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

meta_reports/admin/dbviews/missing_screening_ogtt_admin/__init__.py

@@ -1,2 +1,7 @@
 from .note_model_admin import MissingOgttNoteModelAdmin
 from .unmanaged_model_admin import MissingScreeningOgttAdmin
+
+__all__ = [
+    "MissingOgttNoteModelAdmin",
+    "MissingScreeningOgttAdmin",
+]

meta_reports/admin/dbviews/missing_screening_ogtt_admin/note_model_admin.py

@@ -1,6 +1,7 @@
 from django.contrib import admin
 from django_audit_fields import audit_fieldset_tuple
-from edc_qareports.modeladmin_mixins import NoteModelAdminMixin
+from edc_model_admin.mixins import TemplatesModelAdminMixin
+from edc_sites.admin import SiteModelAdminMixin
 
 from ....admin_site import meta_reports_admin
 from ....forms import MissingOgttNoteForm
@@ -9,7 +10,8 @@ from ....models import MissingOgttNote
 
 @admin.register(MissingOgttNote, site=meta_reports_admin)
 class MissingOgttNoteModelAdmin(
-    NoteModelAdminMixin,
+    SiteModelAdminMixin,
+    TemplatesModelAdminMixin,
     admin.ModelAdmin,
 ):
     """A modeladmin class for the Note model."""
@@ -46,8 +48,30 @@ class MissingOgttNoteModelAdmin(
         audit_fieldset_tuple,
     )
 
-    radio_fields = {
+    radio_fields = {  # noqa: RUF012
         "ogtt_units": admin.VERTICAL,
         "result_status": admin.VERTICAL,
         "fasting": admin.VERTICAL,
     }
+
+    list_display = (
+        "subject_identifier",
+        "note",
+        "status",
+        "report_datetime",
+    )
+
+    # radio_fields = {"status": admin.VERTICAL}
+
+    list_filter = (
+        "report_datetime",
+        "status",
+        "report_model",
+        "user_created",
+        "user_modified",
+    )
+
+    search_fields = ("subject_identifier", "name")
+
+    def get_view_only_site_ids_for_user(self, request) -> list[int]:
+        return [s.id for s in request.user.userprofile.sites.all() if s.id != request.site.id]

meta_reports/admin/dbviews/missing_screening_ogtt_admin/unmanaged_model_admin.py

@@ -32,9 +32,9 @@ class MissingScreeningOgttAdmin(
     note_template = "edc_qareports/columns/notes_column.html"
     include_note_column = True
 
-    ordering = ["site", "subject_identifier"]
+    ordering = ("site", "subject_identifier")
 
-    list_display = [
+    list_display = (
         "dashboard",
         "subject_identifier",
         "site",
@@ -49,17 +49,17 @@ class MissingScreeningOgttAdmin(
         "fbg2_datetime",
         "ogtt2_datetime",
         "consented",
-    ]
+    )
 
-    list_filter = [
+    list_filter = (
         ScheduleStatusListFilter,
         "screening_datetime",
         "fbg_datetime",
         "repeated",
         "p3_ltfu",
-    ]
+    )
 
-    search_fields = ["subject_identifier"]
+    search_fields = ("subject_identifier",)
 
     def dashboard(self, obj=None, label=None) -> str:
         url = self.get_subject_dashboard_url(obj=obj)
@@ -69,7 +69,7 @@ class MissingScreeningOgttAdmin(
                 args=(obj.original_id,),
             )
         context = dict(title=_("Go to subject screening"), url=url, label=label)
-        return render_to_string("dashboard_button.html", context=context)
+        return render_to_string("edc_subject_dashboard/dashboard_button.html", context=context)
 
     @admin.display(description="Screen date", ordering="screening_datetime")
     def screening_date(self, obj):

meta_reports/admin/dbviews/on_study_missing_lab_values_admin/__init__.py

@@ -1 +1,3 @@
 from .unmanaged_model_admin import OnStudyMissingLabValuesAdmin
+
+__all__ = ["OnStudyMissingLabValuesAdmin"]

meta_reports/admin/dbviews/on_study_missing_lab_values_admin/unmanaged_model_admin.py

