@daeh I would love to be able to transfer my Papers library without losing at least some of the organisation associated with it but unfortunately I don't know anything about coding but. I have looked at your script but wouldn't even know where to begin! Do you think it's a complete pipe dream to think I could use your code without any basic knowledge of coding? Where would I begin and how much time would it take? Or should I just accept that I will only be able to transfer the basic info from my Papers library?
@Matthias It occurred to me that it might be possible to export to Endnote XML, to import into Zotero, but first script papers to change Papers collections to Endnote keywords - which could import to Zotero tags? That way at least there could be some kind of organisation left?
I am using Daeh's GitHub code to try to convert my Paper3 library to Zotero. I've had Papers since version 1 (when it was just "papers", and it didn't suck), so my directory contains many old files.
I can't find the directory labelled "Library.papers3", but I now realize that this is the directory "Papers Library". So, I disabled the line that checks for the .paper3 extension, and had the program look at /Documents/Papers Library/
The next error is "AttributeError: 'NoneType' object has no attribute 'group'" when reading through the Bibtex file. It seems that the re.search file doesn't handle non-Latin characters properly, and some of my records contain weird characters. I wasn't able to make the code resistant to this, so I simply removed records from the bibtex file until it ran until the end. I've saved these records, so I can add these back after the inport.
Here's an example of a deleted record, in case anyone is able to 'code around this' and commit to GitHub.
@article{J:1998va, author = {Stohr J, Joachim and Padmore, Howard and Anders, S and Stammler, T and Scheinfein, MR}, title = {{PRINCIPLES OF X-RAY MAGNETIC DICHROISM SPECTROMICROSCOPY}}, journal = {Surf. Rev. Let.}, year = {1998}, volume = {5}, pages = {1297--1308}, rating = {0}, date-added = {2009-04-28T23:02:42GMT}, date-modified = {2017-04-23T02:32:03GMT}, url = {http://www.google.ca/search?client=safari&rls=en-us&q=Joachim+Stohr,J.,+Howard+Padmore,+S+Anders,+T+Stammler,+M.R+Scheinfein&ie=UTF-8&oe=UTF-8&redir_esc=&ei=xhv9TLDcGIbmsQPIjJX3DQ}, local-url = {file://localhost/Users/urquhart/Documents/Papers%20Library/1998/StohrJ./Surf.%20Rev.%20Let.%201998%20StohrJ.pdf}, file = {{Surf. Rev. Let. 1998 StohrJ.pdf:/Users/urquhart/Documents/Papers Library/1998/StohrJ./Surf. Rev. Let. 1998 StohrJ.pdf:application/pdf}}, uri = {\url{papers3://publication/uuid/F8B4E327-01A9-4DFA-B94E-A77F98E190BE}} }
After starting this, I kind of lost track of it until very recently. (I don't believe I was notified about the replies and offers of help, so I did not realize those were there until I came back to the topic much later).
Anyway, I now have completed the transition from Papers to Zotero (mostly), of my close to 10K references. So far so good (mostly), given that Papers v3 is ever more useless and the new version continues to be everlastingly delayed. (Continuing a proud Papers tradition (after v1!) of promising more than can be delivered)
Hello 1) I have also a problem to move from papers3 to Zotero : in my case, I don't have a lot of collections so I can reconstruct them "by hand" but I am interested in recovering my annotations and highlights because I use them a lot and have plenty of annotated papers for my research. Could you please tell me how to do this. I am new in Zotero so I know almost nothing, sorry. I have another question : 2) to annotate I use a lot my iPad. If I understood well, I can use zotfile to synchronise my papers this way and recover the annotations I make. But I did not really understand the workflow for this. Can I use any annotation app for this ? how do I "record" the annotations then ? ... It is all unclear for me. Maybe I just have to read more the zotfile help. (I confess I have not yet, since I am for the moment more preoccupied by the first problem).
Thank you in advance for any help you will be able to give me. M.
Hi, I read a lot of the forum and so I know how to do 2) in my above question. BUT I still don't know how to recover all my data (reference+pdf+annotations+highlights) from papers 3. Do you know something about that ? (I have 3GO of documents on Papers3 and run on macOS Catalina+ iPadOS. Now I want to go to Zotero+zotfile (linked files+dropbox)+betterbibtex. Thank you in advance. The forum is really useful to learn !
Hello M. I can't help with the annotations / highlights from Papers. From an early stage I was a bit suspicious of Papers (and lock-in) and decided to do most highlighting using a regular PDF reader program. I believe there is a way to export the PDFs with embedded notes from Papers, but that may be too much work to be useful (i.e. to do one by one, manually).
(As you probably know already - at least the normal notes from papers do get transferred when you use the XML (endnote) format for switching to Zotero)
thanks a lot for your answer. I am arrived to the same conclusion. I can recover my highlights one pdf by one by some trick but I cannot recover my handwritten annotations, and I am afraid that there is no way for that. So I decided to just keep the papers3'copies of those few important annotated pdf files in the app and just recover all the pdf without annotations.
