Very problematic bug in citation formatting - data loss

Michael Glotzer's Avatar

Michael Glotzer

08 Feb, 2017 09:28 PM

Data Loss Bug during with formatting citations in Papers v3

Some references in the database have a citekey of the form
2010Smith10p99999 (type "a") whereas the majority have Smith2010ig (type “b”). These references are associated with references from certain time windows.

If a citation of type a is added alone, it doesn't get formatted but it is retained in the document unformatted so that it can be fixed.

If there are multiple citations in which type a and b are mixed, the “type a” citations are completely dropped from the document with no error or warning.

I don't know why some citations have the type a cite keys, but I have many of them in my library which has been growing from version 1.

There needs to be an automated way to change all the citekeys. Manual deletion of existing citekeys (triggering their re-creation as type “b” is impractical).

Users should be notified of this. I fear that some published papers may lack key citations on account of this bug.

  1. Support Staff 1 Posted by cary on 10 Feb, 2017 09:00 PM

    cary's Avatar

    Hey Michael -

    Thanks so much for taking the time to reach out to us. I'm sorry to hear about this trouble that you're having with Citations.

    When you can, can you please let me know which citation style you're using?

    Thanks so much!



  2. cary closed this discussion on 10 Feb, 2017 09:00 PM.

  3. Michael Glotzer re-opened this discussion on 10 Feb, 2017 11:00 PM

  4. 2 Posted by Michael Glotzer on 10 Feb, 2017 11:00 PM

    Michael Glotzer's Avatar

    That is not a relevant variable. I get the same effect with both nature and JCB.

    This is a serious bug.

    Sent from my iPhone

  5. Support Staff 3 Posted by cary on 13 Feb, 2017 08:41 PM

    cary's Avatar

    Hey Michael -

    Thanks so much for letting me known what the citation style is not a factor. Please allow me a bit of time to have this investigated.



  6. 4 Posted by Michael Glotzer on 13 Feb, 2017 09:48 PM

    Michael Glotzer's Avatar

    This continued delay is not encouraging.

    I had actually reported that these different cite key cause problems about 6 months ago:
    Papers for Mac - Problems #197453

    I am very disappointed because references have been dropping out of my documents with no warning whatsoever!

    Is this program being updated anymore?

    Release Notes / FAQs - Papersapp Support<> - Last update Nov 23, 2015!

    Tweets with replies by Papers (@papersapp) | Twitter<> - Last tweet of any kind 29 Dec 2016

  7. Support Staff 5 Posted by cary on 15 Feb, 2017 07:24 PM

    cary's Avatar

    Hey Michael -

    Thank you so very much for your continued patience. We have been working together here for help find a solution and I have been able to confirm that is a bug.

    While the current version of Papers is continuing to be maintained and supported by the team here, but it will not see any major changes as our developers are currently hard at work on developing the next version of Papers which is due out later this year.

    If you're interested is being a beta tester for this program, you can sign up here.

    As for your current trouble, while we still do not have a proper solution for you yet, I may have an alternative: are you familiar with our sister application ReadCube?

    ReadCube, like Papers, is a reference manager but has been written using entirely different code and may be more successful for you. If you'd like to spend some time with the application, I more be more than happy to provide you with a free subscription to our Pro service (normally $55) and help you get set-up.

    Just let me know!



  8. cary closed this discussion on 15 Feb, 2017 07:24 PM.

  9. Michael Glotzer re-opened this discussion on 15 Feb, 2017 11:31 PM

  10. 6 Posted by Michael Glotzer on 15 Feb, 2017 11:31 PM

    Michael Glotzer's Avatar

    Thanks Cary,

    Initially put this post in the suggestions because I think it is important for other users to know about this bug.
    As we move to a solution, perhaps it should be made private.

    I am glad to hear that papers is still in development.

    I would think it could be fixed by just deleting all the citekeys of the old form - they will be regenerated automatically. Is that a hard thing to arrange?

    Does ReadCube do citations/referencing? That is an essential feature for me.

    I would rather stick with Papers as I like the offline storage and I have a very satisfactory sync solution (resilio sync - previously bitorrent sync, that does peer to peer syncing of different machines; then local sync to iPad).

    Keep me posted -

  11. 7 Posted by Michael Glotzer on 16 Feb, 2017 05:36 PM

    Michael Glotzer's Avatar

    Just to illustrate the severity of this problem

    I made a smart group to identify references with the problematic format

    1963/5917 papers in my library, imported between Jan 4 2007 and April 16 2012 have the Author:Yearp12345 format

  12. Support Staff 8 Posted by cary on 17 Feb, 2017 08:23 PM

    cary's Avatar

    Hey Michael -

    Thanks so much for getting back to me.

    ReadCube does indeed have a citation feature called SmartCite. It is currently in beta but the full version is due out in the next couple of months.

    I do totally understand your wanting to stay with a program which you've invested so much time in.

    I do not have an additional suggestion at this time but I have pinged the development team and we'll see what we can get figured out and will be back in touch as soon as possible.



  13. cary closed this discussion on 17 Feb, 2017 08:23 PM.

  14. Michael Glotzer re-opened this discussion on 28 Feb, 2017 10:07 PM

  15. 9 Posted by Michael Glotzer on 28 Feb, 2017 10:07 PM

    Michael Glotzer's Avatar

    any news on this - I would think it would be a high priority as it is a very problematic bug.

    Why is it so hard to purge the database of cite key entries that contain Pn (where n integer 0-9).

    The program is set up to regenerate the new cite keys already.

  16. Support Staff 10 Posted by Ayie on 01 Mar, 2017 03:48 AM

    Ayie's Avatar


    I'm afraid there is no update on this issue but we will let you know once we make progress.

    Best Wishes,

  17. Ayie closed this discussion on 01 Mar, 2017 03:48 AM.

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