meta-edc 0.3.15__py3-none-any.whl → 0.3.50__py3-none-any.whl

meta_pharmacy/utils/update_initial_pharmacy_data.py

@@ -0,0 +1,146 @@
+from django.contrib.sites.models import Site
+from django.core.exceptions import ObjectDoesNotExist
+from django_pylabels.models import LabelSpecification
+from edc_pharmacy.models import (
+    Assignment,
+    Container,
+    ContainerType,
+    ContainerUnits,
+    Formulation,
+    Location,
+    Product,
+    Supplier,
+)
+from edc_pylabels.models import LabelConfiguration
+from edc_pylabels.site_label_configs import site_label_configs
+
+
+def update_initial_pharmacy_data():
+    update_assignment()
+    update_container()
+    update_location()
+    update_product()
+    update_supplier()
+    update_labels()
+
+
+def update_assignment():
+    """For a trial with just active and placebo.
+
+    Better to get these labels from edc_randomizer.
+    """
+    for assignment in ["placebo", "active"]:
+        try:
+            Assignment.objects.get(name=assignment)
+        except ObjectDoesNotExist:
+            Assignment.objects.create(name=assignment, display_name=assignment.title())
+
+
+def update_container():
+    """Here we order a number of tablets. The manufacturer sends
+    the order in large containers, barrels of about 30K tablets
+    per barrel. We repack/decant into bottles of 128 tablets
+    """
+    tablet_type = ContainerType.objects.get(name="tablet")
+    bottle_type = ContainerType.objects.get(name="bottle")
+    units = ContainerUnits.objects.get(name="tablet")
+    opts = {
+        "tablet": dict(
+            name="tablet",
+            display_name="Tablet",
+            container_type=tablet_type,
+            units=units,
+            qty=1,
+            may_order_as=True,
+            max_per_subject=0,
+        ),
+        "bottle30k": dict(
+            name="bottle30k",
+            display_name="Barrel 30K",
+            container_type=bottle_type,
+            units=units,
+            qty=30000,
+            may_receive_as=True,
+            max_per_subject=0,
+        ),
+        "bottle128": dict(
+            name="bottle128",
+            display_name="Bottle 128",
+            container_type=bottle_type,
+            units=units,
+            qty=128,
+            max_per_subject=3,
+            may_repack_as=True,
+            may_request_as=True,
+            may_dispense_as=True,
+        ),
+    }
+    for name, data in opts.items():
+        try:
+            Container.objects.get(name=name)
+        except ObjectDoesNotExist:
+            Container.objects.create(**data)
+
+
+def update_location():
+    """Base the locations on the sites in the trial plus
+    a "central" pharmacy"""
+    for obj in Location.objects.exclude(name="central"):
+        obj.site_id = Site.objects.get(name=obj.name).id
+        obj.save(update_fields=["site_id"])
+
+
+def update_product():
+    """Define the product, in this case just two; active and placebo.
+
+    Formulation is defined before running this script.
+
+    In this case the formulation is just the study drug/IMP.
+    """
+    formulation = Formulation.objects.get()
+    active = Assignment.objects.get(name="active")
+    placebo = Assignment.objects.get(name="placebo")
+    try:
+        Product.objects.get(formulation=formulation, assignment=active)
+    except ObjectDoesNotExist:
+        Product(assignment=active, formulation=formulation).save()
+    try:
+        Product.objects.get(formulation=formulation, assignment=placebo)
+    except ObjectDoesNotExist:
+        Product(assignment=placebo, formulation=formulation).save()
+
+
+def update_supplier():
+    """In this case MERCK"""
+    try:
+        Supplier.objects.get(name="merck")
+    except ObjectDoesNotExist:
+        Supplier(name="merck").save()
+
+
+def update_labels():
+    """The default label spec is a 2 x 6 label sheet
+
+    Add "label congigs" as registered in the "site_label_configs"
+    global. In this case there are three labels:
+    * a bulk label for the barrels
+    * a generic vertical label for decanted stock (bottles of 128)
+    * a patient label for allocated stock (bottles of 128)
+
+    The patient label will be placed over the generic vertical label
+    once the stock item is allocated to a subject.
+    """
+    try:
+        default = LabelSpecification.objects.get(name="default")
+    except ObjectDoesNotExist:
+        LabelSpecification().save()
+        default = LabelSpecification.objects.get(name="default")
+
+    for name, label_config in site_label_configs.registry.items():
+        LabelConfiguration.objects.create(name=name, label_specification=default)
+    for label_configuration in LabelConfiguration.objects.filter(name__contains="patient"):
+        label_configuration.requires_allocation = True
+        label_configuration.save()
+
+
+__all__ = ["update_initial_pharmacy_data"]

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_prn/admin/pregnancy_notification_admin.py

