Image does not appear in OMERO.iviewer

One more question: the path indicated in the webclient view for an image is root_0/2015-01/12/15-55-32.311/126-Phospho H3 Bod1 siRNA.ome.tiff, on the physical disk containing the data, this is in the OMERO/ManagedRepository directory of the archive. Is this expected? The image does not appear in omero.iviewer, only the thumbnail shows, but I can download it.

Thanks once more!

Yes. That look like a typical, timestamped import directory.

This sounds surprising. If you can see a thumbnail I’d expect you to be able to see the image. Are there any error messages?

~J.

Hi,

Are there any error messages?

Here is the console.log error:

TypeError: e.rdefs is undefined main.js:1:13716
    value http://XX.XX.XX.XX:4080/static/omero_iviewer/main.js?_iviewer-0.9.0:1
    value http://XX.XX.XX.XX:4080/static/omero_iviewer/main.js?_iviewer-0.9.0:1
    success http://XX.XX.XX.XX:4080/static/omero_iviewer/main.js?_iviewer-0.9.0:1
    s http://XX.XX.XX.XX:4080/static/omero_iviewer/vendors.js?_iviewer-0.9.0:80
    fireWith http://XX.XX.XX.XX:4080/static/omero_iviewer/vendors.js?_iviewer-0.9.0:80
    O http://XX.XX.XX.XX:4080/static/omero_iviewer/vendors.js?_iviewer-0.9.0:80
    e http://XX.XX.XX.XX:4080/static/omero_iviewer/vendors.js?_iviewer-0.9.0:80

Today I plan on testing other clients and the python API,

Best,

Guillaume

I had a more detailed error log (I think related to the iviewer issue) while trying to access images through the python API:

image = conn.getObject("Image", 2980)
imshape = (image.getSizeX(), image.getSizeY())
imshape # this is correct
pixels = image.getPrimaryPixels()

arr = pixels.getPlane()

The last line throws the following error:

WARNING:omero.gateway:ResourceError on <class ‘omero.gateway.OmeroGatewaySafeCallWrapper’> to <1e77c468-60a3-464d-bd53-9ea6ad4590dfomero.api.RawPixelsStore> setPixelsId((2980, True, <ServiceOptsDict: {‘omero.client.uuid’: ‘4909870e-6dec-4baf-8b1b-f80a118d0f40’, ‘omero.session.uuid’: ‘13f8131e-5fdc-4d1d-ad9c-e4167a045ee3’}>), {})
Traceback (most recent call last):
File “/opt/tljh/user/lib/python3.7/site-packages/omero/gateway/init.py”, line 4746, in call
return self.f(*args, **kwargs)
File “/opt/tljh/user/lib/python3.7/site-packages/omero_api_RawPixelsStore_ice.py”, line 529, in setPixelsId
return _M_omero.api.RawPixelsStore._op_setPixelsId.invoke(self, ((pixelsId, bypassOriginalFile), _ctx))
omero.ResourceError: exception ::omero::ResourceError
{
serverStackTrace = ome.conditions.ResourceError: Error instantiating pixel buffer: /OMERO/ManagedRepository/root_0\2015-01\12\15-55-32.311/126-Phospho H3 Bod1 siRNA.ome.tiff
at ome.io.nio.PixelsService.createBfPixelBuffer(PixelsService.java:877)
at ome.io.nio.PixelsService._getPixelBuffer(PixelsService.java:631)
at ome.io.nio.PixelsService.getPixelBuffer(PixelsService.java:549)
at ome.services.RawPixelsBean.setPixelsId(RawPixelsBean.java:284)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
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:333)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
at ome.security.basic.EventHandler.invoke(EventHandler.java:154)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
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:179)
at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:282)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
at com.sun.proxy.$Proxy112.setPixelsId(Unknown Source)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:93)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
at com.sun.proxy.$Proxy112.setPixelsId(Unknown Source)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
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.setPixelsId_async(RawPixelsStoreI.java:197)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
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:333)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
at omero.cmd.CallContext.invoke(CallContext.java:85)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
at com.sun.proxy.$Proxy113.setPixelsId_async(Unknown Source)
at omero.api._RawPixelsStoreTie.setPixelsId_async(_RawPixelsStoreTie.java:270)
at omero.api._RawPixelsStoreDisp.___setPixelsId(_RawPixelsStoreDisp.java:668)
at omero.api._RawPixelsStoreDisp.__dispatch(_RawPixelsStoreDisp.java:1759)
at IceInternal.Incoming.invoke(Incoming.java:221)
at Ice.ConnectionI.invokeAll(ConnectionI.java:2536)
at Ice.ConnectionI.dispatch(ConnectionI.java:1145)
at Ice.ConnectionI.message(ConnectionI.java:1056)
at IceInternal.ThreadPool.run(ThreadPool.java:395)
at IceInternal.ThreadPool.access$300(ThreadPool.java:12)
at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)
at java.lang.Thread.run(Thread.java:748)

serverExceptionClass = ome.conditions.ResourceError
message = Error instantiating pixel buffer: /OMERO/ManagedRepository/root_0\2015-01\12\15-55-32.311/126-Phospho H3 Bod1 siRNA.ome.tiff

