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1 | /* | |
2 | * Copyright (c) 2003, the JUNG Project and the Regents of the University | |
3 | * of California | |
4 | * All rights reserved. | |
5 | * | |
6 | * This software is open-source under the BSD license; see either | |
7 | * "license.txt" or | |
8 | * http://jung.sourceforge.net/license.txt for a description. | |
9 | */ | |
10 | package edu.uci.ics.jung.io; | |
11 | ||
12 | import java.io.File; | |
13 | import java.io.FileOutputStream; | |
14 | import java.io.FilenameFilter; | |
15 | import java.io.InputStream; | |
16 | import java.io.PrintStream; | |
17 | import java.io.Reader; | |
18 | import java.util.ArrayList; | |
19 | import java.util.Iterator; | |
20 | import java.util.List; | |
21 | ||
22 | import javax.xml.parsers.SAXParser; | |
23 | import javax.xml.parsers.SAXParserFactory; | |
24 | ||
25 | import org.xml.sax.InputSource; | |
26 | ||
27 | import edu.uci.ics.jung.exceptions.FatalException; | |
28 | import edu.uci.ics.jung.graph.DirectedEdge; | |
29 | import edu.uci.ics.jung.graph.Edge; | |
30 | import edu.uci.ics.jung.graph.Graph; | |
31 | import edu.uci.ics.jung.graph.UndirectedEdge; | |
32 | import edu.uci.ics.jung.graph.Vertex; | |
33 | import edu.uci.ics.jung.graph.decorators.Indexer; | |
34 | import edu.uci.ics.jung.utils.Pair; | |
35 | import edu.uci.ics.jung.utils.PredicateUtils; | |
36 | import edu.uci.ics.jung.utils.UserData; | |
37 | import edu.uci.ics.jung.utils.UserDataContainer; | |
38 | ||
39 | /** | |
40 | * A file reader for GraphML files. Currently, there is only support for directed and undirected graphs. | |
41 | * The elements <port>, <hyperedge>, <endpoint>, and <locator> are simply ignored. <p> | |
42 | * | |
43 | * What follows are the native GraphML attributes that are recognized: <ul> | |
44 | * <li> graph: edgedefault (takes values {"undirected","directed"}; determines whether the graph is directed or undirected) | |
45 | * <li> node: id (Can be any string value; only used to connect up edges) | |
46 | * <li> edge: source, target (take ids; both are used to created either a directed or undirected edge depending | |
47 | * on the type of graph) </ul> <br> | |
48 | * These attributes are not stored as explicit UserDatum instances. All other attributes are read in and stored as | |
49 | * UserDatum String values with the corresponding graph object, i.e. graph, node, or edge. <p> | |
50 | * | |
51 | * A sample file looks like this: <br> | |
52 | * <?xml version="1.0" encoding="iso-8859-1" ?> <br> | |
53 | * <?meta name="GENERATOR" content="XML::Smart 1.3.1" ?> <br> | |
54 | * <?meta name="GENERATOR" content="XML::Smart 1.3.1" ?> <br> | |
55 | * <graph edgedefault="directed" year="1983"> <br> | |
56 | * <node id="1" name="V1" color="red"/> <br> | |
57 | * <node id="2" name="V2" color="blue"/> <br> | |
58 | * <node id="3" name="V3" color="green"/> <br> | |
59 | * <edge source="1" target="2" day="Monday"/> <br> | |
60 | * <edge source="1" target="3" day="Tuesday"/> <br> | |
61 | *<edge source="2" target="3" day="Friday"/> <br> | |
62 | * </graph> <br> | |
63 | * Note: In this example, year, color, and day are user-defined attributes that get stored in the object's UserData | |
64 | * | |
65 | * Assuming we have a Graph g created from the above XML file we can print out the days of | |
66 | * the week for each node as follows: | |
67 | * <pre> | |
68 | * for (Iterator eIt = g.getEdges().iterator(); eIt.hasNext(); ) { | |
69 | * Edge v = (Edge) eIt.next(); | |
70 | * System.out.println(e.getUserDatum("day"); | |
71 | * } | |
72 | * </pre><br> | |
73 | * | |
74 | * @see "http://graphml.graphdrawing.org/" | |
75 | * @author Scott White, John Yesberg | |
76 | */ | |
77 | public class GraphMLFile implements GraphFile { | |
78 | private GraphMLFileHandler mFileHandler; | |
79 | protected boolean directed; | |
80 | protected boolean undirected; | |
81 | ||
82 | /** | |
83 | * Default constructor which uses default GraphMLFileHandler to parse the graph | |
84 | */ | |
85 | 18 | public GraphMLFile() { |
86 | 18 | mFileHandler = new GraphMLFileHandler(); |
87 | 18 | } |
88 | ||
89 | /** | |
