What I need is to add functionality to upload xml file on wordpress page and then sync my custom_table with this xml so the table reflects xml file.
XML file size is now ~6MB but I guess it might grow in the future. During syncing custom_table has to be intact - I mean that changes to the table during syncing have to be atomic - all or nothing.
It is a good idea to do this in normal php script or I should better make some background job for this stuff? For example upload xml file to server and then run in background a job which will parse xml file and put to DB?
6MB is a lot when you are dealing with a slow internet connection and with a script that has a chance of timing out.
I see 3 issues that you are trying to solve here -
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