meta-edc 1.1.10__py3-none-any.whl → 1.1.13__py3-none-any.whl

meta_screening/baker_recipes.py

@@ -1,8 +1,8 @@
 from dateutil.relativedelta import relativedelta
 from django.contrib.sites.models import Site
-from edc_constants.constants import BLACK, FEMALE, NO, NOT_APPLICABLE, YES
+from django.utils import timezone
+from edc_constants.constants import BLACK, FEMALE, NO, NOT_APPLICABLE, NULL_STRING, YES
 from edc_reportable.units import MILLIGRAMS_PER_DECILITER, MILLIMOLES_PER_LITER
-from edc_utils import get_utcnow
 from faker import Faker
 from model_bakery.recipe import Recipe
 
@@ -13,11 +13,11 @@ fake = Faker()
 
 subjectscreening = Recipe(
     SubjectScreening,
-    report_datetime=get_utcnow() - relativedelta(days=1),
+    report_datetime=timezone.now() - relativedelta(days=1),
     screening_consent=YES,
     hospital_identifier="111",
     initials="ZZ",
-    subject_identifier=None,
+    subject_identifier=NULL_STRING,
     gender=FEMALE,
     age_in_years=40,
     ethnicity=BLACK,
@@ -29,7 +29,7 @@ subjectscreening = Recipe(
     staying_nearby_12=YES,
     pregnant=NO,
     site=Site.objects.get_current(),
-    part_two_report_datetime=get_utcnow() - relativedelta(days=1),
+    part_two_report_datetime=timezone.now() - relativedelta(days=1),
     congestive_heart_failure=NO,
     liver_disease=NO,
     alcoholism=NO,
@@ -39,8 +39,8 @@ subjectscreening = Recipe(
     acute_condition=NO,
     metformin_sensitivity=NO,
     advised_to_fast=YES,
-    appt_datetime=get_utcnow() + relativedelta(days=1),
-    part_three_report_datetime=get_utcnow(),
+    appt_datetime=timezone.now() + relativedelta(days=1),
+    part_three_report_datetime=timezone.now(),
     weight=65,
     height=120,
     fasting=YES,
@@ -51,8 +51,8 @@ subjectscreening = Recipe(
     creatinine_units=MILLIGRAMS_PER_DECILITER,
     fbg_value=6.9,
     fbg_units=MILLIMOLES_PER_LITER,
-    fbg_datetime=get_utcnow(),
-    ogtt_base_datetime=get_utcnow(),
+    fbg_datetime=timezone.now(),
+    ogtt_base_datetime=timezone.now(),
     unsuitable_for_study=NO,
     unsuitable_agreed=NOT_APPLICABLE,
     vl_undetectable=YES,

meta_screening/eligibility/__init__.py

@@ -6,3 +6,12 @@ from .eligibility import (
 from .eligibility_part_one import EligibilityPartOne
 from .eligibility_part_three import EligibilityPartThreePhaseThree
 from .eligibility_part_two import EligibilityPartTwo
+
+__all__ = [
+    "EligibilityPartOne",
+    "EligibilityPartThreePhaseThree",
+    "EligibilityPartTwo",
+    "MetaEligibility",
+    "SubjectScreeningEligibilityError",
+    "get_display_label",
+]

meta_screening/eligibility/eligibility.py

@@ -16,7 +16,7 @@ class SubjectScreeningEligibilityError(Exception):
     pass
 
 
-def get_eligible_as_word(
+def get_eligible_as_word(  # noqa: PLR0913
     obj=None,
     eligible_part_one=None,
     eligible_part_two=None,
@@ -90,8 +90,8 @@ class MetaEligibility:
 
     """
 
