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user should not upload the file, JavaScript or any other technology shall automatically get the file from the specified path.
You can schedule the task to periodically check if the file has arrived in a particular folder, then run a PHP method that would read the file and then insert it into the MySQL database.
The scheduling can be done using crontab
This should be a good starting point to read on how to go about it.
http://code.tutsplus.com/tutorials/managing-cron-jobs-with-php--net-19428
If you do not want to use a web interface to do so, try using a MySQL client on your PC. Some of them have import features where you can import CSV files. You can set separator (comma or semicolon) and headers. Other way is to use the online MySQL manager from your hosting provider like PHP MyAdmin
I don't think so, that could be happens using PHP. You have to submit a form to upload a file from local to server.