meta-edc 0.3.7__py3-none-any.whl → 0.3.15__py3-none-any.whl

meta_subject/admin/subject_visit_admin.py

@@ -1,6 +1,7 @@
 from django.contrib import admin
 from django_audit_fields.admin import audit_fieldset_tuple
 from edc_model_admin.history import SimpleHistoryAdmin
+from edc_sites.admin import SiteModelAdminMixin
 from edc_visit_schedule.fieldsets import visit_schedule_fieldset_tuple
 from edc_visit_tracking.modeladmin_mixins import VisitModelAdminMixin
 
@@ -11,7 +12,9 @@ from .modeladmin import ModelAdminMixin
 
 
 @admin.register(SubjectVisit, site=meta_subject_admin)
-class SubjectVisitAdmin(VisitModelAdminMixin, ModelAdminMixin, SimpleHistoryAdmin):
+class SubjectVisitAdmin(
+    VisitModelAdminMixin, SiteModelAdminMixin, ModelAdminMixin, SimpleHistoryAdmin
+):
     show_dashboard_in_list_display_pos = 2
 
     form = SubjectVisitForm

meta_subject/baker_recipes.py

@@ -11,6 +11,7 @@ from .models import (
     BirthOutcomes,
     Delivery,
     FollowupExamination,
+    HealthEconomicsUpdate,
     MedicationAdherence,
     SubjectRequisition,
     SubjectVisit,
@@ -103,3 +104,8 @@ birthoutcomes = Recipe(
     birth_outcome=LIVE_AT_TERM,
     birth_weight=320,
 )
+
+healtheconomicsupdate = Recipe(
+    HealthEconomicsUpdate,
+    report_datetime=get_utcnow(),
+)

meta_subject/choices.py

@@ -10,6 +10,7 @@ from edc_constants.constants import (
     OPEN,
     OTHER,
     PATIENT,
+    PENDING,
     PRESENT,
     PRESENT_WITH_REINFORCEMENT,
     YES,
@@ -80,6 +81,13 @@ DYSLIPIDAEMIA_RX_CHOICES = (
     (NOT_APPLICABLE, _("Not applicable")),
 )
 
+ENDPOINT_CHOICES = (
+    (YES, _(YES)),
+    (PENDING, _("No. A repeat FBG will be scheduled")),
+    (NO, _(NO)),
+    (NOT_APPLICABLE, _("Not applicable")),
+)
+
 FEELING_DURATION_CHOICES = (
     (ALL_OF_THE_TIME, _("All of the time")),
     (MOST_OF_THE_TIME, _("Most of the time")),

meta_subject/constants.py

@@ -1,9 +1,11 @@
 from datetime import date
 
 ALL_OF_THE_TIME = "all_of_the_time"
+AMENDMENT_DATE = date(2023, 11, 24)
 APPT = "appt"
 APPT_OTHER = "other_routine_appt"
 DELIVERY_ACTION = "delivery_action"
+DM_FOLLOWUP_ACTION = "dm_followup_action"
 FOLLOWUP_EXAMINATION_ACTION = "followup-examination-ae"
 GOOD_BIT_OF_THE_TIME = "good_bit_of_the_time"
 LITTLE_OF_THE_TIME = "little_of_the_time"
@@ -16,4 +18,3 @@ NONE_OF_THE_TIME = "none_of_the_time"
 NO_COMPLICATIONS = "no_complications"
 SOME_OF_THE_TIME = "some_of_the_time"
 URINE_PREGNANCY_ACTION = "urine_pregnancy_action"
-AMENDMENT_DATE = date(2023, 11, 24)

meta_subject/form_validators/__init__.py

@@ -1,6 +1,7 @@
 from .birth_outcomes_form_validator import BirthOutcomesFormValidator
 from .delivery_form_validator import DeliveryFormValidator
-from .dm_referral_followup_form_validator import DmReferralFollowupFormValidator
+from .dm_diagnosis_form_validator import DmDiagnosisFormValidator
+from .dm_followup_form_validator import DmFollowupFormValidator
 from .egfr_drop_notification_form_validator import EgfrDropNotificationFormValidator
 from .followup_examination_form_validator import FollowupExaminationFormValidator
 from .glucose_form_validator import GlucoseFormValidator

