clinicedc 2.0.7__py3-none-any.whl → 2.0.8__py3-none-any.whl

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 = {

edc_form_validators/required_field_validator.py

@@ -43,8 +43,8 @@ class RequiredFieldValidator(BaseFormValidator):
     def required_if(
         self,
         *responses: str | int | bool,
-        field: str = None,
-        field_required: str = None,
+        field: str,
+        field_required: str,
         required_msg: str | None = None,
         not_required_msg: str | None = None,
         optional_if_dwta: bool | None = None,
@@ -82,7 +82,7 @@ class RequiredFieldValidator(BaseFormValidator):
                 self.get(field_required, inline_set=inline_set) is not None
             )
         else:
-            field_required_has_value = self.get(field_required, inline_set=inline_set)
+            field_required_has_value = bool(self.get(field_required, inline_set=inline_set))
 
         if field in self.cleaned_data:
             if (DWTA in responses and optional_if_dwta and field_value == DWTA) or (
@@ -117,7 +117,7 @@ class RequiredFieldValidator(BaseFormValidator):
     def required_if_true(
         self,
         condition: bool,
-        field_required: str = None,
+        field_required: str,
         required_msg: str | None = None,
         not_required_msg: str | None = None,
         inverse: bool | None = None,
@@ -145,7 +145,7 @@ class RequiredFieldValidator(BaseFormValidator):
     def not_required_if_true(
         self,
         condition: bool,
-        field: str = None,
+        field: str,
         msg: str | None = None,
         is_instance_field: bool | None = None,
     ) -> bool:
@@ -170,8 +170,8 @@ class RequiredFieldValidator(BaseFormValidator):
 
     def required_if_not_none(
         self,
-        field: str = None,
-        field_required: str = None,
+        field: str,
+        field_required: str,
         required_msg: str | None = None,
         not_required_msg: str | None = None,
         optional_if_dwta: bool | None = None,
@@ -182,6 +182,9 @@ class RequiredFieldValidator(BaseFormValidator):
         """Raises an exception or returns False.
 
         If field is not none, field_required is "required".
+
+        Note: CharFields usually default to an empty string and not NULL.
+           For IntegerFields, zero is a value.
         """
         inverse = True if inverse is None else inverse
         if is_instance_field:
@@ -197,7 +200,7 @@ class RequiredFieldValidator(BaseFormValidator):
         if field_required_evaluate_as_int:
             field_required_has_value = self.cleaned_data.get(field_required) is not None
         else:
-            field_required_has_value = self.cleaned_data.get(field_required)
+            field_required_has_value = bool(self.cleaned_data.get(field_required))
 
         if field_value is not None and not field_required_has_value:
             self.raise_required(field=field_required, msg=required_msg)
@@ -221,8 +224,8 @@ class RequiredFieldValidator(BaseFormValidator):
     def not_required_if(
         self,
         *responses: str | int | bool,
-        field: str = None,
-        field_required: str = None,
+        field: str,
+        field_required: str | None = None,
         field_not_required: str | None = None,
         required_msg: str | None = None,
         not_required_msg: str | None = None,
@@ -259,8 +262,8 @@ class RequiredFieldValidator(BaseFormValidator):
 
     def require_together(
         self,
-        field: str = None,
-        field_required: str = None,
+        field: str,
+        field_required: str,
         required_msg: str | None = None,
         is_instance_field: bool | None = None,
     ) -> bool:
@@ -280,15 +283,15 @@ class RequiredFieldValidator(BaseFormValidator):
         return False
 
     @staticmethod
-    def _inspect_params(
-        *responses: str | int | bool, field: str = None, field_required: str = None
-    ) -> bool:
+    def _inspect_params(*responses: str | int | bool, field: str, field_required: str) -> bool:
         """Inspects params and raises if any are None"""
         if not field:
             errmsg = _("`field` cannot be `None`")
             raise InvalidModelFormFieldValidator(f"{errmsg}.")
         if not responses:
-            errmsg = _(f"At least one valid response for field '{field}' must be provided.")
+            errmsg = _(
+                "At least one valid response for field '{field}' must be provided."
+            ).format(field=field)
             raise InvalidModelFormFieldValidator(errmsg)
         if not field_required:
             raise InvalidModelFormFieldValidator('"field_required" cannot be None.')

