clinicedc 2.0.24__py3-none-any.whl → 2.0.26__py3-none-any.whl

edc_randomization/randomization_list_verifier.py

@@ -6,17 +6,12 @@ from django.core.exceptions import ObjectDoesNotExist
 from django.core.management.color import color_style
 from django.db.utils import OperationalError, ProgrammingError
 
+from .exceptions import InvalidAssignment, RandomizationListError
 from .site_randomizers import site_randomizers
 
 style = color_style()
 
-
-class RandomizationListError(Exception):
-    pass
-
-
-class InvalidAssignment(Exception):
-    pass
+__all__ = ["RandomizationListVerifier"]
 
 
 class RandomizationListVerifier:
@@ -25,12 +20,12 @@ class RandomizationListVerifier:
     def __init__(
         self,
         randomizer_name=None,
-        randomizationlist_path: Path | str = None,
+        randomizationlist_path: Path | str | None = None,
         randomizer_model_cls=None,
         assignment_map=None,
         fieldnames=None,
         sid_count_for_tests=None,
-        required_csv_fieldnames: list[str] | None = None,
+        required_csv_fieldnames: tuple[str, ...] | None = None,
         **kwargs,  # noqa: ARG002
     ):
         self.count: int = 0
@@ -78,28 +73,31 @@ 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)
             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", ""))
+                all_rows, key=lambda row: (row.get("site_name", ""), int(row.get("sid", 0)))
             )
 
-        for index, row in enumerate(sorted_rows, start=1):
-            sys.stdout.write(f"Index: {index}, SID: {row.get('sid')}, Row: {row}\n")
-            message = self.inspect_row(index - 1, row)
-            if message:
-                break
-            if self.sid_count_for_tests and index == self.sid_count_for_tests:
-                break
-
-        if not message and self.count != index:
+        # compare sorted CSV length with DB
+        if len(sorted_rows) != self.randomizer_model_cls.objects.all().count():
+            expected_cnt = len(sorted_rows)
+            actual_cnt = self.randomizer_model_cls.objects.all().count()
             message = (
-                f"Randomization list count is off. Expected {index} (CSV). "
-                f"Got {self.count} (model_cls). See file "
+                f"Randomization list count is off. Expected {expected_cnt} (CSV). "
+                f"Got {actual_cnt} (model_cls). See file "
                 f"{self.randomizationlist_path}. "
                 f"Resolve this issue before using the system."
             )
+        if not message:
+            # compare sorted CSV data to DB
+            for index, row in enumerate(sorted_rows, start=1):
+                sys.stdout.write(f"Index: {index}, SID: {row.get('sid')}, Row: {row}\n")
+                message = self.inspect_row(index - 1, row)
+                if message:
+                    break
         return message
 
     def inspect_row(self, index: int, row) -> str | None:

edc_randomization/randomizer.py

@@ -8,7 +8,7 @@ from typing import TYPE_CHECKING, Any
 
 from django.apps import apps as django_apps
 from django.conf import settings
-from django.core.exceptions import ObjectDoesNotExist, ValidationError
+from django.core.exceptions import ObjectDoesNotExist
 from django.db.models import Q
 
 from edc_registration.utils import get_registered_subject_model_cls
@@ -18,38 +18,22 @@ from .constants import (
     DEFAULT_ASSIGNMENT_MAP,
     RANDOMIZED,
 )
-from .randomization_list_importer import (
+from .exceptions import (
+    AllocationError,
+    AlreadyRandomized,
+    InvalidAssignmentDescriptionMap,
+    RandomizationError,
     RandomizationListAlreadyImported,
-    RandomizationListImporter,
+    RandomizationListFileNotFound,
 )
+from .randomization_list_importer import RandomizationListImporter
 from .utils import get_randomization_list_path
 
 if TYPE_CHECKING:
     from edc_registration.models import RegisteredSubject
 
 
-class InvalidAssignmentDescriptionMap(Exception):  # noqa: N818
-    pass
-
-
-class RandomizationListFileNotFound(Exception):  # noqa: N818
-    pass
-
-
-class RandomizationListNotLoaded(Exception):  # noqa: N818
-    pass
-
-
-class RandomizationError(Exception):
-    pass
-
-
-class AlreadyRandomized(ValidationError):  # noqa: N818
-    pass
-
-
-class AllocationError(Exception):
-    pass
+__all__ = ["Randomizer"]
 
 
 class Randomizer:
@@ -61,8 +45,8 @@ class Randomizer:
     `site_randomizer` by default. To prevent registration set
     settings.EDC_RANDOMIZATION_REGISTER_DEFAULT_RANDOMIZER=False.
 
