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[DL-Learner SVN] SF.net SVN: dl-learner: [457] trunk/src/dl-learner/org/dllearner
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From: <jen...@us...> - 2008-01-29 19:24:54
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Revision: 457
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=457&view=rev
Author: jenslehmann
Date: 2008-01-29 11:24:02 -0800 (Tue, 29 Jan 2008)
Log Message:
-----------
- started to rewrite Cache such that it can be used for arbitrary SPARQL queries (i.e. not only in the extraction algorithm)
- not working yet
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlKnowledgeSource.java
trunk/src/dl-learner/org/dllearner/kb/sparql/TypedSparqlQuery.java
trunk/src/dl-learner/org/dllearner/kb/sparql/TypedSparqlQueryClasses.java
trunk/src/dl-learner/org/dllearner/kb/sparql/test/JenaQueryToResultSpeedTest.java
trunk/src/dl-learner/org/dllearner/kb/sparql/test/TestResultSet.java
trunk/src/dl-learner/org/dllearner/server/ClientState.java
trunk/src/dl-learner/org/dllearner/server/DLLearnerWS.java
Added Paths:
-----------
trunk/src/dl-learner/org/dllearner/kb/sparql/Cache.java
trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQuery.java
Removed Paths:
-------------
trunk/src/dl-learner/org/dllearner/kb/sparql/query/
Copied: trunk/src/dl-learner/org/dllearner/kb/sparql/Cache.java (from rev 456, trunk/src/dl-learner/org/dllearner/kb/sparql/query/Cache.java)
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/Cache.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/Cache.java 2008-01-29 19:24:02 UTC (rev 457)
@@ -0,0 +1,254 @@
+/**
+ * Copyright (C) 2007-2008, Jens Lehmann
+ *
+ * This file is part of DL-Learner.
+ *
+ * DL-Learner is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * DL-Learner is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+package org.dllearner.kb.sparql;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.ObjectInputStream;
+import java.io.ObjectOutputStream;
+import java.io.Serializable;
+import java.security.MessageDigest;
+import java.security.NoSuchAlgorithmException;
+import java.util.HashMap;
+
+import org.apache.log4j.Logger;
+
+import com.hp.hpl.jena.query.ResultSet;
+
+/**
+ * SPARQL query cache to avoid possibly expensive multiple queries. The queries
+ * and their results are written to files. A cache has an associated cache
+ * directory where all files are written.
+ *
+ * Each SPARQL query and its result is written to one file. The name of this
+ * file is a hash of the query. The result of the query is written as JSON
+ * serialisation of the SPARQL XML result, see
+ * http://www.w3.org/TR/rdf-sparql-json-res/.
+ *
+ * Apart from the query and its result, a timestamp of the query is stored.
+ * After a configurable amount of time, query results are considered outdated.
+ * If a cached result of a SPARQL query exists, but is too old, the cache
+ * behaves as if the cached result would not exist.
+ *
+ * @author Sebastian Hellmann
+ * @author Sebastian Knappe
+ * @author Jens Lehmann
+ */
+public class Cache implements Serializable {
+
+ private static Logger logger = Logger.getLogger(Cache.class);
+
+ private static final long serialVersionUID = 843308736471742205L;
+
+ // maps hash of a SPARQL queries to JSON representation
+ // of its results; this
+ private HashMap<String, String> hm;
+
+ private transient String cacheDir = "";
+ private transient String fileEnding = ".cache";
+ private long timestamp;
+
+ // specifies after how many seconds a cached result becomes invalid
+ private long freshnessSeconds = 15 * 24 * 60 * 60;
+
+ /**
+ * Constructor for the cache itself.
+ *
+ * @param cacheDir
+ * Where the base path to the cache is .
