clinicedc 2.0.34__py3-none-any.whl → 2.0.35__py3-none-any.whl

edc_offstudy/model_mixins/offstudy_model_mixin.py

@@ -9,7 +9,7 @@ from edc_identifier.model_mixins import UniqueSubjectIdentifierFieldMixin
 from edc_model.validators import datetime_not_future
 from edc_model_fields.fields import OtherCharField
 from edc_protocol.validators import datetime_not_before_study_start
-from edc_utils import convert_php_dateformat
+from edc_utils.text import convert_php_dateformat
 from edc_visit_schedule.utils import (
     off_all_schedules_or_raise,
     offstudy_datetime_after_all_offschedule_datetimes,

edc_offstudy/modelform_mixins/crf/offstudy_crf_modelform_mixin.py

@@ -1,7 +1,7 @@
 from django import forms
 from django.core.exceptions import ObjectDoesNotExist
 
-from edc_utils import formatted_datetime
+from edc_utils.text import formatted_datetime
 from edc_visit_schedule.site_visit_schedules import site_visit_schedules
 
 from ...utils import OffstudyError, raise_if_offstudy
@@ -54,4 +54,4 @@ class OffstudyCrfModelFormMixin:
                     report_datetime=self.report_datetime,
                 )
             except OffstudyError as e:
-                raise forms.ValidationError(e)
+                raise forms.ValidationError(str(e)) from e

edc_offstudy/utils.py

@@ -7,7 +7,7 @@ from django.apps import apps as django_apps
 from django.core.exceptions import ObjectDoesNotExist
 from django.db import transaction
 
-from edc_utils import formatted_datetime, to_utc
+from edc_utils.text import formatted_datetime
 from edc_visit_schedule.site_visit_schedules import site_visit_schedules
 
 from .exceptions import OffstudyError
@@ -33,9 +33,9 @@ def get_offstudy_model_cls() -> OffstudyModelMixin:
 
 
 def raise_if_offstudy(
+    subject_identifier: str,
+    report_datetime: datetime,
     source_obj: Model | None = None,
-    subject_identifier: str = None,
-    report_datetime: datetime = None,
 ) -> OffstudyModelMixin | None:
     """Returns None or raises OffstudyError"""
     obj = None
@@ -43,7 +43,7 @@ def raise_if_offstudy(
         with transaction.atomic():
             obj = get_offstudy_model_cls().objects.get(
                 subject_identifier=subject_identifier,
-                offstudy_datetime__lt=to_utc(report_datetime),
+                offstudy_datetime__lt=report_datetime,
             )
     except ObjectDoesNotExist:
         pass

edc_pdf_reports/crf_pdf_report.py

@@ -23,8 +23,9 @@ from edc_data_manager.get_longitudinal_value import (
 )
 from edc_protocol.research_protocol_config import ResearchProtocolConfig
 from edc_randomization.auth_objects import RANDO_UNBLINDED
-from edc_utils import formatted_age, get_static_file
+from edc_utils.age import formatted_age
 from edc_utils.date import to_local
+from edc_utils.get_static_file import get_static_file
 
 from .report import Report
 

edc_pdutils/helper.py

@@ -1,3 +1,5 @@
+import contextlib
+
 import pandas as pd
 from django.conf import settings
 
@@ -38,10 +40,8 @@ class Helper:
         """Returns a value as Yes/No/not_sure given
         1, 0 True, False, etc.
         """
-        try:
+        with contextlib.suppress(ValueError):
             value = str(int(value))
-        except ValueError:
-            pass
         if value in ["1", "True"]:
             value = YES
         elif value in ["0", "False"]:

edc_pdutils/utils/convert_dates_from_model.py

@@ -16,9 +16,10 @@ def convert_dates_from_model(
     """
     date_cols = []
     for field_cls in model_cls._meta.get_fields():
-        if field_cls.get_internal_type() in date_datatypes:
-            if field_cls.name in source_df.columns:
-                date_cols.append(field_cls.name)
+        if (field_cls.get_internal_type() in date_datatypes) and (
+            field_cls.name in source_df.columns
+        ):
+            date_cols.append(field_cls.name)  # noqa: PERF401
     if date_cols:
         source_df[date_cols] = source_df[date_cols].apply(pd.to_datetime, errors="coerce")
         if normalize:

edc_pharmacy/admin/actions/confirm_stock.py

@@ -6,7 +6,7 @@ from django.contrib import admin, messages
 from django.db.models import QuerySet
 from django.http import HttpResponseRedirect
 from django.urls import reverse
-from django.utils.translation import gettext
+from django.utils.translation import gettext as _
 
 from ...models import Receive, RepackRequest, Stock
 
@@ -17,7 +17,7 @@ def confirm_repacked_stock_action(modeladmin, request, queryset: QuerySet[Repack
         messages.add_message(
             request,
             messages.ERROR,
-            gettext("Select one and only one item"),
+            _("Select one and only one item"),
         )
     else:
         return confirm_stock_from_queryset(modeladmin, request, queryset)
@@ -30,7 +30,7 @@ def confirm_received_stock_action(modeladmin, request, queryset: QuerySet[Repack
         messages.add_message(
             request,
             messages.ERROR,
-            gettext("Select one and only one item"),
+            _("Select one and only one item"),
         )
     else:
         return confirm_stock_from_queryset(modeladmin, request, queryset)

edc_pharmacy/admin/actions/delete_items_for_stock_request.py

@@ -1,5 +1,5 @@
 from django.contrib import messages
-from django.utils.translation import gettext
+from django.utils.translation import gettext as _
 
 from ...models import StockRequestItem
 
@@ -9,7 +9,7 @@ def delete_items_for_stock_request_action(modeladmin, request, queryset):
         messages.add_message(
             request,
             messages.ERROR,
-            gettext("Select one and only one item"),
+            _("Select one and only one item"),
         )
     else:
         stock_request = queryset.first()
@@ -17,5 +17,6 @@ def delete_items_for_stock_request_action(modeladmin, request, queryset):
         messages.add_message(
             request,
             messages.SUCCESS,
-            gettext(f"Delete {deleted} items for {stock_request}"),
+            _("Delete %(deleted)s items for %(stock_request)s")
+            % dict(deleted=deleted, stock_request=stock_request),
         )

edc_pharmacy/admin/actions/delete_order_items.py

@@ -23,14 +23,18 @@ def delete_order_items_action(modeladmin, request, queryset: QuerySet[OrderItem]
         messages.add_message(
             request,
             messages.SUCCESS,
-            gettext(f"Successfully deleted {success_count} {OrderItem._meta.verbose_name}."),
+            gettext("Successfully deleted %(success_count)s %(verbose_name)s.")
+            % dict(
+                success_count=success_count, verbose_name_plural=OrderItem._meta.verbose_name
+            ),
         )
     if failed_count > 0:
         messages.add_message(
             request,
             messages.ERROR,
             gettext(
-                f"Unable to deleted {failed_count} {OrderItem._meta.verbose_name}. "
+                "Unable to deleted %(failed_count)s %(verbose_name)s. "
                 "Confirmed stock items exist."
-            ),
+            )
+            % dict(failed_count=failed_count, verbose_name=OrderItem._meta.verbose_name),
         )

edc_pharmacy/admin/actions/delete_receive_items.py

@@ -20,14 +20,16 @@ def delete_receive_items_action(modeladmin, request, queryset: QuerySet[ReceiveI
         messages.add_message(
             request,
             messages.SUCCESS,
-            gettext(f"Successfully deleted {success_count} {ReceiveItem._meta.verbose_name}."),
+            gettext("Successfully deleted %(success_count)s %(verbose_name)s.")
+            % dict(success_count=success_count, verbose_name=ReceiveItem._meta.verbose_name),
         )
     if failed_count > 0:
         messages.add_message(
             request,
             messages.ERROR,
             gettext(
-                f"Unable to deleted {failed_count} {ReceiveItem._meta.verbose_name}. "
+                "Unable to deleted %(failed_count)s %(verbose_name)s. "
                 "Confirmed stock items exist."
-            ),
+            )
+            % dict(failed_count=failed_count, verbose_name=ReceiveItem._meta.verbose_name),
         )

edc_pharmacy/admin/actions/process_repack_request.py

@@ -3,7 +3,6 @@ from __future__ import annotations
 from django.contrib import admin, messages
 from django.http import HttpResponseRedirect
 from django.urls import reverse
-from django.utils.html import format_html
 from django.utils.safestring import mark_safe
 
 from edc_utils.celery import run_task_sync_or_async
@@ -34,16 +33,13 @@ def process_repack_request_action(modeladmin, request, queryset):
     messages.add_message(
         request,
         messages.SUCCESS,
-        format_html(
-            "{}",
-            mark_safe(
-                "Repack request submitted. <BR>Next, go to the ACTION menu below and "
-                "(1)`Print labels`. Then (2) Label your stock "
-                "containers with the printed labels. "
-                "Once all stock is labelled, go to the ACTION menu below and "
-                "(3) Select `Confirm repacked and labelled stock`. "
-                f"Scan in the labels to CONFIRM the stock. ({task_id})"
-            ),  # nosec B703, B308
+        mark_safe(  # noqa: S308
+            "Repack request submitted. <BR>Next, go to the ACTION menu below and "
+            "(1)`Print labels`. Then (2) Label your stock "
+            "containers with the printed labels. "
+            "Once all stock is labelled, go to the ACTION menu below and "
+            "(3) Select `Confirm repacked and labelled stock`. "
+            f"Scan in the labels to CONFIRM the stock. ({task_id})"
         ),
     )
     if task_id:

edc_pharmacy/admin/autocomplete_admin.py

@@ -14,4 +14,4 @@ class VisitScheduleAdmin(ModelAdmin):
 @register(SiteProxy, site=edc_pharmacy_admin)
 class SiteProxyAdmin(ModelAdmin):
     ordering = ("name",)
-    search_fields = ["id", "name"]
+    search_fields = ("id", "name")

edc_pharmacy/admin/list_filters.py

@@ -14,14 +14,15 @@ class MedicationsListFilter(SimpleListFilter):
     title = "Medication"
     parameter_name = "medication_name"
 
-    def lookups(self, request, model_admin):
-        medications = []
-        for medication in Medication.objects.all().order_by("name"):
-            medications.append((medication.name, medication.name.replace("_", " ").title()))
+    def lookups(self, request, model_admin) -> tuple[tuple[str, str], ...]:  # noqa: ARG002
+        medications = [
+            (medication.name, medication.name.replace("_", " ").title())
+            for medication in Medication.objects.all().order_by("name")
+        ]
         medications.append(("none", "None"))
         return tuple(medications)
 
-    def queryset(self, request, queryset):
+    def queryset(self, request, queryset):  # noqa: ARG002
         """Returns a queryset if the Medication name is in the list of sites"""
         qs = None
         if self.value():
@@ -40,10 +41,10 @@ class ConfirmedListFilter(SimpleListFilter):
     title = "Confirmed"
     parameter_name = "confirmation"
 
-    def lookups(self, request, model_admin):
+    def lookups(self, request, model_admin) -> tuple[tuple[str, str], ...]:  # noqa: ARG002
         return YES_NO
 
-    def queryset(self, request, queryset):
+    def queryset(self, request, queryset):  # noqa: ARG002
         qs = None
         if self.value():
             if self.value() == YES:
@@ -57,10 +58,10 @@ class AllocationListFilter(SimpleListFilter):
     title = "Allocated"
     parameter_name = "allocated"
 
-    def lookups(self, request, model_admin):
+    def lookups(self, request, model_admin):  # noqa: ARG002
         return YES_NO_NA
 
-    def queryset(self, request, queryset):
+    def queryset(self, request, queryset):  # noqa: ARG002
         qs = None
         if self.value():
             if self.value() == YES:
@@ -88,10 +89,10 @@ class StockItemAllocationListFilter(SimpleListFilter):
     title = "Allocated"
     parameter_name = "allocated"
 
-    def lookups(self, request, model_admin):
+    def lookups(self, request, model_admin):  # noqa: ARG002
         return YES_NO
 
-    def queryset(self, request, queryset):
+    def queryset(self, request, queryset):  # noqa: ARG002
         qs = None
         if self.value():
             if self.value() == YES:
@@ -105,10 +106,10 @@ class StockItemTransferredListFilter(SimpleListFilter):
     title = "Transferred"
     parameter_name = "transferred"
 
-    def lookups(self, request, model_admin):
+    def lookups(self, request, model_admin):  # noqa: ARG002
         return YES_NO
 
-    def queryset(self, request, queryset):
+    def queryset(self, request, queryset):  # noqa: ARG002
         qs = None
         if self.value():
             if self.value() == YES:
@@ -128,10 +129,10 @@ class TransferredListFilter(SimpleListFilter):
     title = "Transferred"
     parameter_name = "transferred"
 
-    def lookups(self, request, model_admin):
+    def lookups(self, request, model_admin):  # noqa: ARG002
         return YES_NO_NA
 
-    def queryset(self, request, queryset):
+    def queryset(self, request, queryset):  # noqa: ARG002
         qs = None
         if self.value():
             if self.value() == YES:
@@ -159,13 +160,14 @@ class AssignmentListFilter(SimpleListFilter):
             count=Count(self.lookup_str)
         )
         if not blinded_user(request):
-            choices = []
-            for name in [ann.get(self.lookup_str) for ann in groupby]:
-                choices.append((name, name or "None"))
+            choices = [
+                (name, name or "None")
+                for name in [ann.get(self.lookup_str) for ann in groupby]
+            ]
             return tuple(choices)
         return ("****", "****"), ("****", "****")
 
-    def queryset(self, request, queryset):
+    def queryset(self, request, queryset):  # noqa: ARG002
         qs = None
         if self.value():
             qs = queryset.filter(**{self.lookup_str: self.value()})
@@ -182,13 +184,13 @@ class HasOrderNumFilter(SimpleListFilter):
     title = "Has Order #"
     parameter_name = "has_order_num"
 
-    def lookups(self, request, model_admin):
+    def lookups(self, request, model_admin):  # noqa: ARG002
         return YES_NO
 
-    def queryset(self, request, queryset):
+    def queryset(self, request, queryset):  # noqa: ARG002
         qs = None
         if self.value():
-            isnull = True if self.value() == NO else False
+            isnull = self.value() == NO
             qs = queryset.filter(receive_item__order_item__order__isnull=isnull)
         return qs
 
@@ -197,13 +199,13 @@ class HasReceiveNumFilter(SimpleListFilter):
     title = "Has Receive #"
     parameter_name = "has_receive_num"
 
-    def lookups(self, request, model_admin):
+    def lookups(self, request, model_admin):  # noqa: ARG002
         return YES_NO
 
-    def queryset(self, request, queryset):
+    def queryset(self, request, queryset):  # noqa: ARG002
         qs = None
         if self.value():
-            isnull = True if self.value() == NO else False
+            isnull = self.value() == NO
             qs = queryset.filter(receive_item__receive__isnull=isnull)
         return qs
 
@@ -212,13 +214,13 @@ class HasRepackNumFilter(SimpleListFilter):
     title = "Has Repack #"
     parameter_name = "has_repack_num"
 
-    def lookups(self, request, model_admin):
+    def lookups(self, request, model_admin):  # noqa: ARG002
         return YES_NO
 
-    def queryset(self, request, queryset):
+    def queryset(self, request, queryset):  # noqa: ARG002
         qs = None
         if self.value():
-            isnull = True if self.value() == NO else False
+            isnull = self.value() == NO
             qs = queryset.filter(repack_request__isnull=isnull)
         return qs
 
@@ -227,10 +229,10 @@ class TransferredFilter(SimpleListFilter):
     title = "Transferred to site"
     parameter_name = "transferred"
 
-    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
         qs = None
         if self.value():
             opts = dict(
@@ -249,10 +251,10 @@ class ConfirmedAtSiteFilter(SimpleListFilter):
     title = "Confirmed at site"
     parameter_name = "confirmed_at_site"
 
-    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
         qs = None
         if self.value():
             opts = dict(
@@ -272,10 +274,10 @@ class StoredAtSiteFilter(SimpleListFilter):
     title = "Stored at site"
     parameter_name = "stored_at_site_now"
 
-    def lookups(self, request, model_admin):
+    def lookups(self, request, model_admin):  # noqa: ARG002
         return YES_NO_NA
 
-    def queryset(self, request, queryset):
+    def queryset(self, request, queryset):  # noqa: ARG002
         qs = None
         if self.value():
             if self.value() == YES:
@@ -315,10 +317,10 @@ class DispensedFilter(SimpleListFilter):
     title = "Dispensed"
     parameter_name = "dispensed"
 
-    def lookups(self, request, model_admin):
+    def lookups(self, request, model_admin):  # noqa: ARG002
         return YES_NO
 
-    def queryset(self, request, queryset):
+    def queryset(self, request, queryset):  # noqa: ARG002
         qs = None
         if self.value():
             opts = dict(
@@ -339,10 +341,10 @@ class HasCodesListFilter(SimpleListFilter):
     title = "Has codes"
     parameter_name = "has_codes"
 
-    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
         qs = None
         if self.value():
             if self.value() == YES:
@@ -356,14 +358,14 @@ class StockRequestItemPendingListFilter(SimpleListFilter):
     title = "Request Status"
     parameter_name = "item_status"
 
-    def lookups(self, request, model_admin):
+    def lookups(self, request, model_admin):  # noqa: ARG002
         return (
             ("not_allocated", "Not allocated"),
             ("allocated_only", "Allocated only"),
             ("transferred", "Allocation and transferred"),
         )
 
-    def queryset(self, request, queryset):
+    def queryset(self, request, queryset):  # noqa: ARG002
         qs = None
         if self.value():
             if self.value() == "not_allocated":
@@ -387,14 +389,14 @@ class OrderItemStatusListFilter(SimpleListFilter):
     title = "Status"
     parameter_name = "order_item_status"
 
-    def lookups(self, request, model_admin):
+    def lookups(self, request, model_admin):  # noqa: ARG002
         return (
             (NEW, _("New")),
             (PARTIAL, _("Partial")),
             (RECEIVED, _("Received")),
         )
 
-    def queryset(self, request, queryset):
+    def queryset(self, request, queryset):  # noqa: ARG002
         qs = None
         if self.value():
             if self.value() == RECEIVED:
@@ -410,10 +412,10 @@ class DecantedListFilter(SimpleListFilter):
     title = "Decanted"
     parameter_name = "decanted"
 
-    def lookups(self, request, model_admin):
+    def lookups(self, request, model_admin):  # noqa: ARG002
         return YES_NO
 
-    def queryset(self, request, queryset):
+    def queryset(self, request, queryset):  # noqa: ARG002
         qs = None
         if self.value():
             if self.value() == YES:
@@ -427,10 +429,10 @@ class StorageBinItemDispensedFilter(SimpleListFilter):
     title = "Dispensed"
     parameter_name = "dispensed"
 
-    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
         qs = None
         if self.value():
             if self.value() == YES:

edc_pharmacy/admin/medication/assignment_admin.py

@@ -28,16 +28,16 @@ class AssignmentAdmin(ModelAdminMixin, admin.ModelAdmin):
         audit_fieldset_tuple,
     )
 
-    list_display: tuple[str, ...] = (
+    list_display = (
         "name",
         "display_name",
         "created",
         "modified",
     )
 
-    search_fields: tuple[str, ...] = ("name", "display_name")
+    search_fields = ("name", "display_name")
 
-    def get_readonly_fields(self, request, obj=None):
+    def get_readonly_fields(self, request, obj=None):  # noqa: ARG002
         if obj:
-            return self.readonly_fields + ("name",)
+            return tuple({*self.readonly_fields, "name"})
         return self.readonly_fields

edc_pharmacy/admin/medication/dosage_guideline_admin.py

@@ -11,7 +11,7 @@ from ..model_admin_mixin import ModelAdminMixin
 class DosageGuidelineAdmin(ModelAdminMixin, admin.ModelAdmin):
     show_object_tools = True
 
-    autocomplete_fields = ["medication"]
+    autocomplete_fields = ("medication",)
 
     form = DosageGuidelineForm
 
@@ -32,5 +32,5 @@ class DosageGuidelineAdmin(ModelAdminMixin, admin.ModelAdmin):
         audit_fieldset_tuple,
     )
 
-    list_display: tuple[str, ...] = ("__str__", "modified", "user_modified")
-    search_fields: tuple[str, ...] = ("medication__name",)
+    list_display = ("__str__", "modified", "user_modified")
+    search_fields = ("medication__name",)

edc_pharmacy/admin/medication/formulation_admin.py

@@ -11,7 +11,7 @@ from ..model_admin_mixin import ModelAdminMixin
 class FormulationAdmin(ModelAdminMixin, admin.ModelAdmin):
     show_object_tools = True
 
-    autocomplete_fields = ["medication"]
+    autocomplete_fields = ("medication",)
 
     form = FormulationForm
 
@@ -45,13 +45,13 @@ class FormulationAdmin(ModelAdminMixin, admin.ModelAdmin):
         audit_fieldset_tuple,
     )
 
-    radio_fields = {
+    radio_fields = {  # noqa: RUF012
         "units": admin.VERTICAL,
         "formulation_type": admin.VERTICAL,
         "route": admin.VERTICAL,
     }
 
-    list_filter: tuple[str, ...] = (
+    list_filter = (
         "imp",
         "strength",
         "units",
@@ -68,6 +68,6 @@ class FormulationAdmin(ModelAdminMixin, admin.ModelAdmin):
         "route",
     )
 
-    search_fields: tuple[str, ...] = ("medication__name",)
+    search_fields = ("medication__name",)
 
-    ordering: tuple[str, ...] = ("medication__name",)
+    ordering = ("medication__name",)

edc_pharmacy/admin/medication/medication_admin.py

@@ -21,8 +21,8 @@ class MedicationAdmin(ModelAdminMixin, admin.ModelAdmin):
         audit_fieldset_tuple,
     )
 
-    list_display: tuple[str, ...] = ("name", "display_name", "created", "modified")
+    list_display = ("name", "display_name", "created", "modified")
 
-    search_fields: tuple[str, ...] = ("name",)
+    search_fields = ("name",)
 
-    ordering: tuple[str, ...] = ("name",)
+    ordering = ("name",)

edc_pharmacy/admin/prescription/rx_admin.py

@@ -76,14 +76,14 @@ class RxAdmin(ModelAdminSubjectDashboardMixin, admin.ModelAdmin):
     )
 
     @admin.display
-    def add_refill(self, obj=None, label=None):
+    def add_refill(self, obj=None, label=None):  # noqa: ARG002
         url = reverse("edc_pharmacy_admin:edc_pharmacy_rxrefill_add")
         url = f"{url}?rx={obj.id}"
         context = dict(title="Add refill", url=url, label="Add refill")
         return render_to_string("edc_subject_dashboard/dashboard_button.html", context=context)
 
     @admin.display
-    def refills(self, obj=None, label=None):
+    def refills(self, obj=None, label=None):  # noqa: ARG002
         url = reverse("edc_pharmacy_admin:edc_pharmacy_rxrefill_changelist")
         url = f"{url}?q={obj.id}"
         context = dict(title="RX items", url=url, label="Refills")