cleanupRemovedModules.php

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<?php
require_once __DIR__ . '/Maintenance.php';

class CleanupRemovedModules extends Maintenance {

    public function __construct() {
        parent::__construct();
        $this->addDescription(
            'Remove cache entries for removed ResourceLoader modules from the database' );
        $this->addOption( 'batchsize', 'Delete rows in batches of this size. Default: 500', false, true );
    }

    public function execute() {
        $dbw = $this->getDB( DB_MASTER );
        $rl = new ResourceLoader( ConfigFactory::getDefaultInstance()->makeConfig( 'main' ) );
        $moduleNames = $rl->getModuleNames();
        $moduleList = implode( ', ', array_map( [ $dbw, 'addQuotes' ], $moduleNames ) );
        $limit = max( 1, intval( $this->getOption( 'batchsize', 500 ) ) );

        $this->output( "Cleaning up module_deps table...\n" );
        $i = 1;
        $modDeps = $dbw->tableName( 'module_deps' );
        do {
            // $dbw->delete() doesn't support LIMIT :(
            $where = $moduleList ? "md_module NOT IN ($moduleList)" : '1=1';
            $dbw->query( "DELETE FROM $modDeps WHERE $where LIMIT $limit", __METHOD__ );
            $numRows = $dbw->affectedRows();
            $this->output( "Batch $i: $numRows rows\n" );
            $i++;
            wfWaitForSlaves();
        } while ( $numRows > 0 );
        $this->output( "done\n" );
    }
}

$maintClass = "CleanupRemovedModules";
require_once RUN_MAINTENANCE_IF_MAIN;