clinicedc 2.0.28__py3-none-any.whl → 2.0.29__py3-none-any.whl

edc_pharmacy/views/transfer_stock_view.py

@@ -54,7 +54,7 @@ class TransferStockView(EdcViewMixin, NavbarViewMixin, EdcProtocolViewMixin, Tem
     def model_cls(self):
         return django_apps.get_model("edc_pharmacy.stocktransfer")
 
-    def post(self, request, *args, **kwargs):
+    def post(self, request, *args, **kwargs):  # noqa: ARG002
         stock_transfer = StockTransfer.objects.get(pk=self.kwargs.get("stock_transfer"))
         stock_codes = request.POST.getlist("codes")
         if stock_codes:

edc_prn/modelform_mixins.py

@@ -8,7 +8,6 @@ from django.utils.text import format_lazy
 from django.utils.translation import gettext_lazy as _
 
 from edc_consent import site_consents
-from edc_consent.consent_definition import ConsentDefinition
 from edc_crf.crf_form_validator_mixins import BaseFormValidatorMixin
 
 
@@ -19,17 +18,17 @@ class PrnFormValidatorMixin(BaseFormValidatorMixin):
 
     @property
     def subject_consent(self):
-        return self.get_consent_definition(
+        return site_consents.get_consent_definition(
             report_datetime=self.report_datetime
         ).model_cls.objects.get(subject_identifier=self.subject_identifier)
 
-    def get_consent_definition(
-        self,
-        report_datetime: datetime = None,
-        fldname: str = None,
-        error_code: str = None,
-    ) -> ConsentDefinition:
-        return site_consents.get_consent_definition(report_datetime=self.report_datetime)
+    # def get_consent_definition(
+    #     self,
+    #     report_datetime: datetime | None = None,
+    #     fldname: str | None = None,
+    #     error_code: str | None = None,
+    # ) -> ConsentDefinition:
+    #     return site_consents.get_consent_definition(report_datetime=self.report_datetime)
 
     @property
     def report_datetime(self) -> datetime:

edc_prn/models.py

@@ -2,6 +2,8 @@
 
 from django.db import models
 
+from edc_constants.constants import NULL_STRING
+
 
 class SingletonPrnModelMixin(models.Model):
     """Enforces one record per subject."""
@@ -11,7 +13,7 @@ class SingletonPrnModelMixin(models.Model):
         max_length=50,
         unique=True,
         help_text="auto updated for unique constraint",
-        null=True,
+        default=NULL_STRING,
         editable=False,
     )
 

edc_prn/site_prn_forms.py

@@ -14,7 +14,7 @@ if TYPE_CHECKING:
     from edc_prn import Prn
 
 
-class AlreadyRegistered(Exception):
+class AlreadyRegistered(Exception):  # noqa: N818
     pass
 
 
@@ -72,7 +72,7 @@ class PrnFormsCollection:
                 except ImportError as e:
                     site_prn_forms.registry = before_import_registry
                     if module_has_submodule(mod, module_name):
-                        raise SitePrnFormsError(str(e))
+                        raise SitePrnFormsError(str(e)) from e
             except ImportError:
                 pass
 

edc_prn/templatetags/edc_prn_extras.py

@@ -23,7 +23,7 @@ def prn_list_items(subject_identifier, **kwargs):
     prn_forms = []
     for prn in site_prn_forms:
         if prn.get_show_on_dashboard(subject_identifier=subject_identifier):
-            prn_forms.append(prn)
+            prn_forms.append(prn)  # noqa: PERF401
     if prn_forms:
         prn_forms = sorted(prn_forms, key=lambda x: x.verbose_name)
     return dict(prn_forms=prn_forms, subject_identifier=subject_identifier)

edc_protocol/middleware.py

@@ -11,7 +11,7 @@ class ResearchProtocolConfigMiddleware:
     def process_view(self, request, *args):
         pass
 
-    def process_template_response(self, request, response):
+    def process_template_response(self, request, response):  # noqa: ARG002
         if not response.context_data:
             response.context_data = {}
         protocol_config = ResearchProtocolConfig()

edc_protocol/research_protocol_config.py

@@ -134,7 +134,9 @@ class ResearchProtocolConfig:
         return getattr(
             settings,
             "EDC_PROTOCOL_SUBJECT_IDENTIFIER_PATTERN",
-            r"%(protocol_number)s\-[0-9\-]+" % dict(protocol_number=self.protocol_number),
+            r"{protocol_number}\-[0-9\-]+".format(
+                **dict(protocol_number=self.protocol_number)
+            ),
         )
 
     @property
@@ -145,14 +147,14 @@ class ResearchProtocolConfig:
     def study_open_datetime(self) -> datetime:
         try:
             study_open_datetime = settings.EDC_PROTOCOL_STUDY_OPEN_DATETIME
-        except AttributeError:
+        except AttributeError as e:
             raise ImproperlyConfigured(
                 self.error_msg1
                 % {
                     "attr": "study_open_datetime",
                     "settings_attr": "EDC_PROTOCOL_STUDY_OPEN_DATETIME",
                 }
-            )
+            ) from e
         if not study_open_datetime:
             raise ImproperlyConfigured(
                 self.error_msg2
@@ -167,14 +169,14 @@ class ResearchProtocolConfig:
     def study_close_datetime(self) -> datetime:
         try:
             study_close_datetime = settings.EDC_PROTOCOL_STUDY_CLOSE_DATETIME
-        except AttributeError:
+        except AttributeError as e:
             raise ImproperlyConfigured(
                 self.error_msg1
                 % {
                     "attr": "study_close_datetime",
                     "settings_attr": "EDC_PROTOCOL_STUDY_CLOSE_DATETIME",
                 }
-            )
+            ) from e
         if not study_close_datetime:
             raise ImproperlyConfigured(
                 self.error_msg2

edc_protocol_incident/admin/protocol_deviation_violation_admin.py

@@ -65,7 +65,7 @@ class ProtocolDeviationViolationAdmin(ModelAdminSubjectDashboardMixin, SimpleHis
         audit_fieldset_tuple,
     )
 
-    radio_fields = {
+    radio_fields = {  # noqa: RUF012
         "action_required": admin.VERTICAL,
         "report_status": admin.VERTICAL,
         "report_type": admin.VERTICAL,

edc_protocol_incident/form_validators/mixins.py

@@ -40,9 +40,12 @@ class IncidentFormvalidatorMixin:
         self.validate_date_not_before_incident("report_closed_datetime")
 
     def validate_date_not_before_incident(self, fld_name):
-        if self.cleaned_data.get(fld_name) and self.cleaned_data.get("incident_datetime"):
-            if self.cleaned_data.get(fld_name) < self.cleaned_data.get("incident_datetime"):
-                self.raise_validation_error(
-                    {fld_name: "May not be before incident date/time"},
-                    error_code=INVALID_ERROR,
-                )
+        if (
+            self.cleaned_data.get(fld_name)
+            and self.cleaned_data.get("incident_datetime")
+            and self.cleaned_data.get(fld_name) < self.cleaned_data.get("incident_datetime")
+        ):
+            self.raise_validation_error(
+                {fld_name: "May not be before incident date/time"},
+                error_code=INVALID_ERROR,
+            )

edc_protocol_incident/modeladmin_mixins.py

@@ -60,7 +60,7 @@ class ProtocolIncidentModelAdminMixin:
         audit_fieldset_tuple,
     )
 
-    radio_fields = {
+    radio_fields = {  # noqa: RUF012
         "action_required": admin.VERTICAL,
         "report_status": admin.VERTICAL,
         "report_type": admin.VERTICAL,

edc_pylabels/admin/label_configuration_admin.py

@@ -29,7 +29,7 @@ class LabelConfigurationAdmin(
     admin.ModelAdmin,
 ):
     show_object_tools = True
-    actions = [print_test_label_sheet_action]
+    actions = (print_test_label_sheet_action,)
     form = LabelConfigurationForm
 
     instructions = (

edc_pylabels/admin/label_specification_admin.py

@@ -26,7 +26,7 @@ class LabelSpecificationAdmin(
     ModelAdminRedirectOnDeleteMixin,
     admin.ModelAdmin,
 ):
-    actions = [copy_label_specification, export_to_csv]
+    actions = (copy_label_specification, export_to_csv)
 
     instructions = (
         "This model captures the dimensions, rows, columns, "

