clinicedc 2.0.27__py3-none-any.whl → 2.0.29__py3-none-any.whl

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:

edc_randomization/randomization_list_importer.py

@@ -2,6 +2,7 @@ from __future__ import annotations
 
 import csv
 import sys
+from itertools import islice
 from pathlib import Path
 from pprint import pprint
 from uuid import uuid4
@@ -72,6 +73,7 @@ class RandomizationListImporter:
         username: str | None = None,
         revision: str | None = None,
         sid_count_for_tests: int | None = None,
+        skip_verify: bool | None = None,
         extra_csv_fieldnames: tuple[str] | None = None,
         **kwargs,  # noqa: ARG002
     ):
@@ -84,6 +86,7 @@ class RandomizationListImporter:
         self.revision = revision
         self.user = username
         self.sid_count_for_tests = sid_count_for_tests
+        self.skip_verify = skip_verify
         self.randomizer_model_cls = randomizer_model_cls
         self.randomizer_name = randomizer_name
         self.assignment_map = assignment_map
@@ -120,8 +123,9 @@ class RandomizationListImporter:
                 )
             )
         rec_count = self._import_csv_to_model()
-        self.verify_messages = self._verify_data(**kwargs)
-        self._summarize_results()
+        if not self.skip_verify:
+            self.verify_messages = self._verify_data(**kwargs)
+            self._summarize_results()
         if self.verbose:
             sys.stdout.write(
                 style.SUCCESS("\nDone.------------------------------------------------\n")
@@ -221,13 +225,15 @@ class RandomizationListImporter:
             sid_count = len(self.get_sid_list())
         with self.randomizationlist_path.open(mode="r") as f:
             reader = csv.DictReader(f)
+            if self.sid_count_for_tests:
+                reader = islice(reader, self.sid_count_for_tests)
             all_rows = [{k: v.strip() for k, v in row.items() if k} for row in reader]
             sorted_rows = sorted(
                 all_rows, key=lambda row: (row.get("site_name", ""), row.get("sid", ""))
             )
             for row in tqdm(sorted_rows, total=sid_count):
-                if self.sid_count_for_tests and len(objs) == self.sid_count_for_tests:
-                    break
+                # if self.sid_count_for_tests and len(objs) == self.sid_count_for_tests:
+                #     break
                 try:
                     self.randomizer_model_cls.objects.get(sid=row["sid"])
                 except ObjectDoesNotExist:

edc_randomization/randomization_list_verifier.py

@@ -1,5 +1,6 @@
 import csv
 import sys
+from itertools import islice
 from pathlib import Path
 
 from django.core.exceptions import ObjectDoesNotExist
@@ -72,15 +73,16 @@ class RandomizationListVerifier:
 
     def verify(self) -> str | None:
         message = None
-
         # read and sort from CSV file
         with self.randomizationlist_path.open(mode="r") as f:
             reader = csv.DictReader(f)
+            if self.sid_count_for_tests:
+                reader = islice(reader, self.sid_count_for_tests)
             all_rows = [{k: v.strip() for k, v in row.items() if k} for row in reader]
             sorted_rows = sorted(
-                all_rows, key=lambda row: (row.get("site_name", ""), int(row.get("sid", 0)))
+                all_rows,
+                key=lambda row: (row.get("site_name", ""), int(row.get("sid", 0))),
             )
-
         # compare sorted CSV length with DB
         if len(sorted_rows) != self.randomizer_model_cls.objects.all().count():
             expected_cnt = len(sorted_rows)

edc_randomization/system_checks.py

@@ -57,7 +57,7 @@ def randomizationlist_check(app_configs, **kwargs) -> list:
         ):
             error_msgs = randomizer.verify_list()
             for error_msg in error_msgs:
-                errors.append(error.cls(error_msg, hint=None, obj=None, id=error.id))
+                errors.append(error.cls(error_msg, hint=None, obj=None, id=error.id))  # noqa: PERF401
         if not settings.DEBUG:
             if not randomizer.get_randomizationlist_path().is_relative_to(settings.ETC_DIR):
                 errors.append(

edc_refusal/admin.py

@@ -41,7 +41,7 @@ class SubjectRefusalModelAdminMixin:
 
     search_fields = ("screening_identifier",)
 
-    radio_fields = {"reason": admin.VERTICAL}
+    radio_fields = {"reason": admin.VERTICAL}  # noqa: RUF012
 
 
 @admin.register(SubjectRefusal, site=edc_refusal_admin)
@@ -70,5 +70,7 @@ class SubjectRefusalAdmin(
             if callable(super().view_on_site):
                 url = super().view_on_site(obj)
             else:
-                raise NoReverseMatch(f"{e}. See subject_dashboard_url_name for {self!r}.")
+                raise NoReverseMatch(
+                    f"{e}. See subject_dashboard_url_name for {self!r}."
+                ) from e
         return url

edc_registration/modeladmin_mixins.py

@@ -10,7 +10,7 @@ class RegisteredSubjectModelAdminMixin(ModelAdminSubjectDashboardMixin, admin.Mo
 
     date_hierarchy = "registration_datetime"
 
-    instructions = []
+    instructions = ()
 
     @staticmethod
     def show_pii(request) -> bool:
@@ -29,25 +29,23 @@ class RegisteredSubjectModelAdminMixin(ModelAdminSubjectDashboardMixin, admin.Mo
     def get_readonly_fields(self, request, obj=None) -> tuple[str, ...]:
         readonly_fields = super().get_readonly_fields(request, obj=obj)
         return (
-            readonly_fields
-            + (
-                "subject_identifier",
-                "sid",
-                "first_name",
-                "last_name",
-                "initials",
-                "dob",
-                "gender",
-                "subject_type",
-                "registration_status",
-                "identity",
-                "screening_identifier",
-                "screening_datetime",
-                "registration_datetime",
-                "randomization_datetime",
-                "consent_datetime",
-            )
-            + audit_fields
+            *readonly_fields,
+            "subject_identifier",
+            "sid",
+            "first_name",
+            "last_name",
+            "initials",
+            "dob",
+            "gender",
+            "subject_type",
+            "registration_status",
+            "identity",
+            "screening_identifier",
+            "screening_datetime",
+            "registration_datetime",
+            "randomization_datetime",
+            "consent_datetime",
+            *audit_fields,
         )
 
     def get_list_display(self, request):

edc_registration/modelform_mixins.py

@@ -21,6 +21,6 @@ class ModelFormSubjectIdentifierMixin(SiteModelFormMixin):
             get_registered_subject_model_cls().objects.get(
                 subject_identifier=subject_identifier
             )
-        except ObjectDoesNotExist:
-            raise forms.ValidationError({"subject_identifier": "Invalid."})
+        except ObjectDoesNotExist as e:
+            raise forms.ValidationError({"subject_identifier": "Invalid."}) from e
         return cleaned_data

edc_registration/models/signals.py

@@ -18,4 +18,4 @@ def update_registered_subject_from_model_on_post_save(
             instance.registration_update_or_create()
         except AttributeError as e:
             if "registration_update_or_create" not in str(e):
-                raise AttributeError(str(e))
+                raise AttributeError(str(e)) from e

edc_registration/utils.py

@@ -15,7 +15,7 @@ if TYPE_CHECKING:
     from edc_registration.models import RegisteredSubject
 
 
-class RegisteredSubjectDoesNotExist(Exception):
+class RegisteredSubjectDoesNotExist(Exception):  # noqa: N818
     pass
 
 

edc_reportable/age_evaluator.py

@@ -13,7 +13,7 @@ class AgeEvaluator(Evaluator):
     def __init__(
         self,
         age_lower: int | None = None,
-        age_upper: int = None,
+        age_upper: int | None = None,
         age_units: str | None = None,
         age_lower_inclusive: bool | None = None,
         age_upper_inclusive: bool | None = None,
@@ -29,15 +29,15 @@ class AgeEvaluator(Evaluator):
     def __repr__(self) -> str:
         return f"{self.__class__.__name__}({self.description(show_as_int=True)})"
 
-    def description(self, value: int = None, **kwargs):
+    def description(self, value: int | None = None, **kwargs):
         kwargs["show_as_int"] = True
         kwargs["placeholder"] = "AGE"
         return super().description(value=value, **kwargs)
 
     def in_bounds_or_raise(
         self,
-        dob: date = None,
-        report_datetime: datetime = None,
+        dob: date | None = None,
+        report_datetime: datetime | None = None,
         age_units: str | None = None,
     ) -> bool:
         report_datetime = report_datetime or timezone.now()

edc_reportable/data/grading_data/daids_july_2017.py

@@ -5,9 +5,9 @@ Creatinine Clearance14 or eGFR, Low
 *Report only one
 NA
 G1 N/A
-G2 < 90 to 60 ml/min or ml/min/1.73 m2 OR 10 to < 30% decrease from participant’s baseline
-G3 < 60 to 30 ml/min or ml/min/1.73 m2 OR 30 to < 50% decrease from participant’s baseline
-G4 < 30 ml/min or ml/min/1.73 m2 OR ≥ 50% decrease from participant’s baseline
+G2 < 90 to 60 ml/min or ml/min/1.73 m2 OR 10 to < 30% decrease from participant's baseline
+G3 < 60 to 30 ml/min or ml/min/1.73 m2 OR 30 to < 50% decrease from participant's baseline
+G4 < 30 ml/min or ml/min/1.73 m2 OR ≥ 50% decrease from participant's baseline
 """
 
 from edc_constants.constants import FEMALE, MALE

edc_reportable/evaluator.py

@@ -6,40 +6,40 @@ from .constants import HIGH_VALUE
 from .exceptions import ValueBoundryError
 
 
-class InvalidUnits(Exception):
+class InvalidUnits(Exception):  # noqa: N818
     pass
 
 
-class InvalidLowerBound(Exception):
+class InvalidLowerBound(Exception):  # noqa: N818
     pass
 
 
-class InvalidLowerLimitNormal(Exception):
+class InvalidLowerLimitNormal(Exception):  # noqa: N818
     pass
 
 
-class InvalidUpperLimitNormal(Exception):
+class InvalidUpperLimitNormal(Exception):  # noqa: N818
     pass
 
 
-class InvalidUpperBound(Exception):
+class InvalidUpperBound(Exception):  # noqa: N818
     pass
 
 
-class InvalidCombination(Exception):
+class InvalidCombination(Exception):  # noqa: N818
     pass
 
 
 class Evaluator:
     def __init__(
         self,
-        name: str = None,
-        lower: int | float = None,
-        upper: int | float = None,
-        units: str = None,
+        name: str | None = None,
+        lower: int | float | None = None,
+        upper: int | float | None = None,
+        units: str | None = None,
         lower_inclusive: bool | None = None,
         upper_inclusive: bool | None = None,
-        **kwargs,
+        **kwargs,  # noqa: ARG002
     ) -> None:
         self.name = name
         if lower is not None and not re.match(r"\d+", str(lower)):
@@ -78,8 +78,8 @@ class Evaluator:
 
     def description(
         self,
-        value: int | float = None,
-        show_as_int: bool = None,
+        value: int | float | None = None,
+        show_as_int: bool | None = None,
         placeholder: str | None = None,
     ) -> str:
         placeholder = placeholder or "x"
@@ -98,7 +98,7 @@ class Evaluator:
             f"{self.upper_operator or ''}{upper} {self.units}"
         )
 
-    def in_bounds_or_raise(self, value: int | float, units: str = None) -> bool:
+    def in_bounds_or_raise(self, value: int | float, units: str) -> bool:
         """Raises a ValueBoundryError exception if condition not met.
 
         The condition is evaluated to True or False as a string
@@ -116,6 +116,6 @@ class Evaluator:
             f"{'' if self.lower is None else self.lower}{self.lower_operator or ''}{value}"
             f"{self.upper_operator or ''}{'' if self.upper is None else self.upper}"
         )
-        if not eval(condition_str):  # nosec B307
+        if not eval(condition_str):  # nosec B307  # noqa: S307
             raise ValueBoundryError(condition_str)
         return True

edc_reportable/exceptions.py

@@ -18,7 +18,7 @@ class SiteReportablesError(Exception):
     pass
 
 
-class AlreadyRegistered(Exception):
+class AlreadyRegistered(Exception):  # noqa: N818
     pass
 
 
@@ -30,13 +30,13 @@ class ValueBoundryError(Exception):
     pass
 
 
-class NotEvaluated(Exception):
+class NotEvaluated(Exception):  # noqa: N818
     pass
 
 
-class BoundariesOverlap(Exception):
+class BoundariesOverlap(Exception):  # noqa: N818
     pass
 
 
-class ConversionNotHandled(Exception):
+class ConversionNotHandled(Exception):  # noqa: N818
     pass

edc_reportable/forms/reportables_form_validator_mixin.py

@@ -23,7 +23,10 @@ class ReportablesFormValidatorMixin:
         return {"age_units": "years"}
 
     def validate_reportable_fields(
-        self, reference_range_collection_name: str, **reportables_evaluator_options
+        self,
+        reference_range_collection_name: str,
+        age_units: str | None = None,
+        **reportables_evaluator_options,
     ):
         """Called in clean() method of the FormValidator.
 
@@ -47,9 +50,10 @@ class ReportablesFormValidatorMixin:
             report_datetime=self.report_datetime,
             value_field_suffix=self.value_field_suffix,
         )
+        age_units = age_units or self.age_units
         options.update(**reportables_evaluator_options)
         reference_range_evaluator = self.reference_range_evaluator_cls(
-            reference_range_collection_name, **options
+            reference_range_collection_name, age_units=age_units, **options
         )
         try:
             reference_range_evaluator.validate_reportable_fields()

edc_reportable/management/commands/export_reportables.py

@@ -50,5 +50,5 @@ class Command(BaseCommand):
             help="Export path/folder",
         )
 
-    def handle(self, *args, **options):
+    def handle(self, *args, **options):  # noqa: ARG002
         export_daids_grading(path=options["path"])

edc_reportable/models/grading_exception.py

@@ -4,7 +4,6 @@ from edc_model.models import BaseUuidModel
 
 
 class GradingException(BaseUuidModel):
-
     reference_range_collection = models.ForeignKey(
         "edc_reportable.ReferenceRangeCollection", on_delete=models.PROTECT
     )
@@ -17,11 +16,7 @@ class GradingException(BaseUuidModel):
     grade4 = models.BooleanField(default=False)
 
     def grades(self) -> list[int]:
-        grades = []
-        for i in range(1, 5):
-            if getattr(self, f"grade{i}"):
-                grades.append(i)
-        return grades
+        return [i for i in range(1, 5) if getattr(self, f"grade{i}")]
 
     class Meta(BaseUuidModel.Meta):
         verbose_name = "Grading Exception"

edc_reportable/models/normal_data.py

@@ -22,8 +22,8 @@ class NormalData(ReferenceModelMixin, BaseUuidModel):
     def value_in_normal_range_or_raise(
         self,
         value: int | float,
-        dob: date = None,
-        report_datetime: datetime = None,
+        dob: date,
+        report_datetime: datetime,
         age_units: str | None = None,
     ) -> bool:
         """Raises a ValueBoundryError exception if condition not met.
@@ -45,7 +45,7 @@ class NormalData(ReferenceModelMixin, BaseUuidModel):
         value_condition_str = self.get_eval_phrase(value)
         if not re.match(pattern, value_condition_str):
             raise ValueError(f"Invalid condition string. Got {value_condition_str}.")
-        if not eval(value_condition_str):  # nosec B307
+        if not eval(value_condition_str):  # nosec B307  # noqa: S307
             raise ValueBoundryError(
                 f"{self.label}: {value_condition_str}{self.units} [{self.gender}]"
             )

edc_reportable/models/reference_range_collection.py

@@ -38,11 +38,7 @@ class ReferenceRangeCollection(BaseUuidModel):
 
         See also model GradingException.
         """
-        grades = []
-        for i in range(1, 5):
-            if getattr(self, f"grade{i}"):
-                grades.append(i)
-        return grades
+        return [i for i in range(1, 5) if getattr(self, f"grade{i}")]
 
     def reportable_grades(self, label: str) -> list[int]:
         if not label:
@@ -96,7 +92,6 @@ class ReferenceRangeCollection(BaseUuidModel):
         gender: str | None = None,
         dob: date | None = None,
         age_units: str | None = None,
-        site: Site | None = None,
     ) -> tuple[bool, NormalData]:
         if subject_identifier:
             rs_obj = RegisteredSubject.objects.get(subject_identifier=subject_identifier)