Details
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Type:
Bug
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: 9.0.2 Minor Release
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Labels:
-
Story Points:0.25
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Sprint:Fall 2018 Sprint 3
Description
On mac and linux (but not windows) I get an exception on the first startup after clearing preferences:
(does not seem to affect the program but I can see in the console)
ERROR c.a.i.p.IgbPreferencesLoadingOrchestrator - No value present
java.util.NoSuchElementException: No value present
(See attached file for the entire console print out)
This is not the case in IGB 9.0.0 or 9.0.1.
Attachments
Activity
| Field | Original Value | New Value |
|---|---|---|
| Comment |
[ From the console:
12:14:05.986 INFO org.amdatu.remote.AbstractComponent - Adding Remote Service Admin: [org.osgi.service.remoteserviceadmin.RemoteServiceAdmin] 12:14:05.992 INFO org.amdatu.remote.AbstractComponent - Configured export filter updated: (service.exported.interfaces=*) 12:14:05.993 INFO org.amdatu.remote.AbstractComponent - Configured import filter updated: (!(endpoint.framework.uuid=548aba5e-14ac-4631-8489-7d528e206830)) 12:14:05.996 INFO o.l.i.p.PairedReadPreprocessor - Initializaing PairedReadPreprocessor 12:14:06.289 INFO o.l.i.q.QuickloadDataProvider - Initializing Quickload Server http://lorainelab-quickload.scidas.org/rnaseq/ 12:14:06.315 INFO c.a.i.p.IgbPreferencesLoadingOrchestrator - Loading server preferences from the Java preferences subsystem 12:14:06.324 ERROR c.a.i.p.IgbPreferencesLoadingOrchestrator - No value present java.util.NoSuchElementException: No value present at java.util.Optional.get(Optional.java:135) ~[na:1.8.0_152] at com.affymetrix.igb.general.DataProviderManager.integrateUserPrefsToDefaultDataProvider(DataProviderManager.java:270) ~[na:na] at com.affymetrix.igb.general.DataProviderManager.initializeDataProvider(DataProviderManager.java:208) ~[na:na] at com.affymetrix.igb.prefs.IgbPreferencesLoadingOrchestrator.lambda$loadFromPersistenceStorage$248(IgbPreferencesLoadingOrchestrator.java:104) ~[na:na] at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:184) ~[na:1.8.0_152] at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193) ~[na:1.8.0_152] at java.util.Spliterators$ArraySpliterator.forEachRemaining(Spliterators.java:948) ~[na:1.8.0_152] at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481) ~[na:1.8.0_152] at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471) ~[na:1.8.0_152] at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:151) ~[na:1.8.0_152] at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:174) ~[na:1.8.0_152] at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234) ~[na:1.8.0_152] at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:418) ~[na:1.8.0_152] at com.affymetrix.igb.prefs.IgbPreferencesLoadingOrchestrator.loadFromPersistenceStorage(IgbPreferencesLoadingOrchestrator.java:102) ~[na:na] at com.affymetrix.igb.prefs.IgbPreferencesLoadingOrchestrator.loadIGBPrefs(IgbPreferencesLoadingOrchestrator.java:72) ~[na:na] at com.affymetrix.igb.prefs.IgbPreferencesLoadingOrchestrator.activate(IgbPreferencesLoadingOrchestrator.java:50) ~[na:na] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:1.8.0_152] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[na:1.8.0_152] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.8.0_152] at java.lang.reflect.Method.invoke(Method.java:498) ~[na:1.8.0_152] at org.apache.felix.scr.impl.helper.BaseMethod.invokeMethod(BaseMethod.java:231) ~[na:na] at org.apache.felix.scr.impl.helper.BaseMethod.access$500(BaseMethod.java:39) ~[na:na] at org.apache.felix.scr.impl.helper.BaseMethod$Resolved.invoke(BaseMethod.java:624) ~[na:na] at org.apache.felix.scr.impl.helper.BaseMethod.invoke(BaseMethod.java:508) ~[na:na] at org.apache.felix.scr.impl.helper.ActivateMethod.invoke(ActivateMethod.java:149) ~[na:na] at org.apache.felix.scr.impl.manager.SingleComponentManager.createImplementationObject(SingleComponentManager.java:315) ~[na:na] at org.apache.felix.scr.impl.manager.SingleComponentManager.createComponent(SingleComponentManager.java:127) ~[na:na] at org.apache.felix.scr.impl.manager.SingleComponentManager.getService(SingleComponentManager.java:871) ~[na:na] at