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

meta_reports/migrations/0061_auto_20251004_0043.py

@@ -0,0 +1,21 @@
+# Generated by Django 5.2.7 on 2025-10-03 21:43
+
+from django.db import migrations
+
+
+def fix_report_models(apps, schema_editor):
+    note_cls = apps.get_model("edc_qareports", "Note")
+    note_cls.objects.filter(report_model="onstudy_missing_values_view").update(
+        report_model="meta_reports.onstudy_missing_values_view"
+    )
+    note_cls.objects.filter(report_model="onstudy_missing_lab_values_view").update(
+        report_model="meta_reports.onstudy_missing_lab_values_view"
+    )
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("meta_reports", "0060_auto_20250926_0242"),
+    ]
+
+    operations = [migrations.RunPython(fix_report_models)]

meta_reports/migrations/0062_auto_20251004_0106.py

@@ -0,0 +1,21 @@
+# Generated by Django 5.2.7 on 2025-10-03 22:06
+
+from django.db import migrations
+
+
+def fix_report_models(apps, schema_editor):
+    note_cls = apps.get_model("edc_qareports", "Note")
+    note_cls.objects.filter(report_model="meta_reports.onstudy_missing_values_view").update(
+        report_model="meta_reports.onstudymissingvalues"
+    )
+    note_cls.objects.filter(
+        report_model="meta_reports.onstudy_missing_lab_values_view"
+    ).update(report_model="meta_reports.onstudymissinglabvalues")
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("meta_reports", "0061_auto_20251004_0043"),
+    ]
+
+    operations = [migrations.RunPython(fix_report_models)]

meta_reports/models/__init__.py

@@ -14,3 +14,20 @@ from .dbviews import (
 from .endpoints import Endpoints
 from .endpoints_proxy import EndpointsProxy
 from .last_imp_refill import LastImpRefill
+
+__all__ = [
+    "NOTE_STATUSES",
+    "Endpoints",
+    "EndpointsProxy",
+    "GlucoseSummary",
+    "ImpSubstitutions",
+    "LastImpRefill",
+    "MissingOgttNote",
+    "MissingScreeningOgtt",
+    "OnStudyMissingLabValues",
+    "OnStudyMissingValues",
+    "PatientHistoryMissingBaselineCd4",
+    "UnattendedThreeInRow",
+    "UnattendedThreeInRow2",
+    "UnattendedTwoInRow",
+]

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

@@ -1,3 +1,4 @@
+from clinicedc_constants import NULL_STRING
 from django.db import models
 from django_db_views.db_view import DBView
 from edc_qareports.model_mixins import QaReportModelMixin, qa_reports_permissions
@@ -6,16 +7,25 @@ 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, default=NULL_STRING)
+
     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, default=NULL_STRING)
+
     ogtt_datetime = models.DateTimeField(null=True)
 
-    fasted = models.CharField(max_length=15, null=True)
+    fasted = models.CharField(max_length=15, default=NULL_STRING)
+
+    fasting_duration_delta = models.DurationField(
+        verbose_name="Fasting duration (hrs)", null=True
+    )
+
+    report_datetime = models.DateTimeField(null=True)
 
     visit_code = models.CharField(max_length=25)
 
@@ -25,11 +35,13 @@ class GlucoseSummary(QaReportModelMixin, DBView):
 
     offstudy_datetime = models.DateTimeField(null=True)
 
+    source = models.CharField(max_length=35, default=NULL_STRING)
+
     view_definition = get_view_definition()
 
     class Meta:
         managed = False
-        db_table = "glucose_summary_view"
+        db_table = "meta_reports_glucosesummaryview"
         verbose_name = "Glucose Summary"
         verbose_name_plural = "Glucose Summary"
         default_permissions = qa_reports_permissions

meta_reports/models/dbviews/glucose_summary/view_definition.py

@@ -3,22 +3,25 @@ from edc_qareports.sql_generator import SqlViewGenerator
 
 def get_view_definition() -> dict:
     subquery = """
-    select v.subject_identifier, fbg_value, fbg_datetime, null as `ogtt_value`, null as `ogtt_datetime`,
+    select v.subject_identifier, fbg_value, fbg_units, fbg_datetime, null as `ogtt_value`, null as `ogtt_units`,
+    null as `ogtt_datetime`,
     case when fasting="fasting" then "Yes" when fasting="non_fasting" then "No" else fasting end as `fasted`,
-    fbg.site_id, v.visit_code, v.visit_code_sequence, v.appointment_id, eos.offstudy_datetime
+    fbg.site_id, v.visit_code, v.visit_code_sequence, v.report_datetime, v.appointment_id, eos.offstudy_datetime,
+    fasting_duration_delta, "meta_subject.glucosefbg" as source
     from meta_subject_glucosefbg as fbg
     left join meta_subject_subjectvisit as v on v.id=fbg.subject_visit_id
     left join meta_prn_endofstudy as eos on v.subject_identifier=eos.subject_identifier
     UNION
-    select v.subject_identifier, fbg_value, fbg_datetime, ogtt_value, ogtt_datetime,
+    select v.subject_identifier, fbg_value, fbg_units, fbg_datetime, ogtt_value, ogtt_units, ogtt_datetime,
     case when fasting="fasting" then "Yes" when fasting="non_fasting" then "No" else fasting end as `fasted`,
-    fbg.site_id, v.visit_code, v.visit_code_sequence, v.appointment_id, eos.offstudy_datetime
+    fbg.site_id, v.visit_code, v.visit_code_sequence, v.report_datetime, v.appointment_id, eos.offstudy_datetime,
+    fasting_duration_delta, "meta_subject.glucose" as source
     from meta_subject_glucose as fbg
     left join meta_subject_subjectvisit as v on v.id=fbg.subject_visit_id
     left join meta_prn_endofstudy as eos on v.subject_identifier=eos.subject_identifier
     """  # noqa
     sql_view = SqlViewGenerator(
-        report_model="meta_reports.glucose_summary_view",
+        report_model="meta_reports.glucosesummaryview",
         ordering=["subject_identifier", "site_id"],
     )
     return {

meta_reports/models/dbviews/imp_substitutions/__init__.py

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

meta_reports/models/dbviews/imp_substitutions/unmanaged_model.py

@@ -1,14 +1,13 @@
+from clinicedc_constants import NOT_EVALUATED
 from django.db import models
 from django_db_views.db_view import DBView
 from edc_constants.choices import YES_NO_NOT_EVALUATED
-from edc_constants.constants import NOT_EVALUATED
 from edc_qareports.model_mixins import QaReportModelMixin, qa_reports_permissions
 
 from .view_definition import get_view_definition
 
 
 class ImpSubstitutions(QaReportModelMixin, DBView):
-
     original_id = models.UUIDField(null=True)
 
     sid = models.IntegerField(verbose_name="Original SID", null=True)

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 clinicedc_constants import COMPLETE, DONE, NOT_APPLICABLE, NOT_AVAILABLE, YES
 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_lab_values/unmanged_model.py

@@ -9,7 +9,6 @@ from .view_definition import get_view_definition
 
 
 class OnStudyMissingLabValues(OnStudyMissingValuesModelMixin, QaReportModelMixin, DBView):
-
     view_definition = get_view_definition()
 
     class Meta:

meta_reports/models/dbviews/on_study_missing_values/__init__.py

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

meta_reports/models/dbviews/on_study_missing_values/qa_cases.py

@@ -1,6 +1,8 @@
-from edc_constants.constants import OTHER, YES
+from clinicedc_constants import OTHER, YES
 from edc_qareports.sql_generator import CrfCase
 
+from meta_visit_schedule.constants import MONTH36, MONTH48
+
 qa_cases = [
     CrfCase(
         label="No HIV Diagnosis date",
@@ -51,4 +53,20 @@ qa_cases = [
             f"and ogtt_performed='{YES}'"
         ),
     ),
+    CrfCase(
+        label="Weight",
+        dbtable="meta_subject_followupvitals",
+        label_lower="meta_subject.followupvitals",
+        where="(crf.weight is null and v.visit_code_sequence==0)",
+    ),
+    CrfCase(
+        label="Waist circumference 36/48m",
+        dbtable="meta_subject_followupvitals",
+        label_lower="meta_subject.followupvitals",
+        where=(
+            f"(crf.waist_circumference_measured=='{YES}' and crf.waist_circumference "
+            "is null) or (crf.waist_circumference is null and v.visit_code in "
+            f"['{MONTH36}','{MONTH48}'] and v.visit_code_sequence==0)"
+        ),
+    ),
 ]

meta_reports/models/dbviews/on_study_missing_values/unmanged_model.py

@@ -9,7 +9,6 @@ from .view_definition import get_view_definition
 
 
 class OnStudyMissingValues(OnStudyMissingValuesModelMixin, QaReportModelMixin, DBView):
-
     view_definition = get_view_definition()
 
     class Meta:

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/patient_history_missing_baseline_cd4/unmanaged_model.py

@@ -6,7 +6,6 @@ from .view_definition import get_view_definition
 
 
 class PatientHistoryMissingBaselineCd4(QaReportModelMixin, DBView):
-
     visit_code = models.CharField(max_length=25)
 
     visit_code_sequence = models.IntegerField()

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_row/unmanaged_model.py

@@ -6,7 +6,6 @@ from .view_definition import get_view_definition
 
 
 class UnattendedThreeInRow(QaReportModelMixin, DBView):
-
     appt_datetime = models.DateTimeField()
 
     first_value = models.CharField(verbose_name="First", max_length=25)

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_three_in_row2/unmanaged_model.py

@@ -6,7 +6,6 @@ from .view_definition import get_view_definition
 
 
 class UnattendedThreeInRow2(QaReportModelMixin, DBView):
-
     first_value = models.CharField(verbose_name="First", max_length=25)
 
     second_value = models.CharField(verbose_name="Second", max_length=25)

meta_reports/models/dbviews/unattended_two_in_row/__init__.py

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

meta_reports/models/dbviews/unattended_two_in_row/unmanaged_model.py

@@ -6,7 +6,6 @@ from .view_definition import get_view_definition
 
 
 class UnattendedTwoInRow(QaReportModelMixin, DBView):
-
     appt_datetime = models.DateTimeField()
 
     first_value = models.CharField(verbose_name="First", max_length=25)

meta_reports/models/endpoints.py

@@ -1,3 +1,4 @@
+from clinicedc_constants import NULL_STRING
 from django.db import models
 from edc_qareports.model_mixins import QaReportModelMixin, qa_reports_permissions
 
@@ -9,7 +10,7 @@ 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=NULL_STRING)
 
     fbg_date = models.DateField(null=True)
 
@@ -17,15 +18,18 @@ 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=NULL_STRING)
 
     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=NULL_STRING)
 
-    class Meta(QaReportModelMixin.Meta):
+    def __str__(self):
+        return f"{self.subject_identifier} {self.visit_code} {self.endpoint_label}"
+
+    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

@@ -3,10 +3,11 @@ 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:
-        subject_identifiers = []
-    cls = GlucoseEndpointsByDate(subject_identifiers=subject_identifiers)
+        cls = GlucoseEndpointsByDate()
+    else:
+        cls = GlucoseEndpointsByDate(subject_identifiers=subject_identifiers)
     cls.run()
     return cls.to_model()

meta_reports/templates/meta_reports/columns/subject_identifier_column.html

@@ -1 +1 @@
-<a title="{{ title }}" href="{{ url }}?q={{ subject_identifier }}">{{ label|default:subject_identifier }}</a>
+<a title="{{ title }}" href="{{ url }}?q={{ subject_identifier }}">{{ label|default:subject_identifier }}</a>

meta_reports/templates/meta_reports/endpoints_all_change_list_note.html

@@ -9,4 +9,4 @@ Unlike other reports, this report does not automatically update, but you can upd
 <UL>
     <LI>Place a check mark next to one or more subjects and select 'Regenerate selected report data' from the Action menu.</LI>
     <li>If you select more than 5 subjects, records for ALL subjects will be refreshed.</li>
-</UL>
+</UL>

meta_reports/templates/meta_reports/endpoints_change_list_note.html

@@ -9,4 +9,4 @@ Unlike other reports, this report does not automatically update, but you can upd
 <UL>
     <LI>Place a check mark next to one or more subjects and select 'Regenerate selected report data' from the Action menu.</LI>
     <li>If you select more than 5 subjects, records for ALL subjects will be refreshed.</li>
-</UL>
+</UL>

meta_reports/templates/meta_reports/last_imp_refill/changelist_note.html

@@ -0,0 +1,13 @@
+{% load i18n %}
+{% trans "This report fetches the most recent Study Medication report where IMP was refilled and adds the subject's next visit. Subjects taken 'Off Schedule' are not included in this report. To update ALL rows in this report, tick at least one row and select 'Update report' action below." %}
+<BR><BR>
+{% trans "This report has additional search features for numeric columns" %}:
+<code>days_since</code>, <code>days_until</code>, <code>imp_visit_code</code> {% trans "and" %} <code>next_visit_code</code>.
+<BR><BR>
+{%  trans "For example, type" %}
+<code>days_until>=25</code>
+{%  trans "in the search below to show rows for subjects who have an appointment 25 or more days from the date this report was created. You might also try typing" %}
+<code>days_since>365</code> or <code>days_until<0</code>.
+<BR><BR>
+{%  trans "This also works" %}:
+<code>next_visit_code>=1060</code>.

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",
+]