meta-edc 0.3.15__py3-none-any.whl → 0.3.50__py3-none-any.whl

meta_reports/tasks.py

@@ -0,0 +1,12 @@
+from celery import shared_task
+
+
+@shared_task
+def update_endpoints_table(subject_identifiers: list[str] | None = None):
+    from meta_analytics.dataframes import GlucoseEndpointsByDate
+
+    if len(subject_identifiers) > 5:
+        subject_identifiers = []
+    cls = GlucoseEndpointsByDate(subject_identifiers=subject_identifiers)
+    cls.run()
+    return cls.to_model()

meta_reports/templates/meta_reports/columns/subject_identifier_column.html

@@ -0,0 +1 @@
+<a title="{{ title }}" href="{{ url }}?q={{ subject_identifier }}">{{ label|default:subject_identifier }}</a>

meta_reports/templates/meta_reports/endpoints_all_change_list_note.html

@@ -0,0 +1,12 @@
+Endpoints report shows subjects who have reached the protocol endpoint.
+<BR>
+<i>This report INCLUDES subjects who are no longer on-study. See also the <a href="{% url 'meta_reports_admin:meta_reports_endpoints_changelist' %}">Endpoints (DM)</a> report.</i>
+<BR>
+Pay attention to the "LAST_UPDATED" column. This tells you the last time the report was updated per subject.
+<BR>
+<BR>
+Unlike other reports, this report does not automatically update, but you can update it :
+<UL>
+    <LI>Place a check mark next to one or more subjects and select 'Regenerate selected report data' from the Action menu.</LI>
+    <li>If you select more than 5 subjects, records for ALL subjects will be refreshed.</li>
+</UL>

meta_reports/templates/meta_reports/endpoints_change_list_note.html

@@ -0,0 +1,12 @@
+Endpoints report shows subjects who have reached the protocol endpoint and should enroll to the DM Referral Schedule.
+<BR>
+<i>The report EXCLUDES subjects who are no longer on-study. See also the <a href="{% url 'meta_reports_admin:meta_reports_endpointsproxy_changelist' %}">Endpoints (DM): All</a> report.</i></i>
+<BR>
+Pay attention to the "LAST_UPDATED" column. This tells you the last time the report was updated per subject.
+<BR>
+<BR>
+Unlike other reports, this report does not automatically update, but you can update it :
+<UL>
+    <LI>Place a check mark next to one or more subjects and select 'Regenerate selected report data' from the Action menu.</LI>
+    <li>If you select more than 5 subjects, records for ALL subjects will be refreshed.</li>
+</UL>

meta_reports/tests/test_sql_gen.py

@@ -0,0 +1,5 @@
+from django.test import TestCase
+
+
+class TestSqlGen(TestCase):
+    pass

meta_reports/urls.py

@@ -0,0 +1,8 @@
+from django.urls.conf import path
+from django.views.generic import RedirectView
+
+app_name = "meta_reports"
+
+urlpatterns = [
+    path("", RedirectView.as_view(url=f"/{app_name}/admin/"), name="home_url"),
+]

meta_screening/admin/subject_screening_admin.py

@@ -79,6 +79,7 @@ class SubjectScreeningAdmin(ModelAdminSubjectDashboardMixin, SimpleHistoryAdmin)
         "hospital_identifier",
         "initials",
         "reasons_ineligible",
+        "id",
     )
 
     readonly_fields = (

meta_screening/migrations/0067_alter_historicalscreeningpartone_report_datetime_and_more.py

@@ -0,0 +1,84 @@
+# Generated by Django 4.2.11 on 2024-06-03 16:46
+
+from django.db import migrations, models
+import edc_model.validators.date
+import edc_protocol.validators
+import edc_utils.date
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        (
+            "meta_screening",
+            "0066_alter_historicalscreeningpartone_fasting_duration_delta_and_more",
+        ),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="historicalscreeningpartone",
+            name="report_datetime",
+            field=models.DateTimeField(
+                default=edc_utils.date.get_utcnow,
+                help_text="Date and time of report.",
+                validators=[
+                    edc_protocol.validators.datetime_not_before_study_start,
+                    edc_model.validators.date.datetime_not_future,
+                ],
+                verbose_name="Report Date and Time",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="historicalscreeningpartthree",
+            name="report_datetime",
+            field=models.DateTimeField(
+                default=edc_utils.date.get_utcnow,
+                help_text="Date and time of report.",
+                validators=[
+                    edc_protocol.validators.datetime_not_before_study_start,
+                    edc_model.validators.date.datetime_not_future,
+                ],
+                verbose_name="Report Date and Time",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="historicalscreeningparttwo",
+            name="report_datetime",
+            field=models.DateTimeField(
+                default=edc_utils.date.get_utcnow,
+                help_text="Date and time of report.",
+                validators=[
+                    edc_protocol.validators.datetime_not_before_study_start,
+                    edc_model.validators.date.datetime_not_future,
+                ],
+                verbose_name="Report Date and Time",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="historicalsubjectscreening",
+            name="report_datetime",
+            field=models.DateTimeField(
+                default=edc_utils.date.get_utcnow,
+                help_text="Date and time of report.",
+                validators=[
+                    edc_protocol.validators.datetime_not_before_study_start,
+                    edc_model.validators.date.datetime_not_future,
+                ],
+                verbose_name="Report Date and Time",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="subjectscreening",
+            name="report_datetime",
+            field=models.DateTimeField(
+                default=edc_utils.date.get_utcnow,
+                help_text="Date and time of report.",
+                validators=[
+                    edc_protocol.validators.datetime_not_before_study_start,
+                    edc_model.validators.date.datetime_not_future,
+                ],
+                verbose_name="Report Date and Time",
+            ),
+        ),
+    ]

