Installation

git clone https://github.com/AD-SDL/ot2_module.git
cd ot2_module
pip install -r requirements.txt
pip install -e .

This installs ot2_driver as a package

Note: This module was developed using Python 3.9

Getting the OT2 setup for ssh

This is not required (or used) for the HTTP driver When setting up an ssh key to connect to the opentrons, it is helpful to make a new one without a passphrase. For more information on setting up an ssh connection see:

Note, you have to have the Opentrons App installed

• https://support.opentrons.com/en/articles/3203681-setting-up-ssh-access-to-your-ot-2
• https://support.opentrons.com/en/articles/3287453-connecting-to-your-ot-2-with-ssh

For prototyping in the RPL, connect via the wire and wait for the robot to become visible on the application. Click settings then network settings and if you intend on running via the wire, use the wired-ip in the robot configuration file. If you intend to use the wireless IP, you must connect to the snowcrash network, but this does not have internet access.

Robot config

Below is an example of what I refer to as the robot_config

# OT2 in lab
- ip: IP.ADDRESS
  ssh_key: full/path/to/ssh/key # optional of http, just have a dummy string for now
  model: OT2
  version: 5 # If unsure, leave at 5

Running the driver

If you would like to use the script as I have made it, I have provided command line descriptions and example commands below

usage: ot2_driver_ssh.py [-h] -rc ROBOT_CONFIG [-pc PROTOCOL_CONFIG] [-rf RESOURCE_FILE] [-s] [-d] [-v] [-po PROTOCOL_OUT] [-ro RESOURCE_OUT]

optional arguments:
  -h, --help            show this help message and exit
  -rc ROBOT_CONFIG, --robot_config ROBOT_CONFIG
                        Path to config for OT2(s), must be present even if simulating, can contain dummy data however
  -pc PROTOCOL_CONFIG, --protocol_config PROTOCOL_CONFIG
                        Path to protocol config or protocol.py
  -rf RESOURCE_FILE, --resource_file RESOURCE_FILE
                        Path to resource file that currently exists
  -po PROTOCOL_OUT, --protocol_out PROTOCOL_OUT
                        Optional, name/location for protocol file to be saved to
  -ro RESOURCE_OUT, --resource_out RESOURCE_OUT
                        Optional, name/location for resources used file to be saved to
  -s, --simulate        Simulate the run, don't actually connect to the opentrons
  -d, --delete          Delete resource files and protocol files when done, default false
  -v, --verbose         Print status along the way

To run the protopiler/example_configs/basic_config.yaml with verbose settings and default outs, run the following

python ot2_driver_ssh.py -rc [insert/robot/config/path] -pc protopiler/example_configs/basic_config.yaml -v

To run the protopiler/example_configs/basic_config.yaml with verbose settings and specify the output files, run the following

python ot2_driver_ssh.py -rc [insert/robot/config/path] -pc protopiler/example_configs/basic_config.yaml -po ./test_protocol.py -ro ./test_resources.json -v

To run your own protocol.py file, replace data in the -pc option with the path to your protocol.py file

python ot2_driver_ssh.py -rc [insert/robot/config/path] -pc ./test_protocol.py

The process is the same for the HTTP driver

If you would like to write your own code using the ot2 driver you can start with something like this

# would have to specify path to ot2_driver_ssh.py if not in directory
from ot2_driver_ssh import OT2_Driver

# Load one ot2
for ot2_raw_cfg in yaml.safe_load(open(`robot_config_path`)):
    ot2 =OT2_Driver(OT2_Config(**ot2_raw_cfg))

# if you need to compile the protocol from yaml
if "py" not in str(`protocol_config`):

    protocol_file, resource_file = ot2.compile_protocol(
        config_path=`protocol_config`,
        resource_file=`resource_file`,
        protocol_out=`protocol_out`,
        resource_out=`resource_out`,
    )


# Transfer the protocol to the ot2
transfer_returncode = ot2.transfer(protocol_file)
if returncode:
    print("Exception raised when transferring...")

# Execute the protocol
ot2.execute(protocol_file)

Updating the Code on node computer

1. cd ~/wei_ws/src/ot2_module
2. git pull
3. pip install -e .

Running Dev Tools

1. Install pip install -r requirements/dev.txt
2. Run make in project root