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

Closes eXist-db/exist#5680

Author: adamretter

exist-core/pom.xml

@@ -691,6 +691,7 @@
                                 <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>
@@ -736,24 +737,29 @@
                                 <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/collections/triggers/XQueryStartupTrigger.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>
@@ -909,11 +915,13 @@
                                 <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/collections/triggers/XQueryStartupTrigger.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>
@@ -928,13 +936,16 @@
                                 <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>
@@ -1006,6 +1017,7 @@
                                 <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>

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;

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

@@ -195,10 +195,7 @@ public int getPosition() {
     }
 
     public boolean declaresNamespacePrefixes() {
-        if(namespaceMappings == null) {
-            return false;
-        }
-        return namespaceMappings.size() > 0;
+        return namespaceMappings != null && !namespaceMappings.isEmpty();
     }
 
     /**
@@ -474,13 +471,13 @@ public static void readNamespaceDecls(final List<String[]> namespaces, final Val
     }
 
     public void addNamespaceMapping(final String prefix, final String ns) {
-        if(prefix == null) {
+        if (prefix == null) {
             return;
         }
 
-        if(namespaceMappings == null) {
+        if (namespaceMappings == null) {
             namespaceMappings = new HashMap<>(1);
-        } else if(namespaceMappings.containsKey(prefix)) {
+        } else if (namespaceMappings.containsKey(prefix)) {
             return;
         }
 
@@ -1364,8 +1361,13 @@ public void setChildCount(final int count) {
     }
 
     public void setNamespaceMappings(final Map<String, String> map) {
-        this.namespaceMappings = new HashMap<>(map);
-        for(final String ns : namespaceMappings.values()) {
+        if (this.namespaceMappings == null) {
+            this.namespaceMappings = new HashMap<>(map);
+        } else {
+            this.namespaceMappings.clear();
+            this.namespaceMappings.putAll(map);
+        }
+        for (final String ns : namespaceMappings.values()) {
             ownerDocument.getBrokerPool().getSymbols().getNSSymbol(ns);
         }
     }
@@ -1544,7 +1546,7 @@ public void insertBefore(final Txn transaction, final NodeList nodes, final Node
             }
 
             final IStoredNode<?> following = (IStoredNode<?>) refChild;
-            final IStoredNode<?> previous = (IStoredNode<?>) following.getPreviousSibling();
+            final IStoredNode<?> previous = (IStoredNode<?>) ((StoredNode<?>) following).getPreviousSibling(true);
             if(previous == null) {
                 // there's no sibling node before the new node
                 final NodeId newId = following.getNodeId().insertBefore();
@@ -1676,8 +1678,11 @@ public void update(final Txn transaction, final NodeList newContent) throws DOME
      * Update a child node. This method will only update the child node
      * but not its potential descendant nodes.
      *
-     * @param oldChild to be replace
+     * @param oldChild to be replaced
      * @param newChild to be added
+     *
+     * @return the new node
+     *
      * @throws DOMException in case of a DOM error
      */
     @Override
@@ -1699,7 +1704,7 @@ public IStoredNode updateChild(final Txn transaction, final Node oldChild, final
             attr.setValue(StringValue.trimWhitespace(StringValue.collapseWhitespace(attr.getValue())));
             attr.setType(AttrImpl.ID);
         }
-        IStoredNode<?> previousNode = (IStoredNode<?>) oldNode.getPreviousSibling();
+        IStoredNode<?> previousNode = (IStoredNode<?>) ((StoredNode<?>) oldNode).getPreviousSibling(true);
         if(previousNode == null) {
             previousNode = this;
         } else {
@@ -1872,13 +1877,16 @@ public boolean visit(final IStoredNode node) {
     }
 
     /**
-     * Replaces the oldNode with the newChild
+     * Replaces the oldChild with the newChild
      *
      * @param transaction the transaction
      * @param newChild to replace oldChild
-     * @param oldChild to be replace by newChild
+     * @param oldChild to be replaced by newChild
+     *
      * @return The new node (this differs from the {@link org.w3c.dom.Node#replaceChild(Node, Node)} specification)
+     *
      * @throws DOMException in case of a DOM error
+     *
      * @see org.w3c.dom.Node#replaceChild(org.w3c.dom.Node, org.w3c.dom.Node)
      */
     @Override
@@ -1893,7 +1901,7 @@ public Node replaceChild(final Txn transaction, final Node newChild, final Node
         }
 
         final NodePath thisPath = getPath();
-        IStoredNode<?> previous = (IStoredNode<?>) oldNode.getPreviousSibling();
+        IStoredNode<?> previous = (IStoredNode<?>) ((StoredNode<?>) oldNode).getPreviousSibling(true);
         if(previous == null) {
             previous = this;
         } else {