Re: [Taverna-hackers] Flow error on taverna workbench 2.2.0

Thu, 10 Mar 2011 06:44:42 -0800 

On 10/03/2011 14:10, javier wrote:

I have a flow that works in taverna 2.1.2 but fails to open on 2.2.0.



I can't get it to open in 2.1.2 either. Did you just save the workflow 
or has it gone through an editor? The "!" seem to be there to break up 
long lines. I've deleted them and re-merged the lines in the attached 
workflow.


Alan


<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow"; version="1" 
producedBy="taverna-2.1.2"><dataflow id="1092a2a8-5a3a-48e1-8ce6-fd9ad9efcc94" 
role="top"><name>Workflow7</name><inputPorts><port><name>sequence</name><depth>0</depth><granularDepth>0</granularDepth><annotations><annotation_chain
 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
  <annotationAssertions>
    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
      <annotationBean 
class="net.sf.taverna.t2.annotation.annotationbeans.ExampleValue">
        <text>&gt;gi|74663652|sp|Q874A6|Q874A6_9APHY RBPa precursor
MAFKQLLTAALSIALALPFSQAAITRRVACPDGVNTATNAACCALFAVRDDIQQNLFDGGECGEEVHESL
RLTFHDAIGISPSLAATGKFGGGGADGSIMIFDDIEPNFHANNGVDEIINAQKPFVAKHNMTAGDFIQFA
GAVGVSNCPGAPQLSFFLGRPAATQPAPDGLVPEPFDSVTDILNRFADAGGFTIQEVVWLLASHSIAAAD
HVDPTIPGSPFDSTPEIFDTQFFVETLLKGTLFPGTSGNQGEVESPLAGEIRLQSDADFARDSRTACEWQ
SFVNNQPRMQVLFKAAMQKLSILGHDLTQMIDCSDVIPVPPSTAVRGSHLPAGNTLDDIEQACASTPFPS
LTADPGPATSVAPVPPS

&gt;gi|121808615|sp|Q3SC77|Q3SC77_9APHY Versatile peroxidase
MAFKQLAAALSIALALPFSQAAITRRVACPDGVNTATNAACCALFAVRDDIQQNLFDGGECGEEVHESLR
LTFHDAIGISPSIAATGKFGGGGADGSIMIFDDIEPNFHANNGVDEIISAQKPFVAKHNMTAGDFIQFAG
AVGVSNCPGAPQLSFFLGRPAATQPAPDGLVPEPFDSVTDILNRFADAGGFTTQEVVWLLASHSIAAADH
VDPTIPGSPFDSTPEIFDTQFFVETLLKGTLFPGTSGNQGEVESPLAGEIRLQSDADFARDSRTACEWQS
FVNNQPRMQVLFKAAMQKLSILGHDLTQMIDCSDVIPVPPSTAVRGSHLPAGNTLDDIEQACASTPFPTL
TADPGPATSVAPVPPS</text>
      </annotationBean>
      <date>2011-03-03 21:34:45.78 UYST</date>
      <creators />
      <curationEventList />
    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
  </annotationAssertions>
</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port><port><name>params</name><depth>0</depth><granularDepth>0</granularDepth><annotations><annotation_chain
 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
  <annotationAssertions>
    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
      <annotationBean 
class="net.sf.taverna.t2.annotation.annotationbeans.ExampleValue">
        <text>-OUTPUTTREE=nj</text>
      </annotationBean>
      <date>2011-03-02 01:02:32.125 UYST</date>
      <creators />
      <curationEventList />
    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
  </annotationAssertions>
</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain
 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
  <annotationAssertions>
    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
      <annotationBean 
class="net.sf.taverna.t2.annotation.annotationbeans.ExampleValue">
        <text>-OUTPUTTREE=nj -KIMURA=1 -TREE=1</text>
      </annotationBean>
      <date>2011-03-02 01:03:20.828 UYST</date>
      <creators />
      <curationEventList />
    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
  </annotationAssertions>
</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain
 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
  <annotationAssertions>
    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
      <annotationBean 
class="net.sf.taverna.t2.annotation.annotationbeans.ExampleValue">
        <text>-OUTPUTTREE=nj -KIMURA=1</text>
      </annotationBean>
      <date>2011-03-02 01:06:46.31 UYST</date>
      <creators />
      <curationEventList />
    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
  </annotationAssertions>
</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain
 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
  <annotationAssertions>
    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
      <annotationBean 
class="net.sf.taverna.t2.annotation.annotationbeans.ExampleValue">
        <text>-outputtree=nj  -KIMURA=1</text>
      </annotationBean>
      <date>2011-03-02 01:05:45.203 UYST</date>
      <creators />
      <curationEventList />
    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
  </annotationAssertions>
</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain
 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
  <annotationAssertions>
    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
      <annotationBean 
class="net.sf.taverna.t2.annotation.annotationbeans.ExampleValue">
        <text>-outputtree=nj  -KIMURA=1 -TREE=1</text>
      </annotationBean>
      <date>2011-03-02 01:05:17.296 UYST</date>
      <creators />
      <curationEventList />
    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
  </annotationAssertions>
</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain
 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
  <annotationAssertions>
    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
      <annotationBean 
class="net.sf.taverna.t2.annotation.annotationbeans.ExampleValue">
        <text>-OUTPUTTREE=nj  -KIMURA=1</text>
      </annotationBean>
      <date>2011-03-02 01:05:58.250 UYST</date>
      <creators />
      <curationEventList />
    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
  </annotationAssertions>
</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain
 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
  <annotationAssertions>
    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
      <annotationBean 
class="net.sf.taverna.t2.annotation.annotationbeans.ExampleValue">
        <text>-OUTPUTTREE=nj -KIMURA=1</text>
      </annotationBean>
      <date>2011-03-02 01:02:49.812 UYST</date>
      <creators />
      <curationEventList />
    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
  </annotationAssertions>
</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port></inputPorts><outputPorts><port><name>result</name><annotations
 /></port><port><name>result2</name><annotations 
/></port></outputPorts><processors><processor><name>analyzeSimple</name><inputPorts><port><name>query</name><depth>0</depth></port></inputPorts><outputPorts><port><name>Result</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations
 
