clinicedc 2.0.7__py3-none-any.whl → 2.0.9__py3-none-any.whl

edc_dashboard/view_mixins/url_request_context_mixin.py

@@ -30,10 +30,11 @@ class UrlRequestContextMixin:
     @classmethod
     def urls(
         cls,
-        namespace: str = None,
-        label: str = None,
-        identifier_label: str = None,
-        identifier_pattern: str = None,
+        *,
+        label: str,
+        identifier_pattern: str,
+        namespace: str | None = None,
+        identifier_label: str | None = None,
     ) -> list[URLPattern]:
         label = (
             label
@@ -62,5 +63,5 @@ class UrlRequestContextMixin:
                 f"Url name not defined in url_names. "
                 f"Expected one of {url_names.registry}. Got {e}. "
                 f"Hint: check if dashboard middleware is loaded."
-            )
+            ) from e
         return url_data

edc_data_manager/admin/data_query_admin.py

@@ -45,7 +45,7 @@ class DataQueryAdmin(SiteModelAdminMixin, ModelAdminSubjectDashboardMixin, Simpl
 
     locked_column_template_name = "edc_data_manager/columns/locked.html"
 
-    status_column_context = {
+    status_column_context = {  # noqa: RUF012
         "NEW": NEW,
         "OPEN": OPEN,
         "FEEDBACK": FEEDBACK,
@@ -61,13 +61,13 @@ class DataQueryAdmin(SiteModelAdminMixin, ModelAdminSubjectDashboardMixin, Simpl
 
     actions = (toggle_dm_status,)
 
-    radio_fields = {
+    radio_fields = {  # noqa: RUF012
         "status": admin.VERTICAL,
         "site_response_status": admin.VERTICAL,
         "query_priority": admin.VERTICAL,
     }
 
-    autocomplete_fields = [
+    autocomplete_fields = (
         "sender",
         "recipients",
         "data_dictionaries",
@@ -75,7 +75,7 @@ class DataQueryAdmin(SiteModelAdminMixin, ModelAdminSubjectDashboardMixin, Simpl
         "visit_schedule",
         "registered_subject",
         "dm_user",
-    ]
+    )
 
     list_display = (
         "wrapped_title",
@@ -201,11 +201,10 @@ class DataQueryAdmin(SiteModelAdminMixin, ModelAdminSubjectDashboardMixin, Simpl
     wrapped_title.short_description = "Title"
 
     def formfield_for_manytomany(self, db_field, request, **kwargs):
-        if db_field.name == "data_dictionaries":
-            if request.GET.get("title"):
-                kwargs["queryset"] = DataDictionary.objects.filter(
-                    model_verbose_name=request.GET.get("title")
-                )
+        if db_field.name == "data_dictionaries" and request.GET.get("title"):
+            kwargs["queryset"] = DataDictionary.objects.filter(
+                model_verbose_name=request.GET.get("title")
+            )
         return super().formfield_for_manytomany(db_field, request, **kwargs)
 
     def query_dates(self, obj):
@@ -332,7 +331,8 @@ class DataQueryAdmin(SiteModelAdminMixin, ModelAdminSubjectDashboardMixin, Simpl
             "missed_visit",
             "auto_resolved",
             "registered_subject",
-        ) + action_fields
+            *action_fields,
+        )
         if not request.user.groups.filter(name=DATA_MANAGER):
             extra_fields = (
                 "data_dictionaries",
@@ -350,10 +350,11 @@ class DataQueryAdmin(SiteModelAdminMixin, ModelAdminSubjectDashboardMixin, Simpl
                 "title",
                 "visit_code_sequence",
                 "visit_schedule",
+                *extra_fields,
             )
         if not obj:
             extra_fields = tuple(f for f in extra_fields if f != "registered_subject")
-        return fields + extra_fields
+        return *fields, *extra_fields
 
     def get_subject_dashboard_url_kwargs(self, obj):
         def get_opts():

edc_data_manager/auths.py

@@ -18,45 +18,48 @@ from .auth_objects import (
     data_manager,
 )
 
-site_auths.add_custom_permissions_tuples(
-    model="edc_data_manager.edcpermissions", codename_tuples=custom_codename_tuples
-)
 
-site_auths.add_custom_permissions_tuples(
-    model="edc_data_manager.edcpermissions",
-    codename_tuples=[("edc_data_manager.special_bypassmodelform", "Can bypass modelform")],
-)
+def update_site_auths():
+    site_auths.add_custom_permissions_tuples(
+        model="edc_data_manager.edcpermissions", codename_tuples=custom_codename_tuples
+    )
 
+    site_auths.add_custom_permissions_tuples(
+        model="edc_data_manager.edcpermissions",
+        codename_tuples=[("edc_data_manager.special_bypassmodelform", "Can bypass modelform")],
+    )
 
-# groups
-site_auths.add_group(*data_manager, name=DATA_MANAGER)
-site_auths.add_group(*data_manager, name=DATA_QUERY_VIEW, view_only=True)
+    # groups
+    site_auths.add_group(*data_manager, name=DATA_MANAGER)
+    site_auths.add_group(*data_manager, name=DATA_QUERY_VIEW, view_only=True)
 
-site_auths.add_group(*data_manager, name=DATA_QUERY, view_only=True)
-site_auths.update_group("edc_data_manager.change_dataquery", name=DATA_QUERY)
+    site_auths.add_group(*data_manager, name=DATA_QUERY, view_only=True)
+    site_auths.update_group("edc_data_manager.change_dataquery", name=DATA_QUERY)
 
-site_auths.add_group(
-    "edc_data_manager.export_datadictionary",
-    "edc_data_manager.export_dataquery",
-    "edc_data_manager.export_queryrule",
-    name=DATA_MANAGER_EXPORT,
-)
+    site_auths.add_group(
+        "edc_data_manager.export_datadictionary",
+        "edc_data_manager.export_dataquery",
+        "edc_data_manager.export_queryrule",
+        name=DATA_MANAGER_EXPORT,
+    )
 
-site_auths.add_group(*data_manager, name=DATA_MANAGER_SUPER)
-site_auths.update_group("edc_data_manager.change_dataquery", name=DATA_MANAGER_SUPER)
-site_auths.update_group(
-    "edc_data_manager.export_datadictionary",
-    "edc_data_manager.export_dataquery",
-    "edc_data_manager.export_queryrule",
-    "edc_data_manager.special_bypassmodelform",
-    "edc_data_manager.change_dataquery",
-    name=DATA_MANAGER_SUPER,
-)
+    site_auths.add_group(*data_manager, name=DATA_MANAGER_SUPER)
+    site_auths.update_group("edc_data_manager.change_dataquery", name=DATA_MANAGER_SUPER)
+    site_auths.update_group(
+        "edc_data_manager.export_datadictionary",
+        "edc_data_manager.export_dataquery",
+        "edc_data_manager.export_queryrule",
+        "edc_data_manager.special_bypassmodelform",
+        "edc_data_manager.change_dataquery",
+        name=DATA_MANAGER_SUPER,
+    )
+
+    # roles
+    site_auths.add_role(CELERY_MANAGER, DATA_MANAGER, name=DATA_MANAGER_ROLE)
+    site_auths.add_role(DATA_QUERY, name=SITE_DATA_MANAGER_ROLE)
+    site_auths.update_role(DATA_QUERY, name=CLINICIAN_ROLE)
+    site_auths.update_role(DATA_QUERY, name=NURSE_ROLE)
+    site_auths.update_role(DATA_QUERY, name=CLINICIAN_SUPER_ROLE)
 
 
-# roles
-site_auths.add_role(CELERY_MANAGER, DATA_MANAGER, name=DATA_MANAGER_ROLE)
-site_auths.add_role(DATA_QUERY, name=SITE_DATA_MANAGER_ROLE)
-site_auths.update_role(DATA_QUERY, name=CLINICIAN_ROLE)
-site_auths.update_role(DATA_QUERY, name=NURSE_ROLE)
-site_auths.update_role(DATA_QUERY, name=CLINICIAN_SUPER_ROLE)
+update_site_auths()

edc_data_manager/rule/query_rule_wrapper.py

@@ -2,7 +2,7 @@ from __future__ import annotations
 
 from datetime import datetime
 from decimal import Decimal
-from typing import TYPE_CHECKING, LiteralString
+from typing import TYPE_CHECKING
 
 from tqdm import tqdm
 
@@ -17,12 +17,12 @@ if TYPE_CHECKING:
 class QueryRuleWrapper:
     def __init__(
         self,
-        query_rule_obj: QueryRule = None,
-        subject_identifiers: list[LiteralString] = None,
-        visit_schedule_obj: QueryVisitSchedule = None,
-        timepoint: Decimal = None,
-        entry_status: str = None,
-        now: datetime = None,
+        query_rule_obj: QueryRule | None = None,
+        subject_identifiers: list[str] | None = None,
+        visit_schedule_obj: QueryVisitSchedule | None = None,
+        timepoint: Decimal | None = None,
+        entry_status: str | None = None,
+        now: datetime | None = None,
         verbose: bool | None = None,
     ):
         self.now = now

edc_export/archive_exporter.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+from pathlib import Path
 from tempfile import mkdtemp
 from typing import TYPE_CHECKING
 
@@ -17,7 +18,7 @@ if TYPE_CHECKING:
     from django.contrib.auth.models import User
 
 
-class ArchiveExporterNothingExported(Exception):
+class ArchiveExporterNothingExported(Exception):  # noqa: N818
     pass
 
 
@@ -56,7 +57,7 @@ class ArchiveExporter:
         for model in models:
             csv_exporter = self.csv_exporter_cls(
                 model=model,
-                export_folder=tmp_folder,
+                export_folder=Path(tmp_folder),
                 decrypt=decrypt,
                 site_ids=sites.get_site_ids_for_user(
                     user=user, site_id=sites.get_current_site().site_id

edc_export/auths.py

@@ -4,34 +4,38 @@ from edc_auth.utils import remove_default_model_permissions_from_edc_permissions
 from .auth_objects import export_codenames
 from .constants import DATA_EXPORTER_ROLE, EXPORT, EXPORT_PII
 
-site_auths.add_post_update_func(
-    "edc_export",
-    remove_default_model_permissions_from_edc_permissions,
-)
 
-site_auths.add_custom_permissions_tuples(
-    model="edc_export.edcpermissions",
-    codename_tuples=[
-        (
-            "edc_export.export_visitschedule",
-            "Can export the visit schedule",
-        ),
-        (
-            "edc_export.view_export_dashboard",
-            "Can view export dashboard",
-        ),
-        (
-            "edc_export.export_subjectschedulehistory",
-            "Can export subject schedule history",
-        ),
-        (
-            "edc_export.export_pii",
-            "Can export PII",
-        ),
-    ],
-)
+def update_site_auths():
+    site_auths.add_post_update_func(
+        "edc_export",
+        remove_default_model_permissions_from_edc_permissions,
+    )
 
+    site_auths.add_custom_permissions_tuples(
+        model="edc_export.edcpermissions",
+        codename_tuples=[
+            (
+                "edc_export.export_visitschedule",
+                "Can export the visit schedule",
+            ),
+            (
+                "edc_export.view_export_dashboard",
+                "Can view export dashboard",
+            ),
+            (
+                "edc_export.export_subjectschedulehistory",
+                "Can export subject schedule history",
+            ),
+            (
+                "edc_export.export_pii",
+                "Can export PII",
+            ),
+        ],
+    )
 
-site_auths.add_group(*export_codenames, name=EXPORT)
-site_auths.add_role(EXPORT, name=DATA_EXPORTER_ROLE)
-site_auths.add_group("edc_export.export_pii", name=EXPORT_PII)
+    site_auths.add_group(*export_codenames, name=EXPORT)
+    site_auths.add_role(EXPORT, name=DATA_EXPORTER_ROLE)
+    site_auths.add_group("edc_export.export_pii", name=EXPORT_PII)
+
+
+update_site_auths()

edc_export/model_exporter/model_exporter.py

@@ -102,7 +102,10 @@ class ModelExporter:
             if f in self.export_fields or f in self.audit_fields or f in self.required_fields:
                 self._field_names.pop(self._field_names.index(f))
         self._field_names = (
-            self.export_fields + self.required_fields + self.field_names + self.audit_fields
+            *self.export_fields,
+            *self.required_fields,
+            *self.field_names,
+            *self.audit_fields,
         )
 
     @property

edc_facility/auths.py

@@ -2,6 +2,11 @@ from edc_auth.site_auths import site_auths
 
 from .auth_objects import EDC_FACILITY, EDC_FACILITY_SUPER, EDC_FACILITY_VIEW, codenames
 
-site_auths.add_group(*codenames, name=EDC_FACILITY_VIEW, view_only=True)
-site_auths.add_group(*codenames, name=EDC_FACILITY, no_delete=True)
-site_auths.add_group(*codenames, name=EDC_FACILITY_SUPER)
+
+def update_site_auths():
+    site_auths.add_group(*codenames, name=EDC_FACILITY_VIEW, view_only=True)
+    site_auths.add_group(*codenames, name=EDC_FACILITY, no_delete=True)
+    site_auths.add_group(*codenames, name=EDC_FACILITY_SUPER)
+
+
+update_site_auths()

edc_facility/facility.py

@@ -7,8 +7,7 @@ from zoneinfo import ZoneInfo
 
 import arrow
 from arrow import Arrow
-from dateutil._common import weekday
-from dateutil.relativedelta import relativedelta
+from dateutil.relativedelta import relativedelta, weekday
 from django.conf import settings
 from django.utils import timezone
 
@@ -36,19 +35,18 @@ class Facility:
     def __init__(
         self,
         name: str | None = None,
-        days: list | None = None,
+        days: list[weekday] | None = None,
         slots: list[int] | None = None,
         best_effort_available_datetime: datetime | None = None,
     ):
-        self.days = []
+        self.days = days
         self.name = name
         if not name:
             raise FacilityError(f"Name cannot be None. See {self!r}")
         self.best_effort_available_datetime = (
             True if best_effort_available_datetime is None else best_effort_available_datetime
         )
-        for day in days:
-            self.days.append(getattr(day, "weekday", weekday(day)))
+        self.weekdays = [d.weekday for d in self.days]
         self.slots = slots or [99999 for _ in self.days]
         self.config = dict(zip([str(d) for d in self.days], self.slots, strict=False))
         self.holidays = self.holiday_cls()
@@ -69,9 +67,9 @@ class Facility:
             slots_per_day = 0
         return slots_per_day
 
-    @property
-    def weekdays(self) -> list[int]:
-        return [d.weekday for d in self.days]
+    # @property
+    # def weekdays(self) -> list[int]:
+    #     return [d.weekday for d in self.days]
 
     @staticmethod
     def open_slot_on(arr) -> Arrow:
@@ -132,6 +130,7 @@ class Facility:
         reverse_delta=None,
         taken_datetimes=None,
         schedule_on_holidays=None,
+        **kwargs,  # noqa: ARG002
     ):
         """Returns an arrow object for a datetime equal to or
         close to the suggested datetime.

edc_form_label/custom_label_condition.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import contextlib
 from typing import TYPE_CHECKING
 
 from django.apps import apps as django_apps
@@ -28,20 +29,24 @@ class CustomLabelCondition:
         """
         return
 
-    def get_additional_options(self, request=None, obj=None, model=None):
+    def get_additional_options(self, request=None, obj=None, model=None):  # noqa: ARG002
         return {}
 
     @property
     def appointment(self) -> Appointment | None:
         """Returns the appointment instance for this request or None."""
-        return django_apps.get_model(self.appointment_model).objects.get(
-            pk=self.request.GET.get("appointment")
-        )
+        with contextlib.suppress(ObjectDoesNotExist):
+            return django_apps.get_model(self.appointment_model).objects.get(
+                pk=self.request.GET.get("appointment")
+            )
+        return None
 
     @property
     def previous_appointment(self) -> Appointment | None:
         """Returns the previous appointment for this request or None."""
-        return self.appointment.previous_by_timepoint
+        with contextlib.suppress(ObjectDoesNotExist):
+            return self.appointment.previous_by_timepoint
+        return None
 
     @property
     def previous_visit(self):
@@ -73,10 +78,8 @@ class CustomLabelCondition:
         """
         previous_obj = None
         if self.previous_visit:
-            try:
+            with contextlib.suppress(ObjectDoesNotExist):
                 previous_obj = self.model.objects.get(
                     **{f"{self.model.related_visit_model_attr()}": self.previous_visit}
                 )
-            except ObjectDoesNotExist:
-                pass
         return previous_obj

edc_form_label/form_label.py

@@ -41,5 +41,5 @@ class FormLabel:
             except KeyError as e:
                 raise CustomFormLabelError(
                     f"Custom label template has invalid keys. See {label}. Got {e}."
-                )
+                ) from e
         return label

edc_form_runners/auths.py

@@ -9,10 +9,15 @@ from .auth_objects import (
     codenames,
 )
 
-site_auths.add_group(*codenames, name=EDC_FORM_RUNNERS_VIEW, view_only=True)
-site_auths.add_group(*codenames, name=EDC_FORM_RUNNERS, no_delete=True)
-site_auths.add_group(*codenames, name=EDC_FORM_RUNNERS_SUPER)
 
-site_auths.update_role(EDC_FORM_RUNNERS_VIEW, name=AUDITOR_ROLE)
-site_auths.update_role(EDC_FORM_RUNNERS, name=CLINICIAN_ROLE)
-site_auths.update_role(EDC_FORM_RUNNERS_SUPER, name=DATA_MANAGER_ROLE)
+def update_site_auths():
+    site_auths.add_group(*codenames, name=EDC_FORM_RUNNERS_VIEW, view_only=True)
+    site_auths.add_group(*codenames, name=EDC_FORM_RUNNERS, no_delete=True)
+    site_auths.add_group(*codenames, name=EDC_FORM_RUNNERS_SUPER)
+
+    site_auths.update_role(EDC_FORM_RUNNERS_VIEW, name=AUDITOR_ROLE)
+    site_auths.update_role(EDC_FORM_RUNNERS, name=CLINICIAN_ROLE)
+    site_auths.update_role(EDC_FORM_RUNNERS_SUPER, name=DATA_MANAGER_ROLE)
+
+
+update_site_auths()

edc_form_validators/applicable_field_validator.py

@@ -1,6 +1,6 @@
 from typing import Any
 
-from edc_constants.constants import NOT_APPLICABLE
+from edc_constants.constants import NOT_APPLICABLE, NULL_STRING
 
 from .base_form_validator import (
     APPLICABLE_ERROR,
@@ -33,8 +33,8 @@ class ApplicableFieldValidator(BaseFormValidator):
     def applicable_if(
         self,
         *responses: Any,
-        field: str = None,
-        field_applicable: str = None,
+        field: str,
+        field_applicable: str,
         inverse: bool | None = None,
         is_instance_field: bool | None = None,
         msg: str | None = None,
@@ -95,8 +95,8 @@ class ApplicableFieldValidator(BaseFormValidator):
     def applicable(
         self,
         *responses: Any,
-        field: str = None,
-        field_applicable: str = None,
+        field: str,
+        field_applicable: str,
         inverse: bool | None = None,
         is_instance_field: bool | None = None,
         msg: str | None = None,
@@ -117,7 +117,8 @@ class ApplicableFieldValidator(BaseFormValidator):
             field_applicable_value = self.get(field_applicable)
 
             if field_value in responses and (
-                field_applicable_value is None or field_applicable_value == not_applicable
+                field_applicable_value in (NULL_STRING, not_applicable)
+                or field_applicable_value is None
             ):
                 self.raise_applicable(field_applicable, msg=msg, applicable_msg=applicable_msg)
             elif (

edc_form_validators/base_form_validator.py

@@ -1,10 +1,11 @@
 from __future__ import annotations
 
+import contextlib
 from copy import copy
 from typing import Any
 
 from django.core.exceptions import NON_FIELD_ERRORS
-from django.forms import ValidationError, forms
+from django.forms import ValidationError
 
 APPLICABLE_ERROR = "applicable"
 INVALID_ERROR = "invalid"
@@ -14,7 +15,7 @@ REQUIRED_ERROR = "required"
 OUT_OF_RANGE_ERROR = "out_of_range"
 
 
-class InvalidModelFormFieldValidator(Exception):
+class InvalidModelFormFieldValidator(Exception):  # noqa: N818
     def __init__(self, message, code=None):
         message = f"Invalid field validator. Got '{message}'"
         super().__init__(message)
@@ -119,13 +120,13 @@ class BaseFormValidator:
         """
         try:
             self._clean()
-        except forms.ValidationError as e:
+        except ValidationError as e:
             self.capture_error_message(e)
             self.capture_error_code(e)
-            raise forms.ValidationError(e)
+            raise ValidationError(e) from e
         return self.cleaned_data
 
-    def capture_error_message(self, e: forms.ValidationError) -> None:
+    def capture_error_message(self, e: ValidationError) -> None:
         try:
             self._errors.update(**e.error_dict)
         except AttributeError:
@@ -134,11 +135,9 @@ class BaseFormValidator:
             except AttributeError:
                 self._errors.update({NON_FIELD_ERRORS: str(e)})
 
-    def capture_error_code(self, e: forms.ValidationError) -> None:
-        try:
+    def capture_error_code(self, e: ValidationError) -> None:
+        with contextlib.suppress(AttributeError):
             self._error_codes.append(e.code)
-        except AttributeError:
-            pass
 
     def get_inline_field_value(self, field=None, inline_set=None):
         """Returns the value of the first inline field that has a value."""

edc_form_validators/other_specify_field_validator.py

@@ -41,20 +41,14 @@ class OtherSpecifyFieldValidator(BaseFormValidator):
             cleaned_data.get(field), fk_stored_field_name, cleaned_data.get(field)
         )
 
-        if (
-            field_value is not None
-            and field_value == other
-            and not cleaned_data.get(other_specify_field)
-        ):
+        if field_value and field_value == other and not cleaned_data.get(other_specify_field):
             ref = "" if not ref else f" ref: {ref}"
             message = {other_specify_field: required_msg or f"This field is required.{ref}"}
             self._errors.update(message)
             self._error_codes.append(REQUIRED_ERROR)
             raise ValidationError(message, code=REQUIRED_ERROR)
         if (
-            field_value is not None
-            and field_value != other
-            and cleaned_data.get(other_specify_field)
+            field_value and field_value != other and cleaned_data.get(other_specify_field)
         ) or (field_value is None and cleaned_data.get(other_specify_field)):
             ref = "" if not ref else f" ref: {ref}"
             message = {