Pylabrobot error while setup initialize_pipetting_channels

isaacguerreiro · May 3, 2023, 12:17am

I’m having some problems regarding the setup step of the PyLabRobot. So, I’m getting an error when trying to initialize_pipetting_channels.

Some important context:

I’m using WSL as my workspace, so I had to attach the USB device from Windows to WSL. Conectar dispositivos USB | Microsoft Learn
I also had to create an udev rule because I was getting access denied from pyUSB. USBError: [Errno 13] Access denied (insufficient permissions) Ubuntu 16.04 · Issue #237 · pyusb/pyusb · GitHub
At first I was the pylabrobot library imported by pip install (apparently it was an outdated version?) and I was getting another error related to ISWAP.

INFO:pylabrobot.liquid_handling.backends.hamilton.STAR:Finding Hamilton USB device...                                                                                                                                                                                            
INFO:pylabrobot.liquid_handling.backends.hamilton.STAR:Found Hamilton USB device.                                                                                                                                                                                                
INFO:pylabrobot.liquid_handling.backends.hamilton.STAR:Found endpoints.                                                                                                                                                                                                  
Write:                                                                                                                                                                                                                                                                                  
ENDPOINT 0x2: Bulk OUT ===============================                                                                                                                                                                                                                           
bLength          :    0x7 (7 bytes)                                                                                                                                                                                                                                              
bDescriptorType  :    0x5 Endpoint                                                                                                                                                                                                                                               
bEndpointAddress :    0x2 OUT                                                                                                                                                                                                                                                    
bmAttributes     :    0x2 Bulk                                                                                                                                                                                                                                                   
wMaxPacketSize   :   0x40 (64 bytes)                                                                                                                                                                                                                                             
bInterval        :    0x0                                                                                                                                                                                                                                                 
Read:                                                                                                                                                                                                                                                                                   
ENDPOINT 0x81: Bulk IN ===============================                                                                                                                                                                                                                           
bLength          :    0x7 (7 bytes)                                                                                                                                                                                                                                              
bDescriptorType  :    0x5 Endpoint                                                                                                                                                                                                                                               
bEndpointAddress :   0x81 IN                                                                                                                                                                                                                                                     
bmAttributes     :    0x2 Bulk                                                                                                                                                                                                                                                   
wMaxPacketSize   :   0x40 (64 bytes)                                                                                                                                                                                                                                             
bInterval        :    0x0                                                                                                                                                                                                                                                 
INFO:pylabrobot.liquid_handling.backends.hamilton.STAR:Sent command: C0QWid0001                                                                                                                                                                                                  
INFO:pylabrobot.liquid_handling.backends.hamilton.STAR:Received response:
C0QWid0001er00/00qw0                                                                                                                                                                                    
INFO:pylabrobot.liquid_handling.backends.hamilton.STAR:Running backend initialization procedure.                                                                                                                                                                                  
INFO:pylabrobot.liquid_handling.backends.hamilton.STAR:Sent command: C0VIid0002                                                                                                                                                                                                  
INFO:pylabrobot.liquid_handling.backends.hamilton.STAR:Received response: C0VIid0002er00/00                                                                                                                                                                                      
INFO:pylabrobot.liquid_handling.backends.hamilton.STAR:Sent command:
C0DIid0003xp08000&yp4050 3782 3514 3246 2978 2710 2442 2175tp2450tz1220te3600tm1&tt04ti0                                                                                                                    
INFO:pylabrobot.liquid_handling.backends.hamilton.STAR:Received response: C0DIid0003er01/31                                                                                                                                                                                      
INFO:pylabrobot.liquid_handling.backends.hamilton.STAR:Sent command: R0QWid0004                                                                                                                                                                                                  
INFO:pylabrobot.liquid_handling.backends.hamilton.STAR:Received response: R0QWid0004qw0                                                                                                                                                                                          
INFO:pylabrobot.liquid_handling.backends.hamilton.STAR:Sent command: C0FIid0005                                                                                                                                                                                                  
INFO:pylabrobot.liquid_handling.backends.hamilton.STAR:Received response: C0FIid0005er00/00                                                                                                                                                                                      
INFO:pylabrobot.liquid_handling.backends.hamilton.STAR:Sent command: C0PGid0006th2840                                                                                                                                                                                            
INFO:pylabrobot.liquid_handling.backends.hamilton.STAR:Received response: C0PGid0006er99/00
R002/91                                                                                                                                                                              
Traceback (most recent call last):                                                                                                                                                                                                                                                 
File "protocol.py", line 17, in <module>                                                                                                                                                                                                                                           
asyncio.run(protocol())                                                                                                                                                                                                                                                        
File "/usr/lib/python3.8/asyncio/runners.py", line 44, in run                                                                                                                                                                                                                      
return loop.run_until_complete(main)                                                                                                                                                                                                                                           
File "/usr/lib/python3.8/asyncio/base_events.py", line 616, in run_until_complete                                                                                                                                                                                                  
return future.result()                                                                                                                                                                                                                                                         
File "protocol.py", line 15, in protocol                                                                                                                                                                                                                                           
await lh.setup()                                                                                                                                                                                                                                                               
File "/home/isaacguerreir/.local/lib/python3.8/site
packages/pylabrobot/liquid_handling/liquid_handler.py", line 104, in setup                                                                                                                                                     
self.backend.setup()                                                                                                                                                                                                                                                           
File "/home/isaacguerreir/.local/lib/python3.8/site
packages/pylabrobot/liquid_handling/backends/hamilton/STAR.py", line 481, in setup                                                                                                                                             
self.park_iswap()                                                                                                                                                                                                                                                              
File "/home/isaacguerreir/.local/lib/python3.8/site
packages/pylabrobot/liquid_handling/backends/hamilton/STAR.py", line 4088, in park_iswap                                                                                                                                       
command_output = self.send_command(                                                                                                                                                                                                                                            
File "/home/isaacguerreir/.local/lib/python3.8/site
packages/pylabrobot/liquid_handling/backends/hamilton/STAR.py", line 365, in send_command                                                                                                                                      
return self.parse_response(res, fmt)                                                                                                                                                                                                                                           
File "/home/isaacguerreir/.local/lib/python3.8/site
packages/pylabrobot/liquid_handling/backends/hamilton/STAR.py", line 299, in parse_response                                                                                                                                    
raise he                                                                                                                                                                                                                                                                     
pylabrobot.liquid_handling.backends.hamilton.errors.HamiltonFirmwareError: {'ISWAP': HardwareError('iSWAP not initialized. Call star.initialize_iswap().')}

