fix(server): prevent graph clear API from clearing meta table in MySQL backend storage

hugegraph-server/hugegraph-mysql/src/main/java/org/apache/hugegraph/backend/store/mysql/MysqlStore.java

@@ -24,6 +24,7 @@
 import java.util.List;
 import java.util.Map;
 import java.util.concurrent.ConcurrentHashMap;
+import java.util.stream.Collectors;
 
 import org.apache.hugegraph.backend.BackendException;
 import org.apache.hugegraph.backend.id.Id;
@@ -54,7 +55,6 @@ public abstract class MysqlStore extends AbstractBackendStore<Session> {
     private final BackendStoreProvider provider;
 
     private final Map<HugeType, MysqlTable> tables;
-
     private MysqlSessions sessions;
 
     public MysqlStore(final BackendStoreProvider provider,
@@ -336,7 +336,7 @@ protected void clearTables() {
 
     protected void truncateTables() {
         Session session = this.sessions.session();
-        for (MysqlTable table : this.tables()) {
+        for (MysqlTable table : this.getTruncatedTables()) {
             table.truncate(session);
         }
     }
@@ -345,6 +345,14 @@ protected Collection<MysqlTable> tables() {
         return this.tables.values();
     }
 
+    protected Collection<MysqlTable> getTruncatedTables() {
+        // Exclude meta table to preserve system metadata during graph clear
+        return this.tables.entrySet().stream()
+                          .filter(e -> !(HugeType.META == e.getKey()))
+                          .map(Map.Entry::getValue)
+                          .collect(Collectors.toList());
+    }
+
     @Override
     protected final MysqlTable table(HugeType type) {
         assert type != null;

hugegraph-server/hugegraph-test/src/main/java/org/apache/hugegraph/unit/UnitTestSuite.java

@@ -46,6 +46,8 @@
 import org.apache.hugegraph.unit.id.IdTest;
 import org.apache.hugegraph.unit.id.IdUtilTest;
 import org.apache.hugegraph.unit.id.SplicingIdGeneratorTest;
+import org.apache.hugegraph.unit.mysql.BaseMysqlUnitTest;
+import org.apache.hugegraph.unit.mysql.MysqlTest;
 import org.apache.hugegraph.unit.mysql.MysqlUtilTest;
 import org.apache.hugegraph.unit.mysql.WhereBuilderTest;
 import org.apache.hugegraph.unit.rocksdb.RocksDBCountersTest;
@@ -130,6 +132,8 @@
         /* mysql */
         MysqlUtilTest.class,
         WhereBuilderTest.class,
+        BaseMysqlUnitTest.class,
+        MysqlTest.class,
 
         /* rocksdb */
         RocksDBSessionsTest.class,

hugegraph-server/hugegraph-test/src/main/java/org/apache/hugegraph/unit/mysql/BaseMysqlUnitTest.java

@@ -0,0 +1,66 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements.  See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You 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 org.apache.hugegraph.unit.mysql;
+
+import org.apache.commons.configuration2.Configuration;
+import org.apache.hugegraph.backend.store.mysql.MysqlSessions;
+import org.apache.hugegraph.backend.store.mysql.MysqlStoreProvider;
+import org.apache.hugegraph.config.HugeConfig;
+import org.apache.hugegraph.testutil.Utils;
+import org.apache.hugegraph.unit.BaseUnitTest;
+import org.junit.After;
+
+public class BaseMysqlUnitTest extends BaseUnitTest {
+
+    private static final String GRAPH_NAME = "test_graph";
+
+    protected HugeConfig config;
+    protected MysqlStoreProvider provider;
+    protected MysqlSessions sessions;
+
+    public void setup() throws Exception {
+        Configuration conf = Utils.getConf();
+        this.config = new HugeConfig(conf);
+        this.provider = new MysqlStoreProvider();
+        this.provider.open(GRAPH_NAME);
+        this.provider.loadSystemStore(config).open(config);
+        this.provider.loadGraphStore(config).open(config);
+        this.provider.loadSchemaStore(config).open(config);
+        this.provider.init();
+        this.sessions = new MysqlSessions(config, GRAPH_NAME, this.provider.loadGraphStore(config).store());
+        this.sessions.open();
+    }
+
+    @After
+    public void down() {
+        if (this.provider != null) {
+            try {
+                this.provider.close();
+            } catch (Exception e) {
+                LOG.warn("Mysql provider close failed ", e);
+            }
+        }
+        if (this.sessions != null) {
+            try {
+                this.sessions.close();
+            } catch (Exception e) {
+                LOG.warn("Mysql sessions close failed ", e);
+            }
+        }
+    }
+}

hugegraph-server/hugegraph-test/src/main/java/org/apache/hugegraph/unit/mysql/MysqlTest.java

@@ -0,0 +1,115 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements.  See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You 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 org.apache.hugegraph.unit.mysql;
+
+import org.apache.hugegraph.backend.store.BackendStore;
+import org.apache.hugegraph.backend.store.mysql.MysqlSessions;
+import org.apache.hugegraph.backend.store.mysql.ResultSetWrapper;
+import org.apache.hugegraph.testutil.Assert;
+import org.junit.Before;
+import org.junit.Test;
+
+import java.sql.SQLException;
+
+public class MysqlTest extends BaseMysqlUnitTest {
+
+    @Before
+    public void setUp() throws Exception {
+        super.setup();
+    }
+
+    @Test
+    public void testMysqlMetaVersion() throws SQLException {
+        BackendStore systemStore = this.provider.loadSystemStore(config);
+
+        // Record system version before truncation
+        String beforeVersion = systemStore.storedVersion();
+
+        // Get sessions for direct table operations
+        MysqlSessions.Session session = this.sessions.session();
+        session.open();
+
+        // Get the actual table names from the store
+        String vertexTable = "g_v";
+        String edgeOutTable = "g_oe";
+        String edgeInTable = "g_ie";
+
+        // Insert test vertex data directly using simple SQL
+        String insertVertex = String.format(
+                "INSERT INTO %s (ID, LABEL, PROPERTIES, EXPIRED_TIME) VALUES ('test_vertex', 1, " +
+                "'{\"name\":\"test_vertex\"}', 0)",
+                vertexTable
+        );
+        session.execute(insertVertex);
+
+        // Insert test edge data directly using simple SQL
+        String insertEdgeOut = String.format(
+                "INSERT INTO %s (OWNER_VERTEX, DIRECTION, LABEL, SUB_LABEL, SORT_VALUES, " +
+                "OTHER_VERTEX, PROPERTIES, EXPIRED_TIME) VALUES ('test_vertex', 0, 1, 0, '', " +
+                "'target_vertex', '{\"weight\":1.0}', 0)",
+                edgeOutTable
+        );
+        session.execute(insertEdgeOut);
+
+        String insertEdgeIn = String.format(
+                "INSERT INTO %s (OWNER_VERTEX, DIRECTION, LABEL, SUB_LABEL, SORT_VALUES, " +
+                "OTHER_VERTEX, PROPERTIES, EXPIRED_TIME) VALUES ('target_vertex', 1, 1, 0, '', " +
+                "'test_vertex', '{\"weight\":1.0}', 0)",
+                edgeInTable
+        );
+        session.execute(insertEdgeIn);
+
+        // Verify data exists by querying
+        String selectVertex = String.format("SELECT * FROM %s WHERE ID = 'test_vertex'", vertexTable);
+        String selectEdgeOut = String.format(
+                "SELECT * FROM %s WHERE OWNER_VERTEX = 'test_vertex' AND DIRECTION = 0",
+                edgeOutTable);
+        String selectEdgeIn = String.format(
+                "SELECT * FROM %s WHERE OWNER_VERTEX = 'target_vertex' AND DIRECTION = 1",
+                edgeInTable);
+        try (
+                ResultSetWrapper vResult = session.select(selectVertex);
+                ResultSetWrapper oeResult = session.select(selectEdgeOut);
+                ResultSetWrapper ieResult = session.select(selectEdgeIn);
+        ) {
+            Assert.assertTrue("vertex data should exist", vResult.next());
+            Assert.assertTrue("out edge data should exist", oeResult.next());
+            Assert.assertTrue("in edge data should exist", ieResult.next());
+        }
+
+        // Execute truncate operation, clears all graph data but preserves system tables
+        this.provider.truncate();
+
+        // Verify system version remains unchanged after truncation
+        String afterVersion = systemStore.storedVersion();
+        Assert.assertNotNull("System metadata version should exist", afterVersion);
+        Assert.assertEquals("System metadata version should remain unchanged after truncation",
+                            beforeVersion, afterVersion);
+
+        // Verify data has been cleared
+        try (
+                ResultSetWrapper vResult = session.select(selectVertex);
+                ResultSetWrapper oeResult = session.select(selectEdgeOut);
+                ResultSetWrapper ieResult = session.select(selectEdgeIn);
+        ) {
+            Assert.assertFalse("vertex data should not exist", vResult.next());
+            Assert.assertFalse("out edge data should not exist", oeResult.next());
+            Assert.assertFalse("in edge data should not exist", ieResult.next());
+        }
+    }
+}