I\'ve written a big sql script that creates a CSV file. I want to call a cronjob every night to create a fresh CSV file and have it available on the website.
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No, there's no way to overwrite it. From the docs:
file_name cannot be an existing file, which among other things prevents files such as /etc/passwd and database tables from being destroyed.
It might be a better idea to use a different filename each night, as having multiple backups means you can recover from problems that have existed for more than a day. You could then maintain a symlink that always points at the latest complete csv.