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From: <seb...@us...> - 2012-02-22 17:57:05
|
Revision: 3582
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3582&view=rev
Author: sebastianwtr
Date: 2012-02-22 17:56:55 +0000 (Wed, 22 Feb 2012)
Log Message:
-----------
[tbsl exploration] start new implementation
Modified Paths:
--------------
trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/exploration/Sparql/SparqlObject.java
Added Paths:
-----------
trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/exploration/Sparql/Hypothesis.java
trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/exploration/Sparql/Template.java
trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/exploration/Sparql/TemplateBuilder.java
trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/exploration/Sparql/testClass_new.java
Added: trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/exploration/Sparql/Hypothesis.java
===================================================================
--- trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/exploration/Sparql/Hypothesis.java (rev 0)
+++ trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/exploration/Sparql/Hypothesis.java 2012-02-22 17:56:55 UTC (rev 3582)
@@ -0,0 +1,31 @@
+package org.dllearner.algorithm.tbsl.exploration.Sparql;
+
+public class Hypothesis {
+private String variable;
+private String uri;
+private float rank;
+public String getUri() {
+ return uri;
+}
+public void setUri(String uri) {
+ this.uri = uri;
+}
+public String getVariable() {
+ return variable;
+}
+public void setVariable(String variable) {
+ this.variable = variable;
+}
+public float getRank() {
+ return rank;
+}
+public void setRank(float rank) {
+ this.rank = rank;
+}
+
+public Hypothesis(String variable, String uri, float rank){
+ setRank(rank);
+ setVariable(variable);
+ setUri(uri);
+}
+}
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 2012-02-14 15:44:21 UTC (rev 3581)
+++ trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/exploration/Sparql/SparqlObject.java 2012-02-22 17:56:55 UTC (rev 3582)
@@ -2204,16 +2204,7 @@
}
private String createAnswer(String string){
-
- /*Pattern p = Pattern.compile (".*<td>(.*)</td>.*");
- Matcher m = p.matcher (string);
- String result="";
- while (m.find()) {
- if(m.group(1)!=null)
- result = result+" "+ m.group(1);
- }
- */
Pattern p = Pattern.compile (".*\\<td\\>(.*)\\</td\\>.*");
string = string.replace("<table class=\"sparql\" border=\"1\">", "").replace("<tr>","").replace("</tr>", "").replace("</table>", "");
Matcher m = p.matcher (string);
@@ -2235,18 +2226,7 @@
}
private ArrayList<String> createAnswerArray(String string){
- //<td>Klaus Wowereit</td>
-
- //get with regex all between <td> </td>
-
- /*Pattern p = Pattern.compile (".*<td>(.*)</td>.*");
- Matcher m = p.matcher (string);
- ArrayList<String> result=new ArrayList<String>();
- while (m.find()) {
- if(m.group(1)!=null)
- result.add(m.group(1));
- }*/
Pattern p = Pattern.compile (".*\\<td\\>(.*)\\</td\\>.*");
string = string.replace("<table class=\"sparql\" border=\"1\">", "").replace("<tr>","").replace("</tr>", "").replace("</table>", "");
Matcher m = p.matcher (string);
@@ -2309,14 +2289,8 @@
return query;
}
-
-
-
-
}
-
-
/*
* Backup original Iteration function
*
Added: trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/exploration/Sparql/Template.java
===================================================================
--- trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/exploration/Sparql/Template.java (rev 0)
+++ trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/exploration/Sparql/Template.java 2012-02-22 17:56:55 UTC (rev 3582)
@@ -0,0 +1,87 @@
+package org.dllearner.algorithm.tbsl.exploration.Sparql;
+
+import java.util.ArrayList;
+
+public class Template {
+
+ private ArrayList<ArrayList<String>> condition = new ArrayList<ArrayList<String>>();
+ private ArrayList<ArrayList<Hypothesis>> hypotesen = new ArrayList<ArrayList<Hypothesis>>();
+ private String selectTerm;
+ private String having;
+ private String filter;
+ private String OrderBy;
+ private String limit;
+
+ public String getHaving() {
+ return having;
+ }
+ public void setHaving(String having) {
+ this.having = having;
+ }
+ public String getFilter() {
+ return filter;
+ }
+ public void setFilter(String filter) {
+ this.filter = filter;
+ }
+ public String getOrderBy() {
+ return OrderBy;
+ }
+ public void setOrderBy(String orderBy) {
+ OrderBy = orderBy;
+ }
+ public String getLimit() {
+ return limit;
+ }
+ public void setLimit(String limit) {
+ this.limit = limit;
+ }
+
+ public String getSelectTerm() {
+ return selectTerm;
+ }
+ public void setSelectTerm(String selectTerm) {
+ this.selectTerm = selectTerm;
+ }
+
+
+ public Template(ArrayList<ArrayList<String>>condition_new, String having_new, String filter_new, String SelectTerm_new, String OrderBy_new, String limit_new){
+ setCondition(condition_new);
+ setHaving(having_new);
+ setFilter(filter_new);
+ setOrderBy(OrderBy_new);
+ setLimit(limit_new);
+ setSelectTerm(SelectTerm_new);
+ }
+ public ArrayList<ArrayList<String>> getCondition() {
+ return condition;
+ }
+ public void setCondition(ArrayList<ArrayList<String>> condition) {
+ this.condition = condition;
+ }
+ public ArrayList<ArrayList<Hypothesis>> getHypotesen() {
+ return hypotesen;
+ }
+ public void setHypotesen(ArrayList<ArrayList<Hypothesis>> hypotesen) {
+ this.hypotesen = hypotesen;
+ }
+
+ public void addHypothese(ArrayList<Hypothesis> ht){
+ this.hypotesen.add(ht);
+ }
+
+
+ public void printAll(){
+ System.out.println("###### Template ######");
+ System.out.println("condition: "+condition);
+ System.out.println("hypotesen: "+hypotesen);
+ System.out.println("selectTerm: "+selectTerm);
+ System.out.println("having: "+having);
+ System.out.println("filter: "+filter);
+ System.out.println("OrderBy: "+OrderBy);
+ System.out.println("limit: "+limit);
+ System.out.println("###### Template printed ######\n");
+ }
+
+}
+
Added: trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/exploration/Sparql/TemplateBuilder.java
===================================================================
--- trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/exploration/Sparql/TemplateBuilder.java (rev 0)
+++ trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/exploration/Sparql/TemplateBuilder.java 2012-02-22 17:56:55 UTC (rev 3582)
@@ -0,0 +1,121 @@
+package org.dllearner.algorithm.tbsl.exploration.Sparql;
+
+import java.net.MalformedURLException;
+import java.sql.SQLException;
+import java.util.ArrayList;
+import java.util.Set;
+
+import org.dllearner.algorithm.tbsl.sparql.BasicQueryTemplate;
+import org.dllearner.algorithm.tbsl.sparql.Path;
+import org.dllearner.algorithm.tbsl.sparql.SPARQL_Filter;
+import org.dllearner.algorithm.tbsl.sparql.SPARQL_Having;
+import org.dllearner.algorithm.tbsl.sparql.SPARQL_Term;
+import org.dllearner.algorithm.tbsl.templator.BasicTemplator;
+
+public class TemplateBuilder {
+
+ static BasicTemplator btemplator;
+
+
+public TemplateBuilder() throws MalformedURLException, ClassNotFoundException, SQLException{
+
+ TemplateBuilder.btemplator = new BasicTemplator();
+ //btemplator.UNTAGGED_INPUT = false;
+ //Object_new.myindex = new mySQLDictionary();
+ }
+
+
+ public ArrayList<Template> createTemplates(String question){
+ ArrayList<Template> resultArrayList = new ArrayList<Template>();
+ Set<BasicQueryTemplate> querytemps = btemplator.buildBasicQueries(question);
+ for (BasicQueryTemplate bqt : querytemps) {
+ ArrayList<ArrayList<String>> condition = new ArrayList<ArrayList<String>>();
+ ArrayList<ArrayList<Hypothesis>> hypotesen = new ArrayList<ArrayList<Hypothesis>>();
+ String selectTerm = "";
+ String having= "";
+ String filter= "";
+ String OrderBy= "";
+ String limit= "";
+ String condition_String = "";
+
+ boolean addTemplate=true;
+ try{
+ for(SPARQL_Term terms :bqt.getSelTerms()) selectTerm=selectTerm+(terms.toString())+" ";
+ }
+ catch (Exception e){
+ selectTerm="";
+ addTemplate=false;
+ }
+
+ ArrayList<String> temp_array = new ArrayList<String>();
+ try{
+ for(Path conditions1: bqt.getConditions()) condition_String=condition_String+(conditions1.toString())+".";
+ for(Path conditions1: bqt.getConditions()) {
+ temp_array.clear();
+ String[] tmp_array = conditions1.toString().split(" -- ");
+ for(String s: tmp_array){
+ temp_array.add(s);
+ }
+ condition.add(temp_array);
+ }
+
+ }
+ catch (Exception e){
+ condition_String="";
+ addTemplate=false;
+ }
+
+ try{
+ for(SPARQL_Filter tmp : bqt.getFilters()) filter=filter+tmp+" ";
+ }
+ catch(Exception e){
+ filter="";
+ addTemplate=false;
+ }
+ try{
+ for(SPARQL_Having tmp : bqt.getHavings()) having=having+tmp+" ";
+ }
+ catch(Exception e){
+ having="";
+ addTemplate=false;
+ }
+
+ //if there is no order by, replace with ""
+ OrderBy="ORDER BY ";
+ try{
+ for(SPARQL_Term tmp : bqt.getOrderBy()) {
+ System.out.println("Yeah");
+ OrderBy=OrderBy+tmp+" ";
+ }
+ if((bqt.getOrderBy()).size()==0)OrderBy="";
+ }
+ catch(Exception e){
+ OrderBy="";
+ addTemplate=false;
+ }
+
+
+ try{
+ limit="LIMIT "+bqt.getLimit();
+
+ if(bqt.getLimit()==0)limit="";
+ }
+ catch(Exception e){
+ limit="";
+ addTemplate=false;
+ }
+
+ Template template = new Template(condition, having, filter, selectTerm,OrderBy, limit);
+
+ //TODO: Add Hypothesis
+ //TODO: Take Template like it is and change Condition
+
+
+ resultArrayList.add(template);
+ }
+ for(Template temp : resultArrayList){
+ temp.printAll();
+ }
+ return resultArrayList;
+ }
+}
Added: trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/exploration/Sparql/testClass_new.java
===================================================================
--- trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/exploration/Sparql/testClass_new.java (rev 0)
+++ trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/exploration/Sparql/testClass_new.java 2012-02-22 17:56:55 UTC (rev 3582)
@@ -0,0 +1,21 @@
+package org.dllearner.algorithm.tbsl.exploration.Sparql;
+
+import java.net.MalformedURLException;
+import java.sql.SQLException;
+
+public class testClass_new {
+
+ /**
+ * @param args
+ * @throws SQLException
+ * @throws ClassNotFoundException
+ * @throws MalformedURLException
+ */
+ public static void main(String[] args) throws MalformedURLException, ClassNotFoundException, SQLException {
+ // TODO Auto-generated method stub
+ TemplateBuilder testobject = new TemplateBuilder();
+ String question = "Which books are written by Daniele Steel?";
+ testobject.createTemplates(question);
+ }
+
+}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lor...@us...> - 2012-02-14 15:44:32
|
Revision: 3581
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3581&view=rev
Author: lorenz_b
Date: 2012-02-14 15:44:21 +0000 (Tue, 14 Feb 2012)
Log Message:
-----------
Somes updates needed because of new SOLR BOA index.
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 2012-02-14 10:14:06 UTC (rev 3580)
+++ trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/learning/SPARQLTemplateBasedLearner.java 2012-02-14 15:44:21 UTC (rev 3581)
@@ -16,6 +16,7 @@
import java.util.Map.Entry;
import java.util.Set;
import java.util.SortedSet;
+import java.util.TreeMap;
import java.util.TreeSet;
import org.apache.log4j.Logger;
@@ -193,7 +194,7 @@
String boaPatternIndexUrl = options.fetch("solr.boa.properties.url");
String boaPatternIndexSearchField = options.fetch("solr.boa.properties.searchfield");
- SolrSearch patternBasedPropertyIndex = new SolrSearch(boaPatternIndexUrl, boaPatternIndexSearchField, "nlr");
+ SolrSearch patternBasedPropertyIndex = new SolrSearch(boaPatternIndexUrl, boaPatternIndexSearchField, "nlr-no-var");
//first BOA pattern then label based
// property_index = new HierarchicalSolrSearch(patternBasedPropertyIndex, labelBasedPropertyIndex);
@@ -641,18 +642,37 @@
}
private Set<WeightedQuery> getWeightedSPARQLQueries(Set<Template> templates){
+ logger.info("Generating SPARQL query candidates...");
+ Map<Slot, Set<Allocation>> slot2Allocations2 = new TreeMap<Slot, Set<Allocation>>(new Comparator<Slot>() {
+
+ @Override
+ public int compare(Slot o1, Slot o2) {
+ if(o1.getSlotType() == o2.getSlotType()){
+ return o1.getToken().compareTo(o2.getToken());
+ } else {
+ return -1;
+ }
+ }
+ });
+
+
Map<Slot, Set<Allocation>> slot2Allocations = new HashMap<Slot, Set<Allocation>>();
Set<WeightedQuery> allQueries = new TreeSet<WeightedQuery>();
Set<Allocation> allocations;
+
for(Template t : templates){
+ logger.info("Processing template:\n" + t.toString());
allocations = new TreeSet<Allocation>();
for(Slot slot : t.getSlots()){
- allocations = computeAllocations(slot, 50);
-
+ allocations = slot2Allocations2.get(slot);
+ if(allocations == null){
+ allocations = computeAllocations(slot, 20);
+ slot2Allocations2.put(slot, allocations);
+ }
slot2Allocations.put(slot, allocations);
//for tests add the property URI with http://dbpedia.org/property/ namespace
@@ -702,14 +722,14 @@
queries.addAll(tmp);
tmp.clear();
}
-
+
for(Slot slot : sortedSlots){
- if(!slot2Allocations.get(slot).isEmpty()){System.out.println(slot2Allocations.get(slot));
+ if(!slot2Allocations.get(slot).isEmpty()){
for(Allocation a : slot2Allocations.get(slot)){
for(WeightedQuery query : queries){
Query q = new Query(query.getQuery());
- boolean drop = false;
+ 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();
@@ -779,7 +799,7 @@
}
}
}
- }
+ }*/
if(!drop){
@@ -811,6 +831,7 @@
}
template2Queries.put(t, qList);
}
+ logger.info("...done in ");
return allQueries;
}
@@ -859,7 +880,6 @@
// }
// }
- 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
@@ -885,9 +905,11 @@
}
private Set<Allocation> computeAllocations(Slot slot, int limit){
+ logger.info("Computing allocations for " + slot);
SortedSet<Allocation> allocations = computeAllocations(slot);
if(allocations.isEmpty()){
+ logger.info("...done.");
return allocations;
}
@@ -906,7 +928,7 @@
}
}
});
-
+ logger.info("...done.");
return new TreeSet<Allocation>(l.subList(0, Math.min(limit, allocations.size())));
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lor...@us...> - 2012-02-14 10:14:17
|
Revision: 3580
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3580&view=rev
Author: lorenz_b
Date: 2012-02-14 10:14:06 +0000 (Tue, 14 Feb 2012)
Log Message:
-----------
Updated SOLR URI.
Modified Paths:
--------------
trunk/components-ext/src/main/resources/tbsl/tbsl.properties
Modified: trunk/components-ext/src/main/resources/tbsl/tbsl.properties
===================================================================
--- trunk/components-ext/src/main/resources/tbsl/tbsl.properties 2012-02-09 16:15:27 UTC (rev 3579)
+++ trunk/components-ext/src/main/resources/tbsl/tbsl.properties 2012-02-14 10:14:06 UTC (rev 3580)
@@ -1,4 +1,4 @@
-solr.server.url = http://139.18.2.173:8080/apache-solr-3.3.0
+solr.server.url = http://139.18.2.173:8080/solr
solr.classes.url = ${solr.server.url}/dbpedia_classes
solr.classes.searchfield = label
solr.yago.classes.url = ${solr.server.url}/yago_classes
@@ -8,7 +8,7 @@
solr.properties.url = ${solr.server.url}/dbpedia_properties
solr.properties.searchfield = label
solr.boa.properties.url = ${solr.server.url}/boa_pattern
-solr.boa.properties.searchfield = nlr
+solr.boa.properties.searchfield = nlr-no-var
solr.query.limit = 20
sparql.endpoint.url = http://live.dbpedia.org/sparql
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <seb...@us...> - 2012-02-09 16:15:38
|
Revision: 3579
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3579&view=rev
Author: sebastianwtr
Date: 2012-02-09 16:15:27 +0000 (Thu, 09 Feb 2012)
Log Message:
-----------
[tbsl-exploration] some minor changes
Modified Paths:
--------------
trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/exploration/Sparql/GetRessourcePropertys.java
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/queryInformation.java
trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/exploration/exploration_main/exploration_main.java
Modified: trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/exploration/Sparql/GetRessourcePropertys.java
===================================================================
--- trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/exploration/Sparql/GetRessourcePropertys.java 2012-02-08 13:48:02 UTC (rev 3578)
+++ trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/exploration/Sparql/GetRessourcePropertys.java 2012-02-09 16:15:27 UTC (rev 3579)
@@ -20,7 +20,8 @@
//String Prefix="http://greententacle.techfak.uni-bielefeld.de:5171/sparql";
String Prefix="http://dbpedia.org/sparql";
- //String Prefix="http://purpurtentacle.techfak.uni-bielefeld.de:8892/sparql";
+ //String Prefix="http://purpurtentacle.techfak.uni-bielefeld.de:8890/sparql";
+ //String Prefix="http://greententacle.techfak.uni-bielefeld.de:5171/sparql";
public HashMap<String,String> getPropertys(String element, String side, int timeToTimeoutOnServer) throws IOException{
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 2012-02-08 13:48:02 UTC (rev 3578)
+++ trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/exploration/Sparql/SparqlObject.java 2012-02-09 16:15:27 UTC (rev 3579)
@@ -58,7 +58,7 @@
static int explorationdepthwordnet=2;
static int iterationdepth =0;
static int numberofanswers=1;
- static double LevenstheinMin = 0.9;
+ static double LevenstheinMin = 0.8;
static WordNet wordnet;
BasicTemplator btemplator;
Templator templator;
@@ -71,7 +71,8 @@
//change here and in getRessourcePropertys
//String Prefix="http://greententacle.techfak.uni-bielefeld.de:5171/sparql";
String Prefix="http://dbpedia.org/sparql";
- //String Prefix="http://purpurtentacle.techfak.uni-bielefeld.de:8892/sparql";
+ //String Prefix="http://greententacle.techfak.uni-bielefeld.de:5171/sparql";
+ //String Prefix="http://purpurtentacle.techfak.uni-bielefeld.de:8890/sparql";
//Konstruktor
@@ -650,11 +651,20 @@
// TODO Auto-generated catch block
e.printStackTrace();
}*/
+ System.out.println(property_to_compare_with + " : "+property_to_compare_with_uri +" : "+uri_isA_Resource);
if(fall.contains("WORDNET")) new_queries=doWordnet(query,property_to_compare_with,property_to_compare_with_uri,list_of_properties);
if(fall.contains("LEVENSTHEIN")) new_queries=doLevensthein(query,property_to_compare_with_uri,property_to_compare_with_uri,list_of_properties);
-
+ /* BufferedReader in1 = new BufferedReader(new InputStreamReader(System.in));
+ String line;
+
+ try {
+ line = in1.readLine();
+ } catch (IOException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }*/
return new_queries;
}
@@ -703,6 +713,9 @@
//System.out.println("URI from Resource "+ resource +": "+getUriFromIndex(resource.toLowerCase(),0));
System.out.println("URI from Resource "+ resource +": "+queryObject.getHashValue(resource.toLowerCase()));
+ HashMap<String, String> bla = queryObject.getHashMap();
+ System.out.println("INhalt Hasmap QueryObject:");
+ for (String z: bla.keySet()) System.out.println(z);
//gets Propertys left or right from the resource!
try {
@@ -756,7 +769,7 @@
double nld=Levenshtein.nld(property_to_compare_with.toLowerCase(), key);
//check if nld is greater than Levensthein
- if(nld>=LevenstheinMin){
+ if(nld>=LevenstheinMin||key.contains(lemmatiser.stem(property_to_compare_with))||property_to_compare_with.contains(lemmatiser.stem(key))){
//if its so, replace old uri with the new one
String querynew=query;
//String replacement = getUriFromIndex(property_to_compare_with.toLowerCase(),1);
@@ -913,19 +926,31 @@
ArrayList<String> semantics=new ArrayList<String>();
ArrayList<String> tmp_semantics=new ArrayList<String>();
ArrayList<String> result_SemanticsMatchProperties=new ArrayList<String>();
- semantics.add(property);
+ if(property.contains("_")){
+ String[] fix = property.split("_");
+ //here add also lemmatiser
+ for(String s: fix) semantics.add(s);
+ }
+ else semantics.add(property);
System.out.println("Semantics: "+ semantics);
- //first check, if there is a singular form in the wordnet dictionary.. eg children -> child
- String _temp_=myindex.getWordnetHelp(property);
- if(_temp_==null){
- tmp_semantics=semantics;
+ for(String s: semantics){
+ //first check, if there is a singular form in the wordnet dictionary.. eg children -> child
+ //String _temp_=myindex.getWordnetHelp(property);
+ String _temp_=myindex.getWordnetHelp(s);
+ if(_temp_!=null){
+ //tmp_semantics=semantics;
+ tmp_semantics.add(_temp_);
+ tmp_semantics.add(s);
+ }
+ else tmp_semantics.add(s);
+ /*
+ else{
+ semantics.clear();
+ semantics.add(_temp_);
+ tmp_semantics=semantics;
+ }*/
}
- else{
- semantics.clear();
- semantics.add(_temp_);
- tmp_semantics=semantics;
- }
System.out.println("tmp_semantics: "+ tmp_semantics);
Boolean goOnAfterWordnet = true;
@@ -965,11 +990,12 @@
key=key.replace("@en","");
for(String b : semantics){
- if(key.contains(b.toLowerCase())){
+ if(key.contains(b.toLowerCase())||key.contains(lemmatiser.stem(b.toLowerCase()))||b.toLowerCase().contains(lemmatiser.stem(key))){
if(!result_SemanticsMatchProperties.contains(key)){
result_SemanticsMatchProperties.add(key);
String query_tmp=query;
//String replacement = getUriFromIndex(property_to_compare_with.toLowerCase(),1);
+ System.out.println("URI of property: "+uri_of_property);
String replacement = uri_of_property;
if(!query_tmp.contains(replacement)){
replacement=replacement.replace("ontology", "property");
@@ -1765,6 +1791,21 @@
}
else{
result="NONE";
+ String tmp11=originalString;
+ String hotfix ="http://dbpedia.org/resource/"+tmp11;
+ if(tmp11.contains("_")){
+ String[] newarraytmp=tmp11.split("_");
+ String tmpneu="";
+ for(String s :newarraytmp){
+ tmpneu+= "_"+ Character.toUpperCase(s.charAt(0)) + s.substring(1);
+ }
+ tmpneu=tmpneu.replaceFirst("_", "");
+ hotfix ="http://dbpedia.org/resource/"+tmpneu;
+ hotfix=hotfix.replace("/__", "/");
+ System.out.println("Hotfix: "+hotfix);
+ }
+ result=hotfix;
+
}
}
catch(Exception e){
Modified: trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/exploration/Sparql/queryInformation.java
===================================================================
--- trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/exploration/Sparql/queryInformation.java 2012-02-08 13:48:02 UTC (rev 3578)
+++ trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/exploration/Sparql/queryInformation.java 2012-02-09 16:15:27 UTC (rev 3579)
@@ -39,6 +39,8 @@
public String getHashValue(String key) {
key=key.toLowerCase();
+ key=key.replace(" ", "");
+ key=key.replace("_", " ");
String result ="NONE";
try{
result=this.hashMap.get(key);
@@ -51,6 +53,9 @@
}
public void setHashValue(String key, String value) {
+ key=key.replace(" ", "");
+ key=key.replace("_", " ");
+ value=value.replace("__", "");
this.hashMap.put(key.toLowerCase(), value);
}
Modified: trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/exploration/exploration_main/exploration_main.java
===================================================================
--- trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/exploration/exploration_main/exploration_main.java 2012-02-08 13:48:02 UTC (rev 3578)
+++ trunk/components-ext/src/main/java/org/dllearner/algorithm/tbsl/exploration/exploration_main/exploration_main.java 2012-02-09 16:15:27 UTC (rev 3579)
@@ -165,17 +165,17 @@
//queryInformation tmpquery;
//only question, which are not yago files
if(s.isYago()==true)yago_querys=yago_querys+1;
- if(s.isYago()==false){
+ //if(s.isYago()==false){
queryInformation tmpquery=sparql.create_Sparql_query(s);
if(!tmpquery.getResult().isEmpty()) {
list_of_resultstructs.add(sparql.create_Sparql_query(s));
anzahl_query_with_answers=anzahl_query_with_answers+1;
}
- }
+ //}
}
- /*
- //Print to Console
+
+ /* //Print to Console
System.out.println("\n#############\n Result:");
for(queryInformation s : list_of_resultstructs){
System.out.println(s.getResult());
@@ -221,9 +221,15 @@
queryInformation result = new queryInformation(line,"0","",false,false,false,"non",false);
result= sparql.create_Sparql_query(newQuery);
ArrayList<String> ergebnis = result.getResult();
+ //get eacht result only once!
+ Set<String> setString = new HashSet<String>();
for(String i: ergebnis){
- System.out.println(i);
+ setString.add(i);
+ //System.out.println(i);
}
+ for(String z: setString){
+ System.out.println(z);
+ }
long endTime= System.currentTimeMillis();
System.out.println("\n The complete answering of the Question took "+(endTime-startTime)+" ms");
}
@@ -311,7 +317,13 @@
xmlDocument="<?xml version=\"1.0\" ?><dataset id=\""+s.getXMLtype()+"\">";
}
tmp="<question id=\""+s.getId()+"\"><string>"+s.getQuery()+"</string>\n<answers>";
- for(String i : s.getResult()){
+
+ //to get all answers only once!
+ Set<String> setString = new HashSet<String>();
+ for(String z: s.getResult()){
+ setString.add(z);
+ }
+ for(String i : setString){
String input="";
if(i.contains("http")) input="<uri>"+i+"</uri>\n";
else if (i.contains("true")||i.contains("false")) input="<boolean>"+i+"</boolean>\n";
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|
|
From: <lor...@us...> - 2012-02-08 13:48:13
|
Revision: 3578
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3578&view=rev
Author: lorenz_b
Date: 2012-02-08 13:48:02 +0000 (Wed, 08 Feb 2012)
Log Message:
-----------
Fixed bug.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/utilities/JustificationBasedCoherentOntologyExtractor.java
Modified: trunk/components-core/src/main/java/org/dllearner/utilities/JustificationBasedCoherentOntologyExtractor.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/utilities/JustificationBasedCoherentOntologyExtractor.java 2012-02-08 13:23:08 UTC (rev 3577)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/JustificationBasedCoherentOntologyExtractor.java 2012-02-08 13:48:02 UTC (rev 3578)
@@ -115,7 +115,9 @@
this.ontology = ontology;
this.incoherentOntology = getOntologyWithoutAnnotations(ontology);
- File diffFile = new File(new File(ontology.getOWLOntologyManager().getOntologyDocumentIRI(ontology).toURI()).getParent() + "/" + DIFF_ONTOLOGY_NAME);
+ new File("log").mkdir();
+
+ File diffFile = new File("log/" + DIFF_ONTOLOGY_NAME);
try {
if(diffFile.exists()){
diffOntology = manager.loadOntologyFromOntologyDocument(diffFile);
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|
|
From: <lor...@us...> - 2012-02-08 13:23:18
|
Revision: 3577
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3577&view=rev
Author: lorenz_b
Date: 2012-02-08 13:23:08 +0000 (Wed, 08 Feb 2012)
Log Message:
-----------
Reading ontologies from BZIP2.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/utilities/JustificationBasedCoherentOntologyExtractor.java
Modified: trunk/components-core/src/main/java/org/dllearner/utilities/JustificationBasedCoherentOntologyExtractor.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/utilities/JustificationBasedCoherentOntologyExtractor.java 2012-02-08 11:49:16 UTC (rev 3576)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/JustificationBasedCoherentOntologyExtractor.java 2012-02-08 13:23:08 UTC (rev 3577)
@@ -1,7 +1,9 @@
package org.dllearner.utilities;
+import java.io.BufferedInputStream;
import java.io.BufferedOutputStream;
import java.io.File;
+import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
@@ -682,8 +684,11 @@
boolean computeParallel = Boolean.valueOf(args[3]);
System.out.println("Loading ontology...");
- File file = new File(filename);
- OWLOntology schema = man.loadOntologyFromOntologyDocument(file);
+ InputStream is = new BufferedInputStream(new FileInputStream(filename));
+ if(args[0].endsWith("bz2")){
+ is = new CompressorStreamFactory().createCompressorInputStream("bzip2", is);
+ }
+ OWLOntology schema = man.loadOntologyFromOntologyDocument(is);
man.removeAxioms(schema, schema.getAxioms(AxiomType.TRANSITIVE_OBJECT_PROPERTY));
// OWLOntology cleaned = man.createOntology(IRI.create("http://dbpedia_cleaned.owl"));
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|
|
From: <lor...@us...> - 2012-02-08 11:49:26
|
Revision: 3576
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3576&view=rev
Author: lorenz_b
Date: 2012-02-08 11:49:16 +0000 (Wed, 08 Feb 2012)
Log Message:
-----------
Remove only axioms not contained in the original DBpedia ontology.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/utilities/JustificationBasedCoherentOntologyExtractor.java
Modified: trunk/components-core/src/main/java/org/dllearner/utilities/JustificationBasedCoherentOntologyExtractor.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/utilities/JustificationBasedCoherentOntologyExtractor.java 2012-02-07 21:43:20 UTC (rev 3575)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/JustificationBasedCoherentOntologyExtractor.java 2012-02-08 11:49:16 UTC (rev 3576)
@@ -4,6 +4,10 @@
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.net.MalformedURLException;
+import java.net.URL;
import java.security.MessageDigest;
import java.security.NoSuchAlgorithmException;
import java.util.Collections;
@@ -20,6 +24,8 @@
import openlink.util.MD5;
+import org.apache.commons.compress.compressors.CompressorException;
+import org.apache.commons.compress.compressors.CompressorStreamFactory;
import org.mindswap.pellet.RBox;
import org.semanticweb.HermiT.Configuration;
import org.semanticweb.HermiT.Reasoner;
@@ -39,6 +45,7 @@
import org.semanticweb.owlapi.model.OWLOntologyStorageException;
import org.semanticweb.owlapi.model.OWLTransitiveObjectPropertyAxiom;
import org.semanticweb.owlapi.model.RemoveAxiom;
+import org.semanticweb.owlapi.owllink.builtin.requests.LoadOntologies;
import org.semanticweb.owlapi.reasoner.IllegalConfigurationException;
import org.semanticweb.owlapi.reasoner.OWLReasoner;
import org.semanticweb.owlapi.reasoner.OWLReasonerConfiguration;
@@ -83,12 +90,15 @@
//whether to debug classes and properties in parallel
private boolean computeParallel = false;
+ private OWLOntology dbpediaOntology;
+
public JustificationBasedCoherentOntologyExtractor() {
try {
md5 = MessageDigest.getInstance("MD5");
} catch (NoSuchAlgorithmException e) {
e.printStackTrace();
}
+ dbpediaOntology = loadDBpediaOntology();
}
static {PelletExplanation.setup();}
@@ -185,19 +195,14 @@
}
logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
- while(!unsatClasses.isEmpty()){
- //get frequency for each axiom
- Map<OWLAxiom, Integer> axiom2CountMap = getAxiomFrequency(entity2Explanations);
+ if(computeParallel){
+ cnt += unsatPropCnt;
+ }
+
+ while(cnt >= 0){
+ //we remove the most appropriate axiom from the ontology
+ removeAppropriateAxiom();
- //get a sorted list of entries with the highest axiom count first
- List<Entry<OWLAxiom, Integer>> sortedEntries = MapUtils.sortByValues(axiom2CountMap);
- for(Entry<OWLAxiom, Integer> entry : sortedEntries){
-// System.out.println(entry.getKey() + ":" + entry.getValue());
- }
- //we remove the most frequent axiom from the ontology
- OWLAxiom toRemove = sortedEntries.get(0).getKey();
- removeAxiom(toRemove);
-
//recompute the unsatisfiable classes
logger.info("Reclassifying...");
startTime = System.currentTimeMillis();
@@ -229,6 +234,9 @@
save("log/dbpedia_" + cnt + "cls" + unsatPropCnt + "prop.owl");
cnt = rootCnt + derivedCnt;
unsatPropCnt = unsatObjectProperties.size();
+ if(computeParallel){
+ cnt += unsatPropCnt;
+ }
}
//recompute explanations if necessary
@@ -251,15 +259,9 @@
entity2ModuleMap.putAll(extractModules(unsatObjectProperties));
while(!unsatObjectProperties.isEmpty()){
- //get frequency for each axiom
- Map<OWLAxiom, Integer> axiom2CountMap = getAxiomFrequency(entity2Explanations);
+ //we remove the most appropriate axiom from the ontology
+ removeAppropriateAxiom();
- //get a sorted list of entries with the highest axiom count first
- List<Entry<OWLAxiom, Integer>> sortedEntries = MapUtils.sortByValues(axiom2CountMap);
- //we remove the most frequent axiom from the ontology
- OWLAxiom toRemove = sortedEntries.get(0).getKey();
- removeAxiom(toRemove);
-
//recompute the unsatisfiable classes
logger.info("Reclassifying...");
startTime = System.currentTimeMillis();
@@ -324,18 +326,9 @@
logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
while(!unsatClasses.isEmpty()){
- //get frequency for each axiom
- Map<OWLAxiom, Integer> axiom2CountMap = getAxiomFrequency(entity2Explanations);
+ //we remove the most appropriate axiom from the ontology
+ removeAppropriateAxiom();
- //get a sorted list of entries with the highest axiom count first
- List<Entry<OWLAxiom, Integer>> sortedEntries = MapUtils.sortByValues(axiom2CountMap);
- for(Entry<OWLAxiom, Integer> entry : sortedEntries){
-// System.out.println(entry.getKey() + ":" + entry.getValue());
- }
- //we remove the most frequent axiom from the ontology
- OWLAxiom toRemove = sortedEntries.get(0).getKey();
- removeAxiom(toRemove);
-
//recompute the unsatisfiable classes
logger.info("Reclassifying...");
startTime = System.currentTimeMillis();
@@ -375,13 +368,24 @@
return getOntologyWithAnnotations(incoherentOntology);
}
- private void removeAxiom(OWLAxiom axiom){
- logger.info("Removing axiom " + axiom + ".");
- manager.removeAxiom(incoherentOntology, axiom);
- manager.addAxiom(diffOntology, axiom);
- manager.applyChange(new RemoveAxiom(incoherentOntology, axiom));
- removeFromExplanations(entity2Explanations, axiom);
- removeFromModules(axiom);
+ private void removeAppropriateAxiom(){
+ //get frequency for each axiom
+ Map<OWLAxiom, Integer> axiom2CountMap = getAxiomFrequency(entity2Explanations);
+ //get a sorted list of entries with the highest axiom count first
+ List<Entry<OWLAxiom, Integer>> sortedEntries = MapUtils.sortByValues(axiom2CountMap);
+ //we remove the most frequent axiom from the ontology which is not contained in the original DBpedia ontology
+ for(Entry<OWLAxiom, Integer> e : sortedEntries){
+ OWLAxiom axiom = e.getKey();
+ if(!dbpediaOntology.containsAxiomIgnoreAnnotations(axiom)){
+ logger.info("Removing axiom " + axiom + ".");
+ manager.removeAxiom(incoherentOntology, axiom);
+ manager.addAxiom(diffOntology, axiom);
+ manager.applyChange(new RemoveAxiom(incoherentOntology, axiom));
+ removeFromExplanations(entity2Explanations, axiom);
+ removeFromModules(axiom);
+ return;
+ }
+ }
}
private void save(String fileName){
@@ -603,6 +607,28 @@
return module;
}
+ private OWLOntology loadDBpediaOntology() {
+ long startTime = System.currentTimeMillis();
+ logger.info("Loading DBpedia reference ontology...");
+ OWLOntology ontology = null;
+ try {
+ URL dbpediaURL = new URL("http://downloads.dbpedia.org/3.7/dbpedia_3.7.owl.bz2");
+ InputStream is = dbpediaURL.openStream();
+ is = new CompressorStreamFactory().createCompressorInputStream("bzip2", is);
+ ontology = OWLManager.createOWLOntologyManager().loadOntologyFromOntologyDocument(is);
+ } catch (MalformedURLException e) {
+ e.printStackTrace();
+ } catch (OWLOntologyCreationException e) {
+ e.printStackTrace();
+ } catch (IOException e) {
+ e.printStackTrace();
+ } catch (CompressorException e) {
+ e.printStackTrace();
+ }
+ logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
+ return ontology;
+ }
+
// private Map<OWLClass, OWLOntology> extractModules(Set<OWLClass> classes){
// Map<OWLClass, OWLOntology> cls2ModuleMap = new HashMap<OWLClass, OWLOntology>();
// for(OWLClass cls : classes){
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|
|
From: <lor...@us...> - 2012-02-07 21:43:27
|
Revision: 3575
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3575&view=rev
Author: lorenz_b
Date: 2012-02-07 21:43:20 +0000 (Tue, 07 Feb 2012)
Log Message:
-----------
Added method to check if axiom is already entailed by DBpedia ontology.
Modified Paths:
--------------
trunk/scripts/src/main/java/org/dllearner/scripts/SPARQLSampleDebugging.java
Modified: trunk/scripts/src/main/java/org/dllearner/scripts/SPARQLSampleDebugging.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/SPARQLSampleDebugging.java 2012-02-07 09:53:33 UTC (rev 3574)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/SPARQLSampleDebugging.java 2012-02-07 21:43:20 UTC (rev 3575)
@@ -12,6 +12,7 @@
import java.io.PrintWriter;
import java.io.StringReader;
import java.io.UnsupportedEncodingException;
+import java.net.MalformedURLException;
import java.net.URL;
import java.sql.Connection;
import java.sql.DriverManager;
@@ -30,6 +31,7 @@
import java.util.TreeSet;
import java.util.prefs.Preferences;
+import org.apache.commons.compress.compressors.CompressorException;
import org.apache.commons.compress.compressors.CompressorStreamFactory;
import org.apache.log4j.ConsoleAppender;
import org.apache.log4j.FileAppender;
@@ -65,7 +67,13 @@
import org.semanticweb.owlapi.model.OWLOntologyCreationException;
import org.semanticweb.owlapi.model.OWLOntologyManager;
import org.semanticweb.owlapi.model.OWLOntologyStorageException;
+import org.semanticweb.owlapi.reasoner.ClassExpressionNotInProfileException;
+import org.semanticweb.owlapi.reasoner.FreshEntitiesException;
+import org.semanticweb.owlapi.reasoner.InconsistentOntologyException;
import org.semanticweb.owlapi.reasoner.InferenceType;
+import org.semanticweb.owlapi.reasoner.OWLReasoner;
+import org.semanticweb.owlapi.reasoner.ReasonerInterruptedException;
+import org.semanticweb.owlapi.reasoner.TimeOutException;
import uk.ac.manchester.cs.owl.owlapi.OWLDataFactoryImpl;
@@ -109,11 +117,18 @@
private OWLDataFactory factory = new OWLDataFactoryImpl();
+ private OWLOntology dbpediaOntology;
+ private OWLReasoner dbpediaReasoner;
+ private OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
+
static {PelletExplanation.setup();}
public SPARQLSampleDebugging(SparqlEndpoint endpoint) {
this.endpoint = endpoint;
initDBConnection();
+ dbpediaOntology = loadDBpediaOntology();
+ dbpediaReasoner = PelletReasonerFactory.getInstance().createNonBufferingReasoner(dbpediaOntology);
+ dbpediaReasoner.precomputeInferences(InferenceType.CLASS_HIERARCHY);
}
private void initDBConnection() {
@@ -302,6 +317,30 @@
return ontology;
}
+ private OWLOntology loadDBpediaOntology() {
+ long startTime = System.currentTimeMillis();
+ logger.info("Loading DBpedia reference ontology...");
+ OWLOntology ontology = null;
+ try {
+ URL dbpediaURL = new URL("http://downloads.dbpedia.org/3.7/dbpedia_3.7.owl.bz2");
+ InputStream is = dbpediaURL.openStream();
+ is = new CompressorStreamFactory().createCompressorInputStream("bzip2", is);
+ ontology = OWLManager.createOWLOntologyManager().loadOntologyFromOntologyDocument(is);
+ } catch (MalformedURLException e) {
+ e.printStackTrace();
+ } catch (OWLOntologyCreationException e) {
+ e.printStackTrace();
+ } catch (IOException e) {
+ e.printStackTrace();
+ } catch (CompressorException e) {
+ e.printStackTrace();
+ }
+ logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
+ return ontology;
+ }
+
+
+
private OWLOntology convert(Model model) {
ByteArrayOutputStream baos = new ByteArrayOutputStream();
model.write(baos, "N-TRIPLE");
@@ -470,16 +509,13 @@
explanations.addAll(computeInconsistencyExplanationsByIrreflexivityPattern(reference, model));
explanations.addAll(computeInconsistencyExplanationsByFunctionalityPattern(reference, model));
logger.info("Found " + explanations.size() + " explanations.");
- for(Set<OWLAxiom> exp : explanations){
- logger.info(exp + "\n");
- }
Map<AxiomType, Integer> axiomType2CountMap = new HashMap<AxiomType, Integer>();
ManchesterSyntaxExplanationRenderer renderer = new ManchesterSyntaxExplanationRenderer();
try {
FileWriter out = new FileWriter( "log/justifications.txt" );
renderer.startRendering(out );
for(Set<OWLAxiom> explanation : explanations){
- logger.info(explanation);
+ logger.info(explanation + "\n");
out.flush();
try {
renderer.render( Collections.singleton(explanation) );
@@ -702,6 +738,42 @@
return properties;
}
+ private boolean isLearnedAxiom(OWLAxiom axiom){
+ return !dbpediaReasoner.isEntailed(axiom);
+ }
+
+ private boolean containsUnsatisfiableObjectProperty(Set<OWLAxiom> justification){
+ boolean value = false;
+
+ OWLReasoner reasoner = null;
+ try {
+ OWLOntology ontology = manager.createOntology(justification);
+ manager.removeAxioms(ontology, ontology.getABoxAxioms(true));
+ reasoner = PelletReasonerFactory.getInstance().createNonBufferingReasoner(ontology);
+ for(OWLObjectProperty p : ontology.getObjectPropertiesInSignature()){
+ boolean satisfiable = reasoner.isSatisfiable(factory.getOWLObjectExactCardinality(1, p));
+ if(!satisfiable){
+ value = true;
+ break;
+ }
+ }
+ } catch (TimeOutException e) {
+ e.printStackTrace();
+ } catch (ClassExpressionNotInProfileException e) {
+ e.printStackTrace();
+ } catch (FreshEntitiesException e) {
+ e.printStackTrace();
+ } catch (InconsistentOntologyException e) {
+ e.printStackTrace();
+ } catch (ReasonerInterruptedException e) {
+ e.printStackTrace();
+ } catch (OWLOntologyCreationException e) {
+ e.printStackTrace();
+ }
+ reasoner.dispose();
+ return value;
+ }
+
public void removeAxiomsWithNamespace(Set<String> namespaces){
}
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|
|
From: <lor...@us...> - 2012-02-07 09:53:39
|
Revision: 3574
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3574&view=rev
Author: lorenz_b
Date: 2012-02-07 09:53:33 +0000 (Tue, 07 Feb 2012)
Log Message:
-----------
Continued option to debug classes and properties in one step or sequentially.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/utilities/JustificationBasedCoherentOntologyExtractor.java
Modified: trunk/components-core/src/main/java/org/dllearner/utilities/JustificationBasedCoherentOntologyExtractor.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/utilities/JustificationBasedCoherentOntologyExtractor.java 2012-02-07 09:48:07 UTC (rev 3573)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/JustificationBasedCoherentOntologyExtractor.java 2012-02-07 09:53:33 UTC (rev 3574)
@@ -129,7 +129,9 @@
//compute the unsatisfiable object properties and their corresponding modules
unsatObjectProperties = getUnsatisfiableObjectProperties(reasoner);
logger.info("Found unsatisfiable object properties: " + unsatObjectProperties.size());
- entity2ModuleMap.putAll(extractModules(unsatObjectProperties));
+ if(computeParallel){
+ entity2ModuleMap.putAll(extractModules(unsatObjectProperties));
+ }
//start main process, either preferring root classes or not
if(preferRoots){
@@ -240,9 +242,14 @@
System.gc();
}
+ entity2Explanations.clear();
+ entity2ModuleMap.clear();
+
if(!computeParallel){
unsatObjectProperties = getUnsatisfiableObjectProperties(reasoner);
logger.info("Remaining unsatisfiable object properties: " + unsatObjectProperties.size());
+
+ entity2ModuleMap.putAll(extractModules(unsatObjectProperties));
while(!unsatObjectProperties.isEmpty()){
//get frequency for each axiom
Map<OWLAxiom, Integer> axiom2CountMap = getAxiomFrequency(entity2Explanations);
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|
|
From: <lor...@us...> - 2012-02-07 09:48:13
|
Revision: 3573
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3573&view=rev
Author: lorenz_b
Date: 2012-02-07 09:48:07 +0000 (Tue, 07 Feb 2012)
Log Message:
-----------
Added option to debug classes and properties in one step or sequentially.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/utilities/JustificationBasedCoherentOntologyExtractor.java
Modified: trunk/components-core/src/main/java/org/dllearner/utilities/JustificationBasedCoherentOntologyExtractor.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/utilities/JustificationBasedCoherentOntologyExtractor.java 2012-02-06 20:22:07 UTC (rev 3572)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/JustificationBasedCoherentOntologyExtractor.java 2012-02-07 09:48:07 UTC (rev 3573)
@@ -80,6 +80,9 @@
private Set<OWLTransitiveObjectPropertyAxiom> removedTransitiveAxioms;
private Set<OWLObjectProperty> unsatObjectProperties;
+ //whether to debug classes and properties in parallel
+ private boolean computeParallel = false;
+
public JustificationBasedCoherentOntologyExtractor() {
try {
md5 = MessageDigest.getInstance("MD5");
@@ -101,7 +104,7 @@
this.incoherentOntology = getOntologyWithoutAnnotations(ontology);
File diffFile = new File(new File(ontology.getOWLOntologyManager().getOntologyDocumentIRI(ontology).toURI()).getParent() + "/" + DIFF_ONTOLOGY_NAME);
- try {System.out.println(diffFile);
+ try {
if(diffFile.exists()){
diffOntology = manager.loadOntologyFromOntologyDocument(diffFile);
} else {
@@ -175,7 +178,9 @@
logger.info("Computing initial explanations...");
startTime = System.currentTimeMillis();
entity2Explanations.putAll(getInitialExplanations(unsatClasses));
- entity2Explanations.putAll(getInitialExplanations(unsatObjectProperties));
+ if(computeParallel){
+ entity2Explanations.putAll(getInitialExplanations(unsatObjectProperties));
+ }
logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
while(!unsatClasses.isEmpty()){
@@ -211,8 +216,10 @@
logger.info("Remaining unsatisfiable classes: " + (rootCnt + derivedCnt) + "(" + rootCnt + " roots).");
//recompute unsatisfiable object properties
- unsatObjectProperties = getUnsatisfiableObjectProperties(reasoner);
- logger.info("Remaining unsatisfiable object properties: " + unsatObjectProperties.size());
+ if(computeParallel){
+ unsatObjectProperties = getUnsatisfiableObjectProperties(reasoner);
+ logger.info("Remaining unsatisfiable object properties: " + unsatObjectProperties.size());
+ }
//save
if(cnt - (rootCnt+derivedCnt) >= 1 || (unsatPropCnt - unsatObjectProperties.size()) >= 1){
@@ -226,11 +233,52 @@
logger.info("Recomputing explanations...");
startTime = System.currentTimeMillis();
refillExplanations(unsatClasses, entity2Explanations);
- refillExplanations(unsatObjectProperties, entity2Explanations);
+ if(computeParallel){
+ refillExplanations(unsatObjectProperties, entity2Explanations);
+ }
logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
System.gc();
}
+ if(!computeParallel){
+ unsatObjectProperties = getUnsatisfiableObjectProperties(reasoner);
+ logger.info("Remaining unsatisfiable object properties: " + unsatObjectProperties.size());
+ while(!unsatObjectProperties.isEmpty()){
+ //get frequency for each axiom
+ Map<OWLAxiom, Integer> axiom2CountMap = getAxiomFrequency(entity2Explanations);
+
+ //get a sorted list of entries with the highest axiom count first
+ List<Entry<OWLAxiom, Integer>> sortedEntries = MapUtils.sortByValues(axiom2CountMap);
+ //we remove the most frequent axiom from the ontology
+ OWLAxiom toRemove = sortedEntries.get(0).getKey();
+ removeAxiom(toRemove);
+
+ //recompute the unsatisfiable classes
+ logger.info("Reclassifying...");
+ startTime = System.currentTimeMillis();
+ reasoner.classify();
+ logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
+
+ //recompute unsatisfiable object properties
+ unsatObjectProperties = getUnsatisfiableObjectProperties(reasoner);
+ logger.info("Remaining unsatisfiable object properties: " + unsatObjectProperties.size());
+
+ //save
+ if((unsatPropCnt - unsatObjectProperties.size()) >= 1){
+ save("log/dbpedia_" + cnt + "cls" + unsatPropCnt + "prop.owl");
+ unsatPropCnt = unsatObjectProperties.size();
+ }
+
+ //recompute explanations if necessary
+ logger.info("Recomputing explanations...");
+ startTime = System.currentTimeMillis();
+ refillExplanations(unsatObjectProperties, entity2Explanations);
+ logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
+
+ System.gc();
+ }
+ }
+
try {
incoherentOntology.getOWLOntologyManager().saveOntology(getOntologyWithAnnotations(incoherentOntology), new RDFXMLOntologyFormat(), new BufferedOutputStream(new FileOutputStream("log/dbpedia_coherent.owl")));
} catch (OWLOntologyStorageException e) {
@@ -238,7 +286,6 @@
} catch (FileNotFoundException e) {
e.printStackTrace();
}
- System.out.println(incoherentOntology.getLogicalAxiomCount());
return getOntologyWithAnnotations(incoherentOntology);
}
@@ -584,17 +631,22 @@
this.numberOfJustifications = numberOfJustifications;
}
+ public void setComputeParallel(boolean computeParallel) {
+ this.computeParallel = computeParallel;
+ }
+
public static void main(String[] args) throws Exception{
Logger.getLogger(RBox.class.getName()).setLevel(Level.OFF);
OWLOntologyManager man = OWLManager.createOWLOntologyManager();
- if(args.length != 3){
- System.out.println("USAGE: JustificationBasedCoherentOntologyExtractor <incoherent.owl> <numberOfJustifcations> <preferRootClasses(true|false)>");
+ if(args.length != 4){
+ System.out.println("USAGE: JustificationBasedCoherentOntologyExtractor <incoherent.owl> <numberOfJustifcations> <preferRootClasses(true|false)> <computeParallel(true|false)>");
System.exit(0);
}
String filename = args[0];
int numberOfJustifications = Integer.parseInt(args[1]);
boolean preferRoots = Boolean.valueOf(args[2]);
+ boolean computeParallel = Boolean.valueOf(args[3]);
System.out.println("Loading ontology...");
File file = new File(filename);
@@ -620,6 +672,7 @@
JustificationBasedCoherentOntologyExtractor extractor = new JustificationBasedCoherentOntologyExtractor();
extractor.setNumberOfJustifications(numberOfJustifications);
+ extractor.setComputeParallel(computeParallel);
OWLOntology coherentOntology = extractor.getCoherentOntology(schema, preferRoots);
System.out.println("Coherent ontology contains " + coherentOntology.getLogicalAxiomCount() + " logical axioms.");
}
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|
|
From: <lor...@us...> - 2012-02-06 20:22:18
|
Revision: 3572
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3572&view=rev
Author: lorenz_b
Date: 2012-02-06 20:22:07 +0000 (Mon, 06 Feb 2012)
Log Message:
-----------
Added exclusion skipping to answer loading method.
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 2012-02-06 15:27:51 UTC (rev 3571)
+++ trunk/components-ext/src/test/java/org/dllearner/algorithm/tbsl/Evaluation.java 2012-02-06 20:22:07 UTC (rev 3572)
@@ -203,7 +203,7 @@
String question;
Object answer;
for(Entry<Integer, String> entry : id2Query.entrySet()){
- if(testID != -1 && entry.getKey() != testID)continue;
+ if(testID != -1 && entry.getKey() != testID || (exclusions.contains(entry.getKey())))continue;
questionId = entry.getKey();
question = entry.getValue();
try {
@@ -484,8 +484,9 @@
logger.error("Template generation failed");
errorCode = "NT";
latex.addSummaryTableEntry(questionId, extractSentence(question), precision, recall, errorCode);
- } catch(Exception e){
+ } catch(Exception e){cnt++;
e.printStackTrace();
+ errorCode = "ERR";
logger.error("ERROR");
latex.addSummaryTableEntry(questionId, extractSentence(question), precision, recall, errorCode);
}
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|
|
From: <lor...@us...> - 2012-02-06 15:28:02
|
Revision: 3571
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3571&view=rev
Author: lorenz_b
Date: 2012-02-06 15:27:51 +0000 (Mon, 06 Feb 2012)
Log Message:
-----------
Added missing getter and setter methods, needed for usage of ConfigHelper.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/CELOE.java
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 2012-02-06 14:15:12 UTC (rev 3570)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/celoe/CELOE.java 2012-02-06 15:27:51 UTC (rev 3571)
@@ -32,6 +32,7 @@
import org.apache.log4j.Logger;
import org.dllearner.core.AbstractCELA;
+import org.dllearner.core.AbstractKnowledgeSource;
import org.dllearner.core.AbstractLearningProblem;
import org.dllearner.core.AbstractReasonerComponent;
import org.dllearner.core.ComponentAnn;
@@ -45,10 +46,12 @@
import org.dllearner.core.owl.NamedClass;
import org.dllearner.core.owl.Restriction;
import org.dllearner.core.owl.Thing;
+import org.dllearner.kb.OWLFile;
import org.dllearner.learningproblems.ClassLearningProblem;
import org.dllearner.learningproblems.PosNegLP;
import org.dllearner.learningproblems.PosNegLPStandard;
import org.dllearner.learningproblems.PosOnlyLP;
+import org.dllearner.reasoning.FastInstanceChecker;
import org.dllearner.refinementoperators.OperatorInverter;
import org.dllearner.refinementoperators.RefinementOperator;
import org.dllearner.refinementoperators.RhoDRDown;
@@ -1037,4 +1040,56 @@
this.maxExecutionTimeInSecondsAfterImprovement = maxExecutionTimeInSecondsAfterImprovement;
}
+ public boolean isSingleSuggestionMode() {
+ return singleSuggestionMode;
+ }
+
+ public void setSingleSuggestionMode(boolean singleSuggestionMode) {
+ this.singleSuggestionMode = singleSuggestionMode;
+ }
+
+ public int getMaxClassExpressionTests() {
+ return maxClassExpressionTests;
+ }
+
+ public void setMaxClassExpressionTests(int maxClassExpressionTests) {
+ this.maxClassExpressionTests = maxClassExpressionTests;
+ }
+
+ public int getMaxClassExpressionTestsAfterImprovement() {
+ return maxClassExpressionTestsAfterImprovement;
+ }
+
+ public void setMaxClassExpressionTestsAfterImprovement(
+ int maxClassExpressionTestsAfterImprovement) {
+ this.maxClassExpressionTestsAfterImprovement = maxClassExpressionTestsAfterImprovement;
+ }
+
+ public double getMaxDepth() {
+ return maxDepth;
+ }
+
+ public void setMaxDepth(double maxDepth) {
+ this.maxDepth = maxDepth;
+ }
+
+ public static void main(String[] args) throws Exception{
+ AbstractKnowledgeSource ks = new OWLFile("../examples/family/father_oe.owl");
+ ks.init();
+
+ AbstractReasonerComponent rc = new FastInstanceChecker(ks);
+ rc.init();
+
+ ClassLearningProblem lp = new ClassLearningProblem(rc);
+ lp.setClassToDescribe(new NamedClass("http://example.com/father#father"));
+ lp.init();
+
+ CELOE alg = new CELOE(lp, rc);
+ alg.setMaxExecutionTimeInSeconds(10);
+ alg.init();
+
+ alg.start();
+
+ }
+
}
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|
|
From: <lor...@us...> - 2012-02-06 14:15:23
|
Revision: 3570
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3570&view=rev
Author: lorenz_b
Date: 2012-02-06 14:15:12 +0000 (Mon, 06 Feb 2012)
Log Message:
-----------
Added CLI option to return only axioms which not already exist in KB.
Modified Paths:
--------------
trunk/interfaces/src/main/java/org/dllearner/cli/Enrichment.java
trunk/interfaces/src/main/java/org/dllearner/cli/GlobalEnrichment.java
Modified: trunk/interfaces/src/main/java/org/dllearner/cli/Enrichment.java
===================================================================
--- trunk/interfaces/src/main/java/org/dllearner/cli/Enrichment.java 2012-02-06 13:48:50 UTC (rev 3569)
+++ trunk/interfaces/src/main/java/org/dllearner/cli/Enrichment.java 2012-02-06 14:15:12 UTC (rev 3570)
@@ -209,6 +209,7 @@
private int nrOfAxiomsToLearn = 10;
private double threshold = 0.7;
private int chunksize = 1000;
+ private boolean omitExistingAxioms;
private boolean useInference;
private SPARQLReasoner reasoner;
@@ -232,7 +233,7 @@
private Set<OWLAxiom> learnedOWLAxioms;
private Set<EvaluatedAxiom> learnedEvaluatedAxioms;
- public Enrichment(SparqlEndpoint se, Entity resource, double threshold, int nrOfAxiomsToLearn, boolean useInference, boolean verbose, int chunksize, int maxExecutionTimeInSeconds) {
+ public Enrichment(SparqlEndpoint se, Entity resource, double threshold, int nrOfAxiomsToLearn, boolean useInference, boolean verbose, int chunksize, int maxExecutionTimeInSeconds, boolean omitExistingAxioms) {
this.se = se;
this.resource = resource;
this.verbose = verbose;
@@ -241,6 +242,7 @@
this.useInference = useInference;
this.chunksize = chunksize;
this.maxExecutionTimeInSeconds = maxExecutionTimeInSeconds;
+ this.omitExistingAxioms = omitExistingAxioms;
try {
cacheDir = "cache" + File.separator + URLEncoder.encode(se.getURL().toString(), "UTF-8");
@@ -426,6 +428,7 @@
ks2.setCacheDir(cacheDir);
ks2.setRecursionDepth(2);
ks2.setCloseAfterRecursion(true);
+ ks2.setDissolveBlankNodes(false);
ks2.setSaveExtractedFragment(true);
startTime = System.currentTimeMillis();
System.out.print("getting knowledge base fragment ... ");
@@ -491,6 +494,7 @@
ConfigHelper.configure(learner, "maxExecutionTimeInSeconds",
maxExecutionTimeInSeconds);
((AbstractAxiomLearningAlgorithm)learner).setLimit(chunksize);
+ ((AbstractAxiomLearningAlgorithm)learner).setReturnOnlyNewAxioms(omitExistingAxioms);
learner.init();
if(reasoner != null){
((AbstractAxiomLearningAlgorithm)learner).setReasoner(reasoner);
@@ -809,6 +813,8 @@
"Specifies the chunk size for the query result as the approach is incrementally.").withRequiredArg().ofType(Integer.class).defaultsTo(1000);
parser.acceptsAll(asList("maxExecutionTimeInSeconds"),
"Specifies the max execution time for each algorithm run and each entity.").withRequiredArg().ofType(Integer.class).defaultsTo(10);
+ parser.acceptsAll(asList("omitExistingAxioms"),
+ "Specifies whether return only axioms which not already exist in the knowlegde base.").withOptionalArg().ofType(Boolean.class).defaultsTo(false);
// parse options and display a message for the user in case of problems
OptionSet options = null;
@@ -896,7 +902,8 @@
}
int chunksize = (Integer) options.valueOf("chunksize");
- int runtime = (Integer) options.valueOf("runtime");
+ int maxExecutionTimeInSeconds = (Integer) options.valueOf("maxExecutionTimeInSeconds");
+ boolean omitExistingAxioms = (Boolean) options.valueOf("omitExistingAxioms");
// TODO: some handling for inaccessible files or overwriting existing files
File f = (File) options.valueOf("o");
@@ -907,7 +914,7 @@
System.setOut(printStream);
}
- Enrichment e = new Enrichment(se, resource, threshold, maxNrOfResults, useInference, false, chunksize, runtime);
+ Enrichment e = new Enrichment(se, resource, threshold, maxNrOfResults, useInference, false, chunksize, maxExecutionTimeInSeconds, omitExistingAxioms);
e.start();
SparqlEndpointKS ks = new SparqlEndpointKS(se);
Modified: trunk/interfaces/src/main/java/org/dllearner/cli/GlobalEnrichment.java
===================================================================
--- trunk/interfaces/src/main/java/org/dllearner/cli/GlobalEnrichment.java 2012-02-06 13:48:50 UTC (rev 3569)
+++ trunk/interfaces/src/main/java/org/dllearner/cli/GlobalEnrichment.java 2012-02-06 14:15:12 UTC (rev 3570)
@@ -81,6 +81,7 @@
private static int queryChunkSize = 1000;
private static int maxExecutionTimeInSeconds = 10;
private static boolean useInference = true;
+ private static boolean omitExistingAxioms = false;
// directory for generated schemata
private static String baseDir = "log/lod-enriched/";
@@ -88,7 +89,7 @@
//parameters for thread pool
//Parallel running Threads(Executor) on System
- private static int corePoolSize = 5;
+ private static int corePoolSize = 1;
//Maximum Threads allowed in Pool
private static int maximumPoolSize = 20;
//Keep alive time for waiting threads for jobs(Runnable)
@@ -189,7 +190,8 @@
File log = new File(baseDir + File.separator + "failed" + File.separator + name + ".log");
System.out.println("Enriching " + name + " using " + se.getURL());
- Enrichment e = new Enrichment(se, null, threshold, nrOfAxiomsToLearn, useInference, false, queryChunkSize, maxExecutionTimeInSeconds);
+ Enrichment e = new Enrichment(se, null, threshold, nrOfAxiomsToLearn, useInference,
+ false, queryChunkSize, maxExecutionTimeInSeconds, omitExistingAxioms);
e.maxEntitiesPerType = 3; // hack for faster testing of endpoints
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|
|
From: <lor...@us...> - 2012-02-06 13:49:00
|
Revision: 3569
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3569&view=rev
Author: lorenz_b
Date: 2012-02-06 13:48:50 +0000 (Mon, 06 Feb 2012)
Log Message:
-----------
Added class to merge multiple ontologies on the commandline.
