meta-edc 0.2.24__py3-none-any.whl → 1.4.0__py3-none-any.whl

meta_consent/admin/modeladmin_mixins.py

@@ -0,0 +1,148 @@
+from django.contrib import admin, messages
+from django.core.exceptions import MultipleObjectsReturned, ObjectDoesNotExist
+from django.utils.translation import gettext_lazy as _
+from django_audit_fields.admin import audit_fieldset_tuple
+from edc_consent.actions import (
+    flag_as_verified_against_paper,
+    unflag_as_verified_against_paper,
+)
+from edc_identifier import SubjectIdentifierError, is_subject_identifier_or_raise
+from edc_pharmacy.exceptions import PrescriptionAlreadyExists
+from edc_pharmacy.models import Medication
+from edc_pharmacy.prescribe import create_prescription
+
+from meta_edc.meta_version import get_meta_version
+from meta_pharmacy.constants import METFORMIN
+from meta_screening.models.subject_screening import SubjectScreening
+from meta_subject.models import SubjectVisit
+
+from ..forms import SubjectConsentForm
+from ..models import SubjectConsent
+
+
+class SubjectConsentModelAdminMixin:
+    form = SubjectConsentForm
+
+    actions = (
+        flag_as_verified_against_paper,
+        unflag_as_verified_against_paper,
+        "create_missing_metformin_rx",
+    )
+
+    fieldsets = (
+        (
+            None,
+            {
+                "fields": (
+                    "screening_identifier",
+                    "subject_identifier",
+                    "first_name",
+                    "last_name",
+                    "initials",
+                    "gender",
+                    "language",
+                    "is_literate",
+                    "witness_name",
+                    "consent_datetime",
+                    "dob",
+                    "guardian_name",
+                    "is_dob_estimated",
+                    "identity",
+                    "identity_type",
+                    "confirm_identity",
+                    "is_incarcerated",
+                )
+            },
+        ),
+        (
+            "Review Questions",
+            {
+                "fields": (
+                    "consent_reviewed",
+                    "study_questions",
+                    "assessment_score",
+                    "consent_signature",
+                    "consent_copy",
+                ),
+                "description": _("The following questions are directed to the interviewer."),
+            },
+        ),
+        audit_fieldset_tuple,
+    )
+
+    search_fields = ("subject_identifier", "screening_identifier", "identity")
+
+    radio_fields = {  # noqa: RUF012
+        "gender": admin.VERTICAL,
+        "assessment_score": admin.VERTICAL,
+        "consent_copy": admin.VERTICAL,
+        "consent_reviewed": admin.VERTICAL,
+        "consent_signature": admin.VERTICAL,
+        "is_dob_estimated": admin.VERTICAL,
+        "identity_type": admin.VERTICAL,
+        "is_incarcerated": admin.VERTICAL,
+        "is_literate": admin.VERTICAL,
+        "language": admin.VERTICAL,
+        "study_questions": admin.VERTICAL,
+    }
+
+    def delete_view(self, request, object_id, extra_context=None):
+        """Prevent deletion if SubjectVisit objects exist."""
+        extra_context = extra_context or {}
+        obj = SubjectConsent.objects.get(id=object_id)
+        try:
+            protected = [SubjectVisit.objects.get(subject_identifier=obj.subject_identifier)]
+        except ObjectDoesNotExist:
+            protected = None
+        except MultipleObjectsReturned:
+            protected = SubjectVisit.objects.filter(subject_identifier=obj.subject_identifier)
+        extra_context.update({"protected": protected})
+        return super().delete_view(request, object_id, extra_context)
+
+    def get_next_options(self, request=None, **kwargs):
+        """Returns the key/value pairs from the "next" querystring
+        as a dictionary.
+        """
+        next_options = super().get_next_options(request=request, **kwargs)
+        try:
+            is_subject_identifier_or_raise(next_options["subject_identifier"])
+        except SubjectIdentifierError:
+            next_options["subject_identifier"] = SubjectScreening.objects.get(
+                subject_identifier_as_pk=next_options["subject_identifier"]
+            ).subject_identifier
+        except KeyError:
+            pass
+        return next_options
+
+    @admin.action(permissions=["view"], description=_("Create missing METFORMIN prescription"))
+    def create_missing_metformin_rx(self, request, queryset):
+        medication = Medication.objects.get(name=METFORMIN)
+        total = queryset.count()
+        created = 0
+        exist = 0
+        for instance in queryset:
+            try:
+                create_prescription(
+                    subject_identifier=instance.subject_identifier,
+                    report_datetime=instance.consent_datetime,
+                    randomizer_name=get_meta_version(),
+                    medication_names=[medication.name],
+                    site_id=instance.site.id,
+                )
+            except PrescriptionAlreadyExists:
+                exist += 1
+            else:
+                created += 1
+        messages.success(
+            request,
+            _(
+                "Created %(created)s/%(total)s missing %(display_name)s prescriptions. "
+                "Got %(exist)s/%(total)s prescriptions already exist"
+            )
+            % {
+                "created": created,
+                "exist": exist,
+                "total": total,
+                "display_name": medication.display_name,
+            },
+        )

