Fix NoClassDefError.

.gitignore

@@ -9,6 +9,11 @@ target/
 out/
 nbactions.xml
 
+# Eclipse
+.project
+.classpath
+.settings
+
 # IntelliJ IDEA #
 *.iml
 .idea/
@@ -38,4 +43,8 @@ package-lock.json
 /limes-web-ui/node_modules/
 # misc
 release.properties
-cache/
+cache/
+
+# dependency tree file generiated via `mvn dependency:tree > deptree.txt`
+deptree.txt
+

limes-core/pom.xml

@@ -84,19 +84,19 @@
         <dependency>
             <groupId>org.apache.logging.log4j</groupId>
             <artifactId>log4j-slf4j-impl</artifactId>
-            <version>2.6.1</version>
+            <version>2.17.1</version>
         </dependency>
 
         <dependency>
             <groupId>org.slf4j</groupId>
             <artifactId>log4j-over-slf4j</artifactId>
-            <version>1.7.21</version>
+            <version>1.7.35</version>
         </dependency>
 
         <dependency>
             <groupId>org.slf4j</groupId>
             <artifactId>jcl-over-slf4j</artifactId>
-            <version>1.7.21</version>
+            <version>1.7.35</version>
         </dependency>
 
         <dependency>
@@ -132,30 +132,41 @@
         <dependency>
             <groupId>org.apache.jena</groupId>
             <artifactId>apache-jena-libs</artifactId>
-            <version>4.2.0</version>
+            <version>4.4.0</version>
             <type>pom</type>
         </dependency>
+
+
+        <dependency>
+            <groupId>org.apache.logging.log4j</groupId>
+            <artifactId>log4j-web</artifactId>
+            <version>2.17.1</version>
+            <scope>test</scope>
+        </dependency>
+
+
+        <dependency>
+            <groupId>org.aksw.jenax</groupId>
+            <artifactId>jenax-rx-dataaccess</artifactId>
+            <version>4.4.0-1</version>
+        </dependency>
+
+<!--
         <dependency>
             <groupId>org.aksw.jena-sparql-api</groupId>
             <artifactId>jena-sparql-api-cache-h2</artifactId>
-            <version>3.9.0-1</version>
+            <version>3.17.0-1</version>
             <exclusions>
                 <exclusion>
                     <groupId>org.aksw.jena-sparql-api</groupId>
                     <artifactId>jena-sparql-api-resources-test-config</artifactId>
                 </exclusion>
             </exclusions>
         </dependency>
-        <dependency>
-            <groupId>org.apache.logging.log4j</groupId>
-            <artifactId>log4j-web</artifactId>
-            <version>2.6.2</version>
-            <scope>test</scope>
-        </dependency>
         <dependency>
             <groupId>org.aksw.jena-sparql-api</groupId>
             <artifactId>jena-sparql-api-core</artifactId>
-            <version>3.9.0-1</version>
+            <version>3.17.0-1</version>
             <exclusions>
                 <exclusion>
                     <artifactId>slf4j-api</artifactId>
@@ -171,11 +182,12 @@
                 </exclusion>
             </exclusions>
         </dependency>
+-->
 
         <dependency>
             <groupId>org.apache.jena</groupId>
             <artifactId>jena-core</artifactId>
-            <version>3.9.0</version>
+            <version>4.4.0</version>
             <exclusions>
                 <exclusion>
                     <artifactId>slf4j-api</artifactId>
@@ -190,7 +202,7 @@
         <dependency>
             <groupId>org.apache.jena</groupId>
             <artifactId>jena-arq</artifactId>
-            <version>3.9.0</version>
+            <version>4.4.0</version>
             <exclusions>
                 <exclusion>
                     <artifactId>slf4j-api</artifactId>
@@ -209,7 +221,7 @@
         <dependency>
             <groupId>org.apache.jena</groupId>
             <artifactId>jena-jdbc-driver-mem</artifactId>
-            <version>3.6.0</version>
+            <version>4.4.0</version>
             <exclusions>
                 <exclusion>
                     <artifactId>slf4j-api</artifactId>
@@ -228,7 +240,7 @@
         <dependency>
             <groupId>org.apache.jena</groupId>
             <artifactId>jena-jdbc-driver-remote</artifactId>
-            <version>3.6.0</version>
+            <version>4.4.0</version>
             <exclusions>
                 <exclusion>
                     <artifactId>slf4j-api</artifactId>
@@ -247,7 +259,7 @@
         <dependency>
             <groupId>org.apache.jena</groupId>
             <artifactId>jena-jdbc-driver-tdb</artifactId>
-            <version>3.6.0</version>
+            <version>4.4.0</version>
             <exclusions>
                 <exclusion>
                     <artifactId>slf4j-api</artifactId>
@@ -308,7 +320,11 @@
             <type>jar</type>
             <scope>compile</scope>
         </dependency>
-
+		<dependency>
+		    <groupId>commons-codec</groupId>
+		    <artifactId>commons-codec</artifactId>
+		    <version>1.15</version>
+		</dependency>
         <dependency>
             <groupId>edu.mit</groupId>
             <artifactId>jwi</artifactId>
@@ -335,7 +351,7 @@
         <dependency>
             <groupId>junit</groupId>
             <artifactId>junit</artifactId>
-            <version>4.12</version>
+            <version>4.13.2</version>
         </dependency>
 
