Hi David,
Thanks for you reply.
I'installed the Open Virtuoso SPARQL Query in my SUSE system.
However, when I start the Taverna Workbench I got the follow problem:
When I start Taverna without SADI pluggin
----------------------------------------------------------
WARN 2010-11-26 18:36:26,538
(net.sf.taverna.raven.repository.impl.ArtifactImpl:85) - Unable to
find a version for the dependency log4j:log4j - skipping
WARN 2010-11-26 18:36:26,548
(net.sf.taverna.raven.repository.impl.ArtifactImpl:85) - Unable to
find a version for the dependency junit:junit - skipping
ERROR 2010-11-26 18:36:28,099 (System.err:139) - Central class is
org.biomoby.client.CentralDigestCachedImpl
ERROR 2010-11-26 18:36:53,788 (System.err:139) - Central class is
org.biomoby.client.CentralDigestCachedImpl
----------------------------------------------------------
After I had add SADI plugin, I got the folow WARN and ERRORS
----------------------------------------------------------
WARN 2010-11-26 18:52:54,903
(net.sf.taverna.raven.repository.impl.ArtifactImpl:85) - Unable to
find a version for the dependency log4j:log4j - skipping
WARN 2010-11-26 18:52:54,913
(net.sf.taverna.raven.repository.impl.ArtifactImpl:85) - Unable to
find a version for the dependency junit:junit - skipping
ERROR 2010-11-26 18:52:56,557 (System.err:139) - Central class is
org.biomoby.client.CentralDigestCachedImpl
ERROR 2010-11-26 18:52:56,676 (ca.wilkinsonlab.sadi.common.Config:48)
- Cannot locate configuration source sadi.common.properties
WARN 2010-11-26 18:52:56,682 (ca.wilkinsonlab.sadi.common.Config:56)
- no user-space configuration source sadi.properties
WARN 2010-11-26 18:52:58,646
(net.sf.taverna.t2.servicedescriptions.impl.ServiceDescriptionRegistryImpl:579)
- Provider SADI http://biordf.net/sparql: Failed to find services for
SADI at http://biordf.net/sparql
ca.wilkinsonlab.sadi.common.SADIException:
java.net.SocketTimeoutException: creation failed. Max trials 3
reached. Elapsed time 884 millis (creation timeout 20 sec). Could not
connect to biordf.net/137.82.157.228:80 java.net.SocketException:
Operation not supported
at
ca.wilkinsonlab.sadi.utils.QueryExecutorFactory$VirtuosoSPARQLEndpointQueryExecutor.executeQuery(QueryExecutorFactory.java:134)
at
ca.wilkinsonlab.sadi.client.RegistryBase.executeQuery(RegistryBase.java:108)
at
ca.wilkinsonlab.sadi.client.RegistryImpl.getAllServices(RegistryImpl.java:63)
at
net.sf.taverna.t2.activities.sadi.servicedescriptions.SADIServiceProvider.findServiceDescriptionsAsync(SADIServiceProvider.java:59)
at
net.sf.taverna.t2.servicedescriptions.impl.ServiceDescriptionRegistryImpl$FindServiceDescriptionsThread.run(ServiceDescriptionRegistryImpl.java:670)
WARN 2010-11-26 18:53:00,167
(net.sf.taverna.t2.servicedescriptions.impl.ServiceDescriptionRegistryImpl:579)
- Provider SADI http://biordf.net/sparql: Failed to find services for
SADI at http://biordf.net/sparql
ca.wilkinsonlab.sadi.common.SADIException:
java.net.SocketTimeoutException: creation failed. Max trials 3
reached. Elapsed time 924 millis (creation timeout 20 sec). Could not
connect to biordf.net/137.82.157.228:80 java.net.SocketException:
Operation not supported
at
