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From: <lor...@us...> - 2011-11-06 21:28:54
|
Revision: 3382
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3382&view=rev
Author: lorenz_b
Date: 2011-11-06 21:28:47 +0000 (Sun, 06 Nov 2011)
Log Message:
-----------
Added new method to use redirects.
Modified Paths:
--------------
trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/learning/SPARQLTemplateBasedLearner.java
trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/sparql/Allocation.java
Modified: trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/learning/SPARQLTemplateBasedLearner.java
===================================================================
--- trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/learning/SPARQLTemplateBasedLearner.java 2011-11-06 20:15:33 UTC (rev 3381)
+++ trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/learning/SPARQLTemplateBasedLearner.java 2011-11-06 21:28:47 UTC (rev 3382)
@@ -8,9 +8,9 @@
import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
+import java.util.Comparator;
import java.util.HashMap;
import java.util.HashSet;
-import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
@@ -18,7 +18,6 @@
import java.util.SortedSet;
import java.util.TreeSet;
-import org.apache.log4j.Level;
import org.apache.log4j.Logger;
import org.dllearner.algorithm.qtl.util.ModelGenerator;
import org.dllearner.algorithm.qtl.util.ModelGenerator.Strategy;
@@ -287,7 +286,8 @@
generatedQueries = getWeightedSPARQLQueries(templates);
sparqlQueryCandidates = new ArrayList<Query>();
int i = 0;
- for(WeightedQuery wQ : generatedQueries){System.out.println(wQ);
+ for(WeightedQuery wQ : generatedQueries){
+ System.out.println(wQ.explain());
sparqlQueryCandidates.add(wQ.getQuery());
if(i == maxTestedQueries){
break;
@@ -648,12 +648,8 @@
allocations = new TreeSet<Allocation>();
for(Slot slot : t.getSlots()){
- allocations = computeAllocations(slot);
+ allocations = computeAllocations(slot, 50);
- normProminenceValues(allocations);
-
- computeScore(allocations);
-
slot2Allocations.put(slot, allocations);
//for tests add the property URI with http://dbpedia.org/property/ namespace
@@ -788,6 +784,8 @@
WeightedQuery w = new WeightedQuery(q);
double newScore = query.getScore() + a.getScore();
w.setScore(newScore);
+ w.addAllocations(query.getAllocations());
+ w.addAllocation(a);
tmp.add(w);
}
@@ -836,15 +834,20 @@
}
*/
- private Set<Allocation> computeAllocations(Slot slot){
- Set<Allocation> allocations = new TreeSet<Allocation>();
+ private SortedSet<Allocation> computeAllocations(Slot slot){
+ SortedSet<Allocation> allocations = new TreeSet<Allocation>();
SolrSearch index = getIndexBySlotType(slot);
SolrQueryResultSet rs;
for(String word : slot.getWords()){
- rs = index.getResourcesWithScores(word, 30);
+ if(slot.getSlotType() == SlotType.RESOURCE){
+ rs = index.getResourcesWithScores(word, 250);
+ } else {
+ rs = index.getResourcesWithScores(word, 30);
+ }
+
//debugging
// for(Iterator<SolrQueryResultItem> iter = rs.getItems().iterator();iter.hasNext();){
// SolrQueryResultItem item = iter.next();
@@ -855,16 +858,68 @@
System.out.println(word + "->" + rs);
for(SolrQueryResultItem item : rs.getItems()){
+ double similarity = Similarity.getSimilarity(word, item.getLabel());
+ //get the labels of the redirects and compute the highest similarity
+ if(slot.getSlotType() == SlotType.RESOURCE){
+ Set<String> labels = getRedirectLabels(item.getUri());
+ for(String label : labels){
+ double tmp = Similarity.getSimilarity(word, label);
+ if(tmp > similarity){
+ similarity = tmp;
+ }
+ }
+ }
int prominence = getProminenceValue(item.getUri(), slot.getSlotType());
- double similarity = Similarity.getSimilarity(word, item.getLabel());
allocations.add(new Allocation(item.getUri(), prominence, similarity));
}
}
- return allocations;
+ normProminenceValues(allocations);
+
+ computeScore(allocations);
+ return new TreeSet<Allocation>(allocations);
}
+ private Set<Allocation> computeAllocations(Slot slot, int limit){
+ SortedSet<Allocation> allocations = computeAllocations(slot);
+
+ if(allocations.isEmpty()){
+ return allocations;
+ }
+
+ ArrayList<Allocation> l = new ArrayList<Allocation>(allocations);
+ Collections.sort(l, new Comparator<Allocation>() {
+
+ @Override
+ public int compare(Allocation o1, Allocation o2) {
+ double dif = o1.getScore() - o2.getScore();
+ if(dif < 0){
+ return 1;
+ } else if(dif > 0){
+ return -1;
+ } else {
+ return o1.getUri().compareTo(o2.getUri());
+ }
+ }
+ });
+
+ return new TreeSet<Allocation>(l.subList(0, Math.min(limit, allocations.size())));
+ }
+
+ private Set<String> getRedirectLabels(String uri){
+ Set<String> labels = new HashSet<String>();
+ String query = String.format("SELECT ?label WHERE {?s <http://dbpedia.org/ontology/wikiPageRedirects> <%s>. ?s <%s> ?label.}", uri, RDFS.label.getURI());
+ ResultSet rs = SparqlQuery.convertJSONtoResultSet(cache.executeSelectQuery(endpoint, query));
+ QuerySolution qs;
+ while(rs.hasNext()){
+ qs = rs.next();
+ labels.add(qs.getLiteral("label").getLexicalForm());
+
+ }
+ return labels;
+ }
+
private int getProminenceValue(String uri, SlotType type){
int cnt = 1;
String query = null;
@@ -1417,15 +1472,17 @@
// Logger.getLogger(DefaultHttpParams.class).setLevel(Level.OFF);
// Logger.getLogger(HttpClient.class).setLevel(Level.OFF);
// Logger.getLogger(HttpMethodBase.class).setLevel(Level.OFF);
-// String question = "In which programming language is GIMP written?";
// String question = "Who/WP was/VBD the/DT wife/NN of/IN president/NN Lincoln/NNP";
// String question = "Who/WP produced/VBD the/DT most/JJS films/NNS";
// String question = "Which/WDT country/NN does/VBZ the/DT Airedale/NNP Terrier/NNP come/VBP from/IN";
// String question = "When/WRB was/VBD Capcom/NNP founded/VBD";
- String question = "Is/VBZ there/RB a/DT video/NN game/NN called/VBN Battle/NNP Chess/NNP";
+// String question = "Which/WDT organizations/NNS were/VBD founded/VBN in/IN 1950/CD";
+// String question = "Is/VBZ there/RB a/DT video/NN game/NN called/VBN Battle/NNP Chess/NNP";
// String question = "Which/WDT software/NN has/VBZ been/VBN developed/VBN by/IN organizations/NNS founded/VBN in/IN California/NNP";
// String question = "How/WRB many/JJ films/NNS did/VBD Leonardo/NNP DiCaprio/NNP star/VB in/IN";
// String question = "Which/WDT music/NN albums/NNS contain/VBP the/DT song/NN Last/NNP Christmas/NNP";
+// String question = "Which/WDT companies/NNS are/VBP located/VBN in/IN California/NNP USA/NNP";
+ String question = "Who/WP wrote/VBD the/DT book/NN The/NNP pillars/NNP of/NNP the/NNP Earth/NNP";
SPARQLTemplateBasedLearner learner = new SPARQLTemplateBasedLearner();learner.setUseIdealTagger(true);
// SparqlEndpoint endpoint = new SparqlEndpoint(new URL("http://greententacle.techfak.uni-bielefeld.de:5171/sparql"),
// Collections.<String>singletonList(""), Collections.<String>emptyList());
Modified: trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/sparql/Allocation.java
===================================================================
--- trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/sparql/Allocation.java 2011-11-06 20:15:33 UTC (rev 3381)
+++ trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/sparql/Allocation.java 2011-11-06 21:28:47 UTC (rev 3382)
@@ -78,9 +78,9 @@
@Override
public int compareTo(Allocation o) {
if(o.getScore() < this.score){
+ return 1;
+ } else if(o.getScore() > this.score){
return -1;
- } else if(o.getScore() > this.score){
- return 1;
} else {
return this.uri.compareTo(o.getUri());
}
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|
|
From: <jen...@us...> - 2011-11-06 20:15:40
|
Revision: 3381
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3381&view=rev
Author: jenslehmann
Date: 2011-11-06 20:15:33 +0000 (Sun, 06 Nov 2011)
Log Message:
-----------
small fixes
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/reasoning/FastInstanceChecker.java
trunk/scripts/src/main/java/org/dllearner/scripts/evaluation/NLP2RDFEval.java
Modified: trunk/components-core/src/main/java/org/dllearner/reasoning/FastInstanceChecker.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/reasoning/FastInstanceChecker.java 2011-11-06 14:16:46 UTC (rev 3380)
+++ trunk/components-core/src/main/java/org/dllearner/reasoning/FastInstanceChecker.java 2011-11-06 20:15:33 UTC (rev 3381)
@@ -249,6 +249,9 @@
// System.out.println("FIC: " + description + " " + individual);
if (description instanceof NamedClass) {
+ if(!atomicConcepts.contains(description)) {
+ throw new ReasoningMethodUnsupportedException("Class " + description + " is not contained in knowledge base.");
+ }
return classInstancesPos.get((NamedClass) description).contains(individual);
} else if (description instanceof Negation) {
Description child = description.getChild(0);
Modified: trunk/scripts/src/main/java/org/dllearner/scripts/evaluation/NLP2RDFEval.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/evaluation/NLP2RDFEval.java 2011-11-06 14:16:46 UTC (rev 3380)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/evaluation/NLP2RDFEval.java 2011-11-06 20:15:33 UTC (rev 3381)
@@ -96,7 +96,7 @@
PosNegLP lp = context.getBean(PosNegLP.class);
AbstractCELA la = context.getBean(AbstractCELA.class);
CrossValidation cv = new CrossValidation(la,lp,rs,nrOfFolds,false);
- content += cv.getfMeasure().getMean();
+ content += Math.round(cv.getfMeasure().getMean())+",";
}
content += "\n";
}
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|
|
From: <jen...@us...> - 2011-11-06 14:16:53
|
Revision: 3380
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3380&view=rev
Author: jenslehmann
Date: 2011-11-06 14:16:46 +0000 (Sun, 06 Nov 2011)
Log Message:
-----------
NLP2RDF evaluation script
Modified Paths:
--------------
trunk/interfaces/src/main/java/org/dllearner/cli/CLI.java
trunk/interfaces/src/main/java/org/dllearner/cli/CrossValidation.java
Added Paths:
-----------
trunk/scripts/src/main/java/org/dllearner/scripts/evaluation/NLP2RDFEval.java
Modified: trunk/interfaces/src/main/java/org/dllearner/cli/CLI.java
===================================================================
--- trunk/interfaces/src/main/java/org/dllearner/cli/CLI.java 2011-11-05 19:21:09 UTC (rev 3379)
+++ trunk/interfaces/src/main/java/org/dllearner/cli/CLI.java 2011-11-06 14:16:46 UTC (rev 3380)
@@ -60,6 +60,7 @@
private static Logger rootLogger = Logger.getRootLogger();
private ApplicationContext context;
+ private IConfiguration configuration;
private File confFile;
// some CLI options
@@ -76,10 +77,9 @@
this.confFile = confFile;
}
- public void run() throws IOException { // ApplicationContext context, String algorithmBeanName){
-
- IConfiguration configuration = null;
-
+ // separate init methods, because some scripts may want to just get the application
+ // context from a conf file without actually running it
+ public void init() throws IOException {
if(context == null) {
Resource confFileR = new FileSystemResource(confFile);
List<Resource> springConfigResources = new ArrayList<Resource>();
@@ -88,7 +88,10 @@
ApplicationContextBuilder builder = new DefaultApplicationContextBuilder();
context = builder.buildApplicationContext(configuration,springConfigResources);
}
-
+ }
+
+ public void run() throws IOException {
+
if(writeSpringConfiguration) {
SpringConfigurationXMLBeanConverter converter = new SpringConfigurationXMLBeanConverter();
XmlObject xml;
Modified: trunk/interfaces/src/main/java/org/dllearner/cli/CrossValidation.java
===================================================================
--- trunk/interfaces/src/main/java/org/dllearner/cli/CrossValidation.java 2011-11-05 19:21:09 UTC (rev 3379)
+++ trunk/interfaces/src/main/java/org/dllearner/cli/CrossValidation.java 2011-11-06 14:16:46 UTC (rev 3380)
@@ -283,4 +283,12 @@
}
+ public Stat getfMeasure() {
+ return fMeasure;
+ }
+
+ public Stat getfMeasureTraining() {
+ return fMeasureTraining;
+ }
+
}
Added: trunk/scripts/src/main/java/org/dllearner/scripts/evaluation/NLP2RDFEval.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/evaluation/NLP2RDFEval.java (rev 0)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/evaluation/NLP2RDFEval.java 2011-11-06 14:16:46 UTC (rev 3380)
@@ -0,0 +1,108 @@
+/**
+ * Copyright (C) 2011, Jens Lehmann
+ *
+ * This file is part of DL-Learner.
+ *
+ * DL-Learner is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * DL-Learner is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+package org.dllearner.scripts.evaluation;
+
+import java.io.File;
+import java.io.IOException;
+
+import org.dllearner.cli.CLI;
+import org.dllearner.cli.CrossValidation;
+import org.dllearner.core.AbstractCELA;
+import org.dllearner.core.AbstractReasonerComponent;
+import org.dllearner.learningproblems.PosNegLP;
+import org.dllearner.utilities.Files;
+import org.springframework.context.ApplicationContext;
+
+/**
+ * Currently, the script is NLP2RDF evaluation specific, but may be generalised later.
+ *
+ * - take array of conf files as arguments
+ * - run cross val over them and get basic stats
+ * - output to a CSV file
+ * - run through gnumeric
+ *
+ * @author Jens Lehmann
+ *
+ */
+public class NLP2RDFEval {
+
+ public static void main(String args[]) throws IOException {
+
+ // TODO: convert those things into command line arguments to make the script generic
+ int nrOfFolds = 5;
+
+// String confs[] = new String[] {
+// "../examples/nlp2rdf/learning_7_components/stanford/gas9_vs_nat-gas26.conf",
+// "../examples/nlp2rdf/learning_7_components/opennlp/gas9_vs_nat-gas26.conf",
+// "../examples/nlp2rdf/learning_7_components/gateannie/gas9_vs_nat-gas26.conf",
+// "../examples/nlp2rdf/learning_7_components/dbpedia_spotlight/gas9_vs_nat-gas26.conf",
+// "../examples/nlp2rdf/learning_7_components/dbpedia_spotlight_plus/gas9_vs_nat-gas26.conf",
+// };
+//
+ String baseDir = "../examples/nlp2rdf/learning_7_components/";
+
+ String outputFile = "results.csv";
+ String content = "";
+
+ String[] tools = new String[] {
+ "stanford", "opennlp", "gateannie", "dbpedia_spotlight", "dbpedia_spotlight_plus" //, "combined"
+ };
+
+ String topics[] = new String[] {
+ "gas9_vs_nat-gas26", "copper17_vs_gold35", "oilseed11_vs_soybean35", "veg-oil18_vs_palm-oil17"
+ };
+ // shorter labels for diagram
+ String topiclabels[] = new String[] {
+ "gas", "copper", "oilseed", "veg-oil"
+ };
+
+ for(String tool : tools) {
+ content += "," + tool;
+ }
+ content += "\n";
+
+ // loop through topics
+ for(int i=0; i<topics.length; i++) {
+ content += topiclabels[i] + ",";
+
+ for(String tool : tools) {
+ String conf = baseDir + tool + "/" + topics[i] + ".conf";
+ File confFile = new File(conf);
+ System.out.print("Next file: " + confFile);
+ CLI cli = new CLI(confFile);
+ cli.init();
+ System.out.println("File " + confFile + " initialised.");
+
+ // perform cross validation
+ ApplicationContext context = cli.getContext();
+ AbstractReasonerComponent rs = context.getBean(AbstractReasonerComponent.class);
+ PosNegLP lp = context.getBean(PosNegLP.class);
+ AbstractCELA la = context.getBean(AbstractCELA.class);
+ CrossValidation cv = new CrossValidation(la,lp,rs,nrOfFolds,false);
+ content += cv.getfMeasure().getMean();
+ }
+ content += "\n";
+ }
+
+ Files.createFile(new File(baseDir + outputFile), content);
+
+ }
+
+}
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|
|
From: <lor...@us...> - 2011-11-05 19:21:15
|
Revision: 3379
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3379&view=rev
Author: lorenz_b
Date: 2011-11-05 19:21:09 +0000 (Sat, 05 Nov 2011)
Log Message:
-----------
Fixed compiler errors caused by missing imports.
Modified Paths:
--------------
trunk/scripts/src/main/java/org/dllearner/examples/pdb/PDBWekaLearner.java
Modified: trunk/scripts/src/main/java/org/dllearner/examples/pdb/PDBWekaLearner.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/examples/pdb/PDBWekaLearner.java 2011-11-05 14:55:12 UTC (rev 3378)
+++ trunk/scripts/src/main/java/org/dllearner/examples/pdb/PDBWekaLearner.java 2011-11-05 19:21:09 UTC (rev 3379)
@@ -1,4 +1,9 @@
package org.dllearner.examples.pdb;
+
+import java.io.File;
+import java.io.IOException;
+
+import org.apache.log4j.Logger;
/*
import java.io.File;
import java.io.FileWriter;
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|
|
From: <seb...@us...> - 2011-11-05 14:55:19
|
Revision: 3378
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3378&view=rev
Author: sebastianwtr
Date: 2011-11-05 14:55:12 +0000 (Sat, 05 Nov 2011)
Log Message:
-----------
[tbsl] fixed some bugs
Modified Paths:
--------------
trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/exploration/Sparql/SparqlObject.java
Modified: trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/exploration/Sparql/SparqlObject.java
===================================================================
--- trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/exploration/Sparql/SparqlObject.java 2011-11-05 13:03:30 UTC (rev 3377)
+++ trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/exploration/Sparql/SparqlObject.java 2011-11-05 14:55:12 UTC (rev 3378)
@@ -117,7 +117,7 @@
String s = null;
BufferedReader in = null;
- // Lies Textzeilen aus der Datei in einen Vector:
+ // Liest Textzeilen aus der Datei in einen Vector:
try {
in = new BufferedReader(
new InputStreamReader(
@@ -182,9 +182,9 @@
}
String answer;
answer=sendServerQuestionRequest(query);
- //System.out.println(query);
+ System.out.println(query);
System.out.println("Antwort: " + answer);
- String out=tmp + "\n" + question + ":\n"+answer+"\n";
+ String out=tmp + "\n" + "Question: "+question + "\n"+"Query: " + query +"\n Anwer: "+answer+"\n\n##############################";
BufferedWriter outfile = new BufferedWriter(
new OutputStreamWriter(
@@ -242,8 +242,31 @@
for(SPARQL_Filter tmp : temp.getFilters()) filters=filters+tmp+" ";
//System.out.println("\n");
System.out.println("\n");
- query="PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> "+temp.getQt().toString()+" "+selTerms+" { "+ conditions.replace("--","") + "}"+filters;
+ query="PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> "+temp.getQt().toString()+" "+selTerms+" WHERE { "+ conditions.replace("--","") + "}"+filters;
+ String conditions_new = "";
+ for(Path condition: temp.getConditions()){
+ //make conditions up-side-down
+ String[] tmp_upside = condition.toString().split(" -- ");
+ String tmp_conditions_new="";
+ for(String con : tmp_upside) tmp_conditions_new = con +" "+tmp_conditions_new;
+ //remove all dots befor end
+ tmp_conditions_new=tmp_conditions_new.replace(".", "");
+ //at the end ein .
+ tmp_conditions_new = tmp_conditions_new + ".";
+
+ //conditions_new=tmp_conditions_new;
+
+ conditions_new=conditions_new + tmp_conditions_new;
+ }
+
+
+
+ System.out.println("Conditions: " + conditions);
+ System.out.println("Conditions_new: " + conditions_new);
+
+
+ String query_upside_down = "PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> "+temp.getQt().toString()+" "+selTerms+" WHERE { "+ conditions_new.replace("--","") + "}"+filters;
String[] slots= null;
for(Slot slot : temp.getSlots()){
@@ -262,11 +285,24 @@
else replace="?"+array[0];
//System.out.println("replace: " + replace);
//hier dann den hm wert von array[1] eintragen
- query=query.replace(replace, "<"+hm.get(array[1].toLowerCase())+">");
+ String hm_result=hm.get(array[1].toLowerCase());
+ try
+ {
+ if(hm_result.contains("Category:")) hm_result=hm_result.replace("Category:","");
+ }
+ catch ( Exception e )
+ {
+ //System.out.println( "Das war keine Zahl!" );
+ }
+
+ query=query.replace(replace, "<"+hm_result+">");
+ query_upside_down=query_upside_down.replace(replace, "<"+hm_result+">");
+
}
//System.out.println("Query: "+query);
lstquery.add(query);
+ lstquery.add(query_upside_down);
}
@@ -418,6 +454,7 @@
string=string.replace("</td>","");
string=string.replace("<td>","");
string=string.replace("<th>callret-0</th>", "");
+ string=string.replace("<th>y</th>","");
return string;
}
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|
|
From: <jen...@us...> - 2011-11-05 13:03:37
|
Revision: 3377
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3377&view=rev
Author: jenslehmann
Date: 2011-11-05 13:03:30 +0000 (Sat, 05 Nov 2011)
Log Message:
-----------
short test for NLP2RDF
Modified Paths:
--------------
trunk/interfaces/src/main/java/org/dllearner/cli/CLI.java
trunk/interfaces/src/test/java/org/dllearner/cli/NLP2RDFCLITest.java
Modified: trunk/interfaces/src/main/java/org/dllearner/cli/CLI.java
===================================================================
--- trunk/interfaces/src/main/java/org/dllearner/cli/CLI.java 2011-11-05 07:57:16 UTC (rev 3376)
+++ trunk/interfaces/src/main/java/org/dllearner/cli/CLI.java 2011-11-05 13:03:30 UTC (rev 3377)
@@ -86,7 +86,7 @@
configuration = new ConfParserConfiguration(confFileR);
ApplicationContextBuilder builder = new DefaultApplicationContextBuilder();
- ApplicationContext context = builder.buildApplicationContext(configuration,springConfigResources);
+ context = builder.buildApplicationContext(configuration,springConfigResources);
}
if(writeSpringConfiguration) {
Modified: trunk/interfaces/src/test/java/org/dllearner/cli/NLP2RDFCLITest.java
===================================================================
--- trunk/interfaces/src/test/java/org/dllearner/cli/NLP2RDFCLITest.java 2011-11-05 07:57:16 UTC (rev 3376)
+++ trunk/interfaces/src/test/java/org/dllearner/cli/NLP2RDFCLITest.java 2011-11-05 13:03:30 UTC (rev 3377)
@@ -5,6 +5,8 @@
import org.dllearner.core.AbstractReasonerComponent;
import org.dllearner.core.ReasonerComponent;
+import org.dllearner.core.owl.Individual;
+import org.dllearner.core.owl.ObjectProperty;
import org.junit.Test;
import org.springframework.context.ApplicationContext;
@@ -12,10 +14,22 @@
@Test
public void sampleTest() throws IOException {
- File f = new File("../examples/nlp2rdf/sample/sample1.conf");
+// File f = new File("../examples/nlp2rdf/sample/sample1.conf");
+ File f = new File("../examples/nlp2rdf/learning_initial_6/dbpedia_spotlight_plus/copper17_vs_gold35.conf");
CLI cli = new CLI(f);
cli.run();
ApplicationContext context = cli.getContext();
AbstractReasonerComponent rc = context.getBean(AbstractReasonerComponent.class);
+
+ Individual i = new Individual("http://test.de/TOPICS/copper/COPPER+MEETING+AGREES+GOALS+OF+STUDY+GROUP#offset_592_596_U.S.");
+ System.out.println("all information about " + i + ": ");
+ System.out.println(rc.getObjectPropertyRelationships(i));
+
+ ObjectProperty op = new ObjectProperty("http://ns.aksw.org/scms/means");
+ System.out.println("all relationships with scms:means:");
+ System.out.println(rc.getPropertyMembers(op));
+
+ System.out.println("all object properties:");
+ System.out.println(rc.getObjectProperties());
}
}
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|
|
From: <lor...@us...> - 2011-11-05 07:57:23
|
Revision: 3376
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3376&view=rev
Author: lorenz_b
Date: 2011-11-05 07:57:16 +0000 (Sat, 05 Nov 2011)
Log Message:
-----------
Added GROUP BY to query syntax, to be SPARQL 1.1 conform.
Modified Paths:
--------------
trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/sparql/Query.java
trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/sparql/SPARQL_Term.java
trunk/components-ext/src/test/java/org/dllearner/algorithm/tbsl/Evaluation.java
Modified: trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/sparql/Query.java
===================================================================
--- trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/sparql/Query.java 2011-11-05 07:05:23 UTC (rev 3375)
+++ trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/sparql/Query.java 2011-11-05 07:57:16 UTC (rev 3376)
@@ -143,6 +143,8 @@
public String toString()
{
+ String groupBy = null;
+
String retVal = "";
for (SPARQL_Prefix prefix : prefixes)
{
@@ -153,9 +155,14 @@
{
retVal += "\nSELECT ";
+ String lastSelectTerm = null;
for (SPARQL_Term term : selTerms)
{
retVal += term.toString() + " ";
+ if(selTerms.size() > 1 && term.toString().contains("COUNT")){
+ groupBy = lastSelectTerm;
+ }
+ lastSelectTerm = term.toString();
}
}
else retVal += "\nASK ";
@@ -175,6 +182,10 @@
}
retVal += "}\n";
+
+ if(groupBy != null){
+ retVal += "GROUP BY (" + groupBy + ")\n";
+ }
if (orderBy != null && !orderBy.isEmpty())
{
Modified: trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/sparql/SPARQL_Term.java
===================================================================
--- trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/sparql/SPARQL_Term.java 2011-11-05 07:05:23 UTC (rev 3375)
+++ trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/sparql/SPARQL_Term.java 2011-11-05 07:57:16 UTC (rev 3376)
@@ -87,7 +87,7 @@
// System.err.println("SPARQL_Term: name="+name+",alias="+alias+",agg="+aggregate+",orderBy="+orderBy); // DEBUG
if (aggregate != SPARQL_Aggregate.NONE) {
if (alias != null && !alias.equals(name))
- return aggregate+"(?"+name.toLowerCase()+") AS ?" + alias;
+ return "(" + aggregate+"(?"+name.toLowerCase()+") AS ?" + alias + ")";
else
return aggregate+"(?"+name.toLowerCase()+")";
}
Modified: trunk/components-ext/src/test/java/org/dllearner/algorithm/tbsl/Evaluation.java
===================================================================
--- trunk/components-ext/src/test/java/org/dllearner/algorithm/tbsl/Evaluation.java 2011-11-05 07:05:23 UTC (rev 3375)
+++ trunk/components-ext/src/test/java/org/dllearner/algorithm/tbsl/Evaluation.java 2011-11-05 07:57:16 UTC (rev 3376)
@@ -381,7 +381,7 @@
latex.beginEnumeration();
for(WeightedQuery wQ : generatedQueries){
latex.beginEnumerationItem();
- com.hp.hpl.jena.query.Query q = QueryFactory.create(wQ.getQuery().toString());
+ com.hp.hpl.jena.query.Query q = QueryFactory.create(wQ.getQuery().toString(), Syntax.syntaxARQ);
if(q.toString().contains("http://dbpedia.org/property/")){
q.setPrefix("dbp", "http://dbpedia.org/property/");
}
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|
|
From: <lor...@us...> - 2011-11-05 07:05:30
|
Revision: 3375
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3375&view=rev
Author: lorenz_b
Date: 2011-11-05 07:05:23 +0000 (Sat, 05 Nov 2011)
Log Message:
-----------
Some changes in eval output.
