meta-edc 1.0.3__py3-none-any.whl → 1.0.5__py3-none-any.whl

meta_subject/models/__init__.py

@@ -1,6 +1,7 @@
 from .birth_outcomes import BirthOutcomes
 from .blood_results import (
     BloodResultsFbc,
+    BloodResultsGluDummy,
     BloodResultsHba1c,
     BloodResultsIns,
     BloodResultsLft,
@@ -28,6 +29,7 @@ from .hepatitis_test import HepatitisTest
 from .malaria_test import MalariaTest
 from .medication_adherence import MedicationAdherence
 from .mnsi import Mnsi
+from .next_appointment import NextAppointment
 from .other_arv_regimens import OtherArvRegimens
 from .other_arv_regimens_detail import OtherArvRegimensDetail
 from .patient_history import PatientHistory

meta_subject/models/blood_results/__init__.py

@@ -1,4 +1,5 @@
 from .blood_results_fbc import BloodResultsFbc
+from .blood_results_glu import BloodResultsGluDummy
 from .blood_results_hba1c import BloodResultsHba1c
 from .blood_results_ins import BloodResultsIns
 from .blood_results_lft import BloodResultsLft

meta_subject/models/blood_results/blood_results_glu.py

@@ -0,0 +1,29 @@
+from django.db import models
+from edc_lab.model_mixins import CrfWithRequisitionModelMixin, requisition_fk_options
+from edc_lab_panel.panels import blood_glucose_panel
+from edc_lab_results import BLOOD_RESULTS_GLU_ACTION
+from edc_lab_results.model_mixins import BloodResultsModelMixin, GlucoseModelMixin
+from edc_model.models import BaseUuidModel
+
+from ...model_mixins import CrfWithActionModelMixin
+
+
+# TODO: this is a IFG!!
+class BloodResultsGluDummy(
+    CrfWithActionModelMixin,
+    GlucoseModelMixin,
+    CrfWithRequisitionModelMixin,
+    BloodResultsModelMixin,
+    BaseUuidModel,
+):
+    action_name = BLOOD_RESULTS_GLU_ACTION
+    tracking_identifier_prefix = "GL"
+    lab_panel = blood_glucose_panel
+
+    requisition = models.ForeignKey(
+        limit_choices_to={"panel__name": blood_glucose_panel.name}, **requisition_fk_options
+    )
+
+    class Meta(CrfWithActionModelMixin.Meta, BaseUuidModel.Meta):
+        verbose_name = "Blood Result: Glucose (DUMMY)"
+        verbose_name_plural = "Blood Results: Glucose (DUMMY)"

meta_subject/models/next_appointment.py

@@ -0,0 +1,16 @@
+from __future__ import annotations
+
+from edc_appointment.model_mixins import NextAppointmentCrfModelMixin
+from edc_model.models import BaseUuidModel
+
+from ..model_mixins import CrfModelMixin
+
+__all__ = ["NextAppointment"]
+
+
+class NextAppointment(NextAppointmentCrfModelMixin, CrfModelMixin, BaseUuidModel):
+
+    class Meta(CrfModelMixin.Meta, BaseUuidModel.Meta):
+        verbose_name = "Next Appointment"
+        verbose_name_plural = "Next Appointments"
+        indexes = CrfModelMixin.Meta.indexes + BaseUuidModel.Meta.indexes

meta_subject/tests/tests/test_next_appointment.py

@@ -0,0 +1,231 @@
+from datetime import datetime
+from zoneinfo import ZoneInfo
+
+import time_machine
+from dateutil.relativedelta import relativedelta
+from django.core.exceptions import ValidationError
+from django.test import TestCase, tag
+from edc_appointment.exceptions import AppointmentWindowError
+from edc_constants.constants import CLINIC
+from edc_facility.models import HealthFacilityTypes
+from edc_facility.utils import get_health_facility_model, get_health_facility_model_cls
+from edc_metadata.metadata_handler import MetadataHandlerError
+from edc_sites.utils import get_site_model_cls
+from edc_visit_schedule.models import VisitSchedule
+
+from meta_screening.tests.meta_test_case_mixin import MetaTestCaseMixin
+from meta_screening.tests.options import now
+from meta_subject.models import NextAppointment
+
+
+@time_machine.travel(datetime(2019, 6, 11, 8, 00, tzinfo=ZoneInfo("UTC")))
+class TestNextAppointment(MetaTestCaseMixin, TestCase):
+
+    def setUp(self):
+        super().setUp()
+        self.update_health_facility_model()
+        self.subject_visit = self.get_subject_visit(appt_datetime=now)
+
+    def update_health_facility_model(self):
+        from edc_sites.site import sites as site_sites
+
+        clinic = HealthFacilityTypes.objects.get(name=CLINIC)
+        for site_obj in get_site_model_cls().objects.all():
+            single_site = site_sites.get(site_obj.id)
+            get_health_facility_model_cls().objects.create(
+                name=single_site.name,
+                title=single_site.title,
+                health_facility_type=clinic,
+                mon=True,
+                tue=True,
+                wed=True,
+                thu=True,
+                fri=True,
+                sat=False,
+                sun=False,
+                site_id=site_obj.id,
+            )
+
+    @tag("6")
+    def test_in_visit_crfs(self):
+        dt = self.subject_visit.report_datetime.date() + relativedelta(days=10)
+        for i in range(1, 7):
+            dt = dt + relativedelta(days=1)
+            if dt.weekday() < 6:
+                break
+
+        try:
+            NextAppointment.objects.create(
+                subject_visit=self.subject_visit,
+                report_datetime=self.subject_visit.report_datetime,
+                appt_date=dt,
+                health_facility=get_health_facility_model_cls().objects.all()[0],
+            )
+        except MetadataHandlerError as e:
+            self.fail(f"Unexpected MetadataHandlerError. Got {e}")
+
+    @tag("6")
+    def test_validates_clinic_day(self):
+        dt = self.subject_visit.report_datetime.date() + relativedelta(days=10)
+        for i in range(1, 7):
+            dt = dt + relativedelta(days=1)
+            if dt.weekday() > 5:
+                break
+        with self.assertRaises(ValidationError) as cm:
+            NextAppointment.objects.create(
+                subject_visit=self.subject_visit,
+                report_datetime=self.subject_visit.report_datetime,
+                appt_date=dt,
+                health_facility=get_health_facility_model_cls().objects.all()[0],
+            )
+        self.assertIn("Expected Mon-Fri", str(cm.exception))
+
+    @tag("6")
+    def test_appt_date_on_report_date_raises(self):
+        with self.assertRaises(ValidationError) as cm:
+            NextAppointment.objects.create(
+                subject_visit=self.subject_visit,
+                report_datetime=self.subject_visit.report_datetime,
+                appt_date=self.subject_visit.report_datetime.date(),
+                health_facility=get_health_facility_model_cls().objects.all()[0],
+            )
+        self.assertIn(
+            "Cannot be equal to the report datetime",
+            str(cm.exception),
+        )
+
+    # @tag("6")
+    # def test_next_appt_date_required(self):
+    #     next_appt = self.subject_visit.appointment.next
+    #     with self.assertRaises(NextAppointmentModelError) as cm:
+    #         NextAppointment.objects.create(
+    #             subject_visit=self.subject_visit,
+    #             report_datetime=self.subject_visit.report_datetime,
+    #             health_facility=get_health_facility_model_cls().objects.all()[0],
+    #             visitschedule=VisitSchedule.objects.get(
+    #                 visit_schedule_name=self.subject_visit.visit_schedule.name,
+    #                 timepoint=next_appt.timepoint,
+    #             ),
+    #         )
+    #     self.assertIn(
+    #         "Appointment date or datetime is required",
+    #         str(cm.exception),
+    #     )
+
+    @tag("6")
+    def test_nextappt_appt_date_updates_nextappt_appt_datetime(self):
+        next_appt = self.subject_visit.appointment.next
+        original_next_appt_datetime = self.subject_visit.appointment.next.appt_datetime
+        obj = NextAppointment.objects.create(
+            appt_date=original_next_appt_datetime.date(),
+            subject_visit=self.subject_visit,
+            report_datetime=self.subject_visit.report_datetime,
