Open Microscopy Environment

I created an exporter and im trying to export an image to tiff. I get the following error.

Code: Select all

---------------------------------------------------------------------------
InternalException                         Traceback (most recent call last)

/usr0/local/omero.server/OMERO.server-Beta-4.2.0/<ipython console> in <module>()

/usr0/local/omero.server/OMERO.server-Beta-4.2.0/lib/python/pslid.py in export2Tiff(client, iid)
    137    try:
    138        exporter.addImage( iid )
--> 139        length = exporter.generateTiff()
    140        file = open("~/%s.ome.tiff" % iid, "w" )
    141        while True:

/usr0/local/omero.server/OMERO.server-Beta-4.2.0/lib/python/omero_api_Exporter_ice.pyc in generateTiff(self, _ctx)
     91
     92         def generateTiff(self, _ctx=None):
---> 93             return _M_omero.api.Exporter._op_generateTiff.invoke(self, ((), _ctx))
     94
     95         def generateTiff_async(self, _cb, _ctx=None):

InternalException: exception ::omero::InternalException
{
    serverStackTrace = java.io.IOException: Permission denied
   at java.io.UnixFileSystem.createFileExclusively(Native Method)
   at java.io.File.checkAndCreate(File.java:1704)
   at java.io.File.createTempFile(File.java:1792)
   at omero.util.TempFileManager.createPath(TempFileManager.java:320)
   at omero.util.TempFileManager.create_path(TempFileManager.java:429)
   at ome.services.blitz.impl.ExporterI$2.doWork(ExporterI.java:338)
   at sun.reflect.GeneratedMethodAccessor209.invoke(Unknown Source)
   at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
   at java.lang.reflect.Method.invoke(Method.java:597)
   at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
   at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
   at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
   at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:409)
   at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
   at ome.security.basic.EventHandler.invoke(EventHandler.java:144)
   at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
   at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:111)
   at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
   at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)
   at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
   at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:222)
   at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
   at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:111)
   at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
   at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
   at $Proxy56.doWork(Unknown Source)
   at ome.services.util.Executor$Impl.execute(Executor.java:339)
   at ome.services.blitz.impl.ExporterI.do_tiff(ExporterI.java:315)
   at ome.services.blitz.impl.ExporterI.generateTiff_async(ExporterI.java:185)
   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 = java.io.IOException
    message = Permission denied


nevermind... after a coffee break i figured out i passed the session rather than the client.

Glad you figured out the argument issue, Ivan. But the exception you're getting is most likely caused by your AFS mount. You may need to set the OMERO_TEMPDIR environment variable before starting OMERO:

Code: Select all

bin/omero admin stop
set OMERO_TEMPDIR=/usr/local/tmp
bin/omero admin start


For moe information, see http://trac.openmicroscopy.org.uk/omero/wiki/TempFileManager

Cheers
~Josh