meta-edc 0.3.53__py3-none-any.whl → 1.0.1__py3-none-any.whl

meta_prn/tests/tests/test_eos_events.py

@@ -0,0 +1,134 @@
+from django.test import TestCase
+from edc_action_item.models import ActionItem
+from edc_constants.constants import FEMALE, NEW, PATIENT, YES
+from edc_offstudy.constants import END_OF_STUDY_ACTION
+from edc_pharmacy.models import Medication
+from edc_transfer.constants import SUBJECT_TRANSFER_ACTION, TRANSFERRED
+from edc_utils import get_utcnow
+from edc_visit_schedule.constants import OFFSCHEDULE_ACTION
+
+from meta_lists.models import OffstudyReasons, TransferReasons
+from meta_pharmacy.constants import METFORMIN
+from meta_prn.action_items import OffscheduleAction, SubjectTransferAction
+from meta_prn.constants import OFFSTUDY_MEDICATION_ACTION
+from meta_prn.models import EndOfStudy, OffSchedule, OffStudyMedication, SubjectTransfer
+from meta_screening.tests.meta_test_case_mixin import MetaTestCaseMixin
+
+
+class TestEosEvents(MetaTestCaseMixin, TestCase):
+    def setUp(self):
+        super().setUp()
+        self.subject_screening = self.get_subject_screening(gender=FEMALE)
+        self.subject_consent = self.get_subject_consent(self.subject_screening)
+        self.subject_visit = self.get_subject_visit(
+            subject_screening=self.subject_screening,
+            subject_consent=self.subject_consent,
+        )
+        self.data = dict(
+            subject_visit=self.subject_visit.pk,
+            report_datetime=self.subject_visit.report_datetime,
+        )
+
+    def test_transfer_to_offschedule_in_order(self):
+        SubjectTransferAction(
+            subject_identifier=self.subject_consent.subject_identifier,
+            skip_get_current_site=True,
+            site_id=self.subject_consent.site_id,
+        )
+        action_types = [
+            obj.action_type.name
+            for obj in ActionItem.objects.filter(status=NEW).order_by("action_type__name")
+        ]
+        self.assertEqual(action_types, [SUBJECT_TRANSFER_ACTION])
+
+        # add a subject transfer object, which triggers next action item
+        transfer_reason = TransferReasons.objects.get(name="moved")
+        subject_transfer = SubjectTransfer.objects.create(
+            subject_identifier=self.subject_consent.subject_identifier,
+            initiated_by="patient",
+            may_return=YES,
+            may_contact=YES,
+        )
+        subject_transfer.transfer_reason.add(transfer_reason)
+
+        action_types = [
+            obj.action_type.name
+            for obj in ActionItem.objects.filter(status=NEW).order_by("action_type__name")
+        ]
+        self.assertEqual(action_types, [OFFSCHEDULE_ACTION, OFFSTUDY_MEDICATION_ACTION])
+
+        OffSchedule.objects.create(subject_identifier=self.subject_consent.subject_identifier)
+
+        action_types = [
+            obj.action_type.name
+            for obj in ActionItem.objects.filter(status=NEW).order_by("action_type__name")
+        ]
+        self.assertEqual(action_types, [OFFSTUDY_MEDICATION_ACTION])
+
+        offstudy_rx = OffStudyMedication.objects.create(
+            subject_identifier=self.subject_consent.subject_identifier,
+            stop_date=get_utcnow().date(),
+            last_dose_date=get_utcnow().date(),
+            reason=PATIENT,
+        )
+        offstudy_rx.medications.add(Medication.objects.get(name=METFORMIN))
+
+        action_types = [
+            obj.action_type.name
+            for obj in ActionItem.objects.filter(status=NEW).order_by("action_type__name")
+        ]
+        self.assertEqual(action_types, [END_OF_STUDY_ACTION])
+
+        EndOfStudy.objects.create(
+            subject_identifier=self.subject_consent.subject_identifier,
+            last_seen_date=get_utcnow().date(),
+            offstudy_reason=OffstudyReasons.objects.get(name=TRANSFERRED),
+        )
+
+        action_types = [
+            obj.action_type.name
+            for obj in ActionItem.objects.filter(status=NEW).order_by("action_type__name")
+        ]
+        self.assertEqual(action_types, [])
+
+    def test_transfer_to_offschedule_raises(self):
+
+        OffscheduleAction(
+            subject_identifier=self.subject_consent.subject_identifier,
+            skip_get_current_site=True,
+            site_id=self.subject_consent.site_id,
+        )
+
+        OffSchedule.objects.create(subject_identifier=self.subject_consent.subject_identifier)
+
+        action_types = [
+            obj.action_type.name
+            for obj in ActionItem.objects.filter(status=NEW).order_by("action_type__name")
+        ]
+        self.assertEqual(action_types, [OFFSTUDY_MEDICATION_ACTION])
+
+        offstudy_rx = OffStudyMedication.objects.create(
+            subject_identifier=self.subject_consent.subject_identifier,
+            stop_date=get_utcnow().date(),
+            last_dose_date=get_utcnow().date(),
+            reason=PATIENT,
+        )
+        offstudy_rx.medications.add(Medication.objects.get(name=METFORMIN))
+
+        action_types = [
+            obj.action_type.name
+            for obj in ActionItem.objects.filter(status=NEW).order_by("action_type__name")
+        ]
+        self.assertEqual(action_types, [END_OF_STUDY_ACTION])
+
+        EndOfStudy.objects.create(
+            subject_identifier=self.subject_consent.subject_identifier,
+            last_seen_date=get_utcnow().date(),
+            offstudy_reason=OffstudyReasons.objects.get(name=TRANSFERRED),
+        )
+
+        action_types = [
+            obj.action_type.name
+            for obj in ActionItem.objects.filter(status=NEW).order_by("action_type__name")
+        ]
+        self.assertEqual(action_types, [])

meta_reports/admin/dbviews/imp_substitutions_admin.py

@@ -65,7 +65,7 @@ class ImpSubstitutionsAdmin(
             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)
+        return render_to_string("edc_subject_dashboard/dashboard_button.html", context=context)
 
     @admin.display(description="Subject", ordering="subject_identifier")
     def subject(self, obj):

meta_reports/admin/dbviews/missing_screening_ogtt_admin/unmanaged_model_admin.py

@@ -69,7 +69,7 @@ class MissingScreeningOgttAdmin(
                 args=(obj.original_id,),
             )
         context = dict(title=_("Go to subject screening"), url=url, label=label)
-        return render_to_string("dashboard_button.html", context=context)
+        return render_to_string("edc_subject_dashboard/dashboard_button.html", context=context)
 
     @admin.display(description="Screen date", ordering="screening_datetime")
     def screening_date(self, obj):

meta_reports/admin/dbviews/patient_history_missing_baseline_cd4_admin.py

@@ -55,4 +55,4 @@ class PatientHistoryMissingBaselineCd4Admin(
             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)
+        return render_to_string("edc_subject_dashboard/dashboard_button.html", context=context)

meta_reports/admin/last_imp_refill_admin.py

@@ -2,7 +2,8 @@ from django.contrib import admin, messages
 from django.core.exceptions import FieldDoesNotExist
 from django.db import models
 from django.db.models import QuerySet
-from django.utils.html import format_html
+from django.template.loader import render_to_string
+from django.utils.safestring import mark_safe
 from edc_model_admin.dashboard import ModelAdminDashboardMixin
 from edc_model_admin.list_filters import PastDateListFilter
 from edc_model_admin.mixins import TemplatesModelAdminMixin
@@ -70,24 +71,9 @@ class LastImpRefillAdmin(
 
     change_list_title = "List of most recent IMP refills per subject"
 
-    change_list_note = format_html(
-        """
-        This report fetches the most recent Study Medication report where IMP was
-        refilled and adds the subject's next visit. Subjects taken "Off Schedule"
-        are not included in this report. To update ALL rows in this report, tick
-        at least one row and select 'Update report' action below.
-        <BR><BR>
-        This report has additional search features for numeric columns:
-        <code>days_since</code>, <code>days_until</code>, <code>imp_visit_code</code>
-        and <code>next_visit_code</code>.
-        <BR><BR>For example, type <code>days_until>=25</code> in the search below
-        to show rows for subjects who have an appointment 25 or more days from the
-        date this report was created. You might also try typing
-        <code>days_since>365</code> or <code>days_until<0</code>.
-        <BR><BR>
-        This also works: <code>next_visit_code>=1060</code>.
-        """
-    )
+    change_list_note = mark_safe(
+        render_to_string("meta_reports/last_imp_refill/changelist_note.html")
+    )  # nosec B308, B703
 
     actions = [update_report, export_to_csv]
 

meta_reports/templates/meta_reports/last_imp_refill/changelist_note.html

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

meta_screening/admin/subject_screening_admin.py

@@ -3,6 +3,7 @@ from django.template.loader import render_to_string
 from django.urls.base import reverse
 from django.urls.exceptions import NoReverseMatch
 from django.utils.html import format_html
+from django.utils.safestring import mark_safe
 from django.utils.translation import gettext_lazy as _
 from django_audit_fields.admin import audit_fieldset_tuple
 from edc_constants.constants import YES
@@ -160,7 +161,10 @@ class SubjectScreeningAdmin(ModelAdminSubjectDashboardMixin, SimpleHistoryAdmin)
         ]
         if obj.repeat_glucose_opinion == YES:
             data.append(f"Contact #: {obj.contact_number or '--'}")
-        return format_html("<BR>".join(data))
+        return format_html(
+            "{}",
+            mark_safe("<BR>".join(data)),  # nosec B703, B308
+        )
 
     def reasons(self, obj=None):
         if not obj.reasons_ineligible:
@@ -177,8 +181,14 @@ class SubjectScreeningAdmin(ModelAdminSubjectDashboardMixin, SimpleHistoryAdmin)
             url=f"{screening_listboard_url}?q={obj.screening_identifier}",
             label="Screening",
         )
-        button = render_to_string("dashboard_button.html", context=context)
-        return format_html(button + "<BR>" + eligibility.eligibility_status(add_urls=True))
+        button = render_to_string(
+            "edc_subject_dashboard/dashboard_button.html", context=context
+        )
+        return format_html(
+            "{button}<BR>{status}",
+            button=button,
+            status=eligibility.eligibility_status(add_urls=True),
+        )
 
     def dashboard(self, obj=None, label=None):
         try:

meta_screening/eligibility/eligibility.py

@@ -195,15 +195,22 @@ class MetaEligibility:
                 args=(self.part_three.model_obj.id,),
             )
             status_str = format_html(
-                f'<A href="{url_p1}">P1: {self.part_one.eligible.upper()}</A><BR>'
-                f'<A href="{url_p2}">P2: {self.part_two.eligible.upper()}</A><BR>'
-                f'<A href="{url_p3}">P3: {self.part_three.eligible.upper()}</A><BR>'
+                '<A href="{url_p1}">P1: {p1_eligible}</A>'
+                '<BR><A href="{url_p2}">P2: {p2_eligible}</A>'
+                '<BR><A href="{url_p3}">P3: {p3_eligible}</A><BR>',
+                url_p1=url_p1,
+                p1_eligible=self.part_one.eligible.upper(),
+                url_p2=url_p2,
+                p2_eligible=self.part_two.eligible.upper(),
+                url_p3=url_p3,
+                p3_eligible=self.part_three.eligible.upper(),
             )
         else:
-            status_str = (
-                f"P1: {self.part_one.eligible.upper()}<BR>"
-                f"P2: {self.part_two.eligible.upper()}<BR>"
-                f"P3: {self.part_three.eligible.upper()}<BR>"
+            status_str = format_html(
+                "P1: {p1_eligible}<BR>" "P2: {p2_eligible}<BR>" "P3: {p3_eligible}<BR>",
+                p1_eligible=self.part_one.eligible.upper(),
+                p2_eligible=self.part_two.eligible.upper(),
+                p3_eligible=self.part_three.eligible.upper(),
             )
         display_label = self.display_label
         if "PENDING" in display_label:

meta_screening/model_mixins/part_one_fields_model_mixin.py

@@ -1,5 +1,4 @@
 from django.db import models
-from django.utils.html import format_html
 from django.utils.safestring import mark_safe
 from django_crypto_fields.fields import EncryptedCharField
 from edc_constants.choices import SELECTION_METHOD, YES_NO, YES_NO_NA, YESDEFAULT_NO
@@ -11,10 +10,10 @@ from ..constants import PREG_YES_NO_NA
 
 class PartOneFieldsModelMixin(models.Model):
     screening_consent = models.CharField(
-        verbose_name=format_html(
+        verbose_name=mark_safe(
             "Has the subject given his/her verbal consent to be screened for "
             "the <u>META Phase 3</u> trial?"
-        ),
+        ),  # nosec B308
         max_length=15,
         choices=YES_NO,
     )
@@ -26,7 +25,9 @@ class PartOneFieldsModelMixin(models.Model):
     )
 
     meta_phase_two = models.CharField(
-        verbose_name=format_html("Was the subject enrolled in the <u>META Phase 2</u> trial?"),
+        verbose_name=mark_safe(
+            "Was the subject enrolled in the <u>META Phase 2</u> trial?"
+        ),  # nosec B308
         max_length=15,
         choices=YES_NO,
         null=True,
@@ -44,9 +45,9 @@ class PartOneFieldsModelMixin(models.Model):
     )
 
     art_six_months = models.CharField(
-        verbose_name=format_html(
+        verbose_name=mark_safe(
             "Has the patient been on anti-retroviral therapy for <u>at least 6 months</u>"
-        ),
+        ),  # nosec B308
         max_length=15,
         choices=YES_NO_NA,
     )
@@ -59,10 +60,10 @@ class PartOneFieldsModelMixin(models.Model):
     )
 
     vl_undetectable = models.CharField(
-        verbose_name=format_html(
+        verbose_name=mark_safe(
             "Does the patient have a viral load measure of less than 1000 copies per ml "
             "taken <u>within the last 12 months</u>"
-        ),
+        ),  # nosec B308
         max_length=15,
         choices=YES_NO_NA,
     )
@@ -86,10 +87,10 @@ class PartOneFieldsModelMixin(models.Model):
     )
 
     staying_nearby_12 = models.CharField(
-        verbose_name=format_html(
+        verbose_name=mark_safe(
             "Is the patient planning to remain in the catchment area "
             "for <u>at least 12 months</u>"
-        ),
+        ),  # nosec B308
         max_length=15,
         choices=YES_NO,
         null=True,
@@ -101,18 +102,18 @@ class PartOneFieldsModelMixin(models.Model):
     )
 
     continue_part_two = models.CharField(
-        verbose_name=mark_safe(  # nosec B308
+        verbose_name=mark_safe(
             "Continue with <U>part two</U> of the screening process?"
-        ),
+        ),  # nosec B308
         max_length=15,
         choices=YESDEFAULT_NO,
         default=YES,
-        help_text=mark_safe(  # nosec B308
+        help_text=mark_safe(
             "<B>Important</B>: This response will be be automatically "
             "set to YES if:<BR><BR>"
             "- the participant meets the eligibility criteria for part one, or;<BR><BR>"
             "- the eligibility criteria for part two is already complete.<BR>"
-        ),
+        ),  # nosec B308
     )
 
     class Meta:

meta_subject/admin/birth_outcome_admin.py

@@ -72,7 +72,7 @@ class BirthOutcomesAdmin(
         url = reverse("meta_subject_admin:meta_subject_delivery_changelist")
         url = f"{url}?q={obj.subject_identifier}"
         context = dict(title="Delivery", url=url, label="Delivery")
-        return render_to_string("dashboard_button.html", context=context)
+        return render_to_string("edc_subject_dashboard/dashboard_button.html", context=context)
 
     def get_subject_dashboard_url_kwargs(self, obj):
         return dict(subject_identifier=obj.subject_identifier)

meta_subject/admin/delivery_admin.py

@@ -116,4 +116,4 @@ class DeliveryAdmin(
         url = reverse("meta_subject_admin:meta_subject_birthoutcomes_changelist")
         url = f"{url}?q={obj.subject_identifier}"
         context = dict(title="Outcomes", url=url, label="Outcomes")
-        return render_to_string("dashboard_button.html", context=context)
+        return render_to_string("edc_subject_dashboard/dashboard_button.html", context=context)

meta_subject/form_validators/dm_endpoint_form_validator.py

@@ -2,6 +2,7 @@ from django.core.exceptions import ObjectDoesNotExist
 from django.template.loader import render_to_string
 from django.urls import reverse
 from django.utils.html import format_html
+from django.utils.safestring import mark_safe
 from edc_crf.crf_form_validator import CrfFormValidator
 from edc_form_validators import INVALID_ERROR
 
@@ -28,7 +29,8 @@ class DmEndpointFormValidator(CrfFormValidator):
             self.raise_validation_error(
                 {
                     "__all__": format_html(
-                        f"Subject has not reached the protocol endpoint. See {link}"
+                        "Subject has not reached the protocol endpoint. See {link}",
+                        link=mark_safe(link),  # nosec B703, B308
                     )
                 },
                 INVALID_ERROR,

meta_subject/models/diabetes/dm_followup.py

@@ -1,6 +1,6 @@
 from django.core.validators import MaxValueValidator, MinValueValidator
 from django.db import models
-from django.utils.html import format_html
+from django.utils.safestring import mark_safe
 from edc_action_item.models import ActionItem
 from edc_adherence.choices import MISSED_PILLS
 from edc_constants.choices import YES_NO, YES_NO_NA
@@ -186,10 +186,10 @@ class DmFollowup(CrfWithActionModelMixin, BaseUuidModel):
     )
 
     visual_score_confirmed = models.IntegerField(
-        verbose_name=format_html(
+        verbose_name=mark_safe(
             "<B><font color='orange'>Interviewer</font></B>: "
             "please transcribe the score indicated from above."
-        ),
+        ),  # nosec B308
         validators=[MinValueValidator(0), MaxValueValidator(100)],
         help_text="%",
         null=True,

tests/test_settings.py

@@ -74,7 +74,6 @@ project_settings = DefaultTestSettings(
         subject_dashboard_template="meta_dashboard/subject/dashboard.html",
         subject_review_listboard_template="edc_review_dashboard/subject_review_listboard.html",
     ),
-    EDC_BOOTSTRAP=3,
     EMAIL_BACKEND="django.core.mail.backends.locmem.EmailBackend",
     EMAIL_CONTACTS={
         "ae_reports": "someone@example.com",

meta_dashboard/templates/meta_dashboard/bootstrap3/subject/dashboard.html

@@ -1,14 +0,0 @@
-{% extends 'edc_subject_dashboard/bootstrap3/dashboard.html' %}
-
-{% load static %}
-
-{% block locator_information %}{% endblock locator_information %}
-
-{% block top_bar %}
-
-    {% include "meta_dashboard/bootstrap3/subject/dashboard/top_bar.html" %}
-
-{% endblock top_bar %}
-
-
-{% block side_bar %}{% include 'meta_dashboard/bootstrap3/subject/dashboard/sidebar.html' %}{% endblock side_bar %}