meta-edc 0.3.15__py3-none-any.whl → 0.3.50__py3-none-any.whl

meta_reports/admin/modeladmin_mixins.py

@@ -0,0 +1,112 @@
+from typing import Type
+
+from django.conf import settings
+from django.contrib import admin
+from django.contrib.admin import SimpleListFilter
+from django.db.models import QuerySet
+from django.template.loader import render_to_string
+from django.urls import reverse
+from edc_model_admin.dashboard import ModelAdminDashboardMixin
+from edc_model_admin.mixins import TemplatesModelAdminMixin
+from edc_qareports.modeladmin_mixins import QaReportModelAdminMixin
+from edc_sites.admin import SiteModelAdminMixin
+from edc_sites.admin.list_filters import SiteListFilter
+from edc_visit_schedule.admin import ScheduleStatusListFilter
+
+from ..tasks import update_endpoints_table
+
+
+def update_endpoints_table_action(modeladmin, request, queryset):
+    subject_identifiers = []
+    if queryset.count() != modeladmin.model.objects.count():
+        subject_identifiers = [o.subject_identifier for o in queryset]
+    if settings.CELERY_ENABLED:
+        return update_endpoints_table.delay(subject_identifiers)
+    return update_endpoints_table(subject_identifiers)
+
+
+update_endpoints_table_action.short_description = "Regenerate report for selected subjects"
+
+
+class EndpointsModelAdminMixin(
+    QaReportModelAdminMixin,
+    SiteModelAdminMixin,
+    ModelAdminDashboardMixin,
+    TemplatesModelAdminMixin,
+):
+    queryset_filter: dict | None = None
+    actions = [update_endpoints_table_action]
+    qa_report_list_display_insert_pos = 3
+    ordering = ["-fbg_date"]
+    list_display = [
+        "dashboard",
+        "subject",
+        "visit",
+        "fbg_date",
+        "fast",
+        "fbg",
+        "ogtt",
+        "endpoint",
+        "last_updated",
+        "offstudy_date",
+        "offstudy_reason",
+    ]
+
+    list_filter = [
+        "endpoint_label",
+        ScheduleStatusListFilter,
+        SiteListFilter,
+    ]
+
+    search_fields = ["subject_identifier"]
+
+    def get_queryset(self, request) -> QuerySet:
+        qs = super().get_queryset(request)
+        if self.queryset_filter:
+            qs = qs.filter(**self.queryset_filter)
+        return qs
+
+    def get_list_filter(self, request) -> tuple[str | Type[SimpleListFilter], ...]:
+        list_filter = super().get_list_filter(request)
+        list_filter = list_filter + (SiteListFilter,)
+        return list_filter
+
+    @admin.display(description="subject", ordering="subject_identifier")
+    def subject(self, obj=None):
+        return obj.subject_identifier
+
+    @admin.display(description="visit", ordering="visit_code")
+    def visit(self, obj=None):
+        return obj.visit_code
+
+    # @admin.display(description="FBG DATE", ordering="fbg_date")
+    # def fbg_date(self, obj=None):
+    #     return obj.fbg_datetime.date() if obj.fbg_datetime else None
+
+    @admin.display(description="FAST", ordering="fasting")
+    def fast(self, obj=None):
+        return obj.fasting
+
+    @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
+
+    @admin.display(description="endpoint", ordering="endpoint_label")
+    def endpoint(self, obj=None):
+        url = reverse("meta_reports_admin:meta_reports_glucosesummary_changelist")
+        return render_to_string(
+            "meta_reports/columns/subject_identifier_column.html",
+            {
+                "subject_identifier": obj.subject_identifier,
+                "url": url,
+                "label": obj.endpoint_label,
+            },
+        )
+
+    @admin.display(description="last_updated", ordering="created")
+    def last_updated(self, obj=None):
+        return obj.created

meta_reports/admin_site.py

@@ -0,0 +1,5 @@
+from edc_model_admin.admin_site import EdcAdminSite
+
+from .apps import AppConfig
+
+meta_reports_admin = EdcAdminSite(name="meta_reports_admin", app_label=AppConfig.name)

meta_reports/apps.py

@@ -1,22 +1,7 @@
 from django.apps import AppConfig as DjangoAppConfig
-from django.conf import settings
-from edc_facility.apps import AppConfig as BaseEdcFacilityAppConfig
 
