clinicedc 2.0.41__py3-none-any.whl → 2.0.42__py3-none-any.whl

edc_visit_tracking/form_validators/visit_missed_form_validator.py

@@ -1,4 +1,5 @@
-from edc_constants.constants import ALIVE, NO, OTHER, UNKNOWN, YES
+from clinicedc_constants import ALIVE, NO, OTHER, UNKNOWN, YES
+
 from edc_form_validators import FormValidator
 
 

edc_visit_tracking/managers.py

@@ -2,12 +2,11 @@ from __future__ import annotations
 
 from typing import TYPE_CHECKING
 
+from clinicedc_constants import INCOMPLETE, NOT_APPLICABLE, OTHER
 from django.contrib.sites.managers import CurrentSiteManager as DjangoCurrentSiteManager
 from django.core.exceptions import ObjectDoesNotExist
 from django.db import IntegrityError, models, transaction
 
-from edc_constants.constants import INCOMPLETE, NOT_APPLICABLE, OTHER
-
 from .constants import MISSED_VISIT
 from .exceptions import RelatedVisitReasonError
 

edc_visit_tracking/model_mixins/subject_visit_missed_model_mixin.py

@@ -1,9 +1,9 @@
+from clinicedc_constants import NO, NOT_APPLICABLE
 from django.core.validators import MinValueValidator
 from django.db import models
 from django.utils.translation import gettext_lazy as _
 
 from edc_constants.choices import ALIVE_DEAD_UNKNOWN, YES_NO, YES_NO_NA
-from edc_constants.constants import NO, NOT_APPLICABLE
 from edc_model import models as edc_models
 from edc_model.validators import date_not_future
 from edc_protocol.validators import date_not_before_study_start

edc_visit_tracking/model_mixins/visit_model_mixin/caretaker_fields_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
 
 
 class CaretakerFieldsMixin(models.Model):

edc_visit_tracking/model_mixins/visit_model_mixin/visit_model_fields_mixin.py

@@ -1,8 +1,8 @@
+from clinicedc_constants import ALIVE, NOT_APPLICABLE, YES
 from django.db import models
 from django.utils import timezone
 
 from edc_constants.choices import ALIVE_DEAD_UNKNOWN_NA_MISSED, YES_NO
-from edc_constants.constants import ALIVE, NOT_APPLICABLE, YES
 from edc_model.validators import date_not_future, datetime_not_future
 from edc_model_fields.fields import OtherCharField
 from edc_protocol.validators import (

edc_visit_tracking/model_mixins/visit_model_mixin/visit_model_mixin.py

@@ -1,12 +1,12 @@
 from typing import Any
 
+from clinicedc_constants import NO, YES
 from django.db import models
 from django.db.models.deletion import PROTECT
 
 from edc_appointment.appointment_status_updater import AppointmentStatusUpdater
 from edc_appointment.constants import MISSED_APPT
 from edc_consent.model_mixins import RequiresConsentFieldsModelMixin
-from edc_constants.constants import NO, YES
 from edc_document_status.model_mixins import DocumentStatusModelMixin
 from edc_identifier.model_mixins import NonUniqueSubjectIdentifierFieldMixin
 from edc_metadata.model_mixins import MetadataHelperModelMixin

edc_visit_tracking/modeladmin_mixins/crf_model_admin_mixin.py

@@ -3,8 +3,9 @@ from __future__ import annotations
 from typing import TYPE_CHECKING
 from uuid import UUID
 
+from clinicedc_constants import UUID_PATTERN
+
 from edc_consent.fieldsets import REQUIRES_CONSENT_FIELDS
-from edc_constants.constants import UUID_PATTERN
 
 if TYPE_CHECKING:
     from django.core.handlers.wsgi import WSGIRequest

edc_visit_tracking/modeladmin_mixins/visit_model_admin_mixin.py

@@ -2,12 +2,12 @@ from __future__ import annotations
 
 from typing import TYPE_CHECKING
 
+from clinicedc_constants import OTHER
 from django.contrib import admin
 from django.core.exceptions import ObjectDoesNotExist
 from django_audit_fields.admin import audit_fieldset_tuple
 
 from edc_appointment.utils import get_appointment_model_cls
-from edc_constants.constants import OTHER
 from edc_document_status.fieldsets import document_status_fieldset_tuple
 from edc_document_status.modeladmin_mixins import DocumentStatusModelAdminMixin
 from edc_visit_schedule.fieldsets import (

edc_visit_tracking/models/signals.py

@@ -1,8 +1,8 @@
+from clinicedc_constants import NOT_APPLICABLE, PATIENT
 from django.db.models.signals import post_delete, post_save
 from django.dispatch import receiver
 
 from edc_appointment.constants import ONTIME_APPT
-from edc_constants.constants import NOT_APPLICABLE, PATIENT
 from edc_metadata import REQUIRED
 from edc_metadata.metadata import CrfMetadataGetter
 from edc_pharmacy.constants import IN_PROGRESS_APPT

edc_visit_tracking/view_utils/related_visit_button.py

@@ -3,6 +3,7 @@ from __future__ import annotations
 from dataclasses import dataclass, field
 from typing import TYPE_CHECKING, TypeVar
 
+from clinicedc_constants import INCOMPLETE
 from django.utils.translation import gettext as _
 
 from edc_appointment.constants import (
@@ -12,7 +13,6 @@ from edc_appointment.constants import (
     INCOMPLETE_APPT,
     SKIPPED_APPT,
 )
-from edc_constants.constants import INCOMPLETE
 from edc_view_utils import ADD, CHANGE, VIEW, DashboardModelButton
 
 if TYPE_CHECKING:

edc_vitals/form_validators/blood_pressure_form_validator_mixin.py

@@ -1,7 +1,6 @@
+from clinicedc_constants import YES
 from django import forms
 
-from edc_constants.constants import YES
-
 from ..utils import calculate_avg_bp, has_severe_htn
 
 

edc_constants/constants.py

@@ -1,250 +0,0 @@
-import re
-
-UUID_PATTERN = re.compile(
-    "[a-f0-9]{8}-?[a-f0-9]{4}-?4[a-f0-9]{3}-?[89ab][a-f0-9]{3}-?[a-f0-9]{12}"
-)
-
-ABNORMAL = "ABNORMAL"
-ABSENT = "absent"
-ADDITIONAL = True
-AFTERNOON = "afternoon"
-AGREE = "agree"
-ALIVE = "alive"
-ALWAYS = "always"
-ANONYMOUS = "anonymous"
-ANYTIME = "anytime"
-AWAITING_RESULTS = "awaiting_results"
-BLACK = "black"
-BOTH = "both"
-BY_BIRTH = "BY_BIRTH"
-CANCELLED = "cancelled"
-CHOL = "chol"
-CLINIC = "clinic"
-CLINICAL_ENDPOINT = "clinical_endpoint"
-CLINICAL_WITHDRAWAL = "clinical_withdrawal"
-CLINICIAN = "clinician"
-CLOSED = "closed"
-COLLATERAL_HISTORY = "collateral_history"
-COMPLETE = "COMPLETE"
-COMMUNITY = "community"
-CONFIRMED = "confirmed"
-CONSENTED = "consented"
-CONTINUOUS = "continuous"
-CONTROL = "control"
-CREATE = "CREATE"
-DEAD = "dead"
-DECEASED = "dead"
-DECLINED = "Declined"
-DECREASED = "decreased"
-DEFAULTED = "defaulted"
-DEFAULTER = "defaulter"
-DELETE = "DELETE"
-DELIVERY = "delivery"
-DIABETES = "diabetes"
-DISAGREE = "disagree"
-DIVORCED = "divorced"
-DM = "dm"
-DONE = "done"
-DONT_KNOW = "dont_know"
-DWTA = "DWTA"  # don't want to answer
-ERROR = "ERROR"
-ESTIMATED = "estimated"
-EVENING = "evening"
-FAILED_ELIGIBILITY = "failed eligibility"
-FALSE = "false"
-FASTING = "fasting"
-FEEDBACK = "feedback"
-FEMALE = "F"
-FORMER_SMOKER = "former_smoker"
-FREE_OF_CHARGE = "free"
-FUTURE_DATE = "future_date"
-GRADE0 = "0"
-GRADE1 = "1"
-GRADE2 = "2"
-GRADE3 = "3"
-GRADE4 = "4"
-GRADE5 = "5"
-HEADACHE = "headache"
-HELD = "held"
-HIDE_FORM = "NOT_REQUIRED"
-HIGH = "high"
-HIGH_PRIORITY = "high"
-HIV = "HIV"
-HOME = "home"
-HOSPITAL = "hospital"
-HOSPITALIZED = "hospitalized"
-HOSPITAL_NOTES = "hospital_notes"
-HOSPITAL_OR_CLINIC = "hospital_or_clinic"
-HTN = "htn"
-HYPERTENSION = "hypertension"
-IGNORE = "ignore"
-IN_PROGRESS = "in_progress"
-INCOMPLETE = "INCOMPLETE"
-IND = "IND"
-INITIAL = "initial"
-INPATIENT = "inpatient"
-INSERT = "INSERT"
-INSURANCE = "insurance"
-INTEGRATED = "integrated"
-INTEGRATED_CLINIC = "integrated_clinic"
-INTERVENTION = "intervention"
-INVESTIGATOR = "investigator"
-INVESTIGATOR_DECISION = "investigator_decision"
-IN_PERSON = "in_person"
-IS_NULL = "is_null"
-LAST_MONTH = "last_month"
-LAST_WEEK = "last_week"
-LIVE = "live"
-LOW = "low"
-LOW_PRIORITY = "low"
-MALE = "M"
-MALIGNANCY = "malignancy"
-MARRIED = "married"
-MEDIUM_PRIORITY = "medium"
-MEASURED = "measured"
-MICROSCOPY = "microscopy"
-MOBILE_NUMBER = "mobile_no"
-MODIFIED = "modified"
-MONTHLY = "monthly"
-MORNING = "morning"
-MULTI_MORBIDITY = "multi"
-NAIVE = "NAIVE"
-NCD = "NCD"
-NEG = "NEG"
-NEUTRAL = "neutral"
-NEVER = "NEVER"
-NEW = "New"
-NEW_FIELD = "new_field"
-NEXT_OF_KIN = "next_of_kin"
-NEXT_WEEK = "next_week"
-NO = "No"
-NONE = "none"
-NONSMOKER = "nonsmoker"
-NON_BLACK = "non_black"
-NON_FASTING = "non_fasting"
-NORMAL = "NORMAL"
-NOT_ADDITIONAL = False
-NOT_ANSWERED = "not_answered"
-NOT_APPLICABLE = "N/A"
-NOT_AVAILABLE = "not_available"
-NOT_DONE = "not_done"
-NOT_ESTIMATED = "not_estimated"
-NOT_EVALUATED = "not_evaluated"
-NOT_EXAMINED = "not_examined"
-NOT_NULL = "not_null"
-NOT_RECORDED = "not_recorded"
-NOT_REQUIRED = "not_required"
-NOT_SURE = "not_sure"
-NOT_TESTED = "not_tested"
-NO_EXAM = "NO_EXAM"
-NO_UNCONFIRMED = "no_unconfirmed"
-NULL_STRING = ""
-OBSERVATION = "observation"
-OK = "OK"
-OFF_STUDY = "off study"
-OFF_STUDY_VISIT = "off study"
-OMANG = "OMANG"
-ON_ART = "on_art"
-ON_STUDY = "on study"
-ONGOING = "ongoing"
-OPEN = "open"
-OPTION_RETIRED = "OPTION_RETIRED"
-OPTIONAL = True
-OTHER = "OTHER"
-OTHER_PLEASE_SPECIFY_TEXT = "Other, please specify below ..."
-OUTPATIENT_CARDS = "outpatient_cards"
-OUTPATIENT = "outpatient"
-OWN_CASH = "own_cash"
-PARTIAL = "PARTIAL"
-PARTICIPANT = "participant"
-PAST_DATE = "past_date"
-PATIENT = "patient"
-PATIENT_CLUB = "club"
-PATIENT_REPRESENTATIVE = "patient_representative"
-PENDING = "PENDING"
-PER_PROTOCOL = "per_protocol"
-POS = "POS"
-PREGNANCY = "pregnancy"
-PRESENT = "present"
-PRESENT_WITH_REINFORCEMENT = "present_with_reinforcement"
-PRIMARY = "primary"
-PRINT = "PRINT"
-PRIVATE = "private"
-PURPOSIVELY_SELECTED = "purposively_selected"
-QUERY = "QUERY"
-QUESTION_RETIRED = "QUESTION_RETIRED"
-RANDOM_SAMPLING = "random_sampling"
-RAPID_TEST = "rapid_test"
-RARELY = "rarely"
-RECEIVED = "received"
-REDUCED = "reduced"
-REFILL = "refill"
-REFUSED = "REFUSED"
-RELATIVE = "relative"
-RESOLVED = "resolved"
-RESTARTED = "restarted"
-ROUTINE_VISIT = "routine_visit"
-SAE = "sae"
-SCREENED = "SCREENED"
-SECONDARY = "secondary"
-SEQUENTIAL = "sequential"
-SEROCONVERSION = "seroconversion"
-SHOW_FORM = "NEW"
-SINGLE = "single"
-SMOKER = "smoker"
-SOMETIMES = "sometimes"
-STEROIDS = "steroids"
-STOPPED = "stopped"
-STRONGLY_AGREE = "strongly_agree"
-STRONGLY_DISAGREE = "strongly_disagree"
-STUDY_DEFINED_TIMEPOINT = "study_defined_timepoint"
-SUBJECT = "subject"
-SYSTEMATIC = "systematic"
-TBD = "tbd"  # to be determined
-TELEPHONE = "telephone"
-TERTIARY = "tertiary"
-TEST = "test"
-THIS_MONTH = "this_month"
-THIS_WEEK = "this_week"
-TIMEPOINT = "timepoint"
-TODAY = "today"
-TOMORROW = "tomorrow"
-TOXICITY = "toxicity"
-TRUE = "true"
-TUBERCULOSIS = "TB"
-UNK = "UNK"
-UNKNOWN = "unknown"
-UNWELL_VISIT = "unwell_visit"
-UPDATE = "UPDATE"
-VERY_OFTEN = "very_often"
-VIEW = "VIEW"
-VISUAL_LOSS = "visual_loss"
-WARN = "warn"
-WEEKDAYS = "weekdays"
-WEEKENDS = "weekends"
-WEEKLY = "weekly"
-WIDOWED = "widowed"
-YEARLY = "yearly"
-YES = "Yes"
-YESTERDAY = "yesterday"
-
-# operators
-EQ = "="
-GT = ">"
-GTE = ">="
-LT = "<"
-LTE = "<="
-
-# days of the week
-MONDAY = "monday"
-TUESDAY = "tuesday"
-WEDNESDAY = "wednesday"
-THURSDAY = "thursday"
-FRIDAY = "friday"
-SATURDAY = "saturday"
-SUNDAY = "sunday"
-
-VERY_DIFFICULT = "very_difficult"
-DIFFICULT = "difficult"
-EASY = "easy"
-VERY_EASY = "very_easy"

edc_constants/disease_constants.py

@@ -1,22 +0,0 @@
-ANAEMIA = "anaemia"
-BACTERAEMIA = "bacteraemia"
-BACTERAEMIA_SEPSIS = "bacteraemia_sepsis"
-BACTERIAL_PNEUMONIA = "bacterial_pneumonia"
-CM_IRIS = "cm_iris"
-CM_RELAPSE = "cm_relapse"
-CM_RELAPSE_IRIS = "cm_relapse_iris"
-CN_PALSY_LEFT_OTHER = "cn_palsy_left_other"
-CN_PALSY_RIGHT_OTHER = "cn_palsy_right_other"
-COVID_19 = "covid_19"
-CRYPTOCOCCAL_MENINGITIS = "cm"
-DIARRHOEA = "diarrhoea"
-DIARRHOEAL_WASTING = "diarrhoeal_wasting"
-FOCAL_NEUROLOGIC_DEFICIT_OTHER = "focal_neurologic_deficit_other"
-NEUTROPAENIA = "neutropaenia"
-PNEUMONIA = "pneumonia"
-RENAL_IMPAIRMENT = "renal_impairment"
-SEPSIS = "sepsis"
-TB_EXTRAPULMONARY = "tb_extrapulmonary"
-TB_PULMONARY = "tb_pulmonary"
-THERAPEUTIC_LP = "therapeutic_lp"
-THROMBOCYTOPENIA = "thrombocytopenia"

edc_egfr/calculators/__init__.py

@@ -1,4 +0,0 @@
-from .base_egrfr import EgfrCalculatorError
-from .egfr_ckd_epi import EgfrCkdEpi
-from .egfr_cockcroft_gault import EgfrCockcroftGault
-from .percent_change import egfr_percent_change

edc_egfr/calculators/base_egrfr.py

@@ -1,56 +0,0 @@
-from __future__ import annotations
-
-from edc_constants.constants import FEMALE, MALE
-from edc_reportable import MICROMOLES_PER_LITER, MILLIGRAMS_PER_DECILITER
-from edc_reportable.utils import convert_units
-
-
-class EgfrCalculatorError(Exception):
-    pass
-
-
-class BaseEgfr:
-    def __init__(
-        self,
-        gender: str | None = None,
-        age_in_years: int | float | None = None,
-        creatinine_value: float | int | None = None,
-        creatinine_units: str | None = None,
-        **kwargs,  # noqa
-    ):
-        """Expects creatinine (scr) in umols/L.
-
-        Converts to creatinine to mg/dL for the calculation.
-        """
-        self.scr = {}
-        if not gender or gender not in [MALE, FEMALE]:
-            raise EgfrCalculatorError(
-                f"Invalid gender. Expected one of {MALE}, {FEMALE}. Got {gender}."
-            )
-        self.gender = gender
-        if not (18 <= (age_in_years or 0) < 120):
-            raise EgfrCalculatorError(
-                f"Invalid age. See {self.__class__.__name__}. Got {age_in_years}"
-            )
-        self.age_in_years = float(age_in_years) if age_in_years else None
-        if creatinine_value and creatinine_units:
-            self.scr.update(
-                {
-                    MILLIGRAMS_PER_DECILITER: convert_units(
-                        label="creatinine",
-                        value=float(creatinine_value),
-                        units_from=creatinine_units,
-                        units_to=MILLIGRAMS_PER_DECILITER,
-                    )
-                }
-            )
-            self.scr.update(
-                {
-                    MICROMOLES_PER_LITER: convert_units(
-                        label="creatinine",
-                        value=float(creatinine_value),
-                        units_from=creatinine_units,
-                        units_to=MICROMOLES_PER_LITER,
-                    )
-                }
-            )

edc_egfr/calculators/egfr_ckd_epi.py

@@ -1,68 +0,0 @@
-from __future__ import annotations
-
-from edc_constants.constants import BLACK, FEMALE
-from edc_reportable import MILLIGRAMS_PER_DECILITER
-
-from .base_egrfr import BaseEgfr, EgfrCalculatorError
-
-# TODO: https://www.rcpa.edu.au/Manuals/RCPA-Manual/
-#  Pathology-Tests/C/Creatinine-clearance-Cockcroft-and-Gault
-
-
-class EgfrCkdEpi(BaseEgfr):
-    """Reference https://nephron.com/epi_equation
-
-    CKD-EPI Creatinine equation (2009)
-
-    Levey AS, Stevens LA, et al. A New Equation to Estimate Glomerular
-    Filtration Rate. Ann Intern Med. 2009; 150:604-612.
-    """
-
-    def __init__(self, ethnicity: str = None, **kwargs):
-        self.ethnicity = ethnicity
-        super().__init__(**kwargs)
-
-    @property
-    def value(self) -> float | None:
-        if (
-            self.gender
-            and self.age_in_years
-            and self.ethnicity
-            and self.scr.get(MILLIGRAMS_PER_DECILITER)
-        ):
-            scr = self.scr.get(MILLIGRAMS_PER_DECILITER)
-            return float(
-                141.000
-                * (min(scr / self.kappa, 1.000) ** self.alpha)
-                * (max(scr / self.kappa, 1.000) ** -1.209)
-                * self.age_factor
-                * self.gender_factor
-                * self.ethnicity_factor
-            )
-        opts = dict(
-            gender=self.gender,
-            age_in_years=self.age_in_years,
-            ethnicity=self.ethnicity,
-            scr=self.scr.get(MILLIGRAMS_PER_DECILITER),
-        )
-        raise EgfrCalculatorError(f"Unable to calculate. Insufficient information. Got {opts}")
-
-    @property
-    def alpha(self) -> float:
-        return float(-0.329 if self.gender == FEMALE else -0.411)
-
-    @property
-    def kappa(self) -> float:
-        return float(0.7 if self.gender == FEMALE else 0.9)
-
-    @property
-    def ethnicity_factor(self) -> float:
-        return float(1.159 if self.ethnicity == BLACK else 1.000)
-
-    @property
-    def gender_factor(self) -> float:
-        return float(1.018 if self.gender == FEMALE else 1.000)
-
-    @property
-    def age_factor(self) -> float:
-        return float(0.993**self.age_in_years)

