Add PDF files but keep them in my papers directory

Hi everyone,

I’ve looked around on the web and in this forum a fair bit but have not been able to find an answer to this.

I like to keep all my papers in a dropbox folder so that I can access them from anywhere. I also edit and mark them up in Adobe Acrobat. But, I like EndNote’s ability to preview papers in the windows. However, when I add PDF files to EndNote’s database, it makes a copy of the PDF and moves it into a random folder.

Is there any way to add PDFs to EndNote but leave them in the directory I want them to be in?


have you taken a look at the check-box at the bottom of the “Attach File”-window? (says “Copy this file to the default file attachment folder and create a relative link.”

if you uncheck it, than Endnote should use absolute links and not copy the pdf.

But that is only for the files where the box is unchecked. Means you have to redo the attachments for the others you already have in your library (as they are still with a relative link)

As noted, even when you’ve unticked the box for “move my PDFs”, EN will automatically move some PDFs into its internal storage (e.g., those it discovers with “Find Full Text”). I’m sure there’s a reason, but it sure is frustrating. I’m a Mac User, so I have access to AppleScript and have written a script to rename such PDFs and move them to where I want them. Not ideal, but largely solves the problem. I suspect there is an equivalent on the Windows side, but don’t know it. (By the way, EN’s AppleScript dictionary is pretty awesome and a really under-appreciated feature of the program).


I am happy to try that when I add files individually. Is there a way to do that when you import pdfs from a whole folder?


I was not complete in my thought. I am trying to add PDFs from a large directory in batch format, but whenever I add a PDF to have EndNote create a reference (as opposed to adding a PDF to an already-existing reference), EndNote moves the PDF to a different folder.


That is how it works.  The only work flow that allows one to keep the PDFs in their original location, is the manual one (and only when the appropriate preference to do so is selected).  Any automated addition of PDFs copies them to the relative Endnote folder structure and that preference has no effect. 

Any idea why? Should that be somehting I put forward as a suggestion? Seems like an odd way of doing things but maybe I’m wrong. I was hoping there would be an automated way to add files but from a specified directory without them being moved out.

I suspect it was a developers choice.  It has been discussed before by users, and I can look for the threads.  In practice, it is probably easier to back up and maintain relative links as opposed to absolute links.  But I am just a user and unassociated with Endnote or TR, so I can’t really say.  

Bumping an old thread here because no luck resolving this elsewhere. 

I’ve been researching my area for a couple of years now and have a ton of annotated pdf’s filed in set file structure that I don’t want to change.  I haven’t used endnote for a few years so running through the tutorials now and was really pleased to see the import function … yet when I run the import, I end up with a completely meaningless numeric folders duplicating the PDF.

I feel like I’m missing a really basic point here because from the forums and online it looks like this issue comes up regularly but doesn’t seem to have been sorted out.  Does this mean then that all users have their PDF’s in these meaningless numeric folders and only access them through endnote ever after?  Surely it wouldn’t be difficult to have e.g., subfolders within PDF by Group name and an Unassigned for those that haven’t been put in groups?    At least that gives a bit more structure to it.

Thanks for any info.


Yeah, I gave up trying to get this to work. I just keep all my PDFs in a folder and view them through reader instead of endnote, and I don’t import them. It’s a huge annoyance.

Thanks Lord Smurf.  It’s somehow helps hearing others are feeling the same pain.  Hopefully the developers come up with something on this down the track.

I ended up speaking to Endnote and they confirmed the point.  So I’m in a real quandry with what to do.  Do I :

  1.  Just bite the bullet and import them all and lose the logical directory structure?  Part of me wonders if I’m just being “change averse” and need to get over it and just do this.  What’s stopping me doing this is that, as far as I can see it, it means I’m forever bound to using Endnote to find those docs going forward because my logical file structure is gone?  Is that right or is there another way  around this?

  2.  Keep the files in the original folders and then have to go to one of the databases and manually import the refs?

It’s a tough one.  

Just wanted to add my sympathy. I agree with the problem, especially considering the Endnote has no true way of organizing files within the program (too few levels of subgroups).