dear nicklas,
thank you for the prompt answer and apologies for the lack of info.
here the info requested.
thank you
sergio
i am running a test base 2.3.2 on mysql 5.1.14-beta (i must apologies
again, i was thinking to be running on the reccomended 5.0)
the stack (as in base report) is
net.sf.basedb.core.BaseException: Table 'base2dynamic.D2Spot' doesn't
exist
at net.sf.basedb.core.AbstractSqlQuery.iterate(AbstractSqlQuery.java:193)
at
net.sf.basedb.core.BioAssaySet.countSpotsAndReporters(BioAssaySet.java:1096)
at net.sf.basedb.core.BioAssaySet.onBeforeCommit(BioAssaySet.java:315)
at net.sf.basedb.core.DbControl.commit(DbControl.java:365)
at
se.lu.thep.affymetrix.AbstractExternalBinaryPlugin.run(AbstractExternalBinaryPlugin.java:264)
at
net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java:88)
at
net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:420)
at java.lang.Thread.run(Unknown Source)
Caused by: com.mysql.jdbc.exceptions.MySQLSyntaxErrorException: Table
'base2dynamic.D2Spot' doesn't exist
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:936)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:2870)
at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1573)
at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:1665)
at com.mysql.jdbc.Connection.execSQL(Connection.java:3176)
at
com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:1153)
at
com.mysql.jdbc.PreparedStatement.executeQuery(PreparedStatement.java:1266)
the tomcat log reports:
14:03:50,901 ERROR ql:192 - SELECT COUNT(*) AS `spotCount`, COUNT(DISTINCT
`pos`.`reporter_id`) AS `reporterCount` FROM `base2dynamic`.`D2Spot` `spt`
LEFT
JOIN `base2dynamic`.`D2Pos` AS `pos` ON `pos`.`cube` = `spt`.`cube` AND
`pos`.`position` = `spt`.`position` WHERE `spt`.`cube` = 2 AND
`spt`.`layer` = 1
com.mysql.jdbc.exceptions.MySQLSyntaxErrorException: Table
'base2dynamic.D2Spot' doesn't exist
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:936)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:2870)
at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1573)
at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:1665)
at com.mysql.jdbc.Connection.execSQL(Connection.java:3176)
at
com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:1153)
at
com.mysql.jdbc.PreparedStatement.executeQuery(PreparedStatement.java:1266)
at
com.mchange.v2.c3p0.impl.NewProxyPreparedStatement.executeQuery(NewProxyPreparedStatement.java:76)
at
net.sf.basedb.core.AbstractSqlQuery.iterate(AbstractSqlQuery.java:184)
at
net.sf.basedb.core.BioAssaySet.countSpotsAndReporters(BioAssaySet.java:1096)
at
net.sf.basedb.core.BioAssaySet.onBeforeCommit(BioAssaySet.java:315)
at net.sf.basedb.core.DbControl.commit(DbControl.java:365)
at
se.lu.thep.affymetrix.AbstractExternalBinaryPlugin.run(AbstractExternalBinaryPlugin.java:264)
at
net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java:88)
at
net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:420)
at java.lang.Thread.run(Unknown Source)
14:03:51,359 ERROR jobqueue:434 - Exception while executing job:
Job[id=11; name=Run plugin: PLIER plug-in]
net.sf.basedb.core.BaseException: Table 'base2dynamic.D2Spot' doesn't
exist
at
net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:428)
at java.lang.Thread.run(Unknown Source)
Caused by: net.sf.basedb.core.BaseException: Table 'base2dynamic.D2Spot'
doesn't exist
at
net.sf.basedb.core.AbstractSqlQuery.iterate(AbstractSqlQuery.java:193)
at
net.sf.basedb.core.BioAssaySet.countSpotsAndReporters(BioAssaySet.java:1096)
at
net.sf.basedb.core.BioAssaySet.onBeforeCommit(BioAssaySet.java:315)
at net.sf.basedb.core.DbControl.commit(DbControl.java:365)
at
se.lu.thep.affymetrix.AbstractExternalBinaryPlugin.run(AbstractExternalBinaryPlugin.java:264)
at
net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java:88)
at
net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:420)
... 1 more
Caused by: com.mysql.jdbc.exceptions.MySQLSyntaxErrorException: Table
'base2dynamic.D2Spot' doesn't exist
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:936)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:2870)
at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1573)
at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:1665)
at com.mysql.jdbc.Connection.execSQL(Connection.java:3176)
at
com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:1153)
at
com.mysql.jdbc.PreparedStatement.executeQuery(PreparedStatement.java:1266)
at
com.mchange.v2.c3p0.impl.NewProxyPreparedStatement.executeQuery(NewProxyPreparedStatement.java:76)
at
net.sf.basedb.core.AbstractSqlQuery.iterate(AbstractSqlQuery.java:184)
... 7 more
On Wed, 8 Aug 2007, Nicklas Nordborg wrote:
> Sergio Contrino wrote:
>> dear base,
>> i was attempting to 'create a new bioassay root' for an experiment with
>> the array affymetrix 250sty, using Plier.
>> i get the error
>>
>> Error: Table 'base2dynamic.D2Spot' doesn't exist
>>
>
> This error is a bit strange since the table should automatically be
> created if it doesn't exist. Maybe there is something going wrong with
> the creation which isn't reported as a failure. In any case, I need more
> information to be able to start looking for the problem:
>
> * Any related error messages and stack traces that are present in the
> Tomcat log file or displayed in the browser
> * Which database you are using (name and version)
> * Which BASE version you are using
>
> /Nicklas
>
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