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[DL-Learner SVN] SF.net SVN: dl-learner:[3853] branches/hmm
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From: <ki...@us...> - 2012-09-27 16:33:19
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Revision: 3853
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3853&view=rev
Author: kirdie
Date: 2012-09-27 16:33:12 +0000 (Thu, 27 Sep 2012)
Log Message:
-----------
reintegrated the old approach to the learner2.
Modified Paths:
--------------
branches/hmm/components-core/src/main/java/org/dllearner/kb/sparql/ExtractionDBCache.java
branches/hmm/components-ext/pom.xml
branches/hmm/components-ext/src/main/java/org/dllearner/algorithm/tbsl/learning/SPARQLTemplateBasedLearner2.java
branches/hmm/components-ext/src/test/java/org/dllearner/algorithm/tbsl/learning/QueryTestData.java
branches/hmm/components-ext/src/test/java/org/dllearner/algorithm/tbsl/learning/SPARQLTemplateBasedLearner3Test.java
Modified: branches/hmm/components-core/src/main/java/org/dllearner/kb/sparql/ExtractionDBCache.java
===================================================================
--- branches/hmm/components-core/src/main/java/org/dllearner/kb/sparql/ExtractionDBCache.java 2012-09-27 13:18:05 UTC (rev 3852)
+++ branches/hmm/components-core/src/main/java/org/dllearner/kb/sparql/ExtractionDBCache.java 2012-09-27 16:33:12 UTC (rev 3853)
@@ -31,9 +31,7 @@
import java.sql.ResultSet;
import java.sql.SQLException;
import java.sql.Statement;
-
import org.dllearner.utilities.Helper;
-
import com.hp.hpl.jena.query.ResultSetFactory;
import com.hp.hpl.jena.query.ResultSetRewindable;
import com.hp.hpl.jena.rdf.model.Model;
Modified: branches/hmm/components-ext/pom.xml
===================================================================
--- branches/hmm/components-ext/pom.xml 2012-09-27 13:18:05 UTC (rev 3852)
+++ branches/hmm/components-ext/pom.xml 2012-09-27 16:33:12 UTC (rev 3853)
@@ -34,10 +34,10 @@
<groupId>com.jamonapi</groupId>
<artifactId>jamon</artifactId>
</dependency>
- <dependency>
+ <!-- <dependency>
<groupId>org.aksw.commons</groupId>
<artifactId>sparql</artifactId>
- </dependency>
+ </dependency> -->
<dependency>
<groupId>org.apache.solr</groupId>
Modified: branches/hmm/components-ext/src/main/java/org/dllearner/algorithm/tbsl/learning/SPARQLTemplateBasedLearner2.java
===================================================================
--- branches/hmm/components-ext/src/main/java/org/dllearner/algorithm/tbsl/learning/SPARQLTemplateBasedLearner2.java 2012-09-27 13:18:05 UTC (rev 3852)
+++ branches/hmm/components-ext/src/main/java/org/dllearner/algorithm/tbsl/learning/SPARQLTemplateBasedLearner2.java 2012-09-27 16:33:12 UTC (rev 3853)
@@ -9,15 +9,20 @@
import java.util.Comparator;
import java.util.HashMap;
import java.util.HashSet;
+import java.util.Iterator;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Set;
-import java.util.SortedMap;
import java.util.SortedSet;
import java.util.TreeMap;
import java.util.TreeSet;
+import java.util.concurrent.Callable;
+import java.util.concurrent.ExecutionException;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
+import java.util.concurrent.Future;
import org.apache.commons.collections15.MultiMap;
import org.apache.log4j.Logger;
import org.dllearner.algorithm.tbsl.nlp.Lemmatizer;
@@ -49,7 +54,6 @@
import org.dllearner.common.index.IndexResultItem;
import org.dllearner.common.index.IndexResultSet;
import org.dllearner.common.index.MappingBasedIndex;
-import org.dllearner.common.index.SOLRIndex;
import org.dllearner.common.index.SPARQLDatatypePropertiesIndex;
import org.dllearner.common.index.SPARQLIndex;
import org.dllearner.common.index.SPARQLObjectPropertiesIndex;
@@ -70,7 +74,6 @@
import org.dllearner.kb.sparql.SparqlEndpoint;
import org.dllearner.kb.sparql.SparqlQuery;
import org.dllearner.reasoning.SPARQLReasoner;
-import org.ini4j.InvalidFileFormatException;
import org.ini4j.Options;
import org.semanticweb.owlapi.model.IRI;
import org.semanticweb.owlapi.util.SimpleIRIShortFormProvider;
@@ -83,10 +86,6 @@
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
import com.hp.hpl.jena.sparql.engine.http.QueryEngineHTTP;
-import com.hp.hpl.jena.sparql.expr.ExprAggregator;
-import com.hp.hpl.jena.sparql.expr.ExprVar;
-import com.hp.hpl.jena.sparql.expr.aggregate.AggCount;
-import com.hp.hpl.jena.sparql.expr.aggregate.Aggregator;
import com.jamonapi.Monitor;
import com.jamonapi.MonitorFactory;
@@ -95,19 +94,18 @@
* */
public class SPARQLTemplateBasedLearner2 implements SparqlQueryLearningAlgorithm
{
- public static boolean useHMM = true;
-
+ private static final boolean USE_HMM = false;
+ /** synonyms are great but are not used yet by the HMM algorithm. **/
+ private static final boolean HMM_USE_SYNONYMS = false;
+ /** The minimum score of items that are accepted from the Sindice search BOA index. **/
+ private static final Double BOA_THRESHOLD = 0.9;
enum Mode {BEST_QUERY, BEST_NON_EMPTY_QUERY}
private Mode mode = Mode.BEST_QUERY;
/** used to create a label out of the URI when there is no label available in the SPARQL endpoint.*/
private static SimpleIRIShortFormProvider sfp = new SimpleIRIShortFormProvider();
+ private static final Logger logger = Logger.getLogger(SPARQLTemplateBasedLearner2.class);
- private static final Logger logger = Logger.getLogger(SPARQLTemplateBasedLearner2.class);
- /** synonyms are great but are not used yet by the HMM algorithm. **/
- private static final boolean CREATE_SYNONYMS = false;
- /** The minimum score of items that are accepted from the Sindice search BOA index. **/
- private static final Double BOA_THRESHOLD = 0.9;
private Monitor templateMon = MonitorFactory.getTimeMonitor("template");
private Monitor sparqlMon = MonitorFactory.getTimeMonitor("sparql");
@@ -403,7 +401,7 @@
logger.debug("Generating SPARQL query templates...");
templateMon.start();
if(multiThreaded){
- templates = templateGenerator.buildTemplatesMultiThreaded(question,CREATE_SYNONYMS);
+ templates = templateGenerator.buildTemplatesMultiThreaded(question,!USE_HMM||HMM_USE_SYNONYMS);
} else {
templates = templateGenerator.buildTemplates(question);
}
@@ -420,7 +418,7 @@
}
//get the weighted query candidates
- generatedQueries = getWeightedSPARQLQueries(templates);
+ generatedQueries = getWeightedSPARQLQueries(templates,USE_HMM);
sparqlQueryCandidates = new ArrayList<WeightedQuery>();
int i = 0;
for(WeightedQuery wQ : generatedQueries){
@@ -519,13 +517,15 @@
}
- public Set<String> getRelevantKeywords(){
- return relevantKeywords;
- }
+ public Set<String> getRelevantKeywords(){return relevantKeywords;}
- // just for testing the HMM integration, getWeightedSPARQLQueriesOld is the original one
- private SortedSet<WeightedQuery> getWeightedSPARQLQueries(Set<Template> templates)
+ private SortedSet<WeightedQuery> getWeightedSPARQLQueries(Set<Template> templates, boolean hmm)
{
+ return hmm?getWeightedSPARQLQueriesWithHMM(templates):getWeightedSPARQLQueriesWithoutHMM(templates);
+ }
+
+ private SortedSet<WeightedQuery> getWeightedSPARQLQueriesWithHMM(Set<Template> templates)
+ {
// for testing
for(Template template: templates)
{
@@ -621,7 +621,7 @@
return null;
}
- private SortedSet<WeightedQuery> getWeightedSPARQLQueriesOld(Set<Template> templates){
+ private SortedSet<WeightedQuery> getWeightedSPARQLQueriesWithoutHMM(Set<Template> templates){
logger.debug("Generating SPARQL query candidates...");
Map<Slot, Set<Allocation>> slot2Allocations = new TreeMap<Slot, Set<Allocation>>(new Comparator<Slot>() {
@@ -1295,6 +1295,7 @@
}
return indexResultItems;
}
+
class SlotProcessor implements Callable<Map<Slot, SortedSet<Allocation>>>{
private Slot slot;
Modified: branches/hmm/components-ext/src/test/java/org/dllearner/algorithm/tbsl/learning/QueryTestData.java
===================================================================
--- branches/hmm/components-ext/src/test/java/org/dllearner/algorithm/tbsl/learning/QueryTestData.java 2012-09-27 13:18:05 UTC (rev 3852)
+++ branches/hmm/components-ext/src/test/java/org/dllearner/algorithm/tbsl/learning/QueryTestData.java 2012-09-27 16:33:12 UTC (rev 3853)
@@ -11,7 +11,6 @@
import java.io.ObjectOutputStream;
import java.io.PrintWriter;
import java.io.Serializable;
-import java.io.StringWriter;
import java.util.Collection;
import java.util.HashSet;
import java.util.Set;
@@ -37,11 +36,11 @@
public class QueryTestData implements Serializable
{
+ private static final long serialVersionUID = 1L;
public SortedMap<Integer, String> id2Question = new ConcurrentSkipListMap<Integer, String>();
public SortedMap<Integer, String> id2Query = new ConcurrentSkipListMap<Integer, String>();
public SortedMap<Integer, Set<String>> id2Answers = new ConcurrentSkipListMap<Integer, Set<String>>();
public SortedMap<Integer, LearnStatus> id2LearnStatus = new ConcurrentSkipListMap<Integer, LearnStatus>();
- private static final int MAXIMUM_QUESTIONS = Integer.MAX_VALUE;
private static final String persistancePath = "cache/"+SPARQLTemplateBasedLearner3Test.class.getSimpleName()+'/'+QueryTestData.class.getSimpleName();
@@ -85,8 +84,9 @@
/** reads test data from a QALD2 benchmark XML file, including questions, queries and answers.
* each question needs to have a query but not necessarily an answer.
* @param file a QALD benchmark XML file
+ * @param MAX_NUMBER_OF_QUESTIONS the maximum number of questions read from the file.
* @return the test data read from the XML file */
- public static QueryTestData readQaldXml(final File file)
+ public static QueryTestData readQaldXml(final File file, int MAX_NUMBER_OF_QUESTIONS)
{
QueryTestData testData = new QueryTestData();
try {
@@ -99,7 +99,7 @@
for(int i = 0; i < questionNodes.getLength(); i++)
{
- if(i>=MAXIMUM_QUESTIONS) break; // TODO: remove later?
+ if(i>MAX_NUMBER_OF_QUESTIONS) break;
String question;
String query;
Set<String> answers = new HashSet<String>();
Modified: branches/hmm/components-ext/src/test/java/org/dllearner/algorithm/tbsl/learning/SPARQLTemplateBasedLearner3Test.java
===================================================================
--- branches/hmm/components-ext/src/test/java/org/dllearner/algorithm/tbsl/learning/SPARQLTemplateBasedLearner3Test.java 2012-09-27 13:18:05 UTC (rev 3852)
+++ branches/hmm/components-ext/src/test/java/org/dllearner/algorithm/tbsl/learning/SPARQLTemplateBasedLearner3Test.java 2012-09-27 16:33:12 UTC (rev 3853)
@@ -55,7 +55,6 @@
import org.dllearner.algorithm.tbsl.nlp.WordNet;
import org.dllearner.algorithm.tbsl.templator.Templator;
import org.dllearner.algorithm.tbsl.util.Knowledgebase;
-import org.dllearner.common.index.HierarchicalIndex;
import org.dllearner.common.index.Index;
import org.dllearner.common.index.MappingBasedIndex;
import org.dllearner.common.index.SOLRIndex;
@@ -104,6 +103,7 @@
private static final File evaluationFolder = new File("cache/evaluation");
private static final boolean DBPEDIA_PRETAGGED = true;
private static final boolean OXFORD_PRETAGGED = false;
+ private static final int MAX_NUMBER_OF_QUESTIONS = 10;
@Test public void testDBpedia() throws Exception
{
@@ -120,28 +120,28 @@
test("Oxford 19 working questions", file,null,null,null,loadOxfordModel(),getOxfordMappingIndex());
}
-// /*@Test*/ public void testOxford() throws Exception
-// {
-// Model model = loadOxfordModel();
-// QueryTestData testData = QueryTestData.readQaldXml(new File("log/oxford_working_questions.xml"));
-// // answers are not included at least in the first query TODO: check, why
-// testData.generateAnswers(null, null, model);
-// QueryTestData newTestData = generateTestDataMultiThreaded(testData.id2Question, null, model,getOxfordMappingIndex() , OXFORD_PRETAGGED);
-// newTestData.generateAnswers(null, null, model);
-// for(int i : testData.id2Question.keySet())
-// {
-// logger.info("Comparing answers for question "+testData.id2Question.get(i));
-// String referenceQuery = testData.id2Query.get(i);
-// String newQuery = newTestData.id2Query.get(i);
-// if(!referenceQuery.equals(newQuery))
-// {
-// logger.warn("not equal, reference query: "+referenceQuery+", new query: "+newQuery);
-// Collection<String> referenceAnswers = testData.id2Answers.get(i);
-// Collection<String> newAnswers = newTestData.id2Answers.get(i);
-// if(!referenceAnswers.equals(newAnswers)) fail("not equal, reference answers: "+referenceAnswers+", new answers: "+newAnswers);
-// }
-// }
-// }
+ // /*@Test*/ public void testOxford() throws Exception
+ // {
+ // Model model = loadOxfordModel();
+ // QueryTestData testData = QueryTestData.readQaldXml(new File("log/oxford_working_questions.xml"));
+ // // answers are not included at least in the first query TODO: check, why
+ // testData.generateAnswers(null, null, model);
+ // QueryTestData newTestData = generateTestDataMultiThreaded(testData.id2Question, null, model,getOxfordMappingIndex() , OXFORD_PRETAGGED);
+ // newTestData.generateAnswers(null, null, model);
+ // for(int i : testData.id2Question.keySet())
+ // {
+ // logger.info("Comparing answers for question "+testData.id2Question.get(i));
+ // String referenceQuery = testData.id2Query.get(i);
+ // String newQuery = newTestData.id2Query.get(i);
+ // if(!referenceQuery.equals(newQuery))
+ // {
+ // logger.warn("not equal, reference query: "+referenceQuery+", new query: "+newQuery);
+ // Collection<String> referenceAnswers = testData.id2Answers.get(i);
+ // Collection<String> newAnswers = newTestData.id2Answers.get(i);
+ // if(!referenceAnswers.equals(newAnswers)) fail("not equal, reference answers: "+referenceAnswers+", new answers: "+newAnswers);
+ // }
+ // }
+ // }
/** For debugging one question in particular.
*/
@@ -164,23 +164,23 @@
*/
/*@Test*/ public void testSingleQueryDBpedia()
{
-// Logger.getLogger(Templator.class).setLevel(Level.DEBUG);
-// Logger.getLogger(Parser.class).setLevel(Level.DEBUG);
-// Logger.getLogger(SPARQLTemplateBasedLearner2.class).setLevel(Level.DEBUG);
+ // Logger.getLogger(Templator.class).setLevel(Level.DEBUG);
+ // Logger.getLogger(Parser.class).setLevel(Level.DEBUG);
+ // Logger.getLogger(SPARQLTemplateBasedLearner2.class).setLevel(Level.DEBUG);
// String question = "houses for less than 900000 pounds";
String question = "Give/VB me/PRP all/DT video/JJ games/NNS published/VBN by/IN Mean/NNP Hamster/NNP Software/NNP";
-// String question = "give me all video games published by mean hamster software";
-// String question = "Give me all video games published by Mean Hamster Software";
-// question = new StanfordPartOfSpeechTagger().tag(question);
-// System.out.println(question);
+ // String question = "give me all video games published by mean hamster software";
+ // String question = "Give me all video games published by Mean Hamster Software";
+ // question = new StanfordPartOfSpeechTagger().tag(question);
+ // System.out.println(question);
-// Model model = loadOxfordModel();
+ // Model model = loadOxfordModel();
QueryTestData testData = new QueryTestData();
new LearnQueryCallable(question, 0, testData, dbpediaLiveKnowledgebase, true).call();
logger.info("learned query: "+testData.id2Query.get(0));
}
-
- /*@Test*/ public void generateXMLOxford() throws IOException
+
+ /*@Test*/ public void generateXMLOxford() throws IOException
{
boolean ADD_POS_TAGS = true;
PartOfSpeechTagger posTagger = null;
@@ -192,7 +192,7 @@
for(String line;(line=in.readLine())!=null;)
{
j++;
- // if(j>5) break; // TODO: remove later
+ if(j>5) break; // TODO: remove later
String question = line.replace("question: ", "").trim();
if(ADD_POS_TAGS&&!OXFORD_PRETAGGED) {question = posTagger.tag(question);}
if(!line.trim().isEmpty()) {questions.add(question);}
@@ -291,7 +291,7 @@
public void test(String title, final File referenceXML,final SparqlEndpoint endpoint,ExtractionDBCache cache,Knowledgebase kb, Model model, MappingBasedIndex index)
throws ParserConfigurationException, SAXException, IOException, TransformerException, ComponentInitException, NoTemplateFoundException
- {
+ {
evaluateAndWrite(title,referenceXML,endpoint,cache,kb,model,index);
generateHTML(title);
@@ -318,7 +318,7 @@
logger.info("Old test data not loadable, creating it and exiting.");
}
learnedTestData.write();*/
- }
+ }
private File generateTestDataIfNecessary(final File referenceXML,final SparqlEndpoint endpoint,ExtractionDBCache cache) throws ParserConfigurationException, SAXException, IOException, TransformerException
{
@@ -335,9 +335,10 @@
}
private void evaluateAndWrite(String title,final File updatedReferenceXML, final SparqlEndpoint endpoint,ExtractionDBCache cache,
- Knowledgebase kb, Model model, MappingBasedIndex index)
+ Knowledgebase kb, Model model, MappingBasedIndex index)
{
- QueryTestData referenceTestData = QueryTestData.readQaldXml(updatedReferenceXML);
+
+ QueryTestData referenceTestData = QueryTestData.readQaldXml(updatedReferenceXML,MAX_NUMBER_OF_QUESTIONS);
logger.info(title+" subset loaded with "+referenceTestData.id2Question.size()+" questions.");
long startLearning = System.currentTimeMillis();
@@ -352,11 +353,6 @@
evaluation.write();
}
- private void evaluateAndWrite()
- {
-
- }
-
/** evaluates a data set against a reference.
* @param reference the test data assumed to be correct. needs to contain the answers for all queries.
* @param suspect the test data to compare with the reference.
@@ -673,8 +669,8 @@
// try {testData.id2Answers.put(i,getUris(endpoint, learnedQuery));}
// catch(Exception e) {logger.warn("Error with learned query "+learnedQuery+" for question "+question+" at endpoint "+endpoint+": "+e.getLocalizedMessage());}
- long end = System.currentTimeMillis();
- // logger.debug(String.format("Generated query \"%s\" after %d ms", learnedQuery,end-start));
+ // long end = System.currentTimeMillis();
+ // logger.trace(String.format("Generated query \"%s\" after %d ms", learnedQuery,end-start));
// logger.info(String.format("Learned queries for %d of %d questions.",successes,id2Question.size()));
@@ -779,7 +775,7 @@
// int successfullTestThreadRuns = 0;
/** */
- private static final String DBPEDIA_LIVE_ENDPOINT_URL_STRING = "http://live.dbpedia.org/sparql";
+ // private static final String DBPEDIA_LIVE_ENDPOINT_URL_STRING = "http://live.dbpedia.org/sparql";
private static final Logger logger = Logger.getLogger(SPARQLTemplateBasedLearner3Test.class);
@@ -806,7 +802,7 @@
Index propertiesIndex = new SOLRIndex("http://dbpedia.aksw.org:8080/solr/dbpedia_properties");
SOLRIndex boa_propertiesIndex = new SOLRIndex("http://139.18.2.173:8080/solr/boa_fact_detail");
boa_propertiesIndex.setSortField("boa-score");
-// propertiesIndex = new HierarchicalIndex(boa_propertiesIndex, propertiesIndex);
+ // propertiesIndex = new HierarchicalIndex(boa_propertiesIndex, propertiesIndex);
MappingBasedIndex mappingIndex= new MappingBasedIndex(
SPARQLTemplateBasedLearner2.class.getClassLoader().getResource("test/dbpedia_class_mappings.txt").getPath(),
SPARQLTemplateBasedLearner2.class.getClassLoader().getResource("test/dbpedia_resource_mappings.txt").getPath(),
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