[ome-users] OMERO/CellProfiler error

[Laurent Guerard]

Hi guys,

Thanks to the LoadData module in CellProfiler we are using OMERO and 
CellProfiler to avoid having to transfer files back and forth, and it 
works super nicely.

However, a user just told us that running a pipeline on 6 different CSV, 
one for each plate, worked but running it on one CSV containing info 
about 6 plates didn't. I've tried reproducing the errors but so far no luck.

Would you guys know what this could be about ? Here is the error message.

> Traceback (most recent call last): File "cellprofiler\pipeline.pyc", 
> line 1956, in run_image_set File "cellprofiler\pipeline.pyc", line 
> 2067, in run_module File "cellprofiler\modules\loaddata.pyc", line 
> 1069, in run File "cellprofiler\measurements.pyc", line 1616, in 
> get_image File "cellprofiler\modules\loadimages.pyc", line 3230, in 
> provide_image File "bioformats\formatreader.pyc", line 784, in read 
> File "javabridge\jutil.pyc", line 931, in method File 
> "javabridge\jutil.pyc", line 862, in call File "javabridge\jutil.pyc", 
> line 829, in fn JavaException: omero.InternalException 
> serverStackTrace = "ome.conditions.InternalException: Wrapped 
> Exception: (java.lang.NullPointerException): null at 
> loci.formats.in.MetamorphReader.initFile(MetamorphReader.java:399) at 
> loci.formats.FormatReader.setId(FormatReader.java:1426) at 
> loci.formats.in.CellWorxReader.getReader(CellWorxReader.java:727) at 
> loci.formats.in.CellWorxReader.openBytes(CellWorxReader.java:185) at 
> loci.formats.ImageReader.openBytes(ImageReader.java:453) at 
> loci.formats.ChannelFiller.openBytes(ChannelFiller.java:156) at 
> loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:225) at 
> loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:147) at 
> loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:342) at 
> ome.io.bioformats.BfPixelsWrapper.getWholePlane(BfPixelsWrapper.java:359) 
> at 
> ome.io.bioformats.BfPixelsWrapper.getPlane(BfPixelsWrapper.java:256) 
> at 
> ome.io.bioformats.BfPixelBuffer.getPlaneDirect(BfPixelBuffer.java:191) 
> at ome.services.RawPixelsBean.getPlane(RawPixelsBean.java:386) at 
> sun.reflect.GeneratedMethodAccessor2265.invoke(Unknown Source) at 
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) 
> at java.lang.reflect.Method.invoke(Method.java:498) 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:154) at 
> org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) 
> at 
> ome.tools.hibernate.SessionHandler.doStateful(SessionHandler.java:216) 
> at ome.tools.hibernate.SessionHandler.invoke(SessionHandler.java:200) 
> 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$Interceptor.invoke(ProxyCleanupFilter.java:249) 
> at 
> org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) 
> at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at 
> org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) 
> at 
> org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202) 
> at com.sun.proxy.$Proxy107.getPlane(Unknown Source) at 
> sun.reflect.GeneratedMethodAccessor2265.invoke(Unknown Source) at 
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) 
> at java.lang.reflect.Method.invoke(Method.java:498) 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:93) 
> 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 com.sun.proxy.$Proxy107.getPlane(Unknown Source) at 
> sun.reflect.GeneratedMethodAccessor2267.invoke(Unknown Source) at 
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) 
> at java.lang.reflect.Method.invoke(Method.java:498) at 
> ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:172) 
> at ome.services.throttling.Callback.run(Callback.java:56) at 
> ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:56) 
> at 
> ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:140) 
> at 
> ome.services.blitz.impl.RawPixelsStoreI.getPlane_async(RawPixelsStoreI.java:102) 
> at sun.reflect.GeneratedMethodAccessor2266.invoke(Unknown Source) at 
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) 
> at java.lang.reflect.Method.invoke(Method.java:498) at 
> org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307) 
> at 
> org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183) 
> at 
> org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150) 
> at omero.cmd.CallContext.invoke(CallContext.java:78) at 
> org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) 
> at 
> org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202) 
> at com.sun.proxy.$Proxy108.getPlane_async(Unknown Source) at 
> omero.api._RawPixelsStoreTie.getPlane_async(_RawPixelsStoreTie.java:138) 
> at 
> omero.api._RawPixelsStoreDisp.___getPlane(_RawPixelsStoreDisp.java:1001) 
> at 
> omero.api._RawPixelsStoreDisp.__dispatch(_RawPixelsStoreDisp.java:1410) 
> at IceInternal.Incoming.invoke(Incoming.java:222) at 
> Ice.ConnectionI.invokeAll(ConnectionI.java:2482) at 
> Ice.ConnectionI.dispatch(ConnectionI.java:1258) at 
> Ice.ConnectionI.message(ConnectionI.java:1213) at 
> IceInternal.ThreadPool.run(ThreadPool.java:321) at 
> IceInternal.ThreadPool.access$300(ThreadPool.java:12) at 
> IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:693) at 
> java.lang.Thread.run(Thread.java:748) " serverExceptionClass = 
> "ome.conditions.InternalException" message = " Wrapped Exception: 
> (java.lang.NullPointerException): null" 


Thanks !

Best,

---------------
Laurent Guerard