Index: /BH13SPARQLBuilder/src/org/biohackathon/SPARQLBuilder/OWL/OWLQueryBuilderImpl.java =================================================================== --- /BH13SPARQLBuilder/src/org/biohackathon/SPARQLBuilder/OWL/OWLQueryBuilderImpl.java (revision 58) +++ /BH13SPARQLBuilder/src/org/biohackathon/SPARQLBuilder/OWL/OWLQueryBuilderImpl.java (revision 59) @@ -55,74 +55,50 @@ String sparqlEndpoint = "http://lsd.dbcls.jp/sparql"; // String keyword = "artiste"; - String[] keyword = {"Player","Soccer"}; + String[] keyword = { "Player", "Soccer" }; String[] graphURIs = new String[0]; - //keyword = null; + // keyword = null; OWLQueryBuilder builder = new OWLQueryBuilderImpl(sparqlEndpoint); - - builder.getOWLClasses(null,keyword,false); -/* - SClass[] clz = builder.getOWLClasses(graphURIs, keyword, false); - for (SClass cls : clz) { - System.out.println(cls); - } - clz = builder.countInstances(null, clz); - for (SClass cls : clz) { - System.out.println(cls); - } -*/ - - - /* System.out.println("CLS"); - - String uri = "http://purl.jp/bio/10/lsd/ontology/201209#EnglishEntry"; - - ClassLink[] cls = null; - try{ - cls = builder.getNextClass(null, uri, 100, false); - }catch(Exception ex) { - ex.printStackTrace(); - } - - System.out.println("Solutions: "); - if (cls != null) { - for (ClassLink cl : cls) { - System.out.println(cl.toString()); - } - cls = builder.countLinks(null, uri, cls); - for (ClassLink cl : cls) { - System.out.println(cl.toString()); - } - } -*/ -/* - - String uri = "http://purl.jp/bio/10/lsd/ontology/201209#EnglishEntry"; - - ClassLink[] cls = null; - - System.out.println("CLS-INS"); - cls = null; - try{ - cls = builder.getNextClassViaInstanceLink(null, uri, 100); - }catch(Exception ex){ - ex.printStackTrace(); - } - if (cls != null) { - for (ClassLink cl : cls) { - System.out.println(cl.toString()); - } - } -*/ + + builder.getOWLClasses(null, keyword, false); /* - System.out.println("Instances"); - Instance[] ins = builder.getInstances(null, "\"A.C. Reed\"@en"); - if (ins != null) { - for (Instance in : ins) { - System.out.println(in.toString()); - } - } -*/ + * SClass[] clz = builder.getOWLClasses(graphURIs, keyword, false); for + * (SClass cls : clz) { System.out.println(cls); } clz = + * builder.countInstances(null, clz); for (SClass cls : clz) { + * System.out.println(cls); } + */ + + /* + * System.out.println("CLS"); + * + * String uri = + * "http://purl.jp/bio/10/lsd/ontology/201209#EnglishEntry"; + * + * ClassLink[] cls = null; try{ cls = builder.getNextClass(null, uri, + * 100, false); }catch(Exception ex) { ex.printStackTrace(); } + * + * System.out.println("Solutions: "); if (cls != null) { for (ClassLink + * cl : cls) { System.out.println(cl.toString()); } cls = + * builder.countLinks(null, uri, cls); for (ClassLink cl : cls) { + * System.out.println(cl.toString()); } } + */ + /* + * + * String uri = + * "http://purl.jp/bio/10/lsd/ontology/201209#EnglishEntry"; + * + * ClassLink[] cls = null; + * + * System.out.println("CLS-INS"); cls = null; try{ cls = + * builder.getNextClassViaInstanceLink(null, uri, 100); }catch(Exception + * ex){ ex.printStackTrace(); } if (cls != null) { for (ClassLink cl : + * cls) { System.out.println(cl.toString()); } } + */ + /* + * System.out.println("Instances"); Instance[] ins = + * builder.getInstances(null, "\"A.C. Reed\"@en"); if (ins != null) { + * for (Instance in : ins) { System.out.println(in.toString()); } } + */ /* * System.out.println("INS-INS"); ins = builder.getInstances(null, @@ -136,7 +112,4 @@ } - - - /** * 譏守､ｺ逧�↓RDF縺ｧ譖ｸ縺九ｌ縺ｦ縺�ｋ繧ｯ繝ｩ繧ｹ繧貞叙蠕励☆繧� @@ -153,5 +126,5 @@ * @since 28.01.2014 */ - public SClass[] getOWLClasses(String[] graphURIs, String[] keywords, + public SClass[] getOWLClasses(String[] graphURIs, String[] keywords,縲€String language, boolean countInstances) throws Exception { StringBuffer queryStr = new StringBuffer(); @@ -173,9 +146,8 @@ queryStr.append("WHERE{\n"); - // + // queryStr.append(" {?c rdf:type rdfs:Class} UNION {?c rdf:type owl:Class}\n"); -// queryStr.append(" ?i rdf:type ?c.\n"); - - + // queryStr.append(" ?i rdf:type ?c.\n"); + if (countInstances) { queryStr.append(" ?c rdfs:label ?label.\n"); @@ -188,28 +160,24 @@ // queryStr.append(keyword); // queryStr.append("."); - - // TODO OR relationship between keywords + + // TODO OR relationship between keywords if (keywords != null && keywords.length != 0) { - queryStr.append(" ?c rdfs:label "); - queryStr.append("?keywords") - .append(".\n"); - queryStr.append(" filter("); - - for (int i=0;i0) queryStr.append(" or \n "); - - queryStr.append("regex(str(") - .append("?keywords") - .append("),\""); - queryStr.append(keywords[i]); - queryStr.append("\", \"i\" )"); - - } - queryStr.append(")\n"); - - } - + queryStr.append("?keywords").append(".\n"); + queryStr.append(" filter("); + + for (int i = 0; i < keywords.length; i++) { + if (i > 0) + queryStr.append(" or \n "); + + queryStr.append("regex(str(").append("?keywords") + .append("),\""); + queryStr.append(keywords[i]); + queryStr.append("\", \"i\" )"); + } + queryStr.append(")\n"); + + } + if (countInstances) { queryStr.append("} GROUP BY ?c ?pLabel"); @@ -218,61 +186,40 @@ } System.out.println(queryStr.toString()); - - - /* Query query = QueryFactory.create(queryStr.toString()); - - - QueryExecution qexec = null; - try{ - long start = System.currentTimeMillis(); - qexec = QueryExecutionFactory.sparqlService(endpointURI, - query); - long end = System.currentTimeMillis(); - System.out.println("EXEC TIME: " + (end-start)); - }catch(Exception ex){ - ex.printStackTrace(); - throw ex; - } - - ResultSet results = qexec.execSelect(); - HashMap classMap = new HashMap(); - for (; results.hasNext();) { - QuerySolution sol = results.next(); - Resource res = sol.getResource("c"); - if (res != null) { - String uri = res.getURI(); - int numOfInstances = 0; - if (countInstances) { - numOfInstances = sol.getLiteral("numOfInstances").getInt(); - } - // System.out.println(numOfInstances); - Literal labelLiteral = sol.getLiteral("pLabel"); - SClass sClass = null; - if (classMap.containsKey(uri)) { - sClass = classMap.get(uri); - } else { - sClass = new SClass(uri, null, numOfInstances); - classMap.put(uri, sClass); - } - if (labelLiteral != null) { - String label = labelLiteral.getString(); - String lang = labelLiteral.getLanguage(); - sClass.addLabel(new Label(label, lang)); - } - } - } - qexec.close(); - return classMap.values().toArray(new SClass[0]);*/ + + /* + * Query query = QueryFactory.create(queryStr.toString()); + * + * + * QueryExecution qexec = null; try{ long start = + * System.currentTimeMillis(); qexec = + * QueryExecutionFactory.sparqlService(endpointURI, query); long end = + * System.currentTimeMillis(); System.out.println("EXEC TIME: " + + * (end-start)); }catch(Exception ex){ ex.printStackTrace(); throw ex; } + * + * ResultSet results = qexec.execSelect(); HashMap + * classMap = new HashMap(); for (; results.hasNext();) + * { QuerySolution sol = results.next(); Resource res = + * sol.getResource("c"); if (res != null) { String uri = res.getURI(); + * int numOfInstances = 0; if (countInstances) { numOfInstances = + * sol.getLiteral("numOfInstances").getInt(); } // + * System.out.println(numOfInstances); Literal labelLiteral = + * sol.getLiteral("pLabel"); SClass sClass = null; if + * (classMap.containsKey(uri)) { sClass = classMap.get(uri); } else { + * sClass = new SClass(uri, null, numOfInstances); classMap.put(uri, + * sClass); } if (labelLiteral != null) { String label = + * labelLiteral.getString(); String lang = labelLiteral.getLanguage(); + * sClass.addLabel(new Label(label, lang)); } } } qexec.close(); return + * classMap.values().toArray(new SClass[0]); + */ return null; } - public SClass[] listClasses(String[] graphURIs, boolean countInstances) throws Exception{ - - //TODO + public SClass[] listClasses(String[] graphURIs, boolean countInstances) + throws Exception { + + // TODO return null; } - - /** * 縲€繧､繝ｳ繧ｹ繧ｿ繝ｳ繧ｹ繧貞叙蠕励☆繧� @@ -368,6 +315,7 @@ public ClassLink[] getNextClass(String[] graphURIs, String originClass, int limit, boolean countLinks) throws Exception { - ClassLink[] cLinks = getNextClassSub(graphURIs, originClass, limit, false); - if( countLinks ){ + ClassLink[] cLinks = getNextClassSub(graphURIs, originClass, limit, + false); + if (countLinks) { cLinks = countLinks(graphURIs, originClass, cLinks); } @@ -375,7 +323,7 @@ } - private ClassLink[] getNextClassSub(String[] graphURIs, String originClass, + private ClassLink[] getNextClassSub(String[] graphURIs, String originClass, int limit, boolean countLinks) throws Exception { - StringBuffer queryStr = new StringBuffer(); + StringBuffer queryStr = new StringBuffer(); queryStr.append("PREFIX owl: \n"); queryStr.append("PREFIX rdfs: \n"); @@ -434,5 +382,5 @@ queryStr.append(" ?p ?pDirection ?c.\n"); -// queryStr.append(" ?s rdf:type ?c.\n"); + // queryStr.append(" ?s rdf:type ?c.\n"); if (countLinks) { @@ -452,23 +400,22 @@ Query query = QueryFactory.create(queryStr.toString()); QueryExecution qexec = null; - try{ - qexec = QueryExecutionFactory.sparqlService(endpointURI, - query); - }catch(Exception ex){ + try { + qexec = QueryExecutionFactory.sparqlService(endpointURI, query); + } catch (Exception ex) { ex.printStackTrace(); throw ex; } - + ResultSet results = null; - try{ + try { long start = System.currentTimeMillis(); results = qexec.execSelect(); long end = System.currentTimeMillis(); - System.out.println("EXEC TIME: " + (end-start)); - }catch(Exception ex){ + System.out.println("EXEC TIME: " + (end - start)); + } catch (Exception ex) { ex.printStackTrace(); throw ex; } - + ArrayList solCLs = new ArrayList(); for (; results.hasNext();) { @@ -505,5 +452,5 @@ } ClassLink cl = new ClassLink(proURI, clsURI, direction, - numOfLinks, 0, 0, 0, 0 ); + numOfLinks, 0, 0, 0, 0); solCLs.add(cl); } @@ -559,5 +506,5 @@ } -System.out.println(queryStr.toString()); + System.out.println(queryStr.toString()); Query query = QueryFactory.create(queryStr.toString()); @@ -566,10 +513,10 @@ ResultSet results = null; - try{ + try { long start = System.currentTimeMillis(); results = qexec.execSelect(); long end = System.currentTimeMillis(); - System.out.println("EXEC TIME: " + (end-start)); - }catch(Exception ex){ + System.out.println("EXEC TIME: " + (end - start)); + } catch (Exception ex) { ex.printStackTrace(); throw ex; @@ -591,10 +538,14 @@ numOfLinks = sol.getLiteral("numOfForwardLinks").getInt(); numOfLinks += sol.getLiteral("numOfReverseLinks").getInt(); - numOfLinkedInstances = sol.getLiteral("numOfLinkedInstances").getInt(); - numOfOriginInstances = sol.getLiteral("numOfOriginInstances").getInt(); + numOfLinkedInstances = sol.getLiteral( + "numOfLinkedInstances").getInt(); + numOfOriginInstances = sol.getLiteral( + "numOfOriginInstances").getInt(); direction = Direction.both; } else { - numOfLinkedInstances = sol.getLiteral("numOfLinkedInstances").getInt(); - numOfOriginInstances = sol.getLiteral("numOfOriginInstances").getInt(); + numOfLinkedInstances = sol.getLiteral( + "numOfLinkedInstances").getInt(); + numOfOriginInstances = sol.getLiteral( + "numOfOriginInstances").getInt(); numOfLinks = sol.getLiteral("numOfForwardLinks").getInt(); direction = Direction.forward; @@ -604,6 +555,8 @@ direction = Direction.reverse; propURI = proReverse.getURI(); - numOfLinkedInstances = sol.getLiteral("numOfOriginInstances").getInt(); - numOfOriginInstances = sol.getLiteral("numOfLinkedInstances").getInt(); + numOfLinkedInstances = sol.getLiteral("numOfOriginInstances") + .getInt(); + numOfOriginInstances = sol.getLiteral("numOfLinkedInstances") + .getInt(); numOfLinks = sol.getLiteral("numOfReverseLinks").getInt(); } @@ -611,5 +564,7 @@ // System.out.println(propURI + " " + clsURI + " " + direction); - ClassLink cl = new ClassLink(propURI, clsURI, direction, numOfLinks, numOfOriginInstances, numOfLinkedInstances, 0, 0); + ClassLink cl = new ClassLink(propURI, clsURI, direction, + numOfLinks, numOfOriginInstances, numOfLinkedInstances, 0, + 0); solCLs.add(cl); } @@ -889,10 +844,12 @@ if (lit != null) { int numOfOriginClassInstances = lit.getInt(); - classLink.setNumOfOriginClassInstances(numOfOriginClassInstances); + classLink + .setNumOfOriginClassInstances(numOfOriginClassInstances); } lit = sol.getLiteral("numOfLinkedClassInstances"); if (lit != null) { int numOfLinkedClassInstances = lit.getInt(); - classLink.setNumOfLinkedClassInstances(numOfLinkedClassInstances); + classLink + .setNumOfLinkedClassInstances(numOfLinkedClassInstances); } } @@ -933,10 +890,9 @@ } } - + System.out.println(queryStr.toString()); query = QueryFactory.create(queryStr.toString()); - qexec = QueryExecutionFactory.sparqlService( - endpointURI, query); + qexec = QueryExecutionFactory.sparqlService(endpointURI, query); results = qexec.execSelect(); @@ -947,5 +903,6 @@ if (lit != null) { int numOfOriginClassInstances = lit.getInt(); - classLink.setNumOfOriginClassInstances(numOfOriginClassInstances); + classLink + .setNumOfOriginClassInstances(numOfOriginClassInstances); } } @@ -986,10 +943,9 @@ } } - + System.out.println(queryStr.toString()); query = QueryFactory.create(queryStr.toString()); - qexec = QueryExecutionFactory.sparqlService( - endpointURI, query); + qexec = QueryExecutionFactory.sparqlService(endpointURI, query); results = qexec.execSelect(); @@ -1000,14 +956,14 @@ if (lit != null) { int numOfLinkedClassInstances = lit.getInt(); - classLink.setNumOfLinkedClassInstances(numOfLinkedClassInstances); + classLink + .setNumOfLinkedClassInstances(numOfLinkedClassInstances); } } qexec.close(); - + } return classLinks; } - public SClass[] countInstances(String[] graphURIs, SClass[] classes) throws Exception { Index: /BH13SPARQLBuilder/src/org/biohackathon/SPARQLBuilder/OWL/OWLQueryBuilder.java =================================================================== --- /BH13SPARQLBuilder/src/org/biohackathon/SPARQLBuilder/OWL/OWLQueryBuilder.java (revision 55) +++ /BH13SPARQLBuilder/src/org/biohackathon/SPARQLBuilder/OWL/OWLQueryBuilder.java (revision 59) @@ -25,5 +25,5 @@ * @since 28.01.2014 */ - public SClass[] getOWLClasses(String[] graphURIs, String[] keyword, boolean countInstances) throws Exception; + public SClass[] getOWLClasses(String[] graphURIs, String[] keyword, String language, boolean countInstances) throws Exception; public SClass[] listClasses(String[] graphURIs, boolean countInstances) throws Exception;