I have upgraded a couple of servers. All are running in OpenSuse 10.2. In my case, I noticed that servers that contain BASE 1 migrated data fails the upgrade whereas all servers with only "new" data was successfully upgraded.
Jari Keith Ching wrote: > mirrored databases.. different OS and mysql versions > > successful update from 2.1.2 -> 2.2.0 using mysql 5.0.18-standard on MacOSX > > [86%] --Updating schema version: 25 -> 27... > [87%] --Updating schema version: 27 -> 28... > [87%] --Updating schema version: 28 -> 29... > [90%] Database updated successfully. > [95%] Installing web application... > [100%] Web application installed successfully. > > > arrghh.. failed update from 2.1.2 -> 2.2.0 using mysql 5.0.27-standard > on RHEL4 > > [0%] Building database.......... > [30%] Database built successfully. > [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...17:05:23,535 ERROR > Update:1150 - updateToSchemaVersion29: FAILED > net.sf.basedb.core.BaseException: Object with id: 2 was not of the > specified subclass: net.sf.basedb.core.data.MeasuredBioMaterialData > (Discriminator: 1914725632) > 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: 2 was not > of the specified subclass: > net.sf.basedb.core.data.MeasuredBioMaterialData (Discriminator: 1914725632) > 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: 2 was not of the > specified subclass: net.sf.basedb.core.data.MeasuredBioMaterialData > (Discriminator: 1914725632) > > > net.sf.basedb.core.BaseException: Object with id: 2 was not of the > specified subclass: net.sf.basedb.core.data.MeasuredBioMaterialData > (Discriminator: 1914725632) > 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: 2 was not > of the specified subclass: > net.sf.basedb.core.data.MeasuredBioMaterialData (Discriminator: 1914725632) > 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 > > > -keith > > > Jari Häkkinen wrote: >> I have successfully upgraded from 2.1.2 to 2.2. This is of course not >> exactly the same upgrade as Chris. >> >> >> Jari >> >> >> Nicklas Nordborg wrote: >> >>> Chris Wiita wrote: >>> >>>> I attempted a update to Base2.2 from a 2.1.1 installation. Executing >>>> updatedb.sh worked until the "Updating database" step: >>>> >>> I really don't know why this is happening. The error message says >>> something about "Discriminator: 0" but we never use a 0, only the values >>> 1, 2, 3 and 4, which have the following meaning: >>> >>> 1 = Biosource >>> 2 = Sample >>> 3 = Extract >>> 4 = Labeled extract >>> >>> Can you check the "BioMaterials" table and check if any row have a value >>> in the "discriminator" column that is not in the 1-4 range? >>> >>> If there are such values they must be changed to one of the above. Then >>> we have to ask the question how they got there in the first place. >>> >>> If there are only 1-4 the error message complaining about >>> "Discriminator: 0" is a bit confusing and is something that we need to >>> investigate further to see if we can reproduce the error. >>> >>> Another option is to manually change the schema version to 29, but then >>> you will not get the changes between 28 and 29. Luckily, this change >>> doesn't involve any changes to the database. It only recalculates the >>> remaining quantity of all biomaterials since a bug may have caused them >>> to be incorrect. See ticket #466: http://base.thep.lu.se/ticket/466 >>> >>> I don't think it was a good idea to run the update script from an >>> earlier version. I really don't know if that might have messed things up >>> more or not. I'll add a ticket to make sure that the update script >>> checks the schema version and doesn't execute if it is too high. In any >>> case it is good that the main program does the check and refuses to >>> start since it can lead to incorrect data beeing inserted into the >>> database. >>> >>> It is not possible to revert back to an earlier version. You can only do >>> this if you have made a backup of the database. >>> >>> /Nicklas >>> >>> >>>> ---------- >>>> [75%] Updating database... >>>> [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 >>>> >>>> [90%] Database update failed: Object with id: 1 was not of the >>>> specified subclass: net.sf.basedb.core.data.MeasuredBioMaterialData >>>> (Discriminator: 0) >>>> >>>> >>>> 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 >>>> ---------- >>>> >>>> First, what could this be? I'm running a mysql database, the >>>> base.config is set up properly, and no BASE files have ever been >>>> modified--it's a very vanilla installation. It seemed like a minor >>>> error, so I just switched back to my old 2.1.1 installation (switching >>>> folders, ensuring the www link in my tomcat webapp directory was >>>> correct). I ran updatedb.sh on that install (perhaps mistakenly), and >>>> got a error from it, as follows. >>>> >>>> ---------- >>>> [75%] Updating database... >>>> [90%] Database updated successfully. >>>> [95%] Installing web application...12:15:20,332 ERROR Application:401 >>>> - Schema version mismatch: database schema version=28; expected=20; >>>> Please update the BASE code before starting. >>>> >>>> >>>> net.sf.basedb.core.BaseException: Schema version mismatch: database >>>> schema version=28; expected=20; Please update the BASE code before >>>> starting. >>>> at net.sf.basedb.core.Application.start(Application.java:402) >>>> at net.sf.basedb.core.Application.start(Application.java:317) >>>> at net.sf.basedb.install.Webclient.install(Webclient.java:92) >>>> at net.sf.basedb.install.InitDB.main(InitDB.java:72) >>>> ---------- >>>> >>>> >>>> If it's reporting a successful database update, I would think the schema >>>> version would have to be consistent, so the mismatch at the last step >>>> doesn't make sense. Ignoring the error and attempting to load the BASE >>>> interface returns the following 500 server error: >>>> >>>> ---------- >>>> >>>> type Exception report >>>> message >>>> description The server encountered an internal error () that prevented >>>> it from fulfilling this request. >>>> exception >>>> >>>> net.sf.basedb.core.BaseException: Schema version mismatch: database >>>> schema version=28; expected=20; Please update the BASE code before >>>> starting. >>>> net.sf.basedb.core.Application.start(Application.java:402) >>>> net.sf.basedb.core.Application.start(Application.java:301) >>>> net.sf.basedb.core.Application.getSessionControl(Application.java:736) >>>> net.sf.basedb.clients.web.Base.getSessionControl(Base.java:111) >>>> org.apache.jsp.index_jsp._jspService(index_jsp.java:66) >>>> org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:97) >>>> javax.servlet.http.HttpServlet.service(HttpServlet.java:802) >>>> >>>> org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:332) >>>> >>>> org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:314) >>>> org.apache.jasper.servlet.JspServlet.service(JspServlet.java:264) >>>> javax.servlet.http.HttpServlet.service(HttpServlet.java:802) >>>> >>>> net.sf.basedb.clients.web.servlet.CharacterEncodingFilter.doFilter(CharacterEncodingFilter.java:71) >>>> >>>> ---------- >>>> >>>> So 2.2's update script will update the version 28 to 29 (by the looks of >>>> it) except it isn't working on my install--did it update the schema >>>> earlier in the script (to 28), so that the database is no longer >>>> compatible with the 2.1.1 version (which appears to want version 20)? >>>> If the 2.2 update isn't an obvious fix, is there a way to revert to the >>>> 2.1 schema? Thanks. >>>> >>>> --Chris Wiita >>>> >>>> ------------------------------------------------------------------------- >>>> Using Tomcat but need to do more? Need to support web services, security? >>>> Get stuff done quickly with pre-integrated technology to make your job >>>> easier. >>>> Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo >>>> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 >>>> _______________________________________________ >>>> The BASE general discussion mailing list >>>> basedb-users@lists.sourceforge.net >>>> unsubscribe: send a mail with subject "unsubscribe" to >>>> [EMAIL PROTECTED] >>>> >>> ------------------------------------------------------------------------- >>> Using Tomcat but need to do more? Need to support web services, security? >>> Get stuff done quickly with pre-integrated technology to make your job >>> easier. >>> Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo >>> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 >>> _______________________________________________ >>> The BASE general discussion mailing list >>> basedb-users@lists.sourceforge.net >>> unsubscribe: send a mail with subject "unsubscribe" to >>> [EMAIL PROTECTED] >>> >> >> > > -- > Keith Ching, Ph.D. > Bioinformatics, Laboratory of Gene Regulation > Ludwig Institute for Cancer Research > 9500 Gilman Drive, #0653 > CMM East, Room 3020 > La Jolla, CA 92093-0653 > > [EMAIL PROTECTED] > 858-822-5767 > > > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------- > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job easier. > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > > > ------------------------------------------------------------------------ > > _______________________________________________ > The BASE general discussion mailing list > basedb-users@lists.sourceforge.net > unsubscribe: send a mail with subject "unsubscribe" to > [EMAIL PROTECTED] -- Jari Hakkinen, PhD Complex Systems Division mailto:[EMAIL PROTECTED] Department of Theoretical Physics phone: +46 (0)46 2229347 Lund University fax: +46 (0)46 2229686 Solvegatan 14a, SE-223 62 Lund, Sweden http://www.thep.lu.se ------------------------------------------------------------------------- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier. Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 _______________________________________________ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
