clinicedc 2.0.40__py3-none-any.whl → 2.0.42__py3-none-any.whl

edc_dx_review/model_mixins/factory/rx_initial_review_model_mixin_factory.py

@@ -1,9 +1,9 @@
 from __future__ import annotations
 
+from clinicedc_constants import NOT_APPLICABLE, YES
 from django.db import models
 
 from edc_constants.choices import YES_NO, YES_NO_NA
-from edc_constants.constants import NOT_APPLICABLE, YES
 from edc_model.models import DurationYMDField
 from edc_model.validators import date_not_future
 

edc_dx_review/model_mixins/followup_review/followup_review_model_mixin.py

@@ -1,7 +1,7 @@
+from clinicedc_constants import NOT_APPLICABLE
 from django.db import models
 
 from edc_constants.choices import YES_NO_NA
-from edc_constants.constants import NOT_APPLICABLE
 
 
 class FollowupReviewModelMixin(models.Model):

edc_dx_review/model_mixins/followup_review/hiv_followup_review_model_mixin.py

@@ -1,7 +1,7 @@
+from clinicedc_constants import NOT_APPLICABLE
 from django.db import models
 
 from edc_constants.choices import YES_NO_NA
-from edc_constants.constants import NOT_APPLICABLE
 
 from .followup_review_model_mixin import FollowupReviewModelMixin
 

edc_dx_review/model_mixins/initial_review/chol_initial_review_model_mixin.py

@@ -1,7 +1,7 @@
+from clinicedc_constants import NOT_APPLICABLE
 from django.db import models
 
 from edc_constants.choices import YES_NO
-from edc_constants.constants import NOT_APPLICABLE
 
 from ...choices import CHOL_MANAGEMENT
 from ..dx_location_model_mixin import DxLocationModelMixin

edc_dx_review/model_mixins/initial_review/hiv_initial_model_mixins.py

@@ -1,13 +1,12 @@
+from clinicedc_constants import COPIES_PER_MILLILITER, NOT_APPLICABLE, YES
 from django.core.validators import MaxValueValidator, MinValueValidator
 from django.db import models
-
 from edc_constants.choices import YES_NO, YES_NO_NA, YES_NO_PENDING_NA
-from edc_constants.constants import NOT_APPLICABLE, YES
 from edc_lab.choices import VL_QUANTIFIER_NA
 from edc_model import estimated_date_from_ago
 from edc_model import models as edc_models
 from edc_model.validators import date_not_future
-from edc_reportable import CELLS_PER_MILLIMETER_CUBED_DISPLAY, COPIES_PER_MILLILITER
+from edc_reportable.units import CELLS_PER_MILLIMETER_CUBED_DISPLAY
 
 
 class HivArvInitiationModelMixin(models.Model):

edc_dx_review/model_mixins/initial_review/ncd_initial_review_model_mixin.py

@@ -1,7 +1,7 @@
+from clinicedc_constants import YES
 from django.db import models
 
 from edc_constants.choices import YES_NO
-from edc_constants.constants import YES
 from edc_model import models as edc_models
 from edc_model.utils import duration_to_date
 

edc_dx_review/utils.py

@@ -3,12 +3,12 @@ from __future__ import annotations
 from datetime import date, datetime
 from typing import TYPE_CHECKING
 
+from clinicedc_constants import HIV, YES
 from django import forms
 from django.apps import apps as django_apps
 from django.conf import settings
 from django.core.exceptions import ObjectDoesNotExist
 
-from edc_constants.constants import HIV, YES
 from edc_model.utils import model_exists_or_raise
 from edc_visit_schedule.baseline import VisitScheduleBaselineError
 from edc_visit_schedule.utils import is_baseline

edc_egfr/__init__.py

@@ -1 +0,0 @@
-from .calculators import EgfrCkdEpi, EgfrCockcroftGault

edc_egfr/egfr.py

@@ -4,18 +4,19 @@ from datetime import date, datetime
 from decimal import Decimal
 from typing import TYPE_CHECKING, Any
 
+from clinicedc_constants import NEW
+from clinicedc_constants.units import EGFR_UNITS, PERCENT
+from clinicedc_utils import EgfrCkdEpi2009, EgfrCockcroftGault, egfr_percent_change
+from clinicedc_utils.constants import CKD_EPI, COCKCROFT_GAULT
 from dateutil.relativedelta import relativedelta
 from django.core.exceptions import ObjectDoesNotExist
 from django.db import transaction
 from django.utils import timezone
 
-from edc_constants.constants import NEW
 from edc_reportable.models import ReferenceRangeCollection
-from edc_reportable.units import EGFR_UNITS, PERCENT
 from edc_reportable.utils import get_grade_for_value
 from edc_utils.age import age
 
-from .calculators import EgfrCkdEpi, EgfrCockcroftGault, egfr_percent_change
 from .get_drop_notification_model import get_egfr_drop_notification_model_cls
 
 if TYPE_CHECKING:
@@ -27,7 +28,7 @@ class EgfrError(Exception):
 
 
 class Egfr:
-    calculators: dict = {"ckd-epi": EgfrCkdEpi, "cockcroft-gault": EgfrCockcroftGault}  # noqa: RUF012
+    calculators: dict = {CKD_EPI: EgfrCkdEpi2009, COCKCROFT_GAULT: EgfrCockcroftGault}  # noqa: RUF012
 
     def __init__(
         self,
@@ -54,16 +55,11 @@ class Egfr:
         self._egfr_grade = None
         self._egfr_drop_value: Decimal | None = None
         self._egfr_drop_grade = None
+        self._formula_name = formula_name
         self.assay_date: date | None = None
         self.related_visit = None
-
         self.baseline_egfr_value = baseline_egfr_value
-        if formula_name not in self.calculators:
-            raise EgfrError(
-                f"Invalid formula_name. Expected one of {list(self.calculators.keys())}. "
-                f"Got {formula_name}."
-            )
-        self.calculator_cls = self.calculators.get(formula_name)
+        self.calculator_cls = self.calculators.get(self.formula_name)
         self.age_in_years = age_in_years
         self.dob = dob
         self.weight_in_kgs = weight_in_kgs
@@ -121,6 +117,15 @@ class Egfr:
 
         self.on_percent_drop_threshold_reached()
 
+    @property
+    def formula_name(self) -> str:
+        if self._formula_name not in self.calculators:
+            raise EgfrError(
+                f"Invalid formula_name. Expected one of {list(self.calculators.keys())}. "
+                f"Got {self._formula_name}."
+            )
+        return self._formula_name
+
     def on_value_threshold_reached(self) -> None:
         """A hook to respond if egfr value is at or beyond the value
         threshold.
@@ -141,14 +146,17 @@ class Egfr:
     @property
     def egfr_value(self) -> float:
         if self._egfr_value is None:
-            self._egfr_value = self.calculator_cls(
+            opts = dict(
                 gender=self.gender,
-                ethnicity=self.ethnicity,
                 age_in_years=self.age_in_years,
                 creatinine_value=self.creatinine_value,
                 creatinine_units=self.creatinine_units,
-                weight=self.get_weight_in_kgs(),
-            ).value
+            )
+            if self.formula_name == COCKCROFT_GAULT:
+                opts.update(weight=self.get_weight_in_kgs())
+            elif self.formula_name == CKD_EPI:
+                opts.update(ethnicity=self.ethnicity)
+            self._egfr_value = self.calculator_cls(**opts).value
         return self._egfr_value
 
     @property

edc_egfr/form_validator_mixins/egfr_form_validator_mixins.py

@@ -1,56 +1,61 @@
+from clinicedc_utils import (
+    ConversionNotHandled,
+    EgfrCalculatorError,
+    EgfrCkdEpi2009,
+    EgfrCkdEpi2021,
+    EgfrCockcroftGault,
+)
 from django import forms
 
 from edc_form_validators import INVALID_ERROR
-from edc_reportable import ConversionNotHandled
-from edc_vitals.calculators import CalculatorError
-
-from ..calculators import EgfrCalculatorError, EgfrCkdEpi, EgfrCockcroftGault
 
