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AcquiredStructureAnalyzer.java @ 269

リビジョン 269, 15.9 KB (コミッタ: nori, 9 年前)
クローラー結果としてCrawledDataset が扱えるようにの暫定版

行番号
1	package org.biohackathon.SPARQLBuilder.OWL;
2
3	import java.util.*;
4
5	import jp.riken.accc.db.sparqlBuilderMetadata.crawler.dataStructure.sparql.JenaModelGenerator;
6	import jp.riken.accc.db.sparqlBuilderMetadata.crawler.dataStructure.sparql.URICollection;
7	import jp.riken.accc.db.sparqlBuilderMetadata.crawler.dataStructure.sparql.crawler.CrawledMetadata;
8	import jp.riken.accc.db.sparqlBuilderMetadata.crawler.dataStructure.sparql.crawler.Dataset;
9
10	import com.hp.hpl.jena.query.Query;
11	import com.hp.hpl.jena.query.QueryExecution;
12	import com.hp.hpl.jena.query.QueryExecutionFactory;
13	import com.hp.hpl.jena.query.QueryFactory;
14	import com.hp.hpl.jena.query.QuerySolution;
15	import com.hp.hpl.jena.query.ResultSet;
16	import com.hp.hpl.jena.rdf.model.Literal;
17	import com.hp.hpl.jena.rdf.model.Model;
18	import com.hp.hpl.jena.rdf.model.Property;
19	import com.hp.hpl.jena.rdf.model.Resource;
20
21	//public class OWLQueryBuilderForCrawlerImpl implements OWLQueryBuilder {
22	public class AcquiredStructureAnalyzer implements RDFSchemaAnalyzer {
23
24	private CrawledMetadata crawledMetadata = null;
25
26	public String getEndpointURI(){
27	return crawledMetadata.getEndpointURI();
28	}
29
30	public String[] getGraphURIs(){
31	return crawledMetadata.getGraphURIs();
32	}
33
34	/*
35	public static void main(String[] args) throws Exception{
36
37	JenaModelGenerator jmGene = new JenaModelGenerator("c:\\temp\\biosamplesF11.ttl");
38	// JenaModelGenerator jmGene = new JenaModelGenerator("c:\\temp\\reactomeF18s.ttl");
39	AcquiredStructureAnalyzer impl
40	= new AcquiredStructureAnalyzer(jmGene.getEndpointURI(), jmGene.getGraphURIs(), jmGene.getModel());
41
42	System.out.println("--------------------------");
43	SClass[] scs = impl.getOWLClasses(null, null, null, true);
44	System.out.println("list classes:---------------");
45	for(SClass sc: scs){
46	System.out.println(sc.toString());
47	}
48	System.out.println("--------------------------");
49
50	// ClassLink[] cls = impl.getNextClass(null,"http://www.biopax.org/release/biopax-level3.owl#Protein",100,true );
51	// for(ClassLink cl: cls){
52	// System.out.println(cl.toString());
53	// }
54	// System.out.println("--------------------------");
55
56	}
57	*/
58
59	public AcquiredStructureAnalyzer(CrawledMetadata crawledMetadata){
60	this.crawledMetadata = crawledMetadata;
61	}
62
63	private String filterGraphURIs(String orgGraphURIs){
64	// TODO
65	return orgGraphURIs;
66	}
67
68
69	public SClass[] listClasses(String graphURI, boolean countInstances) throws Exception{
70	return getOWLClasses(graphURI, null, null, countInstances);
71	}
72
73
74
75
76	public SClass[] getOWLClasses(String graphURI, String[] keywords, String language, boolean countInstances) throws Exception{
77	return getOWLClassList(graphURI, keywords, language, countInstances).toArray(new SClass[0]);
78	}
79
80	public List<SClass> getOWLClassList(String graphURI, String[] keywords, String language, boolean countInstances) throws Exception{
81	String targetGraphURI = filterGraphURIs(graphURI);
82
83	Dataset dataset = crawledMetadata.getDataset(targetGraphURI);
84
85
86	StringBuffer queryStr = new StringBuffer();
87	queryStr.append("PREFIX owl: <http://www.w3.org/2002/07/owl#>\n");
88	queryStr.append("PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>\n");
89	queryStr.append("PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>\n");
90	queryStr.append("SELECT DISTINCT ?c ?pLabel ?entities\n");
91	if (targetGraphURI != null) {
92	queryStr.append("FROM <");
93	queryStr.append(targetGraphURI);
94	queryStr.append(">\n");
95	}
96	queryStr.append("WHERE{\n");
97	queryStr.append(" ?cp <").append(URICollection.PROPERTY_VOID_CLASS).append("> ?c. \n");
98	queryStr.append(" ?cp <");
99	queryStr.append(URICollection.PROPERTY_VOID_ENTITIES);
100	queryStr.append("> ?entities. \n");
101	queryStr.append(" OPTIONAL{ ?c <");
102	queryStr.append(URICollection.PROPERTY_RDFS_LABEL);
103	queryStr.append("> ?pLabel. }\n");
104
105	if (keywords != null && keywords.length != 0) {
106
107	queryStr.append(" ?c rdfs:label ");
108	queryStr.append("?keywords").append(".\n");
109	queryStr.append(" filter((LANG(?keywords) = \'").append(language);
110	queryStr.append("\') && \n (");
111
112	for (int i = 0; i < keywords.length; i++) {
113	if (i > 0)
114	queryStr.append(" \|\| \n ");
115
116	queryStr.append("regex(str(").append("?keywords")
117	.append("),\"");
118	queryStr.append(keywords[i]);
119	queryStr.append("\", \"i\" )");
120
121	}
122	queryStr.append("))\n");
123
124	}
125	queryStr.append("}");
126	System.out.println(queryStr.toString());
127
128	Query query = QueryFactory.create(queryStr.toString());
129
130	QueryExecution qexec = null;
131	ResultSet results = null;
132	try {
133	// long start = System.currentTimeMillis();
134	qexec = QueryExecutionFactory.create(query, dataset.getModel());
135	results = qexec.execSelect();
136	// long end = System.currentTimeMillis();
137	// System.out.println("EXEC TIME: " + (end - start));
138	} catch (Exception ex) {
139	ex.printStackTrace();
140	throw ex;
141	}
142
143	HashMap<String, SClass> classMap = new HashMap<String, SClass>();
144	for (; results.hasNext();) {
145	QuerySolution sol = results.next();
146	Resource res = sol.getResource("c");
147	if (res != null && res.getURI() != null) {
148	String uri = res.getURI();
149	int numOfInstances = 0;
150	if (countInstances) {
151	numOfInstances = sol.getLiteral("entities").getInt();
152	} //
153	Literal labelLiteral = sol.getLiteral("pLabel");
154	SClass sClass = null;
155	if (classMap.containsKey(uri)) {
156	sClass = classMap.get(uri);
157	} else {
158	sClass = new SClass(uri, null, numOfInstances);
159	classMap.put(uri, sClass);
160	}
161	if (labelLiteral != null) {
162	String label = labelLiteral.getString();
163	String lang = labelLiteral.getLanguage();
164	sClass.addLabel(new Label(label, lang));
165	}
166	}
167	}
168	qexec.close();
169	return new LinkedList<SClass>(classMap.values());
170	}
171
172	/*
173
174	public Instance[] getInstances(String[] graphURIs, String keyword) throws Exception;
175	*/
176
177
178	public ClassLink[] getNextClass(String graphURI, String originClass, int limit, boolean countLinks) throws Exception{
179	String targetGraphURI = filterGraphURIs(graphURI);
180	Dataset dataset = crawledMetadata.getDataset(targetGraphURI);
181
182
183	StringBuffer queryStr = new StringBuffer();
184	queryStr.append("PREFIX owl: <http://www.w3.org/2002/07/owl#>\n");
185	queryStr.append("PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>\n");
