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Can't create dataset via API (DatasetServiceBean.isIdentifierUniqueInDatabase) #3855

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pdurbin opened this issue May 24, 2017 · 5 comments
Closed

Can't create dataset via API (DatasetServiceBean.isIdentifierUniqueInDatabase) #3855

pdurbin opened this issue May 24, 2017 · 5 comments
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@kcondon
Labels
Feature: API Type: Bug a defect
Milestone
4.6.2 - Tabular M...

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@pdurbin
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pdurbin commented May 24, 2017

As of 2054db2 on the "develop" branch (we're close to tagging 4.6.2) I can't create a dataset via API. I'm using the testCreateDataset in DatasetsIT.java. Here's the stacktrace, which has something about DatasetServiceBean.isIdentifierUniqueInDatabase:

[2017-05-24T15:46:04.112-0400] [glassfish 4.1] [WARNING] [AS-EJB-00056] [javax.enterprise.ejb.container] [tid: _ThreadID=106 _ThreadName=http-listener-1(5)] [timeMillis: 1495655164112] [levelValue: 900] [[
  A system exception occurred during an invocation on EJB DatasetServiceBean, method: public boolean edu.harvard.iq.dataverse.DatasetServiceBean.isIdentifierUniqueInDatabase(java.lang.String,java.lang.String,java.lang.String,java.lang.String)]]

[2017-05-24T15:46:04.113-0400] [glassfish 4.1] [WARNING] [] [javax.enterprise.ejb.container] [tid: _ThreadID=106 _ThreadName=http-listener-1(5)] [timeMillis: 1495655164113] [levelValue: 900] [[
  