edc_pylabels/auth_objects.py

@@ -11,5 +11,5 @@ for app_config in django_apps.get_app_configs():
         for model_cls in app_config.get_models():
             app_name, model_name = model_cls._meta.label_lower.split(".")
             for prefix in ["add", "change", "view", "delete"]:
-                codenames.append(f"{app_name}.{prefix}_{model_name}")
+                codenames.append(f"{app_name}.{prefix}_{model_name}")  # noqa: PERF401
 codenames.sort()

edc_pylabels/site_label_configs.py

@@ -11,7 +11,7 @@ from django.core.management.color import color_style
 from django.utils.module_loading import module_has_submodule
 
 
-class AlreadyRegistered(Exception):
+class AlreadyRegistered(Exception):  # noqa: N818
     pass
 
 
@@ -104,7 +104,7 @@ class SiteLabelConfigs:
                 except ImportError as e:
                     site_label_configs.registry = before_import_registry
                     if module_has_submodule(mod, module_name):
-                        raise SitePharmacyError(str(e))
+                        raise SitePharmacyError(str(e)) from e
             except ImportError:
                 pass
 

edc_qareports/admin/qa_report_log_admin.py

@@ -17,15 +17,15 @@ class QaReportLogAdmin(
     TemplatesModelAdminMixin,
     admin.ModelAdmin,
 ):
-    ordering = ["-accessed"]
+    ordering = ("-accessed",)
 
-    list_display = ["report", "username", "site", "accessed", "report_model"]
+    list_display = ("report", "username", "site", "accessed", "report_model")
 
-    list_filter = ["accessed", "report_model", "username", "site"]
+    list_filter = ("accessed", "report_model", "username", "site")
 
-    search_fields = ["report_model", "username"]
+    search_fields = ("report_model", "username")
 
-    readonly_fields = ["report_model", "username", "site", "accessed"]
+    readonly_fields = ("report_model", "username", "site", "accessed")
 
     @admin.display(description="Report", ordering="report_model")
     def report(self, obj=None):

edc_qareports/admin/qa_report_log_summary_admin.py

@@ -17,7 +17,7 @@ class QaReportLogSummaryAdmin(
     TemplatesModelAdminMixin,
     admin.ModelAdmin,
 ):
-    ordering = ["-last_accessed"]
+    ordering = ("-last_accessed",)
 
     list_display = (
         "username",

edc_qareports/forms/note_form.py

@@ -18,15 +18,14 @@ class NoteForm(
     FormValidatorMixin,
     forms.ModelForm,
 ):
-
     report_datetime_field_attr = "report_datetime"
     form_validator_cls = NoteFormValidator
 
     class Meta:
         model = Note
         fields = "__all__"
-        help_text = {"subject_identifier": "(read-only)", "name": "(read-only)"}
-        widgets = {
+        help_text = {"subject_identifier": "(read-only)", "name": "(read-only)"}  # noqa: RUF012
+        widgets = {  # noqa: RUF012
             "report_model": forms.TextInput(attrs={"readonly": "readonly"}),
             "subject_identifier": forms.TextInput(attrs={"readonly": "readonly"}),
             "name": forms.TextInput(attrs={"readonly": "readonly"}),

edc_qareports/modeladmin_mixins/list_filters.py

@@ -17,7 +17,7 @@ class NoteStatusListFilter(SimpleListFilter):
         self.note_model_cls = model_admin.note_model_cls
         super().__init__(request, params, model, model_admin)
 
-    def lookups(self, request, model_admin):
+    def lookups(self, request, model_admin):  # noqa: ARG002
         status_dict = {tpl[0]: tpl[1] for tpl in self.note_model_status_choices}
         names = [(NEW, status_dict.get(NEW, "New"))]
         qs = (
@@ -27,7 +27,7 @@ class NoteStatusListFilter(SimpleListFilter):
         )
 
         for obj in qs:
-            names.append((f"{obj.get('status')}", status_dict[obj.get("status")]))
+            names.append((f"{obj.get('status')}", status_dict[obj.get("status")]))  # noqa: PERF401
         return tuple(names)
 
     @staticmethod
@@ -39,22 +39,26 @@ class NoteStatusListFilter(SimpleListFilter):
         )
         for obj in qs:
             return obj.get("report_model")
+        return ""
 
