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Uncaught exception occured in Thread. Illegal character [?] in URL imported from Citavi. #7882

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ThiloteE opened this issue Jul 4, 2021 · 10 comments · Fixed by #7948
Closed
1 task done

Uncaught exception occured in Thread. Illegal character [?] in URL imported from Citavi. #7882

ThiloteE opened this issue Jul 4, 2021 · 10 comments · Fixed by #7948
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bug Confirmed bugs or reports that are very likely to be bugs external files good first issue An issue intended for project-newcomers. Varies in difficulty.

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@ThiloteE
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ThiloteE commented Jul 4, 2021

JabRef version 5.3--2021-07-02--eed637a on Windows 10 10.0 amd64; Java 16.0.1

20210704 Fragezeichen Error

Steps to reproduce the behavior:

  1. import .bib file originating from citavi
  2. imported file has to have a URL that contains a "?"
  3. Error
Log File 
java.nio.file.InvalidPathException: Illegal character [?] in path at index 23: //books.google.de/books?hl=de&lr=&id=Tj0mBgAAQBAJ&oi=fnd&pg=PA115&ots=_gWwXjRTk8&sig=Tlbx9LR6LeFPor8PluqWGWdhRsI#v=onepage&q&f=false
  at java.base/sun.nio.fs.WindowsPathParser.nextSlash(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.resolve(Unknown Source)
  at [email protected]/org.jabref.model.util.FileHelper.find(Unknown Source)
  at [email protected]/org.jabref.model.util.FileHelper.lambda$find$0(Unknown Source)
  at java.base/java.util.stream.ReferencePipeline$7$1.accept(Unknown Source)
  at java.base/java.util.ArrayList$ArrayListSpliterator.tryAdvance(Unknown Source)
  at java.base/java.util.stream.ReferencePipeline.forEachWithCancel(Unknown Source)
  at java.base/java.util.stream.AbstractPipeline.copyIntoWithCancel(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.FindOps$FindOp.evaluateSequential(Unknown Source)
  at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source)
  at java.base/java.util.stream.ReferencePipeline.findFirst(Unknown Source)
  at [email protected]/org.jabref.model.util.FileHelper.find(Unknown Source)
  at [email protected]/org.jabref.model.util.FileHelper.find(Unknown Source)
  at [email protected]/org.jabref.gui.actions.ActionHelper.lambda$isFilePresentForSelectedEntry$5(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 [email protected]/javafx.beans.binding.ObjectBinding.get(Unknown Source)
  at [email protected]/javafx.beans.binding.ObjectExpression.getValue(Unknown Source)
  at [email protected]/com.tobiasdiez.easybind.optional.PreboundOptionalBinding$3.computeValue(Unknown Source)
  at [email protected]/javafx.beans.binding.ObjectBinding.get(Unknown Source)
  at [email protected]/javafx.beans.binding.ObjectExpression.getValue(Unknown Source)
  at [email protected]/javafx.beans.binding.BooleanExpression$2.computeValue(Unknown Source)
  at [email protected]/javafx.beans.binding.BooleanBinding.get(Unknown Source)
  at [email protected]/javafx.beans.property.BooleanPropertyBase.get(Unknown Source)
  at [email protected]/javafx.beans.property.ReadOnlyBooleanWrapper$ReadOnlyPropertyImpl.get(Unknown Source)
  at [email protected]/javafx.beans.binding.Bindings$52.computeValue(Unknown Source)
  at [email protected]/javafx.beans.binding.BooleanBinding.get(Unknown Source)
  at [email protected]/javafx.beans.property.BooleanPropertyBase.get(Unknown Source)
  at [email protected]/javafx.beans.property.BooleanPropertyBase.get(Unknown Source)
  at [email protected]/javafx.beans.binding.BooleanExpression.getValue(Unknown Source)
  at [email protected]/javafx.beans.binding.BooleanExpression.getValue(Unknown Source)
  at [email protected]/com.sun.javafx.binding.ExpressionHelper$SingleChange.fireValueChangedEvent(Unknown Source)
  at [email protected]/com.sun.javafx.binding.ExpressionHelper.fireValueChangedEvent(Unknown Source)
  at [email protected]/javafx.beans.property.BooleanPropertyBase.fireValueChangedEvent(Unknown Source)