 
 class AppConfig(DjangoAppConfig):
     name = "meta_reports"
     verbose_name = "META Reports"
-
-
-if settings.APP_NAME == "meta_reports":
-    from dateutil.relativedelta import FR, MO, SA, SU, TH, TU, WE
-
-    class EdcFacilityAppConfig(BaseEdcFacilityAppConfig):
-        country = "tanzania"
-        definitions = {
-            "7-day-clinic": dict(
-                days=[MO, TU, WE, TH, FR, SA, SU],
-                slots=[100, 100, 100, 100, 100, 100, 100],
-            ),
-            "5-day-clinic": dict(days=[MO, TU, WE, TH, FR], slots=[100, 100, 100, 100, 100]),
-        }
+    include_in_administration_section = True

meta_reports/forms/__init__.py

@@ -0,0 +1 @@
+from .missing_ogtt_note_form import MissingOgttNoteForm

meta_reports/forms/missing_ogtt_note_form.py

@@ -0,0 +1,33 @@
+from django import forms
+from edc_constants.constants import NO, YES
+from edc_form_validators import FormValidator, FormValidatorMixin
+from edc_glucose.form_validators import OgttFormValidatorMixin
+from edc_glucose.utils import validate_glucose_as_millimoles_per_liter
+
+from ..models import MissingOgttNote
+
+
+class MissingOgttNoteFormValidator(OgttFormValidatorMixin, FormValidator):
+
+    def clean(self):
+        self.applicable_if(YES, field="result_status", field_applicable="fasting")
+        self.required_if(YES, NO, field="fasting", field_required="ogtt_base_datetime")
+        self.required_if(YES, NO, field="fasting", field_required="ogtt_datetime")
+        self.required_if(YES, NO, field="fasting", field_required="ogtt_value")
+        self.applicable_if(YES, NO, field="fasting", field_applicable="ogtt_units")
+        validate_glucose_as_millimoles_per_liter("ogtt", self.cleaned_data)
+        self.validate_ogtt_dates()
+        self.validate_ogtt_time_interval()
+
+
+class MissingOgttNoteForm(FormValidatorMixin, forms.ModelForm):
+    form_validator_cls = MissingOgttNoteFormValidator
+
+    class Meta:
+        model = MissingOgttNote
+        fields = "__all__"
+        help_text = {"subject_identifier": "(read-only)", "name": "(read-only)"}
+        widgets = {
+            "report_model": forms.TextInput(attrs={"readonly": "readonly"}),
+            "subject_identifier": forms.TextInput(attrs={"readonly": "readonly"}),
+        }

meta_reports/management/commands/generate_endpoints.py

@@ -0,0 +1,13 @@
+from django.core.management import BaseCommand
+
+from meta_analytics.dataframes import GlucoseEndpointsByDate
+
+
+class Command(BaseCommand):
+
+    def handle(self, *args, **options):
+        print("Generating endpoints...")
+        cls = GlucoseEndpointsByDate()
+        cls.run()
+        cls.to_model()
+        print("Generating endpoints... done.")

meta_reports/migrations/0001_initial.py

@@ -0,0 +1,87 @@
+# Generated by Django 4.2.11 on 2024-06-06 19:15
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    initial = True
+
+    dependencies = []
+
+    operations = [
+        migrations.CreateModel(
+            name="UnattendedThreeInRow",
+            fields=[
+                (
+                    "id",
+                    models.BigAutoField(
+                        auto_created=True, primary_key=True, serialize=False, verbose_name="ID"
+                    ),
+                ),
+                ("subject_identifier", models.CharField(max_length=25)),
+                ("appt_datetime", models.DateTimeField()),
+                ("first", models.CharField(max_length=25)),
+                ("second", models.CharField(max_length=25)),
+                ("third", models.CharField(max_length=25)),
+                ("interval_days", models.IntegerField()),
+                ("from_now_days", models.IntegerField()),
+                ("created", models.DateTimeField()),
+            ],
+            options={
+                "verbose_name": "Unattended: Three in a row",
+                "verbose_name_plural": "Unattended: Three in a row",
+                "db_table": "unattended_three_in_row_view",
+                "managed": False,
+            },
+        ),
+        migrations.CreateModel(
+            name="UnattendedThreeInRow2",
+            fields=[
+                (
+                    "id",
+                    models.BigAutoField(
+                        auto_created=True, primary_key=True, serialize=False, verbose_name="ID"
+                    ),
+                ),
+                ("subject_identifier", models.CharField(max_length=25)),
+                ("first", models.CharField(max_length=25)),
+                ("second", models.CharField(max_length=25)),
+                ("third", models.CharField(max_length=25)),
+                ("interval_days", models.IntegerField()),
+                ("from_now_days", models.IntegerField()),
+                ("missed_count", models.IntegerField()),
+                ("created", models.DateTimeField()),
+            ],
+            options={
+                "verbose_name": "Unattended: Three in a row (with missed)",
+                "verbose_name_plural": "Unattended: Three in a row (with missed)",
+                "db_table": "unattended_three_in_row2_view",
+                "managed": False,
+            },
+        ),
+        migrations.CreateModel(
+            name="UnattendedTwoInRow",
+            fields=[
+                (
+                    "id",
+                    models.BigAutoField(
+                        auto_created=True, primary_key=True, serialize=False, verbose_name="ID"
+                    ),
+                ),
+                ("subject_identifier", models.CharField(max_length=25)),
+                ("appt_datetime", models.DateTimeField()),
+                ("first", models.CharField(max_length=25)),
+                ("second", models.CharField(max_length=25)),
+                ("interval_days", models.IntegerField()),
+                ("from_now_days", models.IntegerField()),
+                ("created", models.DateTimeField()),
+            ],
+            options={
+                "verbose_name": "Unattended: Two in a row",
+                "verbose_name_plural": "Unattended: Two in a row",
+                "db_table": "unattended_two_in_row_view",
+                "managed": False,
+            },
+        ),
+    ]

meta_reports/migrations/0002_patienthistorymissingbaselinecd4_and_more.py

@@ -0,0 +1,64 @@
+# Generated by Django 4.2.11 on 2024-06-18 02:04
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("meta_reports", "0001_initial"),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name="PatientHistoryMissingBaselineCd4",
+            fields=[
+                (
+                    "id",
+                    models.BigAutoField(
+                        auto_created=True, primary_key=True, serialize=False, verbose_name="ID"
+                    ),
+                ),
+                ("report_model", models.CharField(max_length=50)),
+                ("subject_identifier", models.CharField(max_length=25)),
+                ("created", models.DateTimeField()),
+                ("visit_code", models.CharField(max_length=25)),
+                ("visit_code_sequence", models.IntegerField()),
+                ("cd4", models.IntegerField(verbose_name="Last CD4")),
+                ("cd4_date", models.DateField(verbose_name="Date of last CD4")),
+                ("user_created", models.CharField(max_length=25)),
+                ("user_modified", models.CharField(max_length=25)),
+                ("modified", models.DateTimeField()),
+            ],
+            options={
+                "verbose_name": "Patient History: Missing Baseline Cd4",
+                "verbose_name_plural": "Missing Baseline Cd4",
+                "db_table": "patient_history_missing_baseline_cd4",
+                "managed": False,
+            },
+        ),
+        migrations.AlterModelOptions(
+            name="unattendedthreeinrow",
+            options={
+                "managed": False,
+                "verbose_name": "R100: Unattended appointments: Three in a row",
+                "verbose_name_plural": "R100: Unattended appointments: Three in a row",
+            },
+        ),
+        migrations.AlterModelOptions(
+            name="unattendedthreeinrow2",
+            options={
+                "managed": False,
+                "verbose_name": "R110: Unattended appointments: Three in a row (with missed)",
+                "verbose_name_plural": "R110: Unattended appointments: Three in a row (with missed)",
+            },
+        ),
+        migrations.AlterModelOptions(
+            name="unattendedtwoinrow",
+            options={
+                "managed": False,
+                "verbose_name": "R120: Unattended appointments: Two in a row",
+                "verbose_name_plural": "R120: Unattended appointments: Two in a row",
+            },
+        ),
+    ]

meta_reports/migrations/0003_auto_20240618_0505.py

@@ -0,0 +1,12 @@
+# Generated by Django 4.2.11 on 2024-06-18 02:05
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("meta_reports", "0002_patienthistorymissingbaselinecd4_and_more"),
+    ]
+
+    operations = []

meta_reports/migrations/0004_alter_patienthistorymissingbaselinecd4_table.py

@@ -0,0 +1,17 @@
+# Generated by Django 4.2.11 on 2024-06-18 03:43
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("meta_reports", "0003_auto_20240618_0505"),
+    ]
+
+    operations = [
+        migrations.AlterModelTable(
+            name="patienthistorymissingbaselinecd4",
+            table="patient_history_missing_baseline_cd4_view",
+        ),
+    ]