-    def queryset(self, request, queryset):
-        if self.value() and self.value() != "none":
-            if report_model := self.report_model(queryset):
-                if self.value() == NEW:
-                    qs = self.note_model_cls.objects.values("subject_identifier").filter(
-                        report_model=report_model
-                    )
-                    queryset = queryset.exclude(
-                        subject_identifier__in=[obj.get("subject_identifier") for obj in qs]
-                    )
-                elif self.value() in [tpl[0] for tpl in self.note_model_status_choices]:
-                    qs = self.note_model_cls.objects.values("subject_identifier").filter(
-                        report_model=report_model, status=self.value()
-                    )
-                    queryset = queryset.filter(
-                        subject_identifier__in=[obj.get("subject_identifier") for obj in qs]
-                    )
+    def queryset(self, request, queryset):  # noqa: ARG002
+        if (
+            self.value()
+            and self.value() != "none"
+            and (report_model := self.report_model(queryset))
+        ):
+            if self.value() == NEW:
+                qs = self.note_model_cls.objects.values("subject_identifier").filter(
+                    report_model=report_model
+                )
+                queryset = queryset.exclude(
+                    subject_identifier__in=[obj.get("subject_identifier") for obj in qs]
+                )
+            elif self.value() in [tpl[0] for tpl in self.note_model_status_choices]:
+                qs = self.note_model_cls.objects.values("subject_identifier").filter(
+                    report_model=report_model, status=self.value()
+                )
+                queryset = queryset.filter(
+                    subject_identifier__in=[obj.get("subject_identifier") for obj in qs]
+                )
         return queryset

edc_qareports/modeladmin_mixins/note_modeladmin_mixin.py

@@ -32,7 +32,7 @@ class NoteModelAdminMixin(
     """A modeladmin mixin class for the Note model."""
 
     form = NoteForm
-    ordering = ["site", "subject_identifier"]
+    ordering = ("site", "subject_identifier")
 
     note_template_name = "edc_qareports/qa_report_note.html"
 
@@ -52,26 +52,26 @@ class NoteModelAdminMixin(
         audit_fieldset_tuple,
     )
 
-    list_display = [
+    list_display = (
         "dashboard",
         "subject_identifier",
         "report",
         "status",
         "report_note",
         "report_datetime",
-    ]
+    )
 
-    radio_fields = {"status": admin.VERTICAL}
+    radio_fields = {"status": admin.VERTICAL}  # noqa: RUF012
 
-    list_filter = [
+    list_filter = (
         "report_datetime",
         "status",
         "report_model",
         "user_created",
         "user_modified",
-    ]
+    )
 
-    search_fields = ["subject_identifier", "name"]
+    search_fields = ("subject_identifier", "name")
 
     @admin.display(description="Report", ordering="report_name")
     def report(self, obj=None):

edc_qareports/modeladmin_mixins/on_study_missing_values_modeladmin_mixin.py

@@ -23,9 +23,9 @@ class OnStudyMissingValuesModelAdminMixin(
     include_note_column: bool = True
     site_list_display_insert_pos: int = 2
     qa_report_list_display_insert_pos = 4
-    ordering = ["site", "subject_identifier"]
+    ordering = ("site", "subject_identifier")
 
-    list_display = [
+    list_display = (
         "dashboard",
         "render_button",
         "subject",
@@ -35,16 +35,16 @@ class OnStudyMissingValuesModelAdminMixin(
         "visit",
         "report_date",
         "created",
-    ]
+    )
 
-    list_filter = [
+    list_filter = (
         ScheduleStatusListFilter,
         "label",
         "visit_code",
         "report_datetime",
-    ]
+    )
 
-    search_fields = ["subject_identifier", "label"]
+    search_fields = ("subject_identifier", "label")
 
