meta-edc 0.3.39__py3-none-any.whl → 1.4.0__py3-none-any.whl

meta_screening/eligibility/eligibility_part_three/base_eligibility_part_three.py

@@ -1,15 +1,21 @@
-from edc_constants.constants import NEG, NO, NOT_APPLICABLE
-from edc_egfr import EgfrCkdEpi
-from edc_egfr.calculators import EgfrCalculatorError
-from edc_reportable import (
+import contextlib
+
+from clinicedc_constants import (
     MICROMOLES_PER_LITER,
     MILLIMOLES_PER_LITER,
+    NEG,
+    NO,
+    NOT_APPLICABLE,
+)
+from clinicedc_utils import (
     ConversionNotHandled,
-    calculate_bmi,
+    EgfrCalculatorError,
+    EgfrCkdEpi2009,
     convert_units,
 )
 from edc_screening.fc import FC
 from edc_screening.screening_eligibility import ScreeningEligibility
+from edc_vitals.calculators import calculate_bmi
 
 
 class BaseEligibilityPartThree(ScreeningEligibility):
@@ -40,16 +46,14 @@ 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:
-            self.calculated_egfr_value = EgfrCkdEpi(
+        with contextlib.suppress(EgfrCalculatorError):
+            self.calculated_egfr_value = EgfrCkdEpi2009(
                 gender=self.model_obj.gender,
                 age_in_years=self.model_obj.age_in_years,
                 ethnicity=self.model_obj.gender,
                 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
@@ -82,64 +86,79 @@ class BaseEligibilityPartThree(ScreeningEligibility):
 
     @property
     def converted_creatinine_value(self):
-        try:
-            value = convert_units(
-                self.creatinine_value,
-                units_from=self.creatinine_units,
-                units_to=MICROMOLES_PER_LITER,
-            )
-        except ConversionNotHandled as e:
-            raise ConversionNotHandled(f"Creatinine. {e}")
+        value = None
+        if self.creatinine_value and self.creatinine_units:
+            try:
+                value = convert_units(
+                    label="creatinine",
+                    value=self.creatinine_value,
+                    units_from=self.creatinine_units,
+                    units_to=MICROMOLES_PER_LITER,
+                )
+            except ConversionNotHandled as e:
+                raise ConversionNotHandled(f"Creatinine. {e}") from e
         if value and float(value) > 999999.9999:
             raise ConversionNotHandled("Creatinine value is absurd.")
         return value
 
     @property
     def converted_fbg_value(self):
-        try:
-            value = convert_units(
-                self.fbg_value,
-                units_from=self.fbg_units,
-                units_to=MILLIMOLES_PER_LITER,
-            )
-        except ConversionNotHandled as e:
-            raise ConversionNotHandled(f"FBG. {e}")
+        value = None
+        if self.fbg_value and self.fbg_units:
+            try:
+                value = convert_units(
+                    label="glucose",
+                    value=self.fbg_value,
+                    units_from=self.fbg_units,
+                    units_to=MILLIMOLES_PER_LITER,
+                )
+            except ConversionNotHandled as e:
+                raise ConversionNotHandled(f"FBG. {e}") from e
         return value
 
     @property
     def converted_fbg2_value(self):
-        try:
-            value = convert_units(
-                self.fbg2_value,
-                units_from=self.fbg2_units,
-                units_to=MILLIMOLES_PER_LITER,
-            )
-        except ConversionNotHandled as e:
-            raise ConversionNotHandled(f"FBG2. {e}")
+        value = None
+        if self.fbg2_value and self.fbg2_units:
+            try:
+                value = convert_units(
+                    label="glucose",
+                    value=self.fbg2_value,
+                    units_from=self.fbg2_units,
+                    units_to=MILLIMOLES_PER_LITER,
+                )
+            except ConversionNotHandled as e:
+                raise ConversionNotHandled(f"FBG2. {e}") from e
         return value
 
     @property
     def converted_ogtt_value(self):
-        try:
-            value = convert_units(
-                self.ogtt_value,
-                units_from=self.ogtt_units,
-                units_to=MILLIMOLES_PER_LITER,
-            )
-        except ConversionNotHandled as e:
-            raise ConversionNotHandled(f"OGTT. {e}")
+        value = None
+        if self.ogtt_value and self.ogtt_units:
+            try:
+                value = convert_units(
+                    label="glucose",
+                    value=self.ogtt_value,
+                    units_from=self.ogtt_units,
+                    units_to=MILLIMOLES_PER_LITER,
+                )
+            except ConversionNotHandled as e:
+                raise ConversionNotHandled(f"OGTT. {e}") from e
         return value
 