meta_screening/tests/holidays.csv

@@ -12,4 +12,4 @@
 2019-12-01,Mawlid Day,tanzania
 2019-12-09,Independence Day,tanzania
 2019-12-25,Christmas Day,tanzania
-2019-12-26,Boxing Day,tanzania
+2019-12-26,Boxing Day,tanzania

meta_screening/tests/meta_test_case_mixin.py

@@ -19,6 +19,7 @@ from edc_sites.utils import add_or_update_django_sites
 from edc_visit_tracking.constants import SCHEDULED
 from model_bakery import baker
 
+from meta_consent.models import SubjectConsent, SubjectConsentV1Ext
 from meta_edc.meta_version import PHASE_THREE
 from meta_pharmacy.prepare_meta_pharmacy import prepare_meta_pharmacy
 from meta_sites.sites import domain_suffix
@@ -143,6 +144,20 @@ class MetaTestCaseMixin(AppointmentTestCaseMixin):
             consent_datetime=consent_datetime or subject_screening.report_datetime,
         )
 
+    @staticmethod
+    def get_subject_consent_extended(
+        subject_consent: SubjectConsent,
+        consent_datetime: datetime = None,
+    ):
+        return SubjectConsentV1Ext.objects.create(
+            subject_consent=subject_consent,
+            report_datetime=consent_datetime,
+            agrees_to_extension=YES,
+            user_created="erikvw",
+            user_modified="erikvw",
+            site=subject_consent.site,
+        )
+
     def get_subject_visit(
         self,
         visit_code: str | None = None,

meta_sites/tests/test_sites.py

@@ -1,5 +1,5 @@
 from django.test import TestCase
-from edc_sites import InvalidSiteError
+from edc_sites.exceptions import InvalidSiteError
 from edc_sites.site import sites
 
 

meta_subject/action_items.py

@@ -8,7 +8,7 @@ from edc_lab_results.action_items import (
     BloodResultsFbcAction,
     BloodResultsHba1cAction,
     BloodResultsLftAction,
-    BloodResultsLipidAction,
+    BloodResultsLipidsAction,
 )
 from edc_lab_results.action_items import (
     BloodResultsRftAction as BaseBloodResultsRftAction,
@@ -175,7 +175,7 @@ class DmFollowAction(ActionWithNotification):
 def register_actions():
     for action_item_cls in [
         BloodResultsFbcAction,
-        BloodResultsLipidAction,
+        BloodResultsLipidsAction,
         BloodResultsLftAction,
         BloodResultsRftAction,
         BloodResultsHba1cAction,

meta_subject/admin/__init__.py

@@ -3,13 +3,14 @@ from .birth_outcome_admin import BirthOutcomesAdmin
 from .blood_results import (
     BloodResultsFbcAdmin,
     BloodResultsLftAdmin,
+    BloodResultsLipidsAdmin,
     BloodResultsRftAdmin,
 )
 from .complications_admin import ComplicationsAdmin
 from .complications_glycemia_admin import ComplicationsGlycemiaAdmin
 from .concomitant_medication_admin import ConcomitantMedicationAdmin
 from .delivery_admin import DeliveryAdmin
-from .diabetes import DmFollowupAdmin
+from .diabetes import DmEndpointAdmin, DmFollowupAdmin
 from .egfr_drop_notification_admin import EgfrDropNotificationAdmin
 from .eq5d3l_admin import Eq5d3lAdmin
 from .followup_examination_admin import FollowupExaminationAdmin

