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Is there some way to create a layer file through web mapping application. If I expose data through a map service is there a way to create a .lyr file?

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I've never tried it but you could use the mapping application to allow the user to select what they want in the lyr file (data source, name, symbology, etc.), then use Python (specifically, SaveToLayerFile_management) to save the lyr file. –  Michael Todd Jul 26 '11 at 22:16
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I wrote a PrintSOE (ServerObjectExtention) which creates for each mapservice layer a lyr-file on mapservice startup. The purpose is to create large-format and high-quality printout's.

These lyr-files are accessible over the arcgisoutput-directory. It would be possible to access these lyr-files by a simple url.

You can find the project with full sources here: http://www.arcgis.com/home/item.html?id=6809086326ea4c76bf026a32bb9dd698

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