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

edc_dx_review/migrations/0004_remove_diagnosislocations_edc_dx_revi_name_a39b40_idx_and_more.py

@@ -0,0 +1,20 @@
+# Generated by Django 4.2.7 on 2023-12-04 22:19
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("edc_dx_review", "0003_alter_diagnosislocations_options_and_more"),
+    ]
+
+    operations = [
+        migrations.RemoveIndex(
+            model_name="diagnosislocations",
+            name="edc_dx_revi_name_a39b40_idx",
+        ),
+        migrations.RemoveIndex(
+            model_name="reasonsfortesting",
+            name="edc_dx_revi_name_0b2844_idx",
+        ),
+    ]

edc_dx_review/model_mixins/__init__.py

@@ -0,0 +1,20 @@
+from .clinical_review_baseline_model_mixin import ClinicalReviewBaselineModelMixin
+from .clinical_review_followup import (
+    ClinicalReviewCholModelMixin,
+    ClinicalReviewDmModelMixin,
+    ClinicalReviewHivModelMixin,
+    ClinicalReviewHtnModelMixin,
+    ClinicalReviewModelMixin,
+)
+from .dx_location_model_mixin import DxLocationModelMixin
+from .factory import (
+    dx_initial_review_model_mixin_factory,
+    rx_initial_review_model_mixin_factory,
+)
+from .followup_review import FollowupReviewModelMixin, HivFollowupReviewModelMixin
+from .initial_review import (
+    CholInitialReviewModelMixin,
+    HivArvInitiationModelMixin,
+    HivArvMonitoringModelMixin,
+    NcdInitialReviewModelMixin,
+)

edc_dx_review/model_mixins/clinical_review_baseline_model_mixin.py

@@ -0,0 +1,25 @@
+from django.db import models
+from edc_constants.choices import YES_NO
+from edc_constants.constants import YES
+from edc_crf.model_mixins import SingletonCrfModelMixin
+from edc_dx import raise_on_unknown_diagnosis_labels
+from edc_visit_schedule.utils import raise_if_not_baseline
+
+
+class ClinicalReviewBaselineModelMixin(SingletonCrfModelMixin, models.Model):
+    complications = models.CharField(
+        verbose_name="Since last seen, has the patient had any complications",
+        max_length=15,
+        choices=YES_NO,
+        help_text="If YES, complete the `Complications` CRF",
+    )
+
+    def save(self, *args, **kwargs):
+        raise_if_not_baseline(self.related_visit)
+        raise_on_unknown_diagnosis_labels(self, "_dx", YES)
+        super().save(*args, **kwargs)
+
+    class Meta:
+        abstract = True
+        verbose_name = "Clinical Review: Baseline"
+        verbose_name_plural = "Clinical Review: Baseline"

edc_dx_review/model_mixins/clinical_review_followup/__init__.py

@@ -0,0 +1,5 @@
+from .clinical_review_followup_chol_model_mixin import ClinicalReviewCholModelMixin
+from .clinical_review_followup_dm_model_mixin import ClinicalReviewDmModelMixin
+from .clinical_review_followup_hiv_model_mixin import ClinicalReviewHivModelMixin
+from .clinical_review_followup_htn_model_mixin import ClinicalReviewHtnModelMixin
+from .clinical_review_followup_model_mixin import ClinicalReviewModelMixin

edc_dx_review/model_mixins/clinical_review_followup/clinical_review_followup_chol_model_mixin.py

