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Cite the AMDIS paper #603

Merged
merged 1 commit into from
Feb 14, 2025
Merged

Cite the AMDIS paper #603

merged 1 commit into from
Feb 14, 2025

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Mailaender
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@eselmeister eselmeister merged commit 2d79bce into OpenChrom:develop Feb 14, 2025
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@Mailaender Mailaender deleted the amdis-literature branch February 14, 2025 16:09
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I didn't check the code in detail. Reading the bytes fails:

!ENTRY net.openchrom.chromatogram.msd.peak.detector.supplier.amdis 2 0 2025-02-15 16:14:48.496
!MESSAGE Cannot invoke "java.io.InputStream.readAllBytes()" because the return value of "java.lang.Class.getResourceAsStream(String)" is null
!STACK 0
java.lang.NullPointerException: Cannot invoke "java.io.InputStream.readAllBytes()" because the return value of "java.lang.Class.getResourceAsStream(String)" is null
	at net.openchrom.chromatogram.msd.peak.detector.supplier.amdis.settings.AbstractProcessSettings.createLiteratureReference(AbstractProcessSettings.java:130)
	at net.openchrom.chromatogram.msd.peak.detector.supplier.amdis.settings.AbstractProcessSettings.getLiteratureReferences(AbstractProcessSettings.java:122)
	at org.eclipse.chemclipse.chromatogram.msd.peak.detector.core.PeakDetectorMSD.getPeakDetectorSupport(PeakDetectorMSD.java:134)
	at org.eclipse.chemclipse.chromatogram.msd.peak.detector.core.PeakDetectorMSDProcessTypeSupplier.getProcessorSuppliers(PeakDetectorMSDProcessTypeSupplier.java:48)
	at org.eclipse.chemclipse.processing.internal.OSGiProcessSupplierContext.addProcessTypeSupplier(OSGiProcessSupplierContext.java:68)
	at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103)
	at java.base/java.lang.reflect.Method.invoke(Method.java:580)
	at org.apache.felix.scr.impl.inject.methods.BaseMethod.invokeMethod(BaseMethod.java:257)
	at org.apache.felix.scr.impl.inject.methods.BaseMethod.access$500(BaseMethod.java:41)
	at org.apache.felix.scr.impl.inject.methods.BaseMethod$Resolved.invoke(BaseMethod.java:701)
	at org.apache.felix.scr.impl.inject.methods.BaseMethod.invoke(BaseMethod.java:544)
	at org.apache.felix.scr.impl.inject.methods.BindMethod.invoke(BindMethod.java:42)
	at org.apache.felix.scr.impl.manager.DependencyManager.doInvokeBindMethod(DependencyManager.java:2099)
	at org.apache.felix.scr.impl.manager.DependencyManager.bindDependency(DependencyManager.java:1916)
	at org.apache.felix.scr.impl.manager.DependencyManager.bind(DependencyManager.java:1903)
	at org.apache.felix.scr.impl.manager.SingleComponentManager.createImplementationObject(SingleComponentManager.java:320)
	at org.apache.felix.scr.impl.manager.SingleComponentManager.createComponent(SingleComponentManager.java:115)
	at org.apache.felix.scr.impl.manager.SingleComponentManager.getService(SingleComponentManager.java:1002)
	at org.apache.felix.scr.impl.manager.SingleComponentManager.getServiceInternal(SingleComponentManager.java:975)
	at org.apache.felix.scr.impl.manager.SingleComponentManager.getService(SingleComponentManager.java:920)
	at org.eclipse.osgi.internal.serviceregistry.ServiceFactoryUse$1.run(ServiceFactoryUse.java:226)
	at java.base/java.security.AccessController.doPrivileged(AccessController.java:319)
	at org.eclipse.osgi.internal.serviceregistry.ServiceFactoryUse.factoryGetService(ServiceFactoryUse.java:223)
	at org.eclipse.osgi.internal.serviceregistry.ServiceFactoryUse.getService(ServiceFactoryUse.java:118)
	at org.eclipse.osgi.internal.serviceregistry.ServiceConsumer$2.getService(ServiceConsumer.java:48)
	at org.eclipse.osgi.internal.serviceregistry.ServiceRegistrationImpl.getService(ServiceRegistrationImpl.java:580)
	at org.eclipse.osgi.internal.serviceregistry.ServiceRegistry.getService(ServiceRegistry.java:548)
	at org.eclipse.osgi.internal.framework.BundleContextImpl.getService(BundleContextImpl.java:672)
	at org.osgi.util.tracker.ServiceTracker.addingService(ServiceTracker.java:419)
	at org.osgi.util.tracker.ServiceTracker$Tracked.customizerAdding(ServiceTracker.java:947)
	at org.osgi.util.tracker.ServiceTracker$Tracked.customizerAdding(ServiceTracker.java:1)
	at org.osgi.util.tracker.AbstractTracked.trackAdding(AbstractTracked.java:257)
	at org.osgi.util.tracker.AbstractTracked.trackInitial(AbstractTracked.java:184)
	at org.osgi.util.tracker.ServiceTracker.open(ServiceTracker.java:324)
	at org.osgi.util.tracker.ServiceTracker.open(ServiceTracker.java:267)
	at org.eclipse.chemclipse.ux.extension.xxd.ui.Activator.startServices(Activator.java:167)
	at org.eclipse.chemclipse.ux.extension.xxd.ui.Activator.start(Activator.java:63)
	at org.eclipse.osgi.internal.framework.BundleContextImpl$2.run(BundleContextImpl.java:833)
	at org.eclipse.osgi.internal.framework.BundleContextImpl$2.run(BundleContextImpl.java:1)
	at java.base/java.security.AccessController.doPrivileged(AccessController.java:571)
	at org.eclipse.osgi.internal.framework.BundleContextImpl.startActivator(BundleContextImpl.java:825)
	at org.eclipse.osgi.internal.framework.BundleContextImpl.start(BundleContextImpl.java:775)
	at org.eclipse.osgi.internal.framework.EquinoxBundle.startWorker0(EquinoxBundle.java:1057)
	at org.eclipse.osgi.internal.framework.EquinoxBundle$EquinoxModule.startWorker(EquinoxBundle.java:387)
	at org.eclipse.osgi.container.Module.doStart(Module.java:639)
	at org.eclipse.osgi.container.Module.start(Module.java:498)
	at org.eclipse.osgi.framework.util.SecureAction.start(SecureAction.java:528)
	at org.eclipse.osgi.internal.hooks.EclipseLazyStarter.postFindLocalClass(EclipseLazyStarter.java:122)
	at org.eclipse.osgi.internal.loader.classpath.ClasspathManager.findLocalClass(ClasspathManager.java:620)
	at org.eclipse.osgi.internal.loader.ModuleClassLoader.findLocalClass(ModuleClassLoader.java:348)
	at org.eclipse.osgi.internal.loader.BundleLoader.findLocalClass(BundleLoader.java:414)
	at org.eclipse.osgi.internal.loader.BundleLoader.findClass0(BundleLoader.java:520)
	at org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:434)
	at org.eclipse.osgi.internal.loader.ModuleClassLoader.loadClass(ModuleClassLoader.java:174)
	at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:526)
	at org.eclipse.osgi.internal.framework.EquinoxBundle.loadClass(EquinoxBundle.java:643)
	at org.eclipse.e4.ui.internal.workbench.ReflectionContributionFactory.createFromBundle(ReflectionContributionFactory.java:88)
	at org.eclipse.e4.ui.internal.workbench.ReflectionContributionFactory.doCreate(ReflectionContributionFactory.java:59)
	at org.eclipse.e4.ui.internal.workbench.ReflectionContributionFactory.create(ReflectionContributionFactory.java:42)
	at org.eclipse.e4.ui.internal.workbench.addons.HandlerProcessingAddon.processActiveHandler(HandlerProcessingAddon.java:134)
	at org.eclipse.e4.ui.internal.workbench.addons.HandlerProcessingAddon.postConstruct(HandlerProcessingAddon.java:52)
	at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103)
	at java.base/java.lang.reflect.Method.invoke(Method.java:580)
	at org.eclipse.e4.core.internal.di.MethodRequestor.execute(MethodRequestor.java:56)
	at org.eclipse.e4.core.internal.di.InjectorImpl.processAnnotated(InjectorImpl.java:977)
	at org.eclipse.e4.core.internal.di.InjectorImpl.internalInject(InjectorImpl.java:139)
	at org.eclipse.e4.core.internal.di.InjectorImpl.internalMake(InjectorImpl.java:386)
	at org.eclipse.e4.core.internal.di.InjectorImpl.make(InjectorImpl.java:326)
	at org.eclipse.e4.core.contexts.ContextInjectionFactory.make(ContextInjectionFactory.java:228)
	at org.eclipse.e4.ui.internal.workbench.ReflectionContributionFactory.createFromBundle(ReflectionContributionFactory.java:93)
	at org.eclipse.e4.ui.internal.workbench.ReflectionContributionFactory.doCreate(ReflectionContributionFactory.java:59)
	at org.eclipse.e4.ui.internal.workbench.ReflectionContributionFactory.create(ReflectionContributionFactory.java:37)
	at org.eclipse.e4.ui.internal.workbench.swt.E4Application.createE4Workbench(E4Application.java:273)
	at org.eclipse.ui.internal.Workbench.lambda$3(Workbench.java:592)
	at org.eclipse.core.databinding.observable.Realm.runWithDefault(Realm.java:339)
	at org.eclipse.ui.internal.Workbench.createAndRunWorkbench(Workbench.java:570)
	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.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103)
	at java.base/java.lang.reflect.Method.invoke(Method.java:580)
	at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:668)
	at org.eclipse.equinox.launcher.Main.basicRun(Main.java:605)
	at org.eclipse.equinox.launcher.Main.run(Main.java:1481)
	at org.eclipse.equinox.launcher.Main.main(Main.java:1454)

eselmeister added a commit that referenced this pull request Feb 15, 2025
@eselmeister
Amend #603 - Cite the AMDIS paper
8e2f1fb
@eselmeister
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The given file name differs from the DOI. The fix has been pushed above.

@Mailaender
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It caused problems with the GitHub actions year linter, so I renamed it, but forgot to update in source code.

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@Mailaender @eselmeister