Problems with Medip-chip data analysis using batman

chitra24 · 06-05-2012, 08:56 AM

Hi,
I am using Batman tool for the medip-chip data analysis,
Though there is a post already existing related to this, I couldnt find the solutions to my problems!

The steps i Have dont so far with batman as mentioned in the manual (http://td-blade.gurdon.cam.ac.uk/sof...lpha-0.2.3.pdf ) is
1. Java Installation( already installed and compatiable with batman requirements)
2. Identifing the database server
3. Initializing the Batman database
4. Register the experiments That Im going to analyze and the problem arises in
5.Registering the array design
using the command
java batman.LoadProbesApplication $DBOPTS probes.gff
My gff files are prepared to the requirement of batman

the error i get in this step is
RETURN_GENERATED_KEYS to Statement.executeUpdate() or Connection.prepareStatement().
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1073)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:987)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:982)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:927)
at com.mysql.jdbc.StatementImpl.getGeneratedKeys(StatementImpl.java:1966)
at org.apache.commons.dbcp.DelegatingPreparedStatement.getGeneratedKeys(DelegatingPreparedStatement.java:325)
at batman.LoadProbes$1.recordLine(LoadProbes.java:78)

Please help me with this !

Thanks and looking forward for the answer

dpryan · 01-14-2013, 06:10 AM

Should someone else run into this same error (like I just did) in the future, the fix is to edit "src/batman/LoadProbes.java". Change the line that reads :

Code:

"insert into medip_roi (roi_name) values (?)"

so that it instead reads:

Code:

"insert into medip_roi (roi_name) values (?)", PreparedStatement.RETURN_GENERATED_KEYS

Note, you may need to go into the database and delete previously added ROIs and probe names:

Code:

delete from medip_probe;
delete from medip_roi;

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06-05-2012, 08:56 AM	#1
chitra24 Junior Member Location: netherlands Join Date: Jan 2010 Posts: 2	Problems with Medip-chip data analysis using batman Hi, I am using Batman tool for the medip-chip data analysis, Though there is a post already existing related to this, I couldnt find the solutions to my problems! The steps i Have dont so far with batman as mentioned in the manual (http://td-blade.gurdon.cam.ac.uk/sof...lpha-0.2.3.pdf ) is 1. Java Installation( already installed and compatiable with batman requirements) 2. Identifing the database server 3. Initializing the Batman database 4. Register the experiments That Im going to analyze and the problem arises in 5.Registering the array design using the command java batman.LoadProbesApplication $DBOPTS probes.gff My gff files are prepared to the requirement of batman the error i get in this step is RETURN_GENERATED_KEYS to Statement.executeUpdate() or Connection.prepareStatement(). at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1073) at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:987) at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:982) at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:927) at com.mysql.jdbc.StatementImpl.getGeneratedKeys(StatementImpl.java:1966) at org.apache.commons.dbcp.DelegatingPreparedStatement.getGeneratedKeys(DelegatingPreparedStatement.java:325) at batman.LoadProbes$1.recordLine(LoadProbes.java:78) Please help me with this ! Thanks and looking forward for the answer

01-14-2013, 06:10 AM	#2
dpryan Devon Ryan Location: Freiburg, Germany Join Date: Jul 2011 Posts: 3,480	Should someone else run into this same error (like I just did) in the future, the fix is to edit "src/batman/LoadProbes.java". Change the line that reads : Code: "insert into medip_roi (roi_name) values (?)" so that it instead reads: Code: "insert into medip_roi (roi_name) values (?)", PreparedStatement.RETURN_GENERATED_KEYS Note, you may need to go into the database and delete previously added ROIs and probe names: Code: delete from medip_probe; delete from medip_roi;