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

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.

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

pip install virtualenv virtualenvwrapper

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

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

cd ChRIS_store
workon chris_store_env
pip install httpie
pip install python-swiftclient
pip install django-storage-swift

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

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.

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 chris_store_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 chris_store_chris_store_dev_run_1 python manage.py test --exclude-tag integration

To run only the Integration tests:

docker exec -it chris_store_chris_store_dev_run_1 python manage.py test --tag integration

To run all the tests:

docker exec -it chris_store_chris_store_dev_run_1 python manage.py test

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

docker exec -it chris_store_chris_store_dev_run_1 coverage run --source=plugins,users manage.py test
docker exec -it chris_store_chris_store_dev_run_1 coverage report

http -a cubeadmin:cubeadmin1234 http://localhost:8010/api/v1/

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 cubeadmin:cubeadmin1234 -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

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

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

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

./docker-destroy.sh

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