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I'm looking for a way to automate not just importing PDFs, but importing 2 pdfs per page while also rotating them. Example image below:
The red boxes show the two different PDF pages put 2-up on Indesign page. Notice they are also rotated 90 degrees. To accomplish this the rectangle frame for each pdf needs to be set and positioned on each page, then the actual PDF needs to be positioned in that frame so everything can be read. I've done it by hand before, but there's about 160 PDF pages, so automation would be amazing.
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After some quick tests, I'd say this is a job for a script. My first thought was to place graphics frames on a parent page, then apply rotation, fitting etc. to them; at worst, they'd have to be detached on the document page with Ctrl-Shift-click to allow placement of the PDFs.
Unfortunately, neither rotation nor fitting seems to be saved by Object Styles, making it a highly manual process using any built-in ID features.
You can, however, cut and paste those frames with all properties intact, and once you have a master pair set up, it might be efficient to just paste them across several pages and do manual placement in each. If you include a placeholder PDF, it seems that fitting to frame is preserved when you re-Place the content file.
I think only a script can do it all from scratch. But maybe I've missed something.
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Why do you have to do it that way - one under the other? Why not side-by-side?
How will you print it?
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A script would nice but you CAN do it with Data Merge.
You would have to extract the PDF into individual pages into a folder, and make a data file of the list of file names with "@images" at the top like so:
 After you have done that, prepare your InDesign document by creating a graphic frame the size you need it (vertically first, then rotate that frame -90°). Position it where you want, making note of the top and side margins you want, like my example with 3p top margin and 1p side margins.
Set up your data merge by selecting your data file and drag "image" to your graphic frame, like so:
 Then, select Multiple Records. Set up your margins, and spacing between. Your items butted up against each other so put in "0" (0p0). The bottom margin may need to adjust a bit so that you can physically fit two images on top of each other. You will see this in Preview. Under Options, select your Fitting Options. Unfortunately, if you wanted a specific %, there's no option for that.. Just resize your graphic frame so that the Fitting works the way you want.
 That should do it. Create merged document.
If you need help creating the data merge document from a folder of individual PDF pages, let me know.
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