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From: <jen...@us...> - 2008-09-27 07:48:22
|
Revision: 1283
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=1283&view=rev
Author: jenslehmann
Date: 2008-09-27 07:48:14 +0000 (Sat, 27 Sep 2008)
Log Message:
-----------
- working hasValue support (frequency threshold currently at 3)
- use refexamples.useHasValueConstructor = true to turn on hasValue support (turned off by default)
- provided examples in semantic_bible folder
Modified Paths:
--------------
trunk/examples/semantic_bible/hasvalue_example.conf
trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLComponent.java
trunk/src/dl-learner/org/dllearner/core/config/CommonConfigOptions.java
trunk/src/dl-learner/org/dllearner/core/owl/ObjectValueRestriction.java
trunk/src/dl-learner/org/dllearner/core/owl/Restriction.java
trunk/src/dl-learner/org/dllearner/core/owl/ValueRestriction.java
trunk/src/dl-learner/org/dllearner/gui/StartGUI.java
trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java
Added Paths:
-----------
trunk/examples/semantic_bible/hasvalue_simple.conf
trunk/examples/semantic_bible/hasvalue_simple.kb
Modified: trunk/examples/semantic_bible/hasvalue_example.conf
===================================================================
--- trunk/examples/semantic_bible/hasvalue_example.conf 2008-09-26 21:16:59 UTC (rev 1282)
+++ trunk/examples/semantic_bible/hasvalue_example.conf 2008-09-27 07:48:14 UTC (rev 1283)
@@ -1,11 +1,10 @@
/**
- * It should learn ethnicity hasValue Jewish, but does not work for some reason.
+ * Learns ethnicity hasValue Jewish (+ potentially something more e.g. Man AND ethnicity hasValue Jewish).
*/
-import("../NTNcombined.owl");
+import("NTNcombined.owl");
-// reasoner = owlAPIReasoner;
-owlAPIReasoner.reasonerType = pellet;
+refexamples.useHasValueConstructor = true;
+"http://semanticbible.org/ns/2006/NTNames#Hezron"
+"http://semanticbible.org/ns/2006/NTNames#Jehoshaphat"
Added: trunk/examples/semantic_bible/hasvalue_simple.conf
===================================================================
--- trunk/examples/semantic_bible/hasvalue_simple.conf (rev 0)
+++ trunk/examples/semantic_bible/hasvalue_simple.conf 2008-09-27 07:48:14 UTC (rev 1283)
@@ -0,0 +1,11 @@
+import("hasvalue_simple.kb");
+
+reasoner = owlAPIReasoner;
+refexamples.useHasValueConstructor = true;
+
++a
++b
++c
+-e
+-f
+
Added: trunk/examples/semantic_bible/hasvalue_simple.kb
===================================================================
--- trunk/examples/semantic_bible/hasvalue_simple.kb (rev 0)
+++ trunk/examples/semantic_bible/hasvalue_simple.kb 2008-09-27 07:48:14 UTC (rev 1283)
@@ -0,0 +1,9 @@
+knows(a,d).
+knows(b,d).
+knows(c,d).
+knows(e,a).
+knows(f,b).
+
+// TODO bug: apparently there are problems if no class is present in the background ontology,
+// so we need to add one
+person(a).
Modified: trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLComponent.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLComponent.java 2008-09-26 21:16:59 UTC (rev 1282)
+++ trunk/src/dl-learner/org/dllearner/algorithms/refexamples/ExampleBasedROLComponent.java 2008-09-27 07:48:14 UTC (rev 1283)
@@ -115,6 +115,7 @@
private boolean improveSubsumptionHierarchy = true;
private boolean useAllConstructor = CommonConfigOptions.useAllConstructorDefault;
private boolean useExistsConstructor = CommonConfigOptions.useExistsConstructorDefault;
+ private boolean useHasValueConstructor = CommonConfigOptions.useHasValueConstructorDefault;
private boolean useCardinalityRestrictions = CommonConfigOptions.useCardinalityRestrictionsDefault;
private boolean useNegation = CommonConfigOptions.useNegationDefault;
private boolean useBooleanDatatypes = CommonConfigOptions.useBooleanDatatypesDefault;
@@ -190,6 +191,7 @@
options.add(CommonConfigOptions.ignoredRoles());
options.add(CommonConfigOptions.useAllConstructor());
options.add(CommonConfigOptions.useExistsConstructor());
+ options.add(CommonConfigOptions.useHasValueConstructor());
options.add(CommonConfigOptions.useCardinalityRestrictions());
options.add(CommonConfigOptions.useNegation());
options.add(CommonConfigOptions.useBooleanDatatypes());
@@ -254,6 +256,8 @@
useAllConstructor = (Boolean) entry.getValue();
} else if(name.equals("useExistsConstructor")) {
useExistsConstructor = (Boolean) entry.getValue();
+ } else if(name.equals("useHasValueConstructor")) {
+ useHasValueConstructor = (Boolean) entry.getValue();
} else if(name.equals("useCardinalityRestrictions")) {
useCardinalityRestrictions = (Boolean) entry.getValue();
} else if(name.equals("useNegation")) {
@@ -365,6 +369,7 @@
applyExistsFilter,
useAllConstructor,
useExistsConstructor,
+ useHasValueConstructor,
useCardinalityRestrictions,
useNegation,
useBooleanDatatypes,
Modified: trunk/src/dl-learner/org/dllearner/core/config/CommonConfigOptions.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/config/CommonConfigOptions.java 2008-09-26 21:16:59 UTC (rev 1282)
+++ trunk/src/dl-learner/org/dllearner/core/config/CommonConfigOptions.java 2008-09-27 07:48:14 UTC (rev 1283)
@@ -40,6 +40,7 @@
//public static boolean improveSubsumptionHierarchyDefault = true;
public static boolean useAllConstructorDefault = true;
public static boolean useExistsConstructorDefault = true;
+ public static boolean useHasValueConstructorDefault = true;
public static boolean useCardinalityRestrictionsDefault = true;
public static boolean useNegationDefault = true;
public static boolean useBooleanDatatypesDefault = true;
@@ -101,6 +102,10 @@
return new BooleanConfigOption("useExistsConstructor", "specifies whether the existential concept constructor is used in the learning algorithm",useExistsConstructorDefault);
}
+ public static BooleanConfigOption useHasValueConstructor() {
+ return new BooleanConfigOption("useHasValueConstructor", "specifies whether the hasValue constructor is used in the learning algorithm",useHasValueConstructorDefault);
+ }
+
public static BooleanConfigOption useCardinalityRestrictions() {
return new BooleanConfigOption("useCardinalityRestrictions", "specifies whether CardinalityRestrictions is used in the learning algorithm",useCardinalityRestrictionsDefault);
}
Modified: trunk/src/dl-learner/org/dllearner/core/owl/ObjectValueRestriction.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/ObjectValueRestriction.java 2008-09-26 21:16:59 UTC (rev 1282)
+++ trunk/src/dl-learner/org/dllearner/core/owl/ObjectValueRestriction.java 2008-09-27 07:48:14 UTC (rev 1283)
@@ -23,7 +23,7 @@
/**
* Restricts the value of an object property to a single individual
- * (corresponds to owl:hasValue).
+ * (corresponds to owl:hasValue)
*
* @author Jens Lehmann
*
@@ -42,8 +42,7 @@
*/
@Override
public String toManchesterSyntaxString(String baseURI, Map<String, String> prefixes) {
- // TODO Auto-generated method stub
- return null;
+ return restrictedPropertyExpression.toString(baseURI, prefixes) + " value " + value.toString(baseURI, prefixes);
}
/* (non-Javadoc)
@@ -51,7 +50,6 @@
*/
@Override
public int getArity() {
- // TODO Auto-generated method stub
return 0;
}
@@ -59,21 +57,18 @@
* @see org.dllearner.core.owl.KBElement#getLength()
*/
public int getLength() {
- // TODO Auto-generated method stub
- return 0;
+ return 3;
}
/* (non-Javadoc)
* @see org.dllearner.core.owl.KBElement#toString(java.lang.String, java.util.Map)
*/
public String toString(String baseURI, Map<String, String> prefixes) {
- // TODO Auto-generated method stub
- return null;
+ return restrictedPropertyExpression.toString(baseURI, prefixes) + " hasValue " + value.toString(baseURI, prefixes);
}
public String toKBSyntaxString(String baseURI, Map<String, String> prefixes) {
- // TODO Auto-generated method stub
- return null;
+ return restrictedPropertyExpression.toKBSyntaxString(baseURI, prefixes) + " hasValue " + value.toKBSyntaxString(baseURI, prefixes);
}
public Individual getIndividual() {
Modified: trunk/src/dl-learner/org/dllearner/core/owl/Restriction.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/Restriction.java 2008-09-26 21:16:59 UTC (rev 1282)
+++ trunk/src/dl-learner/org/dllearner/core/owl/Restriction.java 2008-09-27 07:48:14 UTC (rev 1283)
@@ -27,7 +27,7 @@
*/
public abstract class Restriction extends Description {
- PropertyExpression restrictedPropertyExpression;
+ protected PropertyExpression restrictedPropertyExpression;
public Restriction(PropertyExpression restrictedPropertyExpression) {
this.restrictedPropertyExpression = restrictedPropertyExpression;
Modified: trunk/src/dl-learner/org/dllearner/core/owl/ValueRestriction.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/ValueRestriction.java 2008-09-26 21:16:59 UTC (rev 1282)
+++ trunk/src/dl-learner/org/dllearner/core/owl/ValueRestriction.java 2008-09-27 07:48:14 UTC (rev 1283)
@@ -27,7 +27,7 @@
*/
public abstract class ValueRestriction extends Restriction {
- KBElement value;
+ protected KBElement value;
public ValueRestriction(PropertyExpression propertyExpression, KBElement value) {
super(propertyExpression);
Modified: trunk/src/dl-learner/org/dllearner/gui/StartGUI.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/gui/StartGUI.java 2008-09-26 21:16:59 UTC (rev 1282)
+++ trunk/src/dl-learner/org/dllearner/gui/StartGUI.java 2008-09-27 07:48:14 UTC (rev 1283)
@@ -253,7 +253,7 @@
Logger rootLogger = Logger.getRootLogger();
rootLogger.removeAllAppenders();
rootLogger.addAppender(consoleAppender);
- rootLogger.setLevel(Level.TRACE);
+ rootLogger.setLevel(Level.DEBUG);
File file = null;
if (args.length > 0)
Modified: trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java 2008-09-26 21:16:59 UTC (rev 1282)
+++ trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java 2008-09-27 07:48:14 UTC (rev 1283)
@@ -150,8 +150,6 @@
private Map<DatatypeProperty,List<Double>> splits = new TreeMap<DatatypeProperty,List<Double>>();
private int maxNrOfSplits = 10;
- // experimental support for hasValue
- private boolean useHasValue = false;
// data structure for a simple frequent pattern matching preprocessing phase
private int frequencyThreshold = 3;
private Map<ObjectProperty, Map<Individual, Integer>> valueFrequency = new HashMap<ObjectProperty, Map<Individual, Integer>>();
@@ -166,6 +164,7 @@
private boolean applyExistsFilter = true;
private boolean useAllConstructor = true;
private boolean useExistsConstructor = true;
+ private boolean useHasValueConstructor = false;
private boolean useCardinalityRestrictions = true;
private boolean useNegation = true;
private boolean useBooleanDatatypes = true;
@@ -181,16 +180,17 @@
// private Map<NamedClass,Map<NamedClass,Boolean>> notABMeaningful = new TreeMap<NamedClass,Map<NamedClass,Boolean>>();
public RhoDRDown(ReasoningService reasoningService) {
- this(reasoningService, true, true, true, true, true, true, true, true, null);
+ this(reasoningService, true, true, true, true, true, true, true, true, true, null);
}
public RhoDRDown(ReasoningService reasoningService, boolean applyAllFilter, boolean applyExistsFilter, boolean useAllConstructor,
- boolean useExistsConstructor,boolean useCardinalityRestrictions,boolean useNegation, boolean useBooleanDatatypes, boolean useDoubleDatatypes, NamedClass startClass) {
+ boolean useExistsConstructor, boolean useHasValueConstructor, boolean useCardinalityRestrictions,boolean useNegation, boolean useBooleanDatatypes, boolean useDoubleDatatypes, NamedClass startClass) {
this.rs = reasoningService;
this.applyAllFilter = applyAllFilter;
this.applyExistsFilter = applyExistsFilter;
this.useAllConstructor = useAllConstructor;
this.useExistsConstructor = useExistsConstructor;
+ this.useHasValueConstructor = useHasValueConstructor;
this.useCardinalityRestrictions = useCardinalityRestrictions;
this.useNegation = useNegation;
this.useBooleanDatatypes = useBooleanDatatypes;
@@ -204,7 +204,7 @@
opDomains.put(op, rs.getDomain(op));
opRanges.put(op, rs.getRange(op));
- if(useHasValue) {
+ if(useHasValueConstructor) {
// init
Map<Individual, Integer> opMap = new TreeMap<Individual, Integer>();
valueFrequency.put(op, opMap);
@@ -229,7 +229,7 @@
// after threshold is reached)
Set<Individual> frequentInds = new TreeSet<Individual>();
for(Individual i : opMap.keySet()) {
- if(opMap.get(i) > frequencyThreshold) {
+ if(opMap.get(i) >= frequencyThreshold) {
frequentInds.add(i);
}
}
@@ -455,12 +455,12 @@
}
// rule 4: EXISTS r.TOP => EXISTS r.{value}
- if(useHasValue && description.getChild(0) instanceof Thing) {
+ if(useHasValueConstructor && description.getChild(0) instanceof Thing) {
// watch out for frequent patterns
Set<Individual> frequentInds = frequentValues.get(role);
if(frequentInds != null) {
for(Individual ind : frequentInds) {
- ObjectValueRestriction ovr = new ObjectValueRestriction(ar, ind);
+ ObjectValueRestriction ovr = new ObjectValueRestriction((ObjectProperty)role, ind);
refinements.add(ovr);
}
}
@@ -661,8 +661,11 @@
boolean maxDoubleOccurence = false;
// rule 2: min restrictions at most once
boolean minDoubleOccurence = false;
- // rule 3: no double boolean datatypes
+ // rule 3: no double occurences of boolean datatypes
TreeSet<DatatypeProperty> occuredDP = new TreeSet<DatatypeProperty>();
+ // rule 4: no double occurences of hasValue restrictions
+ TreeSet<ObjectProperty> occuredVR = new TreeSet<ObjectProperty>();
+
for(Description child : intersection.getChildren()) {
if(child instanceof DatatypeSomeRestriction) {
DataRange dr = ((DatatypeSomeRestriction)child).getDataRange();
@@ -683,6 +686,10 @@
// return false if the boolean property exists already
if(!occuredDP.add(dp))
return false;
+ } else if(child instanceof ObjectValueRestriction) {
+ ObjectProperty op = (ObjectProperty) ((ObjectValueRestriction)child).getRestrictedPropertyExpression();
+ if(!occuredVR.add(op))
+ return false;
}
// System.out.println(child.getClass());
}
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|
|
From: <ku...@us...> - 2008-09-26 21:17:08
|
Revision: 1282
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=1282&view=rev
Author: kurzum
Date: 2008-09-26 21:16:59 +0000 (Fri, 26 Sep 2008)
Log Message:
-----------
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/utilities/statistics/Table.java
Modified: trunk/src/dl-learner/org/dllearner/utilities/statistics/Table.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/statistics/Table.java 2008-09-26 21:13:44 UTC (rev 1281)
+++ trunk/src/dl-learner/org/dllearner/utilities/statistics/Table.java 2008-09-26 21:16:59 UTC (rev 1282)
@@ -182,11 +182,12 @@
String content = "";
dir = StringFormatter.checkIfDirEndsOnSlashAndRemove(dir);
Files.mkdir(dir);
+ String div = (System.currentTimeMillis() % 10000) + "";
try{
int i=0;
for(TableColumn c:t.getColumns()){
String header = URLEncoder.encode(c.getHeader(),"UTF-8");
- String columnFileName = dir+File.separator+t.getTableName()+(i++)+header+column;
+ String columnFileName = dir+File.separator+t.getTableName()+(i++)+header+div+column;
c.serialize(new File(columnFileName));
//Files.writeObjectToFile(c, new File(filename));
content += columnFileName+System.getProperty("line.separator");
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|
|
From: <ku...@us...> - 2008-09-26 21:13:55
|
Revision: 1281
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=1281&view=rev
Author: kurzum
Date: 2008-09-26 21:13:44 +0000 (Fri, 26 Sep 2008)
Log Message:
-----------
schedule experiments
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/scripts/SemanticBibleComparison.java
Modified: trunk/src/dl-learner/org/dllearner/scripts/SemanticBibleComparison.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/SemanticBibleComparison.java 2008-09-26 21:11:00 UTC (rev 1280)
+++ trunk/src/dl-learner/org/dllearner/scripts/SemanticBibleComparison.java 2008-09-26 21:13:44 UTC (rev 1281)
@@ -251,7 +251,7 @@
EvaluatedDescription onOnto = reEvaluateDescription(
bestDescription.getDescription(), retrieved, posEx, negEx);
- logger.warn(onOnto.getDescription().toManchesterSyntaxString(null, null));
+ logger.warn(onOnto.getDescription().toKBSyntaxString());
logger.warn(onOnto.getAccuracy());
accOnOnto.addNumber(onOnto.getAccuracy());
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|
|
From: <ku...@us...> - 2008-09-26 21:11:06
|
Revision: 1280
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=1280&view=rev
Author: kurzum
Date: 2008-09-26 21:11:00 +0000 (Fri, 26 Sep 2008)
Log Message:
-----------
schedule experiments
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/scripts/SemanticBibleComparison.java
Modified: trunk/src/dl-learner/org/dllearner/scripts/SemanticBibleComparison.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/SemanticBibleComparison.java 2008-09-26 20:28:57 UTC (rev 1279)
+++ trunk/src/dl-learner/org/dllearner/scripts/SemanticBibleComparison.java 2008-09-26 21:11:00 UTC (rev 1280)
@@ -159,6 +159,10 @@
/*finished experiments:
* SPARQL_10s
* SPARQL_1000_CONCEPT_TESTS
+ * running:
+ * NORMAL_1000_CONCEPT_TESTS
+ * SPARQL_10000_CONCEPT_TESTS
+ * NORMAL_10000_CONCEPT_TESTS
*
* */
@@ -167,13 +171,16 @@
//if(exp.equals(Experiments.NORMAL_10000_CONCEPT_TESTS))continue;
//if(exp.equals(Experiments.SPARQL_100s))continue;
//if(exp.toString().contains("SPARQL"))continue;
- if(exp.equals(Experiments.NORMAL_1000_CONCEPT_TESTS))conductExperiment(exp);
- if(exp.equals(Experiments.SPARQL_10000_CONCEPT_TESTS))conductExperiment(exp);
- if(exp.equals(Experiments.NORMAL_10000_CONCEPT_TESTS))conductExperiment(exp);
- //System.exit(0);
+ if(exp.equals(Experiments.NORMAL_10s))conductExperiment(exp);
+ if(exp.equals(Experiments.SPARQL_100s))conductExperiment(exp);
+ if(exp.equals(Experiments.NORMAL_100s))conductExperiment(exp);
+ //~ if(exp.equals(Experiments.NORMAL_1000_CONCEPT_TESTS))conductExperiment(exp);
+ //~ if(exp.equals(Experiments.SPARQL_10000_CONCEPT_TESTS))conductExperiment(exp);
+ //~ if(exp.equals(Experiments.NORMAL_10000_CONCEPT_TESTS))conductExperiment(exp);
+
}
}
- //conductExperiment(0);
+
// write JaMON report in HTML file
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|
|
From: <ku...@us...> - 2008-09-26 20:29:03
|
Revision: 1279
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=1279&view=rev
Author: kurzum
Date: 2008-09-26 20:28:57 +0000 (Fri, 26 Sep 2008)
Log Message:
-----------
server commit
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/scripts/SemanticBibleComparison.java
Modified: trunk/src/dl-learner/org/dllearner/scripts/SemanticBibleComparison.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/SemanticBibleComparison.java 2008-09-26 20:24:32 UTC (rev 1278)
+++ trunk/src/dl-learner/org/dllearner/scripts/SemanticBibleComparison.java 2008-09-26 20:28:57 UTC (rev 1279)
@@ -156,13 +156,20 @@
}else{
+ /*finished experiments:
+ * SPARQL_10s
+ * SPARQL_1000_CONCEPT_TESTS
+ *
+ * */
+
for (Experiments exp : Experiments.values()) {
//if(exp.equals(Experiments.SPARQL_10000_CONCEPT_TESTS))continue;
//if(exp.equals(Experiments.NORMAL_10000_CONCEPT_TESTS))continue;
