Ruby library for parsing, serializing, and manipulating GEXF graphs
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README.md

Gexf.rb

A Ruby library for generating, parsing, and serializing graphs expressed in the GEXF format. Currently, this project implements only a subset of the GEXF specification: the definition of a basic graph topology, and the association of data attributes to nodes and edges. I will possibly implement the rest of the specification later on (i.e. dynamics, hyrarchy, and Phylogeny), as I consolidate the code.

Notice

This gem is not under active development anymore. However, you are wellcome to contribute pull requests, I will do my best to find the time for reviewing and possibly merging them.

Installation

gem install gexf

Usage

The following snippet initializes a GEXF graph, and defines three node attributes:

require 'rubygems'
require 'gexf'

graph = GEXF::Graph.new

graph.define_node_attribute(:url)
graph.define_node_attribute(:indegree, :type    => GEXF::Attribute::INTEGER)
graph.define_node_attribute(:frog,     :type    => GEXF::Attribute::BOOLEAN,
                                       :default => true)

Attribute values can be associated to nodes or edges by using the same syntax used to get/set Ruby Hash keys (symbols are automatically converted into strings).

gephi               = graph.create_node(:label => 'Gephi')
gephi[:url]         = 'http://gephi.org'
gephi[:indegree]    = 1

webatlas            = graph.create_node(:label => 'WebAtlas')
webatlas[:url]      = 'http://webatlas.fr'
webatlas[:indegree] = 2

rtgi                = graph.create_node(:label => 'RTGI')
rtgi[:url]          = 'http://rtgi.fr'
rtgi[:indegree]     = 1

blab                = graph.create_node(:label => 'BarabasiLab')
blab[:url]          = "http://barabasilab.com"
blab[:indegree]     = 1
blab[:frog]         = false

Once associated to a graph, nodes and edges behave as collections, implementing and exposing most of the methods in Ruby's Enumerable module:

graph.nodes.select { |node| !node[:frog] }.map(&:label)
=> 'BarabasiLab'

Edges can be created by calling the graph.create_edges, or more coincisely, by calling connect on the source node.

gephi.connect_to(webatlas)
gephi.connect_to(rtgi)
webatlas.connect_to(gephi)
rtgi.connect_to(webatlas)
gephi.connect_to(blab)

As it is the case for graph.nodes, also edges are enumerable:

graph.edges.count
=> 5

The complete set of edges can be accessed from the main graph object, or fetched on a single node basis:

webatlas.incoming_connections.map { |edge| edge.source.label }
=> ["Gephi", "RTGI"]

Parsing a GEXF document

Gexf.rb provides a basic SAX parser which allows to import GEXF documents into a graph objects suitable to be queried and manipulated. To parse a GEXF file into a graph, just call the GEXF helper method (which is a shortcat to GEXF::Document.parse(file))

require 'gexf'
require 'open-uri'

file  = File.open('http://gexf.net/data/data.gexf', 'r')
graph = GEXF(file)
file.close

graph.nodes.count
=> 4

Exporting a graph into an XML document

A graph object can be easily serialized to XML by just calling:

graph.to_xml
=> "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<gexf xmlns='\"http://www.gexf.net/1.2draft' xmlns....>"

Alternatively, one can obtain the same output by instantiating GEXF::XmlSerializer and calling the serialize! method.

serializer = GEXF::XmlSerializer.new(graph)
serializer.serialize!

Unit tests

Gexf.rb comes with a fairly decent RSpec test suite. The suite can be run from the project directory by issuing the following command:

bundle exec spec -f d spec

Contributors

  • Andrea Fiore
  • Erik Doernenburg
  • Thiago Bueno