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

edc_registration/auths.py

@@ -4,27 +4,32 @@ from edc_auth.constants import PII, PII_VIEW
 from edc_auth.site_auths import site_auths
 from edc_export.constants import EXPORT
 
-if django_apps.is_installed("edc_export"):
-    site_auths.update_group("edc_registration.export_registeredsubject", name=EXPORT)
-site_auths.update_group(
-    "edc_registration.display_dob",
-    "edc_registration.display_firstname",
-    "edc_registration.display_identity",
-    "edc_registration.display_initials",
-    "edc_registration.display_lastname",
-    "edc_registration.view_historicalregisteredsubject",
-    "edc_registration.view_registeredsubject",
-    name=PII,
-)
 
-site_auths.update_group(
-    "edc_registration.display_dob",
-    "edc_registration.display_firstname",
-    "edc_registration.display_identity",
-    "edc_registration.display_initials",
-    "edc_registration.display_lastname",
-    "edc_registration.view_historicalregisteredsubject",
-    "edc_registration.view_registeredsubject",
-    name=PII_VIEW,
-)
-site_auths.add_pii_model("edc_registration.registeredsubject")
+def update_site_auths() -> None:
+    if django_apps.is_installed("edc_export"):
+        site_auths.update_group("edc_registration.export_registeredsubject", name=EXPORT)
+    site_auths.update_group(
+        "edc_registration.display_dob",
+        "edc_registration.display_firstname",
+        "edc_registration.display_identity",
+        "edc_registration.display_initials",
+        "edc_registration.display_lastname",
+        "edc_registration.view_historicalregisteredsubject",
+        "edc_registration.view_registeredsubject",
+        name=PII,
+    )
+
+    site_auths.update_group(
+        "edc_registration.display_dob",
+        "edc_registration.display_firstname",
+        "edc_registration.display_identity",
+        "edc_registration.display_initials",
+        "edc_registration.display_lastname",
+        "edc_registration.view_historicalregisteredsubject",
+        "edc_registration.view_registeredsubject",
+        name=PII_VIEW,
+    )
+    site_auths.add_pii_model("edc_registration.registeredsubject")
+
+
+update_site_auths()

edc_registration/model_mixins/updates_or_creates_registered_subject_model_mixin.py

@@ -5,7 +5,9 @@ from typing import TYPE_CHECKING
 
 from django.core.exceptions import ObjectDoesNotExist
 from django.db import models
+from django.db.models import CharField, TextField
 
+from edc_constants.constants import NULL_STRING
 from edc_model import DEFAULT_BASE_FIELDS
 
 from ..utils import get_registered_subject_model_cls
@@ -99,13 +101,20 @@ class UpdatesOrCreatesRegistrationModelMixin(models.Model):
         """
         registration_options = {}
         rs = self.registration_model()
-        for k, v in self.__dict__.items():
-            if k not in DEFAULT_BASE_FIELDS + ["_state"]:
+        for fname, value in self.__dict__.items():
+            if fname not in (*DEFAULT_BASE_FIELDS, "_state"):
                 try:
-                    getattr(rs, k)
-                    registration_options.update({k: v})
+                    getattr(rs, fname)
                 except AttributeError:
                     pass
+                else:
+                    value = (  # noqa: PLW2901
+                        NULL_STRING
+                        if value is None
+                        and isinstance(rs._meta.get_field(fname), (CharField, TextField))
+                        else value
+                    )
+                    registration_options.update({fname: value})
         registration_identifier = registration_options.get("registration_identifier")
         if registration_identifier:
             registration_options["registration_identifier"] = self.to_string(

edc_registration/models/registered_subject.py

@@ -143,7 +143,7 @@ class RegisteredSubject(UniqueSubjectIdentifierModelMixin, SiteModelMixin, BaseU
 
     def save(self, *args, **kwargs):
         if self.identity:
-            self.additional_key = None
+            self.additional_key = ""
         self.set_uuid_as_subject_identifier_if_none()
         self.raise_on_duplicate("subject_identifier")
         self.raise_on_duplicate("identity")

edc_reportable/utils/get_reference_range_collection.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import contextlib
 from typing import TYPE_CHECKING
 
