Jabref: Groups issues on JabRef 4 OSX

[juanmduran]

Hi, I'm having issues with adding, deleting, etc groups JabRef 4 on OSX. Basically, it stops working.

I've also experience problems with groups on earlier versions (3.8.2), such as references are not added to a group, or JabRef mess them up in different groups.

Anyone knows about these issues? I really need my groups, its a great feature.

Thanks!

[tobiasdiez]

So it just stops working without error message? Do you see some errors reported in the Help -> Event log?

@chochreiner can you reproduce these errors on OSX?

[boceckts]

JabRef 4.0.0-dev--snapshot--2017-04-08--master--65dccbf8a
Mac OS X 10.12.1 x86_64
Java 1.8.0_77

I can confirm this very strange behaviour. After clicking on the "+" sign in the groups tab JabRef freezes without an exception. After I waited more than ten minutes it still didn't respond and only showed the spinning wheel for my mouse pointer.

When executing the jar in a terminal I could see the following log statements.

Other JavaFX dialogs can be used normally. Also there was no message/exception in the event log present when I opened the dialog before clicking the "+" in the groups tab.

[tobiasdiez]

That is indeed very strange. @boceckts may I ask you to investigate this problem further as I have no Mac to debug it myself? Does JabRef still frezzes with other group related changes (e.g. delete of a group?). Is the dropdown menu the reason? The group edit dialog?

[boceckts]

I will have a look into it.

[juanmduran]

Thanks everyone, I really appreciate the quick response.

@tobiasdiez yes, it just dies. No error message, nothing. And this regardless of the size of the .bib

It is also strange that it says: All entries 5141, when a) I don't have any entries, and b) I can't expand to see any of these spooky entries. In fact, JabRef dies not only when clicking "+", but when any action is selected with the left-click menu.

As for the log file, I can't see anything. When Jabref freezes, I kill it, and then the log is empty (other than showing which .bib file I recently open).

I've tried to run it on a terminal, but it won't start. Here's the output:

java version "1.8.0_60"
Java(TM) SE Runtime Environment (build 1.8.0_60-b27)
Java HotSpot(TM) 64-Bit Server VM (build 25.60-b23, mixed mode)
OSX 10.12.4

2017-04-08 16:50:29,944 JavaFX Application Thread ERROR Appenders contains an invalid element or attribute "ApplicationInsightsAppender"
2017-04-08 16:50:29,953 JavaFX Application Thread ERROR Unable to locate appender "applicationInsightsAppender" for logger config "root"
16:50:31.277 [AWT-EventQueue-0] WARN org.jabref.logic.remote.server.RemoteListenerServerLifecycle - Port is blocked
java.net.BindException: Address already in use
at java.net.PlainSocketImpl.socketBind(Native Method) ~[?:1.8.0_60]
at java.net.AbstractPlainSocketImpl.bind(AbstractPlainSocketImpl.java:387) ~[?:1.8.0_60]
at java.net.ServerSocket.bind(ServerSocket.java:375) ~[?:1.8.0_60]
at java.net.ServerSocket.(ServerSocket.java:237) ~[?:1.8.0_60]
at org.jabref.logic.remote.server.RemoteListenerServer.(RemoteListenerServer.java:26) ~[JabRef-4.0.0-dev--snapshot--2017-04-08--master--65dccbf8a.jar:?]
at org.jabref.logic.remote.server.RemoteListenerServerThread.(RemoteListenerServerThread.java:18) ~[JabRef-4.0.0-dev--snapshot--2017-04-08--master--65dccbf8a.jar:?]
at org.jabref.logic.remote.server.RemoteListenerServerLifecycle.open(RemoteListenerServerLifecycle.java:43) ~[JabRef-4.0.0-dev--snapshot--2017-04-08--master--65dccbf8a.jar:?]
at org.jabref.JabRefMain.start(JabRefMain.java:110) ~[JabRef-4.0.0-dev--snapshot--2017-04-08--master--65dccbf8a.jar:?]
at org.jabref.JabRefMain.lambda$start$0(JabRefMain.java:53) ~[JabRef-4.0.0-dev--snapshot--2017-04-08--master--65dccbf8a.jar:?]
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) [?:1.8.0_60]
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756) [?:1.8.0_60]
at java.awt.EventQueue.access$500(EventQueue.java:97) [?:1.8.0_60]
at java.awt.EventQueue$3.run(EventQueue.java:709) [?:1.8.0_60]
at java.awt.EventQueue$3.run(EventQueue.java:703) [?:1.8.0_60]
at java.security.AccessController.doPrivileged(Native Method) ~[?:1.8.0_60]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) [?:1.8.0_60]
at java.awt.EventQueue.dispatchEvent(EventQueue.java:726) [?:1.8.0_60]
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) [?:1.8.0_60]
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) [?:1.8.0_60]
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) [?:1.8.0_60]
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) [?:1.8.0_60]
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) [?:1.8.0_60]
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) [?:1.8.0_60]
16:50:31.286 [AWT-EventQueue-0] INFO org.jabref.JabRefMain - Arguments passed on to running JabRef instance. Shutting down.

