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

edc_data_manager/migrations/0041_alter_dataquery_dm_user_and_more.py

@@ -0,0 +1,164 @@
+# Generated by Django 5.2.6 on 2025-09-18 00:24
+
+import django.db.models.deletion
+import django.utils.timezone
+import uuid
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("edc_data_manager", "0040_alter_datadictionary_device_created_and_more"),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="dataquery",
+            name="dm_user",
+            field=models.ForeignKey(
+                blank=True,
+                help_text="Please select a name from the list",
+                null=True,
+                on_delete=django.db.models.deletion.PROTECT,
+                related_name="+",
+                to="edc_data_manager.datamanageruser",
+                verbose_name="DM resolved by",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="dataquery",
+            name="locked_reason",
+            field=models.TextField(
+                blank=True,
+                default="",
+                help_text="If required, the reason the query cannot be resolved.",
+                verbose_name="Reason query locked",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="dataquery",
+            name="plan_of_action",
+            field=models.TextField(
+                blank=True,
+                default="",
+                help_text="If required, provide a plan of action",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="dataquery",
+            name="report_datetime",
+            field=models.DateTimeField(
+                default=django.utils.timezone.now, verbose_name="Query date"
+            ),
+        ),
+        migrations.AlterField(
+            model_name="dataquery",
+            name="rule_reference",
+            field=models.CharField(
+                default=uuid.uuid4, max_length=150, verbose_name="Query rule reference"
+            ),
+        ),
+        migrations.AlterField(
+            model_name="dataquery",
+            name="sender",
+            field=models.ForeignKey(
+                help_text="Please select a name from the list",
+                on_delete=django.db.models.deletion.PROTECT,
+                related_name="+",
+                to="edc_data_manager.datamanageruser",
+                verbose_name="Query raised by",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="dataquery",
+            name="site_response_text",
+            field=models.TextField(blank=True, default=""),
+        ),
+        migrations.AlterField(
+            model_name="dataquery",
+            name="subject_identifier",
+            field=models.CharField(default="", editable=False, max_length=50),
+        ),
+        migrations.AlterField(
+            model_name="dataquery",
+            name="title",
+            field=models.CharField(default="", max_length=150),
+        ),
+        migrations.AlterField(
+            model_name="historicaldataquery",
+            name="dm_user",
+            field=models.ForeignKey(
+                blank=True,
+                db_constraint=False,
+                help_text="Please select a name from the list",
+                null=True,
+                on_delete=django.db.models.deletion.DO_NOTHING,
+                related_name="+",
+                to="edc_data_manager.datamanageruser",
+                verbose_name="DM resolved by",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="historicaldataquery",
+            name="locked_reason",
+            field=models.TextField(
+                blank=True,
+                default="",
+                help_text="If required, the reason the query cannot be resolved.",
+                verbose_name="Reason query locked",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="historicaldataquery",
+            name="plan_of_action",
+            field=models.TextField(
+                blank=True,
+                default="",
+                help_text="If required, provide a plan of action",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="historicaldataquery",
+            name="report_datetime",
+            field=models.DateTimeField(
+                default=django.utils.timezone.now, verbose_name="Query date"
+            ),
+        ),
+        migrations.AlterField(
+            model_name="historicaldataquery",
+            name="rule_reference",
+            field=models.CharField(
+                default=uuid.uuid4, max_length=150, verbose_name="Query rule reference"
+            ),
+        ),
+        migrations.AlterField(
+            model_name="historicaldataquery",
+            name="sender",
+            field=models.ForeignKey(
+                blank=True,
+                db_constraint=False,
+                help_text="Please select a name from the list",
+                null=True,
+                on_delete=django.db.models.deletion.DO_NOTHING,
+                related_name="+",
+                to="edc_data_manager.datamanageruser",
+                verbose_name="Query raised by",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="historicaldataquery",
+            name="site_response_text",
+            field=models.TextField(blank=True, default=""),
+        ),
+        migrations.AlterField(
+            model_name="historicaldataquery",
+            name="subject_identifier",
+            field=models.CharField(default="", editable=False, max_length=50),
+        ),
+        migrations.AlterField(
+            model_name="historicaldataquery",
+            name="title",
+            field=models.CharField(default="", max_length=150),
+        ),
+    ]

