Hello,
I fixed the problem: it was caused by an empty column field inside the
extended-properties.xml
The system spec:
BASE 2.1.2
mysql: 5.0.15
java: jdk-1.5.0_06
apache-tomcat: 5.5.17
jakarta-tomcat-connectors-1.2.15
OS: linux 64bit
The complete error:
****
14:06:49,992 ERROR jobqueue:434 - Exception while executing job:
Job[id=2; name=Run plugin: Reporter importer]
net.sf.basedb.core.BaseException: could not execute query on line 2: 1
xxx 2...
at
net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:428)
at java.lang.Thread.run(Thread.java:595)
Caused by: net.sf.basedb.core.BaseException: could not execute query on
line 2: 1 xxx 2...
at
net.sf.basedb.plugins.AbstractFlatFileImporter.doImport(AbstractFlatFileImporter.java:581)
at
net.sf.basedb.plugins.AbstractFlatFileImporter.run(AbstractFlatFileImporter.java:432)
at
net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java:82)
at
net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:420)
... 1 more
Caused by: net.sf.basedb.core.BaseException: could not execute query
at
net.sf.basedb.core.HibernateUtil.loadData(HibernateUtil.java:1120)
at
net.sf.basedb.core.ReporterBatcher.getByExternalId(ReporterBatcher.java:252)
at
net.sf.basedb.core.ReporterBatcher.getByExternalId(ReporterBatcher.java:226)
at
net.sf.basedb.plugins.ReporterFlatFileImporter.handleData(ReporterFlatFileImporter.java:492)
at
net.sf.basedb.plugins.AbstractFlatFileImporter.doImport(AbstractFlatFileImporter.java:559)
... 4 more
Caused by: org.hibernate.exception.SQLGrammarException: could not
execute query
at
org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:67)
at
org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:43)
at org.hibernate.loader.Loader.doList(Loader.java:2147)
at
org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2028)
at org.hibernate.loader.Loader.list(Loader.java:2023)
at org.hibernate.loader.hql.QueryLoader.list(QueryLoader.java:393)
at
org.hibernate.hql.ast.QueryTranslatorImpl.list(QueryTranslatorImpl.java:338)
at
org.hibernate.engine.query.HQLQueryPlan.performList(HQLQueryPlan.java:172)
at
org.hibernate.impl.StatelessSessionImpl.list(StatelessSessionImpl.java:467)
at org.hibernate.impl.QueryImpl.list(QueryImpl.java:79)
at
net.sf.basedb.core.HibernateUtil.loadData(HibernateUtil.java:1114)
... 8 more
Caused by: java.sql.SQLException: Unknown column 'reporterda0_.' in
'field list'
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:2975)
at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1600)
at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:1695)
at com.mysql.jdbc.Connection.execSQL(Connection.java:3004)
at
com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:1128)
at
com.mysql.jdbc.PreparedStatement.executeQuery(PreparedStatement.java:1222)
at
com.mchange.v2.c3p0.impl.NewProxyPreparedStatement.executeQuery(NewProxyPreparedStatement.java:76)
at
org.hibernate.jdbc.AbstractBatcher.getResultSet(AbstractBatcher.java:186)
at org.hibernate.loader.Loader.getResultSet(Loader.java:1668)
at org.hibernate.loader.Loader.doQuery(Loader.java:662)
at
org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:224)
at org.hibernate.loader.Loader.doList(Loader.java:2144)
... 16 more
****
Cheers,
Reha
Nicklas Nordborg wrote:
> Reha Yildirimman wrote:
>
>> Hello,
>>
>> I am trying to import Reporter into a new reporter list inside a
>> fresh,new base2 installation, getting the following error:
>> ****
>> Caused by: java.sql.SQLException: Unknown column 'reporterda0_.' in
>> 'field list'
>>
>
> Can you please submit the entire stacktrace and also a step-by-step
> description of how to reproduce the error. Also include information
> about which version of BASE you are using, which database you are using,
> the Java version, and any other information that you think is important.
> All of this should be available in the About box or on the error message
> page.
>
> /Nicklas
>
>
>> ****
>> I cannot find the column 'reporterda0_.' inside any mysql table or
>> inside extended-properties.xml/raw-data-types.xml ...
>> When I try to access the - empty - Reporters part I get the following error:
>> ****
>> could not execute query using scroll
>> ****
>>
>> Does anybody have a clue ? The file containing the list of reporters is
>> a tab-delimited file with 6 columns, the first with the ID,
>> the other 5 columns with annotations
>>
>> Thanks alot in advance for your help.
>>
>> Cheers,
>>
>> Reha
>>
>> -------------------------------------------
>> Reha Yildirimman
>> Max-Planck-Institute for Molecular Genetics
>> Department Lehrach (Vertebrate Genomics)
>> Ihnestr. 73
>> 14195 Berlin
>> Germany
>> -------------------------------------------
>>
>> -------------------------------------------------------------------------
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>
>
> -------------------------------------------------------------------------
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