You can turn on logging in the log4j.properties file. It is located in
the WEB-INF/classes directory (where the base.config is).
In any case... it is not possible to use formulas referencing raw data
information in the 'Columns' settings. This is for reporter annotations
only. Change the formula to 'pos()' instead.
/Nicklas
On 2010-02-23 16:33, Matsalla, Chad wrote:
> Greetings,
>
> I'm using base-2.14.0 on geronimo 2.1.3.
>
> I'm trying to run a base1 plugin that used to work. Unfortunately, I don't
> remember what version of base last successfully ran this plugin.
>
> The error I'm getting is this[1].
>
> In the plugin configuration, I have this in the Columns section of the
> plugin Configuration:
> "position\treporter"
> I have a formula that maps 'position' to raw('position')
>
> I really have no idea where to begin trying to troubleshoot this. Can
> somebody help?
>
> The exception looks like an SQL exception. It would be really helpful to see
> the query itself. When I tried to turn on SQL profiling in the JDBC
> connection string[2], I get a whole bunch of 'Not Serializable' errors and
> the system won't start.
>
> How can I find out the sql of the query that's being executed?
>
> Thank you for your help,
>
> Chad Matsalla
>
>
>
>
> [1]
> View job -- Run plugin: Base1PluginExecuter
> net.sf.basedb.core.BaseException: Unknown column 'raw.position' in 'field
> list'
> at net.sf.basedb.core.QueryExecutor.getFutureResult(QueryExecutor.java:194)
> at net.sf.basedb.core.QueryExecutor.executeQuery(QueryExecutor.java:91)
> at net.sf.basedb.core.AbstractSqlQuery.iterate(AbstractSqlQuery.java:198)
> at net.sf.basedb.core.DynamicQuery.iterate(DynamicQuery.java:46)
> at
> net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter.cacheReporter
> Data(AbstractBioAssaySetExporter.java:579)
> at
> net.sf.basedb.util.export.spotdata.SerialBaseFileExporter.beginExport(Serial
> BaseFileExporter.java:76)
> at
> net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter.doExport(Abst
> ractBioAssaySetExporter.java:276)
> at
> net.sf.basedb.plugins.Base1PluginExecuter.exportData(Base1PluginExecuter.jav
> a:859)
> at
> net.sf.basedb.plugins.Base1PluginExecuter.run(Base1PluginExecuter.java:596)
> at
> net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java
> :110)
> at
> net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:506)
> at java.lang.Thread.run(Thread.java:619)
> Caused by: com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException:
> Unknown column 'raw.position' in 'field list'
> at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
> at
> sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAcces
> sorImpl.java:39)
> at
> sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstruc
> torAccessorImpl.java:27)
> at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
> at com.mysql.jdbc.Util.handleNewInstance(Util.java:406)
> at com.mysql.jdbc.Util.getInstance(Util.java:381)
> at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1030)
> at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:956)
> at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3536)
> at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3468)
> at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1957)
> at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2107)
> at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2648)
> at
> com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:2086
> )
> at
> com.mysql.jdbc.PreparedStatement.executeQuery(PreparedStatement.java:2237)
> at
> com.mchange.v2.c3p0.impl.NewProxyPreparedStatement.executeQuery(NewProxyPrep
> aredStatement.java:76)
> at
> net.sf.basedb.core.QueryExecutor$FutureResultSet.call(QueryExecutor.java:224
> )
> at
> net.sf.basedb.core.QueryExecutor$FutureResultSet.call(QueryExecutor.java:212
> )
> at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
> at java.util.concurrent.FutureTask.run(FutureTask.java:138)
> at
> java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.ja
> va:886)
> at
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:9
> 08)
> ... 1 more
> Properties Stack trace Parameters
>
> Restart job
> Re-configure job
> Close
>
> [2]
> jdbc:mysql://$SERVER/base_2_14_0?useCursorFetch=true&defaultFetchSize=1000&u
> seServerPrepStmps=true&characterEncoding=utf8&logger=com.mysql.jdbc.log.Stan
> dardLogger&profileSQL=true
>
>
> ------------------------------------------------------------------------------
> Download Intel® Parallel Studio Eval
> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
> See why Intel Parallel Studio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev
> _______________________________________________
> The BASE general discussion mailing list
> basedb-users@lists.sourceforge.net
> unsubscribe: send a mail with subject "unsubscribe" to
> basedb-users-requ...@lists.sourceforge.net
------------------------------------------------------------------------------
Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
_______________________________________________
The BASE general discussion mailing list
basedb-users@lists.sourceforge.net
unsubscribe: send a mail with subject "unsubscribe" to
basedb-users-requ...@lists.sourceforge.net
