fix(submission): Add management command to reassign root_uuid to prevent 409 conflict when re-editing an already edited submission (#5888)

### 📣 Summary
Add management command `clean_duplicated_submissions_root_uuid` to
reassign `root_uuid` to prevents conflict errors (HTTP 409) when editing
a submission multiple times in a row.

### 📖 Description
This PR fixes an issue where edited submissions would trigger a 409
Conflict error if a user tried to edit them again.

The problem emerged after switching to the new root_uuid field
(introduced in the fix for #5852, PR #5861) to identify submissions more
reliably. However, submissions that had not yet been fully backfilled
with root_uuid data caused conflicts when edited repeatedly

Author: noliveleger

kobo/apps/openrosa/apps/logger/management/commands/clean_duplicated_submissions_root_uuid.py

@@ -0,0 +1,122 @@
+import time
+
+from django.conf import settings
+from django.core.management.base import BaseCommand, CommandError
+from django.core.management import call_command
+from django.db.utils import IntegrityError
+
+from kobo.apps.openrosa.apps.logger.models.instance import Instance
+from kobo.apps.openrosa.apps.logger.xform_instance_parser import (
+    set_meta,
+    add_uuid_prefix,
+)
+
+
+class Command(BaseCommand):
+
+    help = """
+    Create a unique `root_uuid` for submissions saved before the `2.025.02` release,
+    when their current `root_uuid` is already used by another submission
+    within the same project."
+    """
+
+    def add_arguments(self, parser):
+        super().add_arguments(parser)
+
+        parser.add_argument(
+            '--xform',
+            help="Specify a XForm's `id_string`",
+        )
+
+    def handle(self, *args, **options):
+        self._verbosity = options['verbosity']
+
+        if not (xform_id_string := options.get('xform')):
+            raise CommandError("XForm's `id_string` must be specified")
+
+        # First
+        try:
+            exit_code = call_command(
+                'clean_duplicated_submissions',
+                verbosity=self._verbosity,
+                xform=xform_id_string,
+            )
+        except Exception as e:
+            exit_code = 1
+            error = str(e)
+        else:
+            error = ''
+
+        if exit_code:
+            raise CommandError(
+                f'`clean_duplicated_submissions` command has completed '
+                f'with errors: {error}'
+            )
+
+        # Retrieve all instances with the same `uuid`
+        queryset = Instance.objects.filter(
+            xform__id_string=xform_id_string, root_uuid__isnull=True
+        )
+
+        for instance in queryset.iterator():
+            try:
+                instance._populate_root_uuid()  # noqa
+                if self._verbosity >= 1:
+                    self.stdout.write(
+                        f'Processing root_uuid `{instance.root_uuid}`…'
+                    )
+                # Bypass Instance.save() mechanism
+                Instance.objects.filter(pk=instance.pk).update(
+                    root_uuid=instance.root_uuid
+                )
+            except IntegrityError as e:
+                if 'unique_root_uuid_per_xform' not in str(e):
+                    self.stderr.write(
+                        f'Could not update instance #{instance.pk} '
+                        f'- uuid: {instance.uuid}'
+                    )
+
+                if self._verbosity >= 2:
+                    self.stdout.write('\tConflict detected!')
+
+                xml_hash = Instance.objects.values_list(
+                    'xml_hash', flat=True
+                ).get(root_uuid=instance.root_uuid)
+                # Only consider different hashes, because if there are the
+                # same, they should have been handled by clean_duplicated_submissions
+                # management command
+                if xml_hash != instance.xml_hash:
+                    old_uuid = instance.uuid
+                    now = int(time.time() * 1000)
+                    instance.root_uuid = (
+                        f'CONFLICT-{now}-{xform_id_string}-{old_uuid}'
+                    )
+                    instance.xml = set_meta(
+                        instance.xml,
+                        'rootUuid',
+                        add_uuid_prefix(instance.root_uuid),
+                    )
+                    instance.xml_hash = instance.get_hash(instance.xml)
+                    if self._verbosity >= 2:
+                        self.stdout.write(
+                            f'\tOld root_uuid: {old_uuid}, '
+                            f'New UUID: {instance.root_uuid}'
+                        )
+                    # Bypass Instance.save() mechanism
+                    Instance.objects.filter(pk=instance.pk).update(
+                        xml=instance.xml,
+                        xml_hash=instance.xml_hash,
+                        root_uuid=instance.root_uuid
+                    )
+                    doc = settings.MONGO_DB.instances.find_one(
+                        {'_id': instance.pk}
+                    )
+                    doc['meta/rootUuid'] = add_uuid_prefix(instance.root_uuid)
+                    settings.MONGO_DB.instances.replace_one(
+                        {'_id': instance.pk}, doc, upsert=True
+                    )
+            except AssertionError:
+                self.stderr.write(
+                    f'Could not update root_uuid of instance #{instance.pk} '
+                    f'- uuid: {instance.uuid}'
+                )