-    assignment_map: {<assignment:str)>: <allocation:int>, ...}
-    assignment_description_map: {<assignment:str)>: <description:str>, ...}
+    assignment_map: {<assignment:str>: <allocation:int>, ...}
+    assignment_description_map: {<assignment:str>: <description:str>, ...}
 
 
     Usage:
@@ -101,7 +85,7 @@ class Randomizer:
     )
     filename: str = "randomization_list.csv"
     randomizationlist_folder: Path | str = get_randomization_list_path()
-    extra_csv_fieldnames: list[str] | None = None
+    extra_csv_fieldnames: tuple[str] | None = None
     trial_is_blinded: bool = True
     importer_cls: Any = RandomizationListImporter
     apps = None  # if not using django_apps

edc_randomization/site_randomizers.py

@@ -7,26 +7,12 @@ from typing import TYPE_CHECKING
 from django.apps import apps as django_apps
 from django.utils.module_loading import import_module, module_has_submodule
 
+from .exceptions import AlreadyRegistered, NotRegistered, RegistryNotLoaded
+
 if TYPE_CHECKING:
     from edc_randomization.randomizer import Randomizer
 
 
-class RegistryNotLoaded(Exception):
-    pass
-
-
-class NotRegistered(Exception):
-    pass
-
-
-class AlreadyRegistered(Exception):
-    pass
-
-
-class SiteRandomizerError(Exception):
-    pass
-
-
 class SiteRandomizers:
     """Main controller of :class:`SiteRandomizers` objects.
 

edc_randomization/system_checks.py

@@ -3,7 +3,7 @@ import sys
 from dataclasses import dataclass
 
 from django.conf import settings
-from django.core.checks import Error, Warning
+from django.core.checks import Error, Warning  # noqa: A004
 from django.core.exceptions import ImproperlyConfigured
 from django.core.management import color_style
 

edc_randomization/utils.py

@@ -14,17 +14,10 @@ from django_pandas.io import read_frame
 from edc_pdutils.constants import SYSTEM_COLUMNS
 from edc_sites.site import sites
 
+from .exceptions import RandomizationListExporterError, SubjectNotRandomization
 from .site_randomizers import site_randomizers
 
 
-class RandomizationListExporterError(Exception):
-    pass
-
-
-class SubjectNotRandomization(Exception):  # noqa: N818
-    pass
-
-
 def get_randomization_list_path() -> Path:
     return Path(
         getattr(
@@ -149,7 +142,7 @@ def generate_fake_randomization_list(
 
 def export_randomization_list(
     randomizer_name: str, path: str | None = None, username: str | None = None
-):
+) -> Path:
     randomizer_cls = site_randomizers.get(randomizer_name)
 
     try:
@@ -184,4 +177,4 @@ def export_randomization_list(
     )
     df.to_csv(**opts)
     sys.stdout.write(f"{filename!s}\n")
-    return filename
+    return Path(filename)

edc_review_dashboard/middleware.py

@@ -1,3 +1,5 @@
+import contextlib
+
 from django.conf import settings
 
 from .dashboard_templates import dashboard_templates
@@ -10,12 +12,10 @@ class DashboardMiddleware:
     def __call__(self, request):
         return self.get_response(request)
 
-    def process_view(self, request, *args) -> None:
+    def process_view(self, request, *args) -> None:  # noqa: ARG002
         template_data = dashboard_templates
-        try:
+        with contextlib.suppress(AttributeError):
             template_data.update(settings.REVIEW_DASHBOARD_BASE_TEMPLATES)
-        except AttributeError:
-            pass
         request.template_data.update(**template_data)
 
     def process_template_response(self, request, response):

edc_review_dashboard/views/subject_review_listboard_view.py

@@ -49,15 +49,15 @@ class SubjectReviewListboardView(
     listboard_view_permission_codename = "edc_review_dashboard.view_subject_review_listboard"
 
     navbar_selected_item = "subject_review"
-    ordering = ["subject_identifier", "visit_code", "visit_code_sequence"]
+    ordering = ("subject_identifier", "visit_code", "visit_code_sequence")
     paginate_by = 25
     search_form_url = "subject_review_listboard_url"
-    search_fields = [
+    search_fields = (
         "subject_identifier",
         "visit_code",
         "user_created",
         "user_modified",
-    ]
+    )
 
