meta-edc 1.1.14__py3-none-any.whl → 1.1.17__py3-none-any.whl

meta_prn/models/dm_referral.py

@@ -1,5 +1,6 @@
 from django.db import models
 from edc_action_item.models import ActionModelMixin
+from edc_constants.constants import NULL_STRING
 from edc_identifier.model_mixins import UniqueSubjectIdentifierFieldMixin
 from edc_model.models import BaseUuidModel
 from edc_sites.model_mixins import SiteModelMixin
@@ -14,7 +15,6 @@ class DmReferral(
     UniqueSubjectIdentifierFieldMixin,
     BaseUuidModel,
 ):
-
     action_name = DM_REFFERAL_ACTION
 
     report_datetime = models.DateTimeField(
@@ -30,7 +30,7 @@ class DmReferral(
             "Please provide a brief history of the "
             "diabetes diagnosis that lead to this referral"
         ),
-        null=True,
+        default=NULL_STRING,
         blank=False,
     )
 

meta_prn/models/end_of_study.py

@@ -6,6 +6,7 @@ from edc_constants.constants import (
     DELIVERY,
     DIABETES,
     NOT_APPLICABLE,
+    NULL_STRING,
     OTHER,
     PREGNANCY,
     TOXICITY,
@@ -73,7 +74,7 @@ class EndOfStudy(ActionModelMixin, SiteModelMixin, OffstudyModelMixin, BaseUuidM
         verbose_name="If OTHER, please specify",
         max_length=500,
         blank=True,
-        null=True,
+        default=NULL_STRING,
     )
 
     # TODO: 6m off drug and duration ?? See SOP
@@ -118,8 +119,7 @@ class EndOfStudy(ActionModelMixin, SiteModelMixin, OffstudyModelMixin, BaseUuidM
 
     clinical_withdrawal_reason = models.CharField(
         verbose_name=(
-            "If the patient was withdrawn on CLINICAL grounds, "
-            "please specify PRIMARY reason"
+            "If the patient was withdrawn on CLINICAL grounds, please specify PRIMARY reason"
         ),
         max_length=25,
         choices=CLINICAL_WITHDRAWAL_REASONS,
@@ -130,14 +130,14 @@ class EndOfStudy(ActionModelMixin, SiteModelMixin, OffstudyModelMixin, BaseUuidM
         verbose_name="If withdrawn for 'other' condition, please explain",
         max_length=500,
         blank=True,
-        null=True,
+        default=NULL_STRING,
     )
 
     clinical_withdrawal_investigator_decision = models.TextField(
         verbose_name="If withdrawl was an 'investigator decision', please explain ...",
         max_length=500,
         blank=True,
-        null=True,
+        default=NULL_STRING,
     )
 
     toxicity_withdrawal_reason = models.CharField(
@@ -151,7 +151,7 @@ class EndOfStudy(ActionModelMixin, SiteModelMixin, OffstudyModelMixin, BaseUuidM
         verbose_name="If 'other toxicity', please specify ...",
         max_length=500,
         blank=True,
-        null=True,
+        default=NULL_STRING,
     )
 
     transfer_date = models.DateField(
@@ -173,7 +173,7 @@ class EndOfStudy(ActionModelMixin, SiteModelMixin, OffstudyModelMixin, BaseUuidM
         verbose_name="Please provide further details if possible",
         max_length=500,
         blank=True,
-        null=True,
+        default=NULL_STRING,
     )
 
     class Meta(OffstudyModelMixin.Meta):

meta_prn/models/loss_to_followup.py

@@ -1,7 +1,7 @@
 from django.db import models
 from edc_action_item.models.action_model_mixin import ActionModelMixin
 from edc_constants.choices import YES_NO
-from edc_constants.constants import OTHER
+from edc_constants.constants import NULL_STRING, OTHER
 from edc_identifier.model_mixins import UniqueSubjectIdentifierFieldMixin
 from edc_ltfu.constants import LTFU_ACTION
 from edc_model.models import BaseUuidModel, OtherCharField
@@ -48,7 +48,7 @@ class LossToFollowup(
 
     home_visit_detail = models.TextField(
         verbose_name="If YES, provide any further details of the home visit",
-        null=True,
+        default=NULL_STRING,
         blank=False,
     )
 
@@ -64,13 +64,13 @@ class LossToFollowup(
         verbose_name=(
             "Please give details of the circumstances that have led to this decision."
         ),
-        null=True,
+        default=NULL_STRING,
         blank=False,
     )
 
     class Meta(BaseUuidModel.Meta):
         verbose_name = "Loss to Follow Up"
         verbose_name_plural = "Loss to Follow Up"
-        indexes = [
-            models.Index(fields=["subject_identifier", "action_identifier", "site", "id"])
-        ]
+        indexes = (
+            models.Index(fields=("subject_identifier", "action_identifier", "site", "id")),
+        )

meta_prn/models/off_study_medication.py

@@ -1,5 +1,6 @@
 from django.db import models
 from edc_action_item.models import ActionModelMixin
+from edc_constants.constants import NULL_STRING
 from edc_identifier.model_mixins import UniqueSubjectIdentifierFieldMixin
 from edc_model.models import BaseUuidModel
 from edc_pharmacy.models import Medication
@@ -46,13 +47,13 @@ class OffStudyMedication(
 
     reason_other = models.TextField(
         verbose_name="If other, please specify ...",
-        null=True,
+        default=NULL_STRING,
         blank=True,
     )
 
     comment = models.TextField(
         verbose_name="Any additional comments",
-        null=True,
+        default=NULL_STRING,
         blank=True,
     )
 

meta_prn/models/pregnancy_notification.py

@@ -1,7 +1,7 @@
 from django.db import models
 from edc_action_item.models import ActionModelMixin
 from edc_constants.choices import YES_NO, YES_NO_UNSURE
-from edc_constants.constants import YES
+from edc_constants.constants import NULL_STRING, YES
 from edc_identifier.model_mixins import NonUniqueSubjectIdentifierFieldMixin
 from edc_model.models import BaseUuidModel
 from edc_sites.model_mixins import SiteModelMixin
@@ -44,7 +44,7 @@ class PregnancyNotification(
 
     unconfirmed_details = models.TextField(
         verbose_name="If no, please provide details",
-        null=True,
+        default=NULL_STRING,
         blank=True,
     )
 
@@ -97,4 +97,4 @@ class PregnancyNotification(
     class Meta(BaseUuidModel.Meta):
         verbose_name = "Pregnancy Notification"
         verbose_name_plural = "Pregnancy Notifications"
-        unique_together = ["subject_identifier", "edd"]
+        unique_together = ("subject_identifier", "edd")

meta_prn/models/protocol_incident.py

@@ -1,5 +1,6 @@
 from django.db import models
 from edc_action_item.models import ActionItem, ActionModelMixin
+from edc_constants.constants import NULL_STRING
 from edc_identifier.model_mixins import NonUniqueSubjectIdentifierFieldMixin
 from edc_model.models import BaseUuidModel
 from edc_protocol_incident.constants import PROTOCOL_INCIDENT_ACTION
@@ -26,7 +27,9 @@ class ProtocolIncident(
         related_name="meta_prn_action_item",
     )
 
-    action_required_old = models.CharField(max_length=45, choices=ACTION_REQUIRED, null=True)
+    action_required_old = models.CharField(
+        max_length=45, choices=ACTION_REQUIRED, default=NULL_STRING
+    )
 
     def natural_key(self):
         return (self.action_identifier,)

