RawFileStore et al. should keep size in sync

[jamoore]

I had an interesting problem while working on the scripting engine: I attempt to hack a file under /OMERO/Files leaving it a bit larger than the size in the table. This caused all downloads to fail, since the length was taken from the database.

We should probably include some sanity checks in preparation for multiple repositories.

Possibilities:

• on setFileId check the the size and timestamp for discrepancies

[jmoore]

#1961 contains a portion of this, specifically for script param integration.

[jmoore]

See #2095

[jmoore]

(In [6568]) fix #1961, see #1501 - Adding save to RFS.close

This commit checks both the size and the sha1 of
file objects on RawFileStore.close(). This
adds an EventLog and therefore kicks off indexing
(see #2098)

[jmoore]

(In [6602]) fix #2161 - adding RFS.save (see #1961, #1501)

[jmoore]

One issue with this will be that if a session times out, it becomes difficult to close it:

2010-04-14 08:38:30,794 ERROR [ ome.services.blitz.impl.ServiceFactoryI] (.Server-23) Error destroying servant: 86:24:41:32:7aa3f55e:127f91236d3:-7ee9omero.api.RawFileStore=omero.api._RawFileStoreTie@5456cf60
ome.conditions.SessionTimeoutException: Session (started=2010-04-14 08:26:06.718, hits=366, last access=2010-04-14 08:26:07.501) exceeded timeToIdle (600000) by 143292 ms
	at ome.services.sessions.state.SessionCache.getElementNullOrThrowOnTimeout(SessionCache.java:307)
	at ome.services.sessions.state.SessionCache.getSessionContext(SessionCache.java:235)
	at ome.services.sessions.SessionManagerImpl.getSessionStats(SessionManagerImpl.java:510)
	at ome.services.sessions.stats.PerSessionStats.stats(PerSessionStats.java:31)
	at ome.services.sessions.stats.DelegatingStats.loadedObjects(DelegatingStats.java:43)
	at ome.services.sessions.stats.DelegatingStats.loadedObjects(DelegatingStats.java:44)
	at ome.security.basic.OmeroInterceptor.onLoad(OmeroInterceptor.java:128)
	at org.hibernate.event.def.DefaultPreLoadEventListener.onPreLoad(DefaultPreLoadEventListener.java:41)
	at org.hibernate.engine.TwoPhaseLoad.initializeEntity(TwoPhaseLoad.java:149)
	at org.hibernate.loader.Loader.initializeEntitiesAndCollections(Loader.java:898)
	at org.hibernate.loader.Loader.doQuery(Loader.java:773)
	at org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:270)
	at org.hibernate.loader.Loader.loadEntity(Loader.java:1933)
	at org.hibernate.loader.entity.AbstractEntityLoader.load(AbstractEntityLoader.java:86)
	at org.hibernate.loader.entity.AbstractEntityLoader.load(AbstractEntityLoader.java:76)
	at org.hibernate.persister.entity.AbstractEntityPersister.load(AbstractEntityPersister.java:3270)
	at org.hibernate.event.def.DefaultLoadEventListener.loadFromDatasource(DefaultLoadEventListener.java:496)
	at org.hibernate.event.def.DefaultLoadEventListener.doLoad(DefaultLoadEventListener.java:477)
	at org.hibernate.event.def.DefaultLoadEventListener.load(DefaultLoadEventListener.java:227)
	at org.hibernate.event.def.DefaultLoadEventListener.onLoad(DefaultLoadEventListener.java:147)
	at org.hibernate.impl.SessionImpl.fireLoad(SessionImpl.java:1080)
	at org.hibernate.impl.SessionImpl.immediateLoad(SessionImpl.java:1018)
	at org.hibernate.proxy.AbstractLazyInitializer.initialize(AbstractLazyInitializer.java:176)
	at org.hibernate.Hibernate.initialize(Hibernate.java:346)
	at ome.logic.QueryImpl$1.doInHibernate(QueryImpl.java:173)
	at org.springframework.orm.hibernate3.HibernateTemplate.doExecute(HibernateTemplate.java:406)
	at org.springframework.orm.hibernate3.HibernateTemplate.execute(HibernateTemplate.java:339)
	at ome.logic.QueryImpl.get(QueryImpl.java:156)
        ...
	at $Proxy64.close(Unknown Source)
	at ome.services.blitz.impl.AbstractAmdServant.close_async(AbstractAmdServant.java:216)
	at ome.services.blitz.impl.AbstractAmdServant.close(AbstractAmdServant.java:190)
	at ome.services.blitz.impl.ServiceFactoryI.doDestroy(ServiceFactoryI.java:709)
	at ome.services.blitz.impl.ServiceFactoryI.destroy(ServiceFactoryI.java:639)
	at Glacier2._SessionDisp.___destroy(_SessionDisp.java:82)
	at omero.api._ServiceFactoryDisp.__dispatch(_ServiceFactoryDisp.java:1231)
	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)
2010-04-14 08:38:30,795 INFO  [ ome.services.blitz.impl.ServiceFactoryI] (.Server-23) Unregistered servant:2838932c-f3be-40c7-9629-ba1e74d12563/86:24:41:32:7aa3f55e:127f91236d3:-7ee9omero.api.RawFileStore(omero.api._RawFileStoreTie@5456cf60)

[jmoore]

This has been working well for RFS. Opened #2348 as a carry on for other methods.

[jmoore]

(In [7015]) fix #2396 - rfs.save is needed. See #1501, #2161