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

meta_analytics/utils.py

@@ -0,0 +1,81 @@
+import pandas as pd
+from great_tables import GT, html, loc, style
+
+
+def df_as_great_table(
+    df_table: pd.DataFrame,
+    title=None,
+    subtitle=None,
+):
+    """Used by monitoring report"""
+    return (
+        GT(df_table)
+        .tab_header(title=html(f'<div class="table-header">{title}</div>'), subtitle=subtitle)
+        .cols_align(align="left", columns=[0, 1])
+        .cols_align(align="right", columns=list(range(2, len(df_table.columns))))
+        .opt_stylize(style=3)
+        .opt_row_striping(row_striping=True)
+        .opt_vertical_padding(scale=1.2)
+        .opt_horizontal_padding(scale=1.0)
+        .tab_options(
+            table_width="100%",
+            stub_background_color="snow",
+            row_group_border_bottom_style="hidden",
+            row_group_padding=0.5,
+            row_group_background_color="snow",
+            table_background_color="snow",
+            table_font_size=10,
+        )
+        .tab_style(
+            style=[style.fill(color="snow"), style.text(color="black")],
+            locations=loc.body(
+                columns=list(range(0, len(df_table.columns))),
+                rows=list(range(0, len(df_table))),
+            ),
+        )
+        .tab_style(
+            style=[style.fill(color="lightgray"), style.text(color="black")],
+            locations=loc.body(
+                columns=[0],
+                rows=list(range(0, len(df_table))),
+            ),
+        )
+    )
+
+
+def df_as_great_table2(
+    df_table: pd.DataFrame,
+    title=None,
+    subtitle=None,
+    rowname_col: str | None = None,
+    groupname_col: str | None = None,
+):
+    """Used by monitoring report"""
+    rowname_col = rowname_col or "label"
+    groupname_col = groupname_col or "visit_code"
+    return (
+        GT(df_table, rowname_col=rowname_col, groupname_col=groupname_col)
+        .tab_header(title=html(f'<div class="table-header">{title}</div>'), subtitle=subtitle)
+        .cols_align(align="left", columns=[0, 1])
+        .cols_align(align="right", columns=list(range(2, len(df_table.columns))))
+        .opt_stylize(style=3)
+        .opt_row_striping(row_striping=True)
+        .opt_vertical_padding(scale=1.2)
+        .opt_horizontal_padding(scale=1.0)
+        .tab_options(
+            table_width="100%",
+            stub_background_color="snow",
+            row_group_border_bottom_style="hidden",
+            row_group_padding=0.5,
+            row_group_background_color="snow",
+            table_background_color="snow",
+            table_font_size=10,
+        )
+        .tab_style(
+            style=[style.fill(color="snow"), style.text(color="black")],
+            locations=loc.body(
+                columns=list(range(0, len(df_table.columns))),
+                rows=list(range(0, len(df_table))),
+            ),
+        )
+    )

meta_auth/auths.py

@@ -1,5 +1,4 @@
 from edc_action_item.auth_objects import ACTION_ITEM, ACTION_ITEM_EXPORT
-from edc_adverse_event.constants import TMG_ROLE
 from edc_appointment.auth_objects import APPOINTMENT_EXPORT
 from edc_auth.constants import (
     AUDITOR,
@@ -10,6 +9,7 @@ from edc_auth.constants import (
     CLINICIAN_SUPER_ROLE,
     NURSE_ROLE,
     PII,
+    TMG_ROLE,
 )
 from edc_auth.site_auths import site_auths
 from edc_data_manager.auth_objects import DATA_MANAGER_EXPORT, DATA_MANAGER_ROLE

meta_consent/action_items.py

@@ -1,7 +1,8 @@
-from edc_action_item import Action, site_action_items
-from edc_constants.constants import HIGH_PRIORITY
+from clinicedc_constants import HIGH_PRIORITY
+from edc_action_item.action import Action
+from edc_action_item.site_action_items import site_action_items
 
-from .constants import RECONSENT_ACTION
+from .constants import CONSENT_V1_EXTENSION_ACTION, RECONSENT_ACTION
 
 
 class ReconsentAction(Action):
@@ -23,4 +24,22 @@ class ReconsentAction(Action):
         return False
 
 
+class ConsentV1ExtensionAction(Action):
+    name = CONSENT_V1_EXTENSION_ACTION
+    display_name = "Ask to extend followup (required)"
+    reference_model = "meta_consent.subjectconsentv1ext"
+    priority = HIGH_PRIORITY
+    show_on_dashboard = True
+    show_link_to_changelist = True
+    admin_site_name = "meta_consent_admin"
+    show_link_to_add = True
+    create_by_user = True
+    singleton = True
+    instructions = "Participant must complete as soon as able. "
+
+    def reopen_action_item_on_change(self):
+        return False
+
+
 site_action_items.register(ReconsentAction)
+site_action_items.register(ConsentV1ExtensionAction)

meta_consent/admin/__init__.py

@@ -1,2 +1,9 @@
 from .subject_consent_admin import SubjectConsentAdmin
 from .subject_consent_v1_admin import SubjectConsentV1Admin
+from .subject_consent_v1_ext_admin import SubjectConsentV1ExtAdmin
+
+__all__ = [
+    "SubjectConsentAdmin",
+    "SubjectConsentV1Admin",
+    "SubjectConsentV1ExtAdmin",
+]

meta_consent/admin/actions/__init__.py

@@ -1 +1,3 @@
 from .create_missing_prescriptions import create_missing_metformin_rx
+
+__all__ = ["create_missing_metformin_rx"]

meta_consent/admin/actions/create_missing_prescriptions.py

@@ -9,7 +9,7 @@ from meta_pharmacy.constants import METFORMIN
 
 
 @admin.action(permissions=["view"], description="Create missing METFORMIN prescription")
-def create_missing_metformin_rx(modeladmin, request, queryset):
+def create_missing_metformin_rx(modeladmin, request, queryset):  # noqa: ARG001
     medication = Medication.objects.get(name=METFORMIN)
     total = queryset.count()
     subject_identifiers = queryset.values_list("subject_identifier", flat=True)
@@ -24,7 +24,7 @@ def create_missing_metformin_rx(modeladmin, request, queryset):
                 subject_identifier=instance.subject_identifier,
                 report_datetime=instance.consent_datetime,
                 randomizer_name=get_meta_version(),
-                medications=[medication],
+                medication_names=[medication.name],
                 site_id=instance.site.id,
             )
         except PrescriptionAlreadyExists:

meta_consent/admin/list_filters.py

@@ -0,0 +1,22 @@
+from clinicedc_constants import NO, NOT_APPLICABLE, YES
+from django.contrib.admin import SimpleListFilter
+from edc_constants.choices import YES_NO_NA
+
+
+class AgreesListFilter(SimpleListFilter):
+    title = "Agrees"
+    parameter_name = "agrees"
+
+    def lookups(self, request, model_admin):  # noqa: ARG002
+        return YES_NO_NA
+
+    def queryset(self, request, queryset):  # noqa: ARG002
+        qs = None
+        if self.value():
+            if self.value() == YES:
+                qs = queryset.filter(agrees_to_extension=YES)
+            elif self.value() == NO:
+                qs = queryset.filter(agrees_to_extension=NO)
+            elif self.value() == NOT_APPLICABLE:
+                qs = queryset.filter(agrees_to_extension=NOT_APPLICABLE)
+        return qs

meta_consent/admin/modeladmin_mixins.py

@@ -21,14 +21,13 @@ from ..models import SubjectConsent
 
 
 class SubjectConsentModelAdminMixin:
-
     form = SubjectConsentForm
 
-    actions = [
+    actions = (
         flag_as_verified_against_paper,
         unflag_as_verified_against_paper,
         "create_missing_metformin_rx",
-    ]
+    )
 
     fieldsets = (
         (
@@ -73,7 +72,7 @@ class SubjectConsentModelAdminMixin:
 
     search_fields = ("subject_identifier", "screening_identifier", "identity")
 
-    radio_fields = {
+    radio_fields = {  # noqa: RUF012
         "gender": admin.VERTICAL,
         "assessment_score": admin.VERTICAL,
         "consent_copy": admin.VERTICAL,
@@ -127,7 +126,7 @@ class SubjectConsentModelAdminMixin:
                     subject_identifier=instance.subject_identifier,
                     report_datetime=instance.consent_datetime,
                     randomizer_name=get_meta_version(),
-                    medications=[medication],
+                    medication_names=[medication.name],
                     site_id=instance.site.id,
                 )
             except PrescriptionAlreadyExists:

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

@@ -1,7 +1,7 @@
+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
 
@@ -13,10 +13,10 @@ 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"),
@@ -26,10 +26,10 @@ opts = dict(
     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",
 )
@@ -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

@@ -1,6 +1,10 @@
+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.research_protocol_config import ResearchProtocolConfig
 
 consent_v1 = ConsentDefinition(
@@ -18,6 +22,15 @@ consent_v1 = ConsentDefinition(
         "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(consent_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

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

meta_consent/forms/__init__.py

@@ -1,3 +1,11 @@
 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_v1_ext_form.py

@@ -0,0 +1,47 @@
+from clinicedc_constants import NOT_APPLICABLE
+from django import forms
+from edc_consent.modelform_mixins import ReviewFieldsModelFormMixin
+from edc_form_validators import FormValidatorMixin
+from edc_sites.forms import SiteModelFormMixin
+from edc_utils.date import to_local
+
+from ..consents import consent_v1_ext
+from ..models import SubjectConsentV1Ext
+
+
+class SubjectConsentV1ExtForm(
+    SiteModelFormMixin, ReviewFieldsModelFormMixin, FormValidatorMixin, forms.ModelForm
+):
+    def clean(self):
+        cleaned_data = super().clean()
+        start_datetime = to_local(consent_v1_ext.start)
+        if (
+            cleaned_data.get("report_datetime")
+            and cleaned_data.get("report_datetime") < start_datetime
+        ):
+            dt = start_datetime.date().strftime("%Y-%m-%d")
+            raise forms.ValidationError(
+                {"report_datetime": f"Cannot be before consent approval date {dt}."}
+            )
+
+        if cleaned_data.get("agrees_to_extension") == NOT_APPLICABLE:
+            raise forms.ValidationError({"agrees_to_extension": "Invalid option"})
+        return cleaned_data
+
+    widgets = {  # noqa: RUF012
+        "subject_identifier": forms.TextInput(attrs={"readonly": "readonly"}),
+    }
+
+    class Meta:
+        model = SubjectConsentV1Ext
+        fields = "__all__"
+        labels = {  # noqa: RUF012
+            "study_questions": (
+                "I have answered all questions the participant had about the "
+                "follow-up extension"
+            ),
+            "assessment_score": (
+                "I have asked the participant questions about the follow-up extension and "
+                "the participant has demonstrated understanding"
+            ),
+        }

meta_consent/forms/subject_reconsent_form.py

@@ -23,15 +23,15 @@ class SubjectReconsentForm(
                 subject_identifier=cleaned_data.get("subject_identifier"),
                 identity=cleaned_data.get("identity"),
             )
-        except ObjectDoesNotExist:
-            raise forms.ValidationError({"identity": "Identity number does not match."})
+        except ObjectDoesNotExist as e:
+            raise forms.ValidationError({"identity": "Identity number does not match."}) from e
         return cleaned_data
 
     class Meta:
         model = SubjectReconsent
         fields = "__all__"
-        help_text = {"action_identifier": "(read-only)", "subject_identifier": "(read-only)"}
-        widgets = {
+        help_text = {"action_identifier": "(read-only)", "subject_identifier": "(read-only)"}  # noqa: RUF012
+        widgets = {  # noqa: RUF012
             "action_identifier": forms.TextInput(attrs={"readonly": "readonly"}),
             "subject_identifier": forms.TextInput(attrs={"readonly": "readonly"}),
         }

meta_consent/management/commands/create_missing_prescriptions.py

@@ -1,3 +1,5 @@
+import sys
+
 from django.core.management.base import BaseCommand, CommandError
 from edc_pharmacy.exceptions import PrescriptionAlreadyExists
 from edc_pharmacy.models import Medication, Rx
@@ -12,7 +14,7 @@ from meta_pharmacy.constants import METFORMIN
 class Command(BaseCommand):
     help = "Create missing prescriptions"
 
