On 05/02/2014 16:22, Dmitry wrote:
I do not understand that question. Do you mean for complex datatypes
that are (for example) the body of a REST PUT?
I mean the XML ("application/xml") that is passed in POST (and usually
returned as a result).
http://www.rcsb.org/pdb/rest/describePDB?structureId=4hhb
returns XML which Taverna can't parse further (?)
You can process it further, for example using XPath. However, there are
no nice capabilities for constructing or splitting data types.
So, in this case the template would be:
http://www.rcsb.org/pdb/rest/describePDB?structureId={structureId}
Yes. You can see the template in the REST service in the attached workflow.
Right?
Alan
<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow"; version="1"
producedBy="taverna-2.4.0"><dataflow id="019283dd-e9fb-4a7b-8422-f90f97dc7a4e"
role="top"><name>Workflow1</name><inputPorts
/><outputPorts><port><name>REST_Service_responseBody</name><annotations
/></port><port><name>REST_Service_status</name><annotations
/></port></outputPorts><processors><processor><name>REST_Service</name><inputPorts><port><name>structureId</name><depth>0</depth></port></inputPorts><outputPorts><port><name>responseBody</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>status</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations
/><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>rest-activity</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.activities.rest.RESTActivity</class><inputMap><map
from="structureId" to="structureId" /></inputMap><outputMap><map from="status"
to="status" /><map from="responseBody" to="responseBody"
/></outputMap><configBean
encoding="xstream"><net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean
xmlns="">
<httpMethod>GET</httpMethod>
<urlSignature>http://www.rcsb.org/pdb/rest/describePDB?structureId={structureId}</urlSignature>
<acceptsHeaderValue>application/xml</acceptsHeaderValue>
<contentTypeForUpdates>application/xml</contentTypeForUpdates>
<outgoingDataFormat>String</outgoingDataFormat>
<sendHTTPExpectRequestHeader>false</sendHTTPExpectRequestHeader>
<showRedirectionOutputPort>false</showRedirectionOutputPort>
<showActualUrlPort>false</showActualUrlPort>
<showResponseHeadersPort>false</showResponseHeadersPort>
<escapeParameters>true</escapeParameters>
<otherHTTPHeaders />
<activityInputs>
<entry>
<string>structureId</string>
<java-class>java.lang.String</java-class>
</entry>
</activityInputs>
</net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean></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="structureId" depth="0"
/></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>structureId_value</name><inputPorts
/><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations
/><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap
/><outputMap><map from="value" to="value" /></outputMap><configBean
encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean
xmlns="">
<value>4hhb</value>
</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></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
/></iteration></iterationStrategyStack></processor></processors><conditions
/><datalinks><datalink><sink
type="processor"><processor>REST_Service</processor><port>structureId</port></sink><source
type="processor"><processor>structureId_value</processor><port>value</port></source></datalink><datalink><sink
type="dataflow"><port>REST_Service_responseBody</port></sink><source
type="processor"><processor>REST_Service</processor><port>responseBody</port></source></datalink><datalink><sink
type="dataflow"><port>REST_Service_status</port></sink><source
type="processor"><processor>REST_Service</processor><port>status</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>019283dd-e9fb-4a7b-8422-f90f97dc7a4e</identification>
</annotationBean>
<date>2014-02-05 16:29:30.238 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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