clinicedc 2.0.7__py3-none-any.whl → 2.0.8__py3-none-any.whl

edc_consent/auths.py

@@ -6,15 +6,21 @@ from edc_auth.utils import remove_default_model_permissions_from_edc_permissions
 
 from .auth_objects import consent_codenames, navbar_tuples
 
-site_auths.add_post_update_func(
-    "edc_consent",
-    remove_default_model_permissions_from_edc_permissions,
-)
-
-site_auths.add_custom_permissions_tuples(
-    model="edc_consent.edcpermissions", codename_tuples=navbar_tuples
-)
-
-site_auths.update_group(*consent_codenames, name=PII, no_delete=True)
-site_auths.update_group(*consent_codenames, name=PII_VIEW, view_only=True)
-site_auths.add_pii_model(settings.SUBJECT_CONSENT_MODEL)
+
+def update_site_auths():
+
+    site_auths.add_post_update_func(
+        "edc_consent",
+        remove_default_model_permissions_from_edc_permissions,
+    )
+
+    site_auths.add_custom_permissions_tuples(
+        model="edc_consent.edcpermissions", codename_tuples=navbar_tuples
+    )
+
+    site_auths.update_group(*consent_codenames, name=PII, no_delete=True)
+    site_auths.update_group(*consent_codenames, name=PII_VIEW, view_only=True)
+    site_auths.add_pii_model(settings.SUBJECT_CONSENT_MODEL)
+
+
+update_site_auths()

edc_constants/constants.py

@@ -135,6 +135,7 @@ NOT_SURE = "not_sure"
 NOT_TESTED = "not_tested"
 NO_EXAM = "NO_EXAM"
 NO_UNCONFIRMED = "no_unconfirmed"
+NULL_STRING = ""
 OBSERVATION = "observation"
 OK = "OK"
 OFF_STUDY = "off study"

edc_crf/auths.py

@@ -0,0 +1,5 @@
+def update_site_auths():
+    return None
+
+
+update_site_auths()

edc_dashboard/auths.py

@@ -3,11 +3,15 @@ from edc_auth.utils import remove_default_model_permissions_from_edc_permissions
 
 from .auth_objects import dashboard_tuples
 
-site_auths.add_post_update_func(
-    "edc_dashboard", remove_default_model_permissions_from_edc_permissions
-)
 
+def update_site_auths():
+    site_auths.add_post_update_func(
+        "edc_dashboard", remove_default_model_permissions_from_edc_permissions
+    )
 
-site_auths.add_custom_permissions_tuples(
-    model="edc_dashboard.edcpermissions", codename_tuples=dashboard_tuples
-)
+    site_auths.add_custom_permissions_tuples(
+        model="edc_dashboard.edcpermissions", codename_tuples=dashboard_tuples
+    )
+
+
+update_site_auths()

edc_dashboard/url_config.py

@@ -20,12 +20,13 @@ if TYPE_CHECKING:
 class UrlConfig:
     def __init__(
         self,
-        url_name: str = None,
-        namespace: str = None,
-        view_class: type[View | UrlRequestContextMixin] = None,
-        label: str = None,
-        identifier_label: str = None,
-        identifier_pattern: str = None,
+        *,
+        url_name: str,
+        namespace: str,
+        view_class: type[View | UrlRequestContextMixin],
+        label: str,
+        identifier_label: str,
+        identifier_pattern: str,
     ):
         self.identifier_label = identifier_label
         self.identifier_pattern = identifier_pattern
@@ -39,102 +40,108 @@ class UrlConfig:
     @property
     def dashboard_urls(self) -> list[URLPattern]:
         """Returns url patterns."""
-        urlpatterns = [
+        return [
             re_path(
-                "%(label)s/"
-                "(?P<%(identifier_label)s>%(identifier_pattern)s)/"
+                "{label}/"
+                "(?P<{identifier_label}>{identifier_pattern})/"
                 r"(?P<visit_schedule_name>\w+)/"
                 r"(?P<schedule_name>\w+)/"
                 r"(?P<visit_code>\w+)/"
-                r"(?P<unscheduled>\w+)/"
-                % {
-                    "label": self.label,
-                    "identifier_label": self.identifier_label,
-                    "identifier_pattern": self.identifier_pattern,
-                },
+                r"(?P<unscheduled>\w+)/".format(
+                    **dict(
+                        label=self.label,
+                        identifier_label=self.identifier_label,
+                        identifier_pattern=self.identifier_pattern,
+                    )
+                ),
                 self.view_class.as_view(),
                 name=self.url_name,
             ),
             re_path(
-                "%(label)s/"
-                "(?P<%(identifier_label)s>%(identifier_pattern)s)/"
+                "{label}/"
+                "(?P<{identifier_label}>{identifier_pattern})/"
                 r"(?P<visit_schedule_name>\w+)/"
                 r"(?P<schedule_name>\w+)/"
-                r"(?P<visit_code>\w+)/"
-                % dict(
-                    label=self.label,
-                    identifier_label=self.identifier_label,
-                    identifier_pattern=self.identifier_pattern,
+                r"(?P<visit_code>\w+)/".format(
+                    **dict(
+                        label=self.label,
+                        identifier_label=self.identifier_label,
+                        identifier_pattern=self.identifier_pattern,
+                    )
                 ),
                 self.view_class.as_view(),
                 name=self.url_name,
             ),
             re_path(
-                "%(label)s/"
-                "(?P<%(identifier_label)s>%(identifier_pattern)s)/"
-                "(?P<appointment>%(uuid_pattern)s)/"
+                "{label}/"
+                "(?P<{identifier_label}>{identifier_pattern})/"
+                "(?P<appointment>{uuid_pattern})/"
                 r"(?P<scanning>\d)/"
-                r"(?P<error>\d)/"
-                % dict(
-                    label=self.label,
-                    identifier_label=self.identifier_label,
-                    identifier_pattern=self.identifier_pattern,
-                    uuid_pattern=UUID_PATTERN.pattern,
+                r"(?P<error>\d)/".format(
+                    **dict(
+                        label=self.label,
+                        identifier_label=self.identifier_label,
+                        identifier_pattern=self.identifier_pattern,
+                        uuid_pattern=UUID_PATTERN.pattern,
+                    )
                 ),
                 self.view_class.as_view(),
                 name=self.url_name,
             ),
             re_path(
-                "%(label)s/"
-                "(?P<%(identifier_label)s>%(identifier_pattern)s)/"
-                "(?P<appointment>%(uuid_pattern)s)/"
-                r"(?P<reason>\w+)/"
-                % dict(
-                    label=self.label,
-                    identifier_label=self.identifier_label,
-                    identifier_pattern=self.identifier_pattern,
-                    uuid_pattern=UUID_PATTERN.pattern,
+                "{label}/"
+                "(?P<{identifier_label}>{identifier_pattern})/"
+                "(?P<appointment>{uuid_pattern})/"
+                r"(?P<reason>\w+)/".format(
+                    **dict(
+                        label=self.label,
+                        identifier_label=self.identifier_label,
+                        identifier_pattern=self.identifier_pattern,
+                        uuid_pattern=UUID_PATTERN.pattern,
+                    )
                 ),
                 self.view_class.as_view(),
                 name=self.url_name,
             ),
             re_path(
-                "%(label)s/"
-                "(?P<%(identifier_label)s>%(identifier_pattern)s)/"
-                "(?P<appointment>%(uuid_pattern)s)/"
-                % dict(
-                    label=self.label,
-                    identifier_label=self.identifier_label,
-                    identifier_pattern=self.identifier_pattern,
-                    uuid_pattern=UUID_PATTERN.pattern,
+                "{label}/"
+                "(?P<{identifier_label}>{identifier_pattern})/"
+                "(?P<appointment>{uuid_pattern})/".format(
+                    **dict(
+                        label=self.label,
+                        identifier_label=self.identifier_label,
+                        identifier_pattern=self.identifier_pattern,
+                        uuid_pattern=UUID_PATTERN.pattern,
+                    )
                 ),
                 self.view_class.as_view(),
                 name=self.url_name,
             ),
             re_path(
-                "%(label)s/"
-                "(?P<%(identifier_label)s>%(identifier_pattern)s)/"
-                r"(?P<schedule_name>\w+)/"
-                % dict(
-                    label=self.label,
-                    identifier_label=self.identifier_label,
-                    identifier_pattern=self.identifier_pattern,
+                "{label}/"
+                "(?P<{identifier_label}>{identifier_pattern})/"
+                r"(?P<schedule_name>\w+)/".format(
+                    **dict(
+                        label=self.label,
+                        identifier_label=self.identifier_label,
+                        identifier_pattern=self.identifier_pattern,
+                    )
                 ),
                 self.view_class.as_view(),
                 name=self.url_name,
             ),
             re_path(
-                "%(label)s/(?P<%(identifier_label)s>%(identifier_pattern)s)/"
-                % dict(
-                    label=self.label,
-                    identifier_label=self.identifier_label,
-                    identifier_pattern=self.identifier_pattern,
+                "{label}/(?P<{identifier_label}>{identifier_pattern})/".format(
+                    **dict(
+                        label=self.label,
+                        identifier_label=self.identifier_label,
+                        identifier_pattern=self.identifier_pattern,
+                    )
                 ),
                 self.view_class.as_view(),
                 name=self.url_name,
             ),
         ]
-        return urlpatterns
 
     @property
     def listboard_urls(self) -> list[URLPattern]:
@@ -142,52 +149,54 @@ class UrlConfig:
 
         configs = [(listboard_url, listboard_view_class, label), (), ...]
         """
-        urlpatterns = [
+        return [
             re_path(
-                "%(label)s/(?P<%(identifier_label)s>%(identifier_pattern)s)/"
-                r"(?P<page>\d+)/"
-                % dict(
-                    label=self.label,
-                    identifier_label=self.identifier_label,
-                    identifier_pattern=self.identifier_pattern,
+                "{label}/(?P<{identifier_label}>{identifier_pattern})/"
+                r"(?P<page>\d+)/".format(
+                    **dict(
+                        label=self.label,
+                        identifier_label=self.identifier_label,
+                        identifier_pattern=self.identifier_pattern,
+                    )
                 ),
                 self.view_class.as_view(),
                 name=self.url_name,
             ),
             re_path(
-                "%(label)s/(?P<%(identifier_label)s>%(identifier_pattern)s)/"
-                % dict(
-                    label=self.label,
-                    identifier_label=self.identifier_label,
-                    identifier_pattern=self.identifier_pattern,
+                "{label}/(?P<{identifier_label}>{identifier_pattern})/".format(
+                    **dict(
+                        label=self.label,
+                        identifier_label=self.identifier_label,
+                        identifier_pattern=self.identifier_pattern,
+                    )
                 ),
                 self.view_class.as_view(),
                 name=self.url_name,
             ),
             re_path(
-                r"%(label)s/(?P<page>\d+)/" % dict(label=self.label),
+                r"{label}/(?P<page>\d+)/".format(**dict(label=self.label)),
                 self.view_class.as_view(),
                 name=self.url_name,
             ),
             re_path(
-                r"%(label)s/" % dict(label=self.label),
+                r"{label}/".format(**dict(label=self.label)),
                 self.view_class.as_view(),
                 name=self.url_name,
             ),
         ]
-        return urlpatterns
 
     @property
     def review_listboard_urls(self) -> list[URLPattern]:
         url_patterns = [
             re_path(
-                "%(label)s/(?P<%(identifier_label)s>%(identifier_pattern)s)/"
-                "(?P<appointment>%(uuid_pattern)s)/"
-                % dict(
-                    label=self.label,
-                    identifier_label=self.identifier_label,
-                    identifier_pattern=self.identifier_pattern,
-                    uuid_pattern=UUID_PATTERN.pattern,
+                "{label}/(?P<{identifier_label}>{identifier_pattern})/"
+                "(?P<appointment>{uuid_pattern})/".format(
+                    **dict(
+                        label=self.label,
+                        identifier_label=self.identifier_label,
+                        identifier_pattern=self.identifier_pattern,
+                        uuid_pattern=UUID_PATTERN.pattern,
+                    )
                 ),
                 self.view_class.as_view(),
                 name=self.url_name,

edc_dashboard/url_names.py

@@ -3,11 +3,11 @@ from __future__ import annotations
 from dataclasses import dataclass, field
 
 
-class AlreadyRegistered(Exception):
+class AlreadyRegistered(Exception):  # noqa: N818
     pass
 
 
-class InvalidDashboardUrlName(Exception):
+class InvalidDashboardUrlName(Exception):  # noqa: N818
     pass
 
 
@@ -16,12 +16,12 @@ class UrlNames:
     registry: dict[str, str] = field(default_factory=dict)
 
     def register(
-        self, name: str = None, url: str = None, namespace: str | None = None
+        self, name: str | None = None, url: str | None = None, namespace: str | None = None
     ) -> None:
         name = name or url
         complete_url = f"{namespace}:{url}" if namespace else url
         if name in self.registry:
-            raise AlreadyRegistered(f"Url already registered. Got {name}.")
+            raise AlreadyRegistered(f"Url already registered. Got {complete_url}.")
         self.registry.update({name: complete_url})
 
     def register_from_dict(self, **urldata: str) -> None:

edc_dashboard/view_mixins/url_request_context_mixin.py

@@ -30,10 +30,11 @@ class UrlRequestContextMixin:
     @classmethod
     def urls(
         cls,
-        namespace: str = None,
-        label: str = None,
-        identifier_label: str = None,
-        identifier_pattern: str = None,
+        *,
+        label: str,
+        identifier_pattern: str,
+        namespace: str | None = None,
+        identifier_label: str | None = None,
     ) -> list[URLPattern]:
         label = (
             label
@@ -62,5 +63,5 @@ class UrlRequestContextMixin:
                 f"Url name not defined in url_names. "
                 f"Expected one of {url_names.registry}. Got {e}. "
                 f"Hint: check if dashboard middleware is loaded."
-            )
+            ) from e
         return url_data

edc_data_manager/admin/data_query_admin.py

@@ -45,7 +45,7 @@ class DataQueryAdmin(SiteModelAdminMixin, ModelAdminSubjectDashboardMixin, Simpl
 
     locked_column_template_name = "edc_data_manager/columns/locked.html"
 
-    status_column_context = {
+    status_column_context = {  # noqa: RUF012
         "NEW": NEW,
         "OPEN": OPEN,
         "FEEDBACK": FEEDBACK,
@@ -61,13 +61,13 @@ class DataQueryAdmin(SiteModelAdminMixin, ModelAdminSubjectDashboardMixin, Simpl
 
     actions = (toggle_dm_status,)
 
-    radio_fields = {
+    radio_fields = {  # noqa: RUF012
         "status": admin.VERTICAL,
         "site_response_status": admin.VERTICAL,
         "query_priority": admin.VERTICAL,
     }
 
-    autocomplete_fields = [
+    autocomplete_fields = (
         "sender",
         "recipients",
         "data_dictionaries",
@@ -75,7 +75,7 @@ class DataQueryAdmin(SiteModelAdminMixin, ModelAdminSubjectDashboardMixin, Simpl
         "visit_schedule",
         "registered_subject",
         "dm_user",
-    ]
+    )
 
     list_display = (
         "wrapped_title",
@@ -201,11 +201,10 @@ class DataQueryAdmin(SiteModelAdminMixin, ModelAdminSubjectDashboardMixin, Simpl
     wrapped_title.short_description = "Title"
 
     def formfield_for_manytomany(self, db_field, request, **kwargs):
-        if db_field.name == "data_dictionaries":
-            if request.GET.get("title"):
-                kwargs["queryset"] = DataDictionary.objects.filter(
-                    model_verbose_name=request.GET.get("title")
-                )
+        if db_field.name == "data_dictionaries" and request.GET.get("title"):
+            kwargs["queryset"] = DataDictionary.objects.filter(
+                model_verbose_name=request.GET.get("title")
+            )
         return super().formfield_for_manytomany(db_field, request, **kwargs)
 
     def query_dates(self, obj):
@@ -332,7 +331,8 @@ class DataQueryAdmin(SiteModelAdminMixin, ModelAdminSubjectDashboardMixin, Simpl
             "missed_visit",
             "auto_resolved",
             "registered_subject",
-        ) + action_fields
+            *action_fields,
+        )
         if not request.user.groups.filter(name=DATA_MANAGER):
             extra_fields = (
                 "data_dictionaries",
@@ -350,10 +350,11 @@ class DataQueryAdmin(SiteModelAdminMixin, ModelAdminSubjectDashboardMixin, Simpl
                 "title",
                 "visit_code_sequence",
                 "visit_schedule",
+                *extra_fields,
             )
         if not obj:
             extra_fields = tuple(f for f in extra_fields if f != "registered_subject")
-        return fields + extra_fields
+        return *fields, *extra_fields
 
     def get_subject_dashboard_url_kwargs(self, obj):
         def get_opts():

edc_data_manager/auths.py

@@ -18,45 +18,48 @@ from .auth_objects import (
     data_manager,
 )
 
-site_auths.add_custom_permissions_tuples(
-    model="edc_data_manager.edcpermissions", codename_tuples=custom_codename_tuples
-)
 
-site_auths.add_custom_permissions_tuples(
-    model="edc_data_manager.edcpermissions",
-    codename_tuples=[("edc_data_manager.special_bypassmodelform", "Can bypass modelform")],
-)
+def update_site_auths():
+    site_auths.add_custom_permissions_tuples(
+        model="edc_data_manager.edcpermissions", codename_tuples=custom_codename_tuples
+    )
 
+    site_auths.add_custom_permissions_tuples(
+        model="edc_data_manager.edcpermissions",
+        codename_tuples=[("edc_data_manager.special_bypassmodelform", "Can bypass modelform")],
+    )
 
-# groups
-site_auths.add_group(*data_manager, name=DATA_MANAGER)
-site_auths.add_group(*data_manager, name=DATA_QUERY_VIEW, view_only=True)
+    # groups
+    site_auths.add_group(*data_manager, name=DATA_MANAGER)
+    site_auths.add_group(*data_manager, name=DATA_QUERY_VIEW, view_only=True)
 
-site_auths.add_group(*data_manager, name=DATA_QUERY, view_only=True)
-site_auths.update_group("edc_data_manager.change_dataquery", name=DATA_QUERY)
+    site_auths.add_group(*data_manager, name=DATA_QUERY, view_only=True)
+    site_auths.update_group("edc_data_manager.change_dataquery", name=DATA_QUERY)
 
-site_auths.add_group(
-    "edc_data_manager.export_datadictionary",
-    "edc_data_manager.export_dataquery",
-    "edc_data_manager.export_queryrule",
-    name=DATA_MANAGER_EXPORT,
-)
+    site_auths.add_group(
+        "edc_data_manager.export_datadictionary",
+        "edc_data_manager.export_dataquery",
+        "edc_data_manager.export_queryrule",
+        name=DATA_MANAGER_EXPORT,
+    )
 
-site_auths.add_group(*data_manager, name=DATA_MANAGER_SUPER)
-site_auths.update_group("edc_data_manager.change_dataquery", name=DATA_MANAGER_SUPER)
-site_auths.update_group(
-    "edc_data_manager.export_datadictionary",
-    "edc_data_manager.export_dataquery",
-    "edc_data_manager.export_queryrule",
-    "edc_data_manager.special_bypassmodelform",
-    "edc_data_manager.change_dataquery",
-    name=DATA_MANAGER_SUPER,
-)
+    site_auths.add_group(*data_manager, name=DATA_MANAGER_SUPER)
+    site_auths.update_group("edc_data_manager.change_dataquery", name=DATA_MANAGER_SUPER)
+    site_auths.update_group(
+        "edc_data_manager.export_datadictionary",
+        "edc_data_manager.export_dataquery",
+        "edc_data_manager.export_queryrule",
+        "edc_data_manager.special_bypassmodelform",
+        "edc_data_manager.change_dataquery",
+        name=DATA_MANAGER_SUPER,
+    )
+
+    # roles
+    site_auths.add_role(CELERY_MANAGER, DATA_MANAGER, name=DATA_MANAGER_ROLE)
+    site_auths.add_role(DATA_QUERY, name=SITE_DATA_MANAGER_ROLE)
+    site_auths.update_role(DATA_QUERY, name=CLINICIAN_ROLE)
+    site_auths.update_role(DATA_QUERY, name=NURSE_ROLE)
+    site_auths.update_role(DATA_QUERY, name=CLINICIAN_SUPER_ROLE)
 
 
-# roles
-site_auths.add_role(CELERY_MANAGER, DATA_MANAGER, name=DATA_MANAGER_ROLE)
-site_auths.add_role(DATA_QUERY, name=SITE_DATA_MANAGER_ROLE)
-site_auths.update_role(DATA_QUERY, name=CLINICIAN_ROLE)
-site_auths.update_role(DATA_QUERY, name=NURSE_ROLE)
-site_auths.update_role(DATA_QUERY, name=CLINICIAN_SUPER_ROLE)
+update_site_auths()

edc_data_manager/rule/query_rule_wrapper.py

@@ -2,7 +2,7 @@ from __future__ import annotations
 
 from datetime import datetime
 from decimal import Decimal
-from typing import TYPE_CHECKING, LiteralString
+from typing import TYPE_CHECKING
 
 from tqdm import tqdm
 
@@ -17,12 +17,12 @@ if TYPE_CHECKING:
 class QueryRuleWrapper:
     def __init__(
         self,
-        query_rule_obj: QueryRule = None,
-        subject_identifiers: list[LiteralString] = None,
-        visit_schedule_obj: QueryVisitSchedule = None,
-        timepoint: Decimal = None,
-        entry_status: str = None,
-        now: datetime = None,
+        query_rule_obj: QueryRule | None = None,
+        subject_identifiers: list[str] | None = None,
+        visit_schedule_obj: QueryVisitSchedule | None = None,
+        timepoint: Decimal | None = None,
+        entry_status: str | None = None,
+        now: datetime | None = None,
         verbose: bool | None = None,
     ):
         self.now = now

edc_export/archive_exporter.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+from pathlib import Path
 from tempfile import mkdtemp
 from typing import TYPE_CHECKING
 
@@ -17,7 +18,7 @@ if TYPE_CHECKING:
     from django.contrib.auth.models import User
 
 
-class ArchiveExporterNothingExported(Exception):
+class ArchiveExporterNothingExported(Exception):  # noqa: N818
     pass
 
 
@@ -56,7 +57,7 @@ class ArchiveExporter:
         for model in models:
             csv_exporter = self.csv_exporter_cls(
                 model=model,
-                export_folder=tmp_folder,
+                export_folder=Path(tmp_folder),
                 decrypt=decrypt,
                 site_ids=sites.get_site_ids_for_user(
                     user=user, site_id=sites.get_current_site().site_id