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

meta_screening/migrations/0064_remove_historicalscreeningpartone_fasting_duration_minutes_and_more.py

@@ -0,0 +1,126 @@
+# Generated by Django 4.2.11 on 2024-05-16 00:51
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        (
+            "meta_screening",
+            "0063_alter_historicalscreeningpartone_fasting_duration_str_and_more",
+        ),
+    ]
+
+    operations = [
+        migrations.RemoveField(
+            model_name="historicalscreeningpartone",
+            name="fasting_duration_minutes",
+        ),
+        migrations.RemoveField(
+            model_name="historicalscreeningpartone",
+            name="repeat_fasting_duration_minutes",
+        ),
+        migrations.RemoveField(
+            model_name="historicalscreeningpartthree",
+            name="fasting_duration_minutes",
+        ),
+        migrations.RemoveField(
+            model_name="historicalscreeningpartthree",
+            name="repeat_fasting_duration_minutes",
+        ),
+        migrations.RemoveField(
+            model_name="historicalscreeningparttwo",
+            name="fasting_duration_minutes",
+        ),
+        migrations.RemoveField(
+            model_name="historicalscreeningparttwo",
+            name="repeat_fasting_duration_minutes",
+        ),
+        migrations.RemoveField(
+            model_name="historicalsubjectscreening",
+            name="fasting_duration_minutes",
+        ),
+        migrations.RemoveField(
+            model_name="historicalsubjectscreening",
+            name="repeat_fasting_duration_minutes",
+        ),
+        migrations.RemoveField(
+            model_name="subjectscreening",
+            name="fasting_duration_minutes",
+        ),
+        migrations.RemoveField(
+            model_name="subjectscreening",
+            name="repeat_fasting_duration_minutes",
+        ),
+        migrations.AddField(
+            model_name="historicalscreeningpartone",
+            name="fasting_duration_delta",
+            field=models.DurationField(
+                blank=True, help_text="system calculated value", null=True
+            ),
+        ),
+        migrations.AddField(
+            model_name="historicalscreeningpartone",
+            name="repeat_fasting_duration_delta",
+            field=models.DurationField(
+                blank=True, help_text="system calculated value", null=True
+            ),
+        ),
+        migrations.AddField(
+            model_name="historicalscreeningpartthree",
+            name="fasting_duration_delta",
+            field=models.DurationField(
+                blank=True, help_text="system calculated value", null=True
+            ),
+        ),
+        migrations.AddField(
+            model_name="historicalscreeningpartthree",
+            name="repeat_fasting_duration_delta",
+            field=models.DurationField(
+                blank=True, help_text="system calculated value", null=True
+            ),
+        ),
+        migrations.AddField(
+            model_name="historicalscreeningparttwo",
+            name="fasting_duration_delta",
+            field=models.DurationField(
+                blank=True, help_text="system calculated value", null=True
+            ),
+        ),
+        migrations.AddField(
+            model_name="historicalscreeningparttwo",
+            name="repeat_fasting_duration_delta",
+            field=models.DurationField(
+                blank=True, help_text="system calculated value", null=True
+            ),
+        ),
+        migrations.AddField(
+            model_name="historicalsubjectscreening",
+            name="fasting_duration_delta",
+            field=models.DurationField(
+                blank=True, help_text="system calculated value", null=True
+            ),
+        ),
+        migrations.AddField(
+            model_name="historicalsubjectscreening",
+            name="repeat_fasting_duration_delta",
+            field=models.DurationField(
+                blank=True, help_text="system calculated value", null=True
+            ),
+        ),
+        migrations.AddField(
+            model_name="subjectscreening",
+            name="fasting_duration_delta",
+            field=models.DurationField(
+                blank=True, help_text="system calculated value", null=True
+            ),
+        ),
+        migrations.AddField(
+            model_name="subjectscreening",
+            name="repeat_fasting_duration_delta",
+            field=models.DurationField(
+                blank=True, help_text="system calculated value", null=True
+            ),
+        ),
+    ]