Modified Paths:
--------------
trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/learning/SPARQLTemplateBasedLearner.java
trunk/components-ext/src/test/java/org/dllearner/algorithm/tbsl/Evaluation.java
Modified: trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/learning/SPARQLTemplateBasedLearner.java
===================================================================
--- trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/learning/SPARQLTemplateBasedLearner.java 2011-11-04 15:22:54 UTC (rev 3374)
+++ trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/learning/SPARQLTemplateBasedLearner.java 2011-11-05 07:05:23 UTC (rev 3375)
@@ -119,6 +119,8 @@
private Map<Template, Collection<? extends Query>> template2Queries;
private Map<Slot, List<String>> slot2URI;
+ private Set<WeightedQuery> generatedQueries;
+
private Map<String, String> prefixMap;
private Lemmatizer lemmatizer = new LingPipeLemmatizer();// StanfordLemmatizer();
@@ -282,10 +284,10 @@
// sparqlQueryCandidates = getNBestQueryCandidatesForTemplates(template2Queries);
//get the weighted query candidates
- Set<WeightedQuery> weightedQueries = getWeightedSPARQLQueries(templates);
+ generatedQueries = getWeightedSPARQLQueries(templates);
sparqlQueryCandidates = new ArrayList<Query>();
int i = 0;
- for(WeightedQuery wQ : weightedQueries){System.out.println(wQ);
+ for(WeightedQuery wQ : generatedQueries){System.out.println(wQ);
sparqlQueryCandidates.add(wQ.getQuery());
if(i == maxTestedQueries){
break;
@@ -302,6 +304,22 @@
}
+ public Set<WeightedQuery> getGeneratedQueries() {
+ return generatedQueries;
+ }
+
+ public Set<WeightedQuery> getGeneratedQueries(int topN) {
+ Set<WeightedQuery> topNQueries = new TreeSet<WeightedQuery>();
+ int max = Math.min(topN, generatedQueries.size());
+ for(WeightedQuery wQ : generatedQueries){
+ topNQueries.add(wQ);
+ if(topNQueries.size() == max){
+ break;
+ }
+ }
+ return topNQueries;
+ }
+
public List<String> getSPARQLQueries() throws NoTemplateFoundException{
logger.info("Generating SPARQL query templates...");
mon.start();
@@ -1253,7 +1271,10 @@
logger.info("Testing query:\n" + query);
boolean result = executeAskQuery(query);
learnedSPARQLQueries.put(query, result);
- if(stopIfQueryResultNotEmpty && result){
+// if(stopIfQueryResultNotEmpty && result){
+// return;
+// }
+ if(stopIfQueryResultNotEmpty){
return;
}
logger.info("Result: " + result);
@@ -1400,7 +1421,8 @@
// String question = "Who/WP was/VBD the/DT wife/NN of/IN president/NN Lincoln/NNP";
// String question = "Who/WP produced/VBD the/DT most/JJS films/NNS";
// String question = "Which/WDT country/NN does/VBZ the/DT Airedale/NNP Terrier/NNP come/VBP from/IN";
- String question = "When/WRB was/VBD Capcom/NNP founded/VBD";
+// String question = "When/WRB was/VBD Capcom/NNP founded/VBD";
+ String question = "Is/VBZ there/RB a/DT video/NN game/NN called/VBN Battle/NNP Chess/NNP";
// String question = "Which/WDT software/NN has/VBZ been/VBN developed/VBN by/IN organizations/NNS founded/VBN in/IN California/NNP";
// String question = "How/WRB many/JJ films/NNS did/VBD Leonardo/NNP DiCaprio/NNP star/VB in/IN";
// String question = "Which/WDT music/NN albums/NNS contain/VBP the/DT song/NN Last/NNP Christmas/NNP";
Modified: trunk/components-ext/src/test/java/org/dllearner/algorithm/tbsl/Evaluation.java
===================================================================
--- trunk/components-ext/src/test/java/org/dllearner/algorithm/tbsl/Evaluation.java 2011-11-04 15:22:54 UTC (rev 3374)
+++ trunk/components-ext/src/test/java/org/dllearner/algorithm/tbsl/Evaluation.java 2011-11-05 07:05:23 UTC (rev 3375)
@@ -37,8 +37,10 @@
import org.dllearner.algorithm.tbsl.learning.NoTemplateFoundException;
import org.dllearner.algorithm.tbsl.learning.SPARQLTemplateBasedLearner;
import org.dllearner.algorithm.tbsl.sparql.Query;
+import org.dllearner.algorithm.tbsl.sparql.SPARQL_Prefix;
import org.dllearner.algorithm.tbsl.sparql.Slot;
import org.dllearner.algorithm.tbsl.sparql.Template;
+import org.dllearner.algorithm.tbsl.sparql.WeightedQuery;
import org.dllearner.algorithm.tbsl.util.LatexWriter;
import org.dllearner.kb.sparql.ExtractionDBCache;
import org.dllearner.kb.sparql.SparqlEndpoint;
@@ -49,8 +51,10 @@
import org.w3c.dom.NodeList;
import org.xml.sax.SAXException;
+import com.hp.hpl.jena.query.QueryFactory;
import com.hp.hpl.jena.query.QuerySolution;
import com.hp.hpl.jena.query.ResultSet;
+import com.hp.hpl.jena.query.Syntax;
import com.hp.hpl.jena.rdf.model.RDFNode;
import com.hp.hpl.jena.sparql.engine.http.QueryEngineHTTP;
import com.hp.hpl.jena.sparql.vocabulary.FOAF;
@@ -369,32 +373,34 @@
latex.endEnumeration();
//get the generated SPARQL query candidates
- Map<Template, Collection<? extends Query>> template2Queries = stbl.getTemplates2SPARQLQueries();
+ Set<WeightedQuery> generatedQueries = stbl.getGeneratedQueries(15);
//write generated queries subsection
- latex.beginSubsection("Top " + topN2Print + " generated queries per template");
- int k = 1;
- List<Query> queries;
- for(Template t : templates){
- latex.beginSubSubsection("Template " + k);
- queries = new ArrayList<Query>(template2Queries.get(t));
- if(!queries.isEmpty()){
- latex.beginEnumeration();
- }
- //print top n queries to latex file
- int max = Math.min(topN2Print, queries.size());
- for(int j = 0; j < max; j++){
+ latex.beginSubsection("Top " + 15 + " generated queries");
+ if(!generatedQueries.isEmpty()){
+ latex.beginEnumeration();
+ for(WeightedQuery wQ : generatedQueries){
latex.beginEnumerationItem();
- latex.addListing(queries.get(j).toString());
+ com.hp.hpl.jena.query.Query q = QueryFactory.create(wQ.getQuery().toString());
+ if(q.toString().contains("http://dbpedia.org/property/")){
+ q.setPrefix("dbp", "http://dbpedia.org/property/");
+ }
+ if(q.toString().contains("http://dbpedia.org/ontology/")){
+ q.setPrefix("dbo", "http://dbpedia.org/ontology/");
+ }
+ if(q.toString().contains("http://dbpedia.org/resource/")){
+ q.setPrefix("dbr", "http://dbpedia.org/resource/");
+ }
+ String queryString = q.toString();
+ String requestURL = new QueryEngineHTTP(endpoint.getURL().toString(), queryString).toString();
+// System.out.println(requestURL);
+ queryString = queryString + "\n" + "Score(" + wQ.getScore() + ")";
+ latex.addListing(queryString);
latex.endEnumerationItem();
}
- if(!queries.isEmpty()){
- latex.endEnumeration();
- }
- k++;
+ latex.endEnumeration();
}
-
//get the URIs for each template slot
latex.beginSubsection("Covered entities");
Map<Slot, List<String>> slot2URIsMap = stbl.getSlot2URIs();
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|
|
From: <lor...@us...> - 2011-11-04 15:23:00
|
Revision: 3374
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3374&view=rev
Author: lorenz_b
Date: 2011-11-04 15:22:54 +0000 (Fri, 04 Nov 2011)
Log Message:
-----------
Added comparable interface.
Modified Paths:
--------------
trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/sparql/Allocation.java
Modified: trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/sparql/Allocation.java
===================================================================
--- trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/sparql/Allocation.java 2011-11-04 15:03:03 UTC (rev 3373)
+++ trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/sparql/Allocation.java 2011-11-04 15:22:54 UTC (rev 3374)
@@ -1,7 +1,7 @@
package org.dllearner.algorithm.tbsl.sparql;
-public class Allocation {
+public class Allocation implements Comparable<Allocation>{
private String uri;
@@ -74,6 +74,17 @@
return false;
return true;
}
+
+ @Override
+ public int compareTo(Allocation o) {
+ if(o.getScore() < this.score){
+ return -1;
+ } else if(o.getScore() > this.score){
+ return 1;
+ } else {
+ return this.uri.compareTo(o.getUri());
+ }
+ }
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|
|
From: <lor...@us...> - 2011-11-04 15:03:18
|
Revision: 3373
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3373&view=rev
Author: lorenz_b
Date: 2011-11-04 15:03:03 +0000 (Fri, 04 Nov 2011)
Log Message:
-----------
Some small changes.
Modified Paths:
--------------
trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/learning/SPARQLTemplateBasedLearner.java
Modified: trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/learning/SPARQLTemplateBasedLearner.java
===================================================================
--- trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/learning/SPARQLTemplateBasedLearner.java 2011-11-04 12:51:33 UTC (rev 3372)
+++ trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/learning/SPARQLTemplateBasedLearner.java 2011-11-04 15:03:03 UTC (rev 3373)
@@ -627,7 +627,7 @@
Set<Allocation> allocations;
for(Template t : templates){
- allocations = new HashSet<Allocation>();
+ allocations = new TreeSet<Allocation>();
for(Slot slot : t.getSlots()){
allocations = computeAllocations(slot);
@@ -639,6 +639,7 @@
slot2Allocations.put(slot, allocations);
//for tests add the property URI with http://dbpedia.org/property/ namespace
+ //TODO should be replaced by usage of a separate SOLR index
Set<Allocation> tmp = new HashSet<Allocation>();
if(slot.getSlotType() == SlotType.PROPERTY || slot.getSlotType() == SlotType.SYMPROPERTY){
for(Allocation a : allocations){
@@ -690,9 +691,7 @@
for(Allocation a : slot2Allocations.get(slot)){
for(WeightedQuery query : queries){
Query q = new Query(query.getQuery());
- if(a.getUri().equals("http://dbpedia.org/ontology/developer") && q.toString().contains("/Organisation>") && q.toString().contains("/Software>")){
- System.out.println("YES:\n" + query);
- }
+
boolean drop = false;
if(slot.getSlotType() == SlotType.PROPERTY || slot.getSlotType() == SlotType.SYMPROPERTY){
for(SPARQL_Triple triple : q.getTriplesWithVar(slot.getAnchor())){
@@ -713,17 +712,21 @@
allRanges.remove("http://www.w3.org/2002/07/owl#Thing");
String typeURI = typeTriple.getValue().getName().substring(1,typeTriple.getValue().getName().length()-1);
Set<String> allTypes = getSuperClasses(typeURI);
- allTypes.add(typeTriple.getValue().getName());
- if(typeURI.equals("http://dbpedia.org/ontology/Organisation") && a.getUri().equals("http://dbpedia.org/ontology/developer")){
- System.out.println("RANGES: " + allRanges);
- System.out.println("TYPES: " + allTypes);
- }
+ allTypes.add(typeURI);
+// if(typeURI.equals("http://dbpedia.org/ontology/Organisation") && a.getUri().equals("http://dbpedia.org/ontology/developer")){
+// System.out.println("RANGES: " + allRanges);
+// System.out.println("TYPES: " + allTypes);
+// }
if(!org.mindswap.pellet.utils.SetUtils.intersects(allRanges, allTypes)){
drop = true;
+// if(typeURI.equals("http://dbpedia.org/ontology/Organisation") && a.getUri().equals("http://dbpedia.org/ontology/developer") && q.toString().contains("/Software>")){
+// System.out.println("RANGES: " + allRanges);
+// System.out.println("TYPES: " + allTypes);
+// System.out.println("DROPPING: \n" + q.toString());
+// }
} else {
- if(typeURI.equals("http://dbpedia.org/ontology/Organisation") && a.getUri().equals("http://dbpedia.org/ontology/developer"))
- System.out.println("DROPPING: \n" + q.toString());
+
}
}
} else {
@@ -745,16 +748,16 @@
String typeURI = typeTriple.getValue().getName().substring(1,typeTriple.getValue().getName().length()-1);
Set<String> allTypes = getSuperClasses(typeURI);
allTypes.add(typeTriple.getValue().getName());
- if(typeURI.equals("http://dbpedia.org/ontology/Organisation") && a.getUri().equals("http://dbpedia.org/ontology/developer")){
- System.out.println("DOMAINS: " + allDomains);
- System.out.println("TYPES: " + allTypes);
- }
+// if(typeURI.equals("http://dbpedia.org/ontology/Organisation") && a.getUri().equals("http://dbpedia.org/ontology/developer")){
+// System.out.println("DOMAINS: " + allDomains);
+// System.out.println("TYPES: " + allTypes);
+// }
if(!org.mindswap.pellet.utils.SetUtils.intersects(allDomains, allTypes)){
drop = true;
+// System.out.println("DROPPING: \n" + q.toString());
} else {
- if(typeURI.equals("http://dbpedia.org/ontology/Organisation") && a.getUri().equals("http://dbpedia.org/ontology/developer"))
- System.out.println("DROPPING: \n" + q.toString());
+
}
}
}
@@ -816,13 +819,13 @@
*/
private Set<Allocation> computeAllocations(Slot slot){
- Set<Allocation> allocations = new HashSet<Allocation>();
+ Set<Allocation> allocations = new TreeSet<Allocation>();
SolrSearch index = getIndexBySlotType(slot);
SolrQueryResultSet rs;
for(String word : slot.getWords()){
- rs = index.getResourcesWithScores(word, 10);
+ rs = index.getResourcesWithScores(word, 30);
//debugging
// for(Iterator<SolrQueryResultItem> iter = rs.getItems().iterator();iter.hasNext();){
@@ -832,7 +835,7 @@
// }
// }
-// System.out.println(word + "->" + rs);
+ System.out.println(word + "->" + rs);
for(SolrQueryResultItem item : rs.getItems()){
int prominence = getProminenceValue(item.getUri(), slot.getSlotType());
double similarity = Similarity.getSimilarity(word, item.getLabel());
@@ -1397,7 +1400,8 @@
// String question = "Who/WP was/VBD the/DT wife/NN of/IN president/NN Lincoln/NNP";
// String question = "Who/WP produced/VBD the/DT most/JJS films/NNS";
// String question = "Which/WDT country/NN does/VBZ the/DT Airedale/NNP Terrier/NNP come/VBP from/IN";
- String question = "Which/WDT software/NN has/VBZ been/VBN developed/VBN by/IN organizations/NNS founded/VBN in/IN California/NNP";
+ String question = "When/WRB was/VBD Capcom/NNP founded/VBD";
+// String question = "Which/WDT software/NN has/VBZ been/VBN developed/VBN by/IN organizations/NNS founded/VBN in/IN California/NNP";
// String question = "How/WRB many/JJ films/NNS did/VBD Leonardo/NNP DiCaprio/NNP star/VB in/IN";
// String question = "Which/WDT music/NN albums/NNS contain/VBP the/DT song/NN Last/NNP Christmas/NNP";
SPARQLTemplateBasedLearner learner = new SPARQLTemplateBasedLearner();learner.setUseIdealTagger(true);
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|
|
From: <lor...@us...> - 2011-11-04 12:51:40
|
Revision: 3372
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3372&view=rev
Author: lorenz_b
Date: 2011-11-04 12:51:33 +0000 (Fri, 04 Nov 2011)
Log Message:
-----------
Added constructors with POS tagger.
Modified Paths:
--------------
trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/learning/SPARQLTemplateBasedLearner.java
trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/templator/Templator.java
Modified: trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/learning/SPARQLTemplateBasedLearner.java
===================================================================
--- trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/learning/SPARQLTemplateBasedLearner.java 2011-11-03 19:32:25 UTC (rev 3371)
+++ trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/learning/SPARQLTemplateBasedLearner.java 2011-11-04 12:51:33 UTC (rev 3372)
@@ -5,10 +5,12 @@
import java.io.IOException;
import java.net.URL;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
+import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
@@ -22,6 +24,7 @@
import org.dllearner.algorithm.qtl.util.ModelGenerator.Strategy;
import org.dllearner.algorithm.tbsl.nlp.Lemmatizer;
import org.dllearner.algorithm.tbsl.nlp.LingPipeLemmatizer;
+import org.dllearner.algorithm.tbsl.nlp.PartOfSpeechTagger;
import org.dllearner.algorithm.tbsl.search.HierarchicalSolrSearch;
import org.dllearner.algorithm.tbsl.search.SolrQueryResultItem;
import org.dllearner.algorithm.tbsl.search.SolrQueryResultSet;
@@ -68,6 +71,10 @@
public class SPARQLTemplateBasedLearner implements SparqlQueryLearningAlgorithm{
+ //for debugging
+ List<String> exclusions = Arrays.asList(new String[]{"http://dbpedia.org/ontology/GeopoliticalOrganisation",
+ "http://dbpedia.org/ontology/Non-ProfitOrganisation"});
+
enum Ranking{
LUCENE, SIMILARITY, NONE
}
@@ -140,6 +147,20 @@
templateGenerator = new Templator();
}
+ public SPARQLTemplateBasedLearner(Options options, PartOfSpeechTagger tagger){
+ init(options);
+
+ Set<String> predicateFilters = new HashSet<String>();
+ predicateFilters.add("http://dbpedia.org/ontology/wikiPageWikiLink");
+ predicateFilters.add("http://dbpedia.org/property/wikiPageUsesTemplate");
+
+ prefixMap = Prefixes.getPrefixes();
+
+ modelGenenerator = new ModelGenerator(endpoint, predicateFilters);
+
+ templateGenerator = new Templator(tagger);
+ }
+
/*
* Only for Evaluation useful.
*/
@@ -635,7 +656,7 @@
Query cleanQuery = t.getQuery();
queries.add(new WeightedQuery(cleanQuery));
- Set<WeightedQuery> tmp = new HashSet<WeightedQuery>();
+ Set<WeightedQuery> tmp = new TreeSet<WeightedQuery>();
List<Slot> sortedSlots = new ArrayList<Slot>();
Set<Slot> classSlots = new HashSet<Slot>();
for(Slot slot : t.getSlots()){
@@ -669,8 +690,8 @@
for(Allocation a : slot2Allocations.get(slot)){
for(WeightedQuery query : queries){
Query q = new Query(query.getQuery());
- if(a.getUri().equals("http://dbpedia.org/ontology/developer") && q.toString().contains("/Organisation>")){
- System.out.println("YES");
+ if(a.getUri().equals("http://dbpedia.org/ontology/developer") && q.toString().contains("/Organisation>") && q.toString().contains("/Software>")){
+ System.out.println("YES:\n" + query);
}
boolean drop = false;
if(slot.getSlotType() == SlotType.PROPERTY || slot.getSlotType() == SlotType.SYMPROPERTY){
@@ -701,7 +722,8 @@
if(!org.mindswap.pellet.utils.SetUtils.intersects(allRanges, allTypes)){
drop = true;
} else {
-// System.out.println("DROPPING: \n" + q.toString());
+ if(typeURI.equals("http://dbpedia.org/ontology/Organisation") && a.getUri().equals("http://dbpedia.org/ontology/developer"))
+ System.out.println("DROPPING: \n" + q.toString());
}
}
} else {
@@ -731,7 +753,8 @@
if(!org.mindswap.pellet.utils.SetUtils.intersects(allDomains, allTypes)){
drop = true;
} else {
-// System.out.println("DROPPING: \n" + q.toString());
+ if(typeURI.equals("http://dbpedia.org/ontology/Organisation") && a.getUri().equals("http://dbpedia.org/ontology/developer"))
+ System.out.println("DROPPING: \n" + q.toString());
}
}
}
@@ -801,6 +824,14 @@
for(String word : slot.getWords()){
rs = index.getResourcesWithScores(word, 10);
+ //debugging
+// for(Iterator<SolrQueryResultItem> iter = rs.getItems().iterator();iter.hasNext();){
+// SolrQueryResultItem item = iter.next();
+// if(exclusions.contains(item.getUri())){
+// iter.remove();
+// }
+// }
+
// System.out.println(word + "->" + rs);
for(SolrQueryResultItem item : rs.getItems()){
int prominence = getProminenceValue(item.getUri(), slot.getSlotType());
@@ -1364,12 +1395,11 @@
// Logger.getLogger(HttpMethodBase.class).setLevel(Level.OFF);
// String question = "In which programming language is GIMP written?";
// String question = "Who/WP was/VBD the/DT wife/NN of/IN president/NN Lincoln/NNP";
- String question = "Who/WP produced/VBD the/DT most/JJS films/NNS";
+// String question = "Who/WP produced/VBD the/DT most/JJS films/NNS";
// String question = "Which/WDT country/NN does/VBZ the/DT Airedale/NNP Terrier/NNP come/VBP from/IN";
-// String question = "Which/WDT software/NN has/VBZ been/VBN developed/VBN by/IN organizations/NNS founded/VBN in/IN California/NNP";
+ String question = "Which/WDT software/NN has/VBZ been/VBN developed/VBN by/IN organizations/NNS founded/VBN in/IN California/NNP";
// String question = "How/WRB many/JJ films/NNS did/VBD Leonardo/NNP DiCaprio/NNP star/VB in/IN";
-
-// String question = "Give me all books written by authors influenced by Ernest Hemingway.";
+// String question = "Which/WDT music/NN albums/NNS contain/VBP the/DT song/NN Last/NNP Christmas/NNP";
SPARQLTemplateBasedLearner learner = new SPARQLTemplateBasedLearner();learner.setUseIdealTagger(true);
// SparqlEndpoint endpoint = new SparqlEndpoint(new URL("http://greententacle.techfak.uni-bielefeld.de:5171/sparql"),
// Collections.<String>singletonList(""), Collections.<String>emptyList());
Modified: trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/templator/Templator.java
===================================================================
--- trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/templator/Templator.java 2011-11-03 19:32:25 UTC (rev 3371)
+++ trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/templator/Templator.java 2011-11-04 12:51:33 UTC (rev 3372)
@@ -41,6 +41,7 @@
PartOfSpeechTagger tagger;
LTAGLexicon g;
LTAG_Lexicon_Constructor LTAG_Constructor = new LTAG_Lexicon_Constructor();
+
Parser p;
Preprocessor pp;
@@ -53,9 +54,14 @@
boolean ONE_SCOPE_ONLY = true;
boolean UNTAGGED_INPUT = true;
- boolean USE_NER = false;
+ boolean USE_NER = true;
public Templator() {
+ this(new StanfordPartOfSpeechTagger());
+ }
+
+ public Templator(final PartOfSpeechTagger tagger) {
+ this.tagger = tagger;
List<InputStream> grammarFiles = new ArrayList<InputStream>();
for(int i = 0; i < GRAMMAR_FILES.length; i++){
@@ -64,8 +70,6 @@
g = LTAG_Constructor.construct(grammarFiles);
- tagger = new StanfordPartOfSpeechTagger();
-// tagger = new ApachePartOfSpeechTagger();
p = new Parser();
p.SHOW_GRAMMAR = true;
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <chr...@us...> - 2011-11-03 19:32:31
|
Revision: 3371
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3371&view=rev
Author: christinaunger
Date: 2011-11-03 19:32:25 +0000 (Thu, 03 Nov 2011)
Log Message:
-----------
[tbsl] yet another two bug fixes (template generation)
Modified Paths:
--------------
trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/ltag/parser/GrammarFilter.java
trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/templator/SlotBuilder.java
trunk/components-ext/src/main/resources/tbsl/lexicon/english.lex
Modified: trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/ltag/parser/GrammarFilter.java
===================================================================
--- trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/ltag/parser/GrammarFilter.java 2011-11-03 17:28:10 UTC (rev 3370)
+++ trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/ltag/parser/GrammarFilter.java 2011-11-03 19:32:25 UTC (rev 3371)
@@ -298,11 +298,11 @@
}
semName = semName.substring(1);
- out.add(new Pair<String,String>("(NP NP* ADJ:'"+ w +"' " + rawNames + ")", "<x,l1,<e,t>,[ l1:[ y | SLOT_title(x,y), regex(y,'" + semName + "') ] ], [],[],[ SLOT_title/PROPERTY/title^name ]>"));
+ out.add(new Pair<String,String>("(NP NP* ADJ:'"+ w +"' " + rawNames + ")", "<x,l1,<e,t>,[ l1:[ y | SLOT_title(x,y), regex(y,'" + semName + "') ] ], [],[],[ SLOT_title/PROPERTY/title^name^label ]>"));
out.add(new Pair<String,String>("(NP NP* ADJ:'"+ w +"' " + rawNames + ")", "<x,l1,<e,t>,[ l1:[|] ],[],[],[ x/RESOURCE/"+semName+"]>"));
- out.add(new Pair<String,String>("(DP DP* ADJ:'"+ w +"' " + rawNames + ")", "<x,l1,<<e,t>,t>,[ l1:[ y | SLOT_title(x,y), regex(y,'" + semName + "') ] ], [],[],[ SLOT_title/PROPERTY/title^name ]>"));
+ out.add(new Pair<String,String>("(DP DP* ADJ:'"+ w +"' " + rawNames + ")", "<x,l1,<<e,t>,t>,[ l1:[ y | SLOT_title(x,y), regex(y,'" + semName + "') ] ], [],[],[ SLOT_title/PROPERTY/title^name^label ]>"));
out.add(new Pair<String,String>("(DP DP* ADJ:'"+ w +"' " + rawNames + ")", "<x,l1,<<e,t>,t>,[ l1:[|] ],[],[],[ x/RESOURCE/"+semName+"]>"));
- out.add(new Pair<String,String>("(ADJ ADJ:'"+ w +"' " + rawNames + ")", "<x,l1,<e,t>,[ l1:[ y | SLOT_title(x,y), regex(y,'" + semName + "') ] ], [],[],[ SLOT_title/PROPERTY/title^name ]>"));
+ out.add(new Pair<String,String>("(ADJ ADJ:'"+ w +"' " + rawNames + ")", "<x,l1,<e,t>,[ l1:[ y | SLOT_title(x,y), regex(y,'" + semName + "') ] ], [],[],[ SLOT_title/PROPERTY/title^name^label ]>"));
out.add(new Pair<String,String>("(ADJ ADJ:'"+ w +"' " + rawNames + ")", "<x,l1,<e,t>,[ l1:[|] ],[],[],[ x/RESOURCE/"+semName+"]>"));
return out;
Modified: trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/templator/SlotBuilder.java
===================================================================
--- trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/templator/SlotBuilder.java 2011-11-03 17:28:10 UTC (rev 3370)
+++ trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/templator/SlotBuilder.java 2011-11-03 19:32:25 UTC (rev 3371)
@@ -261,7 +261,8 @@
String[] vEntry = {token,
"(S DP[subj] (VP V:'" + token + "' DP[obj]))",
"<x,l1,t,[ l1:[|], l4:[ | SLOT_" + token + "(x,y) ] ],[(l2,x,subj,<<e,t>,t>),(l3,y,obj,<<e,t>,t>)],[ l2<l1,l3<l1,l4<scope(l2),l4<scope(l3) ],[" + symslot + "]>" +
- " ;; <x,l1,t,[ l1:[|], l4:[ | empty(x,y) ] ],[(l2,x,subj,<<e,t>,t>),(l3,y,obj,<<e,t>,t>)],[ l2<l1,l3<l1,l4<scope(l2),l4<scope(l3) ],[]>"};
+ " ;; <x,l1,t,[ l1:[|], l4:[ | empty(x,y) ] ],[(l2,x,subj,<<e,t>,t>),(l3,y,obj,<<e,t>,t>)],[ l2<l1,l3<l1,l4<scope(l2),l4<scope(l3) ],[]>" +
+ " ;; <x,l1,t,[ l1:[|], l4:[ | empty(y,x) ] ],[(l2,x,subj,<<e,t>,t>),(l3,y,obj,<<e,t>,t>)],[ l2<l1,l3<l1,l4<scope(l2),l4<scope(l3) ],[]>"};
result.add(vEntry);
}
else if (pos.equals("VB")) {
Modified: trunk/components-ext/src/main/resources/tbsl/lexicon/english.lex
===================================================================
--- trunk/components-ext/src/main/resources/tbsl/lexicon/english.lex 2011-11-03 17:28:10 UTC (rev 3370)
+++ trunk/components-ext/src/main/resources/tbsl/lexicon/english.lex 2011-11-03 19:32:25 UTC (rev 3371)
@@ -69,7 +69,6 @@
at least || (DP DET:'at' DET:'least' NUM[num] NP[noun]) || <y,l1,<<e,t>,t>,[l1:[ y,j |count(a,y,j), greaterorequal(j,x) ]],[(l2,y,noun,<e,t>),(l3,x,num,e)],[ l1=l2, l2=l3 ],[]>
at most || (DP DET:'at' DET:'most' NUM[num] NP[noun]) || <y,l1,<<e,t>,t>,[l1:[ y,j | count(a,y,j), smallerorequal(j,x) ]],[(l2,y,noun,<e,t>),(l3,x,num,e)],[ l1=l2, l2=l3 ],[]>
exactly || (DP DET:'exactly' NUM[num] NP[noun]) || <y,l1,<<e,t>,t>,[l1:[ y,j | count(y,j), equals(j,x) ]],[(l2,y,noun,<e,t>),(l3,x,num,e)],[ l1=l2, l2=l3 ],[]>
- s || (DP DP* DET:'s' NP[noun]) || -
other || (NP ADJ:'other' NP*) || <x,l1,<e,t>,[ l1:[ | ] ], [],[],[]>
total || (NP ADJ:'total' NP[np]) || <s,l1,<e,t>,[ l1:[ ?s | sum(a,x,s) ] ], [ (l2,x,np,<e,t>) ],[ l2=l1 ],[]>
@@ -86,7 +85,7 @@
the least || (DET DET:'the' DET:'least') || <y, l1, e, [ l1:[ | l2:[ y | ] THELEAST y l3:[|] ] ], [], [],[]>
// CHEAT!
- highest || (NP ADJ:'highest' NP*) || <x, l1, e, [ l1:[ | maximum(a,x,x) ] ], [], [],[]> ;; <x, l1, e, [ l1:[ j | SLOT_high(x,j), maximum(a,j,j) ] ],[],[],[ SLOT_high/PROPERTY/height^elevation ]>
+ highest || (NP ADJ:'highest' NP*) || <x, l1, e, [ l1:[ | maximum(x) ] ], [], [],[]> ;; <x, l1, e, [ l1:[ j | SLOT_high(x,j), maximum(j) ] ],[],[],[ SLOT_high/PROPERTY/height^elevation ]>
// COUNT
more than || (DP DET:'more' DET:'than' NUM[num] NP[np]) || <y,l1,<<e,t>,t>,[ l1:[ y,c | count(y,c), greater(c,z) ] ],[(l2,y,np,<e,t>),(l3,z,num,e)],[l2=l1,l3=l1],[]> ;; <y,l1,<<e,t>,t>,[ l1:[ y | greater(y,z) ] ],[(l2,y,np,<e,t>),(l3,z,num,e)],[l2=l1,l3=l1],[]>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <km...@us...> - 2011-11-03 17:28:21
|
Revision: 3370
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3370&view=rev
Author: kmpf
Date: 2011-11-03 17:28:10 +0000 (Thu, 03 Nov 2011)
Log Message:
-----------
Changed *.conf format.
