Mercurial > repos > bernhardlutz > graphconverter

changeset 1:29cc4ec84a56 draft

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Deleted selected files
author bernhardlutz
date Fri, 28 Feb 2014 09:46:52 -0500
parents fe01a054a6b2
children 89b606a49225
files 3_molecules.gspan convert_graph.py convert_graph.xml deps.txt gspantest2 jsonex jsonwiki neu.gml neu.xgmml neu.xml neu2.gml test-data/bsp_graph.gml test-data/bsp_graph.gml~ test-data/graph2.gexf test.gexf test.gml test.gspan test.json test.xgmml test.xml test.yaml tool_dependencies.xml xgmml_networkx.py xgmml_networkx.pyc
diffstat 23 files changed, 0 insertions(+), 1693 deletions(-) [+]
line wrap: on
line diff
--- a/3_molecules.gspan	Fri Feb 28 08:57:44 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,129 +0,0 @@
-t # id 1
-v 0 O 
-v 1 O 
-v 2 O 
-v 3 O 
-v 4 C 
-v 5 C 
-v 6 C 
-v 7 C 
-v 8 C 
-v 9 C 
-v 10 C 
-v 11 C 
-v 12 C 
-v 13 H 
-v 14 H 
-v 15 H 
-v 16 H 
-v 17 H 
-v 18 H 
-v 19 H 
-v 20 H 
-e 0 4 1
-e 0 11 1
-e 1 10 1
-e 1 20 1
-e 2 10 2
-e 3 11 2
-e 4 5 1
-e 4 6 2
-e 5 7 2
-e 5 10 1
-e 6 8 1
-e 6 13 1
-e 7 9 1
-e 7 14 1
-e 8 9 2
-e 8 15 1
-e 9 16 1
-e 11 12 1
-e 12 17 1
-e 12 18 1
-e 12 19 1
-t # id 2
-v 0 O 
-v 1 O 
-v 2 O 
-v 3 O 
-v 4 C 
-v 5 C 
-v 6 C 
-v 7 C 
-v 8 C 
-v 9 C 
-v 10 C 
-v 11 C 
-v 12 C 
-v 13 H 
-v 14 H 
-v 15 H 
-v 16 H 
-v 17 H 
-v 18 H 
-v 19 H 
-v 20 H 
-e 0 4 1
-e 0 11 1
-e 1 10 1
-e 1 20 1
-e 2 10 2
-e 3 11 2
-e 4 5 1
-e 4 6 2
-e 5 7 2
-e 5 10 1
-e 6 8 1
-e 6 13 1
-e 7 9 1
-e 7 14 1
-e 8 9 2
-e 8 15 1
-e 9 16 1
-e 11 12 1
-e 12 17 1
-e 12 18 1
-e 12 19 1
-t # id 3
-v 0 O 
-v 1 O 
-v 2 O 
-v 3 O 
-v 4 C 
-v 5 C 
-v 6 C 
-v 7 C 
-v 8 C 
-v 9 C 
-v 10 C 
-v 11 C 
-v 12 C 
-v 13 H 
-v 14 H 
-v 15 H 
-v 16 H 
-v 17 H 
-v 18 H 
-v 19 H 
-v 20 H 
-e 0 4 1
-e 0 11 1
-e 1 10 1
-e 1 20 1
-e 2 10 2
-e 3 11 2
-e 4 5 1
-e 4 6 2
-e 5 7 2
-e 5 10 1
-e 6 8 1
-e 6 13 1
-e 7 9 1
-e 7 14 1
-e 8 9 2
-e 8 15 1
-e 9 16 1
-e 11 12 1
-e 12 17 1
-e 12 18 1
-e 12 19 1
--- a/convert_graph.py	Fri Feb 28 08:57:44 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,129 +0,0 @@
-#!/usr/bin/env python
-# Aufruf convert_graph.py --infile datei --informat typ --outfile ausgabedatei --outformat ausgabetyp
-
-import sys, os
-import networkx as nx
-import argparse
-import json
-
-from xgmml_networkx import XGMMLParserHelper, XGMMLWriter
-from networkx.readwrite import json_graph
-
-#supported graph_types
-graph_types = ["gml", "yaml", "gspan", "xgmml", "gexf", "graphml", "json", "pajek"]
-
-func_dic_read= {'gml': nx.read_gml, 'yaml':nx.read_yaml, 'gexf': nx.read_gexf,
-    'graphml': nx.read_graphml, 'pajek': nx.read_pajek}
-    
-func_dic_write= {'gml': nx.write_gml, 'yaml':nx.write_yaml, 'gexf': nx.write_gexf,
-    'graphml': nx.write_graphml, 'pajek': nx.write_pajek}
-
-#completely supported types by networkx
-completely_supported_types = ["gml", "gexf", "yaml", "graphml", "pajek"]
-
-def read_gspan(infile):
-    G = nx.Graph()
-    idoffset=0
-    old_id_start=0
-    for line in infile:
-        line_split=line.split(" ")
-        if line[0] == "v":
-            G.add_node(idoffset, label=line_split[2].strip())
-            idoffset+=1
-        elif line[0] == "e":
-            G.add_edge(old_id_start+int(line_split[1]), old_id_start+int(line_split[2]), label=line_split[3].strip())
-        elif line[0] == "t":
-        # its a new subgraph
-            #idoffset*=1
-            old_id_start=idoffset
-    #print(nx.is_connected(G))
-    return G
-    
-
-def write_gspan(graph, outfile):
-    # get all subgraphs only works with undirected
-    subgraphs=nx.connected_components(graph.to_undirected())
-    id_count=1
-    node_count=0
-    #get labels
-    label_dic=nx.get_node_attributes(graph,'label')
-    for s in subgraphs:
-        node_count_tree=0
-        node_dict={}
-        outfile.write("t # id "+str(id_count)+"\n")
-        # for every node in subgraph
-        for v in sorted(s):
-        # node id restart from 0 for every sub graph
-            node_dict[v]=node_count_tree
-            outfile.write("v "+str(node_count_tree)+" "+label_dic[v]+" \n")
-            node_count_tree+=1
-            node_count+=1
-            
-        # all edges adjacent to a node of s
-        edges=nx.edges(graph, s)
-        for e in sorted(edges):
-            #print(graph[e[0]][e[1]])
-            outfile.write("e "+str(node_dict[e[0]])+" "+str(node_dict[e[1]])+" "+graph[e[0]][e[1]]['label']+"\n")
-            
-        id_count+=1
-def read_json(file):
-    json_string=file.read()
-    print(json_string)
-    json_dict=json.loads(json_string)
-    print(json_dict)
-    return nx.Graph()
-    
-def write_json(graph, outfile):
-    json_dict=json_graph.node_link_data(graph)
-    json_string=json.dumbs(json_dict)
-    outfile.write(json_string)
-    print("did it")
-    
-def main( args ):
-
-    if args.informat not in graph_types:
-        print "EXCEPTION COMPUTER EXPLODING"
-    # everything networkx can do by itself ;)
-    elif args.informat in completely_supported_types:
-        function = func_dic_read[args.informat]
-        graph = function(args.infile)
-    elif args.informat == "gspan":
-        graph = read_gspan(args.infile)
-    elif args.informat == "json":
-        graph = read_json(args.infile)
-    elif args.informat == "xgmml":
-        xgmml=XGMMLParserHelper()
-        xgmml.parseFile(args.infile)
-        graph=xgmml.graph()
-
-
-
-    if args.outformat in completely_supported_types:
-        function = func_dic_write[args.outformat]
-        function(graph, args.outfile)
-    elif args.outformat == "gspan":
-        write_gspan(graph, args.outfile)
-    elif args.outformat == "json":
-        write_json(graph, args.outfile)
-    elif args.outformat == "xgmml":  
-    #xgmml=XGMMLParserHelper(graph)
-    #xgmml.parseFile(open(sys.argv[1]))
-        a=XGMMLWriter(args.outfile, graph, "MyGraph")
-    
-if __name__ == "__main__":
-    
-    parser = argparse.ArgumentParser()
-    parser.add_argument('--infile', type=argparse.FileType('r'),
-        help="Specify the input file representing a graph")
-    parser.add_argument('--outfile', type=argparse.FileType('w'),
-        help="Specify one output file")
-    parser.add_argument('--informat', type=str,
-        help="Specify the format of the input graph", choices = graph_types)
-    parser.add_argument('--outformat', type=str,
-        help="Specify the format of the output graph", choices = graph_types)
-    if len(sys.argv) < 8:
-        print "Too few arguments..."
-        parser.print_help()
-        exit(1)
-    args = parser.parse_args()
-    main( args )
--- a/convert_graph.xml	Fri Feb 28 08:57:44 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,44 +0,0 @@
-<tool id="graph_converter" name="Graph Converter" version="0.1.0">
-    <description>Convert between different Graphformats</description>
-    <version_command>echo "0.1.0"</version_command>
-    <requirements>
-        <requirement type="set_environment">GRAPHCONVERTER_SCRIPT_PATH</requirement>
-    </requirements>
-    <command>
-        python \$GRAPHCONVERTER_SCRIPT_PATH/convert_graph.py --infile $inputfile --informat $informat --outfile $outfile --outformat $outformat
-    </command>
-
-    <inputs>
-        <param format="txt" name="inputfile" type="data" label="Graph to convert" />
-        <param name="informat" multiple="false" type="select" label="Input Format">
-            <option value="gml">GML</option>
-            <option value="gexf">GEXF</option>
-            <option value="gspan">GSPAN</option>
-            <option value="graphml">GRAPHML</option>
-            <option value="json">JSON</option>
-            <option value="pajek">PAJEK</option>
-            <option value="pajek">XGMML</option>
-            <option value="yaml">YAML</option>
-        </param>
-        <param name="outformat" multiple="false" type="select" label="Output Format">
-            <option value="gml">GML</option>
-            <option value="gexf">GEXF</option>
-            <option value="gspan">GSPAN</option>
-            <option value="graphml">GRAPHML</option>
-            <option value="json">JSON</option>
-            <option value="pajek">PAJEK</option>
-            <option value="pajek">XGMML</option>
-            <option value="yaml">YAML</option>
-        </param>
-    </inputs>
-    <outputs>
-        <data format="txt " name="output" />
-    </outputs>
-    <tests>
-    </tests>
-    <help>
-**What it does**
-
-This tool converts a file representing a graph into another format.
