JabRef error if keyword group has no name #9776

alfureu · 2023-04-18T02:36:19Z

Update: Read on at #9776 (comment)

JabRef version

5.9 (latest release)

Operating system

macOS

Details on version and operating system

macOS 13.3.1

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

import a biblatex library created on linux machine and with the special field priority
error opening (does not open)

JabRef 5.9--2023-01-08--76253f1a7
Mac OS X 13.3.1 aarch64 
Java 19.0.1 
JavaFX 19+11

Appendix

...

Log File

java.lang.NumberFormatException: For input string: "priority"
	at java.base/java.lang.NumberFormatException.forInputString(Unknown Source)
	at java.base/java.lang.Integer.parseInt(Unknown Source)
	at java.base/java.lang.Integer.parseInt(Unknown Source)
	at org.jabref@5.9.60000/org.jabref.logic.importer.util.GroupsParser.keywordGroupFromString(Unknown Source)
	at org.jabref@5.9.60000/org.jabref.logic.importer.util.GroupsParser.fromString(Unknown Source)
	at org.jabref@5.9.60000/org.jabref.logic.importer.util.GroupsParser.importGroups(Unknown Source)
	at org.jabref@5.9.60000/org.jabref.logic.importer.util.MetaDataParser.parse(Unknown Source)
	at org.jabref@5.9.60000/org.jabref.logic.importer.util.MetaDataParser.parse(Unknown Source)
	at org.jabref@5.9.60000/org.jabref.logic.importer.fileformat.BibtexParser.parseFileContent(Unknown Source)
	at org.jabref@5.9.60000/org.jabref.logic.importer.fileformat.BibtexParser.parse(Unknown Source)
	at org.jabref@5.9.60000/org.jabref.logic.importer.fileformat.BibtexImporter.importDatabase(Unknown Source)
	at org.jabref@5.9.60000/org.jabref.logic.importer.fileformat.BibtexImporter.importDatabase(Unknown Source)
	at org.jabref@5.9.60000/org.jabref.logic.importer.OpenDatabase.loadDatabase(Unknown Source)
	at org.jabref@5.9.60000/org.jabref.gui.importer.actions.OpenDatabaseAction.loadDatabase(Unknown Source)
	at org.jabref@5.9.60000/org.jabref.gui.importer.actions.OpenDatabaseAction.lambda$openTheFile$1(Unknown Source)
	at org.jabref@5.9.60000/org.jabref.gui.util.BackgroundTask$1.call(Unknown Source)
	at org.jabref@5.9.60000/org.jabref.gui.util.DefaultTaskExecutor$1.call(Unknown Source)
	at org.jabref.merged.module@5.9.60000/javafx.concurrent.Task$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)

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

koppor · 2023-04-18T07:28:27Z

Which JabRef version was run on the Linux machine? I would assume 3.8.2.

koppor · 2023-04-18T07:29:40Z

Can you send the whole bib file to us? Find my email adress in my GitHub profile. - The stacktrace org.jabref@5.9.60000/org.jabref.logic.importer.util.GroupsParser.keywordGroupFromString indicates that something else is going on.

alfureu · 2023-04-18T17:13:52Z

Which JabRef version was run on the Linux machine? I would assume 3.8.2.

I am running v5.9 also on the Linux machine (Fedora 37 and flatpak install from Software store)

alfureu · 2023-04-18T17:18:38Z

Can you send the whole bib file to us? Find my email adress in my GitHub profile. - The stacktrace org.jabref@5.9.60000/org.jabref.logic.importer.util.GroupsParser.keywordGroupFromString indicates that something else is going on.

I am not sure I can send it to you as the whole bib file is rather huge (25+ MB) and is a part of a research project. The thing is, this is a bib file collated from multiple sources of various quality for a larger review (hence we use the priority classification). It contains non-Latin characters as well, just checked and the file is encoded as UTF-8 with LF with some non-ASCII characters (checked with VScode). I need to change whether I can open this file on a Windows 10 machine JabRef too... will feed back once I get access to such a machine

Siedlerchr · 2023-04-18T17:18:48Z

Can you try to open the file with the latest development version? I vaguely remember something about this
https://builds.jabref.org/main/
(It will report as broken on mac, but then you can allow the app in the Apple security because it's not signed/notarized)

Siedlerchr · 2023-04-18T17:23:07Z

On may you need to execute xattr -d com.apple.quarantine /Applications/JabRef.app in the terminal

alfureu · 2023-04-18T17:28:22Z

Can you try to open the file with the latest development version? I vaguely remember something about this https://builds.jabref.org/main/ (It will report as broken on mac, but then you can allow the app in the Apple security because it's not signed/notarized)

I tried to open it, and it provided the following error:

java.lang.NumberFormatException: For input string: "priority"
	at java.base/java.lang.NumberFormatException.forInputString(Unknown Source)
	at java.base/java.lang.Integer.parseInt(Unknown Source)
	at java.base/java.lang.Integer.parseInt(Unknown Source)
	at org.jabref@5.10.554/org.jabref.logic.importer.util.GroupsParser.keywordGroupFromString(Unknown Source)
	at org.jabref@5.10.554/org.jabref.logic.importer.util.GroupsParser.fromString(Unknown Source)
	at org.jabref@5.10.554/org.jabref.logic.importer.util.GroupsParser.importGroups(Unknown Source)
	at org.jabref@5.10.554/org.jabref.logic.importer.util.MetaDataParser.parse(Unknown Source)
	at org.jabref@5.10.554/org.jabref.logic.importer.util.MetaDataParser.parse(Unknown Source)
	at org.jabref@5.10.554/org.jabref.logic.importer.fileformat.BibtexParser.parseFileContent(Unknown Source)
	at org.jabref@5.10.554/org.jabref.logic.importer.fileformat.BibtexParser.parse(Unknown Source)
	at org.jabref@5.10.554/org.jabref.logic.importer.fileformat.BibtexImporter.importDatabase(Unknown Source)
	at org.jabref@5.10.554/org.jabref.logic.importer.fileformat.BibtexImporter.importDatabase(Unknown Source)
	at org.jabref@5.10.554/org.jabref.logic.importer.OpenDatabase.loadDatabase(Unknown Source)
	at org.jabref@5.10.554/org.jabref.gui.importer.actions.OpenDatabaseAction.loadDatabase(Unknown Source)
	at org.jabref@5.10.554/org.jabref.gui.importer.actions.OpenDatabaseAction.lambda$openTheFile$1(Unknown Source)
	at org.jabref@5.10.554/org.jabref.gui.util.BackgroundTask$1.call(Unknown Source)
	at org.jabref@5.10.554/org.jabref.gui.util.DefaultTaskExecutor$1.call(Unknown Source)
	at org.jabref.merged.module@5.10.554/javafx.concurrent.Task$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)

alfureu · 2023-04-18T17:33:56Z

Can you send the whole bib file to us? Find my email adress in my GitHub profile. - The stacktrace org.jabref@5.9.60000/org.jabref.logic.importer.util.GroupsParser.keywordGroupFromString indicates that something else is going on.

I tried to send the file to your email, hopefully it will go through.

Siedlerchr · 2023-04-18T18:08:40Z

Thanks! Received it!

Siedlerchr · 2023-04-18T18:44:49Z

@alfureu Good news. I found the issue and a fix for you is simple. The problem is that the Keyword Group for the field priority did not have a name! At the end of the file, where the group metadata is defined
replace:

2 KeywordGroup:\;0\;priority\;prio1\;1\;0\;1\;0x8a8a8aff\;\;\;;
with
2 KeywordGroup:Test\;0\;priority\;prio1\;1\;0\;1\;0x8a8a8aff\;\;\;;

and voila it works again :)

I will do more tests to find how this could be even possible to prevent such cases in the future.

alfureu · 2023-04-18T18:48:19Z

Hm, this is interesting. Literally what I did was that I saved the bib file in JabRef on Linux, and I tried to open it on JabRef macOS. No idea what is happening between these. I was also surprised that the file does not open. Thanks for looking into this!

Siedlerchr · 2023-04-18T19:00:30Z

I could reproduce this now with another library. Saving is not a problem, but on opening the parser fails to properly parse the group structure (off by one)

alfureu · 2023-04-18T19:12:15Z

amazing, I was able to open the file in JabRef on macOS. Thanks again, great work! Will leave the ticket open until it gets fixed in the code by the devs

ShuaijuLv · 2023-05-20T07:03:36Z

Hi, I am the university of adelaide student. Our group would like to sovle the issue. I think the solution above consider abnormally formatted data. Can I have the test file?

github-actions · 2023-05-20T07:44:24Z

As a general advice for newcomers: check out Contributing for a start. Also, guidelines for setting up a local workspace is worth having a look at.

Feel free to ask here at GitHub, if you have any issue related questions. If you have questions about how to setup your workspace use JabRef's Gitter chat. Try to open a (draft) pull-request early on, so that people can see you are working on the issue and so that they can see the direction the pull request is heading towards. This way, you will likely receive valuable feedback.

Siedlerchr · 2023-05-20T08:52:06Z

To test this. Create a new library, add some entries and create a new automatic keyword group without a name.
save the library and reopen

koppor added the bug Confirmed bugs or reports that are very likely to be bugs label Apr 18, 2023

Siedlerchr changed the title ~~JabRef error if priority field enabled on macOS~~ JabRef error if keyword group has no name Apr 18, 2023

Siedlerchr added the groups label Apr 18, 2023

koppor added this to the v5.10 milestone Apr 29, 2023

koppor removed this from the v5.10 milestone May 8, 2023

ThiloteE assigned ShuaijuLv May 20, 2023

ThiloteE added the FirstTimeCodeContribution Triggers GitHub Greeter Workflow label May 20, 2023

Siedlerchr mentioned this issue May 30, 2023

fix group parser if group has no name #9964

Closed

6 tasks

koppor unassigned ShuaijuLv Jul 31, 2023

Siedlerchr added the good first issue An issue intended for project-newcomers. Varies in difficulty. label Sep 8, 2023

This was referenced Sep 8, 2023

Fix NPE when adding new aux group #10352

Merged

Fix groups validator #10369

Merged

koppor closed this as completed in #10369 Sep 11, 2023

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JabRef error if keyword group has no name #9776

JabRef error if keyword group has no name #9776

alfureu commented Apr 18, 2023 •

edited by koppor

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alfureu commented Apr 18, 2023

Siedlerchr commented Apr 18, 2023 •

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alfureu commented Apr 18, 2023

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alfureu commented Apr 18, 2023

ShuaijuLv commented May 20, 2023

github-actions bot commented May 20, 2023

Siedlerchr commented May 20, 2023

JabRef error if keyword group has no name #9776

JabRef error if keyword group has no name #9776

Comments

alfureu commented Apr 18, 2023 • edited by koppor Loading

JabRef version

Operating system

Details on version and operating system

Checked with the latest development build

Steps to reproduce the behaviour

Appendix

koppor commented Apr 18, 2023

koppor commented Apr 18, 2023

alfureu commented Apr 18, 2023

alfureu commented Apr 18, 2023

Siedlerchr commented Apr 18, 2023 • edited Loading

Siedlerchr commented Apr 18, 2023

alfureu commented Apr 18, 2023

alfureu commented Apr 18, 2023

Siedlerchr commented Apr 18, 2023

Siedlerchr commented Apr 18, 2023

alfureu commented Apr 18, 2023

Siedlerchr commented Apr 18, 2023

alfureu commented Apr 18, 2023

ShuaijuLv commented May 20, 2023

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Siedlerchr commented May 20, 2023

alfureu commented Apr 18, 2023 •

edited by koppor

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Siedlerchr commented Apr 18, 2023 •

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