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

edc_lab_dashboard/views/action_views/receive_view.py

@@ -1,12 +1,12 @@
 from django.apps import apps as django_apps
 from django.contrib import messages
+from django.utils import timezone
 
 from edc_constants.constants import YES
 from edc_dashboard.view_mixins import EdcViewMixin
 from edc_lab import Specimen
 from edc_lab.labels import AliquotLabel
 from edc_lab.site_labs import site_labs
-from edc_utils import get_utcnow
 
 from ...view_mixins import ProcessRequisitionViewMixin
 from .action_view import ActionView
@@ -38,7 +38,7 @@ class ReceiveView(EdcViewMixin, ProcessRequisitionViewMixin, ActionView):
             updated += (
                 model_cls.objects.filter(pk__in=self.selected_items, is_drawn=YES)
                 .exclude(received=True)
-                .update(received=True, received_datetime=get_utcnow())
+                .update(received=True, received_datetime=timezone.now())
             )
         if updated:
             message = f"{updated} requisitions received."

edc_lab_dashboard/views/action_views/verify_box_item_view.py

@@ -1,8 +1,8 @@
 from django.contrib import messages
+from django.utils import timezone
 
 from edc_dashboard.view_mixins import EdcViewMixin
 from edc_lab import SHIPPED
-from edc_utils import get_utcnow
 
 from ...view_mixins import BoxViewMixin
 from .action_view import ActionView
@@ -48,7 +48,7 @@ class VerifyBoxItemView(EdcViewMixin, BoxViewMixin, ActionView):
                 if self.box_item:
                     if self.box_item == box_item_in_position:
                         box_item_in_position.verified = 1
-                        box_item_in_position.verified_datetime = get_utcnow()
+                        box_item_in_position.verified_datetime = timezone.now()
                         self.next_position()
                         self.redirect_querystring.pop("alert")
                     else:

edc_lab_results/calculate_missing.py

@@ -1,3 +1,4 @@
+import contextlib
 from typing import Any
 
 
@@ -20,11 +21,10 @@ def calculate_missing(obj: Any, panel: Any) -> tuple[int, str | None]:
     missing = []
     for utest_id in panel.utest_ids:
         for field in fields:
-            try:
-                utest_id, _ = utest_id
-            except ValueError:
-                pass
-            if field == utest_id or field == f"{utest_id}_value":
-                if getattr(obj, field) is None:
-                    missing.append(field)
-    return len(missing), ",".join(missing) if missing else None
+            with contextlib.suppress(ValueError):
+                utest_id, _ = utest_id  # noqa: PLW2901
+            if field == utest_id or (
+                field == f"{utest_id}_value" and getattr(obj, field) is None
+            ):
+                missing.append(field)
+    return len(missing), ",".join(missing) if missing else ""

edc_lab_results/form_validator_mixins/blood_results_form_validator_mixin.py

@@ -51,13 +51,13 @@ class BloodResultsFormValidatorMixin(
                     self.required_if_not_none(
                         field=f"{utest_id}{self.value_field_suffix or ''}",
                         field_required=f"{utest_id}_abnormal",
-                        field_required_evaluate_as_int=True,
+                        field_required_evaluate_as_int=False,
                     )
                 if f"{utest_id}_reportable" in self.cleaned_data:
                     self.required_if_not_none(
                         field=f"{utest_id}{self.value_field_suffix or ''}",
                         field_required=f"{utest_id}_reportable",
-                        field_required_evaluate_as_int=True,
+                        field_required_evaluate_as_int=False,
                     )
                 self.evaluate_value(prefix=utest_id)
             self.validate_reportable_fields(

edc_lab_results/get_summary.py

@@ -18,36 +18,37 @@ def get_summary(obj) -> tuple[list[str], list[str], list[str]]:
         except ValueError:
             utest_id = field_name
         reference_range_collection = get_reference_range_collection(obj)
-        if units := getattr(obj, f"{utest_id}_units", None):
-            if value := getattr(obj, field_name):
-                opts.update(units=units, label=utest_id)
+        if (units := getattr(obj, f"{utest_id}_units", None)) and (
+            value := getattr(obj, field_name)
+        ):
+            opts.update(units=units, label=utest_id)
+            try:
+                grading_data, grading_eval_phrase = reference_range_collection.get_grade(
+                    value, **opts
+                )
+            except NotEvaluated as e:
+                errors.append(f"{e}.")
+                grading_data = None
+                grading_eval_phrase = None
+            if (
+                grading_data
+                and grading_data.grade
+                in reference_range_collection.reportable_grades(utest_id)
+            ):
+                setattr(obj, f"{utest_id}_grade", grading_data.grade)
+                setattr(obj, f"{utest_id}_grade_description", grading_data.description)
+                reportable.append(f"{grading_eval_phrase}")
+            else:
                 try:
-                    grading_data, grading_eval_phrase = reference_range_collection.get_grade(
+                    is_normal, normal_data = reference_range_collection.is_normal(
                         value, **opts
                     )
                 except NotEvaluated as e:
                     errors.append(f"{e}.")
-                    grading_data = None
-                    grading_eval_phrase = None
-                if (
-                    grading_data
-                    and grading_data.grade
-                    in reference_range_collection.reportable_grades(utest_id)
-                ):
-                    setattr(obj, f"{utest_id}_grade", grading_data.grade)
-                    setattr(obj, f"{utest_id}_grade_description", grading_data.description)
-                    reportable.append(f"{grading_eval_phrase}")
                 else:
-                    try:
-                        is_normal, normal_data = reference_range_collection.is_normal(
-                            value, **opts
+                    if is_normal is False:
+                        abnormal.append(
+                            f"{normal_data.label}: {value} {units} "
+                            f"{normal_data.phrase} Abnormal"
                         )
-                    except NotEvaluated as e:
-                        errors.append(f"{e}.")
-                    else:
-                        if is_normal is False:
-                            abnormal.append(
-                                f"{normal_data.label}: {value} {units} "
-                                f"{normal_data.phrase} Abnormal"
-                            )
     return reportable, abnormal, errors

edc_lab_results/model_mixins/blood_result_model_mixin.py

@@ -16,12 +16,12 @@ class BloodResultsFieldsModelMixin(models.Model):
         choices=YES_NO,
         max_length=25,
         help_text=(
-            "Abnormal results present at baseline or continuing from " "baseline not included."
+            "Abnormal results present at baseline or continuing from baseline not included."
         ),
     )
 
     results_reportable = models.CharField(
-        verbose_name=("If any results are abnormal, are results within grade 3 or above?"),
+        verbose_name="If any results are abnormal, are results within grade 3 or above?",
         max_length=25,
         choices=YES_NO_NA,
         help_text=(
@@ -30,13 +30,13 @@ class BloodResultsFieldsModelMixin(models.Model):
         ),
     )
 
-    summary = models.TextField(null=True, blank=True)
+    summary = models.TextField(default="", blank=True)
 
-    reportable_summary = models.TextField(null=True, blank=True)
+    reportable_summary = models.TextField(default="", blank=True)
 
-    abnormal_summary = models.TextField(null=True, blank=True)
+    abnormal_summary = models.TextField(default="", blank=True)
 
-    errors = models.TextField(null=True, blank=True)
+    errors = models.TextField(default="", blank=True)
 
     missing_count = models.IntegerField(
         default=0,
@@ -45,7 +45,7 @@ class BloodResultsFieldsModelMixin(models.Model):
     )
 
     missing = models.TextField(
-        null=True,
+        default="",
         editable=False,
         help_text="calculated string of field names that have been left blank",
     )
@@ -70,6 +70,8 @@ class BloodResultsMethodsModelMixin(models.Model):
         return get_summary(self)
 
     def get_summary_options(self: Any) -> dict:
+        # note: gender and dob are queried from RegisteredSubject
+        # in reportables
         return dict(
             subject_identifier=self.subject_visit.subject_identifier,
             report_datetime=self.report_datetime,

edc_lab_results/model_mixins/fbg_model_mixin.py

@@ -37,13 +37,13 @@ class FbgModelMixin(
         verbose_name="Was a point-of-care test used?",
         max_length=15,
         choices=YES_NO,
-        null=True,
+        default="",
     )
     fasting = models.CharField(
         verbose_name="Was this fasting or non-fasting?",
         max_length=25,
         choices=FASTING_CHOICES,
-        null=True,
+        default="",
         blank=False,
     )
 