@@ -0,0 +1,54 @@
+from django.db import models
+from django.utils.html import format_html
+from django.utils.safestring import mark_safe
+from edc_constants.choices import YES_NO_NA
+from edc_constants.constants import NOT_APPLICABLE
+from edc_model import models as edc_models
+
+from ...utils import get_list_model_app
+
+
+class ClinicalReviewCholModelMixin(models.Model):
+    chol_test = models.CharField(
+        verbose_name="Since last seen, was the patient tested for high cholesterol?",
+        max_length=15,
+        choices=YES_NO_NA,
+        default=NOT_APPLICABLE,
+        help_text=format_html(
+            "{}",
+            mark_safe(
+                "Note: Select `not applicable` if diagnosis previously reported. <BR>"
+                "`Since last seen` includes today.<BR>"
+                "If `yes', complete the initial review CRF<BR>"
+                "If `not applicable`, complete the review CRF."
+            ),  # nosec B308, B703
+        ),
+    )
+
+    chol_test_date = models.DateField(
+        verbose_name="Date test requested",
+        null=True,
+        blank=True,
+    )
+
+    chol_reason = models.ManyToManyField(
+        f"{get_list_model_app()}.reasonsfortesting",
+        related_name="chol_reason",
+        verbose_name="Why was the patient tested for cholesterol?",
+        blank=True,
+    )
+
+    chol_reason_other = edc_models.OtherCharField()
+
+    chol_dx = models.CharField(
+        verbose_name=format_html(
+            "As of today, was the patient <u>{text}</u> diagnosed with high cholesterol?",
+            text="newly",
+        ),
+        max_length=15,
+        choices=YES_NO_NA,
+        default=NOT_APPLICABLE,
+    )
+
+    class Meta:
+        abstract = True

edc_dx_review/model_mixins/clinical_review_followup/clinical_review_followup_dm_model_mixin.py

@@ -0,0 +1,54 @@
+from django.db import models
+from django.utils.html import format_html
+from django.utils.safestring import mark_safe
+from edc_constants.choices import YES_NO_NA
+from edc_constants.constants import NOT_APPLICABLE
+from edc_model import models as edc_models
+
+from ...utils import get_list_model_app
+
+
+class ClinicalReviewDmModelMixin(models.Model):
+    dm_test = models.CharField(
+        verbose_name="Since last seen, was the patient tested for diabetes?",
+        max_length=15,
+        choices=YES_NO_NA,
+        default=NOT_APPLICABLE,
+        help_text=format_html(
+            "{html}",
+            html=mark_safe(
+                "Note: Select `not applicable` if diagnosis previously reported. <BR>"
+                "`Since last seen` includes today.<BR>"
+                "If `yes', complete the initial review CRF<BR>"
+                "If `not applicable`, complete the review CRF."
+            ),  # nosec B308, B703
+        ),
+    )
+
+    dm_test_date = models.DateField(
+        verbose_name="Date test requested",
+        null=True,
+        blank=True,
+    )
+
+    dm_reason = models.ManyToManyField(
+        f"{get_list_model_app()}.reasonsfortesting",
+        related_name="dm_reason",
+        verbose_name="Why was the patient tested for diabetes?",
+        blank=True,
+    )
+
+    dm_reason_other = edc_models.OtherCharField()
+
+    dm_dx = models.CharField(
+        verbose_name=format_html(
+            "As of today, was the patient <u>{text}</u> diagnosed with diabetes?",
+            text="newly",
+        ),
+        max_length=15,
+        choices=YES_NO_NA,
+        default=NOT_APPLICABLE,
+    )
+
+    class Meta:
+        abstract = True

edc_dx_review/model_mixins/clinical_review_followup/clinical_review_followup_hiv_model_mixin.py

@@ -0,0 +1,54 @@
+from django.db import models
+from django.utils.html import format_html
+from django.utils.safestring import mark_safe
+from edc_constants.choices import YES_NO_NA
+from edc_constants.constants import NOT_APPLICABLE
+from edc_model import models as edc_models
+
+from ...utils import get_list_model_app
+
+
+class ClinicalReviewHivModelMixin(models.Model):
+    hiv_test = models.CharField(
+        verbose_name="Since last seen, was the patient tested for HIV infection?",
+        max_length=15,
+        choices=YES_NO_NA,
+        default=NOT_APPLICABLE,
+        help_text=format_html(
+            "{html}",
+            html=mark_safe(
+                "Note: Select `not applicable` if diagnosis previously reported. <BR>"
+                "`Since last seen` includes today.<BR>"
+                "If `yes', complete the initial review CRF<BR>"
+                "If `not applicable`, complete the review CRF."
+            ),  # nosec B308, B703
+        ),
+    )
+
+    hiv_test_date = models.DateField(
+        verbose_name="Date test requested",
+        null=True,
+        blank=True,
+    )
+
+    hiv_reason = models.ManyToManyField(
+        f"{get_list_model_app()}.reasonsfortesting",
+        related_name="hiv_test_reason",
+        verbose_name="Why was the patient tested for HIV infection?",
+        blank=True,
+    )
+
+    hiv_reason_other = edc_models.OtherCharField()
+
+    hiv_dx = models.CharField(
+        verbose_name=format_html(
+            "As of today, was the patient <u>{text}</u> diagnosed with HIV infection?",
+            text="newly",
+        ),
+        max_length=15,
+        choices=YES_NO_NA,
+        default=NOT_APPLICABLE,
+    )
+
+    class Meta:
+        abstract = True

edc_dx_review/model_mixins/clinical_review_followup/clinical_review_followup_htn_model_mixin.py

@@ -0,0 +1,56 @@
+from django.db import models
+from django.utils.html import format_html
+from django.utils.safestring import mark_safe
+from edc_constants.choices import YES_NO_NA
+from edc_constants.constants import NOT_APPLICABLE
+from edc_model import models as edc_models
+
+from ...utils import get_list_model_app
+
+
+class ClinicalReviewHtnModelMixin(models.Model):
+    htn_test = models.CharField(
+        verbose_name="Since last seen, was the patient tested for hypertension?",
+        max_length=15,
+        choices=YES_NO_NA,
+        default=NOT_APPLICABLE,
+        help_text=format_html(
+            "{html}",
+            html=mark_safe(
+                "Note: Select `not applicable` if diagnosis previously reported. <BR>"
+                "`Since last seen` includes today.<BR>"
+                "If `yes', complete the initial review CRF<BR>"
+                "If `not applicable`, complete the review CRF."
+            ),  # nosec B308, B703
+        ),
+    )
+
+    htn_test_date = models.DateField(
+        verbose_name="Date test requested",
+        null=True,
+        blank=True,
+    )
+
+    htn_reason = models.ManyToManyField(
+        f"{get_list_model_app()}.reasonsfortesting",
+        related_name="htn_test_reason",
+        verbose_name="Why was the patient tested for hypertension?",
+        blank=True,
+    )
+
+    htn_reason_other = edc_models.OtherCharField()
+
+    htn_dx = models.CharField(
+        verbose_name=format_html(
+            "{html}",
+            html=mark_safe(
+                "As of today, was the patient <u>newly</u> diagnosed with hypertension?"
+            ),  # nosec B308, B703
+        ),
+        max_length=15,
+        choices=YES_NO_NA,
+        default=NOT_APPLICABLE,
+    )
+
+    class Meta:
+        abstract = True

edc_dx_review/model_mixins/clinical_review_followup/clinical_review_followup_model_mixin.py

@@ -0,0 +1,25 @@
+from django.db import models
+from edc_constants.choices import YES_NO
+from edc_constants.constants import YES
+from edc_crf.model_mixins import SingletonCrfModelMixin
+from edc_dx import raise_on_unknown_diagnosis_labels
+from edc_visit_schedule.utils import raise_if_baseline
+
+
+class ClinicalReviewModelMixin(SingletonCrfModelMixin, models.Model):
+    complications = models.CharField(
+        verbose_name="Since last seen, has the patient had any complications",
+        max_length=15,
+        choices=YES_NO,
+        help_text="If YES, complete the `Complications` CRF",
+    )
+
+    def save(self, *args, **kwargs):
+        raise_if_baseline(self.related_visit)
+        raise_on_unknown_diagnosis_labels(self, "_test", YES)
+        super().save(*args, **kwargs)
+
+    class Meta:
+        abstract = True
+        verbose_name = "Clinical Review"
+        verbose_name_plural = "Clinical Review"

edc_dx_review/model_mixins/dx_location_model_mixin.py

@@ -0,0 +1,17 @@
+from django.db import models
+from edc_model import models as edc_models
+
+
+class DxLocationModelMixin(models.Model):
+    dx_location = models.ForeignKey(
+        "edc_dx_review.diagnosislocations",
+        verbose_name="Where was the diagnosis made?",
+        on_delete=models.PROTECT,
+        null=True,
+        blank=False,
+    )
+
+    dx_location_other = edc_models.OtherCharField()
+
+    class Meta:
+        abstract = True

