| 1 | package org.biohackathon.SPARQLBuilder.OWL;
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| 2 |
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| 3 | import java.util.ArrayList;
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| 4 | import java.util.HashMap;
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| 5 |
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| 6 | import jp.riken.accc.db.rdf.crawler.dataStructure.sparql.JenaModelGenerator;
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| 7 |
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| 8 | import com.hp.hpl.jena.query.Query;
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| 9 | import com.hp.hpl.jena.query.QueryExecution;
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| 10 | import com.hp.hpl.jena.query.QueryExecutionFactory;
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| 11 | import com.hp.hpl.jena.query.QueryFactory;
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| 12 | import com.hp.hpl.jena.query.QuerySolution;
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| 13 | import com.hp.hpl.jena.query.ResultSet;
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| 14 | import com.hp.hpl.jena.rdf.model.Literal;
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| 15 | import com.hp.hpl.jena.rdf.model.Model;
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| 16 | import com.hp.hpl.jena.rdf.model.Property;
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| 17 | import com.hp.hpl.jena.rdf.model.Resource;
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| 18 |
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| 19 | //public class OWLQueryBuilderForCrawlerImpl implements OWLQueryBuilder {
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| 20 | public class AcquiredStructureAnalyzer implements RDFSchemaAnalyzer {
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| 21 |
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| 22 | private Model model = null;
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| 23 | private String endpointURI = null;
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| 24 | private String[] graphURIs = null;
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| 25 |
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| 26 | public String getEndpointURI(){
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| 27 | return endpointURI;
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| 28 | }
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| 29 |
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| 30 | public String[] getGraphURIs(){
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| 31 | return graphURIs;
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| 32 | }
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| 33 |
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| 34 |
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| 35 | public static void main(String[] args) throws Exception{
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| 36 | JenaModelGenerator jmGene = new JenaModelGenerator("c:\\temp\\dberdf.ttl");
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| 37 | AcquiredStructureAnalyzer impl
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| 38 | = new AcquiredStructureAnalyzer(jmGene.getEndpointURI(), jmGene.getGraphURIs(), jmGene.getModel());
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| 39 | System.out.println("--------------------------");
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| 40 | SClass[] scs = impl.getOWLClasses(null, null, null, true);
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| 41 | System.out.println("list classes:---------------");
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| 42 | for(SClass sc: scs){
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| 43 | System.out.println(sc.toString());
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| 44 | }
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| 45 | System.out.println("--------------------------");
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| 46 |
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| 47 | ClassLink[] cls = impl.getNextClass(null,"http://purl.org/allie/ontology/201108#EachPair",100,true );
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| 48 | for(ClassLink cl: cls){
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| 49 | System.out.println(cl.toString());
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| 50 | }
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| 51 | System.out.println("--------------------------");
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| 52 |
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| 53 | }
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| 54 |
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| 55 |
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| 56 | public AcquiredStructureAnalyzer(String endpointURI, String[] graphURIs, Model model){
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| 57 | this.model = model;
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| 58 | this.endpointURI = endpointURI;
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| 59 | this.graphURIs = graphURIs;
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| 60 | }
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| 61 |
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| 62 | private String[] filterGraphURIs(String[] orgGraphURIs){
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| 63 | // TODO
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| 64 | return graphURIs;
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| 65 | }
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| 66 |
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| 67 |
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| 68 | public SClass[] listClasses(String[] graphURIs, boolean countInstances) throws Exception{
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| 69 | return getOWLClasses(graphURIs, null, null, countInstances);
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| 70 | }
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| 71 |
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| 72 |
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| 73 |
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| 74 |
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| 75 | public SClass[] getOWLClasses(String[] graphURIs, String[] keywords, String language, boolean countInstances) throws Exception{
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| 76 | String[] targetGraphURIs = filterGraphURIs(graphURIs);
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| 77 |
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| 78 | StringBuffer queryStr = new StringBuffer();
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| 79 | queryStr.append("PREFIX owl: <http://www.w3.org/2002/07/owl#>\n");
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| 80 | queryStr.append("PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>\n");
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| 81 | queryStr.append("PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>\n");
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| 82 | queryStr.append("SELECT DISTINCT ?c ?pLabel ?numOfInstances\n");
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| 83 | // if (targetGraphURIs != null) {
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| 84 | // for (String graphURI : targetGraphURIs) {
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| 85 | // queryStr.append("FROM <");
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| 86 | // queryStr.append(graphURI);
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| 87 | // queryStr.append(">\n");
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| 88 | // }
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| 89 | // }
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| 90 | queryStr.append("WHERE{\n");
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| 91 | queryStr.append(" ?c rdf:type rdfs:Class. \n");
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| 92 | queryStr.append(" ?c <http://sparqlbuilder.org/numberOfInstances> ?numOfInstances. \n");
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| 93 | queryStr.append(" OPTIONAL{ ?c rdfs:label ?pLabel. }\n");
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| 94 |
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| 95 | if (keywords != null && keywords.length != 0) {
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| 96 |
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| 97 | queryStr.append(" ?c rdfs:label ");
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| 98 | queryStr.append("?keywords").append(".\n");
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| 99 | queryStr.append(" filter((LANG(?keywords) = \'").append(language);
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| 100 | queryStr.append("\') && \n (");
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| 101 |
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| 102 | for (int i = 0; i < keywords.length; i++) {
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| 103 | if (i > 0)
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| 104 | queryStr.append(" || \n ");
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| 105 |
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| 106 | queryStr.append("regex(str(").append("?keywords")
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| 107 | .append("),\"");
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| 108 | queryStr.append(keywords[i]);
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| 109 | queryStr.append("\", \"i\" )");
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| 110 |
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| 111 | }
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| 112 | queryStr.append("))\n");
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| 113 |
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| 114 | }
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| 115 | queryStr.append("}");
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| 116 | System.out.println(queryStr.toString());
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| 117 |
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| 118 | Query query = QueryFactory.create(queryStr.toString());
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| 119 |
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| 120 | QueryExecution qexec = null;
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| 121 | ResultSet results = null;
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| 122 | try {
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| 123 | // long start = System.currentTimeMillis();
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| 124 | qexec = QueryExecutionFactory.create(query, model);
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| 125 | results = qexec.execSelect();
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| 126 | // long end = System.currentTimeMillis();
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| 127 | // System.out.println("EXEC TIME: " + (end - start));
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| 128 | } catch (Exception ex) {
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| 129 | ex.printStackTrace();
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| 130 | throw ex;
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| 131 | }
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| 132 |
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| 133 | HashMap<String, SClass> classMap = new HashMap<String, SClass>();
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| 134 | for (; results.hasNext();) {
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| 135 | QuerySolution sol = results.next();
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| 136 | Resource res = sol.getResource("c");
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| 137 | if (res != null && res.getURI() != null) {
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| 138 | String uri = res.getURI();
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| 139 | int numOfInstances = 0;
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| 140 | if (countInstances) {
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| 141 | numOfInstances = sol.getLiteral("numOfInstances").getInt();
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| 142 | } //
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| 143 | Literal labelLiteral = sol.getLiteral("pLabel");
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| 144 | SClass sClass = null;
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| 145 | if (classMap.containsKey(uri)) {
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| 146 | sClass = classMap.get(uri);
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| 147 | } else {
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| 148 | sClass = new SClass(uri, null, numOfInstances);
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| 149 | classMap.put(uri, sClass);
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| 150 | }
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| 151 | if (labelLiteral != null) {
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| 152 | String label = labelLiteral.getString();
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| 153 | String lang = labelLiteral.getLanguage();
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| 154 | sClass.addLabel(new Label(label, lang));
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| 155 | }
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| 156 | }
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| 157 | }
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| 158 | qexec.close();
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| 159 | return classMap.values().toArray(new SClass[0]);
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| 160 | }
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| 161 |
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| 162 | /*
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| 163 |
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| 164 | public Instance[] getInstances(String[] graphURIs, String keyword) throws Exception;
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| 165 | */
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| 166 |
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| 167 |
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| 168 | public ClassLink[] getNextClass(String[] graphURIs, String originClass, int limit, boolean countLinks) throws Exception{