edc_data_manager/models/data_query.py

@@ -6,6 +6,7 @@ from django.db import models
 from django.db.models.deletion import PROTECT
 from django.template.loader import render_to_string
 from django.urls.base import reverse
+from django.utils import timezone
 
 from edc_action_item.models.action_model_mixin import ActionModelMixin
 from edc_constants.constants import CLOSED, RESOLVED
@@ -13,7 +14,6 @@ from edc_dashboard.url_names import InvalidDashboardUrlName, url_names
 from edc_model.models import BaseUuidModel
 from edc_sites.managers import CurrentSiteManager
 from edc_sites.model_mixins import SiteModelMixin
-from edc_utils.date import get_utcnow
 from edc_visit_tracking.utils import get_related_visit_model_cls
 
 from ..action_items import DATA_QUERY_ACTION
@@ -28,7 +28,7 @@ from .requisition_panel import RequisitionPanel
 class DataQuery(DataQueryModelMixin, ActionModelMixin, SiteModelMixin, BaseUuidModel):
     action_name = DATA_QUERY_ACTION
 
-    subject_identifier = models.CharField(max_length=50, null=True, editable=False)
+    subject_identifier = models.CharField(max_length=50, default="", editable=False)
 
     registered_subject = models.ForeignKey(
         QuerySubject,
@@ -83,7 +83,7 @@ class DataQuery(DataQueryModelMixin, ActionModelMixin, SiteModelMixin, BaseUuidM
     )
 
     rule_reference = models.CharField(
-        verbose_name="Query rule reference", max_length=150, null=True, default=uuid4
+        verbose_name="Query rule reference", max_length=150, default=uuid4
     )
 
     objects = models.Manager()
@@ -107,7 +107,7 @@ class DataQuery(DataQueryModelMixin, ActionModelMixin, SiteModelMixin, BaseUuidM
             and self.site_response_text.strip() == AUTO_RESOLVED
         ):
             self.status = CLOSED
-            self.resolved_datetime = get_utcnow()
+            self.resolved_datetime = timezone.now()
             self.dm_user = self.sender
 
     def form_and_numbers_to_string(self):
@@ -192,7 +192,7 @@ class DataQuery(DataQueryModelMixin, ActionModelMixin, SiteModelMixin, BaseUuidM
     class Meta(BaseUuidModel.Meta):
         verbose_name = "Data Query"
         verbose_name_plural = "Data Queries"
-        unique_together = ["registered_subject", "rule_reference", "visit_schedule"]
+        unique_together = ("registered_subject", "rule_reference", "visit_schedule")
         indexes = (
             models.Index(
                 fields=[

edc_data_manager/models/model_mixins.py

@@ -1,8 +1,8 @@
 from django.db import models
 from django.db.models import PROTECT
+from django.utils import timezone
 
 from edc_constants.constants import CLOSED, NEW, NORMAL, OPEN, RESOLVED
-from edc_utils import get_utcnow
 
 from ..choices import DM_STATUS, QUERY_PRIORITY, RESPONSE_STATUS
 from ..constants import CLOSED_WITH_ACTION
@@ -10,16 +10,16 @@ from .user import DataManagerUser, QueryUser
 
 
 class DataQueryModelMixin(models.Model):
-    report_datetime = models.DateTimeField(verbose_name="Query date", default=get_utcnow)
+    report_datetime = models.DateTimeField(verbose_name="Query date", default=timezone.now)
 
-    title = models.CharField(max_length=150, null=True, blank=False)
+    title = models.CharField(max_length=150, default="", blank=False)
 
     sender = models.ForeignKey(
         DataManagerUser,
         related_name="+",
         on_delete=PROTECT,
         verbose_name="Query raised by",
-        help_text="Select a name from the list",
+        help_text="Please select a name from the list",
     )
 
     recipients = models.ManyToManyField(
@@ -43,7 +43,7 @@ class DataQueryModelMixin(models.Model):
         verbose_name="Site resolved on", null=True, blank=True
     )
 
-    site_response_text = models.TextField(null=True, blank=True)
+    site_response_text = models.TextField(default="", blank=True)
 
     site_response_status = models.CharField(
         verbose_name="Site status", max_length=25, choices=RESPONSE_STATUS, default=NEW
@@ -60,7 +60,7 @@ class DataQueryModelMixin(models.Model):
         on_delete=PROTECT,
         null=True,
         blank=True,
-        help_text="select a name from the list",
+        help_text="Please select a name from the list",
     )
 
     resolved_datetime = models.DateTimeField(
@@ -70,7 +70,7 @@ class DataQueryModelMixin(models.Model):
     auto_resolved = models.BooleanField(default=False)
 
     plan_of_action = models.TextField(
-        null=True, blank=True, help_text="If required, provide a plan of action"
+        default="", blank=True, help_text="If required, provide a plan of action"
     )
 
     locked = models.BooleanField(
@@ -80,7 +80,7 @@ class DataQueryModelMixin(models.Model):
 
     locked_reason = models.TextField(
         verbose_name="Reason query locked",
-        null=True,
+        default="",
         blank=True,
         help_text="If required, the reason the query cannot be resolved.",
     )

edc_data_manager/rule/query_rule_wrapper.py

@@ -2,7 +2,7 @@ from __future__ import annotations
 
 from datetime import datetime
 from decimal import Decimal
-from typing import TYPE_CHECKING, LiteralString
+from typing import TYPE_CHECKING
 
 from tqdm import tqdm
 
@@ -17,12 +17,12 @@ if TYPE_CHECKING:
 class QueryRuleWrapper:
     def __init__(
         self,
-        query_rule_obj: QueryRule = None,
-        subject_identifiers: list[LiteralString] = None,
-        visit_schedule_obj: QueryVisitSchedule = None,
-        timepoint: Decimal = None,
-        entry_status: str = None,
-        now: datetime = None,
+        query_rule_obj: QueryRule | None = None,
+        subject_identifiers: list[str] | None = None,
+        visit_schedule_obj: QueryVisitSchedule | None = None,
+        timepoint: Decimal | None = None,
+        entry_status: str | None = None,
+        now: datetime | None = None,
         verbose: bool | None = None,
     ):
         self.now = now

edc_data_manager/rule/rule_runner.py

@@ -5,9 +5,10 @@ from datetime import datetime
 from decimal import Decimal
 from typing import TYPE_CHECKING
 
+from django.utils import timezone
+
 from edc_metadata import KEYED, REQUIRED
 from edc_metadata.metadata_inspector import MetaDataInspector
-from edc_utils import get_utcnow
 
 from ..models import QueryVisitSchedule
 from .query_rule_wrapper import QueryRuleWrapper
@@ -24,7 +25,7 @@ class RuleRunner:
         verbose: bool | None = None,
     ):
         self.query_rule_obj = query_rule_obj  # query rule model instance
-        self.now = now or get_utcnow()
+        self.now = now or timezone.now()
         self.verbose = verbose
 
     @property
@@ -39,7 +40,7 @@ class RuleRunner:
         created_counter = 0
         resolved_counter = 0
         query_rules_data = query_rules_data or self.query_rules_data
-        for key, wrapped_query_rules in query_rules_data.items():
+        for _, wrapped_query_rules in query_rules_data.items():
             for wrapped_query_rule in wrapped_query_rules:
                 if self.verbose:
                     sys.stdout.write(f"     - running {wrapped_query_rule}\n")

edc_document_status/model_mixins.py

@@ -17,7 +17,7 @@ class DocumentStatusModelMixin(models.Model):
 
     document_status_comments = models.TextField(
         verbose_name="Any comments related to status of this document",
-        null=True,
+        default="",
         blank=True,
         help_text="for example, why some data is still pending",
     )

edc_egfr/egfr.py

@@ -8,12 +8,13 @@ from zoneinfo import ZoneInfo
 from dateutil.relativedelta import relativedelta
 from django.core.exceptions import ObjectDoesNotExist
 from django.db import transaction
+from django.utils import timezone
 
 from edc_constants.constants import NEW
 from edc_reportable.models import ReferenceRangeCollection
 from edc_reportable.units import EGFR_UNITS, PERCENT
 from edc_reportable.utils import get_grade_for_value
-from edc_utils import age, get_utcnow
+from edc_utils.age import age
 
