Fix #1705 : MySQL connection might be lost after long operations

lib/Alchemy/Phrasea/Helper/User/Manage.php

@@ -163,6 +163,7 @@ class Manage extends Helper
         $stmt = $conn->prepare($sql);
         $stmt->execute(array(':email' => $email));
         $row = $stmt->fetch(\PDO::FETCH_ASSOC);
+        $stmt->closeCursor();
         $count = count($row);
 
         if (!is_array($row) || $count == 0) {

lib/classes/ACL.php

@@ -1130,6 +1130,7 @@ class ACL implements cache_cacheableInterface
                 throw new Exception('Error while deleteing some rights');
             }
         }
+        $stmt_del->closeCursor();
         $this->delete_data_from_cache(self::CACHE_RIGHTS_BAS);
 
         return $this;
@@ -1188,6 +1189,7 @@ class ACL implements cache_cacheableInterface
             if (!$this->has_access_to_sbas($sbas_id))
                 $stmt_ins->execute(array(':sbas_id' => $sbas_id, ':usr_id'  => $usr_id));
         }
+        $stmt_ins->closeCursor();
         $this->delete_data_from_cache(self::CACHE_RIGHTS_SBAS);
 
         return $this;
@@ -1305,6 +1307,7 @@ class ACL implements cache_cacheableInterface
         if (!$stmt_up->execute($params)) {
             throw new Exception('Error while updating some rights');
         }
+        $stmt_up->closeCursor();
         $this->delete_data_from_cache(self::CACHE_RIGHTS_SBAS);
 
         return $this;

lib/classes/User/Adapter.php

@@ -1420,6 +1420,7 @@ class User_Adapter implements User_Interface, cache_cacheableInterface
                 ':prop'   => $prop,
                 ':value'  => $value
             ));
+            $stmt->closeCursor();
             $this->delete_data_from_cache();
         } catch (\Exception $e) {
 

lib/classes/collection.php

@@ -81,6 +81,7 @@ class collection implements cache_cacheableInterface
         $stmt = $connbas->prepare($sql);
         $stmt->execute(array(':coll_id' => $this->coll_id));
         $row = $stmt->fetch(PDO::FETCH_ASSOC);
+        $stmt->closeCursor();
 
         if ( ! $row)
             throw new Exception('Unknown collection ' . $this->coll_id . ' on ' . $this->databox->get_dbname());

lib/classes/connection.php

@@ -167,6 +167,7 @@ class connection
     public static function close_PDO_connection($name)
     {
         if (isset(self::$_PDO_instance[$name])) {
+            self::$_PDO_instance[$name]->disconnect();
             self::$_PDO_instance[$name] = null;
             unset(self::$_PDO_instance[$name]);
         }

lib/classes/connection/abstract.php

@@ -15,11 +15,12 @@
  * @license     http://opensource.org/licenses/gpl-3.0 GPLv3
  * @link        www.phraseanet.com
  */
-abstract class connection_abstract extends PDO
+abstract class connection_abstract
 {
     protected $name;
     protected $credentials = array();
     protected $multi_db = true;
+    protected $connection;
 
     public function get_credentials()
     {
@@ -42,8 +43,12 @@ abstract class connection_abstract extends PDO
 
     public function ping()
     {
+        if (null === $this->connection) {
+            $this->initConn();
+        }
+
         try {
-            $this->query('SELECT 1');
+            $this->connection->query('SELECT 1');
         } catch (PDOException $e) {
             return false;
         }
@@ -51,41 +56,16 @@ abstract class connection_abstract extends PDO
         return true;
     }
 
-    /**
-     *
-     * @param  string       $statement
-     * @param  array        $driver_options
-     * @return PDOStatement
-     */
-    public function prepare($statement, $driver_options = array())
-    {
-        return parent::prepare($statement, $driver_options);
-    }
-
-    /**
-     *
-     * @return boolean
-     */
-    public function beginTransaction()
-    {
-        return parent::beginTransaction();
-    }
-
-    /**
-     *
-     * @return boolean
-     */
-    public function commit()
-    {
-        return parent::commit();
-    }
-
     /**
      *
      * @return string
      */
     public function server_info()
     {
-        return parent::getAttribute(constant("PDO::ATTR_SERVER_VERSION"));
+        if (null === $this->connection) {
+            $this->initConn();
+        }
+
+        return $this->connection->getAttribute(constant("PDO::ATTR_SERVER_VERSION"));
     }
 }

lib/classes/connection/interface.php

@@ -17,7 +17,6 @@
  */
 interface connection_interface
 {
-
     public function ping();
 
     public function get_name();
@@ -28,11 +27,5 @@ interface connection_interface
 
     public function close();
 
-    public function prepare($statement, $driver_options = array());
-
-    public function beginTransaction();
-
-    public function commit();
-
     public function server_info();
 }

lib/classes/connection/pdo.php

@@ -36,42 +36,45 @@ class connection_pdo extends connection_abstract implements connection_interface
     {
         $this->debug = $debug;
         $this->name = $name;
-        if ($dbname)
-            $dsn = 'mysql:dbname=' . $dbname . ';host=' . $hostname . ';port=' . $port . ';';
-        else
-            $dsn = 'mysql:host=' . $hostname . ';port=' . $port . ';';
 
         $this->credentials['hostname'] = $hostname;
         $this->credentials['port'] = $port;
         $this->credentials['user'] = $user;
         $this->credentials['password'] = $passwd;
+
         if ($dbname)
             $this->credentials['dbname'] = $dbname;
 
-        parent::__construct($dsn, $user, $passwd, $options);
+        $this->initConn();
-
-        $this->setAttribute(PDO::ATTR_ERRMODE, PDO::ERRMODE_EXCEPTION);
-        $this->query("
-      SET character_set_results = 'utf8', character_set_client = 'utf8',
-      character_set_connection = 'utf8', character_set_database = 'utf8',
-      character_set_server = 'utf8'");
 
         return $this;
     }
 
+    protected function initConn()
+    {
+        $this->connection = null;
+
+        if (isset($this->credentials['dbname']))
+            $dsn = 'mysql:dbname=' . $this->credentials['dbname'] . ';host=' . $this->credentials['hostname'] . ';port=' . $this->credentials['port'] . ';';
+        else
+            $dsn = 'mysql:host=' . $this->credentials['hostname'] . ';port=' . $this->credentials['port'] . ';';
+
+        $this->connection = new \PDO($dsn, $this->credentials['user'], $this->credentials['password'], array());
+
+        $this->connection->setAttribute(PDO::ATTR_ERRMODE, PDO::ERRMODE_EXCEPTION);
+        $this->connection->exec("
+            SET character_set_results = 'utf8', character_set_client = 'utf8',
+            character_set_connection = 'utf8', character_set_database = 'utf8',
+            character_set_server = 'utf8'");
+    }
+
     /**
      *
-     * @param  type         $statement
+     * @return void
-     * @param  type         $driver_options
-     * @return PDOStatement
      */
-    public function prepare($statement, $driver_options = array())
+    public function disconnect()
     {
-        if ($this->debug) {
+        $this->connection = null;
-            return new connection_pdoStatementDebugger(parent::prepare($statement, $driver_options));
-        } else {
-            return parent::prepare($statement, $driver_options);
-        }
     }
 
     /**
@@ -83,6 +86,48 @@ class connection_pdo extends connection_abstract implements connection_interface
         connection::close_PDO_connection($this->name);
     }
 
+    public function __call($method, $args)
+    {
+        if (null === $this->connection) {
+            $this->initConn();
+        }
+
+        if (!method_exists($this->connection, $method)) {
+            throw new \BadMethodCallException(sprintf('Method %s does not exist', $method));
+        }
+
+        $tries = 0;
+
+        do {
+            $tries++;
+            try {
+                set_error_handler(function ($errno, $errstr) {
+                    if (false !== strpos($errstr, 'Error while sending QUERY packet')) {
+                        throw new \Exception('MySQL server has gone away');
+                    }
+                    throw new \Exception($errstr);
+                });
+
+                if ('prepare' === $method && $this->debug) {
+                    $ret = new connection_pdoStatementDebugger(call_user_func_array(array($this->connection, $method), $args));
+                } else {
+                    $ret = call_user_func_array(array($this->connection, $method), $args);
+                }
+                restore_error_handler();
+
+                return $ret;
+            } catch (\Exception $e) {
+                restore_error_handler();
+
+                $found = (false !== strpos($e->getMessage(), 'MySQL server has gone away')) || (false !== strpos($e->getMessage(), 'errno=32 Broken pipe'));
+                if ($tries >= 2 || !$found) {
+                    throw $e;
+                }
+                $this->initConn();
+            }
+        } while (true);
+    }
+
     /**
      *
      * @param  string         $message

lib/classes/databox.php

@@ -1009,6 +1009,7 @@ class databox extends base
                 unset($e);
             }
         }
+        $stmt->closeCursor();
 
         $user->ACL()->give_access_to_base($base_ids);
         foreach ($base_ids as $base_id) {
@@ -1022,8 +1023,6 @@ class databox extends base
             );
         }
 
-        $stmt->closeCursor();
-
         return $this;
     }
 

lib/classes/databox/field.php

@@ -413,6 +413,7 @@ class databox_field implements cache_cacheableInterface
 
         $stmt = $connbas->prepare($sql);
         $stmt->execute($params);
+        $stmt->closeCursor();
 
         if ($this->renamed) {
             caption_field::rename_all_metadatas($this);

lib/classes/patch/370alpha7a.php

@@ -65,6 +65,7 @@ class patch_370alpha7a implements patchInterface
             $stmt = $conn->prepare($sql);
             $stmt->execute();
             $rs = $stmt->fetchAll();
+            $stmt->closeCursor();
         } catch (\PDOException $e) {
             // table not found
             if ($e->getCode() == '42S02') {

lib/classes/patch/370alpha8a.php

@@ -72,8 +72,8 @@ class patch_370alpha8a implements patchInterface
         if (($stmt = $conn->prepare($sql)) !== FALSE) {
             $stmt->execute();
             $ttasks = $row = $stmt->fetchAll();
-            $stmt->closeCursor();
         }
+        $stmt->closeCursor();
 
         $tdom = array();     // key = period
         $taskstodel = array();

lib/classes/patchthesaurus/204.php

@@ -74,7 +74,7 @@ class patchthesaurus_204
 
                 $sql2 = "UPDATE record SET status=((status | 15) & ~2)";
 
-                $stmt = $connbas->prepare($sql);
+                $stmt = $connbas->prepare($sql2);
                 $stmt->execute();
                 $stmt->closeCursor();
             }

lib/classes/record/adapter.php

@@ -1055,6 +1055,7 @@ class record_adapter implements record_Interface, cache_cacheableInterface
                 ':record_id' => $this->record_id
             )
         );
+        $stmt->closeCursor();
 
         $this->reindex();
 
@@ -1181,6 +1182,7 @@ class record_adapter implements record_Interface, cache_cacheableInterface
         $sql = 'UPDATE record SET jeton=(jeton | ' . JETON_MAKE_SUBDEF . ') WHERE record_id = :record_id';
         $stmt = $connbas->prepare($sql);
         $stmt->execute(array(':record_id' => $this->get_record_id()));
+        $stmt->closeCursor();
 
         return $this;
     }
@@ -1197,6 +1199,7 @@ class record_adapter implements record_Interface, cache_cacheableInterface
             WHERE record_id= :record_id';
         $stmt = $connbas->prepare($sql);
         $stmt->execute(array(':record_id' => $this->record_id));
+        $stmt->closeCursor();
 
         return $this;
     }
@@ -1264,6 +1267,7 @@ class record_adapter implements record_Interface, cache_cacheableInterface
             ':originalname'     => null,
             ':mime'             => null,
         ));
+        $stmt->closeCursor();
 