meta_consent/admin/subject_consent_admin.py

@@ -1,147 +1,19 @@
-from django.contrib import admin, messages
-from django.core.exceptions import MultipleObjectsReturned, ObjectDoesNotExist
-from django_audit_fields.admin import audit_fieldset_tuple
-from edc_consent.actions import (
-    flag_as_verified_against_paper,
-    unflag_as_verified_against_paper,
-)
+from django.contrib import admin
 from edc_consent.modeladmin_mixins import ModelAdminConsentMixin
-from edc_identifier import SubjectIdentifierError, is_subject_identifier_or_raise
 from edc_model_admin.dashboard import ModelAdminSubjectDashboardMixin
 from edc_model_admin.history import SimpleHistoryAdmin
-from edc_pharmacy.exceptions import PrescriptionAlreadyExists
-from edc_pharmacy.models import Medication
-from edc_pharmacy.prescribe import create_prescription
-
-from meta_edc.meta_version import get_meta_version
-from meta_pharmacy.constants import METFORMIN
-from meta_screening.models.subject_screening import SubjectScreening
-from meta_subject.models import SubjectVisit
 
 from ..admin_site import meta_consent_admin
 from ..forms import SubjectConsentForm
 from ..models import SubjectConsent
+from .modeladmin_mixins import SubjectConsentModelAdminMixin
 
