Export subdatabase from .aux file on macOS command line

I’m using JabRef 5.7--2022-08-05--73c111c (installed via Homebrew) on macOS 12.5. If I open my main .bib file in the GUI and use Tools > New sublibrary based on aux file..., I can successfully create and save a subdatabase with only the entries from an .aux file.

However, when I close the GUI and try to use the command line with the same files, it doesn’t work. When I run the following command:

/Applications/JabRef.app/Contents/runtime/Contents/Home/bin/JabRef --nogui --debug --console --aux "report.aux,references.bib" /Users/james.turner/references/bibliography.bib

the output is the following:

Aug 29, 2022 4:00:53 PM com.sun.javafx.application.PlatformImpl startup
WARNING: Unsupported JavaFX configuration: classes were loaded from 'module org.jabref.merged.module', isAutomatic: false, isOpen: true
2022-08-29 16:00:53 [JavaFX Application Thread] org.jabref.logic.net.ssl.TrustStoreManager.createTruststoreFileIfNotExist()
INFO: Trust store path: /Users/james.turner/Library/Application Support/JabRef/ssl/truststore.jks
use java property -Dtinylog.level=debug
keys in library 142
found in AUX file 1
resolved 1
not found 0
crossreferenced entries included 0
strings included 0
nested AUX files 1
Saving: references.bib

It should create a file named references.bib with a single entry. However, even though it says Saving: references.bib, it doesn’t actually create the references.bib file. Instead, it creates an empty file named references.bib.tmp.

Am I doing something wrong? Please let me know if any additional information would be helpful.

Could you please try the latest development version? There was a significant commit recently that fixed a lot of issues related to file saving. Please create a backup of your library before doing so.

.tmp points to a temporary file being created (Sometimes this is necessary). Usually these temp files should not remain though.

Okay, I can confirm this!

JabRef-5.8.dmg (2022-09-02) from https://builds.jabref.org/main/ has the same behavior.

@jturner314-nrl I’ve just created and merged a PR to fix this issue :sweat_smile:. Please try the new version later.
Build takes roughly 30 minutes to be ready.

That fixed it! Thanks so much! The latest JabRef-5.8.dmg from https://builds.jabref.org/main/ works without issues.

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