 from django.core.exceptions import ObjectDoesNotExist
@@ -21,10 +22,8 @@ def get_reference_range_collection(obj) -> ReferenceRangeCollection:
             name = obj.requisition.panel_object.reference_range_collection_name
         except AttributeError:
             name = obj.panel_object.reference_range_collection_name
-        try:
+        with contextlib.suppress(ObjectDoesNotExist):
             reference_range_collection = reference_range_colllection_model_cls().objects.get(
                 name=name
             )
-        except ObjectDoesNotExist:
-            pass
     return reference_range_collection

edc_reportable/utils/load_data.py

@@ -60,7 +60,7 @@ def load_reference_ranges(
     collection_name: str,
     normal_data: dict[str, list[Formula]],
     grading_data: dict[str, list[Formula]],
-    reportable_grades: list[int],
+    reportable_grades: list[int] | None = None,
     reportable_grades_exceptions: dict[str, list[int]] | None = None,
     keep_existing: bool | None = None,
     create_missing_normal: bool | None = None,

edc_review_dashboard/auths.py

@@ -10,23 +10,28 @@ from edc_auth.utils import remove_default_model_permissions_from_edc_permissions
 
 REVIEW = "REVIEW"
 
-site_auths.add_post_update_func(
-    "edc_review_dashboard", remove_default_model_permissions_from_edc_permissions
-)
 
-site_auths.add_custom_permissions_tuples(
-    model="edc_review_dashboard.edcpermissions",
-    codename_tuples=[
-        (
-            "edc_review_dashboard.view_subject_review_listboard",
-            "Can access subject review listboard",
-        )
-    ],
-)
-site_auths.add_group("edc_review_dashboard.view_subject_review_listboard", name=REVIEW)
+def update_site_auths():
+    site_auths.add_post_update_func(
+        "edc_review_dashboard", remove_default_model_permissions_from_edc_permissions
+    )
+
+    site_auths.add_custom_permissions_tuples(
+        model="edc_review_dashboard.edcpermissions",
+        codename_tuples=[
+            (
+                "edc_review_dashboard.view_subject_review_listboard",
+                "Can access subject review listboard",
+            )
+        ],
+    )
+    site_auths.add_group("edc_review_dashboard.view_subject_review_listboard", name=REVIEW)
+
+    site_auths.update_role(REVIEW, name=AUDITOR_ROLE)
+    site_auths.update_role(REVIEW, name=TMG_ROLE)
+    site_auths.update_role(REVIEW, name=CLINICIAN_ROLE)
+    site_auths.update_role(REVIEW, name=CLINICIAN_SUPER_ROLE)
+    site_auths.update_role(REVIEW, name=NURSE_ROLE)
+
 
-site_auths.update_role(REVIEW, name=AUDITOR_ROLE)
-site_auths.update_role(REVIEW, name=TMG_ROLE)
-site_auths.update_role(REVIEW, name=CLINICIAN_ROLE)
-site_auths.update_role(REVIEW, name=CLINICIAN_SUPER_ROLE)
-site_auths.update_role(REVIEW, name=NURSE_ROLE)
+update_site_auths()

edc_screening/age_evaluator.py

@@ -8,11 +8,11 @@ from edc_reportable.exceptions import ValueBoundryError
 
 class AgeEvaluator(ReportableAgeEvaluator):
     def __init__(self, **kwargs) -> None:
-        self.reasons_ineligible: str | None = None
+        self.reasons_ineligible: str = ""
         super().__init__(**kwargs)
 
     def eligible(self, age: int | None = None) -> bool:
-        self.reasons_ineligible = None
+        self.reasons_ineligible = ""
         eligible = False
         if age:
             try:
@@ -26,7 +26,7 @@ class AgeEvaluator(ReportableAgeEvaluator):
         return eligible
 
     def in_bounds_or_raise(self, age: int = None, **kwargs):
-        self.reasons_ineligible = None
+        self.reasons_ineligible = ""
         dob = localtime(timezone.now() - relativedelta(years=age)).date()
         age_units = "years"
         report_datetime = localtime(timezone.now())

edc_screening/auths.py

@@ -9,38 +9,43 @@ from edc_auth.utils import remove_default_model_permissions_from_edc_permissions
 
 from .auth_objects import SCREENING, SCREENING_ROLE, SCREENING_SUPER, SCREENING_VIEW
 
