Added script to fix embargo after migration. [skip ci]

ops/scripts/migration_fix_embargo.py

+from nomad import infrastructure
+from nomad import processing
+from nomad import search
+
+infrastructure.setup_logging()
+calcs = infrastructure.setup_mongo().fairdi_nomad_migration.calc
+index = infrastructure.setup_mongo().coe_migration.source_calc
+uploads_col = infrastructure.setup_mongo().fairdi_nomad_migration.upload
+infrastructure.setup_elastic()
+
+
+def check_and_fix(upload):
+    example = calcs.find_one({'upload_id': upload, 'metadata.pid': {'$exists': True}})
+    pid = example['metadata']['pid']
+    truth = index.find_one({'_id': pid})
+
+    if truth['metadata']['with_embargo'] != example['metadata']['with_embargo']:
+        print('need to fix %s' % upload)
+
+        calcs.update_many(
+            {'upload_id': upload, 'metadata.with_embargo': True},
+            {'$set': {'changed': True, 'metadata.with_embargo': False}})
+
+        calcs.update_many(
+            {'upload_id': upload, 'metadata.with_embargo': False, 'changed': True},
+            {'$unset': {'changed': 1}, '$set': {'metadata.with_embargo': True}})
+
+        upload_proc = processing.Upload.get_by_id(upload)
+        upload_with_metadata = upload_proc.to_upload_with_metadata(upload_proc.metadata)
+        calcs_with_metadata = upload_with_metadata.calcs
+        search.publish(calcs_with_metadata)
+
+
+for upload in calcs.distinct('upload_id'):
+    check_and_fix(upload)