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https://github.com/fnndsc/chris_store

Backend for ChRIS plugin apps store
https://github.com/fnndsc/chris_store

django django-rest-framework docker kubernetes medical openshift pipelines python3 swift-storage

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Backend for ChRIS plugin apps store

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README 

        
# ![ChRIS logo](https://github.com/FNNDSC/ChRIS_store/blob/master/docs/assets/logo_chris.png) ChRIS_store

[![Build Status](https://travis-ci.org/FNNDSC/ChRIS_store.svg?branch=master)](https://travis-ci.org/FNNDSC/ChRIS_store)

![License][license-badge]

![Last Commit][last-commit-badge]



Backend for the ChRIS store. This is a Django-PostgreSQL project that houses descriptions of ChRIS plugin-apps and workflows for registering to a ChRIS CUBE instance.



## ChRIS store development, testing and deployment



### 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. A production deployment of the ChRIS store backend services is also explained.



### Preconditions



#### Install latest Docker and Docker Compose 



Currently tested platforms:

* ``Ubuntu 18.04+ and MAC OS X 10.14+ and Fedora 31+`` ([Additional instructions for Fedora](https://github.com/mairin/ChRIS_store/wiki/Getting-the-ChRIS-Store-to-work-on-Fedora))

* ``Docker 18.06.0+``

* ``Docker Compose 1.27.0+``



#### On a Linux machine make sure to add your computer user to the ``docker`` group 



Consult this page: https://docs.docker.com/engine/install/linux-postinstall/



### TL;DR



If you read nothing else on this page, and just want to get an instance of the ChRIS store backend services up and 

running with no mess, no fuss:



```bash

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

cd ChRIS_store

./make.sh down ; ./make.sh up

```



The resulting instance uses the default Django development server and therefore is not suitable for production.



### Production deployment on a single-machine Docker Swarm cluster



#### To get the production system up:



Start a local Docker Swarm cluster if not already started:



```bash

docker swarm init --advertise-addr 127.0.0.1

```



Fetch source code:



```bash

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

cd ChRIS_store

```



Create ``secrets`` directory:



```bash

mkdir swarm/prod/secrets

```



Now copy all the required secret configuration files into the ``secrets`` directory, please take a look at 

[this](https://github.com/FNNDSC/ChRIS_store/wiki/ChRIS-store-backend-production-services-secret-configuration-files) 

wiki page to learn more about these files 



Deploy ChRIS store backend containers:



```bash

./deploy.sh up

```



#### To tear down:



Remove ChRIS store backend containers:



```bash

cd ChRIS_store

./deploy.sh down

```



Remove the local Docker Swarm cluster if desired:



```bash

docker swarm leave --force

```



### Development



### Instantiate ChRIS Store dev environment



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



```bash

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

./make.sh up

```

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 the Unit and Integration tests within the container running the Django server:



To run only the Unit tests:



```bash

cd ChRIS_store

docker-compose -f docker-compose_dev.yml exec chris_store_dev python manage.py test --exclude-tag integration

```



To run only the Integration tests:



```bash

docker-compose -f docker-compose_dev.yml exec chris_store_dev python manage.py test --tag integration

```



To run all the tests:



```bash

docker-compose -f docker-compose_dev.yml exec chris_store_dev python manage.py test 

```



#### Check code coverage of the automated tests

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



```bash

docker-compose -f docker-compose_dev.yml exec chris_store_dev coverage run --source=plugins,pipelines,users manage.py test

docker-compose -f docker-compose_dev.yml exec chris_store_dev coverage report

```



### Using [HTTPie](https://httpie.org/) to play with the REST API 



#### A simple GET request:

```bash

http 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:

```bash

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

```

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

```bash

http -a cubeadmin:cubeadmin1234 -f POST http://localhost:8010/api/v1/plugins/ dock_image=fnndsc/pl-simplefsapp descriptor_file@/tmp/json/SimpleFSApp.json public_repo=https://github.com/FNNDSC/pl-simplefsapp name=pl-simplefsapp

```



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

```bash

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"}]}'

```



### Destroy ChRIS Store dev environment



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



```bash

./make.sh down

```



### REST API Documentation



Available [here](https://fnndsc.github.io/ChRIS_store).



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

```



[license-badge]: https://img.shields.io/github/license/fnndsc/chris_store.svg

[last-commit-badge]: https://img.shields.io/github/last-commit/fnndsc/chris_store.svg



### Learn More



If you are interested in contributing or joining us, Check [here](http://chrisproject.org/join-us).