How to migrate from Papers3 to Bookends

A place for users to ask each other questions, make suggestions, and discuss Bookends.
Posts: 30
Joined: Thu Jan 05, 2006 7:03 pm
Location: Idaho

Re: How to migrate from Papers3 to Bookends

Post by JamesAFoster »

The migration process might be simpler if you keep the Papers3 attachment names. Here is a protocol for that. But I haven't tested it:

1. create new Bookends library
2. In Papers3, go to the "Library" prefs and uncheck the checkbox next to "Rename files in library folder as:", then click the "Apply" button
3. Export PDFs (good ones) from Papers3 to ~/Documents/Bookends/Attachments
4. export Papers3 xml format (because I had about 1,000 papers3 entries without any pdfs at all)
5. import xml into bookends
6. in preferences: remove arbitrary attachments (probably not necessary)
7. Refs/Global Change/Remove Orphaned Attachments, in entire library (probably not necessary)
8. Remove Duplicates (Bookends chooses duplicates without attachments, which were added in 5; it also has other smart choices such as removing entries with missing data when other entries exist with those data)

Also consider cleaning things up with Refs/Global changes. This can fix duplicates with different case styles, or missing fields.
james a. foster

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Re: How to migrate from Papers3 to Bookends

Post by Jon »

In my testing it looks like PDFs that have been synced in Papers 3 have UUIDs for names (not human-readable). Even if you uncheck "Rename files in library folder" in Papers preferences, the exported PDF names are readable (author and date). So the attachment names imported by Bookends won't match the names of the exported PDFs.

If you or anyone else has a workaround for this please post it.

Sonny Software

Posts: 33
Joined: Thu Jul 19, 2007 10:04 am
Location: Germany

Re: How to migrate from Papers3 to Bookends

Post by msteffens »

I've written a "Papers To Bookends" export script that should enable Bookends to honor the annotations in the PDFs exported by Papers. For more info, please see the script's Readme file and follow the steps in the "Known Issues" section: ... o_Bookends

In the Bookends forums, this script is discussed here:


HTH, Matthias

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Joined: Tue Jan 02, 2018 3:17 pm

Re: How to migrate from Papers3 to Bookends

Post by albiracer »

As my first post here - and after spending quite a bit of time over the last two days figuring out how to move my Papers 3 library over to Bookends and get it working with iCloud syncing for attachments - I wanted to say a quick thanks to Matthias for this script, and to others who have contributed to the forums. Thanks to that work, I finally figured things out. Just FYI for others who may be doing the same, I found the script to have trouble with references for which the pdf was actually marked "missing" in Papers 3 - of which there were more than I would have expected in my library. I had to delete all imported references (and attachments) in Bookends once, go back to Papers 3 to delete the offending "missing pdf" references and then move through all remaining Papers 3 references looking for other missing pdfs, and then re-run the script a second time to get things to work. So, some grooming of the Papers 3 library might speed the transition.


Posts: 33
Joined: Thu Jul 19, 2007 10:04 am
Location: Germany

Re: How to migrate from Papers3 to Bookends

Post by msteffens »

Hi Ben,

thanks for the kind words, and for reporting the script's issue with missing PDFs. I've uploaded an updated script version which fixes this issue. I.e., the script now ignores any missing PDFs (it just logs their papers to and imports only their publication metadata.

Btw, you can use the script below to select all publications in your Papers library which have missing PDFs.

Cheers, Matthias

Code: Select all

-- Selects all publications in your Papers library whose PDF is missing.
-- Before running this script, please make sure that you've selected the "All Papers" collection in Library mode.

-- NOTE: This script will handle all of the papers in your Papers library, but not any of the manuscripts defined in your library.

tell application id "com.mekentosj.papers3"
	tell front library window to set selected mode to Library Mode
	set pubList to every publication item
	set pubsWithMissingPDFs to {}
	repeat with aPub in pubList
		set f to primary file item of aPub
		if f is not missing value then
			if full path of f is "" or full path of f is missing value then
				copy aPub to end of pubsWithMissingPDFs
			end if
		end if
	end repeat
	tell front library window to set selected publications to pubsWithMissingPDFs
	display dialog "Did select publications with missing PDF: " & (count of pubsWithMissingPDFs) & linefeed & linefeed & "To create a new collection for these papers, choose 'File > New Collection > Collection from Selection'." buttons {"OK"} default button "OK" with icon 1
end tell

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