From 828827d7a2d40345d068958a6e5785fe9ac905bc Mon Sep 17 00:00:00 2001
From: Ivkovic <Sinisa Ivkovic>
Date: Wed, 10 Jan 2024 09:51:48 -0500
Subject: [PATCH] Fix updating samples in Patient record and migration

---
 file_system/models.py        |  1 +
 populate_patients_samples.py | 11 +++++++++++
 2 files changed, 12 insertions(+)
 create mode 100644 populate_patients_samples.py

diff --git a/file_system/models.py b/file_system/models.py
index 43c835785..089e6b1eb 100644
--- a/file_system/models.py
+++ b/file_system/models.py
@@ -352,6 +352,7 @@ def create_or_update_patient(self, patient_id, sex, sample):
                 patient = Patient.objects.create(patient_id=patient_id, sex=sex)
             if sample not in patient.samples:
                 patient.samples.append(sample)
+                patient.save(do_not_version=True)
             return patient
 
     def save(self, *args, **kwargs):
diff --git a/populate_patients_samples.py b/populate_patients_samples.py
new file mode 100644
index 000000000..390d662f7
--- /dev/null
+++ b/populate_patients_samples.py
@@ -0,0 +1,11 @@
+from django.conf import settings
+from file_system.models import Patient
+from file_system.repository import FileRepository
+
+
+def populate_patient_samples():
+    from_lims = FileRepository.filter(file_group=settings.IMPORT_FILE_GROUP, values_metadata="cmoPatientId").all()
+    for p in Patient.objects.filter(patient_id__in=from_lims).all():
+        samples = FileRepository.filter(metadata={"cmoPatientId": p.patient_id}, values_metadata="primaryId").all()
+        p.samples = list(samples)
+        p.save()