meta-edc 0.3.39__py3-none-any.whl → 1.4.0__py3-none-any.whl

meta_subject/migrations/0237_historicalhivexitreview_singleton_field_and_more.py

@@ -0,0 +1,68 @@
+# Generated by Django 5.2.7 on 2025-10-14 00:32
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        (
+            "meta_subject",
+            "0236_alter_historicalhivexitreview_other_current_arv_regimen_and_more",
+        ),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="historicalhivexitreview",
+            name="singleton_field",
+            field=models.CharField(
+                db_index=True,
+                default="",
+                editable=False,
+                help_text="auto updated for unique constraint",
+                max_length=50,
+                verbose_name="subject identifier",
+            ),
+            preserve_default=False,
+        ),
+        migrations.AddField(
+            model_name="hivexitreview",
+            name="singleton_field",
+            field=models.CharField(
+                default="",
+                editable=False,
+                help_text="auto updated for unique constraint",
+                max_length=50,
+                unique=True,
+                verbose_name="subject identifier",
+            ),
+            preserve_default=False,
+        ),
+        migrations.AlterField(
+            model_name="healtheconomicsupdate",
+            name="singleton_field",
+            field=models.CharField(
+                default="",
+                editable=False,
+                help_text="auto updated for unique constraint",
+                max_length=50,
+                unique=True,
+                verbose_name="subject identifier",
+            ),
+            preserve_default=False,
+        ),
+        migrations.AlterField(
+            model_name="historicalhealtheconomicsupdate",
+            name="singleton_field",
+            field=models.CharField(
+                db_index=True,
+                default="",
+                editable=False,
+                help_text="auto updated for unique constraint",
+                max_length=50,
+                verbose_name="subject identifier",
+            ),
+            preserve_default=False,
+        ),
+    ]

meta_subject/migrations/0238_historicalhivexitreview_available_and_more.py

@@ -0,0 +1,88 @@
+# Generated by Django 5.2.7 on 2025-10-14 12:56
+
+import django.db.models.deletion
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        (
+            "meta_lists",
+            "0020_alter_abnormalfootappearanceobservations_extra_value_and_more",
+        ),
+        ("meta_subject", "0237_historicalhivexitreview_singleton_field_and_more"),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="historicalhivexitreview",
+            name="available",
+            field=models.CharField(
+                choices=[("Yes", "Yes"), ("No", "No")],
+                default="Yes",
+                max_length=25,
+                verbose_name="Are HIV test result and treatment information available?",
+            ),
+        ),
+        migrations.AddField(
+            model_name="historicalhivexitreview",
+            name="comment",
+            field=models.TextField(
+                blank=True,
+                default="",
+                help_text="May be left blank.",
+                verbose_name="Any other comment?",
+            ),
+        ),
+        migrations.AddField(
+            model_name="historicalhivexitreview",
+            name="not_available_reason",
+            field=models.TextField(
+                blank=True,
+                default="",
+                verbose_name="If not available, please explain ...",
+            ),
+        ),
+        migrations.AddField(
+            model_name="hivexitreview",
+            name="available",
+            field=models.CharField(
+                choices=[("Yes", "Yes"), ("No", "No")],
+                default="Yes",
+                max_length=25,
+                verbose_name="Are HIV test result and treatment information available?",
+            ),
+        ),
+        migrations.AddField(
+            model_name="hivexitreview",
+            name="comment",
+            field=models.TextField(
+                blank=True,
+                default="",
+                help_text="May be left blank.",
+                verbose_name="Any other comment?",
+            ),
+        ),
+        migrations.AddField(
+            model_name="hivexitreview",
+            name="not_available_reason",
+            field=models.TextField(
+                blank=True,
+                default="",
+                verbose_name="If not available, please explain ...",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="hivexitreview",
+            name="current_arv_regimen",
+            field=models.ForeignKey(
+                blank=True,
+                null=True,
+                on_delete=django.db.models.deletion.PROTECT,
+                related_name="last_arv_regimen",
+                to="meta_lists.arvregimens",
+                verbose_name="Which antiretroviral therapy regimen is the patient currently on?",
+            ),
+        ),
+    ]

