soil_mask_workflow.jx

{
  "define": {
    "WORKSPACE_DIR_NAME": "workspace",
    "RESULT_FILENAME": "result.json",
    "WORKSPACE_DIR": RELATIVE_WORKING_FOLDER + WORKSPACE_DIR_NAME,
    "RUN_RESULTS": WORKSPACE_DIR + "/" + RESULT_FILENAME,
    "CACHE_RESULTS_SCRIPT": SCRIPT_FOLDER + "cache_results.py",
    "DOCKER_MOUNT_POINT": "/mnt/",
    "DOCKER_RUN_PARAMS": DATA_FOLDER_NAME + "/odm_orthophoto.tif",
    "PATH_MAPS": DOCKER_MOUNT_POINT + ":" + RELATIVE_WORKING_FOLDER,
    "LOCAL_RESULT_FILE": CACHE_DIR + RESULT_FILENAME
  },
  "rules": [
    {
      "command": "echo Creating cache folder \\\"${CACHE_DIR}\\\" && mkdir -p \"${CACHE_DIR}\" ",
      "environment": {
        "CACHE_DIR": CACHE_DIR,
      },
      "inputs": [],
      "output": [
        CACHE_DIR
      ]
    },
    {
      "command": "echo Creating workspace \\\"${WORKSPACE_DIR}\\\" && mkdir -p \"${WORKSPACE_DIR}\" && chmod a+w \"${WORKSPACE_DIR}\" ",
      "environment": {
        "WORKSPACE_DIR": WORKSPACE_DIR
      },
      "inputs": [],
      "outputs": [
        WORKSPACE_DIR
      ]
    },
    {
      "command": "docker run --rm --name sm_transformer -v \"${IMAGE_MOUNT_SOURCE}:${DOCKER_MOUNT_POINT}\" ${DOCKER_IMAGE} -d --metadata \"${METADATA}\" --working_space \"${WORKSPACE_DIR}\" ${DOCKER_RUN_PARAMS}",
      "environment": {
        "IMAGE_MOUNT_SOURCE": IMAGE_MOUNT_SOURCE,
        "DOCKER_MOUNT_POINT": DOCKER_MOUNT_POINT,
        "DOCKER_IMAGE": DOCKER_IMAGE,
        "METADATA": EXPERIMENT_METADATA_RELATIVE_PATH,
        "WORKSPACE_DIR": WORKSPACE_DIR,
        "DOCKER_RUN_PARAMS": DOCKER_RUN_PARAMS
      },
      "inputs": [
        WORKSPACE_DIR
      ],
      "outputs": [
        RUN_RESULTS
      ]
    },
    {
      "command": "echo Copying results \\\"${RUN_RESULTS}\\\" to \\\"${CACHE_DIR}\\\" && mkdir -p \"${CACHE_DIR}\/\" && cp \"${RUN_RESULTS}\" \"${CACHE_DIR}\/\" ",
      "environment": {
        "RUN_RESULTS": RUN_RESULTS,
        "CACHE_DIR": CACHE_DIR
      },
      "inputs": [
        RUN_RESULTS
      ],
      "outputs": [
        LOCAL_RESULT_FILE
      ]
    },
    {
      "command": "echo Processing results && python3 \"${CACHE_RESULTS_SCRIPT}\" --maps \"${PATH_MAPS}\" --extra_files \"${METADATA}\" \"${RUN_RESULTS}\" \"${CACHE_DIR}\" ",
      "environment": {
        "CACHE_RESULTS_SCRIPT": CACHE_RESULTS_SCRIPT,
        "PATH_MAPS": PATH_MAPS,
        "METADATA": EXPERIMENT_METADATA_RELATIVE_PATH,
        "RUN_RESULTS": RUN_RESULTS,
        "CACHE_DIR": CACHE_DIR
      },
      "inputs": [
        LOCAL_RESULT_FILE
      ],
      "outputs": [
        CACHE_DIR + EXPERIMENT_METADATA_FILENAME
      ]
    },
    {
      "command": "echo copying \\\"${CACHE_DIR}${FILE_NAME}\\\" \\\"${RESULTS_FILE_PATH}\\\" && cp \"${CACHE_DIR}${FILE_NAME}\" \"${RESULTS_FILE_PATH}\"",
      "environment": {
        "CACHE_DIR": CACHE_DIR,
        "FILE_NAME": FILE_NAME,
        "RESULTS_FILE_PATH": RESULTS_FILE_PATH
      },
      "inputs": [
        CACHE_DIR + EXPERIMENT_METADATA_FILENAME
      ],
      "outputs": [
        RESULTS_FILE_PATH + FILE_NAME
      ]
    } for FILE_NAME in RESULTS_FILE_NAMES
  ]
}