clinicedc 2.0.6__py3-none-any.whl → 2.0.8__py3-none-any.whl

edc_reportable/models/reference_range_collection.py

@@ -20,7 +20,6 @@ if TYPE_CHECKING:
 
 
 class ReferenceRangeCollection(BaseUuidModel):
-
     name = models.CharField(max_length=50, unique=True)
 
     grade1 = models.BooleanField(default=False)
@@ -60,13 +59,13 @@ class ReferenceRangeCollection(BaseUuidModel):
 
     def get_grade(
         self,
-        value: float | int = None,
-        label: str = None,
-        units: str = None,
+        value: float | int | None = None,
+        label: str | None = None,
+        units: str | None = None,
         subject_identifier: str | None = None,
-        report_datetime: datetime = None,
-        gender: str = None,
-        dob: date = None,
+        report_datetime: datetime | None = None,
+        gender: str | None = None,
+        dob: date | None = None,
         age_units: str | None = None,
         site: Site | None = None,
     ) -> tuple[GradingData | None, str | None]:
@@ -89,13 +88,13 @@ class ReferenceRangeCollection(BaseUuidModel):
 
     def is_normal(
         self,
-        value: float | int = None,
-        label: str = None,
-        units: str = None,
+        value: float | int | None = None,
+        label: str | None = None,
+        units: str | None = None,
         subject_identifier: str | None = None,
-        report_datetime: datetime = None,
-        gender: str = None,
-        dob: date = None,
+        report_datetime: datetime | None = None,
+        gender: str | None = None,
+        dob: date | None = None,
         age_units: str | None = None,
         site: Site | None = None,
     ) -> tuple[bool, NormalData]:

edc_reportable/post_migrate_signals.py

@@ -19,7 +19,7 @@ def load_mw():
         model_cls.objects.get_or_create(label=label, mw=mw)
 
 
-def post_migrate_load_reference_ranges(sender=None, **kwargs):  # noqa
+def post_migrate_load_reference_ranges(sender=None, **kwargs):
     sys.stdout.write(style.MIGRATE_HEADING("Loading reference ranges (reportables):\n"))
     load_mw()
     load_all_reference_ranges()

edc_reportable/utils/convert_units.py

@@ -20,18 +20,16 @@ __all__ = ["convert_units"]
 def get_mw(label):
     try:
         molecular_weight = molecular_weight_model_cls().objects.get(label=label)
-    except ObjectDoesNotExist:
+    except ObjectDoesNotExist as e:
         raise ConversionNotHandled(
             f"Conversion not handled. Molecular weight not found for {label}."
-        )
+        ) from e
     else:
         mw = molecular_weight.mw
     return mw
 
 
-def micromoles_per_liter_to(
-    *, label: str = None, value: float | int = None, units_to: str = None
-) -> dict:
+def micromoles_per_liter_to(*, label: str, value: float | int, units_to: str) -> dict:
     if units_to == MICROMOLES_PER_LITER:
         return {MICROMOLES_PER_LITER: float(value)}
     if units_to == MILLIMOLES_PER_LITER:
@@ -44,8 +42,8 @@ def micromoles_per_liter_to(
 
 
 def milligrams_per_deciliter_to(
-    *, label: str = None, value: float | int = None, units_to: str = None
-) -> dict[str:float]:
+    *, label: str, value: float | int, units_to: str
+) -> dict[str, float]:
     if units_to == MILLIGRAMS_PER_DECILITER:
         return {MILLIGRAMS_PER_DECILITER: float(value)}
     if units_to == MILLIMOLES_PER_LITER:
@@ -63,10 +61,10 @@ class UnitsConverter:
     def __init__(
         self,
         *,
-        label: str = None,
-        value: int | float | None = None,
-        units_from: str | None = None,
-        units_to: str | None = None,
+        label: str,
+        value: int | float,
+        units_from: str,
+        units_to: str,
         places: int | None = None,
     ):
         self.label = label
@@ -97,7 +95,7 @@ class UnitsConverter:
                 f"Conversion not handled. Tried {self.label} from {self.units_from} "
                 f"to {self.units_to}. "
                 f"Got {e} when rounding {converted_value} to {self.places} places."
-            )
+            ) from e
         return converted_value
 