edc_dx_review/model_mixins/factory/__init__.py

@@ -0,0 +1,4 @@
+from .baseline_review_model_mixin_factory import baseline_review_model_mixin_factory
+from .dx_initial_review_model_mixin_factory import dx_initial_review_model_mixin_factory
+from .followup_review_model_mixin_factory import followup_review_model_mixin_factory
+from .rx_initial_review_model_mixin_factory import rx_initial_review_model_mixin_factory

edc_dx_review/model_mixins/factory/baseline_review_model_mixin_factory.py

@@ -0,0 +1,55 @@
+from __future__ import annotations
+
+from django.db import models
+from edc_constants.choices import YES_NO
+from edc_constants.constants import CHOL, DM, HIV, HTN, NO
+from edc_dx import get_diagnosis_labels
+
+default_prompts = {
+    HIV.lower(): "Has the patient ever tested <U>positive</U> for HIV infection?",
+    DM: "Has the patient ever been diagnosed with DIABETES?",
+    HTN: "Has the patient ever been diagnosed with HYPERTENSION?",
+    CHOL: "Has the patient ever been diagnosed with HIGH CHOLESTEROL?",
+}
+
+
+def baseline_review_model_mixin_factory(prompts: dict[str, str] | None = None):
+    prompts = prompts or default_prompts
+
+    class AbstractModel(models.Model):
+        class Meta:
+            abstract = True
+
+    opts = {}
+    for cond, label in get_diagnosis_labels().items():
+        opts.update(
+            {
+                f"{cond}_dx": models.CharField(
+                    verbose_name=prompts.get(cond),
+                    max_length=15,
+                    choices=YES_NO,
+                ),
+                f"{cond}_dx_at_screening": models.CharField(
+                    verbose_name=f"Was a diagnosis of {label.upper()} reported at screening?",
+                    max_length=15,
+                    choices=YES_NO,
+                ),
+            }
+        )
+
+    opts.update(
+        {
+            "protocol_incident": models.CharField(
+                verbose_name=(
+                    "Do any of the above diagnosis differ from those reported at screening?"
+                ),
+                max_length=15,
+                choices=YES_NO,
+                default=NO,
+            )
+        }
+    )
+    for name, fld_cls in opts.items():
+        AbstractModel.add_to_class(name, fld_cls)
+
+    return AbstractModel

edc_dx_review/model_mixins/factory/calculate_date.py

@@ -0,0 +1,43 @@
+from __future__ import annotations
+
+from datetime import date
+
+from django.db import models
+from edc_constants.constants import NO, NOT_APPLICABLE, YES
+from edc_model import duration_to_date
+
+
+def calculate_date(
+    instance: models.Model, fld_prefix: str, reference_field: str
+) -> tuple[date | None, str]:
+    """Returns tuple date and YES/NO/NA.
+
+    The date is either the actual date or an estimated date
+    based on the ago field value.
+    ."""
+    calculated_date: date | None = None
+    is_estimated: str = NOT_APPLICABLE
+    report_datetime = getattr(instance, reference_field)
+    rx_date = getattr(instance, f"{fld_prefix}_date")
+    rx_ago = getattr(instance, f"{fld_prefix}_ago")
+    if rx_ago and not rx_date and report_datetime:
+        if rx_ago and not rx_date:
+            calculated_date = duration_to_date(rx_ago, report_datetime)
+            is_estimated = YES
+        elif rx_date:
+            calculated_date = rx_date
+            is_estimated = NO
+
+        else:
+            calculated_date = None
+            is_estimated = NOT_APPLICABLE
+    return calculated_date, is_estimated
+
+
+def update_calculated_date(instance: models.Model, fld_prefix: str, reference_field: str):
+    """Wrapper for model save method"""
+    calculated_date, is_calculated = calculate_date(
+        instance=instance, fld_prefix=fld_prefix, reference_field=reference_field
+    )
+    setattr(instance, f"{fld_prefix}_calculated_date", calculated_date)
+    setattr(instance, f"{fld_prefix}_date_is_estimated", is_calculated)

