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] -- 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]