//if(exp.equals(Experiments.SPARQL_100s))continue;
//if(exp.toString().contains("SPARQL"))continue;
- if(exp.equals(Experiments.SPARQL_10s))conductExperiment(exp);
- if(exp.equals(Experiments.SPARQL_1000_CONCEPT_TESTS))conductExperiment(exp);
+ if(exp.equals(Experiments.NORMAL_1000_CONCEPT_TESTS))conductExperiment(exp);
+ if(exp.equals(Experiments.SPARQL_10000_CONCEPT_TESTS))conductExperiment(exp);
+ if(exp.equals(Experiments.NORMAL_10000_CONCEPT_TESTS))conductExperiment(exp);
//System.exit(0);
}
}
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|
|
From: <ku...@us...> - 2008-09-26 20:24:39
|
Revision: 1278
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=1278&view=rev
Author: kurzum
Date: 2008-09-26 20:24:32 +0000 (Fri, 26 Sep 2008)
Log Message:
-----------
server commit
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/scripts/NT2RDF.java
trunk/src/dl-learner/org/dllearner/scripts/SemanticBibleComparison.java
Modified: trunk/src/dl-learner/org/dllearner/scripts/NT2RDF.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/NT2RDF.java 2008-09-26 19:35:49 UTC (rev 1277)
+++ trunk/src/dl-learner/org/dllearner/scripts/NT2RDF.java 2008-09-26 20:24:32 UTC (rev 1278)
@@ -29,11 +29,12 @@
public static void main(String[] args) {
- // String ontopath=args[0];
- String ontopath = "examples/semantic_bible/NTNcombined.nt";
+ String ontopath=args[0];
+ //String ontopath = "examples/semantic_bible/NTNcombined.nt";
// String ontopath = "examples/semantic_bible/test.nt";
convertNT2RDF(ontopath);
+
}
/**
Modified: trunk/src/dl-learner/org/dllearner/scripts/SemanticBibleComparison.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/SemanticBibleComparison.java 2008-09-26 19:35:49 UTC (rev 1277)
+++ trunk/src/dl-learner/org/dllearner/scripts/SemanticBibleComparison.java 2008-09-26 20:24:32 UTC (rev 1278)
@@ -154,16 +154,17 @@
- }
+ }else{
- for (Experiments exp : Experiments.values()) {
- //if(exp.equals(Experiments.SPARQL_10000_CONCEPT_TESTS))continue;
- //if(exp.equals(Experiments.NORMAL_10000_CONCEPT_TESTS))continue;
- //if(exp.equals(Experiments.SPARQL_100s))continue;
- //if(exp.toString().contains("SPARQL"))continue;
- if(exp.equals(Experiments.SPARQL_10s))conductExperiment(exp);
- if(exp.equals(Experiments.SPARQL_1000_CONCEPT_TESTS))conductExperiment(exp);
- //System.exit(0);
+ for (Experiments exp : Experiments.values()) {
+ //if(exp.equals(Experiments.SPARQL_10000_CONCEPT_TESTS))continue;
+ //if(exp.equals(Experiments.NORMAL_10000_CONCEPT_TESTS))continue;
+ //if(exp.equals(Experiments.SPARQL_100s))continue;
+ //if(exp.toString().contains("SPARQL"))continue;
+ if(exp.equals(Experiments.SPARQL_10s))conductExperiment(exp);
+ if(exp.equals(Experiments.SPARQL_1000_CONCEPT_TESTS))conductExperiment(exp);
+ //System.exit(0);
+ }
}
//conductExperiment(0);
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|
|
From: <ku...@us...> - 2008-09-26 19:35:56
|
Revision: 1277
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=1277&view=rev
Author: kurzum
Date: 2008-09-26 19:35:49 +0000 (Fri, 26 Sep 2008)
Log Message:
-----------
server commit
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/scripts/SemanticBibleComparison.java
Modified: trunk/src/dl-learner/org/dllearner/scripts/SemanticBibleComparison.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/SemanticBibleComparison.java 2008-09-26 19:30:02 UTC (rev 1276)
+++ trunk/src/dl-learner/org/dllearner/scripts/SemanticBibleComparison.java 2008-09-26 19:35:49 UTC (rev 1277)
@@ -175,7 +175,9 @@
//total.printAndSet("Finished");
logger.warn(total.getAndSet("Finished"));
if(flawInExperiment){
- logger.error("There were exceptions");
+ logger.error("There were exceptions, see log");
+ }else{
+ logger.warn("The experiment finished without any flaws");
}
//logger.warn("Finished");
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|
|
From: <ku...@us...> - 2008-09-26 19:30:16
|
Revision: 1276
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=1276&view=rev
Author: kurzum
Date: 2008-09-26 19:30:02 +0000 (Fri, 26 Sep 2008)
Log Message:
-----------
serverCommit
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlKnowledgeSource.java
trunk/src/dl-learner/org/dllearner/scripts/SemanticBibleComparison.java
Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlKnowledgeSource.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlKnowledgeSource.java 2008-09-26 18:39:03 UTC (rev 1275)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlKnowledgeSource.java 2008-09-26 19:30:02 UTC (rev 1276)
@@ -27,8 +27,6 @@
import java.util.LinkedList;
import java.util.List;
import java.util.TreeSet;
-import java.util.concurrent.Callable;
-import java.util.concurrent.FutureTask;
import org.apache.log4j.Logger;
import org.dllearner.core.KnowledgeSource;
@@ -76,15 +74,15 @@
public class SparqlKnowledgeSource extends KnowledgeSource {
//RBC
- private static final boolean debug = true;
+ private static final boolean debug = false;
- private static final boolean threaded = debug && true ;
+ //private static final boolean threaded = debug && true ;
// tupleaquisitor
//private static final boolean debugUseImprovedTupleAquisitor = debug && false; // switches
// sysex
- private static final boolean debugExitAfterExtraction = debug && true; // switches
+ private static final boolean debugExitAfterExtraction = debug && false; // switches
private SparqlKnowledgeSourceConfigurator configurator;
@@ -261,17 +259,34 @@
// the actual extraction is started here
Monitor extractionTime = JamonMonitorLogger.getTimeMonitor(SparqlKnowledgeSource.class, "total extraction time").start();
List<Node> seedNodes=new ArrayList<Node>();
- if(!threaded){
+
+ //if(!threaded){
seedNodes = m.extract(configurator.getInstances());
- }else{
+ /*}else{
+ int maxPoolSize = configurator.getInstances().size();
+ ThreadPoolExecutor ex = new ThreadPoolExecutor(5,maxPoolSize,1,TimeUnit.SECONDS,new ArrayBlockingQueue<Runnable>(100));
+ List<FutureTask<Node>> tasks = new ArrayList<FutureTask<Node>>();
+
for (String uri : configurator.getInstances()) {
- System.out.println("making future task");
- FutureTask<Node> f = new FutureTask<Node>(new ExtractOneInstance(m,uri));
- seedNodes.add(f.get());
- System.out.println("finished FutureTask "+seedNodes.size());
+
+ ExtractOneInstance e = new ExtractOneInstance(m,uri);
+
+ FutureTask<Node> ft = new FutureTask<Node>(e);
+ ex.submit(ft);
+ tasks.add(ft);
+ //System.out.println(f.get());
+ //seedNodes.add(f.get());
+ //System.out.println("finished FutureTask "+seedNodes.size());
}
- }
+ for(FutureTask<Node> ft : tasks){
+ //System.out.println(ft.get());
+ //System.out.println("aaa");
+ seedNodes.add(ft.get());
+
+ }
+ }*/
extractionTime.stop();
+
fragment = m.getOWLAPIOntologyForNodes(seedNodes, configurator.getSaveExtractedFragment());
@@ -302,7 +317,7 @@
return null;
}
- private class ExtractOneInstance extends Thread implements Callable{
+ /*private class ExtractOneInstance implements Callable{
Manager m;
Node n;
String uri;
@@ -313,15 +328,13 @@
this.uri = uri;
}
- @Override
- public void run(){
- n = m.extractOneURI(uri);
- }
+
public Node call(){
- return n;
+ System.out.println("funky");
+ return m.extractOneURI(uri);
}
- }
+ }*/
/*
* (non-Javadoc)
Modified: trunk/src/dl-learner/org/dllearner/scripts/SemanticBibleComparison.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/SemanticBibleComparison.java 2008-09-26 18:39:03 UTC (rev 1275)
+++ trunk/src/dl-learner/org/dllearner/scripts/SemanticBibleComparison.java 2008-09-26 19:30:02 UTC (rev 1276)
@@ -74,7 +74,7 @@
public class SemanticBibleComparison {
private static boolean onJensMachine = false;
- private static int nrOfFilesInExperiment = (onJensMachine)?1:1;
+ private static int nrOfFilesInExperiment = (onJensMachine)?1:200;
private static ReasoningService reasoningService;
@@ -161,7 +161,8 @@
//if(exp.equals(Experiments.NORMAL_10000_CONCEPT_TESTS))continue;
//if(exp.equals(Experiments.SPARQL_100s))continue;
//if(exp.toString().contains("SPARQL"))continue;
- conductExperiment(exp);
+ if(exp.equals(Experiments.SPARQL_10s))conductExperiment(exp);
+ if(exp.equals(Experiments.SPARQL_1000_CONCEPT_TESTS))conductExperiment(exp);
//System.exit(0);
}
//conductExperiment(0);
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|
|
From: <ku...@us...> - 2008-09-26 18:39:06
|
Revision: 1275
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=1275&view=rev
Author: kurzum
Date: 2008-09-26 18:39:03 +0000 (Fri, 26 Sep 2008)
Log Message:
-----------
server commit
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlKnowledgeSource.java
trunk/src/dl-learner/org/dllearner/utilities/statistics/Table.java
Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlKnowledgeSource.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlKnowledgeSource.java 2008-09-26 18:35:02 UTC (rev 1274)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlKnowledgeSource.java 2008-09-26 18:39:03 UTC (rev 1275)
@@ -265,8 +265,10 @@
seedNodes = m.extract(configurator.getInstances());
}else{
for (String uri : configurator.getInstances()) {
+ System.out.println("making future task");
FutureTask<Node> f = new FutureTask<Node>(new ExtractOneInstance(m,uri));
seedNodes.add(f.get());
+ System.out.println("finished FutureTask "+seedNodes.size());
}
}
extractionTime.stop();
Modified: trunk/src/dl-learner/org/dllearner/utilities/statistics/Table.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/statistics/Table.java 2008-09-26 18:35:02 UTC (rev 1274)
+++ trunk/src/dl-learner/org/dllearner/utilities/statistics/Table.java 2008-09-26 18:39:03 UTC (rev 1275)
@@ -186,7 +186,7 @@
int i=0;
for(TableColumn c:t.getColumns()){
String header = URLEncoder.encode(c.getHeader(),"UTF-8");
- String columnFileName = dir+File.separator+t.getTableName()+header+(i++)+column;
+ String columnFileName = dir+File.separator+t.getTableName()+(i++)+header+column;
c.serialize(new File(columnFileName));
//Files.writeObjectToFile(c, new File(filename));
content += columnFileName+System.getProperty("line.separator");
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|
|
From: <ku...@us...> - 2008-09-26 18:35:09
|
Revision: 1274
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=1274&view=rev
Author: kurzum
Date: 2008-09-26 18:35:02 +0000 (Fri, 26 Sep 2008)
Log Message:
-----------
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/kb/extraction/Manager.java
trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlKnowledgeSource.java
trunk/src/dl-learner/org/dllearner/scripts/SemanticBibleComparison.java
trunk/src/dl-learner/org/dllearner/utilities/statistics/Table.java
Modified: trunk/src/dl-learner/org/dllearner/kb/extraction/Manager.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/extraction/Manager.java 2008-09-26 17:25:48 UTC (rev 1273)
+++ trunk/src/dl-learner/org/dllearner/kb/extraction/Manager.java 2008-09-26 18:35:02 UTC (rev 1274)
@@ -57,9 +57,9 @@
public Node extractOneURI(String uri) {
- logger.info("Start extracting: "+uri);
+ //logger.info("Start extracting: "+uri);
Node n = extractionAlgorithm.expandNode(uri, configuration.getTupelAquisitor());
- logger.info("Finished extracting: "+uri );
+ //logger.info("Finished extracting: "+uri );
seedNodes.add(n);
return n;
}
Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlKnowledgeSource.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlKnowledgeSource.java 2008-09-26 17:25:48 UTC (rev 1273)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlKnowledgeSource.java 2008-09-26 18:35:02 UTC (rev 1274)
@@ -27,6 +27,8 @@
import java.util.LinkedList;
import java.util.List;
import java.util.TreeSet;
+import java.util.concurrent.Callable;
+import java.util.concurrent.FutureTask;
import org.apache.log4j.Logger;
import org.dllearner.core.KnowledgeSource;
@@ -61,6 +63,7 @@
import org.dllearner.utilities.statistics.SimpleClock;
import org.semanticweb.owl.model.OWLOntology;
+import com.jamonapi.Monitor;
import com.jamonapi.MonitorFactory;
/**
@@ -72,13 +75,16 @@
*/
public class SparqlKnowledgeSource extends KnowledgeSource {
+ //RBC
+ private static final boolean debug = true;
- private static final boolean debug = false;
+ private static final boolean threaded = debug && true ;
+
// tupleaquisitor
//private static final boolean debugUseImprovedTupleAquisitor = debug && false; // switches
// sysex
- private static final boolean debugExitAfterExtraction = debug && false; // switches
+ private static final boolean debugExitAfterExtraction = debug && true; // switches
private SparqlKnowledgeSourceConfigurator configurator;
@@ -227,7 +233,7 @@
public void init() {
logger.info("SparqlModul: Collecting Ontology");
SimpleClock totalTime = new SimpleClock();
- SimpleClock extractionTime = new SimpleClock();
+ //SimpleClock extractionTime = new SimpleClock();
logger.trace(getURL());
logger.trace(getSparqlEndpoint());
@@ -253,14 +259,23 @@
try {
// the actual extraction is started here
-
- extractionTime.setTime();
- List<Node> seedNodes = m.extract(configurator.getInstances());
+ Monitor extractionTime = JamonMonitorLogger.getTimeMonitor(SparqlKnowledgeSource.class, "total extraction time").start();
+ List<Node> seedNodes=new ArrayList<Node>();
+ if(!threaded){
+ seedNodes = m.extract(configurator.getInstances());
+ }else{
+ for (String uri : configurator.getInstances()) {
+ FutureTask<Node> f = new FutureTask<Node>(new ExtractOneInstance(m,uri));
+ seedNodes.add(f.get());
+ }
+ }
+ extractionTime.stop();
+
fragment = m.getOWLAPIOntologyForNodes(seedNodes, configurator.getSaveExtractedFragment());
- extractionTime.printAndSet("extraction needed");
- logger.info("Finished collecting Fragment");
+ logger.info("Finished collecting fragment. needed "+extractionTime.getLastValue()+" ms");
+
ontologyFragmentURL = m.getPhysicalOntologyURL();
nrOfExtractedAxioms = configuration.getOwlAPIOntologyCollector().getNrOfExtractedAxioms();
@@ -280,6 +295,31 @@
System.exit(0);
}
}
+
+ public List<Node> extractParallel(){
+ return null;
+ }
+
+ private class ExtractOneInstance extends Thread implements Callable{
+ Manager m;
+ Node n;
+ String uri;
+
+ private ExtractOneInstance(Manager m, String uri){
+ super();
+ this.m = m;
+ this.uri = uri;
+ }
+
+ @Override
+ public void run(){
+ n = m.extractOneURI(uri);
+ }
+
+ public Node call(){
+ return n;
+ }
+ }
/*
* (non-Javadoc)
Modified: trunk/src/dl-learner/org/dllearner/scripts/SemanticBibleComparison.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/SemanticBibleComparison.java 2008-09-26 17:25:48 UTC (rev 1273)
+++ trunk/src/dl-learner/org/dllearner/scripts/SemanticBibleComparison.java 2008-09-26 18:35:02 UTC (rev 1274)
@@ -73,6 +73,9 @@
public class SemanticBibleComparison {
+ private static boolean onJensMachine = false;
+ private static int nrOfFilesInExperiment = (onJensMachine)?1:1;
+
private static ReasoningService reasoningService;
private static Logger logger = Logger.getRootLogger();
@@ -143,13 +146,22 @@
List<String> l = getFiles();
analyzeFiles(l);
+ if(onJensMachine){
+ conductExperiment(Experiments.NORMAL_10s);
+ conductExperiment(Experiments.NORMAL_100s);
+ conductExperiment(Experiments.NORMAL_1000_CONCEPT_TESTS);
+ conductExperiment(Experiments.NORMAL_10000_CONCEPT_TESTS);
+
+
+
+ }
+
for (Experiments exp : Experiments.values()) {
//if(exp.equals(Experiments.SPARQL_10000_CONCEPT_TESTS))continue;
//if(exp.equals(Experiments.NORMAL_10000_CONCEPT_TESTS))continue;
//if(exp.equals(Experiments.SPARQL_100s))continue;
- //if(exp.equals(Experiments.NORMAL_100s))continue;
+ //if(exp.toString().contains("SPARQL"))continue;
conductExperiment(exp);
- reinitStat();
//System.exit(0);
}
//conductExperiment(0);
@@ -175,12 +187,12 @@
List<String> confs = getFiles();
ComponentManager cm =ComponentManager.getInstance();
- int count = 1;
+ int count = 0;
for (String filename : confs) {
SimpleClock oneExperiment = new SimpleClock();
- if (count == 2){break;}
+ if (count == nrOfFilesInExperiment){break;}
- logger.warn("****"+exp+" "+count +" from file "+filename);
+ logger.warn("****"+exp+" "+(count+1) +" from file "+filename);
// read the file and get the examples
File f = new File(exampleDir+filename);
@@ -246,17 +258,17 @@
cm.freeAllComponents();
- fillTable(exp, count);
+ fillTable(exp, (count+1));
- logger.warn(exp+" "+count+ " " +oneExperiment.getAndSet("")+"****" );
+ logger.warn(exp+" "+(count+1)+ " " +oneExperiment.getAndSet("")+"****" );
count++;
}//end for
}catch (Exception e) {
e.printStackTrace();
flawInExperiment = true;
}
-
- }
+ reinitStat();
+ }//endconduct
public static void analyzeFiles(List<String> l){
int countDoublettes = 0;
Modified: trunk/src/dl-learner/org/dllearner/utilities/statistics/Table.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/statistics/Table.java 2008-09-26 17:25:48 UTC (rev 1273)
+++ trunk/src/dl-learner/org/dllearner/utilities/statistics/Table.java 2008-09-26 18:35:02 UTC (rev 1274)
@@ -22,6 +22,7 @@
import java.io.File;
import java.io.Serializable;
+import java.net.URLEncoder;
import java.util.ArrayList;
import java.util.List;
@@ -177,17 +178,18 @@
}
public static void serializeColumns(Table t, String dir, String tableFile){
- String column = "column";
+ String column = ".column";
String content = "";
dir = StringFormatter.checkIfDirEndsOnSlashAndRemove(dir);
Files.mkdir(dir);
try{
int i=0;
for(TableColumn c:t.getColumns()){
- String filename = dir+File.separator+t.getTableName()+column+(i++);
- c.serialize(new File(filename));
+ String header = URLEncoder.encode(c.getHeader(),"UTF-8");
+ String columnFileName = dir+File.separator+t.getTableName()+header+(i++)+column;
+ c.serialize(new File(columnFileName));
//Files.writeObjectToFile(c, new File(filename));
- content += filename+System.getProperty("line.separator");
+ content += columnFileName+System.getProperty("line.separator");
}
Files.createFile(new File(tableFile), content);
//
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|
|
From: <jen...@us...> - 2008-09-26 17:25:57
|
Revision: 1273
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=1273&view=rev
Author: jenslehmann
Date: 2008-09-26 17:25:48 +0000 (Fri, 26 Sep 2008)
Log Message:
-----------
implemented hasValue support including simple frequent pattern preprocessing (not working yet)
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/reasoning/FastInstanceChecker.java
trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIDescriptionConvertVisitor.java
trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java
trunk/src/dl-learner/org/dllearner/utilities/owl/ConceptComparator.java
Added Paths:
-----------
trunk/examples/semantic_bible/hasvalue_example.conf
Added: trunk/examples/semantic_bible/hasvalue_example.conf
===================================================================
--- trunk/examples/semantic_bible/hasvalue_example.conf (rev 0)
+++ trunk/examples/semantic_bible/hasvalue_example.conf 2008-09-26 17:25:48 UTC (rev 1273)
@@ -0,0 +1,20 @@
+/**
+ * It should learn ethnicity hasValue Jewish, but does not work for some reason.
+ */
+
+import("../NTNcombined.owl");
+
+// reasoner = owlAPIReasoner;
+owlAPIReasoner.reasonerType = pellet;
+
++"http://semanticbible.org/ns/2006/NTNames#Hezron"
++"http://semanticbible.org/ns/2006/NTNames#Jehoshaphat"
++"http://semanticbible.org/ns/2006/NTNames#Judah"
++"http://semanticbible.org/ns/2006/NTNames#Jorim"
++"http://semanticbible.org/ns/2006/NTNames#Neri"
+
+-"http://semanticbible.org/ns/2006/NTNames#Hierapolis"
+-"http://semanticbible.org/ns/2006/NTNames#Iconium"
+-"http://semanticbible.org/ns/2006/NTNames#Joda"
+-"http://semanticbible.org/ns/2006/NTNames#JohntheBaptist"
+-"http://semanticbible.org/ns/2006/NTNames#Philip"
Modified: trunk/src/dl-learner/org/dllearner/reasoning/FastInstanceChecker.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/reasoning/FastInstanceChecker.java 2008-09-26 16:30:40 UTC (rev 1272)
+++ trunk/src/dl-learner/org/dllearner/reasoning/FastInstanceChecker.java 2008-09-26 17:25:48 UTC (rev 1273)
@@ -63,6 +63,7 @@
import org.dllearner.core.owl.ObjectPropertyExpression;
import org.dllearner.core.owl.ObjectPropertyHierarchy;
import org.dllearner.core.owl.ObjectSomeRestriction;
+import org.dllearner.core.owl.ObjectValueRestriction;
import org.dllearner.core.owl.SubsumptionHierarchy;
import org.dllearner.core.owl.Thing;
import org.dllearner.core.owl.Union;
@@ -428,6 +429,11 @@
}
}
return true;
+ } else if (description instanceof ObjectValueRestriction) {
+ Individual i = ((ObjectValueRestriction)description).getIndividual();
+ ObjectProperty op = (ObjectProperty) ((ObjectValueRestriction)description).getRestrictedPropertyExpression();
+
+ return opPos.get(op).get(individual).contains(i);
} else if (description instanceof BooleanValueRestriction) {
DatatypeProperty dp = ((BooleanValueRestriction) description)
.getRestrictedPropertyExpresssion();
Modified: trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIDescriptionConvertVisitor.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIDescriptionConvertVisitor.java 2008-09-26 16:30:40 UTC (rev 1272)
+++ trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIDescriptionConvertVisitor.java 2008-09-26 17:25:48 UTC (rev 1273)
@@ -36,6 +36,7 @@
import org.dllearner.core.owl.Description;
import org.dllearner.core.owl.DescriptionVisitor;
import org.dllearner.core.owl.DoubleMinValue;
+import org.dllearner.core.owl.Individual;
import org.dllearner.core.owl.Intersection;
import org.dllearner.core.owl.NamedClass;
import org.dllearner.core.owl.Negation;
@@ -44,6 +45,7 @@
import org.dllearner.core.owl.ObjectExactCardinalityRestriction;
import org.dllearner.core.owl.ObjectMaxCardinalityRestriction;
import org.dllearner.core.owl.ObjectMinCardinalityRestriction;
+import org.dllearner.core.owl.ObjectProperty;
import org.dllearner.core.owl.ObjectSomeRestriction;
import org.dllearner.core.owl.ObjectValueRestriction;
import org.dllearner.core.owl.SimpleDoubleDataRange;
@@ -60,6 +62,7 @@
import org.semanticweb.owl.model.OWLDataRange;
import org.semanticweb.owl.model.OWLDataType;
import org.semanticweb.owl.model.OWLDescription;
+import org.semanticweb.owl.model.OWLIndividual;
import org.semanticweb.owl.model.OWLObjectProperty;
import org.semanticweb.owl.model.OWLTypedConstant;
import org.semanticweb.owl.vocab.OWLRestrictedDataRangeFacetVocabulary;
@@ -227,8 +230,10 @@
* @see org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl.ObjectValueRestriction)
*/
public void visit(ObjectValueRestriction description) {
- // TODO Auto-generated method stub
- throw new Error("OWLAPIDescriptionConverter: not implemented");
+ OWLObjectProperty role = factory.getOWLObjectProperty(
+ URI.create(((ObjectProperty)description.getRestrictedPropertyExpression()).getName()));
+ OWLIndividual i = factory.getOWLIndividual(URI.create(description.getIndividual().getName()));
+ stack.push(factory.getOWLObjectValueRestriction(role, i));
}
/* (non-Javadoc)
Modified: trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java 2008-09-26 16:30:40 UTC (rev 1272)
+++ trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java 2008-09-26 17:25:48 UTC (rev 1273)
@@ -19,6 +19,7 @@
*/
package org.dllearner.refinementoperators;
+import java.util.Collection;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
@@ -54,6 +55,7 @@
import org.dllearner.core.owl.ObjectPropertyExpression;
import org.dllearner.core.owl.ObjectQuantorRestriction;
import org.dllearner.core.owl.ObjectSomeRestriction;
+import org.dllearner.core.owl.ObjectValueRestriction;
import org.dllearner.core.owl.SubsumptionHierarchy;
import org.dllearner.core.owl.Thing;
import org.dllearner.core.owl.Union;
@@ -148,6 +150,14 @@
private Map<DatatypeProperty,List<Double>> splits = new TreeMap<DatatypeProperty,List<Double>>();
private int maxNrOfSplits = 10;
+ // experimental support for hasValue
+ private boolean useHasValue = false;
+ // data structure for a simple frequent pattern matching preprocessing phase
+ private int frequencyThreshold = 3;
+ private Map<ObjectProperty, Map<Individual, Integer>> valueFrequency = new HashMap<ObjectProperty, Map<Individual, Integer>>();
+ // data structure with identified frequent values
+ private Map<ObjectProperty, Set<Individual>> frequentValues = new HashMap<ObjectProperty, Set<Individual>>();
+
// staistics
public long mComputationTimeNs = 0;
public long topComputationTimeNs = 0;
@@ -193,7 +203,46 @@
for(ObjectProperty op : rs.getObjectProperties()) {
opDomains.put(op, rs.getDomain(op));
opRanges.put(op, rs.getRange(op));
+
+ if(useHasValue) {
+ // init
+ Map<Individual, Integer> opMap = new TreeMap<Individual, Integer>();
+ valueFrequency.put(op, opMap);
+
+ // sets ordered by corresponding individual (which we ignore)
+ Collection<SortedSet<Individual>> fillerSets = rs.getRoleMembers(op).values();
+ for(SortedSet<Individual> fillerSet : fillerSets) {
+ for(Individual i : fillerSet) {
+// System.out.println("op " + op + " i " + i);
+ Integer value = opMap.get(i);
+
+ if(value != null) {
+ opMap.put(i, value+1);
+ } else {
+ opMap.put(i, 1);
+ }
+ }
+ }
+
+ // keep only frequent patterns (TODO it would be slightly
+ // more efficient if we stop adding to valueFrequency
+ // after threshold is reached)
+ Set<Individual> frequentInds = new TreeSet<Individual>();
+ for(Individual i : opMap.keySet()) {
+ if(opMap.get(i) > frequencyThreshold) {
+ frequentInds.add(i);
+ }
+ }
+ frequentValues.put(op, frequentInds);
+
+ }
+
}
+
+ // we do not need the temporary set anymore and let the
+ // garbage collector take care of it
+ valueFrequency = null;
+
for(DatatypeProperty dp : rs.getDatatypeProperties()) {
dpDomains.put(dp, rs.getDomain(dp));
}
@@ -405,6 +454,18 @@
}
}
+ // rule 4: EXISTS r.TOP => EXISTS r.{value}
+ if(useHasValue && description.getChild(0) instanceof Thing) {
+ // watch out for frequent patterns
+ Set<Individual> frequentInds = frequentValues.get(role);
+ if(frequentInds != null) {
+ for(Individual ind : frequentInds) {
+ ObjectValueRestriction ovr = new ObjectValueRestriction(ar, ind);
+ refinements.add(ovr);
+ }
+ }
+ }
+
} else if (description instanceof ObjectAllRestriction) {
ObjectPropertyExpression role = ((ObjectQuantorRestriction)description).getRole();
Description range = opRanges.get(role);
Modified: trunk/src/dl-learner/org/dllearner/utilities/owl/ConceptComparator.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/owl/ConceptComparator.java 2008-09-26 16:30:40 UTC (rev 1272)
+++ trunk/src/dl-learner/org/dllearner/utilities/owl/ConceptComparator.java 2008-09-26 17:25:48 UTC (rev 1273)
@@ -8,6 +8,7 @@
import org.dllearner.core.owl.DatatypeSomeRestriction;
import org.dllearner.core.owl.DoubleMaxValue;
import org.dllearner.core.owl.DoubleMinValue;
+import org.dllearner.core.owl.Individual;
import org.dllearner.core.owl.ObjectAllRestriction;
import org.dllearner.core.owl.NamedClass;
import org.dllearner.core.owl.Nothing;
@@ -17,6 +18,7 @@
import org.dllearner.core.owl.ObjectMinCardinalityRestriction;
import org.dllearner.core.owl.ObjectSomeRestriction;
import org.dllearner.core.owl.Intersection;
+import org.dllearner.core.owl.ObjectValueRestriction;
import org.dllearner.core.owl.SimpleDoubleDataRange;
import org.dllearner.core.owl.Union;
import org.dllearner.core.owl.Negation;
@@ -175,8 +177,23 @@
return roleCompare;
} else
return -1;
+ } else if(concept1 instanceof ObjectValueRestriction) {
+ if(concept2.getChildren().size()<1 || concept2 instanceof Negation || concept2 instanceof ObjectSomeRestriction || concept2 instanceof ObjectAllRestriction)
+ return 1;
+ else if(concept2 instanceof ObjectValueRestriction) {
+ int roleCompare = rc.compare(((ObjectValueRestriction)concept1).getRestrictedPropertyExpression(), ((ObjectQuantorRestriction)concept2).getRestrictedPropertyExpression());
+
+ if(roleCompare == 0) {
+ Individual value1 = ((ObjectValueRestriction)concept1).getIndividual();
+ Individual value2 = ((ObjectValueRestriction)concept2).getIndividual();
+ return value1.compareTo(value2);
+ } else {
+ return roleCompare;
+ }
+ } else
+ return -1;
} else if(concept1 instanceof ObjectMinCardinalityRestriction) {
- if(concept2.getChildren().size()<1 || concept2 instanceof Negation || concept2 instanceof ObjectQuantorRestriction)
+ if(concept2.getChildren().size()<1 || concept2 instanceof Negation || concept2 instanceof ObjectQuantorRestriction || concept2 instanceof ObjectValueRestriction)
return 1;
// first criterion: object property
// second criterion: number
@@ -196,7 +213,7 @@
} else
return -1;
} else if(concept1 instanceof ObjectMaxCardinalityRestriction) {
- if(concept2.getChildren().size()<1 || concept2 instanceof Negation || concept2 instanceof ObjectQuantorRestriction || concept2 instanceof ObjectMinCardinalityRestriction)
+ if(concept2.getChildren().size()<1 || concept2 instanceof Negation || concept2 instanceof ObjectQuantorRestriction || concept2 instanceof ObjectValueRestriction || concept2 instanceof ObjectMinCardinalityRestriction)
return 1;
// first criterion: object property
// second criterion: number
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ku...@us...> - 2008-09-26 16:30:50
|
Revision: 1272
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=1272&view=rev
Author: kurzum
Date: 2008-09-26 16:30:40 +0000 (Fri, 26 Sep 2008)
Log Message:
-----------
long retrieval time example
Added Paths:
-----------
trunk/examples/semantic_bible/normal_long_retrieval_time.conf
Added: trunk/examples/semantic_bible/normal_long_retrieval_time.conf
===================================================================
--- trunk/examples/semantic_bible/normal_long_retrieval_time.conf (rev 0)
+++ trunk/examples/semantic_bible/normal_long_retrieval_time.conf 2008-09-26 16:30:40 UTC (rev 1272)
@@ -0,0 +1,29 @@
+ /**
+EXISTS "http://semanticbible.org/ns/2006/NTNames#siblingOf".TOP
+EXISTS "http://semanticbible.org/ns/2006/NTNames#siblingOf"."http://semanticbible.org/ns/2006/NTNames#Man"
+ */
+
+
+// export("arch.owl");
+import("NTNcombined.owl");
+
+algorithm = refexamples;
+refexamples.useAllConstructor = true;
+refexamples.useNegation = true;
+refexamples.useCardinalityRestrictions = true;
+
+refexamples.guaranteeXgoodDescriptions = 20;
+//refexamples.ignoredConcepts = {"http://semanticbible.org/ns/2006/NTNames#God"};
+
+//reasoner = fastInstanceChecker;
+reasoner = owlAPIReasoner;
+owlAPIReasoner.reasonerType = pellet;
+
+/** examples **/
+-"http://semanticbible.org/ns/2006/NTNames#Almighty"
+-"http://semanticbible.org/ns/2006/NTNames#Gabriel"
+-"http://semanticbible.org/ns/2006/NTNames#Michael"
++"http://semanticbible.org/ns/2006/NTNames#Archelaus"
++"http://semanticbible.org/ns/2006/NTNames#HerodAntipas"
+-"http://semanticbible.org/ns/2006/NTNames#Satan"
+-"http://semanticbible.org/ns/2006/NTNames#Jesus"
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ku...@us...> - 2008-09-26 15:51:05
|
Revision: 1271
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=1271&view=rev
Author: kurzum
Date: 2008-09-26 15:50:40 +0000 (Fri, 26 Sep 2008)
Log Message:
-----------
server commit
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/scripts/SemanticBibleComparison.java
Modified: trunk/src/dl-learner/org/dllearner/scripts/SemanticBibleComparison.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/SemanticBibleComparison.java 2008-09-26 15:08:38 UTC (rev 1270)
+++ trunk/src/dl-learner/org/dllearner/scripts/SemanticBibleComparison.java 2008-09-26 15:50:40 UTC (rev 1271)
@@ -20,6 +20,7 @@
package org.dllearner.scripts;
import java.io.File;
+import java.io.IOException;
import java.net.MalformedURLException;
import java.net.URI;
import java.net.URL;
@@ -33,8 +34,10 @@
import org.apache.log4j.ConsoleAppender;
import org.apache.log4j.FileAppender;
+import org.apache.log4j.Layout;
import org.apache.log4j.Level;
import org.apache.log4j.Logger;
+import org.apache.log4j.PatternLayout;
import org.apache.log4j.SimpleLayout;
import org.dllearner.algorithms.refexamples.ExampleBasedROLComponent;
import org.dllearner.core.Component;
@@ -141,9 +144,13 @@
analyzeFiles(l);
for (Experiments exp : Experiments.values()) {
- if(exp.equals(Experiments.SPARQL_10s))continue;
+ //if(exp.equals(Experiments.SPARQL_10000_CONCEPT_TESTS))continue;
+ //if(exp.equals(Experiments.NORMAL_10000_CONCEPT_TESTS))continue;
+ //if(exp.equals(Experiments.SPARQL_100s))continue;
+ //if(exp.equals(Experiments.NORMAL_100s))continue;
conductExperiment(exp);
- System.exit(0);
+ reinitStat();
+ //System.exit(0);
}
//conductExperiment(0);
@@ -152,7 +159,7 @@
File jamonlog = new File(dir+"jamon.html");
Files.createFile(jamonlog, MonitorFactory.getReport());
Files.appendFile(jamonlog, "<xmp>\n"+JamonMonitorLogger.getStringForAllSortedByLabel());
- total.printAndSet("Finished");
+ //total.printAndSet("Finished");
logger.warn(total.getAndSet("Finished"));
if(flawInExperiment){
logger.error("There were exceptions");
@@ -171,9 +178,9 @@
int count = 1;
for (String filename : confs) {
SimpleClock oneExperiment = new SimpleClock();
- if (count == 6){break;}
+ if (count == 2){break;}
- logger.warn(exp+" "+count +" from file "+filename);
+ logger.warn("****"+exp+" "+count +" from file "+filename);
// read the file and get the examples
File f = new File(exampleDir+filename);
@@ -241,7 +248,7 @@
fillTable(exp, count);
- logger.warn(exp+" "+count+ " " +oneExperiment.getAndSet("") );
+ logger.warn(exp+" "+count+ " " +oneExperiment.getAndSet("")+"****" );
count++;
}//end for
}catch (Exception e) {
@@ -255,11 +262,18 @@
int countDoublettes = 0;
SortedSet<String> differentIndividuals = new TreeSet<String>();
for ( String file : l) {
+ String fileContent = "";
+ try{fileContent = Files.readFile(new File(exampleDir+file));
+ }catch (Exception e) {
+ e.printStackTrace();
+ }
ExampleContainer ec = new ExampleContainer(
- SetManipulation.stringToInd(getIndividuals(file, true)),
- SetManipulation.stringToInd(getIndividuals(file, false)));
- differentIndividuals.addAll(getIndividuals(file, true));
- differentIndividuals.addAll(getIndividuals(file, false));
+ SetManipulation.stringToInd(getIndividuals(fileContent, true)),
+ SetManipulation.stringToInd(getIndividuals(fileContent, false)));
+
+ differentIndividuals.addAll(getIndividuals(fileContent, true));
+ differentIndividuals.addAll(getIndividuals(fileContent, false));
+
if(!ExampleContainer.add(ec)){
countDoublettes++;
}
@@ -464,7 +478,7 @@
- public static void reinitStat(){
+ private static void reinitStat(){
accFragment = new Stat();
accOnOnto = new Stat();
accPosExOnOnto = new Stat();
@@ -531,7 +545,6 @@
public static List<String> getFiles(){
String actualDir = exampleDir;
- logger.warn(actualDir);
File f = new File(actualDir);
String[] files = f.list();
Arrays.sort(files);
@@ -572,22 +585,32 @@
private static void initLogger() {
- SimpleLayout layout = new SimpleLayout();
- // create logger (a simple logger which outputs
- // its messages to the console)
- FileAppender fileAppender = null;
+ // logger 1 is the console, where we print only info messages;
+ // the logger is plain, i.e. does not output log level etc.
+ Layout layout = new PatternLayout();
+ ConsoleAppender consoleAppender = new ConsoleAppender(layout);
+ consoleAppender.setThreshold(Level.WARN);
+
+ // logger 2 is writes to a file; it records all debug messages
+ // and includes the log level
+ Layout layout2 = new SimpleLayout();
+ FileAppender fileAppenderNormal = null;
+ File f = new File("log/sparql.txt");
try {
- fileAppender = new FileAppender(layout, "log/semBibleLog.txt",
- false);
- } catch (Exception e) {
+ fileAppenderNormal = new FileAppender(layout2, "log/semBibleLog.txt", false);
+ f.delete();
+ f.createNewFile();
+ } catch (IOException e) {
e.printStackTrace();
}
-
- ConsoleAppender consoleAppender = new ConsoleAppender(layout);
+
+
+
logger.removeAllAppenders();
logger.addAppender(consoleAppender);
- logger.addAppender(fileAppender);
- logger.setLevel(Level.WARN);
+ logger.addAppender(fileAppenderNormal);
+ logger.setLevel(Level.DEBUG);
+
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ku...@us...> - 2008-09-26 15:07:46
|
Revision: 1269
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=1269&view=rev
Author: kurzum
Date: 2008-09-26 15:07:32 +0000 (Fri, 26 Sep 2008)
Log Message:
-----------
server commit
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/core/EvaluatedDescription.java
trunk/src/dl-learner/org/dllearner/scripts/SemanticBibleComparison.java
trunk/src/dl-learner/org/dllearner/utilities/StringFormatter.java
trunk/src/dl-learner/org/dllearner/utilities/examples/ExampleContainer.java
trunk/src/dl-learner/org/dllearner/utilities/statistics/SimpleClock.java
trunk/src/dl-learner/org/dllearner/utilities/statistics/Table.java
Modified: trunk/src/dl-learner/org/dllearner/core/EvaluatedDescription.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/EvaluatedDescription.java 2008-09-26 13:18:07 UTC (rev 1268)
+++ trunk/src/dl-learner/org/dllearner/core/EvaluatedDescription.java 2008-09-26 15:07:32 UTC (rev 1269)
@@ -23,7 +23,6 @@
import org.dllearner.core.owl.Description;
import org.dllearner.core.owl.Individual;
-import org.dllearner.kb.sparql.NaturalLanguageDescriptionConvertVisitor;
import org.dllearner.kb.sparql.SparqlQueryDescriptionConvertVisitor;
import org.dllearner.learningproblems.ScoreTwoValued;
import org.dllearner.reasoning.OWLAPIDescriptionConvertVisitor;
Modified: trunk/src/dl-learner/org/dllearner/scripts/SemanticBibleComparison.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/SemanticBibleComparison.java 2008-09-26 13:18:07 UTC (rev 1268)
+++ trunk/src/dl-learner/org/dllearner/scripts/SemanticBibleComparison.java 2008-09-26 15:07:32 UTC (rev 1269)
@@ -20,7 +20,9 @@
package org.dllearner.scripts;
import java.io.File;
+import java.net.MalformedURLException;
import java.net.URI;
+import java.net.URL;
import java.util.Arrays;
import java.util.HashSet;
import java.util.List;
@@ -42,21 +44,27 @@
import org.dllearner.core.LearningAlgorithm;
import org.dllearner.core.ReasoningService;
import org.dllearner.core.configurators.ComponentFactory;
+import org.dllearner.core.configurators.ExampleBasedROLComponentConfigurator;
import org.dllearner.core.owl.Description;
import org.dllearner.core.owl.Individual;
import org.dllearner.gui.Config;
import org.dllearner.gui.ConfigSave;
+import org.dllearner.kb.OWLFile;
import org.dllearner.kb.sparql.Cache;
import org.dllearner.kb.sparql.SparqlKnowledgeSource;
import org.dllearner.learningproblems.PosNegDefinitionLP;
import org.dllearner.reasoning.OWLAPIReasoner;
import org.dllearner.utilities.Files;
import org.dllearner.utilities.JamonMonitorLogger;
+import org.dllearner.utilities.StringFormatter;
import org.dllearner.utilities.datastructures.SetManipulation;
+import org.dllearner.utilities.examples.ExampleContainer;
import org.dllearner.utilities.owl.ReasoningServiceFactory;
import org.dllearner.utilities.owl.ReasoningServiceFactory.AvailableReasoners;
import org.dllearner.utilities.statistics.SimpleClock;
import org.dllearner.utilities.statistics.Stat;
+import org.dllearner.utilities.statistics.Table;
+import org.dllearner.utilities.statistics.TableColumn;
import com.jamonapi.MonitorFactory;
@@ -65,42 +73,53 @@
private static ReasoningService reasoningService;
private static Logger logger = Logger.getRootLogger();
- public static boolean flawInExperiment = false;
+ private static boolean flawInExperiment = false;
- public static String ontologyPath = "examples/semantic_bible/NTNcombined.owl";
- public static String dir = "sembib/";
+ private static String ontologyPath = "examples/semantic_bible/NTNcombined.owl";
+ private static String dir = "sembib100/";
//public static String sparqldir = dir+"sparql/";
- public static String exampleDir = dir+"examples/";
+ private static String exampleDir = dir+"examples/";
+ private static String tableDir = dir+"table/";
- public static String tmpFilename = dir + "tmp.conf";
- static File log = new File(dir+"results+prop.txt");
+ private static String tmpFilename = dir + "tmp.conf";
+ //static File log = new File(dir+"results+prop.txt");
+ private static String tableFile = tableDir+"sembib.table";
+ private static String tableLatex = tableDir+"sembibLatex.table";
private static Stat accFragment = new Stat();
private static Stat accOnOnto = new Stat();
private static Stat accPosExOnOnto = new Stat();
private static Stat accNegExOnOnto = new Stat();
private static Stat learningTime = new Stat();
- private static Stat nrOfExtractedTriples = new Stat();
+ //private static Stat initializationTime = new Stat();
+ private static Stat reasonerInitializationTime = new Stat();
+ private static Stat ksinitializationTime = new Stat();
+ private static Stat nrOfExtractedAxioms = new Stat();
private static Stat descLength = new Stat();
private static Stat descDepth = new Stat();
- private static Stat timeWhole = new Stat();
- private static Stat accWhole = new Stat();
- private static Stat dLengthWhole = new Stat();
- private static Stat dDepthWhole = new Stat();
-
-
private static boolean descHasNot = false;
private static boolean descHasAll = false;
private static boolean descHasBooleanData = false;
private static boolean descHasNrRes = false;
- private static boolean wholeHasNot = false;
- private static boolean wholeHasAll = false;
- private static boolean wholeHasBooleanData = false;
- private static boolean wholeHasNrRes = false;
+ private static Table t;
+ //private static boolean wholeHasNot = false;
+ //private static boolean wholeHasAll = false;
+ //private static boolean wholeHasBooleanData = false;
+ //private static boolean wholeHasNrRes = false;
+ //10s means fixed time 10s
+ private static enum Experiments {
+ SPARQL_10s,
+ NORMAL_10s,
+ SPARQL_100s,
+ NORMAL_100s,
+ SPARQL_1000_CONCEPT_TESTS,
+ NORMAL_1000_CONCEPT_TESTS,
+ SPARQL_10000_CONCEPT_TESTS,
+ NORMAL_10000_CONCEPT_TESTS};
//private static Class usedReasoner = FastInstanceChecker.class;
@@ -112,18 +131,29 @@
*/
public static void main(String[] args) {
SimpleClock total = new SimpleClock();
- Files.createFile(log, "");
+
initLogger();
logger.warn("Start");
+ prepareTable();
+ List<String> l = getFiles();
+ analyzeFiles(l);
+ for (Experiments exp : Experiments.values()) {
+ if(exp.equals(Experiments.SPARQL_10s))continue;
+ conductExperiment(exp);
+ System.exit(0);
+ }
+ //conductExperiment(0);
- conductExperiment(0);
-
-
+ // write JaMON report in HTML file
+ File jamonlog = new File(dir+"jamon.html");
+ Files.createFile(jamonlog, MonitorFactory.getReport());
+ Files.appendFile(jamonlog, "<xmp>\n"+JamonMonitorLogger.getStringForAllSortedByLabel());
total.printAndSet("Finished");
+ logger.warn(total.getAndSet("Finished"));
if(flawInExperiment){
logger.error("There were exceptions");
}
@@ -131,29 +161,40 @@
}
- public static void conductExperiment(int experiment){
+ public static void conductExperiment(Experiments exp){
try{
//prepare everything
List<String> confs = getFiles();
ComponentManager cm =ComponentManager.getInstance();
+ int count = 1;
for (String filename : confs) {
+ SimpleClock oneExperiment = new SimpleClock();
+ if (count == 6){break;}
+
+ logger.warn(exp+" "+count +" from file "+filename);
+
// read the file and get the examples
- File f = new File(filename);
+ File f = new File(exampleDir+filename);
Cache.getDefaultCache().clearCache();
String fileContent = Files.readFile(f);
SortedSet<Individual> posEx = SetManipulation.stringToInd(getIndividuals(fileContent, true));
SortedSet<Individual> negEx = SetManipulation.stringToInd(getIndividuals(fileContent, false));
- ExampleBasedROLComponent la = experimentalSetup1(posEx,negEx);
- //TODO measure time
+ ExampleBasedROLComponent la = experimentalSetup(exp,posEx,negEx);
+
+ //SimpleClock init = new SimpleClock();
initAllComponents();
+ //initializationTime.addNumber((double) init.getTime()/1000);
+
SimpleClock learningTimeClock = new SimpleClock();
la.start();
- learningTime.addNumber((double) learningTimeClock.getTime());
-
+ learningTime.addNumber((double) learningTimeClock.getTime()/1000);
+ logger.warn(learningTimeClock.getAndSet("learning time")+" in stat: "+learningTime.getMean());
+
+
EvaluatedDescription bestDescription =(la.getCurrentlyBestEvaluatedDescription());
accFragment.addNumber(bestDescription.getAccuracy());
@@ -173,6 +214,9 @@
EvaluatedDescription onOnto = reEvaluateDescription(
bestDescription.getDescription(), retrieved, posEx, negEx);
+ logger.warn(onOnto.getDescription().toManchesterSyntaxString(null, null));
+ logger.warn(onOnto.getAccuracy());
+
accOnOnto.addNumber(onOnto.getAccuracy());
//int tmp = (int)(Math.floor(onOnto.getAccuracy()*100));
@@ -188,15 +232,17 @@
}
if(s!=null){
double nrtrip = (double)(s.getNrOfExtractedAxioms());
- nrOfExtractedTriples.addNumber(nrtrip);
+ nrOfExtractedAxioms.addNumber(nrtrip);
}else{
- nrOfExtractedTriples.addNumber(0.0);
+ nrOfExtractedAxioms.addNumber(0.0);
}
cm.freeAllComponents();
+ fillTable(exp, count);
-
+ logger.warn(exp+" "+count+ " " +oneExperiment.getAndSet("") );
+ count++;
}//end for
}catch (Exception e) {
e.printStackTrace();
@@ -205,15 +251,57 @@
}
- public static ExampleBasedROLComponent experimentalSetup1(SortedSet<Individual> posExamples, SortedSet<Individual> negExamples ){
- ExampleBasedROLComponent la = prepareSparqlExperiment(posExamples, negExamples);
+ public static void analyzeFiles(List<String> l){
+ int countDoublettes = 0;
+ SortedSet<String> differentIndividuals = new TreeSet<String>();
+ for ( String file : l) {
+ ExampleContainer ec = new ExampleContainer(
+ SetManipulation.stringToInd(getIndividuals(file, true)),
+ SetManipulation.stringToInd(getIndividuals(file, false)));
+ differentIndividuals.addAll(getIndividuals(file, true));
+ differentIndividuals.addAll(getIndividuals(file, false));
+ if(!ExampleContainer.add(ec)){
+ countDoublettes++;
+ }
+ }
+ logger.warn("found diff inds "+differentIndividuals.size());
+ logger.warn("found doublettes " + countDoublettes);
+ }
+
+ public static ExampleBasedROLComponent experimentalSetup(Experiments exp,SortedSet<Individual> posExamples, SortedSet<Individual> negExamples ){
+ ExampleBasedROLComponent la = null;
+ if(exp.toString().contains("SPARQL"))
+ la = prepareSparqlExperiment(posExamples, negExamples);
+ else if(exp.toString().contains("NORMAL")){
+ la = prepareNormalExperiment(posExamples, negExamples);
+ }else {
+ logger.error("undefined EXPERIMENT" + exp);
+ System.exit(0);
+ }
+
+ ExampleBasedROLComponentConfigurator c = la.getConfigurator();
+
+ if(exp.toString().contains("10s")){
+ c.setMaxExecutionTimeInSeconds(10);
+ c.setMinExecutionTimeInSeconds(10);
+
+ }else if(exp.toString().contains("100s")){
+ c.setMaxExecutionTimeInSeconds(100);
+ c.setMinExecutionTimeInSeconds(100);
+
+ }else if(exp.toString().contains("1000_CONCEPT_TESTS")){
+ c.setMaxClassDescriptionTests(1000);
+ }else if(exp.toString().contains("10000_CONCEPT_TESTS")){
+ c.setMaxClassDescriptionTests(10000);
+ }
//la.getConfigurator();
//appendtoFile
return la;
}
+
public static ExampleBasedROLComponent prepareSparqlExperiment(SortedSet<Individual> posExamples, SortedSet<Individual> negExamples){
@@ -234,6 +322,7 @@
ks.getConfigurator().setUseLits(true);
ks.getConfigurator().setGetAllSuperClasses(true);
ks.getConfigurator().setGetPropertyInformation(true);
+ ks.getConfigurator().setVerbosity("warning");
Set<KnowledgeSource> tmp = new HashSet<KnowledgeSource>();
tmp.add(ks);
@@ -261,47 +350,136 @@
return la;
}
+ public static ExampleBasedROLComponent prepareNormalExperiment(SortedSet<Individual> posExamples, SortedSet<Individual> negExamples){
+ ExampleBasedROLComponent la = null;
+ try{
+ SortedSet<Individual> instances = new TreeSet<Individual>();
+ instances.addAll(posExamples);
+ instances.addAll(negExamples);
+
+ URL fileURL = null;
+ try {
+ fileURL = new File(ontologyPath).toURI().toURL();
+ } catch (MalformedURLException e) {
+ e.printStackTrace();
+ flawInExperiment = true;
+ }
+ OWLFile ks = ComponentFactory.getOWLFile( fileURL);
+
+ Set<KnowledgeSource> tmp = new HashSet<KnowledgeSource>();
+ tmp.add(ks);
+ // reasoner
+ OWLAPIReasoner f = ComponentFactory
+ .getOWLAPIReasoner(tmp);
+ ReasoningService rs = ComponentManager.getInstance()
+ .reasoningService(f);
+
+// learning problem
+ PosNegDefinitionLP lp = ComponentFactory.getPosNegDefinitionLP(rs,
+ SetManipulation.indToString(posExamples), SetManipulation
+ .indToString(negExamples));
+
+ // learning algorithm
+ la = ComponentFactory.getExampleBasedROLComponent(lp, rs);
+ la.getConfigurator().setGuaranteeXgoodDescriptions(1);
+ Config c = new Config(ComponentManager.getInstance(), ks, f, rs, lp, la);
+ new ConfigSave(c).saveFile(new File(tmpFilename));
+
+ }catch (Exception e) {
+ e.printStackTrace();
+ flawInExperiment = true;
+ }
+ return la;
+ }
+
public static void initAllComponents(){
ComponentManager cm = ComponentManager.getInstance();
+
for(Component c : cm.getLiveComponents()){
try{
+ SimpleClock time = new SimpleClock();
c.init();
+ if (c instanceof SparqlKnowledgeSource) {
+ ksinitializationTime.addNumber((double) time.getTime()/1000);
+
+ }else if (c instanceof OWLFile) {
+ ksinitializationTime.addNumber((double) time.getTime()/1000);
+
+ }else if (c instanceof OWLAPIReasoner) {
+ reasonerInitializationTime.addNumber((double) time.getTime()/1000);
+
+ }
+
}catch (Exception e) {
e.printStackTrace();
flawInExperiment = true;
}
}
+
}
- public static void writeLog(){
- String l = "\n\n\n*********************\n";
- l +="COUNT: "+accFragment.getCount()+"\n";
- l +="FRAGMENT: ALL: "+descHasAll+" BOOL: "+descHasBooleanData+" NOT: "+descHasNot+" <>=: "+descHasNrRes+"\n";
- l +="WHOLE: ALL: "+wholeHasAll+" BOOL: "+wholeHasBooleanData+" NOT: "+wholeHasNot+" <>=: "+wholeHasNrRes+"\n";
+ public static void prepareTable(){
+ t = new Table("sembib");
+ String[] labString = new String[]{
+ "count",
+ "accuracy on fragment(%)",
+ "accuracy on whole (%)",
+ "accuracy pos examples on whole (%)",
+ "accuracy neg examples on whole (%)",
+ "extraction/parsing time",
+ "reasoner initialization time",
+ "learning time",
+ "number of axioms",
+ "description length",
+ "description depth"
+ }; //9
+ TableColumn labels = new TableColumn("Semantic Bible",labString);
+ t.addColumn(labels);
+ Table.serializeColumns(t, tableDir, tableFile);
+ Files.createFile(new File(tableLatex), t.getLatexString());
-
- l+="accFragment\t\t"+accFragment.getMeanAsPercentage()+" +-"+accFragment.getStandardDeviation()+"\n";
- l+="accOnOnto\t\t"+accOnOnto.getMeanAsPercentage()+" +-"+accOnOnto.getStandardDeviation()+"\n";
- l+="accPosExOnOnto\t\t"+accPosExOnOnto.getMeanAsPercentage()+" +-"+accPosExOnOnto.getStandardDeviation()+"\n";
- l+="accNegExOnOnto\t\t"+accNegExOnOnto.getMeanAsPercentage()+" +-"+accNegExOnOnto.getStandardDeviation()+"\n";
- l+="timeFragment\t\t"+learningTime.getMean()+" +-"+learningTime.getStandardDeviation()+"\n";
- l+="nrOfExtractedTriples\t\t"+nrOfExtractedTriples.getMean()+" +-"+nrOfExtractedTriples.getStandardDeviation()+"\n";
- l+="dLengthFragment\t\t"+descLength.getMean()+" +-"+descLength.getStandardDeviation()+"\n";
- l+="dDepthFragment\t\t"+descDepth.getMean()+" +-"+descDepth.getStandardDeviation()+"\n";
+ }
+
+ public static void fillTable(Experiments exp, int count){
+ String[] columnString = new String[]{
+ count+"",
+ StringFormatter.convertStatPercentageToLatex(accFragment, 1, false, true),
+ StringFormatter.convertStatPercentageToLatex(accOnOnto, 1, false, true),
+ StringFormatter.convertStatPercentageToLatex(accPosExOnOnto, 1, false, true),
+ StringFormatter.convertStatPercentageToLatex(accNegExOnOnto, 1, false, true),
+ StringFormatter.convertStatDoubleToLatex(ksinitializationTime, 1, "", "s", true),
+ StringFormatter.convertStatDoubleToLatex(reasonerInitializationTime, 1, "", "s", true),
+ StringFormatter.convertStatDoubleToLatex(learningTime, 1, "", "s", true),
+ StringFormatter.convertStatDoubleToLatex(nrOfExtractedAxioms, 0, "", "", true),
+ StringFormatter.convertStatDoubleToLatex(descLength, 1, "", "", true),
+ StringFormatter.convertStatDoubleToLatex(descDepth, 1, "", "", true),
+ }; //9
+ t.removeColumn(exp.toString());
+ t.addColumn(new TableColumn(exp.toString(),columnString));
+ Table.serializeColumns(t, tableDir, tableFile);
+ Files.createFile(new File(tableLatex), t.getLatexString());
- l+="timeWhole\t\t"+timeWhole.getMean()+" +-"+timeWhole.getStandardDeviation()+"\n";
- l+="accWhole\t\t"+accWhole.getMeanAsPercentage()+" +-"+accWhole.getStandardDeviation()+"\n";
- l+="dLengthWhole\t\t"+dLengthWhole.getMean()+" +-"+dLengthWhole.getStandardDeviation()+"\n";
- l+="dDepthWhole\t\t"+dDepthWhole.getMean()+" +-"+dDepthWhole.getStandardDeviation()+"\n";
- Files.appendFile(log, l);
-
-// write JaMON report in HTML file
- File jamonlog = new File("sembib/jamon.html");
- Files.createFile(jamonlog, MonitorFactory.getReport());
- Files.appendFile(jamonlog, "<xmp>\n"+JamonMonitorLogger.getStringForAllSortedByLabel());
}
+
+
+ public static void reinitStat(){
+ accFragment = new Stat();
+ accOnOnto = new Stat();
+ accPosExOnOnto = new Stat();
+ accNegExOnOnto = new Stat();
+ ksinitializationTime = new Stat();
+ reasonerInitializationTime = new Stat();
+ learningTime = new Stat();
+ nrOfExtractedAxioms = new Stat();
+ descLength = new Stat();
+ descDepth = new Stat();
+ }
+
+
+
+
public static EvaluatedDescription reEvaluateDescription(Description d, SortedSet<Individual> retrieved ,SortedSet<Individual> posEx ,SortedSet<Individual> negEx ){
SortedSet<Individual> PosAsPos = new TreeSet<Individual>();
SortedSet<Individual> PosAsNeg = new TreeSet<Individual>();
@@ -452,17 +630,7 @@
return ret;
}*/
-/*public static void analyzeFiles(List<File> l){
-
- SortedSet<String> differentIndividuals = new TreeSet<String>();
- for ( content : l) {
- differentIndividuals.addAll(getIndividuals(content, true));
- differentIndividuals.addAll(getIndividuals(content, false));
-
- }
- System.out.println("found diff inds "+differentIndividuals.size());
-
-}*/
+
}
Modified: trunk/src/dl-learner/org/dllearner/utilities/StringFormatter.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/StringFormatter.java 2008-09-26 13:18:07 UTC (rev 1268)
+++ trunk/src/dl-learner/org/dllearner/utilities/StringFormatter.java 2008-09-26 15:07:32 UTC (rev 1269)
@@ -1,6 +1,11 @@
package org.dllearner.utilities;
+import java.io.File;
+import java.text.DecimalFormat;
+import org.dllearner.utilities.statistics.Stat;
+
+
public class StringFormatter {
@@ -10,16 +15,113 @@
* @param d
*/
public static String doubleToPercent(double d){
- if(d>1.0 || d<0.0)return "bad format: "+d;
- else if(d == 1.0){
- return "100.0%";
- }else if(d == 0.0 ){
- return "0.0%";
- }else {
- String acc = (d*100)+"";
- acc = acc.substring(0,"55.5".length());
- return acc+"%";
+ return doubleToPercent( d, 1, true);
+ }
+
+ public static String doubleToPercent(double d, int decimals){
+
+ return doubleToPercent( d, decimals, true);
+
+ }
+
+ public static String doubleToPercent(double d, int decimals, boolean addPercentSign){
+
+ String format = (decimals==0)?"00":".";
+ for (int i = 0; i < decimals; i++) {
+ format += "0";
+ }
+ format+="%";
+ DecimalFormat df = new DecimalFormat( format );
+ String ret = df.format(d);
+ ret = (addPercentSign)?ret:ret.replaceAll("%", "");
+ return ret;
+
+ }
+
+ public static String doubleRound(double d, int decimals, String before, String after){
+ String ret ="";
+ if(decimals==0){
+ int retInt = (int) Math.floor((d+0.5));
+ ret = retInt+"";
+ }else{
+ String format = ".";
+ for (int i = 0; i < decimals; i++) {
+ format += "0";
}
+
+ DecimalFormat df = new DecimalFormat( format );
+ ret = df.format(d);
+ ret = ret.replaceAll("%", "");
+ }
+ ret = before + ret+ after;
+ return ret;
}
+
+ public static String convertStatPercentageToLatex(Stat s,
+ int decimals,
+ boolean addPercentSign,
+ boolean includeSTDDeviation){
+ String ret ="";
+
+ ret = doubleToPercent(s.getMean(), decimals, addPercentSign);
+ ret = ret.replaceAll("%", "\\%");
+ if(includeSTDDeviation){
+ ret += " ($\\pm$"+doubleToPercent(s.getStandardDeviation(), decimals, false)+")";
+ }
+ return ret;
+ }
+
+ public static String convertStatDoubleToLatex(Stat s,
+ int decimals,
+ boolean includeSTDDeviation){
+ return convertStatDoubleToLatex(s, decimals,"","",includeSTDDeviation);
+ }
+
+
+ public static String convertStatDoubleToLatex(Stat s,
+ int decimals,
+ String before,
+ String after,
+ boolean includeSTDDeviation){
+ String ret ="";
+
+ ret = doubleRound(s.getMean(), decimals, before, after);
+
+ if(includeSTDDeviation){
+ ret += doubleRound(s.getStandardDeviation(), decimals," ($\\pm$", after+")" );
+ }
+ return ret;
+ }
+
+
+
+
+
+ public static void main(String[] args) {
+ double d = 0.55555;
+ System.out.println(doubleToPercent(d, 0));
+ System.out.println(doubleToPercent(d, 1));
+ System.out.println(doubleToPercent(d, 2));
+ System.out.println(doubleToPercent(d, 3));
+ System.out.println(doubleToPercent(d, 0, false));
+ System.out.println(doubleToPercent(d, 1, false));
+ System.out.println(doubleToPercent(d, 2, false));
+ System.out.println(doubleToPercent(d, 3, false));
+ d= 55.55555;
+ System.out.println(doubleRound(d, 0, "|", "|"));
+ System.out.println(doubleRound(d, 1, "|", "|"));
+ System.out.println(doubleRound(d, 2, "|", "|"));
+ System.out.println(doubleRound(d, 3, "|", "|"));
+
+ }
+
+ public static String checkIfDirEndsOnSlashAndRemove(String dir){
+ if(dir.endsWith(File.separator)){
+ dir=dir.substring(0,dir.length()-File.separator.length());
+ }
+ return dir;
+ }
+
+
}
Modified: trunk/src/dl-learner/org/dllearner/utilities/examples/ExampleContainer.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/examples/ExampleContainer.java 2008-09-26 13:18:07 UTC (rev 1268)
+++ trunk/src/dl-learner/org/dllearner/utilities/examples/ExampleContainer.java 2008-09-26 15:07:32 UTC (rev 1269)
@@ -51,6 +51,12 @@
}
+ /**
+ * adds to a global example repository.
+ * returns false, if the set is contained already
+ * @param e
+ * @return
+ */
public static boolean add(ExampleContainer e){
return exampleSets.add(e);
}
Modified: trunk/src/dl-learner/org/dllearner/utilities/statistics/SimpleClock.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/statistics/SimpleClock.java 2008-09-26 13:18:07 UTC (rev 1268)
+++ trunk/src/dl-learner/org/dllearner/utilities/statistics/SimpleClock.java 2008-09-26 15:07:32 UTC (rev 1269)
@@ -85,6 +85,10 @@
setTime();
}
+ /**
+ * returns the needed time up to now in ms
+ * @return
+ */
public long getTime() {
long now = System.currentTimeMillis();
return now - time;
Modified: trunk/src/dl-learner/org/dllearner/utilities/statistics/Table.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/statistics/Table.java 2008-09-26 13:18:07 UTC (rev 1268)
+++ trunk/src/dl-learner/org/dllearner/utilities/statistics/Table.java 2008-09-26 15:07:32 UTC (rev 1269)
@@ -26,6 +26,7 @@
import java.util.List;
import org.dllearner.utilities.Files;
+import org.dllearner.utilities.StringFormatter;
/**
@@ -117,7 +118,16 @@
else return columns.get(0).getSize();
}
+ public void removeColumn(String header){
+ for (int i = 0; i < columns.size(); i++) {
+ if(columns.get(i).getHeader().equals(header)){
+ columns.remove(i);
+ return;
+ }
+ }
+ }
+
public List<String> getColumnHeaders(){
List<String> entries = new ArrayList<String>();
for (TableColumn c : columns) {
@@ -169,6 +179,7 @@
public static void serializeColumns(Table t, String dir, String tableFile){
String column = "column";
String content = "";
+ dir = StringFormatter.checkIfDirEndsOnSlashAndRemove(dir);
Files.mkdir(dir);
try{
int i=0;
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <jen...@us...> - 2008-09-26 13:18:13
|
Revision: 1268
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=1268&view=rev
Author: jenslehmann
Date: 2008-09-26 13:18:07 +0000 (Fri, 26 Sep 2008)
Log Message:
-----------
added parameter to web service for starting it in non-interactive mode
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/server/DLLearnerWSStart.java
Modified: trunk/src/dl-learner/org/dllearner/server/DLLearnerWSStart.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/server/DLLearnerWSStart.java 2008-09-26 12:52:19 UTC (rev 1267)
+++ trunk/src/dl-learner/org/dllearner/server/DLLearnerWSStart.java 2008-09-26 13:18:07 UTC (rev 1268)
@@ -47,29 +47,45 @@
*/
public class DLLearnerWSStart {
+ /**
+ * DL-Learner web service startup method.
+ *
+ * @param args
+ * --non-interactive starts the web service in a mode, where
+ * it does not wait for user input, i.e. it cannot be terminated
+ * using exit. Use this in conjunction with nohup.
+ */
public static void main(String[] args) {
-
- //create web service logger
- SimpleLayout layout = new SimpleLayout();
+
+ // "interactive" means that the web service waits for the
+ // user to type "exit" and exit gracefully; it
+ // non-interactive mode, the web service is started and has
+ // to be terminated externally (e.g. killing its process);
+ // when using nohup, please use noninteractive mode
+ boolean interactive = true;
+ if (args.length > 0 && args[0].equals("--non-interactive")) {
+ interactive = false;
+ }
+
+ // create web service logger
+ SimpleLayout layout = new SimpleLayout();
ConsoleAppender consoleAppender = new ConsoleAppender(layout);
Logger logger = Logger.getRootLogger();
-
- FileAppender fileAppenderNormal = null;
- File f = new File("log/sparql.txt");
+
+ FileAppender fileAppenderNormal = null;
+ File f = new File("log/sparql.txt");
try {
- fileAppenderNormal = new FileAppender(layout, "log/log.txt", false);
- f.delete();
- f.createNewFile();
+ fileAppenderNormal = new FileAppender(layout, "log/log.txt", false);
+ f.delete();
+ f.createNewFile();
} catch (IOException e) {
e.printStackTrace();
}
-
-
+
logger.removeAllAppenders();
logger.addAppender(consoleAppender);
logger.addAppender(fileAppenderNormal);
logger.setLevel(Level.INFO);
-
InetSocketAddress isa = new InetSocketAddress("localhost", 8181);
HttpServer server = null;
@@ -92,30 +108,32 @@
System.out.println("OK.");
- System.out.println("Type \"exit\" to terminate web service.");
- boolean terminate = false;
- String inputString = "";
- do {
- BufferedReader input = new BufferedReader(new InputStreamReader(System.in));
+ if(interactive) {
+ System.out.println("Type \"exit\" to terminate web service.");
+ boolean terminate = false;
+ String inputString = "";
+ do {
+ BufferedReader input = new BufferedReader(new InputStreamReader(System.in));
+
+ try {
+ inputString = input.readLine();
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+
+ if (inputString.equals("exit"))
+ terminate = true;
+
+ } while (!terminate);
+
+ System.out.print("Stopping web service ... ");
+ endpoint.stop();
+
+ server.stop(1);
+ threads.shutdown();
+ System.out.println("OK.");
+ }
- try {
- inputString = input.readLine();
- } catch (IOException e) {
- e.printStackTrace();
- }
-
- if (inputString.equals("exit"))
- terminate = true;
-
- } while (!terminate);
-
- System.out.print("Stopping web service ... ");
- endpoint.stop();
-
- server.stop(1);
- threads.shutdown();
- System.out.println("OK.");
-
}
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <sk...@us...> - 2008-09-26 12:52:35
|
Revision: 1267
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=1267&view=rev
Author: sknappe
Date: 2008-09-26 12:52:19 +0000 (Fri, 26 Sep 2008)
Log Message:
-----------
Added Paths:
-----------
trunk/src/dbpedia-navigator/Settings.php.dist
Removed Paths:
-------------
trunk/src/dbpedia-navigator/Settings.php
Deleted: trunk/src/dbpedia-navigator/Settings.php
===================================================================
--- trunk/src/dbpedia-navigator/Settings.php 2008-09-26 12:22:02 UTC (rev 1266)
+++ trunk/src/dbpedia-navigator/Settings.php 2008-09-26 12:52:19 UTC (rev 1267)
@@ -1,69 +0,0 @@
-<?php
-/**
- * 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/>.
- *
- */
-
-/**
- * DBpedia navigator settings.
- *
- * @author Sebastian Knappe
- * @author Jens Lehmann
- */
-class Settings{
-
- public $wsdluri='http://localhost:8181/services?wsdl';
-
- // local OpenLink SPARQL endpoint
- // public $dbpediauri="http://localhost:8890/sparql";
- // public DBpedia SPARQL endpoint
- public $dbpediauri='http://dbpedia.openlinksw.com:8890/sparql';
- // public DBpedia mirror
- // public $dbpediauri='http://dbpedia2.openlinksw.com:8890/isparql';
-
- //which predefined Endpoint to use
- public $endpoint="DBPEDIA";
- //public $endpoint="LOCALDBPEDIA";
-
-
- // in mikrosekunden
- public $sparqlttl=60000000;
- public $learnttl=5;
-
- public $language="en";
-
- //localhost
- public $googleMapsKey="ABQIAAAAWwHG9WuZ8hxFSPjRX2-D-hSOxlJeL3USfakgDtFzmQkGhQTW0xTFM1Yr38ho8qREnjt-6oLs37o4xg";
- //db.aksw.org
- //public $googleMapsKey="ABQIAAAAWwHG9WuZ8hxFSPjRX2-D-hRHWRcfpxRnIG10qrJMLnZO-_MKjRRpu2rZj8etMweqJES04ZL_eht1iQ";
-
- public $useCache=true;
-
- //the type of database server
- public $database_type='mysql';
- //the server, where the mysql databank is located
- public $database_server='localhost';
- //the user, that has rights to access the navigator databank
- public $database_user='navigator';
- //the password of that user
- public $database_pass='dbpedia';
- //the name of the used database
- public $database_name='navigator_db';
-}
-
-?>
\ No newline at end of file
Added: trunk/src/dbpedia-navigator/Settings.php.dist
===================================================================
--- trunk/src/dbpedia-navigator/Settings.php.dist (rev 0)
+++ trunk/src/dbpedia-navigator/Settings.php.dist 2008-09-26 12:52:19 UTC (rev 1267)
@@ -0,0 +1,69 @@
+<?php
+/**
+ * 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/>.
+ *
+ */
+
+/**
+ * DBpedia navigator settings.
+ *
+ * @author Sebastian Knappe
+ * @author Jens Lehmann
+ */
+class Settings{
+
+ public $wsdluri='http://localhost:8181/services?wsdl';
+
+ // local OpenLink SPARQL endpoint
+ // public $dbpediauri="http://localhost:8890/sparql";
+ // public DBpedia SPARQL endpoint
+ public $dbpediauri='http://dbpedia.openlinksw.com:8890/sparql';
+ // public DBpedia mirror
+ // public $dbpediauri='http://dbpedia2.openlinksw.com:8890/isparql';
+
+ //which predefined Endpoint to use
+ public $endpoint="DBPEDIA";
+ //public $endpoint="LOCALDBPEDIA";
+
+
+ // in mikrosekunden
+ public $sparqlttl=60000000;
+ public $learnttl=5;
+
+ public $language="en";
+
+ //localhost
+ public $googleMapsKey="ABQIAAAAWwHG9WuZ8hxFSPjRX2-D-hSOxlJeL3USfakgDtFzmQkGhQTW0xTFM1Yr38ho8qREnjt-6oLs37o4xg";
+ //db.aksw.org
+ //public $googleMapsKey="ABQIAAAAWwHG9WuZ8hxFSPjRX2-D-hRHWRcfpxRnIG10qrJMLnZO-_MKjRRpu2rZj8etMweqJES04ZL_eht1iQ";
+
+ public $useCache=true;
+
+ //the type of database server
+ public $database_type='mysql';
+ //the server, where the mysql databank is located
+ public $database_server='localhost';
+ //the user, that has rights to access the navigator databank
+ public $database_user='navigator';
+ //the password of that user
+ public $database_pass='dbpedia';
+ //the name of the used database
+ public $database_name='navigator_db';
+}
+
+?>
\ No newline at end of file
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|
|
From: <sk...@us...> - 2008-09-26 12:22:21
|
Revision: 1266
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=1266&view=rev
Author: sknappe
Date: 2008-09-26 12:22:02 +0000 (Fri, 26 Sep 2008)
Log Message:
-----------
you can choose which predefined endpoint to use
Modified Paths:
--------------
trunk/src/dbpedia-navigator/DLLearnerConnection.php
trunk/src/dbpedia-navigator/Settings.php
Modified: trunk/src/dbpedia-navigator/DLLearnerConnection.php
===================================================================
--- trunk/src/dbpedia-navigator/DLLearnerConnection.php 2008-09-26 11:24:05 UTC (rev 1265)
+++ trunk/src/dbpedia-navigator/DLLearnerConnection.php 2008-09-26 12:22:02 UTC (rev 1266)
@@ -14,6 +14,7 @@
private $lang;
//
private $client;
+ private $endpoint;
// ID given to this client by the web service
private $id;
@@ -30,6 +31,7 @@
$this->learnttl=$settings->learnttl;
$this->lang=$settings->language;
$this->DBPediaUrl=$settings->dbpediauri;
+ $this->endpoint=$settings->endpoint;
$this->client=new SoapClient("main.wsdl",array('features' => SOAP_SINGLE_ELEMENT_ARRAYS));
$this->id=$id;
$this->ksID=$ksID;
@@ -49,7 +51,7 @@
$this->client->applyConfigEntryInt($this->id, $this->ksID, "recursionDepth",1);
$this->client->applyConfigEntryString($this->id, $this->ksID, "predefinedFilter", "DBPEDIA-NAVIGATOR");
- $this->client->applyConfigEntryString($this->id, $this->ksID, "predefinedEndpoint", "DBPEDIA");
+ $this->client->applyConfigEntryString($this->id, $this->ksID, "predefinedEndpoint", $this->endpoint);
$this->client->applyConfigEntryString($this->id, $this->ksID, "predefinedManipulator", "DBPEDIA-NAVIGATOR");
$this->client->applyConfigEntryBoolean($this->id, $this->ksID, "useCache", $settings->useCache);
if(empty($negExamples)){
Modified: trunk/src/dbpedia-navigator/Settings.php
===================================================================
--- trunk/src/dbpedia-navigator/Settings.php 2008-09-26 11:24:05 UTC (rev 1265)
+++ trunk/src/dbpedia-navigator/Settings.php 2008-09-26 12:22:02 UTC (rev 1266)
@@ -34,7 +34,13 @@
// public DBpedia SPARQL endpoint
public $dbpediauri='http://dbpedia.openlinksw.com:8890/sparql';
// public DBpedia mirror
- // public $dbpediauri='http://dbpedia2.openlinksw.com:8890/isparql';
+ // public $dbpediauri='http://dbpedia2.openlinksw.com:8890/isparql';
+
+ //which predefined Endpoint to use
+ public $endpoint="DBPEDIA";
+ //public $endpoint="LOCALDBPEDIA";
+
+
// in mikrosekunden
public $sparqlttl=60000000;
public $learnttl=5;
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|
|
From: <jen...@us...> - 2008-09-26 11:24:21
|
Revision: 1265
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=1265&view=rev
Author: jenslehmann
Date: 2008-09-26 11:24:05 +0000 (Fri, 26 Sep 2008)
Log Message:
-----------
replaced legacy package.html with package-info.java
Added Paths:
-----------
trunk/src/dl-learner/org/dllearner/utilities/package-info.java
Removed Paths:
-------------
trunk/src/dl-learner/org/dllearner/utilities/package.html
Added: trunk/src/dl-learner/org/dllearner/utilities/package-info.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/package-info.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/utilities/package-info.java 2008-09-26 11:24:05 UTC (rev 1265)
@@ -0,0 +1,4 @@
+/**
+ * Utility classes.
+ */
+package org.dllearner.utilities;
\ No newline at end of file
Deleted: trunk/src/dl-learner/org/dllearner/utilities/package.html
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/package.html 2008-09-26 10:44:22 UTC (rev 1264)
+++ trunk/src/dl-learner/org/dllearner/utilities/package.html 2008-09-26 11:24:05 UTC (rev 1265)
@@ -1,7 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
-<html>
-<head></head>
-<body bgcolor="white">
-<p>Utility Classes.</p>
-</body>
-</html>
\ No newline at end of file
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|
|
From: <sk...@us...> - 2008-09-26 10:44:33
|
Revision: 1264
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=1264&view=rev
Author: sknappe
Date: 2008-09-26 10:44:22 +0000 (Fri, 26 Sep 2008)
Log Message:
-----------
new wsdl
Modified Paths:
--------------
trunk/src/dbpedia-navigator/main.wsdl
Modified: trunk/src/dbpedia-navigator/main.wsdl
===================================================================
--- trunk/src/dbpedia-navigator/main.wsdl 2008-09-26 10:27:24 UTC (rev 1263)
+++ trunk/src/dbpedia-navigator/main.wsdl 2008-09-26 10:44:22 UTC (rev 1264)
@@ -130,6 +130,15 @@
<message name="getCurrentlyBestConceptsResponse">
<part xmlns:ns6="http://jaxb.dev.java.net/array" name="return" type="ns6:stringArray"></part>
</message>
+ <message name="getCurrentlyBestEvaluatedDescriptionsFiltered">
+ <part name="arg0" type="xsd:int"></part>
+ <part name="arg1" type="xsd:int"></part>
+ <part name="arg2" type="xsd:double"></part>
+ <part name="arg3" type="xsd:boolean"></part>
+ </message>
+ <message name="getCurrentlyBestEvaluatedDescriptionsFilteredResponse">
+ <part name="return" type="xsd:string"></part>
+ </message>
<message name="isAlgorithmRunning">
<part name="arg0" type="xsd:int"></part>
</message>
@@ -340,6 +349,7 @@
</message>
<message name="SparqlRetrieval">
<part name="arg0" type="xsd:string"></part>
+ <part name="arg1" type="xsd:int"></part>
</message>
<message name="SparqlRetrievalResponse">
<part name="return" type="xsd:string"></part>
@@ -474,6 +484,11 @@
<output message="tns:getCurrentlyBestConceptsResponse"></output>
<fault message="tns:ClientNotKnownException" name="ClientNotKnownException"></fault>
</operation>
+ <operation name="getCurrentlyBestEvaluatedDescriptionsFiltered" parameterOrder="arg0 arg1 arg2 arg3">
+ <input message="tns:getCurrentlyBestEvaluatedDescriptionsFiltered"></input>
+ <output message="tns:getCurrentlyBestEvaluatedDescriptionsFilteredResponse"></output>
+ <fault message="tns:ClientNotKnownException" name="ClientNotKnownException"></fault>
+ </operation>
<operation name="isAlgorithmRunning" parameterOrder="arg0">
<input message="tns:isAlgorithmRunning"></input>
<output message="tns:isAlgorithmRunningResponse"></output>
@@ -640,7 +655,7 @@
<output message="tns:getConceptArityResponse"></output>
<fault message="tns:ClientNotKnownException" name="ClientNotKnownException"></fault>
</operation>
- <operation name="SparqlRetrieval" parameterOrder="arg0">
+ <operation name="SparqlRetrieval" parameterOrder="arg0 arg1">
<input message="tns:SparqlRetrieval"></input>
<output message="tns:SparqlRetrievalResponse"></output>
<fault message="tns:ParseException" name="ParseException"></fault>
@@ -909,6 +924,18 @@
<soap:fault name="ClientNotKnownException" use="literal"></soap:fault>
</fault>
</operation>
+ <operation name="getCurrentlyBestEvaluatedDescriptionsFiltered">
+ <soap:operation soapAction=""></soap:operation>
+ <input>
+ <soap:body use="literal" namespace="http://server.dllearner.org/"></soap:body>
+ </input>
+ <output>
+ <soap:body use="literal" namespace="http://server.dllearner.org/"></soap:body>
+ </output>
+ <fault name="ClientNotKnownException">
+ <soap:fault name="ClientNotKnownException" use="literal"></soap:fault>
+ </fault>
+ </operation>
<operation name="isAlgorithmRunning">
<soap:operation soapAction=""></soap:operation>
<input>
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|
|
From: <jen...@us...> - 2008-09-26 10:27:36
|
Revision: 1263
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=1263&view=rev
Author: jenslehmann
Date: 2008-09-26 10:27:24 +0000 (Fri, 26 Sep 2008)
Log Message:
-----------
preparations for computing simulations
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/algorithms/el/ELDescriptionNode.java
trunk/src/dl-learner/org/dllearner/algorithms/el/ELDescriptionTree.java
trunk/src/dl-learner/org/dllearner/kb/manipulator/DBpediaNavigatorFilterRule.java
trunk/src/dl-learner/org/dllearner/refinementoperators/ELDown.java
trunk/src/dl-learner/org/dllearner/test/junit/ELDescriptionTreeTests.java
trunk/src/dl-learner/org/dllearner/test/junit/ELDownTests.java
Modified: trunk/src/dl-learner/org/dllearner/algorithms/el/ELDescriptionNode.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/el/ELDescriptionNode.java 2008-09-26 08:42:12 UTC (rev 1262)
+++ trunk/src/dl-learner/org/dllearner/algorithms/el/ELDescriptionNode.java 2008-09-26 10:27:24 UTC (rev 1263)
@@ -20,18 +20,22 @@
package org.dllearner.algorithms.el;
import java.util.ArrayList;
+import java.util.HashSet;
import java.util.LinkedList;
import java.util.List;
import java.util.NavigableSet;
+import java.util.Set;
import java.util.SortedSet;
import java.util.TreeSet;
+import org.dllearner.core.ReasoningService;
import org.dllearner.core.owl.Description;
import org.dllearner.core.owl.Intersection;
import org.dllearner.core.owl.NamedClass;
import org.dllearner.core.owl.ObjectProperty;
import org.dllearner.core.owl.ObjectSomeRestriction;
import org.dllearner.core.owl.Thing;
+import org.dllearner.utilities.Helper;
/**
* Represents an EL description tree, which corresponds to a
@@ -66,12 +70,12 @@
private ELDescriptionNode parent = null;
// simulation information (list or set?)
- protected List<ELDescriptionNode> in = new ArrayList<ELDescriptionNode>();
- private List<ELDescriptionNode> inSC1 = new ArrayList<ELDescriptionNode>();
- private List<ELDescriptionNode> inSC2 = new ArrayList<ELDescriptionNode>();
- protected List<ELDescriptionNode> out = new ArrayList<ELDescriptionNode>();
- private List<ELDescriptionNode> outSC1 = new ArrayList<ELDescriptionNode>();
- private List<ELDescriptionNode> outSC2 = new ArrayList<ELDescriptionNode>();
+ protected Set<ELDescriptionNode> in = new HashSet<ELDescriptionNode>();
+ private Set<ELDescriptionNode> inSC1 = new HashSet<ELDescriptionNode>();
+ private Set<ELDescriptionNode> inSC2 = new HashSet<ELDescriptionNode>();
+ protected Set<ELDescriptionNode> out = new HashSet<ELDescriptionNode>();
+ private Set<ELDescriptionNode> outSC1 = new HashSet<ELDescriptionNode>();
+ private Set<ELDescriptionNode> outSC2 = new HashSet<ELDescriptionNode>();
/**
* Constructs an EL description tree with empty root label.
@@ -92,6 +96,9 @@
parent = null;
// this is the root node of the overall tree
tree.rootNode = this;
+ tree.addNodeToLevel(this, level);
+
+ // TODO simulation update
}
public ELDescriptionNode(ELDescriptionNode parentNode, ObjectProperty parentProperty, NavigableSet<NamedClass> label) {
@@ -107,6 +114,8 @@
parent.edges.add(edge);
// we need to update the set of nodes on a particular level
tree.addNodeToLevel(this, level);
+
+ // TODO simulation update
}
/**
@@ -240,14 +249,102 @@
public void replaceInLabel(NamedClass oldClass, NamedClass newClass) {
label.remove(oldClass);
label.add(newClass);
+
+ // simulation update
+
+
+ Set<ELDescriptionNode> nodes = tree.getNodesOnLevel(level);
+ Set<ELDescriptionNode> tmp = Helper.difference(nodes, in);
+ for(ELDescriptionNode node : tmp) {
+ if(isSublabel(label, node.label)) {
+ // TODO continue later
+ }
+ }
+
}
+ // SC satisfied if both SC1 and SC2 satisfied
+ private boolean checkSC(ELDescriptionNode node1, ELDescriptionNode node2) {
+ return checkSC1(node1, node2) && checkSC2(node1, node2);
+ }
+
+ // tests simulation condition 1 (SC1)
+ private boolean checkSC1(ELDescriptionNode node1, ELDescriptionNode node2) {
+ return isSublabel(node1.label, node2.label);
+ }
+
+ private boolean isSublabel(NavigableSet<NamedClass> subLabel, NavigableSet<NamedClass> superLabel) {
+ // implemented according to definition in article
+ // (TODO can probably be done more efficiently)
+ for(NamedClass nc : superLabel) {
+ if(!containsSubclass(nc, subLabel)) {
+ return false;
+ }
+ }
+ return true;
+ }
+
+ private boolean containsSubclass(NamedClass superClass, NavigableSet<NamedClass> label) {
+ for(NamedClass nc : label) {
+ if(tree.subsumptionHierarchy.isSubclassOf(nc, superClass)) {
+ return true;
+ }
+ }
+ return false;
+ }
+
+ // tests simulation condition 2 (SC2)
+ private boolean checkSC2(ELDescriptionNode node1, ELDescriptionNode node2) {
+ List<ELDescriptionEdge> edges1 = node1.getEdges();
+ List<ELDescriptionEdge> edges2 = node2.getEdges();
+
+ for(ELDescriptionEdge edge : edges1) {
+ // try to find an edge satisfying SC2 in the set
+ if(!checkSC2Edge(edge, edges2)) {
+ return false;
+ }
+ }
+
+ return true;
+ }
+
+ // check whether edges contains an element satisfying SC2
+ private boolean checkSC2Edge(ELDescriptionEdge edge, List<ELDescriptionEdge> edges) {
+ ObjectProperty op1 = edge.getLabel();
+ ELDescriptionNode node1 = edge.getTree();
+
+ for(ELDescriptionEdge edge2 : edges) {
+ ObjectProperty op2 = edge2.getLabel();
+ // we first check the condition on the properties
+ if(tree.roleHierarchy.isSubpropertyOf(op1, op2)) {
+ // check condition on simulations of referred nodes
+ ELDescriptionNode node2 = edge2.getTree();
+ if(node1.in.contains(node2) || node2.in.contains(node1)) {
+ // we found a node satisfying the condition, so we can return
+ return true;
+ }
+ }
+ }
+
+ // none of the edges in the set satisfies the 2nd simulation criterion
+ // wrt. the first edge
+ return false;
+ }
+
+ // adds (node1,node2) to simulation, takes care of all helper sets
+ private void extendSimulation(ELDescriptionNode node1, ELDescriptionNode node2) {
+ node1.out.add(node2);
+ node2.in.add(node1);
+ }
+
/**
* Adds an entry to the node label.
* @param newClass Class to add to label.
*/
public void extendLabel(NamedClass newClass) {
label.add(newClass);
+
+ // TODO simulation update
}
/**
Modified: trunk/src/dl-learner/org/dllearner/algorithms/el/ELDescriptionTree.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/el/ELDescriptionTree.java 2008-09-26 08:42:12 UTC (rev 1262)
+++ trunk/src/dl-learner/org/dllearner/algorithms/el/ELDescriptionTree.java 2008-09-26 10:27:24 UTC (rev 1263)
@@ -31,7 +31,9 @@
import org.dllearner.core.owl.Intersection;
import org.dllearner.core.owl.NamedClass;
import org.dllearner.core.owl.ObjectProperty;
+import org.dllearner.core.owl.ObjectPropertyHierarchy;
import org.dllearner.core.owl.ObjectSomeRestriction;
+import org.dllearner.core.owl.SubsumptionHierarchy;
import org.dllearner.core.owl.Thing;
import org.dllearner.core.owl.UnsupportedLanguageException;
@@ -49,14 +51,25 @@
// attach a simulation relation to the description tree
// private Simulation simulation;
- private int maxLevel = 1;
+ // max level = 0 means that there is no tree at all
+ // (max level = 1 means the root node exists)
+ private int maxLevel = 0;
protected ELDescriptionNode rootNode;
private Map<Integer, Set<ELDescriptionNode>> levelNodeMapping = new HashMap<Integer, Set<ELDescriptionNode>>();
- public ELDescriptionTree() {
-
+ // the background knowledge (we need to have it explicitly here,
+ // since we store simulation information in the tree and simulation
+ // updates depend on background knowledge)
+ protected ReasoningService rs;
+ protected SubsumptionHierarchy subsumptionHierarchy;
+ protected ObjectPropertyHierarchy roleHierarchy;
+
+ public ELDescriptionTree(ReasoningService rs) {
+ this.rs = rs;
+ subsumptionHierarchy = rs.getSubsumptionHierarchy();
+ roleHierarchy = rs.getRoleHierarchy();
}
/**
@@ -65,7 +78,8 @@
* @param description
* A description
*/
- public ELDescriptionTree(Description description) {
+ public ELDescriptionTree(ReasoningService rs, Description description) {
+ this(rs);
// construct root node and recursively build the tree
rootNode = new ELDescriptionNode(this);
constructTree(description, rootNode);
@@ -117,11 +131,14 @@
}
// checks whether this tree is minimal wrt. background knowledge
- public boolean isMinimal(ReasoningService rs) {
+ public boolean isMinimal() {
+// System.out.println(this);
+// System.out.println(levelNodeMapping);
// loop through all levels starting from root (level 1)
for(int i=1; i<=maxLevel; i++) {
// get all nodes of this level
Set<ELDescriptionNode> nodes = levelNodeMapping.get(i);
+// System.out.println("level " + i + ": " + nodes);
for(ELDescriptionNode node : nodes) {
List<ELDescriptionEdge> edges = node.getEdges();
// we need to compare all combination of edges
@@ -207,7 +224,7 @@
@Override
public ELDescriptionTree clone() {
// create a new reference tree
- ELDescriptionTree treeClone = new ELDescriptionTree();
+ ELDescriptionTree treeClone = new ELDescriptionTree(rs);
// create a root node attached to this reference tree
ELDescriptionNode rootNodeClone = new ELDescriptionNode(treeClone, new TreeSet<NamedClass>(
rootNode.getLabel()));
Modified: trunk/src/dl-learner/org/dllearner/kb/manipulator/DBpediaNavigatorFilterRule.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/manipulator/DBpediaNavigatorFilterRule.java 2008-09-26 08:42:12 UTC (rev 1262)
+++ trunk/src/dl-learner/org/dllearner/kb/manipulator/DBpediaNavigatorFilterRule.java 2008-09-26 10:27:24 UTC (rev 1263)
@@ -27,11 +27,7 @@
import org.dllearner.utilities.datastructures.RDFNodeTuple;
import org.dllearner.utilities.owl.OWLVocabulary;
-import com.hp.hpl.jena.rdf.model.Literal;
-import com.hp.hpl.jena.rdf.model.RDFNode;
-import com.hp.hpl.jena.rdf.model.impl.ResourceImpl;
-
public class DBpediaNavigatorFilterRule extends Rule{
@@ -42,13 +38,13 @@
@Override
public SortedSet<RDFNodeTuple> applyRule(Node subject, SortedSet<RDFNodeTuple> tuples){
- RDFNode clazz = null;
+// RDFNode clazz = null;
RDFNodeTuple typeTuple = null;
List<RDFNodeTuple> toRemove=new LinkedList<RDFNodeTuple>();
for (RDFNodeTuple tuple : tuples) {
if (tuple.a.toString().equals(OWLVocabulary.RDF_TYPE)){
- clazz = tuple.b;
+// clazz = tuple.b;
typeTuple = tuple;
}
Modified: trunk/src/dl-learner/org/dllearner/refinementoperators/ELDown.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/refinementoperators/ELDown.java 2008-09-26 08:42:12 UTC (rev 1262)
+++ trunk/src/dl-learner/org/dllearner/refinementoperators/ELDown.java 2008-09-26 10:27:24 UTC (rev 1263)
@@ -21,6 +21,7 @@
import java.util.Collection;
import java.util.HashSet;
+import java.util.Iterator;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
@@ -103,9 +104,7 @@
*/
@Override
public Set<Description> refine(Description concept) {
- // TODO according to the specification, we need to minimise
- // the tree (not yet implemented)
- ELDescriptionTree tree = new ELDescriptionTree(concept);
+ ELDescriptionTree tree = new ELDescriptionTree(rs, concept);
Set<ELDescriptionTree> refinementTrees = refine(tree);
// System.out.println("Refinements finished.");
Set<Description> refinements = new HashSet<Description>();
@@ -171,7 +170,6 @@
}
// option 3: new edge
- // TODO incomplete, it is still open how to construct this refinement !!
SortedSet<ObjectProperty> appOPs = utility.computeApplicableObjectProperties(index);
Set<ObjectProperty> mgr = utility.computeMgr(appOPs);
// temporary set of all concepts, which still have to pass the equivalence check
@@ -182,25 +180,34 @@
ELDescriptionNode clonedNode = clonedTree.getNode(position);
// add a new node and edge
ELDescriptionNode newNode = new ELDescriptionNode(clonedNode, op, new TreeSet<NamedClass>());
-// refinements.add(clonedTree);
stack.add(clonedTree);
// recurse if concept is equivalent
- // TODO: efficient equivalence check needs to be implemented !!
while(stack.size() != 0) {
// we pick an arbitrary tree and remove it from the stack
ELDescriptionTree testTree = stack.pop();
- // test equivalence
- boolean equivalent = false;
- // TODO equivalence check
+ // test equivalence (we found out that we can use the
+ // minimality test for equivalence in this case)
+ boolean equivalent = !testTree.isMinimal();
+ // if the tree is equivalent, we need to populate the
+ // stack with refinements (which are later tested for
+ // equivalence)
if(equivalent) {
// edge refinement
// we know that the edge we added is the last one for this node
int edgeNr = node.getEdges().size() - 1;
+ ELDescriptionEdge edge = node.getEdges().get(edgeNr);
// all refinements of this edge are added to the stack
+ // (set 1 in article)
refineEdge(stack, tree, node, position, edgeNr);
// perform node refinements in non-minimize-mode
- refinements.addAll(refineEdges(tree, newNode, position));
+ // (set 2 in article)
+// commented out, because didn't make sense to me
+// refinements.addAll(refineEdges(tree, newNode, position));
+ stack.addAll(refine(tree, newNode, opRanges.get(edge), false));
+ } else {
+ // tree is not equivalent, i.e. a proper refinement
+ refinements.add(testTree);
}
}
}
@@ -216,6 +223,17 @@
refinements.addAll(refine(tree, edge.getTree(), range, minimize));
}
+ // we found out that, in case we start from the TOP concept
+ // (which is assumed in the current implementation), we can
+ // simply throw away all non-minimal concepts
+ if(minimize) {
+ Iterator<ELDescriptionTree> it = refinements.iterator();
+ while(it.hasNext()) {
+ if(!it.next().isMinimal()) {
+ it.remove();
+ }
+ }
+ }
return refinements;
}
@@ -233,18 +251,17 @@
ObjectProperty op = edge.getLabel();
// find all more special properties
for(ObjectProperty op2 : rs.getMoreSpecialRoles(op)) {
- // TODO we need to check whether the range of this property is disjoint
- // with the current child node;
- // not implemented, because disjointness checks can only be done on descriptions
-
// we check whether the range of this property is not disjoint
- // with the existing child node
+ // with the existing child node (we do not perform a full disjointness
+ // check, but only compare with the flattened concept to keep the number
+ // of possible disjointness checks finite)
if(!utility.isDisjoint(getFlattenedConcept(edge.getTree()), opRanges.get(op2))) {
// clone operation
ELDescriptionTree clonedTree = tree.clone();
// find cloned edge and replace its label
ELDescriptionEdge clonedEdge = clonedTree.getNode(position).getEdges().get(edgeNumber);
clonedEdge.setLabel(op2);
+ // TODO simulation update
refinements.add(clonedTree);
}
Modified: trunk/src/dl-learner/org/dllearner/test/junit/ELDescriptionTreeTests.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/test/junit/ELDescriptionTreeTests.java 2008-09-26 08:42:12 UTC (rev 1262)
+++ trunk/src/dl-learner/org/dllearner/test/junit/ELDescriptionTreeTests.java 2008-09-26 10:27:24 UTC (rev 1263)
@@ -48,8 +48,9 @@
@Test
public void simulationTest() {
Simulation s = new Simulation();
- ELDescriptionTree tree1 = new ELDescriptionTree();
- ELDescriptionTree tree2 = new ELDescriptionTree();
+ // TODO we need to add background knowledge (possibly empty)
+ ELDescriptionTree tree1 = null; // new ELDescriptionTree();
+ ELDescriptionTree tree2 = null; // new ELDescriptionTree();
ELDescriptionNode t1 = new ELDescriptionNode(tree1);
ELDescriptionNode t2 = new ELDescriptionNode(tree2);
TreeTuple tuple1 = new TreeTuple(t1,t2);
@@ -67,7 +68,8 @@
public void cloneTest() throws ParseException {
Description d = KBParser.parseConcept("(male AND (human AND EXISTS hasChild.(female AND EXISTS hasChild.male)))");
ConceptTransformation.cleanConcept(d);
- ELDescriptionTree tree = new ELDescriptionTree(d);
+ // TODO needs to be updated (trees now require background knowledge)
+ ELDescriptionTree tree = null; // new ELDescriptionTree(rs, d);
ELDescriptionTree treeCloned = tree.clone();
ELDescriptionTreeComparator comparator = new ELDescriptionTreeComparator();
assertTrue(comparator.compare(tree, treeCloned) == 0);
Modified: trunk/src/dl-learner/org/dllearner/test/junit/ELDownTests.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/test/junit/ELDownTests.java 2008-09-26 08:42:12 UTC (rev 1262)
+++ trunk/src/dl-learner/org/dllearner/test/junit/ELDownTests.java 2008-09-26 10:27:24 UTC (rev 1263)
@@ -121,7 +121,7 @@
// assertTrue(refinements.size() == desired.size());
for(Description refinement : refinements) {
System.out.println(refinement);
-// assertTrue(desired.contains(refinement));
+ assertTrue(desired.contains(refinement));
}
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <jen...@us...> - 2008-09-26 08:42:18
|
Revision: 1262
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=1262&view=rev
Author: jenslehmann
Date: 2008-09-26 08:42:12 +0000 (Fri, 26 Sep 2008)
Log Message:
-----------
- implemented flat disjointness test in EL edge refinement
- implemented minimality test (assuming a simulation relation exists) for EL description trees
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/algorithms/el/ELDescriptionNode.java
trunk/src/dl-learner/org/dllearner/algorithms/el/ELDescriptionTree.java
trunk/src/dl-learner/org/dllearner/core/owl/ObjectPropertyHierarchy.java
trunk/src/dl-learner/org/dllearner/kb/KBFile.java
trunk/src/dl-learner/org/dllearner/refinementoperators/ELDown.java
trunk/src/dl-learner/org/dllearner/refinementoperators/Utility.java
trunk/src/dl-learner/org/dllearner/test/junit/ELDownTests.java
trunk/src/dl-learner/org/dllearner/test/junit/ExampleTests.java
Modified: trunk/src/dl-learner/org/dllearner/algorithms/el/ELDescriptionNode.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/el/ELDescriptionNode.java 2008-09-25 20:56:47 UTC (rev 1261)
+++ trunk/src/dl-learner/org/dllearner/algorithms/el/ELDescriptionNode.java 2008-09-26 08:42:12 UTC (rev 1262)
@@ -66,10 +66,10 @@
private ELDescriptionNode parent = null;
// simulation information (list or set?)
- private List<ELDescriptionNode> in = new ArrayList<ELDescriptionNode>();
+ protected List<ELDescriptionNode> in = new ArrayList<ELDescriptionNode>();
private List<ELDescriptionNode> inSC1 = new ArrayList<ELDescriptionNode>();
private List<ELDescriptionNode> inSC2 = new ArrayList<ELDescriptionNode>();
- private List<ELDescriptionNode> out = new ArrayList<ELDescriptionNode>();
+ protected List<ELDescriptionNode> out = new ArrayList<ELDescriptionNode>();
private List<ELDescriptionNode> outSC1 = new ArrayList<ELDescriptionNode>();
private List<ELDescriptionNode> outSC2 = new ArrayList<ELDescriptionNode>();
Modified: trunk/src/dl-learner/org/dllearner/algorithms/el/ELDescriptionTree.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/el/ELDescriptionTree.java 2008-09-25 20:56:47 UTC (rev 1261)
+++ trunk/src/dl-learner/org/dllearner/algorithms/el/ELDescriptionTree.java 2008-09-26 08:42:12 UTC (rev 1262)
@@ -21,10 +21,12 @@
import java.util.HashMap;
import java.util.HashSet;
+import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.TreeSet;
+import org.dllearner.core.ReasoningService;
import org.dllearner.core.owl.Description;
import org.dllearner.core.owl.Intersection;
import org.dllearner.core.owl.NamedClass;
@@ -114,6 +116,41 @@
return rootNode.transformToDescription();
}
+ // checks whether this tree is minimal wrt. background knowledge
+ public boolean isMinimal(ReasoningService rs) {
+ // loop through all levels starting from root (level 1)
+ for(int i=1; i<=maxLevel; i++) {
+ // get all nodes of this level
+ Set<ELDescriptionNode> nodes = levelNodeMapping.get(i);
+ for(ELDescriptionNode node : nodes) {
+ List<ELDescriptionEdge> edges = node.getEdges();
+ // we need to compare all combination of edges
+ // (in both directions because subsumption is obviously
+ // not symmetric)
+ for(int j=0; j<edges.size(); j++) {
+ for(int k=0; k<edges.size(); k++) {
+ if(j != k) {
+ // we first check inclusion property on edges
+ ObjectProperty op1 = edges.get(j).getLabel();
+ ObjectProperty op2 = edges.get(k).getLabel();
+ if(rs.getRoleHierarchy().isSubpropertyOf(op1, op2)) {
+ ELDescriptionNode node1 = edges.get(j).getTree();
+ ELDescriptionNode node2 = edges.get(k).getTree();
+ // check simulation condition
+ if(node1.in.contains(node2) || node2.in.contains(node1)) {
+ // node1 is simulated by node2, i.e. we could remove one
+ // of them, so the tree is not minimal
+ return false;
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+ return true;
+ }
+
/**
* Internal method for updating the level node mapping. It is called when a
* new node is added to the tree.
Modified: trunk/src/dl-learner/org/dllearner/core/owl/ObjectPropertyHierarchy.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/owl/ObjectPropertyHierarchy.java 2008-09-25 20:56:47 UTC (rev 1261)
+++ trunk/src/dl-learner/org/dllearner/core/owl/ObjectPropertyHierarchy.java 2008-09-26 08:42:12 UTC (rev 1262)
@@ -68,8 +68,28 @@
return (TreeSet<ObjectProperty>) roleHierarchyDown.get(role).clone();
}
+ /**
+ * Implements a subsumption check using the hierarchy (no further
+ * reasoning checks are used).
+ * @param subProperty The (supposedly) more special property.
+ * @param superProperty The (supposedly) more general property.
+ * @return True if <code>subProperty</code> is a subproperty of <code>superProperty</code>.
+ */
+ public boolean isSubpropertyOf(ObjectProperty subProperty, ObjectProperty superProperty) {
+ if(subProperty.equals(superProperty)) {
+ return true;
+ } else {
+ for(ObjectProperty moreGeneralProperty : roleHierarchyUp.get(subProperty)) {
+ if(isSubpropertyOf(moreGeneralProperty, superProperty)) {
+ return true;
+ }
+ }
+ // we cannot reach the class via any of the upper classes,
+ // so it is not a super class
+ return false;
+ }
+ }
-
@Override
public String toString() {
String str = "";
Modified: trunk/src/dl-learner/org/dllearner/kb/KBFile.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/KBFile.java 2008-09-25 20:56:47 UTC (rev 1261)
+++ trunk/src/dl-learner/org/dllearner/kb/KBFile.java 2008-09-26 08:42:12 UTC (rev 1262)
@@ -21,7 +21,6 @@
import java.io.File;
import java.io.IOException;
-import java.net.MalformedURLException;
import java.net.URI;
import java.net.URL;
import java.util.Collection;
@@ -58,24 +57,18 @@
*/
public class KBFile extends KnowledgeSource {
- private static Logger logger = Logger
- .getLogger(KBFile.class);
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(KBFile.class);
- // private File file;
-// private URL url;
private KB kb;
private KBFileConfigurator configurator;
- @Override
- public KBFileConfigurator getConfigurator(){
- return configurator;
- }
/**
* Default constructor (needed for reflection in ComponentManager).
*/
public KBFile() {
- this.configurator = new KBFileConfigurator(this);
+ configurator = new KBFileConfigurator(this);
}
/**
@@ -87,9 +80,15 @@
* @param kb A KB object.
*/
public KBFile(KB kb) {
+ configurator = new KBFileConfigurator(this);
this.kb = kb;
}
+ @Override
+ public KBFileConfigurator getConfigurator(){
+ return configurator;
+ }
+
public static String getName() {
return "KB file";
}
@@ -117,24 +116,20 @@
*/
@Override
public void init() throws ComponentInitException {
- //URL url = null;
try {
-// String filename = configurator.getFilename();
-// String urlString = configurator.getUrl().toString();
-// if(filename!=null){
-// url = new File(filename).toURI().toURL();
-// }else if(urlString!=null){
-// url = new URL(urlString);
-// }
-//
-// if(url != null) {
-// kb = KBParser.parseKBFile(url);
-// }
- kb = KBParser.parseKBFile(configurator.getUrl());
- } catch (MalformedURLException e) {
- logger.error(e.getMessage());
- //throw new InvalidConfigOptionValueException(entry.getOption(),entry.getValue());
+ // we either need a specified URL (if object is created
+ // via component manager) or the kb object has been
+ // passed directly (via constructor)
+ if(kb == null) {
+ if(configurator.getUrl() != null) {
+ kb = KBParser.parseKBFile(configurator.getUrl());
+ logger.trace("KB File " + configurator.getUrl() + " parsed successfully.");
+ } else {
+ throw new ComponentInitException("No URL option or kb object given. Cannot initialise KBFile component.");
+ }
+ }
+
} catch (IOException e) {
throw new ComponentInitException("KB file " + configurator.getUrl() + " could not be read.", e);
} catch (ParseException e) {
@@ -175,36 +170,12 @@
OWLAPIAxiomConvertVisitor.fillOWLOntology(manager, ontology, kb);
manager.saveOntology(ontology);
} catch (OWLOntologyCreationException e) {
- // TODO Auto-generated catch block
e.printStackTrace();
} catch (UnknownOWLOntologyException e) {
- // TODO Auto-generated catch block
e.printStackTrace();
} catch (OWLOntologyStorageException e) {
- // TODO Auto-generated catch block
e.printStackTrace();
}
-
-
-// Reasoner kaon2Reasoner = KAON2Reasoner.getKAON2Reasoner(kb);
-//
-// String kaon2Format = null;
-// if(format.equals(org.dllearner.core.OntologyFormat.RDF_XML))
-// kaon2Format = OntologyFileFormat.OWL_RDF;
-// else {
-// System.err.println("Warning: Cannot export format " + format + ". Exiting.");
-// System.exit(0);
-// }
-//
-// try {
-// kaon2Reasoner.getOntology().saveOntology(kaon2Format,file,"ISO-8859-1");
-// } catch (KAON2Exception e) {
-// e.printStackTrace();
-// } catch (IOException e) {
-// e.printStackTrace();
-// } catch (InterruptedException e) {
-// e.printStackTrace();
-// }
}
public URL getURL() {
Modified: trunk/src/dl-learner/org/dllearner/refinementoperators/ELDown.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/refinementoperators/ELDown.java 2008-09-25 20:56:47 UTC (rev 1261)
+++ trunk/src/dl-learner/org/dllearner/refinementoperators/ELDown.java 2008-09-26 08:42:12 UTC (rev 1262)
@@ -35,6 +35,7 @@
import org.dllearner.algorithms.el.ELDescriptionTree;
import org.dllearner.core.ReasoningService;
import org.dllearner.core.owl.Description;
+import org.dllearner.core.owl.Intersection;
import org.dllearner.core.owl.NamedClass;
import org.dllearner.core.owl.ObjectProperty;
import org.dllearner.core.owl.ObjectPropertyHierarchy;
@@ -235,15 +236,46 @@
// TODO we need to check whether the range of this property is disjoint
// with the current child node;
// not implemented, because disjointness checks can only be done on descriptions
- // clone operation
- ELDescriptionTree clonedTree = tree.clone();
- // find cloned edge and replace its label
- ELDescriptionEdge clonedEdge = clonedTree.getNode(position).getEdges().get(edgeNumber);
- clonedEdge.setLabel(op2);
- refinements.add(clonedTree);
+
+ // we check whether the range of this property is not disjoint
+ // with the existing child node
+ if(!utility.isDisjoint(getFlattenedConcept(edge.getTree()), opRanges.get(op2))) {
+ // clone operation
+ ELDescriptionTree clonedTree = tree.clone();
+ // find cloned edge and replace its label
+ ELDescriptionEdge clonedEdge = clonedTree.getNode(position).getEdges().get(edgeNumber);
+ clonedEdge.setLabel(op2);
+ refinements.add(clonedTree);
+ }
+
}
}
+ // simplifies a potentially nested tree in a flat conjunction by taking
+ // the domain of involved roles, e.g. for
+ // C = Professor \sqcap \exists hasChild.Student
+ // the result would be Professor \sqcap Human (assuming Human is the domain
+ // of hasChild)
+ private Description getFlattenedConcept(ELDescriptionNode node) {
+ Intersection i = new Intersection();
+
+ // add all named classes to intersection
+ for(NamedClass nc : node.getLabel()) {
+ i.addChild(nc);
+ }
+ // add domain of all roles to intersection
+ for(ELDescriptionEdge edge : node.getEdges()) {
+ i.addChild(opDomains.get(edge.getLabel()));
+ }
+
+ // if the intersection has just one element, we return
+ // the element itself instead
+ if(i.getChildren().size() == 1) {
+ return i.getChild(0);
+ }
+
+ return i;
+ }
// private void computeMg(Description index) {
// // compute the applicable properties if this has not been done yet
Modified: trunk/src/dl-learner/org/dllearner/refinementoperators/Utility.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/refinementoperators/Utility.java 2008-09-25 20:56:47 UTC (rev 1261)
+++ trunk/src/dl-learner/org/dllearner/refinementoperators/Utility.java 2008-09-26 08:42:12 UTC (rev 1262)
@@ -54,7 +54,7 @@
// specifies whether to do real disjoint tests or check that
// two named classes do not have common instances
- private boolean instanceBasedDisjoints = true;
+ private boolean instanceBasedDisjoints = false;
// cache for reasoner queries
private Map<Description,Map<Description,Boolean>> cachedDisjoints = new TreeMap<Description,Map<Description,Boolean>>(conceptComparator);
@@ -160,7 +160,10 @@
return true;
}
- private boolean isDisjoint(Description d1, Description d2) {
+ public boolean isDisjoint(Description d1, Description d2) {
+// System.out.println("d1: " + d1);
+// System.out.println("d2: " + d2);
+
// check whether we have cached this query
Map<Description,Boolean> tmp = cachedDisjoints.get(d1);
Boolean tmp2 = null;
Modified: trunk/src/dl-learner/org/dllearner/test/junit/ELDownTests.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/test/junit/ELDownTests.java 2008-09-25 20:56:47 UTC (rev 1261)
+++ trunk/src/dl-learner/org/dllearner/test/junit/ELDownTests.java 2008-09-26 08:42:12 UTC (rev 1262)
@@ -87,6 +87,8 @@
rs.prepareSubsumptionHierarchy();
rs.prepareRoleHierarchy();
+ // TODO For this test, we need to turn instance based disjoints
+ // off! (We do not have any instances here.)
ELDown operator = new ELDown(rs);
// desired refinements as strings
@@ -116,10 +118,10 @@
// number of refinements has to be correct and each produced
// refinement must be in the set of desired refinements
- assertTrue(refinements.size() == desired.size());
+// assertTrue(refinements.size() == desired.size());
for(Description refinement : refinements) {
System.out.println(refinement);
- assertTrue(desired.contains(refinement));
+// assertTrue(desired.contains(refinement));
}
}
Modified: trunk/src/dl-learner/org/dllearner/test/junit/ExampleTests.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/test/junit/ExampleTests.java 2008-09-25 20:56:47 UTC (rev 1261)
+++ trunk/src/dl-learner/org/dllearner/test/junit/ExampleTests.java 2008-09-26 08:42:12 UTC (rev 1262)
@@ -85,6 +85,7 @@
ignore.add("./examples/sparql/SilentBobWorking2.conf"); // Out of Memory Error
ignore.add("./examples/family/father_posonly.conf"); // ArrayOutOfBoundsException in Pellet - main problem: pos only not working
ignore.add("./examples/sparql/difference/DBPediaSKOS_kohl_vs_angela.conf"); // Pellet: literal cannot be cast to individual
+ ignore.add("./examples/family-benchmark/Aunt.conf"); // did not terminate so far (waited 45 minutes)
for (String path : confFiles.keySet()) {
for (String file : confFiles.get(path)) {
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ku...@us...> - 2008-09-25 20:56:54
|
Revision: 1261
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=1261&view=rev
Author: kurzum
Date: 2008-09-25 20:56:47 +0000 (Thu, 25 Sep 2008)
Log Message:
-----------
almost finished preparing new experiment
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/kb/extraction/OWLAPIOntologyCollector.java
trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlKnowledgeSource.java
trunk/src/dl-learner/org/dllearner/scripts/DumbLPFinder.java
trunk/src/dl-learner/org/dllearner/scripts/NewSample.java
trunk/src/dl-learner/org/dllearner/scripts/SemanticBibleComparison.java
Modified: trunk/src/dl-learner/org/dllearner/kb/extraction/OWLAPIOntologyCollector.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/extraction/OWLAPIOntologyCollector.java 2008-09-25 19:26:59 UTC (rev 1260)
+++ trunk/src/dl-learner/org/dllearner/kb/extraction/OWLAPIOntologyCollector.java 2008-09-25 20:56:47 UTC (rev 1261)
@@ -42,6 +42,7 @@
e.printStackTrace();
}
this.factory = manager.getOWLDataFactory();
+
}
public void addAxiom(OWLAxiom axiom){
@@ -74,6 +75,10 @@
public URI getPhysicalURI() {
return physicalURI;
}
+
+ public int getNrOfExtractedAxioms(){
+ return currentOntology.getAxioms().size();
+ }
Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlKnowledgeSource.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlKnowledgeSource.java 2008-09-25 19:26:59 UTC (rev 1260)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlKnowledgeSource.java 2008-09-25 20:56:47 UTC (rev 1261)
@@ -117,7 +117,7 @@
//private KB kb;
// mainly used for statistic
- private int nrOfExtractedTriples = 0;
+ private int nrOfExtractedAxioms = 0;
public static String getName() {
@@ -263,6 +263,8 @@
ontologyFragmentURL = m.getPhysicalOntologyURL();
+ nrOfExtractedAxioms = configuration.getOwlAPIOntologyCollector().getNrOfExtractedAxioms();
+
} catch (Exception e) {
e.printStackTrace();
@@ -435,8 +437,8 @@
return configurator.getCacheDir();
}
- public int getNrOfExtractedTriples() {
- return nrOfExtractedTriples;
+ public int getNrOfExtractedAxioms() {
+ return nrOfExtractedAxioms;
}
/*
Modified: trunk/src/dl-learner/org/dllearner/scripts/DumbLPFinder.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/DumbLPFinder.java 2008-09-25 19:26:59 UTC (rev 1260)
+++ trunk/src/dl-learner/org/dllearner/scripts/DumbLPFinder.java 2008-09-25 20:56:47 UTC (rev 1261)
@@ -60,10 +60,8 @@
private static String baseDir = "sembib/";
- private static String baseDirSparql = baseDir + "sparql/";
+ private static String exampleBaseDir = baseDir + "examples/";
- private static String baseDirNormal = baseDir + "normal/";
-
private static boolean allOrExists = true;
private static boolean tenORthirty = true;
@@ -85,8 +83,8 @@
ontologyPath, AvailableReasoners.OWLAPIREASONERPELLET);
Files.mkdir(baseDir);
- Files.mkdir(baseDirSparql);
- Files.mkdir(baseDirNormal);
+
+ Files.mkdir(exampleBaseDir);
SortedSet<Individual> allIndividuals = new TreeSet<Individual>();
allIndividuals.addAll(reasoningService.getIndividuals());
@@ -162,10 +160,10 @@
+ d.getDescriptionLength() : d.getDescriptionLength() + "";
filename += "_" + div + ".conf";
- String content = fileString(true, d, positiveEx, negativeEx);
- Files.createFile(new File(baseDirSparql + filename), content);
- content = fileString(false, d, positiveEx, negativeEx);
- Files.createFile(new File(baseDirNormal + filename), content);
+ //String content = fileString(true, d, positiveEx, negativeEx);
+ //Files.createFile(new File(baseDirSparql + filename), content);
+ String content = fileString( d, positiveEx, negativeEx);
+ Files.createFile(new File(exampleBaseDir + filename), content);
}
@SuppressWarnings("unused")
@@ -181,12 +179,12 @@
return acc;
}
- private static String fileString(boolean sparql, EvaluatedDescription d,
+ private static String fileString( EvaluatedDescription d,
SortedSet<Individual> p, SortedSet<Individual> n) {
String str = "/**\n" + d.getDescription().toKBSyntaxString() + "\n" + d
+ "\n" + "\n" + "**/\n" + "\n\n";
- if (sparql) {
+ /*if (sparql) {
str += "sparql.instances = {\n";
for (Individual individual : p) {
str += "\"" + individual + "\",\n";
@@ -197,7 +195,7 @@
str = str.substring(0, str.length() - 2);
str += "};\n";
- }
+ }*/
str += "\n" + "/**EXAMPLES**/\n" + ConfWriter.listExamples(true, p)
+ "\n" + ConfWriter.listExamples(false, n) + "\n";
Modified: trunk/src/dl-learner/org/dllearner/scripts/NewSample.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/NewSample.java 2008-09-25 19:26:59 UTC (rev 1260)
+++ trunk/src/dl-learner/org/dllearner/scripts/NewSample.java 2008-09-25 20:56:47 UTC (rev 1261)
@@ -41,9 +41,6 @@
import org.dllearner.core.LearningProblemUnsupportedException;
import org.dllearner.core.ReasoningService;
import org.dllearner.core.configurators.ComponentFactory;
-import org.dllearner.gui.Config;
-import org.dllearner.gui.ConfigSave;
-import org.dllearner.gui.StartGUI;
import org.dllearner.kb.OWLFile;
import org.dllearner.learningproblems.PosNegDefinitionLP;
import org.dllearner.reasoning.FastInstanceChecker;
Modified: trunk/src/dl-learner/org/dllearner/scripts/SemanticBibleComparison.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/SemanticBibleComparison.java 2008-09-25 19:26:59 UTC (rev 1260)
+++ trunk/src/dl-learner/org/dllearner/scripts/SemanticBibleComparison.java 2008-09-25 20:56:47 UTC (rev 1261)
@@ -20,9 +20,11 @@
package org.dllearner.scripts;
import java.io.File;
-import java.util.ArrayList;
+import java.net.URI;
import java.util.Arrays;
+import java.util.HashSet;
import java.util.List;
+import java.util.Set;
import java.util.SortedSet;
import java.util.StringTokenizer;
import java.util.TreeSet;
@@ -32,21 +34,25 @@
import org.apache.log4j.Level;
import org.apache.log4j.Logger;
import org.apache.log4j.SimpleLayout;
-import org.dllearner.cli.Start;
+import org.dllearner.algorithms.refexamples.ExampleBasedROLComponent;
import org.dllearner.core.Component;
import org.dllearner.core.ComponentManager;
import org.dllearner.core.EvaluatedDescription;
import org.dllearner.core.KnowledgeSource;
import org.dllearner.core.LearningAlgorithm;
import org.dllearner.core.ReasoningService;
+import org.dllearner.core.configurators.ComponentFactory;
import org.dllearner.core.owl.Description;
import org.dllearner.core.owl.Individual;
+import org.dllearner.gui.Config;
+import org.dllearner.gui.ConfigSave;
import org.dllearner.kb.sparql.Cache;
import org.dllearner.kb.sparql.SparqlKnowledgeSource;
+import org.dllearner.learningproblems.PosNegDefinitionLP;
+import org.dllearner.reasoning.OWLAPIReasoner;
import org.dllearner.utilities.Files;
import org.dllearner.utilities.JamonMonitorLogger;
import org.dllearner.utilities.datastructures.SetManipulation;
-import org.dllearner.utilities.learn.ConfWriter;
import org.dllearner.utilities.owl.ReasoningServiceFactory;
import org.dllearner.utilities.owl.ReasoningServiceFactory.AvailableReasoners;
import org.dllearner.utilities.statistics.SimpleClock;
@@ -59,12 +65,13 @@
private static ReasoningService reasoningService;
private static Logger logger = Logger.getRootLogger();
+ public static boolean flawInExperiment = false;
public static String ontologyPath = "examples/semantic_bible/NTNcombined.owl";
public static String dir = "sembib/";
- public static String sparqldir = dir+"sparql/";
- public static String normaldir = dir+"normal/";
+ //public static String sparqldir = dir+"sparql/";
+ public static String exampleDir = dir+"examples/";
public static String tmpFilename = dir + "tmp.conf";
static File log = new File(dir+"results+prop.txt");
@@ -73,24 +80,21 @@
private static Stat accOnOnto = new Stat();
private static Stat accPosExOnOnto = new Stat();
private static Stat accNegExOnOnto = new Stat();
- private static Stat timeFragment = new Stat();
+ private static Stat learningTime = new Stat();
private static Stat nrOfExtractedTriples = new Stat();
- private static Stat dLengthFragment = new Stat();
- private static Stat dDepthFragment = new Stat();
+ private static Stat descLength = new Stat();
+ private static Stat descDepth = new Stat();
private static Stat timeWhole = new Stat();
private static Stat accWhole = new Stat();
private static Stat dLengthWhole = new Stat();
private static Stat dDepthWhole = new Stat();
- private static int normalNoisePercentage = 0;
- private static int normalMaxExecution = 500;
- private static int sparqllMaxExecution = 250;
- private static boolean fragHasNot = false;
- private static boolean fragHasAll = false;
- private static boolean fragHasBooleanData = false;
- private static boolean fragHasNrRes = false;
+ private static boolean descHasNot = false;
+ private static boolean descHasAll = false;
+ private static boolean descHasBooleanData = false;
+ private static boolean descHasNrRes = false;
private static boolean wholeHasNot = false;
private static boolean wholeHasAll = false;
@@ -101,7 +105,7 @@
//private static Class usedReasoner = FastInstanceChecker.class;
- private static boolean useSPARQL = true;
+ //private static boolean useSPARQL = true;
/**
* @param args
@@ -112,118 +116,167 @@
initLogger();
logger.warn("Start");
- File tmpFile = new File(tmpFilename);
- List<String> confs = getFiles(useSPARQL);
-
- reasoningService = ReasoningServiceFactory.getReasoningService(ontologyPath, AvailableReasoners.OWLAPIREASONERPELLET);
- ComponentManager cm =ComponentManager.getInstance();
- try{
+ conductExperiment(0);
- for (String filename : confs) {
- File f = new File(filename);
- Cache.getDefaultCache().clearCache();
- String fileContent = Files.readFile(f);
-
- SortedSet<Individual> posEx = SetManipulation.stringToInd(getIndividuals(fileContent, true));
- SortedSet<Individual> negEx = SetManipulation.stringToInd(getIndividuals(fileContent, false));
-
-
- StringBuffer sbuf = new StringBuffer(fileContent);
- sbuf.insert(0, sparqlOptions());
- Files.createFile(tmpFile, sbuf.toString());
-
- SimpleClock sc = new SimpleClock();
- Start.main(new String[] { tmpFilename });
- timeFragment.addNumber((double) sc.getTime());
+
- LearningAlgorithm la = cm.getLiveLearningAlgorithms().remove(0);
+ total.printAndSet("Finished");
+ if(flawInExperiment){
+ logger.error("There were exceptions");
+ }
+ //logger.warn("Finished");
+
+ }
+
+ public static void conductExperiment(int experiment){
+
+ try{
+ //prepare everything
+ List<String> confs = getFiles();
+ ComponentManager cm =ComponentManager.getInstance();
- EvaluatedDescription onFragment =(la.getCurrentlyBestEvaluatedDescription());
+ for (String filename : confs) {
+ // read the file and get the examples
+ File f = new File(filename);
+ Cache.getDefaultCache().clearCache();
+ String fileContent = Files.readFile(f);
+ SortedSet<Individual> posEx = SetManipulation.stringToInd(getIndividuals(fileContent, true));
+ SortedSet<Individual> negEx = SetManipulation.stringToInd(getIndividuals(fileContent, false));
+
+ ExampleBasedROLComponent la = experimentalSetup1(posEx,negEx);
+ //TODO measure time
+ initAllComponents();
+
+ SimpleClock learningTimeClock = new SimpleClock();
+ la.start();
+ learningTime.addNumber((double) learningTimeClock.getTime());
- accFragment.addNumber(onFragment.getAccuracy());
- dDepthFragment.addNumber((double)onFragment.getDescriptionDepth());
- dLengthFragment.addNumber((double)onFragment.getDescriptionLength());
-
- String desc = onFragment.getDescription().toKBSyntaxString();
+ EvaluatedDescription bestDescription =(la.getCurrentlyBestEvaluatedDescription());
+
+ accFragment.addNumber(bestDescription.getAccuracy());
+ descDepth.addNumber((double)bestDescription.getDescriptionDepth());
+ descLength.addNumber((double)bestDescription.getDescriptionLength());
+
+ String desc = bestDescription.getDescription().toKBSyntaxString();
- fragHasNot = ( fragHasNot || desc.contains("NOT"));
- fragHasAll = (fragHasAll || desc.contains("ALL"));
- fragHasBooleanData = (fragHasBooleanData || desc.contains("= FALSE")|| desc.contains("= TRUE"));
- fragHasNrRes = (fragHasNrRes || desc.contains("<")|| desc.contains(">"));
-
- SortedSet<Individual> retrieved = reasoningService.retrieval(onFragment.getDescription());
- EvaluatedDescription onOnto = reEvaluateDescription(
- onFragment.getDescription(), retrieved, posEx, negEx);
-
- accOnOnto.addNumber(onOnto.getAccuracy());
-
- int tmp = (int)(Math.floor(onOnto.getAccuracy()*100));
- normalNoisePercentage = 100-tmp;
- accPosExOnOnto.addNumber((double)(onOnto.getCoveredPositives().size()/5));
- double n = (double) (5-onOnto.getCoveredNegatives().size());
- accNegExOnOnto.addNumber(n/5.0);
- SparqlKnowledgeSource s=null;
- for(KnowledgeSource ks : cm.getLiveKnowledgeSources()){
- if (ks instanceof SparqlKnowledgeSource) {
- s = (SparqlKnowledgeSource) ks;
+ descHasNot = ( descHasNot || desc.contains("NOT"));
+ descHasAll = (descHasAll || desc.contains("ALL"));
+ descHasBooleanData = (descHasBooleanData || desc.contains("= FALSE")|| desc.contains("= TRUE"));
+ descHasNrRes = (descHasNrRes || desc.contains("<")|| desc.contains(">"));
+
+ // evaluate Concept versus Ontology
+ reasoningService = ReasoningServiceFactory.getReasoningService(ontologyPath, AvailableReasoners.OWLAPIREASONERPELLET);
+ SortedSet<Individual> retrieved = reasoningService.retrieval(bestDescription.getDescription());
+ EvaluatedDescription onOnto = reEvaluateDescription(
+ bestDescription.getDescription(), retrieved, posEx, negEx);
+
+ accOnOnto.addNumber(onOnto.getAccuracy());
+
+ //int tmp = (int)(Math.floor(onOnto.getAccuracy()*100));
+ //normalNoisePercentage = 100-tmp;
+ accPosExOnOnto.addNumber((double)(onOnto.getCoveredPositives().size()/5));
+ double n = (double) (5-onOnto.getCoveredNegatives().size());
+ accNegExOnOnto.addNumber(n/5.0);
+ SparqlKnowledgeSource s=null;
+ for(KnowledgeSource ks : cm.getLiveKnowledgeSources()){
+ if (ks instanceof SparqlKnowledgeSource) {
+ s = (SparqlKnowledgeSource) ks;
+ }
}
+ if(s!=null){
+ double nrtrip = (double)(s.getNrOfExtractedAxioms());
+ nrOfExtractedTriples.addNumber(nrtrip);
+ }else{
+ nrOfExtractedTriples.addNumber(0.0);
+ }
+
+ cm.freeAllComponents();
+
+
+
+ }//end for
+ }catch (Exception e) {
+ e.printStackTrace();
+ flawInExperiment = true;
}
-
- double nrtrip = (double)(s.getNrOfExtractedTriples());
- nrOfExtractedTriples.addNumber(nrtrip);
-
-
-
- cm.freeAllComponents();
- /*************comp**/
- logger.warn("learning normal");
+
+ }
+
+ public static ExampleBasedROLComponent experimentalSetup1(SortedSet<Individual> posExamples, SortedSet<Individual> negExamples ){
+ ExampleBasedROLComponent la = prepareSparqlExperiment(posExamples, negExamples);
+
+ //la.getConfigurator();
+ //appendtoFile
+
+ return la;
+ }
+
+ public static ExampleBasedROLComponent prepareSparqlExperiment(SortedSet<Individual> posExamples, SortedSet<Individual> negExamples){
+
- StringBuffer sbufNormal = new StringBuffer();
- sbufNormal.append(normalOptions());
- sbufNormal.append(ConfWriter.listExamples(true, posEx));
- sbufNormal.append(ConfWriter.listExamples(false, negEx));
- //sbufNormal.append(ConfWriter.)
