Use "?" for parameter markers in both native query and query translation

src/integrationTest/java/com/mongodb/hibernate/BasicCrudIntegrationTests.java

@@ -237,6 +237,37 @@ void testGetByPrimaryKeyWithNullValueField() {
         }
     }
 
+    @Nested
+    class NativeQueryTests {
+
+        @Test
+        void testNative() {
+            var book = new Book();
+            book.id = 1;
+            book.title = "In Search of Lost Time";
+            book.publishYear = 1913;
+
+            sessionFactoryScope.inTransaction(session -> session.persist(book));
+
+            var nativeQuery =
+                    """
+                    {
+                        aggregate: "books",
+                        pipeline: [
+                            { $match :  { _id: { $eq: :id } } },
+                            { $project: { _id: 1, publishYear: 1, title: 1, author: 1 } }
+                        ]
+                    }
+                    """;
+            sessionFactoryScope.inTransaction(session -> {
+                var query = session.createNativeQuery(nativeQuery, Book.class)
+                        .setParameter("id", book.id);
+                var queriedBook = query.getSingleResult();
+                assertThat(queriedBook).usingRecursiveComparison().isEqualTo(book);
+            });
+        }
+    }
+
     private static void assertCollectionContainsExactly(BsonDocument expectedDoc) {
         assertThat(mongoCollection.find()).containsExactly(expectedDoc);
     }

src/main/java/com/mongodb/hibernate/internal/translate/AbstractMqlTranslator.java

@@ -56,9 +56,13 @@
 import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
+
+import org.bson.BsonUndefined;
+import org.bson.json.Converter;
 import org.bson.json.JsonMode;
 import org.bson.json.JsonWriter;
 import org.bson.json.JsonWriterSettings;
+import org.bson.json.StrictJsonWriter;
 import org.hibernate.engine.spi.SessionFactoryImplementor;
 import org.hibernate.internal.util.collections.Stack;
 import org.hibernate.persister.entity.EntityPersister;
@@ -151,7 +155,9 @@
 
 abstract class AbstractMqlTranslator<T extends JdbcOperation> implements SqlAstTranslator<T> {
     private static final JsonWriterSettings JSON_WRITER_SETTINGS =
-            JsonWriterSettings.builder().outputMode(JsonMode.EXTENDED).build();
+            JsonWriterSettings.builder().outputMode(JsonMode.EXTENDED)
+                    .undefinedConverter((bsonUndefined, strictJsonWriter) -> strictJsonWriter.writeRaw("?"))
+                    .build();
 
     private final SessionFactoryImplementor sessionFactory;
 

src/main/java/com/mongodb/hibernate/jdbc/MongoParameterRecognizer.java

@@ -0,0 +1,99 @@
+/*
+ * Copyright 2025-present MongoDB, Inc.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package com.mongodb.hibernate.jdbc;
+
+class MongoParameterRecognizer {
+
+    static String replace(String json) {
+        StringBuilder builder = new StringBuilder(json.length());
+
+        int i = 0;
+        while (i < json.length()) {
+            char c = json.charAt(i++);
+            switch (c) {
+                case '{':
+                case '}':
+                case '[':
+                case ']':
+                case ':':
+                case ',':
+                case ' ':
+                    builder.append(c);
+                    break;
+                case '\'':
+                case '"':
+                    i = scanString(c, i, json, builder);
+                    break;
+                case '?':
+                    builder.append("{$undefined: true}");
+                    break;
+                default:
+                    if (c == '-' || Character.isDigit(c)) {
+                        i = scanNumber(c, i, json, builder);
+                    } else if (c == '$' || c == '_' || Character.isLetter(c)) {
+                        i = scanUnquotedString(c, i, json, builder);
+                    } else {
+                        builder.append(c);  // or throw exception, as this isn't valid JSON
+                    }
+            }
+        }
+        return builder.toString();
+    }
+
+    private static int scanNumber(char firstCharacter, int startIndex, String json, StringBuilder builder) {
+        builder.append(firstCharacter);
+        int i = startIndex;
+        char c = json.charAt(i++);
+        while (i < json.length() && Character.isDigit(c)) {
+            builder.append(c);
+            c = json.charAt(i++);
+        }
+        return i - 1;
+    }
+
+    private static int scanUnquotedString(final char firstCharacter, final int startIndex, final String json, final StringBuilder builder) {
+        builder.append(firstCharacter);
+        int i = startIndex;
+        char c = json.charAt(i++);
+        while (i < json.length() && Character.isLetterOrDigit(c)) {
+            builder.append(c);
+            c = json.charAt(i++);
+        }
+        return i - 1;
+    }
+
+    private static int scanString(final char quoteCharacter, final int startIndex, final String json, final StringBuilder builder) {
+        int i = startIndex;
+        builder.append(quoteCharacter);
+        while (i < json.length()) {
+            char c = json.charAt(i++);
+            if (c == '\\') {
+                builder.append(c);
+                if (i < json.length()) {
+                    c = json.charAt(i++);
+                    builder.append(c);
+                }
+            } else if (c == quoteCharacter) {
+                builder.append(c);
+                return i;
+            } else {
+                builder.append(c);
+            }
+        }
+        return i;
+    }
+}

src/main/java/com/mongodb/hibernate/jdbc/MongoPreparedStatement.java

@@ -61,7 +61,7 @@ final class MongoPreparedStatement extends MongoStatement implements PreparedSta
             MongoDatabase mongoDatabase, ClientSession clientSession, MongoConnection mongoConnection, String mql)
             throws SQLSyntaxErrorException {
         super(mongoDatabase, clientSession, mongoConnection);
-        this.command = MongoStatement.parse(mql);
+        this.command = MongoStatement.parse(MongoParameterRecognizer.replace(mql));
         this.parameterValueSetters = new ArrayList<>();
         parseParameters(command, parameterValueSetters);
     }

src/main/java/com/mongodb/hibernate/jdbc/MongoResultSet.java

@@ -210,13 +210,18 @@ public double getDouble(int columnIndex) throws SQLException {
     @Override
     public ResultSetMetaData getMetaData() throws SQLException {
         checkClosed();
-        return new MongoResultSetMetadata();
+        return new MongoResultSetMetadata(fieldNames);
     }
 
     @Override
     public int findColumn(String columnLabel) throws SQLException {
         checkClosed();
-        throw new SQLFeatureNotSupportedException("To be implemented in scope of native query tickets");
+        for (int i = 0; i < fieldNames.size(); i++) {
+            if (fieldNames.get(i).equals(columnLabel)) {
+                return i + 1;
+            }
+        }
+        throw new SQLException("Unknown column label " + columnLabel);
     }
 
     @Override
@@ -263,5 +268,22 @@ private void checkColumnIndex(int columnIndex) throws SQLException {
         }
     }
 
-    private static final class MongoResultSetMetadata implements ResultSetMetaDataAdapter {}
+    private static final class MongoResultSetMetadata implements ResultSetMetaDataAdapter {
+        private final List<String> fieldNames;
+
+        public MongoResultSetMetadata(List<String> fieldNames) {
+            this.fieldNames = fieldNames;
+        }
+
+        @Override
+        public int getColumnCount() {
+            return fieldNames.size();
+        }
+
+
+        @Override
+        public String getColumnLabel(int column) {
+            return fieldNames.get(column - 1);
+        }
+    }
 }