ADRCPathViewer

This is a development workspace for a pathology viewer for the ADRC @ Emory using the DSA CodeBase. The repo contains two parts. The web service which used Python Flask and OpenSlide to serve whole-slide images, serve static pages and endpoints to the database. The web applications which contains the viewer.

Prerequisites

virtualenv: to create a virtual python enviroment for the ADRC project

pip install virtualenv

openslide: to serve whole-slide images. Follow the instructions here to install openslide

Instuctions

Make a parent directory for our ADRC project. Move into the directory after you create it:

mkdir ADRC_ROOT

cd ADRC_ROOT

Clone the ADRC repo

git clone https://github.com/dgutman/ADRCPathViewer.git

Create the flask environment for testing using python virtualenv

virtualenv adrc_env

Activate the environment

source adrc_env/bin/activate

Within the environment install Flask, bson, Pillow, gunicorn, openslide-python, pymongo and wheel

pip install bson Pillow gunicorn openslide-python pymongo wheel

Browse to ADRC_ROOT/app/webservice

cd ADRC_ROOT/app/webservice

Run the web service using gunicorn on port 8001, in the foreground

gunicorn --bind 0.0.0.0:8001 wsgi

Or you can run gunicorn in the background

gunicorn --bind 0.0.0.0:8001 wsgi &

Configure Nginx

If you want you can setup Nginx to proxy requests to the ADRC web service.

Create a new server block configuration file in Nginx sites-available directory

sudo vi /etc/nginx/sites-available/adrc

Tell Nginx to listen on port 8000 and to route the traffic to the web service running on port 8001. To do so copy the following into adrc server block file

server {
    listen 0.0.0.0:8000;

    location / {
            proxy_pass http://0.0.0.0:8001;
    }
}

To enable the Nginx server block configuration we've just created, link the file to the sites-enabled directory:

sudo ln -s /etc/nginx/sites-available/adrc /etc/nginx/sites-enabled

Test the server block syntax by typing

sudo nginx -t

If there are no issues in the syntax restart Nginx

sudo service nginx restart

You should now be able to go to your server's domain name (domain_name:8000) or IP address in your web browser and see the ADRC application.

Application configurations

You make changes to the application configurations in app.cfg, some of the settings you can change are:

db_host: localhost (default)

db_port: 27017 (default)

db_name: your mongodb collection name

ws_host: 0.0.0.0 (default web service address)

ws_port: web service port

static_dir: location of static pages relative to the directory where the blueprint is located

slides_dir: location of the whole-slide images

tile_size: 256 (default)

overlap: 1 (default)

limit_bounds: 0 (default)

slide_cache_size: 1000 (default)

deepzoom_format: jpeg (default)