Load a Protocol from Autoprotocol JSON #219

Activity

1. bmiles commented on Nov 1, 2019

   

   bmiles

   on Nov 1, 2019

   Contributor

   More actions

   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?
2. opensean commented on Nov 6, 2019

   

   opensean

   on Nov 6, 2019

   Author

   More actions

   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