edc_egfr/calculators/egfr_cockcroft_gault.py

@@ -1,62 +0,0 @@
-from __future__ import annotations
-
-from decimal import Decimal
-
-from edc_constants.constants import FEMALE
-from edc_reportable import MICROMOLES_PER_LITER
-
-from .base_egrfr import BaseEgfr, EgfrCalculatorError
-
-
-class EgfrCockcroftGault(BaseEgfr):
-    """Reference https://www.mdcalc.com/creatinine-clearance-cockcroft-gault-equation
-
-    Cockcroft-Gault
-
-    eGFR (mL/min) = { (140 – age (years)) x weight (kg) x constant*} /
-    serum creatinine (μmol/L)
-    *constant = 1.23 for males and 1.05 for females
-
-    Cockcroft-Gault CrCl, mL/min =
-        (140 – age) × (weight, kg) × (0.85 if female) / (72 × SCr(mg/dL))
-
-    or:
-
-    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2763564/
-
-    GFR = 141 × min(Scr/κ, 1)α × max(Scr/κ, 1)-1.209 × 0.993Age
-    """  # noqa: RUF002
-
-    def __init__(self, weight: int | float | Decimal | None = None, **kwargs):
-        self.weight = float(weight) if weight else None
-        super().__init__(**kwargs)
-
-    @property
-    def value(self) -> float:
-        """Returns the eGFR value or raises.
-
-        eGFR (mL/min) = { (140 – age (years)) x weight (kg) x constant*} /
-        serum creatinine (μmol/L)
-
-        *constant = 1.23 for males and 1.05 for females
-        """  # noqa: RUF002
-        if (
-            self.gender
-            and self.age_in_years
-            and self.weight
-            and self.scr.get(MICROMOLES_PER_LITER)
-        ):
-            gender_factor = 1.05 if self.gender == FEMALE else 1.23
-            adjusted_age = 140.00 - self.age_in_years
-            return (adjusted_age * self.weight * gender_factor) / float(
-                self.scr.get(MICROMOLES_PER_LITER)
-            )
-        opts = dict(
-            gender=self.gender,
-            age_in_years=self.age_in_years,
-            weight=self.weight,
-            scr=self.scr.get(MICROMOLES_PER_LITER),
-        )
-        raise EgfrCalculatorError(
-            f"Unable to calculate egfr_value. Insufficient information. Got {opts}."
-        )

edc_egfr/calculators/percent_change.py

@@ -1,7 +0,0 @@
-def egfr_percent_change(egfr_value: float, baseline_egfr_value: float) -> float:
-    """Returns the percent change from baseline"""
-    if egfr_value and baseline_egfr_value:
-        return 100 * (
-            (float(baseline_egfr_value) - float(egfr_value)) / float(baseline_egfr_value)
-        )
-    return 0.0

edc_reportable/data/molecular_weights.py

@@ -1,11 +0,0 @@
-# in g/mol
-molecular_weights = dict(
-    glucose=180.16,
-    chol=386.65,
-    trig=885,
-    creatinine=113.12,
-    urea=60.06,
-    tbil=584.6,
-    haemoglobin=64500,
-    albumin=66000,
-)