 from .calculators import EgfrCkdEpi, EgfrCockcroftGault, egfr_percent_change
 from .get_drop_notification_model import get_egfr_drop_notification_model_cls
@@ -27,7 +28,7 @@ class EgfrError(Exception):
 
 
 class Egfr:
-    calculators: dict = {"ckd-epi": EgfrCkdEpi, "cockcroft-gault": EgfrCockcroftGault}
+    calculators: dict = {"ckd-epi": EgfrCkdEpi, "cockcroft-gault": EgfrCockcroftGault}  # noqa: RUF012
 
     def __init__(
         self,
@@ -78,7 +79,7 @@ class Egfr:
                     name=reference_range_collection_name
                 )
             except ObjectDoesNotExist as e:
-                raise ObjectDoesNotExist(f"{e} Got {reference_range_collection_name}")
+                raise ObjectDoesNotExist(f"{e} Got {reference_range_collection_name}") from e
         else:
             self.reference_range_collection = reference_range_collection
         self.report_datetime = report_datetime
@@ -134,9 +135,12 @@ class Egfr:
         """A hook to respond if egfr percent drop from baseline
         is at or beyond the percent drop threshold.
         """
-        if self.egfr_drop_value and self.percent_drop_threshold is not None:
-            if self.egfr_drop_value >= self.percent_drop_threshold:
-                self.create_or_update_egfr_drop_notification()
+        if (
+            self.egfr_drop_value
+            and self.percent_drop_threshold is not None
+            and self.egfr_drop_value >= self.percent_drop_threshold
+        ):
+            self.create_or_update_egfr_drop_notification()
 
     @property
     def egfr_value(self) -> float:
@@ -226,7 +230,7 @@ class Egfr:
                 obj.weight = self.get_weight_in_kgs()
                 obj.egfr_percent_change = self.egfr_drop_value
                 obj.creatinine_date = self.assay_date
-                obj.modified = get_utcnow()
+                obj.modified = timezone.now()
                 obj.save()
         obj.refresh_from_db()
         return obj

edc_egfr/model_mixins/egfr_model_mixin.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import contextlib
 from decimal import Decimal
 
 from django.core.exceptions import ObjectDoesNotExist
@@ -104,13 +105,8 @@ class EgfrModelMixin(
                 appointment__timepoint=self.baseline_timepoint,
                 visit_code_sequence=0,
             )
-        with transaction.atomic():
-            try:
-                egfr_value = self.__class__.objects.get(
-                    subject_visit=baseline_visit
-                ).egfr_value
-            except ObjectDoesNotExist:
-                pass
+        with transaction.atomic(), contextlib.suppress(ObjectDoesNotExist):
+            egfr_value = self.__class__.objects.get(subject_visit=baseline_visit).egfr_value
         return egfr_value
 
     def get_weight_in_kgs_for_egfr(self) -> Decimal | None:

edc_export/admin/data_request_admin.py

@@ -1,4 +1,5 @@
 from django.contrib import admin
+from django.utils import timezone
 from django_audit_fields import ModelAdminAuditFieldsMixin
 from django_revision.modeladmin_mixin import ModelAdminRevisionMixin
 
@@ -11,7 +12,6 @@ from edc_model_admin.mixins import (
     TemplatesModelAdminMixin,
 )
 from edc_sites.admin import SiteModelAdminMixin
-from edc_utils import get_utcnow
 
 from ..admin_site import edc_export_admin
 from ..forms import DataRequestForm
@@ -66,7 +66,7 @@ class DataRequestAdmin(
     def export_selected(self, request, queryset):
         for obj in queryset:
             DataRequestHistory.objects.create(data_request=obj)
-            rows_updated = queryset.update(exported_datetime=get_utcnow())
+            rows_updated = queryset.update(exported_datetime=timezone.now())
             if rows_updated == 1:
                 message_bit = "1 data request was"
             else:

edc_export/archive_exporter.py

@@ -1,11 +1,13 @@
 from __future__ import annotations
 
+from pathlib import Path
 from tempfile import mkdtemp
 from typing import TYPE_CHECKING
 
