clinicedc 2.0.7__py3-none-any.whl → 2.0.8__py3-none-any.whl

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()

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_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/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

@@ -11,7 +11,7 @@ style = color_style()
 class PreloadData:
     def __init__(
         self,
-        list_data: dict[str, list[tuple[str | int, str]]] | None = 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,
@@ -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_locator/auths.py

@@ -1,17 +1,22 @@
 from edc_auth.constants import PII, PII_VIEW
 from edc_auth.site_auths import site_auths
 
-site_auths.update_group(
-    "edc_locator.add_subjectlocator",
-    "edc_locator.change_subjectlocator",
-    "edc_locator.view_historicalsubjectlocator",
-    "edc_locator.view_subjectlocator",
-    name=PII,
-)
 
-site_auths.update_group(
-    "edc_locator.view_historicalsubjectlocator",
-    "edc_locator.view_subjectlocator",
-    name=PII_VIEW,
-)
-site_auths.add_pii_model("edc_locator.subjectlocator")
+def update_site_auths():
+    site_auths.update_group(
+        "edc_locator.add_subjectlocator",
+        "edc_locator.change_subjectlocator",
+        "edc_locator.view_historicalsubjectlocator",
+        "edc_locator.view_subjectlocator",
+        name=PII,
+    )
+
+    site_auths.update_group(
+        "edc_locator.view_historicalsubjectlocator",
+        "edc_locator.view_subjectlocator",
+        name=PII_VIEW,
+    )
+    site_auths.add_pii_model("edc_locator.subjectlocator")
+
+
+update_site_auths()

edc_metadata/auths.py

@@ -1,12 +1,16 @@
 from django.apps import apps as django_apps
 
 from edc_auth.site_auths import site_auths
+from edc_export.constants import EXPORT
 
-if django_apps.is_installed("edc_export"):
-    from edc_export.constants import EXPORT
 
-    site_auths.update_group(
-        "edc_metadata.export_crfmetadata",
-        "edc_metadata.export_requisitionmetadata",
-        name=EXPORT,
-    )
+def update_site_auths():
+    if django_apps.is_installed("edc_export"):
+        site_auths.update_group(
+            "edc_metadata.export_crfmetadata",
+            "edc_metadata.export_requisitionmetadata",
+            name=EXPORT,
+        )
+
+
+update_site_auths()

edc_metadata/metadata/metadata.py

@@ -110,7 +110,7 @@ class CrfCreator(SourceModelMetadataMixin):
                             metadata_obj = self.metadata_model_cls.objects.create(**opts)
                         except IntegrityError as e:
                             msg = f"Integrity error creating. Tried with {opts}. Got {e}."
-                            raise CreatesMetadataError(msg)
+                            raise CreatesMetadataError(msg) from e
             else:
                 if not registered:
                     metadata_obj.delete()

edc_metadata/metadata_rules/crf/crf_rule.py

@@ -14,7 +14,7 @@ if TYPE_CHECKING:
         pass
 
 
-class CrfRuleModelConflict(Exception):
+class CrfRuleModelConflict(Exception):  # noqa: N818
     pass
 
 

edc_metadata/metadata_rules/metadata_rule_evaluator.py

@@ -29,9 +29,11 @@ class MetadataRuleEvaluator:
         if not self.app_labels:
             for rule_groups in site_metadata_rules.registry.values():
                 for rule_group in rule_groups:
-                    if rule_group._meta.related_visit_model == self.related_visit_model:
-                        if rule_group._meta.app_label not in self.app_labels:
-                            self.app_labels.append(rule_group._meta.app_label)
+                    if (
+                        rule_group._meta.related_visit_model == self.related_visit_model
+                        and rule_group._meta.app_label not in self.app_labels
+                    ):
+                        self.app_labels.append(rule_group._meta.app_label)
 
     def evaluate_rules(self) -> None:
         for app_label in self.app_labels:

edc_metadata/metadata_rules/rule.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import contextlib
 from typing import TYPE_CHECKING
 
 from edc_appointment.constants import MISSED_APPT
@@ -91,8 +92,6 @@ class Rule:
         try:
             field_names = [self.predicate.attr]
         except AttributeError:
-            try:
+            with contextlib.suppress(AttributeError):
                 field_names = self.predicate.attrs
-            except AttributeError:
-                pass
         return field_names

edc_metadata/metadata_rules/rule_evaluator.py

@@ -77,5 +77,5 @@ class RuleEvaluator:
                     f"Registered subject required for rule {self!r}. "
                     f"subject_identifier='{self.related_visit.subject_identifier}'. "
                     f"Got {e}."
-                )
+                ) from e
         return self._registered_subject

edc_metadata/model_mixins/updates/updates_crf_metadata_model_mixin.py

@@ -50,16 +50,19 @@ class UpdatesCrfMetadataModelMixin(UpdatesMetadataModelMixin):
         return django_apps.get_model(metadata_model)
 