@@ -55,7 +55,7 @@ class FbgModelMixin(
 
     def get_summary_options(self) -> dict:
         opts = super().get_summary_options()
-        fasting = True if self.fasting == FASTING else False
+        fasting = self.fasting == FASTING
         opts.update(fasting=fasting)
         return opts
 

edc_lab_results/model_mixins/glucose_model_mixin.py

@@ -34,13 +34,13 @@ class GlucoseModelMixin(
         verbose_name="Was a point-of-care test used?",
         max_length=15,
         choices=YES_NO,
-        null=True,
+        default="",
     )
     fasting = models.CharField(
         verbose_name="Was this fasting or non-fasting?",
         max_length=25,
         choices=FASTING_CHOICES,
-        null=True,
+        default="",
         blank=False,
     )
 
@@ -52,7 +52,7 @@ class GlucoseModelMixin(
 
     def get_summary_options(self: Any) -> dict:
         opts = super().get_summary_options()
-        fasting = True if self.fasting == FASTING else False
+        fasting = self.fasting == FASTING
         opts.update(fasting=fasting)
         return opts
 

edc_lab_results/model_mixins/hba1c_model_mixin.py

@@ -10,18 +10,18 @@ class Hba1cModelMixin(BaseHba1cModelMixin, models.Model):
         verbose_name="Was a point-of-care test used?",
         max_length=15,
         choices=YES_NO,
-        null=True,
+        default="",
     )
 
     hba1c_abnormal = models.CharField(
-        verbose_name="abnormal", choices=YES_NO, max_length=25, null=True, blank=True
+        verbose_name="abnormal", choices=YES_NO, max_length=25, default="", blank=True
     )
 
     hba1c_reportable = models.CharField(
         verbose_name="reportable",
         choices=REPORTABLE,
         max_length=25,
-        null=True,
+        default="",
         blank=True,
     )
 

edc_label/auths.py

@@ -2,4 +2,9 @@ from edc_auth.site_auths import site_auths
 
 from .auth_objects import LABELING, codenames
 
-site_auths.add_group(*codenames, name=LABELING, no_delete=False)
+
+def update_site_auths():
+    site_auths.add_group(*codenames, name=LABELING, no_delete=False)
+
+
+update_site_auths()

edc_label/label_template.py

@@ -1,4 +1,4 @@
-import os
+from pathlib import Path
 from string import Template
 
 from django.apps import apps as django_apps
@@ -19,27 +19,27 @@ class LabelTemplate:
             zpl_label_template = django_apps.get_model(
                 "edc_label.zpllabeltemplates"
             ).objects.get(name=self.template_name)
-        except ObjectDoesNotExist:
+        except ObjectDoesNotExist as e:
             if static_files_path:
-                path = finders.find(os.path.join(static_files_path, template_name))
+                path = finders.find(str(Path(static_files_path) / template_name))
             else:
                 app_config = django_apps.get_app_config("edc_label")
                 try:
                     path = app_config.label_templates[template_name]
-                except KeyError:
+                except KeyError as e:
                     raise LabelTemplateError(
                         f"Invalid label template name. "
                         f"Expected one of {list(app_config.label_templates.keys())}. "
                         f"Got '{template_name}'. "
                         f"See edc_label.app_config."
-                    )
-            if not os.path.exists(path or ""):
+                    ) from e
+            if not path or not Path(path).exists():
                 raise LabelTemplateError(
                     f"Invalid label template path. "
                     f"Looking for  template '{template_name}'. "
                     f"Got {path}. See edc_label.app_config."
-                )
-            with open(path) as f:
+                ) from e
+            with Path(path).open("r") as f:
                 self.template = f.read()
         else:
             self.template = zpl_label_template.zpl_data.strip()

edc_label/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_label/migrations/0007_alter_zpllabeltemplates_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_label", "0006_alter_zpllabeltemplates_revision"),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="zpllabeltemplates",
+            name="device_created",
+            field=models.CharField(
+                blank=True, default="", max_length=10, verbose_name="Device created"
+            ),
+        ),
+        migrations.AlterField(
+            model_name="zpllabeltemplates",
+            name="device_modified",
+            field=models.CharField(
+                blank=True, default="", max_length=10, verbose_name="Device modified"
+            ),
+        ),
+        migrations.AlterField(
+            model_name="zpllabeltemplates",
+            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="zpllabeltemplates",
+            name="locale_modified",
+            field=models.CharField(
+                blank=True,
+                default="",
+                help_text="Auto-updated by Modeladmin",
+                max_length=10,
+                verbose_name="Locale modified",
+            ),
+        ),
+    ]

edc_list_data/list_model_maker.py

@@ -33,7 +33,7 @@ class ListModelMaker:
         try:
             self.name, self.display_name = row
         except ValueError as e:
-            raise ListModelMakerError(e)
+            raise ListModelMakerError(e) from e
         except TypeError as e:
             if "Row" not in str(e):
                 raise
@@ -46,7 +46,7 @@ class ListModelMaker:
         opts = dict(
             display_index=self.display_index,
             display_name=self.display_name,
-            extra_value=self.extra_value,
+            extra_value=self.extra_value or "",
         )
         if "custom_name" in [f.name for f in self.model_cls._meta.get_fields()]:
             opts.update(custom_name=self.custom_name)

edc_list_data/load_list_data.py

@@ -1,5 +1,7 @@
 from __future__ import annotations
 
+import contextlib
+
 from django.apps import AppConfig
 
 from .list_model_maker import ListModelMaker, ListModelMakerError
@@ -10,7 +12,7 @@ class LoadListDataError(Exception):
 
 
 def load_list_data(
-    list_data: dict = None, model_name: str | None = None, apps: AppConfig | None = None
+    list_data: dict | None = None, model_name: str | None = None, apps: AppConfig | None = None
 ) -> int:
     """Loads data into a list model.
 
@@ -24,25 +26,20 @@ def load_list_data(
          (name2, display_name),...],
         ...}
     """
-    if model_name:
-        model_names = [model_name]
-    else:
-        model_names = [k for k in list_data]
+    model_names = [model_name] if model_name else [k for k in list_data]
     n = 0
-    for model_name in model_names:
+    for _model_name in model_names:
         try:
-            data = list_data.get(model_name)()
+            data = list_data.get(_model_name)()
         except TypeError:
-            data = list_data.get(model_name)
+            data = list_data.get(_model_name)
         try:
             for display_index, row in enumerate(data):
-                try:
-                    row = row()
-                except TypeError:
-                    pass
-                maker = ListModelMaker(display_index, row, model_name, apps=apps)
+                with contextlib.suppress(TypeError):
+                    row = row()  # noqa: PLW2901
+                maker = ListModelMaker(display_index, row, _model_name, apps=apps)
                 maker.create_or_update()
         except ListModelMakerError as e:
-            raise LoadListDataError(f"{e} See {list_data.get(model_name)}.")
+            raise LoadListDataError(f"{e} See {list_data.get(_model_name)}.") from e
         n += 1
     return n

edc_list_data/load_model_data.py

@@ -1,3 +1,5 @@
+import contextlib
+
 from django.apps import AppConfig
 from django.apps import apps as django_apps
 from django.core.exceptions import ObjectDoesNotExist
@@ -34,10 +36,8 @@ def load_model_data(model_data: dict, apps: AppConfig | None = None) -> int:
             try:
                 obj = model.objects.get(**{unique_field: opts.get(unique_field)})
             except ObjectDoesNotExist:
-                try:
+                with contextlib.suppress(IntegrityError):
                     model.objects.create(**opts)
-                except IntegrityError:
-                    pass
             else:
                 for key, value in opts.items():
                     setattr(obj, key, value)

edc_list_data/model_mixins.py

@@ -18,7 +18,11 @@ class BaseListModelMixin(models.Model):
         help_text="This is the stored value, required",
     )
 
-    plural_name = models.CharField(verbose_name="Plural name", max_length=250, null=True)
+    plural_name = models.CharField(
+        verbose_name="Plural name",
+        max_length=250,
+        default="",
+    )
 
     display_name = models.CharField(
         verbose_name="Name",
@@ -34,10 +38,14 @@ class BaseListModelMixin(models.Model):
     )
 
     field_name = models.CharField(
-        max_length=25, editable=False, null=True, blank=True, help_text="Not required"
+        max_length=25,
+        editable=False,
+        default="",
+        blank=True,
+        help_text="Not required",
     )
 
-    extra_value = models.CharField(max_length=250, null=True)
+    extra_value = models.CharField(max_length=250, default="")
 
     version = models.CharField(max_length=35, editable=False, default="1.0")
 
@@ -85,7 +93,7 @@ class ListModelMixin2(BaseListModelMixin):
 
     custom_name = models.CharField(
         max_length=25,
-        null=True,
+        default="",
         blank=True,
         help_text="A custom name/value to use on export instead of or in addition to `name`",
     )

edc_list_data/post_migrate_signals.py

@@ -6,7 +6,7 @@ style = color_style()
 
 
 def post_migrate_list_data(sender=None, **kwargs):
-    from .site_list_data import get_autodiscover_enabled, site_list_data
+    from .site_list_data import get_autodiscover_enabled, site_list_data  # noqa: PLC0415
 
     if get_autodiscover_enabled():
         sys.stdout.write(style.MIGRATE_HEADING("Updating list data:\n"))

edc_list_data/preload_data.py

@@ -11,9 +11,9 @@ style = color_style()
 class PreloadData:
     def __init__(
         self,
-        list_data: dict[str, list[tuple[str | int, str]]] = None,
-        model_data: dict = None,
-        list_data_model_name: str = None,
+        list_data: dict[str, list[tuple[str | int, str]]],
+        model_data: dict | None = None,
+        list_data_model_name: str | None = None,
         apps: AppConfig = None,
     ) -> None:
         self.list_data = list_data
@@ -24,7 +24,7 @@ class PreloadData:
         if self.model_data:
             self.item_count += self.load_model_data()
 
-    def load_list_data(self, model_name: str = None, apps: AppConfig | None = None) -> int:
+    def load_list_data(self, model_name: str, apps: AppConfig | None = None) -> int:
         return load_list_data(self.list_data, model_name=model_name, apps=apps)
 
     def load_model_data(self, apps: AppConfig | None = None) -> int:

edc_list_data/row.py

@@ -24,7 +24,7 @@ class Row:
 @dataclass
 class AsListData:
     data: tuple[tuple[str, str, str], ...] | Choices
-    rows: list[Row, ...] | None = field(default_factory=list, init=False)
+    rows: list[Row] | None = field(default_factory=list, init=False)
 
     def __post_init__(self):
         for tpl in self.data:

edc_list_data/site_list_data.py

@@ -1,3 +1,4 @@
+import contextlib
 import copy
 import sys
 from importlib import import_module
@@ -51,7 +52,7 @@ class SiteListData:
         if app_name and app_name in self.app_names:
             raise AlreadyLoaded(f"App already loaded. Got {app_name}.")
         self.app_names.append(app_name)
-        opts = copy.deepcopy(self._get_options(module))
+        opts = {k: v for k, v in self._get_options(module).items()}
         sys.stdout.write(f"   - registered {self.module_name} from '{module.__name__}'\n")
         if opts.get(self.module_name):
             self._replace_list_data_or_raise_on_duplicate(module, opts)
@@ -60,6 +61,8 @@ class SiteListData:
     def load_data(self) -> None:
         """Calls `load` class with each list_data dictionary module to
         update database `list` tables.
+
+        See post_migrate_list_data.
         """
         style = color_style()
         for module_name, opts in self.registry.items():
@@ -142,10 +145,8 @@ class SiteListData:
         ):
             sys.stdout.write(f" * checking sites for `{self.module_name}` ...\n")
             for app_name in django_apps.app_configs:
-                try:
+                with contextlib.suppress(ModuleNotFoundError):
                     self._import_and_register(app_name)
-                except ModuleNotFoundError:
-                    pass
 
     def _import_and_register(self, app_name: str) -> None:
         mod = import_module(app_name)
@@ -155,7 +156,7 @@ class SiteListData:
         except ImportError as e:
             site_list_data.registry = before_import_registry
             if module_has_submodule(mod, self.module_name):
-                raise SiteListDataError(f"{e} See {app_name}.{self.module_name}")
+                raise SiteListDataError(f"{e} See {app_name}.{self.module_name}") from e
         else:
             self.register(module, app_name=app_name)
 

edc_listboard/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,
                     ),
                 ),
                 (