Custom entry types might crash JabRef on start

[Doc73]

JabRef version

5.13 (latest release)

Operating system

GNU / Linux

Details on version and operating system

Debian Unstable Gnome AMD64

Checked with the latest development build (copy version output from About dialog)

• 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. $ /opt/jabref/bin/JabRef
2. Here is the result:

Messages are not initialized before accessing key: Display help on command line options
2024-04-01 23:52:12 [main] org.jabref.Launcher.main()
ERROR: Unexpected exception: java.lang.IllegalArgumentException: Fields [PAGES] already added
	at org.jabref@5.13.60000/org.jabref.model.entry.BibEntryTypeBuilder.withImportantFields(Unknown Source)
	at org.jabref@5.13.60000/org.jabref.logic.importer.util.MetaDataParser.parseCustomEntryType(Unknown Source)
	at org.jabref@5.13.60000/org.jabref.preferences.JabRefPreferences.lambda$getBibEntryTypes$5(Unknown Source)
	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source)
	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source)
	at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source)
	at java.base/java.util.Spliterators$ArraySpliterator.forEachRemaining(Unknown Source)
	at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source)
	at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source)
	at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source)
	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source)
	at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source)
	at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source)
	at org.jabref@5.13.60000/org.jabref.preferences.JabRefPreferences.getBibEntryTypes(Unknown Source)
	at org.jabref@5.13.60000/org.jabref.preferences.JabRefPreferences.lambda$getCustomEntryTypesRepository$3(Unknown Source)
	at java.base/java.lang.Iterable.forEach(Unknown Source)
	at org.jabref@5.13.60000/org.jabref.preferences.JabRefPreferences.getCustomEntryTypesRepository(Unknown Source)
	at org.jabref@5.13.60000/org.jabref.Launcher.initGlobals(Unknown Source)
	at org.jabref@5.13.60000/org.jabref.Launcher.main(Unknown Source)

Appendix

...

Log File

Messages are not initialized before accessing key: Display help on command line options
2024-04-01 23:52:12 [main] org.jabref.Launcher.main()
ERROR: Unexpected exception: java.lang.IllegalArgumentException: Fields [PAGES] already added
	at org.jabref@5.13.60000/org.jabref.model.entry.BibEntryTypeBuilder.withImportantFields(Unknown Source)
	at org.jabref@5.13.60000/org.jabref.logic.importer.util.MetaDataParser.parseCustomEntryType(Unknown Source)
	at org.jabref@5.13.60000/org.jabref.preferences.JabRefPreferences.lambda$getBibEntryTypes$5(Unknown Source)
	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source)
	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source)
	at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source)
	at java.base/java.util.Spliterators$ArraySpliterator.forEachRemaining(Unknown Source)
	at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source)
	at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source)
	at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source)
	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source)
	at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source)
	at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source)
	at org.jabref@5.13.60000/org.jabref.preferences.JabRefPreferences.getBibEntryTypes(Unknown Source)
	at org.jabref@5.13.60000/org.jabref.preferences.JabRefPreferences.lambda$getCustomEntryTypesRepository$3(Unknown Source)
	at java.base/java.lang.Iterable.forEach(Unknown Source)
	at org.jabref@5.13.60000/org.jabref.preferences.JabRefPreferences.getCustomEntryTypesRepository(Unknown Source)
	at org.jabref@5.13.60000/org.jabref.Launcher.initGlobals(Unknown Source)
	at org.jabref@5.13.60000/org.jabref.Launcher.main(Unknown Source)```

</details>

[Doc73]

P. S.: downgraded to v. 5.12, still working

[Siedlerchr]

Thanks for the report, seems like an issue with custom entry types. Do you have a custom entry type with the field Pages? Maybe the field is added twice? Domenico Cufalo ***@***.***> schrieb am Di., 2. Apr. 2024, 00:11:

…

P. S.: downgraded to v. 5.12, still working — Reply to this email directly, view it on GitHub <#11127 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AACOFZHWEX2HPFMRNRT7IKLY3HLPXAVCNFSM6AAAAABFSIMM4GVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMZQGY2TQOBRGE> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[koppor]

@Doc73 Please open the file in a text editor, scroll to the very and and paste the selctor_keywords entries here.

