[bugfix] Fix issues with Saxon to eXist-db XDM conversion and vice-versa

Closes eXist-db/exist#5680

Author: adamretter

exist-core/pom.xml

@@ -690,6 +690,7 @@
                                 <include>src/test/java/org/exist/xquery/value/DateTimeTypesTest.java</include>
                                 <include>src/test/java/org/exist/xquery/functions/fn/FunXmlToJsonTest.java</include>
                                 <include>src/test/java/org/exist/xquery/functions/fn/ParsingFunctionsTest.java</include>
+                                <include>src/test/java/org/exist/xquery/functions/fn/transform/ConvertTest.java</include>
                                 <include>src/test/java/org/exist/xquery/functions/fn/transform/FunTransformITTest.java</include>
                                 <include>src/test/java/org/exist/xquery/functions/xmldb/XMLDBStoreTest.java</include>
                                 <include>src/test/java/org/exist/xquery/functions/xquery3/SerializeTest.java</include>
@@ -717,6 +718,7 @@
                                 <include>src/test/resources-filtered/org/exist/storage/statistics/conf.xml</include>
                                 <include>src/test/resources-filtered/org/exist/xquery/functions/transform/transform-from-pkg-test.conf.xml</include>
                                 <include>src/main/antlr/org/exist/xquery/parser/XQueryTree.g</include>
+                                <include>src/main/java/org/exist/Indexer.java</include>
                                 <include>src/main/java/org/exist/backup/SystemExport.java</include>
                                 <include>src/main/java/org/exist/client/ClientFrame.java</include>
                                 <include>src/main/java/org/exist/client/Connection.java</include>
@@ -734,23 +736,28 @@
                                 <include>src/main/java/org/exist/collections/Collection.java</include>
                                 <include>src/main/java/org/exist/collections/CollectionConfiguration.java</include>
                                 <include>src/main/java/org/exist/collections/CollectionConfigurationManager.java</include>
+                                <include>src/main/java/org/exist/collections/MutableCollection.java</include>
                                 <include>src/main/java/org/exist/collections/triggers/CollectionTrigger.java</include>
                                 <include>src/main/java/org/exist/collections/triggers/DocumentTrigger.java</include>
                                 <include>src/main/java/org/exist/config/Configuration.java</include>
                                 <include>src/main/java/org/exist/config/ConfigurationImpl.java</include>
+                                <include>src/main/java/org/exist/dom/memtree/AttrImpl.java</include>
                                 <include>src/main/java/org/exist/dom/memtree/DocumentImpl.java</include>
                                 <include>src/main/java/org/exist/dom/memtree/DOMIndexer.java</include>
                                 <include>src/main/java/org/exist/dom/memtree/ElementImpl.java</include>
                                 <include>src/main/java/org/exist/dom/memtree/MemTreeBuilder.java</include>
                                 <include>src/main/java/org/exist/dom/memtree/NodeImpl.java</include>
                                 <include>src/main/java/org/exist/dom/persistent/AbstractCharacterData.java</include>
+                                <include>src/main/java/org/exist/dom/persistent/AttrImpl.java</include>
                                 <include>src/main/java/org/exist/dom/persistent/CommentImpl.java</include>
                                 <include>src/main/java/org/exist/dom/persistent/DocumentImpl.java</include>
                                 <include>src/main/java/org/exist/dom/persistent/DocumentSet.java</include>
                                 <include>src/main/java/org/exist/dom/persistent/ElementImpl.java</include>
                                 <include>src/main/java/org/exist/dom/persistent/NodeProxy.java</include>
                                 <include>src/test/java/org/exist/dom/persistent/NodeTest.java</include>
+                                <include>src/test/java/org/exist/dom/persistent/PersistentDomTest.java</include>