After getting that pip install pylabrobot was not getting the last version of the library I made an installation using the source code. After that, I received a problem regarding initializing the pipetting channels.
At first, I thought maybe some labware was being impediment to setup the machine, so I remove all of them, but it seems not be this.

SOURCE CODE

import asyncio
import logging

from pylabrobot.resources.hamilton import STARLetDeck
from pylabrobot.liquid_handling.backends.simulation.simulator_backend import SimulatorBackend
from pylabrobot.liquid_handling import LiquidHandler
from pylabrobotliquid_handling.liquid_handling.backends import STAR

logging.basicConfig(level = logging.DEBUG)

async def protocol():
    backend = STAR()
    lh = LiquidHandler(backend=backend, deck=STARLetDeck())

    await lh.setup()

asyncio.run(protocol())

/usr/lib/python3/dist-packages/requests/__init__.py:89: RequestsDependencyWarning: urllib3 (2.0.1) or chardet (3.0.4) doesn't match a supported version!                                                                                                                            warnings.warn("urllib3 ({}) or chardet ({}) doesn't match a supported "                                                                                                                                                                                                         DEBUG:asyncio:Using selector: EpollSelector                                                                                                                                                                                                                                       INFO:pylabrobot.liquid_handling.backends.USBBackend:Finding USB device...
INFO:pylabrobot.liquid_handling.backends.USBBackend:Found USB device.
INFO:pylabrobot.liquid_handling.backends.USBBackend:Found endpoints.
Write:
       ENDPOINT 0x2: Bulk OUT ===============================
       bLength          :    0x7 (7 bytes)
       bDescriptorType  :    0x5 Endpoint
       bEndpointAddress :    0x2 OUT
       bmAttributes     :    0x2 Bulk
       wMaxPacketSize   :   0x40 (64 bytes)
       bInterval        :    0x0
Read:
       ENDPOINT 0x81: Bulk IN ===============================
       bLength          :    0x7 (7 bytes)
       bDescriptorType  :    0x5 Endpoint
       bEndpointAddress :   0x81 IN
       bmAttributes     :    0x2 Bulk
       wMaxPacketSize   :   0x40 (64 bytes)
       bInterval        :    0x0
INFO:pylabrobot.liquid_handling.backends.USBBackend:Sent command: C0RTid0001
DEBUG:pylabrobot.liquid_handling.backends.hamilton.STAR:Starting reading thread...
DEBUG:pylabrobot.liquid_handling.backends.USBBackend:Received data: bytearray(b'C0RTid0001er00/00rt0 0 0 0 0 0 0 0')                                                                                                                                                              INFO:pylabrobot.liquid_handling.backends.hamilton.STAR:Received response: C0RTid0001er00/00rt0 0 0 0 0 0 0 0                                                                                                                                                                      DEBUG:pylabrobot.liquid_handling.backends.hamilton.STAR:Reading thread stopped.
INFO:pylabrobot.liquid_handling.backends.USBBackend:Sent command: C0QMid0002
DEBUG:pylabrobot.liquid_handling.backends.hamilton.STAR:Starting reading thread...
DEBUG:pylabrobot.liquid_handling.backends.USBBackend:Received data: bytearray(b'C0QMid0002er00/00ka010001xt30xa30xw08000xl03xr00xm03500xx11400ys090xu3700xv3700yu0060kl360kc0yx0060ke00000000xn00xo00ym0060kr0km360')
