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knime-ip / knip

KNIME Image Processing Extension
https://www.knime.com/community/image-processing
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AP-21672: fix registration of LogService implementation #529

Closed bernd-wiswedel closed 2 months ago

bernd-wiswedel commented 3 months ago

Details are in the (private) KNIME AP ticket tracker (https://knime-com.atlassian.net/browse/AP-21672)

This fix registers the existing 'Plugin' definition with the class discovery, which was largely inspired from looking at other Service implementation and debugging code. There are more definitions, such as DefaultLabelingService, DefaultMemoryService, KNIPThreadService, which are probably also not properly registered/discovered. Given my limited knowledge about KNIP and scijava I refrain from changing it blindly.

This fix here fixes the concrete issue. On the AP side, starting with 5.2.6, there will be better error handling in case a 3rd party extension (like this one) causes trouble.

Full stack trace:
!MESSAGE An error occurred while automatically activating bundle org.knime.jsnippets (1649). !STACK 0
org.osgi.framework.BundleException: Exception in org.knime.base.node.jsnippet.JavaSnippetActivator.start() of bundle org.knime.jsnippets.
    at org.eclipse.osgi.internal.framework.BundleContextImpl.startActivator(BundleContextImpl.java:839)
    at org.eclipse.osgi.internal.framework.BundleContextImpl.start(BundleContextImpl.java:767)
    at org.eclipse.osgi.internal.framework.EquinoxBundle.startWorker0(EquinoxBundle.java:1032)
    at org.eclipse.osgi.internal.framework.EquinoxBundle$EquinoxModule.startWorker(EquinoxBundle.java:371)
    at org.eclipse.osgi.container.Module.doStart(Module.java:605)
    at org.eclipse.osgi.container.Module.start(Module.java:468)
    at org.eclipse.osgi.framework.util.SecureAction.start(SecureAction.java:513)
    at org.eclipse.osgi.internal.hooks.EclipseLazyStarter.postFindLocalClass(EclipseLazyStarter.java:117)
    at org.eclipse.osgi.internal.loader.classpath.ClasspathManager.findLocalClass(ClasspathManager.java:570)
    at org.eclipse.osgi.internal.loader.ModuleClassLoader.findLocalClass(ModuleClassLoader.java:335)
    at org.eclipse.osgi.internal.loader.BundleLoader.findLocalClass(BundleLoader.java:397)
    at org.eclipse.osgi.internal.loader.BundleLoader.findClass0(BundleLoader.java:500)
    at org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:416)
    at org.eclipse.osgi.internal.loader.ModuleClassLoader.loadClass(ModuleClassLoader.java:168)
    at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:525)
    at org.knime.bigdata.spark.node.StandardSparkNodeFactoryProvider.<init>(StandardSparkNodeFactoryProvider.java:215)
    at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:77)
    at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
    at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499)
    at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:480)
    at org.eclipse.core.internal.registry.osgi.RegistryStrategyOSGI.createExecutableExtension(RegistryStrategyOSGI.java:204)
    at org.eclipse.core.internal.registry.ExtensionRegistry.createExecutableExtension(ExtensionRegistry.java:920)
    at org.eclipse.core.internal.registry.ConfigurationElement.createExecutableExtension(ConfigurationElement.java:246)
    at org.eclipse.core.internal.registry.ConfigurationElementHandle.createExecutableExtension(ConfigurationElementHandle.java:63)
    at org.knime.bigdata.spark.core.version.SparkProviderRegistry.registerExtensions(SparkProviderRegistry.java:74)
    at org.knime.bigdata.spark.core.version.SparkProviderRegistry.registerExtensions(SparkProviderRegistry.java:46)
    at org.knime.bigdata.spark.core.node.SparkNodeFactoryRegistry.getInstance(SparkNodeFactoryRegistry.java:62)
    at org.knime.bigdata.spark.core.node.SparkNodeFactoryRegistry.getNodeIds(SparkNodeFactoryRegistry.java:114)
    at org.knime.bigdata.spark.core.node.SparkNodeSetFactory.getNodeFactoryIds(SparkNodeSetFactory.java:47)
    at org.knime.core.node.extension.NodeSetFactoryExtension.from(NodeSetFactoryExtension.java:296)
    at java.base/java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:197)
    at java.base/java.util.Spliterators$ArraySpliterator.forEachRemaining(Spliterators.java:992)
    at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:509)
    at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:499)
    at java.base/java.util.stream.Nodes$CollectorTask.doLeaf(Nodes.java:2183)
    at java.base/java.util.stream.Nodes$CollectorTask.doLeaf(Nodes.java:2149)
    at java.base/java.util.stream.AbstractTask.compute(AbstractTask.java:327)
    at java.base/java.util.concurrent.CountedCompleter.exec(CountedCompleter.java:754)
    at java.base/java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java:373)
    at java.base/java.util.concurrent.ForkJoinPool$WorkQueue.topLevelExec(ForkJoinPool.java:1182)
    at java.base/java.util.concurrent.ForkJoinPool.scan(ForkJoinPool.java:1655)
    at java.base/java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1622)
    at java.base/java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:165)
Caused by: java.lang.ExceptionInInitializerError
    at org.knime.knip.base.data.img.ImgPlusCellFactory.getDataType(ImgPlusCellFactory.java:116)
    at org.knime.core.data.DataTypeRegistry.availableDataTypes(DataTypeRegistry.java:227)
    at org.knime.core.data.convert.java.DataCellToJavaConverterRegistry.parseAnnotations(DataCellToJavaConverterRegistry.java:481)
    at org.knime.core.data.convert.java.DataCellToJavaConverterRegistry.<init>(DataCellToJavaConverterRegistry.java:436)
    at org.knime.core.data.convert.java.DataCellToJavaConverterRegistry.<clinit>(DataCellToJavaConverterRegistry.java:427)
    at org.knime.base.node.jsnippet.JavaSnippet.cacheCustomTypeClasspaths(JavaSnippet.java:1262)
    at org.knime.base.node.jsnippet.JavaSnippetActivator.start(JavaSnippetActivator.java:68)
    at org.eclipse.osgi.internal.framework.BundleContextImpl$2.run(BundleContextImpl.java:818)
    at org.eclipse.osgi.internal.framework.BundleContextImpl$2.run(BundleContextImpl.java:1)
    at java.base/java.security.AccessController.doPrivileged(AccessController.java:569)
    at org.eclipse.osgi.internal.framework.BundleContextImpl.startActivator(BundleContextImpl.java:810)
    ... 43 more
Caused by: java.lang.IllegalArgumentException: Invalid service: org.scijava.event.DefaultEventService
    at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:281)
    at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:232)
    at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:195)
    at org.scijava.service.ServiceHelper.loadServices(ServiceHelper.java:167)
    at org.scijava.Context.<init>(Context.java:281)
    at org.scijava.Context.<init>(Context.java:237)
    at org.scijava.Context.<init>(Context.java:213)
    at org.knime.knip.core.KNIPGateway.<init>(KNIPGateway.java:145)
    at org.knime.knip.core.KNIPGateway.getInstance(KNIPGateway.java:153)
    at org.knime.knip.core.KNIPGateway.cache(KNIPGateway.java:193)
    at org.knime.knip.base.data.img.ImgPlusCell.<clinit>(ImgPlusCell.java:120)
    ... 54 more
Caused by: java.lang.IllegalArgumentException: No compatible service: org.scijava.log.LogService
    at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:244)
    at org.scijava.service.ServiceHelper.createServiceRecursively(ServiceHelper.java:341)
    at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:270)
    ... 64 more

AP-21672 (Broken Community Extension might break PortType#availablePortTypes (should try-catch ExceptionInInitializationError))

gab1one commented 3 months ago

Mhm this seems to be caused by a bug in the KNIP build system, these plugin / service registrations should be discovered from annotations and added to the plugin jar. Will investigate this .