clinicedc 2.0.7__py3-none-any.whl → 2.0.9__py3-none-any.whl

edc_form_validators/required_field_validator.py

@@ -43,8 +43,8 @@ class RequiredFieldValidator(BaseFormValidator):
     def required_if(
         self,
         *responses: str | int | bool,
-        field: str = None,
-        field_required: str = None,
+        field: str,
+        field_required: str,
         required_msg: str | None = None,
         not_required_msg: str | None = None,
         optional_if_dwta: bool | None = None,
@@ -82,7 +82,7 @@ class RequiredFieldValidator(BaseFormValidator):
                 self.get(field_required, inline_set=inline_set) is not None
             )
         else:
-            field_required_has_value = self.get(field_required, inline_set=inline_set)
+            field_required_has_value = bool(self.get(field_required, inline_set=inline_set))
 
         if field in self.cleaned_data:
             if (DWTA in responses and optional_if_dwta and field_value == DWTA) or (
@@ -117,7 +117,7 @@ class RequiredFieldValidator(BaseFormValidator):
     def required_if_true(
         self,
         condition: bool,
-        field_required: str = None,
+        field_required: str,
         required_msg: str | None = None,
         not_required_msg: str | None = None,
         inverse: bool | None = None,
@@ -145,7 +145,7 @@ class RequiredFieldValidator(BaseFormValidator):
     def not_required_if_true(
         self,
         condition: bool,
-        field: str = None,
+        field: str,
         msg: str | None = None,
         is_instance_field: bool | None = None,
     ) -> bool:
@@ -170,8 +170,8 @@ class RequiredFieldValidator(BaseFormValidator):
 
     def required_if_not_none(
         self,
-        field: str = None,
-        field_required: str = None,
+        field: str,
+        field_required: str,
         required_msg: str | None = None,
         not_required_msg: str | None = None,
         optional_if_dwta: bool | None = None,
@@ -182,6 +182,9 @@ class RequiredFieldValidator(BaseFormValidator):
         """Raises an exception or returns False.
 
         If field is not none, field_required is "required".
+
+        Note: CharFields usually default to an empty string and not NULL.
+           For IntegerFields, zero is a value.
         """
         inverse = True if inverse is None else inverse
         if is_instance_field:
@@ -197,7 +200,7 @@ class RequiredFieldValidator(BaseFormValidator):
         if field_required_evaluate_as_int:
             field_required_has_value = self.cleaned_data.get(field_required) is not None
         else:
-            field_required_has_value = self.cleaned_data.get(field_required)
+            field_required_has_value = bool(self.cleaned_data.get(field_required))
 
         if field_value is not None and not field_required_has_value:
             self.raise_required(field=field_required, msg=required_msg)
@@ -221,8 +224,8 @@ class RequiredFieldValidator(BaseFormValidator):
     def not_required_if(
         self,
         *responses: str | int | bool,
-        field: str = None,
-        field_required: str = None,
+        field: str,
+        field_required: str | None = None,
         field_not_required: str | None = None,
         required_msg: str | None = None,
         not_required_msg: str | None = None,
@@ -259,8 +262,8 @@ class RequiredFieldValidator(BaseFormValidator):
 
     def require_together(
         self,
-        field: str = None,
-        field_required: str = None,
+        field: str,
+        field_required: str,
         required_msg: str | None = None,
         is_instance_field: bool | None = None,
     ) -> bool:
@@ -280,15 +283,15 @@ class RequiredFieldValidator(BaseFormValidator):
         return False
 
     @staticmethod
-    def _inspect_params(
-        *responses: str | int | bool, field: str = None, field_required: str = None
-    ) -> bool:
+    def _inspect_params(*responses: str | int | bool, field: str, field_required: str) -> bool:
         """Inspects params and raises if any are None"""
         if not field:
             errmsg = _("`field` cannot be `None`")
             raise InvalidModelFormFieldValidator(f"{errmsg}.")
         if not responses:
-            errmsg = _(f"At least one valid response for field '{field}' must be provided.")
+            errmsg = _(
+                "At least one valid response for field '{field}' must be provided."
+            ).format(field=field)
             raise InvalidModelFormFieldValidator(errmsg)
         if not field_required:
             raise InvalidModelFormFieldValidator('"field_required" cannot be None.')

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

@@ -1,5 +1,7 @@
+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
@@ -8,6 +10,9 @@ from django.utils import timezone
 
 from .utils import convert_to_human_readable
 
+if TYPE_CHECKING:
+    from edc_identifier.models import IdentifierModel
+
 
 class DuplicateIdentifierError(Exception):
     pass
@@ -195,7 +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.
         """
@@ -210,5 +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_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

edc_lab/migrations/0038_alter_aliquot_slug_alter_box_slug_alter_boxitem_slug_and_more.py

@@ -0,0 +1,112 @@
+# Generated by Django 5.2.6 on 2025-09-22 12:31
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("edc_lab", "0037_alter_historicalorder_order_datetime_and_more"),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="aliquot",
+            name="slug",
+            field=models.CharField(
+                db_index=True,
+                default="",
+                editable=False,
+                help_text="Hold slug field values for quick search. Excludes encrypted fields",
+                max_length=250,
+            ),
+        ),
+        migrations.AlterField(
+            model_name="box",
+            name="slug",
+            field=models.CharField(
+                db_index=True,
+                default="",
+                editable=False,
+                help_text="Hold slug field values for quick search. Excludes encrypted fields",
+                max_length=250,
+            ),
+        ),
+        migrations.AlterField(
+            model_name="boxitem",
+            name="slug",
+            field=models.CharField(
+                db_index=True,
+                default="",
+                editable=False,
+                help_text="Hold slug field values for quick search. Excludes encrypted fields",
+                max_length=250,
+            ),
+        ),
+        migrations.AlterField(
+            model_name="historicalaliquot",
+            name="slug",
+            field=models.CharField(
+                db_index=True,
+                default="",
+                editable=False,
+                help_text="Hold slug field values for quick search. Excludes encrypted fields",
+                max_length=250,
+            ),
+        ),
+        migrations.AlterField(
+            model_name="historicalbox",
+            name="slug",
+            field=models.CharField(
+                db_index=True,
+                default="",
+                editable=False,
+                help_text="Hold slug field values for quick search. Excludes encrypted fields",
+                max_length=250,
+            ),
+        ),
+        migrations.AlterField(
+            model_name="historicalboxitem",
+            name="slug",
+            field=models.CharField(
+                db_index=True,
+                default="",
+                editable=False,
+                help_text="Hold slug field values for quick search. Excludes encrypted fields",
+                max_length=250,
+            ),
+        ),
+        migrations.AlterField(
+            model_name="historicalmanifest",
+            name="slug",
+            field=models.CharField(
+                db_index=True,
+                default="",
+                editable=False,
+                help_text="Hold slug field values for quick search. Excludes encrypted fields",
+                max_length=250,
+            ),
+        ),
+        migrations.AlterField(
+            model_name="manifest",
+            name="slug",
+            field=models.CharField(
+                db_index=True,
+                default="",
+                editable=False,
+                help_text="Hold slug field values for quick search. Excludes encrypted fields",
+                max_length=250,
+            ),
+        ),
+        migrations.AlterField(
+            model_name="manifestitem",
+            name="slug",
+            field=models.CharField(
+                db_index=True,
+                default="",
+                editable=False,
+                help_text="Hold slug field values for quick search. Excludes encrypted fields",
+                max_length=250,
+            ),
+        ),
+    ]

edc_lab/model_mixins/requisition/requisition_model_mixin.py

@@ -136,15 +136,13 @@ class RequisitionModelMixin(
 
     def get_search_slug_fields(self):
         fields = super().get_search_slug_fields()
-        fields.extend(
-            [
-                "subject_identifier",
-                "requisition_identifier",
-                "human_readable_identifier",
-                "identifier_prefix",
-            ]
+        return (
+            *fields,
+            "subject_identifier",
+            "requisition_identifier",
+            "human_readable_identifier",
+            "identifier_prefix",
         )
-        return fields
 
     class Meta(NonUniqueSubjectIdentifierFieldMixin.Meta):
         abstract = True

edc_lab/models/aliquot.py

@@ -24,13 +24,13 @@ class Aliquot(
     BaseUuidModel,
 ):
     def get_search_slug_fields(self):
-        return [
+        return (
             "aliquot_identifier",
             "human_readable_identifier",
             "subject_identifier",
             "parent_identifier",
             "requisition_identifier",
-        ]
+        )
 
     objects = Manager()
 

edc_lab/models/manifest/manifest.py

@@ -21,12 +21,12 @@ class Manifest(ManifestModelMixin, PdfReportModelMixin, SearchSlugModelMixin, Ba
     pdf_report_cls = ManifestPdfReport
 
     def get_search_slug_fields(self):
-        return [
+        return (
             "manifest_identifier",
             "human_readable_identifier",
             "shipper.name",
             "consignee.name",
-        ]
+        )
 
     consignee = models.ForeignKey(Consignee, verbose_name="Consignee", on_delete=PROTECT)
 

edc_lab/models/manifest/manifest_item.py

@@ -17,7 +17,7 @@ class ManifestItemManager(SearchSlugManager, models.Manager):
 
 class ManifestItem(SiteModelMixin, SearchSlugModelMixin, VerifyModelMixin, BaseUuidModel):
     def get_search_slug_fields(self):
-        return ["identifier", "human_readable_identifier"]
+        return "identifier", "human_readable_identifier"
 
     manifest = models.ForeignKey(Manifest, on_delete=PROTECT)
 

edc_lab_dashboard/auths.py

@@ -8,16 +8,21 @@ from edc_lab_dashboard.auth_objects import (
     lab_navbar_tuples,
 )
 
-site_auths.add_post_update_func(
-    "edc_lab_dashboard", remove_default_model_permissions_from_edc_permissions
-)
 
-site_auths.add_custom_permissions_tuples(
-    model="edc_lab_dashboard.edcpermissions", codename_tuples=lab_navbar_tuples
-)
-site_auths.add_custom_permissions_tuples(
-    model="edc_lab_dashboard.edcpermissions", codename_tuples=lab_dashboard_tuples
-)
+def update_site_auths():
+    site_auths.add_post_update_func(
+        "edc_lab_dashboard", remove_default_model_permissions_from_edc_permissions
+    )
+
+    site_auths.add_custom_permissions_tuples(
+        model="edc_lab_dashboard.edcpermissions", codename_tuples=lab_navbar_tuples
+    )
+    site_auths.add_custom_permissions_tuples(
+        model="edc_lab_dashboard.edcpermissions", codename_tuples=lab_dashboard_tuples
+    )
+
+    site_auths.update_group(*lab_dashboard_codenames, *lab_navbar_codenames, name=LAB)
+    site_auths.update_group(*lab_dashboard_codenames, *lab_navbar_codenames, name=LAB_VIEW)
+
 
-site_auths.update_group(*lab_dashboard_codenames, *lab_navbar_codenames, name=LAB)
-site_auths.update_group(*lab_dashboard_codenames, *lab_navbar_codenames, name=LAB_VIEW)
+update_site_auths()

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

@@ -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_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()