flow_definition.json

{
  "Comment": "Transfer and run Tomopy",
  "StartAt": "FacilityChoice",
  "States": {
    "FacilityChoice": {
      "Type": "Choice",
      "Choices": [
        {
          "Variable": "$.input.compute_site",
          "StringEquals": "ALCF",
          "Next": "ALCFConfig"
        }
      ],
      "Default": "NERSCConfig"
    },
    "ALCFConfig": {
      "Type": "Pass",
      "Parameters": {
        "site.$": "$.input.compute_configs.ALCF"
      },
      "ResultPath": "$.input.compute",
      "Next": "TransferInput"
    },
    "NERSCConfig": {
      "Type": "Pass",
      "Parameters": {
        "site.$": "$.input.compute_configs.NERSC"
      },
      "ResultPath": "$.input.compute",
      "Next": "TransferInput"
    },
    "TransferInput": {
      "Comment": "Transfer input file",
      "Type": "Action",
      "ActionUrl": "https://actions.automate.globus.org/transfer/transfer",
      "Parameters": {
        "source_endpoint_id.$": "$.input.source.id",
        "destination_endpoint_id.$": "$.input.compute.site.transfer_endpoint",
        "transfer_items": [
          {
            "source_path.=": "`$.input.source.path` + `$.input.input_filename`",
            "destination_path.=": "`$.input.compute.site.staging_path` + `$.input.input_filename`",
            "recursive": false
          }
        ]
      },
      "ResultPath": "$.TransferInput",
      "WaitTime": 300,
      "Next": "Tomopy"
    },
    "Tomopy": {
      "Comment": "Perform Tomopy analysis",
      "Type": "Action",
      "ActionUrl": "https://compute.actions.globus.org/fxap",
      "Parameters": {
        "endpoint.$": "$.input.compute.site.compute_endpoint",
        "function.$": "$.input.compute_function_id",
        "kwargs": {
          "save_folder.$": "$.input.compute.site.output_path",
          "collection_path.$": "$.input.compute.site.collection_path",
          "filename.=": "`$.input.compute.site.collection_path` + `$.input.compute.site.staging_path` + `$.input.input_filename`",
          "command.$": "$.input.compute_function_kwargs.command",
          "reconstruction_type.$": "$.input.compute_function_kwargs.reconstruction_type"
        }
      },
      "ResultPath": "$.TomopyOutput",
      "WaitTime": 600,
      "Next": "TransferResults"
    },
    "TransferResults": {
      "Comment": "Transfer results",
      "Type": "Action",
      "ActionUrl": "https://actions.automate.globus.org/transfer/transfer",
      "Parameters": {
        "source_endpoint_id.$": "$.input.compute.site.transfer_endpoint",
        "destination_endpoint_id.$": "$.input.source.id",
        "transfer_items": [
          {
            "source_path.$": "$.TomopyOutput.details.result[0][1]",
            "destination_path.=": "`$.input.result_path` + `$.TomopyOutput.details.result[0][0]`",
            "recursive": false
          }
        ]
      },
      "ResultPath": "$.TransferFiles",
      "WaitTime": 300,
      "End": true
    }
  }
}