Bug:Saving rendering settings

[jburel]

Rendering settings are not saved in Insight (clicking the floppy disk icon doesn't save them) - they revert to the defaults after accessing the image again. In web client, changing the rendering settings causes an infinite "Loading..." and/or a 404.

[jburel]

user-1/private-1 (rendering settings on own data)

[jburel]

Saving rendering settings by group owner in private group creates the following exception

settingsorg.openmicroscopy.shoola.env.rnd.RenderingServiceException: An error occurred while saving the current settings.

omero.InternalException
    serverStackTrace = "ome.conditions.InternalException:  Wrapped Exception: (java.lang.NullPointerException):
                        null
                        	at ome.security.basic.BasicACLVoter.objectBelongsToUser(BasicACLVoter.java:320)
                        	at ome.security.basic.BasicACLVoter.allowUpdateOrDelete(BasicACLVoter.java:222)
                        	at ome.security.basic.BasicACLVoter.postProcess(BasicACLVoter.java:296)
                        	at ome.tools.hibernate.ProxyCleanupFilter.filter(ProxyCleanupFilter.java:119)
                        	at ome.util.ContextFilter.filter(ContextFilter.java:160)
                        	at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:244)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:116)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
                        	at $Proxy65.doWork(Unknown Source)
                        	at ome.services.util.Executor$Impl.execute(Executor.java:406)
                        	at ome.services.util.Executor$Impl.execute(Executor.java:350)
                        	at ome.services.RenderingBean.createNewRenderingDef(RenderingBean.java:1871)
                        	at ome.services.RenderingBean.saveCurrentSettings(RenderingBean.java:765)
                        	at sun.reflect.GeneratedMethodAccessor2275.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.ServiceHandler.invoke(ServiceHandler.java:116)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
                        	at $Proxy89.saveCurrentSettings(Unknown Source)
                        	at sun.reflect.GeneratedMethodAccessor2275.invoke(Unknown Source)

[jburel <j.burel@…>]

(In [70f55a90943c720152cca0b8cf2f7adee66d0902/ome.git] on branch develop) Review closing logic if failure to save settings (see #8818)

[jburel]

Moved from sprint 2012-05-22 (15)

[jburel]

java.lang.Exception: Abnormal termination due to an uncaught exception. java.lang.NullPointerException at org.openmicroscopy.shoola.agents.metadata.rnd.DomainPane.setSelectedChannel(DomainPane.java:917) at org.openmicroscopy.shoola.agents.metadata.rnd.DomainPane.resetDefaultRndSettings(DomainPane.java:844) at org.openmicroscopy.shoola.agents.metadata.rnd.RendererUI.resetDefaultRndSettings(RendererUI.java:185) at org.openmicroscopy.shoola.agents.metadata.rnd.RendererComponent.refresh(RendererComponent.java:1066) at org.openmicroscopy.shoola.agents.treeviewer.view.TreeViewerModel.refreshRenderer(TreeViewerModel.java:1030) at org.openmicroscopy.shoola.agents.treeviewer.view.TreeViewerWin.refreshRenderer(TreeViewerWin.java:1153) at org.openmicroscopy.shoola.agents.treeviewer.view.TreeViewerControl.windowGainedFocus(TreeViewerControl.java:1485) at 

[jmoore]

Pushed following partial fix to will/sprint16-bugfixes:

commit b9a57fa8789e614fd824739b646545cb8ed60e27
Author: jmoore <josh@glencoesoftware.com>
Date:   Mon May 28 10:28:44 2012 +0200

    Force load owner and group if null in details (See #8818)
    
    During post-processing in BasicACLVoter, the owner and group
    fields can be null which lead to a NPE on objectBelongsToUser.
    This was masking a ReadOnlyGroupSecurityViolation which still
    needs to be fixed.

Now the issue I'm seeing is:

