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By default Views uses 'views_plugin_query_default' plugin. How can I alter something so that Views could use another class for building queries?

I found one good example how to write Views query plugins: building views query plugins

But this example is for custom tables. But I need to have my own query builder for ordinary node, terms and users tables.

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Firstly you will need to have defined your query plugin to Views using hook_views_plugins():

function MYMODULE_views_plugins() {
  return array(
    'query' => array(
      'myplugin' => array(
        'title' => 'My custom plugin',
        'handler' => 'MyCustomQueryClass',
      ),
    ),
  );
}

Then, you should be able to override the query class used for any of the built-in tables using hook_views_data_alter() and setting the query class key in the table base property:

function MYMODULE_views_data_alter(&$data) {
    $data['node']['table']['base']['query class'] = 'myplugin';
}

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