I have a CSV file that contains a lot of integer values. Is it better to insert these individual values in bulk as in a full transaction or should I be inserting the CSV file itself into the MySQL?
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Insert the individual values in bulk. In other words, each row of the csv file should become a row in the database with the same number of columns.
Using Notepad++ you can use a regex find and replace to easily convert your CSV into a very large insert statement. Replace