JabRef freezes when importing unlinked PDF files into Database

[onewiki]

JabRef version on 3.7

Steps to reproduce:

1. .Quality - Find unlinked files
2. Apply to the selected files (PDF)
3. Shows "Importing into Database" and the program freezes

Put the excerpt of the log file here

[koppor]

We had a similar issue #410

[stefan-kolb]

Thank you for your report 😄
I can reproduce the behavior and we will work on a fix for this issue. Stay tuned.

[stefan-kolb]

@lenhard Maybe a problem caused by the chnages in the thread executor? Code where this functionality here happens is in FindUnlinkedFilesDialog.java starting from line 523

[stefan-kolb]

If I debug this and set a breakpoint in line 550 the dialog is enabled again afterwards, so this should be some timing problem with the threads.

[stefan-kolb]

If I remove the invokeLater commands it works for me, so there exists some scheduling problem here?

        JabRefExecutorService.INSTANCE.execute(() -> {
            List<String> errors = new LinkedList<>();
            creatorManager.addEntriesFromFiles(fileList, databaseContext.getDatabase(), frame.getCurrentBasePanel(),
                    entryType, checkBoxWhyIsThereNoGetSelectedStupidSwing, new ChangeListener() {

                        int counter;

                        @Override
                        public void stateChanged(ChangeEvent e) {
                            counter++;
                            progressBarImporting.setValue(counter);
                            progressBarImporting.setString(Localization.lang("%0 of %1", Integer.toString(counter),
                                        Integer.toString(progressBarImporting.getMaximum())));
                        }
                    }, errors);
            importFinishedHandler(errors);
        });

[lenhard]

@stefan-kolb The threading changes were merged last Friday, whereas this issue was reported 15 days ago, so the changes in the threading PR cannot be the cause.

I can confirm that this is a threading issue. Sometimes the import works fine, sometimes it blocks. I does not make a difference if you execute it on the EDT (what the SwingUtilities.invokeLater() did) or not. It is likely a bug inside FindUnlinkedFilesDialog, since this class implements thread scheduling itself (seach for threadState). My guess is that the class always had this issue.

Since this class is a good example of terrible engineering, a rewrite would probably be the least painful fix.

[stefan-kolb]

@JabRef/developers This one is a blocker for v3.8

[lenhard]

@stefan-kolb As discussed in private chat: no it is not.

Unfortunately, we cannot find your commit on master (or any other branch), otherwise we would have merged it. Therefore, we are moving this to 4.0

[andrewufrank]

i would appreciate to be informed if there is a new fix in a new build for this problem. i am happy to run it with the debug option. i have currently JabRef-3.8.2-dev--snapshot--2017-01-16--master--9e48a5ff8.jar
. anything better to test? any workaround possible? would a different jre or jdk help (see error message?)
thank you for this feature - it will be very useful when it works reliably.

the current error message i get is:

frank@santafe:~/Downloads$ java -jar JabRef-3.8.2-dev--snapshot--2017-01-16--master--9e48a5ff8.jar
09:44:42.628 [AWT-EventQueue-1] WARN net.sf.jabref.JabRefGUI - There seem to be problems with OpenJDK and the default GTK Look&Feel. Using Metal L&F instead. Change to another L&F with caution.
09:44:42.642 [AWT-EventQueue-1] INFO net.sf.jabref.logic.importer.OpenDatabase - Opening: /home/frank/Templates/5273_geoinfo_biblio/geoinfo_bib/paperCollection.bib
09:46:52.727 [SwingWorker-pool-3-thread-1] WARN net.sf.jabref.gui.worker.VersionWorker - Could not connect to the updateserver.
java.net.ConnectException: Connection timed out (Connection timed out)
at java.net.PlainSocketImpl.socketConnect(Native Method) ~[?:1.8.0_111]
at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:350) ~[?:1.8.0_111]
at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:206) ~[?:1.8.0_111]
at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:188) ~[?:1.8.0_111]
at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392) ~[?:1.8.0_111]
at java.net.Socket.connect(Socket.java:589) ~[?:1.8.0_111]
at sun.security.ssl.SSLSocketImpl.connect(SSLSocketImpl.java:668) ~[?:1.8.0_111]
at sun.security.ssl.BaseSSLSocketImpl.connect(BaseSSLSocketImpl.java:173) ~[?:1.8.0_111]
at sun.net.NetworkClient.doConnect(NetworkClient.java:180) ~[?:1.8.0_111]
at sun.net.www.http.HttpClient.openServer(HttpClient.java:432) ~[?:1.8.0_111]
at sun.net.www.http.HttpClient.openServer(HttpClient.java:527) ~[?:1.8.0_111]
at sun.net.www.protocol.https.HttpsClient.(HttpsClient.java:264) ~[?:1.8.0_111]
at sun.net.www.protocol.https.HttpsClient.New(HttpsClient.java:367) ~[?:1.8.0_111]
at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.getNewHttpClient(AbstractDelegateHttpsURLConnection.java:191) ~[?:1.8.0_111]
at sun.net.www.protocol.http.HttpURLConnection.plainConnect0(HttpURLConnection.java:1138) ~[?:1.8.0_111]
at sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:1032) ~[?:1.8.0_111]
at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(AbstractDelegateHttpsURLConnection.java:177) ~[?:1.8.0_111]
at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1546) ~[?:1.8.0_111]
at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1474) ~[?:1.8.0_111]
at sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(HttpsURLConnectionImpl.java:254) ~[?:1.8.0_111]
at net.sf.jabref.logic.util.Version.getAllAvailableVersions(Version.java:93) ~[JabRef-3.8.2-dev--snapshot--2017-01-16--master--9e48a5ff8.jar:?]
at net.sf.jabref.gui.worker.VersionWorker.doInBackground(VersionWorker.java:55) [JabRef-3.8.2-dev--snapshot--2017-01-16--master--9e48a5ff8.jar:?]
at net.sf.jabref.gui.worker.VersionWorker.doInBackground(VersionWorker.java:29) [JabRef-3.8.2-dev--snapshot--2017-01-16--master--9e48a5ff8.jar:?]
at javax.swing.SwingWorker$1.call(SwingWorker.java:295) [?:1.8.0_111]
at java.util.concurrent.FutureTask.run(FutureTask.java:266) [?:1.8.0_111]
at javax.swing.SwingWorker.run(SwingWorker.java:334) [?:1.8.0_111]
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) [?:1.8.0_111]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) [?:1.8.0_111]
at java.lang.Thread.run(Thread.java:745) [?:1.8.0_111]

[koppor]

@andrewufrank Please try again the latest build from https://builds.jabref.org/master/