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ome / ZarrReader

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NPE: Using idr0138 #48

Closed jburel closed 1 year ago

jburel commented 1 year ago 

packages/omeroweb/webgateway/views.py\", line 1564, in imageData_json\n    rv = imageMarshal(image, key=key, request=request)\n  File \"/opt/omero/web/venv3/lib64/python3.6/site-packages/omeroweb/webgateway/marshal.py\", line 187, in imageMarshal\n    width, height = image._re.getTileSize()\n  File \"/opt/omero/web/venv3/lib64/python3.6/site-packages/omero/gateway/__init__.py\", line 4858, in __call__\n    return self.handle_exception(e, *args, **kwargs)\n  File \"/opt/omero/web/venv3/lib64/python3.6/site-packages/omeroweb/webclient/webclient_gateway.py\", line 2109, in handle_exception\n    super(OmeroWebSafeCallWrapper, self).handle_exception(e, *args, **kwargs)\n  File \"/opt/omero/web/venv3/lib64/python3.6/site-packages/omero/gateway/__init__.py\", line 4855, in __call__\n    return self.f(*args, **kwargs)\n  File \"/opt/omero/web/venv3/lib64/python3.6/site-packages/omero_api_PyramidService_ice.py\", line 354, in getTileSize\n    return _M_omero.api.PyramidService._op_getTileSize.invoke(self, ((), _ctx))\nomero.InternalException: exception ::omero::InternalException\n{\n    serverStackTrace = ome.conditions.InternalException:  Wrapped Exception: (java.lang.NullPointerException):\nnull\n\tat loci.formats.in.ZarrReader.getOptimalTileWidth(ZarrReader.java:144)\n\tat loci.formats.ImageReader.getOptimalTileWidth(ImageReader.java:741)\n\tat loci.formats.ReaderWrapper.getOptimalTileWidth(ReaderWrapper.java:573)\n\tat loci.formats.ReaderWrapper.getOptimalTileWidth(ReaderWrapper.java:573)\n\tat loci.formats.ReaderWrapper.getOptimalTileWidth(ReaderWrapper.java:573)\n\tat ome.io.bioformats.BfPixelBuffer.getTileSize(BfPixelBuffer.java:567)\n\tat omeis.providers.re.Renderer.getTileSize(Renderer.java:1003)\n\tat ome.services.RenderingBean.getTileSize(RenderingBean.java:1751)\n\tat jdk.internal.reflect.GeneratedMethodAccessor1766.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy117.getTileSize(Unknown Source)\n\tat jdk.internal.reflect.GeneratedMethodAccessor1766.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:93)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy117.getTileSize(Unknown Source)\n\tat jdk.internal.reflect.GeneratedMethodAccessor1769.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:172)\n\tat ome.services.throttling.Callback.run(Callback.java:56)\n\tat ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:56)\n\tat ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:140)\n\tat ome.services.blitz.impl.AbstractPyramidServant.getTileSize_async(AbstractPyramidServant.java:59)\n\tat jdk.internal.reflect.GeneratedMethodAccessor1768.invoke(Unknown Source)\n\tat java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\n\tat java.base/java.lang.reflect.Method.invoke(Method.java:566)\n\tat org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\n\tat omero.cmd.CallContext.invoke(CallContext.java:85)\n\tat org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\n\tat org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)\n\tat com.sun.proxy.$Proxy119.getTileSize_async(Unknown Source)\n\tat omero.api._RenderingEngineTie.getTileSize_async(_RenderingEngineTie.java:84)\n\tat omero.api._PyramidServiceDisp.___getTileSize(_PyramidServiceDisp.java:311)\n\tat omero.api._RenderingEngineDisp.__dispatch(_RenderingEngineDisp.java:2377)\n\tat IceInternal.Incoming.invoke(Incoming.java:221)\n\tat Ice.ConnectionI.invokeAll(ConnectionI.java:2536)\n\tat Ice.ConnectionI.dispatch(ConnectionI.java:1145)\n\tat Ice.ConnectionI.message(ConnectionI.java:1056)\n\tat IceInternal.ThreadPool.run(ThreadPool.java:395)\n\tat IceInternal.ThreadPool.access$300(ThreadPool.java:12)\n\tat IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)\n\tat java.base/java.lang.Thread.run(Thread.java:829)\n\n    serverExceptionClass = ome.conditions.InternalException\n    message =  Wrapped Exception: (java.lang.NullPointerException):\nnull\n}\n"}
jburel commented 1 year ago

Closing the issue, i was looking at data not correctly imported