clinicedc 2.0.28__py3-none-any.whl → 2.0.29__py3-none-any.whl

edc_randomization/system_checks.py

@@ -57,7 +57,7 @@ def randomizationlist_check(app_configs, **kwargs) -> list:
         ):
             error_msgs = randomizer.verify_list()
             for error_msg in error_msgs:
-                errors.append(error.cls(error_msg, hint=None, obj=None, id=error.id))
+                errors.append(error.cls(error_msg, hint=None, obj=None, id=error.id))  # noqa: PERF401
         if not settings.DEBUG:
             if not randomizer.get_randomizationlist_path().is_relative_to(settings.ETC_DIR):
                 errors.append(

edc_refusal/admin.py

@@ -41,7 +41,7 @@ class SubjectRefusalModelAdminMixin:
 
     search_fields = ("screening_identifier",)
 
-    radio_fields = {"reason": admin.VERTICAL}
+    radio_fields = {"reason": admin.VERTICAL}  # noqa: RUF012
 
 
 @admin.register(SubjectRefusal, site=edc_refusal_admin)
@@ -70,5 +70,7 @@ class SubjectRefusalAdmin(
             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

edc_registration/modeladmin_mixins.py

@@ -10,7 +10,7 @@ class RegisteredSubjectModelAdminMixin(ModelAdminSubjectDashboardMixin, admin.Mo
 
     date_hierarchy = "registration_datetime"
 
-    instructions = []
+    instructions = ()
 
     @staticmethod
     def show_pii(request) -> bool:
@@ -29,25 +29,23 @@ class RegisteredSubjectModelAdminMixin(ModelAdminSubjectDashboardMixin, admin.Mo
     def get_readonly_fields(self, request, obj=None) -> tuple[str, ...]:
         readonly_fields = super().get_readonly_fields(request, obj=obj)
         return (
-            readonly_fields
-            + (
-                "subject_identifier",
-                "sid",
-                "first_name",
-                "last_name",
-                "initials",
-                "dob",
-                "gender",
-                "subject_type",
-                "registration_status",
-                "identity",
-                "screening_identifier",
-                "screening_datetime",
-                "registration_datetime",
-                "randomization_datetime",
-                "consent_datetime",
-            )
-            + audit_fields
+            *readonly_fields,
+            "subject_identifier",
+            "sid",
+            "first_name",
+            "last_name",
+            "initials",
+            "dob",
+            "gender",
+            "subject_type",
+            "registration_status",
+            "identity",
+            "screening_identifier",
+            "screening_datetime",
+            "registration_datetime",
+            "randomization_datetime",
+            "consent_datetime",
+            *audit_fields,
         )
 
     def get_list_display(self, request):

edc_registration/modelform_mixins.py

@@ -21,6 +21,6 @@ class ModelFormSubjectIdentifierMixin(SiteModelFormMixin):
             get_registered_subject_model_cls().objects.get(
                 subject_identifier=subject_identifier
             )
-        except ObjectDoesNotExist:
-            raise forms.ValidationError({"subject_identifier": "Invalid."})
+        except ObjectDoesNotExist as e:
+            raise forms.ValidationError({"subject_identifier": "Invalid."}) from e
         return cleaned_data

edc_registration/models/signals.py

@@ -18,4 +18,4 @@ def update_registered_subject_from_model_on_post_save(
             instance.registration_update_or_create()
         except AttributeError as e:
             if "registration_update_or_create" not in str(e):
-                raise AttributeError(str(e))
+                raise AttributeError(str(e)) from e

edc_registration/utils.py

@@ -15,7 +15,7 @@ if TYPE_CHECKING:
     from edc_registration.models import RegisteredSubject
 
 
-class RegisteredSubjectDoesNotExist(Exception):
+class RegisteredSubjectDoesNotExist(Exception):  # noqa: N818
     pass
 
 

edc_reportable/age_evaluator.py

@@ -13,7 +13,7 @@ class AgeEvaluator(Evaluator):
     def __init__(
         self,
         age_lower: int | None = None,
-        age_upper: int = None,
+        age_upper: int | None = None,
         age_units: str | None = None,
         age_lower_inclusive: bool | None = None,
         age_upper_inclusive: bool | None = None,
@@ -29,15 +29,15 @@ class AgeEvaluator(Evaluator):
     def __repr__(self) -> str:
         return f"{self.__class__.__name__}({self.description(show_as_int=True)})"
 
