meta-edc 0.3.7__py3-none-any.whl → 0.3.50__py3-none-any.whl

meta_prn/migrations/0058_dmreferral_referral_note_and_more.py

@@ -0,0 +1,29 @@
+# Generated by Django 4.2.11 on 2024-04-04 16:47
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("meta_prn", "0057_historicalonscheduledmreferral_and_more"),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="dmreferral",
+            name="referral_note",
+            field=models.TextField(
+                null=True,
+                verbose_name="Please provide a brief history of the diabetes diagnosis that lead to this referral",
+            ),
+        ),
+        migrations.AddField(
+            model_name="historicaldmreferral",
+            name="referral_note",
+            field=models.TextField(
+                null=True,
+                verbose_name="Please provide a brief history of the diabetes diagnosis that lead to this referral",
+            ),
+        ),
+    ]

meta_prn/migrations/0059_alter_historicaloffstudymedication_reason_and_more.py

@@ -0,0 +1,53 @@
+# Generated by Django 5.0.4 on 2024-04-18 23:46
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("meta_prn", "0058_dmreferral_referral_note_and_more"),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="historicaloffstudymedication",
+            name="reason",
+            field=models.CharField(
+                choices=[
+                    ("pregnancy", "Pregnancy"),
+                    ("sae", "Participant is experiencing a serious adverse event"),
+                    (
+                        "clinician",
+                        "Other condition that justifies discontinuation of treatment in the clinician's opinion (specify below)",
+                    ),
+                    ("investigator", " Investigator decision"),
+                    ("referral", "Referral to Diabetes clinic"),
+                    ("patient", "Patient decision"),
+                    ("OTHER", "Other reason (specify below)"),
+                ],
+                max_length=25,
+                verbose_name="Reason for stopping study medication",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="offstudymedication",
+            name="reason",
+            field=models.CharField(
+                choices=[
+                    ("pregnancy", "Pregnancy"),
+                    ("sae", "Participant is experiencing a serious adverse event"),
+                    (
+                        "clinician",
+                        "Other condition that justifies discontinuation of treatment in the clinician's opinion (specify below)",
+                    ),
+                    ("investigator", " Investigator decision"),
+                    ("referral", "Referral to Diabetes clinic"),
+                    ("patient", "Patient decision"),
+                    ("OTHER", "Other reason (specify below)"),
+                ],
+                max_length=25,
+                verbose_name="Reason for stopping study medication",
+            ),
+        ),
+    ]

meta_prn/models/__init__.py

@@ -1,8 +1,19 @@
+from .dm_referral import DmReferral
 from .end_of_study import EndOfStudy
 from .loss_to_followup import LossToFollowup
 from .off_study_medication import OffStudyMedication
-from .offschedule import OffSchedule, OffSchedulePostnatal, OffSchedulePregnancy
-from .onschedule import OnSchedule, OnSchedulePostnatal, OnSchedulePregnancy
+from .offschedule import (
+    OffSchedule,
+    OffScheduleDmReferral,
+    OffSchedulePostnatal,
+    OffSchedulePregnancy,
+)
+from .onschedule import (
+    OnSchedule,
+    OnScheduleDmReferral,
+    OnSchedulePostnatal,
+    OnSchedulePregnancy,
+)
 from .pregnancy_notification import PregnancyNotification
 from .protocol_incident import ProtocolIncident
 from .signals import (

meta_prn/models/dm_referral.py

@@ -0,0 +1,39 @@
+from django.db import models
+from edc_action_item.models import ActionModelMixin
+from edc_identifier.model_mixins import UniqueSubjectIdentifierFieldMixin
+from edc_model.models import BaseUuidModel
+from edc_sites.model_mixins import SiteModelMixin
+from edc_utils.date import get_utcnow
+
+from ..constants import DM_REFFERAL_ACTION
+
+
+class DmReferral(
+    SiteModelMixin,
+    ActionModelMixin,
+    UniqueSubjectIdentifierFieldMixin,
+    BaseUuidModel,
+):
+
+    action_name = DM_REFFERAL_ACTION
+
+    report_datetime = models.DateTimeField(
+        verbose_name="Report date and time", default=get_utcnow
+    )
+
+    referral_date = models.DateField(
+        verbose_name="Date of referral to diabetes clinic",
+    )
+
+    referral_note = models.TextField(
+        verbose_name=(
+            "Please provide a brief history of the "
+            "diabetes diagnosis that lead to this referral"
+        ),
+        null=True,
+        blank=False,
+    )
+
+    class Meta(ActionModelMixin.Meta, BaseUuidModel.Meta):
+        verbose_name = "Diabetes referral"
+        verbose_name_plural = "Diabetes referral"

meta_prn/models/offschedule.py

@@ -4,7 +4,11 @@ from edc_sites.model_mixins import SiteModelMixin
 from edc_visit_schedule.constants import OFFSCHEDULE_ACTION
 from edc_visit_schedule.model_mixins import OffScheduleModelMixin
 
-from ..constants import OFFSCHEDULE_POSTNATAL_ACTION, OFFSCHEDULE_PREGNANCY_ACTION
+from ..constants import (
+    OFFSCHEDULE_DM_REFERRAL_ACTION,
+    OFFSCHEDULE_POSTNATAL_ACTION,
+    OFFSCHEDULE_PREGNANCY_ACTION,
+)
 
 
 class OffSchedule(SiteModelMixin, ActionModelMixin, OffScheduleModelMixin, BaseUuidModel):
@@ -34,3 +38,13 @@ class OffSchedulePostnatal(
     class Meta(OffScheduleModelMixin.Meta, BaseUuidModel.Meta):
         verbose_name = "Off-schedule: post-natal"
         verbose_name_plural = "Off-schedule: post-natal"
+
+
+class OffScheduleDmReferral(
+    SiteModelMixin, ActionModelMixin, OffScheduleModelMixin, BaseUuidModel
+):
+    action_name = OFFSCHEDULE_DM_REFERRAL_ACTION
+
+    class Meta(OffScheduleModelMixin.Meta, BaseUuidModel.Meta):
+        verbose_name = "Off-schedule: DM Referral"
+        verbose_name_plural = "Off-schedule: DM Referral"

meta_prn/models/onschedule.py

@@ -18,3 +18,9 @@ class OnSchedulePregnancy(OnScheduleModelMixin, SiteModelMixin, BaseUuidModel):
 class OnSchedulePostnatal(OnScheduleModelMixin, SiteModelMixin, BaseUuidModel):
     class Meta(OnScheduleModelMixin.Meta):
         pass
+
+
+class OnScheduleDmReferral(OnScheduleModelMixin, SiteModelMixin, BaseUuidModel):
+    class Meta(OnScheduleModelMixin.Meta, BaseUuidModel.Meta):
+        verbose_name = "On-schedule: DM Referral"
+        verbose_name_plural = "On-schedule: DM Referral"

meta_prn/models/signals.py

@@ -5,8 +5,15 @@ from edc_constants.constants import YES
 from edc_visit_schedule.site_visit_schedules import site_visit_schedules
 
 from meta_subject.models import SubjectVisit, UrinePregnancy
-from meta_visit_schedule.constants import SCHEDULE, SCHEDULE_PREGNANCY, VISIT_SCHEDULE
+from meta_visit_schedule.constants import (
+    SCHEDULE,
+    SCHEDULE_DM_REFERRAL,
+    SCHEDULE_PREGNANCY,
+    VISIT_SCHEDULE,
+)
 
+from . import OffScheduleDmReferral
+from .dm_referral import DmReferral
 from .offschedule import OffSchedule
 from .pregnancy_notification import PregnancyNotification
 
@@ -63,3 +70,36 @@ def update_urine_pregnancy_on_pregnancy_notification_on_post_save(
                 notified_datetime=instance.report_datetime,
                 notified=True,
             )
+
+
+@receiver(
+    post_save,
+    weak=False,
+    sender=DmReferral,
+    dispatch_uid="update_schedule_on_dm_referral_post_save",
+)
+def update_schedule_on_dm_referral_post_save(sender, instance, raw, **kwargs):
+    if not raw:
+        try:
+            OffScheduleDmReferral.objects.get(subject_identifier=instance.subject_identifier)
+        except ObjectDoesNotExist:
+            last_subject_visit = (
+                SubjectVisit.objects.filter(
+                    subject_identifier=instance.subject_identifier,
+                    schedule_name=SCHEDULE,
+                )
+                .order_by("report_datetime")
+                .last()
+            )
+            visit_schedule = site_visit_schedules.get_visit_schedule(
+                visit_schedule_name=VISIT_SCHEDULE
+            )
+            schedule = visit_schedule.schedules.get(SCHEDULE)
+            schedule.take_off_schedule(
+                instance.subject_identifier, last_subject_visit.report_datetime
+            )
+            schedule = visit_schedule.schedules.get(SCHEDULE_DM_REFERRAL)
+            schedule.put_on_schedule(
+                onschedule_datetime=last_subject_visit.report_datetime,
+                subject_identifier=instance.subject_identifier,
+            )

meta_prn/tests/tests/test_dm_referral.py

@@ -0,0 +1,203 @@
+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_reports/__init__.py

@@ -0,0 +1 @@
+from .tasks import update_endpoints_table

meta_reports/admin/__init__.py

@@ -0,0 +1,15 @@
+from .dbviews import (
+    GlucoseSummaryAdmin,
+    ImpSubstitutionsAdmin,
+    MissingOgttNoteModelAdmin,
+    MissingScreeningOgttAdmin,
+    OnStudyMissingLabValuesAdmin,
+    OnStudyMissingValuesAdmin,
+    PatientHistoryMissingBaselineCd4Admin,
+    UnattendedThreeInRow2Admin,
+    UnattendedThreeInRowAdmin,
+    UnattendedTwoInRowAdmin,
+)
+from .endpoints_admin import EndpointsAdmin
+from .endpoints_all_admin import EndpointsAllAdmin
+from .last_imp_refill_admin import LastImpRefillAdmin

