Open Microscopy Environment

Hi,
Directory listing works and the Python command returns "True"
I found this information (http://support.microsoft.com/kb/937624) which sounded like it might be relevant but then I noticed I already had UAC disabled.
The way I've got 4.2.0 working is with the OMERO.master service set to log on as the domain user that has full access to the network share and local admin rights on the computer. It only starts when set it that way and with the repository in UNC format rather than using the mapped drive's letter. So long as I don't ever use omero admin stop which deletes the service from the list and causes it to start up next time as a local service, the log on as setting sticks, even after rebooting.

Sorry to ask but does the mechanism that checks whether the path exists handle those extra backslashes correctly?
Thanks again.

Hi Andrew,

we're still not clear on what's going on in your situation. Our current plan is to update the script to only issue a warning and not fail. See http://trac.openmicroscopy.org.uk/omero/ticket/3513 This should be ready within the next week or two. If you'd like, we can provide you a patch to prevent the failure in your code base.

Cheers,
~Josh.

Hi,
I've just tried 4.2.2.
When I stopped 4.2.0 it removes the OMERO.master service from the services list (along with my adjusted Log on as settings)
Starting 4.2.2 fails because it reverts to logging on as a Local System which can't access the mapped network drive containing the repository. Previously I'd then have re-entered the domain account in the service's Log on as settings but this latest version stops the service after detecting the startup failure and it disappears from the service list so I can't do that fix any more...

Hi Andrew,

sorry to hear that you're still having problems. The deployment on Windows is unfortunately more complex than we would like, so hopefully you can bare with us a bit more.

"bin\omero admin start" is a wrapper around a call to "sc create" followed by "sc start". In turn, "bin\omero admin stop" is a wrapper around "sc stop" and "sc delete". Therefore, once "bin\omero admin start" succeeds, you can use all the regular Windows utilities, like sc.exe or the services manager, to stop OMERO without having the service removed completely.

Hope that helps.
~Josh

OK I've got 4.2.2 running by changing the log on as settings and restarting the service using the Windows services interface after doing omero admin start but before it fails and is stopped and deleted. You get 5 minutes before it times-out.
As for the pie-chart I now get "Unable to create chart" where the graph should be in the 4.2.2 Insight client.
Here's the corresponding section of the log:

