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[DL-Learner SVN] SF.net SVN: dl-learner:[3522] trunk
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From: <lor...@us...> - 2012-01-03 08:51:00
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Revision: 3522
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3522&view=rev
Author: lorenz_b
Date: 2012-01-03 08:50:54 +0000 (Tue, 03 Jan 2012)
Log Message:
-----------
Enabled separate cache for each endpoint to avoid concurrency problems when running several threads in parallel.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/kb/sparql/SPARQLTasks.java
trunk/interfaces/src/main/java/org/dllearner/cli/Enrichment.java
trunk/interfaces/src/main/java/org/dllearner/cli/GlobalEnrichment.java
Modified: trunk/components-core/src/main/java/org/dllearner/kb/sparql/SPARQLTasks.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/kb/sparql/SPARQLTasks.java 2012-01-03 04:33:55 UTC (rev 3521)
+++ trunk/components-core/src/main/java/org/dllearner/kb/sparql/SPARQLTasks.java 2012-01-03 08:50:54 UTC (rev 3522)
@@ -33,6 +33,7 @@
import org.dllearner.utilities.datastructures.StringTuple;
import org.dllearner.utilities.owl.OWLVocabulary;
+import com.clarkparsia.owlapiv3.OWL;
import com.hp.hpl.jena.query.QuerySolution;
import com.hp.hpl.jena.query.ResultSet;
import com.hp.hpl.jena.query.ResultSetFactory;
@@ -710,6 +711,9 @@
}
}
+ //remove trivial classes
+ classes.remove(OWL.Nothing.toStringID());
+ classes.remove(OWL.Thing.toStringID());
return classes;
}
Modified: trunk/interfaces/src/main/java/org/dllearner/cli/Enrichment.java
===================================================================
--- trunk/interfaces/src/main/java/org/dllearner/cli/Enrichment.java 2012-01-03 04:33:55 UTC (rev 3521)
+++ trunk/interfaces/src/main/java/org/dllearner/cli/Enrichment.java 2012-01-03 08:50:54 UTC (rev 3522)
@@ -29,6 +29,7 @@
import java.io.IOException;
import java.io.OutputStream;
import java.io.PrintStream;
+import java.io.UnsupportedEncodingException;
import java.lang.reflect.InvocationTargetException;
import java.math.BigInteger;
import java.net.MalformedURLException;
@@ -36,6 +37,7 @@
import java.net.URI;
import java.net.URISyntaxException;
import java.net.URL;
+import java.net.URLEncoder;
import java.security.SecureRandom;
import java.text.DecimalFormat;
import java.util.ArrayList;
@@ -104,6 +106,7 @@
import org.dllearner.core.owl.ObjectProperty;
import org.dllearner.core.owl.SubClassAxiom;
import org.dllearner.kb.SparqlEndpointKS;
+import org.dllearner.kb.sparql.ExtractionDBCache;
import org.dllearner.kb.sparql.SPARQLTasks;
import org.dllearner.kb.sparql.SparqlEndpoint;
import org.dllearner.kb.sparql.SparqlKnowledgeSource;
@@ -208,6 +211,8 @@
private boolean useInference;
private SPARQLReasoner reasoner;
+ private ExtractionDBCache cache;
+ private String cacheDir = "cache";
// lists of algorithms to apply
private List<Class<? extends AxiomLearningAlgorithm>> objectPropertyAlgorithms;
@@ -234,6 +239,14 @@
this.nrOfAxiomsToLearn = nrOfAxiomsToLearn;
this.useInference = useInference;
+ try {
+ cacheDir = "cache" + File.separator + URLEncoder.encode(se.getURL().toString(), "UTF-8");
+ } catch (UnsupportedEncodingException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ cache = new ExtractionDBCache(cacheDir);
+
objectPropertyAlgorithms = new LinkedList<Class<? extends AxiomLearningAlgorithm>>();
objectPropertyAlgorithms.add(DisjointObjectPropertyAxiomLearner.class);
objectPropertyAlgorithms.add(EquivalentObjectPropertyAxiomLearner.class);
@@ -282,7 +295,7 @@
// ks.setSupportsSPARQL_1_1(supportsSPARQL_1_1);
if(useInference){
- reasoner = new SPARQLReasoner(ks);
+ reasoner = new SPARQLReasoner(ks, cache);
System.out.print("Precomputing subsumption hierarchy ... ");
long startTime = System.currentTimeMillis();
reasoner.prepareSubsumptionHierarchy();
@@ -332,7 +345,13 @@
runDataPropertyAlgorithms(ks, (DatatypeProperty) resource);
} else if(resource instanceof NamedClass) {
System.out.println(resource + " appears to be a class. Running appropriate algorithms.\n");
- runClassLearningAlgorithms(ks, (NamedClass) resource);
+ try {
+ runClassLearningAlgorithms(ks, (NamedClass) resource);
+ } catch (Exception e) {
+ System.out.println(e.getCause());
+ } catch (Error e) {
+ System.out.println(e.getCause());
+ }
} else {
throw new Error("The type " + resource.getClass() + " of resource " + resource + " cannot be handled by this enrichment tool.");
}
@@ -401,6 +420,7 @@
ks2.setDefaultGraphURIs(new TreeSet<String>(ks.getEndpoint().getDefaultGraphURIs()));
ks2.setUseLits(false);
ks2.setUseCacheDatabase(true);
+ ks2.setCacheDir(cacheDir);
ks2.setRecursionDepth(2);
ks2.setCloseAfterRecursion(true);
ks2.setSaveExtractedFragment(true);
Modified: trunk/interfaces/src/main/java/org/dllearner/cli/GlobalEnrichment.java
===================================================================
--- trunk/interfaces/src/main/java/org/dllearner/cli/GlobalEnrichment.java 2012-01-03 04:33:55 UTC (rev 3521)
+++ trunk/interfaces/src/main/java/org/dllearner/cli/GlobalEnrichment.java 2012-01-03 08:50:54 UTC (rev 3522)
@@ -31,6 +31,7 @@
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
+import java.util.TreeMap;
import java.util.TreeSet;
import java.util.concurrent.ArrayBlockingQueue;
import java.util.concurrent.ThreadPoolExecutor;
@@ -74,7 +75,7 @@
//parameters for thread pool
//Parallel running Threads(Executor) on System
- private static int corePoolSize = 10;
+ private static int corePoolSize = 1;
//Maximum Threads allowed in Pool
private static int maximumPoolSize = 20;
//Keep alive time for waiting threads for jobs(Runnable)
@@ -103,7 +104,7 @@
Logger.getRootLogger().addAppender(consoleAppender);
// get all SPARQL endpoints and their graphs - the key is a name-identifier
- Map<String,SparqlEndpoint> endpoints = new HashMap<String,SparqlEndpoint>();
+ Map<String,SparqlEndpoint> endpoints = new TreeMap<String,SparqlEndpoint>();
String query = "";
query += "PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> \n";
@@ -130,7 +131,7 @@
ResultSet rs = sq.send();
while(rs.hasNext()) {
QuerySolution qs = rs.next();
- String endpoint = qs.get("endpoint").toString();
+ String endpoint = qs.get("endpoint").toString();System.out.println(endpoint);
String shortName = qs.get("shortName").toString();
endpoints.put(shortName, new SparqlEndpoint(new URL(endpoint)));
}
@@ -170,18 +171,20 @@
// run enrichment script - we make a case distinguish to see which kind of problems we get
// (could be interesting for statistics later on)
try {
- e.start();
- success = true;
- } catch(StackOverflowError error) {
try {
+ e.start();
+ success = true;
+ } catch (Exception ex){
+ ex.printStackTrace(new PrintStream(log));
+ } catch(StackOverflowError error) {
error.printStackTrace(new PrintStream(log));
- } catch (FileNotFoundException e1) {
- // TODO Auto-generated catch block
- e1.printStackTrace();
+ Files.appendToFile(log, "stack overflows could be caused by cycles in class hierarchies");
+ error.printStackTrace();
}
- Files.appendToFile(log, "stack overflows could be caused by cycles in class hierarchies");
- error.printStackTrace();
- } catch(ResultSetException ex) {
+ } catch (FileNotFoundException e2) {
+ e2.printStackTrace();
+ }
+ /*catch(ResultSetException ex) {
try {
ex.printStackTrace(new PrintStream(log));
} catch (FileNotFoundException e1) {
@@ -202,7 +205,7 @@
}
catch(Exception ex) {
System.out.println("class of exception: " + ex.getClass());
- }
+ }*/
// save results to a file (TODO: check if enrichment format
if(success) {
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