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I am developping an app using Ionic in Ubuntu. And installed phpmyadmin and it is running correctly (http://localhost/phpmyadmin).

How should I set up Ionic to connect to phpmyadmin and run my queries?

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PHPMyAdmin is a tool to work with MySQL databases. You don't want to connect it with Ionic.

What you want is to run queries on MySQL. The problem is that the app made with Ionic will not be in the same network as the MySQL server this might make it unsafe.

What you need is to write a WEB application that your Ionic app will use to do actions which will then execute SQL queries to the database.

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thx a lot, so how do I do that? do you have any advice or link?
It's a deep and dark forest. You're probably not skilled enough. To start looking, you'll first need to learn a programming language that you can use to create a web service (PHP, Python, Node or mostly anything, really). Then do it. Then you do HTTP requests with Ionic. There's plenty of resources on google.

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