Error when starting KOMET "Assemblage nid not found"

Description

I've placed the current change sets here (https://www.dropbox.com/s/tlwmzmm4855kx8s/changesets.zip?dl=0). If I start KOMET without these changesets, there is not error, but with these changesets, I get the error below, and I don't know how to find the assemblage with UUID 6e2f04f7-28dd-4318-8576-c5adf02511bd.

This is preventing me from testing issue 666 and 667 because my preferences depend on this assemblage and so they are not being displayed (per the attached image)

2018-09-17 09:45:12,087 ERROR [RunLevelControllerThread-1537191900804] (TaxonomyProvider.java:248) - error processing taxonomy update
java.lang.RuntimeException: No assemblage nid available for -2140332205 6e2f04f7-28dd-4318-8576-c5adf02511bd
at sh.isaac.provider.datastore.FileSystemDataStore.lambda$getElementSequenceForNid$6(FileSystemDataStore.java:898) ~[filesystem-datastore-4.53-SNAPSHOT.jar:?]
at java.util.OptionalInt.orElseThrow(OptionalInt.java:189) ~[?:1.8.0_144]
at sh.isaac.provider.datastore.FileSystemDataStore.getElementSequenceForNid(FileSystemDataStore.java:897) ~[filesystem-datastore-4.53-SNAPSHOT.jar:?]
at sh.isaac.provider.datastore.DatastoreLocator.getElementSequenceForNid(DatastoreLocator.java:362) ~[datastore-locator-4.53-SNAPSHOT.jar:?]
at sh.isaac.model.collections.SpinedIntIntArrayMap.accumulateAndGet(SpinedIntIntArrayMap.java:337) ~[model-4.53-SNAPSHOT.jar:?]
at sh.isaac.provider.datastore.FileSystemDataStore.accumulateAndGetTaxonomyData(FileSystemDataStore.java:701) ~[filesystem-datastore-4.53-SNAPSHOT.jar:?]
at sh.isaac.provider.datastore.DatastoreLocator.accumulateAndGetTaxonomyData(DatastoreLocator.java:270) ~[datastore-locator-4.53-SNAPSHOT.jar:?]
at sh.isaac.provider.datastore.taxonomy.TaxonomyProvider.accumulateAndGetTaxonomyData(TaxonomyProvider.java:407) ~[chronology-4.53-SNAPSHOT.jar:?]
at sh.isaac.provider.datastore.chronology.ChronologyUpdate.updateIsaRel(ChronologyUpdate.java:488) ~[chronology-4.53-SNAPSHOT.jar:?]
at sh.isaac.provider.datastore.chronology.ChronologyUpdate.processRelationshipRoot(ChronologyUpdate.java:364) ~[chronology-4.53-SNAPSHOT.jar:?]
at sh.isaac.provider.datastore.chronology.ChronologyUpdate.processNewLogicGraph(ChronologyUpdate.java:335) ~[chronology-4.53-SNAPSHOT.jar:?]
at sh.isaac.provider.datastore.chronology.ChronologyUpdate.processVersionNode(ChronologyUpdate.java:392) ~[chronology-4.53-SNAPSHOT.jar:?]
at sh.isaac.provider.datastore.chronology.ChronologyUpdate.handleTaxonomyUpdate(ChronologyUpdate.java:157) ~[chronology-4.53-SNAPSHOT.jar:?]
