Merge pull request #39 from jiahao/cjh/read_graphml

Provide read_graphml

src/LightGraphs.jl

@@ -69,7 +69,7 @@ module LightGraphs
     a_star,
 
     # persistence
-    readgraph,
+    readgraph, read_graphml,
 
     # randgraphs
     erdos_renyi, watts_strogatz

src/persistence.jl

@@ -62,3 +62,83 @@ function write(
     close(f)
     return res
 end
+
+
+
+_HAS_LIGHTXML = try
+        using LightXML
+        true
+    catch
+        false
+    end
+
+if _HAS_LIGHTXML
+
+#@doc """
+#Reads in a GraphML file as an array of Graphs or Digraphs
+#
+#Input:
+#
+#    filename
+#
+#Returns:
+#
+#    An array of (name, AbstractGraph) tuple
+#""" ->
+function read_graphml(filename::String)
+    xdoc = parse_file(filename)
+    xroot = root(xdoc)  # an instance of XMLElement
+    name(xroot) == "graphml" || error("Not a GraphML file")
+
+    # traverse all its child nodes and print element names
+    graphs = (String, AbstractGraph)[]
+    for c in child_nodes(xroot)  # c is an instance of XMLNode
+        if is_elementnode(c)
+            e = XMLElement(c)  # this makes an XMLElement instance
+            if name(e) == "graph"
+                nodes = Dict{String,Int}()
+                edges = (Int, Int)[]
+                graphname = has_attribute(e, "id") ? attribute(e, "id") : nothing
+                edgedefault = attribute(e, "edgedefault")
+                isdirected = edgedefault=="directed" ? true :
+                             edgedefault=="undirected" ? false : error("Unknown value of edgedefault: $edgedefault")
+            else
+                error("Unknown node $(name(e))")
+            end
+
+            nodeid = 1
+            for f in child_elements(e)
+                if name(f) == "node"
+                    nodes[attribute(f, "id")] = nodeid
+                    nodeid += 1
+                elseif name(f) == "edge"
+                    n1 = attribute(f, "source")
+                    n2 = attribute(f, "target")
+                    push!(edges, (nodes[n1], nodes[n2]))
+                else
+                    error("Unknown node $(name(f))")
+                end
+            end
+            #Put data in graph
+            g = (isdirected ? DiGraph : Graph)(length(nodes))
+            for (n1, n2) in edges
+                add_edge!(g, n1, n2)
+            end
+            push!(graphs, (graphname, g))
+        end
+    end
+    graphs
+end
+
+else
+
+#@doc """
+#Reads in a GraphML file as an array of Graphs or Digraphs
+#
+#Requires the LightXML package to be insta.
+#""" ->
+function read_graphml(filename::String)
+    error("needs LightXML")
+end
+
+end

test/data/grafo1853.13.graphml

@@ -0,0 +1,35 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- This file was written by the internal XML-Handler of Y-Files.-->
+<!DOCTYPE graphml SYSTEM "http://www.graphdrawing.org/dtds/graphml.dtd">
+<graphml>
+<graph edgedefault="undirected" id="G">
+<node id="n0"/>
+<node id="n1"/>
+<node id="n2"/>
+<node id="n3"/>
+<node id="n4"/>
+<node id="n5"/>
+<node id="n6"/>
+<node id="n7"/>
+<node id="n8"/>
+<node id="n9"/>
+<node id="n10"/>
+<node id="n11"/>
+<node id="n12"/>
+<edge id="e0" source="n0" target="n1"/>
+<edge id="e1" source="n0" target="n3"/>
+<edge id="e2" source="n4" target="n5"/>
+<edge id="e3" source="n6" target="n1"/>
+<edge id="e4" source="n4" target="n1"/>
+<edge id="e5" source="n4" target="n3"/>
+<edge id="e6" source="n7" target="n1"/>
+<edge id="e7" source="n2" target="n7"/>
+<edge id="e8" source="n2" target="n8"/>
+<edge id="e9" source="n9" target="n6"/>
+<edge id="e10" source="n8" target="n10"/>
+<edge id="e11" source="n5" target="n11"/>
+<edge id="e12" source="n11" target="n2"/>
+<edge id="e13" source="n12" target="n11"/>
+<edge id="e14" source="n12" target="n7"/>
+</graph>
+</graphml>

test/persistence.jl

@@ -7,3 +7,23 @@
 @test length(sprint(write, p2)) == 51
 
 rm(f)
+
+_HAVE_LIGHTXML = try
+        using LightXML
+        true
+    catch
+        false
+    end
+
+if _HAVE_LIGHTXML
+#Try reading in a GraphML file from the Rome Graph collection
+#http://www.graphdrawing.org/data/
+let Gs = read_graphml("data/grafo1853.13.graphml")
+    @test length(Gs) == 1
+    @test Gs[1][1] == "G" #Name of graph
+    G = Gs[1][2]
+    @test nv(G) == 13
+    @test ne(G) == 15
+end
+end # _HAVE_LIGHTXML
+