clinicedc 2.0.14__py3-none-any.whl → 2.0.16__py3-none-any.whl

edc_dx_review/model_mixins/factory/dx_initial_review_model_mixin_factory.py

@@ -3,6 +3,7 @@ from __future__ import annotations
 from datetime import date
 
 from django.db import models
+
 from edc_constants.choices import YES_NO
 from edc_constants.constants import NOT_APPLICABLE, YES
 from edc_dx import Diagnoses
@@ -36,7 +37,7 @@ def dx_initial_review_methods_model_mixin_factory():
 
         @property
         def diagnoses(self):
-            subject_identifier = getattr(self, "subject_identifier")
+            subject_identifier = self.subject_identifier
             return Diagnoses(
                 subject_identifier=subject_identifier,
                 report_datetime=getattr(self, get_report_datetime_field_name()),

edc_dx_review/model_mixins/factory/followup_review_model_mixin_factory.py

@@ -1,6 +1,7 @@
 from __future__ import annotations
 
 from django.db import models
+
 from edc_constants.choices import YES_NO_NA
 from edc_constants.constants import CHOL, DM, HIV, HTN, NOT_APPLICABLE
 from edc_dx import get_diagnosis_labels

edc_dx_review/model_mixins/factory/rx_initial_review_model_mixin_factory.py

@@ -1,6 +1,7 @@
 from __future__ import annotations
 
 from django.db import models
+
 from edc_constants.choices import YES_NO, YES_NO_NA
 from edc_constants.constants import NOT_APPLICABLE, YES
 from edc_model.models import DurationYMDField

edc_dx_review/model_mixins/followup_review/followup_review_model_mixin.py

@@ -1,4 +1,5 @@
 from django.db import models
+
 from edc_constants.choices import YES_NO_NA
 from edc_constants.constants import NOT_APPLICABLE
 

edc_dx_review/model_mixins/followup_review/hiv_followup_review_model_mixin.py

@@ -1,4 +1,5 @@
 from django.db import models
+
 from edc_constants.choices import YES_NO_NA
 from edc_constants.constants import NOT_APPLICABLE
 

edc_dx_review/model_mixins/initial_review/chol_initial_review_model_mixin.py

@@ -1,4 +1,5 @@
 from django.db import models
+
 from edc_constants.choices import YES_NO
 from edc_constants.constants import NOT_APPLICABLE
 

edc_dx_review/model_mixins/initial_review/hiv_initial_model_mixins.py

@@ -1,5 +1,6 @@
 from django.core.validators import MaxValueValidator, MinValueValidator
 from django.db import models
+
 from edc_constants.choices import YES_NO, YES_NO_NA, YES_NO_PENDING_NA
 from edc_constants.constants import NOT_APPLICABLE, YES
 from edc_lab.choices import VL_QUANTIFIER_NA

edc_dx_review/model_mixins/initial_review/ncd_initial_review_model_mixin.py

@@ -1,4 +1,5 @@
 from django.db import models
+
 from edc_constants.choices import YES_NO
 from edc_constants.constants import YES
 from edc_model import models as edc_models

edc_dx_review/radio_fields.py

@@ -1,10 +1,10 @@
-from typing import Dict
 
 from django.contrib import admin
+
 from edc_dx import get_diagnosis_labels_prefixes
 
 
-def get_clinical_review_cond_radio_fields() -> Dict[str, int]:
+def get_clinical_review_cond_radio_fields() -> dict[str, int]:
     radio_fields = {}
     for prefix in get_diagnosis_labels_prefixes():
         cond = prefix.lower()
@@ -17,7 +17,7 @@ def get_clinical_review_cond_radio_fields() -> Dict[str, int]:
     return radio_fields
 
 
-def get_clinical_review_baseline_cond_radio_fields() -> Dict[str, int]:
+def get_clinical_review_baseline_cond_radio_fields() -> dict[str, int]:
     radio_fields = {}
     for prefix in get_diagnosis_labels_prefixes():
         cond = prefix.lower()

edc_dx_review/utils.py

@@ -7,6 +7,7 @@ from django import forms
 from django.apps import apps as django_apps
 from django.conf import settings
 from django.core.exceptions import ObjectDoesNotExist
+
 from edc_constants.constants import HIV, YES
 from edc_model.utils import model_exists_or_raise
 from edc_visit_schedule.baseline import VisitScheduleBaselineError
@@ -78,7 +79,7 @@ def get_extra_attrs():
         "review": "review",
     }
     try:
-        data = getattr(settings, "EDC_DX_REVIEW_EXTRA_ATTRS")
+        data = settings.EDC_DX_REVIEW_EXTRA_ATTRS
     except AttributeError:
         pass
     else:

