Details
Description
Big stacktrace of a problem when using the free text search for a PDB lookup. This seems to be caused by a mismatch between api (javax.ws.rs-api-2.1.1.jar) and implementation of (jersey-{core,client,json}-1.19.jar).
Fix via updated and correct API jars in branch with this issue number.
java.lang.ExceptionInInitializerError
at com.sun.jersey.json.impl.provider.entity.JSONRootElementProvider$Wadl.<init>(JSONRootElementProvider.java:138)
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:490)
at com.sun.jersey.core.spi.component.ComponentConstructor._getInstance(ComponentConstructor.java:210)
at com.sun.jersey.core.spi.component.ComponentConstructor.getInstance(ComponentConstructor.java:180)
at com.sun.jersey.core.spi.component.ProviderFactory.__getComponentProvider(ProviderFactory.java:166)
at com.sun.jersey.core.spi.component.ProviderFactory.getComponentProvider(ProviderFactory.java:137)
at com.sun.jersey.core.spi.component.ProviderServices.getComponent(ProviderServices.java:283)
at com.sun.jersey.core.spi.component.ProviderServices.getServices(ProviderServices.java:163)
at com.sun.jersey.core.spi.factory.MessageBodyFactory.initReaders(MessageBodyFactory.java:176)
at com.sun.jersey.core.spi.factory.MessageBodyFactory.init(MessageBodyFactory.java:162)
at com.sun.jersey.api.client.Client.init(Client.java:343)
at com.sun.jersey.api.client.Client.access$000(Client.java:119)
at com.sun.jersey.api.client.Client$1.f(Client.java:192)
at com.sun.jersey.api.client.Client$1.f(Client.java:188)
at com.sun.jersey.spi.inject.Errors.processWithErrors(Errors.java:193)
at com.sun.jersey.api.client.Client.<init>(Client.java:188)
at com.sun.jersey.api.client.Client.<init>(Client.java:171)
at com.sun.jersey.api.client.Client.create(Client.java:683)
at jalview.fts.service.pdb.PDBFTSRestClient.executeRequest(PDBFTSRestClient.java:83)
at jalview.fts.service.pdb.PDBFTSPanel$1.run(PDBFTSPanel.java:99)
Caused by: java.lang.RuntimeException: java.lang.ClassNotFoundException: org.glassfish.jersey.internal.RuntimeDelegateImpl
at javax.ws.rs.ext.RuntimeDelegate.findDelegate(RuntimeDelegate.java:130)
at javax.ws.rs.ext.RuntimeDelegate.getInstance(RuntimeDelegate.java:97)
at javax.ws.rs.core.MediaType.valueOf(MediaType.java:172)
at com.sun.jersey.core.header.MediaTypes.<clinit>(MediaTypes.java:65)
... 23 more
Caused by: java.lang.ClassNotFoundException: org.glassfish.jersey.internal.RuntimeDelegateImpl
at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:583)
at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:178)
at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:521)
at java.base/java.lang.Class.forName0(Native Method)
at java.base/java.lang.Class.forName(Class.java:315)
at javax.ws.rs.ext.FactoryFinder.newInstance(FactoryFinder.java:87)
at javax.ws.rs.ext.FactoryFinder.find(FactoryFinder.java:185)
at javax.ws.rs.ext.RuntimeDelegate.findDelegate(RuntimeDelegate.java:112)
... 26 more
Exception in thread "Thread-18" java.lang.NoClassDefFoundError: Could not initialize class com.sun.jersey.core.header.MediaTypes
at com.sun.jersey.core.spi.factory.MessageBodyFactory.initReaders(MessageBodyFactory.java:182)
at com.sun.jersey.core.spi.factory.MessageBodyFactory.initReaders(MessageBodyFactory.java:176)
at com.sun.jersey.core.spi.factory.MessageBodyFactory.init(MessageBodyFactory.java:162)
at com.sun.jersey.api.client.Client.init(Client.java:343)
at com.sun.jersey.api.client.Client.access$000(Client.java:119)
at com.sun.jersey.api.client.Client$1.f(Client.java:192)
at com.sun.jersey.api.client.Client$1.f(Client.java:188)
at com.sun.jersey.spi.inject.Errors.processWithErrors(Errors.java:193)
at com.sun.jersey.api.client.Client.<init>(Client.java:188)
at com.sun.jersey.api.client.Client.<init>(Client.java:171)
at com.sun.jersey.api.client.Client.create(Client.java:683)
at jalview.fts.service.pdb.PDBFTSRestClient.executeRequest(PDBFTSRestClient.java:83)
at jalview.fts.service.pdb.PDBFTSPanel$1.run(PDBFTSPanel.java:99)
Fix via updated and correct API jars in branch with this issue number.
java.lang.ExceptionInInitializerError
at com.sun.jersey.json.impl.provider.entity.JSONRootElementProvider$Wadl.<init>(JSONRootElementProvider.java:138)
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:490)
at com.sun.jersey.core.spi.component.ComponentConstructor._getInstance(ComponentConstructor.java:210)
at com.sun.jersey.core.spi.component.ComponentConstructor.getInstance(ComponentConstructor.java:180)
at com.sun.jersey.core.spi.component.ProviderFactory.__getComponentProvider(ProviderFactory.java:166)
at com.sun.jersey.core.spi.component.ProviderFactory.getComponentProvider(ProviderFactory.java:137)
at com.sun.jersey.core.spi.component.ProviderServices.getComponent(ProviderServices.java:283)
at com.sun.jersey.core.spi.component.ProviderServices.getServices(ProviderServices.java:163)
at com.sun.jersey.core.spi.factory.MessageBodyFactory.initReaders(MessageBodyFactory.java:176)
at com.sun.jersey.core.spi.factory.MessageBodyFactory.init(MessageBodyFactory.java:162)
at com.sun.jersey.api.client.Client.init(Client.java:343)
at com.sun.jersey.api.client.Client.access$000(Client.java:119)
at com.sun.jersey.api.client.Client$1.f(Client.java:192)
at com.sun.jersey.api.client.Client$1.f(Client.java:188)
at com.sun.jersey.spi.inject.Errors.processWithErrors(Errors.java:193)
at com.sun.jersey.api.client.Client.<init>(Client.java:188)
at com.sun.jersey.api.client.Client.<init>(Client.java:171)
at com.sun.jersey.api.client.Client.create(Client.java:683)
at jalview.fts.service.pdb.PDBFTSRestClient.executeRequest(PDBFTSRestClient.java:83)
at jalview.fts.service.pdb.PDBFTSPanel$1.run(PDBFTSPanel.java:99)
Caused by: java.lang.RuntimeException: java.lang.ClassNotFoundException: org.glassfish.jersey.internal.RuntimeDelegateImpl
at javax.ws.rs.ext.RuntimeDelegate.findDelegate(RuntimeDelegate.java:130)
at javax.ws.rs.ext.RuntimeDelegate.getInstance(RuntimeDelegate.java:97)
at javax.ws.rs.core.MediaType.valueOf(MediaType.java:172)
at com.sun.jersey.core.header.MediaTypes.<clinit>(MediaTypes.java:65)
... 23 more
Caused by: java.lang.ClassNotFoundException: org.glassfish.jersey.internal.RuntimeDelegateImpl
at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:583)
at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:178)
at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:521)
at java.base/java.lang.Class.forName0(Native Method)
at java.base/java.lang.Class.forName(Class.java:315)
at javax.ws.rs.ext.FactoryFinder.newInstance(FactoryFinder.java:87)
at javax.ws.rs.ext.FactoryFinder.find(FactoryFinder.java:185)
at javax.ws.rs.ext.RuntimeDelegate.findDelegate(RuntimeDelegate.java:112)
... 26 more
Exception in thread "Thread-18" java.lang.NoClassDefFoundError: Could not initialize class com.sun.jersey.core.header.MediaTypes
at com.sun.jersey.core.spi.factory.MessageBodyFactory.initReaders(MessageBodyFactory.java:182)
at com.sun.jersey.core.spi.factory.MessageBodyFactory.initReaders(MessageBodyFactory.java:176)
at com.sun.jersey.core.spi.factory.MessageBodyFactory.init(MessageBodyFactory.java:162)
at com.sun.jersey.api.client.Client.init(Client.java:343)
at com.sun.jersey.api.client.Client.access$000(Client.java:119)
at com.sun.jersey.api.client.Client$1.f(Client.java:192)
at com.sun.jersey.api.client.Client$1.f(Client.java:188)
at com.sun.jersey.spi.inject.Errors.processWithErrors(Errors.java:193)
at com.sun.jersey.api.client.Client.<init>(Client.java:188)
at com.sun.jersey.api.client.Client.<init>(Client.java:171)
at com.sun.jersey.api.client.Client.create(Client.java:683)
at jalview.fts.service.pdb.PDBFTSRestClient.executeRequest(PDBFTSRestClient.java:83)
at jalview.fts.service.pdb.PDBFTSPanel$1.run(PDBFTSPanel.java:99)