JabRef does not open after csv file was edited by hand

[swiss-cottage]

JabRef version

5.4 (latest release)

Operating system

Windows

Details on version and operating system

Windows 10 21H2

Checked with the latest development build

• I made a backup of my libraries before testing the latest development version.
• I have tested the latest development version and the problem persists

Steps to reproduce the behaviour

1. edit csv file of journal abbreviations by hand
2. JabRef won't start anymore
3. Reinstalled in hope of fixing this; to no avail
4. Ran the command C:\Program Files\JabRef\runtime\bin>JabRef.bat that I found on another thread: the output is below.

Appendix

...

Log File

Jan 02, 2022 4:50:38 PM com.sun.javafx.application.PlatformImpl startup
WARNING: Unsupported JavaFX configuration: classes were loaded from 'module org.jabref.merged.module', isAutomatic: false, isOpen: true
2022-01-02 16:50:38 [JavaFX Application Thread] org.jabref.logic.net.URLDownload.bypassSSLVerification()
WARN: Fix SSL exceptions by accepting ALL certificates
2022-01-02 16:50:38 [JavaFX Application Thread] org.jabref.gui.JabRefMain.start()
ERROR: Unexpected exception: java.lang.IllegalStateException: IOException reading next record: java.io.IOException: (line 18) invalid char between encapsulated token and delimiter
at [email protected]/org.apache.commons.csv.CSVParser$CSVRecordIterator.getNextRecord(Unknown Source)
at [email protected]/org.apache.commons.csv.CSVParser$CSVRecordIterator.hasNext(Unknown Source)
at [email protected]/org.jabref.logic.journals.AbbreviationParser.readJournalList(Unknown Source)
at [email protected]/org.jabref.logic.journals.AbbreviationParser.readJournalListFromFile(Unknown Source)
at [email protected]/org.jabref.logic.journals.AbbreviationParser.readJournalListFromFile(Unknown Source)
at [email protected]/org.jabref.logic.journals.JournalAbbreviationLoader.readJournalListFromFile(Unknown Source)
at [email protected]/org.jabref.logic.journals.JournalAbbreviationLoader.loadRepository(Unknown Source)
at [email protected]/org.jabref.gui.JabRefMain.applyPreferences(Unknown Source)
at [email protected]/org.jabref.gui.JabRefMain.start(Unknown Source)
at [email protected]/com.sun.javafx.application.LauncherImpl.lambda$launchApplication1$9(Unknown Source)
at [email protected]/com.sun.javafx.application.PlatformImpl.lambda$runAndWait$12(Unknown Source)
at [email protected]/com.sun.javafx.application.PlatformImpl.lambda$runLater$10(Unknown Source)
at java.base/java.security.AccessController.doPrivileged(Unknown Source)
at [email protected]/com.sun.javafx.application.PlatformImpl.lambda$runLater$11(Unknown Source)
at [email protected]/com.sun.glass.ui.InvokeLaterDispatcher$Future.run(Unknown Source)
at [email protected]/com.sun.glass.ui.win.WinApplication._runLoop(Native Method)
at [email protected]/com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(Unknown Source)
at java.base/java.lang.Thread.run(Unknown Source)
Caused by: java.io.IOException: (line 18) invalid char between encapsulated token and delimiter
at [email protected]/org.apache.commons.csv.Lexer.parseEncapsulatedToken(Unknown Source)
at [email protected]/org.apache.commons.csv.Lexer.nextToken(Unknown Source)
at [email protected]/org.apache.commons.csv.CSVParser.nextRecord(Unknown Source)
... 18 more

[swiss-cottage]

I have now renamed the offending csv file and JabRef starts again. Cannot understand how it knew where to look after it was uninstalled but it must have a settings file somewhere that was not deleted during the uninstall.

[Siedlerchr]

The error message indicates that there was a Syntax mistake in the file. What file did you edit exactly?
Maybe you missed some Semicolon?
Jabref stores it preferences in the registry.

[swiss-cottage]

I am sure I have made some syntax error with either " " or \' for French accents. The editing of the journal abbrv file directly in JabRef is somewhat difficult; if one forgets to press ENTER, the entry is lost. But the functionality of having the abbrv list is great. I have a small regret that the built-in abbrv are not consistent, e.g., The Annals of Applied Probability are abbreviated without full stops.

[Siedlerchr]

@swiss-cottage The built-in journal abbreviations are assembled/combined from the ones in this repository: https://github.com/JabRef/abbrv.jabref.org
You are welcome to add/correct the entries

[swiss-cottage]

@Siedlerchr I have found the issue: the file "journal_abbreviations_webofscience.csv" has no dots and I am guessing it overwrites some of the dotted entries. Certainly, in the files "journal_abbreviations_ams" and "journal_abbreviations_mathematics.csv" the dots are present and correct. This is not something that I can fix but perhaps it is not difficult to exclude the undotted file?

[Siedlerchr]

Thanks for the investigation. I guess this refs the issue here JabRef/abbrv.jabref.org#79 (comment)