}
ERROR:omero.gateway:Failed to getPlane() or getTile() from rawPixelsStore
Traceback (most recent call last):
File “/opt/tljh/user/lib/python3.7/site-packages/omero/gateway/init.py”, line 7361, in getTiles
rawPixelsStore = self._prepareRawPixelsStore()
File “/opt/tljh/user/lib/python3.7/site-packages/omero/gateway/init.py”, line 7258, in _prepareRawPixelsStore
ps.setPixelsId(self._obj.id.val, True, self._conn.SERVICE_OPTS)
File “/opt/tljh/user/lib/python3.7/site-packages/omero/gateway/init.py”, line 4749, in call
return self.handle_exception(e, *args, **kwargs)
File “/opt/tljh/user/lib/python3.7/site-packages/omero/gateway/init.py”, line 4746, in call
return self.f(*args, **kwargs)
File “/opt/tljh/user/lib/python3.7/site-packages/omero_api_RawPixelsStore_ice.py”, line 529, in setPixelsId
return _M_omero.api.RawPixelsStore._op_setPixelsId.invoke(self, ((pixelsId, bypassOriginalFile), _ctx))
omero.ResourceError: exception ::omero::ResourceError
{
serverStackTrace = ome.conditions.ResourceError: Error instantiating pixel buffer: /OMERO/ManagedRepository/root_0\2015-01\12\15-55-32.311/126-Phospho H3 Bod1 siRNA.ome.tiff
at ome.io.nio.PixelsService.createBfPixelBuffer(PixelsService.java:877)
at ome.io.nio.PixelsService._getPixelBuffer(PixelsService.java:631)
at ome.io.nio.PixelsService.getPixelBuffer(PixelsService.java:549)
at ome.services.RawPixelsBean.setPixelsId(RawPixelsBean.java:284)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
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:333)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
at ome.security.basic.EventHandler.invoke(EventHandler.java:154)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
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:179)
at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:282)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
at com.sun.proxy.$Proxy112.setPixelsId(Unknown Source)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:93)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
at com.sun.proxy.$Proxy112.setPixelsId(Unknown Source)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
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.setPixelsId_async(RawPixelsStoreI.java:197)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
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:333)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
at omero.cmd.CallContext.invoke(CallContext.java:85)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
at com.sun.proxy.$Proxy113.setPixelsId_async(Unknown Source)
at omero.api._RawPixelsStoreTie.setPixelsId_async(_RawPixelsStoreTie.java:270)
at omero.api._RawPixelsStoreDisp.___setPixelsId(_RawPixelsStoreDisp.java:668)
at omero.api._RawPixelsStoreDisp.__dispatch(_RawPixelsStoreDisp.java:1759)
at IceInternal.Incoming.invoke(Incoming.java:221)
at Ice.ConnectionI.invokeAll(ConnectionI.java:2536)
at Ice.ConnectionI.dispatch(ConnectionI.java:1145)
at Ice.ConnectionI.message(ConnectionI.java:1056)
at IceInternal.ThreadPool.run(ThreadPool.java:395)
at IceInternal.ThreadPool.access$300(ThreadPool.java:12)
at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)
at java.lang.Thread.run(Thread.java:748)

serverExceptionClass = ome.conditions.ResourceError
message = Error instantiating pixel buffer: /OMERO/ManagedRepository/root_0\2015-01\12\15-55-32.311/126-Phospho H3 Bod1 siRNA.ome.tiff

}


ResourceError Traceback (most recent call last)
in
9 pixels = image.getPrimaryPixels()
10
—> 11 pixels.getPlane()

/opt/tljh/user/lib/python3.7/site-packages/omero/gateway/init.py in getPlane(self, theZ, theC, theT)
7329 30% faster.
7330 “”"
-> 7331 planeList = list(self.getPlanes([(theZ, theC, theT)]))
7332 return planeList[0]
7333

/opt/tljh/user/lib/python3.7/site-packages/omero/gateway/init.py in getTiles(self, zctTileList)
7396 exc = e
7397 if exc is not None:
-> 7398 raise exc
7399
7400 def getTile(self, theZ=0, theC=0, theT=0, tile=None):

