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[DL-Learner SVN] SF.net SVN: dl-learner:[1115] trunk
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From: <jen...@us...> - 2008-08-20 20:05:16
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Revision: 1115
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=1115&view=rev
Author: jenslehmann
Date: 2008-08-20 20:05:10 +0000 (Wed, 20 Aug 2008)
Log Message:
-----------
some fixes as result of example unit tests
Modified Paths:
--------------
trunk/examples/carcinogenesis/train.conf
trunk/examples/lymphography/lymphography_Class1.conf
trunk/examples/lymphography/lymphography_Class2.conf
trunk/examples/lymphography/lymphography_Class3.conf
trunk/examples/lymphography/lymphography_Class4.conf
trunk/examples/sparql/AristotlePos.conf
trunk/examples/sparql/govtrack.conf
trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java
trunk/src/dl-learner/org/dllearner/test/junit/ExampleTests.java
trunk/src/dl-learner/org/dllearner/utilities/Helper.java
trunk/src/dl-learner/org/dllearner/utilities/statistics/SimpleClock.java
Removed Paths:
-------------
trunk/examples/test.conf
Modified: trunk/examples/carcinogenesis/train.conf
===================================================================
--- trunk/examples/carcinogenesis/train.conf 2008-08-20 19:25:05 UTC (rev 1114)
+++ trunk/examples/carcinogenesis/train.conf 2008-08-20 20:05:10 UTC (rev 1115)
@@ -2,7 +2,8 @@
reasoner = fastInstanceChecker;
algorithm = refexamples;
-refexamples.noisePercentage = 28;
+// refexamples.noisePercentage = 28;
+refexamples.noisePercentage = 32;
refexamples.startClass = "http://dl-learner.org/carcinogenesis#Compound";
refexamples.writeSearchTree = false;
refexamples.searchTreeFile = "log/carcinogenesis/searchTree.log";
Modified: trunk/examples/lymphography/lymphography_Class1.conf
===================================================================
--- trunk/examples/lymphography/lymphography_Class1.conf 2008-08-20 19:25:05 UTC (rev 1114)
+++ trunk/examples/lymphography/lymphography_Class1.conf 2008-08-20 20:05:10 UTC (rev 1115)
@@ -17,15 +17,6 @@
*/
-
-reasoner = dig;
-//reasoner = fastRetrieval;
-
-algorithm = refinement;
-//refinement.heuristic = flexible;
-//algorithm = refexamples;
-
-
refinement.ignoredConcepts = {
"http://www.example.org/lymphography#Target1_NormalFind",
"http://www.example.org/lymphography#Target2_Metastases",
Modified: trunk/examples/lymphography/lymphography_Class2.conf
===================================================================
--- trunk/examples/lymphography/lymphography_Class2.conf 2008-08-20 19:25:05 UTC (rev 1114)
+++ trunk/examples/lymphography/lymphography_Class2.conf 2008-08-20 20:05:10 UTC (rev 1115)
@@ -13,16 +13,8 @@
it will need a lot of time to find a solution, in case it exists at all.
Mainly used as a test case for improving the algorithms (example 4 uses
a new experimental version of the refinement algorithm)
-
-
*/
-reasoner = dig;
-//reasoner = fastRetrieval;
-algorithm = refinement;
-//refinement.heuristic = flexible;
-//algorithm = refexamples;
-
refinement.ignoredConcepts = {
"http://www.example.org/lymphography#Target1_NormalFind",
"http://www.example.org/lymphography#Target2_Metastases",
@@ -30,12 +22,10 @@
"http://www.example.org/lymphography#Target4_Fibrosis"
};
-
-
-
refinement.useAllConstructor = false;
refinement.useExistsConstructor = true;
refinement.useNegation = false;
+
import("lymphography.owl");
/*Class2*/
Modified: trunk/examples/lymphography/lymphography_Class3.conf
===================================================================
--- trunk/examples/lymphography/lymphography_Class3.conf 2008-08-20 19:25:05 UTC (rev 1114)
+++ trunk/examples/lymphography/lymphography_Class3.conf 2008-08-20 20:05:10 UTC (rev 1115)
@@ -17,15 +17,6 @@
*/
-
-
-reasoner = dig;
-//reasoner = fastRetrieval;
-
-algorithm = refinement;
-//refinement.heuristic = flexible;
-//algorithm = refexamples;
-
refinement.ignoredConcepts = {
"http://www.example.org/lymphography#Target1_NormalFind",
"http://www.example.org/lymphography#Target2_Metastases",
Modified: trunk/examples/lymphography/lymphography_Class4.conf
===================================================================
--- trunk/examples/lymphography/lymphography_Class4.conf 2008-08-20 19:25:05 UTC (rev 1114)
+++ trunk/examples/lymphography/lymphography_Class4.conf 2008-08-20 20:05:10 UTC (rev 1115)
@@ -13,18 +13,8 @@
it will need a lot of time to find a solution, in case it exists at all.
Mainly used as a test case for improving the algorithms (example 4 uses
a new experimental version of the refinement algorithm)
-
-
*/
-
-//reasoner = dig;
-reasoner = fastRetrieval;
-
-//algorithm = refinement;
-//refinement.heuristic = flexible;
-algorithm = refexamples;
-
refexamples.ignoredConcepts = {
"http://www.example.org/lymphography#Target1_NormalFind",
"http://www.example.org/lymphography#Target2_Metastases",
Modified: trunk/examples/sparql/AristotlePos.conf
===================================================================
--- trunk/examples/sparql/AristotlePos.conf 2008-08-20 19:25:05 UTC (rev 1114)
+++ trunk/examples/sparql/AristotlePos.conf 2008-08-20 20:05:10 UTC (rev 1115)
@@ -18,7 +18,8 @@
algorithm = refexamples;
reasoner = fastInstanceChecker;
-problem = posOnlyDefinitionLP;
+// comment this out to enable positive only learning
+// problem = posOnlyDefinitionLP;
sparql.instances = {
"http://dbpedia.org/resource/Democritus",
@@ -33,9 +34,10 @@
+"http://dbpedia.org/resource/Pythagoras"
+"http://dbpedia.org/resource/Philolaus"
+"http://dbpedia.org/resource/Archytas"
-/*
+
+// comment this out to enable positive only learning
-"http://dbpedia.org/resource/Socrates"
-"http://dbpedia.org/resource/Plato"
-"http://dbpedia.org/resource/Zeno_of_Elea"
-"http://dbpedia.org/resource/Democritus"
-*/
+
Modified: trunk/examples/sparql/govtrack.conf
===================================================================
--- trunk/examples/sparql/govtrack.conf 2008-08-20 19:25:05 UTC (rev 1114)
+++ trunk/examples/sparql/govtrack.conf 2008-08-20 20:05:10 UTC (rev 1115)
@@ -7,7 +7,7 @@
reasoner = owlAPI;
// reasoner = fastInstanceChecker;
-import("http://rdfabout.com/sparql/","SPARQL");
+import("http://www.govtrack.us/sparql","SPARQL");
sparql.instances = {
"http://www.rdfabout.com/rdf/usgov/congress/people/A000069",
Deleted: trunk/examples/test.conf
===================================================================
--- trunk/examples/test.conf 2008-08-20 19:25:05 UTC (rev 1114)
+++ trunk/examples/test.conf 2008-08-20 20:05:10 UTC (rev 1115)
@@ -1,13 +0,0 @@
-import("father.kb");
-reasoner = "fastInstanceChecker";
-problem = "posNegDefinition";
-
-+"http://localhost/foo#markus"
-+"http://localhost/foo#michelle"
-+"http://localhost/foo#stefan"
-
--"http://localhost/foo#anna"
--"http://localhost/foo#bernd"
--"http://localhost/foo#gabi"
-
-algorithm = "refexamples";
Modified: trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java 2008-08-20 19:25:05 UTC (rev 1114)
+++ trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java 2008-08-20 20:05:10 UTC (rev 1115)
@@ -451,7 +451,9 @@
System.out.println("solution: " + bestNode.getConcept());
System.out.println("maxPosOnlyExpansion: " + maxPosOnlyExpansion);
System.out.println("best child of this node: " + bestChild);
- System.out.println(bestNode.getChildConcepts());
+ if(bestNode.getChildConcepts().size()<100) {
+ System.out.println(bestNode.getChildConcepts());
+ }
System.out.println("TODO: needs to be integrated with other stopping criteria");
System.out
.println("You tried to use this algorithm for positive only learning, which is not recommended (yet).");
Modified: trunk/src/dl-learner/org/dllearner/test/junit/ExampleTests.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/test/junit/ExampleTests.java 2008-08-20 19:25:05 UTC (rev 1114)
+++ trunk/src/dl-learner/org/dllearner/test/junit/ExampleTests.java 2008-08-20 20:05:10 UTC (rev 1115)
@@ -25,6 +25,8 @@
import java.util.ArrayList;
import java.util.Date;
import java.util.HashMap;
+import java.util.Set;
+import java.util.TreeSet;
import org.apache.log4j.ConsoleAppender;
import org.apache.log4j.FileAppender;
@@ -34,6 +36,7 @@
import org.dllearner.cli.QuickStart;
import org.dllearner.cli.Start;
import org.dllearner.core.ComponentInitException;
+import org.dllearner.core.ComponentManager;
import org.dllearner.utilities.Helper;
import org.junit.Test;
@@ -48,7 +51,7 @@
/**
* This test runs all conf files in the examples directory. Each conf file
* corresponds to one unit test, which is succesful if a concept was
- * learned.
+ * learned. This unit test takes several hours.
*
* @throws ComponentInitException
* If any component initialisation exception occurs in the
@@ -72,18 +75,34 @@
SimpleDateFormat sdf = new SimpleDateFormat("HH:mm:ss");
+ // ignore list (examples which are temporarily not working due
+ // to server downtime, lack of features etc., but should still
+ // remain in the example directory
+ Set<String> ignore = new TreeSet<String>();
+ ignore.add("./examples/sparql/govtrack.conf"); // HTTP 500 Server error
+ ignore.add("./examples/sparql/musicbrainz.conf"); // HTTP 502 error - NullPointer in extraction
+ ignore.add("./examples/sparql/SKOSTEST_local.conf"); // Out of Memory Error
+ ignore.add("./examples/sparql/scrobble.conf"); // HTTP 502 Proxy Error
+ ignore.add("./examples/family-benchmark/Cousin.conf"); // Out of Memory Error
+
for (String path : confFiles.keySet()) {
for (String file : confFiles.get(path)) {
String conf = path + file + ".conf";
- System.out.println("Testing " + conf + " (time: " + sdf.format(new Date()) + ").");
- long startTime = System.nanoTime();
- // start example
- Start start = new Start(new File(conf));
- start.start(false);
- // test is successful if a concept was learned
- assert (start.getLearningAlgorithm().getCurrentlyBestDescription() != null);
- long timeNeeded = System.nanoTime() - startTime;
- System.out.println("Test of " + conf + " completed in " + Helper.prettyPrintNanoSeconds(timeNeeded) + ".");
+ if(ignore.contains(conf)) {
+ System.out.println("Skipping " + conf + " (is on ignore list).");
+ } else {
+ System.out.println("Testing " + conf + " (time: " + sdf.format(new Date()) + ").");
+ long startTime = System.nanoTime();
+ // start example
+ Start start = new Start(new File(conf));
+ start.start(false);
+ // test is successful if a concept was learned
+ assert (start.getLearningAlgorithm().getCurrentlyBestDescription() != null);
+ long timeNeeded = System.nanoTime() - startTime;
+ start.getReasoningService().releaseKB();
+ ComponentManager.getInstance().freeAllComponents();
+ System.out.println("Test of " + conf + " completed in " + Helper.prettyPrintNanoSeconds(timeNeeded) + ".");
+ }
}
}
Modified: trunk/src/dl-learner/org/dllearner/utilities/Helper.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/Helper.java 2008-08-20 19:25:05 UTC (rev 1114)
+++ trunk/src/dl-learner/org/dllearner/utilities/Helper.java 2008-08-20 20:05:10 UTC (rev 1115)
@@ -445,21 +445,20 @@
// ignore some concepts (possibly produced by Jena)
if (conceptName.startsWith("anon")) {
- System.out
- .println(" Ignoring concept "
+ logger.debug(" Ignoring concept "
+ conceptName
+ " (probably an anonymous concept produced by Jena when reading in OWL file).");
it.remove();
} else if (conceptName.startsWith("http://www.w3.org/1999/02/22-rdf-syntax-ns#")) {
- System.out.println(" Ignoring concept " + conceptName
+ logger.debug(" Ignoring concept " + conceptName
+ " (RDF construct produced by Jena when reading in OWL file).");
it.remove();
} else if (conceptName.startsWith("http://www.w3.org/2000/01/rdf-schema#")) {
- System.out.println(" Ignoring concept " + conceptName
+ logger.debug(" Ignoring concept " + conceptName
+ " (RDF Schema construct produced by Jena when reading in OWL file).");
it.remove();
} else if (conceptName.startsWith("http://www.w3.org/2002/07/owl#")) {
- System.out.println(" Ignoring concept " + conceptName
+ logger.debug(" Ignoring concept " + conceptName
+ " (OWL construct produced by Jena when reading in OWL file).");
it.remove();
}
Modified: trunk/src/dl-learner/org/dllearner/utilities/statistics/SimpleClock.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/statistics/SimpleClock.java 2008-08-20 19:25:05 UTC (rev 1114)
+++ trunk/src/dl-learner/org/dllearner/utilities/statistics/SimpleClock.java 2008-08-20 20:05:10 UTC (rev 1115)
@@ -1,78 +1,93 @@
package org.dllearner.utilities.statistics;
/**
- * class for counting time and output it
+ * Copyright (C) 2007-2008, Jens Lehmann
*
+ * This file is part of DL-Learner.
+ *
+ * DL-Learner is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * DL-Learner is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ *
*/
+import org.apache.log4j.Logger;
+
+/**
+ * Class for counting time and outputting it.
+ *
+ * @author Unknown
+ */
public class SimpleClock {
+
+ private static Logger logger = Logger.getLogger(SimpleClock.class);
+
private long time;
-
+
public SimpleClock() {
- time=System.currentTimeMillis();
+ time = System.currentTimeMillis();
}
-
-
-
-
-
+
/**
- * prints time needed
- * and resets the clock
+ * prints time needed and resets the clock
*/
public void printAndSet() {
-
- System.out.println("needed "+getTime()+" ms");
+ logger.info("needed " + getTime() + " ms");
setTime();
}
-
-
+
/**
- * prints time needed
- * and resets the clock
- * @param s String for printing
+ * prints time needed and resets the clock
+ *
+ * @param s
+ * String for printing
*/
public void printAndSet(String s) {
-
- System.out.println(s+" needed "+getTime()+" ms");
+ logger.info(s + " needed " + getTime() + " ms");
setTime();
}
-
+
public String getAndSet(String s) {
-
- String ret = s+" needed "+getTime()+" ms";
+ String ret = s + " needed " + getTime() + " ms";
setTime();
return ret;
-
}
-
-
+
/**
* prints time needed
- *
- * @param s String for printing
+ *
+ * @param s
+ * String for printing
*/
public void print(String s) {
-
- System.out.println(s+" needed "+getTime()+" ms");
-
+ logger.info(s + " needed " + getTime() + " ms");
}
-
+
/**
* resets the clock
*/
public void setTime() {
- time=System.currentTimeMillis();
+ time = System.currentTimeMillis();
}
+
/**
* resets the clock
*/
public void reset() {
setTime();
}
-
+
public long getTime() {
- long now=System.currentTimeMillis();
- return now-time;
+ long now = System.currentTimeMillis();
+ return now - time;
}
-
+
}
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