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JabRef3.5 Export into external SQL-database issues Error Unknown column 'afterword' in 'field list' " #1707

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mtecfred opened this issue Aug 10, 2016 · 5 comments
Closed

JabRef3.5 Export into external SQL-database issues Error Unknown column 'afterword' in 'field list' " #1707

mtecfred opened this issue Aug 10, 2016 · 5 comments

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@mtecfred
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JabRef 3.5 windows nt (unknown) 10.0 x86 Java 1.8.0_25 latestst downloads from yesterday 08/09/2016 JabRef_windows_3_5.exe and JabRef_windows-x64_3_5.exe

Steps to reproduce:

  1. File \ SQL Export into an external SQL-database
    throws the following execption:

"com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Unknown column 'afterword' in 'field list' "

Please advise if there is a walkaround.
Unfortunately I'm not able to fix this bug.

Thanks

Error message console:> 
10:21:42.310 [AWT-EventQueue-0] INFO  net.sf.jabref.importer.OpenDatabaseAction - Opening: C:\Users\Michael\Downloads\2016-8-9_bibtex-2016-2000-all.bib
10:21:42.616 [AWT-EventQueue-0] WARN  net.sf.jabref.importer.fileformat.BibtexParser - Could not parse entry
java.io.IOException: Error in line 1357 or above: Empty text token.
This could be caused by a missing comma between two fields.
    at net.sf.jabref.importer.fileformat.BibtexParser.parseFieldContent(BibtexParser.java:606) ~[JabRef-3.5.jar:?]
    at net.sf.jabref.importer.fileformat.BibtexParser.parseField(BibtexParser.java:554) ~[JabRef-3.5.jar:?]
    at net.sf.jabref.importer.fileformat.BibtexParser.parseEntry(BibtexParser.java:538) ~[JabRef-3.5.jar:?]
    at net.sf.jabref.importer.fileformat.BibtexParser.parseAndAddEntry(BibtexParser.java:221) [JabRef-3.5.jar:?]
    at net.sf.jabref.importer.fileformat.BibtexParser.parseFileContent(BibtexParser.java:191) [JabRef-3.5.jar:?]
    at net.sf.jabref.importer.fileformat.BibtexParser.parse(BibtexParser.java:152) [JabRef-3.5.jar:?]
    at net.sf.jabref.importer.fileformat.BibtexParser.parse(BibtexParser.java:92) [JabRef-3.5.jar:?]
    at net.sf.jabref.importer.fileformat.BibtexImporter.importDatabase(BibtexImporter.java:75) [JabRef-3.5.jar:?]
    at net.sf.jabref.importer.fileformat.ImportFormat.importDatabase(ImportFormat.java:90) [JabRef-3.5.jar:?]
    at net.sf.jabref.importer.fileformat.BibtexImporter.importDatabase(BibtexImporter.java:67) [JabRef-3.5.jar:?]
    at net.sf.jabref.importer.OpenDatabaseAction.loadDatabase(OpenDatabaseAction.java:339) [JabRef-3.5.jar:?]
    at net.sf.jabref.importer.OpenDatabaseAction.loadDatabaseOrAutoSave(OpenDatabaseAction.java:393) [JabRef-3.5.jar:?]
    at net.sf.jabref.JabRefGUI.openLastEditedDatabase(JabRefGUI.java:226) [JabRef-3.5.jar:?]
    at net.sf.jabref.JabRefGUI.openWindow(JabRefGUI.java:106) [JabRef-3.5.jar:?]
    at net.sf.jabref.JabRefGUI.<init>(JabRefGUI.java:70) [JabRef-3.5.jar:?]
    at net.sf.jabref.JabRefMain.lambda$start$1(JabRefMain.java:108) [JabRef-3.5.jar:?]
    at net.sf.jabref.JabRefMain$$Lambda$14/1219090.run(Unknown Source) [JabRef-3.5.jar:?]
    at java.awt.event.InvocationEvent.dispatch(Unknown Source) [?:1.8.0_25]
    at java.awt.EventQueue.dispatchEventImpl(Unknown Source) [?:1.8.0_25]
    at java.awt.EventQueue.access$400(Unknown Source) [?:1.8.0_25]
    at java.awt.EventQueue$3.run(Unknown Source) [?:1.8.0_25]
    at java.awt.EventQueue$3.run(Unknown Source) [?:1.8.0_25]
    at java.security.AccessController.doPrivileged(Native Method) ~[?:1.8.0_25]
    at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) [?:1.8.0_25]
    at java.awt.EventQueue.dispatchEvent(Unknown Source) [?:1.8.0_25]
    at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) [?:1.8.0_25]
    at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) [?:1.8.0_25]