For me it is not so important to recover the highlights if I can't have the handwritten annotations with it, but in case someone is interested : a possibility is to "share" -> "pdf with annotation", for instance sending an email to yourself, and then copy paste the given pdf. I admit that it is a really ugly way to do, but I don't know how to make a script with this. I have read a post of Matthias which could do it, but I don't.
I wish I would have known Zotero before and have written all my annotations in some opened/standardized format. Thank you to all the community of coders who develop zotero.
Upgrade Storage
I am using Daeh's GitHub code to try to convert my Paper3 library to Zotero. I've had Papers since version 1 (when it was just "papers", and it didn't suck), so my directory contains many old files.
I can't find the directory labelled "Library.papers3", but I now realize that this is the directory "Papers Library". So, I disabled the line that checks for the .paper3 extension, and had the program look at /Documents/Papers Library/
The next error is "AttributeError: 'NoneType' object has no attribute 'group'" when reading through the Bibtex file. It seems that the re.search file doesn't handle non-Latin characters properly, and some of my records contain weird characters. I wasn't able to make the code resistant to this, so I simply removed records from the bibtex file until it ran until the end. I've saved these records, so I can add these back after the inport.
Here's an example of a deleted record, in case anyone is able to 'code around this' and commit to GitHub.
@article{J:1998va,
author = {Stohr J, Joachim and Padmore, Howard and Anders, S and Stammler, T and Scheinfein, MR},
title = {{PRINCIPLES OF X-RAY MAGNETIC DICHROISM SPECTROMICROSCOPY}},
journal = {Surf. Rev. Let.},
year = {1998},
volume = {5},
pages = {1297--1308},
rating = {0},
date-added = {2009-04-28T23:02:42GMT},
date-modified = {2017-04-23T02:32:03GMT},
url = {http://www.google.ca/search?client=safari&rls=en-us&q=Joachim+Stohr,J.,+Howard+Padmore,+S+Anders,+T+Stammler,+M.R+Scheinfein&ie=UTF-8&oe=UTF-8&redir_esc=&ei=xhv9TLDcGIbmsQPIjJX3DQ},
local-url = {file://localhost/Users/urquhart/Documents/Papers%20Library/1998/StohrJ./Surf.%20Rev.%20Let.%201998%20StohrJ.pdf},
file = {{Surf. Rev. Let. 1998 StohrJ.pdf:/Users/urquhart/Documents/Papers Library/1998/StohrJ./Surf. Rev. Let. 1998 StohrJ.pdf:application/pdf}},
uri = {\url{papers3://publication/uuid/F8B4E327-01A9-4DFA-B94E-A77F98E190BE}}
}
After starting this, I kind of lost track of it until very recently. (I don't believe I was notified about the replies and offers of help, so I did not realize those were there until I came back to the topic much later).
Anyway, I now have completed the transition from Papers to Zotero (mostly), of my close to 10K references. So far so good (mostly), given that Papers v3 is ever more useless and the new version continues to be everlastingly delayed. (Continuing a proud Papers tradition (after v1!) of promising more than can be delivered)
In case it is helpful to others, the script that I used can be downloaded here:
https://vanderwellab.org/wp-content/uploads/2020/03/Papers-keywords-script.zip
Please see more info within the ZIP file.
Thanks for all your help and inspiration! Sorry for not following up earlier...
Patrick
1) I have also a problem to move from papers3 to Zotero : in my case, I don't have a lot of collections so I can reconstruct them "by hand" but I am interested in recovering my annotations and highlights because I use them a lot and have plenty of annotated papers for my research. Could you please tell me how to do this. I am new in Zotero so I know almost nothing, sorry.
I have another question : 2) to annotate I use a lot my iPad. If I understood well, I can use zotfile to synchronise my papers this way and recover the annotations I make. But I did not really understand the workflow for this. Can I use any annotation app for this ? how do I "record" the annotations then ? ... It is all unclear for me. Maybe I just have to read more the zotfile help. (I confess I have not yet, since I am for the moment more preoccupied by the first problem).
Thank you in advance for any help you will be able to give me.
M.
Thank you in advance. The forum is really useful to learn !
I can't help with the annotations / highlights from Papers. From an early stage I was a bit suspicious of Papers (and lock-in) and decided to do most highlighting using a regular PDF reader program. I believe there is a way to export the PDFs with embedded notes from Papers, but that may be too much work to be useful (i.e. to do one by one, manually).
(As you probably know already - at least the normal notes from papers do get transferred when you use the XML (endnote) format for switching to Zotero)
For me it is not so important to recover the highlights if I can't have the handwritten annotations with it, but in case someone is interested : a possibility is to "share" -> "pdf with annotation", for instance sending an email to yourself, and then copy paste the given pdf.
I admit that it is a really ugly way to do, but I don't know how to make a script with this. I have read a post of Matthias which could do it, but I don't.
I wish I would have known Zotero before and have written all my annotations in some opened/standardized format.
Thank you to all the community of coders who develop zotero.