     #  attr to call SubjectReviewListboardView.urls in urls.py
     urlconfig_getattr = "review_listboard_urls"

edc_screening/age_evaluator.py

@@ -25,7 +25,7 @@ class AgeEvaluator(ReportableAgeEvaluator):
             self.reasons_ineligible = "Age unknown"
         return eligible
 
-    def in_bounds_or_raise(self, age: int = None, **kwargs):
+    def in_bounds_or_raise(self, age: int | None = None, **kwargs):  # noqa: ARG002
         self.reasons_ineligible = ""
         dob = localtime(timezone.now() - relativedelta(years=age)).date()
         age_units = "years"

edc_screening/eligibility.py

@@ -18,14 +18,14 @@ class Eligibility:
     # default to eligible if >=18
     age_evaluator = AgeEvaluator(age_lower=18, age_lower_inclusive=True)
 
-    custom_reasons_dict: dict = {}
+    custom_reasons_dict: dict = {}  # noqa: RUF012
 
     def __init__(
         self,
-        age: int = None,
-        gender: str = None,
-        pregnant: bool = None,
-        breast_feeding: bool = None,
+        age: int | None = None,
+        gender: str | None = None,
+        pregnant: bool | None = None,
+        breast_feeding: bool | None = None,
         **additional_criteria,
     ) -> None:
         self.criteria = dict(**additional_criteria)

edc_screening/exceptions.py

@@ -17,15 +17,15 @@ class ScreeningEligibilityCleanedDataKeyError(Exception):
     pass
 
 
-class ScreeningEligibilityInvalidCombination(Exception):
+class ScreeningEligibilityInvalidCombination(Exception):  # noqa: N818
     pass
 
 
-class RequiredFieldValueMissing(Exception):
+class RequiredFieldValueMissing(Exception):  # noqa: N818
     pass
 
 
-class InvalidScreeningIdentifierFormat(Exception):
+class InvalidScreeningIdentifierFormat(Exception):  # noqa: N818
     def __init__(self, *args, **kwargs):
         self.code = INVALID_SCREENING_IDENTIFIER
         super().__init__(*args, **kwargs)

edc_screening/gender_evaluator.py

@@ -2,7 +2,7 @@ from edc_constants.constants import FEMALE, MALE
 
 
 class GenderEvaluator:
-    eligible_gender = [MALE, FEMALE]
+    eligible_gender = (MALE, FEMALE)
 
     def __init__(self, gender=None, **kwargs) -> None:  # noqa
         self.eligible = False

edc_screening/modelform_mixins.py

@@ -27,7 +27,7 @@ class AlreadyConsentedFormMixin:
             raise forms.ValidationError(self.already_consented_validation_message(url))
         return cleaned_data
 
-    def already_consented_validation_url(self, cleaned_data: dict | None = None) -> str:
+    def already_consented_validation_url(self, cleaned_data: dict | None = None) -> str:  # noqa: ARG002
         url_name = url_names.get("subject_dashboard_url")
         return reverse(
             url_name,

edc_screening/screening_eligibility.py

@@ -2,7 +2,6 @@ from __future__ import annotations
 
 from typing import TYPE_CHECKING
 
-from django.utils.html import format_html
 from django.utils.safestring import mark_safe
 
