diff --git a/ena-submission/scripts/create_project.py b/ena-submission/scripts/create_project.py index 437d037cd..f455158eb 100644 --- a/ena-submission/scripts/create_project.py +++ b/ena-submission/scripts/create_project.py @@ -73,13 +73,13 @@ def construct_project_set_object( Construct project set object, using: - entry in project_table - group_info of corresponding group_id - - config information, such as ingest metadata for that organism + - config information, such as enaDeposition metadata for that organism If test=True add a timestamp to the alias suffix to allow for multiple submissions of the same project for testing. (ENA blocks multiple submissions with the same alias) """ - metadata_dict = config.organisms[entry["organism"]]["ingest"] + metadata_dict = config.organisms[entry["organism"]]["enaDeposition"] if test: alias = XmlAttribute( f"{entry["group_id"]}:{entry["organism"]}:{config.unique_project_suffix}:{datetime.now(tz=pytz.utc)}" diff --git a/ena-submission/scripts/create_sample.py b/ena-submission/scripts/create_sample.py index c0fec4844..c3c361d8f 100644 --- a/ena-submission/scripts/create_sample.py +++ b/ena-submission/scripts/create_sample.py @@ -132,7 +132,7 @@ def construct_sample_set_object( Construct sample set object, using: - entry in sample_table - sample_data_in_submission_table: corresponding entry in submission_table - - config information, such as ingest metadata for that organism + - config information, such as enaDeposition metadata for that organism If test=True add a timestamp to the alias suffix to allow for multiple submissions of the same project for testing. (ENA blocks multiple submissions with the same alias) @@ -140,7 +140,7 @@ def construct_sample_set_object( sample_metadata = sample_data_in_submission_table["metadata"] center_name = sample_data_in_submission_table["center_name"] organism = sample_data_in_submission_table["organism"] - organism_metadata = config.organisms[organism]["ingest"] + organism_metadata = config.organisms[organism]["enaDeposition"] if test: alias = XmlAttribute( f"{entry["accession"]}:{organism}:{config.unique_project_suffix}:{datetime.now(tz=pytz.utc)}" diff --git a/ena-submission/scripts/test_ena_submission.py b/ena-submission/scripts/test_ena_submission.py index 1bee66a27..e81596cfb 100644 --- a/ena-submission/scripts/test_ena_submission.py +++ b/ena-submission/scripts/test_ena_submission.py @@ -48,7 +48,7 @@ def mock_config(): "scientific_name": "Test scientific name", "molecule_type": "genomic RNA", } - config.organisms = {"Test organism": {"ingest": metadata_dict}} + config.organisms = {"Test organism": {"enaDeposition": metadata_dict}} config.metadata_mapping = defaults["metadata_mapping"] config.metadata_mapping_mandatory_field_defaults = defaults[ "metadata_mapping_mandatory_field_defaults"