186	queryStr.append("PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>\n");
187
188	// SELECT
189	queryStr.append("SELECT DISTINCT ?indPropCat ?c ?dat ?d ?p ?numLnkInsStart ?numLnkInsEnd ?numInsDom ?numInsRan ?numTriples\n");
190
191	if (targetGraphURI != null) {
192	queryStr.append("FROM <");
193	queryStr.append(targetGraphURI);
194	queryStr.append(">\n");
195	}
196
197	queryStr.append("WHERE{\n");
198	queryStr.append(" ?cr <").append(URICollection.PROPERTY_RDF_TYPE).append("> <").append(URICollection.RESOURCE_SB_CLASS_RELATION).append(">. \n");
199	queryStr.append(" ?propPart <").append(URICollection.PROPERTY_SB_CLASS_RELATION).append("> ?cr. \n");
200	queryStr.append(" ?propPart <").append(URICollection.PROPERTY_VOID_PROPERTY).append("> ?p. \n");
201
202	queryStr.append(" {");
203	queryStr.append(" ?cr <").append(URICollection.PROPERTY_SB_SUBJECT_CLASS).append("> <" + originClass + ">. \n");
204	queryStr.append(" ?cr <").append(URICollection.PROPERTY_SB_OBJECT_CLASS).append("> ?d. \n");
205	queryStr.append(" ?cr <").append(URICollection.PROPERTY_VOID_DISTINCT_SUBJECTS).append("> ?numLnkInsStart. \n");
206	queryStr.append(" ?cr <").append(URICollection.PROPERTY_VOID_DISTINCT_OBJECTS).append("> ?numLnkInsEnd. \n");
207	queryStr.append(" ?cr <").append(URICollection.PROPERTY_VOID_TRIPLES).append("> ?numTriples. \n");
208	// queryStr.append(" ?cr <http://sparqlbuilder.org/startClassLimitedQ> ?isStartClsLim. \n");
209	// queryStr.append(" ?cr <http://sparqlbuilder.org/endClassLimitedQ> ?isEndClsLim. \n");
210	queryStr.append("}\n");
211	queryStr.append(" UNION\n");
212	queryStr.append(" {");
213	queryStr.append(" ?cr <").append(URICollection.PROPERTY_SB_SUBJECT_CLASS).append("> <" + originClass + ">. \n");
214	queryStr.append(" ?cr <").append(URICollection.PROPERTY_SB_OBJECT_DATATYPE).append("> ?dat. \n");
215	queryStr.append(" ?cr <").append(URICollection.PROPERTY_VOID_DISTINCT_SUBJECTS).append("> ?numLnkInsStart. \n");
216	queryStr.append(" ?cr <").append(URICollection.PROPERTY_VOID_DISTINCT_OBJECTS).append("> ?numLnkInsEnd. \n");
217	queryStr.append(" ?cr <").append(URICollection.PROPERTY_VOID_TRIPLES).append("> ?numTriples. \n");
218	// queryStr.append(" ?cr <http://sparqlbuilder.org/startClassLimitedQ> ?isStartClsLim. \n");
219	// queryStr.append(" ?cr <http://sparqlbuilder.org/endClassLimitedQ> ?isEndClsLim. \n");
220	queryStr.append("}\n");
221	queryStr.append(" UNION\n");
222	queryStr.append(" {");
223	queryStr.append(" ?cr <").append(URICollection.PROPERTY_SB_OBJECT_CLASS).append("> <" + originClass + ">. \n");
224	queryStr.append(" ?cr <").append(URICollection.PROPERTY_SB_SUBJECT_CLASS).append("> ?c. \n");
225	queryStr.append(" ?cr <").append(URICollection.PROPERTY_VOID_DISTINCT_SUBJECTS).append("> ?numLnkInsEnd. \n");
226	queryStr.append(" ?cr <").append(URICollection.PROPERTY_VOID_DISTINCT_OBJECTS).append("> ?numLnkInsStart. \n");
227	queryStr.append(" ?cr <").append(URICollection.PROPERTY_VOID_TRIPLES).append("> ?numTriples. \n");
228	// queryStr.append(" ?cr <http://sparqlbuilder.org/startClassLimitedQ> ?isEndClsLim. \n");
229	// queryStr.append(" ?cr <http://sparqlbuilder.org/endClassLimitedQ> ?isStartClsLim. \n");
230	queryStr.append("}\n");
231
232	// queryStr.append(" ?propPart <").append(URICollection.PROPERTY_RDF_TYPE).append("> <").append(URICollection.PROPERTY_VOID_PROPERTY_PARTITION).append(">. \n");
233	queryStr.append(" ?propPart <").append(URICollection.PROPERTY_SB_PROPERTY_CATEGORY).append("> ?indPropCat. \n");
234
235	queryStr.append(" ?propPart <").append(URICollection.PROPERTY_VOID_DISTINCT_SUBJECTS).append("> ?numInsDom. \n");
236	queryStr.append(" ?propPart <").append(URICollection.PROPERTY_VOID_DISTINCT_OBJECTS).append("> ?numInsRan. \n");
237
238	queryStr.append("}\n");
239
240
241	if (limit > 0) {
242	queryStr.append("limit ");
243	queryStr.append(limit);
244	queryStr.append("\n");
245	}
246
247	// System.out.println("getNextClasses SPARQL Query: ");
248	// System.out.println(queryStr.toString());
249
250	Query query = QueryFactory.create(queryStr.toString());
251	QueryExecution qexec = null;
252	ResultSet results = null;
253	try {
254	long start = System.currentTimeMillis();
255	qexec = QueryExecutionFactory.create(query, dataset.getModel());
256	results = qexec.execSelect();
257	long end = System.currentTimeMillis();
258	System.out.println("EXEC TIME: " + (end - start));
259	} catch (Exception ex) {
260	ex.printStackTrace();
261	throw ex;
262	}
263
264	ArrayList<ClassLink> solCLs = new ArrayList<ClassLink>();
265	for (; results.hasNext();) {
266	QuerySolution sol = results.next();
267	Resource pro = sol.getResource("p");
268	String clsURI = null;
269	String datURI = null;
270	if (pro != null) {
271	int indPropCat = 4;
272	Literal indPropCatLit = sol.getLiteral("indPropCat");
273	if( indPropCatLit != null ){
274	indPropCat = indPropCatLit.getInt();
275	}
276	if( indPropCat < 4 ) {
277	String proURI = pro.getURI();
278	Resource ccls = sol.getResource("c");
279	Resource dcls = sol.getResource("d");
280	Resource dat = sol.getResource("dat");
281	Direction direction = null;
282	if(ccls != null && dcls == null ){
283	// direction forward
284	direction = Direction.reverse;
285	clsURI = ccls.getURI();
286	}else{
287	if( ccls == null && dcls != null ){
288	direction = Direction.forward;
289	clsURI = dcls.getURI();
290	}else{
291	if( ccls == null && dat != null && dcls == null ){
292	clsURI = null;
293	direction = Direction.forward;
294	datURI = dat.getURI();
295	}
296	}
297	}
298
299
300	int numTriples = 0;
301	Literal numTriplesLit = sol.getLiteral("numTriples");
302	if( numTriplesLit != null ){
303	numTriples = numTriplesLit.getInt();
304	}
305
306	int numLnkInsStart = 0;
307	Literal numInsStartLit = sol.getLiteral("numLnkInsStart");
308	if( numInsStartLit != null ){
309	numLnkInsStart = numInsStartLit.getInt();
310	}
311	int numLnkInsEnd = 0;
312	Literal numInsEndLit = sol.getLiteral("numLnkInsEnd");
313	if( numInsEndLit != null ){
314	numLnkInsEnd = numInsEndLit.getInt();
315	}
316
317	int numInsDom = 0;
318	Literal numInsDomLit = sol.getLiteral("numInsDom");
319	if( numInsDomLit != null ){
320	numInsDom = numInsDomLit.getInt();
321	}
322	int numInsRan = 0;
323	Literal numInsRanLit = sol.getLiteral("numInsRan");
324	if( numInsRanLit != null ){
325	numInsRan = numInsRanLit.getInt();
326	}
327
328	boolean isStartClsLim = false;
329	Literal isStartClsLimLit = sol.getLiteral("isStartClsLim");
330	if( isStartClsLimLit != null ){
331	isStartClsLim = isStartClsLimLit.getBoolean();
332	}
333	boolean isEndClsLim = false;
334	Literal isEndClsLimLit = sol.getLiteral("isEndClsLim");
335	if( isEndClsLimLit != null ){
336	isEndClsLim = isEndClsLimLit.getBoolean();
337	}
338