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| 169 | String[] targetGraphURIs = filterGraphURIs(graphURIs);
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| 170 |
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| 171 | StringBuffer queryStr = new StringBuffer();
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| 172 | queryStr.append("PREFIX owl: <http://www.w3.org/2002/07/owl#>\n");
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| 173 | queryStr.append("PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>\n");
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| 174 | queryStr.append("PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>\n");
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| 175 |
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| 176 | // SELECT
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| 177 | queryStr.append("SELECT DISTINCT ?indPropCat ?c ?d ?p ?numLnkInsStart ?numLnkInsEnd ?numInsDom ?numInsRan ?numTriples ?isStartClsLim ?isEndClsLim\n");
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| 178 |
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| 179 | // if (targetGraphURIs != null) {
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| 180 | // for (String graphURI : targetGraphURIs) {
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| 181 | // queryStr.append("FROM <");
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| 182 | // queryStr.append(graphURI);
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| 183 | // queryStr.append(">\n");
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| 184 | // }
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| 185 | // }
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| 186 |
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| 187 | queryStr.append("WHERE{\n");
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| 188 | queryStr.append(" ?cr rdf:type <http://sparqlbuilder.org/ClassRelation>. \n");
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| 189 | // queryStr.append(" <" + originClass + "> <http://sparqlbuilder.org/numberOfInstances> ?numInsStart. \n");
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| 190 | queryStr.append(" {");
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| 191 | queryStr.append(" ?cr <http://sparqlbuilder.org/startClass> <" + originClass + ">. \n");
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| 192 | queryStr.append(" ?cr <http://sparqlbuilder.org/endClass> ?c. \n");
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| 193 | queryStr.append(" ?cr <http://sparqlbuilder.org/property> ?p. \n");
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| 194 | queryStr.append(" ?cr <http://sparqlbuilder.org/numberOfTriples> ?numTriples. \n");
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| 195 | queryStr.append(" ?cr <http://sparqlbuilder.org/numberOfInstancesOfStartClass> ?numLnkInsStart. \n");
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| 196 | queryStr.append(" ?cr <http://sparqlbuilder.org/numberOfInstancesOfEndClass> ?numLnkInsEnd. \n");
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| 197 | queryStr.append(" ?cr <http://sparqlbuilder.org/startClassLimitedQ> ?isStartClsLim. \n");
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| 198 | queryStr.append(" ?cr <http://sparqlbuilder.org/endClassLimitedQ> ?isEndClsLim. \n");
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| 199 | queryStr.append("}\n");
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| 200 | queryStr.append(" UNION\n");
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| 201 | queryStr.append(" {");
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| 202 | queryStr.append(" ?cr <http://sparqlbuilder.org/endClass> <" + originClass + ">. \n");
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| 203 | queryStr.append(" ?cr <http://sparqlbuilder.org/startClass> ?d. \n");
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| 204 | queryStr.append(" ?cr <http://sparqlbuilder.org/property> ?p. \n");
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| 205 | queryStr.append(" ?cr <http://sparqlbuilder.org/numberOfTriples> ?numTriples.\n");
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| 206 | queryStr.append(" ?cr <http://sparqlbuilder.org/numberOfInstancesOfStartClass> ?numLnkInsEnd. \n");
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| 207 | queryStr.append(" ?cr <http://sparqlbuilder.org/numberOfInstancesOfEndClass> ?numLnkInsStart. \n");
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| 208 | queryStr.append(" ?cr <http://sparqlbuilder.org/startClassLimitedQ> ?isEndClsLim. \n");
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| 209 | queryStr.append(" ?cr <http://sparqlbuilder.org/endClassLimitedQ> ?isStartClsLim. \n");
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| 210 | queryStr.append("}\n");
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| 211 |
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| 212 | queryStr.append(" ?pp rdf:type <http://sparqlbuilder.org/PropertyProfile>. \n");
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| 213 | queryStr.append(" ?pp <http://sparqlbuilder.org/property> ?p. \n");
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| 214 | queryStr.append(" ?pp <http://sparqlbuilder.org/individualPropertyCategory> ?indPropCat. \n");
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| 215 | queryStr.append(" ?pp <http://sparqlbuilder.org/numberOfInstancesOfDomainClass> ?numInsDom. \n");
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| 216 | queryStr.append(" ?pp <http://sparqlbuilder.org/numberOfInstancesOfRangeClass> ?numInsRan \n");
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| 217 |
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| 218 |
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| 219 | queryStr.append("}\n");
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| 220 |
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| 221 |
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| 222 | if (limit > 0) {
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| 223 | queryStr.append("limit ");
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| 224 | queryStr.append(limit);
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| 225 | queryStr.append("\n");
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| 226 | }
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| 227 |
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| 228 | // System.out.println("getNextClasses SPARQL Query: ");
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| 229 | System.out.println(queryStr.toString());
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| 230 |
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| 231 | Query query = QueryFactory.create(queryStr.toString());
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| 232 | QueryExecution qexec = null;
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| 233 | ResultSet results = null;
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| 234 | try {
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| 235 | long start = System.currentTimeMillis();
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| 236 | qexec = QueryExecutionFactory.create(query, model);