org.apache.felix.scr.impl.manager.SingleComponentManager.getServiceInternal(SingleComponentManager.java:838) ~[na:na] at org.apache.felix.scr.impl.manager.AbstractComponentManager.activateInternal(AbstractComponentManager.java:850) ~[na:na] at org.apache.felix.scr.impl.manager.DependencyManager$SingleStaticCustomizer.addedService(DependencyManager.java:931) ~[na:na] at org.apache.felix.scr.impl.manager.DependencyManager$SingleStaticCustomizer.addedService(DependencyManager.java:895) ~[na:na] at org.apache.felix.scr.impl.manager.ServiceTracker$Tracked.customizerAdded(ServiceTracker.java:1480) ~[na:na] at org.apache.felix.scr.impl.manager.ServiceTracker$Tracked.customizerAdded(ServiceTracker.java:1401) ~[na:na] at org.apache.felix.scr.impl.manager.ServiceTracker$AbstractTracked.trackAdding(ServiceTracker.java:1210) ~[na:na] at org.apache.felix.scr.impl.manager.ServiceTracker$AbstractTracked.track(ServiceTracker.java:1148) ~[na:na] at org.apache.felix.scr.impl.manager.ServiceTracker$Tracked.serviceChanged(ServiceTracker.java:1432) ~[na:na] at org.apache.felix.framework.util.EventDispatcher.invokeServiceListenerCallback(EventDispatcher.java:987) ~[igb_exe.jar:na] at org.apache.felix.framework.util.EventDispatcher.fireEventImmediately(EventDispatcher.java:838) ~[igb_exe.jar:na] at org.apache.felix.framework.util.EventDispatcher.fireServiceEvent(EventDispatcher.java:545) ~[igb_exe.jar:na] at org.apache.felix.framework.Felix.fireServiceEvent(Felix.java:4560) ~[igb_exe.jar:na] at org.apache.felix.framework.Felix.registerService(Felix.java:3542) ~[igb_exe.jar:na] at org.apache.felix.framework.BundleContextImpl.registerService(BundleContextImpl.java:348) ~[igb_exe.jar:na] at org.apache.felix.scr.impl.manager.AbstractComponentManager$3.register(AbstractComponentManager.java:1003) ~[na:na] at org.apache.felix.scr.impl.manager.AbstractComponentManager$3.register(AbstractComponentManager.java:992) ~[na:na] at org.apache.felix.scr.impl.manager.RegistrationManager.changeRegistration(RegistrationManager.java:134) ~[na:na] at org.apache.felix.scr.impl.manager.AbstractComponentManager.registerService(AbstractComponentManager.java:1044) ~[na:na] at org.apache.felix.scr.impl.manager.AbstractComponentManager.activateInternal(AbstractComponentManager.java:841) ~[na:na] at org.apache.felix.scr.impl.manager.DependencyManager$SingleStaticCustomizer.addedService(DependencyManager.java:931) ~[na:na] at org.apache.felix.scr.impl.manager.DependencyManager$SingleStaticCustomizer.addedService(DependencyManager.java:895) ~[na:na] at org.apache.felix.scr.impl.manager.ServiceTracker$Tracked.customizerAdded(ServiceTracker.java:1480) ~[na:na] at org.apache.felix.scr.impl.manager.ServiceTracker$Tracked.customizerAdded(ServiceTracker.java:1401) ~[na:na] at org.apache.felix.scr.impl.manager.ServiceTracker$AbstractTracked.trackAdding(ServiceTracker.java:1210) ~[na:na] at org.apache.felix.scr.impl.manager.ServiceTracker$AbstractTracked.track(ServiceTracker.java:1148) ~[na:na] at org.apache.felix.scr.impl.manager.ServiceTracker$Tracked.serviceChanged(ServiceTracker.java:1432) ~[na:na] at org.apache.felix.framework.util.EventDispatcher.invokeServiceListenerCallback(EventDispatcher.java:987) ~[igb_exe.jar:na] at org.apache.felix.framework.util.EventDispatcher.fireEventImmediately(EventDispatcher.java:838) ~[igb_exe.jar:na] at org.apache.felix.framework.util.EventDispatcher.fireServiceEvent(EventDispatcher.java:545) ~[igb_exe.jar:na] at org.apache.felix.framework.Felix.fireServiceEvent(Felix.java:4560) ~[igb_exe.jar:na] at org.apache.felix.framework.Felix.registerService(Felix.java:3542) ~[igb_exe.jar:na] at org.apache.felix.framework.BundleContextImpl.registerService(BundleContextImpl.java:348) ~[igb_exe.jar:na] at org.apache.felix.scr.impl.manager.AbstractComponentManager$3.register(AbstractComponentManager.java:1003) ~[na:na] at org.apache.felix.scr.impl.manager.AbstractComponentManager$3.register(AbstractComponentManager.java:992) ~[na:na] at org.apache.felix.scr.impl.manager.RegistrationManager.changeRegistration(RegistrationManager.java:134) ~[na:na] at org.apache.felix.scr.impl.manager.AbstractComponentManager.registerService(AbstractComponentManager.java:1044) ~[na:na] at org.apache.felix.scr.impl.manager.AbstractComponentManager.activateInternal(AbstractComponentManager.java:841) ~[na:na] at org.apache.felix.scr.impl.manager.AbstractComponentManager.enable(AbstractComponentManager.java:419) ~[na:na] at org.apache.felix.scr.impl.config.ConfigurableComponentHolder.enableComponents(ConfigurableComponentHolder.java:376) ~[na:na] at org.apache.felix.scr.impl.BundleComponentActivator.initialize(BundleComponentActivator.java:172) ~[na:na] at org.apache.felix.scr.impl.BundleComponentActivator.