Added Paths:
-----------
trunk/scripts/src/main/java/org/dllearner/scripts/OntologyMerger.java
Added: trunk/scripts/src/main/java/org/dllearner/scripts/OntologyMerger.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/OntologyMerger.java (rev 0)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/OntologyMerger.java 2012-02-06 13:48:50 UTC (rev 3569)
@@ -0,0 +1,58 @@
+package org.dllearner.scripts;
+
+import static java.util.Arrays.asList;
+
+import java.io.File;
+
+import joptsimple.OptionParser;
+import joptsimple.OptionSet;
+
+import org.semanticweb.owlapi.apibinding.OWLManager;
+import org.semanticweb.owlapi.io.RDFXMLOntologyFormat;
+import org.semanticweb.owlapi.model.IRI;
+import org.semanticweb.owlapi.model.OWLOntology;
+import org.semanticweb.owlapi.model.OWLOntologyManager;
+import org.semanticweb.owlapi.util.OWLOntologyMerger;
+
+/**
+ * This class merges several ontologies into a single one.
+ * @author lorenz
+ *
+ */
+public class OntologyMerger {
+
+ /**
+ * @param args
+ */
+ public static void main(String[] args) throws Exception{
+ if(args.length <= 0){
+ System.exit(0);
+ }
+ OptionParser parser = new OptionParser();
+ parser.acceptsAll(asList("o", "output"), "The target output file for the merged ontology.").withRequiredArg();
+ parser.acceptsAll(asList("i", "iri"), "The document IRI for the merged ontology.").withRequiredArg();
+
+ OptionSet os = parser.parse(args);
+
+ String targetFile = "merged.owl";
+ if(os.has("o")){
+ targetFile = (String) os.valueOf("o");;
+ }
+ String documentIRI = "http://www.semanticweb.com/merged";
+ if(os.has("i")){
+ targetFile = (String) os.valueOf("o");;
+ }
+
+ OWLOntologyManager man = OWLManager.createOWLOntologyManager();
+ for(String file : os.nonOptionArguments()){
+ man.loadOntologyFromOntologyDocument(new File(file));
+ }
+
+ OWLOntologyMerger merger = new OWLOntologyMerger(man);
+ OWLOntology merged = merger.createMergedOntology(man, IRI.create(documentIRI));
+
+ man.saveOntology(merged, new RDFXMLOntologyFormat(), IRI.create(targetFile));
+
+ }
+
+}
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|
From: <chr...@us...> - 2012-02-06 13:14:21
|
Revision: 3568
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3568&view=rev
Author: christinaunger
Date: 2012-02-06 13:14:10 +0000 (Mon, 06 Feb 2012)
Log Message:
-----------
[tbsl] added QALD2 evaluation questions
Modified Paths:
--------------
trunk/components-ext/src/test/java/org/dllearner/algorithm/tbsl/Evaluation.java
trunk/components-ext/src/test/java/org/dllearner/algorithm/tbsl/GoldTagger.java
Added Paths:
-----------
trunk/components-ext/questions.txt
trunk/components-ext/src/main/resources/tbsl/evaluation/qald2-dbpedia-train-tagged(ideal).xml
trunk/components-ext/src/main/resources/tbsl/evaluation/qald2-dbpedia-train-tagged.xml
trunk/components-ext/src/main/resources/tbsl/evaluation/qald2-dbpedia-train.xml
Added: trunk/components-ext/questions.txt
===================================================================
--- trunk/components-ext/questions.txt (rev 0)
+++ trunk/components-ext/questions.txt 2012-02-06 13:14:10 UTC (rev 3568)
@@ -0,0 +1,100 @@
+1: Give me all female Russian astronauts
+2: Give me the birthdays of all actors of the television show Charmed
+3: Who is the daughter of Bill Clinton married to
+4: Which river does the Brooklyn Bridge cross
+5: How many monarchical countries are there in Europe
+6: Where did Abraham Lincoln die
+7: Is the wife of President Obama called Michelle
+8: Which states of Germany are governed by the Social Democratic Party
+9: Which US states possess gold minerals
+10: In which country does the Nile start
+11: Which countries have places with more than two caves
+12: Is proinsulin a protein
+13: Which classis does the Millepede belong to
+14: How tall is Claudia Schiffer
+15: Who created Goofy
+16: Give me the capitals of all countries in Africa
+17: Give me all cities in New Jersey with more than 100000 inhabitants
+18: Which museum exhibits The Scream by Munch
+19: Is Egypts largest city also its capital
+20: How many employees does IBM have
+21: Which states border Illinois
+22: In which country is the Limerick Lake
+23: Which television shows were created by Walt Disney
+24: Which mountain is the highest after the Annapurna
+25: In which films directed by Garry Marshall was Julia Roberts starring
+26: Which bridges are of the same type as the Manhattan Bridge
+27: Was US president Jackson involved in a war
+28: Which European countries have a constitutional monarchy
+29: Which awards did WikiLeaks win
+30: Which state of the USA has the highest population density
+31: What is the currency of the Czech Republic
+32: Which countries in the European Union adopted the Euro
+33: What is the area code of Berlin
+34: Which countries have more than two official languages
+35: Who is the owner of Universal Studios
+36: Through which countries does the Yenisei river flow
+37: When did Finland join the EU
+38: Which monarchs of the United Kingdom were married to a German
+39: When was the Battle of Gettysburg
+40: What is the highest mountain in Australia
+41: Give me all soccer clubs in Spain
+42: What are the official languages of the Philippines
+43: Who is the mayor of New York City
+44: Who designed the Brooklyn Bridge
+45: Which telecommunications organizations are located in Belgium
+46: Is Frank Herbert still alive
+47: What is the highest place of Karakoram
+48: Give me the homepage of Forbes
+49: Give me all companies in the advertising industry
+50: What did Bruce Carver die from
+51: Give me all school types
+52: Which presidents were born in 1945
+53: Give me all presidents of the United States
+54: Who was the wife of US president Lincoln
+55: Who developed the video game World of Warcraft
+56: What is the official website of Tom Cruise
+57: List all episodes of the first season of the HBO television series The Sopranos
+58: Who produced the most films
+59: Give me all people with first name Jimmy
+60: Is there a video game called Battle Chess
+61: Which mountains are higher than the Nanga Parbat
+62: Who created Wikipedia
+63: Give me all actors starring in Batman Begins
+64: Which software has been developed by organizations founded in California
+65: Which companies work in the aerospace industry as well as on nuclear reactor technology
+66: Is Christian Bale starring in Batman Begins
+67: Give me the websites of companies with more than 500000 employees
+68: Which actors were born in Germany
+69: Which caves have more than 3 entrances
+70: Give me all films produced by Hal Roach
+71: Give me all video games published by Mean Hamster Software
+72: Which languages are spoken in Estonia
+73: Who owns Aldi
+74: Which capitals in Europe were host cities of the summer olympic games
+75: Who has been the 5th president of the United States of America
+76: How many films did Hal Roach produce
+77: Which music albums contain the song Last Christmas
+78: Give me all books written by Danielle Steel
+79: Which airports are located in California USA
+80: Give me all Canadian Grunge record labels
+81: Which country has the most official languages
+82: In which programming language is GIMP written
+83: Who produced films starring Natalie Portman
+84: Give me all movies with Tom Cruise
+85: In which films did Julia Roberts as well as Richard Gere play
+86: Give me all female German chancellors
+87: Who wrote the book The pillars of the Earth
+88: How many films did Leonardo DiCaprio star in
+89: Give me all soccer clubs in the Premier League
+90: When was Capcom founded
+91: Which organizations were founded in 1950
+92: What is the highest mountain
+93: Was Natalie Portman born in the United States
+94: Which budget did the first movie of Zdenek Sverak have
+95: How many big fires struck Paris during the Middle Ages
+96: Is Jens Friebe a vegan
+97: How often was Michael Jordan divorced
+98: What is the most beautiful painting
+99: Give me all animal species that live in the Teutoburg Forest
+100: When is the movie Worst Case Scenario going to be in cinemas in the Netherlands
Added: trunk/components-ext/src/main/resources/tbsl/evaluation/qald2-dbpedia-train-tagged(ideal).xml
===================================================================
(Binary files differ)
Property changes on: trunk/components-ext/src/main/resources/tbsl/evaluation/qald2-dbpedia-train-tagged(ideal).xml
___________________________________________________________________
Added: svn:mime-type
+ application/xml
Added: trunk/components-ext/src/main/resources/tbsl/evaluation/qald2-dbpedia-train-tagged.xml
===================================================================
(Binary files differ)
Property changes on: trunk/components-ext/src/main/resources/tbsl/evaluation/qald2-dbpedia-train-tagged.xml
___________________________________________________________________
Added: svn:mime-type
+ application/xml
Added: trunk/components-ext/src/main/resources/tbsl/evaluation/qald2-dbpedia-train.xml
===================================================================
(Binary files differ)
Property changes on: trunk/components-ext/src/main/resources/tbsl/evaluation/qald2-dbpedia-train.xml
___________________________________________________________________
Added: svn:mime-type
+ application/xml
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 2012-02-06 12:40:04 UTC (rev 3567)
+++ trunk/components-ext/src/test/java/org/dllearner/algorithm/tbsl/Evaluation.java 2012-02-06 13:14:10 UTC (rev 3568)
@@ -64,7 +64,8 @@
public class Evaluation{
- List<Integer> yagoExclusions = Arrays.asList(new Integer[]{1, 3, 6, 11, 15, 22, 23, 46});
+// List<Integer> yagoExclusions = Arrays.asList(new Integer[]{1, 3, 6, 11, 15, 22, 23, 46});
+ List<Integer> exclusions = Arrays.asList(new Integer[]{1,5,8,9,16,28,30,32,38,51,52,53,74,86,94,95,96,97,98,99,100});
Map<Integer, String> evalCodes = new HashMap<Integer, String>();
private static Logger logger = Logger.getLogger(Evaluation.class);
@@ -97,8 +98,10 @@
prefixMap = new HashMap<String, String>();
prefixMap.put("rdf", RDF.getURI());
prefixMap.put("rdfs", RDFS.getURI());
- prefixMap.put("onto", "http://dbpedia.org/ontology/");
- prefixMap.put("prop", "http://dbpedia.org/property/");
+// prefixMap.put("onto", "http://dbpedia.org/ontology/");
+// prefixMap.put("prop", "http://dbpedia.org/property/");
+ prefixMap.put("dbo", "http://dbpedia.org/ontology/");
+ prefixMap.put("dbp", "http://dbpedia.org/property/");
prefixMap.put("res", "http://dbpedia.org/resource/");
prefixMap.put("foaf", FOAF.getURI());
prefixMap.put("yago", "http://dbpedia.org/class/yago/");
@@ -323,7 +326,7 @@
int i = 0;
int cnt = 0;
for(Entry<Integer, String> entry : id2Question.entrySet()){//if(entry.getKey()==50)continue;
- if((testID != -1 && entry.getKey() != testID) || (yagoExclusions.contains(entry.getKey())))continue;
+ if((testID != -1 && entry.getKey() != testID) || (exclusions.contains(entry.getKey()))) continue;
try {
questionId = entry.getKey();
question = entry.getValue();
Modified: trunk/components-ext/src/test/java/org/dllearner/algorithm/tbsl/GoldTagger.java
===================================================================
--- trunk/components-ext/src/test/java/org/dllearner/algorithm/tbsl/GoldTagger.java 2012-02-06 12:40:04 UTC (rev 3567)
+++ trunk/components-ext/src/test/java/org/dllearner/algorithm/tbsl/GoldTagger.java 2012-02-06 13:14:10 UTC (rev 3568)
@@ -25,8 +25,8 @@
public class GoldTagger {
- static String GOLD = "src/main/resources/tbsl/evaluation/dbpedia-train.xml";
- static String OUT = "target/dbpedia-train-tagged.xml";
+ static String GOLD = "src/main/resources/tbsl/evaluation/qald2-dbpedia-train.xml";
+ static String OUT = "target/qald2-dbpedia-train-tagged.xml";
public static void main(String[] args) {
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|
|
From: <lor...@us...> - 2012-02-06 12:40:15
|
Revision: 3567
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3567&view=rev
Author: lorenz_b
Date: 2012-02-06 12:40:04 +0000 (Mon, 06 Feb 2012)
Log Message:
-----------
Fixed some dependencies for SOLR.
Modified Paths:
--------------
trunk/components-ext/pom.xml
Modified: trunk/components-ext/pom.xml
===================================================================
--- trunk/components-ext/pom.xml 2012-02-06 09:38:22 UTC (rev 3566)
+++ trunk/components-ext/pom.xml 2012-02-06 12:40:04 UTC (rev 3567)
@@ -57,7 +57,6 @@
<dependency>
<groupId>org.apache.solr</groupId>
<artifactId>solr-core</artifactId>
- <version>1.4.1</version>
</dependency>
<!--BEGIN Logging Dependencies-->
@@ -66,16 +65,20 @@
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
- <version>1.5.8</version>
</dependency>
+
+ <dependency>
+ <groupId>org.slf4j</groupId>
+ <artifactId>slf4j-log4j12</artifactId>
+ </dependency>
<!--This is the bridge that ties calls to the slf4j api to the log4j framework. This is a runtime dependency for programs which wish to use log4j as their implementation.-->
- <dependency>
+ <!-- dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-log4j12</artifactId>
<version>1.5.11</version>
<scope>runtime</scope>
- </dependency>
+ </dependency-->
<!-- This is the concrete implementation of the log4j framework - it is a runtime dependency that needs to be used with the slf4j-log4j12 dependency -->
<dependency>
@@ -83,12 +86,12 @@
<artifactId>log4j</artifactId>
</dependency>
- <dependency>
+ <!-- dependency>
<groupId>org.slf4j</groupId>
<artifactId>jcl-over-slf4j</artifactId>
<version>1.5.11</version>
<scope>runtime</scope>
- </dependency>
+ </dependency-->
<!--END Logging Dependencies-->
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|
|
From: <lor...@us...> - 2012-02-06 09:38:33
|
Revision: 3566
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3566&view=rev
Author: lorenz_b
Date: 2012-02-06 09:38:22 +0000 (Mon, 06 Feb 2012)
Log Message:
-----------
Saving diff.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/utilities/JustificationBasedCoherentOntologyExtractor.java
Modified: trunk/components-core/src/main/java/org/dllearner/utilities/JustificationBasedCoherentOntologyExtractor.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/utilities/JustificationBasedCoherentOntologyExtractor.java 2012-02-05 18:27:34 UTC (rev 3565)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/JustificationBasedCoherentOntologyExtractor.java 2012-02-06 09:38:22 UTC (rev 3566)
@@ -26,6 +26,7 @@
import org.semanticweb.owlapi.apibinding.OWLManager;
import org.semanticweb.owlapi.io.RDFXMLOntologyFormat;
import org.semanticweb.owlapi.model.AxiomType;
+import org.semanticweb.owlapi.model.IRI;
import org.semanticweb.owlapi.model.OWLAxiom;
import org.semanticweb.owlapi.model.OWLClass;
import org.semanticweb.owlapi.model.OWLDataFactory;
@@ -56,7 +57,8 @@
public class JustificationBasedCoherentOntologyExtractor implements CoherentOntologyExtractor{
private static final org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(JustificationBasedCoherentOntologyExtractor.class);
-
+ private static final String DIFF_ONTOLOGY_NAME = "diff.owl";
+
private int numberOfJustifications = 10;
// private PelletReasoner reasoner;
private IncrementalClassifier reasoner;
@@ -66,7 +68,11 @@
private OWLOntology ontology;
private OWLDataFactory factory;
+ //we store the removed axioms in it
+ private OWLOntology diffOntology;
+
private Map<OWLEntity, OWLOntology> entity2ModuleMap = new HashMap<OWLEntity, OWLOntology>();
+ private Map<OWLEntity, Set<Set<OWLAxiom>>> entity2Explanations = new HashMap<OWLEntity, Set<Set<OWLAxiom>>>();
private OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
MessageDigest md5;
@@ -94,6 +100,17 @@
this.ontology = ontology;
this.incoherentOntology = getOntologyWithoutAnnotations(ontology);
+ File diffFile = new File(new File(ontology.getOWLOntologyManager().getOntologyDocumentIRI(ontology).toURI()).getParent() + "/" + DIFF_ONTOLOGY_NAME);
+ try {System.out.println(diffFile);
+ if(diffFile.exists()){
+ diffOntology = manager.loadOntologyFromOntologyDocument(diffFile);
+ } else {
+ diffOntology = manager.createOntology(IRI.create("http://diff.org/"));
+ }
+ } catch (OWLOntologyCreationException e1) {
+ e1.printStackTrace();
+ }
+
//only for debugging
removedTransitiveAxioms = incoherentOntology.getAxioms(AxiomType.TRANSITIVE_OBJECT_PROPERTY);
incoherentOntology.getOWLOntologyManager().removeAxioms(incoherentOntology, removedTransitiveAxioms);
@@ -141,6 +158,7 @@
int derivedCnt = derivedUnsatClasses.size();
// Set<OWLClass> unsatClasses = reasoner.getUnsatisfiableClasses().getEntitiesMinusBottom();
int cnt = rootCnt + derivedCnt;
+ int unsatPropCnt = unsatObjectProperties.size();
logger.info("Detected " + cnt + " unsatisfiable classes, " + rootCnt + " of them as root.");
//if the ontology is not incoherent we return it here
@@ -156,7 +174,6 @@
//compute initial explanations for each unsatisfiable class
logger.info("Computing initial explanations...");
startTime = System.currentTimeMillis();
- Map<OWLEntity, Set<Set<OWLAxiom>>> entity2Explanations = new HashMap<OWLEntity, Set<Set<OWLAxiom>>>();
entity2Explanations.putAll(getInitialExplanations(unsatClasses));
entity2Explanations.putAll(getInitialExplanations(unsatObjectProperties));
logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
@@ -172,11 +189,7 @@
}
//we remove the most frequent axiom from the ontology
OWLAxiom toRemove = sortedEntries.get(0).getKey();
- logger.info("Removing axiom " + toRemove + ".");
- man.removeAxiom(incoherentOntology, toRemove);
- man.applyChange(new RemoveAxiom(incoherentOntology, toRemove));
- removeFromExplanations(entity2Explanations, toRemove);
- removeFromModules(toRemove);
+ removeAxiom(toRemove);
//recompute the unsatisfiable classes
logger.info("Reclassifying...");
@@ -202,10 +215,11 @@
logger.info("Remaining unsatisfiable object properties: " + unsatObjectProperties.size());
//save
- if(cnt - (rootCnt+derivedCnt) >= 10){
+ if(cnt - (rootCnt+derivedCnt) >= 1 || (unsatPropCnt - unsatObjectProperties.size()) >= 1){
cnt = rootCnt + derivedCnt;
- save("log/dbpedia_" + cnt + ".owl");
+ save("log/dbpedia_" + cnt + "cls" + unsatPropCnt + "prop.owl");
cnt = rootCnt + derivedCnt;
+ unsatPropCnt = unsatObjectProperties.size();
}
//recompute explanations if necessary
@@ -251,7 +265,6 @@
//compute initial explanations for each unsatisfiable class
logger.info("Computing initial explanations...");
startTime = System.currentTimeMillis();
- Map<OWLEntity, Set<Set<OWLAxiom>>> entity2Explanations = new HashMap<OWLEntity, Set<Set<OWLAxiom>>>();
entity2Explanations.putAll(getInitialExplanations(unsatClasses));
entity2Explanations.putAll(getInitialExplanations(unsatObjectProperties));
logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
@@ -267,11 +280,7 @@
}
//we remove the most frequent axiom from the ontology
OWLAxiom toRemove = sortedEntries.get(0).getKey();