-    eligibility_values = [YES, NO, TBD]
-    default_options = dict(
+    eligibility_values = (YES, NO, TBD)
+    default_options = dict(  # noqa: RUF012
         eligible_value_default=TBD,
         eligible_values_list=[YES, NO, TBD],
         is_eligible_value=YES,
@@ -99,8 +99,8 @@ class MetaEligibility:
 
     def __init__(
         self,
-        model_obj: models.Model = None,
-        defaults: dict = None,
+        model_obj: models.Model | None = None,
+        defaults: dict | None = None,
         update_model=None,
     ):
         self.part_one = None
@@ -162,7 +162,7 @@ class MetaEligibility:
     @property
     def is_eligible(self: Any) -> bool:
         """Returns True if eligible else False"""
-        return True if self.eligible == YES else False
+        return self.eligible == YES
 
     def check_eligibility_values_or_raise(self: Any):
         for response in [
@@ -207,7 +207,7 @@ class MetaEligibility:
             )
         else:
             status_str = format_html(
-                "P1: {p1_eligible}<BR>" "P2: {p2_eligible}<BR>" "P3: {p3_eligible}<BR>",
+                "P1: {p1_eligible}<BR>P2: {p2_eligible}<BR>P3: {p3_eligible}<BR>",
                 p1_eligible=self.part_one.eligible.upper(),
                 p2_eligible=self.part_two.eligible.upper(),
                 p3_eligible=self.part_three.eligible.upper(),

meta_screening/eligibility/eligibility_part_three/__init__.py

@@ -1 +1,3 @@
 from .eligibility_part_three_phase_three import EligibilityPartThreePhaseThree
+
+__all__ = ["EligibilityPartThreePhaseThree"]

meta_screening/eligibility/eligibility_part_three/base_eligibility_part_three.py

@@ -1,3 +1,5 @@
+import contextlib
+
 from edc_constants.constants import NEG, NO, NOT_APPLICABLE
 from edc_egfr import EgfrCkdEpi
 from edc_egfr.calculators import EgfrCalculatorError
@@ -37,7 +39,7 @@ class BaseEligibilityPartThree(ScreeningEligibility):
     def assess_eligibility(self) -> None:
         if self.weight and self.height:
             self.bmi = calculate_bmi(weight_kg=self.weight, height_cm=self.height)
-        try:
+        with contextlib.suppress(EgfrCalculatorError):
             self.calculated_egfr_value = EgfrCkdEpi(
                 gender=self.model_obj.gender,
                 age_in_years=self.model_obj.age_in_years,
@@ -45,8 +47,6 @@ class BaseEligibilityPartThree(ScreeningEligibility):
                 creatinine_value=self.model_obj.creatinine_value,
                 creatinine_units=self.model_obj.creatinine_units,
             ).value
-        except EgfrCalculatorError:
-            pass
 
     def set_fld_attrs_on_model(self) -> None:
         self.model_obj.converted_creatinine_value = self.converted_creatinine_value
@@ -89,7 +89,7 @@ class BaseEligibilityPartThree(ScreeningEligibility):
                     units_to=MICROMOLES_PER_LITER,
                 )
             except ConversionNotHandled as e:
-                raise ConversionNotHandled(f"Creatinine. {e}")
+                raise ConversionNotHandled(f"Creatinine. {e}") from e
         if value and float(value) > 999999.9999:
             raise ConversionNotHandled("Creatinine value is absurd.")
         return value
@@ -106,7 +106,7 @@ class BaseEligibilityPartThree(ScreeningEligibility):
                     units_to=MILLIMOLES_PER_LITER,
                 )
             except ConversionNotHandled as e:
-                raise ConversionNotHandled(f"FBG. {e}")
+                raise ConversionNotHandled(f"FBG. {e}") from e
         return value
 
     @property
@@ -121,7 +121,7 @@ class BaseEligibilityPartThree(ScreeningEligibility):
                     units_to=MILLIMOLES_PER_LITER,
                 )
             except ConversionNotHandled as e:
-                raise ConversionNotHandled(f"FBG2. {e}")
+                raise ConversionNotHandled(f"FBG2. {e}") from e
         return value
 
     @property
@@ -136,7 +136,7 @@ class BaseEligibilityPartThree(ScreeningEligibility):
                     units_to=MILLIMOLES_PER_LITER,
                 )
             except ConversionNotHandled as e:
-                raise ConversionNotHandled(f"OGTT. {e}")
+                raise ConversionNotHandled(f"OGTT. {e}") from e
         return value
 
