CORE-RE

Description:

The main goal of the project is to make these verification tools cost-effective and easily accessible, so journals may implement and enforce more rigorous data policies. This will oblige researchers to in turn adopt more transparent practices and promote reproducible research of the highest quality and integrity throughout the scientific community.

Table of Contents:

• Requirements
• Installation
• Usage
• Contributing
• Credits
• License
• Future Work

Requirements:

Python 3.7+ required

Anaconda is suggested but not required.

Kubernetes and Docker is required for running binderhub. (https://binderhub.readthedocs.io/en/latest/)

@andreyodum/core2 jupyterlab extension to use with jupyterhub (installed automatically)

R and R server (automatically installed by binderhub)

CentOS or RHEL is preferred, but is not required.

Installation:

The CORE-RE project consits of three components: CORE-RE server, binderhub server, and gitlab server.

The latter two can be downlaoded and set up using the following sites:

https://about.gitlab.com/ https://binderhub.readthedocs.io/en/latest/

Setting up CORE-RE server

Install the latest version of Python 3 if you haven't already.

Run the following command:

pip install -r requirements.txt

This will install the following libraries:

authlib==0.10
flask==1.0.2
google-api-python-client
google-auth
virtualenv

Rename config.sample.yaml to config.yaml. Open config.yaml and change parameters accordingly.

config:
  git_config_url: "https://user:secret_token@gitlab_full_url/root/test.git/"
  git_lab_url: "gitlab_full_url"
  git_api_version: "api/v4/"
  git_private_token: "private_git_token"
  receipients: "[email protected]

git_config_url : URL for commiting to gitlab repository from binderhub pod.

git_lab_url: URL for gitlab. Used by CORE-RE to download and commit to repository.

git_api_version: only "api/v4?" is supported at this stage

git_private_token: private token used by CORE-RE server that has global access.

recipients: a list of emails (seperated by comma) to use to email changes in git repository.

Run ./run.sh file to launch the server or run the following commands in the terminal (change the URLS appropriately):

export FN_AUTH_REDIRECT_URI=http://localhost:5000/google/auth
export FN_BASE_URI=http://localhost:5000
export FN_CLIENT_ID=GOOGLE_CLIENT_ID_GOES_HERE
export FN_CLIENT_SECRET=GOOGLE_CLIENT_SECRET_GOES_HERE

export FN_GITHUB_CLIENT_ID=GITHUB_CLIENT_ID_GOES_HERE
export FN_GITHUB_CLIENT_SECRET=GITHUB_CLIENT_SECRET_GOES_HERE

export FLASK_APP=index.py
export FLASK_DEBUG=1
export FN_FLASK_SECRET_KEY=RANDOMSECRETdsjaldsajio

export DATABASE_URL="postgresql://localhost/core"

python -m flask run -p 5000

Setting up Binderhub server

Minikubernetes Instruction

Follow the guide found here: https://github.com/jupyterhub/binderhub/blob/master/CONTRIBUTING.md

or use the following (This guide assumes you are on CentOS):

sudo apt install socat -y

Download and install kubectl

curl -LO https://storage.googleapis.com/kubernetes-release/release/$(curl -s https://storage.googleapis.com/kubernetes-release/release/stable.txt)/bin/linux/amd64/kubectl

chmod +x ./kubectl

sudo mv ./kubectl /usr/local/bin/kubectl

Install VirtualBox

Download the latest version of virtualbox at https://www.virtualbox.org/wiki/Downloads

Install Minikube

curl -Lo minikube https://storage.googleapis.com/minikube/releases/latest/minikube-linux-amd64 \
  && chmod +x minikube

Add minikube executable to the path

sudo install minikube /usr/local/bin

Start Minikube

minikube start

Clone the binderhub repository to your local computer and cd into it.

git clone https://github.com/jupyterhub/binderhub
cd binderhub

Install helm to manage installating JupyterHub and Binderhub on cluster.

curl https://raw.githubusercontent.com/kubernetes/helm/master/scripts/get | bash

Initialize helm in minikube.

helm init

Add JupyterHub helm charts repo

helm repo add jupyterhub https://jupyterhub.github.io/helm-chart/
helm repo update

Install BinderHub and its development requirements

python3 -m pip install -e . -r dev-requirements.txt

Copy the following into your binderhub directory. File Path: binderhub/testing/minikube/binderhub_config.py

# config file for testing with minikube-config.yaml
import subprocess
try:
    minikube_ip = subprocess.check_output(['minikube', 'ip']).decode('utf-8').strip()
except (subprocess.SubprocessError, FileNotFoundError):
    minikube_ip = '192.168.1.100'

c.BinderHub.hub_url = 'http://{}:30123'.format(minikube_ip)
c.BinderHub.hub_api_token = 'aec7d32df938c0f55e54f09244a350cb29ea612907ed4f07be13d9553d18a8e4'
c.BinderHub.use_registry = False
c.BinderHub.build_namespace = 'binder-test'

### The command below is important to allow other hosts to access
### Feel free to change this setting to only allow access from specific domain
c.BinderHub.tornado_settings.update({
        'headers': {
            'Access-Control-Allow-Origin': '*',
        }
})

Install JupyterHub in minikube

./testing/minikube/install-hub

Set up docker daemon

eval $(minikube docker-env)

Start BinderHub with the testing config file

python3 -m binderhub -f testing/minikube/binderhub_config.py

Visit http://localhost:8585

Your binderhub should now be set up on the server.

Kubernetes Instructions

Follow the guide found at: https://binderhub.readthedocs.io/en/latest/create-cloud-resources.html

Setting up GitLab Server

Follow instructions found on https://about.gitlab.com/install/ to set up your own gitlab. There is not really anything you need to do except to get the private token.

Usage

Future work

User Roles

Detection

Contributing

Thank you for your interest in contributing to CORE-RE Project! We welcome any contribution from anybody. If you have any questions, please feel free to reach out to us. If you want to add a feature, please create a fork, add the feature, and create a pull request. If you have an issue, please search if there are existing similar issues using the search bar in the issues tab. If an existing open issue exists, contribute to it. Otherwise, please create a new issue.

Credits

Odum Institute

University of North Carolina at Chapel Hill

License

(MIT)

Copyright 2019 Odum Institute

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.