    at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) [?:1.8.0_25]
    at java.awt.EventDispatchThread.pumpEvents(Unknown Source) [?:1.8.0_25]
    at java.awt.EventDispatchThread.pumpEvents(Unknown Source) [?:1.8.0_25]
    at java.awt.EventDispatchThread.run(Unknown Source) [?:1.8.0_25]
10:21:42.630 [AWT-EventQueue-0] INFO  net.sf.jabref.importer.fileformat.BibtexParser - Dropped comment from database: Bibtex file generated on 2016-8-9 with typo3 si_bibtex plugin. Data from /mtec/publications/2012-2000.html 
10:21:43.171 [AWT-EventQueue-0] WARN  net.sf.jabref.importer.OpenDatabaseAction - Fehler beim Analysieren des Eintrags: 'Error in line 1357 or above: Empty text token.
This could be caused by a missing comma between two fields.'. Eintrag übersprungen.
10:22:16.111 [Spin-0] WARN  net.sf.jabref.sql.SQLUtil - java.sql.SQLWarning: Can't create database 'jabref_db'; database exists
10:22:16.114 [Spin-0] WARN  net.sf.jabref.sql.SQLUtil - java.sql.SQLWarning: Table 'jabref_database' already exists
10:22:16.116 [Spin-0] WARN  net.sf.jabref.sql.SQLUtil - java.sql.SQLWarning: Table 'entry_types' already exists
10:22:16.118 [Spin-0] WARN  net.sf.jabref.sql.SQLUtil - java.sql.SQLWarning: Table 'entries' already exists
10:22:16.120 [Spin-0] WARN  net.sf.jabref.sql.SQLUtil - java.sql.SQLWarning: Table 'strings' already exists
10:22:16.121 [Spin-0] WARN  net.sf.jabref.sql.SQLUtil - java.sql.SQLWarning: Table 'group_types' already exists
10:22:16.123 [Spin-0] WARN  net.sf.jabref.sql.SQLUtil - java.sql.SQLWarning: Table 'groups' already exists
10:22:16.124 [Spin-0] WARN  net.sf.jabref.sql.SQLUtil - java.sql.SQLWarning: Table 'entry_group' already exists
10:22:16.132 [Spin-0] WARN  net.sf.jabref.sql.SQLUtil - java.sql.SQLWarning: Can't create database 'jabref_db'; database exists
10:22:19.934 [Spin-0] INFO  net.sf.jabref.gui.BasePanel - Could not export to SQL database
com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Unknown column 'afterword' in 'field list'
    at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) ~[?:1.8.0_25]
    at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source) ~[?:1.8.0_25]
    at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source) ~[?:1.8.0_25]
    at java.lang.reflect.Constructor.newInstance(Unknown Source) ~[?:1.8.0_25]
    at com.mysql.jdbc.Util.handleNewInstance(Util.java:404) ~[JabRef-3.5.jar:?]
    at com.mysql.jdbc.Util.getInstance(Util.java:387) ~[JabRef-3.5.jar:?]
    at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:942) ~[JabRef-3.5.jar:?]
    at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3966) ~[JabRef-3.5.jar:?]
    at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3902) ~[JabRef-3.5.jar:?]
    at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2526) ~[JabRef-3.5.jar:?]
    at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2673) ~[JabRef-3.5.jar:?]
    at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2545) ~[JabRef-3.5.jar:?]
    at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2503) ~[JabRef-3.5.jar:?]
    at com.mysql.jdbc.StatementImpl.executeInternal(StatementImpl.java:839) ~[JabRef-3.5.jar:?]
    at com.mysql.jdbc.StatementImpl.execute(StatementImpl.java:739) ~[JabRef-3.5.jar:?]
    at net.sf.jabref.sql.SQLUtil.executeQuery(SQLUtil.java:229) ~[JabRef-3.5.jar:?]
    at net.sf.jabref.sql.SQLUtil.processQuery(SQLUtil.java:190) ~[JabRef-3.5.jar:?]
    at net.sf.jabref.sql.exporter.DatabaseExporter.populateEntryTypesTable(DatabaseExporter.java:228) ~[JabRef-3.5.jar:?]
    at net.sf.jabref.sql.exporter.DatabaseExporter.performExport(DatabaseExporter.java:99) ~[JabRef-3.5.jar:?]
    at net.sf.jabref.sql.exporter.DatabaseExporter.exportDatabaseToDBMS(DatabaseExporter.java:401) ~[JabRef-3.5.jar:?]
    at net.sf.jabref.gui.BasePanel$1.run(BasePanel.java:455) [JabRef-3.5.jar:?]
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[?:1.8.0_25]
