command line importer fails
Posted: Tue Feb 07, 2012 10:26 am
Hi
After updating my OMERO test system from 4.2.2 to 4.3.4 I can import images using the GUI importer. But the import fails on the commandline:
1. I have created a project and inside the project two dataasets with ids 1 and 2.
2. using the latest importer (4.3.3) I try to import a set of images to the created dataset(s):
This results in the following error:
Server IP, User name, and password if copied from this command and used in the GUI do work and allow me to import the same files.
Any help on this would be greatly appreciated!
Cheers Juergen
After updating my OMERO test system from 4.2.2 to 4.3.4 I can import images using the GUI importer. But the import fails on the commandline:
1. I have created a project and inside the project two dataasets with ids 1 and 2.
2. using the latest importer (4.3.3) I try to import a set of images to the created dataset(s):
- Code: Select all
./importer-cli -s 192.168.2.181 -u importer -w THE_PASSWORD -d 1 /home/helmerj/rails/metaxpress/transfer-script/input_all/20100825\ rbilly_A*.tif
This results in the following error:
- Code: Select all
java.lang.RuntimeException: omero.SecurityViolation
serverStackTrace = "ome.conditions.SecurityViolation: Cannot read ome.model.containers.Dataset:Id_1
at ome.security.basic.BasicACLVoter.throwLoadViolation(BasicACLVoter.java:112)
at ome.security.CompositeACLVoter.throwLoadViolation(CompositeACLVoter.java:86)
at ome.security.ACLEventListener.onPostLoad(ACLEventListener.java:104)
at org.hibernate.engine.TwoPhaseLoad.initializeEntity(TwoPhaseLoad.java:250)
at org.hibernate.loader.Loader.initializeEntitiesAndCollections(Loader.java:898)
at org.hibernate.loader.Loader.doQuery(Loader.java:773)
at org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:270)
at org.hibernate.loader.Loader.loadEntity(Loader.java:1953)
at org.hibernate.loader.entity.AbstractEntityLoader.load(AbstractEntityLoader.java:86)
at org.hibernate.loader.entity.AbstractEntityLoader.load(AbstractEntityLoader.java:76)
at org.hibernate.persister.entity.AbstractEntityPersister.load(AbstractEntityPersister.java:3270)
at org.hibernate.event.def.DefaultLoadEventListener.loadFromDatasource(DefaultLoadEventListener.java:496)
at org.hibernate.event.def.DefaultLoadEventListener.doLoad(DefaultLoadEventListener.java:477)
at org.hibernate.event.def.DefaultLoadEventListener.load(DefaultLoadEventListener.java:227)
at org.hibernate.event.def.DefaultLoadEventListener.onLoad(DefaultLoadEventListener.java:147)
at org.hibernate.impl.SessionImpl.fireLoad(SessionImpl.java:1082)
at org.hibernate.impl.SessionImpl.immediateLoad(SessionImpl.java:1020)
at org.hibernate.proxy.AbstractLazyInitializer.initialize(AbstractLazyInitializer.java:176)
at org.hibernate.Hibernate.initialize(Hibernate.java:428)
at ome.logic.QueryImpl$1.doInHibernate(QueryImpl.java:174)
at org.springframework.orm.hibernate3.HibernateTemplate.doExecute(HibernateTemplate.java:406)
at org.springframework.orm.hibernate3.HibernateTemplate.execute(HibernateTemplate.java:339)
at ome.logic.QueryImpl.get(QueryImpl.java:157)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
at ome.security.basic.EventHandler.invoke(EventHandler.java:150)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:111)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:231)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:116)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
at $Proxy74.get(Unknown Source)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:83)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
at $Proxy74.get(Unknown Source)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:179)
at ome.services.throttling.Callback.run(Callback.java:56)
at ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:56)
at ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:136)
at ome.services.blitz.impl.QueryI.get_async(QueryI.java:110)
at omero.api._IQueryTie.get_async(_IQueryTie.java:127)
at omero.api._IQueryDisp.___get(_IQueryDisp.java:170)
at omero.api._IQueryDisp.__dispatch(_IQueryDisp.java:516)
at IceInternal.Incoming.invoke(Incoming.java:159)
at Ice.ConnectionI.invokeAll(ConnectionI.java:2037)
at Ice.ConnectionI.message(ConnectionI.java:972)
at IceInternal.ThreadPool.run(ThreadPool.java:577)
at IceInternal.ThreadPool.access$100(ThreadPool.java:12)
at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:971)
"
serverExceptionClass = "ome.conditions.SecurityViolation"
message = "Cannot read ome.model.containers.Dataset:Id_1"
at ome.formats.OMEROMetadataStoreClient.getTarget(OMEROMetadataStoreClient.java:2197)
at ome.formats.importer.ImportLibrary.importCandidates(ImportLibrary.java:278)
at ome.formats.importer.cli.CommandLineImporter.start(CommandLineImporter.java:141)
at ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:395)
Caused by: omero.SecurityViolation
serverStackTrace = "ome.conditions.SecurityViolation: Cannot read ome.model.containers.Dataset:Id_1
at ome.security.basic.BasicACLVoter.throwLoadViolation(BasicACLVoter.java:112)
at ome.security.CompositeACLVoter.throwLoadViolation(CompositeACLVoter.java:86)
at ome.security.ACLEventListener.onPostLoad(ACLEventListener.java:104)
at org.hibernate.engine.TwoPhaseLoad.initializeEntity(TwoPhaseLoad.java:250)
at org.hibernate.loader.Loader.initializeEntitiesAndCollections(Loader.java:898)
at org.hibernate.loader.Loader.doQuery(Loader.java:773)
at org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:270)
at org.hibernate.loader.Loader.loadEntity(Loader.java:1953)
at org.hibernate.loader.entity.AbstractEntityLoader.load(AbstractEntityLoader.java:86)
at org.hibernate.loader.entity.AbstractEntityLoader.load(AbstractEntityLoader.java:76)
at org.hibernate.persister.entity.AbstractEntityPersister.load(AbstractEntityPersister.java:3270)
at org.hibernate.event.def.DefaultLoadEventListener.loadFromDatasource(DefaultLoadEventListener.java:496)
at org.hibernate.event.def.DefaultLoadEventListener.doLoad(DefaultLoadEventListener.java:477)
at org.hibernate.event.def.DefaultLoadEventListener.load(DefaultLoadEventListener.java:227)
at org.hibernate.event.def.DefaultLoadEventListener.onLoad(DefaultLoadEventListener.java:147)
at org.hibernate.impl.SessionImpl.fireLoad(SessionImpl.java:1082)
at org.hibernate.impl.SessionImpl.immediateLoad(SessionImpl.java:1020)
at org.hibernate.proxy.AbstractLazyInitializer.initialize(AbstractLazyInitializer.java:176)
at org.hibernate.Hibernate.initialize(Hibernate.java:428)
at ome.logic.QueryImpl$1.doInHibernate(QueryImpl.java:174)
at org.springframework.orm.hibernate3.HibernateTemplate.doExecute(HibernateTemplate.java:406)
at org.springframework.orm.hibernate3.HibernateTemplate.execute(HibernateTemplate.java:339)
at ome.logic.QueryImpl.get(QueryImpl.java:157)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
at ome.security.basic.EventHandler.invoke(EventHandler.java:150)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:111)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:231)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:116)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
at $Proxy74.get(Unknown Source)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:83)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
at $Proxy74.get(Unknown Source)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:179)
at ome.services.throttling.Callback.run(Callback.java:56)
at ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:56)
at ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:136)
at ome.services.blitz.impl.QueryI.get_async(QueryI.java:110)
at omero.api._IQueryTie.get_async(_IQueryTie.java:127)
at omero.api._IQueryDisp.___get(_IQueryDisp.java:170)
at omero.api._IQueryDisp.__dispatch(_IQueryDisp.java:516)
at IceInternal.Incoming.invoke(Incoming.java:159)
at Ice.ConnectionI.invokeAll(ConnectionI.java:2037)
at Ice.ConnectionI.message(ConnectionI.java:972)
at IceInternal.ThreadPool.run(ThreadPool.java:577)
at IceInternal.ThreadPool.access$100(ThreadPool.java:12)
at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:971)
"
serverExceptionClass = "ome.conditions.SecurityViolation"
message = "Cannot read ome.model.containers.Dataset:Id_1"
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:525)
at java.lang.Class.newInstance0(Class.java:372)
at java.lang.Class.newInstance(Class.java:325)
at IceInternal.BasicStream$DynamicUserExceptionFactory.createAndThrow(BasicStream.java:2243)
at IceInternal.BasicStream.throwException(BasicStream.java:1632)
at IceInternal.Outgoing.throwUserException(Outgoing.java:442)
at omero.api._IQueryDelM.get(_IQueryDelM.java:547)
at omero.api.IQueryPrxHelper.get(IQueryPrxHelper.java:660)
at omero.api.IQueryPrxHelper.get(IQueryPrxHelper.java:632)
at ome.formats.OMEROMetadataStoreClient.getTarget(OMEROMetadataStoreClient.java:2193)
... 3 more
Server IP, User name, and password if copied from this command and used in the GUI do work and allow me to import the same files.
Any help on this would be greatly appreciated!
Cheers Juergen