meta_subject/model_mixins/__init__.py

@@ -1,5 +1,15 @@
 from .arv_history_model_mixin import ArvHistoryModelMixin
+from .arv_review_model_mixin import ArvReviewModelMixin
 from .crf_model_mixin import CrfModelMixin
 from .crf_with_action_model_mixin import CrfWithActionModelMixin
 from .search_slug_model_mixin import SearchSlugModelMixin
 from .vitals_fields_model_mixin import VitalsFieldsModelMixin
+
+__all__ = [
+    "ArvHistoryModelMixin",
+    "ArvReviewModelMixin",
+    "CrfModelMixin",
+    "CrfWithActionModelMixin",
+    "SearchSlugModelMixin",
+    "VitalsFieldsModelMixin",
+]

meta_subject/model_mixins/arv_history_model_mixin.py

@@ -1,13 +1,13 @@
-from django.core.validators import MaxValueValidator, MinValueValidator
 from django.db import models
 from edc_constants.choices import YES_NO
 from edc_model.models import OtherCharField
-from edc_reportable import CELLS_PER_MILLIMETER_CUBED_DISPLAY, COPIES_PER_MILLILITER
 
 from meta_lists.models import ArvRegimens, OiProphylaxis
 
+from .arv_review_model_mixin import ArvReviewModelMixin
 
-class ArvHistoryModelMixin(models.Model):
+
+class ArvHistoryModelMixin(ArvReviewModelMixin, models.Model):
     hiv_diagnosis_date = models.DateField(
         verbose_name="When was the diagnosis of HIV made?", null=True, blank=True
     )
@@ -18,47 +18,6 @@ class ArvHistoryModelMixin(models.Model):
         blank=True,
     )
 
-    viral_load = models.IntegerField(
-        verbose_name="Last viral load",
-        validators=[MinValueValidator(0), MaxValueValidator(999999)],
-        null=True,
-        blank=True,
-        help_text=COPIES_PER_MILLILITER,
-    )
-
-    viral_load_date = models.DateField(
-        verbose_name="Date of last viral load", null=True, blank=True
-    )
-
-    cd4 = models.IntegerField(
-        verbose_name="Last 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 last CD4", null=True, blank=True)
-
-    current_arv_regimen = models.ForeignKey(
-        ArvRegimens,
-        on_delete=models.PROTECT,
-        related_name="current_arv_regimen",
-        verbose_name="Which antiretroviral therapy regimen is the patient currently on?",
-        null=True,
-        blank=False,
-    )
-
-    other_current_arv_regimen = OtherCharField(null=True, blank=True)
-
-    current_arv_regimen_start_date = models.DateField(
-        verbose_name=(
-            "When did the patient start this current antiretroviral therapy regimen?"
-        ),
-        null=True,
-        blank=True,
-    )
-
     has_previous_arv_regimen = models.CharField(
         verbose_name="Has the patient been on any previous regimen?",
         max_length=15,

meta_subject/model_mixins/arv_review_model_mixin.py

@@ -0,0 +1,53 @@
+from clinicedc_constants import COPIES_PER_MILLILITER, NULL_STRING
+from django.core.validators import MaxValueValidator, MinValueValidator
+from django.db import models
+from edc_model.models import OtherCharField
+from edc_reportable.units import CELLS_PER_MILLIMETER_CUBED_DISPLAY
+
+from meta_lists.models import ArvRegimens
+
+
+class ArvReviewModelMixin(models.Model):
+    viral_load = models.IntegerField(
+        verbose_name="Last viral load",
+        validators=[MinValueValidator(0), MaxValueValidator(999999)],
+        null=True,
+        blank=True,
+        help_text=COPIES_PER_MILLILITER,
+    )
+
+    viral_load_date = models.DateField(
+        verbose_name="Date of last viral load", null=True, blank=True
+    )
+
+    cd4 = models.IntegerField(
+        verbose_name="Last 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 last CD4", null=True, blank=True)
+
+    current_arv_regimen = models.ForeignKey(
+        ArvRegimens,
+        on_delete=models.PROTECT,
+        related_name="current_arv_regimen",
+        verbose_name="Which antiretroviral therapy regimen is the patient currently on?",
+        null=True,
+        blank=False,
+    )
+
+    other_current_arv_regimen = OtherCharField(default=NULL_STRING, blank=True)
+
+    current_arv_regimen_start_date = models.DateField(
+        verbose_name=(
+            "When did the patient start this current antiretroviral therapy regimen?"
+        ),
+        null=True,
+        blank=True,
+    )
+
+    class Meta:
+        abstract = True

