C-Command Software Forum

Organising pdf files in EF - without losing the EndNote links?


after having successfully exported my email archive of the last five years (with some 13000 emails) into EagleFiler, I have developed a taste for using it for other things as well.

One that springs to mind is organising the masses of pdf files (mostly academic journal articles) that I have so far largely sitting in a folder in ~/Documents. Organising them with EF would have the advantages of quick preview, the ability to tag them, and to search through all of them very quickly.

However, there is one snag: I have created links to many of this files from my EndNote library. Obviously, as this involved a lot of work, I would like to maintain the links. So I thought I would rename the original folder, create an EF library, and then create an alias of that library’s “Files” folder (which contains the pdfs), and place it under the original folders name in its original place.

However, although accessing that alias in the Finder opens a view to all pdf files, it does not work from EndNote (simply changing the information per record in EndNote through search and replace, by the way, does not work either, which is why this attempt at a workaround was necessary in the first place).

Also, when I use Terminal to “cd” from ~/Documents into the aliased directory, I get an error message stating that it “is not a directory”. OK, it’s an alias, but shouldn’t that be of no concern to the operating system? I thought that this is exactly what aliases are for…

Sorry if this has been overly long, but perhaps someone can think of a solution here. I would hate to have to relink hundreds of pdf files to their EndNote records, which would have to be done manually, as I know of no way to automatize that. (I’m using EndNote X).

Many thanks for any help and thoughts in advance,


Hi - slightly embarrassed to answer my own question, but I wanted to record the solution here in case someone else has the problem.

The solution is easy: don’t create the link in the Finder, but do it in Terminal, using the “ln -s” command. I remembered vaguely that there was a difference between the two, and so, after writing my long post, I tried - and it worked.

Clearly, my workflow is flawed, and teh sequence of trying and writing should have been the other way around :slight_smile:

Thanks anyway,


Yes, you’ve found the solution that I would have recommended, which is to use a symbolic link instead of an alias. Symlinks are lower level than aliases, so most programs will transparently treat a symlink to a folder as a folder. For those who don’t want to use the command line, it is also possible to create symbolic links using Path Finder and some other utilities.

Another option would be to move EagleFiler’s Files folder to where EndNote expects its folder to be and put an alias to the Files folder next to the .eflibrary file. I have not fully tested this, but EaglerFiler is designed such that it should always follow the Files alias to the folder.

I eventually gave up on embedding explicit links in EndNote: they seemed too fragile. Now what I do is copy and paste the file name into the Label or Link fields on Endnote. (And yes, once I started this I usually try to have a file name start with the label e.g. Bohn2002A Greatest paper ever.pdf would be the file name, and Bohn2002A the label.)

Then to find the file, I just use spotlight on the file name or label. This finds the file no matter where it resides, even if I moved it around numerous times. This should work fine with EagleFiler, though I have not been using it long enough to be sure it works in practice as well as in theory.