User Story #1750 (closed)
Opened 14 years ago
Closed 14 years ago
4.2 Database upgrade
Reported by: | jamoore | Owned by: | jamoore |
---|---|---|---|
Priority: | critical | Milestone: | OMERO-Beta4.2 |
Component: | Security | Keywords: | n.a. |
Cc: | ajpatterson | Story Points: | n.a. |
Sprint: | n.a. | Importance: | Mandatory |
Total Remaining Time: | 0.0d | Estimated Remaining Time: | n.a. |
Description (last modified by jburel)
The first big task of the DB upgrade will be making sure permissions are sensible, but other DB changes are being placed here as an umbrella e.g. model evolution (SPW and Filter mainly)
Previous ideas.
- Make all groups private (currently rw-r-r)
- Make all group data private (enums?)
- movie ns to file.mimetype??
- "openmicroscopy.org/omero/movie/mpeg";
- "openmicroscopy.org/omero/movie/qt";
- "openmicroscopy.org/omero/movie/wmv";
Change History (54)
comment:1 Changed 14 years ago by jmoore
- Cc ajpatterson added
- Description modified (diff)
- Importance set to Mandatory
- Sprint set to 2010-04-16 (7)
- Summary changed from Permissions: database upgrade to 4.2 Database upgrade
comment:2 Changed 14 years ago by jmoore
comment:3 Changed 14 years ago by jmoore
comment:4 Changed 14 years ago by jmoore
comment:5 Changed 14 years ago by jmoore
comment:6 Changed 14 years ago by jmoore
comment:7 Changed 14 years ago by jmoore
comment:8 Changed 14 years ago by jmoore
comment:9 Changed 14 years ago by jmoore
comment:10 Changed 14 years ago by jmoore
comment:11 Changed 14 years ago by jburel
- Description modified (diff)
comment:12 Changed 14 years ago by jmoore
(In [6756]) see #1750 - Fixing misspelling of emissionSFilterLinks?
comment:13 Changed 14 years ago by jmoore
comment:14 Changed 14 years ago by jmoore
comment:15 Changed 14 years ago by cxallan
comment:16 Changed 14 years ago by cxallan
comment:17 Changed 14 years ago by wmoore
Rendering Engine:
Traceback (most recent call last): File "test/integration/emanScripts.py", line 189, in testImagesFromRois iId = importImage(session, imagePath, imageName) File "test/integration/emanScripts.py", line 627, in importImage image = scriptUtil.createNewImage(pixelsService, rawPixelStore, renderingEngine, pixelsType, gateway, [plane2D], imageName, "description", dataset=None) File "/Users/will/Documents/workspace/Omero/dist/lib/python/omero/util/script_utils.py", line 666, in createNewImage resetRenderingSettings(renderingEngine, pixelsId, theC, minValue, maxValue) File "/Users/will/Documents/workspace/Omero/dist/lib/python/omero/util/script_utils.py", line 609, in resetRenderingSettings renderingEngine.resetDefaults() File "/Users/will/Documents/workspace/Omero/dist/lib/python/omero_api_RenderingEngine_ice.py", line 387, in resetDefaults return _M_omero.api.RenderingEngine._op_resetDefaults.invoke(self, ((), _ctx)) QueryException: exception ::omero::QueryException { serverStackTrace = ome.services.query.QueryException: Illegal query:select channel from LogicalChannel as channel left outer join fetch channel.filterSet as filter left outer join fetch filter.emFilter as ef left outer join fetch filter.exFilter as exf left outer join fetch ef.transmittanceRange as efTrans left outer join fetch exf.transmittanceRange as exfTrans left outer join fetch channel.secondaryEmissionFilter as emfilter left outer join fetch emfilter.transmittanceRange as emTrans left outer join fetch channel.secondaryExcitationFilter as exfilter left outer join fetch exfilter.transmittanceRange as exTrans left outer join fetch channel.lightSourceSettings as lss left outer join fetch lss.lightSource as ls where channel.id = :id could not resolve property: emFilter of: ome.model.acquisition.FilterSet [select channel from ome.model.core.LogicalChannel as channel left outer join fetch channel.filterSet as filter left outer join fetch filter.emFilter as ef left outer join fetch filter.exFilter as exf left outer join fetch ef.transmittanceRange as efTrans left outer join fetch exf.transmittanceRange as exfTrans left outer join fetch channel.secondaryEmissionFilter as emfilter left outer join fetch emfilter.transmittanceRange as emTrans left outer join fetch channel.secondaryExcitationFilter as exfilter left outer join fetch exfilter.transmittanceRange as exTrans left outer join fetch channel.lightSourceSettings as lss left outer join fetch lss.lightSource as ls where channel.id = :id] at ome.services.query.StringQuery.buildQuery(StringQuery.java:60) at ome.services.query.Query.doInHibernate(Query.java:222) at org.springframework.orm.hibernate3.HibernateTemplate.doExecute(HibernateTemplate.java:406) at