                                 <include>src/main/java/org/exist/dom/persistent/ProcessingInstructionImpl.java</include>
+                                <include>src/main/java/org/exist/dom/persistent/StoredNode.java</include>
                                 <include>src/main/java/org/exist/dom/persistent/SymbolTable.java</include>
                                 <include>src/main/java/org/exist/dom/persistent/TextImpl.java</include>
                                 <include>src/main/java/org/exist/dom/persistent/VirtualNodeSet.java</include>
@@ -838,8 +845,12 @@
                                 <include>src/test/java/org/exist/xquery/XQueryFunctionsTest.java</include>
                                 <include>src/main/java/org/exist/xquery/functions/fn/FunXmlToJson.java</include>
                                 <include>src/main/java/org/exist/xquery/functions/fn/LoadXQueryModule.java</include>
+                                <include>src/main/java/org/exist/xquery/functions/fn/transform/Convert.java</include>
+                                <include>src/main/java/org/exist/xquery/functions/fn/transform/Transform.java</include>
+                                <include>src/main/java/org/exist/xquery/functions/fn/transform/TreeUtils.java</include>
                                 <include>src/main/java/org/exist/xquery/functions/transform/Transform.java</include>
                                 <include>src/test/java/org/exist/xquery/functions/transform/TransformFromPkgTest.java</include>
+                                <include>src/test/java/org/exist/xquery/update/UpdateReplaceTest.java</include>
                                 <include>src/test/java/org/exist/xquery/value/Base64BinaryValueTypeTest.java</include>
                                 <include>src/main/java/org/exist/xslt/XsltURIResolverHelper.java</include>
                                 <include>src/test/resources/org/exist/validation/catalog.xml</include>
@@ -878,6 +889,7 @@
                                 <exclude>src/test/resources-filtered/org/exist/xquery/import-from-pkg-test.conf.xml</exclude>
                                 <exclude>src/test/resources-filtered/org/exist/xquery/functions/transform/transform-from-pkg-test.conf.xml</exclude>
                                 <exclude>src/main/antlr/org/exist/xquery/parser/XQueryTree.g</exclude>
+                                <exclude>src/main/java/org/exist/Indexer.java</exclude>
                                 <exclude>src/main/java/org/exist/backup/SystemExport.java</exclude>
                                 <exclude>src/main/java/org/exist/client/ClientFrame.java</exclude>
                                 <exclude>src/main/java/org/exist/client/Connection.java</exclude>
@@ -895,10 +907,12 @@
                                 <exclude>src/main/java/org/exist/collections/Collection.java</exclude>
                                 <exclude>src/main/java/org/exist/collections/CollectionConfiguration.java</exclude>
                                 <exclude>src/main/java/org/exist/collections/CollectionConfigurationManager.java</exclude>
+                                <exclude>src/main/java/org/exist/collections/MutableCollection.java</exclude>
                                 <exclude>src/main/java/org/exist/collections/triggers/CollectionTrigger.java</exclude>
                                 <exclude>src/main/java/org/exist/collections/triggers/DocumentTrigger.java</exclude>
                                 <exclude>src/main/java/org/exist/config/Configuration.java</exclude>
                                 <exclude>src/main/java/org/exist/config/ConfigurationImpl.java</exclude>
+                                <exclude>src/main/java/org/exist/dom/memtree/AttrImpl.java</exclude>
                                 <exclude>src/main/java/org/exist/dom/memtree/DocumentImpl.java</exclude>
                                 <exclude>src/main/java/org/exist/dom/memtree/DocumentTypeImpl.java</exclude>
                                 <exclude>src/main/java/org/exist/dom/memtree/DOMIndexer.java</exclude>
@@ -913,13 +927,16 @@
                                 <exclude>src/main/java/org/exist/dom/memtree/reference/ProcessingInstructionReferenceImpl.java</exclude>
                                 <exclude>src/main/java/org/exist/dom/memtree/reference/TextReferenceImpl.java</exclude>
                                 <exclude>src/main/java/org/exist/dom/persistent/AbstractCharacterData.java</exclude>
+                                <exclude>src/main/java/org/exist/dom/persistent/AttrImpl.java</exclude>
                                 <exclude>src/main/java/org/exist/dom/persistent/CommentImpl.java</exclude>
                                 <exclude>src/main/java/org/exist/dom/persistent/DocumentImpl.java</exclude>
                                 <exclude>src/main/java/org/exist/dom/persistent/DocumentSet.java</exclude>
                                 <exclude>src/main/java/org/exist/dom/persistent/ElementImpl.java</exclude>
                                 <exclude>src/main/java/org/exist/dom/persistent/NodeProxy.java</exclude>
                                 <exclude>src/test/java/org/exist/dom/persistent/NodeTest.java</exclude>
+                                <exclude>src/test/java/org/exist/dom/persistent/PersistentDomTest.java</exclude>
                                 <exclude>src/main/java/org/exist/dom/persistent/ProcessingInstructionImpl.java</exclude>
+                                <exclude>src/main/java/org/exist/dom/persistent/StoredNode.java</exclude>
                                 <exclude>src/main/java/org/exist/dom/persistent/SymbolTable.java</exclude>
                                 <exclude>src/main/java/org/exist/dom/persistent/TextImpl.java</exclude>
                                 <exclude>src/main/java/org/exist/dom/persistent/VirtualNodeSet.java</exclude>
@@ -987,6 +1004,7 @@
                                 <exclude>src/main/java/org/exist/xquery/functions/fn/LoadXQueryModule.java</exclude>
                                 <exclude>src/main/java/org/exist/xquery/functions/fn/ParsingFunctions.java</exclude>
                                 <exclude>src/test/java/org/exist/xquery/functions/fn/ParsingFunctionsTest.java</exclude>
+                                <exclude>src/test/java/org/exist/xquery/functions/fn/transform/ConvertTest.java</exclude>
                                 <exclude>src/test/java/org/exist/xquery/functions/fn/transform/FunTransformITTest.java</exclude>
                                 <exclude>src/main/java/org/exist/xquery/functions/system/GetUptime.java</exclude>
                                 <exclude>src/main/java/org/exist/xquery/functions/system/Shutdown.java</exclude>
@@ -1016,6 +1034,9 @@
                                 <exclude>src/test/java/org/exist/management/JmxRemoteTest.java</exclude>
                                 <exclude>src/test/java/org/exist/xmldb/CreateCollectionsTest.java</exclude>
                                 <exclude>src/test/java/org/exist/xquery/XQueryFunctionsTest.java</exclude>
+                                <exclude>src/main/java/org/exist/xquery/functions/fn/transform/Convert.java</exclude>
+                                <exclude>src/main/java/org/exist/xquery/functions/fn/transform/Transform.java</exclude>
+                                <exclude>src/main/java/org/exist/xquery/functions/fn/transform/TreeUtils.java</exclude>
                                 <exclude>src/main/java/org/exist/xquery/functions/transform/Transform.java</exclude>
                                 <exclude>src/test/java/org/exist/xquery/functions/transform/TransformFromPkgTest.java</exclude>
                                 <exclude>src/test/java/org/exist/xquery/value/Base64BinaryValueTypeTest.java</exclude>
@@ -1090,6 +1111,7 @@
                                 <exclude>src/test/java/org/exist/xquery/functions/xmldb/XMLDBAuthenticateTest.java</exclude>
                                 <exclude>src/main/java/org/exist/xquery/functions/util/Eval.java</exclude>
                                 <exclude>src/main/java/org/exist/xquery/pragmas/TimePragma.java</exclude>
+                                <exclude>src/test/java/org/exist/xquery/update/UpdateReplaceTest.java</exclude>
                                 <exclude>src/test/java/org/exist/xquery/util/URIUtilsTest.java</exclude>
                                 <exclude>src/main/java/org/exist/xquery/value/ArrayListValueSequence.java</exclude>
                                 <exclude>src/test/java/org/exist/xquery/value/BifurcanMapTest.java</exclude>

exist-core/src/main/java/org/exist/Indexer.java

@@ -1,4 +1,28 @@
 /*
+ * Elemental
+ * Copyright (C) 2024, Evolved Binary Ltd
+ *
+ * [email protected]
+ * https://www.evolvedbinary.com | https://www.elemental.xyz
+ *
+ * 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; version 2.1.
+ *
+ * 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
+ *
+ * NOTE: Parts of this file contain code from 'The eXist-db Authors'.
+ *       The original license header is included below.
+ *
+ * =====================================================================
+ *
  * eXist-db Open Source Native XML Database
  * Copyright (C) 2001 The eXist-db Authors
  *
@@ -591,7 +615,7 @@ public void startElement(final String namespace, final String name, final String
             setPrevious(null);
             node.setOwnerDocument(document);
             node.setAttributes((short) attrLength);
-            if (nsMappings != null && nsMappings.size() > 0) {
+            if (!nsMappings.isEmpty()) {
                 node.setNamespaceMappings(nsMappings);
                 nsMappings.clear();
             }
@@ -615,7 +639,7 @@ public void startElement(final String namespace, final String name, final String
             node.setOwnerDocument(document);
             node.setNodeId(broker.getBrokerPool().getNodeFactory().createInstance(nodeFactoryInstanceCnt++));
             node.setAttributes((short) attrLength);
-            if (nsMappings != null && nsMappings.size() > 0) {
+            if (!nsMappings.isEmpty()) {
                 node.setNamespaceMappings(nsMappings);
                 nsMappings.clear();
             }

exist-core/src/main/java/org/exist/collections/MutableCollection.java

@@ -1,4 +1,28 @@
 /*
+ * Elemental
+ * Copyright (C) 2024, Evolved Binary Ltd
+ *
+ * [email protected]
+ * https://www.evolvedbinary.com | https://www.elemental.xyz
+ *
+ * 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; version 2.1.
+ *
+ * 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
+ *
+ * NOTE: Parts of this file contain code from 'The eXist-db Authors'.
+ *       The original license header is included below.
+ *
+ * =====================================================================
+ *
  * eXist-db Open Source Native XML Database
  * Copyright (C) 2001 The eXist-db Authors
  *
@@ -1160,7 +1184,7 @@ public void storeDocument(final Txn transaction, final DBBroker broker, final Xm
 
     @Override
     public void storeDocument(final Txn transaction, final DBBroker broker, final XmldbURI name, final Node node, @Nullable MimeType mimeType) throws EXistException, PermissionDeniedException, SAXException, LockException, IOException {
-        storeDocument(transaction, broker, name, node, mimeType);
+        storeDocument(transaction, broker, name, node, mimeType, null, null, null, null, null);
     }
 
     @Override

exist-core/src/main/java/org/exist/dom/memtree/AttrImpl.java

@@ -1,4 +1,28 @@
 /*
+ * Elemental
+ * Copyright (C) 2024, Evolved Binary Ltd
+ *
+ * [email protected]
+ * https://www.evolvedbinary.com | https://www.elemental.xyz
+ *
+ * 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; version 2.1.
+ *
+ * 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
+ *
+ * NOTE: Parts of this file contain code from 'The eXist-db Authors'.
+ *       The original license header is included below.
+ *
+ * =====================================================================
+ *
  * eXist-db Open Source Native XML Database
  * Copyright (C) 2001 The eXist-db Authors
  *
@@ -79,6 +103,11 @@ public Node getFirstChild() {
         return null;
     }
 
+    @Override
+    public Node getPreviousSibling() {
+        return null;
+    }
+
     @Override
     public Node getNextSibling() {
         return null;

exist-core/src/main/java/org/exist/dom/persistent/AttrImpl.java

@@ -1,4 +1,28 @@
 /*
+ * Elemental
+ * Copyright (C) 2024, Evolved Binary Ltd
+ *
+ * [email protected]
+ * https://www.evolvedbinary.com | https://www.elemental.xyz
+ *
+ * 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; version 2.1.
+ *
+ * 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
+ *
+ * NOTE: Parts of this file contain code from 'The eXist-db Authors'.
+ *       The original license header is included below.
+ *
+ * =====================================================================
+ *
  * eXist-db Open Source Native XML Database
  * Copyright (C) 2001 The eXist-db Authors
  *
@@ -385,6 +409,11 @@ public Node getFirstChild() {
         return null;
     }
 
+    @Override
+    public Node getPreviousSibling() {
+        return null;
+    }
+
     @Override
     public Node getNextSibling() {
         return null;