+            health_facility=get_health_facility_model_cls().objects.all()[0],
+            visitschedule=VisitSchedule.objects.get(
+                visit_schedule_name=self.subject_visit.visit_schedule.name,
+                timepoint=next_appt.timepoint,
+            ),
+        )
+        self.assertIsNotNone(obj.appt_datetime)
+
+    # @tag("6")
+    # def test_nextappt_appt_datetime_updates_nextappt_appt_date(self):
+    #     next_appt = self.subject_visit.appointment.next
+    #     original_next_appt_datetime = self.subject_visit.appointment.next.appt_datetime
+    #     obj = NextAppointment.objects.create(
+    #         appt_datetime=original_next_appt_datetime,
+    #         subject_visit=self.subject_visit,
+    #         report_datetime=self.subject_visit.report_datetime,
+    #         health_facility=get_health_facility_model_cls().objects.all()[0],
+    #         visitschedule=VisitSchedule.objects.get(
+    #             visit_schedule_name=self.subject_visit.visit_schedule.name,
+    #             timepoint=next_appt.timepoint,
+    #         ),
+    #     )
+    #     self.assertIsNotNone(obj.appt_date)
+
+    @tag("6")
+    def test_next_appt_date_same_as_original_next_appt(self):
+        get_health_facility_model()
+        next_appt = self.subject_visit.appointment.next
+        obj = NextAppointment.objects.create(
+            subject_visit=self.subject_visit,
+            report_datetime=self.subject_visit.report_datetime,
+            appt_date=next_appt.appt_datetime.date(),
+            health_facility=get_health_facility_model_cls().objects.all()[0],
+            visitschedule=VisitSchedule.objects.get(
+                visit_schedule_name=self.subject_visit.visit_schedule.name,
+                timepoint=next_appt.timepoint,
+            ),
+        )
+        next_appt.refresh_from_db()
+        self.assertEqual(next_appt.appt_datetime, obj.appt_datetime)
+
+    @tag("6")
+    def test_updates_next_appointment_datetime(self):
+        next_appt = self.subject_visit.appointment.next
+        original_next_appt_datetime = self.subject_visit.appointment.next.appt_datetime
+        obj = NextAppointment.objects.create(
+            subject_visit=self.subject_visit,
+            report_datetime=self.subject_visit.report_datetime,
+            appt_date=original_next_appt_datetime.date() + relativedelta(days=1),
+            health_facility=get_health_facility_model_cls().objects.all()[0],
+            visitschedule=VisitSchedule.objects.get(
+                visit_schedule_name=self.subject_visit.visit_schedule.name,
+                timepoint=next_appt.timepoint,
+            ),
+        )
+        next_appt.refresh_from_db()
+        self.assertEqual(next_appt.appt_datetime, obj.appt_datetime)
+
+    @tag("6")
+    def test_raises_if_next_appointment_datetime_is_before_current(self):
+        next_appt = self.subject_visit.appointment.next
+        current_appt_datetime = self.subject_visit.appointment.appt_datetime
+        self.assertRaises(
+            ValidationError,
+            NextAppointment.objects.create,
+            subject_visit=self.subject_visit,
+            report_datetime=self.subject_visit.report_datetime,
+            appt_date=current_appt_datetime.date(),
+            health_facility=get_health_facility_model_cls().objects.all()[0],
+            visitschedule=VisitSchedule.objects.get(
+                visit_schedule_name=self.subject_visit.visit_schedule.name,
+                timepoint=next_appt.timepoint,
+            ),
+        )
+
+    @tag("6")
+    def test_raises_on_appt_date_outside_of_window_for_selected_visit_code(self):
+        next_appt = self.subject_visit.appointment.next
+        bad_next_date = self.subject_visit.report_datetime.date() + relativedelta(days=1)
+        self.assertRaises(
+            AppointmentWindowError,
+            NextAppointment.objects.create,
+            subject_visit=self.subject_visit,
+            report_datetime=self.subject_visit.report_datetime,
+            appt_date=bad_next_date,
+            health_facility=get_health_facility_model_cls().objects.all()[0],
+            visitschedule=VisitSchedule.objects.get(
+                visit_schedule_name=self.subject_visit.visit_schedule.name,
+                timepoint=next_appt.timepoint,
+            ),
+        )
+
+    @tag("6")
+    def test_next_is_interim_or_unscheduled(self):
+        dt = self.subject_visit.report_datetime.date() + relativedelta(days=10)
+        for i in range(1, 7):
+            dt = dt + relativedelta(days=1)
+            if dt.weekday() < 6:
+                break
+        NextAppointment.objects.create(
+            subject_visit=self.subject_visit,
+            report_datetime=self.subject_visit.report_datetime,
+            appt_date=dt,
+            health_facility=get_health_facility_model_cls().objects.all()[0],
+            visitschedule=VisitSchedule.objects.get(
+                visit_schedule_name=self.subject_visit.visit_schedule.name,
+                timepoint=self.subject_visit.appointment.timepoint,
+            ),
+        )

meta_visit_schedule/visit_schedules/phase_three/crfs.py

@@ -48,6 +48,7 @@ crfs_d1 = CrfCollection(
     Crf(show_order=360, model="meta_subject.malariatest"),
     Crf(show_order=370, model="meta_subject.urinedipsticktest"),
     Crf(show_order=400, model="meta_subject.studymedication"),
+    Crf(show_order=600, model="meta_subject.nextappointment", required=False),
     name="day1",
 )
 
@@ -61,6 +62,7 @@ crfs_w2 = CrfCollection(
     Crf(show_order=460, model="meta_subject.eq5d3l"),
     Crf(show_order=465, model="meta_subject.sf12"),
     Crf(show_order=480, model="meta_subject.healtheconomicssimple"),
+    Crf(show_order=600, model="meta_subject.nextappointment", required=False),
     name="week2",
 )
 
@@ -75,6 +77,7 @@ crfs_1m = CrfCollection(
     Crf(show_order=465, model="meta_subject.sf12", required=False),
     Crf(show_order=470, model="meta_subject.mnsi"),
     Crf(show_order=480, model="meta_subject.healtheconomicssimple", required=False),
+    Crf(show_order=600, model="meta_subject.nextappointment", required=False),
     name="1m",
 )
 
@@ -91,6 +94,7 @@ crfs_3m = CrfCollection(
     Crf(show_order=465, model="meta_subject.sf12", required=False),
     Crf(show_order=470, model="meta_subject.mnsi", required=False),
     Crf(show_order=500, model="meta_subject.healtheconomicsupdate"),
+    Crf(show_order=600, model="meta_subject.nextappointment", required=False),
     name="3m",
 )
 
@@ -108,6 +112,7 @@ crfs_6m = CrfCollection(
     Crf(show_order=465, model="meta_subject.sf12", required=False),
     Crf(show_order=470, model="meta_subject.mnsi", required=False),
     Crf(show_order=500, model="meta_subject.healtheconomicsupdate", required=False),
+    Crf(show_order=600, model="meta_subject.nextappointment", required=False),
     name="6m",
 )
 
@@ -121,6 +126,7 @@ crfs_9m = CrfCollection(
     Crf(show_order=460, model="meta_subject.eq5d3l", required=False),
     Crf(show_order=465, model="meta_subject.sf12", required=False),
     Crf(show_order=500, model="meta_subject.healtheconomicsupdate", required=False),
+    Crf(show_order=600, model="meta_subject.nextappointment", required=False),
     name="9m",
 )
 
@@ -138,6 +144,7 @@ crfs_12m = CrfCollection(
     Crf(show_order=460, model="meta_subject.eq5d3l", required=False),
     Crf(show_order=465, model="meta_subject.sf12", required=False),
     Crf(show_order=500, model="meta_subject.healtheconomicsupdate", required=False),
+    Crf(show_order=600, model="meta_subject.nextappointment", required=False),
     name="12m",
 )
 
@@ -151,6 +158,7 @@ crfs_15m = CrfCollection(
     Crf(show_order=460, model="meta_subject.eq5d3l", required=False),
     Crf(show_order=465, model="meta_subject.sf12", required=False),
     Crf(show_order=500, model="meta_subject.healtheconomicsupdate", required=False),
+    Crf(show_order=600, model="meta_subject.nextappointment", required=False),
     name="15m",
 )
 
@@ -165,6 +173,7 @@ crfs_18m = CrfCollection(
     Crf(show_order=460, model="meta_subject.eq5d3l", required=False),
     Crf(show_order=465, model="meta_subject.sf12", required=False),
     Crf(show_order=500, model="meta_subject.healtheconomicsupdate", required=False),
+    Crf(show_order=600, model="meta_subject.nextappointment", required=False),
     name="18m",
 )
 
@@ -178,6 +187,7 @@ crfs_21m = CrfCollection(
     Crf(show_order=460, model="meta_subject.eq5d3l", required=False),
     Crf(show_order=465, model="meta_subject.sf12", required=False),
     Crf(show_order=500, model="meta_subject.healtheconomicsupdate", required=False),
+    Crf(show_order=600, model="meta_subject.nextappointment", required=False),
     name="21m",
 )
 
