Error while parsing changed file #8895

MHFrey · 2022-06-10T19:10:13Z

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

Open library
Save library
Check Log
Close and try to reopen library
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)

The text was updated successfully, but these errors were encountered:

Siedlerchr · 2022-06-10T20:47:07Z

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 · 2022-06-11T18:57:12Z

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 · 2022-06-14T08:29:41Z

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

Fixes #8895 Fixes #8870

* Fix charset detection with utf16 and others Fixes #8895 Fixes #8870 * checkstyöe * Fix typo in method names * change newlines * get bytes * Set newline character to LF * Revert "get bytes" This reverts commit 1082f8a. * progress * switch line sep to LF * Please work * Try jitpack * Add manual build of icu4j * Check if we have ascii in the list of charsets * fix checkstyle * Update external-libraries.md * Enocde with UTF-16BE * Fix umlaut * Hack to get test running * Also compare meta data * Add enforced ignorance of malformed characters Source: http://biercoff.com/malformedinputexception-input-length-1-exception-solution-for-scala-and-java/ Co-authored-by: Christoph <siedlerkiller@gmail.com> * checkstyle * IntelliJ now also renders the file correctly * Add test Additionally - Replace unknown characters - Remove obsolete wrapping classes in test * Refine CHANGELOG.md * Remove non-working jpackage reference Co-authored-by: Oliver Kopp <kopp.dev@gmail.com> Co-authored-by: Houssem Nasri <housi.housi2015@gmail.com>

Siedlerchr added the import label Jun 10, 2022

ThiloteE added the unicode unicode related issues label Jun 14, 2022

ThiloteE mentioned this issue Jun 14, 2022

Will not open file (Charset Exception when reading file) #8870

Closed

2 tasks

Siedlerchr added a commit that referenced this issue Jul 3, 2022

Fix charset detection with utf16 and others

dc9b9cb

Fixes #8895 Fixes #8870

Siedlerchr mentioned this issue Jul 3, 2022

Fix charset detection with utf16 and others #8947

Merged

6 tasks

Siedlerchr closed this as completed in #8947 Jul 11, 2022

koppor moved this to Done in Prioritization Nov 10, 2022

koppor added this to Prioritization Nov 10, 2022

Siedlerchr mentioned this issue May 19, 2023

JabRef V5.9 still corrupts my BIB file. #9926

Closed

2 tasks

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Error while parsing changed file #8895

Error while parsing changed file #8895

MHFrey commented Jun 10, 2022

Siedlerchr commented Jun 10, 2022

Siedlerchr commented Jun 11, 2022 •

edited

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ThiloteE commented Jun 14, 2022 •

edited

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Error while parsing changed file #8895

Error while parsing changed file #8895

Comments

MHFrey commented Jun 10, 2022

JabRef version

Operating system

Details on version and operating system

Checked with the latest development build

Steps to reproduce the behaviour

Appendix

Siedlerchr commented Jun 10, 2022

Siedlerchr commented Jun 11, 2022 • edited Loading

ThiloteE commented Jun 14, 2022 • edited Loading

Siedlerchr commented Jun 11, 2022 •

edited

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ThiloteE commented Jun 14, 2022 •

edited

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