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rabix / bunny

[Legacy] Executor for CWL workflows. Executes sbg:draft-2 and CWL 1.0
http://rabix.io
Apache License 2.0
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Very large java stack traces generated in rabix composer logs #453

Open zymergen-mbarton opened 5 years ago

zymergen-mbarton commented 5 years ago

I always see these very large stack traces in the rabix composer output logs. Is there a way to fix this? About 50% of my coworkers whom use rabix composer see this, while the others don't.

WARNING: The following warnings have been detected: WARNING: HK2 service reification failed for [org.glassfish.jersey.message.internal.DataSourceProvider] with an exception:
MultiException stack 1 of 2
java.lang.NoClassDefFoundError: javax/activation/DataSource
    at java.base/java.lang.Class.getDeclaredConstructors0(Native Method)
    at java.base/java.lang.Class.privateGetDeclaredConstructors(Class.java:3110)
    at java.base/java.lang.Class.getDeclaredConstructors(Class.java:2314)
    at org.jvnet.hk2.internal.Utilities$3.run(Utilities.java:1311)
    at org.jvnet.hk2.internal.Utilities$3.run(Utilities.java:1307)
    at java.base/java.security.AccessController.doPrivileged(Native Method)
    at org.jvnet.hk2.internal.Utilities.getAllConstructors(Utilities.java:1307)
    at org.jvnet.hk2.internal.Utilities.findProducerConstructor(Utilities.java:1250)
    at org.jvnet.hk2.internal.DefaultClassAnalyzer.getConstructor(DefaultClassAnalyzer.java:82)
    at org.glassfish.jersey.internal.inject.JerseyClassAnalyzer.getConstructor(JerseyClassAnalyzer.java:144)
    at org.jvnet.hk2.internal.Utilities.getConstructor(Utilities.java:179)
    at org.jvnet.hk2.internal.ClazzCreator.initialize(ClazzCreator.java:129)
    at org.jvnet.hk2.internal.ClazzCreator.initialize(ClazzCreator.java:182)
    at org.jvnet.hk2.internal.SystemDescriptor.internalReify(SystemDescriptor.java:722)
    at org.jvnet.hk2.internal.SystemDescriptor.reify(SystemDescriptor.java:677)
    at org.jvnet.hk2.internal.ServiceLocatorImpl.reifyDescriptor(ServiceLocatorImpl.java:459)
    at org.jvnet.hk2.internal.ServiceLocatorImpl.narrow(ServiceLocatorImpl.java:2181)
    at org.jvnet.hk2.internal.ServiceLocatorImpl.access$1200(ServiceLocatorImpl.java:121)
    at org.jvnet.hk2.internal.ServiceLocatorImpl$9.compute(ServiceLocatorImpl.java:1325)
    at org.jvnet.hk2.internal.ServiceLocatorImpl$9.compute(ServiceLocatorImpl.java:1320)
    at org.glassfish.hk2.utilities.cache.LRUHybridCache$OriginThreadAwareFuture$1.call(LRUHybridCache.java:115)
    at org.glassfish.hk2.utilities.cache.LRUHybridCache$OriginThreadAwareFuture$1.call(LRUHybridCache.java:111)
    at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
    at org.glassfish.hk2.utilities.cache.LRUHybridCache$OriginThreadAwareFuture.run(LRUHybridCache.java:173)
    at org.glassfish.hk2.utilities.cache.LRUHybridCache.compute(LRUHybridCache.java:292)
    at org.jvnet.hk2.internal.ServiceLocatorImpl.internalGetAllServiceHandles(ServiceLocatorImpl.java:1382)
    at org.jvnet.hk2.internal.ServiceLocatorImpl.getAllServiceHandles(ServiceLocatorImpl.java:1307)
    at org.jvnet.hk2.internal.ServiceLocatorImpl.getAllServiceHandles(ServiceLocatorImpl.java:1296)
    at org.glassfish.jersey.internal.inject.Providers.getServiceHandles(Providers.java:354)
    at org.glassfish.jersey.internal.inject.Providers.getCustomProviders(Providers.java:201)
    at org.glassfish.jersey.message.internal.MessageBodyFactory.<init>(MessageBodyFactory.java:221)
    at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
    at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
    at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:488)
    at org.glassfish.hk2.utilities.reflection.ReflectionHelper.makeMe(ReflectionHelper.java:1129)
    at org.jvnet.hk2.internal.ClazzCreator.createMe(ClazzCreator.java:274)
    at org.jvnet.hk2.internal.ClazzCreator.create(ClazzCreator.java:368)
    at org.jvnet.hk2.internal.SystemDescriptor.create(SystemDescriptor.java:470)