ca.wilkinsonlab.sadi.utils.QueryExecutorFactory$VirtuosoSPARQLEndpointQueryExecutor.executeQuery(QueryExecutorFactory.java:134)
at
ca.wilkinsonlab.sadi.client.RegistryBase.executeQuery(RegistryBase.java:108)
at
ca.wilkinsonlab.sadi.client.RegistryImpl.getAllServices(RegistryImpl.java:63)
at
net.sf.taverna.t2.activities.sadi.servicedescriptions.SADIServiceProvider.findServiceDescriptionsAsync(SADIServiceProvider.java:59)
at
net.sf.taverna.t2.servicedescriptions.impl.ServiceDescriptionRegistryImpl$FindServiceDescriptionsThread.run(ServiceDescriptionRegistryImpl.java:670)
WARN 2010-11-26 18:53:08,899
(net.sf.taverna.t2.servicedescriptions.impl.ServiceDescriptionRegistryImpl:579)
- Provider SADI http://biordf.net/sparql: Failed to find services for
SADI at http://biordf.net/sparql
ca.wilkinsonlab.sadi.common.SADIException:
java.net.SocketTimeoutException: creation failed. Max trials 3
reached. Elapsed time 726 millis (creation timeout 20 sec). Could not
connect to biordf.net/137.82.157.228:80 java.net.SocketException:
Operation not supported
at
ca.wilkinsonlab.sadi.utils.QueryExecutorFactory$VirtuosoSPARQLEndpointQueryExecutor.executeQuery(QueryExecutorFactory.java:134)
at
ca.wilkinsonlab.sadi.client.RegistryBase.executeQuery(RegistryBase.java:108)
at
ca.wilkinsonlab.sadi.client.RegistryImpl.getAllServices(RegistryImpl.java:63)
at
net.sf.taverna.t2.activities.sadi.servicedescriptions.SADIServiceProvider.findServiceDescriptionsAsync(SADIServiceProvider.java:59)
at
net.sf.taverna.t2.servicedescriptions.impl.ServiceDescriptionRegistryImpl$FindServiceDescriptionsThread.run(ServiceDescriptionRegistryImpl.java:670)
ERROR 2010-11-26 18:53:12,349 (System.err:139) - Central class is
org.biomoby.client.CentralDigestCachedImpl
WARN 2010-11-26 18:53:14,245
(net.sf.taverna.t2.servicedescriptions.impl.ServiceDescriptionRegistryImpl:579)
- Provider SADI http://biordf.net/sparql: Failed to find services for
SADI at http://biordf.net/sparql
ca.wilkinsonlab.sadi.common.SADIException:
java.net.SocketTimeoutException: creation failed. Max trials 3
reached. Elapsed time 1066 millis (creation timeout 20 sec). Could not
connect to biordf.net/137.82.157.228:80 java.net.SocketException:
Operation not supported
at
ca.wilkinsonlab.sadi.utils.QueryExecutorFactory$VirtuosoSPARQLEndpointQueryExecutor.executeQuery(QueryExecutorFactory.java:134)
at
ca.wilkinsonlab.sadi.client.RegistryBase.executeQuery(RegistryBase.java:108)
at
ca.wilkinsonlab.sadi.client.RegistryImpl.getAllServices(RegistryImpl.java:63)
at
net.sf.taverna.t2.activities.sadi.servicedescriptions.SADIServiceProvider.findServiceDescriptionsAsync(SADIServiceProvider.java:59)
at
net.sf.taverna.t2.servicedescriptions.impl.ServiceDescriptionRegistryImpl$FindServiceDescriptionsThread.run(ServiceDescriptionRegistryImpl.java:670)
WARN 2010-11-26 18:53:24,118
(net.sf.taverna.t2.servicedescriptions.impl.ServiceDescriptionRegistryImpl:579)
- Provider SADI http://biordf.net/sparql: Failed to find services for
SADI at http://biordf.net/sparql
ca.wilkinsonlab.sadi.common.SADIException:
java.net.SocketTimeoutException: creation failed. Max trials 3
reached. Elapsed time 998 millis (creation timeout 20 sec). Could not
connect to biordf.net/137.82.157.228:80 java.net.SocketException:
Operation not supported
at
ca.wilkinsonlab.sadi.utils.QueryExecutorFactory$VirtuosoSPARQLEndpointQueryExecutor.executeQuery(QueryExecutorFactory.java:134)
at
ca.wilkinsonlab.sadi.client.RegistryBase.executeQuery(RegistryBase.java:108)
at
ca.wilkinsonlab.sadi.client.RegistryImpl.getAllServices(RegistryImpl.java:63)
at
net.sf.taverna.t2.activities.sadi.servicedescriptions.SADIServiceProvider.findServiceDescriptionsAsync(SADIServiceProvider.java:59)
at
net.sf.taverna.t2.servicedescriptions.impl.ServiceDescriptionRegistryImpl$FindServiceDescriptionsThread.run(ServiceDescriptionRegistryImpl.java:670)
-------------------------------------------------------------
At last, when I try to Add my own SADI services through SADI pluggins,
I got the follow one;
-------------------------------------------------------------
WARN 2010-11-26 18:58:24,119
(net.sf.taverna.t2.servicedescriptions.impl.ServiceDescriptionRegistryImpl:579)
- Provider SADI http://localhost:8890/sparql: Failed to find services
for SADI at http://localhost:8890/sparql
ca.wilkinsonlab.sadi.common.SADIException:
java.net.SocketTimeoutException: creation failed. Max trials 3
reached. Elapsed time 34 millis (creation timeout 20 sec). Could not
connect to localhost/127.0.0.1:8890 java.net.SocketException:
Operation not supported
at
ca.wilkinsonlab.sadi.utils.QueryExecutorFactory$VirtuosoSPARQLEndpointQueryExecutor.executeQuery(QueryExecutorFactory.java:134)
at
ca.wilkinsonlab.sadi.client.RegistryBase.executeQuery(RegistryBase.java:108)
at
ca.wilkinsonlab.sadi.client.RegistryImpl.getAllServices(RegistryImpl.java:63)
at
net.sf.taverna.t2.activities.sadi.servicedescriptions.SADIServiceProvider.findServiceDescriptionsAsync(SADIServiceProvider.java:59)
at
net.sf.taverna.t2.servicedescriptions.impl.ServiceDescriptionRegistryImpl$FindServiceDescriptionsThread.run(ServiceDescriptionRegistryImpl.java:670)
WARN 2010-11-26 18:58:25,104
(net.sf.taverna.t2.servicedescriptions.impl.ServiceDescriptionRegistryImpl:579)
- Provider SADI http://biordf.net/sparql: Failed to find services for
SADI at http://biordf.net/sparql
ca.wilkinsonlab.sadi.common.SADIException:
java.net.SocketTimeoutException: creation failed. Max trials 3
reached. Elapsed time 1022 millis (creation timeout 20 sec). Could not
connect to biordf.net/137.82.157.228:80 java.net.SocketException:
Operation not supported
at
ca.wilkinsonlab.sadi.utils.QueryExecutorFactory$VirtuosoSPARQLEndpointQueryExecutor.executeQuery(QueryExecutorFactory.java:134)
at
ca.wilkinsonlab.sadi.client.RegistryBase.executeQuery(RegistryBase.java:108)
at
ca.wilkinsonlab.sadi.client.RegistryImpl.getAllServices(RegistryImpl.java:63)
at
net.sf.taverna.t2.activities.sadi.servicedescriptions.SADIServiceProvider.findServiceDescriptionsAsync(SADIServiceProvider.java:59)
at
net.sf.taverna.t2.servicedescriptions.impl.ServiceDescriptionRegistryImpl$FindServiceDescriptionsThread.run(ServiceDescriptionRegistryImpl.java:670)
-------------------------------------------------------------
Can you help me. I cannot fix this error.
Thanks
--
Caio César Batista
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