Opened 16 years ago
Closed 16 years ago
#1204 closed defect (fixed)
Unknown column 'pos.reporter_id' in 'field list' when using 'merge on reporter' in BioAssaySetExporter
Reported by: | Nicklas Nordborg | Owned by: | Nicklas Nordborg |
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Priority: | critical | Milestone: | BASE 2.9.1 |
Component: | coreplugins | Version: | |
Keywords: | Cc: |
Description
- From any experiment with data, select a bioassay set and then the 'Export' button.
- Select 'BASEFile' as the file format on the first screen.
- On the second screen, set 'Average on reporters' to true and select for example ch(1) and ch(2) in the fields list. Do not select any reporter-related formula or anything from the 'Reporter' list.
- Continue the wizard until the end and wait for the job to begin.
It will end with:
net.sf.basedb.core.BaseException: Unknown column 'pos.reporter_id' 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.plugins.BioAssaySetExporter.exportBaseFileSectionSpots(BioAssaySetExporter.java:518) at net.sf.basedb.plugins.BioAssaySetExporter.exportBaseFileMatrix(BioAssaySetExporter.java:326) at net.sf.basedb.plugins.BioAssaySetExporter.performExport(BioAssaySetExporter.java:1322) at net.sf.basedb.core.plugin.AbstractExporterPlugin.run(AbstractExporterPlugin.java:144) at net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java:106) at net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:504) at java.lang.Thread.run(Thread.java:619) Caused by: com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Unknown column 'pos.reporter_id' in 'field list' at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27) at java.lang.reflect.Constructor.newInstance(Constructor.java:513) at com.mysql.jdbc.Util.handleNewInstance(Util.java:406) at com.mysql.jdbc.Util.getInstance(Util.java:381) at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1030) at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:956) at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3491) at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3423) at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1936) at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2060) at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2542) at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:1734) at com.mysql.jdbc.PreparedStatement.executeQuery(PreparedStatement.java:1885) at com.mchange.v2.c3p0.impl.NewProxyPreparedStatement.executeQuery(NewProxyPreparedStatement.java:76) at net.sf.basedb.core.QueryExecutor$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$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) ... 1 more
The generated SQL is:
SELECT AVG(`spt`.`ch1`) AS `a19101568`, AVG(`spt`.`ch2`) AS `a24804944`, `pos`.`reporter_id` AS `_position`, `spt`.`column` AS `_column` FROM `base29dynamic`.`D2Spot` `spt` WHERE `spt`.`cube` = 1 AND `spt`.`layer` = 2 GROUP BY `spt`.`column`, `pos`.`reporter_id` ORDER BY `pos`.`reporter_id` ASC, `spt`.`column` ASC
Eg. it is missing a join to the 'D2Pos' table which contains the 'pos.reporter_id' column.
Change History (2)
comment:1 by , 16 years ago
Owner: | changed from | to
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Status: | new → assigned |
comment:2 by , 16 years ago
Resolution: | → fixed |
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Status: | assigned → closed |
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(In [4694]) Fixes #1204: Unknown column 'pos.reporter_id' in 'field list' when using 'merge on reporter' in BioAssaySetExporter