Most of the time, when exiting Zotero (~80GB/95,000 files, with WebDAV for a backup and sharing across multiple computers), it doesn’t close in a way that allows opening it with its library without the "Welcome to Zotero" screen, followed by the Warning Sync notification. Checking the Zotero folder reveals: “Zotero [conflicted].sqlite” I close Zotero and delete the “ [conflicted]” portion of the file name and reopen Zotero and it is all as it should be. This didn't work today.
Likely my error due to distraction or related to a Grammarly installation, regardless it would not open the library including after multiple system restarts.
In Preferences, the data directory location is now not what it may have been- set to the same folder location for both base and data directories, but now it notifies: "The data directory cannot be set to the same location as the Linked Attachment Base Directory."
I am not sure how to safely resolve this to access my library. Help would be greatly appreciated.
Please start new threads for new issues — your question has nothing to do with the thread you posted to. I've moved this to a new thread.
“Zotero [conflicted].sqlite”
You have your database in some cloud storage folder or other syncing tool. You absolutely should not do that, and we can't help you further as long as that's the case.
Your advice has benefited me over the years- including on this topic previously.
I may have confused settings between my home and work computers as I have not had to change anything for a couple of years- it was working, although unknown if the best, right, and Zotero approved way.
The intent was for cloud storage with files stored/synced via WebDAV (pCloud: https://webdav.pcloud.com/zotero/) to: 1. home computer w/files on an external hard drive 2. work computer w/files on USB flash drive 3. another computer wo/files
In Zotero Preferences:
Home computer (not working with the library) Sync/Settings/Data Syncing: linked to my Zotero account Sync/Settings/File Syncing: on for WebDAV (currently unable to verify pCloud server). Advance/Files and Folders/Linked Attachment Base Directory: E:\1\References\Zotero Advance/Files and Folders/Data Directory Location: currently empty, but my screenshot for the original set up was E:\1\References\Zotero.
Work computer (still seemingly works, but WebDAV sync currently "verification failed") Sync/Settings/Data Syncing: linked to my Zotero account Sync/Settings/File Syncing: on for WebDAV (currently unable to verify pCloud server). Advance/Files and Folders/Linked Attachment Base Directory: (empty) Advance/Files and Folders/Data Directory Location: D:\Zotero (a USB drive)
Uncertain the best way forward for system safety and robustness.
"Zotero [conflicted].sqlite" isn't something that Zotero ever creates, so if you're getting that, your Zotero data directory is in a cloud storage folder of some sort. You would know the details.
Zotero will load the zotero.sqlite file in the data directory at startup. If that contains your data, you'll see your data. I can't help you with the specifics, since I don't know what you have in these folders.
The Linked Attachment Base Directory is something completely unrelated to the data directory, so having that set to the same folder is always wrong.
The [conflicted] portion I attributed to syncing completeness regardless if Zotero used the source/local version, or the cloud version (appears to be local version), and since always basing everything from the local (home computer) as master, it didn't seem to matter.
How do I rectify whatever is the issue with opening Zotero in "Home computer": What happens if I now select "Revert to Absolute Paths" but set the Data Directory to what was in the Linked Attachment directory? When I set this up 3 years ago did it permit the dual paths then?
Is there a user comprehensible and important reason why setting Linked Attachment Base Directory the same as Data Directory always wrong?
If the program has an error now- should I simply reinstall it? I have backed up the .sqlite file and the storage folder. Are those the essentials? Are they salvageable like that?
The [conflicted] portion I attributed to syncing completeness
I don't know what you're saying there, but again, that file should not exist in the folder, its presence means you were or are using some sort of external syncing system on that folder, and we can't help you as long as that's the case.
What happens if I now select "Revert to Absolute Paths" but set the Data Directory to what was in the Linked Attachment directory?
Again, the Linked Attachment Base Directory has absolutely nothing to do with your data directory, your database, what you see when you open Zotero, anything like that. It has nothing to do with this. Read the section I linked to that explains what it's for. You shouldn't be guessing what will happen when you change those settings — you should know which type of files you're referring to and which setting applies.
