Feature/71 store each fault tree in separate graph context

src/main/java/cz/cvut/kbss/analysis/dao/BaseDao.java

@@ -2,31 +2,58 @@
 
 import cz.cvut.kbss.analysis.config.conf.PersistenceConf;
 import cz.cvut.kbss.analysis.exception.PersistenceException;
+import cz.cvut.kbss.analysis.model.AbstractEntity;
 import cz.cvut.kbss.analysis.model.util.EntityToOwlClassMapper;
-import cz.cvut.kbss.analysis.model.util.HasIdentifier;
+import cz.cvut.kbss.analysis.service.IdentifierService;
 import cz.cvut.kbss.jopa.model.EntityManager;
+import cz.cvut.kbss.jopa.model.descriptors.EntityDescriptor;
 
 import java.net.URI;
-import java.util.*;
+import java.util.Collection;
+import java.util.List;
+import java.util.Objects;
+import java.util.Optional;
 
 /**
  * Base implementation of the generic DAO API.
  *
  * @param <T> the entity class this DAO manages
  */
-public abstract class BaseDao<T extends HasIdentifier> implements GenericDao<T> {
+public abstract class BaseDao<T extends AbstractEntity> implements GenericDao<T> {
 
     protected final Class<T> type;
     protected final URI typeUri;
 
     protected final EntityManager em;
     protected final PersistenceConf config;
+    protected final IdentifierService identifierService;
 
-    protected BaseDao(Class<T> type, EntityManager em, PersistenceConf config) {
+    protected BaseDao(Class<T> type, EntityManager em, PersistenceConf config, IdentifierService identifierService) {
         this.type = type;
         this.typeUri = URI.create(EntityToOwlClassMapper.getOwlClassForEntity(type));
         this.em = em;
         this.config = config;
+        this.identifierService = identifierService;
+    }
+
+    public EntityDescriptor getEntityDescriptor(T entity){
+        return new EntityDescriptor();
+    }
+
+    public EntityDescriptor getEntityDescriptor(URI uri){
+        return new EntityDescriptor();
+    }
+
+    public URI getContext(T entity){
+        if(entity.getContext() == null)
+            entity.setContext(getContext(entity.getUri()));
+        return entity.getContext();
+    }
+
+    public URI getContext(URI uri){
+        return em.createNativeQuery("SELECT DISTINCT ?context {GRAPH ?context {?uri a ?type}}", URI.class)
+                .setParameter("uri", uri)
+                .getSingleResult();
     }
 
     @Override
@@ -56,7 +83,8 @@ public List<T> findAll(URI contenxt) {
     public Optional<T> find(URI id) {
         Objects.requireNonNull(id);
         try {
-            return Optional.ofNullable(em.find(type, id));
+            EntityDescriptor entityDescriptor = getEntityDescriptor(id);
+            return Optional.ofNullable(em.find(type, id, entityDescriptor));
         } catch (RuntimeException e) {
             throw new PersistenceException(e);
         }
@@ -66,7 +94,8 @@ public Optional<T> find(URI id) {
     public Optional<T> getReference(URI id) {
         Objects.requireNonNull(id);
         try {
-            return Optional.ofNullable(em.getReference(type, id));
+            EntityDescriptor entityDescriptor = getEntityDescriptor(id);
+            return Optional.ofNullable(em.getReference(type, id, entityDescriptor));
         } catch (RuntimeException e) {
             throw new PersistenceException(e);
         }
@@ -76,7 +105,7 @@ public Optional<T> getReference(URI id) {
     public void persist(T entity) {
         Objects.requireNonNull(entity);
         try {
-            em.persist(entity);
+            _persist(entity);
         } catch (RuntimeException e) {
             throw new PersistenceException(e);
         }
@@ -86,17 +115,23 @@ public void persist(T entity) {
     public void persist(Collection<T> entities) {
         Objects.requireNonNull(entities);
         try {
-            entities.forEach(em::persist);
+            entities.forEach(this::_persist);
         } catch (RuntimeException e) {
             throw new PersistenceException(e);
         }
     }
 