INFO:pylabrobot.liquid_handling.backends.hamilton.STAR:Received response: C0QMid0002er00/00ka010001xt30xa30xw08000xl03xr00xm03500xx11400ys090xu3700xv3700yu0060kl360kc0yx0060ke00000000xn00xo00ym0060kr0km360                                                                     DEBUG:pylabrobot.liquid_handling.backends.hamilton.STAR:Reading thread stopped.
INFO:pylabrobot.liquid_handling.backends.USBBackend:Sent command: C0QWid0003
DEBUG:pylabrobot.liquid_handling.backends.hamilton.STAR:Starting reading thread...
DEBUG:pylabrobot.liquid_handling.backends.USBBackend:Received data: bytearray(b'C0QWid0003er00/00qw0')
INFO:pylabrobot.liquid_handling.backends.hamilton.STAR:Received response: C0QWid0003er00/00qw0
DEBUG:pylabrobot.liquid_handling.backends.hamilton.STAR:Reading thread stopped.
INFO:pylabrobot.liquid_handling.backends.hamilton.STAR:Running backend initialization procedure.
INFO:pylabrobot.liquid_handling.backends.USBBackend:Sent command: C0VIid0004
DEBUG:pylabrobot.liquid_handling.backends.hamilton.STAR:Starting reading thread...
DEBUG:pylabrobot.liquid_handling.backends.USBBackend:Received data: bytearray(b'')
WARNING:pylabrobot.liquid_handling.backends.hamilton.STAR:Could not parse response:
DEBUG:pylabrobot.liquid_handling.backends.USBBackend:Received data: bytearray(b'C0VIid0004er00/00')
INFO:pylabrobot.liquid_handling.backends.hamilton.STAR:Received response: C0VIid0004er00/00
DEBUG:pylabrobot.liquid_handling.backends.hamilton.STAR:Reading thread stopped.
INFO:pylabrobot.liquid_handling.backends.USBBackend:Sent command: C0DIid0005xp08000&yp4050 3783 3516 3249 2982 2715 2448 2181tp2450tz1220te3600tm1&tt04ti0                                                                                                                        DEBUG:pylabrobot.liquid_handling.backends.hamilton.STAR:Starting reading thread...
DEBUG:pylabrobot.liquid_handling.backends.USBBackend:Received data: bytearray(b'C0DIid0005er01/31')
INFO:pylabrobot.liquid_handling.backends.hamilton.STAR:Received response: C0DIid0005er01/31
DEBUG:pylabrobot.liquid_handling.backends.hamilton.STAR:Reading thread stopped.
Traceback (most recent call last):
  File "protocol.py", line 17, in <module>
    asyncio.run(protocol())
  File "/usr/lib/python3.8/asyncio/runners.py", line 44, in run
    return loop.run_until_complete(main)
  File "/usr/lib/python3.8/asyncio/base_events.py", line 616, in run_until_complete
    return future.result()
  File "protocol.py", line 15, in protocol
    await lh.setup()
  File "/home/isaacguerreir/workspace/personal/pylabrobot/pylabrobot/liquid_handling/liquid_handler.py", line 109, in setup
    await self.backend.setup()
  File "/home/isaacguerreir/workspace/personal/pylabrobot/pylabrobot/liquid_handling/backends/hamilton/STAR.py", line 607, in setup
    await self.initialize_pipetting_channels(
  File "/home/isaacguerreir/workspace/personal/pylabrobot/pylabrobot/liquid_handling/backends/hamilton/STAR.py", line 2725, in initialize_pipetting_channels
    return await self.send_command(
  File "/home/isaacguerreir/workspace/personal/pylabrobot/pylabrobot/liquid_handling/backends/hamilton/STAR.py", line 447, in send_command
    return await fut
  File "/home/isaacguerreir/workspace/personal/pylabrobot/pylabrobot/liquid_handling/backends/hamilton/STAR.py", line 506, in _continuously_read
    parsed = self.parse_response(resp, fmt)
  File "/home/isaacguerreir/workspace/personal/pylabrobot/pylabrobot/liquid_handling/backends/hamilton/STAR.py", line 396, in parse_response
    raise he
pylabrobot.liquid_handling.backends.hamilton.errors.HamiltonFirmwareError: HamiltonFirmwareError({'Master': CommandSyntaxError('Unknown parameter (call lh.backend.request_name_of_last_faulty_parameter)')})

