diff --git a/nmdc_automation/models/nmdc.py b/nmdc_automation/models/nmdc.py index 0b59044c..3d9fdde9 100644 --- a/nmdc_automation/models/nmdc.py +++ b/nmdc_automation/models/nmdc.py @@ -81,6 +81,9 @@ def _normalize_mags_record(record: Dict[str, Any]) -> Dict[str, Any]: # for backwards compatibility normalize num_tRNA to num_t_rna if "num_tRNA" in mag: record["mags_list"][i]["num_t_rna"] = mag.pop("num_tRNA") + # strip output_dir if present + if "output_dir" in mag: + record["mags_list"][i].pop("output_dir") # add type to eukaryotic_evaluation if it exists if "eukaryotic_evaluation" in mag: record["mags_list"][i]["eukaryotic_evaluation"]["type"] = "nmdc:EukEval" diff --git a/nmdc_automation/workflow_automation/wfutils.py b/nmdc_automation/workflow_automation/wfutils.py index 9f61bdbe..45ff4c3d 100755 --- a/nmdc_automation/workflow_automation/wfutils.py +++ b/nmdc_automation/workflow_automation/wfutils.py @@ -512,7 +512,7 @@ def make_data_objects(self, output_dir: Union[str, Path] = None) -> List[DataObj def make_workflow_execution(self, data_objects: List[DataObject]) -> WorkflowExecution: """ - Create a workflow execution record for the job. This record includes the basic workflow execution attributes + Create a workflow execution instance for the job. This record includes the basic workflow execution attributes and the data objects generated by the job. Additional workflow-specific attributes can be defined in the workflow execution template and read from a job's output files. The data objects are added to the record as a list of IDs in the "has_output" key.