-site_auths.add_post_update_func(
-    "edc_screening", remove_default_model_permissions_from_edc_permissions
-)
 
-site_auths.add_custom_permissions_tuples(
-    model="edc_screening.edcpermissions",
-    codename_tuples=(
-        ("edc_screening.view_screening_listboard", "Can access Screening listboard"),
-        ("edc_screening.nav_screening_section", "Can access screening section"),
-    ),
-)
+def update_site_auths() -> None:
+    site_auths.add_post_update_func(
+        "edc_screening", remove_default_model_permissions_from_edc_permissions
+    )
 
-site_auths.add_group(
-    "edc_screening.view_screening_listboard",
-    "edc_screening.nav_screening_section",
-    name=SCREENING,
-)
+    site_auths.add_custom_permissions_tuples(
+        model="edc_screening.edcpermissions",
+        codename_tuples=(
+            ("edc_screening.view_screening_listboard", "Can access Screening listboard"),
+            ("edc_screening.nav_screening_section", "Can access screening section"),
+        ),
+    )
 
-site_auths.add_group(
-    "edc_screening.view_screening_listboard",
-    "edc_screening.nav_screening_section",
-    name=SCREENING_SUPER,
-)
+    site_auths.add_group(
+        "edc_screening.view_screening_listboard",
+        "edc_screening.nav_screening_section",
+        name=SCREENING,
+    )
+
+    site_auths.add_group(
+        "edc_screening.view_screening_listboard",
+        "edc_screening.nav_screening_section",
+        name=SCREENING_SUPER,
+    )
+
+    site_auths.add_group(
+        "edc_screening.view_screening_listboard",
+        "edc_screening.nav_screening_section",
+        name=SCREENING_VIEW,
+    )
+
+    site_auths.add_role(SCREENING, name=SCREENING_ROLE)
+    site_auths.update_role(SCREENING, name=CLINICIAN_ROLE)
+    site_auths.update_role(SCREENING, name=NURSE_ROLE)
+    site_auths.update_role(SCREENING_SUPER, name=CLINICIAN_SUPER_ROLE)
+    site_auths.update_role(SCREENING_VIEW, name=AUDITOR_ROLE)
 
-site_auths.add_group(
-    "edc_screening.view_screening_listboard",
-    "edc_screening.nav_screening_section",
-    name=SCREENING_VIEW,
-)
 
-site_auths.add_role(SCREENING, name=SCREENING_ROLE)
-site_auths.update_role(SCREENING, name=CLINICIAN_ROLE)
-site_auths.update_role(SCREENING, name=NURSE_ROLE)
-site_auths.update_role(SCREENING_SUPER, name=CLINICIAN_SUPER_ROLE)
-site_auths.update_role(SCREENING_VIEW, name=AUDITOR_ROLE)
+update_site_auths()

edc_screening/eligibility.py

@@ -45,7 +45,7 @@ class Eligibility:
         self.eligible = all([v for v in self.criteria.values()])
 
         if self.eligible:
-            self.reasons_ineligible = None
+            self.reasons_ineligible = ""
         else:
             self.reasons_ineligible = {k: v for k, v in self.criteria.items() if not v}
             for k, v in self.criteria.items():

edc_screening/gender_evaluator.py

@@ -6,7 +6,7 @@ class GenderEvaluator:
 
     def __init__(self, gender=None, **kwargs) -> None:  # noqa
         self.eligible = False
-        self.reasons_ineligible = None
+        self.reasons_ineligible = ""
         if gender in self.eligible_gender:
             self.eligible = True
         else:

edc_screening/model_mixins/eligibility_model_mixin.py

@@ -45,8 +45,6 @@ class EligibilityModelMixin(EligibilityFieldsModelMixin, models.Model):
         """
         # if self.eligibility_cls:
         self.eligibility_cls(model_obj=self)
-        # self.eligible = eligibility_obj.is_eligible
-        # self.reasons_ineligible = eligibility_obj.reasons_ineligible
         if not self.id:
             self.screening_identifier = self.identifier_cls().identifier
         if self.eligible:

edc_screening/model_mixins/screening_methods_model_mixin.py

@@ -16,7 +16,7 @@ class ScreeningMethodsModeMixin(models.Model):
 