meta_screening/migrations/0065_auto_20240516_0352.py

@@ -0,0 +1,31 @@
+# Generated by Django 4.2.11 on 2024-05-16 00:52
+from django.db import migrations
+from edc_model.utils import duration_hm_to_timedelta
+from tqdm import tqdm
+
+
+def update_duration(apps, schema_editor):
+    model_cls = apps.get_model("meta_screening.subjectscreening")
+    qs = model_cls.objects.all()
+    total = qs.count()
+    for obj in tqdm(qs, total=total):
+        if obj.fasting_duration_str:
+            tdelta = duration_hm_to_timedelta(obj.fasting_duration_str)
+            obj.fasting_duration_delta = tdelta
+            obj.save_base(update_fields=["fasting_duration_delta"])
+        if obj.repeat_fasting_duration_str:
+            tdelta = duration_hm_to_timedelta(obj.repeat_fasting_duration_str)
+            obj.repeat_fasting_duration_delta = tdelta
+            obj.save_base(update_fields=["repeat_fasting_duration_delta"])
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        (
+            "meta_screening",
+            "0064_remove_historicalscreeningpartone_fasting_duration_minutes_and_more",
+        ),
+    ]
+
+    operations = [migrations.RunPython(update_duration)]

meta_screening/migrations/0066_alter_historicalscreeningpartone_fasting_duration_delta_and_more.py

@@ -0,0 +1,103 @@
+# Generated by Django 4.2.11 on 2024-05-16 01:21
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("meta_screening", "0065_auto_20240516_0352"),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="historicalscreeningpartone",
+            name="fasting_duration_delta",
+            field=models.DurationField(
+                blank=True,
+                help_text="system calculated to microseconds. (hours=microseconds/3.6e+9)",
+                null=True,
+            ),
+        ),
+        migrations.AlterField(
+            model_name="historicalscreeningpartone",
+            name="repeat_fasting_duration_delta",
+            field=models.DurationField(
+                blank=True,
+                help_text="system calculated to microseconds. (hours=microseconds/3.6e+9)",
+                null=True,
+            ),
+        ),
+        migrations.AlterField(
+            model_name="historicalscreeningpartthree",
+            name="fasting_duration_delta",
+            field=models.DurationField(
+                blank=True,
+                help_text="system calculated to microseconds. (hours=microseconds/3.6e+9)",
+                null=True,
+            ),
+        ),
+        migrations.AlterField(
+            model_name="historicalscreeningpartthree",
+            name="repeat_fasting_duration_delta",
+            field=models.DurationField(
+                blank=True,
+                help_text="system calculated to microseconds. (hours=microseconds/3.6e+9)",
+                null=True,
+            ),
+        ),
+        migrations.AlterField(
+            model_name="historicalscreeningparttwo",
+            name="fasting_duration_delta",
+            field=models.DurationField(
+                blank=True,
+                help_text="system calculated to microseconds. (hours=microseconds/3.6e+9)",
+                null=True,
+            ),
+        ),
+        migrations.AlterField(
+            model_name="historicalscreeningparttwo",
+            name="repeat_fasting_duration_delta",
+            field=models.DurationField(
+                blank=True,
+                help_text="system calculated to microseconds. (hours=microseconds/3.6e+9)",
+                null=True,
+            ),
+        ),
+        migrations.AlterField(
+            model_name="historicalsubjectscreening",
+            name="fasting_duration_delta",
+            field=models.DurationField(
+                blank=True,
+                help_text="system calculated to microseconds. (hours=microseconds/3.6e+9)",
+                null=True,
+            ),
+        ),
+        migrations.AlterField(
+            model_name="historicalsubjectscreening",
+            name="repeat_fasting_duration_delta",
+            field=models.DurationField(
+                blank=True,
+                help_text="system calculated to microseconds. (hours=microseconds/3.6e+9)",
+                null=True,
+            ),
+        ),
+        migrations.AlterField(
+            model_name="subjectscreening",
+            name="fasting_duration_delta",
+            field=models.DurationField(
+                blank=True,
+                help_text="system calculated to microseconds. (hours=microseconds/3.6e+9)",
+                null=True,
+            ),
+        ),
+        migrations.AlterField(
+            model_name="subjectscreening",
+            name="repeat_fasting_duration_delta",
+            field=models.DurationField(
+                blank=True,
+                help_text="system calculated to microseconds. (hours=microseconds/3.6e+9)",
+                null=True,
+            ),
+        ),
+    ]

