Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

MydasServlet initialisation fails to read config file. #5134

Closed
fdlk opened this issue Aug 9, 2016 · 1 comment
Closed

MydasServlet initialisation fails to read config file. #5134

fdlk opened this issue Aug 9, 2016 · 1 comment

Comments

@fdlk
Copy link
Contributor

fdlk commented Aug 9, 2016

Reproduce

Check out 1.21 branch, clean database and work dir, start molgenis in IntelliJ.

Expected

MydasServlet initializes without problems

Observed

10:02:51.559 [RMI TCP Connection(4)-127.0.0.1] ERROR u.a.e.mydas.controller.MydasServlet - Fatal Exception thrown at initialisation.  None of the datasources will be usable.
java.lang.IllegalArgumentException: is parameter must not be null
    at javax.xml.bind.helpers.AbstractUnmarshallerImpl.unmarshal(AbstractUnmarshallerImpl.java:200) ~[na:1.8.0_91]
    at uk.ac.ebi.mydas.configuration.ConfigurationManager.unmarshal(ConfigurationManager.java:41) ~[mydas-1.6.7.jar:1.6.7]
    at uk.ac.ebi.mydas.controller.DataSourceManager.loadConfiguration(DataSourceManager.java:80) ~[mydas-1.6.7.jar:1.6.7]
    at uk.ac.ebi.mydas.controller.DataSourceManager.init(DataSourceManager.java:62) ~[mydas-1.6.7.jar:1.6.7]
    at uk.ac.ebi.mydas.controller.MydasServlet.init(MydasServlet.java:214) ~[mydas-1.6.7.jar:1.6.7]
    at javax.servlet.GenericServlet.init(GenericServlet.java:158) [servlet-api.jar:3.1.FR]
    at org.apache.catalina.core.StandardWrapper.initServlet(StandardWrapper.java:1238) [catalina.jar:8.0.33]
    at org.apache.catalina.core.StandardWrapper.load(StandardWrapper.java:1041) [catalina.jar:8.0.33]
    at org.apache.catalina.core.StandardContext.loadOnStartup(StandardContext.java:4996) [catalina.jar:8.0.33]
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5285) [catalina.jar:8.0.33]
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:147) [catalina.jar:8.0.33]
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:725) [catalina.jar:8.0.33]
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:701) [catalina.jar:8.0.33]
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:717) [catalina.jar:8.0.33]
    at org.apache.catalina.startup.HostConfig.manageApp(HostConfig.java:1696) [catalina.jar:8.0.33]
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:1.8.0_91]
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[na:1.8.0_91]
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.8.0_91]
    at java.lang.reflect.Method.invoke(Method.java:498) ~[na:1.8.0_91]
    at org.apache.tomcat.util.modeler.BaseModelMBean.invoke(BaseModelMBean.java:300) [tomcat-coyote.jar:8.0.33]
    at com.sun.jmx.interceptor.DefaultMBeanServerInterceptor.invoke(DefaultMBeanServerInterceptor.java:819) [na:1.8.0_91]
    at com.sun.jmx.mbeanserver.JmxMBeanServer.invoke(JmxMBeanServer.java:801) [na:1.8.0_91]
    at org.apache.catalina.mbeans.MBeanFactory.createStandardContext(MBeanFactory.java:484) [catalina.jar:8.0.33]
    at org.apache.catalina.mbeans.MBeanFactory.createStandardContext(MBeanFactory.java:433) [catalina.jar:8.0.33]
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:1.8.0_91]
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[na:1.8.0_91]
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.8.0_91]
    at java.lang.reflect.Method.invoke(Method.java:498) ~[na:1.8.0_91]
    at org.apache.tomcat.util.modeler.BaseModelMBean.invoke(BaseModelMBean.java:300) [tomcat-coyote.jar:8.0.33]
    at com.sun.jmx.interceptor.DefaultMBeanServerInterceptor.invoke(DefaultMBeanServerInterceptor.java:819) [na:1.8.0_91]
    at com.sun.jmx.mbeanserver.JmxMBeanServer.invoke(JmxMBeanServer.java:801) [na:1.8.0_91]
    at javax.management.remote.rmi.RMIConnectionImpl.doOperation(RMIConnectionImpl.java:1468) [na:1.8.0_91]
    at javax.management.remote.rmi.RMIConnectionImpl.access$300(RMIConnectionImpl.java:76) [na:1.8.0_91]
    at javax.management.remote.rmi.RMIConnectionImpl$PrivilegedOperation.run(RMIConnectionImpl.java:1309) [na:1.8.0_91]
    at javax.management.remote.rmi.RMIConnectionImpl.doPrivilegedOperation(RMIConnectionImpl.java:1401) [na:1.8.0_91]
    at javax.management.remote.rmi.RMIConnectionImpl.invoke(RMIConnectionImpl.java:829) [na:1.8.0_91]
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:1.8.0_91]
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[na:1.8.0_91]
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.8.0_91]
    at java.lang.reflect.Method.invoke(Method.java:498) ~[na:1.8.0_91]
    at sun.rmi.server.UnicastServerRef.dispatch(UnicastServerRef.java:324) [na:1.8.0_91]
    at sun.rmi.transport.Transport$1.run(Transport.java:200) [na:1.8.0_91]
    at sun.rmi.transport.Transport$1.run(Transport.java:197) [na:1.8.0_91]
    at java.security.AccessController.doPrivileged(Native Method) [na:1.8.0_91]
    at sun.rmi.transport.Transport.serviceCall(Transport.java:196) [na:1.8.0_91]
    at sun.rmi.transport.tcp.TCPTransport.handleMessages(TCPTransport.java:568) [na:1.8.0_91]
    at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run0(TCPTransport.java:826) [na:1.8.0_91]
    at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.lambda$run$0(TCPTransport.java:683) [na:1.8.0_91]
    at java.security.AccessController.doPrivileged(Native Method) [na:1.8.0_91]
    at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run(TCPTransport.java:682) [na:1.8.0_91]
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) ~[na:1.8.0_91]
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) ~[na:1.8.0_91]
    at java.lang.Thread.run(Thread.java:745) ~[na:1.8.0_91]
@fdlk fdlk added the 1.21.4 label Aug 9, 2016
@fdlk fdlk changed the title MydasServlet initialisation fails MydasServlet initialisation fails to read config file. Aug 9, 2016
@fdlk
Copy link
Contributor Author

fdlk commented Aug 9, 2016

Solution is to run mvn clean install.

@fdlk fdlk closed this as completed Aug 9, 2016
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant