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I am using FME 2015 in order to build a workflow as shown in the image:enter image description here

As you can see in the figure I have an AttributeFilter which takes manually some value. I have to run this workflow multiple times for different values in the Attribute Filter. The issue I face is that once I modify the value (in AttributeFilter) then all the connections between the FeatureMerger and the writter (komvoi) are lost and I have to remake them by clicking..

My question is if there an automatic way to do this connection instead of manually.

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Check out https://blog.safe.com/2010/04/fmeevangelist62/ -- in particular, the part near the bottom about "Use Replace With AttributeCopier".

In short, make all the mappings manually once between FeatureMerger and your output feature type. Then right click on the main connector between those and say "Replace With AttributeCopier". Now you have a transformer that has the mappings you want. You can copy and reuse that transformer (if you have have several places you want the same renaming), or take that transformer and move it earlier in the workflow so that you're just working with the attributes in their destination name sooner rather than later.

Hope this helps.

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The other thing that will help is where the mapping could be reasonably guessed at by FME - for example "NISIDA" is obviously a match for "nisida"

In that scenario, use the Auto-Connect attributes option by right-clicking the feature connection.

I made a short video demo you can find here: http://screencast.com/t/Apb9fh3XKf

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