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

meta_reports/admin/dbviews/missing_screening_ogtt_admin/note_model_admin.py

@@ -0,0 +1,53 @@
+from django.contrib import admin
+from django_audit_fields import audit_fieldset_tuple
+from edc_qareports.modeladmin_mixins import NoteModelAdminMixin
+
+from ....admin_site import meta_reports_admin
+from ....forms import MissingOgttNoteForm
+from ....models import MissingOgttNote
+
+
+@admin.register(MissingOgttNote, site=meta_reports_admin)
+class MissingOgttNoteModelAdmin(
+    NoteModelAdminMixin,
+    admin.ModelAdmin,
+):
+    """A modeladmin class for the Note model."""
+
+    form = MissingOgttNoteForm
+    note_template_name = "edc_qareports/qa_report_note.html"
+
+    fieldsets = (
+        (
+            None,
+            {"fields": ("subject_identifier", "report_datetime", "result_status")},
+        ),
+        (
+            "OGTT",
+            {
+                "fields": (
+                    "fasting",
+                    "ogtt_base_datetime",
+                    "ogtt_datetime",
+                    "ogtt_value",
+                    "ogtt_units",
+                )
+            },
+        ),
+        (
+            "Note",
+            {
+                "fields": (
+                    "note",
+                    "report_model",
+                )
+            },
+        ),
+        audit_fieldset_tuple,
+    )
+
+    radio_fields = {
+        "ogtt_units": admin.VERTICAL,
+        "result_status": admin.VERTICAL,
+        "fasting": admin.VERTICAL,
+    }

meta_reports/admin/dbviews/missing_screening_ogtt_admin/unmanaged_model_admin.py

@@ -0,0 +1,84 @@
+from django.contrib import admin
+from django.template.loader import render_to_string
+from django.urls import reverse
+from django.utils.translation import gettext as _
+from edc_model_admin.dashboard import ModelAdminDashboardMixin
+from edc_model_admin.mixins import TemplatesModelAdminMixin
+from edc_qareports.modeladmin_mixins import (
+    NoteStatusListFilter as BaseNoteStatusListFilter,
+)
+from edc_qareports.modeladmin_mixins import QaReportModelAdminMixin
+from edc_sites.admin import SiteModelAdminMixin
+from edc_visit_schedule.admin import ScheduleStatusListFilter
+
+from ....admin_site import meta_reports_admin
+from ....models import NOTE_STATUSES, MissingScreeningOgtt
+
+
+class NoteStatusListFilter(BaseNoteStatusListFilter):
+    note_model_status_choices = NOTE_STATUSES
+
+
+@admin.register(MissingScreeningOgtt, site=meta_reports_admin)
+class MissingScreeningOgttAdmin(
+    QaReportModelAdminMixin,
+    SiteModelAdminMixin,
+    ModelAdminDashboardMixin,
+    TemplatesModelAdminMixin,
+    admin.ModelAdmin,
+):
+    note_model = "meta_reports.missingogttnote"
+    note_status_list_filter = NoteStatusListFilter
+    note_template = "edc_qareports/columns/notes_column.html"
+    include_note_column = True
+
+    ordering = ["site", "subject_identifier"]
+
+    list_display = [
+        "dashboard",
+        "subject_identifier",
+        "site",
+        "screening_date",
+        "fbg_date",
+        "fbg_value",
+        "ogtt_value",
+        "repeated",
+        "p3_ltfu",
+        "fbg2_value",
+        "ogtt2_value",
+        "fbg2_datetime",
+        "ogtt2_datetime",
+        "consented",
+    ]
+
+    list_filter = [
+        ScheduleStatusListFilter,
+        "screening_datetime",
+        "fbg_datetime",
+        "repeated",
+        "p3_ltfu",
+    ]
+
+    search_fields = ["subject_identifier"]
+
+    def dashboard(self, obj=None, label=None) -> str:
+        url = self.get_subject_dashboard_url(obj=obj)
+        if not url:
+            url = reverse(
+                "meta_screening_admin:meta_screening_subjectscreening_change",
+                args=(obj.original_id,),
+            )
+        context = dict(title=_("Go to subject screening"), url=url, label=label)
+        return render_to_string("dashboard_button.html", context=context)
+
+    @admin.display(description="Screen date", ordering="screening_datetime")
+    def screening_date(self, obj):
+        if obj.screening_datetime:
+            return obj.screening_datetime.date()
+        return None
+
+    @admin.display(description="Fbg date", ordering="fbg_datetime")
+    def fbg_date(self, obj):
+        if obj.fbg_datetime:
+            return obj.fbg_datetime.date()
+        return None

