Zotero Version 6 Released

I’m with you on that. PDF annotations are far too limited. Skim also has its own annotations that overcome those limitations. I personally keep my detailed PDF notes outside the file anyway (in plain text files, diagrams, etc.)

For me, Zotero 6 really erased all doubt that this is the way to go for me. I was also unsure about the annotations not being stored in the pdf-files (because I like to keep things simple and application independent) but I was quickly convince that this is not a problem:

  1. it is easy to switch back and forth between in-database and in-document annotations and doing so doesn’t seem to entail any pitfalls (admittedly, I did not try too hard, so do let me know if you found a scenario where you might lose data when switching back and forth, or where weird stuff happens)
  2. The most important argument for me was, however, that didn’t really see a need for using in-document annotations anymore when I tried the zotero pdf reader in combination with Zotero storage: I can open any pdf from my zotero-library on my ipad, annotate it there, and all annotations are immediately available on my Mac (or on another ipad, for that matter), thanks to the zotero database syncing via zotero storage (incl. all the annotations). No need to make sure to sync the file from the ipad back to the library via my cloud storage provider (previously, it had happened more than once that I knew I had annotated a particular article but couldn’t remember on which device (and in which pdf annotation app) so that it was a pain finding those notes and syncing the pdf back to my library (this had to be done manually because of how iOS sandboxes all applications, making it impossible to annotate a pdf document from my cloud storage while simultaneously keeping it in sync with that storage).
  3. And the best thing is that you do not even need to upgrade your zotero storage to accommodate all your thousands of pdf files because you can also let zotero save your pdfs in any webDAV storage. So I gave up my reluctance to let zotero manage my pdfs (I felt more in control when I handled them myself in my own designated folder in the cloud storage. Since zotero gives me everything I need, in a more convenient way that any other solution, why not also let it handle my files?
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Helpful post @toffy. Thank you.

I sent the following to @toffy as a private message, but the thought it would be more helpful to respond to the whole group.

I’ve setup WebDAV syncing on mine. I get space for WebDAV with Fastmail. so that’s my sync location.

I just followed the setup instructions for WebDAV sync on the Zotero website. Prior to that, I was syncing the storage folder in the Zotero folder using Resilo Sync. So I setup the WebDAV location, waited for it to upload everything (I believe I had to set Zotero to force upload) and then once that was in place, I removed the Resilo Sync and setup the other instances to use WebDAV.

As I was using Resilo, I hadn’t made any changes to the storage location of where Zotero would store files, so if you’ve changed that, you might need to look at that before setting up WebDAV.

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So I have a webDAV server. It works fine. I can connect to it from just about anything and anywhere. Zotero; however, will not connect with it. On iPadOS it reports that I don’t have permission to access the specified folder. (Same credentials that I use logging into my webDAV server from anything, so it seems unlikely that there is actually a permissions error.) On macOS, I receive an error that something is wrong with the certificate. It’s not trusted.

The webDAV is my own self-hosted server.

Is it a self signed certificate or one using Let’s Encrypt or similar?

A quick google suggested self signed certificates can be an issue and may need a cert override file.

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Can you try with some other webDAV server to rule out that the problem is with the configuration of your server? (looks like there is a test server here, for example: https://www.dlp-test.com/WebDAV-Intro/)

When I look at my config on the zotero iOS app, it looks pretty straight forward: under file syncing set it to WebDAV, then enter the URL of the server, username and password. Done.

Oh, perhaps this is it: the app adds /zotero/ to the path. So you have to make sure that directory exists…

The test site worked; it connected but (unsurprisingly) wanted me to create the Zotero folder, which I didn’t do. That was a helpful exercise.

Mine has the /zotero/ folder. Maybe there is something to this certificate issue. I’ll see what I can do about that.

Thank you.