meta-edc 0.3.7__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

@@ -16,14 +16,18 @@ from edc_visit_schedule.constants import OFFSCHEDULE_ACTION
 
 from meta_subject.constants import (
     DELIVERY_ACTION,
+    DM_FOLLOWUP_ACTION,
     MISSED_VISIT_ACTION,
     URINE_PREGNANCY_ACTION,
 )
 
 from .constants import (
+    DM_REFFERAL_ACTION,
+    OFFSCHEDULE_DM_REFERRAL_ACTION,
     OFFSCHEDULE_PREGNANCY_ACTION,
     OFFSTUDY_MEDICATION_ACTION,
     PREGNANCY_NOTIFICATION_ACTION,
+    REFERRAL,
     UNBLINDING_REQUEST_ACTION,
     UNBLINDING_REVIEW_ACTION,
 )
@@ -56,7 +60,7 @@ class OffscheduleAction(ActionWithNotification):
         if pregnancy_notification and pregnancy_notification.may_contact in [YES, NOT_SURE]:
             next_actions = [OFFSTUDY_MEDICATION_ACTION]
         else:
-            next_actions = [OFFSTUDY_MEDICATION_ACTION, END_OF_STUDY_ACTION]
+            next_actions = [OFFSTUDY_MEDICATION_ACTION]
         return next_actions
 
 
@@ -86,8 +90,10 @@ class EndOfStudyAction(ActionWithNotification):
     display_name = "Submit End of Study Report"
     notification_display_name = "End of Study Report"
     parent_action_names = [
-        OFFSCHEDULE_ACTION,
+        # OFFSCHEDULE_ACTION,
+        OFFSTUDY_MEDICATION_ACTION,
         OFFSCHEDULE_PREGNANCY_ACTION,
+        OFFSCHEDULE_DM_REFERRAL_ACTION,
     ]
     reference_model = "meta_prn.endofstudy"
     show_link_to_changelist = True
@@ -125,6 +131,41 @@ class PregnancyNotificationAction(ActionWithNotification):
     priority = HIGH_PRIORITY
 
 
+class DmReferralAction(ActionWithNotification):
+    """Action to put subject on dm_referral schedule"""
+
+    name = DM_REFFERAL_ACTION
+    display_name = "Diabetes referral"
+    notification_display_name = "Diabetes referral"
+    parent_action_names = [OFFSTUDY_MEDICATION_ACTION]
+    reference_model = "meta_prn.dmreferral"
+    show_link_to_changelist = True
+    show_link_to_add = True
+    admin_site_name = "meta_prn_admin"
+    priority = HIGH_PRIORITY
+    singleton = True
+
+    def get_next_actions(self):
+        next_actions = [DM_FOLLOWUP_ACTION]
+        return next_actions
+
+
+class OffscheduleDmReferralAction(ActionWithNotification):
+    name = OFFSCHEDULE_DM_REFERRAL_ACTION
+    display_name = "Submit Off-Schedule (Diabetes Referral)"
+    notification_display_name = "Off-Schedule (Diabetes Referral)"
+    parent_action_names = [DM_FOLLOWUP_ACTION]
+    reference_model = "meta_prn.offscheduledmreferral"
+    show_link_to_changelist = True
+    admin_site_name = "meta_prn_admin"
+    priority = HIGH_PRIORITY
+    singleton = True
+
+    def get_next_actions(self):
+        next_actions = [END_OF_STUDY_ACTION]
+        return next_actions
+
+
 class OffStudyMedicationAction(ActionWithNotification):
     name = OFFSTUDY_MEDICATION_ACTION
     display_name = "Withdrawal Study Medication"
@@ -142,6 +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
@@ -212,3 +260,5 @@ site_action_items.register(SubjectTransferAction)
 site_action_items.register(UnblindingRequestAction)
 site_action_items.register(UnblindingReviewAction)
 site_action_items.register(OffStudyMedicationAction)
+site_action_items.register(DmReferralAction)
+site_action_items.register(OffscheduleDmReferralAction)

meta_prn/admin/__init__.py

@@ -1,10 +1,13 @@
+from .dm_referral_admin import DmReferralAdmin
 from .end_of_study_admin import EndOfStudyAdmin
 from .loss_to_followup_admin import LossToFollowupAdmin
 from .off_study_medication_admin import OffStudyMedicationAdmin
 from .offschedule_admin import OffScheduleAdmin
+from .offschedule_dm_referral_admin import OffScheduleDmReferralAdmin
 from .offschedule_postnatal_admin import OffSchedulePostnatalAdmin
 from .offschedule_pregnancy_admin import OffSchedulePregnancyAdmin
 from .onschedule_admin import OnScheduleAdmin
+from .onschedule_dm_referral_admin import OnScheduleDmReferralAdmin
 from .pregnancy_notification_admin import PregnancyNotificationAdmin
 from .protocol_incident_admin import ProtocolIncidentAdmin
 from .subject_transfer_admin import SubjectTransferAdmin

meta_prn/admin/dm_referral_admin.py

@@ -0,0 +1,49 @@
+from django.contrib import admin
+from django_audit_fields.admin import audit_fieldset_tuple
+from edc_action_item import ActionItemModelAdminMixin, action_fieldset_tuple
+from edc_model_admin.dashboard import ModelAdminSubjectDashboardMixin
+from edc_model_admin.history import SimpleHistoryAdmin
+from edc_sites.admin import SiteModelAdminMixin
+
+from ..admin_site import meta_prn_admin
+from ..forms import DmReferralForm
+from ..models import DmReferral
+
+
+@admin.register(DmReferral, site=meta_prn_admin)
+class DmReferralAdmin(
+    SiteModelAdminMixin,
+    ModelAdminSubjectDashboardMixin,
+    ActionItemModelAdminMixin,
+    SimpleHistoryAdmin,
+):
+    form = DmReferralForm
+
+    fieldsets = (
+        (None, {"fields": ("subject_identifier", "report_datetime")}),
+        ("Referral to Diabetes clinic", {"fields": ("referral_date",)}),
+        (
+            "Diabetes diagnosis",
+            {
+                "fields": ("referral_note",),
+            },
+        ),
+        action_fieldset_tuple,
+        audit_fieldset_tuple,
+    )
+
+    list_display = (
+        "subject_identifier",
+        "dashboard",
+        "report_datetime",
+        "referral_date_as_col",
+    )
+
+    list_filter = (
+        "report_datetime",
+        "referral_date",
+    )
+
+    @admin.display(description="Referral date", ordering="referral_date")
+    def referral_date_as_col(self, obj=None):
+        return obj.referral_date

meta_prn/admin/offschedule_dm_referral_admin.py

@@ -0,0 +1,47 @@
+from typing import Tuple
+
+from django.contrib import admin
+from django.utils.html import format_html
+from django_audit_fields import audit_fieldset_tuple
+from edc_action_item import ActionItemModelAdminMixin, action_fieldset_tuple
+from edc_model_admin.dashboard import ModelAdminSubjectDashboardMixin
+from edc_model_admin.history import SimpleHistoryAdmin
+from edc_sites.admin import SiteModelAdminMixin
+
+from ..admin_site import meta_prn_admin
+from ..forms import OffScheduleDmReferralForm
+from ..models import EndOfStudy, OffScheduleDmReferral
+
+
+@admin.register(OffScheduleDmReferral, site=meta_prn_admin)
+class OffScheduleDmReferralAdmin(
+    SiteModelAdminMixin,
+    ActionItemModelAdminMixin,
+    ModelAdminSubjectDashboardMixin,
+    SimpleHistoryAdmin,
+):
+    instructions = None
+
+    form = OffScheduleDmReferralForm
+
+    additional_instructions = format_html(
+        '<span style="color:orange;font-weight:bold">Note:</span> Detailed '
+        "information about study termination will be asked for on the "
+        f"<b>{EndOfStudy._meta.verbose_name}</b> form"
+    )
+
+    fieldsets = (
+        (None, {"fields": ("subject_identifier", "offschedule_datetime")}),
+        action_fieldset_tuple,
+        audit_fieldset_tuple,
+    )
+
+    def get_list_display(self, request) -> Tuple[str, ...]:
+        list_display = super().get_list_display(request)
+        custom_fields = ("subject_identifier", "dashboard", "offschedule_datetime")
+        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_filter(request)
+        custom_fields = ("offschedule_datetime",)
+        return custom_fields + tuple(f for f in list_filter if f not in custom_fields)

meta_prn/admin/onschedule_dm_referral_admin.py

@@ -0,0 +1,39 @@
+from typing import Tuple
+
+from django.contrib import admin
+from edc_model_admin.dashboard import ModelAdminSubjectDashboardMixin
+from edc_model_admin.history import SimpleHistoryAdmin
+from edc_sites.admin import SiteModelAdminMixin
+
+from ..admin_site import meta_prn_admin
+from ..models import OnScheduleDmReferral
+
+
+@admin.register(OnScheduleDmReferral, site=meta_prn_admin)
+class OnScheduleDmReferralAdmin(
+    SiteModelAdminMixin, ModelAdminSubjectDashboardMixin, SimpleHistoryAdmin
+):
+    instructions = None
+
+    fields = ("subject_identifier", "onschedule_datetime")
+
+    def get_list_display(self, request) -> Tuple[str, ...]:
+        list_display = super().get_list_display(request)
+        custom_fields = ("subject_identifier", "dashboard", "onschedule_datetime")
+        return custom_fields + tuple(
+            f for f in list_display if f not in custom_fields + ("__str__",)
+        )
+
+    def get_list_filter(self, request) -> Tuple[str, ...]:
+        list_filter = super().get_list_filter(request)
+        custom_fields = ("onschedule_datetime",)
+        return custom_fields + tuple(f for f in list_filter if f not in custom_fields)
+
+    def get_readonly_fields(self, request, obj=None) -> Tuple[str, ...]:
+        return (
+            "subject_identifier",
+            "onschedule_datetime",
+        )
+
+    def get_search_fields(self, request) -> Tuple[str, ...]:
+        return tuple(set(super().get_search_fields(request) + ("subject_identifier",)))

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/baker_recipes.py

@@ -4,7 +4,7 @@ from edc_utils import get_utcnow
 from faker import Faker
 from model_bakery.recipe import Recipe
 
-from .models import PregnancyNotification
+from .models import DmReferral, PregnancyNotification
 
 fake = Faker()
 
@@ -19,3 +19,10 @@ pregnancynotification = Recipe(
     unconfirmed_details=None,
     edd=get_utcnow() + relativedelta(months=6),
 )
+
+dmreferral = Recipe(
+    DmReferral,
+    action_identifier=None,
+    subject_identifier=None,
+    report_datetime=get_utcnow(),
+)

meta_prn/choices.py

@@ -1,6 +1,6 @@
 from edc_constants.constants import NOT_APPLICABLE, OTHER, PATIENT, PREGNANCY, UNKNOWN
 
-from .constants import CLINICIAN, INVESTIGATOR, SAE
+from .constants import CLINICIAN, INVESTIGATOR, REFERRAL, SAE
 
 CLINICAL_WITHDRAWAL_REASONS = (
     ("kidney_disease", "Development of chronic kidney disease"),
@@ -95,6 +95,7 @@ WITHDRAWAL_STUDY_MEDICATION_REASONS = (
         "treatment in the clinician's opinion (specify below)",
     ),
     (INVESTIGATOR, " Investigator decision"),
+    (REFERRAL, "Referral to Diabetes clinic"),
     (PATIENT, "Patient decision"),
     (OTHER, "Other reason (specify below)"),
 )

meta_prn/constants.py

@@ -2,17 +2,20 @@ CLINICAL_WITHDRAWAL = "clinical_withdrawal"
 CLINICIAN = "clinician"
 DEATH_REPORT_ACTION = "submit_death_report"
 DEVIATION = "protocol_deviation"
+DM_REFFERAL_ACTION = "dm_refferal_action"
 INVESTIGATOR = "investigator"
 INVESTIGATOR_DECISION = "investigator_decision"
 LATE_EXCLUSION = "late_exclusion"
 LOSS_TO_FOLLOWUP_ACTION = "submit_loss_to_followup"
+OFFSCHEDULE_DM_REFERRAL_ACTION = "offschedule_dm_referral_action"
 OFFSCHEDULE_POSTNATAL_ACTION = "offschedule_postnatal_action"
 OFFSCHEDULE_PREGNANCY_ACTION = "offschedule_pregnancy_action"
+OFFSTUDY_MEDICATION_ACTION = "withdrawal_study_medication_action"
 OTHER_RX_DISCONTINUATION = "other_treatment_discontinuation"
 PREGNANCY_NOTIFICATION_ACTION = "pregancy_notification_action"
 PROTOCOL_DEVIATION_VIOLATION_ACTION = "submit-protocol-deviation-violation"
+REFERRAL = "referral"
 SAE = "sae"
 UNBLINDING_REQUEST_ACTION = "unblinding-request"
 UNBLINDING_REVIEW_ACTION = "unblinding-review"
 VIOLATION = "protocol_violation"
-OFFSTUDY_MEDICATION_ACTION = "withdrawal_study_medication_action"

meta_prn/forms/__init__.py

@@ -1,6 +1,8 @@
+from .dm_referral_form import DmReferralForm
 from .end_of_study_form import EndOfStudyForm
 from .loss_to_followup_form import LossToFollowupForm
 from .off_study_medication_form import OffStudyMedicationForm
+from .offschedule_dm_referral_form import OffScheduleDmReferralForm
 from .offschedule_form import OffScheduleForm
 from .offschedule_pregnancy_form import OffSchedulePregnancyForm
 from .pregnancy_notification_form import PregnancyNotificationForm

meta_prn/forms/dm_referral_form.py

@@ -0,0 +1,40 @@
+from django import forms
+from edc_action_item.forms.action_item_form_mixin import ActionItemFormMixin
+from edc_form_validators.form_validator import FormValidator
+from edc_form_validators.form_validator_mixins import FormValidatorMixin
+from edc_model_form.mixins import BaseModelFormMixin
+from edc_offstudy.modelform_mixins import OffstudyNonCrfModelFormMixin
+from edc_prn.modelform_mixins import PrnFormValidatorMixin
+from edc_sites.forms import SiteModelFormMixin
+
+from ..models import DmReferral
+
+
+class DmReferralFormValidator(PrnFormValidatorMixin, FormValidator):
+    pass
+
+
+class DmReferralForm(
+    SiteModelFormMixin,
+    OffstudyNonCrfModelFormMixin,
+    ActionItemFormMixin,
+    BaseModelFormMixin,
+    FormValidatorMixin,
+    forms.ModelForm,
+):
+    form_validator_cls = DmReferralFormValidator
+
+    # subject_identifier = forms.CharField(
+    #     label="Subject Identifier",
+    #     required=False,
+    #     widget=forms.TextInput(attrs={"readonly": "readonly"}),
+    # )
+
+    class Meta:
+        model = DmReferral
+        fields = "__all__"
+        help_text = {"subject_identifier": "(read-only)", "action_identifier": "(read-only)"}
+        widgets = {
+            "subject_identifier": forms.TextInput(attrs={"readonly": "readonly"}),
+            "action_identifier": forms.TextInput(attrs={"readonly": "readonly"}),
+        }

meta_prn/forms/offschedule_dm_referral_form.py

@@ -0,0 +1,35 @@
+from django import forms
+from edc_action_item.forms.action_item_form_mixin import ActionItemFormMixin
+from edc_form_validators.form_validator import FormValidator
+from edc_form_validators.form_validator_mixins import FormValidatorMixin
+from edc_model_form.mixins import BaseModelFormMixin
+from edc_prn.modelform_mixins import PrnFormValidatorMixin
+from edc_sites.forms import SiteModelFormMixin
+from edc_visit_schedule.modelform_mixins import OffScheduleModelFormMixin
+
+from ..models import OffScheduleDmReferral
+
+
+class OffScheduleDmReferralFormValidator(PrnFormValidatorMixin, FormValidator):
+    pass
+
+
+class OffScheduleDmReferralForm(
+    OffScheduleModelFormMixin,
+    SiteModelFormMixin,
+    ActionItemFormMixin,
+    BaseModelFormMixin,
+    FormValidatorMixin,
+    forms.ModelForm,
+):
+    form_validator_cls = OffScheduleDmReferralFormValidator
+
+    subject_identifier = forms.CharField(
+        label="Subject Identifier",
+        required=False,
+        widget=forms.TextInput(attrs={"readonly": "readonly"}),
+    )
+
+    class Meta:
+        model = OffScheduleDmReferral
+        fields = "__all__"

meta_prn/forms/offschedule_form.py

@@ -25,6 +25,12 @@ class OffScheduleForm(
     form_validator_cls = OffScheduleFormValidator
     report_datetime_field_attr = "offschedule_datetime"
 
+    subject_identifier = forms.CharField(
+        label="Subject Identifier",
+        required=False,
+        widget=forms.TextInput(attrs={"readonly": "readonly"}),
+    )
+
     class Meta:
         model = OffSchedule
         fields = "__all__"

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):