clinicedc 2.0.6__py3-none-any.whl → 2.0.8__py3-none-any.whl

edc_auth/models/user_profile.py

@@ -11,7 +11,7 @@ from edc_export.choices import EXPORT_FORMATS
 from edc_export.constants import CSV
 from edc_notification.model_mixins import NotificationUserProfileModelMixin
 
-from ..auth_objects import CUSTOM_ROLE, STAFF_ROLE
+from ..constants import CUSTOM_ROLE, STAFF_ROLE
 from .role import Role
 
 
@@ -32,21 +32,21 @@ class UserProfile(NotificationUserProfileModelMixin, models.Model):
 
     sites = models.ManyToManyField(Site, blank=True)
 
-    job_title = models.CharField(max_length=100, null=True, blank=True)
+    job_title = models.CharField(max_length=100, default="", blank=True)
 
-    alternate_email = models.EmailField(_("Alternate email address"), blank=True, null=True)
+    alternate_email = models.EmailField(_("Alternate email address"), blank=True, default="")
 
     mobile = models.CharField(
         max_length=25,
         validators=[RegexValidator(regex=r"^\+\d+")],
-        null=True,
+        default="",
         blank=True,
         help_text="e.g. +1234567890",
     )
 
     clinic_label_printer = models.CharField(
         max_length=100,
-        null=True,
+        default="",
         blank=True,
         help_text=format_html(
             'Change in <a href="{href}">{label}</a>',
@@ -57,7 +57,7 @@ class UserProfile(NotificationUserProfileModelMixin, models.Model):
 
     lab_label_printer = models.CharField(
         max_length=100,
-        null=True,
+        default="",
         blank=True,
         help_text=format_html(
             'Change in <a href="{href}">{label}</a>',
@@ -68,7 +68,7 @@ class UserProfile(NotificationUserProfileModelMixin, models.Model):
 
     print_server = models.CharField(
         max_length=100,
-        null=True,
+        default="",
         blank=True,
         help_text=format_html(
             'Change in <a href="{href}">{label}</a>',
@@ -82,7 +82,6 @@ class UserProfile(NotificationUserProfileModelMixin, models.Model):
         max_length=25,
         choices=EXPORT_FORMATS,
         default=CSV,
-        null=True,
         blank=True,
         help_text="Note: requires export permissions",
     )
@@ -101,9 +100,13 @@ class UserProfile(NotificationUserProfileModelMixin, models.Model):
             group_names = [group.name for group in self.user.groups.all()]
             add_group_names = []
             for role in self.roles.all():
-                for group in role.groups.all():
-                    if group.name not in group_names:
-                        add_group_names.append(group.name)
+                add_group_names.extend(
+                    [
+                        group.name
+                        for group in role.groups.all()
+                        if group.name not in group_names
+                    ]
+                )
             add_group_names = list(set(add_group_names))
             for name in add_group_names:
                 self.user.groups.add(Group.objects.get(name=name))

edc_auth/post_migrate_signals.py

@@ -6,7 +6,7 @@ from django.core.management.color import color_style
 style = color_style()
 
 
-def post_migrate_user_groups_and_roles(sender=None, **kwargs):  # noqa
+def post_migrate_user_groups_and_roles(sender=None, **kwargs):
     """Update Groups, Role model with EDC defaults."""
 
     from .auth_updater import AuthUpdater

edc_auth/site_auths.py

@@ -9,30 +9,40 @@ from django.apps import apps as django_apps
 from django.conf import settings
 from django.utils.module_loading import import_module, module_has_submodule
 
-from .auth_objects import default_groups, default_pii_models, default_roles
-
-
-class AlreadyRegistered(Exception):
+from .auth_objects import default_pii_models, get_default_groups, get_default_roles
+from .constants import (
+    CUSTOM_PERMISSIONS_TUPLES_KEY,
+    GROUPS_KEY,
+    PII_MODELS_KEY,
+    POST_UPDATE_FUNCS_KEY,
+    PRE_UPDATE_FUNCS_KEY,
+    ROLES_KEY,
+    UPDATE_GROUPS_KEY,
+    UPDATE_ROLES_KEY,
+)
+
+
+class AlreadyRegistered(Exception):  # noqa: N818
     pass
 
 
-class InvalidGroup(Exception):
+class InvalidGroup(Exception):  # noqa: N818
     pass
 
 
-class InvalidRole(Exception):
+class InvalidRole(Exception):  # noqa: N818
     pass
 
