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answers:

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I develop a public-facing survey website. We get heavy IE6 usage, and it's not going away any time soon. Since we're dealing with the public, we can't tell people to use something else.

I wanted to start using selenium to do automated web testing, but it can't handle javascript alert boxes, which we use for error messages.

I was thinking about migrating to a more web 2.0 error message, but I'm not sure about compatibility with IE6. I couldn't find easily how well IE 6 works with scriptaculous.

If I can't use scriptaculous, what can I use that works in IE6 and is amenable to selenium testing?

A: 

I use prototype and scriptaculous in one of my projects for some really heavy JavaScript functionality and until now, I never had any issue with IE6.

You only have to follow the best practices from the prototype/scriptaculous API and you won't have any issue with IE6.

The only issues you might have are those that are general JavaScript issues of IE6 prototype doesn't have a workaround for.

I also used jQuery for some other functionality and it also works with IE6.

Kau-Boy