clinicedc 2.0.27__py3-none-any.whl → 2.0.29__py3-none-any.whl

edc_auth/utils.py

@@ -1,5 +1,7 @@
 from __future__ import annotations
 
+import contextlib
+import sys
 from pprint import pprint
 from typing import TYPE_CHECKING, Any
 
@@ -24,25 +26,23 @@ def get_user(username: str) -> User | None:
     return user
 
 
-def compare_codenames_for_group(group_name: str = None, expected: list[str] = None) -> None:
+def compare_codenames_for_group(group_name: str, expected: list[str]) -> None:
     group = django_apps.get_model("auth.group").objects.get(name=group_name)
     codenames = [p.codename for p in group.permissions.all()]
     new_expected = []
     for c in expected:
-        try:
+        with contextlib.suppress(IndexError):
             c = c.split(".")[1]
-        except IndexError:
-            pass
         new_expected.append(c)
 
     compared = [c for c in new_expected if c not in codenames]
     if compared:
-        print(group.name, "missing from codenames")
-        pprint(compared)
+        sys.stdout.write(f"{group.name},  missing from codenames\n")
+        pprint(compared)  # noqa: T203
     compared = [c for c in codenames if c not in new_expected]
     if compared:
-        print(group.name, "extra codenames")
-        pprint(compared)
+        sys.stdout.write(f"{group.name},  extra codenames\n")
+        pprint(compared)  # noqa: T203
 
 
 def remove_default_model_permissions_from_edc_permissions(auth_updater: Any, app_label: str):
@@ -119,9 +119,7 @@ def get_codenames_for_user(
     for role in roles.all():
         groups.extend([grp for grp in role.groups.all() if grp not in account_manager_groups])
     if include_groups:
-        for group in user.groups.all():
-            if group not in account_manager_groups:
-                groups.append(group)
+        groups.extend([grp for grp in user.groups.all() if grp not in account_manager_groups])
     groups = list(set(groups))
     for group in groups:
         codenames.extend(

edc_consent/consent_definition.py

@@ -101,7 +101,10 @@ class ConsentDefinition:
 
     @property
     def model(self):
-        from .managers import ConsentObjectsByCdefManager, CurrentSiteByCdefManager
+        from .managers import (  # noqa: PLC0415
+            ConsentObjectsByCdefManager,
+            CurrentSiteByCdefManager,
+        )
 
         model_cls = django_apps.get_model(self._model)
         if not model_cls._meta.proxy:

edc_consent/models/__init__.py

@@ -1,11 +1,11 @@
 from .edc_permissions import EdcPermissions
 from .signals import (
     requires_consent_on_pre_save,
-    # update_appointment_from_consentext_post_save,
+    update_appointment_from_consentext_post_save,
 )
 
 __all__ = [
     "EdcPermissions",
     "requires_consent_on_pre_save",
-    # "update_appointment_from_consentext_post_save",
+    "update_appointment_from_consentext_post_save",
 ]

edc_consent/models/signals.py

@@ -1,9 +1,14 @@
-from django.db.models.signals import pre_save
+import contextlib
+
+from django.db.models.signals import post_save, pre_save
 from django.dispatch import receiver
 
 from edc_sites import site_sites
+from edc_visit_schedule.exceptions import NotOnScheduleError
+from edc_visit_schedule.site_visit_schedules import site_visit_schedules
+from edc_visit_schedule.subject_schedule import SubjectSchedule
 
-from ..model_mixins import RequiresConsentFieldsModelMixin
+from ..model_mixins import ConsentExtensionModelMixin, RequiresConsentFieldsModelMixin
 from ..site_consents import site_consents
 
 
@@ -50,27 +55,28 @@ def requires_consent_on_pre_save(instance, raw, using, update_fields, **kwargs):
         instance.consent_model = consent_definition.model
 
 
-# @receiver(
-#     post_save,
-#     weak=False,
-#     dispatch_uid="update_appointment_from_consentext_post_save",
-# )
-# def update_appointment_from_consentext_post_save(
-#     sender, instance, raw, created, using, **kwargs
-# ):
-#     if (
-#         not raw
-#         and not kwargs.get("update_fields")
-#         and isinstance(instance, (ConsentExtensionModelMixin,))
-#     ):
-#         cdef = site_consents.get_consent_definition(
-#             model=instance.subject_consent._meta.label_lower,
-#             version=instance.subject_consent.version,
-#         )
-#         visit_schedule, schedule = site_visit_schedules.get_by_consent_definition(cdef)
-#         subject_schedule = SubjectSchedule(
-#             instance.subject_consent.subject_identifier,
-#             visit_schedule=visit_schedule,
-#             schedule=schedule,
-#         )
-#         subject_schedule.refresh_appointments()
+@receiver(
+    post_save,
+    weak=False,
+    dispatch_uid="update_appointment_from_consentext_post_save",
+)
+def update_appointment_from_consentext_post_save(
+    sender, instance, raw, created, using, **kwargs
+):
+    if (
+        not raw
+        and not kwargs.get("update_fields")
+        and isinstance(instance, (ConsentExtensionModelMixin,))
+    ):
+        cdef = site_consents.get_consent_definition(
+            model=instance.subject_consent._meta.label_lower,
+            version=instance.subject_consent.version,
+        )
+        for visit_schedule, schedule in site_visit_schedules.get_by_consent_definition(cdef):
+            subject_schedule = SubjectSchedule(
+                instance.subject_consent.subject_identifier,
+                visit_schedule=visit_schedule,
+                schedule=schedule,
+            )
+            with contextlib.suppress(NotOnScheduleError):
+                subject_schedule.refresh_appointments()

edc_model_admin/mixins/model_admin_form_instructions_mixin.py

@@ -46,7 +46,9 @@ class ModelAdminFormInstructionsMixin:
     change_additional_instructions = ()
 
     def get_add_instructions(
-        self, extra_context: dict | None, request: WSGIRequest | None = None
+        self,
+        extra_context: dict | None,
+        request: WSGIRequest | None = None,  # noqa: ARG002
     ):
         extra_context = extra_context or {}
         extra_context["instructions"] = self.add_instructions or self.instructions
@@ -56,7 +58,9 @@ class ModelAdminFormInstructionsMixin:
         return extra_context
 
     def get_change_instructions(
-        self, extra_context: dict | None, request: WSGIRequest | None = None
+        self,
+        extra_context: dict | None,
+        request: WSGIRequest | None = None,  # noqa: ARG002
     ):
         extra_context = extra_context or {}
         extra_context["instructions"] = self.change_instructions or self.instructions
@@ -65,7 +69,9 @@ class ModelAdminFormInstructionsMixin:
         )
         return extra_context
 
-    def add_view(self, request: WSGIRequest, form_url: str = "", extra_context: dict = None):
+    def add_view(
+        self, request: WSGIRequest, form_url: str = "", extra_context: dict | None = None
+    ):
         extra_context = self.get_add_instructions(extra_context, request=request)
         return super().add_view(request, form_url=form_url, extra_context=extra_context)
 

edc_model_admin/mixins/model_admin_protect_pii_mixin.py

@@ -23,20 +23,20 @@ class ModelAdminProtectPiiMixin:
 
     extra_pii_attrs: tuple[str] | None = ()
 
-    def get_extra_pii_attrs(self) -> list[str | tuple[str, str]]:
-        return self.extra_pii_attrs or []
+    def get_extra_pii_attrs(self) -> tuple[str | tuple[str, str]]:
+        return self.extra_pii_attrs
 
     def get_encrypted_fields(self) -> tuple[str, ...]:
-        encrypted_fields = [f.name for f in get_encrypted_fields(self.model)]
-        encrypted_fields.extend(*self.get_extra_pii_attrs())
-        return tuple(set(encrypted_fields))
+        encrypted_fields = tuple([f.name for f in get_encrypted_fields(self.model)])
+        return tuple({*encrypted_fields, *self.get_extra_pii_attrs()})
 
     def get_list_display(self, request) -> tuple[str]:
         list_display = super().get_list_display(request)
         if not request.user.groups.filter(name__in=[PII, PII_VIEW]).exists():
             # TODO: search replace from list_display if extra_pii_attr has tuple
-            list_display = [f for f in list_display if f not in self.get_encrypted_fields()]
-            list_display = tuple(list_display)
+            list_display = tuple(
+                *{f for f in list_display if f not in self.get_encrypted_fields()}
+            )
         return list_display
 
     def get_list_display_links(self, request, list_display) -> list[str] | None:

edc_pharmacy/admin_mixin.py

@@ -7,7 +7,7 @@ class PrintButtonAdminMixin:
     print_server_error = None
 
     def __init__(self, args, *kwargs):
-        super(PrintButtonAdminMixin, self).__init__(*args, **kwargs)
+        super().__init__(*args, **kwargs)
         app_config = django_apps.get_app_config("edc_label")
         self._print_server = None
         self._printers = {}

edc_pharmacy/approve_prescription.py

@@ -8,12 +8,14 @@ class ApprovePrescription:
     def __init__(self, rx_model_obj=None):
         dispense_appointment = rx_model_obj.dispense_appointment
         previous_appointment = dispense_appointment.previous()
-        if previous_appointment:
-            if rx_model_obj.__class__.objects.filter(
+        if (
+            previous_appointment
+            and rx_model_obj.__class__.objects.filter(
                 is_approved=False, dispense_appointment=previous_appointment
-            ).exists():
-                raise PrescriptionApprovalValidatorError(
-                    f"Future prescriptions cannot be approved. Approve "
-                    f"prescriptions for dispensing date "
-                    f"{previous_appointment.appt_datetime}"
-                )
+            ).exists()
+        ):
+            raise PrescriptionApprovalValidatorError(
+                f"Future prescriptions cannot be approved. Approve "
+                f"prescriptions for dispensing date "
+                f"{previous_appointment.appt_datetime}"
+            )

edc_pharmacy/auth_objects.py

@@ -20,7 +20,7 @@ PHARMACY_SUPER_ROLE = "PHARMACY_SUPER_ROLE"
 navbar_codenames = ["edc_pharmacy.nav_pharmacy_section"]
 navbar_tuples = []
 for codename in navbar_codenames:
-    navbar_tuples.append((codename, f"Can access {codename.split('.')[1]}"))
+    navbar_tuples.append((codename, f"Can access {codename.split('.')[1]}"))  # noqa: PERF401
 
 
 # central pharmacist

edc_pharmacy/exceptions.py

@@ -1,4 +1,4 @@
-class ActivePrescriptionRefillOverlap(Exception):
+class ActivePrescriptionRefillOverlap(Exception):  # noqa: N818
     pass
 
 
@@ -6,7 +6,7 @@ class RefillError(Exception):
     pass
 
 
-class ActiveRefillAlreadyExists(Exception):
+class ActiveRefillAlreadyExists(Exception):  # noqa: N818
     pass
 
 
@@ -34,7 +34,7 @@ class PackagingLotNumberMismatchError(Exception):
     pass
 
 
-class PrescriptionAlreadyExists(Exception):
+class PrescriptionAlreadyExists(Exception):  # noqa: N818
     pass
 
 
@@ -42,15 +42,15 @@ class PrescriptionError(Exception):
     pass
 
 
-class PrescriptionExpired(Exception):
+class PrescriptionExpired(Exception):  # noqa: N818
     pass
 
 
-class RefillAlreadyExists(Exception):
+class RefillAlreadyExists(Exception):  # noqa: N818
     pass
 
 
-class PrescriptionNotStarted(Exception):
+class PrescriptionNotStarted(Exception):  # noqa: N818
     pass
 
 
@@ -74,7 +74,7 @@ class InsufficientStockError(Exception):
     pass
 
 
-class InvalidContainer(Exception):
+class InvalidContainer(Exception):  # noqa: N818
     pass
 
 

edc_pharmacy/settings.py

@@ -15,7 +15,7 @@ BASE_DIR = Path(__file__).resolve().parent.parent
 # See https://docs.djangoproject.com/en/5.1/howto/deployment/checklist/
 
 # SECURITY WARNING: keep the secret key used in production secret!
-SECRET_KEY = "django-insecure-+#-*m&byi1w8=#e5nr))^kollb=k1b#rvjffo#+teji^qpm14o"  # nosec B105
+SECRET_KEY = "django-insecure-+#-*m&byi1w8=#e5nr))^kollb=k1b#rvjffo#+teji^qpm14o"  # nosec B105  # noqa: S105
 
 # SECURITY WARNING: don't run with debug turned on in production!
 DEBUG = True

edc_pharmacy/views/add_to_storage_bin_view.py

@@ -95,8 +95,7 @@ class AddToStorageBinView(EdcViewMixin, NavbarViewMixin, EdcProtocolViewMixin, T
     def storage_bin_changelist_url(self) -> str:
         if self.storage_bin:
             url = reverse("edc_pharmacy_admin:edc_pharmacy_storagebin_changelist")
-            url = f"{url}?q={self.storage_bin.bin_identifier}"
-            return url
+            return f"{url}?q={self.storage_bin.bin_identifier}"
         return "/"
 
     def redirect_on_has_duplicates(
@@ -144,30 +143,29 @@ class AddToStorageBinView(EdcViewMixin, NavbarViewMixin, EdcProtocolViewMixin, T
     def redirect_on_invalid_subject_for_location(
         self, stock_codes: list[str], storage_bin: StorageBin
     ) -> HttpResponseRedirect | None:
-        if stock_codes:
-            if (
-                Stock.objects.filter(code__in=stock_codes)
-                .exclude(location=storage_bin.location)
-                .exists()
-            ):
-                qs = Stock.objects.filter(code__in=stock_codes).exclude(
-                    location=storage_bin.location
-                )
-                messages.add_message(
-                    self.request,
-                    messages.ERROR,
-                    f"Stock not from this location. See {[obj.stock.code for obj in qs]}.",
-                )
-                url = reverse(
-                    "edc_pharmacy:add_to_storage_bin_url",
-                    kwargs={
-                        "storage_bin": storage_bin.id,
-                    },
-                )
-                return HttpResponseRedirect(url)
+        if stock_codes and (
+            Stock.objects.filter(code__in=stock_codes)
+            .exclude(location=storage_bin.location)
+            .exists()
+        ):
+            qs = Stock.objects.filter(code__in=stock_codes).exclude(
+                location=storage_bin.location
+            )
+            messages.add_message(
+                self.request,
+                messages.ERROR,
+                f"Stock not from this location. See {[obj.stock.code for obj in qs]}.",
+            )
+            url = reverse(
+                "edc_pharmacy:add_to_storage_bin_url",
+                kwargs={
+                    "storage_bin": storage_bin.id,
+                },
+            )
+            return HttpResponseRedirect(url)
         return None
 
-    def post(self, request, *args, **kwargs):
+    def post(self, request, *args, **kwargs):  # noqa: ARG002
         stock_codes = request.POST.getlist("codes") if request.POST.get("codes") else None
         storage_bin = StorageBin.objects.get(id=kwargs.get("storage_bin"))
         items_to_scan = request.POST.get("items_to_scan") or kwargs.get("items_to_scan")

edc_pharmacy/views/allocate_to_subject_view.py

@@ -96,8 +96,7 @@ class AllocateToSubjectView(EdcViewMixin, NavbarViewMixin, EdcProtocolViewMixin,
     def stock_request_changelist_url(self) -> str:
         if self.stock_request:
             url = reverse("edc_pharmacy_admin:edc_pharmacy_stockrequest_changelist")
-            url = f"{url}?q={self.stock_request.request_identifier}"
-            return url
+            return f"{url}?q={self.stock_request.request_identifier}"
         return "/"
 
     @staticmethod
@@ -120,14 +119,13 @@ class AllocateToSubjectView(EdcViewMixin, NavbarViewMixin, EdcProtocolViewMixin,
                 messages.ERROR,
                 "Nothing saved. Duplicate codes detected in list. Please try again.",
             )
-            url = reverse(
+            return reverse(
                 "edc_pharmacy:allocate_url",
                 kwargs={
                     "stock_request": stock_request.id,
                     "assignment": assignment.id,
                 },
             )
-            return url
         return None
 
     def redirect_on_uncomfirmed_stock_codes(
@@ -153,14 +151,13 @@ class AllocateToSubjectView(EdcViewMixin, NavbarViewMixin, EdcProtocolViewMixin,
                         f"Got {uncomfirmed_codes}. "
                     ),
                 )
-                url = reverse(
+                return reverse(
                     "edc_pharmacy:allocate_url",
                     kwargs={
                         "stock_request": stock_request.id,
                         "assignment": assignment.id,
                     },
                 )
-                return url
         return None
 
     def redirect_on_invalid_stock_codes(
@@ -183,14 +180,13 @@ class AllocateToSubjectView(EdcViewMixin, NavbarViewMixin, EdcProtocolViewMixin,
                 messages.ERROR,
                 f"Nothing saved. Invalid codes detected. Got {invalid_codes}. ",
             )
-            url = reverse(
+            return reverse(
                 "edc_pharmacy:allocate_url",
                 kwargs={
                     "stock_request": stock_request.id,
                     "assignment": assignment.id,
                 },
             )
-            return url
         return None
 
     def redirect_on_has_multiple_container_types(
@@ -211,14 +207,13 @@ class AllocateToSubjectView(EdcViewMixin, NavbarViewMixin, EdcProtocolViewMixin,
                     f"only. See Stock request {stock_request.request_identifier} "
                 ),
             )
-            url = reverse(
+            return reverse(
                 "edc_pharmacy:allocate_url",
                 kwargs={
                     "stock_request": stock_request.id,
                     "assignment": assignment.id,
                 },
             )
-            return url
         return None
 
     def redirect_on_stock_already_allocated(
@@ -234,20 +229,19 @@ class AllocateToSubjectView(EdcViewMixin, NavbarViewMixin, EdcProtocolViewMixin,
             allocated_stock_codes = []
             for stock in Stock.objects.filter(code__in=stock_codes):
                 if stock.allocation:
-                    allocated_stock_codes.append(stock.code)
+                    allocated_stock_codes.append(stock.code)  # noqa: PERF401
             messages.add_message(
                 self.request,
                 messages.ERROR,
                 f"Stock already allocated. Got {','.join(allocated_stock_codes)}.",
             )
-            url = reverse(
+            return reverse(
                 "edc_pharmacy:allocate_url",
                 kwargs={
                     "stock_request": stock_request.id,
                     "assignment": getattr(assignment, "id", None),
                 },
             )
-            return url
         return None
 
     def redirect_on_all_allocated_for_assignment(
@@ -265,14 +259,13 @@ class AllocateToSubjectView(EdcViewMixin, NavbarViewMixin, EdcProtocolViewMixin,
                 )
                 % {"assignment": assignment.display_name.upper()},
             )
-            url = reverse(
+            return reverse(
                 "edc_pharmacy:allocate_url",
                 kwargs={
                     "stock_request": stock_request.id,
                     "assignment": getattr(assignment, "id", None),
                 },
             )
-            return url
         return None
 
     def redirect_on_incorrect_stock_for_assignment(
@@ -292,14 +285,13 @@ class AllocateToSubjectView(EdcViewMixin, NavbarViewMixin, EdcProtocolViewMixin,
                     f"Expected `{assignment.display_name}` only. Check your work."
                 ),
             )
-            url = reverse(
+            return reverse(
                 "edc_pharmacy:allocate_url",
                 kwargs={
                     "stock_request": stock_request.id,
                     "assignment": getattr(assignment, "id", None),
                 },
             )
-            return url
         return None
 
     def get_counts(self, stock_request: StockRequest) -> tuple[int, int]:
@@ -315,7 +307,7 @@ class AllocateToSubjectView(EdcViewMixin, NavbarViewMixin, EdcProtocolViewMixin,
             return remaining_count or 0, total_count
         return 0, 0
 
-    def post(self, request, *args, **kwargs):
+    def post(self, request, *args, **kwargs):  # noqa: ARG002
         stock_codes = request.POST.getlist("codes") if request.POST.get("codes") else None
         subject_identifiers = request.POST.get("subject_identifiers")
         assignment_id = request.POST.get("assignment")

edc_pharmacy/views/celery_task_status_view.py

@@ -4,8 +4,7 @@ from django.views import View
 
 
 class CeleryTaskStatusView(View):
-
-    def get(self, request, *args, **kwargs):
+    def get(self, request, *args, **kwargs):  # noqa: ARG002
         task_id = request.GET.get("task_id")
         response_data = {"task_id": task_id, "status": None}
         try:

edc_pharmacy/views/confirm_stock_from_instance_view.py

@@ -90,7 +90,7 @@ class ConfirmStockFromInstanceView(
     def model_cls(self):
         return django_apps.get_model(f"edc_pharmacy.{self.kwargs.get('model')}")
 
-    def post(self, request, *args, **kwargs):
+    def post(self, request, *args, **kwargs):  # noqa: ARG002
         dct = self.get_values_dict(**kwargs)
         codes = request.POST.getlist("codes")
         confirmed, already_confirmed, invalid = confirm_stock(

edc_pharmacy/views/confirm_stock_from_queryset_view.py

@@ -29,8 +29,8 @@ class ConfirmStockFromQuerySetView(
     navbar_selected_item = "pharmacy"
     codes_per_page = 12
 
-    def get_context_data(self, **kwargs):
-        context = dict(
+    def get_context_data(self, **kwargs):  # noqa: ARG002
+        return dict(
             CONFIRMED=CONFIRMED,
             ALREADY_CONFIRMED=ALREADY_CONFIRMED,
             INVALID=INVALID,
@@ -40,7 +40,6 @@ class ConfirmStockFromQuerySetView(
             source_changelist_url=self.source_changelist_url,
             **self.session_data,
         )
-        return context
 
     @property
     def session_data(self):
@@ -58,10 +57,8 @@ class ConfirmStockFromQuerySetView(
                     [
                         x,
                         ALREADY_CONFIRMED,
-                        _(
-                            "already %(transaction_word)s"
-                            % {"transaction_word": transaction_word}
-                        ),
+                        _("already %(transaction_word)s")
+                        % {"transaction_word": transaction_word},
                     ]
                     for x in session_obj.get("already_confirmed_codes") or []
                 ]
@@ -117,7 +114,7 @@ class ConfirmStockFromQuerySetView(
         label_lower = self.session_data.get("source_label_lower")
         return django_apps.get_model(label_lower)
 
-    def post(self, request, *args, **kwargs):
+    def post(self, request, *args, **kwargs):  # noqa: ARG002
         stock_codes = request.POST.getlist("stock_codes")
         if len(stock_codes) != len(list(set(stock_codes))):
             messages.add_message(

edc_pharmacy/views/dispense_view.py

@@ -85,7 +85,7 @@ class DispenseView(EdcViewMixin, NavbarViewMixin, EdcProtocolViewMixin, Template
             )
         return confirmation_at_site
 
-    def post(self, request, *args, **kwargs):
+    def post(self, request, *args, **kwargs):  # noqa: ARG002
         location_id = request.POST.get("location_id")
         location = Location.objects.get(pk=location_id)
         formulation_id = request.POST.get("formulation_id")

edc_pharmacy/views/move_to_storage_bin_view.py

@@ -11,6 +11,7 @@ from ..models import Stock, StorageBin, StorageBinItem
 from .add_to_storage_bin_view import AddToStorageBinView, StorageBinError
 
 p = inflect.engine()
+MAX_STORAGE_BIN_CAPACITY = 50
 
 
 def move_to_bin(
@@ -25,8 +26,11 @@ def move_to_bin(
     new_capacity = StorageBinItem.objects.filter(storage_bin=storage_bin).count() + len(
         stock_codes
     )
-    if new_capacity > 50:
-        raise StorageBinError(f"Storage bin {storage_bin.name} capacity may not exceeded 50")
+    if new_capacity > MAX_STORAGE_BIN_CAPACITY:
+        raise StorageBinError(
+            f"Storage bin {storage_bin.name} capacity "
+            f"may not exceeded {MAX_STORAGE_BIN_CAPACITY}."
+        )
     if new_capacity > storage_bin.capacity:
         storage_bin.capacity = new_capacity
         storage_bin.save()
@@ -89,7 +93,7 @@ class MoveToStorageBinView(AddToStorageBinView):
             return HttpResponseRedirect(url)
         return None
 
-    def post(self, request, *args, **kwargs):
+    def post(self, request, *args, **kwargs):  # noqa: ARG002
         stock_codes = request.POST.getlist("codes") if request.POST.get("codes") else None
         storage_bin = StorageBin.objects.get(id=kwargs.get("storage_bin"))
         items_to_scan = request.POST.get("items_to_scan") or kwargs.get("items_to_scan")