zotero-better-bibtex: Corrupt DB crashes Zotero on exit

  • Zotero 5.0.89 (archlinux)
  • BBT 5.2.54

Every time I open Zotero, BBT start from scratch, generate citation keys and I have to setup the auto-export profile again. This problem happens some point in time and after that it happens non-stop.

Here is the output from zotero -ZoteroDebug

WARNING: At least one completion condition is taking too long to complete. Conditions: [{"name":"Sqlite.jsm shutdown blocker","state":{"description":"Waiting for connections to close","state":[{"name":"better-bibtex.sqlite#0: waiting for shutdown","state":{"identifier":"better-bibtex.sqlite#0","isCloseRequested":false,"hasDbConn":true,"hasInProgressTransaction":false,"pendingStatements":0,"statementCounter":9},"filename":"resource://gre/modules/Sqlite.jsm","lineNumber":250,"stack":["resource://gre/modules/Sqlite.jsm:ConnectionData:250","resource://gre/modules/Sqlite.jsm:OpenedConnection:1143","resource://gre/modules/Sqlite.jsm:openConnection/</<:953"]}]},"filename":"resource://gre/modules/Sqlite.jsm","lineNumber":148,"stack":["resource://gre/modules/Sqlite.jsm:null:148","resource://gre/modules/XPCOMUtils.jsm:get:194","resource://gre/modules/Sqlite.jsm:ConnectionData:250","resource://gre/modules/Sqlite.jsm:OpenedConnection:1143","resource://gre/modules/Sqlite.jsm:openConnection/</<:953"]}] Barrier: profile-before-change
WARNING: At least one completion condition is taking too long to complete. Conditions: [{"name":"better-bibtex.sqlite#0: waiting for shutdown","state":{"identifier":"better-bibtex.sqlite#0","isCloseRequested":false,"hasDbConn":true,"hasInProgressTransaction":false,"pendingStatements":0,"statementCounter":9},"filename":"resource://gre/modules/Sqlite.jsm","lineNumber":250,"stack":["resource://gre/modules/Sqlite.jsm:ConnectionData:250","resource://gre/modules/Sqlite.jsm:OpenedConnection:1143","resource://gre/modules/Sqlite.jsm:openConnection/</<:953"]}] Barrier: Sqlite.jsm: wait until all connections are closed
FATAL ERROR: AsyncShutdown timeout in profile-before-change Conditions: [{"name":"Sqlite.jsm shutdown blocker","state":{"description":"Waiting for connections to close","state":[{"name":"better-bibtex.sqlite#0: waiting for shutdown","state":{"identifier":"better-bibtex.sqlite#0","isCloseRequested":false,"hasDbConn":true,"hasInProgressTransaction":false,"pendingStatements":0,"statementCounter":9},"filename":"resource://gre/modules/Sqlite.jsm","lineNumber":250,"stack":["resource://gre/modules/Sqlite.jsm:ConnectionData:250","resource://gre/modules/Sqlite.jsm:OpenedConnection:1143","resource://gre/modules/Sqlite.jsm:openConnection/</<:953"]}]},"filename":"resource://gre/modules/Sqlite.jsm","lineNumber":148,"stack":["resource://gre/modules/Sqlite.jsm:null:148","resource://gre/modules/XPCOMUtils.jsm:get:194","resource://gre/modules/Sqlite.jsm:ConnectionData:250","resource://gre/modules/Sqlite.jsm:OpenedConnection:1143","resource://gre/modules/Sqlite.jsm:openConnection/</<:953"]}] At least one completion condition failed to complete within a reasonable amount of time. Causing a crash to ensure that we do not leave the user with an unresponsive process draining resources.
WARNING: No crash reporter available
[169354, Main Thread] ###!!! ABORT: file resource://gre/modules/Sqlite.jsm, line 148
[169354, Main Thread] ###!!! ABORT: file resource://gre/modules/Sqlite.jsm, line 148
[1]    169354 segmentation fault (core dumped)  zotero -ZoteroDebug

I have also included the Zotero Debug output (html) here (which covers mostly the startup part), I saw the below part relevant, if it may help:


			<div id="errors">[JavaScript Error: "{better-bibtex error} +5099 DB.Store.exportDatabaseSQLiteAsync: save of better-bibtex to unopened database "]

[JavaScript Error: "{better-bibtex error} +5177 DB.Store.exportDatabaseSQLiteAsync: save of better-bibtex to unopened database "]

[JavaScript Error: "{better-bibtex error} +5037 DB.Store.exportDatabaseSQLiteAsync: save of better-bibtex to unopened database "]

[JavaScript Error: "{better-bibtex error} +5173 DB.Store.exportDatabaseSQLiteAsync: save of better-bibtex to unopened database "]

[JavaScript Error: "{better-bibtex error} +5195 DB.Store.exportDatabaseSQLiteAsync: save of better-bibtex to unopened database "]

[JavaScript Error: "{better-bibtex error} +5154 DB.Store.exportDatabaseSQLiteAsync: save of better-bibtex to unopened database "]

[JavaScript Error: "{better-bibtex error} +5164 DB.Store.exportDatabaseSQLiteAsync: save of better-bibtex to unopened database "]

[JavaScript Error: "{better-bibtex error} +5091 DB.Store.exportDatabaseSQLiteAsync: save of better-bibtex to unopened database "]

[JavaScript Error: "{better-bibtex error} +5179 DB.Store.exportDatabaseSQLiteAsync: save of better-bibtex to unopened database "]

[JavaScript Error: "{better-bibtex error} +5133 DB.Store.exportDatabaseSQLiteAsync: save of better-bibtex to unopened database "]

[JavaScript Error: "{better-bibtex error} +5115 DB.Store.exportDatabaseSQLiteAsync: save of better-bibtex to unopened database "]

[JavaScript Error: "{better-bibtex error} +5214 DB.Store.exportDatabaseSQLiteAsync: save of better-bibtex to unopened database "]

[JavaScript Error: "{better-bibtex error} +5374 DB.Store.exportDatabaseSQLiteAsync: save of better-bibtex to unopened database "]

[JavaScript Error: "{better-bibtex error} +5228 DB.Store.exportDatabaseSQLiteAsync: save of better-bibtex to unopened database "]

[JavaScript Error: "{better-bibtex error} +5075 DB.Store.exportDatabaseSQLiteAsync: save of better-bibtex to unopened database "]

[JavaScript Error: "{better-bibtex error} +5608 DB.Store.exportDatabaseSQLiteAsync: save of better-bibtex to unopened database "]

[JavaScript Error: "{better-bibtex error} +5203 DB.Store.exportDatabaseSQLiteAsync: save of better-bibtex to unopened database "]

[JavaScript Error: "{better-bibtex error} +5135 DB.Store.exportDatabaseSQLiteAsync: save of better-bibtex to unopened database "]

[JavaScript Error: "{better-bibtex error} +5229 DB.Store.exportDatabaseSQLiteAsync: save of better-bibtex to unopened database "]

[JavaScript Error: "{better-bibtex error} +5072 DB.Store.exportDatabaseSQLiteAsync: save of better-bibtex to unopened database "]

[JavaScript Error: "{better-bibtex error} +5280 DB.Store.exportDatabaseSQLiteAsync: save of better-bibtex to unopened database "]

[JavaScript Error: "{better-bibtex error} +5118 DB.Store.exportDatabaseSQLiteAsync: save of better-bibtex to unopened database "]

[JavaScript Error: "{better-bibtex error} +5162 DB.Store.exportDatabaseSQLiteAsync: save of better-bibtex to unopened database "]

[JavaScript Error: "{better-bibtex error} +5206 DB.Store.exportDatabaseSQLiteAsync: save of better-bibtex to unopened database "]

[JavaScript Error: "{better-bibtex error} +5072 DB.Store.exportDatabaseSQLiteAsync: save of better-bibtex to unopened database "]

version =&gt; 5.0.89, platform =&gt; Linux x86_64, oscpu =&gt; Linux x86_64, locale =&gt; en-US, appName =&gt; Zotero, appVersion =&gt; 5.0.89, extensions =&gt; ZotFile (5.0.16, extension), Zotero LibreOffice Integration (5.0.23.SA.5.0.89, extension), Better BibTex for Zotero (5.2.54, extension)</div>
			<div id="output"><p>(3)(+0000000): {better-bibtex} +null pathSearch: texstudio found at /usr/bin/texstudio </p><p>(3)(+0000000): {better-bibtex} +0 TeXstudio: found at /usr/bin/texstudio </p><p>(3)(+0000001): {better-bibtex} +1 Startup progress: waiting for Zotero locks... </p><p>(3)(+0000003): Using data directory /run/media/mizozhan/Win10/Users/mizozhan/AppData/Roaming/zotero/zotero/4g7pxkf8.default/zotero</p><p>(3)(+0000003):
 IPC: Initializing pipe at 

Export ID: 5072, 5206, 5162, 5118, 5280, 5229, 5135, 5203, 5608, 5475, 5298, 5374, 5214, 5115, 51xx …

Expected behavior: After restarting zotero, BBT shouldn’t start from scratch and it keep the auto export profile created before.

Actual behavior: After restart I lost everything related to BBT and it start from scratch (all citation keys are generated again) and the automatic export profile is lost and I need to recreate it again.

ZoteroDebugOutput.zip

better-bibtex.sqlite

About this issue

  • Original URL
  • State: closed
  • Created 4 years ago
  • Comments: 21 (13 by maintainers)

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Most upvoted comments

6990 should do it.

Wait I think I can replicate the problem