Merge pull request #26 from mjovanovik/develop/2

Merge of the major new version from develop/2

.gitignore

@@ -11,3 +11,6 @@ dependency-reduced-pom.xml
 .classpath
 .project
 .settings/
+.idea/
+GeoSPARQLBenchmark.iml
+src/main/resources/.DS_Store

README.md

@@ -1,5 +1,16 @@
-# GeoSPARQL Benchmark
+# GeoSPARQL Compliance Benchmark
 
-This is the GeoSPARQL Benchmark, integrated into the [HOBBIT Platform](https://github.com/hobbit-project/platform).
+This is the GeoSPARQL Compliance Benchmark, integrated into the [HOBBIT Platform](https://github.com/hobbit-project/platform).
 
-The GeoSPARQL Benchmark (GSB) aims to evaluate GeoSPARQL compliance of RDF storage systems. The current version of the benchmark is based on the [GeoSPARQL subtest](https://github.com/BorderCloud/TFT-tests/tree/master/geosparql) of [Tester-for-Triplestores](https://github.com/BorderCloud/TFT) and the [SPARQLScore](http://sparqlscore.com/) standard conformance test suite.
+The GeoSPARQL Compliance Benchmark aims to evaluate the GeoSPARQL compliance of RDF storage systems. The benchmark uses
+206 SPARQL queries to test the extent to which the benchmarked system supports the 30 requirements defined in the [GeoSPARQL standard](https://www.ogc.org/standards/geosparql).
+
+As a result, the benchmark provides two metrics:
+ * **Correct answers**: The number of correct answers out of all GeoSPARQL queries, i.e. tests.
+ * **GeoSPARQL compliance percentage**: The percentage of compliance with the requirements of the GeoSPARQL standard.
+
+You can find a set of results from the [latest experiments on the hosted instance of the HOBBIT Platform](https://master.project-hobbit.eu/experiments/1612476122572,1612477003063,1612476116049,1612477500164,1612477015896,1612477025778,1612477047489,1612477849872,1612478626265,1612479271411)
+(log in as Guest).
+
+If you want your RDF triplestore tested, you can [add it as a system to the HOBBIT Platform](https://hobbit-project.github.io/system_integration.html),
+and then [run an experiment](https://hobbit-project.github.io/benchmarking.html) using the [hosted instance of the HOBBIT Platform](https://hobbit-project.github.io/master.html).

pom.xml

@@ -29,6 +29,26 @@
 	</properties>
 
 	<dependencies>
+	<!-- https://mvnrepository.com/artifact/org.apache.xml.security/xml-security -->
+<!-- https://mvnrepository.com/artifact/org.apache.santuario/xmlsec -->
+<dependency>
+    <groupId>org.apache.santuario</groupId>
+    <artifactId>xmlsec</artifactId>
+    <version>2.2.1</version>
+</dependency>
+
+
+	<dependency>
+    <groupId>com.fasterxml.jackson.core</groupId>
+    <artifactId>jackson-databind</artifactId>
+    <version>2.11.1</version>
+</dependency>
+	<!-- https://mvnrepository.com/artifact/org.json/json -->
+<dependency>
+    <groupId>org.json</groupId>
+    <artifactId>json</artifactId>
+    <version>20201115</version>
+</dependency>
 		<dependency>
 			<groupId>org.hobbit</groupId>
 			<artifactId>core</artifactId>

src/main/java/org/hobbit/geosparql/GSBDataGenerator.java

@@ -57,8 +57,8 @@ public void close() throws IOException {
     }
 
     private void getFileAndSendData() {
-        String datasetFile = "gsb_dataset/example.rdf";
-        String datasetURI = "http://bordercloud.github.io/TFT-tests/geosparql/illustration/example.rdf";
+        String datasetFile = "gsb_dataset/dataset.rdf";
+        String datasetURI = "http://openlinksw.com/geosparql/dataset.rdf";
 
         try {
             LOGGER.info("Getting file " + datasetFile);           
@@ -91,7 +91,7 @@ public void receiveCommand(byte command, byte[] data) {
                 for (int i=0; i < GSBConstants.GSB_QUERIES.length; i++) {
                     InputStream inputStream = new FileInputStream("gsb_queries/" + GSBConstants.GSB_QUERIES[i]);
                     String fileContent = IOUtils.toString(inputStream);
-                    fileContent = "#Q0" + (i+1) + "\n" + fileContent; // add a comment line at the beginning of the query, to denote the query number (Q01, Q02, ...)
+                    fileContent = "#Q-" + (i+1) + "\n" + fileContent; // add a comment line at the beginning of the query, to denote the query number (#Q-1, #Q-2, ...)
                     byte[] bytesArray = null;
                     bytesArray = RabbitMQUtils.writeString(fileContent);
                     sendDataToTaskGenerator(bytesArray);

src/main/java/org/hobbit/geosparql/GSBSeqTaskGenerator.java

@@ -1,6 +1,7 @@
 package org.hobbit.geosparql;
 
 import java.io.ByteArrayOutputStream;
+import java.io.File;
 import java.io.FileInputStream;
 import java.io.IOException;
 import java.io.InputStream;
@@ -50,6 +51,21 @@ private void internalInit() {
                 ResultSetFormatter.outputAsJSON(outputStream, rsf.fromXML(inputStream));
                 answers[i] = outputStream.toString();
                 inputStream.close();
+                for (int k=1; ; k++) {
+                    String alternativeAnswerFileName = GSBConstants.GSB_ANSWERS[i].replace(".srx","") + "-alternative-" + k + ".srx";
+                    LOGGER.info("Looking for an alternative file called: " + alternativeAnswerFileName);
+                    File alternativeAnswerFile = new File("gsb_answers/" + alternativeAnswerFileName);
+                    if (!alternativeAnswerFile.exists()) break;
+                    else {
+                        LOGGER.info("Alternative file found: " + alternativeAnswerFileName);
+                        InputStream alternativeAnswerInputStream = new FileInputStream(alternativeAnswerFile);
+                        ByteArrayOutputStream alternativeAnswerOutputStream = new ByteArrayOutputStream();
+                        ResultSetFormatter.outputAsJSON(alternativeAnswerOutputStream, rsf.fromXML(alternativeAnswerInputStream));
+                        answers[i] = answers[i] + "======" + alternativeAnswerOutputStream.toString(); // add the detected alternative expected answer with a corresponding delimiter
+                        alternativeAnswerInputStream.close();
+                        LOGGER.info("answers[" + i + "]: " + answers[i]);
+                    }
+                }
             }
         } catch (IOException e) {
             // TODO Auto-generated catch block
@@ -79,10 +95,10 @@ protected void generateTask(byte[] data) throws Exception {
         // Locate the corresponding query answer
         // and send it to the Evaluation Store for evaluation
         String [] parts = dataString.split("\n");
-        String answerIndexString = parts[0].trim().substring(2);
-        int answerIndex = Integer.parseInt(answerIndexString) - 1; // The first line is a comment denoting the query (#Q01, #Q02, ...)
+        String answerIndexString = parts[0].trim().substring(3);
+        int answerIndex = Integer.parseInt(answerIndexString) - 1; // The first line is a comment denoting the query (#Q-1, #Q-2, ...)
         String ans = answers[answerIndex];
-        data = RabbitMQUtils.writeString("#Q0" + (answerIndex+1) + "\n\n" + ans);
+        data = RabbitMQUtils.writeString("#Q-" + (answerIndex+1) + "\n\n" + ans);
         sendTaskToEvalStorage(taskIdString, timestamp, data);
     }
 }

src/main/java/org/hobbit/geosparql/systems/VirtuosoSysAda.java

@@ -127,6 +127,11 @@ public void receiveGeneratedTask(String taskId, byte[] data) {
             }
         }
         else {
+            if (queryString.contains("INFERENCE")) {
+                // Activate inference in Virtuoso
+                queryString = "DEFINE input:inference <myset>\n" + queryString;
+                LOGGER.info("Added an INFERENCE line to a query. This is the new query text:\n" + queryString);
+            }
             QueryExecution qe = queryExecFactory.createQueryExecution(queryString);
             ResultSet results = null;
             ByteArrayOutputStream outputStream = new ByteArrayOutputStream();
@@ -201,7 +206,7 @@ public void receiveCommand(byte command, byte[] data) {
             try {
                 allDataReceivedMutex.acquire();
             } catch (InterruptedException e) {
-                LOGGER.error("Exception while waitting for all data for bulk load " + loadingNumber + " to be recieved.", e);
+                LOGGER.error("Exception while waiting for all data for bulk load " + loadingNumber + " to be received.", e);
             }
             LOGGER.info("All data for bulk load " + loadingNumber + " received. Proceed to the loading...");