meta_screening/models/__init__.py

@@ -1,4 +1,4 @@
-from .icp_referral import IcpReferral
+# from .icp_referral import IcpReferral
 from .proxy_models import ScreeningPartOne, ScreeningPartThree, ScreeningPartTwo
 from .signals import update_p3_ltfu_on_post_save
 from .subject_refusal import SubjectRefusal

meta_screening/tests/meta_test_case_mixin.py

@@ -21,7 +21,7 @@ from model_bakery import baker
 
 from meta_edc.meta_version import PHASE_THREE
 from meta_pharmacy.prepare_meta_pharmacy import prepare_meta_pharmacy
-from meta_sites import fqdn
+from meta_sites.sites import domain_suffix
 from meta_subject.models import SubjectVisit
 from meta_visit_schedule.constants import DAY1
 
@@ -40,7 +40,7 @@ from .options import (
 
 
 class MetaTestCaseMixin(AppointmentTestCaseMixin):
-    fqdn = fqdn
+    fqdn = domain_suffix
 
     default_sites = sites.get_by_country("tanzania", aslist=True)
 

meta_screening/tests/options.py

@@ -54,18 +54,18 @@ def get_part_one_eligible_options():
     return options
 
 
-def get_part_two_eligible_options():
+def get_part_two_eligible_options(report_datetime: datetime = None) -> dict:
     options = dict(
         acute_condition=NO,
         acute_metabolic_acidosis=NO,
         advised_to_fast=YES,
         alcoholism=NO,
         already_fasted=NO,
-        appt_datetime=now + relativedelta(days=10),
+        appt_datetime=report_datetime or (now + relativedelta(days=10)),
         congestive_heart_failure=NO,
         liver_disease=NO,
         metformin_sensitivity=NO,
-        part_two_report_datetime=now,
+        part_two_report_datetime=report_datetime or now,
         renal_function_condition=NO,
         tissue_hypoxia_condition=NO,
         has_dm=NO,

meta_sites/__init__.py

@@ -1 +0,0 @@
-from .sites import all_sites, fqdn  # noqa

meta_sites/sites.py

@@ -1,7 +1,8 @@
+from django.conf import settings
 from edc_sites.single_site import SingleSite
 from edc_sites.site import sites as site_sites
 
-fqdn = "meta3.clinicedc.org"
+domain_suffix = settings.EDC_SITES_DOMAIN_SUFFIX
 languages = ["sw", "en", "mas"]
 
 all_sites = [
@@ -11,7 +12,7 @@ all_sites = [
         title="Hindu Mandal Hospital",
         country="tanzania",
         country_code="tz",
-        domain=f"hindu-mandal.tz.{fqdn}",
+        domain=f"hindu-mandal.tz.{domain_suffix}",
         language_codes=languages,
     ),
     SingleSite(
@@ -20,7 +21,7 @@ all_sites = [
         title="Amana Hospital",
         country="tanzania",
         country_code="tz",
-        domain=f"amana.tz.{fqdn}",
+        domain=f"amana.tz.{domain_suffix}",
         language_codes=languages,
     ),
     SingleSite(
@@ -29,7 +30,7 @@ all_sites = [
         title="Temeke Hospital",
         country="tanzania",
         country_code="tz",
-        domain=f"temeke.tz.{fqdn}",
+        domain=f"temeke.tz.{domain_suffix}",
         language_codes=languages,
     ),
     SingleSite(
@@ -39,7 +40,7 @@ all_sites = [
         country="tanzania",
         country_code="tz",
         language_codes=languages,
-        domain=f"mwananyamala.tz.{fqdn}",
+        domain=f"mwananyamala.tz.{domain_suffix}",
     ),
     SingleSite(
         50,
@@ -48,7 +49,7 @@ all_sites = [
         country="tanzania",
         country_code="tz",
         language_codes=languages,
-        domain=f"mbagala.tz.{fqdn}",
+        domain=f"mbagala.tz.{domain_suffix}",
     ),
     SingleSite(
         60,
@@ -57,7 +58,7 @@ all_sites = [
         country="tanzania",
         country_code="tz",
         language_codes=languages,
-        domain=f"mnazi-moja.tz.{fqdn}",
+        domain=f"mnazi-moja.tz.{domain_suffix}",
     ),
 ]
 

meta_subject/action_items.py

@@ -20,12 +20,15 @@ from edc_visit_schedule.utils import is_baseline
 from edc_visit_tracking.constants import MISSED_VISIT
 
 from meta_prn.constants import (
+    DM_REFFERAL_ACTION,
+    OFFSCHEDULE_DM_REFERRAL_ACTION,
     OFFSCHEDULE_PREGNANCY_ACTION,
     PREGNANCY_NOTIFICATION_ACTION,
 )
 
 from .constants import (
     DELIVERY_ACTION,
+    DM_FOLLOWUP_ACTION,
     FOLLOWUP_EXAMINATION_ACTION,
     MISSED_VISIT_ACTION,
     URINE_PREGNANCY_ACTION,
@@ -150,6 +153,25 @@ class EgfrDropNotificationAction(ActionWithNotification):
         return self.reference_obj.report_status != NEW
 
 
+class DmFollowAction(ActionWithNotification):
+    name = DM_FOLLOWUP_ACTION
+    display_name = "Diabetes Followup"
+    notification_display_name = "Diabetes Followup"
+    parent_action_names = [DM_REFFERAL_ACTION]
+    reference_model = "meta_subject.dmfollowup"
+    show_link_to_changelist = True
+    show_link_to_add = False
+    show_on_dashboard = False
+    create_by_user = False
+    create_by_action = True
+    admin_site_name = "meta_subject_admin"
+    priority = HIGH_PRIORITY
+
+    def get_next_actions(self):
+        next_actions = [OFFSCHEDULE_DM_REFERRAL_ACTION]
+        return next_actions
+
+
 def register_actions():
     for action_item_cls in [
         BloodResultsFbcAction,
@@ -162,6 +184,7 @@ def register_actions():
         UrinePregnancyAction,
         DeliveryAction,
         EgfrDropNotificationAction,
+        DmFollowAction,
     ]:
         try:
             site_action_items.register(action_item_cls)

meta_subject/admin/__init__.py

@@ -9,7 +9,7 @@ from .complications_admin import ComplicationsAdmin
 from .complications_glycemia_admin import ComplicationsGlycemiaAdmin
 from .concomitant_medication_admin import ConcomitantMedicationAdmin
 from .delivery_admin import DeliveryAdmin
-from .dm_referral_followup_admin import DmReferralFollowupAdmin
+from .diabetes import DmFollowupAdmin
 from .egfr_drop_notification_admin import EgfrDropNotificationAdmin
 from .eq5d3l_admin import Eq5d3lAdmin
 from .followup_examination_admin import FollowupExaminationAdmin

meta_subject/admin/birth_outcome_admin.py

@@ -60,15 +60,14 @@ class BirthOutcomesAdmin(
     def get_search_fields(self, request) -> Tuple[str, ...]:
         fields = super().get_search_fields(request)
         custom_fields = (
-            "delivery__action_identifier__subject_visit__subject_identifier",
+            "delivery__subject_visit__subject_identifier",
             "delivery__action_identifier",
-            "delivery__tracking_identifier",
         )
         return tuple(set(fields + custom_fields))
 
