ChRIS plugin apps store
Switch branches/tags
Nothing to show
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Failed to load latest commit information.
docs
requirements
store_backend
utils/ssl_cert
.dockerignore
.env
.gitignore
.travis.yml
Dockerfile
Dockerfile_dev
LICENSE
README.md
decorate.sh
docker-compose.yml
docker-destroy.sh
docker-make.sh

README.md

ChRIS_store

Build Status

Back end for ChRIS Store. This is a Django-MySQL project.

ChRIS Store development and testing

Abstract

This page describes how to quickly get the set of services comprising the backend up and running for development and how to run the automated tests.

Preconditions

Install latest Docker and Docker Compose. Currently tested platforms

  • Docker 17.04.0+
  • Docker Compose 1.10.0+
  • Ubuntu (16.04/17.04/17.10) and MAC OS X 10.11+

Make sure to add your computer user to the docker group in your machine

Install virtualenv

pip install virtualenv virtualenvwrapper

Setup your virtual environments

Create a directory for your virtual environments e.g.:

mkdir ~/Python_Envs

You might want to add to your .bashrc file these two lines:

export WORKON_HOME=~/Python_Envs
source /usr/local/bin/virtualenvwrapper.sh

Then you can source your .bashrc and create a new Python3 virtual environment:

mkvirtualenv --python=python3 chris_store_env

To activate chris_store_env:

workon chris_store_env

To deactivate chris_store_env:

deactivate

Checkout the Github repo

git clone https://github.com/FNNDSC/ChRIS_store.git

Install useful python tools in your virtual environment

cd ChRIS_store
workon chris_store_env
pip install httpie
pip install django-storage-swift
pip install docker

You can also install some python libraries (not all of them) specified in the requirements/base.txt and requirements/local.txt files in the source repo

To list installed dependencies in chris_store_env:

pip freeze --local

Instantiate ChRIS Store

Start ChRIS Store from the repository source directory by running the make bash script

./docker-make.sh

All the steps performed by the above script are properly documented in the script itself.

After running this script all the automated tests should have successfully run and a Django development server should be running in interactive mode in this terminal.

Rerun automated tests after modifying source code

Open another terminal and run

docker ps

Find out from the previous output the name of the container running the Django server in interactive mode (usually chrisstore_chris_store_dev_run_1) and run the Unit tests and Integration tests within that container. For instance to run only the Unit tests:

docker exec -it chrisstore_chris_store_dev_run_1 python manage.py test --exclude-tag integration

To run only the Integration tests:

docker exec -it chrisstore_chris_store_dev_run_1 python manage.py test --tag integration

To run all the tests:

docker exec -it chrisstore_chris_store_dev_run_1 python manage.py test 

Check code coverage of the automated tests

Make sure the store_backend/ dir is world writable. Then type:

docker exec -it chrisstore_chris_store_dev_run_1 coverage run --source=plugins,users manage.py test
docker exec -it chrisstore_chris_store_dev_run_1 coverage report

Using httpie to play with the REST API

A simple GET request:

http -a cube:cube1234 http://localhost:8010/api/v1/

A simple POST request to register a new plugin app in the store:

First save the plugin representation json file by running the plugin with the --savejson flag:

docker run --rm -v /tmp/json:/json fnndsc/pl-simplefsapp simplefsapp.py --savejson /json

Then upload the plugin representation json file to the ChRIS Store as part of the POST request:

http -a cube:cube1234 -f POST http://localhost:8010/api/v1/ dock_image=fnndsc/pl-simplefsapp descriptor_file@/tmp/json/SimpleFSApp.json public_repo=https://github.com/FNNDSC/pl-simplefsapp name=simplefsapp

An unauthenticated POST request to create a new ChRIS store user account:

http POST http://localhost:8010/api/v1/users/ Content-Type:application/vnd.collection+json Accept:application/vnd.collection+json template:='{"data":[{"name":"email","value":"developer@babymri.org"}, {"name":"password","value":"newstoreuser1234"}, {"name":"username","value":"newstoreuser"}]}'

Using swift client to list files in the store_users bucket

swift -A http://127.0.0.1:8080/auth/v1.0 -U chris:chris1234 -K testing list store_users

Destroy ChRIS Store

Stop and remove ChRIS Store services by running the destroy bash script from the repository source directory

./docker-destroy.sh

REST API Documentation

Available here.

Install Sphinx and the http extension (useful to document the REST API)

pip install Sphinx
pip install sphinxcontrib-httpdomain

Build the html documentation

cd docs/
make html