Re: [base] Bug fix release 2.2.1 is available now
Keith Ching wrote: hmm.. i had restored back to 2.1.2, then upgraded to 2.2.1 and it was working ok until i took ownership of some jobs as root.. then went to the trash can. it gave me this error: Object with id: 2 was not of the specified subclass: net.sf.basedb.core.data.BioMaterialData (Discriminator: 1746955520) and now most of the queries bomb out.. biosources, samples, scans, hybs, etc.. We have now been able to reproduce this on a fresh installation by only creating a single new sample. It appears to be bug in MySQL 5.0.27 and/or the JDBC driver (Connector/J 5.0.4). The problem never appears on MySQL 5.0.15 or 5.0.19 (the only two other version that we have available). MySQL has released 5.0.33 but only as source files and we have not tested if this release solves the problem. The problem also disappears in 5.0.27 if the 'useCursorFetch=true' option is removed from the 'db.url' setting in the base.config file. The drawback of removing this option is that the JDBC driver will load all data from a query into memory before returning it to the client. It will not affect regular interaction in the web interface since it only loads a few items at a time. It may cause problems for export and analysis plugins that handle a lot of data. For example, exporting all reporters or the data in a bioassayset. So, there are two possible solutions: * Don't use MySQL 5.0.27 * Remove the 'useCursorFetch=true' setting Which one is best to use is hard to tell. It probably depends on what the server is running. For a test/demo server I would use the second option, and hope that a new MySQL release will fix the problem. For a production server the second option might also be the best one to try first and then if you get out-of-memory problems try upgrading or downgrading MySQL (if that is possible). /Nicklas the tomcat log looks like this: 16:00:59,475 ERROR [jsp]:704 - Servlet.service() for servlet jsp threw exceptionjava.lang.NullPointerExceptionat org.apache.jsp.admin.plugindefinitions.edit_005fplugin_jsp.appendPermissionLetter(edit_005fplugin_jsp.java:65) at org.apache.jsp.admin.plugindefinitions.edit_005fplugin_jsp._jspService(edit_005fplugin_jsp.java:1163) at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:97) then 16:03:12,363 ERROR [jsp]:253 - Servlet.service() for servlet jsp threw exceptionorg.hibernate.exception.DataException: could not read next row of resultsat org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:77) at org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:43) at org.hibernate.loader.Loader.loadSingleRow(Loader.java:268)at org.hibernate.impl.ScrollableResultsImpl.prepareCurrentRow(ScrollableResultsImpl.java:231) at org.hibernate.impl.ScrollableResultsImpl.next(ScrollableResultsImpl.java:100) at net.sf.basedb.core.ScrollIterator.hasNext(ScrollIterator.java:67) at net.sf.basedb.core.ItemResultIterator.hasNext(ItemResultIterator.java:106) ... Caused by: com.mysql.jdbc.exceptions.MySQLDataException: '1340029796353' in column '15' is outside valid range for the datatype INTEGER. at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:893) at com.mysql.jdbc.ResultSet.throwRangeException(ResultSet.java:7391) i'll try to reinstall and reproduce the error. Restarting tomcat did not change anything, i think the db is probably corrupted. -keith Jari Häkkinen wrote: Hi all, We are eager to announce the release of BASE 2.2.1. You can download BASE from http://base.thep.lu.se/wiki/DownloadPage This release does not contain the database upgrade that was not working in 2.2. We have also added a check making it impossible to make a backwardsupgrade, i.e., reverting to an earlier version using the update script. This is of course only available from now on so be careful with the older releases. Of course, all the nice things that was added to 2.2 is still there. A list of fixed and added features in 2.2 is found by clicking on this beast: http://base.thep.lu.se/query?status=newstatus=assignedstatus=reopenedstatus=closedmilestone=BASE+2.2order=id Enjoy, The Lund BASE Team - 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=lnkkid=120709bid=263057dat=121642 ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] Bug fix release 2.2.1 is available now
hmm.. i had restored back to 2.1.2, then upgraded to 2.2.1 and it was working ok until i took ownership of some jobs as root.. then went to the trash can. it gave me this error: Object with id: 2 was not of the specified subclass: net.sf.basedb.core.data.BioMaterialData (Discriminator: 1746955520) and now most of the queries bomb out.. biosources, samples, scans, hybs, etc.. the tomcat log looks like this: 16:00:59,475 ERROR [jsp]:704 - Servlet.service() for servlet jsp threw exceptionjava.lang.NullPointerExceptionat org.apache.jsp.admin.plugindefinitions.edit_005fplugin_jsp.appendPermissionLetter(edit_005fplugin_jsp.java:65) at org.apache.jsp.admin.plugindefinitions.edit_005fplugin_jsp._jspService(edit_005fplugin_jsp.java:1163) at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:97) then 16:03:12,363 ERROR [jsp]:253 - Servlet.service() for servlet jsp threw exceptionorg.hibernate.exception.DataException: could not read next row of resultsat org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:77) at org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:43) at org.hibernate.loader.Loader.loadSingleRow(Loader.java:268)at org.hibernate.impl.ScrollableResultsImpl.prepareCurrentRow(ScrollableResultsImpl.java:231) at org.hibernate.impl.ScrollableResultsImpl.next(ScrollableResultsImpl.java:100) at net.sf.basedb.core.ScrollIterator.hasNext(ScrollIterator.java:67) at net.sf.basedb.core.ItemResultIterator.hasNext(ItemResultIterator.java:106) ... Caused by: com.mysql.jdbc.exceptions.MySQLDataException: '1340029796353' in column '15' is outside valid range for the datatype INTEGER. at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:893) at com.mysql.jdbc.ResultSet.throwRangeException(ResultSet.java:7391) i'll try to reinstall and reproduce the error. Restarting tomcat did not change anything, i think the db is probably corrupted. -keith Jari Häkkinen wrote: Hi all, We are eager to announce the release of BASE 2.2.1. You can download BASE from http://base.thep.lu.se/wiki/DownloadPage This release does not contain the database upgrade that was not working in 2.2. We have also added a check making it impossible to make a backwardsupgrade, i.e., reverting to an earlier version using the update script. This is of course only available from now on so be careful with the older releases. Of course, all the nice things that was added to 2.2 is still there. A list of fixed and added features in 2.2 is found by clicking on this beast: http://base.thep.lu.se/query?status=newstatus=assignedstatus=reopenedstatus=closedmilestone=BASE+2.2order=id Enjoy, The Lund BASE Team -- 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=lnkkid=120709bid=263057dat=121642 ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] Bug fix release 2.2.1 is available now
weird.. at one point 2.2.1 was working.. i restored back to 2.1.2 and it worked.. so i upgraded to 2.2.1 and it blows again w/ the same error.. without doing anything.. maybe i'll try to reinstall 2.2.1 w/ fresh codebase, maybe i messed up the config somewhere.. -keith - 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=lnkkid=120709bid=263057dat=121642 ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
