clinicedc 2.0.41__py3-none-any.whl → 2.0.43__py3-none-any.whl

edc_navbar/system_checks.py

@@ -1,6 +1,7 @@
 from django.apps import apps as django_apps
 from django.core.checks import CheckMessage, Error
 from django.urls import NoReverseMatch
+from edc_dashboard.url_names import InvalidDashboardUrlName
 
 from edc_navbar import site_navbars
 
@@ -32,4 +33,6 @@ def edc_navbar_checks(app_configs, **kwargs) -> list[CheckMessage]:
                 navbar_item.get_url(raise_exception=True)
             except NoReverseMatch as e:
                 errors.append(Error(str(e), id="edc_navbar.E003"))
+            except InvalidDashboardUrlName as e:
+                errors.append(Error(str(e), id="edc_navbar.E004"))
     return errors

edc_offstudy/action_items.py

@@ -1,6 +1,7 @@
+from clinicedc_constants import HIGH_PRIORITY
+
 from edc_action_item.action_with_notification import ActionWithNotification
 from edc_adverse_event.constants import DEATH_REPORT_ACTION
-from edc_constants.constants import HIGH_PRIORITY
 from edc_ltfu.constants import LTFU_ACTION
 from edc_unblinding.constants import UNBLINDING_REVIEW_ACTION
 

edc_offstudy/choices.py

@@ -1,5 +1,6 @@
+from clinicedc_constants import DEAD, OTHER
+
 from edc_consent.constants import CONSENT_WITHDRAWAL
-from edc_constants.constants import DEAD, OTHER
 from edc_visit_tracking.constants import COMPLETED_PROTOCOL_VISIT, LOST_VISIT
 
 OFFSTUDY_REASONS = (

edc_pdf_reports/crf_pdf_report.py

@@ -9,6 +9,14 @@ from django.apps import apps as django_apps
 from django.contrib.auth import get_user_model
 from django.core.exceptions import ObjectDoesNotExist
 from django.utils.text import slugify
+from reportlab.lib import colors
+from reportlab.lib.pagesizes import A4
+from reportlab.lib.units import cm
+from reportlab.lib.utils import ImageReader
+from reportlab.platypus import Paragraph, TableStyle
+from reportlab.platypus.flowables import KeepTogether, Spacer
+from reportlab.platypus.tables import Table
+
 from edc_data_manager.get_longitudinal_value import (
     DataDictionaryError,
     get_longitudinal_value,
@@ -18,19 +26,13 @@ from edc_randomization.auth_objects import RANDO_UNBLINDED
 from edc_utils.age import formatted_age
 from edc_utils.date import to_local
 from edc_utils.get_static_file import get_static_file
-from reportlab.lib import colors
-from reportlab.lib.pagesizes import A4
-from reportlab.lib.units import cm
-from reportlab.lib.utils import ImageReader
-from reportlab.platypus import Paragraph, TableStyle
-from reportlab.platypus.flowables import KeepTogether, Spacer
-from reportlab.platypus.tables import Table
 
 from .report import Report
 
 if TYPE_CHECKING:
     from django.contrib.auth.models import User
     from django.core.handlers.wsgi import WSGIRequest
+
     from edc_crf.model_mixins import CrfModelMixin
     from edc_identifier.model_mixins import UniqueSubjectIdentifierModelMixin
 

edc_pdutils/dataframes/get_subject_consent.py

@@ -1,11 +1,10 @@
 import numpy as np
 import pandas as pd
+from clinicedc_constants import FEMALE, MALE
 from django.apps import apps as django_apps
 from django.db.models import Model
 from django_pandas.io import read_frame
 
-from edc_constants.constants import FEMALE, MALE
-
 from ..utils import convert_dates_from_model
 
