = {
+    old_field_to_new_field = {
         models.BloodCultureOrganism.get_display_name(): "organism",
-        models.GramStain.get_display_name(): "gram_stains",
+        models.GramStain.get_display_name(): "gram_stain",
         models.QuickFISH.get_display_name(): "quick_fish",
         models.GPCStaph.get_display_name(): "gpc_staph",
         models.GPCStrep.get_display_name(): "gpc_strep",
         models.GNR.get_display_name(): "gnr"
     }
 
-    for lab_test in lab_tests:
-        field = lab_test_type_to_field[lab_test.lab_test_type]
-        if field == "gram_stains" and lab_test.result.result:
-            gs = models.GramStainOutcome.objects.get(
-                name=lab_test.result.result
-            )
-            blood_culture_isolate.gram_stains.add(gs)
-        else:
-            setattr(blood_culture_isolate, field, lab_test.result.result)
-
-        blood_culture_isolate.lab_number = lab_test.extras.get("lab_number")
-        blood_culture_isolate.aerobic = lab_test.extras.get("aerobic")
-        blood_culture_isolate.source = lab_test.extras.get("source")
-        blood_culture_isolate.created = lab_test.created
-        blood_culture_isolate.created_by = lab_test.created_by
-        blood_culture_isolate.updated = lab_test.updated
-        blood_culture_isolate.updated_by = lab_test.updated_by
-        dt = lab_test.datetime_ordered
-        if dt:
-            blood_culture_isolate.date_ordered = dt.date()
-
-        blood_culture_isolate.sensitivities.add(
-            *lab_test.sensitive_antibiotics.all()
-        )
-        blood_culture_isolate.resistances.add(
-            *lab_test.resistant_antibiotics.all()
-        )
-
-    # saves the non many to many fields
-    blood_culture_isolate.save()
+    isolate = models.BloodCultureIsolate(
+        blood_culture_set=bcs
+    )
+
+    for old_field, new_field in old_field_to_new_field.items():
+        setattr(isolate, new_field, old_lab_test.extras.get(old_field))
+
+    if old_lab_test.extras.get("aerobic") is True:
+        isolate.aerobic_or_anaerobic = isolate.AEROBIC
+    elif old_lab_test.extras.get("aerobic") is False:
+        isolate.aerobic_or_anaerobic = isolate.ANAEROBIC
+    isolate.created = old_lab_test.created
+    isolate.created_by = old_lab_test.created_by
+    isolate.updated = old_lab_test.updated
+    isolate.updated_by = old_lab_test.updated_by
+    isolate.sensitivities.add(
+        *old_lab_test.sensitive_antibiotics.all()
+    )
+    isolate.resistances.add(
+        *old_lab_test.resistant_antibiotics.all()
+    )
+    isolate.save()
 
 
 @transaction.atomic
 def sync_blood_cultures(patient):
     lab_tests = patient.labtest_set.exclude(lab_test_type__istartswith="up")
-    by_key = defaultdict(list)
     for lab_test in lab_tests:
-        by_key[get_key(lab_test)].append(lab_test)
-
-    for lab_tests in by_key.values():
-        save_blood_culture_isolate(patient, lab_tests)
+        save_blood_culture_isolates(patient, lab_test)
 
 
 class Command(BaseCommand):
     def handle(self, *args, **options):
         for patient in Patient.objects.all():
-            if not patient.bloodcultureisolate_set.exists():
+            if not patient.bloodcultureset_set.exists():
                 sync_blood_cultures(patient)