meta_subject/admin/birth_outcome_admin.py

@@ -5,6 +5,7 @@ from django.core.exceptions import ObjectDoesNotExist
 from django.template.loader import render_to_string
 from django.urls import NoReverseMatch, reverse
 from django_audit_fields.admin import audit_fieldset_tuple
+from edc_crf.fieldset import crf_status_fieldset
 from edc_model_admin.dashboard import ModelAdminSubjectDashboardMixin
 from edc_model_admin.history import SimpleHistoryAdmin
 from edc_registration.models import RegisteredSubject
@@ -35,6 +36,7 @@ class BirthOutcomesAdmin(
                 )
             },
         ),
+        crf_status_fieldset,
         audit_fieldset_tuple,
     )
 

meta_subject/admin/blood_results/__init__.py

@@ -2,5 +2,5 @@ from .blood_results_fbc_admin import BloodResultsFbcAdmin
 from .blood_results_hba1c_admin import BloodResultsHba1cAdmin
 from .blood_results_ins_admin import BloodResultsInsAdmin
 from .blood_results_lft_admin import BloodResultsLftAdmin
-from .blood_results_lipid_admin import BloodResultsLipidAdmin
+from .blood_results_lipids_admin import BloodResultsLipidsAdmin
 from .blood_results_rft_admin import BloodResultsRftAdmin

meta_subject/admin/blood_results/{blood_results_lipid_admin.py → blood_results_lipids_admin.py}

@@ -5,19 +5,19 @@ from edc_lab_results.fieldsets import BloodResultFieldset
 from edc_model_admin.history import SimpleHistoryAdmin
 
 from ...admin_site import meta_subject_admin
-from ...forms import BloodResultsLipidForm
-from ...models import BloodResultsLipid
+from ...forms import BloodResultsLipidsForm
+from ...models import BloodResultsLipids
 from ..modeladmin import CrfModelAdminMixin
 
 
-@admin.register(BloodResultsLipid, site=meta_subject_admin)
-class BloodResultsLipidAdmin(
+@admin.register(BloodResultsLipids, site=meta_subject_admin)
+class BloodResultsLipidsAdmin(
     BloodResultsModelAdminMixin, CrfModelAdminMixin, SimpleHistoryAdmin
 ):
-    form = BloodResultsLipidForm
+    form = BloodResultsLipidsForm
     fieldsets = BloodResultFieldset(
-        BloodResultsLipid.lab_panel,
-        model_cls=BloodResultsLipid,
+        BloodResultsLipids.lab_panel,
+        model_cls=BloodResultsLipids,
         extra_fieldsets=[
             (-1, action_fieldset_tuple),
         ],

meta_subject/admin/diabetes/__init__.py

@@ -1,2 +1,2 @@
-from .dm_diagnosis_admin import DmDiagnosisAdmin
+from .dm_endpoint_admin import DmEndpointAdmin
 from .dm_followup_admin import DmFollowupAdmin

meta_subject/admin/diabetes/dm_endpoint_admin.py

@@ -0,0 +1,35 @@
+from django.contrib import admin
+from django_audit_fields.admin import audit_fieldset_tuple
+from edc_crf.fieldset import crf_status_fieldset
+from edc_form_label.form_label_modeladmin_mixin import FormLabelModelAdminMixin
+from edc_model_admin.history import SimpleHistoryAdmin
+
+from ...admin_site import meta_subject_admin
+from ...forms import DmEndpointForm
+from ...models import DmEndpoint
+from ..modeladmin import CrfModelAdminMixin
+
+
+@admin.register(DmEndpoint, site=meta_subject_admin)
+class DmEndpointAdmin(
+    CrfModelAdminMixin,
+    FormLabelModelAdminMixin,
+    SimpleHistoryAdmin,
+):
+    form = DmEndpointForm
+
+    fieldsets = (
+        (None, {"fields": ("subject_visit", "report_datetime")}),
+        (
+            "Endpoint reached",
+            {
+                "fields": ("endpoint_reached", "comments"),
+            },
+        ),
+        crf_status_fieldset,
+        audit_fieldset_tuple,
+    )
+
+    list_filter = ["endpoint_reached"]
+
+    radio_fields = {"endpoint_reached": admin.VERTICAL}

meta_subject/admin/glucose_fbg_admin.py

@@ -4,6 +4,8 @@ from typing import Type
 
 from django.contrib import admin
 from django.contrib.admin import SimpleListFilter
+from django_audit_fields import audit_fieldset_tuple
+from edc_crf.fieldset import crf_status_fieldset
 from edc_model_admin.history import SimpleHistoryAdmin
 
 from ..admin_site import meta_subject_admin
@@ -50,6 +52,8 @@ class GlucoseFbgAdmin(CrfModelAdminMixin, SimpleHistoryAdmin):
                 "fields": ("repeat_fbg_date",),
             },
         ),
+        crf_status_fieldset,
+        audit_fieldset_tuple,
     ]
 
     radio_fields = {

meta_subject/admin/other_arv_regimens_admin.py

@@ -1,5 +1,6 @@
 from django.contrib import admin
 from django_audit_fields.admin import audit_fieldset_tuple
+from edc_crf.fieldset import crf_status_fieldset
 from edc_model_admin.history import SimpleHistoryAdmin
 from edc_model_admin.mixins import TabularInlineMixin
 
@@ -43,6 +44,7 @@ class OtherArvRegimensAdmin(CrfModelAdminMixin, SimpleHistoryAdmin):
 
     fieldsets = (
         (None, {"fields": ("subject_visit", "report_datetime", "has_other_regimens")}),
+        crf_status_fieldset,
         audit_fieldset_tuple,
     )
 

meta_subject/admin/study_medication_admin.py

@@ -64,6 +64,16 @@ class StudyMedicationAdmin(CrfModelAdminMixin, SimpleHistoryAdmin):
                 ),
             },
         ),
+        (
+            "Dispensed medication",
+            {
+                "description": (
+                    "Type in the stock code on the medication "
+                    "bottle or bottles. Separate by comma."
+                ),
+                "fields": ("stock_codes",),
+            },
+        ),
         crf_status_fieldset,
         audit_fieldset_tuple,
     )

meta_subject/form_validators/__init__.py

@@ -1,6 +1,6 @@
 from .birth_outcomes_form_validator import BirthOutcomesFormValidator
 from .delivery_form_validator import DeliveryFormValidator
-from .dm_diagnosis_form_validator import DmDiagnosisFormValidator
+from .dm_endpoint_form_validator import DmEndpointFormValidator
 from .dm_followup_form_validator import DmFollowupFormValidator
 from .egfr_drop_notification_form_validator import EgfrDropNotificationFormValidator
 from .followup_examination_form_validator import FollowupExaminationFormValidator

meta_subject/form_validators/dm_endpoint_form_validator.py

@@ -0,0 +1,35 @@
+from django.core.exceptions import ObjectDoesNotExist
+from django.template.loader import render_to_string
+from django.urls import reverse
+from django.utils.html import format_html
+from edc_crf.crf_form_validator import CrfFormValidator
+from edc_form_validators import INVALID_ERROR
+
+from meta_reports.models import Endpoints
+from meta_reports.tasks import update_endpoints_table
+
+
+class DmEndpointFormValidator(CrfFormValidator):
+    def clean(self):
+        # recalc from endpoint report to confirm the endpoint has been reached
+        update_endpoints_table(subject_identifiers=[self.subject_identifier])
+        try:
+            Endpoints.objects.get(subject_identifier=self.subject_identifier)
+        except ObjectDoesNotExist:
+            url = reverse("meta_reports_admin:meta_reports_glucosesummary_changelist")
+            link = render_to_string(
+                "meta_reports/columns/subject_identifier_column.html",
+                {
+                    "subject_identifier": self.subject_identifier,
+                    "url": url,
+                    "label": "Glucose Summary",
+                },
+            )
+            self.raise_validation_error(
+                {
+                    "__all__": format_html(
+                        f"Subject has not reached the protocol endpoint. See {link}"
+                    )
+                },
+                INVALID_ERROR,
+            )

meta_subject/forms/__init__.py

@@ -4,13 +4,13 @@ from .blood_results import (
     BloodResultsHba1cForm,
     BloodResultsInsForm,
     BloodResultsLftForm,
-    BloodResultsLipidForm,
+    BloodResultsLipidsForm,
     BloodResultsRftForm,
 )
 from .complications_glycemia_form import ComplicationsGlycemiaForm
 from .concomitant_medication_form import ConcomitantMedicationForm
 from .delivery_form import DeliveryForm
-from .diabetes import DmDiagnosisForm, DmDxResultForm, DmFollowupForm
+from .diabetes import DmEndpointForm, DmFollowupForm
 from .egfr_drop_notification_form import EgfrDropNotificationForm
 from .eq53d3l_form import Eq5d3lForm
 from .followup_examination_form import FollowupExaminationForm

meta_subject/forms/blood_results/__init__.py

@@ -2,5 +2,5 @@ from .blood_results_fbc_form import BloodResultsFbcForm
 from .blood_results_hba1c_form import BloodResultsHba1cForm
 from .blood_results_ins_form import BloodResultsInsForm
 from .blood_results_lft_form import BloodResultsLftForm
-from .blood_results_lipid_form import BloodResultsLipidForm
+from .blood_results_lipids_form import BloodResultsLipidsForm
 from .blood_results_rft_form import BloodResultsRftForm

meta_subject/forms/blood_results/{blood_results_lipid_form.py → blood_results_lipids_form.py}