meta_reports/admin/dbviews/on_study_missing_lab_values_admin/__init__.py

@@ -0,0 +1 @@
+from .unmanaged_model_admin import OnStudyMissingLabValuesAdmin

meta_reports/admin/dbviews/on_study_missing_lab_values_admin/unmanaged_model_admin.py

@@ -0,0 +1,13 @@
+from django.contrib import admin
+from edc_qareports.modeladmin_mixins import OnStudyMissingValuesModelAdminMixin
+
+from ....admin_site import meta_reports_admin
+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

@@ -0,0 +1 @@
+from .unmanaged_model_admin import OnStudyMissingValuesAdmin

meta_reports/admin/dbviews/on_study_missing_values_admin/unmanaged_model_admin.py

@@ -0,0 +1,13 @@
+from django.contrib import admin
+from edc_qareports.modeladmin_mixins import OnStudyMissingValuesModelAdminMixin
+
+from ....admin_site import meta_reports_admin
+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

@@ -0,0 +1,58 @@
+from django.contrib import admin
+from django.core.exceptions import ObjectDoesNotExist
+from django.template.loader import render_to_string
+from django.urls import reverse
+from django.utils.translation import gettext_lazy as _
+from edc_appointment.models import Appointment
+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_visit_schedule.admin import ScheduleStatusListFilter
+from edc_visit_schedule.constants import DAY1
+
+from ...admin_site import meta_reports_admin
+from ...models import PatientHistoryMissingBaselineCd4
+
+
+@admin.register(PatientHistoryMissingBaselineCd4, site=meta_reports_admin)
+class PatientHistoryMissingBaselineCd4Admin(
+    QaReportModelAdminMixin,
+    SiteModelAdminMixin,
+    ModelAdminDashboardMixin,
+    TemplatesModelAdminMixin,
+    admin.ModelAdmin,
+):
+    ordering = ["site", "subject_identifier"]
+    list_display = [
+        "dashboard",
+        "subject_identifier",
+        "cd4",
+        "cd4_date",
+        "site",
+        "user_created",
+        "user_modified",
+        "modified",
+    ]
+
+    list_filter = [ScheduleStatusListFilter]
+
+    search_fields = ["subject_identifier"]
+
+    def dashboard(self, obj=None, label=None) -> str:
+        kwargs = self.get_subject_dashboard_url_kwargs(obj)
+        try:
+            kwargs.update(
+                appointment=str(
+                    Appointment.objects.get(
+                        subject_identifier=obj.subject_identifier,
+                        visit_code=DAY1,
+                        visit_code_sequence=0,
+                    ).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)

meta_reports/admin/dbviews/unattended_three_in_row2_admin.py

@@ -0,0 +1,47 @@
+from django.contrib import admin
+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_visit_schedule.admin import ScheduleStatusListFilter
+
+from ...admin_site import meta_reports_admin
+from ...models import UnattendedThreeInRow2
+
+
+@admin.register(UnattendedThreeInRow2, site=meta_reports_admin)
+class UnattendedThreeInRow2Admin(
+    QaReportModelAdminMixin,
+    SiteModelAdminMixin,
+    ModelAdminDashboardMixin,
+    TemplatesModelAdminMixin,
+    admin.ModelAdmin,
+):
+    ordering = ["site", "subject_identifier"]
+
+    list_display = [
+        "dashboard",
+        "subject",
+        "first_value",
+        "second_value",
+        "third_value",
+        "interval_days",
+        "from_now_days",
+        "site",
+        "missed_count",
+        "created",
+    ]
+
+    list_filter = [
+        "missed_count",
+        ScheduleStatusListFilter,
+        "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):
+        return obj.subject_identifier