-    </help>
-</tool>
--- a/deps.txt	Fri Feb 28 08:57:44 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-libyaml->pyyaml
--- a/gspantest2	Fri Feb 28 08:57:44 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,18 +0,0 @@
-t # id 1
-v 0 O 
-v 3 O  
-e 0 3 1
-t # id 2
-v 0 O 
-v 1 O 
-v 2 O 
-v 3 O 
-e 0 1 1
-e 1 2 1
-e 1 3 1
-
-t # id 3
-v 0 O 
-v 1 O 
-e 0 1 1
-
--- a/jsonex	Fri Feb 28 08:57:44 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,19 +0,0 @@
-{
-    "id": "root",
-    "children": [{
-        id: "n1",
-        labels: [ { text: "n1" } ],
-        width: 100,
-        height: 100,
-    },{
-        id: "n2",
-        labels: [ { text: "n2" } ],
-        width: 100,
-        height: 50
-    }],
-    "edges": [{
-        id: "e1",
-        source: "n1",
-        target: "n2"
-    }]
-}
--- a/jsonwiki	Fri Feb 28 08:57:44 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,16 +0,0 @@
-{
-  "Herausgeber": "Xema",
-  "Nummer": "1234-5678-9012-3456",
-  "Deckung": 2e+6,
-  "Währung": "EURO",
-  "Inhaber": {
-    "Name": "Mustermann",
-    "Vorname": "Max",
-    "männlich": true,
-    "Hobbys": [ "Reiten", "Golfen", "Lesen" ],
-    "Alter": 42,
-    "Kinder": [],
-    "Partner": null
-  }
-}
-
--- a/neu.gml	Fri Feb 28 08:57:44 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,18 +0,0 @@
-graph [
-  directed 1
-  edge_default [ 
-    ]
-  node [
-    id 0
-    label "Word"
-  ]
-  node [
-    id 1
-    label "Hello"
-  ]
-  edge [
-    source 1
-    target 0
-    id "0"
-  ]
-]
--- a/neu.xgmml	Fri Feb 28 08:57:44 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,28 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
-<graph directed="1"  xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns="http://www.cs.rpi.edu/XGMML">
-<att name="selected" value="1" type="boolean" />
-<att name="name" value="xgmml" type="string"/>
-<att name="shared name" value="xgmml" type="string"/>
-
-<node id="1" label="A">
-<att name="weiteresAttribut" value="42" type="string" />
-<att name="id" value="1" type="string" />
-</node>
-<node id="2" label="B">
-<att name="weiteresAttribut" value="43" type="string" />
-<att name="id" value="2" type="string" />
-</node>
-<node id="3" label="C">
-<att name="weiteresAttribut" value="44" type="string" />
-<att name="id" value="3" type="string" />
-</node>
-<edge source="1" target="2">
-<att name="label" value="Kante AB" type="string" />
-</edge>
-<edge source="2" target="3">
-<att name="label" value="Kante BC" type="string" />
-</edge>
-<edge source="3" target="1">
-<att name="label" value="Kante CA" type="string" />
-</edge>
-</graph>
--- a/neu.xml	Fri Feb 28 08:57:44 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
-<graph directed="1"  xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns="http://www.cs.rpi.edu/XGMML">
-<att name="selected" value="1" type="boolean" />
-<att name="name" value="graph" type="string"/>
-<att name="shared name" value="graph" type="string"/>
-
--- a/neu2.gml	Fri Feb 28 08:57:44 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,39 +0,0 @@
-graph [
-  directed 1
-  node [
-    id 1
-    label "A"
-    weiteresAttribut "42"
-  ]
-  node [
-    id 3
-    label "C"
-    weiteresAttribut "44"
-  ]
-  node [
-    id 2
-    label "B"
-    weiteresAttribut "43"
-  ]
-  edge [
-    source 1
-    target 2
-    weiteresAttribut "44"
-    id "3"
-    label "Kante AB"
-  ]
-  edge [
-    source 3
-    target 1
-    weiteresAttribut "44"
-    id "3"
-    label "Kante CA"
-  ]
-  edge [
-    source 2
-    target 3
-    weiteresAttribut "44"
-    id "3"
-    label "Kante BC"
-  ]
-]
--- a/test-data/bsp_graph.gml	Fri Feb 28 08:57:44 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,37 +0,0 @@
-graph [
-	comment "Das ist ein Beispielgraph."
-	directed 1
-	id 42
-	label "Graph"
-	node [
-		id 1
-		label "A"
-		weiteresAttribut 42
-	]
-	node [
-		id 2
-		label "B"
-		weiteresAttribut 43
-	]
-	node [
-		id 3
-		label "C"
-		weiteresAttribut 44
-	]
-	edge [
-		source 1
-		target 2
-		label "Kante AB"
-	]
-	edge [
-		source 2
-		target 3
-		label "Kante BC"
-	]
-	edge [
-		source 3
-		target 1
-		label "Kante CA"
-	]
-]
-
--- a/test-data/bsp_graph.gml~	Fri Feb 28 08:57:44 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,49 +0,0 @@
-    Creator "yFiles"  
-    Version 2.2  
-    graph  
-    [ hierarchic  1  
-      directed  1  
-      node  
-      [ id  0  
-        graphics  
-        [ x 200.0     
-          y 0.0  
-        ]  
-        LabelGraphics  
-        [ text  "January" ]  
-      ]  
-      node  
-      [ id  1  
-        graphics  
-        [ x 425.0  
-          y 75.0  
-        ]  
-        LabelGraphics  
-        [ text  "December"  ]  
-      ]  
-      edge  
-      [ source  1  
-        target  0  
-        graphics  
-        [ Line  
-          [ point  
-            [ x 425.0  
-              y 75.0  
-            ]  
-            point  
-            [ x 425.0  
-              y 0.0  
-            ]  
-            point  
-            [ x 200.0  
-              y 0.0  
-            ]  
-          ]  
-        ]  
-        LabelGraphics  
-        [ text  "Happy New Year!"  
-          model "six_pos"  
-          position  "head"  
-        ]  
-      ]  
-    ]  
--- a/test-data/graph2.gexf	Fri Feb 28 08:57:44 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<gexf xmlns="http://www.gexf.net/1.2draft" version="1.2">
-    <meta lastmodifieddate="2009-03-20">
-        <creator>Gexf.net</creator>
-        <description>A hello world! file</description>
-    </meta>
-    <graph mode="static" defaultedgetype="directed">
-        <nodes>
-            <node id="0" label="Hello" />
-            <node id="1" label="Word" />
-        </nodes>
-        <edges>
-            <edge id="0" source="0" target="1" />
-        </edges>
-    </graph>
-</gexf>
--- a/test.gexf	Fri Feb 28 08:57:44 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,389 +0,0 @@
-<?xml version="1.0" encoding="utf-8"?><gexf version="1.1" xmlns="http://www.gexf.net/1.1draft" xmlns:viz="http://www.gexf.net/1.1draft/viz" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.w3.org/2001/XMLSchema-instance">
-  <graph defaultedgetype="undirected" mode="static">
-    <attributes class="edge" mode="static">
-      <attribute id="0" title="label" type="string" />
-    </attributes>
-    <nodes>
-      <node id="0" label="O" />
-      <node id="1" label="O" />
-      <node id="2" label="O" />
-      <node id="3" label="O" />
-      <node id="4" label="C" />
-      <node id="5" label="C" />
-      <node id="6" label="C" />
-      <node id="7" label="C" />
-      <node id="8" label="C" />
-      <node id="9" label="C" />
-      <node id="10" label="C" />
-      <node id="11" label="C" />
-      <node id="12" label="C" />
-      <node id="13" label="H" />
-      <node id="14" label="H" />
-      <node id="15" label="H" />
-      <node id="16" label="H" />
-      <node id="17" label="H" />
-      <node id="18" label="H" />
-      <node id="19" label="H" />
-      <node id="20" label="H" />
-      <node id="21" label="O" />
-      <node id="22" label="O" />
-      <node id="23" label="O" />
-      <node id="24" label="O" />
-      <node id="25" label="C" />
-      <node id="26" label="C" />
-      <node id="27" label="C" />
-      <node id="28" label="C" />
-      <node id="29" label="C" />
-      <node id="30" label="C" />
-      <node id="31" label="C" />
-      <node id="32" label="C" />
-      <node id="33" label="C" />
-      <node id="34" label="H" />
-      <node id="35" label="H" />
-      <node id="36" label="H" />
-      <node id="37" label="H" />
-      <node id="38" label="H" />
-      <node id="39" label="H" />
-      <node id="40" label="H" />
-      <node id="41" label="H" />
-      <node id="42" label="O" />
-      <node id="43" label="O" />
-      <node id="44" label="O" />
-      <node id="45" label="O" />
-      <node id="46" label="C" />
-      <node id="47" label="C" />
-      <node id="48" label="C" />
-      <node id="49" label="C" />
-      <node id="50" label="C" />
-      <node id="51" label="C" />
-      <node id="52" label="C" />
-      <node id="53" label="C" />
-      <node id="54" label="C" />
-      <node id="55" label="H" />
-      <node id="56" label="H" />
-      <node id="57" label="H" />
-      <node id="58" label="H" />
-      <node id="59" label="H" />
-      <node id="60" label="H" />
-      <node id="61" label="H" />
-      <node id="62" label="H" />
-    </nodes>
-    <edges>
-      <edge id="0" source="0" target="11">
-        <attvalues>
-          <attvalue for="0" value="1" />
-        </attvalues>
-      </edge>
-      <edge id="1" source="0" target="4">
-        <attvalues>
-          <attvalue for="0" value="1" />
-        </attvalues>
-      </edge>
-      <edge id="2" source="1" target="10">
-        <attvalues>
-          <attvalue for="0" value="1" />
-        </attvalues>
-      </edge>
-      <edge id="3" source="1" target="20">
-        <attvalues>
-          <attvalue for="0" value="1" />
-        </attvalues>
-      </edge>
-      <edge id="4" source="2" target="10">
-        <attvalues>
-          <attvalue for="0" value="2" />
-        </attvalues>
-      </edge>
-      <edge id="5" source="3" target="11">
-        <attvalues>
-          <attvalue for="0" value="2" />
-        </attvalues>
-      </edge>
-      <edge id="6" source="4" target="5">
-        <attvalues>
-          <attvalue for="0" value="1" />
-        </attvalues>
-      </edge>
-      <edge id="7" source="4" target="6">
-        <attvalues>
-          <attvalue for="0" value="2" />
-        </attvalues>
-      </edge>
-      <edge id="8" source="5" target="10">
-        <attvalues>
-          <attvalue for="0" value="1" />
-        </attvalues>
-      </edge>
-      <edge id="9" source="5" target="7">
-        <attvalues>
-          <attvalue for="0" value="2" />
-        </attvalues>
-      </edge>
-      <edge id="10" source="6" target="8">
-        <attvalues>
-          <attvalue for="0" value="1" />
-        </attvalues>
-      </edge>
-      <edge id="11" source="6" target="13">
-        <attvalues>
-          <attvalue for="0" value="1" />
-        </attvalues>
-      </edge>
-      <edge id="12" source="7" target="9">
-        <attvalues>
-          <attvalue for="0" value="1" />
-        </attvalues>
-      </edge>
-      <edge id="13" source="7" target="14">
-        <attvalues>
-          <attvalue for="0" value="1" />
-        </attvalues>
-      </edge>
-      <edge id="14" source="8" target="9">
-        <attvalues>
-          <attvalue for="0" value="2" />
-        </attvalues>
-      </edge>
-      <edge id="15" source="8" target="15">
-        <attvalues>
-          <attvalue for="0" value="1" />
-        </attvalues>
-      </edge>
-      <edge id="16" source="9" target="16">
-        <attvalues>
-          <attvalue for="0" value="1" />
-        </attvalues>
-      </edge>
-      <edge id="17" source="11" target="12">
-        <attvalues>
-          <attvalue for="0" value="1" />
-        </attvalues>
-      </edge>
-      <edge id="18" source="12" target="19">
-        <attvalues>
-          <attvalue for="0" value="1" />
-        </attvalues>
-      </edge>
-      <edge id="19" source="12" target="17">
-        <attvalues>
-          <attvalue for="0" value="1" />
-        </attvalues>
-      </edge>
-      <edge id="20" source="12" target="18">
-        <attvalues>
-          <attvalue for="0" value="1" />
-        </attvalues>
-      </edge>
-      <edge id="21" source="21" target="32">
-        <attvalues>
-          <attvalue for="0" value="1" />
-        </attvalues>
-      </edge>
-      <edge id="22" source="21" target="25">
-        <attvalues>
-          <attvalue for="0" value="1" />
-        </attvalues>
-      </edge>
-      <edge id="23" source="22" target="41">
-        <attvalues>
-          <attvalue for="0" value="1" />
-        </attvalues>
-      </edge>
-      <edge id="24" source="22" target="31">
-        <attvalues>
-          <attvalue for="0" value="1" />
-        </attvalues>
-      </edge>
-      <edge id="25" source="23" target="31">
-        <attvalues>
-          <attvalue for="0" value="2" />
-        </attvalues>
-      </edge>
-      <edge id="26" source="24" target="32">
-        <attvalues>
-          <attvalue for="0" value="2" />
-        </attvalues>
-      </edge>
-      <edge id="27" source="25" target="26">
-        <attvalues>
-          <attvalue for="0" value="1" />
-        </attvalues>
-      </edge>
-      <edge id="28" source="25" target="27">
-        <attvalues>
-          <attvalue for="0" value="2" />
-        </attvalues>
-      </edge>
-      <edge id="29" source="26" target="28">
-        <attvalues>
-          <attvalue for="0" value="2" />
-        </attvalues>
-      </edge>
-      <edge id="30" source="26" target="31">
-        <attvalues>
-          <attvalue for="0" value="1" />
-        </attvalues>
-      </edge>
-      <edge id="31" source="27" target="34">
-        <attvalues>
-          <attvalue for="0" value="1" />
-        </attvalues>
-      </edge>
-      <edge id="32" source="27" target="29">
-        <attvalues>
-          <attvalue for="0" value="1" />
-        </attvalues>
-      </edge>
-      <edge id="33" source="28" target="35">
-        <attvalues>
-          <attvalue for="0" value="1" />
-        </attvalues>
-      </edge>
-      <edge id="34" source="28" target="30">
-        <attvalues>
-          <attvalue for="0" value="1" />
-        </attvalues>
-      </edge>
-      <edge id="35" source="29" target="36">
-        <attvalues>
-          <attvalue for="0" value="1" />
-        </attvalues>
-      </edge>
-      <edge id="36" source="29" target="30">
-        <attvalues>
-          <attvalue for="0" value="2" />
-        </attvalues>
-      </edge>
-      <edge id="37" source="30" target="37">
-        <attvalues>
-          <attvalue for="0" value="1" />
-        </attvalues>
-      </edge>
-      <edge id="38" source="32" target="33">
-        <attvalues>
-          <attvalue for="0" value="1" />
-        </attvalues>
-      </edge>
-      <edge id="39" source="33" target="40">
-        <attvalues>
-          <attvalue for="0" value="1" />
-        </attvalues>
-      </edge>
-      <edge id="40" source="33" target="38">
-        <attvalues>
-          <attvalue for="0" value="1" />
-        </attvalues>
-      </edge>
-      <edge id="41" source="33" target="39">
-        <attvalues>
-          <attvalue for="0" value="1" />
-        </attvalues>
-      </edge>
-      <edge id="42" source="42" target="53">
-        <attvalues>
-          <attvalue for="0" value="1" />
-        </attvalues>
-      </edge>
-      <edge id="43" source="42" target="46">
-        <attvalues>
-          <attvalue for="0" value="1" />
-        </attvalues>
-      </edge>
-      <edge id="44" source="43" target="52">
-        <attvalues>
-          <attvalue for="0" value="1" />
-        </attvalues>
-      </edge>
-      <edge id="45" source="43" target="62">
-        <attvalues>
-          <attvalue for="0" value="1" />
-        </attvalues>
-      </edge>
-      <edge id="46" source="44" target="52">
-        <attvalues>
-          <attvalue for="0" value="2" />
-        </attvalues>
-      </edge>
-      <edge id="47" source="45" target="53">
-        <attvalues>
-          <attvalue for="0" value="2" />
-        </attvalues>
-      </edge>
