meta-edc 0.3.26__tar.gz → 0.3.28__tar.gz

{meta_edc-0.3.26 → meta_edc-0.3.28}/CHANGES

@@ -1,12 +1,17 @@
 Changes
 -------
 
+0.3.27
+------
+- bump edc 0.6.5
+
 0.3.26
 ------
 - add signal to recalculate Endpoint record if either model
   GlucoseFBG or  Glucose is saved.
 - queue message on subject dashboard if subject reaches the protocol
   glucose / DM endpoint.
+- bump edc 0.6.4
 
 0.3.25
 ------
@@ -14,7 +19,7 @@ Changes
 - add Endpoints report for ALL endpoints, not just those still
   on study
 - improve navigation between endpoint reports and glucose summary
-
+- bump edc 0.6.3
 
 0.3.24
 ------

{meta_edc-0.3.26 → meta_edc-0.3.28}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: meta-edc
-Version: 0.3.26
+Version: 0.3.28
 Summary: META Trial EDC (http://www.isrctn.com/ISRCTN76157257)
 Home-page: https://github.com/meta-trial/meta-edc
 Author: Erik van Widenfelt
@@ -10,6 +10,7 @@ Keywords: django edc META EDC,clinicedc,clinical trials
 Classifier: Environment :: Web Environment
 Classifier: Framework :: Django
 Classifier: Framework :: Django :: 4.2
+Classifier: Framework :: Django :: 5.1
 Classifier: Intended Audience :: Developers
 Classifier: Intended Audience :: Science/Research
 Classifier: Operating System :: OS Independent
@@ -19,7 +20,7 @@ Requires-Python: >=3.12
 Description-Content-Type: text/x-rst
 License-File: LICENSE
 License-File: AUTHORS
-Requires-Dist: edc==0.6.3
+Requires-Dist: edc==0.6.5
 Requires-Dist: edc-microscopy
 Requires-Dist: beautifulsoup4
 Requires-Dist: edc-analytics

{meta_edc-0.3.26 → meta_edc-0.3.28}/meta_dashboard/views/subject/dashboard/dashboard_view.py

@@ -17,6 +17,7 @@ class DashboardView(SubjectDashboardView):
     history_button_label = _("Audit")
 
     def get_context_data(self, **kwargs) -> dict[str, Any]:
+        """Add message if subject reaches DM Endpoint."""
         context = super().get_context_data(**kwargs)
         try:
             Endpoints.objects.get(subject_identifier=self.subject_identifier)

{meta_edc-0.3.26 → meta_edc-0.3.28}/meta_edc.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: meta-edc
-Version: 0.3.26
+Version: 0.3.28
 Summary: META Trial EDC (http://www.isrctn.com/ISRCTN76157257)
 Home-page: https://github.com/meta-trial/meta-edc
 Author: Erik van Widenfelt
@@ -10,6 +10,7 @@ Keywords: django edc META EDC,clinicedc,clinical trials
 Classifier: Environment :: Web Environment
 Classifier: Framework :: Django
 Classifier: Framework :: Django :: 4.2
+Classifier: Framework :: Django :: 5.1
 Classifier: Intended Audience :: Developers
 Classifier: Intended Audience :: Science/Research
 Classifier: Operating System :: OS Independent
@@ -19,7 +20,7 @@ Requires-Python: >=3.12
 Description-Content-Type: text/x-rst
 License-File: LICENSE
 License-File: AUTHORS
-Requires-Dist: edc==0.6.3
+Requires-Dist: edc==0.6.5
 Requires-Dist: edc-microscopy
 Requires-Dist: beautifulsoup4
 Requires-Dist: edc-analytics

{meta_edc-0.3.26 → meta_edc-0.3.28}/meta_edc.egg-info/SOURCES.txt

@@ -518,11 +518,15 @@ meta_reports/admin/list_filters.py
 meta_reports/admin/modeladmin_mixins.py
 meta_reports/admin/unmanaged/__init__.py
 meta_reports/admin/unmanaged/glucose_summary_admin.py
-meta_reports/admin/unmanaged/missing_screening_ogtt_admin.py
 meta_reports/admin/unmanaged/patient_history_missing_baseline_cd4_admin.py
 meta_reports/admin/unmanaged/unattended_three_in_row2_admin.py
 meta_reports/admin/unmanaged/unattended_three_in_row_admin.py
 meta_reports/admin/unmanaged/unattended_two_in_row_admin.py
+meta_reports/admin/unmanaged/missing_screening_ogtt_admin/__init__.py
+meta_reports/admin/unmanaged/missing_screening_ogtt_admin/note_model_admin.py
+meta_reports/admin/unmanaged/missing_screening_ogtt_admin/unmanaged_model_admin.py
+meta_reports/forms/__init__.py
+meta_reports/forms/missing_ogtt_note_form.py
 meta_reports/management/__init__.py
 meta_reports/management/commands/__init__.py
 meta_reports/management/commands/generate_endpoints.py
@@ -559,6 +563,11 @@ meta_reports/migrations/0030_auto_20240822_1637.py
 meta_reports/migrations/0031_endpointsproxy.py
 meta_reports/migrations/0032_alter_endpointsproxy_options.py
 meta_reports/migrations/0033_auto_20240823_0012.py
+meta_reports/migrations/0034_auto_20240823_1642.py
+meta_reports/migrations/0035_historicalmissingogttnote_missingogttnote.py
+meta_reports/migrations/0036_historicalmissingogttnote_fasting_and_more.py
+meta_reports/migrations/0037_historicalmissingogttnote_result_status_and_more.py
+meta_reports/migrations/0038_alter_historicalmissingogttnote_fasting_and_more.py
 meta_reports/migrations/__init__.py
 meta_reports/models/__init__.py
 meta_reports/models/endpoints.py
@@ -569,6 +578,7 @@ meta_reports/models/dbviews/glucose_summary/__init__.py
 meta_reports/models/dbviews/glucose_summary/unmanaged_model.py
 meta_reports/models/dbviews/glucose_summary/view_definition.py
 meta_reports/models/dbviews/missing_screening_ogtt/__init__.py
+meta_reports/models/dbviews/missing_screening_ogtt/note_model.py
 meta_reports/models/dbviews/missing_screening_ogtt/unmanaged_model.py
 meta_reports/models/dbviews/missing_screening_ogtt/view_definition.py
 meta_reports/models/dbviews/patient_history_missing_baseline_cd4/__init__.py

{meta_edc-0.3.26 → meta_edc-0.3.28}/meta_edc.egg-info/requires.txt

@@ -1,4 +1,4 @@
-edc==0.6.3
+edc==0.6.5
 edc-microscopy
 beautifulsoup4
 edc-analytics

{meta_edc-0.3.26 → meta_edc-0.3.28}/meta_reports/admin/__init__.py

@@ -2,6 +2,7 @@ from .endpoints_admin import EndpointsAdmin
 from .endpoints_all_admin import EndpointsAllAdmin
 from .unmanaged import (
     GlucoseSummaryAdmin,
+    MissingOgttNoteModelAdmin,
     MissingScreeningOgttAdmin,
     PatientHistoryMissingBaselineCd4Admin,
     UnattendedThreeInRow2Admin,

{meta_edc-0.3.26 → meta_edc-0.3.28}/meta_reports/admin/unmanaged/__init__.py

@@ -1,5 +1,8 @@
 from .glucose_summary_admin import GlucoseSummaryAdmin
-from .missing_screening_ogtt_admin import MissingScreeningOgttAdmin
+from .missing_screening_ogtt_admin import (
+    MissingOgttNoteModelAdmin,
+    MissingScreeningOgttAdmin,
+)
 from .patient_history_missing_baseline_cd4_admin import (
     PatientHistoryMissingBaselineCd4Admin,
 )

meta_edc-0.3.28/meta_reports/admin/unmanaged/missing_screening_ogtt_admin/__init__.py

@@ -0,0 +1,2 @@
+from .note_model_admin import MissingOgttNoteModelAdmin
+from .unmanaged_model_admin import MissingScreeningOgttAdmin

meta_edc-0.3.28/meta_reports/admin/unmanaged/missing_screening_ogtt_admin/note_model_admin.py

@@ -0,0 +1,53 @@
+from django.contrib import admin
+from django_audit_fields import audit_fieldset_tuple
+from edc_qareports.modeladmin_mixins import NoteModelAdminMixin
+
+from ....admin_site import meta_reports_admin
+from ....forms import MissingOgttNoteForm
+from ....models import MissingOgttNote
+
+
+@admin.register(MissingOgttNote, site=meta_reports_admin)
+class MissingOgttNoteModelAdmin(
+    NoteModelAdminMixin,
+    admin.ModelAdmin,
+):
+    """A modeladmin class for the Note model."""
+
+    form = MissingOgttNoteForm
+    note_template_name = "edc_qareports/qa_report_note.html"
+
+    fieldsets = (
+        (
+            None,
+            {"fields": ("subject_identifier", "report_datetime", "result_status")},
+        ),
+        (
+            "OGTT",
+            {
+                "fields": (
+                    "fasting",
+                    "ogtt_base_datetime",
+                    "ogtt_datetime",
+                    "ogtt_value",
+                    "ogtt_units",
+                )
+            },
+        ),
+        (
+            "Note",
+            {
+                "fields": (
+                    "note",
+                    "report_model",
+                )
+            },
+        ),
+        audit_fieldset_tuple,
+    )
+
+    radio_fields = {
+        "ogtt_units": admin.VERTICAL,
+        "result_status": admin.VERTICAL,
+        "fasting": admin.VERTICAL,
+    }

meta_edc-0.3.26/meta_reports/admin/unmanaged/missing_screening_ogtt_admin.py → meta_edc-0.3.28/meta_reports/admin/unmanaged/missing_screening_ogtt_admin/unmanaged_model_admin.py

@@ -4,12 +4,19 @@ from django.urls import reverse
 from django.utils.translation import gettext as _
 from edc_model_admin.dashboard import ModelAdminDashboardMixin
 from edc_model_admin.mixins import TemplatesModelAdminMixin
+from edc_qareports.modeladmin_mixins import (
+    NoteStatusListFilter as BaseNoteStatusListFilter,
+)
 from edc_qareports.modeladmin_mixins import QaReportModelAdminMixin
 from edc_sites.admin import SiteModelAdminMixin
 from edc_visit_schedule.admin import ScheduleStatusListFilter
 
-from ...admin_site import meta_reports_admin
-from ...models import MissingScreeningOgtt
+from ....admin_site import meta_reports_admin
+from ....models import NOTE_STATUSES, MissingScreeningOgtt
+
+
+class NoteStatusListFilter(BaseNoteStatusListFilter):
+    note_model_status_choices = NOTE_STATUSES
 
 
 @admin.register(MissingScreeningOgtt, site=meta_reports_admin)
@@ -20,13 +27,19 @@ class MissingScreeningOgttAdmin(
     TemplatesModelAdminMixin,
     admin.ModelAdmin,
 ):
-    ordering = ["site", "screening_identifier"]
+    note_model = "meta_reports.missingogttnote"
+    note_status_list_filter = NoteStatusListFilter
+    note_template = "edc_qareports/columns/notes_column.html"
+    include_note_column = True
+
+    ordering = ["site", "subject_identifier"]
+
     list_display = [
         "dashboard",
-        "screening_identifier",
+        "subject_identifier",
         "site",
-        "screening_datetime",
-        "fbg_datetime",
+        "screening_date",
+        "fbg_date",
         "fbg_value",
         "ogtt_value",
         "repeated",
@@ -46,7 +59,7 @@ class MissingScreeningOgttAdmin(
         "p3_ltfu",
     ]
 
-    search_fields = ["screening_identifier"]
+    search_fields = ["subject_identifier"]
 
     def dashboard(self, obj=None, label=None) -> str:
         url = self.get_subject_dashboard_url(obj=obj)
@@ -57,3 +70,15 @@ class MissingScreeningOgttAdmin(
             )
         context = dict(title=_("Go to subject screening"), url=url, label=label)
         return render_to_string("dashboard_button.html", context=context)
+
+    @admin.display(description="Screen date", ordering="screening_datetime")
+    def screening_date(self, obj):
+        if obj.screening_datetime:
+            return obj.screening_datetime.date()
+        return None
+
+    @admin.display(description="Fbg date", ordering="fbg_datetime")
+    def fbg_date(self, obj):
+        if obj.fbg_datetime:
+            return obj.fbg_datetime.date()
+        return None

meta_edc-0.3.28/meta_reports/forms/__init__.py

@@ -0,0 +1 @@
+from .missing_ogtt_note_form import MissingOgttNoteForm

meta_edc-0.3.28/meta_reports/forms/missing_ogtt_note_form.py

@@ -0,0 +1,33 @@
+from django import forms
+from edc_constants.constants import NO, YES
+from edc_form_validators import FormValidator, FormValidatorMixin
+from edc_glucose.form_validators import OgttFormValidatorMixin
+from edc_glucose.utils import validate_glucose_as_millimoles_per_liter
+
+from ..models import MissingOgttNote
+
+
+class MissingOgttNoteFormValidator(OgttFormValidatorMixin, FormValidator):
+
+    def clean(self):
+        self.applicable_if(YES, field="result_status", field_applicable="fasting")
+        self.required_if(YES, NO, field="fasting", field_required="ogtt_base_datetime")
+        self.required_if(YES, NO, field="fasting", field_required="ogtt_datetime")
+        self.required_if(YES, NO, field="fasting", field_required="ogtt_value")
+        self.applicable_if(YES, NO, field="fasting", field_applicable="ogtt_units")
+        validate_glucose_as_millimoles_per_liter("ogtt", self.cleaned_data)
+        self.validate_ogtt_dates()
+        self.validate_ogtt_time_interval()
+
+
+class MissingOgttNoteForm(FormValidatorMixin, forms.ModelForm):
+    form_validator_cls = MissingOgttNoteFormValidator
+
+    class Meta:
+        model = MissingOgttNote
+        fields = "__all__"
+        help_text = {"subject_identifier": "(read-only)", "name": "(read-only)"}
+        widgets = {
+            "report_model": forms.TextInput(attrs={"readonly": "readonly"}),
+            "subject_identifier": forms.TextInput(attrs={"readonly": "readonly"}),
+        }

meta_edc-0.3.28/meta_reports/migrations/0034_auto_20240823_1642.py

@@ -0,0 +1,54 @@
+# Generated by Django 5.0.8 on 2024-08-23 13:42
+
+import django_db_views.migration_functions
+import django_db_views.operations
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("meta_reports", "0033_auto_20240823_0012"),
+    ]
+
+    operations = [
+        django_db_views.operations.ViewRunPython(
+            code=django_db_views.migration_functions.ForwardViewMigration(
+                "# noqa\n    select *, uuid() as id, now() as created,\n    'meta_reports.missing_screening_ogtt_view' as report_model\n      from (\n        select screening_identifier, site_id, report_datetime as 'screening_datetime', fbg_datetime,\n        converted_fbg_value as fbg_value,  converted_ogtt_value as ogtt_value, repeat_glucose_performed as repeated,\n        p3_ltfu, fbg2_value, ogtt2_value, fbg2_datetime, ogtt2_datetime, consented,\n        screening_identifier as subject_identifier, id as original_id\n        from meta_screening_subjectscreening\n        where converted_fbg_value is not null and converted_ogtt_value is null and unsuitable_agreed != \"Yes\"\n    ) as A\n    order by screening_identifier",
+                "missing_screening_ogtt_view",
+                engine="django.db.backends.mysql",
+            ),
+            reverse_code=django_db_views.migration_functions.BackwardViewMigration(
+                "# noqa\n    select *, uuid() as id, now() as created,\n    'meta_reports.missing_screening_ogtt_view' as report_model\n      from (\n        select screening_identifier, site_id, report_datetime as 'screening_datetime', fbg_datetime,\n        converted_fbg_value as fbg_value,  converted_ogtt_value as ogtt_value, repeat_glucose_performed as repeated,\n        p3_ltfu, fbg2_value, ogtt2_value, fbg2_datetime, ogtt2_datetime, consented, \"\" as subject_identifier,\n        id as original_id\n        from meta_screening_subjectscreening\n        where converted_fbg_value is not null and converted_ogtt_value is null and unsuitable_agreed != \"Yes\"\n    ) as A\n    order by screening_identifier",
+                "missing_screening_ogtt_view",
+                engine="django.db.backends.mysql",
+            ),
+            atomic=False,
+        ),
+        django_db_views.operations.ViewRunPython(
+            code=django_db_views.migration_functions.ForwardViewMigration(
+                "# noqa\n    select *, get_random_uuid() as id, now() as created,\n    'meta_reports.missing_screening_ogtt_view' as report_model\n      from (\n        select screening_identifier, site_id, report_datetime as 'screening_datetime', fbg_datetime,\n        converted_fbg_value as fbg_value,  converted_ogtt_value as ogtt_value, repeat_glucose_performed as repeated,\n        p3_ltfu, fbg2_value, ogtt2_value, fbg2_datetime, ogtt2_datetime, consented,\n        screening_identifier as subject_identifier, id as original_id\n        from meta_screening_subjectscreening\n        where converted_fbg_value is not null and converted_ogtt_value is null and unsuitable_agreed != \"Yes\"\n    ) as A\n    order by screening_identifier",
+                "missing_screening_ogtt_view",
+                engine="django.db.backends.postgresql",
+            ),
+            reverse_code=django_db_views.migration_functions.BackwardViewMigration(
+                "# noqa\n    select *, get_random_uuid() as id, now() as created,\n    'meta_reports.missing_screening_ogtt_view' as report_model\n      from (\n        select screening_identifier, site_id, report_datetime as 'screening_datetime', fbg_datetime,\n        converted_fbg_value as fbg_value,  converted_ogtt_value as ogtt_value, repeat_glucose_performed as repeated,\n        p3_ltfu, fbg2_value, ogtt2_value, fbg2_datetime, ogtt2_datetime, consented, \"\" as subject_identifier,\n        id as original_id\n        from meta_screening_subjectscreening\n        where converted_fbg_value is not null and converted_ogtt_value is null and unsuitable_agreed != \"Yes\"\n    ) as A\n    order by screening_identifier",
+                "missing_screening_ogtt_view",
+                engine="django.db.backends.postgresql",
+            ),
+            atomic=False,
+        ),
+        django_db_views.operations.ViewRunPython(
+            code=django_db_views.migration_functions.ForwardViewMigration(
+                "# noqa\nSELECT *, lower(\n    hex(randomblob(4)) || '-' || hex(randomblob(2)) || '-' || '4' ||\n    substr(hex( randomblob(2)), 2) || '-' ||\n    substr('AB89', 1 + (abs(random()) % 4) , 1)  ||\n    substr(hex(randomblob(2)), 2) || '-' ||\n    hex(randomblob(6))\n  ) as id, datetime() as `created`,\n    'meta_reports.missing_screening_ogtt_view' as report_model\n      from (\n        select screening_identifier, site_id, report_datetime as 'screening_datetime', fbg_datetime,\n        converted_fbg_value as fbg_value,  converted_ogtt_value as ogtt_value, fbg2_value, ogtt2_value,\n        repeat_glucose_performed as repeated, p3_ltfu, fbg2_datetime, ogtt2_datetime, consented,\n        screening_identifier as subject_identifier, id as original_id\n        from meta_screening_subjectscreening\n        where converted_fbg_value is not null and converted_ogtt_value is null and unsuitable_agreed != \"Yes\"\n    ) as A\n    order by screening_identifier",
+                "missing_screening_ogtt_view",
+                engine="django.db.backends.sqlite3",
+            ),
+            reverse_code=django_db_views.migration_functions.BackwardViewMigration(
+                "# noqa\nSELECT *, lower(\n    hex(randomblob(4)) || '-' || hex(randomblob(2)) || '-' || '4' ||\n    substr(hex( randomblob(2)), 2) || '-' ||\n    substr('AB89', 1 + (abs(random()) % 4) , 1)  ||\n    substr(hex(randomblob(2)), 2) || '-' ||\n    hex(randomblob(6))\n  ) as id, datetime() as `created`,\n    'meta_reports.missing_screening_ogtt_view' as report_model\n      from (\n        select screening_identifier, site_id, report_datetime as 'screening_datetime', fbg_datetime,\n        converted_fbg_value as fbg_value,  converted_ogtt_value as ogtt_value, fbg2_value, ogtt2_value,\n        repeat_glucose_performed as repeated, p3_ltfu, fbg2_datetime, ogtt2_datetime, consented, \"\" as subject_identifier,\n        id as original_id\n        from meta_screening_subjectscreening\n        where converted_fbg_value is not null and converted_ogtt_value is null and unsuitable_agreed != \"Yes\"\n    ) as A\n    order by screening_identifier",
+                "missing_screening_ogtt_view",
+                engine="django.db.backends.sqlite3",
+            ),
+            atomic=False,
+        ),
+    ]