Sprint3 review by jburel · Pull Request #328 · ome/openmicroscopy

jburel · 2012-08-31T11:17:24Z

For testing information see https://trac.openmicroscopy.org.uk/ome/ticket/9566

This is only displayed when the objects are not in the same group.

gusferguson · 2012-09-03T08:41:44Z

Tests done as requested.

Re tooltips Insight vs. Importer: - working as expected.

Re wording on script window: I don't think the text of the warning is clear enough. Suggest:

This script can only batch export images from the same group.
Please perform a separate run of the script for each group, selecting only images from a single group to batch export each time.

jburel · 2012-09-03T09:19:55Z

@gusferguson: The target of the script varies from script to script. Some scripts also support more than one type.
cf. Chat discussion, text will become. "This script can only run on data from the same group Please perform a separate run of the script for each group, selecting only data from a single group to run the script on each time."

gusferguson · 2012-09-04T11:52:55Z

Retested with Mac and Windows. Problem with script processing on gretzky. Tested with howe - new dialog box behaved as expected - text clearer. Filing bug ticket.

joshmoore · 2012-09-04T12:20:46Z

Note, I see this in Blitz-0.log:

2012-09-04 12:41:09,159 INFO  [        ome.services.util.ServiceHandler] (l.Server-8)  Executor.doWork -- omero.grid.InteractiveProcessorI.getScriptId
2012-09-04 12:41:09,159 INFO  [        ome.services.util.ServiceHandler] (l.Server-8)  Args:    [null, InternalSF@1093729019]
2012-09-04 12:41:09,160 INFO  [    ome.security.basic.BasicEventContext] (l.Server-8)  cctx:    group=-1
2012-09-04 12:41:09,162 INFO  [         ome.security.basic.EventHandler] (l.Server-8)  Auth:    user=4,group=-1,event=null(User),sess=787c662c-378f-4977-ac12-916d695
bb667
2012-09-04 12:41:09,166 INFO  [                 org.perf4j.TimingLogger] (l.Server-8) start[1346758869159] time[7] tag[omero.call.exception]
2012-09-04 12:41:09,166 WARN  [        ome.services.util.ServiceHandler] (l.Server-8) IllegalArgumentException thrown.

java.lang.IllegalArgumentException: Permissions argument cannot be null.
        at ome.model.internal.Permissions.<init>(Permissions.java:152)
        at ome.security.basic.CurrentDetails.applyContext(CurrentDetails.java:408)        at ome.security.basic.BasicACLVoter.postProcess(BasicACLVoter.java:352)
        at ome.tools.hibernate.ProxyCleanupFilter.filter(ProxyCleanupFilter.java:119)
...
        at omero.grid.ParamsHelper.getOrCreateParams(ParamsHelper.java:94)
        at ome.services.blitz.impl.ScriptI$10.call(ScriptI.java:408)
        at ome.services.throttling.Callback2.run(Callback2.java:49)
        at ome.services.throttling.InThreadThrottlingStrategy.safeRunnableCall(InThreadThrottlingStrategy.java:80)
        at ome.services.blitz.impl.AbstractAmdServant.safeRunnableCall(AbstractAmdServant.java:169)
        at ome.services.blitz.impl.ScriptI.getParams_async(ScriptI.java:406)
...
2012-09-04 12:41:09,166 INFO  [        ome.services.util.ServiceHandler] (l.Server-8)  Excp:    java.lang.IllegalArgumentException: Permissions argument cannot be null.

Which I thought was fixed? Similar to what you saw, Gus?

joshmoore · 2012-09-04T12:25:46Z

Note: this is likely related to issues with gh-309 if you'd like to try again tomorrow.

gusferguson · 2012-09-04T12:31:54Z

Hi Josh

There were certainly similar in my logs - log file attached to ticket - https://trac.openmicroscopy.org.uk/ome/ticket/9574 :

Caused by: omero.ApiUsageException
serverStackTrace = "ome.conditions.ApiUsageException: Permissions argument cannot be null.
at ome.model.internal.Permissions.(Permissions.java:152)
at ome.security.basic.CurrentDetails.applyContext(CurrentDetails.java:408)
at ome.security.basic.BasicACLVoter.postProcess(BasicACLVoter.java:352)
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 omero.grid.InteractiveProcessorI.getScriptId(InteractiveProcessorI.java:486)
at omero.grid.InteractiveProcessorI.(InteractiveProcessorI.java:122)
at ome.services.blitz.impl.SharedResourcesI.acquireProcessor(SharedResourcesI.java:418)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
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 omero.cmd.CallContext.invoke(CallContext.java:59)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
at $Proxy74.acquireProcessor(Unknown Source)
at omero.grid.ParamsHelper.generateScriptParams(ParamsHelper.java:137)
at omero.grid.ParamsHelper.getOrCreateParams(ParamsHelper.java:94)
at ome.services.blitz.impl.ScriptI$10.call(ScriptI.java:408)
at ome.services.throttling.Callback2.run(Callback2.java:49)
at ome.services.throttling.InThreadThrottlingStrategy.safeRunnableCall(InThreadThrottlingStrategy.java:80)
at ome.services.blitz.impl.AbstractAmdServant.safeRunnableCall(AbstractAmdServant.java:169)
at ome.services.blitz.impl.ScriptI.getParams_async(ScriptI.java:406)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
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 omero.cmd.CallContext.invoke(CallContext.java:59)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
at $Proxy91.getParams_async(Unknown Source)
at omero.api._IScriptTie.getParams_async(_IScriptTie.java:85)
at omero.api._IScriptDisp.___getParams(_IScriptDisp.java:347)
at omero.api._IScriptDisp.__dispatch(_IScriptDisp.java:494)
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)

On 4 Sep 2012, at 13:20, Josh Moore wrote:

Note, I see this in Blitz-0.log:

2012-09-04 12:41:09,159 INFO ome.services.util.ServiceHandler Executor.doWork -- omero.grid.InteractiveProcessorI.getScriptId
2012-09-04 12:41:09,159 INFO ome.services.util.ServiceHandler Args: [null, InternalSF@1093729019]
2012-09-04 12:41:09,160 INFO ome.security.basic.BasicEventContext cctx: group=-1
2012-09-04 12:41:09,162 INFO ome.security.basic.EventHandler Auth: user=4,group=-1,event=null(User),sess=787c662c-378f-4977-ac12-916d695
bb667
2012-09-04 12:41:09,166 INFO org.perf4j.TimingLogger start[1346758869159] time[7] tag[omero.call.exception]
2012-09-04 12:41:09,166 WARN ome.services.util.ServiceHandler IllegalArgumentException thrown.

java.lang.IllegalArgumentException: Permissions argument cannot be null.
at ome.model.internal.Permissions.(Permissions.java:152)
at ome.security.basic.CurrentDetails.applyContext(CurrentDetails.java:408) at ome.security.basic.BasicACLVoter.postProcess(BasicACLVoter.java:352)
at ome.tools.hibernate.ProxyCleanupFilter.filter(ProxyCleanupFilter.java:119)
...
at omero.grid.ParamsHelper.getOrCreateParams(ParamsHelper.java:94)
at ome.services.blitz.impl.ScriptI$10.call(ScriptI.java:408)
at ome.services.throttling.Callback2.run(Callback2.java:49)
at ome.services.throttling.InThreadThrottlingStrategy.safeRunnableCall(InThreadThrottlingStrategy.java:80)
at ome.services.blitz.impl.AbstractAmdServant.safeRunnableCall(AbstractAmdServant.java:169)
at ome.services.blitz.impl.ScriptI.getParams_async(ScriptI.java:406)
...
2012-09-04 12:41:09,166 INFO ome.services.util.ServiceHandler Excp: java.lang.IllegalArgumentException: Permissions argument cannot be null.

Which I thought was fixed? Similar to what you saw, Gus?

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gusferguson · 2012-09-04T12:32:32Z

Bug ticket: https://trac.openmicroscopy.org.uk/ome/ticket/9574

jburel · 2012-09-04T12:38:29Z

@gusferguson, @joshmoore: The reported problem is covered by another PR. @gusferguson validated the text using howe. That PR can be merged.

Sprint3 review

gusferguson · 2012-09-05T10:18:13Z

@jburel - The old warning message is still present in the script window and appears even when running the script on a single image or images from the same group. Is this intentional?

jburel · 2012-09-05T10:20:43Z

@gusferguson: Strange... Are you using today's build. If yes could you attach a screenshot to the ticket? Thanks

gusferguson · 2012-09-05T10:28:17Z

Yes using todays. Attached to https://trac.openmicroscopy.org.uk/ome/ticket/9574 - Windows 7 - Parallels Desktop.png

jburel added 3 commits August 31, 2012 11:38

Fix tooltip when importer is a standalone app (see #9566)

7e08dc5

Cleaning.

da30223

Modify wording when running scripts (see #9566)

574eab6

This is only displayed when the objects are not in the same group.

Modify text following comment from Gus.

5092e37

joshmoore added a commit that referenced this pull request Sep 5, 2012

Merge pull request #328 from jburel/sprint3-review

6570ec0

Sprint3 review

joshmoore merged commit 6570ec0 into ome:develop Sep 5, 2012

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Sprint3 review#328

Sprint3 review#328
joshmoore merged 4 commits intoome:developfrom
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jburel commented Aug 31, 2012

Uh oh!

gusferguson commented Sep 3, 2012

Uh oh!

jburel commented Sep 3, 2012

Uh oh!

gusferguson commented Sep 4, 2012

Uh oh!

joshmoore commented Sep 4, 2012

Uh oh!

joshmoore commented Sep 4, 2012

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gusferguson commented Sep 4, 2012

Uh oh!

gusferguson commented Sep 4, 2012

Uh oh!

jburel commented Sep 4, 2012

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gusferguson commented Sep 5, 2012

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jburel commented Sep 5, 2012

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gusferguson commented Sep 5, 2012

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jburel commented Aug 31, 2012

Uh oh!

gusferguson commented Sep 3, 2012

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jburel commented Sep 3, 2012

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gusferguson commented Sep 4, 2012

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joshmoore commented Sep 4, 2012

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joshmoore commented Sep 4, 2012

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gusferguson commented Sep 4, 2012

Uh oh!

gusferguson commented Sep 4, 2012

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jburel commented Sep 4, 2012

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gusferguson commented Sep 5, 2012

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jburel commented Sep 5, 2012

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gusferguson commented Sep 5, 2012

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