meta_reports/migrations/0005_endpoints.py

@@ -0,0 +1,47 @@
+# Generated by Django 4.2.11 on 2024-07-27 00:12
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("sites", "0002_alter_domain_unique"),
+        ("meta_reports", "0004_alter_patienthistorymissingbaselinecd4_table"),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name="Endpoints",
+            fields=[
+                (
+                    "id",
+                    models.BigAutoField(
+                        auto_created=True, primary_key=True, serialize=False, verbose_name="ID"
+                    ),
+                ),
+                ("report_model", models.CharField(max_length=50)),
+                ("subject_identifier", models.CharField(max_length=25)),
+                ("created", models.DateTimeField()),
+                ("visit_code", models.IntegerField()),
+                ("fasting", models.CharField(max_length=10)),
+                ("fbg_datetime", models.DateTimeField()),
+                ("fbg_value", models.FloatField()),
+                ("ogtt_value", models.FloatField()),
+                ("endpoint_label", models.CharField(max_length=25)),
+                ("offstudy_datetime", models.DateTimeField(null=True)),
+                ("offstudy_reason", models.CharField(max_length=250, null=True)),
+                (
+                    "site",
+                    models.ForeignKey(
+                        on_delete=django.db.models.deletion.PROTECT, to="sites.site"
+                    ),
+                ),
+            ],
+            options={
+                "verbose_name": "Endpoints (DM)",
+                "verbose_name_plural": "Endpoints (DM)",
+            },
+        ),
+    ]

meta_reports/migrations/0006_endpoints_baseline_datetime.py

@@ -0,0 +1,18 @@
+# Generated by Django 4.2.11 on 2024-07-27 00:26
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("meta_reports", "0005_endpoints"),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="endpoints",
+            name="baseline_datetime",
+            field=models.DateTimeField(null=True),
+        ),
+    ]

meta_reports/migrations/0007_alter_endpoints_endpoint_label_and_more.py

@@ -0,0 +1,43 @@
+# Generated by Django 4.2.11 on 2024-07-27 00:32
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("meta_reports", "0006_endpoints_baseline_datetime"),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="endpoints",
+            name="endpoint_label",
+            field=models.CharField(max_length=25, null=True),
+        ),
+        migrations.AlterField(
+            model_name="endpoints",
+            name="fasting",
+            field=models.CharField(max_length=10, null=True),
+        ),
+        migrations.AlterField(
+            model_name="endpoints",
+            name="fbg_datetime",
+            field=models.DateTimeField(null=True),
+        ),
+        migrations.AlterField(
+            model_name="endpoints",
+            name="fbg_value",
+            field=models.FloatField(null=True),
+        ),
+        migrations.AlterField(
+            model_name="endpoints",
+            name="ogtt_value",
+            field=models.FloatField(null=True),
+        ),
+        migrations.AlterField(
+            model_name="endpoints",
+            name="visit_code",
+            field=models.IntegerField(null=True),
+        ),
+    ]

meta_reports/migrations/0008_alter_endpoints_endpoint_label.py

@@ -0,0 +1,18 @@
+# Generated by Django 4.2.11 on 2024-07-27 00:34
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("meta_reports", "0007_alter_endpoints_endpoint_label_and_more"),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="endpoints",
+            name="endpoint_label",
+            field=models.CharField(max_length=250, null=True),
+        ),
+    ]

meta_reports/migrations/0009_alter_endpoints_options.py

@@ -0,0 +1,21 @@
+# Generated by Django 4.2.11 on 2024-07-31 01:00
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("meta_reports", "0008_alter_endpoints_endpoint_label"),
+    ]
+
+    operations = [
+        migrations.AlterModelOptions(
+            name="endpoints",
+            options={
+                "default_permissions": ("view", "export", "viewallsites"),
+                "verbose_name": "Endpoints (DM)",
+                "verbose_name_plural": "Endpoints (DM)",
+            },
+        ),
+    ]

meta_reports/migrations/0010_alter_patienthistorymissingbaselinecd4_options_and_more.py

@@ -0,0 +1,49 @@
+# Generated by Django 5.0.7 on 2024-08-12 14:20
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("meta_reports", "0009_alter_endpoints_options"),
+    ]
+
+    operations = [
+        migrations.AlterModelOptions(
+            name="patienthistorymissingbaselinecd4",
+            options={
+                "default_permissions": ("view", "export", "viewallsites"),
+                "managed": False,
+                "verbose_name": "Patient History: Missing Baseline Cd4",
+                "verbose_name_plural": "Missing Baseline Cd4",
+            },
+        ),
+        migrations.AlterModelOptions(
+            name="unattendedthreeinrow",
+            options={
+                "default_permissions": ("view", "export", "viewallsites"),
+                "managed": False,
+                "verbose_name": "R100: Unattended appointments: Three in a row",
+                "verbose_name_plural": "R100: Unattended appointments: Three in a row",
+            },
+        ),
+        migrations.AlterModelOptions(
+            name="unattendedthreeinrow2",
+            options={
+                "default_permissions": ("view", "export", "viewallsites"),
+                "managed": False,
+                "verbose_name": "R110: Unattended appointments: Three in a row (with missed)",
+                "verbose_name_plural": "R110: Unattended appointments: Three in a row (with missed)",
+            },
+        ),
+        migrations.AlterModelOptions(
+            name="unattendedtwoinrow",
+            options={
+                "default_permissions": ("view", "export", "viewallsites"),
+                "managed": False,
+                "verbose_name": "R120: Unattended appointments: Two in a row",
+                "verbose_name_plural": "R120: Unattended appointments: Two in a row",
+            },
+        ),
+    ]

meta_reports/migrations/0011_auto_20240813_0156.py

@@ -0,0 +1,54 @@
+# Generated by Django 5.0.7 on 2024-08-12 22:56
+
+import django_db_views.migration_functions
+import django_db_views.operations
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("meta_reports", "0010_alter_patienthistorymissingbaselinecd4_options_and_more"),
+    ]
+
+    operations = [
+        django_db_views.operations.ViewRunPython(
+            code=django_db_views.migration_functions.ForwardViewMigration(
+                "select *, uuid() as id, now() as created, \n    'meta_reports.patienthistorymissingbaselinecd4' as report_model \n      from (\n        select subject_identifier, v.visit_code, v.visit_code_sequence,cd4,\n          cd4_date, crf.site_id, crf.user_created, crf.user_modified,\n          crf.modified\n        from meta_subject_patienthistory as crf\n        left join meta_subject_subjectvisit as v on crf.subject_visit_id=v.id\n        where cd4 is null or cd4_date is null\n    ) as A\n    order by subject_identifier",
+                "patient_history_missing_baseline_cd4_view",
+                engine="django.db.backends.mysql",
+            ),
+            reverse_code=django_db_views.migration_functions.BackwardViewMigration(
+                "",
+                "patient_history_missing_baseline_cd4_view",
+                engine="django.db.backends.mysql",
+            ),
+            atomic=False,
+        ),
+        django_db_views.operations.ViewRunPython(
+            code=django_db_views.migration_functions.ForwardViewMigration(
+                "select *, get_random_uuid() as id, now() as created, \n    'meta_reports.patienthistorymissingbaselinecd4' as report_model \n      from (\n        select subject_identifier, v.visit_code, v.visit_code_sequence,cd4,\n          cd4_date, crf.site_id, crf.user_created, crf.user_modified,\n          crf.modified\n        from meta_subject_patienthistory as crf\n        left join meta_subject_subjectvisit as v on crf.subject_visit_id=v.id\n        where cd4 is null or cd4_date is null\n    ) as A\n    order by subject_identifier",
+                "patient_history_missing_baseline_cd4_view",
+                engine="django.db.backends.postgresql",
+            ),
+            reverse_code=django_db_views.migration_functions.BackwardViewMigration(
+                "",
+                "patient_history_missing_baseline_cd4_view",
+                engine="django.db.backends.postgresql",
+            ),
+            atomic=False,
+        ),
+        django_db_views.operations.ViewRunPython(
+            code=django_db_views.migration_functions.ForwardViewMigration(
+                "SELECT *, lower(\n    hex(randomblob(4)) || '-' || hex(randomblob(2)) || '-' || '4' ||\n    substr(hex( randomblob(2)), 2) || '-' ||\n    substr('AB89', 1 + (abs(random()) % 4) , 1)  ||\n    substr(hex(randomblob(2)), 2) || '-' ||\n    hex(randomblob(6))\n  ) as id, datetime() as `created`, 'meta_reports.patienthistorymissingbaselinecd4' as report_model \n      from (\n        select subject_identifier, v.visit_code, v.visit_code_sequence,cd4,\n          cd4_date, crf.site_id, crf.user_created, crf.user_modified,\n          crf.modified\n        from meta_subject_patienthistory as crf\n        left join meta_subject_subjectvisit as v on crf.subject_visit_id=v.id\n        where cd4 is null or cd4_date is null\n    ) as A\n    order by subject_identifier",
+                "patient_history_missing_baseline_cd4_view",
+                engine="django.db.backends.sqlite3",
+            ),
+            reverse_code=django_db_views.migration_functions.BackwardViewMigration(
+                "",
+                "patient_history_missing_baseline_cd4_view",
+                engine="django.db.backends.sqlite3",
+            ),
+            atomic=False,
+        ),
+    ]