 
 @admin.register(SubjectConsent, site=meta_consent_admin)
 class SubjectConsentAdmin(
-    ModelAdminConsentMixin, ModelAdminSubjectDashboardMixin, SimpleHistoryAdmin
+    SubjectConsentModelAdminMixin,
+    ModelAdminConsentMixin,
+    ModelAdminSubjectDashboardMixin,
+    SimpleHistoryAdmin,
 ):
-
     form = SubjectConsentForm
-
-    actions = [
-        flag_as_verified_against_paper,
-        unflag_as_verified_against_paper,
-        "create_missing_metformin_rx",
-    ]
-
-    fieldsets = (
-        (
-            None,
-            {
-                "fields": (
-                    "screening_identifier",
-                    "subject_identifier",
-                    "first_name",
-                    "last_name",
-                    "initials",
-                    "gender",
-                    "language",
-                    "is_literate",
-                    "witness_name",
-                    "consent_datetime",
-                    "dob",
-                    "guardian_name",
-                    "is_dob_estimated",
-                    "identity",
-                    "identity_type",
-                    "confirm_identity",
-                    "is_incarcerated",
-                )
-            },
-        ),
-        (
-            "Review Questions",
-            {
-                "fields": (
-                    "consent_reviewed",
-                    "study_questions",
-                    "assessment_score",
-                    "consent_signature",
-                    "consent_copy",
-                ),
-                "description": "The following questions are directed to the interviewer.",
-            },
-        ),
-        audit_fieldset_tuple,
-    )
-
-    search_fields = ("subject_identifier", "screening_identifier", "identity")
-
-    radio_fields = {
-        "gender": admin.VERTICAL,
-        "assessment_score": admin.VERTICAL,
-        "consent_copy": admin.VERTICAL,
-        "consent_reviewed": admin.VERTICAL,
-        "consent_signature": admin.VERTICAL,
-        "is_dob_estimated": admin.VERTICAL,
-        "identity_type": admin.VERTICAL,
-        "is_incarcerated": admin.VERTICAL,
-        "is_literate": admin.VERTICAL,
-        "language": admin.VERTICAL,
-        "study_questions": admin.VERTICAL,
-    }
-
-    def delete_view(self, request, object_id, extra_context=None):
-        """Prevent deletion if SubjectVisit objects exist."""
-        extra_context = extra_context or {}
-        obj = SubjectConsent.objects.get(id=object_id)
-        try:
-            protected = [SubjectVisit.objects.get(subject_identifier=obj.subject_identifier)]
-        except ObjectDoesNotExist:
-            protected = None
-        except MultipleObjectsReturned:
-            protected = SubjectVisit.objects.filter(subject_identifier=obj.subject_identifier)
-        extra_context.update({"protected": protected})
-        return super().delete_view(request, object_id, extra_context)
-
-    def get_next_options(self, request=None, **kwargs):
-        """Returns the key/value pairs from the "next" querystring
-        as a dictionary.
-        """
-        next_options = super().get_next_options(request=request, **kwargs)
-        try:
-            is_subject_identifier_or_raise(next_options["subject_identifier"])
-        except SubjectIdentifierError:
-            next_options["subject_identifier"] = SubjectScreening.objects.get(
-                subject_identifier_as_pk=next_options["subject_identifier"]
-            ).subject_identifier
-        except KeyError:
-            pass
-        return next_options
-
-    @admin.action(permissions=["view"], description="Create missing METFORMIN prescription")
-    def create_missing_metformin_rx(self, request, queryset):
-        medication = Medication.objects.get(name=METFORMIN)
-        total = queryset.count()
-        created = 0
-        exist = 0
-        for instance in queryset:
-            try:
-                create_prescription(
-                    subject_identifier=instance.subject_identifier,
-                    report_datetime=instance.consent_datetime,
-                    randomizer_name=get_meta_version(),
-                    medications=[medication],
-                    site_id=instance.site.id,
-                )
-            except PrescriptionAlreadyExists:
-                exist += 1
-            else:
-                created += 1
-        messages.success(
-            request,
-            f"Created {created}/{total} missing {medication.display_name} prescriptions. "
-            f"Got {exist}/{total} prescriptions already exist",
-        )

meta_consent/admin/subject_consent_v1_admin.py

@@ -0,0 +1,19 @@
+from django.contrib import admin
+from edc_consent.modeladmin_mixins import ModelAdminConsentMixin
+from edc_model_admin.dashboard import ModelAdminSubjectDashboardMixin
+from edc_model_admin.history import SimpleHistoryAdmin
+
+from ..admin_site import meta_consent_admin
+from ..forms import SubjectConsentV1Form
+from ..models import SubjectConsentV1
+from .modeladmin_mixins import SubjectConsentModelAdminMixin
+
+
+@admin.register(SubjectConsentV1, site=meta_consent_admin)
+class SubjectConsentV1Admin(
+    SubjectConsentModelAdminMixin,
+    ModelAdminConsentMixin,
+    ModelAdminSubjectDashboardMixin,
+    SimpleHistoryAdmin,
+):
+    form = SubjectConsentV1Form

