Index: /SPARQLBuilderWWW/nbproject/project.properties
===================================================================
--- /SPARQLBuilderWWW/nbproject/project.properties (revision 123)
+++ /SPARQLBuilderWWW/nbproject/project.properties (revision 197)
@@ -111,5 +111,4 @@
javadoc.windowtitle=
lib.dir=${web.docbase.dir}/WEB-INF/lib
-no.dependencies=false
persistence.xml.dir=${conf.dir}
platform.active=default_platform
@@ -120,5 +119,5 @@
# Space-separated list of JVM arguments used when running a class with a main method or a unit test
# (you may also define separate properties like run-sys-prop.name=value instead of -Dname=value):
-runmain.jvmargs=
+runmain.jvmargs=-Xmx 5000m -Xms 5000m -XX:-UseGCOverheadLimit
source.encoding=UTF-8
source.root=src
Index: /SPARQLBuilderWWW/nbproject/project.xml
===================================================================
--- /SPARQLBuilderWWW/nbproject/project.xml (revision 123)
+++ /SPARQLBuilderWWW/nbproject/project.xml (revision 197)
@@ -94,8 +94,8 @@
-
+
-
+
Index: /SPARQLBuilderWWW/nbproject/genfiles.properties
===================================================================
--- /SPARQLBuilderWWW/nbproject/genfiles.properties (revision 123)
+++ /SPARQLBuilderWWW/nbproject/genfiles.properties (revision 197)
@@ -1,8 +1,8 @@
-build.xml.data.CRC32=d2464d47
+build.xml.data.CRC32=73259a3a
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=d2464d47
+nbproject/build-impl.xml.data.CRC32=73259a3a
nbproject/build-impl.xml.script.CRC32=06c5e70d
nbproject/build-impl.xml.stylesheet.CRC32=99ea4b56@1.67.1.1
Index: /SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/OWL/OWLClassGraph.java
===================================================================
--- /SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/OWL/OWLClassGraph.java (revision 177)
+++ /SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/OWL/OWLClassGraph.java (revision 197)
@@ -44,11 +44,16 @@
public OWLClassGraph(String startClass, String endClass){
super();
+
+ // start & end
this.startClass = startClass;
- addNode(startClass);
this.endClass = endClass;
- addNode(endClass);
+
+ // parameters
nsteps = 3;
limit = 1000;
prunecut = 100;
+
+ // constructing subgraph
+
}
@@ -229,4 +234,11 @@
}
*/
+
+ private void setGraph(RDFSchemaAnalyzer rdfsa, boolean countLink){
+ // BFS
+
+
+ //ClassLink[] classLinks = rdfsa.getNextClass(null, crrlp.classLink.getLinkedClassURI(), limit, countLinks);
+ }
}
Index: /SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/OWL/QueryPathGenerator.java
===================================================================
--- /SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/OWL/QueryPathGenerator.java (revision 177)
+++ /SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/OWL/QueryPathGenerator.java (revision 197)
@@ -18,5 +18,6 @@
private RDFSchemaAnalyzer analyzer = null;
//private OWLClassGraph graph;
-
+ //private PathMatrix matrix = null;
+
private static final String CDIR = "cdata";
@@ -84,5 +85,5 @@
}
try {
- return analyzer.getOWLClasses(null, keywords, null, false);
+ return analyzer.getOWLClasses(null, keywords, null, true);
}catch(Exception e){
System.err.println(e);
Index: /SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/endpointMetadata/MetadataFile.java
===================================================================
--- /SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/endpointMetadata/MetadataFile.java (revision 192)
+++ /SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/endpointMetadata/MetadataFile.java (revision 197)
@@ -324,7 +324,4 @@
}
-
-
-
private void readFile(File file) throws Exception{
System.out.println("readfile: " + file.getAbsolutePath());
Index: /SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/www/CLServlet.java
===================================================================
--- /SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/www/CLServlet.java (revision 196)
+++ /SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/www/CLServlet.java (revision 197)
@@ -83,7 +83,27 @@
for (int i = 0 ; i < classes.length; i++ ){
JsonObjectBuilder job = jbfactory.createObjectBuilder();
- job.add("uri", classes[i].getClassURI());
- job.add("display", classes[i].getClassURI());
- //jab.add(classes[i].getClassURI());
+ String uri = classes[i].getClassURI();
+ job.add("uri", uri);
+ 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") ){
+ label = labels[j].getLabel(); break;
+ }
+ }
+ if ( label == null ){
+ String[] uris = uri.split("/");
+ String tmplabel = uris[uris.length-1];
+ String[] tmplabel2 = tmplabel.split("#");
+ label = tmplabel2[tmplabel2.length-1];
+ }
+
+ StringBuilder displaybuilder = new StringBuilder(label);
+ displaybuilder.append(" (");
+ displaybuilder.append(classes[i].getNumOfInstances());
+ displaybuilder.append(")");
+ job.add("display", displaybuilder.toString());
jab.add(job);
}
Index: /SPARQLBuilderWWW/web/WEB-INF/glassfish-web.xml
===================================================================
--- /SPARQLBuilderWWW/web/WEB-INF/glassfish-web.xml (revision 123)
+++ /SPARQLBuilderWWW/web/WEB-INF/glassfish-web.xml (revision 197)
@@ -2,5 +2,5 @@
- /sbapi
+ /api