@@ -7,7 +7,4 @@ from ....models import OnStudyMissingLabValues
 
 @admin.register(OnStudyMissingLabValues, site=meta_reports_admin)
 class OnStudyMissingLabValuesAdmin(OnStudyMissingValuesModelAdminMixin, admin.ModelAdmin):
-
     include_note_column: bool = True
-
-    instructions = ["ello"]

meta_reports/admin/dbviews/on_study_missing_values_admin/__init__.py

@@ -1 +1,3 @@
 from .unmanaged_model_admin import OnStudyMissingValuesAdmin
+
+__all__ = ["OnStudyMissingValuesAdmin"]

meta_reports/admin/dbviews/on_study_missing_values_admin/unmanaged_model_admin.py

@@ -7,7 +7,6 @@ from ....models import OnStudyMissingValues
 
 @admin.register(OnStudyMissingValues, site=meta_reports_admin)
 class OnStudyMissingValuesAdmin(OnStudyMissingValuesModelAdminMixin, admin.ModelAdmin):
-
     include_note_column: bool = True
     project_reports_admin: str = "meta_reports_admin"
     project_subject_admin: str = "meta_subject_admin"

meta_reports/admin/dbviews/patient_history_missing_baseline_cd4_admin.py

@@ -1,3 +1,5 @@
+import contextlib
+
 from django.contrib import admin
 from django.core.exceptions import ObjectDoesNotExist
 from django.template.loader import render_to_string
@@ -23,8 +25,8 @@ class PatientHistoryMissingBaselineCd4Admin(
     TemplatesModelAdminMixin,
     admin.ModelAdmin,
 ):
-    ordering = ["site", "subject_identifier"]
-    list_display = [
+    ordering = ("site", "subject_identifier")
+    list_display = (
         "dashboard",
         "subject_identifier",
         "cd4",
@@ -33,15 +35,15 @@ class PatientHistoryMissingBaselineCd4Admin(
         "user_created",
         "user_modified",
         "modified",
-    ]
+    )
 
-    list_filter = [ScheduleStatusListFilter]
+    list_filter = (ScheduleStatusListFilter,)
 
-    search_fields = ["subject_identifier"]
+    search_fields = ("subject_identifier",)
 
     def dashboard(self, obj=None, label=None) -> str:
         kwargs = self.get_subject_dashboard_url_kwargs(obj)
-        try:
+        with contextlib.suppress(ObjectDoesNotExist):
             kwargs.update(
                 appointment=str(
                     Appointment.objects.get(
@@ -51,8 +53,6 @@ class PatientHistoryMissingBaselineCd4Admin(
                     ).id
                 )
             )
-        except ObjectDoesNotExist:
-            pass
         url = reverse(self.get_subject_dashboard_url_name(obj=obj), kwargs=kwargs)
         context = dict(title=_("Go to subject's dashboard@1000"), url=url, label=label)
-        return render_to_string("dashboard_button.html", context=context)
+        return render_to_string("edc_subject_dashboard/dashboard_button.html", context=context)

meta_reports/admin/dbviews/unattended_three_in_row2_admin.py

@@ -17,9 +17,9 @@ class UnattendedThreeInRow2Admin(
     TemplatesModelAdminMixin,
     admin.ModelAdmin,
 ):
-    ordering = ["site", "subject_identifier"]
+    ordering = ("site", "subject_identifier")
 
-    list_display = [
+    list_display = (
         "dashboard",
         "subject",
         "first_value",
@@ -30,17 +30,17 @@ class UnattendedThreeInRow2Admin(
         "site",
         "missed_count",
         "created",
-    ]
+    )
 
-    list_filter = [
+    list_filter = (
         "missed_count",
         ScheduleStatusListFilter,
         "first_value",
         "second_value",
         "third_value",
-    ]
+    )
 
-    search_fields = ["id", "subject_identifier", "first_value", "second_value", "third_value"]
+    search_fields = ("id", "subject_identifier", "first_value", "second_value", "third_value")
 