     def from_milligrams_per_deciliter(self) -> float | int:
@@ -106,14 +104,6 @@ class UnitsConverter:
                 label=self.label, value=float(self.value), units_to=self.units_to
             )[self.units_to]
         return self.value
-        # converted_value = None
-        # if self.units_to == MILLIMOLES_PER_LITER:
-        #     converted_value = (float(self.value) * 10.00) / self.get_mw()
-        # elif self.units_to == MICROMOLES_PER_LITER:
-        #     converted_value = (float(self.value) * 10.00**3) / self.get_mw()
-        # elif self.units_to == GRAMS_PER_LITER:
-        #     converted_value = float(self.value) / 100.00
-        # return converted_value
 
     def from_grams_per_liter(self) -> float | int:
         if self.units_to != GRAMS_PER_LITER:
@@ -123,14 +113,6 @@ class UnitsConverter:
                 units_to=self.units_to,
             )[self.units_to]
         return self.value
-        # converted_value = None
-        # if self.units_to == MILLIMOLES_PER_LITER:
-        #     converted_value = (self.value * 1000.00) / self.get_mw()
-        # elif self.units_to == MICROMOLES_PER_LITER:
-        #     converted_value = (self.value * 10.00**6) / self.get_mw()
-        # elif self.units_to == MILLIGRAMS_PER_DECILITER:
-        #     converted_value = float(self.value) * 100.00
-        # return converted_value
 
     def from_millimoles_per_liter(self) -> float | int:
         if self.units_to != MILLIMOLES_PER_LITER:
@@ -138,14 +120,6 @@ class UnitsConverter:
                 label=self.label, value=self.value / 1000, units_to=self.units_to
             )[self.units_to]
         return self.value
-        # converted_value = None
-        # if self.units_to == MICROMOLES_PER_LITER:
-        #     converted_value = self.value * 1000.00
-        # elif self.units_to == GRAMS_PER_LITER:
-        #     converted_value = (self.value * self.get_mw()) / 1000.00
-        # elif self.units_to == MILLIGRAMS_PER_DECILITER:
-        #     converted_value = (self.value * self.get_mw()) / 10.00
-        # return converted_value
 
     def from_micromoles_per_liter(self):
         if self.units_to != MICROMOLES_PER_LITER:
@@ -153,14 +127,6 @@ class UnitsConverter:
                 label=self.label, value=self.value, units_to=self.units_to
             )[self.units_to]
         return self.value
-        # converted_value = None
-        # if self.units_to == MILLIMOLES_PER_LITER:
-        #     converted_value = self.value / 1000.00
-        # elif self.units_to == GRAMS_PER_LITER:
-        #     converted_value = (self.value * self.get_mw()) / 10**6
-        # elif self.units_to == MILLIGRAMS_PER_DECILITER:
-        #     converted_value = (self.value * self.get_mw()) / 10**4
-        # return converted_value
 
     def get_converted_value(self) -> int | float:
         converted_value = None
@@ -182,7 +148,7 @@ class UnitsConverter:
 
 def convert_units(
     *,
-    label: str = None,
+    label: str | None = None,
     value: int | float | None = None,
     units_from: str | None = None,
     units_to: str | None = None,

edc_reportable/utils/get_normal_data_or_raise.py

@@ -5,10 +5,10 @@ from typing import TYPE_CHECKING
 
 from django.core.exceptions import MultipleObjectsReturned, ObjectDoesNotExist
 from django.db.models import Q
+from django.utils import timezone
 
 from edc_model_to_dataframe.constants import SYSTEM_COLUMNS
 from edc_utils import age as get_age
-from edc_utils import get_utcnow
 
 from ..exceptions import NotEvaluated
 from .convert_units import convert_units
@@ -135,7 +135,7 @@ def create_obj_for_new_units_or_raise(
         )
         opts["units"] = units
         opts["auto_created"] = True
-        opts["created"] = get_utcnow()
+        opts["created"] = timezone.now()
         opts["modified"] = opts["created"]
         break
     if opts:

edc_reportable/utils/get_reference_range_collection.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import contextlib
 from typing import TYPE_CHECKING
 
 from django.core.exceptions import ObjectDoesNotExist
@@ -21,10 +22,8 @@ def get_reference_range_collection(obj) -> ReferenceRangeCollection:
             name = obj.requisition.panel_object.reference_range_collection_name
         except AttributeError:
             name = obj.panel_object.reference_range_collection_name
-        try:
+        with contextlib.suppress(ObjectDoesNotExist):
             reference_range_collection = reference_range_colllection_model_cls().objects.get(
                 name=name
             )
-        except ObjectDoesNotExist:
-            pass
     return reference_range_collection

edc_reportable/utils/load_data.py

@@ -58,10 +58,10 @@ def load_all_reference_ranges() -> None:
 
 def load_reference_ranges(
     collection_name: str,
-    normal_data: dict[str, list[Formula]] = None,
-    grading_data: dict[str, list[Formula]] = None,
-    reportable_grades: list[int] = None,
-    reportable_grades_exceptions: dict[str, list[int]] = None,
+    normal_data: dict[str, list[Formula]],
+    grading_data: dict[str, list[Formula]],
+    reportable_grades: list[int] | None = None,
+    reportable_grades_exceptions: dict[str, list[int]] | None = None,
     keep_existing: bool | None = None,
     create_missing_normal: bool | None = None,
 ) -> ReferenceRangeCollection:

edc_reportable/utils/update_grading_data.py

@@ -1,11 +1,11 @@
 from __future__ import annotations
 
+import sys
 from typing import TYPE_CHECKING
 
 from dateutil.relativedelta import relativedelta
 from django.core.exceptions import ObjectDoesNotExist
-
-from edc_utils import get_utcnow
+from django.utils import timezone
 
 from ..exceptions import NotEvaluated
 from ..formula import Formula
@@ -55,7 +55,7 @@ def update_grading_data(
                                     value=value,
                                     units=formula_opts.get("units"),
                                     gender=gender,
-                                    dob=get_utcnow()
+                                    dob=timezone.now()
                                     - relativedelta(
                                         **{
                                             age_opts.get("age_units"): age_opts.get(
@@ -63,12 +63,12 @@ def update_grading_data(
                                             )
                                         }
                                     ),
-                                    report_datetime=get_utcnow(),
+                                    report_datetime=timezone.now(),
                                     age_units=age_opts.get("age_units"),
                                     create_missing_normal=create_missing_normal,
                                 )
                             except NotEvaluated as e:
-                                print(e)
+                                sys.stdout.write(f"{e}\n")
 
 
 def get_reportable_grades(

edc_review_dashboard/auths.py

@@ -10,23 +10,28 @@ from edc_auth.utils import remove_default_model_permissions_from_edc_permissions
 
 REVIEW = "REVIEW"
 
-site_auths.add_post_update_func(
-    "edc_review_dashboard", remove_default_model_permissions_from_edc_permissions
-)
 