org.springframework.orm.hibernate3.HibernateTemplate.execute(HibernateTemplate.java:339) at ome.logic.QueryImpl.execute(QueryImpl.java:141) at ome.logic.QueryImpl.findByQuery(QueryImpl.java:337) at ome.logic.RenderingSettingsImpl.loadLogicalChannel(RenderingSettingsImpl.java:367) at ome.logic.RenderingSettingsImpl.resetChannelBindings(RenderingSettingsImpl.java:744) at ome.logic.RenderingSettingsImpl.resetDefaults(RenderingSettingsImpl.java:566) at ome.logic.RenderingSettingsImpl.resetDefaults(RenderingSettingsImpl.java:485) at ome.logic.RenderingSettingsImpl.resetDefaults(RenderingSettingsImpl.java:1248) at ome.services.RenderingBean$13.doWork(RenderingBean.java:1540) at sun.reflect.GeneratedMethodAccessor193.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:592) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:393) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) at ome.security.basic.EventHandler.invoke(EventHandler.java:144) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:111) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:175) 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 $Proxy54.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:323) at ome.services.RenderingBean._resetDefaults(RenderingBean.java:1537) at ome.services.RenderingBean.resetDefaults(RenderingBean.java:635) 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:592) 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:111) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202) at $Proxy70.resetDefaults(Unknown Source) 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:592) 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 $Proxy70.resetDefaults(Unknown Source) 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:592) 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:132) at ome.services.blitz.impl.RenderingEngineI.resetDefaults_async(RenderingEngineI.java:406) at omero.api._RenderingEngineTie.resetDefaults_async(_RenderingEngineTie.java:281) at omero.api._RenderingEngineDisp.___resetDefaults(_RenderingEngineDisp.java:1266) at omero.api._RenderingEngineDisp.__dispatch(_RenderingEngineDisp.java:1616) 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)
comment:18 Changed 14 years ago by cxallan
- Sprint changed from 2010-04-16 (7) to 2010-04-30 (8)
comment:19 Changed 14 years ago by jmoore
see r6766 for enumerations.
comment:20 Changed 14 years ago by jmoore
comment:21 Changed 14 years ago by jmoore
(In [6783]) see #1750 - 4.2-RC1 DB including fix for #2293 (ScreenPlateWell)
comment:22 Changed 14 years ago by jmoore
(In [6785]) see #1750, #2293 - Commenting out sections of OmeroMetadata? for Chris
comment:23 Changed 14 years ago by cxallan
(In [6788]) Fixed FilterSet? query used during resetDefaults(). (See #1750).
comment:24 Changed 14 years ago by jmoore
- Sprint 2010-04-30 (8) deleted
comment:25 Changed 14 years ago by jmoore
(In [6793]) see #1750 - Reversing plate acquisition / well sample relationship as per xml:ticket:121
comment:26 Changed 14 years ago by jmoore
(In [6795]) see #1750 - Changing timepoint to timestamp (xml:ticket:120)wq
comment:27 Changed 14 years ago by jmoore
comment:28 Changed 14 years ago by jmoore
comment:29 Changed 14 years ago by jmoore
(In [6807]) see #1750 - Fixing RegionsOfInterest example's use of TextI
comment:30 Changed 14 years ago by jmoore
- Description modified (diff)
comment:31 Changed 14 years ago by jburel
- Description modified (diff)
comment:32 Changed 14 years ago by jmoore
comment:33 Changed 14 years ago by jmoore
comment:34 Changed 14 years ago by jmoore
comment:35 Changed 14 years ago by jmoore
comment:36 Changed 14 years ago by jmoore
comment:37 Changed 14 years ago by jmoore
comment:38 Changed 14 years ago by jmoore
comment:39 Changed 14 years ago by jmoore
comment:40 Changed 14 years ago by jmoore
comment:41 Changed 14 years ago by jmoore
comment:42 Changed 14 years ago by jmoore
comment:43 Changed 14 years ago by jmoore
comment:44 Changed 14 years ago by jmoore
comment:45 Changed 14 years ago by jmoore
comment:46 Changed 14 years ago by jmoore
comment:47 Changed 14 years ago by jmoore
comment:48 Changed 14 years ago by jmoore
comment:49 Changed 14 years ago by jmoore
comment:50 Changed 14 years ago by jmoore
comment:51 Changed 14 years ago by jmoore
comment:52 Changed 14 years ago by jmoore
comment:53 Changed 14 years ago by jmoore
comment:54 Changed 14 years ago by jmoore
- Resolution set to fixed
- Status changed from new to closed
Note: all DB modifications will be happening in a single commit tied to this ticket as opposed to the individual tasks because of the interruptions caused by small DB changes.