     @admin.display(description="Subject", ordering="subject_identifier")
     def subject(self, obj):

meta_reports/admin/dbviews/unattended_three_in_row_admin.py

@@ -17,8 +17,8 @@ class UnattendedThreeInRowAdmin(
     TemplatesModelAdminMixin,
     admin.ModelAdmin,
 ):
-    ordering = ["site", "subject_identifier"]
-    list_display = [
+    ordering = ("site", "subject_identifier")
+    list_display = (
         "dashboard",
         "subject_identifier",
         "first_value",
@@ -28,8 +28,8 @@ class UnattendedThreeInRowAdmin(
         "from_now_days",
         "site",
         "created",
-    ]
+    )
 
-    list_filter = [ScheduleStatusListFilter, "first_value", "second_value", "third_value"]
+    list_filter = (ScheduleStatusListFilter, "first_value", "second_value", "third_value")
 
-    search_fields = ["subject_identifier", "first_value", "second_value", "third_value"]
+    search_fields = ("subject_identifier", "first_value", "second_value", "third_value")

meta_reports/admin/dbviews/unattended_two_in_row_admin.py

@@ -17,8 +17,8 @@ class UnattendedTwoInRowAdmin(
     TemplatesModelAdminMixin,
     admin.ModelAdmin,
 ):
-    ordering = ["site", "subject_identifier"]
-    list_display = [
+    ordering = ("site", "subject_identifier")
+    list_display = (
         "dashboard",
         "subject_identifier",
         "first_value",
@@ -27,8 +27,8 @@ class UnattendedTwoInRowAdmin(
         "from_now_days",
         "site",
         "created",
-    ]
+    )
 
-    list_filter = [ScheduleStatusListFilter, "first_value", "second_value"]
+    list_filter = (ScheduleStatusListFilter, "first_value", "second_value")
 
-    search_fields = ["subject_identifier", "first_value", "second_value"]
+    search_fields = ("subject_identifier", "first_value", "second_value")

meta_reports/admin/endpoints_admin.py

@@ -8,7 +8,7 @@ from .modeladmin_mixins import EndpointsModelAdminMixin
 
 @admin.register(Endpoints, site=meta_reports_admin)
 class EndpointsAdmin(EndpointsModelAdminMixin, admin.ModelAdmin):
-    queryset_filter = dict(offstudy_date__isnull=True)
+    queryset_filter = dict(offstudy_date__isnull=True)  # noqa: RUF012
 
     def rendered_change_list_note(self):
         return render_to_string("meta_reports/endpoints_change_list_note.html")

meta_reports/admin/endpoints_all_admin.py

@@ -8,6 +8,5 @@ from .modeladmin_mixins import EndpointsModelAdminMixin
 
 @admin.register(EndpointsProxy, site=meta_reports_admin)
 class EndpointsAllAdmin(EndpointsModelAdminMixin, admin.ModelAdmin):
-
     def rendered_change_list_note(self):
         return render_to_string("meta_reports/endpoints_all_change_list_note.html")

meta_reports/admin/last_imp_refill_admin.py

@@ -1,16 +1,18 @@
+import pandas as pd
 from django.contrib import admin, messages
 from django.core.exceptions import FieldDoesNotExist
 from django.db import models
 from django.db.models import QuerySet
-from django.utils.html import format_html
+from django.template.loader import render_to_string
+from django.utils.safestring import mark_safe
 from edc_model_admin.dashboard import ModelAdminDashboardMixin
 from edc_model_admin.list_filters import PastDateListFilter
 from edc_model_admin.mixins import TemplatesModelAdminMixin
-from edc_pdutils.actions import export_to_csv
 from edc_qareports.modeladmin_mixins import QaReportModelAdminMixin
 from edc_sites.admin import SiteModelAdminMixin
 from edc_sites.admin.list_filters import SiteListFilter
 from edc_utils import get_utcnow
+from rangefilter.filters import DateRangeFilterBuilder
 
 from meta_analytics.dataframes import get_last_imp_visits_df
 
@@ -32,7 +34,7 @@ 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()
@@ -41,21 +43,31 @@ def update_report(modeladmin, request, queryset):
             modeladmin.model(
                 subject_identifier=row["subject_identifier"],
                 site_id=row["site_id"],
-                imp_visit_date=row["imp_visit_date"],
+                imp_visit_date=(
+                    None if pd.isna(row["imp_visit_date"]) else row["imp_visit_date"]
+                ),
                 imp_visit_code=row["imp_visit_code"],
-                next_appt_date=row["next_appt_datetime"],
-                next_visit_code=row["next_visit_code"],
+                next_appt_date=(
+                    None if pd.isna(row["next_appt_datetime"]) else row["next_appt_datetime"]
+                ),
+                next_visit_code=(
+                    None if pd.isna(row["next_visit_code"]) else row["next_visit_code"]
+                ),
                 days_since=row["days_since"].days,
-                days_until=row["days_until"].days,
-                visit_code=str(int(row["imp_visit_code"])),
-                visit_code_sequence=row["imp_visit_code"] % 1,
+                days_until=None if pd.isna(row["days_until"]) else row["days_until"].days,
+                visit_code=(
+                    None if pd.isna(row["imp_visit_code"]) else str(int(row["imp_visit_code"]))
+                ),
+                visit_code_sequence=(
+                    None if pd.isna(row["imp_visit_code"]) else row["imp_visit_code"] % 1
+                ),
                 report_model=modeladmin.model._meta.label_lower,
                 created=now,
             )
             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)
@@ -70,28 +82,13 @@ class LastImpRefillAdmin(
 
     change_list_title = "List of most recent IMP refills per subject"
 
-    change_list_note = format_html(
-        """
-        This report fetches the most recent Study Medication report where IMP was
-        refilled and adds the subject's next visit. Subjects taken "Off Schedule"
-        are not included in this report. To update ALL rows in this report, tick
-        at least one row and select 'Update report' action below.
-        <BR><BR>
-        This report has additional search features for numeric columns:
-        <code>days_since</code>, <code>days_until</code>, <code>imp_visit_code</code>
-        and <code>next_visit_code</code>.
-        <BR><BR>For example, type <code>days_until>=25</code> in the search below
-        to show rows for subjects who have an appointment 25 or more days from the
-        date this report was created. You might also try typing
-        <code>days_since>365</code> or <code>days_until<0</code>.
-        <BR><BR>
-        This also works: <code>next_visit_code>=1060</code>.
-        """
-    )
+    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,)
 
-    list_display = [
+    list_display = (
         "dashboard",
         "subject_identifier",
         "imp_visit_code",
@@ -101,17 +98,17 @@ class LastImpRefillAdmin(
         "next_appt_date",
         "days_until",
         "created",
-    ]
+    )
 
-    list_filter = [
-        ImpVisitDateListFilter,
-        NextApptDateListFilter,
+    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

@@ -1,5 +1,5 @@
+from clinicedc_constants import NO, YES
 from django.contrib.admin import SimpleListFilter
-from edc_constants.constants import NO, YES
 
 from meta_reports.models import Endpoints
 
@@ -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
@@ -16,7 +14,7 @@ from edc_visit_schedule.admin import ScheduleStatusListFilter
 from ..tasks import update_endpoints_table
 
 
-def update_endpoints_table_action(modeladmin, request, queryset):
+def update_endpoints_table_action(modeladmin, request, queryset):  # noqa: ARG001
     subject_identifiers = []
     if queryset.count() != modeladmin.model.objects.count():
         subject_identifiers = [o.subject_identifier for o in queryset]
@@ -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

@@ -1,8 +1,8 @@
 from textwrap import fill
 
 import inflect
+from clinicedc_constants import OTHER, TUBERCULOSIS
 from django.contrib.auth import get_user_model
-from edc_constants.constants import OTHER, TUBERCULOSIS
 from reportlab.lib import colors
 from reportlab.lib.units import cm
 from reportlab.platypus.flowables import Spacer
@@ -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

@@ -1,5 +1,5 @@
+from clinicedc_constants import NO, YES
 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
@@ -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",