PDOException (Unknown column 'url' in 'field list') when upgrading to OJS 3.3.0.6

[luca.g]

I get an error when upgrading from 3.2.1 to 3.3.0.6.

When going to the index/install/installUpgrade address, I get:

Errors occurred during installation:

A database error has occurred: PDOException: SQLSTATE[42S22]: Column not found: 1054 Unknown column 'url' in 'field list' in /var/www/html/clog.glasgow.ac.uk/www/ojs/lib/pkp/lib/vendor/doctrine/dbal/lib/Doctrine/DBAL/Driver/PDOConnection.php:78 Stack trace: #0 /var/www/html/clog.glasgow.ac.uk/www/ojs/lib/pkp/lib/vendor/doctrine/dbal/lib/Doctrine/DBAL/Driver/PDOConnection.php(78): PDO->prepare('select `url`, `...', Array) #1 /var/www/html/clog.glasgow.ac.uk/www/ojs/lib/pkp/lib/vendor/laravel/framework/src/Illuminate/Database/Connection.php(331): Doctrine\DBAL\Driver\PDOConnection->prepare('select `url`, `...') #2 /var/www/html/clog.glasgow.ac.uk/www/ojs/lib/pkp/lib/vendor/laravel/framework/src/Illuminate/Database/Connection.php(664): Illuminate\Database\Connection->Illuminate\Database\{closure}('select `url`, `...', Array) #3 /var/www/html/clog.glasgow.ac.uk/www/ojs/lib/pkp/lib/vendor/laravel/framework/src/Illuminate/Database/Connection.php(631): Illuminate\Database\Connection->runQueryCallback('select `url`, `...', Array, Object(Closure)) #4 /var/www/html/clog.glasgow.ac.uk/www/ojs/lib/pkp/lib/vendor/laravel/framework/src/Illuminate/Database/Connection.php(339): Illuminate\Database\Connection->run('select `url`, `...', Array, Object(Closure)) #5 /var/www/html/clog.glasgow.ac.uk/www/ojs/lib/pkp/lib/vendor/laravel/framework/src/Illuminate/Database/Query/Builder.php(2270): Illuminate\Database\Connection->select('select `url`, `...', Array, true) #6 /var/www/html/clog.glasgow.ac.uk/www/ojs/lib/pkp/lib/vendor/laravel/framework/src/Illuminate/Database/Query/Builder.php(2445): Illuminate\Database\Query\Builder->runSelect() #7 /var/www/html/clog.glasgow.ac.uk/www/ojs/lib/pkp/lib/vendor/laravel/framework/src/Illuminate/Database/Query/Builder.php(2753): Illuminate\Database\Query\Builder->Illuminate\Database\Query\{closure}() #8 /var/www/html/clog.glasgow.ac.uk/www/ojs/lib/pkp/lib/vendor/laravel/framework/src/Illuminate/Database/Query/Builder.php(2447): Illuminate\Database\Query\Builder->onceWithColumns(Array, Object(Closure)) #9 /var/www/html/clog.glasgow.ac.uk/www/ojs/lib/pkp/classes/migration/upgrade/PKPv3_3_0UpgradeMigration.inc.php(246): Illuminate\Database\Query\Builder->pluck('url', 'navigation_menu...') #10 /var/www/html/clog.glasgow.ac.uk/www/ojs/lib/pkp/classes/migration/upgrade/PKPv3_3_0UpgradeMigration.inc.php(121): PKPv3_3_0UpgradeMigration->_makeRemoteUrlLocalizable() #11 /var/www/html/clog.glasgow.ac.uk/www/ojs/lib/pkp/classes/install/Installer.inc.php(405): PKPv3_3_0UpgradeMigration->up() #12 /var/www/html/clog.glasgow.ac.uk/www/ojs/lib/pkp/classes/install/Installer.inc.php(251): Installer->executeAction(Array) #13 /var/www/html/clog.glasgow.ac.uk/www/ojs/lib/pkp/classes/install/Installer.inc.php(174): Installer->executeInstaller() #14 /var/www/html/clog.glasgow.ac.uk/www/ojs/lib/pkp/classes/install/form/UpgradeForm.inc.php(43): Installer->execute() #15 /var/www/html/clog.glasgow.ac.uk/www/ojs/lib/pkp/pages/install/InstallHandler.inc.php(130): UpgradeForm->execute() #16 /var/www/html/clog.glasgow.ac.uk/www/ojs/lib/pkp/classes/core/PKPRouter.inc.php(395): InstallHandler->installUpgrade(Array, Object(Request)) #17 /var/www/html/clog.glasgow.ac.uk/www/ojs/lib/pkp/classes/core/PKPPageRouter.inc.php(246): PKPRouter->_authorizeInitializeAndCallRequest(Array, Object(Request), Array, false) #18 /var/www/html/clog.glasgow.ac.uk/www/ojs/lib/pkp/classes/core/Dispatcher.inc.php(144): PKPPageRouter->route(Object(Request)) #19 /var/www/html/clog.glasgow.ac.uk/www/ojs/lib/pkp/classes/core/PKPApplication.inc.php(362): Dispatcher->dispatch(Object(Request)) #20 /var/www/html/clog.glasgow.ac.uk/www/ojs/index.php(68): PKPApplication->execute() #21 {main} Next Doctrine\DBAL\Driver\PDO\Exception: SQLSTATE[42S22]: Column not found: 1054 Unknown column 'url' in 'field list' in /var/www/html/clog.glasgow.ac.uk/www/ojs/lib/pkp/lib/vendor/doctrine/dbal/lib/Doctrine/DBAL/Driver/PDO/Exception.php:18 Stack trace: #0 /var/www/html/clog.glasgow.ac.uk/www/ojs/lib/pkp/lib/vendor/doctrine/dbal/lib/Doctrine/DBAL/Driver/PDOConnection.php(83): Doctrine\DBAL\Driver\PDO\Exception::new(Object(PDOException)) #1 /var/www/html/clog.glasgow.ac.uk/www/ojs/lib/pkp/lib/vendor/laravel/framework/src/Illuminate/Database/Connection.php(331): Doctrine\DBAL\Driver\PDOConnection->prepare('select `url`, `...') #2 /var/www/html/clog.glasgow.ac.uk/www/ojs/lib/pkp/lib/vendor/laravel/framework/src/Illuminate/Database/Connection.php(664): Illuminate\Database\Connection->Illuminate\Database\{closure}('select `url`, `...', Array) #3 /var/www/html/clog.glasgow.ac.uk/www/ojs/lib/pkp/lib/vendor/laravel/framework/src/Illuminate/Database/Connection.php(631): Illuminate\Database\Connection->runQueryCallback('select `url`, `...', Array, Object(Closure)) #4 /var/www/html/clog.glasgow.ac.uk/www/ojs/lib/pkp/lib/vendor/laravel/framework/src/Illuminate/Database/Connection.php(339): Illuminate\Database\Connection->run('select `url`, `...', Array, Object(Closure)) #5 /var/www/html/clog.glasgow.ac.uk/www/ojs/lib/pkp/lib/vendor/laravel/framework/src/Illuminate/Database/Query/Builder.php(2270): Illuminate\Database\Connection->select('select `url`, `...', Array, true) #6 /var/www/html/clog.glasgow.ac.uk/www/ojs/lib/pkp/lib/vendor/laravel/framework/src/Illuminate/Database/Query/Builder.php(2445): Illuminate\Database\Query\Builder->runSelect() #7 /var/www/html/clog.glasgow.ac.uk/www/ojs/lib/pkp/lib/vendor/laravel/framework/src/Illuminate/Database/Query/Builder.php(2753): Illuminate\Database\Query\Builder->Illuminate\Database\Query\{closure}() #8 /var/www/html/clog.glasgow.ac.uk/www/ojs/lib/pkp/lib/vendor/laravel/framework/src/Illuminate/Database/Query/Builder.php(2447): Illuminate\Database\Query\Builder->onceWithColumns(Array, Object(Closure)) #9 /var/www/html/clog.glasgow.ac.uk/www/ojs/lib/pkp/classes/migration/upgrade/PKPv3_3_0UpgradeMigration.inc.php(246): Illuminate\Database\Query\Builder->pluck('url', 'navigation_menu...') #10 /var/www/html/clog.glasgow.ac.uk/www/ojs/lib/pkp/classes/migration/upgrade/PKPv3_3_0UpgradeMigration.inc.php(121): PKPv3_3_0UpgradeMigration->_makeRemoteUrlLocalizable() #11 /var/www/html/clog.glasgow.ac.uk/www/ojs/lib/pkp/classes/install/Installer.inc.php(405): PKPv3_3_0UpgradeMigration->up() #12 /var/www/html/clog.glasgow.ac.uk/www/ojs/lib/pkp/classes/install/Installer.inc.php(251): Installer->executeAction(Array) #13 /var/www/html/clog.glasgow.ac.uk/www/ojs/lib/pkp/classes/install/Installer.inc.php(174): Installer->executeInstaller() #14 /var/www/html/clog.glasgow.ac.uk/www/ojs/lib/pkp/classes/install/form/UpgradeForm.inc.php(43): Installer->execute() #15 /var/www/html/clog.glasgow.ac.uk/www/ojs/lib/pkp/pages/install/InstallHandler.inc.php(130): UpgradeForm->execute() #16 /var/www/html/clog.glasgow.ac.uk/www/ojs/lib/pkp/classes/core/PKPRouter.inc.php(395): InstallHandler->installUpgrade(Array, Object(Request)) #17 /var/www/html/clog.glasgow.ac.uk/www/ojs/lib/pkp/classes/core/PKPPageRouter.inc.php(246): PKPRouter->_authorizeInitializeAndCallRequest(Array, Object(Request), Array, false) #18 /var/www/html/clog.glasgow.ac.uk/www/ojs/lib/pkp/classes/core/Dispatcher.inc.php(144): PKPPageRouter->route(Object(Request)) #19 /var/www/html/clog.glasgow.ac.uk/www/ojs/lib/pkp/classes/core/PKPApplication.inc.php(362): Dispatcher->dispatch(Object(Request)) #20 /var/www/html/clog.glasgow.ac.uk/www/ojs/index.php(68): PKPApplication->execute() #21 {main} Next Illuminate\Database\QueryException: SQLSTATE[42S22]: Column not found: 1054 Unknown column 'url' in 'field list' (SQL: select `url`, `navigation_menu_item_id` from `navigation_menu_items` where `context_id` = 1) in /var/www/html/clog.glasgow.ac.uk/www/ojs/lib/pkp/lib/vendor/laravel/framework/src/Illuminate/Database/Connection.php:671 Stack trace: #0 /var/www/html/clog.glasgow.ac.uk/www/ojs/lib/pkp/lib/vendor/laravel/framework/src/Illuminate/Database/Connection.php(631): Illuminate\Database\Connection->runQueryCallback('select `url`, `...', Array, Object(Closure)) #1 /var/www/html/clog.glasgow.ac.uk/www/ojs/lib/pkp/lib/vendor/laravel/framework/src/Illuminate/Database/Connection.php(339): Illuminate\Database\Connection->run('select `url`, `...', Array, Object(Closure)) #2 /var/www/html/clog.glasgow.ac.uk/www/ojs/lib/pkp/lib/vendor/laravel/framework/src/Illuminate/Database/Query/Builder.php(2270): Illuminate\Database\Connection->select('select `url`, `...', Array, true) #3 /var/www/html/clog.glasgow.ac.uk/www/ojs/lib/pkp/lib/vendor/laravel/framework/src/Illuminate/Database/Query/Builder.php(2445): Illuminate\Database\Query\Builder->runSelect() #4 /var/www/html/clog.glasgow.ac.uk/www/ojs/lib/pkp/lib/vendor/laravel/framework/src/Illuminate/Database/Query/Builder.php(2753): Illuminate\Database\Query\Builder->Illuminate\Database\Query\{closure}() #5 /var/www/html/clog.glasgow.ac.uk/www/ojs/lib/pkp/lib/vendor/laravel/framework/src/Illuminate/Database/Query/Builder.php(2447): Illuminate\Database\Query\Builder->onceWithColumns(Array, Object(Closure)) #6 /var/www/html/clog.glasgow.ac.uk/www/ojs/lib/pkp/classes/migration/upgrade/PKPv3_3_0UpgradeMigration.inc.php(246): Illuminate\Database\Query\Builder->pluck('url', 'navigation_menu...') #7 /var/www/html/clog.glasgow.ac.uk/www/ojs/lib/pkp/classes/migration/upgrade/PKPv3_3_0UpgradeMigration.inc.php(121): PKPv3_3_0UpgradeMigration->_makeRemoteUrlLocalizable() #8 /var/www/html/clog.glasgow.ac.uk/www/ojs/lib/pkp/classes/install/Installer.inc.php(405): PKPv3_3_0UpgradeMigration->up() #9 /var/www/html/clog.glasgow.ac.uk/www/ojs/lib/pkp/classes/install/Installer.inc.php(251): Installer->executeAction(Array) #10 /var/www/html/clog.glasgow.ac.uk/www/ojs/lib/pkp/classes/install/Installer.inc.php(174): Installer->executeInstaller() #11 /var/www/html/clog.glasgow.ac.uk/www/ojs/lib/pkp/classes/install/form/UpgradeForm.inc.php(43): Installer->execute() #12 /var/www/html/clog.glasgow.ac.uk/www/ojs/lib/pkp/pages/install/InstallHandler.inc.php(130): UpgradeForm->execute() #13 /var/www/html/clog.glasgow.ac.uk/www/ojs/lib/pkp/classes/core/PKPRouter.inc.php(395): InstallHandler->installUpgrade(Array, Object(Request)) #14 /var/www/html/clog.glasgow.ac.uk/www/ojs/lib/pkp/classes/core/PKPPageRouter.inc.php(246): PKPRouter->_authorizeInitializeAndCallRequest(Array, Object(Request), Array, false) #15 /var/www/html/clog.glasgow.ac.uk/www/ojs/lib/pkp/classes/core/Dispatcher.inc.php(144): PKPPageRouter->route(Object(Request)) #16 /var/www/html/clog.glasgow.ac.uk/www/ojs/lib/pkp/classes/core/PKPApplication.inc.php(362): Dispatcher->dispatch(Object(Request)) #17 /var/www/html/clog.glasgow.ac.uk/www/ojs/index.php(68): PKPApplication->execute() #18 {main}

[israel.cefrin]

Hi @luca.g

This user had the same issue you are finding while upgrading. Please, have a look at the procedures he ran to upgrade successfully their OJS:

Problem with upgrading to OJS 3.3.0.3

Hello, thank you. I have used: php -d memory_limit=800M tools/upgrade.php upgrade ERROR: Upgrade failed: DB: SQLSTATE[HY000]: General error: 1215 Cannot add foreign key constraint (SQL: alter table submission_file_revisions add constraint submission_file_revisions_submission_file_id_foreign foreign key (submission_file_id) references submission_files (submission_file_id)) OK after this message I reed the forum and found it should be an issue due to the MyISAM format of the tables, there should…

Best,
Israel Cefrin
PKP Team

[luca.g]

Hello @israel.cefrin ,

the post of the user with the same issue seems to be without answer (second-last post of that thread). I cannot find any field_list table in my database.

I’m still stuck with this problem.

[luca.g]

Hello again,

I have restored a backup of the database and the error is gone.