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
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