Added a wait for SQLite to finish queries before closing the connection

Also:
- Transactions now execute as much as possible on the same connection instead
  of getting a new connection
- More shutdown messages when waiting for things (Like SQLite queries, or db transactions).

Affects issues:
- Possibly fixed #1814

Plan/common/src/main/java/com/djrapitops/plan/delivery/webserver/auth/ActiveCookieStore.java

@@ -71,7 +71,6 @@ public class ActiveCookieStore implements SubSystem {
     }
 
     public static void removeUserCookie(String username) {
-        System.out.println(USERS_BY_COOKIE);
         USERS_BY_COOKIE.entrySet().stream().filter(entry -> entry.getValue().getUsername().equals(username))
                 .findAny()
                 .map(Map.Entry::getKey)

Plan/common/src/main/java/com/djrapitops/plan/settings/locale/lang/PluginLang.java

@@ -58,6 +58,10 @@ public enum PluginLang implements Lang {
     DISABLED_PROCESSING_COMPLETE("Disable - Processing Complete", "Processing complete."),
     DISABLED_UNSAVED_SESSIONS("Disable - Unsaved Session Save", "Saving unfinished sessions.."),
     DISABLED_UNSAVED_SESSIONS_TIMEOUT("Disable - Unsaved Session Save Timeout", "Timeout hit, storing the unfinished sessions on next enable instead."),
+    DISABLED_WAITING_SQLITE("Disable - Waiting SQLite", "Waiting queries to finish to avoid SQLite crashing JVM.."),
+    DISABLED_WAITING_SQLITE_COMPLETE("Disable - Waiting SQLite Complete", "Closed SQLite connection."),
+    DISABLED_WAITING_TRANSACTIONS("Disable - Waiting Transactions", "Waiting for unfinished transactions to avoid data loss.."),
+    DISABLED_WAITING_TRANSACTIONS_COMPLETE("Disable - Waiting Transactions Complete", "Transaction queue closed."),
 
     VERSION_NEWEST("Version - Latest", "You're using the latest version."),
     VERSION_AVAILABLE("Version - New", "New Release (${0}) is available ${1}"),

Plan/common/src/main/java/com/djrapitops/plan/storage/database/SQLDB.java

@@ -24,6 +24,7 @@ import com.djrapitops.plan.settings.config.PlanConfig;
 import com.djrapitops.plan.settings.config.paths.PluginSettings;
 import com.djrapitops.plan.settings.config.paths.TimeSettings;
 import com.djrapitops.plan.settings.locale.Locale;
+import com.djrapitops.plan.settings.locale.lang.PluginLang;
 import com.djrapitops.plan.storage.database.queries.Query;
 import com.djrapitops.plan.storage.database.transactions.Transaction;
 import com.djrapitops.plan.storage.database.transactions.init.CreateIndexTransaction;
@@ -123,6 +124,7 @@ public abstract class SQLDB extends AbstractDatabase {
         }
         transactionExecutor.shutdown();
         try {
+            logger.info(locale.getString(PluginLang.DISABLED_WAITING_TRANSACTIONS));
             Long waitMs = config.getOrDefault(TimeSettings.DB_TRANSACTION_FINISH_WAIT_DELAY, TimeUnit.SECONDS.toMillis(20L));
             if (waitMs > TimeUnit.MINUTES.toMillis(5L)) {
                 logger.warn(TimeSettings.DB_TRANSACTION_FINISH_WAIT_DELAY.getPath() + " was set to over 5 minutes, using 5 min instead.");
@@ -138,6 +140,8 @@ public abstract class SQLDB extends AbstractDatabase {
             }
         } catch (InterruptedException e) {
             Thread.currentThread().interrupt();
+        } finally {
+            logger.info(locale.getString(PluginLang.DISABLED_WAITING_TRANSACTIONS_COMPLETE));
         }
         return Collections.emptyList();
     }

Plan/common/src/main/java/com/djrapitops/plan/storage/database/SQLiteDB.java

@@ -24,6 +24,7 @@ import com.djrapitops.plan.settings.locale.lang.PluginLang;
 import com.djrapitops.plan.storage.file.PlanFiles;
 import com.djrapitops.plan.storage.upkeep.DBKeepAliveTask;
 import com.djrapitops.plan.utilities.MiscUtils;
+import com.djrapitops.plan.utilities.SemaphoreAccessCounter;
 import com.djrapitops.plan.utilities.logging.ErrorContext;
 import com.djrapitops.plan.utilities.logging.ErrorLogger;
 import dagger.Lazy;
@@ -49,6 +50,13 @@ public class SQLiteDB extends SQLDB {
     private Connection connection;
     private Task connectionPingTask;
 
+    /*
+     * In charge of keeping a single thread in control of the connection to avoid
+     * one thread closing the connection while another is executing a statement as
+     * that might lead to a SIGSEGV signal JVM crash.
+     */
+    private final SemaphoreAccessCounter connectionLock = new SemaphoreAccessCounter();
+
     private SQLiteDB(
             File databaseFile,
             Locale locale,
@@ -132,6 +140,7 @@ public class SQLiteDB extends SQLDB {
         if (connection == null) {
             connection = getNewConnection(databaseFile);
         }
+        connectionLock.enter();
         return connection;
     }
 
@@ -140,14 +149,17 @@ public class SQLiteDB extends SQLDB {
         super.close();
         stopConnectionPingTask();
 
+        logger.info(locale.getString(PluginLang.DISABLED_WAITING_SQLITE));
+        connectionLock.waitUntilNothingAccessing();
         if (connection != null) {
             MiscUtils.close(connection);
         }
+        logger.info(locale.getString(PluginLang.DISABLED_WAITING_SQLITE_COMPLETE));
     }
 
     @Override
     public void returnToPool(Connection connection) {
-        // Connection pool not in use, no action required.
+        connectionLock.exit();
     }
 
     @Override

Plan/common/src/main/java/com/djrapitops/plan/storage/database/queries/QueryAPIQuery.java

@@ -42,13 +42,19 @@ public class QueryAPIQuery<T> implements Query<T> {
         Connection connection = null;
         try {
             connection = db.getConnection();
-            try (PreparedStatement preparedStatement = connection.prepareStatement(sql)) {
+            return executeWithConnection(connection);
-                return performQuery.apply(preparedStatement);
-            }
         } catch (SQLException e) {
             throw DBOpException.forCause(sql, e);
         } finally {
             db.returnToPool(connection);
         }
     }
+
+    public T executeWithConnection(Connection connection) {
+        try (PreparedStatement preparedStatement = connection.prepareStatement(sql)) {
+            return performQuery.apply(preparedStatement);
+        } catch (SQLException e) {
+            throw DBOpException.forCause(sql, e);
+        }
+    }
 }

Plan/common/src/main/java/com/djrapitops/plan/storage/database/queries/QueryStatement.java

@@ -48,9 +48,7 @@ public abstract class QueryStatement<T> implements Query<T> {
         Connection connection = null;
         try {
             connection = db.getConnection();
-            try (PreparedStatement preparedStatement = connection.prepareStatement(sql)) {
+            return executeWithConnection(connection);
-                return executeQuery(preparedStatement);
-            }
         } catch (SQLException e) {
             throw DBOpException.forCause(sql, e);
         } finally {
@@ -58,6 +56,14 @@ public abstract class QueryStatement<T> implements Query<T> {
         }
     }
 
+    public T executeWithConnection(Connection connection) {
+        try (PreparedStatement preparedStatement = connection.prepareStatement(sql)) {
+            return executeQuery(preparedStatement);
+        } catch (SQLException e) {
+            throw DBOpException.forCause(sql, e);
+        }
+    }
+
     public T executeQuery(PreparedStatement statement) throws SQLException {
         try {
             statement.setFetchSize(fetchSize);