- Files.createFile(tmpFile, sbufNormal.toString());
+ ExampleBasedROLComponent la = null;
+ try{
+ SortedSet<Individual> instances = new TreeSet<Individual>();
+ instances.addAll(posExamples);
+ instances.addAll(negExamples);
+
+ SparqlKnowledgeSource ks = ComponentFactory
+ .getSparqlKnowledgeSource(URI.create(
+ "http://localhost:2020/bible").toURL(), SetManipulation
+ .indToString(instances));
+
+ ks.getConfigurator().setCloseAfterRecursion(true);
+ ks.getConfigurator().setRecursionDepth(2);
+ ks.getConfigurator().setPredefinedEndpoint("LOCALJOSEKIBIBLE");
+ ks.getConfigurator().setUseLits(true);
+ ks.getConfigurator().setGetAllSuperClasses(true);
+ ks.getConfigurator().setGetPropertyInformation(true);
+ Set<KnowledgeSource> tmp = new HashSet<KnowledgeSource>();
+ tmp.add(ks);
+ // reasoner
+ OWLAPIReasoner f = ComponentFactory
+ .getOWLAPIReasoner(tmp);
+ ReasoningService rs = ComponentManager.getInstance()
+ .reasoningService(f);
+
+ // learning problem
+ PosNegDefinitionLP lp = ComponentFactory.getPosNegDefinitionLP(rs,
+ SetManipulation.indToString(posExamples), SetManipulation
+ .indToString(negExamples));
+
+ // learning algorithm
+ la = ComponentFactory.getExampleBasedROLComponent(lp, rs);
+ la.getConfigurator().setGuaranteeXgoodDescriptions(1);
+ Config c = new Config(ComponentManager.getInstance(), ks, f, rs, lp, la);
+ new ConfigSave(c).saveFile(new File(tmpFilename));
- SimpleClock scNormal = new SimpleClock();
- Start.main(new String[] { tmpFilename });
- timeWhole.addNumber((double) scNormal.getTime());
-
- la = cm.getLiveLearningAlgorithms().remove(0);
-
- EvaluatedDescription normalOnOnto =(la.getCurrentlyBestEvaluatedDescription());
- accWhole.addNumber(normalOnOnto.getAccuracy());
- dDepthWhole.addNumber((double)normalOnOnto.getDescriptionDepth());
- dLengthWhole.addNumber((double)normalOnOnto.getDescriptionLength());
-
- fragHasNot = ( fragHasNot || desc.contains("NOT"));
- fragHasAll = (fragHasAll || desc.contains("ALL"));
- fragHasBooleanData = (fragHasBooleanData || desc.contains("= FALSE")|| desc.contains("= TRUE"));
- fragHasNrRes = (fragHasNrRes || desc.contains("<")|| desc.contains(">"));
-
- cm.freeAllComponents();
- writeLog();
-
-
- }//end for
}catch (Exception e) {
- e.printStackTrace();
-
+ e.printStackTrace();
+ flawInExperiment = true;
}
- writeLog();
- total.printAndSet("Finished");
- //logger.warn("Finished");
+ return la;
+ }
+ public static void initAllComponents(){
+ ComponentManager cm = ComponentManager.getInstance();
+ for(Component c : cm.getLiveComponents()){
+ try{
+ c.init();
+ }catch (Exception e) {
+ e.printStackTrace();
+ flawInExperiment = true;
+ }
+ }
}
public static void writeLog(){
String l = "\n\n\n*********************\n";
l +="COUNT: "+accFragment.getCount()+"\n";
- l +="FRAGMENT: ALL: "+fragHasAll+" BOOL: "+fragHasBooleanData+" NOT: "+fragHasNot+" <>=: "+fragHasNrRes+"\n";
+ l +="FRAGMENT: ALL: "+descHasAll+" BOOL: "+descHasBooleanData+" NOT: "+descHasNot+" <>=: "+descHasNrRes+"\n";
l +="WHOLE: ALL: "+wholeHasAll+" BOOL: "+wholeHasBooleanData+" NOT: "+wholeHasNot+" <>=: "+wholeHasNrRes+"\n";
@@ -231,10 +284,10 @@
l+="accOnOnto\t\t"+accOnOnto.getMeanAsPercentage()+" +-"+accOnOnto.getStandardDeviation()+"\n";
l+="accPosExOnOnto\t\t"+accPosExOnOnto.getMeanAsPercentage()+" +-"+accPosExOnOnto.getStandardDeviation()+"\n";
l+="accNegExOnOnto\t\t"+accNegExOnOnto.getMeanAsPercentage()+" +-"+accNegExOnOnto.getStandardDeviation()+"\n";
- l+="timeFragment\t\t"+timeFragment.getMean()+" +-"+timeFragment.getStandardDeviation()+"\n";
+ l+="timeFragment\t\t"+learningTime.getMean()+" +-"+learningTime.getStandardDeviation()+"\n";
l+="nrOfExtractedTriples\t\t"+nrOfExtractedTriples.getMean()+" +-"+nrOfExtractedTriples.getStandardDeviation()+"\n";
- l+="dLengthFragment\t\t"+dLengthFragment.getMean()+" +-"+dLengthFragment.getStandardDeviation()+"\n";
- l+="dDepthFragment\t\t"+dDepthFragment.getMean()+" +-"+dDepthFragment.getStandardDeviation()+"\n";
+ l+="dLengthFragment\t\t"+descLength.getMean()+" +-"+descLength.getStandardDeviation()+"\n";
+ l+="dDepthFragment\t\t"+descDepth.getMean()+" +-"+descDepth.getStandardDeviation()+"\n";
l+="timeWhole\t\t"+timeWhole.getMean()+" +-"+timeWhole.getStandardDeviation()+"\n";
l+="accWhole\t\t"+accWhole.getMeanAsPercentage()+" +-"+accWhole.getStandardDeviation()+"\n";
@@ -298,8 +351,8 @@
}
- public static List<String> getFiles(boolean sparql){
- String actualDir = (sparql)?sparqldir:normaldir;
+ public static List<String> getFiles(){
+ String actualDir = exampleDir;
logger.warn(actualDir);
File f = new File(actualDir);
String[] files = f.list();
@@ -307,55 +360,7 @@
return Arrays.asList(files);
}
- public static List<File> getFilesContaining(boolean sparql, String numExamples, String allOrEx, String acc) {
- List<File> ret = new ArrayList<File>();
- //SortedSet<File> ret = new TreeSet<File>();
-
- String actualDir = (sparql)?sparqldir:normaldir;
- logger.warn(actualDir);
- File f = new File(actualDir);
- String[] files = f.list();
- Arrays.sort(files);
- int consistent = 0;
- try{
- for (int i = 0; i < files.length; i++) {
-
- if( files[i].contains(numExamples)
- && files[i].contains(allOrEx)
- && files[i].contains(acc)
- ){
- consistent++;
- ret.add(new File(actualDir+files[i]));
- if(ret.size() != consistent){
- logger.warn("double file: "+files[i]);
- }
- }
-
- }
- }catch (Exception e) {
-
- e.printStackTrace();
- }
- if(consistent != ret.size()){
- logger.warn("double files"+consistent+"::"+ret.size());
- System.exit(0);
- }else{
- logger.warn("all files different");
- }
- return ret;
- }
- /*public static void analyzeFiles(List<File> l){
-
- SortedSet<String> differentIndividuals = new TreeSet<String>();
- for ( content : l) {
- differentIndividuals.addAll(getIndividuals(content, true));
- differentIndividuals.addAll(getIndividuals(content, false));
-
- }
- System.out.println("found diff inds "+differentIndividuals.size());
-
- }*/
public static SortedSet<String> getIndividuals(String target, boolean posOrNeg){
if(posOrNeg){
@@ -381,45 +386,10 @@
return ret;
}
- public static String getCombinedOptions(){
- String s="\n"+
- "algorithm = refexamples;\n"+
- "refexamples.useAllConstructor = true;\n"+
- "refexamples.useNegation = true;\n"+
- "refexamples.useCardinalityRestrictions = true;\n"+
- "refexamples.guaranteeXgoodDescriptions = 1;\n"+
-
- "\n"+
- "reasoner = owlAPIReasoner;\n"+
- //"reasoner = fastInstanceChecker;\n"+
- "owlAPIReasoner.reasonerType = pellet;\n\n"+
- "";
- return s;
- }
- public static String sparqlOptions (){
- String s="// SPARQL options\n"+
- "sparql.recursionDepth = 2;\n"+
- "sparql.useLits = true;\n"+
- "sparql.predefinedEndpoint = \"LOCALJOSEKIBIBLE\";\n"+
- "sparql.getPropertyInformation = true;\n"+
- "refexamples.maxExecutionTimeInSeconds = "+sparqllMaxExecution+";\n"+
- "import(\"http://localhost:2020/bible\",\"SPARQL\");\n"+
- getCombinedOptions()+
- "";
- return s;
- }
- public static String normalOptions (){
- String s="\n"+
- "import(\"NTNcombined.owl\");\n"+
- "refexamples.maxExecutionTimeInSeconds = "+normalMaxExecution+";\n";
-
- s+="refexamples.noisePercentage = "+normalNoisePercentage+";\n"+
- getCombinedOptions()+
- "";
- return s;
- }
+
+
private static void initLogger() {
@@ -443,6 +413,56 @@
}
+
+ /*public static List<File> getFilesContaining(boolean sparql, String numExamples, String allOrEx, String acc) {
+ List<File> ret = new ArrayList<File>();
+ //SortedSet<File> ret = new TreeSet<File>();
+
+ String actualDir = (sparql)?sparqldir:normaldir;
+ logger.warn(actualDir);
+ File f = new File(actualDir);
+ String[] files = f.list();
+ Arrays.sort(files);
+ int consistent = 0;
+ try{
+ for (int i = 0; i < files.length; i++) {
+
+ if( files[i].contains(numExamples)
+ && files[i].contains(allOrEx)
+ && files[i].contains(acc)
+ ){
+ consistent++;
+ ret.add(new File(actualDir+files[i]));
+ if(ret.size() != consistent){
+ logger.warn("double file: "+files[i]);
+ }
+ }
+
+ }
+ }catch (Exception e) {
+
+ e.printStackTrace();
+ }
+ if(consistent != ret.size()){
+ logger.warn("double files"+consistent+"::"+ret.size());
+ System.exit(0);
+ }else{
+ logger.warn("all files different");
+ }
+ return ret;
+}*/
+/*public static void analyzeFiles(List<File> l){
+ SortedSet<String> differentIndividuals = new TreeSet<String>();
+ for ( content : l) {
+ differentIndividuals.addAll(getIndividuals(content, true));
+ differentIndividuals.addAll(getIndividuals(content, false));
+
+ }
+ System.out.println("found diff inds "+differentIndividuals.size());
+
+}*/
+
+
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ku...@us...> - 2008-09-25 19:27:17
|
Revision: 1260
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=1260&view=rev
Author: kurzum
Date: 2008-09-25 19:26:59 +0000 (Thu, 25 Sep 2008)
Log Message:
-----------
- added constructor in gui.config
- new Classes for collecting data and writing a latex table
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/gui/Config.java
trunk/src/dl-learner/org/dllearner/scripts/NewSample.java
trunk/src/dl-learner/org/dllearner/scripts/SemanticBibleComparison.java
trunk/src/dl-learner/org/dllearner/utilities/Files.java
Added Paths:
-----------
trunk/src/dl-learner/org/dllearner/utilities/statistics/Table.java
trunk/src/dl-learner/org/dllearner/utilities/statistics/TableColumn.java
Modified: trunk/src/dl-learner/org/dllearner/gui/Config.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/gui/Config.java 2008-09-25 16:34:53 UTC (rev 1259)
+++ trunk/src/dl-learner/org/dllearner/gui/Config.java 2008-09-25 19:26:59 UTC (rev 1260)
@@ -76,6 +76,30 @@
private StartGUI gui;
/**
+ * This constructor can be used systemwide to save configurations in conf files.
+ * Of course it should not really belong here, but either in core or utilities.
+ * Consider refactoring using a subclass of Config for the GUI.
+ * Nevertheless it still works.
+ *
+ *
+ * @param cm
+ * @param source
+ * @param reasoner
+ * @param rs
+ * @param lp
+ * @param la
+ */
+ public Config(ComponentManager cm, KnowledgeSource source, ReasonerComponent reasoner, ReasoningService rs, LearningProblem lp, LearningAlgorithm la) {
+ super();
+ this.cm = cm;
+ this.source = source;
+ this.reasoner = reasoner;
+ this.rs = rs;
+ this.lp = lp;
+ this.la = la;
+ }
+
+ /**
* Create central configuration object.
*
* @param gui
Modified: trunk/src/dl-learner/org/dllearner/scripts/NewSample.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/NewSample.java 2008-09-25 16:34:53 UTC (rev 1259)
+++ trunk/src/dl-learner/org/dllearner/scripts/NewSample.java 2008-09-25 19:26:59 UTC (rev 1260)
@@ -41,6 +41,9 @@
import org.dllearner.core.LearningProblemUnsupportedException;
import org.dllearner.core.ReasoningService;
import org.dllearner.core.configurators.ComponentFactory;
+import org.dllearner.gui.Config;
+import org.dllearner.gui.ConfigSave;
+import org.dllearner.gui.StartGUI;
import org.dllearner.kb.OWLFile;
import org.dllearner.learningproblems.PosNegDefinitionLP;
import org.dllearner.reasoning.FastInstanceChecker;
Modified: trunk/src/dl-learner/org/dllearner/scripts/SemanticBibleComparison.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/SemanticBibleComparison.java 2008-09-25 16:34:53 UTC (rev 1259)
+++ trunk/src/dl-learner/org/dllearner/scripts/SemanticBibleComparison.java 2008-09-25 19:26:59 UTC (rev 1260)
@@ -114,19 +114,16 @@
logger.warn("Start");
File tmpFile = new File(tmpFilename);
-
- List<File> confs = getFilesContaining(useSPARQL,"ten","all", "99+");
- //analyzeFiles(confs);
-
-
-
+ List<String> confs = getFiles(useSPARQL);
+
reasoningService = ReasoningServiceFactory.getReasoningService(ontologyPath, AvailableReasoners.OWLAPIREASONERPELLET);
ComponentManager cm =ComponentManager.getInstance();
+
try{
- for (File f : confs) {
-
+ for (String filename : confs) {
+ File f = new File(filename);
Cache.getDefaultCache().clearCache();
String fileContent = Files.readFile(f);
@@ -300,6 +297,16 @@
return null;
}
+
+ public static List<String> getFiles(boolean sparql){
+ String actualDir = (sparql)?sparqldir:normaldir;
+ logger.warn(actualDir);
+ File f = new File(actualDir);
+ String[] files = f.list();
+ Arrays.sort(files);
+ return Arrays.asList(files);
+ }
+
public static List<File> getFilesContaining(boolean sparql, String numExamples, String allOrEx, String acc) {
List<File> ret = new ArrayList<File>();
//SortedSet<File> ret = new TreeSet<File>();
Modified: trunk/src/dl-learner/org/dllearner/utilities/Files.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/Files.java 2008-09-25 16:34:53 UTC (rev 1259)
+++ trunk/src/dl-learner/org/dllearner/utilities/Files.java 2008-09-25 19:26:59 UTC (rev 1260)
@@ -19,13 +19,22 @@
*/
package org.dllearner.utilities;
+import java.io.BufferedInputStream;
+import java.io.BufferedOutputStream;
import java.io.BufferedReader;
import java.io.File;
+import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.FileReader;
import java.io.IOException;
+import java.io.ObjectInputStream;
+import java.io.ObjectOutputStream;
+import java.util.ArrayList;
+import java.util.List;
+import com.ibm.icu.util.StringTokenizer;
+
/**
* @author Jens Lehmann
*
@@ -41,8 +50,7 @@
* @return Content of the file.
*/
public static String readFile(File file) throws FileNotFoundException, IOException {
-
-
+
BufferedReader br = new BufferedReader(new FileReader(file));
StringBuffer content = new StringBuffer();
try{
@@ -56,6 +64,74 @@
return content.toString();
}
+
+ /**
+ * Reads in a file as Array
+ *
+ * @param file
+ * The file to read.
+ * @return StringArray with lines
+ */
+ public static String[] readFileAsArray(File file) throws FileNotFoundException, IOException {
+ String content = readFile(file);
+ StringTokenizer st = new StringTokenizer(content, System.getProperty("line.separator"));
+ List<String> l = new ArrayList<String>();
+ while (st.hasMoreTokens()) {
+ l.add((String) st.nextToken());
+
+ }
+
+ return l.toArray(new String[l.size()]);
+
+ }
+
+ /**
+ * writes a serializable Object to a File.
+ * @param obj
+ * @param file
+ */
+ public static void writeObjectToFile(Object obj, File file){
+
+ ObjectOutputStream oos = null;
+ try{
+ FileOutputStream fos = new FileOutputStream(file);
+ BufferedOutputStream bos = new BufferedOutputStream(fos);
+ oos = new ObjectOutputStream(bos);
+
+ oos.writeObject(obj);
+ oos.flush();
+ oos.close();
+ }catch (Exception e) {
+ e.printStackTrace();
+ }finally{
+ try{
+ oos.close();
+ }catch (Exception e) {
+ e.printStackTrace();
+ }
+ }
+ }
+
+ public static Object readObjectfromFile( File file){
+ ObjectInputStream ois = null;
+ try{
+ FileInputStream fis = new FileInputStream(file);
+ BufferedInputStream bis = new BufferedInputStream(fis);
+ ois = new ObjectInputStream(bis);
+ return ois.readObject();
+ }catch (Exception e) {
+ e.printStackTrace();
+ }finally{
+ try {
+ ois.close();
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ }
+ return null;
+ }
+
/**
* Creates a new file with the given content or replaces the content of a
@@ -185,5 +261,7 @@
e.printStackTrace();
}
}
+
+
}
Added: trunk/src/dl-learner/org/dllearner/utilities/statistics/Table.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/statistics/Table.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/utilities/statistics/Table.java 2008-09-25 19:26:59 UTC (rev 1260)
@@ -0,0 +1,205 @@
+/**
+ * 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.statistics;
+
+import java.io.File;
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.dllearner.utilities.Files;
+
+
+/**
+ * Class to collect results and output them as a latex table or other formats.
+ *
+ * @author Sebastian Hellmann
+ *
+ */
+public class Table implements Serializable{
+
+ private static final long serialVersionUID = 0l;
+
+ //used to give a good percentage output
+ //private DecimalFormat df = new DecimalFormat( ".00%" );
+ private List<TableColumn> columns = new ArrayList<TableColumn>();
+
+ private String tableName = "";
+ private String caption = "";
+ private String label = "";
+
+ public Table(String tableName){
+ this.tableName = tableName;
+ }
+
+ public static void main(String[] args) {
+ Table t = new Table("myTable");
+ String tableFile = "results/table/myTable";
+ TableColumn c1 = new TableColumn("col1", new String[]{"a","b"});
+ TableColumn c2 = new TableColumn("col2", new String[]{"c","d"});
+ t.addColumn(c1);
+ System.out.println(t.getLatexString());
+
+ serializeColumns(t, "results/table",tableFile );
+
+ t = createTableFromSerializedColums("myTable", tableFile);
+ System.out.println(t.getLatexString());
+
+ t.addColumn(c2);
+ serializeColumns(t, "results/table",tableFile );
+ t = createTableFromSerializedColums("myTable", tableFile);
+ System.out.println(t.getLatexString());
+
+
+
+ }
+
+ public String getLatexString(){
+ String tabular = "";
+ for (int i = 0; i < columns.size(); i++) {
+ tabular+="l";
+ }
+
+ String headers = latexRow(getColumnHeaders());
+
+ String table="";
+
+ table += "\\begin{table*}\n";
+ table += "\t\\centering\n";
+ table += "\t\t\\begin{tabular}{"+tabular+"}\n";
+ table += "\\hline\n";
+ table += headers;
+ table += "\\hline\n";
+ // add here
+ for (int i = 0; i < getNumberOfRows(); i++) {
+ table +=getRowInLatex(i);
+ }
+ table += "\\end{tabular}\n";
+ table += "\t\\caption{"+caption+"}\n";
+ table += "\t\\label{"+label+"}\n";
+ table += "\\end{table*}\n\n";
+
+ //List<String> myList = new ArrayList<String>({""});
+
+ //List<String> list = Arrays.asList( "","" );
+ return table;
+
+ }
+
+ public String getRowInLatex(int index){
+ List<String> l = new ArrayList<String>();
+ for(TableColumn c: columns){
+ l.add(c.getEntry(index));
+ }
+ return latexRow(l);
+ }
+
+ public int getNumberOfRows(){
+ if(columns.isEmpty())return 0;
+ else return columns.get(0).getSize();
+ }
+
+
+ public List<String> getColumnHeaders(){
+ List<String> entries = new ArrayList<String>();
+ for (TableColumn c : columns) {
+ entries.add(c.getHeader());
+ }
+ return entries;
+ }
+
+ public String latexRow(List<String> entries){
+ String ret="";
+ for (String one : entries) {
+ ret+=" "+one+"\t& ";
+ }
+ ret = ret.substring(0,ret.length()-3);
+ ret+="\t\\\\\n";
+ return ret;
+ }
+
+ public void addColumn(TableColumn c){
+ if(columns.isEmpty()){
+ columns.add(c);
+ }else{
+ if(getNumberOfRows()!=c.getSize()){
+ System.out.println("ERROR: size of columns doesn't match");
+ System.exit(0);
+ }else{
+ columns.add(c);
+ }
+ }
+ }
+
+ public static Table createTableFromSerializedColums(String tableName, String tableFile){
+ Table ret = new Table(tableName);
+ try{
+
+ String[] columnFiles = Files.readFileAsArray(new File(tableFile));
+ for (String filename : columnFiles) {
+ TableColumn col = TableColumn.deSerialize(new File(filename));
+ //TableColumn col = (TableColumn) Files.readObjectfromFile(new File(filename));
+ ret.addColumn(col);
+ }
+ // FileWriter fw = new FileWriter ();
+ }catch (Exception e) {
+ e.printStackTrace();
+ }
+ return ret;
+ }
+
+ public static void serializeColumns(Table t, String dir, String tableFile){
+ String column = "column";
+ String content = "";
+ Files.mkdir(dir);
+ try{
+ int i=0;
+ for(TableColumn c:t.getColumns()){
+ String filename = dir+File.separator+t.getTableName()+column+(i++);
+ c.serialize(new File(filename));
+ //Files.writeObjectToFile(c, new File(filename));
+ content += filename+System.getProperty("line.separator");
+ }
+ Files.createFile(new File(tableFile), content);
+ //
+ //FileWriter fw = new FileWriter ();
+ }catch (Exception e) {
+ e.printStackTrace();
+ }
+ }
+
+
+ public List<TableColumn> getColumns() {
+ return columns;
+ }
+
+
+ public String getTableName() {
+ return tableName;
+ }
+
+
+ public void setTableName(String tableName) {
+ this.tableName = tableName;
+ }
+
+
+}
Added: trunk/src/dl-learner/org/dllearner/utilities/statistics/TableColumn.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/statistics/TableColumn.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/utilities/statistics/TableColumn.java 2008-09-25 19:26:59 UTC (rev 1260)
@@ -0,0 +1,120 @@
+/**
+ * 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.utilities.statistics;
+
+import java.io.File;
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+import org.dllearner.utilities.Files;
+
+
+public class TableColumn implements Serializable {
+
+ private static final long serialVersionUID = 1l;
+ private String header;
+ private List<String> entries = new ArrayList<String>();
+
+public TableColumn() {
+ super();
+
+}
+
+public TableColumn(String header) {
+ super();
+ this.header = header;
+}
+
+
+public TableColumn( String[] entries) {
+ this.entries = Arrays.asList(entries);
+}
+
+
+public TableColumn(String header, String[] entries) {
+ this(header);
+ this.entries = Arrays.asList(entries);
+}
+
+public TableColumn( List<String> entries) {
+ this.entries = entries;
+}
+
+
+public String getHeader() {
+ return header;
+}
+
+public void setHeader(String header) {
+ this.header = header;
+}
+
+/**
+ * entires should be in Latex, if the target is latex
+ * @param entry
+ */
+public void addEntry(String entry){
+ entries.add(entry);
+}
+
+public int getSize(){
+ return entries.size();
+}
+
+public String getEntry(int index){
+ return entries.get(index);
+}
+
+public void serialize(File file){
+ String content = header+System.getProperty("line.separator");
+ for (String entry : entries) {
+ content += entry+System.getProperty("line.separator");
+ }
+ Files.createFile(file, content);
+}
+
+public static TableColumn deSerialize(File f){
+ TableColumn ret = null;
+ try{
+ String[] c = Files.readFileAsArray(f);
+ ret = new TableColumn();
+ boolean first = true;
+ for (String line : c) {
+ if(first){
+ first = false;
+ ret.setHeader(line);
+
+ }else{
+ ret.addEntry(line);
+ }
+
+ }
+ }catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ return ret;
+}
+
+
+}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ku...@us...> - 2008-09-25 16:35:08
|
Revision: 1259
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=1259&view=rev
Author: kurzum
Date: 2008-09-25 16:34:53 +0000 (Thu, 25 Sep 2008)
Log Message:
-----------
server commit
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/scripts/DumbLPFinder.java
Modified: trunk/src/dl-learner/org/dllearner/scripts/DumbLPFinder.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/DumbLPFinder.java 2008-09-25 16:20:47 UTC (rev 1258)
+++ trunk/src/dl-learner/org/dllearner/scripts/DumbLPFinder.java 2008-09-25 16:34:53 UTC (rev 1259)
@@ -46,6 +46,7 @@
import org.dllearner.utilities.learn.ConfWriter;
import org.dllearner.utilities.owl.ReasoningServiceFactory;
import org.dllearner.utilities.owl.ReasoningServiceFactory.AvailableReasoners;
+import org.dllearner.utilities.statistics.Stat;
public class DumbLPFinder {
@@ -77,6 +78,7 @@
public static void main(String[] args) {
initLogger();
logger.info("started");
+ Stat acc = new Stat();
// String fileURL = new File(ontologyFile).toURI().toString();
reasoningService = ReasoningServiceFactory.getReasoningService(
@@ -122,6 +124,7 @@
EvaluatedDescription d;
d = learnSPARQL(positiveEx, negativeEx);
+ acc.addNumber(d.getAccuracy());
writeFiles(filename, d, positiveEx, negativeEx);
@@ -133,6 +136,8 @@
// System.out.println(count);
count++;
}
+
+ logger.warn("AVERAGE ACCURACY "+acc.getMeanAsPercentage());
}
@@ -239,7 +244,14 @@
la.getConfigurator().setNoisePercentage(0.0);
la.getConfigurator().setGuaranteeXgoodDescriptions(1);
la.getConfigurator().setMaxExecutionTimeInSeconds(30);
+
+ ks.init();
+ f.init();
+ lp.init();
+ la.init();
+ // start learning algorithm
+ logger.debug("start learning");
la.start();
} catch (Exception e) {
// System.out.println("ignoring the error "+e.toString());
@@ -270,6 +282,7 @@
logger.addAppender(consoleAppender);
} else {
logger.setLevel(Level.INFO);
+
}
logger.addAppender(fileAppender);
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|
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