RDML-Tools

A collection of web applications to visualize, edit and validate RDML files.

Install a local copy for testing

sudo apt-get install -y git-all

git clone --recursive https://github.com/RDML-consortium/rdml-tools.git rdml_tools

cd rdml_tools

Update your local copy

git pull

git submodule update --recursive --remote

Reconnect the submodules (for developpers)

cd server/rdmlpython

git branch

git checkout main

cd schema

git branch

git checkout main

Setup and run the server

The server runs in a terminal

Install the dependencies:

sudo apt install python3 python3-lxml python3-matplotlib python3-flask npm

sudo apt install python3-flask-cors python3-pip python3-numpy python3-scipy

Start the server:

cd rdml_tools

python3 server/server.py

Setup and run the client

The client requires a different terminal

Install the dependencies:

cd rdml_tools/client

npm install

Start the client:

cd rdml_tools/client

npm run dev

Hints on setting up a productive server

This introduction is far from complete and does not cover how to set up nginx or a linux server to run secure on the internet. This should be known and the hints below should be considered as incomplete tips to get you started faster.

Basics

RDML-Tools work in two parts. We need a web server (HTML) to distribute the homepage and its JavaScript code and a different web server (PY) to handle the requests made by this JavScript code, run the Python library and return the results, which are then displayed by the javaScript code. A single nginx machine can handle both functions.

Get the code

sudo apt-get install -y git-all

git clone --recursive https://github.com/RDML-consortium/rdml-tools.git rdml_tools

cd rdml_tools

Create the pages for the HTML server

First the production file has to be created:

cd client

nano .env.production

In .env.production you need three lines:

API_URL=https://PY-SERVER.COM/rdml-tools/api/v1

API_LINK=https://www.HTML-SERVER.COM/rdml-tools/

INDEX_LINK_URL=https://www.HTML-SERVER.COM/rdml-tools/index.html

Adapt the PY-SERVER.COM and HTML-SERVER.COM to your server names and the check the path. Now the HTML files can be created:

cd rdml_tools/client

sudo apt install npm

npm install

npm run bulid

A folder dist will be created and its content should be made available under: https://www.HTML-SERVER.COM/rdml-tools/

Get the PY service running

First install all required tools:

sudo apt install python3 python3-pip python3-lxml

pip3 install gunicorn lxml matplotlib flask flask_cors numpy scipy

sudo npm install pm2 -g

Now we need to create a runscript run.sh:

cd [RDML-TOOLS]/server

nano run.sh

With one line:

export URL_INDEX="https://www.HTML-SERVER.COM/rdml-tools/index.html"; gunicorn --timeout 125 -w 5 -b 0.0.0.0:8798 server:app

Be aware that this will create a service at port 8798 (could be any other).

Now it needs to be started with pm2:

pm2 start --name rdml-tools run.sh

Check how it is running:

pm2 list

Get the PY server running

Now the service is running and the nginx server needs to connect to it. So this is required for nginx serving https://PY-SERVER.COM/:

First you need to adapt the server config:

sudo nano /etc/nginx/sites-available/PY-SERVER.COM

And add the api part in your server (this is not a complete config):

server {
    server_name PY-SERVER.COM;
    [ALL OTHER STUFF]
    location /rdml-tools/api {
        rewrite ^/rdml-tools(.*) $1 break;
        proxy_pass http://127.0.0.1:8798;
        proxy_set_header X-Real-IP $remote_addr;
    }
}

Now activate and restart the server:

sudo ln -s /etc/nginx/sites-available/PY-SERVER.COM /etc/nginx/sites-enabled/

sudo nginx -t

sudo nginx -s reload

Last check if it works

Go to www.HTML-SERVER.COM/rdml-tools/index.html and open LinRegPCR. Load example file LinRegPCR, go to LinRegPCR tab and press Run LinRegPCR. If it calculates and you get a table below, you made it!