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  1. Jalview
  2. JAL-3243

Problem with PDB free text lookup / jersey/javax.ws.rs problem

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    Details

    • Type: Bug
    • Status: Closed
    • Priority: Minor
    • Resolution: Fixed
    • Affects Version/s: None
    • Fix Version/s: 2.11.0
    • Component/s: None
    • Labels:

      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)

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            Assignee:
            soares Ben Soares
            Reporter:
            soares Ben Soares
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              Created:
              Updated:
              Resolved: