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

edc_identifier/migrations/0010_auto_20170112_0602.py

@@ -6,7 +6,7 @@ from django.db import migrations, models
 
 import edc_model_fields.fields.hostname_modification_field
 import edc_model_fields.fields.userfield
-import edc_utils
+import django.utils.timezone
 
 
 class Migration(migrations.Migration):
@@ -16,7 +16,7 @@ class Migration(migrations.Migration):
         migrations.AlterField(
             model_name="historicalidentifierhistory",
             name="created",
-            field=models.DateTimeField(blank=True, default=edc_utils.date.get_utcnow),
+            field=models.DateTimeField(blank=True, default=django.utils.timezone.now),
         ),
         migrations.AlterField(
             model_name="historicalidentifierhistory",
@@ -40,7 +40,7 @@ class Migration(migrations.Migration):
         migrations.AlterField(
             model_name="historicalidentifierhistory",
             name="modified",
-            field=models.DateTimeField(blank=True, default=edc_utils.date.get_utcnow),
+            field=models.DateTimeField(blank=True, default=django.utils.timezone.now),
         ),
         migrations.AlterField(
             model_name="historicalidentifierhistory",
@@ -59,7 +59,7 @@ class Migration(migrations.Migration):
         migrations.AlterField(
             model_name="historicalidentifiertracker",
             name="created",
-            field=models.DateTimeField(blank=True, default=edc_utils.date.get_utcnow),
+            field=models.DateTimeField(blank=True, default=django.utils.timezone.now),
         ),
         migrations.AlterField(
             model_name="historicalidentifiertracker",
@@ -83,7 +83,7 @@ class Migration(migrations.Migration):
         migrations.AlterField(
             model_name="historicalidentifiertracker",
             name="modified",
-            field=models.DateTimeField(blank=True, default=edc_utils.date.get_utcnow),
+            field=models.DateTimeField(blank=True, default=django.utils.timezone.now),
         ),
         migrations.AlterField(
             model_name="historicalidentifiertracker",
@@ -102,7 +102,7 @@ class Migration(migrations.Migration):
         migrations.AlterField(
             model_name="historicalsubjectidentifier",
             name="created",
-            field=models.DateTimeField(blank=True, default=edc_utils.date.get_utcnow),
+            field=models.DateTimeField(blank=True, default=django.utils.timezone.now),
         ),
         migrations.AlterField(
             model_name="historicalsubjectidentifier",
@@ -126,7 +126,7 @@ class Migration(migrations.Migration):
         migrations.AlterField(
             model_name="historicalsubjectidentifier",
             name="modified",
-            field=models.DateTimeField(blank=True, default=edc_utils.date.get_utcnow),
+            field=models.DateTimeField(blank=True, default=django.utils.timezone.now),
         ),
         migrations.AlterField(
             model_name="historicalsubjectidentifier",
@@ -145,7 +145,7 @@ class Migration(migrations.Migration):
         migrations.AlterField(
             model_name="identifierhistory",
             name="created",
-            field=models.DateTimeField(blank=True, default=edc_utils.date.get_utcnow),
+            field=models.DateTimeField(blank=True, default=django.utils.timezone.now),
         ),
         migrations.AlterField(
             model_name="identifierhistory",
@@ -169,7 +169,7 @@ class Migration(migrations.Migration):
         migrations.AlterField(
             model_name="identifierhistory",
             name="modified",
-            field=models.DateTimeField(blank=True, default=edc_utils.date.get_utcnow),
+            field=models.DateTimeField(blank=True, default=django.utils.timezone.now),
         ),
         migrations.AlterField(
             model_name="identifierhistory",
@@ -188,7 +188,7 @@ class Migration(migrations.Migration):
         migrations.AlterField(
             model_name="identifiermodel",
             name="created",
-            field=models.DateTimeField(blank=True, default=edc_utils.date.get_utcnow),
+            field=models.DateTimeField(blank=True, default=django.utils.timezone.now),
         ),
         migrations.AlterField(
             model_name="identifiermodel",
@@ -212,7 +212,7 @@ class Migration(migrations.Migration):
         migrations.AlterField(
             model_name="identifiermodel",
             name="modified",
-            field=models.DateTimeField(blank=True, default=edc_utils.date.get_utcnow),
+            field=models.DateTimeField(blank=True, default=django.utils.timezone.now),
         ),
         migrations.AlterField(
             model_name="identifiermodel",
@@ -231,7 +231,7 @@ class Migration(migrations.Migration):
         migrations.AlterField(
             model_name="identifiertracker",
             name="created",
-            field=models.DateTimeField(blank=True, default=edc_utils.date.get_utcnow),
+            field=models.DateTimeField(blank=True, default=django.utils.timezone.now),
         ),
         migrations.AlterField(
             model_name="identifiertracker",
@@ -255,7 +255,7 @@ class Migration(migrations.Migration):
         migrations.AlterField(
             model_name="identifiertracker",
             name="modified",
-            field=models.DateTimeField(blank=True, default=edc_utils.date.get_utcnow),
+            field=models.DateTimeField(blank=True, default=django.utils.timezone.now),
         ),
         migrations.AlterField(
             model_name="identifiertracker",
@@ -274,7 +274,7 @@ class Migration(migrations.Migration):
         migrations.AlterField(
             model_name="sequence",
             name="created",
-            field=models.DateTimeField(blank=True, default=edc_utils.date.get_utcnow),
+            field=models.DateTimeField(blank=True, default=django.utils.timezone.now),
         ),
         migrations.AlterField(
             model_name="sequence",
@@ -298,7 +298,7 @@ class Migration(migrations.Migration):
         migrations.AlterField(
             model_name="sequence",
             name="modified",
-            field=models.DateTimeField(blank=True, default=edc_utils.date.get_utcnow),
+            field=models.DateTimeField(blank=True, default=django.utils.timezone.now),
         ),
         migrations.AlterField(
             model_name="sequence",
@@ -317,7 +317,7 @@ class Migration(migrations.Migration):
         migrations.AlterField(
             model_name="subjectidentifier",
             name="created",
-            field=models.DateTimeField(blank=True, default=edc_utils.date.get_utcnow),
+            field=models.DateTimeField(blank=True, default=django.utils.timezone.now),
         ),
         migrations.AlterField(
             model_name="subjectidentifier",
@@ -341,7 +341,7 @@ class Migration(migrations.Migration):
         migrations.AlterField(
             model_name="subjectidentifier",
             name="modified",
-            field=models.DateTimeField(blank=True, default=edc_utils.date.get_utcnow),
+            field=models.DateTimeField(blank=True, default=django.utils.timezone.now),
         ),
         migrations.AlterField(
             model_name="subjectidentifier",

