Merge branch 'release/0.1.9'

VERSION

@@ -1 +1 @@
-0.1.8
+0.1.9

ambition_prn/action_items.py

@@ -1,4 +1,5 @@
 from django.apps import apps as django_apps
+from django.conf import settings
 from django.core.exceptions import ObjectDoesNotExist, MultipleObjectsReturned
 from django.utils.safestring import mark_safe
 from edc_action_item import Action, HIGH_PRIORITY, site_action_items
@@ -52,10 +53,18 @@ class DeathReportAction(Action):
     admin_site_name = 'ambition_prn_admin'
     priority = HIGH_PRIORITY
     singleton = True
+    email_contacts = [settings.EMAIL_CONTACTS.get('tmg')]
 
     def get_next_actions(self):
         self.delete_if_new(action_cls=DeathReportTmgAction)
-        next_actions = [DeathReportTmgAction]
+
+        if self.action_item_model_cls().objects.filter(
+                related_reference_identifier=self.reference_obj.action_identifier,
+                action_type__name=DeathReportTmgAction.name).count() < 2:
+            next_actions = [DeathReportTmgAction]
+        else:
+            next_actions = []
+
         on_schedule_w10_model_cls = django_apps.get_model(
             'ambition_prn.onschedulew10')
         try:
@@ -81,24 +90,34 @@ class DeathReportTmgAction(Action):
     admin_site_name = 'ambition_prn_admin'
     instructions = mark_safe(
         f'This report is to be completed by the TMG only.')
+    email_recipients = [settings.EMAIL_CONTACTS.get('tmg')]
 
     def close_action_item_on_save(self):
         self.delete_if_new(action_cls=self)
         return self.reference_obj.report_status == CLOSED
 
     def get_next_actions(self):
+        """Returns a next DeathReportTmgAction if the
+        submitted report does not match the cause of death
+        of the original death report.
+
+        Also, no more than two DeathReportTmgAction can exist.
+        """
         next_actions = []
         self.delete_if_new(action_cls=self)
-        try:
-            self.reference_model_cls().objects.get(
-                death_report=self.reference_obj.death_report)
-        except MultipleObjectsReturned:
-            pass
-        else:
-            if self.reference_obj.report_status == CLOSED:
-                if (self.reference_obj.death_report.cause_of_death
-                        != self.reference_obj.cause_of_death):
-                    next_actions = [self]
+        if self.action_item_model_cls().objects.filter(
+                action_identifier=self.reference_obj.action_identifier,
+                action_type__name=self.name).count() < 2:
+            try:
+                self.reference_model_cls().objects.get(
+                    death_report=self.reference_obj.death_report)
+            except MultipleObjectsReturned:
+                pass
+            else:
+                if self.reference_obj.report_status == CLOSED:
+                    if (self.reference_obj.death_report.cause_of_death
+                            != self.reference_obj.cause_of_death):
+                        next_actions = [self]
         return next_actions
 
 

ambition_prn/choices.py

@@ -5,6 +5,7 @@
 from .constants import AZT_3TC_with_EFV_NVP_or_DTG, TDF_3TC_FTC_with_ATZ_r_or_Lopinavir_r
 from .constants import TDF_3TC_FTC_with_EFV_or_NVP
 from .constants import TUBERCULOSIS, DEVIATION, VIOLATION, CONSENT_WITHDRAWAL
+from .constants import CRYTOCOCCAL_MENINGITIS, MALIGNANCY
 
 ACTION_REQUIRED = (
     ('remain_on_study', 'Participant to remain on trial'),
@@ -15,13 +16,13 @@
 
 
 CAUSE_OF_DEATH = (
-    ('cryptococcal_meningitis', 'Cryptococcal meningitis'),
+    (CRYTOCOCCAL_MENINGITIS, 'Cryptococcal meningitis'),
     ('Cryptococcal_meningitis_relapse_IRIS',
      'Cryptococcal meningitis relapse/IRIS'),
     (TUBERCULOSIS, 'TB'),
     ('bacteraemia', 'Bacteraemia'),
     ('bacterial_pneumonia', 'Bacterial pneumonia'),
-    ('malignancy', 'Malignancy'),
+    (MALIGNANCY, 'Malignancy'),
     ('art_toxicity', 'ART toxicity'),
     ('IRIS_non_CM', 'IRIS non-CM'),
     ('diarrhea_wasting', 'Diarrhea/wasting'),

ambition_prn/constants.py

@@ -1,7 +1,10 @@
 AZT_3TC_with_ATZ_r_or_Lopinavir_r = 'AZT_3TC_with_ATZ_r_or_Lopinavir_r'
 AZT_3TC_with_EFV_NVP_or_DTG = 'AZT_3TC_with_EFV_NVP_or_DTG'
 CONSENT_WITHDRAWAL = 'consent_withdrawn'
+CRYTOCOCCAL_MENINGITIS = 'cryptococcal_meningitis'
+CRYTOCOCCAL_MENINGITIS = 'cryptococcal_meningitis'
 DEVIATION = 'protocol_deviation'
+MALIGNANCY = 'malignancy'
 MEDICATION_NONCOMPLIANCE = 'medication_noncompliance'
 TDF_3TC_FTC_with_ATZ_r_or_Lopinavir_r = 'TDF_3TC_FTC_with_ATZ_r_or_Lopinavir_r'
 TDF_3TC_FTC_with_EFV_or_NVP = 'TDF_3TC_FTC_with_EFV_or_NVP'

ambition_prn/mommy_recipes.py

@@ -2,6 +2,7 @@
 from faker import Faker
 from model_mommy.recipe import Recipe
 
+from .constants import CRYTOCOCCAL_MENINGITIS
 from .models import DeathReport, StudyTerminationConclusion, StudyTerminationConclusionW10
 from .models import ProtocolDeviationViolation, DeathReportTmg
 
@@ -11,13 +12,13 @@
     DeathReport,
     study_day=1,
     death_as_inpatient=YES,
-    cause_of_death='art_toxicity',
+    cause_of_death=CRYTOCOCCAL_MENINGITIS,
     cause_of_death_other=None,
     action_identifier=None,
-    tracking_identifier=None,
-    tb_site='meningitis',
-    narrative=(
-        'adverse event resulted in death due to cryptococcal meningitis'))
+    tracking_identifier=None)
+#     tb_site='meningitis',
+#     narrative=(
+#         'adverse event resulted in death due to cryptococcal meningitis'))
 
 studyterminationconclusion = Recipe(
     StudyTerminationConclusion,
@@ -29,7 +30,6 @@
     action_identifier=None,
     tracking_identifier=None)
 
-
 protocoldeviationviolation = Recipe(
     ProtocolDeviationViolation,
     action_identifier=None,
@@ -38,4 +38,6 @@
 deathreporttmg = Recipe(
     DeathReportTmg,
     action_identifier=None,
+    cause_of_death=CRYTOCOCCAL_MENINGITIS,
+    cause_of_death_agreed=YES,
     tracking_identifier=None)

ambition_prn/settings.py

@@ -156,6 +156,7 @@
 COUNTRY = 'botswana'
 HOLIDAY_FILE = os.path.join(BASE_DIR, APP_NAME, 'tests', 'holidays.csv')
 
+EMAIL_CONTACTS = {}
 
 if 'test' in sys.argv:
 

ambition_prn/tests/test_action.py

@@ -1,14 +1,16 @@
 from ambition_rando.tests import AmbitionTestCaseMixin
+from django.core.exceptions import ObjectDoesNotExist
+from django.db.utils import IntegrityError
 from django.test import TestCase, tag
-from edc_action_item import SingletonActionItemError
 from edc_action_item.models.action_item import ActionItem
-from edc_constants.constants import CLOSED, NEW
+from edc_base.utils import get_utcnow
+from edc_constants.constants import CLOSED, NEW, NO
 from edc_facility.import_holidays import import_holidays
 from edc_registration.models import RegisteredSubject
 from model_mommy import mommy
 
-from ..action_items import DeathReportAction
-from django.db.utils import IntegrityError
+from ..action_items import DeathReportAction, DEATH_REPORT_TMG_ACTION
+from ..constants import CRYTOCOCCAL_MENINGITIS, MALIGNANCY
 
 
 class TestDeathReport(AmbitionTestCaseMixin, TestCase):
@@ -89,3 +91,129 @@ def test_death_report_closes_action(self):
         obj = ActionItem.objects.get(
             action_identifier=death_report.action_identifier)
         self.assertEqual(obj.status, CLOSED)
+
+    def test_add_tmg_death_report_action_cause_matches(self):
+
+        death_report_action = DeathReportAction(
+            subject_identifier=self.subject_identifier)
+        death_report = mommy.make_recipe(
+            'ambition_prn.deathreport',
+            subject_identifier=self.subject_identifier,
+            cause_of_death=CRYTOCOCCAL_MENINGITIS)
+        self.assertEqual(death_report_action.action_identifier,
+                         death_report.action_identifier)
+
+        # assert death report creates one TMG Death Report Action
+        self.assertEqual(ActionItem.objects.filter(
+            action_type__name=DEATH_REPORT_TMG_ACTION).count(), 1)
+
+        # fill in TMG report with matching cause of death
+        death_report_tmg = mommy.make_recipe(
+            'ambition_prn.deathreporttmg',
+            subject_identifier=self.subject_identifier,
+            death_report=death_report,
+            cause_of_death=CRYTOCOCCAL_MENINGITIS,
+            related_reference_identifier=death_report_action.action_identifier,
+            parent_reference_identifier=death_report_action.action_identifier
+        )
+        self.assertEqual(
+            death_report_tmg.parent_reference_identifier,
+            death_report.action_identifier)
+
+        self.assertEqual(
+            death_report_tmg.related_reference_identifier,
+            death_report.action_identifier)
+
+        # assert a second TMG Death Report Action is NOT created
+        # because the cause of death matches
+        self.assertEqual(ActionItem.objects.filter(
+            action_type__name=DEATH_REPORT_TMG_ACTION).count(), 1)
+
+    def test_add_two_tmg_death_report_action_cause_not_matching(self):
+
+        death_report_action = DeathReportAction(
+            subject_identifier=self.subject_identifier)
+        death_report = mommy.make_recipe(
+            'ambition_prn.deathreport',
+            subject_identifier=self.subject_identifier,
+            cause_of_death=CRYTOCOCCAL_MENINGITIS)
+
+        # assert death report creates one TMG Death Report Action
+        try:
+            action_item = ActionItem.objects.get(
+                action_type__name=DEATH_REPORT_TMG_ACTION)
+        except ObjectDoesNotExist:
+            self.fail('Action item unexpectedly does not exist')
+
+        self.assertEqual(ActionItem.objects.filter(
+            action_type__name=DEATH_REPORT_TMG_ACTION).count(), 1)
+
+        # fill in TMG report with non-matching cause of death
+        death_report_tmg1 = mommy.make_recipe(
+            'ambition_prn.deathreporttmg',
+            subject_identifier=self.subject_identifier,
+            death_report=death_report,
+            cause_of_death=MALIGNANCY,
+            cause_of_death_agreed=NO,
+            report_status=CLOSED,
+            report_closed_datetime=get_utcnow(),
+            action_identifier=action_item.action_identifier,
+            related_reference_identifier=death_report.action_identifier,
+            parent_reference_identifier=death_report.action_identifier)
+
+        action_item = ActionItem.objects.get(
+            action_identifier=death_report_tmg1.action_identifier,
+            action_type__name=DEATH_REPORT_TMG_ACTION)
+
+        # assert a second TMG Death Report Action is created
+        # by death_report_tmg because the cause of death matches
+        self.assertEqual(ActionItem.objects.filter(
+            related_reference_identifier=death_report.action_identifier,
+            action_type__name=DEATH_REPORT_TMG_ACTION,
+            status=CLOSED).count(), 1)
+        self.assertEqual(ActionItem.objects.filter(
+            related_reference_identifier=death_report.action_identifier,
+            action_type__name=DEATH_REPORT_TMG_ACTION,
+            status=NEW).count(), 1)
+        self.assertEqual(ActionItem.objects.filter(
+            action_type__name=DEATH_REPORT_TMG_ACTION).count(), 2)
+
+        # resave
+        death_report_tmg1.save()
+
+        # still 2
+        self.assertEqual(ActionItem.objects.filter(
+            action_type__name=DEATH_REPORT_TMG_ACTION).count(), 2)
+
+        # fill in second TMG report with any cause of death
+        death_report_tmg2 = mommy.make_recipe(
+            'ambition_prn.deathreporttmg',
+            subject_identifier=self.subject_identifier,
+            death_report=death_report,
+            cause_of_death=MALIGNANCY,
+            related_reference_identifier=death_report_action.action_identifier,
+            parent_reference_identifier=death_report_tmg1.action_identifier)
+
+        # still 2
+        self.assertEqual(ActionItem.objects.filter(
+            action_type__name=DEATH_REPORT_TMG_ACTION).count(), 2)
+
+        death_report_tmg2.save()
+
+        # still 2
+        self.assertEqual(ActionItem.objects.filter(
+            action_type__name=DEATH_REPORT_TMG_ACTION).count(), 2)
+
+        # resave
+        death_report.save()
+
+        # still 2
+        self.assertEqual(ActionItem.objects.filter(
+            action_type__name=DEATH_REPORT_TMG_ACTION).count(), 2)
+
+        # resave
+        death_report_tmg1.save()
+
+        # still 2
+        self.assertEqual(ActionItem.objects.filter(
+            action_type__name=DEATH_REPORT_TMG_ACTION).count(), 2)