bug: Cannot use Jupyter Notebook to communicate with the device on v8.0.0

[smeng9]

Overview

Our lab need access to the opentrons' Jupyter notebook server to run some automated protocol.

However we cannot connect to the device because it is always busy. Additionally a few files like /data/robot_settings.json are missing.

Steps to reproduce

We followed the steps on https://docs.opentrons.com/v2/new_advanced_running.html?highlight=jupyter#protocol-structure to create a new cell with the following content

import opentrons.execute
protocol = opentrons.execute.get_protocol_api("2.20")
protocol.home()

However it did not run and throws the following error below.

Current behavior

/data/robot_settings.json not found. Loading defaults
Exception in Thread Manager build
Traceback (most recent call last):
File "/opt/opentrons-robot-server/opentrons/hardware_control/thread_manager.py", line 314, in _build_and_start_loop
managed_obj = loop.run_until_complete(builder(*args, loop=loop, **kwargs))
File "/usr/lib/python3.10/asyncio/base_events.py", line 649, in run_until_complete
return future.result()
File "/opt/opentrons-robot-server/opentrons/hardware_control/ot3api.py", line 382, in build_hardware_controller
backend = await OT3Controller.build(
File "/opt/opentrons-robot-server/opentrons/hardware_control/backends/ot3controller.py", line 294, in build
inst = cls(
File "/opt/opentrons-robot-server/opentrons/hardware_control/backends/ot3controller.py", line 323, in init
self._drivers = self._build_system_hardware(
File "/opt/opentrons-robot-server/opentrons/hardware_control/backends/ot3controller.py", line 448, in _build_system_hardware
gpio = OT3GPIO("hardware_control")
File "/opt/opentrons-robot-server/opentrons_hardware/drivers/gpio/init.py", line 50, in init
self._estop_out_line.request(
OSError: [Errno 16] Device or resource busy
from_conf None default {<InstrumentProbeType.PRIMARY: 1>: '/data/pressure_sensor_data.csv'}

---

ThreadManagerException Traceback (most recent call last)
Input In [3], in <cell line: 2>()
1 import opentrons.execute
----> 2 protocol = opentrons.execute.get_protocol_api("2.19")

File /opt/opentrons-robot-server/opentrons/execute.py:180, in get_protocol_api(version, bundled_labware, bundled_data, extra_labware)
177 robot_type = _get_robot_type()
178 deck_type = guess_deck_type_from_global_config()
--> 180 hardware_controller = _get_global_hardware_controller(robot_type)
182 if checked_version < ENGINE_CORE_API_VERSION:
183 context = _create_live_context_non_pe(
184 api_version=checked_version,
185 deck_type=deck_type,
(...)
189 extra_labware=extra_labware,
190 )

File /opt/opentrons-robot-server/opentrons/execute.py:708, in _get_global_hardware_controller(robot_type)
704 if robot_type == "OT-3 Standard":
705 # Conditional import because this isn't installed on OT-2s.
706 from opentrons.hardware_control.ot3api import OT3API
--> 708 _THREAD_MANAGED_HW = ThreadManager(
709 OT3API.build_hardware_controller,
710 feature_flags=HardwareFeatureFlags.build_from_ff(),
711 )
712 else:
713 _THREAD_MANAGED_HW = ThreadManager(
714 OT2API.build_hardware_controller,
715 feature_flags=HardwareFeatureFlags.build_from_ff(),
716 )

File /opt/opentrons-robot-server/opentrons/hardware_control/thread_manager.py:289, in ThreadManager.init(self, builder, *args, **kwargs)
287 thread.start()
288 if blocking:
--> 289 object.getattribute(self, "managed_thread_ready_blocking")()

File /opt/opentrons-robot-server/opentrons/hardware_control/thread_manager.py:294, in ThreadManager.managed_thread_ready_blocking(self)
292 object.getattribute(self, "_is_running").wait()
293 if not object.getattribute(self, "managed_obj"):
--> 294 raise ThreadManagerException("Failed to create Managed Object")

ThreadManagerException: Failed to create Managed Object

Expected behavior

Device should get the protocol API without a problem

Operating system

Mac

System and robot setup or anything else?

8.0.0
Wi-Fi
Opentrons Flex