meta-edc 1.1.8__py3-none-any.whl → 1.1.12__py3-none-any.whl

meta_edc-1.1.8.dist-info/WHEEL

@@ -1,5 +0,0 @@
-Wheel-Version: 1.0
-Generator: setuptools (80.9.0)
-Root-Is-Purelib: true
-Tag: py3-none-any
-

meta_edc-1.1.8.dist-info/licenses/AUTHORS.rst

@@ -1,8 +0,0 @@
-Maintainers
-===========
-- Erik van Widenfelt (`erikvw <https://github.com/erikvw>`__)
-
-Authors
-=======
-- Erik van Widenfelt (`erikvw <https://github.com/erikvw>`_)
-- Jonathan Willitts (`JonathanWillitts <https://github.com/JonathanWillitts>`_)

meta_edc-1.1.8.dist-info/top_level.txt

@@ -1,20 +0,0 @@
-meta_ae
-meta_analytics
-meta_auth
-meta_consent
-meta_dashboard
-meta_data_manager
-meta_edc
-meta_export
-meta_labs
-meta_lists
-meta_pharmacy
-meta_prn
-meta_rando
-meta_reports
-meta_screening
-meta_sites
-meta_stats
-meta_subject
-meta_visit_schedule
-tests

meta_labs/tests/test_labs.py

@@ -1,27 +0,0 @@
-from django.test import TestCase
-from edc_lab.models import Panel
-from edc_lab.site_labs import site_labs
-
-from ..lab_profiles import subject_lab_profile
-
-
-class TestLabs(TestCase):
-    def setUp(self):
-        site_labs._registry = {}
-        site_labs.loaded = False
-        site_labs.register(lab_profile=subject_lab_profile)
-
-    def test_(self):
-        obj = site_labs.get(lab_profile_name="subject_lab_profile")
-        self.assertEqual(obj, subject_lab_profile)
-
-    def test_lab_profile_model(self):
-        obj = site_labs.get(lab_profile_name="subject_lab_profile")
-        self.assertEqual("meta_subject.subjectrequisition", obj.requisition_model)
-
-    def test_panel_model(self):
-        for panel in site_labs.get(lab_profile_name="subject_lab_profile").panels.values():
-            self.assertEqual(panel.requisition_model, "meta_subject.subjectrequisition")
-
-    def test_panels_exist(self):
-        self.assertGreater(Panel.objects.all().count(), 0)

meta_labs/tests/test_reportables.py

@@ -1,70 +0,0 @@
-from django.test import TestCase, tag
-from edc_lab import site_labs
-from edc_reportable.models import GradingData, NormalData, ReferenceRangeCollection
-from edc_reportable.utils import load_reference_ranges
-
-
-class TestReportables(TestCase):
-    @tag("37")
-    def test_load_reference_ranges(self):
-
-        from meta_labs.reportables import (
-            collection_name,
-            grading_data,
-            normal_data,
-            reportable_grades,
-            reportable_grades_exceptions,
-        )
-
-        load_reference_ranges(
-            collection_name=collection_name,
-            grading_data=grading_data,
-            normal_data=normal_data,
-            reportable_grades=reportable_grades,
-            reportable_grades_exceptions=reportable_grades_exceptions,
-        )
-        self.assertTrue(ReferenceRangeCollection.objects.filter(name=collection_name).exists())
-        reference_range_collection = ReferenceRangeCollection.objects.get(name=collection_name)
-
-        for panel_name, requisition_panel in site_labs.lab_profiles.get(
-            "subject_lab_profile"
-        ).panels.items():
-            for utest_id in requisition_panel.utest_ids:
-                try:
-                    utest_id, _ = utest_id
-                except ValueError:
-                    pass
-                if not NormalData.objects.filter(label=utest_id).exists():
-                    print(f"{utest_id} does not exist in NormalData")
-                if not GradingData.objects.filter(label=utest_id).exists():
-                    print(f"{utest_id} does not exist in GradingData")
-
-        for panel_name, requisition_panel in site_labs.lab_profiles.get(
-            "subject_lab_profile"
-        ).panels.items():
-            for utest_id in requisition_panel.utest_ids:
-                try:
-                    utest_id, _ = utest_id
-                except ValueError:
-                    pass
-                self.assertTrue(
-                    NormalData.objects.filter(label=utest_id).exists(),
-                    msg=f"{utest_id} does not exist in NormalData",
-                )
-                self.assertTrue(
-                    GradingData.objects.filter(label=utest_id).exists(),
-                    msg=f"{utest_id} does not exist in GradingData",
-                )
-
-        self.assertEqual(
-            NormalData.objects.filter(
-                reference_range_collection=reference_range_collection
-            ).count(),
-            88,
-        )
-        self.assertEqual(
-            GradingData.objects.filter(
-                reference_range_collection=reference_range_collection
-            ).count(),
-            180,
-        )

meta_labs/tests/urls.py

@@ -1,4 +0,0 @@
-from django.contrib import admin
-from django.urls import path
-
-urlpatterns = [path("admin/", admin.site.urls)]

meta_lists/tests/test_lists.py

@@ -1,8 +0,0 @@
-from django.test import TestCase
-from edc_list_data.site_list_data import site_list_data
-
-
-class TestList(TestCase):
-    def test_(self):
-        site_list_data.initialize()
-        site_list_data.autodiscover()

meta_pharmacy/notebooks/pharmacy.ipynb

@@ -1,41 +0,0 @@
-{
- "cells": [
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "0",
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "1",
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "Python 3",
-   "language": "python",
-   "name": "python3"
-  },
-  "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 2
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython2",
-   "version": "2.7.6"
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 5
-}

meta_prn/tests/tests/test_actions.py

@@ -1,97 +0,0 @@
-from django.core.exceptions import ObjectDoesNotExist
-from django.test import TestCase
-from edc_action_item.models import ActionItem
-from edc_appointment.models import Appointment
-from edc_constants.constants import FEMALE
-from edc_utils import get_utcnow
-from edc_visit_schedule.constants import MONTH1
-from model_bakery.baker import make_recipe
-
-from meta_prn.models import OffSchedulePregnancy
-from meta_screening.tests.meta_test_case_mixin import MetaTestCaseMixin
-from meta_visit_schedule.constants import DELIVERY
-
-
-class TestMetadataRules(MetaTestCaseMixin, TestCase):
-    def setUp(self):
-        super().setUp()
-        self.subject_screening = self.get_subject_screening(gender=FEMALE)
-        self.subject_consent = self.get_subject_consent(self.subject_screening)
-        self.subject_visit = self.get_subject_visit(
-            subject_screening=self.subject_screening,
-            subject_consent=self.subject_consent,
-        )
-        self.data = dict(
-            subject_visit=self.subject_visit.pk,
-            report_datetime=self.subject_visit.report_datetime,
-        )
-
-    def test_pregnancy_actions(self):
-        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)
-
-        urine_pregnancy = make_recipe(
-            "meta_subject.urinepregnancy",
-            subject_visit=subject_visit,
-            report_datetime=get_utcnow(),
-            assay_date=get_utcnow().date(),
-        )
-
-        try:
-            ActionItem.objects.get(
-                action_identifier=urine_pregnancy.action_identifier,
-                action_type__reference_model="meta_subject.urinepregnancy",
-            )
-        except ObjectDoesNotExist:
-            self.fail("ActionItem for urinepregnancy unexpectedly does not exist")
-
-        try:
-            ActionItem.objects.get(
-                parent_action_item__action_identifier=urine_pregnancy.action_identifier,
-                action_type__reference_model="meta_prn.pregnancynotification",
-            )
-        except ObjectDoesNotExist:
-            self.fail("ActionItem for pregnancynotification unexpectedly does not exist")
-
-        make_recipe(
-            "meta_prn.pregnancynotification",
-            subject_identifier=subject_visit.subject_identifier,
-        )
-
-        try:
-            appointment = Appointment.objects.get(visit_code=DELIVERY)
-        except ObjectDoesNotExist:
-            self.fail("delivery appointment unexpectedly does not exist")
-
-        subject_visit = self.get_subject_visit(
-            subject_screening=self.subject_screening,
-            subject_consent=self.subject_consent,
-            visit_code=DELIVERY,
-            visit_code_sequence=0,
-            appt_datetime=appointment.appt_datetime,
-        )
-
-        delivery = make_recipe(
-            "meta_subject.delivery",
-            subject_visit=subject_visit,
-        )
-
-        try:
-            ActionItem.objects.get(
-                parent_action_item__action_identifier=delivery.action_identifier,
-                action_type__reference_model="meta_prn.offschedulepregnancy",
-            )
-        except ObjectDoesNotExist:
-            self.fail("ActionItem for offschedulepregnancy unexpectedly does not exist")
-
-        offschedule_pregancy = OffSchedulePregnancy.objects.get(
-            subject_identifier=delivery.subject_visit.subject_identifier
-        )
-        try:
-            ActionItem.objects.get(
-                parent_action_item__action_identifier=offschedule_pregancy.action_identifier,
-                action_type__reference_model="meta_prn.endofstudy",
-            )
-        except ObjectDoesNotExist:
-            self.fail("ActionItem for endofstudy unexpectedly does not exist")

meta_prn/tests/tests/test_dm_referral.py

@@ -1,203 +0,0 @@
-from dateutil.relativedelta import relativedelta
-from django.core.exceptions import ObjectDoesNotExist
-from django.test import TestCase
-from edc_action_item.models import ActionItem
-from edc_appointment.constants import COMPLETE_APPT
-from edc_appointment.models import Appointment
-from edc_constants.constants import CLOSED, FEMALE, NEW, NO, PATIENT, YES
-from edc_pharmacy.constants import IN_PROGRESS_APPT
-from edc_utils import get_utcnow
-from edc_visit_schedule.constants import MONTH1, OFFSCHEDULE_ACTION
-from edc_visit_tracking.constants import SCHEDULED
-
-from meta_lists.models import MissedReferralReasons
-from meta_prn.constants import (
-    OFFSCHEDULE_DM_REFERRAL_ACTION,
-    OFFSTUDY_MEDICATION_ACTION,
-)
-from meta_prn.models import DmReferral, OnScheduleDmReferral
-from meta_screening.tests.meta_test_case_mixin import MetaTestCaseMixin
-from meta_subject.constants import DM_FOLLOWUP_ACTION
-from meta_subject.models import DmEndpoint, DmFollowup, SubjectVisit
-from meta_visit_schedule.constants import DM_BASELINE, DM_FOLLOWUP, SCHEDULE_DM_REFERRAL
-
-
-class TestDmReferral(MetaTestCaseMixin, TestCase):
-    def setUp(self):
-        super().setUp()
-        self.subject_visit = self.get_subject_visit(gender=FEMALE)
-
-    def test_dm_referral_puts_subject_on_dm_followup_schedule(self):
-        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)
-        dm_referral = DmReferral.objects.create(
-            subject_identifier=subject_visit.subject_identifier,
-            report_datetime=get_utcnow(),
-            referral_date=get_utcnow(),
-        )
-        self.assertIsNotNone(dm_referral.report_datetime)
-        self.assertIsNotNone(dm_referral.referral_date)
-        self.assertIsNotNone(dm_referral.action_identifier)
-
-        # verify subject is on DM Followup schedule
-        try:
-            OnScheduleDmReferral.objects.get(
-                subject_identifier=subject_visit.subject_identifier
-            )
-        except ObjectDoesNotExist:
-            self.fail("OnScheduleDmReferral unexpectedly does not exist")
-
-    def test_dm_referral_action_creates_offschedule_action(self):
-        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)
-        dm_referral = DmReferral.objects.create(
-            subject_identifier=subject_visit.subject_identifier,
-            report_datetime=get_utcnow(),
-            referral_date=get_utcnow(),
-        )
-        self.assertIsNotNone(dm_referral.report_datetime)
-        self.assertIsNotNone(dm_referral.referral_date)
-        self.assertIsNotNone(dm_referral.action_identifier)
-
-        try:
-            ActionItem.objects.get(
-                subject_identifier=subject_visit.subject_identifier,
-                action_type__name=OFFSCHEDULE_ACTION,
-                status=CLOSED,
-            )
-        except ObjectDoesNotExist:
-            self.fail(f"{OFFSCHEDULE_ACTION} Action item unexpectedly does not exist")
-
-    def test_dm_referral_creates_offstudy_med_action(self):
-        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)
-        dm_referral = DmReferral.objects.create(
-            subject_identifier=subject_visit.subject_identifier,
-            report_datetime=get_utcnow(),
-            referral_date=get_utcnow(),
-        )
-        self.assertIsNotNone(dm_referral.report_datetime)
-        self.assertIsNotNone(dm_referral.referral_date)
-        self.assertIsNotNone(dm_referral.action_identifier)
-
-        # verify action items are created
-        try:
-            ActionItem.objects.get(
-                subject_identifier=subject_visit.subject_identifier,
-                action_type__name=OFFSTUDY_MEDICATION_ACTION,
-                status=NEW,
-            )
-        except ObjectDoesNotExist:
-            self.fail(f"{OFFSTUDY_MEDICATION_ACTION} Action item unexpectedly does not exist")
-
-    def test_dm_referral_creates_dm_followup_action(self):
-        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)
-        dm_referral = DmReferral.objects.create(
-            subject_identifier=subject_visit.subject_identifier,
-            report_datetime=get_utcnow(),
-            referral_date=get_utcnow(),
-        )
-        self.assertIsNotNone(dm_referral.report_datetime)
-        self.assertIsNotNone(dm_referral.referral_date)
-        self.assertIsNotNone(dm_referral.action_identifier)
-
-        try:
-            ActionItem.objects.get(
-                subject_identifier=subject_visit.subject_identifier,
-                action_type__name=DM_FOLLOWUP_ACTION,
-                status=NEW,
-            )
-        except ObjectDoesNotExist:
-            self.fail(f"{DM_FOLLOWUP_ACTION} Action item unexpectedly does not exist")
-
-    def test_dm_referral2(self):
-        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)
-        referral_datetime = subject_visit.report_datetime
-        DmReferral.objects.create(
-            subject_identifier=subject_visit.subject_identifier,
-            report_datetime=referral_datetime,
-            referral_date=referral_datetime.date(),
-        )
-
-        # Add DM Baseline
-        appointment = Appointment.objects.get(
-            subject_identifier=subject_visit.subject_identifier,
-            schedule_name=SCHEDULE_DM_REFERRAL,
-            visit_code=DM_BASELINE,
-        )
-        appointment.appt_status = IN_PROGRESS_APPT
-        appointment.save()
-
-        subject_visit = SubjectVisit.objects.create(
-            appointment=appointment,
-            subject_identifier=subject_visit.subject_identifier,
-            report_datetime=appointment.appt_datetime,
-            reason=SCHEDULED,
-            info_source=PATIENT,
-        )
-
-        DmEndpoint.objects.create(
-            subject_visit=subject_visit,
-            report_datetime=get_utcnow(),
-            dx_date=referral_datetime.date(),
-            dx_initiated_by="fbg_confirmed",
-            dx_tmg=YES,
-            dx_tmg_date=referral_datetime.date(),
-        )
-
-        # Add DM Followup
-        followup_datetime = referral_datetime + relativedelta(months=6)
-        appointment = Appointment.objects.get(
-            subject_identifier=subject_visit.subject_identifier,
-            schedule_name=SCHEDULE_DM_REFERRAL,
-            visit_code=DM_FOLLOWUP,
-        )
-        appointment.appt_status = IN_PROGRESS_APPT
-        appointment.save()
-
-        subject_visit = SubjectVisit.objects.create(
-            appointment=appointment,
-            subject_identifier=subject_visit.subject_identifier,
-            report_datetime=appointment.appt_datetime,
-            reason=SCHEDULED,
-            info_source=PATIENT,
-        )
-
-        dm_followup = DmFollowup.objects.create(
-            subject_visit=subject_visit,
-            report_datetime=followup_datetime,
-            referral_date=referral_datetime.date(),
-            attended=NO,
-            on_dm_medications=NO,
-        )
-        dm_followup.missed_referral_reasons.set([MissedReferralReasons.objects.all()[0]])
-
-        appointment.appt_status = COMPLETE_APPT
-        appointment.save()
-
-        try:
-            ActionItem.objects.get(
-                subject_identifier=subject_visit.subject_identifier,
-                action_type__name=DM_FOLLOWUP_ACTION,
-                status=CLOSED,
-            )
-        except ObjectDoesNotExist:
-            self.fail(f"{DM_FOLLOWUP_ACTION} Action item unexpectedly does not exist")
-
-        try:
-            ActionItem.objects.get(
-                subject_identifier=subject_visit.subject_identifier,
-                action_type__name=OFFSCHEDULE_DM_REFERRAL_ACTION,
-                status=NEW,
-            )
-        except ObjectDoesNotExist:
-            self.fail(
-                f"{OFFSCHEDULE_DM_REFERRAL_ACTION} Action item unexpectedly does not exist"
-            )

