A simple SBGN-ML renderering API

This application is a simple REST API to render SBGN-ML files. Both synchronous and asynchronous requests are available.

You can test it at https://vincent-noel.github.io/SBGNRenderAPI/

It is based on Newt, which is executed from Selenium using Chromedriver. It comes with a simple python library which implements this wrapper and can be used independently of the API.

Run with docker and docker-compose

git clone https://github.com/vincent-noel/SBGNRenderAPI.git
cd SBGNRenderAPI
sudo docker-compose up -d

Using the API

When running via docker, the api is available at

http://localhost:8082/render

A public rendering API is available at

https://sbgnrender.vincent.science/render

Rendering

Endpoint : http://localhost:8082/render

Method : POST

Files:

• file : the sbgn-ml file to render

Parameters:

• format : image format (svg|png|jpg) (optional, default=png)
• scale : scaling value (optional, default 3 for jpg/png, 1 for svg)
• max_width : maximum width (optional, default depends on scale)
• max_height : maximum height (optional, default depends on scale)
• quality : JPG quality (optional, default 1, only for jpg)
• layout : true|false (optional, default false)
• async (true|false) (optional, default=false)

Returns:

• if async = false, rendered image
• if async = true, a json object with the identifier of the rendering

Example of synchronous request using python

import requests

files = {'file': open('sbgnml.xml','rb')}
values = {
    'format': 'png',
    'bg': '#fff',
    'scale': 1,
    'max_width': 5000,
    'max_height': 5000,
}
api_url = "http://localhost:8082/render"

r = requests.post(api_url, files=files, data=values)
with open('network.png', 'wb') as f:
    f.write(r.content)

Getting status of rendering for asynchronous request

Endpoint : http://localhost:8082/status/\<id>

Method : GET

Parameter:

• id : the identifier of the rendering

Returns:

• a json object with the rendering status

Getting renderer image for asynchronous request

Endpoint : http://localhost:8082/rendered/\<id>

Method : GET

Parameter:

• id : the identifier of the rendering

Returns:

• renderer image

Example of asynchronous request using python

import requests, time

# Launching the rendering as asynchronous, and getting the id to check its status/requesting the renderer image
files = {'file': open('sbgnml.xml','rb')}
values = {'async': True}

r = requests.post("http://localhost:8082/render", files=files, data=values)
rendering_id = r.json()['id']

# Checking it's status to see if it's rendered
finished = False
while not finished:
    r = requests.get("http://localhost:8082/status/%s" % rendering_id)
    status = r.json()['status']
    finished = (status == 'ready')
    time.sleep(1)
    
# Then requesting the renderered image
r = requests.get("http://localhost:8082/rendered/%s" % rendering_id)
with open('network_async.png', 'wb') as f:
    f.write(r.content)

Installation

• Installation (Ubuntu/Debian)

# Installing dependencies
sudo apt install git python3-pip chromium-driver
curl -sL https://deb.nodesource.com/setup_12.x | sudo bash - 
sudo apt-get install nodejs 

# Downloading this tool
git clone https://github.com/vincent-noel/newt.git
cd newt/sbgnrender

# Building JS bundle
npm install 
npm run build-bundle-js

# Installing python library
cd .. 
sudo pip3 install .

• Running the server

python3 api/RendererAPI.py

SBGNRender Python library

This API comes with a python package which is the one running newt. To install it, the simplest way is via PyPI :

sudo pip3 install sbgnrender

This library depends on ChromeDriver, which can be installed on ubuntu/debian systems with

sudo apt install chromium-chromedriver

On Ubuntu 19.x and later, chromium installation is using snap package manager, which causes a problem while writing and accessing temporary files. The current workaround is to change chromium temporary directory permissions with :

sudo chmod 711 /tmp/snap.chromium

After installing the library, usage is the following :

from sbgnrender import renderSBGN

renderSBGN(
    input_file,  // Path as a string
    output_file, // Path as a string
    format,      // Format as a string : svg, png, jpg
    scale,       // Scale of the network (default 1 for svg, 3 for jpg/png)
    bg,          // Background color as HTML String (ex #fff for white), None for transparent (available for png/svg),
    max_width,   // Maximum width in pixels
    min_width,   // Minimum width in pixels
    quality,     // Quality (available for jpg)
    layout,      // Perform automatic layout
    verbose      // True | False
)

While installing via Pypi is advised, if you want to install it from this repository you can do the following:

sudo apt install chromium-chromedriver
curl -sL https://deb.nodesource.com/setup_12.x | sudo bash - 
sudo apt-get install nodejs 

git clone https://github.com/vincent-noel/newt.git
cd newt/sbgnrender
npm install
npm run build-bundle-js
cd ..
sudo pip3 install .

Software

This application is distributed under GNU Lesser General Public License.

Copyright

A Simple SBGN Rendering API, Copyright (C) 2020 Institut Curie, 26 rue d'Ulm, Paris, France

A Simple SBGN Rendering API is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.

A Simple SBGN Rendering API is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.

You should have received a copy of the GNU Lesser General Public License along with this library; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA