Using an export to save to tiff

[icaoberg]

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


[icaoberg]

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

[jmoore]

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