meta-edc 1.0.7__py3-none-any.whl → 1.1.0__py3-none-any.whl

meta_screening/tests/tests/test_screening_part_three.py

@@ -4,11 +4,8 @@ from decimal import Decimal
 from dateutil.relativedelta import relativedelta
 from django.test import TestCase
 from edc_constants.constants import FEMALE, NO, NOT_APPLICABLE, POS, TBD, YES
-from edc_reportable import (
-    MICROMOLES_PER_LITER,
-    MILLIMOLES_PER_LITER,
-    ConversionNotHandled,
-)
+from edc_reportable import MICROMOLES_PER_LITER, MILLIMOLES_PER_LITER
+from edc_reportable.utils import convert_units
 from edc_utils.date import get_utcnow
 
 from meta_screening.constants import (
@@ -292,20 +289,20 @@ class TestScreeningPartThree(TestCase):
         obj.ogtt_value = 3.0
         obj.ogtt_units = MICROMOLES_PER_LITER
         obj.ogtt_datetime = get_utcnow()
-        try:
-            obj.save()
-        except ConversionNotHandled:
-            pass
-        else:
-            self.fail("ConversionNotHandled unexpectedly not raised.")
+        obj.save()
 
         obj.refresh_from_db()
+        obj.ogtt_value = convert_units(
+            label="glucose",
+            value=3.0,
+            units_from=MICROMOLES_PER_LITER,
+            units_to=MILLIMOLES_PER_LITER,
+        )
         obj.ogtt_units = MILLIMOLES_PER_LITER
         obj.save()
 
-        self.assertIn(ineligible_reason, obj.reasons_ineligible_part_three)
-        self.assertEqual(obj.eligible_part_three, TBD)
-        self.assertFalse(obj.eligible)
+        self.assertEqual(obj.eligible_part_three, YES)
+        self.assertTrue(obj.eligible)
         self.assertFalse(obj.consented)
 
         obj.ogtt_base_datetime = get_utcnow()

meta_subject/action_items.py

@@ -2,7 +2,7 @@ from django.apps import apps as django_apps
 from edc_action_item import Action, ActionWithNotification, site_action_items
 from edc_action_item.site_action_items import AlreadyRegistered
 from edc_adverse_event.constants import AE_INITIAL_ACTION
-from edc_constants.constants import HIGH_PRIORITY, NEW, NONE, POS, YES
+from edc_constants.constants import GRADE3, GRADE4, HIGH_PRIORITY, NEW, NONE, POS, YES
 from edc_egfr.constants import EGFR_DROP_NOTIFICATION_ACTION
 from edc_lab_results.action_items import BloodResultsFbcAction
 from edc_lab_results.action_items import (
@@ -17,7 +17,6 @@ from edc_lab_results.action_items import (
     BloodResultsRftAction as BaseBloodResultsRftAction,
 )
 from edc_ltfu.constants import LTFU_ACTION
-from edc_reportable import GRADE3, GRADE4
 from edc_visit_schedule.constants import OFFSCHEDULE_ACTION
 from edc_visit_schedule.utils import is_baseline
 from edc_visit_tracking.constants import MISSED_VISIT

meta_subject/choices.py

@@ -3,6 +3,8 @@ from edc_constants.constants import (
     ABSENT,
     CLOSED,
     DEAD,
+    GRADE3,
+    GRADE4,
     NEW,
     NO,
     NO_EXAM,
@@ -15,7 +17,6 @@ from edc_constants.constants import (
     PRESENT_WITH_REINFORCEMENT,
     YES,
 )
-from edc_reportable.constants import GRADE3, GRADE4
 from edc_visit_tracking.constants import MISSED_VISIT, SCHEDULED, UNSCHEDULED
 
 from meta_ae.choices import INFORMANT_RELATIONSHIP

meta_subject/forms/blood_results/blood_results_rft_form.py

@@ -3,21 +3,78 @@ from django.utils.safestring import mark_safe
 from edc_action_item.forms import ActionItemCrfFormMixin
 from edc_crf.crf_form_validator import CrfFormValidator
 from edc_crf.modelform_mixins import CrfModelFormMixin
+from edc_egfr.form_validator_mixins import EgfrCkdEpiFormValidatorMixin
 from edc_lab_panel.panels import rft_panel
 from edc_lab_results.form_validator_mixins import BloodResultsFormValidatorMixin
-from edc_reportable import BmiFormValidatorMixin
+from edc_registration.models import RegisteredSubject
+from edc_utils import age
+from edc_visit_schedule.utils import is_baseline
+from edc_vitals.form_validators import BmiFormValidatorMixin
 
