Error in Syncing PDF files with offline client

piggyback

Report ID:D80147135

Hello,

I moved to a new system and tried to sync my entries. This worked with the sqlite entries but not with the PDF attachments. While syncing there was no error message. The PDF are marked with the icon for a working link but I can't open them.

A new PDF is linked properly but it's stored in the default C:/user/storage folder.

It seems that my settings for a different root are ignored.

Cheers Dominik

dstillman

Sorry about that. There was a problem with longer uploads in Zotero 5.0.75 that should be fixed in 5.0.76, available now via Help → Check for Updates.

piggyback

Hello, thanks dstillman,

I've realized the issue with long uploads as well.

My finding is different (local sync):
- OK: entry sync / sqlite-content
- NOK: user defined PDF root

My new root is displayed in the settings, but ignored: existing PDF are refused, new are stored in the default root.

Cheers Dominik

dstillman

Linked files aren't synced by Zotero.

piggyback

what did i do wrong to sync them?

dstillman

I'm not sure what you're asking. Zotero just doesn't sync linked files. If you want to use Zotero's file syncing, you need to use stored files.

https://www.zotero.org/support/attaching_files#file_copies_and_links

piggyback

That’s my point, thanks. Syncing via sqlite works, but file linking in a different root doesn’t.

I’ve defined a new root for my files, but zotero can’t open the files. The pdf icon is ok, no broken links. New pdf will be stored in the default root for file storage.

dstillman

Sorry, I'm still not following. When referring to things, please use the actual words you see in the Zotero interface or documentation. For example, I don't know what you mean by "defined a new root for my files" or "file linking in a different root".

Again, if you just add a file to Zotero, by default it's going to be stored within the Zotero data directory. If you're creating linked files manually or by using ZotFile, they'll be stored elsewhere.

piggyback

OK. I've been storing my pdf files since several years within a manual defined base directory without any problems.

I moved to a new system, linked to that folder again. Now, I can't open the files anymore. I've installed Zotero to another system, the same problem occurs.

In the preferences, my manual defined base directory is displayed, Zotero prefers the default directory.

dstillman

OK, got it.

So assuming the files exist on your current system, either you've chosen the wrong base directory — such that the relative paths don't match up — or the base directory was wrong on the computer where you created the files, causing them to be stored as absolute paths instead.

If you view the debug output (Help → Debug Output Logging) for trying to open a file, you can see the path it's trying to use. You can also use the Zutilo plugin to modify paths in batch (if, for example, they're still set to an absolute path from the other computer).

piggyback

Thanks, I'll check it tonight with the debug output.

The files exist, I can localize them manually. The paths are relative.

piggyback

Unfortunately I can't find the path within the log file.

I've decided to use the default base directory. This works properly & proofs that my files exist and the path was relative.

I still assume that there's something wrong with the function in the current Zotero releases. That's why the behaviour is different to the previous releases (4.n).

That happens currently:
1. I've defined my base directory manually (partition D) in the preferences. Zotero 'pretends' that it can't localize my files there (error message when I try to open a PDF).
2. But in the background Zotero syncs the files from partition D to partition C / default base directory. In fact, Zotero copies file by file.

This takes a lot of time so I haven't realized earlier what happens.

dstillman

Unfortunately I can't find the path within the log file.

It's logged every time you try to open a file that's missing, but you can also generate a Debug ID for that and we can tell you what the path is.

I still assume that there's something wrong with the function in the current Zotero releases.

No, there's not — this functionality hasn't changed in years. You're likely just misunderstanding how it works.

Zotero 'pretends' that it can't localize my files there (error message when I try to open a PDF).

If you get that message, it means the file doesn't exist where the path is set. This is a configuration problem on your end, not a bug in Zotero.

But in the background Zotero syncs the files from partition D to partition C / default base directory. In fact, Zotero copies file by file.

This absolutely doesn't happen.

Again, I think you're confused about how all of this works. If you provide a Debug ID for an attempt to open a file, we can tell you where it's looking and tell you how to fix it.

piggyback

This is my ID D7615041. Do you read my base directory in the debug report as well?

dstillman

Don't use "Restart with Logging Enabled…" — it creates too much unnecessary output. Just click the parent item, start debug output logging, double-click on the child attachment to get the error, and submit it.

dstillman

If you could say what file (or the beginning of the filename) you're trying to open, that would also be helpful. But from the looks of it, you're not trying to open any linked files, so the Linked Attachment Base Directory setting is irrelevant. All the files shown as not found in the debug output are in the 'storage' directory within the Zotero data directory on your C: drive, so they're simply stored files. Those were A) deleted/moved on disk, B) created on another computer and not synced, or C) created on this computer but with Zotero pointed at a different data directory from where it's pointed now.

Note, too, that you have your data directory in a bizarre, nonstandard location:

C:\Users\[…]\zotero\Profiles\gu62px27.default\zotero

It looks like at some point in the past you moved an entire Zotero or Firefox profile directory to your home folder, and then pointed Zotero at the 'zotero' folder within. While that's not inherently a problem, it's confusing and nonstandard, and I'd strongly recommend just moving the last 'zotero' — the actual data directory — to your home directory as 'Zotero' (with a capital 'Z'). When you restart Zotero, it should notice that your custom data directory is missing and ask if you want to use the default location, and you can say yes. You can then get rid of that extra 'zotero\Profiles\gu62px27.default' stuff.

piggyback

Thanks, I'll check it by the week-end. I assume B) is the problem.

piggyback

This is my Debug ID: D53934721

Please don't be confused, this is from another system with the standard directory to avoid legacy problems.

I tried to open this PDF: Software-Drives_2030_v1-0_online.pdf

Additional information
- Base directory in Preferences: D:\DB\Zotero\storage
- File(s) can be localized and opened with win search there.
- There's no chain symbol with the PDF in Zotero.

Thanks in advance.

dstillman

Attachment file 'C:\Users\[…]\Zotero\storage\8UG48FMS\Software-Drives_2030_v1-0_online.pdf' not found

OK, so again, this is a stored file, not a linked file, so the Linked Attachment Base Directory setting is irrelevant. This file doesn't exist online and likely never has, so it didn't sync to this computer.

See Files Not Syncing.

piggyback

I'm trying to sync the items but I get this error message: "The note “XXX” is too long to sync. Shorten the note and sync again." for this and other notes. These are old notes synced to Zotero a couple of times.

Does this error belong to the upload issues in 5.0.75 you mentioned previously?

Debug ID: 876735802