Dockerize

[northwestwitch]

This PR adds a minimal Dockerfile that allows to build both the frontend and the backend of this app.

fix #96

The code in the Dockerfile is the following:

FROM python:3.8-alpine3.12

MAINTAINER Chiara Rasi

RUN apk update
RUN apk add make automake gcc g++ linux-headers curl libcurl curl-dev \
  zlib-dev bzip2-dev xz-dev libffi-dev curl libressl-dev bash \
  && rm -rf /var/cache/apk/*s

WORKDIR /home/worker/app
COPY . /home/worker/app

RUN pip install -r requirements.txt
RUN pip install -e .

RUN adduser -D worker
RUN chown worker:worker -R /home/worker
USER worker

It basically just installs all the requirements and the beacon on a container and then instructs to run any commands as a non-root user.

I've reasoned that since both frontend and backend belong to the same app they should share this basic module.

The additional layers such as the mongodb connection and the specific instructions might also be added in a modular way. At this regard I've included a docker-compose with a complete demo of the app that does the following:

• Instantiates and runs a mongodb
• Adds a container with the backend that adds demo data to the database
• Runs a server on localhost:5000 allowing requests from outside the container.

How to prepare for test:

• Have installed docker and docker-compose
• clone this repo branch on a local computer and cd to cgbeacon2

How to test:

• Stop eventual mongodb database running on your local machine
• Run the demo using the following command:
  docker-compose up
• From another terminal, send a request to the / endpoint of the app:
  curl -X GET 'http://127.0.0.1:5000/apiv1.0/

Expected outcome:

• When running docker-compose there should be 3 container created: mongodb, beacon-cli, and beacon-web.
• mongodb container should successfully create the database, running on port 27017
• beacon-cli should be able to connect and populate database with data
• beacon-web should be able to connect, accept incoming requests and send responses
• The request sent from the other terminal should receive a response from the containers server.

Review:

• Code approved by
• Tests executed by CR

This version is a:

• MAJOR - when you make incompatible API changes
• MINOR - when you add functionality in a backwards compatible manner
• PATCH - when you make backwards compatible bug fixes or documentation/instructions

[northwestwitch]

Hi @eriksjolund and @moonso. I know you're working with dockerizing other repos for the new server. Could you take a look at this PR and tell me what you think of my solution? Any suggestions?

Another way of doing it is creating 2 Dockerfiles based on mongo, one for the backend and one for the frontend, but I like the modularity..

[northwestwitch]

Tests:

Start the docker-compose and get all 3 containers to work and do what they should do: 🆗

Database gets populated with data: 🆗

Sending a request from another terminal should trigger a response: 🆗

[northwestwitch]

I'm hosting the image on my docker hub now because I don't have access to the clinicalgenomics one, but I plan to move the images there

[moonso]

Great @northwestwitch !! I had some comments but everything looks awesome

[moonso]

Suggested change

	docker-compose run beacon-cli /bin/bash
	docker-compose run -d beacon-cli

You can use -d to run the container in background. Also you could add

CMD ["/bin/bash"]

to the Dockerfile instead

[northwestwitch]

If I include the CMD command in the Dockerfile it's not usable any more for launching the server.

[northwestwitch]

I can't use -d here because then it won't be interactive any more. I'd just get the ID of the image and I won't be able to type and run commands in the shell

[moonso]

It would be nice if there was some test data and instruction for how to populate the database for testing only

[northwestwitch]

Good idea, I'll add the command to load the demo data!

[northwestwitch]

The command to load the data is actually already included in the demo, but I'll comment about it in the readme and the docs

[moonso]

Suggested change

	LABEL maintainer="Chiara Rasi <chiara.rasi@scilifelab.se>"

You could also add some more labels here to describe the container. Have a look at @jemten and @henrikstranneheim examples in MIP for inspiration

[northwestwitch]

I'll check, thanks!

[moonso]

Very nice! Again the test data would be nice here as well

[northwestwitch]

👍