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[DL-Learner SVN] SF.net SVN: dl-learner:[3068] trunk
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From: <jen...@us...> - 2011-08-18 09:22:47
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Revision: 3068
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3068&view=rev
Author: jenslehmann
Date: 2011-08-18 09:22:41 +0000 (Thu, 18 Aug 2011)
Log Message:
-----------
- extended ConfigHelper with methods to get all config options and their values
- worked on RDF output generation of enrichment script
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/core/config/ConfigHelper.java
trunk/components-core/src/main/java/org/dllearner/core/config/ConfigOption.java
trunk/interfaces/src/main/java/org/dllearner/cli/Enrichment.java
Modified: trunk/components-core/src/main/java/org/dllearner/core/config/ConfigHelper.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/core/config/ConfigHelper.java 2011-08-18 09:22:16 UTC (rev 3067)
+++ trunk/components-core/src/main/java/org/dllearner/core/config/ConfigHelper.java 2011-08-18 09:22:41 UTC (rev 3068)
@@ -74,6 +74,58 @@
}
/**
+ *
+ * @param component The component to analyse.
+ * @return All config options of the component with their respective value.
+ */
+ public static Map<ConfigOption,String> getConfigOptionValuesString(Component component) {
+ Map<ConfigOption,String> optionValues = new HashMap<ConfigOption,String>();
+ Field[] fields = getConfigOptions(component).getClass().getDeclaredFields();
+ for(Field field : fields) {
+ ConfigOption option = field.getAnnotation(ConfigOption.class);
+ if(option != null) {
+ Class<? extends PropertyEditor> editorClass = option.propertyEditorClass();
+ PropertyEditor editor = null;
+ try {
+ editor = editorClass.newInstance();
+ Object object = field.get(component);
+ editor.setValue(object);
+ String value = editor.getAsText();
+ optionValues.put(option, value);
+ } catch (InstantiationException e) {
+ e.printStackTrace();
+ } catch (IllegalAccessException e) {
+ e.printStackTrace();
+ }
+ }
+ }
+ return optionValues;
+ }
+
+ /**
+ *
+ * @param component The component to analyse.
+ * @return All config options of the component with their respective value.
+ */
+ public static Map<ConfigOption,Object> getConfigOptionValues(Component component) {
+ Map<ConfigOption,Object> optionValues = new HashMap<ConfigOption,Object>();
+ Field[] fields = getConfigOptions(component).getClass().getDeclaredFields();
+ for(Field field : fields) {
+ ConfigOption option = field.getAnnotation(ConfigOption.class);
+ if(option != null) {
+ try {
+ optionValues.put(option, field.get(component));
+ } catch (IllegalArgumentException e1) {
+ e1.printStackTrace();
+ } catch (IllegalAccessException e1) {
+ e1.printStackTrace();
+ }
+ }
+ }
+ return optionValues;
+ }
+
+ /**
* Returns all config options for the given component.
* @param component
* @return
Modified: trunk/components-core/src/main/java/org/dllearner/core/config/ConfigOption.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/core/config/ConfigOption.java 2011-08-18 09:22:16 UTC (rev 3067)
+++ trunk/components-core/src/main/java/org/dllearner/core/config/ConfigOption.java 2011-08-18 09:22:41 UTC (rev 3068)
@@ -19,6 +19,7 @@
*/
package org.dllearner.core.config;
+import java.beans.PropertyEditor;
import java.lang.annotation.Retention;
import java.lang.annotation.RetentionPolicy;
@@ -49,7 +50,7 @@
* An implementation of the Property Editor to use
* @return
*/
- Class<?> propertyEditorClass();
+ Class<? extends PropertyEditor> propertyEditorClass();
/**
* Returns whether this option is required for initializing the component.
Modified: trunk/interfaces/src/main/java/org/dllearner/cli/Enrichment.java
===================================================================
--- trunk/interfaces/src/main/java/org/dllearner/cli/Enrichment.java 2011-08-18 09:22:16 UTC (rev 3067)
+++ trunk/interfaces/src/main/java/org/dllearner/cli/Enrichment.java 2011-08-18 09:22:41 UTC (rev 3068)
@@ -21,6 +21,8 @@
import static java.util.Arrays.asList;
+import java.io.File;
+import java.io.FileOutputStream;
import java.io.IOException;
import java.lang.reflect.InvocationTargetException;
import java.math.BigInteger;
@@ -35,6 +37,7 @@
import java.util.HashSet;
import java.util.LinkedList;
import java.util.List;
+import java.util.Map;
import java.util.Map.Entry;
import java.util.Set;
import java.util.SortedSet;
@@ -79,6 +82,7 @@
import org.dllearner.core.LearningProblemUnsupportedException;
import org.dllearner.core.Score;
import org.dllearner.core.config.ConfigHelper;
+import org.dllearner.core.config.ConfigOption;
import org.dllearner.core.configurators.CELOEConfigurator;
import org.dllearner.core.owl.Axiom;
import org.dllearner.core.owl.DatatypeProperty;
@@ -135,21 +139,29 @@
// data structure for holding the result of an algorithm run
private class AlgorithmRun {
- private LearningAlgorithm algorithm;
+ // we only store the algorithm class and not the learning algorithm object,
+ // since otherwise we run into memory problems for full enrichment
+ private Class<? extends LearningAlgorithm> algorithm;
private List<EvaluatedAxiom> axioms;
-
- public AlgorithmRun(LearningAlgorithm algorithm, List<EvaluatedAxiom> axioms) {
+ private Map<ConfigOption,String> parameters;
+
+ public AlgorithmRun(Class<? extends LearningAlgorithm> algorithm, List<EvaluatedAxiom> axioms, Map<ConfigOption,String> parameters) {
this.algorithm = algorithm;
this.axioms = axioms;
+ this.parameters = parameters;
}
- public LearningAlgorithm getAlgorithm() {
+ public Class<? extends LearningAlgorithm> getAlgorithm() {
return algorithm;
}
public List<EvaluatedAxiom> getAxioms() {
return axioms;
}
+
+ public Map<ConfigOption, String> getParameters() {
+ return parameters;
+ }
}
private static Logger logger = Logger.getLogger(Enrichment.class);
@@ -177,8 +189,8 @@
private List<Class<? extends LearningAlgorithm>> classAlgorithms;
// list of generated axioms while script is running
+ private List<AlgorithmRun> algorithmRuns;
-
private CommonPrefixMap prefixes = new CommonPrefixMap();
public Enrichment(SparqlEndpoint se, Entity resource, boolean verbose) {
@@ -209,6 +221,8 @@
classAlgorithms.add(DisjointClassesLearner.class);
classAlgorithms.add(SimpleSubclassLearner.class);
classAlgorithms.add(CELOE.class);
+
+ algorithmRuns = new LinkedList<AlgorithmRun>();
}
@SuppressWarnings("unchecked")
@@ -318,7 +332,7 @@
ks2.getConfigurator().setDefaultGraphURIs(new TreeSet<String>(ks.getEndpoint().getDefaultGraphURIs()));
ks2.getConfigurator().setUseLits(false);
ks2.getConfigurator().setUseCacheDatabase(true);
- ks2.getConfigurator().setRecursionDepth(1);
+ ks2.getConfigurator().setRecursionDepth(2);
ks2.getConfigurator().setCloseAfterRecursion(true);
// ks2.getConfigurator().setSaveExtractedFragment(true);
System.out.println("getting fragment ... ");
@@ -371,7 +385,7 @@
evaluatedAxioms.add(new EvaluatedAxiom(axiom, score));
}
- toRDF(evaluatedAxioms, la, ks);
+ algorithmRuns.add(new AlgorithmRun(CELOE.class, evaluatedAxioms, ConfigHelper.getConfigOptionValuesString(la)));
cm.freeAllComponents();
return evaluatedAxioms;
}
@@ -409,7 +423,7 @@
.getCurrentlyBestEvaluatedAxioms(nrOfAxiomsToLearn);
System.out.println(prettyPrint(learnedAxioms));
- toRDF(learnedAxioms, learner, ks);
+ algorithmRuns.add(new AlgorithmRun(learner.getClass(), learnedAxioms, ConfigHelper.getConfigOptionValuesString(learner)));
return learnedAxioms;
}
@@ -437,11 +451,11 @@
/*
* Generates list of OWL axioms.
*/
- private void toRDF(List<EvaluatedAxiom> evalAxioms, LearningAlgorithm algorithm, SparqlEndpointKS ks){
- toRDF(evalAxioms, algorithm, ks, null);
+ private List<OWLAxiom> toRDF(List<EvaluatedAxiom> evalAxioms, Class<? extends LearningAlgorithm> algorithm, Map<ConfigOption,String> parameters, SparqlEndpointKS ks){
+ return toRDF(evalAxioms, algorithm, parameters, ks, null);
}
- private void toRDF(List<EvaluatedAxiom> evalAxioms, LearningAlgorithm algorithm, SparqlEndpointKS ks, String defaultNamespace){
+ private List<OWLAxiom> toRDF(List<EvaluatedAxiom> evalAxioms, Class<? extends LearningAlgorithm> algorithm, Map<ConfigOption,String> parameters, SparqlEndpointKS ks, String defaultNamespace){
if(defaultNamespace == null || defaultNamespace.isEmpty()){
defaultNamespace = DEFAULT_NS;
}
@@ -464,7 +478,7 @@
ax = f.getOWLClassAssertionAxiom(EnrichmentVocabulary.AlgorithmRun, algorithmRunInd);
axioms.add(ax);
//generate instance for algorithm
- String algorithmName = algorithm.getClass().getAnnotation(ComponentAnn.class).name();
+ String algorithmName = algorithm.getAnnotation(ComponentAnn.class).name();
String algorithmID = "http://dl-learner.org#" + algorithmName.replace(" ", "_");
OWLIndividual algorithmInd = f.getOWLNamedIndividual(IRI.create(algorithmID));
//add label to algorithm instance
@@ -474,7 +488,7 @@
ax = f.getOWLAnnotationAssertionAxiom(algorithmInd.asOWLNamedIndividual().getIRI(), labelAnno);
axioms.add(ax);
//add version to algorithm
- ax = f.getOWLDataPropertyAssertionAxiom(EnrichmentVocabulary.version, algorithmInd, algorithm.getClass().getAnnotation(ComponentAnn.class).version());
+ ax = f.getOWLDataPropertyAssertionAxiom(EnrichmentVocabulary.version, algorithmInd, algorithm.getAnnotation(ComponentAnn.class).version());
axioms.add(ax);
//add algorithm instance to algorithm run instance
ax = f.getOWLObjectPropertyAssertionAxiom(EnrichmentVocabulary.usedAlgorithm,
@@ -512,9 +526,10 @@
}
- printManchesterOWLSyntax(axioms, defaultNamespace);
- printTurtleSyntax(axioms);
+// printManchesterOWLSyntax(axioms, defaultNamespace);
+// printTurtleSyntax(axioms);
// printNTriplesSyntax(axioms);
+ return axioms;
}
private String generateId(){
@@ -546,6 +561,16 @@
}
}
+ private Model getModel(List<OWLAxiom> axioms) {
+ Model model = ModelFactory.createDefaultModel();
+ try {
+ Conversion.OWLAPIOntology2JenaModel(OWLManager.createOWLOntologyManager().createOntology(new HashSet<OWLAxiom>(axioms)), model);
+ } catch (OWLOntologyCreationException e) {
+ e.printStackTrace();
+ }
+ return model;
+ }
+
/*
* Write axioms in Turtle syntax.
*/
@@ -578,6 +603,10 @@
}
}
+ public List<AlgorithmRun> getAlgorithmRuns() {
+ return algorithmRuns;
+ }
+
public static void main(String[] args) throws IOException, ComponentInitException, IllegalArgumentException, SecurityException, InstantiationException, IllegalAccessException, InvocationTargetException, NoSuchMethodException, LearningProblemUnsupportedException {
SimpleLayout layout = new SimpleLayout();
@@ -598,9 +627,9 @@
parser.acceptsAll(asList("r", "resource"),
"The resource for which enrichment axioms should be suggested.").withOptionalArg().ofType(URI.class);
parser.acceptsAll(asList("o", "output"), "Specify a file where the output can be written.")
- .withOptionalArg();
+ .withOptionalArg().ofType(File.class);
parser.acceptsAll(asList("f", "format"),
- "Format of the generated output (plain, html, rdf).").withOptionalArg()
+ "Format of the generated output (plain, html, rdf/xml, turtle, manchester, sparul).").withOptionalArg()
.ofType(String.class).defaultsTo("plain");
// parse options and display a message for the user in case of problems
@@ -651,8 +680,31 @@
Enrichment e = new Enrichment(se, resource, verbose);
e.start();
- // TODO: print output in correct format
+ SparqlEndpointKS ks = new SparqlEndpointKS(se);
+ // TODO: some handling for inaccessible files or overwriting existing files
+ File f = (File) options.valueOf("o");
+
+ // print output in correct format
+ if(options.has("f")) {
+ // TODO: handle other formats
+ if(options.valueOf("f").equals("turtle")) {
+ List<AlgorithmRun> runs = e.getAlgorithmRuns();
+ List<OWLAxiom> axioms = new LinkedList<OWLAxiom>();
+ for(AlgorithmRun run : runs) {
+ axioms.addAll(e.toRDF(run.getAxioms(), run.getAlgorithm(), run.getParameters(), ks));
+ }
+ Model model = e.getModel(axioms);
+ if(options.has("o")) {
+ model.write(new FileOutputStream(f));
+ } else {
+ System.out.println("ENRICHMENT[");
+ model.write(System.out);
+ System.out.println("]");
+ }
+ }
+ }
+
}
}
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