339	ClassLink cl = new ClassLink(proURI, clsURI, datURI, direction,
340	numTriples, numInsDom, numInsRan, numLnkInsStart, numLnkInsEnd, isStartClsLim, isEndClsLim);
341	solCLs.add(cl);
342
343	}
344	}
345	}
346	qexec.close();
347	return solCLs.toArray(new ClassLink[0]);
348	}
349
350
351
352	/*
353
354	public ClassLink[] getNextClassViaInstanceLink(String[] graphURIs, String originClass, int limit) throws Exception;
355
356	public Path[] getPaths(String startClass, String endClass, int mode, boolean countLinks) throws Exception;
357
358	public String createSPARQL(Path path) throws Exception;
359
360	InstanceLink[] getNextInstancesViaInstanceLink(String[] graphURIs, String originInstance,
361	int limit) throws Exception;
362	*/
363
364	public LabelMap[] getLabels(String graphURI, String[] resourceURIs,
365	String language) throws Exception {
366	// if (resourceURI == null \|\| resourceURIs.length == 0) {
367	// return new LabelMap[0];
368	// }
369
370	String targetGraphURI = filterGraphURIs(graphURI);
371	Dataset dataset = crawledMetadata.getDataset(targetGraphURI);
372
373
374	StringBuffer queryStr = new StringBuffer();
375	queryStr.append("PREFIX owl: <http://www.w3.org/2002/07/owl#>\n");
376	queryStr.append("PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>\n");
377	queryStr.append("PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>\n");
378	queryStr.append("SELECT DISTINCT ?res ?label \n");
379	if (targetGraphURI != null) {
380	queryStr.append("FROM <");
381	queryStr.append(targetGraphURI);
382	queryStr.append(">\n");
383	}
384	queryStr.append("WHERE{\n");
385	queryStr.append(" ?res rdfs:label ?label.\n");
386	queryStr.append(" FILTER(?res IN (");
387	boolean f = false;
388	for (String resourceURI : resourceURIs) {
389	if (f) {
390	queryStr.append(", ");
391	}
392	f = true;
393	queryStr.append("<");
394	queryStr.append(resourceURI);
395	queryStr.append(">");
396	}
397	queryStr.append("))\n");
398	queryStr.append("}");
399
400	// System.out.println(queryStr.toString());
401
402	Query query = QueryFactory.create(queryStr.toString());
403	QueryExecution qexec = QueryExecutionFactory.create(query, dataset.getModel());
404
405	ResultSet results = qexec.execSelect();
406	HashMap<String, LabelMap> lMap = new HashMap<String, LabelMap>();
407	for (; results.hasNext();) {
408	QuerySolution sol = results.next();
409	String uri = sol.getResource("res").getURI();
410	Literal literal = sol.getLiteral("label");
411	if (literal != null) {
412	String label = literal.getString();
413	String lang = literal.getLanguage();
414	if (language != null && language.equals(lang)) {
415	Label lbl = new Label(label, lang);
416	if (lMap.containsKey(uri)) {
417	LabelMap lm = lMap.get(uri);
418	lm.addLabel(lbl);
419	} else {
420	LabelMap lm = new LabelMap(uri, new Label[] { lbl });
421	lMap.put(uri, lm);
422	}
423	}
424	}
425	}
426	return lMap.values().toArray(new LabelMap[0]);
427	}
428
429	/*
430	public ClassLink[] countLinks(String[] graphURIs, String startClassURI, ClassLink[] classLinks) throws Exception;
431	public SClass[] countInstances(String[] graphURIs, SClass[] classes) throws Exception;
432
433	*/
434
435	}

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root/SPARQLBuilderWWW2016/src/java/org/biohackathon/SPARQLBuilder/OWL/AcquiredStructureAnalyzer.java @ 269

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