From 64e74148f943b60b238a2858ad9a63aef83aee52 Mon Sep 17 00:00:00 2001 From: Michael Thornton Date: Wed, 31 Jan 2024 13:07:25 -0800 Subject: [PATCH] improve logging in re-id tool --- nmdc_automation/re_iding/scripts/re_id_tool.py | 16 +++++++++++++--- 1 file changed, 13 insertions(+), 3 deletions(-) diff --git a/nmdc_automation/re_iding/scripts/re_id_tool.py b/nmdc_automation/re_iding/scripts/re_id_tool.py index 718de1c6..7fecb88e 100755 --- a/nmdc_automation/re_iding/scripts/re_id_tool.py +++ b/nmdc_automation/re_iding/scripts/re_id_tool.py @@ -109,10 +109,16 @@ def extract_records(ctx, study_id, api_base_url): ) continue db.omics_processing_set.append(omics_processing_record) - for data_object_id in omics_processing_record["has_output"]: + + omics_processing_has_outputs = omics_processing_record.get("has_output", []) + if not omics_processing_has_outputs: + logger.warning(f"OmicsProcessing: no has_output for: {omics_id}") + logger.warning(f"omics_processing_record: {omics_processing_record}") + for data_object_id in omics_processing_has_outputs: data_object_record = api_client.get_data_object(data_object_id) if not data_object_record: - logger.warning(f"no data object found for {data_object_id}") + logger.warning(f"DataObjectNotFound: {data_object_id}") + logger.warning(f"omics_processing_record: {omics_processing_record}") continue data_object_type = data_object_record.get("data_object_type") data_object_description = data_object_record.get("description") @@ -161,7 +167,11 @@ def extract_records(ctx, study_id, api_base_url): data_object_id ) if not data_object_record: - logger.warning(f"no data object found for {data_object_id}") + logger.warning(f"DataObjectNotFound {data_object_id}") + logger.warning(f"workflow_record: {workflow_record['id']}, {workflow_record['type']}, {workflow_record['name']}") + logger.warning(f"has_input: {workflow_record.get('has_input')}") + logger.warning(f"has_output: {workflow_record.get('has_output')}") + logger.warning(f"omics_processing_record: {omics_processing_record['id']}, {omics_processing_record['omics_type']['has_raw_value']}") continue data_object_type = data_object_record.get("data_object_type") data_object_description = data_object_record.get("description")