meta_prn/models/signals.py

@@ -24,7 +24,7 @@ from .pregnancy_notification import PregnancyNotification
     sender=PregnancyNotification,
     dispatch_uid="update_schedule_on_pregnancy_notification_post_save",
 )
-def update_schedule_on_pregnancy_notification_post_save(sender, instance, raw, **kwargs):
+def update_schedule_on_pregnancy_notification_post_save(sender, instance, raw, **kwargs):  # noqa: ARG001
     if not raw:
         try:
             OffSchedule.objects.get(subject_identifier=instance.subject_identifier)
@@ -58,18 +58,20 @@ def update_schedule_on_pregnancy_notification_post_save(sender, instance, raw, *
     dispatch_uid="update_urine_pregnancy_on_pregnancy_notification_on_post_save",
 )
 def update_urine_pregnancy_on_pregnancy_notification_on_post_save(
-    sender, instance, raw, **kwargs
+    sender,  # noqa: ARG001
+    instance,
+    raw,
+    **kwargs,  # noqa: ARG001
 ):
-    if not raw:
-        if instance.bhcg_confirmed == YES:
-            UrinePregnancy.objects.filter(
-                subject_visit__subject_identifier=instance.subject_identifier,
-                notified=False,
-                assay_date__lte=instance.report_datetime.date(),
-            ).update(
-                notified_datetime=instance.report_datetime,
-                notified=True,
-            )
+    if not raw and instance.bhcg_confirmed == YES:
+        UrinePregnancy.objects.filter(
+            subject_visit__subject_identifier=instance.subject_identifier,
+            notified=False,
+            assay_date__lte=instance.report_datetime.date(),
+        ).update(
+            notified_datetime=instance.report_datetime,
+            notified=True,
+        )
 
 
 @receiver(
@@ -78,7 +80,7 @@ def update_urine_pregnancy_on_pregnancy_notification_on_post_save(
     sender=DmReferral,
     dispatch_uid="update_schedule_on_dm_referral_post_save",
 )
-def update_schedule_on_dm_referral_post_save(sender, instance, raw, **kwargs):
+def update_schedule_on_dm_referral_post_save(sender, instance, raw, **kwargs):  # noqa: ARG001
     if not raw:
         try:
             OffScheduleDmReferral.objects.get(subject_identifier=instance.subject_identifier)

meta_prn/models/subject_transfer.py

@@ -8,7 +8,6 @@ class SubjectTransfer(
     SubjectTransferModelMixin,
     BaseUuidModel,
 ):
-
     transfer_reason = models.ManyToManyField(
         f"{settings.LIST_MODEL_APP_LABEL}.transferreasons",
         verbose_name="Reason for transfer",

meta_reports/admin/dbviews/imp_substitutions_admin.py

@@ -49,7 +49,7 @@ class ImpSubstitutionsAdmin(
         "allocated_datetime",
     )
 
-    search_fields = ["subject_identifier", "sid", "dispensed_sid"]
+    search_fields = ("subject_identifier", "sid", "dispensed_sid")
 
     def dashboard(self, obj=None, label=None) -> str:
         kwargs = self.get_subject_dashboard_url_kwargs(obj)

meta_reports/admin/dbviews/on_study_missing_values_admin/unmanaged_model_admin.py

@@ -7,7 +7,6 @@ from ....models import OnStudyMissingValues
 
 @admin.register(OnStudyMissingValues, site=meta_reports_admin)
 class OnStudyMissingValuesAdmin(OnStudyMissingValuesModelAdminMixin, admin.ModelAdmin):
-
     include_note_column: bool = True
     project_reports_admin: str = "meta_reports_admin"
     project_subject_admin: str = "meta_subject_admin"

meta_reports/admin/endpoints_all_admin.py

@@ -8,6 +8,5 @@ from .modeladmin_mixins import EndpointsModelAdminMixin
 
 @admin.register(EndpointsProxy, site=meta_reports_admin)
 class EndpointsAllAdmin(EndpointsModelAdminMixin, admin.ModelAdmin):
-
     def rendered_change_list_note(self):
         return render_to_string("meta_reports/endpoints_all_change_list_note.html")

meta_reports/admin/modeladmin_mixins.py

@@ -14,7 +14,7 @@ from edc_visit_schedule.admin import ScheduleStatusListFilter
 from ..tasks import update_endpoints_table
 
 
-def update_endpoints_table_action(modeladmin, request, queryset):
+def update_endpoints_table_action(modeladmin, request, queryset):  # noqa: ARG001
     subject_identifiers = []
     if queryset.count() != modeladmin.model.objects.count():
         subject_identifiers = [o.subject_identifier for o in queryset]

meta_reports/models/dbviews/imp_substitutions/unmanaged_model.py

@@ -8,7 +8,6 @@ from .view_definition import get_view_definition
 
 
 class ImpSubstitutions(QaReportModelMixin, DBView):
-
     original_id = models.UUIDField(null=True)
 
     sid = models.IntegerField(verbose_name="Original SID", null=True)

meta_reports/models/dbviews/on_study_missing_lab_values/unmanged_model.py

@@ -9,7 +9,6 @@ from .view_definition import get_view_definition
 
 
 class OnStudyMissingLabValues(OnStudyMissingValuesModelMixin, QaReportModelMixin, DBView):
-
     view_definition = get_view_definition()
 
     class Meta:

meta_reports/models/dbviews/on_study_missing_values/unmanged_model.py

@@ -9,7 +9,6 @@ from .view_definition import get_view_definition
 
 
 class OnStudyMissingValues(OnStudyMissingValuesModelMixin, QaReportModelMixin, DBView):
-
     view_definition = get_view_definition()
 
     class Meta:

meta_reports/models/dbviews/patient_history_missing_baseline_cd4/unmanaged_model.py

@@ -6,7 +6,6 @@ from .view_definition import get_view_definition
 
 
 class PatientHistoryMissingBaselineCd4(QaReportModelMixin, DBView):
-
     visit_code = models.CharField(max_length=25)
 
     visit_code_sequence = models.IntegerField()

meta_reports/models/dbviews/unattended_three_in_row/unmanaged_model.py

@@ -6,7 +6,6 @@ from .view_definition import get_view_definition
 
 
 class UnattendedThreeInRow(QaReportModelMixin, DBView):
-
     appt_datetime = models.DateTimeField()
 
     first_value = models.CharField(verbose_name="First", max_length=25)

meta_reports/models/dbviews/unattended_three_in_row2/unmanaged_model.py

@@ -6,7 +6,6 @@ from .view_definition import get_view_definition
 
 
 class UnattendedThreeInRow2(QaReportModelMixin, DBView):
-
     first_value = models.CharField(verbose_name="First", max_length=25)
 
     second_value = models.CharField(verbose_name="Second", max_length=25)

meta_reports/models/dbviews/unattended_two_in_row/unmanaged_model.py

@@ -6,7 +6,6 @@ from .view_definition import get_view_definition
 
 
 class UnattendedTwoInRow(QaReportModelMixin, DBView):
-
     appt_datetime = models.DateTimeField()
 
     first_value = models.CharField(verbose_name="First", max_length=25)

meta_screening/admin/fieldsets.py

@@ -1,4 +1,3 @@
-
 from django.utils.safestring import mark_safe
 
 from ..forms import (

meta_screening/admin/screening_part_one_admin.py

@@ -1,4 +1,3 @@
-
 from django.contrib import admin
 from django_audit_fields.admin import audit_fieldset_tuple
 from edc_sites.admin import SiteModelAdminMixin

meta_screening/forms/field_lists.py

@@ -1,4 +1,3 @@
-
 part_one_fields: tuple[str, ...] = (
     "report_datetime",
     "screening_consent",

meta_subject/admin/birth_outcome_admin.py

@@ -66,7 +66,7 @@ class BirthOutcomesAdmin(
         return tuple(set(fields + custom_fields))
 
     @admin.display
-    def delivery_report(self, obj=None, label=None):
+    def delivery_report(self, obj=None, label=None):  # noqa: ARG002
         url = reverse("meta_subject_admin:meta_subject_delivery_changelist")
         url = f"{url}?q={obj.subject_identifier}"
         context = dict(title="Delivery", url=url, label="Delivery")
@@ -90,5 +90,7 @@ class BirthOutcomesAdmin(
                 if callable(super().view_on_site):
                     url = super().view_on_site(obj)
                 else:
-                    raise NoReverseMatch(f"{e}. See subject_dashboard_url_name for {self!r}.")
+                    raise NoReverseMatch(
+                        f"{e}. See subject_dashboard_url_name for {self!r}."
+                    ) from e
         return url

meta_subject/admin/fields.py

@@ -1,12 +1,12 @@
-def get_blood_pressure_fields():
-    return [
+def get_blood_pressure_fields() -> tuple[str, ...]:
+    return (
         "sys_blood_pressure_one",
         "dia_blood_pressure_one",
         "sys_blood_pressure_two",
         "dia_blood_pressure_two",
         "severe_htn",
-    ]
+    )
 
 
-def get_respiratory_o2_fields():
-    return ["respiratory_rate"]
+def get_respiratory_o2_fields() -> tuple[str, ...]:
+    return ("respiratory_rate",)

meta_subject/admin/fieldsets.py

@@ -1,5 +1,5 @@
 def get_htn_fieldset(part=None):
-    fields = [
+    fields = (
         "htn_diagnosis",
         "on_htn_treatment",
         "htn_treatment",
@@ -9,11 +9,11 @@ def get_htn_fieldset(part=None):
         "dyslipidaemia_rx",
         "concomitant_conditions",
         "concomitant_medications",
-    ]
+    )
 
     return (
         f"Part {part}: Hypertension",
-        {"fields": tuple(fields)},
+        {"fields": fields},
     )
 
 
@@ -22,7 +22,7 @@ def get_hiv_fieldset(part=None):
     if part:
         title = f"Part {part}: {title}"
     # TODO: previous_arv_regimen_start_date is PHASE 3 only
-    fields = [
+    fields = (
         "hiv_diagnosis_date",
         "arv_initiation_date",
         "viral_load",
@@ -39,7 +39,7 @@ def get_hiv_fieldset(part=None):
         "on_oi_prophylaxis",
         "oi_prophylaxis",
         "other_oi_prophylaxis",
-    ]
+    )
     return (
         title,
         {"fields": fields},

meta_subject/admin/glucose_admin.py

@@ -84,13 +84,11 @@ class GlucoseAdmin(CrfModelAdminMixin, SimpleHistoryAdmin):
         list_display = list(list_display)
         list_display.insert(3, "ogtt_value")
         list_display.insert(3, "fbg_value")
-        list_display = tuple(list_display)
-        return list_display
+        return tuple(list_display)
 
     def get_list_filter(self, request) -> tuple[str | type[SimpleListFilter], ...]:
         list_filter = super().get_list_filter(request)
         list_filter = list(list_filter)
         list_filter.insert(2, OgttListFilter)
         list_filter.insert(2, FbgListFilter)
-        list_filter = tuple(list_filter)
-        return list_filter
+        return tuple(list_filter)

meta_subject/admin/glucose_fbg_admin.py

@@ -17,7 +17,7 @@ from .modeladmin import CrfModelAdminMixin
 class GlucoseFbgAdmin(CrfModelAdminMixin, SimpleHistoryAdmin):
     form = GlucoseFbgForm
 
-    fieldsets = [
+    fieldsets = (
         (None, {"fields": ("subject_visit", "report_datetime")}),
         (
             "Fasting",
@@ -52,9 +52,9 @@ class GlucoseFbgAdmin(CrfModelAdminMixin, SimpleHistoryAdmin):
         ),
         crf_status_fieldset,
         audit_fieldset_tuple,
-    ]
+    )
 
-    radio_fields = {
+    radio_fields = {  # noqa: RUF012
         "fasting": admin.VERTICAL,
         "fbg_units": admin.VERTICAL,
         "fbg_performed": admin.VERTICAL,
@@ -69,12 +69,10 @@ class GlucoseFbgAdmin(CrfModelAdminMixin, SimpleHistoryAdmin):
         list_display = list(list_display)
         # list_display.insert(3, "ogtt")
         list_display.insert(3, "fbg")
-        list_display = tuple(list_display)
-        return list_display
+        return tuple(list_display)
 
     def get_list_filter(self, request) -> tuple[str | type[SimpleListFilter], ...]:
         list_filter = super().get_list_filter(request)
         list_filter = list(list_filter)
         list_filter.insert(2, GlucoseListFilter)
-        list_filter = tuple(list_filter)
-        return list_filter
+        return tuple(list_filter)

meta_subject/admin/list_filters.py

@@ -13,14 +13,14 @@ class GlucoseListFilter(SimpleListFilter):
     parameter_name = "glucose_value"
     model_cls = GlucoseFbg
 
-    def lookups(self, request, model_admin):
+    def lookups(self, request, model_admin):  # noqa: ARG002
         return (
             (NORMAL, "Normal"),
             (HIGH, "High"),
             (VERY_HIGH, "Very high"),
         )
 
-    def queryset(self, request, queryset):
+    def queryset(self, request, queryset):  # noqa: ARG002
         qs = None
         if self.value():
             if self.value() == NORMAL:
@@ -52,7 +52,7 @@ class OgttListFilter(SimpleListFilter):
             (HIGH, "High"),
         )
 
-    def queryset(self, request, queryset):
+    def queryset(self, request, queryset):  # noqa: ARG002
         qs = None
         if self.value():
             if self.value() == NORMAL:

meta_subject/admin/next_appointment_admin.py

@@ -16,5 +16,4 @@ __all__ = ["NextAppointmentAdmin"]
 class NextAppointmentAdmin(
     CrfModelAdminMixin, NextAppointmentCrfModelAdminMixin, SimpleHistoryAdmin
 ):
-
     form = NextAppointmentForm

meta_subject/form_validators/glucose_form_validator.py

@@ -70,11 +70,13 @@ class GlucoseFormValidator(FbgOgttFormValidatorMixin, CrfFormValidator):
 
     def is_endpoint(self):
         value = NO
-        if (self.cleaned_data.get("fbg_value") >= Decimal("7.0") and self.cleaned_data.get(
-            "ogtt_value"
-        ) >= Decimal("11.1")) or (self.cleaned_data.get("fbg_value") < Decimal("7.0") and self.cleaned_data.get(
-            "ogtt_value"
-        ) >= Decimal("11.1")):
+        if (
+            self.cleaned_data.get("fbg_value") >= Decimal("7.0")
+            and self.cleaned_data.get("ogtt_value") >= Decimal("11.1")
+        ) or (
+            self.cleaned_data.get("fbg_value") < Decimal("7.0")
+            and self.cleaned_data.get("ogtt_value") >= Decimal("11.1")
+        ):
             value = YES
         elif self.cleaned_data.get("fbg_value") >= Decimal("7.0") and self.cleaned_data.get(
             "ogtt_value"

meta_subject/forms/blood_results/blood_results_hba1c_form.py

@@ -9,7 +9,7 @@ from ...models import BloodResultsHba1c
 
 
 class BloodResultsHba1cFormValidator(BloodResultsFormValidatorMixin, CrfFormValidator):
-    panels = [hba1c_poc_panel, hba1c_panel]
+    panels = (hba1c_poc_panel, hba1c_panel)
 
 
 class BloodResultsHba1cForm(ActionItemCrfFormMixin, CrfModelFormMixin, forms.ModelForm):

meta_subject/forms/subject_requisition_form.py

@@ -20,7 +20,7 @@ class SubjectRequisitionForm(RequisitionModelFormMixin, forms.ModelForm):
         cleaned_data = super().clean()
         if cleaned_data.get("reason_not_drawn") == NOT_REQUIRED:
             raise forms.ValidationError(
-                {"reason_not_drawn": "Invalid choice. Not expected " "for this panel"}
+                {"reason_not_drawn": "Invalid choice. Not expected for this panel"}
             )
         return cleaned_data
 

meta_subject/models/blood_results/__init__.py

@@ -15,4 +15,3 @@ __all__ = [
     "BloodResultsLipids",
     "BloodResultsRft",
 ]
-

meta_subject/models/next_appointment.py

@@ -9,7 +9,6 @@ __all__ = ["NextAppointment"]
 
 
 class NextAppointment(NextAppointmentCrfModelMixin, CrfModelMixin, BaseUuidModel):
-
     class Meta(CrfModelMixin.Meta, BaseUuidModel.Meta):
         verbose_name = "Next Appointment"
         verbose_name_plural = "Next Appointments"