-from ...models import BloodResultsRft
+from meta_visit_schedule.constants import DAY1
+
+from ...models import BloodResultsRft, FollowupVitals, PhysicalExam, SubjectVisit
 
 
 class BloodResultsRftFormValidator(
-    BloodResultsFormValidatorMixin, BmiFormValidatorMixin, CrfFormValidator
+    BloodResultsFormValidatorMixin,
+    EgfrCkdEpiFormValidatorMixin,
+    BmiFormValidatorMixin,
+    CrfFormValidator,
 ):
     panel = rft_panel
 
     def clean(self):
         super().clean()
         self.validate_bmi()
+        if self.cleaned_data.get("creatinine_value") and self.cleaned_data.get(
+            "creatinine_units"
+        ):
+
+            if is_baseline(self.related_visit):
+                baseline_egfr_value = None
+            else:
+                baseline_visit = SubjectVisit.objects.get(
+                    subject_identifier=self.related_visit.subject_identifier,
+                    visit_code=DAY1,
+                    visit_code_sequence=0,
+                )
+                baseline_egfr_value = BloodResultsRft.objects.get(
+                    subject_visit=baseline_visit
+                ).egfr_value
+            rs = RegisteredSubject.objects.get(
+                subject_identifier=self.related_visit.subject_identifier
+            )
+            age_in_years = age(rs.dob, self.report_datetime).years
+
+            self.validate_egfr(
+                gender=rs.gender,
+                age_in_years=age_in_years,
+                ethnicity=rs.ethnicity,
+                weight_in_kgs=self.get_weight_in_kgs(),
+                baseline_egfr_value=baseline_egfr_value,
+            )
+
+    def get_weight_in_kgs(self) -> float | None:
+        if is_baseline(self.related_visit):
+            obj = (
+                PhysicalExam.objects.filter(
+                    subject_visit=self.related_visit, weight__isnull=False
+                )
+                .order_by("report_datetime")
+                .last()
+            )
+        else:
+            obj = (
+                FollowupVitals.objects.filter(
+                    subject_visit=self.related_visit, weight__isnull=False
+                )
+                .order_by("report_datetime")
+                .last()
+            )
+        if obj:
+            return obj.weight
+        return None
 
 
 class BloodResultsRftForm(ActionItemCrfFormMixin, CrfModelFormMixin, forms.ModelForm):

meta_subject/migrations/0223_bloodresultsfbc_errors_bloodresultsgludummy_errors_and_more.py

@@ -0,0 +1,83 @@
+# Generated by Django 5.2.3 on 2025-06-25 20:55
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("meta_subject", "0222_alter_historicalstudymedication_stock_codes_and_more"),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="bloodresultsfbc",
+            name="errors",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="bloodresultsgludummy",
+            name="errors",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="bloodresultshba1c",
+            name="errors",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="bloodresultsins",
+            name="errors",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="bloodresultslft",
+            name="errors",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="bloodresultslipids",
+            name="errors",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="bloodresultsrft",
+            name="errors",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="historicalbloodresultsfbc",
+            name="errors",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="historicalbloodresultsgludummy",
+            name="errors",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="historicalbloodresultshba1c",
+            name="errors",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="historicalbloodresultsins",
+            name="errors",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="historicalbloodresultslft",
+            name="errors",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="historicalbloodresultslipids",
+            name="errors",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="historicalbloodresultsrft",
+            name="errors",
+            field=models.TextField(blank=True, null=True),
+        ),
+    ]

