Merge branch 'master' into snyk-upgrade-eeaf18052c6af32ced9fa5a85d26205c

# Conflicts: # qanary_pipeline-template/pom.xml
WDAqua · Oct 11, 2023 · 5340060 · 5340060
2 parents a1b9931 + 07a8b23
commit 5340060
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diff --git a/.github/workflows/codeql-analysis.yml b/.github/workflows/codeql-analysis.yml
@@ -38,7 +38,7 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL

diff --git a/.github/workflows/docker-deployment.yml b/.github/workflows/docker-deployment.yml
@@ -11,11 +11,11 @@ jobs:
         STARDOG_PASSWORD: ${{ secrets.STARDOG_PASSWORD }}
     steps:
       - name: Docker Login
-        uses: docker/login-action@v2
+        uses: docker/login-action@v3
         with:
           username: ${{ secrets.DOCKER_USER }}
           password: ${{ secrets.DOCKER_PASSWORD }}
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Build the Docker images and Push to Dockerhub
         run: bash -c ./service_config/build_images.sh
       - name: Init update

diff --git a/.github/workflows/maven.yml b/.github/workflows/maven.yml
@@ -15,7 +15,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up JDK 17
       uses: actions/setup-java@v3
       with:

diff --git a/qanary-configuration-frontend/package-lock.json b/qanary-configuration-frontend/package-lock.json
diff --git a/qanary-configuration-frontend/package.json b/qanary-configuration-frontend/package.json
@@ -3,7 +3,7 @@
   "version": "1.0.3",
   "private": true,
   "dependencies": {
-    "@babel/core": "7.20.12",
+    "@babel/core": "7.21.0",
     "@testing-library/jest-dom": "^5.16.5",
     "@testing-library/react": "^12.1.2",
     "@testing-library/user-event": "^7.2.1",
@@ -34,7 +34,7 @@
     ]
   },
   "devDependencies": {
-    "@babel/core": "7.20.12",
+    "@babel/core": "7.21.0",
     "axios": "^0.21.2"
   }
 }
diff --git a/qanary_commons/pom.xml b/qanary_commons/pom.xml
@@ -2,20 +2,20 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>eu.wdaqua.qanary</groupId>
 	<artifactId>qa.commons</artifactId>
-	<version>3.8.2</version>
+	<version>3.8.5</version>
 	<parent>
 		<groupId>org.springframework.boot</groupId>
 		<artifactId>spring-boot-starter-parent</artifactId>
 		<version>2.6.7</version>
-		<relativePath /> <!-- lookup parent from repository -->
+		<relativePath/> <!-- lookup parent from repository -->
 	</parent>
 
 	<properties>
 		<java.version>11</java.version>
 		<spring-boot-admin.version>2.7.10</spring-boot-admin.version>
 		<maven.compiler.source>${java.version}</maven.compiler.source>
 		<maven.compiler.target>${java.version}</maven.compiler.target>
-		<jena.version>4.7.0</jena.version>
+		<jena.version>4.9.0</jena.version>
 		<stardog.version>[8.0.0,9.0.0)</stardog.version>
 		<mockito.version>4.4.0</mockito.version><!-- last working version -->
 	</properties>

diff --git a/qanary_commons/src/main/java/eu/wdaqua/qanary/commons/QanaryQuestion.java b/qanary_commons/src/main/java/eu/wdaqua/qanary/commons/QanaryQuestion.java
@@ -585,14 +585,16 @@ public List<SparqlAnnotation> getSparqlResults() throws SparqlQueryFailed {
 				+ "  } \n" //
 				+ "  OPTIONAL { ?a qa:score ?confidence . } \n" //
 				+ "  OPTIONAL { ?a qa:overKnowledgeGraph ?kb . } \n" //
-				+ "  ?a oa:annotatedAt ?time1 . \n" //
-				+ "  { \n" //
-				+ "   SELECT ?time1 { \n" //
-				+ "    ?a a qa:AnnotationOfAnswerSPARQL . \n" //
-				+ "    ?a oa:annotatedAt ?time1 . \n" //
-				+ "   } \n" //
-				+ "	  ORDER BY DESC(?time1) \n" //
-				+ "	  LIMIT 1 \n" //
+				+ "  OPTIONAL { \n" //
+				+ "	?a oa:annotatedAt ?time1 . \n" //
+				+ "  	{ \n" //
+				+ "  	SELECT ?time1 { \n" //
+				+ "  		?a a qa:AnnotationOfAnswerSPARQL . \n" //
+				+ "  		?a oa:annotatedAt ?time1 . \n" //
+				+ "  	} \n" //
+				+ "	ORDER BY DESC(?time1) \n" //
+				+ "	LIMIT 1 \n" //
+				+ "  	} \n" //
 				+ "  } \n" //
 				+ "} \n" //
 				+ "ORDER BY DESC(?score) \n";
@@ -622,11 +624,11 @@ public class SparqlAnnotation {
 	}
 