<init>(BundleComponentActivator.java:120) ~[na:na] at org.apache.felix.scr.impl.Activator.loadComponents(Activator.java:258) ~[na:na] at org.apache.felix.scr.impl.Activator.access$000(Activator.java:45) ~[na:na] at org.apache.felix.scr.impl.Activator$ScrExtension.start(Activator.java:185) ~[na:na] at org.apache.felix.utils.extender.AbstractExtender.createExtension(AbstractExtender.java:259) ~[na:na] at org.apache.felix.utils.extender.AbstractExtender.modifiedBundle(AbstractExtender.java:232) ~[na:na] at org.osgi.util.tracker.BundleTracker$Tracked.customizerModified(BundleTracker.java:479) ~[igb_exe.jar:na] at org.osgi.util.tracker.BundleTracker$Tracked.customizerModified(BundleTracker.java:414) ~[igb_exe.jar:na] at org.osgi.util.tracker.AbstractTracked.track(AbstractTracked.java:232) ~[igb_exe.jar:na] at org.osgi.util.tracker.BundleTracker$Tracked.bundleChanged(BundleTracker.java:443) ~[igb_exe.jar:na] at org.apache.felix.framework.util.EventDispatcher.invokeBundleListenerCallback(EventDispatcher.java:913) ~[igb_exe.jar:na] at org.apache.felix.framework.util.EventDispatcher.fireEventImmediately(EventDispatcher.java:834) ~[igb_exe.jar:na] at org.apache.felix.framework.util.EventDispatcher.fireBundleEvent(EventDispatcher.java:516) ~[igb_exe.jar:na] at org.apache.felix.framework.Felix.fireBundleEvent(Felix.java:4544) ~[igb_exe.jar:na] at org.apache.felix.framework.Felix.startBundle(Felix.java:2166) ~[igb_exe.jar:na] at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1365) ~[igb_exe.jar:na] at org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:308) ~[igb_exe.jar:na] at java.lang.Thread.run(Thread.java:748) ~[na:1.8.0_152] 12:14:06.326 INFO c.a.i.p.IgbPreferencesLoadingOrchestrator - Completed loading server preferences from the Java preferences subsystem 12:14:06.377 INFO c.a.igb.IgbServiceDependencyManager - AnnotationContextMenuRegistryI now available. 12:14:06.377 INFO c.a.igb.IgbServiceDependencyManager - ChromosomeSynonymLookupService now available. 12:14:06.378 INFO c.a.igb.IgbServiceDependencyManager - Console Service now available. 12:14:06.378 INFO c.a.igb.IgbServiceDependencyManager - FrameManagerService now available. 12:14:06.378 INFO c.a.igb.IgbServiceDependencyManager - GenomeVersionSynonymLookupService now available. 12:14:06.378 INFO c.a.igb.IgbServiceDependencyManager - QuickloadFactory now available. 12:14:06.378 INFO c.a.igb.IgbServiceDependencyManager - SpeciesSynonymLookupService now available. 12:14:06.378 INFO c.a.igb.IgbServiceDependencyManager - Window Service now available. 12:14:06.378 INFO c.a.igb.IgbServiceDependencyManager - Igb Module Service Dependencies are now available. 12:14:06.379 INFO com.affymetrix.igb.Activator - Starting IGB ] |
| Attachment | Console_FirstStartupAfterResetPrefs.txt [ 14154 ] |
| Description |
On mac and linux (but not windows) I get an exception on the first startup after clearing preferences:
(does not seem to affect the program but I can see in the console) ERROR c.a.i.p.IgbPreferencesLoadingOrchestrator - No value present java.util.NoSuchElementException: No value present This is not the case in IGB 9.0.0 or 9.0.1. |
On mac and linux (but not windows) I get an exception on the first startup after clearing preferences:
(does not seem to affect the program but I can see in the console) ERROR c.a.i.p.IgbPreferencesLoadingOrchestrator - No value present java.util.NoSuchElementException: No value present (See attached file for the entire console print out) This is not the case in IGB 9.0.0 or 9.0.1. |
| Attachment | Error.PNG [ 14155 ] |
| Assignee | Ann Loraine [ aloraine ] | Sneha Ramesh Watharkar [ jdaly ] |
| Status | Open [ 1 ] | In Progress [ 3 ] |
Fixed the error:
You can see the work here -> https://bitbucket.org/swathark/integrated-genome-browser/branch/IGBF-1415-Fix
Ivory Blakley: Its a small fix. Please review or test once on Mac. I checked on Windows and the error is no more seen.