         <dependency>
@@ -363,6 +379,10 @@
                     <groupId>log4j</groupId>
                     <artifactId>log4j</artifactId>
                 </exclusion>
+                <exclusion>
+                    <groupId>junit-addons</groupId>
+                    <artifactId>junit-addons</artifactId>
+                </exclusion>
             </exclusions>
         </dependency>
         <dependency>

limes-core/src/main/java/org/aksw/limes/core/controller/Controller.java

@@ -17,7 +17,14 @@
  */
 package org.aksw.limes.core.controller;
 
-import org.aksw.commons.util.Files;
+import static org.fusesource.jansi.Ansi.ansi;
+import static org.fusesource.jansi.Ansi.Color.RED;
+
+import java.io.File;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.util.function.Function;
+
 import org.aksw.limes.core.evaluation.oracle.OracleFactory;
 import org.aksw.limes.core.exceptions.UnsupportedMLImplementationException;
 import org.aksw.limes.core.execution.engine.ExecutionEngineFactory;
@@ -35,18 +42,16 @@
 import org.aksw.limes.core.io.serializer.ISerializer;
 import org.aksw.limes.core.io.serializer.SerializerFactory;
 import org.aksw.limes.core.measures.mapper.MappingOperations;
-import org.apache.commons.cli.*;
+import org.apache.commons.cli.BasicParser;
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.CommandLineParser;
+import org.apache.commons.cli.HelpFormatter;
+import org.apache.commons.cli.Options;
+import org.apache.commons.cli.ParseException;
 import org.apache.commons.lang3.time.StopWatch;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import java.io.File;
-import java.io.IOException;
-import java.util.function.Function;
-
-import static org.fusesource.jansi.Ansi.Color.RED;
-import static org.fusesource.jansi.Ansi.ansi;
-
 /**
  * This is the default LIMES Controller used to run the software as CLI.
  *
@@ -116,9 +121,9 @@ public static void main(String[] args) {
                         format = cmd.getOptionValue('F');
                     }
                     AMapping reference = OracleFactory.getOracle(cmd.getOptionValue('g'), format, "simple").getMapping();
-                    Files.writeToFile(statFile, result.getStatistics(reference), false);
+                    Files.writeString(statFile.toPath(), result.getStatistics(reference));
                 } else {
-                    Files.writeToFile(statFile, result.getStatistics(), false);
+                    Files.writeString(statFile.toPath(), result.getStatistics());
                 }
             } catch (IOException e) {
                 logger.error("Error writing JSON statistics file:");
@@ -204,7 +209,7 @@ static LimesResult getMapping(Configuration config, int limit, ActiveLearningOra
             sourceCache = getSubCache.apply(sourceCache);
             targetCache = getSubCache.apply(targetCache);
         }
-        // 4. Apply preprocessing 
+        // 4. Apply preprocessing
         sourceCache = Preprocessor.applyFunctionsToCache(sourceCache, config.getSourceInfo().getFunctions());
         targetCache = Preprocessor.applyFunctionsToCache(targetCache, config.getTargetInfo().getFunctions());
 

limes-core/src/main/java/org/aksw/limes/core/io/query/FileQueryModule.java

@@ -21,7 +21,7 @@
 import org.aksw.limes.core.io.config.KBInfo;
 import org.apache.jena.rdf.model.Model;
 import org.apache.jena.rdf.model.ModelFactory;
-import org.apache.jena.rdf.model.RDFReader;
+import org.apache.jena.rdf.model.RDFReaderI;
 import org.apache.jena.riot.RiotNotFoundException;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -60,7 +60,7 @@ public FileQueryModule(KBInfo kbinfo) {
                     logger.error(MarkerFactory.getMarker("FATAL"),"endpoint could not be loaded as a file or resource");
                     throw new RuntimeException(e);
                 }
-                RDFReader r = model.getReader(kb.getType());
+                RDFReaderI r = model.getReader(kb.getType());
                 InputStreamReader reader = new InputStreamReader(in, "UTF8");
                 r.read(model, reader, null);
                 reader.close();

limes-core/src/main/java/org/aksw/limes/core/io/query/ResilientSparqlQueryModule.java

@@ -17,25 +17,30 @@
  */
 package org.aksw.limes.core.io.query;
 
-import org.aksw.jena_sparql_api.cache.core.QueryExecutionFactoryCacheEx;
-import org.aksw.jena_sparql_api.cache.extra.CacheFrontend;
-import org.aksw.jena_sparql_api.cache.h2.CacheUtilsH2;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.sql.SQLException;
+import java.util.concurrent.TimeUnit;
+
+import org.aksw.commons.io.cache.AdvancedRangeCacheConfigImpl;
+import org.aksw.commons.io.util.PathUtils;
+import org.aksw.commons.io.util.UriToPathUtils;
+import org.aksw.jena_sparql_api.cache.advanced.QueryExecutionFactoryRangeCache;
 import org.aksw.jena_sparql_api.core.FluentQueryExecutionFactory;
-import org.aksw.jena_sparql_api.core.QueryExecutionFactory;
 import org.aksw.jena_sparql_api.core.SparqlServiceReference;
 import org.aksw.jena_sparql_api.pagination.core.QueryExecutionFactoryPaginated;
+import org.aksw.jenax.arq.connection.core.QueryExecutionFactory;
 import org.aksw.limes.core.io.cache.ACache;
 import org.aksw.limes.core.io.config.KBInfo;
+import org.apache.jena.query.Query;
 import org.apache.jena.query.QueryExecution;
+import org.apache.jena.query.QueryFactory;
 import org.apache.jena.query.QuerySolution;
 import org.apache.jena.query.ResultSet;
 import org.apache.jena.sparql.core.DatasetDescription;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import java.sql.SQLException;
-import java.util.concurrent.TimeUnit;
-
 
 /**
  * @author Mohamed Sherif (sherif@informatik.uni-leipzig.de)
@@ -79,11 +84,12 @@ public ResilientSparqlQueryModule(KBInfo kbinfo, Logger logger, int retryCount,
      */
     public void fillCache(ACache cache, boolean sparql) {
         long startTime = System.currentTimeMillis();
-        String query = generateQuery();
+        String queryStr = generateQuery();
+        Query query = QueryFactory.create(queryStr);
 
         logger.info("Querying the endpoint.");
         //run query
-        org.aksw.jena_sparql_api.core.QueryExecutionFactory qef = null;
+        QueryExecutionFactory qef = null;
         try {
             qef = initQueryExecution(kb);
         } catch (Exception e) {
@@ -147,30 +153,44 @@ protected QueryExecutionFactory initQueryExecution(KBInfo kbInfo) throws ClassNo
 
         SparqlServiceReference ssr = new SparqlServiceReference(kbInfo.getEndpoint(), dd);
 
+        // Since jenax 4.4.0-1 there is a new advanced range cache that unifies caching and pagination
+
+        int pageSize = kbInfo.getPageSize();
+
         qef = FluentQueryExecutionFactory
                 .http(ssr)
                 .config()
                 .withRetry(retryCount, retryDelayInMS, TimeUnit.MILLISECONDS)
                 .withDelay(requestDelayInMs, TimeUnit.MILLISECONDS)
-                .withPagination(pageSize)
+                // Only apply pagination if there is a page size
+                // and no configured cache folder
+                .compose(internalQef -> pageSize > 0 && cacheDirectory == null
+                    ? new QueryExecutionFactoryPaginated(internalQef, pageSize)
+                    : internalQef)
                 .end()
                 .create();
 
         if (cacheDirectory != null) {
-            String dbName = kbInfo.getEndpoint().replaceAll("[:/]", "_");
-            CacheFrontend cacheFrontend = CacheUtilsH2.createCacheFrontend(dbName, true, timeToLive);
-            qef = new QueryExecutionFactoryCacheEx(qef, cacheFrontend);
+            // Javaify the endpoint url - e.g. http://dbpedia.org/sparql becomes org/dbepdia/sparql
+            String[] pathSegments = UriToPathUtils.toPathSegments(kbInfo.getEndpoint());
+            Path cacheFolder = PathUtils.resolve(Paths.get(cacheDirectory), pathSegments);
+
+            AdvancedRangeCacheConfigImpl cacheConfig = AdvancedRangeCacheConfigImpl.createDefault();
+            cacheConfig.setMaxRequestSize(pageSize > 0 ? pageSize : Integer.MAX_VALUE);
+
+            qef = QueryExecutionFactoryRangeCache.create(qef, cacheFolder, 100, cacheConfig);
         } else {
             logger.info("The cache directory has not been set. Creating an uncached SPARQL client.");
         }
 
-        try {
-            qef = new QueryExecutionFactoryPaginated(qef, pageSize);
-            return qef;
-        } catch (Exception e) {
-            logger.warn("Couldn't create Factory with pagination. Returning Factory without pagination. Exception: " +
-                    e.getLocalizedMessage());
-            return qef;
-        }
+        return qef;
+//        try {
+//            qef = new QueryExecutionFactoryPaginated(qef, pageSize);
+//            return qef;
+//        } catch (Exception e) {
+//            logger.warn("Couldn't create Factory with pagination. Returning Factory without pagination. Exception: " +
+//                    e.getLocalizedMessage());
+//            return qef;
+//        }
     }
 }