[juanmduran]

Hi again, dunno if this is useful, but I've been playing around with older versions and this is what I found out:

3.7, 3.8 and up: static groups can be created but references dragged and drop (or "Add to group") work ONLY in the following case: first, save one reference, immediately after save a second reference. Only the first reference is saved in the selected group. It does NOT work by dragging (or saving) one reference at the time (and then clicking on the group), or dragging (or saving) two or more references at once. I've also noticed that some of the references disappear after adding new ones.

Thanks

[boceckts]

Thank you for your great support in this issue @juanmduran. From the console log I can see that you had another instance of JabRef running, which is why it "won't start". Other than that there is unfortunately no log statement regarding the groups issue.

I have looked into the code and it seems that the old Swing Dialog is still used to create/edit the groups however the displayed TreeView component is now in JavaFX. This means we have to be very careful to execute the Swing stuff in the EDT and to execute the JavaFX stuff on the JavaFX Application Thread.

Wrapping the call inside of all the methods which are called on the Java FX Application Thread and want to open a Swing dialog, makes the group actions work again.

@tobiasdiez
However it still behaved strange. Adding and removing group/subgroup seemed to work as expected, but editing a group still showed me the old name in the tree view, adding and removing selected entries also didn't update the view...

The strange thing is that it works on Windows(?) but not on Mac OS X?...So much for the Platform independency 😁

[tobiasdiez]

Mhh strange. There appears to be some issues on MacOS when JavaXF and Swing need to communicate. But good that you could isolate the underlying issue and fix it. I think the update problems are still inconvenient but not as worse as a not responding JabRef. Can you please open a PR with the fix so that it can be included in the beta release at the weekend. Thanks.

[boceckts]

I just found out that the method removeSubgroups isn't even getting called, seems like a copy paste error when assigning the actions to the menu items. I will create a pull request later and have a look if the rest of the groups actions are working as expected or if I can fix it.

[juanmduran]

@boceckts, sorry you're right. Here's my output running the .jar

The last two lines show up when I click "+"

Thanks again to all of you.

dyn-mit-239:Downloads Juan$ java -jar JabRef-4.0.0-dev--snapshot--2017-04-11--master--d206fb8b1.jar
2017-04-11 16:13:19,375 JavaFX Application Thread ERROR Appenders contains an invalid element or attribute "ApplicationInsightsAppender"
2017-04-11 16:13:19,385 JavaFX Application Thread ERROR Unable to locate appender "applicationInsightsAppender" for logger config "root"
AI: INFO 11-04-2017 16:13, 17: Configuration file has been successfully found as resource
AI: INFO 11-04-2017 16:13, 17: 'MaxTelemetryBufferCapacity': null value is replaced with '500'
AI: INFO 11-04-2017 16:13, 17: 'FlushIntervalInSeconds': null value is replaced with '5'
AI: TRACE 11-04-2017 16:13, 17: Using Http Client version 4.3+
AI: INFO 11-04-2017 16:13, 17: 'Channel.MaxTransmissionStorageCapacityInMB': null value is replaced with '10'
AI: INFO 11-04-2017 16:13, 17: Configuration file has been successfully found as resource
AI: INFO 11-04-2017 16:13, 17: 'MaxTelemetryBufferCapacity': null value is replaced with '500'
AI: INFO 11-04-2017 16:13, 17: 'FlushIntervalInSeconds': null value is replaced with '5'
AI: INFO 11-04-2017 16:13, 17: 'Channel.MaxTransmissionStorageCapacityInMB': null value is replaced with '10'
AI: TRACE 11-04-2017 16:13, 17: InProcessTelemetryChannel sending telemetry
AI: ERROR 11-04-2017 16:13, 31: Failed to send, Bad request : {"itemsReceived":1,"itemsAccepted":0,"errors":[{"index":0,"statusCode":400,"message":"Unknown domain type 'Microsoft.ApplicationInsights.SessionStateData'"}]}
16:13:25.800 [AWT-EventQueue-0] INFO org.jabref.logic.importer.OpenDatabase - Opening: /Users/Juan/Dropbox/00_PAPERS/BibTex/biblioZotero.bib
File: grouptree.fxml not found, attempting with camel case
Apr 11, 2017 4:13:27 PM javafx.fxml.FXMLLoader$ValueElement processValue
WARNING: Loading FXML document with JavaFX API of version 8.0.112 by JavaFX runtime of version 8.0.60
File: grouptree.css not found, attempting with camel case
AI: TRACE 11-04-2017 16:13, 17: InProcessTelemetryChannel sending telemetry
AI: TRACE 11-04-2017 16:13, 12: InProcessTelemetryChannel sending telemetry

[boceckts]

No worries and thank you for your great collaboration.
The changes I made in #2727 should do the trick.

