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I want to simply process a layer by writing a tool script in a toolbox without having to connect any database, so I think I may have to set up a workspace environment in ArcMap, but I'm not sure if I need to do anything else.

Essentially I want to find a Python version of the ArcObjects IWorkspace.ExecuteSQL method.

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i'm not that clear what you're asking for, but... have you reviewed the doc for ArcSDESQLExecute ? Edit: also see GP Considerations for working with SDE –  gotchula Dec 31 '12 at 21:20

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For file geodatabases, I do not think this is possible through arcpy, but it is using GDAL/OGR: ogr2ogr / GDAL remove features in FileGDB while in use by ArcGIS Server map service

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