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

edc_identifier/models.py

@@ -1,6 +1,7 @@
 from django.db import models
 from django.db.models import UniqueConstraint
 
+from edc_constants.constants import NULL_STRING
 from edc_model.models import BaseUuidModel
 from edc_sites.model_mixins import SiteModelMixin
 
@@ -25,21 +26,21 @@ class IdentifierModel(SiteModelMixin, BaseUuidModel):
 
     name = models.CharField(max_length=100)
 
-    subject_identifier = models.CharField(max_length=50, default="")
+    subject_identifier = models.CharField(max_length=50, default=NULL_STRING)
 
     sequence_number = models.IntegerField(default=1)
 
-    linked_identifier = models.CharField(max_length=50, default="")
+    linked_identifier = models.CharField(max_length=50, default=NULL_STRING)
 
     device_id = models.IntegerField()
 
-    protocol_number = models.CharField(max_length=25, default="")
+    protocol_number = models.CharField(max_length=25, default=NULL_STRING)
 
-    model = models.CharField(max_length=100, default="")
+    model = models.CharField(max_length=100, default=NULL_STRING)
 
-    identifier_type = models.CharField(max_length=100, default="")
+    identifier_type = models.CharField(max_length=100, default=NULL_STRING)
 
-    identifier_prefix = models.CharField(max_length=25, default="")
+    identifier_prefix = models.CharField(max_length=25, default=NULL_STRING)
 
     objects = IdentifierModelManager()
 

edc_identifier/research_identifier.py

@@ -21,7 +21,7 @@ class IdentifierMissingTemplateValue(Exception):  # noqa: N818
 
 
 class ResearchIdentifier:
-    label: str = None  # e.g. subject_identifier, plot_identifier, etc
+    label: str | None = None  # e.g. subject_identifier, plot_identifier, etc
     identifier_type: str | None = None  # e.g. 'subject', 'infant', 'plot', a.k.a subject_type
     template: str | None = None
     padding: int = 5

edc_identifier/short_identifier.py

@@ -100,7 +100,7 @@ class ShortIdentifier:
             tries += 1
             random_string = "".join(
                 [
-                    random.choice(allowed_chars)  # nosec B311
+                    random.choice(allowed_chars)  # nosec B311  # noqa: S311
                     for _ in range(self.random_string_length)
                 ]
             )

edc_identifier/simple_identifier.py

@@ -8,6 +8,8 @@ from django.core.exceptions import ObjectDoesNotExist
 from django.db import models
 from django.utils import timezone
 
+from edc_constants.constants import NULL_STRING
+
 from .utils import convert_to_human_readable
 
 if TYPE_CHECKING:
@@ -22,10 +24,13 @@ class IdentifierError(Exception):
     pass
 
 
+IDENTIFER_PREFIX_LENGTH = 2
+
+
 class SimpleIdentifier:
     random_string_length: int = 5
     template: str = "{device_id}{random_string}"
-    identifier_prefix: str = None
+    identifier_prefix: str = NULL_STRING
 
     def __init__(
         self,
@@ -90,7 +95,7 @@ class SimpleSequentialIdentifier:
         random_number: int = choice(range(1000, 9999))  # nosec B311
         sequence: str = f"{sequence}{random_number}"
         chk: int = int(sequence) % 11
-        self.identifier: str = f"{self.prefix or ''}{sequence}{chk}"
+        self.identifier: str = f"{self.prefix or NULL_STRING}{sequence}{chk}"
 
     def __str__(self) -> str:
         return self.identifier
@@ -111,12 +116,13 @@ class SimpleUniqueIdentifier:
     model: str = "edc_identifier.identifiermodel"
     template: str = "{device_id}{random_string}"
     identifier_prefix: str | None = None
+    identifier_prefix_length: int = 2
     identifier_cls = SimpleIdentifier
     make_human_readable: bool | None = None
 
     def __init__(
         self,
-        model: str = None,
+        model: str | None = None,
         identifier_attr: str | None = None,
         identifier_type: str | None = None,
         identifier_prefix: str | None = None,
@@ -140,9 +146,13 @@ class SimpleUniqueIdentifier:
         self.identifier_attr = identifier_attr or self.identifier_attr
         self.identifier_type = identifier_type or self.identifier_type
         self.identifier_prefix = identifier_prefix or self.identifier_prefix
-        if self.identifier_prefix and len(self.identifier_prefix) != 2:
+        if (
+            self.identifier_prefix
+            and len(self.identifier_prefix) != self.identifier_prefix_length
+        ):
             raise IdentifierError(
-                f"Expected identifier_prefix of length=2. Got {len(identifier_prefix)}"
+                f"Expected identifier_prefix of length={self.identifier_prefix_length}. "
+                f"Got {len(identifier_prefix)}"
             )
         self.make_human_readable = make_human_readable or self.make_human_readable
         self.device_id = django_apps.get_app_config("edc_device").device_id

edc_identifier/subject_identifier.py

@@ -10,8 +10,8 @@ class SubjectIdentifier(ResearchIdentifier):
     label: str = "subjectidentifier"
     padding: int = 4
 
-    def __init__(self, last_name: str = None, **kwargs):
-        self.last_name = last_name
+    def __init__(self, last_name: str | None = None, **kwargs):
+        self.last_name = last_name or ""
         super().__init__(**kwargs)
 
     def pre_identifier(self) -> None:

edc_identifier/utils.py

@@ -14,23 +14,22 @@ def is_subject_identifier_or_raise(subject_identifier, reference_obj=None, raise
     * If `subject_identifier` is None, does nothing, unless
       `raise_on_none` is `True`.
     """
-    if subject_identifier or raise_on_none:
-        if not re.match(
-            ResearchProtocolConfig().subject_identifier_pattern,
-            subject_identifier or "",
-        ):
-            reference_msg = ""
-            if reference_obj:
-                reference_msg = f"See {reference_obj!r}. "
-            raise SubjectIdentifierError(
-                f"Invalid format for subject identifier. {reference_msg}"
-                f"Got `{subject_identifier or ''}`. "
-                f"Expected pattern `{ResearchProtocolConfig().subject_identifier_pattern}`"
-            )
+    valid_subject_identifier = subject_identifier and re.match(
+        ResearchProtocolConfig().subject_identifier_pattern, subject_identifier or ""
+    )
+    if not valid_subject_identifier or (not subject_identifier and raise_on_none):
+        reference_msg = ""
+        if reference_obj:
+            reference_msg = f"See {reference_obj!r}. "
+        raise SubjectIdentifierError(
+            f"Invalid format for subject identifier. {reference_msg}"
+            f"Got `{subject_identifier or ''}`. "
+            f"Expected pattern `{ResearchProtocolConfig().subject_identifier_pattern}`"
+        )
     return subject_identifier
 
 
-def get_human_phrase(no_hyphen: bool = None) -> str:
+def get_human_phrase(no_hyphen: bool | None = None) -> str:
     """Returns 6 digits split by a '-', e.g. DEC-96E.
 
     There are 213,127,200 permutations from an unambiguous alphabet.

edc_listboard/view_mixins/search_listboard_view_mixin.py

@@ -13,12 +13,12 @@ from edc_model_admin.utils import add_to_messages_once
 
 
 class SearchListboardMixin:
-    search_fields = ["slug"]
+    search_fields = ("slug",)
 
     default_querystring_attrs: str = "q"
     alternate_search_attr: str = "subject_identifier"
     default_lookup = "icontains"
-    operators: list[str] = [
+    operators: tuple[str, ...] = (
         "exact",
         "iexact",
         "contains",
@@ -33,7 +33,7 @@ class SearchListboardMixin:
         "endswith",
         "istartswith",
         "iendswith",
-    ]
+    )
 
     def __init__(self, **kwargs):
         self._search_term = None
@@ -66,12 +66,11 @@ class SearchListboardMixin:
 
     @property
     def search_term(self) -> str | None:
-        if not self._search_term:
-            if search_term := self.raw_search_term:
-                self._search_term = escape(search_term).strip()
+        if (not self._search_term) and (search_term := self.raw_search_term):
+            self._search_term = escape(search_term).strip()
         return self._search_term
 
-    def get_search_fields(self) -> list[str]:
+    def get_search_fields(self) -> tuple[str, ...]:
         """Override to add additional search fields"""
         return self.search_fields
 

edc_metadata/view_mixins/metadata_view_mixin.py

@@ -16,16 +16,19 @@ class MetadataViewError(Exception):
 
 class MetadataViewMixin:
     panel_model: str = "edc_lab.panel"
-    metadata_show_status: list[str] = [REQUIRED, KEYED]
+    metadata_show_status: tuple[str] = (REQUIRED, KEYED)
 
     def get_context_data(self, **kwargs) -> dict:
         if self.appointment:
             # always refresh metadata / run rules
             refresh_metadata_for_timepoint(self.appointment, allow_create=True)
             referer = self.request.headers.get("Referer")
-            if referer and "subject_review_listboard" in referer:
-                if self.appointment.related_visit:
-                    update_appt_status_for_timepoint(self.appointment.related_visit)
+            if (
+                referer
+                and "subject_review_listboard" in referer
+                and self.appointment.related_visit
+            ):
+                update_appt_status_for_timepoint(self.appointment.related_visit)
             crf_qs = self.get_crf_metadata()
             requisition_qs = self.get_requisition_metadata()
             kwargs.update(crfs=crf_qs, requisitions=requisition_qs)

edc_navbar/navbar.py

@@ -29,7 +29,7 @@ class Navbar:
 
     def get(self, name: str) -> NavbarItem | None:
         try:
-            navbar_item = [nb for nb in self.navbar_items if nb.name == name][0]
+            navbar_item = next(nb for nb in self.navbar_items if nb.name == name)
         except IndexError:
             navbar_item = None
         return navbar_item
@@ -37,7 +37,7 @@ class Navbar:
     def set_active(self, name: str) -> None:
         if name:
             for navbar_item in self.navbar_items:
-                navbar_item.active = True if navbar_item.name == name else False
+                navbar_item.active = navbar_item.name == name
 
     def show_user_permissions(self, user: User = None) -> dict[str, dict[str, bool]]:
         """Returns the permissions required to access this Navbar

edc_randomization/admin.py

@@ -17,6 +17,8 @@ from .auth_objects import RANDO_UNBLINDED
 from .blinding import user_is_blinded
 from .site_randomizers import site_randomizers
 
+__all__ = ["RandomizationListModelAdmin", "print_pharmacy_labels"]
+
 
 @admin.action(permissions=["view"], description="Print labels for pharmacy")
 def print_pharmacy_labels(modeladmin, request, queryset):
@@ -59,7 +61,7 @@ class RandomizationListModelAdmin(TemplatesModelAdminMixin, admin.ModelAdmin):
 
     search_fields = ("subject_identifier", "sid")
 
-    def get_fieldsets(self, request, obj=None):
+    def get_fieldsets(self, request, obj=None):  # noqa: ARG002
         return (
             (None, {"fields": self.get_fieldnames(request)}),
             audit_fieldset_tuple,

edc_randomization/apps.py

@@ -1,8 +1,4 @@
-import os
-from warnings import warn
-
 from django.apps import AppConfig as DjangoAppConfig
-from django.conf import settings
 from django.core.checks.registry import register
 
 from .system_checks import randomizationlist_check
@@ -17,10 +13,11 @@ class AppConfig(DjangoAppConfig):
     def ready(self):
         register(randomizationlist_check, deploy=True)
 
-    @property
-    def randomization_list_path(self):
-        warn(
-            "Use of settings.RANDOMIZATION_LIST_PATH has been deprecated. "
-            "See site_randomizers in edc_randomization"
-        )
-        return os.path.join(settings.RANDOMIZATION_LIST_PATH)
+    # @property
+    # def randomization_list_path(self):
+    #     warn(
+    #         "Use of settings.RANDOMIZATION_LIST_PATH has been deprecated. "
+    #         "See site_randomizers in edc_randomization",
+    #         stacklevel=2,
+    #     )
+    #     return os.path.join(settings.RANDOMIZATION_LIST_PATH)

edc_randomization/auth_objects.py

@@ -2,6 +2,15 @@ import sys
 
 from .site_randomizers import site_randomizers
 
+__all__ = [
+    "RANDO_BLINDED",
+    "RANDO_UNBLINDED",
+    "get_rando_permissions_codenames",
+    "get_rando_permissions_tuples",
+    "make_randomizationlist_view_only",
+    "update_rando_group_permissions",
+]
+
 RANDO_UNBLINDED = "RANDO_UNBLINDED"
 RANDO_BLINDED = "RANDO_BLINDED"
 

edc_randomization/blinding.py

@@ -4,7 +4,6 @@ from django import forms
 from django.conf import settings
 from django.contrib.auth import get_user_model
 from django.core.exceptions import ImproperlyConfigured, ObjectDoesNotExist
-from django.utils.html import format_html
 from django.utils.safestring import mark_safe
 
 from .auth_objects import RANDO_UNBLINDED
@@ -43,13 +42,11 @@ def user_is_blinded(username) -> bool:
     return blinded
 
 
-def user_is_blinded_from_request(request):
-    if user_is_blinded(request.user.username) or (
+def user_is_blinded_from_request(request) -> bool:
+    return user_is_blinded(request.user.username) or (
         not user_is_blinded(request.user.username)
         and RANDO_UNBLINDED not in [g.name for g in request.user.groups.all()]
-    ):
-        return True
-    return False
+    )
 
 
 def raise_if_prohibited_from_unblinded_rando_group(username: str, groups: Iterable) -> None:
@@ -61,12 +58,9 @@ def raise_if_prohibited_from_unblinded_rando_group(username: str, groups: Iterab
     if RANDO_UNBLINDED in [grp.name for grp in groups] and user_is_blinded(username):
         raise forms.ValidationError(
             {
-                "groups": format_html(
-                    "{}",
-                    mark_safe(
-                        "This user is not unblinded and may not added "
-                        "to the <U>RANDO_UNBLINDED</U> group."
-                    ),  # nosec B703 B308
+                "groups": mark_safe(
+                    "This user is not unblinded and may not added "
+                    "to the <U>RANDO_UNBLINDED</U> group."
                 )
             }
         )

edc_randomization/decorators.py

@@ -1,11 +1,10 @@
 from typing import Any
 
+from .exceptions import RegisterRandomizerError
 from .randomizer import Randomizer
 from .site_randomizers import site_randomizers
 
-
-class RegisterRandomizerError(Exception):
-    pass
+__all__ = ["register"]
 
 
 def register(site=None, **kwargs) -> Any:

edc_randomization/exceptions.py

@@ -0,0 +1,73 @@
+from django.core.exceptions import ValidationError
+
+
+class InvalidAssignment(Exception):  # noqa: N818
+    pass
+
+
+class RandomizationListImportError(Exception):
+    pass
+
+
+class RandomizationListAlreadyImported(Exception):  # noqa: N818
+    pass
+
+
+class RandomizationListError(Exception):
+    pass
+
+
+class RegistryNotLoaded(Exception):  # noqa: N818
+    pass
+
+
+class NotRegistered(Exception):  # noqa: N818
+    pass
+
+
+class AlreadyRegistered(Exception):  # noqa: N818
+    pass
+
+
+class SiteRandomizerError(Exception):
+    pass
+
+
+class RandomizationListExporterError(Exception):
+    pass
+
+
+class SubjectNotRandomization(Exception):  # noqa: N818
+    pass
+
+
+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
+
+
+class RegisterRandomizerError(Exception):
+    pass
+
+
+class RandomizationListModelError(Exception):
+    pass

edc_randomization/model_mixins.py

@@ -7,12 +7,11 @@ from django_crypto_fields.fields import EncryptedCharField
 from edc_model.models import HistoricalRecords
 from edc_sites.managers import CurrentSiteManager
 
+from .exceptions import RandomizationListModelError
 from .randomizer import RandomizationError
 from .site_randomizers import site_randomizers
 
-
-class RandomizationListModelError(Exception):
-    pass
+__all__ = ["RandomizationListManager", "RandomizationListModelMixin"]
 
 
 class RandomizationListManager(models.Manager):

edc_randomization/randomization_list_importer.py

@@ -12,21 +12,16 @@ from tqdm import tqdm
 
 from edc_sites.site import sites as site_sites
 
+from .exceptions import (
+    InvalidAssignment,
+    RandomizationListAlreadyImported,
+    RandomizationListImportError,
+)
 from .randomization_list_verifier import RandomizationListVerifier
 
 style = color_style()
 
