Index: /SPARQLBuilderWWW/nbproject/project.properties
===================================================================
--- /SPARQLBuilderWWW/nbproject/project.properties (revision 197)
+++ /SPARQLBuilderWWW/nbproject/project.properties (revision 248)
@@ -31,6 +31,13 @@
file.reference.agraph-4.5.jar=/Users/atsuko/src/java/SPARQLBuilder2014/lib2/agraph-4.5.jar
file.reference.commons-codec-1.3.jar=/Users/atsuko/src/java/SPARQLBuilder2014/lib2/commons-codec-1.3.jar
-file.reference.commons-httpclient-3.1-src.zip=/Users/atsuko/src/java/SPARQLBuilder2014/lib2/commons-httpclient-3.1-src.zip
+file.reference.commons-codec-1.9.jar=/Users/atsuko/src/java/SPARQLBuilder2014/lib2/commons-codec-1.9.jar
file.reference.commons-httpclient-3.1.jar=/Users/atsuko/src/java/SPARQLBuilder2014/lib2/commons-httpclient-3.1.jar
+file.reference.commons-logging-1.2.jar=/Users/atsuko/src/java/SPARQLBuilder2014/lib2/commons-logging-1.2.jar
+file.reference.fluent-hc-4.4.jar=/Users/atsuko/src/java/SPARQLBuilder2014/lib2/fluent-hc-4.4.jar
+file.reference.httpclient-4.4.jar=/Users/atsuko/src/java/SPARQLBuilder2014/lib2/httpclient-4.4.jar
+file.reference.httpclient-cache-4.4.jar=/Users/atsuko/src/java/SPARQLBuilder2014/lib2/httpclient-cache-4.4.jar
+file.reference.httpclient-win-4.4.jar=/Users/atsuko/src/java/SPARQLBuilder2014/lib2/httpclient-win-4.4.jar
+file.reference.httpcore-4.4.jar=/Users/atsuko/src/java/SPARQLBuilder2014/lib2/httpcore-4.4.jar
+file.reference.httpmime-4.4.jar=/Users/atsuko/src/java/SPARQLBuilder2014/lib2/httpmime-4.4.jar
file.reference.icu4j-3.4.4.jar=/Users/atsuko/src/java/SPARQLBuilder2014/lib2/icu4j-3.4.4.jar
file.reference.jena-arq-2.11.2.jar=/Users/atsuko/src/java/SPARQLBuilder2014/lib2/jena-arq-2.11.2.jar
@@ -40,4 +47,6 @@
file.reference.jena-iri-0.9.0-incubating.jar=/Users/atsuko/src/java/SPARQLBuilder2014/lib2/jena-iri-0.9.0-incubating.jar
file.reference.jena-iri-1.0.2.jar=/Users/atsuko/src/java/SPARQLBuilder2014/lib2/jena-iri-1.0.2.jar
+file.reference.jna-4.1.0.jar=/Users/atsuko/src/java/SPARQLBuilder2014/lib2/jna-4.1.0.jar
+file.reference.jna-platform-4.1.0.jar=/Users/atsuko/src/java/SPARQLBuilder2014/lib2/jna-platform-4.1.0.jar
file.reference.json.jar=/Users/atsuko/src/java/SPARQLBuilder2014/lib2/json.jar
file.reference.jsonic-1.2.8.jar=/Users/atsuko/src/java/SPARQLBuilder2014/lib2/jsonic-1.2.8.jar
@@ -66,5 +75,4 @@
${file.reference.agraph-4.5.jar}:\
${file.reference.commons-codec-1.3.jar}:\
- ${file.reference.commons-httpclient-3.1-src.zip}:\
${file.reference.commons-httpclient-3.1.jar}:\
${file.reference.icu4j-3.4.4.jar}:\
@@ -84,5 +92,15 @@
${file.reference.xercesImpl.jar}:\
${file.reference.xml-apis-1.4.01.jar}:\
- ${file.reference.xml-apis.jar}
+ ${file.reference.xml-apis.jar}:\
+ ${file.reference.httpclient-4.4.jar}:\
+ ${file.reference.httpclient-cache-4.4.jar}:\
+ ${file.reference.httpclient-win-4.4.jar}:\
+ ${file.reference.commons-codec-1.9.jar}:\
+ ${file.reference.commons-logging-1.2.jar}:\
+ ${file.reference.fluent-hc-4.4.jar}:\
+ ${file.reference.httpcore-4.4.jar}:\
+ ${file.reference.httpmime-4.4.jar}:\
+ ${file.reference.jna-4.1.0.jar}:\
+ ${file.reference.jna-platform-4.1.0.jar}
# Space-separated list of extra javac options
javac.compilerargs=
Index: /SPARQLBuilderWWW/nbproject/project.xml
===================================================================
--- /SPARQLBuilderWWW/nbproject/project.xml (revision 197)
+++ /SPARQLBuilderWWW/nbproject/project.xml (revision 248)
@@ -13,8 +13,4 @@
${file.reference.commons-codec-1.3.jar}
- WEB-INF/lib
-
-
- ${file.reference.commons-httpclient-3.1-src.zip}
WEB-INF/lib
@@ -91,4 +87,44 @@
WEB-INF/lib
+
+ ${file.reference.httpclient-4.4.jar}
+ WEB-INF/lib
+
+
+ ${file.reference.httpclient-cache-4.4.jar}
+ WEB-INF/lib
+
+
+ ${file.reference.httpclient-win-4.4.jar}
+ WEB-INF/lib
+
+
+ ${file.reference.commons-codec-1.9.jar}
+ WEB-INF/lib
+
+
+ ${file.reference.commons-logging-1.2.jar}
+ WEB-INF/lib
+
+
+ ${file.reference.fluent-hc-4.4.jar}
+ WEB-INF/lib
+
+
+ ${file.reference.httpcore-4.4.jar}
+ WEB-INF/lib
+
+
+ ${file.reference.httpmime-4.4.jar}
+ WEB-INF/lib
+
+
+ ${file.reference.jna-4.1.0.jar}
+ WEB-INF/lib
+
+
+ ${file.reference.jna-platform-4.1.0.jar}
+ WEB-INF/lib
+
Index: /SPARQLBuilderWWW/nbproject/genfiles.properties
===================================================================
--- /SPARQLBuilderWWW/nbproject/genfiles.properties (revision 197)
+++ /SPARQLBuilderWWW/nbproject/genfiles.properties (revision 248)
@@ -1,8 +1,8 @@
-build.xml.data.CRC32=73259a3a
+build.xml.data.CRC32=1e8e9335
build.xml.script.CRC32=15bad33c
build.xml.stylesheet.CRC32=651128d4@1.67.1.1
# This file is used by a NetBeans-based IDE to track changes in generated files such as build-impl.xml.
# Do not edit this file. You may delete it but then the IDE will never regenerate such files for you.
-nbproject/build-impl.xml.data.CRC32=73259a3a
-nbproject/build-impl.xml.script.CRC32=06c5e70d
+nbproject/build-impl.xml.data.CRC32=1e8e9335
+nbproject/build-impl.xml.script.CRC32=acb6c008
nbproject/build-impl.xml.stylesheet.CRC32=99ea4b56@1.67.1.1
Index: /SPARQLBuilderWWW/nbproject/build-impl.xml
===================================================================
--- /SPARQLBuilderWWW/nbproject/build-impl.xml (revision 123)
+++ /SPARQLBuilderWWW/nbproject/build-impl.xml (revision 248)
@@ -1000,5 +1000,4 @@
-
@@ -1019,4 +1018,14 @@
+
+
+
+
+
+
+
+
+
+
@@ -1025,5 +1034,4 @@
-
@@ -1044,4 +1052,14 @@
+
+
+
+
+
+
+
+
+
+
Index: /SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/OWL/EndpointAccess.java
===================================================================
--- /SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/OWL/EndpointAccess.java (revision 248)
+++ /SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/OWL/EndpointAccess.java (revision 248)
@@ -0,0 +1,198 @@
+/*
+ * 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;
+
+import com.hp.hpl.jena.query.*;
+import com.hp.hpl.jena.sparql.engine.http.QueryEngineHTTP;
+import java.util.*;
+
+/**
+ *
+ * @author atsuko
+ */
+public class EndpointAccess {
+ static public boolean checkPath(String startClass, List classlinks, String sparqlEndpoint){
+ // SPARQL Query construction
+ StringBuilder queryStr = new StringBuilder();
+ queryStr.append("PREFIX rdfs: \n");
+ queryStr.append("PREFIX rdf: \n");
+ queryStr.append("ASK { \n");
+
+ ListIterator cit = classlinks.listIterator();
+ queryStr.append("?r0").append(" rdf:type <").append(startClass).append("> .\n");
+ int i = 0;
+ while( cit.hasNext() ){
+ ClassLink link = cit.next();
+ //String next = link.getLinkedClassURI();
+ String sval = "?r".concat(Integer.toString(i));
+ String oval = "?r".concat(Integer.toString(i+1));
+ queryStr.append(oval).append(" rdf:type <").append(link.getLinkedClassURI()).append("> .\n");
+ if( link.getDirection() == Direction.forward ){
+ queryStr.append(sval).append(" <").append(link.getPropertyURI()).append("> ")
+ .append(oval).append(" .\n");
+ }else{
+ queryStr.append(oval).append(" <").append(link.getPropertyURI()).append("> ")
+ .append(sval).append(" .\n");
+ }
+ i++;
+ }
+ queryStr.append("} \n");
+
+ String sparqlQuery = queryStr.toString();
+ Query query = QueryFactory.create(sparqlQuery, Syntax.syntaxARQ);
+ /*
+ QueryEngineHTTP httpQuery = new QueryEngineHTTP(sparqlEndpoint, query);
+ boolean res = httpQuery.execAsk();
+ httpQuery.close();
+ */
+ QueryExecution qexec = QueryExecutionFactory.sparqlService(sparqlEndpoint, query);
+ boolean res = qexec.execAsk();
+ qexec.close();
+ return res;
+ }
+
+ static public boolean checkSimplePath(List nodes, OWLClassGraph ocg, String sparqlEndpoint){
+ // SPARQL Query construction
+ StringBuilder queryStr = new StringBuilder();
+ queryStr.append("PREFIX rdfs: \n");
+ queryStr.append("PREFIX rdf: \n");
+ queryStr.append("ASK { \n");
+
+ ListIterator cit = nodes.listIterator();
+ queryStr.append("?r0").append(" rdf:type <").append(ocg.labels.get(cit.next())).append("> .\n");
+ int i = 0;
+ while( cit.hasNext() ){
+ String cURI = ocg.labels.get(cit.next());
+ //String next = link.getLinkedClassURI();
+ String sval = "?r".concat(Integer.toString(i));
+ String pval = "?p".concat(Integer.toString(i));
+ String oval = "?r".concat(Integer.toString(i+1));
+ queryStr.append(oval).append(" rdf:type <").append(cURI).append("> .\n");
+ queryStr.append("{{");
+ queryStr.append(sval).append(" ").append(pval).append(" ")
+ .append(oval).append(" }\n UNION\n {");
+ queryStr.append(oval).append(" ").append(pval).append(" ")
+ .append(sval).append(" }}\n");
+ i++;
+ }
+ queryStr.append("} \n");
+
+ String sparqlQuery = queryStr.toString();
+ System.out.println("Ask Simple");
+ System.out.println(sparqlQuery);
+ Query query = QueryFactory.create(sparqlQuery, Syntax.syntaxARQ);
+ /*
+ QueryEngineHTTP httpQuery = new QueryEngineHTTP(sparqlEndpoint, query);
+ boolean res = httpQuery.execAsk();
+ httpQuery.close();
+ */
+ QueryExecution qexec = QueryExecutionFactory.sparqlService(sparqlEndpoint, query);
+ boolean res = qexec.execAsk();
+ qexec.close();
+ return res;
+ }
+
+ static public boolean check3SimplePath(Integer node1, Integer node2, Integer node3, OWLClassGraph ocg, String sparqlEndpoint){
+ // SPARQL Query construction
+ StringBuilder queryStr = new StringBuilder();
+ queryStr.append("PREFIX rdfs: \n");
+ queryStr.append("PREFIX rdf: \n");
+ queryStr.append("ASK { \n");
+
+ queryStr.append("?n1").append(" rdf:type <").append(ocg.labels.get(node1)).append("> .\n");
+ queryStr.append("?n2").append(" rdf:type <").append(ocg.labels.get(node2)).append("> .\n");
+ queryStr.append("?n3").append(" rdf:type <").append(ocg.labels.get(node3)).append("> .\n");
+
+ queryStr.append("{{");
+ queryStr.append("?n1").append(" ").append("?p1").append(" ")
+ .append("?n2").append(" }\n UNION\n {");
+ queryStr.append("?n2").append(" ").append("?p1").append(" ")
+ .append("?n1").append(" }}\n");
+
+ queryStr.append("{{");
+ queryStr.append("?n2").append(" ").append("?p2").append(" ")
+ .append("?n3").append(" }\n UNION\n {");
+ queryStr.append("?n3").append(" ").append("?p2").append(" ")
+ .append("?n2").append(" }}\n");
+
+ queryStr.append("} \n");
+
+ String sparqlQuery = queryStr.toString();
+ System.out.println("Ask Simple3");
+ System.out.println(sparqlQuery);
+ Query query = QueryFactory.create(sparqlQuery, Syntax.syntaxARQ);
+ /*
+ QueryEngineHTTP httpQuery = new QueryEngineHTTP(sparqlEndpoint, query);
+ boolean res = httpQuery.execAsk();
+ httpQuery.close();
+ */
+ QueryExecution qexec = QueryExecutionFactory.sparqlService(sparqlEndpoint, query);
+ boolean res = qexec.execAsk();
+ qexec.close();
+ return res;
+ }
+
+ static public boolean check3SimplePathwithJoin(Integer node1, Integer node2, Integer node3, OWLClassGraph ocg, String sparqlEndpoint){
+ StringBuilder queryStr = new StringBuilder();
+ queryStr.append("PREFIX rdf: \n");
+ queryStr.append("SELECT DISTINCT ?n2 { \n");
+
+ queryStr.append("?n1").append(" rdf:type <").append(ocg.labels.get(node1)).append("> .\n");
+ queryStr.append("?n2").append(" rdf:type <").append(ocg.labels.get(node2)).append("> .\n");
+
+ queryStr.append("{{");
+ queryStr.append("?n1").append(" ").append("?p1").append(" ")
+ .append("?n2").append(" }\n UNION\n {");
+ queryStr.append("?n2").append(" ").append("?p1").append(" ")
+ .append("?n1").append(" }}\n");
+
+ queryStr.append("} \n");
+
+ String sparqlQuery = queryStr.toString();
+ System.out.println("SELECT Simple3 by Join");
+ System.out.println(sparqlQuery);
+ Query query = QueryFactory.create(sparqlQuery, Syntax.syntaxARQ);
+ QueryExecution qexec = QueryExecutionFactory.sparqlService(sparqlEndpoint, query);
+ ResultSet res1 = qexec.execSelect();
+ qexec.close();
+
+ queryStr = new StringBuilder();
+ queryStr.append("PREFIX rdf: \n");
+ queryStr.append("SELECT DISTINCT ?n2 { \n");
+
+ queryStr.append("?n2").append(" rdf:type <").append(ocg.labels.get(node2)).append("> .\n");
+ queryStr.append("?n3").append(" rdf:type <").append(ocg.labels.get(node3)).append("> .\n");
+
+ queryStr.append("{{");
+ queryStr.append("?n2").append(" ").append("?p2").append(" ")
+ .append("?n3").append(" }\n UNION\n {");
+ queryStr.append("?n3").append(" ").append("?p2").append(" ")
+ .append("?n2").append(" }}\n");
+
+ queryStr.append("} \n");
+
+ sparqlQuery = queryStr.toString();
+ System.out.println("SELECT Simple3 by Join 2");
+ System.out.println(sparqlQuery);
+ query = QueryFactory.create(sparqlQuery, Syntax.syntaxARQ);
+ qexec = QueryExecutionFactory.sparqlService(sparqlEndpoint, query);
+ ResultSet res2 = qexec.execSelect();
+ qexec.close();
+
+ Set res1hash = new HashSet();
+ while(res1.hasNext()){
+ String resstr = res1.next().toString();
+ res1hash.add(resstr);
+ }
+ while(res2.hasNext()){
+ if ( res1hash.contains(res2.next().toString())){
+ return true;
+ }
+ }
+ return false;
+ }
+}
Index: /SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/OWL/OWLClassGraph.java
===================================================================
--- /SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/OWL/OWLClassGraph.java (revision 228)
+++ /SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/OWL/OWLClassGraph.java (revision 248)
@@ -19,5 +19,10 @@
List nodeType;
ArrayList> connectionTable;
-
+ String sparqlEndpoint;
+ Set visited;
+ boolean askcheck;
+ List> edgeweight;
+ List nodeweight;
+
public class LinkAndPath{
String originalClassURI; // originalClasssURI -classLink.propertyURI-> classLink.linkedClassURL
@@ -46,50 +51,21 @@
}
-/*
- public OWLClassGraph(String startClass, String endClass){
- super();
-
- // start & end
- this.startClass = startClass;
- this.endClass = endClass;
-
- // parameters
- nsteps = 3;
- limit = 1000;
- th = 5;
- }
-*/
-
-/*
- public OWLClassGraph(String startClass, String endClass, int th){
- super();
-
- // start & end
- this.startClass = startClass;
- this.endClass = endClass;
- // th of instances
- this.th = th;
-
- // parameters
- nsteps = 3;
- limit = 1000;
- }
-*/
-
- public OWLClassGraph(){
+ public OWLClassGraph(){ // not used
super();
nodeType = new LinkedList();
- //setClassGraph(rdfsa);
- //connectionTable = createConnectionTable();
- }
-
-
- public OWLClassGraph(RDFSchemaAnalyzer rdfsa){
+ }
+
+ public OWLClassGraph(RDFSchemaAnalyzer rdfsa){ // not used
super();
nodeType = new LinkedList();
- //setClassGraph(rdfsa);
- //connectionTable = createConnectionTable();
- }
-
+ }
+
+ public OWLClassGraph(RDFSchemaAnalyzer rdfsa, String sparqlEndpoint, String startClass, boolean askcheck){ // used
+ super();
+ nodeType = new LinkedList();
+ this.askcheck = askcheck;
+ setPartClassGraph(rdfsa, sparqlEndpoint, startClass);
+ }
+
public int getNumberOfEdge(String url){
Integer node = labelednodes.get(url);
@@ -98,4 +74,11 @@
}
return adjlist.get(node).size();
+ }
+
+ public boolean visitedNode(String classURI){
+ if ( visited.contains(labelednodes.get(classURI)) ){
+ return true;
+ }
+ return false;
}
@@ -138,40 +121,8 @@
return connectionTable.get(node);
}
-
- 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(String startClass, String endClass){
-
+ //int asked = 0;
+ Map checkedpaths = new HashMap();
List> paths = new ArrayList<>();
List> simplePaths = new LinkedList<>();
@@ -195,4 +146,35 @@
List nextpath = new LinkedList(crrpath); // copy
nextpath.add(nextnode);
+ // tmp
+ if ( i >= 1 ){
+ 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.check3SimplePathwithJoin(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);
@@ -206,4 +188,8 @@
ListIterator> pit = simplePaths.listIterator();
+ //int i = 0;
+ //int j = 0;
+ System.out.println("SPATH:");
+ System.out.println(simplePaths.size());
while( pit.hasNext()){
List spath = pit.next();
@@ -211,12 +197,15 @@
paths.addAll(convertedPaths);
}
+ System.out.println("PATH:");
+ System.out.println(paths.size());
return paths;
}
+
private List> convertSimplePathToPaths(List simplePath){
List> paths = new LinkedList>();
- //List> multiedges = new LinkedList>();
ListIterator spit = simplePath.listIterator();
Integer start = spit.next();
+ String startClass = this.labels.get(start);
Integer end = spit.next();
List edges = gadjlist.get(start).get(end);
@@ -242,5 +231,8 @@
List addedpath = new LinkedList(basepath);
addedpath.add(cl);
- tmppaths.add(addedpath);
+ // check
+ //if ( EndpointAccess.checkPath(startClass, addedpath, sparqlEndpoint) ){
+ tmppaths.add(addedpath);
+ //}
}
}
@@ -252,45 +244,4 @@
/*
- 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 List> searchPathsbyVisitingNodes(RDFSchemaAnalyzer rdfsa, boolean countLinks,
String startClass, String endClass){
@@ -365,16 +316,4 @@
}
addEdge(i, n, classLinks[j]);
- /*
- ClassLink rev = new ClassLink( classLinks[j].getPropertyURI(),
- //classLinks[j].getLinkedClassURI(),
- classes[i].getClassURI(),
- classLinks[j].getLinkedLiteralDatatypeURI(),
- classLinks[j].getDirection(), classLinks[j].getNumOfLinks(),
- classLinks[j].getNumOfOriginInstances(), classLinks[j].getNumOfLinkedInstances(),
- classLinks[j].getNumOfOriginClassInstances(), classLinks[j].getNumOfLinkedClassInstances(),
- classLinks[j].isDomainClassLimitedQ(), classLinks[j].isRangeClassLimitedQ() );
- rev.setDirection(Direction.reverse);
- addEdge(n, i, rev);
- */
}
}
@@ -383,8 +322,14 @@
}
}
- }
-
- public void setPartClassGraph(RDFSchemaAnalyzer rdfsa, String startClass){
- // setNodes
+ }*/
+
+ public void setPartClassGraph(RDFSchemaAnalyzer rdfsa, String sparqlEndpoint, String startClass){
+ // set endpoint
+ this.sparqlEndpoint = sparqlEndpoint;
+
+ visited = new HashSet();
+ edgeweight = new LinkedList>();
+ nodeweight = new LinkedList();
+ // setNodes for all classes
SClass[] classes = null;
try{
@@ -396,10 +341,13 @@
addNode(classes[i].getClassURI());
nodeType.add("class");
- }
- int nedge = 0;
+ edgeweight.add(new HashMap());
+ nodeweight.add(classes[i].getNumOfInstances());
+ }
+ // setEdges
+ //int nedge = 0;
Integer snode = labelednodes.get(startClass);
Set nodes = new HashSet();
nodes.add(snode);
- Set visited = new HashSet();
+ visited.add(snode);
for (int i = 0 ; i < nsteps; i++ ){
Iterator nit = nodes.iterator();
@@ -407,36 +355,16 @@
while ( nit.hasNext() ){
Integer crr = nit.next();
- visited.add(crr);
try{
ClassLink[] classLinks = rdfsa.getNextClass(null, labels.get(crr), limit, true);
for (int j = 0 ; j < classLinks.length; j++){
Integer nn = labelednodes.get(classLinks[j].getLinkedClassURI());
+ if ( nn == null ){
+ continue;
+ }
if ( !visited.contains(nn) ){
nextnodes.add(nn);
}
- if ( nn != null ){
- addEdge(crr, nn, classLinks[j]);
- /*
- }else{
- nn = labelednodes.get(classLinks[j].getLinkedLiteralDatatypeURI());
- if ( nn == null ){
- addNode(classLinks[j].getLinkedLiteralDatatypeURI());
- n = nodeType.size();
- nodeType.add("literal");
- }
- addEdge(i, n, classLinks[j]);
- /*
- ClassLink rev = new ClassLink( classLinks[j].getPropertyURI(),
- //classLinks[j].getLinkedClassURI(),
- classes[i].getClassURI(),
- classLinks[j].getLinkedLiteralDatatypeURI(),
- classLinks[j].getDirection(), classLinks[j].getNumOfLinks(),
- classLinks[j].getNumOfOriginInstances(), classLinks[j].getNumOfLinkedInstances(),
- classLinks[j].getNumOfOriginClassInstances(), classLinks[j].getNumOfLinkedClassInstances(),
- classLinks[j].isDomainClassLimitedQ(), classLinks[j].isRangeClassLimitedQ() );
- rev.setDirection(Direction.reverse);
- addEdge(n, i, rev);
- */
- }
+ addEdge(crr, nn, classLinks[j]);
+ updateWeight(crr, nn, classLinks[j]);
}
}catch(Exception e){
@@ -445,8 +373,9 @@
}
nodes = nextnodes;
+ visited.addAll(nodes);
}
}
- private ArrayList> createConnectionTable(){
+ private ArrayList> createConnectionTable(){ // not used
ArrayList> ct = new ArrayList>();
for (int i = 0; i < labels.size(); i++ ){ // each node
@@ -457,5 +386,5 @@
}
- private HashSet createConnectionList(Integer node){
+ private HashSet createConnectionList(Integer node){ // not used
HashSet cl = new HashSet();
HashSet crrnodes = new HashSet();
@@ -482,3 +411,147 @@
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(node2, crr);
+ }
+ if ( crr < edge.getNumOfOriginClassInstances() ){
+ crr = edge.getNumOfOriginInstances();
+ weight.put(node1, crr);
+ }
+ }
+
+ // 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;
+ }
+ */
+
}
Index: /SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/OWL/QueryPathGenerator.java
===================================================================
--- /SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/OWL/QueryPathGenerator.java (revision 228)
+++ /SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/OWL/QueryPathGenerator.java (revision 248)
@@ -18,4 +18,5 @@
private RDFSchemaAnalyzer analyzer = null;
private OWLClassGraph graph;
+ private boolean askcheck;
private static final String CDIR = "cdata";
@@ -50,11 +51,15 @@
factory = new RDFSchemaAnalyzerFactory(CDIR);
}
-
+
public QueryPathGenerator(String sparqlEndpoint){
factory = new RDFSchemaAnalyzerFactory(CDIR);
setSPARQLendpoint(sparqlEndpoint);
- setOWLClassGraph();
}
-
+
+ public void setOWLClassGraph(String startClass){
+ graph = new OWLClassGraph(analyzer, sparqlEndpoint, startClass, askcheck);
+ }
+
+/*
public QueryPathGenerator(String sparqlEndpoint, String crawlFileName){
factory = new RDFSchemaAnalyzerFactory(crawlFileName);
@@ -62,4 +67,5 @@
setOWLClassGraph();
}
+ */
public SClass[] getClasses(String keyword){
@@ -79,12 +85,11 @@
}
- public Path[] getPaths(String startClass, String endClass, boolean countLink){
+ public Path[] getPaths(String startClass, String endClass, boolean askcheck){
+ this.askcheck = askcheck;
if ( graph == null ){
- setOWLClassGraph();
+ //System.err.println("Class graph is null.");
+ setOWLClassGraph(startClass);
}
- graph.setPartClassGraph(analyzer, startClass);
return graph.getPaths(startClass, endClass);
- //return graph.getPaths(startClass, endClass, analyzer);
- //return graph.getPaths_old(analyzer, true, startClass, endClass);
}
@@ -135,12 +140,14 @@
}
+ /*
private void setOWLClassGraph(){
- graph = new OWLClassGraph(analyzer);
- }
+ //graph = new OWLClassGraph(analyzer);
+ graph = new OWLClassGraph();
+ }*/
public OWLClassGraph getOWLClassGraph(){
- if ( graph == null ){
+ /*if ( graph == null ){
graph = new OWLClassGraph(analyzer);
- }
+ }*/
return graph;
}
Index: /SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/OWL/Path.java
===================================================================
--- /SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/OWL/Path.java (revision 221)
+++ /SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/OWL/Path.java (revision 248)
@@ -86,7 +86,9 @@
json_str+= classLinks.get(i).toJSONString3(classes);
}
- json_str+="]";
+ json_str+="]";
}
- json_str+="}";
+ json_str += ",";
+ json_str +="\"score\":\""+width+"\"";
+ json_str +="}";
return json_str;
@@ -139,4 +141,3 @@
//throw new UnsupportedOperationException("Not supported yet."); //To change body of generated methods, choose Tools | Templates.
}
-
}
Index: /SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/www/PLServlet.java
===================================================================
--- /SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/www/PLServlet.java (revision 221)
+++ /SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/www/PLServlet.java (revision 248)
@@ -74,4 +74,5 @@
String st = request.getParameter("startclass");
String en = request.getParameter("endclass");
+ String ask = request.getParameter("ask");
HttpSession session = request.getSession();
@@ -81,5 +82,13 @@
}
SClass[] classes = qpg.getClasses(null);
- Path[] paths = qpg.getPaths(st, en, true);
+ Path[] paths = null;
+ if ( ask == null ){
+ paths = qpg.getPaths(st, en, false);
+ }else if ( ask.equalsIgnoreCase("true")){
+ paths = qpg.getPaths(st, en, true);
+ }else{
+ paths = qpg.getPaths(st, en, false);
+ }
+
String jsonstr = "[";
for(int i = 0; i< paths.length; i++){
Index: /SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/www/CLServlet.java
===================================================================
--- /SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/www/CLServlet.java (revision 228)
+++ /SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/www/CLServlet.java (revision 248)
@@ -74,4 +74,5 @@
PrintWriter out = response.getWriter();
String ep = request.getParameter("ep");
+ String classURI = request.getParameter("class");
HttpSession session = request.getSession();
QueryPathGenerator qpg = (QueryPathGenerator)session.getAttribute("qpg");
@@ -82,4 +83,8 @@
qpg.setSPARQLendpoint(ep);
//OWLClassGraph ocg = qpg.getOWLClassGraph();
+ if ( classURI != null ){
+ qpg.setOWLClassGraph(classURI);
+ }
+
SClass[] classes = qpg.getClasses(null);
for (int i = 0 ; i < classes.length; i++ ){
@@ -88,4 +93,9 @@
// continue;
//}
+ if ( classURI != null ){
+ if ( qpg.getOWLClassGraph().visitedNode(classURI) == false ){
+ continue;
+ }
+ }
Label[] labels = classes[i].getLabels();
String label = null;
@@ -113,6 +123,23 @@
JsonArrayBuilder jab = jbfactory.createArrayBuilder();
Iterator cit = sortedClasses.iterator();
+ List tmpclasses = new LinkedList();
+ JsonObjectBuilder job = jbfactory.createObjectBuilder();
while( cit.hasNext() ){
- JsonObjectBuilder job = jbfactory.createObjectBuilder();
+ String classinfo = cit.next();
+ String[] data = classinfo.split(" ");
+ if (data.length != 3 ){
+ System.out.println("data is wrong?");
+ }
+ if (data[0].matches("^[0-9]*$")){
+ tmpclasses.add(classinfo);
+ }else{
+ job.add("uri", data[2]);
+ job.add("label", data[0]);
+ job.add("number", data[1]);
+ jab.add(job);
+ }
+ }
+ cit = tmpclasses.iterator();
+ while( cit.hasNext() ){
String classinfo = cit.next();
String[] data = classinfo.split(" ");
@@ -124,5 +151,5 @@
job.add("number", data[1]);
jab.add(job);
- }
+ }
JsonArray ja = jab.build();
out.print(ja);
Index: /SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/www/SPServlet.java
===================================================================
--- /SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/www/SPServlet.java (revision 229)
+++ /SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/www/SPServlet.java (revision 248)
@@ -179,7 +179,5 @@
private String convertPath2SPARQL(Path path) throws Exception{
-
- ArrayList classname =new ArrayList() ;
-
+ ArrayList classname =new ArrayList() ;
if( path == null ){
throw new Exception("Path is null.");
Index: /SPARQLBuilderWWW/cdata_old/chemblF.ttl
===================================================================
--- /SPARQLBuilderWWW/cdata_old/chemblF.ttl (revision 248)
+++ /SPARQLBuilderWWW/cdata_old/chemblF.ttl (revision 248)
@@ -0,0 +1,14234 @@
+@base .
+<> a ;
+
+ .
+
+[ a ;
+ false ;
+ ;
+ "181458"^^ ;
+
+ "11592790"^^ ;
+ "11592790"^^ ;
+ ;
+ ;
+ false
+] .
+
+[ a ;
+ false ;
+ ;
+ "2"^^ ;
+
+ "6"^^ ;
+ "6"^^ ;
+ ;
+ ;
+ false
+] .
+
+[ a ;
+ "2"^^ ;
+
+ "3"^^ ;
+
+ "1"^^ ;
+ "3"^^ ;
+
+] .
+
+[ a ;
+ "4"^^ ;
+
+ "0"^^ ;
+
+ "3"^^ ;
+ "0"^^ ;
+
+] .
+
+
+ a ;
+
+ "PharmGKB Cross Reference"^^ ;
+ "1000"^^ .
+
+[ a ;
+ false ;
+ ;
+ "58"^^ ;
+
+ "58"^^ ;
+ "58"^^ ;
+ ;
+ ;
+ false
+] .
+
+
+
+ "has attribute"^^ .
+
+
+
+ ;
+
+ "ChEMBL Activity Entity Published Type"^^ ;
+
+ .
+
+[ a ;
+ false ;
+ ;
+ "1613"^^ ;
+
+ "1623"^^ ;
+ "1623"^^ ;
+ ;
+ ;
+ false
+] .
+
+[ a ;
+ "2"^^ ;
+
+ "1"^^ ;
+
+ "1"^^ ;
+ "1"^^ ;
+
+] .
+
+
+ a ;
+
+ "TIMBAL Cross Reference"^^ ;
+ "44"^^ .
+
+[ a ;
+ "2"^^ ;
+
+ "850"^^ ;
+
+ "839"^^ ;
+ "850"^^ ;
+
+] .
+
+
+
+ .
+
+
+
+ .
+
+[ a ;
+ ;
+ false ;
+