"Open File" doesn't lead anywhere

[siainbuletin]

JabRef version

5.12 (latest release)

Operating system

Windows

Details on version and operating system

Windows 11 v23H2 (OS Build 22631.3235)

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. Open my BibLaTeX file exported from Zotero with the file directory set on the Zotero/storage folder.
2. Click on an article that has an associated PDF (the correct path is associated in the BibLaTex entry, as seen below):

3. Pressing F4 or going to the context menu simply directs me to my regular C:/Users//Documents directory.

Appendix

...

Log File

2024-03-02 17:15:58 [JavaFX-Launcher] sun.util.logging.internal.LoggingProviderImpl$JULWrapper.log()
WARN: Unsupported JavaFX configuration: classes were loaded from 'module org.jabref.merged.module', isAutomatic: false, isOpen: true
2024-03-02 17:15:59 [JavaFX Application Thread] org.jabref.gui.StateManager.setActiveDatabase()
INFO: No open database detected
2024-03-02 17:15:59 [JavaFX Application Thread] org.jabref.gui.theme.ThemeManager.updateThemeSettings()
INFO: Not updating theme because it hasn't changed
2024-03-02 17:15:59 [JavaFX Application Thread] org.jabref.gui.theme.ThemeManager.updateThemeSettings()
INFO: Theme set to Theme{type=DEFAULT, name=''} with base css StyleSheet{jrt:/org.jabref/org/jabref/gui/Base.css}
2024-03-02 17:15:59 [JavaFX Application Thread] org.jabref.gui.theme.ThemeManager.updateThemeSettings()
INFO: Not updating theme because it hasn't changed
2024-03-02 17:15:59 [JavaFX Application Thread] org.jabref.gui.theme.ThemeManager.updateThemeSettings()
INFO: Theme set to Theme{type=DEFAULT, name=''} with base css StyleSheet{jrt:/org.jabref/org/jabref/gui/Base.css}
2024-03-02 17:15:59 [JavaFX Application Thread] sun.util.logging.internal.LoggingProviderImpl$JULWrapper.log()
WARN: Resource "" not found.
2024-03-02 17:16:01 [JavaFX Application Thread] sun.util.logging.internal.LoggingProviderImpl$JULWrapper.log()
WARN: Resource "" not found.
2024-03-02 17:16:11 [pool-1-thread-1] org.jabref.gui.JabRefDialogService.notify()
INFO: Opening: 'A:\bib\My Library.bib'
2024-03-02 17:16:13 [JavaFX Application Thread] org.jabref.gui.FallbackExceptionHandler.uncaughtException()
ERROR: Uncaught exception occurred in Thread[#60,JavaFX Application Thread,5,main]: java.nio.file.InvalidPathException: Trailing char < > at index 16:  Analitica primă 
	at java.base/sun.nio.fs.WindowsPathParser.normalize(Unknown Source)
	at java.base/sun.nio.fs.WindowsPathParser.parse(Unknown Source)
	at java.base/sun.nio.fs.WindowsPathParser.parse(Unknown Source)
	at java.base/sun.nio.fs.WindowsPath.parse(Unknown Source)
	at java.base/sun.nio.fs.WindowsFileSystem.getPath(Unknown Source)
	at java.base/java.nio.file.Path.of(Unknown Source)
	at [email protected]/org.jabref.logic.importer.util.FileFieldParser.convert(Unknown Source)
	at [email protected]/org.jabref.logic.importer.util.FileFieldParser.parse(Unknown Source)
	at [email protected]/org.jabref.logic.importer.util.FileFieldParser.parse(Unknown Source)
	at [email protected]/org.jabref.model.entry.BibEntry.getFiles(Unknown Source)
	at [email protected]/org.jabref.logic.pdf.search.indexing.IndexingTaskManager.updateIndex(Unknown Source)
	at [email protected]/org.jabref.gui.LibraryTab.onDatabaseLoadingSucceed(Unknown Source)
	at [email protected]/org.jabref.gui.util.DefaultTaskExecutor.lambda$getJavaFXTask$4(Unknown Source)
	at [email protected]/com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(Unknown Source)
	at [email protected]/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(Unknown Source)
	at [email protected]/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(Unknown Source)
	at [email protected]/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
	at [email protected]/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
	at [email protected]/com.sun.javafx.event.EventUtil.fireEventImpl(Unknown Source)
	at [email protected]/com.sun.javafx.event.EventUtil.fireEvent(Unknown Source)
	at [email protected]/javafx.event.Event.fireEvent(Unknown Source)
	at [email protected]/javafx.concurrent.EventHelper.fireEvent(Unknown Source)
	at [email protected]/javafx.concurrent.Task.fireEvent(Unknown Source)
	at [email protected]/javafx.concurrent.Task.setState(Unknown Source)
	at [email protected]/javafx.concurrent.Task$TaskCallable.lambda$call$1(Unknown Source)
	at [email protected]/com.sun.javafx.application.PlatformImpl.lambda$runLater$10(Unknown Source)
	at java.base/java.security.AccessController.doPrivileged(Unknown Source)
	at [email protected]/com.sun.javafx.application.PlatformImpl.lambda$runLater$11(Unknown Source)
	at [email protected]/com.sun.glass.ui.InvokeLaterDispatcher$Future.run(Unknown Source)
	at [email protected]/com.sun.glass.ui.win.WinApplication._runLoop(Native Method)
	at [email protected]/com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(Unknown Source)
	at java.base/java.lang.Thread.run(Unknown Source)

[HoussemNasri]

Try to add a colon : just before the file path, like this file = {:A:\Zotero\storage...

[HoussemNasri]

It turns out JabRef has a cleanup action for this case. After selecting all entries, go to the menu bar and select Quality > Cleanup entries. Select Upgrade external PDF/PS links to use the 'File' field, then click OK.

[Siedlerchr]

Can you please verify that with the newest development version as well?
Refs #9129
The FieldFieldParser needs to probably be adjusted (see the tests as well)=

[siainbuletin]

@HoussemNasri Just performed the cleanup on this one file, ended up with this string:

Please note that I have next to no knowledge of anything related to programming, so I might've done something else along the way. I'm currently trying to migrate from Zotero as it's gotten incredibly sluggish with processing my files and not even my 32gb ram, i9-12th generation pc can run it smoothly. For context, I have a ridiculous bib database (>8k entries)

@Siedlerchr Currently backing up again and installing the latest branch to see what happens.

[ThiloteE]

Is there a better solution than a cleanup action? Something more automatic?

[Siedlerchr]

For solving the issue:
0. Prepare a bib entry with such a file link

1. Add a new test case for

   jabref/src/test/java/org/jabref/logic/importer/util/FileFieldParserTest.java

   Line 40 in 71a0b62

   private static Stream<Arguments> stringsToParseTest() throws Exception {

2. Adjust the logic of the FileFieldParser

[HoussemNasri]

Just performed the cleanup on this one file, ended up with this string:

Yeah, I just performed that on a Windows machine and got the same result. It seems JabRef is not dealing well with backslashes in the file path. It worked when I used double backslashes instead of one.

Can you please verify that with the newest development version as well?

I reproduced it on the development version too.

[koppor]

This refs #10871.

@siainbuletin How did you get the content in the file field? Did you add the path manually?

[siainbuletin]

@koppor No, the initial path which wouldn't open is just what is set up by the Better BibLaTeX export function in Zotero. The second is what I got when I ran Cleanup entries, as @HoussemNasri told me to. I didn't tinker with anything manually.

[HoussemNasri]

Makes sense, I just tried the default Zotero export function and it has double backslashes and uses the same file field format as jabref which is description:path:filetype. If the description and filetype are not specified it should be :path:

[koppor]

JabRef has some auto detection magic if the first colon is ommitted and just a path contained. There should be test cades around...

[siainbuletin]

Any news on this? Possible workarounds?

[Siedlerchr]

@siainbuletin
I'm taking a look at it. A simple workaround is to add a colon before the file path in the file field

e.g. :A:\Zotero..\.pdf that works

[Siedlerchr]

@siainbuletin You could try this version now, it should be able to parse the file paths now https://builds.jabref.org/pull/11038/merge