 

edc_pdutils/dataframes/get_subject_visit.py

@@ -4,17 +4,7 @@ from django_pandas.io import read_frame
 
 from edc_appointment.models import AppointmentType
 
-from ..utils import convert_dates_from_model
-
-
-def convert_visit_code_to_float(df):
-    """Convert visit_code to float using visit_code_sequence"""
-    df["visit_code"] = df["visit_code"].astype(float)
-    df["visit_code_sequence"] = df["visit_code_sequence"].astype(float)
-    df["visit_code_sequence"] = df["visit_code_sequence"].apply(
-        lambda x: x / 10.0 if x > 0.0 else 0.0
-    )
-    df["visit_code"] = df["visit_code"] + df["visit_code_sequence"]
+from ..utils import convert_dates_from_model, convert_visit_code_to_float
 
 
 def get_subject_visit(

edc_pdutils/helper.py

@@ -1,10 +1,9 @@
 import contextlib
 
 import pandas as pd
+from clinicedc_constants import NO, YES
 from django.conf import settings
 
-from edc_constants.constants import NO, YES
-
 
 class Helper:
     to_dataframe_cls = None

edc_pdutils/mappings.py

@@ -1,3 +1,3 @@
-from edc_constants.constants import NO, YES
+from clinicedc_constants import NO, YES
 
 yes_no = {True: YES, False: NO}

edc_pdutils/tables/crf.py

@@ -1,7 +1,6 @@
 import numpy as np
 import pandas as pd
-
-from edc_constants.constants import YES
+from clinicedc_constants import YES
 
 from ..mappings import yes_no
 from .table import Table

edc_pdutils/tables/requisition.py

@@ -1,7 +1,6 @@
 import numpy as np
 import pandas as pd
-
-from edc_constants.constants import YES
+from clinicedc_constants import YES
 
 from ..mappings import yes_no
 from .table import Table

edc_pdutils/utils/__init__.py

@@ -3,6 +3,7 @@ from .convert_numbers_to_float64_int64 import convert_numbers_to_float64_int64
 from .convert_numbers_to_nullable_dtype import convert_numbers_to_nullable_dtype
 from .convert_numerics_from_model import convert_numerics_from_model
 from .convert_timedelta_from_model import convert_timedelta_from_model
+from .convert_visit_code_to_float import convert_visit_code_to_float
 from .datetime_to_date import datetime_to_date
 from .decrypt import DecryptError, decrypt
 from .get_export_folder import get_export_folder

edc_pdutils/utils/convert_visit_code_to_float.py

@@ -0,0 +1,8 @@
+def convert_visit_code_to_float(df):
+    """Convert visit_code to float using visit_code_sequence"""
+    df["visit_code"] = df["visit_code"].astype(float)
+    df["visit_code_sequence"] = df["visit_code_sequence"].astype(float)
+    df["visit_code_sequence"] = df["visit_code_sequence"].apply(
+        lambda x: x / 10.0 if x > 0.0 else 0.0
+    )
+    df["visit_code"] = df["visit_code"] + df["visit_code_sequence"]

edc_pdutils/utils/decrypt.py

@@ -1,10 +1,11 @@
+import contextlib
+
 import numpy as np
 import pandas as pd
+from django.core.exceptions import ImproperlyConfigured
 
-try:
+with contextlib.suppress(ModuleNotFoundError, ImproperlyConfigured):
     from django_crypto_fields.field_cryptor import FieldCryptor
-except ModuleNotFoundError:
-    pass
 
 
 class DecryptError(Exception):
@@ -13,7 +14,7 @@ class DecryptError(Exception):
 
 def decrypt(row, column_name, algorithm, access_mode):
     value = np.nan
-    if pd.notnull(row[column_name]):
+    if pd.notna(row[column_name]):
         field_cryptor = FieldCryptor(algorithm, access_mode)
         value = field_cryptor.decrypt(row[column_name])
         if value.startswith("enc1::"):

edc_pdutils/utils/missing_subject_identifiers.py

@@ -3,11 +3,9 @@ from warnings import warn
 import pandas as pd
 from django.apps import apps as django_apps
 
-from edc_model_to_dataframe.model_to_dataframe import ModelToDataframe
-
 
 def missing_subject_identifiers(
-    self, model=None, subject_identifiers=None, remove_uuids=None, verbose=None
+    model=None, subject_identifiers=None, remove_uuids=None, verbose=None
 ):
     """Returns a series of subject_identifiers not in model.
 
@@ -16,6 +14,8 @@ def missing_subject_identifiers(
             model='edc_registration.registeredsubject',
             subject_identifiers=[a list of subject identifiers])
     """
+    from edc_model_to_dataframe.model_to_dataframe import ModelToDataframe  # noqa: PLC0415
+
     # convert list of subject identifiers to a dataframe
     df_subject_identifiers = pd.DataFrame(subject_identifiers, columns=["subject_identifier"])
     df_subject_identifiers["identifier"] = df_subject_identifiers["subject_identifier"]
@@ -43,6 +43,7 @@ def missing_subject_identifiers(
     if len(df_missing.index) > 0 and verbose:
         warn(
             f"There are {len(df_missing['identifier'])} subject identifiers "
-            f"missing from {model}."
+            f"missing from {model}.",
+            stacklevel=2,
         )
     return df_missing["identifier"]

edc_pharmacy/action_items.py

@@ -1,6 +1,7 @@
+from clinicedc_constants import HIGH_PRIORITY
+
 from edc_action_item.action import Action
 from edc_action_item.site_action_items import site_action_items
-from edc_constants.constants import HIGH_PRIORITY
 
 from .constants import PRESCRIPTION_ACTION
 

edc_pharmacy/admin/list_filters.py

@@ -1,10 +1,10 @@
+from clinicedc_constants import NEW, NO, NOT_APPLICABLE, PARTIAL, RECEIVED, YES
 from django.contrib.admin import SimpleListFilter
 from django.contrib.sites.shortcuts import get_current_site
 from django.db.models import Count, F, Q
 from django.utils.translation import gettext as _
 
 from edc_constants.choices import YES_NO, YES_NO_NA
-from edc_constants.constants import NEW, NO, NOT_APPLICABLE, PARTIAL, RECEIVED, YES
 
 from ..models import Medication, Rx
 from ..utils import blinded_user

edc_pharmacy/admin/stock/allocation_admin.py

@@ -1,3 +1,4 @@
+from clinicedc_constants import NO, YES
 from django.contrib import admin
 from django.contrib.admin import SimpleListFilter
 from django.template.loader import render_to_string
@@ -6,7 +7,6 @@ from django.utils.translation import gettext
 from django_audit_fields import audit_fieldset_tuple
 from rangefilter.filters import DateRangeFilterBuilder
 
-from edc_constants.constants import NO, YES
 from edc_model_admin.history import SimpleHistoryAdmin
 from edc_utils.date import to_local
 

edc_pharmacy/admin/stock/order_item_admin.py

@@ -1,5 +1,6 @@
 from decimal import Decimal
 
+from clinicedc_constants import NEW, PARTIAL, RECEIVED
 from django.contrib import admin, messages
 from django.template.loader import render_to_string
 from django.urls import reverse
@@ -7,7 +8,6 @@ from django.utils.safestring import mark_safe
 from django.utils.translation import gettext as _
 from django_audit_fields.admin import audit_fieldset_tuple
 
-from edc_constants.constants import NEW, PARTIAL, RECEIVED
 from edc_model_admin.history import SimpleHistoryAdmin
 from edc_utils import message_in_queue
 

edc_pharmacy/admin/stock/stock_request_admin.py

@@ -1,5 +1,6 @@
 from celery.result import AsyncResult
 from celery.states import SUCCESS
+from clinicedc_constants import CANCELLED, COMPLETE, PENDING
 from django.contrib import admin
 from django.template.loader import render_to_string
 from django.urls import reverse
@@ -8,7 +9,6 @@ from django.utils.translation import gettext as _
 from django_audit_fields import audit_fieldset_tuple
 from rangefilter.filters import DateRangeFilterBuilder
 
-from edc_constants.constants import CANCELLED, COMPLETE, PENDING
 from edc_model_admin.history import SimpleHistoryAdmin
 from edc_utils.date import to_local
 

edc_pharmacy/admin/stock/stock_transfer_admin.py

@@ -1,3 +1,4 @@
+from clinicedc_constants import NO, PARTIAL, YES
 from django.contrib import admin
 from django.contrib.admin import SimpleListFilter
 from django.db.models import Count
@@ -6,7 +7,6 @@ from django.urls import reverse
 from django_audit_fields import audit_fieldset_tuple
 from rangefilter.filters import DateRangeFilterBuilder
 
-from edc_constants.constants import NO, PARTIAL, YES
 from edc_model_admin.history import SimpleHistoryAdmin
 from edc_utils.date import to_local
 

edc_pharmacy/admin/stock/stock_transfer_item_admin.py

@@ -1,3 +1,4 @@
+from clinicedc_constants import NO, YES
 from django.contrib import admin
 from django.contrib.admin import SimpleListFilter
 from django.core.exceptions import ObjectDoesNotExist
@@ -6,7 +7,6 @@ from django.urls import reverse
 from django_audit_fields import audit_fieldset_tuple
 from rangefilter.filters import DateRangeFilterBuilder
 
-from edc_constants.constants import NO, YES
 from edc_model_admin.history import SimpleHistoryAdmin
 from edc_utils.date import to_local
 

edc_pharmacy/choices.py

@@ -1,7 +1,6 @@
+from clinicedc_constants import COMPLETE, NEW, NOT_APPLICABLE, OTHER
 from django.utils.translation import gettext as _
 
-from edc_constants.constants import COMPLETE, NEW, NOT_APPLICABLE, OTHER
-
 from .constants import (
     ALLOCATED,
     AVAILABLE,

edc_pharmacy/form_validators/crf/study_medication_form_validator.py

@@ -3,9 +3,9 @@ from __future__ import annotations
 from datetime import datetime
 from typing import TYPE_CHECKING
 
+from clinicedc_constants import NO, YES
 from django.core.exceptions import ObjectDoesNotExist
 
-from edc_constants.constants import NO, YES
 from edc_crf.crf_form_validator import CrfFormValidator
 from edc_form_validators import INVALID_ERROR
 from edc_utils.text import formatted_datetime

edc_pharmacy/list_data.py

@@ -1,4 +1,4 @@
-from edc_constants.constants import NOT_APPLICABLE, OTHER
+from clinicedc_constants import NOT_APPLICABLE, OTHER
 
 from .constants import PER_DAY, PER_HR, SINGLE
 

edc_pharmacy/model_mixins/study_medication_crf_model_mixin.py

@@ -2,11 +2,11 @@ from __future__ import annotations
 
 from typing import TYPE_CHECKING
 
+from clinicedc_constants import YES
 from django.apps import apps as django_apps
 from django.core.exceptions import ObjectDoesNotExist
 
 from edc_appointment.utils import get_next_appointment
-from edc_constants.constants import YES
 from edc_utils.text import formatted_datetime
 from edc_visit_tracking.utils import get_next_related_visit
 

edc_pharmacy/model_mixins/study_medication_refill_model_mixin.py

@@ -1,11 +1,11 @@
 from uuid import uuid4
 
+from clinicedc_constants import YES
 from django.core.validators import RegexValidator
 from django.db import models
 from django.db.models import PROTECT
 
 from edc_constants.choices import YES_NO
-from edc_constants.constants import YES
 
 
 class StudyMedicationRefillModelMixin(models.Model):

edc_pharmacy/models/model_mixins.py

@@ -1,7 +1,6 @@
+from clinicedc_constants import NULL_STRING
 from django.db import models
 
-from edc_constants.constants import NULL_STRING
-
 
 class AddressModelMixin(models.Model):
     address_one = models.CharField(max_length=255, default=NULL_STRING, blank=True)

edc_pharmacy/models/prescription/rx.py

@@ -1,12 +1,12 @@
 from uuid import uuid4
 
+from clinicedc_constants import NEW
 from django.core.exceptions import ObjectDoesNotExist
 from django.db import models
 from django.db.models import PROTECT, Index
 from django.utils import timezone
 
 from edc_action_item.models import ActionModelMixin
-from edc_constants.constants import NEW
 from edc_identifier.model_mixins import NonUniqueSubjectIdentifierFieldMixin
 from edc_model.models import BaseUuidModel
 from edc_randomization.site_randomizers import site_randomizers

edc_pharmacy/models/signals.py

@@ -3,11 +3,11 @@ from __future__ import annotations
 from decimal import Decimal
 
 from celery.states import PENDING
+from clinicedc_constants import COMPLETE, PARTIAL
 from django.db.models import Sum
 from django.db.models.signals import post_delete, post_save
 from django.dispatch import receiver
 
-from edc_constants.constants import COMPLETE, PARTIAL
 from edc_utils.celery import get_task_result, run_task_sync_or_async
 
 from ..exceptions import InsufficientStockError

edc_pharmacy/models/stock/order.py

@@ -1,7 +1,7 @@
+from clinicedc_constants import NEW
 from django.db import models
 from sequences import get_next_value
 
-from edc_constants.constants import NEW
 from edc_model.models import BaseUuidModel, HistoricalRecords
 
 from ...choices import ORDER_CHOICES

edc_pharmacy/models/stock/order_item.py

@@ -1,7 +1,7 @@
+from clinicedc_constants import NEW
 from django.db import models
 from sequences import get_next_value
 
-from edc_constants.constants import NEW
 from edc_model.models import BaseUuidModel, HistoricalRecords
 
 from ...choices import ORDER_CHOICES
@@ -16,7 +16,6 @@ class Manager(models.Manager):
 
 
 class OrderItem(BaseUuidModel):
-
     order_item_identifier = models.CharField(
         max_length=36,
         unique=True,

edc_pharmacy/models/stock/stock_request.py

@@ -1,8 +1,8 @@
+from clinicedc_constants import CANCELLED, CLOSED, OPEN
 from django.db import models
 from django.utils import timezone
 from sequences import get_next_value
 
-from edc_constants.constants import CANCELLED, CLOSED, OPEN
 from edc_model.models import BaseUuidModel, HistoricalRecords
 from edc_registration.models import RegisteredSubject
 

edc_pharmacy/views/confirm_stock_from_queryset_view.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+from clinicedc_constants import CONFIRMED
 from django.apps import apps as django_apps
 from django.conf import settings
 from django.contrib import messages
@@ -9,7 +10,7 @@ from django.urls import reverse
 from django.utils.decorators import method_decorator
 from django.utils.translation import gettext as _
 from django.views.generic.base import TemplateView
-from edc_constants.constants import CONFIRMED
+
 from edc_dashboard.view_mixins import EdcViewMixin
 from edc_navbar import NavbarViewMixin
 from edc_protocol.view_mixins import EdcProtocolViewMixin

edc_pharmacy/views/confirmation_at_site_view.py

@@ -4,6 +4,7 @@ import contextlib
 import uuid
 from uuid import uuid4
 
+from clinicedc_constants import CONFIRMED
 from django.conf import settings
 from django.contrib import messages
 from django.contrib.auth.decorators import login_required
@@ -15,7 +16,6 @@ from django.urls import reverse
 from django.utils.decorators import method_decorator
 from django.views.generic.base import TemplateView
 
-from edc_constants.constants import CONFIRMED
 from edc_dashboard.view_mixins import EdcViewMixin
 from edc_navbar import NavbarViewMixin
 from edc_protocol.view_mixins import EdcProtocolViewMixin

edc_prn/models.py

@@ -1,9 +1,8 @@
 # do not delete
 
+from clinicedc_constants import NULL_STRING
 from django.db import models
 
-from edc_constants.constants import NULL_STRING
-
 
 class SingletonPrnModelMixin(models.Model):
     """Enforces one record per subject."""

edc_protocol_incident/action_items.py

@@ -1,5 +1,6 @@
+from clinicedc_constants import CLOSED, HIGH_PRIORITY
+
 from edc_action_item.action_with_notification import ActionWithNotification
-from edc_constants.constants import CLOSED, HIGH_PRIORITY
 
 from .constants import (
     PROTOCOL_DEVIATION_VIOLATION_ACTION,

edc_protocol_incident/choices.py

@@ -1,4 +1,4 @@
-from edc_constants.constants import CLOSED, OPEN
+from clinicedc_constants import CLOSED, OPEN
 
 from .constants import DEVIATION, VIOLATION, WITHDRAWN
 

edc_protocol_incident/form_validators/mixins.py

@@ -1,4 +1,5 @@
-from edc_constants.constants import CLOSED
+from clinicedc_constants import CLOSED
+
 from edc_form_validators import INVALID_ERROR
 from edc_protocol_incident.constants import WITHDRAWN
 

edc_protocol_incident/form_validators/protocol_deviation_violation_form_validator.py