-
-class RandomizationListImportError(Exception):
-    pass
-
-
-class RandomizationListAlreadyImported(Exception):
-    pass
-
-
-class InvalidAssignment(Exception):
-    pass
+__all__ = ["RandomizationListImporter"]
 
 
 class RandomizationListImporter:
@@ -67,19 +62,20 @@ class RandomizationListImporter:
     def __init__(
         self,
         randomizer_model_cls=None,
-        randomizer_name: str = None,
-        randomizationlist_path: Path | str = None,
-        assignment_map: dict[str, int] = None,
-        verbose: bool = None,
-        overwrite: bool = None,
-        add: bool = None,
-        dryrun: bool = None,
-        username: str = None,
-        revision: str = None,
-        sid_count_for_tests: int = None,
-        extra_csv_fieldnames: list[str] | None = None,
-        **kwargs,
+        randomizer_name: str | None = None,
+        randomizationlist_path: Path | str | None = None,
+        assignment_map: dict[str, int] | None = None,
+        verbose: bool | None = None,
+        overwrite: bool | None = None,
+        add: bool | None = None,
+        dryrun: bool | None = None,
+        username: str | None = None,
+        revision: str | None = None,
+        sid_count_for_tests: int | None = None,
+        extra_csv_fieldnames: tuple[str] | None = None,
+        **kwargs,  # noqa: ARG002
     ):
+        extra_csv_fieldnames = extra_csv_fieldnames or ()
         self.verify_messages: str | None = None
         self.add = add
         self.overwrite = overwrite
@@ -92,7 +88,7 @@ class RandomizationListImporter:
         self.randomizer_name = randomizer_name
         self.assignment_map = assignment_map
         self.randomizationlist_path: Path = Path(randomizationlist_path).expanduser()
-        self.required_csv_fieldnames.extend(extra_csv_fieldnames or [])
+        self.required_csv_fieldnames = (*self.required_csv_fieldnames, *extra_csv_fieldnames)
 
         if self.dryrun:
             sys.stdout.write(
@@ -156,7 +152,7 @@ class RandomizationListImporter:
         index = 0
         with self.randomizationlist_path.open(mode="r") as csvfile:
             reader = csv.DictReader(csvfile)
-            for index, row in enumerate(reader):
+            for index, _ in enumerate(reader):
                 if index == 0:
                     continue
         if index == 0:
@@ -178,11 +174,11 @@ class RandomizationListImporter:
                 elif index == 1:
                     if self.dryrun:
                         row_as_dict = {k: v for k, v in row.items()}
-                        print(" -->  First row:")
-                        print(f" -->  {list(row_as_dict.keys())}")
-                        print(f" -->  {list(row_as_dict.values())}")
+                        sys.stdout.write(" -->  First row:\n")
+                        sys.stdout.write(f" -->  {list(row_as_dict.keys())}\n")
+                        sys.stdout.write(f" -->  {list(row_as_dict.values())}\n")
                         obj = self.randomizer_model_cls(**self.get_import_options(row))
-                        pprint(obj.__dict__)
+                        pprint(obj.__dict__)  # noqa: T203
                 else:
                     break
 
@@ -223,12 +219,15 @@ class RandomizationListImporter:
             sid_count = self.sid_count_for_tests
         else:
             sid_count = len(self.get_sid_list())
-        with self.randomizationlist_path.open(mode="r") as csvfile:
-            reader = csv.DictReader(csvfile)
-            for row in tqdm(reader, total=sid_count):
+        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", ""))
+            )
+            for row in tqdm(sorted_rows, total=sid_count):
                 if self.sid_count_for_tests and len(objs) == self.sid_count_for_tests:
                     break
-                row = {k: v.strip() for k, v in row.items()}
                 try:
                     self.randomizer_model_cls.objects.get(sid=row["sid"])
                 except ObjectDoesNotExist:
@@ -300,7 +299,7 @@ class RandomizationListImporter:
             **self.get_extra_import_options(row),
         )
 
-    def get_extra_import_options(self, row):
+    def get_extra_import_options(self, row):  # noqa: ARG002
         return {}
 
     @staticmethod
@@ -314,9 +313,9 @@ class RandomizationListImporter:
         """Returns the site name or raises"""
         try:
             site_name = self.get_site_names()[row["site_name"].lower()]
-        except KeyError:
+        except KeyError as e:
             raise RandomizationListImportError(
                 f"Invalid site. Got {row['site_name']}. "
                 f"Expected one of {self.get_site_names().keys()}"
-            )
+            ) from e
         return site_name