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I have 3 different components: 1) a file server with different shares 2) SharePoint 2010 Server, Enterprise license 3) a custom .NET 3.5 web site

What I want to be able to do is have SharePoint index the necessary share on my file server (easy, set up a content source for it), and then from the web site, perform a query against the SharePoint search indexer, and return the results to the web site for processing and display.

Is it possible to do this, or does the query have to be done from within a SharePoint site?

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It is possible, you can use SharePoint Search Web Service for the task. Only tricky part is the authentication but if you're using Windows authentication in your custom .NET site and on SharePoint you should be able to run these queries without explicitly having to pass any usernames/passwords to SharePoint.

Example here.

You can use e.g., this tool to test your search queries.

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Perfect. Having some trouble with the indexer failing on TIFF files at the momment (Access denied errors), but once I get that sorted, I'll look to putting this in, and I'll mark you up. –  Evan M. Feb 1 '12 at 21:47
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