@Comment{jabref-meta: selector_keywords:example;example-2;}

[Siedlerchr]

@koppor This has nothing to do with content selectors, it's about custom entry entry types, but yes they might exist there as well but the stack trace looks like it's coming from the value in the prefs

[Doc73]

@koppor I have not this line, but I use custom entry type. I'm not at home. Tomorrow evening I will send other infos

[Siedlerchr]

I can reproduce it now easily:

@Comment{jabref-entrytype: asdfasdf: req[pages] opt[pages]}

jabref/src/main/java/org/jabref/model/entry/BibEntryTypeBuilder.java

Lines 39 to 41 in 5cb70df

	if (!containedFields.isEmpty()) {
	throw new IllegalArgumentException("Fields " + containedFields + " already added");
	}

Hah and it is the exact line I called out in the review #11013 (review)

[Siedlerchr]

@Doc73 This version should work again https://builds.jabref.org/pull/11132/merge
The culprit is that you somehwere have a custom entry type with duplicated fields e.g. the field pages is both in required and optional fields

[Doc73]

@Siedlerchr I'll do the tests tomorrow, but I am nearly sure that I have no duplicate fields in my custom types, because I have given a look at the file itself (unfortunately, I can't past the text with my phone)

[Doc73]

I succeeded!

@Comment{jabref-meta: databaseType:biblatex;}

@Comment{jabref-meta: fileDirectoryLatex-domenico-debian:/home/domenico/Documenti/myLatexProjects/Scholia in Platonem;}

@Comment{jabref-meta: grouping:
0 AllEntriesGroup:;
1 KeywordGroup:Editiones\;1\;keywords\;editiones\;0\;0\;1\;0x008080ff\;\;\;;
1 KeywordGroup:Auctores\;1\;keywords\;auctores\;0\;0\;1\;0xff0000ff\;\;\;;
1 KeywordGroup:Studi\;1\;keywords\;studi\;0\;0\;1\;0x0000ffff\;\;\;;
1 KeywordGroup:Sigle\;1\;keywords\;sigle\;0\;0\;1\;0xffff00ff\;\;\;;
1 KeywordGroup:Scholia\;1\;keywords\;scholia\;0\;0\;1\;0x008000ff\;\;\;;
1 KeywordGroup:Extra\;1\;keywords\;extra\;0\;0\;1\;0x00ff00ff\;\;\;;
1 KeywordGroup:Philigranae\;1\;keywords\;philigranae\;0\;0\;1\;\;\;\;;
1 KeywordGroup:Manuscripti\;1\;keywords\;manuscripti\;0\;0\;1\;\;\;\;;
1 KeywordGroup:Palaeographia\;1\;keywords\;paleografia\;0\;0\;1\;0x800080ff\;\;\;;
1 KeywordGroup:Atti\;0\;keywords\;atti\;0\;0\;1\;0x669966ff\;\;\;;
1 KeywordGroup:MIEI\;1\;keywords\;mio\;0\;0\;1\;0x00ffffff\;\;\;;
1 KeywordGroup:Italian\;1\;keywords\;italian\;0\;0\;1\;\;\;\;;
2 KeywordGroup:Religio\;1\;keywords\;religio\;0\;0\;1\;\;\;\;;
2 KeywordGroup:Duecento\;1\;keywords\;duecento\;0\;0\;1\;\;\;\;;
2 KeywordGroup:Volgare\;1\;keywords\;volgare\;0\;0\;1\;\;\;\;;
2 KeywordGroup:Dante\;1\;keywords\;dante\;0\;0\;1\;\;\;\;;
2 KeywordGroup:General\;1\;keywords\;general\;0\;0\;1\;\;\;\;;
2 KeywordGroup:Prosa Duecento\;1\;keywords\;prosaduecento\;0\;0\;0\;\;\;\;;
2 KeywordGroup:Medioevo\;0\;keywords\;medioevo\;0\;0\;1\;0x8a8a8aff\;\;\;;
}

@Comment{jabref-entrytype: bookinarticle: req[author;bookauthor;date;journal;pages;title;volume] opt[keywords;mainsubtitle;maintitle;note;number;substitle]}

@Comment{jabref-entrytype: bookinincollection: req[author;bookauthor;booktitle;date;location;maintitle;pages;publisher;title] opt[booksubtitle;edition;editor;keywords;mainsubtitle;number;series;substitle;volume]}

@Comment{jabref-entrytype: manuscript: req[collection;library;location;shelfmark] opt[bookpagination;columns;dating;layer;pages;pagetotal;pagination;shortcollection;shorthand;shortlibrary;support]}

@Comment{jabref-entrytype: review: req[author;journal;pages;title;volume;date] opt[number;month;part;eid;note;keywords]}

@Comment{
Local Variables:
bibtex-dialect: biblatex
End:
}

[Siedlerchr]

Sorry for the trouble we caused, and thank you so much for immediately testing! That's really helpful.

I think we cleaned the existing entry types as well to remove duplicates, it might have been some leftover still in the preferences

[Doc73]

@Siedlerchr
I did my tests in my desktop with Debian Stable. Version 5.13 doesn't start, but the version of https://builds.jabref.org/main/ works fine.
Many thanks!