     @property
@@ -151,7 +151,7 @@ class BaseEligibilityPartThree(ScreeningEligibility):
                     units_to=MILLIMOLES_PER_LITER,
                 )
             except ConversionNotHandled as e:
-                raise ConversionNotHandled(f"OGTT2. {e}")
+                raise ConversionNotHandled(f"OGTT2. {e}") from e
         return value
 
     def set_eligible_model_field(self):

meta_screening/eligibility/eligibility_part_three/eligibility_part_three_phase_three.py

@@ -52,20 +52,19 @@ class EligibilityPartThreePhaseThree(BaseEligibilityPartThree):
         ):
             self.eligible = TBD
             self.reasons_ineligible.update(fbg_ogtt_incomplete=FBG_OGTT_INCOMPLETE)
-        else:
-            if self.ogtt_category == PRE_DM:
-                self.eligible = YES
-            elif self.ogtt_category == DM:
-                self.eligible = NO
-                self.reasons_ineligible.update(hi_ogtt=HI_OGTT)
-            elif self.fbg_category == PRE_DM and self.ogtt_category == NORMAL:
-                self.eligible = YES
-            elif self.fbg_category == NORMAL and self.ogtt_category == NORMAL:
-                self.eligible = NO
-                self.reasons_ineligible.update(normal_fbg_ogtt=NORMAL_FBG_OGTT)
-            elif self.fbg_category == DM and self.ogtt_category == NORMAL:
-                self.eligible = NO
-                self.reasons_ineligible.update(hi_fbg=HI_FBG)
+        elif self.ogtt_category == PRE_DM:
+            self.eligible = YES
+        elif self.ogtt_category == DM:
+            self.eligible = NO
+            self.reasons_ineligible.update(hi_ogtt=HI_OGTT)
+        elif self.fbg_category == PRE_DM and self.ogtt_category == NORMAL:
+            self.eligible = YES
+        elif self.fbg_category == NORMAL and self.ogtt_category == NORMAL:
+            self.eligible = NO
+            self.reasons_ineligible.update(normal_fbg_ogtt=NORMAL_FBG_OGTT)
+        elif self.fbg_category == DM and self.ogtt_category == NORMAL:
+            self.eligible = NO
+            self.reasons_ineligible.update(hi_fbg=HI_FBG)
         if self.calculated_egfr_value and self.calculated_egfr_value < 45.0:
             self.reasons_ineligible.update(egfr_low=EGFR_LT_45)
             self.eligible = NO

meta_screening/form_validators/__init__.py

@@ -3,3 +3,11 @@ from .screening_part_three import ScreeningPartThreeFormValidator
 from .screening_part_two import ScreeningPartTwoFormValidator
 from .subject_refusal import SubjectRefusalFormValidator
 from .subject_screening import SubjectScreeningFormValidator
+
+__all__ = [
+    "ScreeningPartOneFormValidator",
+    "ScreeningPartThreeFormValidator",
+    "ScreeningPartTwoFormValidator",
+    "SubjectRefusalFormValidator",
+    "SubjectScreeningFormValidator",
+]

meta_screening/forms/__init__.py

@@ -16,3 +16,23 @@ from .screening_part_three_form import ScreeningPartThreeForm
 from .screening_part_two_form import ScreeningPartTwoForm
 from .subject_refusal_form import SubjectRefusalForm
 from .subject_screening_form import SubjectScreeningForm
+
+__all__ = [
+    "ScreeningPartOneForm",
+    "ScreeningPartThreeForm",
+    "ScreeningPartTwoForm",
+    "SubjectRefusalForm",
+    "SubjectScreeningForm",
+    "calculated_fields",
+    "field_lists",
+    "part_one_fields",
+    "part_three_comment_fields",
+    "part_three_fbg_fields",
+    "part_three_fields",
+    "part_three_glucose_fields",
+    "part_three_ogtt_fields",
+    "part_three_other_fields",
+    "part_three_pregnancy_fields",
+    "part_three_vitals_fields",
+    "part_two_fields",
+]

meta_screening/forms/field_lists.py

@@ -1,6 +1,5 @@
-from typing import Tuple
 
-part_one_fields: Tuple[str, ...] = (
+part_one_fields: tuple[str, ...] = (
     "report_datetime",
     "screening_consent",
     "meta_phase_two",
@@ -22,7 +21,7 @@ part_one_fields: Tuple[str, ...] = (
 )
 