at sh.isaac.provider.datastore.taxonomy.TaxonomyProvider.updateTaxonomy(TaxonomyProvider.java:246) ~[chronology-4.53-SNAPSHOT.jar:?]
at sh.isaac.provider.commit.CommitProvider.postProcessImportNoChecks(CommitProvider.java:572) ~[commit-4.53-SNAPSHOT.jar:?]
at sh.isaac.provider.commit.ChangeSetLoadProvider.lambda$readChangesetFiles$2(ChangeSetLoadProvider.java:169) ~[commit-4.53-SNAPSHOT.jar:?]
at java.lang.Iterable.forEach(Iterable.java:75) [?:1.8.0_144]
at sh.isaac.provider.commit.ChangeSetLoadProvider.readChangesetFiles(ChangeSetLoadProvider.java:145) [commit-4.53-SNAPSHOT.jar:?]
at sh.isaac.provider.commit.ChangeSetLoadProvider.startMe(ChangeSetLoadProvider.java:267) [commit-4.53-SNAPSHOT.jar:?]
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[?:1.8.0_144]
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[?:1.8.0_144]
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:1.8.0_144]
at java.lang.reflect.Method.invoke(Method.java:498) ~[?:1.8.0_144]
at org.glassfish.hk2.utilities.reflection.ReflectionHelper.invoke(ReflectionHelper.java:1287) [hk2-utils-2.5.0-b60.jar:?]
at org.jvnet.hk2.internal.ClazzCreator.postConstructMe(ClazzCreator.java:333) [hk2-locator-2.5.0-b60.jar:?]
at org.jvnet.hk2.internal.ClazzCreator.create(ClazzCreator.java:375) [hk2-locator-2.5.0-b60.jar:?]
at org.jvnet.hk2.internal.AutoActiveDescriptor.create(AutoActiveDescriptor.java:172) [hk2-locator-2.5.0-b60.jar:?]
at org.jvnet.hk2.internal.SystemDescriptor.create(SystemDescriptor.java:479) [hk2-locator-2.5.0-b60.jar:?]
at org.glassfish.hk2.runlevel.internal.AsyncRunLevelContext.findOrCreate(AsyncRunLevelContext.java:305) [hk2-runlevel-2.5.0-b60.jar:?]
at org.glassfish.hk2.runlevel.RunLevelContext.findOrCreate(RunLevelContext.java:89) [hk2-runlevel-2.5.0-b60.jar:?]
at org.jvnet.hk2.internal.Utilities.createService(Utilities.java:2126) [hk2-locator-2.5.0-b60.jar:?]
at org.jvnet.hk2.internal.ServiceHandleImpl.getService(ServiceHandleImpl.java:116) [hk2-locator-2.5.0-b60.jar:?]
at org.jvnet.hk2.internal.ServiceHandleImpl.getService(ServiceHandleImpl.java:90) [hk2-locator-2.5.0-b60.jar:?]
at org.glassfish.hk2.runlevel.internal.CurrentTaskFuture$QueueRunner.oneJob(CurrentTaskFuture.java:1237) [hk2-runlevel-2.5.0-b60.jar:?]
at org.glassfish.hk2.runlevel.internal.CurrentTaskFuture$QueueRunner.run(CurrentTaskFuture.java:1168) [hk2-runlevel-2.5.0-b60.jar:?]
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) [?:1.8.0_144]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) [?:1.8.0_144]
at java.lang.Thread.run(Thread.java:748) [?:1.8.0_144]

Environment

None

Activity

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Saif Baig
September 18, 2018, 2:13 PM

The first time I started KOMET with the changesets I got the the same error type (assemblage nid not found), but now for a difference assemblage UUID. If I close it and run it again, that error goes away.

However, I still get the same screen with no options for the java preferences with the error beow. Just to make sure I sent the right changesets and preferences zip file, I'm including a new dropbox link here (https://www.dropbox.com/s/jb0j89rkpn70hfx/changesets%20%26%20preferences.zip?dl=0)

Here's the error:
2018-09-18 10:08:13,322 ERROR [JavaFX Application Thread] (PreferencesTreeItem.java:86) - sh.isaac.komet.preferences.GeneralPreferences
java.lang.ClassNotFoundException: sh.isaac.komet.preferences.GeneralPreferences
at java.net.URLClassLoader.findClass(URLClassLoader.java:381) ~[?:1.8.0_144]
at java.lang.ClassLoader.loadClass(ClassLoader.java:424) ~[?:1.8.0_144]
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:335) ~[?:1.8.0_144]
at java.lang.ClassLoader.loadClass(ClassLoader.java:357) ~[?:1.8.0_144]
at java.lang.Class.forName0(Native Method) ~[?:1.8.0_144]
at java.lang.Class.forName(Class.java:264) ~[?:1.8.0_144]
at sh.isaac.komet.preferences.PreferencesTreeItem.from(PreferencesTreeItem.java:75) ~[komet-preferences-4.53-SNAPSHOT.jar:?]
at sh.isaac.komet.preferences.PreferencesTreeItem.<init>(PreferencesTreeItem.java:51) ~[komet-preferences-4.53-SNAPSHOT.jar:?]
at sh.isaac.komet.preferences.PreferencesTreeItem.from(PreferencesTreeItem.java:81) ~[komet-preferences-4.53-SNAPSHOT.jar:?]
at sh.isaac.komet.preferences.KometPreferencesImpl.loadPreferences(KometPreferencesImpl.java:63) ~[komet-preferences-4.53-SNAPSHOT.jar:?]
at sh.komet.fx.stage.MainApp.start(MainApp.java:150) ~[classes/:?]
at com.sun.javafx.application.LauncherImpl.lambda$launchApplication1$162(LauncherImpl.java:863) ~[jfxrt.jar:?]
at com.sun.javafx.application.PlatformImpl.lambda$runAndWait$175(PlatformImpl.java:326) ~[jfxrt.jar:?]
at com.sun.javafx.application.PlatformImpl.lambda$null$173(PlatformImpl.java:295) ~[jfxrt.jar:?]
at java.security.AccessController.doPrivileged(Native Method) ~[?:1.8.0_144]
at com.sun.javafx.application.PlatformImpl.lambda$runLater$174(PlatformImpl.java:294) ~[jfxrt.jar:?]
at com.sun.glass.ui.InvokeLaterDispatcher$Future.run(InvokeLaterDispatcher.java:95) [jfxrt.jar:?]
2018-09-18 10:08:13,332 ERROR [JavaFX Application Thread] (PreferencesTreeItem.java:86) - sh.isaac.komet.preferences.ChangeSetPreferences
java.lang.ClassNotFoundException: sh.isaac.komet.preferences.ChangeSetPreferences
at java.net.URLClassLoader.findClass(URLClassLoader.java:381) ~[?:1.8.0_144]
at java.lang.ClassLoader.loadClass(ClassLoader.java:424) ~[?:1.8.0_144]
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:335) ~[?:1.8.0_144]
at java.lang.ClassLoader.loadClass(ClassLoader.java:357) ~[?:1.8.0_144]
at java.lang.Class.forName0(Native Method) ~[?:1.8.0_144]
at java.lang.Class.forName(Class.java:264) ~[?:1.8.0_144]
at sh.isaac.komet.preferences.PreferencesTreeItem.from(PreferencesTreeItem.java:75) ~[komet-preferences-4.53-SNAPSHOT.jar:?]
at sh.isaac.komet.preferences.PreferencesTreeItem.<init>(PreferencesTreeItem.java:51) ~[komet-preferences-4.53-SNAPSHOT.jar:?]
at sh.isaac.komet.preferences.PreferencesTreeItem.from(PreferencesTreeItem.java:81) ~[komet-preferences-4.53-SNAPSHOT.jar:?]
at sh.isaac.komet.preferences.KometPreferencesImpl.loadPreferences(KometPreferencesImpl.java:63) ~[komet-preferences-4.53-SNAPSHOT.jar:?]
at sh.komet.fx.stage.MainApp.start(MainApp.java:150) ~[classes/:?]
at com.sun.javafx.application.LauncherImpl.lambda$launchApplication1$162(LauncherImpl.java:863) ~[jfxrt.jar:?]
at com.sun.javafx.application.PlatformImpl.lambda$runAndWait$175(PlatformImpl.java:326) ~[jfxrt.jar:?]
at com.sun.javafx.application.PlatformImpl.lambda$null$173(PlatformImpl.java:295) ~[jfxrt.jar:?]
at java.security.AccessController.doPrivileged(Native Method) ~[?:1.8.0_144]
at com.sun.javafx.application.PlatformImpl.lambda$runLater$174(PlatformImpl.java:294) ~[jfxrt.jar:?]
at com.sun.glass.ui.InvokeLaterDispatcher$Future.run(InvokeLaterDispatcher.java:95) [jfxrt.jar:?]
2018-09-18 10:08:13,337 ERROR [JavaFX Application Thread] (PreferencesTreeItem.java:86) - sh.isaac.komet.preferences.AttachmentActionPreferences
java.lang.ClassNotFoundException: sh.isaac.komet.preferences.AttachmentActionPreferences
at java.net.URLClassLoader.findClass(URLClassLoader.java:381) ~[?:1.8.0_144]
at java.lang.ClassLoader.loadClass(ClassLoader.java:424) ~[?:1.8.0_144]
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:335) ~[?:1.8.0_144]
at java.lang.ClassLoader.loadClass(ClassLoader.java:357) ~[?:1.8.0_144]
at java.lang.Class.forName0(Native Method) ~[?:1.8.0_144]
at java.lang.Class.forName(Class.java:264) ~[?:1.8.0_144]
at sh.isaac.komet.preferences.PreferencesTreeItem.from(PreferencesTreeItem.java:75) ~[komet-preferences-4.53-SNAPSHOT.jar:?]
at sh.isaac.komet.preferences.PreferencesTreeItem.<init>(PreferencesTreeItem.java:51) ~[komet-preferences-4.53-SNAPSHOT.jar:?]
at sh.isaac.komet.preferences.PreferencesTreeItem.from(PreferencesTreeItem.java:81) ~[komet-preferences-4.53-SNAPSHOT.jar:?]
at sh.isaac.komet.preferences.KometPreferencesImpl.loadPreferences(KometPreferencesImpl.java:63) ~[komet-preferences-4.53-SNAPSHOT.jar:?]
at sh.komet.fx.stage.MainApp.start(MainApp.java:150) ~[classes/:?]
at com.sun.javafx.application.LauncherImpl.lambda$launchApplication1$162(LauncherImpl.java:863) ~[jfxrt.jar:?]
at com.sun.javafx.application.PlatformImpl.lambda$runAndWait$175(PlatformImpl.java:326) ~[jfxrt.jar:?]
at com.sun.javafx.application.PlatformImpl.lambda$null$173(PlatformImpl.java:295) ~[jfxrt.jar:?]
at java.security.AccessController.doPrivileged(Native Method) ~[?:1.8.0_144]
at com.sun.javafx.application.PlatformImpl.lambda$runLater$174(PlatformImpl.java:294) ~[jfxrt.jar:?]
at com.sun.glass.ui.InvokeLaterDispatcher$Future.run(InvokeLaterDispatcher.java:95) [jfxrt.jar:?]
2018-09-18 10:08:13,342 ERROR [JavaFX Application Thread] (PreferencesTreeItem.java:86) - sh.isaac.komet.preferences.LogicActionPreferences
java.lang.ClassNotFoundException: sh.isaac.komet.preferences.LogicActionPreferences
at java.net.URLClassLoader.findClass(URLClassLoader.java:381) ~[?:1.8.0_144]
at java.lang.ClassLoader.loadClass(ClassLoader.java:424) ~[?:1.8.0_144]
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:335) ~[?:1.8.0_144]
at java.lang.ClassLoader.loadClass(ClassLoader.java:357) ~[?:1.8.0_144]
at java.lang.Class.forName0(Native Method) ~[?:1.8.0_144]
at java.lang.Class.forName(Class.java:264) ~[?:1.8.0_144]
at sh.isaac.komet.preferences.PreferencesTreeItem.from(PreferencesTreeItem.java:75) ~[komet-preferences-4.53-SNAPSHOT.jar:?]
at sh.isaac.komet.preferences.PreferencesTreeItem.<init>(PreferencesTreeItem.java:51) ~[komet-preferences-4.53-SNAPSHOT.jar:?]
at sh.isaac.komet.preferences.PreferencesTreeItem.from(PreferencesTreeItem.java:81) ~[komet-preferences-4.53-SNAPSHOT.jar:?]
at sh.isaac.komet.preferences.KometPreferencesImpl.loadPreferences(KometPreferencesImpl.java:63) ~[komet-preferences-4.53-SNAPSHOT.jar:?]
at sh.komet.fx.stage.MainApp.start(MainApp.java:150) ~[classes/:?]
at com.sun.javafx.application.LauncherImpl.lambda$launchApplication1$162(LauncherImpl.java:863) ~[jfxrt.jar:?]
at com.sun.javafx.application.PlatformImpl.lambda$runAndWait$175(PlatformImpl.java:326) ~[jfxrt.jar:?]
at com.sun.javafx.application.PlatformImpl.lambda$null$173(PlatformImpl.java:295) ~[jfxrt.jar:?]
at java.security.AccessController.doPrivileged(Native Method) ~[?:1.8.0_144]
at com.sun.javafx.application.PlatformImpl.lambda$runLater$174(PlatformImpl.java:294) ~[jfxrt.jar:?]
at com.sun.glass.ui.InvokeLaterDispatcher$Future.run(InvokeLaterDispatcher.java:95) [jfxrt.jar:?]

Saif Baig
September 18, 2018, 2:18 PM
Edited

Below is the error for the "No assembage nid available" when you run KOMET for the first time with the changesets. That error goes away if you close and reopen KOMET. The GeneralPreferences error always appears.

2018-09-18 10:17:21,476 ERROR [RunLevelControllerThread-1537280228156] (TaxonomyProvider.java:248) - error processing taxonomy update
java.lang.RuntimeException: No assemblage nid available for -2140332110 2cf4f983-5a4e-457f-9544-bff4a2ea12e8

Saif Baig
September 20, 2018, 3:05 PM

Though the error is still showing, the problems associated with it are gone. So this can be closed.

Assignee

Saif Baig

Reporter

Saif Baig

Labels

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Fix versions

Priority

Blocker
Configure