diff --git a/ena-submission/scripts/create_assembly.py b/ena-submission/scripts/create_assembly.py index ab66c6c68..41718c4dc 100644 --- a/ena-submission/scripts/create_assembly.py +++ b/ena-submission/scripts/create_assembly.py @@ -7,6 +7,7 @@ import click import pytz import yaml +from call_loculus import get_group_info from ena_submission_helper import ( CreationResult, create_chromosome_list, @@ -134,6 +135,17 @@ def create_manifest_object( sample_accession = sample_table_entry["result"]["ena_sample_accession"] study_accession = project_table_entry["result"]["bioproject_accession"] + address_string = project_table_entry["center_name"] + if config.is_broker: + try: + group_info = get_group_info(config, project_table_entry["group_id"])[0]["group"] + address = group_info["address"] + address_string = (f'{address.get("line1", "")}, {address.get("line2", "")}, ' + f'{address.get("city", "")}, {address.get("state", "")}, ' + f'{address.get("postalCode", "")}, {address.get("country")}') + except Exception as e: + logger.error(f"Was unable to create address, setting address to center_name due to {e}") + metadata = submission_table_entry["metadata"] unaligned_nucleotide_sequences = submission_table_entry["unaligned_nucleotide_sequences"] organism_metadata = config.organisms[group_key["organism"]]["enaDeposition"] @@ -205,6 +217,7 @@ def create_manifest_object( description=description, moleculetype=moleculetype, authors=authors, + address=address_string, ) diff --git a/ena-submission/scripts/test_ena_submission.py b/ena-submission/scripts/test_ena_submission.py index e81596cfb..9e2c1e211 100644 --- a/ena-submission/scripts/test_ena_submission.py +++ b/ena-submission/scripts/test_ena_submission.py @@ -240,7 +240,10 @@ def test_create_manifest(self): study_accession = "Test Study Accession" sample_accession = "Test Sample Accession" results_in_sample_table = {"result": {"ena_sample_accession": sample_accession}} - results_in_project_table = {"result": {"bioproject_accession": study_accession}} + results_in_project_table = { + "result": {"bioproject_accession": study_accession}, + "center_name": "generic_center_name", + } manifest = create_manifest_object( config, results_in_sample_table,