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From: <ku...@us...> - 2008-04-25 14:34:12
|
Revision: 827
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=827&view=rev
Author: kurzum
Date: 2008-04-25 07:33:54 -0700 (Fri, 25 Apr 2008)
Log Message:
-----------
intermediate commit
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java
trunk/src/dl-learner/org/dllearner/scripts/SPARQLMassLearning.java
trunk/src/dl-learner/org/dllearner/utilities/AutomaticExampleFinderSPARQL.java
trunk/src/dl-learner/org/dllearner/utilities/ConfWriter.java
Modified: trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java 2008-04-25 10:48:36 UTC (rev 826)
+++ trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java 2008-04-25 14:33:54 UTC (rev 827)
@@ -413,17 +413,17 @@
logger.info("best node " + candidatesStable.last().getShortDescription(nrOfPositiveExamples, nrOfNegativeExamples, baseURI));
logger.info("\nsolutions ( top 5 ):");
int show=1;
+ String manchester="MANCHESTER:\n";
+ String KBSyntax="KBSyntax:\n";
for(Description c : solutions) {
logger.info(show+": " + c.toString(baseURI,null) + " (length " + c.getLength() +", depth " + c.getDepth() + ")");
- //TODO remove this line maybe
// watch for String.replace Quick hack
- logger.info(" MANCHESTER: " +
- c.toManchesterSyntaxString(baseURI, new HashMap<String,String>()).
- replace("\"", ""));
- logger.info(" KBSyntax: " + c.toKBSyntaxString());
- if(show>=5){break;}
- show++;
+ manchester+=show+": "+c.toManchesterSyntaxString(baseURI, new HashMap<String,String>()).replace("\"", "")+"\n";
+ KBSyntax+=show+": " + c.toKBSyntaxString()+"\n";
+ if(show>=5){break;} show++;
}
+ logger.debug(manchester);
+ logger.debug(KBSyntax);
}
logger.debug("size of candidate set: " + candidates.size());
Modified: trunk/src/dl-learner/org/dllearner/scripts/SPARQLMassLearning.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/SPARQLMassLearning.java 2008-04-25 10:48:36 UTC (rev 826)
+++ trunk/src/dl-learner/org/dllearner/scripts/SPARQLMassLearning.java 2008-04-25 14:33:54 UTC (rev 827)
@@ -31,15 +31,15 @@
boolean useRelated = false;
boolean useSuperClasses = false;
boolean useParallelClasses = true;
- int poslimit = 15;
- int neglimit = 200;
+ int poslimit = 10;
+ int neglimit = 20;
try {
//logger.setLevel(Level.TRACE);
- Logger.getLogger(SparqlKnowledgeSource.class).setLevel(Level.TRACE);
- System.out.println(Logger.getLogger(SparqlQuery.class).getLevel());
+ Logger.getLogger(SparqlKnowledgeSource.class).setLevel(Level.INFO);
+ //System.out.println(Logger.getLogger(SparqlQuery.class).getLevel());
/*System.out.println(Level.DEBUG.getClass());
System.out.println(Level.toLevel("INFO"));
@@ -49,11 +49,12 @@
//concepts.add("(EXISTS \"monarch\".TOP AND EXISTS \"predecessor\".(\"Knight\" OR \"Secretary\"))");
SortedSet<String> concepts = new TreeSet<String>();
- //concepts.add("(\"http://dbpedia.org/class/yago/HeadOfState110164747\" AND (\"http://dbpedia.org/class/yago/Negotiator110351874\" AND \"http://dbpedia.org/class/yago/Representative110522035\"))");
+ concepts.add("(\"http://dbpedia.org/class/yago/HeadOfState110164747\" AND (\"http://dbpedia.org/class/yago/Negotiator110351874\" AND \"http://dbpedia.org/class/yago/Representative110522035\"))");
//concepts.add("\"http://dbpedia.org/class/yago/Person100007846\"");
- concepts.add("\"http://dbpedia.org/class/yago/FieldMarshal110086821\"");
+ //concepts.add("\"http://dbpedia.org/class/yago/FieldMarshal110086821\"");
//concepts.add("http://dbpedia.org/resource/Category:Prime_Ministers_of_the_United_Kingdom");
//concepts.add("http://dbpedia.org/resource/Category:Grammy_Award_winners");
+ //concepts.add("EXISTS \"http://dbpedia.org/property/grammyawards\".TOP");
SortedSet<String> posExamples = new TreeSet<String>();
SortedSet<String> negExamples = new TreeSet<String>();
@@ -78,6 +79,7 @@
//System.exit(0);
String tmp = concepts.first().replace("http://dbpedia.org/resource/Category:", "").replace("\"","");
tmp = tmp.replace("http://dbpedia.org/class/yago/", "");
+ tmp = tmp.replace("http://dbpedia.org/property/", "");
String confname = URLEncoder.encode(tmp, "UTF-8")+".conf";
//
ConfWriter cf=new ConfWriter();
Modified: trunk/src/dl-learner/org/dllearner/utilities/AutomaticExampleFinderSPARQL.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/AutomaticExampleFinderSPARQL.java 2008-04-25 10:48:36 UTC (rev 826)
+++ trunk/src/dl-learner/org/dllearner/utilities/AutomaticExampleFinderSPARQL.java 2008-04-25 14:33:54 UTC (rev 827)
@@ -189,7 +189,7 @@
SparqlQuery sq = new SparqlQuery(query, se);
String JSON = c.executeSparqlQuery(sq);
- //System.out.println(JSON);
+ //System.out.println("JSON:\n"+JSON);
rs = SparqlQuery.JSONtoResultSet(JSON);
} catch (Exception e) {
Modified: trunk/src/dl-learner/org/dllearner/utilities/ConfWriter.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/ConfWriter.java 2008-04-25 10:48:36 UTC (rev 826)
+++ trunk/src/dl-learner/org/dllearner/utilities/ConfWriter.java 2008-04-25 14:33:54 UTC (rev 827)
@@ -54,6 +54,7 @@
"sparql.predefinedEndpoint = \"DBPEDIA\";\n" +
"refexamples.minExecutionTimeInSeconds = 30;\n" +
"refexamples.maxExecutionTimeInSeconds = 30;\n" +
+ "//refexamples.guaranteeXgoodDescriptions = 10;\n" +
"refexamples.logLevel=\"TRACE\";\n" +
"refexamples.noisePercentage = 0.10;\n" +
"refexamples.writeSearchTree = true;\n" +
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ku...@us...> - 2008-04-25 10:48:48
|
Revision: 826
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=826&view=rev
Author: kurzum
Date: 2008-04-25 03:48:36 -0700 (Fri, 25 Apr 2008)
Log Message:
-----------
added string for testing
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQueryDescriptionConvertVisitor.java
Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQueryDescriptionConvertVisitor.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQueryDescriptionConvertVisitor.java 2008-04-25 10:47:06 UTC (rev 825)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQueryDescriptionConvertVisitor.java 2008-04-25 10:48:36 UTC (rev 826)
@@ -160,6 +160,7 @@
s.add(conj);
s.add("(\"http://dbpedia.org/class/yago/Person100007846\" OR \"http://dbpedia.org/class/yago/Head110162991\")");
s.add("NOT \"http://dbpedia.org/class/yago/Person100007846\"");
+ s.add("(\"http://dbpedia.org/class/yago/HeadOfState110164747\" AND (\"http://dbpedia.org/class/yago/Negotiator110351874\" AND \"http://dbpedia.org/class/yago/Representative110522035\"))");
for (String kbsyntax : s) {
result.put(kbsyntax,SparqlQueryDescriptionConvertVisitor.getSparqlQuery(kbsyntax));
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ku...@us...> - 2008-04-25 10:47:21
|
Revision: 825
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=825&view=rev
Author: kurzum
Date: 2008-04-25 03:47:06 -0700 (Fri, 25 Apr 2008)
Log Message:
-----------
hacked double point .. bug
see http://sourceforge.net/tracker/index.php?func=detail&aid=1951521&group_id=203619&atid=986319
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQueryDescriptionConvertVisitor.java
Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQueryDescriptionConvertVisitor.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQueryDescriptionConvertVisitor.java 2008-04-25 09:28:21 UTC (rev 824)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQueryDescriptionConvertVisitor.java 2008-04-25 10:47:06 UTC (rev 825)
@@ -94,7 +94,13 @@
Description d = KBParser.parseConcept(description);
SparqlQueryDescriptionConvertVisitor visitor=new SparqlQueryDescriptionConvertVisitor();
d.accept(visitor);
- return visitor.getSparqlQuery();
+
+ //TODO ERROR see replace HACK
+ String ret = visitor.getSparqlQuery();
+ while (ret.contains("..")) {
+ ret = ret.replace("..", ".");
+ }
+ return ret;
}
public static String getSparqlQuery(String description, int limit) throws ParseException
@@ -102,7 +108,12 @@
Description d = KBParser.parseConcept(description);
SparqlQueryDescriptionConvertVisitor visitor=new SparqlQueryDescriptionConvertVisitor();
d.accept(visitor);
- return visitor.getSparqlQuery(limit);
+ //TODO ERROR see replace HACK
+ String ret = visitor.getSparqlQuery(limit);
+ while (ret.contains("..")) {
+ ret = ret.replace("..", ".");
+ }
+ return ret;
}
/**
@@ -213,6 +224,8 @@
* @see org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl.Intersection)
*/
public void visit(Intersection description) {
+ //TODO ERROR see replace HACK
+
logger.trace("Intersection");
description.getChild(0).accept(this);
query+=".";
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ku...@us...> - 2008-04-25 09:28:26
|
Revision: 824
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=824&view=rev
Author: kurzum
Date: 2008-04-25 02:28:21 -0700 (Fri, 25 Apr 2008)
Log Message:
-----------
applied new options
Modified Paths:
--------------
trunk/examples/sparql/Aristotle.conf
trunk/examples/sparql/DBPediaYAGOWomanInPolitics.conf
trunk/examples/sparql/SilentBobWorking1.conf
trunk/examples/sparql/SilentBobWorking2.conf
trunk/examples/sparql/difference/DBPediaSKOS_kohl_vs_angela.conf
trunk/examples/sparql/difference/DifferenceDBPediaYAGO_angela_vs_hillary.conf
trunk/examples/sparql/difference/DifferenceDBPediaYAGO_angela_vs_hillary_ignoredConcepts.conf
trunk/examples/sparql/difference/DifferenceDBPediaYAGO_hillary_vs_angela.conf
trunk/examples/sparql/difference/DifferenceDBPediaYAGO_hillary_vs_angela_ignoredConcepts.conf
trunk/examples/sparql/hierarchy/Hierarchy0DBPediaYAGOChanBrit_monarch.conf
trunk/examples/sparql/hierarchy/Hierarchy1DBPediaYAGOChanBrit_pred_Knight.conf
trunk/examples/sparql/navigation/Navigation0DBPediaYAGOAristotle.conf
trunk/examples/sparql/navigation/Navigation1DBPediaYAGOAristotle.conf
trunk/examples/sparql/navigation/Navigation2DBPediaYAGOAristotle.conf
Modified: trunk/examples/sparql/Aristotle.conf
===================================================================
--- trunk/examples/sparql/Aristotle.conf 2008-04-25 09:28:05 UTC (rev 823)
+++ trunk/examples/sparql/Aristotle.conf 2008-04-25 09:28:21 UTC (rev 824)
@@ -11,10 +11,9 @@
sparql.recursionDepth = 1;
//predefined filter (1 = YAGO based learning)
-sparql.predefinedFilter = 5;
+sparql.predefinedFilter = "YAGO";
+sparql.predefinedEndpoint = "DBPEDIA";
-sparql.predefinedEndpoint = 1;
-
import("http://dbpedia.openlinksw.com:8890/sparql","SPARQL");
sparql.instances = {
Modified: trunk/examples/sparql/DBPediaYAGOWomanInPolitics.conf
===================================================================
--- trunk/examples/sparql/DBPediaYAGOWomanInPolitics.conf 2008-04-25 09:28:05 UTC (rev 823)
+++ trunk/examples/sparql/DBPediaYAGOWomanInPolitics.conf 2008-04-25 09:28:21 UTC (rev 824)
@@ -20,11 +20,10 @@
//predefined filter (1 = YAGO based learning)
// 2 = SKOS, more Options are needed then though. replacePredicate, breakSuperClassRetrievalAfter
-sparql.predefinedFilter = 5;
+sparql.predefinedFilter = "YAGO";
+sparql.predefinedEndpoint = "DBPEDIA";
-sparql.predefinedEndpoint = 1;
-
import("http://dbpedia.openlinksw.com:8890/sparql","SPARQL");
sparql.instances = {
Modified: trunk/examples/sparql/SilentBobWorking1.conf
===================================================================
--- trunk/examples/sparql/SilentBobWorking1.conf 2008-04-25 09:28:05 UTC (rev 823)
+++ trunk/examples/sparql/SilentBobWorking1.conf 2008-04-25 09:28:21 UTC (rev 824)
@@ -12,11 +12,10 @@
//predefined filter (1 = YAGO based learning)
// 2 = SKOS, more Options are needed then though. replacePredicate, breakSuperClassRetrievalAfter
-sparql.predefinedFilter = 5;
+sparql.predefinedFilter = "YAGO";
+sparql.predefinedEndpoint = "DBPEDIA";
-sparql.predefinedEndpoint = 1;
-
// use DBpedia endpoint
import("http://dbpedia.openlinksw.com:8890/sparql","SPARQL");
Modified: trunk/examples/sparql/SilentBobWorking2.conf
===================================================================
--- trunk/examples/sparql/SilentBobWorking2.conf 2008-04-25 09:28:05 UTC (rev 823)
+++ trunk/examples/sparql/SilentBobWorking2.conf 2008-04-25 09:28:21 UTC (rev 824)
@@ -12,11 +12,10 @@
//predefined filter (1 = YAGO based learning)
// 2 = SKOS, more Options are needed then though. replacePredicate, breakSuperClassRetrievalAfter
-sparql.predefinedFilter = 5;
+sparql.predefinedFilter = "YAGO";
+sparql.predefinedEndpoint = "DBPEDIA";
-sparql.predefinedEndpoint = 1;
-
// use DBpedia endpoint
import("http://dbpedia.openlinksw.com:8890/sparql","SPARQL");
Modified: trunk/examples/sparql/difference/DBPediaSKOS_kohl_vs_angela.conf
===================================================================
--- trunk/examples/sparql/difference/DBPediaSKOS_kohl_vs_angela.conf 2008-04-25 09:28:05 UTC (rev 823)
+++ trunk/examples/sparql/difference/DBPediaSKOS_kohl_vs_angela.conf 2008-04-25 09:28:21 UTC (rev 824)
@@ -70,8 +70,9 @@
//manually after retrieving the specified amount of classes
sparql.breakSuperClassRetrievalAfter=200;
-sparql.predefinedEndpoint = 1;
+sparql.predefinedEndpoint = "DBPEDIA";
+
// use DBpedia endpoint
import("http://dbpedia.openlinksw.com:8890/sparql","SPARQL");
Modified: trunk/examples/sparql/difference/DifferenceDBPediaYAGO_angela_vs_hillary.conf
===================================================================
--- trunk/examples/sparql/difference/DifferenceDBPediaYAGO_angela_vs_hillary.conf 2008-04-25 09:28:05 UTC (rev 823)
+++ trunk/examples/sparql/difference/DifferenceDBPediaYAGO_angela_vs_hillary.conf 2008-04-25 09:28:21 UTC (rev 824)
@@ -25,10 +25,9 @@
//predefined filter (1 = YAGO based learning)
// 2 = SKOS, more Options are needed then though. replacePredicate, breakSuperClassRetrievalAfter
-sparql.predefinedFilter = 1;
+sparql.predefinedFilter = "YAGO";
+sparql.predefinedEndpoint = "DBPEDIA";
-sparql.predefinedEndpoint = 1;
-
// use DBpedia endpoint
import("http://dbpedia.openlinksw.com:8890/sparql","SPARQL");
Modified: trunk/examples/sparql/difference/DifferenceDBPediaYAGO_angela_vs_hillary_ignoredConcepts.conf
===================================================================
--- trunk/examples/sparql/difference/DifferenceDBPediaYAGO_angela_vs_hillary_ignoredConcepts.conf 2008-04-25 09:28:05 UTC (rev 823)
+++ trunk/examples/sparql/difference/DifferenceDBPediaYAGO_angela_vs_hillary_ignoredConcepts.conf 2008-04-25 09:28:21 UTC (rev 824)
@@ -41,10 +41,9 @@
//predefined filter (1 = YAGO based learning)
// 2 = SKOS, more Options are needed then though. replacePredicate, breakSuperClassRetrievalAfter
-sparql.predefinedFilter = 1;
+sparql.predefinedFilter = "YAGO";
+sparql.predefinedEndpoint = "DBPEDIA";
-sparql.predefinedEndpoint = 1;
-
// use DBpedia endpoint
import("http://dbpedia.openlinksw.com:8890/sparql","SPARQL");
Modified: trunk/examples/sparql/difference/DifferenceDBPediaYAGO_hillary_vs_angela.conf
===================================================================
--- trunk/examples/sparql/difference/DifferenceDBPediaYAGO_hillary_vs_angela.conf 2008-04-25 09:28:05 UTC (rev 823)
+++ trunk/examples/sparql/difference/DifferenceDBPediaYAGO_hillary_vs_angela.conf 2008-04-25 09:28:21 UTC (rev 824)
@@ -14,10 +14,9 @@
//predefined filter (1 = YAGO based learning)
// 2 = SKOS, more Options are needed then though. replacePredicate, breakSuperClassRetrievalAfter
-sparql.predefinedFilter = 1;
+sparql.predefinedFilter = "YAGO";
+sparql.predefinedEndpoint = "DBPEDIA";
-sparql.predefinedEndpoint = 1;
-
// use DBpedia endpoint
import("http://dbpedia.openlinksw.com:8890/sparql","SPARQL");
Modified: trunk/examples/sparql/difference/DifferenceDBPediaYAGO_hillary_vs_angela_ignoredConcepts.conf
===================================================================
--- trunk/examples/sparql/difference/DifferenceDBPediaYAGO_hillary_vs_angela_ignoredConcepts.conf 2008-04-25 09:28:05 UTC (rev 823)
+++ trunk/examples/sparql/difference/DifferenceDBPediaYAGO_hillary_vs_angela_ignoredConcepts.conf 2008-04-25 09:28:21 UTC (rev 824)
@@ -53,11 +53,10 @@
//predefined filter (1 = YAGO based learning)
// 2 = SKOS, more Options are needed then though. replacePredicate, breakSuperClassRetrievalAfter
-sparql.predefinedFilter = 1;
+sparql.predefinedFilter = "YAGO";
+sparql.predefinedEndpoint = "DBPEDIA";
-sparql.predefinedEndpoint = 1;
-
// use DBpedia endpoint
import("http://dbpedia.openlinksw.com:8890/sparql","SPARQL");
Modified: trunk/examples/sparql/hierarchy/Hierarchy0DBPediaYAGOChanBrit_monarch.conf
===================================================================
--- trunk/examples/sparql/hierarchy/Hierarchy0DBPediaYAGOChanBrit_monarch.conf 2008-04-25 09:28:05 UTC (rev 823)
+++ trunk/examples/sparql/hierarchy/Hierarchy0DBPediaYAGOChanBrit_monarch.conf 2008-04-25 09:28:21 UTC (rev 824)
@@ -31,10 +31,9 @@
//predefined filter (1 = YAGO based learning)
// 2 = SKOS, more Options are needed then though. replacePredicate, breakSuperClassRetrievalAfter
-sparql.predefinedFilter = 1;
+sparql.predefinedFilter = "YAGO";
+sparql.predefinedEndpoint = "DBPEDIA";
-sparql.predefinedEndpoint = 1;
-
import("http://dbpedia.openlinksw.com:8890/sparql","SPARQL");
sparql.instances={"http://dbpedia.org/resource/Tony_Blair"
Modified: trunk/examples/sparql/hierarchy/Hierarchy1DBPediaYAGOChanBrit_pred_Knight.conf
===================================================================
--- trunk/examples/sparql/hierarchy/Hierarchy1DBPediaYAGOChanBrit_pred_Knight.conf 2008-04-25 09:28:05 UTC (rev 823)
+++ trunk/examples/sparql/hierarchy/Hierarchy1DBPediaYAGOChanBrit_pred_Knight.conf 2008-04-25 09:28:21 UTC (rev 824)
@@ -22,9 +22,9 @@
//predefined filter (1 = YAGO based learning)
// 2 = SKOS, more Options are needed then though. replacePredicate, breakSuperClassRetrievalAfter
-sparql.predefinedFilter = 1;
+sparql.predefinedFilter = "YAGO";
+sparql.predefinedEndpoint = "DBPEDIA";
-sparql.predefinedEndpoint = 1;
import("http://dbpedia.openlinksw.com:8890/sparql","SPARQL");
sparql.instances = {
Modified: trunk/examples/sparql/navigation/Navigation0DBPediaYAGOAristotle.conf
===================================================================
--- trunk/examples/sparql/navigation/Navigation0DBPediaYAGOAristotle.conf 2008-04-25 09:28:05 UTC (rev 823)
+++ trunk/examples/sparql/navigation/Navigation0DBPediaYAGOAristotle.conf 2008-04-25 09:28:21 UTC (rev 824)
@@ -26,11 +26,10 @@
//predefined filter (1 = YAGO based learning)
// 2 = SKOS, more Options are needed then though. replacePredicate, breakSuperClassRetrievalAfter
-sparql.predefinedFilter = 1;
+sparql.predefinedFilter = "YAGO";
+sparql.predefinedEndpoint = "DBPEDIA";
-sparql.predefinedEndpoint = 1;
-
import("http://dbpedia.openlinksw.com:8890/sparql","SPARQL");
sparql.instances = {
Modified: trunk/examples/sparql/navigation/Navigation1DBPediaYAGOAristotle.conf
===================================================================
--- trunk/examples/sparql/navigation/Navigation1DBPediaYAGOAristotle.conf 2008-04-25 09:28:05 UTC (rev 823)
+++ trunk/examples/sparql/navigation/Navigation1DBPediaYAGOAristotle.conf 2008-04-25 09:28:21 UTC (rev 824)
@@ -25,10 +25,9 @@
//predefined filter (1 = YAGO based learning)
// 2 = SKOS, more Options are needed then though. replacePredicate, breakSuperClassRetrievalAfter
-sparql.predefinedFilter = 1;
+sparql.predefinedFilter = "YAGO";
+sparql.predefinedEndpoint = "DBPEDIA";
-sparql.predefinedEndpoint = 1;
-
import("http://dbpedia.openlinksw.com:8890/sparql","SPARQL");
sparql.instances = {
Modified: trunk/examples/sparql/navigation/Navigation2DBPediaYAGOAristotle.conf
===================================================================
--- trunk/examples/sparql/navigation/Navigation2DBPediaYAGOAristotle.conf 2008-04-25 09:28:05 UTC (rev 823)
+++ trunk/examples/sparql/navigation/Navigation2DBPediaYAGOAristotle.conf 2008-04-25 09:28:21 UTC (rev 824)
@@ -14,11 +14,10 @@
//predefined filter (1 = YAGO based learning)
// 2 = SKOS, more Options are needed then though. replacePredicate, breakSuperClassRetrievalAfter
-sparql.predefinedFilter = 1;
+sparql.predefinedFilter = "YAGO";
+sparql.predefinedEndpoint = "DBPEDIA";
-sparql.predefinedEndpoint = 1;
-
import("http://dbpedia.openlinksw.com:8890/sparql","SPARQL");
sparql.instances = {
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ku...@us...> - 2008-04-25 09:28:13
|
Revision: 823
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=823&view=rev
Author: kurzum
Date: 2008-04-25 02:28:05 -0700 (Fri, 25 Apr 2008)
Log Message:
-----------
some changes mostly options and output
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java
trunk/src/dl-learner/org/dllearner/kb/sparql/Cache.java
trunk/src/dl-learner/org/dllearner/kb/sparql/ExtractionAlgorithm.java
trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlKnowledgeSource.java
trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQuery.java
trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQueryDescriptionConvertVisitor.java
trunk/src/dl-learner/org/dllearner/kb/sparql/TypedSparqlQuery.java
trunk/src/dl-learner/org/dllearner/kb/sparql/TypedSparqlQueryClasses.java
trunk/src/dl-learner/org/dllearner/kb/sparql/configuration/SparqlEndpoint.java
trunk/src/dl-learner/org/dllearner/kb/sparql/configuration/SparqlQueryType.java
trunk/src/dl-learner/org/dllearner/scripts/SPARQLMassLearning.java
trunk/src/dl-learner/org/dllearner/test/SparqlExtractionTest.java
trunk/src/dl-learner/org/dllearner/utilities/AutomaticExampleFinderSPARQL.java
trunk/src/dl-learner/org/dllearner/utilities/ConfWriter.java
trunk/src/dl-learner/org/dllearner/utilities/JenaResultSetConvenience.java
trunk/src/dl-learner/org/dllearner/utilities/SimpleClock.java
Added Paths:
-----------
trunk/src/dl-learner/org/dllearner/test/SparqlEndpointTest.java
Modified: trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java 2008-04-24 17:39:36 UTC (rev 822)
+++ trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java 2008-04-25 09:28:05 UTC (rev 823)
@@ -777,7 +777,7 @@
// searchTree += bestNodeString + "\n";
logger.debug(bestNodeString);
- logger.trace(startNode.getStats(nrOfPositiveExamples, nrOfNegativeExamples));
+ logger.trace(bestNode.getStats(nrOfPositiveExamples, nrOfNegativeExamples));
logger.debug(bestNodeStringKBSyntax);
if(bestNode.getCoveredNegatives().size()<=5)logger.trace("covered negs: "+bestNode.getCoveredNegatives());
String expandedNodeString = "next expanded node: " + candidates.last().getShortDescription(nrOfPositiveExamples, nrOfNegativeExamples, baseURI);
@@ -1035,10 +1035,10 @@
return ;
i++;
}
- for (int j = 0; j < solutions.size(); j++) {
+ /*for (int j = 0; j < solutions.size(); j++) {
Description d = solutions.get(j);
logger.trace(d.toString());
- }
+ }*/
}
Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/Cache.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/Cache.java 2008-04-24 17:39:36 UTC (rev 822)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/Cache.java 2008-04-25 09:28:05 UTC (rev 823)
@@ -220,6 +220,7 @@
public String executeSparqlQuery(SparqlQuery query) {
String result = getCacheEntry(query.getQueryString());
if (result != null) {
+ logger.trace("got from cache");
return result;
} else {
query.send();
Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/ExtractionAlgorithm.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/ExtractionAlgorithm.java 2008-04-24 17:39:36 UTC (rev 822)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/ExtractionAlgorithm.java 2008-04-25 09:28:05 UTC (rev 823)
@@ -106,10 +106,11 @@
}
HashSet<String> hadAlready = new HashSet<String>();
- logger.info("Get all superclasses");
+
//p(configuration.toString());
// gets All Class Nodes and expands them further
if (this.configuration.isGetAllSuperClasses()) {
+ logger.info("Get all superclasses");
// Set<Node> classes = new TreeSet<Node>();
Vector<Node> classes = new Vector<Node>();
Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlKnowledgeSource.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlKnowledgeSource.java 2008-04-24 17:39:36 UTC (rev 822)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlKnowledgeSource.java 2008-04-25 09:28:05 UTC (rev 823)
@@ -60,14 +60,17 @@
*/
public class SparqlKnowledgeSource extends KnowledgeSource {
+ //DEFAULTS
+ static int recursionDepthDefault = 1;
+
// ConfigOptions
public URL url;
// String host;
private Set<String> instances = new HashSet<String>();;
private URL dumpFile;
- private int recursionDepth = 1;
- private int predefinedFilter = 0;
- private int predefinedEndpoint = 0;
+ private int recursionDepth = recursionDepthDefault;
+ private String predefinedFilter = null;
+ private String predefinedEndpoint = null;
private Set<String> predList = new HashSet<String>();
private Set<String> objList = new HashSet<String>();
// private Set<String> classList;
@@ -123,11 +126,11 @@
.add(new StringSetConfigOption("instances",
"relevant instances e.g. positive and negative examples in a learning problem"));
options.add(new IntegerConfigOption("recursionDepth",
- "recursion depth of KB fragment selection", 2));
- options.add(new IntegerConfigOption("predefinedFilter",
- "the mode of the SPARQL Filter"));
- options.add(new IntegerConfigOption("predefinedEndpoint",
- "the mode of the SPARQL Filter"));
+ "recursion depth of KB fragment selection", recursionDepthDefault));
+ options.add(new StringConfigOption("predefinedFilter",
+ "the mode of the SPARQL Filter, use one of YAGO,SKOS,YAGOSKOS , YAGOSPECIALHIERARCHY, TEST"));
+ options.add(new StringConfigOption("predefinedEndpoint",
+ "the mode of the SPARQL Filter, use one of DBPEDIA, LOCAL, GOVTRACK, REVYU, MYOPENLINK, FACTBOOK"));
options.add(new StringSetConfigOption("predList",
"list of all ignored roles"));
@@ -207,9 +210,9 @@
// } else if (option.equals("classList")) {
// classList = (Set<String>) entry.getValue();
} else if (option.equals("predefinedEndpoint")) {
- predefinedEndpoint = (Integer) entry.getValue();
+ predefinedEndpoint = ((String) entry.getValue()).toUpperCase();
} else if (option.equals("predefinedFilter")) {
- predefinedFilter = (Integer) entry.getValue();
+ predefinedFilter = ((String) entry.getValue()).toUpperCase();
} else if (option.equals("format")) {
format = (String) entry.getValue();
} else if (option.equals("dumpToFile")) {
@@ -285,8 +288,9 @@
breakSuperClassRetrievalAfter, replacePredicate, replaceObject);
// get Options for endpoints
- if (predefinedEndpoint >= 1) {
- endpoint = SparqlEndpoint.getEndpointByNumber(predefinedEndpoint);
+ if (predefinedEndpoint != null) {
+ //endpoint = SparqlEndpoint.getEndpointByNumber(predefinedEndpoint);
+ endpoint = SparqlEndpoint.getEndpointByName(predefinedEndpoint);
} else {
// TODO this is not optimal, because not all options are used
// like default-graph uri
@@ -295,9 +299,9 @@
// get Options for Filters
- if (predefinedFilter >= 1) {
+ if (predefinedFilter != null) {
sparqlQueryType = SparqlQueryType
- .getFilterByNumber(predefinedFilter);
+ .getFilterByName(predefinedFilter);
} else {
sparqlQueryType = new SparqlQueryType("forbid", objList, predList,
Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQuery.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQuery.java 2008-04-24 17:39:36 UTC (rev 822)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQuery.java 2008-04-25 09:28:05 UTC (rev 823)
@@ -43,6 +43,7 @@
private static Logger logger = Logger.getLogger(SparqlKnowledgeSource.class);
+ public String extraDebugInfo = "";
private boolean isRunning = false;
private String queryString;
private QueryEngineHTTP queryExecution;
@@ -65,6 +66,7 @@
* Sends a SPARQL query using the Jena library.
*/
public ResultSet send() {
+
isRunning = true;
ResultSet rs=null;
logger.trace(queryString);
@@ -84,7 +86,8 @@
//TODO remove after overnext Jena release
HttpQuery.urlLimit = 3*1024 ;
rs = queryExecution.execSelect();
- logger.debug("query SPARQL server, retrieved: "+rs.getResultVars());
+
+ logger.debug("query SPARQL server ["+extraDebugInfo+"], retrieved: "+rs.getResultVars());
json=SparqlQuery.getAsJSON(rs);
logger.trace(rs.getResultVars().toString());
Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQueryDescriptionConvertVisitor.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQueryDescriptionConvertVisitor.java 2008-04-24 17:39:36 UTC (rev 822)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQueryDescriptionConvertVisitor.java 2008-04-25 09:28:05 UTC (rev 823)
@@ -38,6 +38,10 @@
*
*/
public class SparqlQueryDescriptionConvertVisitor implements DescriptionVisitor{
+
+ //private SparqlEndpoint se = null;
+ //private boolean RDFSReasoning = false;
+
private static Logger logger = Logger.getLogger(ComponentManager.class);
@@ -53,6 +57,13 @@
stack.push("subject");
}
+ /*public SparqlQueryDescriptionConvertVisitor(SparqlEndpoint se, boolean RDFSReasoning)
+ {
+ stack.push("subject");
+ this.se = se;
+ this.RDFSReasoning = RDFSReasoning;
+ }*/
+
public String getSparqlQuery()
{
query="SELECT ?subject\nWHERE {"+query;
@@ -69,6 +80,15 @@
return query;
}
+ public static String getSparqlSubclassQuery(String description)
+ { String ret = "SELECT ?subject \n";
+ ret+= "WHERE {\n";
+ ret+=" ?subject <http://www.w3.org/2000/01/rdf-schema#subClassOf> <"+description+"> \n";
+ ret+="}\n";
+
+ return ret;
+ }
+
public static String getSparqlQuery(String description) throws ParseException
{
Description d = KBParser.parseConcept(description);
@@ -85,6 +105,22 @@
return visitor.getSparqlQuery(limit);
}
+ /**
+ * includes subclasses, costly function, because subclasses habe to be recieved first.