-site_auths.add_custom_permissions_tuples(
-    model="edc_review_dashboard.edcpermissions",
-    codename_tuples=[
-        (
-            "edc_review_dashboard.view_subject_review_listboard",
-            "Can access subject review listboard",
-        )
-    ],
-)
-site_auths.add_group("edc_review_dashboard.view_subject_review_listboard", name=REVIEW)
+def update_site_auths():
+    site_auths.add_post_update_func(
+        "edc_review_dashboard", remove_default_model_permissions_from_edc_permissions
+    )
+
+    site_auths.add_custom_permissions_tuples(
+        model="edc_review_dashboard.edcpermissions",
+        codename_tuples=[
+            (
+                "edc_review_dashboard.view_subject_review_listboard",
+                "Can access subject review listboard",
+            )
+        ],
+    )
+    site_auths.add_group("edc_review_dashboard.view_subject_review_listboard", name=REVIEW)
+
+    site_auths.update_role(REVIEW, name=AUDITOR_ROLE)
+    site_auths.update_role(REVIEW, name=TMG_ROLE)
+    site_auths.update_role(REVIEW, name=CLINICIAN_ROLE)
+    site_auths.update_role(REVIEW, name=CLINICIAN_SUPER_ROLE)
+    site_auths.update_role(REVIEW, name=NURSE_ROLE)
+
 
-site_auths.update_role(REVIEW, name=AUDITOR_ROLE)
-site_auths.update_role(REVIEW, name=TMG_ROLE)
-site_auths.update_role(REVIEW, name=CLINICIAN_ROLE)
-site_auths.update_role(REVIEW, name=CLINICIAN_SUPER_ROLE)
-site_auths.update_role(REVIEW, name=NURSE_ROLE)
+update_site_auths()

edc_review_dashboard/migrations/0001_initial.py

@@ -7,6 +7,7 @@ import django_audit_fields.fields.uuid_auto_field
 import django_audit_fields.models.audit_model_mixin
 import django_revision.revision_field
 from django.db import migrations, models
+import django.utils.timezone
 
 
 class Migration(migrations.Migration):
@@ -33,14 +34,14 @@ class Migration(migrations.Migration):
                     "created",
                     models.DateTimeField(
                         blank=True,
-                        default=django_audit_fields.models.audit_model_mixin.utcnow,
+                        default=django.utils.timezone.now,
                     ),
                 ),
                 (
                     "modified",
                     models.DateTimeField(
                         blank=True,
-                        default=django_audit_fields.models.audit_model_mixin.utcnow,
+                        default=django.utils.timezone.now,
                     ),
                 ),
                 (

edc_review_dashboard/migrations/0006_alter_edcpermissions_device_created_and_more.py

@@ -0,0 +1,49 @@
+# Generated by Django 5.2.6 on 2025-09-17 16:53
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("edc_review_dashboard", "0005_alter_edcpermissions_revision"),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="edcpermissions",
+            name="device_created",
+            field=models.CharField(
+                blank=True, default="", max_length=10, verbose_name="Device created"
+            ),
+        ),
+        migrations.AlterField(
+            model_name="edcpermissions",
+            name="device_modified",
+            field=models.CharField(
+                blank=True, default="", max_length=10, verbose_name="Device modified"
+            ),
+        ),
+        migrations.AlterField(
+            model_name="edcpermissions",
+            name="locale_created",
+            field=models.CharField(
+                blank=True,
+                default="",
+                help_text="Auto-updated by Modeladmin",
+                max_length=10,
+                verbose_name="Locale created",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="edcpermissions",
+            name="locale_modified",
+            field=models.CharField(
+                blank=True,
+                default="",
+                help_text="Auto-updated by Modeladmin",
+                max_length=10,
+                verbose_name="Locale modified",
+            ),
+        ),
+    ]

edc_screening/age_evaluator.py

@@ -1,18 +1,18 @@
 from dateutil.relativedelta import relativedelta
+from django.utils import timezone
 from django.utils.timezone import localtime
 
 from edc_reportable.age_evaluator import AgeEvaluator as ReportableAgeEvaluator
 from edc_reportable.exceptions import ValueBoundryError
-from edc_utils.date import get_utcnow
 
 
 class AgeEvaluator(ReportableAgeEvaluator):
     def __init__(self, **kwargs) -> None:
-        self.reasons_ineligible: str | None = None
+        self.reasons_ineligible: str = ""
         super().__init__(**kwargs)
 
