Check that the copy to remote mongo actually copied anything

eva-accession-release-automation/requirements.txt

@@ -1,4 +1,4 @@
-ebi_eva_common_pyutils==0.5.6
+ebi_eva_common_pyutils[internal]==0.6.5
 click==7.1.2
 pytz==2022.6
 pyyaml==5.3.1

eva-accession-release-automation/run_release_in_embassy/copy_accessioning_collections_to_embassy.py

@@ -18,6 +18,7 @@
 import sys
 import traceback
 
+from ebi_eva_common_pyutils.command_utils import run_command_with_output
 from ebi_eva_common_pyutils.config_utils import get_mongo_uri_for_eva_profile
 from ebi_eva_common_pyutils.metadata_utils import get_metadata_connection_handle
 from ebi_eva_common_pyutils.mongo_utils import copy_db
@@ -47,6 +48,13 @@
     "submittedVariantOperationEntity": "inactiveObjects.tax"
 }
 
+def remote_db_is_empty(local_forwarded_port, assembly_accession, destination_db_name):
+    logger.info(f"check if: {assembly_accession} has been copied")
+    command = f"mongosh --eval 'use {destination_db_name}' --eval 'db.stats()' --port {local_forwarded_port} " \
+              "| grep 'dataSize' | awk '{print substr($2,1,length($2)-1)}'"
+    output = run_command_with_output(command)
+    return output.strip() == '0'
+
 
 def mongo_data_copy_to_remote_host(local_forwarded_port, private_config_xml_file, profile, assembly_accession,
                                    taxonomy_id, collections_to_copy_map, dump_dir, destination_db_name):
@@ -119,6 +127,8 @@ def copy_accessioning_collections_to_embassy(private_config_xml_file, profile, t
             mongo_data_copy_to_remote_host(mongo_port, private_config_xml_file, profile, assembly_accession,
                                            taxonomy_id, collections_to_copy_map, dump_dir, destination_db_name)
             exit_code = 0
+            if remote_db_is_empty(mongo_port, assembly_accession, destination_db_name):
+                raise Exception
     except Exception as ex:
         logger.error("Encountered an error while copying species data to Embassy for assemblies in "
                      + release_info["tempmongo_instance"] + "\n" + traceback.format_exc())