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| 237 | results = qexec.execSelect();
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| 238 | long end = System.currentTimeMillis();
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| 239 | System.out.println("EXEC TIME: " + (end - start));
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| 240 | } catch (Exception ex) {
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| 241 | ex.printStackTrace();
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| 242 | throw ex;
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| 243 | }
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| 244 |
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| 245 | ArrayList<ClassLink> solCLs = new ArrayList<ClassLink>();
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| 246 | for (; results.hasNext();) {
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| 247 | QuerySolution sol = results.next();
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| 248 | Resource pro = sol.getResource("p");
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| 249 | String clsURI = null;
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| 250 | if (pro != null) {
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| 251 | int indPropCat = 4;
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| 252 | Literal indPropCatLit = sol.getLiteral("indPropCat");
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| 253 | if( indPropCatLit != null ){
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| 254 | indPropCat = indPropCatLit.getInt();
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| 255 | }
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| 256 | if( indPropCat < 4 ) {
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| 257 | String proURI = pro.getURI();
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| 258 | Resource ccls = sol.getResource("c");
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| 259 | Resource dcls = sol.getResource("d");
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| 260 | Direction direction = null;
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| 261 | if(ccls != null && dcls == null ){
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| 262 | // direction forward
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| 263 | direction = Direction.forward;
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| 264 | clsURI = ccls.getURI();
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| 265 | }else{
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| 266 | if( ccls == null && dcls != null ){
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| 267 | direction = Direction.reverse;
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| 268 | clsURI = dcls.getURI();
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| 269 | }
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| 270 | }
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| 271 |
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| 272 |
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| 273 | int numTriples = 0;
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| 274 | Literal numTriplesLit = sol.getLiteral("numTriples");
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| 275 | if( numTriplesLit != null ){
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| 276 | numTriples = numTriplesLit.getInt();
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| 277 | }
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| 278 |
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| 279 | int numLnkInsStart = 0;
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| 280 | Literal numInsStartLit = sol.getLiteral("numLnkInsStart");
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| 281 | if( numInsStartLit != null ){
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| 282 | numLnkInsStart = numInsStartLit.getInt();
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| 283 | }
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| 284 | int numLnkInsEnd = 0;
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| 285 | Literal numInsEndLit = sol.getLiteral("numLnkInsEnd");
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| 286 | if( numInsEndLit != null ){
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| 287 | numLnkInsEnd = numInsEndLit.getInt();
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| 288 | }
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| 289 |
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| 290 | int numInsDom = 0;
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| 291 | Literal numInsDomLit = sol.getLiteral("numInsDom");
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| 292 | if( numInsDomLit != null ){
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| 293 | numInsDom = numInsDomLit.getInt();
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| 294 | }
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| 295 | int numInsRan = 0;
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| 296 | Literal numInsRanLit = sol.getLiteral("numInsRan");
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| 297 | if( numInsRanLit != null ){
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| 298 | numInsRan = numInsRanLit.getInt();
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| 299 | }
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| 300 |
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| 301 | boolean isStartClsLim = false;
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| 302 | Literal isStartClsLimLit = sol.getLiteral("isStartClsLim");
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| 303 | if( isStartClsLimLit != null ){
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| 304 | isStartClsLim = isStartClsLimLit.getBoolean();
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| 305 | }
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| 306 | boolean isEndClsLim = false;
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| 307 | Literal isEndClsLimLit = sol.getLiteral("isEndClsLim");
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| 308 | if( isEndClsLimLit != null ){
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| 309 | isEndClsLim = isEndClsLimLit.getBoolean();
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| 310 | }
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| 311 |
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| 312 | ClassLink cl = new ClassLink(proURI, clsURI, direction,
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| 313 | numTriples, numInsDom, numInsRan, numLnkInsStart, numLnkInsEnd, isStartClsLim, isEndClsLim);
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| 314 | solCLs.add(cl);
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| 315 |
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| 316 | }
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| 317 | }
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| 318 | }
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| 319 | qexec.close();
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| 320 | return solCLs.toArray(new ClassLink[0]);
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| 321 | }
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| 322 |
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| 323 |
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| 324 |
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| 325 | /*
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| 326 |
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| 327 | public ClassLink[] getNextClassViaInstanceLink(String[] graphURIs, String originClass, int limit) throws Exception;
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| 328 |
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| 329 | public Path[] getPaths(String startClass, String endClass, int mode, boolean countLinks) throws Exception;
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| 330 |
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| 331 | public String createSPARQL(Path path) throws Exception;
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| 332 |
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| 333 | InstanceLink[] getNextInstancesViaInstanceLink(String[] graphURIs, String originInstance,
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| 334 | int limit) throws Exception;
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| 335 | */
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| 336 |
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| 337 | public LabelMap[] getLabels(String[] graphURIs, String[] resourceURIs,
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| 338 | String language) throws Exception {
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| 339 | if (resourceURIs == null || resourceURIs.length == 0) {
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| 340 | return new LabelMap[0];
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| 341 | }
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| 342 | StringBuffer queryStr = new StringBuffer();
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| 343 | queryStr.append("PREFIX owl: <http://www.w3.org/2002/07/owl#>\n");
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| 344 | queryStr.append("PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>\n");
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| 345 | queryStr.append("PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>\n");
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| 346 | queryStr.append("SELECT DISTINCT ?res ?label \n");
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| 347 | if (graphURIs != null) {
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| 348 | for (String graphURI : graphURIs) {
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| 349 | queryStr.append("FROM <");
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| 350 | queryStr.append(graphURI);
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| 351 | queryStr.append(">\n");
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| 352 | }
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| 353 | }
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| 354 | queryStr.append("WHERE{\n");
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| 355 | queryStr.append(" ?res rdfs:label ?label.\n");
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| 356 | queryStr.append(" FILTER(?res IN (");
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| 357 | boolean f = false;
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| 358 | for (String resourceURI : resourceURIs) {
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| 359 | if (f) {
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| 360 | queryStr.append(", ");
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| 361 | }
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| 362 | f = true;
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| 363 | queryStr.append("<");
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| 364 | queryStr.append(resourceURI);
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| 365 | queryStr.append(">");
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| 366 | }
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| 367 | queryStr.append("))\n");
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| 368 | queryStr.append("}");
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| 369 |
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| 370 | System.out.println(queryStr.toString());
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| 371 |
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| 372 | Query query = QueryFactory.create(queryStr.toString());
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| 373 | QueryExecution qexec = QueryExecutionFactory.create(query, model);
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| 374 |
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| 375 | ResultSet results = qexec.execSelect();
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| 376 | HashMap<String, LabelMap> lMap = new HashMap<String, LabelMap>();
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| 377 | for (; results.hasNext();) {
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| 378 | QuerySolution sol = results.next();
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| 379 | String uri = sol.getResource("res").getURI();
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| 380 | Literal literal = sol.getLiteral("label");
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| 381 | if (literal != null) {
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| 382 | String label = literal.getString();
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| 383 | String lang = literal.getLanguage();
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| 384 | if (language != null && language.equals(lang)) {
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| 385 | Label lbl = new Label(label, lang);
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| 386 | if (lMap.containsKey(uri)) {
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| 387 | LabelMap lm = lMap.get(uri);
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| 388 | lm.addLabel(lbl);
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| 389 | } else {
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| 390 | LabelMap lm = new LabelMap(uri, new Label[] { lbl });
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| 391 | lMap.put(uri, lm);
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| 392 | }
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| 393 | }
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| 394 | }
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| 395 | }
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| 396 | return lMap.values().toArray(new LabelMap[0]);
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| 397 | }
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| 398 |
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| 399 | /*
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| 400 | public ClassLink[] countLinks(String[] graphURIs, String startClassURI, ClassLink[] classLinks) throws Exception;
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| 401 | public SClass[] countInstances(String[] graphURIs, SClass[] classes) throws Exception;
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| 402 |
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| 403 | */
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| 404 |
|
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| 405 | }
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