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Task #12978 (closed)

Opened 9 years ago

Closed 8 years ago

Last modified 8 years ago

Bug: Zeiss PlaneInfo population

Reported by: mtbcarroll Owned by: mlinkert
Priority: major Milestone: B-F-5.2.0
Component: Bio-Formats Version: OMERO-5.1.3
Keywords: ZeissLSMReader, OMETiffReader, our-fault, external Cc: audrey.salles@…, bf@…
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: n.a.

Description

On importing the LSM file in https://www.openmicroscopy.org/qa2/qa/feedback/11328/ the OMERO server throws,

ome.conditions.ValidationException: not-null property references a null or transient value: ome.model.core.PlaneInfo.theC; nested exception is org.hibernate.PropertyValueException: not-null property references a null or transient value: ome.model.core.PlaneInfo.theC
	at org.springframework.orm.hibernate3.SessionFactoryUtils.convertHibernateAccessException(SessionFactoryUtils.java:648) ~[org.springframework.orm.jar:3.0.1.RELEASE-A]
	at org.springframework.orm.hibernate3.HibernateAccessor.convertHibernateAccessException(HibernateAccessor.java:412) ~[org.springframework.orm.jar:3.0.1.RELEASE-A]
	at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:117) ~[org.springframework.orm.jar:3.0.1.RELEASE-A]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [org.springframework.aop.jar:3.0.1.RELEASE-A]
	at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108) ~[org.springframework.transaction.jar:3.0.1.RELEASE-A]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [org.springframework.aop.jar:3.0.1.RELEASE-A]
	at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) ~[server.jar:na]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [org.springframework.aop.jar:3.0.1.RELEASE-A]
	at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) ~[server.jar:na]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [org.springframework.aop.jar:3.0.1.RELEASE-A]
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202) [org.springframework.aop.jar:3.0.1.RELEASE-A]
	at com.sun.proxy.$Proxy72.doWork(Unknown Source) ~[na:na]
	at ome.services.util.Executor$Impl.execute(Executor.java:447) ~[server.jar:na]
	at ome.services.util.Executor$Impl.execute(Executor.java:391) ~[server.jar:na]
	at ome.services.throttling.Adapter.run(Adapter.java:51) ~[blitz.jar:na]
	at ome.services.throttling.InThreadThrottlingStrategy.runnableCall(InThreadThrottlingStrategy.java:89) [blitz.jar:na]
	at ome.services.blitz.impl.AbstractAmdServant.runnableCall(AbstractAmdServant.java:163) [blitz.jar:na]
	at ome.services.blitz.impl.MetadataStoreI.saveToDB_async(MetadataStoreI.java:218) [blitz.jar:na]
	at sun.reflect.GeneratedMethodAccessor1675.invoke(Unknown Source) ~[na:na]
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.7.0_60]
	at java.lang.reflect.Method.invoke(Method.java:606) ~[na:1.7.0_60]
	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307) [org.springframework.aop.jar:3.0.1.RELEASE-A]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183) [org.springframework.aop.jar:3.0.1.RELEASE-A]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150) [org.springframework.aop.jar:3.0.1.RELEASE-A]
	at omero.cmd.CallContext.invoke(CallContext.java:78) [blitz.jar:na]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [org.springframework.aop.jar:3.0.1.RELEASE-A]
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202) [org.springframework.aop.jar:3.0.1.RELEASE-A]
	at com.sun.proxy.$Proxy106.saveToDB_async(Unknown Source) [na:na]
	at omero.api._MetadataStoreTie.saveToDB_async(_MetadataStoreTie.java:94) [blitz.jar:na]
	at omero.api._MetadataStoreDisp.___saveToDB(_MetadataStoreDisp.java:271) [blitz.jar:na]
	at omero.api._MetadataStoreDisp.__dispatch(_MetadataStoreDisp.java:419) [blitz.jar:na]
	at IceInternal.Incoming.invoke(Incoming.java:159) [ice.jar:na]
	at Ice.ConnectionI.invokeAll(ConnectionI.java:2357) [ice.jar:na]
	at Ice.ConnectionI.dispatch(ConnectionI.java:1208) [ice.jar:na]
	at Ice.ConnectionI.message(ConnectionI.java:1163) [ice.jar:na]
	at IceInternal.ThreadPool.run(ThreadPool.java:302) [ice.jar:na]
	at IceInternal.ThreadPool.access$300(ThreadPool.java:12) [ice.jar:na]
	at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:643) [ice.jar:na]
	at java.lang.Thread.run(Thread.java:745) [na:1.7.0_60]

Change History (12)

comment:1 Changed 9 years ago by mtbcarroll

  • Cc audrey.salles@… added

comment:2 Changed 9 years ago by mlinkert

  • Milestone changed from Unscheduled to 5.1.4

comment:3 Changed 9 years ago by mlinkert

The underlying cause here is that the image count is incorrect. There should be 5 phases and 5 rotations in addition to 30 Z - following the convention in the .czi reader, this would mean 5 T (phase in ModuloT) and 150 Z (rotation in ModuloZ). This isn't (yet?) in the "Self-contained bugs" column of https://trello.com/b/Uoadzs9k/formats because I don't know where the phase/rotation counts are coming from.

comment:4 Changed 9 years ago by jamoore

  • Milestone changed from 5.1.4 to B-F-5.1.4

Splitting 5.1.4 due to milestone decoupling

comment:5 Changed 9 years ago by sbesson

  • Milestone changed from B-F-5.1.4 to BF-5.1.5

comment:7 Changed 8 years ago by dlindner

Same error (but here not with Zeiss LSM but with an ome.tiff file): https://www.openmicroscopy.org/qa2/qa/feedback/16996/

comment:9 Changed 8 years ago by mlinkert

Still planning to work on this before the end of March - some of these are the same issue, some are similar exceptions but slightly different problems. I'll add more details and/or split up into new cards for anything that isn't done before the end of the month. These should all be plain bug fixes though, so if we run out of time for 5.2.0 then they should be safe for 5.2.1.

comment:10 Changed 8 years ago by mlinkert

  • Keywords OMETiffReader our-fault external added
  • Resolution set to fixed
  • Status changed from new to closed

comment:11 Changed 8 years ago by Melissa Linkert <melissa@…>

(In [66079508d3d50f2da3cabea8e97327b2c2a488eb/bioformats.git] on branch develop) Zeiss LSM: read rotation, phase, and illumination counts

See #12978.

comment:12 Changed 8 years ago by Melissa Linkert <melissa@…>

(In [ce5ffc924b0a6a96e8d11226a68f24c39e05d769/bioformats.git] on branch develop) OME-TIFF: make sure Plane attributes are correctly populated

See #12978

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