microbetag back-end

Basic architecture and firing up

microbetag is hosted in KU Leuven server and is Docker oriented. More specifically, it consists of 3 Docker images:

• a database (services/db/)
• an ngninx (services/nginx)
• the actual app (services/web)

First, each of those images needs to be built. Assuming all 3 images are ready, all you have to do is to fire the docker-compose command. We will discuss how to edit an image later. When the docker-compose command performs, it will start the web-server of microbetag. That means we need a way that this will keep running even when we exit our terminal.

To this end, we init a tmux session:

tmux new -s dockerApp

From within the tmux session, we move to the root folder of this repo /microbetagApp and fire the docker-compose command:

docker-compose up

Attention!

You need to detach from the tmux session; not exit! If you exit, the docker-compose command will be shut and your app will go down. To detach, you need to press: ctrl+b and then d.

You can attach to your running session any time by runnint

tmux attach -t dockerApp

When running htop now on the server and searching for "tmux" in the tree mode, you may see something similar with this:

The app is now up and running! You may check this by just typing to a browser: msysbio.gbiomed.kuleuven.be/.

How to edit the app

As mentioned above, the app consists of 3 Docker images that all 3 of them are used simultaneously. If one is to edit something on the app, they need to move to the corresponding image, edit the code and then rebuild the Docker image. For example, if you are about to edit a route of the app.py script, then you will have to rebuild the microbetagapp-web image:

docker build -f Dockerfile.prod -t microbetagapp-web:latest .

To make sure you can always come back to a working version of the app, a good pracice is to first make a backup tag of your working version running

docker tag <docker_image_id> microbetagapp-web-working-version

and only then rebuild the Docker image.

Once you have rebuild the image, all you need to do is to attach to the tmux session, create a new window (ctrl + b and then c) and fire again the docker-compose up command. This will re-create your web docker container and after a few seconds you app will be up and running once again with your new code.

Remember to detach from the tmux session, not exit!

Notes on the server's environment

Env

I made a new file under /etc/docker/ called daemon.json:

u0156635@gbw-s-msysbio01:/etc/docker$ more daemon.json 
{
  "data-root": "/data/docker"

}

Ports

I changed the mysql port of the vm to 4545 so I can have the 3306 for the container

My database

We need to build the whole database in the vm or wherever (even on a laptop) and then export it to a dbtest_data.sql file. Here is how:

 mysqldump -u [user name] –p [password] [database_name] > [dumpfilename.sql]

To build the SSL keys

Follow the instructions here and remove the pass phrase as shown here.

openssl rsa -in [original.key] -out [new.key]

Links

• Setting up and Running a MySQL Container
• Creating a Self-Signed Certificate With OpenSS

Challenges:

• argparse in nginx

Notes after destroying /data

failed to update store for object type *libnetwork.endpointCnt: Key not found in store

this fixes by running sudo service docker restart

VM overall

consider of crontabs removing for example /tmp folders