    at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source) ~[?:1.8.0_25]
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) ~[?:1.8.0_25]
    at java.lang.reflect.Method.invoke(Unknown Source) ~[?:1.8.0_25]
    at spin.Invocation.evaluate(Invocation.java:175) [JabRef-3.5.jar:?]
    at spin.off.SpinOffEvaluator$1.run(SpinOffEvaluator.java:108) [JabRef-3.5.jar:?]
    at java.lang.Thread.run(Unknown Source) [?:1.8.0_25]
10:33:03.641 [Spin-43] WARN  net.sf.jabref.sql.SQLUtil - java.sql.SQLWarning: Can't create database 'jabref_db'; database exists
10:33:03.645 [Spin-43] WARN  net.sf.jabref.sql.SQLUtil - java.sql.SQLWarning: Table 'jabref_database' already exists
10:33:03.648 [Spin-43] WARN  net.sf.jabref.sql.SQLUtil - java.sql.SQLWarning: Table 'entry_types' already exists
10:33:03.651 [Spin-43] WARN  net.sf.jabref.sql.SQLUtil - java.sql.SQLWarning: Table 'entries' already exists
10:33:03.653 [Spin-43] WARN  net.sf.jabref.sql.SQLUtil - java.sql.SQLWarning: Table 'strings' already exists
10:33:03.654 [Spin-43] WARN  net.sf.jabref.sql.SQLUtil - java.sql.SQLWarning: Table 'group_types' already exists
10:33:03.656 [Spin-43] WARN  net.sf.jabref.sql.SQLUtil - java.sql.SQLWarning: Table 'groups' already exists
10:33:03.658 [Spin-43] WARN  net.sf.jabref.sql.SQLUtil - java.sql.SQLWarning: Table 'entry_group' already exists
10:33:03.666 [Spin-43] WARN  net.sf.jabref.sql.SQLUtil - java.sql.SQLWarning: Can't create database 'jabref_db'; database exists
10:33:06.174 [Spin-43] INFO  net.sf.jabref.gui.BasePanel - Could not export to SQL database
com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Unknown column 'afterword' in 'field list'
    at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) ~[?:1.8.0_25]
    at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source) ~[?:1.8.0_25]
    at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source) ~[?:1.8.0_25]
    at java.lang.reflect.Constructor.newInstance(Unknown Source) ~[?:1.8.0_25]
    at com.mysql.jdbc.Util.handleNewInstance(Util.java:404) ~[JabRef-3.5.jar:?]
    at com.mysql.jdbc.Util.getInstance(Util.java:387) ~[JabRef-3.5.jar:?]
    at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:942) ~[JabRef-3.5.jar:?]
    at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3966) ~[JabRef-3.5.jar:?]
    at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3902) ~[JabRef-3.5.jar:?]
    at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2526) ~[JabRef-3.5.jar:?]
    at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2673) ~[JabRef-3.5.jar:?]
    at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2545) ~[JabRef-3.5.jar:?]
    at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2503) ~[JabRef-3.5.jar:?]
    at com.mysql.jdbc.StatementImpl.executeInternal(StatementImpl.java:839) ~[JabRef-3.5.jar:?]
    at com.mysql.jdbc.StatementImpl.execute(StatementImpl.java:739) ~[JabRef-3.5.jar:?]
    at net.sf.jabref.sql.SQLUtil.executeQuery(SQLUtil.java:229) ~[JabRef-3.5.jar:?]
    at net.sf.jabref.sql.SQLUtil.processQuery(SQLUtil.java:190) ~[JabRef-3.5.jar:?]
    at net.sf.jabref.sql.exporter.DatabaseExporter.populateEntryTypesTable(DatabaseExporter.java:228) ~[JabRef-3.5.jar:?]
    at net.sf.jabref.sql.exporter.DatabaseExporter.performExport(DatabaseExporter.java:99) ~[JabRef-3.5.jar:?]
    at net.sf.jabref.sql.exporter.DatabaseExporter.exportDatabaseToDBMS(DatabaseExporter.java:401) ~[JabRef-3.5.jar:?]
    at net.sf.jabref.gui.BasePanel$1.run(BasePanel.java:455) [JabRef-3.5.jar:?]
    at sun.reflect.GeneratedMethodAccessor26.invoke(Unknown Source) ~[?:?]
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) ~[?:1.8.0_25]
    at java.lang.reflect.Method.invoke(Unknown Source) ~[?:1.8.0_25]
    at spin.Invocation.evaluate(Invocation.java:175) [JabRef-3.5.jar:?]
    at spin.off.SpinOffEvaluator$1.run(SpinOffEvaluator.java:108) [JabRef-3.5.jar:?]
    at java.lang.Thread.run(Unknown Source) [?:1.8.0_25]