90 | * Constructors which allows a subclass of GraphMLFileHandler to be used to parse the graph | |
91 | * @param handler the user-provided GraphML file handler | |
92 | */ | |
93 | 0 | public GraphMLFile(GraphMLFileHandler handler) { |
94 | 0 | mFileHandler = handler; |
95 | 0 | } |
96 | ||
97 | /** | |
98 | * Loads a graph from a GraphML file. | |
99 | * @param filename the fully specified file name | |
100 | * @return the constructed graph | |
101 | */ | |
102 | public Graph load(String filename) { | |
103 | ||
104 | // Use the default (non-validating) parser | |
105 | 3 | SAXParserFactory factory = SAXParserFactory.newInstance(); |
106 | try { | |
107 | // Parse the input | |
108 | 3 | SAXParser saxParser = factory.newSAXParser(); |
109 | 3 | saxParser.parse(new File(filename), mFileHandler); |
110 | ||
111 | 0 | } catch (Exception e) { |
112 | 0 | throw new FatalException("Error loading graphml file: " + filename, e); |
113 | 3 | } |
114 | ||
115 | 3 | return mFileHandler.getGraph(); |
116 | } | |
117 | ||
118 | /** | |
119 | * Loads a graph from a GraphML input stream. | |
120 | * @param stream the input stream which contains the GraphML data | |
121 | * @return the constructed graph | |
122 | * @deprecated generally, InputStreams are less robust than Readers | |
123 | */ | |
124 | public Graph load(InputStream stream) { | |
125 | ||
126 | // Use the default (non-validating) parser | |
127 | 0 | SAXParserFactory factory = SAXParserFactory.newInstance(); |
128 | try { | |
129 | // Parse the input | |
130 | 0 | SAXParser saxParser = factory.newSAXParser(); |
131 | 0 | saxParser.parse(stream, mFileHandler); |
132 | ||
133 | 0 | } catch (Exception e) { |
134 | 0 | throw new FatalException("Error loading graphml file", e); |
135 | 0 | } |
136 | ||
137 | 0 | return mFileHandler.getGraph(); |
138 | } | |
139 | ||
140 | public Graph load( Reader reader ) { | |
141 | ||
142 | // Use the default (non-validating) parser | |
143 | 15 | SAXParserFactory factory = SAXParserFactory.newInstance(); |
144 | try { | |
145 | // Parse the input | |
146 | 15 | SAXParser saxParser = factory.newSAXParser(); |
147 | 15 | InputSource is = new InputSource( reader ); |
148 | 15 | saxParser.parse(is, mFileHandler); |
149 | ||
150 | 0 | } catch (Exception e) { |
151 | 0 | throw new FatalException("Error loading graphml file", e); |
152 | 15 | } |
153 | ||
154 | 15 | return mFileHandler.getGraph(); |
155 | ||
156 | } | |
157 | ||
158 | /** | |
159 | * Loads in a list of graphs whose corresponding filenames pass the file filter and are located in the | |
160 | * specified directory | |
161 | * @param dirName the directory containing the set of files that are to be screened through the file filter | |
162 | * @param filter the file filter | |
163 | * @return a list of graphs | |
164 | */ | |
165 | public List loadGraphCollection(String dirName, FilenameFilter filter) { | |
166 | 0 | File dir = new File(dirName); |
167 | 0 | if (!dir.isDirectory()) { |
168 | 0 | throw new FatalException("Parameter dirName must be a directory"); |
169 | } | |
170 | ||
171 | 0 | String[] files = dir.list(filter); |
172 | ||
173 | 0 | List graphCollection = new ArrayList(); |
174 | 0 | for (int i = 0; i < files.length; i++) { |
175 | 0 | String currentFile = dirName + File.separatorChar + files[i]; |
176 | 0 | GraphMLFile graphmlFile = new GraphMLFile(mFileHandler); |
177 | 0 | Graph graph = graphmlFile.load(currentFile); |
178 | //System.out.println("Graph loaded with " + graph.numVertices() + " nodes and " + graph.numEdges() + " edges."); | |
179 | 0 | graphCollection.add(graph); |
180 | } | |
181 | ||
182 | 0 | return graphCollection; |
183 | } | |
184 | ||
185 | public void save(Graph g, String filename) { | |
186 | PrintStream out; | |
187 | try { | |
188 | 1 | out = new PrintStream(new FileOutputStream(filename, false)); |
189 | 0 | } catch (Exception e) { |
190 | 0 | throw new FatalException("Could not open file \"" + filename + "\" for writing. " + e); |
191 | 1 | } |
192 | 1 | save(g, out); |
193 | 1 | out.close(); |
194 | 1 | } |
195 | ||
196 | ||
197 | ||
198 | public void save(Graph g, PrintStream out) { | |
199 | 1 | out.println("<?xml version=\"1.0\" encoding=\"UTF-8\"?>"); |
200 | 1 | out.println("<graphml xmlns=\"http://graphml.graphdrawing.org/xmlns/graphml\" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" "); |
201 | 1 | out.println("xsi:schemaLocation=\"http://graphml.graphdrawing.org/xmlns/graphml\">"); |
202 | 1 | out.print("<graph edgedefault=\""); |
203 | 1 | boolean directed = PredicateUtils.enforcesEdgeConstraint(g, Graph.DIRECTED_EDGE); |
204 | 1 | boolean undirected = PredicateUtils.enforcesEdgeConstraint(g, Graph.UNDIRECTED_EDGE); |
205 | 1 | if (directed) |
206 | 0 | out.print("directed\" "); |
207 | 1 | else if (undirected) |
208 | 0 | out.print("undirected\" "); |
209 | else // default for mixed graphs | |
210 | { | |
211 | 1 | directed = true; |
212 | 1 | out.print("directed\" "); |
213 | } | |
214 | // throw new IllegalArgumentException("Mixed (directed/undirected) " + | |
215 | // "graphs not currently supported"); | |
216 | ||
217 | 1 | saveUserData(g, out); |
218 | 1 | out.println(" >"); |
219 | 1 | saveVerticesSection(out, g); |
220 | 1 | saveEdgesSection(out, g); |
221 | 1 | out.println("</graph>"); |
222 | 1 | out.println("</graphml>"); |
223 | ||
224 | 1 | } |
225 | ||
226 | private void saveVerticesSection(PrintStream out, Graph g) { | |
227 | 1 | int numVertices = g.getVertices().size(); |
228 | 1 | Indexer id = Indexer.getIndexer(g); |
229 | 4 | for (int i = 0; i < numVertices; i++) { |
230 | 3 | Vertex v = (Vertex) id.getVertex(i); |
231 | 3 | int vId = i+1; |
232 | 3 | out.print("<node id=\"" + vId + "\" "); |
233 | ||
234 | 3 | saveUserData(v, out); |
235 | 3 | out.println("/>"); |
236 | } | |
237 | 1 | } |
238 | ||
239 | private void saveEdgesSection(PrintStream out, Graph g) { | |
240 | 1 | Indexer id = Indexer.getIndexer(g); |
241 | 1 | for (Iterator edgeIterator = g.getEdges().iterator(); edgeIterator.hasNext();) { |
242 | 3 | Edge e = (Edge) edgeIterator.next(); |
243 | 3 | Pair p = e.getEndpoints(); |
244 | 3 | Vertex src = (Vertex) p.getFirst(); |
245 | 3 | Vertex dest = (Vertex) p.getSecond(); |
246 | 3 | int srcId = id.getIndex(src)+1; |
247 | 3 | out.print("<edge source=\"" + srcId + "\" "); |
248 | 3 | int destId = id.getIndex(dest)+1; |
249 | 3 | out.print("target=\"" + destId + "\" "); |
250 | ||
251 | // tag the edges that don't match the default | |
252 | 3 | if (directed) |
253 | { | |
254 | 0 | if (e instanceof UndirectedEdge) |
255 | 0 | out.print("directed=\"false\" "); |
256 | } | |
257 | else // undirected | |
258 | 3 | if (e instanceof DirectedEdge) |
259 | 3 | out.print("directed=\"true\" "); |
260 | ||
261 | 3 | saveUserData(e, out); |
262 | 3 | out.println("/>"); |
263 | } | |
264 | 1 | } |
265 | ||
266 | private void saveUserData(UserDataContainer udc, PrintStream out) { | |
267 | 7 | Iterator udki = udc.getUserDatumKeyIterator(); |
268 | 11 | while (udki.hasNext()) { |
269 | 4 | Object key_obj = udki.next(); |
270 | 4 | if (udc.getUserDatumCopyAction(key_obj) == UserData.REMOVE) |
271 | 1 | continue; |
272 | 3 | String key = key_obj.toString(); |
273 | 3 | if (invalidXMLData(key)) continue; |
274 | 3 | Object o = udc.getUserDatum(key); |
275 | 3 | if (o == null) |
276 | 0 | continue; |
277 | 3 | String datum = o.toString(); |
278 | 3 | if (invalidXMLData(datum)) continue; |
279 | 3 | out.print(key + "=\"" + datum + "\" "); |
280 | } | |
281 | 7 | } |
282 | ||
283 | private boolean invalidXMLData(String str) { | |
284 | 6 | if (str.indexOf("&") >= 0) return true; |
285 | 6 | if (str.indexOf("<") >= 0) return true; |
286 | 6 | if (str.indexOf(">") >= 0) return true; |
287 | 6 | if (str.indexOf("\'") >= 0) return true; |
288 | 6 | if (str.indexOf("\"") >= 0) return true; |
289 | 6 | return false; |
290 | } | |
291 | ||
292 | /** | |
293 | * Allows the user to provide his/her own subclassed GraphML file handerl | |
294 | * @param fileHandler | |
295 | */ | |
296 | public void setGraphMLFileHandler(GraphMLFileHandler fileHandler) { | |
297 | 0 | mFileHandler = fileHandler; |
298 | 0 | } |
299 | } |
this report was generated by version 1.0.5 of jcoverage. |
copyright © 2003, jcoverage ltd. all rights reserved. |