What do you mean by "I can see annotations as child notes"?

If you click on the parent item of one of the affected attachments in your Zotero web library, what's the URL in the address bar?

Thanks for response @dstillman !

I have many annotations and many highlights in Mendeley online library (like, A LOT).
When I open them on Zotero after import, there is parent item, and there is "child item" (a note below parent) that says "extracted annotations". When I open PDF in the reader, these extracted annotations open only in side bar on the right. They are not linked in anyway to the pdf body. No highlights on any PDF.

An example of that would be: https://www.zotero.org/monikaerva/search/lincoln/titleCreatorYear/items/P9SAUVH5/item-list

One more thing - I used ZotFile to put the PDFs on OneDrive. Is that possibly causing the problem?

There's some confusion here. There were "Extracted Annotations" notes created by an old version of ZotFile for Zotero 5 and earlier, but that version doesn't even run in Zotero 6, which has its own annotation support and annotation extraction. So I'm not sure how you ended up with all of those notes unless you previously used Zotero and exported items to Mendeley or something like that. Or you actually performed the import (and the ZotFile annotation extraction on all of these items) using Zotero 5, which didn't import Mendeley annotations.

And, actually, I'm not sure your "Extracted Annotations" notes were from ZotFile at all. There's some code in them that I don't think ZotFile ever used. Do those notes appear in Mendeley? They're not a standard thing there either, so if so, they would've had to have been something you created with some other tool.

If you haven't made changes to the imported items in Zotero, can you provide a Debug ID from Zotero for repeating the import from Mendeley? It will update your previously imported items, but it shouldn't touch other items.

"So I'm not sure how you ended up with all of those notes unless you previously used Zotero and exported items to Mendeley or something like that. Or you actually performed the import (and the ZotFile annotation extraction on all of these items) using Zotero 5, which didn't import Mendeley annotations."

-- this is the first time I'm using Zotero or ZotFile and I have downloaded them yesterday so both of them are the most recent versions. I have not created any other notes with other tool, Mendeley was the only thing I used.

Before I run a Debug ID - could this problem occur because I directly imported through ZotFIle to OneDrive? (installed ZotFile first and then performed the first ever import directly to OneDrive) If yes, maybe I should start the whole process again but without ZotFile? If yes, what's the best way to start over?

Thank you so much

Hi @dstillman ! Indeed, I have deleted my library and account because I realized that troubleshooting this problem is out of my competence and it would take my very long to resolve it. I didn’t want the setting I had to mess up another import and I didn’t know how to reset them completely.

Before I deleted account, first I have deleted ZotFile, reverted files to the the directory folder, and performed another import - it came out as correct one, with highlights and annotations on place, but I couldn’t get rid of the linked files for nothing. I had to open the parent element and look inside for the correct PDF. Otherwise it would automatically go to the broken linked one.

Now that I made a new account and ran import directly (skipping the ZotFile) - it seems to be working like a dream. All the annotations and highlights seem to be on place. It’s soooo much better than Mendeley!!!

Thank you so much for your help, I wouldn’t figure out what’s going on without your help!

Hi @dstillman,

I think I may have had this same issue yesterday.

I'm a new Zotero user (one of 1000s jumping ship from Mendeley!) using macOS Catalina. Yesterday I downloaded Zotero 6 and Zotfile, and set up Zotfile to rename & save pdfs in a Dropbox folder (I have >1GB of pdfs). I did this before running the Mendeley import.

As Monika described, following the successful import, no pdf highlights are showing, and all annotations have been extracted into separate notes (this looks to be a Zotfile function).

Should I delete my library, remove Zotfile, and repeat the import just with default Zotero settings - and then use Zotfile to rename and move pdfs as a batch process?

It would be great if the documentation about importing from Mendeley could be a bit more prescriptive, and explain how to avoid this pitfall.

Many thanks,

Richard

@rgm43: Well, and as I told Monika — if you're seeing "Extracted Annotations" after a Mendeley import, that would actually be from Zotero 5's Mendeley importer, not ZotFile. Zotero 6 doesn't create those.

I think we're going to have to just block the import with an error if ZotFile is enabled, since this creates an awful, confusing import experience.

For the next version, we've blocked the import from proceeding if ZotFile is enabled. Thanks to both of you for the reports.