     @property
-    def metadata_default_entry_status(self: CrfModel) -> str:
+    def metadata_default_entry_status(self: CrfModel) -> str | None:
         """Returns a string that represents the default entry status
         of the CRF in the visit schedule.
         """
         crfs_prn = self.metadata_visit_object.crfs_prn
         if self.related_visit.visit_code_sequence != 0:
-            crfs = self.metadata_visit_object.crfs_unscheduled.forms + crfs_prn.forms
+            crfs = (*self.metadata_visit_object.crfs_unscheduled.forms, *crfs_prn.forms)
         else:
-            crfs = self.metadata_visit_object.crfs.forms + crfs_prn.forms
-        crf = next(c for c in crfs if c.model == self._meta.label_lower)
+            crfs = (*self.metadata_visit_object.crfs.forms, *crfs_prn.forms)
+        try:
+            crf = next(c for c in crfs if c.model == self._meta.label_lower)
+        except StopIteration:
+            return None
         return REQUIRED if crf.required else NOT_REQUIRED
 
     class Meta:

edc_metadata/model_mixins/updates/updates_requisition_metadata_model_mixin.py

@@ -50,7 +50,7 @@ class UpdatesRequisitionMetadataModelMixin(UpdatesMetadataModelMixin):
         return options
 
     @property
-    def metadata_default_entry_status(self: RequisitionModel) -> str:
+    def metadata_default_entry_status(self: RequisitionModel) -> str | None:
         """Returns a string that represents the configured
         entry status of the requisition in the visit schedule.
         """
@@ -64,7 +64,10 @@ class UpdatesRequisitionMetadataModelMixin(UpdatesMetadataModelMixin):
             requisitions = (
                 self.metadata_visit_object.requisitions.forms + requisitions_prn.forms
             )
-        requisition = next(r for r in requisitions if r.panel.name == self.panel.name)
+        try:
+            requisition = next(r for r in requisitions if r.panel.name == self.panel.name)
+        except StopIteration:
+            return None
         return REQUIRED if requisition.required else NOT_REQUIRED
 
     @property

edc_metadata/models/signals.py

@@ -94,14 +94,13 @@ def metadata_reset_on_post_delete(sender, instance, using, **kwargs) -> None:
 def metadata_update_previous_timepoints_for_singleton_on_post_save(
     sender, instance, raw, created, using, **kwargs
 ):
-    if not raw and not kwargs.get("update_fields"):
-        if isinstance(instance, (SingletonCrfModelMixin,)):
-            appointment = (
-                instance.related_visit.appointment.relative_previous_with_related_visit
-            )
-            while appointment:
-                if appointment.related_visit:
-                    refresh_metadata_for_timepoint(
-                        appointment.related_visit, allow_create=False
-                    )
-                appointment = appointment.relative_previous_with_related_visit
+    if (
+        not raw
+        and not kwargs.get("update_fields")
+        and isinstance(instance, (SingletonCrfModelMixin,))
+    ):
+        appointment = instance.related_visit.appointment.relative_previous_with_related_visit
+        while appointment:
+            if appointment.related_visit:
+                refresh_metadata_for_timepoint(appointment.related_visit, allow_create=False)
+            appointment = appointment.relative_previous_with_related_visit

edc_navbar/auths.py

@@ -4,17 +4,22 @@ from edc_auth.utils import remove_default_model_permissions_from_edc_permissions
 
 from .auth_objects import custom_codename_tuples
 
-site_auths.add_post_update_func(
-    "edc_navbar", remove_default_model_permissions_from_edc_permissions
-)
-site_auths.add_custom_permissions_tuples(
-    model="edc_navbar.edcpermissions", codename_tuples=custom_codename_tuples
-)
 
-site_auths.update_group(
-    "edc_navbar.nav_administration",
-    "edc_navbar.nav_home",
-    "edc_navbar.nav_logout",
-    "edc_navbar.nav_public",
-    name=EVERYONE,
-)
+def update_site_auths():
+    site_auths.add_post_update_func(
+        "edc_navbar", remove_default_model_permissions_from_edc_permissions
+    )
+    site_auths.add_custom_permissions_tuples(
+        model="edc_navbar.edcpermissions", codename_tuples=custom_codename_tuples
+    )
+
+    site_auths.update_group(
+        "edc_navbar.nav_administration",
+        "edc_navbar.nav_home",
+        "edc_navbar.nav_logout",
+        "edc_navbar.nav_public",
+        name=EVERYONE,
+    )
+
+
+update_site_auths()

edc_notification/auths.py

@@ -6,7 +6,12 @@ from edc_export.constants import EXPORT
 
 from .auth_objects import NOTIFICATION, codenames
 
-site_auths.add_group(*codenames, name=NOTIFICATION)
-if django_apps.is_installed("edc_export"):
-    site_auths.update_group("edc_notification.export_notification", name=EXPORT)
-site_auths.update_role(NOTIFICATION, name=ACCOUNT_MANAGER_ROLE)
+
+def update_site_auths():
+    site_auths.add_group(*codenames, name=NOTIFICATION)
+    if django_apps.is_installed("edc_export"):
+        site_auths.update_group("edc_notification.export_notification", name=EXPORT)
+    site_auths.update_role(NOTIFICATION, name=ACCOUNT_MANAGER_ROLE)
+
+
+update_site_auths()

edc_notification/notification/graded_event_notification.py

@@ -4,8 +4,8 @@ from .model_notification import ModelNotification
 class GradedEventNotification(ModelNotification):
     grade: int | None = None
     model: str | None = None
-    create_fields = ["ae_grade"]
-    update_fields = ["ae_grade"]
+    create_fields: tuple[str] = ("ae_grade",)
+    update_fields: tuple[str] = ("ae_grade",)
 
     def field_value_condition_on_create(self, field, current_value):
         return str(current_value) == str(self.grade)