meta-edc 0.3.39__py3-none-any.whl → 1.4.0__py3-none-any.whl

meta_subject/tests/tests/test_egfr.py

@@ -1,234 +0,0 @@
-from __future__ import annotations
-
-from copy import deepcopy
-from datetime import datetime
-from decimal import Decimal
-from zoneinfo import ZoneInfo
-
-import time_machine
-from django import forms
-from django.conf import settings
-from django.contrib.sites.models import Site
-from django.test import TestCase
-from edc_action_item import site_action_items
-from edc_action_item.models import ActionItem
-from edc_constants.constants import BLACK, MALE
-from edc_egfr.calculators import egfr_percent_change
-from edc_lab.models import Panel
-from edc_lab_results import BLOOD_RESULTS_EGFR_ACTION, BLOOD_RESULTS_RFT_ACTION
-from edc_registration import get_registered_subject_model_cls
-from edc_reportable import MICROMOLES_PER_LITER, MILLIGRAMS_PER_DECILITER
-from edc_utils import age, get_utcnow
-from edc_utils.round_up import round_half_away_from_zero
-from edc_visit_schedule.constants import OFFSCHEDULE_ACTION
-
-from meta_screening.tests.meta_test_case_mixin import MetaTestCaseMixin
-from meta_screening.tests.options import now
-from meta_subject.forms.blood_results.blood_results_rft_form import (
-    BloodResultsRftFormValidator,
-)
-from meta_subject.models import (
-    BloodResultsRft,
-    EgfrDropNotification,
-    SubjectRequisition,
-)
-
-
-@time_machine.travel(datetime(2019, 6, 11, 8, 00, tzinfo=ZoneInfo("UTC")))
-class TestEgfr(MetaTestCaseMixin, TestCase):
-    def setUp(self):
-        self.subject_visit = self.get_subject_visit(screening_datetime=get_utcnow())
-        panel = Panel.objects.get(name="chemistry_rft")
-        requisition = SubjectRequisition.objects.create(
-            subject_visit=self.subject_visit,
-            panel=panel,
-            requisition_datetime=self.subject_visit.report_datetime,
-        )
-        self.data = dict(
-            subject_visit=self.subject_visit,
-            report_datetime=self.subject_visit.report_datetime,
-            requisition=requisition,
-            assay_datetime=requisition.requisition_datetime,
-            site=Site.objects.get(id=settings.SITE_ID),
-        )
-
-    def tearDown(self) -> None:
-        EgfrDropNotification.objects.all().delete()
-
-    def test_model(self):
-        data = deepcopy(self.data)
-        data.update(creatinine_value=1.1, creatinine_units=MILLIGRAMS_PER_DECILITER)
-        obj = BloodResultsRft.objects.create(**data)
-        self.assertIsNotNone(obj.egfr_value)
-        self.assertIsNotNone(obj.egfr_units)
-
-    def test_ok(self):
-        traveller = time_machine.travel(self.subject_visit.report_datetime)
-        traveller.start()
-        data = dict(
-            subject_visit=self.subject_visit,
-            report_datetime=get_utcnow(),
-        )
-        form = BloodResultsRftFormValidator(cleaned_data=data, model=BloodResultsRft)
-        try:
-            form.validate()
-        except forms.ValidationError:
-            pass
-        self.assertEqual({}, form._errors)
-
-    def test_egfr_drop(self):
-        data = deepcopy(self.data)
-        data.update(creatinine_value=1.1, creatinine_units=MILLIGRAMS_PER_DECILITER)
-        obj_1000 = BloodResultsRft.objects.create(**data)
-        obj_1000.refresh_from_db()
-        subject_visit = self.get_next_subject_visit(self.subject_visit)
-        panel = Panel.objects.get(name="chemistry_rft")
-        requisition = SubjectRequisition.objects.create(
-            subject_visit=subject_visit,
-            panel=panel,
-            requisition_datetime=subject_visit.report_datetime,
-        )
-        data = dict(
-            subject_visit=subject_visit,
-            requisition=requisition,
-            assay_datetime=requisition.requisition_datetime,
-            site=Site.objects.get(id=settings.SITE_ID),
-        )
-        data.update(creatinine_value=1.5, creatinine_units=MILLIGRAMS_PER_DECILITER)
-        obj_2000 = BloodResultsRft.objects.create(**data)
-        obj_2000.refresh_from_db()
-        self.assertGreaterEqual(
-            float(obj_1000.egfr_value - obj_2000.egfr_value), 0.20 * float(obj_1000.egfr_value)
-        )
-        self.assertEqual(
-            round_half_away_from_zero(float(obj_2000.egfr_drop_value), 2),
-            round_half_away_from_zero(
-                egfr_percent_change(obj_2000.egfr_value, obj_1000.egfr_value), 2
-            ),
-        )
-
-    def test_egfr_drop_percent_drop_cannot_be_negative(self):
-        data = deepcopy(self.data)
-        data.update(creatinine_value=1.1, creatinine_units=MILLIGRAMS_PER_DECILITER)
-        obj_1000 = BloodResultsRft.objects.create(**data)
-        obj_1000.refresh_from_db()
-        subject_visit = self.get_next_subject_visit(self.subject_visit)
-        subject_visit.refresh_from_db()
-        panel = Panel.objects.get(name="chemistry_rft")
-        requisition = SubjectRequisition.objects.create(
-            subject_visit=subject_visit,
-            panel=panel,
-            requisition_datetime=subject_visit.report_datetime,
-        )
-        data = dict(
-            subject_visit=subject_visit,
-            requisition=requisition,
-            assay_datetime=requisition.requisition_datetime,
-            site=Site.objects.get(id=settings.SITE_ID),
-        )
-        data.update(creatinine_value=0.58, creatinine_units=MILLIGRAMS_PER_DECILITER)
-        obj_2000 = BloodResultsRft.objects.create(**data)
-        obj_2000.refresh_from_db()
-        self.assertLess(float(obj_1000.egfr_value - obj_2000.egfr_value), 0.0)
-        self.assertEqual(float(obj_2000.egfr_drop_value), 0.0)
-
-    def test_egfr_below_45(self):
-        data = deepcopy(self.data)
-        data.update(creatinine_value=1.1, creatinine_units=MILLIGRAMS_PER_DECILITER)
-        BloodResultsRft.objects.create(**data)
-        subject_visit = self.get_next_subject_visit(self.subject_visit)
-        panel = Panel.objects.get(name="chemistry_rft")
-        requisition = SubjectRequisition.objects.create(
-            subject_visit=subject_visit,
-            panel=panel,
-            requisition_datetime=subject_visit.report_datetime,
-        )
-        data = dict(
-            subject_visit=subject_visit,
-            requisition=requisition,
-            assay_datetime=requisition.requisition_datetime,
-            site=Site.objects.get(id=settings.SITE_ID),
-        )
-        data.update(creatinine_value=2.0, creatinine_units=MILLIGRAMS_PER_DECILITER)
-        obj_2000 = BloodResultsRft.objects.create(**data)
-        obj_2000.save()
-        obj_2000.refresh_from_db()
-
-        self.assertTrue(obj_2000.egfr_value < 45)
-
-        self.assertIn(BLOOD_RESULTS_EGFR_ACTION, site_action_items.registry)
-        self.assertTrue(
-            site_action_items.registry.get(BLOOD_RESULTS_EGFR_ACTION).reference_model,
-            "meta_subject.bloodresultrft",
-        )
-        self.assertTrue(
-            ActionItem.objects.get(
-                subject_identifier=subject_visit.subject_identifier,
-                action_type__name=OFFSCHEDULE_ACTION,
-            )
-        )
-        self.assertTrue(
-            ActionItem.objects.get(
-                subject_identifier=subject_visit.subject_identifier,
-                action_type__name=BLOOD_RESULTS_RFT_ACTION,
-                action_identifier=obj_2000.action_identifier,
-            )
-        )
-
-    def test_egfr_ethnicity(self):
-        subject_visit = self.get_subject_visit(
-            ethnicity=BLACK, age_in_years=60, appt_datetime=now, gender=MALE
-        )
-        rs = get_registered_subject_model_cls().objects.get(
-            subject_identifier=subject_visit.subject_identifier
-        )
-        self.assertEqual(rs.ethnicity, BLACK)
-        self.assertEqual(
-            age(rs.dob, reference_dt=subject_visit.report_datetime.date()).years, 60
-        )
-
-        panel = Panel.objects.get(name="chemistry_rft")
-        requisition = SubjectRequisition.objects.create(
-            subject_visit=subject_visit,
-            panel=panel,
-            requisition_datetime=subject_visit.report_datetime,
-            drawn_datetime=subject_visit.report_datetime,
-        )
-        data = dict(
-            subject_visit=subject_visit,
-            requisition=requisition,
-            assay_datetime=requisition.requisition_datetime,
-            report_datetime=requisition.requisition_datetime,
-            site=Site.objects.get(id=settings.SITE_ID),
-        )
-        data = deepcopy(data)
-        data.update(creatinine_value=152.0, creatinine_units=MICROMOLES_PER_LITER)
-        obj_1000 = BloodResultsRft.objects.create(**data)
-        obj_1000.refresh_from_db()
-        self.assertEqual(round_half_away_from_zero(obj_1000.egfr_value, 3), Decimal("49.030"))
-        self.assertEqual(round_half_away_from_zero(obj_1000.egfr_value, 2), Decimal("49.03"))
-        self.assertEqual(round_half_away_from_zero(obj_1000.egfr_value, 1), Decimal("49.0"))
-        self.assertEqual(round_half_away_from_zero(obj_1000.egfr_value), Decimal("49"))
-
-        subject_visit = self.get_next_subject_visit(subject_visit)
-        subject_visit.refresh_from_db()
-        panel = Panel.objects.get(name="chemistry_rft")
-        requisition = SubjectRequisition.objects.create(
-            subject_visit=subject_visit,
-            panel=panel,
-            requisition_datetime=subject_visit.report_datetime,
-        )
-        data = dict(
-            subject_visit=subject_visit,
-            requisition=requisition,
-            assay_datetime=requisition.requisition_datetime,
-            report_datetime=requisition.requisition_datetime,
-            site=Site.objects.get(id=settings.SITE_ID),
-        )
-        data.update(creatinine_value=150.8, creatinine_units=MICROMOLES_PER_LITER)
-        obj_2000 = BloodResultsRft.objects.create(**data)
-        obj_2000.refresh_from_db()
-        self.assertEqual(round_half_away_from_zero(obj_2000.egfr_value, 3), Decimal("49.503"))
-        self.assertEqual(round_half_away_from_zero(obj_2000.egfr_value, 2), Decimal("49.50"))
-        self.assertEqual(round_half_away_from_zero(obj_2000.egfr_value, 1), Decimal("49.5"))
-        self.assertEqual(round_half_away_from_zero(obj_2000.egfr_value), Decimal("50"))

meta_subject/tests/tests/test_fixes.py

@@ -1,64 +0,0 @@
-from dateutil.relativedelta import relativedelta
-from django.conf import settings
-from django.contrib.sites.models import Site
-from django.test import TestCase
-from edc_constants.constants import COMPLETE, NO, YES
-from edc_utils import get_utcnow
-
-from meta_screening.tests.meta_test_case_mixin import MetaTestCaseMixin
-from meta_screening.tests.options import now
-from meta_subject.forms import PhysicalExamForm
-
-
-class TestFixes(MetaTestCaseMixin, TestCase):
-    def test_crf_ok_despite_mismatch_between_screening_age_and_calculated_consent_age(self):
-        screening_datetime = get_utcnow()
-        subject_screening = self.get_subject_screening(
-            report_datetime=screening_datetime,
-            eligibility_datetime=screening_datetime,
-            age_in_years=20,
-        )
-        # Consent, with DOB indicating 2 years older than age specified in screening
-        subject_consent = self.get_subject_consent(
-            subject_screening,
-            consent_datetime=screening_datetime,
-            dob=(screening_datetime - relativedelta(years=subject_screening.age_in_years + 2)),
-        )
-        subject_visit = self.get_subject_visit(
-            subject_screening=subject_screening,
-            subject_consent=subject_consent,
-            appt_datetime=screening_datetime,
-        )
-
-        # Test can validate PhysicalExamForm (or any CRF)
-        data = {
-            "abdominal_tenderness": NO,
-            "dia_blood_pressure": 100,
-            "abdominal_tenderness_description": None,
-            "enlarged_liver": YES,
-            "heart_rate": 40,
-            "irregular_heartbeat": NO,
-            "irregular_heartbeat_description": None,
-            "jaundice": YES,
-            "oxygen_saturation": 10,
-            "peripheral_oedema": NO,
-            "report_datetime": now,
-            "respiratory_rate": 30,
-            "sys_blood_pressure": 80,
-            "temperature": 37,
-            "waist_circumference": 100,
-            "weight": 65,
-            "crf_status": COMPLETE,
-            "site": Site.objects.get(id=settings.SITE_ID),
-        }
-        data.update(
-            subject_visit=subject_visit.pk,
-            report_datetime=subject_visit.report_datetime,
-        )
-
-        form = PhysicalExamForm(data=data)
-        try:
-            form.is_valid()
-        except ValueError as e:
-            self.fail(f"ValueError unexpectedly raised. Got {e}")
-        self.assertEqual(form._errors, {})

