Fix multiple processes with migration (#52)

* Migration to fix multiple processes

* Improvements

* Fix multiple processes migration curation by counting only distinct processes

* Migration multiple processes curation - Save version of deleted processes

* Add explanation for migration and delete flag

* Upgrade FMS version from 3.1.1 to 3.1.2

backend/VERSION

@@ -1 +1 @@
-3.1.1
+3.1.2

backend/fms_core/migrations/0019_v3_1_2.py

@@ -0,0 +1,83 @@
+from django.conf import settings
+from django.db import migrations
+from django.contrib.auth.models import User
+import reversion
+import datetime
+
+'''
+This migration will fix an issue that occurred in release 3.1, 
+where multiple Process objects would erroneously be generated for each Sample part of a template 
+(i.e. Transfer, Extraction, etc.)
+There should have only been one Process object created per template.
+'''
+
+ADMIN_USERNAME='biobankadmin'
+
+def fix_process_data(apps, schema_editor):
+    Version = apps.get_model("reversion", "Version")
+    Revision = apps.get_model("reversion", "Revision")
+    ProcessSample = apps.get_model("fms_core", "ProcessSample")
+    Process = apps.get_model("fms_core", "Process")
+
+    affected_revisions_ids = Revision.objects.filter(date_created__range=["2021-04-29", "2021-05-01"]).values_list('id', flat=True)
+
+    for revision_id in affected_revisions_ids:
+        # Getting all ProcessSample created in this revision
+        list_affected_process_samples_ids = list(Version.objects.filter(content_type__model='processsample',
+                                                              revision_id=revision_id).values_list('object_id', flat=True))
+
+        if len(list_affected_process_samples_ids) > 1:
+            process_samples = ProcessSample.objects.filter(id__in=list_affected_process_samples_ids)
+
+            # Getting all distinct Processes related to those ProcessSample
+            list_process_ids = list(process_samples.values_list('process_id', flat=True).distinct())
+
+            # Checks if many processes were created instead of only one
+            if len(list_process_ids) > 1:
+                # First Process; the only one that will be kept
+                first_process_id = min(list_process_ids)
+
+                processes_to_delete = Process.objects.filter(pk__in=list_process_ids).exclude(pk=first_process_id)
+
+                with reversion.create_revision(manage_manually=True):
+                    reversion.set_comment("Curation of multiple processes into one process per template")
+                    reversion.set_user(User.objects.get(username=ADMIN_USERNAME))
+
+                    # Change process_id for ProcessSample now pointing to the wrong processes
+                    for ps in process_samples:
+                        ps.process_id = first_process_id
+                        ps.save()
+                        reversion.add_to_revision(ps)
+
+                    # Delete Processes unused (should not have been created in first place)
+                    for process in processes_to_delete:
+                        process.comment = f'Deleted in curation {datetime.datetime.now().strftime("%Y-%m-%d")} v3.1.2 combined multiple processes - ' + process.comment
+                        process.deleted = True
+                        process.save()
+                        reversion.add_to_revision(process)
+
+                    # Update First Process for this revision batch with comment reflecting the current curation
+                    first_process = Process.objects.get(id=first_process_id)
+                    first_process.comment += f' - Curated {datetime.datetime.now().strftime("%Y-%m-%d")} v3.1.2 combined multiple processes'
+                    first_process.save()
+                    reversion.add_to_revision(first_process)
+
+
+                # Delete all processes to be deleted (has to be done outside of the previous Revision scope)
+                for process in processes_to_delete:
+                    process.delete()
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        migrations.swappable_dependency(settings.AUTH_USER_MODEL),
+        ('fms_core', '0018_v3_1_0'),
+    ]
+
+    operations = [
+        migrations.RunPython(
+            fix_process_data,
+            reverse_code=migrations.RunPython.noop,
+        ),
+    ]