     @admin.display
     def delivery_report(self, obj=None, label=None):
-        url = reverse("meta_prn_admin:meta_prn_delivery_changelist")
+        url = reverse("meta_subject_admin:meta_subject_delivery_changelist")
         url = f"{url}?q={obj.subject_identifier}"
         context = dict(title="Delivery", url=url, label="Delivery")
         return render_to_string("dashboard_button.html", context=context)

meta_subject/admin/delivery_admin.py

@@ -109,7 +109,6 @@ class DeliveryAdmin(
     search_fields = (
         "subject_visit__subject_identifier",
         "action_identifier",
-        "tracking_identifier",
     )
 
     @admin.display

meta_subject/admin/diabetes/__init__.py

@@ -0,0 +1,2 @@
+from .dm_diagnosis_admin import DmDiagnosisAdmin
+from .dm_followup_admin import DmFollowupAdmin

meta_subject/admin/diabetes/dm_diagnosis_admin.py

@@ -0,0 +1,89 @@
+from django.contrib import admin
+from django_audit_fields.admin import audit_fieldset_tuple
+from edc_crf.fieldset import crf_status_fieldset
+from edc_form_label.form_label_modeladmin_mixin import FormLabelModelAdminMixin
+from edc_model_admin.history import SimpleHistoryAdmin
+from edc_model_admin.mixins import TabularInlineMixin
+
+from ...admin_site import meta_subject_admin
+from ...forms import DmDiagnosisForm, DmDxResultForm
+from ...models import DmDiagnosis, DmDxResult
+from ..modeladmin import CrfModelAdminMixin
+
+
+class DmDxResultInline(
+    TabularInlineMixin,
+    admin.TabularInline,
+):
+
+    form = DmDxResultForm
+    extra = 1
+    view_on_site = False
+    min_num = 1
+    insert_before_fieldset = "Comments"
+    verbose_name_plural = "Results used in the decision to diagnose"
+
+    fieldsets = (
+        [
+            "Lab results",
+            {
+                "description": "List the lab results used for this decision",
+                "fields": (
+                    "report_date",
+                    "utestid",
+                    "value",
+                    "fasted",
+                    "comment",
+                ),
+            },
+        ],
+    )
+
+    def get_formset(self, request, obj=None, **kwargs):
+        formset = super().get_formset(request, obj=None, **kwargs)
+        formset.validate_min = True
+        return formset
+
+    model = DmDxResult
+    form = DmDxResultForm
+
+
+@admin.register(DmDiagnosis, site=meta_subject_admin)
+class DmDiagnosisAdmin(
+    CrfModelAdminMixin,
+    FormLabelModelAdminMixin,
+    SimpleHistoryAdmin,
+):
+    form = DmDiagnosisForm
+
+    inlines = [DmDxResultInline]
+
+    fieldsets = (
+        (None, {"fields": ("subject_visit", "report_datetime")}),
+        (
+            "Diagnosis",
+            {
+                "fields": (
+                    "dx_date",
+                    "dx_initiated_by",
+                    "dx_initiated_by_other",
+                    "dx_tmg",
+                    "dx_tmg_date",
+                    "dx_no_tmg_reason",
+                ),
+            },
+        ),
+        (
+            "Comments",
+            {
+                "fields": ("comments",),
+            },
+        ),
+        crf_status_fieldset,
+        audit_fieldset_tuple,
+    )
+
+    radio_fields = {
+        "dx_initiated_by": admin.VERTICAL,
+        "dx_tmg": admin.VERTICAL,
+    }

meta_subject/admin/{dm_referral_followup_admin.py → diabetes/dm_followup_admin.py}

@@ -1,21 +1,25 @@
 from django.contrib import admin
 from django_audit_fields.admin import audit_fieldset_tuple
+from edc_action_item import ActionItemModelAdminMixin, action_fieldset_tuple
 from edc_adherence.model_admin_mixin import get_visual_score_fieldset_tuple
 from edc_crf.fieldset import crf_status_fieldset
 from edc_form_label.form_label_modeladmin_mixin import FormLabelModelAdminMixin
 from edc_model_admin.history import SimpleHistoryAdmin
 
