Problems getting started


#1

I downloaded 4.3.1 running it under Java 1.8.0 on CentOS 6, binary compatible with RedHa6. I have not found any good introduction on the net so I am trying different things. I do not know if I am doing anything wrong but the software seems flaky. I have, as an example, not been able to save any library, the software simply hangs. Getting references from Pubmed does not seem to work seamlesslessly and sometimes I get various exceptions in the console etc.

I am loath to invest more time or suggest it to others until I have been assured that I am doing something wrong.


(Christoph) #2

Hi,

first of all you might try the current development version. There have been a lot of bug fixes since 4.3.1
https://builds.jabref.org/master/
Another thing is to make sure you have either the latest java 1.8 installed (either the openjdk +openfjx) or the oracle version (https://tecadmin.net/install-java-8-on-centos-rhel-and-fedora/).

I would have suggested to try the snap version, but it seems snaps are only supported from Cent OS 7.6+
I hope this helps.

Best regards


#3

I am using the following version of java:
java version “1.8.0_202”
Java™ SE Runtime Environment (build 1.8.0_202-b08)
Java HotSpot™ 64-Bit Server VM (build 25.202-b08, mixed mode)

Is the above version of java not sufficient?

I have also seen that there were problems with Fedora 23 and 27 not unlike some of mine. The version I am running, 4.3.1, is supposed to be stable but my experience so far is far from what I would expect…


(Christoph) #4

The java version is right.
Please try the development version. Although it’s a development version, it is very stable to use and many bugs have been resolved.
But remember to make a backup of your bib file before.


#5

Well, I do not have a bib file since JabRef was never able to save the library, I lost it twice. This must be a very fundamental bug that I should never have encountered, or?


(Christoph) #6

Yes,

this is very odd. Please try the latest development version and report back if it works and if not, please report any errors


#7

Will do. I do have two other questions:

  • Is there a good online resource for learning JabRef (beyond the simple slides I have found on a couple of university websites)?
  • Given that I have multiple PDF-files which I found in 4.3.1 I could import into JabRef - but without being able to retrieve the abstract from each article into the abstract field of JabRef - is this possible in some semi-automated fashion?

Thank you.


(Christoph) #8

Hi

We have a help which covers the major topics http://help.jabref.org/ although some of the pages are a bit outdated.
A complete changelog what has been changed and fixed since 4.x can be found here.
https://github.com/JabRef/jabref/blob/master/CHANGELOG.md

Regarding your second point
JabRef has the option to look up metadata for existing entries. It might be able to get the abstract for some things. It uses CrossRef as basis. For some entries it might work and even provide an abstract.

Regards


#9

Yes, I have seen the help but it is not really a resource for learning JabRef.

As for importing, I am thinking of PubMed - where can I find instructions for how do that?


(Christoph) #10

Medline/Pubmed

Library -> New entry (CTRL + N) , ID Type -> Medline/Pubmed
Here you enter the ID of the article

If you want to search for an article based on title you can use the Web Search
http://help.jabref.org/en/Medline


#11

OK but again, I have a PDF file already and would like to get the metadata on this publication from PubMed. Doable? How? Typing each article title in PubMed search entry box is tedious and time-consuming. I did try using a DOI item for one article in 4.3.1 but again the program hang…


(Christoph) #12

You could do the new entry way as I outlined above, then create the new entry and merge it with the existing ones. Select both entries, right click: Merge

For the frezes. One thing I just remember is, you could try to start JabRef with the following parameters:
java -Djavafx.embed.singleThread=true -jar JabRef.jar


#13

Running 5.0. Imported 92 pdf-files into a Bibtex library and then tried to save it but failed because of the following:
org.jabref.logic.exporter.SaveException: Error in field ‘title’: Unescaped ‘}’ character without opening bracket ends string prematurely.
at org.jabref.gui.exporter.SaveDatabaseAction.saveDatabase(SaveDatabaseAction.java:87)
at org.jabref.gui.exporter.SaveDatabaseAction.doSave(SaveDatabaseAction.java:124)
at org.jabref.gui.exporter.SaveDatabaseAction.save(SaveDatabaseAction.java:166)
at org.jabref.gui.exporter.SaveDatabaseAction.saveAs(SaveDatabaseAction.java:214)
at org.jabref.gui.exporter.SaveDatabaseAction.save(SaveDatabaseAction.java:170)
at org.jabref.gui.BasePanel.runCommand(BasePanel.java:631)
at org.jabref.gui.actions.OldDatabaseCommandWrapper.execute(OldDatabaseCommandWrapper.java:37)
at org.jabref.gui.actions.JabRefAction.lambda$new$697(JabRefAction.java:29)
at org.controlsfx.control.action.Action.handle(Action.java:419)
at org.controlsfx.control.action.Action.handle(Action.java:64)
at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86)
at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:238)
at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191)
at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58)
at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74)
at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49)
at javafx.event.Event.fireEvent(Event.java:198)
at javafx.scene.control.MenuItem.fire(MenuItem.java:462)
at com.sun.javafx.scene.control.skin.ContextMenuContent$MenuItemContainer.doSelect(ContextMenuContent.java:1405)
at com.sun.javafx.scene.control.skin.ContextMenuContent$MenuItemContainer.lambda$createChildren$599(ContextMenuContent.java:1358)
at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:218)
at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80)
at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:238)
at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191)
at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59)
at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58)
at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74)
at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54)
at javafx.event.Event.fireEvent(Event.java:198)
at javafx.scene.Scene$MouseHandler.process(Scene.java:3757)
at javafx.scene.Scene$MouseHandler.access$1500(Scene.java:3485)
at javafx.scene.Scene.impl_processMouseEvent(Scene.java:1762)
at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2494)
at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:394)
at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:295)
at java.security.AccessController.doPrivileged(Native Method)
at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$350(GlassViewEventHandler.java:432)
at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:389)
at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:431)
at com.sun.glass.ui.View.handleMouseEvent(View.java:555)
at com.sun.glass.ui.View.notifyMouse(View.java:937)
at com.sun.glass.ui.gtk.GtkApplication._runLoop(Native Method)
at com.sun.glass.ui.gtk.GtkApplication.lambda$null$208(GtkApplication.java:245)
at java.lang.Thread.run(Thread.java:748)


(Christoph) #14

As the error mesage indicates you have somewhere an entry with a title field where there is an ending curly brace }which does not have an opening brace {.

Only way is to open the file in a text editor and search through the entries.
As you are under Linux, you could use vim for this:

For further, to help you find the right entry I enhanced the error messages to print the value of the field which is problematic. That should help you locating it.
Try this version;
https://builds.jabref.org/improveErrorMessageOnSave/


#15

You were correct, when 4.3.1 had revised the names of the PDF-files when importing them into a library, it had inserted { and } into several filenames. Not sure why since this had to be corrected manually by modifying those filenames.


#16

Just downloaded the snapshot to another computer running CentOS 7 and java as below:
openjdk version “1.8.0_191”
OpenJDK Runtime Environment (build 1.8.0_191-b12)
OpenJDK 64-Bit Server VM (build 25.191-b12, mixed mode)

However, running the snapshot gives me:
Error: Could not find or load main class org.jabref.JabRefMain

Is there a problem with the snapshot dated March 5th?


(Tobias Diez) #17

You are probably missing the the openjfx package on this computer.
http://help.jabref.org/en/Installation#centos-6-or-7-and-oracle-java