meta_subject/model_mixins/search_slug_model_mixin.py

@@ -4,8 +4,7 @@ from edc_search.model_mixins import SearchSlugModelMixin as Base
 class SearchSlugModelMixin(Base):
     def get_search_slug_fields(self):
         fields = super().get_search_slug_fields()
-        fields.append("subject_identifier")
-        return fields
+        return *fields, "subject_identifier"
 
     class Meta:
         abstract = True

meta_subject/model_mixins/vitals_fields_model_mixin.py

@@ -1,11 +1,44 @@
+from clinicedc_constants import NO
 from django.core.validators import MaxValueValidator, MinValueValidator
 from django.db import models
+from edc_constants.choices import YES_NO
 from edc_vitals.models import WeightField
 
 
 class VitalsFieldsModelMixin(models.Model):
     weight = WeightField(null=True)
 
+    waist_circumference_measured = models.CharField(
+        verbose_name="Was the patient's waist circumference measured today?",
+        max_length=15,
+        choices=YES_NO,
+        help_text=(
+            "Waist circumference may be provided at anytime "
+            "but is required at 36 and 48 months"
+        ),
+        default=NO,
+    )
+
+    waist_circumference = models.DecimalField(
+        verbose_name="Waist circumference",
+        max_digits=5,
+        decimal_places=1,
+        validators=[MinValueValidator(50.0), MaxValueValidator(175.0)],
+        help_text="in centimeters",
+        null=True,
+        blank=True,
+    )
+
+    waist_circumference_comment = models.TextField(
+        verbose_name="If waist circumference not measured, please explain ...",
+        help_text=(
+            "A reason not measured may be provided at anytime "
+            "but is required at 36 and 48 months"
+        ),
+        default="",
+        blank=True,
+    )
+
     # 10
     heart_rate = models.IntegerField(
         verbose_name="Heart rate:",

meta_subject/models/__init__.py

@@ -1,6 +1,7 @@
 from .birth_outcomes import BirthOutcomes
 from .blood_results import (
     BloodResultsFbc,
+    BloodResultsGluDummy,
     BloodResultsHba1c,
     BloodResultsIns,
     BloodResultsLft,
@@ -25,9 +26,11 @@ from .health_economics import (
     HealthEconomicsUpdate,
 )
 from .hepatitis_test import HepatitisTest
+from .hiv_exit_review import HivExitReview
 from .malaria_test import MalariaTest
 from .medication_adherence import MedicationAdherence
 from .mnsi import Mnsi
+from .next_appointment import NextAppointment
 from .other_arv_regimens import OtherArvRegimens
 from .other_arv_regimens_detail import OtherArvRegimensDetail
 from .patient_history import PatientHistory
@@ -46,3 +49,52 @@ from .subject_visit import SubjectVisit
 from .subject_visit_missed import SubjectVisitMissed
 from .urine_dipstick_test import UrineDipstickTest
 from .urine_pregnancy import UrinePregnancy
+
+__all__ = [
+    "BirthOutcomes",
+    "BloodResultsFbc",
+    "BloodResultsGluDummy",
+    "BloodResultsHba1c",
+    "BloodResultsIns",
+    "BloodResultsLft",
+    "BloodResultsLipids",
+    "BloodResultsRft",
+    "Complications",
+    "ComplicationsGlycemia",
+    "ConcomitantMedication",
+    "Delivery",
+    "DietAndLifestyle",
+    "DmEndpoint",
+    "DmFollowup",
+    "EgfrDropNotification",
+    "Eq5d3l",
+    "FollowupExamination",
+    "FollowupVitals",
+    "Glucose",
+    "GlucoseFbg",
+    "HealthEconomics",
+    "HealthEconomicsSimple",
+    "HealthEconomicsUpdate",
+    "HepatitisTest",
+    "HivExitReview",
+    "MalariaTest",
+    "MedicationAdherence",
+    "Mnsi",
+    "NextAppointment",
+    "OtherArvRegimens",
+    "OtherArvRegimensDetail",
+    "PatientHistory",
+    "PhysicalExam",
+    "PregnancyUpdate",
+    "Sf12",
+    "StudyMedication",
+    "SubjectRequisition",
+    "SubjectVisit",
+    "SubjectVisitMissed",
+    "UrineDipstickTest",
+    "UrinePregnancy",
+    "study_medication_on_pre_save",
+    "update_glucose_endpoints_for_subject_on_post_save",
+    "update_pregnancy_notification_on_delivery_post_save",
+    "update_schedule_on_delivery_post_save",
+]

meta_subject/models/birth_outcomes.py

@@ -15,7 +15,7 @@ from .delivery import Delivery
 class Manager(models.Manager):
     use_in_migrations = True
 
-    def get_by_natural_key(
+    def get_by_natural_key(  # noqa: PLR0913
         self,
         birth_order,
         subject_identifier,
@@ -97,5 +97,5 @@ class BirthOutcomes(
     class Meta(BaseUuidModel.Meta):
         verbose_name = "Birth Outcomes"
         verbose_name_plural = "Birth Outcomes"
-        indexes = [Index(fields=["delivery", "birth_order"])]
-        unique_together = ["delivery", "birth_order"]
+        indexes = (Index(fields=["delivery", "birth_order"]),)
+        unique_together = ("delivery", "birth_order")

meta_subject/models/blood_results/__init__.py

@@ -1,6 +1,17 @@
 from .blood_results_fbc import BloodResultsFbc
+from .blood_results_glu import BloodResultsGluDummy
 from .blood_results_hba1c import BloodResultsHba1c
 from .blood_results_ins import BloodResultsIns
 from .blood_results_lft import BloodResultsLft
 from .blood_results_lipids import BloodResultsLipids
 from .blood_results_rft import BloodResultsRft
+
+__all__ = [
+    "BloodResultsFbc",
+    "BloodResultsGluDummy",
+    "BloodResultsHba1c",
+    "BloodResultsIns",
+    "BloodResultsLft",
+    "BloodResultsLipids",
+    "BloodResultsRft",
+]

meta_subject/models/blood_results/blood_results_glu.py

@@ -0,0 +1,29 @@
+from django.db import models
+from edc_lab.model_mixins import CrfWithRequisitionModelMixin, requisition_fk_options
+from edc_lab_panel.panels import blood_glucose_panel
+from edc_lab_results import BLOOD_RESULTS_GLU_ACTION
+from edc_lab_results.model_mixins import BloodResultsModelMixin, GlucoseModelMixin
+from edc_model.models import BaseUuidModel
+
+from ...model_mixins import CrfWithActionModelMixin
+
+
+# TODO: this is a IFG!!
+class BloodResultsGluDummy(
+    CrfWithActionModelMixin,
+    GlucoseModelMixin,
+    CrfWithRequisitionModelMixin,
+    BloodResultsModelMixin,
+    BaseUuidModel,
+):
+    action_name = BLOOD_RESULTS_GLU_ACTION
+    tracking_identifier_prefix = "GL"
+    lab_panel = blood_glucose_panel
+
+    requisition = models.ForeignKey(
+        limit_choices_to={"panel__name": blood_glucose_panel.name}, **requisition_fk_options
+    )
+
+    class Meta(CrfWithActionModelMixin.Meta, BaseUuidModel.Meta):
+        verbose_name = "Blood Result: Glucose (DUMMY)"
+        verbose_name_plural = "Blood Results: Glucose (DUMMY)"

meta_subject/models/blood_results/blood_results_hba1c.py

@@ -18,7 +18,6 @@ class BloodResultsHba1c(
     BaseUuidModel,
 ):
     action_name = BLOOD_RESULTS_HBA1C_ACTION
-    tracking_identifier_prefix = "HA"
     lab_panel = hba1c_panel
 
     requisition = models.ForeignKey(

meta_subject/models/blood_results/blood_results_ins.py

@@ -18,7 +18,6 @@ class BloodResultsIns(
     BaseUuidModel,
 ):
     action_name = BLOOD_RESULTS_INSULIN_ACTION
-    tracking_identifier_prefix = "IN"
     lab_panel = insulin_panel
 
     requisition = models.ForeignKey(

meta_subject/models/blood_results/blood_results_lft.py

@@ -31,7 +31,6 @@ class BloodResultsLft(
     BaseUuidModel,
 ):
     action_name = BLOOD_RESULTS_LFT_ACTION
-    tracking_identifier_prefix = "LF"
     lab_panel = lft_panel
 
     requisition = models.ForeignKey(

meta_subject/models/delivery.py

@@ -1,12 +1,12 @@
 # TODO: urine_bhcg form (probably not necessary)
 # TODO: if pos, take of study drug and estimate
 #  delivery date for the pregnancy outcomes form. See Form 25/26
+from clinicedc_constants import NOT_APPLICABLE, PATIENT, YES
 from django.apps import apps as django_apps
 from django.core.validators import MaxValueValidator, MinValueValidator
 from django.db import models
 from django_crypto_fields.fields import EncryptedTextField
 from edc_constants.choices import YES_NO, YES_NO_NA
-from edc_constants.constants import NOT_APPLICABLE, PATIENT, YES
 from edc_model.models import BaseUuidModel
 from edc_model.validators import datetime_not_future
 from edc_model_fields.fields import OtherCharField
@@ -38,8 +38,6 @@ class Delivery(
 
     action_name = DELIVERY_ACTION
 
-    tracking_identifier_prefix = "DL"
-
     report_datetime = models.DateTimeField(
         verbose_name="Report Date and Time", default=get_utcnow
     )
@@ -54,7 +52,7 @@ class Delivery(
 
     info_not_available_reason = models.TextField(
         verbose_name="If the report was not available, please explain?",
-        null=True,
+        default="",
         blank=True,
     )
 
@@ -112,7 +110,7 @@ class Delivery(
             "please give name of the facility"
         ),
         max_length=150,
-        null=True,
+        default="",
         blank=True,
     )
 
@@ -162,4 +160,4 @@ class Delivery(
     class Meta(CrfWithActionModelMixin.Meta, BaseUuidModel.Meta):
         verbose_name = "Delivery"
         verbose_name_plural = "Delivery"
-        unique_together = ["subject_visit", "delivery_datetime"]
+        unique_together = ("subject_visit", "delivery_datetime")

meta_subject/models/diabetes/__init__.py

@@ -1,2 +1,4 @@
 from .dm_endpoint import DmEndpoint
 from .dm_followup import DmFollowup
+
+__all__ = ["DmEndpoint", "DmFollowup"]

meta_subject/models/diabetes/dm_endpoint.py

@@ -1,6 +1,6 @@
+from clinicedc_constants import QUESTION_RETIRED
 from django.db import models
 from edc_constants.choices import YES_NO, YES_NO_RETIRED
-from edc_constants.constants import QUESTION_RETIRED
 from edc_model.models import BaseUuidModel
 from edc_model_fields.fields import OtherCharField
 
