fix conflict

dspace-api/src/main/java/org/dspace/authorize/dao/impl/ResourcePolicyDAOImpl.java

@@ -113,9 +113,9 @@ public void deleteByDsoAndAction(Context context, DSpaceObject dso, int actionId
 
     @Override
     public void deleteByDsoAndType(Context context, DSpaceObject dso, String type) throws SQLException {
-        String queryString = "delete from ResourcePolicy where dSpaceObject= :dso AND rptype = :rptype";
+        String queryString = "delete from ResourcePolicy where dSpaceObject.id = :dsoId AND rptype = :rptype";
         Query query = createQuery(context, queryString);
-        query.setParameter("dso", dso);
+        query.setParameter("dsoId", dso.getID());
         query.setString("rptype", type);
         query.executeUpdate();
     }

dspace-api/src/main/java/org/dspace/content/DSpaceObject.java

@@ -8,6 +8,8 @@
 package org.dspace.content;
 
 import org.apache.commons.collections.CollectionUtils;
+import org.apache.commons.lang3.builder.EqualsBuilder;
+import org.apache.commons.lang3.builder.HashCodeBuilder;
 import org.dspace.authorize.ResourcePolicy;
 import org.dspace.handle.Handle;
 import org.hibernate.annotations.GenericGenerator;
@@ -44,7 +46,7 @@ public abstract class DSpaceObject implements Serializable
     // Order by is here to ensure that the oldest handle is retrieved first,
     // multiple handles are assigned to the latest version of an item the original handle will have the lowest identifier
     // This handle is the prefered handle.
-    @OrderBy("handle_id ASC")
+    @OrderBy("id ASC")
     private List<Handle> handles = new ArrayList<>();
 
     @OneToMany(fetch = FetchType.LAZY, mappedBy = "dSpaceObject", cascade={CascadeType.PERSIST}, orphanRemoval = false)
@@ -192,4 +194,5 @@ public void clearModified() {
     protected void setModified() {
         this.modified = true;
     }
+
 }

dspace-api/src/main/java/org/dspace/content/DSpaceObjectServiceImpl.java

@@ -205,31 +205,16 @@ public List<MetadataValue> getMetadata(T dso, String schema, String element, Str
 
     @Override
     public void addMetadata(Context context, T dso, String schema, String element, String qualifier, String lang, List<String> values) throws SQLException {
-        String fieldKey = metadataAuthorityService.makeFieldKey(schema, element, qualifier);
-        if (metadataAuthorityService.isAuthorityControlled(fieldKey))
-        {
-            List<String> authorities = new ArrayList<String>();
-            List<Integer> confidences = new ArrayList<Integer>();
-            for (int i = 0; i < values.size(); ++i)
-            {
-                if(dso instanceof Item)
-                {
-                    getAuthoritiesAndConfidences(fieldKey, ((Item) dso).getOwningCollection(), values, authorities, confidences, i);
-                }else{
-                    getAuthoritiesAndConfidences(fieldKey, null, values, authorities, confidences, i);
-                }
-            }
-            addMetadata(context, dso, schema, element, qualifier, lang, values, authorities, confidences);
-        }
-        else
-        {
-            addMetadata(context, dso, schema, element, qualifier, lang, values, null, null);
+        MetadataField metadataField = metadataFieldService.findByElement(context, schema, element, qualifier);
+        if (metadataField == null) {
+            throw new SQLException("bad_dublin_core schema=" + schema + "." + element + "." + qualifier);
         }
+
+        addMetadata(context, dso, metadataField, lang, values);
     }
 
     @Override
     public void addMetadata(Context context, T dso, String schema, String element, String qualifier, String lang, List<String> values, List<String> authorities, List<Integer> confidences) throws SQLException {
-
         // We will not verify that they are valid entries in the registry
         // until update() is called.
         MetadataField metadataField = metadataFieldService.findByElement(context, schema, element, qualifier);
@@ -321,27 +306,23 @@ public void addMetadata(Context context, T dso, MetadataField metadataField, Str
 
     @Override
     public void addMetadata(Context context, T dso, MetadataField metadataField, String language, List<String> values) throws SQLException {
-        String fieldKey = metadataAuthorityService.makeFieldKey(metadataField.getMetadataSchema().getName(), metadataField.getElement(), metadataField.getQualifier());
-        if (metadataAuthorityService.isAuthorityControlled(fieldKey))
-        {
-            List<String> authorities = new ArrayList<String>();
-            List<Integer> confidences = new ArrayList<Integer>();
-            for (int i = 0; i < values.size(); ++i)
-            {
-                if(dso instanceof Item)
-                {
-                    getAuthoritiesAndConfidences(fieldKey, ((Item) dso).getOwningCollection(), values, authorities, confidences, i);
-                }else{
-                    getAuthoritiesAndConfidences(fieldKey, null, values, authorities, confidences, i);
+        if(metadataField != null) {
+            String fieldKey = metadataAuthorityService.makeFieldKey(metadataField.getMetadataSchema().getName(), metadataField.getElement(), metadataField.getQualifier());
+            if (metadataAuthorityService.isAuthorityControlled(fieldKey)) {
+                List<String> authorities = new ArrayList<String>();
+                List<Integer> confidences = new ArrayList<Integer>();
+                for (int i = 0; i < values.size(); ++i) {
+                    if (dso instanceof Item) {
+                        getAuthoritiesAndConfidences(fieldKey, ((Item) dso).getOwningCollection(), values, authorities, confidences, i);
+                    } else {
+                        getAuthoritiesAndConfidences(fieldKey, null, values, authorities, confidences, i);
+                    }
                 }
+                addMetadata(context, dso, metadataField, language, values, authorities, confidences);
+            } else {
+                addMetadata(context, dso, metadataField, language, values, null, null);
             }
-            addMetadata(context, dso, metadataField, language, values, authorities, confidences);
         }
-        else
-        {
-            addMetadata(context, dso, metadataField, language, values, null, null);
-        }
-
     }
 
     @Override

dspace-api/src/main/java/org/dspace/content/ItemServiceImpl.java

@@ -26,7 +26,6 @@
 import org.dspace.eperson.Group;
 import org.dspace.event.Event;
 import org.dspace.harvest.HarvestedItem;
-import org.dspace.harvest.factory.HarvestServiceFactory;
 import org.dspace.harvest.service.HarvestedItemService;
 import org.dspace.identifier.IdentifierException;
 import org.dspace.identifier.service.IdentifierService;
@@ -622,7 +621,7 @@ protected void rawDelete(Context context, Item item) throws AuthorizeException,
         // Remove any Handle
         handleService.unbindHandle(context, item);
 
-                // remove version attached to the item
+        // remove version attached to the item
         removeVersion(context, item);
 
         // Finally remove item row

dspace-api/src/main/java/org/dspace/content/dao/impl/ItemDAOImpl.java

@@ -201,7 +201,7 @@ public Iterator<Item> findByMetadataQuery(Context context, List<List<MetadataFie
 
     @Override
     public Iterator<Item> findByAuthorityValue(Context context, MetadataField metadataField, String authority, boolean inArchive) throws SQLException {
-        Query query = createQuery(context, "SELECT item FROM Item as item join item.metadata metadatavalue WHERE item.inArchive=:in_archive AND metadatavalue.metadataField = :metadata_field AND metadatavalue.authority = :authority");
+        Query query = createQuery(context, "SELECT item FROM Item as item join item.metadata metadatavalue WHERE item.inArchive=:in_archive AND metadatavalue.metadataField = :metadata_field AND metadatavalueq = :authority");
         query.setParameter("in_archive", inArchive);
         query.setParameter("metadata_field", metadataField);
         query.setParameter("authority", authority);

dspace-api/src/main/java/org/dspace/core/Context.java

@@ -7,9 +7,6 @@
  */
 package org.dspace.core;
 
-import java.sql.SQLException;
-import java.util.*;
-
 import org.apache.log4j.Logger;
 import org.dspace.eperson.EPerson;
 import org.dspace.eperson.Group;
@@ -22,6 +19,9 @@
 import org.dspace.utils.DSpace;
 import org.springframework.util.CollectionUtils;
 
+import java.sql.SQLException;
+import java.util.*;
+
 /**
  * Class representing the context of a particular DSpace operation. This stores
  * information such as the current authenticated user and the database
@@ -89,9 +89,13 @@ protected Context(EventService eventService, DBConnection dbConnection)  {
         init();
     }
 
+
     /**
      * Construct a new context object with default options. A database connection is opened.
      * No user is authenticated.
+     *
+     * @exception SQLException
+     *                if there was an error obtaining a database connection
      */
     public Context()
     {
@@ -154,6 +158,10 @@ DBConnection getDBConnection()
         return dbConnection;
     }
 
+    public void enableBatchMode(boolean batchModeEnabled) throws SQLException {
+        dbConnection.setOptimizedForBatchProcessing(batchModeEnabled);
+    }
+
 
     public DatabaseConfigVO getDBConfig() throws SQLException
     {
@@ -346,30 +354,53 @@ public void complete() throws SQLException
         if(!isValid())
             log.info("complete() was called on a closed Context object. No changes to commit.");
 
-        // FIXME: Might be good not to do a commit() if nothing has actually
-        // been written using this connection
         try
         {
             // As long as we have a valid, writeable database connection,
             // commit any changes made as part of the transaction
-            if (isValid() && !isReadOnly())
-            {
-                dispatchEvents();
-            }
+            commit();
         }
         finally
         {
             if(dbConnection != null)
             {
-                //Commit our changes
-                dbConnection.commit();
                 // Free the DB connection
                 dbConnection.closeDBConnection();
                 dbConnection = null;
             }
         }
     }
 
+    public void commit() throws SQLException
+    {
+        // If Context is no longer open/valid, just note that it has already been closed
+        if(!isValid()) {
+            log.info("commit() was called on a closed Context object. No changes to commit.");
+        }
+
+        // Our DB Connection (Hibernate) will decide if an actual commit is required or not
+        try
+        {
+            // As long as we have a valid, writeable database connection,
+            // commit any changes made as part of the transaction
+            if (isValid() && !isReadOnly())
+            {
+                dispatchEvents();
+            }
+
+        } finally {
+            if(log.isDebugEnabled()) {
+                log.debug("Cache size on commit is " + getCacheSize());
+            }
+
+            if(dbConnection != null)
+            {
+                //Commit our changes
+                dbConnection.commit();
+            }
+        }
+    }
+
 
     public void dispatchEvents()
     {
@@ -594,6 +625,20 @@ public void shutDownDatabase() throws SQLException {
     }
 
 	public void clearCache() throws SQLException {
+        if(log.isDebugEnabled()) {
+            log.debug("Cache size before clear cache is " + getCacheSize());
+        }
+
+        UUID epersonId = getCurrentUser().getID();
+
 		this.getDBConnection().clearCache();
+
+        if(epersonId != null) {
+            setCurrentUser(EPersonServiceFactory.getInstance().getEPersonService().find(this, epersonId));
+        }
 	}
+
+    public long getCacheSize() throws SQLException {
+        return this.getDBConnection().getCacheSize();
+    }
 }

dspace-api/src/main/java/org/dspace/core/DBConnection.java

@@ -41,4 +41,8 @@ public interface DBConnection<T> {
     public DatabaseConfigVO getDatabaseConfig() throws SQLException;
 
     public void clearCache() throws SQLException;
+
+    public void setOptimizedForBatchProcessing(boolean batchOptimized) throws SQLException;
+
+    public long getCacheSize() throws SQLException;
 }

dspace-api/src/main/java/org/dspace/core/HibernateDBConnection.java

@@ -8,6 +8,7 @@
 package org.dspace.core;
 
 import org.dspace.storage.rdbms.DatabaseConfigVO;
+import org.hibernate.FlushMode;
 import org.hibernate.Session;
 import org.hibernate.SessionFactory;
 import org.hibernate.Transaction;
@@ -32,10 +33,13 @@ public class HibernateDBConnection implements DBConnection<Session> {
     @Qualifier("sessionFactory")
     private SessionFactory sessionFactory;
 
+    private boolean batchModeEnabled = false;
+
     @Override
     public Session getSession() throws SQLException {
         if(!isTransActionAlive()){
             sessionFactory.getCurrentSession().beginTransaction();
+            configureBatchMode();
         }
         return sessionFactory.getCurrentSession();
     }
@@ -74,6 +78,7 @@ public void closeDBConnection() throws SQLException {
     public void commit() throws SQLException {
         if(isTransActionAlive() && !getTransaction().wasRolledBack())
         {
+            getSession().flush();
             getTransaction().commit();
         }
     }
@@ -110,6 +115,26 @@ public DatabaseConfigVO getDatabaseConfig() throws SQLException {
 
 	@Override
 	public void clearCache() throws SQLException {
-		this.getSession().clear();
+        getSession().flush();
+		getSession().clear();
 	}
+
+    @Override
+    public long getCacheSize() throws SQLException {
+        return getSession().getStatistics().getEntityCount();
+    }
+
+    @Override
+    public void setOptimizedForBatchProcessing(final boolean batchOptimized) throws SQLException {
+        this.batchModeEnabled = batchOptimized;
+        configureBatchMode();
+    }
+
+    private void configureBatchMode() throws SQLException {
+        if(batchModeEnabled) {
+            getSession().setFlushMode(FlushMode.ALWAYS);
+        } else {
+            getSession().setFlushMode(FlushMode.AUTO);
+        }
+    }
 }

dspace-api/src/main/java/org/dspace/eperson/dao/impl/GroupDAOImpl.java

@@ -97,7 +97,7 @@ public Group findByName(final Context context, final String name) throws SQLExce
         query.setParameter("name", name);
         query.setCacheable(true);
 
-        return uniqueResult(query);
+        return singleResult(query);
     }
 
     @Override
@@ -123,7 +123,7 @@ public Group findByNameAndEPerson(Context context, String groupName, EPerson ePe
             query.setParameter("eperson_id", ePerson.getID());
             query.setCacheable(true);
 
-            return uniqueResult(query);
+            return singleResult(query);
         }
     }
 

dspace-api/src/main/java/org/dspace/handle/Handle.java

@@ -7,6 +7,8 @@
  */
 package org.dspace.handle;
 
+import org.apache.commons.lang3.builder.EqualsBuilder;
+import org.apache.commons.lang3.builder.HashCodeBuilder;
 import org.dspace.content.DSpaceObject;
 import org.dspace.core.Context;
 
@@ -78,4 +80,26 @@ public void setResourceTypeId(Integer resourceTypeId) {
     public Integer getResourceTypeId() {
         return resourceTypeId;
     }
+
+    public boolean equals(final Object o) {
+        if (this == o) return true;
+
+        if (o == null || getClass() != o.getClass()) return false;
+
+        Handle handle1 = (Handle) o;
+
+        return new EqualsBuilder()
+                .append(id, handle1.id)
+                .append(handle, handle1.handle)
+                .append(resourceTypeId, handle1.resourceTypeId)
+                .isEquals();
+    }
+
+    public int hashCode() {
+        return new HashCodeBuilder(17, 37)
+                .append(id)
+                .append(handle)
+                .append(resourceTypeId)
+                .toHashCode();
+    }
 }