 
-part_two_fields: Tuple[str, ...] = (
+part_two_fields: tuple[str, ...] = (
     "part_two_report_datetime",
     "congestive_heart_failure",
     "liver_disease",
@@ -42,7 +41,7 @@ part_two_fields: Tuple[str, ...] = (
 )
 
 
-part_three_vitals_fields: Tuple[str, ...] = (
+part_three_vitals_fields: tuple[str, ...] = (
     "height",
     "weight",
     "sys_blood_pressure_one",
@@ -53,7 +52,7 @@ part_three_vitals_fields: Tuple[str, ...] = (
 )
 
 
-part_three_fbg_fields: Tuple[str, ...] = (
+part_three_fbg_fields: tuple[str, ...] = (
     "fasting",
     "fasting_duration_str",
     "fbg_datetime",
@@ -62,39 +61,39 @@ part_three_fbg_fields: Tuple[str, ...] = (
 )
 
 
-part_three_repeat_fbg_fields: Tuple[str, ...] = (
+part_three_repeat_fbg_fields: tuple[str, ...] = (
     "fbg2_datetime",
     "fbg2_value",
     "fbg2_units",
 )
 
-part_three_ogtt_fields: Tuple[str, ...] = (
+part_three_ogtt_fields: tuple[str, ...] = (
     "ogtt_base_datetime",
     "ogtt_datetime",
     "ogtt_value",
     "ogtt_units",
 )
 
-part_three_repeat_ogtt_fields: Tuple[str, ...] = (
+part_three_repeat_ogtt_fields: tuple[str, ...] = (
     "ogtt2_base_datetime",
     "ogtt2_datetime",
     "ogtt2_value",
     "ogtt2_units",
 )
 
-part_three_glucose_fields: Tuple[str, ...] = (
+part_three_glucose_fields: tuple[str, ...] = (
     *part_three_fbg_fields,
     *part_three_ogtt_fields,
     *("repeat_glucose_opinion", "repeat_appt_datetime", "contact_number"),
 )
 
-part_three_pregnancy_fields: Tuple[str, ...] = (
+part_three_pregnancy_fields: tuple[str, ...] = (
     "urine_bhcg_performed",
     "urine_bhcg_value",
     "urine_bhcg_date",
 )
 
-part_three_other_fields: Tuple[str, ...] = (
+part_three_other_fields: tuple[str, ...] = (
     "creatinine_performed",
     "creatinine_value",
     "creatinine_units",
@@ -103,25 +102,25 @@ part_three_other_fields: Tuple[str, ...] = (
     "hba1c_value",
 )
 
-part_three_creatinine_fields: Tuple[str, ...] = (
+part_three_creatinine_fields: tuple[str, ...] = (
     "creatinine_performed",
     "creatinine_value",
     "creatinine_units",
 )
 
-part_three_hba1c_fields: Tuple[str, ...] = (
+part_three_hba1c_fields: tuple[str, ...] = (
     "hba1c_performed",
     "hba1c_datetime",
     "hba1c_value",
 )
 
-part_three_comment_fields: Tuple[str, ...] = (
+part_three_comment_fields: tuple[str, ...] = (
     "unsuitable_for_study",
     "reasons_unsuitable",
     "unsuitable_agreed",
 )
 
-calculated_fields: Tuple[str, ...] = (
+calculated_fields: tuple[str, ...] = (
     "sys_blood_pressure_avg",
     "dia_blood_pressure_avg",
     "calculated_bmi_value",
@@ -138,7 +137,7 @@ calculated_fields: Tuple[str, ...] = (
 )
 
