Does OPS feed in to it easily? Do you use an automated file prep software at all?
OnPrintShop (OPS) is what runs our website for those of you who don't know. Yes it does feed in nicely, but that's because it's been custom built from the ground up to do so. OPS has a fairly robust API that allows us to integrate with it. We have asked OPS to add additional fields and connectivity to their API over the years and they have done a good job of doing that. Most recently they are working on giving us a customer facing reorder link and the ability to replace customer artwork with our preflighted artwork. This means that when you go to our site and place a reorder, you will be reordering with our preflighted artwork, saving us time and making the product more consistent.
If you were going to do it, I would have Filemaker pull data directly from OPS using the API, I would then use the plugin called FM books to connect to Quickbooks to push and pull data for accounting. If I had to rebuild it by myself, that's probably what I would do.
What we do is we use a program called OpenSync that creates a mySQL database. OpenSync keeps the SQL database in sync with quickbooks, and we connect to that database in Filemaker. I also have a good friend that is a Javascript/myPHP/SQL developer, so he uses that mySQL database to connect to the OnPrintShop API.
It's a less robust system since it relies on more parts, but it allowed me to focus on just connecting Filemaker to one external data source. When I started this 3 years ago, I had no idea what I was doing, so that made it a little easier.
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In terms of automated file prep, we are still working this out. We use FM to move our files around taking advantage of a program called Super Container by 360works. It runs on a Mac Mini and a 23TB NAS drive we have locally. We take advantage of the mac/supercontainer's ability to quickly generate thumbnails of even the largest files (otherwise we are a windows shop).
We currently use Pitstop server, Switch, and a slew of hotfolders to automate some of our preflight processes. We export XML and CSV files and drop them in the hot folders with the artwork. Pitstop server grabs them and runs through a few basic automatons, then gives us the file back. Filemaker picks it up from there. We do all our nesting within Zund's Prepcenter. It's all far from automated, but we're getting there little by little.
I would look into Pitstop Server, Caldera Prime Center, Tilia Griffin/Phoenix and/or Printfactory if I were you.