-      <edge id="48" source="46" target="48">
-        <attvalues>
-          <attvalue for="0" value="2" />
-        </attvalues>
-      </edge>
-      <edge id="49" source="46" target="47">
-        <attvalues>
-          <attvalue for="0" value="1" />
-        </attvalues>
-      </edge>
-      <edge id="50" source="47" target="49">
-        <attvalues>
-          <attvalue for="0" value="2" />
-        </attvalues>
-      </edge>
-      <edge id="51" source="47" target="52">
-        <attvalues>
-          <attvalue for="0" value="1" />
-        </attvalues>
-      </edge>
-      <edge id="52" source="48" target="50">
-        <attvalues>
-          <attvalue for="0" value="1" />
-        </attvalues>
-      </edge>
-      <edge id="53" source="48" target="55">
-        <attvalues>
-          <attvalue for="0" value="1" />
-        </attvalues>
-      </edge>
-      <edge id="54" source="49" target="56">
-        <attvalues>
-          <attvalue for="0" value="1" />
-        </attvalues>
-      </edge>
-      <edge id="55" source="49" target="51">
-        <attvalues>
-          <attvalue for="0" value="1" />
-        </attvalues>
-      </edge>
-      <edge id="56" source="50" target="57">
-        <attvalues>
-          <attvalue for="0" value="1" />
-        </attvalues>
-      </edge>
-      <edge id="57" source="50" target="51">
-        <attvalues>
-          <attvalue for="0" value="2" />
-        </attvalues>
-      </edge>
-      <edge id="58" source="51" target="58">
-        <attvalues>
-          <attvalue for="0" value="1" />
-        </attvalues>
-      </edge>
-      <edge id="59" source="53" target="54">
-        <attvalues>
-          <attvalue for="0" value="1" />
-        </attvalues>
-      </edge>
-      <edge id="60" source="54" target="59">
-        <attvalues>
-          <attvalue for="0" value="1" />
-        </attvalues>
-      </edge>
-      <edge id="61" source="54" target="60">
-        <attvalues>
-          <attvalue for="0" value="1" />
-        </attvalues>
-      </edge>
-      <edge id="62" source="54" target="61">
-        <attvalues>
-          <attvalue for="0" value="1" />
-        </attvalues>
-      </edge>
-    </edges>
-  </graph>
-</gexf>
--- a/test.gml	Fri Feb 28 08:57:44 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,569 +0,0 @@
-graph [
-  node [
-    id 0
-    label "O"
-  ]
-  node [
-    id 1
-    label "O"
-  ]
-  node [
-    id 2
-    label "O"
-  ]
-  node [
-    id 3
-    label "O"
-  ]
-  node [
-    id 4
-    label "C"
-  ]
-  node [
-    id 5
-    label "C"
-  ]
-  node [
-    id 6
-    label "C"
-  ]
-  node [
-    id 7
-    label "C"
-  ]
-  node [
-    id 8
-    label "C"
-  ]
-  node [
-    id 9
-    label "C"
-  ]
-  node [
-    id 10
-    label "C"
-  ]
-  node [
-    id 11
-    label "C"
-  ]
-  node [
-    id 12
-    label "C"
-  ]
-  node [
-    id 13
-    label "H"
-  ]
-  node [
-    id 14
-    label "H"
-  ]
-  node [
-    id 15
-    label "H"
-  ]
-  node [
-    id 16
-    label "H"
-  ]
-  node [
-    id 17
-    label "H"
-  ]
-  node [
-    id 18
-    label "H"
-  ]
-  node [
-    id 19
-    label "H"
-  ]
-  node [
-    id 20
-    label "H"
-  ]
-  node [
-    id 21
-    label "O"
-  ]
-  node [
-    id 22
-    label "O"
-  ]
-  node [
-    id 23
-    label "O"
-  ]
-  node [
-    id 24
-    label "O"
-  ]
-  node [
-    id 25
-    label "C"
-  ]
-  node [
-    id 26
-    label "C"
-  ]
-  node [
-    id 27
-    label "C"
-  ]
-  node [
-    id 28
-    label "C"
-  ]
-  node [
-    id 29
-    label "C"
-  ]
-  node [
-    id 30
-    label "C"
-  ]
-  node [
-    id 31
-    label "C"
-  ]
-  node [
-    id 32
-    label "C"
-  ]
-  node [
-    id 33
-    label "C"
-  ]
-  node [
-    id 34
-    label "H"
-  ]
-  node [
-    id 35
-    label "H"
-  ]
-  node [
-    id 36
-    label "H"
-  ]
-  node [
-    id 37
-    label "H"
-  ]
-  node [
-    id 38
-    label "H"
-  ]
-  node [
-    id 39
-    label "H"
-  ]
-  node [
-    id 40
-    label "H"
-  ]
-  node [
-    id 41
-    label "H"
-  ]
-  node [
-    id 42
-    label "O"
-  ]
-  node [
-    id 43
-    label "O"
-  ]
-  node [
-    id 44
-    label "O"
-  ]
-  node [
-    id 45
-    label "O"
-  ]
-  node [
-    id 46
-    label "C"
-  ]
-  node [
-    id 47
-    label "C"
-  ]
-  node [
-    id 48
-    label "C"
-  ]
-  node [
-    id 49
-    label "C"
-  ]
-  node [
-    id 50
-    label "C"
-  ]
-  node [
-    id 51
-    label "C"
-  ]
-  node [
-    id 52
-    label "C"
-  ]
-  node [
-    id 53
-    label "C"
-  ]
-  node [
-    id 54
-    label "C"
-  ]
-  node [
-    id 55
-    label "H"
-  ]
-  node [
-    id 56
-    label "H"
-  ]
-  node [
-    id 57
-    label "H"
-  ]
-  node [
-    id 58
-    label "H"
-  ]
-  node [
-    id 59
-    label "H"
-  ]
-  node [
-    id 60
-    label "H"
-  ]
-  node [
-    id 61
-    label "H"
-  ]
-  node [
-    id 62
-    label "H"
-  ]
-  edge [
-    source 0
-    target 11
-    label "1"
-  ]
-  edge [
-    source 0
-    target 4
-    label "1"
-  ]
-  edge [
-    source 1
-    target 10
-    label "1"
-  ]
-  edge [
-    source 1
-    target 20
-    label "1"
-  ]
-  edge [
-    source 2
-    target 10
-    label "2"
-  ]
-  edge [
-    source 3
-    target 11
-    label "2"
-  ]
-  edge [
-    source 4
-    target 5
-    label "1"
-  ]
-  edge [
-    source 4
-    target 6
-    label "2"
-  ]
-  edge [
-    source 5
-    target 10
-    label "1"
-  ]
-  edge [
-    source 5
-    target 7
-    label "2"
-  ]
-  edge [
-    source 6
-    target 8
-    label "1"
-  ]
-  edge [
-    source 6
-    target 13
-    label "1"
-  ]
-  edge [
-    source 7
-    target 9
-    label "1"
-  ]
-  edge [
-    source 7
-    target 14
-    label "1"
-  ]
-  edge [
-    source 8
-    target 9
-    label "2"
-  ]
-  edge [
-    source 8
-    target 15
-    label "1"
-  ]
-  edge [
-    source 9
-    target 16
-    label "1"
-  ]
-  edge [
-    source 11
-    target 12
-    label "1"
-  ]
-  edge [
-    source 12
-    target 19
-    label "1"
-  ]
-  edge [
-    source 12
-    target 17
-    label "1"
-  ]
-  edge [
-    source 12
-    target 18
-    label "1"
-  ]
-  edge [
-    source 21
-    target 32
-    label "1"
-  ]
-  edge [
-    source 21
-    target 25
-    label "1"
-  ]
-  edge [
-    source 22
-    target 41
-    label "1"
-  ]
-  edge [
-    source 22
-    target 31
-    label "1"
-  ]
-  edge [
-    source 23
-    target 31
-    label "2"
-  ]
-  edge [
-    source 24
-    target 32
-    label "2"
-  ]
-  edge [
-    source 25
-    target 26
-    label "1"
-  ]
-  edge [
-    source 25
-    target 27
-    label "2"
-  ]
-  edge [
-    source 26
-    target 28
-    label "2"
-  ]
-  edge [
-    source 26
-    target 31
-    label "1"
-  ]
-  edge [
-    source 27
-    target 34
-    label "1"
-  ]
-  edge [
-    source 27
-    target 29
-    label "1"
-  ]
-  edge [
-    source 28
-    target 35
-    label "1"
-  ]
-  edge [
-    source 28
-    target 30
-    label "1"
-  ]
-  edge [
-    source 29
-    target 36
-    label "1"
-  ]
-  edge [
-    source 29
-    target 30
-    label "2"
-  ]
-  edge [
-    source 30
-    target 37
-    label "1"
-  ]
-  edge [
-    source 32
-    target 33
-    label "1"
-  ]
-  edge [
-    source 33
-    target 40
-    label "1"
-  ]
-  edge [
-    source 33
-    target 38
-    label "1"
-  ]
-  edge [
-    source 33
-    target 39
-    label "1"
-  ]
-  edge [
-    source 42
-    target 53
-    label "1"
-  ]
-  edge [
-    source 42
-    target 46
-    label "1"
-  ]
-  edge [
-    source 43
-    target 52
-    label "1"
-  ]
-  edge [
-    source 43
-    target 62
-    label "1"
-  ]
-  edge [
-    source 44
-    target 52
-    label "2"
-  ]
-  edge [
-    source 45
-    target 53
-    label "2"
-  ]
-  edge [
-    source 46
-    target 48
-    label "2"
-  ]
-  edge [
-    source 46
-    target 47
-    label "1"
-  ]
-  edge [
-    source 47
-    target 49
-    label "2"
-  ]
-  edge [
-    source 47
-    target 52
-    label "1"
-  ]
-  edge [
-    source 48
-    target 50
-    label "1"
-  ]
-  edge [
-    source 48
-    target 55
-    label "1"
-  ]
-  edge [
-    source 49
-    target 56
-    label "1"
-  ]
-  edge [
-    source 49
-    target 51
-    label "1"
-  ]
-  edge [
-    source 50
-    target 57
-    label "1"
-  ]
-  edge [
-    source 50
-    target 51
-    label "2"
-  ]
-  edge [
-    source 51
-    target 58
-    label "1"
-  ]
-  edge [
-    source 53
-    target 54
-    label "1"
-  ]
-  edge [
-    source 54
-    target 59
-    label "1"
-  ]
-  edge [
-    source 54
-    target 60
-    label "1"
-  ]
-  edge [
-    source 54
-    target 61
-    label "1"
-  ]
-]
--- a/test.gspan	Fri Feb 28 08:57:44 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,7 +0,0 @@
-t # id 1
-v 0 A 
-v 1 B 
-v 2 C 
-e 0 1 Kante AB
-e 1 2 Kante BC
-e 2 0 Kante CA
--- a/test.xgmml	Fri Feb 28 08:57:44 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
-<graph directed="1"  xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns="http://www.cs.rpi.edu/XGMML">
-<att name="selected" value="1" type="boolean" />
-<att name="name" value="MyGraph" type="string"/>
-<att name="shared name" value="MyGraph" type="string"/>
-
-<node id="0" label="Word">
-<att name="id" value="0" type="string" />
-</node>
-<node id="1" label="Hello">
-<att name="id" value="1" type="string" />
-</node>
-<edge source="1" target="0">
-<att name="id" value="0" type="string" />
-</edge>
-</graph>
--- a/test.xml	Fri Feb 28 08:57:44 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
-<graph directed="1"  xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns="http://www.cs.rpi.edu/XGMML">
-<att name="selected" value="1" type="boolean" />
-<att name="name" value="MeinGraph" type="string"/>
-<att name="shared name" value="MeinGraph" type="string"/>
-
--- a/test.yaml	Fri Feb 28 08:57:44 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,28 +0,0 @@
-!!python/object:networkx.classes.digraph.DiGraph
-adj: &id001
-  !!python/unicode '1':
-    !!python/unicode '2': &id003 {!!python/unicode 'id': !!python/unicode '3', !!python/unicode 'label': !!python/unicode 'Kante
-        AB', !!python/unicode 'weiteresAttribut': !!python/unicode '44'}
-  !!python/unicode '2':
-    !!python/unicode '3': &id004 {!!python/unicode 'id': !!python/unicode '3', !!python/unicode 'label': !!python/unicode 'Kante
-        BC', !!python/unicode 'weiteresAttribut': !!python/unicode '44'}
-  !!python/unicode '3':
-    !!python/unicode '1': &id002 {!!python/unicode 'id': !!python/unicode '3', !!python/unicode 'label': !!python/unicode 'Kante
-        CA', !!python/unicode 'weiteresAttribut': !!python/unicode '44'}
-edge: *id001
-graph: {}
-node:
-  !!python/unicode '1': {!!python/unicode 'id': !!python/unicode '1', label: !!python/unicode 'A',
-    !!python/unicode 'weiteresAttribut': !!python/unicode '42'}
-  !!python/unicode '2': {!!python/unicode 'id': !!python/unicode '2', label: !!python/unicode 'B',
-    !!python/unicode 'weiteresAttribut': !!python/unicode '43'}
-  !!python/unicode '3': {!!python/unicode 'id': !!python/unicode '3', label: !!python/unicode 'C',
-    !!python/unicode 'weiteresAttribut': !!python/unicode '44'}
-pred:
-  !!python/unicode '1':
-    !!python/unicode '3': *id002
-  !!python/unicode '2':
-    !!python/unicode '1': *id003
-  !!python/unicode '3':
-    !!python/unicode '2': *id004
-succ: *id001
--- a/tool_dependencies.xml	Fri Feb 28 08:57:44 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,5 +0,0 @@
-<tool_dependency>
-    <set_environment version="1.0">
-        <environment_variable name="GRAPHCONVERTER_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
-    </set_environment>
-</tool_dependency>
--- a/xgmml_networkx.py	Fri Feb 28 08:57:44 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,124 +0,0 @@
-__author__ = "Yasunobu OKAMURA"
-__copyright__ = "Copyright (c) 2012 Y.Okamura"
-__license__ = "GPL v3+"
-
-import xml.parsers.expat
-import networkx as nx
-
-class XGMMLParserHelper(object):
-    """
-    """
-    
-    def __init__(self, graph=nx.DiGraph()):
-        """
-        
-        Arguments:
-        - `graph`: Network X graph object
-        """
-        self._graph = graph
-        self._parser = xml.parsers.expat.ParserCreate()
-        self._parser.StartElementHandler = self._start_element
-        self._parser.EndElementHandler = self._end_element
-        self._tagstack = list()
-
-        self._current_attr = dict()
-        self._current_obj = dict()
-
-    def _start_element(self, tag, attr):
-        """
-        
-        Arguments:
-        - `self`:
-        - `tag`:
-        - `attr`:
-        """
-
-        self._tagstack.append(tag)
-
-        if tag == 'node' or tag == 'edge':
-            self._current_obj = dict(attr)
-
-        if tag == 'att' and (self._tagstack[-2] == 'node' or self._tagstack[-2] == 'edge'):
-            if attr['type'] == 'string':
-                self._current_attr[attr['name']] = attr['value']
-            elif attr['type'] == 'real':
-                self._current_attr[attr['name']] = float(attr['value'])
-            elif attr['type'] == 'integer':
-                self._current_attr[attr['name']] = int(attr['value'])
-            elif attr['type'] == 'boolean':
-                self._current_attr[attr['name']] = bool(attr['value'])
-            else:
-                raise NotImplementedError(attr['type'])
-
-    def _end_element(self, tag):
-        """
-        
-        Arguments:
-        - `self`:
-        - `tag`:
-        """
-
-        if tag == 'node':
-            self._graph.add_node(self._current_obj['id'], label=self._current_obj['label'], **self._current_attr)
-            #print 'add node', self._current_obj
-        elif tag == 'edge':
-            self._graph.add_edge(self._current_obj['source'], self._current_obj['target'], **self._current_attr)
-
-        self._tagstack.pop()
-
-    def parseFile(self, file):
-        """
-        
-        Arguments:
-        - `self`:
-        - `file`:
-        """
-
-        self._parser.ParseFile(file)
-
-    def graph(self):
-        """
-        
-        Arguments:
-        - `self`:
-        """
-
-        return self._graph
-
-def XGMMLWriter(file, graph, graph_name):
-    """
-    
-    Arguments:
-    - `graph`:
-    """
-
-    print >>file, """<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
-<graph directed="1"  xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns="http://www.cs.rpi.edu/XGMML">
-<att name="selected" value="1" type="boolean" />
-<att name="name" value="{0}" type="string"/>
-<att name="shared name" value="{0}" type="string"/>
-""".format(graph_name)
-
-
-    for onenode in graph.nodes(data=True):
-        id = onenode[0]
-        attr = dict(onenode[1])
-
-        if 'label' in attr:
-            label = attr['label']
-            del attr['label']
-        else:
-            label = id
-        
-        print >>file, '<node id="{id}" label="{label}">'.format(id=id, label=label)
-        for k, v in attr.iteritems():
-            print >>file, '<att name="{}" value="{}" type="string" />'.format(k, v)
-        print >>file, '</node>'
-        
-    for oneedge in graph.edges(data=True):
-        print >>file, '<edge source="{}" target="{}">'.format(oneedge[0], oneedge[1])
-        for k, v in oneedge[2].iteritems():
-            print >>file, '<att name="{}" value="{}" type="string" />'.format(k, v)
-        print >>file, '</edge>'
-    print >>file, '</graph>'
-
Binary file xgmml_networkx.pyc has changed