clinicedc 2.0.11__py3-none-any.whl → 2.0.13__py3-none-any.whl

edc_dx_review/model_mixins/followup_review/hiv_followup_review_model_mixin.py

@@ -0,0 +1,32 @@
+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
+
+
+class HivFollowupReviewModelMixin(FollowupReviewModelMixin, models.Model):
+    dx = models.CharField(
+        verbose_name="Has the patient been infected with HIV?",
+        max_length=15,
+        choices=YES_NO_NA,
+        default=NOT_APPLICABLE,
+    )
+
+    arv_initiated = models.CharField(
+        verbose_name="Has the patient started antiretroviral therapy (ART)?",
+        max_length=15,
+        choices=YES_NO_NA,
+        default=NOT_APPLICABLE,
+        help_text="Select `not applicable` if previously reported.",
+    )
+    arv_initiation_actual_date = models.DateField(
+        verbose_name="Date started antiretroviral therapy (ART)",
+        null=True,
+        blank=True,
+    )
+
+    class Meta(FollowupReviewModelMixin.Meta):
+        abstract = True
+        verbose_name = "HIV Review"
+        verbose_name_plural = "HIV Review"

edc_dx_review/model_mixins/initial_review/__init__.py

@@ -0,0 +1,6 @@
+from .chol_initial_review_model_mixin import CholInitialReviewModelMixin
+from .hiv_initial_model_mixins import (
+    HivArvInitiationModelMixin,
+    HivArvMonitoringModelMixin,
+)
+from .ncd_initial_review_model_mixin import NcdInitialReviewModelMixin

edc_dx_review/model_mixins/initial_review/chol_initial_review_model_mixin.py

@@ -0,0 +1,34 @@
+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
+from .ncd_initial_review_model_mixin import NcdInitialReviewModelMixin
+
+
+class CholInitialReviewModelMixin(
+    DxLocationModelMixin,
+    NcdInitialReviewModelMixin,
+):
+    ncd_condition_label = "cholesterol"
+
+    managed_by = models.CharField(
+        verbose_name="How is the patient's cholesterol managed?",
+        max_length=25,
+        choices=CHOL_MANAGEMENT,
+        default=NOT_APPLICABLE,
+    )
+
+    chol_performed = models.CharField(
+        verbose_name=(
+            "Has the patient had their cholesterol measured in the last few months?"
+        ),
+        max_length=15,
+        choices=YES_NO,
+    )
+
+    class Meta:
+        abstract = True
+        verbose_name = "High Cholesterol Initial Review"
+        verbose_name_plural = "High Cholesterol Initial Reviews"

edc_dx_review/model_mixins/initial_review/hiv_initial_model_mixins.py

@@ -0,0 +1,119 @@
+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
+
+
+class HivArvInitiationModelMixin(models.Model):
+    arv_initiated = models.CharField(
+        verbose_name="Has the patient started antiretroviral therapy (ART)?",
+        max_length=15,
+        choices=YES_NO,
+        default=YES,
+    )
+
+    arv_initiation_ago = edc_models.DurationYMDField(
+        verbose_name="How long ago did the patient start ART?",
+        null=True,
+        blank=True,
+    )
+
+    arv_initiation_actual_date = models.DateField(
+        verbose_name="Date started antiretroviral therapy (ART)",
+        validators=[date_not_future],
+        null=True,
+        blank=True,
+        help_text="Calculated based on response to `arv_initiation_ago`",
+    )
+
+    arv_initiation_estimated_date = models.DateField(
+        verbose_name="Estimated Date started antiretroviral therapy (ART)",
+        validators={date_not_future},
+        null=True,
+        editable=False,
+        help_text="Calculated based on response to `arv_initiation_ago`",
+    )
+
+    arv_initiation_date_is_estimated = models.CharField(
+        verbose_name="Was the ART start date estimated?",
+        max_length=15,
+        choices=YES_NO,
+        default=YES,
+        editable=False,
+    )
+
+    def save(self, *args, **kwargs):
+        self.dx_estimated_date = estimated_date_from_ago(instance=self, ago_field="dx_ago")
+        self.arv_initiation_estimated_date = estimated_date_from_ago(
+            instance=self, ago_field="arv_initiation_ago"
+        )
+        super().save(*args, **kwargs)
+
+    @property
+    def best_art_initiation_date(self):
+        return self.arv_initiation_actual_date or self.arv_initiation_estimated_date
+
+    class Meta:
+        abstract = True
+
+
+class HivArvMonitoringModelMixin(models.Model):
+    # Viral Load
+    has_vl = models.CharField(
+        verbose_name="Is the patient's most recent viral load result available?",
+        max_length=25,
+        choices=YES_NO_PENDING_NA,
+        default=NOT_APPLICABLE,
+    )
+    vl = models.IntegerField(
+        verbose_name="Most recent viral load",
+        validators=[MinValueValidator(0), MaxValueValidator(9999999)],
+        null=True,
+        blank=True,
+        help_text=COPIES_PER_MILLILITER,
+    )
+
+    vl_quantifier = models.CharField(
+        max_length=10,
+        choices=VL_QUANTIFIER_NA,
+        null=True,
+        blank=True,
+    )
+
+    vl_date = models.DateField(
+        verbose_name="Date of most recent viral load",
+        validators=[date_not_future],
+        null=True,
+        blank=True,
+    )
+
+    # CD4
+    has_cd4 = models.CharField(
+        verbose_name="Is the patient's most recent CD4 result available?",
+        max_length=25,
+        choices=YES_NO_NA,
+        default=NOT_APPLICABLE,
+    )
+
+    cd4 = models.IntegerField(
+        verbose_name="Most recent CD4",
+        validators=[MinValueValidator(0), MaxValueValidator(3000)],
+        null=True,
+        blank=True,
+        help_text=CELLS_PER_MILLIMETER_CUBED_DISPLAY,
+    )
+
+    cd4_date = models.DateField(
+        verbose_name="Date of most recent CD4",
+        validators=[date_not_future],
+        null=True,
+        blank=True,
+    )
+
+    class Meta:
+        abstract = True

edc_dx_review/model_mixins/initial_review/ncd_initial_review_model_mixin.py

@@ -0,0 +1,42 @@
+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
+
+
+class NcdInitialReviewModelMixin(models.Model):
+    ncd_condition_label: str = None
+
+    med_start_ago = edc_models.DurationYMDField(
+        verbose_name=(
+            "If the patient is taking medicines for ncd_condition_label, "
+            "how long have they been taking these?"
+        ),
+        null=True,
+        blank=True,
+    )
+
+    med_start_estimated_date = models.DateField(
+        verbose_name="Estimated medication start date",
+        null=True,
+        editable=False,
+    )
+
+    med_start_date_is_estimated = models.CharField(
+        verbose_name="Was the medication start date estimated?",
+        max_length=15,
+        choices=YES_NO,
+        default=YES,
+        editable=False,
+    )
+
+    def save(self, *args, **kwargs):
+        if self.med_start_ago:
+            self.med_start_estimated_date = duration_to_date(
+                self.med_start_ago, self.report_datetime
+            )
+        super().save(*args, **kwargs)
+
+    class Meta:
+        abstract = True

edc_dx_review/models.py

@@ -0,0 +1,20 @@
+from edc_list_data.model_mixins import ListModelManager, ListModelMixin
+from edc_model.models import HistoricalRecords
+
+
+class ReasonsForTesting(ListModelMixin):
+    objects = ListModelManager()
+    history = HistoricalRecords()
+
+    class Meta(ListModelMixin.Meta):
+        verbose_name = "Reasons for Testing"
+        verbose_name_plural = "Reasons for Testing"
+
+
+class DiagnosisLocations(ListModelMixin):
+    objects = ListModelManager()
+    history = HistoricalRecords()
+
+    class Meta(ListModelMixin.Meta):
+        verbose_name = "Diagnosis Locations"
+        verbose_name_plural = "Diagnosis Locations"