edc_identifier/migrations/0011_alter_identifiermodel_device_created_and_more.py

@@ -0,0 +1,79 @@
+# Generated by Django 5.2.6 on 2025-09-17 15:50
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("edc_identifier", "0010_alter_identifiermodel_revision"),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="identifiermodel",
+            name="device_created",
+            field=models.CharField(
+                blank=True, default="", max_length=10, verbose_name="Device created"
+            ),
+        ),
+        migrations.AlterField(
+            model_name="identifiermodel",
+            name="device_modified",
+            field=models.CharField(
+                blank=True, default="", max_length=10, verbose_name="Device modified"
+            ),
+        ),
+        migrations.AlterField(
+            model_name="identifiermodel",
+            name="identifier_prefix",
+            field=models.CharField(default="", max_length=25),
+        ),
+        migrations.AlterField(
+            model_name="identifiermodel",
+            name="identifier_type",
+            field=models.CharField(default="", max_length=100),
+        ),
+        migrations.AlterField(
+            model_name="identifiermodel",
+            name="linked_identifier",
+            field=models.CharField(default="", max_length=50),
+        ),
+        migrations.AlterField(
+            model_name="identifiermodel",
+            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="identifiermodel",
+            name="locale_modified",
+            field=models.CharField(
+                blank=True,
+                default="",
+                help_text="Auto-updated by Modeladmin",
+                max_length=10,
+                verbose_name="Locale modified",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="identifiermodel",
+            name="model",
+            field=models.CharField(default="", max_length=100),
+        ),
+        migrations.AlterField(
+            model_name="identifiermodel",
+            name="protocol_number",
+            field=models.CharField(default="", max_length=25),
+        ),
+        migrations.AlterField(
+            model_name="identifiermodel",
+            name="subject_identifier",
+            field=models.CharField(default="", max_length=50),
+        ),
+    ]

edc_identifier/model_mixins.py

@@ -44,7 +44,7 @@ class SubjectIdentifierAdditionalFieldsModelMixin(models.Model):
     subject_identifier_aka = models.CharField(
         verbose_name="Subject Identifier a.k.a",
         max_length=50,
-        null=True,
+        default="",
         editable=False,
         help_text="track a previously allocated identifier.",
     )

edc_identifier/models.py

@@ -25,21 +25,21 @@ class IdentifierModel(SiteModelMixin, BaseUuidModel):
 
     name = models.CharField(max_length=100)
 
-    subject_identifier = models.CharField(max_length=50, null=True)
+    subject_identifier = models.CharField(max_length=50, default="")
 
     sequence_number = models.IntegerField(default=1)
 
-    linked_identifier = models.CharField(max_length=50, null=True)
+    linked_identifier = models.CharField(max_length=50, default="")
 
     device_id = models.IntegerField()
 
-    protocol_number = models.CharField(max_length=25, null=True)
+    protocol_number = models.CharField(max_length=25, default="")
 
-    model = models.CharField(max_length=100, null=True)
+    model = models.CharField(max_length=100, default="")
 
-    identifier_type = models.CharField(max_length=100, null=True)
+    identifier_type = models.CharField(max_length=100, default="")
 
-    identifier_prefix = models.CharField(max_length=25, null=True)
+    identifier_prefix = models.CharField(max_length=25, default="")
 
     objects = IdentifierModelManager()
 
@@ -51,9 +51,9 @@ class IdentifierModel(SiteModelMixin, BaseUuidModel):
 
     class Meta(BaseUuidModel.Meta):
         app_label = "edc_identifier"
-        constraints = [
+        constraints = (
             UniqueConstraint(
                 fields=["name", "identifier"], name="%(app_label)s_%(class)s_name_uniq"
-            )
-        ]
+            ),
+        )
         indexes = BaseUuidModel.Meta.indexes

edc_identifier/research_identifier.py

@@ -16,7 +16,7 @@ if TYPE_CHECKING:
     from .models import IdentifierModel
 
 
-class IdentifierMissingTemplateValue(Exception):
+class IdentifierMissingTemplateValue(Exception):  # noqa: N818
     pass
 
 
@@ -38,6 +38,7 @@ class ResearchIdentifier:
         identifier: str | None = None,
     ) -> None:
         self._identifier = None
+        self._sequence_number = None
         self.requesting_model = requesting_model
         if not self.requesting_model:
             raise IdentifierError("Invalid requesting_model. Got None")
@@ -121,10 +122,10 @@ class ResearchIdentifier:
         for key in keys:
             try:
                 value = getattr(self, key)
-            except AttributeError:
+            except AttributeError as e:
                 raise IdentifierMissingTemplateValue(
                     f"Required option not provided. Got '{key}'."
-                )
+                ) from e
             else:
                 if value:
                     template_opts.update({key: value})
@@ -141,15 +142,15 @@ class ResearchIdentifier:
     @property
     def sequence_number(self) -> int:
         """Returns the next sequence number to use."""
-        try:
-            identifier_model = (
+        if self._sequence_number is None:
+            if identifier_model := (
                 self.identifier_model_cls.objects.filter(
                     name=self.label, device_id=self.device_id, site=self.site
                 )
                 .order_by("-sequence_number")
                 .first()
-            )
-            sequence_number = identifier_model.sequence_number + 1
-        except AttributeError:
-            sequence_number = 1
-        return sequence_number
+            ):
+                self._sequence_number = identifier_model.sequence_number + 1
+            else:
+                self._sequence_number = 1
+        return self._sequence_number

edc_identifier/simple_identifier.py

@@ -1,15 +1,18 @@
+from __future__ import annotations
+
 from secrets import choice
-from typing import Any
+from typing import TYPE_CHECKING, Any
 
 from django.apps import apps as django_apps
 from django.core.exceptions import ObjectDoesNotExist
 from django.db import models
 from django.utils import timezone
 
-from edc_utils import get_utcnow
-
 from .utils import convert_to_human_readable
 
+if TYPE_CHECKING:
+    from edc_identifier.models import IdentifierModel
+
 
 class DuplicateIdentifierError(Exception):
     pass
@@ -83,7 +86,7 @@ class SimpleSequentialIdentifier:
     prefix: str | None = None
 
     def __init__(self):
-        sequence: int = int(get_utcnow().timestamp())
+        sequence: int = int(timezone.now().timestamp())
         random_number: int = choice(range(1000, 9999))  # nosec B311
         sequence: str = f"{sequence}{random_number}"
         chk: int = int(sequence) % 11
@@ -197,7 +200,7 @@ class SimpleUniqueIdentifier:
     def model_cls(self) -> type[models.Model]:
         return django_apps.get_model(self.model)
 
-    def update_identifier_model(self, **kwargs) -> bool:
+    def update_identifier_model(self, **kwargs) -> bool | IdentifierModel:
         """Attempts to update identifier_model and returns True (or instance)
         if successful else False if identifier already exists.
         """
@@ -212,5 +215,6 @@ class SimpleUniqueIdentifier:
         try:
             self.model_cls.objects.get(identifier=self.identifier)
         except ObjectDoesNotExist:
+            opts = {k: v for k, v in opts.items() if v is not None}
             return self.model_cls.objects.create(**opts)
         return False

edc_identifier/subject_identifier.py

@@ -1,5 +1,6 @@
+from django.utils import timezone
+
 from edc_registration import get_registered_subject_model_cls
-from edc_utils import get_utcnow
 
 from .research_identifier import ResearchIdentifier
 
@@ -26,5 +27,5 @@ class SubjectIdentifier(ResearchIdentifier):
             site=self.site,
             subject_type=self.identifier_type,
             last_name=self.last_name,
-            registration_datetime=get_utcnow(),
+            registration_datetime=timezone.now(),
         )

edc_lab/auths.py

@@ -9,6 +9,7 @@ from edc_auth.constants import (
     PII_VIEW,
 )
 from edc_auth.site_auths import site_auths
+from edc_export.constants import EXPORT
 
 from .auth_objects import (
     LAB,
@@ -18,26 +19,28 @@ from .auth_objects import (
     lab_view_codenames,
 )
 
-site_auths.add_group(*lab_codenames, name=LAB)
-site_auths.add_group(*lab_view_codenames, name=LAB_VIEW)
-
-if django_apps.is_installed("edc_export"):
-    from edc_export.constants import EXPORT
-
-    site_auths.update_group(
-        "edc_lab.export_aliquot",
-        "edc_lab.export_box",
-        "edc_lab.export_boxitem",
-        "edc_lab.export_boxtype",
-        "edc_lab.export_order",
-        "edc_lab.export_panel",
-        "edc_lab.export_result",
-        "edc_lab.export_resultitem",
-        name=EXPORT,
-    )
-
-
-site_auths.add_role(ADMINISTRATION, EVERYONE, LAB, PII_VIEW, name=LAB_TECHNICIAN_ROLE)
-site_auths.update_role(LAB, name=CLINICIAN_ROLE)
-site_auths.update_role(LAB, name=NURSE_ROLE)
-site_auths.update_role(LAB_VIEW, name=AUDITOR_ROLE)
+
+def update_site_auths():
+    site_auths.add_group(*lab_codenames, name=LAB)
+    site_auths.add_group(*lab_view_codenames, name=LAB_VIEW)
+
+    if django_apps.is_installed("edc_export"):
+        site_auths.update_group(
+            "edc_lab.export_aliquot",
+            "edc_lab.export_box",
+            "edc_lab.export_boxitem",
+            "edc_lab.export_boxtype",
+            "edc_lab.export_order",
+            "edc_lab.export_panel",
+            "edc_lab.export_result",
+            "edc_lab.export_resultitem",
+            name=EXPORT,
+        )
+
+    site_auths.add_role(ADMINISTRATION, EVERYONE, LAB, PII_VIEW, name=LAB_TECHNICIAN_ROLE)
+    site_auths.update_role(LAB, name=CLINICIAN_ROLE)
+    site_auths.update_role(LAB, name=NURSE_ROLE)
+    site_auths.update_role(LAB_VIEW, name=AUDITOR_ROLE)
+
+
+update_site_auths()

edc_lab/lab/aliquot_creator.py

@@ -90,18 +90,15 @@ class AliquotCreator:
             parent_segment=self.parent_segment,
         )
 
-        parent_identifier = parent_identifier or aliquot_identifier_obj.identifier
-
-        aliquot = self.aliquot_model_cls.objects.create(
+        return self.aliquot_model_cls.objects.create(
             aliquot_identifier=aliquot_identifier_obj.identifier,
             aliquot_type=aliquot_type.name,
             alpha_code=aliquot_type.alpha_code,
             count=count,
             numeric_code=aliquot_type.numeric_code,
-            parent_identifier=parent_identifier,
+            parent_identifier=parent_identifier or aliquot_identifier_obj.identifier,
             identifier_prefix=self.identifier_prefix,
-            is_primary=True if self.is_primary else False,
-            requisition_identifier=self.requisition_identifier,
-            subject_identifier=self.subject_identifier,
+            is_primary=bool(self.is_primary),
+            requisition_identifier=self.requisition_identifier or "",
+            subject_identifier=self.subject_identifier or "",
         )
-        return aliquot

edc_lab/lab/primary_aliquot.py

@@ -1,3 +1,11 @@
+from __future__ import annotations
+
+from typing import TYPE_CHECKING
+
+if TYPE_CHECKING:
+    from edc_lab import AliquotCreator, AliquotType
+
+
 class PrimaryAliquotError(Exception):
     pass
 
@@ -11,11 +19,12 @@ class PrimaryAliquot:
 
     def __init__(
         self,
-        aliquot_type=None,
-        subject_identifier=None,
-        requisition_identifier=None,
-        identifier_prefix=None,
-        aliquot_creator_cls=None,
+        *,
+        aliquot_creator_cls: type[AliquotCreator],
+        aliquot_type: AliquotType | None = None,
+        subject_identifier: str | None = None,
+        requisition_identifier: str | None = None,
+        identifier_prefix: str | None = None,
     ):
         self._object = None
         self.aliquot_creator_cls = aliquot_creator_cls