@@ -57,11 +57,15 @@ class PregnancyNotificationAdmin(
             "subject_identifier",
             "dashboard",
             "edd",
-            "may_contact",
+            "contact_agreed",
         )
         return custom_fields + tuple(f for f in list_display if f not in custom_fields)
 
     def get_list_filter(self, request) -> Tuple[str, ...]:
-        list_filter = super().get_list_display(request)
+        list_filter = super().get_list_filter(request)
         custom_fields = ("edd", "may_contact")
         return custom_fields + tuple(f for f in list_filter if f not in custom_fields)
+
+    @admin.display(description="May contact?", ordering="may_contact")
+    def contact_agreed(self, obj):
+        return obj.may_contact

meta_prn/migrations/0034_auto_20220630_1110.py

@@ -37,9 +37,9 @@ def update_for_protocol_incident(apps, schema_editor):
         ).update(action_type=action_type)
 
         # update crf metadata if there is any
-        action_item_model_cls.objects.filter(
-            reference_model="meta_prn.protocoldeviationviolation"
-        ).update(reference_model="meta_prn.protocolincident")
+        # action_item_model_cls.objects.filter(
+        #     reference_model="meta_prn.protocoldeviationviolation"
+        # ).update(reference_model="meta_prn.protocolincident")
 
 
 class Migration(migrations.Migration):

meta_prn/migrations/0035_auto_20220630_1140.py

@@ -18,70 +18,73 @@ def create_missing_offschedule(apps, schema_editor):
     subject_schedule_history_model_cls = apps.get_model(
         "edc_visit_schedule.subjectschedulehistory"
     )
-    action_type = action_type_model_cls.objects.get(name=OFFSCHEDULE_ACTION)
+    try:
+        action_type = action_type_model_cls.objects.get(name=OFFSCHEDULE_ACTION)
+    except ObjectDoesNotExist:
+        pass
+    else:
+        # update subject_schedule_history
+        subject_schedule_history_model_cls.objects.filter(
+            offschedule_model="meta_prn.endofstudy"
+        ).update(offschedule_model="meta_prn.offschedule")
 
-    # update subject_schedule_history
-    subject_schedule_history_model_cls.objects.filter(
-        offschedule_model="meta_prn.endofstudy"
-    ).update(offschedule_model="meta_prn.offschedule")
-
-    sql = (
-        "Select eos.id, eos.subject_identifier from meta_prn_endofstudy as eos "
-        "left join meta_prn_offschedule as off on eos.subject_identifier = off.subject_identifier "
-        "where off.id is null"
-    )
-    qs = eos_model_cls.objects.raw(sql)
+        sql = (
+            "Select eos.id, eos.subject_identifier from meta_prn_endofstudy as eos "
+            "left join meta_prn_offschedule as off on eos.subject_identifier = off.subject_identifier "
+            "where off.id is null"
+        )
+        qs = eos_model_cls.objects.raw(sql)
 
-    qs = [obj for obj in qs]
-    total = len(qs)
+        qs = [obj for obj in qs]
+        total = len(qs)
 
-    # create missing offschedule model instances
-    for eos in tqdm(qs, total=total):
-        # create action items model instances
-        tracking_identifier = uuid4().hex
-        try:
-            action_item = action_item_model_cls.objects.get(
-                subject_identifier=eos.subject_identifier, action_type=action_type
-            )
-        except ObjectDoesNotExist:
-            action_item = action_item_model_cls(
-                action_identifier=uuid4().hex.upper(),
+        # create missing offschedule model instances
+        for eos in tqdm(qs, total=total):
+            # create action items model instances
+            tracking_identifier = uuid4().hex
+            try:
+                action_item = action_item_model_cls.objects.get(
+                    subject_identifier=eos.subject_identifier, action_type=action_type
+                )
+            except ObjectDoesNotExist:
+                action_item = action_item_model_cls(
+                    action_identifier=uuid4().hex.upper(),
+                    subject_identifier=eos.subject_identifier,
+                    action_type=action_type,
+                    report_datetime=eos.offschedule_datetime,
+                    priority=HIGH_PRIORITY,
+                    status=NEW,
+                    auto_created=True,
+                    reference_model="meta_prn.offschedule",
+                )
+                action_item.save()
+                action_item.refresh_from_db()
+                if not action_item.action_identifier:
+                    raise ValueError("Action identifier cannot be null")
+            action_item.status = NEW
+            action_item.save()
+            action_item.refresh_from_db()
+            offschedule = offschedule_model_cls(
                 subject_identifier=eos.subject_identifier,
-                action_type=action_type,
+                action_identifier=action_item.action_identifier,
+                tracking_identifier=tracking_identifier,
+                action_item=action_item,
                 report_datetime=eos.offschedule_datetime,
-                priority=HIGH_PRIORITY,
-                status=NEW,
-                auto_created=True,
-                reference_model="meta_prn.offschedule",
+                offschedule_datetime=eos.offschedule_datetime,
+                site_id=eos.site.id,
             )
+            action_item.status = CLOSED
             action_item.save()
-            action_item.refresh_from_db()
-            if not action_item.action_identifier:
-                raise ValueError("Action identifier cannot be null")
-        action_item.status = NEW
-        action_item.save()
-        action_item.refresh_from_db()
-        offschedule = offschedule_model_cls(
-            subject_identifier=eos.subject_identifier,
-            action_identifier=action_item.action_identifier,
-            tracking_identifier=tracking_identifier,
-            action_item=action_item,
-            report_datetime=eos.offschedule_datetime,
-            offschedule_datetime=eos.offschedule_datetime,
-            site_id=eos.site.id,
-        )
-        action_item.status = CLOSED
-        action_item.save()
-        offschedule.save()
-        eos.parent_action_item = action_item
-        eos.action_item.status = NEW
-        eos.action_item.save()
-        eos.action_item.refresh_from_db()
-        eos.refresh_from_db()
-        eos.save()
+            offschedule.save()
+            eos.parent_action_item = action_item
+            eos.action_item.status = NEW
+            eos.action_item.save()
+            eos.action_item.refresh_from_db()
+            eos.refresh_from_db()
+            eos.save()
 
-    for obj in eos_model_cls.objects.all():
-        obj.save()
+        for obj in eos_model_cls.objects.all():
+            obj.save()
 
 
 class Migration(migrations.Migration):

meta_prn/tests/tests/test_dm_referral.py

@@ -1,6 +1,6 @@
 from dateutil.relativedelta import relativedelta
 from django.core.exceptions import ObjectDoesNotExist
-from django.test import TestCase, tag
+from django.test import TestCase
 from edc_action_item.models import ActionItem
 from edc_appointment.constants import COMPLETE_APPT
 from edc_appointment.models import Appointment
@@ -18,11 +18,10 @@ from meta_prn.constants import (
 from meta_prn.models import DmReferral, OnScheduleDmReferral
 from meta_screening.tests.meta_test_case_mixin import MetaTestCaseMixin
 from meta_subject.constants import DM_FOLLOWUP_ACTION
-from meta_subject.models import DmDiagnosis, DmFollowup, SubjectVisit
+from meta_subject.models import DmEndpoint, DmFollowup, SubjectVisit
 from meta_visit_schedule.constants import DM_BASELINE, DM_FOLLOWUP, SCHEDULE_DM_REFERRAL
 
 
-@tag("1")
 class TestDmReferral(MetaTestCaseMixin, TestCase):
     def setUp(self):
         super().setUp()
@@ -49,7 +48,6 @@ class TestDmReferral(MetaTestCaseMixin, TestCase):
         except ObjectDoesNotExist:
             self.fail("OnScheduleDmReferral unexpectedly does not exist")
 
-    @tag("1")
     def test_dm_referral_action_creates_offschedule_action(self):
         subject_visit = self.get_next_subject_visit(self.subject_visit)
         subject_visit = self.get_next_subject_visit(subject_visit)
@@ -117,7 +115,6 @@ class TestDmReferral(MetaTestCaseMixin, TestCase):
         except ObjectDoesNotExist:
             self.fail(f"{DM_FOLLOWUP_ACTION} Action item unexpectedly does not exist")
 
-    @tag("1")
     def test_dm_referral2(self):
         subject_visit = self.get_next_subject_visit(self.subject_visit)
         subject_visit = self.get_next_subject_visit(subject_visit)
@@ -146,7 +143,7 @@ class TestDmReferral(MetaTestCaseMixin, TestCase):
             info_source=PATIENT,
         )
 
-        DmDiagnosis.objects.create(
+        DmEndpoint.objects.create(
             subject_visit=subject_visit,
             report_datetime=get_utcnow(),
             dx_date=referral_datetime.date(),

meta_reports/__init__.py

@@ -0,0 +1 @@
+from .tasks import update_endpoints_table

meta_reports/admin/__init__.py

@@ -0,0 +1,15 @@
+from .dbviews import (
+    GlucoseSummaryAdmin,
+    ImpSubstitutionsAdmin,
+    MissingOgttNoteModelAdmin,
+    MissingScreeningOgttAdmin,
+    OnStudyMissingLabValuesAdmin,
+    OnStudyMissingValuesAdmin,
+    PatientHistoryMissingBaselineCd4Admin,
+    UnattendedThreeInRow2Admin,
+    UnattendedThreeInRowAdmin,
+    UnattendedTwoInRowAdmin,
+)
+from .endpoints_admin import EndpointsAdmin
+from .endpoints_all_admin import EndpointsAllAdmin
+from .last_imp_refill_admin import LastImpRefillAdmin

meta_reports/admin/dbviews/__init__.py

@@ -0,0 +1,14 @@
+from .glucose_summary_admin import GlucoseSummaryAdmin
+from .imp_substitutions_admin import ImpSubstitutionsAdmin
+from .missing_screening_ogtt_admin import (
+    MissingOgttNoteModelAdmin,
+    MissingScreeningOgttAdmin,
+)
+from .on_study_missing_lab_values_admin import OnStudyMissingLabValuesAdmin
+from .on_study_missing_values_admin import OnStudyMissingValuesAdmin
+from .patient_history_missing_baseline_cd4_admin import (
+    PatientHistoryMissingBaselineCd4Admin,
+)
+from .unattended_three_in_row2_admin import UnattendedThreeInRow2Admin
+from .unattended_three_in_row_admin import UnattendedThreeInRowAdmin
+from .unattended_two_in_row_admin import UnattendedTwoInRowAdmin

meta_reports/admin/dbviews/glucose_summary_admin.py

@@ -0,0 +1,116 @@
+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 edc_constants.constants import YES
+from edc_glucose.list_filters import FbgListFilter, OgttListFilter
+from edc_model_admin.dashboard import ModelAdminDashboardMixin
+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 ...admin_site import meta_reports_admin
+from ...models import Endpoints, EndpointsProxy, GlucoseSummary
+from ..list_filters import EndpointListFilter
+
+
+@admin.register(GlucoseSummary, site=meta_reports_admin)
+class GlucoseSummaryAdmin(
+    QaReportModelAdminMixin,
+    SiteModelAdminMixin,
+    ModelAdminDashboardMixin,
+    TemplatesModelAdminMixin,
+    admin.ModelAdmin,
+):
+    ordering = ["site", "subject_identifier", "fbg_datetime"]
+    include_note_column = False
+    list_display = [
+        "dashboard",
+        "subject_identifier_link",
+        "site",
+        "visit",
+        "fasted",
+        "fbg_date",
+        "fbg_value",
+        "ogtt_value",
+        "ogtt_date",
+        "endpoint",
+        "offstudy_date",
+    ]
+
+    list_filter = [
+        ScheduleStatusListFilter,
+        "fasted",
+        FbgListFilter,
+        OgttListFilter,
+        "fbg_datetime",
+        "ogtt_datetime",
+        EndpointListFilter,
+    ]
+
+    search_fields = ["subject_identifier"]
+
+    @admin.display(description="visit", ordering="visit_code")
+    def visit(self, obj=None):
+        return f"{obj.visit_code}.{obj.visit_code_sequence}"
+
+    @admin.display(description="Endpoint")
+    def endpoint(self, obj=None):
+        try:
+            endpoint_obj = Endpoints.objects.get(subject_identifier=obj.subject_identifier)
+        except ObjectDoesNotExist:
+            value = None
+        else:
+            if endpoint_obj.offstudy_date:
+                url = reverse("meta_reports_admin:meta_reports_endpointsproxy_changelist")
+                title = f"Go to {EndpointsProxy._meta.verbose_name}"
+            else:
+                url = reverse("meta_reports_admin:meta_reports_endpoints_changelist")
+                title = f"Go to {Endpoints._meta.verbose_name}"
+            value = render_to_string(
+                "meta_reports/columns/subject_identifier_column.html",
+                {
+                    "subject_identifier": obj.subject_identifier,
+                    "url": url,
+                    "label": YES,
+                    "title": title,
+                },
+            )
+        return value
+
+    @admin.display(description="Subject Idenfifier", ordering="subject_identifier")
+    def subject_identifier_link(self, obj=None):
+        url = reverse("meta_reports_admin:meta_reports_glucosesummary_changelist")
+        return render_to_string(
+            "meta_reports/columns/subject_identifier_column.html",
+            {
+                "subject_identifier": obj.subject_identifier,
+                "url": url,
+                "title": "Click to filter for this subject only",
+            },
+        )
+
+    def get_subject_dashboard_url_kwargs(self, obj) -> dict:
+        return dict(
+            subject_identifier=obj.subject_identifier,
+            appointment=obj.appointment_id,
+        )
+
+    @admin.display(description="Fbg date", ordering="fbg_datetime")
+    def fbg_date(self, obj):
+        if obj.fbg_datetime:
+            return obj.fbg_datetime.date()
+        return None
+
+    @admin.display(description="OGTT date", ordering="ogtt_datetime")
+    def ogtt_date(self, obj):
+        if obj.ogtt_datetime:
+            return obj.ogtt_datetime.date()
+        return None
+
+    @admin.display(description="Offstudy date", ordering="offstudy_datetime")
+    def offstudy_date(self, obj):
+        if obj.offstudy_datetime:
+            return obj.offstudy_datetime.date()
+        return None

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/admin/dbviews/missing_screening_ogtt_admin/__init__.py

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