  at [email protected]/javafx.beans.property.BooleanPropertyBase.markInvalid(Unknown Source)
  at [email protected]/javafx.beans.property.BooleanPropertyBase$Listener.invalidated(Unknown Source)
  at [email protected]/com.sun.javafx.binding.ExpressionHelper$SingleInvalidation.fireValueChangedEvent(Unknown Source)
  at [email protected]/com.sun.javafx.binding.ExpressionHelper.fireValueChangedEvent(Unknown Source)
  at [email protected]/javafx.beans.property.BooleanPropertyBase.fireValueChangedEvent(Unknown Source)
  at [email protected]/javafx.beans.property.BooleanPropertyBase.markInvalid(Unknown Source)
  at [email protected]/javafx.beans.property.BooleanPropertyBase$Listener.invalidated(Unknown Source)
  at [email protected]/com.sun.javafx.binding.ExpressionHelper$SingleInvalidation.fireValueChangedEvent(Unknown Source)
  at [email protected]/com.sun.javafx.binding.ExpressionHelper.fireValueChangedEvent(Unknown Source)
  at [email protected]/javafx.beans.binding.BooleanBinding.invalidate(Unknown Source)
  at [email protected]/com.sun.javafx.binding.BindingHelperObserver.invalidated(Unknown Source)
  at [email protected]/com.sun.javafx.binding.ExpressionHelper$SingleInvalidation.fireValueChangedEvent(Unknown Source)
  at [email protected]/com.sun.javafx.binding.ExpressionHelper.fireValueChangedEvent(Unknown Source)
  at [email protected]/javafx.beans.property.ReadOnlyBooleanPropertyBase.fireValueChangedEvent(Unknown Source)
  at [email protected]/javafx.beans.property.ReadOnlyBooleanWrapper.fireValueChangedEvent(Unknown Source)
  at [email protected]/javafx.beans.property.BooleanPropertyBase.markInvalid(Unknown Source)
  at [email protected]/javafx.beans.property.BooleanPropertyBase$Listener.invalidated(Unknown Source)
  at [email protected]/com.sun.javafx.binding.ExpressionHelper$SingleInvalidation.fireValueChangedEvent(Unknown Source)
  at [email protected]/com.sun.javafx.binding.ExpressionHelper.fireValueChangedEvent(Unknown Source)
  at [email protected]/javafx.beans.binding.BooleanBinding.invalidate(Unknown Source)
  at [email protected]/com.sun.javafx.binding.BindingHelperObserver.invalidated(Unknown Source)
  at [email protected]/com.sun.javafx.binding.ExpressionHelper$SingleInvalidation.fireValueChangedEvent(Unknown Source)
  at [email protected]/com.sun.javafx.binding.ExpressionHelper.fireValueChangedEvent(Unknown Source)
  at [email protected]/javafx.beans.binding.ObjectBinding.invalidate(Unknown Source)
  at [email protected]/com.sun.javafx.binding.BindingHelperObserver.invalidated(Unknown Source)
  at [email protected]/com.sun.javafx.collections.ListListenerHelper$Generic.fireValueChangedEvent(Unknown Source)
  at [email protected]/com.sun.javafx.collections.ListListenerHelper.fireValueChangedEvent(Unknown Source)
  at [email protected]/javafx.collections.ObservableListBase.fireChange(Unknown Source)
  at [email protected]/javafx.collections.ListChangeBuilder.commit(Unknown Source)
  at [email protected]/javafx.collections.ListChangeBuilder.endChange(Unknown Source)
  at [email protected]/javafx.collections.ObservableListBase.endChange(Unknown Source)
  at [email protected]/javafx.collections.ModifiableObservableListBase.setAll(Unknown Source)
  at [email protected]/org.jabref.gui.StateManager.setSelectedEntries(Unknown Source)
  at [email protected]/org.jabref.gui.LibraryTab.lambda$createMainTable$14(Unknown Source)
  at [email protected]/com.sun.javafx.collections.ListListenerHelper$Generic.fireValueChangedEvent(Unknown Source)
  at [email protected]/com.sun.javafx.collections.ListListenerHelper.fireValueChangedEvent(Unknown Source)
  at [email protected]/javafx.collections.ObservableListBase.fireChange(Unknown Source)
  at [email protected]/javafx.collections.ListChangeBuilder.commit(Unknown Source)
  at [email protected]/javafx.collections.ListChangeBuilder.endChange(Unknown Source)
  at [email protected]/javafx.collections.ObservableListBase.endChange(Unknown Source)
  at [email protected]/com.sun.javafx.scene.control.SelectedItemsReadOnlyObservableList.lambda$new$0(Unknown Source)
  at [email protected]/com.sun.javafx.collections.ListListenerHelper$Generic.fireValueChangedEvent(Unknown Source)
  at [email protected]/com.sun.javafx.collections.ListListenerHelper.fireValueChangedEvent(Unknown Source)
  at [email protected]/javafx.collections.ObservableListBase.fireChange(Unknown Source)
  at [email protected]/javafx.collections.ListChangeBuilder.commit(Unknown Source)
  at [email protected]/javafx.collections.ListChangeBuilder.endChange(Unknown Source)
  at [email protected]/javafx.collections.ObservableListBase.endChange(Unknown Source)
  at [email protected]/com.sun.javafx.scene.control.ReadOnlyUnbackedObservableList._endChange(Unknown Source)
  at [email protected]/javafx.scene.control.MultipleSelectionModelBase$SelectedIndicesList._endChange(Unknown Source)
  at [email protected]/javafx.scene.control.ControlUtils.updateSelectedIndices(Unknown Source)
  at [email protected]/javafx.scene.control.TableView$TableViewArrayListSelectionModel.fireCustomSelectedCellsListChangeEvent(Unknown Source)
  at [email protected]/javafx.scene.control.TableView$TableViewArrayListSelectionModel.clearAndSelect(Unknown Source)
  at [email protected]/javafx.scene.control.TableView$TableViewSelectionModel.clearAndSelect(Unknown Source)
  at [email protected]/com.sun.javafx.scene.control.behavior.TableViewBehaviorBase.selectCell(Unknown Source)
  at [email protected]/com.sun.javafx.scene.control.behavior.TableViewBehaviorBase.selectPreviousRow(Unknown Source)
  at [email protected]/com.sun.javafx.scene.control.behavior.TableViewBehaviorBase.lambda$new$10(Unknown Source)
  at [email protected]/com.sun.javafx.scene.control.inputmap.InputMap.handle(Unknown Source)
  at [email protected]/com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(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.CompositeEventDispatcher.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.BasicEventDispatcher.dispatchEvent(Unknown Source)
  at [email protected]/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(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.BasicEventDispatcher.dispatchEvent(Unknown Source)
  at [email protected]/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(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.BasicEventDispatcher.dispatchEvent(Unknown Source)
  at [email protected]/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(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.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.scene.Scene$KeyHandler.process(Unknown Source)
  at [email protected]/javafx.scene.Scene.processKeyEvent(Unknown Source)
  at [email protected]/javafx.scene.Scene$ScenePeerListener.keyEvent(Unknown Source)
  at [email protected]/com.sun.javafx.tk.quantum.GlassViewEventHandler$KeyEventNotification.run(Unknown Source)
  at [email protected]/com.sun.javafx.tk.quantum.GlassViewEventHandler$KeyEventNotification.run(Unknown Source)
  at java.base/java.security.AccessController.doPrivileged(Unknown Source)
  at [email protected]/com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleKeyEvent$1(Unknown Source)
  at [email protected]/com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(Unknown Source)
  at [email protected]/com.sun.javafx.tk.quantum.GlassViewEventHandler.handleKeyEvent(Unknown Source)
  at [email protected]/com.sun.glass.ui.View.handleKeyEvent(Unknown Source)
  at [email protected]/com.sun.glass.ui.View.notifyKey(Unknown Source)
  at [email protected]/com.sun.glass.ui.win.WinApplication._runLoop(Native Method)
  at [email protected]/com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(Unknown Source)
  at java.base/java.lang.Thread.run(Unknown Source)
@Siedlerchr
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Can you please check if the citavi export has the url listed with the prefix http or http:// ?
//books.google.de/books?hl=
From the error message it seems the prefix is missing and therefore JabRef does not recognize this as an url and tries to parse it as a local file path

@Siedlerchr Siedlerchr added the status: waiting-for-feedback The submitter or other users need to provide more information about the issue label Jul 5, 2021
@ThiloteE
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ThiloteE commented Jul 5, 2021

This is the BibTex source that caused the error; You can see it is https instead of http or http://

@incollection{Sturm.2004,
author = {Sturm, Roland},
title = {Staatst{"a}tigkeit im europ{"a}ischen Mehrebenensystem - Der Beitrag der Policy-Forschung zur Analyse von EU-governance-Prozessen},
urldate = {20.12.2020},
pages = {117--132},
publisher = {{VS Verlag f{"u}r Sozialwissenschaften}},
isbn = {978-3-8100-4034-3},
editor = {Holtmann, Everhard},
booktitle = {Staatsentwicklung und Policyforschung},
year = {2004},
address = {Wiesbaden},
doi = {10.1007/978-3-322-80971-1{\textunderscore }10},
file = {https://books.google.de/books?hl=de&lr=&id=Tj0mBgAAQBAJ&oi=fnd&pg=PA115&ots=_gWwXjRTk8&sig=Tlbx9LR6LeFPor8PluqWGWdhRsI#v=onepage&q&f=false}
}

Here you can see the entry in citavi:

20210704 Fragezeichen Error - Citavi entry

Don't worry, in Citavi, there also is a https:// in front, it just doesn't show in the UI outside of the edit entry field.

@Siedlerchr
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Thanks, indeed, I can reproduce this partly. It is incorrectly assumed to be a file

@Siedlerchr Siedlerchr added external files bug Confirmed bugs or reports that are very likely to be bugs and removed status: waiting-for-feedback The submitter or other users need to provide more information about the issue labels Jul 5, 2021
@Siedlerchr
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The problem is that the file field is in incorrect format. The file field parser splits it somehow into https+ the rest of the url

@ThiloteE
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Thank you. I understand now. I will change the "file" to "url", which should do the trick.

On first glance solutions to workaround:

  • Code into JabRef to detect links in files
  • Citavi has to change how they export bib files.

I don't think i can do more here. Good luck and thank you :-)

@ThiloteE
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Just saying, when i enter the URL in Citavi, it doesn't stick to the URL field, but the URL immediately "turns" into a "local web file". It is the one in the bottom red rectangle.

@Siedlerchr
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Ah thanks for the clarification. Im thinking of a search and replace Regex

@Siedlerchr Siedlerchr added the good first issue An issue intended for project-newcomers. Varies in difficulty. label Jul 30, 2021
Siedlerchr added a commit that referenced this issue Jul 30, 2021
@Siedlerchr
Fix file field parser not recognizing online urls
c372987 
Fixes #7882
@Siedlerchr Siedlerchr mentioned this issue Jul 30, 2021
Merged
3 tasks
Siedlerchr added a commit that referenced this issue Jul 31, 2021
@Siedlerchr
Fix file field parser not recognizing online urls (#7948)
720fd8e 
* Fix file field parser not recognizing online urls

Fixes #7882

* checkstyle

* fix test
@Siedlerchr
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Siedlerchr commented Jul 31, 2021 •
edited
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@ThiloteE JabRef should now be able to parse the file field correctly, I added a fix.

The new version is currently building, will take roughly 20 minutes
We would like to ask you to use a development build from https://builds.jabref.org/main and report back if it works for you. Please remember to make a backup of your library before trying-out this version.

@ThiloteE
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works like a charm via

JabRef 5.4--2021-07-31--720fd8e
Windows 10 10.0 amd64
Java 16.0.1
JavaFX 16+8

good job! :)

for everybody that stumbles upon this thread in future:
the solution looks like this:

image

@koppor
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koppor commented Aug 2, 2021

Refs #98

@ThiloteE ThiloteE mentioned this issue Sep 24, 2021
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@Siedlerchr Siedlerchr mentioned this issue Feb 20, 2022
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@koppor koppor moved this to Done in Prioritization Nov 10, 2022
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Fix file field parser not recognizing online urls JabRef/jabref
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@Siedlerchr @koppor @ThiloteE