meta_consent/admin/subject_consent_v1_ext_admin.py

@@ -0,0 +1,93 @@
+from django.contrib import admin
+from django.utils.translation import gettext_lazy as _
+from django_audit_fields import audit_fieldset_tuple
+from edc_model_admin.dashboard import ModelAdminSubjectDashboardMixin
+from edc_model_admin.history import SimpleHistoryAdmin
+
+from ..admin_site import meta_consent_admin
+from ..forms import SubjectConsentV1ExtForm
+from ..models import SubjectConsentV1Ext
+from .list_filters import AgreesListFilter
+
+
+@admin.register(SubjectConsentV1Ext, site=meta_consent_admin)
+class SubjectConsentV1ExtAdmin(
+    ModelAdminSubjectDashboardMixin,
+    SimpleHistoryAdmin,
+):
+    form = SubjectConsentV1ExtForm
+
+    additional_instructions = (
+        "This consent offers the participant the option to agree to "
+        "extend clinic followup from the original 36 months to 48 months. "
+    )
+
+    fieldsets = (
+        (
+            None,
+            {
+                "fields": (
+                    "subject_consent",
+                    "report_datetime",
+                    "agrees_to_extension",
+                )
+            },
+        ),
+        (
+            "Review Questions",
+            {
+                "fields": (
+                    "consent_reviewed",
+                    "study_questions",
+                    "assessment_score",
+                    "consent_signature",
+                    "consent_copy",
+                ),
+                "description": _("The following questions are directed to the interviewer."),
+            },
+        ),
+        audit_fieldset_tuple,
+    )
+
+    list_display = (
+        "subject_consent",
+        "report_date",
+        "agrees",
+    )
+
+    list_filter = (
+        "report_datetime",
+        AgreesListFilter,
+    )
+
+    radio_fields = {  # noqa: RUF012
+        "agrees_to_extension": admin.VERTICAL,
+        "consent_reviewed": admin.VERTICAL,
+        "study_questions": admin.VERTICAL,
+        "assessment_score": admin.VERTICAL,
+        "consent_signature": admin.VERTICAL,
+        "consent_copy": admin.VERTICAL,
+    }
+
+    def get_readonly_fields(self, request, obj=None) -> tuple[str, ...]:  # noqa: ARG002
+        if obj:
+            return ("subject_consent",)
+        return ()
+
+    def formfield_for_foreignkey(self, db_field, request, **kwargs):
+        if db_field.name == "subject_consent":
+            subject_identifier = request.GET.get("subject_identifier")
+            kwargs["queryset"] = db_field.related_model.objects.filter(
+                subject_identifier=subject_identifier
+            )
+        return super().formfield_for_foreignkey(db_field, request, **kwargs)
+
+    @admin.display(description="Agrees")
+    def agrees(self, obj):
+        return obj.agrees_to_extension
+
+    @admin.display(description="Report date")
+    def report_date(self, obj):
+        if obj:
+            return obj.report_datetime.date()
+        return None

meta_consent/baker_recipes.py

@@ -1,24 +1,22 @@
+from clinicedc_constants import NO, NULL_STRING, YES
 from dateutil.relativedelta import relativedelta
 from django.contrib.sites.models import Site
-from edc_constants.constants import NO, YES
-from edc_utils import get_utcnow
+from django.utils import timezone
 from faker import Faker
 from model_bakery.recipe import Recipe, seq
 
-from .models import SubjectConsent, SubjectReconsent
+from .models import SubjectConsent, SubjectConsentV1, SubjectReconsent
 
 fake = Faker()
 
-
-subjectconsent = Recipe(
-    SubjectConsent,
+opts = dict(
     assessment_score=YES,
     confirm_identity=seq("12315678"),
     consent_copy=YES,
-    consent_datetime=get_utcnow(),
+    consent_datetime=timezone.now(),
     consent_reviewed=YES,
     consent_signature=YES,
-    dob=get_utcnow() - relativedelta(years=25),
+    dob=timezone.now() - relativedelta(years=25),
     first_name=fake.first_name,
     gender="M",
     identity=seq("12315678"),
@@ -28,13 +26,15 @@ subjectconsent = Recipe(
     is_incarcerated=NO,
     is_literate=YES,
     last_name=fake.last_name,
-    screening_identifier=None,
+    screening_identifier=NULL_STRING,
     study_questions=YES,
     site=Site.objects.get_current(),
-    subject_identifier=None,
+    subject_identifier=NULL_STRING,
     user_created="erikvw",
     user_modified="erikvw",
 )
+subjectconsent = Recipe(SubjectConsent, **opts)
+subjectconsentv1 = Recipe(SubjectConsentV1, **opts)
 