javax.ejb.TransactionRolledbackLocalException: Exception thrown from bean
	at com.sun.ejb.containers.EJBContainerTransactionManager.checkExceptionClientTx(EJBContainerTransactionManager.java:662)
	at com.sun.ejb.containers.EJBContainerTransactionManager.postInvokeTx(EJBContainerTransactionManager.java:507)
	at com.sun.ejb.containers.BaseContainer.postInvokeTx(BaseContainer.java:4566)
	at com.sun.ejb.containers.BaseContainer.postInvoke(BaseContainer.java:2074)
	at com.sun.ejb.containers.BaseContainer.postInvoke(BaseContainer.java:2044)
	at com.sun.ejb.containers.EJBLocalObjectInvocationHandler.invoke(EJBLocalObjectInvocationHandler.java:220)
	at com.sun.ejb.containers.EJBLocalObjectInvocationHandlerDelegate.invoke(EJBLocalObjectInvocationHandlerDelegate.java:88)
	at com.sun.proxy.$Proxy451.isIdentifierUniqueInDatabase(Unknown Source)
	at edu.harvard.iq.dataverse.__EJB31_Generated__DatasetServiceBean__Intf____Bean__.isIdentifierUniqueInDatabase(Unknown Source)
	at edu.harvard.iq.dataverse.engine.command.impl.CreateDatasetCommand.execute(CreateDatasetCommand.java:78)
	at edu.harvard.iq.dataverse.engine.command.impl.CreateDatasetCommand.execute(CreateDatasetCommand.java:31)
	at edu.harvard.iq.dataverse.EjbDataverseEngine.submit(EjbDataverseEngine.java:207)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.glassfish.ejb.security.application.EJBSecurityManager.runMethod(EJBSecurityManager.java:1081)
	at org.glassfish.ejb.security.application.EJBSecurityManager.invoke(EJBSecurityManager.java:1153)
	at com.sun.ejb.containers.BaseContainer.invokeBeanMethod(BaseContainer.java:4786)
	at com.sun.ejb.EjbInvocation.invokeBeanMethod(EjbInvocation.java:656)
	at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:822)
	at com.sun.ejb.EjbInvocation.proceed(EjbInvocation.java:608)
	at org.jboss.weld.ejb.AbstractEJBRequestScopeActivationInterceptor.aroundInvoke(AbstractEJBRequestScopeActivationInterceptor.java:46)
	at org.jboss.weld.ejb.SessionBeanInterceptor.aroundInvoke(SessionBeanInterceptor.java:52)
	at sun.reflect.GeneratedMethodAccessor106.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at com.sun.ejb.containers.interceptors.AroundInvokeInterceptor.intercept(InterceptorManager.java:883)
	at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:822)
	at com.sun.ejb.EjbInvocation.proceed(EjbInvocation.java:608)
	at com.sun.ejb.containers.interceptors.SystemInterceptorProxy.doCall(SystemInterceptorProxy.java:163)
	at com.sun.ejb.containers.interceptors.SystemInterceptorProxy.aroundInvoke(SystemInterceptorProxy.java:140)
	at sun.reflect.GeneratedMethodAccessor108.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at com.sun.ejb.containers.interceptors.AroundInvokeInterceptor.intercept(InterceptorManager.java:883)
	at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:822)
	at com.sun.ejb.containers.interceptors.InterceptorManager.intercept(InterceptorManager.java:369)
	at com.sun.ejb.containers.BaseContainer.__intercept(BaseContainer.java:4758)
	at com.sun.ejb.containers.BaseContainer.intercept(BaseContainer.java:4746)
	at com.sun.ejb.containers.EJBLocalObjectInvocationHandler.invoke(EJBLocalObjectInvocationHandler.java:212)
	at com.sun.ejb.containers.EJBLocalObjectInvocationHandlerDelegate.invoke(EJBLocalObjectInvocationHandlerDelegate.java:88)
	at com.sun.proxy.$Proxy461.submit(Unknown Source)
	at edu.harvard.iq.dataverse.__EJB31_Generated__EjbDataverseEngine__Intf____Bean__.submit(Unknown Source)
	at edu.harvard.iq.dataverse.api.AbstractApiBean.execCommand(AbstractApiBean.java:411)
	at edu.harvard.iq.dataverse.api.Dataverses.createDataset(Dataverses.java:244)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.glassfish.ejb.security.application.EJBSecurityManager.runMethod(EJBSecurityManager.java:1081)
	at org.glassfish.ejb.security.application.EJBSecurityManager.invoke(EJBSecurityManager.java:1153)
	at com.sun.ejb.containers.BaseContainer.invokeBeanMethod(BaseContainer.java:4786)
	at com.sun.ejb.EjbInvocation.invokeBeanMethod(EjbInvocation.java:656)
	at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:822)
	at com.sun.ejb.EjbInvocation.proceed(EjbInvocation.java:608)
	at org.jboss.weld.ejb.AbstractEJBRequestScopeActivationInterceptor.aroundInvoke(AbstractEJBRequestScopeActivationInterceptor.java:46)
	at org.jboss.weld.ejb.SessionBeanInterceptor.aroundInvoke(SessionBeanInterceptor.java:52)
	at sun.reflect.GeneratedMethodAccessor106.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at com.sun.ejb.containers.interceptors.AroundInvokeInterceptor.intercept(InterceptorManager.java:883)
	at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:822)
	at com.sun.ejb.EjbInvocation.proceed(EjbInvocation.java:608)
	at com.sun.ejb.containers.interceptors.SystemInterceptorProxy.doCall(SystemInterceptorProxy.java:163)
	at com.sun.ejb.containers.interceptors.SystemInterceptorProxy.aroundInvoke(SystemInterceptorProxy.java:140)
	at sun.reflect.GeneratedMethodAccessor108.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at com.sun.ejb.containers.interceptors.AroundInvokeInterceptor.intercept(InterceptorManager.java:883)
	at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:822)
	at com.sun.ejb.containers.interceptors.InterceptorManager.intercept(InterceptorManager.java:369)
	at com.sun.ejb.containers.BaseContainer.__intercept(BaseContainer.java:4758)
	at com.sun.ejb.containers.BaseContainer.intercept(BaseContainer.java:4746)
	at com.sun.ejb.containers.EJBLocalObjectInvocationHandler.invoke(EJBLocalObjectInvocationHandler.java:212)
	at com.sun.ejb.containers.EJBLocalObjectInvocationHandlerDelegate.invoke(EJBLocalObjectInvocationHandlerDelegate.java:88)
	at com.sun.proxy.$Proxy510.createDataset(Unknown Source)
	at edu.harvard.iq.dataverse.api.__EJB31_Generated__Dataverses__Intf____Bean__.createDataset(Unknown Source)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.glassfish.jersey.server.model.internal.ResourceMethodInvocationHandlerFactory$1.invoke(ResourceMethodInvocationHandlerFactory.java:81)
	at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher$1.run(AbstractJavaResourceMethodDispatcher.java:151)
	at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.invoke(AbstractJavaResourceMethodDispatcher.java:171)
	at org.glassfish.jersey.server.model.internal.JavaResourceMethodDispatcherProvider$ResponseOutInvoker.doDispatch(JavaResourceMethodDispatcherProvider.java:152)
	at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.dispatch(AbstractJavaResourceMethodDispatcher.java:104)
	at org.glassfish.jersey.server.model.ResourceMethodInvoker.invoke(ResourceMethodInvoker.java:387)
	at org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:331)
	at org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:103)
	at org.glassfish.jersey.server.ServerRuntime$1.run(ServerRuntime.java:271)
	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:297)
	at org.glassfish.jersey.server.ServerRuntime.process(ServerRuntime.java:254)
	at org.glassfish.jersey.server.ApplicationHandler.handle(ApplicationHandler.java:1028)
	at org.glassfish.jersey.servlet.WebComponent.service(WebComponent.java:372)
	at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:381)
	at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:344)
	at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:221)
	at org.apache.catalina.core.StandardWrapper.service(StandardWrapper.java:1682)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:344)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:214)
	at org.ocpsoft.rewrite.servlet.RewriteFilter.doFilter(RewriteFilter.java:205)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:256)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:214)
	at edu.harvard.iq.dataverse.api.ApiBlockingFilter.doFilter(ApiBlockingFilter.java:162)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:256)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:214)
	at edu.harvard.iq.dataverse.api.ApiRouter.doFilter(ApiRouter.java:30)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:256)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:214)
	at org.apache.catalina.core.ApplicationDispatcher.doInvoke(ApplicationDispatcher.java:873)
	at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:739)
	at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:575)
	at org.apache.catalina.core.ApplicationDispatcher.doDispatch(ApplicationDispatcher.java:546)
	at org.apache.catalina.core.ApplicationDispatcher.dispatch(ApplicationDispatcher.java:428)
	at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:378)
	at edu.harvard.iq.dataverse.api.ApiRouter.doFilter(ApiRouter.java:34)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:256)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:214)
	at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:316)
	at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:160)
	at org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:734)
	at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:673)
	at com.sun.enterprise.web.WebPipeline.invoke(WebPipeline.java:99)
	at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:174)
	at org.apache.catalina.connector.CoyoteAdapter.doService(CoyoteAdapter.java:415)
	at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:282)
	at com.sun.enterprise.v3.services.impl.ContainerMapper$HttpHandlerCallable.call(ContainerMapper.java:459)
	at com.sun.enterprise.v3.services.impl.ContainerMapper.service(ContainerMapper.java:167)
	at org.glassfish.grizzly.http.server.HttpHandler.runService(HttpHandler.java:201)
	at org.glassfish.grizzly.http.server.HttpHandler.doHandle(HttpHandler.java:175)
	at org.glassfish.grizzly.http.server.HttpServerFilter.handleRead(HttpServerFilter.java:235)
	at org.glassfish.grizzly.filterchain.ExecutorResolver$9.execute(ExecutorResolver.java:119)
	at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeFilter(DefaultFilterChain.java:284)
	at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeChainPart(DefaultFilterChain.java:201)
	at org.glassfish.grizzly.filterchain.DefaultFilterChain.execute(DefaultFilterChain.java:133)
	at org.glassfish.grizzly.filterchain.DefaultFilterChain.process(DefaultFilterChain.java:112)
	at org.glassfish.grizzly.ProcessorExecutor.execute(ProcessorExecutor.java:77)
	at org.glassfish.grizzly.nio.transport.TCPNIOTransport.fireIOEvent(TCPNIOTransport.java:561)
	at org.glassfish.grizzly.strategies.AbstractIOStrategy.fireIOEvent(AbstractIOStrategy.java:112)
	at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.run0(WorkerThreadIOStrategy.java:117)
	at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.access$100(WorkerThreadIOStrategy.java:56)
	at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy$WorkerThreadRunnable.run(WorkerThreadIOStrategy.java:137)
	at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.doWork(AbstractThreadPool.java:565)
	at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.run(AbstractThreadPool.java:545)
	at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.NullPointerException
	at edu.harvard.iq.dataverse.DatasetServiceBean.isIdentifierUniqueInDatabase(DatasetServiceBean.java:277)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.glassfish.ejb.security.application.EJBSecurityManager.runMethod(EJBSecurityManager.java:1081)
	at org.glassfish.ejb.security.application.EJBSecurityManager.invoke(EJBSecurityManager.java:1153)
	at com.sun.ejb.containers.BaseContainer.invokeBeanMethod(BaseContainer.java:4786)
	at com.sun.ejb.EjbInvocation.invokeBeanMethod(EjbInvocation.java:656)
	at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:822)
	at com.sun.ejb.EjbInvocation.proceed(EjbInvocation.java:608)
	at org.jboss.weld.ejb.AbstractEJBRequestScopeActivationInterceptor.aroundInvoke(AbstractEJBRequestScopeActivationInterceptor.java:46)
	at org.jboss.weld.ejb.SessionBeanInterceptor.aroundInvoke(SessionBeanInterceptor.java:52)
	at sun.reflect.GeneratedMethodAccessor106.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at com.sun.ejb.containers.interceptors.AroundInvokeInterceptor.intercept(InterceptorManager.java:883)
	at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:822)
	at com.sun.ejb.EjbInvocation.proceed(EjbInvocation.java:608)
	at com.sun.ejb.containers.interceptors.SystemInterceptorProxy.doCall(SystemInterceptorProxy.java:163)
	at com.sun.ejb.containers.interceptors.SystemInterceptorProxy.aroundInvoke(SystemInterceptorProxy.java:140)
	at sun.reflect.GeneratedMethodAccessor108.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at com.sun.ejb.containers.interceptors.AroundInvokeInterceptor.intercept(InterceptorManager.java:883)
	at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:822)
	at com.sun.ejb.containers.interceptors.InterceptorManager.intercept(InterceptorManager.java:369)
	at com.sun.ejb.containers.BaseContainer.__intercept(BaseContainer.java:4758)
	at com.sun.ejb.containers.BaseContainer.intercept(BaseContainer.java:4746)
	at com.sun.ejb.containers.EJBLocalObjectInvocationHandler.invoke(EJBLocalObjectInvocationHandler.java:212)
	... 145 more
]]

[2017-05-24T15:46:04.126-0400] [glassfish 4.1] [SEVERE] [] [edu.harvard.iq.dataverse.api.AbstractApiBean] [tid: _ThreadID=106 _ThreadName=http-listener-1(5)] [timeMillis: 1495655164126] [levelValue: 1000] [[
  Error while executing command [DatasetCreate dataset:null]
edu.harvard.iq.dataverse.engine.command.exception.CommandException: Command [DatasetCreate dataset:null] failed: null
	at edu.harvard.iq.dataverse.EjbDataverseEngine.submit(EjbDataverseEngine.java:211)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.glassfish.ejb.security.application.EJBSecurityManager.runMethod(EJBSecurityManager.java:1081)
	at org.glassfish.ejb.security.application.EJBSecurityManager.invoke(EJBSecurityManager.java:1153)
	at com.sun.ejb.containers.BaseContainer.invokeBeanMethod(BaseContainer.java:4786)
	at com.sun.ejb.EjbInvocation.invokeBeanMethod(EjbInvocation.java:656)
	at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:822)
	at com.sun.ejb.EjbInvocation.proceed(EjbInvocation.java:608)
	at org.jboss.weld.ejb.AbstractEJBRequestScopeActivationInterceptor.aroundInvoke(AbstractEJBRequestScopeActivationInterceptor.java:46)
	at org.jboss.weld.ejb.SessionBeanInterceptor.aroundInvoke(SessionBeanInterceptor.java:52)
	at sun.reflect.GeneratedMethodAccessor106.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at com.sun.ejb.containers.interceptors.AroundInvokeInterceptor.intercept(InterceptorManager.java:883)
	at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:822)
	at com.sun.ejb.EjbInvocation.proceed(EjbInvocation.java:608)
	at com.sun.ejb.containers.interceptors.SystemInterceptorProxy.doCall(SystemInterceptorProxy.java:163)
	at com.sun.ejb.containers.interceptors.SystemInterceptorProxy.aroundInvoke(SystemInterceptorProxy.java:140)
	at sun.reflect.GeneratedMethodAccessor108.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at com.sun.ejb.containers.interceptors.AroundInvokeInterceptor.intercept(InterceptorManager.java:883)
	at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:822)
	at com.sun.ejb.containers.interceptors.InterceptorManager.intercept(InterceptorManager.java:369)
	at com.sun.ejb.containers.BaseContainer.__intercept(BaseContainer.java:4758)
	at com.sun.ejb.containers.BaseContainer.intercept(BaseContainer.java:4746)
	at com.sun.ejb.containers.EJBLocalObjectInvocationHandler.invoke(EJBLocalObjectInvocationHandler.java:212)
	at com.sun.ejb.containers.EJBLocalObjectInvocationHandlerDelegate.invoke(EJBLocalObjectInvocationHandlerDelegate.java:88)
	at com.sun.proxy.$Proxy461.submit(Unknown Source)
	at edu.harvard.iq.dataverse.__EJB31_Generated__EjbDataverseEngine__Intf____Bean__.submit(Unknown Source)
	at edu.harvard.iq.dataverse.api.AbstractApiBean.execCommand(AbstractApiBean.java:411)
	at edu.harvard.iq.dataverse.api.Dataverses.createDataset(Dataverses.java:244)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.glassfish.ejb.security.application.EJBSecurityManager.runMethod(EJBSecurityManager.java:1081)
	at org.glassfish.ejb.security.application.EJBSecurityManager.invoke(EJBSecurityManager.java:1153)
	at com.sun.ejb.containers.BaseContainer.invokeBeanMethod(BaseContainer.java:4786)
	at com.sun.ejb.EjbInvocation.invokeBeanMethod(EjbInvocation.java:656)
	at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:822)
	at com.sun.ejb.EjbInvocation.proceed(EjbInvocation.java:608)
	at org.jboss.weld.ejb.AbstractEJBRequestScopeActivationInterceptor.aroundInvoke(AbstractEJBRequestScopeActivationInterceptor.java:46)
	at org.jboss.weld.ejb.SessionBeanInterceptor.aroundInvoke(SessionBeanInterceptor.java:52)
	at sun.reflect.GeneratedMethodAccessor106.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at com.sun.ejb.containers.interceptors.AroundInvokeInterceptor.intercept(InterceptorManager.java:883)
	at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:822)
	at com.sun.ejb.EjbInvocation.proceed(EjbInvocation.java:608)
	at com.sun.ejb.containers.interceptors.SystemInterceptorProxy.doCall(SystemInterceptorProxy.java:163)
	at com.sun.ejb.containers.interceptors.SystemInterceptorProxy.aroundInvoke(SystemInterceptorProxy.java:140)
	at sun.reflect.GeneratedMethodAccessor108.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at com.sun.ejb.containers.interceptors.AroundInvokeInterceptor.intercept(InterceptorManager.java:883)
	at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:822)
	at com.sun.ejb.containers.interceptors.InterceptorManager.intercept(InterceptorManager.java:369)
	at com.sun.ejb.containers.BaseContainer.__intercept(BaseContainer.java:4758)
	at com.sun.ejb.containers.BaseContainer.intercept(BaseContainer.java:4746)
	at com.sun.ejb.containers.EJBLocalObjectInvocationHandler.invoke(EJBLocalObjectInvocationHandler.java:212)
	at com.sun.ejb.containers.EJBLocalObjectInvocationHandlerDelegate.invoke(EJBLocalObjectInvocationHandlerDelegate.java:88)
	at com.sun.proxy.$Proxy510.createDataset(Unknown Source)
	at edu.harvard.iq.dataverse.api.__EJB31_Generated__Dataverses__Intf____Bean__.createDataset(Unknown Source)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.glassfish.jersey.server.model.internal.ResourceMethodInvocationHandlerFactory$1.invoke(ResourceMethodInvocationHandlerFactory.java:81)
	at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher$1.run(AbstractJavaResourceMethodDispatcher.java:151)
	at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.invoke(AbstractJavaResourceMethodDispatcher.java:171)
	at org.glassfish.jersey.server.model.internal.JavaResourceMethodDispatcherProvider$ResponseOutInvoker.doDispatch(JavaResourceMethodDispatcherProvider.java:152)
	at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.dispatch(AbstractJavaResourceMethodDispatcher.java:104)
	at org.glassfish.jersey.server.model.ResourceMethodInvoker.invoke(ResourceMethodInvoker.java:387)
	at org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:331)
	at org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:103)
	at org.glassfish.jersey.server.ServerRuntime$1.run(ServerRuntime.java:271)
	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:297)
	at org.glassfish.jersey.server.ServerRuntime.process(ServerRuntime.java:254)
	at org.glassfish.jersey.server.ApplicationHandler.handle(ApplicationHandler.java:1028)
	at org.glassfish.jersey.servlet.WebComponent.service(WebComponent.java:372)
	at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:381)
	at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:344)
	at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:221)
	at org.apache.catalina.core.StandardWrapper.service(StandardWrapper.java:1682)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:344)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:214)
	at org.ocpsoft.rewrite.servlet.RewriteFilter.doFilter(RewriteFilter.java:205)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:256)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:214)
	at edu.harvard.iq.dataverse.api.ApiBlockingFilter.doFilter(ApiBlockingFilter.java:162)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:256)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:214)
	at edu.harvard.iq.dataverse.api.ApiRouter.doFilter(ApiRouter.java:30)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:256)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:214)
	at org.apache.catalina.core.ApplicationDispatcher.doInvoke(ApplicationDispatcher.java:873)
	at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:739)
	at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:575)
	at org.apache.catalina.core.ApplicationDispatcher.doDispatch(ApplicationDispatcher.java:546)
	at org.apache.catalina.core.ApplicationDispatcher.dispatch(ApplicationDispatcher.java:428)
	at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:378)
	at edu.harvard.iq.dataverse.api.ApiRouter.doFilter(ApiRouter.java:34)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:256)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:214)
	at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:316)
	at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:160)
	at org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:734)
	at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:673)
	at com.sun.enterprise.web.WebPipeline.invoke(WebPipeline.java:99)
	at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:174)
	at org.apache.catalina.connector.CoyoteAdapter.doService(CoyoteAdapter.java:415)
	at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:282)
	at com.sun.enterprise.v3.services.impl.ContainerMapper$HttpHandlerCallable.call(ContainerMapper.java:459)
	at com.sun.enterprise.v3.services.impl.ContainerMapper.service(ContainerMapper.java:167)
	at org.glassfish.grizzly.http.server.HttpHandler.runService(HttpHandler.java:201)
	at org.glassfish.grizzly.http.server.HttpHandler.doHandle(HttpHandler.java:175)
	at org.glassfish.grizzly.http.server.HttpServerFilter.handleRead(HttpServerFilter.java:235)
	at org.glassfish.grizzly.filterchain.ExecutorResolver$9.execute(ExecutorResolver.java:119)
	at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeFilter(DefaultFilterChain.java:284)
	at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeChainPart(DefaultFilterChain.java:201)
	at org.glassfish.grizzly.filterchain.DefaultFilterChain.execute(DefaultFilterChain.java:133)
	at org.glassfish.grizzly.filterchain.DefaultFilterChain.process(DefaultFilterChain.java:112)
	at org.glassfish.grizzly.ProcessorExecutor.execute(ProcessorExecutor.java:77)
	at org.glassfish.grizzly.nio.transport.TCPNIOTransport.fireIOEvent(TCPNIOTransport.java:561)
	at org.glassfish.grizzly.strategies.AbstractIOStrategy.fireIOEvent(AbstractIOStrategy.java:112)
	at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.run0(WorkerThreadIOStrategy.java:117)
	at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.access$100(WorkerThreadIOStrategy.java:56)
	at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy$WorkerThreadRunnable.run(WorkerThreadIOStrategy.java:137)
	at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.doWork(AbstractThreadPool.java:565)
	at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.run(AbstractThreadPool.java:545)
	at java.lang.Thread.run(Thread.java:745)
Caused by: javax.ejb.TransactionRolledbackLocalException: Exception thrown from bean
	at com.sun.ejb.containers.EJBContainerTransactionManager.checkExceptionClientTx(EJBContainerTransactionManager.java:662)
	at com.sun.ejb.containers.EJBContainerTransactionManager.postInvokeTx(EJBContainerTransactionManager.java:507)
	at com.sun.ejb.containers.BaseContainer.postInvokeTx(BaseContainer.java:4566)
	at com.sun.ejb.containers.BaseContainer.postInvoke(BaseContainer.java:2074)
	at com.sun.ejb.containers.BaseContainer.postInvoke(BaseContainer.java:2044)
	at com.sun.ejb.containers.EJBLocalObjectInvocationHandler.invoke(EJBLocalObjectInvocationHandler.java:220)
	at com.sun.ejb.containers.EJBLocalObjectInvocationHandlerDelegate.invoke(EJBLocalObjectInvocationHandlerDelegate.java:88)
	at com.sun.proxy.$Proxy451.isIdentifierUniqueInDatabase(Unknown Source)
	at edu.harvard.iq.dataverse.__EJB31_Generated__DatasetServiceBean__Intf____Bean__.isIdentifierUniqueInDatabase(Unknown Source)
	at edu.harvard.iq.dataverse.engine.command.impl.CreateDatasetCommand.execute(CreateDatasetCommand.java:78)
	at edu.harvard.iq.dataverse.engine.command.impl.CreateDatasetCommand.execute(CreateDatasetCommand.java:31)
	at edu.harvard.iq.dataverse.EjbDataverseEngine.submit(EjbDataverseEngine.java:207)
	... 139 more
Caused by: java.lang.NullPointerException
	at edu.harvard.iq.dataverse.DatasetServiceBean.isIdentifierUniqueInDatabase(DatasetServiceBean.java:277)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.glassfish.ejb.security.application.EJBSecurityManager.runMethod(EJBSecurityManager.java:1081)
	at org.glassfish.ejb.security.application.EJBSecurityManager.invoke(EJBSecurityManager.java:1153)
	at com.sun.ejb.containers.BaseContainer.invokeBeanMethod(BaseContainer.java:4786)
	at com.sun.ejb.EjbInvocation.invokeBeanMethod(EjbInvocation.java:656)
	at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:822)
	at com.sun.ejb.EjbInvocation.proceed(EjbInvocation.java:608)
	at org.jboss.weld.ejb.AbstractEJBRequestScopeActivationInterceptor.aroundInvoke(AbstractEJBRequestScopeActivationInterceptor.java:46)
	at org.jboss.weld.ejb.SessionBeanInterceptor.aroundInvoke(SessionBeanInterceptor.java:52)
	at sun.reflect.GeneratedMethodAccessor106.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at com.sun.ejb.containers.interceptors.AroundInvokeInterceptor.intercept(InterceptorManager.java:883)
	at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:822)
	at com.sun.ejb.EjbInvocation.proceed(EjbInvocation.java:608)
	at com.sun.ejb.containers.interceptors.SystemInterceptorProxy.doCall(SystemInterceptorProxy.java:163)
	at com.sun.ejb.containers.interceptors.SystemInterceptorProxy.aroundInvoke(SystemInterceptorProxy.java:140)
	at sun.reflect.GeneratedMethodAccessor108.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at com.sun.ejb.containers.interceptors.AroundInvokeInterceptor.intercept(InterceptorManager.java:883)
	at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:822)
	at com.sun.ejb.containers.interceptors.InterceptorManager.intercept(InterceptorManager.java:369)
	at com.sun.ejb.containers.BaseContainer.__intercept(BaseContainer.java:4758)
	at com.sun.ejb.containers.BaseContainer.intercept(BaseContainer.java:4746)
	at com.sun.ejb.containers.EJBLocalObjectInvocationHandler.invoke(EJBLocalObjectInvocationHandler.java:212)
	... 145 more
]]
@pdurbin pdurbin added the Type: Bug a defect label May 24, 2017
@pdurbin pdurbin added this to the 4.6.2 - Tabular Mapping milestone May 24, 2017
pdurbin added a commit that referenced this issue May 24, 2017
@pdurbin
prevent NullPointerException when creating dataset #3855
4c62e24
@pdurbin pdurbin mentioned this issue May 24, 2017
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pdurbin commented May 24, 2017

