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ChemClipse Project
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Delete targets fails if a scan/peak contains NIST-DB entries #1722

Closed eselmeister closed 6 months ago

eselmeister commented 6 months ago 
!ENTRY org.eclipse.chemclipse.ux.extension.xxd.ui 2 0 2024-04-03 11:13:07.001
!MESSAGE While executing the operation, an exception occurred
!STACK 0
org.eclipse.core.commands.ExecutionException: While executing the operation, an exception occurred
    at org.eclipse.core.commands.operations.DefaultOperationHistory.execute(DefaultOperationHistory.java:496)
    at org.eclipse.chemclipse.ux.extension.xxd.ui.swt.ExtendedPeakScanListUI.deletePeaksOrIdentifications(ExtendedPeakScanListUI.java:525)
    at org.eclipse.chemclipse.ux.extension.xxd.ui.swt.ExtendedPeakScanListUI$10.widgetSelected(ExtendedPeakScanListUI.java:863)
    at org.eclipse.swt.widgets.TypedListener.handleEvent(TypedListener.java:252)
    at org.eclipse.swt.widgets.EventTable.sendEvent(EventTable.java:89)
    at org.eclipse.swt.widgets.Display.sendEvent(Display.java:5855)
    at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:1529)
    at org.eclipse.swt.widgets.Display.runDeferredEvents(Display.java:5065)
    at org.eclipse.swt.widgets.Display.readAndDispatch(Display.java:4517)
    at org.eclipse.e4.ui.internal.workbench.swt.PartRenderingEngine$5.run(PartRenderingEngine.java:1151)
    at org.eclipse.core.databinding.observable.Realm.runWithDefault(Realm.java:339)
    at org.eclipse.e4.ui.internal.workbench.swt.PartRenderingEngine.run(PartRenderingEngine.java:1042)
    at org.eclipse.e4.ui.internal.workbench.E4Workbench.createAndRunUI(E4Workbench.java:152)
    at org.eclipse.ui.internal.Workbench.lambda$3(Workbench.java:639)
    at org.eclipse.core.databinding.observable.Realm.runWithDefault(Realm.java:339)
    at org.eclipse.ui.internal.Workbench.createAndRunWorkbench(Workbench.java:546)
    at org.eclipse.ui.PlatformUI.createAndRunWorkbench(PlatformUI.java:173)
    at org.eclipse.chemclipse.rcp.app.ui.internal.support.ApplicationSupportDefault.start(ApplicationSupportDefault.java:25)
    at org.eclipse.chemclipse.rcp.app.ui.Application.start(Application.java:27)
    at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:208)
    at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:143)
    at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:109)
    at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:439)
    at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:271)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.base/java.lang.reflect.Method.invoke(Method.java:568)
    at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:651)
    at org.eclipse.equinox.launcher.Main.basicRun(Main.java:588)
    at org.eclipse.equinox.launcher.Main.run(Main.java:1459)
    at org.eclipse.equinox.launcher.Main.main(Main.java:1432)
Caused by: org.apache.commons.lang3.SerializationException: ClassNotFoundException while reading cloned object data
    at org.apache.commons.lang3.SerializationUtils.clone(SerializationUtils.java:152)
    at org.eclipse.chemclipse.ux.extension.xxd.ui.operations.DeleteScanTargetsOperation.execute(DeleteScanTargetsOperation.java:71)
    at org.eclipse.core.commands.operations.DefaultOperationHistory.execute(DefaultOperationHistory.java:488)
    ... 31 more
Caused by: java.lang.ClassNotFoundException: org.eclipse.chemclipse.msd.identifier.supplier.nist.core.support.NISTIdentificationTarget
    at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:641)
    at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:188)
    at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:520)
    at org.eclipse.osgi.internal.framework.ContextFinder.loadClass(ContextFinder.java:150)
    at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:520)
    at java.base/java.lang.Class.forName0(Native Method)
    at java.base/java.lang.Class.forName(Class.java:467)
    at org.apache.commons.lang3.SerializationUtils$ClassLoaderAwareObjectInputStream.resolveClass(SerializationUtils.java:108)
    at java.base/java.io.ObjectInputStream.readNonProxyDesc(ObjectInputStream.java:2045)
    at java.base/java.io.ObjectInputStream.readClassDesc(ObjectInputStream.java:1909)
    at java.base/java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:2235)
    at java.base/java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1744)
    at java.base/java.io.ObjectInputStream.readObject(ObjectInputStream.java:514)
    at java.base/java.io.ObjectInputStream.readObject(ObjectInputStream.java:472)
    at java.base/java.util.HashSet.readObject(HashSet.java:345)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.base/java.lang.reflect.Method.invoke(Method.java:568)
    at java.base/java.io.ObjectStreamClass.invokeReadObject(ObjectStreamClass.java:1231)
    at java.base/java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:2434)
    at java.base/java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:2268)
    at java.base/java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1744)
    at java.base/java.io.ObjectInputStream$FieldValues.<init>(ObjectInputStream.java:2617)
    at java.base/java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:2468)
    at java.base/java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:2268)
    at java.base/java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1744)
    at java.base/java.io.ObjectInputStream.readObject(ObjectInputStream.java:514)
    at java.base/java.io.ObjectInputStream.readObject(ObjectInputStream.java:472)
    at org.apache.commons.lang3.SerializationUtils.clone(SerializationUtils.java:148)
    ... 33 more

!ENTRY org.eclipse.chemclipse.ux.extension.xxd.ui 2 0 2024-04-03 11:13:11.763
!MESSAGE While executing the operation, an exception occurred
!STACK 0
org.eclipse.core.commands.ExecutionException: While executing the operation, an exception occurred
    at org.eclipse.core.commands.operations.DefaultOperationHistory.execute(DefaultOperationHistory.java:496)
    at org.eclipse.chemclipse.ux.extension.xxd.ui.swt.ExtendedPeakScanListUI.deletePeaksOrIdentifications(ExtendedPeakScanListUI.java:525)
    at org.eclipse.chemclipse.ux.extension.xxd.ui.swt.ExtendedPeakScanListUI$10.widgetSelected(ExtendedPeakScanListUI.java:863)
    at org.eclipse.swt.widgets.TypedListener.handleEvent(TypedListener.java:252)
    at org.eclipse.swt.widgets.EventTable.sendEvent(EventTable.java:89)
    at org.eclipse.swt.widgets.Display.sendEvent(Display.java:5855)
    at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:1529)
    at org.eclipse.swt.widgets.Display.runDeferredEvents(Display.java:5065)
    at org.eclipse.swt.widgets.Display.readAndDispatch(Display.java:4517)
    at org.eclipse.e4.ui.internal.workbench.swt.PartRenderingEngine$5.run(PartRenderingEngine.java:1151)
    at org.eclipse.core.databinding.observable.Realm.runWithDefault(Realm.java:339)
    at org.eclipse.e4.ui.internal.workbench.swt.PartRenderingEngine.run(PartRenderingEngine.java:1042)
    at org.eclipse.e4.ui.internal.workbench.E4Workbench.createAndRunUI(E4Workbench.java:152)
    at org.eclipse.ui.internal.Workbench.lambda$3(Workbench.java:639)
    at org.eclipse.core.databinding.observable.Realm.runWithDefault(Realm.java:339)
    at org.eclipse.ui.internal.Workbench.createAndRunWorkbench(Workbench.java:546)
    at org.eclipse.ui.PlatformUI.createAndRunWorkbench(PlatformUI.java:173)
    at org.eclipse.chemclipse.rcp.app.ui.internal.support.ApplicationSupportDefault.start(ApplicationSupportDefault.java:25)
    at org.eclipse.chemclipse.rcp.app.ui.Application.start(Application.java:27)
    at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:208)
    at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:143)
    at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:109)
    at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:439)
    at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:271)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.base/java.lang.reflect.Method.invoke(Method.java:568)
    at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:651)
    at org.eclipse.equinox.launcher.Main.basicRun(Main.java:588)
    at org.eclipse.equinox.launcher.Main.run(Main.java:1459)
    at org.eclipse.equinox.launcher.Main.main(Main.java:1432)
Caused by: org.apache.commons.lang3.SerializationException: ClassNotFoundException while reading cloned object data
    at org.apache.commons.lang3.SerializationUtils.clone(SerializationUtils.java:152)
    at org.eclipse.chemclipse.ux.extension.xxd.ui.operations.DeleteScanTargetsOperation.execute(DeleteScanTargetsOperation.java:71)
    at org.eclipse.core.commands.operations.DefaultOperationHistory.execute(DefaultOperationHistory.java:488)
    ... 31 more
Caused by: java.lang.ClassNotFoundException: org.eclipse.chemclipse.msd.identifier.supplier.nist.core.support.NISTIdentificationTarget
    at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:641)
    at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:188)
    at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:520)
    at org.eclipse.osgi.internal.framework.ContextFinder.loadClass(ContextFinder.java:150)
    at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:520)
    at java.base/java.lang.Class.forName0(Native Method)
    at java.base/java.lang.Class.forName(Class.java:467)
    at org.apache.commons.lang3.SerializationUtils$ClassLoaderAwareObjectInputStream.resolveClass(SerializationUtils.java:108)
    at java.base/java.io.ObjectInputStream.readNonProxyDesc(ObjectInputStream.java:2045)
    at java.base/java.io.ObjectInputStream.readClassDesc(ObjectInputStream.java:1909)
    at java.base/java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:2235)
    at java.base/java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1744)
    at java.base/java.io.ObjectInputStream.readObject(ObjectInputStream.java:514)
    at java.base/java.io.ObjectInputStream.readObject(ObjectInputStream.java:472)
    at java.base/java.util.HashSet.readObject(HashSet.java:345)
    at java.base/jdk.internal.reflect.GeneratedMethodAccessor53.invoke(Unknown Source)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.base/java.lang.reflect.Method.invoke(Method.java:568)
    at java.base/java.io.ObjectStreamClass.invokeReadObject(ObjectStreamClass.java:1231)
    at java.base/java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:2434)
    at java.base/java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:2268)
    at java.base/java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1744)
    at java.base/java.io.ObjectInputStream$FieldValues.<init>(ObjectInputStream.java:2617)
    at java.base/java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:2468)
    at java.base/java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:2268)
    at java.base/java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1744)
    at java.base/java.io.ObjectInputStream.readObject(ObjectInputStream.java:514)
    at java.base/java.io.ObjectInputStream.readObject(ObjectInputStream.java:472)
    at org.apache.commons.lang3.SerializationUtils.clone(SerializationUtils.java:148)
    ... 33 more