-    def handle(self, *args, **options):
+    def handle(self, *args, **options):  # noqa: ARG002
         medication = Medication.objects.get(name=METFORMIN)
         subject_identifiers = Rx.objects.values_list("subject_identifier", flat=True).all()
         subject_consents_wo_rx = SubjectConsent.objects.exclude(
@@ -25,10 +27,10 @@ class Command(BaseCommand):
                     subject_identifier=instance.subject_identifier,
                     report_datetime=instance.consent_datetime,
                     randomizer_name=get_meta_version(),
-                    medications=[medication],
+                    medication_names=[medication.name],
                     site_id=instance.site.id,
                 )
             except PrescriptionAlreadyExists:
                 pass
             except CommandError as e:
-                print(f"Failed for {instance.subject_identifier}. Got {e}")
+                sys.stdout.write(f"Failed for {instance.subject_identifier}. Got {e}\n")

meta_consent/migrations/0001_initial.py

@@ -8,7 +8,7 @@ import django.db.models.deletion
 import django_audit_fields.fields.hostname_modification_field
 import django_audit_fields.fields.userfield
 import django_audit_fields.fields.uuid_auto_field
-import django_audit_fields.models.audit_model_mixin
+import django.utils.timezone
 import django_crypto_fields.fields.encrypted_char_field
 import django_crypto_fields.fields.encrypted_text_field
 import django_crypto_fields.fields.firstname_field
@@ -55,14 +55,14 @@ class Migration(migrations.Migration):
                     "created",
                     models.DateTimeField(
                         blank=True,
-                        default=django_audit_fields.models.audit_model_mixin.utcnow,
+                        default=django.utils.timezone.now,
                     ),
                 ),
                 (
                     "modified",
                     models.DateTimeField(
                         blank=True,
-                        default=django_audit_fields.models.audit_model_mixin.utcnow,
+                        default=django.utils.timezone.now,
                     ),
                 ),
                 (
@@ -288,14 +288,14 @@ class Migration(migrations.Migration):
                     "created",
                     models.DateTimeField(
                         blank=True,
-                        default=django_audit_fields.models.audit_model_mixin.utcnow,
+                        default=django.utils.timezone.now,
                     ),
                 ),
                 (
                     "modified",
                     models.DateTimeField(
                         blank=True,
-                        default=django_audit_fields.models.audit_model_mixin.utcnow,
+                        default=django.utils.timezone.now,
                     ),
                 ),
                 (
@@ -773,14 +773,14 @@ class Migration(migrations.Migration):
                     "created",
                     models.DateTimeField(
                         blank=True,
-                        default=django_audit_fields.models.audit_model_mixin.utcnow,
+                        default=django.utils.timezone.now,
                     ),
                 ),
                 (
                     "modified",
                     models.DateTimeField(
                         blank=True,
-                        default=django_audit_fields.models.audit_model_mixin.utcnow,
+                        default=django.utils.timezone.now,
                     ),
                 ),
                 (
@@ -1043,14 +1043,14 @@ class Migration(migrations.Migration):
                     "created",
                     models.DateTimeField(
                         blank=True,
-                        default=django_audit_fields.models.audit_model_mixin.utcnow,
+                        default=django.utils.timezone.now,
                     ),
                 ),
                 (
                     "modified",
                     models.DateTimeField(
                         blank=True,
-                        default=django_audit_fields.models.audit_model_mixin.utcnow,
+                        default=django.utils.timezone.now,
                     ),
                 ),
                 (

meta_consent/migrations/0024_historicalsubjectconsentv1.py

@@ -8,7 +8,7 @@ import django.db.models.deletion
 import django_audit_fields.fields.hostname_modification_field
 import django_audit_fields.fields.userfield
 import django_audit_fields.fields.uuid_auto_field
-import django_audit_fields.models.audit_model_mixin
+import django.utils.timezone
 import django_crypto_fields.fields.encrypted_char_field
 import django_crypto_fields.fields.encrypted_text_field
 import django_crypto_fields.fields.firstname_field
@@ -24,7 +24,6 @@ import uuid
 
 
 class Migration(migrations.Migration):
-
     dependencies = [
         ("sites", "0002_alter_domain_unique"),
         migrations.swappable_dependency(settings.AUTH_USER_MODEL),
@@ -48,15 +47,11 @@ class Migration(migrations.Migration):
                 ),
                 (
                     "created",
-                    models.DateTimeField(
-                        blank=True, default=django_audit_fields.models.audit_model_mixin.utcnow
-                    ),
+                    models.DateTimeField(blank=True, default=django.utils.timezone.now),
                 ),
                 (
                     "modified",
-                    models.DateTimeField(
-                        blank=True, default=django_audit_fields.models.audit_model_mixin.utcnow
-                    ),
+                    models.DateTimeField(blank=True, default=django.utils.timezone.now),
                 ),
                 (
                     "user_created",