Bug: script replace group.annotationLinks

[wmoore]

On a newly build develop server: (NB: didn't see this on howe - FS only).

$ bin/omero script replace 4 omero/export_scripts/Batch_Image_Export.py 
Using session a38fd6a8-19a0-4c5e-a6eb-5fd35073fb72 (root@localhost:4064). Idle timeout: 10.0 min. Current group: system
Traceback (most recent call last):
  File "/Users/will/Desktop/OMERO/dist/bin/omero", line 125, in <module>
    rv = omero.cli.argv()
  File "/Users/will/Desktop/OMERO/dist/lib/python/omero/cli.py", line 1195, in argv
    cli.invoke(args[1:])
  File "/Users/will/Desktop/OMERO/dist/lib/python/omero/cli.py", line 745, in invoke
    stop = self.onecmd(line, previous_args)
  File "/Users/will/Desktop/OMERO/dist/lib/python/omero/cli.py", line 814, in onecmd
    self.execute(line, previous_args)
  File "/Users/will/Desktop/OMERO/dist/lib/python/omero/cli.py", line 894, in execute
    args.func(args)
  File "/Users/will/Desktop/OMERO/dist/lib/python/omero/plugins/script.py", line 590, in replace
    scriptSvc.editScript(ofile, scriptText)
  File "/Users/will/Desktop/OMERO/dist/lib/python/omero_api_IScript_ice.py", line 583, in editScript
    return _M_omero.api.IScript._op_editScript.invoke(self, ((fileObject, scriptText), _ctx))
omero.InternalException: exception ::omero::InternalException
{
    serverStackTrace = ome.conditions.InternalException:  Wrapped Exception: (org.springframework.orm.hibernate3.HibernateSystemException):
Exception occurred inside getter of ome.model.meta.ExperimenterGroup.annotationLinks; nested exception is org.hibernate.PropertyAccessException: Exception occurred inside getter of ome.model.meta.ExperimenterGroup.annotationLinks
	at org.springframework.orm.hibernate3.SessionFactoryUtils.convertHibernateAccessException(SessionFactoryUtils.java:679)
	at org.springframework.orm.hibernate3.HibernateAccessor.convertHibernateAccessException(HibernateAccessor.java:412)
	at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:117)
	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:241)
	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 $Proxy66.doWork(Unknown Source)
	at ome.services.util.Executor$Impl.execute(Executor.java:416)
	at ome.services.util.Executor$Impl.execute(Executor.java:360)
	at ome.services.scripts.ScriptRepoHelper.update(ScriptRepoHelper.java:434)
	at ome.services.blitz.impl.ScriptI$6.call(ScriptI.java:289)
	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.editScript_async(ScriptI.java:259)
	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 $Proxy81.editScript_async(Unknown Source)
	at omero.api._IScriptTie.editScript_async(_IScriptTie.java:87)
	at omero.api._IScriptDisp.___editScript(_IScriptDisp.java:473)
	at omero.api._IScriptDisp.__dispatch(_IScriptDisp.java:658)
	at IceInternal.Incoming.invoke(Incoming.java:159)
	at Ice.ConnectionI.invokeAll(ConnectionI.java:2357)
	at Ice.ConnectionI.dispatch(ConnectionI.java:1208)
	at Ice.ConnectionI.message(ConnectionI.java:1163)
	at IceInternal.ThreadPool.run(ThreadPool.java:302)
	at IceInternal.ThreadPool.access$300(ThreadPool.java:12)
	at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:643)
	at java.lang.Thread.run(Thread.java:680)

    serverExceptionClass = ome.conditions.InternalException
    message =  Wrapped Exception: (org.springframework.orm.hibernate3.HibernateSystemException):
Exception occurred inside getter of ome.model.meta.ExperimenterGroup.annotationLinks; nested exception is org.hibernate.PropertyAccessException: Exception occurred inside getter of ome.model.meta.ExperimenterGroup.annotationLinks
}

[jamoore]

PR filed: ​https://github.com/openmicroscopy/openmicroscopy/pull/1291

[jmoore <josh@…>]

(In [e0a558bd2d0bbc43177705f141dfaa30438e718e/ome.git] on branch develop) Pass context to script helper (Fix #10970)

ScriptI was failing to pass the Ice.Current.ctx
value down to the script helper for use with
Executor.execute(Map<String, String>, ...)

bin/omero script replace now works as expected

Note: it still modifies the ID of the script!

[jmoore <josh@…>]

(In [9ec1621739b55ae8109eb5ae16a7d9df0d23654f/ome.git] on branch develop) Also load hasher actively (See #10970)

[Josh Moore <josh@…>]

(In [0afde412262e13976decfeec61ed4a82e0f812fe/ome.git] on branch develop) Merge pull request #1291 from joshmoore/10970-script-replace

Pass context to script helper (Fix #10970)

[jmoore <josh@…>]

(In [180b3b0a96470fb86438b1bfaa30d3464679b093/ome.git]on branches master, dev_4_4) Pass context to script helper (Fix #10970)

ScriptI was failing to pass the Ice.Current.ctx
value down to the script helper for use with
Executor.execute(Map<String, String>, ...)

bin/omero script replace now works as expected

Note: it still modifies the ID of the script!