edc_form_describer/form_describer.py

@@ -1,12 +1,13 @@
 from __future__ import annotations
 
+import contextlib
 import re
 import string
 import sys
-from datetime import datetime
 from math import floor
 
 from django.core.management.color import color_style
+from django.utils import timezone
 
 from edc_fieldsets.fieldsets import Fieldsets
 from edc_model.constants import DEFAULT_BASE_FIELDS
@@ -57,14 +58,20 @@ class FormDescriber:
         self.markdown: list[str] = []
         add_timestamp = True if add_timestamp is None else add_timestamp
         self.anchor_prefix = anchor_prefix or self.anchor_prefix
-        timestamp = datetime.today().strftime("%Y-%m-%d %H:%M")
+        timestamp = timezone.now().strftime("%Y-%m-%d %H:%M")
         self.level = level or self.level
         self.conditional_fieldset = None
         self.admin_cls = admin_cls
         try:
             self.model_cls = admin_cls.model
         except AttributeError:
-            self.model_cls = admin_cls.form._meta.model
+            try:
+                self.model_cls = admin_cls.form._meta.model
+            except AttributeError as e:
+                raise FormDescriberError(
+                    f"Unable to determine admin class model. Got {admin_cls}"
+                ) from e
+
         self.visit_code = visit_code
         self.models_fields = {fld.name: fld for fld in self.model_cls._meta.get_fields()}
 
@@ -115,7 +122,7 @@ class FormDescriber:
     def anchor(self):
         allow = string.ascii_letters + string.digits + "-"
         slug = self.verbose_name.lower().replace(" ", "-")
-        slug = re.sub("[^%s]" % allow, "", slug)
+        slug = re.sub(f"[^{allow}]", "", slug)
         return f"{self.anchor_prefix}-{slug}"
 
     def describe(self):
@@ -135,7 +142,7 @@ class FormDescriber:
 
         for fieldset_name, fieldset in self.fieldsets:
             if fieldset_name not in ["Audit"]:
-                fieldset_name = fieldset_name or "Main"
+                fieldset_name = fieldset_name or "Main"  # noqa: PLW2901
                 self.markdown.append(f"\n**Section: {fieldset_name}**")
                 if fieldset.get("classes") != "collapse":
                     for fname in fieldset.get("fields"):
@@ -172,10 +179,8 @@ class FormDescriber:
             self.markdown.append(f"* custom_prompt: *{self.custom_form_labels.get(fname)}*")
         self.markdown.append(f"- db_table: {self.model_cls._meta.db_table}")
         self.markdown.append(f"- column: {field_cls.name}")
-        try:
+        with contextlib.suppress(AttributeError):
             self.markdown.append(f"- metadata: {field_cls.metadata}")
-        except AttributeError:
-            pass
         self.markdown.append(f"- type: {field_cls.get_internal_type()}")
         if field_cls.max_length:
             self.markdown.append(f"- length: {field_cls.max_length}")

edc_form_describer/forms_reference.py

@@ -1,8 +1,9 @@
-from datetime import datetime
 from importlib.metadata import version
+from pathlib import Path
 
 from django.apps import apps as django_apps
 from django.conf import settings
+from django.utils import timezone
 
 from .form_describer import FormDescriber
 from .markdown_writer import MarkdownWriter
@@ -36,24 +37,20 @@ class FormsReference:
         self.add_per_form_timestamp = (
             True if add_per_form_timestamp is None else add_per_form_timestamp
         )
-        self.timestamp = datetime.today().strftime("%Y-%m-%d %H:%M")
+        self.timestamp = timezone.now().strftime("%Y-%m-%d %H:%M")
         for visit_schedule in self.visit_schedules:
             self.plans.update({visit_schedule.name: {}})
             for schedule in visit_schedule.schedules.values():
                 for visit_code, visit in schedule.visits.items():
-                    crfs = []
-                    requisitions = []
-                    for c in visit.crfs:
-                        crfs.append(c.model)
-                    for r in visit.requisitions:
-                        requisitions.append(r.panel.name)
+                    crfs = [c.model for c in visit.crfs]
+                    requisitions = [r.panel.name for r in visit.requisitions]
                     self.plans[visit_schedule.name].update(
                         {visit_code: {"crfs": crfs, "requisitions": requisitions}}
                     )
 
     def to_file(
         self,
-        path: str | None = None,
+        path: Path | str | None = None,
         overwrite: bool | None = None,
         pad: int | None = None,
     ):
@@ -95,23 +92,25 @@ class FormsReference:
                     for index, model in enumerate(documents.get("crfs")):
                         model_cls = django_apps.get_model(model)
                         admin_cls = self.admin_site._registry.get(model_cls)
-                        describer = self.describer_cls(
-                            admin_cls=admin_cls,
-                            include_hidden_fields=self.include_hidden_fields,
-                            visit_code=visit_code,
-                            level=self.h4,
-                            anchor_prefix=self.anchor_prefix,
-                            add_timestamp=self.add_per_form_timestamp,
-                        )
-                        describer.markdown.append("\n")
-                        anchor = f"{self.get_anchor(describer.anchor)}"
-                        toc.append(
-                            f'{index + 1}. <a href="#{anchor}">{describer.verbose_name}</a>'
-                        )
-                        markdown.extend(describer.markdown)
+                        if admin_cls:
+                            describer = self.describer_cls(
+                                admin_cls=admin_cls,
+                                include_hidden_fields=self.include_hidden_fields,
+                                visit_code=visit_code,
+                                level=self.h4,
+                                anchor_prefix=self.anchor_prefix,
+                                add_timestamp=self.add_per_form_timestamp,
+                            )
+                            describer.markdown.append("\n")
+                            anchor = f"{self.get_anchor(describer.anchor)}"
+                            toc.append(
+                                f'{index + 1}. <a href="#{anchor}">{describer.verbose_name}</a>'
+                            )
+                            markdown.extend(describer.markdown)
                     markdown.append(f"{self.h4} Requisitions\n")
-                    for panel_name in documents.get("requisitions"):
-                        markdown.append(f"* {panel_name}\n")
+                    markdown.extend(
+                        [f"* {panel_name}\n" for panel_name in documents.get("requisitions")]
+                    )
             markdown = self.insert_toc(toc, markdown)
             markdown.insert(0, f"{self.h1} {self.title}")
             markdown.append(

edc_form_describer/make_forms_reference.py

@@ -1,6 +1,5 @@
 from __future__ import annotations
 
-import os
 import sys
 from importlib import import_module
 
@@ -16,11 +15,10 @@ style = color_style()
 
 
 def make_forms_reference(
-    app_label: str = None,
-    admin_site_name: str = None,
-    visit_schedule_name: str = None,
-    title: str = None,
-    path: str | None = None,
+    app_label: str,
+    admin_site_name: str,
+    visit_schedule_name: str,
+    title: str | None = None,
 ):
     module = import_module(app_label)
     admin_site = getattr(module.admin_site, admin_site_name)
@@ -29,9 +27,9 @@ def make_forms_reference(
     sys.stdout.write(
         style.MIGRATE_HEADING(f"Refreshing CRF reference document for {app_label}\n")
     )
-    doc_folder = os.path.join(settings.BASE_DIR, "docs")
-    if not os.path.exists(doc_folder):
-        os.mkdir(doc_folder)
+    doc_folder = settings.BASE_DIR / "docs"
+    if not doc_folder.exists():
+        doc_folder.mkdir()
 
     forms = FormsReference(
         visit_schedules=[visit_schedule],
@@ -40,8 +38,8 @@ def make_forms_reference(
         add_per_form_timestamp=False,
     )
 
-    path = os.path.join(doc_folder, "forms_reference.md")
+    path = doc_folder / f"forms_reference_{app_label}.md"
     forms.to_file(path=path, overwrite=True)
 
-    print(path)
-    print("Done.")
+    sys.stdout.write(f"{path}\n")
+    sys.stdout.write("Done.\n")

edc_form_describer/management/commands/make_forms_reference.py

@@ -17,16 +17,16 @@ style = color_style()
 
 
 def update_forms_reference(
-    app_label: str = None,
-    admin_site_name: str = None,
-    visit_schedule_name: str = None,
-    title: str = None,
+    app_label: str,
+    admin_site_name: str,
+    visit_schedule_name: str,
+    title: str | None = None,
     filename: str | None = None,
     doc_folder: str | None = None,
 ):
     module = import_module(app_label)
     default_doc_folder = Path(settings.BASE_DIR / "docs")
-    filename = filename or "forms_reference.md"
+    filename = filename or f"forms_reference_{app_label}.md"
     admin_site = getattr(module.admin_site, admin_site_name)
     visit_schedule = site_visit_schedules.get_visit_schedule(visit_schedule_name)
     title = title or _("%(title_app)s Forms Reference") % dict(title_app=app_label.upper())
@@ -47,8 +47,8 @@ def update_forms_reference(
     path = doc_folder / filename
     forms.to_file(path=path, overwrite=True)
 
-    print(path)
-    print("Done.")
+    sys.stdout.write(f"{path}\n")
+    sys.stdout.write("Done\n")
 
 
 class Command(BaseCommand):
@@ -85,7 +85,7 @@ class Command(BaseCommand):
             default=None,
         )
 
-    def handle(self, *args, **options):
+    def handle(self, *args, **options):  # noqa: ARG002
         app_label = options["app_label"]
         admin_site_name = options["admin_site_name"]
         visit_schedule_name = options["visit_schedule_name"]

edc_form_describer/markdown_writer.py

@@ -1,7 +1,8 @@
 from __future__ import annotations
 
-import os
-from datetime import datetime
+from pathlib import Path
+
+from django.utils import timezone
 
 
 class MarkdownWriter:
@@ -11,23 +12,23 @@ class MarkdownWriter:
     @staticmethod
     def get_path(path: str | None = None, overwrite: bool | None = None) -> str:
         if not path:
-            timestamp = datetime.today().strftime("%Y%m%d%H%M")
+            timestamp = timezone.now().strftime("%Y%m%d%H%M")
             path = f"forms_{timestamp}.md"
-        if os.path.exists(path):
+        if Path(path).exists():
             if overwrite:
-                os.remove(path)
+                Path(path).unlink()
             else:
                 raise FileExistsError(f"File exists. Got '{path}'")
         return path
 
     @staticmethod
-    def to_markdown(markdown: list[str] = None) -> str:
+    def to_markdown(markdown: list[str]) -> str:
         """Returns the markdown as a text string."""
         return "\n".join(markdown)
 
     def to_file(
         self,
-        markdown: list[str] = None,
+        markdown: list[str],
         pad: int | None = None,
         append: bool | None = None,
         prepend: bool | None = None,
@@ -42,9 +43,9 @@ class MarkdownWriter:
         else:
             self._write(markdown)
 
-    def _write(self, markdown: str = None, mode: str | None = None) -> None:
+    def _write(self, markdown: str, mode: str | None = None) -> None:
         mode = mode or "w"
-        with open(self.path, mode) as f:
+        with Path(self.path).open(mode) as f:
             f.write(markdown)
 
     def _append(self, markdown) -> None:
@@ -53,7 +54,7 @@ class MarkdownWriter:
 
     def _prepend(self, markdown=None) -> None:
         mode = "r+"
-        with open(self.path, mode) as f:
+        with Path(self.path).open(mode) as f:
             content = f.read()
             f.seek(0, 0)
             f.write(markdown + "\n" + content)

edc_randomization/randomizer.py

@@ -22,6 +22,7 @@ from .randomization_list_importer import (
     RandomizationListAlreadyImported,
     RandomizationListImporter,
 )
+from .utils import get_randomization_list_path
 
 if TYPE_CHECKING:
     from edc_registration.models import RegisteredSubject
@@ -99,11 +100,7 @@ class Randomizer:
         DEFAULT_ASSIGNMENT_DESCRIPTION_MAP,
     )
     filename: str = "randomization_list.csv"
-    randomizationlist_folder: Path | str = getattr(
-        settings,
-        "EDC_RANDOMIZATION_LIST_PATH",
-        Path(settings.BASE_DIR).expanduser() / ".etc",
-    )
+    randomizationlist_folder: Path | str = get_randomization_list_path()
     extra_csv_fieldnames: list[str] | None = None
     trial_is_blinded: bool = True
     importer_cls: Any = RandomizationListImporter

edc_randomization/utils.py

@@ -25,6 +25,16 @@ class SubjectNotRandomization(Exception):  # noqa: N818
     pass
 
 
+def get_randomization_list_path() -> Path:
+    return Path(
+        getattr(
+            settings,
+            "EDC_RANDOMIZATION_LIST_PATH",
+            settings.ETC_DIR,
+        )
+    ).expanduser()
+
+
 def get_assignment_for_subject(
     subject_identifier: str,
     randomizer_name: str,

edc_visit_schedule/schedule/schedule.py

@@ -45,7 +45,7 @@ class ScheduleNameError(Exception):
     pass
 
 
-class AlreadyRegisteredVisit(Exception):
+class AlreadyRegisteredVisit(Exception):  # noqa: N818
     pass
 
 
@@ -69,15 +69,15 @@ class Schedule:
 
     def __init__(
         self,
-        name=None,
-        verbose_name: str = None,
-        onschedule_model: str = None,
-        offschedule_model: str = None,
-        loss_to_followup_model: str = None,
-        appointment_model: str | None = None,
-        history_model: str | None = None,
+        name: str,
+        onschedule_model: str,
+        offschedule_model: str,
         consent_definitions: list[ConsentDefinition] | ConsentDefinition = None,
+        loss_to_followup_model: str | None = None,
+        appointment_model: str | None = None,
         offstudymedication_model: str | None = None,
+        history_model: str | None = None,
+        verbose_name: str | None = None,
         sequence: str | None = None,
         base_timepoint: float | Decimal | None = None,
     ):
@@ -146,10 +146,10 @@ class Schedule:
 
     def visits_for_subject(
         self,
-        subject_identifier: str = None,
-        report_datetime: datetime = None,
-        site_id: int = None,
-        consent_definition: ConsentDefinition = None,
+        subject_identifier: str,
+        report_datetime: datetime,
+        site_id: int | None = None,
+        consent_definition: ConsentDefinition | None = None,
     ) -> VisitCollection:
         """Returns a deep copy of visits collection filtered for a
         given consented subject.
@@ -352,7 +352,7 @@ class Schedule:
 
     def get_consent_definition(
         self,
-        report_datetime: datetime = None,
+        report_datetime: datetime,
         site: SingleSite = None,
         consent_definition: ConsentDefinition = None,
     ) -> ConsentDefinition:

edc_visit_tracking/action_items.py

@@ -26,12 +26,11 @@ class VisitMissedAction(ActionWithNotification):
 
     def get_next_actions(self) -> list[Action]:
         next_actions: list[Action] = []
-        next_actions = self.append_to_next_if_required(
+        return self.append_to_next_if_required(
             next_actions=next_actions,
             action_name=self.get_loss_to_followup_action_name(),
             required=self.is_ltfu(),
         )
-        return next_actions
 
 
 class MissedVisitAction(VisitMissedAction):

edc_visit_tracking/apps.py

@@ -12,7 +12,7 @@ class AppConfig(DjangoAppConfig):
     verbose_name = "Edc Visit Tracking"
     report_datetime_allowance: int = 30
     allow_crf_report_datetime_before_visit: bool = False
-    reason_field: dict = {}
+    reason_field: dict = {}  # noqa: RUF012
 
     def ready(self):
         register(context_processors_check)

edc_visit_tracking/context_processors.py

@@ -2,11 +2,10 @@ from .constants import DEFERRED_VISIT, LOST_VISIT, MISSED_VISIT, SCHEDULED, UNSC
 
 
 def constants(request) -> dict:
-    dct = dict(
+    return dict(
         DEFERRED_VISIT=DEFERRED_VISIT,
         LOST_VISIT=LOST_VISIT,
         MISSED_VISIT=MISSED_VISIT,
         SCHEDULED=SCHEDULED,
         UNSCHEDULED=UNSCHEDULED,
     )
-    return dct

edc_visit_tracking/crf_date_validator.py

@@ -14,11 +14,11 @@ class CrfReportDateAllowanceError(Exception):
     pass
 
 
-class CrfReportDateBeforeStudyStart(Exception):
+class CrfReportDateBeforeStudyStart(Exception):  # noqa: N818
     pass
 
 
-class CrfReportDateIsFuture(Exception):
+class CrfReportDateIsFuture(Exception):  # noqa: N818
     pass
 
 
@@ -58,13 +58,13 @@ class CrfDateValidator:
             datetime_not_before_study_start(self.report_datetime)
         except ValidationError as e:
             message = e.message if hasattr(e, "message") else str(e)
-            raise CrfReportDateBeforeStudyStart(message)
+            raise CrfReportDateBeforeStudyStart(message) from e
         # datetime_not_future
         try:
             datetime_not_future(self.report_datetime)
         except ValidationError as e:
             message = e.message if hasattr(e, "message") else str(e)
-            raise CrfReportDateIsFuture(message)
+            raise CrfReportDateIsFuture(message) from e
 
         formatted_visit_datetime = self.visit_report_datetime.strftime(
             convert_php_dateformat(settings.SHORT_DATE_FORMAT)