I just made pull request #3856 and put it in Code Review at https://waffle.io/IQSS/dataverse

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pdurbin commented May 24, 2017

In case it's helpful, here are the database settings on my laptop:

$ curl -s http://localhost:8080/api/admin/settings | jq .
{
  "status": "OK",
  "data": {
    ":Authority": "10.5072/FK2",
    ":DoiSeparator": "/",
    ":ExcludeDatasetContactEmailFromExport": "true",
    ":FileFixityChecksumAlgorithm": "SHA-1",
    ":AllowSignUp": "yes",
    ":UploadMethods": "dcm/rsync+ssh",
    ":DebugShibAccountType": "datasetIdentifier=3813",
    "BuiltinUsers.KEY": "burrito",
    ":DoiProvider": "EZID",
    ":ComputeBaseUrl": "https://giji.massopencloud.org/application/dataverse/jobs?containerName=",
    ":DataCaptureModuleUrl": "http://localhost:8888",
    ":GeoconnectCreateEditMaps": "true",
    ":BlockedApiPolicy": "localhost-only",
    ":GeoconnectViewMaps": "true",
    ":DoiIdentifierGetsDatasetDatabaseId": "true",
    ":Protocol": "doi",
    ":SignUpUrl": "/dataverseuser.xhtml?editMode=CREATE",
    ":DoiIdentifierType": "sequentialNumber"
  }
}

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pdurbin commented May 25, 2017

@sekmiller is working on a fix. We chatted this morning and I pointed him to this script I use to create datasets on the phoenix server using JSON: https://github.com/IQSS/dataverse/blob/v4.6.1/scripts/search/tests/create-all-and-test#L10

sekmiller added a commit that referenced this issue May 25, 2017
@sekmiller
#3855 -move create identifier to create dataset command
95d5ea5
@kcondon kcondon assigned kcondon and unassigned sekmiller May 25, 2017
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pdurbin commented May 25, 2017

I would like the definition of done for this issue to be that mvn test -Dtest=DataversesIT,DatasetsIT,SwordIT,AdminIT,BuiltinUsersIT,UsersIT,UtilIT,ConfirmEmailIT,FileMetadataIT,FilesIT,SearchIT -Ddataverse.test.baseurl=$DATAVERSE_SERVER doesn't give any errors, just like for 4.6.1. Right now I'm seeing a lot of errors on http://phoenix.dataverse.org as of 2054db2:

https://build.hmdc.harvard.edu:8443/job/phoenix.dataverse.org-apitest-develop/103/console ends with "Tests run: 54, Failures: 12, Errors: 8, Skipped: 6" and here's how the failures look on a graph:

screen shot 2017-05-25 at 2 12 33 pm

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pdurbin commented May 25, 2017

On my laptop, I'm testing various branches and running mvn test -Dtest=DataversesIT,DatasetsIT,SwordIT,AdminIT,BuiltinUsersIT,UsersIT,UtilIT,ConfirmEmailIT,FileMetadataIT,FilesIT,SearchIT.

As of 2054db2 (develop branch) on my laptop, I'm getting this from the mvn test command above:

  • Tests run: 54, Failures: 15, Errors: 9, Skipped: 6

As of 95d5ea5 (3855-cannot-create-dataset) on my laptop, I'm getting this from the mvn test command above:

  • Tests run: 53, Failures: 1, Errors: 6, Skipped: 6
Tests in error: 
  testServiceDocument(edu.harvard.iq.dataverse.api.SwordIT): Failed to parse the JSON document
  testCreateDataverseCreateDatasetUploadFileDownloadFileEditTitle(edu.harvard.iq.dataverse.api.SwordIT): Failed to parse the JSON document
  testCreateAndDeleteDatasetInRoot(edu.harvard.iq.dataverse.api.SwordIT): Failed to parse the JSON document
  testCreateDatasetPublishDestroy(edu.harvard.iq.dataverse.api.SwordIT): Failed to parse the JSON document
  testDeleteFiles(edu.harvard.iq.dataverse.api.SwordIT): Failed to parse the JSON document
  convertNonBcryptUserFromBuiltinToShib(edu.harvard.iq.dataverse.api.UsersIT): Failed to parse the JSON document

@pdurbin pdurbin self-assigned this May 25, 2017
sekmiller added a commit that referenced this issue May 25, 2017
@sekmiller
#3855 Only check for duplicate on create when identifier is created o…
794d524 
…n create dataset
pdurbin added a commit that referenced this issue May 25, 2017
@pdurbin
run createsequence.sql to get tests passing #3855
d278773
sekmiller added a commit that referenced this issue May 25, 2017
@sekmiller
#3855 Reduce noise on duplicate lookup.
8266216
sekmiller added a commit that referenced this issue May 25, 2017
@sekmiller
#3855 - Only try to delete identifier if it exists remotely
b0e967b
sekmiller added a commit that referenced this issue May 25, 2017
@sekmiller
#3855 Remove more error logging
6f28f26
kcondon added a commit that referenced this issue May 25, 2017
@kcondon
Merge pull request #3856 from IQSS/3855-cannot-create-dataset
cb0e38f 
prevent NullPointerException when creating dataset #3855
@kcondon kcondon closed this as completed May 25, 2017
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