+ */
+ public Cache(String cacheDir) {
+ this.cacheDir = cacheDir + File.separator;
+ if (!new File(cacheDir).exists()) {
+ logger
+ .info("Created directory: " + cacheDir + " : " + new File(cacheDir).mkdir()
+ + ".");
+ }
+ }
+
+ /**
+ * constructor for single cache object(one entry)
+ *
+ * @param sparqlQuery
+ * query
+ * @param content
+ * that is the sparql query result as xml
+ */
+ private Cache(String sparqlQuery, String content) {
+ // this.content = c;
+ // this.sparqlquery = sparql;
+ this.timestamp = System.currentTimeMillis();
+ this.hm = new HashMap<String, String>();
+ hm.put(sparqlQuery, content);
+ }
+
+ private String getHash(String string) {
+ // calculate md5 hash of the string (code is somewhat
+ // difficult to read, but there doesn't seem to be a
+ // single function call in Java for md5 hashing)
+ MessageDigest md5 = null;
+ try {
+ md5 = MessageDigest.getInstance("MD5");
+ } catch (NoSuchAlgorithmException e) {
+ e.printStackTrace();
+ }
+ md5.reset();
+ md5.update(string.getBytes());
+ byte[] result = md5.digest();
+
+ StringBuffer hexString = new StringBuffer();
+ for (int i = 0; i < result.length; i++) {
+ hexString.append(Integer.toHexString(0xFF & result[i]));
+ }
+ return hexString.toString();
+ }
+
+ private String getFilename(String sparqlQuery) {
+ return getHash(sparqlQuery) + fileEnding;
+ }
+
+ /**
+ * Gets the query result for a SPARQL query.
+ *
+ * @param sparqlQuery
+ * SPARQL query to check.
+ * @return Query result or null if no result has been found or it is
+ * outdated.
+ */
+ public String get(String sparqlQuery) {
+ Cache c = readFromFile(getFilename(sparqlQuery));
+ if (c == null)
+ return null;
+ // System.out.println(" file found");
+ if (!c.checkFreshness())
+ return null;
+ // System.out.println("fresh");
+ String xml = "";
+ try {
+ xml = c.hm.get(sparqlQuery);
+ } catch (Exception e) {
+ return null;
+ }
+ return xml;
+ }
+
+ /**
+ * @param key
+ * is the resource, the identifier
+ * @param sparqlquery
+ * is the query used as another identifier
+ * @param content
+ * is the result of the query
+ */
+ public void put(String sparqlQuery, String content) {
+ String hash = getHash(sparqlQuery);
+ Cache c = readFromFile(hash);
+ if (c == null) {
+ c = new Cache(sparqlQuery, content);
+ putIntoFile(hash, c);
+ } else {
+ c.hm.put(sparqlQuery, content);
+ putIntoFile(hash, c);
+ }
+
+ }
+
+ public void checkFile(String Filename) {
+ if (!new File(Filename).exists()) {
+ try {
+ new File(Filename).createNewFile();
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ }
+
+ }
+
+ /**
+ * puts a cache entry in a file
+ *
+ * @param filename
+ * @param c
+ */
+ protected void putIntoFile(String filename, Cache c) {
+ try {
+ // FileWriter fw=new FileWriter(new File(Filename),true);
+ FileOutputStream fos = new FileOutputStream(filename, false);
+ ObjectOutputStream o = new ObjectOutputStream(fos);
+ o.writeObject(c);
+ fos.flush();
+ fos.close();
+ } catch (Exception e) {
+ System.out.println("Not in cache creating: " + filename);
+ }
+ }
+
+ /**
+ * reads a cache entry from a file
+ *
+ * @param Filename
+ * @return cache entry
+ */
+ protected Cache readFromFile(String Filename) {
+ Cache content = null;
+ try {
+ FileInputStream fos = new FileInputStream(Filename);
+ ObjectInputStream o = new ObjectInputStream(fos);
+ content = (Cache) o.readObject();
+ } catch (IOException e) {
+ e.printStackTrace();
+ } catch (ClassNotFoundException e) {
+ e.printStackTrace();
+ }
+ return content;
+ }
+
+ private boolean checkFreshness() {
+ if ((System.currentTimeMillis() - this.timestamp) <= (freshnessSeconds * 1000))
+ // fresh
+ return true;
+ else
+ return false;
+ }
+
+ /**
+ * Takes a SPARQL query (which has not been evaluated yet) as argument and
+ * returns a result set. The result set is taken from this cache if the
+ * query is stored here. Otherwise the query is send and its result added to
+ * the cache and returned. Convenience method.
+ *
+ * @param query
+ * The SPARQL query.
+ * @return Jena result set.
+ */
+ public ResultSet executeSparqlQuery(SparqlQuery query) {
+ if (hm.containsKey(query.getQueryString())) {
+ String result = hm.get(query.getQueryString());
+ return SparqlQuery.JSONtoResultSet(result);
+ } else {
+ query.send();
+ return query.getResultSet();
+ }
+ }
+
+}
Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlKnowledgeSource.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlKnowledgeSource.java 2008-01-29 17:34:13 UTC (rev 456)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlKnowledgeSource.java 2008-01-29 19:24:02 UTC (rev 457)
@@ -46,7 +46,6 @@
import org.dllearner.core.dl.KB;
import org.dllearner.kb.sparql.configuration.SparqlEndpoint;
import org.dllearner.kb.sparql.configuration.SparqlQueryType;
-import org.dllearner.kb.sparql.query.SparqlQuery;
import org.dllearner.parser.KBParser;
import org.dllearner.reasoning.DIGConverter;
import org.dllearner.reasoning.JenaOWLDIGConverter;
Copied: trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQuery.java (from rev 456, trunk/src/dl-learner/org/dllearner/kb/sparql/query/SparqlQuery.java)
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQuery.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlQuery.java 2008-01-29 19:24:02 UTC (rev 457)
@@ -0,0 +1,204 @@
+/**
+ * Copyright (C) 2007-2008, Jens Lehmann
+ *
+ * This file is part of DL-Learner.
+ *
+ * DL-Learner is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * DL-Learner is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+package org.dllearner.kb.sparql;
+
+import java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
+import java.nio.charset.Charset;
+import java.util.Iterator;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.dllearner.kb.sparql.configuration.SparqlEndpoint;
+
+import com.hp.hpl.jena.query.ResultSet;
+import com.hp.hpl.jena.query.ResultSetFactory;
+import com.hp.hpl.jena.query.ResultSetFormatter;
+import com.hp.hpl.jena.sparql.core.ResultBinding;
+import com.hp.hpl.jena.sparql.engine.http.QueryEngineHTTP;
+
+/**
+ * Represents one SPARQL query. It includes support for stopping the SPARQL
+ * query (which may be necessary if a timeout is reached).
+ *
+ * @author Jens Lehmann
+ *
+ */
+public class SparqlQuery {
+
+ private static Logger logger = Logger.getLogger(SparqlKnowledgeSource.class);
+
+ private boolean isRunning = false;
+ // TODO: declare as private
+ protected String queryString;
+ private QueryEngineHTTP queryExecution;
+ private SparqlEndpoint endpoint;
+ // TODO: declare as private
+ protected ResultSet rs = null;
+
+ /**
+ * Standard constructor.
+ *
+ * @param queryString
+ * @param endpoint
+ */
+ public SparqlQuery(String queryString, SparqlEndpoint endpoint) {
+ this.queryString = queryString;
+ this.endpoint = endpoint;
+ }
+
+ @Deprecated
+ public void setIsRunning(boolean running) {
+ this.isRunning = running;
+ }
+
+ /**
+ * Sends a SPARQL query using the Jena library.
+ */
+ public ResultSet send() {
+ isRunning = true;
+ logger.info(queryString);
+
+ String service = endpoint.getURL().toString();
+ logger.info(endpoint.getURL().toString());
+ // Jena access to SPARQL endpoint
+ queryExecution = new QueryEngineHTTP(service, queryString);
+ for (String dgu : endpoint.getDefaultGraphURIs()) {
+ queryExecution.addDefaultGraph(dgu);
+ }
+ for (String ngu : endpoint.getNamedGraphURIs()) {
+ queryExecution.addNamedGraph(ngu);
+ }
+ logger.info("query SPARQL server");
+
+ rs = queryExecution.execSelect();
+ logger.info(rs.getResultVars().toString());
+ isRunning = false;
+ return rs;
+ }
+
+ public void stop() {
+ queryExecution.abort();
+ isRunning = false;
+ }
+
+ public String getQueryString() {
+ return queryString;
+ }
+
+ public ResultSet getResultSet() {
+ return rs;
+ }
+
+ public boolean isRunning() {
+ return isRunning;
+ }
+
+ public boolean hasCompleted() {
+ return (rs != null);
+ }
+
+ /**
+ * TODO define the format
+ *
+ * @return
+ */
+ @Deprecated
+ @SuppressWarnings( { "unchecked" })
+ public String[][] getAsStringArray() {
+ if (rs == null)
+ this.send();
+ System.out.println("Starting Query");
+ List<ResultBinding> l = ResultSetFormatter.toList(rs);
+ List<String> resultVars = rs.getResultVars();
+ String[][] array = new String[l.size()][resultVars.size()];
+ Iterator<String> iter = resultVars.iterator();
+ int i = 0, j = 0;
+
+ for (ResultBinding resultBinding : l) {
+ while (iter.hasNext()) {
+ String varName = (String) iter.next();
+ array[i][j] = resultBinding.get(varName).toString();
+ j++;
+ }
+ iter = resultVars.iterator();
+ i++;
+ j = 0;
+ }
+ System.out.println("Query complete");
+ return array;
+ }
+
+ /**
+ * sends a query and returns XML
+ *
+ * @return String xml
+ */
+ public static String getAsXMLString(ResultSet resultSet) {
+ //if (rs == null)
+ // this.send();
+ return ResultSetFormatter.asXMLString(resultSet);
+ }
+
+ /**
+ * sends a query and returns complicated Jena List with ResultBindings
+ *
+ *
+ * @return jena List<ResultBinding>
+ */
+ @Deprecated
+ @SuppressWarnings( { "unchecked" })
+ public List<ResultBinding> getAsList() {
+ if (rs == null)
+ this.send();
+ return ResultSetFormatter.toList(rs);
+ }
+
+ /**
+ * Converts Jena result set to JSON.
+ *
+ * @param resultSet The result set to transform.
+ * @return JSON representation of the result set.
+ */
+ public static String getAsJSON(ResultSet resultSet) {
+ // if (rs == null)
+ // this.send();
+ ByteArrayOutputStream baos = new ByteArrayOutputStream();
+ ResultSetFormatter.outputAsJSON(baos, resultSet);
+ // possible Jena bug: Jena modifies the result set during
+ // JSON transformation, so we need to get it back
+ resultSet = JSONtoResultSet(baos.toString());
+ return baos.toString();
+ }
+
+ /**
+ * Converts from JSON to internal Jena format.
+ *
+ * @param json
+ * A JSON representation if a SPARQL query result.
+ * @return A Jena ResultSet.
+ */
+ public static ResultSet JSONtoResultSet(String json) {
+ ByteArrayInputStream bais = new ByteArrayInputStream(json
+ .getBytes(Charset.forName("UTF-8")));
+ return ResultSetFactory.fromJSON(bais);
+ }
+
+}
Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/TypedSparqlQuery.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/TypedSparqlQuery.java 2008-01-29 17:34:13 UTC (rev 456)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/TypedSparqlQuery.java 2008-01-29 19:24:02 UTC (rev 457)
@@ -25,8 +25,6 @@
import java.util.Set;
import org.dllearner.kb.sparql.configuration.Configuration;
-import org.dllearner.kb.sparql.query.Cache;
-import org.dllearner.kb.sparql.query.CachedSparqlQuery;
import org.dllearner.utilities.StringTuple;
import com.hp.hpl.jena.query.ResultSet;
@@ -85,13 +83,12 @@
String sparqlQueryString = sparqlQueryMaker
.makeSubjectQueryUsingFilters(uri.toString());
- CachedSparqlQuery csq = new CachedSparqlQuery(configuration
- .getSparqlEndpoint(), cache, uri.toString(), sparqlQueryString);
+// CachedSparqlQuery csq = new CachedSparqlQuery(configuration
+// .getSparqlEndpoint(), cache, uri.toString(), sparqlQueryString);
+ SparqlQuery query = new SparqlQuery(sparqlQueryString, configuration.getSparqlEndpoint());
+ ResultSet rs = cache.executeSparqlQuery(query);
- // TODO optimize
- ResultSet rs = csq.getAsResultSet();
-
List<ResultBinding> l = ResultSetFormatter.toList(rs);
p(l.toString());
for (ResultBinding resultBinding : l) {
Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/TypedSparqlQueryClasses.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/TypedSparqlQueryClasses.java 2008-01-29 17:34:13 UTC (rev 456)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/TypedSparqlQueryClasses.java 2008-01-29 19:24:02 UTC (rev 457)
@@ -25,7 +25,6 @@
import java.util.Set;
import org.dllearner.kb.sparql.configuration.Configuration;
-import org.dllearner.kb.sparql.query.CachedSparqlQuery;
import org.dllearner.utilities.StringTuple;
import com.hp.hpl.jena.query.ResultSet;
@@ -64,11 +63,9 @@
+ " FILTER (!regex(str(?object),'http://xmlns.com/foaf/0.1/'))"
+ "}";
- CachedSparqlQuery csq = new CachedSparqlQuery(configuration
- .getSparqlEndpoint(), cache, uri.toString(), sparqlQueryString);
-
- // TODO optimize
- ResultSet rs = csq.getAsResultSet();
+ SparqlQuery query = new SparqlQuery(sparqlQueryString, configuration.getSparqlEndpoint());
+ ResultSet rs = cache.executeSparqlQuery(query);
+
List<ResultBinding> l = ResultSetFormatter.toList(rs);
for (ResultBinding resultBinding : l) {
Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/test/JenaQueryToResultSpeedTest.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/test/JenaQueryToResultSpeedTest.java 2008-01-29 17:34:13 UTC (rev 456)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/test/JenaQueryToResultSpeedTest.java 2008-01-29 19:24:02 UTC (rev 457)
@@ -19,8 +19,8 @@
*/
package org.dllearner.kb.sparql.test;
+import org.dllearner.kb.sparql.SparqlQuery;
import org.dllearner.kb.sparql.configuration.SparqlEndpoint;
-import org.dllearner.kb.sparql.query.SparqlQuery;
import com.hp.hpl.jena.query.ResultSet;
Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/test/TestResultSet.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/test/TestResultSet.java 2008-01-29 17:34:13 UTC (rev 456)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/test/TestResultSet.java 2008-01-29 19:24:02 UTC (rev 457)
@@ -25,8 +25,8 @@
import java.io.ObjectOutputStream;
import java.util.List;
+import org.dllearner.kb.sparql.SparqlQuery;
import org.dllearner.kb.sparql.configuration.SparqlEndpoint;
-import org.dllearner.kb.sparql.query.SparqlQuery;
import com.hp.hpl.jena.query.ResultSet;
import com.hp.hpl.jena.sparql.core.ResultBinding;
Modified: trunk/src/dl-learner/org/dllearner/server/ClientState.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/server/ClientState.java 2008-01-29 17:34:13 UTC (rev 456)
+++ trunk/src/dl-learner/org/dllearner/server/ClientState.java 2008-01-29 19:24:02 UTC (rev 457)
@@ -34,7 +34,7 @@
import org.dllearner.core.ReasoningService;
import org.dllearner.kb.OWLFile;
import org.dllearner.kb.sparql.SparqlKnowledgeSource;
-import org.dllearner.kb.sparql.query.SparqlQuery;
+import org.dllearner.kb.sparql.SparqlQuery;
/**
* Stores the state of a DL-Learner client session.
Modified: trunk/src/dl-learner/org/dllearner/server/DLLearnerWS.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/server/DLLearnerWS.java 2008-01-29 17:34:13 UTC (rev 456)
+++ trunk/src/dl-learner/org/dllearner/server/DLLearnerWS.java 2008-01-29 19:24:02 UTC (rev 457)
@@ -47,7 +47,7 @@
import org.dllearner.core.dl.Individual;
import org.dllearner.kb.OWLFile;
import org.dllearner.kb.sparql.SparqlKnowledgeSource;
-import org.dllearner.kb.sparql.query.SparqlQuery;
+import org.dllearner.kb.sparql.SparqlQuery;
import org.dllearner.learningproblems.PosNegDefinitionLP;
import org.dllearner.learningproblems.PosNegInclusionLP;
import org.dllearner.learningproblems.PosOnlyDefinitionLP;
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