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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

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.

comment:3 Changed 14 years ago by jmoore

(In [6737]) see #1750 - Initial support for arrays in Hibernate and blitz (cF NDIM)

comment:4 Changed 14 years ago by jmoore

(In [6738]) see #1750 - Adding slightly modified sql array support from Hibernate forum

comment:5 Changed 14 years ago by jmoore

(In [6739]) see #1750 - 4.2 Database mapping changes

comment:6 Changed 14 years ago by jmoore

(In [6741]) see #1750 - RC1 SQL for 4.2 DB, code and tests compile. Needs review!

comment:7 Changed 14 years ago by jmoore

(In [6744]) see #1750 - Build fixes for simplifying model creation / testing

NB: This allows the following usage of bin/omero db script

   FILE=`omero db script "" "" ome | perl -pe 's/^Saving to (.*?)$/$1/'`
   psql omero -f $FILE

comment:8 Changed 14 years ago by jmoore

(In [6749]) see #1750 - More test fixes

comment:9 Changed 14 years ago by jmoore

(In [6751]) see #1750 - Making SqlArray Java 6 compatible

comment:10 Changed 14 years ago by jmoore

(In [6752]) see #1750 - But for Java5 we have to remove the @Override annotation on SqlArray.free()

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

(In [6758]) see #1750, #2287 - Fixing FilterSet links and the naming of linked objects

comment:14 Changed 14 years ago by jmoore

(In [6759]) see #1750 - Re-adding PlateAcquisition start and end time

comment:15 Changed 14 years ago by cxallan

(In [6762]) Fixed server side metadata store issues that arose from data model updates. (See #1750)

comment:16 Changed 14 years ago by cxallan

(In [6763]) Fixed reference tests that arose from data model updates; tests all pass. (See #1750)

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

(In [6776]) see #1750 - Fixing TextI reference in OmeroPopo.py

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

(In [6796]) see #1750 - Compile fix r6795

comment:28 Changed 14 years ago by jmoore

(In [6799]) see #1750 - more compile fixes

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

(In [7000]) see #1750, #2353 - Modifying annotations (+term;-uri/query/tb)

comment:33 Changed 14 years ago by jmoore

(In [7001]) see #1750 - Making WellSample.plateAcquisition nullable

comment:34 Changed 14 years ago by jmoore

(In [7320]) DB 4.2-RC10. See #1750

comment:35 Changed 14 years ago by jmoore

(In [7325]) Initial version of OMERO4.2__0 upgrade script (See #1750)

comment:36 Changed 14 years ago by jmoore

(In [7327]) Possible unit-test system for DB upgrades. (See #1750)

comment:37 Changed 14 years ago by jmoore

(In [7328]) Minor fixes to mappings and renaming to OMERO4.20. (See #1750)

comment:38 Changed 14 years ago by jmoore

(In [7329]) OMERO4.2__0 scripts with working upgrade. (See #1750)

comment:39 Changed 14 years ago by jmoore

(In [7330]) Updating internal use of original_metadata.txt to match OMERO4.2__0. (See #1750, #1753)

comment:40 Changed 14 years ago by jmoore

(In [7338]) Fixing OMERO4.2__0 for PostgreSQL 8.2+ (See #1750)

comment:41 Changed 14 years ago by jmoore

(In [7371]) Moving 4.1 scripts to 'user' group (See #1750)

comment:42 Changed 14 years ago by jmoore

(In [7394]) Working omero report before refactoring (See #1750)

comment:43 Changed 14 years ago by jmoore

(In [7395]) Report now embedded into OMERO4.1__0.sql with \i and using ACTION variable (See #1750)

comment:44 Changed 14 years ago by jmoore

(In [7406]) Removing now unneeded ome_nextval(unknown) functions (See #1750, r7338)

comment:45 Changed 14 years ago by jmoore

(In [7428]) Adding user photo handling to db upgrade script (See #1750)

comment:46 Changed 14 years ago by jmoore

(In [7486]) Ignoring all non-system permissions on update (See #1750, #1434)

comment:47 Changed 14 years ago by jmoore

(In [7492]) DB 4.2__0 improvements (See #1750 & #2204, Fix #2565 & #2573)

comment:48 Changed 14 years ago by jmoore

(In [7502]) Adding example SQL cleanup script (See #1750)

comment:49 Changed 14 years ago by jmoore

(In [7504]) Replacing missing exception in report (See #1750)

comment:50 Changed 14 years ago by jmoore

(In [7505]) Scripts updated for PG 8.1 with working upgrade (See #1750 & #2204)

comment:51 Changed 14 years ago by jmoore

(In [7508]) Storing seq_table values in new _lock_ids (See #1750)

comment:52 Changed 14 years ago by jmoore

(In [7512]) Lowering all group permissions on upgrade (See #1750, #2204)

comment:53 Changed 14 years ago by jmoore

(In [7515]) Inserting all of the permissions report file in to OMERO4.1__0.sql to prevent errors (See #1750)

comment:54 Changed 14 years ago by jmoore

  • Resolution set to fixed
  • Status changed from new to closed
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