     @property
     def converted_ogtt2_value(self):
-        try:
-            value = convert_units(
-                self.ogtt2_value,
-                units_from=self.ogtt2_units,
-                units_to=MILLIMOLES_PER_LITER,
-            )
-        except ConversionNotHandled as e:
-            raise ConversionNotHandled(f"OGTT2. {e}")
+        value = None
+        if self.ogtt2_value and self.ogtt2_units:
+            try:
+                value = convert_units(
+                    label="glucose",
+                    value=self.ogtt2_value,
+                    units_from=self.ogtt2_units,
+                    units_to=MILLIMOLES_PER_LITER,
+                )
+            except ConversionNotHandled as 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

@@ -1,6 +1,6 @@
 from typing import Any
 
-from edc_constants.constants import DM, NO, NORMAL, NOT_APPLICABLE, PENDING, TBD, YES
+from clinicedc_constants import DM, NO, NORMAL, NOT_APPLICABLE, PENDING, TBD, YES
 from edc_screening.fc import FC
 
 from ...constants import (
@@ -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/eligibility/eligibility_part_two.py

@@ -1,4 +1,4 @@
-from edc_constants.constants import NO, NOT_APPLICABLE, YES
+from clinicedc_constants import NO, NOT_APPLICABLE, YES
 from edc_screening.fc import FC
 from edc_screening.screening_eligibility import ScreeningEligibility
 

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/form_validators/screening_part_one.py

@@ -1,5 +1,5 @@
+from clinicedc_constants import MALE, YES
 from django import forms
-from edc_constants.constants import MALE, YES
 from edc_form_validators import FormValidator
 from edc_prn.modelform_mixins import PrnFormValidatorMixin
 

meta_screening/form_validators/screening_part_three.py

@@ -2,8 +2,8 @@ from __future__ import annotations
 
 from datetime import datetime
 
+from clinicedc_constants import NO, YES
 from django import forms
-from edc_constants.constants import NO, YES
 from edc_egfr.form_validator_mixins import EgfrCkdEpiFormValidatorMixin
 from edc_form_validators import INVALID_ERROR, FormValidator
 from edc_glucose.form_validators import (
@@ -74,7 +74,11 @@ class ScreeningPartThreeFormValidator(
         self.validate_creatinine_required_fields()
         self.required_if(YES, field="hba1c_performed", field_required="hba1c_datetime")
         self.required_if(YES, field="hba1c_performed", field_required="hba1c_value")
-        self.validate_egfr()
+        self.validate_egfr(
+            gender=self.instance.gender,
+            age_in_years=self.instance.age_in_years,
+            ethnicity=self.instance.ethnicity,
+        )
         self.validate_suitability_for_study()
 
     @property

meta_screening/form_validators/screening_part_two.py

@@ -2,8 +2,8 @@ from __future__ import annotations
 
 from datetime import datetime
 
+from clinicedc_constants import NO, YES
 from django import forms
-from edc_constants.constants import NO, YES
 from edc_form_validators import INVALID_ERROR, FormValidator
 from edc_prn.modelform_mixins import PrnFormValidatorMixin
 from edc_utils import formatted_datetime, get_utcnow, to_utc

meta_screening/form_validators/subject_refusal.py

@@ -1,4 +1,4 @@
-from edc_constants.constants import OTHER
+from clinicedc_constants import OTHER
 from edc_form_validators import FormValidator
 from edc_prn.modelform_mixins import PrnFormValidatorMixin
 

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 +1,4 @@
-from typing import Tuple
-
-part_one_fields: Tuple[str, ...] = (
+part_one_fields: tuple[str, ...] = (
     "report_datetime",
     "screening_consent",
     "meta_phase_two",
@@ -22,7 +20,7 @@ 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 +40,7 @@ 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 +51,7 @@ 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 +60,39 @@ 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 +101,25 @@ 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 +136,7 @@ calculated_fields: Tuple[str, ...] = (
 )
 
 
-part_three_labs: Tuple[str, ...] = (
+part_three_labs: tuple[str, ...] = (
     "haemoglobin_value",
     "wbc_value",
     "ast_value",
@@ -149,7 +147,7 @@ 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,
                     ),
                 ),
                 (