clinicedc 2.0.0__py3-none-any.whl → 2.0.2__py3-none-any.whl

edc_auth/migrations/0016_auto_20191026_2153.py

@@ -7,9 +7,7 @@ class Migration(migrations.Migration):
     dependencies = [("edc_auth", "0015_auto_20191026_2149")]
 
     operations = [
-        migrations.RenameField(
-            model_name="role", old_name="short_name", new_name="name"
-        ),
+        migrations.RenameField(model_name="role", old_name="short_name", new_name="name"),
         migrations.AlterField(
             model_name="role",
             name="display_name",

edc_auth/migrations/0025_permissions.py

@@ -1,12 +1,12 @@
 # Generated by Django 3.2.13 on 2022-08-24 20:47
 
 import _socket
-from django.db import migrations, models
 import django_audit_fields.fields.hostname_modification_field
 import django_audit_fields.fields.userfield
 import django_audit_fields.fields.uuid_auto_field
 import django_audit_fields.models.audit_model_mixin
 import django_revision.revision_field
+from django.db import migrations, models
 
 
 class Migration(migrations.Migration):

edc_auth/migrations/0029_alter_edcpermissions_device_created_and_more.py

@@ -1,8 +1,8 @@
 # Generated by Django 4.2.4 on 2023-08-23 01:13
 
 import _socket
-from django.db import migrations, models
 import django_audit_fields.fields.hostname_modification_field
+from django.db import migrations, models
 
 
 class Migration(migrations.Migration):
@@ -14,16 +14,12 @@ class Migration(migrations.Migration):
         migrations.AlterField(
             model_name="edcpermissions",
             name="device_created",
-            field=models.CharField(
-                blank=True, max_length=10, verbose_name="Device created"
-            ),
+            field=models.CharField(blank=True, max_length=10, verbose_name="Device created"),
         ),
         migrations.AlterField(
             model_name="edcpermissions",
             name="device_modified",
-            field=models.CharField(
-                blank=True, max_length=10, verbose_name="Device modified"
-            ),
+            field=models.CharField(blank=True, max_length=10, verbose_name="Device modified"),
         ),
         migrations.AlterField(
             model_name="edcpermissions",
@@ -49,16 +45,12 @@ class Migration(migrations.Migration):
         migrations.AlterField(
             model_name="role",
             name="device_created",
-            field=models.CharField(
-                blank=True, max_length=10, verbose_name="Device created"
-            ),
+            field=models.CharField(blank=True, max_length=10, verbose_name="Device created"),
         ),
         migrations.AlterField(
             model_name="role",
             name="device_modified",
-            field=models.CharField(
-                blank=True, max_length=10, verbose_name="Device modified"
-            ),
+            field=models.CharField(blank=True, max_length=10, verbose_name="Device modified"),
         ),
         migrations.AlterField(
             model_name="role",

edc_auth/migrations/0034_alter_edcpermissions_revision_alter_role_revision.py

@@ -0,0 +1,38 @@
+# Generated by Django 5.2.4 on 2025-09-10 03:24
+
+import django_revision.revision_field
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("edc_auth", "0001_squashed_0033_alter_userprofile_is_multisite_viewer"),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="edcpermissions",
+            name="revision",
+            field=django_revision.revision_field.RevisionField(
+                blank=True,
+                editable=False,
+                help_text="System field. From git repository (tag:branch:commit), project metadata, project toml, project VERSION, or settings.",
+                max_length=75,
+                null=True,
+                verbose_name="Revision",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="role",
+            name="revision",
+            field=django_revision.revision_field.RevisionField(
+                blank=True,
+                editable=False,
+                help_text="System field. From git repository (tag:branch:commit), project metadata, project toml, project VERSION, or settings.",
+                max_length=75,
+                null=True,
+                verbose_name="Revision",
+            ),
+        ),
+    ]

edc_auth/models/__init__.py

@@ -10,7 +10,5 @@ from .signals import (
 )
 from .user_profile import UserProfile
 
