Error while parsing changed file

[MHFrey]

JabRef version

5.6 (latest release)

Operating system

Windows

Details on version and operating system

WIndows 10 Pro 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. Open library
2. Save library
3. Check Log
4. Close and try to reopen library
5. Error opening file '(filename unknown)'. Input lentgh = 1

Appendix

...

Log File

Error when Saving============================================
Trust store path: C:\Users\frey\AppData\Local\org.jabref\ssl\truststore.jks
Not updating theme because it hasn't changed
Theme set to Theme{type=DEFAULT, name=''} with base css StyleSheet{jrt:/org.jabref/org/jabref/gui/Base.css}
Index path for C:\Users\frey\Documents\My_Documents\Papers\JabRef\MHF.bib is C:\Users\frey\AppData\Local\org.jabref\JabRef\lucene91
Saving library...
Library saved
Error while parsing changed file.
java.nio.charset.MalformedInputException: Input length = 1
	at java.base/java.nio.charset.CoderResult.throwException(Unknown Source)
	at java.base/sun.nio.cs.StreamDecoder.implRead(Unknown Source)
	at java.base/sun.nio.cs.StreamDecoder.read(Unknown Source)
	at java.base/java.io.InputStreamReader.read(Unknown Source)
	at java.base/java.io.BufferedReader.fill(Unknown Source)
	at java.base/java.io.BufferedReader.read(Unknown Source)
	at java.base/java.io.FilterReader.read(Unknown Source)
	at java.base/java.io.PushbackReader.read(Unknown Source)
	at org.jabref@5.6.60000/org.jabref.logic.importer.fileformat.BibtexParser.read(Unknown Source)
	at org.jabref@5.6.60000/org.jabref.logic.importer.fileformat.BibtexParser.consumeUncritically(Unknown Source)
	at org.jabref@5.6.60000/org.jabref.logic.importer.fileformat.BibtexParser.parseFileContent(Unknown Source)
	at org.jabref@5.6.60000/org.jabref.logic.importer.fileformat.BibtexParser.parse(Unknown Source)
	at org.jabref@5.6.60000/org.jabref.logic.importer.fileformat.BibtexImporter.importDatabase(Unknown Source)
	at org.jabref@5.6.60000/org.jabref.logic.importer.fileformat.BibtexImporter.importDatabase(Unknown Source)
	at org.jabref@5.6.60000/org.jabref.logic.importer.OpenDatabase.loadDatabase(Unknown Source)
	at org.jabref@5.6.60000/org.jabref.gui.collab.ChangeScanner.scanForChanges(Unknown Source)
	at org.jabref@5.6.60000/org.jabref.gui.util.BackgroundTask$1.call(Unknown Source)
	at org.jabref@5.6.60000/org.jabref.gui.util.DefaultTaskExecutor$1.call(Unknown Source)
	at org.jabref.merged.module@5.6.60000/javafx.concurrent.Task$TaskCallable.call(Unknown Source)
	at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
	at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
	at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
	at java.base/java.lang.Thread.run(Unknown Source)

Error when Reopening=================================================
Trust store path: C:\Users\frey\AppData\Local\org.jabref\ssl\truststore.jks
Not updating theme because it hasn't changed
Theme set to Theme{type=DEFAULT, name=''} with base css StyleSheet{jrt:/org.jabref/org/jabref/gui/Base.css}
Error opening file 'C:\Users\frey\Documents\My_Documents\Papers\JabRef\MHF.bib'
java.nio.charset.MalformedInputException: Input length = 1
	at java.base/java.nio.charset.CoderResult.throwException(Unknown Source)
	at java.base/sun.nio.cs.StreamDecoder.implRead(Unknown Source)
	at java.base/sun.nio.cs.StreamDecoder.read(Unknown Source)
	at java.base/java.io.InputStreamReader.read(Unknown Source)
	at java.base/java.io.BufferedReader.fill(Unknown Source)
	at java.base/java.io.BufferedReader.read(Unknown Source)
	at java.base/java.io.FilterReader.read(Unknown Source)
	at java.base/java.io.PushbackReader.read(Unknown Source)
	at org.jabref@5.6.60000/org.jabref.logic.importer.fileformat.BibtexParser.read(Unknown Source)
	at org.jabref@5.6.60000/org.jabref.logic.importer.fileformat.BibtexParser.consumeUncritically(Unknown Source)
	at org.jabref@5.6.60000/org.jabref.logic.importer.fileformat.BibtexParser.parseFileContent(Unknown Source)
	at org.jabref@5.6.60000/org.jabref.logic.importer.fileformat.BibtexParser.parse(Unknown Source)
	at org.jabref@5.6.60000/org.jabref.logic.importer.fileformat.BibtexImporter.importDatabase(Unknown Source)
	at org.jabref@5.6.60000/org.jabref.logic.importer.fileformat.BibtexImporter.importDatabase(Unknown Source)
	at org.jabref@5.6.60000/org.jabref.logic.importer.OpenDatabase.loadDatabase(Unknown Source)
	at org.jabref@5.6.60000/org.jabref.gui.JabRefGUI.openLastEditedDatabases(Unknown Source)
	at org.jabref@5.6.60000/org.jabref.gui.JabRefGUI.openDatabases(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.application.PlatformImpl.lambda$runLater$10(Unknown Source)
	at java.base/java.security.AccessController.doPrivileged(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.application.PlatformImpl.lambda$runLater$11(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.glass.ui.InvokeLaterDispatcher$Future.run(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.glass.ui.win.WinApplication._runLoop(Native Method)
	at org.jabref.merged.module@5.6.60000/com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(Unknown Source)
	at java.base/java.lang.Thread.run(Unknown Source)

[Siedlerchr]

Thanks for the report. The error message looks similar to #8870
There seems to be something wrong with detecting the char set.

Can you open the bib file in an application like Notepad++ and check the encoding? JabRef always tries to Write and Read in UTF-8.
And second, would it be possible for you to make the bib file available to us? (You can send it privately to web@jabref.org

[Siedlerchr]

Thanks a lot for the files. I could reproduce this on my machine as well.
The problem lies in our approach to automatically identify the charset. Later on, we try to check if the first line contains the encoding comment. However, if the wrong charset previously was identified as e.g. UTF8, but it is like UTF16BE the String comparsion fails, because java compares the chars on a byte level and those obviously don't match in different charsets.

[ThiloteE]

Cause could maybe be: JabRef#75 (comment)
Refs #8506