Skip to content

SynBioDex/SBOL-Validator

master
Switch branches/tags
Code

Latest commit

 

Git stats

Files

Permalink
Failed to load latest commit information.
Type
Name
Latest commit message
Commit time
 
 
src
 
 
 
 
 
 
 
 

SBOL Validator

Build Status
A web-based validator for SBOL files backed by libSBOLj's validation runtimes. This validator offers support for SBOL2, SBOL1.1, and GenBank. Furthermore, it is accessible through a web GUI or a RESTful API.

The validator can be found here with an API endpoint found at https://validator.sbolstandard.org/validate.

Installation

First, bit about the way the application is structured. There are two main parts:

  • The web frontend -- static HTML, CSS, and JavaScript files served by a webserver (nginx setup instructions below)
  • The REST API backend -- a Python Flask application served by uwsgi.

Prerequisites

You should have Git installed. To do that, execute the appropriate command for your system.

OS Command
Ubuntu sudo apt-get install git
Mac brew install git

First, clone the repository into its own folder on your computer. To do so, navigate to the directory where you'd like to place this folder and run the command git clone https://www.github.com/SynBioDex/SBOL-Validator.git to create a new directory containing a clone of the validator. The setup is now ready to begin.

Setting up the backend

Prerequisites

Install all of the necessary packages onto your system with the appropriate command for your system.

OS Command
Ubuntu sudo apt-get install python3 python3-pip
Mac brew install python3 pip3 pyvenv
Set up virtual environment

Create a virtual environment for the validator in the parent directory. You can use the example commands below to create a virtualenv called sbol-validator-venv.

OS Command
Ubuntu virtualenv sbol-validator-venv
Mac pyvenv sbol-validator-venv

Activate this virtualenv using the command source sbol-validator-venv/bin/activate (note: for the remainder of this guide, it will be assumed that your virtualenv is named sbol-validator-venv -- if it isn't, you'll have to use common sense to find out where to substitute the name you used.) You should see (sbol-validator-venv) before your command prompt if you've correctly activated the virtualenv.

Navigate into the SBOL-Validator directory. Run the command pip install -r requirements.txt to install all of the necessary Python packages for the validator.

This should be all that you need to run the backend manually. To test this, set the environment variable FLASK_APP to validationapi.api and run the command python -m flask run from within the .../SBOL-Validator/src directory. You should see the following message:

Unable to import uWSGI application.
This probably means that you're running the application manually.
If you are, ignore this message.
 * Serving Flask app "validationapi.api"
 * Running on http://127.0.0.1:5000/ (Press CTRL+C to quit)
Set up Systemd service

To ensure that the application is managed by the system and restarted if it crashes or if the system powers off, we will create a Systemd unit file.

Create a systemd unit file called sbol-validator.service as root user in /etc/systemd/system. In it, paste the following content:

[Unit]
Description=uWSGI instance to serve SBOL Validator
After=network.target

[Service]
User=nginx
Group=nginx
WorkingDirectory=/PATH/TO/YOUR/VALIDATOR/SBOL-Validator/src
Environment="PATH=/PATH/TO/YOUR/VALIDATOR/sbol-validator-venv/bin"
ExecStart=/PATH/TO/YOUR/VALIDATOR/sbol-validator-venv/bin/uwsgi --ini sbol-validator.ini

[Install]
WantedBy=multi-user.target

Be sure to replace /PATH/TO/YOUR/VALIDATOR/ with the actual path to your validator.

Ensure that the configuration is correct with sudo systemctl restart sbol-validator. If you see no errors, the validation service is up and running! To make sure that it runs at startup, run sudo systemctl enable sbol-validator.

Setting up the frontend

Prerequisites

First, install nginx. Nginx will serve the static files for the frontend and direct any requests for the backend to uWSGI.

OS Command
Ubuntu sudo apt-get install nginx
Mac brew install nginx
Create nginx configuration

Navigate to the /etc/nginx/sites-available/ directory and create the file sbol-validator.conf.

Copy the following into the file:

server {
    listen 80;
    server_name server_domain_or_IP;
   
    location /sbol-validator/ {
        alias /PATH/TO/YOUR/VALIDATOR/SBOL-Validator/src/validation-form/;
        index html/form.html;
    }
    
    location /validate/ {
        include uwsgi_params;
        uwsgi_pass unix:/PATH/TO/YOUR/VALIDATOR/SBOL-Validator/src/sbol-validator.sock;
    }
    
    location /update/ {
        include uwsgi_params;
        uwsgi_pass unix:/PATH/TO/YOUR/VALIDATOR/SBOL-Validator/src/sbol-validator.sock;
    }
}

Once you've saved this, check that there are no typos with the command sudo nginx -t. If everything is correct, restart nginx with sudo service nginx restart.

With that, your validator should be online!

API

The API documentation can be found here

Docker

The application is packaged into two Docker containers to make things simpler to deploy and manage. The container images are automatically built when the GitHub repository is updated and pushed to Docker Hub. Their image names are zachzundel/sbolvalidator and zachzundel/sbolconverter, and the latest build is available at the snapshot tag for each.

To deploy the containers on your system, create a Systemd unitfile to manage and run the container. An example file for the SBOL validator is shown below. The unit file should be placed in the /etc/systemd/system/ directory.

[Unit]
Description=SBOL Validator

# This unitfile depends on the Docker service
Requires=docker.service network-online.target
After=docker.service network-online.target

[Service]
# Pulling the Docker image can take a while, so don't timeout
TimeoutStartSec=0

Restart=always

# Before starting, stop any existing containers...
ExecStartPre=-/usr/bin/docker stop %n

# ...remove them...
ExecStartPre=-/usr/bin/docker rm %n

# ...and pull any new ones.
ExecStartPre=-/usr/bin/docker pull zachzundel/sbolvalidator:snapshot

ExecStart=/usr/bin/docker run --rm --name %n --publish 9000:80 zachzundel/sbolvalidator:snapshot
ExecStop=/usr/bin/docker stop %n

[Install]
WantedBy=multi-user.target

If the file is named validator.service, it can then be started with the command systemctl start validator, it can be configured to start automatically with systemctl enable validator, and its status can be checked with systemctl status validator.

Deployment

The validator is deployed on the SBOL standard webserver, as is the converter. They are configured in a manner shown above. A GitHub action is configured to automatically update the services when a new image is pushed to Docker Hub.