-if settings.APP_NAME == "edc_auth" and (
-    "test" in sys.argv or "runtests.py" in sys.argv
-):
+if settings.APP_NAME == "edc_auth" and ("test" in sys.argv or "runtests.py" in sys.argv):
     from ..tests.models import *  # noqa

edc_auth/models/signals.py

@@ -6,9 +6,7 @@ from django.dispatch import receiver
 from .user_profile import UserProfile
 
 
-@receiver(
-    post_save, weak=False, sender=User, dispatch_uid="update_user_profile_on_post_save"
-)
+@receiver(post_save, weak=False, sender=User, dispatch_uid="update_user_profile_on_post_save")
 def update_user_profile_on_post_save(sender, instance, raw, **kwargs):
     if not raw:
         try:
@@ -17,9 +15,7 @@ def update_user_profile_on_post_save(sender, instance, raw, **kwargs):
             UserProfile.objects.create(user=instance)
 
 
-@receiver(
-    m2m_changed, weak=False, dispatch_uid="update_user_groups_on_role_m2m_changed"
-)
+@receiver(m2m_changed, weak=False, dispatch_uid="update_user_groups_on_role_m2m_changed")
 def update_user_groups_on_role_m2m_changed(sender, action, instance, pk_set, **kwargs):
     try:
         through = instance.roles.through

edc_auth/models/user_profile.py

@@ -34,9 +34,7 @@ class UserProfile(NotificationUserProfileModelMixin, models.Model):
 
     job_title = models.CharField(max_length=100, null=True, blank=True)
 
-    alternate_email = models.EmailField(
-        _("Alternate email address"), blank=True, null=True
-    )
+    alternate_email = models.EmailField(_("Alternate email address"), blank=True, null=True)
 
     mobile = models.CharField(
         max_length=25,

edc_auth/password_setter.py

@@ -58,9 +58,7 @@ class PasswordSetter:
         self._reset(users)
 
     def reset_users(self, usernames: List[str]) -> None:
-        users = User.objects.filter(
-            username__in=usernames, is_active=True, is_staff=True
-        )
+        users = User.objects.filter(username__in=usernames, is_active=True, is_staff=True)
         self._reset(users)
 
     def reset_user(self, username: str) -> None:

edc_auth/system_checks.py

@@ -14,11 +14,7 @@ def check_etc_dir(app_configs, **kwargs) -> list[CheckMessage]:
     except AttributeError:
         pass
     else:
-        if (
-            not settings.DEBUG
-            and settings.ETC_DIR
-            and not settings.ETC_DIR.startswith("/etc")
-        ):
+        if not settings.DEBUG and settings.ETC_DIR and not settings.ETC_DIR.startswith("/etc"):
             errors.append(
                 Warning(
                     "Insecure configuration. Use root level etc folder. "

edc_auth/urls_for_accounts.py

@@ -25,9 +25,7 @@ if allow_password_reset:
             views.PasswordChangeDoneView.as_view(),
             name="password_change_done",
         ),
-        path(
-            "password_reset/", views.PasswordResetView.as_view(), name="password_reset"
-        ),
+        path("password_reset/", views.PasswordResetView.as_view(), name="password_reset"),
         path(
             "password_reset/done/",
             views.PasswordResetDoneView.as_view(),

edc_auth/utils.py

@@ -24,9 +24,7 @@ def get_user(username: str) -> User | None:
     return user
 
 
-def compare_codenames_for_group(
-    group_name: str = None, expected: list[str] = None
-) -> None:
+def compare_codenames_for_group(group_name: str = None, expected: list[str] = None) -> None:
     group = django_apps.get_model("auth.group").objects.get(name=group_name)
     codenames = [p.codename for p in group.permissions.all()]
     new_expected = []
@@ -47,9 +45,7 @@ def compare_codenames_for_group(
         pprint(compared)
 
 
-def remove_default_model_permissions_from_edc_permissions(
-    auth_updater: Any, app_label: str
-):
+def remove_default_model_permissions_from_edc_permissions(auth_updater: Any, app_label: str):
     for group in auth_updater.group_model_cls.objects.all():
         auth_updater.remove_permissions_by_codenames(
             group=group,
@@ -121,9 +117,7 @@ def get_codenames_for_user(
     roles = roles or user.userprofile.roles
 
     for role in roles.all():
-        groups.extend(
-            [grp for grp in role.groups.all() if grp not in account_manager_groups]
-        )
+        groups.extend([grp for grp in role.groups.all() if grp not in account_manager_groups])
     if include_groups:
         for group in user.groups.all():
             if group not in account_manager_groups:

edc_consent/actions.py

@@ -10,9 +10,7 @@ def verify_consent(request=None, consent_obj=None):
         consent_obj.is_verified = True
         consent_obj.is_verified_datetime = get_utcnow()
         consent_obj.verified_by = request.user.username
-        consent_obj.save(
-            update_fields=["is_verified", "is_verified_datetime", "verified_by"]
-        )
+        consent_obj.save(update_fields=["is_verified", "is_verified_datetime", "verified_by"])
     return consent_obj
 
 
@@ -20,9 +18,7 @@ def unverify_consent(consent_obj=None):
     consent_obj.is_verified = False
     consent_obj.is_verified_datetime = None
     consent_obj.verified_by = None
-    consent_obj.save(
-        update_fields=["is_verified", "is_verified_datetime", "verified_by"]
-    )
+    consent_obj.save(update_fields=["is_verified", "is_verified_datetime", "verified_by"])
     return consent_obj
 
 
@@ -48,9 +44,7 @@ def flag_as_verified_against_paper(modeladmin, request, queryset, **kwargs):  #
             )
 
 
-flag_as_verified_against_paper.short_description = (
-    "Verify consent against paper document"
-)
+flag_as_verified_against_paper.short_description = "Verify consent against paper document"
 
 
 def unflag_as_verified_against_paper(modeladmin, request, queryset, **kwargs):  # noqa

edc_consent/consent_definition.py

@@ -1,8 +1,8 @@
 from __future__ import annotations
 
-from dataclasses import dataclass, field, KW_ONLY
+from dataclasses import KW_ONLY, dataclass, field
 from datetime import datetime
-from typing import Type, TYPE_CHECKING
+from typing import TYPE_CHECKING, Type
 
 from django.apps import apps as django_apps
 from django.core.exceptions import ObjectDoesNotExist
@@ -13,6 +13,7 @@ from edc_screening.utils import get_subject_screening_model
 from edc_sites import site_sites
 from edc_utils import ceil_secs, floor_secs, formatted_date, formatted_datetime
 from edc_utils.date import to_local
+
 from .exceptions import (
     ConsentDefinitionError,
     ConsentDefinitionValidityPeriodError,
@@ -82,9 +83,7 @@ class ConsentDefinition:
         if MALE not in self.gender and FEMALE not in self.gender:
             raise ConsentDefinitionError(f"Invalid gender. Got {self.gender}.")
         if not self.start.tzinfo:
-            raise ConsentDefinitionError(
-                f"Naive datetime not allowed. Got {self.start}."
-            )
+            raise ConsentDefinitionError(f"Naive datetime not allowed. Got {self.start}.")
         elif str(self.start.tzinfo).upper() != "UTC":
             raise ConsentDefinitionError(
                 f"Start date must be UTC. Got {self.start} / {self.start.tzinfo}."
@@ -140,9 +139,7 @@ class ConsentDefinition:
         if self.country:
             sites = site_sites.get_by_country(self.country, aslist=True)
         elif self.site_ids:
-            sites = [
-                s for s in site_sites.all(aslist=True) if s.site_id in self.site_ids
-            ]
+            sites = [s for s in site_sites.all(aslist=True) if s.site_id in self.site_ids]
         else:
             sites = [s for s in site_sites.all(aslist=True)]
         return sites

edc_consent/consent_definition_extension.py

@@ -23,9 +23,7 @@ if TYPE_CHECKING:
 
     from .consent_definition import ConsentDefinition
 
-    class ConsentLikeModel(
-        SiteModelMixin, UniqueSubjectIdentifierModelMixin, BaseUuidModel
-    ):
+    class ConsentLikeModel(SiteModelMixin, UniqueSubjectIdentifierModelMixin, BaseUuidModel):
         _meta: ...
 
