Output

Build and Run Commands

Local or AWS

git clone https://github.com/SWOT-Confluence/output.git

cd output

docker build -t output .

HPC

singularity build output.simg docker://travissimmons/output

singularity run –bind mnt/input:/mnt/data/input,mnt/flpe:/mnt/data/flpe,mnt/moi:/mnt/data/moi,mnt/diagnostics:/mnt/data/diagnostics,mnt/offline:/mnt/data/offline,mnt/validation:/mnt/data/validation,mnt/output:/mnt/data/output output.simg -s local -j /app/metadata/metadata.json -m input priors prediagnostics momma neobam metroman sic4dvar sad moi offline validation swot -i 0

Arguments

def create_args(): “"”Create and return argparser with arguments.”””

arg_parser = argparse.ArgumentParser(description="Append results of Confluence workflow execution to the SoS.")
arg_parser.add_argument("-i",
                        "--index",
                        type=int,
                        help="Index to specify input data to execute on, value of -235 indicates AWS selection")
arg_parser.add_argument("-c",
                        "--contjson",
                        type=str,
                        help="Name of the continent JSON file",
                        default="continent.json")
arg_parser.add_argument("-r",
                        "--runtype",
                        type=str,
                        choices=["constrained", "unconstrained"],
                        help="Current run type of workflow: 'constrained' or 'unconstrained'",
                        default="constrained")
arg_parser.add_argument("-m",
                        "--modules",
                        nargs="+",
                        default=[],
                        help="List of modules executed in current workflow.")
arg_parser.add_argument("-j",
                        "--metadatajson",
                        type=Path,
                        default=Path(__file__).parent / "metadata" / "metadata.json",
                        help="Path to JSON file that contains global attribute values")
arg_parser.add_argument("-u",
                        "--podaacupload",
                        action="store_true",
                        help="Indicate requirement to upload to PO.DAAC S3 Bucket")
arg_parser.add_argument("-b",
                        "--podaacbucket",
                        type=str,
                        help="Name of PO.DAAC S3 bucket to upload to")
arg_parser.add_argument("-s",
                        "--sosbucket",
                        type=str,
                        default="confluence-sos",
                        help="Name of SoS S3 bucket to upload to")
return arg_parser

Dev notes….