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.NullPointerException        at 
> 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 results        at 
> 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=new&status=assigned&status=reopened&status=closed&milestone=BASE+2.2&order=id
>>
>>
>> Enjoy,
>>
>> The Lund BASE Team
>>   
> 



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