@@ -5,16 +5,16 @@ from edc_crf.modelform_mixins import CrfModelFormMixin
 from edc_lab_panel.panels import lipids_panel
 from edc_lab_results.form_validator_mixins import BloodResultsFormValidatorMixin
 
-from ...models import BloodResultsLipid
+from ...models import BloodResultsLipids
 
 
-class BloodResultsLipidFormValidator(BloodResultsFormValidatorMixin, CrfFormValidator):
+class BloodResultsLipidsFormValidator(BloodResultsFormValidatorMixin, CrfFormValidator):
     panel = lipids_panel
 
 
-class BloodResultsLipidForm(ActionItemCrfFormMixin, CrfModelFormMixin, forms.ModelForm):
-    form_validator_cls = BloodResultsLipidFormValidator
+class BloodResultsLipidsForm(ActionItemCrfFormMixin, CrfModelFormMixin, forms.ModelForm):
+    form_validator_cls = BloodResultsLipidsFormValidator
 
     class Meta(ActionItemCrfFormMixin.Meta):
-        model = BloodResultsLipid
+        model = BloodResultsLipids
         fields = "__all__"

meta_subject/forms/diabetes/__init__.py

@@ -1,3 +1,2 @@
-from .dm_diagnosis_form import DmDiagnosisForm
-from .dm_dx_result_form import DmDxResultForm
+from .dm_endpoint_form import DmEndpointForm
 from .dm_followup_form import DmFollowupForm

meta_subject/forms/diabetes/dm_endpoint_form.py

@@ -0,0 +1,13 @@
+from django import forms
+from edc_crf.modelform_mixins import CrfModelFormMixin
+
+from ...form_validators import DmEndpointFormValidator
+from ...models import DmEndpoint
+
+
+class DmEndpointForm(CrfModelFormMixin, forms.ModelForm):
+    form_validator_cls = DmEndpointFormValidator
+
+    class Meta:
+        model = DmEndpoint
+        fields = "__all__"

meta_subject/forms/study_medication_form.py

@@ -1,9 +1,12 @@
+import re
+
 from django import forms
 from edc_crf.modelform_mixins import CrfModelFormMixin
 from edc_form_validators import INVALID_ERROR
 from edc_pharmacy.form_validators import (
     StudyMedicationFormValidator as BaseStudyMedicationFormValidator,
 )
+from edc_pharmacy.models import Stock
 from edc_visit_schedule.constants import DAY1
 
 from ..models import StudyMedication
@@ -13,6 +16,7 @@ class StudyMedicationFormValidator(BaseStudyMedicationFormValidator):
     def clean(self):
         super().clean()
         self.validate_half_dose_at_baseline()
+        self.validate_stock_codes_are_dispensed()
 
     def validate_half_dose_at_baseline(self):
         """Require 1000mg dose at baseline"""
@@ -32,6 +36,37 @@ class StudyMedicationFormValidator(BaseStudyMedicationFormValidator):
                         {"dosage_guideline": "Invalid. Expected 1000mg/day at baseline"}
                     )
 
+    def validate_stock_codes_are_dispensed(self):
+        if self.cleaned_data.get("stock_codes"):
+            pattern = re.compile("^([A-Z0-9]{6})(,[A-Z0-9]{6})*$")
+            if not pattern.match(self.cleaned_data.get("stock_codes")):
+                raise forms.ValidationError(
+                    {
+                        "stock_codes": (
+                            "Invalid format. Enter one or more valid codes separated by comma"
+                        )
+                    }
+                )
+            for stock_code in self.cleaned_data.get("stock_codes").split(","):
+                try:
+                    Stock.objects.get(
+                        code=stock_code,
+                        dispensed=True,
+                        allocation__registered_subject__subject_identifier=(
+                            self.subject_identifier
+                        ),
+                    )
+                except Stock.DoesNotExist:
+                    raise forms.ValidationError(
+                        {
+                            "stock_codes": (
+                                f"Invalid. Got {stock_code}. "
+                                "Either not allocated to this subject or not dispensed. "
+                                "Please check the bottle or check with your pharmacist."
+                            )
+                        }
+                    )
+
 
 class StudyMedicationForm(CrfModelFormMixin, forms.ModelForm):
     form_validator_cls = StudyMedicationFormValidator