Sprint 1 - Running jfx.zip throws errors

Description

Error encountered at step 3 of the following instructions:
1. upzip -jfx.zip file on your computer where you can get to from a terminal window...
2. open terminal window and navigate to the folder jfx/app
3. Start the application as follows:
java -jar application-4.42-SNAPSHOT-jfx.jar
Make sure it launches ok. Running the app will create a /to-import folder
4. Choose the memory configuration you want to use (high/low)...under "task" menu upper right hand side of viewer app...app will quit
5. put data file in /to-import folder
6. relaunch app
java -Xmx6G -Xms6G -jar application-4.42-SNAPSHOT-jfx.jar
7. choose "import... from tasks menu...this can take up to 30 mins....on my machine...make note of time you started import and monitor if application is hung (on mac i open the activity viewer) the terminal window will also display information that will tell you the progress...

Error:

c:\Temp\jfx\app>java -jar application-4.42-SNAPSHOT-jfx.jar
2017-12-05 07:15:06,194 INFO [JavaFX Application Thread] api.LookupService (LookupService.java:336) - Looking for HK2 annotations skipping inhabitant files; and scanning in the packages: [sh, one, org.ihtsdo, org.glassfish, com.informatics]
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
2017-12-05 07:15:06,820 INFO [JavaFX Application Thread] api.LookupService (LookupService.java:353) - HK2 initialized. Identifed 63 services
java.util.prefs.BackingStoreException: Can't rename data\preferences\preferences-tmp.xml to data\preferences\preferences.xml
at sh.isaac.komet.preferences.IsaacPreferencesImpl.syncSpi(IsaacPreferencesImpl.java:213)
at java.util.prefs.AbstractPreferences.sync2(Unknown Source)
at java.util.prefs.AbstractPreferences.sync(Unknown Source)
at sh.isaac.komet.preferences.IsaacPreferencesWrapper.sync(IsaacPreferencesWrapper.java:177)
at sh.isaac.komet.preferences.PreferencesProvider.startMe(PreferencesProvider.java:171)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at org.glassfish.hk2.utilities.reflection.ReflectionHelper.invoke(ReflectionHelper.java:1287)
at org.jvnet.hk2.internal.ClazzCreator.postConstructMe(ClazzCreator.java:333)
at org.jvnet.hk2.internal.ClazzCreator.create(ClazzCreator.java:375)
at org.jvnet.hk2.internal.AutoActiveDescriptor.create(AutoActiveDescriptor.java:172)
at org.jvnet.hk2.internal.SystemDescriptor.create(SystemDescriptor.java:479)
at org.glassfish.hk2.runlevel.internal.AsyncRunLevelContext.findOrCreate(AsyncRunLevelContext.java:305)
at org.glassfish.hk2.runlevel.RunLevelContext.findOrCreate(RunLevelContext.java:85)
at org.jvnet.hk2.internal.Utilities.createService(Utilities.java:2126)
at org.jvnet.hk2.internal.ServiceHandleImpl.getService(ServiceHandleImpl.java:116)
at org.jvnet.hk2.internal.ServiceHandleImpl.getService(ServiceHandleImpl.java:90)
at org.glassfish.hk2.runlevel.internal.CurrentTaskFuture$QueueRunner.oneJob(CurrentTaskFuture.java:1237)
at org.glassfish.hk2.runlevel.internal.CurrentTaskFuture$QueueRunner.run(CurrentTaskFuture.java:1168)
at org.glassfish.hk2.runlevel.internal.CurrentTaskFuture$UpOneLevel.run(CurrentTaskFuture.java:786)
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
2017-12-05 07:15:07,014 ERROR [RunLevelControllerThread-1512483306827] preferences.PreferencesProvider (PreferencesProvider.java:178) - java.util.prefs.BackingStoreException: Can't rename data\preferences\preferences-tmp.xml to data\preferences\preferences.xml
Exception in Application start method
java.lang.reflect.InvocationTargetException
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at com.sun.javafx.application.LauncherImpl.launchApplicationWithArgs(LauncherImpl.java:389)
at com.sun.javafx.application.LauncherImpl.launchApplication(LauncherImpl.java:328)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at sun.launcher.LauncherHelper$FXHelper.main(Unknown Source)
Caused by: java.lang.RuntimeException: Exception in Application start method
at com.sun.javafx.application.LauncherImpl.launchApplication1(LauncherImpl.java:917)
at com.sun.javafx.application.LauncherImpl.lambda$launchApplication$155(LauncherImpl.java:182)
at java.lang.Thread.run(Unknown Source)
Caused by: A MultiException has 1 exceptions. They are:
1. org.glassfish.hk2.api.MultiException: A MultiException has 2 exceptions. They are:
1. java.lang.RuntimeException: java.util.prefs.BackingStoreException: Can't rename data\preferences\preferences-tmp.xml to data\preferences\preferences.xml
2. java.lang.IllegalStateException: Unable to perform operation: post construct on sh.isaac.komet.preferences.PreferencesProvider

at org.glassfish.hk2.runlevel.internal.CurrentTaskFuture$UpOneLevel.fail(CurrentTaskFuture.java:801)
at org.glassfish.hk2.runlevel.internal.CurrentTaskFuture$UpOneLevel.access$3200(CurrentTaskFuture.java:653)
at org.glassfish.hk2.runlevel.internal.CurrentTaskFuture$QueueRunner.oneJob(CurrentTaskFuture.java:1247)
at org.glassfish.hk2.runlevel.internal.CurrentTaskFuture$QueueRunner.run(CurrentTaskFuture.java:1168)
at org.glassfish.hk2.runlevel.internal.CurrentTaskFuture$UpOneLevel.run(CurrentTaskFuture.java:786)
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
... 1 more
Exception running application sh.komet.fx.stage.MainApp

c:\Temp\jfx\app>

Environment

None

Assignee

Keith Campbell

Reporter

Eric Hwang

Labels

None

Epic Link

Fix versions

Priority

Blocker
Configure