meta_subject/migrations/0224_bloodresultsfbc_abnormal_summary_and_more.py

@@ -0,0 +1,153 @@
+# Generated by Django 5.2.3 on 2025-06-25 23:57
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("meta_subject", "0223_bloodresultsfbc_errors_bloodresultsgludummy_errors_and_more"),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="bloodresultsfbc",
+            name="abnormal_summary",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="bloodresultsfbc",
+            name="reportable_summary",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="bloodresultsgludummy",
+            name="abnormal_summary",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="bloodresultsgludummy",
+            name="reportable_summary",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="bloodresultshba1c",
+            name="abnormal_summary",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="bloodresultshba1c",
+            name="reportable_summary",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="bloodresultsins",
+            name="abnormal_summary",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="bloodresultsins",
+            name="reportable_summary",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="bloodresultslft",
+            name="abnormal_summary",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="bloodresultslft",
+            name="reportable_summary",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="bloodresultslipids",
+            name="abnormal_summary",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="bloodresultslipids",
+            name="reportable_summary",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="bloodresultsrft",
+            name="abnormal_summary",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="bloodresultsrft",
+            name="reportable_summary",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="historicalbloodresultsfbc",
+            name="abnormal_summary",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="historicalbloodresultsfbc",
+            name="reportable_summary",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="historicalbloodresultsgludummy",
+            name="abnormal_summary",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="historicalbloodresultsgludummy",
+            name="reportable_summary",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="historicalbloodresultshba1c",
+            name="abnormal_summary",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="historicalbloodresultshba1c",
+            name="reportable_summary",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="historicalbloodresultsins",
+            name="abnormal_summary",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="historicalbloodresultsins",
+            name="reportable_summary",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="historicalbloodresultslft",
+            name="abnormal_summary",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="historicalbloodresultslft",
+            name="reportable_summary",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="historicalbloodresultslipids",
+            name="abnormal_summary",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="historicalbloodresultslipids",
+            name="reportable_summary",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="historicalbloodresultsrft",
+            name="abnormal_summary",
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name="historicalbloodresultsrft",
+            name="reportable_summary",
+            field=models.TextField(blank=True, null=True),
+        ),
+    ]

meta_subject/tests/tests/test_egfr.py

@@ -205,8 +205,8 @@ class TestEgfr(MetaTestCaseMixin, TestCase):
         data.update(creatinine_value=152.0, creatinine_units=MICROMOLES_PER_LITER)
         obj_1000 = BloodResultsRft.objects.create(**data)
         obj_1000.refresh_from_db()
-        self.assertEqual(round_half_away_from_zero(obj_1000.egfr_value, 3), Decimal("49.030"))
-        self.assertEqual(round_half_away_from_zero(obj_1000.egfr_value, 2), Decimal("49.03"))
+        self.assertEqual(round_half_away_from_zero(obj_1000.egfr_value, 3), Decimal("49.019"))
+        self.assertEqual(round_half_away_from_zero(obj_1000.egfr_value, 2), Decimal("49.02"))
         self.assertEqual(round_half_away_from_zero(obj_1000.egfr_value, 1), Decimal("49.0"))
         self.assertEqual(round_half_away_from_zero(obj_1000.egfr_value), Decimal("49"))
 
@@ -228,7 +228,7 @@ class TestEgfr(MetaTestCaseMixin, TestCase):
         data.update(creatinine_value=150.8, creatinine_units=MICROMOLES_PER_LITER)
         obj_2000 = BloodResultsRft.objects.create(**data)
         obj_2000.refresh_from_db()
-        self.assertEqual(round_half_away_from_zero(obj_2000.egfr_value, 3), Decimal("49.503"))
-        self.assertEqual(round_half_away_from_zero(obj_2000.egfr_value, 2), Decimal("49.50"))
+        self.assertEqual(round_half_away_from_zero(obj_2000.egfr_value, 3), Decimal("49.492"))
+        self.assertEqual(round_half_away_from_zero(obj_2000.egfr_value, 2), Decimal("49.49"))
         self.assertEqual(round_half_away_from_zero(obj_2000.egfr_value, 1), Decimal("49.5"))
-        self.assertEqual(round_half_away_from_zero(obj_2000.egfr_value), Decimal("50"))
+        self.assertEqual(round_half_away_from_zero(obj_2000.egfr_value), Decimal("49"))