Hi all,
Is there any way to get Taverna 2.1b2 to produce more precise reasons
for the loading of a workflow failing? The workflow file I'm writing
from Seahawk isn't loading, even though the workflow validates against
the T2Flow XSD:
http://taverna.googlecode.com/svn/taverna/dev/xsd/trunk/t2flow/t2flow.xsd
so I'm guessing it's a logic/labelling error somewhere. But all I get
is a "...OpenException: Could not parse Scufl file" which doesn't help
pinpoint it at all :-)
As a minor point, shouldn't it say Could not parse T2Flow file, or
something generic that covers them both? Or is it actually trying to
parse it as a Scufl...which would be a major issue of course (the file
is given the .t2flow suffix).
Thanks for any help you can provide,
Paul
P.S. A simple workflow with this issue is attached.
<?xml version="1.0" encoding="UTF-8"?>
<workflow producedBy="Seahawk 1.0" version="1" xmlns="http://taverna.sf.net/2008/xml/t2flow";>
<dataflow id="8bed1d6d-c8ec-42d5-baa3-66b652ec4e12" role="top">
<name>q</name>
<inputPorts>
<port>
<name>id</name>
<depth>0</depth>
<granularDepth>0</granularDepth>
</port>
</inputPorts>
<outputPorts>
<port>
<name>taxonomy</name>
</port>
</outputPorts>
<processors>
<processor>
<name>ID2Taxonomy</name>
<inputPorts>
<port>
<name>Object(id)</name>
<depth>0</depth>
</port>
</inputPorts>
<outputPorts>
<port>
<name>TaxonScientificName(taxonomy)</name>
<depth>0</depth>
<granularDepth>0</granularDepth>
</port>
<port>
<name>output</name>
<depth>0</depth>
<granularDepth>0</granularDepth>
</port>
</outputPorts>
<annotations/>
<activities>
<activity>
<class>net.sf.taverna.t2.activities.biomoby.BiomobyActivity</class>
<inputMap>
<map from="Object(id)" to="Object(id)"/>
</inputMap>
<outputMap>
<map from="TaxonScientificName(taxonomy)" to="TaxonScientificName(taxonomy)"/>
<map from="output" to="output"/>
</outputMap>
<configBean encoding="xstream">
<net.sf.taverna.t2.activities.biomoby.BiomobyActivityConfigurationBean xmlns="">
<mobyEndpoint>http://moby.ucalgary.ca/moby/MOBY-Central.pl</mobyEndpoint>
<serviceName>ID2Taxonomy</serviceName>
<category>moby</category>
<serviceType>Retrieval</serviceType>
<secondaries/>
</net.sf.taverna.t2.activities.biomoby.BiomobyActivityConfigurationBean>
</configBean>
</activity>
</activities>
<dispatchStack>
<dispatchLayer>
<raven>
<group>net.sf.taverna.t2.core</group>
<artifact>workflowmodel-impl</artifact>
<version>0.8</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>0.8</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>0.8</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>0.8</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>0.8</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 depth="0" name="Object(id)"/>
</cross>
</strategy>
</iteration>
</iterationStrategyStack>
</processor>
</processors>
<conditions/>
<datalinks>
<datalink>
<sink type="processor">
<processor>ID2Taxonomy</processor>
<port>Object(id)</port>
</sink>
<source type="dataflow">
<port>id</port>
</source>
</datalink>
<datalink>
<sink type="dataflow">
<port>taxonomy</port>
</sink>
<source type="processor">
<processor>ID2Taxonomy</processor>
<port>taxonomy</port>
</source>
</datalink>
</datalinks>
</dataflow>
</workflow>
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