========================== Beckman Biomek Driver Page ========================== This page has all the information specific to the Beckman Biomek driver and adapter. Supported Beckman Biomek versions --------------------------------- Beckman Biomek 5.1.10 Beckman Biomek Installer ------------------------ You can download the latest installer `here `_. Beckman Biomek Adapter :file:`config.yaml` File ----------------------------------------------- .. code-block:: yaml :caption: :file:`config.yaml` log: level: "DEBUG" loggerLevels: - logger: "tutorial" level: "DEBUG" artificial: host: your-instance.artificial.com lab: lab_1a2b3c-4d5e-6f7g-8h9i-123456abcdef adapter: name: BiomekTutorialAdapter remoteConfig: False allowAnySequenceId: True # Useful when running in a local dev container plugin: # all resources this adapter can connect to resource: name: "Biomek i7" # user friendly name, unique in the adapter id: "asset_name" driver: name: "biomek" # Driver name, this is a non-configurable string that needs to match the driver identity url: "http://biomek.webaddress.com:49835" # URL of the hardware and driver resource_simulation: false # Set to true to run simulation without hardware driver_simulation: false # Set to true to run simulation without a driver cert_file: "adapter/certs/ca.crt" workspace_name: "C:/biomek_files/Biomek i7.bif" # Modify to use desired workspace name asset_sync: devices: # device string names/prefix must match resource id above "asset_name": { rid: "d1234567-34d0-4391-be64-7aef4e0b28be" } #. Fill in the correct URL and port for the Biomek device. (The IPv4 URL can be obtained on the device by running ipconfig in a command window. The port is listed in the running driver server window). #. Fill in the workspace path to match the installation location on the Biomek device. #. You may update the resource name above if you wish (any unique string will work). #. If you wish to run in simulation without hardware or without a driver, change resource_simulation or driver_simulation to true, respectively. #. Under asset_sync, match at least one of your devices to a Digital Twin asset ID. You can fill out the rest of the devices later. Consult the corresponding step in :doc:`tutorial_adapter_hardware_setup`. #. Update the artificial section to the correct host and lab. Consult the corresponding step in :doc:`tutorial_adapter_hardware_setup` for how to do this. Beckman Biomek Adapter :file:`adapter/main/plugin.py` File ---------------------------------------------------------- .. code-block:: python :caption: :file:`adapter/main/plugin.py` file from artificial.adapter_common import ActionModulePlugin, ability_name, action_modules from artificial.adapter_common.plugin import PluginContext, plugin_config from artificial.biomek.actions import BiomekActions from artificial.biomek.core import BiomekResource from artificial.biomek.event_handler import BiomekEventHandler from artificial.biomek.models import PluginConfig from artificial.logging import get_logger from artificial.resource_base.asset_syncer import ResourceAssetSyncer from artificial.resource_base.models import SyncConfig # from .simulators.labware_simulator import BiomekDriverLabwareMock as LabwareSimulator logger = get_logger(__name__) @ability_name('biomek') @action_modules(BiomekActions) class AdapterPlugin(ActionModulePlugin): """assemble resources components with resource configuration""" _cfg = plugin_config(PluginConfig) # this will make PluginConfig show up in the adapter config UI async def setup(self, pctx: PluginContext) -> None: prog_config = pctx.config plugin_conf = self._cfg sync_config: SyncConfig = pctx.raw_config.to_dataclass(SyncConfig, 'adapter.asset_sync') logger.debug(f'sync_config loaded: {sync_config}') # all resources in the adapter use the same res_syncer syncer = pctx.asset_sync_manager_v1(f'ResourceSyncer-{prog_config.adapter.name}') res_syncer = ResourceAssetSyncer(syncer, sync_config) await res_syncer.initialize() # create instances of resources for this adapter resource = BiomekResource( pctx.alabPyBase, lab_id=prog_config.artificial.labId, adapter_id=prog_config.adapter.name, resource_id=plugin_conf.resource.id, name=plugin_conf.resource.name, res_syncer=res_syncer, ) if resource: resource.set_driver(driver_config=plugin_conf.resource.driver, simulator=None) await resource.set_health_monitors(pctx.lab.health) module = BiomekActions(resource) self.add_module(module) # subscribe the driver events event_handler = BiomekEventHandler(resource) resource.add_event_handler(event_handler) Beckman Biomek Adapter :file:`adapter/main/__main__.py` File ------------------------------------------------------------ Copy the following list of actors into the file in place of the example actors. .. code-block:: python actors = [ ActorConfig(id='biomek', abilities={'run_protocol': 1, 'substrate': 1, 'biomek': 1}), ] Beckman Biomek Adapter :file:`pyproject.toml` Dependencies ----------------------------------------------------------------------------- Run ``uv add artificial-biomek-adapter==1.1.*`` in the terminal to add the required packages to the :code:`[project]` section. Your :file:`pyproject.toml` file should now include ``artificial-biomek-adapter`` in the project dependencies section: .. code-block:: python [project] dependencies = [ "artificial-biomek-adapter==1.1.*" ] Beckman Biomek Simple Connectivity Workflow ------------------------------------------- This workflow will run a method of your choosing and log a message in the UI upon successful completion. You will define which method to run in the request UI by inputting the method name with its full path (e.g., :file:`C://Methods//mymethod.med`). A couple of notes: #. After copying this code into a file, remember to replace the lab_guid in the workflow heading with the one from your Lab (most easily found by opening the Lab in Artificial and looking in the browser address bar). Consult :doc:`tutorial_adding_tutorial_workflow` for more info. #. Update the variables in the Workflow to match your protocol. .. code-block:: python from typing import List from artificial.workflows.decorators import parameter, workflow from artificial.workflows.runtime import show_info from stubs.stubs_actions import VariableType, run_protocol_to_completion @workflow('Simple Biomek Connectivity Test Workflow', 'simple_biomek_connectivity_test_workflow', 'lab_8ff750d9-b8c9-4a1b-b433-05437ce87ef2', interactive=True, quick=True) @parameter('biomek_method_name', {'required': True, 'uiTitle': 'Biomek Method Name'}) async def simple_biomek_connectivity_test_workflow(biomek_method_name: str = 'alab-test') -> None: params: List[VariableType] = [ VariableType(var_name='run_now', var_value='true', var_type='TrueFalse'), VariableType(var_name='nplates', var_value='2', var_type='Numeric'), ] await run_protocol_to_completion(biomek_method_name, params) # when no path specified, driver's workspace is used await show_info('Congratulations, you successfully ran your hardware!', 'Hardware Success')