[tobiasdiez]

This should be fixed in the latest development version. Could you please check the build from http://builds.jabref.org/master/. Thanks!

[juanmduran]

Works perfect. Thank you guys!

[juanmduran]

Ok guys, so a little work on the groups shows the following issues:

• The groups are not saved after quitting. Restarting JabRef means creating the groups again. Mind you that the entry "groups" in a given reference remains.
• For "automatically create groups" (e.g., by keyword), it does not "automatically" add a new reference when a new keyword is added to that reference.
• Working with groups seems to randomly freeze JabRef. I can't figure out in what specific situations. E.g., I just double clicked and it is now freeze.

[Siedlerchr]

@juanmduran I cannot confirm the first issue of your list. When I create groups and save the db, the groups are definitively there.

[juanmduran]

@Siedlerchr I should've probably mentioned that I'm running it on OSX Sierra 10.12.4. The above discussions show that there are a few issues with groups in JabRef for Mac.

Triple check and the problem is still there. I've tried with Static groups, dynamic groups, and Automatically created groups. Same result: when I quit, the groups in the group interface are not there anymore (thou, again, the entry "group" in a given reference remains correct).

[tobiasdiez]

Your second problem is a known issue. You can switch to a second db and then back to your first and the subgroups are refreshed (as a workaround).

I've never seen that groups are not saved correctly and this should be completely independent of the used OS. Can you please give a step by step procedure how this issue can be reproduced (maybe in a new github issue).

[mvt91]

Hello,
Lat be I'm late and the problem is solved and closed but...
With the last development release(s), I've the same problem.
After a "double clic" on e line to show the details of the bibref reference I chooses, JabRef (JabRef-4.0.0-dev--snapshot--2017-06-18--master--c0ca85e07.jar) freezes.
Linux Mint Cinnamon 18.1, last update with
openjdk version "1.8.0_131"
OpenJDK Runtime Environment (build 1.8.0_131-8u131-b11-0ubuntu1.16.04.2-b11)
OpenJDK 64-Bit Server VM (build 25.131-b11, mixed mode)

" AI: INFO 19-06-2017 16:34, 19: Configuration file has been successfully found as resource
16:34:22.884 [AWT-EventQueue-0] INFO org.jabref.logic.importer.OpenDatabase - Opening: /home/tidy/Documents/Biblio/Cur_BibFiles/170619PmId.bib
File: grouptree.fxml not found, attempting with camel case
Jun 19, 2017 4:34:24 PM javafx.fxml.FXMLLoader$ValueElement processValue
WARNING: Loading FXML document with JavaFX API of version 8.0.112 by JavaFX runtime of version 8.0.60
File: grouptree.css not found, attempting with camel case
Jun 19, 2017 4:34:57 PM javafx.fxml.FXMLLoader$ValueElement processValue
WARNING: Loading FXML document with JavaFX API of version 8.0.112 by JavaFX runtime of version 8.0.60
Jun 19, 2017 4:34:57 PM javafx.fxml.FXMLLoader$ValueElement processValue
WARNING: Loading FXML document with JavaFX API of version 8.0.112 by JavaFX runtime of version 8.0.60
Jun 19, 2017 4:34:57 PM javafx.fxml.FXMLLoader$ValueElement processValue
WARNING: Loading FXML document with JavaFX API of version 8.0.112 by JavaFX runtime of version 8.0.60
Jun 19, 2017 4:34:57 PM javafx.fxml.FXMLLoader$ValueElement processValue
WARNING: Loading FXML document with JavaFX API of version 8.0.112 by JavaFX runtime of version 8.0.60
Jun 19, 2017 4:34:57 PM javafx.fxml.FXMLLoader$ValueElement processValue
WARNING: Loading FXML document with JavaFX API of version 8.0.112 by JavaFX runtime of version 8.0.60
Jun 19, 2017 4:34:57 PM javafx.fxml.FXMLLoader$ValueElement processValue
WARNING: Loading FXML document with JavaFX API of version 8.0.112 by JavaFX runtime of version 8.0.60
Jun 19, 2017 4:34:57 PM javafx.fxml.FXMLLoader$ValueElement processValue
WARNING: Loading FXML document with JavaFX API of version 8.0.112 by JavaFX runtime of version 8.0.60
Jun 19, 2017 4:34:57 PM javafx.fxml.FXMLLoader$ValueElement processValue
WARNING: Loading FXML document with JavaFX API of version 8.0.112 by JavaFX runtime of version 8.0.60
Jun 19, 2017 4:34:57 PM javafx.fxml.FXMLLoader$ValueElement processValue
WARNING: Loading FXML document with JavaFX API of version 8.0.112 by JavaFX runtime of version 8.0.60
Jun 19, 2017 4:34:57 PM javafx.fxml.FXMLLoader$ValueElement processValue
WARNING: Loading FXML document with JavaFX API of version 8.0.112 by JavaFX runtime of version 8.0.60
Jun 19, 2017 4:34:57 PM javafx.fxml.FXMLLoader$ValueElement processValue
WARNING: Loading FXML document with JavaFX API of version 8.0.112 by JavaFX runtime of version 8.0.60
"