meta_subject/tests/tests/test_followup.py

@@ -1,52 +0,0 @@
-from django.conf import settings
-from django.contrib.sites.models import Site
-from django.test import TestCase
-from model_bakery.baker import make_recipe
-
-from meta_screening.tests.meta_test_case_mixin import MetaTestCaseMixin
-from meta_subject.forms import FollowupExaminationForm
-
-
-class TestFollowup(MetaTestCaseMixin, TestCase):
-    def setUp(self):
-        super().setUp()
-
-        self.subject_visit = self.get_subject_visit()
-
-        self.data = {
-            "site": Site.objects.get(id=settings.SITE_ID),
-            "report_datetime": None,
-            "subject_visit": None,
-            "symptoms_detail": None,
-            "attended_clinic": None,
-            "admitted_hospital": None,
-            "attended_clinic_detail": None,
-            "prescribed_medication": None,
-            "prescribed_medication_detail": None,
-            "attended_clinic_sae": None,
-            "any_other_problems": None,
-            "any_other_problems_detail": None,
-            "any_other_problems_sae": None,
-            "any_other_problems_sae_grade": None,
-            "art_change": None,
-            "art_change_reason": None,
-            "art_new_regimen_other": None,
-            "abdominal_tenderness": None,
-            "enlarged_liver": None,
-            "jaundice": None,
-            "comment": None,
-            "lactic_acidosis": None,
-            "hepatomegaly": None,
-            "referral": None,
-            "referral_reason": None,
-        }
-        self.data.update(
-            subject_visit=self.subject_visit.pk,
-            report_datetime=self.subject_visit.report_datetime,
-        )
-
-    def test_ok(self):
-        subject_visit = self.get_next_subject_visit(self.subject_visit)
-        obj = make_recipe("meta_subject.followupexamination", subject_visit=subject_visit)
-        form = FollowupExaminationForm(instance=obj)
-        form.is_valid()

meta_subject/tests/tests/test_manager_order.py

@@ -1,11 +0,0 @@
-from django.apps import apps as django_apps
-from django.test import TestCase
-from edc_sites.managers import CurrentSiteManager
-
-
-class TestManagers(TestCase):
-    def test_default_model_manager_not_site_manager(self):
-        app_label = "meta_subject"
-        app_config = django_apps.get_app_config(app_label)
-        for model_cls in app_config.get_models():
-            self.assertFalse(isinstance(model_cls._default_manager, (CurrentSiteManager,)))