-from ..admin_site import meta_subject_admin
-from ..forms.dm_referral_followup import DmReferralFollowupForm
-from ..models import DmReferralFollowup
-from .modeladmin import CrfModelAdminMixin
+from ...admin_site import meta_subject_admin
+from ...forms import DmFollowupForm
+from ...models import DmFollowup
+from ..modeladmin import CrfModelAdminMixin
 
 
-@admin.register(DmReferralFollowup, site=meta_subject_admin)
-class DmReferralFollowupAdmin(
-    CrfModelAdminMixin, FormLabelModelAdminMixin, SimpleHistoryAdmin
+@admin.register(DmFollowup, site=meta_subject_admin)
+class DmFollowupAdmin(
+    CrfModelAdminMixin,
+    FormLabelModelAdminMixin,
+    ActionItemModelAdminMixin,
+    SimpleHistoryAdmin,
 ):
-    form = DmReferralFollowupForm
+    form = DmFollowupForm
 
     fieldsets = (
         (None, {"fields": ("subject_visit", "report_datetime")}),
@@ -49,6 +53,7 @@ class DmReferralFollowupAdmin(
             "Diabetes treatment",
             {
                 "fields": (
+                    "treatment_prescribed",
                     "dm_treatments",
                     "on_dm_medications",
                     "dm_medications_init_date",
@@ -68,6 +73,7 @@ class DmReferralFollowupAdmin(
         ),
         get_visual_score_fieldset_tuple(),
         crf_status_fieldset,
+        action_fieldset_tuple,
         audit_fieldset_tuple,
     )
 
@@ -86,4 +92,5 @@ class DmReferralFollowupAdmin(
         "on_dm_medications": admin.VERTICAL,
         "medications_adherent": admin.VERTICAL,
         "last_missed_pill": admin.VERTICAL,
+        "treatment_prescribed": admin.VERTICAL,
     }

meta_subject/admin/glucose_admin.py

@@ -32,7 +32,7 @@ class GlucoseAdmin(CrfModelAdminMixin, SimpleHistoryAdmin):
             },
         ),
         (
-            "FBG",
+            "Blood Glucose",
             {
                 "fields": (
                     "fbg_performed",

meta_subject/admin/glucose_fbg_admin.py

@@ -19,27 +19,53 @@ class GlucoseFbgAdmin(CrfModelAdminMixin, SimpleHistoryAdmin):
 
     fieldsets = [
         (None, {"fields": ("subject_visit", "report_datetime")}),
-        ("Fasting", {"fields": ["fasting"]}),
-        ("Result", {"fields": ["assay_datetime", "glucose_value", "glucose_units"]}),
+        (
+            "Fasting",
+            {
+                "fields": (
+                    "fasting",
+                    "fasting_duration_str",
+                )
+            },
+        ),
+        (
+            "Blood Glucose",
+            {
+                "fields": (
+                    "fbg_performed",
+                    "fbg_not_performed_reason",
+                    "fbg_datetime",
+                    "fbg_value",
+                    "fbg_units",
+                )
+            },
+        ),
+        (
+            "Confirmation appointment",
+            {
+                "description": (
+                    "If blood glucose value is >= 7.0 mmol/L, schedule an "
+                    "appointment within 1 week to confirm"
+                ),
+                "fields": ("repeat_fbg_date",),
+            },
+        ),
     ]
 
     radio_fields = {
         "fasting": admin.VERTICAL,
-        "glucose_units": admin.VERTICAL,
+        "fbg_units": admin.VERTICAL,
+        "fbg_performed": admin.VERTICAL,
     }
 
     @admin.display(description="FBG", ordering="fbg_value")
     def fbg(self, obj=None):
         return obj.fbg_value
 
-    @admin.display(description="OGTT", ordering="ogtt_value")
-    def ogtt(self, obj=None):
-        return obj.ogtt_value
-
     def get_list_display(self, request) -> tuple[str, ...]:
         list_display = super().get_list_display(request)
         list_display = list(list_display)
-        list_display.insert(3, "ogtt")
+        # list_display.insert(3, "ogtt")
         list_display.insert(3, "fbg")
         list_display = tuple(list_display)
         return list_display