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journallist.mv mvstore exception #6482

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ilippert opened this issue May 14, 2020 · 3 comments
Closed
1 task done

journallist.mv mvstore exception #6482

ilippert opened this issue May 14, 2020 · 3 comments
Labels
bug Confirmed bugs or reports that are very likely to be bugs
Milestone
v5.2

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@ilippert
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JabRef 5.1--2020-05-14--09111be
Linux 5.6.11-200.fc31.x86_64 amd64
Java 14.0.1

I have edited the biblatex source in the entry editor and got this exception.

Log File 
java.lang.IllegalStateException: Reading from file nio:/tmp/journal6841416217601125907/journalList.mv failed at 1745057 (length -1), read 0, remaining 1024 [1.4.200/1]
  at org.jabref.merged.module@5.1.394/org.h2.mvstore.DataUtils.newIllegalStateException(Unknown Source)
  at org.jabref.merged.module@5.1.394/org.h2.mvstore.DataUtils.readFully(Unknown Source)
  at org.jabref.merged.module@5.1.394/org.h2.mvstore.FileStore.readFully(Unknown Source)
  at org.jabref.merged.module@5.1.394/org.h2.mvstore.Chunk.readBufferForPage(Unknown Source)
  at org.jabref.merged.module@5.1.394/org.h2.mvstore.MVStore.readBufferForPage(Unknown Source)
  at org.jabref.merged.module@5.1.394/org.h2.mvstore.MVStore.readPage(Unknown Source)
  at org.jabref.merged.module@5.1.394/org.h2.mvstore.MVMap.readPage(Unknown Source)
  at org.jabref.merged.module@5.1.394/org.h2.mvstore.Page$NonLeaf.getChildPage(Unknown Source)
  at org.jabref.merged.module@5.1.394/org.h2.mvstore.Page.get(Unknown Source)
  at org.jabref.merged.module@5.1.394/org.h2.mvstore.MVMap.get(Unknown Source)
  at org.jabref.merged.module@5.1.394/org.h2.mvstore.MVMap.get(Unknown Source)
  at org.jabref.merged.module@5.1.394/org.h2.mvstore.MVMap.containsKey(Unknown Source)
  at org.jabref/org.jabref.logic.journals.JournalAbbreviationRepository.isAbbreviatedName(Unknown Source)
  at org.jabref/org.jabref.logic.integrity.AbbreviationChecker.checkValue(Unknown Source)
  at org.jabref/org.jabref.gui.fieldeditors.AbstractEditorViewModel.lambda$new$0(Unknown Source)
  at org.jabref.merged.module@5.1.394/de.saxsys.mvvmfx.utils.validation.FunctionBasedValidator.lambda$new$1(Unknown Source)
  at org.jabref.merged.module@5.1.394/de.saxsys.mvvmfx.utils.validation.FunctionBasedValidator.validate(Unknown Source)
  at org.jabref.merged.module@5.1.394/de.saxsys.mvvmfx.utils.validation.FunctionBasedValidator.lambda$new$0(Unknown Source)
  at org.jabref.merged.module@5.1.394/com.sun.javafx.binding.ExpressionHelper$Generic.fireValueChangedEvent(Unknown Source)
  at org.jabref.merged.module@5.1.394/com.sun.javafx.binding.ExpressionHelper.fireValueChangedEvent(Unknown Source)
  at org.jabref.merged.module@5.1.394/javafx.beans.property.StringPropertyBase.fireValueChangedEvent(Unknown Source)
  at org.jabref.merged.module@5.1.394/javafx.beans.property.StringPropertyBase.markInvalid(Unknown Source)
  at org.jabref.merged.module@5.1.394/javafx.beans.property.StringPropertyBase.set(Unknown Source)
  at org.jabref.merged.module@5.1.394/javafx.beans.property.StringPropertyBase.set(Unknown Source)
  at org.jabref.merged.module@5.1.394/javafx.beans.property.StringProperty.setValue(Unknown Source)
  at org.jabref.merged.module@5.1.394/javafx.beans.property.StringProperty.setValue(Unknown Source)
  at org.jabref/org.jabref.gui.util.BindingsHelper$BidirectionalBinding.updateLocked(Unknown Source)
  at org.jabref/org.jabref.gui.util.BindingsHelper$BidirectionalBinding.changedB(Unknown Source)
  at org.jabref.merged.module@5.1.394/com.sun.javafx.binding.ExpressionHelper$SingleChange.fireValueChangedEvent(Unknown Source)
  at org.jabref.merged.module@5.1.394/com.sun.javafx.binding.ExpressionHelper.fireValueChangedEvent(Unknown Source)
  at org.jabref.merged.module@5.1.394/javafx.beans.binding.ObjectBinding.invalidate(Unknown Source)
  at org.jabref.merged.module@5.1.394/com.sun.javafx.binding.BindingHelperObserver.invalidated(Unknown Source)
  at org.jabref.merged.module@5.1.394/com.sun.javafx.collections.MapListenerHelper$Generic.fireValueChangedEvent(Unknown Source)
  at org.jabref.merged.module@5.1.394/com.sun.javafx.collections.MapListenerHelper.fireValueChangedEvent(Unknown Source)
  at org.jabref.merged.module@5.1.394/com.sun.javafx.collections.ObservableMapWrapper.callObservers(Unknown Source)
  at org.jabref.merged.module@5.1.394/com.sun.javafx.collections.ObservableMapWrapper.put(Unknown Source)
  at org.jabref/org.jabref.model.entry.BibEntry.setField(Unknown Source)
  at org.jabref/org.jabref.model.entry.BibEntry.setField(Unknown Source)
  at org.jabref/org.jabref.gui.entryeditor.SourceTab.storeSource(Unknown Source)
  at org.jabref/org.jabref.gui.entryeditor.SourceTab.lambda$setupSourceEditor$4(Unknown Source)
  at org.jabref.merged.module@5.1.394/com.sun.javafx.binding.ExpressionHelper$Generic.fireValueChangedEvent(Unknown Source)
  at org.jabref.merged.module@5.1.394/com.sun.javafx.binding.ExpressionHelper.fireValueChangedEvent(Unknown Source)
  at org.jabref.merged.module@5.1.394/javafx.beans.property.ReadOnlyBooleanPropertyBase.fireValueChangedEvent(Unknown Source)
  at org.jabref.merged.module@5.1.394/javafx.scene.Node$FocusedProperty.notifyListeners(Unknown Source)
  at org.jabref.merged.module@5.1.394/javafx.scene.Scene$12.invalidated(Unknown Source)
  at org.jabref.merged.module@5.1.394/javafx.beans.property.ObjectPropertyBase.markInvalid(Unknown Source)
  at org.jabref.merged.module@5.1.394/javafx.beans.property.ObjectPropertyBase.set(Unknown Source)
  at org.jabref.merged.module@5.1.394/javafx.scene.Scene$KeyHandler.setFocusOwner(Unknown Source)
  at org.jabref.merged.module@5.1.394/javafx.scene.Scene$KeyHandler.requestFocus(Unknown Source)
  at org.jabref.merged.module@5.1.394/javafx.scene.Scene.requestFocus(Unknown Source)
  at org.jabref.merged.module@5.1.394/javafx.scene.Node.requestFocus(Unknown Source)
  at org.jabref.merged.module@5.1.394/com.sun.javafx.scene.control.behavior.TableViewBehaviorBase.mousePressed(Unknown Source)
  at org.jabref.merged.module@5.1.394/com.sun.javafx.scene.control.inputmap.InputMap.handle(Unknown Source)
  at org.jabref.merged.module@5.1.394/com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(Unknown Source)
  at org.jabref.merged.module@5.1.394/com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(Unknown Source)
  at org.jabref.merged.module@5.1.394/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(Unknown Source)
  at org.jabref.merged.module@5.1.394/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(Unknown Source)
  at org.jabref.merged.module@5.1.394/com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(Unknown Source)
  at org.jabref.merged.module@5.1.394/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
  at org.jabref.merged.module@5.1.394/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
  at org.jabref.merged.module@5.1.394/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
  at org.jabref.merged.module@5.1.394/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
  at org.jabref.merged.module@5.1.394/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
  at org.jabref.merged.module@5.1.394/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
  at org.jabref.merged.module@5.1.394/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
  at org.jabref.merged.module@5.1.394/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
  at org.jabref.merged.module@5.1.394/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
  at org.jabref.merged.module@5.1.394/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
  at org.jabref.merged.module@5.1.394/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
  at org.jabref.merged.module@5.1.394/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
  at org.jabref.merged.module@5.1.394/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
  at org.jabref.merged.module@5.1.394/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
  at org.jabref.merged.module@5.1.394/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
  at org.jabref.merged.module@5.1.394/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
  at org.jabref.merged.module@5.1.394/com.sun.javafx.event.EventUtil.fireEventImpl(Unknown Source)
  at org.jabref.merged.module@5.1.394/com.sun.javafx.event.EventUtil.fireEvent(Unknown Source)
  at org.jabref.merged.module@5.1.394/javafx.event.Event.fireEvent(Unknown Source)
  at org.jabref.merged.module@5.1.394/javafx.scene.Scene$MouseHandler.process(Unknown Source)
  at org.jabref.merged.module@5.1.394/javafx.scene.Scene.processMouseEvent(Unknown Source)
  at org.jabref.merged.module@5.1.394/javafx.scene.Scene$ScenePeerListener.mouseEvent(Unknown Source)
  at org.jabref.merged.module@5.1.394/com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(Unknown Source)
  at org.jabref.merged.module@5.1.394/com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(Unknown Source)
  at java.base/java.security.AccessController.doPrivileged(Unknown Source)
  at org.jabref.merged.module@5.1.394/com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(Unknown Source)
  at org.jabref.merged.module@5.1.394/com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(Unknown Source)
  at org.jabref.merged.module@5.1.394/com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(Unknown Source)
  at org.jabref.merged.module@5.1.394/com.sun.glass.ui.View.handleMouseEvent(Unknown Source)
  at org.jabref.merged.module@5.1.394/com.sun.glass.ui.View.notifyMouse(Unknown Source)
  at org.jabref.merged.module@5.1.394/com.sun.glass.ui.gtk.GtkApplication._runLoop(Native Method)
  at org.jabref.merged.module@5.1.394/com.sun.glass.ui.gtk.GtkApplication.lambda$runLoop$11(Unknown Source)
  at java.base/java.lang.Thread.run(Unknown Source)
Caused by: java.nio.channels.ClosedChannelException
  at java.base/sun.nio.ch.FileChannelImpl.ensureOpen(Unknown Source)
  at java.base/sun.nio.ch.FileChannelImpl.read(Unknown Source)
  at org.jabref.merged.module@5.1.394/org.h2.store.fs.FileNio.read(Unknown Source)
  ... 90 more
@Siedlerchr Siedlerchr added the bug Confirmed bugs or reports that are very likely to be bugs label May 15, 2020
@tobiasdiez tobiasdiez added this to the v5.1 milestone May 16, 2020
@koppor koppor modified the milestones: v5.1, v5.2 Jul 27, 2020
@Siedlerchr
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Does this error stil occur?