         $story_id = $databox->get_connection()->lastInsertId();
 
@@ -1319,6 +1323,7 @@ class record_adapter implements record_Interface, cache_cacheableInterface
             ':originalname'     => $file->getOriginalName(),
             ':mime'             => $file->getFile()->getMimeType(),
         ));
+        $stmt->closeCursor();
 
         $record_id = $databox->get_connection()->lastInsertId();
 

lib/classes/task/period/RecordMover.php

@@ -761,10 +761,10 @@ class task_period_RecordMover extends task_appboxAbstract
             while (($row = $stmt->fetch(PDO::FETCH_ASSOC))) {
                 $result['rids'][] = $row['record_id'];
             }
-            $stmt->closeCursor();
         } else {
             $result['err'] = $connbas->last_error();
         }
+        $stmt->closeCursor();
 
         return $result;
     }

tests/Alchemy/Tests/Phrasea/Application/OAuth2Test.php

@@ -70,6 +70,7 @@ class oauthv2_application_test extends \PhraseanetWebTestCaseAuthenticatedAbstra
         $t = array(':id' => $app->get_id());
         $stmt = $conn->prepare($sql);
         $stmt->execute($t);
+        $stmt->closeCursor();
         $sql = '
       DELETE FROM api_accounts
       WHERE api_account_id  = :id
@@ -78,6 +79,7 @@ class oauthv2_application_test extends \PhraseanetWebTestCaseAuthenticatedAbstra
         $t = array(':id' => $acc->get_id());
         $stmt = $conn->prepare($sql);
         $stmt->execute($t);
+        $stmt->closeCursor();
     }
 
     /**
@@ -119,6 +121,7 @@ class oauthv2_application_test extends \PhraseanetWebTestCaseAuthenticatedAbstra
         $stmt = $conn->prepare($sql);
         $stmt->execute($t);
         $result = $stmt->fetch(\PDO::FETCH_ASSOC);
+        $stmt->closeCursor();
 
         return $result;
     }
@@ -131,6 +134,7 @@ class oauthv2_application_test extends \PhraseanetWebTestCaseAuthenticatedAbstra
         $stmt = $conn->prepare($sql);
         $stmt->execute($t);
         $row = $stmt->fetch(\PDO::FETCH_ASSOC);
+        $stmt->closeCursor();
 
         return new \API_OAuth2_Account(self::$DI['app'], $row["api_account_id"]);
     }

tests/Alchemy/Tests/Phrasea/Authentication/Phrasea/NativeAuthenticationTest.php

@@ -5,7 +5,7 @@ namespace Alchemy\Tests\Phrasea\Authentication\Phrasea;
 use Alchemy\Phrasea\Authentication\Phrasea\NativeAuthentication;
 use Alchemy\Phrasea\Authentication\Exception\AccountLockedException;
 
-class NativeAuthenticationTest extends \PHPUnit_Framework_TestCase
+class NativeAuthenticationTest extends \PhraseanetPHPUnitAbstract
 {
     /**
      * @dataProvider provideReservedUsernames
@@ -16,7 +16,7 @@ class NativeAuthenticationTest extends \PHPUnit_Framework_TestCase
 
         $encoder = $this->getEncoderMock();
         $oldEncoder = $this->getOldEncoderMock();
-        $conn = $this->getMock('connection_interface');
+        $conn = $this->createConnectionMock();
         $request = $this->getRequestMock();
 
         $auth = new NativeAuthentication($encoder, $oldEncoder, $conn);
@@ -180,7 +180,7 @@ class NativeAuthenticationTest extends \PHPUnit_Framework_TestCase
         $encoder = $this->getEncoderMock();
         $oldEncoder = $this->getOldEncoderMock();
 
-        $conn = $this->getMock('connection_interface');
+        $conn = $this->createConnectionMock();
 
         $statement = $this->getMock('PDOStatement');
         $statement
@@ -248,7 +248,7 @@ class NativeAuthenticationTest extends \PHPUnit_Framework_TestCase
 
     private function getConnectionMock($username, $row = null)
     {
-        $conn = $this->getMock('connection_interface');
+        $conn = $this->createConnectionMock();
 
         $statement = $this->getMock('PDOStatement');
 

tests/Alchemy/Tests/Phrasea/SearchEngine/PhraseaEngineTest.php

@@ -90,6 +90,7 @@ class PhraseaEngineTest extends SearchEngineAbstractTest
 
             break;
         }
+        $stmt->closeCursor();
 
         $date = new \DateTime('-1 months');
 

tests/classes/PhraseanetPHPUnitAbstract.php

@@ -107,6 +107,8 @@ abstract class PhraseanetPHPUnitAbstract extends WebTestCase
 
         parent::setUp();
 
+        connection::close_connections();
+
         \PHPUnit_Framework_Error_Warning::$enabled = true;
         \PHPUnit_Framework_Error_Notice::$enabled = true;
 
@@ -989,4 +991,9 @@ abstract class PhraseanetPHPUnitAbstract extends WebTestCase
             ->disableOriginalConstructor()
             ->getMock();
     }
+
+    public function createConnectionMock()
+    {
+        return $this->getMock('connection_interface', array('close', 'get_credentials', 'server_info', 'prepare', 'beginTransaction', 'commit', 'ping', 'get_name', 'is_multi_db'));
+    }
 }

tests/classes/PhraseanetWebTestCaseAuthenticatedAbstract.php

@@ -136,10 +136,12 @@ abstract class PhraseanetWebTestCaseAuthenticatedAbstract extends PhraseanetPHPU
             ->get_connection()
             ->prepare('DROP DATABASE IF EXISTS `unit_test_db`');
         $stmt->execute();
+        $stmt->closeCursor();
         $stmt = self::$DI['app']['phraseanet.appbox']
             ->get_connection()
             ->prepare('DELETE FROM sbas WHERE dbname = "unit_test_db"');
         $stmt->execute();
+        $stmt->closeCursor();
     }
 
     protected function createDatabase()

tests/classes/Session/Session_LoggerTest.php

@@ -47,6 +47,7 @@ class Session_LoggerTest extends PhraseanetPHPUnitAbstract
         $stmt->execute($params);
         $this->assertEquals(1, $stmt->rowCount());
         $row = $stmt->fetch(PDO::FETCH_ASSOC);
+        $stmt->closeCursor();
         $this->assertEquals($this->object->get_id(), $row['id']);
         $log_id = $this->object->get_id();
         $ses_id = self::$DI['app']['session']->get('session_id');
@@ -67,5 +68,6 @@ class Session_LoggerTest extends PhraseanetPHPUnitAbstract
         $this->assertEquals(1, $stmt->rowCount());
         $row = $stmt->fetch(PDO::FETCH_ASSOC);
         $this->assertEquals($log_id, $row['id']);
+        $stmt->closeCursor();
     }
 }

tests/classes/connectionTest.php

@@ -0,0 +1,13 @@
+<?php
+
+class connectionTest extends \PhraseanetPHPUnitAbstract
+{
+    public function testMysqlTimeoutIsHandled()
+    {
+        $conn = connection::getPDOConnection(self::$DI['app']);
+        $conn->exec('SET @@local.wait_timeout= 1');
+        usleep(1200000);
+        $conn->exec('SHOW DATABASES');
+        connection::close_connections();
+    }
+}