Modified Paths:
--------------
trunk/scripts/src/main/java/org/dllearner/examples/pdb/AminoAcids.java
trunk/scripts/src/main/java/org/dllearner/examples/pdb/HelixRDFCreator.java
trunk/scripts/src/main/java/org/dllearner/examples/pdb/PDBIdRdfModel.java
trunk/scripts/src/main/java/org/dllearner/examples/pdb/PDBWekaLearner.java
Modified: trunk/scripts/src/main/java/org/dllearner/examples/pdb/AminoAcids.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/examples/pdb/AminoAcids.java 2011-11-03 15:02:37 UTC (rev 3369)
+++ trunk/scripts/src/main/java/org/dllearner/examples/pdb/AminoAcids.java 2011-11-03 17:28:10 UTC (rev 3370)
@@ -90,6 +90,33 @@
return resprint;
}
+ public static HashMap<Resource, StringBuffer> getAminoAcidStringBufferMap(String init){
+ // put all amino acid resources and the their conf-files together
+ HashMap<Resource, StringBuffer> resourceString = new HashMap<Resource, StringBuffer>(30);
+ resourceString.put(ALA, new StringBuffer(init));
+ resourceString.put(CYS, new StringBuffer(init));
+ resourceString.put(ASP, new StringBuffer(init));
+ resourceString.put(GLU, new StringBuffer(init));
+ resourceString.put(PHE, new StringBuffer(init));
+ resourceString.put(GLY, new StringBuffer(init));
+ resourceString.put(HIS, new StringBuffer(init));
+ resourceString.put(ILE, new StringBuffer(init));
+ resourceString.put(LYS, new StringBuffer(init));
+ resourceString.put(LEU, new StringBuffer(init));
+ resourceString.put(MET, new StringBuffer(init));
+ resourceString.put(ASN, new StringBuffer(init));
+ resourceString.put(PRO, new StringBuffer(init));
+ resourceString.put(GLN, new StringBuffer(init));
+ resourceString.put(ARG, new StringBuffer(init));
+ resourceString.put(SER, new StringBuffer(init));
+ resourceString.put(THR, new StringBuffer(init));
+ resourceString.put(VAL, new StringBuffer(init));
+ resourceString.put(TRP, new StringBuffer(init));
+ resourceString.put(TYR, new StringBuffer(init));
+ resourceString.put(SEL, new StringBuffer(init));
+ return resourceString;
+ }
+
public static HashMap<Resource, String> getAminoAcidArffAttributeMap(){
HashMap<Resource, String> resdata = new HashMap<Resource, String>(30);
resdata.put(ALA, new String("2,0,0.5,?,?"));
Modified: trunk/scripts/src/main/java/org/dllearner/examples/pdb/HelixRDFCreator.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/examples/pdb/HelixRDFCreator.java 2011-11-03 15:02:37 UTC (rev 3369)
+++ trunk/scripts/src/main/java/org/dllearner/examples/pdb/HelixRDFCreator.java 2011-11-03 17:28:10 UTC (rev 3370)
@@ -101,16 +101,16 @@
* load = true -> load alle .rdf, .conf and .arff Files that can be found within the directory dataDir
* load = false -> don't load anything
*/
- Boolean dlLearn = true;
- Boolean wekaLearn = true;
+ Boolean dlLearn = false;
+ Boolean wekaLearn = false;
int dataSet = 5;
/*
* data for test purpose
*/
-// PdbProtein testProtein = new PdbProtein("1XFF");
- PDBProtein testProtein = new PDBProtein("1XFF", "A");
+ PDBProtein testProtein = new PDBProtein("1XFF");
+// PDBProtein testProtein = new PDBProtein("1LMB", "3");
/*
* create a training data set
@@ -233,14 +233,14 @@
try {
String line = protein.getPdbID() + "." + protein.getChainID() + "." + protein.getSpecies() + "\n";
FileWriter out = new FileWriter(speciesProteins, true);
- _logger.debug("Write " + line + "to file " + speciesProteins.getPath() + speciesProteins.getName());
+ _logger.debug("Write " + line + "to file " + speciesProteins.getPath());
out.write(line);
out.close();
} catch (FileNotFoundException e) {
- _logger.error("Could not find file " + speciesProteins.getPath() + speciesProteins.getName());
+ _logger.error("Could not find file " + speciesProteins.getPath() );
e.printStackTrace();
} catch (IOException e) {
- _logger.error("Something went wrong while trying to write to " + speciesProteins.getPath() + speciesProteins.getName());
+ _logger.error("Something went wrong while trying to write to " + speciesProteins.getPath() );
e.printStackTrace();
}
}
@@ -325,33 +325,53 @@
try
{
PDBProtein protein = model.getProtein();
- // the file with all amino acids
+
+ // the .conf file that contains all positives and negatives
String confFilePath = pdbDir + protein.getConfFileName();
PrintStream confFile = new PrintStream (new File(confFilePath));
- // add import statements to confFile
- String importStmt = new String("import(\"../AA_properties.owl\");\n" +
- "import(\"" + protein.getRdfFileName() + "\");\n");
- confFile.println(importStmt);
-
- HashMap<Resource, File> confFilePerResidue = AminoAcids.getAllConfFiles(pdbDir, protein.getConfFileName());
- HashMap<Resource, PrintStream> resprint = AminoAcids.getAminoAcidPrintStreamMap(confFilePerResidue);
- Property type = ResourceFactory.createProperty("http://www.w3.org/1999/02/22-rdf-syntax-ns#", "type");
+ // knowledge source definition
+ String ks = new String ("// knowledge source definition\n" +
+ "ks.type = \"OWL File\"\n" +
+ "ks.fileName = \"AA_properties.owl\"\n" +
+ "\n" +
+ "ks.type = \"OWL File\"\n" +
+ "ks.fileName = \"" + protein.getRdfFileName() + "\"\n");
+ // learning problem
+ StringBuffer lp = new StringBuffer ("// learning problem\n" +
+ "lp.type = \"posNegStandard\"" +
+ "\n" +
+ "lp.positiveExamples = { ");
- // add import statements to <PDB ID>_<Amino Acid>.conf files
- Iterator<Resource> keys = resprint.keySet().iterator();
- while (keys.hasNext()){
- resprint.get(keys.next()).println(importStmt);
+ // separate files that contain only positives and negatives of a distinct type
+ HashMap<Resource, File> confFilePerResidue =
+ AminoAcids.getAllConfFiles(pdbDir, protein.getConfFileName());
+ HashMap<Resource, PrintStream> resprint =
+ AminoAcids.getAminoAcidPrintStreamMap(confFilePerResidue);
+ HashMap<Resource, StringBuffer> resourceStringBuffer =
+ AminoAcids.getAminoAcidStringBufferMap(lp.toString());
+
+ // add knowledge source definition to <PDB ID>.conf files
+ confFile.println(ks);
+
+ // add knowledge source definition to <PDB ID>_<Amino Acid>.conf files
+ Iterator<Resource> resources = resprint.keySet().iterator();
+ while (resources.hasNext()){
+ resprint.get(resources.next()).println(ks);
}
- // add every amino acid in positive list to <PDB ID>.conf and its corresponding <PDB ID>_<Amino Acid>.conf
+
ArrayList<Resource> positives = model.getPositives();
+
+ Property type = ResourceFactory.createProperty("http://www.w3.org/1999/02/22-rdf-syntax-ns#", "type");
+
+ // add positive examples to <PDB ID>.conf and corresponding <PDB ID>_<Amino Acid>.conf files
for (int i = 0 ; i < positives.size() ; i++ ) {
- confFile.println("+\"" + positives.get(i).getURI() + "\"");
+ lp.append("\"" + positives.get(i).getURI() + "\", ");
try{
Statement spo = model.getModel().getProperty(positives.get(i), type);
- resprint.get(spo.getResource()).println("+\"" + positives.get(i).getURI() + "\"");
+ resourceStringBuffer.get(spo.getResource()).append("\"" + positives.get(i).getURI() + "\", ");
} catch (NullPointerException e) {
// What was the Object that probably caused the pain?
_logger.error("Object probably not in our HashMap: " +
@@ -360,13 +380,29 @@
}
}
+ if (lp.toString().contains(","))
+ lp.deleteCharAt(lp.lastIndexOf(","));
+ lp.append("}\n" +
+ "lp.negativeExamples = { ");
+
+ resources = resourceStringBuffer.keySet().iterator();
+ while (resources.hasNext()){
+ Resource residue = resources.next();
+ if (resourceStringBuffer.get(residue).toString().contains(","))
+ resourceStringBuffer.get(residue).deleteCharAt(
+ resourceStringBuffer.get(residue).lastIndexOf(","));
+ resourceStringBuffer.get(residue).append("}\n" +
+ "lp.negativeExamples = { ");
+ }
+
+
// add every amino acid in negative list to <PDB ID>.conf and its corresponding <PDB ID>_<Amino Acid>.conf
ArrayList<Resource> negatives = model.getNegatives();
for (int i = 0 ; i < negatives.size() ; i++ ) {
- confFile.println("-\"" + negatives.get(i).getURI() + "\"");
+ lp.append("\"" + negatives.get(i).getURI() + "\", ");
try{
Statement spo = model.getModel().getProperty(negatives.get(i), type);
- resprint.get(spo.getResource()).println("-\"" + negatives.get(i).getURI() + "\"");
+ resourceStringBuffer.get(spo.getResource()).append("\"" + negatives.get(i).getURI() + "\", ");
} catch (NullPointerException e) {
// What was the Object that probably caused the pain?
_logger.error("Object probably not in our HashMap: " +
@@ -374,7 +410,26 @@
e.printStackTrace();
}
}
+
+ // add learning problem to <PDB ID>.conf file
+ // and write learning problem to file
+ if (lp.toString().contains(","))
+ lp.deleteCharAt(lp.lastIndexOf(","));
+ lp.append("}\n");
+ confFile.println(lp);
+ // add learning problem to <PDB ID>_<Amino Acid>.conf files
+ // and write learning problem to file
+ resources = resourceStringBuffer.keySet().iterator();
+ while (resources.hasNext()){
+ Resource residue = resources.next();
+ if (resourceStringBuffer.get(residue).toString().contains(","))
+ resourceStringBuffer.get(residue).deleteCharAt(
+ resourceStringBuffer.get(residue).lastIndexOf(","));
+ resourceStringBuffer.get(residue).append("}\n");
+ resprint.get(residue).println(resourceStringBuffer.get(residue));
+ }
+
// Important - free up resources used running the query
confFile.close();
@@ -382,7 +437,6 @@
while ( newkeys.hasNext() ){
resprint.get(newkeys.next()).close();
}
-
}
catch (IOException e)
{
@@ -409,16 +463,16 @@
* ATTRIBUTES
*/
// Integer declaring Position in chain
- String attributes = "@ATTRIBUTE hydrophob NUMERIC\n" + // Hydrophilic = 0; Hydrophobic = 1; Very_hydrophobic = 2
+ StringBuffer attributes = new StringBuffer("@ATTRIBUTE hydrophob NUMERIC\n" + // Hydrophilic = 0; Hydrophobic = 1; Very_hydrophobic = 2
"@ATTRIBUTE charge NUMERIC\n" + // Negative = -1; Neutral = 0; Positive = 1
"@ATTRIBUTE size NUMERIC\n" + // Large = 2; Small = 1; Tiny = 0.5
"@ATTRIBUTE aromaticity NUMERIC\n" + // Aliphatic = 0; Aromatic = 1
- "@ATTRIBUTE hydrogen_bonding NUMERIC\n"; // Donor = 1; Donor/Acceptor = 0; Acceptor = -1
+ "@ATTRIBUTE hydrogen_bonding NUMERIC\n"); // Donor = 1; Donor/Acceptor = 0; Acceptor = -1
for (int i = -8; i <= 8; i++) {
- attributes += "@ATTRIBUTE aa_position_" + i + " {A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y}\n"; // amino acid at position $i from current amino acid
+ attributes.append("@ATTRIBUTE aa_position_" + i + " {A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y}\n"); // amino acid at position $i from current amino acid
}
- attributes += "@ATTRIBUTE in_helix NUMERIC\n"; // Helix = 1 Other = 0
+ attributes.append("@ATTRIBUTE in_helix NUMERIC\n"); // Helix = 1 Other = 0
_logger.debug(attributes);
out.println(attributes);
@@ -443,32 +497,32 @@
Resource currentAA = firstAA;
Resource nextAA = firstAA;
- int i = 0;
- String dataLine;
- do {
- dataLine = "";
+
+
+ for ( int i = 0; currentAA.hasProperty(iib); i++ ) {
+ StringBuffer dataLine = new StringBuffer("");
currentAA = nextAA;
NodeIterator niter = model.getModel().listObjectsOfProperty(currentAA, type);
while (niter.hasNext()){
Resource key = niter.next().asResource();
if (resdata.containsKey(key)){
- dataLine += resdata.get(key) +",";
+ dataLine.append( resdata.get(key) + "," );
}
}
for (int j = (i - 8); j <= (i + 8) ; j++){
try {
- dataLine += protein.getSequence().charAt(j) + ",";
+ dataLine.append( protein.getSequence().charAt(j) + "," );
} catch (IndexOutOfBoundsException e) {
- dataLine += "?,";
+ dataLine.append( "?," );
}
}
if (positives.contains(currentAA)){
- dataLine += "1";
+ dataLine.append( "1" );
} else if (negatives.contains(currentAA)){
- dataLine += "0";
+ dataLine.append( "0" );
}
@@ -479,8 +533,7 @@
}
_logger.info(dataLine);
out.println(dataLine);
- i++;
- } while (currentAA.hasProperty(iib)) ;
+ }
}
} catch (FileNotFoundException e){
e.printStackTrace();
Modified: trunk/scripts/src/main/java/org/dllearner/examples/pdb/PDBIdRdfModel.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/examples/pdb/PDBIdRdfModel.java 2011-11-03 15:02:37 UTC (rev 3369)
+++ trunk/scripts/src/main/java/org/dllearner/examples/pdb/PDBIdRdfModel.java 2011-11-03 17:28:10 UTC (rev 3370)
@@ -37,7 +37,9 @@
this._protein = protein;
this._pdbIdModel = this.getPdbRdfModel();
this.getProtein().setSequence(extractSequence(_pdbIdModel));
+ System.out.println("Sequence: " + this.getProtein().getSequence());
this.getProtein().setSpecies(extractSpecies(_pdbIdModel));
+ System.out.println("Species: " + this.getProtein().getSpecies());
createPositivesAndNegatives();
}
@@ -98,11 +100,12 @@
"PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> " +
"PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> " +
"PREFIX fn: <http://www.w3.org/2005/xpath-functions#> " +
- "CONSTRUCT {<http://bio2rdf.org/pdb:" + this.getProtein().getPdbID() + "/extraction/source/gene/organism> rdfs:label ?species. }" +
- "WHERE { ?x1 <http://purl.org/dc/terms/isPartOf> ?x2 ." +
- " ?x1 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ?x3 ." +
- " ?x1 <http://bio2rdf.org/pdb:isImmediatelyBefore> ?x4 ." +
- " ?x5 rdfs:label ?species FILTER (str(?x5) = fn:concat(str(?x2), '/extraction/source/gene/organism')) . }";
+ "CONSTRUCT { pdb:" + this.getProtein().getPdbID() + "/extraction/source/gene/organism rdfs:label ?species. }" +
+ "WHERE { ?x1 dcterms:isPartOf ?x2 ." +
+ " ?x1 rdf:type> ?x3 ." +
+ " ?x1 pdb:isImmediatelyBefore ?x4 ." +
+ " ?x5 rdfs:label ?species " +
+ " FILTER (str(?x5) = fn:concat(str(?x2), '/extraction/source/gene/organism')) . }";
// System.out.println(queryString);
@@ -189,36 +192,37 @@
"PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> " +
"PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> " +
"PREFIX fn: <http://www.w3.org/2005/xpath-functions#> " +
- "CONSTRUCT { ?x1 <http://bio2rdf.org/pdb:beginsAt> ?x2 ." +
- " ?x1 <http://bio2rdf.org/pdb:endsAt> ?x3 . " +
- " ?x5 <http://purl.org/dc/terms/isPartOf> ?x4 . " +
- " ?x5 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ?x6 ." +
- " ?x5 <http://bio2rdf.org/pdb:isImmediatelyBefore> ?x7 ." +
+ "CONSTRUCT { ?x1 pdb:beginsAt ?x2 ." +
+ " ?x1 pdb:endsAt ?x3 . " +
+ " ?x5 dcterms:isPartOf ?x4 . " +
+ " ?x5 rdf:type ?x6 ." +
+ " ?x5 pdb:isImmediatelyBefore ?x7 ." +
" ?organism rdfs:label ?organismName ." +
- " ?seq <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://bio2rdf.org/pdb:PolymerSequence> ." +
+ " ?seq rdf:type pdb:PolymerSequence ." +
" ?seq pdb:hasValue ?sequence. } " +
- "WHERE { ?x1 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://bio2rdf.org/pdb:Helix> ." +
- " ?x1 <http://bio2rdf.org/pdb:beginsAt> ?x2 ." +
- " ?x1 <http://bio2rdf.org/pdb:endsAt> ?x3 ." +
- " ?x3 <http://purl.org/dc/terms/isPartOf> ?x4 ." +
- " ?x4 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://bio2rdf.org/pdb:Polypeptide(L)> ." +
- " ?x5 <http://purl.org/dc/terms/isPartOf> ?x4 ." +
- " ?x5 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ?x6 .";
+ "WHERE { ?x1 rdf:type pdb:Helix ." +
+ " ?x1 pdb:beginsAt ?x2 ." +
+ " ?x1 pdb:endsAt ?x3 ." +
+ " ?x3 dcterms:isPartOf ?x4 ." +
+ " ?x4 rdf:type <http://bio2rdf.org/pdb:Polypeptide(L)> ." +
+ " ?x5 dcterms:isPartOf ?x4 ." +
+ " ?x5 rdf:type ?x6 .";
if (chainID.length() == 1 && pdbID.length() == 4)
{
queryString +=
- " ?x5 <http://bio2rdf.org/pdb:hasChainPosition> ?x8 ." +
- " ?x8 <http://purl.org/dc/terms/isPartOf> <http://bio2rdf.org/pdb:" +
+ " ?x5 pdb:hasChainPosition ?x8 ." +
+ " ?x8 dcterms:isPartOf pdb:" +
pdbID.toUpperCase() +
"/chain_" + chainID.toUpperCase() + "> .";
}
queryString +=
- " ?organism rdfs:label ?organismName FILTER (str(?organism) = fn:concat(str(?x4), '/extraction/source/gene/organism')) . " +
- " ?seq <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://bio2rdf.org/pdb:PolymerSequence> . " +
+ " ?organism rdfs:label ?organismName " +
+ "FILTER (str(?organism) = fn:concat(str(?x4), '/extraction/source/gene/organism')) . " +
+ " ?seq rdf:type pdb:PolymerSequence . " +
" ?seq pdb:hasValue ?sequence ." +
// with the Optional clause i get the information by which amino acid
// a amino acid is followed
- " OPTIONAL { ?x5 <http://bio2rdf.org/pdb:isImmediatelyBefore> ?x7 . } .}";
+ " OPTIONAL { ?x5 pdb:isImmediatelyBefore ?x7 . } .}";
System.out.println(queryString);
Query query = QueryFactory.create(queryString);
Modified: trunk/scripts/src/main/java/org/dllearner/examples/pdb/PDBWekaLearner.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/examples/pdb/PDBWekaLearner.java 2011-11-03 15:02:37 UTC (rev 3369)
+++ trunk/scripts/src/main/java/org/dllearner/examples/pdb/PDBWekaLearner.java 2011-11-03 17:28:10 UTC (rev 3370)
@@ -1,5 +1,5 @@
package org.dllearner.examples.pdb;
-
+/*
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
@@ -10,7 +10,7 @@
import org.apache.log4j.Level;
import org.apache.log4j.Logger;
import org.apache.log4j.SimpleLayout;
-/*
+
import weka.classifiers.Evaluation;
import weka.classifiers.bayes.NaiveBayes;
import weka.core.Instances;
@@ -22,7 +22,7 @@
private static Logger logger = Logger.getRootLogger();
public PDBWekaLearner (File arffFile) throws IOException{
- /*
+ /*
// create logger (configure this to your needs)
SimpleLayout layout = new SimpleLayout();
FileAppender fileAppender = new FileAppender(layout, "log/sample_log.txt", false);
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|
|
From: <lor...@us...> - 2011-11-03 15:02:43
|
Revision: 3369
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3369&view=rev
Author: lorenz_b
Date: 2011-11-03 15:02:37 +0000 (Thu, 03 Nov 2011)
Log Message:
-----------
Changed eval output.
Modified Paths:
--------------
trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/util/LatexWriter.java
trunk/components-ext/src/test/java/org/dllearner/algorithm/tbsl/Evaluation.java
Modified: trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/util/LatexWriter.java
===================================================================
--- trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/util/LatexWriter.java 2011-11-03 14:29:32 UTC (rev 3368)
+++ trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/util/LatexWriter.java 2011-11-03 15:02:37 UTC (rev 3369)
@@ -61,8 +61,8 @@
sb.append("\\end{document}");
}
- public void beginSection(String title){
- sb.append("\\section{").append(title).append("}").append("\\label{" + cnt++ + "}\n");
+ public void beginSection(String title, int id){
+ sb.append("\\section{").append(title).append("}").append("\\label{" + id + "}\n");
}
public void beginSubsection(String title){
Modified: trunk/components-ext/src/test/java/org/dllearner/algorithm/tbsl/Evaluation.java
===================================================================
--- trunk/components-ext/src/test/java/org/dllearner/algorithm/tbsl/Evaluation.java 2011-11-03 14:29:32 UTC (rev 3368)
+++ trunk/components-ext/src/test/java/org/dllearner/algorithm/tbsl/Evaluation.java 2011-11-03 15:02:37 UTC (rev 3369)
@@ -317,7 +317,7 @@
String errorCode = "";
LatexWriter latex = new LatexWriter();
int i = 0;
- for(Entry<Integer, String> entry : id2Question.entrySet()){if(entry.getKey()==50)continue;
+ for(Entry<Integer, String> entry : id2Question.entrySet()){//if(entry.getKey()==50)continue;
if((testID != -1 && entry.getKey() != testID) || (yagoExclusions.contains(entry.getKey())))continue;
try {
questionId = entry.getKey();
@@ -333,7 +333,7 @@
//write new section for query
- latex.beginSection(extractSentence(question));
+ latex.beginSection(extractSentence(question), questionId);
//write subsection for target
latex.beginSubsection("Target");
//write subsubsection for target query
@@ -616,7 +616,7 @@
//write new section for query
- latex.beginSection(question);
+ latex.beginSection(question, questionId);
//write subsection for target
latex.beginSubsection("Target");
//write subsubsection for target query
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|
|
From: <lor...@us...> - 2011-11-03 14:29:38
|
Revision: 3368
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3368&view=rev
Author: lorenz_b
Date: 2011-11-03 14:29:32 +0000 (Thu, 03 Nov 2011)
Log Message:
-----------
Small changes in dbprop handling.
Modified Paths:
--------------
trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/learning/SPARQLTemplateBasedLearner.java
trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/sparql/Allocation.java
Modified: trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/learning/SPARQLTemplateBasedLearner.java
===================================================================
--- trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/learning/SPARQLTemplateBasedLearner.java 2011-11-03 14:04:11 UTC (rev 3367)
+++ trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/learning/SPARQLTemplateBasedLearner.java 2011-11-03 14:29:32 UTC (rev 3368)
@@ -595,6 +595,7 @@
double score = alpha * a.getSimilarity() + beta * a.getProminence();
a.setScore(score);
}
+
}
private Set<WeightedQuery> getWeightedSPARQLQueries(Set<Template> templates){
@@ -615,6 +616,18 @@
computeScore(allocations);
slot2Allocations.put(slot, allocations);
+
+ //for tests add the property URI with http://dbpedia.org/property/ namespace
+ Set<Allocation> tmp = new HashSet<Allocation>();
+ if(slot.getSlotType() == SlotType.PROPERTY || slot.getSlotType() == SlotType.SYMPROPERTY){
+ for(Allocation a : allocations){
+ String uri = "http://dbpedia.org/property/" + a.getUri().substring(a.getUri().lastIndexOf("/")+1);
+ Allocation newA = new Allocation(uri, a.getSimilarity(), a.getProminence());
+ newA.setScore(a.getScore()-0.000001);
+ tmp.add(newA);
+ }
+ }
+ allocations.addAll(tmp);
}
@@ -787,15 +800,7 @@
SolrQueryResultSet rs;
for(String word : slot.getWords()){
rs = index.getResourcesWithScores(word, 10);
- //for tests add the property URI with http://dbpedia.org/property/ namespace
- Set<SolrQueryResultItem> tmp = new HashSet<SolrQueryResultItem>();
- if(slot.getSlotType() == SlotType.PROPERTY || slot.getSlotType() == SlotType.SYMPROPERTY){
- for(SolrQueryResultItem i : rs.getItems()){
- String uri = "http://dbpedia.org/property/" + i.getUri().substring(i.getUri().lastIndexOf("/")+1);
- tmp.add(new SolrQueryResultItem(i.getLabel(), uri));
- }
- }
- rs.addItems(tmp);
+
// System.out.println(word + "->" + rs);
for(SolrQueryResultItem item : rs.getItems()){
int prominence = getProminenceValue(item.getUri(), slot.getSlotType());
@@ -1359,9 +1364,10 @@
// Logger.getLogger(HttpMethodBase.class).setLevel(Level.OFF);
// String question = "In which programming language is GIMP written?";
// String question = "Who/WP was/VBD the/DT wife/NN of/IN president/NN Lincoln/NNP";
-// String question = "Who/WP produced/VBD the/DT most/JJS films/NNS";
- String question = "Which/WDT country/NN does/VBZ the/DT Airedale/NNP Terrier/NNP come/VBP from/IN";
+ String question = "Who/WP produced/VBD the/DT most/JJS films/NNS";
+// String question = "Which/WDT country/NN does/VBZ the/DT Airedale/NNP Terrier/NNP come/VBP from/IN";
// String question = "Which/WDT software/NN has/VBZ been/VBN developed/VBN by/IN organizations/NNS founded/VBN in/IN California/NNP";
+// String question = "How/WRB many/JJ films/NNS did/VBD Leonardo/NNP DiCaprio/NNP star/VB in/IN";
// String question = "Give me all books written by authors influenced by Ernest Hemingway.";
SPARQLTemplateBasedLearner learner = new SPARQLTemplateBasedLearner();learner.setUseIdealTagger(true);
Modified: trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/sparql/Allocation.java
===================================================================
--- trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/sparql/Allocation.java 2011-11-03 14:04:11 UTC (rev 3367)
+++ trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/sparql/Allocation.java 2011-11-03 14:29:32 UTC (rev 3368)
@@ -10,7 +10,7 @@
private double score;
- public Allocation(String uri, int prominence, double similarity) {
+ public Allocation(String uri, double prominence, double similarity) {
this.uri = uri;
this.prominence = prominence;
this.similarity = similarity;
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|
|
From: <lor...@us...> - 2011-11-03 14:04:18
|
Revision: 3367
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3367&view=rev
Author: lorenz_b
Date: 2011-11-03 14:04:11 +0000 (Thu, 03 Nov 2011)
Log Message:
-----------
Omit YAGO question in eval.
Modified Paths:
--------------
trunk/components-ext/src/test/java/org/dllearner/algorithm/tbsl/Evaluation.java
Modified: trunk/components-ext/src/test/java/org/dllearner/algorithm/tbsl/Evaluation.java
===================================================================
--- trunk/components-ext/src/test/java/org/dllearner/algorithm/tbsl/Evaluation.java 2011-11-03 14:02:03 UTC (rev 3366)
+++ trunk/components-ext/src/test/java/org/dllearner/algorithm/tbsl/Evaluation.java 2011-11-03 14:04:11 UTC (rev 3367)
@@ -60,6 +60,9 @@
public class Evaluation{
+ List<Integer> yagoExclusions = Arrays.asList(new Integer[]{1, 3, 6, 11, 15, 22, 23, 46});
+ Map<Integer, String> evalCodes = new HashMap<Integer, String>();
+
private static Logger logger = Logger.getLogger(Evaluation.class);
private static String PROPERTIES_PATH = "tbsl/evaluation/evaluation.properties";
private static final boolean USE_IDEAL_TAGGER = true;
@@ -95,6 +98,8 @@
prefixMap.put("res", "http://dbpedia.org/resource/");
prefixMap.put("foaf", FOAF.getURI());
prefixMap.put("yago", "http://dbpedia.org/class/yago/");
+
+
}
public void init() throws FileNotFoundException, IOException{
@@ -312,8 +317,8 @@
String errorCode = "";
LatexWriter latex = new LatexWriter();
int i = 0;
- for(Entry<Integer, String> entry : id2Question.entrySet()){//if(entry.getKey()==50)continue;
- if(testID != -1 && entry.getKey() != testID)continue;
+ for(Entry<Integer, String> entry : id2Question.entrySet()){if(entry.getKey()==50)continue;
+ if((testID != -1 && entry.getKey() != testID) || (yagoExclusions.contains(entry.getKey())))continue;
try {
questionId = entry.getKey();
question = entry.getValue();
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|
|
From: <lor...@us...> - 2011-11-03 14:02:10
|
Revision: 3366
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3366&view=rev
Author: lorenz_b
Date: 2011-11-03 14:02:03 +0000 (Thu, 03 Nov 2011)
Log Message:
-----------
Added dbprop: hack.
Modified Paths:
--------------
trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/learning/SPARQLTemplateBasedLearner.java
trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/sparql/Allocation.java
Modified: trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/learning/SPARQLTemplateBasedLearner.java
===================================================================
--- trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/learning/SPARQLTemplateBasedLearner.java 2011-11-03 08:26:17 UTC (rev 3365)
+++ trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/learning/SPARQLTemplateBasedLearner.java 2011-11-03 14:02:03 UTC (rev 3366)
@@ -7,7 +7,6 @@
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
-import java.util.Comparator;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
@@ -17,7 +16,7 @@
import java.util.SortedSet;
import java.util.TreeSet;
-import org.apache.commons.collections.SetUtils;
+import org.apache.log4j.Level;
import org.apache.log4j.Logger;
import org.dllearner.algorithm.qtl.util.ModelGenerator;
import org.dllearner.algorithm.qtl.util.ModelGenerator.Strategy;
@@ -42,7 +41,6 @@
import org.dllearner.algorithm.tbsl.util.Prefixes;
import org.dllearner.algorithm.tbsl.util.Similarity;
import org.dllearner.algorithm.tbsl.util.SolrQueryResultStringSimilarityComparator;
-import org.dllearner.algorithm.tbsl.util.StringSimilarityComparator;
import org.dllearner.core.ComponentInitException;
import org.dllearner.core.Oracle;
import org.dllearner.core.SparqlQueryLearningAlgorithm;
@@ -63,6 +61,7 @@
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
import com.hp.hpl.jena.sparql.engine.http.QueryEngineHTTP;
+import com.hp.hpl.jena.vocabulary.OWL;
import com.hp.hpl.jena.vocabulary.RDFS;
import com.jamonapi.Monitor;
import com.jamonapi.MonitorFactory;
@@ -571,43 +570,54 @@
}
*/
- private Set<WeightedQuery> getWeightedSPARQLQueries(Set<Template> templates){
+ private void normProminenceValues(Set<Allocation> allocations){
+ double min = 0;
+ double max = 0;
+ for(Allocation a : allocations){
+ if(a.getProminence() < min){
+ min = a.getProminence();
+ }
+ if(a.getProminence() > max){
+ max = a.getProminence();
+ }
+ }
+ for(Allocation a : allocations){
+ double prominence = a.getProminence()/(max-min);
+ a.setProminence(prominence);
+ }
+ }
+
+ private void computeScore(Set<Allocation> allocations){
double alpha = 0.8;
double beta = 1 - alpha;
+
+ for(Allocation a : allocations){
+ double score = alpha * a.getSimilarity() + beta * a.getProminence();
+ a.setScore(score);
+ }
+ }
+
+ private Set<WeightedQuery> getWeightedSPARQLQueries(Set<Template> templates){
+
Map<Slot, Set<Allocation>> slot2Allocations = new HashMap<Slot, Set<Allocation>>();
Set<WeightedQuery> allQueries = new TreeSet<WeightedQuery>();
- Set<Allocation> allAllocations;
+ Set<Allocation> allocations;
for(Template t : templates){
- allAllocations = new HashSet<Allocation>();
+ allocations = new HashSet<Allocation>();
for(Slot slot : t.getSlots()){
- Set<Allocation> allocations = computeAllocation(slot);
- allAllocations.addAll(allocations);
- slot2Allocations.put(slot, allocations);
- }
-
- int min = Integer.MAX_VALUE;
- int max = Integer.MIN_VALUE;
- for(Allocation a : allAllocations){
- if(a.getInDegree() < min){
- min = a.getInDegree();
- }
- if(a.getInDegree() > max){
- max = a.getInDegree();
- }
- }
- for(Allocation a : allAllocations){
- double prominence = a.getInDegree()/(max-min);
- a.setProminence(prominence);
+ allocations = computeAllocations(slot);
- double score = alpha * a.getSimilarity() + beta * a.getProminence();
- a.setScore(score);
+ normProminenceValues(allocations);
+ computeScore(allocations);
+
+ slot2Allocations.put(slot, allocations);
}
-// System.out.println(allAllocations);
+
Set<WeightedQuery> queries = new HashSet<WeightedQuery>();
Query cleanQuery = t.getQuery();
queries.add(new WeightedQuery(cleanQuery));
@@ -642,11 +652,13 @@
}
for(Slot slot : sortedSlots){
- if(!slot2Allocations.get(slot).isEmpty()){
+ if(!slot2Allocations.get(slot).isEmpty()){System.out.println(slot2Allocations.get(slot));
for(Allocation a : slot2Allocations.get(slot)){
for(WeightedQuery query : queries){
Query q = new Query(query.getQuery());
-
+ if(a.getUri().equals("http://dbpedia.org/ontology/developer") && q.toString().contains("/Organisation>")){
+ System.out.println("YES");
+ }
boolean drop = false;
if(slot.getSlotType() == SlotType.PROPERTY || slot.getSlotType() == SlotType.SYMPROPERTY){
for(SPARQL_Triple triple : q.getTriplesWithVar(slot.getAnchor())){
@@ -655,33 +667,38 @@
// System.out.println(triple);
for(SPARQL_Triple typeTriple : q.getRDFTypeTriples(objectVar)){
// System.out.println(typeTriple);
- Set<String> ranges = getRanges(a.getUri());
-// System.out.println(a);
- if(!ranges.isEmpty()){
- Set<String> allRanges = new HashSet<String>();
- for(String range : ranges){
- allRanges.addAll(getSuperClasses(range));
+ if(isObjectProperty(a.getUri())){
+ Set<String> ranges = getRanges(a.getUri());
+// System.out.println(a);
+ if(!ranges.isEmpty()){
+ Set<String> allRanges = new HashSet<String>();
+ for(String range : ranges){
+ allRanges.addAll(getSuperClasses(range));
+ }
+ allRanges.addAll(ranges);
+ allRanges.remove("http://www.w3.org/2002/07/owl#Thing");
+ String typeURI = typeTriple.getValue().getName().substring(1,typeTriple.getValue().getName().length()-1);
+ Set<String> allTypes = getSuperClasses(typeURI);
+ allTypes.add(typeTriple.getValue().getName());
+ if(typeURI.equals("http://dbpedia.org/ontology/Organisation") && a.getUri().equals("http://dbpedia.org/ontology/developer")){
+ System.out.println("RANGES: " + allRanges);
+ System.out.println("TYPES: " + allTypes);
+ }
+
+ if(!org.mindswap.pellet.utils.SetUtils.intersects(allRanges, allTypes)){
+ drop = true;
+ } else {
+// System.out.println("DROPPING: \n" + q.toString());
+ }
}
- allRanges.addAll(ranges);
- allRanges.remove("http://www.w3.org/2002/07/owl#Thing");
- String typeURI = typeTriple.getValue().getName().substring(1,typeTriple.getValue().getName().length()-1);
- Set<String> allTypes = getSuperClasses(typeURI);
- allTypes.add(typeTriple.getValue().getName());
-// if(typeURI.equals("http://dbpedia.org/ontology/Actor") && a.getUri().equals("http://dbpedia.org/ontology/birthPlace")){
-// System.out.println("RANGES: " + allRanges);
-// System.out.println("TYPES: " + allTypes);
-// }
-
- if(!org.mindswap.pellet.utils.SetUtils.intersects(allRanges, allTypes)){
- drop = true;
- } else {
- System.out.println("DROPPING: \n" + q.toString());
- }
+ } else {
+ drop = true;
}
+
}
for(SPARQL_Triple typeTriple : q.getRDFTypeTriples(subjectVar)){
// System.out.println(typeTriple);
- Set<String> domains = getDomains(a.getUri());System.out.println(a.getUri() + ":" + domains);
+ Set<String> domains = getDomains(a.getUri());
// System.out.println(a);
if(!domains.isEmpty()){
Set<String> allDomains = new HashSet<String>();
@@ -693,15 +710,15 @@
String typeURI = typeTriple.getValue().getName().substring(1,typeTriple.getValue().getName().length()-1);
Set<String> allTypes = getSuperClasses(typeURI);
allTypes.add(typeTriple.getValue().getName());
-// if(typeURI.equals("http://dbpedia.org/ontology/Actor") && a.getUri().equals("http://dbpedia.org/ontology/birthPlace")){
-// System.out.println("DOMAINS: " + allDomains);
-// System.out.println("TYPES: " + allTypes);
-// }
+ if(typeURI.equals("http://dbpedia.org/ontology/Organisation") && a.getUri().equals("http://dbpedia.org/ontology/developer")){
+ System.out.println("DOMAINS: " + allDomains);
+ System.out.println("TYPES: " + allTypes);
+ }
if(!org.mindswap.pellet.utils.SetUtils.intersects(allDomains, allTypes)){
drop = true;
} else {
- System.out.println("DROPPING: \n" + q.toString());
+// System.out.println("DROPPING: \n" + q.toString());
}
}
}
@@ -762,15 +779,24 @@
}
*/
- private Set<Allocation> computeAllocation(Slot slot){
+ private Set<Allocation> computeAllocations(Slot slot){
Set<Allocation> allocations = new HashSet<Allocation>();
SolrSearch index = getIndexBySlotType(slot);
SolrQueryResultSet rs;
for(String word : slot.getWords()){
- rs = index.getResourcesWithScores(word, 10);System.out.println(word + "->" + rs);
-
+ rs = index.getResourcesWithScores(word, 10);
+ //for tests add the property URI with http://dbpedia.org/property/ namespace
+ Set<SolrQueryResultItem> tmp = new HashSet<SolrQueryResultItem>();
+ if(slot.getSlotType() == SlotType.PROPERTY || slot.getSlotType() == SlotType.SYMPROPERTY){
+ for(SolrQueryResultItem i : rs.getItems()){
+ String uri = "http://dbpedia.org/property/" + i.getUri().substring(i.getUri().lastIndexOf("/")+1);
+ tmp.add(new SolrQueryResultItem(i.getLabel(), uri));
+ }
+ }
+ rs.addItems(tmp);
+// System.out.println(word + "->" + rs);
for(SolrQueryResultItem item : rs.getItems()){
int prominence = getProminenceValue(item.getUri(), slot.getSlotType());
double similarity = Similarity.getSimilarity(word, item.getLabel());
@@ -1295,6 +1321,15 @@
return domains;
}
+ private boolean isObjectProperty(String property){
+ String query = String.format("SELECT * WHERE {<%s> a <%s>}", property, OWL.ObjectProperty.getURI());
+ ResultSet rs = SparqlQuery.convertJSONtoResultSet(cache.executeSelectQuery(endpoint, query));
+ if(rs.hasNext()){
+ return true;
+ }
+ return false;
+ }
+
private Set<String> getSuperClasses(String cls){
Set<String> superClasses = new HashSet<String>();
@@ -1325,7 +1360,8 @@
// String question = "In which programming language is GIMP written?";
// String question = "Who/WP was/VBD the/DT wife/NN of/IN president/NN Lincoln/NNP";
// String question = "Who/WP produced/VBD the/DT most/JJS films/NNS";
- String question = "Which/WDT actors/NNS were/VBD born/VBN in/IN Germany/NNP";
+ String question = "Which/WDT country/NN does/VBZ the/DT Airedale/NNP Terrier/NNP come/VBP from/IN";
+// String question = "Which/WDT software/NN has/VBZ been/VBN developed/VBN by/IN organizations/NNS founded/VBN in/IN California/NNP";
// String question = "Give me all books written by authors influenced by Ernest Hemingway.";
SPARQLTemplateBasedLearner learner = new SPARQLTemplateBasedLearner();learner.setUseIdealTagger(true);
Modified: trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/sparql/Allocation.java
===================================================================
--- trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/sparql/Allocation.java 2011-11-03 08:26:17 UTC (rev 3365)
+++ trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/sparql/Allocation.java 2011-11-03 14:02:03 UTC (rev 3366)
@@ -4,16 +4,15 @@
public class Allocation {
private String uri;
- private int inDegree;
private double similarity;
private double prominence;
private double score;
- public Allocation(String uri, int inDegree, double similarity) {
+ public Allocation(String uri, int prominence, double similarity) {
this.uri = uri;
- this.inDegree = inDegree;
+ this.prominence = prominence;
this.similarity = similarity;
}
@@ -21,10 +20,6 @@
return uri;
}
- public int getInDegree() {
- return inDegree;
- }
-
public double getSimilarity() {
return similarity;
}
@@ -47,7 +42,7 @@
@Override
public String toString() {
- return uri + "(similarity: " + similarity + "; prominence: " + inDegree + ")";
+ return uri + "(score: " + score + "; similarity: " + similarity + "; prominence: " + prominence + ")";
}
@Override
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lor...@us...> - 2011-11-03 08:26:23
|
Revision: 3365
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3365&view=rev
Author: lorenz_b
Date: 2011-11-03 08:26:17 +0000 (Thu, 03 Nov 2011)
Log Message:
-----------
Continued type checking.
Modified Paths:
--------------
trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/learning/SPARQLTemplateBasedLearner.java
trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/search/SolrQueryResultSet.java
Modified: trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/learning/SPARQLTemplateBasedLearner.java
===================================================================
--- trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/learning/SPARQLTemplateBasedLearner.java 2011-11-02 22:28:33 UTC (rev 3364)
+++ trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/learning/SPARQLTemplateBasedLearner.java 2011-11-03 08:26:17 UTC (rev 3365)
@@ -667,7 +667,7 @@
String typeURI = typeTriple.getValue().getName().substring(1,typeTriple.getValue().getName().length()-1);
Set<String> allTypes = getSuperClasses(typeURI);
allTypes.add(typeTriple.getValue().getName());
-// if(typeURI.equals("http://dbpedia.org/ontology/Film") && a.getUri().equals("http://dbpedia.org/ontology/starring")){
+// if(typeURI.equals("http://dbpedia.org/ontology/Actor") && a.getUri().equals("http://dbpedia.org/ontology/birthPlace")){
// System.out.println("RANGES: " + allRanges);
// System.out.println("TYPES: " + allTypes);
// }
@@ -693,7 +693,7 @@
String typeURI = typeTriple.getValue().getName().substring(1,typeTriple.getValue().getName().length()-1);
Set<String> allTypes = getSuperClasses(typeURI);
allTypes.add(typeTriple.getValue().getName());
-// if(typeURI.equals("http://dbpedia.org/ontology/Film") && a.getUri().equals("http://dbpedia.org/ontology/starring")){
+// if(typeURI.equals("http://dbpedia.org/ontology/Actor") && a.getUri().equals("http://dbpedia.org/ontology/birthPlace")){
// System.out.println("DOMAINS: " + allDomains);
// System.out.println("TYPES: " + allTypes);
// }
@@ -769,7 +769,7 @@
SolrQueryResultSet rs;
for(String word : slot.getWords()){
- rs = index.getResourcesWithScores(word, 3);
+ rs = index.getResourcesWithScores(word, 10);System.out.println(word + "->" + rs);
for(SolrQueryResultItem item : rs.getItems()){
int prominence = getProminenceValue(item.getUri(), slot.getSlotType());
@@ -1297,8 +1297,13 @@
private Set<String> getSuperClasses(String cls){
Set<String> superClasses = new HashSet<String>();
- for(Description d : reasoner.getClassHierarchy().getSuperClasses(new NamedClass(cls))){
+
+ for(Description d : reasoner.getClassHierarchy().getSuperClasses((new NamedClass(cls)))){
superClasses.add(((NamedClass)d).getName());
+ for(Description sup : reasoner.getClassHierarchy().getSuperClasses(d)){
+ superClasses.add(((NamedClass)sup).getName());
+ }
+
}
return superClasses;
}
@@ -1319,8 +1324,8 @@
// Logger.getLogger(HttpMethodBase.class).setLevel(Level.OFF);
// String question = "In which programming language is GIMP written?";
// String question = "Who/WP was/VBD the/DT wife/NN of/IN president/NN Lincoln/NNP";
- String question = "Who/WP produced/VBD the/DT most/JJS films/NNS";
-// String question = "Give/VB me/PRP all/DT soccer/NN clubs/NNS in/IN the/DT Premier/NNP League/NNP";
+// String question = "Who/WP produced/VBD the/DT most/JJS films/NNS";
+ String question = "Which/WDT actors/NNS were/VBD born/VBN in/IN Germany/NNP";
// String question = "Give me all books written by authors influenced by Ernest Hemingway.";
SPARQLTemplateBasedLearner learner = new SPARQLTemplateBasedLearner();learner.setUseIdealTagger(true);
Modified: trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/search/SolrQueryResultSet.java
===================================================================
--- trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/search/SolrQueryResultSet.java 2011-11-02 22:28:33 UTC (rev 3364)
+++ trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/search/SolrQueryResultSet.java 2011-11-03 08:26:17 UTC (rev 3365)
@@ -27,6 +27,9 @@
this.items.addAll(rs.getItems());
}
-
+ @Override
+ public String toString() {
+ return items.toString();
+ }
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lor...@us...> - 2011-11-02 22:28:40
|
Revision: 3364
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3364&view=rev
Author: lorenz_b
Date: 2011-11-02 22:28:33 +0000 (Wed, 02 Nov 2011)
Log Message:
-----------
Added simple type restriction to ignore invalid queries.
Modified Paths:
--------------
trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/learning/SPARQLTemplateBasedLearner.java
trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/sparql/Allocation.java
Modified: trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/learning/SPARQLTemplateBasedLearner.java
===================================================================
--- trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/learning/SPARQLTemplateBasedLearner.java 2011-11-02 19:32:53 UTC (rev 3363)
+++ trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/learning/SPARQLTemplateBasedLearner.java 2011-11-02 22:28:33 UTC (rev 3364)
@@ -200,6 +200,7 @@
modelGenenerator = new ModelGenerator(endpoint, predicateFilters);
reasoner = new SPARQLReasoner(new SparqlEndpointKS(endpoint));
+ reasoner.setCache(cache);
reasoner.prepareSubsumptionHierarchy();
}
@@ -358,6 +359,7 @@
}
}
+ /*
private Set<WeightedQuery> getWeightedSPARQLQueries(Set<Template> templates){
double alpha = 0.8;
double beta = 1 - alpha;
@@ -417,17 +419,20 @@
if(!slot2Allocations.get(slot).isEmpty()){
for(Allocation a : slot2Allocations.get(slot)){
for(WeightedQuery query : queries){
- Query reversedQuery = new Query(query.getQuery());
- reversedQuery.getTriplesWithVar(slot.getAnchor()).iterator().next().reverse();
//check if the query is possible
if(slot.getSlotType() == SlotType.SYMPROPERTY){
+ Query reversedQuery = new Query(query.getQuery());
+ reversedQuery.getTriplesWithVar(slot.getAnchor()).iterator().next().reverse();
+
boolean drop = false;
- for(SPARQL_Triple triple : query.getQuery().getTriplesWithVar(slot.getAnchor())){
- System.out.println(triple);
- for(SPARQL_Triple typeTriple : query.getQuery().getRDFTypeTriples(triple.getValue().getName())){
- System.out.println(typeTriple);
+ for(SPARQL_Triple triple : reversedQuery.getTriplesWithVar(slot.getAnchor())){
+ String objectVar = triple.getValue().getName();
+ String subjectVar = triple.getVariable().getName();
+// System.out.println(triple);
+ for(SPARQL_Triple typeTriple : reversedQuery.getRDFTypeTriples(objectVar)){
+// System.out.println(typeTriple);
Set<String> ranges = getRanges(a.getUri());
- System.out.println(a);
+// System.out.println(a);
if(!ranges.isEmpty()){
Set<String> allRanges = new HashSet<String>();
for(String range : ranges){
@@ -436,14 +441,38 @@
String typeURI = typeTriple.getValue().getName().substring(1,typeTriple.getValue().getName().length()-1);
Set<String> allTypes = getSuperClasses(typeURI);
allTypes.add(typeTriple.getValue().getName());
- System.out.println("RANGES: " + ranges);
- System.out.println("TYPES: " + allTypes);
+// System.out.println("RANGES: " + ranges);
+// System.out.println("TYPES: " + allTypes);
if(!org.mindswap.pellet.utils.SetUtils.intersects(allRanges, allTypes)){
drop = true;
+ } else {
+ System.out.println("DROPPING: \n" + reversedQuery.toString());
}
}
}
+ for(SPARQL_Triple typeTriple : reversedQuery.getRDFTypeTriples(subjectVar)){
+// System.out.println(typeTriple);
+ Set<String> domains = getDomains(a.getUri());
+// System.out.println(a);
+ if(!domains.isEmpty()){
+ Set<String> allDomains = new HashSet<String>();
+ for(String domain : domains){
+ allDomains.addAll(getSuperClasses(domain));
+ }
+ String typeURI = typeTriple.getValue().getName().substring(1,typeTriple.getValue().getName().length()-1);
+ Set<String> allTypes = getSuperClasses(typeURI);
+ allTypes.add(typeTriple.getValue().getName());
+// System.out.println("DOMAINS: " + domains);
+// System.out.println("TYPES: " + allTypes);
+
+ if(!org.mindswap.pellet.utils.SetUtils.intersects(allDomains, allTypes)){
+ drop = true;
+ } else {
+ System.out.println("DROPPING: \n" + reversedQuery.toString());
+ }
+ }
+ }
}
if(!drop){
@@ -454,21 +483,245 @@
tmp.add(w);
}
-
+ }
+ Query q = new Query(query.getQuery());
+ boolean drop = false;
+ if(slot.getSlotType() == SlotType.PROPERTY || slot.getSlotType() == SlotType.SYMPROPERTY){
+ for(SPARQL_Triple triple : q.getTriplesWithVar(slot.getAnchor())){
+ String objectVar = triple.getValue().getName();
+ String subjectVar = triple.getVariable().getName();
+// System.out.println(triple);
+ for(SPARQL_Triple typeTriple : q.getRDFTypeTriples(objectVar)){
+// System.out.println(typeTriple);
+ Set<String> ranges = getRanges(a.getUri());
+// System.out.println(a);
+ if(!ranges.isEmpty()){
+ Set<String> allRanges = new HashSet<String>();
+ for(String range : ranges){
+ allRanges.addAll(getSuperClasses(range));
+ }
+ String typeURI = typeTriple.getValue().getName().substring(1,typeTriple.getValue().getName().length()-1);
+ Set<String> allTypes = getSuperClasses(typeURI);
+ allTypes.add(typeTriple.getValue().getName());
+// System.out.println("RANGES: " + ranges);
+// System.out.println("TYPES: " + allTypes);
+
+ if(!org.mindswap.pellet.utils.SetUtils.intersects(allRanges, allTypes)){
+ drop = true;
+ } else {
+ System.out.println("DROPPING: \n" + q.toString());
+ }
+ }
+ }
+ for(SPARQL_Triple typeTriple : q.getRDFTypeTriples(subjectVar)){
+// System.out.println(typeTriple);
+ Set<String> domains = getDomains(a.getUri());
+// System.out.println(a);
+ if(!domains.isEmpty()){
+ Set<String> allDomains = new HashSet<String>();
+ for(String domain : domains){
+ allDomains.addAll(getSuperClasses(domain));
+ }
+ String typeURI = typeTriple.getValue().getName().substring(1,typeTriple.getValue().getName().length()-1);
+ Set<String> allTypes = getSuperClasses(typeURI);
+ allTypes.add(typeTriple.getValue().getName());
+// System.out.println("DOMAINS: " + domains);
+// System.out.println("TYPES: " + allTypes);
+
+ if(!org.mindswap.pellet.utils.SetUtils.intersects(allDomains, allTypes)){
+ drop = true;
+ } else {
+ System.out.println("DROPPING: \n" + q.toString());
+ }
+ }
+ }
+ }
+ }
- }
+
+ if(!drop){
+ q.replaceVarWithURI(slot.getAnchor(), a.getUri());
+ WeightedQuery w = new WeightedQuery(q);
+ double newScore = query.getScore() + a.getScore();
+ w.setScore(newScore);
+ tmp.add(w);
+ }
+
+
+ }
+ }
+ queries.clear();
+ queries.addAll(tmp);System.out.println(tmp);
+ tmp.clear();
+ }
+
+ }
+ for(WeightedQuery q : queries){
+ q.setScore(q.getScore()/t.getSlots().size());
+ }
+ allQueries.addAll(queries);
+ List<Query> qList = new ArrayList<Query>();
+ for(WeightedQuery wQ : queries){//System.err.println(wQ.getQuery());
+ qList.add(wQ.getQuery());
+ }
+ template2Queries.put(t, qList);
+ }
+ return allQueries;
+ }
+ */
+
+ private Set<WeightedQuery> getWeightedSPARQLQueries(Set<Template> templates){
+ double alpha = 0.8;
+ double beta = 1 - alpha;
+ Map<Slot, Set<Allocation>> slot2Allocations = new HashMap<Slot, Set<Allocation>>();
+
+ Set<WeightedQuery> allQueries = new TreeSet<WeightedQuery>();
+
+ Set<Allocation> allAllocations;
+ for(Template t : templates){
+ allAllocations = new HashSet<Allocation>();
+
+ for(Slot slot : t.getSlots()){
+ Set<Allocation> allocations = computeAllocation(slot);
+ allAllocations.addAll(allocations);
+ slot2Allocations.put(slot, allocations);
+ }
+
+ int min = Integer.MAX_VALUE;
+ int max = Integer.MIN_VALUE;
+ for(Allocation a : allAllocations){
+ if(a.getInDegree() < min){
+ min = a.getInDegree();
+ }
+ if(a.getInDegree() > max){
+ max = a.getInDegree();
+ }
+ }
+ for(Allocation a : allAllocations){
+ double prominence = a.getInDegree()/(max-min);
+ a.setProminence(prominence);
+
+ double score = alpha * a.getSimilarity() + beta * a.getProminence();
+ a.setScore(score);
+
+ }
+// System.out.println(allAllocations);
+
+ Set<WeightedQuery> queries = new HashSet<WeightedQuery>();
+ Query cleanQuery = t.getQuery();
+ queries.add(new WeightedQuery(cleanQuery));
+
+ Set<WeightedQuery> tmp = new HashSet<WeightedQuery>();
+ List<Slot> sortedSlots = new ArrayList<Slot>();
+ Set<Slot> classSlots = new HashSet<Slot>();
+ for(Slot slot : t.getSlots()){
+ if(slot.getSlotType() == SlotType.CLASS){
+ sortedSlots.add(slot);
+ classSlots.add(slot);
+ }
+ }
+ for(Slot slot : t.getSlots()){
+ if(!sortedSlots.contains(slot)){
+ sortedSlots.add(slot);
+ }
+ }
+ //add for each SYMPROPERTY Slot the reversed query
+ for(Slot slot : sortedSlots){
+ for(WeightedQuery wQ : queries){
+ if(slot.getSlotType() == SlotType.SYMPROPERTY){
+ Query reversedQuery = new Query(wQ.getQuery());
+ reversedQuery.getTriplesWithVar(slot.getAnchor()).iterator().next().reverse();
+ tmp.add(new WeightedQuery(reversedQuery));
+ }
+ tmp.add(wQ);
+ }
+ queries.clear();
+ queries.addAll(tmp);
+ tmp.clear();
+ }
+
+ for(Slot slot : sortedSlots){
+ if(!slot2Allocations.get(slot).isEmpty()){
+ for(Allocation a : slot2Allocations.get(slot)){
+ for(WeightedQuery query : queries){
Query q = new Query(query.getQuery());
- q.replaceVarWithURI(slot.getAnchor(), a.getUri());
- WeightedQuery w = new WeightedQuery(q);
- double newScore = query.getScore() + a.getScore();
- w.setScore(newScore);
- tmp.add(w);
+
+ boolean drop = false;
+ if(slot.getSlotType() == SlotType.PROPERTY || slot.getSlotType() == SlotType.SYMPROPERTY){
+ for(SPARQL_Triple triple : q.getTriplesWithVar(slot.getAnchor())){
+ String objectVar = triple.getValue().getName();
+ String subjectVar = triple.getVariable().getName();
+// System.out.println(triple);
+ for(SPARQL_Triple typeTriple : q.getRDFTypeTriples(objectVar)){
+// System.out.println(typeTriple);
+ Set<String> ranges = getRanges(a.getUri());
+// System.out.println(a);
+ if(!ranges.isEmpty()){
+ Set<String> allRanges = new HashSet<String>();
+ for(String range : ranges){
+ allRanges.addAll(getSuperClasses(range));
+ }
+ allRanges.addAll(ranges);
+ allRanges.remove("http://www.w3.org/2002/07/owl#Thing");
+ String typeURI = typeTriple.getValue().getName().substring(1,typeTriple.getValue().getName().length()-1);
+ Set<String> allTypes = getSuperClasses(typeURI);
+ allTypes.add(typeTriple.getValue().getName());
+// if(typeURI.equals("http://dbpedia.org/ontology/Film") && a.getUri().equals("http://dbpedia.org/ontology/starring")){
+// System.out.println("RANGES: " + allRanges);
+// System.out.println("TYPES: " + allTypes);
+// }
+
+ if(!org.mindswap.pellet.utils.SetUtils.intersects(allRanges, allTypes)){
+ drop = true;
+ } else {
+ System.out.println("DROPPING: \n" + q.toString());
+ }
+ }
+ }
+ for(SPARQL_Triple typeTriple : q.getRDFTypeTriples(subjectVar)){
+// System.out.println(typeTriple);
+ Set<String> domains = getDomains(a.getUri());System.out.println(a.getUri() + ":" + domains);
+// System.out.println(a);
+ if(!domains.isEmpty()){
+ Set<String> allDomains = new HashSet<String>();
+ for(String domain : domains){
+ allDomains.addAll(getSuperClasses(domain));
+ }
+ allDomains.addAll(domains);
+ allDomains.remove("http://www.w3.org/2002/07/owl#Thing");
+ String typeURI = typeTriple.getValue().getName().substring(1,typeTriple.getValue().getName().length()-1);
+ Set<String> allTypes = getSuperClasses(typeURI);
+ allTypes.add(typeTriple.getValue().getName());
+// if(typeURI.equals("http://dbpedia.org/ontology/Film") && a.getUri().equals("http://dbpedia.org/ontology/starring")){
+// System.out.println("DOMAINS: " + allDomains);
+// System.out.println("TYPES: " + allTypes);
+// }
+
+ if(!org.mindswap.pellet.utils.SetUtils.intersects(allDomains, allTypes)){
+ drop = true;
+ } else {
+ System.out.println("DROPPING: \n" + q.toString());
+ }
+ }
+ }
+ }
+ }
+
+
+ if(!drop){
+ q.replaceVarWithURI(slot.getAnchor(), a.getUri());
+ WeightedQuery w = new WeightedQuery(q);
+ double newScore = query.getScore() + a.getScore();
+ w.setScore(newScore);
+ tmp.add(w);
+ }
+
}
}
queries.clear();
- queries.addAll(tmp);
+ queries.addAll(tmp);//System.out.println(tmp);
tmp.clear();
}
@@ -478,7 +731,7 @@
}
allQueries.addAll(queries);
List<Query> qList = new ArrayList<Query>();
- for(WeightedQuery wQ : queries){
+ for(WeightedQuery wQ : queries){//System.err.println(wQ.getQuery());
qList.add(wQ.getQuery());
}
template2Queries.put(t, qList);
@@ -516,7 +769,7 @@
SolrQueryResultSet rs;
for(String word : slot.getWords()){
- rs = index.getResourcesWithScores(word, 10);
+ rs = index.getResourcesWithScores(word, 3);
for(SolrQueryResultItem item : rs.getItems()){
int prominence = getProminenceValue(item.getUri(), slot.getSlotType());
Modified: trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/sparql/Allocation.java
===================================================================
--- trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/sparql/Allocation.java 2011-11-02 19:32:53 UTC (rev 3363)
+++ trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/sparql/Allocation.java 2011-11-02 22:28:33 UTC (rev 3364)
@@ -49,6 +49,36 @@
public String toString() {
return uri + "(similarity: " + similarity + "; prominence: " + inDegree + ")";
}
+
+ @Override
+ public int hashCode() {
+ final int prime = 31;
+ int result = 1;
+ long temp;
+ temp = Double.doubleToLongBits(score);
+ result = prime * result + (int) (temp ^ (temp >>> 32));
+ result = prime * result + ((uri == null) ? 0 : uri.hashCode());
+ return result;
+ }
+
+ @Override
+ public boolean equals(Object obj) {
+ if (this == obj)
+ return true;
+ if (obj == null)
+ return false;
+ if (getClass() != obj.getClass())
+ return false;
+ Allocation other = (Allocation) obj;
+ if (Double.doubleToLongBits(score) != Double.doubleToLongBits(other.score))
+ return false;
+ if (uri == null) {
+ if (other.uri != null)
+ return false;
+ } else if (!uri.equals(other.uri))
+ return false;
+ return true;
+ }
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <jen...@us...> - 2011-11-02 19:33:00
|
Revision: 3363
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3363&view=rev
Author: jenslehmann
Date: 2011-11-02 19:32:53 +0000 (Wed, 02 Nov 2011)
Log Message:
-----------
cross validation for the new command line interface
Modified Paths:
--------------
trunk/interfaces/src/main/java/org/dllearner/cli/CLI.java
Added Paths:
-----------
trunk/examples/cross-validation/
trunk/examples/cross-validation/father.conf
trunk/examples/cross-validation/father.owl
trunk/examples/cross-validation/father.xml
trunk/interfaces/src/main/java/org/dllearner/cli/CrossValidation.java
Added: trunk/examples/cross-validation/father.conf
===================================================================
--- trunk/examples/cross-validation/father.conf (rev 0)
+++ trunk/examples/cross-validation/father.conf 2011-11-02 19:32:53 UTC (rev 3363)
@@ -0,0 +1,33 @@
+/**
+ * Father Example
+ *
+ * possible solution:
+ * male AND EXISTS hasChild.TOP
+ *
+ * Copyright (C) 2007, Jens Lehmann
+ */
+
+// perform cross validation
+cli.type = "org.dllearner.cli.CLI"
+cli.writeSpringConfiguration = true
+cli.performCrossValidation = true
+cli.nrOfFolds = 3
+
+// declare some prefixes to use as abbreviations
+prefixes = [ ("ex","http://example.com/father#") ]
+
+// knowledge source definition
+ks.type = "OWL File"
+ks.fileName = "father.owl"
+
+// reasoner
+reasoner.type = "fast instance checker"
+reasoner.sources = { ks }
+
+// learning problem
+lp.type = "posNegStandard"
+lp.positiveExamples = { "ex:stefan", "ex:markus", "ex:martin" }
+lp.negativeExamples = { "ex:heinz", "ex:anna", "ex:michelle" }
+
+// create learning algorithm to run
+alg.type = "ocel"
Added: trunk/examples/cross-validation/father.owl
===================================================================
--- trunk/examples/cross-validation/father.owl (rev 0)
+++ trunk/examples/cross-validation/father.owl 2011-11-02 19:32:53 UTC (rev 3363)
@@ -0,0 +1,35 @@
+<?xml version="1.0"?>
+<rdf:RDF
+ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+ xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
+ xmlns="http://example.com/father#"
+ xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
+ xmlns:owl="http://www.w3.org/2002/07/owl#"
+ xml:base="http://example.com/father">
+ <owl:Ontology rdf:about=""/>
+ <owl:Class rdf:ID="female"/>
+ <owl:Class rdf:ID="male">
+ <owl:equivalentClass>
+ <owl:Class>
+ <owl:complementOf rdf:resource="#female"/>
+ </owl:Class>
+ </owl:equivalentClass>
+ </owl:Class>
+ <owl:ObjectProperty rdf:ID="hasChild"/>
+ <male rdf:ID="markus">
+ <hasChild>
+ <female rdf:ID="anna">
+ <hasChild>
+ <male rdf:ID="heinz"/>
+ </hasChild>
+ </female>
+ </hasChild>
+ </male>
+ <male rdf:ID="stefan">
+ <hasChild rdf:resource="#markus"/>
+ </male>
+ <female rdf:ID="michelle"/>
+ <male rdf:ID="martin">
+ <hasChild rdf:resource="#heinz"/>
+ </male>
+</rdf:RDF>
Added: trunk/examples/cross-validation/father.xml
===================================================================
--- trunk/examples/cross-validation/father.xml (rev 0)
+++ trunk/examples/cross-validation/father.xml 2011-11-02 19:32:53 UTC (rev 3363)
@@ -0,0 +1,32 @@
+<beans xmlns="http://www.springframework.org/schema/beans">
+ <bean class="org.dllearner.algorithms.ocel.OCEL" name="alg"/>
+ <bean class="org.dllearner.kb.OWLFile" name="ks">
+ <property name="fileName" value="father.owl"/>
+ </bean>
+ <bean class="org.dllearner.learningproblems.PosNegLPStandard" name="lp">
+ <property name="positiveExamples">
+ <set>
+ <value>http://example.com/father#markus</value>
+ <value>http://example.com/father#stefan</value>
+ <value>http://example.com/father#martin</value>
+ </set>
+ </property>
+ <property name="negativeExamples">
+ <set>
+ <value>http://example.com/father#heinz</value>
+ <value>http://example.com/father#anna</value>
+ <value>http://example.com/father#michelle</value>
+ </set>
+ </property>
+ </bean>
+ <bean class="org.dllearner.cli.CLI" name="cli">
+ <property name="writeSpringConfiguration"/>
+ </bean>
+ <bean class="org.dllearner.reasoning.FastInstanceChecker" name="reasoner">
+ <property name="sources">
+ <set>
+ <ref bean="ks"/>
+ </set>
+ </property>
+ </bean>
+</beans>
\ No newline at end of file
Modified: trunk/interfaces/src/main/java/org/dllearner/cli/CLI.java
===================================================================
--- trunk/interfaces/src/main/java/org/dllearner/cli/CLI.java 2011-11-02 14:37:35 UTC (rev 3362)
+++ trunk/interfaces/src/main/java/org/dllearner/cli/CLI.java 2011-11-02 19:32:53 UTC (rev 3363)
@@ -38,8 +38,10 @@
import org.dllearner.confparser3.ConfParserConfiguration;
import org.dllearner.confparser3.ParseException;
import org.dllearner.core.AbstractCELA;
+import org.dllearner.core.AbstractReasonerComponent;
import org.dllearner.core.LearningAlgorithm;
import org.dllearner.core.ReasoningMethodUnsupportedException;
+import org.dllearner.learningproblems.PosNegLP;
import org.dllearner.utilities.Files;
import org.springframework.context.ApplicationContext;
import org.springframework.core.io.FileSystemResource;
@@ -57,59 +59,65 @@
private static Logger logger = Logger.getLogger(CLI.class);
private static Logger rootLogger = Logger.getRootLogger();
- private boolean writeSpringConfiguration = false;
private ApplicationContext context;
+ private File confFile;
- public CLI(File file) throws IOException{
- Resource confFile = new FileSystemResource(file);
+ // some CLI options
+ private boolean writeSpringConfiguration = false;
+ private boolean performCrossValidation = false;
+ private int nrOfFolds = 10;
+
+ public CLI() {
- List<Resource> springConfigResources = new ArrayList<Resource>();
+ }
+
+ public CLI(File confFile) {
+ this();
+ this.confFile = confFile;
+ }
+
+ public void run() throws IOException { // ApplicationContext context, String algorithmBeanName){
+
+ IConfiguration configuration = null;
+
+ if(context == null) {
+ Resource confFileR = new FileSystemResource(confFile);
+ List<Resource> springConfigResources = new ArrayList<Resource>();
+ configuration = new ConfParserConfiguration(confFileR);
- //DL-Learner Configuration Object
- IConfiguration configuration = new ConfParserConfiguration(confFile);
-
- ApplicationContextBuilder builder = new DefaultApplicationContextBuilder();
- context = builder.buildApplicationContext(configuration,springConfigResources);
-
- // a lot of debugging stuff
-// FastInstanceChecker fi = context.getBean("reasoner", FastInstanceChecker.class);
-// System.out.println(fi.getClassHierarchy());
-// NamedClass male = new NamedClass("http://localhost/foo#male");
-// System.out.println(fi.getIndividuals(new NamedClass("http://localhost/foo#male")));
-// System.out.println(fi.getIndividuals().size());
-// System.out.println("has type: " + fi.hasTypeImpl(male, new Individual("http://localhost/foo#bernd")));
-//
-// PosNegLPStandard lp = context.getBean("lp", PosNegLPStandard.class);
-// System.out.println(lp.getPositiveExamples());
-// System.out.println(lp.getNegativeExamples());
-// System.out.println(lp.getAccuracy(new NamedClass("http://localhost/foo#male")));
-
- // get a CLI bean if it exists
- CLI cli = null;
- if(context.getBeansOfType(CLI.class).size()>0) {
- System.out.println();
- cli = context.getBean(CLI.class);
+ ApplicationContextBuilder builder = new DefaultApplicationContextBuilder();
+ ApplicationContext context = builder.buildApplicationContext(configuration,springConfigResources);
+ }
+
+ if(writeSpringConfiguration) {
SpringConfigurationXMLBeanConverter converter = new SpringConfigurationXMLBeanConverter();
- XmlObject xml = converter.convert(configuration);
- String springFilename = file.getCanonicalPath().replace(".conf", ".xml");
+ XmlObject xml;
+ if(configuration == null) {
+ Resource confFileR = new FileSystemResource(confFile);
+ configuration = new ConfParserConfiguration(confFileR);
+ xml = converter.convert(configuration);
+ } else {
+ xml = converter.convert(configuration);
+ }
+ String springFilename = confFile.getCanonicalPath().replace(".conf", ".xml");
File springFile = new File(springFilename);
if(springFile.exists()) {
logger.warn("Cannot write Spring configuration, because " + springFilename + " already exists.");
} else {
Files.createFile(springFile, xml.toString());
- }
-// SpringConfigurationXMLBeanConverter converter;
- }
-
- // start algorithm in conf file
-// LearningAlgorithm algorithm = context.getBean("alg",LearningAlgorithm.class);
-// algorithm.start();
- }
+ }
+ }
+
+ if(performCrossValidation) {
+ AbstractReasonerComponent rs = context.getBean(AbstractReasonerComponent.class);
+ PosNegLP lp = context.getBean(PosNegLP.class);
+ AbstractCELA la = context.getBean(AbstractCELA.class);
+ new CrossValidation(la,lp,rs,nrOfFolds,false);
+ } else {
+ LearningAlgorithm algorithm = context.getBean(LearningAlgorithm.class);
+ algorithm.start();
+ }
- public void run() { // ApplicationContext context, String algorithmBeanName){
- LearningAlgorithm algorithm = context.getBean(LearningAlgorithm.class);
-// LearningAlgorithm algorithm = context.getBean(algorithmBeanName, LearningAlgorithm.class);
- algorithm.start();
}
public boolean isWriteSpringConfiguration() {
@@ -150,12 +158,61 @@
System.exit(0);
}
- CLI cli = new CLI(file);
+ Resource confFile = new FileSystemResource(file);
+
+ List<Resource> springConfigResources = new ArrayList<Resource>();
+
+ //DL-Learner Configuration Object
+ IConfiguration configuration = new ConfParserConfiguration(confFile);
+
+ ApplicationContextBuilder builder = new DefaultApplicationContextBuilder();
+ ApplicationContext context = builder.buildApplicationContext(configuration,springConfigResources);
+
+ // TODO: later we could check which command line interface is specified in the conf file
+ // for now we just use the default one
+
+ CLI cli;
+ if(context.containsBean("cli")) {
+ cli = (CLI) context.getBean("cli");
+ } else {
+ cli = new CLI();
+ }
+ cli.setContext(context);
+ cli.setConfFile(file);
cli.run();
+
}
+ public void setContext(ApplicationContext context) {
+ this.context = context;
+ }
+
public ApplicationContext getContext() {
return context;
}
+ public File getConfFile() {
+ return confFile;
+ }
+
+ public void setConfFile(File confFile) {
+ this.confFile = confFile;
+ }
+
+ public boolean isPerformCrossValidation() {
+ return performCrossValidation;
+ }
+
+ public void setPerformCrossValidation(boolean performCrossValiation) {
+ this.performCrossValidation = performCrossValiation;
+ }
+
+ public int getNrOfFolds() {
+ return nrOfFolds;
+ }
+
+ public void setNrOfFolds(int nrOfFolds) {
+ this.nrOfFolds = nrOfFolds;
+ }
+
}
Added: trunk/interfaces/src/main/java/org/dllearner/cli/CrossValidation.java
===================================================================
--- trunk/interfaces/src/main/java/org/dllearner/cli/CrossValidation.java (rev 0)
+++ trunk/interfaces/src/main/java/org/dllearner/cli/CrossValidation.java 2011-11-02 19:32:53 UTC (rev 3363)
@@ -0,0 +1,286 @@
+/**
+ * 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.cli;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.text.DecimalFormat;
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Random;
+import java.util.Set;
+
+import org.apache.log4j.ConsoleAppender;
+import org.apache.log4j.Level;
+import org.apache.log4j.Logger;
+import org.apache.log4j.SimpleLayout;
+import org.dllearner.core.ComponentInitException;
+import org.dllearner.core.ComponentManager;
+import org.dllearner.core.AbstractCELA;
+import org.dllearner.core.AbstractLearningProblem;
+import org.dllearner.core.AbstractReasonerComponent;
+import org.dllearner.core.owl.Description;
+import org.dllearner.core.owl.Individual;
+import org.dllearner.learningproblems.Heuristics;
+import org.dllearner.learningproblems.PosNegLP;
+import org.dllearner.learningproblems.PosOnlyLP;
+import org.dllearner.utilities.Helper;
+import org.dllearner.utilities.datastructures.Datastructures;
+import org.dllearner.utilities.statistics.Stat;
+import org.dllearner.utilities.Files;
+
+/**
+ * Performs cross validation for the given problem. Supports
+ * k-fold cross-validation and leave-one-out cross-validation.
+ *
+ * @author Jens Lehmann
+ *
+ */
+public class CrossValidation {
+
+ private static Logger logger = Logger.getRootLogger();
+
+ // statistical values
+ private Stat runtime = new Stat();
+ private Stat accuracy = new Stat();
+ private Stat length = new Stat();
+ private Stat accuracyTraining = new Stat();
+ private Stat fMeasure = new Stat();
+ private Stat fMeasureTraining = new Stat();
+ private static boolean writeToFile = false;
+ private static File outputFile;
+
+ public CrossValidation(AbstractCELA la, PosNegLP lp, AbstractReasonerComponent rs, int folds, boolean leaveOneOut) {
+
+ DecimalFormat df = new DecimalFormat();
+
+ // the training and test sets used later on
+ List<Set<Individual>> trainingSetsPos = new LinkedList<Set<Individual>>();
+ List<Set<Individual>> trainingSetsNeg = new LinkedList<Set<Individual>>();
+ List<Set<Individual>> testSetsPos = new LinkedList<Set<Individual>>();
+ List<Set<Individual>> testSetsNeg = new LinkedList<Set<Individual>>();
+
+ // get examples and shuffle them too
+ Set<Individual> posExamples = ((PosNegLP)lp).getPositiveExamples();
+ List<Individual> posExamplesList = new LinkedList<Individual>(posExamples);
+ Collections.shuffle(posExamplesList, new Random(1));
+ Set<Individual> negExamples = ((PosNegLP)lp).getNegativeExamples();
+ List<Individual> negExamplesList = new LinkedList<Individual>(negExamples);
+ Collections.shuffle(negExamplesList, new Random(2));
+
+ // sanity check whether nr. of folds makes sense for this benchmark
+ if(!leaveOneOut && (posExamples.size()<folds && negExamples.size()<folds)) {
+ System.out.println("The number of folds is higher than the number of "
+ + "positive/negative examples. This can result in empty test sets. Exiting.");
+ System.exit(0);
+ }
+
+ if(leaveOneOut) {
+ // note that leave-one-out is not identical to k-fold with
+ // k = nr. of examples in the current implementation, because
+ // with n folds and n examples there is no guarantee that a fold
+ // is never empty (this is an implementation issue)
+ int nrOfExamples = posExamples.size() + negExamples.size();
+ for(int i = 0; i < nrOfExamples; i++) {
+ // ...
+ }
+ System.out.println("Leave-one-out not supported yet.");
+ System.exit(1);
+ } else {
+ // calculating where to split the sets, ; note that we split
+ // positive and negative examples separately such that the
+ // distribution of positive and negative examples remains similar
+ // (note that there are better but more complex ways to implement this,
+ // which guarantee that the sum of the elements of a fold for pos
+ // and neg differs by at most 1 - it can differ by 2 in our implementation,
+ // e.g. with 3 folds, 4 pos. examples, 4 neg. examples)
+ int[] splitsPos = calculateSplits(posExamples.size(),folds);
+ int[] splitsNeg = calculateSplits(negExamples.size(),folds);
+
+// System.out.println(splitsPos[0]);
+// System.out.println(splitsNeg[0]);
+
+ // calculating training and test sets
+ for(int i=0; i<folds; i++) {
+ Set<Individual> testPos = getTestingSet(posExamplesList, splitsPos, i);
+ Set<Individual> testNeg = getTestingSet(negExamplesList, splitsNeg, i);
+ testSetsPos.add(i, testPos);
+ testSetsNeg.add(i, testNeg);
+ trainingSetsPos.add(i, getTrainingSet(posExamples, testPos));
+ trainingSetsNeg.add(i, getTrainingSet(negExamples, testNeg));
+ }
+
+ }
+
+ // run the algorithm
+ for(int currFold=0; currFold<folds; currFold++) {
+
+ Set<String> pos = Datastructures.individualSetToStringSet(trainingSetsPos.get(currFold));
+ Set<String> neg = Datastructures.individualSetToStringSet(trainingSetsNeg.get(currFold));
+ lp.setPositiveExamples(trainingSetsPos.get(currFold));
+ lp.setNegativeExamples(trainingSetsNeg.get(currFold));
+
+ try {
+ lp.init();
+ la.init();
+ } catch (ComponentInitException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+
+ long algorithmStartTime = System.nanoTime();
+ la.start();
+ long algorithmDuration = System.nanoTime() - algorithmStartTime;
+ runtime.addNumber(algorithmDuration/(double)1000000000);
+
+ Description concept = la.getCurrentlyBestDescription();
+
+ Set<Individual> tmp = rs.hasType(concept, testSetsPos.get(currFold));
+ Set<Individual> tmp2 = Helper.difference(testSetsPos.get(currFold), tmp);
+ Set<Individual> tmp3 = rs.hasType(concept, testSetsNeg.get(currFold));
+
+ outputWriter("test set errors pos: " + tmp2);
+ outputWriter("test set errors neg: " + tmp3);
+
+ // calculate training accuracies
+ int trainingCorrectPosClassified = getCorrectPosClassified(rs, concept, trainingSetsPos.get(currFold));
+ int trainingCorrectNegClassified = getCorrectNegClassified(rs, concept, trainingSetsNeg.get(currFold));
+ int trainingCorrectExamples = trainingCorrectPosClassified + trainingCorrectNegClassified;
+ double trainingAccuracy = 100*((double)trainingCorrectExamples/(trainingSetsPos.get(currFold).size()+
+ trainingSetsNeg.get(currFold).size()));
+ accuracyTraining.addNumber(trainingAccuracy);
+ // calculate test accuracies
+ int correctPosClassified = getCorrectPosClassified(rs, concept, testSetsPos.get(currFold));
+ int correctNegClassified = getCorrectNegClassified(rs, concept, testSetsNeg.get(currFold));
+ int correctExamples = correctPosClassified + correctNegClassified;
+ double currAccuracy = 100*((double)correctExamples/(testSetsPos.get(currFold).size()+
+ testSetsNeg.get(currFold).size()));
+ accuracy.addNumber(currAccuracy);
+ // calculate training F-Score
+ int negAsPosTraining = rs.hasType(concept, trainingSetsNeg.get(currFold)).size();
+ double precisionTraining = trainingCorrectPosClassified + negAsPosTraining == 0 ? 0 : trainingCorrectPosClassified / (double) (trainingCorrectPosClassified + negAsPosTraining);
+ double recallTraining = trainingCorrectPosClassified / (double) trainingSetsPos.get(currFold).size();
+ fMeasureTraining.addNumber(100*Heuristics.getFScore(recallTraining, precisionTraining));
+ // calculate test F-Score
+ int negAsPos = rs.hasType(concept, testSetsNeg.get(currFold)).size();
+ double precision = correctPosClassified + negAsPos == 0 ? 0 : correctPosClassified / (double) (correctPosClassified + negAsPos);
+ double recall = correctPosClassified / (double) testSetsPos.get(currFold).size();
+// System.out.println(precision);System.out.println(recall);
+ fMeasure.addNumber(100*Heuristics.getFScore(recall, precision));
+
+ length.addNumber(concept.getLength());
+
+ outputWriter("fold " + currFold + ":");
+ outputWriter(" training: " + pos.size() + " positive and " + neg.size() + " negative examples");
+ outputWriter(" testing: " + correctPosClassified + "/" + testSetsPos.get(currFold).size() + " correct positives, "
+ + correctNegClassified + "/" + testSetsNeg.get(currFold).size() + " correct negatives");
+ outputWriter(" concept: " + concept);
+ outputWriter(" accuracy: " + df.format(currAccuracy) + "% (" + df.format(trainingAccuracy) + "% on training set)");
+ outputWriter(" length: " + df.format(concept.getLength()));
+ outputWriter(" runtime: " + df.format(algorithmDuration/(double)1000000000) + "s");
+
+ }
+
+ outputWriter("");
+ outputWriter("Finished " + folds + "-folds cross-validation.");
+ outputWriter("runtime: " + statOutput(df, runtime, "s"));
+ outputWriter("length: " + statOutput(df, length, ""));
+ outputWriter("F-Measure on training set: " + statOutput(df, fMeasureTraining, "%"));
+ outputWriter("F-Measure: " + statOutput(df, fMeasure, "%"));
+ outputWriter("predictive accuracy on training set: " + statOutput(df, accuracyTraining, "%"));
+ outputWriter("predictive accuracy: " + statOutput(df, accuracy, "%"));
+
+ }
+
+ private int getCorrectPosClassified(AbstractReasonerComponent rs, Description concept, Set<Individual> testSetPos) {
+ return rs.hasType(concept, testSetPos).size();
+ }
+
+ private int getCorrectNegClassified(AbstractReasonerComponent rs, Description concept, Set<Individual> testSetNeg) {
+ return testSetNeg.size() - rs.hasType(concept, testSetNeg).size();
+ }
+
+ public static Set<Individual> getTestingSet(List<Individual> examples, int[] splits, int fold) {
+ int fromIndex;
+ // we either start from 0 or after the last fold ended
+ if(fold == 0)
+ fromIndex = 0;
+ else
+ fromIndex = splits[fold-1];
+ // the split corresponds to the ends of the folds
+ int toIndex = splits[fold];
+
+// System.out.println("from " + fromIndex + " to " + toIndex);
+
+ Set<Individual> testingSet = new HashSet<Individual>();
+ // +1 because 2nd element is exclusive in subList method
+ testingSet.addAll(examples.subList(fromIndex, toIndex));
+ return testingSet;
+ }
+
+ public static Set<Individual> getTrainingSet(Set<Individual> examples, Set<Individual> testingSet) {
+ return Helper.difference(examples, testingSet);
+ }
+
+ // takes nr. of examples and the nr. of folds for this examples;
+ // returns an array which says where each fold ends, i.e.
+ // splits[i] is the index of the last element of fold i in the examples
+ public static int[] calculateSplits(int nrOfExamples, int folds) {
+ int[] splits = new int[folds];
+ for(int i=1; i<=folds; i++) {
+ // we always round up to the next integer
+ splits[i-1] = (int)Math.ceil(i*nrOfExamples/(double)folds);
+ }
+ return splits;
+ }
+
+ public static String statOutput(DecimalFormat df, Stat stat, String unit) {
+ String str = "av. " + df.format(stat.getMean()) + unit;
+ str += " (deviation " + df.format(stat.getStandardDeviation()) + unit + "; ";
+ str += "min " + df.format(stat.getMin()) + unit + "; ";
+ str += "max " + df.format(stat.getMax()) + unit + ")";
+ return str;
+ }
+
+ public Stat getAccuracy() {
+ return accuracy;
+ }
+
+ public Stat getLength() {
+ return length;
+ }
+
+ public Stat getRuntime() {
+ return runtime;
+ }
+
+ private void outputWriter(String output) {
+ if(writeToFile) {
+ Files.appendFile(outputFile, output +"\n");
+ System.out.println(output);
+ } else {
+ System.out.println(output);
+ }
+
+ }
+
+}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lor...@us...> - 2011-11-02 14:37:45
|
Revision: 3362
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3362&view=rev
Author: lorenz_b
Date: 2011-11-02 14:37:35 +0000 (Wed, 02 Nov 2011)
Log Message:
-----------
Changed handling of count results with value 0.
Modified Paths:
--------------
trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/learning/SPARQLTemplateBasedLearner.java
trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/sparql/Query.java
trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/sparql/WeightedQuery.java
Modified: trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/learning/SPARQLTemplateBasedLearner.java
===================================================================
--- trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/learning/SPARQLTemplateBasedLearner.java 2011-11-02 14:07:30 UTC (rev 3361)
+++ trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/learning/SPARQLTemplateBasedLearner.java 2011-11-02 14:37:35 UTC (rev 3362)
@@ -7,6 +7,7 @@
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
+import java.util.Comparator;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
@@ -16,6 +17,7 @@
import java.util.SortedSet;
import java.util.TreeSet;
+import org.apache.commons.collections.SetUtils;
import org.apache.log4j.Logger;
import org.dllearner.algorithm.qtl.util.ModelGenerator;
import org.dllearner.algorithm.qtl.util.ModelGenerator.Strategy;
@@ -31,6 +33,7 @@
import org.dllearner.algorithm.tbsl.sparql.RatedQuery;
import org.dllearner.algorithm.tbsl.sparql.SPARQL_Prefix;
import org.dllearner.algorithm.tbsl.sparql.SPARQL_QueryType;
+import org.dllearner.algorithm.tbsl.sparql.SPARQL_Triple;
import org.dllearner.algorithm.tbsl.sparql.Slot;
import org.dllearner.algorithm.tbsl.sparql.SlotType;
import org.dllearner.algorithm.tbsl.sparql.Template;
@@ -43,9 +46,13 @@
import org.dllearner.core.ComponentInitException;
import org.dllearner.core.Oracle;
import org.dllearner.core.SparqlQueryLearningAlgorithm;
+import org.dllearner.core.owl.Description;
+import org.dllearner.core.owl.NamedClass;
+import org.dllearner.kb.SparqlEndpointKS;
import org.dllearner.kb.sparql.ExtractionDBCache;
import org.dllearner.kb.sparql.SparqlEndpoint;
import org.dllearner.kb.sparql.SparqlQuery;
+import org.dllearner.reasoning.SPARQLReasoner;
import org.ini4j.InvalidFileFormatException;
import org.ini4j.Options;
@@ -56,6 +63,7 @@
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
import com.hp.hpl.jena.sparql.engine.http.QueryEngineHTTP;
+import com.hp.hpl.jena.vocabulary.RDFS;
import com.jamonapi.Monitor;
import com.jamonapi.MonitorFactory;
@@ -109,6 +117,8 @@
private Lemmatizer lemmatizer = new LingPipeLemmatizer();// StanfordLemmatizer();
+ private SPARQLReasoner reasoner;
+
public SPARQLTemplateBasedLearner() throws InvalidFileFormatException, FileNotFoundException, IOException{
this(OPTIONS_FILE);
}
@@ -188,6 +198,9 @@
predicateFilters.add("http://dbpedia.org/ontology/wikiPageWikiLink");
predicateFilters.add("http://dbpedia.org/property/wikiPageUsesTemplate");
modelGenenerator = new ModelGenerator(endpoint, predicateFilters);
+
+ reasoner = new SPARQLReasoner(new SparqlEndpointKS(endpoint));
+ reasoner.prepareSubsumptionHierarchy();
}
public void setQuestion(String question){
@@ -251,7 +264,7 @@
Set<WeightedQuery> weightedQueries = getWeightedSPARQLQueries(templates);
sparqlQueryCandidates = new ArrayList<Query>();
int i = 0;
- for(WeightedQuery wQ : weightedQueries){
+ for(WeightedQuery wQ : weightedQueries){System.out.println(wQ);
sparqlQueryCandidates.add(wQ.getQuery());
if(i == maxTestedQueries){
break;
@@ -346,7 +359,7 @@
}
private Set<WeightedQuery> getWeightedSPARQLQueries(Set<Template> templates){
- double alpha = 0.7;
+ double alpha = 0.8;
double beta = 1 - alpha;
Map<Slot, Set<Allocation>> slot2Allocations = new HashMap<Slot, Set<Allocation>>();
@@ -355,6 +368,7 @@
Set<Allocation> allAllocations;
for(Template t : templates){
allAllocations = new HashSet<Allocation>();
+
for(Slot slot : t.getSlots()){
Set<Allocation> allocations = computeAllocation(slot);
allAllocations.addAll(allocations);
@@ -386,25 +400,71 @@
queries.add(new WeightedQuery(cleanQuery));
Set<WeightedQuery> tmp = new HashSet<WeightedQuery>();
+ List<Slot> sortedSlots = new ArrayList<Slot>();
+ Set<Slot> classSlots = new HashSet<Slot>();
for(Slot slot : t.getSlots()){
+ if(slot.getSlotType() == SlotType.CLASS){
+ sortedSlots.add(slot);
+ classSlots.add(slot);
+ }
+ }
+ for(Slot slot : t.getSlots()){
+ if(!sortedSlots.contains(slot)){
+ sortedSlots.add(slot);
+ }
+ }
+ for(Slot slot : sortedSlots){
if(!slot2Allocations.get(slot).isEmpty()){
for(Allocation a : slot2Allocations.get(slot)){
for(WeightedQuery query : queries){
- if(slot.getSlotType() == SlotType.SYMPROPERTY){
Query reversedQuery = new Query(query.getQuery());
reversedQuery.getTriplesWithVar(slot.getAnchor()).iterator().next().reverse();
- reversedQuery.replaceVarWithURI(slot.getAnchor(), a.getUri());
- WeightedQuery w = new WeightedQuery(reversedQuery);
+ //check if the query is possible
+ if(slot.getSlotType() == SlotType.SYMPROPERTY){
+ boolean drop = false;
+ for(SPARQL_Triple triple : query.getQuery().getTriplesWithVar(slot.getAnchor())){
+ System.out.println(triple);
+ for(SPARQL_Triple typeTriple : query.getQuery().getRDFTypeTriples(triple.getValue().getName())){
+ System.out.println(typeTriple);
+ Set<String> ranges = getRanges(a.getUri());
+ System.out.println(a);
+ if(!ranges.isEmpty()){
+ Set<String> allRanges = new HashSet<String>();
+ for(String range : ranges){
+ allRanges.addAll(getSuperClasses(range));
+ }
+ String typeURI = typeTriple.getValue().getName().substring(1,typeTriple.getValue().getName().length()-1);
+ Set<String> allTypes = getSuperClasses(typeURI);
+ allTypes.add(typeTriple.getValue().getName());
+ System.out.println("RANGES: " + ranges);
+ System.out.println("TYPES: " + allTypes);
+
+ if(!org.mindswap.pellet.utils.SetUtils.intersects(allRanges, allTypes)){
+ drop = true;
+ }
+ }
+ }
+ }
+
+ if(!drop){
+ reversedQuery.replaceVarWithURI(slot.getAnchor(), a.getUri());
+ WeightedQuery w = new WeightedQuery(reversedQuery);
+ double newScore = query.getScore() + a.getScore();
+ w.setScore(newScore);
+ tmp.add(w);
+ }
+
+
+
+
+ }
+ Query q = new Query(query.getQuery());
+ q.replaceVarWithURI(slot.getAnchor(), a.getUri());
+ WeightedQuery w = new WeightedQuery(q);
double newScore = query.getScore() + a.getScore();
w.setScore(newScore);
tmp.add(w);
- }
- Query q = new Query(query.getQuery());
- q.replaceVarWithURI(slot.getAnchor(), a.getUri());
- WeightedQuery w = new WeightedQuery(q);
- double newScore = query.getScore() + a.getScore();
- w.setScore(newScore);
- tmp.add(w);
+
}
}
queries.clear();
@@ -425,6 +485,29 @@
}
return allQueries;
}
+
+/*
+ * for(SPARQL_Triple triple : t.getQuery().getTriplesWithVar(slot.getAnchor())){System.out.println(triple);
+ for(SPARQL_Triple typeTriple : t.getQuery().getRDFTypeTriples(triple.getVariable().getName())){
+ System.out.println(typeTriple);
+ for(Allocation a : allocations){
+ Set<String> domains = getDomains(a.getUri());
+ System.out.println(a);
+ System.out.println(domains);
+ for(Slot s : classSlots){
+ if(s.getAnchor().equals(triple.getVariable().getName())){
+ for(Allocation all : slot2Allocations.get(s)){
+ if(!domains.contains(all.getUri())){
+ System.out.println("DROP " + a);
+ }
+ }
+ }
+ }
+ }
+
+
+ }
+ */
private Set<Allocation> computeAllocation(Slot slot){
Set<Allocation> allocations = new HashSet<Allocation>();
@@ -829,10 +912,21 @@
logger.info("Testing query:\n" + query);
List<String> results = getResultFromRemoteEndpoint(query);
if(!results.isEmpty()){
- learnedSPARQLQueries.put(query, results);
- if(stopIfQueryResultNotEmpty){
- return;
+ try{
+ int cnt = Integer.parseInt(results.get(0));
+ if(cnt > 0){
+ learnedSPARQLQueries.put(query, results);
+ if(stopIfQueryResultNotEmpty){
+ return;
+ }
+ }
+ } catch (NumberFormatException e){
+ learnedSPARQLQueries.put(query, results);
+ if(stopIfQueryResultNotEmpty){
+ return;
+ }
}
+
}
logger.info("Result: " + results);
}
@@ -884,7 +978,7 @@
logger.info("Done in " + mon.getLastValue() + "ms.");
}
- private List<String> getResultFromRemoteEndpoint(String query){System.out.println(query);
+ private List<String> getResultFromRemoteEndpoint(String query){
List<String> resources = new ArrayList<String>();
try {
String queryString = query;
@@ -897,7 +991,12 @@
while(rs.hasNext()){
qs = rs.next();
projectionVar = qs.varNames().next();
- resources.add(qs.get(projectionVar).toString());
+ if(qs.get(projectionVar).isLiteral()){
+ resources.add(qs.get(projectionVar).asLiteral().getLexicalForm());
+ } else if(qs.get(projectionVar).isURIResource()){
+ resources.add(qs.get(projectionVar).asResource().getURI());
+ }
+
}
} catch (Exception e) {
logger.error("Query execution failed.", e);
@@ -917,8 +1016,42 @@
return resources;
}
+ private Set<String> getDomains(String property){
+ Set<String> domains = new HashSet<String>();
+ String query = String.format("SELECT ?domain WHERE {<%s> <%s> ?domain}", property, RDFS.domain.getURI());
+ ResultSet rs = SparqlQuery.convertJSONtoResultSet(cache.executeSelectQuery(endpoint, query));
+ QuerySolution qs;
+ while(rs.hasNext()){
+ qs = rs.next();
+ domains.add(qs.getResource("domain").getURI());
+ }
+
+ return domains;
+ }
+ private Set<String> getRanges(String property){
+ Set<String> domains = new HashSet<String>();
+ String query = String.format("SELECT ?range WHERE {<%s> <%s> ?range}", property, RDFS.range.getURI());
+ ResultSet rs = SparqlQuery.convertJSONtoResultSet(cache.executeSelectQuery(endpoint, query));
+ QuerySolution qs;
+ while(rs.hasNext()){
+ qs = rs.next();
+ domains.add(qs.getResource("range").getURI());
+ }
+
+ return domains;
+ }
+ private Set<String> getSuperClasses(String cls){
+ Set<String> superClasses = new HashSet<String>();
+ for(Description d : reasoner.getClassHierarchy().getSuperClasses(new NamedClass(cls))){
+ superClasses.add(((NamedClass)d).getName());
+ }
+ return superClasses;
+ }
+
+
+
/**
* @param args
@@ -932,7 +1065,9 @@
// Logger.getLogger(HttpClient.class).setLevel(Level.OFF);
// Logger.getLogger(HttpMethodBase.class).setLevel(Level.OFF);
// String question = "In which programming language is GIMP written?";
- String question = "Who/WP are/VBP the/DT presidents/NNS of/IN the/DT United/NNP States/NNPS";
+// String question = "Who/WP was/VBD the/DT wife/NN of/IN president/NN Lincoln/NNP";
+ String question = "Who/WP produced/VBD the/DT most/JJS films/NNS";
+// String question = "Give/VB me/PRP all/DT soccer/NN clubs/NNS in/IN the/DT Premier/NNP League/NNP";
// String question = "Give me all books written by authors influenced by Ernest Hemingway.";
SPARQLTemplateBasedLearner learner = new SPARQLTemplateBasedLearner();learner.setUseIdealTagger(true);
Modified: trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/sparql/Query.java
===================================================================
--- trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/sparql/Query.java 2011-11-02 14:07:30 UTC (rev 3361)
+++ trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/sparql/Query.java 2011-11-02 14:37:35 UTC (rev 3362)
@@ -423,6 +423,28 @@
}
return triples;
}
+
+ public List<SPARQL_Triple> getRDFTypeTriples(){
+ List<SPARQL_Triple> triples = new ArrayList<SPARQL_Triple>();
+
+ for(SPARQL_Triple triple : conditions){
+ if(triple.getProperty().equals("rdf:type")){
+ triples.add(triple);
+ }
+ }
+ return triples;
+ }
+
+ public List<SPARQL_Triple> getRDFTypeTriples(String var){
+ List<SPARQL_Triple> triples = new ArrayList<SPARQL_Triple>();
+
+ for(SPARQL_Triple triple : conditions){
+ if(triple.getProperty().toString().equals("rdf:type") && triple.getVariable().getName().equals(var)){
+ triples.add(triple);
+ }
+ }
+ return triples;
+ }
@Override
public int hashCode() {
Modified: trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/sparql/WeightedQuery.java
===================================================================
--- trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/sparql/WeightedQuery.java 2011-11-02 14:07:30 UTC (rev 3361)
+++ trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/sparql/WeightedQuery.java 2011-11-02 14:37:35 UTC (rev 3362)
@@ -33,7 +33,16 @@
return -1;
} else if(o.getScore() > this.score){
return 1;
- } else return query.toString().compareTo(o.getQuery().toString());
+ } else {
+ int filter = Boolean.valueOf(query.getFilters().isEmpty()).compareTo(Boolean.valueOf(o.getQuery().getFilters().isEmpty()));
+ if(filter == 0){
+ return query.toString().compareTo(o.getQuery().toString());
+ } else {
+ return filter;
+ }
+ }
+
+
}
@Override
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <jen...@us...> - 2011-11-02 14:07:37
|
Revision: 3361
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3361&view=rev
Author: jenslehmann
Date: 2011-11-02 14:07:30 +0000 (Wed, 02 Nov 2011)
Log Message:
-----------
- fixed a difficult to find bug in the refinement operator for string datatypes (related to an optimisation using property ranges)
- added support for single quoted strings in manchester parser (allows to use strings in conf files)
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/CELOE.java
trunk/components-core/src/main/java/org/dllearner/parser/ManchesterSyntaxParser.java
trunk/components-core/src/main/java/org/dllearner/parser/ManchesterSyntaxParserTokenManager.java
trunk/components-core/src/main/java/org/dllearner/parser/manchester.jj
trunk/components-core/src/main/java/org/dllearner/refinementoperators/RhoDRDown.java
trunk/components-core/src/test/java/org/dllearner/test/junit/ParserTests.java
trunk/examples/nlp2rdf/reuters_gold_vs_copper/learn.conf
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/CELOE.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/CELOE.java 2011-11-02 12:46:04 UTC (rev 3360)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/CELOE.java 2011-11-02 14:07:30 UTC (rev 3361)
@@ -453,7 +453,7 @@
// for(Description refinement : refinements) {
// System.out.println("refinement: " + refinement);
// }
-// if(loop % 100 == 0) {
+// if((loop+1) % 500 == 0) {
// System.out.println(getMinimumHorizontalExpansion() + " - " + getMaximumHorizontalExpansion());
// System.exit(0);
// }
Modified: trunk/components-core/src/main/java/org/dllearner/parser/ManchesterSyntaxParser.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/parser/ManchesterSyntaxParser.java 2011-11-02 12:46:04 UTC (rev 3360)
+++ trunk/components-core/src/main/java/org/dllearner/parser/ManchesterSyntaxParser.java 2011-11-02 14:07:30 UTC (rev 3361)
@@ -190,11 +190,6 @@
finally { jj_save(5, xla); }
}
- private boolean jj_3R_3() {
- if (jj_scan_token(STRING)) return true;
- return false;
- }
-
private boolean jj_3R_8() {
if (jj_scan_token(21)) return true;
if (jj_3R_2()) return true;
@@ -366,6 +361,11 @@
return false;
}
+ private boolean jj_3R_3() {
+ if (jj_scan_token(STRING)) return true;
+ return false;
+ }
+
/** Generated Token Manager. */
public ManchesterSyntaxParserTokenManager token_source;
SimpleCharStream jj_input_stream;
Modified: trunk/components-core/src/main/java/org/dllearner/parser/ManchesterSyntaxParserTokenManager.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/parser/ManchesterSyntaxParserTokenManager.java 2011-11-02 12:46:04 UTC (rev 3360)
+++ trunk/components-core/src/main/java/org/dllearner/parser/ManchesterSyntaxParserTokenManager.java 2011-11-02 14:07:30 UTC (rev 3361)
@@ -18,11 +18,11 @@
{
case 0:
if ((active0 & 0x40000L) != 0L)
- return 31;
+ return 34;
return -1;
case 1:
if ((active0 & 0x40000L) != 0L)
- return 31;
+ return 34;
return -1;
default :
return -1;
@@ -83,7 +83,7 @@
if ((active0 & 0x20000L) != 0L)
return jjStopAtPos(1, 17);
else if ((active0 & 0x40000L) != 0L)
- return jjStartNfaWithStates_0(1, 18, 31);
+ return jjStartNfaWithStates_0(1, 18, 34);
break;
case 79:
return jjMoveStringLiteralDfa2_0(active0, 0xc00L);
@@ -220,7 +220,7 @@
private int jjMoveNfa_0(int startState, int curPos)
{
int startsAt = 0;
- jjnewStateCnt = 31;
+ jjnewStateCnt = 34;
int i = 1;
jjstateSet[0] = startState;
int kind = 0x7fffffff;
@@ -235,15 +235,6 @@
{
switch(jjstateSet[--i])
{
- case 31:
- if ((0xbfffffffffffdbffL & l) != 0L)
- jjCheckNAddTwoStates(4, 5);
- else if (curChar == 62)
- {
- if (kind > 20)
- kind = 20;
- }
- break;
case 0:
if ((0x3fe000000000000L & l) != 0L)
{
@@ -255,15 +246,26 @@
{
if (kind > 8)
kind = 8;
- jjCheckNAdd(28);
+ jjCheckNAdd(31);
}
else if (curChar == 47)
jjAddStates(3, 5);
else if (curChar == 60)
+ jjCheckNAddTwoStates(7, 8);
+ else if (curChar == 39)
jjCheckNAddTwoStates(4, 5);
else if (curChar == 34)
jjCheckNAddTwoStates(1, 2);
break;
+ case 34:
+ if ((0xbfffffffffffdbffL & l) != 0L)
+ jjCheckNAddTwoStates(7, 8);
+ else if (curChar == 62)
+ {
+ if (kind > 20)
+ kind = 20;
+ }
+ break;
case 1:
if ((0xfffffffbffffdbffL & l) != 0L)
jjCheckNAddTwoStates(1, 2);
@@ -273,131 +275,143 @@
kind = 19;
break;
case 3:
- if (curChar == 60)
+ if (curChar == 39)
jjCheckNAddTwoStates(4, 5);
break;
case 4:
- if ((0xbfffffffffffdbffL & l) != 0L)
+ if ((0xfffffffbffffdbffL & l) != 0L)
jjCheckNAddTwoStates(4, 5);
break;
case 5:
+ if (curChar == 39 && kind > 19)
+ kind = 19;
+ break;
+ case 6:
+ if (curChar == 60)
+ jjCheckNAddTwoStates(7, 8);
+ break;
+ case 7:
+ if ((0xbfffffffffffdbffL & l) != 0L)
+ jjCheckNAddTwoStates(7, 8);
+ break;
+ case 8:
if (curChar == 62 && kind > 20)
kind = 20;
break;
- case 6:
+ case 9:
if (curChar == 47)
jjAddStates(3, 5);
break;
- case 7:
+ case 10:
if (curChar == 47)
jjCheckNAddStates(6, 8);
break;
- case 8:
+ case 11:
if ((0xffffffffffffdbffL & l) != 0L)
jjCheckNAddStates(6, 8);
break;
- case 9:
+ case 12:
if ((0x2400L & l) != 0L && kind > 5)
kind = 5;
break;
- case 10:
+ case 13:
if (curChar == 10 && kind > 5)
kind = 5;
break;
- case 11:
+ case 14:
if (curChar == 13)
- jjstateSet[jjnewStateCnt++] = 10;
+ jjstateSet[jjnewStateCnt++] = 13;
break;
- case 12:
+ case 15:
if (curChar == 42)
- jjCheckNAddTwoStates(13, 14);
+ jjCheckNAddTwoStates(16, 17);
break;
- case 13:
+ case 16:
if ((0xfffffbffffffffffL & l) != 0L)
- jjCheckNAddTwoStates(13, 14);
+ jjCheckNAddTwoStates(16, 17);
break;
- case 14:
+ case 17:
if (curChar == 42)
jjCheckNAddStates(9, 11);
break;
- case 15:
+ case 18:
if ((0xffff7bffffffffffL & l) != 0L)
- jjCheckNAddTwoStates(16, 14);
+ jjCheckNAddTwoStates(19, 17);
break;
- case 16:
+ case 19:
if ((0xfffffbffffffffffL & l) != 0L)
- jjCheckNAddTwoStates(16, 14);
+ jjCheckNAddTwoStates(19, 17);
break;
- case 17:
+ case 20:
if (curChar == 47 && kind > 6)
kind = 6;
break;
- case 18:
+ case 21:
if (curChar == 42)
- jjstateSet[jjnewStateCnt++] = 12;
+ jjstateSet[jjnewStateCnt++] = 15;
break;
- case 19:
+ case 22:
if (curChar == 42)
- jjCheckNAddTwoStates(20, 21);
+ jjCheckNAddTwoStates(23, 24);
break;
- case 20:
+ case 23:
if ((0xfffffbffffffffffL & l) != 0L)
- jjCheckNAddTwoStates(20, 21);
+ jjCheckNAddTwoStates(23, 24);
break;
- case 21:
+ case 24:
if (curChar == 42)
jjCheckNAddStates(12, 14);
break;
- case 22:
+ case 25:
if ((0xffff7bffffffffffL & l) != 0L)
- jjCheckNAddTwoStates(23, 21);
+ jjCheckNAddTwoStates(26, 24);
break;
- case 23:
+ case 26:
if ((0xfffffbffffffffffL & l) != 0L)
- jjCheckNAddTwoStates(23, 21);
+ jjCheckNAddTwoStates(26, 24);
break;
- case 24:
+ case 27:
if (curChar == 47 && kind > 7)
kind = 7;
break;
- case 25:
+ case 28:
if ((0x3fe000000000000L & l) == 0L)
break;
if (kind > 8)
kind = 8;
jjCheckNAddStates(0, 2);
break;
- case 26:
+ case 29:
if ((0x3ff000000000000L & l) == 0L)
break;
if (kind > 8)
kind = 8;
- jjCheckNAdd(26);
+ jjCheckNAdd(29);
break;
- case 27:
+ case 30:
if ((0x3ff000000000000L & l) != 0L)
- jjCheckNAddTwoStates(27, 28);
+ jjCheckNAddTwoStates(30, 31);
break;
- case 28:
+ case 31:
if (curChar != 46)
break;
if (kind > 9)
kind = 9;
- jjCheckNAdd(29);
+ jjCheckNAdd(32);
break;
- case 29:
+ case 32:
if ((0x3ff000000000000L & l) == 0L)
break;
if (kind > 9)
kind = 9;
- jjCheckNAdd(29);
+ jjCheckNAdd(32);
break;
- case 30:
+ case 33:
if (curChar != 48)
break;
if (kind > 8)
kind = 8;
- jjCheckNAdd(28);
+ jjCheckNAdd(31);
break;
default : break;
}
@@ -410,32 +424,36 @@
{
switch(jjstateSet[--i])
{
- case 31:
- case 4:
+ case 34:
+ case 7:
if ((0xffffffffefffffffL & l) != 0L)
- jjCheckNAddTwoStates(4, 5);
+ jjCheckNAddTwoStates(7, 8);
break;
case 1:
if ((0xffffffffefffffffL & l) != 0L)
jjAddStates(15, 16);
break;
- case 8:
+ case 4:
+ if ((0xffffffffefffffffL & l) != 0L)
+ jjAddStates(17, 18);
+ break;
+ case 11:
jjAddStates(6, 8);
break;
- case 13:
- jjCheckNAddTwoStates(13, 14);
- break;
- case 15:
case 16:
- jjCheckNAddTwoStates(16, 14);
+ jjCheckNAddTwoStates(16, 17);
break;
- case 20:
- jjCheckNAddTwoStates(20, 21);
+ case 18:
+ case 19:
+ jjCheckNAddTwoStates(19, 17);
break;
- case 22:
case 23:
- jjCheckNAddTwoStates(23, 21);
+ jjCheckNAddTwoStates(23, 24);
break;
+ case 25:
+ case 26:
+ jjCheckNAddTwoStates(26, 24);
+ break;
default : break;
}
} while(i != startsAt);
@@ -448,37 +466,41 @@
{
switch(jjstateSet[--i])
{
- case 31:
- case 4:
+ case 34:
+ case 7:
if ((jjbitVec0[i2] & l2) != 0L)
- jjCheckNAddTwoStates(4, 5);
+ jjCheckNAddTwoStates(7, 8);
break;
case 1:
if ((jjbitVec0[i2] & l2) != 0L)
jjAddStates(15, 16);
break;
- case 8:
+ case 4:
if ((jjbitVec0[i2] & l2) != 0L)
- jjAddStates(6, 8);
+ jjAddStates(17, 18);
break;
- case 13:
+ case 11:
if ((jjbitVec0[i2] & l2) != 0L)
- jjCheckNAddTwoStates(13, 14);
+ jjAddStates(6, 8);
break;
- case 15:
case 16:
if ((jjbitVec0[i2] & l2) != 0L)
- jjCheckNAddTwoStates(16, 14);
+ jjCheckNAddTwoStates(16, 17);
break;
- case 20:
+ case 18:
+ case 19:
if ((jjbitVec0[i2] & l2) != 0L)
- jjCheckNAddTwoStates(20, 21);
+ jjCheckNAddTwoStates(19, 17);
break;
- case 22:
case 23:
if ((jjbitVec0[i2] & l2) != 0L)
- jjCheckNAddTwoStates(23, 21);
+ jjCheckNAddTwoStates(23, 24);
break;
+ case 25:
+ case 26:
+ if ((jjbitVec0[i2] & l2) != 0L)
+ jjCheckNAddTwoStates(26, 24);
+ break;
default : break;
}
} while(i != startsAt);
@@ -490,15 +512,15 @@
kind = 0x7fffffff;
}
++curPos;
- if ((i = jjnewStateCnt) == (startsAt = 31 - (jjnewStateCnt = startsAt)))
+ if ((i = jjnewStateCnt) == (startsAt = 34 - (jjnewStateCnt = startsAt)))
return curPos;
try { curChar = input_stream.readChar(); }
catch(java.io.IOException e) { return curPos; }
}
}
static final int[] jjnextStates = {
- 26, 27, 28, 7, 18, 19, 8, 9, 11, 14, 15, 17, 21, 22, 24, 1,
- 2,
+ 29, 30, 31, 10, 21, 22, 11, 12, 14, 17, 18, 20, 24, 25, 27, 1,
+ 2, 4, 5,
};
/** Token literal values. */
@@ -518,8 +540,8 @@
0xfeL,
};
protected SimpleCharStream input_stream;
-private final int[] jjrounds = new int[31];
-private final int[] jjstateSet = new int[62];
+private final int[] jjrounds = new int[34];
+private final int[] jjstateSet = new int[68];
protected char curChar;
/** Constructor. */
public ManchesterSyntaxParserTokenManager(SimpleCharStream stream){
@@ -546,7 +568,7 @@
{
int i;
jjround = 0x80000001;
- for (i = 31; i-- > 0;)
+ for (i = 34; i-- > 0;)
jjrounds[i] = 0x80000000;
}
Modified: trunk/components-core/src/main/java/org/dllearner/parser/manchester.jj
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/parser/manchester.jj 2011-11-02 12:46:04 UTC (rev 3360)
+++ trunk/components-core/src/main/java/org/dllearner/parser/manchester.jj 2011-11-02 14:07:30 UTC (rev 3361)
@@ -64,7 +64,8 @@
| < NOT: "not" >
| < GE: ">=" >
| < LE: "<=" >
- | < STRING: "\"" (~["\"","\\","\n","\r"])* "\"" >
+ // support single quotes and double quotes
+ | < STRING: "\"" (~["\"","\\","\n","\r"])* "\"" | "'" (~["\"","\\","\n","\r"])* "'">
| < URI: "<" (~[">","\\","\n","\r"])* ">" >
}
Modified: trunk/components-core/src/main/java/org/dllearner/refinementoperators/RhoDRDown.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/refinementoperators/RhoDRDown.java 2011-11-02 12:46:04 UTC (rev 3360)
+++ trunk/components-core/src/main/java/org/dllearner/refinementoperators/RhoDRDown.java 2011-11-02 14:07:30 UTC (rev 3361)
@@ -145,6 +145,7 @@
private Map<NamedClass, Set<ObjectProperty>> appOP = new TreeMap<NamedClass, Set<ObjectProperty>>();
private Map<NamedClass, Set<DatatypeProperty>> appBD = new TreeMap<NamedClass, Set<DatatypeProperty>>();
private Map<NamedClass, Set<DatatypeProperty>> appDD = new TreeMap<NamedClass, Set<DatatypeProperty>>();
+ private Map<NamedClass, Set<DatatypeProperty>> appSD = new TreeMap<NamedClass, Set<DatatypeProperty>>();
// most general applicable properties
private Map<NamedClass,Set<ObjectProperty>> mgr = new TreeMap<NamedClass,Set<ObjectProperty>>();
@@ -838,6 +839,7 @@
private void computeTopRefinements(int maxLength, NamedClass domain) {
long topComputationTimeStartNs = System.nanoTime();
+// System.out.println("computing top refinements for " + domain + " up to length " + maxLength);
if(domain == null && m.size() == 0)
computeM();
@@ -957,6 +959,12 @@
topARefinementsLength.put(domain,maxLength);
topComputationTimeNs += System.nanoTime() - topComputationTimeStartNs;
+
+// if(domain == null) {
+// System.out.println("computed top refinements: " + topRefinementsCumulative.get(maxLength));
+// } else {
+// System.out.println("computed top refinements: " + topARefinementsCumulative.get(domain).get(maxLength));
+// }
}
// compute M_\top
@@ -1046,6 +1054,8 @@
}
m.put(4,m4);
+// System.out.println("m: " + m);
+
mComputationTimeNs += System.nanoTime() - mComputationTimeStartNs;
}
@@ -1183,7 +1193,7 @@
}
mA.get(nc).put(4,m4);
-// System.out.println(mA.get(nc));
+// System.out.println("m for " + nc + ": " + mA.get(nc));
mComputationTimeNs += System.nanoTime() - mComputationTimeStartNs;
}
@@ -1330,7 +1340,7 @@
private void computeMgsdRecursive(NamedClass domain, Set<DatatypeProperty> currProperties, Set<DatatypeProperty> mgsdTmp) {
for(DatatypeProperty prop : currProperties) {
- if(appDD.get(domain).contains(prop))
+ if(appSD.get(domain).contains(prop))
mgsdTmp.add(prop);
else
computeMgsdRecursive(domain, reasoner.getSubProperties(prop), mgsdTmp);
@@ -1372,7 +1382,19 @@
if(!isDisjoint(domain,d))
applicableDDPs.add(role);
}
- appDD.put(domain, applicableDDPs);
+ appDD.put(domain, applicableDDPs);
+
+ // string datatype properties
+ Set<DatatypeProperty> mostGeneralSDPs = reasoner.getStringDatatypeProperties();
+ Set<DatatypeProperty> applicableSDPs = new TreeSet<DatatypeProperty>();
+ for(DatatypeProperty role : mostGeneralSDPs) {
+// Description d = (NamedClass) rs.getDomain(role);
+ Description d = reasoner.getDomain(role);
+// System.out.println("domain: " + d);
+ if(!isDisjoint(domain,d))
+ applicableSDPs.add(role);
+ }
+ appSD.put(domain, applicableSDPs);
}
// returns true of the intersection contains elements disjoint
Modified: trunk/components-core/src/test/java/org/dllearner/test/junit/ParserTests.java
===================================================================
--- trunk/components-core/src/test/java/org/dllearner/test/junit/ParserTests.java 2011-11-02 12:46:04 UTC (rev 3360)
+++ trunk/components-core/src/test/java/org/dllearner/test/junit/ParserTests.java 2011-11-02 14:07:30 UTC (rev 3361)
@@ -68,6 +68,8 @@
"(<http://example.com/prop> some (<http://example.com/class1> and <http://example.com/class2>))",
// another nested expression
"(<http://nlp2rdf.lod2.eu/schema/string/Document> and (<http://nlp2rdf.lod2.eu/schema/string/subStringTrans> some <http://www.w3.org/2002/07/owl#Thing>))",
+ // a test with a single quoted string
+ "(<http://nlp2rdf.lod2.eu/schema/string/Document> and (<http://nlp2rdf.lod2.eu/schema/string/subStringTrans> some ( <http://nlp2rdf.lod2.eu/schema/sso/lemma> value 'copper')))"
};
// loop through all test cases
Modified: trunk/examples/nlp2rdf/reuters_gold_vs_copper/learn.conf
===================================================================
--- trunk/examples/nlp2rdf/reuters_gold_vs_copper/learn.conf 2011-11-02 12:46:04 UTC (rev 3360)
+++ trunk/examples/nlp2rdf/reuters_gold_vs_copper/learn.conf 2011-11-02 14:07:30 UTC (rev 3361)
@@ -36,9 +36,10 @@
alg.type = "celoe"
// alg.writeSearchTree = true
alg.replaceSearchTree = true
-alg.maxExecutionTimeInSeconds = 100
+alg.maxExecutionTimeInSeconds = 10
alg.maxNrOfResults = 10
alg.startClass = "(<http://nlp2rdf.lod2.eu/schema/string/Document> and (<http://nlp2rdf.lod2.eu/schema/string/subStringTrans> some <http://www.w3.org/2002/07/owl#Thing>))"
+// solution:
+// alg.startClass = "(<http://nlp2rdf.lod2.eu/schema/string/Document> and (<http://nlp2rdf.lod2.eu/schema/string/subStringTrans> some ( <http://nlp2rdf.lod2.eu/schema/sso/lemma> value 'copper')))"
-
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <jen...@us...> - 2011-11-02 12:46:10
|
Revision: 3360
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3360&view=rev
Author: jenslehmann
Date: 2011-11-02 12:46:04 +0000 (Wed, 02 Nov 2011)
Log Message:
-----------
improvements of Manchester syntax parser
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/parser/ManchesterSyntaxParser.java
trunk/components-core/src/main/java/org/dllearner/parser/manchester.jj
trunk/components-core/src/test/java/org/dllearner/test/junit/ParserTests.java
trunk/examples/nlp2rdf/reuters_gold_vs_copper/learn.conf
Modified: trunk/components-core/src/main/java/org/dllearner/parser/ManchesterSyntaxParser.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/parser/ManchesterSyntaxParser.java 2011-11-02 12:26:53 UTC (rev 3359)
+++ trunk/components-core/src/main/java/org/dllearner/parser/ManchesterSyntaxParser.java 2011-11-02 12:46:04 UTC (rev 3360)
@@ -42,14 +42,18 @@
jj_consume_token(22);
{if (true) return new Union(c1,c2);}
} else if (jj_2_3(2147483647)) {
+ jj_consume_token(21);
s = URI();
jj_consume_token(SOME);
c = ClassExpression();
+ jj_consume_token(22);
{if (true) return new ObjectSomeRestriction(new ObjectProperty(s),c);}
} else if (jj_2_4(2147483647)) {
+ jj_consume_token(21);
s = URI();
jj_consume_token(ONLY);
c = ClassExpression();
+ jj_consume_token(22);
{if (true) return new ObjectAllRestriction(new ObjectProperty(s),c);}
} else {
switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
@@ -192,9 +196,11 @@
}
private boolean jj_3R_8() {
+ if (jj_scan_token(21)) return true;
if (jj_3R_2()) return true;
if (jj_scan_token(SOME)) return true;
if (jj_3R_1()) return true;
+ if (jj_scan_token(22)) return true;
return false;
}
@@ -291,6 +297,7 @@
}
private boolean jj_3_4() {
+ if (jj_scan_token(21)) return true;
if (jj_3R_2()) return true;
if (jj_scan_token(ONLY)) return true;
return false;
@@ -306,6 +313,7 @@
}
private boolean jj_3_3() {
+ if (jj_scan_token(21)) return true;
if (jj_3R_2()) return true;
if (jj_scan_token(SOME)) return true;
return false;
@@ -350,9 +358,11 @@
}
private boolean jj_3R_9() {
+ if (jj_scan_token(21)) return true;
if (jj_3R_2()) return true;
if (jj_scan_token(ONLY)) return true;
if (jj_3R_1()) return true;
+ if (jj_scan_token(22)) return true;
return false;
}
Modified: trunk/components-core/src/main/java/org/dllearner/parser/manchester.jj
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/parser/manchester.jj 2011-11-02 12:26:53 UTC (rev 3359)
+++ trunk/components-core/src/main/java/org/dllearner/parser/manchester.jj 2011-11-02 12:46:04 UTC (rev 3360)
@@ -84,11 +84,11 @@
| LOOKAHEAD( "(" ClassExpression() <OR>)
"(" c1=ClassExpression() <OR> c2=ClassExpression() ")"
{return new Union(c1,c2);}
- | LOOKAHEAD( URI() <SOME>)
- s=URI() <SOME> c=ClassExpression()
+ | LOOKAHEAD( "(" URI() <SOME>)
+ "(" s=URI() <SOME> c=ClassExpression() ")"
{return new ObjectSomeRestriction(new ObjectProperty(s),c); }
- | LOOKAHEAD( URI() <ONLY>)
- s=URI() <ONLY> c=ClassExpression()
+ | LOOKAHEAD( "(" URI() <ONLY>)
+ "(" s=URI() <ONLY> c=ClassExpression() ")"
{return new ObjectAllRestriction(new ObjectProperty(s),c); }
| <NOT> c=ClassExpression()
{return new Negation(c); }
Modified: trunk/components-core/src/test/java/org/dllearner/test/junit/ParserTests.java
===================================================================
--- trunk/components-core/src/test/java/org/dllearner/test/junit/ParserTests.java 2011-11-02 12:26:53 UTC (rev 3359)
+++ trunk/components-core/src/test/java/org/dllearner/test/junit/ParserTests.java 2011-11-02 12:46:04 UTC (rev 3360)
@@ -53,9 +53,9 @@
// simple URI
"<http://example.com/foo>",
// existential restriction
- "<http://example.com/prop> some <http://example.com/class>",
+ "(<http://example.com/prop> some <http://example.com/class>)",
// universal restriction
- "<http://example.com/prop> only <http://example.com/class>",
+ "(<http://example.com/prop> only <http://example.com/class>)",
// intersection
"(<http://example.com/class1> and <http://example.com/class2>)",
// disjunction
@@ -65,7 +65,9 @@
// has value with string
"(<http://example.com/prop> value \"string\")",
// nested expression
- "<http://example.com/prop> some (<http://example.com/class1> and <http://example.com/class2>)",
+ "(<http://example.com/prop> some (<http://example.com/class1> and <http://example.com/class2>))",
+ // another nested expression
+ "(<http://nlp2rdf.lod2.eu/schema/string/Document> and (<http://nlp2rdf.lod2.eu/schema/string/subStringTrans> some <http://www.w3.org/2002/07/owl#Thing>))",
};
// loop through all test cases
Modified: trunk/examples/nlp2rdf/reuters_gold_vs_copper/learn.conf
===================================================================
--- trunk/examples/nlp2rdf/reuters_gold_vs_copper/learn.conf 2011-11-02 12:26:53 UTC (rev 3359)
+++ trunk/examples/nlp2rdf/reuters_gold_vs_copper/learn.conf 2011-11-02 12:46:04 UTC (rev 3360)
@@ -34,11 +34,11 @@
op.useStringDatatypes = true
//op.frequencyThreshold = 1
alg.type = "celoe"
-alg.writeSearchTree = true
+// alg.writeSearchTree = true
alg.replaceSearchTree = true
alg.maxExecutionTimeInSeconds = 100
alg.maxNrOfResults = 10
+alg.startClass = "(<http://nlp2rdf.lod2.eu/schema/string/Document> and (<http://nlp2rdf.lod2.eu/schema/string/subStringTrans> some <http://www.w3.org/2002/07/owl#Thing>))"
-
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <jen...@us...> - 2011-11-02 12:27:00
|
Revision: 3359
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3359&view=rev
Author: jenslehmann
Date: 2011-11-02 12:26:53 +0000 (Wed, 02 Nov 2011)
Log Message:
-----------
- wrote Manchester syntax parser
- added a unit test for it
- integrated support for using class expressions in conf files (via property editor)
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/CELOE.java
trunk/components-core/src/main/java/org/dllearner/core/config/ClassExpressionPropertyEditor.java
trunk/components-core/src/main/java/org/dllearner/core/owl/StringValueRestriction.java
trunk/components-core/src/main/java/org/dllearner/utilities/owl/ManchesterOWLSyntaxParser.java
trunk/components-core/src/test/java/org/dllearner/test/junit/OWLAPITests.java
trunk/components-core/src/test/java/org/dllearner/test/junit/ParserTests.java
trunk/examples/father.conf
Added Paths:
-----------
trunk/components-core/src/main/java/org/dllearner/parser/ManchesterSyntaxParser.java
trunk/components-core/src/main/java/org/dllearner/parser/ManchesterSyntaxParserConstants.java
trunk/components-core/src/main/java/org/dllearner/parser/ManchesterSyntaxParserTokenManager.java
trunk/components-core/src/main/java/org/dllearner/parser/manchester.jj
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/CELOE.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/CELOE.java 2011-11-02 09:08:56 UTC (rev 3358)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/CELOE.java 2011-11-02 12:26:53 UTC (rev 3359)
@@ -49,6 +49,8 @@
import org.dllearner.core.owl.Individual;
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.Restriction;
import org.dllearner.core.owl.Thing;
import org.dllearner.learningproblems.ClassLearningProblem;
@@ -262,7 +264,10 @@
minimizer = new DescriptionMinimizer(reasoner);
- startClass = Thing.instance;
+ // start at owl:Thing by default
+ if(startClass == null) {
+ startClass = Thing.instance;
+ }
// singleSuggestionMode = configurator.getSingleSuggestionMode();
Modified: trunk/components-core/src/main/java/org/dllearner/core/config/ClassExpressionPropertyEditor.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/core/config/ClassExpressionPropertyEditor.java 2011-11-02 09:08:56 UTC (rev 3358)
+++ trunk/components-core/src/main/java/org/dllearner/core/config/ClassExpressionPropertyEditor.java 2011-11-02 12:26:53 UTC (rev 3359)
@@ -7,6 +7,8 @@
import java.beans.PropertyEditor;
import org.dllearner.core.owl.Description;
+import org.dllearner.parser.ManchesterSyntaxParser;
+import org.dllearner.parser.ParseException;
import org.dllearner.utilities.owl.ManchesterOWLSyntaxParser;
import org.semanticweb.owlapi.expression.ParserException;
@@ -68,14 +70,12 @@
@Override
public void setAsText(String arg0) throws IllegalArgumentException {
- System.out.println(arg0);
// we assume that the start class string is given in Manchester syntax
try {
- description = ManchesterOWLSyntaxParser.getDescription(arg0);
- } catch (ParserException e) {
+ description = ManchesterSyntaxParser.parseClassExpression(arg0);
+ } catch (ParseException e) {
throw new IllegalArgumentException(e);
}
- System.out.println(description);
}
@Override
Modified: trunk/components-core/src/main/java/org/dllearner/core/owl/StringValueRestriction.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/core/owl/StringValueRestriction.java 2011-11-02 09:08:56 UTC (rev 3358)
+++ trunk/components-core/src/main/java/org/dllearner/core/owl/StringValueRestriction.java 2011-11-02 12:26:53 UTC (rev 3359)
@@ -42,7 +42,7 @@
@Override
public String toManchesterSyntaxString(String baseURI, Map<String,String> prefixes) {
- return restrictedPropertyExpression.toString(baseURI, prefixes) + " value " +"\"" +value.toManchesterSyntaxString(baseURI, prefixes)+"\"";
+ return restrictedPropertyExpression.toString(baseURI, prefixes) + " value " + value.toManchesterSyntaxString(baseURI, prefixes);
}
@Override
Added: trunk/components-core/src/main/java/org/dllearner/parser/ManchesterSyntaxParser.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/parser/ManchesterSyntaxParser.java (rev 0)
+++ trunk/components-core/src/main/java/org/dllearner/parser/ManchesterSyntaxParser.java 2011-11-02 12:26:53 UTC (rev 3359)
@@ -0,0 +1,641 @@
+/* Generated By:JavaCC: Do not edit this line. ManchesterSyntaxParser.java */
+package org.dllearner.parser;
+
+import org.dllearner.core.owl.*;
+import java.io.*;
+import java.net.URL;
+
+public class ManchesterSyntaxParser implements ManchesterSyntaxParserConstants {
+
+ public static Description parseClassExpression(String classExpression) throws ParseException {
+ ManchesterSyntaxParser parser = new ManchesterSyntaxParser(new StringReader(classExpression));
+ return parser.ClassExpression();
+ }
+
+ final public Description ClassExpression() throws ParseException {
+ Description c,c1,c2;
+ String s,s1,s2;
+ int i;
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case TOP:
+ jj_consume_token(TOP);
+ {if (true) return new Thing();}
+ break;
+ case BOTTOM:
+ jj_consume_token(BOTTOM);
+ {if (true) return new Nothing();}
+ break;
+ default:
+ jj_la1[0] = jj_gen;
+ if (jj_2_1(2147483647)) {
+ jj_consume_token(21);
+ c1 = ClassExpression();
+ jj_consume_token(AND);
+ c2 = ClassExpression();
+ jj_consume_token(22);
+ {if (true) return new Intersection(c1,c2);}
+ } else if (jj_2_2(2147483647)) {
+ jj_consume_token(21);
+ c1 = ClassExpression();
+ jj_consume_token(OR);
+ c2 = ClassExpression();
+ jj_consume_token(22);
+ {if (true) return new Union(c1,c2);}
+ } else if (jj_2_3(2147483647)) {
+ s = URI();
+ jj_consume_token(SOME);
+ c = ClassExpression();
+ {if (true) return new ObjectSomeRestriction(new ObjectProperty(s),c);}
+ } else if (jj_2_4(2147483647)) {
+ s = URI();
+ jj_consume_token(ONLY);
+ c = ClassExpression();
+ {if (true) return new ObjectAllRestriction(new ObjectProperty(s),c);}
+ } else {
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case NOT:
+ jj_consume_token(NOT);
+ c = ClassExpression();
+ {if (true) return new Negation(c);}
+ break;
+ case GE:
+ jj_consume_token(GE);
+ i = Integer();
+ s = URI();
+ jj_consume_token(23);
+ c = ClassExpression();
+ {if (true) return new ObjectMinCardinalityRestriction(i,new ObjectProperty(s),c);}
+ break;
+ case LE:
+ jj_consume_token(LE);
+ i = Integer();
+ s = URI();
+ jj_consume_token(23);
+ c = ClassExpression();
+ {if (true) return new ObjectMaxCardinalityRestriction(i,new ObjectProperty(s),c);}
+ break;
+ default:
+ jj_la1[1] = jj_gen;
+ if (jj_2_5(4)) {
+ jj_consume_token(21);
+ s1 = URI();
+ jj_consume_token(24);
+ s2 = URI();
+ jj_consume_token(22);
+ {if (true) return new ObjectValueRestriction(new ObjectProperty(s1), new Individual(s2));}
+ } else if (jj_2_6(4)) {
+ jj_consume_token(21);
+ s1 = URI();
+ jj_consume_token(24);
+ s2 = String();
+ jj_consume_token(22);
+ {if (true) return new StringValueRestriction(new DatatypeProperty(s1), s2);}
+ } else {
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case URI:
+ s = URI();
+ {if (true) return new NamedClass(s);}
+ break;
+ default:
+ jj_la1[2] = jj_gen;
+ jj_consume_token(-1);
+ throw new ParseException();
+ }
+ }
+ }
+ }
+ }
+ throw new Error("Missing return statement in function");
+ }
+
+ final public double Double() throws ParseException {
+ Token t;
+ t = jj_consume_token(DOUBLE);
+ {if (true) return new Double(t.image);}
+ throw new Error("Missing return statement in function");
+ }
+
+ final public int Integer() throws ParseException {
+ Token t;
+ t = jj_consume_token(NUMBER);
+ {if (true) return new Integer(t.image);}
+ throw new Error("Missing return statement in function");
+ }
+
+ final public String String() throws ParseException {
+ Token t;
+ String s;
+ t = jj_consume_token(STRING);
+ // cut quotes
+ s = t.image;
+ s = s.substring(1, s.length() - 1);
+ {if (true) return s;}
+ throw new Error("Missing return statement in function");
+ }
+
+ final public String URI() throws ParseException {
+ Token t;
+ String s;
+ t = jj_consume_token(URI);
+ // cut "<" and ">"
+ s = t.image;
+ s = s.substring(1, s.length() - 1);
+ {if (true) return s;}
+ throw new Error("Missing return statement in function");
+ }
+
+ private boolean jj_2_1(int xla) {
+ jj_la = xla; jj_lastpos = jj_scanpos = token;
+ try { return !jj_3_1(); }
+ catch(LookaheadSuccess ls) { return true; }
+ finally { jj_save(0, xla); }
+ }
+
+ private boolean jj_2_2(int xla) {
+ jj_la = xla; jj_lastpos = jj_scanpos = token;
+ try { return !jj_3_2(); }
+ catch(LookaheadSuccess ls) { return true; }
+ finally { jj_save(1, xla); }
+ }
+
+ private boolean jj_2_3(int xla) {
+ jj_la = xla; jj_lastpos = jj_scanpos = token;
+ try { return !jj_3_3(); }
+ catch(LookaheadSuccess ls) { return true; }
+ finally { jj_save(2, xla); }
+ }
+
+ private boolean jj_2_4(int xla) {
+ jj_la = xla; jj_lastpos = jj_scanpos = token;
+ try { return !jj_3_4(); }
+ catch(LookaheadSuccess ls) { return true; }
+ finally { jj_save(3, xla); }
+ }
+
+ private boolean jj_2_5(int xla) {
+ jj_la = xla; jj_lastpos = jj_scanpos = token;
+ try { return !jj_3_5(); }
+ catch(LookaheadSuccess ls) { return true; }
+ finally { jj_save(4, xla); }
+ }
+
+ private boolean jj_2_6(int xla) {
+ jj_la = xla; jj_lastpos = jj_scanpos = token;
+ try { return !jj_3_6(); }
+ catch(LookaheadSuccess ls) { return true; }
+ finally { jj_save(5, xla); }
+ }
+
+ private boolean jj_3R_3() {
+ if (jj_scan_token(STRING)) return true;
+ return false;
+ }
+
+ private boolean jj_3R_8() {
+ if (jj_3R_2()) return true;
+ if (jj_scan_token(SOME)) return true;
+ if (jj_3R_1()) return true;
+ return false;
+ }
+
+ private boolean jj_3R_7() {
+ if (jj_scan_token(21)) return true;
+ if (jj_3R_1()) return true;
+ if (jj_scan_token(OR)) return true;
+ if (jj_3R_1()) return true;
+ if (jj_scan_token(22)) return true;
+ return false;
+ }
+
+ private boolean jj_3R_6() {
+ if (jj_scan_token(21)) return true;
+ if (jj_3R_1()) return true;
+ if (jj_scan_token(AND)) return true;
+ if (jj_3R_1()) return true;
+ if (jj_scan_token(22)) return true;
+ return false;
+ }
+
+ private boolean jj_3R_5() {
+ if (jj_scan_token(BOTTOM)) return true;
+ return false;
+ }
+
+ private boolean jj_3R_1() {
+ Token xsp;
+ xsp = jj_scanpos;
+ if (jj_3R_4()) {
+ jj_scanpos = xsp;
+ if (jj_3R_5()) {
+ jj_scanpos = xsp;
+ if (jj_3R_6()) {
+ jj_scanpos = xsp;
+ if (jj_3R_7()) {
+ jj_scanpos = xsp;
+ if (jj_3R_8()) {
+ jj_scanpos = xsp;
+ if (jj_3R_9()) {
+ jj_scanpos = xsp;
+ if (jj_3R_10()) {
+ jj_scanpos = xsp;
+ if (jj_3R_11()) {
+ jj_scanpos = xsp;
+ if (jj_3R_12()) {
+ jj_scanpos = xsp;
+ if (jj_3_5()) {
+ jj_scanpos = xsp;
+ if (jj_3_6()) {
+ jj_scanpos = xsp;
+ if (jj_3R_13()) return true;
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+ return false;
+ }
+
+ private boolean jj_3R_4() {
+ if (jj_scan_token(TOP)) return true;
+ return false;
+ }
+
+ private boolean jj_3R_14() {
+ if (jj_scan_token(NUMBER)) return true;
+ return false;
+ }
+
+ private boolean jj_3R_13() {
+ if (jj_3R_2()) return true;
+ return false;
+ }
+
+ private boolean jj_3R_2() {
+ if (jj_scan_token(URI)) return true;
+ return false;
+ }
+
+ private boolean jj_3_6() {
+ if (jj_scan_token(21)) return true;
+ if (jj_3R_2()) return true;
+ if (jj_scan_token(24)) return true;
+ if (jj_3R_3()) return true;
+ if (jj_scan_token(22)) return true;
+ return false;
+ }
+
+ private boolean jj_3_4() {
+ if (jj_3R_2()) return true;
+ if (jj_scan_token(ONLY)) return true;
+ return false;
+ }
+
+ private boolean jj_3_5() {
+ if (jj_scan_token(21)) return true;
+ if (jj_3R_2()) return true;
+ if (jj_scan_token(24)) return true;
+ if (jj_3R_2()) return true;
+ if (jj_scan_token(22)) return true;
+ return false;
+ }
+
+ private boolean jj_3_3() {
+ if (jj_3R_2()) return true;
+ if (jj_scan_token(SOME)) return true;
+ return false;
+ }
+
+ private boolean jj_3R_12() {
+ if (jj_scan_token(LE)) return true;
+ if (jj_3R_14()) return true;
+ if (jj_3R_2()) return true;
+ if (jj_scan_token(23)) return true;
+ if (jj_3R_1()) return true;
+ return false;
+ }
+
+ private boolean jj_3_2() {
+ if (jj_scan_token(21)) return true;
+ if (jj_3R_1()) return true;
+ if (jj_scan_token(OR)) return true;
+ return false;
+ }
+
+ private boolean jj_3R_11() {
+ if (jj_scan_token(GE)) return true;
+ if (jj_3R_14()) return true;
+ if (jj_3R_2()) return true;
+ if (jj_scan_token(23)) return true;
+ if (jj_3R_1()) return true;
+ return false;
+ }
+
+ private boolean jj_3R_10() {
+ if (jj_scan_token(NOT)) return true;
+ if (jj_3R_1()) return true;
+ return false;
+ }
+
+ private boolean jj_3_1() {
+ if (jj_scan_token(21)) return true;
+ if (jj_3R_1()) return true;
+ if (jj_scan_token(AND)) return true;
+ return false;
+ }
+
+ private boolean jj_3R_9() {
+ if (jj_3R_2()) return true;
+ if (jj_scan_token(ONLY)) return true;
+ if (jj_3R_1()) return true;
+ return false;
+ }
+
+ /** Generated Token Manager. */
+ public ManchesterSyntaxParserTokenManager token_source;
+ SimpleCharStream jj_input_stream;
+ /** Current token. */
+ public Token token;
+ /** Next token. */
+ public Token jj_nt;
+ private int jj_ntk;
+ private Token jj_scanpos, jj_lastpos;
+ private int jj_la;
+ private int jj_gen;
+ final private int[] jj_la1 = new int[3];
+ static private int[] jj_la1_0;
+ static {
+ jj_la1_init_0();
+ }
+ private static void jj_la1_init_0() {
+ jj_la1_0 = new int[] {0xc00,0x70000,0x100000,};
+ }
+ final private JJCalls[] jj_2_rtns = new JJCalls[6];
+ private boolean jj_rescan = false;
+ private int jj_gc = 0;
+
+ /** Constructor with InputStream. */
+ public ManchesterSyntaxParser(java.io.InputStream stream) {
+ this(stream, null);
+ }
+ /** Constructor with InputStream and supplied encoding */
+ public ManchesterSyntaxParser(java.io.InputStream stream, String encoding) {
+ try { jj_input_stream = new SimpleCharStream(stream, encoding, 1, 1); } catch(java.io.UnsupportedEncodingException e) { throw new RuntimeException(e); }
+ token_source = new ManchesterSyntaxParserTokenManager(jj_input_stream);
+ token = new Token();
+ jj_ntk = -1;
+ jj_gen = 0;
+ for (int i = 0; i < 3; i++) jj_la1[i] = -1;
+ for (int i = 0; i < jj_2_rtns.length; i++) jj_2_rtns[i] = new JJCalls();
+ }
+
+ /** Reinitialise. */
+ public void ReInit(java.io.InputStream stream) {
+ ReInit(stream, null);
+ }
+ /** Reinitialise. */
+ public void ReInit(java.io.InputStream stream, String encoding) {
+ try { jj_input_stream.ReInit(stream, encoding, 1, 1); } catch(java.io.UnsupportedEncodingException e) { throw new RuntimeException(e); }
+ token_source.ReInit(jj_input_stream);
+ token = new Token();
+ jj_ntk = -1;
+ jj_gen = 0;
+ for (int i = 0; i < 3; i++) jj_la1[i] = -1;
+ for (int i = 0; i < jj_2_rtns.length; i++) jj_2_rtns[i] = new JJCalls();
+ }
+
+ /** Constructor. */
+ public ManchesterSyntaxParser(java.io.Reader stream) {
+ jj_input_stream = new SimpleCharStream(stream, 1, 1);
+ token_source = new ManchesterSyntaxParserTokenManager(jj_input_stream);
+ token = new Token();
+ jj_ntk = -1;
+ jj_gen = 0;
+ for (int i = 0; i < 3; i++) jj_la1[i] = -1;
+ for (int i = 0; i < jj_2_rtns.length; i++) jj_2_rtns[i] = new JJCalls();
+ }
+
+ /** Reinitialise. */
+ public void ReInit(java.io.Reader stream) {
+ jj_input_stream.ReInit(stream, 1, 1);
+ token_source.ReInit(jj_input_stream);
+ token = new Token();
+ jj_ntk = -1;
+ jj_gen = 0;
+ for (int i = 0; i < 3; i++) jj_la1[i] = -1;
+ for (int i = 0; i < jj_2_rtns.length; i++) jj_2_rtns[i] = new JJCalls();
+ }
+
+ /** Constructor with generated Token Manager. */
+ public ManchesterSyntaxParser(ManchesterSyntaxParserTokenManager tm) {
+ token_source = tm;
+ token = new Token();
+ jj_ntk = -1;
+ jj_gen = 0;
+ for (int i = 0; i < 3; i++) jj_la1[i] = -1;
+ for (int i = 0; i < jj_2_rtns.length; i++) jj_2_rtns[i] = new JJCalls();
+ }
+
+ /** Reinitialise. */
+ public void ReInit(ManchesterSyntaxParserTokenManager tm) {
+ token_source = tm;
+ token = new Token();
+ jj_ntk = -1;
+ jj_gen = 0;
+ for (int i = 0; i < 3; i++) jj_la1[i] = -1;
+ for (int i = 0; i < jj_2_rtns.length; i++) jj_2_rtns[i] = new JJCalls();
+ }
+
+ private Token jj_consume_token(int kind) throws ParseException {
+ Token oldToken;
+ if ((oldToken = token).next != null) token = token.next;
+ else token = token.next = token_source.getNextToken();
+ jj_ntk = -1;
+ if (token.kind == kind) {
+ jj_gen++;
+ if (++jj_gc > 100) {
+ jj_gc = 0;
+ for (int i = 0; i < jj_2_rtns.length; i++) {
+ JJCalls c = jj_2_rtns[i];
+ while (c != null) {
+ if (c.gen < jj_gen) c.first = null;
+ c = c.next;
+ }
+ }
+ }
+ return token;
+ }
+ token = oldToken;
+ jj_kind = kind;
+ throw generateParseException();
+ }
+
+ static private final class LookaheadSuccess extends java.lang.Error { }
+ final private LookaheadSuccess jj_ls = new LookaheadSuccess();
+ private boolean jj_scan_token(int kind) {
+ if (jj_scanpos == jj_lastpos) {
+ jj_la--;
+ if (jj_scanpos.next == null) {
+ jj_lastpos = jj_scanpos = jj_scanpos.next = token_source.getNextToken();
+ } else {
+ jj_lastpos = jj_scanpos = jj_scanpos.next;
+ }
+ } else {
+ jj_scanpos = jj_scanpos.next;
+ }
+ if (jj_rescan) {
+ int i = 0; Token tok = token;
+ while (tok != null && tok != jj_scanpos) { i++; tok = tok.next; }
+ if (tok != null) jj_add_error_token(kind, i);
+ }
+ if (jj_scanpos.kind != kind) return true;
+ if (jj_la == 0 && jj_scanpos == jj_lastpos) throw jj_ls;
+ return false;
+ }
+
+
+/** Get the next Token. */
+ final public Token getNextToken() {
+ if (token.next != null) token = token.next;
+ else token = token.next = token_source.getNextToken();
+ jj_ntk = -1;
+ jj_gen++;
+ return token;
+ }
+
+/** Get the specific Token. */
+ final public Token getToken(int index) {
+ Token t = token;
+ for (int i = 0; i < index; i++) {
+ if (t.next != null) t = t.next;
+ else t = t.next = token_source.getNextToken();
+ }
+ return t;
+ }
+
+ private int jj_ntk() {
+ if ((jj_nt=token.next) == null)
+ return (jj_ntk = (token.next=token_source.getNextToken()).kind);
+ else
+ return (jj_ntk = jj_nt.kind);
+ }
+
+ private java.util.List<int[]> jj_expentries = new java.util.ArrayList<int[]>();
+ private int[] jj_expentry;
+ private int jj_kind = -1;
+ private int[] jj_lasttokens = new int[100];
+ private int jj_endpos;
+
+ private void jj_add_error_token(int kind, int pos) {
+ if (pos >= 100) return;
+ if (pos == jj_endpos + 1) {
+ jj_lasttokens[jj_endpos++] = kind;
+ } else if (jj_endpos != 0) {
+ jj_expentry = new int[jj_endpos];
+ for (int i = 0; i < jj_endpos; i++) {
+ jj_expentry[i] = jj_lasttokens[i];
+ }
+ jj_entries_loop: for (java.util.Iterator<?> it = jj_expentries.iterator(); it.hasNext();) {
+ int[] oldentry = (int[])(it.next());
+ if (oldentry.length == jj_expentry.length) {
+ for (int i = 0; i < jj_expentry.length; i++) {
+ if (oldentry[i] != jj_expentry[i]) {
+ continue jj_entries_loop;
+ }
+ }
+ jj_expentries.add(jj_expentry);
+ break jj_entries_loop;
+ }
+ }
+ if (pos != 0) jj_lasttokens[(jj_endpos = pos) - 1] = kind;
+ }
+ }
+
+ /** Generate ParseException. */
+ public ParseException generateParseException() {
+ jj_expentries.clear();
+ boolean[] la1tokens = new boolean[25];
+ if (jj_kind >= 0) {
+ la1tokens[jj_kind] = true;
+ jj_kind = -1;
+ }
+ for (int i = 0; i < 3; i++) {
+ if (jj_la1[i] == jj_gen) {
+ for (int j = 0; j < 32; j++) {
+ if ((jj_la1_0[i] & (1<<j)) != 0) {
+ la1tokens[j] = true;
+ }
+ }
+ }
+ }
+ for (int i = 0; i < 25; i++) {
+ if (la1tokens[i]) {
+ jj_expentry = new int[1];
+ jj_expentry[0] = i;
+ jj_expentries.add(jj_expentry);
+ }
+ }
+ jj_endpos = 0;
+ jj_rescan_token();
+ jj_add_error_token(0, 0);
+ int[][] exptokseq = new int[jj_expentries.size()][];
+ for (int i = 0; i < jj_expentries.size(); i++) {
+ exptokseq[i] = jj_expentries.get(i);
+ }
+ return new ParseException(token, exptokseq, tokenImage);
+ }
+
+ /** Enable tracing. */
+ final public void enable_tracing() {
+ }
+
+ /** Disable tracing. */
+ final public void disable_tracing() {
+ }
+
+ private void jj_rescan_token() {
+ jj_rescan = true;
+ for (int i = 0; i < 6; i++) {
+ try {
+ JJCalls p = jj_2_rtns[i];
+ do {
+ if (p.gen > jj_gen) {
+ jj_la = p.arg; jj_lastpos = jj_scanpos = p.first;
+ switch (i) {
+ case 0: jj_3_1(); break;
+ case 1: jj_3_2(); break;
+ case 2: jj_3_3(); break;
+ case 3: jj_3_4(); break;
+ case 4: jj_3_5(); break;
+ case 5: jj_3_6(); break;
+ }
+ }
+ p = p.next;
+ } while (p != null);
+ } catch(LookaheadSuccess ls) { }
+ }
+ jj_rescan = false;
+ }
+
+ private void jj_save(int index, int xla) {
+ JJCalls p = jj_2_rtns[index];
+ while (p.gen > jj_gen) {
+ if (p.next == null) { p = p.next = new JJCalls(); break; }
+ p = p.next;
+ }
+ p.gen = jj_gen + xla - jj_la; p.first = token; p.arg = xla;
+ }
+
+ static final class JJCalls {
+ int gen;
+ Token first;
+ int arg;
+ JJCalls next;
+ }
+
+}
Added: trunk/components-core/src/main/java/org/dllearner/parser/ManchesterSyntaxParserConstants.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/parser/ManchesterSyntaxParserConstants.java (rev 0)
+++ trunk/components-core/src/main/java/org/dllearner/parser/ManchesterSyntaxParserConstants.java 2011-11-02 12:26:53 UTC (rev 3359)
@@ -0,0 +1,78 @@
+/* Generated By:JavaCC: Do not edit this line. ManchesterSyntaxParserConstants.java */
+package org.dllearner.parser;
+
+
+/**
+ * Token literal values and constants.
+ * Generated by org.javacc.parser.OtherFilesGen#start()
+ */
+public interface ManchesterSyntaxParserConstants {
+
+ /** End of File. */
+ int EOF = 0;
+ /** RegularExpression Id. */
+ int SINGLE_LINE_COMMENT = 5;
+ /** RegularExpression Id. */
+ int FORMAL_COMMENT = 6;
+ /** RegularExpression Id. */
+ int MULTI_LINE_COMMENT = 7;
+ /** RegularExpression Id. */
+ int NUMBER = 8;
+ /** RegularExpression Id. */
+ int DOUBLE = 9;
+ /** RegularExpression Id. */
+ int TOP = 10;
+ /** RegularExpression Id. */
+ int BOTTOM = 11;
+ /** RegularExpression Id. */
+ int AND = 12;
+ /** RegularExpression Id. */
+ int OR = 13;
+ /** RegularExpression Id. */
+ int SOME = 14;
+ /** RegularExpression Id. */
+ int ONLY = 15;
+ /** RegularExpression Id. */
+ int NOT = 16;
+ /** RegularExpression Id. */
+ int GE = 17;
+ /** RegularExpression Id. */
+ int LE = 18;
+ /** RegularExpression Id. */
+ int STRING = 19;
+ /** RegularExpression Id. */
+ int URI = 20;
+
+ /** Lexical state. */
+ int DEFAULT = 0;
+
+ /** Literal token values. */
+ String[] tokenImage = {
+ "<EOF>",
+ "\" \"",
+ "\"\\t\"",
+ "\"\\n\"",
+ "\"\\r\"",
+ "<SINGLE_LINE_COMMENT>",
+ "<FORMAL_COMMENT>",
+ "<MULTI_LINE_COMMENT>",
+ "<NUMBER>",
+ "<DOUBLE>",
+ "\"TOP\"",
+ "\"BOTTOM\"",
+ "\"and\"",
+ "\"or\"",
+ "\"some\"",
+ "\"only\"",
+ "\"not\"",
+ "\">=\"",
+ "\"<=\"",
+ "<STRING>",
+ "<URI>",
+ "\"(\"",
+ "\")\"",
+ "\".\"",
+ "\"value\"",
+ };
+
+}
Added: trunk/components-core/src/main/java/org/dllearner/parser/ManchesterSyntaxParserTokenManager.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/parser/ManchesterSyntaxParserTokenManager.java (rev 0)
+++ trunk/components-core/src/main/java/org/dllearner/parser/ManchesterSyntaxParserTokenManager.java 2011-11-02 12:26:53 UTC (rev 3359)
@@ -0,0 +1,692 @@
+/* Generated By:JavaCC: Do not edit this line. ManchesterSyntaxParserTokenManager.java */
+package org.dllearner.parser;
+import org.dllearner.core.owl.*;
+import java.io.*;
+import java.net.URL;
+
+/** Token Manager. */
+public class ManchesterSyntaxParserTokenManager implements ManchesterSyntaxParserConstants
+{
+
+ /** Debug output. */
+ public java.io.PrintStream debugStream = System.out;
+ /** Set debug output. */
+ public void setDebugStream(java.io.PrintStream ds) { debugStream = ds; }
+private final int jjStopStringLiteralDfa_0(int pos, long active0)
+{
+ switch (pos)
+ {
+ case 0:
+ if ((active0 & 0x40000L) != 0L)
+ return 31;
+ return -1;
+ case 1:
+ if ((active0 & 0x40000L) != 0L)
+ return 31;
+ return -1;
+ default :
+ return -1;
+ }
+}
+private final int jjStartNfa_0(int pos, long active0)
+{
+ return jjMoveNfa_0(jjStopStringLiteralDfa_0(pos, active0), pos + 1);
+}
+private int jjStopAtPos(int pos, int kind)
+{
+ jjmatchedKind = kind;
+ jjmatchedPos = pos;
+ return pos + 1;
+}
+private int jjMoveStringLiteralDfa0_0()
+{
+ switch(curChar)
+ {
+ case 40:
+ return jjStopAtPos(0, 21);
+ case 41:
+ return jjStopAtPos(0, 22);
+ case 46:
+ return jjStopAtPos(0, 23);
+ case 60:
+ return jjMoveStringLiteralDfa1_0(0x40000L);
+ case 62:
+ return jjMoveStringLiteralDfa1_0(0x20000L);
+ case 66:
+ return jjMoveStringLiteralDfa1_0(0x800L);
+ case 84:
+ return jjMoveStringLiteralDfa1_0(0x400L);
+ case 97:
+ return jjMoveStringLiteralDfa1_0(0x1000L);
+ case 110:
+ return jjMoveStringLiteralDfa1_0(0x10000L);
+ case 111:
+ return jjMoveStringLiteralDfa1_0(0xa000L);
+ case 115:
+ return jjMoveStringLiteralDfa1_0(0x4000L);
+ case 118:
+ return jjMoveStringLiteralDfa1_0(0x1000000L);
+ default :
+ return jjMoveNfa_0(0, 0);
+ }
+}
+private int jjMoveStringLiteralDfa1_0(long active0)
+{
+ try { curChar = input_stream.readChar(); }
+ catch(java.io.IOException e) {
+ jjStopStringLiteralDfa_0(0, active0);
+ return 1;
+ }
+ switch(curChar)
+ {
+ case 61:
+ if ((active0 & 0x20000L) != 0L)
+ return jjStopAtPos(1, 17);
+ else if ((active0 & 0x40000L) != 0L)
+ return jjStartNfaWithStates_0(1, 18, 31);
+ break;
+ case 79:
+ return jjMoveStringLiteralDfa2_0(active0, 0xc00L);
+ case 97:
+ return jjMoveStringLiteralDfa2_0(active0, 0x1000000L);
+ case 110:
+ return jjMoveStringLiteralDfa2_0(active0, 0x9000L);
+ case 111:
+ return jjMoveStringLiteralDfa2_0(active0, 0x14000L);
+ case 114:
+ if ((active0 & 0x2000L) != 0L)
+ return jjStopAtPos(1, 13);
+ break;
+ default :
+ break;
+ }
+ return jjStartNfa_0(0, active0);
+}
+private int jjMoveStringLiteralDfa2_0(long old0, long active0)
+{
+ if (((active0 &= old0)) == 0L)
+ return jjStartNfa_0(0, old0);
+ try { curChar = input_stream.readChar(); }
+ catch(java.io.IOException e) {
+ jjStopStringLiteralDfa_0(1, active0);
+ return 2;
+ }
+ switch(curChar)
+ {
+ case 80:
+ if ((active0 & 0x400L) != 0L)
+ return jjStopAtPos(2, 10);
+ break;
+ case 84:
+ return jjMoveStringLiteralDfa3_0(active0, 0x800L);
+ case 100:
+ if ((active0 & 0x1000L) != 0L)
+ return jjStopAtPos(2, 12);
+ break;
+ case 108:
+ return jjMoveStringLiteralDfa3_0(active0, 0x1008000L);
+ case 109:
+ return jjMoveStringLiteralDfa3_0(active0, 0x4000L);
+ case 116:
+ if ((active0 & 0x10000L) != 0L)
+ return jjStopAtPos(2, 16);
+ break;
+ default :
+ break;
+ }
+ return jjStartNfa_0(1, active0);
+}
+private int jjMoveStringLiteralDfa3_0(long old0, long active0)
+{
+ if (((active0 &= old0)) == 0L)
+ return jjStartNfa_0(1, old0);
+ try { curChar = input_stream.readChar(); }
+ catch(java.io.IOException e) {
+ jjStopStringLiteralDfa_0(2, active0);
+ return 3;
+ }
+ switch(curChar)
+ {
+ case 84:
+ return jjMoveStringLiteralDfa4_0(active0, 0x800L);
+ case 101:
+ if ((active0 & 0x4000L) != 0L)
+ return jjStopAtPos(3, 14);
+ break;
+ case 117:
+ return jjMoveStringLiteralDfa4_0(active0, 0x1000000L);
+ case 121:
+ if ((active0 & 0x8000L) != 0L)
+ return jjStopAtPos(3, 15);
+ break;
+ default :
+ break;
+ }
+ return jjStartNfa_0(2, active0);
+}
+private int jjMoveStringLiteralDfa4_0(long old0, long active0)
+{
+ if (((active0 &= old0)) == 0L)
+ return jjStartNfa_0(2, old0);
+ try { curChar = input_stream.readChar(); }
+ catch(java.io.IOException e) {
+ jjStopStringLiteralDfa_0(3, active0);
+ return 4;
+ }
+ switch(curChar)
+ {
+ case 79:
+ return jjMoveStringLiteralDfa5_0(active0, 0x800L);
+ case 101:
+ if ((active0 & 0x1000000L) != 0L)
+ return jjStopAtPos(4, 24);
+ break;
+ default :
+ break;
+ }
+ return jjStartNfa_0(3, active0);
+}
+private int jjMoveStringLiteralDfa5_0(long old0, long active0)
+{
+ if (((active0 &= old0)) == 0L)
+ return jjStartNfa_0(3, old0);
+ try { curChar = input_stream.readChar(); }
+ catch(java.io.IOException e) {
+ jjStopStringLiteralDfa_0(4, active0);
+ return 5;
+ }
+ switch(curChar)
+ {
+ case 77:
+ if ((active0 & 0x800L) != 0L)
+ return jjStopAtPos(5, 11);
+ break;
+ default :
+ break;
+ }
+ return jjStartNfa_0(4, active0);
+}
+private int jjStartNfaWithStates_0(int pos, int kind, int state)
+{
+ jjmatchedKind = kind;
+ jjmatchedPos = pos;
+ try { curChar = input_stream.readChar(); }
+ catch(java.io.IOException e) { return pos + 1; }
+ return jjMoveNfa_0(state, pos + 1);
+}
+static final long[] jjbitVec0 = {
+ 0x0L, 0x0L, 0xffffffffffffffffL, 0xffffffffffffffffL
+};
+private int jjMoveNfa_0(int startState, int curPos)
+{
+ int startsAt = 0;
+ jjnewStateCnt = 31;
+ int i = 1;
+ jjstateSet[0] = startState;
+ int kind = 0x7fffffff;
+ for (;;)
+ {
+ if (++jjround == 0x7fffffff)
+ ReInitRounds();
+ if (curChar < 64)
+ {
+ long l = 1L << curChar;
+ do
+ {
+ switch(jjstateSet[--i])
+ {
+ case 31:
+ if ((0xbfffffffffffdbffL & l) != 0L)
+ jjCheckNAddTwoStates(4, 5);
+ else if (curChar == 62)
+ {
+ if (kind > 20)
+ kind = 20;
+ }
+ break;
+ case 0:
+ if ((0x3fe000000000000L & l) != 0L)
+ {
+ if (kind > 8)
+ kind = 8;
+ jjCheckNAddStates(0, 2);
+ }
+ else if (curChar == 48)
+ {
+ if (kind > 8)
+ kind = 8;
+ jjCheckNAdd(28);
+ }
+ else if (curChar == 47)
+ jjAddStates(3, 5);
+ else if (curChar == 60)
+ jjCheckNAddTwoStates(4, 5);
+ else if (curChar == 34)
+ jjCheckNAddTwoStates(1, 2);
+ break;
+ case 1:
+ if ((0xfffffffbffffdbffL & l) != 0L)
+ jjCheckNAddTwoStates(1, 2);
+ break;
+ case 2:
+ if (curChar == 34 && kind > 19)
+ kind = 19;
+ break;
+ case 3:
+ if (curChar == 60)
+ jjCheckNAddTwoStates(4, 5);
+ break;
+ case 4:
+ if ((0xbfffffffffffdbffL & l) != 0L)
+ jjCheckNAddTwoStates(4, 5);
+ break;
+ case 5:
+ if (curChar == 62 && kind > 20)
+ kind = 20;
+ break;
+ case 6:
+ if (curChar == 47)
+ jjAddStates(3, 5);
+ break;
+ case 7:
+ if (curChar == 47)
+ jjCheckNAddStates(6, 8);
+ break;
+ case 8:
+ if ((0xffffffffffffdbffL & l) != 0L)
+ jjCheckNAddStates(6, 8);
+ break;
+ case 9:
+ if ((0x2400L & l) != 0L && kind > 5)
+ kind = 5;
+ break;
+ case 10:
+ if (curChar == 10 && kind > 5)
+ kind = 5;
+ break;
+ case 11:
+ if (curChar == 13)
+ jjstateSet[jjnewStateCnt++] = 10;
+ break;
+ case 12:
+ if (curChar == 42)
+ jjCheckNAddTwoStates(13, 14);
+ break;
+ case 13:
+ if ((0xfffffbffffffffffL & l) != 0L)
+ jjCheckNAddTwoStates(13, 14);
+ break;
+ case 14:
+ if (curChar == 42)
+ jjCheckNAddStates(9, 11);
+ break;
+ case 15:
+ if ((0xffff7bffffffffffL & l) != 0L)
+ jjCheckNAddTwoStates(16, 14);
+ break;
+ case 16:
+ if ((0xfffffbffffffffffL & l) != 0L)
+ jjCheckNAddTwoStates(16, 14);
+ break;
+ case 17:
+ if (curChar == 47 && kind > 6)
+ kind = 6;
+ break;
+ case 18:
+ if (curChar == 42)
+ jjstateSet[jjnewStateCnt++] = 12;
+ break;
+ case 19:
+ if (curChar == 42)
+ jjCheckNAddTwoStates(20, 21);
+ break;
+ case 20:
+ if ((0xfffffbffffffffffL & l) != 0L)
+ jjCheckNAddTwoStates(20, 21);
+ break;
+ case 21:
+ if (curChar == 42)
+ jjCheckNAddStates(12, 14);
+ break;
+ case 22:
+ if ((0xffff7bffffffffffL & l) != 0L)
+ jjCheckNAddTwoStates(23, 21);
+ break;
+ case 23:
+ if ((0xfffffbffffffffffL & l) != 0L)
+ jjCheckNAddTwoStates(23, 21);
+ break;
+ case 24:
+ if (curChar == 47 && kind > 7)
+ kind = 7;
+ break;
+ case 25:
+ if ((0x3fe000000000000L & l) == 0L)
+ break;
+ if (kind > 8)
+ kind = 8;
+ jjCheckNAddStates(0, 2);
+ break;
+ case 26:
+ if ((0x3ff000000000000L & l) == 0L)
+ break;
+ if (kind > 8)
+ kind = 8;
+ jjCheckNAdd(26);
+ break;
+ case 27:
+ if ((0x3ff000000000000L & l) != 0L)
+ jjCheckNAddTwoStates(27, 28);
+ break;
+ case 28:
+ if (curChar != 46)
+ break;
+ if (kind > 9)
+ kind = 9;
+ jjCheckNAdd(29);
+ break;
+ case 29:
+ if ((0x3ff000000000000L & l) == 0L)
+ break;
+ if (kind > 9)
+ kind = 9;
+ jjCheckNAdd(29);
+ break;
+ case 30:
+ if (curChar != 48)
+ break;
+ if (kind > 8)
+ kind = 8;
+ jjCheckNAdd(28);
+ break;
+ default : break;
+ }
+ } while(i != startsAt);
+ }
+ else if (curChar < 128)
+ {
+ long l = 1L << (curChar & 077);
+ do
+ {
+ switch(jjstateSet[--i])
+ {
+ case 31:
+ case 4:
+ if ((0xffffffffefffffffL & l) != 0L)
+ jjCheckNAddTwoStates(4, 5);
+ break;
+ case 1:
+ if ((0xffffffffefffffffL & l) != 0L)
+ jjAddStates(15, 16);
+ break;
+ case 8:
+ jjAddStates(6, 8);
+ break;
+ case 13:
+ jjCheckNAddTwoStates(13, 14);
+ break;
+ case 15:
+ case 16:
+ jjCheckNAddTwoStates(16, 14);
+ break;
+ case 20:
+ jjCheckNAddTwoStates(20, 21);
+ break;
+ case 22:
+ case 23:
+ jjCheckNAddTwoStates(23, 21);
+ break;
+ default : break;
+ }
+ } while(i != startsAt);
+ }
+ else
+ {
+ int i2 = (curChar & 0xff) >> 6;
+ long l2 = 1L << (curChar & 077);
+ do
+ {
+ switch(jjstateSet[--i])
+ {
+ case 31:
+ case 4:
+ if ((jjbitVec0[i2] & l2) != 0L)
+ jjCheckNAddTwoStates(4, 5);
+ break;
+ case 1:
+ if ((jjbitVec0[i2] & l2) != 0L)
+ jjAddStates(15, 16);
+ break;
+ case 8:
+ if ((jjbitVec0[i2] & l2) != 0L)
+ jjAddStates(6, 8);
+ break;
+ case 13:
+ if ((jjbitVec0[i2] & l2) != 0L)
+ jjCheckNAddTwoStates(13, 14);
+ break;
+ case 15:
+ case 16:
+ if ((jjbitVec0[i2] & l2) != 0L)
+ jjCheckNAddTwoStates(16, 14);
+ break;
+ case 20:
+ if ((jjbitVec0[i2] & l2) != 0L)
+ jjCheckNAddTwoStates(20, 21);
+ break;
+ case 22:
+ case 23:
+ if ((jjbitVec0[i2] & l2) != 0L)
+ jjCheckNAddTwoStates(23, 21);
+ break;
+ default : break;
+ }
+ } while(i != startsAt);
+ }
+ if (kind != 0x7fffffff)
+ {
+ jjmatchedKind = kind;
+ jjmatchedPos = curPos;
+ kind = 0x7fffffff;
+ }
+ ++curPos;
+ if ((i = jjnewStateCnt) == (startsAt = 31 - (jjnewStateCnt = startsAt)))
+ return curPos;
+ try { curChar = input_stream.readChar(); }
+ catch(java.io.IOException e) { return curPos; }
+ }
+}
+static final int[] jjnextStates = {
+ 26, 27, 28, 7, 18, 19, 8, 9, 11, 14, 15, 17, 21, 22, 24, 1,
+ 2,
+};
+
+/** Token literal values. */
+public static final String[] jjstrLiteralImages = {
+"", null, null, null, null, null, null, null, null, null, "\124\117\120",
+"\102\117\124\124\117\115", "\141\156\144", "\157\162", "\163\157\155\145", "\157\156\154\171",
+"\156\157\164", "\76\75", "\74\75", null, null, "\50", "\51", "\56", "\166\141\154\165\145", };
+
+/** Lexer state names. */
+public static final String[] lexStateNames = {
+ "DEFAULT",
+};
+static final long[] jjtoToken = {
+ 0x1ffff01L,
+};
+static final long[] jjtoSkip = {
+ 0xfeL,
+};
+protected SimpleCharStream input_stream;
+private final int[] jjrounds = new int[31];
+private final int[] jjstateSet = new int[62];
+protected char curChar;
+/** Constructor. */
+public ManchesterSyntaxParserTokenManager(SimpleCharStream stream){
+ if (SimpleCharStream.staticFlag)
+ throw new Error("ERROR: Cannot use a static CharStream class with a non-static lexical analyzer.");
+ input_stream = stream;
+}
+
+/** Constructor. */
+public ManchesterSyntaxParserTokenManager(SimpleCharStream stream, int lexState){
+ this(stream);
+ SwitchTo(lexState);
+}
+
+/** Reinitialise parser. */
+public void ReInit(SimpleCharStream stream)
+{
+ jjmatchedPos = jjnewStateCnt = 0;
+ curLexState = defaultLexState;
+ input_stream = stream;
+ ReInitRounds();
+}
+private void ReInitRounds()
+{
+ int i;
+ jjround = 0x80000001;
+ for (i = 31; i-- > 0;)
+ jjrounds[i] = 0x80000000;
+}
+
+/** Reinitialise parser. */
+public void ReInit(SimpleCharStream stream, int lexState)
+{
+ ReInit(stream);
+ SwitchTo(lexState);
+}
+
+/** Switch to specified lex state. */
+public void SwitchTo(int lexState)
+{
+ if (lexState >= 1 || lexState < 0)
+ throw new TokenMgrError("Error: Ignoring invalid lexical state : " + lexState + ". State unchanged.", TokenMgrError.INVALID_LEXICAL_STATE);
+ else
+ curLexState = lexState;
+}
+
+protected Token jjFillToken()
+{
+ final Token t;
+ final String curTokenImage;
+ final int beginLine;
+ final int endLine;
+ final int beginColumn;
+ final int endColumn;
+ String im = jjstrLiteralImages[jjmatchedKind];
+ curTokenImage = (im == null) ? input_stream.GetImage() : im;
+ beginLine = input_stream.getBeginLine();
+ beginColumn = input_stream.getBeginColumn();
+ endLine = input_stream.getEndLine();
+ endColumn = input_stream.getEndColumn();
+ t = Token.newToken(jjmatchedKind, curTokenImage);
+
+ t.beginLine = beginLine;
+ t.endLine = endLine;
+ t.beginColumn = beginColumn;
+ t.endColumn = endColumn;
+
+ return t;
+}
+
+int curLexState = 0;
+int defaultLexState = 0;
+int jjnewStateCnt;
+int jjround;
+int jjmatchedPos;
+int jjmatchedKind;
+
+/** Get the next Token. */
+public Token getNextToken()
+{
+ Token matchedToken;
+ int curPos = 0;
+
+ EOFLoop :
+ for (;;)
+ {
+ try
+ {
+ curChar = input_stream.BeginToken();
+ }
+ catch(java.io.IOException e)
+ {
+ jjmatchedKind = 0;
+ matchedToken = jjFillToken();
+ return matchedToken;
+ }
+
+ try { input_stream.backup(0);
+ while (curChar <= 32 && (0x100002600L & (1L << curChar)) != 0L)
+ curChar = input_stream.BeginToken();
+ }
+ catch (java.io.IOException e1) { continue EOFLoop; }
+ jjmatchedKind = 0x7fffffff;
+ jjmatchedPos = 0;
+ curPos = jjMoveStringLiteralDfa0_0();
+ if (jjmatchedKind != 0x7fffffff)
+ {
+ if (jjmatchedPos + 1 < curPos)
+ input_stream.backup(curPos - jjmatchedPos - 1);
+ if ((jjtoToken[jjmatchedKind >> 6] & (1L << (jjmatchedKind & 077))) != 0L)
+ {
+ matchedToken = jjFillToken();
+ return matchedToken;
+ }
+ else
+ {
+ continue EOFLoop;
+ }
+ }
+ int error_line = input_stream.getEndLine();
+ int error_column = input_stream.getEndColumn();
+ String error_after = null;
+ boolean EOFSeen = false;
+ try { input_stream.readChar(); input_stream.backup(1); }
+ catch (java.io.IOException e1) {
+ EOFSeen = true;
+ error_after = curPos <= 1 ? "" : input_stream.GetImage();
+ if (curChar == '\n' || curChar == '\r') {
+ error_line++;
+ error_column = 0;
+ }
+ else
+ error_column++;
+ }
+ if (!EOFSeen) {
+ input_stream.backup(1);
+ error_after = curPos <= 1 ? "" : input_stream.GetImage();
+ }
+ throw new TokenMgrError(EOFSeen, curLexState, error_line, error_column, error_after, curChar, TokenMgrError.LEXICAL_ERROR);
+ }
+}
+
+private void jjCheckNAdd(int state)
+{
+ if (jjrounds[state] != jjround)
+ {
+ jjstateSet[jjnewStateCnt++] = state;
+ jjrounds[state] = jjround;
+ }
+}
+private void jjAddStates(int start, int end)
+{
+ do {
+ jjstateSet[jjnewStateCnt++] = jjnextStates[start];
+ } while (start++ != end);
+}
+private void jjCheckNAddTwoStates(int state1, int state2)
+{
+ jjCheckNAdd(state1);
+ jjCheckNAdd(state2);
+}
+
+private void jjCheckNAddStates(int start, int end)
+{
+ do {
+ jjCheckNAdd(jjnextStates[start]);
+ } while (start++ != end);
+}
+
+}
Added: trunk/components-core/src/main/java/org/dllearner/parser/manchester.jj
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/parser/manchester.jj (rev 0)
+++ trunk/components-core/src/main/java/org/dllearner/parser/manchester.jj 2011-11-02 12:26:53 UTC (rev 3359)
@@ -0,0 +1,159 @@
+/**
+ * Copyright (C) 2011, 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/>.
+ *
+ */
+
+options {
+ JDK_VERSION = "1.5";
+ STATIC = false;
+}
+
+PARSER_BEGIN(ManchesterSyntaxParser)
+package org.dllearner.parser;
+
+import org.dllearner.core.owl.*;
+import java.io.*;
+import java.net.URL;
+
+public class ManchesterSyntaxParser {
+
+ public static Description parseClassExpression(String classExpression) throws ParseException {
+ ManchesterSyntaxParser parser = new ManchesterSyntaxParser(new StringReader(classExpression));
+ return parser.ClassExpression();
+ }
+
+}
+PARSER_END(ManchesterSyntaxParser)
+
+SKIP :
+{
+ " "
+| "\t"
+| "\n"
+| "\r"
+| <SINGLE_LINE_COMMENT: "//" (~["\n","\r"])* ("\n"|"\r"|"\r\n")>
+| <FORMAL_COMMENT: "/**" (~["*"])* "*" ("*" | (~["*","/"] (~["*"])* "*"))* "/">
+| <MULTI_LINE_COMMENT: "/*" (~["*"])* "*" ("*" | (~["*","/"] (~["*"])* "*"))* "/">
+}
+
+TOKEN :
+{
+ < NUMBER: (["1"-"9"] (["0"-"9"])* | "0") >
+ | < DOUBLE: (["1"-"9"] (["0"-"9"])* | "0") "." (["0"-"9"])* >
+ | < TOP: "TOP" >
+ | < BOTTOM: "BOTTOM" >
+ | < AND: "and" >
+ | < OR: "or" >
+ | < SOME: "some" >
+ | < ONLY: "only" >
+ | < NOT: "not" >
+ | < GE: ">=" >
+ | < LE: "<=" >
+ | < STRING: "\"" (~["\"","\\","\n","\r"])* "\"" >
+ | < URI: "<" (~[">","\\","\n","\r"])* ">" >
+}
+
+Description ClassExpression() :
+{
+ Description c,c1,c2;
+ String s,s1,s2;
+ int i;
+}
+{
+ <TOP> {return new Thing();}
+ | <BOTTOM> {return new Nothing();}
+ // parse until next AND or OR
+ | LOOKAHEAD( "(" ClassExpression() <AND>)
+ "(" c1=ClassExpression() <AND> c2=ClassExpression() ")"
+ {return new Intersection(c1,c2);}
+ | LOOKAHEAD( "(" ClassExpression() <OR>)
+ "(" c1=ClassExpression() <OR> c2=ClassExpression() ")"
+ {return new Union(c1,c2);}
+ | LOOKAHEAD( URI() <SOME>)
+ s=URI() <SOME> c=ClassExpression()
+ {return new ObjectSomeRestriction(new ObjectProperty(s),c); }
+ | LOOKAHEAD( URI() <ONLY>)
+ s=URI() <ONLY> c=ClassExpression()
+ {return new ObjectAllRestriction(new ObjectProperty(s),c); }
+ | <NOT> c=ClassExpression()
+ {return new Negation(c); }
+ | <GE> i=Integer() s=URI() "." c=ClassExpression()
+ {return new ObjectMinCardinalityRestriction(i,new ObjectProperty(s),c);}
+ | <LE> i=Integer() s=URI() "." c=ClassExpression()
+ {return new ObjectMaxCardinalityRestriction(i,new ObjectProperty(s),c);}
+ | LOOKAHEAD(4)
+ "(" s1=URI() "value" s2=URI() ")"
+ { return new ObjectValueRestriction(new ObjectProperty(s1), new Individual(s2)); }
+ | LOOKAHEAD(4)
+ "(" s1=URI() "value" s2=String() ")"
+ { return new StringValueRestriction(new DatatypeProperty(s1), s2); }
+ // if none of the other cases matches, it is just a named class
+ | s = URI() {return new NamedClass(s);}
+}
+
+double Double() :
+{
+ Token t;
+}
+{
+ t=<DOUBLE>
+ {
+ return new Double(t.image);
+ }
+}
+
+int Integer() :
+{
+ Token t;
+}
+{
+ t=<NUMBER>
+ {
+ return new Integer(t.image);
+ }
+}
+
+String String() :
+{
+ Token t;
+ String s;
+}
+{
+ t=<STRING>
+ {
+ // cut quotes
+ s = t.image;
+ s = s.substring(1, s.length() - 1);
+ return s;
+ }
+}
+
+String URI() :
+{
+ Token t;
+ String s;
+}
+{
+ t=<URI>
+ {
+ // cut "<" and ">"
+ s = t.image;
+ s = s.substring(1, s.length() - 1);
+ return s;
+ }
+}
\ No newline at end of file
Modified: trunk/components-core/src/main/java/org/dllearner/utilities/owl/ManchesterOWLSyntaxParser.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/utilities/owl/ManchesterOWLSyntaxParser.java 2011-11-02 09:08:56 UTC (rev 3358)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/owl/ManchesterOWLSyntaxParser.java 2011-11-02 12:26:53 UTC (rev 3359)
@@ -22,6 +22,8 @@
import org.coode.owlapi.manchesterowlsyntax.ManchesterOWLSyntaxEditorParser;
import org.dllearner.core.owl.Description;
import org.dllearner.kb.sparql.SparqlQueryDescriptionConvertVisitor;
+import org.dllearner.parser.ManchesterSyntaxParser;
+import org.dllearner.parser.ParseException;
import org.semanticweb.owlapi.apibinding.OWLManager;
import org.semanticweb.owlapi.expression.ParserException;
import org.semanticweb.owlapi.model.OWLClassExpression;
@@ -42,14 +44,16 @@
return parser.parseClassExpression();
}
- public static Description getDescription(String manchesterSyntaxDescription) throws ParserException {
- OWLClassExpression d = getOWLAPIDescription(manchesterSyntaxDescription);
- return DLLearnerDescriptionConvertVisitor.getDLLearnerDescription(d);
+ public static Description getDescription(String manchesterSyntaxDescription) throws ParseException {
+// OWLClassExpression d = getOWLAPIDescription(manchesterSyntaxDescription);
+// return DLLearnerDescriptionConvertVisitor.getDLLearnerDescription(d);
+ return ManchesterSyntaxParser.parseClassExpression(manchesterSyntaxDescription);
}
+
- public static void main(String args[]) throws ParserException {
- Description d = ManchesterOWLSyntaxParser.getDescription("hasP SOME A");
- SparqlQueryDescriptionConvertVisitor.getSparqlQuery(d, 10, false, false);
- }
+// public static void main(String args[]) throws ParserException {
+// Description d = ManchesterOWLSyntaxParser.getDescription("hasP SOME A");
+// SparqlQueryDescriptionConvertVisitor.getSparqlQuery(d, 10, false, false);
+// }
}
Modified: trunk/components-core/src/test/java/org/dllearner/test/junit/OWLAPITests.java
===================================================================
--- trunk/components-core/src/test/java/org/dllearner/test/junit/OWLAPITests.java 2011-11-02 09:08:56 UTC (rev 3358)
+++ trunk/components-core/src/test/java/org/dllearner/test/junit/OWLAPITests.java 2011-11-02 12:26:53 UTC (rev 3359)
@@ -20,9 +20,9 @@
package org.dllearner.test.junit;
import org.dllearner.core.owl.Description;
+import org.dllearner.parser.ParseException;
import org.dllearner.utilities.owl.ManchesterOWLSyntaxParser;
import org.junit.Test;
-import org.semanticweb.owlapi.expression.ParserException;
/**
*
@@ -34,7 +34,7 @@
public class OWLAPITests {
@Test
- public void testManchesterSyntaxParser() throws ParserException {
+ public void testManchesterSyntaxParser() throws ParseException {
// String s = "BIGPROP SOME smallclass";
// String s = "<http://test.de/prop> some <http://test.de/Class>";
String s = "<http://test.de/Class>";
Modified: trunk/components-core/src/test/java/org/dllearner/test/junit/ParserTests.java
===================================================================
--- trunk/components-core/src/test/java/org/dllearner/test/junit/ParserTests.java 2011-11-02 09:08:56 UTC (rev 3358)
+++ trunk/components-core/src/test/java/org/dllearner/test/junit/ParserTests.java 2011-11-02 12:26:53 UTC (rev 3359)
@@ -24,6 +24,7 @@
import org.dllearner.core.owl.Description;
import org.dllearner.kb.sparql.SparqlQueryDescriptionConvertVisitor;
import org.dllearner.parser.KBParser;
+import org.dllearner.parser.ManchesterSyntaxParser;
import org.dllearner.parser.ParseException;
import org.junit.Test;
@@ -47,6 +48,36 @@
}
@Test
+ public void ManchesterParserTest() throws ParseException {
+ String[] tests = new String[] {
+ // simple URI
+ "<http://example.com/foo>",
+ // existential restriction
+ "<http://example.com/prop> some <http://example.com/class>",
+ // universal restriction
+ "<http://example.com/prop> only <http://example.com/class>",
+ // intersection
+ "(<http://example.com/class1> and <http://example.com/class2>)",
+ // disjunction
+ "(<http://example.com/class1> or <http://example.com/class2>)",
+ // has value
+ "(<http://example.com/prop> value <http://example.com/ind>)",
+ // has value with string
+ "(<http://example.com/prop> value \"string\")",
+ // nested expression
+ "<http://example.com/prop> some (<http://example.com/class1> and <http://example.com/class2>)",
+ };
+
+ // loop through all test cases
+ for(String test : tests) {
+ System.out.print(test + " --> ");
+ Description d = ManchesterSyntaxParser.parseClassExpression(test);
+ System.out.println(d.toManchesterSyntaxString(null, null));
+ }
+
+ }
+
+ @Test
public void ParseAndSPARQLConvertTest() throws ParseException {
// add your test strings here (do not use prefixes)
String[] kbArray = new String[] {
Modified: trunk/examples/father.conf
===================================================================
--- trunk/examples/father.conf 2011-11-02 09:08:56 UTC (rev 3358)
+++ trunk/examples/father.conf 2011-11-02 12:26:53 UTC (rev 3359)
@@ -25,4 +25,3 @@
// create learning algorithm to run
alg.type = "ocel"
-
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|
|
From: <jen...@us...> - 2011-11-02 09:09:03
|
Revision: 3358
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3358&view=rev
Author: jenslehmann
Date: 2011-11-02 09:08:56 +0000 (Wed, 02 Nov 2011)
Log Message:
-----------
registered editor for class expressions (not working yet)
Modified Paths:
--------------
trunk/components-core/src/test/java/org/dllearner/test/junit/OWLAPITests.java
trunk/examples/nlp2rdf/reuters_gold_vs_copper/learn.conf
trunk/interfaces/src/main/java/org/dllearner/configuration/spring/CustomPropertyEditorRegistrar.java
Added Paths:
-----------
trunk/components-core/src/main/java/org/dllearner/core/config/ClassExpressionPropertyEditor.java
Added: trunk/components-core/src/main/java/org/dllearner/core/config/ClassExpressionPropertyEditor.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/core/config/ClassExpressionPropertyEditor.java (rev 0)
+++ trunk/components-core/src/main/java/org/dllearner/core/config/ClassExpressionPropertyEditor.java 2011-11-02 09:08:56 UTC (rev 3358)
@@ -0,0 +1,92 @@
+package org.dllearner.core.config;
+
+import java.awt.Component;
+import java.awt.Graphics;
+import java.awt.Rectangle;
+import java.beans.PropertyChangeListener;
+import java.beans.PropertyEditor;
+
+import org.dllearner.core.owl.Description;
+import org.dllearner.utilities.owl.ManchesterOWLSyntaxParser;
+import org.semanticweb.owlapi.expression.ParserException;
+
+public class ClassExpressionPropertyEditor implements PropertyEditor {
+
+ private Description description;
+
+ @Override
+ public void addPropertyChangeListener(PropertyChangeListener arg0) {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public String getAsText() {
+ return description.toManchesterSyntaxString(null, null);
+ }
+
+ @Override
+ public Component getCustomEditor() {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String getJavaInitializationString() {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public String[] getTags() {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public Object getValue() {
+ return description;
+ }
+
+ @Override
+ public boolean isPaintable() {
+ // TODO Auto-generated method stub
+ return false;
+ }
+
+ @Override
+ public void paintValue(Graphics arg0, Rectangle arg1) {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void removePropertyChangeListener(PropertyChangeListener arg0) {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void setAsText(String arg0) throws IllegalArgumentException {
+ System.out.println(arg0);
+ // we assume that the start class string is given in Manchester syntax
+ try {
+ description = ManchesterOWLSyntaxParser.getDescription(arg0);
+ } catch (ParserException e) {
+ throw new IllegalArgumentException(e);
+ }
+ System.out.println(description);
+ }
+
+ @Override
+ public void setValue(Object arg0) {
+ description = (Description) arg0;
+ }
+
+ @Override
+ public boolean supportsCustomEditor() {
+ // TODO Auto-generated method stub
+ return false;
+ }
+
+}
Modified: trunk/components-core/src/test/java/org/dllearner/test/junit/OWLAPITests.java
===================================================================
--- trunk/components-core/src/test/java/org/dllearner/test/junit/OWLAPITests.java 2011-11-02 08:43:43 UTC (rev 3357)
+++ trunk/components-core/src/test/java/org/dllearner/test/junit/OWLAPITests.java 2011-11-02 09:08:56 UTC (rev 3358)
@@ -21,6 +21,7 @@
import org.dllearner.core.owl.Description;
import org.dllearner.utilities.owl.ManchesterOWLSyntaxParser;
+import org.junit.Test;
import org.semanticweb.owlapi.expression.ParserException;
/**
@@ -32,7 +33,7 @@
*/
public class OWLAPITests {
-// @Test
+ @Test
public void testManchesterSyntaxParser() throws ParserException {
// String s = "BIGPROP SOME smallclass";
// String s = "<http://test.de/prop> some <http://test.de/Class>";
Modified: trunk/examples/nlp2rdf/reuters_gold_vs_copper/learn.conf
===================================================================
--- trunk/examples/nlp2rdf/reuters_gold_vs_copper/learn.conf 2011-11-02 08:43:43 UTC (rev 3357)
+++ trunk/examples/nlp2rdf/reuters_gold_vs_copper/learn.conf 2011-11-02 09:08:56 UTC (rev 3358)
@@ -34,9 +34,9 @@
op.useStringDatatypes = true
//op.frequencyThreshold = 1
alg.type = "celoe"
-// alg.writeSearchTree = true
+alg.writeSearchTree = true
alg.replaceSearchTree = true
-alg.maxExecutionTimeInSeconds = 10
+alg.maxExecutionTimeInSeconds = 100
alg.maxNrOfResults = 10
Modified: trunk/interfaces/src/main/java/org/dllearner/configuration/spring/CustomPropertyEditorRegistrar.java
===================================================================
--- trunk/interfaces/src/main/java/org/dllearner/configuration/spring/CustomPropertyEditorRegistrar.java 2011-11-02 08:43:43 UTC (rev 3357)
+++ trunk/interfaces/src/main/java/org/dllearner/configuration/spring/CustomPropertyEditorRegistrar.java 2011-11-02 09:08:56 UTC (rev 3358)
@@ -1,5 +1,7 @@
package org.dllearner.configuration.spring;
+import org.dllearner.core.config.ClassExpressionPropertyEditor;
+import org.dllearner.core.owl.Description;
import org.springframework.beans.PropertyEditorRegistrar;
import org.springframework.beans.PropertyEditorRegistry;
@@ -17,6 +19,7 @@
@Override
public void registerCustomEditors(PropertyEditorRegistry registry) {
//Register any custom editors here.
-
+ ClassExpressionPropertyEditor ce = new ClassExpressionPropertyEditor();
+ registry.registerCustomEditor(Description.class, ce);
}
}
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