Code: Select all

2010-12-21 11:39:37,870 INFO  [ ome.services.blitz.impl.ServiceFactoryI] (l.Server-6) Added servant to adapter: b3b6669d-7f94-47e2-a67f-6a8d27b986ba/b48e27ee-591f-4644-b81a-7f2e17747b8aomero.api.IRepositoryInfo(omero.api._IRepositoryInfoTie@11f0fe3)
2010-12-21 11:39:37,886 INFO  [        ome.services.util.ServiceHandler] (l.Server-2)  Meth:   interface ome.api.IRepositoryInfo.getFreeSpaceInKilobytes
2010-12-21 11:39:37,886 INFO  [        ome.services.util.ServiceHandler] (l.Server-2)  Args:   ()
2010-12-21 11:39:37,901 INFO  [         ome.security.basic.EventHandler] (l.Server-2)  Auth:   user=52,group=54,event=5973(User),sess=b3b6669d-7f94-47e2-a67f-6a8d27b986ba
2010-12-21 11:39:37,901 ERROR [            ome.logic.RepositoryInfoImpl] (l.Server-2) Error retrieving usage in KB.
java.lang.NullPointerException
   at org.apache.commons.io.FileSystemUtils.freeSpaceWindows(FileSystemUtils.java:217)
   at org.apache.commons.io.FileSystemUtils.freeSpaceOS(FileSystemUtils.java:194)
   at org.apache.commons.io.FileSystemUtils.freeSpaceKb(FileSystemUtils.java:166)
   at ome.tools.FileSystem.free(FileSystem.java:90)
   at ome.logic.RepositoryInfoImpl.getFreeSpaceInKilobytes(RepositoryInfoImpl.java:161)
   at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
   at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
   at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
   at java.lang.reflect.Method.invoke(Unknown Source)
   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.security.basic.EventHandler.invoke(EventHandler.java:157)
   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:231)
   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 $Proxy69.getFreeSpaceInKilobytes(Unknown Source)
   at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
   at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
   at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
   at java.lang.reflect.Method.invoke(Unknown Source)
   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.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:83)
   at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
   at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:40)
   at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
   at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
   at $Proxy69.getFreeSpaceInKilobytes(Unknown Source)
   at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
   at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
   at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
   at java.lang.reflect.Method.invoke(Unknown Source)
   at ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:179)
   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:136)
   at ome.services.blitz.impl.RepositoryInfoI.getFreeSpaceInKilobytes_async(RepositoryInfoI.java:42)
   at omero.api._IRepositoryInfoTie.getFreeSpaceInKilobytes_async(_IRepositoryInfoTie.java:64)
   at omero.api._IRepositoryInfoDisp.___getFreeSpaceInKilobytes(_IRepositoryInfoDisp.java:132)
   at omero.api._IRepositoryInfoDisp.__dispatch(_IRepositoryInfoDisp.java:218)
   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)
2010-12-21 11:39:37,901 INFO  [                 org.perf4j.TimingLogger] (l.Server-2) start[1292931577886] time[15] tag[omero.call.exception]
2010-12-21 11:39:37,901 INFO  [        ome.services.util.ServiceHandler] (l.Server-2)  Excp:   ome.conditions.ResourceError
2010-12-21 11:39:37,917 INFO  [        ome.services.util.ServiceHandler] (l.Server-1)  Meth:   interface ome.api.IQuery.findAllByQuery
2010-12-21 11:39:37,917 INFO  [        ome.services.util.ServiceHandler] (l.Server-1)  Args:   [select f from OriginalFile as f left outer join fetch f.details.owner as o where o.id = :userID, ome.parameters.Parameters@c50443]
2010-12-21 11:39:37,917 INFO  [         ome.security.basic.EventHandler] (l.Server-1)  Auth:   user=52,group=54,event=null(User),sess=b3b6669d-7f94-47e2-a67f-6a8d27b986ba
2010-12-21 11:39:37,917 INFO  [                 org.perf4j.TimingLogger] (l.Server-1) start[1292931577917] time[0] tag[omero.call.success.ome.logic.QueryImpl.findAllByQuery]
2010-12-21 11:39:37,917 INFO  [        ome.services.util.ServiceHandler] (l.Server-1)  Rslt:   ()
2010-12-21 11:39:37,933 INFO  [        ome.services.util.ServiceHandler] (l.Server-5)  Meth:   interface ome.api.IQuery.findAllByQuery
2010-12-21 11:39:37,933 INFO  [        ome.services.util.ServiceHandler] (l.Server-5)  Args:   [select distinct g from ExperimenterGroup g left outer join fetch g.groupExperimenterMap m left outer join fetch m.child u left outer join fetch u.groupExperimenterMap m2 left outer join fetch m2.parent where g.id = :id, ome.parameters.Parameters@ebe108]
2010-12-21 11:39:37,933 INFO  [         ome.security.basic.EventHandler] (l.Server-5)  Auth:   user=52,group=54,event=null(User),sess=b3b6669d-7f94-47e2-a67f-6a8d27b986ba
2010-12-21 11:39:37,948 INFO  [                 org.perf4j.TimingLogger] (l.Server-5) start[1292931577933] time[15] tag[omero.call.success.ome.logic.QueryImpl.findAllByQuery]
2010-12-21 11:39:37,948 INFO  [        ome.services.util.ServiceHandler] (l.Server-5)  Rslt:   (ome.model.meta.ExperimenterGroup:Id_54)


I'm sure the graph would look lovely but we can live without it.
Next job: getting the web admin interface onto IIS...
Thanks

ahar wrote:OK I've got 4.2.2 running by changing the log on as settings and restarting the service using the Windows services interface after doing omero admin start but before it fails and is stopped and deleted. You get 5 minutes before it times-out.

Good to hear. Another tip: you can use "bin\omero admin startasync" to prevent the 5 minute timeout, or you can cancel the command while the 5 minute timer is running, without the server being deleted.

As for the pie-chart I now get "Unable to create chart" where the graph should be in the 4.2.2 Insight client.

Yep, all looks as intended. The underlying library simply can't handle your configuration, and so the clients now display the "Unable to create chart" message.

I'm sure the graph would look lovely but we can live without it.
Next job: getting the web admin interface onto IIS...
Thanks

Be sure to let us know how it goes. Our impression that the IIS installation was comparatively straight-forward.

Cheers,
~Josh