Index: /SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/OWL/OWLClassGraph.java =================================================================== --- /SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/OWL/OWLClassGraph.java (revision 252) +++ /SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/OWL/OWLClassGraph.java (revision 254) @@ -12,6 +12,4 @@ public class OWLClassGraph extends LabeledMultiDigraph{ - //String startClass; - //String endClass; int nsteps = 4; int limit = 100; @@ -23,5 +21,4 @@ String sparqlEndpoint; Set visited; - boolean askcheck; List> edgeweight; List nodeweight; @@ -62,12 +59,10 @@ super(); nodeType = new LinkedList(); - this.askcheck = false; setClassGraph(rdfsa); } - public OWLClassGraph(RDFSchemaAnalyzer rdfsa, String sparqlEndpoint, String startClass, boolean askcheck){ // used + public OWLClassGraph(RDFSchemaAnalyzer rdfsa, String sparqlEndpoint, String startClass){ // used super(); nodeType = new LinkedList(); - this.askcheck = askcheck; setPartClassGraph(rdfsa, sparqlEndpoint, startClass); } @@ -124,8 +119,4 @@ } - public HashSet getConnectionList(Integer node){ - return connectionTable.get(node); - } - private List> searchPaths(String startClass, String endClass){ //int asked = 0; @@ -168,35 +159,4 @@ List nextpath = new LinkedList(crrpath); // copy nextpath.add(nextnode); - // tmp - if ( i >= 1 && askcheck == true ){ - int wn = nodeweight.get(crrnode); - int in = edgeweight.get(crrpath.get(crrpath.size()-2)).get(crrnode); - int out = edgeweight.get(nextnode).get(crrnode); - if ( wn > in + out ){ - /* - String key1 = nextnode.toString().concat("-").concat(crrpath.get(crrpath.size()-1).toString()) - .concat("-").concat(crrpath.get(crrpath.size()-2).toString()); - String key2 = crrpath.get(crrpath.size()-2).toString().concat("-").concat(crrpath.get(crrpath.size()-1).toString()) - .concat("-").concat(nextnode.toString()); - if ( checkedpaths.containsKey(key1) ){ - if ( checkedpaths.get(key1) == false ){ - continue; - } - }else if ( checkedpaths.containsKey(key2) ){ - if ( checkedpaths.get(key2) == false ){ - continue; - } - }else{ - boolean chk = EndpointAccess.check3SimplePath(nextnode, crrpath.get(crrpath.size()-1), - crrpath.get(crrpath.size()-2), this, sparqlEndpoint); - checkedpaths.put(key1, chk); - if ( chk == false ){ - continue; - } - } - */ - continue; - } - } if ( nextnode.equals(enode) ){ simplePaths.add(nextpath); @@ -241,7 +201,7 @@ addedpath.add(cl); // check - if (checkPath(startClass, addedpath)){ + //if (checkPath(startClass, addedpath)){ tmppaths.add(addedpath); - } + //} } } @@ -348,188 +308,28 @@ } } - } - - - private ArrayList> createConnectionTable(){ // not used - ArrayList> ct = new ArrayList>(); - for (int i = 0; i < labels.size(); i++ ){ // each node - HashSet cl = createConnectionList(i); - ct.add(cl); - } - return ct; - } + } - private HashSet createConnectionList(Integer node){ // not used - HashSet cl = new HashSet(); - HashSet crrnodes = new HashSet(); - crrnodes.add(node); - cl.add(node); - for ( int i = 0 ; i < nsteps; i++ ){ - Set nextnodes = new HashSet(); - Iterator cit = crrnodes.iterator(); - while ( cit.hasNext() ){ - Integer crr = cit.next(); - Set nexts = gadjlist.get(crr).keySet(); - Iterator nit = nexts.iterator(); - while ( nit.hasNext() ){ - Integer next = nit.next(); - if ( !cl.contains(next) ){ - nextnodes.add(next); - cl.add(next); - } - } - } - crrnodes.clear(); - crrnodes.addAll(nextnodes); - } - return cl; - } - - - private void updateWeight(Integer node1, Integer node2, ClassLink edge){ - Map weight = edgeweight.get(node1); - Integer crr = weight.get(node2); - if (crr == null ){ - crr = edge.getNumOfLinkedClassInstances(); - weight.put(node2, crr); - } - if ( crr < edge.getNumOfLinkedClassInstances() ){ - crr = edge.getNumOfLinkedClassInstances(); - weight.put(node2, crr); - } - weight = edgeweight.get(node2); - crr = weight.get(node1); - if (crr == null ){ - crr = edge.getNumOfOriginClassInstances(); - weight.put(node1, crr); - } - if ( crr < edge.getNumOfOriginClassInstances() ){ - crr = edge.getNumOfOriginInstances(); - weight.put(node1, crr); - } - } - - private boolean checkPath(String startClass, List paths){ - // KOKO - return true; - } - // old codes - /* - public Path[] getPaths_old(RDFSchemaAnalyzer rdfsa, boolean countLink, String startClass, String endClass){ - List> paths = null; - paths = searchPathsbyVisitingNodes(rdfsa, countLink, startClass, endClass); - NavigableSet sortedpath = new TreeSet(); - ListIterator> pit = paths.listIterator(); - int j = 0; - while ( pit.hasNext() ){ - Path path = new Path(); - path.setStartClass(startClass); - List crrpath = pit.next(); - path.setClassLinks(crrpath); - ListIterator cit = crrpath.listIterator(); - int min = Integer.MAX_VALUE; - while ( cit.hasNext() ){ - ClassLink cl = cit.next(); - if ( cl.getNumOfLinks() < min ){ - min = cl.getNumOfLinks(); - } - } - path.setWidth(min); - sortedpath.add(path); - j++; - } - Path[] patharray = new Path[paths.size()]; - Iterator pait = sortedpath.descendingIterator(); - int i = 0; - while ( pait.hasNext() ){ - patharray[i] = pait.next(); - i++; - } - return patharray; - } - - private List> searchPaths_old(String startClass, String endClass){ - - List> paths = new ArrayList<>(); - List> simplePaths = new LinkedList<>(); - Integer snode = labelednodes.get(startClass); - Integer enode = labelednodes.get(endClass); - List> lp = new LinkedList<>(); - List ini = new LinkedList(); // initial path - ini.add(snode); - lp.add(ini); - for (int i = 0; i < nsteps; i++ ){ - ListIterator> lit = lp.listIterator(); - List> nextlp = new LinkedList<>(); - while ( lit.hasNext() ){ - List crrpath = lit.next(); - Integer crrnode = crrpath.get(crrpath.size()-1); - Set nexts = gadjlist.get(crrnode).keySet(); - Iterator nit = nexts.iterator(); - while( nit.hasNext() ){ - Integer nextnode = nit.next(); - if ( crrpath.contains(nextnode) ){ continue; } - List nextpath = new LinkedList(crrpath); // copy - nextpath.add(nextnode); - if ( nextnode.equals(enode) ){ - simplePaths.add(nextpath); - continue; - } - nextlp.add(nextpath); - } - } - lp = nextlp; - } - - ListIterator> pit = simplePaths.listIterator(); - while( pit.hasNext()){ - List spath = pit.next(); - List> convertedPaths = convertSimplePathToPaths(spath); - paths.addAll(convertedPaths); - } - return paths; - } - */ - /* - private List> searchPaths(RDFSchemaAnalyzer rdfsa, boolean countLinks){ - List> paths = new ArrayList<>(); - List lp = new LinkedList<>(); - lp.add(new LinkAndPath(new ClassLink("",startClass,null,Direction.both,0,0,0,0,0,false,false), new LinkedList(), "")); - try{ - for ( int i = 0; i < nsteps; i++ ){ - ListIterator lit = lp.listIterator(); - List nextlp = new LinkedList<>(); - while ( lit.hasNext() ){ - LinkAndPath crrlp = lit.next(); - ClassLink[] classLinks = rdfsa.getNextClass(null, crrlp.classLink.getLinkedClassURI(), limit, countLinks); - for ( int j = 0 ; j < classLinks.length; j++ ){ - List crrpath = new LinkedList<>(crrlp.path); - crrpath.add(classLinks[j]); - if ( classLinks[j].getLinkedClassURI() == null ){ continue; } - if ( classLinks[j].getLinkedClassURI().equals(endClass) ){ - paths.add(new LinkedList<>(crrpath)); - continue; - } - if ( countLinks == true && classLinks[j].getNumOfLinks() <= th){ - continue; - } - if ( i >= 2 ){ - if ( crrlp.classLink.getPropertyURI().equals(classLinks[j].getPropertyURI()) && - crrlp.classLink.getDirection() != classLinks[j].getDirection() && - crrlp.originalClassURI.equals( classLinks[j].getLinkedClassURI()) ){ - continue; - } - } - nextlp.add(new LinkAndPath(classLinks[j], crrpath, crrlp.classLink.getLinkedClassURI())); - } - } - lp = nextlp; - } - }catch(Exception e){ - System.err.println(e); - } - return paths; - } - */ - + private void updateWeight(Integer node1, Integer node2, ClassLink edge){ + Map weight = edgeweight.get(node1); + Integer crr = weight.get(node2); + if (crr == null ){ + crr = edge.getNumOfLinkedClassInstances(); + weight.put(node2, crr); + } + if ( crr < edge.getNumOfLinkedClassInstances() ){ + crr = edge.getNumOfLinkedClassInstances(); + weight.put(node2, crr); + } + weight = edgeweight.get(node2); + crr = weight.get(node1); + if (crr == null ){ + crr = edge.getNumOfOriginClassInstances(); + weight.put(node1, crr); + } + if ( crr < edge.getNumOfOriginClassInstances() ){ + crr = edge.getNumOfOriginInstances(); + weight.put(node1, crr); + } + } + } Index: /SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/OWL/SimpleTree.java =================================================================== --- /SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/OWL/SimpleTree.java (revision 133) +++ /SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/OWL/SimpleTree.java (revision 254) @@ -122,5 +122,5 @@ * */ - + /* public static void main (String[] args) { @@ -145,5 +145,5 @@ - } + }*/ } Index: /SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/OWL/StructureCrawler.java =================================================================== --- /SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/OWL/StructureCrawler.java (revision 133) +++ /SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/OWL/StructureCrawler.java (revision 254) @@ -15,4 +15,5 @@ // this is just for a test + /* public static void main(String[] args) throws Exception{ StructureCrawler sc = new StructureCrawler(new File("c:\\cdata")); @@ -29,5 +30,5 @@ } } - + */ Index: /SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/OWL/ClassLink.java =================================================================== --- /SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/OWL/ClassLink.java (revision 221) +++ /SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/OWL/ClassLink.java (revision 254) @@ -166,5 +166,53 @@ return json_str; } - + + public String toJSONString4(QueryPathGenerator qpg) { + String json_str ="{"; + + if( propertyURI != null ) { + //json_str+="\"propertyURI\":"+"\""+propertyURI+"\","; + json_str+="\"predicate\":"+"\""+propertyURI+"\","; + } + else{ + json_str+="\"predicate\":"+"\"propertyURI\","; + } + if( linkedClassURI != null ){ + //json_str+="\"linkedClassURI\":"+"\""+linkedClassURI+"\","; + json_str+="\"linkedClass\":"+"\""+linkedClassURI+"\","; + } + else{ + //json_str+="\"linkedClassURI\":"+"\"linkedClassURI\","; + json_str+="\"linkedClass\":"+"\""+linkedClassURI+"\","; + } + if( linkedLiteralDatatypeURI != null ){ + json_str+="\"linkedLiteralDatatypeURI\":"+"\""+linkedLiteralDatatypeURI+"\","; + } + else{ + json_str+="\"linkedLiteralDatatypeURI\":"+"\"linkedLiteralDatatypeURI\","; + } + if( direction != null ){ + json_str+="\"direction\":"+"\""+direction.toString()+"\","; + } + else{ + json_str+="\"direction\":"+"\"direction\","; + } + if ( linkedClassURI != null ){ + String label = qpg.getClassLabel(linkedClassURI); + json_str+="\"label\":"+"\""+label+"\""; + }else if ( linkedLiteralDatatypeURI != null ){ + String url[] = linkedLiteralDatatypeURI.split("/"); + String tmplabel = url[url.length-1]; + String[] tmplabel2 = tmplabel.split("#"); + String label = tmplabel2[tmplabel2.length-1]; + json_str+="\"label\":"+"\""+label+"\""; + }else{ + json_str+="\"label\":"+"\""+"\"No Label\""+"\""; + } + json_str+="}"; + + return json_str; + } + + public int getNumOfLinks() { return numOfLinks; Index: /SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/OWL/OWLLabelReader.java =================================================================== --- /SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/OWL/OWLLabelReader.java (revision 254) +++ /SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/OWL/OWLLabelReader.java (revision 254) @@ -0,0 +1,43 @@ +/* + * To change this license header, choose License Headers in Project Properties. + * To change this template file, choose Tools | Templates + * and open the template in the editor. + */ +package org.biohackathon.SPARQLBuilder.OWL; + +/** + * + * @author atsuko + */ + +import java.util.*; +import java.io.*; + +public class OWLLabelReader { + static Map readLabels(String dir){ + Map labels = new HashMap (); + File fdir = new File(dir); + if ( fdir.exists() ){ + File[] files = fdir.listFiles(); + for (int i = 0 ; i < files.length; i++ ){ + try{ + BufferedReader in = new BufferedReader(new FileReader(files[i])); + String buf; + while( (buf = in.readLine()) != null){ + String[] data = buf.split("[\\s]+"); + if ( data[1].equals("") ){ + String[] lit = data[2].split("\""); + labels.put(data[0].substring(1,data[0].length() -1 ), lit[1]); + //System.out.println(data[0].substring(1,data[0].length() -1 )); + //System.out.println(lit[1]); + } + } + in.close(); + }catch(IOException e){ + System.err.println(e); + } + } + } + return labels; + } +} Index: /SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/OWL/AcquiredStructureAnalyzer.java =================================================================== --- /SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/OWL/AcquiredStructureAnalyzer.java (revision 173) +++ /SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/OWL/AcquiredStructureAnalyzer.java (revision 254) @@ -33,5 +33,5 @@ } - + /* public static void main(String[] args) throws Exception{ @@ -56,5 +56,5 @@ } - + */ public AcquiredStructureAnalyzer(String endpointURI, String[] graphURIs, Model model){ Index: /SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/OWL/QueryPathGenerator.java =================================================================== --- /SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/OWL/QueryPathGenerator.java (revision 251) +++ /SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/OWL/QueryPathGenerator.java (revision 254) @@ -20,8 +20,11 @@ private RDFSchemaAnalyzer analyzer = null; private OWLClassGraph graph; - private boolean askcheck; + + private Map clabels; private static final String CDIR = "cdata"; - + private static final String ODIR = "owldata"; + + /* public static void main(String[] args){ QueryPathGenerator qpg = new QueryPathGenerator(); @@ -87,4 +90,5 @@ } } + */ public QueryPathGenerator(){ @@ -98,6 +102,5 @@ public void setOWLClassGraph(String startClass){ - //graph = new OWLClassGraph(analyzer, sparqlEndpoint, startClass, askcheck); - graph = new OWLClassGraph(analyzer, sparqlEndpoint, startClass, true); + graph = new OWLClassGraph(analyzer, sparqlEndpoint, startClass); } @@ -123,5 +126,4 @@ setOWLClassGraph(startClass); } - graph.askcheck = askcheck; return graph.getPaths(startClass, endClass); } @@ -144,4 +146,39 @@ } + public String getClassLabel(String classURI){ + return clabels.get(classURI); + } + + public void setClassLabels(SClass[] classes){ + clabels = new HashMap(); + Map extLabels = getClassLabelsFromExternal(); + + for ( int i = 0 ; i < classes.length; i++ ){ + String classURI = classes[i].getClassURI(); + + Label[] labels = classes[i].getLabels(); + String label = null; + for ( int j = 0 ; j < labels.length; j++ ){ + if ( labels[j].getLanguage() == null ){ + label = labels[j].getLabel(); + break; + }else if ( labels[j].getLanguage().equals("en") || labels[j].getLanguage().equals("") ){ + label = labels[j].getLabel(); + break; + } + } + if ( label == null ){ + label = extLabels.get(classURI); + } + if ( label == null ){ + String[] uris = classURI.split("/"); + String tmplabel = uris[uris.length-1]; + String[] tmplabel2 = tmplabel.split("#"); + label = tmplabel2[tmplabel2.length-1]; + } + clabels.put(classURI, label); + } + } + public static String getClassLabelfromList(String classURI, SClass[] classes){ if ( classURI == null ){ @@ -152,5 +189,5 @@ if ( classURI.equals(classes[i].getClassURI()) ){ return getClassLabelfromClass(classes[i]); - } + } } return ""; @@ -173,4 +210,8 @@ } + public Map getClassLabelsFromExternal(){ + return OWLLabelReader.readLabels(ODIR); + } + public OWLClassGraph getOWLClassGraph(){ /*if ( graph == null ){ Index: /SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/OWL/Path.java =================================================================== --- /SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/OWL/Path.java (revision 251) +++ /SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/OWL/Path.java (revision 254) @@ -78,5 +78,5 @@ // label json_str+="\"label\":\""+QueryPathGenerator.getClassLabelfromList(startClass, classes)+"\","; - if (classLinks != null && classLinks.size() != 0) { + if (classLinks != null && classLinks.size() != 0) { json_str+="\"classLinks\":["; @@ -95,4 +95,25 @@ } + public String toJSONString4(QueryPathGenerator qpg){ + String json_str=""; + json_str+="{\"startClass\":\""+ startClass+"\","; + // label + json_str+="\"label\":\""+qpg.getClassLabel(startClass)+"\","; + if (classLinks != null && classLinks.size() != 0) { + json_str+="\"classLinks\":["; + + JSONObject[] classLinkObjs = new JSONObject[classLinks.size()]; + for (int i = 0; i < classLinks.size(); i++) { + if(i>0){json_str += "," ;} + json_str+= classLinks.get(i).toJSONString4(qpg); + } + json_str+="]"; + } + json_str += ","; + json_str +="\"score\":\""+width+"\""; + json_str +="}"; + + return json_str; + } public String getStartClass() {