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

edc_qareports/modeladmin_mixins/list_filters.py

@@ -44,21 +44,17 @@ class NoteStatusListFilter(SimpleListFilter):
         if self.value() and self.value() != "none":
             if report_model := self.report_model(queryset):
                 if self.value() == NEW:
-                    qs = self.note_model_cls.objects.values(
-                        "subject_identifier"
-                    ).filter(report_model=report_model)
+                    qs = self.note_model_cls.objects.values("subject_identifier").filter(
+                        report_model=report_model
+                    )
                     queryset = queryset.exclude(
-                        subject_identifier__in=[
-                            obj.get("subject_identifier") for obj in qs
-                        ]
+                        subject_identifier__in=[obj.get("subject_identifier") for obj in qs]
                     )
                 elif self.value() in [tpl[0] for tpl in self.note_model_status_choices]:
-                    qs = self.note_model_cls.objects.values(
-                        "subject_identifier"
-                    ).filter(report_model=report_model, status=self.value())
+                    qs = self.note_model_cls.objects.values("subject_identifier").filter(
+                        report_model=report_model, status=self.value()
+                    )
                     queryset = queryset.filter(
-                        subject_identifier__in=[
-                            obj.get("subject_identifier") for obj in qs
-                        ]
+                        subject_identifier__in=[obj.get("subject_identifier") for obj in qs]
                     )
         return queryset

edc_qareports/modeladmin_mixins/note_modeladmin_mixin.py

@@ -94,7 +94,5 @@ class NoteModelAdminMixin(
         return render_to_string(self.note_template_name, context)
 
     def redirect_url(self, request, obj, post_url_continue=None) -> str | None:
-        redirect_url = super().redirect_url(
-            request, obj, post_url_continue=post_url_continue
-        )
+        redirect_url = super().redirect_url(request, obj, post_url_continue=post_url_continue)
         return f"{redirect_url}?q={obj.subject_identifier}"

edc_qareports/modeladmin_mixins/on_study_missing_values_modeladmin_mixin.py

@@ -96,12 +96,8 @@ class OnStudyMissingValuesModelAdminMixin(
                 appointment=self.related_visit(obj).appointment.id,
             ),
         )
-        context = dict(
-            title=_("Go to subject's dashboard"), url=dashboard_url, label=label
-        )
-        return render_to_string(
-            "edc_subject_dashboard/dashboard_button.html", context=context
-        )
+        context = dict(title=_("Go to subject's dashboard"), url=dashboard_url, label=label)
+        return render_to_string("edc_subject_dashboard/dashboard_button.html", context=context)
 
     @staticmethod
     def crf_admin_site_name(crf_model_cls) -> str:

edc_qareports/modeladmin_mixins/qa_report_modeladmin_mixin.py

@@ -83,9 +83,7 @@ class QaReportModelAdminMixin:
     @admin.display(description="Notes")
     def notes(self, obj=None) -> str:
         """Returns url to add or edit qa_report note model."""
-        note_app_label, note_model_name = self.note_model_cls._meta.label_lower.split(
-            "."
-        )
+        note_app_label, note_model_name = self.note_model_cls._meta.label_lower.split(".")
         note_url_name = f"{note_app_label}_{note_model_name}"
 
         report_app_label, report_model_name = self.model._meta.label_lower.split(".")

edc_qareports/sql_generator/crf_case.py

@@ -24,11 +24,7 @@ class CrfCase:
     @property
     def sql(self):
         sql = CrfSubquery(**self.__dict__).sql
-        vendor = (
-            "postgres"
-            if connection.vendor.startswith("postgres")
-            else connection.vendor
-        )
+        vendor = "postgres" if connection.vendor.startswith("postgres") else connection.vendor
         return sqlglot.transpile(sql, read="mysql", write=vendor)[0]
 
     @property

edc_qareports/sql_generator/sql_view_generator.py

@@ -25,9 +25,7 @@ class SqlViewGenerator:
     )
 
     def __post_init__(self):
-        ordering = [
-            f"{fld[1:]} desc" if fld.startswith("~") else fld for fld in self.ordering
-        ]
+        ordering = [f"{fld[1:]} desc" if fld.startswith("~") else fld for fld in self.ordering]
         self.order_by = ", ".join(ordering) or "subject_identifier"
         self.footer = f") as A ORDER BY {self.order_by}"
 

edc_qareports/utils.py

@@ -4,7 +4,8 @@ from warnings import warn
 
 from django.apps import apps as django_apps
 from django.conf import settings
-from django.db import connection, OperationalError
+from django.db import OperationalError, connection
+
 from edc_auth.get_app_codenames import get_app_codenames
 
 
@@ -19,9 +20,7 @@ def read_unmanaged_model_sql(
         uuid_func = "gen_random_uuid()"
 
     if not fullpath:
-        fullpath = (
-            Path(settings.BASE_DIR) / app_name / "models" / "unmanaged" / filename
-        )
+        fullpath = Path(settings.BASE_DIR) / app_name / "models" / "unmanaged" / filename
     else:
         fullpath = Path(fullpath)
 
@@ -85,9 +84,7 @@ def recreate_db_view(model_cls, drop: bool | None = None, verbose: bool | None =
     """
     drop = True if drop is None else drop
     try:
-        sql = model_cls.view_definition.get(
-            settings.DATABASES["default"]["ENGINE"]
-        )  # noqa
+        sql = model_cls.view_definition.get(settings.DATABASES["default"]["ENGINE"])  # noqa
     except AttributeError as e:
         raise AttributeError(
             f"Is this model linked to a view? Declare model with `DBView`. Got {e}"

edc_randomization/admin.py

@@ -157,9 +157,7 @@ def register_admin():
     site_randomizers.autodiscover()
     for randomizer_cls in site_randomizers._registry.values():
         model = randomizer_cls.model_cls()
-        admin_cls = type(
-            f"{model.__name__}ModelAdmin", (RandomizationListModelAdmin,), {}
-        )
+        admin_cls = type(f"{model.__name__}ModelAdmin", (RandomizationListModelAdmin,), {})
         try:
             edc_randomization_admin.register(model, admin_cls)
         except AlreadyRegistered:

edc_randomization/auths.py

@@ -13,11 +13,7 @@ site_auths.add_post_update_func(
     "edc_randomization", remove_default_model_permissions_from_edc_permissions
 )
 
-site_auths.add_group(
-    get_rando_permissions_codenames, name=RANDO_BLINDED, view_only=True
-)
-site_auths.add_group(
-    get_rando_permissions_codenames, name=RANDO_UNBLINDED, view_only=True
-)
+site_auths.add_group(get_rando_permissions_codenames, name=RANDO_BLINDED, view_only=True)
+site_auths.add_group(get_rando_permissions_codenames, name=RANDO_UNBLINDED, view_only=True)
 site_auths.add_post_update_func("edc_randomization", update_rando_group_permissions)
 site_auths.add_post_update_func("edc_randomization", make_randomizationlist_view_only)

edc_randomization/blinding.py

@@ -52,9 +52,7 @@ def user_is_blinded_from_request(request):
     return False
 
 
-def raise_if_prohibited_from_unblinded_rando_group(
-    username: str, groups: Iterable
-) -> None:
+def raise_if_prohibited_from_unblinded_rando_group(username: str, groups: Iterable) -> None:
     """A user form validation to prevent adding an unlisted
     user to the RANDO_UNBLINDED group.
 

edc_randomization/migrations/0001_initial.py

@@ -9,9 +9,10 @@ import django_audit_fields.fields.uuid_auto_field
 import django_audit_fields.models.audit_model_mixin
 import django_crypto_fields.fields.encrypted_char_field
 import django_revision.revision_field
-import edc_sites.models
 from django.db import migrations, models
 
+import edc_sites.models
+
 
 class Migration(migrations.Migration):
     initial = True
@@ -141,9 +142,7 @@ class Migration(migrations.Migration):
             ],
             options={
                 "ordering": ("site_name", "sid"),
-                "permissions": (
-                    ("display_randomization", "Can display randomization"),
-                ),
+                "permissions": (("display_randomization", "Can display randomization"),),
                 "abstract": False,
                 "unique_together": {("site_name", "sid")},
             },

edc_randomization/migrations/0009_edcpermissions.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_randomization/migrations/0011_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="historicalrandomizationlist",
             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="historicalrandomizationlist",
             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="historicalrandomizationlist",
@@ -84,16 +76,12 @@ class Migration(migrations.Migration):
         migrations.AlterField(
             model_name="randomizationlist",
             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="randomizationlist",
             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="randomizationlist",

edc_randomization/migrations/0013_alter_edcpermissions_revision_and_more.py

@@ -0,0 +1,50 @@
+# 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_randomization", "0012_alter_randomizationlist_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",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="historicalrandomizationlist",
+            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="randomizationlist",
+            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_randomization/model_mixins.py

@@ -42,9 +42,7 @@ class RandomizationListModelMixin(models.Model):
 
     site_name = models.CharField(max_length=100)
 
-    allocation = EncryptedCharField(
-        verbose_name="Original integer allocation", null=True
-    )
+    allocation = EncryptedCharField(verbose_name="Original integer allocation", null=True)
 
     allocated = models.BooleanField(default=False)
 
@@ -82,8 +80,7 @@ class RandomizationListModelMixin(models.Model):
         except ObjectDoesNotExist:
             site_names = [obj.name for obj in Site.objects.all()]
             raise RandomizationListModelError(
-                f"Invalid site name. Got {self.site_name}. "
-                f"Expected one of {site_names}."
+                f"Invalid site name. Got {self.site_name}. " f"Expected one of {site_names}."
             )
         super().save(*args, **kwargs)
 

edc_randomization/randomization_list_importer.py

@@ -128,9 +128,7 @@ class RandomizationListImporter:
         self._summarize_results()
         if self.verbose:
             sys.stdout.write(
-                style.SUCCESS(
-                    "\nDone.------------------------------------------------\n"
-                )
+                style.SUCCESS("\nDone.------------------------------------------------\n")
             )
         return rec_count, self.randomizationlist_path
 
@@ -176,8 +174,7 @@ class RandomizationListImporter:
                     for fieldname in self.required_csv_fieldnames:
                         if fieldname not in row:
                             raise RandomizationListImportError(
-                                "Invalid header. Missing column "
-                                f"`{fieldname}`. Got {row}"
+                                "Invalid header. Missing column " f"`{fieldname}`. Got {row}"
                             )
                 elif index == 1:
                     if self.dryrun:
@@ -311,8 +308,7 @@ class RandomizationListImporter:
     def get_site_names() -> dict[str, str]:
         """A dict of site names for the target randomizer."""
         return {
-            single_site.name: single_site.name
-            for single_site in site_sites.all().values()
+            single_site.name: single_site.name for single_site in site_sites.all().values()
         }
 
     def validate_site_name(self, row) -> str:

edc_randomization/randomization_list_verifier.py

@@ -44,9 +44,7 @@ class RandomizationListVerifier:
 
         randomizer_cls = site_randomizers.get(randomizer_name)
         if not randomizer_cls:
-            raise RandomizationListError(
-                f"Randomizer not registered. Got `{randomizer_name}`"
-            )
+            raise RandomizationListError(f"Randomizer not registered. Got `{randomizer_name}`")
         self.fieldnames = fieldnames or self.required_csv_fieldnames
         try:
             self.count = self.randomizer_model_cls.objects.all().count()
@@ -62,10 +60,7 @@ class RandomizationListVerifier:
                 )
 
             else:
-                if (
-                    not self.randomizationlist_path
-                    or not self.randomizationlist_path.exists()
-                ):
+                if not self.randomizationlist_path or not self.randomizationlist_path.exists():
                     self.messages.append(
                         f"Randomization list file does not exist but SIDs "
                         f"have been loaded. Expected file "

edc_randomization/randomizer.py

@@ -3,13 +3,14 @@ from __future__ import annotations
 import warnings
 from datetime import datetime
 from pathlib import Path
-from typing import Any, Type, TYPE_CHECKING
+from typing import TYPE_CHECKING, Any, Type
 
 from django.apps import apps as django_apps
 from django.conf import settings
 from django.core.exceptions import ObjectDoesNotExist, ValidationError
 
 from edc_registration.utils import get_registered_subject_model_cls
+
 from .constants import (
     DEFAULT_ASSIGNMENT_DESCRIPTION_MAP,
     DEFAULT_ASSIGNMENT_MAP,
@@ -182,9 +183,7 @@ class Randomizer:
         self.registration_obj.sid = self.sid
         self.registration_obj.randomization_datetime = self.model_obj.allocated_datetime
         self.registration_obj.registration_status = RANDOMIZED
-        self.registration_obj.randomization_list_model = (
-            self.model_obj._meta.label_lower
-        )
+        self.registration_obj.randomization_list_model = self.model_obj._meta.label_lower
         self.registration_obj.save()
         # requery
         self._registration_obj = self.get_registration_model_cls().objects.get(
@@ -301,9 +300,7 @@ class Randomizer:
                 self._registration_obj = self.get_unallocated_registration_obj()
             except ObjectDoesNotExist:
                 try:
-                    obj = self.get_registration_model_cls().objects.get(
-                        **self.identifier_opts
-                    )
+                    obj = self.get_registration_model_cls().objects.get(**self.identifier_opts)
                 except ObjectDoesNotExist:
                     raise RandomizationError(
                         f"{self.identifier_object_name.title()} does not exist. "

edc_randomization/site_randomizers.py

@@ -115,9 +115,7 @@ class SiteRandomizers:
                         before_import_registry = copy.copy(site_randomizers._registry)
                         import_module(f"{app}.{module_name}")
                         if verbose:
-                            sys.stdout.write(
-                                " * registered randomizer from " f"'{app}'\n"
-                            )
+                            sys.stdout.write(" * registered randomizer from " f"'{app}'\n")
                     except Exception as e:
                         if f"No module named '{app}.{module_name}'" not in str(e):
                             raise

edc_randomization/system_checks.py

@@ -60,9 +60,7 @@ def randomizationlist_check(app_configs, **kwargs) -> list:
             for error_msg in error_msgs:
                 errors.append(error.cls(error_msg, hint=None, obj=None, id=error.id))
         if not settings.DEBUG:
-            if not randomizer.get_randomizationlist_path().is_relative_to(
-                settings.ETC_DIR
-            ):
+            if not randomizer.get_randomizationlist_path().is_relative_to(settings.ETC_DIR):
                 errors.append(
                     Warning(
                         "Insecure configuration. Randomization list file must be "

edc_randomization/utils.py

@@ -119,9 +119,7 @@ def generate_fake_randomization_list(
     # get site ID and write the file
     site_id = sites.get_by_attr("name", site_name)
     with open(filename, "a+", newline="") as f:
-        writer = csv.DictWriter(
-            f, fieldnames=["sid", "assignment", "site_name", "country"]
-        )
+        writer = csv.DictWriter(f, fieldnames=["sid", "assignment", "site_name", "country"])
         if write_header:
             writer.writeheader()
         for j in range(1, int(slots)):
@@ -147,9 +145,7 @@ def export_randomization_list(
         user = get_user_model().objects.get(username=username)
     except ObjectDoesNotExist:
         raise RandomizationListExporterError(f"User `{username}` does not exist")
-    if not user.has_perm(
-        randomizer_cls.model_cls()._meta.label_lower.replace(".", ".view_")
-    ):
+    if not user.has_perm(randomizer_cls.model_cls()._meta.label_lower.replace(".", ".view_")):
         raise RandomizationListExporterError(
             f"User `{username}` does not have "
             f"permission to view '{randomizer_cls.model_cls()._meta.label_lower}'"

edc_refusal/admin.py

@@ -70,7 +70,5 @@ class SubjectRefusalAdmin(
             if callable(super().view_on_site):
                 url = super().view_on_site(obj)
             else:
-                raise NoReverseMatch(
-                    f"{e}. See subject_dashboard_url_name for {repr(self)}."
-                )
+                raise NoReverseMatch(f"{e}. See subject_dashboard_url_name for {repr(self)}.")
         return url

edc_refusal/forms.py

@@ -21,8 +21,7 @@ class ScreeningFormMixin:
     def clean(self):
         cleaned_data = super().clean()
         screening_identifier = (
-            cleaned_data.get("screening_identifier")
-            or self.instance.screening_identifier
+            cleaned_data.get("screening_identifier") or self.instance.screening_identifier
         )
         if screening_identifier:
             subject_screening = get_subject_screening_model_cls().objects.get(

edc_refusal/migrations/0001_initial.py

@@ -1,13 +1,14 @@
 # Generated by Django 3.2.4 on 2021-07-14 21:55
 
 import _socket
-from django.db import migrations, models
 import django.db.models.deletion
 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
+
 import edc_model.models.fields.other_charfield
 import edc_sites.models
 import edc_utils.date

edc_refusal/migrations/0002_historicalsubjectrefusal.py

@@ -1,18 +1,20 @@
 # Generated by Django 3.2.4 on 2021-07-15 00:37
 
+import uuid
+
 import _socket
-from django.conf import settings
-from django.db import migrations, models
 import django.db.models.deletion
 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
+import simple_history.models
+from django.conf import settings
+from django.db import migrations, models
+
 import edc_model.models.fields.other_charfield
 import edc_utils.date
-import simple_history.models
-import uuid
 
 
 class Migration(migrations.Migration):

edc_refusal/migrations/0004_refusalreasons_plural_name.py

@@ -12,8 +12,6 @@ class Migration(migrations.Migration):
         migrations.AddField(
             model_name="refusalreasons",
             name="plural_name",
-            field=models.CharField(
-                max_length=250, null=True, verbose_name="Plural name"
-            ),
+            field=models.CharField(max_length=250, null=True, verbose_name="Plural name"),
         ),
     ]

edc_refusal/migrations/0005_alter_subjectrefusal_options_and_more.py

@@ -1,9 +1,10 @@
 # Generated by Django 4.2.1 on 2023-07-05 02:16
 
 import django.db.models.manager
-import edc_sites.models
 from django.db import migrations
 
+import edc_sites.models
+
 
 class Migration(migrations.Migration):
     dependencies = [

edc_refusal/migrations/0006_alter_subjectrefusal_managers.py

@@ -1,9 +1,10 @@
 # Generated by Django 4.2.1 on 2023-07-07 19:32
 
 import django.db.models.manager
-import edc_sites.models
 from django.db import migrations
 
+import edc_sites.models
+
 
 class Migration(migrations.Migration):
     dependencies = [

edc_refusal/migrations/0008_alter_historicalsubjectrefusal_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="historicalsubjectrefusal",
             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="historicalsubjectrefusal",
             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="historicalsubjectrefusal",
@@ -49,16 +45,12 @@ class Migration(migrations.Migration):
         migrations.AlterField(
             model_name="subjectrefusal",
             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="subjectrefusal",
             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="subjectrefusal",