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Task #8922 (new)

Opened 7 years ago

Last modified 3 years ago

Bug: setting ROI shape to None

Reported by: cblackburn Owned by:
Priority: minor Milestone: ROI
Component: Services Version: n.a.
Keywords: n.a. Cc: cxallan, jamoore, jburel, sylittlewood
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: n.a.

Description

The is a test in roi.py which references #3703 

        roi = omero.model.RoiI()
        roi.addShape(omero.model.RectangleI())
        roi.addShape(omero.model.RectangleI())
        roi.setShape(0, None)

This test fails as there is no setShape() method. The same effect can be achieved using,

        ...
        roi.addShape(rect2)
        roi._shapesSeq[0] = None

However, this causes the exception below when saveAndReturnObject() is called in the Pixels object.

Not sure if this is a bug or the sort of thing you expect when you hack around like this. Is the test still relevant?

Change History (7)

comment:1 Changed 7 years ago by cblackburn 

======================================================================
ERROR: test3703 (__main__.TestRois)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test/integration/rois.py", line 47, in test3703
    pix = self.update.saveAndReturnObject(pix)
  File "/Users/cblackburn/Work/repos/ome/dist/lib/python/omero_api_IUpdate_ice.py", line 97, in saveAndReturnObject
    return _M_omero.api.IUpdate._op_saveAndReturnObject.invoke(self, ((obj, ), _ctx))
InternalException: exception ::omero::InternalException
{
    serverStackTrace = ome.conditions.InternalException: Session is dirty. Cannot properly reset security system. Must rollback.
 Session=SessionImpl(PersistenceContext[entityKeys=[EntityKey[ome.model.meta.Experimenter#2923], EntityKey[ome.model.enums.EventType#4], EntityKey[ome.model.meta.Session#8249], EntityKey[ome.model.core.Image#20088], EntityKey[ome.model.meta.Event#35621], EntityKey[ome.model.core.Pixels#19988], EntityKey[ome.model.roi.ImageROILink#53], EntityKey[ome.model.meta.ExperimenterGroup#2931], EntityKey[ome.model.roi.Rectangle#54], EntityKey[ome.model.meta.Event#35622], EntityKey[ome.model.enums.DimensionOrder#1], EntityKey[ome.model.enums.PixelType#1], EntityKey[ome.model.roi.ROI#53]],collectionKeys=[CollectionKey[ome.model.core.Pixels.pixelsFileMapsCountPerOwner#19988], CollectionKey[ome.model.meta.Experimenter.groupExperimenterMap#2923], CollectionKey[ome.model.core.Image.roiLinksCountPerOwner#20088], CollectionKey[ome.model.core.Pixels.thumbnails#19988], CollectionKey[ome.model.roi.ROI.shapes#53], CollectionKey[ome.model.core.Image.roiLinks#20088], CollectionKey[ome.model.roi.ROI.imageLinks#53], CollectionKey[ome.model.core.Image.datasetLinks#20088], CollectionKey[ome.model.meta.ExperimenterGroup.annotationLinks#2931], CollectionKey[ome.model.meta.Session.annotationLinks#8249], CollectionKey[ome.model.core.Image.annotationLinksCountPerOwner#20088], CollectionKey[ome.model.core.Image.datasetLinksCountPerOwner#20088], CollectionKey[ome.model.core.Pixels.annotationLinksCountPerOwner#19988], CollectionKey[ome.model.meta.Session.annotationLinksCountPerOwner#8249], CollectionKey[ome.model.meta.ExperimenterGroup.annotationLinksCountPerOwner#2931], CollectionKey[ome.model.core.Pixels.planes#19988], CollectionKey[ome.model.core.Pixels.annotationLinks#19988], CollectionKey[ome.model.core.Image.annotationLinks#20088], CollectionKey[ome.model.meta.Session.events#8249], CollectionKey[ome.model.meta.Event.logs#35622], CollectionKey[ome.model.core.Pixels.pixelsFileMaps#19988], CollectionKey[ome.model.meta.Event.logs#35621], CollectionKey[ome.model.core.Pixels.settings#19988], CollectionKey[ome.model.meta.ExperimenterGroup.groupExperimenterMap#2931], CollectionKey[ome.model.core.Image.microbeamManipulationLinksCountPerOwner#20088], CollectionKey[ome.model.meta.Experimenter.annotationLinksCountPerOwner#2923], CollectionKey[ome.model.roi.ROI.annotationLinks#53], CollectionKey[ome.model.core.Pixels.channels#19988], CollectionKey[ome.model.roi.ROI.microbeamManipulationLinks#53], CollectionKey[ome.model.core.Image.microbeamManipulationLinks#20088], CollectionKey[ome.model.meta.Experimenter.annotationLinks#2923]]];ActionQueue[insertions=[] updates=[] deletions=[] collectionCreations=[] collectionRemovals=[] collectionUpdates=[]])
	at ome.security.basic.EventHandler.invoke(EventHandler.java:200)
	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 $Proxy82.saveAndReturnObject(Unknown Source)
	at sun.reflect.GeneratedMethodAccessor928.invoke(Unknown Source)
	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:98)
	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 $Proxy82.saveAndReturnObject(Unknown Source)
	at sun.reflect.GeneratedMethodAccessor952.invoke(Unknown Source)
	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:137)
	at ome.services.blitz.impl.UpdateI.saveAndReturnObject_async(UpdateI.java:64)
	at sun.reflect.GeneratedMethodAccessor951.invoke(Unknown Source)
	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 omero.cmd.CallContext.invoke(CallContext.java:59)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
	at $Proxy83.saveAndReturnObject_async(Unknown Source)
	at omero.api._IUpdateTie.saveAndReturnObject_async(_IUpdateTie.java:92)
	at omero.api._IUpdateDisp.___saveAndReturnObject(_IUpdateDisp.java:185)
	at omero.api._IUpdateDisp.__dispatch(_IUpdateDisp.java:365)
	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.InternalException
    message = Session is dirty. Cannot properly reset security system. Must rollback.
 Session=SessionImpl(PersistenceContext[entityKeys=[EntityKey[ome.model.meta.Experimenter#2923], EntityKey[ome.model.enums.EventType#4], EntityKey[ome.model.meta.Session#8249], EntityKey[ome.model.core.Image#20088], EntityKey[ome.model.meta.Event#35621], EntityKey[ome.model.core.Pixels#19988], EntityKey[ome.model.roi.ImageROILink#53], EntityKey[ome.model.meta.ExperimenterGroup#2931], EntityKey[ome.model.roi.Rectangle#54], EntityKey[ome.model.meta.Event#35622], EntityKey[ome.model.enums.DimensionOrder#1], EntityKey[ome.model.enums.PixelType#1], EntityKey[ome.model.roi.ROI#53]],collectionKeys=[CollectionKey[ome.model.core.Pixels.pixelsFileMapsCountPerOwner#19988], CollectionKey[ome.model.meta.Experimenter.groupExperimenterMap#2923], CollectionKey[ome.model.core.Image.roiLinksCountPerOwner#20088], CollectionKey[ome.model.core.Pixels.thumbnails#19988], CollectionKey[ome.model.roi.ROI.shapes#53], CollectionKey[ome.model.core.Image.roiLinks#20088], CollectionKey[ome.model.roi.ROI.imageLinks#53], CollectionKey[ome.model.core.Image.datasetLinks#20088], CollectionKey[ome.model.meta.ExperimenterGroup.annotationLinks#2931], CollectionKey[ome.model.meta.Session.annotationLinks#8249], CollectionKey[ome.model.core.Image.annotationLinksCountPerOwner#20088], CollectionKey[ome.model.core.Image.datasetLinksCountPerOwner#20088], CollectionKey[ome.model.core.Pixels.annotationLinksCountPerOwner#19988], CollectionKey[ome.model.meta.Session.annotationLinksCountPerOwner#8249], CollectionKey[ome.model.meta.ExperimenterGroup.annotationLinksCountPerOwner#2931], CollectionKey[ome.model.core.Pixels.planes#19988], CollectionKey[ome.model.core.Pixels.annotationLinks#19988], CollectionKey[ome.model.core.Image.annotationLinks#20088], CollectionKey[ome.model.meta.Session.events#8249], CollectionKey[ome.model.meta.Event.logs#35622], CollectionKey[ome.model.core.Pixels.pixelsFileMaps#19988], CollectionKey[ome.model.meta.Event.logs#35621], CollectionKey[ome.model.core.Pixels.settings#19988], CollectionKey[ome.model.meta.ExperimenterGroup.groupExperimenterMap#2931], CollectionKey[ome.model.core.Image.microbeamManipulationLinksCountPerOwner#20088], CollectionKey[ome.model.meta.Experimenter.annotationLinksCountPerOwner#2923], CollectionKey[ome.model.roi.ROI.annotationLinks#53], CollectionKey[ome.model.core.Pixels.channels#19988], CollectionKey[ome.model.roi.ROI.microbeamManipulationLinks#53], CollectionKey[ome.model.core.Image.microbeamManipulationLinks#20088], CollectionKey[ome.model.meta.Experimenter.annotationLinks#2923]]];ActionQueue[insertions=[] updates=[] deletions=[] collectionCreations=[] collectionRemovals=[] collectionUpdates=[]])
}

comment:2 Changed 7 years ago by jburel

Referencing ticket #8084 has changed sprint.

comment:3 Changed 7 years ago by jmoore

  • Milestone changed from OMERO-Beta4.4 to OMERO-Beta4.5

Pushing with the schema work. This is somewhat hacky, but we should still try to prevent issues.

comment:4 Changed 7 years ago by ajpatterson

Referencing ticket #8084 has changed sprint.

comment:5 Changed 3 years ago by jamoore

  • Cc changed from cxallan,jamoore,jburel,sylittlewood to cxallan, jamoore, jburel, sylittlewood
  • Milestone changed from 5.x to ROI

comment:6 Changed 3 years ago by jamoore

Referencing ticket #8084 has changed sprint.

comment:7 Changed 3 years ago by jamoore

Referencing ticket #8084 has changed sprint.

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