Is it possible to run java command line app from python in AWS EC2?
Since you're just making a command line call to the Java app, the path of least resistance would just be to make that call from another server using ssh. You can easily adapt the command you've been using with subprocess.call to use ssh -- more or less, subprocess.call(['ssh', '{user}@{server}', command]) (although have fun figuring out the quotation marks). As an aside on those lines, I usually find using '-o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null' stabilizes scripted SSH calls in my environment. 
The more involved thing will be setting up the environments to properly run the components you need. You'll need to set up ssh configs so that your django app can ssh over and set up -- probably with private key verification. Then, you'll need to make sure that your EC2 security groups are set up to allow the ssh access to your java server on port 22, where sshd listens by default. 
None of this is that hairy, but all the same, it might be stabler to just wrap your Java service in a HTTP server that your Django app can hit. Anyway, hope this is helpful.
I am working on some machine learning for chemical modelling in python. I need to run a java app (from command line through python subprocess.call) and a python webserver. Is this possible on AWS EC2?
I currently have this setup running on my mac but I am curious on how to set it up on aws.
Thanks in advance!