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"sha256:a07157588a12518c9d4034df3fbbee09c814741a33ff63c05fa29d26a2404166"}, +] diff --git a/pyproject.toml b/pyproject.toml index 47f83ff..469fe96 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -9,8 +9,9 @@ authors = [ {name = "Tobias Ginsburg", email = "tginsburg@anl.gov"}, ] dependencies = [ - "madsci.node_module>=0.1.9", - "pandas" + "madsci.node_module~=0.5.0", + "madsci.client~=0.5.0", + "madsci.common~=0.5.0" ] requires-python = ">=3.9.1" readme = "README.md" diff --git a/src/ot2_interface/ot2_driver_http.py b/src/ot2_interface/ot2_driver_http.py index fff26fa..0511d32 100644 --- a/src/ot2_interface/ot2_driver_http.py +++ b/src/ot2_interface/ot2_driver_http.py @@ -1,4 +1,5 @@ """Driver implemented using HTTP protocol supported by Opentrons""" + import subprocess import time from enum import Enum @@ -7,9 +8,10 @@ import requests import yaml +from urllib3 import Retry + from ot2_interface.config import OT2_Config, PathLike, parse_ot2_args from ot2_interface.protopiler.protopiler import ProtoPiler -from urllib3 import Retry class RobotStatus(Enum): @@ -157,7 +159,9 @@ def transfer(self, protocol_path: PathLike) -> Tuple[str, str]: # create the run run_url = f"{self.base_url}/runs" run_json = {"data": {"protocolId": protocol_id}} - run_resp = requests.post(url=run_url, headers=self.headers, json=run_json) + run_resp = requests.post( + url=run_url, headers=self.headers, json=run_json, timeout=60 + ) run_id = run_resp.json()["data"]["id"] diff --git a/src/ot2_rest_node.py b/src/ot2_rest_node.py index 9867feb..7762069 100644 --- a/src/ot2_rest_node.py +++ b/src/ot2_rest_node.py @@ -3,39 +3,28 @@ import traceback from pathlib import Path -from typing import Any -from urllib.error import HTTPError, URLError +from typing import Any, Optional -import requests -from madsci.client.resource_client import ResourceClient -from madsci.common.types.action_types import ActionFailed, ActionSucceeded -from madsci.common.types.auth_types import OwnershipInfo from madsci.common.types.node_types import RestNodeConfig -from madsci.common.types.resource_types.definitions import ( - ContainerResourceDefinition, - SlotResourceDefinition, -) +from madsci.common.types.resource_types import Container, Pool, Slot, Stack from madsci.node_module.helpers import action from madsci.node_module.rest_node_module import RestNode from ot2_interface.ot2_driver_http import OT2_Config, OT2_Driver from typing_extensions import Annotated -from urllib3.exceptions import ConnectTimeoutError class OT2NodeConfig(RestNodeConfig): """Configuration for the OT2 node module.""" - __test__ = False - - ot2_ip: str + ot2_ip: Optional[str] = None "ip of opentrons device" class OT2Node(RestNode): """Node module for Opentrons Robots""" - __test__ = False - ot2_interface: OT2_Driver + ot2_interface: OT2_Driver = None + config: OT2NodeConfig = OT2NodeConfig() config_model = OT2NodeConfig def startup_handler(self) -> None: @@ -46,60 +35,307 @@ def startup_handler(self) -> None: self.protocols_folder_path = str( temp_dir / self.node_definition.node_name / "protocols/" ) - if self.config.resource_server_url: - self.resource_client = ResourceClient(self.config.resource_server_url) - self.resource_owner = OwnershipInfo(node_id=self.node_definition.node_id) - self.deck = self.resource_client.init_resource( - ContainerResourceDefinition( - resource_name="ot2_" + self.node_definition.node_name + "_deck", - owner=self.resource_owner, - ) - ) + # Create templates + self._create_ot2_templates() + + # Create deck instance + self.deck = self.resource_client.create_resource_from_template( + template_name="ot2_deck", + resource_name=f"ot2_{self.node_definition.node_name}_deck", + add_to_database=True, + ) - for i in range(1, 13): - rec_def = SlotResourceDefinition( - resource_name="ot2_" - + self.node_definition.node_name - + "_deck" - + str(i), - owner=self.resource_owner, - ) - try: - self.resource_client.set_child( - self.deck, str(i), self.resource_client.init_resource(rec_def) - ) - except Exception: - print("Already has child") - self.pipette_slots = {} - self.pipette_slots["left"] = self.resource_client.init_resource( - SlotResourceDefinition( - resource_name="ot2_" - + self.node_definition.node_name - + "_left_pipette_slot", - owner=self.resource_owner, - ) + # Create 12 deck slots (1-11 standard, 12 is trash) + for i in range(1, 13): + slot_name = f"ot2_{self.node_definition.node_name}_deck_slot_{i}" + template_name = "ot2_trash_slot" if i == 12 else "ot2_deck_slot" + + slot = self.resource_client.create_resource_from_template( + template_name=template_name, + resource_name=slot_name, + add_to_database=True, ) - self.pipette_slots["right"] = self.resource_client.init_resource( - SlotResourceDefinition( - resource_name="ot2_" - + self.node_definition.node_name - + "_right_pipette_slot", - owner=self.resource_owner, - ) + + try: + self.resource_client.set_child(self.deck, str(i), slot) + except Exception: + self.logger.log(f"Deck slot {i} already exists") + + # Create pipette mount slots + self.pipette_slots = {} + for mount in ["left", "right"]: + mount_slot = self.resource_client.create_resource_from_template( + template_name="ot2_pipette_mount", + resource_name=f"ot2_{self.node_definition.node_name}_{mount}_mount", + add_to_database=True, ) + self.pipette_slots[mount] = mount_slot + + if self.config.ot2_ip is None: + raise ValueError("OT2 IP address is not configured.") + try: + self.ot2_interface = OT2_Driver(OT2_Config(ip=self.config.ot2_ip)) + except Exception as e: + self.logger.error(f"Failed to connect to OT2: {e}") + raise e - else: - self.resource_client = None - self.deck_slots = None - # TODO: eventual path for resources? - # TODO: setup logs folder path? self.run_id = None - self.ip = self.config.ot2_ip - # TODO: check if resource and protocols folders exist, if not create them - self.ot2_interface = None - self.connect_robot() self.startup_has_run = True - self.logger.log("OT2 node initialized!") + self.logger.info("OT2 node initialized!") + + def _create_ot2_templates(self) -> None: + """Create all OT2-specific resource templates.""" + + # 0. Deck container template + deck_container = Container( + resource_name="ot2_deck", + resource_class="OT2Deck", + capacity=12, + attributes={ + "deck_type": "OT2", + "slot_count": 12, + "sbs_compatible": True, + "description": "OT2 deck with 11 standard slots plus trash bin", + }, + ) + + self.resource_client.init_template( + resource=deck_container, + template_name="ot2_deck", + description="Template for OT2 deck container. Holds 11 deck slots plus trash bin.", + required_overrides=["resource_name"], + tags=["ot2", "deck", "container"], + created_by=self.node_definition.node_id, + version="1.0.0", + ) + + # 1. Deck slot template (standard slots 1-11) + deck_slot = Slot( + resource_name="ot2_deck_slot", + resource_class="OT2DeckSlot", + capacity=1, + attributes={ + "slot_type": "deck_position", + "sbs_compatible": True, + "description": "OT2 deck slot for labware", + }, + ) + + self.resource_client.init_template( + resource=deck_slot, + template_name="ot2_deck_slot", + description="Template for OT2 deck slot. Standard SBS-compatible position.", + required_overrides=["resource_name"], + tags=["ot2", "deck", "slot"], + created_by=self.node_definition.node_id, + version="1.0.0", + ) + + # 2. Trash bin template (slot 12) - Stack type for collecting tips/waste + trash_bin = Stack( + resource_name="ot2_trash", + resource_class="OT2TrashBin", + attributes={ + "container_type": "trash_bin", + "removable": True, + "description": "OT2 removable trash bin at slot 12", + }, + ) + + self.resource_client.init_template( + resource=trash_bin, + template_name="ot2_trash_slot", + description="Template for OT2 trash bin slot.", + required_overrides=["resource_name"], + tags=["ot2", "trash", "stack"], + created_by=self.node_definition.node_id, + version="1.0.0", + ) + + # 3. Pipette mount template + pipette_mount = Slot( + resource_name="ot2_pipette_mount", + resource_class="OT2PipetteMount", + capacity=1, + attributes={ + "mount_type": "pipette_mount", + "description": "OT2 pipette mount (left or right)", + }, + ) + + self.resource_client.init_template( + resource=pipette_mount, + template_name="ot2_pipette_mount", + description="Template for OT2 pipette mount slot.", + required_overrides=["resource_name"], + tags=["ot2", "pipette", "mount", "slot"], + created_by=self.node_definition.node_id, + version="1.0.0", + ) + + # 4. P20 Single-Channel Pipette + p20_single = Pool( + resource_name="ot2_p20_single", + resource_class="OT2_P20_Single", + capacity=20.0, + attributes={ + "pipette_type": "p20_single_gen2", + "channels": 1, + "min_volume": 1.0, + "max_volume": 20.0, + "accuracy_1ul": {"random_error_pct": 15.0, "systematic_error_pct": 5.0}, + "accuracy_10ul": {"random_error_pct": 2.0, "systematic_error_pct": 1.0}, + "accuracy_20ul": {"random_error_pct": 1.5, "systematic_error_pct": 0.8}, + "description": "P20 Single-Channel pipette (1-20 µL)", + }, + ) + + self.resource_client.init_template( + resource=p20_single, + template_name="ot2_p20_single_pipette", + description="Template for OT2 P20 Single-Channel pipette (1-20 µL).", + required_overrides=["resource_name"], + tags=["ot2", "pipette", "p20", "single-channel", "pool"], + created_by=self.node_definition.node_id, + version="1.0.0", + ) + + # 5. P300 Single-Channel Pipette + p300_single = Pool( + resource_name="ot2_p300_single", + resource_class="OT2_P300_Single", + capacity=300.0, + attributes={ + "pipette_type": "p300_single_gen2", + "channels": 1, + "min_volume": 20.0, + "max_volume": 300.0, + "accuracy_20ul": {"random_error_pct": 4.0, "systematic_error_pct": 2.5}, + "accuracy_150ul": { + "random_error_pct": 1.0, + "systematic_error_pct": 0.4, + }, + "accuracy_300ul": { + "random_error_pct": 0.6, + "systematic_error_pct": 0.3, + }, + "description": "P300 Single-Channel pipette (20-300 µL)", + }, + ) + + self.resource_client.init_template( + resource=p300_single, + template_name="ot2_p300_single_pipette", + description="Template for OT2 P300 Single-Channel pipette (20-300 µL).", + required_overrides=["resource_name"], + tags=["ot2", "pipette", "p300", "single-channel", "pool"], + created_by=self.node_definition.node_id, + version="1.0.0", + ) + + # 6. P1000 Single-Channel Pipette + p1000_single = Pool( + resource_name="ot2_p1000_single", + resource_class="OT2_P1000_Single", + capacity=1000.0, + attributes={ + "pipette_type": "p1000_single_gen2", + "channels": 1, + "min_volume": 100.0, + "max_volume": 1000.0, + "accuracy_100ul": { + "random_error_pct": 2.0, + "systematic_error_pct": 1.0, + }, + "accuracy_500ul": { + "random_error_pct": 1.0, + "systematic_error_pct": 0.2, + }, + "accuracy_1000ul": { + "random_error_pct": 0.7, + "systematic_error_pct": 0.15, + }, + "description": "P1000 Single-Channel pipette (100-1000 µL)", + }, + ) + + self.resource_client.init_template( + resource=p1000_single, + template_name="ot2_p1000_single_pipette", + description="Template for OT2 P1000 Single-Channel pipette (100-1000 µL).", + required_overrides=["resource_name"], + tags=["ot2", "pipette", "p1000", "single-channel", "pool"], + created_by=self.node_definition.node_id, + version="1.0.0", + ) + + # 7. P20 8-Channel Pipette + p20_multi = Pool( + resource_name="ot2_p20_multi", + resource_class="OT2_P20_Multi", + capacity=20.0, + attributes={ + "pipette_type": "p20_multi_gen2", + "channels": 8, + "min_volume": 1.0, + "max_volume": 20.0, + "accuracy_1ul": { + "random_error_pct": 20.0, + "systematic_error_pct": 10.0, + }, + "accuracy_10ul": {"random_error_pct": 3.0, "systematic_error_pct": 2.0}, + "accuracy_20ul": {"random_error_pct": 2.2, "systematic_error_pct": 1.5}, + "fill_96well_time_seconds": 22, + "description": "P20 8-Channel pipette (1-20 µL)", + }, + ) + + self.resource_client.init_template( + resource=p20_multi, + template_name="ot2_p20_multi_pipette", + description="Template for OT2 P20 8-Channel pipette (1-20 µL).", + required_overrides=["resource_name"], + tags=["ot2", "pipette", "p20", "8-channel", "multi-channel", "pool"], + created_by=self.node_definition.node_id, + version="1.0.0", + ) + + # 8. P300 8-Channel Pipette + p300_multi = Pool( + resource_name="ot2_p300_multi", + resource_class="OT2_P300_Multi", + capacity=300.0, + attributes={ + "pipette_type": "p300_multi_gen2", + "channels": 8, + "min_volume": 20.0, + "max_volume": 300.0, + "accuracy_20ul": { + "random_error_pct": 10.0, + "systematic_error_pct": 4.0, + }, + "accuracy_150ul": { + "random_error_pct": 2.5, + "systematic_error_pct": 0.8, + }, + "accuracy_300ul": { + "random_error_pct": 1.5, + "systematic_error_pct": 0.5, + }, + "fill_96well_time_seconds": 26, + "description": "P300 8-Channel pipette (20-300 µL)", + }, + ) + + self.resource_client.init_template( + resource=p300_multi, + template_name="ot2_p300_multi_pipette", + description="Template for OT2 P300 8-Channel pipette (20-300 µL).", + required_overrides=["resource_name"], + tags=["ot2", "pipette", "p300", "8-channel", "multi-channel", "pool"], + created_by=self.node_definition.node_id, + version="1.0.0", + ) def shutdown_handler(self) -> None: """Called to shutdown the node. Should be used to close connections to devices or release any other resources.""" @@ -113,34 +349,9 @@ def state_handler(self) -> None: """Periodically called to update the current state of the node.""" if self.ot2_interface is not None: self.node_state = { - # "test_status_code": self.ot2_interface.status_code, + "ot2_status_code": self.ot2_interface.get_robot_status(), } - def connect_robot(self) -> None: - """Description: Connects to the ot2""" - try: - self.ot2_interface = OT2_Driver(OT2_Config(ip=self.config.ot2_ip)) - - except ConnectTimeoutError as connection_err: - self.node_status.errored = True - print("Connection error code: " + connection_err) - - except HTTPError as http_error: - print("HTTP error code: " + http_error) - - except URLError as url_err: - print("Url error code: " + url_err) - - except requests.exceptions.ConnectionError as conn_err: - print("Connection error code: " + str(conn_err)) - - except Exception as error_msg: - self.node_status.errored = True - print("-------" + str(error_msg) + " -------") - - else: - self.logger.log("OT2 node online") - @action(name="run_protocol", description="run a given opentrons protocol") def run_protocol( self, @@ -149,7 +360,7 @@ def run_protocol( dict[str, Any], "Parameters for insertion into the protocol" ] = {}, # TODO: whether or not to use existing resources? - ): + ) -> Annotated[dict[str, Any], "ot2 action log"]: """ Run a given protocol on the ot2 """ @@ -168,7 +379,6 @@ def run_protocol( if self.resource_client is not None: self.parse_logs(self.ot2_interface.get_run_log(run_id)) - response = ActionFailed() if response_flag == "succeeded": # TODO logging pass @@ -180,16 +390,14 @@ def run_protocol( # ) # if resource_config_path: # response.resources = str(resource_config_path) - response = ActionSucceeded( - data={"log_value": self.ot2_interface.get_run_log(run_id)} - ) + return self.ot2_interface.get_run_log(run_id) elif response_flag == "stopped": pass # Path(logs_folder_path).mkdir(parents=True, exist_ok=True) # with open(Path(logs_folder_path) / f"{run_id}.json", "w") as f: # json.dump(state.ot2.get_run_log(run_id), f, indent=2) # return StepFileResponse(status=StepStatus.FAILED, files={"log": f.name}) - response = ActionFailed() + raise Exception("Run was stopped") elif response_flag == "failed": pass # response = StepResponse() @@ -197,13 +405,9 @@ def run_protocol( # response.error = "an error occurred" # if resource_config_path: # response.resources = str(resource_config_path) - response = ActionFailed() - return response + raise Exception("Run failed: " + response_msg) else: - response["action_msg"] = "Required 'protocol' file was not provided" - print(response.action_msg) - - return response + raise Exception("No protocol file found") def execute(self, protocol_path, payload=None, resource_config=None): """