meta-edc 1.1.10__py3-none-any.whl → 1.1.13__py3-none-any.whl

meta_reports/models/dbviews/__init__.py

@@ -7,3 +7,17 @@ from .patient_history_missing_baseline_cd4 import PatientHistoryMissingBaselineC
 from .unattended_three_in_row import UnattendedThreeInRow
 from .unattended_three_in_row2 import UnattendedThreeInRow2
 from .unattended_two_in_row import UnattendedTwoInRow
+
+__all__ = [
+    "NOTE_STATUSES",
+    "GlucoseSummary",
+    "ImpSubstitutions",
+    "MissingOgttNote",
+    "MissingScreeningOgtt",
+    "OnStudyMissingLabValues",
+    "OnStudyMissingValues",
+    "PatientHistoryMissingBaselineCd4",
+    "UnattendedThreeInRow",
+    "UnattendedThreeInRow2",
+    "UnattendedTwoInRow",
+]

meta_reports/models/dbviews/glucose_summary/__init__.py

@@ -1,2 +1,4 @@
 from .unmanaged_model import GlucoseSummary
 from .view_definition import get_view_definition
+
+__all__ = ["GlucoseSummary", "get_view_definition"]

meta_reports/models/dbviews/glucose_summary/unmanaged_model.py

@@ -6,20 +6,19 @@ from .view_definition import get_view_definition
 
 
 class GlucoseSummary(QaReportModelMixin, DBView):
-
     fbg_value = models.DecimalField(max_digits=8, decimal_places=2, null=True)
 
-    fbg_units = models.CharField(max_length=15, null=True)
+    fbg_units = models.CharField(max_length=15, default="")
 
     fbg_datetime = models.DateTimeField(null=True)
 
     ogtt_value = models.DecimalField(max_digits=8, decimal_places=2, null=True)
 
-    ogtt_units = models.CharField(max_length=15, null=True)
+    ogtt_units = models.CharField(max_length=15, default="")
 
     ogtt_datetime = models.DateTimeField(null=True)
 
-    fasted = models.CharField(max_length=15, null=True)
+    fasted = models.CharField(max_length=15, default="")
 
     fasting_duration_delta = models.DurationField(
         verbose_name="Fasting duration (hrs)", null=True
@@ -35,7 +34,7 @@ class GlucoseSummary(QaReportModelMixin, DBView):
 
     offstudy_datetime = models.DateTimeField(null=True)
 
-    source = models.CharField(max_length=35, null=True)
+    source = models.CharField(max_length=35, default="")
 
     view_definition = get_view_definition()
 

meta_reports/models/dbviews/imp_substitutions/__init__.py

@@ -1 +1,3 @@
 from .unmanaged_model import ImpSubstitutions
+
+__all__ = ["ImpSubstitutions"]

meta_reports/models/dbviews/imp_substitutions/view_definition.py

@@ -9,7 +9,7 @@ def get_view_definition() -> dict:
         from meta_pharmacy_substitutions as s left join meta_rando_randomizationlist as r
         on r.subject_identifier=s.subject_identifier
         order by s.subject_identifier
-        """  # noqa
+        """
     sql_view = SqlViewGenerator(
         report_model="meta_reports.imp_subjectitutions_view",
         ordering=["subject_identifier", "site_id"],

meta_reports/models/dbviews/missing_screening_ogtt/__init__.py

@@ -1,2 +1,4 @@
 from .note_model import NOTE_STATUSES, MissingOgttNote
 from .unmanaged_model import MissingScreeningOgtt
+
+__all__ = ["NOTE_STATUSES", "MissingOgttNote", "MissingScreeningOgtt"]

meta_reports/models/dbviews/missing_screening_ogtt/note_model.py

@@ -1,7 +1,7 @@
 from django.db import models
 from edc_constants.choices import YES_NO, YES_NO_NA
 from edc_constants.constants import COMPLETE, DONE, NOT_APPLICABLE, NOT_AVAILABLE, YES
-from edc_glucose.model_mixins import (
+from edc_glucose.model_mixin_factories import (
     fasting_model_mixin_factory,
     ogtt_model_mixin_factory,
 )

meta_reports/models/dbviews/missing_screening_ogtt/unmanaged_model.py

@@ -6,7 +6,6 @@ from .view_definition import get_view_definition
 
 
 class MissingScreeningOgtt(QaReportModelMixin, DBView):
-
     screening_datetime = models.DateTimeField(null=True)
 
     fbg_datetime = models.DateTimeField(null=True)
@@ -23,9 +22,11 @@ class MissingScreeningOgtt(QaReportModelMixin, DBView):
 
     ogtt2_datetime = models.DateTimeField(null=True)
 
-    repeated = models.CharField(null=True, max_length=25, help_text="repeat_glucose_performed")
+    repeated = models.CharField(
+        default="", max_length=25, help_text="repeat_glucose_performed"
+    )
 
-    p3_ltfu = models.CharField(null=True, max_length=25)
+    p3_ltfu = models.CharField(default="", max_length=25)
 
     consented = models.BooleanField(null=True)
 

meta_reports/models/dbviews/on_study_missing_lab_values/__init__.py

@@ -1 +1,3 @@
 from .unmanged_model import OnStudyMissingLabValues
+
+__all__ = ["OnStudyMissingLabValues"]

meta_reports/models/dbviews/on_study_missing_lab_values/qa_cases.py

@@ -1,8 +1,10 @@
+import contextlib
+
 from edc_lab_panel.constants import FBC, LFT, LIPIDS, RFT
 from edc_lab_panel.panels import fbc_panel, lft_panel, lipids_panel, rft_panel
 from edc_qareports.sql_generator import CrfCase, RequisitionCase
 
-qa_cases = [
+qa_cases: list[RequisitionCase | CrfCase] = [
     RequisitionCase(
         label="FBC requisitioned but not entered",
         dbtable="meta_subject_bloodresultsfbc",
@@ -32,10 +34,8 @@ qa_cases = [
 panels = {FBC: fbc_panel, RFT: rft_panel, LFT: lft_panel, LIPIDS: lipids_panel}
 for abbrev, panel in panels.items():
     for utest_id in panel.utest_ids:
-        try:
-            utest_id, _ = utest_id
-        except ValueError:
-            pass
+        with contextlib.suppress(ValueError):
+            utest_id, _ = utest_id  # noqa: PLW2901
         qa_cases.append(
             CrfCase(
                 label=f"{abbrev.upper()}: missing {utest_id} value/units",
@@ -45,9 +45,11 @@ for abbrev, panel in panels.items():
             )
         )
 
-    CrfCase(
-        label="No UREA value",
-        dbtable="meta_subject_bloodresultsrft",
-        label_lower="meta_subject.bloodresultsrft",
-        where="crf.urea_value is null or crf.urea_units is null",
-    ),
+    (
+        CrfCase(
+            label="No UREA value",
+            dbtable="meta_subject_bloodresultsrft",
+            label_lower="meta_subject.bloodresultsrft",
+            where="crf.urea_value is null or crf.urea_units is null",
+        ),
+    )

meta_reports/models/dbviews/on_study_missing_values/__init__.py

@@ -1 +1,3 @@
 from .unmanged_model import OnStudyMissingValues
+
+__all__ = ["OnStudyMissingValues"]

meta_reports/models/dbviews/patient_history_missing_baseline_cd4/__init__.py

@@ -1 +1,3 @@
 from .unmanaged_model import PatientHistoryMissingBaselineCd4
+
+__all__ = ["PatientHistoryMissingBaselineCd4"]

meta_reports/models/dbviews/unattended_three_in_row/__init__.py

@@ -1 +1,3 @@
 from .unmanaged_model import UnattendedThreeInRow
+
+__all__ = ["UnattendedThreeInRow"]

meta_reports/models/dbviews/unattended_three_in_row2/__init__.py

@@ -1 +1,3 @@
 from .unmanaged_model import UnattendedThreeInRow2
+
+__all__ = ["UnattendedThreeInRow2"]

meta_reports/models/dbviews/unattended_two_in_row/__init__.py

@@ -1 +1,3 @@
 from .unmanaged_model import UnattendedTwoInRow
+
+__all__ = ["UnattendedTwoInRow"]

meta_reports/models/endpoints.py

@@ -9,7 +9,7 @@ class Endpoints(QaReportModelMixin, models.Model):
 
     visit_code = models.IntegerField(null=True)
 
-    fasting = models.CharField(max_length=10, null=True)
+    fasting = models.CharField(max_length=10, default="")
 
     fbg_date = models.DateField(null=True)
 
@@ -17,18 +17,18 @@ class Endpoints(QaReportModelMixin, models.Model):
 
     ogtt_value = models.FloatField(null=True)
 
-    endpoint_label = models.CharField(max_length=250, null=True)
+    endpoint_label = models.CharField(max_length=250, default="")
 
     baseline_date = models.DateField(null=True)
 
     offstudy_date = models.DateField(null=True)
 
-    offstudy_reason = models.CharField(max_length=250, null=True)
+    offstudy_reason = models.CharField(max_length=250, default="")
 
     def __str__(self):
         return f"{self.subject_identifier} {self.visit_code} {self.endpoint_label}"
 
-    class Meta(QaReportModelMixin.Meta):
+    class Meta(QaReportModelMixin.Meta):  # noqa: DJ012
         verbose_name = "Endpoints (DM)"
         verbose_name_plural = "Endpoints (DM)"
         default_permissions = qa_reports_permissions

meta_reports/models/last_imp_refill.py

@@ -4,7 +4,6 @@ from edc_qareports.model_mixins import QaReportModelMixin, qa_reports_permission
 
 
 class LastImpRefill(QaReportModelMixin, models.Model):
-
     reference_date = models.DateField(null=True)
 
     imp_visit_code = models.FloatField(null=True)
@@ -15,7 +14,7 @@ class LastImpRefill(QaReportModelMixin, models.Model):
 
     next_appt_date = models.DateField(null=True)
 
-    visit_code = models.CharField(max_length=15, null=True)
+    visit_code = models.CharField(max_length=15, default="")
 
     visit_code_sequence = models.IntegerField(null=True)
 
@@ -28,7 +27,7 @@ class LastImpRefill(QaReportModelMixin, models.Model):
     def recreate_db_view(self, **kwargs):
         raise NotImplementedError()
 
-    class Meta(QaReportModelMixin.Meta):
+    class Meta(QaReportModelMixin.Meta):  # noqa: DJ012
         verbose_name = "Last IMP Refill"
         verbose_name_plural = "Last IMP Refills"
         default_permissions = qa_reports_permissions

meta_reports/pdf_report.py

@@ -20,7 +20,7 @@ def get_weight_for_timepoint(subject_identifier=None, reference_dt=None):
 
 
 class MetaCrfPdfReport(CrfPdfReport):
-    logo_data = {
+    logo_data = {  # noqa: RUF012
         "app_label": "meta_edc",
         "filename": "meta_logo.png",
         "first_page": (4.0 * cm, 0.83 * cm),
@@ -34,7 +34,7 @@ class MetaCrfPdfReport(CrfPdfReport):
             subject_identifier=self.subject_identifier
         ).get_drug_assignment_display()
 
-    def draw_demographics(self, story, **kwargs):
+    def draw_demographics(self, story, **kwargs):  # noqa: ARG002
         model_obj = getattr(self, self.model_attr)
         weight = get_weight_for_timepoint(
             subject_identifier=self.subject_identifier,

meta_reports/tasks.py

@@ -3,7 +3,7 @@ from celery import shared_task
 
 @shared_task
 def update_endpoints_table(subject_identifiers: list[str] | None = None):
-    from meta_analytics.dataframes import GlucoseEndpointsByDate
+    from meta_analytics.dataframes import GlucoseEndpointsByDate  # noqa: PLC0415
 
     if len(subject_identifiers) > 5:
         cls = GlucoseEndpointsByDate()

meta_screening/admin/__init__.py

@@ -3,3 +3,11 @@ from .screening_part_three_admin import ScreeningPartThreeAdmin
 from .screening_part_two_admin import ScreeningPartTwoAdmin
 from .subject_refusal_admin import SubjectRefusalAdmin
 from .subject_screening_admin import SubjectScreeningAdmin
+
+__all__ = [
+    "ScreeningPartOneAdmin",
+    "ScreeningPartThreeAdmin",
+    "ScreeningPartTwoAdmin",
+    "SubjectRefusalAdmin",
+    "SubjectScreeningAdmin",
+]

meta_screening/admin/fieldsets.py

@@ -1,4 +1,3 @@
-from typing import Tuple
 
 from django.utils.safestring import mark_safe
 
@@ -20,7 +19,7 @@ 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 +32,7 @@ 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 +47,7 @@ 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 +66,7 @@ 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 +86,47 @@ 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 +143,14 @@ 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

@@ -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

@@ -1,4 +1,3 @@
-from typing import Tuple
 
 from django.contrib import admin
 from django_audit_fields.admin import audit_fieldset_tuple
@@ -35,7 +34,7 @@ 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

@@ -97,7 +97,7 @@ 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,
@@ -145,11 +145,11 @@ 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
@@ -163,7 +163,7 @@ class SubjectScreeningAdmin(ModelAdminSubjectDashboardMixin, SimpleHistoryAdmin)
             data.append(f"Contact #: {obj.contact_number or '--'}")
         return format_html(
             "{}",
-            mark_safe("<BR>".join(data)),  # nosec B703, B308
+            mark_safe("<BR>".join(data)),  # noqa: S308
         )
 
     def reasons(self, obj=None):