The o2r platform

Leveraging reproducible research by providing a powerful user interface for the o2r Web API.

Libraries

AngularJS
Bootstrap

Dependencies

bower

Install

bower install

Run only platform project in a container

docker build --tag platform .

docker run -d -p 80:80 platform

Configure

Create a copy of the file client/app/config/configSample.js and name it client/app/config/config.js. You can configure the required application settings in this file ../config.js:

window.__env.server = /*String containing server address*/;
window.__env.api = /*String containing base api*/;
window.__env.sizeRestriction = /*integer*/;
window.__env.disableTracking = /*true/false, default is true*/;
window.__env.enableDebug = /*true/false, default is false*/;
window.__env.piwik = /*String containing Piwik server address*/;
window.__env.userLevels = {};
window.__env.userLevels.admin = /*Integer containing the required user level for admin status*/;
window.__env.userLevels.regular = /*Integer containing the required user level for regular status*/;
window.__env.userLevels.restricted = /*Integer containing the required user level for restricted status*/;

Development environment with Docker Compose

You can start all required o2r microservices (using latest images from Docker Hub) with just two commands using docker-compose (version 1.9.0+) and Docker (version 1.13.0+).

First, read the instructions on "Basics" and "Prerequisites" to prepare your host machine in the reference-implementation project.

This project contains one docker-compose configuration (file docker-compose.yml) to run all microservices & databases, and mount the client application directly from the source directory client. If you see an error related to the MongoDB in the first "up", abort and restart.

The client must be build on the host!

Running the platform

The services can be started using docker-compose on the following platforms

Unix based systems
Windows with Docker for Windows

by running:

docker-compose up

The platform is available at http://localhost.

Configuration (optional)

The platform provides two options to pass on environment variables to configure authorization, remote repositories and the Slack monitoring bot:

The .env file contains default values to configure the platform to work with the offline OAuth server [o2r-guestlister]https://github.com/o2r-project/o2r-guestlister). Note that quotation marks are not parsed but instead treated as part of the variable value. For more information on how the .env file works, see the docker-compose documentation.
Environment variables defined in the shell have priority over the values set in the .env file and can to override the default configuration, for example to use ORCID as the OAuth server:

OAUTH_CLIENT_ID=<...> OAUTH_CLIENT_SECRET=<...> OAUTH_URL_CALLBACK=<...> SHIPPER_REPO_TOKENS=<...> docker-compose up

Strings containing quotation marks (e.g. SHIPPER_REPO_TOKENS) have to be escaped when used in the shell. For details on configuring the platform to use ORCID instead of the o2r-guestlister, see the ORCID section in the reference implementation documentation.

The environment parameters are as follows:

OAUTH_CLIENT_ID identifier for the platform with auth provider
OAUTH_CLIENT_SECRET password for identification with the auth provider
OAUTH_URL_CALLBACK the URL that the authentication service redirects the user to, important to complete the authentication, probably http://localhost/api/v1/auth/login
SHIPPER_REPO_TOKENS a JSON object, that holds the authentication tokens for shipping to remote repositories such as Zenodo (optional). Must have the (unescaped) form {"zenodo": "$ZENODO_TOKEN", "zenodo_sandbox": "$ZENODO_SANDBOX_TOKEN", "download": "" }. Replace $ZENODO_TOKEN etc. with your personal access token.
SLACK_BOT_TOKEN and SLACK_VERIFICATION_TOKEN, required for monitoring with Slack (optional)

Configuration with Docker for Windows

When using the shell to provide environmental variables, these must be passed separately on Windows, followed by the docker-compose commands:

$env:OAUTH_CLIENT_ID = <...>
$env:OAUTH_CLIENT_SECRET = <...>
$env:OAUTH_URL_CALLBACK = <...>
$env:ZENODO_TOKEN = <...>
docker-compose up

Restart from scratch

You can remove all containers and images by o2r with the following two commands on Linux:

docker ps -a | grep o2r | awk '{print $1}' | xargs docker rm -f
docker images | grep o2r | awk '{print $3}' | xargs docker rmi --force

Use non-default version of o2r-meta and containerit

Two core steps for compendium creation are provided by the standalone tools o2r-meta and containerit. These tools are used in a containerized version with different version tags (o2r-meta, containerit) and the specific tool can be selected via an environment variable for both muncher and loader in the compose configuration (see comments in the file).

For metadata extraction and brokering, see the respective loader configuration property LOADER_META_TOOL_CONTAINER and muncher configuration property MUNCHER_META_TOOL_CONTAINER. For testing metadata tools under development setting the property to o2rproject/o2r-meta:dev can be useful.

For container manifest creation, see the muncher configuration property MUNCHER_CONTAINERIT_IMAGE.

Note

(Re-)starting containers manually might cause problems with the platform due to newly assigned IP-addressees. To avoid this problem, restart the platform container after (re-)starting other containers manually.

User levels

The o2r microservices require users to have specific user level to be allowed certain tasks. By default, users may create compendia, but if you want to develop features for editors or admins, you can adjust a user's level in the admin view (.

Proxy for o2r microservices

If you run the o2r microservices locally as a developer (e.g. by manually starting each microservice via npm start), it is useful to run a local nginx to make all API endpoints available under one port (80), and use the same nginx to serve the application in this repo. A nginx configuration file to achieve this is dev/nginx-microservices.conf.

docker run --rm --name o2r-platform --network="host" -p 80:80 -v $(pwd)/dev/nginx-microservices.conf:/etc/nginx/nginx.conf:ro -v $(pwd)/client:/usr/share/nginx/html:ro -v $(pwd)/dev:/etc/nginx/html/dev:ro nginx:stable-alpine

# bash inside the container for debugging IPs:
docker exec -it o2r-platform /bin/bash
# get the host machine IP from inside the container (use this if the default 172.17.0.1 does not work):
ip addr show docker0 | grep -Po 'inet \K[\d.]+'

Note: If you want to run this in a Makefile, $(CURDIR) will come in handy to create the mount paths instead of using $(pwd).

WebSocket testing

The compose configuration also makes a simple test page for WebSockets available at http://localhost/dev/socket.html (based on file dev/socket.html).

Platform Version

1.0.0

Timmimim/o2r-platform