Merge pull request #329 from dschiese/updatedComponents

Updated components

qanary-component-KG2KG-TranslateAnnotationsOfInstance/pom.xml

@@ -6,7 +6,7 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>eu.wdaqua.qanary.component</groupId>
     <artifactId>qanary-component-KG2KG-TranslateAnnotationsOfInstance</artifactId>
-    <version>0.1.4</version>
+    <version>0.2.0</version>
     <name>Qanary component KG2KG Translation of AnnotationOfInstance</name>
     <parent>
         <groupId>org.springframework.boot</groupId>

qanary-component-KG2KG-TranslateAnnotationsOfInstance/src/main/java/eu/wdaqua/qanary/component/KG2KGTranslateAnnotationsOfInstance.java

@@ -35,7 +35,7 @@ public class KG2KGTranslateAnnotationsOfInstance extends QanaryComponent {
     - depending on what is given the other resource is returned
      */
 
-    private static final String ANNOTATION_OF_INSTANCE_RESOURCES_QUERY = "/queries/annotationsOfInstanceResourceQuery.rq";
+    private static final String ANNOTATION_OF_INSTANCE_RESOURCES_QUERY = "/queries/select_all_AnnotationOfInstance.rq";
     private static final String DBPEDIA_TO_WIKIDATA_QUERY = "/queries/dbpediaToWikidata.rq";
     private static final String WIKIDATA_TO_DBPEDIA_QUERY = "/queries/wikidataToDbpedia.rq";
     private static final String INSERT_ANNOTATION_QUERY = "/queries/insert_one_annotation.rq";
@@ -99,7 +99,7 @@ public ResultSet fetchAnnotations(String graphID, final QanaryUtils qanaryUtils)
      */
     public String getRequestQuery(String graphID) throws IOException {
         QuerySolutionMap bindingsForQuery = new QuerySolutionMap();
-        bindingsForQuery.add("graphID", ResourceFactory.createResource(graphID));
+        bindingsForQuery.add("graph", ResourceFactory.createResource(graphID));
 
         return QanaryTripleStoreConnector.readFileFromResourcesWithMap(ANNOTATION_OF_INSTANCE_RESOURCES_QUERY, bindingsForQuery);
     }
@@ -109,9 +109,9 @@ public List<AnnotationOfInstancePojo> createAnnotationObjets(ResultSet resultSet
 
         while (resultSet.hasNext()) {
             QuerySolution entry = resultSet.next();
-            String entryResource = entry.get("resource").toString();
+            String entryResource = entry.get("hasBody").toString();
             double score = entry.get("score").asLiteral().getDouble();
-            String targetQuestion = entry.get("targetQuestion").toString();
+            String targetQuestion = entry.get("hasSource").toString();
             int start = entry.get("start").asLiteral().getInt();
             int end = entry.get("end").asLiteral().getInt();
             String annotationId = entry.get("annotationId").toString();

qanary-component-NED-AGDISTIS/pom.xml

@@ -4,8 +4,7 @@
     <modelVersion>4.0.0</modelVersion>
     <artifactId>qanary-component-NED-AGDISTIS</artifactId>
     <groupId>eu.wdaqua.qanary.component</groupId>
-    <version>4.4.0</version>
-
+    <version>4.5.0</version>
     <parent>
         <groupId>org.springframework.boot</groupId>
         <artifactId>spring-boot-starter-parent</artifactId>

qanary-component-NED-AGDISTIS/src/main/java/eu/wdaqua/qanary/component/agdistis/ned/Agdistis.java

@@ -48,7 +48,7 @@
 public class Agdistis extends QanaryComponent {
     private static final Logger LOGGER = LoggerFactory.getLogger(Agdistis.class);
 
-    private final String FILENAME_SPOTS_FROM_GRAPH = "/queries/select_all_spots_from_graph.rq";
+    private final String FILENAME_SPOTS_FROM_GRAPH = "/queries/select_all_AnnotationOfSpotInstance.rq";
     private final String FILENAME_INSERT_ANNOTATION = "/queries/insert_one_annotation.rq";
 
     private final String applicationName;

qanary-component-NED-AGDISTIS/src/test/java/eu/wdaqua/qanary/component/agdistis/ned/AgdistisMockedTest.java

@@ -72,7 +72,7 @@ public void init() throws URISyntaxException, QanaryExceptionNoOrMultipleQuestio
         ReflectionTestUtils.setField(this.mockedAgdistis, "myRestTemplate", this.myRestTemplate);
         ReflectionTestUtils.setField(this.mockedAgdistis, "myCacheOfResponses", this.myCacheOfResponses);
         ReflectionTestUtils.setField(this.mockedAgdistis, "apiUrl", this.apiUrl);
-        ReflectionTestUtils.setField(this.mockedAgdistis, "FILENAME_SPOTS_FROM_GRAPH", "/queries/select_all_spots_from_graph.rq");
+        ReflectionTestUtils.setField(this.mockedAgdistis, "FILENAME_SPOTS_FROM_GRAPH", "/queries/select_all_AnnotationOfSpotInstance.rq");
         ReflectionTestUtils.setField(this.mockedAgdistis, "FILENAME_INSERT_ANNOTATION", "/queries/insert_one_annotation.rq");
 
         this.mockedQanaryQuestion = Mockito.mock(QanaryQuestion.class);

qanary-component-NED-DiambiguationClass-OKBQA/pom.xml

@@ -5,7 +5,7 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>eu.wdaqua.qanary.component</groupId>
     <artifactId>qanary-component-NED-DiambiguationClass-OKBQA</artifactId>
-    <version>3.1.4</version>
+    <version>3.2.0</version>
 
     <parent>
         <groupId>org.springframework.boot</groupId>

qanary-component-NED-DiambiguationClass-OKBQA/src/main/java/eu/wdaqua/qanary/component/diambiguationclass/ned/DiambiguationClass.java

@@ -51,7 +51,7 @@ public class DiambiguationClass extends QanaryComponent {
 
     private final String applicationName;
     private String FILENAME_INSERT_ANNOTATION = "/queries/insert_one_annotation.rq";
-    private String FILENAME_SELECT_ANNOTATED_LANGUAGES = "/queries/select_annotated_languages.rq";
+    private String FILENAME_SELECT_ANNOTATED_LANGUAGES = "/queries/select_all_AnnotationOfQuestionLanguage.rq";
 
     public DiambiguationClass(@Value("${spring.application.name}") final String applicationName) {
         this.applicationName = applicationName;

qanary-component-NED-Tagme/pom.xml

@@ -5,7 +5,7 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>eu.wdaqua.qanary.component</groupId>
     <artifactId>qanary-component-NED-Tagme</artifactId>
-    <version>3.2.0</version>
+    <version>3.3.0</version>
     <parent>
         <groupId>org.springframework.boot</groupId>
         <artifactId>spring-boot-starter-parent</artifactId>

qanary-component-NED-Tagme/src/main/resources/queries/insert_one_annotation.rq

@@ -12,8 +12,8 @@ GRAPH ?graph {
             a oa:TextPositionSelector ;
             oa:start ?start ;
             oa:end  ?end ;
-            qa:score ?score .
-        ] .
+            qa:score ?score
+        ]
     ] .
     ?a oa:hasBody ?answer ;
     oa:annotatedBy ?application ;
@@ -22,4 +22,4 @@ GRAPH ?graph {
 WHERE {
     BIND (IRI(str(RAND())) AS ?a) .
     BIND (now() as ?time) .
-}
+}

qanary-component-QB-BirthDataWikidata/pom.xml

@@ -6,7 +6,6 @@
 	<groupId>eu.wdaqua.qanary.component</groupId>
 	<artifactId>qanary-component-QB-BirthDataWikidata</artifactId>
 	<version>3.4.0</version>
-
 	<parent>
 		<groupId>org.springframework.boot</groupId>
 		<artifactId>spring-boot-starter-parent</artifactId>
@@ -34,6 +33,11 @@
 				</exclusion>
 			</exclusions>
 		</dependency>
+		<dependency>
+			<groupId>eu.wdaqua.qanary</groupId>
+			<artifactId>qa.commons</artifactId>
+			<version>[3.5.4,4.0.0]</version>
+		</dependency>
 		<dependency>
 			<groupId>org.apache.logging.log4j</groupId>
 			<artifactId>log4j-to-slf4j</artifactId>

qanary-component-QB-BirthDataWikidata/src/main/java/eu/wdaqua/component/qb/birthdata/wikidata/BirthDataQueryBuilder.java

