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

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)

edc_notification/notification/model_notification.py

@@ -17,10 +17,10 @@ class ModelNotification(Notification):
 
     model: str | None = None  # label_lower format
 
-    model_operations = [CREATE, UPDATE, DELETE]
+    model_operations: tuple[str] = (CREATE, UPDATE, DELETE)
 
-    create_fields = ["created"]
-    update_fields = ["modified"]
+    create_fields: tuple[str] = ("created",)
+    update_fields: tuple[str] = ("modified",)
 
     email_body_template: str = (
         "\n\nDo not reply to this email\n\n"
@@ -177,30 +177,3 @@ class ModelNotification(Notification):
         )
 
         return opts
-
-    # @property
-    # def test_template_options(self) -> dict:
-    #     class Site:
-    #         domain = "gaborone.example.com"
-    #         name = "gaborone"
-    #         id = 99
-    #
-    #     class Meta:
-    #         label_lower = self.model
-    #
-    #     class DummyHistory:
-    #         def __init__(self, objects):
-    #             self._objects = objects
-    #
-    #         def all(self):
-    #             return self._objects
-    #
-    #     class DummyInstance:
-    #         id = 99
-    #         subject_identifier = "123456910"
-    #         site = Site()
-    #         _meta = Meta()
-    #
-    #     instance = DummyInstance()
-    #     instance.history = DummyHistory(objects=[instance])
-    #     return dict(instance=instance)

edc_notification/notification/new_model_notification.py

@@ -3,4 +3,4 @@ from .model_notification import ModelNotification
 
 
 class NewModelNotification(ModelNotification):
-    model_operations = [CREATE]
+    model_operations = (CREATE,)

edc_notification/notification/notification.py

@@ -214,7 +214,7 @@ class Notification:
 
     def send_email(
         self,
-        email_to: list[str],
+        email_to: list[str] | None = None,
         fail_silently: bool | None = None,
         email_body_template: str | None = None,
         **kwargs,

edc_notification/notification/updated_model_notification.py

@@ -3,9 +3,9 @@ from .model_notification import ModelNotification
 
 
 class UpdatedModelNotification(ModelNotification):
-    model_operations = [UPDATE]
+    model_operations = (UPDATE,)
 
-    update_fields = ["modified"]
+    update_fields = ("modified",)
 
     email_subject_template = (
         "*UPDATE* {test_subject_line}{protocol_name}: "

edc_offstudy/auths.py

@@ -8,10 +8,15 @@ from edc_auth.site_auths import site_auths
 
 from .auth_objects import OFFSTUDY, OFFSTUDY_SUPER, OFFSTUDY_VIEW, codenames
 
-site_auths.add_group(*codenames, name=OFFSTUDY, no_delete=True)
-site_auths.add_group(*codenames, name=OFFSTUDY_SUPER)
-site_auths.add_group(*codenames, name=OFFSTUDY_VIEW, view_only=True)
-site_auths.update_role(OFFSTUDY, name=CLINICIAN_ROLE)
-site_auths.update_role(OFFSTUDY, name=NURSE_ROLE)
-site_auths.update_role(OFFSTUDY_SUPER, name=CLINICIAN_SUPER_ROLE)
-site_auths.update_role(OFFSTUDY_VIEW, name=AUDITOR_ROLE)
+
+def update_site_auths():
+    site_auths.add_group(*codenames, name=OFFSTUDY, no_delete=True)
+    site_auths.add_group(*codenames, name=OFFSTUDY_SUPER)
+    site_auths.add_group(*codenames, name=OFFSTUDY_VIEW, view_only=True)
+    site_auths.update_role(OFFSTUDY, name=CLINICIAN_ROLE)
+    site_auths.update_role(OFFSTUDY, name=NURSE_ROLE)
+    site_auths.update_role(OFFSTUDY_SUPER, name=CLINICIAN_SUPER_ROLE)
+    site_auths.update_role(OFFSTUDY_VIEW, name=AUDITOR_ROLE)
+
+
+update_site_auths()

edc_pdutils/df_exporters/csv_model_exporter.py

@@ -30,6 +30,7 @@ class CsvModelExporter:
         **kwargs,
     ):
         self.model = model or queryset.model._meta.label_lower
+        self.export_folder = export_folder
         self.df_maker = self.df_maker_cls(
             model=model,
             queryset=queryset,
@@ -46,8 +47,10 @@ class CsvModelExporter:
 
     def to_csv(self):
         dataframe = self.df_maker.dataframe
-        return self.csv_exporter.to_csv(dataframe=dataframe)
+        return self.csv_exporter.to_csv(dataframe=dataframe, export_folder=self.export_folder)
 
     def to_stata(self):
         dataframe = self.df_maker.dataframe
-        return self.csv_exporter.to_stata(dataframe=dataframe)
+        return self.csv_exporter.to_stata(
+            dataframe=dataframe, export_folder=self.export_folder
+        )

edc_pharmacy/auths.py

@@ -18,21 +18,25 @@ from .auth_objects import (
     prescriber_codenames,
 )
 
-site_auths.add_post_update_func(
-    "edc_pharmacy", remove_default_model_permissions_from_edc_permissions
-)
-site_auths.add_custom_permissions_tuples(
-    model="edc_pharmacy.edcpermissions", codename_tuples=navbar_tuples
-)
 
-site_auths.add_group(*pharmacy_codenames, name=PHARMACY_VIEW, view_only=True)
-site_auths.add_group(*prescriber_codenames, name=PHARMACY_PRESCRIBER, no_delete=True)
-site_auths.add_group(*pharmacy_site_codenames, name=PHARMACY_SITE, no_delete=False)
-site_auths.add_group(*pharmacy_codenames, name=PHARMACY, no_delete=False)
+def update_site_auths() -> None:
+    site_auths.add_post_update_func(
+        "edc_pharmacy", remove_default_model_permissions_from_edc_permissions
+    )
+    site_auths.add_custom_permissions_tuples(
+        model="edc_pharmacy.edcpermissions", codename_tuples=navbar_tuples
+    )
+
+    site_auths.add_group(*pharmacy_codenames, name=PHARMACY_VIEW, view_only=True)
+    site_auths.add_group(*prescriber_codenames, name=PHARMACY_PRESCRIBER, no_delete=True)
+    site_auths.add_group(*pharmacy_site_codenames, name=PHARMACY_SITE, no_delete=False)
+    site_auths.add_group(*pharmacy_codenames, name=PHARMACY, no_delete=False)
+
+    site_auths.add_role(PHARMACY_VIEW, name=PHARMACY_AUDITOR_ROLE)
+    site_auths.add_role(PHARMACY_PRESCRIBER, name=PHARMACY_PRESCRIBER_ROLE)
+    site_auths.add_role(PHARMACY_SITE, PYLABELS, name=SITE_PHARMACIST_ROLE)
+    site_auths.add_role(PHARMACY, PYLABELS, name=PHARMACIST_ROLE)
+    site_auths.add_role(PHARMACY, name=PHARMACY_SUPER_ROLE)
 
 
-site_auths.add_role(PHARMACY_VIEW, name=PHARMACY_AUDITOR_ROLE)
-site_auths.add_role(PHARMACY_PRESCRIBER, name=PHARMACY_PRESCRIBER_ROLE)
-site_auths.add_role(PHARMACY_SITE, PYLABELS, name=SITE_PHARMACIST_ROLE)
-site_auths.add_role(PHARMACY, PYLABELS, name=PHARMACIST_ROLE)
-site_auths.add_role(PHARMACY, name=PHARMACY_SUPER_ROLE)
+update_site_auths()

edc_pharmacy/models/medication/formulation.py

@@ -61,18 +61,17 @@ class Formulation(BaseUuidModel):
     def save(self, *args, **kwargs):
         self.description = self.get_description()
         if not self.imp:
-            self.imp_description = None
+            self.imp_description = ""
         else:
             self.imp_description = (
                 self.imp_description if self.imp_description else self.description
             )
         super().save(*args, **kwargs)
 
-    def get_description(self):
+    def get_description(self) -> str:
         return (
             f"{self.medication} {round_half_away_from_zero(self.strength, 0)}"
             f"{self.get_units_display()} "
-            # f"{self.get_formulation_type_display()} "
             f"{self.get_route_display()}"
         )
 
@@ -80,7 +79,6 @@ class Formulation(BaseUuidModel):
         return (
             f"{self.medication} {round_half_away_from_zero(self.strength, 0)}"
             f"{self.get_units_display()} "
-            # f"{self.get_formulation_type_display()} "
         )
 
     def get_description_with_assignment(self, assignment: Assignment) -> str:
@@ -103,9 +101,9 @@ class Formulation(BaseUuidModel):
     class Meta(BaseUuidModel.Meta):
         verbose_name = "Formulation"
         verbose_name_plural = "Formulations"
-        constraints = [
+        constraints = (
             UniqueConstraint(
                 fields=["medication", "strength", "units", "formulation_type"],
                 name="%(app_label)s_%(class)s_med_stren_uniq",
-            )
-        ]
+            ),
+        )

edc_pharmacy/prescribe/create_prescription.py

@@ -30,11 +30,11 @@ def create_prescription(
     for medication_name in medication_names:
         try:
             obj = medication_model_cls.objects.get(name__iexact=medication_name)
-        except ObjectDoesNotExist:
+        except ObjectDoesNotExist as e:
             raise PrescriptionError(
                 "Unable to create prescription. Medication does not exist. "
                 f"Got {medication_name}"
-            )
+            ) from e
         else:
             medications.append(obj)
     try:
@@ -51,7 +51,7 @@ def create_prescription(
         try:
             rx = rx_model_cls.objects.create(**opts)
         except ObjectDoesNotExist as e:
-            raise CommandError(f"Site does not exists. site_id={site_id}. Got {e}")
+            raise CommandError(f"Site does not exists. site_id={site_id}. Got {e}") from e
         for obj in medications:
             rx.medications.add(obj)
     else:

edc_pharmacy/utils/confirm_stock.py

@@ -15,7 +15,7 @@ def confirm_stock(
     stock_codes: list[str],
     fk_attr: str | None = None,
     confirmed_by: str | None = None,
-    user_created: str = None,
+    user_created: str | None = None,
 ) -> tuple[list[str], list[str], list[str]]:
     """Confirm stock instances given a list of stock codes
     and a request/receive pk.