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Short Description
Badges for reproducible research
Full Description

o2r badger

API for retrieving scalable badges for scientific publications. Used by the o2r-extender, which is a Chrome extension that integrates these badges into several research aggregators.

Based on the Badges for computational geoscience containers study project at ifgi.

Badges:

  • executable: Information about executability and reproducibility of a publication.
  • licence: The license type.
  • spatial: Where research took place.
  • releasetime: The publication date.
  • peerreview: If and by which process the publication was peer reviewed.

Services and what they are used for:

  • o2r: executable, licence, location
  • crossref: releasetime
  • DOAJ: peerreview

Note that the badger will only find results if the respective service has the publication listed.

Requirements

Installation

There are three options to get the badger running on your system.

1) with Docker, via Docker Hub

docker pull o2rproject/o2r-badger

# Start the badger:
docker run -it -e DEBUG=* -p 8089:8089 o2rproject/o2r-badger

2) with Docker, locally build image

First, clone the repository: git clone https://github.com/o2r-project/o2r-badger

This project includes a Dockerfile which can be built with:

docker build -t badger -f Dockerfile.local .

## Start the badger:
docker run -it -e DEBUG=* -p 8089:8089 badger

3) with Node.js

git clone https://github.com/o2r-project/o2r-badger
cd o2r-badger
npm install --production

# Start the badger:
DEBUG=* npm start

The badger is running and can be accessed via http://localhost:8089/. To display badges for common research aggregators, install the o2r-extender, a chrome extension. More info here

Examples

1) GET (peer review badge, small):

curl http://localhost:8089/api/1.0/badge/peerreview/10.5194%2Fgmdd-8-3905-2015

Returns a small badge for the DOI 10.5194/gmdd-8-3905-2015:

2) POST (license badge, extended):

curl -o output.svg -H "Content-Type: application/json" --data '{  
   "id":"opxYU",
   "created":"2016-08-19T13:59:13.134Z",
   "metadata":{  
      "licence":{  
         "data":"Against-DRM",
         "text":"CC-BY-4.0",
         "code":"AAL"
      }
   }
}' http://localhost:8089/api/1.0/badge/licence/extended

Will return a big badge for the license data contained in the json document (o2r compendium):

API Documentation (Version 0.2)

Small badges:

GET /api/1.0/badge/:type/:doi

The badger can also create a badge for information that is sent via a POST request (see the example above):

POST /api/1.0/badge/:type

Extended badges:

GET /api/1.0/badge/:type/:doi/extended

POST /api/1.0/badge/:type/extended

Path paramters

  • :type: Badge type, one of executable, spatial, licence, releasetime or peerreview
  • :doi: A DOI to identify the publication, in the form 10.999/test

The DOI must be URL encoded!

Body parameters (for extended badges only)

  • format - The image format for extended badges. May be svg or png
  • width - The image width for extended badges

Error responses

If the badger finds no data for a given DOI a grey "n/a" badge is returned:

If there is an unexpected error during execution, or if the services are not accessbile, an error will be returned:

404 Not found
{"error":"error accessing crossref API"}

Configuration

Most relevant configuration can be done via the following environment variables when starting the service.
They are picked up in the file config/config.js where all configuration settings can be changed.

  • BADGER_PORT
    Defines the port the badger is listening to. Defaults to 8089.
  • BADGER_O2R_HOST
    The address used to query the o2r API . Defaults to https://o2r.uni-muenster.de.
  • BADGER_TEST_ENDPOINT
    The address used for tests. Defaults to http://localhost

Other settings in config.js without corresponding environment variable:

  • c.net.proxy
    Proxy used for all outgoing requests (o2r, crossref, doaj). Not tested.
  • c.ext.crossref
    Crossref API endpoint.
  • c.ext.o2r
    o2r endpoint. Can be modified via BADGER_O2R_HOST.
  • c.ext.doajArticles and c.ext.doajJournals
    DOAJ search endpoint for articles and journals.

Development

First install the badger locally:

npm install

Then start it with npm start or in your development environment.

For tests run npm test.

Study project documentation (shortened)

This work is based on the study project "Badges for computational geoscience containers", see here and the original code repos.
We thank the valuable contributions of the students in this project.

1 Scalable badges (geocontainer-badges/scalability)

This project provides an API for retrieving a scalable badge as svg or png.

2 Spatial information badges (geocontainer-badges/spatial-information)

This badge will provide the user information about where a research took place.
The base for receiving those information is a bounding box in json format.
For the small badge, the mean center of the bounding box is calculated and sended via reverse geocoding to the geocoding service geonames.org. This service sends back
the country and if available also the district.
For the extended badge, the spatial information can be requested via the o2r API /spatial/o2r/:id/extended. When requesting the API, the user receives a Leaflet Map
where the bounding box of the research location is highlighted.

3 Executability badges (geocontainer-badges/executable-code)

The project developed an API for retrieving information on the executability of compendia.
It was established in the context of the o2r project.
The information about the executablility of a compendia are requested from the o2r API.

4 License badges (geocontainer-badges/licencing)

The project's aim is to provide an API, which gives information about the licencing of a research compendium.

The API is specified as: /api/1.0/badge/licence/:id/:extended?. With :id specifying the ID of the research compendium and :extended is optional. If extended is given in the URL, the big badges are sent to the client. Otherwise, small badges from shields.io are the response.
For licences of code (software) the list of licences available at Open Definition Licenses Service
with this json file is provided.
For licences of data and text of the research compendia the licences from Open Definition is used
with the list in this json file.

5 Release date badges (geocontainer-badges/release)

In this project we developed an API for retrieving badges which provide information about the release date of a compendium.

API to receive a release-badge for a compendium with a specific DOI (testing locally):
http://localhost:8089/api/1.0/badge/releasetime/:id/

with id being an URL-encoded DOI of an published compendium. To receive a "big badge" for a paper page, "extended" has to be added at the end of the API.

The information about the release date are requested through the crossref API.

6 Peer-review badges (geocontainer-badges/peer-review)

Our Task

Creating badges to check if a journel is peer reviewed or not.

Components of our task:

  • Application Sever (Badge API)
  • API for DOAJ (Directory of Open Access Journals)
  • API for Shields.io (A platform that serves fast and scalable information images a s badges)
  • Web Client
  • Docker Container

Usage

The following API calls are supported (localhost might need to be replaced by a custom host name or IP address):

As you will notice currently the only service supported is DOAJ, with a DOI as identifier. An example request would be:

Known issues and limitations

  • There are only 'peer-reviewed' journals in the DOAJ so we just get a green badge in return having no case of 'non peer-reviewed'.

Licence

This project is licensed under Apache License 2.0.

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lukaslohoff
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