[TAV-700] Column 'thing' too short in LogBook database schema Created: 2007-12-19  Updated: 2008-02-15  Resolved: 2008-02-15

Status: Resolved
Project: myGrid
Component/s: Provenance
Affects Version/s: None
Fix Version/s: 1.7.1

Type: Bug Priority: Major
Reporter: Stuart Owen Assignee: Ian Dunlop
Resolution: Fixed Votes: 0
Labels: None
Remaining Estimate: Not Specified
Time Spent: Not Specified
Original Estimate: Not Specified


 Description   

Reported by one of our users:

I am running a workflow with a text file like input and splitting it
into several lines to finally get a "list of lists" (I'm using local
processors and regex to do it).

Results window show everything well, but logbook say in results tab
window : "Problem Retrieving Data from Store - No Data Matching the
Given LSID Value"

Looking at java console appears:

com.mysql.jdbc.MysqlDataTruncation: Data truncation: Data too long for
column 'thing' at row 1
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:2868)
at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1573)
at com.mysql.jdbc.ServerPreparedStatement.serverExecute(ServerPreparedStatement.java:1169)
at com.mysql.jdbc.ServerPreparedStatement.executeInternal(ServerPreparedStatement.java:693)
at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1404)
at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1318)
at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1303)
at uk.org.mygrid.provenance.dataservice.AbstractJDBCDataService.storeDataThing(AbstractJDBCDataService.java:345)
at uk.ac.man.cs.img.mygrid.provenance.knowledge.taverna.ProvenanceGenerator.store(ProvenanceGenerator.java:1419)
at uk.ac.man.cs.img.mygrid.provenance.knowledge.taverna.ProvenanceGenerator.processCompletedWithIteration(ProvenanceGenerator.java:518)
at org.embl.ebi.escience.scufl.enactor.implementation.WorkflowEventDispatcher.sendAnEvent(WorkflowEventDispatcher.java:203)
at org.embl.ebi.escience.scufl.enactor.implementation.WorkflowEventDispatcher.fireEvents(WorkflowEventDispatcher.java:184)
at org.embl.ebi.escience.scufl.enactor.implementation.WorkflowEventDispatcher$NotifyThread.run(WorkflowEventDispatcher.java:250)
com.mysql.jdbc.MysqlDataTruncation: Data truncation: Data too long for
column 'thing' at row 1
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:2868)
at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1573)
at com.mysql.jdbc.ServerPreparedStatement.serverExecute(ServerPreparedStatement.java:1169)
at com.mysql.jdbc.ServerPreparedStatement.executeInternal(ServerPreparedStatement.java:693)
at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1404)
at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1318)
at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1303)
at uk.org.mygrid.provenance.dataservice.AbstractJDBCDataService.storeDataThing(AbstractJDBCDataService.java:345)
at uk.ac.man.cs.img.mygrid.provenance.knowledge.taverna.ProvenanceGenerator.store(ProvenanceGenerator.java:1419)
at uk.ac.man.cs.img.mygrid.provenance.knowledge.taverna.ProvenanceGenerator.workflowCompleted(ProvenanceGenerator.java:426)
at org.embl.ebi.escience.scufl.enactor.implementation.WorkflowEventDispatcher.sendAnEvent(WorkflowEventDispatcher.java:199)
at org.embl.ebi.escience.scufl.enactor.implementation.WorkflowEventDispatcher.fireEvents(WorkflowEventDispatcher.java:184)
at org.embl.ebi.escience.scufl.enactor.implementation.WorkflowEventDispatcher$NotifyThread.run(WorkflowEventDispatcher.java:250)



 Comments   
Comment by Ian Dunlop [ 2007-12-19 ]

Looks like the table is using TEXT field(max size 65k in mySQL). Code is in rdf-provenance module, uk.org.mygrid.provenance.dataservice.MySQLDataService createTables method:

"CREATE TABLE IF NOT EXISTS datathings (id INT UNSIGNED NOT NULL AUTO_INCREMENT,"
+ " thing TEXT NOT NULL,"
+ " PRIMARY KEY(id)) TYPE = InnoDB;"

Could set the field size to MEDIUMTEXT or LONGTEXT (although there could be performance issues which arise).

Comment by June Finch (Inactive) [ 2007-12-20 ]

Should be considered within 1.7.1 timescales.

Comment by Stuart Owen [ 2008-01-07 ]

I've had a reply that setting the size to MEDIUMTEXT fixed the problem. We need to update the plugin to set this as the default field size.

This doesn't need to released as part of 1.7.1 but can be released as an independant plugin update.

Comment by Ian Dunlop [ 2008-01-07 ]

Changed it to MEDIUMTEXT, need to test it against some meaningful data - any ideas?

Comment by Ian Dunlop [ 2008-02-15 ]

I think it works OK now but needs some testing to say for sure

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