    at org.jvnet.hk2.internal.SingletonContext$1.compute(SingletonContext.java:82)
    at org.jvnet.hk2.internal.SingletonContext$1.compute(SingletonContext.java:70)
    at org.glassfish.hk2.utilities.cache.Cache$OriginThreadAwareFuture$1.call(Cache.java:97)
    at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
    at org.glassfish.hk2.utilities.cache.Cache$OriginThreadAwareFuture.run(Cache.java:154)
    at org.glassfish.hk2.utilities.cache.Cache.compute(Cache.java:199)
    at org.jvnet.hk2.internal.SingletonContext.findOrCreate(SingletonContext.java:121)
    at org.jvnet.hk2.internal.Utilities.createService(Utilities.java:2065)
    at org.jvnet.hk2.internal.ServiceLocatorImpl.internalGetService(ServiceLocatorImpl.java:761)
    at org.jvnet.hk2.internal.ServiceLocatorImpl.getUnqualifiedService(ServiceLocatorImpl.java:768)
    at org.jvnet.hk2.internal.IterableProviderImpl.get(IterableProviderImpl.java:110)
    at org.glassfish.jersey.client.RequestProcessingInitializationStage.apply(RequestProcessingInitializationStage.java:97)
    at org.glassfish.jersey.client.RequestProcessingInitializationStage.apply(RequestProcessingInitializationStage.java:67)
    at org.glassfish.jersey.process.internal.Stages$LinkedStage.apply(Stages.java:308)
    at org.glassfish.jersey.process.internal.Stages.process(Stages.java:171)
    at org.glassfish.jersey.client.ClientRuntime$2.run(ClientRuntime.java:156)
    at org.glassfish.jersey.internal.Errors$1.call(Errors.java:271)
    at org.glassfish.jersey.internal.Errors$1.call(Errors.java:267)
    at org.glassfish.jersey.internal.Errors.process(Errors.java:315)
    at org.glassfish.jersey.internal.Errors.process(Errors.java:297)
    at org.glassfish.jersey.internal.Errors.process(Errors.java:267)
    at org.glassfish.jersey.process.internal.RequestScope.runInScope(RequestScope.java:340)
    at org.glassfish.jersey.client.ClientRuntime$3.run(ClientRuntime.java:209)
    at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:514)
    at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
    at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1167)
    at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:641)
    at java.base/java.lang.Thread.run(Thread.java:844)
Caused by: java.lang.ClassNotFoundException: javax.activation.DataSource
    at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:582)
    at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:185)
    at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:496)
    ... 67 more
MultiException stack 2 of 2
java.lang.IllegalArgumentException: Errors were discovered while reifying SystemDescriptor(
    implementation=org.glassfish.jersey.message.internal.DataSourceProvider
    contracts={javax.ws.rs.ext.MessageBodyReader,javax.ws.rs.ext.MessageBodyWriter}
    scope=javax.inject.Singleton
    qualifiers={}
    descriptorType=CLASS
    descriptorVisibility=NORMAL
    metadata=
    rank=0
    loader=org.glassfish.hk2.utilities.binding.AbstractBinder$2@16cd6a6b
    proxiable=null
    proxyForSameScope=null
    analysisName=null
    id=12
    locatorId=1
    identityHashCode=2047823520
    reified=false)
    at org.jvnet.hk2.internal.SystemDescriptor.reify(SystemDescriptor.java:688)
    at org.jvnet.hk2.internal.ServiceLocatorImpl.reifyDescriptor(ServiceLocatorImpl.java:459)
    at org.jvnet.hk2.internal.ServiceLocatorImpl.narrow(ServiceLocatorImpl.java:2181)
    at org.jvnet.hk2.internal.ServiceLocatorImpl.access$1200(ServiceLocatorImpl.java:121)
    at org.jvnet.hk2.internal.ServiceLocatorImpl$9.compute(ServiceLocatorImpl.java:1325)
    at org.jvnet.hk2.internal.ServiceLocatorImpl$9.compute(ServiceLocatorImpl.java:1320)
    at org.glassfish.hk2.utilities.cache.LRUHybridCache$OriginThreadAwareFuture$1.call(LRUHybridCache.java:115)
    at org.glassfish.hk2.utilities.cache.LRUHybridCache$OriginThreadAwareFuture$1.call(LRUHybridCache.java:111)
    at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
    at org.glassfish.hk2.utilities.cache.LRUHybridCache$OriginThreadAwareFuture.run(LRUHybridCache.java:173)
    at org.glassfish.hk2.utilities.cache.LRUHybridCache.compute(LRUHybridCache.java:292)
    at org.jvnet.hk2.internal.ServiceLocatorImpl.internalGetAllServiceHandles(ServiceLocatorImpl.java:1382)
    at org.jvnet.hk2.internal.ServiceLocatorImpl.getAllServiceHandles(ServiceLocatorImpl.java:1307)
    at org.jvnet.hk2.internal.ServiceLocatorImpl.getAllServiceHandles(ServiceLocatorImpl.java:1296)
    at org.glassfish.jersey.internal.inject.Providers.getServiceHandles(Providers.java:354)
    at org.glassfish.jersey.internal.inject.Providers.getCustomProviders(Providers.java:201)
    at org.glassfish.jersey.message.internal.MessageBodyFactory.<init>(MessageBodyFactory.java:221)
    at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
    at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
    at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:488)
    at org.glassfish.hk2.utilities.reflection.ReflectionHelper.makeMe(ReflectionHelper.java:1129)
    at org.jvnet.hk2.internal.ClazzCreator.createMe(ClazzCreator.java:274)
    at org.jvnet.hk2.internal.ClazzCreator.create(ClazzCreator.java:368)
    at org.jvnet.hk2.internal.SystemDescriptor.create(SystemDescriptor.java:470)
    at org.jvnet.hk2.internal.SingletonContext$1.compute(SingletonContext.java:82)
    at org.jvnet.hk2.internal.SingletonContext$1.compute(SingletonContext.java:70)
    at org.glassfish.hk2.utilities.cache.Cache$OriginThreadAwareFuture$1.call(Cache.java:97)
    at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
    at org.glassfish.hk2.utilities.cache.Cache$OriginThreadAwareFuture.run(Cache.java:154)
    at org.glassfish.hk2.utilities.cache.Cache.compute(Cache.java:199)
    at org.jvnet.hk2.internal.SingletonContext.findOrCreate(SingletonContext.java:121)
    at org.jvnet.hk2.internal.Utilities.createService(Utilities.java:2065)
    at org.jvnet.hk2.internal.ServiceLocatorImpl.internalGetService(ServiceLocatorImpl.java:761)
    at org.jvnet.hk2.internal.ServiceLocatorImpl.getUnqualifiedService(ServiceLocatorImpl.java:768)
    at org.jvnet.hk2.internal.IterableProviderImpl.get(IterableProviderImpl.java:110)
    at org.glassfish.jersey.client.RequestProcessingInitializationStage.apply(RequestProcessingInitializationStage.java:97)
    at org.glassfish.jersey.client.RequestProcessingInitializationStage.apply(RequestProcessingInitializationStage.java:67)
    at org.glassfish.jersey.process.internal.Stages$LinkedStage.apply(Stages.java:308)
    at org.glassfish.jersey.process.internal.Stages.process(Stages.java:171)
    at org.glassfish.jersey.client.ClientRuntime$2.run(ClientRuntime.java:156)
    at org.glassfish.jersey.internal.Errors$1.call(Errors.java:271)
    at org.glassfish.jersey.internal.Errors$1.call(Errors.java:267)
    at org.glassfish.jersey.internal.Errors.process(Errors.java:315)
    at org.glassfish.jersey.internal.Errors.process(Errors.java:297)
    at org.glassfish.jersey.internal.Errors.process(Errors.java:267)
    at org.glassfish.jersey.process.internal.RequestScope.runInScope(RequestScope.java:340)
    at org.glassfish.jersey.client.ClientRuntime$3.run(ClientRuntime.java:209)
    at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:514)
    at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
    at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1167)
    at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:641)
    at java.base/java.lang.Thread.run(Thread.java:844)
ghost commented 5 years ago

Thanks for reporting this. Are there any salient differences in the two groups of users? OS, OS build, java version? I'll move this to the Rabix Executor (Bunny repo)

zymergen-mbarton commented 5 years ago 
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by com.google.inject.internal.cglib.core.$ReflectUtils$1 (file:/Applications/rabix-composer.app/Contents/Resources/app.asar.unpacked/executor/lib/rabix-cli.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of com.google.inject.internal.cglib.core.$ReflectUtils$1
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release

We also see these errors too.