Illegal character in query: pipe character in file field

[ryan-carpenter]

JabRef version

Other (please describe below)

Operating system

GNU / Linux

Details on version and operating system

No response

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

• [x] I made a backup of my libraries before testing the latest development version.
• [x] I have tested the latest development version and the problem persists

Steps to reproduce the behaviour

I think this exception was trigger by searching full text online, which added a URL to the file field. The important part is that a pipe character in the URL raised an exception that recurred until l I killed JabRef and removed the offending URL from the .bib file.

1. Add a URL containing a pipe (|) character to the file field (URLs from GALE ONEFILE, containing the string &docId=GALE|)

Appendix

JabRef 6.0--2024-09-25--91d0709 Linux 6.9.9-1-default amd64 Java 21.0.2 JavaFX 23+29

Log File

java.lang.IllegalArgumentException: Illegal character in query at index 58: https://go.gale.com/ps/i.do?p=HRCA&u=googlescholar&id=GALE|A653693412&v=2.1&it=r&sid=googleScholar&asid=68b1dec7
	at java.base/java.net.URI.create(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 java.base/java.util.Optional.map(Unknown Source)
	at [email protected]/com.tobiasdiez.easybind.optional.PreboundOptionalBinding$1.computeValue(Unknown Source)
	at [email protected]/com.tobiasdiez.easybind.optional.PreboundOptionalBinding$1.computeValue(Unknown Source)
	at javafx.base@23/javafx.beans.binding.ObjectBinding.get(Unknown Source)
	at javafx.base@23/javafx.beans.binding.ObjectExpression.getValue(Unknown Source)
	at [email protected]/com.tobiasdiez.easybind.optional.PreboundOptionalBinding$3.computeValue(Unknown Source)
	at javafx.base@23/javafx.beans.binding.ObjectBinding.get(Unknown Source)
	at javafx.base@23/javafx.beans.binding.ObjectExpression.getValue(Unknown Source)
	at javafx.controls@23/javafx.scene.control.TableCell.updateItem(Unknown Source)
	at javafx.controls@23/javafx.scene.control.TableCell.indexChanged(Unknown Source)
	at javafx.controls@23/javafx.scene.control.IndexedCell.updateIndex(Unknown Source)
	at javafx.controls@23/javafx.scene.control.skin.TableRowSkinBase.updateCells(Unknown Source)
	at javafx.controls@23/javafx.scene.control.skin.TableRowSkinBase.checkState(Unknown Source)
	at javafx.controls@23/javafx.scene.control.skin.TableRowSkinBase.computePrefHeight(Unknown Source)
	at javafx.controls@23/javafx.scene.control.Control.computePrefHeight(Unknown Source)
	at javafx.graphics@23/javafx.scene.Parent.prefHeight(Unknown Source)
	at javafx.graphics@23/javafx.scene.layout.Region.prefHeight(Unknown Source)
	at javafx.controls@23/javafx.scene.control.skin.VirtualFlow.resizeCell(Unknown Source)
	at javafx.controls@23/javafx.scene.control.skin.VirtualFlow.getCell(Unknown Source)
	at javafx.controls@23/javafx.scene.control.skin.VirtualFlow.getOrCreateCellSize(Unknown Source)
	at javafx.controls@23/javafx.scene.control.skin.VirtualFlow.getOrCreateCellSize(Unknown Source)
	at javafx.controls@23/javafx.scene.control.skin.VirtualFlow.recalculateAndImproveEstimatedSize(Unknown Source)
	at javafx.controls@23/javafx.scene.control.skin.VirtualFlow.recalculateAndImproveEstimatedSize(Unknown Source)
	at javafx.controls@23/javafx.scene.control.skin.VirtualFlow.recalculateEstimatedSize(Unknown Source)
	at javafx.controls@23/javafx.scene.control.skin.VirtualFlow.layoutChildren(Unknown Source)
	at javafx.graphics@23/javafx.scene.Parent.layout(Unknown Source)
	at javafx.graphics@23/javafx.scene.Parent.layout(Unknown Source)
	at javafx.graphics@23/javafx.scene.Parent.layout(Unknown Source)
	at javafx.graphics@23/javafx.scene.Parent.layout(Unknown Source)
	at javafx.graphics@23/javafx.scene.Parent.layout(Unknown Source)
	at javafx.graphics@23/javafx.scene.Parent.layout(Unknown Source)
	at javafx.graphics@23/javafx.scene.Parent.layout(Unknown Source)
	at javafx.graphics@23/javafx.scene.Parent.layout(Unknown Source)
	at javafx.graphics@23/javafx.scene.Parent.layout(Unknown Source)
	at javafx.graphics@23/javafx.scene.Parent.layout(Unknown Source)
	at javafx.graphics@23/javafx.scene.Scene.doLayoutPass(Unknown Source)
	at javafx.graphics@23/javafx.scene.Scene$ScenePulseListener.pulse(Unknown Source)
	at javafx.graphics@23/com.sun.javafx.tk.Toolkit.lambda$runPulse$2(Unknown Source)
	at java.base/java.security.AccessController.doPrivileged(Unknown Source)
	at javafx.graphics@23/com.sun.javafx.tk.Toolkit.runPulse(Unknown Source)
	at javafx.graphics@23/com.sun.javafx.tk.Toolkit.firePulse(Unknown Source)
	at javafx.graphics@23/com.sun.javafx.tk.quantum.QuantumToolkit.pulse(Unknown Source)
	at javafx.graphics@23/com.sun.javafx.tk.quantum.QuantumToolkit.pulse(Unknown Source)
	at javafx.graphics@23/com.sun.javafx.tk.quantum.QuantumToolkit.pulseFromQueue(Unknown Source)
	at javafx.graphics@23/com.sun.javafx.tk.quantum.QuantumToolkit.lambda$runToolkit$11(Unknown Source)
	at javafx.graphics@23/com.sun.glass.ui.InvokeLaterDispatcher$Future.run(Unknown Source)
	at javafx.graphics@23/com.sun.glass.ui.gtk.GtkApplication._runLoop(Native Method)
	at javafx.graphics@23/com.sun.glass.ui.gtk.GtkApplication.lambda$runLoop$10(Unknown Source)
	at java.base/java.lang.Thread.run(Unknown Source)
Caused by: java.net.URISyntaxException: Illegal character in query at index 58: https://go.gale.com/ps/i.do?p=HRCA&u=googlescholar&id=GALE|A653693412&v=2.1&it=r&sid=googleScholar&asid=68b1dec7
	at java.base/java.net.URI$Parser.fail(Unknown Source)
	at java.base/java.net.URI$Parser.checkChars(Unknown Source)
	at java.base/java.net.URI$Parser.parseHierarchical(Unknown Source)
	at java.base/java.net.URI$Parser.parse(Unknown Source)
	at java.base/java.net.URI.<init>(Unknown Source)
	... 53 more