     @staticmethod
     def get_search_slug_fields():
-        return ["screening_identifier", "subject_identifier", "reference"]
+        return "screening_identifier", "subject_identifier", "reference"
 
     @property
     def estimated_dob(self: SubjectScreeningModelStub) -> date:

edc_screening/screening_eligibility.py

@@ -174,7 +174,7 @@ class ScreeningEligibility:
         setattr(
             self.model_obj,
             self.reasons_ineligible_fld_name,
-            "|".join(self.reasons_ineligible.values()) or None,
+            "|".join(self.reasons_ineligible.values()) or "",
         )
         self.set_eligible_model_field()
         self.set_fld_attrs_on_model()
@@ -229,9 +229,7 @@ class ScreeningEligibility:
         }
 
     def formatted_reasons_ineligible(self) -> str:
-        str_values = "<BR>".join(
-            [x for x in self.reasons_ineligible.values() if x is not None]
-        )
+        str_values = "<BR>".join([x for x in self.reasons_ineligible.values() if x])
         return format_html(
             "{}",
             mark_safe(str_values),  # nosec B703 B308

edc_screening/utils.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import contextlib
 import re
 from typing import TYPE_CHECKING, Any
 
@@ -33,14 +34,15 @@ def get_subject_screening_model_cls() -> Any:
     return django_apps.get_model(get_subject_screening_model())
 
 
-def format_reasons_ineligible(*str_values: str, delimiter=None) -> str:
+def format_reasons_ineligible(*str_values: str | None, delimiter: str | None = None) -> str:
     reasons = None
     delimiter = delimiter or "|"
-    str_values = tuple(x for x in str_values if x is not None)
+    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)),  # nosec B703 B308
+            mark_safe(delimiter.join(str_values)),  # noqa: S308
         )
     return reasons
 
@@ -73,10 +75,10 @@ def get_subject_screening_or_raise(
             )
     except ObjectDoesNotExist as e:
         if is_modelform:
-            raise forms.ValidationError("Not allowed. Screening form not found.")
+            raise forms.ValidationError("Not allowed. Screening form not found.") from e
         raise ObjectDoesNotExist(
             f"{e} screening_identifier={screening_identifier}. Perhaps catch this in the form."
-        )
+        ) from e
     return subject_screening
 
 
@@ -101,10 +103,8 @@ def is_eligible_or_raise(
     )
 
     url_name = url_name or "screening_listboard_url"
-    try:
+    with contextlib.suppress(InvalidDashboardUrlName):
         url_name = url_names.get(url_name)
-    except InvalidDashboardUrlName:
-        pass
 
     if not subject_screening.eligible:
         try:
@@ -128,7 +128,7 @@ def is_eligible_or_raise(
         else:
             msg = format_html(
                 'Not allowed. Subject is not eligible. See subject <A href="{}">{}</A>',
-                mark_safe(url),  # nosec B308 B703
+                mark_safe(url),  # noqa: S308
                 subject_screening.screening_identifier,
             )
         raise forms.ValidationError(msg)

edc_search/generate_slug.py

@@ -0,0 +1,26 @@
+from __future__ import annotations
+
+from django.utils.text import slugify
+from django_crypto_fields.utils import get_encrypted_field_names
+
+SLUG_SEP = "|"
+
+
+def generate_slug(obj, fields) -> str | None:
+    """Returns a slug of the char values of the fields
+    listed on the models get_search_slug_fields() method.
+
+    Excludes any encrypted fields if listed.
+    """
+    slug = None
+    if obj and fields:
+        values = []
+        for field in (f for f in fields if f not in get_encrypted_field_names(obj)):
+            v = obj
+            for f in field.split("."):
+                v = getattr(v, f)
+            if isinstance(v, str):
+                values.append(v[:50])  # truncate value
+        slugs = [slugify(v) for v in list(set(values)) if v]
+        slug = SLUG_SEP.join(slugs)[:250]
+    return slug

edc_search/model_mixins.py

@@ -1,42 +1,31 @@
 from django.db import models
+from tqdm import tqdm
 
-from .updater import SearchSlugUpdater
+from .generate_slug import generate_slug
 
 
 class SearchSlugManager(models.Manager):
-    search_slug_updater_cls = SearchSlugUpdater
-    search_slug_field_name = "slug"
-
     def update_search_slugs(self) -> None:
-        for obj in self.all():
-            updater = self.search_slug_updater_cls(
-                fields=obj.get_search_slug_fields(), model_obj=obj
-            )
-            setattr(obj, self.search_slug_field_name, updater.slug)
-            obj.save_base(update_fields=[self.search_slug_field_name])
+        qs = self.all()
+        for obj in tqdm(qs, total=qs.count()):
+            obj.slug = generate_slug(obj, obj.get_search_slug_fields()) or ""
+            obj.save_base(update_fields=["slug"])
 
 
 class SearchSlugModelMixin(models.Model):
-    search_slug_warning = None
-    search_slug_updater_cls = SearchSlugUpdater
-
-    def get_search_slug_fields(self) -> tuple[str] | None:
-        return None
+    def get_search_slug_fields(self) -> tuple[str, ...]:
+        return ()
 
     slug = models.CharField(
         max_length=250,
         default="",
         editable=False,
         db_index=True,
-        help_text="a field used for quick search",
+        help_text="Hold slug field values for quick search. Excludes encrypted fields",
     )
 
     def save(self, *args, **kwargs):
-        updater = self.search_slug_updater_cls(
-            fields=self.get_search_slug_fields(), model_obj=self
-        )
-        self.search_slug_warning = updater.warning
-        self.slug = updater.slug
+        self.slug = generate_slug(self, self.get_search_slug_fields()) or ""
         super().save(*args, **kwargs)
 
     class Meta:

edc_sites/auths.py

@@ -1,6 +1,11 @@
 from edc_auth.site_auths import site_auths
 from edc_auth.utils import remove_default_model_permissions_from_edc_permissions
 
-site_auths.add_post_update_func(
-    "edc_sites", remove_default_model_permissions_from_edc_permissions
-)
+
+def update_site_auths() -> None:
+    site_auths.add_post_update_func(
+        "edc_sites", remove_default_model_permissions_from_edc_permissions
+    )
+
+
+update_site_auths()

edc_subject_dashboard/auths.py

@@ -7,30 +7,35 @@ from edc_auth.constants import (
 from edc_auth.site_auths import site_auths
 from edc_auth.utils import remove_default_model_permissions_from_edc_permissions
 
-site_auths.add_post_update_func(
-    "edc_subject_dashboard", remove_default_model_permissions_from_edc_permissions
-)
-
 SUBJECT_VIEW = "SUBJECT_VIEW"
 
-site_auths.add_custom_permissions_tuples(
-    model="edc_subject_dashboard.edcpermissions",
-    codename_tuples=(
-        (
-            "edc_subject_dashboard.view_subject_listboard",
-            "Can access subject listboard",
+
+def update_site_auths() -> None:
+    site_auths.add_post_update_func(
+        "edc_subject_dashboard", remove_default_model_permissions_from_edc_permissions
+    )
+
+    site_auths.add_custom_permissions_tuples(
+        model="edc_subject_dashboard.edcpermissions",
+        codename_tuples=(
+            (
+                "edc_subject_dashboard.view_subject_listboard",
+                "Can access subject listboard",
+            ),
+            ("edc_subject_dashboard.nav_subject_section", "Can access nav_subject_section"),
         ),
-        ("edc_subject_dashboard.nav_subject_section", "Can access nav_subject_section"),
-    ),
-)
+    )
+
+    site_auths.add_group(
+        "edc_subject_dashboard.view_subject_listboard",
+        "edc_subject_dashboard.nav_subject_section",
+        name=SUBJECT_VIEW,
+    )
+
+    site_auths.update_role(SUBJECT_VIEW, name=CLINICIAN_ROLE)
+    site_auths.update_role(SUBJECT_VIEW, name=NURSE_ROLE)
+    site_auths.update_role(SUBJECT_VIEW, name=CLINICIAN_SUPER_ROLE)
+    site_auths.update_role(SUBJECT_VIEW, name=AUDITOR_ROLE)
 
-site_auths.add_group(
-    "edc_subject_dashboard.view_subject_listboard",
-    "edc_subject_dashboard.nav_subject_section",
-    name=SUBJECT_VIEW,
-)
 
-site_auths.update_role(SUBJECT_VIEW, name=CLINICIAN_ROLE)
-site_auths.update_role(SUBJECT_VIEW, name=NURSE_ROLE)
-site_auths.update_role(SUBJECT_VIEW, name=CLINICIAN_SUPER_ROLE)
-site_auths.update_role(SUBJECT_VIEW, name=AUDITOR_ROLE)
+update_site_auths()

edc_timepoint/apps.py

@@ -1,7 +1,6 @@
 import sys
 
 from django.apps import AppConfig as DjangoAppConfig
-from django.conf import settings
 
 from edc_appointment.constants import COMPLETE_APPT
 
@@ -35,23 +34,3 @@ class AppConfig(DjangoAppConfig):
         for model in self.timepoints:
             sys.stdout.write(f" * '{model}' is a timepoint model.\n")
         sys.stdout.write(f" Done loading {self.verbose_name}.\n")
-
-
-if settings.APP_NAME == "edc_timepoint":
-    from dateutil.relativedelta import FR, MO, SA, SU, TH, TU, WE
-
-    from edc_facility.apps import AppConfig as BaseEdcFacilityAppConfig
-
-    class EdcFacilityAppConfig(BaseEdcFacilityAppConfig):
-        definitions = {
-            "7-day-clinic": dict(
-                days=[MO, TU, WE, TH, FR, SA, SU],
-                slots=[100, 100, 100, 100, 100, 100, 100],
-            ),
-            "5-day-clinic": dict(days=[MO, TU, WE, TH, FR], slots=[100, 100, 100, 100, 100]),
-            "3-day-clinic": dict(
-                days=[TU, WE, TH],
-                slots=[100, 100, 100],
-                best_effort_available_datetime=True,
-            ),
-        }

edc_unblinding/auths.py

@@ -9,7 +9,12 @@ from .auth_objects import (
     unblinding_reviewers,
 )
 
-site_auths.add_group(*unblinding_requestors, name=UNBLINDING_REQUESTORS)
-site_auths.add_group(*unblinding_reviewers, name=UNBLINDING_REVIEWERS)
-site_auths.add_role(UNBLINDING_REQUESTORS, name=UNBLINDING_REQUESTORS_ROLE)
-site_auths.add_role(UNBLINDING_REVIEWERS, name=UNBLINDING_REVIEWERS_ROLE)
+
+def update_site_auths() -> None:
+    site_auths.add_group(*unblinding_requestors, name=UNBLINDING_REQUESTORS)
+    site_auths.add_group(*unblinding_reviewers, name=UNBLINDING_REVIEWERS)
+    site_auths.add_role(UNBLINDING_REQUESTORS, name=UNBLINDING_REQUESTORS_ROLE)
+    site_auths.add_role(UNBLINDING_REVIEWERS, name=UNBLINDING_REVIEWERS_ROLE)
+
+
+update_site_auths()

edc_utils/__init__.py

@@ -8,7 +8,7 @@ from .get_static_file import get_static_file
 from .get_uuid import get_uuid
 from .message_in_queue import message_in_queue
 from .round_up import round_half_away_from_zero, round_half_up, round_up
-from .show_urls import show_url_names, show_urls
+from .show_urls import show_namespaces, show_url_names, show_urls, show_urls_from_patterns
 from .text import (
     convert_from_camel,
     convert_php_dateformat,
@@ -48,8 +48,10 @@ __all__ = [
     "round_half_up",
     "round_up",
     "safe_allowed_chars",
+    "show_namespaces",
     "show_url_names",
     "show_urls",
+    "show_urls_from_patterns",
     "to_local",
     "to_utc",
     "truncate_string",