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Task #9919 (closed)

Opened 11 years ago

Closed 9 years ago

Bug: OME-tiff export: handle Pyramids

Reported by: jamoore Owned by: wmoore
Priority: minor Milestone: 5.1.3
Component: Web Version: 5.0.8
Keywords: n.a. Cc: cxallan
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: n.a.

Description

I tried to export a bad pyramid while testing #9904. The green check showed up despite the failure.

WARNING:omero.gateway:ApiUsageException on <class 'omero.gateway.OmeroGatewaySafeCallWrapper'> to <86:24:41:e4:5664dc63:13b07a76d02:-7eeaomero.api.Exporter> generateTiff((<ServiceOptsDict: {'omero.session.uuid': '31c96118-5809-4e6c-9065-1f5d30b94be0', 'omero.client.uuid': '430bd574-d6b7-40e7-acfb-c2ad16239aac'}>,), {})
Traceback (most recent call last):
  File "/home/hudson/hudson/workspace/OMERO-merge-4.4/src/dist/lib/python/omero/gateway/__init__.py", line 3335, in __call__
    return self.f(*args, **kwargs)
  File "/home/hudson/hudson/workspace/OMERO-merge-4.4/src/dist/lib/python/omero_api_Exporter_ice.py", line 93, in generateTiff
    return _M_omero.api.Exporter._op_generateTiff.invoke(self, ((), _ctx))
ApiUsageException: exception ::omero::ApiUsageException
{
    serverStackTrace = ome.conditions.ApiUsageException: Cannot load image: 4449
	at ome.services.blitz.impl.OmeroMetadata.initialize(OmeroMetadata.java:247)
	at ome.services.blitz.impl.ExporterI$2.doWork(ExporterI.java:347)
...
	at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:971)

    serverExceptionClass = ome.conditions.ApiUsageException
    message = Cannot load image: 4449
}
Traceback (most recent call last):
  File "./script", line 513, in <module>
    runScript()
  File "./script", line 499, in runScript
    fileAnnotation, message = batchImageExport(conn, scriptParams)
  File "./script", line 346, in batchImageExport
    saveAsOmeTiff(conn, img, folder_name)
  File "./script", line 165, in saveAsOmeTiff
    fileSize, block_gen = image.exportOmeTiff(bufsize=65536)
  File "/home/hudson/hudson/workspace/OMERO-merge-4.4/src/dist/lib/python/omero/gateway/__init__.py", line 6572, in exportOmeTiff
    size = e.generateTiff(self._conn.SERVICE_OPTS)
  File "/home/hudson/hudson/workspace/OMERO-merge-4.4/src/dist/lib/python/omero/gateway/__init__.py", line 3338, in __call__
    return self.handle_exception(e, *args, **kwargs)
  File "/home/hudson/hudson/workspace/OMERO-merge-4.4/src/dist/lib/python/omero/gateway/__init__.py", line 3335, in __call__
    return self.f(*args, **kwargs)
  File "/home/hudson/hudson/workspace/OMERO-merge-4.4/src/dist/lib/python/omero_api_Exporter_ice.py", line 93, in generateTiff
    return _M_omero.api.Exporter._op_generateTiff.invoke(self, ((), _ctx))
omero.ApiUsageException: exception ::omero::ApiUsageException
{
    serverStackTrace = ome.conditions.ApiUsageException: Cannot load image: 4449
	at ome.services.blitz.impl.OmeroMetadata.initialize(OmeroMetadata.java:247)
	at ome.services.blitz.impl.ExporterI$2.doWork(ExporterI.java:347)
	at sun.reflect.GeneratedMethodAccessor259.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
...
	at $Proxy105.generateTiff_async(Unknown Source)
	at omero.api._ExporterTie.generateTiff_async(_ExporterTie.java:71)
	at omero.api._ExporterDisp.___generateTiff(_ExporterDisp.java:175)
	at omero.api._ExporterDisp.__dispatch(_ExporterDisp.java:248)
	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.ApiUsageException
    message = Cannot load image: 4449
}

Attachments (2)

ss-web-ome-tiff-export-bug.png (302.7 KB) - added by jmoore 11 years ago.
Screen Shot 2015-06-16 at 12.54.07.png (26.1 KB) - added by wmoore 9 years ago.
Improved handling of Big images by Batch Image Export script

Download all attachments as: .zip

Change History (7)

Changed 11 years ago by jmoore

comment:1 Changed 11 years ago by wmoore

Hmmm - the green 'tick' in the activities window tells you that there was no error in the scripting service. The OME-TIFF export script "Batch_Image_Export.py" could check if the ome-tiff was created, and if not, then return an appropriate message, but the scripting service doesn't provide a way to return "Script Failed" status, right? This is what we'd need if we want the scripts to display their status in this way (or I guess we could decide on a convention between the clients, in the same way as we've done with the "Message" return parameter.

comment:2 Changed 11 years ago by jmoore

Will, it seems like no exception is being thrown by the script. If one is, or the exit code is otherwise not 0, then the script should be marked as failed.

comment:3 Changed 11 years ago by wmoore

  • Summary changed from Bug: web ome-tiff export is green on failed export to Bug: OME-tiff export: handle Pyramids

We should add a check to see if the image is a Pyramid, and if so return a suitable 'message'. Not sure if Batch Image Export will work with any Pyramids, even for rendering planes??

comment:4 Changed 9 years ago by jburel

  • Milestone changed from 5.x to 5.1.3
  • Version set to 5.0.8

Moving to 5.1.3 for review

Changed 9 years ago by wmoore

Improved handling of Big images by Batch Image Export script

comment:5 Changed 9 years ago by wmoore

  • Resolution set to worksforme
  • Status changed from new to closed

Seems we have improved handling of Big Images by Batch_Image_Export script now https://trac.openmicroscopy.org/ome/attachment/ticket/9919/Screen%20Shot%202015-06-16%20at%2012.54.07.png

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