Load a Protocol from Autoprotocol JSON

[opensean]

Hello,

Is there way to load a protocol from a json file?

For example, the protocol can be serialized to JSON using:

# serialize the protocol as Autoprotocol JSON
print(json.dumps(p.as_dict(), indent=2))

How do I go the other way? Ideally, something like:

with open("protocol.json", "r") as f:
    p = Protocol.from_dict(json.load(f))

[bmiles]

Hey Sean, that's a cool idea, it isn't supported in Ap-py. I'd be interested to hear how that could be done?

[opensean]

I spent some time looking at the code and came across some differences between the spec and this package. For example, spec for a container_ref does not include the container type, which is required by autoprotocol-python to generate a Container.

  "refs": {
    String: {
      "id": Option<String>,
      "new": Option<String>,
      "store": Option<{
        "where": Option<Enum(
          "cold_80",
          "cold_20",
          "cold_4",
          "ambient",
          "warm_30",
          "warm_37"
        )>
      }>,
      "discard": Option<Boolean>,
      "cover": Option<String>
    }
  }
}

The missing container type means I can't do this

def from_json(path):
    """
    Load an Autoprotocol formatted JSON.

    Args:
        path (str):  file path.

    Returns:
        [autoprotocol.container.Container], autoprotocol.protocol.Protocol
    """
    containers = []
    with open(path, "r") as f:
        p_dict = json.load(f)
        p = Protocol()
        for k,v in p_dict["refs"].items():

            ## get storage info

            storage = v.get("store", None)
            if storage:
                storage = v["store"]["where"]


            ## cont_type is not available in spec unless it is a "new" 
            ## container e.g,
            ##
            ## "sample_plate_1": {
            ##   "new": "96-pcr",
            ##   "discard": true
            ## }
            cont_type = v.get("new", None)

            ## create container, this will break without cont_type
            c =  Container(v.get("id", None), cont_type, name = k,
                           storage = storage,
                           cover = v.get("cover", None))

            containers.append(c)

            ## create Ref and add to protocol
            r = Ref(k, v, c)

            p.refs[k] = r


        ## create instructions
        for i in p_dict["instructions"]:

            ## insert code here

            ## p._append_and_return(Instruction)

    return containers, p

I haven't explored rebuilding the instructions yet