>
@koppor
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koppor commented Aug 10, 2016

We completely reworked the database code. We now offer concurrent editing at the database. Unfortunately, the schema had to change completely.

Please try the most recent recent build at: https://builds.jabref.org/master/

A documentation is in preparation at JabRef/blog.jabref.org#1

@koppor koppor added the status: waiting-for-feedback The submitter or other users need to provide more information about the issue label Aug 10, 2016
@mtecfred
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mtecfred commented Aug 10, 2016 •
edited
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Thanks so far for the update. Unfortunately the Oracle DBMS Driver is
not available in both versions, see attached file.

With version 2.11 it is working fine.

net.sf.jabref.shared.DBMSConnector - Oracle-Driver not available

Am 10.08.2016 um 12:01 schrieb Oliver Kopp:

We completely reworked the database code. We now offer concurrent
editing at the database. Unfortunately, the schema had to change
completely.

Please try the most recent recent build at:
https://builds.jabref.org/master/

A documentation is in preparation at JabRef/blog.jabref.org#1
JabRef/blog.jabref.org#1

—
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#1707 (comment),
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https://github.com/notifications/unsubscribe-auth/AT-Y7TIeyiaKF-2n3eLW-Z5BL76tekUqks5qeaGWgaJpZM4Jg8iv.

Michael Freude

Institute of Medical Technology

Hamburg University of Technology

Am Schwarzenberg-Campus 3 1.046

21073 Hamburg

Fon: +49 (0) 40 42878 2196

Fax: +49 (0) 40 42878 4693

http://mtec.et8.tuhh.de

14:50:52.145 [AWT-EventQueue-0] WARN net.sf.jabref.logic.l10n.Localization - Warning: no message translation for "The text after the last line starting with # will be used" for locale de
14:50:52.148 [AWT-EventQueue-0] WARN net.sf.jabref.logic.l10n.Localization - Warning: no message translation for "The text after the last line starting with # will be used" for locale de
C:\Program Files (x86)\JabRef\JabRef.exe

14:50:52.148 [AWT-EventQueue-0] WARN net.sf.jabref.logic.l10n.Localization - Warning: no message translation for "The text after the last line starting with # will be used" for locale de
14:50:52.207 [AWT-EventQueue-0] INFO net.sf.jabref.importer.OpenDatabaseAction - Opening: C:\Users\Michael\Downloads\2016-8-9_bibtex-2016-2000-all.bib
14:50:52.416 [AWT-EventQueue-0] WARN net.sf.jabref.importer.fileformat.BibtexParser - Could not parse entry
java.io.IOException: Error in line 1394 or above: Empty text token.
This could be caused by a missing comma between two fields.
at net.sf.jabref.importer.fileformat.BibtexParser.parseFieldContent(BibtexParser.java:599) ~[JabRef-3.6dev--snapshot--2016-08-10--master--4c1c13b.jar:?]
at net.sf.jabref.importer.fileformat.BibtexParser.parseField(BibtexParser.java:547) ~[JabRef-3.6dev--snapshot--2016-08-10--master--4c1c13b.jar:?]
at net.sf.jabref.importer.fileformat.BibtexParser.parseEntry(BibtexParser.java:531) ~[JabRef-3.6dev--snapshot--2016-08-10--master--4c1c13b.jar:?]
at net.sf.jabref.importer.fileformat.BibtexParser.parseAndAddEntry(BibtexParser.java:227) [JabRef-3.6dev--snapshot--2016-08-10--master--4c1c13b.jar:?]
at net.sf.jabref.importer.fileformat.BibtexParser.parseFileContent(BibtexParser.java:197) [JabRef-3.6dev--snapshot--2016-08-10--master--4c1c13b.jar:?]
at net.sf.jabref.importer.fileformat.BibtexParser.parse(BibtexParser.java:158) [JabRef-3.6dev--snapshot--2016-08-10--master--4c1c13b.jar:?]
at net.sf.jabref.importer.fileformat.BibtexParser.parse(BibtexParser.java:98) [JabRef-3.6dev--snapshot--2016-08-10--master--4c1c13b.jar:?]
at net.sf.jabref.importer.fileformat.BibtexImporter.importDatabase(BibtexImporter.java:78) [JabRef-3.6dev--snapshot--2016-08-10--master--4c1c13b.jar:?]
at net.sf.jabref.importer.fileformat.ImportFormat.importDatabase(ImportFormat.java:90) [JabRef-3.6dev--snapshot--2016-08-10--master--4c1c13b.jar:?]
at net.sf.jabref.importer.fileformat.BibtexImporter.importDatabase(BibtexImporter.java:70) [JabRef-3.6dev--snapshot--2016-08-10--master--4c1c13b.jar:?]
at net.sf.jabref.importer.OpenDatabaseAction.loadDatabase(OpenDatabaseAction.java:341) [JabRef-3.6dev--snapshot--2016-08-10--master--4c1c13b.jar:?]
at net.sf.jabref.importer.OpenDatabaseAction.loadDatabaseOrAutoSave(OpenDatabaseAction.java:395) [JabRef-3.6dev--snapshot--2016-08-10--master--4c1c13b.jar:?]
at net.sf.jabref.JabRefGUI.openLastEditedDatabases(JabRefGUI.java:236) [JabRef-3.6dev--snapshot--2016-08-10--master--4c1c13b.jar:?]
at net.sf.jabref.JabRefGUI.openWindow(JabRefGUI.java:113) [JabRef-3.6dev--snapshot--2016-08-10--master--4c1c13b.jar:?]
at net.sf.jabref.JabRefGUI.(JabRefGUI.java:79) [JabRef-3.6dev--snapshot--2016-08-10--master--4c1c13b.jar:?]
at net.sf.jabref.JabRefMain.lambda$start$1(JabRefMain.java:118) [JabRef-3.6dev--snapshot--2016-08-10--master--4c1c13b.jar:?]
at net.sf.jabref.JabRefMain$$Lambda$14/8870505.run(Unknown Source) [JabRef-3.6dev--snapshot--2016-08-10--master--4c1c13b.jar:?]
at java.awt.event.InvocationEvent.dispatch(Unknown Source) [?:1.8.0_25]
at java.awt.EventQueue.dispatchEventImpl(Unknown Source) [?:1.8.0_25]
at java.awt.EventQueue.access$400(Unknown Source) [?:1.8.0_25]
at java.awt.EventQueue$3.run(Unknown Source) [?:1.8.0_25]
at java.awt.EventQueue$3.run(Unknown Source) [?:1.8.0_25]
at java.security.AccessController.doPrivileged(Native Method) ~[?:1.8.0_25]
at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) [?:1.8.0_25]
at java.awt.EventQueue.dispatchEvent(Unknown Source) [?:1.8.0_25]
at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) [?:1.8.0_25]
at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) [?:1.8.0_25]
at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) [?:1.8.0_25]
at java.awt.EventDispatchThread.pumpEvents(Unknown Source) [?:1.8.0_25]
at java.awt.EventDispatchThread.pumpEvents(Unknown Source) [?:1.8.0_25]
at java.awt.EventDispatchThread.run(Unknown Source) [?:1.8.0_25]
14:50:52.655 [AWT-EventQueue-0] WARN net.sf.jabref.importer.OpenDatabaseAction - Fehler beim Analysieren des Eintrags: 'Error in line 1394 or above: Empty text token.
This could be caused by a missing comma between two fields.'. Eintrag übersprungen.
14:50:53.804 [AWT-EventQueue-0] WARN net.sf.jabref.logic.l10n.Localization - Warning: no message translation for "Export cited" for locale de
14:50:53.855 [AWT-EventQueue-0] WARN net.sf.jabref.logic.l10n.Localization - Warning: no menu item translation for "Manage protected terms" for locale de
14:51:06.852 [AWT-EventQueue-0] INFO net.sf.jabref.shared.DBMSConnector - Oracle-Treiber nicht verfügbar.

-------------- x64 Version :

10:21:42.310 [AWT-EventQueue-0] INFO net.sf.jabref.importer.OpenDatabaseAction - Opening: C:\Users\Michael\Downloads\2016-8-9_bibtex-2016-2000-all.bib
10:21:42.616 [AWT-EventQueue-0] WARN net.sf.jabref.importer.fileformat.BibtexParser - Could not parse entry
java.io.IOException: Error in line 1357 or above: Empty text token.
This could be caused by a missing comma between two fields.
at net.sf.jabref.importer.fileformat.BibtexParser.parseFieldContent(BibtexParser.java:606) ~[JabRef-3.5.jar:?]
at net.sf.jabref.importer.fileformat.BibtexParser.parseField(BibtexParser.java:554) ~[JabRef-3.5.jar:?]
at net.sf.jabref.importer.fileformat.BibtexParser.parseEntry(BibtexParser.java:538) ~[JabRef-3.5.jar:?]
at net.sf.jabref.importer.fileformat.BibtexParser.parseAndAddEntry(BibtexParser.java:221) [JabRef-3.5.jar:?]
at net.sf.jabref.importer.fileformat.BibtexParser.parseFileContent(BibtexParser.java:191) [JabRef-3.5.jar:?]
at net.sf.jabref.importer.fileformat.BibtexParser.parse(BibtexParser.java:152) [JabRef-3.5.jar:?]
at net.sf.jabref.importer.fileformat.BibtexParser.parse(BibtexParser.java:92) [JabRef-3.5.jar:?]
at net.sf.jabref.importer.fileformat.BibtexImporter.importDatabase(BibtexImporter.java:75) [JabRef-3.5.jar:?]
at net.sf.jabref.importer.fileformat.ImportFormat.importDatabase(ImportFormat.java:90) [JabRef-3.5.jar:?]
at net.sf.jabref.importer.fileformat.BibtexImporter.importDatabase(BibtexImporter.java:67) [JabRef-3.5.jar:?]
at net.sf.jabref.importer.OpenDatabaseAction.loadDatabase(OpenDatabaseAction.java:339) [JabRef-3.5.jar:?]
at net.sf.jabref.importer.OpenDatabaseAction.loadDatabaseOrAutoSave(OpenDatabaseAction.java:393) [JabRef-3.5.jar:?]
at net.sf.jabref.JabRefGUI.openLastEditedDatabase(JabRefGUI.java:226) [JabRef-3.5.jar:?]
at net.sf.jabref.JabRefGUI.openWindow(JabRefGUI.java:106) [JabRef-3.5.jar:?]
at net.sf.jabref.JabRefGUI.(JabRefGUI.java:70) [JabRef-3.5.jar:?]
at net.sf.jabref.JabRefMain.lambda$start$1(JabRefMain.java:108) [JabRef-3.5.jar:?]
at net.sf.jabref.JabRefMain$$Lambda$14/1219090.run(Unknown Source) [JabRef-3.5.jar:?]
at java.awt.event.InvocationEvent.dispatch(Unknown Source) [?:1.8.0_25]
at java.awt.EventQueue.dispatchEventImpl(Unknown Source) [?:1.8.0_25]
at java.awt.EventQueue.access$400(Unknown Source) [?:1.8.0_25]
at java.awt.EventQueue$3.run(Unknown Source) [?:1.8.0_25]
at java.awt.EventQueue$3.run(Unknown Source) [?:1.8.0_25]
at java.security.AccessController.doPrivileged(Native Method) ~[?:1.8.0_25]
at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) [?:1.8.0_25]
at java.awt.EventQueue.dispatchEvent(Unknown Source) [?:1.8.0_25]
at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) [?:1.8.0_25]
at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) [?:1.8.0_25]
at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) [?:1.8.0_25]
at java.awt.EventDispatchThread.pumpEvents(Unknown Source) [?:1.8.0_25]
at java.awt.EventDispatchThread.pumpEvents(Unknown Source) [?:1.8.0_25]
at java.awt.EventDispatchThread.run(Unknown Source) [?:1.8.0_25]
10:21:42.630 [AWT-EventQueue-0] INFO net.sf.jabref.importer.fileformat.BibtexParser - Dropped comment from database: Bibtex file generated on 2016-8-9 with typo3 si_bibtex plugin. Data from /mtec/publications/2012-2000.html
10:21:43.171 [AWT-EventQueue-0] WARN net.sf.jabref.importer.OpenDatabaseAction - Fehler beim Analysieren des Eintrags: 'Error in line 1357 or above: Empty text token.
This could be caused by a missing comma between two fields.'. Eintrag übersprungen.
10:22:16.111 [Spin-0] WARN net.sf.jabref.sql.SQLUtil - java.sql.SQLWarning: Can't create database 'jabref_db'; database exists
10:22:16.114 [Spin-0] WARN net.sf.jabref.sql.SQLUtil - java.sql.SQLWarning: Table 'jabref_database' already exists
10:22:16.116 [Spin-0] WARN net.sf.jabref.sql.SQLUtil - java.sql.SQLWarning: Table 'entry_types' already exists
10:22:16.118 [Spin-0] WARN net.sf.jabref.sql.SQLUtil - java.sql.SQLWarning: Table 'entries' already exists
10:22:16.120 [Spin-0] WARN net.sf.jabref.sql.SQLUtil - java.sql.SQLWarning: Table 'strings' already exists
10:22:16.121 [Spin-0] WARN net.sf.jabref.sql.SQLUtil - java.sql.SQLWarning: Table 'group_types' already exists
10:22:16.123 [Spin-0] WARN net.sf.jabref.sql.SQLUtil - java.sql.SQLWarning: Table 'groups' already exists
10:22:16.124 [Spin-0] WARN net.sf.jabref.sql.SQLUtil - java.sql.SQLWarning: Table 'entry_group' already exists
10:22:16.132 [Spin-0] WARN net.sf.jabref.sql.SQLUtil - java.sql.SQLWarning: Can't create database 'jabref_db'; database exists
10:22:19.934 [Spin-0] INFO net.sf.jabref.gui.BasePanel - Could not export to SQL database
com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Unknown column 'afterword' in 'field list'
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) ~[?:1.8.0_25]
at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source) ~[?:1.8.0_25]
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source) ~[?:1.8.0_25]
at java.lang.reflect.Constructor.newInstance(Unknown Source) ~[?:1.8.0_25]
at com.mysql.jdbc.Util.handleNewInstance(Util.java:404) ~[JabRef-3.5.jar:?]
at com.mysql.jdbc.Util.getInstance(Util.java:387) ~[JabRef-3.5.jar:?]
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:942) ~[JabRef-3.5.jar:?]
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3966) ~[JabRef-3.5.jar:?]
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3902) ~[JabRef-3.5.jar:?]
at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2526) ~[JabRef-3.5.jar:?]
at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2673) ~[JabRef-3.5.jar:?]
at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2545) ~[JabRef-3.5.jar:?]
at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2503) ~[JabRef-3.5.jar:?]
at com.mysql.jdbc.StatementImpl.executeInternal(StatementImpl.java:839) ~[JabRef-3.5.jar:?]
at com.mysql.jdbc.StatementImpl.execute(StatementImpl.java:739) ~[JabRef-3.5.jar:?]
at net.sf.jabref.sql.SQLUtil.executeQuery(SQLUtil.java:229) ~[JabRef-3.5.jar:?]
at net.sf.jabref.sql.SQLUtil.processQuery(SQLUtil.java:190) ~[JabRef-3.5.jar:?]
at net.sf.jabref.sql.exporter.DatabaseExporter.populateEntryTypesTable(DatabaseExporter.java:228) ~[JabRef-3.5.jar:?]
at net.sf.jabref.sql.exporter.DatabaseExporter.performExport(DatabaseExporter.java:99) ~[JabRef-3.5.jar:?]
at net.sf.jabref.sql.exporter.DatabaseExporter.exportDatabaseToDBMS(DatabaseExporter.java:401) ~[JabRef-3.5.jar:?]
at net.sf.jabref.gui.BasePanel$1.run(BasePanel.java:455) [JabRef-3.5.jar:?]
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[?:1.8.0_25]
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source) ~[?:1.8.0_25]
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) ~[?:1.8.0_25]
at java.lang.reflect.Method.invoke(Unknown Source) ~[?:1.8.0_25]
at spin.Invocation.evaluate(Invocation.java:175) [JabRef-3.5.jar:?]
at spin.off.SpinOffEvaluator$1.run(SpinOffEvaluator.java:108) [JabRef-3.5.jar:?]
at java.lang.Thread.run(Unknown Source) [?:1.8.0_25]
10:33:03.641 [Spin-43] WARN net.sf.jabref.sql.SQLUtil - java.sql.SQLWarning: Can't create database 'jabref_db'; database exists
10:33:03.645 [Spin-43] WARN net.sf.jabref.sql.SQLUtil - java.sql.SQLWarning: Table 'jabref_database' already exists
10:33:03.648 [Spin-43] WARN net.sf.jabref.sql.SQLUtil - java.sql.SQLWarning: Table 'entry_types' already exists
10:33:03.651 [Spin-43] WARN net.sf.jabref.sql.SQLUtil - java.sql.SQLWarning: Table 'entries' already exists
10:33:03.653 [Spin-43] WARN net.sf.jabref.sql.SQLUtil - java.sql.SQLWarning: Table 'strings' already exists
10:33:03.654 [Spin-43] WARN net.sf.jabref.sql.SQLUtil - java.sql.SQLWarning: Table 'group_types' already exists
10:33:03.656 [Spin-43] WARN net.sf.jabref.sql.SQLUtil - java.sql.SQLWarning: Table 'groups' already exists
10:33:03.658 [Spin-43] WARN net.sf.jabref.sql.SQLUtil - java.sql.SQLWarning: Table 'entry_group' already exists
10:33:03.666 [Spin-43] WARN net.sf.jabref.sql.SQLUtil - java.sql.SQLWarning: Can't create database 'jabref_db'; database exists
10:33:06.174 [Spin-43] INFO net.sf.jabref.gui.BasePanel - Could not export to SQL database
com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Unknown column 'afterword' in 'field list'
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) ~[?:1.8.0_25]
at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source) ~[?:1.8.0_25]
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source) ~[?:1.8.0_25]
at java.lang.reflect.Constructor.newInstance(Unknown Source) ~[?:1.8.0_25]
at com.mysql.jdbc.Util.handleNewInstance(Util.java:404) ~[JabRef-3.5.jar:?]
at com.mysql.jdbc.Util.getInstance(Util.java:387) ~[JabRef-3.5.jar:?]
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:942) ~[JabRef-3.5.jar:?]
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3966) ~[JabRef-3.5.jar:?]
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3902) ~[JabRef-3.5.jar:?]
at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2526) ~[JabRef-3.5.jar:?]
at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2673) ~[JabRef-3.5.jar:?]
at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2545) ~[JabRef-3.5.jar:?]
at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2503) ~[JabRef-3.5.jar:?]
at com.mysql.jdbc.StatementImpl.executeInternal(StatementImpl.java:839) ~[JabRef-3.5.jar:?]
at com.mysql.jdbc.StatementImpl.execute(StatementImpl.java:739) ~[JabRef-3.5.jar:?]
at net.sf.jabref.sql.SQLUtil.executeQuery(SQLUtil.java:229) ~[JabRef-3.5.jar:?]
at net.sf.jabref.sql.SQLUtil.processQuery(SQLUtil.java:190) ~[JabRef-3.5.jar:?]
at net.sf.jabref.sql.exporter.DatabaseExporter.populateEntryTypesTable(DatabaseExporter.java:228) ~[JabRef-3.5.jar:?]
at net.sf.jabref.sql.exporter.DatabaseExporter.performExport(DatabaseExporter.java:99) ~[JabRef-3.5.jar:?]
at net.sf.jabref.sql.exporter.DatabaseExporter.exportDatabaseToDBMS(DatabaseExporter.java:401) ~[JabRef-3.5.jar:?]
at net.sf.jabref.gui.BasePanel$1.run(BasePanel.java:455) [JabRef-3.5.jar:?]
at sun.reflect.GeneratedMethodAccessor26.invoke(Unknown Source) ~[?:?]
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) ~[?:1.8.0_25]
at java.lang.reflect.Method.invoke(Unknown Source) ~[?:1.8.0_25]
at spin.Invocation.evaluate(Invocation.java:175) [JabRef-3.5.jar:?]
at spin.off.SpinOffEvaluator$1.run(SpinOffEvaluator.java:108) [JabRef-3.5.jar:?]
at java.lang.Thread.run(Unknown Source) [?:1.8.0_25]

@koppor
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koppor commented Aug 10, 2016

That means, you could connect to Oracle using the 2.11 version?

@mtecfred
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Yes, I'm able to connect to a remote database and to export the whole
JabRef contents into a former created remote database.

I checked it via sql console at the remote system and also with MS
Access via odbc connection.

I also can import it back from the remote sql-server by using an empty
JabRef file that is filled by the new import.

JabRef Version 2.11 © 2003-2015

Am 10.08.2016 um 16:10 schrieb Oliver Kopp:

That means, you could connect to Oracle using the 2.11 version?

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@koppor koppor removed the status: waiting-for-feedback The submitter or other users need to provide more information about the issue label Oct 20, 2016
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koppor commented Oct 20, 2016

I'll close this as we do not support old 3.x versions actively.

We created a help page on migrating data from pre-3.6 databases: https://help.jabref.org/en/SQLDatabaseMigration

The missing Oracle driver is not an issue if you use Postgres or MySQL.

Please also check the latest build at https://builds.jabref.org/master/ and Postgres: In this combination, JabRef offers live update in case more than one client is connected.

Please contact me in case you have issues with the 3.6 or 3.7dev version.

@koppor koppor closed this as completed Oct 20, 2016
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