@opentrons/shared-data 0.0.1-alpha.20 → 0.0.1-alpha.21

package/python/opentrons_shared_data/pipette/scripts/build_json_script.py

@@ -1,469 +0,0 @@
-import argparse
-import csv
-import json
-from ast import literal_eval
-from typing import Optional, Dict, Union, Any, List
-from pathlib import Path
-from pydantic import BaseModel
-import math
-
-from ... import get_shared_data_root
-from ..pipette_definition import (
-    PipetteGeometryDefinition,
-    PipetteLiquidPropertiesDefinition,
-    PipettePhysicalPropertiesDefinition,
-    PlungerPositions,
-    SupportedTipsDefinition,
-    MotorConfigurations,
-    PartialTipDefinition,
-    AvailableSensorDefinition,
-    PickUpTipConfigurations,
-    PressFitPickUpTipConfiguration,
-    DropTipConfigurations,
-    PlungerEjectDropTipConfiguration,
-)
-
-from ..dev_types import PipetteModelSpec
-
-
-PIPETTE_DEFINITION_ROOT = Path("pipette") / "definitions" / "2"
-GEOMETRY_ROOT = get_shared_data_root() / PIPETTE_DEFINITION_ROOT / "geometry"
-GENERAL_ROOT = get_shared_data_root() / PIPETTE_DEFINITION_ROOT / "general"
-LIQUID_ROOT = get_shared_data_root() / PIPETTE_DEFINITION_ROOT / "liquid"
-
-GENERAL_SCHEMA = "#/pipette/schemas/2/pipettePropertiesSchema.json"
-LIQUID_SCHEMA = "#/pipette/schemas/2/pipetteLiquidPropertiesSchema.json"
-GEOMETRY_SCHEMA = "#/pipette/schemas/2/pipetteGeometryPropertiesSchema.json"
-
-
-def _build_pickup_tip_data(
-    model_configurations: Optional[PipetteModelSpec] = None,
-) -> PickUpTipConfigurations:
-    presses = 0
-    increment = 0
-    distance = 0.0
-    if model_configurations:
-        current = model_configurations["pickUpCurrent"]["value"]
-        speed = model_configurations["pickUpSpeed"]["value"]
-        presses = model_configurations["pickUpPresses"]["value"]
-        increment = int(model_configurations["pickUpIncrement"]["value"])
-        distance = model_configurations["pickUpDistance"]["value"]
-    else:
-        print("Handling pick up tip configurations\n")
-        speed = float(input("please provide the speed\n"))
-        presses = int(input("please provide the number of presses for force pick up\n"))
-        increment = int(
-            input(
-                "please provide the increment to move the pipette down for force pickup\n"
-            )
-        )
-        distance = float(
-            input("please provide the starting distance for pick up tip\n")
-        )
-    print(f"TODO: Current {current} is not used yet")
-    return PickUpTipConfigurations(
-        pressFit=PressFitPickUpTipConfiguration(
-            speed=speed,
-            presses=presses,
-            increment=increment,
-            distance=distance,
-            currentByTipCount={},
-        )
-    )
-
-
-def _build_drop_tip_data(
-    model_configurations: Optional[PipetteModelSpec] = None,
-) -> DropTipConfigurations:
-    if model_configurations:
-        current = model_configurations["dropTipCurrent"]["value"]
-        speed = model_configurations["dropTipSpeed"]["value"]
-    else:
-        print("Handling drop tip configurations\n")
-        speed = float(input("please provide the speed\n"))
-    return DropTipConfigurations(
-        plungerEject=PlungerEjectDropTipConfiguration(
-            current=current,
-            speed=speed,
-        )
-    )
-
-
-def _build_plunger_positions(
-    model_configurations: Optional[PipetteModelSpec] = None,
-) -> PlungerPositions:
-    if model_configurations:
-        top = model_configurations["top"]["value"]
-        bottom = model_configurations["bottom"]["value"]
-        blow_out = model_configurations["blowout"]["value"]
-        drop_tip = model_configurations["dropTip"]["value"]
-    else:
-        print("Handling plunger motor positions\n")
-        top = float(input("Please provide the top plunger position\n"))
-        bottom = float(input("Please provide the bottom plunger position\n"))
-        blow_out = float(input("Please provide the blow out plunger position\n"))
-        drop_tip = float(input("Please provide the drop tip plunger position\n"))
-    return PlungerPositions(top=top, bottom=bottom, blowout=blow_out, drop=drop_tip)
-
-
-def _build_motor_configurations(
-    model_configurations: Optional[PipetteModelSpec] = None,
-) -> MotorConfigurations:
-    if model_configurations:
-        run = model_configurations["plungerCurrent"]["value"]
-        idle = model_configurations.get("idleCurrent", run)
-    else:
-        print("Handling default plunger motor currents\n")
-        idle = float(
-            input("Please provide the default idle current of the plunger motor\n")
-        )
-        run = float(
-            input("Please provide the default run current of the plunger motor\n")
-        )
-    return MotorConfigurations(idle=idle, run=run)
-
-
-def _build_partial_tip_configurations(channels: int) -> PartialTipDefinition:
-    if channels == 8:
-        return PartialTipDefinition(
-            partialTipSupported=True, availableConfigurations=[1, 2, 3, 4, 5, 6, 7, 8]
-        )
-    elif channels == 96:
-        return PartialTipDefinition(
-            partialTipSupported=True, availableConfigurations=[1, 8, 12, 96]
-        )
-    else:
-        return PartialTipDefinition(partialTipSupported=False)
-
-
-def build_geometry_model_v2(
-    input_dictionary: Dict[str, Any]
-) -> PipetteGeometryDefinition:
-    return PipetteGeometryDefinition.parse_obj(input_dictionary)
-
-
-def build_liquid_model_v2(
-    input_dictionary: Dict[str, Any],
-    supported_tip_configurations: Dict[str, SupportedTipsDefinition],
-) -> PipetteLiquidPropertiesDefinition:
-    if input_dictionary:
-        if input_dictionary.get("partialTipConfigurations"):
-            return PipetteLiquidPropertiesDefinition.parse_obj(
-                {**input_dictionary, "supportedTips": supported_tip_configurations}
-            )
-        else:
-            return PipetteLiquidPropertiesDefinition.parse_obj(
-                {
-                    **input_dictionary,
-                    "supportedTips": supported_tip_configurations,
-                }
-            )
-    max_volume = int(input("please provide the max volume of the pipette\n"))
-    min_volume = float(input("please provide the min volume of the pipette\n"))
-    default_tipracks = input(
-        "please input the load names of default tipracks separated by commas\n"
-    )
-    list_default_tipracks = default_tipracks.split(",")
-    return PipetteLiquidPropertiesDefinition.parse_obj(
-        {
-            "supportedTips": supported_tip_configurations,
-            "maxVolume": max_volume,
-            "minVolume": min_volume,
-            "defaultTipracks": list_default_tipracks,
-        }
-    )
-
-
-def build_physical_model_v2(
-    input_dictionary: Optional[Dict[str, Any]], pipette_type: Optional[str] = None
-) -> PipettePhysicalPropertiesDefinition:
-    if input_dictionary:
-        available_sensors = AvailableSensorDefinition(
-            sensors=input_dictionary.pop("availableSensors", [])
-        )
-        back_compat_names = input_dictionary.pop("backCompatNames", [])
-        return PipettePhysicalPropertiesDefinition.parse_obj(
-            {
-                **input_dictionary,
-                "availableSensors": available_sensors,
-                "backCompatNames": back_compat_names,
-            }
-        )
-    print(f"Handling general pipette information for {pipette_type}\n")
-    display_name = input("please provide the product name of the pipette\n")
-
-    display_category = input("please provide the model generation of the pipette\n")
-    input_available_sensors = input(
-        "Please provide a list of available sensors, separated by comma\n"
-    )
-    channels = input(f"Please provide the number of channels your {pipette_type} has\n")
-    shaft_diam = float(input(f"Please provide the shaft diameter of {pipette_type}\n"))
-    shaft_ul_per_mm = float(
-        input(f"Please provide the uL to mm conversion for {pipette_type}\n")
-    )
-    pick_up_tip_configurations = _build_pickup_tip_data()
-    drop_tip_configurations = _build_drop_tip_data()
-    plunger_positions = _build_plunger_positions()
-    plunger_motor_configurations = _build_motor_configurations()
-    partial_tip_configurations = _build_partial_tip_configurations(int(channels))
-
-    back_compat_names_str = input(
-        "Please list compatible pipette names separated by commas or hit enter if none"
-    )
-    if back_compat_names_str:
-        back_compat_names = [i.strip() for i in back_compat_names_str.split(",")]
-    else:
-        back_compat_names = []
-    return PipettePhysicalPropertiesDefinition.parse_obj(
-        {
-            "displayName": display_name,
-            "model": pipette_type,
-            "displayCategory": display_category,
-            "pickUpTipConfigurations": pick_up_tip_configurations,
-            "dropTipConfigurations": drop_tip_configurations,
-            "plungerMotorConfigurations": plunger_motor_configurations,
-            "plungerPositionsConfigurations": plunger_positions,
-            "availableSensors": AvailableSensorDefinition(
-                sensors=input_available_sensors.split(",")
-            ),
-            "partialTipConfigurations": partial_tip_configurations,
-            "channels": channels,
-            "shaftDiameter": shaft_diam,
-            "shaftULperMM": shaft_ul_per_mm,
-            "backCompatNames": back_compat_names,
-        }
-    )
-
-
-def build_supported_tips(input_dictionary: Dict[str, Any]) -> SupportedTipsDefinition:
-    return SupportedTipsDefinition.parse_obj(input_dictionary)
-
-
-def save_to_file(
-    directorypath: Path,
-    file_name: str,
-    data: Union[BaseModel, Dict[str, Any]],
-    schema_path: str,
-) -> None:
-    """
-    Function used to save data to a file
-    """
-
-    directorypath.mkdir(parents=True, exist_ok=True)
-    filepath = directorypath / f"{file_name}.json"
-    if isinstance(data, BaseModel):
-        # We have to rely on the json serialization of the
-        # pydantic model to properly convert special objects
-        # such as (pipetteModelType) to a string. However,
-        # we also want to add in a new key on top of the
-        # data in the pydantic model so we need to convert it
-        # back to a dictionary before saving to file.
-        json_basemodel = data.json(by_alias=True)
-        dict_basemodel = json.loads(json_basemodel)
-        dict_basemodel["$otSharedSchema"] = schema_path
-        filepath.write_text(
-            json.dumps(dict_basemodel, ensure_ascii=False), encoding="utf-8"
-        )
-    else:
-        data["$otSharedSchema"] = schema_path
-        filepath.write_text(json.dumps(data, ensure_ascii=False), encoding="utf-8")
-
-
-def migrate_new_blow_out_configs_v2() -> None:
-    pipette_volumes = {
-        1: ["p10", "p50", "p300", "p1000"],
-        2: ["p20", "p300", "p1000"],
-        3: ["p50", "p1000"],
-    }
-
-    for pipette_gen in range(1, 4):  # gen 1, gen 2, gen 3
-        print(f"\nTaking data for gen{pipette_gen} pipettes:")
-        # overwrite and pass in dict with user input for each gen
-        shaft_diameters = {
-            vol: float(input(f"Enter shaft diameter for gen{pipette_gen} {vol}: "))
-            for vol in pipette_volumes[pipette_gen]
-        }
-        fill_blowout_configs(pipette_gen, shaft_diameters, pipette_volumes[pipette_gen])
-
-
-def fill_blowout_configs(
-    pipette_gen: int, shaft_diameters: Dict[str, float], volumes: List[str]
-) -> None:
-
-    general_config_files = Path(GENERAL_ROOT).glob("*")
-    for pipette_type in general_config_files:  # single, eight, 96-channel
-        for volume in volumes:  # pipette max volume- p10, p20, p50, etc.
-            shaft_diameter = shaft_diameters[volume]
-            # calculate uL per mm, default blowout vol
-            ul_per_mm = math.pi * (shaft_diameter / 2) ** 2
-            # get path for every file version for the pipette gen at hand
-            volume_path = Path(pipette_type / volume)
-            for general_file_version in volume_path.glob(f"{str(pipette_gen)}_*.json"):
-                with open(general_file_version, "r") as file:
-                    general_config_dict = json.load(file)
-                general_config_dict["shaftDiameter"] = round(shaft_diameter, 3)
-                general_config_dict["shaftULperMM"] = round(ul_per_mm, 3)
-
-                # get file path to pass into save_to_file
-                gen_path = GENERAL_ROOT / pipette_type / volume
-                version_str = str(general_file_version).split("/")[-1][:-5]
-                save_to_file(gen_path, version_str, general_config_dict, GENERAL_SCHEMA)
-
-
-def build_new_pipette_model_v2(
-    pipette_functions_dict: Dict[str, Any], pipette_model_csv: str
-) -> None:
-    """
-    Build a brand new pipette model from user inputted data.
-    """
-    top_level_pipette_model = {}
-    with open(pipette_model_csv, "r") as f:
-        reader = csv.reader(f)
-        current_key = None
-        for row in reader:
-            if row[0]:
-                current_key = row[0]
-                top_level_pipette_model[current_key] = {row[1]: literal_eval(row[2])}
-            elif current_key:
-                top_level_pipette_model[current_key][row[1]] = literal_eval(row[2])
-            else:
-                continue
-    geometry_model = build_geometry_model_v2(top_level_pipette_model["geometry"])
-    liquid_model = build_liquid_model_v2(
-        top_level_pipette_model["liquid"],
-        pipette_functions_dict,
-    )
-    liquid_model_dict = liquid_model.dict(by_alias=True)
-    liquid_model_dict["supportedTips"] = {
-        k.name: v for k, v in liquid_model_dict["supportedTips"].items()
-    }
-    pipette_type = f"p{liquid_model.max_volume}"
-    physical_model = build_physical_model_v2(
-        {
-            **top_level_pipette_model["general"],
-            "plungerMotorConfigurations": top_level_pipette_model[
-                "plungerMotorConfigurations"
-            ],
-            "plungerPositionsConfigurations": top_level_pipette_model[
-                "plungerPositionsConfigurations"
-            ],
-            "pickUpTipConfigurations": top_level_pipette_model[
-                "pickUpTipConfigurations"
-            ],
-            "dropTipConfigurations": top_level_pipette_model["dropTipConfigurations"],
-            "partialTipConfigurations": _build_partial_tip_configurations(
-                top_level_pipette_model["general"]["channels"]
-            ),
-        },
-        pipette_type,
-    )
-
-    major_version = input("please provide the major version of this pipette model\n")
-    minor_version = input("please provide the minor version of this pipette model\n")
-
-    file_name = f"{major_version}_{minor_version}"
-    current_pipette_path = Path(physical_model.channels.name.lower()) / pipette_type
-
-    save_to_file(
-        GEOMETRY_ROOT / current_pipette_path, file_name, geometry_model, GEOMETRY_SCHEMA
-    )
-    save_to_file(
-        GENERAL_ROOT / current_pipette_path, file_name, physical_model, GENERAL_SCHEMA
-    )
-    save_to_file(
-        LIQUID_ROOT / current_pipette_path, file_name, liquid_model_dict, LIQUID_SCHEMA
-    )
-
-
-def main() -> None:
-    """Entry point."""
-    parser = argparse.ArgumentParser(
-        description="96 channel tip handling testing script."
-    )
-    parser.add_argument(
-        "--path_to_pipette_model",
-        type=str,
-        help="the csv filled with data to build a pipette model",
-        default=None,
-    )
-    parser.add_argument(
-        "--migrate_blowout_configs",
-        type=bool,
-        help="If true, migrate new blowout configs to existing json files",
-        default=False,
-    )
-
-    args = parser.parse_args()
-    if args.migrate_blowout_configs:
-        migrate_new_blow_out_configs_v2()
-    else:
-        using_csv = "" if args.path_to_pipette_model else "out"
-        print(f"Building new pipette function with{using_csv} using csv")
-
-        next_tip = True
-        pipette_functions_dict: Dict[str, Any] = {}
-        while next_tip:
-            print("Preparing pipetting function table from csv\n")
-            tip_volume = input("Please provide the next tip volume\n")
-            tiprack = input(
-                "Please provide the tiprack/tip type associated with this data\n"
-            )
-            path_to_data = input("Please provide the data path to the csv\n")
-            csv_dict = pipette_functions_dict.get(f"t{tip_volume}", {})
-            with open(path_to_data, "r") as f:
-                reader = csv.reader(f)
-                pipetting_key = None
-                for row in reader:
-                    current_key_exists = csv_dict.get(row[0])
-                    if row[0] == "aspirate" or row[0] == "dispense":
-                        pipetting_key = row[0]
-                        if current_key_exists:
-                            csv_dict[pipetting_key][f"{tiprack}"].append(
-                                [float(row[1]), float(row[2]), float(row[3])]
-                            )
-                        else:
-                            csv_dict[pipetting_key] = {
-                                f"{tiprack}": [
-                                    [float(row[1]), float(row[2]), float(row[3])]
-                                ]
-                            }
-                    elif pipetting_key and not row[0]:
-                        csv_dict[pipetting_key][f"{tiprack}"].append(
-                            [float(row[1]), float(row[2]), float(row[3])]
-                        )
-                    else:
-                        pipetting_key = None
-                        if current_key_exists:
-                            continue
-                        csv_dict[row[0]] = row[1]
-            pipette_functions_dict[f"t{tip_volume}"] = csv_dict
-            cont = input("Additional tips? Please enter y/n")
-
-            next_tip = cont == "y" or cont == "yes"
-        converted_pipette_functions_dict = {
-            k: build_supported_tips(d) for k, d in pipette_functions_dict.items()
-        }
-
-        print(
-            "Please review the aspirate and dispense functions once the pipette model is built.\n"
-        )
-        build_new_pipette_model_v2(
-            converted_pipette_functions_dict, args.path_to_pipette_model
-        )
-
-
-if __name__ == "__main__":
-    """
-    A script to automate building a pipette configuration definition.
-
-    This script can either perform migrations from a v1 -> v2 schema format
-    or build a brand new script from scratch.
-
-    When building a new pipette configuration model, you will either need
-    to provide CSVs or use command line inputs.
-
-    If you choose CSVs you will need one CSV for the general pipette configuration
-    data (such as pipette model or number of channels) and one for every tip
-    type that this pipette model can support.
-    """
-    main()