 subjectreconsent = Recipe(
     SubjectReconsent,
@@ -43,7 +43,7 @@ subjectreconsent = Recipe(
     assessment_score=YES,
     study_questions=YES,
     consent_copy=YES,
-    action_identifier=None,
+    action_identifier=NULL_STRING,
     user_created="erikvw",
     user_modified="erikvw",
 )

meta_consent/consents.py

@@ -1,17 +1,36 @@
-from edc_consent.consent import Consent
+from datetime import datetime
+from zoneinfo import ZoneInfo
+
+from clinicedc_constants import FEMALE, MALE
+from edc_consent.consent_definition import ConsentDefinition
+from edc_consent.consent_definition_extension import ConsentDefinitionExtension
 from edc_consent.site_consents import site_consents
-from edc_constants.constants import FEMALE, MALE
-from edc_protocol import Protocol
+from edc_protocol.research_protocol_config import ResearchProtocolConfig
 
-v1 = Consent(
-    "meta_consent.subjectconsent",
+consent_v1 = ConsentDefinition(
+    "meta_consent.subjectconsentv1",
     version="1",
-    start=Protocol().study_open_datetime,
-    end=Protocol().study_close_datetime,
+    start=ResearchProtocolConfig().study_open_datetime,
+    end=ResearchProtocolConfig().study_close_datetime,
     age_min=18,
     age_is_adult=18,
     age_max=110,
     gender=[MALE, FEMALE],
+    screening_model=[
+        "meta_screening.subjectscreening",
+        "meta_screening.screeningpartone",
+        "meta_screening.screeningparttwo",
+        "meta_screening.screeningpartthree",
+    ],
+    timepoints=list(range(1, 14 + 1)),
+)
+
+consent_v1_ext = ConsentDefinitionExtension(
+    "meta_consent.subjectconsentv1ext",
+    version="1.1",
+    start=datetime(2024, 12, 16, tzinfo=ZoneInfo("UTC")),
+    extends=consent_v1,
+    timepoints=[15, 16, 17, 18],
 )
 
-site_consents.register(v1)
+site_consents.register(consent_v1, extended_by=consent_v1_ext)

meta_consent/constants.py

@@ -1 +1,2 @@
 RECONSENT_ACTION = "reconsent"
+CONSENT_V1_EXTENSION_ACTION = "consent_v1_ext"

meta_consent/form_validators/__init__.py

@@ -0,0 +1,3 @@
+from .subject_consent_form_validator import SubjectConsentFormValidator
+
+__all__ = ["SubjectConsentFormValidator"]

meta_consent/form_validators/subject_consent_form_validator.py

@@ -0,0 +1,30 @@
+from django import forms
+from django.conf import settings
+from django.utils.translation import gettext_lazy as _
+from edc_consent.form_validators import SubjectConsentFormValidatorMixin
+from edc_form_validators import FormValidator
+
+
+class SubjectConsentFormValidator(SubjectConsentFormValidatorMixin, FormValidator):
+    def validate_identity(self) -> None:
+        """Override to validate `identity_type` is a hospital
+        number and `identity` matches the screening form.
+        """
+        if self.cleaned_data.get("identity_type") != "hospital_no":
+            raise forms.ValidationError({"identity_type": _("Expected 'hospital number'.")})
+
+        if self.subject_screening.hospital_identifier != (
+            self.cleaned_data.get("identity") or getattr(self.instance, "identity", "")
+        ):
+            raise forms.ValidationError(
+                {
+                    "identity": (
+                        _("The hospital identifier does not match that reported at screening.")
+                    )
+                }
+            )
+
+    def validate_consent_datetime(self):
+        if getattr(settings, "EDC_CONSENT_BYPASS_CONSENT_DATETIME_VALIDATION", False):
+            return None
+        return super().validate_consent_datetime()

