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Dear all, I am trying one of the examples on this page: http://www.tizag.com/xmlTutorial/xpathattribute.php The t2 workflow is attached. The workflow gives an error document that ends with: Invalid XPath _expression_: inventory/snack/ch...@supplier Unexpected '@' I was able to correct this by placing a '\' before the @ symbol, because I remembered that such a thing would be needed in java too. Would it be possible to remove these Java peculiarities from the use of String constants in Taverna? Or at least point this out to users when they get an error (with a link to a help page perhaps)? Ideally, workflows should not show that Taverna is java-based, should it? Thanks, Marco. --
Marco
Roos (PhD)
BioSemantics group, Human Genetics department, Leiden University Medical Centre Albinusdreef 2 (Building 2, room S3-46) 2333 ZA Leiden Tel. +31 (0) 71 526 9450 Adaptive Information Disclosure group, Informatics Institute, University of Amsterdam Kruislaan 403 ( room N2.30) 1098 SJ Amsterdam Tel. +31 (0) 20 525 7522 Communities: Professional: LinkedIn, myExperiment Personal: Hyves |
<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow"; version="1" producedBy="taverna-2.1-beta-2"><dataflow id="85db9935-d94c-4200-959e-4bcd41053444" role="top"><name>Workflow18</name><inputPorts /><outputPorts><port><name>output</name></port></outputPorts><processors><processor><name>xml_doc</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>0.8</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><inventory> <drink> <lemonade supplier="mother" id="1"> <price>$2.50</price> <amount>20</amount> </lemonade> <pop supplier="store" id="2"> <price>$1.50</price> <amount>10</amount> </pop> </drink> <snack> <chips supplier="store" id="3"> <price>$4.50</price> <amount>60</amount> <calories>180</calories> </chips> </snack> </inventory> </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>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 /></iteration></iterationStrategyStack></processor><processor><name>XPath_From_Text</name><inputPorts><port><name>xml-text</name><depth>0</depth></port><port><name>xpath</name><depth>0</depth></port></inputPorts><outputPorts><port><name>nodelist</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>localworker-activity</artifact><version>0.8</version></raven><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap><map from="xml-text" to="xml-text" /><map from="xpath" to="xpath" /></inputMap><outputMap><map from="nodelist" to="nodelist" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns=""> <script>import org.dom4j.Document; import org.dom4j.Node; import org.dom4j.io.SAXReader;
SAXReader reader = new SAXReader(false);
reader.setIncludeInternalDTDDeclarations(false);
reader.setIncludeExternalDTDDeclarations(false);
Document document = reader.read(new StringReader(xmltext));
List nodelist = document.selectNodes(xpath);
// Process the elements in the nodelist
ArrayList outputList = new ArrayList();
ArrayList outputXmlList = new ArrayList();
String val = null;
String xmlVal = null;
for (Iterator iter = nodelist.iterator(); iter.hasNext();) {
Node element = (Node) iter.next();
xmlVal = element.asXML();
val = element.getStringValue();
if (val != null && !val.equals("")) {
outputList.add(val);
outputXmlList.add(xmlVal);
}
}
List nodelist=outputList;
List nodelistAsXML=outputXmlList;</script>
<dependencies>
<string>dom4j:dom4j:1.6</string>
</dependencies>
<classLoaderSharing>workflow</classLoaderSharing>
<localDependencies />
<artifactDependencies>
<net.sf.taverna.raven.repository.BasicArtifact>
<groupId>dom4j</groupId>
<artifactId>dom4j</artifactId>
<version>1.6</version>
<hashCode>716010169</hashCode>
<string>dom4j:dom4j:1.6</string>
</net.sf.taverna.raven.repository.BasicArtifact>
</artifactDependencies>
<inputs>
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
<handledReferenceSchemes />
<translatedElementType>java.lang.String</translatedElementType>
<allowsLiteralValues>true</allowsLiteralValues>
<name>xpath</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>xml-text</name>
<depth>0</depth>
<mimeTypes>
<string>'text/xml'</string>
</mimeTypes>
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
</inputs>
<outputs>
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
<granularDepth>1</granularDepth>
<name>nodelist</name>
<depth>1</depth>
<mimeTypes>
<string>l('text/plain')</string>
</mimeTypes>
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
<granularDepth>1</granularDepth>
<name>nodelistAsXML</name>
<depth>1</depth>
<mimeTypes>
<string>l('text/plain')</string>
</mimeTypes>
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
</outputs>
</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean><annotations
/></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
name="xml-text" depth="0" /><port name="xpath" depth="0"
/></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>xpath</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>0.8</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>inventory/snack/ch...@supplier </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>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
/></iteration></iterationStrategyStack></processor></processors><conditions
/><datalinks><datalink><sink
type="processor"><processor>XPath_From_Text</processor><port>xml-text</port></sink><source
type="processor"><processor>xml_doc</processor><port>value</port></source></datalink><datalink><sink
type="processor"><processor>XPath_From_Text</processor><port>xpath</port></sink><source
type="processor"><processor>xpath</processor><port>value</port></source></datalink><datalink><sink
type="dataflow"><port>output</port></sink><source
type="processor"><processor>XPath_From_Text</processor><port>nodelist</port></source></datalink></datalinks><annotations
/></dataflow></workflow>------------------------------------------------------------------------------ This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-dev2dev
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