Hello Alan,
I thought the ones with working services were OK
I thought too...
I just try to execute a moby workflow (a dumb one) and get an exception.
After investigating a little bit I found that there are several
JAXB/JAX-WS implementations in repository.
Because I can not remove them (taverna just downloads them back), I
removed "META-INF/services" dirs from the jars and
could be able to run the workflow...
Any comments?
Cheers,
Dmitry
java.util.ServiceConfigurationError: javax.xml.ws.spi.Provider: Provider
com.sun.xml.ws.spi.ProviderImpl could not be instantiated:
java.lang.NoClassDefFoundError: javax/xml/bind/annotation/AccessorOrder
at java.util.ServiceLoader.fail(Unknown Source)
at java.util.ServiceLoader.access$100(Unknown Source)
at java.util.ServiceLoader$LazyIterator.next(Unknown Source)
at java.util.ServiceLoader$1.next(Unknown Source)
at javax.xml.ws.spi.Provider.getProviderUsingServiceLoader(Unknown
Source)
at javax.xml.ws.spi.Provider.provider(Unknown Source)
at javax.xml.ws.Service.<init>(Unknown Source)
at javax.xml.ws.Service.create(Unknown Source)
at
net.sf.taverna.t2.activities.biomoby.ExecuteAsyncMobyService.launchMobyAsyncService(ExecuteAsyncMobyService.java:514)
at
net.sf.taverna.t2.activities.biomoby.ExecuteAsyncMobyService.executeMobyAsyncService(ExecuteAsyncMobyService.java:324)
at
net.sf.taverna.t2.activities.biomoby.BiomobyActivity.executeService(BiomobyActivity.java:1311)
at
net.sf.taverna.t2.activities.biomoby.BiomobyActivity.access$400(BiomobyActivity.java:60)
at
net.sf.taverna.t2.activities.biomoby.BiomobyActivity$1.run(BiomobyActivity.java:694)
at java.lang.Thread.run(Unknown Source)
Caused by: java.lang.NoClassDefFoundError:
javax/xml/bind/annotation/AccessorOrder
at
com.sun.xml.bind.v2.model.impl.RuntimeModelBuilder.createClassInfo(RuntimeModelBuilder.java:59)
at
com.sun.xml.bind.v2.model.impl.RuntimeModelBuilder.createClassInfo(RuntimeModelBuilder.java:41)
at
com.sun.xml.bind.v2.model.impl.ModelBuilder.getClassInfo(ModelBuilder.java:123)
at
com.sun.xml.bind.v2.model.impl.RuntimeModelBuilder.getClassInfo(RuntimeModelBuilder.java:49)
at
com.sun.xml.bind.v2.model.impl.RuntimeModelBuilder.getClassInfo(RuntimeModelBuilder.java:41)
at
com.sun.xml.bind.v2.model.impl.ModelBuilder.getTypeInfo(ModelBuilder.java:189)
at
com.sun.xml.bind.v2.model.impl.ModelBuilder.getTypeInfo(ModelBuilder.java:204)
at
com.sun.xml.bind.v2.runtime.JAXBContextImpl.getTypeInfoSet(JAXBContextImpl.java:327)
at
com.sun.xml.bind.v2.runtime.JAXBContextImpl.<init>(JAXBContextImpl.java:198)
at
com.sun.xml.bind.v2.ContextFactory.createContext(ContextFactory.java:76)
at
com.sun.xml.bind.v2.ContextFactory.createContext(ContextFactory.java:55)
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 javax.xml.bind.ContextFinder.newInstance(Unknown Source)
at javax.xml.bind.ContextFinder.newInstance(Unknown Source)
at javax.xml.bind.ContextFinder.find(Unknown Source)
at javax.xml.bind.JAXBContext.newInstance(Unknown Source)
at javax.xml.bind.JAXBContext.newInstance(Unknown Source)
at com.sun.xml.ws.spi.ProviderImpl$2.run(ProviderImpl.java:220)
at com.sun.xml.ws.spi.ProviderImpl$2.run(ProviderImpl.java:218)
at java.security.AccessController.doPrivileged(Native Method)
at
com.sun.xml.ws.spi.ProviderImpl.getEPRJaxbContext(ProviderImpl.java:217)
at com.sun.xml.ws.spi.ProviderImpl.<clinit>(ProviderImpl.java:88)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Unknown Source)
... 12 more
Caused by: java.lang.ClassNotFoundException:
javax.xml.bind.annotation.AccessorOrder
at
net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass(LocalArtifactClassLoader.java:343)
at
net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass(LocalArtifactClassLoader.java:276)
at java.lang.ClassLoader.loadClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
... 39 more
On 10/1/2012 12:37 PM, Alan R Williams wrote:
On 01/10/2012 11:31, Dmitry wrote:
Hello,
Hello Dmitry
I am facing a problem with BioMoby workflows.
The problem looks like in clashing with JAX-WS library installed in
maven and Java6/7 internal JAX-WS.
I can execute workflow successfully cheating Taverna's repository.
Probably I (we) have to remove all JAXB/JAX-WS dependencies given that
Taverna now is compiled for Java6 and it is already has JAX-WS/JAXB
implementation.
What happens when you run BioMoby workflows? I thought the ones with
working services were OK, and the example ones used to work in Taverna
2.4 (before the problems with the services).
