Elixys Hardware Software API

pyelixys is a library for communicating with the Sofie Biosciences Elixys hardware. The the hardware is a design based upon the mbed development board. It communicates with the hardware using the websocket protocol. This library abstracts the hardware to python objects.

It is distributed under the 3-Clause BSD License

Developing with pyelixys

First, install pip.

sudo apt-get install python-setuptools

Next, install the virtual environment - virtualenv.

pip install virtualenv

Now setup the pyelixys sandbox environment

virtualenv pyelixys
cd pyelixys

Active the sandbox environment

source bin/activate

Clone the repository

git clone git@github.com:henryeherman/pyelixys.git
cd pyelixys

Install the python dependencies by executing the install dependencies script in the root of pyelixys

./install_dependencies.sh

If installing on linux, you will need numpy. (This should be installed by running the install dependencies script). To install numpy in a virtualenv requires the python dev package. Before installing the requirements with pip run the following command.

sudo apt-get install python2.7-dev

Working with the HAL & the Hardware Simulator

To run the Elixys host server and gain access to system object, which gives access to all features the Elixys Robot, run the following command from the root of the virtual environment. The system object will be loaded as the variable s.

python -m pyelixys.hal.system

The simulator is automatically started if configured the controlbox and/or synthesizer options are set to True

The hardware simulator object and all corresponding status information is accessible from the variable s.simulator.

Working with the Database

By default pyelixys is configured to use a sqlite file based database. It will appear in the root of your virtual environment as soon as you initialized it. To initialize it run:

sudo python -m pyelixys.web.database.model

If the database does not exist, it will now! The filename of the database is located in the dbconf.ini and can be fount in database directory. This will execute the setup of the database and return the user in an Ipython terminal upon completion. At this point, a user may run additional scripts or commands. To exit Ipython, type exit.

The database is accessed through the wonderful sqlalchemy library, and the models can be found in model.py

Initializing Data in the Database

Developers might like to start with some default data. This can be done by populating the database with data. In order to populate the database with data, simply run:

python -m pyelixys.web.database.populatedb

This shall store a user with default settings onto the database. If the database did not already exist it will now! The user shall be returned to an an Ipython terminal upon completion. At this point, a user may run additional scripts or commands. To exit Ipython, type exit.

Working with the Sequence Manager

The Sequence Manager pyelixys.sequence.sequencemanager allows the host to load sequences from the database and run them on the elixys robot. It has access to the database model pyelixys.web.database.model and the system hardware pyelixys.hal.system. The webserver sequence requests should be sent to the sequencemanager.

To run the sequencemanager simply run:

python -m pyelixys.sequence.sequencemanager

Doing so will load the a sequence and start an IPython shell. The sequencemanager is load as sm.

Starting the Webserver

To run the Elixys web server, perform the following command in the root of the virtual environment. The runserver shall run on port 80 and requires sudo permissions to execute.

sudo python runserver.py

The webserver shall handle all web requests to and from the Elixys server. To access the webserver, open a browser and visit the URL: localhost. You will be required to enter your creditionals. Examples of URLs to visit include: localhost/state localhost/config localhost/runstate