. . . . . . . . . . . . . . . . . . . . . Dr Alexandra Nenadic myGrid project School of Computer Science University of Manchester E-mail: [email protected] Web: http://www.cs.man.ac.uk/~nenadic Office: +44 (0)161 275 0672 . . . . . . . . . . . . . . . . . . . . .
Hi,The exception you get (i.e. HttpHostConnectException) appears to be related to opening a TCP socket to the host,
long before the GET request for a specific URL is sent.I can open and run your wf just fine (with the .txt input you provided). The only obvious difference that I see is that I am running Java 6.
Could you try just calling a simple "Get page from URL" Beanshell service using the the following URL "http://www.uniprot.org/uniprot/Q99102"; (see the attached wf)?
Alex On 15/03/2011 12:03, Peter Li wrote:
Hi Alex, I can confirm we have the 0.3.1 version of the REST plugin installed in Taverna 2.2. When I open Paul's REST workflow, the processor is grayed out. See pic. When I write a new workflow containing a REST activity, the processor isn't greyed out - its a blue colour. If I try to run the workflow though, it says that connection to the web server is refused. Peter. ________________________________________ From: Alex Nenadic [[email protected]] Sent: 15 March 2011 11:14 To: [email protected] Cc: Peter Li Subject: Re: [Taverna-users] Problem with REST service Hi Pete, Make sure you have the latest REST activity plugin v0.3.1 installed in the Taverna Workbench 2.2 - that made the workflow work for me fine. Let us know if this does not help you. Alex On 15/03/2011 10:58, Peter Li wrote: Hi there, We're having problems with using the REST service here in South Africa at the Taverna workshop that I've not seen before. I've attached the error message that I get when running the attached workflow. The training PCs are running behind a proxy but that appears to be set ok - other workflows using web service are running ok. When I check the URL on a web browser, it seems to access the page ok too. Taverna 2.2 is running on Windows XP with Java 1.5.0_12. Any ideas? Thanks, Peter ------------------------------------------------------------------------------ Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d _______________________________________________ taverna-users mailing list [email protected]<mailto:[email protected]> [email protected]<mailto:[email protected]> Web site: http://www.taverna.org.uk Mailing lists: http://www.taverna.org.uk/about/contact-us/ ------------------------------------------------------------------------------ Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d _______________________________________________ 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/
<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow"; version="1" producedBy="taverna-2.2.0"><dataflow id="53239d39-79d4-4a05-936f-ead5c51b4699" role="top"><name>Workflow5</name><inputPorts /><outputPorts><port><name>contents</name><annotations /></port></outputPorts><processors><processor><name>Get_Web_Page_from_URL</name><inputPorts><port><name>url</name><depth>0</depth></port></inputPorts><outputPorts><port><name>contents</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>localworker-activity</artifact><version>1.2</version></raven><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap><map from="url" to="url" /></inputMap><outputMap><map from="contents" to="contents" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns=""> <localworkerName>org.embl.ebi.escience.scuflworkers.java.WebPageFetcher</localworkerName> <script>URL inputURL = null; if (base != void) { inputURL = new URL(new URL(base), url); } else { inputURL = new URL(url); } URLConnection con = inputURL.openConnection(); InputStream in = con.getInputStream(); InputStreamReader isr = new InputStreamReader(in); Reader inReader = new BufferedReader(isr); StringBuffer buf = new StringBuffer(); int ch; while ((ch = inReader.read()) > -1) { buf.append((char)ch); } inReader.close(); contents = buf.toString(); //String NEWLINE = System.getProperty("line.separator"); // //URL inputURL = null; //if (base != void) { // inputURL = new URL(new URL(base), url); //} else { // inputURL = new URL(url); //} //StringBuffer result = new StringBuffer(); //BufferedReader reader = new BufferedReader(new InputStreamReader(inputURL.openStream())); //String line = null; //while ((line = reader.readLine()) != null) { // result.append(line); // result.append(NEWLINE); //} // //contents = result.toString(); </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>url</name> <depth>0</depth> <mimeTypes> <string>'text/x-taverna-web-url'</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>base</name> <depth>0</depth> <mimeTypes> <string>'text/x-taverna-web-url'</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>contents</name> <depth>0</depth> <mimeTypes> <string>'text/plain,text/html'</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>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="url" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>url_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>1.2</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>http://www.uniprot.org/uniprot/Q99102</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>1.2</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 /></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>Get_Web_Page_from_URL</processor><port>url</port></sink><source type="processor"><processor>url_value</processor><port>value</port></source></datalink><datalink><sink type="dataflow"><port>contents</port></sink><source type="processor"><processor>Get_Web_Page_from_URL</processor><port>contents</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>6a9741f1-5874-4e7a-ab0f-f28e89ed942f</identification> </annotationBean> <date>2011-03-15 12:24:38.34 GMT</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>42f1f0d0-951e-4778-8e05-d9f6f5e5c496</identification> </annotationBean> <date>2011-03-15 12:24:18.815 GMT</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>53239d39-79d4-4a05-936f-ead5c51b4699</identification> </annotationBean> <date>2011-03-15 12:25:05.465 GMT</date> <creators /> <curationEventList /> </net.sf.taverna.t2.annotation.AnnotationAssertionImpl> </annotationAssertions> </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
------------------------------------------------------------------------------ Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d
_______________________________________________ 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/