meta_subject/tests/tests/test_medication_adherence.py

@@ -1,75 +0,0 @@
-from copy import deepcopy
-
-from django.conf import settings
-from django.contrib.sites.models import Site
-from django.test import TestCase
-from edc_constants.constants import COMPLETE, NEVER, NO, YES
-from model_bakery.baker import make_recipe
-
-from meta_screening.tests.meta_test_case_mixin import MetaTestCaseMixin
-from meta_subject.forms import MedicationAdherenceForm
-
-
-class TestMedicationAdherence(MetaTestCaseMixin, TestCase):
-    def setUp(self):
-        super().setUp()
-
-        self.subject_visit = self.get_subject_visit()
-
-        self.data = dict(
-            site=None,
-            crf_status=COMPLETE,
-            subject_visit=None,
-            report_datetime=None,
-            visual_score_slider=90,
-            visual_score_confirmed=90,
-            last_missed_pill=NEVER,
-            pill_count_performed=YES,
-            pill_count=3,
-            missed_pill_reason=[],
-            other_missed_pill_reason=None,
-        )
-        self.data.update(
-            subject_visit=self.subject_visit.pk,
-            report_datetime=self.subject_visit.report_datetime,
-            site=Site.objects.get(id=settings.SITE_ID),
-        )
-
-    def test_ok(self):
-        subject_visit = self.get_next_subject_visit(self.subject_visit)
-        obj = make_recipe("meta_subject.medicationadherence", subject_visit=subject_visit)
-        form = MedicationAdherenceForm(instance=obj)
-        form.is_valid()
-        self.assertIsNone(form._errors)
-
-    def test_pill_count(self):
-        """Assert pill count logic.
-
-        Note: tests repeated from edc-adherence
-        """
-        data = deepcopy(self.data)
-        subject_visit = self.get_next_subject_visit(self.subject_visit)
-        data.update(
-            subject_visit=subject_visit,
-            report_datetime=subject_visit.report_datetime,
-            pill_count_performed=YES,
-            pill_count=0,
-        )
-        form = MedicationAdherenceForm(data=data)
-        form.is_valid()
-        self.assertEqual({}, form._errors)
-
-        data.update(pill_count=1)
-        form = MedicationAdherenceForm(data=data)
-        form.is_valid()
-        self.assertEqual({}, form._errors)
-
-        data.update(pill_count_performed=NO, pill_count=0)
-        form = MedicationAdherenceForm(data=data)
-        form.is_valid()
-        self.assertIn("pill_count", form._errors)
-
-        data.update(pill_count_performed=NO, pill_count=None)
-        form = MedicationAdherenceForm(data=data)
-        form.is_valid()
-        self.assertEqual({}, form._errors)

meta_subject/tests/tests/test_metadata_rules.py

@@ -1,135 +0,0 @@
-from dateutil.relativedelta import relativedelta
-from django.test import TestCase, tag
-from edc_appointment.models import Appointment
-from edc_constants.constants import FEMALE, MALE, YES
-from edc_utils import get_utcnow
-from edc_visit_schedule.constants import MONTH1
-from model_bakery.baker import make_recipe
-
-from meta_consent.models import SubjectConsent
-from meta_screening.models import SubjectScreening
-from meta_screening.tests.meta_test_case_mixin import MetaTestCaseMixin
-from meta_subject.forms import FollowupExaminationForm
-from meta_visit_schedule.constants import DELIVERY, MONTH3, SCHEDULE_PREGNANCY
-
-
-class TestMetadataRules(MetaTestCaseMixin, TestCase):
-    def test_ok(self):
-        self.subject_visit = self.get_subject_visit(gender=FEMALE)
-        subject_visit = self.get_next_subject_visit(self.subject_visit)
-        obj = make_recipe("meta_subject.followupexamination", subject_visit=subject_visit)
-        form = FollowupExaminationForm(instance=obj)
-        form.is_valid()
-
-    def test_pregnancy_not_required_for_male(self):
-        self.subject_visit = self.get_subject_visit(gender=MALE)
-        subject_visit = self.get_next_subject_visit(self.subject_visit)
-        subject_visit = self.get_next_subject_visit(subject_visit)
-        self.assertEqual(subject_visit.visit_code, MONTH1)
-
-        self.assertNotIn(
-            "meta_subject.urinepregnancy",
-            [obj.model for obj in self.get_crf_metadata(subject_visit)],
-        )
-
-        subject_visit = self.get_next_subject_visit(subject_visit)
-        self.assertNotIn(
-            "meta_subject.urinepregnancy",
-            [obj.model for obj in self.get_crf_metadata(subject_visit)],
-        )
-
-    def test_pregnancy_and_notification(self):
-        self.subject_visit = self.get_subject_visit(gender=FEMALE)
-        subject_visit = self.get_next_subject_visit(self.subject_visit)
-        subject_visit = self.get_next_subject_visit(subject_visit)
-        urine_pregnancy = make_recipe(
-            "meta_subject.urinepregnancy",
-            subject_visit=subject_visit,
-            report_datetime=get_utcnow(),
-            assay_date=get_utcnow().date(),
-        )
-        self.assertFalse(urine_pregnancy.notified)
-        self.assertIsNone(urine_pregnancy.notified_datetime)
-        self.assertEqual(
-            subject_visit.subject_identifier,
-            urine_pregnancy.subject_visit.subject_identifier,
-        )
-        make_recipe(
-            "meta_prn.pregnancynotification",
-            subject_identifier=subject_visit.subject_identifier,
-        )
-
-    def test_only_pregnancy_update_required_after_pregnancy_notification(self):
-        self.subject_visit = self.get_subject_visit(gender=FEMALE)
-        subject_visit = self.get_next_subject_visit(self.subject_visit)
-        subject_visit = self.get_next_subject_visit(subject_visit)
-        urine_pregnancy = make_recipe(
-            "meta_subject.urinepregnancy",
-            subject_visit=subject_visit,
-            report_datetime=subject_visit.report_datetime,
-            assay_date=subject_visit.report_datetime.date(),
-        )
-        self.assertFalse(urine_pregnancy.notified)
-        self.assertIsNone(urine_pregnancy.notified_datetime)
-        self.assertEqual(
-            subject_visit.subject_identifier,
-            urine_pregnancy.subject_visit.subject_identifier,
-        )
-        make_recipe(
-            "meta_prn.pregnancynotification",
-            subject_identifier=subject_visit.subject_identifier,
-            report_datetime=subject_visit.report_datetime,
-            bhcg_confirmed=YES,
-            unconfirmed_details="blah blah",
-            edd=subject_visit.report_datetime + relativedelta(months=6),
-        )
-
-        Appointment.objects.get(
-            subject_identifier=subject_visit.subject_identifier,
-            schedule_name=SCHEDULE_PREGNANCY,
-        )
-        subject_screening = SubjectScreening.objects.get(
-            subject_identifier=subject_visit.subject_identifier
-        )
-        subject_consent = SubjectConsent.objects.get(
-            subject_identifier=subject_visit.subject_identifier
-        )
-        subject_visit = self.get_subject_visit(
-            visit_code=DELIVERY,
-            subject_screening=subject_screening,
-            subject_consent=subject_consent,
-        )
-        self.assertEqual(
-            ["meta_subject.delivery"],
-            [obj.model for obj in self.get_crf_metadata(subject_visit)],
-        )
-
-    @tag("4")
-    def test_health_economics_update_required(self):
-        """Assert healtheconomicsupdate is required starting w/1030"""
-        self.subject_visit = self.get_subject_visit(gender=FEMALE)
-        subject_visit = self.get_next_subject_visit(self.subject_visit)
-        subject_visit = self.get_next_subject_visit(subject_visit)
-        subject_visit = self.get_next_subject_visit(subject_visit)
-        self.assertEqual(subject_visit.visit_code, MONTH3)
-        self.assertIn(
-            "meta_subject.healtheconomicsupdate",
-            [obj.model for obj in self.get_crf_metadata(subject_visit)],
-        )
-
-        subject_visit = self.get_next_subject_visit(subject_visit)
-        self.assertIn(
-            "meta_subject.healtheconomicsupdate",
-            [obj.model for obj in self.get_crf_metadata(subject_visit)],
-        )
-        make_recipe(
-            "meta_subject.healtheconomicsupdate",
-            subject_visit=subject_visit,
-            report_datetime=subject_visit.report_datetime,
-        )
-
-        subject_visit = self.get_next_subject_visit(subject_visit)
-        self.assertNotIn(
-            "meta_subject.healtheconomicsupdate",
-            [obj.model for obj in self.get_crf_metadata(subject_visit)],
-        )