@@ -44,7 +44,6 @@
 @Component
 public class BirthDataQueryBuilder extends QanaryComponent {
 	private static final Logger logger = LoggerFactory.getLogger(BirthDataQueryBuilder.class);
-
 	public static final String FILENAME_ANNOTATIONS = "/queries/getAnnotation.rq";
 	public static final String FILENAME_ANNOTATIONS_NAMED_ENTITY_FILTERED_FOR_WIKIDATA = "/queries/getAnnotationOfNamedEntityLinkedToSpecificKnowledgeGraph.rq";
 

qanary-component-QB-BirthDataWikidata/src/test/java/eu/wdaqua/component/birthdatawikidata/qb/QueryTest.java

@@ -14,6 +14,8 @@
 import org.springframework.test.context.web.WebAppConfiguration;
 
 import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Paths;
 
 import static org.junit.jupiter.api.Assertions.*;
 
@@ -27,7 +29,7 @@ class QueryTest {
     void filenameAnnotationsQueryTest() throws IOException {
         QuerySolutionMap bindingsForFirstname = new QuerySolutionMap();
         bindingsForFirstname.add("graph", ResourceFactory.createResource("urn:graph"));
-        bindingsForFirstname.add("value", ResourceFactory.createStringLiteral("FIRST_NAME"));
+        bindingsForFirstname.add("hasBody", ResourceFactory.createStringLiteral("FIRST_NAME"));
 
         String sparqlCheckFirstname = QanaryTripleStoreConnector.readFileFromResourcesWithMap(
                 TestConfiguration.FILENAME_ANNOTATIONS, bindingsForFirstname
@@ -37,17 +39,18 @@ void filenameAnnotationsQueryTest() throws IOException {
         assertFalse(sparqlCheckFirstname.isEmpty());
         assertFalse(sparqlCheckFirstname.isBlank());
 
-        assertEquals(TestConfiguration.getTestQuery("queries/getAnnotationTest.rq"), sparqlCheckFirstname);
+        assertEquals(TestConfiguration.getTestQuery("queries/getAnnotationTest.rq").concat("\n"),sparqlCheckFirstname);
     }
 
     @Test
     void filenameAnnotationsFilteredQueryTest() throws IOException {
         QuerySolutionMap bindingsForAnnotation = new QuerySolutionMap();
         bindingsForAnnotation.add("graph", ResourceFactory.createResource("urn:graph"));
-        bindingsForAnnotation.add("source", ResourceFactory.createResource("urn:source"));
-        bindingsForAnnotation.add("filterStart", ResourceFactory.createTypedLiteral(String.valueOf(5), XSDDatatype.XSDint));
+        bindingsForAnnotation.add("hasSource", ResourceFactory.createResource("urn:source"));
+        bindingsForAnnotation.add("start", ResourceFactory.createTypedLiteral(String.valueOf(5), XSDDatatype.XSDint));
 
         String sparqlGetAnnotation = QanaryTripleStoreConnector.readFileFromResourcesWithMap(
+
                 TestConfiguration.FILENAME_ANNOTATIONS_NAMED_ENTITY_FILTERED_FOR_WIKIDATA,
                 bindingsForAnnotation
         );
@@ -56,7 +59,7 @@ void filenameAnnotationsFilteredQueryTest() throws IOException {
         assertFalse(sparqlGetAnnotation.isEmpty());
         assertFalse(sparqlGetAnnotation.isBlank());
 
-        assertEquals(TestConfiguration.getTestQuery("queries/getAnnotationFilteredTest.rq"), sparqlGetAnnotation);
+        assertEquals(TestConfiguration.getTestQuery("queries/getAnnotationFilteredTest.rq").concat("\n"), sparqlGetAnnotation);
     }
 
     @Test
@@ -73,7 +76,7 @@ void questionAnswerFromWikidataByPersonTest() throws IOException {
         assertFalse(sparql.isEmpty());
         assertFalse(sparql.isBlank());
 
-        assertEquals(TestConfiguration.getTestQuery("queries/getQuestionAnswerFromWikidataByPersonTest.rq"), sparql);
+        assertEquals(TestConfiguration.getTestQuery("queries/getQuestionAnswerFromWikidataByPersonTest.rq").concat("\n"), sparql);
     }
 
     @Test
@@ -90,7 +93,7 @@ void wikidataQueryFirstAndLastNameTest() throws IOException {
         assertFalse(sparql.isEmpty());
         assertFalse(sparql.isBlank());
 
-        assertEquals(TestConfiguration.getTestQuery("queries/getQuestionAnswerFromWikidataByFirstnameLastnameTest.rq"), sparql);
+        assertEquals(TestConfiguration.getTestQuery("queries/getQuestionAnswerFromWikidataByFirstnameLastnameTest.rq").concat("\n"), sparql);
     }
 
 }

qanary-component-QB-BirthDataWikidata/src/test/java/eu/wdaqua/component/birthdatawikidata/qb/TestConfiguration.java

@@ -1,13 +1,20 @@
 package eu.wdaqua.component.birthdatawikidata.qb;
 
-import java.io.IOException;
+import org.springframework.core.io.ClassPathResource;
+import org.springframework.util.ResourceUtils;
+
+import java.io.*;
 import java.nio.file.Files;
+import java.nio.file.Path;
 import java.nio.file.Paths;
+import java.util.Scanner;
+import java.util.stream.Collectors;
 
 import eu.wdaqua.component.qb.birthdata.wikidata.BirthDataQueryBuilder;
 
 @org.springframework.boot.test.context.TestConfiguration
 public class TestConfiguration {
+
     protected static final String FILENAME_ANNOTATIONS = BirthDataQueryBuilder.FILENAME_ANNOTATIONS;
     protected static final String FILENAME_ANNOTATIONS_NAMED_ENTITY_FILTERED_FOR_WIKIDATA = BirthDataQueryBuilder.FILENAME_ANNOTATIONS_NAMED_ENTITY_FILTERED_FOR_WIKIDATA; 
     protected static final String FILENAME_WIKIDATA_BIRTHDATA_QUERY_PERSON = BirthDataQueryBuilder.FILENAME_WIKIDATA_BIRTHDATA_QUERY_PERSON;
@@ -20,9 +27,17 @@ public class TestConfiguration {
      * @throws IOException
      */
     protected static String getTestQuery(String testQueryFilename) throws IOException {
-        String path = TestConfiguration.class.getClassLoader().getResource(testQueryFilename).getPath();
+//        String path = TestConfiguration.class.getClassLoader().getResource(testQueryFilename).getPath();
+//        File file = ResourceUtils.getFile(ResourceUtils.CLASSPATH_URL_PREFIX + testQueryFilename);
+//        return new String(Files.readAllBytes(file.toPath()));
 
-        return new String(Files.readAllBytes(Paths.get(path)));
+        try (InputStream inputStream = TestConfiguration.class.getClassLoader().getResourceAsStream(testQueryFilename)) {
+            if (inputStream != null) {
+                BufferedReader reader = new BufferedReader(new InputStreamReader(inputStream));
+                return reader.lines().collect(Collectors.joining("\n"));
+            } else {
+                throw new IOException("Resource not found: " + testQueryFilename);
+            }
+        }
     }
-
 }

qanary-component-QB-BirthDataWikidata/src/test/resources/queries/getAnnotationFilteredTest.rq

@@ -1,6 +1,5 @@
 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#>
 
 SELECT  *
@@ -19,4 +18,3 @@ WHERE
     FILTER ( ?start = "5"^^<http://www.w3.org/2001/XMLSchema#int> )
     FILTER regex(?wikidataResource, ?regexForResourceFilter, "i")
   }
-ORDER BY DESC(?annotationScore)

qanary-component-QB-BirthDataWikidata/src/test/resources/queries/getAnnotationTest.rq

@@ -1,20 +1,25 @@
 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#>
 
 SELECT  *
 FROM <urn:graph>
 WHERE
-  { ?annotation  oa:hasBody  ?wikidataResource ;
-              qa:score      ?annotationScore ;
-              oa:hasTarget  ?target
-    FILTER ( ?wikidataResource = "FIRST_NAME" )
-    ?target   oa:hasSource    ?source ;
-              oa:hasSelector  ?textSelector .
-    ?textSelector
-              rdf:type        oa:TextPositionSelector ;
+  { ?annotationId
+              rdf:type        qa:AnnotationOfInstance ;
+              oa:hasTarget    _:b0 .
+    _:b0      rdf:type        oa:SpecificResource ;
+              oa:hasSource    ?hasSource ;
+              oa:hasSelector  _:b1 .
+    _:b1      rdf:type        oa:TextPositionSelector ;
               oa:start        ?start ;
-              oa:end          ?end
+              oa:end          ?end .
+    ?annotationId
+              oa:hasBody      "FIRST_NAME" ;
+              oa:annotatedBy  ?annotatedBy ;
+              oa:annotatedAt  ?annotatedAt
+    OPTIONAL
+      { ?annotationId
+                  qa:score  ?score
+      }
   }
-ORDER BY DESC(?annotationScore)

qanary-component-QB-ComicCharacterAlterEgoSimpleDBpedia/pom.xml

@@ -5,8 +5,7 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>eu.wdaqua.qanary.component</groupId>
     <artifactId>qanary-component-QB-ComicCharacterAlterEgoSimpleDBpedia</artifactId>
-    <version>3.2.4</version>
-
+    <version>3.3.0</version>
     <parent>
         <groupId>org.springframework.boot</groupId>
         <artifactId>spring-boot-starter-parent</artifactId>

qanary-component-QB-ComicCharacterAlterEgoSimpleDBpedia/src/main/java/eu/wdaqua/qanary/component/comiccharacteralteregoaimpledbpedia/qb/ComicCharacterAlterEgoSimpleDBpediaQueryBuilder.java

@@ -38,7 +38,7 @@ public class ComicCharacterAlterEgoSimpleDBpediaQueryBuilder extends QanaryCompo
     private final String applicationName;
 
     private String FILENAME_INSERT_ANNOTATION = "/queries/insert_one_annotation.rq";
-    private String FILENAME_SELECT_ANNOTATION = "/queries/select_annotation.rq";
+    private String FILENAME_SELECT_ANNOTATION = "/queries/select_all_AnnotationOfSpotInstance.rq";
     private String FILENAME_DBPEDIA_QUERY = "/queries/dbpedia_query.rq";
 
     public ComicCharacterAlterEgoSimpleDBpediaQueryBuilder(@Value("${spring.application.name}") final String applicationName) {
@@ -75,7 +75,7 @@ public QanaryMessage process(QanaryMessage myQanaryMessage) throws Exception {
 
         QuerySolutionMap bindingsForSelect = new QuerySolutionMap();
         bindingsForSelect.add("graph", ResourceFactory.createResource(qanaryQuestion.getOutGraph().toASCIIString()));
-        bindingsForSelect.add("targetQuestion", ResourceFactory.createResource(qanaryQuestion.getUri().toASCIIString()));
+        bindingsForSelect.add("hasSource", ResourceFactory.createResource(qanaryQuestion.getUri().toASCIIString()));
 
         // get the template of the INSERT query
         String sparql = this.loadQueryFromFile(FILENAME_SELECT_ANNOTATION, bindingsForSelect);
@@ -89,8 +89,8 @@ public QanaryMessage process(QanaryMessage myQanaryMessage) throws Exception {
         while (resultSet.hasNext()) {
             QuerySolution result = resultSet.next();
             logger.info("result: \n{}", result);
-            int start = result.get("startOfSpecificResource").asLiteral().getInt();
-            int end = result.get("endOfSpecificResource").asLiteral().getInt();
+            int start = result.get("start").asLiteral().getInt();
+            int end = result.get("end").asLiteral().getInt();
             String name = question.substring(start, end);
             logger.warn("annotation found for name '{}' (at {},{})", name, start, end);