My workaround for cites with multiple files and "ghost" bad attachments

I think my message was yet again deleted, which drives me nuts, especially since I’m disabled.


I saw an old post about a problem that took a huge amount of time to deal with - well over 100 hours. Count the hours actually. Which is horrible for me since I’m still recovering from a disability - my right wrist and arm broke partly or fully in seven places. l thought I’d post my way of dealing with the problems as a general post.

My summary below gives you my workarounds to the problems of cites with bad links, duplicate pdfs within a cite and some things that might help you avoid them in the future.

You actually have two problems -

  1. First, I see you have what I call “ghost files”, where Endnote have a link where it lost its connection to the pdf, which is probably floating around somewhere in the database. You can recognize these because they look different and don’t open up.

  2. You also have many cites with multiple pdfs files attached to single citations.

It takes a lot of steps if you want to fully deal with the situation, these steps fix the problem despite its wasted time and frustration.

Below I listed how I deal with the problem, which works.

To get rid of the - what I call fake “ghost files” - do this:

  1. Put your cursor at the top level of the database (showing all cites).

From the menu, select Tools → Find Broken Attachments - and wait for Endnote to identify the list of ghost files.

Copy all the “ghost” cites from that database to a new empty one, perhaps named something like “broken cites.enl”.

At that point, I suggest you temporarily keep two copies of the broken files - temporarily for now, save the broken files from your original database in a new group called “broken links” because when you copy the cites over, the bad links disappear. Which is a good thing unless you are trying to figure out which file is associated with which cite. This allows you to go back as needed to the original database to look at the link and name of the missing pdf.

At that point, if your bad cites just included a ghost file - or a ghost file and a real pdf, it’s possible you have now fixed both problems - ghost files and duplicates.

Or, you may find that most of the cites have no attachments at all.


SECOND PROBLEM: Multiple files

You can do several things though it’s a royal pain in the neck.

If your problem cites includes both the “ghost” files as well as double files, you may as well work off the broken enl folder, since you have already removed the nonexistent links to files Endnote can’t find…

Then, identify the remaining cites that have duplicate pdfs by creating a smart group that searches for cites with attachments that include a carriage return in the file attachment. The carriage return is an option in smart group settings. (right-click on create groups - select smart group - then open up options)

The cites that show up in that folder presumably are the ones that have multiple pdfs.

Temporarily copy the cites identified in this smart group to a new database called something like “many pdfs.enl” and work off of that for now. Don’t delete the ones in your original folder until later - put it in a folder identifying these for you to delete at a later time.

There are two ways you can fix this.

a. Move the “pdf folder” in the “many” database somewhere to another folder so when you open the “many pdfs.enl” file, it has lost all its pdfs. You may need to copy those to a new file again to get rid of the bad links - keep all of these until you’ve dealt with the problem and then you can combine the cites that now have the problem fixed…

Then, have doublekiller (see below) delete all the extra duplicates in the pdf file, so all you have are the originals.

Next, open the new database, which should only have cites, and import the pdf folder that already had its duplicates removed. Be sure you listed to import the folder without its duplicates Hopefully, that Endnote database will recognize and attach those pdfs. If you still see files in the smart folders pointing to files with duplicates, you may need to deal with these individually. While deleting the cites you don’t need.

b. Have doublekiller (described below) work directly off the double cites. This may or may not fix the problem so you may have single pdfs in each cite. Hopefully.

c. Deal with the cites you don’t care about individually.

In the future, although you can’t prevent this happening any longer, there are a couple of things you might do. Won’t keep dupes out every time, but it should reduce the risk.

One option to get rid of the identical doubles beforehand is to just ignore it and let them be.

a. First, when importing, be sure the “discard duplicates.” is set to on beforehand.

b. Second, once you have the pdfs, move them to a separate folder so these don’t get doubled the second time when you by download online or importing from a folder. You can always move it back.

c. Make sure that any files you import from a folder on your computer do not have duplicates.

i. I do this by using a program called “doublekiller Pro” which is very old but incredibly useful – and really works. You can buy it at BigBankEnterpricses

It’s inexpensive, but because it’s so old it will only work if you set the property settings of the app to run on Vista and run as Administrator. And then as you are opening it, right click your mouse and select “run as administrator”. Amazingly, I haven’t seen another program since that works so well. I’ve written to the guy who developed it, telling him what a massive help it was - he was surprised anyone was even using it anymore. But it’s fantastic.

I can also find duplicates with doublekiller by searching the pdf folder of the Endnote database. First time I used it, it found well over a hundred duplicates floating around in my database. Instead of deleting the extras, you might select all the duplicates and click the option to export it to a folder on your desktop. Otherwise you may find you have some cites that are empty and others still floating around. Then, you are stuck with duplicates again in some places. So just get rid of them all by exporting the file.