+    protected void _persist(T entity){
+        EntityDescriptor entityDescriptor = getEntityDescriptor(entity);
+        em.persist(entity, entityDescriptor);
+    }
+
     @Override
     public T update(T entity) {
         Objects.requireNonNull(entity);
         try {
-            return em.merge(entity);
+            EntityDescriptor entityDescriptor = getEntityDescriptor(entity);
+            return em.merge(entity, entityDescriptor);
         } catch (RuntimeException e) {
             throw new PersistenceException(e);
         }
@@ -106,7 +141,8 @@ public T update(T entity) {
     public void remove(T entity) {
         Objects.requireNonNull(entity);
         try {
-            em.remove(em.merge(entity));
+            EntityDescriptor entityDescriptor = getEntityDescriptor(entity);
+            em.remove(em.merge(entity,entityDescriptor));
         } catch (RuntimeException e) {
             throw new PersistenceException(e);
         }
@@ -135,8 +171,13 @@ public boolean exists(URI id) {
         }
     }
 
+    /**
+     * Checks if the input id exists in current persistence context.
+     * @param id Entity identifier
+     * @return
+     */
     @Override
-    public boolean existsInContext(URI id) {
+    public boolean existsInPersistenceContext(URI id) {
         Objects.requireNonNull(id);
         return em.find(type, id) != null;
     }

src/main/java/cz/cvut/kbss/analysis/dao/BehaviorDao.java

@@ -4,6 +4,7 @@
 import cz.cvut.kbss.analysis.exception.ResourceException;
 import cz.cvut.kbss.analysis.model.Behavior;
 import cz.cvut.kbss.analysis.resources.ResourceUtils;
+import cz.cvut.kbss.analysis.service.IdentifierService;
 import cz.cvut.kbss.analysis.util.Vocabulary;
 import cz.cvut.kbss.jopa.model.EntityManager;
 
@@ -15,8 +16,8 @@
 
 public abstract class BehaviorDao<T extends Behavior> extends NamedEntityDao<T>{
     public static URI P_IS_IMPAIRING = URI.create(Vocabulary.s_p_is_impairing);
-    public BehaviorDao(Class<T> type, EntityManager em, PersistenceConf config) {
-        super(type, em, config);
+    public BehaviorDao(Class<T> type, EntityManager em, PersistenceConf config, IdentifierService identifierService) {
+        super(type, em, config, identifierService);
     }
 
     public Set<URI> getTransitiveRequiredBehaviors(URI behaviorURI){

src/main/java/cz/cvut/kbss/analysis/dao/ComponentDao.java

@@ -1,22 +1,18 @@
 package cz.cvut.kbss.analysis.dao;
 
 import cz.cvut.kbss.analysis.config.conf.PersistenceConf;
-import cz.cvut.kbss.analysis.exception.PersistenceException;
 import cz.cvut.kbss.analysis.model.Component;
-import cz.cvut.kbss.analysis.model.FailureMode;
-import cz.cvut.kbss.analysis.util.Vocabulary;
+import cz.cvut.kbss.analysis.service.IdentifierService;
 import cz.cvut.kbss.jopa.model.EntityManager;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Repository;
 
-import java.net.URI;
-
 @Repository
 public class ComponentDao extends NamedEntityDao<Component> {
 
     @Autowired
-    public ComponentDao(EntityManager em, PersistenceConf config) {
-        super(Component.class, em, config);
+    public ComponentDao(EntityManager em, PersistenceConf config, IdentifierService identifierService) {
+        super(Component.class, em, config, identifierService);
     }
 
 }

src/main/java/cz/cvut/kbss/analysis/dao/FailureModeDao.java

@@ -2,6 +2,7 @@
 
 import cz.cvut.kbss.analysis.config.conf.PersistenceConf;
 import cz.cvut.kbss.analysis.model.FailureMode;
+import cz.cvut.kbss.analysis.service.IdentifierService;
 import cz.cvut.kbss.jopa.model.EntityManager;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Repository;
@@ -10,8 +11,8 @@
 public class FailureModeDao extends BehaviorDao<FailureMode> {
 
     @Autowired
-    public FailureModeDao(EntityManager em, PersistenceConf config) {
-        super(FailureMode.class, em, config);
+    public FailureModeDao(EntityManager em, PersistenceConf config, IdentifierService identifierService) {
+        super(FailureMode.class, em, config, identifierService);
     }
 
