Missing attachments and Error for synchronization after reset file sync

Since we had missing attachments on the target Storage after syncing from the Zotero Storage we reset the sync history locally on the target instance
and tried to start the synchronization manually, but got an Error.

Debug-ID: 1552311293
including logs while resetting the sync history

The storage folder of the target Zotero instance is located on a Synology NAS.

We tried the sync reset options after searching in the forums and reading the docs
https://www.zotero.org/support/kb/files_not_syncing
https://www.zotero.org/support/kb/sync_reset_options
  • [JavaScript Error: "Error: Error(s) encountered during statement execution: disk I/O error [QUERY: SELECT itemID FROM items JOIN itemAttachments USING (itemID) WHERE libraryID=? AND itemTypeID=? AND linkMode IN (?, ?, ?)] [PARAMS: 7, 3, 0, 1, 4] [ERROR: disk I/O error]" {file: "chrome://zotero/content/xpcom/db.js" line: 782}]
    That's a Report ID, not a Debug ID as requested in Files Not Syncing, but it also points to a more general problem with your Zotero installation.

    Do you have your entire Zotero data directory on a NAS? This is the kind of error you would get if you did.

    A disk I/O error is a general, unspecified problem with Zotero's ability to access your disk. If you have your Zotero data directory on a network drive or external disk, you should move it back to the local disk to avoid these kinds of problems.

    If your data directory is already on a local disk, there may be an actual problem with your disk, and you should check it for errors. It could potentially also be caused by security software interfering with Zotero's ability to access the disk.
  • Thank you for the feedback.

    My bad with the ID, I guess, I overlooked the message while copying.

    Yes, the entire Zotero directory is on the NAS.

    It had no problems syncing the entries itself to the database but failed with the attachments after some days lafter (it's a large collection) leading to an incomplete number of attachments.

    Is there a way I could get further information regarding the disk I/O error?
    Would the debug log help?
  • edited April 23, 2022
    I'm afraid there's nothing really we can say other than that you should move the data directory back to the local drive to avoid problems. Network shares just don't always behave the same as local disks, particularly for database usage, and if Zotero is getting an error accessing the disk, there's nothing we can do about that.
  • I'm unsure if the reset of the synchronization failed, since the log reports timeouts.

    Debug Log:

    version => 6.0.5, platform => Win32, oscpu => Windows NT 10.0; WOW64, locale => de, appName => Zotero, appVersion => 6.0.5, extensions => Storage Scanner for Zotero (5.0.11, extension), Zotero LibreOffice Integration (6.0.0.SA.6.0.5, extension), Zotero Word for Windows Integration (6.0.0.SA.6.0.5, extension)

    (3)(+11510688): itemTree.render(). Displaying Item Tree

    (3)(+0010194): Unverifying storage

    (3)(+0000018): Username not set before getting Zotero.Sync.Storage.WebDAV.password

    (3)(+0000002): [ConcurrentCaller] Running function (0/4 running, 0 queued)

    (3)(+0000001): HTTP GET https://api.zotero.org/keys/current

    (3)(+0000433): HTTP GET https://api.zotero.org/keys/current succeeded with 200

    (3)(+0000002): [ConcurrentCaller] Done with function (0/4 running, 0 queued)

    (3)(+0000002): { "userID": 1053660 "username": "Wernerb2" "displayName": "" "access": { "user": { "library": true "files": true "notes": true "write": true } "groups": { "all": { "library": true "write": true } } } }

    (3)(+0000006): [ConcurrentCaller] All tasks are done

    (4)(+0028699): Beginning DB transaction zjPMrN5t

    (4)(+0000003): SELECT itemID FROM items JOIN itemAttachments USING (itemID) WHERE libraryID=? AND itemTypeID=? AND linkMode IN (?, ?, ?) [1, 3, 0, 1, 4]

    (4)(+0005101): Waiting for DB transaction zjPMrN5t to finish to start vgPv3JIO

    (5)(+0000000): Zotero.DBConnection.prototype.waitForTransaction@chrome://zotero/content/xpcom/db.js:573:43 Zotero.DBConnection.prototype.executeTransaction@chrome://zotero/content/xpcom/db.js:443:13 resetAllSyncStates@chrome://zotero/content/xpcom/storage/storageLocal.js:575:12 reset@chrome://zotero/content/preferences/preferences_sync.js:858:19 onclick@chrome://zotero/content/preferences/preferences.xul:1:1

    (4)(+0005487): Waiting for DB transaction zjPMrN5t to finish to start GPjBxFgO

    (5)(+0000001): Zotero.DBConnection.prototype.waitForTransaction@chrome://zotero/content/xpcom/db.js:573:43 Zotero.DBConnection.prototype.executeTransaction@chrome://zotero/content/xpcom/db.js:443:13 resetAllSyncStates@chrome://zotero/content/xpcom/storage/storageLocal.js:575:12 reset@chrome://zotero/content/preferences/preferences_sync.js:858:19 onclick@chrome://zotero/content/preferences/preferences.xul:1:1

    (4)(+0004776): Waiting for DB transaction zjPMrN5t to finish to start ujBEn1p1

    (5)(+0000000): Zotero.DBConnection.prototype.waitForTransaction@chrome://zotero/content/xpcom/db.js:573:43 Zotero.DBConnection.prototype.executeTransaction@chrome://zotero/content/xpcom/db.js:443:13 resetAllSyncStates@chrome://zotero/content/xpcom/storage/storageLocal.js:575:12 reset@chrome://zotero/content/preferences/preferences_sync.js:858:19 onclick@chrome://zotero/content/preferences/preferences.xul:1:1

    (4)(+0006743): Waiting for DB transaction zjPMrN5t to finish to start 40f1pSjg

    (5)(+0000001): Zotero.DBConnection.prototype.waitForTransaction@chrome://zotero/content/xpcom/db.js:573:43 Zotero.DBConnection.prototype.executeTransaction@chrome://zotero/content/xpcom/db.js:443:13 resetAllSyncStates@chrome://zotero/content/xpcom/storage/storageLocal.js:575:12 reset@chrome://zotero/content/preferences/preferences_sync.js:858:19 onclick@chrome://zotero/content/preferences/preferences.xul:1:1

    (1)(+0013000): Timed out waiting for transaction vgPv3JIO

    (1)(+0005494): Timed out waiting for transaction GPjBxFgO

    (1)(+0004779): Timed out waiting for transaction ujBEn1p1

    (4)(+0003750): Waiting for DB transaction zjPMrN5t to finish to start WuJbPVDe

    (5)(+0000000): Zotero.DBConnection.prototype.waitForTransaction@chrome://zotero/content/xpcom/db.js:573:43 Zotero.DBConnection.prototype.executeTransaction@chrome://zotero/content/xpcom/db.js:443:13 resetAllSyncStates@chrome://zotero/content/xpcom/storage/storageLocal.js:575:12 reset@chrome://zotero/content/preferences/preferences_sync.js:858:19 onclick@chrome://zotero/content/preferences/preferences.xul:1:1

    (1)(+0002991): Timed out waiting for transaction 40f1pSjg

    (4)(+0004650): Waiting for DB transaction zjPMrN5t to finish to start 4ppSyE1r

    (5)(+0000001): Zotero.DBConnection.prototype.waitForTransaction@chrome://zotero/content/xpcom/db.js:573:43 Zotero.DBConnection.prototype.executeTransaction@chrome://zotero/content/xpcom/db.js:443:13 resetAllSyncStates@chrome://zotero/content/xpcom/storage/storageLocal.js:575:12 reset@chrome://zotero/content/preferences/preferences_sync.js:858:19 onclick@chrome://zotero/content/preferences/preferences.xul:1:1

    (4)(+0007934): Waiting for DB transaction zjPMrN5t to finish to start 0YZclI9W

    (5)(+0000000): Zotero.DBConnection.prototype.waitForTransaction@chrome://zotero/content/xpcom/db.js:573:43 Zotero.DBConnection.prototype.executeTransaction@chrome://zotero/content/xpcom/db.js:443:13 resetAllSyncStates@chrome://zotero/content/xpcom/storage/storageLocal.js:575:12 reset@chrome://zotero/content/preferences/preferences_sync.js:858:19 onclick@chrome://zotero/content/preferences/preferences.xul:1:1

    (4)(+0008247): Waiting for DB transaction zjPMrN5t to finish to start 3ws3Uh8M

    (5)(+0000000): Zotero.DBConnection.prototype.waitForTransaction@chrome://zotero/content/xpcom/db.js:573:43 Zotero.DBConnection.prototype.executeTransaction@chrome://zotero/content/xpcom/db.js:443:13 resetAllSyncStates@chrome://zotero/content/xpcom/storage/storageLocal.js:575:12 reset@chrome://zotero/content/preferences/preferences_sync.js:858:19 onclick@chrome://zotero/content/preferences/preferences.xul:1:1

    (4)(+0004768): Waiting for DB transaction zjPMrN5t to finish to start VtiAcMqw

    (5)(+0000001): Zotero.DBConnection.prototype.waitForTransaction@chrome://zotero/content/xpcom/db.js:573:43 Zotero.DBConnection.prototype.executeTransaction@chrome://zotero/content/xpcom/db.js:443:13 resetAllSyncStates@chrome://zotero/content/xpcom/storage/storageLocal.js:575:12 reset@chrome://zotero/content/preferences/preferences_sync.js:858:19 onclick@chrome://zotero/content/preferences/preferences.xul:1:1

    (1)(+0001411): Timed out waiting for transaction WuJbPVDe

    (1)(+0007653): Timed out waiting for transaction 4ppSyE1r

    (4)(+0005081): UPDATE itemAttachments SET syncState=? WHERE itemID IN (SELECT itemID FROM items JOIN itemAttachments USING (itemID) WHERE libraryID=? AND itemTypeID=? AND linkMode IN (?, ?, ?)) [0, 1, 3, 0, 1, 4]

    (1)(+0002847): Timed out waiting for transaction 0YZclI9W

    (4)(+0001175): Waiting for DB transaction zjPMrN5t to finish to start 6V1gBk0F

    (5)(+0000000): Zotero.DBConnection.prototype.waitForTransaction@chrome://zotero/content/xpcom/db.js:573:43 Zotero.DBConnection.prototype.executeTransaction@chrome://zotero/content/xpcom/db.js:443:13 resetAllSyncStates@chrome://zotero/content/xpcom/storage/storageLocal.js:575:12 reset@chrome://zotero/content/preferences/preferences_sync.js:858:19 onclick@chrome://zotero/content/preferences/preferences.xul:1:1

    (1)(+0007073): Timed out waiting for transaction 3ws3Uh8M

    (1)(+0004770): Timed out waiting for transaction VtiAcMqw

    (4)(+0001470): Waiting for DB transaction zjPMrN5t to finish to start ZVMbEDXe

    (5)(+0000000): Zotero.DBConnection.prototype.waitForTransaction@chrome://zotero/content/xpcom/db.js:573:43 Zotero.DBConnection.prototype.executeTransaction@chrome://zotero/content/xpcom/db.js:443:13 resetAllSyncStates@chrome://zotero/content/xpcom/storage/storageLocal.js:575:12 reset@chrome://zotero/content/preferences/preferences_sync.js:858:19 onclick@chrome://zotero/content/preferences/preferences.xul:1:1

    (1)(+0016953): Timed out waiting for transaction 6V1gBk0F

    (1)(+0013049): Timed out waiting for transaction ZVMbEDXe
  • edited April 24, 2022
    Please don't open multiple threads for the same issue — I've merged this back into one thread.

    Unless you've moved your data directory back to the local disk, we can't help you further.
  • The second one was meant to be a more general question, because I don't know how to interpret these timeouts.

    Are they directly related to the action of resetting the sync history or not?
    I didn't get an error in the UI while doing it but there are timeout even though no synchronization was active at the time.
  • edited April 25, 2022
    If you can reproduce this with the database on a local disk, start a new thread and provide a Debug ID for Zotero startup through getting these errors, using the "Restart with Logging Enabled…" option.

    Otherwise the first thing to do is to move your database to a local disk.
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