[HoussemNasri]

Seems like a problem with the underlying URI implementation in the JDK, they implement RFC2396 + RFC2732 while the usage of pipe characters is only supported in RFC3986.

Source: https://github.com/gatling/gatling/issues/1981#issuecomment-47118450.

Solution: Encode pipe characters as %7C before passing them into the URI.

raised an exception that recurred until l I killed JabRef and removed the offending URL from the .bib file.

This is bad. This type of exceptions should never make the program unusable.

[jiaxin0103]

hi @ryan-carpenter , Is this issue still available for contribution? I have a student assignment that requires contributing to an open-source project, and I’m interested in contributing to this one.Could you assign this issue to me?

[ThiloteE]

@jiaxin0103 Please have a look at https://github.com/orgs/JabRef/projects/5 and choose a "free to take" issue, as it depends on the JDK. It would be needed to open a PR over there, if a solution is found.

Edit: Sorry, this is not search related. My bad. Not sure, why I completely missed HoussemNasri's comment.

[koppor]

I think, this can be done inside JabRef, too. As stated at https://github.com/JabRef/jabref/issues/11876#issuecomment-2395122403, one needs to recode the pipe sign into %7C.

Replace all calls to URI.create with a new method.

1. Create a new method create in org.jabref.gui.fieldeditors.URLUtil. That method returns an URL It makes use of createUri and then calls toUrl()
2. Create a new method createUri in org.jabref.gui.fieldeditors.URLUtil. That method returns an URI.
3. Replace all calls of URI.create(...).toURL() by URLUtil.create(...).
4. Replace all calls of URI.create(...) by URLUtil.createUri(...).

The method in step 2 does that escaping.

Test cases need to be added to org.jabref.logic.net.URLUtilTest.

[koppor]

@jiaxin0103 Please reply with /assign-me if you want to take this issue.

[ghost]

Hello @koppor , I would like to work on this problem.

[koppor]

/assign @hitalo-siriano

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