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I think the answer should be easy but I can't find it.

maybe I've been put in the wrong direction finding sites telling how to clear my flood table like so:

drush php-eval 'db_query("DELETE FROM `flood`");'

But I think is should be like this so it also works for prefixed tables:

drush php-eval 'db_query("DELETE FROM `{flood}`");'

Or does db_query() works different in drush php-eval? As far as I know it just executes php but does it has the drupal 'library' available or not?

Now I could just try and see what happens but I think it's good to really know if there's a difference or not in running db_query() from drush or from code.

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I don't know this for definite but conceptually speaking, if Drush didn't use a standard Drupal bootstrap to perform these tasks it would have to re-implement all of that functionality itself.

Drush uses your site's settings.php file for the database connection, which leads me to believe it will also have access to things like $db_prefix.

I think it's safe to say exactly the same thing is happening when you run db_query() from Drush as if you run it from any other bootstrapped instance of Drupal.

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    Yes, that is absolutely correct for php-eval: the code will execute in the same environment that it does when running from within a Drupal site, so prefixed tables will be handled for {flood} and similar. However, please note that the sql-query command avoids modifying your query in any way unless you specify the --db-prefix option. The sql-query version of the above example would therefore be: drush sql-query --db-prefix 'DELETE FROM {flood};' (please excuse quoting variation; stack exchange code filter in effect)
    – greg_1_anderson
    Commented Sep 24, 2012 at 16:09

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