Thanks.
Best regards

[Siedlerchr]

Could you please exactly describe the freezing? There is a slight delay for showing the entry editor when you do a double click on the entry. Does the entry editor show up?

[mvt91]

Hi Siedlerchr ,
I launch JabRef and load a .bib file (about 1400 - 1500 refs).
When I select (just a clic) a line, I can see the content at the bottom of the window. If I "double clic" on the line to show all the properties (tabbed display format at the bottom of the windows, include the bibtex "raw text", JabRef freezes. The sole solution is to kill the process. If needed, I can try to do the same command on some previous release (last 3 or 4 dev snapshot - 11, 14, 15 and 18 june - and a 3.8.2 release).
I just tried with the same last snapshot release under windows 8.1. The program works well. May be this an issue with openJDK under Mint 8.1 (or Ubuntu like linuxes)
Best regards

[Siedlerchr]

Okay, that narrows it down a bit. Could you please try to install the
Oracle hee?
For ubuntu there is an external repo
http://www.webupd8.org/2012/09/install-oracle-java-8-in-ubuntu-via-ppa.html?m=1

Am 19.06.2017 6:38 nachm. schrieb "mvt91" [e-mail]:

Hi Siedlerchr ,
I launch JabRef and load a .bib file (about 1400 - 1500 refs).
When I select (just a clic) a line, I can see the content at the bottom of
the window. If I "double clic" on the line to show all the properties
(tabbed display format at the bottom of the windows, include the bibtex
"raw text", JabRef freezes. The sole solution is to kill the process. If
needed, I can try to do the same command on some previous release (last 3
or 4 dev snapshot - 11, 14, 15 and 18 june - and a 3.8.2 release).
I just tried with the same last snapshot release under windows 8.1. The
program works well. May be this an issue with openJDK under Mint 8.1 (or
Ubuntu like linuxes)
Best regards

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[mvt91]

I tried the last release (snapshot) under windows 8.1 (with Oracle Java). It works well.
I'll try Oracle under Mint in a few days. I hope the next WE.
Thanks

[mvt91]

Hi Siedlerchr ,,

Sorry for the delay.
Under Linux Mint Cinnamon 18.1, I removed OpenJDK :
sudo apt-get update && sudo apt-get remove openjdk*
sudo apt-get autoremove && sudo apt-get clean

I download the last JDK release from Oracle website :
jdk-8u131-linux-x64.tar.gz

I did these commands :
sudo mkdir -p -v /opt/java/64

Into ~/Download dir :
tar -zxvf jdk-8u131-linux-x64.tar.gz
sudo mv -v jdk-8u131-linux-x64* /opt/java/64

sudo update-alternatives --install "/usr/bin/java" "java" "/opt/java/64/jdk1.8.0_131/jre/bin/java" 1
sudo update-alternatives --set java /opt/java/64/jdk1.8.0_131/jre/bin/java

~/java -version
java version "1.8.0_131"
Java(TM) SE Runtime Environment (build 1.8.0_131-b11)
Java HotSpot(TM) 64-Bit Server VM (build 25.131-b11, mixed mode)

Running JabRef last snapshot (17-06-26) :
java -jar JabRef-4.0.0-dev--snapshot--2017-06-26--master--c3f60f813.jar
AI: INFO 27-06-2017 11:33, 19: Configuration file has been successfully found as resource
11:33:49.603 [AWT-EventQueue-0] INFO org.jabref.logic.importer.OpenDatabase - Opening: /home/tidy/Documents/Biblio/Cur_BibFiles/170619PmId.bib
File: grouptree.fxml not found, attempting with camel case
File: grouptree.css not found, attempting with camel case

Opening the last opened file (by default)
Double clic on the first entry
Jabref freezes...

May I try something else ?

Note : the external repository for java was mentioned to be use with older releases of Ubuntu (eg. <13.x, release not maintained)

Just a question : Do I have to create a new thread. This one is closed and relative to MacOS ?

Thanks