meta_prn/tests/tests/test_eos_events.py

@@ -1,134 +0,0 @@
-from django.test import TestCase
-from edc_action_item.models import ActionItem
-from edc_constants.constants import FEMALE, NEW, PATIENT, YES
-from edc_offstudy.constants import END_OF_STUDY_ACTION
-from edc_pharmacy.models import Medication
-from edc_transfer.constants import SUBJECT_TRANSFER_ACTION, TRANSFERRED
-from edc_utils import get_utcnow
-from edc_visit_schedule.constants import OFFSCHEDULE_ACTION
-
-from meta_lists.models import OffstudyReasons, TransferReasons
-from meta_pharmacy.constants import METFORMIN
-from meta_prn.action_items import OffscheduleAction, SubjectTransferAction
-from meta_prn.constants import OFFSTUDY_MEDICATION_ACTION
-from meta_prn.models import EndOfStudy, OffSchedule, OffStudyMedication, SubjectTransfer
-from meta_screening.tests.meta_test_case_mixin import MetaTestCaseMixin
-
-
-class TestEosEvents(MetaTestCaseMixin, TestCase):
-    def setUp(self):
-        super().setUp()
-        self.subject_screening = self.get_subject_screening(gender=FEMALE)
-        self.subject_consent = self.get_subject_consent(self.subject_screening)
-        self.subject_visit = self.get_subject_visit(
-            subject_screening=self.subject_screening,
-            subject_consent=self.subject_consent,
-        )
-        self.data = dict(
-            subject_visit=self.subject_visit.pk,
-            report_datetime=self.subject_visit.report_datetime,
-        )
-
-    def test_transfer_to_offschedule_in_order(self):
-        SubjectTransferAction(
-            subject_identifier=self.subject_consent.subject_identifier,
-            skip_get_current_site=True,
-            site_id=self.subject_consent.site_id,
-        )
-        action_types = [
-            obj.action_type.name
-            for obj in ActionItem.objects.filter(status=NEW).order_by("action_type__name")
-        ]
-        self.assertEqual(action_types, [SUBJECT_TRANSFER_ACTION])
-
-        # add a subject transfer object, which triggers next action item
-        transfer_reason = TransferReasons.objects.get(name="moved")
-        subject_transfer = SubjectTransfer.objects.create(
-            subject_identifier=self.subject_consent.subject_identifier,
-            initiated_by="patient",
-            may_return=YES,
-            may_contact=YES,
-        )
-        subject_transfer.transfer_reason.add(transfer_reason)
-
-        action_types = [
-            obj.action_type.name
-            for obj in ActionItem.objects.filter(status=NEW).order_by("action_type__name")
-        ]
-        self.assertEqual(action_types, [OFFSCHEDULE_ACTION, OFFSTUDY_MEDICATION_ACTION])
-
-        OffSchedule.objects.create(subject_identifier=self.subject_consent.subject_identifier)
-
-        action_types = [
-            obj.action_type.name
-            for obj in ActionItem.objects.filter(status=NEW).order_by("action_type__name")
-        ]
-        self.assertEqual(action_types, [OFFSTUDY_MEDICATION_ACTION])
-
-        offstudy_rx = OffStudyMedication.objects.create(