edc_dx_review/model_mixins/factory/dx_initial_review_model_mixin_factory.py

@@ -0,0 +1,97 @@
+from __future__ import annotations
+
+from datetime import date
+
+from django.db import models
+from edc_constants.choices import YES_NO
+from edc_constants.constants import NOT_APPLICABLE, YES
+from edc_dx import Diagnoses
+from edc_model.models import DurationYMDField
+from edc_model.utils import get_report_datetime_field_name
+from edc_model.validators import date_not_future
+
+from .calculate_date import update_calculated_date
+
+
+class InitialReviewModelError(Exception):
+    pass
+
+
+def dx_initial_review_methods_model_mixin_factory():
+    class AbstractModel(models.Model):
+        fld_prefix: str | None = None
+
+        def save(self, *args, **kwargs):
+            if not self.diagnoses.get_dx_by_model(self) == YES:
+                raise InitialReviewModelError(
+                    "No diagnosis has been recorded. See clinical review. "
+                    "Perhaps catch this in the form."
+                )
+            update_calculated_date(
+                self,
+                fld_prefix=self.fld_prefix,
+                reference_field=get_report_datetime_field_name(),
+            )
+            super().save(*args, **kwargs)
+
+        @property
+        def diagnoses(self):
+            subject_identifier = getattr(self, "subject_identifier")
+            return Diagnoses(
+                subject_identifier=subject_identifier,
+                report_datetime=getattr(self, get_report_datetime_field_name()),
+                lte=True,
+            )
+
+        def get_best_dx_date(self) -> date:
+            return getattr(self, f"{self.fld_prefix}_date") or getattr(
+                self, f"{self.fld_prefix}_calculated_date"
+            )
+
+        class Meta:
+            abstract = True
+
+    return AbstractModel
+
+
+def dx_initial_review_model_mixin_factory(fld_prefix: str | None = None):
+    fld_prefix = fld_prefix or "dx"
+
+    class AbstractModel(dx_initial_review_methods_model_mixin_factory(), models.Model):
+        class Meta:
+            abstract = True
+
+    opts = {
+        "fld_prefix": fld_prefix,
+        f"{fld_prefix}_date": models.DateField(
+            verbose_name="Date patient diagnosed",
+            null=True,
+            blank=True,
+            validators=[date_not_future],
+            help_text="If possible, provide the exact date here instead of estimating.",
+        ),
+        f"{fld_prefix}_ago": DurationYMDField(
+            verbose_name="If date not known, how long ago was the patient diagnosed?",
+            null=True,
+            blank=True,
+            help_text="If possible, provide the exact date above instead of estimating here.",
+        ),
+        f"{fld_prefix}_calculated_date": models.DateField(
+            verbose_name="Estimated diagnosis date",
+            null=True,
+            help_text=f"Calculated based on response to `{fld_prefix}dx_ago`",
+            editable=False,
+        ),
+        f"{fld_prefix}_date_is_estimated": models.CharField(
+            verbose_name="Was the diagnosis date estimated?",
+            max_length=15,
+            choices=YES_NO,
+            default=NOT_APPLICABLE,
+            editable=False,
+        ),
+    }
+
+    for name, fld_cls in opts.items():
+        AbstractModel.add_to_class(name, fld_cls)
+
+    return AbstractModel

edc_dx_review/model_mixins/factory/followup_review_model_mixin_factory.py

@@ -0,0 +1,39 @@
+from __future__ import annotations
+
+from django.db import models
+from edc_constants.choices import YES_NO_NA
+from edc_constants.constants import CHOL, DM, HIV, HTN, NOT_APPLICABLE
+from edc_dx import get_diagnosis_labels
+
+default_prompts = {
+    HIV.lower(): "Since last seen, has the patient tested <U>positive</U> for HIV infection?",
+    DM: "Since last seen, has the patient been diagnosed with Diabetes?",
+    HTN: "Since last seen, has the patient been diagnosed with Hypertension?",
+    CHOL: "Since last seen, has the patient been diagnosed with High Cholesterol?",
+}
+
+
+def followup_review_model_mixin_factory(prompts: dict[str, str] | None = None):
+    prompts = prompts or default_prompts
+
+    class AbstractModel(models.Model):
+        class Meta:
+            abstract = True
+
+    opts = {}
+    for dx in get_diagnosis_labels():
+        opts.update(
+            {
+                f"{dx}_dx": models.CharField(
+                    verbose_name=prompts.get(dx),
+                    max_length=15,
+                    choices=YES_NO_NA,
+                    default=NOT_APPLICABLE,
+                )
+            }
+        )
+
+    for name, fld_cls in opts.items():
+        AbstractModel.add_to_class(name, fld_cls)
+
+    return AbstractModel

edc_dx_review/model_mixins/factory/rx_initial_review_model_mixin_factory.py

@@ -0,0 +1,69 @@
+from __future__ import annotations
+
+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
+
+from .calculate_date import update_calculated_date
+
+
+def rx_initial_review_model_mixin_factory(
+    fld_prefix: str | None = None, verbose_name_label: str | None = None
+):
+    fld_prefix = fld_prefix or "rx_init"
+
+    class AbstractModel(models.Model):
+        def save(self, *args, **kwargs):
+            update_calculated_date(
+                self, fld_prefix=fld_prefix, reference_field="report_datetime"
+            )
+            super().save(*args, **kwargs)
+
+        class Meta:
+            abstract = True
+
+    opts = {
+        "fld_prefix": fld_prefix,
+        f"{fld_prefix}": models.CharField(
+            verbose_name=f"Has the patient started {verbose_name_label}?",
+            max_length=15,
+            choices=YES_NO_NA,
+            default=YES,
+        ),
+        f"{fld_prefix}_date": models.DateField(
+            verbose_name=f"Date started {verbose_name_label}",
+            validators=[date_not_future],
+            null=True,
+            blank=True,
+            help_text="If possible, provide the exact date here instead of estimating.",
+        ),
+        f"{fld_prefix}_ago": DurationYMDField(
+            verbose_name=(
+                f"If date not known, how long ago did the patient start {verbose_name_label}?"
+            ),
+            null=True,
+            blank=True,
+            help_text="If possible, provide the exact date above instead of estimating here.",
+        ),
+        f"{fld_prefix}_calculated_date": models.DateField(
+            verbose_name=f"Estimated date started {verbose_name_label}",
+            validators=[date_not_future],
+            null=True,
+            editable=False,
+            help_text="Calculated based on response to `rx_init_ago`",
+        ),
+        f"{fld_prefix}_date_is_estimated": models.CharField(
+            verbose_name=f"Was {verbose_name_label} start date estimated?",
+            max_length=15,
+            choices=YES_NO,
+            default=NOT_APPLICABLE,
+            editable=False,
+        ),
+    }
+
+    for name, fld_cls in opts.items():
+        AbstractModel.add_to_class(name, fld_cls)
+
+    return AbstractModel

edc_dx_review/model_mixins/followup_review/__init__.py

@@ -0,0 +1,2 @@
+from .followup_review_model_mixin import FollowupReviewModelMixin
+from .hiv_followup_review_model_mixin import HivFollowupReviewModelMixin

edc_dx_review/model_mixins/followup_review/followup_review_model_mixin.py

@@ -0,0 +1,22 @@
+from django.db import models
+from edc_constants.choices import YES_NO_NA
+from edc_constants.constants import NOT_APPLICABLE
+
+
+class FollowupReviewModelMixin(models.Model):
+    care_delivery = models.CharField(
+        verbose_name=(
+            "Was care for this `condition` delivered in an integrated care clinic today?"
+        ),
+        max_length=25,
+        choices=YES_NO_NA,
+        default=NOT_APPLICABLE,
+        help_text="Select `not applicable` if site was not selected for integrated care.",
+    )
+
+    care_delivery_other = models.TextField(
+        verbose_name="If NO, please explain", null=True, blank=True
+    )
+
+    class Meta:
+        abstract = True