     def eligible(self, age: int | None = None) -> bool:
-        self.reasons_ineligible = None
+        self.reasons_ineligible = ""
         eligible = False
         if age:
             try:
@@ -26,10 +26,10 @@ class AgeEvaluator(ReportableAgeEvaluator):
         return eligible
 
     def in_bounds_or_raise(self, age: int = None, **kwargs):
-        self.reasons_ineligible = None
-        dob = localtime(get_utcnow() - relativedelta(years=age)).date()
+        self.reasons_ineligible = ""
+        dob = localtime(timezone.now() - relativedelta(years=age)).date()
         age_units = "years"
-        report_datetime = localtime(get_utcnow())
+        report_datetime = localtime(timezone.now())
         return super().in_bounds_or_raise(
             dob=dob, report_datetime=report_datetime, age_units=age_units
         )

edc_screening/auths.py

@@ -9,38 +9,43 @@ from edc_auth.utils import remove_default_model_permissions_from_edc_permissions
 
 from .auth_objects import SCREENING, SCREENING_ROLE, SCREENING_SUPER, SCREENING_VIEW
 
-site_auths.add_post_update_func(
-    "edc_screening", remove_default_model_permissions_from_edc_permissions
-)
 
-site_auths.add_custom_permissions_tuples(
-    model="edc_screening.edcpermissions",
-    codename_tuples=(
-        ("edc_screening.view_screening_listboard", "Can access Screening listboard"),
-        ("edc_screening.nav_screening_section", "Can access screening section"),
-    ),
-)
+def update_site_auths() -> None:
+    site_auths.add_post_update_func(
+        "edc_screening", remove_default_model_permissions_from_edc_permissions
+    )
 
-site_auths.add_group(
-    "edc_screening.view_screening_listboard",
-    "edc_screening.nav_screening_section",
-    name=SCREENING,
-)
+    site_auths.add_custom_permissions_tuples(
+        model="edc_screening.edcpermissions",
+        codename_tuples=(
+            ("edc_screening.view_screening_listboard", "Can access Screening listboard"),
+            ("edc_screening.nav_screening_section", "Can access screening section"),
+        ),
+    )
 
-site_auths.add_group(
-    "edc_screening.view_screening_listboard",
-    "edc_screening.nav_screening_section",
-    name=SCREENING_SUPER,
-)
+    site_auths.add_group(
+        "edc_screening.view_screening_listboard",
+        "edc_screening.nav_screening_section",
+        name=SCREENING,
+    )
+
+    site_auths.add_group(
+        "edc_screening.view_screening_listboard",
+        "edc_screening.nav_screening_section",
+        name=SCREENING_SUPER,
+    )
+
+    site_auths.add_group(
+        "edc_screening.view_screening_listboard",
+        "edc_screening.nav_screening_section",
+        name=SCREENING_VIEW,
+    )
+
+    site_auths.add_role(SCREENING, name=SCREENING_ROLE)
+    site_auths.update_role(SCREENING, name=CLINICIAN_ROLE)
+    site_auths.update_role(SCREENING, name=NURSE_ROLE)
+    site_auths.update_role(SCREENING_SUPER, name=CLINICIAN_SUPER_ROLE)
+    site_auths.update_role(SCREENING_VIEW, name=AUDITOR_ROLE)
 
-site_auths.add_group(
-    "edc_screening.view_screening_listboard",
-    "edc_screening.nav_screening_section",
-    name=SCREENING_VIEW,
-)
 
-site_auths.add_role(SCREENING, name=SCREENING_ROLE)
-site_auths.update_role(SCREENING, name=CLINICIAN_ROLE)
-site_auths.update_role(SCREENING, name=NURSE_ROLE)
-site_auths.update_role(SCREENING_SUPER, name=CLINICIAN_SUPER_ROLE)
-site_auths.update_role(SCREENING_VIEW, name=AUDITOR_ROLE)
+update_site_auths()

edc_screening/eligibility.py

@@ -45,7 +45,7 @@ class Eligibility:
         self.eligible = all([v for v in self.criteria.values()])
 
         if self.eligible:
-            self.reasons_ineligible = None
+            self.reasons_ineligible = ""
         else:
             self.reasons_ineligible = {k: v for k, v in self.criteria.items() if not v}
             for k, v in self.criteria.items():

edc_screening/gender_evaluator.py

@@ -6,7 +6,7 @@ class GenderEvaluator:
 
     def __init__(self, gender=None, **kwargs) -> None:  # noqa
         self.eligible = False
-        self.reasons_ineligible = None
+        self.reasons_ineligible = ""
         if gender in self.eligible_gender:
             self.eligible = True
         else:

edc_screening/migrations/0001_initial.py

@@ -7,6 +7,7 @@ import django_audit_fields.fields.uuid_auto_field
 import django_audit_fields.models.audit_model_mixin
 import django_revision.revision_field
 from django.db import migrations, models
+import django.utils.timezone
 
 
 class Migration(migrations.Migration):
@@ -33,14 +34,14 @@ class Migration(migrations.Migration):
                     "created",
                     models.DateTimeField(
                         blank=True,
-                        default=django_audit_fields.models.audit_model_mixin.utcnow,
+                        default=django.utils.timezone.now,
                     ),
                 ),
                 (
                     "modified",
                     models.DateTimeField(
                         blank=True,
-                        default=django_audit_fields.models.audit_model_mixin.utcnow,
+                        default=django.utils.timezone.now,
                     ),
                 ),
                 (

edc_screening/migrations/0005_alter_edcpermissions_device_created_and_more.py

@@ -0,0 +1,49 @@
+# Generated by Django 5.2.6 on 2025-09-17 16:53
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("edc_screening", "0004_alter_edcpermissions_revision"),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="edcpermissions",
+            name="device_created",
+            field=models.CharField(
+                blank=True, default="", max_length=10, verbose_name="Device created"
+            ),
+        ),
+        migrations.AlterField(
+            model_name="edcpermissions",
+            name="device_modified",
+            field=models.CharField(
+                blank=True, default="", max_length=10, verbose_name="Device modified"
+            ),
+        ),
+        migrations.AlterField(
+            model_name="edcpermissions",
+            name="locale_created",
+            field=models.CharField(
+                blank=True,
+                default="",
+                help_text="Auto-updated by Modeladmin",
+                max_length=10,
+                verbose_name="Locale created",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="edcpermissions",
+            name="locale_modified",
+            field=models.CharField(
+                blank=True,
+                default="",
+                help_text="Auto-updated by Modeladmin",
+                max_length=10,
+                verbose_name="Locale modified",
+            ),
+        ),
+    ]

edc_screening/model_mixins/eligibility_model_mixin.py

@@ -1,6 +1,5 @@
 from django.db import models
-
-from edc_utils import get_utcnow
+from django.utils import timezone
 
 from ..screening_eligibility import ScreeningEligibility
 
@@ -9,7 +8,7 @@ class EligibilityFieldsModelMixin(models.Model):
     eligible = models.BooleanField(default=False)
 
     reasons_ineligible = models.TextField(
-        verbose_name="Reason not eligible", max_length=150, null=True
+        verbose_name="Reason not eligible", max_length=150, default=""
     )
 
     eligibility_datetime = models.DateTimeField(
@@ -46,13 +45,11 @@ class EligibilityModelMixin(EligibilityFieldsModelMixin, models.Model):
         """
         # if self.eligibility_cls:
         self.eligibility_cls(model_obj=self)
-        # self.eligible = eligibility_obj.is_eligible
-        # self.reasons_ineligible = eligibility_obj.reasons_ineligible
         if not self.id:
             self.screening_identifier = self.identifier_cls().identifier
         if self.eligible:
             self.eligibility_datetime = self.get_report_datetime_for_eligibility_datetime()
-            self.real_eligibility_datetime = get_utcnow()
+            self.real_eligibility_datetime = timezone.now()
         else:
             self.eligibility_datetime = None
             self.real_eligibility_datetime = None