meta-edc 1.1.8__py3-none-any.whl → 1.1.12__py3-none-any.whl

meta_reports/admin/last_imp_refill_admin.py

@@ -35,7 +35,7 @@ class NextApptDateListFilter(PastDateListFilter):
     field_name = "next_appt_date"
 
 
-def update_report(modeladmin, request, queryset):
+def update_report(modeladmin, request, queryset):  # noqa: ARG001
     now = get_utcnow()
     modeladmin.model.objects.all().delete()
     df = get_last_imp_visits_df()
@@ -68,7 +68,7 @@ def update_report(modeladmin, request, queryset):
             for _, row in df.iterrows()
         ]
         created = len(modeladmin.model.objects.bulk_create(data))
-        messages.success(request, "{} records were successfully created.".format(created))
+        messages.success(request, f"{created} records were successfully created.")
 
 
 @admin.register(LastImpRefill, site=meta_reports_admin)
@@ -83,13 +83,13 @@ class LastImpRefillAdmin(
 
     change_list_title = "List of most recent IMP refills per subject"
 
-    change_list_note = mark_safe(
+    change_list_note = mark_safe(  # noqa: S308
         render_to_string("meta_reports/last_imp_refill/changelist_note.html")
     )  # nosec B308, B703
 
-    actions = [update_report, export_to_csv]
+    actions = (update_report, export_to_csv)
 
-    list_display = [
+    list_display = (
         "dashboard",
         "subject_identifier",
         "imp_visit_code",
@@ -99,17 +99,17 @@ class LastImpRefillAdmin(
         "next_appt_date",
         "days_until",
         "created",
-    ]
+    )
 
-    list_filter = [
+    list_filter = (
         ("imp_visit_date", DateRangeFilterBuilder()),
         ("next_appt_date", DateRangeFilterBuilder()),
         "imp_visit_code",
         "next_visit_code",
         SiteListFilter,
-    ]
+    )
 
-    search_fields = ["subject_identifier"]
+    search_fields = ("subject_identifier",)
 
     def get_queryset(self, request) -> QuerySet:
         qs = super().get_queryset(request)

meta_reports/admin/list_filters.py

@@ -8,13 +8,13 @@ class EndpointListFilter(SimpleListFilter):
     title = "Endpoint"
     parameter_name = "endpoint"
 
-    def lookups(self, request, model_admin):
+    def lookups(self, request, model_admin):  # noqa: ARG002
         return (
             (YES, YES),
             (NO, NO),
         )
 
-    def queryset(self, request, queryset):
+    def queryset(self, request, queryset):  # noqa: ARG002
         if self.value() == YES:
             return queryset.filter(
                 subject_identifier__in=Endpoints.objects.values_list(

meta_reports/admin/modeladmin_mixins.py

@@ -1,5 +1,3 @@
-from typing import Type
-
 from django.conf import settings
 from django.contrib import admin
 from django.contrib.admin import SimpleListFilter
@@ -35,10 +33,10 @@ class EndpointsModelAdminMixin(
     TemplatesModelAdminMixin,
 ):
     queryset_filter: dict | None = None
-    actions = [update_endpoints_table_action]
+    actions = (update_endpoints_table_action,)
     qa_report_list_display_insert_pos = 3
-    ordering = ["-fbg_date"]
-    list_display = [
+    ordering = ("-fbg_date",)
+    list_display = (
         "dashboard",
         "subject",
         "visit",
@@ -50,15 +48,15 @@ class EndpointsModelAdminMixin(
         "last_updated",
         "offstudy_date",
         "offstudy_reason",
-    ]
+    )
 
-    list_filter = [
+    list_filter = (
         "endpoint_label",
         ScheduleStatusListFilter,
         SiteListFilter,
-    ]
+    )
 
-    search_fields = ["subject_identifier"]
+    search_fields = ("subject_identifier",)
 
     def get_queryset(self, request) -> QuerySet:
         qs = super().get_queryset(request)
@@ -66,10 +64,9 @@ class EndpointsModelAdminMixin(
             qs = qs.filter(**self.queryset_filter)
         return qs
 
-    def get_list_filter(self, request) -> tuple[str | Type[SimpleListFilter], ...]:
+    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
+        return *list_filter, SiteListFilter
 
     @admin.display(description="subject", ordering="subject_identifier")
     def subject(self, obj=None):
@@ -79,10 +76,6 @@ class EndpointsModelAdminMixin(
     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

meta_reports/death_report.py

@@ -24,7 +24,7 @@ class DeathPdfReport(MetaCrfPdfReport):
         super().__init__(**kwargs)
         self.death_report = death_report
 
-    def get_report_story(self, **kwargs):
+    def get_report_story(self, **kwargs):  # noqa: ARG002
         story = []
 
         self.draw_demographics(story)

meta_reports/forms/__init__.py

@@ -1 +1,3 @@
 from .missing_ogtt_note_form import MissingOgttNoteForm
+
+__all__ = ["MissingOgttNoteForm"]

meta_reports/forms/missing_ogtt_note_form.py

@@ -8,7 +8,6 @@ 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")
@@ -26,8 +25,8 @@ class MissingOgttNoteForm(FormValidatorMixin, forms.ModelForm):
     class Meta:
         model = MissingOgttNote
         fields = "__all__"
-        help_text = {"subject_identifier": "(read-only)", "name": "(read-only)"}
-        widgets = {
+        help_text = {"subject_identifier": "(read-only)", "name": "(read-only)"}  # noqa: RUF012
+        widgets = {  # noqa: RUF012
             "report_model": forms.TextInput(attrs={"readonly": "readonly"}),
             "subject_identifier": forms.TextInput(attrs={"readonly": "readonly"}),
         }

meta_reports/management/commands/generate_endpoints.py

@@ -1,13 +1,14 @@
+import sys
+
 from django.core.management import BaseCommand
 
 from meta_analytics.dataframes import GlucoseEndpointsByDate
 
 
 class Command(BaseCommand):
-
-    def handle(self, *args, **options):
-        print("Generating endpoints...")
+    def handle(self, *args, **options):  # noqa: ARG002
+        sys.stdout.write("Generating endpoints...\n")
         cls = GlucoseEndpointsByDate()
         cls.run()
         cls.to_model()
-        print("Generating endpoints... done.")
+        sys.stdout.write("Generating endpoints... done.\n")

meta_reports/migrations/0035_historicalmissingogttnote_missingogttnote.py

@@ -6,7 +6,7 @@ import django.db.models.manager
 import django_audit_fields.fields.hostname_modification_field
 import django_audit_fields.fields.userfield
 import django_audit_fields.fields.uuid_auto_field
-import django_audit_fields.models.audit_model_mixin
+import django.utils.timezone
 import django_revision.revision_field
 import edc_model.validators.date
 import edc_sites.managers
@@ -18,7 +18,6 @@ from django.db import migrations, models
 
 
 class Migration(migrations.Migration):
-
     dependencies = [
         ("meta_reports", "0034_auto_20240823_1642"),
         ("sites", "0002_alter_domain_unique"),
@@ -42,15 +41,11 @@ class Migration(migrations.Migration):
                 ),
                 (
                     "created",
-                    models.DateTimeField(
-                        blank=True, default=django_audit_fields.models.audit_model_mixin.utcnow
-                    ),
+                    models.DateTimeField(blank=True, default=django.utils.timezone.now),
                 ),
                 (
                     "modified",
-                    models.DateTimeField(
-                        blank=True, default=django_audit_fields.models.audit_model_mixin.utcnow
-                    ),
+                    models.DateTimeField(blank=True, default=django.utils.timezone.now),
                 ),
                 (
                     "user_created",
@@ -262,15 +257,11 @@ class Migration(migrations.Migration):
                 ),
                 (
                     "created",
-                    models.DateTimeField(
-                        blank=True, default=django_audit_fields.models.audit_model_mixin.utcnow
-                    ),
+                    models.DateTimeField(blank=True, default=django.utils.timezone.now),
                 ),
                 (
                     "modified",
-                    models.DateTimeField(
-                        blank=True, default=django_audit_fields.models.audit_model_mixin.utcnow
-                    ),
+                    models.DateTimeField(blank=True, default=django.utils.timezone.now),
                 ),
                 (
                     "user_created",

meta_reports/migrations/0059_alter_endpoints_created_and_more.py

@@ -0,0 +1,161 @@
+# Generated by Django 5.2.6 on 2025-09-24 05:45
+
+import django.utils.timezone
+import django_revision.revision_field
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("meta_reports", "0058_auto_20250422_2232"),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="endpoints",
+            name="created",
+            field=models.DateTimeField(default=django.utils.timezone.now),
+        ),
+        migrations.AlterField(
+            model_name="endpoints",
+            name="endpoint_label",
+            field=models.CharField(default="", max_length=250),
+        ),
+        migrations.AlterField(
+            model_name="endpoints",
+            name="fasting",
+            field=models.CharField(default="", max_length=10),
+        ),
+        migrations.AlterField(
+            model_name="endpoints",
+            name="offstudy_reason",
+            field=models.CharField(default="", max_length=250),
+        ),
+        migrations.AlterField(
+            model_name="historicalmissingogttnote",
+            name="device_created",
+            field=models.CharField(
+                blank=True, default="", max_length=10, verbose_name="Device created"
+            ),
+        ),
+        migrations.AlterField(
+            model_name="historicalmissingogttnote",
+            name="device_modified",
+            field=models.CharField(
+                blank=True, default="", max_length=10, verbose_name="Device modified"
+            ),
+        ),
+        migrations.AlterField(
+            model_name="historicalmissingogttnote",
+            name="locale_created",
+            field=models.CharField(
+                blank=True,
+                default="",
+                help_text="Auto-updated by Modeladmin",
+                max_length=10,
+                verbose_name="Locale created",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="historicalmissingogttnote",
+            name="locale_modified",
+            field=models.CharField(
+                blank=True,
+                default="",
+                help_text="Auto-updated by Modeladmin",
+                max_length=10,
+                verbose_name="Locale modified",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="historicalmissingogttnote",
+            name="note",
+            field=models.TextField(blank=True, default=""),
+        ),
+        migrations.AlterField(
+            model_name="historicalmissingogttnote",
+            name="report_datetime",
+            field=models.DateTimeField(default=django.utils.timezone.now),
+        ),
+        migrations.AlterField(
+            model_name="historicalmissingogttnote",
+            name="revision",
+            field=django_revision.revision_field.RevisionField(
+                blank=True,
+                default="",
+                editable=False,
+                help_text="System field. From git repository (tag:branch:commit), project metadata, project toml, project VERSION, or settings.",
+                max_length=75,
+                verbose_name="Revision",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="lastimprefill",
+            name="created",
+            field=models.DateTimeField(default=django.utils.timezone.now),
+        ),
+        migrations.AlterField(
+            model_name="lastimprefill",
+            name="visit_code",
+            field=models.CharField(default="", max_length=15),
+        ),
+        migrations.AlterField(
+            model_name="missingogttnote",
+            name="device_created",
+            field=models.CharField(
+                blank=True, default="", max_length=10, verbose_name="Device created"
+            ),
+        ),
+        migrations.AlterField(
+            model_name="missingogttnote",
+            name="device_modified",
+            field=models.CharField(
+                blank=True, default="", max_length=10, verbose_name="Device modified"
+            ),
+        ),
+        migrations.AlterField(
+            model_name="missingogttnote",
+            name="locale_created",
+            field=models.CharField(
+                blank=True,
+                default="",
+                help_text="Auto-updated by Modeladmin",
+                max_length=10,
+                verbose_name="Locale created",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="missingogttnote",
+            name="locale_modified",
+            field=models.CharField(
+                blank=True,
+                default="",
+                help_text="Auto-updated by Modeladmin",
+                max_length=10,
+                verbose_name="Locale modified",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="missingogttnote",
+            name="note",
+            field=models.TextField(blank=True, default=""),
+        ),
+        migrations.AlterField(
+            model_name="missingogttnote",
+            name="report_datetime",
+            field=models.DateTimeField(default=django.utils.timezone.now),
+        ),
+        migrations.AlterField(
+            model_name="missingogttnote",
+            name="revision",
+            field=django_revision.revision_field.RevisionField(
+                blank=True,
+                default="",
+                editable=False,
+                help_text="System field. From git repository (tag:branch:commit), project metadata, project toml, project VERSION, or settings.",
+                max_length=75,
+                verbose_name="Revision",
+            ),
+        ),
+    ]

meta_reports/models/__init__.py

@@ -14,3 +14,20 @@ from .dbviews import (
 from .endpoints import Endpoints
 from .endpoints_proxy import EndpointsProxy
 from .last_imp_refill import LastImpRefill
+
+__all__ = [
+    "NOTE_STATUSES",
+    "Endpoints",
+    "EndpointsProxy",
+    "GlucoseSummary",
+    "ImpSubstitutions",
+    "LastImpRefill",
+    "MissingOgttNote",
+    "MissingScreeningOgtt",
+    "OnStudyMissingLabValues",
+    "OnStudyMissingValues",
+    "PatientHistoryMissingBaselineCd4",
+    "UnattendedThreeInRow",
+    "UnattendedThreeInRow2",
+    "UnattendedTwoInRow",
+]

meta_reports/models/dbviews/__init__.py

@@ -7,3 +7,17 @@ from .patient_history_missing_baseline_cd4 import PatientHistoryMissingBaselineC
 from .unattended_three_in_row import UnattendedThreeInRow
 from .unattended_three_in_row2 import UnattendedThreeInRow2
 from .unattended_two_in_row import UnattendedTwoInRow
+
+__all__ = [
+    "NOTE_STATUSES",
+    "GlucoseSummary",
+    "ImpSubstitutions",
+    "MissingOgttNote",
+    "MissingScreeningOgtt",
+    "OnStudyMissingLabValues",
+    "OnStudyMissingValues",
+    "PatientHistoryMissingBaselineCd4",
+    "UnattendedThreeInRow",
+    "UnattendedThreeInRow2",
+    "UnattendedTwoInRow",
+]

meta_reports/models/dbviews/glucose_summary/__init__.py

@@ -1,2 +1,4 @@
 from .unmanaged_model import GlucoseSummary
 from .view_definition import get_view_definition
+
+__all__ = ["GlucoseSummary", "get_view_definition"]

meta_reports/models/dbviews/glucose_summary/unmanaged_model.py

@@ -6,20 +6,19 @@ from .view_definition import get_view_definition
 
 
 class GlucoseSummary(QaReportModelMixin, DBView):
-
     fbg_value = models.DecimalField(max_digits=8, decimal_places=2, null=True)
 
-    fbg_units = models.CharField(max_length=15, null=True)
+    fbg_units = models.CharField(max_length=15, default="")
 
     fbg_datetime = models.DateTimeField(null=True)
 
     ogtt_value = models.DecimalField(max_digits=8, decimal_places=2, null=True)
 
-    ogtt_units = models.CharField(max_length=15, null=True)
+    ogtt_units = models.CharField(max_length=15, default="")
 
     ogtt_datetime = models.DateTimeField(null=True)
 
-    fasted = models.CharField(max_length=15, null=True)
+    fasted = models.CharField(max_length=15, default="")
 
     fasting_duration_delta = models.DurationField(
         verbose_name="Fasting duration (hrs)", null=True
@@ -35,7 +34,7 @@ class GlucoseSummary(QaReportModelMixin, DBView):
 
     offstudy_datetime = models.DateTimeField(null=True)
 
-    source = models.CharField(max_length=35, null=True)
+    source = models.CharField(max_length=35, default="")
 
     view_definition = get_view_definition()
 

meta_reports/models/dbviews/imp_substitutions/__init__.py

@@ -1 +1,3 @@
 from .unmanaged_model import ImpSubstitutions
+
+__all__ = ["ImpSubstitutions"]

meta_reports/models/dbviews/imp_substitutions/view_definition.py

@@ -9,7 +9,7 @@ def get_view_definition() -> dict:
         from meta_pharmacy_substitutions as s left join meta_rando_randomizationlist as r
         on r.subject_identifier=s.subject_identifier
         order by s.subject_identifier
-        """  # noqa
+        """
     sql_view = SqlViewGenerator(
         report_model="meta_reports.imp_subjectitutions_view",
         ordering=["subject_identifier", "site_id"],

meta_reports/models/dbviews/missing_screening_ogtt/__init__.py

@@ -1,2 +1,4 @@
 from .note_model import NOTE_STATUSES, MissingOgttNote
 from .unmanaged_model import MissingScreeningOgtt
+
+__all__ = ["NOTE_STATUSES", "MissingOgttNote", "MissingScreeningOgtt"]

meta_reports/models/dbviews/missing_screening_ogtt/note_model.py

@@ -1,7 +1,7 @@
 from django.db import models
 from edc_constants.choices import YES_NO, YES_NO_NA
 from edc_constants.constants import COMPLETE, DONE, NOT_APPLICABLE, NOT_AVAILABLE, YES
-from edc_glucose.model_mixins import (
+from edc_glucose.model_mixin_factories import (
     fasting_model_mixin_factory,
     ogtt_model_mixin_factory,
 )

meta_reports/models/dbviews/missing_screening_ogtt/unmanaged_model.py

@@ -6,7 +6,6 @@ from .view_definition import get_view_definition
 
 
 class MissingScreeningOgtt(QaReportModelMixin, DBView):
-
     screening_datetime = models.DateTimeField(null=True)
 
     fbg_datetime = models.DateTimeField(null=True)
@@ -23,9 +22,11 @@ class MissingScreeningOgtt(QaReportModelMixin, DBView):
 
     ogtt2_datetime = models.DateTimeField(null=True)
 
-    repeated = models.CharField(null=True, max_length=25, help_text="repeat_glucose_performed")
+    repeated = models.CharField(
+        default="", max_length=25, help_text="repeat_glucose_performed"
+    )
 
-    p3_ltfu = models.CharField(null=True, max_length=25)
+    p3_ltfu = models.CharField(default="", max_length=25)
 
     consented = models.BooleanField(null=True)
 

meta_reports/models/dbviews/on_study_missing_lab_values/__init__.py

@@ -1 +1,3 @@
 from .unmanged_model import OnStudyMissingLabValues
+
+__all__ = ["OnStudyMissingLabValues"]

meta_reports/models/dbviews/on_study_missing_lab_values/qa_cases.py

@@ -1,8 +1,10 @@
+import contextlib
+
 from edc_lab_panel.constants import FBC, LFT, LIPIDS, RFT
 from edc_lab_panel.panels import fbc_panel, lft_panel, lipids_panel, rft_panel
 from edc_qareports.sql_generator import CrfCase, RequisitionCase
 
-qa_cases = [
+qa_cases: list[RequisitionCase | CrfCase] = [
     RequisitionCase(
         label="FBC requisitioned but not entered",
         dbtable="meta_subject_bloodresultsfbc",
@@ -32,10 +34,8 @@ qa_cases = [
 panels = {FBC: fbc_panel, RFT: rft_panel, LFT: lft_panel, LIPIDS: lipids_panel}
 for abbrev, panel in panels.items():
     for utest_id in panel.utest_ids:
-        try:
-            utest_id, _ = utest_id
-        except ValueError:
-            pass
+        with contextlib.suppress(ValueError):
+            utest_id, _ = utest_id  # noqa: PLW2901
         qa_cases.append(
             CrfCase(
                 label=f"{abbrev.upper()}: missing {utest_id} value/units",
@@ -45,9 +45,11 @@ for abbrev, panel in panels.items():
             )
         )
 
-    CrfCase(
-        label="No UREA value",
-        dbtable="meta_subject_bloodresultsrft",
-        label_lower="meta_subject.bloodresultsrft",
-        where="crf.urea_value is null or crf.urea_units is null",
-    ),
+    (
+        CrfCase(
+            label="No UREA value",
+            dbtable="meta_subject_bloodresultsrft",
+            label_lower="meta_subject.bloodresultsrft",
+            where="crf.urea_value is null or crf.urea_units is null",
+        ),
+    )

meta_reports/models/dbviews/on_study_missing_values/__init__.py

@@ -1 +1,3 @@
 from .unmanged_model import OnStudyMissingValues
+
+__all__ = ["OnStudyMissingValues"]

meta_reports/models/dbviews/on_study_missing_values/qa_cases.py

@@ -1,6 +1,8 @@
 from edc_constants.constants import OTHER, YES
 from edc_qareports.sql_generator import CrfCase
 
+from meta_visit_schedule.constants import MONTH36, MONTH48
+
 qa_cases = [
     CrfCase(
         label="No HIV Diagnosis date",
@@ -51,4 +53,20 @@ qa_cases = [
             f"and ogtt_performed='{YES}'"
         ),
     ),
+    CrfCase(
+        label="Weight",
+        dbtable="meta_subject_followupvitals",
+        label_lower="meta_subject.followupvitals",
+        where="(crf.weight is null and v.visit_code_sequence==0)",
+    ),
+    CrfCase(
+        label="Waist circumference 36/48m",
+        dbtable="meta_subject_followupvitals",
+        label_lower="meta_subject.followupvitals",
+        where=(
+            f"(crf.waist_circumference_measured=='{YES}' and crf.waist_circumference "
+            "is null) or (crf.waist_circumference is null and v.visit_code in "
+            f"['{MONTH36}','{MONTH48}'] and v.visit_code_sequence==0)"
+        ),
+    ),
 ]

meta_reports/models/dbviews/patient_history_missing_baseline_cd4/__init__.py

@@ -1 +1,3 @@
 from .unmanaged_model import PatientHistoryMissingBaselineCd4
+
+__all__ = ["PatientHistoryMissingBaselineCd4"]

meta_reports/models/dbviews/unattended_three_in_row/__init__.py

@@ -1 +1,3 @@
 from .unmanaged_model import UnattendedThreeInRow
+
+__all__ = ["UnattendedThreeInRow"]

meta_reports/models/dbviews/unattended_three_in_row2/__init__.py

@@ -1 +1,3 @@
 from .unmanaged_model import UnattendedThreeInRow2
+
+__all__ = ["UnattendedThreeInRow2"]

meta_reports/models/dbviews/unattended_two_in_row/__init__.py

@@ -1 +1,3 @@
 from .unmanaged_model import UnattendedTwoInRow
+
+__all__ = ["UnattendedTwoInRow"]