 
 class EgfrCkdEpiFormValidatorMixin:
+    calculator_version = 2009
+
+    @property
+    def egfr_calculator_cls(self) -> type[EgfrCkdEpi2009 | EgfrCkdEpi2021]:
+        if self.calculator_version == 2009:  # noqa: PLR2004
+            cls = EgfrCkdEpi2009
+        elif self.calculator_version == 2021:  # noqa: PLR2004
+            cls = EgfrCkdEpi2021
+        else:
+            raise EgfrCalculatorError(
+                f"Invalid calculator version. Got {self.calculator_version}."
+            )
+        return cls
+
     def validate_egfr(
-        self,
-        gender: str = None,
-        age_in_years: int = None,
-        weight_in_kgs: float = None,
-        ethnicity: str = None,
-        baseline_egfr_value: float | None = None,
-    ):
+        self, *, gender: str, age_in_years: int, ethnicity: str | None = None
+    ) -> float | None:
         opts = dict(
             gender=gender,
             age_in_years=age_in_years,
-            weight=weight_in_kgs,
-            ethnicity=ethnicity,
             creatinine_value=self.cleaned_data.get("creatinine_value"),
             creatinine_units=self.cleaned_data.get("creatinine_units"),
-            baseline_egfr_value=baseline_egfr_value,
         )
+        if self.egfr_calculator_cls == EgfrCkdEpi2009:
+            opts.update(ethnicity=ethnicity)
         try:
-            value = EgfrCkdEpi(**opts).value
-        except (EgfrCalculatorError, CalculatorError, ConversionNotHandled) as e:
+            value = self.egfr_calculator_cls(**opts).value
+        except (EgfrCalculatorError, ConversionNotHandled) as e:
             raise forms.ValidationError(e) from e
         return value
 
 
 class EgfrCockcroftGaultFormValidatorMixin:
     def validate_egfr(
-        self,
-        *,
-        gender: str,
-        age_in_years: int,
-        weight_in_kgs: float,
-        ethnicity: str,
-    ):
+        self, *, gender: str, age_in_years: int, weight_in_kgs: float
+    ) -> float | None:
         opts = dict(
             gender=gender,
             age_in_years=age_in_years,
             weight=weight_in_kgs,
-            ethnicity=ethnicity,
             creatinine_value=self.cleaned_data.get("creatinine_value"),
             creatinine_units=self.cleaned_data.get("creatinine_units"),
         )
         try:
             value = EgfrCockcroftGault(**opts).value
-        except (EgfrCalculatorError, CalculatorError, ConversionNotHandled) as e:
+        except (EgfrCalculatorError, ConversionNotHandled) as e:
             self.raise_validation_error({"__all__": str(e)}, INVALID_ERROR, exc=e)
         return value

edc_egfr/model_mixins/egfr_drop_notification_model_mixin.py

@@ -1,10 +1,16 @@
+from clinicedc_constants import (
+    COMPLETE,
+    EGFR_UNITS,
+    INCOMPLETE,
+    MICROMOLES_PER_LITER,
+    NEW,
+    OPEN,
+)
 from django.db import models
 
-from edc_constants.constants import COMPLETE, INCOMPLETE, NEW, OPEN
 from edc_lab.choices import SERUM_CREATININE_UNITS
 from edc_lab_results.model_mixin_factories import reportable_result_model_mixin_factory
 from edc_model import REPORT_STATUS
-from edc_reportable.units import EGFR_UNITS, MICROMOLES_PER_LITER
 from edc_vitals.models import WeightField
 
 

edc_egfr/model_mixins/egfr_model_mixin.py

@@ -3,15 +3,15 @@ from __future__ import annotations
 import contextlib
 from decimal import Decimal
 
+from clinicedc_constants import EGFR_UNITS, PERCENT
+from clinicedc_utils import EgfrCalculatorError
 from django.core.exceptions import ObjectDoesNotExist
 from django.db import models, transaction
 
 from edc_lab_results.model_mixin_factories import reportable_result_model_mixin_factory
 from edc_registration.models import RegisteredSubject
-from edc_reportable.units import EGFR_UNITS, PERCENT
 from edc_reportable.utils import get_reference_range_collection
 
-from ..calculators import EgfrCalculatorError
 from ..egfr import Egfr
 
 

edc_export/management/commands/import_receipts.py

@@ -2,11 +2,10 @@ import csv
 import os
 from datetime import datetime
 
+from clinicedc_constants import CLOSED
 from django.core.exceptions import MultipleObjectsReturned
 from django.core.management.base import BaseCommand, CommandError
 
