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#488 closed defect (fixed)

Upgrade 2.1.1 to 2.2 fails

Reported by:	Nicklas Nordborg	Owned by:	everyone
Priority:	blocker	Milestone:	BASE 2.2.1
Component:	install	Version:	2.2
Keywords:		Cc:

Description (last modified by Nicklas Nordborg)

Here is the stacktrace:

[87%]   --Updating schema version: 28 -> 29...12:06:13,579 ERROR 
Update:1150 - updateToSchemaVersion29: FAILED
net.sf.basedb.core.BaseException: Object with id: 1 was not of the 
specified subclass: net.sf.basedb.core.data.MeasuredBioMaterialData 
(Discriminator: 0)
        at 
net.sf.basedb.core.HibernateUtil.loadList(HibernateUtil.java:1355)
        at 
net.sf.basedb.core.Update.updateToSchemaVersion29(Update.java:1105)
        at net.sf.basedb.core.Update.updateDatabase(Update.java:504)
        at net.sf.basedb.install.InitDB.main(InitDB.java:69)
Caused by: org.hibernate.WrongClassException: Object with id: 1 was not 
of the specified subclass: 
net.sf.basedb.core.data.MeasuredBioMaterialData (Discriminator: 0)
        at org.hibernate.loader.Loader.getInstanceClass(Loader.java:1444)
        at 
org.hibernate.loader.Loader.instanceNotYetLoaded(Loader.java:1275)
        at org.hibernate.loader.Loader.getRow(Loader.java:1197)
        at org.hibernate.loader.Loader.getRowFromResultSet(Loader.java:568)
        at org.hibernate.loader.Loader.doQuery(Loader.java:689)
        at 
org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:224)
        at org.hibernate.loader.Loader.doList(Loader.java:2211)
        at 
org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2095)
        at org.hibernate.loader.Loader.list(Loader.java:2090)
        at org.hibernate.loader.hql.QueryLoader.list(QueryLoader.java:375)
        at 
org.hibernate.hql.ast.QueryTranslatorImpl.list(QueryTranslatorImpl.java:338)
        at 
org.hibernate.engine.query.HQLQueryPlan.performList(HQLQueryPlan.java:172)
        at org.hibernate.impl.SessionImpl.list(SessionImpl.java:1121)
        at org.hibernate.impl.QueryImpl.list(QueryImpl.java:79)
        at 
net.sf.basedb.core.HibernateUtil.loadList(HibernateUtil.java:1351)
        ... 3 more

For more info see the mailing list archive: http://sourceforge.net/mailarchive/forum.php?thread_id=31614751&forum_id=12992

Change History (9)

comment:1 by Nicklas Nordborg, 17 years ago

Summary:	Updade 2.1.1 to 2.2 fails → Upgrade 2.1.1 to 2.2 fails

comment:2 by Nicklas Nordborg, 17 years ago

Description:	modified (diff)

comment:3 by Jari Häkkinen, 17 years ago

I have successfully upgraded from 2.1.2 to 2.2. This is of course not exactly the same upgrade as Chris but it goes from schema 20 to 29 in steps:

[75%] Updating database... [83%] --Updating schema version: 20 -> 23... [85%] --Updating schema version: 23 -> 24... [85%] --NOTE! The "FileValues" table is no longer used by BASE. It may be removed from the database. [85%] --Updating schema version: 24 -> 25... [86%] --Updating schema version: 25 -> 27... [87%] --Updating schema version: 27 -> 28... [87%] --Updating schema version: 28 -> 29... [90%] Database updated successfully.

comment:4 by Jari Häkkinen, 17 years ago

Updating another server gives a similar stack trace as Chrises

[0%]    Building database...................................................
[30%]   Database built successfully.01:49:17,461  WARN BasicResourcePool:972 - Failed to destroy resource: com.mchange.v2.c3p0.impl.NewPooledConnection@dec3c6d
java.lang.InterruptedException
        at com.mysql.jdbc.Connection.realClose(Connection.java:4796)
        at com.mysql.jdbc.Connection.close(Connection.java:2172)
        at com.mchange.v2.c3p0.impl.NewPooledConnection.close(NewPooledConnection.java:474)
        at com.mchange.v2.c3p0.impl.NewPooledConnection.close(NewPooledConnection.java:191)
        at com.mchange.v2.c3p0.impl.C3P0PooledConnectionPool$1PooledConnectionResourcePoolManager.destroyResource(C3P0PooledConnectionPool.java:470)
        at com.mchange.v2.resourcepool.BasicResourcePool$1DestroyResourceTask.run(BasicResourcePool.java:964)
        at com.mchange.v2.resourcepool.BasicResourcePool.destroyResource(BasicResourcePool.java:989)
        at com.mchange.v2.resourcepool.BasicResourcePool.removeResource(BasicResourcePool.java:1406)
        at com.mchange.v2.resourcepool.BasicResourcePool.removeResource(BasicResourcePool.java:1378)
        at com.mchange.v2.resourcepool.BasicResourcePool.access$300(BasicResourcePool.java:32)
        at com.mchange.v2.resourcepool.BasicResourcePool$1RefurbishCheckinResourceTask.run(BasicResourcePool.java:1245)
        at com.mchange.v2.async.ThreadPoolAsynchronousRunner$PoolThread.run(ThreadPoolAsynchronousRunner.java:547)

[35%]   Initialising database...
[36%]   --Creating quota types...
[37%]   --Creating quota...
[39%]   --Creating roles...
[40%]   --Creating users...
[42%]   --Creating groups...
[43%]   --Creating keys...
[44%]   --Creating protocol types...
[46%]   --Creating hardware types...
[47%]   --Creating hardware...
[49%]   --Creating software types...
[50%]   --Creating software...
[51%]   --Creating directories...
[53%]   --Creating file types...
[54%]   --Creating MIME types...
[56%]   --Creating plate geometries...
[57%]   --Creating plate mappings...
[58%]   --Creating labels...
[60%]   --Creating annotation types...
[61%]   --Creating clients...
[63%]   --Creating news...
[64%]   --Creating plugin definitions...
[67%]   --Creating formulas...
[68%]   --Creating job agents...
[70%]   Database initialised successfully.
[75%]   Updating database...
[83%]   --Updating schema version: 20 -> 23...
[85%]   --Updating schema version: 23 -> 24...
[85%]   --NOTE! The "FileValues" table is no longer used by BASE. It may be removed from the database.
[85%]   --Updating schema version: 24 -> 25...
[86%]   --Updating schema version: 25 -> 27...
[87%]   --Updating schema version: 27 -> 28...
[87%]   --Updating schema version: 28 -> 29...01:49:33,223 ERROR Update:1150 - updateToSchemaVersion29: FAILED
net.sf.basedb.core.BaseException: Object with id: 1 was not of the specified subclass: net.sf.basedb.core.data.MeasuredBioMaterialData (Discriminator: 24733184)
        at net.sf.basedb.core.HibernateUtil.loadList(HibernateUtil.java:1355)
        at net.sf.basedb.core.Update.updateToSchemaVersion29(Update.java:1105)
        at net.sf.basedb.core.Update.updateDatabase(Update.java:504)
        at net.sf.basedb.install.InitDB.main(InitDB.java:69)
Caused by: org.hibernate.WrongClassException: Object with id: 1 was not of the specified subclass: net.sf.basedb.core.data.MeasuredBioMaterialData (Discriminator: 24733184)
        at org.hibernate.loader.Loader.getInstanceClass(Loader.java:1444)
        at org.hibernate.loader.Loader.instanceNotYetLoaded(Loader.java:1275)
        at org.hibernate.loader.Loader.getRow(Loader.java:1197)
        at org.hibernate.loader.Loader.getRowFromResultSet(Loader.java:568)
        at org.hibernate.loader.Loader.doQuery(Loader.java:689)
        at org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:224)
        at org.hibernate.loader.Loader.doList(Loader.java:2211)
        at org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2095)
        at org.hibernate.loader.Loader.list(Loader.java:2090)
        at org.hibernate.loader.hql.QueryLoader.list(QueryLoader.java:375)
        at org.hibernate.hql.ast.QueryTranslatorImpl.list(QueryTranslatorImpl.java:338)
        at org.hibernate.engine.query.HQLQueryPlan.performList(HQLQueryPlan.java:172)
        at org.hibernate.impl.SessionImpl.list(SessionImpl.java:1121)
        at org.hibernate.impl.QueryImpl.list(QueryImpl.java:79)
        at net.sf.basedb.core.HibernateUtil.loadList(HibernateUtil.java:1351)
        ... 3 more

[90%]   Database update failed: Object with id: 1 was not of the specified subclass: net.sf.basedb.core.data.MeasuredBioMaterialData (Discriminator: 24733184)


net.sf.basedb.core.BaseException: Object with id: 1 was not of the specified subclass: net.sf.basedb.core.data.MeasuredBioMaterialData (Discriminator: 24733184)
        at net.sf.basedb.core.HibernateUtil.loadList(HibernateUtil.java:1355)
        at net.sf.basedb.core.Update.updateToSchemaVersion29(Update.java:1105)
        at net.sf.basedb.core.Update.updateDatabase(Update.java:504)
        at net.sf.basedb.install.InitDB.main(InitDB.java:69)
Caused by: org.hibernate.WrongClassException: Object with id: 1 was not of the specified subclass: net.sf.basedb.core.data.MeasuredBioMaterialData (Discriminator: 24733184)
        at org.hibernate.loader.Loader.getInstanceClass(Loader.java:1444)
        at org.hibernate.loader.Loader.instanceNotYetLoaded(Loader.java:1275)
        at org.hibernate.loader.Loader.getRow(Loader.java:1197)
        at org.hibernate.loader.Loader.getRowFromResultSet(Loader.java:568)
        at org.hibernate.loader.Loader.doQuery(Loader.java:689)
        at org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:224)
        at org.hibernate.loader.Loader.doList(Loader.java:2211)
        at org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2095)
        at org.hibernate.loader.Loader.list(Loader.java:2090)
        at org.hibernate.loader.hql.QueryLoader.list(QueryLoader.java:375)
        at org.hibernate.hql.ast.QueryTranslatorImpl.list(QueryTranslatorImpl.java:338)
        at org.hibernate.engine.query.HQLQueryPlan.performList(HQLQueryPlan.java:172)
        at org.hibernate.impl.SessionImpl.list(SessionImpl.java:1121)
        at org.hibernate.impl.QueryImpl.list(QueryImpl.java:79)
        at net.sf.basedb.core.HibernateUtil.loadList(HibernateUtil.java:1351)
        ... 3 more

comment:5 by Jari Häkkinen, 17 years ago

Trying to run the update script once more on the same database gives the same stack trace as Chris, i.e.

[87%]   --Updating schema version: 28 -> 29...01:54:32,610 ERROR Update:1150 - updateToSchemaVersion29: FAILED
net.sf.basedb.core.BaseException: Object with id: 1 was not of the specified subclass: net.sf.basedb.core.data.MeasuredBioMaterialData (Discriminator: 0)

comment:6 by Jari Häkkinen, 17 years ago

I upgraded a couple of more servers. I noticed that servers that contain BASE 1 migrated data fails the upgrade whereas all servers with only "new" data was successfully upgraded.

comment:7 by Martin Svensson, 17 years ago

(In [3120]) References #488. Update schema version without validating the measured biomaterial. Will make the upgrade to work, but some measured biomaterial can have wrong value in remaining quantity.

comment:8 by Johan Enell, 17 years ago

(In [3121]) References #488. Update schema version without validating the measured ?\226?\128?\166

comment:9 by Jari Häkkinen, 17 years ago

Resolution:	→ fixed
Status:	new → closed

This issue is returned to the original ticket:466. The upgrade problem is removed in release 2.2.1.

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