 
-class RoleAlreadyExists(Exception):
+class RoleAlreadyExists(Exception):  # noqa: N818
     pass
 
 
-class GroupAlreadyExists(Exception):
+class GroupAlreadyExists(Exception):  # noqa: N818
     pass
 
 
-class PiiModelAlreadyExists(Exception):
+class PiiModelAlreadyExists(Exception):  # noqa: N818
     pass
 
 
@@ -96,39 +106,39 @@ class SiteAuths:
 
     def initialize(self):
         self.registry = {
-            "groups": default_groups,
-            "roles": default_roles,
-            "update_groups": {},
-            "update_roles": {},
-            "custom_permissions_tuples": {},
-            "pre_update_funcs": [],
-            "post_update_funcs": [],
-            "pii_models": default_pii_models,
+            GROUPS_KEY: get_default_groups(),
+            ROLES_KEY: get_default_roles(),
+            UPDATE_GROUPS_KEY: {},
+            UPDATE_ROLES_KEY: {},
+            CUSTOM_PERMISSIONS_TUPLES_KEY: {},
+            PRE_UPDATE_FUNCS_KEY: [],
+            POST_UPDATE_FUNCS_KEY: [],
+            PII_MODELS_KEY: default_pii_models,
         }
 
     def clear(self):
         self.registry = {
-            "groups": {},
-            "roles": {},
-            "update_groups": {},
-            "update_roles": {},
-            "custom_permissions_tuples": {},
-            "pre_update_funcs": [],
-            "post_update_funcs": [],
-            "pii_models": [],
+            GROUPS_KEY: {},
+            ROLES_KEY: {},
+            UPDATE_GROUPS_KEY: {},
+            UPDATE_ROLES_KEY: {},
+            CUSTOM_PERMISSIONS_TUPLES_KEY: {},
+            PRE_UPDATE_FUNCS_KEY: [],
+            POST_UPDATE_FUNCS_KEY: [],
+            PII_MODELS_KEY: [],
         }
 
     def clear_values(self):
         registry = deepcopy(self.registry)
         self.registry = {
-            "groups": {k: [] for k in registry.get("groups")},
-            "roles": {k: [] for k in self.registry.get("roles")},
-            "update_groups": {},
-            "update_roles": {},
-            "custom_permissions_tuples": {},
-            "pre_update_funcs": [],
-            "post_update_funcs": [],
-            "pii_models": [],
+            GROUPS_KEY: {k: [] for k in registry.get(GROUPS_KEY)},
+            ROLES_KEY: {k: [] for k in self.registry.get(ROLES_KEY)},
+            UPDATE_GROUPS_KEY: {},
+            UPDATE_ROLES_KEY: {},
+            CUSTOM_PERMISSIONS_TUPLES_KEY: {},
+            PRE_UPDATE_FUNCS_KEY: [],
+            POST_UPDATE_FUNCS_KEY: [],
+            PII_MODELS_KEY: [],
         }
 
     @property
@@ -136,15 +146,15 @@ class SiteAuths:
         return getattr(settings, "EDC_AUTH_SKIP_SITE_AUTHS", False)
 
     def add_pre_update_func(self, func):
-        self.registry["pre_update_funcs"].append(func)
+        self.registry[PRE_UPDATE_FUNCS_KEY].append(func)
 
     def add_post_update_func(self, app_label: str, func: Callable):
-        self.registry["post_update_funcs"].append((app_label, func))
+        self.registry[POST_UPDATE_FUNCS_KEY].append((app_label, func))
 
     def add_pii_model(self, model_name):
-        if model_name in self.registry["pii_models"]:
+        if model_name in self.registry[PII_MODELS_KEY]:
             raise PiiModelAlreadyExists(f"PII model already exists. Got {model_name}")
-        self.registry["pii_models"].append(model_name)
+        self.registry[PII_MODELS_KEY].append(model_name)
 
     def add_groups(self, data: dict):
         for name, codenames in data.items():
@@ -162,7 +172,7 @@ class SiteAuths:
         convert_to_export=None,
         no_delete=None,
     ):
-        if name in self.registry["groups"]:
+        if name in self.registry[GROUPS_KEY]:
             raise GroupAlreadyExists(f"Group name already exists. Got {name}.")
         if no_delete:
             codenames_or_func = self.remove_delete_codenames(codenames_or_func)
@@ -170,18 +180,18 @@ class SiteAuths:
             codenames_or_func = self.get_view_only_codenames(codenames_or_func)
         if convert_to_export:
             codenames_or_func = self.convert_to_export_codenames(codenames_or_func)
-        self.registry["groups"].update({name: codenames_or_func})
+        self.registry[GROUPS_KEY].update({name: codenames_or_func})
 
     def add_role(self, *group_names, name=None):
-        if name in self.registry["roles"]:
+        if name in self.registry[ROLES_KEY]:
             raise RoleAlreadyExists(f"Role name already exists. Got {name}.")
         group_names = list(set(group_names))
-        self.registry["roles"].update({name: group_names})
+        self.registry[ROLES_KEY].update({name: group_names})
 
     def update_group(
         self, *codenames_or_func, name=None, key=None, view_only=None, no_delete=None
     ) -> None:
-        key = key or "update_groups"
+        key = key or UPDATE_GROUPS_KEY
         if no_delete:
             codenames_or_func = self.remove_delete_codenames(codenames_or_func)
         if view_only:
@@ -191,30 +201,30 @@ class SiteAuths:
         try:
             existing_codenames = list(set(existing_codenames))
         except TypeError as e:
-            raise TypeError(f"{e}. Got {name}")
+            raise TypeError(f"{e}. Got {name}") from e
         existing_codenames.extend(codenames_or_func)
         existing_codenames = list(set(existing_codenames))
         self.registry[key].update({name: existing_codenames})
 
     def update_role(self, *group_names, name=None, key=None) -> None:
-        key = key or "update_roles"
+        key = key or UPDATE_ROLES_KEY
         group_names = list(set(group_names))
-        existing_group_names = deepcopy(self.registry[key].get(name)) or []
-        existing_group_names = list(set(existing_group_names))
+        existing_group_names = [
+            name for name in self.registry[key].get(name) or [] if name not in group_names
+        ]
         existing_group_names.extend(group_names)
-        existing_group_names = list(set(existing_group_names))
         self.registry[key].update({name: existing_group_names})
 
     def add_custom_permissions_tuples(
         self, model: str, codename_tuples: tuple[tuple[str, str], ...]
     ):
         try:
-            self.registry["custom_permissions_tuples"][model]
+            self.registry[CUSTOM_PERMISSIONS_TUPLES_KEY][model]
         except KeyError:
-            self.registry["custom_permissions_tuples"].update({model: []})
+            self.registry[CUSTOM_PERMISSIONS_TUPLES_KEY].update({model: []})
         for codename_tuple in codename_tuples:
-            if codename_tuple not in self.registry["custom_permissions_tuples"][model]:
-                self.registry["custom_permissions_tuples"][model].append(codename_tuple)
+            if codename_tuple not in self.registry[CUSTOM_PERMISSIONS_TUPLES_KEY][model]:
+                self.registry[CUSTOM_PERMISSIONS_TUPLES_KEY][model].append(codename_tuple)
 
     @staticmethod
     def get_view_only_codenames(codenames):
@@ -225,7 +235,8 @@ class SiteAuths:
         Does not remove `edc_navbar`, 'nav_' or `edc_dashboard`
         codenames.
         """
-        callables = [lambda: view_only_wrapper(c) for c in codenames if callable(c)]
+        # callables = [lambda: view_only_wrapper(c) for c in codenames if callable(c)]
+        callables = [lambda c=c: view_only_wrapper(c) for c in codenames if callable(c)]
         view_only_codenames = [
             codename
             for codename in codenames
@@ -263,27 +274,27 @@ class SiteAuths:
 
     @property
     def roles(self):
-        return self.registry["roles"]
+        return self.registry[ROLES_KEY]
 
     @property
     def groups(self):
-        return self.registry["groups"]
+        return self.registry[GROUPS_KEY]
 
     @property
     def pii_models(self):
-        return self.registry["pii_models"]
+        return self.registry[PII_MODELS_KEY]
 
     @property
     def pre_update_funcs(self):
-        return self.registry["pre_update_funcs"]
+        return self.registry[PRE_UPDATE_FUNCS_KEY]
 
     @property
     def post_update_funcs(self) -> tuple[str, Callable]:
-        return self.registry["post_update_funcs"]
+        return self.registry[POST_UPDATE_FUNCS_KEY]
 
     @property
     def custom_permissions_tuples(self):
-        return self.registry["custom_permissions_tuples"]
+        return self.registry[CUSTOM_PERMISSIONS_TUPLES_KEY]
 
     def verify_and_populate(
         self, app_name: str | None = None, warn_only: bool | None = None
@@ -294,28 +305,30 @@ class SiteAuths:
         * Updates data from `update_groups` -> `groups`
         * Updates data from `update_roles` -> `roles`
         """
-        for name, codenames in self.registry["update_groups"].items():
-            if name not in self.registry["groups"]:
+        for name, codenames in self.registry[UPDATE_GROUPS_KEY].items():
+            if name not in self.registry[GROUPS_KEY]:
                 msg = (
                     f"Cannot update group. Group name does not exist. See app={app_name}"
                     f"update_groups['groups']={codenames}. Got {name}"
                 )
                 if warn_only:
-                    warn(msg)
+                    warn(msg, stacklevel=2)
                 else:
                     raise InvalidGroup(msg)
-            self.update_group(*codenames, name=name, key="groups")
-        for name, group_names in self.registry["update_roles"].items():
-            if name not in self.registry["roles"]:
+            self.update_group(*codenames, name=name, key=GROUPS_KEY)
+        self.registry[UPDATE_GROUPS_KEY] = {}
+        for name, group_names in self.registry[UPDATE_ROLES_KEY].items():
+            if name not in self.registry[ROLES_KEY]:
                 msg = (
                     f"Cannot update role. Role name does not exist. See app={app_name}. "
                     f"update_roles['groups']={group_names}. Got {name}"
                 )
                 if warn_only:
-                    warn(msg)
+                    warn(msg, stacklevel=2)
                 else:
                     raise InvalidRole(msg)
-            self.update_role(*group_names, name=name, key="roles")
+            self.update_role(*group_names, name=name, key=ROLES_KEY)
+        self.registry[UPDATE_ROLES_KEY] = {}
 
     def autodiscover(self, module_name=None, verbose=True):
         """Autodiscovers in the auths.py file of any INSTALLED_APP."""
@@ -335,7 +348,7 @@ class SiteAuths:
                     except ImportError as e:
                         site_auths.registry = before_import_registry
                         if module_has_submodule(mod, module_name):
-                            raise SiteAuthError(str(e))
+                            raise SiteAuthError(str(e)) from e
                 except ImportError:
                     pass
             self.verify_and_populate(app_name=app_name)

edc_consent/actions.py

@@ -1,13 +1,12 @@
 from django.contrib import messages
-
-from edc_utils import get_utcnow
+from django.utils import timezone
 
 
 def verify_consent(request=None, consent_obj=None):
     if consent_obj.is_verified:
         return None
     consent_obj.is_verified = True
-    consent_obj.is_verified_datetime = get_utcnow()
+    consent_obj.is_verified_datetime = timezone.now()
     consent_obj.verified_by = request.user.username
     consent_obj.save(update_fields=["is_verified", "is_verified_datetime", "verified_by"])
     return consent_obj
@@ -21,7 +20,7 @@ def unverify_consent(consent_obj=None):
     return consent_obj
 
 
-def flag_as_verified_against_paper(modeladmin, request, queryset, **kwargs):  # noqa
+def flag_as_verified_against_paper(modeladmin, request, queryset, **kwargs):
     """Flags instance as verified against the paper document."""
     for consent_obj in queryset:
         if not consent_obj.open_data_queries.count() > 0:
@@ -46,7 +45,7 @@ def flag_as_verified_against_paper(modeladmin, request, queryset, **kwargs):  #
 flag_as_verified_against_paper.short_description = "Verify consent against paper document"
 
 
-def unflag_as_verified_against_paper(modeladmin, request, queryset, **kwargs):  # noqa
+def unflag_as_verified_against_paper(modeladmin, request, queryset, **kwargs):
     """Unflags instance as verified."""
     for consent_obj in queryset:
         unverify_consent(consent_obj)

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_consent/migrations/0001_initial.py

@@ -7,6 +7,7 @@ import django_audit_fields.fields.uuid_auto_field
 import django_audit_fields.models.audit_model_mixin
 import django_revision.revision_field
 from django.db import migrations, models
+import django.utils.timezone
 
 
 class Migration(migrations.Migration):
@@ -33,14 +34,14 @@ class Migration(migrations.Migration):
                     "created",
                     models.DateTimeField(
                         blank=True,
-                        default=django_audit_fields.models.audit_model_mixin.utcnow,
+                        default=django.utils.timezone.now,
                     ),
                 ),
                 (
                     "modified",
                     models.DateTimeField(
                         blank=True,
-                        default=django_audit_fields.models.audit_model_mixin.utcnow,
+                        default=django.utils.timezone.now,
                     ),
                 ),
                 (

edc_consent/migrations/0006_alter_edcpermissions_device_created_and_more.py

@@ -0,0 +1,49 @@
+# Generated by Django 5.2.6 on 2025-09-17 16:53
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("edc_consent", "0005_alter_edcpermissions_revision"),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="edcpermissions",
+            name="device_created",
+            field=models.CharField(
+                blank=True, default="", max_length=10, verbose_name="Device created"
+            ),
+        ),
+        migrations.AlterField(
+            model_name="edcpermissions",
+            name="device_modified",
+            field=models.CharField(
+                blank=True, default="", max_length=10, verbose_name="Device modified"
+            ),
+        ),
+        migrations.AlterField(
+            model_name="edcpermissions",
+            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="edcpermissions",
+            name="locale_modified",
+            field=models.CharField(
+                blank=True,
+                default="",
+                help_text="Auto-updated by Modeladmin",
+                max_length=10,
+                verbose_name="Locale modified",
+            ),
+        ),
+    ]

edc_consent/model_mixins/consent_extension_model_mixin.py

@@ -1,10 +1,10 @@
 from django.db import models
+from django.utils import timezone
 from django.utils.translation import gettext as _
 from django_crypto_fields.fields import EncryptedTextField
 
 from edc_constants.choices import YES_NO_NA
 from edc_identifier.model_mixins import UniqueSubjectIdentifierModelMixin
-from edc_utils import get_utcnow
 
 from .. import site_consents
 from ..consent_definition_extension import ConsentDefinitionExtension
@@ -14,11 +14,10 @@ ___all__ = ["ConsentExtensionModelMixin"]
 
 
 class ConsentExtensionModelMixin(UniqueSubjectIdentifierModelMixin, models.Model):
-
     # declare with an FK your subject consent!
     subject_consent = models.ForeignKey("mysubjectconsent", on_delete=models.PROTECT)
 
-    report_datetime = models.DateTimeField(default=get_utcnow)
+    report_datetime = models.DateTimeField(default=timezone.now)
 
     agrees_to_extension = models.CharField(
         verbose_name=_(
@@ -35,14 +34,14 @@ class ConsentExtensionModelMixin(UniqueSubjectIdentifierModelMixin, models.Model
     consent_extension_version = models.CharField(
         verbose_name="Consent extension version",
         max_length=10,
-        null=True,
+        default="",
         editable=False,
     )
 
     consent_extension_definition_name = models.CharField(
         verbose_name="Consent extension definition",
         max_length=50,
-        null=True,
+        default="",
         editable=False,
     )
 

edc_consent/model_mixins/requires_consent_fields_model_mixin.py

@@ -4,9 +4,9 @@ from django.db import models
 class RequiresConsentFieldsModelMixin(models.Model):
     """See pre-save signal that checks if subject is consented"""
 
-    consent_model = models.CharField(max_length=50, null=True, blank=True)
+    consent_model = models.CharField(max_length=50, default="", blank=True)
 
-    consent_version = models.CharField(max_length=10, null=True, blank=True)
+    consent_version = models.CharField(max_length=10, default="", blank=True)
 
     class Meta:
         abstract = True

edc_consent/utils.py

@@ -76,7 +76,7 @@ def verify_initials_against_full_name(
     first_name: str | None = None,
     last_name: str | None = None,
     initials: str | None = None,
-    **kwargs,  # noqa
+    **kwargs,
 ) -> None:
     if first_name and initials and last_name:
         try:

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_crf/migrations/0001_initial.py

@@ -7,6 +7,7 @@ import django_audit_fields.fields.uuid_auto_field
 import django_audit_fields.models.audit_model_mixin
 import django_revision.revision_field
 from django.db import migrations, models
+import django.utils.timezone
 
 
 class Migration(migrations.Migration):
@@ -33,14 +34,14 @@ class Migration(migrations.Migration):
                     "created",
                     models.DateTimeField(
                         blank=True,
-                        default=django_audit_fields.models.audit_model_mixin.utcnow,
+                        default=django.utils.timezone.now,
                     ),
                 ),
                 (
                     "modified",
                     models.DateTimeField(
                         blank=True,
-                        default=django_audit_fields.models.audit_model_mixin.utcnow,
+                        default=django.utils.timezone.now,
                     ),
                 ),
                 (