I'm having problems after the update. No highlights or notes were imported. Is there a problem with this version? Are there any extra steps to be taken to get everything imported? Sorry about my English
The importer in the latest beta will now import annotations on PDFs in your personal library that were opened from group libraries. As discussed, Mendeley stores those as group annotations but displays them in the personal library. (@glanciano, @MACorreia, @bailh, @e2henrik)
We've also made some changes that should dramatically speed up Mendeley imports, as well as introduced a new importer that can import from an online Mendeley library instead of a local database.
Hi! I'm new to Zotero and am trying to get started by importing my Mendeley library. This appeared to work, except that the "Publication" field has been left empty for every entry. Can I fix this after import (perhaps using something like the lookup from DOI option in Mendeley)? Or can I re-import in a way that preserves this information? Thanks!
This appeared to work, except that the "Publication" field has been left empty for every entry.
@dagewa: Sorry, that was a bug in the new online importer. Fixed now in the latest beta — thanks for reporting. If you upgrade to the latest beta via Help → Check for Updates and do another import, it should fill in the Publication field on previously imported items.
Let us know if you notice any other problems in the imported data.
@dstillman that's great, thanks! The second import correctly pulled in the Publication field. Whlie doing this I noticed a lot of duplications in my library, but I suspect these are present in Mendeley too. I will try clearing up the duplicates on that side and then import again.
I’m completely sold now! Thank you so much for all of the work you all are doing on this iOS app and desktop beta. I couldn’t wait to finish my thesis so I could give Mendeley the boot - no way am I suffering through my dissertation as I have with the thesis. So glitchy, and there has been a steady removal of important features and functionality in the desktop app over the past several months followed by completely ending support of their iOS app. Just didn’t seem like a developer that understood/cared about the needs of their user demographic. Then I learned that Mendeley is now owned by Elsevier. That answered all my questions - goodbye Mendeley!
I’ve been searching reviews/comparisons of ref managers for several months and Zotero consistently rises to the top (not because it’s free but what a bonus!). Been playing around with the iOS beta and what a dream! I also really appreciate your responsiveness, openness, and professionalism as I read through these discussion threads. It seems you guys get it and I’m really happy to be boarding the Zotero train!
The import functionality for highlights and annotations is wonderful. The native reader is already better than Mendeley with more features (come through dark mode!) and the iOS connectivity is exactly what we need. Oh, and the ability to create cited notes that can be imported into MS Word? I don’t think I could have imagined that but freaking love it! Now being able to export my Mendeley annotations to Zotero seals the deal for me.
As I’m still just getting to know Zotero, I don’t need extra storage yet, but went ahead and upgraded just to show some support of the platform. I’m sure I’ll buy the unlimited plan after fully migrating. Is there another way to directly support this iOS app development? I’m so in! Thank you again and keep up the great work!
@dstillman: On the issue of annotations on PDFs in Mendeley group libraries (which I've since moved to regular collections in Mendeley, as instructed above), the Zotero importer is successfully bringing over annotations that are *from that Mendeley account*. But not annotations made by other Mendeley accounts on the same documents (which are all displayed together in Mendeley).
Any expectation that the importer could deal with that use case in the near future?
This might very understandably be a bridge to far to expect the importer to handle! But I wanted to check if it might before I go ahead and start dealing with fixing the fragmentation of my annotations from this situation on an ad hoc basis.
Thanks for all you do! I'm excited to get out of Mendeley and into the open source world of Zotero.
@ah123: Currently, we're intentionally importing only annotations you created yourself. We could reconsider importing other people's annotations if there's demand. We'd have to make some changes in order to store and display the usernames, since unlike Zotero group annotations those wouldn't map to actual Zotero users.
@dstillman: Thanks for that insight. I had what's probably a pretty idiosyncratic workflow where there was a subset of my documents that I annotated at different times from both a work and a personal Mendeley account that I controlled. So, in my case, I don't care what account a given annotation is associated with, since they're both me. But obviously you can't necessarily accommodate all of these weird use cases.
(To be clear, I have no desire to continue that two-account workflow in Zotero. I'm just trying move everything over into one consolidated library at this point.)
I'm having a similar issue as @glanciano, @MACorreia . I imported my Mendeley library 2 months ago with no issues. I use Zotfile and I basically deleted everything from my library and my bin to change the Zotfile main folder of my files 2 weeks ago.
I've not been able to recover all my annotations since then. I recently managed to erase everything again and get everything back once more. Now I don't have any annotation on most files but I have some annotations on a few of them. (very strange)
I don't use any Mendeley group and I made all the annotations I have on my Mendeley files.
@fgr1: ZotFile will delete the Zotero/Mendeley annotations for any attachments it converts to linked files. Don’t use it if you want to import Mendeley annotations.
@dstillman is there any way to prevent this? I do not have enough storage on Zotero, what you're proposing is not an option for me unfortunately. Would webDAV or any alternative to ZotFile solve the problem?
webDAV would work, yes. ZotFile could also be made to work, but it's not a super quick fix and the developer isn't spending much time on it these days, so not sure if that'll happen.
@adamsmith@dstillman Thanks for the response. You confirmed my suspicions that ZotFile simply doesn't do annotations. I have considered the webDAV but for the time being I am not in a particular rush although I want to escape mendeley as soon as it becomes viable.
Zotero clearly has far superior functionality so I can't wait till it can happen!
@hadifalex: To be clear, you can also just add a Zotero storage subscription, or not sync files at all and just store them locally. ZotFile is an unmaintained third-party plugin, so it's not something I would recommend waiting for.
@adamsmith@dstillman Thanks for your answer. I am still looking for any solution to preserve the notes while using another drive (e.g. google drive) for file storage. Is creating a symbolic link to a new Zotero storage location without 3rd party software a possible solution?
By using something like mklink /D .../Zotero/storage "Drive location" to get a symbolic link, do I keep the Mendeley annotations?
If I do, can I still use Zotfile to do some sort of renaming of pdf files without it affecting the notes export?
@fgr1 - Did you ever end up figuring out how to preserve notes while using Google Drive etc. for file storage? I'm out of Zotero file storage and had assumed that my annotations would be transferred if I switch to Linked Files, but now I'm concerned I'll lose them after reading this thread. I also have a bunch of things in Mendeley needing to be imported (and that also have annotations/notes).
@dstillman - Apologies - I thought I'd read that linked files allow for the functionality of stored files (annotations, tags, etc. - just not Groups), so I'm a bit confused now. Apologies if I'm just missing some clearer breakdown of the limitations of switching to linked files. (Btw, I hope this comment is okay; I just didn't want to clutter up the forums by posting this as a separate question, given that it is related to this post's topic, and it's kind of taking forever to sift through all of the prior posts to find out the specific risks of using Linked Files and/or simply not syncing the files to Zotero. The latter route seems like the best bet if annotations/tags/notes are still retained in the data sync.)
The problem described above where ZotFile deletes annotations when you convert stored files to linked files is fixed in ZotFile 5.1.0. (We submitted the fix ourselves.)
@dstillman - Thank you once again for the swift reply! That's great to hear that the annotation deletion issue has been fixed.
I did read through the Stored/Linked Files documentation earlier, plus lots of forums, and I eventually concluded that linking files isn't really necessary for me (I'm ok with giving up control of manual file organization) and may risk problems (although I still don't quite understand what those might be). But my main issue now is that I don't understand why we're discouraged from the symlink option (the last option listed in the "sync" documentation) if we're not advanced users. (I would not consider myself advanced.) My intuitive thought was that the best solution for me*** is to uncheck File Sync and then point Google Drive for Desktop to Zotero's storage folder on my computer. But the documentation says that this is an advanced technique, making me hesitant to proceed. It *sounds* simple...Are there risks to this I'm unaware of? To clarify, I use Google Drive for Desktop only to back up a couple of important folders on my computer; I do not ever edit/touch the files in these local folders via the cloud/G-Drive on the web (unlike the rest of my Google Drive) because the main purpose is backup. I only edit those files locally. I would treat the Zotero storage folder the same (or rather, I wouldn't touch it at all and would let Zotero do its usual file management locally). Please let me know if I'm missing something about why this might be a bad idea. I greatly appreciate it.
(***I am low-income and unfortunately can't buy Zotero storage yet, thus my needing an alternative.)
That's not a symlink. I don't know anything about how the Google Drive desktop app works, sorry. If it's not interacting with the zotero.sqlite file in the root of the Zotero data directory, though, it's probably OK.
Yeah, sorry, haha; I'm not very familiar with the term. I just assumed that it was referring to what I was describing since I didn't see another sync description that matched it. I definitely know to avoid letting GDrive touch the zotero.sqlite file, though, or anything besides the "storage" subfolder...I'm just hoping to back up the PDFs in case of hard drive failure but don't want to lose the features I have with Zotero File Sync (except Group sharing or accessing the files from Zotero web, which I don't think I need yet at this stage of my degree.) So long as using the cloud to back up my storage files doesn't affect anything else in terms of functionality (e.g., my tags/annotations/notes/collections or ability to import new papers), then I think/hope I'm okay.
Thank you again. I do genuinely hope to someday make more $$ and support you guys!
