[Solved] lib/pkp/tools/parseCitations.php in 3.3.0.4 throws an Exception

Nason_Bimbe · April 5, 2021, 9:54pm

Running php lib/pkp/tools/parseCitations.php all

Throws the following Exception
PHP Fatal error: Uncaught Error: Call to a member function getConnection() on null in /[]/lib/pkp/lib/vendor/laravel/framework/src/Illuminate/Database/Capsule/Manager.php:74
Stack trace:
#0 /[]/lib/pkp/lib/vendor/laravel/framework/src/Illuminate/Database/Capsule/Manager.php(200): Illuminate\Database\Capsule\Manager::connection()
#1 /[]/lib/pkp/classes/db/DAO.inc.php(94): Illuminate\Database\Capsule\Manager::__callStatic()
#2 /[]/lib/pkp/classes/context/ContextDAO.inc.php(77): DAO->retrieveRange()
#3 /[]/lib/pkp/tools/parseCitations.php(56): ContextDAO->getAll()
#4 /[]/lib/pkp/tools/parseCitations.php(107): CitationsParsingTool->execute()
#5 {main}
thrown in /[]/lib/pkp/lib/vendor/laravel/framework/src/Illuminate/Database/Capsule/Manager.php on line 74

Using the solution at Unable to upgrade 3.3.0.2: Call to a member function getConnection() on null · Issue #6703 · pkp/pkp-lib · GitHub solves the problem by adding
Application::get()->initializeDatabaseConnection(); in the constructor of lib/pkp/tools/parseCitations.php

This need to be added to the codebase in GitHub

Cheers
Nason

asmecher · April 9, 2021, 5:16pm

Hi @Nason_Bimbe,

The connection initialization should be taken care of here:

github.com

pkp/pkp-lib/blob/stable-3_3_0/classes/core/PKPApplication.inc.php#L169


		import('classes.i18n.AppLocale');

		PKPString::init();

		$microTime = Core::microtime();
		Registry::set('system.debug.startTime', $microTime);

		$notes = array();
		Registry::set('system.debug.notes', $notes);

		if (Config::getVar('general', 'installed')) $this->initializeDatabaseConnection();

		// Register custom autoloader functions for namespaces
		spl_autoload_register(function($class) {
			$prefix = 'PKP\\';
			$rootPath = BASE_SYS_DIR . "/lib/pkp/classes";
			customAutoload($rootPath, $prefix, $class);
		});
		spl_autoload_register(function($class) {
			$prefix = 'APP\\';
			$rootPath = BASE_SYS_DIR . "/classes";

Is it possible that you were running the script with installed set to Off in config.inc.php?

Regards,
Alec Smecher
Public Knowledge Project Team

Nason_Bimbe · April 9, 2021, 6:05pm

Hi @asmecher,
Just tested it again, you are correct I was running it with installed set to Off in config.inc.php. So I was running it after upgrading after resolving the issue described at Upgrade error: Duplicate entry 'xxx-yyy' for key 'citations_publication_seq' · Issue #5626 · pkp/pkp-lib · GitHub so ran it before reverting installed to On

Thanks
Nason

asmecher · April 9, 2021, 7:20pm

Hi @Nason_Bimbe,

Great, thanks for the follow-up!

Regards,
Alec Smecher
Public Knowledge Project Team