meta_subject/form_validators/dm_diagnosis_form_validator.py

@@ -0,0 +1,38 @@
+from edc_constants.constants import NO, YES
+from edc_crf.crf_form_validator import CrfFormValidator
+from edc_form_validators import INVALID_ERROR
+
+
+class DmDiagnosisFormValidator(CrfFormValidator):
+    def clean(self):
+        # dx_date must be on or before report datetime
+        if (
+            self.cleaned_data.get("report_datetime")
+            and self.cleaned_data.get("dx_date")
+            and self.cleaned_data.get("dx_date")
+            > self.cleaned_data.get("report_datetime").date()
+        ):
+            self.raise_validation_error(
+                {"dx_date": "Invalid. Expected a date on or before the report date above. "},
+                INVALID_ERROR,
+            )
+
+        self.required_if(YES, field="dx_tmg", field_required="dx_tmg_date")
+
+        if (
+            self.cleaned_data.get("dx_tmg_date")
+            and self.cleaned_data.get("dx_date")
+            and self.cleaned_data.get("dx_tmg_date") > self.cleaned_data.get("dx_date")
+        ):
+            self.raise_validation_error(
+                {
+                    "dx_tmg_date": (
+                        "Invalid. Expected a date on or before the diagnosis date above. "
+                    )
+                },
+                INVALID_ERROR,
+            )
+
+        self.required_if(NO, field="dx_tmg", field_required="dx_no_tmg_reason")
+
+        # TODO: do we check for lab results listed in the inline?

meta_subject/form_validators/dm_dx_result_form_validator.py

@@ -0,0 +1,7 @@
+from edc_form_validators import FormValidator
+
+
+class DmDiagnosisFormValidator(FormValidator):
+    def clean(self):
+        self.required_if_true(self.cleaned_data.get("report_date"), field_required="utestid")
+        self.required_if_true(self.cleaned_data.get("utestid"), field_required="value")

meta_subject/form_validators/{dm_referral_followup_form_validator.py → dm_followup_form_validator.py}

@@ -1,11 +1,15 @@
 from django import forms
+from django.core.exceptions import ObjectDoesNotExist
 from edc_constants.constants import NO, OTHER, YES
 from edc_crf.crf_form_validator import CrfFormValidator
 from edc_form_validators import INVALID_ERROR
+from edc_utils import formatted_date
 from edc_utils.date import to_local
 
+from meta_prn.models import DmReferral
 
-class DmReferralFollowupFormValidator(CrfFormValidator):
+
+class DmFollowupFormValidator(CrfFormValidator):
     def clean(self):
 
         # referral_date must be before report datetime
@@ -15,10 +19,31 @@ class DmReferralFollowupFormValidator(CrfFormValidator):
             and self.cleaned_data.get("referral_date") >= to_local(self.report_datetime).date()
         ):
             self.raise_validation_error(
-                {"referral_date": "Invalid. Cannot be on or after report date"},
+                {"referral_date": "Invalid. Expected a date prior to the report date above."},
                 INVALID_ERROR,
             )
 
+        # try to match referral date to the referal form
+        try:
+            dm_referral = DmReferral.objects.get(subject_identifier=self.subject_identifier)
+        except ObjectDoesNotExist:
+            self.raise_validation_error(
+                {"__all__": "Original Referral form not found."}, INVALID_ERROR
+            )
+        else:
+            if dm_referral.referral_date != self.cleaned_data.get("referral_date"):
+                referral_dt = formatted_date(dm_referral.referral_date)
+                report_dt = formatted_date(to_local(dm_referral.report_datetime).date())
+                self.raise_validation_error(
+                    {
+                        "referral_date": (
+                            f"Invalid. Expected `{referral_dt}` "
+                            f"based on the referral form submitted on {report_dt}."
+                        )
+                    },
+                    INVALID_ERROR,
+                )
+
         # Diabetes clinic attendance
         self.m2m_required_if(
             NO,
@@ -147,6 +172,20 @@ class DmReferralFollowupFormValidator(CrfFormValidator):
                 INVALID_ERROR,
             )
 
+        # dm_medications_init_date must be on or after attended_date
+        if self.cleaned_data.get("dm_medications_init_date") and self.cleaned_data.get(
+            "dm_medications_init_date"
+        ) < self.cleaned_data.get("attended_date"):
+            self.raise_validation_error(
+                {
+                    "dm_medications_init_date": (
+                        "Invalid. Expected a date on or after date patient "
+                        "attended the health facility."
+                    )
+                },
+                INVALID_ERROR,
+            )
+
         self.m2m_required_if(
             YES,
             field="on_dm_medications",

meta_subject/forms/__init__.py

@@ -10,6 +10,7 @@ from .blood_results import (
 from .complications_glycemia_form import ComplicationsGlycemiaForm
 from .concomitant_medication_form import ConcomitantMedicationForm
 from .delivery_form import DeliveryForm
+from .diabetes import DmDiagnosisForm, DmDxResultForm, DmFollowupForm
 from .egfr_drop_notification_form import EgfrDropNotificationForm
 from .eq53d3l_form import Eq5d3lForm
 from .followup_examination_form import FollowupExaminationForm

meta_subject/forms/diabetes/__init__.py

@@ -0,0 +1,3 @@
+from .dm_diagnosis_form import DmDiagnosisForm
+from .dm_dx_result_form import DmDxResultForm
+from .dm_followup_form import DmFollowupForm

meta_subject/forms/diabetes/dm_diagnosis_form.py

@@ -0,0 +1,13 @@
+from django import forms
+from edc_crf.modelform_mixins import CrfModelFormMixin
+
+from ...form_validators import DmDiagnosisFormValidator
+from ...models import DmDiagnosis
+
+
+class DmDiagnosisForm(CrfModelFormMixin, forms.ModelForm):
+    form_validator_cls = DmDiagnosisFormValidator
+
+    class Meta:
+        model = DmDiagnosis
+        fields = "__all__"

meta_subject/forms/diabetes/dm_dx_result_form.py

@@ -0,0 +1,11 @@
+from django import forms
+
+from ...models import DmDxResult
+
+
+class DmDxResultForm(forms.ModelForm):
+    # form_validator_cls = DmDxResultFormValidator
+
+    class Meta:
+        model = DmDxResult
+        fields = "__all__"

meta_subject/forms/diabetes/dm_followup_form.py

@@ -0,0 +1,25 @@
+from django import forms
+from edc_action_item.forms import ActionItemCrfFormMixin
+from edc_crf.modelform_mixins import CrfModelFormMixin
+from edc_model_fields.widgets import SliderWidget
+
+from ...form_validators import DmFollowupFormValidator
+from ...models import DmFollowup
+
+
+class DmFollowupForm(CrfModelFormMixin, ActionItemCrfFormMixin, forms.ModelForm):
+    form_validator_cls = DmFollowupFormValidator
+
+    visual_score_slider = forms.CharField(
+        label="Visual Score", widget=SliderWidget(attrs={"min": 0, "max": 100})
+    )
+
+    class Meta:
+        model = DmFollowup
+        fields = "__all__"
+        help_text = {"action_identifier": "(read-only)"}
+        widgets = {
+            "action_identifier": forms.TextInput(
+                attrs={"required": False, "readonly": "readonly"}
+            ),
+        }

meta_subject/forms/glucose_fbg_form.py

@@ -1,31 +1,53 @@
+from decimal import Decimal
+
 from django import forms
+from edc_constants.constants import NO, YES
 from edc_crf.crf_form_validator import CrfFormValidator
 from edc_crf.modelform_mixins import CrfModelFormMixin
 from edc_form_validators import INVALID_ERROR
 from edc_glucose.utils import validate_glucose_as_millimoles_per_liter
-from edc_lab_results.form_validator_mixins import (
-    BloodResultsFormValidatorMixin,
-    BloodResultsGluFormValidatorMixin,
-)
 
 from ..models import GlucoseFbg
 
 
-class GlucoseFbgFormValidator(
-    BloodResultsGluFormValidatorMixin, BloodResultsFormValidatorMixin, CrfFormValidator
-):
+class GlucoseFbgFormValidator(CrfFormValidator):
     def clean(self):
-        if (
-            self.cleaned_data.get("report_datetime")
-            and self.cleaned_data.get("assay_datetime")
-            and self.cleaned_data.get("assay_datetime")
-            < self.cleaned_data.get("report_datetime")
-        ):
+        converted_value = None
+        self.required_if(YES, field="fasting", field_required="fasting_duration_str")
+        self.required_if(NO, field="fbg_performed", field_required="fbg_not_performed_reason")
+        self.required_if(YES, field="fbg_performed", field_required="fbg_datetime")
+        if self.cleaned_data.get("fbg_datetime") and self.cleaned_data.get(
+            "fbg_datetime"
+        ) < self.cleaned_data.get("report_datetime"):
             self.raise_validation_error(
-                {"assay_datetime": "Cannot be before report date"}, INVALID_ERROR
+                {"fbg_datetime": "Invalid. Must be on or after report date above"},
+                INVALID_ERROR,
+            )
+        self.required_if(YES, field="fbg_performed", field_required="fbg_value")
+        if self.cleaned_data.get("fbg_value") is not None:
+            converted_value = validate_glucose_as_millimoles_per_liter(
+                "fbg", self.cleaned_data
             )
-        if self.cleaned_data.get("glucose_value") is not None:
-            validate_glucose_as_millimoles_per_liter("glucose", self.cleaned_data)
+
+        self.applicable_if(YES, field="fbg_performed", field_applicable="fbg_units")
+
+        # repeat_fbg_date
+        condition = converted_value and converted_value >= Decimal("7.0")
+        self.required_if_true(condition, field_required="repeat_fbg_date")
+        if self.cleaned_data.get("repeat_fbg_date") and self.cleaned_data.get("fbg_datetime"):
+            diffdays = (
+                self.cleaned_data.get("repeat_fbg_date")
+                - self.cleaned_data.get("fbg_datetime").date()
+            ).days
+            if not (7 <= diffdays <= 10):
+                self.raise_validation_error(
+                    {
+                        "repeat_fbg_date": (
+                            f"Must be 7 to 10 days from date measured above. Got {diffdays}."
+                        )
+                    },
+                    INVALID_ERROR,
+                )
 
 
 class GlucoseFbgForm(CrfModelFormMixin, forms.ModelForm):

meta_subject/forms/subject_visit_form.py

@@ -5,6 +5,9 @@ from edc_offstudy.modelform_mixins import OffstudyNonCrfModelFormMixin
 from edc_visit_tracking.form_validators import VisitFormValidator
 from edc_visit_tracking.modelform_mixins import VisitTrackingModelFormMixin
 
+from meta_prn.models import OffStudyMedication
+from meta_visit_schedule.constants import SCHEDULE_DM_REFERRAL
+
 from ..models import SubjectVisit
 
 
@@ -21,6 +24,19 @@ class SubjectVisitForm(
 ):
     form_validator_cls = SubjectVisitFormValidator
 
+    def clean(self):
+        cleaned_data = super().clean()
+        if (
+            self.cleaned_data.get("appointment").schedule_name == SCHEDULE_DM_REFERRAL
+            and not OffStudyMedication.objects.filter(
+                subject_identifier=self.subject_identifier
+            ).exists()
+        ):
+            raise forms.ValidationError(
+                f"Submit form `{OffStudyMedication._meta.verbose_name}` first."
+            )
+        return cleaned_data
+
     class Meta:
         model = SubjectVisit
         fields = "__all__"

meta_subject/metadata_rules/metadata_rules.py

@@ -41,6 +41,20 @@ class HealthEconomicsRuleGroup(CrfRuleGroup):
         source_model = "meta_subject.subjectvisit"
 
 
+@register()
+class HealthEconomicsUpdateRuleGroup(CrfRuleGroup):
+    hecon = CrfRule(
+        predicate=pc.health_economics_update_required,
+        consequence=REQUIRED,
+        alternative=NOT_REQUIRED,
+        target_models=["healtheconomicsupdate"],
+    )
+
+    class Meta:
+        app_label = "meta_subject"
+        source_model = "meta_subject.subjectvisit"
+
+
 @register()
 class HbA1cCrfRuleGroup(CrfRuleGroup):
     hba1c = CrfRule(

meta_subject/metadata_rules/predicates.py

@@ -173,6 +173,28 @@ class Predicates(PersistantSingletonMixin):
                 required = True
         return required
 
+    def health_economics_update_required(self, visit, **kwargs) -> bool:
+        """Returns true if `healtheconomicsupdate` was not completed at
+        month 3 or ever.
+
+        `healtheconomicsupdate` is a singleton CRF.
+        """
+        required = False
+        model_cls = django_apps.get_model(f"{self.app_label}.healtheconomicsupdate")
+        try:
+            obj = model_cls.objects.get(
+                subject_visit__subject_identifier=visit.subject_identifier,
+            )
+        except ObjectDoesNotExist:
+            obj = None
+        if (
+            not obj
+            and visit.appointment.visit_code_sequence == 0
+            and visit.appointment.visit_code not in [DAY1, WEEK2, MONTH1]
+        ):
+            required = True
+        return required
+
     def mnsi_required(self, visit, **kwargs) -> bool:
         """Returns True if MNSI assessment was not performed at the
         1M, 3M or 6M visits.

meta_subject/migrations/0181_dmreferralfollowup_action_identifier_and_more.py

@@ -0,0 +1,143 @@
+# Generated by Django 4.2.11 on 2024-04-03 19:45
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("edc_action_item", "0037_remove_actionitem_reference_model_and_more"),
+        ("meta_subject", "0180_dmreferralfollowup_missed_referral_reasons_and_more"),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="dmreferralfollowup",
+            name="action_identifier",
+            field=models.CharField(blank=True, max_length=50, null=True, unique=True),
+        ),
+        migrations.AddField(
+            model_name="dmreferralfollowup",
+            name="action_item",
+            field=models.ForeignKey(
+                blank=True,
+                null=True,
+                on_delete=django.db.models.deletion.PROTECT,
+                to="edc_action_item.actionitem",
+            ),
+        ),
+        migrations.AddField(
+            model_name="dmreferralfollowup",
+            name="action_item_reason",
+            field=models.TextField(editable=False, null=True),
+        ),
+        migrations.AddField(
+            model_name="dmreferralfollowup",
+            name="parent_action_identifier",
+            field=models.CharField(
+                blank=True,
+                help_text="action identifier that links to parent reference model instance.",
+                max_length=30,
+                null=True,
+            ),
+        ),
+        migrations.AddField(
+            model_name="dmreferralfollowup",
+            name="parent_action_item",
+            field=models.ForeignKey(
+                blank=True,
+                null=True,
+                on_delete=django.db.models.deletion.PROTECT,
+                related_name="+",
+                to="edc_action_item.actionitem",
+            ),
+        ),
+        migrations.AddField(
+            model_name="dmreferralfollowup",
+            name="related_action_identifier",
+            field=models.CharField(
+                blank=True,
+                help_text="action identifier that links to related reference model instance.",
+                max_length=30,
+                null=True,
+            ),
+        ),
+        migrations.AddField(
+            model_name="dmreferralfollowup",
+            name="related_action_item",
+            field=models.ForeignKey(
+                blank=True,
+                null=True,
+                on_delete=django.db.models.deletion.PROTECT,
+                related_name="+",
+                to="edc_action_item.actionitem",
+            ),
+        ),
+        migrations.AddField(
+            model_name="historicaldmreferralfollowup",
+            name="action_identifier",
+            field=models.CharField(blank=True, db_index=True, max_length=50, null=True),
+        ),
+        migrations.AddField(
+            model_name="historicaldmreferralfollowup",
+            name="action_item",
+            field=models.ForeignKey(
+                blank=True,
+                db_constraint=False,
+                null=True,
+                on_delete=django.db.models.deletion.DO_NOTHING,
+                related_name="+",
+                to="edc_action_item.actionitem",
+            ),
+        ),
+        migrations.AddField(
+            model_name="historicaldmreferralfollowup",
+            name="action_item_reason",
+            field=models.TextField(editable=False, null=True),
+        ),
+        migrations.AddField(
+            model_name="historicaldmreferralfollowup",
+            name="parent_action_identifier",
+            field=models.CharField(
+                blank=True,
+                help_text="action identifier that links to parent reference model instance.",
+                max_length=30,
+                null=True,
+            ),
+        ),
+        migrations.AddField(
+            model_name="historicaldmreferralfollowup",
+            name="parent_action_item",
+            field=models.ForeignKey(
+                blank=True,
+                db_constraint=False,
+                null=True,
+                on_delete=django.db.models.deletion.DO_NOTHING,
+                related_name="+",
+                to="edc_action_item.actionitem",
+            ),
+        ),
+        migrations.AddField(
+            model_name="historicaldmreferralfollowup",
+            name="related_action_identifier",
+            field=models.CharField(
+                blank=True,
+                help_text="action identifier that links to related reference model instance.",
+                max_length=30,
+                null=True,
+            ),
+        ),
+        migrations.AddField(
+            model_name="historicaldmreferralfollowup",
+            name="related_action_item",
+            field=models.ForeignKey(
+                blank=True,
+                db_constraint=False,
+                null=True,
+                on_delete=django.db.models.deletion.DO_NOTHING,
+                related_name="+",
+                to="edc_action_item.actionitem",
+            ),
+        ),
+    ]