-from edc_constants.constants import CLOSED
-
 from ...models import ExportPlan, ExportReceipt, ExportTransaction
 
 

edc_export/model_exporter/object_history_helpers.py

@@ -1,10 +1,9 @@
+from clinicedc_constants import NEW
 from django.apps import apps as django_apps
 from django.core import serializers
 from django.core.exceptions import MultipleObjectsReturned, ObjectDoesNotExist
 from django.utils import timezone
 
-from edc_constants.constants import NEW
-
 from ..constants import EXPORTED, INSERT, UPDATE
 
 

edc_export/models/object_history.py

@@ -1,8 +1,8 @@
+from clinicedc_constants import CLOSED, NEW
 from django.db import models
 from django.urls import reverse
 from django_crypto_fields.fields import EncryptedTextField
 
-from edc_constants.constants import CLOSED, NEW
 from edc_model.models import BaseUuidModel, HistoricalRecords
 
 from ..constants import CANCELLED, EXPORTED

edc_export/models/upload_export_receipt_file.py

@@ -3,10 +3,10 @@ import os
 import re
 from datetime import datetime
 
+from clinicedc_constants import UUID_PATTERN
 from django.db import models
 from django.db.models import Index
 
-from edc_constants.constants import UUID_PATTERN
 from edc_model.models import BaseUuidModel
 
 from .file_history import FileHistory

edc_facility/list_data.py

@@ -1,4 +1,4 @@
-from edc_constants.constants import DM, HIV, HTN, NCD, OTHER
+from clinicedc_constants import DM, HIV, HTN, NCD, OTHER
 
 list_data = {
     "edc_facility.healthfacilitytypes": [

edc_fieldsets/fieldsets_modeladmin_mixin.py

@@ -1,8 +1,7 @@
+from clinicedc_constants import UUID_PATTERN
 from django.apps import apps as django_apps
 from django.core.exceptions import ObjectDoesNotExist
 
-from edc_constants.constants import UUID_PATTERN
-
 from .fieldsets import Fieldsets
 
 

edc_form_validators/applicable_field_validator.py

@@ -1,6 +1,6 @@
 from typing import Any
 
-from edc_constants.constants import NOT_APPLICABLE, NULL_STRING
+from clinicedc_constants import NOT_APPLICABLE, NULL_STRING
 
 from .base_form_validator import (
     APPLICABLE_ERROR,

edc_form_validators/date_validator.py

@@ -2,9 +2,9 @@ from __future__ import annotations
 
 from datetime import date, datetime
 
+from clinicedc_constants import EQ, GT, GTE, LT, LTE
 from django.conf import settings
 
-from edc_constants.constants import EQ, GT, GTE, LT, LTE
 from edc_model import estimated_date_from_ago
 from edc_utils.date import to_local
 from edc_utils.text import convert_php_dateformat

edc_form_validators/many_to_many_field_validator.py

@@ -1,7 +1,6 @@
+from clinicedc_constants import NOT_APPLICABLE, OTHER
 from django.forms import ValidationError
 
-from edc_constants.constants import NOT_APPLICABLE, OTHER
-
 from .base_form_validator import (
     APPLICABLE_ERROR,
     NOT_APPLICABLE_ERROR,

edc_form_validators/other_specify_field_validator.py

@@ -1,9 +1,8 @@
 from typing import Any
 
+from clinicedc_constants import OTHER
 from django.forms import ValidationError
 
-from edc_constants.constants import OTHER
-
 from .base_form_validator import NOT_REQUIRED_ERROR, REQUIRED_ERROR, BaseFormValidator
 
 

edc_form_validators/required_field_validator.py

@@ -1,10 +1,9 @@
 from copy import copy
 
+from clinicedc_constants import DWTA, NOT_APPLICABLE, NULL_STRING
 from django.db.models import QuerySet
 from django.utils.translation import gettext_lazy as _
 
-from edc_constants.constants import DWTA, NOT_APPLICABLE, NULL_STRING
-
 from .base_form_validator import (
     NOT_REQUIRED_ERROR,
     REQUIRED_ERROR,

edc_glucose/form_validators/fasting_form_validator.py

@@ -1,6 +1,6 @@
 from __future__ import annotations
 
-from edc_constants.constants import YES
+from clinicedc_constants import YES
 
 
 class FastingFormValidatorMixin:

edc_glucose/form_validators/glucose_form_validator.py

@@ -1,10 +1,10 @@
+from clinicedc_constants import DM
+
+from edc_crf.crf_form_validator_mixins import CrfFormValidatorMixin
 from edc_dx_review.utils import (
     raise_if_clinical_review_does_not_exist,
     raise_if_initial_review_does_not_exist,
 )
-
-from edc_constants.constants import DM
-from edc_crf.crf_form_validator_mixins import CrfFormValidatorMixin
 from edc_form_validators import FormValidator
 from edc_visit_schedule.utils import raise_if_baseline
 

edc_glucose/form_validators/glucose_form_validator_mixin.py

@@ -1,9 +1,8 @@
 from __future__ import annotations
 
+from clinicedc_constants import YES
 from dateutil.relativedelta import relativedelta
 
-from edc_constants.constants import YES
-
 from ..utils import validate_glucose_as_millimoles_per_liter
 
 INVALID_GLUCOSE_DATE = "INVALID_GLUCOSE_DATE"

edc_glucose/form_validators/ogtt_form_validator_mixin.py

@@ -1,9 +1,8 @@
 from __future__ import annotations
 
+from clinicedc_constants import NO
 from django import forms
 
-from edc_constants.constants import NO
-
 
 class OgttFormValidatorMixin:
     def validate_ogtt_required_fields(

edc_glucose/model_mixin_factories/fasting_model_mixin_factory.py

@@ -1,7 +1,7 @@
+from clinicedc_constants import NOT_APPLICABLE
 from django.db import models
 
 from edc_constants.choices import YES_NO_NA
-from edc_constants.constants import NOT_APPLICABLE
 from edc_model.utils import duration_hm_to_timedelta
 from edc_model.validators import hm_validator
 

edc_glucose/model_mixin_factories/fbg_model_mixin_factory.py

@@ -1,8 +1,7 @@
+from clinicedc_constants import EQ, NOT_APPLICABLE
 from django.db import models
 
-from edc_constants.constants import NOT_APPLICABLE
 from edc_lab.choices import GLUCOSE_UNITS_NA, RESULT_QUANTIFIER
-from edc_lab.constants import EQ
 
 from ..constants import GLUCOSE_HIGH_READING
 

edc_glucose/model_mixin_factories/glucose_model_mixin_factory.py

@@ -1,8 +1,8 @@
 from __future__ import annotations
 
+from clinicedc_constants import NOT_APPLICABLE
 from django.db import models
 
-from edc_constants.constants import NOT_APPLICABLE
 from edc_lab.choices import GLUCOSE_UNITS_NA, RESULT_QUANTIFIER_NA
 
 from ..constants import GLUCOSE_HIGH_READING

edc_glucose/model_mixin_factories/ogtt_model_mixin_factory.py

@@ -1,10 +1,9 @@
+from clinicedc_constants import EQ, NOT_APPLICABLE
 from django.db import models
 from django.utils.html import format_html
 from django.utils.safestring import mark_safe
 
-from edc_constants.constants import NOT_APPLICABLE
 from edc_lab.choices import GLUCOSE_UNITS_NA, RESULT_QUANTIFIER
-from edc_lab.constants import EQ
 from edc_model.validators import datetime_not_future
 
 from ..constants import GLUCOSE_HIGH_READING

edc_glucose/model_mixins/hba1c_model_mixin.py

@@ -1,8 +1,6 @@
+from clinicedc_constants import EQ, PERCENT
 from django.db import models
 
-from edc_lab.constants import EQ
-from edc_reportable import PERCENT
-
 from ..constants import GLUCOSE_HIGH_READING
 
 

edc_glucose/utils.py

@@ -1,9 +1,9 @@
 from decimal import Decimal
 
+from clinicedc_constants import MILLIMOLES_PER_LITER
+from clinicedc_utils import ConversionNotHandled, convert_units
 from django import forms
 
