ChRIS_ultron_backEnd

The core backend service for the ChRIS distributed software platform, also known by the anacronym "CUBE". Internally the service is implemented as a Django-PostgreSQL project offering a collection+json REST API. Important ancillary components include the pfcon and pman file transfer and remote process management microservices.

ChRIS development, testing and deployment

Abstract

This page describes how to quickly get the set of services comprising the ChRIS backend up and running for CUBE development and how to run the automated tests. A production deployment of the ChRIS backend services is also explained.

Preconditions

Install latest Docker and Docker Compose.

Currently tested platforms:

• Docker 18.06.0+
• Docker Compose 1.27.0+
• Ubuntu 18.04+ and MAC OS X 10.14+

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 backend services up and running with no mess, no fuss:

Start a local Docker Swarm cluster if not already started:

docker swarm init --advertise-addr 127.0.0.1

Get the source code from CUBE repo:

git clone https://github.com/FNNDSC/ChRIS_ultron_backend
cd ChRIS_ultron_backend

Run full CUBE instantiation with tests:

./unmake.sh ; sudo rm -fr CHRIS_REMOTE_FS; rm -fr CHRIS_REMOTE_FS; ./make.sh

Or skip unit and integration tests and the intro:

./unmake.sh ; sudo rm -fr CHRIS_REMOTE_FS; rm -fr CHRIS_REMOTE_FS; ./make.sh -U -I -s

Once the system is "up" you can add more compute plugins to the ecosystem:

./postscript.sh

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

Production deployments

For convenience a deploy.sh bash script is provided as part of the Github repo's source code. Internally the script uses the docker stack or Kustomize tools to deploy on a Swarm or Kubernetes cluster respectively.

Fetch the repo's source code:

git clone https://github.com/FNNDSC/ChRIS_ultron_backend
cd ChRIS_ultron_backend

Deploy on a single-machine Docker Swarm cluster:

• Create appropriate secrets subdirectory:

mkdir swarm/prod/secrets

• Copy all the required secret configuration files into the secrets directory, please take a look at this wiki page to learn more about these files.

• Deploy CUBE backend containers:

./deploy.sh up

• Tear down and remove CUBE backend containers:

cd ChRIS_ultron_backend
./deploy.sh down

Deploy on a Kubernetes cluster:

• Create appropriate secrets subdirectory:

mkdir kubernetes/prod/secrets

• Copy all the required secret configuration files into the secrets directory, please take a look at this wiki page to learn more about these files.

Single-machine deployment:

• Deploy CUBE backend containers:

./deploy.sh -O kubernetes up

• Tear down and remove CUBE backend containers:

cd ChRIS_ultron_backend
./deploy.sh -O kubernetes down

Multi-machine deployment (with NFS-based persistent storage):

• Deploy CUBE backend containers:

./deploy.sh -O kubernetes -T nfs -P <nfs_server_ip> -S <storeBase> -D <storageBase> up

• Both storeBase and storageBase are explained in the header documentation of the deploy.sh script.

• Tear down and remove CUBE backend containers:

cd ChRIS_ultron_backend
./deploy.sh -O kubernetes -T nfs -P <nfs_server_ip> down

Development

Docker Swarm-based development environment:

Start a local Docker Swarm cluster if not already started:

docker swarm init --advertise-addr 127.0.0.1

Start CUBE from the repository source directory by running the make bash script

git clone https://github.com/FNNDSC/ChRIS_ultron_backEnd.git
cd ChRIS_ultron_backEnd
./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.

Later you can stop and remove CUBE services and storage space by running the following bash script from the repository source directory:

./unmake.sh

Then remove the local Docker Swarm cluster if desired:

docker swarm leave --force

Kubernetes-based development environment:

Install single-node Kubernetes cluster. On MAC OS Docker Desktop includes a standalone Kubernetes server and client. Consult this page https://docs.docker.com/desktop/kubernetes/. On Linux there is a simple MicroK8s installation. Consult this page https://microk8s.io. Then create the required alias:

snap alias microk8s.kubectl kubectl
microk8s.kubectl config view --raw > $HOME/.kube/config

Start the Kubernetes cluster:

microk8s start

Start CUBE from the repository source directory by running the make bash script

git clone https://github.com/FNNDSC/ChRIS_ultron_backEnd.git
cd ChRIS_ultron_backEnd
export HOSTIP=<IP address of this machine>
./make.sh -O kubernetes

Later you can stop and remove CUBE services and storage space by running the following bash script from the repository source directory:

./unmake.sh -O kubernetes

Stop the Kubernetes cluster if desired:

microk8s stop

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:

cd ChRIS_ultron_backEnd
docker-compose -f docker-compose_dev.yml exec chris_dev python manage.py test --exclude-tag integration

To run only the Integration tests:

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

To run all the tests:

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

After running the Integration tests the ./CHRIS_REMOTE_FS directory must be empty otherwise it means some error has occurred and you should manually empty it.

Check code coverage of the automated tests

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

docker-compose -f docker-compose_dev.yml exec chris_dev coverage run --source=feeds,plugins,uploadedfiles,users manage.py test
docker-compose -f docker-compose_dev.yml exec chris_dev coverage report

Using HTTPie client to play with the REST API

A simple GET request to retrieve the user-specific list of feeds:

http -a cube:cube1234 http://localhost:8000/api/v1/

A simple POST request to run the plugin with id 1:

http -a cube:cube1234 POST http://localhost:8000/api/v1/plugins/1/instances/ Content-Type:application/vnd.collection+json Accept:application/vnd.collection+json template:='{"data":[{"name":"dir","value":"cube/"}]}'

Then keep making the following GET request until the "status" descriptor in the response becomes "finishedSuccessfully":

http -a cube:cube1234 http://localhost:8000/api/v1/plugins/instances/1/

Using swift client to list files in the users bucket

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

Documentation

REST API reference

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

ChRIS REST API design.

Available here.

ChRIS backend database design.

Available here.

Wiki.

Available here.

Learn More

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