 from edc_constants.constants import NO, PENDING, TBD, YES
@@ -33,7 +32,7 @@ class ScreeningEligibility:
     eligible_fld_name: str = "eligible"
     eligible_value_default: str = TBD
     default_display_label = TBD
-    eligible_values_list: list = [YES, NO, TBD]
+    eligible_values_list: list = (YES, NO, TBD)
     ineligible_display_label: str = "INELIGIBLE"
     is_eligible_value: str = YES
     is_ineligible_value: str = NO
@@ -44,9 +43,9 @@ class ScreeningEligibility:
     def __init__(
         self,
         model_obj: SubjectScreeningModel | EligibilityModelMixin = None,
-        cleaned_data: dict = None,
+        cleaned_data: dict | None = None,
         eligible_value_default: str | None = None,
-        eligible_values_list: list | None = None,
+        eligible_values_list: tuple[str, ...] | None = None,
         is_eligible_value: str | None = None,
         is_ineligible_value: str | None = None,
         eligible_display_label: str | None = None,
@@ -126,7 +125,7 @@ class ScreeningEligibility:
     @property
     def is_eligible(self) -> bool:
         """Returns True if eligible else False"""
-        return True if self.eligible == self.is_eligible_value else False
+        return self.eligible == self.is_eligible_value
 
     def _assess_eligibility(self) -> None:
         self.set_fld_attrs_on_self()
@@ -136,30 +135,29 @@ class ScreeningEligibility:
             self.reasons_ineligible.update(**missing_data)
             self.eligible = self.eligible_value_default  # probably TBD
         for fldattr, fc in self.get_required_fields().items():
-            if fldattr not in missing_data:
-                if fc and fc.value:
-                    msg = fc.msg if fc.msg else fldattr.title().replace("_", " ")
-                    is_callable = False
-                    try:
-                        value = fc.value(getattr(self, fldattr))
-                    except TypeError:
-                        value = fc.value
-                    else:
-                        is_callable = True
-                    if (
-                        (isinstance(value, str) and getattr(self, fldattr) != value)
-                        or (
-                            isinstance(value, (list, tuple))
-                            and getattr(self, fldattr) not in value
-                        )
-                        or (
-                            isinstance(value, range)
-                            and not (min(value) <= getattr(self, fldattr) <= max(value))
-                        )
-                        or (is_callable and value is False)
-                    ):
-                        self.reasons_ineligible.update({fldattr: msg})
-                        self.eligible = self.is_ineligible_value  # probably NO
+            if fldattr not in missing_data and fc and fc.value:
+                msg = fc.msg if fc.msg else fldattr.title().replace("_", " ")
+                is_callable = False
+                try:
+                    value = fc.value(getattr(self, fldattr))
+                except TypeError:
+                    value = fc.value
+                else:
+                    is_callable = True
+                if (
+                    (isinstance(value, str) and getattr(self, fldattr) != value)
+                    or (
+                        isinstance(value, (list, tuple))
+                        and getattr(self, fldattr) not in value
+                    )
+                    or (
+                        isinstance(value, range)
+                        and not (min(value) <= getattr(self, fldattr) <= max(value))
+                    )
+                    or (is_callable and value is False)
+                ):
+                    self.reasons_ineligible.update({fldattr: msg})
+                    self.eligible = self.is_ineligible_value  # probably NO
         if self.is_eligible:
             if self.is_eligible and not self.get_required_fields():
                 self.eligible = self.eligible_value_default
@@ -194,7 +192,7 @@ class ScreeningEligibility:
                     "does not exist on class. "
                     f"See {self.__class__.__name__}. "
                     f"Got {e}"
-                )
+                ) from e
             if self.model_obj:
                 try:
                     value = (
@@ -207,7 +205,7 @@ class ScreeningEligibility:
                         "Attribute does not exist on model. "
                         f"See {self.model_obj.__class__.__name__}. "
                         f"Got {e}"
-                    )
+                    ) from e
             else:
                 value = self.cleaned_data.get(fldattr)
             setattr(self, fldattr, value)
@@ -230,10 +228,7 @@ class ScreeningEligibility:
 
     def formatted_reasons_ineligible(self) -> str:
         str_values = "<BR>".join([x for x in self.reasons_ineligible.values() if x])
-        return format_html(
-            "{}",
-            mark_safe(str_values),  # nosec B703 B308
-        )
+        return mark_safe(str_values)  # noqa: S308
 
     @property
     def display_label(self) -> str:

edc_screening/utils.py

@@ -40,10 +40,8 @@ def format_reasons_ineligible(*str_values: str | None, delimiter: str | None = N
     str_values = str_values or []
     str_values = tuple(x for x in str_values if x)
     if str_values:
-        reasons = format_html(
-            "{}",
-            mark_safe(delimiter.join(str_values)),  # noqa: S308
-        )
+        formatted_string = delimiter.join(str_values)
+        reasons = mark_safe(formatted_string)  # noqa: S308
     return reasons
 
