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.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
>
--
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
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