 }

src/main/java/cz/cvut/kbss/analysis/dao/FailureModesRowDao.java

@@ -2,12 +2,15 @@
 
 import cz.cvut.kbss.analysis.config.conf.PersistenceConf;
 import cz.cvut.kbss.analysis.model.FailureModesRow;
+import cz.cvut.kbss.analysis.service.IdentifierService;
 import cz.cvut.kbss.jopa.model.EntityManager;
+import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Repository;
 
 @Repository
 public class FailureModesRowDao extends BaseDao<FailureModesRow> {
-    protected FailureModesRowDao(EntityManager em, PersistenceConf config) {
-        super(FailureModesRow.class, em, config);
+    @Autowired
+    protected FailureModesRowDao(EntityManager em, PersistenceConf config, IdentifierService identifierService) {
+        super(FailureModesRow.class, em, config, identifierService);
     }
 }

src/main/java/cz/cvut/kbss/analysis/dao/FailureModesTableDao.java

@@ -2,12 +2,13 @@
 
 import cz.cvut.kbss.analysis.config.conf.PersistenceConf;
 import cz.cvut.kbss.analysis.model.FailureModesTable;
+import cz.cvut.kbss.analysis.service.IdentifierService;
 import cz.cvut.kbss.jopa.model.EntityManager;
 import org.springframework.stereotype.Repository;
 
 @Repository
 public class FailureModesTableDao extends NamedEntityDao<FailureModesTable> {
-    protected FailureModesTableDao(EntityManager em, PersistenceConf config) {
-        super(FailureModesTable.class, em, config);
+    protected FailureModesTableDao(EntityManager em, PersistenceConf config, IdentifierService identifierService) {
+        super(FailureModesTable.class, em, config, identifierService);
     }
 }

src/main/java/cz/cvut/kbss/analysis/dao/FaultEventDao.java

@@ -4,16 +4,21 @@
 import cz.cvut.kbss.analysis.exception.PersistenceException;
 import cz.cvut.kbss.analysis.model.FaultEvent;
 import cz.cvut.kbss.analysis.model.diagram.Rectangle;
+import cz.cvut.kbss.analysis.service.IdentifierService;
 import cz.cvut.kbss.analysis.util.Vocabulary;
 import cz.cvut.kbss.jopa.model.EntityManager;
+import cz.cvut.kbss.jopa.model.descriptors.EntityDescriptor;
+import cz.cvut.kbss.jopa.model.metamodel.EntityType;
+import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Repository;
 
 import java.net.URI;
 
 @Repository
 public class FaultEventDao extends NamedEntityDao<FaultEvent> {
-    protected FaultEventDao(EntityManager em, PersistenceConf config) {
-        super(FaultEvent.class, em, config);
+    @Autowired
+    protected FaultEventDao(EntityManager em, PersistenceConf config, IdentifierService identifierService) {
+        super(FaultEvent.class, em, config, identifierService);
     }
 
     public boolean isChild(URI faultEventIri) {
@@ -25,12 +30,39 @@ public boolean isChild(URI faultEventIri) {
                 .getSingleResult();
     }
 
+    @Override
+    public EntityDescriptor getEntityDescriptor(FaultEvent entity) {
+        URI graph = getContext(entity);
+        return getEntityDescriptorInContext(graph);
+    }
+
+    @Override
+    public EntityDescriptor getEntityDescriptor(URI uri) {
+        URI graph = getContext(uri);
+        return getEntityDescriptorInContext(graph);
+    }
+
+    protected EntityDescriptor getEntityDescriptorInContext(URI graph){
+        EntityDescriptor entityDescriptor = new EntityDescriptor(graph);
+        EntityType<FaultEvent> fe = em.getMetamodel().entity(FaultEvent.class);
+        entityDescriptor.addAttributeContext(fe.getAttribute("supertypes"), null);
+        entityDescriptor.addAttributeContext(fe.getAttribute("behavior"), null);
+
+        return entityDescriptor;
+    }
+
+    public EntityDescriptor getRectangleDescriptor(URI uri){
+        URI graph = getContext(uri);
+        EntityDescriptor entityDescriptor = new EntityDescriptor(graph);
+        return entityDescriptor;
+    }
+
     public Rectangle update(Rectangle rect){
         try{
-            return em.merge(rect);
+            EntityDescriptor entityDescriptor = getRectangleDescriptor(rect.getUri());
+            return em.merge(rect, entityDescriptor);
         }catch (RuntimeException e){
             throw new PersistenceException(e);
         }
     }
-
 }

src/main/java/cz/cvut/kbss/analysis/dao/FaultEventScenarioDao.java

@@ -2,12 +2,23 @@
 
 import cz.cvut.kbss.analysis.config.conf.PersistenceConf;
 import cz.cvut.kbss.analysis.model.FaultEventScenario;
+import cz.cvut.kbss.analysis.service.IdentifierService;
 import cz.cvut.kbss.jopa.model.EntityManager;
+import cz.cvut.kbss.jopa.model.descriptors.EntityDescriptor;
+import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Repository;
 
+import java.net.URI;
+
 @Repository
 public class FaultEventScenarioDao extends BaseDao<FaultEventScenario> {
-    protected FaultEventScenarioDao(EntityManager em, PersistenceConf config) {
-        super(FaultEventScenario.class, em, config);
+    @Autowired
+    protected FaultEventScenarioDao(EntityManager em, PersistenceConf config, IdentifierService identifierService) {
+        super(FaultEventScenario.class, em, config, identifierService);
+    }
+
+    @Override
+    public EntityDescriptor getEntityDescriptor(URI uri) {
+        return super.getEntityDescriptor(uri);
     }
 }

src/main/java/cz/cvut/kbss/analysis/dao/FaultTreeDao.java

@@ -2,8 +2,10 @@
 
 import cz.cvut.kbss.analysis.config.conf.PersistenceConf;
 import cz.cvut.kbss.analysis.model.FaultTree;
+import cz.cvut.kbss.analysis.service.IdentifierService;
 import cz.cvut.kbss.analysis.util.Vocabulary;
 import cz.cvut.kbss.jopa.model.EntityManager;
+import cz.cvut.kbss.jopa.model.descriptors.EntityDescriptor;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Repository;
 
@@ -13,8 +15,8 @@
 public class FaultTreeDao extends NamedEntityDao<FaultTree> {
 
     @Autowired
-    protected FaultTreeDao(EntityManager em, PersistenceConf config) {
-        super(FaultTree.class, em, config);
+    protected FaultTreeDao(EntityManager em, PersistenceConf config, IdentifierService identifierService) {
+        super(FaultTree.class, em, config, identifierService);
     }
 
     public boolean isRootEvent(URI faultEventIri) {
@@ -26,4 +28,17 @@ public boolean isRootEvent(URI faultEventIri) {
                 .getSingleResult();
     }
 
+    @Override
+    public EntityDescriptor getEntityDescriptor(FaultTree entity) {
+        if(entity.getUri() == null)
+            entity.setUri(identifierService.generateNewInstanceUri(typeUri.toString()));
+        EntityDescriptor entityDescriptor = new EntityDescriptor(entity.getUri());
+        return entityDescriptor;
+    }
+
+    @Override
+    public EntityDescriptor getEntityDescriptor(URI uri) {
+        EntityDescriptor entityDescriptor = new EntityDescriptor(uri);
+        return entityDescriptor;
+    }
 }

src/main/java/cz/cvut/kbss/analysis/dao/FunctionDao.java

@@ -4,6 +4,7 @@
 import cz.cvut.kbss.analysis.model.Behavior;
 import cz.cvut.kbss.analysis.model.Component;
 import cz.cvut.kbss.analysis.model.Function;
+import cz.cvut.kbss.analysis.service.IdentifierService;
 import cz.cvut.kbss.analysis.util.Vocabulary;
 import cz.cvut.kbss.jopa.model.EntityManager;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -17,8 +18,8 @@ public class FunctionDao extends BehaviorDao<Function> {
     public static URI P_HAS_FUNCTION = URI.create(Vocabulary.s_p_has_function);
 
     @Autowired
-    protected FunctionDao(EntityManager em, PersistenceConf config) {
-        super(Function.class, em, config);
+    protected FunctionDao(EntityManager em, PersistenceConf config, IdentifierService identifierService) {
+        super(Function.class, em, config, identifierService);
     }
 
     public Component getComponent(URI functionUri) {