@@ -1,4 +1,5 @@
-from edc_constants.constants import YES
+from clinicedc_constants import YES
+
 from edc_form_validators import FormValidator
 
 from ..constants import VIOLATION

edc_protocol_incident/form_validators/protocol_incident_form_validator.py

@@ -1,4 +1,5 @@
-from edc_constants.constants import YES
+from clinicedc_constants import YES
+
 from edc_form_validators import INVALID_ERROR, FormValidator
 from edc_prn.modelform_mixins import PrnFormValidatorMixin
 from edc_utils.date import to_local

edc_protocol_incident/list_data.py

@@ -1,4 +1,4 @@
-from edc_constants.constants import NOT_APPLICABLE, OTHER
+from clinicedc_constants import NOT_APPLICABLE, OTHER
 
 list_data = {
     "edc_protocol_incident.protocolviolations": [

edc_protocol_incident/model_mixins/protocol_deviation_violation_model_mixin.py

@@ -1,8 +1,8 @@
+from clinicedc_constants import NOT_APPLICABLE
 from django.db import models
 from django.utils import timezone
 
 from edc_constants.choices import YES_NO_NA
-from edc_constants.constants import NOT_APPLICABLE
 from edc_model import REPORT_STATUS
 from edc_model.validators import datetime_not_future
 

edc_protocol_incident/modeladmin_mixins.py

@@ -1,8 +1,8 @@
+from clinicedc_constants import CLOSED, OPEN
 from django.contrib import admin
 from django.utils.html import format_html
 from django_audit_fields.admin import audit_fieldset_tuple
 
-from edc_constants.constants import CLOSED, OPEN
 from edc_protocol_incident.constants import WITHDRAWN
 
 

edc_qareports/choices.py

@@ -1,4 +1,4 @@
-from edc_constants.constants import NOT_AVAILABLE, PENDING
+from clinicedc_constants import NOT_AVAILABLE, PENDING
 
 NOTE_STATUSES = (
     (PENDING, "Data is pending"),

edc_qareports/migrations/0017_auto_20240816_0256.py

@@ -3,7 +3,7 @@
 from django.db import migrations
 from django.db.migrations import RunPython
 
-from edc_constants.constants import FEEDBACK, PENDING
+from clinicedc_constants import FEEDBACK, PENDING
 
 
 def update_status(apps, schema_editor):
@@ -17,7 +17,6 @@ def update_status(apps, schema_editor):
 
 
 class Migration(migrations.Migration):
-
     dependencies = [
         ("edc_qareports", "0016_alter_note_options_alter_qareportlog_options"),
     ]

edc_qareports/modeladmin_mixins/list_filters.py

@@ -1,8 +1,7 @@
+from clinicedc_constants import NEW
 from django.contrib.admin import SimpleListFilter
 from django.db.models import Count, QuerySet
 
-from edc_constants.constants import NEW
-
 from ..choices import NOTE_STATUSES
 
 

edc_qareports/modeladmin_mixins/qa_report_modeladmin_mixin.py

@@ -1,3 +1,4 @@
+from clinicedc_constants import NEW
 from django.apps import apps as django_apps
 from django.contrib import admin
 from django.core.exceptions import ObjectDoesNotExist
@@ -5,7 +6,6 @@ from django.template.loader import render_to_string
 from django.urls import reverse
 from django.utils.translation import gettext as _
 
-from edc_constants.constants import NEW
 from edc_utils import truncate_string
 
 from ..models import QaReportLog

edc_qareports/sql_generator/requisition_subquery.py

@@ -1,7 +1,7 @@
 from dataclasses import dataclass, field
 from string import Template
 
-from edc_constants.constants import YES
+from clinicedc_constants import YES
 
 from .crf_subquery import CrfSubquery
 

edc_refusal/forms.py

@@ -1,8 +1,9 @@
+from clinicedc_constants import OTHER
 from django import forms
 from django.core.exceptions import ObjectDoesNotExist
 from django.urls.base import reverse
 from django.utils.html import format_html
-from edc_constants.constants import OTHER
+
 from edc_dashboard.url_names import url_names
 from edc_form_validators import FormValidator, FormValidatorMixin
 from edc_registration.models import RegisteredSubject

edc_refusal/list_data.py

@@ -1,4 +1,4 @@
-from edc_constants.constants import OTHER
+from clinicedc_constants import OTHER
 
 list_data = {
     "edc_refusal.refusalreasons": [