     class ConsentExtensionLikeModel(
@@ -59,9 +57,7 @@ class ConsentDefinitionExtension:
 
     model: str = field(compare=False)
     _ = KW_ONLY
-    start: datetime = field(
-        default=ResearchProtocolConfig().study_open_datetime, compare=True
-    )
+    start: datetime = field(default=ResearchProtocolConfig().study_open_datetime, compare=True)
     version: str = field(default="1", compare=False)
     extends: ConsentDefinition = field(default=None, compare=False)
     timepoints: list[int] | None = field(default_factory=list, compare=False)
@@ -75,9 +71,7 @@ class ConsentDefinitionExtension:
         self.name = f"{self.model}-{self.version}"
         self.sort_index = self.name
         if not self.start.tzinfo:
-            raise ConsentDefinitionError(
-                f"Naive datetime not allowed. Got {self.start}."
-            )
+            raise ConsentDefinitionError(f"Naive datetime not allowed. Got {self.start}.")
         elif str(self.start.tzinfo) != "UTC":
             raise ConsentDefinitionError(f"Start date must be UTC. Got {self.start}.")
         self.extends.check_date_within_study_period()
@@ -118,9 +112,7 @@ class ConsentDefinitionExtension:
         if self.country:
             sites = site_sites.get_by_country(self.country, aslist=True)
         elif self.site_ids:
-            sites = [
-                s for s in site_sites.all(aslist=True) if s.site_id in self.site_ids
-            ]
+            sites = [s for s in site_sites.all(aslist=True) if s.site_id in self.site_ids]
         else:
             sites = [s for s in site_sites.all(aslist=True)]
         return sites

edc_consent/field_mixins/citizen_fields_mixin.py

@@ -13,8 +13,7 @@ class CitizenFieldsMixin(models.Model):
 
     legal_marriage = models.CharField(
         verbose_name=(
-            "If not a citizen, is the participant legally "
-            "married to a Botswana citizen?"
+            "If not a citizen, is the participant legally " "married to a Botswana citizen?"
         ),
         max_length=3,
         choices=YES_NO_NA,
@@ -26,8 +25,7 @@ class CitizenFieldsMixin(models.Model):
 
     marriage_certificate = models.CharField(
         verbose_name=(
-            "[Interviewer] Has the participant produced "
-            "the marriage certificate as proof? "
+            "[Interviewer] Has the participant produced " "the marriage certificate as proof? "
         ),
         max_length=3,
         choices=YES_NO_NA,

edc_consent/field_mixins/identity_fields_mixin.py

@@ -36,8 +36,7 @@ class IdentityFieldsMixin(CryptoMixin, models.Model):
     def save(self, *args, **kwargs):
         if self.identity != self.confirm_identity:
             raise IdentityFieldsMixinError(
-                "'Identity' must match 'confirm_identity'. "
-                "Catch this error on the form"
+                "'Identity' must match 'confirm_identity'. " "Catch this error on the form"
             )
         super().save(*args, **kwargs)
 

edc_consent/field_mixins/personal_fields_mixin.py

@@ -35,12 +35,17 @@ class BaseFieldsMixin(models.Model):
         help_text=format_html(
             "{text1}.<BR>{text2}",
             text1=_("Required only if participant is a minor"),
-            text2=_(
-                "Format is 'LASTNAME, FIRSTNAME'. All uppercase separated by a comma."
-            ),
+            text2=_("Format is 'LASTNAME, FIRSTNAME'. All uppercase separated by a comma."),
         ),
     )
 
+    ethnicity = models.CharField(
+        max_length=15,
+        help_text=_("from screening"),
+        editable=False,
+        null=True,
+    )
+
     subject_type = models.CharField(max_length=25)
 
     class Meta:

edc_consent/field_mixins/site_fields_mixin.py

@@ -6,8 +6,7 @@ class SiteFieldsMixin(models.Model):
         verbose_name="Site",
         max_length=25,
         help_text=(
-            "This refers to the site or 'clinic area' where the "
-            "subject is being consented."
+            "This refers to the site or 'clinic area' where the " "subject is being consented."
         ),
     )
 

edc_consent/form_validators/subject_consent_form_validator.py

@@ -8,9 +8,10 @@ from django.conf import settings
 from edc_form_validators import INVALID_ERROR
 from edc_screening.form_validator_mixins import SubjectScreeningFormValidatorMixin
 from edc_sites.site import sites
-from edc_utils import age, AgeValueError
+from edc_utils import AgeValueError, age
 from edc_utils.date import to_local, to_utc
 from edc_utils.text import convert_php_dateformat
+
 from ..site_consents import site_consents
 
 
@@ -62,9 +63,7 @@ class SubjectConsentFormValidatorMixin(SubjectScreeningFormValidatorMixin):
                     self.raise_validation_error(
                         {"consent_datetime": "This field is required."}, INVALID_ERROR
                     )
-                self._consent_datetime = to_utc(
-                    self.cleaned_data.get("consent_datetime")
-                )
+                self._consent_datetime = to_utc(self.cleaned_data.get("consent_datetime"))
             else:
                 self._consent_datetime = self.instance.consent_datetime
         return self._consent_datetime
@@ -81,10 +80,7 @@ class SubjectConsentFormValidatorMixin(SubjectScreeningFormValidatorMixin):
 
     def validate_age(self) -> None:
         """Validate age matches that on the screening form."""
-        if (
-            self.dob
-            and self.screening_age_in_years != self.subject_screening.age_in_years
-        ):
+        if self.dob and self.screening_age_in_years != self.subject_screening.age_in_years:
             self.raise_validation_error(
                 {
                     "dob": "Age mismatch. The date of birth entered does "

edc_consent/migrations/0001_initial.py

@@ -1,12 +1,12 @@
 # Generated by Django 3.2.13 on 2022-08-25 01:51
 
 import _socket
-from django.db import migrations, models
 import django_audit_fields.fields.hostname_modification_field
 import django_audit_fields.fields.userfield
 import django_audit_fields.fields.uuid_auto_field
 import django_audit_fields.models.audit_model_mixin
 import django_revision.revision_field
+from django.db import migrations, models
 
 
 class Migration(migrations.Migration):

edc_consent/migrations/0002_alter_edcpermissions_device_created_and_more.py

@@ -1,8 +1,8 @@
 # Generated by Django 4.2.4 on 2023-08-23 01:13
 
 import _socket
-from django.db import migrations, models
 import django_audit_fields.fields.hostname_modification_field
+from django.db import migrations, models
 
 
 class Migration(migrations.Migration):
@@ -14,16 +14,12 @@ class Migration(migrations.Migration):
         migrations.AlterField(
             model_name="edcpermissions",
             name="device_created",
-            field=models.CharField(
-                blank=True, max_length=10, verbose_name="Device created"
-            ),
+            field=models.CharField(blank=True, max_length=10, verbose_name="Device created"),
         ),
         migrations.AlterField(
             model_name="edcpermissions",
             name="device_modified",
-            field=models.CharField(
-                blank=True, max_length=10, verbose_name="Device modified"
-            ),
+            field=models.CharField(blank=True, max_length=10, verbose_name="Device modified"),
         ),
         migrations.AlterField(
             model_name="edcpermissions",

edc_consent/migrations/0005_alter_edcpermissions_revision.py

@@ -0,0 +1,26 @@
+# Generated by Django 5.2.4 on 2025-09-10 03:24
+
+import django_revision.revision_field
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("edc_consent", "0004_alter_edcpermissions_options_and_more"),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="edcpermissions",
+            name="revision",
+            field=django_revision.revision_field.RevisionField(
+                blank=True,
+                editable=False,
+                help_text="System field. From git repository (tag:branch:commit), project metadata, project toml, project VERSION, or settings.",
+                max_length=75,
+                null=True,
+                verbose_name="Revision",
+            ),
+        ),
+    ]

edc_consent/model_mixins/consent_extension_model_mixin.py

@@ -5,6 +5,7 @@ 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
 from ..exceptions import ConsentExtensionDefinitionModelError
@@ -29,9 +30,7 @@ class ConsentExtensionModelMixin(UniqueSubjectIdentifierModelMixin, models.Model
         help_text=_("See above for the definition of extended followup."),
     )
 
-    comment = EncryptedTextField(
-        verbose_name="Comment", max_length=250, blank=True, null=True
-    )
+    comment = EncryptedTextField(verbose_name="Comment", max_length=250, blank=True, null=True)
 
     consent_extension_version = models.CharField(
         verbose_name="Consent extension version",

edc_consent/model_mixins/consent_model_mixin.py

@@ -16,17 +16,13 @@ from ..managers import ConsentObjectsManager
 from .consent_version_model_mixin import ConsentVersionModelMixin
 
 
-class ConsentModelMixin(
-    ConsentVersionModelMixin, VerificationFieldsMixin, models.Model
-):
+class ConsentModelMixin(ConsentVersionModelMixin, VerificationFieldsMixin, models.Model):
     """Mixin for a Consent model class such as SubjectConsent.
 
     Declare with edc_identifier's NonUniqueSubjectIdentifierModelMixin
     """
 
-    screening_identifier = models.CharField(
-        verbose_name="Screening identifier", max_length=50
-    )
+    screening_identifier = models.CharField(verbose_name="Screening identifier", max_length=50)
 
     screening_datetime = models.DateTimeField(
         verbose_name="Screening datetime", null=True, editable=False
@@ -59,9 +55,7 @@ class ConsentModelMixin(
         help_text="Used for randomization against a prepared rando-list.",
     )
 
-    comment = EncryptedTextField(
-        verbose_name="Comment", max_length=250, blank=True, null=True
-    )
+    comment = EncryptedTextField(verbose_name="Comment", max_length=250, blank=True, null=True)
 
     dm_comment = models.CharField(
         verbose_name="Data Management comment",

edc_consent/modeladmin_mixins/consent_model_admin_mixin.py

@@ -70,9 +70,7 @@ class ConsentModelAdminMixin:
         fields = ("subject_identifier", "subject_identifier_as_pk")
         if obj:
             return (
-                fields
-                + ("consent_datetime", "identity", "confirm_identity")
-                + readonly_fields
+                fields + ("consent_datetime", "identity", "confirm_identity") + readonly_fields
             )
         else:
             return fields + readonly_fields
@@ -131,16 +129,12 @@ class ConsentModelAdminMixin:
     def delete_view(self, request, object_id, extra_context=None):
         """Prevent deletion if SubjectVisit objects exist."""
         extra_context = extra_context or {}
-        subject_consent_model_cls = django_apps.get_model(
-            settings.SUBJECT_CONSENT_MODEL
-        )
+        subject_consent_model_cls = django_apps.get_model(settings.SUBJECT_CONSENT_MODEL)
         related_visit_model_cls = django_apps.get_model(settings.SUBJECT_VISIT_MODEL)
         obj = subject_consent_model_cls.objects.get(id=object_id)
         try:
             protected = [
-                related_visit_model_cls.objects.get(
-                    subject_identifier=obj.subject_identifier
-                )
+                related_visit_model_cls.objects.get(subject_identifier=obj.subject_identifier)
             ]
         except ObjectDoesNotExist:
             protected = None
@@ -155,18 +149,14 @@ class ConsentModelAdminMixin:
         """Returns the key/value pairs from the "next" querystring
         as a dictionary.
         """
-        subject_screening_model_cls = django_apps.get_model(
-            settings.SUBJECT_SCREENING_MODEL
-        )
+        subject_screening_model_cls = django_apps.get_model(settings.SUBJECT_SCREENING_MODEL)
         next_options = super().get_next_options(request=request, **kwargs)
         try:
             is_subject_identifier_or_raise(next_options["subject_identifier"])
         except SubjectIdentifierError:
-            next_options["subject_identifier"] = (
-                subject_screening_model_cls.objects.get(
-                    subject_identifier_as_pk=next_options["subject_identifier"]
-                ).subject_identifier
-            )
+            next_options["subject_identifier"] = subject_screening_model_cls.objects.get(
+                subject_identifier_as_pk=next_options["subject_identifier"]
+            ).subject_identifier
         except KeyError:
             pass
         return next_options