covmatic-localwebserver 2.5.1

Package for the COVMATIC LocalWebServer

LocalWebServer

This software is part of the Covmatic project.
Visit the website https://covmatic.org/ for more documentation and information.

Table of Contents

• Installation
• Setup
• Execution
• LocalWebServer
• TempDeck

Installation

You can install the Covmatic LocalWebServer via pip:

<python> -m pip install covmatic-localwebserver

Where <python> should be changed for the Python instance you wish to install the LocalWebServer onto. We will be following this convention for all the next instructions.

Troubleshooting

In some cases, the opentrons package fails to install as a dependency of this package. If it happens, please install the opentrons package separately.

<python> -m pip install opentrons
<python> -m pip install covmatic-localwebserver

Setup

To set up the LocalWebServer application, run

<python> -m covmatic_lws.setup

This will create a desktop link and open in a text editor the file covmatic.conf in your user home directory. To create a link also for the TempDeck GUI, please run

<python> -m covmatic_lws.setup --tempdeck-desktop

This functionality is supported in Windows and Linux.

If you are running another OS, please open the covmatic.conf file manually. If you would like an automatic desktop link creator for your OS, please open an issue on GitHub.

Configuration

The file covmatic.conf stores configuration settings for running the LocalWebServer. The most important settings are

• ip: the ip address or hostname of the Opentrons robot you want to connect to
• ssh-key: SSH key file path (default is ~/ot2_ssh_key). Please, make sure you have the correct SSH key file in the specified path
• pwd: the passphrase for the SSH key used when connecting to the Opentrons robot
• web-app: the webapp url (including, eventually, https://) that is concatenated with the station name retrieved from the robot
• web-app-fixed: the url (including, eventually, https://) that will not be concatenated with the retrieved station name To learn how to set up SSH on your Opentrons robot, please refer to the official guide.

An example configuration file would be

ip=robot-name.local
pwd=pass
web-app=https://covmatic-web-app.com

Other useful settings are:

• app: the Opentrons App filepath (default is C:/Program Files/Opentrons/Opentrons.exe)
• station: the name of the default station protocol (default is A)
• lang: the default message language (default is ENG)

For a complete list of settings, run

<python> -m covmatic_lws -h

Execution

To start the Covmatic LocalWebServer gui, run

<python> -m covmatic_lws.gui

To start the Covmatic TempDeck gui, run

<python> -m covmatic_lws.gui.tempdeck

If you ran the setup program, you will have desktop entries for these applications

Linux

• The Covmatic app (blue icon) is the LocalWebServer GUI
• The TempDeck app (red icon) is the TempDeck GUI

Windows

• The Covmatic Localwebser link (blue icon) is the LocalWebServer GUI
• The Covmatic TempDeck link (red icon) is the TempDeck GUI

LocalWebServer GUI

The LocalWebServer GUI has a main window where you can see

• The Covmatic logo
• The robot ip/hostname
• Two columns of buttons

Please, check that the ip/hostname corresponds to the robot you want to connect to. If the robot is offline, (disconnected) will show under the robot's ip/hostname.

In the first column you will find buttons for functions strictly related to robot

• Package version button. This button shows the current version of the protocol package installed on the robot. It should read Stations <version>. If the button is blue, the package is up to date. If the button is white, the package is outdated: by clicking the button, you can update the package to the latest version (this may take a minute). The button should then turn blue, displaying the updated version number.
• Robot lights button. This button allows for turning on and off the robot rail lights. If the button is blue, the lights are on. If the button is white, the lights are off. By clicking the button, you can toggle the lights.
• Home button. This button sends the robot deck home. Please, don't use this button when a protocol is running, as it may crash the process.
• Protocol upload button. This button opens (or closes) the Protocol upload window.
• Jupyter button. This buttons opens the robot's Jupyter server in a web browser.
• Run Log button. This button opens (or closes) the run log window. The run log window displays the protocol run log in real time. It is reset at the start of a new run.

In the second column you will find buttons related to services external to the robot

• Opentrons button. This button launches the Opentrons app. You will need this app for calibration procedures. If the app doesn't open, please check that the app's path matches the path specified in the configuration file
• LocalWebServer button. This button allows for turning on and off the local web server. If the button is blue, the server is on. If the button is white, the server is off. By clicking the button, you can toggle the server state.
• WebApp button. This button opens the web app in a web browser. If the web-app setting is unset, this button is disabled.

Protocol upload

The protocol upload window allows you to specify protocol parameters and upload the generated protocol file to the robot.

• Station menu. This menu allows you to specify which station protocol to use. The default choice is regulated by the station setting
• Number of samples entry. This entry field allows you to specify the number of samples that you want to process in your protocol
• Next tips. Here you can see which tip locations will be the next to be picked by the robot (for each type of tip rack).
• Save button. Save protocol file to a custom path.
• Upload button. Upload file to the robot. If this is not clicked, no changes are made to the robot's protocol.
• Language menu. This menu allows you to choose the message language. The default choice is regulated by the lang setting
• Reset tips button. This button resets the tip log. The robot will start picking tips from the first position of each rack. This button has immediate effect on the robot.

TempDeck GUI

This GUI allows you to control multiple Opentrons Temperature modules (the TempDeck) connected via USB to your laptop. You can find more information about it here.

There is an entry field where you can specify the target temperature. There are 3 buttons

• Refresh button. Rescan the USB ports to update the list of connected TempDecks.
• Set button. Set the temperature of all connected TempDecks to the specified temperature.
• Deactivate button. Deactivate all connected TempDeks.