@@ -189,13 +199,14 @@ crfs_24m = CrfCollection(
     Crf(show_order=220, model="meta_subject.bloodresultsrft"),
     Crf(show_order=230, model="meta_subject.bloodresultslft"),
     Crf(show_order=240, model="meta_subject.bloodresultsfbc"),
-    Crf(show_order=250, model="meta_subject.bloodresultslipids"),
+    # Crf(show_order=250, model="meta_subject.bloodresultslipids"),
     Crf(show_order=300, model="meta_subject.studymedication"),
     Crf(show_order=310, model="meta_subject.medicationadherence"),
     Crf(show_order=460, model="meta_subject.eq5d3l", required=False),
     Crf(show_order=465, model="meta_subject.sf12", required=False),
     Crf(show_order=470, model="meta_subject.mnsi"),
     Crf(show_order=500, model="meta_subject.healtheconomicsupdate", required=False),
+    Crf(show_order=600, model="meta_subject.nextappointment", required=False),
     name="24m",
 )
 
@@ -209,6 +220,7 @@ crfs_27m = CrfCollection(
     Crf(show_order=465, model="meta_subject.sf12", required=False),
     Crf(show_order=470, model="meta_subject.mnsi", required=False),
     Crf(show_order=500, model="meta_subject.healtheconomicsupdate", required=False),
+    Crf(show_order=600, model="meta_subject.nextappointment", required=False),
     name="27m",
 )
 
@@ -223,6 +235,7 @@ crfs_30m = CrfCollection(
     Crf(show_order=465, model="meta_subject.sf12", required=False),
     Crf(show_order=470, model="meta_subject.mnsi", required=False),
     Crf(show_order=500, model="meta_subject.healtheconomicsupdate", required=False),
+    Crf(show_order=600, model="meta_subject.nextappointment", required=False),
     name="30m",
 )
 
@@ -236,6 +249,7 @@ crfs_33m = CrfCollection(
     Crf(show_order=465, model="meta_subject.sf12", required=False),
     Crf(show_order=470, model="meta_subject.mnsi", required=False),
     Crf(show_order=500, model="meta_subject.healtheconomicsupdate", required=False),
+    Crf(show_order=600, model="meta_subject.nextappointment", required=False),
     name="33m",
 )
 
@@ -254,6 +268,7 @@ crfs_36m = CrfCollection(
     Crf(show_order=465, model="meta_subject.sf12"),
     Crf(show_order=470, model="meta_subject.mnsi"),
     Crf(show_order=500, model="meta_subject.healtheconomicsupdate", required=False),
+    Crf(show_order=600, model="meta_subject.nextappointment", required=False),
     name="36m",
 )
 
@@ -267,6 +282,7 @@ crfs_39m = CrfCollection(
     Crf(show_order=465, model="meta_subject.sf12", required=False),
     Crf(show_order=470, model="meta_subject.mnsi", required=False),
     Crf(show_order=500, model="meta_subject.healtheconomicsupdate", required=False),
+    Crf(show_order=600, model="meta_subject.nextappointment", required=False),
     name="39m",
 )
 
@@ -281,6 +297,7 @@ crfs_42m = CrfCollection(
     Crf(show_order=465, model="meta_subject.sf12", required=False),
     Crf(show_order=470, model="meta_subject.mnsi", required=False),
     Crf(show_order=500, model="meta_subject.healtheconomicsupdate", required=False),
+    Crf(show_order=600, model="meta_subject.nextappointment", required=False),
     name="42m",
 )
 
@@ -294,6 +311,7 @@ crfs_45m = CrfCollection(
     Crf(show_order=465, model="meta_subject.sf12", required=False),
     Crf(show_order=470, model="meta_subject.mnsi", required=False),
     Crf(show_order=500, model="meta_subject.healtheconomicsupdate", required=False),
+    Crf(show_order=600, model="meta_subject.nextappointment", required=False),
     name="45m",
 )
 
@@ -312,5 +330,6 @@ crfs_48m = CrfCollection(
     Crf(show_order=465, model="meta_subject.sf12"),
     Crf(show_order=470, model="meta_subject.mnsi"),
     Crf(show_order=500, model="meta_subject.healtheconomicsupdate", required=False),
+    Crf(show_order=600, model="meta_subject.nextappointment", required=False),
     name="48m",
 )

meta_visit_schedule/visit_schedules/phase_three/schedule_pregnancy.py

@@ -28,7 +28,7 @@ visit = Visit(
     timepoint=200,
     rbase=relativedelta(days=0),
     rlower=relativedelta(days=0),
-    rupper=relativedelta(months=12),
+    rupper=relativedelta(months=24),
     crfs=crfs_pregnancy,
     crfs_prn=crfs_prn or default_crfs_prn,
     crfs_missed=crfs_missed,