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Sneha Ramesh Watharkar [ jdaly ] | Ivory Blakley [ ieclabau ] |
| Assignee | Ivory Blakley [ ieclabau ] |
| Status | Needs 1st Level Review [ 10005 ] | Ready for Pull Request [ 10304 ] |
| Assignee | Sneha Ramesh Watharkar [ jdaly ] |
| Summary | Fix Error on startup after reseting preferences | Fix Error on startup after resetting preferences |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Assignee | Sneha Ramesh Watharkar [ jdaly ] | Ann Loraine [ aloraine ] |
| Fix Version/s | 9.0.2 Minor Release [ 10600 ] | |
| Story Points | 0.25 | |
| Labels | Intermediate |
| Status | Reviewing Pull Request [ 10303 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | Open [ 1 ] |
| Rank | Ranked higher |
| Rank | Ranked higher |
| Status | Open [ 1 ] | Needs 1st Level Review [ 10005 ] |
Needs functional testing on Mac before pull request can proceed.
| Assignee | Ann Loraine [ aloraine ] |
| Summary | Fix Error on startup after resetting preferences | Fix exception on startup after resetting preferences |
| Status | Needs 1st Level Review [ 10005 ] | Reviewing [ 10301 ] |
| Assignee | Nowlan Freese [ nfreese ] |
Tested on Mac
Appears to be fixed on Mac.
9.0.2 Behavior (Sneha fix)
User selects: Open Preferences Window icon > Other Options > Reset Preference to Defaults
-No error is shown in console
9.0.1 Behavior
User selects: Open Preferences Window icon > Other Options > Reset Preference to Defaults
-The error is shown in console
ERROR c.a.i.p.IgbPreferencesLoadingOrchestrator - No value present
java.util.NoSuchElementException: No value present
9.0.0 Behavior
User selects: Open Preferences Window icon > Other Options > Reset Preference to Defaults
-No error is shown in console
| Assignee | Nowlan Freese [ nfreese ] |
| Status | Reviewing [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Assignee | Sneha Ramesh Watharkar [ jdaly ] |
| Status | Ready for Pull Request [ 10304 ] | Reviewing Pull Request [ 10303 ] |
Re-reviewing pull request following validation that the fix works on Mac.
| Assignee | Sneha Ramesh Watharkar [ jdaly ] | Ann Loraine [ aloraine ] |
| Status | Reviewing Pull Request [ 10303 ] | Needs Testing [ 10002 ] |
Merged and moved to Needs Testing,
| Assignee | Ann Loraine [ aloraine ] |
Moving back. to "In Progress" (branch not ready for review as yet)
| Assignee | Pranav Sanjay Tambvekar [ ptambvek ] |
| Status | Needs Testing [ 10002 ] | Testing In Progress [ 10003 ] |
Tested on Windows:
no error observed.
>clone team-repo, build and run 'run_igb.bat' on master.
>Open Preferences Window icon > Other Options > Reset Preference to Defaults
>No error was shown in the console.
| Assignee | Pranav Sanjay Tambvekar [ ptambvek ] | Sneha Ramesh Watharkar [ jdaly ] |
| Resolution | Done [ 10000 ] | |
| Status | Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Workflow | Loraine Lab Workflow [ 18120 ] | Fall 2019 Workflow Update [ 19947 ] |
| Workflow | Fall 2019 Workflow Update [ 19947 ] | Revised Fall 2019 Workflow Update [ 22068 ] |
This error appears in Windows too. Attaching image for reference.
Assigning it to myself and working on that.