Hi!
I'm using the command line to run a workflow but I have a MySQL Exception. I
searched the web and found this error happened also in Taverna 2.2 but couldn't
found if it was fixed. Any idea about this? The workflow runs ok but later on I
can't see the provenance data correctly in the workbench. Here's the command
and exception
I appreciate any advice!
regards
Guzmán
C:\Archivos de programa\Taverna Workbench 2.3.0>executeworkflow.bat -provenance
-dbproperties DataAndProvenance-6BD3F5C1-C68D-4893-8D9B-2F46FA1DDB19.config blas
t_ncbi_result_xml.t2flow -inputvalue Databases uniprotkb_swissprot -inputvalue E
mail [email protected] -inputvalue Program blastp -inputfile Sequence sequence
s_short.txt -inputdelimiter Sequence "\n" -inputvalue Sequence_type protein
ERROR 2011-11-07 09:08:42,984 (net.sf.taverna.t2.provenance.connector.MySQLProve
nanceConnector:345) - There was a problem creating the Provenance database datab
ase:
com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Table 'datalink' alre
ady exists
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Sou
rce)
at java.lang.reflect.Constructor.newInstance(Unknown Source)
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:1031)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:957)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3376)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3308)
at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1837)
at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:1961)
at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2537)
at com.mysql.jdbc.StatementImpl.executeUpdate(StatementImpl.java:1564)
at com.mysql.jdbc.StatementImpl.executeUpdate(StatementImpl.java:1485)
at org.apache.commons.dbcp.DelegatingStatement.executeUpdate(DelegatingS
tatement.java:228)
at org.apache.commons.dbcp.DelegatingStatement.executeUpdate(DelegatingS
tatement.java:228)
at net.sf.taverna.t2.provenance.connector.MySQLProvenanceConnector.creat
eDatabase(MySQLProvenanceConnector.java:319)
at net.sf.taverna.t2.provenance.connector.ProvenanceConnector.init(Prove
nanceConnector.java:291)
at net.sf.taverna.t2.commandline.CommandLineLauncher.createInvocationCon
text(CommandLineLauncher.java:356)
at net.sf.taverna.t2.commandline.CommandLineLauncher.setupAndExecute(Com
mandLineLauncher.java:240)
at net.sf.taverna.t2.commandline.CommandLineLauncher.launch(CommandLineL
auncher.java:111)
at net.sf.taverna.raven.launcher.Launcher.launchMain(Launcher.java:150)
at net.sf.taverna.raven.launcher.Launcher.main(Launcher.java:66)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at net.sf.taverna.raven.prelauncher.PreLauncher.runLauncher(PreLauncher.
java:115)
at net.sf.taverna.raven.prelauncher.PreLauncher.launchArgs(PreLauncher.j
ava:69)
at net.sf.taverna.raven.prelauncher.PreLauncher.main(PreLauncher.java:47
)
Outputs will be saved to the directory: C:\Archivos de programa\Taverna Workbenc
h 2.3.0\NCBI_BLAST__SOAP__output_45
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