Upgrade Storage
Sorry about my English
How exactly are you importing, and what are the exact steps you're taking to determine that highlights and notes weren't imported?
We've also made some changes that should dramatically speed up Mendeley imports, as well as introduced a new importer that can import from an online Mendeley library instead of a local database.
I can confirm that my annotations from the group library are correctly imported now. Many thanks!
Let us know if you notice any other problems in the imported data.
I’ve been searching reviews/comparisons of ref managers for several months and Zotero consistently rises to the top (not because it’s free but what a bonus!). Been playing around with the iOS beta and what a dream! I also really appreciate your responsiveness, openness, and professionalism as I read through these discussion threads. It seems you guys get it and I’m really happy to be boarding the Zotero train!
The import functionality for highlights and annotations is wonderful. The native reader is already better than Mendeley with more features (come through dark mode!) and the iOS connectivity is exactly what we need. Oh, and the ability to create cited notes that can be imported into MS Word? I don’t think I could have imagined that but freaking love it! Now being able to export my Mendeley annotations to Zotero seals the deal for me.
As I’m still just getting to know Zotero, I don’t need extra storage yet, but went ahead and upgraded just to show some support of the platform. I’m sure I’ll buy the unlimited plan after fully migrating. Is there another way to directly support this iOS app development? I’m so in! Thank you again and keep up the great work!
Any expectation that the importer could deal with that use case in the near future?
This might very understandably be a bridge to far to expect the importer to handle! But I wanted to check if it might before I go ahead and start dealing with fixing the fragmentation of my annotations from this situation on an ad hoc basis.
Thanks for all you do! I'm excited to get out of Mendeley and into the open source world of Zotero.
(To be clear, I have no desire to continue that two-account workflow in Zotero. I'm just trying move everything over into one consolidated library at this point.)
I've not been able to recover all my annotations since then. I recently managed to erase everything again and get everything back once more. Now I don't have any annotation on most files but I have some annotations on a few of them. (very strange)
I don't use any Mendeley group and I made all the annotations I have on my Mendeley files.
Thanks for the response. You confirmed my suspicions that ZotFile simply doesn't do annotations. I have considered the webDAV but for the time being I am not in a particular rush although I want to escape mendeley as soon as it becomes viable.
Zotero clearly has far superior functionality so I can't wait till it can happen!
Many thanks again!
Thanks for your answer. I am still looking for any solution to preserve the notes while using another drive (e.g. google drive) for file storage. Is creating a symbolic link to a new Zotero storage location without 3rd party software a possible solution?
By using something like
mklink /D .../Zotero/storage "Drive location"
to get a symbolic link, do I keep the Mendeley annotations?
If I do, can I still use Zotfile to do some sort of renaming of pdf files without it affecting the notes export?
@dstillman - Apologies - I thought I'd read that linked files allow for the functionality of stored files (annotations, tags, etc. - just not Groups), so I'm a bit confused now. Apologies if I'm just missing some clearer breakdown of the limitations of switching to linked files. (Btw, I hope this comment is okay; I just didn't want to clutter up the forums by posting this as a separate question, given that it is related to this post's topic, and it's kind of taking forever to sift through all of the prior posts to find out the specific risks of using Linked Files and/or simply not syncing the files to Zotero. The latter route seems like the best bet if annotations/tags/notes are still retained in the data sync.)
For general limitations of linked files, see Stored Files and Linked Files.
I did read through the Stored/Linked Files documentation earlier, plus lots of forums, and I eventually concluded that linking files isn't really necessary for me (I'm ok with giving up control of manual file organization) and may risk problems (although I still don't quite understand what those might be). But my main issue now is that I don't understand why we're discouraged from the symlink option (the last option listed in the "sync" documentation) if we're not advanced users. (I would not consider myself advanced.) My intuitive thought was that the best solution for me*** is to uncheck File Sync and then point Google Drive for Desktop to Zotero's storage folder on my computer. But the documentation says that this is an advanced technique, making me hesitant to proceed. It *sounds* simple...Are there risks to this I'm unaware of? To clarify, I use Google Drive for Desktop only to back up a couple of important folders on my computer; I do not ever edit/touch the files in these local folders via the cloud/G-Drive on the web (unlike the rest of my Google Drive) because the main purpose is backup. I only edit those files locally. I would treat the Zotero storage folder the same (or rather, I wouldn't touch it at all and would let Zotero do its usual file management locally). Please let me know if I'm missing something about why this might be a bad idea. I greatly appreciate it.
(***I am low-income and unfortunately can't buy Zotero storage yet, thus my needing an alternative.)
Thank you again. I do genuinely hope to someday make more $$ and support you guys!