-            subject_identifier=self.subject_consent.subject_identifier,
-            stop_date=get_utcnow().date(),
-            last_dose_date=get_utcnow().date(),
-            reason=PATIENT,
-        )
-        offstudy_rx.medications.add(Medication.objects.get(name=METFORMIN))
-
-        action_types = [
-            obj.action_type.name
-            for obj in ActionItem.objects.filter(status=NEW).order_by("action_type__name")
-        ]
-        self.assertEqual(action_types, [END_OF_STUDY_ACTION])
-
-        EndOfStudy.objects.create(
-            subject_identifier=self.subject_consent.subject_identifier,
-            last_seen_date=get_utcnow().date(),
-            offstudy_reason=OffstudyReasons.objects.get(name=TRANSFERRED),
-        )
-
-        action_types = [
-            obj.action_type.name
-            for obj in ActionItem.objects.filter(status=NEW).order_by("action_type__name")
-        ]
-        self.assertEqual(action_types, [])
-
-    def test_transfer_to_offschedule_raises(self):
-
-        OffscheduleAction(
-            subject_identifier=self.subject_consent.subject_identifier,
-            skip_get_current_site=True,
-            site_id=self.subject_consent.site_id,
-        )
-
-        OffSchedule.objects.create(subject_identifier=self.subject_consent.subject_identifier)
-
-        action_types = [
-            obj.action_type.name
-            for obj in ActionItem.objects.filter(status=NEW).order_by("action_type__name")
-        ]
-        self.assertEqual(action_types, [OFFSTUDY_MEDICATION_ACTION])
-
-        offstudy_rx = OffStudyMedication.objects.create(
-            subject_identifier=self.subject_consent.subject_identifier,
-            stop_date=get_utcnow().date(),
-            last_dose_date=get_utcnow().date(),
-            reason=PATIENT,
-        )
-        offstudy_rx.medications.add(Medication.objects.get(name=METFORMIN))
-
-        action_types = [
-            obj.action_type.name
-            for obj in ActionItem.objects.filter(status=NEW).order_by("action_type__name")
-        ]
-        self.assertEqual(action_types, [END_OF_STUDY_ACTION])
-
-        EndOfStudy.objects.create(
-            subject_identifier=self.subject_consent.subject_identifier,
-            last_seen_date=get_utcnow().date(),
-            offstudy_reason=OffstudyReasons.objects.get(name=TRANSFERRED),
-        )
-
-        action_types = [
-            obj.action_type.name
-            for obj in ActionItem.objects.filter(status=NEW).order_by("action_type__name")
-        ]
-        self.assertEqual(action_types, [])

meta_prn/tests/tests/test_manager_order.py

@@ -1,14 +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_models(self):
-        app_config = django_apps.get_app_config("meta_prn")
-        for model_cls in app_config.get_models():
-            if "historical" not in model_cls._meta.label_lower:
-                self.assertFalse(
-                    isinstance(model_cls._default_manager, (CurrentSiteManager,)),
-                    msg=model_cls._meta.label_lower,
-                )