PDF sync with Google Drive loses annotations in Mac OS

Support
1

Hi all,

I wonder if any Paperpile users have encountered the following issue in Mac OS before. This could be a Google Drive and version management issue.

Basically, I organised the PDF to be read in one folder, say Folder A (both in Paperpile and Google Drive). I made annotations (highlights, free text) using a e-ink reader and sync to Google Drive. All works fine and I can see the annotations were updated in the Google Drive on my Mac OS.

Once I finished reading the PDF, I moved the PDF out from Folder A to Folder B via Paperpile. I can see that a copy of the PDF file (with all annotations preserved) was moved to Trash in Mac OS. Then, after a while (1 minute or 2), I can see a PDF appear in Folder B (Google Drive). However, the version of that PDF is not the latest version (some old versions).

This is not the first time I encountered this issue. It has been an issue for me in the last few weeks now - I cannot recall when exactly it start happening though. I don’t want to think about the possibility of losing all my annotations in the past few months.

My workaround is go the Folder B in paperpile, delete the attachment from Paperpile, wait for the file to disappear from Google Drive, then recover the latest PDF file from Trash (Mac OS), and use that version to upload to the paperpile entry.

Any suggestion or pointer would be helpful. I suspect it is more a Google Drive issue because using an external PDF reader to read & annotate PDFs organised by paperpile on my Mac OS also is an issue. Occasionally, the PDF reader will make the file “read-only” and notified me that the file was in Trash.

This is really strange! Would appreciate any suggestion. Thanks!

Here is my configuration/version:

Paperpile web v57 (81bcb5)
Chrome extension v1.5.713 (b71a8e)
Mac OS 14.2.1 (23C71)

2

Thanks for the report, @zhao.paperpile, and sorry to read about the lost work. Could I trouble you to let us know which publication(s) you have noticed this happening with, so the team can investigate?

Sometimes external programs modify PDFs in a way that makes Paperpile fall back to re-uploading. We try to bring in annotations from changes in GDrive back to Paperpile and avoid trashing PDFs unless absolutely necessary, so this definitely shouldn’t happen. It’s not unlikely there was a change on Google’s side which could be causing this disruption on ours — the team is looking into it.

3

Sure @vicente. It happened pretty consistently. Yesterday, I moved three of these papers from my folder “p0” to “_pending_export_filed”:

Papuga et al. 2018…
Tsafnat et al. 2024…
Joshanloo 2024…

Here is a screenshot of the “annotated” pdfs but in Bin now:

image

image
image729Ă—535 78.8 KB

If I checked the PDFs under the folder _pending_export_filed, the three files are blank without my annotations.

image
image1530Ă—142 26.8 KB

Hope that helps and please let me know if I can provide any more information to help you troubleshoot this issue further.

4

This morning, I also realised that it is not just moving the publication around folders in Paperpile. It seems any update to existing PDFs will trigger the updated PDFs (with annotation) moved to Trash and the file in the Google Drive replaced with a version without annotation :slightly_frowning_face:

I have two examples here:

image
image788Ă—88 5.5 KB

Donaldson et al., 2023 - I annotated it yesterday and this entry is still in my p0 folder (not moved). But I checked the PDF file under p0/ in Google Drive, it was without annotations but the one in Trash has the annotations.

Also, another case:

Rush et al., 2003 - This PDF has been filed away a while ago under the folder “_in_bookends” but this was moved to Trash (just saw this file). This version has the annotations but the one now in Google Drive has no annotations.

image
image831Ă—33 6.71 KB

Really strange! :exploding_head:

5

Additional information - hope it helps. My google drive sync setting is set to “Mirror files” rather than “Streaming”.

image

6

Another piece of information - because I really want to get this fixed so that I can continue to use Paperpile - currently it is slowing down my workflow considerably (e.g., checking Trash everyday and see if there is any paper → Go the Paperpile check the PDF attached → Remove the PDF attached → Re-upload the one in the Trash).

Today, I tried to export a bibtex file from a list of entries under a folder called “_pending_export_filed”. However, all the “file” attribute in the bibtex file (for all entries) appeared to prefix with the folder "“All Papers/Other/” which I can’t find the files under that folder in Google Drive.

Please ignore if this is not related to the problem above. Thanks.

@ARTICLE{Tsafnat2024-aq,
  title     = "Converge or collide? Making sense of a plethora of open data
               standards in health care",
  author    = "Tsafnat, Guy and Dunscombe, Rachel and Gabriel, Davera and
               Grieve, Grahame and Reich, Christian",
  journal   = "Journal of medical internet research",
  publisher = "JMIR Publications Inc.",
  volume    =  26,
  number    =  1,
  pages     = "e55779",
  abstract  = "Practitioners of digital health are familiar with disjointed data
               environments that often inhibit effective communication among
               different elements of the ecosystem. This fragmentation leads in
               turn to issues such as inconsistencies in services versus
               payments, wastage, and notably, care delivered being less than
               best-practice. Despite the long-standing recognition of
               interoperable data as a potential solution, efforts in achieving
               interoperability have been disjointed and inconsistent, resulting
               in numerous incompatible standards, despite the widespread
               agreement that fewer standards would enhance interoperability.
               This paper introduces a framework for understanding health care
               data needs, discussing the challenges and opportunities of open
               data standards in the field. It emphasizes the necessity of
               acknowledging diverse data standards, each catering to specific
               viewpoints and needs, while proposing a categorization of health
               care data into three domains, each with its distinct
               characteristics and challenges, along with outlining overarching
               design requirements applicable to all domains and specific
               requirements unique to each domain.",
  month     =  apr,
  year      =  2024,
  url       = "https://www.jmir.org/2024/1/e55779",
  file      = "All Papers/Other/Tsafnat et al. 2024 - Converge or collide - Making sense of a plethora of open data standards in health care.pdf",
  doi       = "10.2196/55779",
  issn      = "1439-4456,1438-8871",
  language  = "en"
}

Thanks,
7

Thank you so much for the details, @zhao.paperpile — the debugging information you shared helped make the team’s investigation super effective! They were able to craft a fix; following some testing it should go live before the end of next week. Will reach out here once it’s implemented.

8

Perfect @vicente thank you for being so responsive and I look forward for the fix,

9

Hi @zhao.paperpile ,

the fix is now live. We try to resolve the externally-edited annotations and bring them to Paperpile correctly again.

In general this gets triggered when we synchronise some changes from Paperpile back to Google Drive, so one reliable way to test it now for a specific pub is to toggle the Star of the publication in question or Settings > Data and files > Resync.

Let me know how it looks with your external program :+1:

1 Like
10

Thanks for this @jirka, I will give it a try and see if the problem still persists.

11

Hi @jirka,

Just letting you know that since the fix was published, I haven’t encounter any of the reported issue so far, i.e., no PDF is moved to “Trash” even I selected the re-sync function.

Thank you so much and I can start enjoying Paperpile again! Much appreciate your help.

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