Hi Paolo!
I wanted to test the sample client API but I'm having some trouble.
I'm using a mysql db, the kegg pathway workflow example using
[[mmmu:26416],[mmu:328788]] as input.
Here's the error. Any idea of what I may be doing wrong?
Thanks
Guzmán
INFO 2010-06-08 00:45:04,500
(net.sf.taverna.t2.provenance.lineageservice.mysql.MySQLProvenanceWriter:39) -
Using MySQLProvenanceWriter as an extension of RDFProvenanceWriter
INFO 2010-06-08 00:45:04,500
(net.sf.taverna.t2.provenance.api.ProvenanceAccess:175) - Provenance
being captured using: MySQL Provenance Connector
INFO 2010-06-08 00:45:04,750
(net.sf.taverna.t2.provenance.lineageservice.ProvenanceAnalysis:116) -
chosen OPMmanager:
net.sf.taverna.t2.provenance.lineageservice.ext.pc3.PANSTARRSOPMManager not
available, reverting to default
INFO 2010-06-08 00:45:05,765
(net.sf.taverna.t2.provenance.api.ProvenanceAccess:190) - using writer
of type: class
net.sf.taverna.t2.provenance.lineageservice.mysql.MySQLProvenanceWriter
INFO 2010-06-08 00:45:05,765
(net.sf.taverna.t2.provenance.api.client.ProvenanceBaseClient:126) -
query returns output values in addition to inputs: true
INFO 2010-06-08 00:45:05,765
(net.sf.taverna.t2.provenance.api.client.ProvenanceBaseClient:133) -
OPM.recordArtifactValues: true
INFO 2010-06-08 00:45:05,765
(net.sf.taverna.t2.provenance.api.client.ProvenanceBaseClient:140) -
OPM.computeGraph: true
INFO 2010-06-08 00:45:05,765
(net.sf.taverna.t2.provenance.api.client.ProvenanceBaseClient:147) -
query.returnDataValues: true
INFO 2010-06-08 00:45:05,765
(net.sf.taverna.t2.provenance.api.client.ProvenanceAPISampleClient:84)
- executing query src/main/resources/completeGraph.xml
INFO 2010-06-08 00:45:05,781
(net.sf.taverna.t2.provenance.api.ProvenanceQueryParser:431) - no
explicit scope for the query: using latest run id
6b58477e-9dde-4dfd-9c8d-c9d8790d96aa and top level workflow id
c9665664-4ddd-4ce9-99c3-76992bd530a9
INFO 2010-06-08 00:45:05,781
(net.sf.taverna.t2.provenance.api.client.ProvenanceAPISampleClient:95)
- YOUR QUERY:
**** QUERY SCOPE: ****
workflow name: c9665664-4ddd-4ce9-99c3-76992bd530a9
runs:
6b58477e-9dde-4dfd-9c8d-c9d8790d96aa
**** TARGET PORTS: ****
PORT: ****
workflow: c9665664-4ddd-4ce9-99c3-76992bd530a9
processor: KeggGenes2KeggPathways
port: paths_per_gene
path to value: ALL
PORT: ****
workflow: c9665664-4ddd-4ce9-99c3-76992bd530a9
processor: KeggGenes2KeggPathways
port: commonPathways
path to value: ALL
**** SELECTED PROCESSORS: ****
INFO 2010-06-08 00:45:05,781
(net.sf.taverna.t2.provenance.lineageservice.ProvenanceAnalysis:238) -
************
lineage query: [instance, workflow, proc, port, path] =
[6b58477e-9dde-4dfd-9c8d-c9d8790d96aa,c9665664-4ddd-4ce9-99c3-76992bd530a9,KeggGenes2KeggPathways,paths_per_gene,[ALL]]
***********
INFO 2010-06-08 00:45:05,781
(net.sf.taverna.t2.provenance.lineageservice.ProvenanceAnalysis:301) -
return outputs: true
WARN 2010-06-08 00:45:05,796
(net.sf.taverna.t2.provenance.lineageservice.ProvenanceAnalysis:316) -
ALL specified for paths but no varBindings found. nothing to compute
INFO 2010-06-08 00:45:05,796
(net.sf.taverna.t2.provenance.lineageservice.ProvenanceAnalysis:238) -
************
lineage query: [instance, workflow, proc, port, path] =
[6b58477e-9dde-4dfd-9c8d-c9d8790d96aa,c9665664-4ddd-4ce9-99c3-76992bd530a9,KeggGenes2KeggPathways,commonPathways,[ALL]]
***********
INFO 2010-06-08 00:45:05,796
(net.sf.taverna.t2.provenance.lineageservice.ProvenanceAnalysis:301) -
return outputs: true
WARN 2010-06-08 00:45:05,796
(net.sf.taverna.t2.provenance.lineageservice.ProvenanceAnalysis:316) -
ALL specified for paths but no varBindings found. nothing to compute
Exception in thread "main" java.lang.IllegalArgumentException: No
soportado: indent-number
at
org.apache.xalan.processor.TransformerFactoryImpl.setAttribute(TransformerFactoryImpl.java:485)
at org.tupeloproject.util.Xml.newTransformer(Xml.java:155)
at org.tupeloproject.util.Xml.transform(Xml.java:210)
at org.tupeloproject.rdf.xml.RdfXmlWriter.write(RdfXmlWriter.java:215)
at
net.sf.taverna.t2.provenance.opm.OPMManager.writeGraph(OPMManager.java:329)
at
net.sf.taverna.t2.provenance.lineageservice.ProvenanceAnalysis.lineageQuery(ProvenanceAnalysis.java:256)
at
net.sf.taverna.t2.provenance.api.ProvenanceAccess.executeQuery(ProvenanceAccess.java:217)
at
net.sf.taverna.t2.provenance.api.client.ProvenanceAPISampleClient.queryProvenance(ProvenanceAPISampleClient.java:99)
at
net.sf.taverna.t2.provenance.api.client.ProvenanceAPISampleClient.main(ProvenanceAPISampleClient.java:63)
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