+ * @param description
+ * @param limit
+ * @param se
+ * @return
+ * @throws ParseException
+ */
+ /*public static String getSparqlQueryIncludingSubclasses(String description, int limit, SparqlEndpoint se) throws ParseException
+ { if(limit==0)limit=99999;
+ Description d = KBParser.parseConcept(description);
+ SparqlQueryDescriptionConvertVisitor visitor=new SparqlQueryDescriptionConvertVisitor(se, true);
+ d.accept(visitor);
+ return visitor.getSparqlQuery(limit);
+ }*/
+
public static String getSparqlQuery(Description description)
{
SparqlQueryDescriptionConvertVisitor visitor=new SparqlQueryDescriptionConvertVisitor();
@@ -235,9 +271,12 @@
* @see org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl.NamedClass)
*/
public void visit(NamedClass description) {
+
logger.trace("NamedClass");
query+="?"+stack.peek()+" a <"+description.getName()+">";
}
+
+
/* (non-Javadoc)
* @see org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.algorithms.gp.ADC)
Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/TypedSparqlQuery.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/TypedSparqlQuery.java 2008-04-24 17:39:36 UTC (rev 822)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/TypedSparqlQuery.java 2008-04-25 09:28:05 UTC (rev 823)
@@ -87,6 +87,7 @@
// .getSparqlEndpoint(), cache, uri.toString(), sparqlQueryString);
SparqlQuery query = new SparqlQuery(sparqlQueryString, configuration.getSparqlEndpoint());
+ query.extraDebugInfo=uri.toString();
ResultSet rs = SparqlQuery.JSONtoResultSet(cache.executeSparqlQuery(query));
List<ResultBinding> l = ResultSetFormatter.toList(rs);
Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/TypedSparqlQueryClasses.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/TypedSparqlQueryClasses.java 2008-04-24 17:39:36 UTC (rev 822)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/TypedSparqlQueryClasses.java 2008-04-25 09:28:05 UTC (rev 823)
@@ -64,6 +64,7 @@
+ "}";
SparqlQuery query = new SparqlQuery(sparqlQueryString, configuration.getSparqlEndpoint());
+ query.extraDebugInfo=uri.toString();
ResultSet rs = SparqlQuery.JSONtoResultSet(cache.executeSparqlQuery(query));
List<ResultBinding> l = ResultSetFormatter.toList(rs);
Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/configuration/SparqlEndpoint.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/configuration/SparqlEndpoint.java 2008-04-24 17:39:36 UTC (rev 822)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/configuration/SparqlEndpoint.java 2008-04-25 09:28:05 UTC (rev 823)
@@ -61,7 +61,7 @@
return namedGraphURIs;
}
- public static SparqlEndpoint getEndpointByNumber(int i) {
+ /*public static SparqlEndpoint getEndpointByNumber(int i) {
switch (i) {
case 0:break;
@@ -80,6 +80,25 @@
return worldFactBook();
}
return null;
+ }*/
+
+ public static SparqlEndpoint getEndpointByName(String name) {
+
+
+
+ if (name.equals("DBPEDIA"))
+ return dbpediaEndpoint();
+ if (name.equals("LOCALJOSECKI"))
+ return localJoseki();
+ if (name.equals("GOVTRACK"))
+ return govTrack();
+ if (name.equals("REVYU"))
+ return revyu();
+ if (name.equals("MYOPENLINK"))
+ return myopenlink();
+ if (name.equals("FACTBOOK"))
+ return worldFactBook();
+ return null;
}
public static SparqlEndpoint dbpediaEndpoint() {
Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/configuration/SparqlQueryType.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/configuration/SparqlQueryType.java 2008-04-24 17:39:36 UTC (rev 822)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/configuration/SparqlQueryType.java 2008-04-25 09:28:05 UTC (rev 823)
@@ -65,22 +65,20 @@
//System.out.println("added filter: "+filter);
}
- public static SparqlQueryType getFilterByNumber(int i) {
-
- switch (i) {
- case 0:break;
- //should not be filled
- case 1:
+ public static SparqlQueryType getFilterByName(String name) {
+
+
+ if (name.equals("YAGO"))
return YagoFilter();
- case 2:
+ if (name.equals("SKOS"))
return SKOS();
- case 3:
+ if (name.equals("YAGOSKOS"))
return YAGOSKOS();
- case 4:
+ if (name.equals("YAGOSPECIALHIERARCHY"))
return YagoSpecialHierarchy();
- case 5:
+ if (name.equals("TEST"))
return test();
- }
+
return null;
}
Modified: trunk/src/dl-learner/org/dllearner/scripts/SPARQLMassLearning.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/SPARQLMassLearning.java 2008-04-24 17:39:36 UTC (rev 822)
+++ trunk/src/dl-learner/org/dllearner/scripts/SPARQLMassLearning.java 2008-04-25 09:28:05 UTC (rev 823)
@@ -9,6 +9,8 @@
import org.apache.log4j.Logger;
import org.apache.log4j.SimpleLayout;
import org.dllearner.kb.sparql.Cache;
+import org.dllearner.kb.sparql.SparqlKnowledgeSource;
+import org.dllearner.kb.sparql.SparqlQuery;
import org.dllearner.kb.sparql.configuration.SparqlEndpoint;
import org.dllearner.utilities.AutomaticExampleFinderSPARQL;
import org.dllearner.utilities.ConfWriter;
@@ -26,32 +28,47 @@
init();
//vars
- boolean useRelated = true;
- boolean useSuperClasses = true;
- int poslimit = 10;
- int neglimit = 10;
+ boolean useRelated = false;
+ boolean useSuperClasses = false;
+ boolean useParallelClasses = true;
+ int poslimit = 15;
+ int neglimit = 200;
+
try {
-
- //System.out.println(logger.setLevel(TRACE));
+ //logger.setLevel(Level.TRACE);
+ Logger.getLogger(SparqlKnowledgeSource.class).setLevel(Level.TRACE);
+ System.out.println(Logger.getLogger(SparqlQuery.class).getLevel());
+
/*System.out.println(Level.DEBUG.getClass());
System.out.println(Level.toLevel("INFO"));
- System.out.println(Level.INFO);
- System.exit(0);*/
+ System.out.println(Level.INFO);*/
+ //System.exit(0);
SimpleClock sc=new SimpleClock();
+ //concepts.add("(EXISTS \"monarch\".TOP AND EXISTS \"predecessor\".(\"Knight\" OR \"Secretary\"))");
+
SortedSet<String> concepts = new TreeSet<String>();
+ //concepts.add("(\"http://dbpedia.org/class/yago/HeadOfState110164747\" AND (\"http://dbpedia.org/class/yago/Negotiator110351874\" AND \"http://dbpedia.org/class/yago/Representative110522035\"))");
//concepts.add("\"http://dbpedia.org/class/yago/Person100007846\"");
- //concepts.add("\"http://dbpedia.org/class/yago/FieldMarshal110086821\"");
- concepts.add("http://dbpedia.org/resource/Category:Prime_Ministers_of_the_United_Kingdom");
+ concepts.add("\"http://dbpedia.org/class/yago/FieldMarshal110086821\"");
+ //concepts.add("http://dbpedia.org/resource/Category:Prime_Ministers_of_the_United_Kingdom");
+ //concepts.add("http://dbpedia.org/resource/Category:Grammy_Award_winners");
+
SortedSet<String> posExamples = new TreeSet<String>();
SortedSet<String> negExamples = new TreeSet<String>();
String url = "http://dbpedia.openlinksw.com:8890/sparql";
//HashMap<String, ResultSet> result = new HashMap<String, ResultSet>();
//HashMap<String, String> result2 = new HashMap<String, String>();
+ //System.out.println(concepts.first());
+ //logger.setLevel(Level.TRACE);
+ AutomaticExampleFinderSPARQL ae= new AutomaticExampleFinderSPARQL( se);
+ //System.out.println(new JenaResultSetConvenience(ae.queryConcept(concepts.first(), 0)).getStringListForVariable("?subject") );;
+ //System.out.println(new JenaResultSetConvenience(ae.queryConcept(concepts.first(), 0)).getStringListForVariable("?subject").size() );;
+ //ae.getSubClasses(concepts.first());
+ //System.exit(0);
- AutomaticExampleFinderSPARQL ae= new AutomaticExampleFinderSPARQL( se);
- ae.init(concepts.first(), useRelated, useSuperClasses, poslimit, neglimit);
+ ae.init(concepts.first(), useRelated, useSuperClasses,useParallelClasses, poslimit, neglimit);
posExamples = ae.getPosExamples();
negExamples = ae.getNegExamples();
@@ -59,13 +76,14 @@
System.out.println(posExamples);
System.out.println(negExamples);
//System.exit(0);
- String concept = concepts.first().replace("http://dbpedia.org/resource/Category:", "");
- concept = concept.replace("http://dbpedia.org/class/yago/", "");
- String confname = URLEncoder.encode(concept, "UTF-8")+".conf";
+ String tmp = concepts.first().replace("http://dbpedia.org/resource/Category:", "").replace("\"","");
+ tmp = tmp.replace("http://dbpedia.org/class/yago/", "");
+ String confname = URLEncoder.encode(tmp, "UTF-8")+".conf";
//
ConfWriter cf=new ConfWriter();
cf.addToStats("relearned concept: "+concepts.first());
+ //System.exit(0);
//"relearned concept: ";
cf.writeSPARQL(confname, posExamples, negExamples, url, new TreeSet<String>());
//new LearnSparql().learn(posExamples, negExamples, "http://dbpedia.openlinksw.com:8890/sparql", new TreeSet<String>());
Added: trunk/src/dl-learner/org/dllearner/test/SparqlEndpointTest.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/test/SparqlEndpointTest.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/test/SparqlEndpointTest.java 2008-04-25 09:28:05 UTC (rev 823)
@@ -0,0 +1,85 @@
+package org.dllearner.test;
+
+import java.util.HashSet;
+import java.util.Set;
+
+import org.apache.log4j.ConsoleAppender;
+import org.apache.log4j.Level;
+import org.apache.log4j.Logger;
+import org.apache.log4j.SimpleLayout;
+import org.dllearner.kb.sparql.SparqlKnowledgeSource;
+import org.dllearner.kb.sparql.SparqlQuery;
+import org.dllearner.kb.sparql.configuration.SparqlEndpoint;
+import org.dllearner.utilities.JenaResultSetConvenience;
+import org.dllearner.utilities.SimpleClock;
+
+import com.hp.hpl.jena.query.ResultSet;
+
+public class SparqlEndpointTest {
+ private static Logger logger = Logger.getRootLogger();
+ static Set<String> working = new HashSet<String>();
+ static Set<String> notworking = new HashSet<String>();
+
+ public static void main(String[] args) {
+ SimpleLayout layout = new SimpleLayout();
+ ConsoleAppender consoleAppender = new ConsoleAppender(layout);
+ logger.removeAllAppenders();
+ logger.addAppender(consoleAppender);
+ logger.setLevel(Level.DEBUG);
+ Logger.getLogger(SparqlKnowledgeSource.class).setLevel(Level.INFO);
+
+
+
+ Set<SparqlEndpoint> set = new HashSet<SparqlEndpoint>();
+ set.add(SparqlEndpoint.dbpediaEndpoint());
+ set.add(SparqlEndpoint.govTrack());
+ set.add(SparqlEndpoint.localJoseki());
+ set.add(SparqlEndpoint.myopenlink());
+ set.add(SparqlEndpoint.worldFactBook());
+ set.add(SparqlEndpoint.revyu());
+
+
+ int i=1;
+ for (SparqlEndpoint sparqlEndpoint : set) {
+ testEndPoint(sparqlEndpoint);
+ logger.info("finished "+i+" of "+set.size());
+ i++;
+ }
+ logger.info("**************");
+ for (String str : working) {
+ logger.info(str);
+ }
+ for (String str : notworking) {
+ logger.info(str);
+
+ }
+ //set.add(SparqlEndpoint.);
+
+ }
+
+
+ public static void testEndPoint(SparqlEndpoint se) {
+ SimpleClock sc = new SimpleClock();
+ try{
+
+ String query ="" +
+ "SELECT DISTINCT ?c " +
+ "WHERE {[] a ?c }" +
+ "LIMIT 100";
+
+ query ="SELECT DISTINCT ?c WHERE {[] a ?c }LIMIT 100";
+
+ SparqlQuery s = new SparqlQuery(query,se);
+
+ s.send();
+ String result = s.getResult();
+ ResultSet rs = SparqlQuery.JSONtoResultSet(result);
+
+ JenaResultSetConvenience jsr = new JenaResultSetConvenience(rs);
+ int i = jsr.getStringListForVariable("c").size();
+
+ working.add(sc.getAndSet("endpoint working: "+se.getURL()+" ("+((i==100)?"more than 100 concepts":"about "+i+" concepts")+" )"));
+ }catch (Exception e) {notworking.add(sc.getAndSet("endpoint NOT working: "+se.getURL()));}
+ }
+
+}
Modified: trunk/src/dl-learner/org/dllearner/test/SparqlExtractionTest.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/test/SparqlExtractionTest.java 2008-04-24 17:39:36 UTC (rev 822)
+++ trunk/src/dl-learner/org/dllearner/test/SparqlExtractionTest.java 2008-04-25 09:28:05 UTC (rev 823)
@@ -49,7 +49,7 @@
URI u2 = new URI("http://dbpedia.org/resource/Angela_Merkel");
m.useConfiguration(
- SparqlQueryType.getFilterByNumber(1),SparqlEndpoint.getEndpointByNumber(1),
+ SparqlQueryType.getFilterByName("DBPEDIA"),SparqlEndpoint.getEndpointByName("YAGO"),
new Manipulator("",200,new LinkedList<StringTuple>(),new LinkedList<StringTuple>()),
1,true,true);
//, ,
Modified: trunk/src/dl-learner/org/dllearner/utilities/AutomaticExampleFinderSPARQL.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/AutomaticExampleFinderSPARQL.java 2008-04-24 17:39:36 UTC (rev 822)
+++ trunk/src/dl-learner/org/dllearner/utilities/AutomaticExampleFinderSPARQL.java 2008-04-25 09:28:05 UTC (rev 823)
@@ -30,11 +30,12 @@
negExamples = new TreeSet<String>();
}
- public void init(String concept, boolean useRelated, boolean useSuperclasses, int poslimit, int neglimit) {
+ public void init(String concept, boolean useRelated, boolean useSuperclasses,boolean useParallelClasses, int poslimit, int neglimit) {
makePositiveExamplesFromConcept( concept);
SortedSet<String> keepForClean = new TreeSet<String>();
keepForClean.addAll(this.posExamples);
this.posExamples = SetManipulation.fuzzyShrink(this.posExamples, poslimit);
+ logger.trace("shrinking: pos Example size: "+posExamples.size());
if(useRelated) {
dbpediaMakeNegativeExamplesFromRelatedInstances(this.posExamples);
@@ -42,10 +43,16 @@
if(useSuperclasses) {
dbpediaMakeNegativeExamplesFromSuperClasses(concept);
}
+ if(useParallelClasses) {
+ dbpediaMakeNegativeExamplesFromClassesOfInstances();
+ }
//clean
negExamples.removeAll(keepForClean);
+ logger.trace("neg Example size after cleaning: "+negExamples.size());
this.negExamples = SetManipulation.fuzzyShrink(negExamples, neglimit);
- logger.debug("Finished examples for concept :"+concept);
+ logger.debug("pos Example size after shrinking: "+posExamples.size());
+ logger.debug("neg Example size after shrinking: "+negExamples.size());
+ logger.debug("Finished examples for concept: "+concept);
}
public SortedSet<String> getPosOnly(String concept, int limit){
@@ -54,6 +61,7 @@
}
private void makePositiveExamplesFromConcept(String concept){
+ logger.debug("making Positive Examples from Concept: "+concept);
if(concept.contains("http://dbpedia.org/resource/Category:")) {
this.posExamples = new JenaResultSetConvenience(querySKOSConcept(concept,0))
.getStringListForVariable("subject");
@@ -61,6 +69,7 @@
this.posExamples = new JenaResultSetConvenience(queryConcept(concept,0))
.getStringListForVariable("subject");
}
+ logger.debug(" pos Example size: "+posExamples.size());
}
@@ -68,9 +77,11 @@
private void dbpediaMakeNegativeExamplesFromRelatedInstances(SortedSet<String> subject) {
+ logger.debug("making examples from related instances");
for (String string : subject) {
dbpediaMakeNegativeExamplesFromRelatedInstances(string);
}
+ logger.debug(" negExample size: "+negExamples.size());
}
@@ -92,6 +103,7 @@
JenaResultSetConvenience rsc = new JenaResultSetConvenience(rs);
this.negExamples.addAll(rsc.getStringListForVariable("o"));
+
}
@@ -101,14 +113,42 @@
superClasses.add(concept.replace("\"", ""));
//logger.debug("before"+superClasses);
superClasses = dbpediaGetSuperClasses( superClasses, 4);
- logger.debug("getting negExamples from "+superClasses.size()+" superclasses");
+ logger.debug("making neg Examples from "+superClasses.size()+" superclasses");
JenaResultSetConvenience rsc;
for (String oneSuperClass : superClasses) {
rsc = new JenaResultSetConvenience(queryConcept("\""+oneSuperClass+"\"", 0));
this.negExamples.addAll(rsc.getStringListForVariable("subject"));
}
+ logger.debug(" neg Example size: "+negExamples.size());
}
+
+ private void dbpediaMakeNegativeExamplesFromClassesOfInstances() {
+ logger.debug("making neg Examples from parallel classes");
+ SortedSet<String> classes = new TreeSet<String>();
+ //superClasses.add(concept.replace("\"", ""));
+ //logger.debug("before"+superClasses);
+ //superClasses = dbpediaGetSuperClasses( superClasses, 4);
+ //logger.debug("getting negExamples from "+superClasses.size()+" superclasses");
+ JenaResultSetConvenience rsc;
+ ResultSet rs=null;
+ for (String instance : posExamples) {
+ //System.out.println(instance);
+ rs = getClassesForInstance(instance);
+ //System.out.println(ResultSetFormatter.asXMLString(rs));
+ rsc = new JenaResultSetConvenience(rs);
+ classes.addAll(rsc.getStringListForVariable("subject"));
+ //System.out.println(classes);
+ }
+ logger.debug("getting negExamples from "+classes.size()+" parallel classes");
+ for (String oneClass : classes) {
+
+ rsc = new JenaResultSetConvenience(queryConcept("\""+oneClass+"\"",0));
+ this.negExamples.addAll(rsc.getStringListForVariable("subject"));
+ }
+ logger.debug("neg Example size: "+negExamples.size());
+
+ }
private SortedSet<String> dbpediaGetSuperClasses(SortedSet<String> superClasses, int depth) {
SortedSet<String> ret = new TreeSet<String>();
@@ -181,7 +221,30 @@
return rs;
}
+
+ public ResultSet getClassesForInstance(String instance) {
+ ResultSet rs = null;
+ try {
+
+ String query = "SELECT ?subject WHERE { \n " +
+ "<" + instance + ">"+
+ " a " +
+ "?subject " +
+ "\n" +
+ "}";
+ SparqlQuery sq = new SparqlQuery(query, se);
+ //System.out.println(query);
+ String JSON = c.executeSparqlQuery(sq);
+ //System.out.println(JSON);
+ rs = SparqlQuery.JSONtoResultSet(JSON);
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ return rs;
+ }
+
public SortedSet<String> getPosExamples() {
return posExamples;
}
@@ -191,5 +254,41 @@
}
+ /**
+ * NOT WORKING
+ * @param description
+ */
+ public void getSubClasses(String description) {
+ ResultSet rs = null;
+ try {
+ String query = SparqlQueryDescriptionConvertVisitor
+ .getSparqlSubclassQuery(description.replace("\"", ""));
+
+ rs = new SparqlQuery(query, se).send();
+ System.out.println(query);
+ //System.out.println(SparqlQuery.getAsXMLString(rs));
+ System.out.println(rs.getResultVars());
+ SortedSet<String> remainingClasses = new JenaResultSetConvenience(rs).getStringListForVariable("subject");
+ SortedSet<String> alreadyQueried = new TreeSet<String>();
+ alreadyQueried.add(description);
+ while (remainingClasses.size()!=0){
+ String tmp = remainingClasses.first();
+ remainingClasses.remove(tmp);
+ query = SparqlQueryDescriptionConvertVisitor
+ .getSparqlSubclassQuery(tmp);
+ alreadyQueried.add(tmp);
+ rs = new SparqlQuery(query, se).send();
+ remainingClasses.addAll(new JenaResultSetConvenience(rs).getStringListForVariable("subject"));
+ }
+ //System.out.println(JSON);
+ System.out.println(alreadyQueried);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ }
+
+
}
Modified: trunk/src/dl-learner/org/dllearner/utilities/ConfWriter.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/ConfWriter.java 2008-04-24 17:39:36 UTC (rev 822)
+++ trunk/src/dl-learner/org/dllearner/utilities/ConfWriter.java 2008-04-25 09:28:05 UTC (rev 823)
@@ -50,11 +50,15 @@
String standardSettings =
"sparql.recursionDepth = 1;\n" +
- "sparql.predefinedFilter = 1;\n" +
- "sparql.predefinedEndpoint = 1;\n" +
- "refexamples.minExecutionTimeInSeconds = 10;\n" +
- "refexamples.maxExecutionTimeInSeconds = 10;\n" +
- "refexamples.logLevel=\"TRACE\";\n" ;
+ "sparql.predefinedFilter = \"YAGO\";\n" +
+ "sparql.predefinedEndpoint = \"DBPEDIA\";\n" +
+ "refexamples.minExecutionTimeInSeconds = 30;\n" +
+ "refexamples.maxExecutionTimeInSeconds = 30;\n" +
+ "refexamples.logLevel=\"TRACE\";\n" +
+ "refexamples.noisePercentage = 0.10;\n" +
+ "refexamples.writeSearchTree = true;\n" +
+ "refexamples.searchTreeFile = \"searchTree.txt\";\n"+
+ "refexamples.replaceSearchTree = true;\n\n" ;
// "sparql.format = \"KB\";\n\n";
Modified: trunk/src/dl-learner/org/dllearner/utilities/JenaResultSetConvenience.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/JenaResultSetConvenience.java 2008-04-24 17:39:36 UTC (rev 822)
+++ trunk/src/dl-learner/org/dllearner/utilities/JenaResultSetConvenience.java 2008-04-25 09:28:05 UTC (rev 823)
@@ -20,6 +20,7 @@
public SortedSet<String> getStringListForVariable(String var){
SortedSet<String> result = new TreeSet<String>();
+ //String s=ResultSetFormatter.asXMLString(this.rs);
List<ResultBinding> l = ResultSetFormatter.toList(this.rs);
for (ResultBinding resultBinding : l) {
Modified: trunk/src/dl-learner/org/dllearner/utilities/SimpleClock.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/SimpleClock.java 2008-04-24 17:39:36 UTC (rev 822)
+++ trunk/src/dl-learner/org/dllearner/utilities/SimpleClock.java 2008-04-25 09:28:05 UTC (rev 823)
@@ -37,7 +37,15 @@
time=now;
}
+ public String getAndSet(String s) {
+ long now=System.currentTimeMillis();
+ String ret = s+" needed "+(now-time)+" ms";
+ time=now;
+ return ret;
+
+ }
+
/**
* prints time needed
*
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ton...@us...> - 2008-04-24 17:39:48
|
Revision: 822
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=822&view=rev
Author: tonytacker
Date: 2008-04-24 10:39:36 -0700 (Thu, 24 Apr 2008)
Log Message:
-----------
removed a warning
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/gui/RunPanel.java
Modified: trunk/src/dl-learner/org/dllearner/gui/RunPanel.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/gui/RunPanel.java 2008-04-24 08:43:22 UTC (rev 821)
+++ trunk/src/dl-learner/org/dllearner/gui/RunPanel.java 2008-04-24 17:39:36 UTC (rev 822)
@@ -39,7 +39,7 @@
private JButton runButton, stopButton, treeButton;
private JTextArea infoArea;
private Config config;
- private StartGUI startGUI;
+ //private StartGUI startGUI;
private ThreadRun thread;
@@ -65,7 +65,7 @@
super(new BorderLayout());
this.config = config;
- this.startGUI = startGUI;
+ //this.startGUI = startGUI;
runButton = new JButton("Run");
runButton.addActionListener(this);
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ku...@us...> - 2008-04-24 08:43:39
|
Revision: 821
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=821&view=rev
Author: kurzum
Date: 2008-04-24 01:43:22 -0700 (Thu, 24 Apr 2008)
Log Message:
-----------
small changes
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java
trunk/src/dl-learner/org/dllearner/algorithms/refinement/ROLearner.java
trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQuery.java
trunk/src/dl-learner/org/dllearner/scripts/SPARQLMassLearning.java
trunk/src/dl-learner/org/dllearner/utilities/AutomaticExampleFinderSPARQL.java
trunk/src/dl-learner/org/dllearner/utilities/ConfWriter.java
Modified: trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java 2008-04-23 12:42:53 UTC (rev 820)
+++ trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java 2008-04-24 08:43:22 UTC (rev 821)
@@ -394,10 +394,8 @@
Files.appendFile(searchTreeFile, treeString);
}
+ handleStoppingConditions();
- if(maxExecutionTimeReached()) { stop=true;}
- solutionFound = (guaranteeXgoodDescriptions() );
- solutionFound = (minExecutionTimeReached()&& solutionFound);
//logger.info(minExecutionTimeReached()+"aaaaaaa "+solutions.size()+"::"+guaranteeXgoodDescriptions);
//logger.info(solutionFound+"aaaaaaa "+stop);
@@ -1055,10 +1053,19 @@
return startNode;
}
+ private void handleStoppingConditions(){
+ solutionFound = (guaranteeXgoodDescriptions() );
+ solutionFound = (minExecutionTimeReached()&& solutionFound);
+ if(maxExecutionTimeReached()) {
+ stop();
+ if(solutions.size()>0)solutionFound = true;
+ }
+ }
+
private boolean guaranteeXgoodDescriptions(){
if(guaranteeXgoodShown)return true;
if(solutions.size()>guaranteeXgoodDescriptions){
- logger.info("Minimum number of good descriptions reached, stopping now...");
+ logger.info("Minimum number ("+guaranteeXgoodDescriptions+") of good descriptions reached, stopping now...");
guaranteeXgoodShown=true;
return true;}
else return false;
@@ -1072,7 +1079,7 @@
long needed = System.currentTimeMillis()- this.runtime;
long maxMilliSeconds = maxExecutionTimeInSeconds *1000 ;
if(maxMilliSeconds<needed){
- logger.info("Maximum time reached, stopping now...");
+ logger.info("Maximum time ("+maxExecutionTimeInSeconds+" seconds) reached, stopping now...");
maxExecutionTimeShown=true;
return true;}
else return false;
@@ -1088,7 +1095,7 @@
long needed = System.currentTimeMillis()- this.runtime;
long minMilliSeconds = minExecutionTimeInSeconds *1000 ;
if(minMilliSeconds<needed){
- logger.info("Minimum time reached, stopping when next solution is found");
+ logger.info("Minimum time ("+minExecutionTimeInSeconds+" seconds) reached, stopping when next solution is found");
minExecutionTimeShown=true;
return true;}
else return false;
Modified: trunk/src/dl-learner/org/dllearner/algorithms/refinement/ROLearner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/refinement/ROLearner.java 2008-04-23 12:42:53 UTC (rev 820)
+++ trunk/src/dl-learner/org/dllearner/algorithms/refinement/ROLearner.java 2008-04-24 08:43:22 UTC (rev 821)
@@ -72,6 +72,7 @@
private boolean useAllConstructor = CommonConfigOptions.useAllConstructorDefault;
private boolean useExistsConstructor = CommonConfigOptions.useExistsConstructorDefault;
//this was added so you can switch algorithm without removing everything not applicable
+ @SuppressWarnings("unused")
private boolean useCardinalityRestrictions = CommonConfigOptions.useCardinalityRestrictionsDefault;
private boolean useNegation = CommonConfigOptions.useNegationDefault;
//TODO different standard options to CommonConfigOptions
@@ -81,11 +82,11 @@
//extended Options
private int maxExecutionTimeInSeconds = CommonConfigOptions.maxExecutionTimeInSecondsDefault;
- private boolean maxExecutionTimeShown=false;
+ private boolean maxExecutionTimeShown = false;
private int minExecutionTimeInSeconds = CommonConfigOptions.minExecutionTimeInSecondsDefault;
- private boolean minExecutionTimeShown=false;
+ private boolean minExecutionTimeShown = false;
private int guaranteeXgoodDescriptions = CommonConfigOptions.guaranteeXgoodDescriptionsDefault;
- private boolean guaranteeXgoodShown=false;
+ private boolean guaranteeXgoodShown = false;
private boolean quiet = false;
@@ -415,9 +416,7 @@
algorithmStartTime = System.nanoTime();
//second set of lines below, sometimes doesn't go into while, see above
- if(maxExecutionTimeReached()) { stop=true;}
- solutionFound = (guaranteeXgoodDescriptions() );
- solutionFound = (minExecutionTimeReached()&& solutionFound);
+ handleStoppingConditions();
// TODO: effizienter Traversal der Subsumption-Hierarchie
// TODO: Äquivalenzen nutzen
@@ -528,10 +527,8 @@
if(!quiet)
logger.debug("--- loop " + loop + " finished ---");
+ handleStoppingConditions();
- solutionFound = (guaranteeXgoodDescriptions() );
- solutionFound = (minExecutionTimeReached()&& solutionFound);
- if(maxExecutionTimeReached()) {solutionFound=true; stop=true;}
}//end while
@@ -1091,11 +1088,19 @@
return startNode;
}
+ private void handleStoppingConditions(){
+ solutionFound = (guaranteeXgoodDescriptions() );
+ solutionFound = (minExecutionTimeReached()&& solutionFound);
+ if(maxExecutionTimeReached()) { stop();
+ if(solutions.size()>0)solutionFound = true;
+ }
+ }
+
private boolean guaranteeXgoodDescriptions(){
if(guaranteeXgoodShown)return true;
if(solutions.size()>guaranteeXgoodDescriptions){
- logger.info("Minimum number of good descriptions reached, stopping now...");
+ logger.info("Minimum number ("+guaranteeXgoodDescriptions+") of good descriptions reached, stopping now...");
guaranteeXgoodShown=true;
return true;}
else return false;
@@ -1109,13 +1114,15 @@
long needed = System.currentTimeMillis()- this.runtime;
long maxMilliSeconds = maxExecutionTimeInSeconds *1000 ;
if(maxMilliSeconds<needed){
- logger.info("Maximum time reached, stopping now...");
+ logger.info("Maximum time ("+maxExecutionTimeInSeconds+" seconds) reached, stopping now...");
maxExecutionTimeShown=true;
return true;}
else return false;
}
+
+
/**
* true if minExecutionTime reached
* @return true
@@ -1125,7 +1132,7 @@
long needed = System.currentTimeMillis()- this.runtime;
long minMilliSeconds = minExecutionTimeInSeconds *1000 ;
if(minMilliSeconds<needed){
- logger.info("Minimum time reached, stopping when next solution is found");
+ logger.info("Minimum time ("+minExecutionTimeInSeconds+" seconds) reached, stopping when next solution is found");
minExecutionTimeShown=true;
return true;}
else return false;
Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQuery.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQuery.java 2008-04-23 12:42:53 UTC (rev 820)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQuery.java 2008-04-24 08:43:22 UTC (rev 821)
@@ -79,12 +79,14 @@
for (String ngu : endpoint.getNamedGraphURIs()) {
queryExecution.addNamedGraph(ngu);
}
- logger.info("query SPARQL server");
+
try{
//TODO remove after overnext Jena release
HttpQuery.urlLimit = 3*1024 ;
rs = queryExecution.execSelect();
+ logger.debug("query SPARQL server, retrieved: "+rs.getResultVars());
json=SparqlQuery.getAsJSON(rs);
+
logger.trace(rs.getResultVars().toString());
} catch (Exception e){
sendException=new SparqlQueryException(e.getMessage());
Modified: trunk/src/dl-learner/org/dllearner/scripts/SPARQLMassLearning.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/SPARQLMassLearning.java 2008-04-23 12:42:53 UTC (rev 820)
+++ trunk/src/dl-learner/org/dllearner/scripts/SPARQLMassLearning.java 2008-04-24 08:43:22 UTC (rev 821)
@@ -1,5 +1,6 @@
package org.dllearner.scripts;
+import java.net.URLEncoder;
import java.util.SortedSet;
import java.util.TreeSet;
@@ -27,21 +28,22 @@
//vars
boolean useRelated = true;
boolean useSuperClasses = true;
- int poslimit = 300;
- int neglimit = 600;
+ int poslimit = 10;
+ int neglimit = 10;
try {
//System.out.println(logger.setLevel(TRACE));
- System.out.println(Level.DEBUG.getClass());
+ /*System.out.println(Level.DEBUG.getClass());
System.out.println(Level.toLevel("INFO"));
System.out.println(Level.INFO);
- System.exit(0);
+ System.exit(0);*/
SimpleClock sc=new SimpleClock();
SortedSet<String> concepts = new TreeSet<String>();
//concepts.add("\"http://dbpedia.org/class/yago/Person100007846\"");
- concepts.add("\"http://dbpedia.org/class/yago/FieldMarshal110086821\"");
+ //concepts.add("\"http://dbpedia.org/class/yago/FieldMarshal110086821\"");
+ concepts.add("http://dbpedia.org/resource/Category:Prime_Ministers_of_the_United_Kingdom");
SortedSet<String> posExamples = new TreeSet<String>();
SortedSet<String> negExamples = new TreeSet<String>();
String url = "http://dbpedia.openlinksw.com:8890/sparql";
@@ -57,10 +59,15 @@
System.out.println(posExamples);
System.out.println(negExamples);
//System.exit(0);
+ String concept = concepts.first().replace("http://dbpedia.org/resource/Category:", "");
+ concept = concept.replace("http://dbpedia.org/class/yago/", "");
+ String confname = URLEncoder.encode(concept, "UTF-8")+".conf";
+ //
+ ConfWriter cf=new ConfWriter();
+ cf.addToStats("relearned concept: "+concepts.first());
-
- //
- new ConfWriter().writeSPARQL("aaa.conf", posExamples, negExamples, url, new TreeSet<String>());
+ //"relearned concept: ";
+ cf.writeSPARQL(confname, posExamples, negExamples, url, new TreeSet<String>());
//new LearnSparql().learn(posExamples, negExamples, "http://dbpedia.openlinksw.com:8890/sparql", new TreeSet<String>());
sc.printAndSet("Finished");
Modified: trunk/src/dl-learner/org/dllearner/utilities/AutomaticExampleFinderSPARQL.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/AutomaticExampleFinderSPARQL.java 2008-04-23 12:42:53 UTC (rev 820)
+++ trunk/src/dl-learner/org/dllearner/utilities/AutomaticExampleFinderSPARQL.java 2008-04-24 08:43:22 UTC (rev 821)
@@ -54,9 +54,13 @@
}
private void makePositiveExamplesFromConcept(String concept){
+ if(concept.contains("http://dbpedia.org/resource/Category:")) {
+ this.posExamples = new JenaResultSetConvenience(querySKOSConcept(concept,0))
+ .getStringListForVariable("subject");
+ }else {
this.posExamples = new JenaResultSetConvenience(queryConcept(concept,0))
.getStringListForVariable("subject");
-
+ }
}
@@ -154,7 +158,30 @@
return rs;
}
+
+ public ResultSet querySKOSConcept(String SKOSconcept,int limit) {
+ if(limit==0)limit=99999;
+ //
+ ResultSet rs = null;
+ try {
+
+ String query = "SELECT * WHERE { \n " +
+ "?subject " +
+ "<http://www.w3.org/2004/02/skos/core#subject> " +
+ "<" + SKOSconcept + "> \n" +
+ "} LIMIT "+limit;
+ SparqlQuery sq = new SparqlQuery(query, se);
+ String JSON = c.executeSparqlQuery(sq);
+ //System.out.println(JSON);
+ rs = SparqlQuery.JSONtoResultSet(JSON);
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ return rs;
+ }
+
public SortedSet<String> getPosExamples() {
return posExamples;
}
Modified: trunk/src/dl-learner/org/dllearner/utilities/ConfWriter.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/ConfWriter.java 2008-04-23 12:42:53 UTC (rev 820)
+++ trunk/src/dl-learner/org/dllearner/utilities/ConfWriter.java 2008-04-24 08:43:22 UTC (rev 821)
@@ -10,130 +10,136 @@
public class ConfWriter {
-
- public String workingDir="examples/stest/";
-
-
- public void writeROLLearnerOWLFileInd(String filename,SortedSet<Individual> pos,SortedSet<Individual> neg,
- String owlFile, SortedSet<String> ignoredConcepts){
-
- writeROLLearnerOWLFile( filename,toString( pos),toString( neg),
- owlFile, ignoredConcepts);
+ StringBuffer stats = new StringBuffer("/**STATS:\n");
+
+ public String workingDir = "examples/stest/";
+
+ public void writeROLLearnerOWLFileInd(String filename, SortedSet<Individual> pos,
+ SortedSet<Individual> neg, String owlFile, SortedSet<String> ignoredConcepts) {
+
+ writeROLLearnerOWLFile(filename, toString(pos), toString(neg), owlFile, ignoredConcepts);
}
-
- public void writeROLLearnerOWLFile(String filename,SortedSet<String> pos,SortedSet<String> neg,
- String owlFile, SortedSet<String> ignoredConcepts){
-
+
+ public void writeROLLearnerOWLFile(String filename, SortedSet<String> pos,
+ SortedSet<String> neg, String owlFile, SortedSet<String> ignoredConcepts) {
+
String prefix = "refexamples";
StringBuffer buf = new StringBuffer();
buf.append("import(\"" + owlFile + "\");\n\n");
-
- buf.append(getIgnoredConcepts(ignoredConcepts,prefix));
-
+
+ buf.append(getIgnoredConcepts(ignoredConcepts, prefix));
+
buf.append(getStandard(prefix));
-
- buf.append( getPosAndNeg( pos, neg));
-
-
- writeToFile(filename, buf.toString());
-
+
+ buf.append(getPosAndNeg(pos, neg));
+
+ stats.append(ignoredConcepts + "\n");
+ stats.append("No of positive Examples: " + pos.size() + "\n");
+ stats.append("No of negative Examples: " + neg.size() + "\n");
+ stats.append("\n**/\n\n");
+
+ writeToFile(filename, stats.toString() + buf.toString());
+
}
-
- public void writeSPARQL(String filename,SortedSet<String> pos,SortedSet<String> neg,
- String uri, SortedSet<String> ignoredConcepts){
-
- String prefixAlgortihm = "refexamples";
- String prefixSparql = "sparql";
-
- String standardSettings="sparql.recursionDepth = 1;\n" +
- "sparql.predefinedFilter = 1;\n" +
- "sparql.predefinedEndpoint = 1;\n";
- //"sparql.format = \"KB\";\n\n";
-
- StringBuffer buf = new StringBuffer();
- buf.append("import(\"" + uri + "\",\"SPARQL\");\n\n");
-
- buf.append(standardSettings);
-
- buf.append(getIgnoredConcepts(ignoredConcepts,prefixAlgortihm));
-
- buf.append(getStandard(prefixAlgortihm));
-
- buf.append(sparqlInstances(pos, neg, prefixSparql));
-
- buf.append( getPosAndNeg( pos, neg));
-
-
- writeToFile(filename, buf.toString());
-
-}
-
- public String sparqlInstances(SortedSet<String> pos,SortedSet<String> neg,String prefix){
+
+ public void writeSPARQL(String filename, SortedSet<String> pos, SortedSet<String> neg,
+ String uri, SortedSet<String> ignoredConcepts) {
+
+ String prefixAlgortihm = "refexamples";
+ String prefixSparql = "sparql";
+
+ String standardSettings =
+ "sparql.recursionDepth = 1;\n" +
+ "sparql.predefinedFilter = 1;\n" +
+ "sparql.predefinedEndpoint = 1;\n" +
+ "refexamples.minExecutionTimeInSeconds = 10;\n" +
+ "refexamples.maxExecutionTimeInSeconds = 10;\n" +
+ "refexamples.logLevel=\"TRACE\";\n" ;
+
+
+ // "sparql.format = \"KB\";\n\n";
+
+ StringBuffer buf = new StringBuffer();
+ buf.append("import(\"" + uri + "\",\"SPARQL\");\n\n");
+
+ buf.append(standardSettings);
+ buf.append(getIgnoredConcepts(ignoredConcepts, prefixAlgortihm));
+ buf.append(getStandard(prefixAlgortihm));
+ buf.append(sparqlInstances(pos, neg, prefixSparql));
+ buf.append(getPosAndNeg(pos, neg));
+
+ stats.append(ignoredConcepts + "\n");
+ stats.append("No of positive Examples: " + pos.size() + "\n");
+ stats.append("No of negative Examples: " + neg.size() + "\n");
+ stats.append("\n**/\n\n");
+
+ writeToFile(filename, stats.toString() + buf.toString());
+
+ }
+
+ public String sparqlInstances(SortedSet<String> pos, SortedSet<String> neg, String prefix) {
SortedSet<String> ret = new TreeSet<String>();
ret.addAll(pos);
ret.addAll(neg);
-
+
return getStringSet(ret, prefix, "instances");
-
+
}
-
- public String getPosAndNeg(SortedSet<String> pos,SortedSet<String> neg){
- StringBuffer buf = new StringBuffer();
- buf.append("\n\n");
- for (String individuals : pos) {
- buf.append("+\"" + individuals + "\"\n");
-
- }
- buf.append("\n\n");
- for (String individuals : neg) {
-
- buf.append("-\"" + individuals + "\"\n");
- }
-
- return buf.toString();
+ public String getPosAndNeg(SortedSet<String> pos, SortedSet<String> neg) {
+ StringBuffer buf = new StringBuffer();
+ buf.append("\n\n");
+ for (String individuals : pos) {
+ buf.append("+\"" + individuals + "\"\n");
+
+ }
+ buf.append("\n\n");
+ for (String individuals : neg) {
+
+ buf.append("-\"" + individuals + "\"\n");
+ }
+
+ return buf.toString();
}
-
- public String getIgnoredConcepts(SortedSet<String> ignoredConcepts,String prefix){
- return getStringSet(ignoredConcepts,prefix, "ignoredConcepts");
+ public String getIgnoredConcepts(SortedSet<String> ignoredConcepts, String prefix) {
+
+ return getStringSet(ignoredConcepts, prefix, "ignoredConcepts");
}
-
- public String getStringSet(SortedSet<String> set,String prefix, String type){
- if(set.size()==0)return "\n";
- String ret = prefix+"."+type+"={\n";
- int x=0;
+
+ public String getStringSet(SortedSet<String> set, String prefix, String type) {
+ if (set.size() == 0)
+ return "\n";
+ String ret = prefix + "." + type + "={\n";
+ int x = 0;
for (String string : set) {
- if(x>0)ret+=",";
- ret+="\""+string+"\"\n";
+ if (x > 0)
+ ret += ",";
+ ret += "\"" + string + "\"\n";
x++;
}
- ret+="};\n";
+ ret += "};\n";
return ret;
}
-
- public String getStandard(String prefix){
- String ret =
- "algorithm = "+prefix+";\n"+
- "reasoner=fastInstanceChecker;\n\n"+
-
- prefix+".useAllConstructor = false;\n"+
- prefix+".useExistsConstructor = true;\n"+
- prefix+".useCardinalityRestrictions = false;\n"+
- prefix+".useNegation = false;\n";
-
+
+ public String getStandard(String prefix) {
+ String ret = "algorithm = " + prefix + ";\n" + "reasoner=fastInstanceChecker;\n\n" +
+
+ prefix + ".useAllConstructor = false;\n" + prefix + ".useExistsConstructor = true;\n"
+ + prefix + ".useCardinalityRestrictions = false;\n" + prefix
+ + ".useNegation = false;\n";
+
return ret;
-
+
}
-
-
- protected void writeToFile(String filename, String content) {
+
+ protected void writeToFile(String filename, String content) {
// create the file we want to use
- File file = new File(workingDir+filename);
+ File file = new File(workingDir + filename);
try {
file.createNewFile();
- FileOutputStream fos = new FileOutputStream(workingDir+filename, false);
+ FileOutputStream fos = new FileOutputStream(workingDir + filename, false);
// ObjectOutputStream o = new ObjectOutputStream(fos);
fos.write(content.getBytes());
fos.flush();
@@ -142,14 +148,17 @@
e.printStackTrace();
}
}
-
- protected SortedSet<String> toString(SortedSet<Individual> set ){
+
+ protected SortedSet<String> toString(SortedSet<Individual> set) {
SortedSet<String> ret = new TreeSet<String>();
for (Individual ind : set) {
ret.add(ind.toString());
}
return ret;
}
-
-
+
+ public void addToStats(String add) {
+ stats.append(add);
+ }
+
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ku...@us...> - 2008-04-23 12:42:58
|
Revision: 820
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=820&view=rev
Author: kurzum
Date: 2008-04-23 05:42:53 -0700 (Wed, 23 Apr 2008)
Log Message:
-----------
output changes, logfile is now created by default in "the_log.txt"
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java
trunk/src/dl-learner/org/dllearner/algorithms/refinement/ROLearner.java
trunk/src/dl-learner/org/dllearner/cli/Start.java
trunk/src/dl-learner/org/dllearner/kb/sparql/ExtractionAlgorithm.java
trunk/src/dl-learner/org/dllearner/kb/sparql/datastructure/Node.java
Modified: trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java 2008-04-23 09:28:15 UTC (rev 819)
+++ trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java 2008-04-23 12:42:53 UTC (rev 820)
@@ -255,8 +255,8 @@
this.useOverlyGeneralList = useOverlyGeneralList;
this.useShortConceptConstruction = useShortConceptConstruction;
this.baseURI = rs.getBaseURI();
- this.maxExecutionTimeInSeconds=maxExecutionTimeInSeconds;
- this.minExecutionTimeInSeconds=minExecutionTimeInSeconds;
+ this.maxExecutionTimeInSeconds = maxExecutionTimeInSeconds;
+ this.minExecutionTimeInSeconds = minExecutionTimeInSeconds;
this.guaranteeXgoodDescriptions = guaranteeXgoodDescriptions;
@@ -1037,6 +1037,10 @@
return ;
i++;
}
+ for (int j = 0; j < solutions.size(); j++) {
+ Description d = solutions.get(j);
+ logger.trace(d.toString());
+ }
}
Modified: trunk/src/dl-learner/org/dllearner/algorithms/refinement/ROLearner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/refinement/ROLearner.java 2008-04-23 09:28:15 UTC (rev 819)
+++ trunk/src/dl-learner/org/dllearner/algorithms/refinement/ROLearner.java 2008-04-23 12:42:53 UTC (rev 820)
@@ -69,11 +69,16 @@
private boolean useShortConceptConstruction = true;
private double horizontalExpansionFactor = 0.6;
private boolean improveSubsumptionHierarchy = true;
- private boolean useAllConstructor = true;
- private boolean useExistsConstructor = true;
- private boolean useNegation = true;
+ private boolean useAllConstructor = CommonConfigOptions.useAllConstructorDefault;
+ private boolean useExistsConstructor = CommonConfigOptions.useExistsConstructorDefault;
+ //this was added so you can switch algorithm without removing everything not applicable
+ private boolean useCardinalityRestrictions = CommonConfigOptions.useCardinalityRestrictionsDefault;
+ private boolean useNegation = CommonConfigOptions.useNegationDefault;
+ //TODO different standard options to CommonConfigOptions
private boolean useBooleanDatatypes = false;
+
+
//extended Options
private int maxExecutionTimeInSeconds = CommonConfigOptions.maxExecutionTimeInSecondsDefault;
private boolean maxExecutionTimeShown=false;
@@ -228,7 +233,8 @@
options.add(CommonConfigOptions.ignoredRoles());
options.add(CommonConfigOptions.useAllConstructor());
options.add(CommonConfigOptions.useExistsConstructor());
- options.add(CommonConfigOptions.useNegation());
+ options.add(CommonConfigOptions.useNegation());
+ options.add(CommonConfigOptions.useCardinalityRestrictions());
options.add(CommonConfigOptions.useBooleanDatatypes());
options.add(CommonConfigOptions.maxExecutionTimeInSeconds());
options.add(CommonConfigOptions.minExecutionTimeInSeconds());
@@ -282,6 +288,8 @@
useAllConstructor = (Boolean) entry.getValue();
} else if(name.equals("useExistsConstructor")) {
useExistsConstructor = (Boolean) entry.getValue();
+ }else if(name.equals("useCardinalityRestrictions")) {
+ useCardinalityRestrictions = (Boolean) entry.getValue();
} else if(name.equals("useNegation")) {
useNegation = (Boolean) entry.getValue();
} else if(name.equals("useBooleanDatatypes")) {
@@ -304,6 +312,7 @@
@Override
public void init() {
logger.setLevel(Level.toLevel(logLevel,Level.toLevel(CommonConfigOptions.logLevelDefault)));
+
if(searchTreeFile == null)
searchTreeFile = new File(defaultSearchTreeFile);
@@ -405,6 +414,11 @@
algorithmStartTime = System.nanoTime();
+ //second set of lines below, sometimes doesn't go into while, see above
+ if(maxExecutionTimeReached()) { stop=true;}
+ solutionFound = (guaranteeXgoodDescriptions() );
+ solutionFound = (minExecutionTimeReached()&& solutionFound);
+
// TODO: effizienter Traversal der Subsumption-Hierarchie
// TODO: Äquivalenzen nutzen
// TODO: Gibt es auch eine andere Abbruchbedingung? Es könnte sein, dass irgendwann keine
@@ -506,7 +520,7 @@
Files.createFile(searchTreeFile, treeString);
else
Files.appendFile(searchTreeFile, treeString);
- }
+ }//write search tree
// Anzahl Schleifendurchläufe
loop++;
@@ -514,13 +528,15 @@
if(!quiet)
logger.debug("--- loop " + loop + " finished ---");
- }
+
+ solutionFound = (guaranteeXgoodDescriptions() );
+ solutionFound = (minExecutionTimeReached()&& solutionFound);
+ if(maxExecutionTimeReached()) {solutionFound=true; stop=true;}
+ }//end while
- if(maxExecutionTimeReached()) { stop=true;}
- solutionFound = (guaranteeXgoodDescriptions() );
- solutionFound = (minExecutionTimeReached()&& solutionFound);
+
// Suchbaum in Datei schreiben
// if(writeSearchTree)
// Files.createFile(searchTreeFile, searchTree);
@@ -542,18 +558,23 @@
if(solutionFound) {
logger.info("\nsolutions:");
+ int show=1;
for(Description c : solutions) {
- logger.info(" " + c.toString(baseURI,null) + " (length " + c.getLength() +", depth " + c.getDepth() + ")");
+ logger.info(show+": " +c.toString(baseURI,null) + " (length " + c.getLength() +", depth " + c.getDepth() + ")");
//TODO remove this line maybe
// watch for String.replace Quick hack
- logger.info(" MANCHESTER: " +
+ logger.info(" MANCHESTER: " +
c.toManchesterSyntaxString(baseURI, new HashMap<String,String>()).
replace("\"", ""));
- logger.info(" KBSyntax: " + c.toKBSyntaxString());
+ logger.info(" KBSyntax: " + c.toKBSyntaxString());
+ if(show>=5){break;}
+ show++;
}
}
logger.info(" horizontal expansion: " + minimumHorizontalExpansion + " to " + maximumHorizontalExpansion);
logger.info(" size of candidate set: " + candidates.size());
+ //logger.trace("test");
+ //logger.trace(solutions.size());
printBestSolutions(0);
printStatistics(true);
@@ -1018,13 +1039,13 @@
}
public void printBestSolutions(int nrOfSolutions){
- if(!logLevel.equalsIgnoreCase("TRACE"))return;
+ if(!logLevel.equalsIgnoreCase("TRACE")){return;}
if(nrOfSolutions==0)nrOfSolutions=solutions.size();
int i=0;
- for(;i==nrOfSolutions; i++) {
+ for(;i<nrOfSolutions; i++) {
Description d = solutions.get(i);
logger.trace(" " + d.toString(baseURI,null) + " (length " + d.getLength() + " " +
- ""+getSolutionScore(d) );
+ "" );
}
}
Modified: trunk/src/dl-learner/org/dllearner/cli/Start.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/cli/Start.java 2008-04-23 09:28:15 UTC (rev 819)
+++ trunk/src/dl-learner/org/dllearner/cli/Start.java 2008-04-23 12:42:53 UTC (rev 820)
@@ -35,6 +35,7 @@
import java.util.TreeSet;
import org.apache.log4j.ConsoleAppender;
+import org.apache.log4j.FileAppender;
import org.apache.log4j.Level;
import org.apache.log4j.Logger;
import org.apache.log4j.SimpleLayout;
@@ -117,8 +118,13 @@
// its messages to the console)
SimpleLayout layout = new SimpleLayout();
ConsoleAppender consoleAppender = new ConsoleAppender(layout);
- logger.removeAllAppenders();
+ FileAppender fileAppender =null; ;
+ try{
+ fileAppender = new FileAppender(layout,"the_log.txt",false);
+ }catch (Exception e) {e.printStackTrace();}
+ logger.removeAllAppenders();
logger.addAppender(consoleAppender);
+ logger.addAppender(fileAppender);
logger.setLevel(Level.DEBUG);
Start start = null;
Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/ExtractionAlgorithm.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/ExtractionAlgorithm.java 2008-04-23 09:28:15 UTC (rev 819)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/ExtractionAlgorithm.java 2008-04-23 12:42:53 UTC (rev 820)
@@ -128,10 +128,10 @@
configuration);
if (this.configuration.isCloseAfterRecursion()) {
while (instances.size() > 0) {
- logger.info("Getting classes for remaining instances: "
+ logger.trace("Getting classes for remaining instances: "
+ instances.size());
Node next = instances.remove(0);
- logger.info("Getting classes for: " + next);
+ logger.trace("Getting classes for: " + next);
classes.addAll(next.expand(tsqc, manipulator));
if (classes.size() >= manipulator.breakSuperClassRetrievalAfter) {
break;
@@ -141,14 +141,14 @@
Vector<Node> tmp = new Vector<Node>();
int i = 0;
while (classes.size() > 0) {
- logger.info("Remaining classes: " + classes.size());
+ logger.trace("Remaining classes: " + classes.size());
// Iterator<Node> it=classes.iterator();
// Node next =(Node) it.next();
// classes.remove(next);
Node next = classes.remove(0);
if (!hadAlready.contains(next.getURI().toString())) {
- logger.info("Expanding: " + next);
+ logger.trace("Getting SuperClass for: " + next);
// System.out.println(hadAlready.size());
hadAlready.add(next.getURI().toString());
tmp = next.expand(typedSparqlQuery, manipulator);
Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/datastructure/Node.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/datastructure/Node.java 2008-04-23 09:28:15 UTC (rev 819)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/datastructure/Node.java 2008-04-23 12:42:53 UTC (rev 820)
@@ -78,7 +78,7 @@
@Override
public String toString() {
- return "Node: " + uri + ":" + this.getClass();
+ return "Node: " + uri + ":" + this.getClass().getSimpleName();
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ku...@us...> - 2008-04-23 09:28:22
|
Revision: 819
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=819&view=rev
Author: kurzum
Date: 2008-04-23 02:28:15 -0700 (Wed, 23 Apr 2008)
Log Message:
-----------
changed tasks:
build is now without javadoc generation
full_release is everything
also added "-Xmx1024m" by default to scripts (only bat now)
Modified Paths:
--------------
trunk/build.xml
Modified: trunk/build.xml
===================================================================
--- trunk/build.xml 2008-04-23 09:20:23 UTC (rev 818)
+++ trunk/build.xml 2008-04-23 09:28:15 UTC (rev 819)
@@ -24,7 +24,11 @@
</path>
<!-- build target -->
- <target name="build" depends="createScripts,javadoc">
+ <target name="full_release" depends="javadoc,build" description="full release, javadoc, scripts">
+ </target>
+
+ <!-- build target -->
+ <target name="build" depends="createScripts" description="fast build including scripts, no javadoc">
<!-- write current build date into Info.java -->
<echo file="${source_dir}/org/dllearner/Info.java" append="false">
@@ -179,8 +183,8 @@
<map from="${removeprefix}" to="."/>
</pathconvert>
- <echo file="bin/quickstart.bat" message="java -cp ${pathStringWin} org.dllearner.cli.QuickStart"/>
- <echo file="bin/dllearner.bat" message="java -cp ${pathStringWin} org.dllearner.cli.Start %*"/>
+ <echo file="bin/quickstart.bat" message="java -Xmx1024m -cp ${pathStringWin} org.dllearner.cli.QuickStart"/>
+ <echo file="bin/dllearner.bat" message="java -Xmx1024m -cp ${pathStringWin} org.dllearner.cli.Start %*"/>
<echo file="bin/ws.bat" message="java -cp ${pathStringWin} org.dllearner.server.DLLearnerWSStart %*"/>
<echo file="bin/quickstart" message="java -cp ${pathStringUnix} org.dllearner.cli.QuickStart"/>
<echo file="bin/dllearner" message="java -cp ${pathStringUnix} org.dllearner.cli.Start $@"/>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ku...@us...> - 2008-04-23 09:20:26
|
Revision: 818
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=818&view=rev
Author: kurzum
Date: 2008-04-23 02:20:23 -0700 (Wed, 23 Apr 2008)
Log Message:
-----------
small output changes
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java
trunk/src/dl-learner/org/dllearner/algorithms/refinement/ROLearner.java
Modified: trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java 2008-04-23 08:04:01 UTC (rev 817)
+++ trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java 2008-04-23 09:20:23 UTC (rev 818)
@@ -1028,6 +1028,7 @@
public void printBestSolutions(int nrOfSolutions){
+ if(!logger.getLevel().toString().equalsIgnoreCase("TRACE"))return;
if(nrOfSolutions==0)nrOfSolutions=candidatesStable.size();
int i=0;
for(ExampleBasedNode n : candidatesStable.descendingSet()) {
Modified: trunk/src/dl-learner/org/dllearner/algorithms/refinement/ROLearner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/refinement/ROLearner.java 2008-04-23 08:04:01 UTC (rev 817)
+++ trunk/src/dl-learner/org/dllearner/algorithms/refinement/ROLearner.java 2008-04-23 09:20:23 UTC (rev 818)
@@ -554,6 +554,7 @@
}
logger.info(" horizontal expansion: " + minimumHorizontalExpansion + " to " + maximumHorizontalExpansion);
logger.info(" size of candidate set: " + candidates.size());
+ printBestSolutions(0);
printStatistics(true);
if(stop)
@@ -1015,6 +1016,18 @@
public Description getBestSolution() {
return candidatesStable.last().getConcept();
}
+
+ public void printBestSolutions(int nrOfSolutions){
+ if(!logLevel.equalsIgnoreCase("TRACE"))return;
+ if(nrOfSolutions==0)nrOfSolutions=solutions.size();
+ int i=0;
+ for(;i==nrOfSolutions; i++) {
+ Description d = solutions.get(i);
+ logger.trace(" " + d.toString(baseURI,null) + " (length " + d.getLength() + " " +
+ ""+getSolutionScore(d) );
+ }
+
+ }
@Override
public synchronized List<Description> getBestSolutions(int nrOfSolutions) {
@@ -1036,6 +1049,14 @@
else
return learningProblem.computeScore(getBestSolution());
}
+
+
+ public Score getSolutionScore(Description d) {
+ if(posOnly)
+ return posOnlyLearningProblem.computeScore(d);
+ else
+ return learningProblem.computeScore(d);
+ }
@Override
public void stop() {
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ku...@us...> - 2008-04-23 08:04:22
|
Revision: 817
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=817&view=rev
Author: kurzum
Date: 2008-04-23 01:04:01 -0700 (Wed, 23 Apr 2008)
Log Message:
-----------
ne config doc
Modified Paths:
--------------
trunk/doc/configOptions.txt
Property Changed:
----------------
trunk/doc/
Property changes on: trunk/doc
___________________________________________________________________
Name: svn:ignore
- javadoc
+ javadoc
configOptions_old.txt
Modified: trunk/doc/configOptions.txt
===================================================================
--- trunk/doc/configOptions.txt 2008-04-23 08:03:44 UTC (rev 816)
+++ trunk/doc/configOptions.txt 2008-04-23 08:04:01 UTC (rev 817)
@@ -621,6 +621,12 @@
default value: 1
CLI usage: refexamples.guaranteeXgoodDescriptions = 1;
+option name: logLevel
+description: determines the logLevel for this component, can be {TRACE, DEBUG, INFO}
+values: class org.dllearner.core.config.StringConfigOption
+default value: DEBUG
+CLI usage: refexamples.logLevel = DEBUG;
+
option name: noisePercentage
description: the (approximated) percentage of noise within the examples
values: class org.dllearner.core.config.DoubleConfigOption min 0.0 max 100.0
@@ -759,4 +765,28 @@
default value: true
CLI usage: refinement.useBooleanDatatypes = true;
+option name: maxExecutionTimeInSeconds
+description: algorithm will stop after specified seconds
+values: class org.dllearner.core.config.IntegerConfigOption
+default value: 0
+CLI usage: refinement.maxExecutionTimeInSeconds = 0;
+option name: minExecutionTimeInSeconds
+description: algorithm will run at least specified seconds
+values: class org.dllearner.core.config.IntegerConfigOption
+default value: 0
+CLI usage: refinement.minExecutionTimeInSeconds = 0;
+
+option name: guaranteeXgoodDescriptions
+description: algorithm will run until X good (100%) concept descritpions are found
+values: class org.dllearner.core.config.IntegerConfigOption
+default value: 1
+CLI usage: refinement.guaranteeXgoodDescriptions = 1;
+
+option name: logLevel
+description: determines the logLevel for this component, can be {TRACE, DEBUG, INFO}
+values: class org.dllearner.core.config.StringConfigOption
+default value: DEBUG
+CLI usage: refinement.logLevel = DEBUG;
+
+
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ku...@us...> - 2008-04-23 08:04:01
|
Revision: 816
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=816&view=rev
Author: kurzum
Date: 2008-04-23 01:03:44 -0700 (Wed, 23 Apr 2008)
Log Message:
-----------
new options loglevel and stopping for ROLLearner and refexamples
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/Info.java
trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLComponent.java
trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java
trunk/src/dl-learner/org/dllearner/algorithms/refinement/ROLearner.java
trunk/src/dl-learner/org/dllearner/core/config/CommonConfigOptions.java
trunk/src/dl-learner/org/dllearner/scripts/SPARQLMassLearning.java
trunk/src/dl-learner/org/dllearner/utilities/LearnSparql.java
Modified: trunk/src/dl-learner/org/dllearner/Info.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/Info.java 2008-04-22 18:11:28 UTC (rev 815)
+++ trunk/src/dl-learner/org/dllearner/Info.java 2008-04-23 08:03:44 UTC (rev 816)
@@ -3,6 +3,6 @@
package org.dllearner;
public class Info {
- public static final String build = "2008-03-31";
+ public static final String build = "2008-04-23";
}
\ No newline at end of file
Modified: trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLComponent.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLComponent.java 2008-04-22 18:11:28 UTC (rev 815)
+++ trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLComponent.java 2008-04-23 08:03:44 UTC (rev 816)
@@ -26,6 +26,8 @@
import java.util.List;
import java.util.Set;
+import org.apache.log4j.Level;
+import org.apache.log4j.Logger;
import org.dllearner.core.LearningAlgorithm;
import org.dllearner.core.LearningProblem;
import org.dllearner.core.ReasoningService;
@@ -75,6 +77,9 @@
// actual algorithm
private ExampleBasedROLearner algorithm;
+ private static Logger logger = Logger
+ .getLogger(ExampleBasedROLearner.class);
+ private String logLevel = CommonConfigOptions.logLevelDefault;
// learning problem to solve and background knowledge
private ReasoningService rs;
@@ -172,6 +177,7 @@
options.add(CommonConfigOptions.maxExecutionTimeInSeconds());
options.add(CommonConfigOptions.minExecutionTimeInSeconds());
options.add(CommonConfigOptions.guaranteeXgoodDescriptions());
+ options.add(CommonConfigOptions.getLogLevel());
DoubleConfigOption noisePercentage = new DoubleConfigOption("noisePercentage", "the (approximated) percentage of noise within the examples");
noisePercentage.setLowerLimit(0);
noisePercentage.setUpperLimit(100);
@@ -239,6 +245,8 @@
minExecutionTimeInSeconds = (Integer) entry.getValue();
}else if(name.equals("guaranteeXgoodDescriptions")) {
guaranteeXgoodDescriptions = (Integer) entry.getValue();
+ } else if(name.equals("logLevel")) {
+ logLevel = ((String)entry.getValue()).toUpperCase();
}
}
@@ -247,7 +255,8 @@
*/
@Override
public void init() {
-
+
+ logger.setLevel(Level.toLevel(logLevel,Level.toLevel(CommonConfigOptions.logLevelDefault)));
if(searchTreeFile == null)
searchTreeFile = new File(defaultSearchTreeFile);
@@ -308,7 +317,7 @@
rs,
applyAllFilter,
applyExistsFilter,
- useAllConstructor,
+ useAllConstructor,
useExistsConstructor,
useCardinalityRestrictions,
useNegation,
@@ -380,10 +389,10 @@
}
- public void printBestSolutions(int nrOfSolutions){
+ /*public void printBestSolutions(int nrOfSolutions){
algorithm.printBestSolutions(nrOfSolutions);
- }
+ }*/
Modified: trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java 2008-04-22 18:11:28 UTC (rev 815)
+++ trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java 2008-04-23 08:03:44 UTC (rev 816)
@@ -75,8 +75,9 @@
public class ExampleBasedROLearner {
private static Logger logger = Logger
- .getLogger(ExampleBasedROLearner.class);
+ .getLogger(ExampleBasedROLearner.class);
+
// basic setup: learning problem and reasoning service
private ReasoningService rs;
private PosNegLP learningProblem;
@@ -221,6 +222,7 @@
int minExecutionTimeInSeconds,
int guaranteeXgoodDescriptions
) {
+
if(learningProblem instanceof PosNegLP) {
PosNegLP lp = (PosNegLP) learningProblem;
this.learningProblem = lp;
@@ -257,6 +259,7 @@
this.minExecutionTimeInSeconds=minExecutionTimeInSeconds;
this.guaranteeXgoodDescriptions = guaranteeXgoodDescriptions;
+
// logger.setLevel(Level.DEBUG);
}
@@ -424,7 +427,9 @@
show++;
}
}
+
logger.debug("size of candidate set: " + candidates.size());
+ printBestSolutions(0);
printStatistics(true);
if(stop)
@@ -774,9 +779,9 @@
// searchTree += bestNodeString + "\n";
logger.debug(bestNodeString);
- logger.debug(startNode.getStats(nrOfPositiveExamples, nrOfNegativeExamples));
+ logger.trace(startNode.getStats(nrOfPositiveExamples, nrOfNegativeExamples));
logger.debug(bestNodeStringKBSyntax);
- if(bestNode.getCoveredNegatives().size()<=3)logger.debug("covered negs: "+bestNode.getCoveredNegatives());
+ if(bestNode.getCoveredNegatives().size()<=5)logger.trace("covered negs: "+bestNode.getCoveredNegatives());
String expandedNodeString = "next expanded node: " + candidates.last().getShortDescription(nrOfPositiveExamples, nrOfNegativeExamples, baseURI);
// searchTree += expandedNodeString + "\n";
logger.debug(expandedNodeString);
@@ -1023,10 +1028,10 @@
public void printBestSolutions(int nrOfSolutions){
-
+ if(nrOfSolutions==0)nrOfSolutions=candidatesStable.size();
int i=0;
for(ExampleBasedNode n : candidatesStable.descendingSet()) {
- System.out.println(n.getShortDescription(nrOfPositiveExamples, nrOfNegativeExamples, baseURI));
+ logger.trace(n.getShortDescription(nrOfPositiveExamples, nrOfNegativeExamples, baseURI));
if(i==nrOfSolutions)
return ;
i++;
@@ -1060,12 +1065,7 @@
if(maxExecutionTimeInSeconds==0)return false;
if(maxExecutionTimeShown)return true;
long needed = System.currentTimeMillis()- this.runtime;
- //millisec /100
- //seconds /1000
long maxMilliSeconds = maxExecutionTimeInSeconds *1000 ;
- //System.out.println("max"+maxMilliSeconds);
- //System.out.println(needed);
-
if(maxMilliSeconds<needed){
logger.info("Maximum time reached, stopping now...");
maxExecutionTimeShown=true;
@@ -1080,14 +1080,8 @@
*/
private boolean minExecutionTimeReached(){
if(minExecutionTimeShown)return true;
- //if(minExecutionTimeInSeconds==0)return true;
long needed = System.currentTimeMillis()- this.runtime;
- //millisec /100
- //seconds /1000
long minMilliSeconds = minExecutionTimeInSeconds *1000 ;
- //System.out.println("min"+minMilliSeconds);
- //System.out.println(needed);
-
if(minMilliSeconds<needed){
logger.info("Minimum time reached, stopping when next solution is found");
minExecutionTimeShown=true;
Modified: trunk/src/dl-learner/org/dllearner/algorithms/refinement/ROLearner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/refinement/ROLearner.java 2008-04-22 18:11:28 UTC (rev 815)
+++ trunk/src/dl-learner/org/dllearner/algorithms/refinement/ROLearner.java 2008-04-23 08:03:44 UTC (rev 816)
@@ -12,6 +12,7 @@
import java.util.SortedSet;
import java.util.TreeSet;
+import org.apache.log4j.Level;
import org.apache.log4j.Logger;
import org.dllearner.core.LearningAlgorithm;
import org.dllearner.core.LearningProblem;
@@ -25,12 +26,12 @@
import org.dllearner.core.config.DoubleConfigOption;
import org.dllearner.core.config.InvalidConfigOptionValueException;
import org.dllearner.core.config.StringConfigOption;
-import org.dllearner.core.owl.NamedClass;
import org.dllearner.core.owl.Description;
import org.dllearner.core.owl.Intersection;
-import org.dllearner.core.owl.Union;
+import org.dllearner.core.owl.NamedClass;
import org.dllearner.core.owl.ObjectProperty;
import org.dllearner.core.owl.Thing;
+import org.dllearner.core.owl.Union;
import org.dllearner.learningproblems.PosNegLP;
import org.dllearner.learningproblems.PosOnlyDefinitionLP;
import org.dllearner.refinementoperators.RhoDown;
@@ -44,6 +45,8 @@
private static Logger logger = Logger
.getLogger(LearningAlgorithm.class);
+ private String logLevel = CommonConfigOptions.logLevelDefault;
+
public enum Heuristic { LEXICOGRAPHIC, FLEXIBLE }
// configuration options
@@ -71,6 +74,15 @@
private boolean useNegation = true;
private boolean useBooleanDatatypes = false;
+ //extended Options
+ private int maxExecutionTimeInSeconds = CommonConfigOptions.maxExecutionTimeInSecondsDefault;
+ private boolean maxExecutionTimeShown=false;
+ private int minExecutionTimeInSeconds = CommonConfigOptions.minExecutionTimeInSecondsDefault;
+ private boolean minExecutionTimeShown=false;
+ private int guaranteeXgoodDescriptions = CommonConfigOptions.guaranteeXgoodDescriptionsDefault;
+ private boolean guaranteeXgoodShown=false;
+
+
private boolean quiet = false;
private boolean stop = false;
@@ -151,6 +163,7 @@
private int conceptTestsReasoner = 0;
// Zeitvariablen
+ private long runtime;
private long algorithmStartTime;
private long propernessCalcTimeNs = 0;
private long propernessCalcReasoningTimeNs = 0;
@@ -217,6 +230,10 @@
options.add(CommonConfigOptions.useExistsConstructor());
options.add(CommonConfigOptions.useNegation());
options.add(CommonConfigOptions.useBooleanDatatypes());
+ options.add(CommonConfigOptions.maxExecutionTimeInSeconds());
+ options.add(CommonConfigOptions.minExecutionTimeInSeconds());
+ options.add(CommonConfigOptions.guaranteeXgoodDescriptions());
+ options.add(CommonConfigOptions.getLogLevel());
return options;
}
@@ -269,6 +286,14 @@
useNegation = (Boolean) entry.getValue();
} else if(name.equals("useBooleanDatatypes")) {
useBooleanDatatypes = (Boolean) entry.getValue();
+ }else if(name.equals("maxExecutionTimeInSeconds")) {
+ maxExecutionTimeInSeconds = (Integer) entry.getValue();
+ }else if(name.equals("minExecutionTimeInSeconds")) {
+ minExecutionTimeInSeconds = (Integer) entry.getValue();
+ }else if(name.equals("guaranteeXgoodDescriptions")) {
+ guaranteeXgoodDescriptions = (Integer) entry.getValue();
+ } else if(name.equals("logLevel")) {
+ logLevel = ((String)entry.getValue()).toUpperCase();
}
}
@@ -278,6 +303,7 @@
*/
@Override
public void init() {
+ logger.setLevel(Level.toLevel(logLevel,Level.toLevel(CommonConfigOptions.logLevelDefault)));
if(searchTreeFile == null)
searchTreeFile = new File(defaultSearchTreeFile);
@@ -351,7 +377,7 @@
@Override
@SuppressWarnings("unchecked")
public void start() {
-
+ runtime=System.currentTimeMillis();
// Suche wird mit Top-Konzept gestartet
Thing top = new Thing();
Node topNode = new Node(top);
@@ -490,6 +516,11 @@
}
+ if(maxExecutionTimeReached()) { stop=true;}
+ solutionFound = (guaranteeXgoodDescriptions() );
+ solutionFound = (minExecutionTimeReached()&& solutionFound);
+
+
// Suchbaum in Datei schreiben
// if(writeSearchTree)
// Files.createFile(searchTreeFile, searchTree);
@@ -1017,5 +1048,46 @@
public Node getStartNode() {
return startNode;
}
+
+ private boolean guaranteeXgoodDescriptions(){
+ if(guaranteeXgoodShown)return true;
+ if(solutions.size()>guaranteeXgoodDescriptions){
+ logger.info("Minimum number of good descriptions reached, stopping now...");
+ guaranteeXgoodShown=true;
+ return true;}
+ else return false;
+
+ }
+
+
+ private boolean maxExecutionTimeReached(){
+ if(maxExecutionTimeInSeconds==0)return false;
+ if(maxExecutionTimeShown)return true;
+ long needed = System.currentTimeMillis()- this.runtime;
+ long maxMilliSeconds = maxExecutionTimeInSeconds *1000 ;
+ if(maxMilliSeconds<needed){
+ logger.info("Maximum time reached, stopping now...");
+ maxExecutionTimeShown=true;
+ return true;}
+ else return false;
+
+ }
+
+ /**
+ * true if minExecutionTime reached
+ * @return true
+ */
+ private boolean minExecutionTimeReached(){
+ if(minExecutionTimeShown)return true;
+ long needed = System.currentTimeMillis()- this.runtime;
+ long minMilliSeconds = minExecutionTimeInSeconds *1000 ;
+ if(minMilliSeconds<needed){
+ logger.info("Minimum time reached, stopping when next solution is found");
+ minExecutionTimeShown=true;
+ return true;}
+ else return false;
+
+ }
+
}
Modified: trunk/src/dl-learner/org/dllearner/core/config/CommonConfigOptions.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/config/CommonConfigOptions.java 2008-04-22 18:11:28 UTC (rev 815)
+++ trunk/src/dl-learner/org/dllearner/core/config/CommonConfigOptions.java 2008-04-23 08:03:44 UTC (rev 816)
@@ -43,6 +43,7 @@
public static int maxExecutionTimeInSecondsDefault = 0;
public static int minExecutionTimeInSecondsDefault = 0;
public static int guaranteeXgoodDescriptionsDefault = 1;
+ public static String logLevelDefault = "DEBUG";
//public static double noisePercentageDefault = 0.0;
@@ -119,5 +120,9 @@
public static IntegerConfigOption guaranteeXgoodDescriptions() {
return new IntegerConfigOption("guaranteeXgoodDescriptions", "algorithm will run until X good (100%) concept descritpions are found",guaranteeXgoodDescriptionsDefault);
- }
+ }
+
+ public static StringConfigOption getLogLevel() {
+ return new StringConfigOption("logLevel", "determines the logLevel for this component, can be {TRACE, DEBUG, INFO}",logLevelDefault);
+ }
}
Modified: trunk/src/dl-learner/org/dllearner/scripts/SPARQLMassLearning.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/SPARQLMassLearning.java 2008-04-22 18:11:28 UTC (rev 815)
+++ trunk/src/dl-learner/org/dllearner/scripts/SPARQLMassLearning.java 2008-04-23 08:03:44 UTC (rev 816)
@@ -11,7 +11,6 @@
import org.dllearner.kb.sparql.configuration.SparqlEndpoint;
import org.dllearner.utilities.AutomaticExampleFinderSPARQL;
import org.dllearner.utilities.ConfWriter;
-import org.dllearner.utilities.LearnSparql;
import org.dllearner.utilities.SimpleClock;
public class SPARQLMassLearning {
@@ -34,6 +33,11 @@
try {
+ //System.out.println(logger.setLevel(TRACE));
+ System.out.println(Level.DEBUG.getClass());
+ System.out.println(Level.toLevel("INFO"));
+ System.out.println(Level.INFO);
+ System.exit(0);
SimpleClock sc=new SimpleClock();
SortedSet<String> concepts = new TreeSet<String>();
//concepts.add("\"http://dbpedia.org/class/yago/Person100007846\"");
@@ -57,7 +61,7 @@
//
new ConfWriter().writeSPARQL("aaa.conf", posExamples, negExamples, url, new TreeSet<String>());
- new LearnSparql().learn(posExamples, negExamples, "http://dbpedia.openlinksw.com:8890/sparql", new TreeSet<String>());
+ //new LearnSparql().learn(posExamples, negExamples, "http://dbpedia.openlinksw.com:8890/sparql", new TreeSet<String>());
sc.printAndSet("Finished");
} catch (Exception e) {
Modified: trunk/src/dl-learner/org/dllearner/utilities/LearnSparql.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/LearnSparql.java 2008-04-22 18:11:28 UTC (rev 815)
+++ trunk/src/dl-learner/org/dllearner/utilities/LearnSparql.java 2008-04-23 08:03:44 UTC (rev 816)
@@ -72,6 +72,7 @@
cm.applyConfigEntry(la,"minExecutionTimeInSeconds",0);
cm.applyConfigEntry(la,"maxExecutionTimeInSeconds",900);
cm.applyConfigEntry(la,"guaranteeXgoodDescriptions",999999);
+ cm.applyConfigEntry(la,"logLevel","TRACE");
//cm.applyConfigEntry(la,"quiet",false);
if(ignoredConcepts.size()>0)
@@ -82,7 +83,7 @@
la.start();
//System.out.println("best"+la(20));
- ((ExampleBasedROLComponent)la).printBestSolutions(10000);
+ //((ExampleBasedROLComponent)la).printBestSolutions(10000);
}catch (Exception e) {e.printStackTrace();}
//System.out.println( la.getBestSolution());;
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <hee...@us...> - 2008-04-22 18:11:38
|
Revision: 815
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=815&view=rev
Author: heeroyuy
Date: 2008-04-22 11:11:28 -0700 (Tue, 22 Apr 2008)
Log Message:
-----------
small changes
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/tools/protege/ActionHandler.java
trunk/src/dl-learner/org/dllearner/tools/protege/ButtonList.java
trunk/src/dl-learner/org/dllearner/tools/protege/DLLearnerModel.java
trunk/src/dl-learner/org/dllearner/tools/protege/META-INF/MANIFEST.MF
trunk/src/dl-learner/org/dllearner/tools/protege/SuggestEquivalentClassView.java
Modified: trunk/src/dl-learner/org/dllearner/tools/protege/ActionHandler.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/protege/ActionHandler.java 2008-04-22 17:43:49 UTC (rev 814)
+++ trunk/src/dl-learner/org/dllearner/tools/protege/ActionHandler.java 2008-04-22 18:11:28 UTC (rev 815)
@@ -4,7 +4,8 @@
import java.awt.event.*;
import java.util.Observable;
-public class ActionHandler extends Observable implements ActionListener, ItemListener {
+
+public class ActionHandler extends Observable implements ActionListener, ItemListener, MouseListener {
private DLLearnerModel model;
private SuggestEquivalentClassView view;
private Thread dlLearner;
@@ -17,8 +18,8 @@
if(z.getActionCommand().equals("RUN"))
{
+ model.setDLLearnerModel(view.getPositiveVector(), view.getNegativeVector(),view.getUri());
dlLearner = new Thread(model);
- System.out.println("test");
view.getStartButton().setEnabled(false);
view.getStopButton().setEnabled(true);
dlLearner.start();
@@ -26,21 +27,27 @@
if(z.getActionCommand().equals("Cancel"))
{
- System.out.println(dlLearner.isInterrupted());
model.getLearningAlgorithm().stop();
- view.destroyListener();
view.getStartButton().setEnabled(true);
view.getStopButton().setEnabled(false);
- System.out.println(dlLearner.isInterrupted());
String error = "Learning aborted";
dlLearner.interrupt();
- System.out.println(dlLearner.isInterrupted());
view.renderErrorMessage(error);
}
if(z.getActionCommand().equals("ADD"))
{
- String message ="Ausgezeichnet *Mr.Burns*";
+ String suggest=view.getSuggestionList().getSelectedValue().toString();
+ for(int i = 0;i<model.getSolutions().length;i++)
+ {
+ if(model.getSolutions()[i].toString().equals(suggest))
+ {
+ model.changeDLLearnerDescriptionsToOWLDescriptions(model.getSolutions()[i]);
+ System.out.println(model.getSolutions()[i].toString());
+ }
+ }
+
+ String message ="Concept added";
view.renderErrorMessage(message);
}
}
@@ -51,15 +58,34 @@
}
- public void textValueChanged(TextEvent t)
+ public void mouseReleased(MouseEvent m)
{
+ }
+
+ public void mouseEntered(MouseEvent m)
+ {
}
- public void destroyThread()
+ public void mouseClicked(MouseEvent m)
{
- view.getStartButton().setEnabled(true);
- view.getStopButton().setEnabled(false);
+ System.out.println("mouseClicked: ");
}
+
+ public void mouseExited(MouseEvent m)
+ {
+
+ }
+
+ public void mousePressed(MouseEvent m)
+ {
+
+ }
+ public void textValueChanged(TextEvent t)
+ {
+
+ }
+
+
}
Modified: trunk/src/dl-learner/org/dllearner/tools/protege/ButtonList.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/protege/ButtonList.java 2008-04-22 17:43:49 UTC (rev 814)
+++ trunk/src/dl-learner/org/dllearner/tools/protege/ButtonList.java 2008-04-22 18:11:28 UTC (rev 815)
@@ -14,7 +14,7 @@
public ButtonList(OWLEditorKit editorKit)
{
super(editorKit.getOWLModelManager().getOWLOntologyManager());
- addSection(new OWLEquivalentClassesAxiomFrameSection(editorKit, this));
+ //addSection(new SuggestButton(editorKit, this));
addSection(new SuggestEquivalentClassButton(editorKit, this));
addSection(new OWLSubClassAxiomFrameSection(editorKit, this));
addSection(new InheritedAnonymousClassesFrameSection(editorKit, this));
Modified: trunk/src/dl-learner/org/dllearner/tools/protege/DLLearnerModel.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/protege/DLLearnerModel.java 2008-04-22 17:43:49 UTC (rev 814)
+++ trunk/src/dl-learner/org/dllearner/tools/protege/DLLearnerModel.java 2008-04-22 18:11:28 UTC (rev 815)
@@ -3,16 +3,31 @@
import org.dllearner.core.ComponentManager;
import org.dllearner.kb.OWLFile;
+import java.util.HashSet;
import java.util.Observable;
import java.util.Set;
import java.util.TreeSet;
import java.util.Vector;
import java.io.*;
+import org.dllearner.core.owl.Description;
import javax.swing.JCheckBox;
import org.dllearner.algorithms.refinement.*;
+//import org.coode.manchesterowlsyntax.ManchesterOWLSyntaxEditorParser;
import org.dllearner.core.*;
import org.dllearner.reasoning.*;
import org.dllearner.learningproblems.*;
+import org.semanticweb.owl.apibinding.OWLManager;
+import org.semanticweb.owl.model.AddAxiom;
+import org.semanticweb.owl.model.OWLAxiom;
+import org.semanticweb.owl.model.OWLClass;
+import org.semanticweb.owl.model.OWLDataFactory;
+import org.semanticweb.owl.model.OWLDescription;
+import org.semanticweb.owl.model.OWLOntology;
+import org.dllearner.reasoning.OWLAPIReasoner;
+import org.semanticweb.owl.model.OWLOntologyChangeException;
+import org.semanticweb.owl.model.OWLOntologyManager;
+import org.semanticweb.owl.model.OWLOntologyStorageException;
+import org.semanticweb.owl.model.UnknownOWLOntologyException;
public class DLLearnerModel extends Observable implements Runnable{
private String[] componenten={"org.dllearner.kb.OWLFile","org.dllearner.reasoning.OWLAPIReasoner",
@@ -22,12 +37,15 @@
private Vector<JCheckBox> positiv;
private Vector<JCheckBox> negativ;
private ComponentManager cm;
- private ReasonerComponent reasoner;
+ //private ReasonerComponent reasoner;
private ReasoningService rs;
private static final int anzahl = 10;
- private String[] description = new String[anzahl];
+ private Description[] description = new Description[anzahl];
private LearningProblem lp;
private LearningAlgorithm la = null;
+ OWLAPIReasoner reasoner;
+
+
public DLLearnerModel()
{
@@ -52,6 +70,7 @@
}
public void run()
{
+ resetSuggestionList();
ComponentManager.setComponentClasses(componenten);
// get singleton instance of component manager
cm = ComponentManager.getInstance();
@@ -120,13 +139,17 @@
// start the algorithm and print the best concept found
la.start();
- System.out.println(la.getSolutionScore());
- description[0]=la.getBestSolution().toString();
+ description = new Description[la.getBestSolutions(anzahl).size()];
+ for(int j = 0;j<la.getBestSolutions(anzahl).size();j++)
+ {
+ description[j]=la.getBestSolutions(anzahl).get(j);
+ }
setChanged();
notifyObservers(description);
+
}
- public String[] getSolutions()
+ public Description[] getSolutions()
{
return description;
}
@@ -171,20 +194,67 @@
return uri;
}
- public void setDescriptionList(String[] list)
+ public void setDescriptionList(Description[] list)
{
description=list;
}
- public String[] getSollutions()
- {
- return description;
- }
public LearningAlgorithm getLearningAlgorithm()
{
return la;
}
+
+ public void resetSuggestionList()
+ {
+ /*for(int i=0;i<description.length;i++)
+ {
+ description[i]="";
+ }*/
+ }
+
+ public void changeDLLearnerDescriptionsToOWLDescriptions(Description desc)
+ {
+ OWLDescription newConceptOWLAPI = OWLAPIDescriptionConvertVisitor.getOWLDescription(desc);
+ System.out.println(newConceptOWLAPI);
+ //OWLDescription oldConceptOWLAPI = OWLAPIDescriptionConvertVisitor.getOWLDescription(concept);
+ }
+
+ public void addAxiomToOWL(Description desc,Description concept){
+ OWLDescription newConceptOWLAPI = OWLAPIDescriptionConvertVisitor.getOWLDescription(desc);
+ OWLDescription oldConceptOWLAPI = OWLAPIDescriptionConvertVisitor.getOWLDescription(concept);
+
+ OWLOntology ontology = reasoner.getOWLAPIOntologies().get(0);
+
+ OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
+
+ OWLDataFactory factory = manager.getOWLDataFactory();
+
+ Set<OWLDescription> ds = new HashSet<OWLDescription>();
+ ds.add(newConceptOWLAPI);
+ ds.add(oldConceptOWLAPI);
+
+ OWLAxiom axiomOWLAPI = factory.getOWLEquivalentClassesAxiom(ds);
+
+
+ AddAxiom axiom = new AddAxiom(ontology, axiomOWLAPI);
+ try {
+ manager.applyChange(axiom);
+ } catch (OWLOntologyChangeException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ try {
+ manager.saveOntology(ontology);
+ } catch (UnknownOWLOntologyException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ } catch (OWLOntologyStorageException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ }
+
}
Modified: trunk/src/dl-learner/org/dllearner/tools/protege/META-INF/MANIFEST.MF
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/protege/META-INF/MANIFEST.MF 2008-04-22 17:43:49 UTC (rev 814)
+++ trunk/src/dl-learner/org/dllearner/tools/protege/META-INF/MANIFEST.MF 2008-04-22 18:11:28 UTC (rev 815)
@@ -6,7 +6,7 @@
Bundle-Description: blablabla
Bundle-Vendor: blablabla
Bundle-DocURL: blablabla
-Bundle-ClassPath: .,lib/junit-4.4.jar,log4j.jar,lib/pellet/pellet.jar,lib/pellet/aterm-java-1.6.jar,lib/pellet/relaxngDatatype.jar,lib/pellet/xsdlib.jar,lib/jena/commons-logging-1.1.jar
+Bundle-ClassPath: .,lib/junit-4.4.jar,lib/pellet/pellet.jar,lib/pellet/aterm-java-1.6.jar,lib/pellet/relaxngDatatype.jar,lib/pellet/xsdlib.jar,lib/jena/commons-logging-1.1.jar
Import-Package: org.osgi.framework,org.apache.log4j
Export-Package: lib
Bundle-Version: 1.0.0
Modified: trunk/src/dl-learner/org/dllearner/tools/protege/SuggestEquivalentClassView.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/protege/SuggestEquivalentClassView.java 2008-04-22 17:43:49 UTC (rev 814)
+++ trunk/src/dl-learner/org/dllearner/tools/protege/SuggestEquivalentClassView.java 2008-04-22 18:11:28 UTC (rev 815)
@@ -5,6 +5,7 @@
import java.awt.GridLayout;
import java.util.*;
+import org.semanticweb.owl.model.OWLAxiom;
import org.semanticweb.owl.model.OWLClass;
import org.protege.editor.owl.ui.frame.OWLFrame;
import javax.swing.JButton;
@@ -13,6 +14,8 @@
import javax.swing.JComponent;
import javax.swing.JLabel;
import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import org.dllearner.core.owl.Description;
import javax.swing.JList;
import org.protege.editor.owl.OWLEditorKit;
@@ -34,13 +37,15 @@
private JList suggest;
private Object[] instances;
private JLabel neg;
+ private JScrollPane scrollPane;
+ private JScrollPane suggestScroll;
private final static Color Color_RED = Color.red;
private JButton cancel;
private JLabel errorMessage;
private ActionHandler action;
private DLLearnerModel model;
- private String[] descriptions = new String[10];
- //private OWLFrame<OWLClass> aktuell;
+ private Description[] descriptions = new Description[10];
+ private OWLFrame<OWLClass> aktuell;
private SuggestEquivalentClassView view;
public void update(Observable m,Object c)
@@ -54,11 +59,15 @@
public SuggestEquivalentClassView(OWLEditorKit editorKit, OWLDescription description, OWLFrame<OWLClass> h) {
editor = editorKit;
- //aktuell = h;
+ scrollPane = new JScrollPane(JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED,JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED);
+ suggestScroll = new JScrollPane(JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED,JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED);
+ aktuell = h;
model = new DLLearnerModel();
errorMessage = new JLabel();
+ System.out.println("test: "+aktuell.getRootObject());
errorMessage.setForeground(Color_RED);
- suggest = new JList(descriptions);
+ suggest = new JList();
+ suggest.setEnabled(true);
learner = new JPanel();
learner.setLayout(null);
learner.setPreferredSize(new Dimension(600, 480));
@@ -70,7 +79,6 @@
accept.setPreferredSize(new Dimension(290,50));
option = new JPanel(new GridLayout(0,2));
cancel.setEnabled(false);
- option.setPreferredSize(new Dimension(290,0));
model.addObserver(this);
}
@@ -91,9 +99,10 @@
}
- public void makeView()
+ public JComponent makeView()
{
- suggest = new JList(descriptions);
+ suggest = new JList();
+
option.add(pos);
option.add(neg);
instances=editor.getOWLModelManager().getActiveOntology().getReferencedIndividuals().toArray();
@@ -111,26 +120,48 @@
option.add(positive.get(j));
option.add(negative.get(j));
}
- //test.add(option);
- option.setBounds(0, 0, 490, 250);
- run.setBounds(0,260,200,30);
+ for(int j = 0; j<positive.size();j++)
+ {
+ Object[] test=editor.getOWLModelManager().getActiveOntology().getClassAssertionAxioms(aktuell.getRootObject()).toArray();
+ for(int i = 0;i<test.length;i++)
+ {
+ String k = test[i].toString();
+ String l = instances[j].toString();
+ if(k.contains(l)&&positive.get(j).getText().contains(l))
+ {
+ JCheckBox n=positive.get(j);
+ n.setSelected(true);
+ positive.set(j, n);
+ }
+ }
+
+
+
+ }
+ scrollPane.setViewportView(option);
+ scrollPane.setBounds(0, 0, 490, 250);
+ run.setBounds(0,260,200,30);
cancel.setBounds(210,260,200,30);
- suggest.setBounds(0,300,490,110);
+ suggestScroll.setBounds(0,300,490,110);
+ suggestScroll.setViewportView(suggest);
+ suggestScroll.setVisible(true);
+ //suggest.setBounds(0,300,490,110);
accept.setBounds(0,420,200,30);
errorMessage.setBounds(210,420,300,30);
System.out.println("blub2");
- learner.add(option);
+ learner.add(scrollPane);
learner.add(run);
learner.add(cancel);
learner.add(suggest);
learner.add(accept);
learner.add(errorMessage);
addListener();
- model.setDLLearnerModel(positive,negative,getUri());
+ return learner;
}
public JComponent getEditorComponent()
{
+ System.out.println("das ist ein test");
makeView();
return learner;
}
@@ -145,13 +176,11 @@
option.removeAll();
}
suggest.removeAll();
+ model.resetSuggestionList();
+ learner.removeAll();
positive.removeAllElements();
negative.removeAllElements();
errorMessage.setText("");
- for(int i=0; i<descriptions.length;i++)
- {
- descriptions[i]="";
- }
}
/**
* Methode die alle Buttons und CheckBoxes an dem ActionListener anmeldet
@@ -161,6 +190,7 @@
run.addActionListener(this.action);
accept.addActionListener(this.action);
cancel.addActionListener(this.action);
+
for(int i=0;i<positive.size();i++)
{
positive.get(i).addItemListener(action);
@@ -171,22 +201,7 @@
negative.get(i).addItemListener(action);
}
}
- public void destroyListener()
- {
- run.removeActionListener(this.action);
- accept.removeActionListener(this.action);
- System.out.println("hihihihi");
- cancel.removeActionListener(this.action);
- for(int i=0;i<positive.size();i++)
- {
- positive.get(i).removeItemListener(action);
- }
-
- for(int i=0;i<negative.size();i++)
- {
- negative.get(i).removeItemListener(action);
- }
- }
+
public void setSuggestedClass()
{
//TODO: Description umwandeln und in ontologie einfuegen
@@ -212,14 +227,7 @@
{
return super.getEditedObjects();
}
- private void resetPanel()
- {
- option.removeAll();
- System.out.println("blub1");
- positive.removeAllElements();
- negative.removeAllElements();
- learner.removeAll();
- }
+
public void release()
{
@@ -232,25 +240,50 @@
run.setEnabled(true);
cancel.setEnabled(false);
System.out.println("blub");
+ System.out.println(((DLLearnerModel)model).getSolutions().length);
descriptions = ((DLLearnerModel)model).getSolutions();
- resetPanel();
- makeView();
+ suggest=new JList(descriptions);
+ //learner.remove(3);
+ suggest.setBounds(0,300,490,110);
+ learner.add(suggest);
+ unsetJCheckBoxen();
+ suggest.addMouseListener(action);
+
+ returnLearner();
+
}
}
- public void disableRunButtons()
+ public JComponent returnLearner()
{
- run.setEnabled(false);
- cancel.setEnabled(true);
- resetPanel();
- makeView();
+ return learner;
}
public void renderErrorMessage(String s)
{
errorMessage.setText(s);
}
-
+ private void unsetJCheckBoxen()
+ {
+ for(int j=0;j<positive.size();j++)
+ {
+ if(positive.get(j).isSelected())
+ {
+ JCheckBox i = positive.get(j);
+ i.setSelected(false);
+ positive.set(j, i);
+ }
+ }
+ for(int j=0;j<negative.size();j++)
+ {
+ if(negative.get(j).isSelected())
+ {
+ JCheckBox i = negative.get(j);
+ i.setSelected(false);
+ negative.set(j, i);
+ }
+ }
+ }
public JButton getStartButton()
{
return run;
@@ -260,4 +293,24 @@
{
return cancel;
}
+
+ public Vector<JCheckBox> getPositiveVector()
+ {
+ return positive;
+ }
+
+ public Vector<JCheckBox> getNegativeVector()
+ {
+
+ return negative;
+ }
+
+ public JList getSuggestionList()
+ {
+ return suggest;
+ }
+
+
+
+
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ku...@us...> - 2008-04-22 17:43:54
|
Revision: 814
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=814&view=rev
Author: kurzum
Date: 2008-04-22 10:43:49 -0700 (Tue, 22 Apr 2008)
Log Message:
-----------
new configoption.txt configgenerator moved to scripts
Modified Paths:
--------------
trunk/doc/configOptions.txt
trunk/src/dl-learner/org/dllearner/utilities/LearnSparql.java
Added Paths:
-----------
trunk/src/dl-learner/org/dllearner/scripts/ConfigDocumentationGenerator.java
Removed Paths:
-------------
trunk/src/dl-learner/org/dllearner/core/config/ConfigDocumentationGenerator.java
Modified: trunk/doc/configOptions.txt
===================================================================
--- trunk/doc/configOptions.txt 2008-04-22 17:34:43 UTC (rev 813)
+++ trunk/doc/configOptions.txt 2008-04-22 17:43:49 UTC (rev 814)
@@ -603,6 +603,24 @@
default value: true
CLI usage: refexamples.useBooleanDatatypes = true;
+option name: maxExecutionTimeInSeconds
+description: algorithm will stop after specified seconds
+values: class org.dllearner.core.config.IntegerConfigOption
+default value: 0
+CLI usage: refexamples.maxExecutionTimeInSeconds = 0;
+
+option name: minExecutionTimeInSeconds
+description: algorithm will run at least specified seconds
+values: class org.dllearner.core.config.IntegerConfigOption
+default value: 0
+CLI usage: refexamples.minExecutionTimeInSeconds = 0;
+
+option name: guaranteeXgoodDescriptions
+description: algorithm will run until X good (100%) concept descritpions are found
+values: class org.dllearner.core.config.IntegerConfigOption
+default value: 1
+CLI usage: refexamples.guaranteeXgoodDescriptions = 1;
+
option name: noisePercentage
description: the (approximated) percentage of noise within the examples
values: class org.dllearner.core.config.DoubleConfigOption min 0.0 max 100.0
Deleted: trunk/src/dl-learner/org/dllearner/core/config/ConfigDocumentationGenerator.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/config/ConfigDocumentationGenerator.java 2008-04-22 17:34:43 UTC (rev 813)
+++ trunk/src/dl-learner/org/dllearner/core/config/ConfigDocumentationGenerator.java 2008-04-22 17:43:49 UTC (rev 814)
@@ -1,45 +0,0 @@
-/**
- * Copyright (C) 2007, 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/>.
- *
- */
-package org.dllearner.core.config;
-
-import java.io.File;
-
-import org.dllearner.core.ComponentManager;
-
-/**
- * Collects information about all used configuration options and
- * writes them into a file. This way the documentation is always
- * in sync with the source code.
- *
- * @author Jens Lehmann
- *
- */
-public class ConfigDocumentationGenerator {
-
- /**
- * @param args
- */
- public static void main(String[] args) {
- File file = new File("doc/configOptions.txt");
- ComponentManager cm = ComponentManager.getInstance();
- cm.writeConfigDocumentation(file);
- }
-
-}
Copied: trunk/src/dl-learner/org/dllearner/scripts/ConfigDocumentationGenerator.java (from rev 808, trunk/src/dl-learner/org/dllearner/core/config/ConfigDocumentationGenerator.java)
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/ConfigDocumentationGenerator.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/scripts/ConfigDocumentationGenerator.java 2008-04-22 17:43:49 UTC (rev 814)
@@ -0,0 +1,46 @@
+/**
+ * Copyright (C) 2007, 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/>.
+ *
+ */
+package org.dllearner.scripts;
+
+import java.io.File;
+
+import org.dllearner.core.ComponentManager;
+
+/**
+ * Collects information about all used configuration options and
+ * writes them into a file. This way the documentation is always
+ * in sync with the source code.
+ *
+ * @author Jens Lehmann
+ *
+ */
+public class ConfigDocumentationGenerator {
+
+ /**
+ * @param args
+ */
+ public static void main(String[] args) {
+ File file = new File("doc/configOptions.txt");
+ ComponentManager cm = ComponentManager.getInstance();
+ cm.writeConfigDocumentation(file);
+ System.out.println("Done");
+ }
+
+}
Modified: trunk/src/dl-learner/org/dllearner/utilities/LearnSparql.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/LearnSparql.java 2008-04-22 17:34:43 UTC (rev 813)
+++ trunk/src/dl-learner/org/dllearner/utilities/LearnSparql.java 2008-04-22 17:43:49 UTC (rev 814)
@@ -70,7 +70,7 @@
cm.applyConfigEntry(la,"useCardinalityRestrictions",false);
cm.applyConfigEntry(la,"useNegation",false);
cm.applyConfigEntry(la,"minExecutionTimeInSeconds",0);
- cm.applyConfigEntry(la,"maxExecutionTimeInSeconds",1800);
+ cm.applyConfigEntry(la,"maxExecutionTimeInSeconds",900);
cm.applyConfigEntry(la,"guaranteeXgoodDescriptions",999999);
//cm.applyConfigEntry(la,"quiet",false);
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ku...@us...> - 2008-04-22 17:35:02
|
Revision: 813
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=813&view=rev
Author: kurzum
Date: 2008-04-22 10:34:43 -0700 (Tue, 22 Apr 2008)
Log Message:
-----------
small changes
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/scripts/SPARQLMassLearning.java
trunk/src/dl-learner/org/dllearner/utilities/LearnSparql.java
Modified: trunk/src/dl-learner/org/dllearner/scripts/SPARQLMassLearning.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/SPARQLMassLearning.java 2008-04-22 17:29:06 UTC (rev 812)
+++ trunk/src/dl-learner/org/dllearner/scripts/SPARQLMassLearning.java 2008-04-22 17:34:43 UTC (rev 813)
@@ -28,8 +28,8 @@
//vars
boolean useRelated = true;
boolean useSuperClasses = true;
- int poslimit = 50;
- int neglimit = 100;
+ int poslimit = 300;
+ int neglimit = 600;
try {
Modified: trunk/src/dl-learner/org/dllearner/utilities/LearnSparql.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/LearnSparql.java 2008-04-22 17:29:06 UTC (rev 812)
+++ trunk/src/dl-learner/org/dllearner/utilities/LearnSparql.java 2008-04-22 17:34:43 UTC (rev 813)
@@ -69,9 +69,9 @@
cm.applyConfigEntry(la,"useExistsConstructor",true);
cm.applyConfigEntry(la,"useCardinalityRestrictions",false);
cm.applyConfigEntry(la,"useNegation",false);
- cm.applyConfigEntry(la,"minExecutionTimeInSeconds",100);
- cm.applyConfigEntry(la,"maxExecutionTimeInSeconds",100);
- cm.applyConfigEntry(la,"guaranteeXgoodDescriptions",1);
+ cm.applyConfigEntry(la,"minExecutionTimeInSeconds",0);
+ cm.applyConfigEntry(la,"maxExecutionTimeInSeconds",1800);
+ cm.applyConfigEntry(la,"guaranteeXgoodDescriptions",999999);
//cm.applyConfigEntry(la,"quiet",false);
if(ignoredConcepts.size()>0)
@@ -82,7 +82,7 @@
la.start();
//System.out.println("best"+la(20));
- ((ExampleBasedROLComponent)la).printBestSolutions(200);
+ ((ExampleBasedROLComponent)la).printBestSolutions(10000);
}catch (Exception e) {e.printStackTrace();}
//System.out.println( la.getBestSolution());;
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ku...@us...> - 2008-04-22 17:29:31
|
Revision: 812
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=812&view=rev
Author: kurzum
Date: 2008-04-22 10:29:06 -0700 (Tue, 22 Apr 2008)
Log Message:
-----------
Script done, validation still needed, incorporated superclasses with negative examples
made an extra class AutomaticExampleFinderSPARQL for reuse in ORE tool
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java
trunk/src/dl-learner/org/dllearner/kb/sparql/Cache.java
trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQueryDescriptionConvertVisitor.java
trunk/src/dl-learner/org/dllearner/utilities/LearnSparql.java
Added Paths:
-----------
trunk/src/dl-learner/org/dllearner/scripts/SPARQLMassLearning.java
trunk/src/dl-learner/org/dllearner/utilities/AutomaticExampleFinderSPARQL.java
trunk/src/dl-learner/org/dllearner/utilities/SetManipulation.java
Removed Paths:
-------------
trunk/src/dl-learner/org/dllearner/scripts/SPARQLPreparation.java
Modified: trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java 2008-04-22 17:15:27 UTC (rev 811)
+++ trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java 2008-04-22 17:29:06 UTC (rev 812)
@@ -776,6 +776,7 @@
logger.debug(bestNodeString);
logger.debug(startNode.getStats(nrOfPositiveExamples, nrOfNegativeExamples));
logger.debug(bestNodeStringKBSyntax);
+ if(bestNode.getCoveredNegatives().size()<=3)logger.debug("covered negs: "+bestNode.getCoveredNegatives());
String expandedNodeString = "next expanded node: " + candidates.last().getShortDescription(nrOfPositiveExamples, nrOfNegativeExamples, baseURI);
// searchTree += expandedNodeString + "\n";
logger.debug(expandedNodeString);
Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/Cache.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/Cache.java 2008-04-22 17:15:27 UTC (rev 811)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/Cache.java 2008-04-22 17:29:06 UTC (rev 812)
@@ -73,6 +73,13 @@
private long freshnessSeconds = 15 * 24 * 60 * 60;
/**
+ * same ad Cache(String) default is "cache"
+ */
+ public Cache() {
+ this("cache");
+ }
+
+ /**
* Constructor for the cache itself.
*
* @param cacheDir
Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQueryDescriptionConvertVisitor.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQueryDescriptionConvertVisitor.java 2008-04-22 17:15:27 UTC (rev 811)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQueryDescriptionConvertVisitor.java 2008-04-22 17:29:06 UTC (rev 812)
@@ -6,7 +6,9 @@
import java.util.Stack;
import java.util.TreeSet;
+import org.apache.log4j.Logger;
import org.dllearner.algorithms.gp.ADC;
+import org.dllearner.core.ComponentManager;
import org.dllearner.core.owl.DatatypeExactCardinalityRestriction;
import org.dllearner.core.owl.DatatypeMaxCardinalityRestriction;
import org.dllearner.core.owl.DatatypeMinCardinalityRestriction;
@@ -37,7 +39,8 @@
*/
public class SparqlQueryDescriptionConvertVisitor implements DescriptionVisitor{
- public static boolean debug_flag=false;
+ private static Logger logger = Logger.getLogger(ComponentManager.class);
+
private Stack<String> stack = new Stack<String>();
@@ -131,42 +134,42 @@
* @see org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl.Negation)
*/
public void visit(Negation description) {
- print("Negation");
+ logger.trace("Negation");
}
/* (non-Javadoc)
* @see org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl.ObjectAllRestriction)
*/
public void visit(ObjectAllRestriction description) {
- print("ObjectAllRestriction");
+ logger.trace("ObjectAllRestriction");
}
/* (non-Javadoc)
* @see org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl.ObjectSomeRestriction)
*/
public void visit(ObjectSomeRestriction description) {
- print("ObjectSomeRestriction");
+ logger.trace("ObjectSomeRestriction");
query+="?"+stack.peek()+" <"+description.getRole()+"> ?object"+currentObject+".";
stack.push("object"+currentObject);
currentObject++;
description.getChild(0).accept(this);
stack.pop();
- print(description.getRole().toString());
- print(description.getChild(0).toString());
+ logger.trace(description.getRole().toString());
+ logger.trace(description.getChild(0).toString());
}
/* (non-Javadoc)
* @see org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl.Nothing)
*/
public void visit(Nothing description) {
- print("Nothing");
+ logger.trace("Nothing");
}
/* (non-Javadoc)
* @see org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl.Thing)
*/
public void visit(Thing description) {
- print("Thing");
+ logger.trace("Thing");
}
@@ -174,7 +177,7 @@
* @see org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl.Intersection)
*/
public void visit(Intersection description) {
- print("Intersection");
+ logger.trace("Intersection");
description.getChild(0).accept(this);
query+=".";
description.getChild(1).accept(this);
@@ -185,7 +188,7 @@
* @see org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl.Union)
*/
public void visit(Union description) {
- print("Union");
+ logger.trace("Union");
query+="{";
description.getChild(0).accept(this);
query+="} UNION {";
@@ -197,42 +200,42 @@
* @see org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl.ObjectMinCardinalityRestriction)
*/
public void visit(ObjectMinCardinalityRestriction description) {
- print("ObjectMinCardinalityRestriction");
+ logger.trace("ObjectMinCardinalityRestriction");
}
/* (non-Javadoc)
* @see org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl.ObjectExactCardinalityRestriction)
*/
public void visit(ObjectExactCardinalityRestriction description) {
- print("ObjectExactCardinalityRestriction");
+ logger.trace("ObjectExactCardinalityRestriction");
}
/* (non-Javadoc)
* @see org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl.ObjectMaxCardinalityRestriction)
*/
public void visit(ObjectMaxCardinalityRestriction description) {
- print("ObjectMaxCardinalityRestriction");
+ logger.trace("ObjectMaxCardinalityRestriction");
}
/* (non-Javadoc)
* @see org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl.ObjectValueRestriction)
*/
public void visit(ObjectValueRestriction description) {
- print("ObjectValueRestriction");
+ logger.trace("ObjectValueRestriction");
}
/* (non-Javadoc)
* @see org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl.DatatypeValueRestriction)
*/
public void visit(DatatypeValueRestriction description) {
- print("DatatypeValueRestriction");
+ logger.trace("DatatypeValueRestriction");
}
/* (non-Javadoc)
* @see org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl.NamedClass)
*/
public void visit(NamedClass description) {
- print("NamedClass");
+ logger.trace("NamedClass");
query+="?"+stack.peek()+" a <"+description.getName()+">";
}
@@ -240,44 +243,37 @@
* @see org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.algorithms.gp.ADC)
*/
public void visit(ADC description) {
- print("ADC");
+ logger.trace("ADC");
}
/* (non-Javadoc)
* @see org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl.DatatypeMinCardinalityRestriction)
*/
public void visit(DatatypeMinCardinalityRestriction description) {
- print("DatatypeMinCardinalityRestriction");
+ logger.trace("DatatypeMinCardinalityRestriction");
}
/* (non-Javadoc)
* @see org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl.DatatypeExactCardinalityRestriction)
*/
public void visit(DatatypeExactCardinalityRestriction description) {
- print("DatatypeExactCardinalityRestriction");
+ logger.trace("DatatypeExactCardinalityRestriction");
}
/* (non-Javadoc)
* @see org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl.DatatypeMaxCardinalityRestriction)
*/
public void visit(DatatypeMaxCardinalityRestriction description) {
- print("DatatypeMaxCardinalityRestriction");
+ logger.trace("DatatypeMaxCardinalityRestriction");
}
/* (non-Javadoc)
* @see org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl.DatatypeSomeRestriction)
*/
public void visit(DatatypeSomeRestriction description) {
- print("DatatypeSomeRestriction");
+ logger.trace("DatatypeSomeRestriction");
}
- /**
- * TODO should be replaced by logger.debug or sth like that
- * @param str
- */
- public void print(String str){
- if(debug_flag)System.out.println(str);
- }
}
Copied: trunk/src/dl-learner/org/dllearner/scripts/SPARQLMassLearning.java (from rev 810, trunk/src/dl-learner/org/dllearner/scripts/SPARQLPreparation.java)
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/SPARQLMassLearning.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/scripts/SPARQLMassLearning.java 2008-04-22 17:29:06 UTC (rev 812)
@@ -0,0 +1,118 @@
+package org.dllearner.scripts;
+
+import java.util.SortedSet;
+import java.util.TreeSet;
+
+import org.apache.log4j.ConsoleAppender;
+import org.apache.log4j.Level;
+import org.apache.log4j.Logger;
+import org.apache.log4j.SimpleLayout;
+import org.dllearner.kb.sparql.Cache;
+import org.dllearner.kb.sparql.configuration.SparqlEndpoint;
+import org.dllearner.utilities.AutomaticExampleFinderSPARQL;
+import org.dllearner.utilities.ConfWriter;
+import org.dllearner.utilities.LearnSparql;
+import org.dllearner.utilities.SimpleClock;
+
+public class SPARQLMassLearning {
+
+ static Cache c;
+ static SparqlEndpoint se;
+ private static Logger logger = Logger.getRootLogger();
+ /**
+ * @param args
+ */
+ public static void main(String[] args) {
+ init();
+
+ //vars
+ boolean useRelated = true;
+ boolean useSuperClasses = true;
+ int poslimit = 50;
+ int neglimit = 100;
+
+
+ try {
+
+ SimpleClock sc=new SimpleClock();
+ SortedSet<String> concepts = new TreeSet<String>();
+ //concepts.add("\"http://dbpedia.org/class/yago/Person100007846\"");
+ concepts.add("\"http://dbpedia.org/class/yago/FieldMarshal110086821\"");
+ SortedSet<String> posExamples = new TreeSet<String>();
+ SortedSet<String> negExamples = new TreeSet<String>();
+ String url = "http://dbpedia.openlinksw.com:8890/sparql";
+ //HashMap<String, ResultSet> result = new HashMap<String, ResultSet>();
+ //HashMap<String, String> result2 = new HashMap<String, String>();
+
+ AutomaticExampleFinderSPARQL ae= new AutomaticExampleFinderSPARQL( se);
+ ae.init(concepts.first(), useRelated, useSuperClasses, poslimit, neglimit);
+
+ posExamples = ae.getPosExamples();
+ negExamples = ae.getNegExamples();
+
+ System.out.println(posExamples);
+ System.out.println(negExamples);
+ //System.exit(0);
+
+
+ //
+ new ConfWriter().writeSPARQL("aaa.conf", posExamples, negExamples, url, new TreeSet<String>());
+ new LearnSparql().learn(posExamples, negExamples, "http://dbpedia.openlinksw.com:8890/sparql", new TreeSet<String>());
+
+ sc.printAndSet("Finished");
+ } catch (Exception e) {
+ e.printStackTrace();
+
+ }
+
+ }
+
+ /***************************************************************************
+ * *********************OLDCODE String
+ * conj="(\"http://dbpedia.org/class/yago/Person100007846\" AND
+ * \"http://dbpedia.org/class/yago/Head110162991\")";
+ *
+ *
+ * concepts.add("EXISTS \"http://dbpedia.org/property/disambiguates\".TOP");
+ * concepts.add("EXISTS
+ * \"http://dbpedia.org/property/successor\".\"http://dbpedia.org/class/yago/Person100007846\"");
+ * concepts.add("EXISTS \"http://dbpedia.org/property/successor\"."+conj);
+ * //concepts.add("ALL \"http://dbpedia.org/property/disambiguates\".TOP");
+ * //concepts.add("ALL
+ * \"http://dbpedia.org/property/successor\".\"http://dbpedia.org/class/yago/Person100007846\"");
+ * concepts.add("\"http://dbpedia.org/class/yago/Person100007846\"");
+ * concepts.add(conj);
+ * concepts.add("(\"http://dbpedia.org/class/yago/Person100007846\" OR
+ * \"http://dbpedia.org/class/yago/Head110162991\")");
+ *
+ * //concepts.add("NOT \"http://dbpedia.org/class/yago/Person100007846\"");
+ *
+ * for (String kbsyntax : concepts) {
+ * result.put(kbsyntax,queryConcept(kbsyntax)); }
+ * System.out.println("************************"); for (String string :
+ * result.keySet()) { System.out.println("KBSyntayString: "+string);
+ * System.out.println("Query:\n"+result.get(string).hasNext());
+ * System.out.println("************************"); }
+ **************************************************************************/
+
+
+
+
+
+ public static void init() {
+
+ se = SparqlEndpoint.dbpediaEndpoint();
+ // create logger (a simple logger which outputs
+ // its messages to the console)
+ SimpleLayout layout = new SimpleLayout();
+ ConsoleAppender consoleAppender = new ConsoleAppender(layout);
+ logger.removeAllAppenders();
+ logger.addAppender(consoleAppender);
+ logger.setLevel(Level.DEBUG);
+
+
+ }
+
+
+
+}
Deleted: trunk/src/dl-learner/org/dllearner/scripts/SPARQLPreparation.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/SPARQLPreparation.java 2008-04-22 17:15:27 UTC (rev 811)
+++ trunk/src/dl-learner/org/dllearner/scripts/SPARQLPreparation.java 2008-04-22 17:29:06 UTC (rev 812)
@@ -1,176 +0,0 @@
-package org.dllearner.scripts;
-
-import java.util.Random;
-import java.util.SortedSet;
-import java.util.TreeSet;
-
-import javax.sound.midi.SysexMessage;
-
-import org.apache.log4j.ConsoleAppender;
-import org.apache.log4j.Level;
-import org.apache.log4j.Logger;
-import org.apache.log4j.SimpleLayout;
-import org.dllearner.kb.sparql.Cache;
-import org.dllearner.kb.sparql.SparqlQuery;
-import org.dllearner.kb.sparql.SparqlQueryDescriptionConvertVisitor;
-import org.dllearner.kb.sparql.configuration.SparqlEndpoint;
-import org.dllearner.utilities.ConfWriter;
-import org.dllearner.utilities.JenaResultSetConvenience;
-import org.dllearner.utilities.LearnSparql;
-import org.dllearner.utilities.SimpleClock;
-
-import com.hp.hpl.jena.query.ResultSet;
-
-public class SPARQLPreparation {
-
- static Cache c;
- static SparqlEndpoint se;
- private static Logger logger = Logger.getRootLogger();
- /**
- * @param args
- */
- public static void main(String[] args) {
- init();
- try {
-
-
-
- SimpleClock sc=new SimpleClock();
- SortedSet<String> concepts = new TreeSet<String>();
- //concepts.add("\"http://dbpedia.org/class/yago/Person100007846\"");
- concepts.add("\"http://dbpedia.org/class/yago/FieldMarshal110086821\"");
- SortedSet<String> posExamples = new TreeSet<String>();
- SortedSet<String> negExamples = new TreeSet<String>();
- String url = "http://dbpedia.openlinksw.com:8890/sparql";
- //HashMap<String, ResultSet> result = new HashMap<String, ResultSet>();
- //HashMap<String, String> result2 = new HashMap<String, String>();
-
- //System.out.println(concepts.first());
- posExamples = new JenaResultSetConvenience(queryConcept(concepts.first(),0))
- .getStringListForVariable("subject");
-
- for (String string : posExamples) {
- negExamples.addAll( getObjects(string));
- //if(neg.size()>=1)System.out.println(neg);
- }
-
- /*for (String string2 : negExamples) {
- if(posExamples.contains(string2)){
- System.out.println(string2);
- negExamples.remove(string2);
- };
- }*/
- //System.out.println(negExamples.size());
- negExamples.removeAll(posExamples);
- posExamples=shrink(posExamples,5);
- negExamples=shrink(negExamples,posExamples.size());
- //System.out.println(posExamples.first()));
- //System.out.println(posExamples.size());
- //System.out.println(negExamples.size());
-
- //
- new ConfWriter().writeSPARQL("aaa.conf", posExamples, negExamples, url, new TreeSet<String>());
- new LearnSparql().learn(posExamples, negExamples, "http://dbpedia.openlinksw.com:8890/sparql", new TreeSet<String>());
-
- sc.printAndSet("Finished");
- } catch (Exception e) {
- e.printStackTrace();
-
- }
-
- }
-
- /***************************************************************************
- * *********************OLDCODE String
- * conj="(\"http://dbpedia.org/class/yago/Person100007846\" AND
- * \"http://dbpedia.org/class/yago/Head110162991\")";
- *
- *
- * concepts.add("EXISTS \"http://dbpedia.org/property/disambiguates\".TOP");
- * concepts.add("EXISTS
- * \"http://dbpedia.org/property/successor\".\"http://dbpedia.org/class/yago/Person100007846\"");
- * concepts.add("EXISTS \"http://dbpedia.org/property/successor\"."+conj);
- * //concepts.add("ALL \"http://dbpedia.org/property/disambiguates\".TOP");
- * //concepts.add("ALL
- * \"http://dbpedia.org/property/successor\".\"http://dbpedia.org/class/yago/Person100007846\"");
- * concepts.add("\"http://dbpedia.org/class/yago/Person100007846\"");
- * concepts.add(conj);
- * concepts.add("(\"http://dbpedia.org/class/yago/Person100007846\" OR
- * \"http://dbpedia.org/class/yago/Head110162991\")");
- *
- * //concepts.add("NOT \"http://dbpedia.org/class/yago/Person100007846\"");
- *
- * for (String kbsyntax : concepts) {
- * result.put(kbsyntax,queryConcept(kbsyntax)); }
- * System.out.println("************************"); for (String string :
- * result.keySet()) { System.out.println("KBSyntayString: "+string);
- * System.out.println("Query:\n"+result.get(string).hasNext());
- * System.out.println("************************"); }
- **************************************************************************/
-
- static SortedSet<String> getObjects(String subject) {
- // SortedSet<String> result = new TreeSet<String>();
-
- String query = "SELECT * WHERE { \n" + "<" + subject + "> " + "?p ?o. \n"
- + "FILTER (REGEX(str(?o), 'http://dbpedia.org/resource/')).\n"
- + "FILTER (!REGEX(str(?p), 'http://www.w3.org/2004/02/skos'))\n"
- + "}";
- //System.out.println(query);
- String JSON = (c.executeSparqlQuery(new SparqlQuery(query, se)));
- //System.out.println(JSON);
- ResultSet rs =SparqlQuery.JSONtoResultSet(JSON);
- JenaResultSetConvenience rsc = new JenaResultSetConvenience(rs);
- return rsc.getStringListForVariable("o");
- }
-
- public static ResultSet queryConcept(String concept,int limit) {
- ResultSet rs = null;
- try {
- String query = SparqlQueryDescriptionConvertVisitor
- .getSparqlQuery(concept,limit);
-
- SparqlQuery sq = new SparqlQuery(query, se);
- String JSON = c.executeSparqlQuery(sq);
- //System.out.println(JSON);
- rs = SparqlQuery.JSONtoResultSet(JSON);
-
- } catch (Exception e) {
- e.printStackTrace();
- }
-
- return rs;
- }
-
- public static void init() {
- SparqlQueryDescriptionConvertVisitor.debug_flag = false;
- c = new Cache("cache");
- se = SparqlEndpoint.dbpediaEndpoint();
- // create logger (a simple logger which outputs
- // its messages to the console)
- SimpleLayout layout = new SimpleLayout();
- ConsoleAppender consoleAppender = new ConsoleAppender(layout);
- logger.removeAllAppenders();
- logger.addAppender(consoleAppender);
- logger.setLevel(Level.DEBUG);
-
-
- }
-
- public static SortedSet<String> shrink(SortedSet<String> s, int limit) {
- SortedSet<String> ret = new TreeSet<String>();
- Random r = new Random();
- double treshold = ((double)limit)/s.size();
- //System.out.println("treshold"+howmany);
- //System.out.println("treshold"+allRetrieved.size());
- System.out.println("treshold"+treshold);
-
- for (String oneInd : s) {
- if(r.nextDouble()<treshold) {
- ret.add(oneInd);
-
- }
- }
- return ret;
- }
-
-}
Added: trunk/src/dl-learner/org/dllearner/utilities/AutomaticExampleFinderSPARQL.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/AutomaticExampleFinderSPARQL.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/utilities/AutomaticExampleFinderSPARQL.java 2008-04-22 17:29:06 UTC (rev 812)
@@ -0,0 +1,168 @@
+package org.dllearner.utilities;
+
+import java.util.SortedSet;
+import java.util.TreeSet;
+
+import org.apache.log4j.Logger;
+import org.dllearner.core.ComponentManager;
+import org.dllearner.kb.sparql.Cache;
+import org.dllearner.kb.sparql.SparqlQuery;
+import org.dllearner.kb.sparql.SparqlQueryDescriptionConvertVisitor;
+import org.dllearner.kb.sparql.configuration.SparqlEndpoint;
+
+import com.hp.hpl.jena.query.ResultSet;
+
+public class AutomaticExampleFinderSPARQL {
+
+ private static Logger logger = Logger
+ .getLogger(ComponentManager.class);
+
+ private Cache c;
+ private SparqlEndpoint se;
+ private SortedSet<String> posExamples;
+ private SortedSet<String> negExamples;
+
+
+ public AutomaticExampleFinderSPARQL(SparqlEndpoint se){
+ this.c=new Cache();
+ this.se=se;
+ posExamples = new TreeSet<String>();
+ negExamples = new TreeSet<String>();
+ }
+
+ public void init(String concept, boolean useRelated, boolean useSuperclasses, int poslimit, int neglimit) {
+ makePositiveExamplesFromConcept( concept);
+ SortedSet<String> keepForClean = new TreeSet<String>();
+ keepForClean.addAll(this.posExamples);
+ this.posExamples = SetManipulation.fuzzyShrink(this.posExamples, poslimit);
+
+ if(useRelated) {
+ dbpediaMakeNegativeExamplesFromRelatedInstances(this.posExamples);
+ }
+ if(useSuperclasses) {
+ dbpediaMakeNegativeExamplesFromSuperClasses(concept);
+ }
+ //clean
+ negExamples.removeAll(keepForClean);
+ this.negExamples = SetManipulation.fuzzyShrink(negExamples, neglimit);
+ logger.debug("Finished examples for concept :"+concept);
+ }
+
+ public SortedSet<String> getPosOnly(String concept, int limit){
+ makePositiveExamplesFromConcept( concept);
+ return SetManipulation.fuzzyShrink(this.posExamples, limit);
+ }
+
+ private void makePositiveExamplesFromConcept(String concept){
+ this.posExamples = new JenaResultSetConvenience(queryConcept(concept,0))
+ .getStringListForVariable("subject");
+
+ }
+
+
+
+
+
+ private void dbpediaMakeNegativeExamplesFromRelatedInstances(SortedSet<String> subject) {
+ for (String string : subject) {
+ dbpediaMakeNegativeExamplesFromRelatedInstances(string);
+ }
+ }
+
+
+ /**
+ *
+ * @param subject
+ * @return
+ */
+ private void dbpediaMakeNegativeExamplesFromRelatedInstances(String subject) {
+ // SortedSet<String> result = new TreeSet<String>();
+
+ String query = "SELECT * WHERE { \n" + "<" + subject + "> " + "?p ?o. \n"
+ + "FILTER (REGEX(str(?o), 'http://dbpedia.org/resource/')).\n"
+ + "FILTER (!REGEX(str(?p), 'http://www.w3.org/2004/02/skos'))\n"
+ + "}";
+
+ String JSON = (c.executeSparqlQuery(new SparqlQuery(query, se)));
+ ResultSet rs =SparqlQuery.JSONtoResultSet(JSON);
+ JenaResultSetConvenience rsc = new JenaResultSetConvenience(rs);
+ this.negExamples.addAll(rsc.getStringListForVariable("o"));
+
+ }
+
+
+ private void dbpediaMakeNegativeExamplesFromSuperClasses(String concept) {
+
+ SortedSet<String> superClasses = new TreeSet<String>();
+ superClasses.add(concept.replace("\"", ""));
+ //logger.debug("before"+superClasses);
+ superClasses = dbpediaGetSuperClasses( superClasses, 4);
+ logger.debug("getting negExamples from "+superClasses.size()+" superclasses");
+ JenaResultSetConvenience rsc;
+ for (String oneSuperClass : superClasses) {
+
+ rsc = new JenaResultSetConvenience(queryConcept("\""+oneSuperClass+"\"", 0));
+ this.negExamples.addAll(rsc.getStringListForVariable("subject"));
+ }
+ }
+
+ private SortedSet<String> dbpediaGetSuperClasses(SortedSet<String> superClasses, int depth) {
+ SortedSet<String> ret = new TreeSet<String>();
+ SortedSet<String> tmpset = new TreeSet<String>();
+ ret.addAll(superClasses);
+ //logger.debug(superClasses);
+ JenaResultSetConvenience rsc;
+
+ String query = "";
+ for (; depth != 0 ; depth--) {
+ for (String oneSuperClass : superClasses) {
+ //logger.debug("one"+oneSuperClass);
+ //tmp = oneSuperClass.replace("\"", "");
+ query = "SELECT * WHERE { \n" + "<" + oneSuperClass + "> "
+ + "<http://www.w3.org/2000/01/rdf-schema#subClassOf> ?superclass. \n"
+ + "}";
+ String JSON = (c.executeSparqlQuery(new SparqlQuery(query, se)));
+ ResultSet rs =SparqlQuery.JSONtoResultSet(JSON);
+ rsc = new JenaResultSetConvenience(rs);
+ tmpset.addAll(rsc.getStringListForVariable("superclass"));
+ }
+ ret.addAll(tmpset);
+ //logger.debug(ret);
+ superClasses.clear();
+ superClasses.addAll(tmpset);
+ tmpset.clear();
+ }
+ //logger.debug(concept);
+ //logger.debug(query);
+ return ret;
+ }
+
+ public ResultSet queryConcept(String concept,int limit) {
+ ResultSet rs = null;
+ try {
+ String query = SparqlQueryDescriptionConvertVisitor
+ .getSparqlQuery(concept,limit);
+
+ SparqlQuery sq = new SparqlQuery(query, se);
+ String JSON = c.executeSparqlQuery(sq);
+ //System.out.println(JSON);
+ rs = SparqlQuery.JSONtoResultSet(JSON);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ return rs;
+ }
+
+ public SortedSet<String> getPosExamples() {
+ return posExamples;
+ }
+
+ public SortedSet<String> getNegExamples() {
+ return negExamples;
+ }
+
+
+
+}
Modified: trunk/src/dl-learner/org/dllearner/utilities/LearnSparql.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/LearnSparql.java 2008-04-22 17:15:27 UTC (rev 811)
+++ trunk/src/dl-learner/org/dllearner/utilities/LearnSparql.java 2008-04-22 17:29:06 UTC (rev 812)
@@ -12,7 +12,6 @@
import org.dllearner.core.LearningProblem;
import org.dllearner.core.ReasonerComponent;
import org.dllearner.core.ReasoningService;
-import org.dllearner.core.owl.Individual;
import org.dllearner.kb.sparql.SparqlKnowledgeSource;
import org.dllearner.learningproblems.PosNegDefinitionLP;
import org.dllearner.learningproblems.PosNegLP;
@@ -21,6 +20,7 @@
public class LearnSparql {
+
public void learn(SortedSet<String> posExamples,SortedSet<String> negExamples,
String uri, SortedSet<String> ignoredConcepts){
@@ -58,8 +58,8 @@
lp = new PosNegDefinitionLP(rs);
//cm.applyConfigEntry(lp, "positiveExamples",toInd(posExamples));
- ((PosNegLP) lp).setPositiveExamples(toInd(posExamples));
- ((PosNegLP) lp).setNegativeExamples(toInd(negExamples));
+ ((PosNegLP) lp).setPositiveExamples(SetManipulation.stringToInd(posExamples));
+ ((PosNegLP) lp).setNegativeExamples(SetManipulation.stringToInd(negExamples));
//cm.applyConfigEntry(lp, "negativeExamples",toInd(negExamples));
lp.init();
@@ -69,8 +69,9 @@
cm.applyConfigEntry(la,"useExistsConstructor",true);
cm.applyConfigEntry(la,"useCardinalityRestrictions",false);
cm.applyConfigEntry(la,"useNegation",false);
- cm.applyConfigEntry(la,"minExecutionTimeInSeconds",0);
- cm.applyConfigEntry(la,"guaranteeXgoodDescriptions",20);
+ cm.applyConfigEntry(la,"minExecutionTimeInSeconds",100);
+ cm.applyConfigEntry(la,"maxExecutionTimeInSeconds",100);
+ cm.applyConfigEntry(la,"guaranteeXgoodDescriptions",1);
//cm.applyConfigEntry(la,"quiet",false);
if(ignoredConcepts.size()>0)
@@ -81,18 +82,12 @@
la.start();
//System.out.println("best"+la(20));
- ((ExampleBasedROLComponent)la).printBestSolutions(20);
+ ((ExampleBasedROLComponent)la).printBestSolutions(200);
}catch (Exception e) {e.printStackTrace();}
//System.out.println( la.getBestSolution());;
}
- protected SortedSet<Individual> toInd(SortedSet<String> set ){
- SortedSet<Individual> ret = new TreeSet<Individual>();
- for (String ind : set) {
- ret.add(new Individual(ind));
- }
- return ret;
- }
+
}
Added: trunk/src/dl-learner/org/dllearner/utilities/SetManipulation.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/SetManipulation.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/utilities/SetManipulation.java 2008-04-22 17:29:06 UTC (rev 812)
@@ -0,0 +1,43 @@
+package org.dllearner.utilities;
+
+import java.util.Random;
+import java.util.SortedSet;
+import java.util.TreeSet;
+
+import org.dllearner.core.owl.Individual;
+
+public class SetManipulation {
+
+
+ /**
+ * shrinks a set to the limit
+ * size will be roughly the same as limit, but can be more or less a bit
+ * @param set
+ * @param limit
+ * @return
+ */
+ public static SortedSet<String> fuzzyShrink(SortedSet<String> set, int limit) {
+ SortedSet<String> ret = new TreeSet<String>();
+ Random r = new Random();
+ double treshold = ((double)limit)/set.size();
+ //System.out.println("treshold"+howmany);
+ //System.out.println("treshold"+allRetrieved.size());
+ //System.out.println("treshold"+treshold);
+
+ for (String oneInd : set) {
+ if(r.nextDouble()<treshold) {
+ ret.add(oneInd);
+
+ }
+ }
+ return ret;
+ }
+
+ public static SortedSet<Individual> stringToInd(SortedSet<String> set ){
+ SortedSet<Individual> ret = new TreeSet<Individual>();
+ for (String ind : set) {
+ ret.add(new Individual(ind));
+ }
+ return ret;
+ }
+}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ton...@us...> - 2008-04-22 17:15:37
|
Revision: 811
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=811&view=rev
Author: tonytacker
Date: 2008-04-22 10:15:27 -0700 (Tue, 22 Apr 2008)
Log Message:
-----------
- reinit on run-button
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/gui/RunPanel.java
Modified: trunk/src/dl-learner/org/dllearner/gui/RunPanel.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/gui/RunPanel.java 2008-04-22 15:23:38 UTC (rev 810)
+++ trunk/src/dl-learner/org/dllearner/gui/RunPanel.java 2008-04-22 17:15:27 UTC (rev 811)
@@ -143,7 +143,6 @@
// start
if (e.getSource() == runButton && config.getLearningAlgorithm() != null
&& !config.getThreadIsRunning()) {
- startGUI.init();
thread = new ThreadRun(config);
config.getReasoningService().resetStatistics();
thread.start();
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ku...@us...> - 2008-04-22 15:23:48
|
Revision: 810
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=810&view=rev
Author: kurzum
Date: 2008-04-22 08:23:38 -0700 (Tue, 22 Apr 2008)
Log Message:
-----------
moved some classes to new package scripts, because, they are neither utitlity classes nor test classes, but scripts.
Added Paths:
-----------
trunk/src/dl-learner/org/dllearner/scripts/
trunk/src/dl-learner/org/dllearner/scripts/CloseOntology.java
trunk/src/dl-learner/org/dllearner/scripts/CrossValidation.java
trunk/src/dl-learner/org/dllearner/scripts/NT2RDF.java
trunk/src/dl-learner/org/dllearner/scripts/SPARQLPreparation.java
Removed Paths:
-------------
trunk/src/dl-learner/org/dllearner/test/SPARQLPreparation.java
trunk/src/dl-learner/org/dllearner/utilities/CloseOntology.java
trunk/src/dl-learner/org/dllearner/utilities/CrossValidation.java
trunk/src/dl-learner/org/dllearner/utilities/NT2RDF.java
Copied: trunk/src/dl-learner/org/dllearner/scripts/CloseOntology.java (from rev 808, trunk/src/dl-learner/org/dllearner/utilities/CloseOntology.java)
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/CloseOntology.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/scripts/CloseOntology.java 2008-04-22 15:23:38 UTC (rev 810)
@@ -0,0 +1,66 @@
+package org.dllearner.scripts;
+
+import java.io.File;
+import java.net.URI;
+import java.util.HashSet;
+import java.util.Set;
+
+import org.dllearner.core.KnowledgeSource;
+import org.dllearner.kb.OWLFile;
+import org.dllearner.reasoning.OWLAPIReasoner;
+import org.dllearner.utilities.OntologyCloserOWLAPI;
+
+/**
+ * Script for closing an ontology OWLAPI produces extensive filesizes, when
+ * exporting output file ist named like input file, but recieves a
+ * "_closedConcise" at the end.
+ *
+ * Counts all roles of individuals and adds an Intersection (Concise) of
+ * ExactCardinalityRestriction to the ABox
+ *
+ */
+public class CloseOntology {
+
+ /**
+ * @param argument0
+ * simply the path to the owl ontology "examples/test.owl"
+ */
+ public static void main(String[] args) {
+ String ontopath="";
+ //ontopath="examples/carcinogenesis/carcinogenesis.owl";
+ // inputURI
+ //ontopath = args[0];
+ File file = new File(ontopath);
+ URI inputURI = file.toURI();
+
+ // outputURI
+ String ending = ontopath.substring(ontopath.lastIndexOf(".") + 1);
+ ontopath = ontopath.replace("." + ending, "_closedConcise." + ending);
+ file = new File(ontopath);
+ URI outputURI = file.toURI();
+
+ try {
+ // initializing reasoner
+ OWLFile owlFile = new OWLFile();
+ owlFile.setURL(inputURI.toURL());
+ Set<KnowledgeSource> ks = new HashSet<KnowledgeSource>();
+ ks.add(owlFile);
+ OWLAPIReasoner owlapireasoner = new OWLAPIReasoner(ks);
+ owlapireasoner.init();
+
+ // close
+ OntologyCloserOWLAPI oc = new OntologyCloserOWLAPI(owlapireasoner);
+ oc.testForTransitiveProperties(true);
+ System.out.println("Attempting to close");
+ oc.applyNumberRestrictionsConcise();
+ System.out.println("Finished, preparing output");
+
+ // save
+ oc.writeOWLFile(outputURI);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+ }
+
+}
Copied: trunk/src/dl-learner/org/dllearner/scripts/CrossValidation.java (from rev 808, trunk/src/dl-learner/org/dllearner/utilities/CrossValidation.java)
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/CrossValidation.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/scripts/CrossValidation.java 2008-04-22 15:23:38 UTC (rev 810)
@@ -0,0 +1,318 @@
+/**
+ * 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/>.
+ *
+ */
+package org.dllearner.scripts;
+
+import java.io.File;
+import java.text.DecimalFormat;
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Random;
+import java.util.Set;
+
+import org.apache.log4j.ConsoleAppender;
+import org.apache.log4j.Level;
+import org.apache.log4j.Logger;
+import org.apache.log4j.SimpleLayout;
+import org.dllearner.cli.Start;
+import org.dllearner.core.ComponentInitException;
+import org.dllearner.core.ComponentManager;
+import org.dllearner.core.LearningAlgorithm;
+import org.dllearner.core.LearningProblem;
+import org.dllearner.core.ReasoningService;
+import org.dllearner.core.owl.Description;
+import org.dllearner.core.owl.Individual;
+import org.dllearner.learningproblems.PosNegLP;
+import org.dllearner.learningproblems.PosOnlyLP;
+import org.dllearner.utilities.Datastructures;
+import org.dllearner.utilities.Helper;
+import org.dllearner.utilities.Stat;
+
+/**
+ * Performs cross validation for the given problem. Supports
+ * k-fold cross-validation and leave-one-out cross-validation.
+ *
+ * @author Jens Lehmann
+ *
+ */
+public class CrossValidation {
+
+ private static Logger logger = Logger.getRootLogger();
+
+ public static void main(String[] args) {
+ File file = new File(args[0]);
+
+ boolean leaveOneOut = false;
+ int folds = 10;
+
+ // use second argument as number of folds; if not specified
+ // leave one out cross validation is used
+ if(args.length > 1)
+ folds = Integer.parseInt(args[1]);
+ else
+ leaveOneOut = true;
+
+ if(folds < 2) {
+ System.out.println("At least 2 fold needed.");
+ System.exit(0);
+ }
+
+ // create logger (a simple logger which outputs
+ // its messages to the console)
+ SimpleLayout layout = new SimpleLayout();
+ ConsoleAppender consoleAppender = new ConsoleAppender(layout);
+ logger.removeAllAppenders();
+ logger.addAppender(consoleAppender);
+ logger.setLevel(Level.WARN);
+ // disable OWL API info output
+ java.util.logging.Logger.getLogger("").setLevel(java.util.logging.Level.WARNING);
+
+ new CrossValidation(file, folds, leaveOneOut);
+
+ }
+
+ public CrossValidation(File file, int folds, boolean leaveOneOut) {
+
+ DecimalFormat df = new DecimalFormat();
+ ComponentManager cm = ComponentManager.getInstance();
+
+ // the first read of the file is used to detect the examples
+ // and set up the splits correctly according to our validation
+ // method
+ Start start = null;
+ try {
+ start = new Start(file);
+ } catch (ComponentInitException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+
+ LearningProblem lp = start.getLearningProblem();
+ ReasoningService rs = start.getReasoningService();
+
+ // the training and test sets used later on
+ List<Set<Individual>> trainingSetsPos = new LinkedList<Set<Individual>>();
+ List<Set<Individual>> trainingSetsNeg = new LinkedList<Set<Individual>>();
+ List<Set<Individual>> testSetsPos = new LinkedList<Set<Individual>>();
+ List<Set<Individual>> testSetsNeg = new LinkedList<Set<Individual>>();
+
+ if(lp instanceof PosNegLP) {
+
+ // get examples and shuffle them to
+ Set<Individual> posExamples = ((PosNegLP)lp).getPositiveExamples();
+ List<Individual> posExamplesList = new LinkedList<Individual>(posExamples);
+ Collections.shuffle(posExamplesList, new Random(1));
+ Set<Individual> negExamples = ((PosNegLP)lp).getNegativeExamples();
+ List<Individual> negExamplesList = new LinkedList<Individual>(negExamples);
+ Collections.shuffle(negExamplesList, new Random(2));
+
+ // sanity check whether nr. of folds makes sense for this benchmark
+ if(!leaveOneOut && (posExamples.size()<folds && negExamples.size()<folds)) {
+ System.out.println("The number of folds is higher than the number of "
+ + "positive/negative examples. This can result in empty test sets. Exiting.");
+ System.exit(0);
+ }
+
+ if(leaveOneOut) {
+ // note that leave-one-out is not identical to k-fold with
+ // k = nr. of examples in the current implementation, because
+ // with n folds and n examples there is no guarantee that a fold
+ // is never empty (this is an implementation issue)
+ int nrOfExamples = posExamples.size() + negExamples.size();
+ for(int i = 0; i < nrOfExamples; i++) {
+ // ...
+ }
+ System.out.println("Leave-one-out not supported yet.");
+ System.exit(1);
+ } else {
+ // calculating where to split the sets, ; note that we split
+ // positive and negative examples separately such that the
+ // distribution of positive and negative examples remains similar
+ // (note that there better but more complex ways to implement this,
+ // which guarantee that the sum of the elements of a fold for pos
+ // and neg differs by at most 1 - it can differ by 2 in our implementation,
+ // e.g. with 3 folds, 4 pos. examples, 4 neg. examples)
+ int[] splitsPos = calculateSplits(posExamples.size(),folds);
+ int[] splitsNeg = calculateSplits(negExamples.size(),folds);
+
+// System.out.println(splitsPos[0]);
+// System.out.println(splitsNeg[0]);
+
+ // calculating training and test sets
+ for(int i=0; i<folds; i++) {
+ Set<Individual> testPos = getTestingSet(posExamplesList, splitsPos, i);
+ Set<Individual> testNeg = getTestingSet(negExamplesList, splitsNeg, i);
+ testSetsPos.add(i, testPos);
+ testSetsNeg.add(i, testNeg);
+ trainingSetsPos.add(i, getTrainingSet(posExamples, testPos));
+ trainingSetsNeg.add(i, getTrainingSet(negExamples, testNeg));
+ }
+
+ }
+
+ } else if(lp instanceof PosOnlyLP) {
+ System.out.println("Cross validation for positive only learning not supported yet.");
+ System.exit(0);
+ // Set<Individual> posExamples = ((PosOnlyLP)lp).getPositiveExamples();
+ // int[] splits = calculateSplits(posExamples.size(),folds);
+ } else {
+ System.out.println("Cross validation for learning problem " + lp + " not supported.");
+ System.exit(0);
+ }
+
+ // statistical values
+ Stat runtime = new Stat();
+ Stat accuracy = new Stat();
+ Stat length = new Stat();
+
+ // run the algorithm
+ for(int currFold=0; currFold<folds; currFold++) {
+ // we always perform a full initialisation to make sure that
+ // no objects are reused
+ try {
+ start = new Start(file);
+ } catch (ComponentInitException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ lp = start.getLearningProblem();
+ Set<String> pos = Datastructures.individualSetToStringSet(trainingSetsPos.get(currFold));
+ Set<String> neg = Datastructures.individualSetToStringSet(trainingSetsNeg.get(currFold));
+ cm.applyConfigEntry(lp, "positiveExamples", pos);
+ cm.applyConfigEntry(lp, "negativeExamples", neg);
+// System.out.println("pos: " + pos.size());
+// System.out.println("neg: " + neg.size());
+// System.exit(0);
+
+ // es fehlt init zwischendurch
+
+ LearningAlgorithm la = start.getLearningAlgorithm();
+ // init again, because examples have changed
+ try {
+ la.init();
+ } catch (ComponentInitException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ long algorithmStartTime = System.nanoTime();
+ la.start();
+ long algorithmDuration = System.nanoTime() - algorithmStartTime;
+ runtime.addNumber(algorithmDuration/(double)1000000000);
+
+ Description concept = la.getBestSolution();
+
+ Set<Individual> tmp = rs.instanceCheck(concept, testSetsPos.get(currFold));
+ Set<Individual> tmp2 = Helper.difference(testSetsPos.get(currFold), tmp);
+ Set<Individual> tmp3 = rs.instanceCheck(concept, testSetsNeg.get(currFold));
+
+ System.out.println("test set errors pos: " + tmp2);
+ System.out.println("test set errors neg: " + tmp3);
+
+ // calculate training accuracies
+ int trainingCorrectPosClassified = getCorrectPosClassified(rs, concept, trainingSetsPos.get(currFold));
+ int trainingCorrectNegClassified = getCorrectNegClassified(rs, concept, trainingSetsNeg.get(currFold));
+ int trainingCorrectExamples = trainingCorrectPosClassified + trainingCorrectNegClassified;
+ double trainingAccuracy = 100*((double)trainingCorrectExamples/(trainingSetsPos.get(currFold).size()+
+ trainingSetsNeg.get(currFold).size()));
+
+ // calculate test accuracies
+ int correctPosClassified = getCorrectPosClassified(rs, concept, testSetsPos.get(currFold));
+ int correctNegClassified = getCorrectNegClassified(rs, concept, testSetsNeg.get(currFold));
+ int correctExamples = correctPosClassified + correctNegClassified;
+ double currAccuracy = 100*((double)correctExamples/(testSetsPos.get(currFold).size()+
+ testSetsNeg.get(currFold).size()));
+ accuracy.addNumber(currAccuracy);
+
+ length.addNumber(concept.getLength());
+
+ System.out.println("fold " + currFold + " (" + file + "):");
+ System.out.println(" training: " + pos.size() + " positive and " + neg.size() + " negative examples");
+ System.out.println(" testing: " + correctPosClassified + "/" + testSetsPos.get(currFold).size() + " correct positives, "
+ + correctNegClassified + "/" + testSetsNeg.get(currFold).size() + " correct negatives");
+ System.out.println(" concept: " + concept);
+ System.out.println(" accuracy: " + df.format(currAccuracy) + "% (" + df.format(trainingAccuracy) + "% on training set)");
+ System.out.println(" length: " + df.format(concept.getLength()));
+ System.out.println(" runtime: " + df.format(algorithmDuration/(double)1000000000) + "s");
+
+ // free all resources
+ start.getReasoningService().releaseKB();
+ cm.freeAllComponents();
+ }
+
+ System.out.println();
+ System.out.println("Finished " + folds + "-folds cross-validation on " + file + ".");
+ System.out.println("runtime: " + statOutput(df, runtime, "s"));
+ System.out.println("length: " + statOutput(df, length, ""));
+ System.out.println("accuracy: " + statOutput(df, accuracy, "%"));
+
+ }
+
+ private int getCorrectPosClassified(ReasoningService rs, Description concept, Set<Individual> testSetPos) {
+ return rs.instanceCheck(concept, testSetPos).size();
+ }
+
+ private int getCorrectNegClassified(ReasoningService rs, Description concept, Set<Individual> testSetNeg) {
+ return testSetNeg.size() - rs.instanceCheck(concept, testSetNeg).size();
+ }
+
+ private Set<Individual> getTestingSet(List<Individual> examples, int[] splits, int fold) {
+ int fromIndex;
+ // we either start from 0 or after the last fold ended
+ if(fold == 0)
+ fromIndex = 0;
+ else
+ fromIndex = splits[fold-1];
+ // the split corresponds to the ends of the folds
+ int toIndex = splits[fold];
+
+// System.out.println("from " + fromIndex + " to " + toIndex);
+
+ Set<Individual> testingSet = new HashSet<Individual>();
+ // +1 because 2nd element is exclusive in subList method
+ testingSet.addAll(examples.subList(fromIndex, toIndex));
+ return testingSet;
+ }
+
+ private Set<Individual> getTrainingSet(Set<Individual> examples, Set<Individual> testingSet) {
+ return Helper.difference(examples, testingSet);
+ }
+
+ // takes nr. of examples and the nr. of folds for this examples;
+ // returns an array which says where each fold ends, i.e.
+ // splits[i] is the index of the last element of fold i in the examples
+ private int[] calculateSplits(int nrOfExamples, int folds) {
+ int[] splits = new int[folds];
+ for(int i=1; i<=folds; i++) {
+ // we always round up to the next integer
+ splits[i-1] = (int)Math.ceil(i*nrOfExamples/(double)folds);
+ }
+ return splits;
+ }
+
+ private String statOutput(DecimalFormat df, Stat stat, String unit) {
+ String str = "av. " + df.format(stat.getMean()) + unit;
+ str += " (deviation " + df.format(stat.getStandardDeviation()) + unit + "; ";
+ str += "min " + df.format(stat.getMin()) + unit + "; ";
+ str += "max " + df.format(stat.getMax()) + unit + ")";
+ return str;
+ }
+
+}
Copied: trunk/src/dl-learner/org/dllearner/scripts/NT2RDF.java (from rev 808, trunk/src/dl-learner/org/dllearner/utilities/NT2RDF.java)
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/NT2RDF.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/scripts/NT2RDF.java 2008-04-22 15:23:38 UTC (rev 810)
@@ -0,0 +1,35 @@
+package org.dllearner.scripts;
+import java.io.File;
+import java.net.URI;
+
+import org.semanticweb.owl.apibinding.OWLManager;
+import org.semanticweb.owl.io.RDFXMLOntologyFormat;
+import org.semanticweb.owl.model.OWLOntology;
+import org.semanticweb.owl.model.OWLOntologyManager;
+public class NT2RDF {
+
+
+ public static void main(String[] args) {
+ try {
+ String ontopath=args[0];
+ URI inputURI = new File(ontopath).toURI();
+
+ // outputURI
+ String ending = ontopath.substring(ontopath.lastIndexOf(".") + 1);
+ ontopath = ontopath.replace("." + ending, ".rdf" );
+ URI outputURI = new File(ontopath).toURI();
+
+ OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
+ OWLOntology ontology = manager.loadOntologyFromPhysicalURI(inputURI);
+ manager.saveOntology(ontology, new RDFXMLOntologyFormat(), outputURI);
+ // Remove the ontology from the manager
+ manager.removeOntology(ontology.getURI());
+ }
+ catch (Exception e) {
+ System.out.println("The ontology could not be created: " + e.getMessage());
+ }
+
+ }
+ }
+
+
Copied: trunk/src/dl-learner/org/dllearner/scripts/SPARQLPreparation.java (from rev 809, trunk/src/dl-learner/org/dllearner/test/SPARQLPreparation.java)
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/SPARQLPreparation.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/scripts/SPARQLPreparation.java 2008-04-22 15:23:38 UTC (rev 810)
@@ -0,0 +1,176 @@
+package org.dllearner.scripts;
+
+import java.util.Random;
+import java.util.SortedSet;
+import java.util.TreeSet;
+
+import javax.sound.midi.SysexMessage;
+
+import org.apache.log4j.ConsoleAppender;
+import org.apache.log4j.Level;
+import org.apache.log4j.Logger;
+import org.apache.log4j.SimpleLayout;
+import org.dllearner.kb.sparql.Cache;
+import org.dllearner.kb.sparql.SparqlQuery;
+import org.dllearner.kb.sparql.SparqlQueryDescriptionConvertVisitor;
+import org.dllearner.kb.sparql.configuration.SparqlEndpoint;
+import org.dllearner.utilities.ConfWriter;
+import org.dllearner.utilities.JenaResultSetConvenience;
+import org.dllearner.utilities.LearnSparql;
+import org.dllearner.utilities.SimpleClock;
+
+import com.hp.hpl.jena.query.ResultSet;
+
+public class SPARQLPreparation {
+
+ static Cache c;
+ static SparqlEndpoint se;
+ private static Logger logger = Logger.getRootLogger();
+ /**
+ * @param args
+ */
+ public static void main(String[] args) {
+ init();
+ try {
+
+
+
+ SimpleClock sc=new SimpleClock();
+ SortedSet<String> concepts = new TreeSet<String>();
+ //concepts.add("\"http://dbpedia.org/class/yago/Person100007846\"");
+ concepts.add("\"http://dbpedia.org/class/yago/FieldMarshal110086821\"");
+ SortedSet<String> posExamples = new TreeSet<String>();
+ SortedSet<String> negExamples = new TreeSet<String>();
+ String url = "http://dbpedia.openlinksw.com:8890/sparql";
+ //HashMap<String, ResultSet> result = new HashMap<String, ResultSet>();
+ //HashMap<String, String> result2 = new HashMap<String, String>();
+
+ //System.out.println(concepts.first());
+ posExamples = new JenaResultSetConvenience(queryConcept(concepts.first(),0))
+ .getStringListForVariable("subject");
+
+ for (String string : posExamples) {
+ negExamples.addAll( getObjects(string));
+ //if(neg.size()>=1)System.out.println(neg);
+ }
+
+ /*for (String string2 : negExamples) {
+ if(posExamples.contains(string2)){
+ System.out.println(string2);
+ negExamples.remove(string2);
+ };
+ }*/
+ //System.out.println(negExamples.size());
+ negExamples.removeAll(posExamples);
+ posExamples=shrink(posExamples,5);
+ negExamples=shrink(negExamples,posExamples.size());
+ //System.out.println(posExamples.first()));
+ //System.out.println(posExamples.size());
+ //System.out.println(negExamples.size());
+
+ //
+ new ConfWriter().writeSPARQL("aaa.conf", posExamples, negExamples, url, new TreeSet<String>());
+ new LearnSparql().learn(posExamples, negExamples, "http://dbpedia.openlinksw.com:8890/sparql", new TreeSet<String>());
+
+ sc.printAndSet("Finished");
+ } catch (Exception e) {
+ e.printStackTrace();
+
+ }
+
+ }
+
+ /***************************************************************************
+ * *********************OLDCODE String
+ * conj="(\"http://dbpedia.org/class/yago/Person100007846\" AND
+ * \"http://dbpedia.org/class/yago/Head110162991\")";
+ *
+ *
+ * concepts.add("EXISTS \"http://dbpedia.org/property/disambiguates\".TOP");
+ * concepts.add("EXISTS
+ * \"http://dbpedia.org/property/successor\".\"http://dbpedia.org/class/yago/Person100007846\"");
+ * concepts.add("EXISTS \"http://dbpedia.org/property/successor\"."+conj);
+ * //concepts.add("ALL \"http://dbpedia.org/property/disambiguates\".TOP");
+ * //concepts.add("ALL
+ * \"http://dbpedia.org/property/successor\".\"http://dbpedia.org/class/yago/Person100007846\"");
+ * concepts.add("\"http://dbpedia.org/class/yago/Person100007846\"");
+ * concepts.add(conj);
+ * concepts.add("(\"http://dbpedia.org/class/yago/Person100007846\" OR
+ * \"http://dbpedia.org/class/yago/Head110162991\")");
+ *
+ * //concepts.add("NOT \"http://dbpedia.org/class/yago/Person100007846\"");
+ *
+ * for (String kbsyntax : concepts) {
+ * result.put(kbsyntax,queryConcept(kbsyntax)); }
+ * System.out.println("************************"); for (String string :
+ * result.keySet()) { System.out.println("KBSyntayString: "+string);
+ * System.out.println("Query:\n"+result.get(string).hasNext());
+ * System.out.println("************************"); }
+ **************************************************************************/
+
+ static SortedSet<String> getObjects(String subject) {
+ // SortedSet<String> result = new TreeSet<String>();
+
+ String query = "SELECT * WHERE { \n" + "<" + subject + "> " + "?p ?o. \n"
+ + "FILTER (REGEX(str(?o), 'http://dbpedia.org/resource/')).\n"
+ + "FILTER (!REGEX(str(?p), 'http://www.w3.org/2004/02/skos'))\n"
+ + "}";
+ //System.out.println(query);
+ String JSON = (c.executeSparqlQuery(new SparqlQuery(query, se)));
+ //System.out.println(JSON);
+ ResultSet rs =SparqlQuery.JSONtoResultSet(JSON);
+ JenaResultSetConvenience rsc = new JenaResultSetConvenience(rs);
+ return rsc.getStringListForVariable("o");
+ }
+
+ public static ResultSet queryConcept(String concept,int limit) {
+ ResultSet rs = null;
+ try {
+ String query = SparqlQueryDescriptionConvertVisitor
+ .getSparqlQuery(concept,limit);
+
+ SparqlQuery sq = new SparqlQuery(query, se);
+ String JSON = c.executeSparqlQuery(sq);
+ //System.out.println(JSON);
+ rs = SparqlQuery.JSONtoResultSet(JSON);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ return rs;
+ }
+
+ public static void init() {
+ SparqlQueryDescriptionConvertVisitor.debug_flag = false;
+ c = new Cache("cache");
+ se = SparqlEndpoint.dbpediaEndpoint();
+ // create logger (a simple logger which outputs
+ // its messages to the console)
+ SimpleLayout layout = new SimpleLayout();
+ ConsoleAppender consoleAppender = new ConsoleAppender(layout);
+ logger.removeAllAppenders();
+ logger.addAppender(consoleAppender);
+ logger.setLevel(Level.DEBUG);
+
+
+ }
+
+ public static SortedSet<String> shrink(SortedSet<String> s, int limit) {
+ SortedSet<String> ret = new TreeSet<String>();
+ Random r = new Random();
+ double treshold = ((double)limit)/s.size();
+ //System.out.println("treshold"+howmany);
+ //System.out.println("treshold"+allRetrieved.size());
+ System.out.println("treshold"+treshold);
+
+ for (String oneInd : s) {
+ if(r.nextDouble()<treshold) {
+ ret.add(oneInd);
+
+ }
+ }
+ return ret;
+ }
+
+}
Deleted: trunk/src/dl-learner/org/dllearner/test/SPARQLPreparation.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/test/SPARQLPreparation.java 2008-04-22 15:19:07 UTC (rev 809)
+++ trunk/src/dl-learner/org/dllearner/test/SPARQLPreparation.java 2008-04-22 15:23:38 UTC (rev 810)
@@ -1,176 +0,0 @@
-package org.dllearner.test;
-
-import java.util.Random;
-import java.util.SortedSet;
-import java.util.TreeSet;
-
-import javax.sound.midi.SysexMessage;
-
-import org.apache.log4j.ConsoleAppender;
-import org.apache.log4j.Level;
-import org.apache.log4j.Logger;
-import org.apache.log4j.SimpleLayout;
-import org.dllearner.kb.sparql.Cache;
-import org.dllearner.kb.sparql.SparqlQuery;
-import org.dllearner.kb.sparql.SparqlQueryDescriptionConvertVisitor;
-import org.dllearner.kb.sparql.configuration.SparqlEndpoint;
-import org.dllearner.utilities.ConfWriter;
-import org.dllearner.utilities.JenaResultSetConvenience;
-import org.dllearner.utilities.LearnSparql;
-import org.dllearner.utilities.SimpleClock;
-
-import com.hp.hpl.jena.query.ResultSet;
-
-public class SPARQLPreparation {
-
- static Cache c;
- static SparqlEndpoint se;
- private static Logger logger = Logger.getRootLogger();
- /**
- * @param args
- */
- public static void main(String[] args) {
- init();
- try {
-
-
-
- SimpleClock sc=new SimpleClock();
- SortedSet<String> concepts = new TreeSet<String>();
- //concepts.add("\"http://dbpedia.org/class/yago/Person100007846\"");
- concepts.add("\"http://dbpedia.org/class/yago/FieldMarshal110086821\"");
- SortedSet<String> posExamples = new TreeSet<String>();
- SortedSet<String> negExamples = new TreeSet<String>();
- String url = "http://dbpedia.openlinksw.com:8890/sparql";
- //HashMap<String, ResultSet> result = new HashMap<String, ResultSet>();
- //HashMap<String, String> result2 = new HashMap<String, String>();
-
- //System.out.println(concepts.first());
- posExamples = new JenaResultSetConvenience(queryConcept(concepts.first(),0))
- .getStringListForVariable("subject");
-
- for (String string : posExamples) {
- negExamples.addAll( getObjects(string));
- //if(neg.size()>=1)System.out.println(neg);
- }
-
- /*for (String string2 : negExamples) {
- if(posExamples.contains(string2)){
- System.out.println(string2);
- negExamples.remove(string2);
- };
- }*/
- //System.out.println(negExamples.size());
- negExamples.removeAll(posExamples);
- posExamples=shrink(posExamples,5);
- negExamples=shrink(negExamples,posExamples.size());
- //System.out.println(posExamples.first()));
- //System.out.println(posExamples.size());
- //System.out.println(negExamples.size());
-
- //
- new ConfWriter().writeSPARQL("aaa.conf", posExamples, negExamples, url, new TreeSet<String>());
- new LearnSparql().learn(posExamples, negExamples, "http://dbpedia.openlinksw.com:8890/sparql", new TreeSet<String>());
-
- sc.printAndSet("Finished");
- } catch (Exception e) {
- e.printStackTrace();
-
- }
-
- }
-
- /***************************************************************************
- * *********************OLDCODE String
- * conj="(\"http://dbpedia.org/class/yago/Person100007846\" AND
- * \"http://dbpedia.org/class/yago/Head110162991\")";
- *
- *
- * concepts.add("EXISTS \"http://dbpedia.org/property/disambiguates\".TOP");
- * concepts.add("EXISTS
- * \"http://dbpedia.org/property/successor\".\"http://dbpedia.org/class/yago/Person100007846\"");
- * concepts.add("EXISTS \"http://dbpedia.org/property/successor\"."+conj);
- * //concepts.add("ALL \"http://dbpedia.org/property/disambiguates\".TOP");
- * //concepts.add("ALL
- * \"http://dbpedia.org/property/successor\".\"http://dbpedia.org/class/yago/Person100007846\"");
- * concepts.add("\"http://dbpedia.org/class/yago/Person100007846\"");
- * concepts.add(conj);
- * concepts.add("(\"http://dbpedia.org/class/yago/Person100007846\" OR
- * \"http://dbpedia.org/class/yago/Head110162991\")");
- *
- * //concepts.add("NOT \"http://dbpedia.org/class/yago/Person100007846\"");
- *
- * for (String kbsyntax : concepts) {
- * result.put(kbsyntax,queryConcept(kbsyntax)); }
- * System.out.println("************************"); for (String string :
- * result.keySet()) { System.out.println("KBSyntayString: "+string);
- * System.out.println("Query:\n"+result.get(string).hasNext());
- * System.out.println("************************"); }
- **************************************************************************/
-
- static SortedSet<String> getObjects(String subject) {
- // SortedSet<String> result = new TreeSet<String>();
-
- String query = "SELECT * WHERE { \n" + "<" + subject + "> " + "?p ?o. \n"
- + "FILTER (REGEX(str(?o), 'http://dbpedia.org/resource/')).\n"
- + "FILTER (!REGEX(str(?p), 'http://www.w3.org/2004/02/skos'))\n"
- + "}";
- //System.out.println(query);
- String JSON = (c.executeSparqlQuery(new SparqlQuery(query, se)));
- //System.out.println(JSON);
- ResultSet rs =SparqlQuery.JSONtoResultSet(JSON);
- JenaResultSetConvenience rsc = new JenaResultSetConvenience(rs);
- return rsc.getStringListForVariable("o");
- }
-
- public static ResultSet queryConcept(String concept,int limit) {
- ResultSet rs = null;
- try {
- String query = SparqlQueryDescriptionConvertVisitor
- .getSparqlQuery(concept,limit);
-
- SparqlQuery sq = new SparqlQuery(query, se);
- String JSON = c.executeSparqlQuery(sq);
- //System.out.println(JSON);
- rs = SparqlQuery.JSONtoResultSet(JSON);
-
- } catch (Exception e) {
- e.printStackTrace();
- }
-
- return rs;
- }
-
- public static void init() {
- SparqlQueryDescriptionConvertVisitor.debug_flag = false;
- c = new Cache("cache");
- se = SparqlEndpoint.dbpediaEndpoint();
- // create logger (a simple logger which outputs
- // its messages to the console)
- SimpleLayout layout = new SimpleLayout();
- ConsoleAppender consoleAppender = new ConsoleAppender(layout);
- logger.removeAllAppenders();
- logger.addAppender(consoleAppender);
- logger.setLevel(Level.DEBUG);
-
-
- }
-
- public static SortedSet<String> shrink(SortedSet<String> s, int limit) {
- SortedSet<String> ret = new TreeSet<String>();
- Random r = new Random();
- double treshold = ((double)limit)/s.size();
- //System.out.println("treshold"+howmany);
- //System.out.println("treshold"+allRetrieved.size());
- System.out.println("treshold"+treshold);
-
- for (String oneInd : s) {
- if(r.nextDouble()<treshold) {
- ret.add(oneInd);
-
- }
- }
- return ret;
- }
-
-}
Deleted: trunk/src/dl-learner/org/dllearner/utilities/CloseOntology.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/CloseOntology.java 2008-04-22 15:19:07 UTC (rev 809)
+++ trunk/src/dl-learner/org/dllearner/utilities/CloseOntology.java 2008-04-22 15:23:38 UTC (rev 810)
@@ -1,65 +0,0 @@
-package org.dllearner.utilities;
-
-import java.io.File;
-import java.net.URI;
-import java.util.HashSet;
-import java.util.Set;
-
-import org.dllearner.core.KnowledgeSource;
-import org.dllearner.kb.OWLFile;
-import org.dllearner.reasoning.OWLAPIReasoner;
-
-/**
- * Script for closing an ontology OWLAPI produces extensive filesizes, when
- * exporting output file ist named like input file, but recieves a
- * "_closedConcise" at the end.
- *
- * Counts all roles of individuals and adds an Intersection (Concise) of
- * ExactCardinalityRestriction to the ABox
- *
- */
-public class CloseOntology {
-
- /**
- * @param argument0
- * simply the path to the owl ontology "examples/test.owl"
- */
- public static void main(String[] args) {
- String ontopath="";
- //ontopath="examples/carcinogenesis/carcinogenesis.owl";
- // inputURI
- //ontopath = args[0];
- File file = new File(ontopath);
- URI inputURI = file.toURI();
-
- // outputURI
- String ending = ontopath.substring(ontopath.lastIndexOf(".") + 1);
- ontopath = ontopath.replace("." + ending, "_closedConcise." + ending);
- file = new File(ontopath);
- URI outputURI = file.toURI();
-
- try {
- // initializing reasoner
- OWLFile owlFile = new OWLFile();
- owlFile.setURL(inputURI.toURL());
- Set<KnowledgeSource> ks = new HashSet<KnowledgeSource>();
- ks.add(owlFile);
- OWLAPIReasoner owlapireasoner = new OWLAPIReasoner(ks);
- owlapireasoner.init();
-
- // close
- OntologyCloserOWLAPI oc = new OntologyCloserOWLAPI(owlapireasoner);
- oc.testForTransitiveProperties(true);
- System.out.println("Attempting to close");
- oc.applyNumberRestrictionsConcise();
- System.out.println("Finished, preparing output");
-
- // save
- oc.writeOWLFile(outputURI);
-
- } catch (Exception e) {
- e.printStackTrace();
- }
- }
-
-}
Deleted: trunk/src/dl-learner/org/dllearner/utilities/CrossValidation.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/CrossValidation.java 2008-04-22 15:19:07 UTC (rev 809)
+++ trunk/src/dl-learner/org/dllearner/utilities/CrossValidation.java 2008-04-22 15:23:38 UTC (rev 810)
@@ -1,315 +0,0 @@
-/**
- * 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/>.
- *
- */
-package org.dllearner.utilities;
-
-import java.io.File;
-import java.text.DecimalFormat;
-import java.util.Collections;
-import java.util.HashSet;
-import java.util.LinkedList;
-import java.util.List;
-import java.util.Random;
-import java.util.Set;
-
-import org.apache.log4j.ConsoleAppender;
-import org.apache.log4j.Level;
-import org.apache.log4j.Logger;
-import org.apache.log4j.SimpleLayout;
-import org.dllearner.cli.Start;
-import org.dllearner.core.ComponentInitException;
-import org.dllearner.core.ComponentManager;
-import org.dllearner.core.LearningAlgorithm;
-import org.dllearner.core.LearningProblem;
-import org.dllearner.core.ReasoningService;
-import org.dllearner.core.owl.Description;
-import org.dllearner.core.owl.Individual;
-import org.dllearner.learningproblems.PosNegLP;
-import org.dllearner.learningproblems.PosOnlyLP;
-
-/**
- * Performs cross validation for the given problem. Supports
- * k-fold cross-validation and leave-one-out cross-validation.
- *
- * @author Jens Lehmann
- *
- */
-public class CrossValidation {
-
- private static Logger logger = Logger.getRootLogger();
-
- public static void main(String[] args) {
- File file = new File(args[0]);
-
- boolean leaveOneOut = false;
- int folds = 10;
-
- // use second argument as number of folds; if not specified
- // leave one out cross validation is used
- if(args.length > 1)
- folds = Integer.parseInt(args[1]);
- else
- leaveOneOut = true;
-
- if(folds < 2) {
- System.out.println("At least 2 fold needed.");
- System.exit(0);
- }
-
- // create logger (a simple logger which outputs
- // its messages to the console)
- SimpleLayout layout = new SimpleLayout();
- ConsoleAppender consoleAppender = new ConsoleAppender(layout);
- logger.removeAllAppenders();
- logger.addAppender(consoleAppender);
- logger.setLevel(Level.WARN);
- // disable OWL API info output
- java.util.logging.Logger.getLogger("").setLevel(java.util.logging.Level.WARNING);
-
- new CrossValidation(file, folds, leaveOneOut);
-
- }
-
- public CrossValidation(File file, int folds, boolean leaveOneOut) {
-
- DecimalFormat df = new DecimalFormat();
- ComponentManager cm = ComponentManager.getInstance();
-
- // the first read of the file is used to detect the examples
- // and set up the splits correctly according to our validation
- // method
- Start start = null;
- try {
- start = new Start(file);
- } catch (ComponentInitException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
-
- LearningProblem lp = start.getLearningProblem();
- ReasoningService rs = start.getReasoningService();
-
- // the training and test sets used later on
- List<Set<Individual>> trainingSetsPos = new LinkedList<Set<Individual>>();
- List<Set<Individual>> trainingSetsNeg = new LinkedList<Set<Individual>>();
- List<Set<Individual>> testSetsPos = new LinkedList<Set<Individual>>();
- List<Set<Individual>> testSetsNeg = new LinkedList<Set<Individual>>();
-
- if(lp instanceof PosNegLP) {
-
- // get examples and shuffle them to
- Set<Individual> posExamples = ((PosNegLP)lp).getPositiveExamples();
- List<Individual> posExamplesList = new LinkedList<Individual>(posExamples);
- Collections.shuffle(posExamplesList, new Random(1));
- Set<Individual> negExamples = ((PosNegLP)lp).getNegativeExamples();
- List<Individual> negExamplesList = new LinkedList<Individual>(negExamples);
- Collections.shuffle(negExamplesList, new Random(2));
-
- // sanity check whether nr. of folds makes sense for this benchmark
- if(!leaveOneOut && (posExamples.size()<folds && negExamples.size()<folds)) {
- System.out.println("The number of folds is higher than the number of "
- + "positive/negative examples. This can result in empty test sets. Exiting.");
- System.exit(0);
- }
-
- if(leaveOneOut) {
- // note that leave-one-out is not identical to k-fold with
- // k = nr. of examples in the current implementation, because
- // with n folds and n examples there is no guarantee that a fold
- // is never empty (this is an implementation issue)
- int nrOfExamples = posExamples.size() + negExamples.size();
- for(int i = 0; i < nrOfExamples; i++) {
- // ...
- }
- System.out.println("Leave-one-out not supported yet.");
- System.exit(1);
- } else {
- // calculating where to split the sets, ; note that we split
- // positive and negative examples separately such that the
- // distribution of positive and negative examples remains similar
- // (note that there better but more complex ways to implement this,
- // which guarantee that the sum of the elements of a fold for pos
- // and neg differs by at most 1 - it can differ by 2 in our implementation,
- // e.g. with 3 folds, 4 pos. examples, 4 neg. examples)
- int[] splitsPos = calculateSplits(posExamples.size(),folds);
- int[] splitsNeg = calculateSplits(negExamples.size(),folds);
-
-// System.out.println(splitsPos[0]);
-// System.out.println(splitsNeg[0]);
-
- // calculating training and test sets
- for(int i=0; i<folds; i++) {
- Set<Individual> testPos = getTestingSet(posExamplesList, splitsPos, i);
- Set<Individual> testNeg = getTestingSet(negExamplesList, splitsNeg, i);
- testSetsPos.add(i, testPos);
- testSetsNeg.add(i, testNeg);
- trainingSetsPos.add(i, getTrainingSet(posExamples, testPos));
- trainingSetsNeg.add(i, getTrainingSet(negExamples, testNeg));
- }
-
- }
-
- } else if(lp instanceof PosOnlyLP) {
- System.out.println("Cross validation for positive only learning not supported yet.");
- System.exit(0);
- // Set<Individual> posExamples = ((PosOnlyLP)lp).getPositiveExamples();
- // int[] splits = calculateSplits(posExamples.size(),folds);
- } else {
- System.out.println("Cross validation for learning problem " + lp + " not supported.");
- System.exit(0);
- }
-
- // statistical values
- Stat runtime = new Stat();
- Stat accuracy = new Stat();
- Stat length = new Stat();
-
- // run the algorithm
- for(int currFold=0; currFold<folds; currFold++) {
- // we always perform a full initialisation to make sure that
- // no objects are reused
- try {
- start = new Start(file);
- } catch (ComponentInitException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- lp = start.getLearningProblem();
- Set<String> pos = Datastructures.individualSetToStringSet(trainingSetsPos.get(currFold));
- Set<String> neg = Datastructures.individualSetToStringSet(trainingSetsNeg.get(currFold));
- cm.applyConfigEntry(lp, "positiveExamples", pos);
- cm.applyConfigEntry(lp, "negativeExamples", neg);
-// System.out.println("pos: " + pos.size());
-// System.out.println("neg: " + neg.size());
-// System.exit(0);
-
- // es fehlt init zwischendurch
-
- LearningAlgorithm la = start.getLearningAlgorithm();
- // init again, because examples have changed
- try {
- la.init();
- } catch (ComponentInitException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- long algorithmStartTime = System.nanoTime();
- la.start();
- long algorithmDuration = System.nanoTime() - algorithmStartTime;
- runtime.addNumber(algorithmDuration/(double)1000000000);
-
- Description concept = la.getBestSolution();
-
- Set<Individual> tmp = rs.instanceCheck(concept, testSetsPos.get(currFold));
- Set<Individual> tmp2 = Helper.difference(testSetsPos.get(currFold), tmp);
- Set<Individual> tmp3 = rs.instanceCheck(concept, testSetsNeg.get(currFold));
-
- System.out.println("test set errors pos: " + tmp2);
- System.out.println("test set errors neg: " + tmp3);
-
- // calculate training accuracies
- int trainingCorrectPosClassified = getCorrectPosClassified(rs, concept, trainingSetsPos.get(currFold));
- int trainingCorrectNegClassified = getCorrectNegClassified(rs, concept, trainingSetsNeg.get(currFold));
- int trainingCorrectExamples = trainingCorrectPosClassified + trainingCorrectNegClassified;
- double trainingAccuracy = 100*((double)trainingCorrectExamples/(trainingSetsPos.get(currFold).size()+
- trainingSetsNeg.get(currFold).size()));
-
- // calculate test accuracies
- int correctPosClassified = getCorrectPosClassified(rs, concept, testSetsPos.get(currFold));
- int correctNegClassified = getCorrectNegClassified(rs, concept, testSetsNeg.get(currFold));
- int correctExamples = correctPosClassified + correctNegClassified;
- double currAccuracy = 100*((double)correctExamples/(testSetsPos.get(currFold).size()+
- testSetsNeg.get(currFold).size()));
- accuracy.addNumber(currAccuracy);
-
- length.addNumber(concept.getLength());
-
- System.out.println("fold " + currFold + " (" + file + "):");
- System.out.println(" training: " + pos.size() + " positive and " + neg.size() + " negative examples");
- System.out.println(" testing: " + correctPosClassified + "/" + testSetsPos.get(currFold).size() + " correct positives, "
- + correctNegClassified + "/" + testSetsNeg.get(currFold).size() + " correct negatives");
- System.out.println(" concept: " + concept);
- System.out.println(" accuracy: " + df.format(currAccuracy) + "% (" + df.format(trainingAccuracy) + "% on training set)");
- System.out.println(" length: " + df.format(concept.getLength()));
- System.out.println(" runtime: " + df.format(algorithmDuration/(double)1000000000) + "s");
-
- // free all resources
- start.getReasoningService().releaseKB();
- cm.freeAllComponents();
- }
-
- System.out.println();
- System.out.println("Finished " + folds + "-folds cross-validation on " + file + ".");
- System.out.println("runtime: " + statOutput(df, runtime, "s"));
- System.out.println("length: " + statOutput(df, length, ""));
- System.out.println("accuracy: " + statOutput(df, accuracy, "%"));
-
- }
-
- private int getCorrectPosClassified(ReasoningService rs, Description concept, Set<Individual> testSetPos) {
- return rs.instanceCheck(concept, testSetPos).size();
- }
-
- private int getCorrectNegClassified(ReasoningService rs, Description concept, Set<Individual> testSetNeg) {
- return testSetNeg.size() - rs.instanceCheck(concept, testSetNeg).size();
- }
-
- private Set<Individual> getTestingSet(List<Individual> examples, int[] splits, int fold) {
- int fromIndex;
- // we either start from 0 or after the last fold ended
- if(fold == 0)
- fromIndex = 0;
- else
- fromIndex = splits[fold-1];
- // the split corresponds to the ends of the folds
- int toIndex = splits[fold];
-
-// System.out.println("from " + fromIndex + " to " + toIndex);
-
- Set<Individual> testingSet = new HashSet<Individual>();
- // +1 because 2nd element is exclusive in subList method
- testingSet.addAll(examples.subList(fromIndex, toIndex));
- return testingSet;
- }
-
- private Set<Individual> getTrainingSet(Set<Individual> examples, Set<Individual> testingSet) {
- return Helper.difference(examples, testingSet);
- }
-
- // takes nr. of examples and the nr. of folds for this examples;
- // returns an array which says where each fold ends, i.e.
- // splits[i] is the index of the last element of fold i in the examples
- private int[] calculateSplits(int nrOfExamples, int folds) {
- int[] splits = new int[folds];
- for(int i=1; i<=folds; i++) {
- // we always round up to the next integer
- splits[i-1] = (int)Math.ceil(i*nrOfExamples/(double)folds);
- }
- return splits;
- }
-
- private String statOutput(DecimalFormat df, Stat stat, String unit) {
- String str = "av. " + df.format(stat.getMean()) + unit;
- str += " (deviation " + df.format(stat.getStandardDeviation()) + unit + "; ";
- str += "min " + df.format(stat.getMin()) + unit + "; ";
- str += "max " + df.format(stat.getMax()) + unit + ")";
- return str;
- }
-
-}
Deleted: trunk/src/dl-learner/org/dllearner/utilities/NT2RDF.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/NT2RDF.java 2008-04-22 15:19:07 UTC (rev 809)
+++ trunk/src/dl-learner/org/dllearner/utilities/NT2RDF.java 2008-04-22 15:23:38 UTC (rev 810)
@@ -1,35 +0,0 @@
-package org.dllearner.utilities;
-import java.io.File;
-import java.net.URI;
-
-import org.semanticweb.owl.apibinding.OWLManager;
-import org.semanticweb.owl.io.RDFXMLOntologyFormat;
-import org.semanticweb.owl.model.OWLOntology;
-import org.semanticweb.owl.model.OWLOntologyManager;
-public class NT2RDF {
-
-
- public static void main(String[] args) {
- try {
- String ontopath=args[0];
- URI inputURI = new File(ontopath).toURI();
-
- // outputURI
- String ending = ontopath.substring(ontopath.lastIndexOf(".") + 1);
- ontopath = ontopath.replace("." + ending, ".rdf" );
- URI outputURI = new File(ontopath).toURI();
-
- OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
- OWLOntology ontology = manager.loadOntologyFromPhysicalURI(inputURI);
- manager.saveOntology(ontology, new RDFXMLOntologyFormat(), outputURI);
- // Remove the ontology from the manager
- manager.removeOntology(ontology.getURI());
- }
- catch (Exception e) {
- System.out.println("The ontology could not be created: " + e.getMessage());
- }
-
- }
- }
-
-
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|
|
From: <ku...@us...> - 2008-04-22 15:19:20
|
Revision: 809
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=809&view=rev
Author: kurzum
Date: 2008-04-22 08:19:07 -0700 (Tue, 22 Apr 2008)
Log Message:
-----------
finished sparql script, some fine tuning needed
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java
trunk/src/dl-learner/org/dllearner/kb/sparql/ExtractionAlgorithm.java
trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQuery.java
trunk/src/dl-learner/org/dllearner/test/SPARQLPreparation.java
trunk/src/dl-learner/org/dllearner/utilities/LearnSparql.java
Modified: trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java 2008-04-22 13:31:50 UTC (rev 808)
+++ trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java 2008-04-22 15:19:07 UTC (rev 809)
@@ -103,8 +103,11 @@
//extended Options
private long maxExecutionTimeInSeconds;
+ private boolean maxExecutionTimeShown=false;
private long minExecutionTimeInSeconds;
+ private boolean minExecutionTimeShown=false;
private int guaranteeXgoodDescriptions;
+ private boolean guaranteeXgoodShown=false;
// if set to false we do not test properness; this may seem wrong
// but the disadvantage of properness testing are additional reasoner
@@ -185,6 +188,7 @@
private int conceptTestsReasoner = 0;
// time variables
+ private long runtime;
private long algorithmStartTime;
private long propernessCalcTimeNs = 0;
private long propernessCalcReasoningTimeNs = 0;
@@ -257,7 +261,7 @@
}
public void start() {
-
+ runtime=System.currentTimeMillis();
// TODO: write a JUnit test for this problem (long-lasting or infinite loops because
// redundant children of a node are called recursively after when the node is extended
// twice)
@@ -387,26 +391,37 @@
Files.appendFile(searchTreeFile, treeString);
}
+
+ if(maxExecutionTimeReached()) { stop=true;}
+ solutionFound = (guaranteeXgoodDescriptions() );
+ solutionFound = (minExecutionTimeReached()&& solutionFound);
+ //logger.info(minExecutionTimeReached()+"aaaaaaa "+solutions.size()+"::"+guaranteeXgoodDescriptions);
+ //logger.info(solutionFound+"aaaaaaa "+stop);
+
+
// Anzahl Schleifendurchläufe
loop++;
- }
- if(maxExecutionTimeReached()) { stop=true;}
- boolean minSolutionrequirement = (solutions.size()>guaranteeXgoodDescriptions);
+ }//end while
+
- if(solutionFound && minExecutionTimeReached() && minSolutionrequirement) {
+
+ if(solutionFound ) {
logger.info("best node " + candidatesStable.last().getShortDescription(nrOfPositiveExamples, nrOfNegativeExamples, baseURI));
- logger.info("\nsolutions:");
+ logger.info("\nsolutions ( top 5 ):");
+ int show=1;
for(Description c : solutions) {
- logger.info(" " + c.toString(baseURI,null) + " (length " + c.getLength() +", depth " + c.getDepth() + ")");
+ logger.info(show+": " + c.toString(baseURI,null) + " (length " + c.getLength() +", depth " + c.getDepth() + ")");
//TODO remove this line maybe
// watch for String.replace Quick hack
- logger.info(" MANCHESTER: " +
+ logger.info(" MANCHESTER: " +
c.toManchesterSyntaxString(baseURI, new HashMap<String,String>()).
replace("\"", ""));
- logger.info(" KBSyntax: " + c.toKBSyntaxString());
+ logger.info(" KBSyntax: " + c.toKBSyntaxString());
+ if(show>=5){break;}
+ show++;
}
}
logger.debug("size of candidate set: " + candidates.size());
@@ -1029,13 +1044,31 @@
return startNode;
}
+ private boolean guaranteeXgoodDescriptions(){
+ if(guaranteeXgoodShown)return true;
+ if(solutions.size()>guaranteeXgoodDescriptions){
+ logger.info("Minimum number of good descriptions reached, stopping now...");
+ guaranteeXgoodShown=true;
+ return true;}
+ else return false;
+
+ }
+
+
private boolean maxExecutionTimeReached(){
if(maxExecutionTimeInSeconds==0)return false;
- long needed = System.nanoTime()- this.algorithmStartTime;
+ if(maxExecutionTimeShown)return true;
+ long needed = System.currentTimeMillis()- this.runtime;
//millisec /100
//seconds /1000
- long maxNanoSeconds = maxExecutionTimeInSeconds *100*1000 ;
- if(maxNanoSeconds<needed)return true;
+ long maxMilliSeconds = maxExecutionTimeInSeconds *1000 ;
+ //System.out.println("max"+maxMilliSeconds);
+ //System.out.println(needed);
+
+ if(maxMilliSeconds<needed){
+ logger.info("Maximum time reached, stopping now...");
+ maxExecutionTimeShown=true;
+ return true;}
else return false;
}
@@ -1045,12 +1078,19 @@
* @return true
*/
private boolean minExecutionTimeReached(){
+ if(minExecutionTimeShown)return true;
//if(minExecutionTimeInSeconds==0)return true;
- long needed = System.nanoTime()- this.algorithmStartTime;
+ long needed = System.currentTimeMillis()- this.runtime;
//millisec /100
//seconds /1000
- long minNanoSeconds = minExecutionTimeInSeconds *100*1000 ;
- if(minNanoSeconds<needed)return true;
+ long minMilliSeconds = minExecutionTimeInSeconds *1000 ;
+ //System.out.println("min"+minMilliSeconds);
+ //System.out.println(needed);
+
+ if(minMilliSeconds<needed){
+ logger.info("Minimum time reached, stopping when next solution is found");
+ minExecutionTimeShown=true;
+ return true;}
else return false;
}
Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/ExtractionAlgorithm.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/ExtractionAlgorithm.java 2008-04-22 13:31:50 UTC (rev 808)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/ExtractionAlgorithm.java 2008-04-22 15:19:07 UTC (rev 809)
@@ -23,6 +23,7 @@
import java.util.HashSet;
import java.util.Vector;
+import org.apache.log4j.Logger;
import org.dllearner.kb.sparql.configuration.Configuration;
import org.dllearner.kb.sparql.datastructure.ClassNode;
import org.dllearner.kb.sparql.datastructure.InstanceNode;
@@ -40,7 +41,8 @@
private int recursionDepth = 1;
// private boolean getAllSuperClasses = true;
// private boolean closeAfterRecursion = true;
- private boolean print_flag = false;
+ private static Logger logger = Logger
+ .getLogger(ExtractionAlgorithm.class);
public ExtractionAlgorithm(Configuration Configuration) {
this.configuration = Configuration;
@@ -79,7 +81,7 @@
System.out.println(n);
Vector<Node> v = new Vector<Node>();
v.add(n);
- p("StartVector: " + v);
+ logger.info("StartVector: " + v);
// n.expand(tsp, this.Manipulator);
// Vector<Node> second=
for (int x = 1; x <= recursionDepth; x++) {
@@ -87,7 +89,7 @@
Vector<Node> tmp = new Vector<Node>();
while (v.size() > 0) {
Node tmpNode = v.remove(0);
- p("Expanding " + tmpNode);
+ logger.info("Expanding " + tmpNode);
// System.out.println(this.Manipulator);
// these are the new not expanded nodes
// the others are saved in connection with the original node
@@ -97,14 +99,14 @@
tmp.addAll(tmpVec);
}
v = tmp;
- System.out.println("Recursion counter: " + x + " with " + v.size()
+ logger.info("Recursion counter: " + x + " with " + v.size()
+ " Nodes remaining, needed: "
+ (System.currentTimeMillis() - time) + "ms");
time = System.currentTimeMillis();
}
HashSet<String> hadAlready = new HashSet<String>();
- p("Get all superclasses");
+ logger.info("Get all superclasses");
//p(configuration.toString());
// gets All Class Nodes and expands them further
if (this.configuration.isGetAllSuperClasses()) {
@@ -126,10 +128,10 @@
configuration);
if (this.configuration.isCloseAfterRecursion()) {
while (instances.size() > 0) {
- p("Getting classes for remaining instances: "
+ logger.info("Getting classes for remaining instances: "
+ instances.size());
Node next = instances.remove(0);
- p("Getting classes for: " + next);
+ logger.info("Getting classes for: " + next);
classes.addAll(next.expand(tsqc, manipulator));
if (classes.size() >= manipulator.breakSuperClassRetrievalAfter) {
break;
@@ -139,14 +141,14 @@
Vector<Node> tmp = new Vector<Node>();
int i = 0;
while (classes.size() > 0) {
- p("Remaining classes: " + classes.size());
+ logger.info("Remaining classes: " + classes.size());
// Iterator<Node> it=classes.iterator();
// Node next =(Node) it.next();
// classes.remove(next);
Node next = classes.remove(0);
if (!hadAlready.contains(next.getURI().toString())) {
- p("Expanding: " + next);
+ logger.info("Expanding: " + next);
// System.out.println(hadAlready.size());
hadAlready.add(next.getURI().toString());
tmp = next.expand(typedSparqlQuery, manipulator);
@@ -172,9 +174,6 @@
}
- void p(String s) {
- if (print_flag)
- System.out.println(s);
- }
+
}
Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQuery.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQuery.java 2008-04-22 13:31:50 UTC (rev 808)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQuery.java 2008-04-22 15:19:07 UTC (rev 809)
@@ -67,10 +67,10 @@
public ResultSet send() {
isRunning = true;
ResultSet rs=null;
- logger.info(queryString);
+ logger.trace(queryString);
String service = endpoint.getURL().toString();
- logger.info(endpoint.getURL().toString());
+ logger.trace(endpoint.getURL().toString());
// Jena access to SPARQL endpoint
queryExecution = new QueryEngineHTTP(service, queryString);
for (String dgu : endpoint.getDefaultGraphURIs()) {
@@ -81,14 +81,14 @@
}
logger.info("query SPARQL server");
try{
- //TODO after overnext Jena release
+ //TODO remove after overnext Jena release
HttpQuery.urlLimit = 3*1024 ;
rs = queryExecution.execSelect();
json=SparqlQuery.getAsJSON(rs);
- logger.info(rs.getResultVars().toString());
+ logger.trace(rs.getResultVars().toString());
} catch (Exception e){
sendException=new SparqlQueryException(e.getMessage());
- logger.info("Exception when querying Sparql Endpoint");
+ logger.error("Exception when querying Sparql Endpoint");
}
isRunning = false;
return rs;
Modified: trunk/src/dl-learner/org/dllearner/test/SPARQLPreparation.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/test/SPARQLPreparation.java 2008-04-22 13:31:50 UTC (rev 808)
+++ trunk/src/dl-learner/org/dllearner/test/SPARQLPreparation.java 2008-04-22 15:19:07 UTC (rev 809)
@@ -4,6 +4,12 @@
import java.util.SortedSet;
import java.util.TreeSet;
+import javax.sound.midi.SysexMessage;
+
+import org.apache.log4j.ConsoleAppender;
+import org.apache.log4j.Level;
+import org.apache.log4j.Logger;
+import org.apache.log4j.SimpleLayout;
import org.dllearner.kb.sparql.Cache;
import org.dllearner.kb.sparql.SparqlQuery;
import org.dllearner.kb.sparql.SparqlQueryDescriptionConvertVisitor;
@@ -19,7 +25,7 @@
static Cache c;
static SparqlEndpoint se;
-
+ private static Logger logger = Logger.getRootLogger();
/**
* @param args
*/
@@ -27,6 +33,8 @@
init();
try {
+
+
SimpleClock sc=new SimpleClock();
SortedSet<String> concepts = new TreeSet<String>();
//concepts.add("\"http://dbpedia.org/class/yago/Person100007846\"");
@@ -52,13 +60,13 @@
negExamples.remove(string2);
};
}*/
- System.out.println(negExamples.size());
+ //System.out.println(negExamples.size());
negExamples.removeAll(posExamples);
posExamples=shrink(posExamples,5);
negExamples=shrink(negExamples,posExamples.size());
//System.out.println(posExamples.first()));
- System.out.println(posExamples.size());
- System.out.println(negExamples.size());
+ //System.out.println(posExamples.size());
+ //System.out.println(negExamples.size());
//
new ConfWriter().writeSPARQL("aaa.conf", posExamples, negExamples, url, new TreeSet<String>());
@@ -137,6 +145,14 @@
SparqlQueryDescriptionConvertVisitor.debug_flag = false;
c = new Cache("cache");
se = SparqlEndpoint.dbpediaEndpoint();
+ // create logger (a simple logger which outputs
+ // its messages to the console)
+ SimpleLayout layout = new SimpleLayout();
+ ConsoleAppender consoleAppender = new ConsoleAppender(layout);
+ logger.removeAllAppenders();
+ logger.addAppender(consoleAppender);
+ logger.setLevel(Level.DEBUG);
+
}
Modified: trunk/src/dl-learner/org/dllearner/utilities/LearnSparql.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/LearnSparql.java 2008-04-22 13:31:50 UTC (rev 808)
+++ trunk/src/dl-learner/org/dllearner/utilities/LearnSparql.java 2008-04-22 15:19:07 UTC (rev 809)
@@ -24,6 +24,7 @@
public void learn(SortedSet<String> posExamples,SortedSet<String> negExamples,
String uri, SortedSet<String> ignoredConcepts){
+
ComponentManager cm = ComponentManager.getInstance();
LearningAlgorithm la = null;
ReasoningService rs = null;
@@ -68,8 +69,8 @@
cm.applyConfigEntry(la,"useExistsConstructor",true);
cm.applyConfigEntry(la,"useCardinalityRestrictions",false);
cm.applyConfigEntry(la,"useNegation",false);
- cm.applyConfigEntry(la,"minExecutionTimeInSeconds",10);
- cm.applyConfigEntry(la,"guaranteeXgoodDescriptions",10);
+ cm.applyConfigEntry(la,"minExecutionTimeInSeconds",0);
+ cm.applyConfigEntry(la,"guaranteeXgoodDescriptions",20);
//cm.applyConfigEntry(la,"quiet",false);
if(ignoredConcepts.size()>0)
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|
|
From: <lor...@us...> - 2008-04-22 13:31:55
|
Revision: 808
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=808&view=rev
Author: lorenz_b
Date: 2008-04-22 06:31:50 -0700 (Tue, 22 Apr 2008)
Log Message:
-----------
added method moveIndividual() to class ORE
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/tools/ore/ORE.java
Modified: trunk/src/dl-learner/org/dllearner/tools/ore/ORE.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/ore/ORE.java 2008-04-22 13:26:06 UTC (rev 807)
+++ trunk/src/dl-learner/org/dllearner/tools/ore/ORE.java 2008-04-22 13:31:50 UTC (rev 808)
@@ -180,6 +180,7 @@
OWLDescription newConceptOWLAPI = OWLAPIDescriptionConvertVisitor.getOWLDescription(desc);
OWLDescription oldConceptOWLAPI = OWLAPIDescriptionConvertVisitor.getOWLDescription(concept);
+
OWLOntology ontology = reasoner.getOWLAPIOntologies().get(0);
OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
@@ -192,7 +193,6 @@
OWLAxiom axiomOWLAPI = factory.getOWLEquivalentClassesAxiom(ds);
-
AddAxiom axiom = new AddAxiom(ontology, axiomOWLAPI);
try {
@@ -214,9 +214,6 @@
public void deleteIndividual(Individual ind){
-
-
-
OWLOntology ontology = reasoner.getOWLAPIOntologies().get(0);
OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
@@ -244,10 +241,52 @@
}
remover.reset();
-
+ try {
+ manager.saveOntology(ontology);
+ } catch (UnknownOWLOntologyException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ } catch (OWLOntologyStorageException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ }
+ public void moveIndividual(Individual ind, Description oldDescription, Description newDescription){
+
+ OWLOntology ontology = reasoner.getOWLAPIOntologies().get(0);
+
+ OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
+ OWLDataFactory factory = manager.getOWLDataFactory();
+ OWLIndividual individualOWLAPI = null;
+
+
+ try {
+ individualOWLAPI = factory.getOWLIndividual( new URI(ind.getName()));
+ } catch (URISyntaxException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+
+ //Loeschen
+ OWLEntityRemover remover = new OWLEntityRemover(manager, Collections.singleton(ontology));
+ individualOWLAPI.accept(remover);
+
+ try {
+ manager.applyChanges(remover.getChanges());
+ } catch (OWLOntologyChangeException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ remover.reset();
+
+ //Hinzufuegen
+
+
}
+
+
public static void main(String[] args){
@@ -262,7 +301,6 @@
System.err.println("Concepts :" + rs.getAtomicConcepts());
-
test.setConcept(new NamedClass("http://example.com/father#father"));
test.setPosNegExamples();
System.out.println(test.posExamples);
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|
|
From: <ku...@us...> - 2008-04-22 13:26:09
|
Revision: 807
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=807&view=rev
Author: kurzum
Date: 2008-04-22 06:26:06 -0700 (Tue, 22 Apr 2008)
Log Message:
-----------
fixed log level
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/core/ComponentManager.java
Modified: trunk/src/dl-learner/org/dllearner/core/ComponentManager.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/ComponentManager.java 2008-04-22 13:07:07 UTC (rev 806)
+++ trunk/src/dl-learner/org/dllearner/core/ComponentManager.java 2008-04-22 13:26:06 UTC (rev 807)
@@ -40,6 +40,7 @@
import java.util.TreeMap;
import java.util.TreeSet;
+import org.apache.log4j.Logger;
import org.dllearner.cli.Start;
import org.dllearner.core.config.ConfigEntry;
import org.dllearner.core.config.ConfigOption;
@@ -61,6 +62,9 @@
*/
public class ComponentManager {
+ private static Logger logger = Logger
+ .getLogger(ComponentManager.class);
+
private ComponentPool pool = new ComponentPool();
// these variables are valid for the complete lifetime of a DL-Learner session
@@ -213,10 +217,10 @@
*/
@SuppressWarnings( { "unchecked" })
public <T> void applyConfigEntry(Component component, String optionName, T value) {
- System.out.println(component);
- System.out.println(optionName);
- System.out.println(value);
- System.out.println(value.getClass());
+ logger.trace(component);
+ logger.trace(optionName);
+ logger.trace(value);
+ logger.trace(value.getClass());
// first we look whether the component is registered
if (components.contains(component.getClass())) {
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|
|
From: <ku...@us...> - 2008-04-22 13:07:12
|
Revision: 806
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=806&view=rev
Author: kurzum
Date: 2008-04-22 06:07:07 -0700 (Tue, 22 Apr 2008)
Log Message:
-----------
loads of little changes
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLComponent.java
trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java
trunk/src/dl-learner/org/dllearner/core/ComponentManager.java
trunk/src/dl-learner/org/dllearner/core/config/CommonConfigOptions.java
trunk/src/dl-learner/org/dllearner/examples/KRKModular.java
trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlKnowledgeSource.java
trunk/src/dl-learner/org/dllearner/kb/sparql/configuration/SparqlQueryType.java
trunk/src/dl-learner/org/dllearner/reasoning/FastInstanceChecker.java
trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java
trunk/src/dl-learner/org/dllearner/test/SPARQLPreparation.java
Added Paths:
-----------
trunk/src/dl-learner/org/dllearner/utilities/ConfWriter.java
trunk/src/dl-learner/org/dllearner/utilities/LearnSparql.java
trunk/src/dl-learner/org/dllearner/utilities/NT2RDF.java
Modified: trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLComponent.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLComponent.java 2008-04-21 20:21:36 UTC (rev 805)
+++ trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLComponent.java 2008-04-22 13:07:07 UTC (rev 806)
@@ -38,8 +38,8 @@
import org.dllearner.core.config.DoubleConfigOption;
import org.dllearner.core.config.InvalidConfigOptionValueException;
import org.dllearner.core.config.StringConfigOption;
+import org.dllearner.core.owl.Description;
import org.dllearner.core.owl.NamedClass;
-import org.dllearner.core.owl.Description;
import org.dllearner.core.owl.ObjectProperty;
import org.dllearner.learningproblems.PosNegLP;
import org.dllearner.learningproblems.PosOnlyDefinitionLP;
@@ -99,13 +99,18 @@
private boolean useOverlyGeneralList = true;
private boolean useShortConceptConstruction = true;
private boolean improveSubsumptionHierarchy = true;
- private boolean useAllConstructor = true;
- private boolean useExistsConstructor = true;
- private boolean useCardinalityRestrictions = true;
- private boolean useNegation = true;
- private boolean useBooleanDatatypes = true;
+ private boolean useAllConstructor = CommonConfigOptions.useAllConstructorDefault;
+ private boolean useExistsConstructor = CommonConfigOptions.useExistsConstructorDefault;
+ private boolean useCardinalityRestrictions = CommonConfigOptions.useCardinalityRestrictionsDefault;
+ private boolean useNegation = CommonConfigOptions.useNegationDefault;
+ private boolean useBooleanDatatypes = CommonConfigOptions.useBooleanDatatypesDefault;
private double noisePercentage = 0.0;
private NamedClass startClass = null;
+ //extended Options
+ //in seconds
+ private int maxExecutionTimeInSeconds = CommonConfigOptions.maxExecutionTimeInSecondsDefault;
+ private int minExecutionTimeInSeconds = CommonConfigOptions.minExecutionTimeInSecondsDefault;
+ private int guaranteeXgoodDescriptions = CommonConfigOptions.guaranteeXgoodDescriptionsDefault;
// Variablen zur Einstellung der Protokollierung
// boolean quiet = false;
@@ -164,7 +169,9 @@
options.add(CommonConfigOptions.useCardinalityRestrictions());
options.add(CommonConfigOptions.useNegation());
options.add(CommonConfigOptions.useBooleanDatatypes());
-
+ options.add(CommonConfigOptions.maxExecutionTimeInSeconds());
+ options.add(CommonConfigOptions.minExecutionTimeInSeconds());
+ options.add(CommonConfigOptions.guaranteeXgoodDescriptions());
DoubleConfigOption noisePercentage = new DoubleConfigOption("noisePercentage", "the (approximated) percentage of noise within the examples");
noisePercentage.setLowerLimit(0);
noisePercentage.setUpperLimit(100);
@@ -226,6 +233,12 @@
useBooleanDatatypes = (Boolean) entry.getValue();
} else if(name.equals("startClass")) {
startClass = new NamedClass((String)entry.getValue());
+ }else if(name.equals("maxExecutionTimeInSeconds")) {
+ maxExecutionTimeInSeconds = (Integer) entry.getValue();
+ }else if(name.equals("minExecutionTimeInSeconds")) {
+ minExecutionTimeInSeconds = (Integer) entry.getValue();
+ }else if(name.equals("guaranteeXgoodDescriptions")) {
+ guaranteeXgoodDescriptions = (Integer) entry.getValue();
}
}
@@ -319,7 +332,10 @@
searchTreeFile,
useTooWeakList,
useOverlyGeneralList,
- useShortConceptConstruction
+ useShortConceptConstruction,
+ maxExecutionTimeInSeconds,
+ minExecutionTimeInSeconds,
+ guaranteeXgoodDescriptions
);
// note: used concepts and roles do not need to be passed
// as argument, because it is sufficient to prepare the
@@ -363,4 +379,13 @@
return algorithm.getStartNode();
}
+
+ public void printBestSolutions(int nrOfSolutions){
+
+ algorithm.printBestSolutions(nrOfSolutions);
+ }
+
+
+
+
}
Modified: trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java 2008-04-21 20:21:36 UTC (rev 805)
+++ trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLearner.java 2008-04-22 13:07:07 UTC (rev 806)
@@ -101,6 +101,11 @@
private boolean useOverlyGeneralList = true;
private boolean useShortConceptConstruction = true;
+ //extended Options
+ private long maxExecutionTimeInSeconds;
+ private long minExecutionTimeInSeconds;
+ private int guaranteeXgoodDescriptions;
+
// if set to false we do not test properness; this may seem wrong
// but the disadvantage of properness testing are additional reasoner
// queries and a search bias towards ALL r.something because
@@ -188,6 +193,7 @@
private long redundancyCheckTimeNs = 0;
private long evaluateSetCreationTimeNs = 0;
private long improperConceptsRemovalTimeNs = 0;
+
// prefixes
private String baseURI;
@@ -206,7 +212,10 @@
File searchTreeFile,
boolean useTooWeakList,
boolean useOverlyGeneralList,
- boolean useShortConceptConstruction
+ boolean useShortConceptConstruction,
+ int maxExecutionTimeInSeconds,
+ int minExecutionTimeInSeconds,
+ int guaranteeXgoodDescriptions
) {
if(learningProblem instanceof PosNegLP) {
PosNegLP lp = (PosNegLP) learningProblem;
@@ -239,7 +248,10 @@
this.useTooWeakList = useTooWeakList;
this.useOverlyGeneralList = useOverlyGeneralList;
this.useShortConceptConstruction = useShortConceptConstruction;
- baseURI = rs.getBaseURI();
+ this.baseURI = rs.getBaseURI();
+ this.maxExecutionTimeInSeconds=maxExecutionTimeInSeconds;
+ this.minExecutionTimeInSeconds=minExecutionTimeInSeconds;
+ this.guaranteeXgoodDescriptions = guaranteeXgoodDescriptions;
// logger.setLevel(Level.DEBUG);
}
@@ -317,7 +329,7 @@
long reductionInterval = 500l * 1000000000l;
long currentTime;
- while(!solutionFound && !stop) {
+ while(!solutionFound && !stop ) {
// print statistics at most once a second
currentTime = System.nanoTime();
@@ -352,7 +364,8 @@
candidates.add(bestNode);
// newCandidates has been filled during node expansion
candidates.addAll(newCandidates);
- candidatesStable.addAll(newCandidates);
+ candidatesStable.addAll(newCandidates);
+
// System.out.println("done");
if(writeSearchTree) {
@@ -380,8 +393,10 @@
}
-
- if(solutionFound) {
+ if(maxExecutionTimeReached()) { stop=true;}
+ boolean minSolutionrequirement = (solutions.size()>guaranteeXgoodDescriptions);
+
+ if(solutionFound && minExecutionTimeReached() && minSolutionrequirement) {
logger.info("best node " + candidatesStable.last().getShortDescription(nrOfPositiveExamples, nrOfNegativeExamples, baseURI));
logger.info("\nsolutions:");
for(Description c : solutions) {
@@ -732,6 +747,7 @@
long algorithmRuntime = System.nanoTime() - algorithmStartTime;
if(!finalStats) {
+
ExampleBasedNode bestNode = candidatesStable.last();
// double accuracy = 100 * ((bestNode.getCoveredPositives().size()
// + nrOfNegativeExamples - bestNode.getCoveredNegatives().size())/(double)nrOfExamples);
@@ -989,6 +1005,19 @@
return best;
}
+
+ public void printBestSolutions(int nrOfSolutions){
+
+ int i=0;
+ for(ExampleBasedNode n : candidatesStable.descendingSet()) {
+ System.out.println(n.getShortDescription(nrOfPositiveExamples, nrOfNegativeExamples, baseURI));
+ if(i==nrOfSolutions)
+ return ;
+ i++;
+ }
+
+ }
+
public Score getSolutionScore() {
if(posOnly)
return posOnlyLearningProblem.computeScore(getBestSolution());
@@ -1000,4 +1029,30 @@
return startNode;
}
+ private boolean maxExecutionTimeReached(){
+ if(maxExecutionTimeInSeconds==0)return false;
+ long needed = System.nanoTime()- this.algorithmStartTime;
+ //millisec /100
+ //seconds /1000
+ long maxNanoSeconds = maxExecutionTimeInSeconds *100*1000 ;
+ if(maxNanoSeconds<needed)return true;
+ else return false;
+
+ }
+
+ /**
+ * true if minExecutionTime reached
+ * @return true
+ */
+ private boolean minExecutionTimeReached(){
+ //if(minExecutionTimeInSeconds==0)return true;
+ long needed = System.nanoTime()- this.algorithmStartTime;
+ //millisec /100
+ //seconds /1000
+ long minNanoSeconds = minExecutionTimeInSeconds *100*1000 ;
+ if(minNanoSeconds<needed)return true;
+ else return false;
+
+ }
+
}
Modified: trunk/src/dl-learner/org/dllearner/core/ComponentManager.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/ComponentManager.java 2008-04-21 20:21:36 UTC (rev 805)
+++ trunk/src/dl-learner/org/dllearner/core/ComponentManager.java 2008-04-22 13:07:07 UTC (rev 806)
@@ -213,6 +213,10 @@
*/
@SuppressWarnings( { "unchecked" })
public <T> void applyConfigEntry(Component component, String optionName, T value) {
+ System.out.println(component);
+ System.out.println(optionName);
+ System.out.println(value);
+ System.out.println(value.getClass());
// first we look whether the component is registered
if (components.contains(component.getClass())) {
Modified: trunk/src/dl-learner/org/dllearner/core/config/CommonConfigOptions.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/config/CommonConfigOptions.java 2008-04-21 20:21:36 UTC (rev 805)
+++ trunk/src/dl-learner/org/dllearner/core/config/CommonConfigOptions.java 2008-04-22 13:07:07 UTC (rev 806)
@@ -40,6 +40,9 @@
public static boolean useCardinalityRestrictionsDefault = true;
public static boolean useNegationDefault = true;
public static boolean useBooleanDatatypesDefault = true;
+ public static int maxExecutionTimeInSecondsDefault = 0;
+ public static int minExecutionTimeInSecondsDefault = 0;
+ public static int guaranteeXgoodDescriptionsDefault = 1;
//public static double noisePercentageDefault = 0.0;
@@ -105,4 +108,16 @@
public static BooleanConfigOption useBooleanDatatypes() {
return new BooleanConfigOption("useBooleanDatatypes", "specifies whether boolean datatypes are used in the learning algorothm",useBooleanDatatypesDefault);
}
+
+ public static IntegerConfigOption maxExecutionTimeInSeconds() {
+ return new IntegerConfigOption("maxExecutionTimeInSeconds", "algorithm will stop after specified seconds",maxExecutionTimeInSecondsDefault);
+ }
+
+ public static IntegerConfigOption minExecutionTimeInSeconds() {
+ return new IntegerConfigOption("minExecutionTimeInSeconds", "algorithm will run at least specified seconds",minExecutionTimeInSecondsDefault);
+ }
+
+ public static IntegerConfigOption guaranteeXgoodDescriptions() {
+ return new IntegerConfigOption("guaranteeXgoodDescriptions", "algorithm will run until X good (100%) concept descritpions are found",guaranteeXgoodDescriptionsDefault);
+ }
}
Modified: trunk/src/dl-learner/org/dllearner/examples/KRKModular.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/examples/KRKModular.java 2008-04-21 20:21:36 UTC (rev 805)
+++ trunk/src/dl-learner/org/dllearner/examples/KRKModular.java 2008-04-22 13:07:07 UTC (rev 806)
@@ -32,7 +32,6 @@
import org.dllearner.core.owl.ObjectPropertyAssertion;
import org.dllearner.kb.KBFile;
import org.dllearner.learningproblems.PosNegDefinitionLP;
-import org.dllearner.learningproblems.PosNegLP;
import org.dllearner.parser.KBParser;
import org.dllearner.reasoning.FastInstanceChecker;
import org.dllearner.reasoning.OWLAPIReasoner;
@@ -258,9 +257,12 @@
r.init();
ReasoningService rs = new ReasoningService(r);
+ //cm.learningProblem(lpClass, reasoner)
LearningProblem lp = new PosNegDefinitionLP(rs);
- ((PosNegLP)lp).setPositiveExamples(pos);
- ((PosNegLP)lp).setNegativeExamples(neg);
+ //cm.getConfigOptionValue(lp, "");
+ cm.applyConfigEntry(lp, "positiveExamples",pos);
+ cm.applyConfigEntry(lp, "negativeExamples",neg);
+
lp.init();
la = cm.learningAlgorithm(ExampleBasedROLComponent.class, lp, rs);
Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlKnowledgeSource.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlKnowledgeSource.java 2008-04-21 20:21:36 UTC (rev 805)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlKnowledgeSource.java 2008-04-22 13:07:07 UTC (rev 806)
@@ -405,6 +405,10 @@
// TODO Does this work?
return kb;
}
+
+ public URL getNTripleURL(){
+ return dumpFile;
+ }
/*public static void main(String[] args) throws MalformedURLException {
String query = "SELECT ?pred ?obj\n"
Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/configuration/SparqlQueryType.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/configuration/SparqlQueryType.java 2008-04-21 20:21:36 UTC (rev 805)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/configuration/SparqlQueryType.java 2008-04-22 13:07:07 UTC (rev 806)
@@ -95,6 +95,8 @@
pred.add("http://dbpedia.org/property/wikipage");
pred.add("http://dbpedia.org/property/wikiPageUsesTemplate");
pred.add("http://dbpedia.org/property/relatedInstance");
+ pred.add("http://dbpedia.org/property/owner");
+ pred.add("http://dbpedia.org/property/standard");
Set<String> obj = new HashSet<String>();
//obj.add("http://dbpedia.org/resource/Category:Wikipedia_");
@@ -108,7 +110,7 @@
obj.add("http://www.w3.org/2006/03/wn/wn20/instances/synset");
obj.add("http://www4.wiwiss.fu-berlin.de/flickrwrappr");
obj.add("http://www.w3.org/2004/02/skos/core");
-
+
return new SparqlQueryType("forbid", obj, pred, false);
}
public static SparqlQueryType YagoSpecialHierarchy(){
Modified: trunk/src/dl-learner/org/dllearner/reasoning/FastInstanceChecker.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/reasoning/FastInstanceChecker.java 2008-04-21 20:21:36 UTC (rev 805)
+++ trunk/src/dl-learner/org/dllearner/reasoning/FastInstanceChecker.java 2008-04-22 13:07:07 UTC (rev 806)
@@ -162,8 +162,11 @@
public void init() throws ComponentInitException {
rc = new OWLAPIReasoner(sources);
//TODO make it nice
+
+
rc.setReasonerType(reasonerType);
rc.init();
+
try {
atomicConcepts = rc.getAtomicConcepts();
Modified: trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java 2008-04-21 20:21:36 UTC (rev 805)
+++ trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java 2008-04-22 13:07:07 UTC (rev 806)
@@ -58,6 +58,7 @@
import org.dllearner.core.owl.TypedConstant;
import org.dllearner.core.owl.UntypedConstant;
import org.dllearner.kb.OWLFile;
+import org.dllearner.kb.sparql.SparqlKnowledgeSource;
import org.dllearner.utilities.ConceptComparator;
import org.dllearner.utilities.RoleComparator;
import org.semanticweb.owl.apibinding.OWLManager;
@@ -180,9 +181,15 @@
Set<OWLOntology> allImports = new HashSet<OWLOntology>();
for(KnowledgeSource source : sources) {
- // OWL files are read directly
- if(source instanceof OWLFile) {
- URL url = ((OWLFile)source).getURL();
+
+ if(source instanceof OWLFile || source instanceof SparqlKnowledgeSource ) {
+ URL url=null;
+ if(source instanceof OWLFile){
+ url = ((OWLFile)source).getURL();
+ }
+ else if(source instanceof SparqlKnowledgeSource) {
+ url=((SparqlKnowledgeSource)source).getNTripleURL();
+ }
try {
OWLOntology ontology = manager.loadOntologyFromPhysicalURI(url.toURI());
Modified: trunk/src/dl-learner/org/dllearner/test/SPARQLPreparation.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/test/SPARQLPreparation.java 2008-04-21 20:21:36 UTC (rev 805)
+++ trunk/src/dl-learner/org/dllearner/test/SPARQLPreparation.java 2008-04-22 13:07:07 UTC (rev 806)
@@ -8,7 +8,9 @@
import org.dllearner.kb.sparql.SparqlQuery;
import org.dllearner.kb.sparql.SparqlQueryDescriptionConvertVisitor;
import org.dllearner.kb.sparql.configuration.SparqlEndpoint;
+import org.dllearner.utilities.ConfWriter;
import org.dllearner.utilities.JenaResultSetConvenience;
+import org.dllearner.utilities.LearnSparql;
import org.dllearner.utilities.SimpleClock;
import com.hp.hpl.jena.query.ResultSet;
@@ -24,12 +26,14 @@
public static void main(String[] args) {
init();
try {
+
SimpleClock sc=new SimpleClock();
SortedSet<String> concepts = new TreeSet<String>();
//concepts.add("\"http://dbpedia.org/class/yago/Person100007846\"");
concepts.add("\"http://dbpedia.org/class/yago/FieldMarshal110086821\"");
SortedSet<String> posExamples = new TreeSet<String>();
SortedSet<String> negExamples = new TreeSet<String>();
+ String url = "http://dbpedia.openlinksw.com:8890/sparql";
//HashMap<String, ResultSet> result = new HashMap<String, ResultSet>();
//HashMap<String, String> result2 = new HashMap<String, String>();
@@ -50,11 +54,16 @@
}*/
System.out.println(negExamples.size());
negExamples.removeAll(posExamples);
-
- negExamples=shrink(negExamples,posExamples.size()*2);
+ posExamples=shrink(posExamples,5);
+ negExamples=shrink(negExamples,posExamples.size());
//System.out.println(posExamples.first()));
System.out.println(posExamples.size());
System.out.println(negExamples.size());
+
+ //
+ new ConfWriter().writeSPARQL("aaa.conf", posExamples, negExamples, url, new TreeSet<String>());
+ new LearnSparql().learn(posExamples, negExamples, "http://dbpedia.openlinksw.com:8890/sparql", new TreeSet<String>());
+
sc.printAndSet("Finished");
} catch (Exception e) {
e.printStackTrace();
Added: trunk/src/dl-learner/org/dllearner/utilities/ConfWriter.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/ConfWriter.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/utilities/ConfWriter.java 2008-04-22 13:07:07 UTC (rev 806)
@@ -0,0 +1,155 @@
+package org.dllearner.utilities;
+
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.util.SortedSet;
+import java.util.TreeSet;
+
+import org.dllearner.core.owl.Individual;
+
+public class ConfWriter {
+
+
+ public String workingDir="examples/stest/";
+
+
+ public void writeROLLearnerOWLFileInd(String filename,SortedSet<Individual> pos,SortedSet<Individual> neg,
+ String owlFile, SortedSet<String> ignoredConcepts){
+
+ writeROLLearnerOWLFile( filename,toString( pos),toString( neg),
+ owlFile, ignoredConcepts);
+ }
+
+ public void writeROLLearnerOWLFile(String filename,SortedSet<String> pos,SortedSet<String> neg,
+ String owlFile, SortedSet<String> ignoredConcepts){
+
+ String prefix = "refexamples";
+ StringBuffer buf = new StringBuffer();
+ buf.append("import(\"" + owlFile + "\");\n\n");
+
+ buf.append(getIgnoredConcepts(ignoredConcepts,prefix));
+
+ buf.append(getStandard(prefix));
+
+ buf.append( getPosAndNeg( pos, neg));
+
+
+ writeToFile(filename, buf.toString());
+
+ }
+
+ public void writeSPARQL(String filename,SortedSet<String> pos,SortedSet<String> neg,
+ String uri, SortedSet<String> ignoredConcepts){
+
+ String prefixAlgortihm = "refexamples";
+ String prefixSparql = "sparql";
+
+ String standardSettings="sparql.recursionDepth = 1;\n" +
+ "sparql.predefinedFilter = 1;\n" +
+ "sparql.predefinedEndpoint = 1;\n";
+ //"sparql.format = \"KB\";\n\n";
+
+ StringBuffer buf = new StringBuffer();
+ buf.append("import(\"" + uri + "\",\"SPARQL\");\n\n");
+
+ buf.append(standardSettings);
+
+ buf.append(getIgnoredConcepts(ignoredConcepts,prefixAlgortihm));
+
+ buf.append(getStandard(prefixAlgortihm));
+
+ buf.append(sparqlInstances(pos, neg, prefixSparql));
+
+ buf.append( getPosAndNeg( pos, neg));
+
+
+ writeToFile(filename, buf.toString());
+
+}
+
+ public String sparqlInstances(SortedSet<String> pos,SortedSet<String> neg,String prefix){
+ SortedSet<String> ret = new TreeSet<String>();
+ ret.addAll(pos);
+ ret.addAll(neg);
+
+ return getStringSet(ret, prefix, "instances");
+
+ }
+
+
+ public String getPosAndNeg(SortedSet<String> pos,SortedSet<String> neg){
+ StringBuffer buf = new StringBuffer();
+ buf.append("\n\n");
+ for (String individuals : pos) {
+ buf.append("+\"" + individuals + "\"\n");
+
+ }
+ buf.append("\n\n");
+ for (String individuals : neg) {
+
+ buf.append("-\"" + individuals + "\"\n");
+ }
+
+ return buf.toString();
+ }
+
+ public String getIgnoredConcepts(SortedSet<String> ignoredConcepts,String prefix){
+
+ return getStringSet(ignoredConcepts,prefix, "ignoredConcepts");
+ }
+
+ public String getStringSet(SortedSet<String> set,String prefix, String type){
+ if(set.size()==0)return "\n";
+ String ret = prefix+"."+type+"={\n";
+ int x=0;
+ for (String string : set) {
+ if(x>0)ret+=",";
+ ret+="\""+string+"\"\n";
+ x++;
+ }
+ ret+="};\n";
+ return ret;
+ }
+
+ public String getStandard(String prefix){
+ String ret =
+ "algorithm = "+prefix+";\n"+
+ "reasoner=fastInstanceChecker;\n\n"+
+
+ prefix+".useAllConstructor = false;\n"+
+ prefix+".useExistsConstructor = true;\n"+
+ prefix+".useCardinalityRestrictions = false;\n"+
+ prefix+".useNegation = false;\n";
+
+ return ret;
+
+ }
+
+
+ protected void writeToFile(String filename, String content) {
+ // create the file we want to use
+ File file = new File(workingDir+filename);
+
+ try {
+ file.createNewFile();
+ FileOutputStream fos = new FileOutputStream(workingDir+filename, false);
+ // ObjectOutputStream o = new ObjectOutputStream(fos);
+ fos.write(content.getBytes());
+ fos.flush();
+ fos.close();
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+ }
+
+ protected SortedSet<String> toString(SortedSet<Individual> set ){
+ SortedSet<String> ret = new TreeSet<String>();
+ for (Individual ind : set) {
+ ret.add(ind.toString());
+ }
+ return ret;
+ }
+
+
+}
Added: trunk/src/dl-learner/org/dllearner/utilities/LearnSparql.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/LearnSparql.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/utilities/LearnSparql.java 2008-04-22 13:07:07 UTC (rev 806)
@@ -0,0 +1,97 @@
+package org.dllearner.utilities;
+
+import java.util.HashSet;
+import java.util.Set;
+import java.util.SortedSet;
+import java.util.TreeSet;
+
+import org.dllearner.algorithms.refexamples.ExampleBasedROLComponent;
+import org.dllearner.core.ComponentManager;
+import org.dllearner.core.KnowledgeSource;
+import org.dllearner.core.LearningAlgorithm;
+import org.dllearner.core.LearningProblem;
+import org.dllearner.core.ReasonerComponent;
+import org.dllearner.core.ReasoningService;
+import org.dllearner.core.owl.Individual;
+import org.dllearner.kb.sparql.SparqlKnowledgeSource;
+import org.dllearner.learningproblems.PosNegDefinitionLP;
+import org.dllearner.learningproblems.PosNegLP;
+import org.dllearner.reasoning.FastInstanceChecker;
+
+public class LearnSparql {
+
+
+ public void learn(SortedSet<String> posExamples,SortedSet<String> negExamples,
+ String uri, SortedSet<String> ignoredConcepts){
+
+ ComponentManager cm = ComponentManager.getInstance();
+ LearningAlgorithm la = null;
+ ReasoningService rs = null;
+ LearningProblem lp = null;
+ SparqlKnowledgeSource ks =null;
+ try {
+ Set<KnowledgeSource> sources = new HashSet<KnowledgeSource>();
+
+ ks = cm.knowledgeSource(SparqlKnowledgeSource.class);
+
+ SortedSet<String> instances = new TreeSet<String>();
+ instances.addAll(posExamples);
+ instances.addAll(negExamples);
+ cm.applyConfigEntry(ks, "instances",instances);
+ cm.applyConfigEntry(ks, "url",uri);
+ cm.applyConfigEntry(ks, "recursionDepth",1);
+ cm.applyConfigEntry(ks, "predefinedFilter",1);
+ cm.applyConfigEntry(ks, "predefinedEndpoint",1);
+ //cm.applyConfigEntry(ks, "format","KB");
+
+ ks.init();
+ sources.add(ks);
+ //System.out.println(ks.getNTripleURL());
+ //
+
+ ReasonerComponent r = new FastInstanceChecker(sources);
+ //cm.applyConfigEntry(r,"useAllConstructor",false);
+ //cm.applyConfigEntry(r,"useExistsConstructor",true);
+ r.init();
+ rs = new ReasoningService(r);
+
+ lp = new PosNegDefinitionLP(rs);
+ //cm.applyConfigEntry(lp, "positiveExamples",toInd(posExamples));
+ ((PosNegLP) lp).setPositiveExamples(toInd(posExamples));
+ ((PosNegLP) lp).setNegativeExamples(toInd(negExamples));
+ //cm.applyConfigEntry(lp, "negativeExamples",toInd(negExamples));
+ lp.init();
+
+ la = cm.learningAlgorithm(ExampleBasedROLComponent.class, lp, rs);
+
+ cm.applyConfigEntry(la,"useAllConstructor",false);
+ cm.applyConfigEntry(la,"useExistsConstructor",true);
+ cm.applyConfigEntry(la,"useCardinalityRestrictions",false);
+ cm.applyConfigEntry(la,"useNegation",false);
+ cm.applyConfigEntry(la,"minExecutionTimeInSeconds",10);
+ cm.applyConfigEntry(la,"guaranteeXgoodDescriptions",10);
+
+ //cm.applyConfigEntry(la,"quiet",false);
+ if(ignoredConcepts.size()>0)
+ cm.applyConfigEntry(la,"ignoredConcepts",ignoredConcepts);
+ la.init();
+
+ System.out.println("start learning");
+ la.start();
+
+ //System.out.println("best"+la(20));
+ ((ExampleBasedROLComponent)la).printBestSolutions(20);
+
+ }catch (Exception e) {e.printStackTrace();}
+ //System.out.println( la.getBestSolution());;
+ }
+
+ protected SortedSet<Individual> toInd(SortedSet<String> set ){
+ SortedSet<Individual> ret = new TreeSet<Individual>();
+ for (String ind : set) {
+ ret.add(new Individual(ind));
+ }
+ return ret;
+ }
+
+}
Added: trunk/src/dl-learner/org/dllearner/utilities/NT2RDF.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/NT2RDF.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/utilities/NT2RDF.java 2008-04-22 13:07:07 UTC (rev 806)
@@ -0,0 +1,35 @@
+package org.dllearner.utilities;
+import java.io.File;
+import java.net.URI;
+
+import org.semanticweb.owl.apibinding.OWLManager;
+import org.semanticweb.owl.io.RDFXMLOntologyFormat;
+import org.semanticweb.owl.model.OWLOntology;
+import org.semanticweb.owl.model.OWLOntologyManager;
+public class NT2RDF {
+
+
+ public static void main(String[] args) {
+ try {
+ String ontopath=args[0];
+ URI inputURI = new File(ontopath).toURI();
+
+ // outputURI
+ String ending = ontopath.substring(ontopath.lastIndexOf(".") + 1);
+ ontopath = ontopath.replace("." + ending, ".rdf" );
+ URI outputURI = new File(ontopath).toURI();
+
+ OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
+ OWLOntology ontology = manager.loadOntologyFromPhysicalURI(inputURI);
+ manager.saveOntology(ontology, new RDFXMLOntologyFormat(), outputURI);
+ // Remove the ontology from the manager
+ manager.removeOntology(ontology.getURI());
+ }
+ catch (Exception e) {
+ System.out.println("The ontology could not be created: " + e.getMessage());
+ }
+
+ }
+ }
+
+
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|
|
From: <ku...@us...> - 2008-04-21 20:21:41
|
Revision: 805
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=805&view=rev
Author: kurzum
Date: 2008-04-21 13:21:36 -0700 (Mon, 21 Apr 2008)
Log Message:
-----------
finished script for automatic example choice
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQueryDescriptionConvertVisitor.java
trunk/src/dl-learner/org/dllearner/test/SPARQLPreparation.java
Added Paths:
-----------
trunk/src/dl-learner/org/dllearner/utilities/JenaResultSetConvenience.java
Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQueryDescriptionConvertVisitor.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQueryDescriptionConvertVisitor.java 2008-04-21 19:55:38 UTC (rev 804)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQueryDescriptionConvertVisitor.java 2008-04-21 20:21:36 UTC (rev 805)
@@ -58,6 +58,14 @@
return query;
}
+ public String getSparqlQuery(int limit)
+ { if(limit==0)limit=99999;
+ query="SELECT ?subject\nWHERE {"+query;
+ query+="}\n";
+ query+="LIMIT "+limit;
+ return query;
+ }
+
public static String getSparqlQuery(String description) throws ParseException
{
Description d = KBParser.parseConcept(description);
@@ -66,6 +74,14 @@
return visitor.getSparqlQuery();
}
+ public static String getSparqlQuery(String description, int limit) throws ParseException
+ { if(limit==0)limit=99999;
+ Description d = KBParser.parseConcept(description);
+ SparqlQueryDescriptionConvertVisitor visitor=new SparqlQueryDescriptionConvertVisitor();
+ d.accept(visitor);
+ return visitor.getSparqlQuery(limit);
+ }
+
public static String getSparqlQuery(Description description)
{
SparqlQueryDescriptionConvertVisitor visitor=new SparqlQueryDescriptionConvertVisitor();
Modified: trunk/src/dl-learner/org/dllearner/test/SPARQLPreparation.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/test/SPARQLPreparation.java 2008-04-21 19:55:38 UTC (rev 804)
+++ trunk/src/dl-learner/org/dllearner/test/SPARQLPreparation.java 2008-04-21 20:21:36 UTC (rev 805)
@@ -1,6 +1,6 @@
package org.dllearner.test;
-import java.util.HashMap;
+import java.util.Random;
import java.util.SortedSet;
import java.util.TreeSet;
@@ -8,68 +8,144 @@
import org.dllearner.kb.sparql.SparqlQuery;
import org.dllearner.kb.sparql.SparqlQueryDescriptionConvertVisitor;
import org.dllearner.kb.sparql.configuration.SparqlEndpoint;
-import org.dllearner.parser.ParseException;
+import org.dllearner.utilities.JenaResultSetConvenience;
+import org.dllearner.utilities.SimpleClock;
import com.hp.hpl.jena.query.ResultSet;
public class SPARQLPreparation {
static Cache c;
+ static SparqlEndpoint se;
+
/**
* @param args
*/
public static void main(String[] args) {
+ init();
try {
+ SimpleClock sc=new SimpleClock();
SortedSet<String> concepts = new TreeSet<String>();
- HashMap<String,ResultSet> result = new HashMap<String,ResultSet>();
- HashMap<String,String> result2 = new HashMap<String,String>();
+ //concepts.add("\"http://dbpedia.org/class/yago/Person100007846\"");
+ concepts.add("\"http://dbpedia.org/class/yago/FieldMarshal110086821\"");
+ SortedSet<String> posExamples = new TreeSet<String>();
+ SortedSet<String> negExamples = new TreeSet<String>();
+ //HashMap<String, ResultSet> result = new HashMap<String, ResultSet>();
+ //HashMap<String, String> result2 = new HashMap<String, String>();
- SparqlQueryDescriptionConvertVisitor.debug_flag=false;
- c=new Cache("cache");
- String conj="(\"http://dbpedia.org/class/yago/Person100007846\" AND \"http://dbpedia.org/class/yago/Head110162991\")";
+ //System.out.println(concepts.first());
+ posExamples = new JenaResultSetConvenience(queryConcept(concepts.first(),0))
+ .getStringListForVariable("subject");
+
+ for (String string : posExamples) {
+ negExamples.addAll( getObjects(string));
+ //if(neg.size()>=1)System.out.println(neg);
+ }
+ /*for (String string2 : negExamples) {
+ if(posExamples.contains(string2)){
+ System.out.println(string2);
+ negExamples.remove(string2);
+ };
+ }*/
+ System.out.println(negExamples.size());
+ negExamples.removeAll(posExamples);
- concepts.add("EXISTS \"http://dbpedia.org/property/disambiguates\".TOP");
- concepts.add("EXISTS \"http://dbpedia.org/property/successor\".\"http://dbpedia.org/class/yago/Person100007846\"");
- concepts.add("EXISTS \"http://dbpedia.org/property/successor\"."+conj);
- //concepts.add("ALL \"http://dbpedia.org/property/disambiguates\".TOP");
- //concepts.add("ALL \"http://dbpedia.org/property/successor\".\"http://dbpedia.org/class/yago/Person100007846\"");
- concepts.add("\"http://dbpedia.org/class/yago/Person100007846\"");
- concepts.add(conj);
- concepts.add("(\"http://dbpedia.org/class/yago/Person100007846\" OR \"http://dbpedia.org/class/yago/Head110162991\")");
+ negExamples=shrink(negExamples,posExamples.size()*2);
+ //System.out.println(posExamples.first()));
+ System.out.println(posExamples.size());
+ System.out.println(negExamples.size());
+ sc.printAndSet("Finished");
+ } catch (Exception e) {
+ e.printStackTrace();
+
+ }
+
+ }
+
+ /***************************************************************************
+ * *********************OLDCODE String
+ * conj="(\"http://dbpedia.org/class/yago/Person100007846\" AND
+ * \"http://dbpedia.org/class/yago/Head110162991\")";
+ *
+ *
+ * concepts.add("EXISTS \"http://dbpedia.org/property/disambiguates\".TOP");
+ * concepts.add("EXISTS
+ * \"http://dbpedia.org/property/successor\".\"http://dbpedia.org/class/yago/Person100007846\"");
+ * concepts.add("EXISTS \"http://dbpedia.org/property/successor\"."+conj);
+ * //concepts.add("ALL \"http://dbpedia.org/property/disambiguates\".TOP");
+ * //concepts.add("ALL
+ * \"http://dbpedia.org/property/successor\".\"http://dbpedia.org/class/yago/Person100007846\"");
+ * concepts.add("\"http://dbpedia.org/class/yago/Person100007846\"");
+ * concepts.add(conj);
+ * concepts.add("(\"http://dbpedia.org/class/yago/Person100007846\" OR
+ * \"http://dbpedia.org/class/yago/Head110162991\")");
+ *
+ * //concepts.add("NOT \"http://dbpedia.org/class/yago/Person100007846\"");
+ *
+ * for (String kbsyntax : concepts) {
+ * result.put(kbsyntax,queryConcept(kbsyntax)); }
+ * System.out.println("************************"); for (String string :
+ * result.keySet()) { System.out.println("KBSyntayString: "+string);
+ * System.out.println("Query:\n"+result.get(string).hasNext());
+ * System.out.println("************************"); }
+ **************************************************************************/
+
+ static SortedSet<String> getObjects(String subject) {
+ // SortedSet<String> result = new TreeSet<String>();
+
+ String query = "SELECT * WHERE { \n" + "<" + subject + "> " + "?p ?o. \n"
+ + "FILTER (REGEX(str(?o), 'http://dbpedia.org/resource/')).\n"
+ + "FILTER (!REGEX(str(?p), 'http://www.w3.org/2004/02/skos'))\n"
+ + "}";
+ //System.out.println(query);
+ String JSON = (c.executeSparqlQuery(new SparqlQuery(query, se)));
+ //System.out.println(JSON);
+ ResultSet rs =SparqlQuery.JSONtoResultSet(JSON);
+ JenaResultSetConvenience rsc = new JenaResultSetConvenience(rs);
+ return rsc.getStringListForVariable("o");
+ }
+
+ public static ResultSet queryConcept(String concept,int limit) {
+ ResultSet rs = null;
+ try {
+ String query = SparqlQueryDescriptionConvertVisitor
+ .getSparqlQuery(concept,limit);
- //concepts.add("NOT \"http://dbpedia.org/class/yago/Person100007846\"");
-
- for (String kbsyntax : concepts) {
- result.put(kbsyntax,queryConcept(kbsyntax));
- }
- System.out.println("************************");
- for (String string : result.keySet()) {
- System.out.println("KBSyntayString: "+string);
- System.out.println("Query:\n"+result.get(string).hasNext());
- System.out.println("************************");
- }
- System.out.println("Finished");
+ SparqlQuery sq = new SparqlQuery(query, se);
+ String JSON = c.executeSparqlQuery(sq);
+ //System.out.println(JSON);
+ rs = SparqlQuery.JSONtoResultSet(JSON);
+
} catch (Exception e) {
- // TODO Auto-generated catch block
e.printStackTrace();
+ }
+ return rs;
}
+ public static void init() {
+ SparqlQueryDescriptionConvertVisitor.debug_flag = false;
+ c = new Cache("cache");
+ se = SparqlEndpoint.dbpediaEndpoint();
+
}
- public static ResultSet queryConcept(String concept){
- ResultSet rs =null;
- try{
- String query = SparqlQueryDescriptionConvertVisitor.getSparqlQuery(concept);
- SparqlQuery sq= new SparqlQuery(query,SparqlEndpoint.dbpediaEndpoint());
- String JSON = c.executeSparqlQuery(sq);
+ public static SortedSet<String> shrink(SortedSet<String> s, int limit) {
+ SortedSet<String> ret = new TreeSet<String>();
+ Random r = new Random();
+ double treshold = ((double)limit)/s.size();
+ //System.out.println("treshold"+howmany);
+ //System.out.println("treshold"+allRetrieved.size());
+ System.out.println("treshold"+treshold);
- rs= SparqlQuery.JSONtoResultSet(JSON);
-
- }catch (Exception e) {e.printStackTrace();}
-
- return rs;
+ for (String oneInd : s) {
+ if(r.nextDouble()<treshold) {
+ ret.add(oneInd);
+
+ }
+ }
+ return ret;
}
-
+
}
Added: trunk/src/dl-learner/org/dllearner/utilities/JenaResultSetConvenience.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/JenaResultSetConvenience.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/utilities/JenaResultSetConvenience.java 2008-04-21 20:21:36 UTC (rev 805)
@@ -0,0 +1,36 @@
+package org.dllearner.utilities;
+
+import java.util.List;
+import java.util.SortedSet;
+import java.util.TreeSet;
+
+import com.hp.hpl.jena.query.ResultSet;
+import com.hp.hpl.jena.query.ResultSetFormatter;
+import com.hp.hpl.jena.sparql.core.ResultBinding;
+
+public class JenaResultSetConvenience {
+ ResultSet rs;
+
+ public JenaResultSetConvenience(ResultSet rs) {
+ super();
+ this.rs = rs;
+ }
+
+ @SuppressWarnings("unchecked")
+ public SortedSet<String> getStringListForVariable(String var){
+ SortedSet<String> result = new TreeSet<String>();
+
+ List<ResultBinding> l = ResultSetFormatter.toList(this.rs);
+
+ for (ResultBinding resultBinding : l) {
+
+ result.add(resultBinding.get(var).toString());
+
+ }
+
+ return result;
+
+ }
+
+
+}
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|
|
From: <lor...@us...> - 2008-04-21 19:56:09
|
Revision: 804
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=804&view=rev
Author: lorenz_b
Date: 2008-04-21 12:55:38 -0700 (Mon, 21 Apr 2008)
Log Message:
-----------
added method deleteIndividual() to class ORE
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/tools/ore/ORE.java
Modified: trunk/src/dl-learner/org/dllearner/tools/ore/ORE.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/tools/ore/ORE.java 2008-04-21 14:58:01 UTC (rev 803)
+++ trunk/src/dl-learner/org/dllearner/tools/ore/ORE.java 2008-04-21 19:55:38 UTC (rev 804)
@@ -2,6 +2,9 @@
import java.io.File;
import java.math.BigDecimal;
+import java.net.URI;
+import java.net.URISyntaxException;
+import java.util.Collections;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
@@ -27,11 +30,13 @@
import org.semanticweb.owl.model.OWLAxiom;
import org.semanticweb.owl.model.OWLDataFactory;
import org.semanticweb.owl.model.OWLDescription;
+import org.semanticweb.owl.model.OWLIndividual;
import org.semanticweb.owl.model.OWLOntology;
import org.semanticweb.owl.model.OWLOntologyChangeException;
import org.semanticweb.owl.model.OWLOntologyManager;
import org.semanticweb.owl.model.OWLOntologyStorageException;
import org.semanticweb.owl.model.UnknownOWLOntologyException;
+import org.semanticweb.owl.util.OWLEntityRemover;
public class ORE {
@@ -206,7 +211,44 @@
e.printStackTrace();
}
}
+
+ public void deleteIndividual(Individual ind){
+
+
+
+ OWLOntology ontology = reasoner.getOWLAPIOntologies().get(0);
+
+ OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
+ OWLDataFactory factory = manager.getOWLDataFactory();
+ OWLIndividual individualOWLAPI = null;
+
+ try {
+ individualOWLAPI = factory.getOWLIndividual( new URI(ind.getName()));
+ } catch (URISyntaxException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+
+
+ OWLEntityRemover remover = new OWLEntityRemover(manager, Collections.singleton(ontology));
+
+
+ individualOWLAPI.accept(remover);
+
+ try {
+ manager.applyChanges(remover.getChanges());
+ } catch (OWLOntologyChangeException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ remover.reset();
+
+
+
+
+ }
+
public static void main(String[] args){
ORE test = new ORE();
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|
|
From: <ku...@us...> - 2008-04-21 14:58:05
|
Revision: 803
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=803&view=rev
Author: kurzum
Date: 2008-04-21 07:58:01 -0700 (Mon, 21 Apr 2008)
Log Message:
-----------
test script, changed comment in Cache.java
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/kb/sparql/Cache.java
trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQueryDescriptionConvertVisitor.java
Added Paths:
-----------
trunk/src/dl-learner/org/dllearner/test/SPARQLPreparation.java
Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/Cache.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/Cache.java 2008-04-21 14:33:06 UTC (rev 802)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/Cache.java 2008-04-21 14:58:01 UTC (rev 803)
@@ -202,7 +202,7 @@
/**
* Takes a SPARQL query (which has not been evaluated yet) as argument and
- * returns a result set. The result set is taken from this cache if the
+ * returns a JSON result set. The result set is taken from this cache if the
* query is stored here. Otherwise the query is send and its result added to
* the cache and returned. Convenience method.
*
Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQueryDescriptionConvertVisitor.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQueryDescriptionConvertVisitor.java 2008-04-21 14:33:06 UTC (rev 802)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQueryDescriptionConvertVisitor.java 2008-04-21 14:58:01 UTC (rev 803)
@@ -37,7 +37,7 @@
*/
public class SparqlQueryDescriptionConvertVisitor implements DescriptionVisitor{
- public boolean debug_flag=false;
+ public static boolean debug_flag=false;
private Stack<String> stack = new Stack<String>();
Added: trunk/src/dl-learner/org/dllearner/test/SPARQLPreparation.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/test/SPARQLPreparation.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/test/SPARQLPreparation.java 2008-04-21 14:58:01 UTC (rev 803)
@@ -0,0 +1,75 @@
+package org.dllearner.test;
+
+import java.util.HashMap;
+import java.util.SortedSet;
+import java.util.TreeSet;
+
+import org.dllearner.kb.sparql.Cache;
+import org.dllearner.kb.sparql.SparqlQuery;
+import org.dllearner.kb.sparql.SparqlQueryDescriptionConvertVisitor;
+import org.dllearner.kb.sparql.configuration.SparqlEndpoint;
+import org.dllearner.parser.ParseException;
+
+import com.hp.hpl.jena.query.ResultSet;
+
+public class SPARQLPreparation {
+
+ static Cache c;
+ /**
+ * @param args
+ */
+ public static void main(String[] args) {
+ try {
+ SortedSet<String> concepts = new TreeSet<String>();
+ HashMap<String,ResultSet> result = new HashMap<String,ResultSet>();
+ HashMap<String,String> result2 = new HashMap<String,String>();
+
+ SparqlQueryDescriptionConvertVisitor.debug_flag=false;
+ c=new Cache("cache");
+ String conj="(\"http://dbpedia.org/class/yago/Person100007846\" AND \"http://dbpedia.org/class/yago/Head110162991\")";
+
+
+ concepts.add("EXISTS \"http://dbpedia.org/property/disambiguates\".TOP");
+ concepts.add("EXISTS \"http://dbpedia.org/property/successor\".\"http://dbpedia.org/class/yago/Person100007846\"");
+ concepts.add("EXISTS \"http://dbpedia.org/property/successor\"."+conj);
+ //concepts.add("ALL \"http://dbpedia.org/property/disambiguates\".TOP");
+ //concepts.add("ALL \"http://dbpedia.org/property/successor\".\"http://dbpedia.org/class/yago/Person100007846\"");
+ concepts.add("\"http://dbpedia.org/class/yago/Person100007846\"");
+ concepts.add(conj);
+ concepts.add("(\"http://dbpedia.org/class/yago/Person100007846\" OR \"http://dbpedia.org/class/yago/Head110162991\")");
+
+ //concepts.add("NOT \"http://dbpedia.org/class/yago/Person100007846\"");
+
+ for (String kbsyntax : concepts) {
+ result.put(kbsyntax,queryConcept(kbsyntax));
+ }
+ System.out.println("************************");
+ for (String string : result.keySet()) {
+ System.out.println("KBSyntayString: "+string);
+ System.out.println("Query:\n"+result.get(string).hasNext());
+ System.out.println("************************");
+ }
+ System.out.println("Finished");
+ } catch (Exception e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+
+ }
+
+ }
+
+ public static ResultSet queryConcept(String concept){
+ ResultSet rs =null;
+ try{
+ String query = SparqlQueryDescriptionConvertVisitor.getSparqlQuery(concept);
+ SparqlQuery sq= new SparqlQuery(query,SparqlEndpoint.dbpediaEndpoint());
+ String JSON = c.executeSparqlQuery(sq);
+
+ rs= SparqlQuery.JSONtoResultSet(JSON);
+
+ }catch (Exception e) {e.printStackTrace();}
+
+ return rs;
+ }
+
+}
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