edc_dx_review/radio_fields.py

@@ -0,0 +1,30 @@
+from typing import Dict
+
+from django.contrib import admin
+from edc_dx import get_diagnosis_labels_prefixes
+
+
+def get_clinical_review_cond_radio_fields() -> Dict[str, int]:
+    radio_fields = {}
+    for prefix in get_diagnosis_labels_prefixes():
+        cond = prefix.lower()
+        radio_fields.update(
+            {
+                f"{cond}_dx": admin.VERTICAL,
+                f"{cond}_test": admin.VERTICAL,
+            }
+        )
+    return radio_fields
+
+
+def get_clinical_review_baseline_cond_radio_fields() -> Dict[str, int]:
+    radio_fields = {}
+    for prefix in get_diagnosis_labels_prefixes():
+        cond = prefix.lower()
+        radio_fields.update(
+            {
+                f"{cond}_dx": admin.VERTICAL,
+                f"{cond}_dx_at_screening": admin.VERTICAL,
+            }
+        )
+    return radio_fields

edc_dx_review/utils.py

@@ -0,0 +1,220 @@
+from __future__ import annotations
+
+from datetime import date, datetime
+from typing import TYPE_CHECKING
+
+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
+
+if TYPE_CHECKING:
+    from edc_model.models import BaseUuidModel
+    from edc_visit_tracking.model_mixins import VisitTrackingCrfModelMixin
+
+    class CrfLikeModel(VisitTrackingCrfModelMixin, BaseUuidModel):
+        pass
+
+
+EDC_DX_REVIEW_APP_LABEL = getattr(settings, "EDC_DX_REVIEW_APP_LABEL", "edc_dx_review")
+
+
+class ModelNotDefined(Exception):
+    pass
+
+
+class BaselineModelError(Exception):
+    pass
+
+
+def get_list_model_app():
+    return getattr(
+        settings, "EDC_DX_REVIEW_LIST_MODEL_APP_LABEL", settings.LIST_MODEL_APP_LABEL
+    )
+
+
+def get_clinical_review_baseline_model_cls():
+    clinicalreviewbaseline = get_extra_attrs().get(
+        "clinicalreviewbaseline", "clinicalreviewbaseline"
+    )
+
+    return django_apps.get_model(f"{EDC_DX_REVIEW_APP_LABEL}.{clinicalreviewbaseline}")
+
+
+def get_clinical_review_model_cls():
+    clinicalreview = get_extra_attrs().get("clinicalreview", "clinicalreview")
+    return django_apps.get_model(f"{EDC_DX_REVIEW_APP_LABEL}.{clinicalreview}")
+
+
+def get_medication_model_cls():
+    medications = get_extra_attrs().get("medications", "medications")
+    return django_apps.get_model(f"{EDC_DX_REVIEW_APP_LABEL}.{medications}")
+
+
+def get_initial_review_model_cls(prefix):
+    initialreview = get_extra_attrs().get("initialreview", "initialreview")
+    return django_apps.get_model(f"{EDC_DX_REVIEW_APP_LABEL}.{prefix.lower()}{initialreview}")
+
+
+def get_review_model_cls(prefix):
+    review = get_extra_attrs().get("review", "review")
+    return django_apps.get_model(f"{EDC_DX_REVIEW_APP_LABEL}.{prefix.lower()}{review}")
+
+
+def get_extra_attrs():
+    """Settings from EDC_DX_REVIEW_EXTRA_ATTRS.
+
+    See model name suffixes used in model_cls getters in utils.py.
+    """
+    extra_attrs = {
+        "clinicalreview": "clinicalreview",
+        "clinicalreviewbaseline": "clinicalreviewbaseline",
+        "initialreview": "initialreview",
+        "medications": "medications",
+        "review": "review",
+    }
+    try:
+        data = getattr(settings, "EDC_DX_REVIEW_EXTRA_ATTRS")
+    except AttributeError:
+        pass
+    else:
+        extra_attrs.update(data)
+    return extra_attrs
+
+
+def raise_if_clinical_review_does_not_exist(subject_visit) -> CrfLikeModel:
+    try:
+        baseline = is_baseline(instance=subject_visit)
+    except VisitScheduleBaselineError as e:
+        raise forms.ValidationError(str(e))
+    else:
+        if baseline:
+            model_cls = get_clinical_review_baseline_model_cls()
+        else:
+            model_cls = get_clinical_review_model_cls()
+        try:
+            obj = model_exists_or_raise(subject_visit=subject_visit, model_cls=model_cls)
+        except ObjectDoesNotExist:
+            raise forms.ValidationError(f"Complete {model_cls._meta.verbose_name} CRF first.")
+    return obj
+
+
+def raise_if_both_ago_and_actual_date(
+    cleaned_data: dict | None = None,
+    date_fld: str | None = None,
+    ago_fld: str | None = None,
+    dx_ago: str | None = None,
+    dx_date: date | None = None,
+) -> None:
+    if cleaned_data:
+        dx_ago = cleaned_data.get(date_fld)
+        dx_date = cleaned_data.get(ago_fld)
+    if dx_ago and dx_date:
+        raise forms.ValidationError(
+            {
+                ago_fld: (
+                    "Date conflict. Do not provide a response "
+                    "here if the date of diagnosis is available."
+                )
+            }
+        )
+
+
+def requires_clinical_review_at_baseline(subject_visit):
+    try:
+        get_clinical_review_baseline_model_cls().objects.get(
+            subject_visit__subject_identifier=subject_visit.subject_identifier
+        )
+    except ObjectDoesNotExist:
+        raise forms.ValidationError(
+            "Please complete the "
+            f"{get_clinical_review_baseline_model_cls()._meta.verbose_name} first."
+        )
+
+
+def raise_if_initial_review_does_not_exist(subject_visit, prefix):
+    model_exists_or_raise(
+        subject_visit=subject_visit,
+        model_cls=get_initial_review_model_cls(prefix),
+    )
+
+
+def raise_if_review_does_not_exist(subject_visit, prefix):
+    model_exists_or_raise(
+        subject_visit=subject_visit,
+        model_cls=get_review_model_cls(prefix),
+    )
+
+
+def medications_exists_or_raise(subject_visit) -> bool:
+    if subject_visit:
+        try:
+            get_medication_model_cls().objects.get(subject_visit=subject_visit)
+        except ObjectDoesNotExist:
+            raise forms.ValidationError(
+                f"Complete the `{get_medication_model_cls()._meta.verbose_name}` CRF first."
+            )
+    return True
+
+
+def is_rx_initiated(
+    subject_identifier: str, report_datetime: datetime, instance_id: str | None = None
+) -> bool:
+    """Return True if already initiated"""
+    try:
+        get_initial_review_model_cls(HIV).objects.get(
+            subject_visit__subject_identifier=subject_identifier,
+            report_datetime__lte=report_datetime,
+            rx_init=YES,
+        )
+    except ObjectDoesNotExist:
+        exclude = {}
+        if instance_id:
+            exclude = {"id": instance_id}
+        rx_initiated = (
+            get_review_model_cls(HIV)
+            .objects.filter(
+                subject_visit__subject_identifier=subject_identifier,
+                report_datetime__lte=report_datetime,
+                rx_init=YES,
+            )
+            .exclude(**exclude)
+            .exists()
+        )
+    else:
+        rx_initiated = True
+    return rx_initiated
+
+
+def art_initiation_date(subject_identifier: str, report_datetime: datetime) -> date:
+    """Returns date initiated on ART or None by querying
+    the HIV Initial Review and then the HIV Review.
+    """
+    art_date = None
+    try:
+        initial_review = get_initial_review_model_cls(HIV).objects.get(
+            subject_visit__subject_identifier=subject_identifier,
+            report_datetime__lte=report_datetime,
+        )
+    except ObjectDoesNotExist:
+        pass
+    else:
+        if initial_review.arv_initiated == YES:
+            art_date = initial_review.best_art_initiation_date
+        else:
+            for review in (
+                get_review_model_cls(HIV)
+                .objects.filter(
+                    subject_visit__subject_identifier=subject_identifier,
+                    report_datetime__lte=report_datetime,
+                )
+                .order_by("-report_datetime")
+            ):
+                if review.arv_initiated == YES:
+                    art_date = review.arv_initiation_actual_date
+                    break
+    return art_date

edc_export/migrations/0004_auto_20190305_0123.py

@@ -2,7 +2,7 @@
 
 import django_audit_fields.fields.hostname_modification_field
 import django_audit_fields.fields.userfield
-import django_audit_fields.models.audit_model_mixin
+import django.utils.timezone
 from django.db import migrations, models
 import django.utils.timezone
 

edc_export/migrations/0013_edcpermissions.py

@@ -4,7 +4,7 @@ import _socket
 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_revision.revision_field
 from django.db import migrations, models
 import django.utils.timezone