 	public String getSparqlResult() throws SparqlQueryFailed {
-		// added try and catch to prevent indexOutOfBoundsException, returns empty String if no Query was found
+		// added try and catch to prevent indexOutOfBoundsException and NullPointerException, returns empty String if no Query was found
 		String sparqlResult = "";
 		try {
 			sparqlResult = this.getSparqlResults().get(0).query;
-		} catch (IndexOutOfBoundsException e) {
+		} catch (IndexOutOfBoundsException | NullPointerException e) {
 			logger.warn("No SPARQL Query found, index out of bounds");
 		}
 		return sparqlResult;
@@ -643,21 +645,23 @@ public String getJsonResult() throws SparqlQueryFailed {
 				+ "	?a a qa:AnnotationOfAnswerJson . " //
 				+ "  	?a oa:hasBody ?answer . " //
 				+ " 	?answer rdf:value ?json . " //
-//				+ "  	?a a qa:AnnotationOfAnswerJSON . " //
-//				+ "  	?a oa:hasBody ?json " //
-//				TODO: this should be body of AnswerJson with rdf:value answer
 				+ "}";
 		logger.debug("getJsonResult: SELECT using:\n{}", sparql);
 		ResultSet resultset = this.getQanaryTripleStoreConnector().select(sparql);
 
-		// the default value has to be null to distinguish missing values from empty values
+		// OLD: the default value has to be null to distinguish missing values from empty values
+		// NEW: returning null would result in "null" being part of the response JSON, 
+		//		return an empty string instead.
+		//		This way, a distinction is still possible:
+		//		missing values: ""
+		//		empty values: []
 		String sparqlAnnotation = null; 
 		while (resultset.hasNext()) {
 			sparqlAnnotation = resultset.next().get("json").asLiteral().toString();
 		}
 
 		if (sparqlAnnotation == null) {
-			return sparqlAnnotation;
+			return "";
 		} else {
 			return sparqlAnnotation.replace("\\\"", "\"");
 		}

diff --git a/qanary_commons/src/main/resources/queries/select_all_AnnotationOfAnswerJson.rq b/qanary_commons/src/main/resources/queries/select_all_AnnotationOfAnswerJson.rq
@@ -5,17 +5,17 @@ PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
 PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> 
 PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> 
 
-SELECT * WHERE { 
-	GRAPH ?graph {
-		?annotationAnswer 
-				a				qa:AnnotationOfAnswerJson ;
-				oa:hasTarget	?question ; 
-				oa:hasBody		?answer ; 
-				oa:annotatedBy	?service ; 
-				oa:annotatedAt	?time ; 
-				qa:score		?score . 
-	  	?answer	
-				a				qa:AnswerJson ;
-		   		rdf:value		?answerJson . 
-	}
-}
+SELECT * 
+FROM ?graphURI
+WHERE { 
+	?annotationAnswer 
+		a	qa:AnnotationOfAnswerJson ;
+				oa:hasTarget ?hasTarget ; 
+				oa:hasBody ?hasBody ; 
+				oa:annotatedBy ?annotatedBy ; 
+				oa:annotatedAt ?annotatedAt ; 
+				qa:score ?score . 
+	  	?hasBody	
+			a qa:AnswerJson ;
+		   	rdf:value ?value . 
+}
diff --git a/qanary_commons/src/main/resources/queries/select_all_AnnotationOfAnswerSPARQL.rq b/qanary_commons/src/main/resources/queries/select_all_AnnotationOfAnswerSPARQL.rq
@@ -4,14 +4,15 @@ PREFIX qa: <http://www.wdaqua.eu/qa#>
 PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
 PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
 
