Dropped age column from patient registration and annotated age in p…

…atient viewset (#1966) * drop field `age` and compute age on demand * Update filters and related usages * add min value validator for year of birth * remove age from test utils * remove unnecessary default * Add field `death_datetime` in patient registration * annotate age in days * suggestion from code review * revert unintended changes * skip serializing age * rebase migrations * rebase migrations * drop age from dummy data * Revert "drop age from dummy data" This reverts commit 9964b85. * drop patient registration's age from dummy data * select only `last_consultation` in custom migration Co-authored-by: Aakash Singh <mail@singhaakash.dev> * format code * rebase migrations * rebase migrations --------- Co-authored-by: Aakash Singh <mail@singhaakash.dev>
ohcnetwork · Apr 2, 2024 · 1115a8f · 1115a8f
1 parent e97177b
commit 1115a8f
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Showing 9 changed files with 177 additions and 89 deletions.
diff --git a/care/facility/admin.py b/care/facility/admin.py
@@ -147,7 +147,7 @@ class AmbulanceDriverAdmin(DjangoQLSearchMixin, admin.ModelAdmin):
 
 
 class PatientAdmin(DjangoQLSearchMixin, admin.ModelAdmin):
-    list_display = ("id", "name", "age", "gender")
+    list_display = ("id", "name", "year_of_birth", "gender")
     djangoql_completion_enabled_by_default = True
 
 

diff --git a/care/facility/api/serializers/patient.py b/care/facility/api/serializers/patient.py
@@ -121,13 +121,12 @@ class Meta:
             "created_by",
             "deleted",
             "ongoing_medication",
-            "year_of_birth",
             "meta_info",
             "countries_travelled_old",
             "allergies",
             "external_id",
         )
-        read_only = TIMESTAMP_FIELDS
+        read_only = TIMESTAMP_FIELDS + ("death_datetime",)
 
 
 class PatientContactDetailsSerializer(serializers.ModelSerializer):
@@ -223,12 +222,16 @@ class Meta:
         model = PatientRegistration
         exclude = (
             "deleted",
-            "year_of_birth",
             "countries_travelled_old",
             "external_id",
         )
         include = ("contacted_patients",)
-        read_only = TIMESTAMP_FIELDS + ("last_edited", "created_by", "is_active")
+        read_only = TIMESTAMP_FIELDS + (
+            "last_edited",
+            "created_by",
+            "is_active",
+            "death_datetime",
+        )
 
     # def get_last_consultation(self, obj):
     #     last_consultation = PatientConsultation.objects.filter(patient=obj).last()
@@ -250,13 +253,15 @@ def validate_countries_travelled(self, value):
 
     def validate(self, attrs):
         validated = super().validate(attrs)
-        if (
-            not self.partial
-            and not validated.get("age")
-            and not validated.get("date_of_birth")
+        if not self.partial and not (
+            validated.get("year_of_birth") or validated.get("date_of_birth")
         ):
             raise serializers.ValidationError(
-                {"non_field_errors": ["Either age or date_of_birth should be passed"]}
+                {
+                    "non_field_errors": [
+                        "Either year_of_birth or date_of_birth should be passed"
+                    ]
+                }
             )
 
         if validated.get("is_vaccinated"):

diff --git a/care/facility/api/viewsets/patient.py b/care/facility/api/viewsets/patient.py
@@ -5,7 +5,18 @@
 from django.conf import settings
 from django.contrib.postgres.search import TrigramSimilarity
 from django.db import models
-from django.db.models import Case, OuterRef, Q, Subquery, When
+from django.db.models import (
+    Case,
+    ExpressionWrapper,
+    F,
+    Func,
+    OuterRef,
+    Q,
+    Subquery,
+    Value,
+    When,
+)
+from django.db.models.functions import Coalesce, ExtractDay, Now
 from django.db.models.query import QuerySet
 from django_filters import rest_framework as filters
 from djqscsv import render_to_csv_response
@@ -333,25 +344,61 @@ class PatientViewSet(
     ]
     permission_classes = (IsAuthenticated, DRYPermissions)
     lookup_field = "external_id"
-    queryset = PatientRegistration.objects.all().select_related(
-        "local_body",
-        "district",
-        "state",
-        "ward",
-        "assigned_to",
-        "facility",
-        "facility__ward",
-        "facility__local_body",
-        "facility__district",
-        "facility__state",
-        # "nearest_facility",
-        # "nearest_facility__local_body",
-        # "nearest_facility__district",
-        # "nearest_facility__state",
-        "last_consultation",
-        "last_consultation__assigned_to",
-        "last_edited",
-        "created_by",
+    queryset = (
+        PatientRegistration.objects.all()
+        .select_related(
+            "local_body",
+            "district",
+            "state",
+            "ward",
+            "assigned_to",
+            "facility",
+            "facility__ward",
+            "facility__local_body",
+            "facility__district",
+            "facility__state",
+            # "nearest_facility",
+            # "nearest_facility__local_body",
+            # "nearest_facility__district",
+            # "nearest_facility__state",
+            "last_consultation",
+            "last_consultation__assigned_to",
+            "last_edited",
+            "created_by",
+        )
+        .annotate(
+            coalesced_dob=Coalesce(
+                "date_of_birth",
+                Func(
+                    F("year_of_birth"),
+                    Value(1),
+                    Value(1),
+                    function="MAKE_DATE",
+                    output_field=models.DateField(),
+                ),
+                output_field=models.DateField(),
+            ),
+            age_end=Case(
+                When(death_datetime__isnull=True, then=Now()),
+                default=F("death_datetime__date"),
+            ),
+        )
+        .annotate(
+            age=Func(
+                Value("year"),
+                Func(
+                    F("age_end"),
+                    F("coalesced_dob"),
+                    function="age",
+                ),
+                function="date_part",
+                output_field=models.IntegerField(),
+            ),
+            age_days=ExpressionWrapper(
+                ExtractDay(F("age_end") - F("coalesced_dob")),
+                output_field=models.IntegerField(),
+            ),
+        )
     )
     ordering_fields = [
         "facility__name",

diff --git a/...rations/0424_remove_patientregistration_age_and_add_patientregistration_death_datetime.py b/...rations/0424_remove_patientregistration_age_and_add_patientregistration_death_datetime.py
@@ -0,0 +1,65 @@
+# Generated by Django 4.2.8 on 2024-03-13 07:03
+
+import django.core.validators
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("facility", "0423_patientconsultation_consent_records_and_more"),
+    ]
+
+    def populate_patientregistration_death_datetime(apps, schema_editor):
+        PatientRegistration = apps.get_model("facility", "PatientRegistration")
+
+        patients = (
+            PatientRegistration.objects.only("last_consultation")
+            .filter(last_consultation__death_datetime__isnull=False)
+            .annotate(new_death_datetime=models.F("last_consultation__death_datetime"))
+        )
+
+        for patient in patients:
+            patient.death_datetime = patient.new_death_datetime
+
+        PatientRegistration.objects.bulk_update(
+            patients, ["death_datetime"], batch_size=1000
+        )
+
+    operations = [
+        migrations.RemoveField(
+            model_name="historicalpatientregistration",
+            name="age",
+        ),
+        migrations.RemoveField(
+            model_name="patientregistration",
+            name="age",
+        ),
+        migrations.AddField(
+            model_name="historicalpatientregistration",
+            name="death_datetime",
+            field=models.DateTimeField(default=None, null=True),
+        ),
+        migrations.AddField(
+            model_name="patientregistration",
+            name="death_datetime",
+            field=models.DateTimeField(default=None, null=True),
+        ),
+        migrations.AlterField(
+            model_name="historicalpatientregistration",
+            name="year_of_birth",
+            field=models.IntegerField(
+                null=True, validators=[django.core.validators.MinValueValidator(1900)]
+            ),
+        ),
+        migrations.AlterField(
+            model_name="patientregistration",
+            name="year_of_birth",
+            field=models.IntegerField(
+                null=True, validators=[django.core.validators.MinValueValidator(1900)]
+            ),
+        ),
+        migrations.RunPython(
+            populate_patientregistration_death_datetime,
+            migrations.RunPython.noop,
+        ),
+    ]
diff --git a/care/facility/models/patient.py b/care/facility/models/patient.py
@@ -1,10 +1,10 @@
-import datetime
 import enum
 
 from django.contrib.postgres.aggregates import ArrayAgg
 from django.core.validators import MaxValueValidator, MinValueValidator
 from django.db import models
 from django.db.models import JSONField
+from django.utils import timezone
 from simple_history.models import HistoricalRecords
 
 from care.abdm.models import AbhaNumber
@@ -109,7 +109,6 @@ class TestTypeEnum(enum.Enum):
     # name_old = EncryptedCharField(max_length=200, default="")
     name = models.CharField(max_length=200, default="")
 
-    age = models.PositiveIntegerField(null=True, blank=True)
     gender = models.IntegerField(choices=GENDER_CHOICES, blank=False)
 
     # phone_number_old = EncryptedCharField(max_length=14, validators=[phone_number_regex], default="")
@@ -128,7 +127,8 @@ class TestTypeEnum(enum.Enum):
     pincode = models.IntegerField(default=0, blank=True, null=True)
 
     date_of_birth = models.DateField(default=None, null=True)
-    year_of_birth = models.IntegerField(default=0, null=True)
+    year_of_birth = models.IntegerField(validators=[MinValueValidator(1900)], null=True)
+    death_datetime = models.DateTimeField(default=None, null=True)
 
     nationality = models.CharField(
         max_length=255, default="", verbose_name="Nationality of Patient"
@@ -426,7 +426,7 @@ class TestTypeEnum(enum.Enum):
     objects = BaseManager()
 
     def __str__(self):
-        return "{} - {} - {}".format(self.name, self.age, self.get_gender_display())
+        return f"{self.name} - {self.year_of_birth} - {self.get_gender_display()}"
 
     @property
     def tele_consultation_history(self):
@@ -458,30 +458,13 @@ def save(self, *args, **kwargs) -> None:
         if self.district is not None:
             self.state = self.district.state
 
-        self.year_of_birth = (
-            self.date_of_birth.year
-            if self.date_of_birth is not None
-            else datetime.datetime.now().year - self.age
-        )
-
-        today = datetime.date.today()
-
         if self.date_of_birth:
-            self.age = (
-                today.year
-                - self.date_of_birth.year
-                - (
-                    (today.month, today.day)
-                    < (self.date_of_birth.month, self.date_of_birth.day)
-                )
-            )
-        elif self.year_of_birth:
-            self.age = today.year - self.year_of_birth
+            self.year_of_birth = self.date_of_birth.year
 
         self.date_of_receipt_of_information = (
             self.date_of_receipt_of_information
             if self.date_of_receipt_of_information is not None
-            else datetime.datetime.now()
+            else timezone.now()
         )
 
         self._alias_recovery_to_recovered()

diff --git a/care/facility/models/patient_consultation.py b/care/facility/models/patient_consultation.py
@@ -286,6 +286,20 @@ def get_related_consultation(self):
     def __str__(self):
         return f"{self.patient.name}<>{self.facility.name}"
 
+    def save(self, *args, **kwargs):
+        """
+        # Removing Patient Hospital Change on Referral
+        if not self.pk or self.referred_to is not None:
+            # pk is None when the consultation is created
+            # referred to is not null when the person is being referred to a new facility
+            self.patient.facility = self.referred_to or self.facility
+            self.patient.save()
+        """
+        if self.death_datetime and self.patient.death_datetime != self.death_datetime:
+            self.patient.death_datetime = self.death_datetime
+            self.patient.save(update_fields=["death_datetime"])
+        super(PatientConsultation, self).save(*args, **kwargs)
+
     class Meta:
         constraints = [
             models.CheckConstraint(

diff --git a/care/facility/models/patient_icmr.py b/care/facility/models/patient_icmr.py
@@ -1,6 +1,7 @@
 import datetime
 
 from dateutil.relativedelta import relativedelta
+from django.utils import timezone
 
 from care.facility.models import (
     DISEASE_CHOICES_MAP,
@@ -45,26 +46,18 @@ class Meta:
     #         instance.__class__ = PatientSampleICMR
     #     return instance
 
+    def get_age_delta(self):
+        start = self.date_of_birth or timezone.datetime(self.year_of_birth, 1, 1).date()
+        end = (self.death_datetime or timezone.now()).date()
+        return relativedelta(end, start)
+
     @property
-    def age_years(self):
-        if self.date_of_birth is not None:
-            age_years = relativedelta(datetime.datetime.now(), self.date_of_birth).years
-        else:
-            age_years = relativedelta(
-                datetime.datetime.now(),
-                datetime.datetime(year=self.year_of_birth, month=1, day=1),
-            ).years
-        return age_years
+    def age_years(self) -> int:
+        return self.get_age_delta().year
 
     @property
-    def age_months(self):
-        if self.date_of_birth is None or self.year_of_birth is None:
-            age_months = 0
-        else:
-            age_months = relativedelta(
-                datetime.datetime.now(), self.date_of_birth
-            ).months
-        return age_months
+    def age_months(self) -> int:
+        return self.get_age_delta().months
 
     @property
     def email(self):

diff --git a/care/utils/tests/test_utils.py b/care/utils/tests/test_utils.py
@@ -238,7 +238,6 @@ def create_facility(
     def get_patient_data(cls, district, state) -> dict:
         return {
             "name": "Foo",
-            "age": 32,
             "date_of_birth": date(1992, 4, 1),
             "gender": 2,
             "is_medical_worker": True,