edc_identifier/research_identifier.py

@@ -16,7 +16,7 @@ if TYPE_CHECKING:
     from .models import IdentifierModel
 
 
-class IdentifierMissingTemplateValue(Exception):
+class IdentifierMissingTemplateValue(Exception):  # noqa: N818
     pass
 
 
@@ -38,6 +38,7 @@ class ResearchIdentifier:
         identifier: str | None = None,
     ) -> None:
         self._identifier = None
+        self._sequence_number = None
         self.requesting_model = requesting_model
         if not self.requesting_model:
             raise IdentifierError("Invalid requesting_model. Got None")
@@ -121,10 +122,10 @@ class ResearchIdentifier:
         for key in keys:
             try:
                 value = getattr(self, key)
-            except AttributeError:
+            except AttributeError as e:
                 raise IdentifierMissingTemplateValue(
                     f"Required option not provided. Got '{key}'."
-                )
+                ) from e
             else:
                 if value:
                     template_opts.update({key: value})
@@ -141,15 +142,15 @@ class ResearchIdentifier:
     @property
     def sequence_number(self) -> int:
         """Returns the next sequence number to use."""
-        try:
-            identifier_model = (
+        if self._sequence_number is None:
+            if identifier_model := (
                 self.identifier_model_cls.objects.filter(
                     name=self.label, device_id=self.device_id, site=self.site
                 )
                 .order_by("-sequence_number")
                 .first()
-            )
-            sequence_number = identifier_model.sequence_number + 1
-        except AttributeError:
-            sequence_number = 1
-        return sequence_number
+            ):
+                self._sequence_number = identifier_model.sequence_number + 1
+            else:
+                self._sequence_number = 1
+        return self._sequence_number

edc_identifier/simple_identifier.py

@@ -1,5 +1,7 @@
+from __future__ import annotations
+
 from secrets import choice
-from typing import Any
+from typing import TYPE_CHECKING, Any
 
 from django.apps import apps as django_apps
 from django.core.exceptions import ObjectDoesNotExist
@@ -8,6 +10,9 @@ from django.utils import timezone
 
 from .utils import convert_to_human_readable
 
+if TYPE_CHECKING:
+    from edc_identifier.models import IdentifierModel
+
 
 class DuplicateIdentifierError(Exception):
     pass
@@ -195,7 +200,7 @@ class SimpleUniqueIdentifier:
     def model_cls(self) -> type[models.Model]:
         return django_apps.get_model(self.model)
 
-    def update_identifier_model(self, **kwargs) -> bool:
+    def update_identifier_model(self, **kwargs) -> bool | IdentifierModel:
         """Attempts to update identifier_model and returns True (or instance)
         if successful else False if identifier already exists.
         """
@@ -210,5 +215,6 @@ class SimpleUniqueIdentifier:
         try:
             self.model_cls.objects.get(identifier=self.identifier)
         except ObjectDoesNotExist:
+            opts = {k: v for k, v in opts.items() if v is not None}
             return self.model_cls.objects.create(**opts)
         return False

edc_lab/auths.py

@@ -9,6 +9,7 @@ from edc_auth.constants import (
     PII_VIEW,
 )
 from edc_auth.site_auths import site_auths
+from edc_export.constants import EXPORT
 
 from .auth_objects import (
     LAB,
@@ -18,26 +19,28 @@ from .auth_objects import (
     lab_view_codenames,
 )
 
-site_auths.add_group(*lab_codenames, name=LAB)
-site_auths.add_group(*lab_view_codenames, name=LAB_VIEW)
-
-if django_apps.is_installed("edc_export"):
-    from edc_export.constants import EXPORT
-
-    site_auths.update_group(
-        "edc_lab.export_aliquot",
-        "edc_lab.export_box",
-        "edc_lab.export_boxitem",
-        "edc_lab.export_boxtype",
-        "edc_lab.export_order",
-        "edc_lab.export_panel",
-        "edc_lab.export_result",
-        "edc_lab.export_resultitem",
-        name=EXPORT,
-    )
-
-
-site_auths.add_role(ADMINISTRATION, EVERYONE, LAB, PII_VIEW, name=LAB_TECHNICIAN_ROLE)
-site_auths.update_role(LAB, name=CLINICIAN_ROLE)
-site_auths.update_role(LAB, name=NURSE_ROLE)
-site_auths.update_role(LAB_VIEW, name=AUDITOR_ROLE)
+
+def update_site_auths():
+    site_auths.add_group(*lab_codenames, name=LAB)
+    site_auths.add_group(*lab_view_codenames, name=LAB_VIEW)
+
+    if django_apps.is_installed("edc_export"):
+        site_auths.update_group(
+            "edc_lab.export_aliquot",
+            "edc_lab.export_box",
+            "edc_lab.export_boxitem",
+            "edc_lab.export_boxtype",
+            "edc_lab.export_order",
+            "edc_lab.export_panel",
+            "edc_lab.export_result",
+            "edc_lab.export_resultitem",
+            name=EXPORT,
+        )
+
+    site_auths.add_role(ADMINISTRATION, EVERYONE, LAB, PII_VIEW, name=LAB_TECHNICIAN_ROLE)
+    site_auths.update_role(LAB, name=CLINICIAN_ROLE)
+    site_auths.update_role(LAB, name=NURSE_ROLE)
+    site_auths.update_role(LAB_VIEW, name=AUDITOR_ROLE)
+
+
+update_site_auths()

edc_lab/lab/aliquot_creator.py

@@ -90,18 +90,15 @@ class AliquotCreator:
             parent_segment=self.parent_segment,
         )
 
-        parent_identifier = parent_identifier or aliquot_identifier_obj.identifier
-
-        aliquot = self.aliquot_model_cls.objects.create(
+        return self.aliquot_model_cls.objects.create(
             aliquot_identifier=aliquot_identifier_obj.identifier,
             aliquot_type=aliquot_type.name,
             alpha_code=aliquot_type.alpha_code,
             count=count,
             numeric_code=aliquot_type.numeric_code,
-            parent_identifier=parent_identifier,
+            parent_identifier=parent_identifier or aliquot_identifier_obj.identifier,
             identifier_prefix=self.identifier_prefix,
-            is_primary=True if self.is_primary else False,
-            requisition_identifier=self.requisition_identifier,
-            subject_identifier=self.subject_identifier,
+            is_primary=bool(self.is_primary),
+            requisition_identifier=self.requisition_identifier or "",
+            subject_identifier=self.subject_identifier or "",
         )
-        return aliquot

edc_lab/lab/primary_aliquot.py

@@ -1,3 +1,11 @@
+from __future__ import annotations
+
+from typing import TYPE_CHECKING
+
+if TYPE_CHECKING:
+    from edc_lab import AliquotCreator, AliquotType
+
+
 class PrimaryAliquotError(Exception):
     pass
 
@@ -11,11 +19,12 @@ class PrimaryAliquot:
 
     def __init__(
         self,
-        aliquot_type=None,
-        subject_identifier=None,
-        requisition_identifier=None,
-        identifier_prefix=None,
-        aliquot_creator_cls=None,
+        *,
+        aliquot_creator_cls: type[AliquotCreator],
+        aliquot_type: AliquotType | None = None,
+        subject_identifier: str | None = None,
+        requisition_identifier: str | None = None,
+        identifier_prefix: str | None = None,
     ):
         self._object = None
         self.aliquot_creator_cls = aliquot_creator_cls