 
-part_three_labs: Tuple[str, ...] = (
+part_three_labs: tuple[str, ...] = (
     "haemoglobin_value",
     "wbc_value",
     "ast_value",
@@ -149,7 +148,7 @@ part_three_labs: Tuple[str, ...] = (
 )
 
 
-part_three_fields: Tuple[str, ...] = (
+part_three_fields: tuple[str, ...] = (
     "part_three_report_datetime",
     *part_three_vitals_fields,
     *part_three_pregnancy_fields,

meta_screening/forms/screening_part_one_form.py

@@ -17,9 +17,9 @@ class ScreeningPartOneForm(
         model = ScreeningPartOne
         fields = part_one_fields
 
-        labels = {
+        labels = {  # noqa: RUF012
             "site": "Which study site is this?",
         }
-        help_texts = {
+        help_texts = {  # noqa: RUF012
             "site": "This question is asked to confirm you are logged in to the correct site.",
         }

meta_screening/forms/screening_part_three_form.py

@@ -18,9 +18,11 @@ class ScreeningPartThreeForm(AlreadyConsentedFormMixin, FormValidatorMixin, form
     def clean(self):
         cleaned_data = super().clean()
 
-        if cleaned_data.get("creatinine_value"):
-            if float(cleaned_data.get("creatinine_value")) > GLUCOSE_HIGH_READING:
-                raise forms.ValidationError({"creatinine_value": "Value is absurd."})
+        if (
+            cleaned_data.get("creatinine_value")
+            and float(cleaned_data.get("creatinine_value")) > GLUCOSE_HIGH_READING
+        ):
+            raise forms.ValidationError({"creatinine_value": "Value is absurd."})
         return cleaned_data
 
     class Meta:

meta_screening/forms/screening_part_two_form.py

@@ -12,11 +12,7 @@ class ScreeningPartTwoForm(AlreadyConsentedFormMixin, FormValidatorMixin, forms.
 
     AUTO_NUMBER_START = 17
 
-    def clean(self):
-        cleaned_data = super().clean()
-        return cleaned_data
-
     class Meta:
         model = ScreeningPartTwo
         fields = part_two_fields
-        help_texts = {"contact_number": "(Encryption: RSA local)"}
+        help_texts = {"contact_number": "(Encryption: RSA local)"}  # noqa: RUF012

meta_screening/forms/subject_refusal_form.py

@@ -12,10 +12,6 @@ class SubjectRefusalForm(
 ):
     form_validator_cls = SubjectRefusalFormValidator
 
-    def clean(self):
-        cleaned_data = super().clean()
-        return cleaned_data
-
     class Meta:
         model = SubjectRefusal
         fields = "__all__"

meta_screening/forms/subject_screening_form.py

@@ -12,10 +12,6 @@ class SubjectScreeningForm(
 ):
     form_validator_cls = SubjectScreeningFormValidator
 
-    def clean(self):
-        cleaned_data = super().clean()
-        return cleaned_data
-
     class Meta:
         model = SubjectScreening
         fields = "__all__"

meta_screening/migrations/0001_initial.py

@@ -8,7 +8,7 @@ import django.db.models.deletion
 import django_audit_fields.fields.hostname_modification_field
 import django_audit_fields.fields.userfield
 import django_audit_fields.fields.uuid_auto_field
-import django_audit_fields.models.audit_model_mixin
+import django.utils.timezone
 import django_crypto_fields.fields.encrypted_char_field
 import django_revision.revision_field
 import edc_sites.models
@@ -45,14 +45,14 @@ 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,
                     ),
                 ),
                 (
@@ -839,14 +839,14 @@ 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,
                     ),
                 ),
                 (
@@ -1028,14 +1028,14 @@ 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,
                     ),
                 ),
                 (
@@ -1852,14 +1852,14 @@ 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,
                     ),
                 ),
                 (
@@ -2676,14 +2676,14 @@ 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,
                     ),
                 ),
                 (
@@ -3500,14 +3500,14 @@ 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,
                     ),
                 ),
                 (
@@ -4324,14 +4324,14 @@ 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,
                     ),
                 ),
                 (