     @admin.display(description="Update")
     def render_button(self, obj=None):
@@ -64,7 +64,7 @@ class OnStudyMissingValuesModelAdminMixin(
                 f"&appointment={self.related_visit(obj).appointment.id}"
                 f"&requisition={obj.original_id}"
             )
-            title = _(f"Add {crf_model_cls._meta.verbose_name}")
+            title = _("Add {}") % crf_model_cls._meta.verbose_name
             label = _("Add CRF")
             crf_button = render_to_string(
                 "edc_qareports/columns/add_button.html",
@@ -80,7 +80,7 @@ class OnStudyMissingValuesModelAdminMixin(
                 f"{url}?next={self.admin_site.name}:"
                 f"{self.model._meta.label_lower.replace('.', '_')}_changelist"
             )
-            title = _(f"Change {crf_model_cls._meta.verbose_name}")
+            title = _("Change {}") % crf_model_cls._meta.verbose_name
             label = _("Change CRF")
             crf_button = render_to_string(
                 "edc_qareports/columns/change_button.html",

edc_qareports/modeladmin_mixins/qa_report_modeladmin_mixin.py

@@ -62,13 +62,9 @@ class QaReportModelAdminMixin:
         return tuple(list_filter)
 
     def get_note_model_obj_or_raise(self, obj=None):
-        try:
-            note_model_obj = self.note_model_cls.objects.get(
-                report_model=obj.report_model, subject_identifier=obj.subject_identifier
-            )
-        except ObjectDoesNotExist:
-            raise
-        return note_model_obj
+        return self.note_model_cls.objects.get(
+            report_model=obj.report_model, subject_identifier=obj.subject_identifier
+        )
 
     @admin.display(description="Status")
     def status(self, obj) -> str:

edc_qareports/sql_generator/crf_case.py

@@ -36,5 +36,5 @@ class CrfCase:
             try:
                 cursor.execute(self.sql)
             except OperationalError as e:
-                raise CrfCaseError(f"{e}. See {self}.")
+                raise CrfCaseError(f"{e}. See {self}.") from e
             return cursor.fetchall()

edc_qareports/sql_generator/crf_subquery.py

@@ -59,5 +59,5 @@ class CrfSubquery:
         try:
             sql = self.template.substitute(**opts).replace(";", "")
         except KeyError as e:
-            raise CrfSubqueryError(e)
+            raise CrfSubqueryError(e) from e
         return sql

edc_qareports/sql_generator/requisition_subquery.py

@@ -27,7 +27,7 @@ class RequisitionSubquery(CrfSubquery):
     template: str = field(
         init=False,
         default=Template(
-            "select req.subject_identifier, req.id as original_id, "  # nosec B608
+            "select req.subject_identifier, req.id as original_id, "  # nosec B608  # noqa: S608
             "req.subject_visit_id, req.report_datetime, req.site_id, v.visit_code, "
             "v.visit_code_sequence, "
             "v.schedule_name, req.modified, '${label_lower}' as label_lower, "

edc_qareports/sql_generator/sql_view_generator.py

@@ -30,7 +30,7 @@ class SqlViewGenerator:
         self.footer = f") as A ORDER BY {self.order_by}"
 
     @staticmethod
-    def transpile(sql: str, read: str | None = None, write: str = None) -> str:
+    def transpile(sql: str, read: str | None = None, write: str | None = None) -> str:
         read = read or "mysql"
         sql = sql.replace(";", "")
         return sqlglot.transpile(sql, read=read, write=write)[0]

