meta-edc 0.3.39__py3-none-any.whl → 1.4.0__py3-none-any.whl

meta_screening/admin/fieldsets.py

@@ -1,5 +1,3 @@
-from typing import Tuple
-
 from django.utils.safestring import mark_safe
 
 from ..forms import (
@@ -20,7 +18,7 @@ from ..forms.field_lists import (
 )
 
 
-def get_part_one_fieldset(collapse=None) -> Tuple[str, dict]:
+def get_part_one_fieldset(collapse=None) -> tuple[str, dict]:
     dct = {
         "description": mark_safe(  # nosec B308
             "To be completed by the <u>study clinician</u> or the "
@@ -33,7 +31,7 @@ def get_part_one_fieldset(collapse=None) -> Tuple[str, dict]:
     return "Part 1", dct
 
 
-def get_part_two_fieldset(collapse=None) -> Tuple[str, dict]:
+def get_part_two_fieldset(collapse=None) -> tuple[str, dict]:
     dct = {
         "description": mark_safe(  # nosec B308
             "To be completed by the <u>study clinician</u> or the "
@@ -48,7 +46,7 @@ def get_part_two_fieldset(collapse=None) -> Tuple[str, dict]:
 
 def get_part_three_fieldset(
     collapse=None,
-) -> Tuple[str, dict]:
+) -> tuple[str, dict]:
     dct = {
         "description": mark_safe(  # nosec B308
             "To be completed by the <u>study clinician</u>"
@@ -67,7 +65,7 @@ def get_part_three_glucose_fieldset(collapse=None):
     return "Part 3c:  Glucose Measurements (FBG / OGTT)", dct
 
 
-def get_part_three_repeat_glucose_fieldset(collapse=None) -> Tuple[str, dict]:
+def get_part_three_repeat_glucose_fieldset(collapse=None) -> tuple[str, dict]:
     fields = [
         "repeat_glucose_performed",
         "repeat_fasting",
@@ -87,47 +85,47 @@ def get_part_three_repeat_glucose_fieldset(collapse=None) -> Tuple[str, dict]:
     return "Part 3d: Repeat Glucose Measurements (FBG / OGTT)", dct
 
 
-def get_part_three_other_fieldset(collapse=None) -> Tuple[str, dict]:
+def get_part_three_other_fieldset(collapse=None) -> tuple[str, dict]:
     dct = {"fields": part_three_other_fields}
     if collapse:
         dct.update(classes=("collapse",))
     return "Part 3e: Creatinine / HbA1c", dct
 
 
-def get_part_three_creatinine_fieldset(collapse=None) -> Tuple[str, dict]:
+def get_part_three_creatinine_fieldset(collapse=None) -> tuple[str, dict]:
     dct = {"fields": part_three_creatinine_fields}
     if collapse:
         dct.update(classes=("collapse",))
     return "Part 3e: Creatinine", dct
 
 
-def get_part_three_hba1c_fieldset(collapse=None) -> Tuple[str, dict]:
+def get_part_three_hba1c_fieldset(collapse=None) -> tuple[str, dict]:
     dct = {"fields": part_three_hba1c_fields}
     if collapse:
         dct.update(classes=("collapse",))
     return "Part 3f: HbA1c", dct
 
 
-def get_part_three_report_datetime_fieldset() -> Tuple[str, dict]:
+def get_part_three_report_datetime_fieldset() -> tuple[str, dict]:
     dct = {"fields": ["part_three_report_datetime"]}
     return "Part 3", dct
 
 
-def get_part_three_vitals_fieldset(collapse=None) -> Tuple[str, dict]:
+def get_part_three_vitals_fieldset(collapse=None) -> tuple[str, dict]:
     dct = {"fields": part_three_vitals_fields}
     if collapse:
         dct.update(classes=("collapse",))
     return "Part 3a: Vitals", dct
 
 
-def get_part_three_pregnancy_fieldset(collapse=None) -> Tuple[str, dict]:
+def get_part_three_pregnancy_fieldset(collapse=None) -> tuple[str, dict]:
     dct = {"fields": part_three_pregnancy_fields}
     if collapse:
         dct.update(classes=("collapse",))
     return "Part 3b: Pregnancy", dct
 
 
-def get_p3_screening_appt_update_fields(collapse=None) -> Tuple[str, dict]:
+def get_p3_screening_appt_update_fields(collapse=None) -> tuple[str, dict]:
     dct = {
         "description": mark_safe(  # nosec B308
             '<span style="color:orange;font-weight:bold">IMPORTANT:</span>'
@@ -144,14 +142,14 @@ def get_p3_screening_appt_update_fields(collapse=None) -> Tuple[str, dict]:
     return "Part 3 screening appointment update", dct
 
 
-comments_fieldset: Tuple[str, dict] = (
+comments_fieldset: tuple[str, dict] = (
     "Additional Comments",
     {
         "fields": (*part_three_comment_fields,),
     },
 )
 
-calculated_values_fieldset: Tuple[str, dict] = (
+calculated_values_fieldset: tuple[str, dict] = (
     "Calculated values",
     {
         "classes": ("collapse",),

meta_screening/admin/list_filters.py

@@ -1,7 +1,7 @@
+from clinicedc_constants import NO, NOT_APPLICABLE, PENDING, TBD, YES
 from django.contrib import admin
 from django.db.models import Q
 from edc_appointment.admin import AppointmentListFilter
-from edc_constants.constants import NO, NOT_APPLICABLE, PENDING, TBD, YES
 
 from ..constants import PENDING_REPEAT
 
@@ -11,13 +11,13 @@ class EligibilityPending(admin.SimpleListFilter):
 
     parameter_name = "eligibility_pending"
 
-    def lookups(self, request, model_admin):
+    def lookups(self, request, model_admin):  # noqa: ARG002
         return (
             (PENDING, "Pending"),
             (PENDING_REPEAT, "Pending repeat GLU"),
         )
 
-    def queryset(self, request, queryset):
+    def queryset(self, request, queryset):  # noqa: ARG002
         if self.value() == PENDING_REPEAT:
             return queryset.filter(
                 eligible_part_one=YES,
@@ -35,6 +35,7 @@ class EligibilityPending(admin.SimpleListFilter):
                 p3_ltfu=NOT_APPLICABLE,
                 part_three_report_datetime__isnull=True,
             )
+        return queryset
 
 
 class P3LtfuListFilter(admin.SimpleListFilter):
@@ -42,13 +43,13 @@ class P3LtfuListFilter(admin.SimpleListFilter):
 
     parameter_name = "p3_ltfu_custom"
 
-    def lookups(self, request, model_admin):
+    def lookups(self, request, model_admin):  # noqa: ARG002
         return (
             (YES, "Yes"),
             (NO, "No, lost contact"),
         )
 
-    def queryset(self, request, queryset):
+    def queryset(self, request, queryset):  # noqa: ARG002
         if self.value() == YES:
             return queryset.filter(
                 eligible_part_one=YES,
@@ -69,6 +70,7 @@ class P3LtfuListFilter(admin.SimpleListFilter):
                 | Q(eligible_part_two=TBD)
                 | Q(eligible_part_three=TBD)
             )
+        return queryset
 
 
 class P3ApptListFilter(AppointmentListFilter):

meta_screening/admin/screening_part_one_admin.py

@@ -1,5 +1,3 @@
-from typing import Tuple
-
 from django.contrib import admin
 from django_audit_fields.admin import audit_fieldset_tuple
 from edc_sites.admin import SiteModelAdminMixin
@@ -35,7 +33,7 @@ class ScreeningPartOneAdmin(SiteModelAdminMixin, SubjectScreeningAdmin):
 
     fieldsets = get_fieldsets()
 
-    readonly_fields: Tuple[str, ...] = (
+    readonly_fields: tuple[str, ...] = (
         *part_two_fields,
         *part_three_fields,
         *calculated_fields,

meta_screening/admin/screening_part_three_admin.py

@@ -1,5 +1,4 @@
 from copy import deepcopy
-from typing import Tuple
 
 from django.contrib import admin
 from django_audit_fields.admin import audit_fieldset_tuple
@@ -30,7 +29,7 @@ from .list_filters import EligibilityPending, P3ApptListFilter, P3LtfuListFilter
 from .subject_screening_admin import SubjectScreeningAdmin
 
 
-def get_part_two_fieldset_without_contact_number() -> Tuple[str, dict]:
+def get_part_two_fieldset_without_contact_number() -> tuple[str, dict]:
     """Remove contact number from the part 2 fields"""
     part_two_name, part_two_dct = get_part_two_fieldset(collapse=True)
     part_two_dct = deepcopy(part_two_dct)
@@ -76,7 +75,7 @@ class ScreeningPartThreeAdmin(SiteModelAdminMixin, SubjectScreeningAdmin):
         "refused",
     )
 
-    readonly_fields: Tuple[str, ...] = (
+    readonly_fields: tuple[str, ...] = (
         *part_one_fields,
         *(f for f in part_two_fields if f != "contact_number"),
         *calculated_fields,

meta_screening/admin/screening_part_two_admin.py

@@ -1,5 +1,3 @@
-from typing import Tuple
-
 from django.contrib import admin
 from django_audit_fields.admin import audit_fieldset_tuple
 from edc_sites.admin import SiteModelAdminMixin
@@ -21,12 +19,12 @@ from .fieldsets import (
 from .subject_screening_admin import SubjectScreeningAdmin
 
 
-def get_fieldsets() -> Tuple[
-    Tuple[str, dict],
-    Tuple[str, dict],
-    Tuple[str, dict],
-    Tuple[str, dict],
-    Tuple[str, dict],
+def get_fieldsets() -> tuple[
+    tuple[str, dict],
+    tuple[str, dict],
+    tuple[str, dict],
+    tuple[str, dict],
+    tuple[str, dict],
 ]:
     return (
         get_part_one_fieldset(collapse=True),
@@ -39,12 +37,11 @@ def get_fieldsets() -> Tuple[
 
 @admin.register(ScreeningPartTwo, site=meta_screening_admin)
 class ScreeningPartTwoAdmin(SiteModelAdminMixin, SubjectScreeningAdmin):
-
     form = ScreeningPartTwoForm
 
     fieldsets = get_fieldsets()
 
-    readonly_fields: Tuple[str, ...] = (
+    readonly_fields: tuple[str, ...] = (
         *part_one_fields,
         *part_three_fields,
         *calculated_fields,

meta_screening/admin/subject_refusal_admin.py

@@ -17,7 +17,7 @@ class SubjectRefusalAdmin(
 ):
     form = SubjectRefusalForm
 
-    autocomplete_fields = ["subject_screening"]
+    autocomplete_fields = ("subject_screening",)
 
     post_url_on_delete_name = "screening_listboard_url"
     subject_listboard_url_name = "screening_listboard_url"
@@ -54,7 +54,7 @@ class SubjectRefusalAdmin(
         "subject_screening__initials",
     )
 
-    radio_fields = {"reason": admin.VERTICAL}
+    radio_fields = {"reason": admin.VERTICAL}  # noqa: RUF012
 
     def get_subject_dashboard_url_kwargs(self, obj):
         return dict(screening_identifier=obj.screening_identifier)
@@ -69,5 +69,7 @@ class SubjectRefusalAdmin(
             if callable(super().view_on_site):
                 url = super().view_on_site(obj)
             else:
-                raise NoReverseMatch(f"{e}. See subject_dashboard_url_name for {repr(self)}.")
+                raise NoReverseMatch(
+                    f"{e}. See subject_dashboard_url_name for {self!r}."
+                ) from e
         return url

meta_screening/admin/subject_screening_admin.py

@@ -1,11 +1,12 @@
+from clinicedc_constants import YES
 from django.contrib import admin
 from django.template.loader import render_to_string
 from django.urls.base import reverse
 from django.urls.exceptions import NoReverseMatch
 from django.utils.html import format_html
+from django.utils.safestring import mark_safe
 from django.utils.translation import gettext_lazy as _
 from django_audit_fields.admin import audit_fieldset_tuple
-from edc_constants.constants import YES
 from edc_dashboard.url_names import url_names
 from edc_model_admin.dashboard import ModelAdminSubjectDashboardMixin
 from edc_model_admin.history import SimpleHistoryAdmin
@@ -30,7 +31,8 @@ class SubjectScreeningAdmin(ModelAdminSubjectDashboardMixin, SimpleHistoryAdmin)
     form = SubjectScreeningForm
     list_per_page = 15
     post_url_on_delete_name = "screening_listboard_url"
-    subject_listboard_url_name = "screening_listboard_url"
+    subject_listboard_url_name = "screening_listboard_url"  # :FIXME is this ok?
+    screening_listboard_url_name = "screening_listboard_url"
 
     additional_instructions = (
         "Patients must meet ALL of the inclusion criteria and NONE of the "
@@ -96,7 +98,7 @@ class SubjectScreeningAdmin(ModelAdminSubjectDashboardMixin, SimpleHistoryAdmin)
         "inclusion_d",
     )
 
-    radio_fields = {
+    radio_fields = {  # noqa: RUF012
         "acute_condition": admin.VERTICAL,
         "acute_metabolic_acidosis": admin.VERTICAL,
         "advised_to_fast": admin.VERTICAL,
@@ -144,11 +146,11 @@ class SubjectScreeningAdmin(ModelAdminSubjectDashboardMixin, SimpleHistoryAdmin)
         "vl_undetectable": admin.VERTICAL,
     }
 
-    def post_url_on_delete_kwargs(self, request, obj):
+    def post_url_on_delete_kwargs(self, request, obj):  # noqa: ARG002
         return {}
 
     # TODO: this is a hack!
-    def get_post_url_on_delete_name(self, request) -> str:
+    def get_post_url_on_delete_name(self, request) -> str:  # noqa: ARG002
         return url_names.get(self.post_url_on_delete_name)
 
     @staticmethod
@@ -160,7 +162,10 @@ class SubjectScreeningAdmin(ModelAdminSubjectDashboardMixin, SimpleHistoryAdmin)
         ]
         if obj.repeat_glucose_opinion == YES:
             data.append(f"Contact #: {obj.contact_number or '--'}")
-        return format_html("<BR>".join(data))
+        return format_html(
+            "{}",
+            mark_safe("<BR>".join(data)),  # noqa: S308
+        )
 
     def reasons(self, obj=None):
         if not obj.reasons_ineligible:
@@ -170,15 +175,21 @@ class SubjectScreeningAdmin(ModelAdminSubjectDashboardMixin, SimpleHistoryAdmin)
     def eligibility_status(self, obj=None):
         eligibility = MetaEligibility(obj, update_model=False)
         screening_listboard_url = reverse(
-            url_names.get(self.subject_listboard_url_name), args=(obj.screening_identifier,)
+            url_names.get(self.screening_listboard_url_name), args=(obj.screening_identifier,)
         )
         context = dict(
             title="Go to screening listboard",
             url=f"{screening_listboard_url}?q={obj.screening_identifier}",
             label="Screening",
         )
-        button = render_to_string("dashboard_button.html", context=context)
-        return format_html(button + "<BR>" + eligibility.eligibility_status(add_urls=True))
+        button = render_to_string(
+            "edc_subject_dashboard/dashboard_button.html", context=context
+        )
+        return format_html(
+            "{button}<BR>{status}",
+            button=button,
+            status=eligibility.eligibility_status(add_urls=True),
+        )
 
     def dashboard(self, obj=None, label=None):
         try:
@@ -187,7 +198,7 @@ class SubjectScreeningAdmin(ModelAdminSubjectDashboardMixin, SimpleHistoryAdmin)
                 kwargs=self.get_subject_dashboard_url_kwargs(obj),
             )
         except NoReverseMatch:
-            url = reverse(url_names.get("screening_listboard_url"), kwargs={})
+            url = reverse(self.get_screening_listboard_url_name(), kwargs={})
             context = dict(
                 title="Go to screening listboard",
                 url=f"{url}?q={obj.screening_identifier}",

meta_screening/baker_recipes.py

@@ -1,8 +1,16 @@
+from clinicedc_constants import (
+    BLACK,
+    FEMALE,
+    MILLIGRAMS_PER_DECILITER,
+    MILLIMOLES_PER_LITER,
+    NO,
+    NOT_APPLICABLE,
+    NULL_STRING,
+    YES,
+)
 from dateutil.relativedelta import relativedelta
 from django.contrib.sites.models import Site
-from edc_constants.constants import BLACK, FEMALE, NO, NOT_APPLICABLE, YES
-from edc_reportable.units import MILLIGRAMS_PER_DECILITER, MILLIMOLES_PER_LITER
-from edc_utils import get_utcnow
+from django.utils import timezone
 from faker import Faker
 from model_bakery.recipe import Recipe
 
@@ -13,11 +21,11 @@ fake = Faker()
 
 subjectscreening = Recipe(
     SubjectScreening,
-    report_datetime=get_utcnow() - relativedelta(days=1),
+    report_datetime=timezone.now() - relativedelta(days=1),
     screening_consent=YES,
     hospital_identifier="111",
     initials="ZZ",
-    subject_identifier=None,
+    subject_identifier=NULL_STRING,
     gender=FEMALE,
     age_in_years=40,
     ethnicity=BLACK,
@@ -29,7 +37,7 @@ subjectscreening = Recipe(
     staying_nearby_12=YES,
     pregnant=NO,
     site=Site.objects.get_current(),
-    part_two_report_datetime=get_utcnow() - relativedelta(days=1),
+    part_two_report_datetime=timezone.now() - relativedelta(days=1),
     congestive_heart_failure=NO,
     liver_disease=NO,
     alcoholism=NO,
@@ -39,8 +47,8 @@ subjectscreening = Recipe(
     acute_condition=NO,
     metformin_sensitivity=NO,
     advised_to_fast=YES,
-    appt_datetime=get_utcnow() + relativedelta(days=1),
-    part_three_report_datetime=get_utcnow(),
+    appt_datetime=timezone.now() + relativedelta(days=1),
+    part_three_report_datetime=timezone.now(),
     weight=65,
     height=120,
     fasting=YES,
@@ -51,8 +59,8 @@ subjectscreening = Recipe(
     creatinine_units=MILLIGRAMS_PER_DECILITER,
     fbg_value=6.9,
     fbg_units=MILLIMOLES_PER_LITER,
-    fbg_datetime=get_utcnow(),
-    ogtt_base_datetime=get_utcnow(),
+    fbg_datetime=timezone.now(),
+    ogtt_base_datetime=timezone.now(),
     unsuitable_for_study=NO,
     unsuitable_agreed=NOT_APPLICABLE,
     vl_undetectable=YES,

meta_screening/calculators.py

@@ -1,4 +1,4 @@
-from edc_constants.constants import NO, TBD, YES
+from clinicedc_constants import NO, TBD, YES
 
 
 def calculate_inclusion_field_values_phase_two(obj):

meta_screening/choices.py

@@ -1,4 +1,4 @@
-from edc_constants.constants import BLACK, NO, NOT_APPLICABLE, OTHER, PENDING, YES
+from clinicedc_constants import BLACK, NO, NOT_APPLICABLE, OTHER, PENDING, YES
 
 ETHNICITY = ((BLACK, "Black"), (OTHER, "Other"))
 

meta_screening/constants.py

@@ -1,4 +1,4 @@
-from edc_constants.constants import NO, NOT_APPLICABLE, YES
+from clinicedc_constants import NO, NOT_APPLICABLE, YES
 
 BMI_FBG_OGTT_INCOMPLETE = "BMI/FBG/OGTT incomplete"
 BMI_FBG_OGTT = "BMI/FBG/OGTT"

meta_screening/eligibility/__init__.py

@@ -6,3 +6,12 @@ from .eligibility import (
 from .eligibility_part_one import EligibilityPartOne
 from .eligibility_part_three import EligibilityPartThreePhaseThree
 from .eligibility_part_two import EligibilityPartTwo
+
+__all__ = [
+    "EligibilityPartOne",
+    "EligibilityPartThreePhaseThree",
+    "EligibilityPartTwo",
+    "MetaEligibility",
+    "SubjectScreeningEligibilityError",
+    "get_display_label",
+]

meta_screening/eligibility/eligibility.py

@@ -1,9 +1,9 @@
 from typing import Any
 
+from clinicedc_constants import NO, TBD, YES
 from django.db import models
 from django.urls import reverse
 from django.utils.html import format_html
-from edc_constants.constants import NO, TBD, YES
 from edc_utils import get_utcnow
 
 from ..constants import EGFR_NOT_CALCULATED
@@ -16,7 +16,7 @@ class SubjectScreeningEligibilityError(Exception):
     pass
 
 
-def get_eligible_as_word(
+def get_eligible_as_word(  # noqa: PLR0913
     obj=None,
     eligible_part_one=None,
     eligible_part_two=None,
@@ -90,8 +90,8 @@ class MetaEligibility:
 
     """
 
-    eligibility_values = [YES, NO, TBD]
-    default_options = dict(
+    eligibility_values = (YES, NO, TBD)
+    default_options = dict(  # noqa: RUF012
         eligible_value_default=TBD,
         eligible_values_list=[YES, NO, TBD],
         is_eligible_value=YES,
@@ -99,8 +99,8 @@ class MetaEligibility:
 
     def __init__(
         self,
-        model_obj: models.Model = None,
-        defaults: dict = None,
+        model_obj: models.Model | None = None,
+        defaults: dict | None = None,
         update_model=None,
     ):
         self.part_one = None
@@ -162,7 +162,7 @@ class MetaEligibility:
     @property
     def is_eligible(self: Any) -> bool:
         """Returns True if eligible else False"""
-        return True if self.eligible == YES else False
+        return self.eligible == YES
 
     def check_eligibility_values_or_raise(self: Any):
         for response in [
@@ -195,15 +195,22 @@ class MetaEligibility:
                 args=(self.part_three.model_obj.id,),
             )
             status_str = format_html(
-                f'<A href="{url_p1}">P1: {self.part_one.eligible.upper()}</A><BR>'
-                f'<A href="{url_p2}">P2: {self.part_two.eligible.upper()}</A><BR>'
-                f'<A href="{url_p3}">P3: {self.part_three.eligible.upper()}</A><BR>'
+                '<A href="{url_p1}">P1: {p1_eligible}</A>'
+                '<BR><A href="{url_p2}">P2: {p2_eligible}</A>'
+                '<BR><A href="{url_p3}">P3: {p3_eligible}</A><BR>',
+                url_p1=url_p1,
+                p1_eligible=self.part_one.eligible.upper(),
+                url_p2=url_p2,
+                p2_eligible=self.part_two.eligible.upper(),
+                url_p3=url_p3,
+                p3_eligible=self.part_three.eligible.upper(),
             )
         else:
-            status_str = (
-                f"P1: {self.part_one.eligible.upper()}<BR>"
-                f"P2: {self.part_two.eligible.upper()}<BR>"
-                f"P3: {self.part_three.eligible.upper()}<BR>"
+            status_str = format_html(
+                "P1: {p1_eligible}<BR>P2: {p2_eligible}<BR>P3: {p3_eligible}<BR>",
+                p1_eligible=self.part_one.eligible.upper(),
+                p2_eligible=self.part_two.eligible.upper(),
+                p3_eligible=self.part_three.eligible.upper(),
             )
         display_label = self.display_label
         if "PENDING" in display_label:

meta_screening/eligibility/eligibility_part_one.py

@@ -1,4 +1,4 @@
-from edc_constants.constants import FEMALE, MALE, NO, NOT_APPLICABLE, YES
+from clinicedc_constants import FEMALE, MALE, NO, NOT_APPLICABLE, YES
 from edc_screening.fc import FC
 from edc_screening.screening_eligibility import ScreeningEligibility
 

meta_screening/eligibility/eligibility_part_three/__init__.py

@@ -1 +1,3 @@
 from .eligibility_part_three_phase_three import EligibilityPartThreePhaseThree
+
+__all__ = ["EligibilityPartThreePhaseThree"]