Cheers,
Dmitry
Alan
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<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow"; version="1"
producedBy="taverna-2.4.0"><dataflow id="b061811b-161c-454d-a658-8a43d2999c1a"
role="top"><name>Workflow32</name><inputPorts><port><name>fasta_file</name><depth>0</depth><granularDepth>0</granularDepth><annotations
/></port></inputPorts><outputPorts><port><name>zip_file</name><annotations
/></port></outputPorts><processors><processor><name>runNCBIFormatdb</name><inputPorts><port><name>FASTA(fasta)</name><depth>0</depth></port></inputPorts><outputPorts><port><name>Zip_Encoded(blast_db)</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations
/><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>biomoby-activity</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.activities.biomoby.BiomobyActivity</class><inputMap><map
from="FASTA(fasta)" to="FASTA(fasta)" /></inputMap><outputMap><map
from="Zip_Encoded(blast_db)" to="Zip_Encoded(blast_db)"
/></outputMap><configBean
encoding="xstream"><net.sf.taverna.t2.activities.biomoby.BiomobyActivityConfigurationBean
xmlns="">
<mobyEndpoint>http://moby-dev.inab.org/cgi-bin/MOBY-Central.pl</mobyEndpoint>
<serviceName>runNCBIFormatdb</serviceName>
<authorityName>inb.bsc.es</authorityName>
<category />
<serviceType />
<secondaries>
<entry>
<string>persistent</string>
<string>true</string>
</entry>
<entry>
<string>type</string>
<string>protein</string>
</entry>
<entry>
<string>database</string>
<string>db</string>
</entry>
</secondaries>
</net.sf.taverna.t2.activities.biomoby.BiomobyActivityConfigurationBean></configBean><annotations
/></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean
encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig
xmlns="">
<maxJobs>1</maxJobs>
</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean
encoding="xstream"><null xmlns=""
/></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean
encoding="xstream"><null xmlns=""
/></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean
encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig
xmlns="">
<backoffFactor>1.0</backoffFactor>
<initialDelay>1000</initialDelay>
<maxDelay>5000</maxDelay>
<maxRetries>0</maxRetries>
</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean
encoding="xstream"><null xmlns=""
/></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port
name="FASTA(fasta)" depth="0"
/></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>FASTA</name><inputPorts><port><name>String(content)</name><depth>0</depth></port></inputPorts><outputPorts><port><name>mobyData</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations
/><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>biomoby-activity</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.activities.biomoby.BiomobyObjectActivity</class><inputMap><map
from="String(content)" to="String(content)" /></inputMap><outputMap><map
from="mobyData" to="mobyData" /></outputMap><configBean
encoding="xstream"><net.sf.taverna.t2.activities.biomoby.BiomobyObjectActivityConfigurationBean
xmlns="">
<mobyEndpoint>http://moby-dev.inab.org/cgi-bin/MOBY-Central.pl</mobyEndpoint>
<serviceName>FASTA</serviceName>
<authorityName>www.inab.org</authorityName>
</net.sf.taverna.t2.activities.biomoby.BiomobyObjectActivityConfigurationBean></configBean><annotations
/></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean
encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig
xmlns="">
<maxJobs>1</maxJobs>
</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean
encoding="xstream"><null xmlns=""
/></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean
encoding="xstream"><null xmlns=""
/></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean
encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig
xmlns="">
<backoffFactor>1.0</backoffFactor>
<initialDelay>1000</initialDelay>
<maxDelay>5000</maxDelay>
<maxRetries>0</maxRetries>
</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean
encoding="xstream"><null xmlns=""
/></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port
name="String(content)" depth="0"
/></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>String(content)</name><inputPorts><port><name>value</name><depth>0</depth></port></inputPorts><outputPorts><port><name>mobyData</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations
/><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>biomoby-activity</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.activities.biomoby.BiomobyObjectActivity</class><inputMap><map
from="value" to="value" /></inputMap><outputMap><map from="mobyData"
to="mobyData" /></outputMap><configBean
encoding="xstream"><net.sf.taverna.t2.activities.biomoby.BiomobyObjectActivityConfigurationBean
xmlns="">
<mobyEndpoint>http://moby-dev.inab.org/cgi-bin/MOBY-Central.pl</mobyEndpoint>
<serviceName>String</serviceName>
<authorityName />
</net.sf.taverna.t2.activities.biomoby.BiomobyObjectActivityConfigurationBean></configBean><annotations
/></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean
encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig
xmlns="">
<maxJobs>1</maxJobs>
</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean
encoding="xstream"><null xmlns=""
/></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean
encoding="xstream"><null xmlns=""
/></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean
encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig
xmlns="">
<backoffFactor>1.0</backoffFactor>
<initialDelay>1000</initialDelay>
<maxDelay>5000</maxDelay>
<maxRetries>0</maxRetries>
</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean
encoding="xstream"><null xmlns=""
/></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port
name="value" depth="0"
/></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions
/><datalinks><datalink><sink
type="processor"><processor>runNCBIFormatdb</processor><port>FASTA(fasta)</port></sink><source
type="processor"><processor>FASTA</processor><port>mobyData</port></source></datalink><datalink><sink
type="processor"><processor>FASTA</processor><port>String(content)</port></sink><source
type="processor"><processor>String(content)</processor><port>mobyData</port></source></datalink><datalink><sink
type="processor"><processor>String(content)</processor><port>value</port></sink><source
type="dataflow"><port>fasta_file</port></source></datalink><datalink><sink
type="dataflow"><port>zip_file</port></sink><source
type="processor"><processor>runNCBIFormatdb</processor><port>Zip_Encoded(blast_db)</port></source></datalink></datalinks><annotations><annotation_chain_2_2
encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
<annotationAssertions>
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
<annotationBean
class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
<identification>b061811b-161c-454d-a658-8a43d2999c1a</identification>
</annotationBean>
<date>2012-09-28 10:24:47.427 UTC</date>
<creators />
<curationEventList />
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
</annotationAssertions>
</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>------------------------------------------------------------------------------
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