meta-edc 0.3.33__py3-none-any.whl → 0.3.35__py3-none-any.whl

meta_pharmacy/migrations/0003_auto_20240909_2335.py

@@ -0,0 +1,64 @@
+# Generated by Django 5.1 on 2024-09-09 20:35
+from pathlib import Path
+
+import pandas as pd
+from django.apps import apps as django_apps
+from django.conf import settings
+from django.db import migrations
+from edc_utils import get_utcnow
+from tqdm import tqdm
+
+
+def populate_substitutions(apps, schema_editor):
+    """import CSV file into pandas dataframe and use DF to
+    populate the model.
+
+    CSV file was sent to ERIK on 2024-09-09 in relation to
+    a possible protocol violation where a subject was given the
+    incorrect IMP. The CSV file lists `sid` where a bottle was not ready
+    to dispense and a bottle of `dispensed_sid` was dispensed instead.
+    """
+    path = Path(settings.META_PHARMACY_RX_SUBSTITUTION_FILE).expanduser()
+    df = pd.read_csv(path, header=1)
+    df = df.rename(
+        columns={"MISSING DRUG": "sid", "SUBSTITUTE": "dispensed_sid", "SITE": "site_id"}
+    )
+    df = df.rename(
+        columns={"MISSING DRUG": "sid", "SUBSTITUTE": "dispensed_sid", "SITE": "site_id"}
+    )
+    df["sid"] = df["sid"].apply(pd.to_numeric, errors="coerce")
+    df["dispensed_sid"] = df["dispensed_sid"].apply(pd.to_numeric, errors="coerce")
+    df["site_id"] = df["site_id"].apply(pd.to_numeric, errors="coerce")
+    now = get_utcnow()
+    model_cls = django_apps.get_model("meta_pharmacy.substitutions")
+    df_error = df[df["dispensed_sid"].isna()]
+    df_error = df_error.reset_index()
+    df_ok = df[df["dispensed_sid"].notna()]
+    df_ok = df_ok.reset_index()
+    data = [
+        model_cls(
+            row_index=row["index"],
+            report_datetime=now,
+            site_id=row["site_id"],
+            sid=row["sid"],
+            dispensed_sid=row["dispensed_sid"],
+            user_created="erikvw",
+            created=now,
+            locale_created="en-gb",
+        )
+        for _, row in df_ok.iterrows()
+    ]
+    created = len(model_cls.objects.bulk_create(data))
+    for obj in tqdm(model_cls.objects.all(), total=created):
+        obj.save()
+    if not df_error.empty:
+        print(df_error[["index", "sid"]])
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("meta_pharmacy", "0002_initial"),
+    ]
+
+    operations = [migrations.RunPython(populate_substitutions)]

meta_pharmacy/migrations/0004_alter_historicalsubstitutions_report_datetime_and_more.py

@@ -0,0 +1,23 @@
+# Generated by Django 5.1 on 2024-09-11 00:30
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("meta_pharmacy", "0003_auto_20240909_2335"),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="historicalsubstitutions",
+            name="report_datetime",
+            field=models.DateTimeField(null=True),
+        ),
+        migrations.AlterField(
+            model_name="substitutions",
+            name="report_datetime",
+            field=models.DateTimeField(null=True),
+        ),
+    ]

meta_pharmacy/migrations/0005_auto_20240911_0352.py

@@ -0,0 +1,17 @@
+# Generated by Django 5.1 on 2024-09-11 00:52
+from django.apps import apps as django_apps
+from django.db import migrations
+
+
+def update_report_datetime_as_none(apps, schema_editor):
+    model_cls = django_apps.get_model("meta_pharmacy.substitutions")
+    model_cls.objects.update(report_datetime=None)
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("meta_pharmacy", "0004_alter_historicalsubstitutions_report_datetime_and_more"),
+    ]
+
+    operations = [migrations.RunPython(update_report_datetime_as_none)]

meta_pharmacy/models.py

@@ -0,0 +1,102 @@
+from django.core.exceptions import ObjectDoesNotExist
+from django.db import models
+from django.db.models import Index
+from edc_constants.choices import YES_NO_NOT_EVALUATED
+from edc_constants.constants import NO, NOT_EVALUATED, YES
+from edc_identifier.model_mixins import NonUniqueSubjectIdentifierFieldMixin
+from edc_model.models import BaseUuidModel, HistoricalRecords
+from edc_pharmacy.models import Rx as BaseRx
+from edc_sites.managers import CurrentSiteManager
+from edc_sites.model_mixins import SiteModelMixin
+
+from meta_pharmacy.constants import MISSING_SUBJECT_IDENTIFIER
+from meta_rando.models import RandomizationList
+
+
+class MyManager(models.Manager):
+    use_in_migrations = True
+
+
+class Rx(BaseRx):
+    """A proxy model of edc_pharmacy.Rx.
+
+    For autocomplete only.
+    """
+
+    def save(self, *args, **kwargs):
+        raise NotImplementedError(
+            "This proxy model may not be saved. Permissions should be view only"
+        )
+
+    class Meta:
+        proxy = True
+
+
+class Substitutions(NonUniqueSubjectIdentifierFieldMixin, SiteModelMixin, BaseUuidModel):
+    """A model to capture a CSV file that lists IMP substitutions
+    made where a bottle of `sid` is substituted with a bottle of
+    `dispensed_sid`.
+
+    The IMP substitutions were not done by any approved procedure. SID
+    values are sequential and not designed for human transcription.
+    """
+
+    report_datetime = models.DateTimeField(null=True, blank=False)
+
+    row_index = models.IntegerField(null=True)
+
+    rx = models.ForeignKey(Rx, on_delete=models.PROTECT, null=True, blank=True)
+
+    sid = models.IntegerField(verbose_name="SID")
+
+    visit_no = models.IntegerField("Visit Number", null=True, blank=True)
+
+    dispensed_sid = models.IntegerField(verbose_name="Dispensed SID")
+
+    updated_visit_no = models.IntegerField("Visit Number", null=True, blank=True)
+
+    updated_subject_identifier = models.CharField(
+        max_length=50, verbose_name="Taken from subject", null=True, blank=True
+    )
+
+    arm_match = models.CharField(
+        max_length=15, choices=YES_NO_NOT_EVALUATED, default=NOT_EVALUATED
+    )
+
+    notes = models.TextField(verbose_name="Notes")
+
+    objects = MyManager()
+    on_site = CurrentSiteManager()
+    history = HistoricalRecords(inherit=True)
+
+    def __str__(self):
+        if self.rx:
+            return self.rx.subject_identifier
+        return str(self.sid)
+
+    def save(self, *args, **kwargs):
+        if not self.rx:
+            try:
+                self.rx = Rx.objects.get(rando_sid=self.sid)
+            except ObjectDoesNotExist:
+                self.status = MISSING_SUBJECT_IDENTIFIER
+            else:
+                self.subject_identifier = self.rx.subject_identifier
+        else:
+            self.subject_identifier = self.rx.subject_identifier
+        rando_a = RandomizationList.objects.get(sid=self.sid)
+        rando_b = RandomizationList.objects.get(sid=self.dispensed_sid)
+        if rando_a.assignment != rando_b.assignment:
+            self.arm_match = NO
+        else:
+            self.arm_match = YES
+
+        super().save(*args, **kwargs)
+
+    class Meta(SiteModelMixin.Meta, BaseUuidModel.Meta):
+        verbose_name_plural = "IMP Substitutions"
+        verbose_name = "IMP Substitution"
+        indexes = [
+            Index(fields=["sid", "dispensed_sid", "subject_identifier"]),
+            Index(fields=["row_index"]),
+        ]

meta_pharmacy/urls.py

@@ -0,0 +1,8 @@
+from django.urls.conf import path
+from django.views.generic import RedirectView
+
+app_name = "meta_pharmacy"
+
+urlpatterns = [
+    path("", RedirectView.as_view(url=f"/{app_name}/admin/"), name="home_url"),
+]

meta_prn/action_items.py

@@ -27,6 +27,7 @@ from .constants import (
     OFFSCHEDULE_PREGNANCY_ACTION,
     OFFSTUDY_MEDICATION_ACTION,
     PREGNANCY_NOTIFICATION_ACTION,
+    REFERRAL,
     UNBLINDING_REQUEST_ACTION,
     UNBLINDING_REVIEW_ACTION,
 )
@@ -136,7 +137,7 @@ class DmReferralAction(ActionWithNotification):
     name = DM_REFFERAL_ACTION
     display_name = "Diabetes referral"
     notification_display_name = "Diabetes referral"
-    parent_action_names = None
+    parent_action_names = [OFFSTUDY_MEDICATION_ACTION]
     reference_model = "meta_prn.dmreferral"
     show_link_to_changelist = True
     show_link_to_add = True
@@ -182,6 +183,13 @@ class OffStudyMedicationAction(ActionWithNotification):
     priority = HIGH_PRIORITY
     singleton = True
 
+    def get_next_actions(self):
+        if self.reference_obj.reason == REFERRAL:
+            next_actions = [DM_REFFERAL_ACTION]
+        else:
+            next_actions = [END_OF_STUDY_ACTION]
+        return next_actions
+
 
 class UnblindingRequestAction(ActionWithNotification):
     name = UNBLINDING_REQUEST_ACTION

meta_reports/admin/__init__.py

@@ -1,5 +1,6 @@
 from .dbviews import (
     GlucoseSummaryAdmin,
+    ImpSubstitutionsAdmin,
     MissingOgttNoteModelAdmin,
     MissingScreeningOgttAdmin,
     OnStudyMissingLabValuesAdmin,

meta_reports/admin/dbviews/__init__.py

@@ -1,4 +1,5 @@
 from .glucose_summary_admin import GlucoseSummaryAdmin
+from .imp_substitutions_admin import ImpSubstitutionsAdmin
 from .missing_screening_ogtt_admin import (
     MissingOgttNoteModelAdmin,
     MissingScreeningOgttAdmin,

meta_reports/admin/dbviews/imp_substitutions_admin.py

@@ -0,0 +1,101 @@
+from django.apps import apps as django_apps
+from django.contrib import admin
+from django.core.exceptions import ObjectDoesNotExist
+from django.template.loader import render_to_string
+from django.urls import reverse
+from django.utils.translation import gettext_lazy as _
+from edc_appointment.models import Appointment
+from edc_model_admin.dashboard import ModelAdminDashboardMixin
+from edc_model_admin.list_filters import ReportDateListFilter
+from edc_model_admin.mixins import TemplatesModelAdminMixin
+from edc_qareports.modeladmin_mixins import QaReportModelAdminMixin
+from edc_sites.admin import SiteModelAdminMixin
+from edc_visit_schedule.admin import ScheduleStatusListFilter
+from edc_visit_schedule.constants import DAY1
+
+from ...admin_site import meta_reports_admin
+from ...models import ImpSubstitutions
+
+
+@admin.register(ImpSubstitutions, site=meta_reports_admin)
+class ImpSubstitutionsAdmin(
+    QaReportModelAdminMixin,
+    SiteModelAdminMixin,
+    ModelAdminDashboardMixin,
+    TemplatesModelAdminMixin,
+    admin.ModelAdmin,
+):
+    ordering = ["site", "subject_identifier"]
+    list_display = [
+        "dashboard",
+        "render_button",
+        "subject",
+        "sid",
+        "dispensed_sid",
+        "report_date",
+        "arm_match",
+        "allocated_date",
+        "user_created",
+        "user_modified",
+        "modified",
+    ]
+
+    list_filter = [
+        "arm_match",
+        ScheduleStatusListFilter,
+        ReportDateListFilter,
+        "allocated_datetime",
+    ]
+
+    search_fields = ["subject_identifier", "sid", "dispensed_sid"]
+
+    def dashboard(self, obj=None, label=None) -> str:
+        kwargs = self.get_subject_dashboard_url_kwargs(obj)
+        try:
+            kwargs.update(
+                appointment=str(
+                    Appointment.objects.get(
+                        subject_identifier=obj.subject_identifier,
+                        visit_code=DAY1,
+                        visit_code_sequence=0,
+                    ).id
+                )
+            )
+        except ObjectDoesNotExist:
+            pass
+        url = reverse(self.get_subject_dashboard_url_name(obj=obj), kwargs=kwargs)
+        context = dict(title=_("Go to subject's dashboard@1000"), url=url, label=label)
+        return render_to_string("dashboard_button.html", context=context)
+
+    @admin.display(description="Subject", ordering="subject_identifier")
+    def subject(self, obj):
+        return obj.subject_identifier
+
+    @admin.display(description="Allocated", ordering="allocated_datetime")
+    def allocated_date(self, obj=None):
+        return obj.allocated_datetime.date() if obj.allocated_datetime else None
+
+    @admin.display(description="Update")
+    def render_button(self, obj=None):
+        crf_model_cls = django_apps.get_model("meta_pharmacy", "substitutions")
+        url = reverse(
+            f"meta_pharmacy_admin:{crf_model_cls._meta.label_lower.replace('.', '_')}_change",
+            args=(obj.original_id,),
+        )
+        url = (
+            f"{url}?next={self.admin_site.name}:"
+            f"{self.model._meta.label_lower.replace('.', '_')}_changelist"
+        )
+        title = _(f"View {crf_model_cls._meta.verbose_name}")
+        label = _("View")
+        crf_button = render_to_string(
+            "edc_qareports/columns/change_button.html",
+            context=dict(title=title, url=url, label=label),
+        )
+        return crf_button
+
+    @admin.display(description="Report date", ordering="report_datetime")
+    def report_date(self, obj) -> str | None:
+        if obj.report_datetime:
+            return obj.report_datetime.date()
+        return None

meta_reports/migrations/0017_auto_20240819_1711.py

@@ -9,6 +9,7 @@ class Migration(migrations.Migration):
 
     dependencies = [
         ("meta_reports", "0016_missingscreeningogtt"),
+        ("meta_screening", "0067_alter_historicalscreeningpartone_report_datetime_and_more"),
     ]
 
     operations = [

meta_reports/migrations/0047_impsubstitutions.py

@@ -0,0 +1,56 @@
+# Generated by Django 5.1 on 2024-09-09 20:37
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("meta_reports", "0046_auto_20240829_0250"),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name="ImpSubstitutions",
+            fields=[
+                (
+                    "id",
+                    models.BigAutoField(
+                        auto_created=True, primary_key=True, serialize=False, verbose_name="ID"
+                    ),
+                ),
+                ("report_model", models.CharField(max_length=50)),
+                ("subject_identifier", models.CharField(max_length=25)),
+                ("created", models.DateTimeField()),
+                ("original_id", models.UUIDField(null=True)),
+                ("sid", models.IntegerField(null=True, verbose_name="Original SID")),
+                (
+                    "dispensed_sid",
+                    models.IntegerField(null=True, verbose_name="Dispensed SID"),
+                ),
+                (
+                    "arm_match",
+                    models.CharField(
+                        choices=[
+                            ("Yes", "Yes"),
+                            ("No", "No"),
+                            ("not_evaluated", "Not evaluated"),
+                        ],
+                        default="not_evaluated",
+                        max_length=15,
+                    ),
+                ),
+                ("allocated_datetime", models.DateTimeField(null=True)),
+                ("user_created", models.CharField(max_length=25)),
+                ("user_modified", models.CharField(max_length=25)),
+                ("modified", models.DateTimeField(null=True)),
+            ],
+            options={
+                "verbose_name": "IMP Substitutions",
+                "verbose_name_plural": "IMP Substitutions",
+                "db_table": "imp_subjectitutions_view",
+                "managed": False,
+                "default_permissions": ("view", "export", "viewallsites"),
+            },
+        ),
+    ]

meta_reports/migrations/0048_auto_20240909_2338.py

@@ -0,0 +1,48 @@
+# Generated by Django 5.1 on 2024-09-09 20:38
+
+import django_db_views.migration_functions
+import django_db_views.operations
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("meta_reports", "0047_impsubstitutions"),
+    ]
+
+    operations = [
+        django_db_views.operations.ViewRunPython(
+            code=django_db_views.migration_functions.ForwardViewMigration(
+                "select *, uuid() as id, now() as `created`, 'meta_reports.imp_subjectitutions_view' as `report_model` from (SELECT s.subject_identifier, s.sid, s.dispensed_sid, arm_match, r.allocated_datetime, s.site_id, s.user_created, s.user_modified, s.modified, s.id AS original_id 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) as A ORDER BY subject_identifier, site_id",
+                "imp_subjectitutions_view",
+                engine="django.db.backends.mysql",
+            ),
+            reverse_code=django_db_views.migration_functions.BackwardViewMigration(
+                "", "imp_subjectitutions_view", engine="django.db.backends.mysql"
+            ),
+            atomic=False,
+        ),
+        django_db_views.operations.ViewRunPython(
+            code=django_db_views.migration_functions.ForwardViewMigration(
+                "select *, get_random_uuid() as id, now() as created, 'meta_reports.imp_subjectitutions_view' as report_model from (SELECT s.subject_identifier, s.sid, s.dispensed_sid, arm_match, r.allocated_datetime, s.site_id, s.user_created, s.user_modified, s.modified, s.id AS original_id 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 NULLS FIRST) as A ORDER BY subject_identifier, site_id",
+                "imp_subjectitutions_view",
+                engine="django.db.backends.postgresql",
+            ),
+            reverse_code=django_db_views.migration_functions.BackwardViewMigration(
+                "", "imp_subjectitutions_view", engine="django.db.backends.postgresql"
+            ),
+            atomic=False,
+        ),
+        django_db_views.operations.ViewRunPython(
+            code=django_db_views.migration_functions.ForwardViewMigration(
+                "select *, uuid() as id, datetime() as created, 'meta_reports.imp_subjectitutions_view' as report_model from (SELECT s.subject_identifier, s.sid, s.dispensed_sid, arm_match, r.allocated_datetime, s.site_id, s.user_created, s.user_modified, s.modified, s.id AS original_id 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) as A ORDER BY subject_identifier, site_id",
+                "imp_subjectitutions_view",
+                engine="django.db.backends.sqlite3",
+            ),
+            reverse_code=django_db_views.migration_functions.BackwardViewMigration(
+                "", "imp_subjectitutions_view", engine="django.db.backends.sqlite3"
+            ),
+            atomic=False,
+        ),
+    ]

meta_reports/migrations/0049_auto_20240911_0327.py

@@ -0,0 +1,54 @@
+# Generated by Django 5.1 on 2024-09-11 00:27
+
+import django_db_views.migration_functions
+import django_db_views.operations
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("meta_reports", "0048_auto_20240909_2338"),
+    ]
+
+    operations = [
+        django_db_views.operations.ViewRunPython(
+            code=django_db_views.migration_functions.ForwardViewMigration(
+                "select *, uuid() as id, now() as `created`, 'meta_reports.imp_subjectitutions_view' as `report_model` from (SELECT s.subject_identifier, s.sid, s.dispensed_sid, arm_match, s.report_datetime, r.allocated_datetime, s.site_id, s.user_created, s.user_modified, s.modified, s.id AS original_id 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) as A ORDER BY subject_identifier, site_id",
+                "imp_subjectitutions_view",
+                engine="django.db.backends.mysql",
+            ),
+            reverse_code=django_db_views.migration_functions.BackwardViewMigration(
+                "select *, uuid() as id, now() as `created`, 'meta_reports.imp_subjectitutions_view' as `report_model` from (SELECT s.subject_identifier, s.sid, s.dispensed_sid, arm_match, r.allocated_datetime, s.site_id, s.user_created, s.user_modified, s.modified, s.id AS original_id 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) as A ORDER BY subject_identifier, site_id",
+                "imp_subjectitutions_view",
+                engine="django.db.backends.mysql",
+            ),
+            atomic=False,
+        ),
+        django_db_views.operations.ViewRunPython(
+            code=django_db_views.migration_functions.ForwardViewMigration(
+                "select *, get_random_uuid() as id, now() as created, 'meta_reports.imp_subjectitutions_view' as report_model from (SELECT s.subject_identifier, s.sid, s.dispensed_sid, arm_match, s.report_datetime, r.allocated_datetime, s.site_id, s.user_created, s.user_modified, s.modified, s.id AS original_id 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 NULLS FIRST) as A ORDER BY subject_identifier, site_id",
+                "imp_subjectitutions_view",
+                engine="django.db.backends.postgresql",
+            ),
+            reverse_code=django_db_views.migration_functions.BackwardViewMigration(
+                "select *, get_random_uuid() as id, now() as created, 'meta_reports.imp_subjectitutions_view' as report_model from (SELECT s.subject_identifier, s.sid, s.dispensed_sid, arm_match, r.allocated_datetime, s.site_id, s.user_created, s.user_modified, s.modified, s.id AS original_id 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 NULLS FIRST) as A ORDER BY subject_identifier, site_id",
+                "imp_subjectitutions_view",
+                engine="django.db.backends.postgresql",
+            ),
+            atomic=False,
+        ),
+        django_db_views.operations.ViewRunPython(
+            code=django_db_views.migration_functions.ForwardViewMigration(
+                "select *, uuid() as id, datetime() as created, 'meta_reports.imp_subjectitutions_view' as report_model from (SELECT s.subject_identifier, s.sid, s.dispensed_sid, arm_match, s.report_datetime, r.allocated_datetime, s.site_id, s.user_created, s.user_modified, s.modified, s.id AS original_id 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) as A ORDER BY subject_identifier, site_id",
+                "imp_subjectitutions_view",
+                engine="django.db.backends.sqlite3",
+            ),
+            reverse_code=django_db_views.migration_functions.BackwardViewMigration(
+                "select *, uuid() as id, datetime() as created, 'meta_reports.imp_subjectitutions_view' as report_model from (SELECT s.subject_identifier, s.sid, s.dispensed_sid, arm_match, r.allocated_datetime, s.site_id, s.user_created, s.user_modified, s.modified, s.id AS original_id 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) as A ORDER BY subject_identifier, site_id",
+                "imp_subjectitutions_view",
+                engine="django.db.backends.sqlite3",
+            ),
+            atomic=False,
+        ),
+    ]

meta_reports/models/__init__.py

@@ -1,6 +1,7 @@
 from .dbviews import (
     NOTE_STATUSES,
     GlucoseSummary,
+    ImpSubstitutions,
     MissingOgttNote,
     MissingScreeningOgtt,
     OnStudyMissingLabValues,

meta_reports/models/dbviews/__init__.py

@@ -1,4 +1,5 @@
 from .glucose_summary import GlucoseSummary
+from .imp_substitutions import ImpSubstitutions
 from .missing_screening_ogtt import NOTE_STATUSES, MissingOgttNote, MissingScreeningOgtt
 from .on_study_missing_lab_values import OnStudyMissingLabValues
 from .on_study_missing_values import OnStudyMissingValues

meta_reports/models/dbviews/imp_substitutions/__init__.py

@@ -0,0 +1 @@
+from .unmanaged_model import ImpSubstitutions

meta_reports/models/dbviews/imp_substitutions/unmanaged_model.py

@@ -0,0 +1,39 @@
+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)
+
+    dispensed_sid = models.IntegerField(verbose_name="Dispensed SID", null=True)
+
+    arm_match = models.CharField(
+        max_length=15, choices=YES_NO_NOT_EVALUATED, default=NOT_EVALUATED
+    )
+
+    report_datetime = models.DateTimeField(null=True)
+
+    allocated_datetime = models.DateTimeField(null=True)
+
+    user_created = models.CharField(max_length=25)
+
+    user_modified = models.CharField(max_length=25)
+
+    modified = models.DateTimeField(null=True)
+
+    view_definition = get_view_definition()
+
+    class Meta:
+        managed = False
+        db_table = "imp_subjectitutions_view"
+        verbose_name = "IMP Substitutions"
+        verbose_name_plural = "IMP Substitutions"
+        default_permissions = qa_reports_permissions

meta_reports/models/dbviews/imp_substitutions/view_definition.py

@@ -0,0 +1,21 @@
+from edc_qareports.sql_generator import SqlViewGenerator
+
+
+def get_view_definition() -> dict:
+    subquery = """
+        select s.subject_identifier, s.sid, s.dispensed_sid, arm_match,
+        s.report_datetime, r.allocated_datetime,
+        s.site_id, s.user_created, s.user_modified, s.modified, s.id as original_id
+        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"],
+    )
+    return {
+        "django.db.backends.mysql": sql_view.as_mysql(subquery),
+        "django.db.backends.postgresql": sql_view.as_postgres(subquery),
+        "django.db.backends.sqlite3": sql_view.as_sqlite(subquery),
+    }

meta_reports/models/dbviews/on_study_missing_values/qa_cases.py

@@ -12,7 +12,6 @@ qa_cases = [
         label="No VL value or VL date",
         dbtable="meta_subject_patienthistory",
         label_lower="meta_subject.patienthistory",
-        fld_name="viral_load_date",
         where="crf.viral_load is null or crf.viral_load_date is null",
     ),
     CrfCase(

meta_sites/tests/test_sites.py

@@ -1,5 +1,5 @@
 from django.test import TestCase
-from edc_sites import InvalidSiteError
+from edc_sites.exceptions import InvalidSiteError
 from edc_sites.site import sites