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Need to load new app with lots of old data

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I an converting Pharmacy systems from a 30 year old COBOL system to a SQL*Svr 2005 based system front ended with VB.net and ASP.net GUIs. I can extract and load the data from the old system into whatever format works best for getting it into the new system. I am new to AutoIT and would like some advice on where to begin. How do I pull data from a column/row record format and sequentially load this data into a GUI one record at a time? I know how to write do/while loops, etc., the question is how can I use AutoIT to do this as I need to use the 3rd party vendor GUIs to ensure all the edit checks are included...I cannot write directly to the back end database. A "kick-start" of help would be most appreciated!

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