meta_subject/migrations/0182_rename_dmreferralfollowup_dmfollowup_and_more.py

@@ -0,0 +1,54 @@
+# Generated by Django 4.2.11 on 2024-04-04 14:18
+
+from django.conf import settings
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("sites", "0002_alter_domain_unique"),
+        migrations.swappable_dependency(settings.AUTH_USER_MODEL),
+        ("edc_action_item", "0037_remove_actionitem_reference_model_and_more"),
+        ("meta_lists", "0018_missedreferralreasons"),
+        ("meta_subject", "0181_dmreferralfollowup_action_identifier_and_more"),
+    ]
+
+    operations = [
+        migrations.RenameModel(
+            old_name="DmReferralFollowup",
+            new_name="DmFollowup",
+        ),
+        migrations.RenameModel(
+            old_name="HistoricalDmReferralFollowup",
+            new_name="HistoricalDmFollowup",
+        ),
+        migrations.AlterModelOptions(
+            name="dmfollowup",
+            options={
+                "default_manager_name": "objects",
+                "default_permissions": ("add", "change", "delete", "view", "export", "import"),
+                "verbose_name": "Diabetes follow-up after referral",
+                "verbose_name_plural": "Diabetes follow-up after referral",
+            },
+        ),
+        migrations.AlterModelOptions(
+            name="historicaldmfollowup",
+            options={
+                "get_latest_by": ("history_date", "history_id"),
+                "ordering": ("-history_date", "-history_id"),
+                "verbose_name": "historical Diabetes follow-up after referral",
+                "verbose_name_plural": "historical Diabetes follow-up after referral",
+            },
+        ),
+        migrations.RenameIndex(
+            model_name="dmfollowup",
+            new_name="meta_subjec_subject_dd09d5_idx",
+            old_name="meta_subjec_subject_cfb7da_idx",
+        ),
+        migrations.RenameIndex(
+            model_name="dmfollowup",
+            new_name="meta_subjec_subject_1313a7_idx",
+            old_name="meta_subjec_subject_257846_idx",
+        ),
+    ]

meta_subject/migrations/0183_alter_dmfollowup_on_dm_medications_and_more.py

@@ -0,0 +1,31 @@
+# Generated by Django 4.2.11 on 2024-04-05 20:19
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("meta_subject", "0182_rename_dmreferralfollowup_dmfollowup_and_more"),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="dmfollowup",
+            name="on_dm_medications",
+            field=models.CharField(
+                choices=[("Yes", "Yes"), ("No", "No"), ("N/A", "Not applicable")],
+                max_length=25,
+                verbose_name="Are you currently taking any drug therapy for diabetes?",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="historicaldmfollowup",
+            name="on_dm_medications",
+            field=models.CharField(
+                choices=[("Yes", "Yes"), ("No", "No"), ("N/A", "Not applicable")],
+                max_length=25,
+                verbose_name="Are you currently taking any drug therapy for diabetes?",
+            ),
+        ),
+    ]