 
@@ -120,15 +118,15 @@ def is_eligible_or_raise(
             if url and url_name.endswith("changelist"):
                 url = f"{url}?q={subject_screening.screening_identifier}"
         if not url:
-            msg = format_html(
-                "{}",
+            safe_string = mark_safe(  # noqa: S308
                 "Not allowed. Subject is not eligible. "
-                f"Got {subject_screening.screening_identifier}",
+                f"Got {subject_screening.screening_identifier}.",
             )
         else:
-            msg = format_html(
-                'Not allowed. Subject is not eligible. See subject <A href="{}">{}</A>',
-                mark_safe(url),  # noqa: S308
-                subject_screening.screening_identifier,
+            safe_string = format_html(
+                "Not allowed. Subject is not eligible. See subject "
+                '<A href="{url}">{screening_identifier}</A>',
+                url=url,
+                screening_identifier=subject_screening.screening_identifier,
             )
-        raise forms.ValidationError(msg)
+        raise forms.ValidationError(safe_string)

edc_sites/admin/list_filters.py

@@ -17,10 +17,10 @@ class SiteListFilter(SimpleListFilter):
         else:
             site_ids = sites.get_site_ids_for_user(request=request)
         for site in Site.objects.filter(id__in=site_ids).order_by("id"):
-            names.append((site.id, f"{site.id} {sites.get(site.id).description}"))
+            names.append((site.id, f"{site.id} {sites.get(site.id).description}"))  # noqa: PERF401
         return tuple(names)
 
-    def queryset(self, request, queryset):
+    def queryset(self, request, queryset):  # noqa: ARG002
         if self.value() and self.value() != "none":
             queryset = queryset.filter(site__id=self.value())
         return queryset

edc_sites/admin/site_model_admin_mixin.py

@@ -46,7 +46,7 @@ class SiteModelAdminMixin:
             ]
         return sites.get_view_only_site_ids_for_user(request=request)
 
-    def has_viewallsites_permission(self, request, obj=None) -> bool:
+    def has_viewallsites_permission(self, request, obj=None) -> bool:  # noqa: ARG002
         """Checks if the user has the EDC custom codename
         "viewallsites" for this model.
 
@@ -54,7 +54,7 @@ class SiteModelAdminMixin:
         """
         opts = self.opts
         codename_allsites = get_permission_codename("viewallsites", opts)
-        return request.user.has_perm("%s.%s" % (opts.app_label, codename_allsites))
+        return request.user.has_perm(f"{opts.app_label}.{codename_allsites}")
 
     @admin.display(description="Site", ordering="site__id")
     def site_code(self, obj=None):
@@ -75,7 +75,7 @@ class SiteModelAdminMixin:
         to mulitple sites.
         """
         list_filter = super().get_list_filter(request)
-        list_filter = [x for x in list_filter if x != "site" and x != SiteListFilter]
+        list_filter = [x for x in list_filter if x not in ("site", SiteListFilter)]
         if self.user_may_view_other_sites(request) or self.has_viewallsites_permission(
             request
         ):
@@ -95,25 +95,25 @@ class SiteModelAdminMixin:
             or self.has_viewallsites_permission(request)
         ) and "site" not in list_display:
             list_display = tuple(list_display)
-            list_display = list_display[:pos] + (self.site_code,) + list_display[pos:]
+            list_display = list_display[:pos], self.site_code, list_display[pos:]
         elif "site" in list_display:
             list_display = tuple(
                 [x for x in list_display if x not in ["site", self.site_code]]
             )
-            list_display = list_display[:pos] + (self.site_code,) + list_display[pos:]
+            list_display = list_display[:pos], self.site_code, list_display[pos:]
         return list_display
 
     def get_queryset(self, request) -> QuerySet:
         """Limit modeladmin queryset for the current site only"""
         qs = super().get_queryset(request)
-        site_ids = [request.site.id] + self.get_view_only_site_ids_for_user(request=request)
+        site_ids = (request.site.id, *self.get_view_only_site_ids_for_user(request=request))
         try:
             qs = qs.select_related("site").filter(site_id__in=site_ids)
-        except FieldError:
+        except FieldError as e:
             raise SiteModeAdminMixinError(
                 f"Model missing field `site`. Model `{self.model}`. Did you mean to use "
                 f"the SiteModelAdminMixin? See `{self}`."
-            )
+            ) from e
         return qs
 
     def get_form(self, request, obj=None, change=False, **kwargs):

edc_sites/exceptions.py

@@ -6,5 +6,5 @@ class InvalidSiteForSubjectError(Exception):
     pass
 
 
-class InvalidSiteForUser(Exception):
+class InvalidSiteForUser(Exception):  # noqa: N818
     pass

edc_sites/forms.py

@@ -1 +1,3 @@
-from .modelform_mixins import SiteModelFormMixin  # noqa
+from .modelform_mixins import SiteModelFormMixin
+
+__all__ = ["SiteModelFormMixin"]

edc_sites/management/commands/sync_sites.py

@@ -4,6 +4,8 @@ import sys
 from django.conf import settings
 from django.core.management.base import BaseCommand
 from django.core.management.color import color_style
+from multisite.models import Alias
+from multisite.utils import create_or_sync_canonical_from_all_sites
 
 from edc_sites.site import sites as site_sites
 from edc_sites.utils import add_or_update_django_sites
@@ -15,7 +17,6 @@ class Command(BaseCommand):
     help = "Add / Update django Site model after changes to edc_sites"
 
     def add_arguments(self, parser):
-
         parser.add_argument(
             "--ping-hosts",
             default=False,
@@ -32,26 +33,19 @@ class Command(BaseCommand):
             help="Suggest ALLOWED_HOSTS",
         )
 
-    def handle(self, *args, **options) -> None:
+    def handle(self, *args, **options) -> None:  # noqa: ARG002
         sys.stdout.write("\n\n")
         sys.stdout.write(" Edc Sites : Adding / Updating sites ...     \n")
         add_or_update_django_sites(verbose=True)
-        if (
-            "multisite" in settings.INSTALLED_APPS
-            or "multisite.apps.AppConfig" in settings.INSTALLED_APPS
-        ):
-            from multisite.models import Alias
-            from multisite.utils import create_or_sync_canonical_from_all_sites
-
-            sys.stdout.write("\n Multisite. \n")
-            create_or_sync_canonical_from_all_sites(verbose=True)
+        sys.stdout.write("\n Multisite. \n")
+        create_or_sync_canonical_from_all_sites(verbose=True)
 
-            sys.stdout.write("    multisite.Alias \n")
-            for obj in Alias.objects.all():
-                sys.stdout.write(
-                    f"      - Site model: {obj.site.id}: {obj.domain} "
-                    f"is_canonical={obj.is_canonical}.\n"
-                )
+        sys.stdout.write("    multisite.Alias \n")
+        for obj in Alias.objects.all():
+            sys.stdout.write(
+                f"      - Site model: {obj.site.id}: {obj.domain} "
+                f"is_canonical={obj.is_canonical}.\n"
+            )
         arg = [arg for arg in sys.argv if arg.startswith("--settings")]
         sys.stdout.write(f"\n Settings: reading from {arg}")
         sys.stdout.write("\n\n Current value of settings.ALLOWED_HOSTS\n")

edc_sites/models/site_profile.py

@@ -5,17 +5,19 @@ import json
 from django.contrib.sites.models import Site
 from django.db import models
 
+from edc_constants.constants import NULL_STRING
+
 
 class SiteProfile(models.Model):
     id = models.BigAutoField(primary_key=True)
 
-    country = models.CharField(max_length=250, default="")
+    country = models.CharField(max_length=250, default=NULL_STRING)
 
-    country_code = models.CharField(max_length=15, default="")
+    country_code = models.CharField(max_length=15, default=NULL_STRING)
 
-    languages = models.TextField(default="")
+    languages = models.TextField(default=NULL_STRING)
 
-    title = models.CharField(max_length=250, default="")
+    title = models.CharField(max_length=250, default=NULL_STRING)
 
     site = models.OneToOneField(Site, on_delete=models.PROTECT)