Merge pull request #1314 from mskcc/fix/patient_record

Fix updating samples in Patient record and migration

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):

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()