- logger.info("Removing axiom " + toRemove + ".");
- manager.removeAxiom(incoherentOntology, toRemove);
- manager.applyChange(new RemoveAxiom(incoherentOntology, toRemove));
- removeFromExplanations(entity2Explanations, toRemove);
- removeFromModules(toRemove);
+ removeAxiom(toRemove);
//recompute the unsatisfiable classes
logger.info("Reclassifying...");
@@ -312,10 +321,20 @@
return getOntologyWithAnnotations(incoherentOntology);
}
+ private void removeAxiom(OWLAxiom axiom){
+ logger.info("Removing axiom " + axiom + ".");
+ manager.removeAxiom(incoherentOntology, axiom);
+ manager.addAxiom(diffOntology, axiom);
+ manager.applyChange(new RemoveAxiom(incoherentOntology, axiom));
+ removeFromExplanations(entity2Explanations, axiom);
+ removeFromModules(axiom);
+ }
+
private void save(String fileName){
OWLOntology toSave = getOntologyWithAnnotations(incoherentOntology);
try {
toSave.getOWLOntologyManager().saveOntology(incoherentOntology, new RDFXMLOntologyFormat(), new BufferedOutputStream(new FileOutputStream(fileName)));
+ toSave.getOWLOntologyManager().saveOntology(diffOntology, new RDFXMLOntologyFormat(), new BufferedOutputStream(new FileOutputStream("log/diff.owl")));
} catch (OWLOntologyStorageException e) {
e.printStackTrace();
} catch (FileNotFoundException e) {
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|
|
From: <lor...@us...> - 2012-02-05 18:27:40
|
Revision: 3565
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3565&view=rev
Author: lorenz_b
Date: 2012-02-05 18:27:34 +0000 (Sun, 05 Feb 2012)
Log Message:
-----------
Minor changes to use CLI options for run time and chunk size.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/algorithms/properties/AsymmetricObjectPropertyAxiomLearner.java
trunk/components-core/src/main/java/org/dllearner/algorithms/properties/DisjointObjectPropertyAxiomLearner.java
trunk/components-core/src/main/java/org/dllearner/algorithms/properties/EquivalentObjectPropertyAxiomLearner.java
trunk/components-core/src/main/java/org/dllearner/algorithms/properties/InverseObjectPropertyAxiomLearner.java
trunk/components-core/src/main/java/org/dllearner/algorithms/properties/TransitiveObjectPropertyAxiomLearner.java
trunk/components-core/src/main/java/org/dllearner/core/AbstractAxiomLearningAlgorithm.java
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/properties/AsymmetricObjectPropertyAxiomLearner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/properties/AsymmetricObjectPropertyAxiomLearner.java 2012-02-05 18:25:51 UTC (rev 3564)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/properties/AsymmetricObjectPropertyAxiomLearner.java 2012-02-05 18:27:34 UTC (rev 3565)
@@ -21,6 +21,7 @@
import java.net.URL;
import java.util.ArrayList;
+import java.util.Collections;
import org.dllearner.core.AbstractAxiomLearningAlgorithm;
import org.dllearner.core.ComponentAnn;
@@ -145,7 +146,6 @@
symmetric = qs.getLiteral("symmetric").getInt();
}
int asymmetric = total - symmetric;
-
if(total > 0){
currentlyBestAxioms.add(new EvaluatedAxiom(new AsymmetricObjectPropertyAxiom(propertyToDescribe),
computeScore(total, asymmetric), declaredAsymmetric));
@@ -154,8 +154,9 @@
}
public static void main(String[] args) throws Exception{
- AsymmetricObjectPropertyAxiomLearner l = new AsymmetricObjectPropertyAxiomLearner(new SparqlEndpointKS(new SparqlEndpoint(new URL("http://factforge.net/sparql"))));//.getEndpointDBpediaLiveAKSW()));
- l.setPropertyToDescribe(new ObjectProperty("http://dbpedia.org/ontology/country"));
+ AsymmetricObjectPropertyAxiomLearner l = new AsymmetricObjectPropertyAxiomLearner(new SparqlEndpointKS(new SparqlEndpoint(
+ new URL("http://dbpedia.aksw.org:8902/sparql"), Collections.singletonList("http://dbpedia.org"), Collections.<String>emptyList())));//.getEndpointDBpediaLiveAKSW()));
+ l.setPropertyToDescribe(new ObjectProperty("http://dbpedia.org/ontology/spouse"));
l.setMaxExecutionTimeInSeconds(10);
l.init();
l.start();
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/properties/DisjointObjectPropertyAxiomLearner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/properties/DisjointObjectPropertyAxiomLearner.java 2012-02-05 18:25:51 UTC (rev 3564)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/properties/DisjointObjectPropertyAxiomLearner.java 2012-02-05 18:27:34 UTC (rev 3565)
@@ -138,7 +138,6 @@
private void runSPARQL1_1_Mode() {
//get properties and how often they occur
- int limit = 1000;
int offset = 0;
String queryTemplate = "SELECT ?p COUNT(?s) AS ?count WHERE {?s ?p ?o." +
"{SELECT ?s ?o WHERE {?s <%s> ?o.} LIMIT %d OFFSET %d}" +
@@ -186,7 +185,7 @@
EvaluatedAxiom evalAxiom;
//first create disjoint axioms with properties which not occur and give score of 1
- for(ObjectProperty p : completeDisjointProperties){System.out.println(p);
+ for(ObjectProperty p : completeDisjointProperties){
if(usePropertyPopularity){
int popularity = reasoner.getPropertyCount(p);
//skip if property is not used in kb
@@ -205,7 +204,7 @@
//second create disjoint axioms with other properties and score 1 - (#occurence/#all)
for(Entry<ObjectProperty, Integer> entry : sortByValues(property2Count)){
double[] confidenceInterval = Heuristics.getConfidenceInterval95Wald(all, entry.getValue());
- double accuracy = (confidenceInterval[0] + confidenceInterval[1]) / 2;
+ double accuracy = (confidenceInterval[0] + confidenceInterval[1]) / 2;//System.out.println(entry + ": " + accuracy);
evalAxiom = new EvaluatedAxiom(new DisjointObjectPropertyAxiom(propertyToDescribe, entry.getKey()),
new AxiomScore(1 - accuracy));
axioms.add(evalAxiom);
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/properties/EquivalentObjectPropertyAxiomLearner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/properties/EquivalentObjectPropertyAxiomLearner.java 2012-02-05 18:25:51 UTC (rev 3564)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/properties/EquivalentObjectPropertyAxiomLearner.java 2012-02-05 18:27:34 UTC (rev 3565)
@@ -128,7 +128,6 @@
private void runSPARQL1_1_Mode() {
//get subjects with types
- int limit = 1000;
int offset = 0;
String queryTemplate = "SELECT ?p (COUNT(?s) AS ?count) WHERE {?s ?p ?o." +
"{SELECT ?s ?o WHERE {?s <%s> ?o.} LIMIT %d OFFSET %d}" +
@@ -159,7 +158,7 @@
}
if(!result.isEmpty()){
currentlyBestAxioms = buildAxioms(result);
- offset += 1000;
+ offset += limit;
}
}
@@ -178,9 +177,10 @@
properties.add(propertyToDescribe);
properties.add(entry.getKey());
int popularity = reasoner.getPropertyCount(entry.getKey());
- int total = popularity;//Math.max(popularity, all);
+// int total = popularity;
+ int total = Math.max(popularity, all);
int success = entry.getValue();//System.out.println(entry.getKey());System.out.println(entry.getKey());System.out.println(total);System.out.println(success);
- Score score = computeScore(total, success);
+ Score score = computeScore(total, success);//System.out.println(entry + ": " + score.getAccuracy());
evalAxiom = new EvaluatedAxiom(new EquivalentObjectPropertiesAxiom(properties),score);
axioms.add(evalAxiom);
}
@@ -192,7 +192,7 @@
public static void main(String[] args) throws Exception{
EquivalentObjectPropertyAxiomLearner l = new EquivalentObjectPropertyAxiomLearner(new SparqlEndpointKS(new SparqlEndpoint(
new URL("http://dbpedia.aksw.org:8902/sparql"), Collections.singletonList("http://dbpedia.org"), Collections.<String>emptyList())));//.getEndpointDBpediaLiveAKSW()));
- l.setPropertyToDescribe(new ObjectProperty("http://dbpedia.org/ontology/state"));
+ l.setPropertyToDescribe(new ObjectProperty("http://dbpedia.org/ontology/nationality"));
l.setMaxExecutionTimeInSeconds(10);
l.init();
l.start();
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/properties/InverseObjectPropertyAxiomLearner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/properties/InverseObjectPropertyAxiomLearner.java 2012-02-05 18:25:51 UTC (rev 3564)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/properties/InverseObjectPropertyAxiomLearner.java 2012-02-05 18:27:34 UTC (rev 3565)
@@ -21,6 +21,7 @@
import java.net.URL;
import java.util.ArrayList;
+import java.util.Collections;
import java.util.SortedSet;
import org.dllearner.core.AbstractAxiomLearningAlgorithm;
@@ -142,7 +143,8 @@
}
public static void main(String[] args) throws Exception{
- SparqlEndpointKS ks = new SparqlEndpointKS(new SparqlEndpoint(new URL("http://dbpedia.aksw.org:8902/sparql")));//.getEndpointDBpediaLiveAKSW()));
+ SparqlEndpointKS ks = new SparqlEndpointKS(new SparqlEndpoint(
+ new URL("http://dbpedia.aksw.org:8902/sparql"), Collections.singletonList("http://dbpedia.org"), Collections.<String>emptyList()));//.getEndpointDBpediaLiveAKSW()));
SPARQLReasoner reasoner = new SPARQLReasoner(ks);
reasoner.prepareSubsumptionHierarchy();
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/properties/TransitiveObjectPropertyAxiomLearner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/properties/TransitiveObjectPropertyAxiomLearner.java 2012-02-05 18:25:51 UTC (rev 3564)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/properties/TransitiveObjectPropertyAxiomLearner.java 2012-02-05 18:27:34 UTC (rev 3565)
@@ -19,7 +19,9 @@
package org.dllearner.algorithms.properties;
+import java.net.URL;
import java.util.ArrayList;
+import java.util.Collections;
import org.dllearner.core.AbstractAxiomLearningAlgorithm;
import org.dllearner.core.ComponentAnn;
@@ -143,7 +145,7 @@
qs = rs.next();
transitive = qs.getLiteral("transitive").getInt();
}
-
+ System.out.println(total);
if(total > 0){
currentlyBestAxioms.add(new EvaluatedAxiom(new TransitiveObjectPropertyAxiom(propertyToDescribe),
computeScore(total, transitive), declaredAsTransitive));
@@ -152,9 +154,10 @@
}
public static void main(String[] args) throws Exception{
- SparqlEndpointKS ks = new SparqlEndpointKS(SparqlEndpoint.getEndpointDBpedia());
+ SparqlEndpointKS ks = new SparqlEndpointKS(new SparqlEndpoint(
+ new URL("http://dbpedia.aksw.org:8902/sparql"), Collections.singletonList("http://dbpedia.org"), Collections.<String>emptyList()));
TransitiveObjectPropertyAxiomLearner l = new TransitiveObjectPropertyAxiomLearner(ks);
- l.setPropertyToDescribe(new ObjectProperty("http://dbpedia.org/ontology/subregion"));
+ l.setPropertyToDescribe(new ObjectProperty("http://dbpedia.org/ontology/chairman"));
l.init();
l.start();
System.out.println(l.getCurrentlyBestEvaluatedAxioms(1));
Modified: trunk/components-core/src/main/java/org/dllearner/core/AbstractAxiomLearningAlgorithm.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/core/AbstractAxiomLearningAlgorithm.java 2012-02-05 18:25:51 UTC (rev 3564)
+++ trunk/components-core/src/main/java/org/dllearner/core/AbstractAxiomLearningAlgorithm.java 2012-02-05 18:27:34 UTC (rev 3565)
@@ -84,6 +84,7 @@
protected int fetchedRows;
protected long startTime;
+ protected int limit = 1000;
public AbstractAxiomLearningAlgorithm() {
existingAxioms = new TreeSet<Axiom>(new AxiomComparator());
@@ -136,6 +137,14 @@
public void start() {
}
+ public int getLimit() {
+ return limit;
+ }
+
+ public void setLimit(int limit) {
+ this.limit = limit;
+ }
+
@Override
public void init() throws ComponentInitException {
ks.init();
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lor...@us...> - 2012-02-05 18:25:58
|
Revision: 3564
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3564&view=rev
Author: lorenz_b
Date: 2012-02-05 18:25:51 +0000 (Sun, 05 Feb 2012)
Log Message:
-----------
Added to CLI options to set query chunk size and max execution time in seconds.
Modified Paths:
--------------
trunk/interfaces/src/main/java/org/dllearner/cli/Enrichment.java
trunk/interfaces/src/main/java/org/dllearner/cli/GlobalEnrichment.java
Modified: trunk/interfaces/src/main/java/org/dllearner/cli/Enrichment.java
===================================================================
--- trunk/interfaces/src/main/java/org/dllearner/cli/Enrichment.java 2012-02-02 13:17:12 UTC (rev 3563)
+++ trunk/interfaces/src/main/java/org/dllearner/cli/Enrichment.java 2012-02-05 18:25:51 UTC (rev 3564)
@@ -208,6 +208,7 @@
// some learners)
private int nrOfAxiomsToLearn = 10;
private double threshold = 0.7;
+ private int chunksize = 1000;
private boolean useInference;
private SPARQLReasoner reasoner;
@@ -231,13 +232,15 @@
private Set<OWLAxiom> learnedOWLAxioms;
private Set<EvaluatedAxiom> learnedEvaluatedAxioms;
- public Enrichment(SparqlEndpoint se, Entity resource, double threshold, int nrOfAxiomsToLearn, boolean useInference, boolean verbose) {
+ public Enrichment(SparqlEndpoint se, Entity resource, double threshold, int nrOfAxiomsToLearn, boolean useInference, boolean verbose, int chunksize, int maxExecutionTimeInSeconds) {
this.se = se;
this.resource = resource;
this.verbose = verbose;
this.threshold = threshold;
this.nrOfAxiomsToLearn = nrOfAxiomsToLearn;
this.useInference = useInference;
+ this.chunksize = chunksize;
+ this.maxExecutionTimeInSeconds = maxExecutionTimeInSeconds;
try {
cacheDir = "cache" + File.separator + URLEncoder.encode(se.getURL().toString(), "UTF-8");
@@ -487,6 +490,7 @@
}
ConfigHelper.configure(learner, "maxExecutionTimeInSeconds",
maxExecutionTimeInSeconds);
+ ((AbstractAxiomLearningAlgorithm)learner).setLimit(chunksize);
learner.init();
if(reasoner != null){
((AbstractAxiomLearningAlgorithm)learner).setReasoner(reasoner);
@@ -801,6 +805,11 @@
.withRequiredArg().ofType(File.class);
parser.acceptsAll(asList("a", "annotations"),
"Specifies whether to save scores as annotations.").withOptionalArg().ofType(Boolean.class).defaultsTo(true);
+ parser.acceptsAll(asList("chunksize"),
+ "Specifies the chunk size for the query result as the approach is incrementally.").withRequiredArg().ofType(Integer.class).defaultsTo(1000);
+ parser.acceptsAll(asList("maxExecutionTimeInSeconds"),
+ "Specifies the max execution time for each algorithm run and each entity.").withRequiredArg().ofType(Integer.class).defaultsTo(10);
+
// parse options and display a message for the user in case of problems
OptionSet options = null;
try {
@@ -886,6 +895,9 @@
maxNrOfResults = Integer.MAX_VALUE;
}
+ int chunksize = (Integer) options.valueOf("chunksize");
+ int runtime = (Integer) options.valueOf("runtime");
+
// TODO: some handling for inaccessible files or overwriting existing files
File f = (File) options.valueOf("o");
@@ -895,7 +907,7 @@
System.setOut(printStream);
}
- Enrichment e = new Enrichment(se, resource, threshold, maxNrOfResults, useInference, false);
+ Enrichment e = new Enrichment(se, resource, threshold, maxNrOfResults, useInference, false, chunksize, runtime);
e.start();
SparqlEndpointKS ks = new SparqlEndpointKS(se);
Modified: trunk/interfaces/src/main/java/org/dllearner/cli/GlobalEnrichment.java
===================================================================
--- trunk/interfaces/src/main/java/org/dllearner/cli/GlobalEnrichment.java 2012-02-02 13:17:12 UTC (rev 3563)
+++ trunk/interfaces/src/main/java/org/dllearner/cli/GlobalEnrichment.java 2012-02-05 18:25:51 UTC (rev 3564)
@@ -78,6 +78,8 @@
// parameters
private static double threshold = 0.8;
private static int nrOfAxiomsToLearn = 10;
+ private static int queryChunkSize = 1000;
+ private static int maxExecutionTimeInSeconds = 10;
private static boolean useInference = true;
// directory for generated schemata
@@ -187,7 +189,7 @@
File log = new File(baseDir + File.separator + "failed" + File.separator + name + ".log");
System.out.println("Enriching " + name + " using " + se.getURL());
- Enrichment e = new Enrichment(se, null, threshold, nrOfAxiomsToLearn, useInference, false);
+ Enrichment e = new Enrichment(se, null, threshold, nrOfAxiomsToLearn, useInference, false, queryChunkSize, maxExecutionTimeInSeconds);
e.maxEntitiesPerType = 3; // hack for faster testing of endpoints
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lor...@us...> - 2012-02-02 13:17:22
|
Revision: 3563
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3563&view=rev
Author: lorenz_b
Date: 2012-02-02 13:17:12 +0000 (Thu, 02 Feb 2012)
Log Message:
-----------
Continued integration of debugging unsatisfiable object properties.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/utilities/JustificationBasedCoherentOntologyExtractor.java
Modified: trunk/components-core/src/main/java/org/dllearner/utilities/JustificationBasedCoherentOntologyExtractor.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/utilities/JustificationBasedCoherentOntologyExtractor.java 2012-02-01 14:31:26 UTC (rev 3562)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/JustificationBasedCoherentOntologyExtractor.java 2012-02-02 13:17:12 UTC (rev 3563)
@@ -66,7 +66,6 @@
private OWLOntology ontology;
private OWLDataFactory factory;
- private Map<OWLClass, OWLOntology> cls2ModuleMap = new HashMap<OWLClass, OWLOntology>();
private Map<OWLEntity, OWLOntology> entity2ModuleMap = new HashMap<OWLEntity, OWLOntology>();
private OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
@@ -96,8 +95,8 @@
this.incoherentOntology = getOntologyWithoutAnnotations(ontology);
//only for debugging
- removedTransitiveAxioms = ontology.getAxioms(AxiomType.TRANSITIVE_OBJECT_PROPERTY);
- incoherentOntology.getOWLOntologyManager().removeAxioms(ontology, removedTransitiveAxioms);
+ removedTransitiveAxioms = incoherentOntology.getAxioms(AxiomType.TRANSITIVE_OBJECT_PROPERTY);
+ incoherentOntology.getOWLOntologyManager().removeAxioms(incoherentOntology, removedTransitiveAxioms);
manager = incoherentOntology.getOWLOntologyManager();
factory = manager.getOWLDataFactory();
@@ -107,8 +106,10 @@
reasoner.classify();
logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
- //compute the unsatisfiable object properties
+ //compute the unsatisfiable object properties and their corresponding modules
unsatObjectProperties = getUnsatisfiableObjectProperties(reasoner);
+ logger.info("Found unsatisfiable object properties: " + unsatObjectProperties.size());
+ entity2ModuleMap.putAll(extractModules(unsatObjectProperties));
//start main process, either preferring root classes or not
if(preferRoots){
@@ -147,20 +148,22 @@
return incoherentOntology;
}
//compute the logical modules for each unsatisfiable class
- logger.info("Computing module for each unsatisfiable class...");
+ logger.info("Computing module for each unsatisfiable entity...");
startTime = System.currentTimeMillis();
- cls2ModuleMap = extractModules(unsatClasses);
+ entity2ModuleMap.putAll(extractModules(unsatClasses));
logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
//compute initial explanations for each unsatisfiable class
logger.info("Computing initial explanations...");
startTime = System.currentTimeMillis();
- Map<OWLClass, Set<Set<OWLAxiom>>> cls2Explanations = getInitialExplanationsForUnsatClasses(unsatClasses);
+ Map<OWLEntity, Set<Set<OWLAxiom>>> entity2Explanations = new HashMap<OWLEntity, Set<Set<OWLAxiom>>>();
+ entity2Explanations.putAll(getInitialExplanations(unsatClasses));
+ entity2Explanations.putAll(getInitialExplanations(unsatObjectProperties));
logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
while(!unsatClasses.isEmpty()){
//get frequency for each axiom
- Map<OWLAxiom, Integer> axiom2CountMap = getAxiomFrequency(cls2Explanations);
+ Map<OWLAxiom, Integer> axiom2CountMap = getAxiomFrequency(entity2Explanations);
//get a sorted list of entries with the highest axiom count first
List<Entry<OWLAxiom, Integer>> sortedEntries = MapUtils.sortByValues(axiom2CountMap);
@@ -172,7 +175,7 @@
logger.info("Removing axiom " + toRemove + ".");
man.removeAxiom(incoherentOntology, toRemove);
man.applyChange(new RemoveAxiom(incoherentOntology, toRemove));
- removeFromExplanations(cls2Explanations, toRemove);
+ removeFromExplanations(entity2Explanations, toRemove);
removeFromModules(toRemove);
//recompute the unsatisfiable classes
@@ -194,6 +197,10 @@
logger.info("Remaining unsatisfiable classes: " + (rootCnt + derivedCnt) + "(" + rootCnt + " roots).");
+ //recompute unsatisfiable object properties
+ unsatObjectProperties = getUnsatisfiableObjectProperties(reasoner);
+ logger.info("Remaining unsatisfiable object properties: " + unsatObjectProperties.size());
+
//save
if(cnt - (rootCnt+derivedCnt) >= 10){
cnt = rootCnt + derivedCnt;
@@ -204,7 +211,8 @@
//recompute explanations if necessary
logger.info("Recomputing explanations...");
startTime = System.currentTimeMillis();
- refillExplanations(unsatClasses, cls2Explanations);
+ refillExplanations(unsatClasses, entity2Explanations);
+ refillExplanations(unsatObjectProperties, entity2Explanations);
logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
System.gc();
@@ -237,19 +245,20 @@
//compute the logical modules for each unsatisfiable class
logger.info("Computing module for each unsatisfiable class...");
startTime = System.currentTimeMillis();
- cls2ModuleMap = extractModules(unsatClasses);
+ entity2ModuleMap = extractModules(unsatClasses);
logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
//compute initial explanations for each unsatisfiable class
logger.info("Computing initial explanations...");
startTime = System.currentTimeMillis();
- Map<OWLClass, Set<Set<OWLAxiom>>> cls2Explanations = getInitialExplanationsForUnsatClasses(unsatClasses);
- Map<OWLObjectProperty, Set<Set<OWLAxiom>>> prop2Explanations = getInitialExplanationsForUnsatObjectProperties(unsatObjectProperties);
+ Map<OWLEntity, Set<Set<OWLAxiom>>> entity2Explanations = new HashMap<OWLEntity, Set<Set<OWLAxiom>>>();
+ entity2Explanations.putAll(getInitialExplanations(unsatClasses));
+ entity2Explanations.putAll(getInitialExplanations(unsatObjectProperties));
logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
while(!unsatClasses.isEmpty()){
//get frequency for each axiom
- Map<OWLAxiom, Integer> axiom2CountMap = getAxiomFrequency(cls2Explanations);
+ Map<OWLAxiom, Integer> axiom2CountMap = getAxiomFrequency(entity2Explanations);
//get a sorted list of entries with the highest axiom count first
List<Entry<OWLAxiom, Integer>> sortedEntries = MapUtils.sortByValues(axiom2CountMap);
@@ -261,7 +270,7 @@
logger.info("Removing axiom " + toRemove + ".");
manager.removeAxiom(incoherentOntology, toRemove);
manager.applyChange(new RemoveAxiom(incoherentOntology, toRemove));
- removeFromExplanations(cls2Explanations, toRemove);
+ removeFromExplanations(entity2Explanations, toRemove);
removeFromModules(toRemove);
//recompute the unsatisfiable classes
@@ -272,6 +281,10 @@
logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
logger.info("Remaining unsatisfiable classes: " + unsatClasses.size());
+ //recompute unsatisfiable object properties
+ unsatObjectProperties = getUnsatisfiableObjectProperties(reasoner);
+ logger.info("Remaining unsatisfiable object properties: " + unsatObjectProperties.size());
+
//save
if(cnt - unsatClasses.size() >= 10){
cnt = unsatClasses.size();
@@ -281,7 +294,8 @@
//recompute explanations if necessary
logger.info("Recomputing explanations...");
startTime = System.currentTimeMillis();
- refillExplanations(unsatClasses, cls2Explanations);
+ refillExplanations(unsatClasses, entity2Explanations);
+ refillExplanations(unsatObjectProperties, entity2Explanations);
logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
System.gc();
@@ -310,6 +324,8 @@
}
private Set<OWLObjectProperty> getUnsatisfiableObjectProperties(IncrementalClassifier reasoner){
+ logger.info("Computing unsatisfiable object properties...");
+ long startTime = System.currentTimeMillis();
SortedSet<OWLObjectProperty> properties = new TreeSet<OWLObjectProperty>();
OWLDataFactory f = OWLManager.createOWLOntologyManager().getOWLDataFactory();
for(OWLObjectProperty p : reasoner.getRootOntology().getObjectPropertiesInSignature()){
@@ -319,19 +335,20 @@
properties.add(p);
}
}
+ logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
return properties;
}
private void removeFromModules(OWLAxiom axiom){
OWLOntology module;
- for(Entry<OWLClass, OWLOntology> entry : cls2ModuleMap.entrySet()){
+ for(Entry<? extends OWLEntity, OWLOntology> entry : entity2ModuleMap.entrySet()){
module = entry.getValue();
module.getOWLOntologyManager().removeAxiom(module, axiom);
}
}
- private void removeFromExplanations(Map<OWLClass, Set<Set<OWLAxiom>>> cls2Explanations, OWLAxiom axiom){
- for(Entry<OWLClass, Set<Set<OWLAxiom>>> entry : cls2Explanations.entrySet()){
+ private void removeFromExplanations(Map<OWLEntity, Set<Set<OWLAxiom>>> entity2Explanations, OWLAxiom axiom){
+ for(Entry<OWLEntity, Set<Set<OWLAxiom>>> entry : entity2Explanations.entrySet()){
for (Iterator<Set<OWLAxiom>> iterator = entry.getValue().iterator(); iterator.hasNext();) {
Set<OWLAxiom> explanation = iterator.next();
if(explanation.contains(axiom)){
@@ -341,20 +358,20 @@
}
}
- private void refillExplanations(Set<OWLClass> unsatClasses, Map<OWLClass, Set<Set<OWLAxiom>>> cls2Explanations){
- for(OWLClass unsatClass : unsatClasses){
- Set<Set<OWLAxiom>> precomputedExplanations = cls2Explanations.get(unsatClass);
+ private void refillExplanations(Set<? extends OWLEntity> unsatEntities, Map<OWLEntity, Set<Set<OWLAxiom>>> entity2Explanations){
+ for(OWLEntity unsatClass : unsatEntities){
+ Set<Set<OWLAxiom>> precomputedExplanations = entity2Explanations.get(unsatClass);
if(precomputedExplanations == null || precomputedExplanations.size() < numberOfJustifications){
Set<Set<OWLAxiom>> newExplanations = computeExplanations(unsatClass, numberOfJustifications);
- cls2Explanations.put(unsatClass, newExplanations);
+ entity2Explanations.put(unsatClass, newExplanations);
}
}
}
- private Map<OWLAxiom, Integer> getAxiomFrequency(Map<OWLClass, Set<Set<OWLAxiom>>> cls2Explanations){
+ private Map<OWLAxiom, Integer> getAxiomFrequency(Map<OWLEntity, Set<Set<OWLAxiom>>> entity2Explanations){
Map<OWLAxiom, Integer> axiom2CountMap = new HashMap<OWLAxiom, Integer>();
- for(Entry<OWLClass, Set<Set<OWLAxiom>>> entry : cls2Explanations.entrySet()){
+ for(Entry<OWLEntity, Set<Set<OWLAxiom>>> entry : entity2Explanations.entrySet()){
for(Set<OWLAxiom> explanation : entry.getValue()){
for(OWLAxiom ax : explanation){
Integer cnt = axiom2CountMap.get(ax);
@@ -370,28 +387,22 @@
return axiom2CountMap;
}
- private Map<OWLClass, Set<Set<OWLAxiom>>> getInitialExplanationsForUnsatClasses(Set<OWLClass> unsatClasses){
- Map<OWLClass, Set<Set<OWLAxiom>>> cls2Explanations = new HashMap<OWLClass, Set<Set<OWLAxiom>>>();
+ private Map<OWLEntity, Set<Set<OWLAxiom>>> getInitialExplanations(Set<? extends OWLEntity> unsatEntities){
+ Map<OWLEntity, Set<Set<OWLAxiom>>> cls2Explanations = new HashMap<OWLEntity, Set<Set<OWLAxiom>>>();
- for(OWLClass unsatClass : unsatClasses){
- Set<Set<OWLAxiom>> explanations = computeExplanations(unsatClass);
- cls2Explanations.put(unsatClass, explanations);
+ for(OWLEntity unsatEntity : unsatEntities){
+ Set<Set<OWLAxiom>> explanations = null;
+ if(unsatEntity instanceof OWLClass){
+ explanations = computeExplanations((OWLClass) unsatEntity);
+ } else if(unsatEntity instanceof OWLObjectProperty){
+ explanations = computeExplanations((OWLObjectProperty) unsatEntity);
+ }
+ cls2Explanations.put(unsatEntity, explanations);
}
return cls2Explanations;
}
- private Map<OWLObjectProperty, Set<Set<OWLAxiom>>> getInitialExplanationsForUnsatObjectProperties(Set<OWLObjectProperty> unsatObjProperties){
- Map<OWLObjectProperty, Set<Set<OWLAxiom>>> prop2Explanations = new HashMap<OWLObjectProperty, Set<Set<OWLAxiom>>>();
-
- for(OWLObjectProperty unsatClass : unsatObjProperties){
- Set<Set<OWLAxiom>> explanations = computeExplanations(unsatClass);
- prop2Explanations.put(unsatClass, explanations);
- }
-
- return prop2Explanations;
- }
-
private OWLOntology getOntologyWithoutAnnotations(OWLOntology ontology){
try {
OWLOntologyManager man = ontology.getOWLOntologyManager();
@@ -418,20 +429,26 @@
return ontology;
}
- private Set<Set<OWLAxiom>> computeExplanations(OWLClass unsatClass){
- PelletExplanation expGen = new PelletExplanation(getModule(unsatClass));
- return expGen.getUnsatisfiableExplanations(unsatClass, numberOfJustifications);
+ private Set<Set<OWLAxiom>> computeExplanations(OWLEntity unsatEntity){
+ PelletExplanation expGen = new PelletExplanation(getModule(unsatEntity));
+ if(unsatEntity instanceof OWLClass){
+ return expGen.getUnsatisfiableExplanations((OWLClass) unsatEntity, numberOfJustifications);
+ } else if(unsatEntity instanceof OWLObjectProperty){
+ return expGen.getUnsatisfiableExplanations(factory.getOWLObjectExactCardinality(1, (OWLObjectProperty)unsatEntity), numberOfJustifications);
+ }
+ return null;
}
- private Set<Set<OWLAxiom>> computeExplanations(OWLObjectProperty unsatProp){
- PelletExplanation expGen = new PelletExplanation(getModule(unsatProp));
- return expGen.getUnsatisfiableExplanations(factory.getOWLObjectExactCardinality(1, unsatProp), numberOfJustifications);
+ private Set<Set<OWLAxiom>> computeExplanations(OWLEntity unsatEntity, int limit){
+ PelletExplanation expGen = new PelletExplanation(getModule(unsatEntity));
+ if(unsatEntity instanceof OWLClass){
+ return expGen.getUnsatisfiableExplanations((OWLClass) unsatEntity, limit);
+ } else if(unsatEntity instanceof OWLObjectProperty){
+ return expGen.getUnsatisfiableExplanations(factory.getOWLObjectExactCardinality(1, (OWLObjectProperty)unsatEntity), limit);
+ }
+ return null;
}
- private Set<Set<OWLAxiom>> computeExplanations(OWLClass unsatClass, int limit){
- PelletExplanation expGen = new PelletExplanation(getModule(unsatClass));
- return expGen.getUnsatisfiableExplanations(unsatClass, numberOfJustifications);
- }
private Set<Set<OWLAxiom>> computeExplanationsBlackBox(OWLClass unsatClass, int limit){
BlackBoxExplanation singleExpGen = new BlackBoxExplanation(incoherentOntology, new HermiTReasonerFactory(), hermitReasoner);
@@ -446,33 +463,33 @@
// return expGen.getUnsatisfiableExplanations(unsatClass, NUMBER_OF_JUSTIFICATIONS);
// }
- private OWLOntology getModule(OWLClass cls){
- OWLOntology module = cls2ModuleMap.get(cls);
- new File("log").mkdir();
- if(module == null){
- md5.reset();
- md5.update((ontology.getOWLOntologyManager().getOntologyDocumentIRI(ontology).toString() + cls.toStringID()).getBytes());
- String hash = MD5.asHex(md5.digest());
- String filename = "log/" + hash + ".owl";
- File file = new File(filename);
- if(file.exists()){
- module = loadModule(file);
- } else {
- module = OntologyUtils.getOntologyFromAxioms(
- ModularityUtils.extractModule(incoherentOntology, Collections.singleton((OWLEntity)cls), ModuleType.TOP_OF_BOT));
- try {
- manager.saveOntology(module, new RDFXMLOntologyFormat(), new BufferedOutputStream(new FileOutputStream(filename)));
- } catch (OWLOntologyStorageException e) {
- e.printStackTrace();
- } catch (FileNotFoundException e) {
- e.printStackTrace();
- }
- }
-
- cls2ModuleMap.put(cls, module);
- }
- return module;
- }
+// private OWLOntology getModule(OWLClass cls){
+// OWLOntology module = cls2ModuleMap.get(cls);
+// new File("log").mkdir();
+// if(module == null){
+// md5.reset();
+// md5.update((ontology.getOWLOntologyManager().getOntologyDocumentIRI(ontology).toString() + cls.toStringID()).getBytes());
+// String hash = MD5.asHex(md5.digest());
+// String filename = "log/" + hash + ".owl";
+// File file = new File(filename);
+// if(file.exists()){
+// module = loadModule(file);
+// } else {
+// module = OntologyUtils.getOntologyFromAxioms(
+// ModularityUtils.extractModule(incoherentOntology, Collections.singleton((OWLEntity)cls), ModuleType.TOP_OF_BOT));
+// try {
+// manager.saveOntology(module, new RDFXMLOntologyFormat(), new BufferedOutputStream(new FileOutputStream(filename)));
+// } catch (OWLOntologyStorageException e) {
+// e.printStackTrace();
+// } catch (FileNotFoundException e) {
+// e.printStackTrace();
+// }
+// }
+//
+// cls2ModuleMap.put(cls, module);
+// }
+// return module;
+// }
private OWLOntology getModule(OWLEntity entity){
OWLOntology module = entity2ModuleMap.get(entity);
@@ -531,12 +548,16 @@
// return prop2ModuleMap;
// }
- private <T extends OWLEntity> Map<T, OWLOntology> extractModules(Set<T> entities){
- Map<T, OWLOntology> entity2ModuleMap = new HashMap<T, OWLOntology>();
- for(T entity : entities){
+ private Map<OWLEntity, OWLOntology> extractModules(Set<? extends OWLEntity> entities){
+ logger.info("Computing modules...");
+ long startTime = System.currentTimeMillis();
+ Map<OWLEntity, OWLOntology> entity2ModuleMap = new HashMap<OWLEntity, OWLOntology>();
+ for(OWLEntity entity : entities){
+ logger.info(" for " + entity.toStringID());
OWLOntology module = getModule(entity);
entity2ModuleMap.put(entity, module);
}
+ logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
return entity2ModuleMap;
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lor...@us...> - 2012-02-01 14:31:35
|
Revision: 3562
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3562&view=rev
Author: lorenz_b
Date: 2012-02-01 14:31:26 +0000 (Wed, 01 Feb 2012)
Log Message:
-----------
Started integration of debugging unsatisfiable object properties.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/utilities/JustificationBasedCoherentOntologyExtractor.java
Modified: trunk/components-core/src/main/java/org/dllearner/utilities/JustificationBasedCoherentOntologyExtractor.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/utilities/JustificationBasedCoherentOntologyExtractor.java 2012-02-01 11:36:50 UTC (rev 3561)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/JustificationBasedCoherentOntologyExtractor.java 2012-02-01 14:31:26 UTC (rev 3562)
@@ -11,6 +11,8 @@
import java.util.Iterator;
import java.util.List;
import java.util.Map;
+import java.util.SortedSet;
+import java.util.TreeSet;
import java.util.Map.Entry;
import java.util.Set;
import java.util.logging.Level;
@@ -29,10 +31,12 @@
import org.semanticweb.owlapi.model.OWLDataFactory;
import org.semanticweb.owlapi.model.OWLEntity;
import org.semanticweb.owlapi.model.OWLLogicalAxiom;
+import org.semanticweb.owlapi.model.OWLObjectProperty;
import org.semanticweb.owlapi.model.OWLOntology;
import org.semanticweb.owlapi.model.OWLOntologyCreationException;
import org.semanticweb.owlapi.model.OWLOntologyManager;
import org.semanticweb.owlapi.model.OWLOntologyStorageException;
+import org.semanticweb.owlapi.model.OWLTransitiveObjectPropertyAxiom;
import org.semanticweb.owlapi.model.RemoveAxiom;
import org.semanticweb.owlapi.reasoner.IllegalConfigurationException;
import org.semanticweb.owlapi.reasoner.OWLReasoner;
@@ -47,6 +51,7 @@
import com.clarkparsia.owlapi.explanation.HSTExplanationGenerator;
import com.clarkparsia.owlapi.explanation.PelletExplanation;
import com.clarkparsia.owlapiv3.OntologyUtils;
+import com.clarkparsia.pellet.owlapiv3.PelletReasoner;
public class JustificationBasedCoherentOntologyExtractor implements CoherentOntologyExtractor{
@@ -62,10 +67,14 @@
private OWLDataFactory factory;
private Map<OWLClass, OWLOntology> cls2ModuleMap = new HashMap<OWLClass, OWLOntology>();
+ private Map<OWLEntity, OWLOntology> entity2ModuleMap = new HashMap<OWLEntity, OWLOntology>();
private OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
MessageDigest md5;
+ private Set<OWLTransitiveObjectPropertyAxiom> removedTransitiveAxioms;
+ private Set<OWLObjectProperty> unsatObjectProperties;
+
public JustificationBasedCoherentOntologyExtractor() {
try {
md5 = MessageDigest.getInstance("MD5");
@@ -83,25 +92,34 @@
@Override
public OWLOntology getCoherentOntology(OWLOntology ontology, boolean preferRoots){
- if(preferRoots){
- return computeCoherentOntologyRootBased(ontology);
- } else {
- return computeCoherentOntology(ontology);
- }
- }
-
- private OWLOntology computeCoherentOntologyRootBased(OWLOntology ontology) {
this.ontology = ontology;
this.incoherentOntology = getOntologyWithoutAnnotations(ontology);
//only for debugging
- ontology.getOWLOntologyManager().removeAxioms(ontology, ontology.getAxioms(AxiomType.TRANSITIVE_OBJECT_PROPERTY));
+ removedTransitiveAxioms = ontology.getAxioms(AxiomType.TRANSITIVE_OBJECT_PROPERTY);
+ incoherentOntology.getOWLOntologyManager().removeAxioms(ontology, removedTransitiveAxioms);
+ manager = incoherentOntology.getOWLOntologyManager();
+ factory = manager.getOWLDataFactory();
+
long startTime = System.currentTimeMillis();
reasoner = new IncrementalClassifier(incoherentOntology);
reasoner.classify();
logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
+ //compute the unsatisfiable object properties
+ unsatObjectProperties = getUnsatisfiableObjectProperties(reasoner);
+
+ //start main process, either preferring root classes or not
+ if(preferRoots){
+ return computeCoherentOntologyRootBased(incoherentOntology);
+ } else {
+ return computeCoherentOntology(incoherentOntology);
+ }
+ }
+
+ private OWLOntology computeCoherentOntologyRootBased(OWLOntology ontology) {
+
// startTime = System.currentTimeMillis();
// hermitReasoner = new Reasoner(incoherentOntology);
// hermitReasoner.classifyClasses();
@@ -113,7 +131,7 @@
//compute the unsatisfiable classes
logger.info("Computing root/derived unsatisfiable classes...");
- startTime = System.currentTimeMillis();
+ long startTime = System.currentTimeMillis();
StructureBasedRootClassFinder rootFinder = new StructureBasedRootClassFinder(reasoner);
Set<OWLClass> unsatClasses = rootFinder.getRootUnsatisfiableClasses();
Set<OWLClass> derivedUnsatClasses = rootFinder.getDerivedUnsatisfiableClasses();
@@ -179,14 +197,7 @@
//save
if(cnt - (rootCnt+derivedCnt) >= 10){
cnt = rootCnt + derivedCnt;
- OWLOntology toSave = getOntologyWithAnnotations(incoherentOntology);
- try {
- toSave.getOWLOntologyManager().saveOntology(incoherentOntology, new RDFXMLOntologyFormat(), new BufferedOutputStream(new FileOutputStream("log/dbpedia_" + cnt + ".owl")));
- } catch (OWLOntologyStorageException e) {
- e.printStackTrace();
- } catch (FileNotFoundException e) {
- e.printStackTrace();
- }
+ save("log/dbpedia_" + cnt + ".owl");
cnt = rootCnt + derivedCnt;
}
@@ -211,23 +222,9 @@
}
private OWLOntology computeCoherentOntology(OWLOntology ontology) {
- this.ontology = ontology;
- this.incoherentOntology = getOntologyWithoutAnnotations(ontology);
-
- //only for debugging
- ontology.getOWLOntologyManager().removeAxioms(ontology, ontology.getAxioms(AxiomType.TRANSITIVE_OBJECT_PROPERTY));
-
- long startTime = System.currentTimeMillis();
- reasoner = new IncrementalClassifier(incoherentOntology);
- reasoner.classify();
- logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
-
- OWLOntologyManager man = incoherentOntology.getOWLOntologyManager();
- factory = man.getOWLDataFactory();
-
//compute the unsatisfiable classes
logger.info("Computing unsatisfiable classes...");
- startTime = System.currentTimeMillis();
+ long startTime = System.currentTimeMillis();
logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
Set<OWLClass> unsatClasses = reasoner.getUnsatisfiableClasses().getEntitiesMinusBottom();
int cnt = unsatClasses.size();
@@ -247,6 +244,7 @@
logger.info("Computing initial explanations...");
startTime = System.currentTimeMillis();
Map<OWLClass, Set<Set<OWLAxiom>>> cls2Explanations = getInitialExplanationsForUnsatClasses(unsatClasses);
+ Map<OWLObjectProperty, Set<Set<OWLAxiom>>> prop2Explanations = getInitialExplanationsForUnsatObjectProperties(unsatObjectProperties);
logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
while(!unsatClasses.isEmpty()){
@@ -261,8 +259,8 @@
//we remove the most frequent axiom from the ontology
OWLAxiom toRemove = sortedEntries.get(0).getKey();
logger.info("Removing axiom " + toRemove + ".");
- man.removeAxiom(incoherentOntology, toRemove);
- man.applyChange(new RemoveAxiom(incoherentOntology, toRemove));
+ manager.removeAxiom(incoherentOntology, toRemove);
+ manager.applyChange(new RemoveAxiom(incoherentOntology, toRemove));
removeFromExplanations(cls2Explanations, toRemove);
removeFromModules(toRemove);
@@ -277,14 +275,7 @@
//save
if(cnt - unsatClasses.size() >= 10){
cnt = unsatClasses.size();
- OWLOntology toSave = getOntologyWithAnnotations(incoherentOntology);
- try {
- toSave.getOWLOntologyManager().saveOntology(incoherentOntology, new RDFXMLOntologyFormat(), new BufferedOutputStream(new FileOutputStream("log/dbpedia_" + cnt + ".owl")));
- } catch (OWLOntologyStorageException e) {
- e.printStackTrace();
- } catch (FileNotFoundException e) {
- e.printStackTrace();
- }
+ save("log/dbpedia_" + cnt + ".owl");
}
//recompute explanations if necessary
@@ -307,6 +298,30 @@
return getOntologyWithAnnotations(incoherentOntology);
}
+ private void save(String fileName){
+ OWLOntology toSave = getOntologyWithAnnotations(incoherentOntology);
+ try {
+ toSave.getOWLOntologyManager().saveOntology(incoherentOntology, new RDFXMLOntologyFormat(), new BufferedOutputStream(new FileOutputStream(fileName)));
+ } catch (OWLOntologyStorageException e) {
+ e.printStackTrace();
+ } catch (FileNotFoundException e) {
+ e.printStackTrace();
+ }
+ }
+
+ private Set<OWLObjectProperty> getUnsatisfiableObjectProperties(IncrementalClassifier reasoner){
+ SortedSet<OWLObjectProperty> properties = new TreeSet<OWLObjectProperty>();
+ OWLDataFactory f = OWLManager.createOWLOntologyManager().getOWLDataFactory();
+ for(OWLObjectProperty p : reasoner.getRootOntology().getObjectPropertiesInSignature()){
+// boolean satisfiable = reasoner.isSatisfiable(f.getOWLObjectExactCardinality(1, p));
+ boolean satisfiable = reasoner.isSatisfiable(f.getOWLObjectSomeValuesFrom(p, factory.getOWLThing()));
+ if(!satisfiable){
+ properties.add(p);
+ }
+ }
+ return properties;
+ }
+
private void removeFromModules(OWLAxiom axiom){
OWLOntology module;
for(Entry<OWLClass, OWLOntology> entry : cls2ModuleMap.entrySet()){
@@ -366,6 +381,17 @@
return cls2Explanations;
}
+ private Map<OWLObjectProperty, Set<Set<OWLAxiom>>> getInitialExplanationsForUnsatObjectProperties(Set<OWLObjectProperty> unsatObjProperties){
+ Map<OWLObjectProperty, Set<Set<OWLAxiom>>> prop2Explanations = new HashMap<OWLObjectProperty, Set<Set<OWLAxiom>>>();
+
+ for(OWLObjectProperty unsatClass : unsatObjProperties){
+ Set<Set<OWLAxiom>> explanations = computeExplanations(unsatClass);
+ prop2Explanations.put(unsatClass, explanations);
+ }
+
+ return prop2Explanations;
+ }
+
private OWLOntology getOntologyWithoutAnnotations(OWLOntology ontology){
try {
OWLOntologyManager man = ontology.getOWLOntologyManager();
@@ -397,6 +423,11 @@
return expGen.getUnsatisfiableExplanations(unsatClass, numberOfJustifications);
}
+ private Set<Set<OWLAxiom>> computeExplanations(OWLObjectProperty unsatProp){
+ PelletExplanation expGen = new PelletExplanation(getModule(unsatProp));
+ return expGen.getUnsatisfiableExplanations(factory.getOWLObjectExactCardinality(1, unsatProp), numberOfJustifications);
+ }
+
private Set<Set<OWLAxiom>> computeExplanations(OWLClass unsatClass, int limit){
PelletExplanation expGen = new PelletExplanation(getModule(unsatClass));
return expGen.getUnsatisfiableExplanations(unsatClass, numberOfJustifications);
@@ -415,7 +446,7 @@
// return expGen.getUnsatisfiableExplanations(unsatClass, NUMBER_OF_JUSTIFICATIONS);
// }
- private OWLOntology getModule(OWLClass cls){System.out.println(cls);
+ private OWLOntology getModule(OWLClass cls){
OWLOntology module = cls2ModuleMap.get(cls);
new File("log").mkdir();
if(module == null){
@@ -443,6 +474,35 @@
return module;
}
+ private OWLOntology getModule(OWLEntity entity){
+ OWLOntology module = entity2ModuleMap.get(entity);
+ new File("log").mkdir();
+ if(module == null){
+ md5.reset();
+ md5.update((ontology.getOWLOntologyManager().getOntologyDocumentIRI(ontology).toString() + entity.toStringID()).getBytes());
+ String hash = MD5.asHex(md5.digest());
+ String filename = "log/" + hash + ".owl";
+ File file = new File(filename);
+ if(file.exists()){
+ module = loadModule(file);
+ } else {
+ module = OntologyUtils.getOntologyFromAxioms(
+ ModularityUtils.extractModule(incoherentOntology, Collections.singleton(entity), ModuleType.TOP_OF_BOT));
+ try {
+ manager.saveOntology(module, new RDFXMLOntologyFormat(), new BufferedOutputStream(new FileOutputStream(filename)));
+ } catch (OWLOntologyStorageException e) {
+ e.printStackTrace();
+ } catch (FileNotFoundException e) {
+ e.printStackTrace();
+ }
+ }
+
+ entity2ModuleMap.put(entity, module);
+ }
+ return module;
+ }
+
+
private OWLOntology loadModule(File file){
OWLOntology module = null;
try {
@@ -453,13 +513,31 @@
return module;
}
- private Map<OWLClass, OWLOntology> extractModules(Set<OWLClass> classes){
- Map<OWLClass, OWLOntology> cls2ModuleMap = new HashMap<OWLClass, OWLOntology>();
- for(OWLClass cls : classes){
- OWLOntology module = getModule(cls);
- cls2ModuleMap.put(cls, module);
+// private Map<OWLClass, OWLOntology> extractModules(Set<OWLClass> classes){
+// Map<OWLClass, OWLOntology> cls2ModuleMap = new HashMap<OWLClass, OWLOntology>();
+// for(OWLClass cls : classes){
+// OWLOntology module = getModule(cls);
+// cls2ModuleMap.put(cls, module);
+// }
+// return cls2ModuleMap;
+// }
+//
+// private Map<OWLObjectProperty, OWLOntology> extractModules(Set<OWLObjectProperty> objectProperties){
+// Map<OWLObjectProperty, OWLOntology> prop2ModuleMap = new HashMap<OWLObjectProperty, OWLOntology>();
+// for(OWLObjectProperty prop : objectProperties){
+// OWLOntology module = getModule(prop);
+// prop2ModuleMap.put(prop, module);
+// }
+// return prop2ModuleMap;
+// }
+
+ private <T extends OWLEntity> Map<T, OWLOntology> extractModules(Set<T> entities){
+ Map<T, OWLOntology> entity2ModuleMap = new HashMap<T, OWLOntology>();
+ for(T entity : entities){
+ OWLOntology module = getModule(entity);
+ entity2ModuleMap.put(entity, module);
}
- return cls2ModuleMap;
+ return entity2ModuleMap;
}
public void setNumberOfJustifications(int numberOfJustifications) {
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lor...@us...> - 2012-02-01 11:36:56
|
Revision: 3561
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3561&view=rev
Author: lorenz_b
Date: 2012-02-01 11:36:50 +0000 (Wed, 01 Feb 2012)
Log Message:
-----------
Added renderer for justifications.
Modified Paths:
--------------
trunk/scripts/src/main/java/org/dllearner/scripts/ApproximateDebugging.java
trunk/scripts/src/main/java/org/dllearner/scripts/SPARQLSampleDebugging.java
Modified: trunk/scripts/src/main/java/org/dllearner/scripts/ApproximateDebugging.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/ApproximateDebugging.java 2012-02-01 11:35:39 UTC (rev 3560)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/ApproximateDebugging.java 2012-02-01 11:36:50 UTC (rev 3561)
@@ -1,30 +1,34 @@
package org.dllearner.scripts;
+import java.io.BufferedInputStream;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.File;
+import java.io.FileInputStream;
import java.io.IOException;
+import java.io.InputStream;
import java.io.PrintWriter;
import java.net.URL;
import java.util.Collections;
-import java.util.Comparator;
+import java.util.HashMap;
import java.util.HashSet;
+import java.util.Map;
+import java.util.Map.Entry;
import java.util.Set;
import java.util.SortedSet;
import java.util.TreeSet;
+import org.apache.commons.compress.compressors.CompressorInputStream;
+import org.apache.commons.compress.compressors.CompressorStreamFactory;
import org.apache.log4j.ConsoleAppender;
import org.apache.log4j.FileAppender;
import org.apache.log4j.Level;
import org.apache.log4j.Logger;
import org.apache.log4j.SimpleLayout;
-import org.dllearner.algorithm.qtl.util.ModelGenerator;
-import org.dllearner.algorithm.qtl.util.ModelGenerator.Strategy;
import org.dllearner.kb.sparql.ConciseBoundedDescriptionGenerator;
import org.dllearner.kb.sparql.ConciseBoundedDescriptionGeneratorImpl;
import org.dllearner.kb.sparql.ExtractionDBCache;
import org.dllearner.kb.sparql.SparqlEndpoint;
-import org.dllearner.kb.sparql.SymmetricConciseBoundedDescriptionGeneratorImpl;
import org.mindswap.pellet.PelletOptions;
import org.semanticweb.owlapi.apibinding.OWLManager;
import org.semanticweb.owlapi.io.RDFXMLOntologyFormat;
@@ -35,7 +39,6 @@
import org.semanticweb.owlapi.model.OWLDataFactory;
import org.semanticweb.owlapi.model.OWLDisjointClassesAxiom;
import org.semanticweb.owlapi.model.OWLEntity;
-import org.semanticweb.owlapi.model.OWLException;
import org.semanticweb.owlapi.model.OWLIndividual;
import org.semanticweb.owlapi.model.OWLObjectProperty;
import org.semanticweb.owlapi.model.OWLObjectPropertyAssertionAxiom;
@@ -48,7 +51,6 @@
import uk.ac.manchester.cs.owl.owlapi.OWLDataFactoryImpl;
import uk.ac.manchester.cs.owlapi.modularity.ModuleType;
-import weka.attributeSelection.ConsistencySubsetEval;
import com.clarkparsia.modularity.ModularityUtils;
import com.clarkparsia.owlapi.explanation.PelletExplanation;
@@ -84,6 +86,12 @@
public ApproximateDebugging(OWLOntology schema, OWLOntology data) throws OWLOntologyCreationException {
this.schema = schema;
this.data = data;
+ System.out.println(data.getLogicalAxiomCount());
+ for(OWLAxiom ax : new HashSet<OWLAxiom>(data.getLogicalAxioms())){
+ if(!ax.getDataPropertiesInSignature().isEmpty()){
+ man.removeAxiom(data, ax);
+ }
+ }System.out.println(data.getLogicalAxiomCount());
Set<OWLOntology> ontologies = new HashSet<OWLOntology>();
ontologies.add(schema);
@@ -181,7 +189,8 @@
logger.info("done in " + (System.currentTimeMillis()-startTime) + "ms.");
logger.info("Module size: " + module.size());
reasoner = PelletReasonerFactory.getInstance().createNonBufferingReasoner(OntologyUtils.getOntologyFromAxioms(module));
- expGen = new PelletExplanation(reasoner);
+// expGen = new PelletExplanation(reasoner);
+ expGen = new PelletExplanation(schema, false);
logger.info("Computing explanations...");
startTime = System.currentTimeMillis();
Set<Set<OWLAxiom>> temp = expGen.getUnsatisfiableExplanations(unsatClass, 10);
@@ -231,9 +240,9 @@
}
public Set<Set<OWLAxiom>> computeExplanationsDefault(int limit){
- reasoner = PelletReasonerFactory.getInstance().createNonBufferingReasoner(schema);
+ reasoner = PelletReasonerFactory.getInstance().createNonBufferingReasoner(ontology);
reasoner.isConsistent();
- logger.info("Computing inconsistency explanations with only Pellet...");
+ logger.info("Computing inconsistency explanations with Pellet only...");
long startTime = System.currentTimeMillis();
PelletExplanation expGen = new PelletExplanation(reasoner);
Set<Set<OWLAxiom>> explanations = expGen.getInconsistencyExplanations(limit);
@@ -312,7 +321,7 @@
for(OWLObjectProperty prop : extractObjectProperties(AxiomType.FUNCTIONAL_OBJECT_PROPERTY)){
OWLAxiom axiom = factory.getOWLFunctionalObjectPropertyAxiom(prop);
- String queryString = "SELECT * WHERE {?s <%s> ?o1. ?s <%s> ?o2. FILTER(?o1 != ?o2)}".replace("%s", prop.toStringID());
+ String queryString = "SELECT DISTINCT * WHERE {?s <%s> ?o1. ?s <%s> ?o2. FILTER(?o1 != ?o2)}".replace("%s", prop.toStringID());
Query query = QueryFactory.create(queryString) ;
QueryExecution qexec = QueryExecutionFactory.create(query, model) ;
try {
@@ -427,6 +436,7 @@
for(OWLAxiom ax : ontology.getAxioms(axiomType)){
properties.add(((OWLObjectPropertyCharacteristicAxiom)ax).getProperty().asOWLObjectProperty());
}
+// properties.retainAll(data.getObjectPropertiesInSignature());
return properties;
}
@@ -472,6 +482,11 @@
* @throws Exception
*/
public static void main(String[] args) throws Exception {
+ if(args.length != 1){
+ System.out.println("Usage: ApproximateDebugging <Schema-Ontology>");
+ System.exit(0);
+ }
+
Logger.getRootLogger().setLevel(Level.INFO);
Logger.getRootLogger().removeAllAppenders();
Logger.getRootLogger().addAppender(new ConsoleAppender(new SimpleLayout()));
@@ -487,14 +502,55 @@
Model model = cbdGen.getConciseBoundedDescription(resource, 3);
OWLOntology data = convert(model);
+ InputStream is = new BufferedInputStream(new FileInputStream(args[0]));
+ CompressorInputStream in = new CompressorStreamFactory().createCompressorInputStream("bzip2", is);
+
OWLOntologyManager man = OWLManager.createOWLOntologyManager();
- OWLOntology schema = man.loadOntologyFromOntologyDocument(new File("src/main/resources/dbpedia_0.75_no_datapropaxioms.owl"));
+ OWLOntology schema = man.loadOntologyFromOntologyDocument(in);
ApproximateDebugging debug = new ApproximateDebugging(schema, data);
+
+ Set<Set<OWLAxiom>> explanations2 = debug.computeExplanationsDefault(3);
+ ManchesterSyntaxExplanationRenderer renderer = new ManchesterSyntaxExplanationRenderer();
+ PrintWriter out = new PrintWriter( System.out );
+ renderer.startRendering( out );
+ for(Set<OWLAxiom> exp : explanations2){
+ out.flush();
+ renderer.render( Collections.singleton(exp) );
+ }
+ renderer.endRendering();
+ for(Entry<AxiomType<? extends OWLAxiom>, Integer> entry : getAxiomTypeCount(explanations2).entrySet()){
+ System.out.println(entry.getKey() + ": " + entry.getValue());
+ }
+
Set<Set<OWLAxiom>> explanations1 = debug.computeInconsistencyExplanations();
- Set<Set<OWLAxiom>> explanations2 = debug.computeExplanationsDefault(500);
- System.out.println(explanations1.size());
- System.out.println(explanations2.size());
+ for(Set<OWLAxiom> exp : explanations1){
+ System.out.println(exp);
+ }
+
+ for(Entry<AxiomType<? extends OWLAxiom>, Integer> entry : getAxiomTypeCount(explanations1).entrySet()){
+ System.out.println(entry.getKey() + ": " + entry.getValue());
+ }
+//
+// System.out.println(explanations1.size());
+// System.out.println(explanations2.size());
}
+
+ private static Map<AxiomType<? extends OWLAxiom>, Integer> getAxiomTypeCount(Set<Set<OWLAxiom>> explanations){
+ Map<AxiomType<? extends OWLAxiom>, Integer> axiomType2CountMap = new HashMap<AxiomType<? extends OWLAxiom>, Integer>();
+
+ for(Set<OWLAxiom> exp : explanations){
+ for(OWLAxiom ax : exp){
+ Integer cnt = axiomType2CountMap.get(ax.getAxiomType());
+ if(cnt == null){
+ cnt = Integer.valueOf(0);
+ }
+ cnt = Integer.valueOf(cnt + 1);
+ axiomType2CountMap.put(ax.getAxiomType(), cnt);
+ }
+ }
+
+ return axiomType2CountMap;
+ }
}
Modified: trunk/scripts/src/main/java/org/dllearner/scripts/SPARQLSampleDebugging.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/SPARQLSampleDebugging.java 2012-02-01 11:35:39 UTC (rev 3560)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/SPARQLSampleDebugging.java 2012-02-01 11:36:50 UTC (rev 3561)
@@ -6,6 +6,7 @@
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileReader;
+import java.io.FileWriter;
import java.io.IOException;
import java.io.InputStream;
import java.io.PrintWriter;
@@ -29,7 +30,6 @@
import java.util.TreeSet;
import java.util.prefs.Preferences;
-import org.apache.commons.compress.compressors.CompressorInputStream;
import org.apache.commons.compress.compressors.CompressorStreamFactory;
import org.apache.log4j.ConsoleAppender;
import org.apache.log4j.FileAppender;
@@ -54,6 +54,7 @@
import org.semanticweb.owlapi.model.OWLClass;
import org.semanticweb.owlapi.model.OWLDataFactory;
import org.semanticweb.owlapi.model.OWLDataProperty;
+import org.semanticweb.owlapi.model.OWLException;
import org.semanticweb.owlapi.model.OWLFunctionalDataPropertyAxiom;
import org.semanticweb.owlapi.model.OWLFunctionalObjectPropertyAxiom;
import org.semanticweb.owlapi.model.OWLIndividual;
@@ -473,16 +474,32 @@
logger.info(exp + "\n");
}
Map<AxiomType, Integer> axiomType2CountMap = new HashMap<AxiomType, Integer>();
- for(Set<OWLAxiom> explanation : explanations){
- logger.info(explanation);
- for(OWLAxiom axiom : explanation){
- Integer cnt = axiomType2CountMap.get(axiom.getAxiomType());
- if(cnt == null){
- cnt = Integer.valueOf(0);
+ ManchesterSyntaxExplanationRenderer renderer = new ManchesterSyntaxExplanationRenderer();
+ try {
+ FileWriter out = new FileWriter( "log/justifications.txt" );
+ renderer.startRendering(out );
+ for(Set<OWLAxiom> explanation : explanations){
+ logger.info(explanation);
+ out.flush();
+ try {
+ renderer.render( Collections.singleton(explanation) );
+ } catch (UnsupportedOperationException e) {
+ e.printStackTrace();
+ } catch (OWLException e) {
+ e.printStackTrace();
}
- cnt = Integer.valueOf(cnt + 1);
- axiomType2CountMap.put(axiom.getAxiomType(), cnt);
+ for(OWLAxiom axiom : explanation){
+ Integer cnt = axiomType2CountMap.get(axiom.getAxiomType());
+ if(cnt == null){
+ cnt = Integer.valueOf(0);
+ }
+ cnt = Integer.valueOf(cnt + 1);
+ axiomType2CountMap.put(axiom.getAxiomType(), cnt);
+ }
}
+ renderer.endRendering();
+ } catch (IOException e) {
+ e.printStackTrace();
}
logger.info("Axiom type count:");
for(Entry<AxiomType, Integer> entry : axiomType2CountMap.entrySet()){
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|
|
From: <lor...@us...> - 2012-02-01 11:35:45
|
Revision: 3560
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3560&view=rev
Author: lorenz_b
Date: 2012-02-01 11:35:39 +0000 (Wed, 01 Feb 2012)
Log Message:
-----------
Added method to get all super classes.
Add option to omit existing SubClassOf axioms.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/algorithms/SimpleSubclassLearner.java
trunk/components-core/src/main/java/org/dllearner/core/owl/ClassHierarchy.java
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/SimpleSubclassLearner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/SimpleSubclassLearner.java 2012-01-27 11:55:41 UTC (rev 3559)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/SimpleSubclassLearner.java 2012-02-01 11:35:39 UTC (rev 3560)
@@ -126,7 +126,23 @@
//get existing super classes
SortedSet<Description> existingSuperClasses = reasoner.getSuperClasses(classToDescribe);
if(!existingSuperClasses.isEmpty()){
+ SortedSet<Description> inferredSuperClasses = new TreeSet<Description>();
+ for(Description assertedSup : existingSuperClasses){
+ if(reasoner.isPrepared()){
+ if(reasoner.getClassHierarchy().contains(assertedSup)){
+ for(Description inferredSup : reasoner.getClassHierarchy().getSuperClasses(assertedSup, false)){
+ inferredSuperClasses.add(inferredSup);
+ }
+ }
+ } else {
+ inferredSuperClasses.add(assertedSup);
+ }
+ }
+ existingSuperClasses.addAll(inferredSuperClasses);
logger.info("Existing super classes: " + existingSuperClasses);
+ for(Description sup : existingSuperClasses){
+ existingAxioms.add(new SubClassAxiom(classToDescribe, sup));
+ }
}
Map<Individual, SortedSet<Description>> ind2Types = new HashMap<Individual, SortedSet<Description>>();
@@ -226,9 +242,10 @@
SimpleSubclassLearner l = new SimpleSubclassLearner(ks);
l.setReasoner(reasoner);
+ l.setReturnOnlyNewAxioms(true);
ConfigHelper.configure(l, "maxExecutionTimeInSeconds", 10);
- l.setClassToDescribe(new NamedClass("http://dbpedia.org/ontology/Olympics"));
+ l.setClassToDescribe(new NamedClass("http://dbpedia.org/ontology/SoccerClub"));
l.init();
l.start();
Modified: trunk/components-core/src/main/java/org/dllearner/core/owl/ClassHierarchy.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/core/owl/ClassHierarchy.java 2012-01-27 11:55:41 UTC (rev 3559)
+++ trunk/components-core/src/main/java/org/dllearner/core/owl/ClassHierarchy.java 2012-02-01 11:35:39 UTC (rev 3560)
@@ -111,6 +111,20 @@
// return (TreeSet<Description>) subsumptionHierarchyDown.get(concept).clone();
// }
}
+
+ public SortedSet<Description> getSuperClasses(Description concept, boolean direct) {
+ SortedSet<Description> result = subsumptionHierarchyUp.get(concept);
+ if(result == null) {
+ logger.error("Query for super class of " + concept + " in subsumption hierarchy, but the class is not contained in the (downward) hierarchy, e.g. because the class does not exist or is ignored. Returning empty result instead.");
+ return new TreeSet<Description>();
+ }
+ result.remove(concept);
+ for(Description sub : new HashSet<Description>(result)){
+ result.addAll(getSuperClasses(sub, false));
+ }
+
+ return new TreeSet<Description>(result);
+ }
/**
* Computes the siblings of the specified descriptions. Siblings are all those
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|
|
From: <lor...@us...> - 2012-01-27 11:55:52
|
Revision: 3559
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3559&view=rev
Author: lorenz_b
Date: 2012-01-27 11:55:41 +0000 (Fri, 27 Jan 2012)
Log Message:
-----------
Option to load bzip2 compressed.
Modified Paths:
--------------
trunk/scripts/src/main/java/org/dllearner/scripts/SPARQLSampleDebugging.java
Modified: trunk/scripts/src/main/java/org/dllearner/scripts/SPARQLSampleDebugging.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/SPARQLSampleDebugging.java 2012-01-27 11:51:28 UTC (rev 3558)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/SPARQLSampleDebugging.java 2012-01-27 11:55:41 UTC (rev 3559)
@@ -714,10 +714,11 @@
}
InputStream is = new BufferedInputStream(new FileInputStream(args[0]));
- CompressorInputStream in = new CompressorStreamFactory().createCompressorInputStream("bzip2", is);
+ if(args[0].endsWith("bz2")){
+ is = new CompressorStreamFactory().createCompressorInputStream("bzip2", is);
+ }
+ OWLOntology ontology = OWLManager.createOWLOntologyManager().loadOntologyFromOntologyDocument(is);
- OWLOntology ontology = OWLManager.createOWLOntologyManager().loadOntologyFromOntologyDocument(in);
-
SPARQLSampleDebugging debug = new SPARQLSampleDebugging(endpoint);
// debug.checkFunctionalityViolation(ontology);
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|
|
From: <lor...@us...> - 2012-01-27 11:51:34
|
Revision: 3558
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3558&view=rev
Author: lorenz_b
Date: 2012-01-27 11:51:28 +0000 (Fri, 27 Jan 2012)
Log Message:
-----------
Small update.
Modified Paths:
--------------
trunk/scripts/src/main/java/org/dllearner/scripts/SPARQLSampleDebugging.java
Modified: trunk/scripts/src/main/java/org/dllearner/scripts/SPARQLSampleDebugging.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/SPARQLSampleDebugging.java 2012-01-26 13:43:13 UTC (rev 3557)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/SPARQLSampleDebugging.java 2012-01-27 11:51:28 UTC (rev 3558)
@@ -1,8 +1,9 @@
package org.dllearner.scripts;
+import java.io.BufferedInputStream;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
-import java.io.File;
+import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.IOException;
@@ -28,6 +29,8 @@
import java.util.TreeSet;
import java.util.prefs.Preferences;
+import org.apache.commons.compress.compressors.CompressorInputStream;
+import org.apache.commons.compress.compressors.CompressorStreamFactory;
import org.apache.log4j.ConsoleAppender;
import org.apache.log4j.FileAppender;
import org.apache.log4j.Level;
@@ -35,7 +38,8 @@
import org.apache.log4j.SimpleLayout;
import org.dllearner.algorithm.qtl.util.ModelGenerator;
import org.dllearner.algorithm.qtl.util.ModelGenerator.Strategy;
-import org.dllearner.core.owl.IrreflexiveObjectPropertyAxiom;
+import org.dllearner.kb.sparql.ConciseBoundedDescriptionGenerator;
+import org.dllearner.kb.sparql.ConciseBoundedDescriptionGeneratorImpl;
import org.dllearner.kb.sparql.ExtractionDBCache;
import org.dllearner.kb.sparql.SparqlEndpoint;
import org.dllearner.kb.sparql.SparqlQuery;
@@ -52,14 +56,18 @@
import org.semanticweb.owlapi.model.OWLDataProperty;
import org.semanticweb.owlapi.model.OWLFunctionalDataPropertyAxiom;
import org.semanticweb.owlapi.model.OWLFunctionalObjectPropertyAxiom;
+import org.semanticweb.owlapi.model.OWLIndividual;
import org.semanticweb.owlapi.model.OWLIrreflexiveObjectPropertyAxiom;
import org.semanticweb.owlapi.model.OWLObjectProperty;
+import org.semanticweb.owlapi.model.OWLObjectPropertyCharacteristicAxiom;
import org.semanticweb.owlapi.model.OWLOntology;
import org.semanticweb.owlapi.model.OWLOntologyCreationException;
import org.semanticweb.owlapi.model.OWLOntologyManager;
import org.semanticweb.owlapi.model.OWLOntologyStorageException;
import org.semanticweb.owlapi.reasoner.InferenceType;
+import uk.ac.manchester.cs.owl.owlapi.OWLDataFactoryImpl;
+
import com.clarkparsia.owlapi.explanation.PelletExplanation;
import com.clarkparsia.owlapi.explanation.io.manchester.ManchesterSyntaxExplanationRenderer;
import com.clarkparsia.pellet.owlapiv3.PelletReasoner;
@@ -85,9 +93,9 @@
private ExtractionDBCache cache = new ExtractionDBCache("cache");
private int sampleSize = 10;
- private int depth = 2;
+ private int depth = 3;
private int nrOfChunks = 1;
- private int maxNrOfExplanations = 20;
+ private int maxNrOfExplanations = 10;
private Logger logger = Logger.getLogger(SPARQLSampleDebugging.class);
@@ -98,6 +106,8 @@
private Connection conn;
private PreparedStatement ps;
+ private OWLDataFactory factory = new OWLDataFactoryImpl();
+
static {PelletExplanation.setup();}
public SPARQLSampleDebugging(SparqlEndpoint endpoint) {
@@ -184,7 +194,7 @@
for(int i = 0; i < nrOfChunks; i++){
int offset = (int)(Math.random() * max);
- offset = Math.min(offset, offset-(size/nrOfChunks));
+ offset = Math.min(offset, offset-(size/nrOfChunks));offset = 236242;
query = String.format("SELECT DISTINCT ?s WHERE {?s a ?type} LIMIT %d OFFSET %d", (size/nrOfChunks), offset);
logger.info(query);
@@ -236,10 +246,11 @@
private OWLOntology extractSampleModule(String resource){
logger.info("Extracting sample module...");
long startTime = System.currentTimeMillis();
- ModelGenerator modelGen = new ModelGenerator(endpoint, cache);
- Model model = modelGen.createModel(resource, Strategy.CHUNKS, depth);
+ ConciseBoundedDescriptionGenerator cbdGen = new ConciseBoundedDescriptionGeneratorImpl(endpoint, cache);
+ Model model = cbdGen.getConciseBoundedDescription(resource, 3);
+ OWLOntology data = convert(model);
logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
- return convert(model);
+ return data;
}
@@ -257,7 +268,13 @@
logger.info("Computing explanations...");
long startTime = System.currentTimeMillis();
PelletExplanation expGen = new PelletExplanation(reasoner);
- Set<Set<OWLAxiom>> explanations = expGen.getInconsistencyExplanations(maxNrOfExplanations);
+ Set<Set<OWLAxiom>> explanations = new HashSet<Set<OWLAxiom>>(maxNrOfExplanations);
+ try {
+ explanations = expGen.getInconsistencyExplanations(maxNrOfExplanations);
+ } catch (Exception e) {
+ e.printStackTrace();
+ logger.error(e);
+ }
logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
return explanations;
}
@@ -279,7 +296,7 @@
long startTime = System.currentTimeMillis();
logger.info("Loading reference ontology...");
OWLOntology ontology = OWLManager.createOWLOntologyManager().loadOntologyFromOntologyDocument(
- getClass().getClassLoader().getResourceAsStream("dbpedia_0.75_no_datapropaxioms.owl"));System.out.println(ontology.getLogicalAxiomCount());
+ getClass().getClassLoader().getResourceAsStream("dbpedia_0.75_no_datapropaxioms.owl"));
logger.info("...done in " + (System.currentTimeMillis()-startTime) + "ms.");
return ontology;
}
@@ -435,16 +452,26 @@
OWLOntologyManager man = OWLManager.createOWLOntologyManager();
man.addOntologyChangeListener( reasoner );
Set<String> resources = extractSampleResourcesChunked(sampleSize);
+ Model model;
for(String resource : resources){
- logger.info("Resource " + resource);resource = "http://dbpedia.org/resource/The_Man_Who_Wouldn%27t_Die";
- module = extractSampleModule(Collections.singleton(resource));computeExplanations(convert(module).add(convert(extractSampleModule(resource))));
+ logger.info("###################################################################");
+ logger.info("Resource " + resource);//resource = "http://dbpedia.org/resource/The_Man_Who_Wouldn%27t_Die";
+ module = extractSampleModule(resource);
man.addAxioms(reference, module.getABoxAxioms(true));
+ man.removeAxioms(reference, reference.getAxioms(AxiomType.DATA_PROPERTY_ASSERTION));
boolean isConsistent = reasoner.isConsistent();
logger.info("Consistent: " + isConsistent);
Set<Set<OWLAxiom>> explanations = null;
if(!isConsistent){
explanations = computeExplanations(reasoner);
+ model = convert(reference);
+ explanations.addAll(computeInconsistencyExplanationsByAsymmetryPattern(reference, model));
+ explanations.addAll(computeInconsistencyExplanationsByIrreflexivityPattern(reference, model));
+ explanations.addAll(computeInconsistencyExplanationsByFunctionalityPattern(reference, model));
logger.info("Found " + explanations.size() + " explanations.");
+ for(Set<OWLAxiom> exp : explanations){
+ logger.info(exp + "\n");
+ }
Map<AxiomType, Integer> axiomType2CountMap = new HashMap<AxiomType, Integer>();
for(Set<OWLAxiom> explanation : explanations){
logger.info(explanation);
@@ -457,13 +484,14 @@
axiomType2CountMap.put(axiom.getAxiomType(), cnt);
}
}
+ logger.info("Axiom type count:");
for(Entry<AxiomType, Integer> entry : axiomType2CountMap.entrySet()){
logger.info(entry.getKey() + "\t: " + entry.getValue());
}
}
man.removeAxioms(reference, module.getABoxAxioms(true));
// writeToDB(resource, module.getLogicalAxiomCount(), isConsistent, explanations);
- break;
+// break;
}
}
@@ -501,10 +529,7 @@
} finally { qexec.close() ; }
}
- public void checkFunctionalityViolation(){
- try {
- OWLOntology ontology = loadReferenceOntology();
-
+ public void checkFunctionalityViolation(OWLOntology ontology){
Set<String> properties = new TreeSet<String>();
for(OWLAxiom ax : ontology.getAxioms(AxiomType.FUNCTIONAL_OBJECT_PROPERTY)){
OWLObjectProperty prop = ((OWLFunctionalObjectPropertyAxiom)ax).getProperty().asOWLObjectProperty();
@@ -526,16 +551,9 @@
}
}
- } catch (OWLOntologyCreationException e) {
- e.printStackTrace();
- }
-
}
- public void checkIrreflexivityViolation(){
- try {
- OWLOntology ontology = loadReferenceOntology();
-
+ public void checkIrreflexivityViolation(OWLOntology ontology){
Set<String> properties = new TreeSet<String>();
for(OWLAxiom ax : ontology.getAxioms(AxiomType.IRREFLEXIVE_OBJECT_PROPERTY)){
OWLObjectProperty prop = ((OWLIrreflexiveObjectPropertyAxiom)ax).getProperty().asOWLObjectProperty();
@@ -552,16 +570,9 @@
}
}
- } catch (OWLOntologyCreationException e) {
- e.printStackTrace();
- }
-
}
- public void checkAsymmetryViolation(){
- try {
- OWLOntology ontology = loadReferenceOntology();
-
+ public void checkAsymmetryViolation(OWLOntology ontology){
Set<String> properties = new TreeSet<String>();
for(OWLAxiom ax : ontology.getAxioms(AxiomType.ASYMMETRIC_OBJECT_PROPERTY)){
OWLObjectProperty prop = ((OWLAsymmetricObjectPropertyAxiom)ax).getProperty().asOWLObjectProperty();
@@ -578,11 +589,102 @@
}
}
- } catch (OWLOntologyCreationException e) {
- e.printStackTrace();
+ }
+
+ private Set<Set<OWLAxiom>> computeInconsistencyExplanationsByFunctionalityPattern(OWLOntology ontology, Model model){
+ Set<Set<OWLAxiom>> explanations = new HashSet<Set<OWLAxiom>>();
+
+ for(OWLObjectProperty prop : extractObjectProperties(AxiomType.FUNCTIONAL_OBJECT_PROPERTY, ontology)){
+ OWLAxiom axiom = factory.getOWLFunctionalObjectPropertyAxiom(prop);
+ String queryString = "SELECT DISTINCT * WHERE {?s <%s> ?o1. ?s <%s> ?o2. FILTER(?o1 != ?o2)}".replace("%s", prop.toStringID());
+ Query query = QueryFactory.create(queryString) ;
+ QueryExecution qexec = QueryExecutionFactory.create(query, model) ;
+ try {
+ ResultSet results = qexec.execSelect();
+ for (; results.hasNext();) {
+ Set<OWLAxiom> explanation = new HashSet<OWLAxiom>();
+ explanation.add(axiom);
+ QuerySolution qs = results.next();
+ OWLIndividual subject = factory.getOWLNamedIndividual(IRI.create(qs.getResource("s").getURI()));
+ OWLIndividual object1 = factory.getOWLNamedIndividual(IRI.create(qs.getResource("o1").getURI()));
+ OWLIndividual object2 = factory.getOWLNamedIndividual(IRI.create(qs.getResource("o2").getURI()));
+ OWLAxiom ax = factory.getOWLObjectPropertyAssertionAxiom(prop, subject, object1);
+ explanation.add(ax);
+ ax = factory.getOWLObjectPropertyAssertionAxiom(prop, subject, object2);
+ explanation.add(ax);
+ explanations.add(explanation);
+ }
+ } finally {
+ qexec.close();
+ }
}
+ return explanations;
}
+ private Set<Set<OWLAxiom>> computeInconsistencyExplanationsByAsymmetryPattern(OWLOntology ontology, Model model){
+ Set<Set<OWLAxiom>> explanations = new HashSet<Set<OWLAxiom>>();
+
+ for(OWLObjectProperty prop : extractObjectProperties(AxiomType.ASYMMETRIC_OBJECT_PROPERTY, ontology)){
+ OWLAxiom axiom = factory.getOWLAsymmetricObjectPropertyAxiom(prop);
+ String queryString = "SELECT * WHERE {?s <%s> ?o. ?o <%s> ?s. FILTER(?o != ?s)}".replace("%s", prop.toStringID());
+ Query query = QueryFactory.create(queryString) ;
+ QueryExecution qexec = QueryExecutionFactory.create(query, model) ;
+ try {
+ ResultSet results = qexec.execSelect();
+ for (; results.hasNext();) {
+ Set<OWLAxiom> explanation = new HashSet<OWLAxiom>();
+ explanation.add(axiom);
+ QuerySolution qs = results.nextSolution();
+ OWLIndividual subject = factory.getOWLNamedIndividual(IRI.create(qs.getResource("s").getURI()));
+ OWLIndividual object = factory.getOWLNamedIndividual(IRI.create(qs.getResource("o").getURI()));
+ OWLAxiom ax = factory.getOWLObjectPropertyAssertionAxiom(prop, subject, object);
+ explanation.add(ax);
+ ax = factory.getOWLObjectPropertyAssertionAxiom(prop, object, subject);
+ explanation.add(ax);
+ explanations.add(explanation);
+ }
+ } finally {
+ qexec.close();
+ }
+ }
+ return explanations;
+ }
+
+ private Set<Set<OWLAxiom>> computeInconsistencyExplanationsByIrreflexivityPattern(OWLOntology ontology, Model model){
+ Set<Set<OWLAxiom>> explanations = new HashSet<Set<OWLAxiom>>();
+
+ for(OWLObjectProperty prop : extractObjectProperties(AxiomType.IRREFLEXIVE_OBJECT_PROPERTY, ontology)){
+ OWLAxiom axiom = factory.getOWLIrreflexiveObjectPropertyAxiom(prop);
+ String queryString = "SELECT * WHERE {?s <%s> ?s.}".replace("%s", prop.toStringID());
+ Query query = QueryFactory.create(queryString) ;
+ QueryExecution qexec = QueryExecutionFactory.create(query, model) ;
+ try {
+ ResultSet results = qexec.execSelect();
+ for (; results.hasNext();) {
+ Set<OWLAxiom> explanation = new HashSet<OWLAxiom>();
+ explanation.add(axiom);
+ QuerySolution qs = results.nextSolution();
+ OWLIndividual subject = factory.getOWLNamedIndividual(IRI.create(qs.getResource("s").getURI()));
+ OWLAxiom ax = factory.getOWLObjectPropertyAssertionAxiom(prop, subject, subject);
+ explanation.add(ax);
+ explanations.add(explanation);
+ }
+ } finally {
+ qexec.close();
+ }
+ }
+ return explanations;
+ }
+
+ private SortedSet<OWLObjectProperty> extractObjectProperties(AxiomType<? extends OWLAxiom> axiomType, OWLOntology ontology){
+ SortedSet<OWLObjectProperty> properties = new TreeSet<OWLObjectProperty>();
+ for(OWLAxiom ax : ontology.getAxioms(axiomType)){
+ properties.add(((OWLObjectPropertyCharacteristicAxiom)ax).getProperty().asOWLObjectProperty());
+ }
+// properties.retainAll(data.getObjectPropertiesInSignature());
+ return properties;
+ }
+
public void removeAxiomsWithNamespace(Set<String> namespaces){
}
@@ -611,24 +713,28 @@
System.exit(0);
}
- OWLOntology ontology = OWLManager.createOWLOntologyManager().loadOntologyFromOntologyDocument(IRI.create(new File(args[0]).toURI()));
+ InputStream is = new BufferedInputStream(new FileInputStream(args[0]));
+ CompressorInputStream in = new CompressorStreamFactory().createCompressorInputStream("bzip2", is);
+ OWLOntology ontology = OWLManager.createOWLOntologyManager().loadOntologyFromOntologyDocument(in);
+
SPARQLSampleDebugging debug = new SPARQLSampleDebugging(endpoint);
- debug.checkFunctionalityViolation();
- debug.checkAsymmetryViolation();
- debug.checkIrreflexivityViolation();
+// debug.checkFunctionalityViolation(ontology);
+// debug.checkAsymmetryViolation(ontology);
+// debug.checkIrreflexivityViolation(ontology);
long s1 = System.currentTimeMillis();
debug.runOptimized(ontology);
long s2 = System.currentTimeMillis()-s1;
+ System.out.println(s2);
- long s3 = System.currentTimeMillis();
+ /*long s3 = System.currentTimeMillis();
debug.run(ontology);
long s4 = System.currentTimeMillis()-s3;
System.out.println(s2);
- System.out.println(s4);
+ System.out.println(s4);*/
}
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