meta_consent/forms/__init__.py

@@ -1,2 +1,11 @@
-from .subject_consent_form import SubjectConsentForm, SubjectConsentFormValidator
+from .subject_consent_form import SubjectConsentForm
+from .subject_consent_v1_ext_form import SubjectConsentV1ExtForm
+from .subject_consent_v1_form import SubjectConsentV1Form
 from .subject_reconsent_form import SubjectReconsentForm
+
+__all__ = [
+    "SubjectConsentForm",
+    "SubjectConsentV1ExtForm",
+    "SubjectConsentV1Form",
+    "SubjectReconsentForm",
+]

meta_consent/forms/subject_consent_form.py

@@ -1,45 +1,38 @@
 from django import forms
-from django.conf import settings
-from edc_consent.form_validators import SubjectConsentFormValidatorMixin
+from django.utils.translation import gettext_lazy as _
 from edc_consent.modelform_mixins import ConsentModelFormMixin
-from edc_form_validators import FormValidator, FormValidatorMixin
+from edc_form_validators import FormValidatorMixin
 from edc_sites.forms import SiteModelFormMixin
 
+from ..form_validators import SubjectConsentFormValidator
 from ..models import SubjectConsent
 
-# TODO: Assessment score "The client has completed the
-#  assessment of understanding with a passing score"
-
-
-class SubjectConsentFormValidator(SubjectConsentFormValidatorMixin, FormValidator):
-    def validate_identity(self) -> None:
-        """Override to validate `identity_type` is a hospital
-        number and `identity` matches the screening form.
-        """
-        if self.cleaned_data.get("identity_type") != "hospital_no":
-            raise forms.ValidationError({"identity_type": "Expected 'hospital number'."})
-
-        if self.subject_screening.hospital_identifier != (
-            self.cleaned_data.get("identity") or getattr(self.instance, "identity", "")
-        ):
-            raise forms.ValidationError(
-                {
-                    "identity": (
-                        "The hospital identifier does not match that reported at screening."
-                    )
-                }
-            )
-
-    def validate_consent_datetime(self):
-        if getattr(settings, "EDC_CONSENT_BYPASS_CONSENT_DATETIME_VALIDATION", False):
-            return None
-        return super().validate_consent_datetime()
+help_texts = {
+    "identity": (
+        _(
+            "Use Country ID Number, Passport number, driver's license "
+            "number or Country ID receipt number"
+        )
+    ),
+    "witness_name": (
+        _(
+            "Required only if participant is illiterate. "
+            "Format is 'LASTNAME, FIRSTNAME'. "
+            "All uppercase separated by a comma."
+        )
+    ),
+    "screening_identifier": _("(read-only)"),
+}
+
+
+widgets = {
+    "screening_identifier": forms.TextInput(attrs={"readonly": "readonly"}),
+}
 
 
 class SubjectConsentForm(
     SiteModelFormMixin, ConsentModelFormMixin, FormValidatorMixin, forms.ModelForm
 ):
-
     form_validator_cls = SubjectConsentFormValidator
 
     def validate_gender_of_consent(self):
@@ -51,18 +44,5 @@ class SubjectConsentForm(
     class Meta:
         model = SubjectConsent
         fields = "__all__"
-        help_texts = {
-            "identity": (
-                "Use Country ID Number, Passport number, driver's license "
-                "number or Country ID receipt number"
-            ),
-            "witness_name": (
-                "Required only if participant is illiterate. "
-                "Format is 'LASTNAME, FIRSTNAME'. "
-                "All uppercase separated by a comma."
-            ),
-            "screening_identifier": "(read-only)",
-        }
-        widgets = {
-            "screening_identifier": forms.TextInput(attrs={"readonly": "readonly"}),
-        }
+        help_texts = help_texts
+        widgets = widgets