edc_qareports/sql_generator/subquery_from_dict.py

@@ -1,39 +1,39 @@
-from __future__ import annotations
-
-from typing import TYPE_CHECKING
-
-from .subquery import Subquery
-
-if TYPE_CHECKING:
-    from .qa_case import QaCase
-
-
-def subquery_from_dict(
-    cases: list[dict[str:str, str:str, str:str] | QaCase],
-    as_list: bool | None = False,
-) -> str | list:
-    """Returns an SQL select statement as a union of the select
-    statements of each case.
-
-    args:
-     cases = [{
-         "label_lower": "my_app.hivhistory",
-         "dbtable": "my_app_hivhistory",
-         "field": "hiv_init_date",
-         "label": "missing HIV initiation date",
-         "list_tables": [(list_field, list_dbtable, alias), ...],
-         }, ...]
-
-         Note: `list_field` is the CRF id field, for example:
-            left join <list_dbtable> as <alias> on crf.<list_field>=<alias>.id
-    """
-    subqueries = []
-    for case in cases:
-        try:
-            subquery = case.sql
-        except AttributeError:
-            subquery = Subquery(**case).sql
-        subqueries.append(subquery)
-    if as_list:
-        return subqueries
-    return " UNION ".join(subqueries)
+# from __future__ import annotations
+#
+# from typing import TYPE_CHECKING
+#
+# from .subquery import Subquery
+#
+# if TYPE_CHECKING:
+#     from .qa_case import QaCase
+#
+#
+# def subquery_from_dict(
+#     cases: list[dict[str:str, str:str, str:str] | QaCase],
+#     as_list: bool | None = False,
+# ) -> str | list:
+#     """Returns an SQL select statement as a union of the select
+#     statements of each case.
+#
+#     args:
+#      cases = [{
+#          "label_lower": "my_app.hivhistory",
+#          "dbtable": "my_app_hivhistory",
+#          "field": "hiv_init_date",
+#          "label": "missing HIV initiation date",
+#          "list_tables": [(list_field, list_dbtable, alias), ...],
+#          }, ...]
+#
+#          Note: `list_field` is the CRF id field, for example:
+#             left join <list_dbtable> as <alias> on crf.<list_field>=<alias>.id
+#     """
+#     subqueries = []
+#     for case in cases:
+#         try:
+#             subquery = case.sql
+#         except AttributeError:
+#             subquery = Subquery(**case).sql
+#         subqueries.append(subquery)
+#     if as_list:
+#         return subqueries
+#     return " UNION ".join(subqueries)

edc_qareports/utils.py

@@ -1,3 +1,4 @@
+import contextlib
 import sys
 from pathlib import Path
 from warnings import warn
@@ -27,10 +28,10 @@ def read_unmanaged_model_sql(
     parsed_sql = []
     with fullpath.open("r") as f:
         for line in f:
-            line = line.split("#", maxsplit=1)[0]
-            line = line.split("-- ", maxsplit=1)[0]
-            line = line.replace("\n", "")
-            line = line.strip()
+            line = line.split("#", maxsplit=1)[0]  # noqa: PLW2901
+            line = line.split("-- ", maxsplit=1)[0]  # noqa: PLW2901
+            line = line.replace("\n", "")  # noqa: PLW2901
+            line = line.strip()  # noqa: PLW2901
             if line:
                 parsed_sql.append(line)
 
@@ -88,17 +89,15 @@ def recreate_db_view(model_cls, drop: bool | None = None, verbose: bool | None =
     except AttributeError as e:
         raise AttributeError(
             f"Is this model linked to a view? Declare model with `DBView`. Got {e}"
-        )
+        ) from e
     else:
         sql = sql.replace(";", "")
         if verbose:
-            print(f"create view {model_cls._meta.db_table} as {sql};")
+            sys.stdout.write(f"create view {model_cls._meta.db_table} as {sql};\n")
         with connection.cursor() as c:
             if drop:
-                try:
+                with contextlib.suppress(OperationalError):
                     c.execute(f"drop view {model_cls._meta.db_table};")
-                except OperationalError:
-                    pass
             c.execute(f"create view {model_cls._meta.db_table} as {sql};")
         if verbose:
             sys.stdout.write(
@@ -107,14 +106,14 @@ def recreate_db_view(model_cls, drop: bool | None = None, verbose: bool | None =
 
 
 def recreate_dbview_for_all():
-    from .model_mixins import QaReportModelMixin
+    from .model_mixins import QaReportModelMixin  # noqa: PLC0415
 
     for model_cls in django_apps.get_models():
         if issubclass(model_cls, (QaReportModelMixin,)):
-            print(model_cls)
+            sys.stdout.write(f"{model_cls}\n")
             try:
                 model_cls.recreate_db_view()
             except AttributeError as e:
-                print(e)
+                sys.stdout.write(f"{e}\n")
             except TypeError as e:
-                print(e)
+                sys.stdout.write(f"{e}\n")

edc_randomization/model_mixins.py

@@ -71,7 +71,7 @@ class RandomizationListModelMixin(models.Model):
     def save(self, *args, **kwargs):
         self.randomizer_name = self.randomizer_cls.name
         try:
-            self.assignment_description
+            self.assignment_description  # noqa: B018
         except RandomizationError as e:
             raise RandomizationListModelError(e) from e
         try: