remove consent_version from object create

erikvw · erikvw · commit 50626404607d · 2023-07-31T23:23:20.000-05:00
diff --git a/edc_egfr/egfr.py b/edc_egfr/egfr.py
@@ -2,7 +2,7 @@
 
 from datetime import date, datetime
 from decimal import Decimal
-from typing import Any, Optional
+from typing import TYPE_CHECKING, Any, Optional
 from zoneinfo import ZoneInfo
 
 from dateutil.relativedelta import relativedelta
@@ -16,6 +16,9 @@
 from .calculators import EgfrCkdEpi, EgfrCockcroftGault, egfr_percent_change
 from .get_drop_notification_model import get_egfr_drop_notification_model_cls
 
+if TYPE_CHECKING:
+    from edc_visit_tracking.typing_stubs import RelatedVisitProtocol
+
 
 class EgfrError(Exception):
     pass
@@ -40,7 +43,7 @@ def __init__(
         percent_drop_threshold: Decimal | float | None = None,
         reference_range_collection_name: str | None = None,
         calling_crf: Any | None = None,
-        subject_visit: Any | None = None,
+        related_visit: RelatedVisitProtocol | None = None,
         assay_datetime: datetime | None = None,
         egfr_drop_notification_model: str | None = None,
     ):
@@ -49,7 +52,7 @@ def __init__(
         self._egfr_drop_value: Decimal | None = None
         self._egfr_drop_grade = None
         self.assay_date: date | None = None
-        self.subject_visit = None
+        self.related_visit = None
 
         self.baseline_egfr_value = baseline_egfr_value
         if formula_name not in self.calculators:
@@ -88,14 +91,14 @@ def __init__(
             self.creatinine_units = calling_crf.creatinine_units
             self.creatinine_value = calling_crf.creatinine_value
             self.percent_drop_threshold = calling_crf.percent_drop_threshold
-            self.subject_visit = calling_crf.subject_visit
+            self.related_visit = calling_crf.related_visit
             self.report_datetime = calling_crf.report_datetime
             self.assay_date = calling_crf.assay_datetime.astimezone(ZoneInfo("UTC")).date()
         else:
             self.creatinine_units = creatinine_units
             self.creatinine_value = creatinine_value
             self.percent_drop_threshold = percent_drop_threshold
-            self.subject_visit = subject_visit
+            self.related_visit = related_visit
             self.report_datetime = report_datetime
             if assay_datetime:
                 self.assay_date = assay_datetime.astimezone(ZoneInfo("UTC")).date()
@@ -191,11 +194,11 @@ def create_or_update_egfr_drop_notification(self):
         with transaction.atomic():
             try:
                 obj = self.egfr_drop_notification_model_cls.objects.get(
-                    subject_visit__id=self.subject_visit.id
+                    subject_visit__id=self.related_visit.id
                 )
             except ObjectDoesNotExist:
                 obj = self.egfr_drop_notification_model_cls.objects.create(
-                    subject_visit_id=self.subject_visit.id,
+                    subject_visit_id=self.related_visit.id,
                     report_datetime=self.report_datetime,
                     egfr_value=self.egfr_value,
                     creatinine_date=self.assay_date,
@@ -204,8 +207,7 @@ def create_or_update_egfr_drop_notification(self):
                     weight=self.get_weight_in_kgs(),
                     egfr_percent_change=self.egfr_drop_value,
                     report_status=NEW,
-                    consent_version=self.subject_visit.consent_version,
-                    site_id=self.subject_visit.site.id,
+                    site_id=self.related_visit.site.id,
                 )
             else:
                 obj.egfr_value = self.egfr_value
diff --git a/edc_egfr/tests/tests/test_drop_notification.py b/edc_egfr/tests/tests/test_drop_notification.py
@@ -1,28 +1,39 @@
 from dateutil.relativedelta import relativedelta
 from django.test import TestCase, override_settings
+from edc_appointment.constants import SCHEDULED_APPT
+from edc_appointment.models import Appointment
 from edc_constants.constants import BLACK, CLOSED, COMPLETE, INCOMPLETE, MALE, OPEN
 from edc_lab import site_labs
 from edc_lab.models import Panel
 from edc_lab_panel.panels import rft_panel
+from edc_reference import site_reference_configs
 from edc_registration.models import RegisteredSubject
 from edc_reportable import MICROMOLES_PER_LITER, site_reportables
 from edc_reportable.grading_data.daids_july_2017 import grading_data
 from edc_reportable.normal_data.africa import normal_data
 from edc_utils import get_utcnow
+from edc_visit_schedule import site_visit_schedules
+from edc_visit_schedule.constants import DAY1
+from edc_visit_tracking.constants import SCHEDULED
 
 from edc_egfr.egfr import Egfr
 from egfr_app.lab_profiles import lab_profile
 from egfr_app.models import (
-    Appointment,
     EgfrDropNotification,
     ResultCrf,
     SubjectRequisition,
     SubjectVisit,
 )
+from egfr_app.visit_schedules import visit_schedule
 
 
 class TestEgfr(TestCase):
     def setUp(self) -> None:
+        site_visit_schedules._registry = {}
+        site_visit_schedules.register(visit_schedule)
+        site_reference_configs.register_from_visit_schedule(
+            visit_models={"edc_appointment.appointment": "edc_visit_tracking.subjectvisit"}
+        )
         RegisteredSubject.objects.create(
             subject_identifier="1234",
             gender=MALE,
@@ -33,11 +44,21 @@ def setUp(self) -> None:
             subject_identifier="1234",
             appt_datetime=get_utcnow(),
             timepoint=0,
+            visit_code=DAY1,
+            visit_code_sequence=0,
+            visit_schedule_name="visit_schedule",
+            schedule_name="schedule",
+            appt_reason=SCHEDULED_APPT,
         )
         self.subject_visit = SubjectVisit.objects.create(
             subject_identifier="1234",
             appointment=appointment,
             report_datetime=appointment.appt_datetime,
+            visit_code=DAY1,
+            visit_code_sequence=0,
+            visit_schedule_name="visit_schedule",
+            schedule_name="schedule",
+            reason=SCHEDULED,
         )
 
         panel = Panel.objects.get(name=rft_panel.name)
diff --git a/edc_egfr/tests/tests/test_egfr.py b/edc_egfr/tests/tests/test_egfr.py
@@ -1,9 +1,12 @@
+from _decimal import Decimal
 from dateutil.relativedelta import relativedelta
 from django.test import TestCase, override_settings
+from edc_appointment.models import Appointment
 from edc_constants.constants import BLACK, MALE
 from edc_lab import site_labs
 from edc_lab.models import Panel
 from edc_lab_panel.panels import rft_panel
+from edc_reference import site_reference_configs
 from edc_registration.models import RegisteredSubject
 from edc_reportable import (
     MICROMOLES_PER_LITER,
@@ -14,21 +17,24 @@
 from edc_reportable.normal_data.africa import normal_data
 from edc_utils import get_utcnow
 from edc_utils.round_up import round_half_away_from_zero
+from edc_visit_schedule import site_visit_schedules
+from edc_visit_tracking.constants import SCHEDULED
+from edc_visit_tracking.models import SubjectVisit
 
 from edc_egfr.calculators import EgfrCalculatorError
 from edc_egfr.egfr import Egfr, EgfrError
 from egfr_app.lab_profiles import lab_profile
-from egfr_app.models import (
-    Appointment,
-    EgfrDropNotification,
-    ResultCrf,
-    SubjectRequisition,
-    SubjectVisit,
-)
+from egfr_app.models import EgfrDropNotification, ResultCrf, SubjectRequisition
+from egfr_app.visit_schedules import visit_schedule
 
 
 class TestEgfr(TestCase):
     def setUp(self) -> None:
+        site_visit_schedules._registry = {}
+        site_visit_schedules.register(visit_schedule)
+        site_reference_configs.register_from_visit_schedule(
+            visit_models={"edc_appointment.appointment": "edc_visit_tracking.subjectvisit"}
+        )
         RegisteredSubject.objects.create(
             subject_identifier="1234",
             gender=MALE,
@@ -187,12 +193,21 @@ def test_egfr_drop_with_notify(self):
         appointment = Appointment.objects.create(
             subject_identifier="1234",
             appt_datetime=get_utcnow(),
-            timepoint=0,
+            visit_code="1000",
+            visit_code_sequence=0,
+            timepoint=Decimal("0.0"),
+            schedule_name="schedule",
+            visit_schedule_name="visit_schedule",
         )
         subject_visit = SubjectVisit.objects.create(
             subject_identifier="1234",
             appointment=appointment,
             report_datetime=appointment.appt_datetime,
+            visit_code="1000",
+            visit_code_sequence=0,
+            reason=SCHEDULED,
+            schedule_name="schedule",
+            visit_schedule_name="visit_schedule",
         )
 
         panel = Panel.objects.get(name=rft_panel.name)
diff --git a/egfr_app/models.py b/egfr_app/models.py
@@ -9,6 +9,7 @@
 from edc_screening.model_mixins import ScreeningIdentifierModelMixin
 from edc_sites.models import SiteModelMixin
 from edc_utils import get_utcnow
+from edc_visit_tracking.models import SubjectVisit
 
 from edc_egfr.model_mixins import EgfrDropNotificationModelMixin, EgfrModelMixin
 
@@ -33,47 +34,6 @@ class SubjectScreening(ScreeningIdentifierModelMixin, BaseUuidModel):
     )
 
 
-class Appointment(BaseUuidModel):
-    subject_identifier = models.CharField(max_length=25, null=True)
-
-    appt_datetime = models.DateTimeField(
-        verbose_name="Appointment date and time", db_index=True
-    )
-
-    timepoint = models.IntegerField(default=0)
-
-    visit_code_sequence = models.IntegerField(default=0)
-
-    visit_schedule_name = models.CharField(max_length=25, default="visit_schedule")
-
-    schedule_name = models.CharField(max_length=25, default="schedule")
-
-    class Meta(BaseUuidModel.Meta):
-        pass
-
-
-class SubjectVisit(SiteModelMixin, BaseUuidModel):
-    appointment = models.OneToOneField(
-        Appointment,
-        on_delete=PROTECT,
-    )
-
-    subject_identifier = models.CharField(max_length=25, null=True)
-
-    consent_version = models.CharField(max_length=5, default="1")
-
-    report_datetime = models.DateTimeField()
-
-    visit_code_sequence = models.IntegerField(default=0)
-
-    visit_schedule_name = models.CharField(max_length=25, default="visit_schedule")
-
-    schedule_name = models.CharField(max_length=25, default="schedule")
-
-    class Meta(BaseUuidModel.Meta):
-        app_label = "egfr_app"
-
-
 class SubjectRequisition(PanelModelMixin, BaseUuidModel):
     subject_visit = models.ForeignKey(SubjectVisit, on_delete=PROTECT)
 
diff --git a/egfr_app/visit_schedules.py b/egfr_app/visit_schedules.py
@@ -0,0 +1,67 @@
+from dateutil.relativedelta import relativedelta
+from edc_visit_schedule.schedule import Schedule
+from edc_visit_schedule.visit import Crf, FormsCollection, Visit
+from edc_visit_schedule.visit_schedule import VisitSchedule
+
+crfs = FormsCollection(Crf(show_order=1, model="egfr_app.ResultCrf", required=True))
+
+visit0 = Visit(
+    code="1000",
+    title="Day 1",
+    timepoint=0,
+    rbase=relativedelta(days=0),
+    rlower=relativedelta(days=0),
+    rupper=relativedelta(days=6),
+    crfs=crfs,
+)
+
+visit1 = Visit(
+    code="2000",
+    title="Day 2",
+    timepoint=1,
+    rbase=relativedelta(days=1),
+    rlower=relativedelta(days=0),
+    rupper=relativedelta(days=6),
+    crfs=crfs,
+)
+
+visit2 = Visit(
+    code="3000",
+    title="Day 3",
+    timepoint=2,
+    rbase=relativedelta(days=2),
+    rlower=relativedelta(days=0),
+    rupper=relativedelta(days=6),
+    crfs=crfs,
+)
+
+visit3 = Visit(
+    code="4000",
+    title="Day 4",
+    timepoint=3,
+    rbase=relativedelta(days=3),
+    rlower=relativedelta(days=0),
+    rupper=relativedelta(days=6),
+    crfs=crfs,
+)
+
+schedule = Schedule(
+    name="schedule",
+    onschedule_model="visit_schedule_app.onschedule",
+    offschedule_model="visit_schedule_app.offschedule",
+    appointment_model="edc_appointment.appointment",
+    consent_model="visit_schedule_app.subjectconsent",
+)
+
+schedule.add_visit(visit0)
+schedule.add_visit(visit1)
+schedule.add_visit(visit2)
+schedule.add_visit(visit3)
+
+visit_schedule = VisitSchedule(
+    name="visit_schedule",
+    offstudy_model="visit_schedule_app.subjectoffstudy",
+    death_report_model="visit_schedule_app.deathreport",
+)
+
+visit_schedule.add_schedule(schedule)
diff --git a/runtests.py b/runtests.py
@@ -17,6 +17,7 @@
     BASE_DIR=base_dir,
     APP_NAME=app_name,
     ETC_DIR=os.path.join(base_dir, app_name, "tests", "etc"),
+    SUBJECT_VISIT_MODEL="edc_visit_tracking.subjectvisit",
     INSTALLED_APPS=[
         "django.contrib.admin",
         "django.contrib.auth",
@@ -27,17 +28,20 @@
         "django.contrib.sites",
         "django_crypto_fields.apps.AppConfig",
         "edc_appointment.apps.AppConfig",
-        # "edc_auth.apps.AppConfig",
+        "edc_metadata.apps.AppConfig",
         "edc_action_item.apps.AppConfig",
         "edc_lab.apps.AppConfig",
         "edc_lab_results.apps.AppConfig",
+        "edc_reference.apps.AppConfig",
         "edc_registration.apps.AppConfig",
         "edc_sites.apps.AppConfig",
         "edc_notification.apps.AppConfig",
         "edc_protocol.apps.AppConfig",
         "edc_reportable.apps.AppConfig",
+        "edc_visit_tracking.apps.AppConfig",
         "edc_visit_schedule.apps.AppConfig",
         "edc_timepoint.apps.AppConfig",
+        "visit_schedule_app.apps.AppConfig",
         "edc_egfr.apps.AppConfig",
         "egfr_app.apps.AppConfig",
     ],
