Hi Nicklas,
Nicklas Nordborg writes:
> I think the 'table exists' problem can happen in rare cases if two jobs
> are executed at the same time, the time window between checking if a
> table exists and creating it if it doesn't is small but not zero. This
> means that two different jobs may not see the table and both will try to
> create it... The last one will fail. I guess it is possible to make the
> code more robust in this case, but figured it would maybe not happen
> very often (if at all) since the tables are usually created at the same
> time as the first root bioassay set in an experiment is created. In any
> case, you don't need to worry about database being corrupted.
thanks for the explanation/reassurance (and also for the reply to
the other mail)
> The duplication is a bit more surprising. Are the bioassay sets created
> by the same or different jobs? You can check the jobs table (View ->
> Jobs) if you can't find it out from the experiment analysis page. The
well I stupidly deleted them and emptied the trash, so can't check again,
sorry!
but... I just made a filtered bioassayset (raw('flags') == 0) and get this
duplication again! (no errors reported).
so to answer your question above about the jobs:
View->Jobs says that one JEP Filter Plugin job was completed at 12:07:32
And the two duplicate bioassaysets have exactly the same timestamp.
> one thing that comes to my mind and that could explain both the 'table
> exists' error and the duplication issue is that each job is for some
> reason executed twice (and at the same time). It shouldn't happen, but I
> remember that we had some problems when running test programs and still
> having the web server's job queue active. Every now and then the web
> server would start executing a job that was also started by our test
> program. Some times the one executing on the web server would fail and
> some times the test program. So, do you have any job agents installed,
> or multiple web applications, or anything else that is executing jobs
> from the job queue?
yes we do have some prototype web apps run from separate tomcats which use
instances of the BASE application. I have killed them and did another
filtering and got only one result - no more duplication!
On starting one tomcat and BASE-related webapp again I still don't get
duplication.
I'll post back here again if we see duplication again and can recreate the
conditions. In the meantime, all seems OK again.
cheers,
Bob.
>
> /Nicklas
>
>
> Bob MacCallum wrote:
> > Dear BASE team,
> >
> > I just got the following error while creating a root bioassayset for a
> > small
> > test experiment. My hunch is that it's something bad like a corrupted
> > db...
> >
> > I plan to get 2.5 installed ASAP, but was hoping to do a demo with 2.4.5 to
> > my colleagues later this week.
> >
> > Well I am in luck, I just repeated exactly the same thing and it worked
> > fine.
> >
> > But the odd thing is that I now see that there are three identical-looking
> > bioassaysets in the experiment, even though I only ran the Formula
> > intensity
> > calculator plugin twice. From the "Date" column it is the latter analysis
> > which got duplicated (and the original one seems to work ok). I am not
> > usually a double-clicker, but that might be one explanation.
> >
> > Strange indeed.
> >
> > Here's the stack trace in any case.
> >
> > cheers,
> > Bob.
> >
> > net.sf.basedb.core.BaseException: Table 'D13Pos' already exists
> > at
> > net.sf.basedb.core.HibernateUtil.createVirtualTable(HibernateUtil.java:605)
> > at net.sf.basedb.core.VirtualDb.createTables(VirtualDb.java:290)
> > at
> > net.sf.basedb.core.PositionBatcher.buildInsertSelectSql(PositionBatcher.java:303)
> > at net.sf.basedb.core.PositionBatcher.insert(PositionBatcher.java:246)
> > at
> > net.sf.basedb.util.IntensityCalculatorUtil.createRootBioAssaySet(IntensityCalculatorUtil.java:204)
> > at
> > net.sf.basedb.plugins.IntensityCalculatorPlugin.run(IntensityCalculatorPlugin.java:249)
> > at
> > net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java:89)
> > at
> > net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:421)
> > at java.lang.Thread.run(Thread.java:619)
> > Caused by: com.mysql.jdbc.exceptions.MySQLSyntaxErrorException: Table
> > 'D13Pos' already exists
> > at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:936)
> > at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:2934)
> > at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1616)
> > at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:1708)
> > at com.mysql.jdbc.Connection.execSQL(Connection.java:3249)
> > at com.mysql.jdbc.Statement.executeUpdate(Statement.java:1350)
> > at com.mysql.jdbc.Statement.executeUpdate(Statement.java:1266)
> > at
> > com.mchange.v2.c3p0.impl.NewProxyStatement.executeUpdate(NewProxyStatement.java:64)
> > at
> > net.sf.basedb.core.HibernateUtil.createVirtualTable(HibernateUtil.java:581)
> > ... 8 more
> >
> >
> >
> >
> > Version BASE 2.4.6pre (build #3938; schema #40)
> > Web server Apache Tomcat/5.5.20
> > Database Server MySQL 5.0.21-max-log
> > Database Dialect org.hibernate.dialect.MySQLInnoDBDialect
> > JDBC Driver com.mysql.jdbc.Driver (version 5.0)
> > Java runtime Java(TM) SE Runtime Environment (1.6.0-b105), Sun
> > Microsystems Inc.
> > Operating system Linux amd64 2.6.16.53-0.16-smp
> > Memory Total: 474.6 MB
> > Free: 238.2 MB
> > Max: 910.3 MB
> >
>
>
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--
Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups |
Division of Cell and Molecular Biology | Imperial College London |
Phone +442075941945 | Email [EMAIL PROTECTED]
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