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Article-Level Metrics - Alternative Measures to Gauge the Impact of Research

README.md

Article Level Metrics (ALM), is a Ruby on Rails application started by the Public Library of Science (PLOS). It stores and reports user configurable performance data on research articles. Examples of possible metrics are online usage, citations, social bookmarks, notes, comments, ratings and blog coverage.

For more information on how PLOS uses Article-Level Metrics, see http://article-level-metrics.plos.org/.

Version 2.0 of the application was released in July 2012 and has been updated to be compatible with Ruby 1.9.3, Rails 3.2.x, and to store the results of external API calls in CouchDB. The backend processes have been completely rewritten and now uses delayed_job.

Installation

ALM is a standard Ruby on Rails application with the following requirements:

  • Ruby 1.9.3
  • CouchDB 1.1

CouchDB is used to store the responses from external API calls, MySQL is used for everything else. The application has been tested with Apache/Passenger, but should also run in other deployment environments, e.g. Nginx/Unicorn or WEBrick. ALM uses Ruby on Rails 3.2.3.

In a manual installation the following configuration files have to be created using the examples provided:

  • config/database.yml
  • config/settings.yml

Don't forget to set up the CouchDB URL in settings.yml and include username and password if necessary. Also don't forget to add this to the Apache virtual host file in order to keep Apache from messing up encoded embedded slashes in DOIs:

AllowEncodedSlashes On

Using Vagrant/Chef

This is the preferred way to install the ALM application as a developer. The application will automatically be installed in a self-contained virtual machine. Download and install Virtualbox and Vagrant. Then install the application with:

git clone git://github.com/articlemetrics/alm.git alm
cd alm
# (Optional) Enter usernames, passwords and API keys for external sources in dna.json
vagrant up

If there is an error during installation, you can re-run the installation script with vagrant provision. After installation is finished (this can take up to 10 min on the first run) you can access the ALM application with your web browser at

http://localhost:8080

The Rails application runs in Development mode. The database servers are made available at ports 3307 (MySQL) and 5985 (CouchDB). For SSH use command vagrant ssh, the application root is at /vagrant. The MySQL password is randomly generated and is stored at config/database.yml. Seven sources are preconfigured, 5 of them are not activated because you have to first supply passwords or API keys for them. CiteULike and PubMed Central Citations can be used without further configuration. Ten sample articles from PLOS are provided.

Using a Platform as a Service (PaaS) provider

The ALM application can be installed as a hosted solution with a PaaS provider.

Several providers provide hosting for CouchDB, including Cloudant.

Usage

Setup

Groups and sources are already configured if you installed via Chef/Vagrant, or if you issued the rake db:setup command. You can also add groups and sources later with rake db:seed.

The admin user can be created when using the web interface for the first time. After logging in as admin you can add articles and configure sources.

The following configuration options for sources are stored in settings.yml:

  • job_batch_size: number of articles per job (default 200)
  • max_job_batch_size: maximal number of articles per job (default 1000)
  • default_job_batch_size: number of articles per job (default 202)
  • staleness: refresh interval (default 7 days)
  • batch_time_interval (default 1 hour)

The following configuration options for sources are available via the web interface:

  • timeout (default 30 sec)
  • disable delay (default 10 sec)
  • number of workers for the job queue (default 1)
  • whether the results can be shared via the API (default true)
  • maximum number of failed queries allowed before being disabled (default 200)
  • maximum number of failed queries allowed in a time interval (default 86400 sec)

Through these setup options the behavior of sources can be fine-tuned. Please contact us if you have any questions.

Adding articles

Articles can be added via the web interface (after logging in as admin), or via rake doi_import <DOI_DUMP (see below).

Adding metrics

Metrics are automatically added in the background, using the delayed_job queuing system. The results returned by external APIs are stored in CouchDB.

When we have to update the metrics for an article (determined by the staleness interval), a job is added to the background queue for that source. A delayed_job worker will then process this job in the background. We have to set up a queue and at least one worker for every source. In development mode this is done with foreman, using the configuration in Procfile:

foreman start

In production mode the background processes run via the upstartsystem utility. The Chef/Vagrant setup has the upstart scripts already configured, otherwise this can be done (where USER is the user running the web server) via

rvmsudo foreman export upstart /etc/init -a alm -l /USER/log -u USER

More Documentation

In the Wiki at https://github.com/articlemetrics/alm/wiki.

Follow @plosalm on Twitter

You should follow @plosalm on Twitter for announcements and updates.

Mailing List

Please direct questions about the library to the mailing list.

List your application in the Wiki

Does your project or organization use this application? Add it to the FAQ!

Note on Patches/Pull Requests

  • Fork the project
  • Write tests for your new feature or a test that reproduces a bug
  • Implement your feature or make a bug fix
  • Do not mess with Rakefile, version or history
  • Commit, push and make a pull request. Bonus points for topical branches.

Copyright

Copyright (c) 2009-2012 by Public Library of Science. See LICENSE for details.

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