Caused by: omero.ReadOnlyGroupSecurityViolation
    serverStackTrace = "ome.conditions.ReadOnlyGroupSecurityViolation: Cannot link to ome.model.core.Pixels:Id_1001
                        Current user (rnd8818-leader) is an admin or the owner of
                        the private group (rnd8818=rw----). It is not allowed to
                        link to users' data.
                                at ome.security.basic.OmeroInterceptor.evaluateLinkages(OmeroInterceptor.java:454)
                                at ome.security.basic.OmeroInterceptor.onFlushDirty(OmeroInterceptor.java:179)
                                at org.hibernate.event.def.DefaultFlushEntityEventListener.invokeInterceptor(DefaultFlushEntityEventListener.java:372)
                                at org.hibernate.event.def.DefaultFlushEntityEventListener.handleInterception(DefaultFlushEntityEventListener.java:349)
                                at org.hibernate.event.def.DefaultFlushEntityEventListener.scheduleUpdate(DefaultFlushEntityEventListener.java:287)
                                at org.hibernate.event.def.DefaultFlushEntityEventListener.onFlushEntity(DefaultFlushEntityEventListener.java:155)
                                at org.hibernate.event.def.AbstractFlushingEventListener.flushEntities(AbstractFlushingEventListener.java:219)
                                at org.hibernate.event.def.AbstractFlushingEventListener.flushEverythingToExecutions(AbstractFlushingEventListener.java:99)
                                at org.hibernate.event.def.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:50)
                                at org.hibernate.impl.SessionImpl.flush(SessionImpl.java:1208)
                                at ome.logic.UpdateImpl.afterUpdate(UpdateImpl.java:294)
                                at ome.logic.UpdateImpl.doAction(UpdateImpl.java:312)
                                at ome.logic.UpdateImpl.doAction(UpdateImpl.java:302)
                                at ome.logic.UpdateImpl.saveAndReturnObject(UpdateImpl.java:118)
                                at ome.logic.PixelsImpl.saveRndSettings(PixelsImpl.java:305)

[jburel]

From viewer with latest code.

omero.InternalException
    serverStackTrace = "ome.conditions.InternalException:  Wrapped Exception: (java.lang.NullPointerException):
                        null
                        "
    serverExceptionClass = "ome.conditions.InternalException"
    message = " Wrapped Exception: (java.lang.NullPointerException):
               null"
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
	at java.lang.reflect.Constructor.newInstance(Constructor.java:501)
	at java.lang.Class.newInstance0(Class.java:350)
	at java.lang.Class.newInstance(Class.java:303)
	at IceInternal.BasicStream$DynamicUserExceptionFactory.createAndThrow(BasicStream.java:2243)
	at IceInternal.BasicStream.throwException(BasicStream.java:1632)
	at IceInternal.Outgoing.throwUserException(Outgoing.java:442)
	at omero.api._RenderingEngineDelM.saveCurrentSettings(_RenderingEngineDelM.java:1926)
	at omero.api.RenderingEnginePrxHelper.saveCurrentSettings(RenderingEnginePrxHelper.java:2712)
	at omero.api.RenderingEnginePrxHelper.saveCurrentSettings(RenderingEnginePrxHelper.java:2684)
	at org.openmicroscopy.shoola.env.rnd.RenderingControlProxy.saveCurrentSettings(RenderingControlProxy.java:1285)

[jmoore]

Jean-Marie, can you add a test that reproduces? I'm certainly not seeing that.

[jburel]

A commit was pushed while testing. I do not have the problem now.

[jburel]

Private group-owner

• saving his/her data: ok

Read-only:

• admin:
  • saving his/her data: ok
  • saving settings for other members: ok (update thumbnail insight missing )

• group owner:
  • saving his/her data: ok
  • saving settings for other members:

    Caused by: omero.SecurityViolation
        serverStackTrace = "ome.conditions.SecurityViolation: You are not authorized to change the owner for ome.model.display.RenderingDef:Id_104 from ome.model.meta.Experimenter:Id_3 to ome.model.meta.Experimenter:Id_2
                            	at ome.security.basic.OmeroInterceptor.managedOwner(OmeroInterceptor.java:849)
                            	at ome.security.basic.OmeroInterceptor.checkManagedDetails(OmeroInterceptor.java:747)
                            	at ome.security.basic.OmeroInterceptor.resetDetails(OmeroInterceptor.java:316)
                            	at ome.security.basic.OmeroInterceptor.onFlushDirty(OmeroInterceptor.java:181)
                            	at org.hibernate.event.def.DefaultFlushEntityEventListener.invokeInterceptor(DefaultFlushEntityEventListener.java:372)
                            	at org.hibernate.event.def.DefaultFlushEntityEventListener.handleInterception(DefaultFlushEntityEventListener.java:349)
                            	at org.hibernate.event.def.DefaultFlushEntityEventListener.scheduleUpdate(DefaultFlushEntityEventListener.java:287)
                            	at org.hibernate.event.def.DefaultFlushEntityEventListener.onFlushEntity(DefaultFlushEntityEventListener.java:155)
                            	at org.hibernate.event.def.AbstractFlushingEventListener.flushEntities(AbstractFlushingEventListener.java:219)
                            	at org.hibernate.event.def.AbstractFlushingEventListener.flushEverythingToExecutions(AbstractFlushingEventListener.java:99)
                            	at org.hibernate.event.def.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:50)
                            	at org.hibernate.impl.SessionImpl.flush(SessionImpl.java:1208)
                            	at ome.logic.UpdateImpl.afterUpdate(UpdateImpl.java:294)
                            	at ome.logic.UpdateImpl.doAction(UpdateImpl.java:312)
                            	at ome.logic.UpdateImpl.doAction(UpdateImpl.java:302)
                            	at ome.logic.UpdateImpl.saveAndReturnObject(UpdateImpl.java:118)
                            	at ome.logic.PixelsImpl.saveRndSettings(PixelsImpl.java:305)
    