-    def description(self, value: int = None, **kwargs):
+    def description(self, value: int | None = None, **kwargs):
         kwargs["show_as_int"] = True
         kwargs["placeholder"] = "AGE"
         return super().description(value=value, **kwargs)
 
     def in_bounds_or_raise(
         self,
-        dob: date = None,
-        report_datetime: datetime = None,
+        dob: date | None = None,
+        report_datetime: datetime | None = None,
         age_units: str | None = None,
     ) -> bool:
         report_datetime = report_datetime or timezone.now()

edc_reportable/data/grading_data/daids_july_2017.py

@@ -5,9 +5,9 @@ Creatinine Clearance14 or eGFR, Low
 *Report only one
 NA
 G1 N/A
-G2 < 90 to 60 ml/min or ml/min/1.73 m2 OR 10 to < 30% decrease from participant’s baseline
-G3 < 60 to 30 ml/min or ml/min/1.73 m2 OR 30 to < 50% decrease from participant’s baseline
-G4 < 30 ml/min or ml/min/1.73 m2 OR ≥ 50% decrease from participant’s baseline
+G2 < 90 to 60 ml/min or ml/min/1.73 m2 OR 10 to < 30% decrease from participant's baseline
+G3 < 60 to 30 ml/min or ml/min/1.73 m2 OR 30 to < 50% decrease from participant's baseline
+G4 < 30 ml/min or ml/min/1.73 m2 OR ≥ 50% decrease from participant's baseline
 """
 
 from edc_constants.constants import FEMALE, MALE

edc_reportable/evaluator.py

@@ -6,40 +6,40 @@ from .constants import HIGH_VALUE
 from .exceptions import ValueBoundryError
 
 
-class InvalidUnits(Exception):
+class InvalidUnits(Exception):  # noqa: N818
     pass
 
 
-class InvalidLowerBound(Exception):
+class InvalidLowerBound(Exception):  # noqa: N818
     pass
 
 
-class InvalidLowerLimitNormal(Exception):
+class InvalidLowerLimitNormal(Exception):  # noqa: N818
     pass
 
 
-class InvalidUpperLimitNormal(Exception):
+class InvalidUpperLimitNormal(Exception):  # noqa: N818
     pass
 
 
-class InvalidUpperBound(Exception):
+class InvalidUpperBound(Exception):  # noqa: N818
     pass
 
 
-class InvalidCombination(Exception):
+class InvalidCombination(Exception):  # noqa: N818
     pass
 
 
 class Evaluator:
     def __init__(
         self,
-        name: str = None,
-        lower: int | float = None,
-        upper: int | float = None,
-        units: str = None,
+        name: str | None = None,
+        lower: int | float | None = None,
+        upper: int | float | None = None,
+        units: str | None = None,
         lower_inclusive: bool | None = None,
         upper_inclusive: bool | None = None,
-        **kwargs,
+        **kwargs,  # noqa: ARG002
     ) -> None:
         self.name = name
         if lower is not None and not re.match(r"\d+", str(lower)):
@@ -78,8 +78,8 @@ class Evaluator:
 
     def description(
         self,
-        value: int | float = None,
-        show_as_int: bool = None,
+        value: int | float | None = None,
+        show_as_int: bool | None = None,
         placeholder: str | None = None,
     ) -> str:
         placeholder = placeholder or "x"
@@ -98,7 +98,7 @@ class Evaluator:
             f"{self.upper_operator or ''}{upper} {self.units}"
         )
 
-    def in_bounds_or_raise(self, value: int | float, units: str = None) -> bool:
+    def in_bounds_or_raise(self, value: int | float, units: str) -> bool:
         """Raises a ValueBoundryError exception if condition not met.
 
         The condition is evaluated to True or False as a string
@@ -116,6 +116,6 @@ class Evaluator:
             f"{'' if self.lower is None else self.lower}{self.lower_operator or ''}{value}"
             f"{self.upper_operator or ''}{'' if self.upper is None else self.upper}"
         )
-        if not eval(condition_str):  # nosec B307
+        if not eval(condition_str):  # nosec B307  # noqa: S307
             raise ValueBoundryError(condition_str)
         return True

edc_reportable/exceptions.py

@@ -18,7 +18,7 @@ class SiteReportablesError(Exception):
     pass
 
 
-class AlreadyRegistered(Exception):
+class AlreadyRegistered(Exception):  # noqa: N818
     pass
 
 
@@ -30,13 +30,13 @@ class ValueBoundryError(Exception):
     pass
 
 
-class NotEvaluated(Exception):
+class NotEvaluated(Exception):  # noqa: N818
     pass
 
 
-class BoundariesOverlap(Exception):
+class BoundariesOverlap(Exception):  # noqa: N818
     pass
 
 
-class ConversionNotHandled(Exception):
+class ConversionNotHandled(Exception):  # noqa: N818
     pass

edc_reportable/forms/reportables_form_validator_mixin.py

@@ -23,7 +23,10 @@ class ReportablesFormValidatorMixin:
         return {"age_units": "years"}
 
     def validate_reportable_fields(
-        self, reference_range_collection_name: str, **reportables_evaluator_options
+        self,
+        reference_range_collection_name: str,
+        age_units: str | None = None,
+        **reportables_evaluator_options,
     ):
         """Called in clean() method of the FormValidator.
 
@@ -47,9 +50,10 @@ class ReportablesFormValidatorMixin:
             report_datetime=self.report_datetime,
             value_field_suffix=self.value_field_suffix,
         )
+        age_units = age_units or self.age_units
         options.update(**reportables_evaluator_options)
         reference_range_evaluator = self.reference_range_evaluator_cls(
-            reference_range_collection_name, **options
+            reference_range_collection_name, age_units=age_units, **options
         )
         try:
             reference_range_evaluator.validate_reportable_fields()

edc_reportable/management/commands/export_reportables.py

@@ -50,5 +50,5 @@ class Command(BaseCommand):
             help="Export path/folder",
         )
 
-    def handle(self, *args, **options):
+    def handle(self, *args, **options):  # noqa: ARG002
         export_daids_grading(path=options["path"])

edc_reportable/models/grading_exception.py

@@ -4,7 +4,6 @@ from edc_model.models import BaseUuidModel
 
 
 class GradingException(BaseUuidModel):
-
     reference_range_collection = models.ForeignKey(
         "edc_reportable.ReferenceRangeCollection", on_delete=models.PROTECT
     )
@@ -17,11 +16,7 @@ class GradingException(BaseUuidModel):
     grade4 = models.BooleanField(default=False)
 
     def grades(self) -> list[int]:
-        grades = []
-        for i in range(1, 5):
-            if getattr(self, f"grade{i}"):
-                grades.append(i)
-        return grades
+        return [i for i in range(1, 5) if getattr(self, f"grade{i}")]
 
     class Meta(BaseUuidModel.Meta):
         verbose_name = "Grading Exception"

edc_reportable/models/normal_data.py

@@ -22,8 +22,8 @@ class NormalData(ReferenceModelMixin, BaseUuidModel):
     def value_in_normal_range_or_raise(
         self,
         value: int | float,
-        dob: date = None,
-        report_datetime: datetime = None,
+        dob: date,
+        report_datetime: datetime,
         age_units: str | None = None,
     ) -> bool:
         """Raises a ValueBoundryError exception if condition not met.
@@ -45,7 +45,7 @@ class NormalData(ReferenceModelMixin, BaseUuidModel):
         value_condition_str = self.get_eval_phrase(value)
         if not re.match(pattern, value_condition_str):
             raise ValueError(f"Invalid condition string. Got {value_condition_str}.")
-        if not eval(value_condition_str):  # nosec B307
+        if not eval(value_condition_str):  # nosec B307  # noqa: S307
             raise ValueBoundryError(
                 f"{self.label}: {value_condition_str}{self.units} [{self.gender}]"
             )

edc_reportable/models/reference_range_collection.py

@@ -38,11 +38,7 @@ class ReferenceRangeCollection(BaseUuidModel):
 
         See also model GradingException.
         """
-        grades = []
-        for i in range(1, 5):
-            if getattr(self, f"grade{i}"):
-                grades.append(i)
-        return grades
+        return [i for i in range(1, 5) if getattr(self, f"grade{i}")]
 
     def reportable_grades(self, label: str) -> list[int]:
         if not label:
@@ -96,7 +92,6 @@ class ReferenceRangeCollection(BaseUuidModel):
         gender: str | None = None,
         dob: date | None = None,
         age_units: str | None = None,
-        site: Site | None = None,
     ) -> tuple[bool, NormalData]:
         if subject_identifier:
             rs_obj = RegisteredSubject.objects.get(subject_identifier=subject_identifier)

edc_reportable/utils/get_grade_for_value.py

@@ -19,12 +19,12 @@ __all__ = ["get_grade_for_value"]
 
 def get_grade_for_value(
     reference_range_collection: ReferenceRangeCollection,
-    value: float | int = None,
-    label: str = None,
-    units: str = None,
-    gender: str = None,
-    dob: date = None,
-    report_datetime: datetime = None,
+    value: float | int | None = None,
+    label: str | None = None,
+    units: str | None = None,
+    gender: str | None = None,
+    dob: date | None = None,
+    report_datetime: datetime | None = None,
     age_units: str | None = None,
     site: Site | None = None,
     create_missing_normal: bool | None = None,
@@ -56,11 +56,11 @@ def get_grade_for_value(
         upper_limit = get_upper_limit(normal_data, grading_data)
         value = float(value)
         condition_str = (
-            f'{"" if lower_limit is None else lower_limit}'
-            f'{grading_data.lower_operator or ""}{value}'
-            f'{grading_data.upper_operator or ""}{"" if upper_limit is None else upper_limit}'
+            f"{'' if lower_limit is None else lower_limit}"
+            f"{grading_data.lower_operator or ''}{value}"
+            f"{grading_data.upper_operator or ''}{'' if upper_limit is None else upper_limit}"
         )
-        if eval(condition_str):  # nosec B307
+        if eval(condition_str):  # nosec B307  # noqa: S307
             if not found_grading_data:
                 found_grading_data = grading_data
                 found_condition_str = (
@@ -104,11 +104,11 @@ def get_upper_limit(
 
 def get_grading_data_instances(
     reference_range_collection: ReferenceRangeCollection,
-    label: str = None,
-    units: str = None,
-    gender: str = None,
-    dob: date = None,
-    report_datetime: datetime = None,
+    label: str | None = None,
+    units: str | None = None,
+    gender: str | None = None,
+    dob: date | None = None,
+    report_datetime: datetime | None = None,
     age_units: str | None = None,
     site: Site | None = None,
 ) -> list[GradingData]:

edc_reportable/utils/get_normal_data_or_raise.py

@@ -25,11 +25,11 @@ __all__ = ["get_normal_data_or_raise"]
 
 def get_normal_data_or_raise(
     reference_range_collection: ReferenceRangeCollection = None,
-    label: str = None,
-    units: str = None,
-    gender: str = None,
-    dob: date = None,
-    report_datetime: datetime = None,
+    label: str | None = None,
+    units: str | None = None,
+    gender: str | None = None,
+    dob: date | None = None,
+    report_datetime: datetime | None = None,
     age_units: str | None = None,
     site: Site | None = None,
     create_missing_normal: bool | None = None,
@@ -48,7 +48,7 @@ def get_normal_data_or_raise(
             units=units,
             age_units=age_units,
         )
-    except ObjectDoesNotExist:
+    except ObjectDoesNotExist as e:
         if create_missing_normal:
             opts = dict(
                 reference_range_collection=reference_range_collection,
@@ -68,23 +68,23 @@ def get_normal_data_or_raise(
                 f"age={getattr(age_rdelta, age_units)}{age_units}. "
                 "Perhaps add this to the default normal reference range data or "
                 "pass 'create_missing=True' to convert an existing normal reference."
-            )
-    except MultipleObjectsReturned:
+            ) from e
+    except MultipleObjectsReturned as e:
         raise NotEvaluated(
             f"Value not evaluated. "
             f"Multiple normal references found for `{label}`. "
             f"Using units={units}, gender={gender}, age={getattr(age_rdelta, age_units)}. "
-        )
+        ) from e
     return obj
 
 
 def create_obj_for_new_units_or_raise(
     reference_range_collection: ReferenceRangeCollection = None,
-    label: str = None,
-    units: str = None,
-    gender: str = None,
-    dob: date = None,
-    report_datetime: datetime = None,
+    label: str | None = None,
+    units: str | None = None,
+    gender: str | None = None,
+    dob: date | None = None,
+    report_datetime: datetime | None = None,
     age_units: str | None = None,
 ) -> NormalData | None:
     opts = {}

edc_reportable/utils/in_normal_bounds_or_raise.py

@@ -14,12 +14,12 @@ __all__ = ["in_normal_bounds_or_raise"]
 
 def in_normal_bounds_or_raise(
     reference_range_collection: ReferenceRangeCollection = None,
-    label: str = None,
-    value: int | float = None,
-    units: str = None,
-    gender: str = None,
-    dob: date = None,
-    report_datetime: datetime = None,
+    label: str | None = None,
+    value: int | float | None = None,
+    units: str | None = None,
+    gender: str | None = None,
+    dob: date | None = None,
+    report_datetime: datetime | None = None,
     age_units: str | None = None,
     create_missing_normal: bool | None = None,
 ) -> bool:

edc_reportable/utils/load_data.py

@@ -18,7 +18,7 @@ if TYPE_CHECKING:
     from ..models import ReferenceRangeCollection
 
 
-class AlreadyLoaded(Exception):
+class AlreadyLoaded(Exception):  # noqa: N818
     pass
 
 

edc_reportable/utils/update_grading_exceptions.py

@@ -21,12 +21,12 @@ def update_grading_exceptions(
             reference_range_collection=reference_range_collection
         ).delete()
     for label, grades in reportable_grades_exceptions.items():
-        grades = [int(g) for g in grades]
+        grades = [int(g) for g in grades]  # noqa: PLW2901
         grading_exception_model_cls().objects.get_or_create(
             reference_range_collection=reference_range_collection,
             label=label,
-            grade1=True if 1 in grades else False,
-            grade2=True if 2 in grades else False,
-            grade3=True if 3 in grades else False,
-            grade4=True if 4 in grades else False,
+            grade1=1 in grades,
+            grade2=2 in grades,  # noqa: PLR2004
+            grade3=3 in grades,  # noqa: PLR2004
+            grade4=4 in grades,  # noqa: PLR2004
         )