WIP 369 subAnnotations for all types of axioms

onto-viewer-core/src/main/java/org/edmcouncil/spec/ontoviewer/core/model/property/OwlAxiomPropertyValue.java

@@ -1,9 +1,12 @@
 package org.edmcouncil.spec.ontoviewer.core.model.property;
 
 import java.util.HashMap;
+import java.util.LinkedList;
+import java.util.List;
 import java.util.Map;
 import java.util.Objects;
 import org.edmcouncil.spec.ontoviewer.core.model.OwlType;
+import org.edmcouncil.spec.ontoviewer.core.model.PropertyValue;
 
 /**
  * @author Michał Daniel ([email protected])
@@ -14,6 +17,7 @@ public class OwlAxiomPropertyValue extends PropertyValueAbstract<String> {
   private Map<String, OwlAxiomPropertyEntity> entityMaping = new HashMap<>();
   private boolean inferable = false;
   private RestrictionType restrictionType = RestrictionType.OTHER;
+  private List <PropertyValue> annotationPropertyValues = new LinkedList();
 
   public OwlAxiomPropertyValue() {
     super();
@@ -53,6 +57,10 @@ public String getFullRenderedString() {
     return fullRenderedString;
   }
 
+  public void setAnnotationPropertyValues(List <PropertyValue> annotationPropertyValues) { this.annotationPropertyValues = annotationPropertyValues;}
+
+  public List <PropertyValue> getAnnotationPropertyValues() { return annotationPropertyValues;}
+
   public boolean isInferable() {
     return inferable;
   }

onto-viewer-core/src/main/java/org/edmcouncil/spec/ontoviewer/core/ontology/DetailsManager.java

@@ -69,6 +69,7 @@ public class DetailsManager {
   private final DeprecatedHandler deprecatedHandler;
   private final VersionIriHandler versionIriHandler;
 
+
   public DetailsManager(ApplicationConfigurationService applicationConfigurationService,
       OntologyManager ontologyManager,
       ClassHandler particularClassHandler,

onto-viewer-core/src/main/java/org/edmcouncil/spec/ontoviewer/core/ontology/data/handler/axiom/AxiomsHandler.java

@@ -4,17 +4,27 @@
 import static org.semanticweb.owlapi.model.parameters.Imports.INCLUDED;
 
 import java.util.Iterator;
+import java.util.LinkedList;
 import java.util.Set;
+import java.util.LinkedHashMap;
+import java.util.Map;
 import java.util.stream.Collectors;
 import org.edmcouncil.spec.ontoviewer.core.model.PropertyValue;
+import org.edmcouncil.spec.ontoviewer.core.model.property.OwlAnnotationPropertyValue;
+import org.edmcouncil.spec.ontoviewer.core.model.property.OwlAnnotationPropertyValueWithSubAnnotations;
 import org.edmcouncil.spec.ontoviewer.core.model.property.OwlAxiomPropertyValue;
 import org.edmcouncil.spec.ontoviewer.core.model.property.OwlDetailsProperties;
+import org.edmcouncil.spec.ontoviewer.core.ontology.data.extractor.OwlDataExtractor;
 import org.edmcouncil.spec.ontoviewer.core.ontology.data.handler.StringIdentifier;
+import org.edmcouncil.spec.ontoviewer.core.ontology.data.handler.data.AnnotationsDataHandler;
 import org.edmcouncil.spec.ontoviewer.core.ontology.data.visitor.ContainsVisitors;
 import org.edmcouncil.spec.ontoviewer.core.ontology.factory.ViewerIdentifierFactory;
 import org.edmcouncil.spec.ontoviewer.core.utils.StringUtils;
+import org.edmcouncil.spec.ontoviewer.core.model.OwlType;
 import org.semanticweb.owlapi.model.AxiomType;
 import org.semanticweb.owlapi.model.IRI;
+import org.semanticweb.owlapi.model.OWLAnnotation;
+import org.semanticweb.owlapi.model.OWLAnnotationAssertionAxiom;
 import org.semanticweb.owlapi.model.OWLAnnotationAxiom;
 import org.semanticweb.owlapi.model.OWLAnnotationProperty;
 import org.semanticweb.owlapi.model.OWLAnonymousIndividual;
@@ -29,13 +39,18 @@
 import org.semanticweb.owlapi.model.OWLObjectPropertyAxiom;
 import org.semanticweb.owlapi.model.OWLOntology;
 import org.semanticweb.owlapi.model.OWLSubClassOfAxiom;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.stereotype.Component;
 
 @Component
 public class AxiomsHandler {
-
+private static  final Logger LOG = LoggerFactory.getLogger(AxiomsHandler.class);
   private final AxiomsHelper axiomsHelper;
   private final ContainsVisitors containsVisitors;
+  private OwlDataExtractor dataExtractor = new OwlDataExtractor();
+  private AnnotationsDataHandler annotationsDataHandler;
+
 
   public AxiomsHandler(AxiomsHelper axiomsHelper, ContainsVisitors containsVisitors) {
     this.axiomsHelper = axiomsHelper;
@@ -109,25 +124,49 @@ private <T extends OWLAxiom> OwlDetailsProperties<PropertyValue> handle(
       T axiom = axiomsIterator.next();
 
       String key = axiom.getAxiomType().getName();
+      key = ViewerIdentifierFactory.createId(ViewerIdentifierFactory.Type.axiom, key);
       if (axiom instanceof OWLSubClassOfAxiom) {
         OWLSubClassOfAxiom clazzAxiom = (OWLSubClassOfAxiom) axiom;
         if (clazzAxiom.isGCI()) {
           key = "gci";
         }
       }
-      key = ViewerIdentifierFactory.createId(ViewerIdentifierFactory.Type.axiom, key);
 
-      OwlAxiomPropertyValue axiomPropertyValue = axiomsHelper.prepareAxiomPropertyValue(
-          axiom, iriFragment, splitFragment, fixRenderedIri, true);
+      var axiomAnnotations = axiom.annotations().collect(Collectors.toList());
+      OwlAxiomPropertyValue axiomPropertyValue;
+      if (axiomAnnotations.size() > 0) {
+        LinkedList annotationPropertyValues = new LinkedList();
+        for (OWLAnnotation owlAnnotation : axiomAnnotations) {
+          String value = owlAnnotation.annotationValue().toString();
+          PropertyValue annotationValue = new OwlAnnotationPropertyValue();
+          annotationValue.setType(dataExtractor.extractAnnotationType(owlAnnotation));
+          annotationValue.setValue(value);
+          Map<String, PropertyValue> annotationMap = new LinkedHashMap<>();
+          annotationMap.put(owlAnnotation.getProperty().getIRI().getIRIString(), annotationValue);
+          OwlAnnotationPropertyValueWithSubAnnotations annotationPropertyValue = new OwlAnnotationPropertyValueWithSubAnnotations();
+          annotationPropertyValue.setType(OwlType.AXIOM);
+          annotationPropertyValue.setValue(annotationValue.toString());
+          annotationPropertyValue.setSubAnnotations(annotationMap);
+          annotationPropertyValues.add(annotationPropertyValue);
 
+        }
+        LOG.info("anotated: {}", axiom.annotations().collect(Collectors.toList()));
+
+        axiomPropertyValue = axiomsHelper.prepareAxiomPropertyValue(
+                axiom, iriFragment, splitFragment, fixRenderedIri, true, annotationPropertyValues);
+      } else {
+        axiomPropertyValue = axiomsHelper.prepareAxiomPropertyValue(
+                axiom, iriFragment, splitFragment, fixRenderedIri, true);
+      }
       if (axiomPropertyValue == null) {
         continue;
       }
+
       if (!key.equals(StringIdentifier.subClassOfIriString) || !axiomPropertyValue.getType().equals(TAXONOMY)) {
         result.addProperty(key, axiomPropertyValue);
       }
+      result.sortPropertiesInAlphabeticalOrder();
     }
-    result.sortPropertiesInAlphabeticalOrder();
     return result;
   }
 

onto-viewer-core/src/main/java/org/edmcouncil/spec/ontoviewer/core/ontology/data/handler/axiom/AxiomsHelper.java

@@ -1,11 +1,11 @@
 package org.edmcouncil.spec.ontoviewer.core.ontology.data.handler.axiom;
 
 import com.github.jsonldjava.shaded.com.google.common.collect.ImmutableSet;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.HashSet;
-import java.util.Set;
+
+import java.util.*;
+
 import org.edmcouncil.spec.ontoviewer.core.model.OwlType;
+import org.edmcouncil.spec.ontoviewer.core.model.PropertyValue;
 import org.edmcouncil.spec.ontoviewer.core.model.property.OwlAxiomPropertyValue;
 import org.edmcouncil.spec.ontoviewer.core.model.property.RestrictionType;
 import org.edmcouncil.spec.ontoviewer.core.utils.OwlUtils;
@@ -54,11 +54,25 @@ public AxiomsHelper(OwlUtils owlUtils, Parser parser) {
   }
 //todo 
   public <T extends OWLAxiom> OwlAxiomPropertyValue prepareAxiomPropertyValue(
-      T axiom,
-      String iriFragment,
-      String splitFragment,
-      Boolean fixRenderedIri,
-      boolean bypassClass
+          T axiom,
+          String iriFragment,
+          String splitFragment,
+          Boolean fixRenderedIri,
+          boolean bypassClass,
+          List<PropertyValue> annotationPropertyValues
+  )
+  {
+    OwlAxiomPropertyValue axiomPropertyValue = prepareAxiomPropertyValue(axiom, iriFragment, splitFragment, fixRenderedIri, bypassClass);
+    axiomPropertyValue.setAnnotationPropertyValues(annotationPropertyValues);
+    return axiomPropertyValue;
+  }
+
+  public <T extends OWLAxiom> OwlAxiomPropertyValue prepareAxiomPropertyValue(
+          T axiom,
+          String iriFragment,
+          String splitFragment,
+          Boolean fixRenderedIri,
+          boolean bypassClass
   ) {
     String value = rendering.render(axiom);
     for (String unwantedType : unwantedTypes) {

onto-viewer-core/src/main/java/org/edmcouncil/spec/ontoviewer/core/ontology/data/handler/data/AnnotationsDataHandler.java

@@ -185,7 +185,7 @@ private PropertyValue extractSubAnnotation(OWLAnnotation owlAnnotation) {
     return annotationValue;
   }
 
-  private <T extends HasAnnotationValue> PropertyValue getAnnotationPropertyValue(
+  public  <T extends HasAnnotationValue> PropertyValue getAnnotationPropertyValue(
       T annotationAssertion,
       String value, PropertyValue annotationPropertyValue) {
     if (annotationAssertion.annotationValue().isIRI()) {