meta_reports/admin/dbviews/__init__.py

@@ -0,0 +1,14 @@
+from .glucose_summary_admin import GlucoseSummaryAdmin
+from .imp_substitutions_admin import ImpSubstitutionsAdmin
+from .missing_screening_ogtt_admin import (
+    MissingOgttNoteModelAdmin,
+    MissingScreeningOgttAdmin,
+)
+from .on_study_missing_lab_values_admin import OnStudyMissingLabValuesAdmin
+from .on_study_missing_values_admin import OnStudyMissingValuesAdmin
+from .patient_history_missing_baseline_cd4_admin import (
+    PatientHistoryMissingBaselineCd4Admin,
+)
+from .unattended_three_in_row2_admin import UnattendedThreeInRow2Admin
+from .unattended_three_in_row_admin import UnattendedThreeInRowAdmin
+from .unattended_two_in_row_admin import UnattendedTwoInRowAdmin

meta_reports/admin/dbviews/glucose_summary_admin.py

@@ -0,0 +1,116 @@
+from django.contrib import admin
+from django.core.exceptions import ObjectDoesNotExist
+from django.template.loader import render_to_string
+from django.urls import reverse
+from edc_constants.constants import YES
+from edc_glucose.list_filters import FbgListFilter, OgttListFilter
+from edc_model_admin.dashboard import ModelAdminDashboardMixin
+from edc_model_admin.mixins import TemplatesModelAdminMixin
+from edc_qareports.modeladmin_mixins import QaReportModelAdminMixin
+from edc_sites.admin import SiteModelAdminMixin
+from edc_visit_schedule.admin import ScheduleStatusListFilter
+
+from ...admin_site import meta_reports_admin
+from ...models import Endpoints, EndpointsProxy, GlucoseSummary
+from ..list_filters import EndpointListFilter
+
+
+@admin.register(GlucoseSummary, site=meta_reports_admin)
+class GlucoseSummaryAdmin(
+    QaReportModelAdminMixin,
+    SiteModelAdminMixin,
+    ModelAdminDashboardMixin,
+    TemplatesModelAdminMixin,
+    admin.ModelAdmin,
+):
+    ordering = ["site", "subject_identifier", "fbg_datetime"]
+    include_note_column = False
+    list_display = [
+        "dashboard",
+        "subject_identifier_link",
+        "site",
+        "visit",
+        "fasted",
+        "fbg_date",
+        "fbg_value",
+        "ogtt_value",
+        "ogtt_date",
+        "endpoint",
+        "offstudy_date",
+    ]
+
+    list_filter = [
+        ScheduleStatusListFilter,
+        "fasted",
+        FbgListFilter,
+        OgttListFilter,
+        "fbg_datetime",
+        "ogtt_datetime",
+        EndpointListFilter,
+    ]
+
+    search_fields = ["subject_identifier"]
+
+    @admin.display(description="visit", ordering="visit_code")
+    def visit(self, obj=None):
+        return f"{obj.visit_code}.{obj.visit_code_sequence}"
+
+    @admin.display(description="Endpoint")
+    def endpoint(self, obj=None):
+        try:
+            endpoint_obj = Endpoints.objects.get(subject_identifier=obj.subject_identifier)
+        except ObjectDoesNotExist:
+            value = None
+        else:
+            if endpoint_obj.offstudy_date:
+                url = reverse("meta_reports_admin:meta_reports_endpointsproxy_changelist")
+                title = f"Go to {EndpointsProxy._meta.verbose_name}"
+            else:
+                url = reverse("meta_reports_admin:meta_reports_endpoints_changelist")
+                title = f"Go to {Endpoints._meta.verbose_name}"
+            value = render_to_string(
+                "meta_reports/columns/subject_identifier_column.html",
+                {
+                    "subject_identifier": obj.subject_identifier,
+                    "url": url,
+                    "label": YES,
+                    "title": title,
+                },
+            )
+        return value
+
+    @admin.display(description="Subject Idenfifier", ordering="subject_identifier")
+    def subject_identifier_link(self, obj=None):
+        url = reverse("meta_reports_admin:meta_reports_glucosesummary_changelist")
+        return render_to_string(
+            "meta_reports/columns/subject_identifier_column.html",
+            {
+                "subject_identifier": obj.subject_identifier,
+                "url": url,
+                "title": "Click to filter for this subject only",
+            },
+        )
+
+    def get_subject_dashboard_url_kwargs(self, obj) -> dict:
+        return dict(
+            subject_identifier=obj.subject_identifier,
+            appointment=obj.appointment_id,
+        )
+
+    @admin.display(description="Fbg date", ordering="fbg_datetime")
+    def fbg_date(self, obj):
+        if obj.fbg_datetime:
+            return obj.fbg_datetime.date()
+        return None
+
+    @admin.display(description="OGTT date", ordering="ogtt_datetime")
+    def ogtt_date(self, obj):
+        if obj.ogtt_datetime:
+            return obj.ogtt_datetime.date()
+        return None
+
+    @admin.display(description="Offstudy date", ordering="offstudy_datetime")
+    def offstudy_date(self, obj):
+        if obj.offstudy_datetime:
+            return obj.offstudy_datetime.date()
+        return None