meta_reports/admin/dbviews/unattended_three_in_row_admin.py

@@ -0,0 +1,35 @@
+from django.contrib import admin
+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_visit_schedule.admin import ScheduleStatusListFilter
+
+from ...admin_site import meta_reports_admin
+from ...models import UnattendedThreeInRow
+
+
+@admin.register(UnattendedThreeInRow, site=meta_reports_admin)
+class UnattendedThreeInRowAdmin(
+    QaReportModelAdminMixin,
+    SiteModelAdminMixin,
+    ModelAdminDashboardMixin,
+    TemplatesModelAdminMixin,
+    admin.ModelAdmin,
+):
+    ordering = ["site", "subject_identifier"]
+    list_display = [
+        "dashboard",
+        "subject_identifier",
+        "first_value",
+        "second_value",
+        "third_value",
+        "interval_days",
+        "from_now_days",
+        "site",
+        "created",
+    ]
+
+    list_filter = [ScheduleStatusListFilter, "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

@@ -0,0 +1,34 @@
+from django.contrib import admin
+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_visit_schedule.admin import ScheduleStatusListFilter
+
+from ...admin_site import meta_reports_admin
+from ...models import UnattendedTwoInRow
+
+
+@admin.register(UnattendedTwoInRow, site=meta_reports_admin)
+class UnattendedTwoInRowAdmin(
+    QaReportModelAdminMixin,
+    SiteModelAdminMixin,
+    ModelAdminDashboardMixin,
+    TemplatesModelAdminMixin,
+    admin.ModelAdmin,
+):
+    ordering = ["site", "subject_identifier"]
+    list_display = [
+        "dashboard",
+        "subject_identifier",
+        "first_value",
+        "second_value",
+        "interval_days",
+        "from_now_days",
+        "site",
+        "created",
+    ]
+
+    list_filter = [ScheduleStatusListFilter, "first_value", "second_value"]
+
+    search_fields = ["subject_identifier", "first_value", "second_value"]

meta_reports/admin/endpoints_admin.py

@@ -0,0 +1,14 @@
+from django.contrib import admin
+from django.template.loader import render_to_string
+
+from ..admin_site import meta_reports_admin
+from ..models import Endpoints
+from .modeladmin_mixins import EndpointsModelAdminMixin
+
+
+@admin.register(Endpoints, site=meta_reports_admin)
+class EndpointsAdmin(EndpointsModelAdminMixin, admin.ModelAdmin):
+    queryset_filter = dict(offstudy_date__isnull=True)
+
+    def rendered_change_list_note(self):
+        return render_to_string("meta_reports/endpoints_change_list_note.html")

meta_reports/admin/endpoints_all_admin.py

@@ -0,0 +1,13 @@
+from django.contrib import admin
+from django.template.loader import render_to_string
+
+from ..admin_site import meta_reports_admin
+from ..models import EndpointsProxy
+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

@@ -0,0 +1,181 @@
+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 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 meta_analytics.dataframes import get_last_imp_visits_df
+
+from ..admin_site import meta_reports_admin
+from ..models import LastImpRefill
+
+
+class ImpVisitDateListFilter(PastDateListFilter):
+    title = "IMP visit date"
+
+    parameter_name = "imp_visit_date"
+    field_name = "imp_visit_date"
+
+
+class NextApptDateListFilter(PastDateListFilter):
+    title = "Next appt date"
+
+    parameter_name = "next_appt_date"
+    field_name = "next_appt_date"
+
+
+def update_report(modeladmin, request, queryset):
+    now = get_utcnow()
+    modeladmin.model.objects.all().delete()
+    df = get_last_imp_visits_df()
+    if not df.empty:
+        data = [
+            modeladmin.model(
+                subject_identifier=row["subject_identifier"],
+                site_id=row["site_id"],
+                imp_visit_date=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"],
+                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,
+                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))
+
+
+@admin.register(LastImpRefill, site=meta_reports_admin)
+class LastImpRefillAdmin(
+    QaReportModelAdminMixin,
+    SiteModelAdminMixin,
+    ModelAdminDashboardMixin,
+    TemplatesModelAdminMixin,
+    admin.ModelAdmin,
+):
+    include_note_column = False
+
+    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>.
+        """
+    )
+
+    actions = [update_report, export_to_csv]
+
+    list_display = [
+        "dashboard",
+        "subject_identifier",
+        "imp_visit_code",
+        "imp_visit_date",
+        "days_since",
+        "next_visit_code",
+        "next_appt_date",
+        "days_until",
+        "created",
+    ]
+
+    list_filter = [
+        ImpVisitDateListFilter,
+        NextApptDateListFilter,
+        "imp_visit_code",
+        "next_visit_code",
+        SiteListFilter,
+    ]
+
+    search_fields = ["subject_identifier"]
+
+    def get_queryset(self, request) -> QuerySet:
+        qs = super().get_queryset(request)
+        if qs.count() == 0:
+            update_report(self, request, None)
+            qs = super().get_queryset(request)
+        return qs
+
+    def dataframe_to_model(self):
+        now = get_utcnow()
+        self.model.objects.all().delete()
+        created = 0
+        df = get_last_imp_visits_df()
+        if not df.empty:
+            data = [
+                self.model(
+                    subject_identifier=row["subject_identifier"],
+                    site_id=row["site_id"],
+                    imp_visit_date=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"],
+                    days_since=row["days_since"],
+                    days_until=row["days_until"],
+                    visit_code=str(int(row["imp_visit_code"])),
+                    visit_code_sequence=row["imp_visit_code"] % 1,
+                    report_model=self.model._meta.label_lower,
+                    created=now,
+                )
+                for _, row in df.iterrows()
+            ]
+            created = len(self.model.objects.bulk_create(data))
+        return created
+
+    def get_search_results(self, request, queryset, search_term):
+        value = None
+        fldname = None
+        search_term = search_term.replace(" ", "")
+        operators = {">=": "gte", "<=": "lte", "<": "lt", ">": "gt"}
+        if op := [op for op in operators if op in search_term]:
+            op = op[0]
+            fldname, value = search_term.split(op)
+            try:
+                fldcls = self.model._meta.get_field(fldname)
+            except FieldDoesNotExist:
+                fldname = None
+            else:
+                if isinstance(fldcls, (models.IntegerField,)):
+                    try:
+                        value = int(value)
+                    except ValueError:
+                        value = None
+                elif isinstance(fldcls, (models.FloatField,)):
+                    try:
+                        value = float(value)
+                    except ValueError:
+                        value = None
+        if (
+            value is not None
+            and fldname
+            and fldname in ["days_until", "days_since", "imp_visit_code", "next_visit_code"]
+        ):
+            queryset, use_distinct = super().get_search_results(request, queryset, None)
+            queryset = queryset.filter(**{f"{fldname}__{operators[op]}": value})
+        else:
+            queryset, use_distinct = super().get_search_results(request, queryset, search_term)
+        return queryset, use_distinct

meta_reports/admin/list_filters.py

@@ -0,0 +1,30 @@
+from django.contrib.admin import SimpleListFilter
+from edc_constants.constants import NO, YES
+
+from meta_reports.models import Endpoints
+
+
+class EndpointListFilter(SimpleListFilter):
+    title = "Endpoint"
+    parameter_name = "endpoint"
+
+    def lookups(self, request, model_admin):
+        return (
+            (YES, YES),
+            (NO, NO),
+        )
+
+    def queryset(self, request, queryset):
+        if self.value() == YES:
+            return queryset.filter(
+                subject_identifier__in=Endpoints.objects.values_list(
+                    "subject_identifier", flat=True
+                )
+            )
+        if self.value() == YES:
+            return queryset.exclude(
+                subject_identifier__in=Endpoints.objects.values_list(
+                    "subject_identifier", flat=True
+                )
+            )
+        return queryset