Any ideas of what could be happening?

One possible idea about what is happening for me it’s that the backend is for Hamilton Star, and my machine is a Starlet (my USB is recognized as 08af:8000 Microlab STAR).

Stefan · May 3, 2023, 2:50am

It’s possible that your robot is configured for a different set of USB commands than we are set up for, which is consistent with the firmware issue earlier in Venus. Would you be able to tell us what version of Venus the robot computer (that is known to work with the Hamilton) is running?

isaacguerreiro · May 3, 2023, 2:29pm

Yes. I will be going to the laboratory later today and I will check this.

One interesting thought is that when I was using the pylabrobot from pypi (by installing using the pip install pylabrobot command) version 0.1.4, the initialize_pipetting_channels function was working fine. I actually saw the pipetting channels moving to the zero position and going to the initialize_iswap function and also saw the ISWAP moving around.

So the 0.1.4 version of the initialize_pipetting_channels it’s compatible with the machine. I will try to run both versions and use a debugger to see what the difference between them.

isaacguerreiro · May 4, 2023, 12:37am

When I run initialize_pipetting_channels on version 0.1.4 the answer is C0DIid0003er01/31. Is this an error not caught by the response_parser? I’m interested to know if the pipetting channels are being correctly initialized and if the problem is only when I tried to initialize ISWAP.

Version 0.1.4 run initialize_pipetting_channels without any error returning the response: C0DIid0003er01/31

The last version of the code when trying to run initialize_pipetting_channels returns an error as response: C0DIid0005er01/31

Gareth · May 4, 2023, 10:44am

01/31 is “undefined parameter”, which suggests that as Stefan said, the robot accepts a different parameter set to what the docs say…

isaacguerreiro · May 4, 2023, 3:44pm

Thanks, Gareth! I will have to see the possibility of updating our Hamilton Starlet firmware, so we can use Venus FOUR. Would like to ask if someone knows when the new VENUS software will be released in 2023, maybe it will be nice to time this update so we can have the most up-to-date firmware and software.

luisvillaautomata · May 4, 2023, 3:59pm

That’s a good question for @EricSindelar_Hamilton or @NickHealy_Hamilton

EricSindelar_Hamilton · May 4, 2023, 4:26pm

End of May is the most recent update that we received last week.

isaacguerreiro · May 4, 2023, 4:48pm

Thanks for the update @EricSindelar_Hamilton. Do Hamilton have made a presentation about the new software? I would like to share this with my lab manager.

EricSindelar_Hamilton · May 4, 2023, 5:24pm

Yes, please see this post for a link to the webinar from last month. Once you register, you can view the recording.

https://forums.pylabrobot.org/t/hamilton-slas-2023-info/1118/13?u=ericsindelar_hamilton