-SELECT * 
+SELECT *
+FROM ?graph
 WHERE { 
-	GRAPH ?graph  {
-        ?newAnnotation rdf:type qa:AnnotationOfAnswerSPARQL .
-        ?newAnnotation oa:hasTarget ?targetQuestion .
-        ?newAnnotation oa:hasBody ?selectQueryThatShouldComputeTheAnswer .
-        ?newAnnotation qa:score ?confidence .
-        ?newAnnotation oa:annotatedAt ?time .
-        ?newAnnotation oa:annotatedBy ?application . 
-    }
+        ?annotationId rdf:type qa:AnnotationOfAnswerSPARQL .
+        ?annotationId oa:hasTarget ?hasTarget ;
+        oa:hasBody ?hasBody .
+        OPTIONAL {
+        ?annotationnId qa:score ?score ;
+        }
+        ?annotationId oa:annotatedAt ?annotatedAt ;
+        oa:annotatedBy ?annotatedBy . 
 }
diff --git a/qanary_commons/src/main/resources/queries/select_all_AnnotationOfClass.rq b/qanary_commons/src/main/resources/queries/select_all_AnnotationOfClass.rq
@@ -0,0 +1,16 @@
+PREFIX qa: <http://www.wdaqua.eu/qa#>
+PREFIX oa: <http://www.w3.org/ns/openannotation/core/>
+PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
+
+SELECT *
+FROM ?graph
+WHERE {
+?annotationId a qa:AnnotationOfClass .
+?annotationId oa:hasTarget [
+	a oa:SpecificClass ;
+ 	oa:hasSource ?hasSource ;
+] .
+?annotationId oa:hasBody ?hasBody ;
+    oa:annotatedBy ?annotatedBy ;
+    oa:annotatedAt ?annotatedAt  .
+  }
diff --git a/qanary_commons/src/main/resources/queries/select_all_AnnotationOfInstance.rq b/qanary_commons/src/main/resources/queries/select_all_AnnotationOfInstance.rq
@@ -0,0 +1,24 @@
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX oa: <http://www.w3.org/ns/openannotation/core/>
+PREFIX qa: <http://www.wdaqua.eu/qa#>
+
+SELECT *
+FROM ?graph
+WHERE {
+    ?annotationId rdf:type qa:AnnotationOfInstance .
+    ?annotationId oa:hasTarget [
+                    a oa:SpecificResource;
+                      oa:hasSource ?hasSource;
+                      oa:hasSelector [
+        	                a oa:TextPositionSelector;
+                            oa:start ?start;
+                            oa:end ?end
+                      ]
+    ].
+    ?annotationId oa:hasBody ?hasBody ;
+                  oa:annotatedBy ?annotatedBy ;
+                  oa:annotatedAt ?annotatedAt .
+                  OPTIONAL {
+                      ?annotationId qa:score ?score .
+                  }
+}
diff --git a/qanary_commons/src/main/resources/queries/select_all_AnnotationOfQuestionLanguage.rq b/qanary_commons/src/main/resources/queries/select_all_AnnotationOfQuestionLanguage.rq
@@ -0,0 +1,13 @@
+PREFIX qa: <http://www.wdaqua.eu/qa#>
+PREFIX oa: <http://www.w3.org/ns/openannotation/core/>
+PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> 
+
+SELECT *
+FROM ?graph
+WHERE {
+?annotationId a qa:AnnotationOfQuestionLanguage .
+?annotationId oa:hasTarget ?hasTarget ; 
+  oa:hasBody ?hasBody ;
+  oa:annotatedBy ?annotatedBy ;
+  oa:annotatedAt ?annotatedAt .
+  }
diff --git a/qanary_commons/src/main/resources/queries/select_all_AnnotationOfQuestionTranslation.rq b/qanary_commons/src/main/resources/queries/select_all_AnnotationOfQuestionTranslation.rq
@@ -1,11 +1,14 @@
 PREFIX qa: <http://www.wdaqua.eu/qa#>
 PREFIX oa: <http://www.w3.org/ns/openannotation/core/>
 
-SELECT ?a ?translation ?time
+SELECT *
 FROM ?graph
 WHERE {
-    ?a a qa:AnnotationOfQuestionTranslation .
-    ?a oa:hasTarget ?targetQuestion .
-    ?a oa:hasBody ?translation .
-    FILTER (lang(?translation) = ?language).
+    ?annotationId a qa:AnnotationOfQuestionTranslation .
+    ?annotationId oa:hasTarget ?hasTarget ;
+                  oa:hasBody ?hasBody ;
+                  oa:annotatedBy ?annotatedBy ;
+                  oa:annotatedAt ?annotatedAt .
+    FILTER (lang(?hasBody) = ?language).
 }
+
diff --git a/qanary_commons/src/main/resources/queries/select_all_AnnotationOfRelation.rq b/qanary_commons/src/main/resources/queries/select_all_AnnotationOfRelation.rq
@@ -0,0 +1,29 @@
+
+
+PREFIX qa: <http://www.wdaqua.eu/qa#>
+PREFIX oa: <http://www.w3.org/ns/openannotation/core/>
+
+SELECT *
+FROM ?graph
+WHERE {
+?annotationId a qa:AnnotationOfRelation .
+?annotationId oa:hasTarget [
+    a   oa:SpecificResource;
+        oa:hasSource    ?hasSource 
+    ] .
+  OPTIONAL {
+    ?annotationId oa:hasTarget [
+        oa:hasSelector  [
+            a oa:TextPositionSelector ;
+            oa:start ?start ;
+            oa:end  ?end
+        ] 
+    ] .
+}
+OPTIONAL {
+?annotationId qa:score ?score .
+}
+?annotationId oa:hasBody ?hasBody ;
+    oa:annotatedBy ?annotatedBy ;
+    oa:annotatedAt ?annotatedAt .
+}
diff --git a/qanary_commons/src/main/resources/queries/select_all_AnnotationOfSpotInstance.rq b/qanary_commons/src/main/resources/queries/select_all_AnnotationOfSpotInstance.rq
@@ -0,0 +1,20 @@
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX oa: <http://www.w3.org/ns/openannotation/core/>
+PREFIX qa: <http://www.wdaqua.eu/qa#>
+
+SELECT *
+FROM ?graph
+WHERE {
+    ?annotationId rdf:type qa:AnnotationOfSpotInstance.
+    ?annotationId oa:hasTarget [
+                    a oa:SpecificResource;
+                      oa:hasSource ?hasSource;
+                      oa:hasSelector [
+                            a oa:TextPositionSelector;
+                            oa:start ?start;
+                            oa:end ?end .
+                      ]
+    ].
+    ?annotationId oa:annotatedAt ?annotatedAt ;
+                  oa:annotatedBy ?annotatedBy .
+}
diff --git a/qanary_commons/src/main/resources/queries/select_all_AnnotationOfTextAnswerJson.rq b/qanary_commons/src/main/resources/queries/select_all_AnnotationOfTextAnswerJson.rq
@@ -0,0 +1,19 @@
+PREFIX  qa:   <http://www.wdaqua.eu/qa#>
+PREFIX  oa:   <http://www.w3.org/ns/openannotation/core/>
+PREFIX  dbr:  <http://dbpedia.org/resource/>
+PREFIX  rdf:  <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX  xsd:  <http://www.w3.org/2001/XMLSchema#>
+PREFIX  rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+
+SELECT *
+FROM ?graph
+WHERE {
+    ?annotationId rdf:type qa:AnnotationOfTextAnswerJson .
+    ?annotationId oa:hasTarget ?hasTarget
+    ?annotationId oa:hasBody ?hasBody .
+    ?annotationId oa:annotatedAt ?annotatedAt .
+    ?annotationId oa:annotatedBy ?annotatedBy .
+    ?hasBody rdf:type qa:AnswerJson .
+    ?hasBody rdf:value ?value .
+    qa:AnswerJson rdfs:subClassOf qa:Answer .
+    }
diff --git a/qanary_commons/src/main/resources/queries/select_highestScore_AnnotationOfAnswerSPARQL.rq b/qanary_commons/src/main/resources/queries/select_highestScore_AnnotationOfAnswerSPARQL.rq
@@ -5,8 +5,8 @@ PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
 PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
 
 SELECT * 
+FROM ?graph
 WHERE { 
-	GRAPH ?graph  {
 		?newAnnotation rdf:type qa:AnnotationOfAnswerSPARQL .
 		?newAnnotation oa:hasTarget ?targetQuestion .
 		?newAnnotation oa:hasBody ?selectQueryThatShouldComputeTheAnswer .
@@ -25,6 +25,5 @@ WHERE {
 
 		?newAnnotation oa:annotatedBy ?application . 
 	}
-}
 ORDER BY DESC(?confidence) 
 LIMIT 1
diff --git a/qanary_component-template/pom.xml b/qanary_component-template/pom.xml
@@ -14,7 +14,7 @@
 	</parent>
 	<properties>
 		<java.version>11</java.version>
-		<spring-boot-admin.version>2.6.7</spring-boot-admin.version>
+		<spring-boot-admin.version>2.7.10</spring-boot-admin.version>
 	</properties>
 
 	<dependencies>