When I set this up 3 years ago did it permit the dual paths then?
There just didn't used to be a check for this incorrect configuration. It's always been incorrect. The Linked Attachment Base Directory is for linked attachments, which don't belong in your data directory. The whole point of linked files is that they're stored elsewhere on your computer and not managed by Zotero within its data directory.
Again, I don't know what files you have where, but Zotero reads the zotero.sqlite file in your active Zotero data directory at startup. That needs to be the database you were using previously, and then you'll see your data at startup. Read through that page for an explanation of what files are in the data directory and instructions for restoring from a backup.
There were a number of issues, some of unknown origin. The WebDAV was down, and after an inquiry, was resolved (verified on my work computer). The WebDAV recovery didn't fix the issue with my home computer whose Zotero I then subsequently uninstalled and reinstalled, which resolved the issue (including the Linked Attachment [empty] vs. Data Directory locations).
One of the reasons for the choice to reinstall was the window Zotero/Preferences/Sync/Settings showing incompletely compared to my work computer that showed optional settings below the "Verify Server" button. That window does not permit scrolling, enlarging, or shrinking the window. After the reinstall, I could see these options and text i.e. from "Download files" to "terms and conditions."
Now, however, I can no longer see those options and text again. I cannot verify if those settings are set correctly- e.g. regarding "Sync attachments" etc.
Is there a known cause and solution to this issue?
Sorry but I'm not going to help you until you acknowledge that you had your data directory in some external sync system — resulting in the "conflicted" files — and you confirm that you've stopped using an external sync system on your database.
Now, however, I can no longer see those options and text again. I cannot verify if those settings are set correctly- e.g. regarding "Sync attachments" etc.
The resizing of the pref panes can sometimes be a little glitchy. Just switch to a different preferences pane, close the preferences, reopen the preferences, and switch back to Sync. There's certainly no need to reinstall anything.
Based on your help and Zotero forums, I got something set up and working, I thought correctly. My current questions make clear I am still not very familiar.
I do not acknowledge that I intentionally put my data directory in some external WebDAV store, but maybe I did? Regardless, I can understand how it might appear that way based on the “conflicted” portion. I may have incorrectly set that up initially, or perhaps still do. I am not a programmer, computer, or Zotero expert.
Did a prior Zotero (4.0?) allow an incorrect setup, which in my case might have persisted to newer versions? I don’t recall trying to coerce Zotero into using a Data directory via external sync but DID want the data directories in each computer in my private USB attached drives (backed up) and not on the computer/public or work drives. The same is true for the files stored, but want those shared via WebDAV to source and reference those in one situation also be available in each location/setting.
The “conflicted” portion has been frustrating for a while, but I thought it was due to something else. That seems likely to be now resolved.
If "conflicted" appeared recently and repeatedly — as you seemed to suggest in your initial post — then it's not resolved unless you did something recently to stop using whatever external syncing system you were using. I'm not sure why you're saying it's resolved now, if you don't know what you were using that was causing it.
In any case, I'm not really clear on what your situation is at the moment, but you'll need to work through this using the documentation we provide on the data directory based on what files you have in what locations on your computer:
We recommend using the default data directory location, Zotero syncing, and stored files. Other configurations are more advanced and require more technical knowledge to set up.
Upgrade Storage
“Zotero [conflicted].sqlite”
I close Zotero and delete the “ [conflicted]” portion of the file name and reopen Zotero and it is all as it should be. This didn't work today.
Likely my error due to distraction or related to a Grammarly installation, regardless it would not open the library including after multiple system restarts.
In Preferences, the data directory location is now not what it may have been- set to the same folder location for both base and data directories, but now it notifies:
"The data directory cannot be set to the same location as the Linked Attachment Base Directory."
I am not sure how to safely resolve this to access my library. Help would be greatly appreciated.
https://www.zotero.org/support/kb/data_directory_in_cloud_storage_folder Yes, those settings have nothing to do with each other and should never be set to the same thing.
https://www.zotero.org/support/zotero_data
https://www.zotero.org/support/preferences/advanced#linked_attachment_base_directory
Your advice has benefited me over the years- including on this topic previously.
I may have confused settings between my home and work computers as I have not had to change anything for a couple of years- it was working, although unknown if the best, right, and Zotero approved way.
The intent was for cloud storage with files stored/synced via WebDAV (pCloud: https://webdav.pcloud.com/zotero/) to:
1. home computer w/files on an external hard drive
2. work computer w/files on USB flash drive
3. another computer wo/files
In Zotero Preferences:
Home computer (not working with the library)
Sync/Settings/Data Syncing: linked to my Zotero account
Sync/Settings/File Syncing: on for WebDAV (currently unable to verify pCloud server).
Advance/Files and Folders/Linked Attachment Base Directory: E:\1\References\Zotero
Advance/Files and Folders/Data Directory Location: currently empty, but my screenshot for the original set up was E:\1\References\Zotero.
Work computer (still seemingly works, but WebDAV sync currently "verification failed")
Sync/Settings/Data Syncing: linked to my Zotero account
Sync/Settings/File Syncing: on for WebDAV (currently unable to verify pCloud server).
Advance/Files and Folders/Linked Attachment Base Directory: (empty)
Advance/Files and Folders/Data Directory Location: D:\Zotero (a USB drive)
Uncertain the best way forward for system safety and robustness.
Zotero will load the zotero.sqlite file in the data directory at startup. If that contains your data, you'll see your data. I can't help you with the specifics, since I don't know what you have in these folders.
The Linked Attachment Base Directory is something completely unrelated to the data directory, so having that set to the same folder is always wrong.
How do I rectify whatever is the issue with opening Zotero in "Home computer": What happens if I now select "Revert to Absolute Paths" but set the Data Directory to what was in the Linked Attachment directory? When I set this up 3 years ago did it permit the dual paths then?
Is there a user comprehensible and important reason why setting Linked Attachment Base Directory the same as Data Directory always wrong?
If the program has an error now- should I simply reinstall it? I have backed up the .sqlite file and the storage folder. Are those the essentials? Are they salvageable like that?
I may be overly cautious to play with it.
Thank you for your time and effort.
Again, I don't know what files you have where, but Zotero reads the zotero.sqlite file in your active Zotero data directory at startup. That needs to be the database you were using previously, and then you'll see your data at startup. Read through that page for an explanation of what files are in the data directory and instructions for restoring from a backup.
One of the reasons for the choice to reinstall was the window Zotero/Preferences/Sync/Settings showing incompletely compared to my work computer that showed optional settings below the "Verify Server" button. That window does not permit scrolling, enlarging, or shrinking the window. After the reinstall, I could see these options and text i.e. from "Download files" to "terms and conditions."
Now, however, I can no longer see those options and text again. I cannot verify if those settings are set correctly- e.g. regarding "Sync attachments" etc.
Is there a known cause and solution to this issue?
https://forums.zotero.org/discussion/comment/302475/#Comment_302475
Based on your help and Zotero forums, I got something set up and working, I thought correctly. My current questions make clear I am still not very familiar.
I do not acknowledge that I intentionally put my data directory in some external WebDAV store, but maybe I did? Regardless, I can understand how it might appear that way based on the “conflicted” portion. I may have incorrectly set that up initially, or perhaps still do. I am not a programmer, computer, or Zotero expert.
Did a prior Zotero (4.0?) allow an incorrect setup, which in my case might have persisted to newer versions? I don’t recall trying to coerce Zotero into using a Data directory via external sync but DID want the data directories in each computer in my private USB attached drives (backed up) and not on the computer/public or work drives. The same is true for the files stored, but want those shared via WebDAV to source and reference those in one situation also be available in each location/setting.
The “conflicted” portion has been frustrating for a while, but I thought it was due to something else. That seems likely to be now resolved.
In any case, I'm not really clear on what your situation is at the moment, but you'll need to work through this using the documentation we provide on the data directory based on what files you have in what locations on your computer:
https://www.zotero.org/support/zotero_data
We recommend using the default data directory location, Zotero syncing, and stored files. Other configurations are more advanced and require more technical knowledge to set up.