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

edc_screening/model_mixins/screening_fields_model_mixin.py

@@ -8,6 +8,7 @@ from django.core.validators import (
     RegexValidator,
 )
 from django.db import models
+from django.utils import timezone
 from django_crypto_fields.fields import EncryptedCharField
 
 from edc_constants.choices import GENDER, YES_NO, YES_NO_NA
@@ -15,7 +16,6 @@ from edc_constants.constants import NO, NOT_APPLICABLE
 from edc_model.validators import datetime_not_future
 from edc_protocol.validators import datetime_not_before_study_start
 from edc_sites.model_mixins import SiteModelMixin
-from edc_utils.date import get_utcnow
 
 
 class ScreeningFieldsModeMixin(SiteModelMixin, models.Model):
@@ -34,7 +34,7 @@ class ScreeningFieldsModeMixin(SiteModelMixin, models.Model):
     report_datetime = models.DateTimeField(
         verbose_name="Report Date and Time",
         validators=[datetime_not_before_study_start, datetime_not_future],
-        default=get_utcnow,
+        default=timezone.now,
         help_text="Date and time of report.",
     )
 
@@ -54,7 +54,7 @@ class ScreeningFieldsModeMixin(SiteModelMixin, models.Model):
         validators=[MinValueValidator(0), MaxValueValidator(110)]
     )
 
-    ethnicity = models.CharField(max_length=25, null=True, blank=True)
+    ethnicity = models.CharField(max_length=25, default="", blank=True)
 
     consent_ability = models.CharField(
         verbose_name="Participant or legal guardian/representative able and "
@@ -65,8 +65,7 @@ class ScreeningFieldsModeMixin(SiteModelMixin, models.Model):
 
     unsuitable_for_study = models.CharField(
         verbose_name=(
-            "Is there any other reason the patient is "
-            "deemed to not be suitable for the study?"
+            "Is there any other reason the patient is deemed to not be suitable for the study?"
         ),
         max_length=5,
         choices=YES_NO,
@@ -77,14 +76,13 @@ class ScreeningFieldsModeMixin(SiteModelMixin, models.Model):
     reasons_unsuitable = models.TextField(
         verbose_name="Reason not suitable for the study",
         max_length=150,
-        null=True,
+        default="",
         blank=True,
     )
 
     unsuitable_agreed = models.CharField(
         verbose_name=(
-            "Does the study coordinator agree that the patient "
-            "is not suitable for the study?"
+            "Does the study coordinator agree that the patient is not suitable for the study?"
         ),
         max_length=5,
         choices=YES_NO_NA,

edc_screening/model_mixins/screening_methods_model_mixin.py

@@ -16,7 +16,7 @@ class ScreeningMethodsModeMixin(models.Model):
 
     @staticmethod
     def get_search_slug_fields():
-        return ["screening_identifier", "subject_identifier", "reference"]
+        return "screening_identifier", "subject_identifier", "reference"
 
     @property
     def estimated_dob(self: SubjectScreeningModelStub) -> date:

edc_screening/screening_eligibility.py

@@ -174,7 +174,7 @@ class ScreeningEligibility:
         setattr(
             self.model_obj,
             self.reasons_ineligible_fld_name,
-            "|".join(self.reasons_ineligible.values()) or None,
+            "|".join(self.reasons_ineligible.values()) or "",
         )
         self.set_eligible_model_field()
         self.set_fld_attrs_on_model()
@@ -229,9 +229,7 @@ class ScreeningEligibility:
         }
 
     def formatted_reasons_ineligible(self) -> str:
-        str_values = "<BR>".join(
-            [x for x in self.reasons_ineligible.values() if x is not None]
-        )
+        str_values = "<BR>".join([x for x in self.reasons_ineligible.values() if x])
         return format_html(
             "{}",
             mark_safe(str_values),  # nosec B703 B308

edc_screening/utils.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import contextlib
 import re
 from typing import TYPE_CHECKING, Any
 
@@ -33,14 +34,15 @@ def get_subject_screening_model_cls() -> Any:
     return django_apps.get_model(get_subject_screening_model())
 
 
-def format_reasons_ineligible(*str_values: str, delimiter=None) -> str:
+def format_reasons_ineligible(*str_values: str | None, delimiter: str | None = None) -> str:
     reasons = None
     delimiter = delimiter or "|"
-    str_values = tuple(x for x in str_values if x is not None)
+    str_values = str_values or []
+    str_values = tuple(x for x in str_values if x)
     if str_values:
         reasons = format_html(
             "{}",
-            mark_safe(delimiter.join(str_values)),  # nosec B703 B308
+            mark_safe(delimiter.join(str_values)),  # noqa: S308
         )
     return reasons
 
@@ -73,10 +75,10 @@ def get_subject_screening_or_raise(
             )
     except ObjectDoesNotExist as e:
         if is_modelform:
-            raise forms.ValidationError("Not allowed. Screening form not found.")
+            raise forms.ValidationError("Not allowed. Screening form not found.") from e
         raise ObjectDoesNotExist(
             f"{e} screening_identifier={screening_identifier}. Perhaps catch this in the form."
-        )
+        ) from e
     return subject_screening
 
 
@@ -101,10 +103,8 @@ def is_eligible_or_raise(
     )
 
     url_name = url_name or "screening_listboard_url"
-    try:
+    with contextlib.suppress(InvalidDashboardUrlName):
         url_name = url_names.get(url_name)
-    except InvalidDashboardUrlName:
-        pass
 
     if not subject_screening.eligible:
         try:
@@ -128,7 +128,7 @@ def is_eligible_or_raise(
         else:
             msg = format_html(
                 'Not allowed. Subject is not eligible. See subject <A href="{}">{}</A>',
-                mark_safe(url),  # nosec B308 B703
+                mark_safe(url),  # noqa: S308
                 subject_screening.screening_identifier,
             )
         raise forms.ValidationError(msg)

edc_search/generate_slug.py

@@ -0,0 +1,26 @@
+from __future__ import annotations
+
+from django.utils.text import slugify
+from django_crypto_fields.utils import get_encrypted_field_names
+
+SLUG_SEP = "|"
+
+
+def generate_slug(obj, fields) -> str | None:
+    """Returns a slug of the char values of the fields
+    listed on the models get_search_slug_fields() method.
+
+    Excludes any encrypted fields if listed.
+    """
+    slug = None
+    if obj and fields:
+        values = []
+        for field in (f for f in fields if f not in get_encrypted_field_names(obj)):
+            v = obj
+            for f in field.split("."):
+                v = getattr(v, f)
+            if isinstance(v, str):
+                values.append(v[:50])  # truncate value
+        slugs = [slugify(v) for v in list(set(values)) if v]
+        slug = SLUG_SEP.join(slugs)[:250]
+    return slug

edc_search/model_mixins.py

@@ -1,43 +1,31 @@
 from django.db import models
+from tqdm import tqdm
 
-from .updater import SearchSlugUpdater
+from .generate_slug import generate_slug
 
 
 class SearchSlugManager(models.Manager):
-    search_slug_updater_cls = SearchSlugUpdater
-    search_slug_field_name = "slug"
-
     def update_search_slugs(self) -> None:
-        for obj in self.all():
-            updater = self.search_slug_updater_cls(
-                fields=obj.get_search_slug_fields(), model_obj=obj
-            )
-            setattr(obj, self.search_slug_field_name, updater.slug)
-            obj.save_base(update_fields=[self.search_slug_field_name])
+        qs = self.all()
+        for obj in tqdm(qs, total=qs.count()):
+            obj.slug = generate_slug(obj, obj.get_search_slug_fields()) or ""
+            obj.save_base(update_fields=["slug"])
 
 
 class SearchSlugModelMixin(models.Model):
-    search_slug_warning = None
-    search_slug_updater_cls = SearchSlugUpdater
-
-    def get_search_slug_fields(self) -> list[str]:
-        return []
+    def get_search_slug_fields(self) -> tuple[str, ...]:
+        return ()
 
     slug = models.CharField(
         max_length=250,
         default="",
-        null=True,
         editable=False,
         db_index=True,
-        help_text="a field used for quick search",
+        help_text="Hold slug field values for quick search. Excludes encrypted fields",
     )
 
     def save(self, *args, **kwargs):
-        updater = self.search_slug_updater_cls(
-            fields=self.get_search_slug_fields(), model_obj=self
-        )
-        self.search_slug_warning = updater.warning
-        self.slug = updater.slug
+        self.slug = generate_slug(self, self.get_search_slug_fields()) or ""
         super().save(*args, **kwargs)
 
     class Meta:

edc_sites/auths.py

@@ -1,6 +1,11 @@
 from edc_auth.site_auths import site_auths
 from edc_auth.utils import remove_default_model_permissions_from_edc_permissions
 
-site_auths.add_post_update_func(
-    "edc_sites", remove_default_model_permissions_from_edc_permissions
-)
+
+def update_site_auths() -> None:
+    site_auths.add_post_update_func(
+        "edc_sites", remove_default_model_permissions_from_edc_permissions
+    )
+
+
+update_site_auths()

edc_sites/migrations/0007_edcpermissions.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_sites/migrations/0010_alter_edcpermissions_device_created_and_more.py

@@ -0,0 +1,69 @@
+# Generated by Django 5.2.6 on 2025-09-17 16:53
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("edc_sites", "0009_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",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="siteprofile",
+            name="country",
+            field=models.CharField(default="", max_length=250),
+        ),
+        migrations.AlterField(
+            model_name="siteprofile",
+            name="country_code",
+            field=models.CharField(default="", max_length=15),
+        ),
+        migrations.AlterField(
+            model_name="siteprofile",
+            name="languages",
+            field=models.TextField(default=""),
+        ),
+        migrations.AlterField(
+            model_name="siteprofile",
+            name="title",
+            field=models.CharField(default="", max_length=250),
+        ),
+    ]

edc_sites/model_mixins/site_model_mixin.py

@@ -28,7 +28,7 @@ class SiteModelMixin(models.Model):
         self.update_site_on_save(*args, **kwargs)
         super().save(*args, **kwargs)
 
-    def update_site_on_save(self, *args, **kwargs) -> None:
+    def update_site_on_save(self, *args, **kwargs) -> None:  # noqa: ARG002
         if not self.id:
             if not self.site_id and not self.site:
                 self.site = self.get_site_on_create()
@@ -59,7 +59,7 @@ class SiteModelMixin(models.Model):
                         "Exception raised when trying manager method `get_current()`. "
                         f"Sites registered with `sites` global are {site_ids}. "
                         f"settings.SITE_ID={settings.SITE_ID}. Got {e}."
-                    )
+                    ) from e
         return site_obj
 
     def validate_site_against_current(self) -> None:

edc_sites/site.py

@@ -160,13 +160,13 @@ class Sites:
                     single_site = dataclasses.replace(single_site, domain=domain)
 
                 if single_site.site_id in self._registry:
-                    raise AlreadyRegistered(f"Site already registered. Got `{single_site}`.")  # noqa: TRY003
+                    raise AlreadyRegistered(f"Site already registered. Got `{single_site}`.")
                 if single_site.name in [s.name for s in self._registry.values()]:
-                    raise AlreadyRegisteredName(  # noqa: TRY003
+                    raise AlreadyRegisteredName(
                         f"Site with this name is already registered. Got `{single_site}`."
                     )
                 if single_site.domain in [s.domain for s in self._registry.values()]:
-                    raise AlreadyRegisteredDomain(  # noqa: TRY003
+                    raise AlreadyRegisteredDomain(
                         f"Site with this domain is already registered. Got `{single_site}`."
                     )
                 self._registry.update({single_site.site_id: single_site})
@@ -187,7 +187,7 @@ class Sites:
                 msg = "In fact, no sites have been registered!"
             else:
                 msg = f"Expected one of {[s.site_id for s in self.all(aslist=True)]}."
-            raise SiteNotRegistered(  # noqa: TRY003
+            raise SiteNotRegistered(
                 f"Site not registered. {msg} See {self!r}. Got `{site_id}`."
             )
         return self._registry.get(site_id)
@@ -196,7 +196,7 @@ class Sites:
         for single_site in self._registry.values():
             if getattr(single_site, attrname) == value:
                 return single_site
-        raise SiteDoesNotExist(f"No site exists with `{attrname}`==`{value}`.")  # noqa: TRY003
+        raise SiteDoesNotExist(f"No site exists with `{attrname}`==`{value}`.")
 
     def all(self, aslist: bool | None = None) -> dict[int, SingleSite] | list[SingleSite]:
         if aslist:

edc_sites/system_checks.py

@@ -10,7 +10,7 @@ from edc_sites.site import sites as site_sites
 from edc_sites.utils import get_site_model_cls
 
 
-def sites_check(app_configs, **kwargs):  # noqa
+def sites_check(app_configs, **kwargs):
     errors = []
     if "migrate" not in sys.argv and "makemigrations" not in sys.argv:
         try:

edc_subject_dashboard/auths.py

@@ -7,30 +7,35 @@ from edc_auth.constants import (
 from edc_auth.site_auths import site_auths
 from edc_auth.utils import remove_default_model_permissions_from_edc_permissions
 
-site_auths.add_post_update_func(
-    "edc_subject_dashboard", remove_default_model_permissions_from_edc_permissions
-)
-
 SUBJECT_VIEW = "SUBJECT_VIEW"
 
-site_auths.add_custom_permissions_tuples(
-    model="edc_subject_dashboard.edcpermissions",
-    codename_tuples=(
-        (
-            "edc_subject_dashboard.view_subject_listboard",
-            "Can access subject listboard",
+
+def update_site_auths() -> None:
+    site_auths.add_post_update_func(
+        "edc_subject_dashboard", remove_default_model_permissions_from_edc_permissions
+    )
+
+    site_auths.add_custom_permissions_tuples(
+        model="edc_subject_dashboard.edcpermissions",
+        codename_tuples=(
+            (
+                "edc_subject_dashboard.view_subject_listboard",
+                "Can access subject listboard",
+            ),
+            ("edc_subject_dashboard.nav_subject_section", "Can access nav_subject_section"),
         ),
-        ("edc_subject_dashboard.nav_subject_section", "Can access nav_subject_section"),
-    ),
-)
+    )
+
+    site_auths.add_group(
+        "edc_subject_dashboard.view_subject_listboard",
+        "edc_subject_dashboard.nav_subject_section",
+        name=SUBJECT_VIEW,
+    )
+
+    site_auths.update_role(SUBJECT_VIEW, name=CLINICIAN_ROLE)
+    site_auths.update_role(SUBJECT_VIEW, name=NURSE_ROLE)
+    site_auths.update_role(SUBJECT_VIEW, name=CLINICIAN_SUPER_ROLE)
+    site_auths.update_role(SUBJECT_VIEW, name=AUDITOR_ROLE)
 
-site_auths.add_group(
-    "edc_subject_dashboard.view_subject_listboard",
-    "edc_subject_dashboard.nav_subject_section",
-    name=SUBJECT_VIEW,
-)
 
-site_auths.update_role(SUBJECT_VIEW, name=CLINICIAN_ROLE)
-site_auths.update_role(SUBJECT_VIEW, name=NURSE_ROLE)
-site_auths.update_role(SUBJECT_VIEW, name=CLINICIAN_SUPER_ROLE)
-site_auths.update_role(SUBJECT_VIEW, name=AUDITOR_ROLE)
+update_site_auths()

edc_subject_dashboard/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_subject_dashboard/migrations/0005_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_subject_dashboard", "0004_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_subject_dashboard/requisition_report.py

@@ -1,6 +1,7 @@
 from tempfile import mkdtemp
 
 from django.contrib import messages
+from django.utils import timezone
 from reportlab.graphics.barcode import code39
 from reportlab.lib import colors
 from reportlab.lib.units import cm, mm
@@ -11,7 +12,6 @@ from edc_identifier.utils import convert_to_human_readable
 from edc_lab.model_mixins import RequisitionModelMixin
 from edc_lab.models.manifest.shipper import Shipper
 from edc_pdf_reports import Report
-from edc_utils import get_utcnow
 
 
 class RequisitionReport(Report):
@@ -33,7 +33,7 @@ class RequisitionReport(Report):
         self.consignee = consignee
         self.contact_name = f"{self.user.first_name} {self.user.last_name}"
         self.image_folder = mkdtemp()
-        self.timestamp = get_utcnow().strftime("%Y%m%d%H%M%S")
+        self.timestamp = timezone.now().strftime("%Y%m%d%H%M%S")
         self.report_filename = f"requisition_{self.timestamp}.pdf"
 
     @property
@@ -60,7 +60,9 @@ class RequisitionReport(Report):
                 Paragraph("REFERENCE", self.styles["line_label"]),
             ],
             [
-                Paragraph(get_utcnow().strftime("%Y-%m-%d"), self.styles["line_data_largest"]),
+                Paragraph(
+                    timezone.now().strftime("%Y-%m-%d"), self.styles["line_data_largest"]
+                ),
                 Paragraph(
                     convert_to_human_readable(self.timestamp),
                     self.styles["line_data_largest"],
@@ -173,7 +175,7 @@ class RequisitionReport(Report):
                 Paragraph(self.contact_name, self.styles["line_data_large"]),
                 "",
                 Paragraph(
-                    get_utcnow().strftime("%Y-%m-%d %H:%M"),
+                    timezone.now().strftime("%Y-%m-%d %H:%M"),
                     self.styles["line_data_large"],
                 ),
             ],

edc_subject_dashboard/requisition_verifier.py

@@ -1,10 +1,12 @@
+import contextlib
+
 from django.core.exceptions import ObjectDoesNotExist
+from django.utils import timezone
 
 from edc_appointment.models import Appointment
 from edc_constants.constants import NO, YES
 from edc_lab.constants import TUBE
 from edc_lab.model_mixins import RequisitionModelMixin
-from edc_utils import get_utcnow
 
 
 class RequisitionVerifier:
@@ -22,12 +24,12 @@ class RequisitionVerifier:
         if self.requisition and self.requisition.is_drawn != NO:
             # verification fields
             self.requisition.clinic_verified = YES
-            self.requisition.clinic_verified_datetime = get_utcnow()
+            self.requisition.clinic_verified_datetime = timezone.now()
             # other fields for label printing
             self.requisition.is_drawn = self.requisition.is_drawn or YES
             self.requisition.item_count = self.requisition.item_count or 1
             self.requisition.item_type = self.requisition.item_type or TUBE
-            self.requisition.drawn_datetime = self.requisition.drawn_datetime or get_utcnow()
+            self.requisition.drawn_datetime = self.requisition.drawn_datetime or timezone.now()
             self.requisition.save()
             self.verified = self.requisition.clinic_verified
 
@@ -43,12 +45,10 @@ class RequisitionVerifier:
     def requisition(self):
         """Returns a requisition model instance."""
         if not self._requisition:
-            try:
+            with contextlib.suppress(ObjectDoesNotExist):
                 self._requisition = self.requisition_model_cls.objects.get(
                     requisition_identifier=self.requisition_identifier.strip()
                 )
-            except ObjectDoesNotExist:
-                pass
         return self._requisition
 
     @property

edc_subject_dashboard/templatetags/edc_subject_dashboard_extras.py

@@ -8,6 +8,7 @@ from django import template
 from django.apps import apps as django_apps
 from django.core.exceptions import MultipleObjectsReturned, ObjectDoesNotExist
 from django.urls import reverse
+from django.utils import timezone
 
 from edc_appointment.constants import (
     CANCELLED_APPT,
@@ -26,7 +27,6 @@ from edc_appointment.view_utils import AppointmentButton
 from edc_auth.constants import AUDITOR_ROLE
 from edc_metadata import KEYED, REQUIRED
 from edc_metadata.metadata_helper import MetadataHelper
-from edc_utils import get_utcnow
 from edc_view_utils import PrnButton, render_history_and_query_buttons
 from edc_visit_tracking.view_utils import RelatedVisitButton
 
@@ -171,7 +171,7 @@ def render_crf_totals(appointment: Appointment = None) -> dict[str, bool | int]:
         skipped = True
     elif (
         appointment.appt_status == NEW_APPT
-        and appointment.appt_datetime.date() < get_utcnow().date()
+        and appointment.appt_datetime.date() < timezone.now().date()
     ):
         overdue = True
     else: