meta-edc 1.0.0__py3-none-any.whl → 1.0.2__py3-none-any.whl

{meta_edc-1.0.0.dist-info → meta_edc-1.0.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: meta-edc
-Version: 1.0.0
+Version: 1.0.2
 Summary: META Trial EDC (http://www.isrctn.com/ISRCTN76157257)
 Home-page: https://github.com/meta-trial/meta-edc
 Author: Erik van Widenfelt

{meta_edc-1.0.0.dist-info → meta_edc-1.0.2.dist-info}/RECORD

@@ -345,11 +345,11 @@ meta_pharmacy/models/substitutions.py,sha256=9FjjD4x66B8SxABZR5atan2S5uE4nJH0tn0
 meta_pharmacy/utils/__init__.py,sha256=PiPRCZqgxPiudXWEvQmXOqFZMoj56NEiOeRuYEyE_9w,71
 meta_pharmacy/utils/update_initial_pharmacy_data.py,sha256=Od0QL41unsDEGDBYsVCe8k-T3GpMae0DtHt61vz4sYM,4621
 meta_prn/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-meta_prn/action_items.py,sha256=R83aFDxyOEkmzfJwWMcRYXWXZBcv3hTp_QzHNJPLNPM,9108
+meta_prn/action_items.py,sha256=99NxsonE_iXscoRLZ00lymAgjDqGbhiUhzgTMk9Ib30,9272
 meta_prn/admin_site.py,sha256=E4dJ6ofu9Kp-1SIWIuY3PraVPbEJSWBBqhorJPGUNqU,161
 meta_prn/apps.py,sha256=NEqrwzEW277BAPGeL1H1KdK9e74FqXfYHK6o46BtaJA,280
 meta_prn/baker_recipes.py,sha256=jDGg3btxjtvnsph_AnKoZBDUeTfokMs5iQWnQBJD-jw,660
-meta_prn/choices.py,sha256=QKqCh2mN_Fgt9Z_la_YVeAqlzRxd507TurFVOOc71G0,3210
+meta_prn/choices.py,sha256=Cb55BmvEgLyIhLzWDRw2aMkGr_WOyBgvcOZpVYgxSS8,3336
 meta_prn/constants.py,sha256=Z0atxRnTIj-_bWbfYY0vZIwfmbwaFRpSZqb1-K1B4Jo,1018
 meta_prn/list_data.py,sha256=Se-GxHTuxmU_j17tIdLicKlW6d5E9pVKvYVrTLZQFUo,2336
 meta_prn/pregnancy_action_item_mixin.py,sha256=E_7aFSs_PXkqlRqRbKohWZSnE7rUcFVr0LacF7EjrvM,1018
@@ -463,6 +463,7 @@ meta_prn/tests/urls.py,sha256=JtaYMEhXBim3a2uPLNvyoulbEutvtbTlmH-ez9Ws8u8,270
 meta_prn/tests/tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 meta_prn/tests/tests/test_actions.py,sha256=KjMznJALY4zB3-4WQHubum_B6sE6pyf0_pg9i57Ri9w,3811
 meta_prn/tests/tests/test_dm_referral.py,sha256=FP5NO464D6n6Oe5uAsv9oIPZ08VQsWmBQmhQajIrWKU,8381
+meta_prn/tests/tests/test_eos_events.py,sha256=T4ZMNM2kjseE_Viy9HAM7sx3TyeSsPyv5VXHgBDLFKs,5449
 meta_prn/tests/tests/test_manager_order.py,sha256=KYda9YaWJNf761_YiMcXkxlllt2Al27MYgaWO859DWI,548
 meta_prn/tests/tests/test_pregnancy_notification.py,sha256=anAzrfIAEMles-IH-PGkVBCS0vyUzxBOJ2EQtQBbnOI,3982
 meta_rando/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -490,7 +491,7 @@ meta_reports/utils.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 meta_reports/admin/__init__.py,sha256=om3lFa4YxsZSNlYIi2sZv8li2irOMoSeBtOpPk4V3lk,488
 meta_reports/admin/endpoints_admin.py,sha256=7wZCdC-D-QHI1bb_ucgyDZYlnYD7mWtcZpcH_LftkLs,514
 meta_reports/admin/endpoints_all_admin.py,sha256=_czdezZf9fSjwZJmO-3HbmdXrXP6nk8-HdiweqUzPRE,476
-meta_reports/admin/last_imp_refill_admin.py,sha256=w-0wIanAk7vXwUufd9v_ZEWhYJ3s8Q2fDP3csRRxgls,5946
+meta_reports/admin/last_imp_refill_admin.py,sha256=RKODpodLqQsKx1v4ybqVULo38s2bNXd1nsUpCdPlJ1A,6431
 meta_reports/admin/list_filters.py,sha256=pByBzz9-qGwqBfdZFlByxJUZDTJQXOTWfNLjmK8KF00,870
 meta_reports/admin/modeladmin_mixins.py,sha256=tEZYw0xNMfBvo2RLDrYfi_S9lbZU02dwtLxdRDZob4Q,3663
 meta_reports/admin/dbviews/__init__.py,sha256=2yPu0SO7ZX9yjan0OS9izzws14YYoXcGXmZhwJhax1I,675
@@ -1183,9 +1184,9 @@ tests/etc/user-rsa-restricted-private.pem,sha256=CUcHW9bznWdmmASN00hCzvxFPAFl4N2
 tests/etc/user-rsa-restricted-public.pem,sha256=mt84djoL-uHw6Wc5SJh0zml6VzXulnf8eQSFg7-fheg,450
 tests/etc/user-salt-local.key,sha256=x5anBw9fvbHurczouT3CjrkWb_xs7Ypm1htIJsgiuiw,256
 tests/etc/user-salt-restricted.key,sha256=pxmpcfBRNB-4C6wTvHXz-9fOfJgKIFOjaAF8ZFfa4q4,256
-meta_edc-1.0.0.dist-info/AUTHORS,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-meta_edc-1.0.0.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
-meta_edc-1.0.0.dist-info/METADATA,sha256=XRxGxnPZR6V4r-xp4mPNJzdJSfdwrSXrTHC7goKUUdM,43527
-meta_edc-1.0.0.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
-meta_edc-1.0.0.dist-info/top_level.txt,sha256=RkzjNXwRq2kg_uZ_1bDwPUntijSXoY2YBqtByDwvvrc,244
-meta_edc-1.0.0.dist-info/RECORD,,
+meta_edc-1.0.2.dist-info/AUTHORS,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+meta_edc-1.0.2.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+meta_edc-1.0.2.dist-info/METADATA,sha256=5KWkarvYtcSI6PzhZvKjGItS0aBzrrhQcttY4YtU1Cw,43527
+meta_edc-1.0.2.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
+meta_edc-1.0.2.dist-info/top_level.txt,sha256=RkzjNXwRq2kg_uZ_1bDwPUntijSXoY2YBqtByDwvvrc,244
+meta_edc-1.0.2.dist-info/RECORD,,

meta_prn/action_items.py

@@ -43,6 +43,7 @@ class OffscheduleAction(ActionWithNotification):
         DEATH_REPORT_ACTION,
         LTFU_ACTION,
         BLOOD_RESULTS_RFT_ACTION,
+        SUBJECT_TRANSFER_ACTION,
     ]
     reference_model = "meta_prn.offschedule"
     show_link_to_changelist = True
@@ -72,6 +73,7 @@ class OffschedulePregnancyAction(ActionWithNotification):
         UNBLINDING_REVIEW_ACTION,
         DEATH_REPORT_ACTION,
         LTFU_ACTION,
+        SUBJECT_TRANSFER_ACTION,
         DELIVERY_ACTION,
     ]
     reference_model = "meta_prn.offschedulepregnancy"
@@ -85,6 +87,27 @@ class OffschedulePregnancyAction(ActionWithNotification):
         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,
+        DEATH_REPORT_ACTION,
+        LTFU_ACTION,
+        SUBJECT_TRANSFER_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 EndOfStudyAction(ActionWithNotification):
     name = END_OF_STUDY_ACTION
     display_name = "Submit End of Study Report"
@@ -150,22 +173,6 @@ class DmReferralAction(ActionWithNotification):
         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"

meta_prn/choices.py

@@ -2,6 +2,9 @@ from edc_constants.constants import NOT_APPLICABLE, OTHER, PATIENT, PREGNANCY, U
 
 from .constants import CLINICIAN, INVESTIGATOR, REFERRAL, SAE
 
+# from edc_transfer.constants import TRANSFERRED
+
+
 CLINICAL_WITHDRAWAL_REASONS = (
     ("kidney_disease", "Development of chronic kidney disease"),
     ("liver_disease", "Development of chronic liver disease"),
@@ -96,6 +99,7 @@ WITHDRAWAL_STUDY_MEDICATION_REASONS = (
     ),
     (INVESTIGATOR, " Investigator decision"),
     (REFERRAL, "Referral to Diabetes clinic"),
+    # (TRANSFERRED, "Patient decision to transfer out of catchment area"),
     (PATIENT, "Patient decision"),
     (OTHER, "Other reason (specify below)"),
 )

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/last_imp_refill_admin.py

@@ -1,3 +1,4 @@
+import pandas as pd
 from django.contrib import admin, messages
 from django.core.exceptions import FieldDoesNotExist
 from django.db import models
@@ -42,14 +43,24 @@ def update_report(modeladmin, request, queryset):
             modeladmin.model(
                 subject_identifier=row["subject_identifier"],
                 site_id=row["site_id"],
-                imp_visit_date=row["imp_visit_date"],
+                imp_visit_date=(
+                    None if pd.isna(row["imp_visit_date"]) else row["imp_visit_date"]
+                ),
                 imp_visit_code=row["imp_visit_code"],
-                next_appt_date=row["next_appt_datetime"],
-                next_visit_code=row["next_visit_code"],
+                next_appt_date=(
+                    None if pd.isna(row["next_appt_datetime"]) else row["next_appt_datetime"]
+                ),
+                next_visit_code=(
+                    None if pd.isna(row["next_visit_code"]) else row["next_visit_code"]
+                ),
                 days_since=row["days_since"].days,
-                days_until=row["days_until"].days,
-                visit_code=str(int(row["imp_visit_code"])),
-                visit_code_sequence=row["imp_visit_code"] % 1,
+                days_until=None if pd.isna(row["days_until"]) else row["days_until"].days,
+                visit_code=(
+                    None if pd.isna(row["imp_visit_code"]) else str(int(row["imp_visit_code"]))
+                ),
+                visit_code_sequence=(
+                    None if pd.isna(row["imp_visit_code"]) else row["imp_visit_code"] % 1
+                ),
                 report_model=modeladmin.model._meta.label_lower,
                 created=now,
             )