[6.x.x] Fix errors on update operations

exist-core/src/main/java/org/exist/storage/NativeBroker.java

@@ -3033,8 +3033,7 @@ public Object start() {
                 }
             }.run();
             // create a copy of the old doc to copy the nodes into it
-            final DocumentImpl tempDoc = new DocumentImpl(null, null, doc.getCollection(), doc.getDocId(), doc.getFileURI());
-            tempDoc.copyOf(this, doc, doc);
+            final DocumentImpl tempDoc = new DocumentImpl(null, pool, doc.getCollection(), doc.getDocId(), doc.getFileURI());
             final StreamListener listener = getIndexController().getStreamListener(doc, ReindexMode.STORE);
             // copy the nodes
             final NodeList nodes = doc.getChildNodes();
@@ -3067,7 +3066,7 @@ public Object start() {
             if (LOG.isDebugEnabled()) {
                 LOG.debug("Defragmentation took {} ms.", (System.currentTimeMillis() - start));
             }
-        } catch(final PermissionDeniedException | IOException e) {
+        } catch(IOException e) {
             LOG.error(e);
         }
     }

exist-core/src/main/java/org/exist/test/ExistXmldbEmbeddedServer.java

@@ -42,6 +42,7 @@
 import java.io.IOException;
 import java.nio.file.Path;
 import java.util.Map;
+import java.util.Properties;
 
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.fail;

exist-core/src/test/java/org/exist/xquery/update/UpdateInsertTriggersDefragTest.java

@@ -0,0 +1,98 @@
+/*
+ * eXist-db Open Source Native XML Database
+ * Copyright (C) 2001 The eXist-db Authors
+ *
+ * [email protected]
+ * http://www.exist-db.org
+ *
+ * This library is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation; either
+ * version 2.1 of the License, or (at your option) any later version.
+ *
+ * This library is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this library; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+ */
+package org.exist.xquery.update;
+
+import com.evolvedbinary.j8fu.function.Consumer2E;
+import org.exist.EXistException;
+import org.exist.collections.Collection;
+import org.exist.security.PermissionDeniedException;
+import org.exist.source.StringSource;
+import org.exist.storage.BrokerPool;
+import org.exist.storage.DBBroker;
+import org.exist.storage.txn.Txn;
+import org.exist.test.ExistEmbeddedServer;
+import org.exist.test.TestConstants;
+import org.exist.util.MimeType;
+import org.exist.util.StringInputSource;
+import org.exist.xquery.XPathException;
+import org.exist.xquery.value.Sequence;
+import org.junit.Before;
+import org.junit.ClassRule;
+import org.junit.Test;
+
+import java.io.IOException;
+import java.util.Optional;
+
+import static org.exist.test.Util.executeQuery;
+import static org.exist.test.Util.withCompiledQuery;
+import static org.exist.util.PropertiesBuilder.propertiesBuilder;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
+public class UpdateInsertTriggersDefragTest {
+
+    @ClassRule
+    public static final ExistEmbeddedServer existEmbeddedServer = new ExistEmbeddedServer(propertiesBuilder().put(DBBroker.PROPERTY_XUPDATE_FRAGMENTATION_FACTOR, -1).build(), true, true);
+
+    @Before
+    public void setUp() throws Exception {
+        final BrokerPool brokerPool = existEmbeddedServer.getBrokerPool();
+        try (final DBBroker broker = brokerPool.get(Optional.of(brokerPool.getSecurityManager().getSystemSubject()));
+             final Txn transaction = brokerPool.getTransactionManager().beginTransaction()) {
+
+            // store the test document in the test collection
+            try (final Collection testCollection = broker.getOrCreateCollection(transaction, TestConstants.TEST_COLLECTION_URI)) {
+                broker.storeDocument(transaction, TestConstants.TEST_XML_URI, new StringInputSource("<list><item>initial</item></list>"), MimeType.XML_TYPE, testCollection);
+            }
+
+            transaction.commit();
+        }
+    }
+
+    @Test
+    public void triggerDefragAfterUpdate() throws Exception {
+        final String updateQuery = "update insert <item>new node</item> into doc('" + TestConstants.TEST_COLLECTION_URI + "/" + TestConstants.TEST_XML_URI + "')//list";
+        assertQuery(updateQuery, updateResults ->
+            assertTrue("Update expression returns an empty sequence", updateResults.isEmpty())
+        );
+
+        final String searchQuery = "doc('" + TestConstants.TEST_COLLECTION_URI + "/" + TestConstants.TEST_XML_URI + "')//item";
+        assertQuery(searchQuery, searchResults ->
+            assertEquals("Both items are returned", 2, searchResults.getItemCount())
+        );
+    }
+
+    private void assertQuery(final String query, final Consumer2E<Sequence, XPathException, PermissionDeniedException> assertions) throws EXistException, XPathException, PermissionDeniedException, IOException {
+        final BrokerPool brokerPool = existEmbeddedServer.getBrokerPool();
+        try (final DBBroker broker = brokerPool.get(Optional.of(brokerPool.getSecurityManager().getSystemSubject()));
+             final Txn transaction = brokerPool.getTransactionManager().beginTransaction()) {
+
+            withCompiledQuery(broker, new StringSource(query), compiledQuery -> {
+                final Sequence results = executeQuery(broker, compiledQuery);
+                assertions.accept(results);
+                return null;
+            });
+
+            transaction.commit();
+        }
+    }
+}