[jmoore <josh@…>]

(In [b9a57fa8789e614fd824739b646545cb8ed60e27/ome.git] on branch develop) Force load owner and group if null in details (See #8818)

During post-processing in BasicACLVoter, the owner and group
fields can be null which lead to a NPE on objectBelongsToUser.
This was masking a ReadOnlyGroupSecurityViolation? which still
needs to be fixed.

[jburel]

Moved from sprint 2012-06-05 (16)

[jmoore]

Jean-Marie was working on tests. If you need me to write them, J-M, feel free to pass it back.

[jburel]

Testing written and pushed
The failing tests are in integration/RenderingEngineTest

[jmoore]

Pushed a partial fix to ​https://github.com/joshmoore/openmicroscopy/tree/8818-saveCurrentSettings

This is getting into the deeper mysteries of rdef ownership. Passing to Chris for guidance.

[jmoore]

Chris pointed out that

commit b9a57fa8789e614fd824739b646545cb8ed60e27
Author: jmoore <josh@glencoesoftware.com>
Date:   Mon May 28 10:28:44 2012

    Force load owner and group if null in details (See #8818)
    
    During post-processing in BasicACLVoter, the owner and group
    fields can be null which lead to a NPE on objectBelongsToUser.
    This was masking a ReadOnlyGroupSecurityViolation which still
    needs to be fixed.

is doing the wrong thing. This is related to #8991, so I may be backtracking on all of those changes and finding a different solution (if possible). Otherwise, I'll need to add DB access to BasicACLVoter and lookup the correct details info.

[jmoore]

After rolling back the above commit, I'm no longer getting a NPE at objectBelongsToUser in comment 2 but rather a NPE saying that retrieveRndSettings is returning null.

[jmoore]

Refactoring of retrieveRndSettings from RenderingBean? seems to fix the issue. Pushed to sprint17-bugfixes.

*   2eb7cb4 - (HEAD, sprint17-bugfixes) Merge branch '8818-rnd-settings' into sprint17-bugfixes (30 seconds ago) <jmoore>
|\  
| * 7114d5f - Refactor graph critical logic to IPixels (Fix #8818) (4 minutes ago) <jmoore>
| * aad77be - Reuse retrieveRndSettings outside of execute (See #8818) (4 minutes ago) <jmoore>
| * a379407 - Revert "Force load owner and group if null in details (See #8818)" (4 minutes ago) <jmoore>

[jmoore]

Last issue in #8898 is now reproducing this issue.

[jmoore]

Another fixed pushed to sprint17-bugfixe:

commit 2355f135e7f0803e107135ae674e7904aacd11b4
Author: jmoore <josh@glencoesoftware.com>
Date:   Tue Jun 12 10:03:26 2012

    Handle unmanaged objects for createNewRenderingDef (Fix #8818)
    
    RenderingBean calls createNewRenderingDef in a transaction. That method
    in IRenderingSettings returns an unmanaged, or "transient", object which
    of course has no owner since it hasn't been saved yet. This commit
    assumes objects without an owner and an ID set inherently belong to the
    current user since a later save will set the owner to be the current
    user.

The script I used to reproduce the problem:

import sys
sys.path.insert(0, "lib/python")
import omero
c = omero.client()
p = long(c.getProperty("omero.pixels"))

s = c.createSession()
r = s.createRenderingEngine()
r.lookupPixels(p)
print "%s rdef?" % p, r.lookupRenderingDef(p)
r.load()

start = r.getChannelWindowStart(0)
start += 0.00001

end = r.getChannelWindowEnd(0)
end -= 0.00001

r.setChannelWindow(0, start, end)
r.saveCurrentSettings() # Fails here

r.close()

logged in as user-1 (the leader the current group) where "omero.pixels" points to an image belonging to the same user.