@@ -16,7 +16,7 @@ class DmEndpoint(CrfModelMixin, BaseUuidModel):
         verbose_name="Was the patient referred because the diabetes endpoint was reached?",
         max_length=15,
         choices=YES_NO,
-        null=True,
+        default="",
         blank=False,
         help_text="If YES, the EDC will check for the patient on the Endpoints report.",
     )
@@ -32,7 +32,7 @@ class DmEndpoint(CrfModelMixin, BaseUuidModel):
     )
 
     # retired
-    dx_initiated_by_other = OtherCharField(null=True, blank=True)
+    dx_initiated_by_other = OtherCharField(blank=True)
 
     # retired
     dx_tmg = models.CharField(
@@ -50,11 +50,11 @@ class DmEndpoint(CrfModelMixin, BaseUuidModel):
     # retired
     dx_no_tmg_reason = models.TextField(
         verbose_name="If NO, please explain why this case was not discussed with the TMG",
-        null=True,
+        default="",
         blank=True,
     )
 
-    comments = models.TextField(verbose_name="Any other comments", null=True, blank=True)
+    comments = models.TextField(verbose_name="Any other comments", default="", blank=True)
 
     class Meta(CrfModelMixin.Meta, BaseUuidModel.Meta):
         verbose_name = "Diabetes endpoint"

meta_subject/models/diabetes/dm_followup.py

@@ -1,10 +1,10 @@
+from clinicedc_constants import NOT_APPLICABLE, QUESTION_RETIRED
 from django.core.validators import MaxValueValidator, MinValueValidator
 from django.db import models
-from django.utils.html import format_html
+from django.utils.safestring import mark_safe
 from edc_action_item.models import ActionItem
 from edc_adherence.choices import MISSED_PILLS
 from edc_constants.choices import YES_NO, YES_NO_NA
-from edc_constants.constants import NOT_APPLICABLE, QUESTION_RETIRED
 from edc_model.models import BaseUuidModel
 from edc_model_fields.fields import OtherCharField
 
@@ -22,7 +22,6 @@ from ...model_mixins import CrfWithActionModelMixin
 
 
 class DmFollowup(CrfWithActionModelMixin, BaseUuidModel):
-
     action_name = DM_FOLLOWUP_ACTION
 
     referral_date = models.DateField(
@@ -63,7 +62,7 @@ class DmFollowup(CrfWithActionModelMixin, BaseUuidModel):
     facility_attended = models.CharField(
         verbose_name="If 'Yes', please give the name of the facility you attended",
         max_length=50,
-        null=True,
+        default="",
         blank=True,
     )
 
@@ -181,15 +180,15 @@ class DmFollowup(CrfWithActionModelMixin, BaseUuidModel):
         verbose_name="Visual score",
         max_length=3,
         help_text="%",
-        null=True,
+        default="",
         blank=True,
     )
 
     visual_score_confirmed = models.IntegerField(
-        verbose_name=format_html(
+        verbose_name=mark_safe(
             "<B><font color='orange'>Interviewer</font></B>: "
             "please transcribe the score indicated from above."
-        ),
+        ),  # nosec B308
         validators=[MinValueValidator(0), MaxValueValidator(100)],
         help_text="%",
         null=True,
@@ -200,7 +199,7 @@ class DmFollowup(CrfWithActionModelMixin, BaseUuidModel):
         verbose_name="When was the last time you missed your study pill?",
         max_length=25,
         choices=MISSED_PILLS,
-        null=True,
+        default="",
         blank=True,
     )
 

meta_subject/models/diet_and_lifestyle.py

@@ -8,11 +8,11 @@ from ..model_mixins import CrfModelMixin
 class DietAndLifestyle(CrfModelMixin, BaseUuidModel):
     diet_and_lifestyle = models.CharField(
         verbose_name=(
-            "Has the participant received the META3 " "approved diet and lifetsyle counseling?"
+            "Has the participant received the META3 approved diet and lifetsyle counseling?"
         ),
         max_length=15,
         choices=YES_NO,
-        null=True,
+        default="",
         blank=False,
         help_text="This response is not criteria for eligibility",
     )