@ilippert
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Does this error stil occur?

Thanks for asking.
I am afraid I cannot say. I guess not - I am posting most exceptions I get and it probably has not occurred anymore if I did not post it again. If you give me a note what to check for, what kind of operations to conduct, then I will test the current master for it. I do not know the code well enough (no capacity to read this error code) to know what journallist or the exception code refers to.

@Siedlerchr
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Judging from the error log it seem you edited the journal field in the biblatex source tab. I tried to reproduce this, but could not. And it may be related to another fix which I did to the loading of journal abbreviaton.
Therefore I would vote to close this and you reopen it when you encounter it

@koppor koppor moved this to Done in Prioritization Nov 10, 2022
koppor pushed a commit that referenced this issue May 1, 2023
Squashed 'buildres/csl/csl-styles/' changes from 4728902faa..a985762505
802ad43 
a985762505 Update environmental-and-engineering-geoscience.csl (#6512)
5118058ea0 Update norsk-henvisningsstandard-for-rettsvitenskapelige-tekster.csl (#6515)
e9830d3f5e Create polish-archives-of-internal-medicine.csl (#6399)
05ef543bd6 Update ieee.csl (#6511)
b6e6292e4b Update universite-de-bordeaux-ecole-doctorale-de-droit.csl (#6510)
af38aba0e9 Create la-nouvelle-revue-du-travail.csl (#6400)
4b23d7a03e Create north-pacific-anadromous-fish-commission-bulletin.csl (#6436)
77ea82a242 Create journal-of-dental-traumatology.csl (#6403)
af4578d1a7 Make magnetic-resonance-in-medicine.csl AMA dependent (#6433)
5467a4f901 Create medizinische-universitaet-innsbruck-vancouver.csl (#6484)
8a3c0a2b9b Update united-states-international-trade-commissio (#6487)
789267a9cb Update cardiff-university-harvard.csl (#6482)
252a5b5c08 Locators in palaeontology journal styles (#6496)
3d2bff0794 Update ecosistemas.csl (#6503)
199baca2c6 Bump nokogiri from 1.13.10 to 1.14.3 (#6504)
feffe61ae4 Update universite-du-quebec-a-montreal-etudes-litteraires-et-semiologie.csl (#6505)

git-subtree-dir: buildres/csl/csl-styles
git-subtree-split: a985762505418bd63c26a54c59b48e3ed7426953
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Milestone
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@Siedlerchr @koppor @tobiasdiez @ilippert