Merge pull request #15 from TIBHannover/11-several-ontologies-of-tib-…

…fail-in-ingestion Added null check while parsing anootators
TIBHannover · Jun 3, 2024 · 5d32434 · 5d32434
2 parents 1bf0bcd + f0bbf59
commit 5d32434
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Showing 2 changed files with 37 additions and 30 deletions.
diff --git a/dataload/rdf2json/src/main/java/uk/ac/ebi/rdf2json/annotators/DisjointWithAnnotator.java b/dataload/rdf2json/src/main/java/uk/ac/ebi/rdf2json/annotators/DisjointWithAnnotator.java
@@ -1,4 +1,5 @@
 package uk.ac.ebi.rdf2json.annotators;
+
 import java.util.*;
 import java.util.stream.Collectors;
 
@@ -16,56 +17,62 @@ public static void annotateDisjointWith(OntologyGraph graph) {
 
 		long startTime3 = System.nanoTime();
 
-		for(String id : graph.nodes.keySet()) {
+		for (String id : graph.nodes.keySet()) {
 			OntologyNode c = graph.nodes.get(id);
 
 			if (c.types.contains(OntologyNode.NodeType.ALL_DISJOINT_CLASSES)) {
 
-				PropertyValue membersList  = c.properties.getPropertyValue("http://www.w3.org/2002/07/owl#members");
-				List<PropertyValue> members = RdfListEvaluator.evaluateRdfList(graph.getNodeForPropertyValue(membersList), graph);
+				PropertyValue membersList = c.properties.getPropertyValue("http://www.w3.org/2002/07/owl#members");
+				List<PropertyValue> members = RdfListEvaluator
+						.evaluateRdfList(graph.getNodeForPropertyValue(membersList), graph);
 
-				List<OntologyNode> classNodes = members.stream().map(val -> graph.getNodeForPropertyValue(val)).collect(Collectors.toList());
+				List<OntologyNode> classNodes = members.stream().map(val -> graph.getNodeForPropertyValue(val))
+						.collect(Collectors.toList());
 
-				for(OntologyNode classNodeA : classNodes) {
-					for(OntologyNode classNodeB : classNodes) {
-						if(classNodeB.uri != classNodeA.uri) {
+				for (OntologyNode classNodeA : classNodes) {
+					for (OntologyNode classNodeB : classNodes) {
+						if (classNodeA != null && classNodeB != null && classNodeB.uri != classNodeA.uri) {
 							classNodeA.properties.addProperty("http://www.w3.org/2002/07/owl#disjointWith",
-								PropertyValueURI.fromUri(classNodeB.uri));
+									PropertyValueURI.fromUri(classNodeB.uri));
 						}
 					}
 				}
 
 			} else if (c.types.contains(OntologyNode.NodeType.ALL_DISJOINT_PROPERTIES)) {
 
-				PropertyValue membersList  = c.properties.getPropertyValue("http://www.w3.org/2002/07/owl#members");
-				List<PropertyValue> members = RdfListEvaluator.evaluateRdfList(graph.getNodeForPropertyValue(membersList), graph);
+				PropertyValue membersList = c.properties.getPropertyValue("http://www.w3.org/2002/07/owl#members");
+				List<PropertyValue> members = RdfListEvaluator
+						.evaluateRdfList(graph.getNodeForPropertyValue(membersList), graph);
 
-				List<OntologyNode> propertyNodes = members.stream().map(val -> graph.getNodeForPropertyValue(val)).collect(Collectors.toList());
+				List<OntologyNode> propertyNodes = members.stream().map(val -> graph.getNodeForPropertyValue(val))
+						.collect(Collectors.toList());
 
-				for(OntologyNode propertyNodeA : propertyNodes) {
-					for(OntologyNode propertyNodeB : propertyNodes) {
-						if(propertyNodeB.uri != propertyNodeA.uri) {
+				for (OntologyNode propertyNodeA : propertyNodes) {
+					for (OntologyNode propertyNodeB : propertyNodes) {
+						if (propertyNodeB.uri != propertyNodeA.uri) {
 							propertyNodeA.properties.addProperty("http://www.w3.org/2002/07/owl#propertyDisjointWith",
-								PropertyValueURI.fromUri(propertyNodeB.uri));
+									PropertyValueURI.fromUri(propertyNodeB.uri));
 						}
 					}
 				}
-
-			} else if (c.types.contains(OntologyNode.NodeType.ALL_DIFFERENT)) {
 
-				PropertyValue membersList  = c.properties.getPropertyValue("http://www.w3.org/2002/07/owl#distinctMembers");
-				List<PropertyValue> members = RdfListEvaluator.evaluateRdfList(graph.getNodeForPropertyValue(membersList), graph);
-
-				List<OntologyNode> individualNodes = members.stream()
-					.map(val -> graph.getNodeForPropertyValue(val))
-					.filter(val -> val != null)
-					.collect(Collectors.toList());
+			} else if (c.types.contains(OntologyNode.NodeType.ALL_DIFFERENT)) {
 
-				for(OntologyNode individualNodeA : individualNodes) {
-					for(OntologyNode individualNodeB : individualNodes) {
-						if(individualNodeB.uri != individualNodeA.uri) {
-							individualNodeA.properties.addProperty("http://www.w3.org/2002/07/owl#differentFrom",
-								PropertyValueURI.fromUri(individualNodeB.uri));
+				PropertyValue membersList = c.properties
+						.getPropertyValue("http://www.w3.org/2002/07/owl#distinctMembers");
+				if (membersList != null) {
+					List<PropertyValue> members = RdfListEvaluator
+							.evaluateRdfList(graph.getNodeForPropertyValue(membersList), graph);
+
+					List<OntologyNode> individualNodes = members.stream().map(val -> graph.getNodeForPropertyValue(val))
+							.filter(val -> val != null).collect(Collectors.toList());
+
+					for (OntologyNode individualNodeA : individualNodes) {
+						for (OntologyNode individualNodeB : individualNodes) {
+							if (individualNodeB.uri != individualNodeA.uri) {
+								individualNodeA.properties.addProperty("http://www.w3.org/2002/07/owl#differentFrom",
+										PropertyValueURI.fromUri(individualNodeB.uri));
+							}
 						}
 					}
 				}

diff --git a/dataload/rdf2json/src/main/java/uk/ac/ebi/rdf2json/annotators/RelatedAnnotator.java b/dataload/rdf2json/src/main/java/uk/ac/ebi/rdf2json/annotators/RelatedAnnotator.java
@@ -258,7 +258,7 @@ private static void annotateRelated_Class_subClassOf_Restriction_hasValue(Ontolo
 
 			OntologyNode fillerNode = graph.nodes.get( ((PropertyValueURI) filler).getUri() );
 
-			if(fillerNode.types.contains(OntologyNode.NodeType.INDIVIDUAL)) {
+			if(fillerNode != null && fillerNode.types.contains(OntologyNode.NodeType.INDIVIDUAL)) {
 				// fillerNode is an individual
 				fillerNode.properties.addProperty("relatedTo", new PropertyValueRelated(fillerRestriction, propertyUri, classNode));
 				classNode.properties.addProperty("relatedFrom", new PropertyValueRelated(fillerRestriction, propertyUri, fillerNode));