-from edc_reportable import MILLIMOLES_PER_LITER, ConversionNotHandled
-from edc_reportable.utils import convert_units
 from edc_utils.round_up import round_half_away_from_zero
 
 from .constants import GLUCOSE_HIGH_READING

edc_identifier/model_mixins.py

@@ -1,12 +1,11 @@
 import re
 from uuid import uuid4
 
+from clinicedc_constants import UUID_PATTERN
 from django.apps import apps as django_apps
 from django.core.exceptions import MultipleObjectsReturned, ObjectDoesNotExist
 from django.db import models
 
-from edc_constants.constants import UUID_PATTERN
-
 from .exceptions import IdentifierError
 from .subject_identifier import SubjectIdentifier
 

edc_identifier/models.py

@@ -1,7 +1,7 @@
+from clinicedc_constants import NULL_STRING
 from django.db import models
 from django.db.models import UniqueConstraint
 
-from edc_constants.constants import NULL_STRING
 from edc_model.models import BaseUuidModel
 from edc_sites.model_mixins import SiteModelMixin
 

edc_identifier/simple_identifier.py

@@ -3,13 +3,12 @@ from __future__ import annotations
 from secrets import choice
 from typing import TYPE_CHECKING, Any
 
+from clinicedc_constants import NULL_STRING
 from django.apps import apps as django_apps
 from django.core.exceptions import ObjectDoesNotExist
 from django.db import models
 from django.utils import timezone
 
-from edc_constants.constants import NULL_STRING
-
 from .utils import convert_to_human_readable
 
 if TYPE_CHECKING:

edc_lab/admin/modeladmin_mixins.py

@@ -1,11 +1,11 @@
 from uuid import UUID
 
+from clinicedc_constants import UUID_PATTERN, YES
 from django.contrib import admin
 from django.core.exceptions import ObjectDoesNotExist
 from django.utils.html import format_html
 from django.utils.safestring import mark_safe
 
-from edc_constants.constants import UUID_PATTERN, YES
 from edc_lab.admin.fieldsets import (
     requisition_identifier_fields,
     requisition_verify_fields,

edc_lab/choices.py

@@ -1,25 +1,22 @@
-from django.utils.translation import gettext_lazy as _
-
-from edc_constants.constants import (
+from clinicedc_constants import (
     COMPLETE,
     EQ,
     GT,
     GTE,
     LT,
     LTE,
+    MICROMOLES_PER_LITER,
+    MILLIGRAMS_PER_DECILITER,
+    MILLIMOLES_PER_LITER,
     NOT_APPLICABLE,
     OTHER,
     PARTIAL,
     PENDING,
 )
+from django.utils.translation import gettext_lazy as _
+
 from edc_metadata.constants import NOT_REQUIRED
-from edc_reportable import (
-    MICROMOLES_PER_LITER,
-    MICROMOLES_PER_LITER_DISPLAY,
-    MILLIGRAMS_PER_DECILITER,
-    MILLIMOLES_PER_LITER,
-    MILLIMOLES_PER_LITER_DISPLAY,
-)
+from edc_reportable.units import MICROMOLES_PER_LITER_DISPLAY, MILLIMOLES_PER_LITER_DISPLAY
 
 from .constants import FILL_ACROSS, FILL_DOWN, FINGER_PRICK, TUBE
 

edc_lab/constants.py

@@ -1,5 +1,3 @@
-from edc_constants.constants import EQ, GT, GTE, LT, LTE  # noqa
-
 CONDITION_OK = "OK"
 FILL_ACROSS = "across"
 FILL_DOWN = "down"

edc_lab/form_validators/crf_requisition_form_validator_mixin.py

@@ -3,6 +3,7 @@ from __future__ import annotations
 from typing import TYPE_CHECKING
 
 from django import forms
+
 from edc_utils.date import to_local
 from edc_utils.text import formatted_datetime
 

edc_lab/form_validators/requisition_form_validator_mixin.py

@@ -3,10 +3,10 @@ from __future__ import annotations
 from datetime import datetime
 from typing import TYPE_CHECKING
 
+from clinicedc_constants import NO, YES
 from django import forms
 from django.apps import apps as django_apps
 
-from edc_constants.constants import NO, YES
 from edc_utils.date import to_local
 
 if TYPE_CHECKING: