diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index f027315..3faa11a 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -12,12 +12,12 @@ repos: - id: end-of-file-fixer - id: trailing-whitespace - repo: https://github.com/kynan/nbstripout - rev: 0.6.1 + rev: 0.9.1 hooks: - id: nbstripout - repo: https://github.com/astral-sh/ruff-pre-commit # Ruff version. - rev: v0.14.1 + rev: v0.15.14 hooks: # Run the linter. - id: ruff diff --git a/Dockerfile b/Dockerfile index f952dce..fd9b8e4 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM ghcr.io/ad-sdl/madsci +FROM ghcr.io/ad-sdl/madsci:v0.8.0 LABEL org.opencontainers.image.source=https://github.com/AD-SDL/ot2_module LABEL org.opencontainers.image.description="Drivers and REST API's for the Opentrons OT2 LiquidHandling robots" @@ -13,10 +13,14 @@ RUN mkdir -p ot2_module COPY ./src ot2_module/src COPY ./README.md ot2_module/README.md COPY ./pyproject.toml ot2_module/pyproject.toml -COPY ./tests ot2_module/tests +# Install into the madsci venv (system pip would land in /usr/lib site-packages, +# invisible to the venv interpreter the entrypoint actually runs). RUN --mount=type=cache,target=/root/.cache \ - pip install -e ./ot2_module + uv pip install --python ${MADSCI_VENV}/bin/python -e ./ot2_module + +# Note: do not switch USER here — the base entrypoint runs userdel/useradd as +# root to remap UID/GID to the host's, then drops to the madsci user itself. CMD ["python", "ot2_module/src/ot2_rest_node.py"] diff --git a/definitions/otflex_template.node.yaml b/definitions/otflex_template.node.yaml new file mode 100644 index 0000000..c99d142 --- /dev/null +++ b/definitions/otflex_template.node.yaml @@ -0,0 +1,11 @@ +node_name: otflex_template +node_url: null +node_description: Template for a MADSci Opentrons OT2 node +node_type: device +module_name: otflex_module +module_version: 0.0.2 +capabilities: + admin_commands: [] +commands: {} +is_template: true +config_defaults: {} diff --git a/pdm.lock b/pdm.lock index bd7df65..4602db6 100644 --- a/pdm.lock +++ b/pdm.lock @@ -3,31 +3,35 @@ [metadata] groups = ["default", "dev"] -strategy = ["inherit_metadata"] +strategy = [] lock_version = "4.5.0" -content_hash = "sha256:a726396f25ca848299c4be5c3ed4a81013cc83cdf2c4ec02c88815b46604eab0" +content_hash = "sha256:def0dd6b33bac86cc0a6d4cc9a16bfdd0d4951af9af2a26863ecbcb17194cb3b" [[metadata.targets]] -requires_python = ">=3.9.1" +requires_python = ">=3.10" [[package]] name = "aenum" -version = "3.1.16" -summary = "Advanced Enumerations (compatible with Python's stdlib Enum), NamedTuples, and NamedConstants" -groups = ["default"] +version = "3.1.17" +summary = "" files = [ - {file = "aenum-3.1.16-py3-none-any.whl", hash = "sha256:9035092855a98e41b66e3d0998bd7b96280e85ceb3a04cc035636138a1943eaf"}, + {file = "aenum-3.1.17-py3-none-any.whl", hash = "sha256:8b883a37a04e74cc838ac442bdd28c266eae5bbf13e1342c7ef123ed25230139"}, + {file = "aenum-3.1.17.tar.gz", hash = "sha256:a969a4516b194895de72c875ece355f17c0d272146f7fda346ef74f93cf4d5ba"}, +] + +[[package]] +name = "annotated-doc" +version = "0.0.4" +summary = "" +files = [ + {file = "annotated_doc-0.0.4-py3-none-any.whl", hash = "sha256:571ac1dc6991c450b25a9c2d84a3705e2ae7a53467b5d111c24fa8baabbed320"}, + {file = "annotated_doc-0.0.4.tar.gz", hash = "sha256:fbcda96e87e9c92ad167c2e53839e57503ecfda18804ea28102353485033faa4"}, ] [[package]] name = "annotated-types" version = "0.7.0" -requires_python = ">=3.8" -summary = "Reusable constraint types to use with typing.Annotated" -groups = ["default"] -dependencies = [ - "typing-extensions>=4.0.0; 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Lewis", email="ryan.lewis@anl.gov"}, @@ -9,11 +9,11 @@ authors = [ {name = "Tobias Ginsburg", email = "tginsburg@anl.gov"}, ] dependencies = [ - "madsci.node_module~=0.5.0", - "madsci.client~=0.5.0", - "madsci.common~=0.5.0" + "madsci.node_module~=0.8.0", + "madsci.client~=0.8.0", + "madsci.common~=0.8.0" ] -requires-python = ">=3.9.1" +requires-python = ">=3.10" readme = "README.md" license = {text = "MIT"} diff --git a/scripts/delete_all_runs.py b/scripts/delete_all_runs.py index 7e28056..9d1fa00 100644 --- a/scripts/delete_all_runs.py +++ b/scripts/delete_all_runs.py @@ -1,4 +1,5 @@ """delete all runs""" + from argparse import ArgumentParser import requests diff --git a/src/ot2_interface/config.py b/src/ot2_interface/config.py index 3bb065d..04812f0 100644 --- a/src/ot2_interface/config.py +++ b/src/ot2_interface/config.py @@ -1,4 +1,5 @@ """Stores dataclasses/args/config for the ot2 drivers""" + import json from argparse import ArgumentParser, Namespace from pathlib import Path diff --git a/src/ot2_interface/ot2_driver_http.py b/src/ot2_interface/ot2_driver_http.py index 0511d32..d31a4bd 100644 --- a/src/ot2_interface/ot2_driver_http.py +++ b/src/ot2_interface/ot2_driver_http.py @@ -23,6 +23,7 @@ class RobotStatus(Enum): FAILED = "failed" PAUSED = "paused" OFFLINE = "offline" + STOPPED = "stopped" class RunStatus(Enum): diff --git a/src/ot2_interface/protopiler/config.py b/src/ot2_interface/protopiler/config.py index f33994c..dfeeb67 100644 --- a/src/ot2_interface/protopiler/config.py +++ b/src/ot2_interface/protopiler/config.py @@ -1,4 +1,5 @@ """Dataclasses and other configuration used in the protopiler""" + from pathlib import Path from typing import List, Literal, Optional, TypeVar, Union diff --git a/src/ot2_interface/protopiler/deconstructor.py b/src/ot2_interface/protopiler/deconstructor.py index c1cd8fb..8c060f3 100644 --- a/src/ot2_interface/protopiler/deconstructor.py +++ b/src/ot2_interface/protopiler/deconstructor.py @@ -1,4 +1,5 @@ """Deconstructor, parses a protocol and turns it into a config""" + import re import subprocess from argparse import ArgumentParser diff --git a/src/ot2_interface/protopiler/protopiler.py b/src/ot2_interface/protopiler/protopiler.py index 4f2fcc7..ea501a7 100644 --- a/src/ot2_interface/protopiler/protopiler.py +++ b/src/ot2_interface/protopiler/protopiler.py @@ -1,4 +1,5 @@ """Protopiler is designed to compile a config yaml into a working protocol""" + import argparse import copy from datetime import datetime @@ -7,6 +8,7 @@ from typing import Dict, Generator, List, Optional, Tuple, Union import pandas as pd + from ot2_interface.protopiler.config import ( Clear_Pipette, CommandBase, @@ -501,7 +503,7 @@ def yaml_to_protocol( "#location#", f'"{location}"' ) labware_command = labware_command.replace( - "#nickname#", f'{"module"}' + "#nickname#", f"{'module'}" ) labware_command = labware_command.replace( "#labware_name#", f'"{name}"' diff --git a/src/ot2_interface/protopiler/resource_manager.py b/src/ot2_interface/protopiler/resource_manager.py index 3a54608..665100d 100644 --- a/src/ot2_interface/protopiler/resource_manager.py +++ b/src/ot2_interface/protopiler/resource_manager.py @@ -1,4 +1,5 @@ """Class to manage/keep track of resources used by a protocol""" + import json import re from argparse import ArgumentParser diff --git a/src/ot2_interface/protopiler/test_configs/basic_config.py b/src/ot2_interface/protopiler/test_configs/basic_config.py index 2737708..a8f6938 100644 --- a/src/ot2_interface/protopiler/test_configs/basic_config.py +++ b/src/ot2_interface/protopiler/test_configs/basic_config.py @@ -1,4 +1,5 @@ """basic config module""" + from opentrons import protocol_api metadata = { diff --git a/src/ot2_rest_node.py b/src/ot2_rest_node.py index 7762069..2095d42 100644 --- a/src/ot2_rest_node.py +++ b/src/ot2_rest_node.py @@ -3,21 +3,28 @@ import traceback from pathlib import Path -from typing import Any, Optional +from typing import Any, ClassVar, Optional -from madsci.common.types.node_types import RestNodeConfig +from madsci.common.types.node_types import ( + NodeIntrinsicLocationDefinition, + NodeRepresentationTemplateDefinition, + RestNodeConfig, +) 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 ot2_interface.ot2_driver_http import OT2_Config, OT2_Driver + class OT2NodeConfig(RestNodeConfig): """Configuration for the OT2 node module.""" ot2_ip: Optional[str] = None "ip of opentrons device" + rate_limit_requests: int = 500 + "max number of requests per minute to the ot2 device" class OT2Node(RestNode): @@ -27,13 +34,69 @@ class OT2Node(RestNode): config: OT2NodeConfig = OT2NodeConfig() config_model = OT2NodeConfig + # Location representation templates — registered automatically by template_handler() + location_representation_templates: ClassVar[ + list[NodeRepresentationTemplateDefinition] + ] = [ + NodeRepresentationTemplateDefinition( + template_name="deck_nest_repr", + default_values={"capacity": 1}, + schema_def={ + "type": "object", + "properties": { + "capacity": { + "type": "integer", + "minimum": 1, + "description": "Number of plates the nest can hold", + }, + }, + }, + required_overrides=[], + tags=["deck", "nest"], + version="1.0.0", + description="OT-2 deck nest location template with capacity", + ), + ] + + # Intrinsic locations — auto-created on startup with '{node_name}.' prefix + intrinsic_locations: ClassVar[list[NodeIntrinsicLocationDefinition]] = [ + NodeIntrinsicLocationDefinition( + location_name="deck_nest_1", + description="OT-2 deck nest 1.", + representation_template_name="deck_nest_repr", + # resource_template_name="ot2_deck_slot", + allow_transfers=True, + ), + NodeIntrinsicLocationDefinition( + location_name="deck_nest_3", + description="OT-2 deck nest 3.", + representation_template_name="deck_nest_repr", + # resource_template_name="ot2_deck_slot", + allow_transfers=True, + ), + NodeIntrinsicLocationDefinition( + location_name="deck_nest_4_temp_block", + description="OT-2 deck nest 4 with temperature block.", + representation_template_name="deck_nest_repr", + # resource_template_name="ot2_deck_slot", + allow_transfers=True, + ), + NodeIntrinsicLocationDefinition( + location_name="deck_nest_6_temp_block", + description="OT-2 deck nest 6 with temperature block.", + representation_template_name="deck_nest_repr", + # resource_template_name="ot2_deck_slot", + allow_transfers=True, + ), + ] + def startup_handler(self) -> None: """Called to (re)initialize the node. Should be used to open connections to devices or initialize any other resources.""" self.logger.log("Node initializing...") temp_dir = Path.home() / ".madsci" / ".ot2_temp" temp_dir.mkdir(exist_ok=True) self.protocols_folder_path = str( - temp_dir / self.node_definition.node_name / "protocols/" + temp_dir / self.node_info.node_name / "protocols/" ) # Create templates self._create_ot2_templates() @@ -41,19 +104,18 @@ def startup_handler(self) -> None: # 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", + resource_name=f"{self.node_info.node_name}.deck", add_to_database=True, ) # 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}" + slot_name = f"{self.node_info.node_name}.deck.nest_{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, ) try: @@ -66,8 +128,7 @@ def startup_handler(self) -> None: 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, + resource_name=f"{self.node_info.node_name}.{mount}_mount", ) self.pipette_slots[mount] = mount_slot @@ -93,7 +154,7 @@ def _create_ot2_templates(self) -> None: capacity=12, attributes={ "deck_type": "OT2", - "slot_count": 12, + "nest_count": 12, "sbs_compatible": True, "description": "OT2 deck with 11 standard slots plus trash bin", }, @@ -105,7 +166,7 @@ def _create_ot2_templates(self) -> None: 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, + created_by=self.node_info.node_id, version="1.0.0", ) @@ -127,7 +188,7 @@ def _create_ot2_templates(self) -> None: 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, + created_by=self.node_info.node_id, version="1.0.0", ) @@ -148,7 +209,7 @@ def _create_ot2_templates(self) -> None: description="Template for OT2 trash bin slot.", required_overrides=["resource_name"], tags=["ot2", "trash", "stack"], - created_by=self.node_definition.node_id, + created_by=self.node_info.node_id, version="1.0.0", ) @@ -169,7 +230,7 @@ def _create_ot2_templates(self) -> None: description="Template for OT2 pipette mount slot.", required_overrides=["resource_name"], tags=["ot2", "pipette", "mount", "slot"], - created_by=self.node_definition.node_id, + created_by=self.node_info.node_id, version="1.0.0", ) @@ -196,7 +257,7 @@ def _create_ot2_templates(self) -> None: 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, + created_by=self.node_info.node_id, version="1.0.0", ) @@ -229,7 +290,7 @@ def _create_ot2_templates(self) -> None: 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, + created_by=self.node_info.node_id, version="1.0.0", ) @@ -265,7 +326,7 @@ def _create_ot2_templates(self) -> None: 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, + created_by=self.node_info.node_id, version="1.0.0", ) @@ -296,7 +357,7 @@ def _create_ot2_templates(self) -> None: 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, + created_by=self.node_info.node_id, version="1.0.0", ) @@ -333,7 +394,7 @@ def _create_ot2_templates(self) -> None: 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, + created_by=self.node_info.node_id, version="1.0.0", ) @@ -429,9 +490,7 @@ def execute(self, protocol_path, payload=None, resource_config=None): try: protocol_id, run_id = self.ot2_interface.transfer(protocol_file_path) self.logger.log( - "OT2 " - + self.node_definition.node_name - + " protocol transfer successful" + "OT2 " + self.node_info.node_name + " protocol transfer successful" ) self.run_id = run_id @@ -442,12 +501,12 @@ def execute(self, protocol_path, payload=None, resource_config=None): # poll_OT2_until_run_completion() self.logger.log( "OT2 " - + self.node_definition.node_name + + self.node_info.node_name + " succeeded in executing a protocol" ) response_msg = ( "OT2 " - + self.node_definition.node_name + + self.node_info.node_name + " successfully IDLE running a protocol" ) return "succeeded", response_msg, run_id @@ -455,12 +514,12 @@ def execute(self, protocol_path, payload=None, resource_config=None): elif resp["data"]["status"] == "stopped": self.logger.log( "OT2 " - + self.node_definition.node_name + + self.node_info.node_name + " stopped while executing a protocol" ) response_msg = ( "OT2 " - + self.node_definition.node_name + + self.node_info.node_name + " successfully IDLE after stopping a protocol" ) return "stopped", response_msg, run_id @@ -468,13 +527,13 @@ def execute(self, protocol_path, payload=None, resource_config=None): else: self.logger.log( "OT2 " - + self.node_definition.node_name + + self.node_info.node_name + " failed in executing a protocol" ) self.logger.log(resp["data"]) response_msg = ( "OT2 " - + self.node_definition.node_name + + self.node_info.node_name + " failed running a protocol\n" + str(resp["data"]) ) diff --git a/src/otflex_rest_node.py b/src/otflex_rest_node.py new file mode 100644 index 0000000..9bed32e --- /dev/null +++ b/src/otflex_rest_node.py @@ -0,0 +1,616 @@ +#! /usr/bin/env python3 +"""OT-FLex Node Module implementation""" + +import traceback +from pathlib import Path +from typing import Any, ClassVar, Optional + +from madsci.common.types.node_types import ( + NodeIntrinsicLocationDefinition, + NodeRepresentationTemplateDefinition, + RestNodeConfig, +) +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 typing_extensions import Annotated + +from ot2_interface.ot2_driver_http import OT2_Config, OT2_Driver + + +class OT2NodeConfig(RestNodeConfig): + """Configuration for the OT2 node module.""" + + ot2_ip: Optional[str] = None + "ip of opentrons device" + rate_limit_requests: int = 500 + "max number of requests per minute to the ot2 device" + + +class OT2Node(RestNode): + """Node module for Opentrons Robots""" + + ot2_interface: OT2_Driver = None + config: OT2NodeConfig = OT2NodeConfig() + config_model = OT2NodeConfig + + # Location representation templates — registered automatically by template_handler() + location_representation_templates: ClassVar[ + list[NodeRepresentationTemplateDefinition] + ] = [ + NodeRepresentationTemplateDefinition( + template_name="deck_nest_repr", + default_values={"capacity": 1}, + schema_def={ + "type": "object", + "properties": { + "capacity": { + "type": "integer", + "minimum": 1, + "description": "Number of plates the nest can hold", + }, + }, + }, + required_overrides=[], + tags=["deck", "nest"], + version="1.0.0", + description="OT-Flex deck nest location template with capacity", + ), + ] + + # Intrinsic locations — auto-created on startup with '{node_name}.' prefix + intrinsic_locations: ClassVar[list[NodeIntrinsicLocationDefinition]] = [ + NodeIntrinsicLocationDefinition( + location_name="deck_nest_A4", + description="OT-Flex deck nest A4.", + representation_template_name="deck_nest_repr", + allow_transfers=True, + ), + NodeIntrinsicLocationDefinition( + location_name="deck_nest_B4", + description="OT-Flex deck nest B4.", + representation_template_name="deck_nest_repr", + allow_transfers=True, + ), + ] + + def startup_handler(self) -> None: + """Called to (re)initialize the node. Should be used to open connections to devices or initialize any other resources.""" + self.logger.log("Node initializing...") + temp_dir = Path.home() / ".madsci" / ".ot2_temp" + temp_dir.mkdir(exist_ok=True) + self.protocols_folder_path = str( + temp_dir / self.node_info.node_name / "protocols/" + ) + # 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"{self.node_info.node_name}.deck", + add_to_database=True, + ) + + # Create 12 deck slots (1-11 standard, 12 is trash) + for i in range(1, 13): + slot_name = f"{self.node_info.node_name}.deck.nest_{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, + ) + + 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"{self.node_info.node_name}.{mount}_mount", + ) + 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 + + self.run_id = None + self.startup_has_run = True + self.logger.info("OT-Flex 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", + "nest_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_info.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_info.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_info.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_info.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_info.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_info.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_info.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_info.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_info.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.""" + self.logger.log("Shutting down") + self.shutdown_has_run = True + del self.ot2_interface + self.ot2_interface = None + self.logger.log("Shutdown complete.") + + 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 = { + "otflex_status_code": self.ot2_interface.get_robot_status(), + } + + @action(name="run_protocol", description="run a given opentrons protocol") + def run_protocol( + self, + protocol: Annotated[Path, "Protocol File"], + parameters: Annotated[ + 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 + """ + # TODO: if use existing resources.... (find and use a ot2 json file) + + # get the next protocol file + + if protocol: + with protocol.open(mode="r") as f: + file_text = f.read() + for key in parameters.keys(): + file_text = file_text.replace("$" + key, str(parameters[key])) + with protocol.open(mode="w") as f: + f.write(file_text) + response_flag, response_msg, run_id = self.execute(protocol, parameters) + if self.resource_client is not None: + self.parse_logs(self.ot2_interface.get_run_log(run_id)) + + if response_flag == "succeeded": + # TODO logging + 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.SUCCEEDED, files={"log": f.name} + # ) + # if resource_config_path: + # response.resources = str(resource_config_path) + 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}) + raise Exception("Run was stopped") + elif response_flag == "failed": + pass + # response = StepResponse() + # response.status = StepStatus.FAILED + # response.error = "an error occurred" + # if resource_config_path: + # response.resources = str(resource_config_path) + raise Exception("Run failed: " + response_msg) + else: + raise Exception("No protocol file found") + + def execute(self, protocol_path, payload=None, resource_config=None): + """ + Transfers and Executes the .py protocol file + + Parameters: + ----------- + protocol_path: str + absolute path to the yaml protocol + + Returns + ----------- + response: bool + If the ot2 execution was successful + """ + + protocol_file_path = Path(protocol_path) + self.logger.log(f"{protocol_file_path.resolve()=}") + try: + protocol_id, run_id = self.ot2_interface.transfer(protocol_file_path) + self.logger.log( + "OT2 " + self.node_info.node_name + " protocol transfer successful" + ) + + self.run_id = run_id + resp = self.ot2_interface.execute(run_id) + self.run_id = None + print(resp) + if resp["data"]["status"] == "succeeded": + # poll_OT2_until_run_completion() + self.logger.log( + "OT2 " + + self.node_info.node_name + + " succeeded in executing a protocol" + ) + response_msg = ( + "OT2 " + + self.node_info.node_name + + " successfully IDLE running a protocol" + ) + return "succeeded", response_msg, run_id + + elif resp["data"]["status"] == "stopped": + self.logger.log( + "OT2 " + + self.node_info.node_name + + " stopped while executing a protocol" + ) + response_msg = ( + "OT2 " + + self.node_info.node_name + + " successfully IDLE after stopping a protocol" + ) + return "stopped", response_msg, run_id + + else: + self.logger.log( + "OT2 " + + self.node_info.node_name + + " failed in executing a protocol" + ) + self.logger.log(resp["data"]) + response_msg = ( + "OT2 " + + self.node_info.node_name + + " failed running a protocol\n" + + str(resp["data"]) + ) + return "failed", response_msg, run_id + except Exception as err: + if "no route to host" in str(err.args).lower(): + response_msg = "No route to host error. Ensure that this container \ + has network access to the robot and that the environment \ + variable, robot_ip, matches the ip of the connected robot \ + on the shared LAN." + self.logger.log(response_msg) + + response_msg = f"Error: {traceback.format_exc()}" + print(response_msg) + return False, response_msg, None + + def pause(self) -> None: + """Pause the node.""" + self.logger.log("Pausing node...") + self.ot2_interface.pause(self.run_id) + self.node_status.paused = True + self.logger.log("Node paused.") + return True + + def resume(self) -> None: + """Resume the node.""" + self.logger.log("Resuming node...") + self.ot2_interface.resume(self.run_id) + self.node_status.paused = False + self.logger.log("Node resumed.") + return True + + # TODO: shutdown, safety stop, reset + def shutdown(self) -> None: + """Shutdown the node.""" + self.shutdown_handler() + return True + + def reset(self) -> None: + """Reset the node.""" + self.logger.log("Resetting node...") + result = super().reset() + self.logger.log("Node reset.") + return result + + def safety_stop(self) -> None: + """Stop the node.""" + self.logger.log("Stopping node...") + self.node_status.stopped = True + self.logger.log("Node stopped.") + return True + + def cancel(self) -> None: + """Cancel the node.""" + self.logger.log("Canceling node...") + self.ot2_interface.cancel(self.run_id) + self.node_status.cancelled = True + self.logger.log("Node cancelled.") + return True + + def find_resource(self, logs: Any, command: Any): + """Extract resource information from logs""" + labwares = logs["data"]["labware"] + labware_id = command["params"]["labwareId"] + labware = next(labware for labware in labwares if labware["id"] == labware_id) + resource = self.deck_slots[labware["location"]["slotName"]] + return resource + + def parse_logs(self, logs: Any): + """Extract useful information from the ot2's logs""" + try: + for command in logs["commands"]["data"]: + if command["commandType"] == "aspirate": + resource = self.find_resource(logs, command) + print(resource) + # self.resource_client.decrease_resource(command["params"]["volume"]) + elif command["commandType"] == "dispense": + resource = self.find_resource(logs, command) + print(resource) + # self.resource_client.decrease_resource(command["params"]["volume"]) + elif command["commandType"] == "pickUpTip": + resource = self.find_resource(logs, command) + + print(resource) + elif command["commandType"] == "dropTip": + resource = self.find_resource(logs, command) + + print(resource) + # self.resource_client.decrease_resource(command["params"]["volume"]) + except Exception: + print("Couldn't update resources, no longer tracked") + + +if __name__ == "__main__": + ot2_node = OT2Node() + ot2_node.start_node()