/opt/tljh/user/lib/python3.7/site-packages/omero/gateway/init.py in getTiles(self, zctTileList)
7359 exc = None
7360 try:
-> 7361 rawPixelsStore = self._prepareRawPixelsStore()
7362 for zctTile in zctTileList:
7363 z, c, t, tile = zctTile

/opt/tljh/user/lib/python3.7/site-packages/omero/gateway/init.py in _prepareRawPixelsStore(self)
7256 “”"
7257 ps = self._conn.createRawPixelsStore()
-> 7258 ps.setPixelsId(self._obj.id.val, True, self._conn.SERVICE_OPTS)
7259 return ps
7260

/opt/tljh/user/lib/python3.7/site-packages/omero/gateway/init.py in call(self, *args, **kwargs)
4747 except Exception as e:
4748 self.debug(e.class.name, args, kwargs)
-> 4749 return self.handle_exception(e, *args, **kwargs)
4750
4751 # Extension point for API users who want to customise the semantics of

/opt/tljh/user/lib/python3.7/site-packages/omero/gateway/init.py in call(self, *args, **kwargs)
4744 def call(self, *args, **kwargs):
4745 try:
-> 4746 return self.f(*args, **kwargs)
4747 except Exception as e:
4748 self.debug(e.class.name, args, kwargs)

/opt/tljh/user/lib/python3.7/site-packages/omero_api_RawPixelsStore_ice.py in setPixelsId(self, pixelsId, bypassOriginalFile, _ctx)
527 “”"
528 def setPixelsId(self, pixelsId, bypassOriginalFile, _ctx=None):
–> 529 return _M_omero.api.RawPixelsStore._op_setPixelsId.invoke(self, ((pixelsId, bypassOriginalFile), _ctx))
530
531 “”"

ResourceError: exception ::omero::ResourceError
{
serverStackTrace = ome.conditions.ResourceError: Error instantiating pixel buffer: /OMERO/ManagedRepository/root_0\2015-01\12\15-55-32.311/126-Phospho H3 Bod1 siRNA.ome.tiff
at ome.io.nio.PixelsService.createBfPixelBuffer(PixelsService.java:877)
at ome.io.nio.PixelsService._getPixelBuffer(PixelsService.java:631)
at ome.io.nio.PixelsService.getPixelBuffer(PixelsService.java:549)
at ome.services.RawPixelsBean.setPixelsId(RawPixelsBean.java:284)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
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:333)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
at ome.security.basic.EventHandler.invoke(EventHandler.java:154)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
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:179)
at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:282)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
at com.sun.proxy.$Proxy112.setPixelsId(Unknown Source)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:93)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
at com.sun.proxy.$Proxy112.setPixelsId(Unknown Source)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
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.setPixelsId_async(RawPixelsStoreI.java:197)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
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:333)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
at omero.cmd.CallContext.invoke(CallContext.java:85)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
at com.sun.proxy.$Proxy113.setPixelsId_async(Unknown Source)
at omero.api._RawPixelsStoreTie.setPixelsId_async(_RawPixelsStoreTie.java:270)
at omero.api._RawPixelsStoreDisp.___setPixelsId(_RawPixelsStoreDisp.java:668)
at omero.api._RawPixelsStoreDisp.__dispatch(_RawPixelsStoreDisp.java:1759)
at IceInternal.Incoming.invoke(Incoming.java:221)
at Ice.ConnectionI.invokeAll(ConnectionI.java:2536)
at Ice.ConnectionI.dispatch(ConnectionI.java:1145)
at Ice.ConnectionI.message(ConnectionI.java:1056)
at IceInternal.ThreadPool.run(ThreadPool.java:395)
at IceInternal.ThreadPool.access$300(ThreadPool.java:12)
at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)
at java.lang.Thread.run(Thread.java:748)

serverExceptionClass = ome.conditions.ResourceError
message = Error instantiating pixel buffer: /OMERO/ManagedRepository/root_0\2015-01\12\15-55-32.311/126-Phospho H3 Bod1 siRNA.ome.tiff

}

Hi Guillaume

Looking at the error you pasted, something does not seem correct in the path /OMERO/ManagedRepository/root_0\2015-01\12\15-55-32.311/126-Phospho H3 Bod1 siRNA.ome.tiff
You have a mixture of / and \, that is probably the source of the problem

Could you compare the path on disk and the value in the DB?

Cheers

Jmarie

Hi Guillaume

This page might be useful
https://docs.openmicroscopy.org/omero/5.3.5/sysadmins/windows-migration.html#restore-data-linux

1 Like

Yes the DB was formerly on a windows machine, so this explains that, good catch!
I’m going to look at that doc, thanks Josh and Jean-Marie!

For quick reference, here is the relevant psql command:

UPDATE pixels SET path = regexp_replace(path,'\\','/','g');

I’ll be testing this very soon.

I worked!

Thanks a lot

Guillaume