HI
Just tried the pathway workflow again and got same error
However i tried another workflow which works from the command line but
not in taverna. This was just my test for the command line tool (it
just concatenates my forname and surname)
andrea@oscar:~/taverna-2.2$ executeworkflow.sh getname.t2flow
-inputvalue forname andrea -inputvalue surname edwards
Outputs will be saved to the directory:
/home/andrea/taverna-2.2/Workflow4_output_1
andrea@oscar:~/taverna-2.2$ cd Workflow4_output
andrea@oscar:~/taverna-2.2/Workflow4_output$ ls
out
andrea@oscar:~/taverna-2.2/Workflow4_output$ head out
andrea edwards
andrea@oscar:~/taverna-2.2/Workflow4_output$
However it does not work inside taverna. I have attached the workflow
cheers
On 18/04/11 16:41, Alan R Williams wrote:
On 18/04/2011 16:26, Andrea Edwards wrote:
HI
Hello
I can run other workflows
What database are you referring to?
Two other users reported a similar problem. It could be solved by
removing the database in which Taverna stores provenance information
(and perhaps data).
However, I would have expected a corrupt database to prevent you running
any workflows. If you send me the input values, I can try to replicate
your problem.
thanks
Alan
------------------------------------------------------------------------------
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<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow"; version="1"
producedBy="taverna-2.2.0"><dataflow id="ed1be37e-5558-434c-9731-4309732d4765"
role="top"><name>Workflow4</name><inputPorts><port><name>forname</name><depth>0</depth><granularDepth>0</granularDepth><annotations
/></port><port><name>surname</name><depth>0</depth><granularDepth>0</granularDepth><annotations
/></port></inputPorts><outputPorts><port><name>out</name><annotations
/></port></outputPorts><processors><processor><name>Beanshell</name><inputPorts><port><name>forname</name><depth>0</depth></port><port><name>surname</name><depth>0</depth></port></inputPorts><outputPorts><port><name>fullname</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations
/><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map
from="forname" to="forname" /><map from="surname" to="surname"
/></inputMap><outputMap><map from="fullname" to="fullname"
/></outputMap><configBean
encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean
xmlns="">
<script>fullname = forname + " " + surname;</script>
<dependencies />
<classLoaderSharing>workflow</classLoaderSharing>
<localDependencies />
<artifactDependencies />
<inputs>
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
<handledReferenceSchemes />
<translatedElementType>java.lang.String</translatedElementType>
<allowsLiteralValues>true</allowsLiteralValues>
<name>forname</name>
<depth>0</depth>
<mimeTypes>
<string>text/plain</string>
</mimeTypes>
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
<handledReferenceSchemes />
<translatedElementType>java.lang.String</translatedElementType>
<allowsLiteralValues>true</allowsLiteralValues>
<name>surname</name>
<depth>0</depth>
<mimeTypes>
<string>text/plain</string>
</mimeTypes>
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
</inputs>
<outputs>
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
<granularDepth>0</granularDepth>
<name>fullname</name>
<depth>0</depth>
<mimeTypes />
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
</outputs>
</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations
/></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.2</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>1.2</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>1.2</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>1.2</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>1.2</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="forname" depth="0" /><port name="surname" depth="0"
/></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions
/><datalinks><datalink><sink
type="processor"><processor>Beanshell</processor><port>forname</port></sink><source
type="dataflow"><port>forname</port></source></datalink><datalink><sink
type="processor"><processor>Beanshell</processor><port>surname</port></sink><source
type="dataflow"><port>surname</port></source></datalink><datalink><sink
type="dataflow"><port>out</port></sink><source
type="processor"><processor>Beanshell</processor><port>fullname</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>0e4b1033-2f7f-412d-b71c-789e42c34add</identification>
</annotationBean>
<date>2011-04-15 01:08:37.658 BST</date>
<creators />
<curationEventList />
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
</annotationAssertions>
</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><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>ed1be37e-5558-434c-9731-4309732d4765</identification>
</annotationBean>
<date>2011-04-15 01:16:59.937 BST</date>
<creators />
<curationEventList />
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
</annotationAssertions>
</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><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>cd1cf6eb-315b-4a31-87d8-44ade0a815b9</identification>
</annotationBean>
<date>2011-04-15 01:05:35.645 BST</date>
<creators />
<curationEventList />
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
</annotationAssertions>
</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><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>afa915dd-0270-416e-9afa-fac4f2ffc574</identification>
</annotationBean>
<date>2011-04-15 01:03:09.562 BST</date>
<creators />
<curationEventList />
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
</annotationAssertions>
</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>------------------------------------------------------------------------------
Benefiting from Server Virtualization: Beyond Initial Workload
Consolidation -- Increasing the use of server virtualization is a top
priority.Virtualization can reduce costs, simplify management, and improve
application availability and disaster protection. Learn more about boosting
the value of server virtualization. http://p.sf.net/sfu/vmware-sfdev2dev
_______________________________________________
taverna-users mailing list
[email protected]
[email protected]
Web site: http://www.taverna.org.uk
Mailing lists: http://www.taverna.org.uk/about/contact-us/