+from django.utils import timezone
+
 from edc_pdutils.df_exporters import CsvModelExporter
 from edc_sites.site import sites
-from edc_utils import get_utcnow
 
 from .files_archiver import FilesArchiver
 from .files_emailer import FilesEmailer, FilesEmailerError
@@ -16,7 +18,7 @@ if TYPE_CHECKING:
     from django.contrib.auth.models import User
 
 
-class ArchiveExporterNothingExported(Exception):
+class ArchiveExporterNothingExported(Exception):  # noqa: N818
     pass
 
 
@@ -55,7 +57,7 @@ class ArchiveExporter:
         for model in models:
             csv_exporter = self.csv_exporter_cls(
                 model=model,
-                export_folder=tmp_folder,
+                export_folder=Path(tmp_folder),
                 decrypt=decrypt,
                 site_ids=sites.get_site_ids_for_user(
                     user=user, site_id=sites.get_current_site().site_id
@@ -85,8 +87,8 @@ class ArchiveExporter:
                     summary="\n".join(summary),
                 )
             except FilesEmailerError as e:
-                raise ArchiveExporterEmailError(e)
+                raise ArchiveExporterEmailError(e) from e
             else:
                 self.emailed_to = user.email
-                self.emailed_datetime = get_utcnow()
+                self.emailed_datetime = timezone.now()
                 self.exported_datetime = self.exported_datetime or self.emailed_datetime

edc_export/auths.py

@@ -4,34 +4,38 @@ from edc_auth.utils import remove_default_model_permissions_from_edc_permissions
 from .auth_objects import export_codenames
 from .constants import DATA_EXPORTER_ROLE, EXPORT, EXPORT_PII
 
-site_auths.add_post_update_func(
-    "edc_export",
-    remove_default_model_permissions_from_edc_permissions,
-)
 
-site_auths.add_custom_permissions_tuples(
-    model="edc_export.edcpermissions",
-    codename_tuples=[
-        (
-            "edc_export.export_visitschedule",
-            "Can export the visit schedule",
-        ),
-        (
-            "edc_export.view_export_dashboard",
-            "Can view export dashboard",
-        ),
-        (
-            "edc_export.export_subjectschedulehistory",
-            "Can export subject schedule history",
-        ),
-        (
-            "edc_export.export_pii",
-            "Can export PII",
-        ),
-    ],
-)
+def update_site_auths():
+    site_auths.add_post_update_func(
+        "edc_export",
+        remove_default_model_permissions_from_edc_permissions,
+    )
 
+    site_auths.add_custom_permissions_tuples(
+        model="edc_export.edcpermissions",
+        codename_tuples=[
+            (
+                "edc_export.export_visitschedule",
+                "Can export the visit schedule",
+            ),
+            (
+                "edc_export.view_export_dashboard",
+                "Can view export dashboard",
+            ),
+            (
+                "edc_export.export_subjectschedulehistory",
+                "Can export subject schedule history",
+            ),
+            (
+                "edc_export.export_pii",
+                "Can export PII",
+            ),
+        ],
+    )
 
-site_auths.add_group(*export_codenames, name=EXPORT)
-site_auths.add_role(EXPORT, name=DATA_EXPORTER_ROLE)
-site_auths.add_group("edc_export.export_pii", name=EXPORT_PII)
+    site_auths.add_group(*export_codenames, name=EXPORT)
+    site_auths.add_role(EXPORT, name=DATA_EXPORTER_ROLE)
+    site_auths.add_group("edc_export.export_pii", name=EXPORT_PII)
+
+
+update_site_auths()

edc_export/files_archiver.py

@@ -5,8 +5,9 @@ import shutil
 import sys
 from typing import TYPE_CHECKING
 
+from django.utils import timezone
+
 from edc_export.utils import get_base_dir
-from edc_utils import get_utcnow
 
 if TYPE_CHECKING:
     from datetime import datetime
@@ -25,7 +26,7 @@ class FilesArchiver:
         date_format: str = None,
         verbose: bool | None = None,
     ):
-        self.exported_datetime: datetime = exported_datetime or get_utcnow()
+        self.exported_datetime: datetime = exported_datetime or timezone.now()
         formatted_date: str = self.exported_datetime.strftime(date_format)
         base_dir: str = get_base_dir()
         archive_name: str = os.path.join(path, f"{user.username}_{formatted_date}")