/><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.1</version></raven><class>net.sf.taverna.t2.activities.wsdl.WSDLActivity</class><inputMap><map
 from="query" to="query" /></inputMap><outputMap><map from="Result" to="Result" 
/></outputMap><configBean 
encoding="xstream"><net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean
 xmlns="">
  <wsdl>http://xml.nig.ac.jp/wsdl/ClustalW.wsdl</wsdl>
  <operation>analyzeSimple</operation>
</net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean></configBean><annotations
 
/></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.1</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>1.1</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>1.1</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>1.1</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>1.1</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="query" depth="0" 
/></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>analyzeParam</name><inputPorts><port><name>query</name><depth>0</depth></port><port><name>param</name><depth>0</depth></port></inputPorts><outputPorts><port><name>Result</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations
 
/><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>1.1</version></raven><class>net.sf.taverna.t2.activities.wsdl.WSDLActivity</class><inputMap><map
 from="param" to="param" /><map from="query" to="query" 
/></inputMap><outputMap><map from="Result" to="Result" 
/></outputMap><configBean 
encoding="xstream"><net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean
 xmlns="">
  <wsdl>http://xml.nig.ac.jp/wsdl/ClustalW.wsdl</wsdl>
  <operation>analyzeParam</operation>
</net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean></configBean><annotations
 
/></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.1</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>1.1</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>1.1</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>1.1</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>1.1</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="query" depth="0" /><port name="param" depth="0" 
/></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions
 /><datalinks><datalink><sink 
type="processor"><processor>analyzeSimple</processor><port>query</port></sink><source
 type="dataflow"><port>sequence</port></source></datalink><datalink><sink 
type="processor"><processor>analyzeParam</processor><port>query</port></sink><source
 type="dataflow"><port>sequence</port></source></datalink><datalink><sink 
type="processor"><processor>analyzeParam</processor><port>param</port></sink><source
 type="dataflow"><port>params</port></source></datalink><datalink><sink 
type="dataflow"><port>result</port></sink><source 
type="processor"><processor>analyzeSimple</processor><port>Result</port></source></datalink><datalink><sink
 type="dataflow"><port>result2</port></sink><source 
type="processor"><processor>analyzeParam</processor><port>Result</port></source></datalink></datalinks><annotations
 /></dataflow></workflow>
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