Plan/common/src/main/java/com/djrapitops/plan/storage/database/transactions/Transaction.java

@@ -22,6 +22,8 @@ import com.djrapitops.plan.storage.database.DBType;
 import com.djrapitops.plan.storage.database.Database;
 import com.djrapitops.plan.storage.database.SQLDB;
 import com.djrapitops.plan.storage.database.queries.Query;
+import com.djrapitops.plan.storage.database.queries.QueryAPIQuery;
+import com.djrapitops.plan.storage.database.queries.QueryStatement;
 import com.djrapitops.plan.utilities.logging.ErrorContext;
 import net.playeranalytics.plugin.scheduling.TimeAmount;
 
@@ -194,8 +196,14 @@ public abstract class Transaction {
     }
 
     protected <T> T query(Query<T> query) {
+        if (query instanceof QueryStatement) {
+            return ((QueryStatement<T>) query).executeWithConnection(connection);
+        } else if (query instanceof QueryAPIQuery) {
+            return ((QueryAPIQuery<T>) query).executeWithConnection(connection);
+        } else {
             return query.executeQuery(db);
         }
+    }
 
     protected boolean execute(Executable executable) {
         return executable.execute(connection);
@@ -226,7 +234,9 @@ public abstract class Transaction {
         transaction.db = db;
         transaction.dbType = dbType;
         transaction.connection = this.connection;
+        if (transaction.shouldBeExecuted()) {
             transaction.performOperations();
+        }
         transaction.connection = null;
         transaction.dbType = null;
         transaction.db = null;

Plan/common/src/main/java/com/djrapitops/plan/storage/database/transactions/patches/Patch.java

@@ -34,20 +34,34 @@ import static com.djrapitops.plan.storage.database.sql.building.Sql.*;
 public abstract class Patch extends OperationCriticalTransaction {
 
     private static final String ALTER_TABLE = "ALTER TABLE ";
+    private boolean appliedPreviously = false;
+    private boolean appliedNow = false;
 
     public abstract boolean hasBeenApplied();
 
     protected abstract void applyPatch();
 
+    public boolean isApplied() {
+        if (!success) throw new IllegalStateException("Asked a Patch if it is applied before it was executed!");
+        return appliedPreviously || appliedNow;
+    }
+
+    public boolean wasApplied() {
+        return appliedNow;
+    }
+
     @Override
     protected boolean shouldBeExecuted() {
-        return !hasBeenApplied();
+        boolean hasBeenApplied = hasBeenApplied();
+        if (hasBeenApplied) appliedPreviously = true;
+        return !hasBeenApplied;
     }
 
     @Override
     protected void performOperations() {
         if (dbType == DBType.MYSQL) disableForeignKeyChecks();
         applyPatch();
+        appliedNow = true;
         if (dbType == DBType.MYSQL) enableForeignKeyChecks();
     }
 

Plan/common/src/main/java/com/djrapitops/plan/storage/upkeep/DBKeepAliveTask.java

@@ -33,14 +33,14 @@ import java.sql.Statement;
  * @author Fuzzlemann
  */
 public class DBKeepAliveTask extends PluginRunnable {
-    private final IReconnect iReconnect;
+    private final Reconnector reconnector;
     private final PluginLogger logger;
     private final ErrorLogger errorLogger;
     private Connection connection;
 
-    public DBKeepAliveTask(Connection connection, IReconnect iReconnect, PluginLogger logger, ErrorLogger errorLogger) {
+    public DBKeepAliveTask(Connection connection, Reconnector reconnector, PluginLogger logger, ErrorLogger errorLogger) {
         this.connection = connection;
-        this.iReconnect = iReconnect;
+        this.reconnector = reconnector;
         this.logger = logger;
         this.errorLogger = errorLogger;
     }
@@ -56,7 +56,7 @@ public class DBKeepAliveTask extends PluginRunnable {
             }
         } catch (SQLException pingException) {
             try {
-                connection = iReconnect.reconnect();
+                connection = reconnector.reconnect();
             } catch (SQLException reconnectionError) {
                 errorLogger.error(reconnectionError, ErrorContext.builder()
                         .whatToDo("Reload Plan and Report this if the issue persists").build());
@@ -68,7 +68,7 @@ public class DBKeepAliveTask extends PluginRunnable {
         }
     }
 
-    public interface IReconnect {
+    public interface Reconnector {
         Connection reconnect() throws SQLException;
     }
 }

Plan/common/src/main/java/com/djrapitops/plan/utilities/SemaphoreAccessCounter.java

@@ -0,0 +1,39 @@
+package com.djrapitops.plan.utilities;
+
+import java.util.concurrent.atomic.AtomicInteger;
+
+public class SemaphoreAccessCounter {
+
+    private final AtomicInteger accessCounter;
+    private final Object lockObject;
+
+    public SemaphoreAccessCounter() {
+        accessCounter = new AtomicInteger(0);
+        lockObject = new Object();
+    }
+
+    public void enter() {
+        accessCounter.incrementAndGet();
+    }
+
+    public void exit() {
+        synchronized (lockObject) {
+            int value = accessCounter.decrementAndGet();
+            if (value == 0) {
+                lockObject.notifyAll();
+            }
+        }
+    }
+
+    public void waitUntilNothingAccessing() {
+        while (accessCounter.get() > 0) {
+            synchronized (lockObject) {
+                try {
+                    lockObject.wait();
+                } catch (InterruptedException e) {
+                    Thread.currentThread().interrupt();
+                }
+            }
+        }
+    }
+}

Plan/common/src/test/java/com/djrapitops/plan/storage/database/DBPatchMySQLRegressionTest.java

@@ -33,6 +33,7 @@ import utilities.mocks.PluginMockComponent;
 import java.nio.file.Path;
 import java.util.Optional;
 
+import static org.junit.jupiter.api.Assertions.assertFalse;
 import static org.junit.jupiter.api.Assertions.assertTrue;
 import static org.junit.jupiter.api.Assumptions.assumeTrue;
 
@@ -152,6 +153,7 @@ class DBPatchMySQLRegressionTest extends DBPatchRegressionTest {
         KillsOptimizationPatch patch = new KillsOptimizationPatch();
         underTest.executeTransaction(patch);
 
-        assertTrue(patch.hasBeenApplied());
+        assertTrue(patch.isApplied());
+        assertFalse(patch.wasApplied());
     }
 }

Plan/common/src/test/java/com/djrapitops/plan/storage/database/DBPatchRegressionTest.java

@@ -86,8 +86,11 @@ abstract class DBPatchRegressionTest {
     void assertPatchesHaveBeenApplied(Patch[] patches) {
         List<String> failed = new ArrayList<>();
         for (Patch patch : patches) {
-            if (!patch.hasBeenApplied()) {
+            if (!patch.isApplied()) {
+                System.out.println("! NOT APPLIED: " + patch.getClass().getSimpleName());
                 failed.add(patch.getClass().getSimpleName());
+            } else {
+                System.out.println("  WAS APPLIED: " + patch.getClass().getSimpleName());
             }
         }
         assertTrue(failed.isEmpty(), "Patches " + failed + " were not applied properly.");

Plan/common/src/test/java/com/djrapitops/plan/storage/database/DatabaseTest.java

@@ -292,7 +292,7 @@ public interface DatabaseTest extends DatabaseTestPreparer {
         // Test expected result
         Optional<BaseUser> updatedBaseUser = db().query(BaseUserQueries.fetchBaseUserOfPlayer(playerUUID));
         assertEquals(0L, updatedBaseUser.isPresent() ? updatedBaseUser.get().getRegistered() : null);
-        assertTrue(testedPatch.hasBeenApplied());
+        assertTrue(testedPatch.isApplied());
     }
 
     @Test