taverna-t2flow 0.2.0 → 0.3.0
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- data/CHANGES.rdoc +16 -0
- data/README.rdoc +30 -21
- data/Rakefile +54 -0
- data/lib/t2flow/model.rb +7 -0
- data/lib/t2flow/parser.rb +7 -2
- data/taverna-t2flow.gemspec +76 -0
- data/test/fixtures/1000.t2flow +244 -0
- data/test/fixtures/1001.t2flow +321 -0
- data/test/fixtures/1002.t2flow +474 -0
- data/test/fixtures/1003.t2flow +292 -0
- data/test/fixtures/1004.t2flow +73 -0
- data/test/fixtures/996.t2flow +193 -0
- data/test/fixtures/997.t2flow +359 -0
- data/test/fixtures/998.t2flow +324 -0
- data/test/fixtures/999.t2flow +604 -0
- data/test/fixtures/basic.t2flow +94 -0
- data/test/fixtures/coordinated.t2flow +63 -0
- data/test/fixtures/linked.t2flow +88 -0
- data/test/fixtures/nested.t2flow +270 -0
- data/test/fixtures/processors.t2flow +174 -0
- data/test/run_tests.rb +7 -0
- data/test/test_bogus_workflows.rb +80 -0
- data/test/test_helper.rb +50 -0
- data/test/test_starter_pack_workflows.rb +132 -0
- metadata +121 -69
- data/ChangeLog.rdoc +0 -7
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<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.1.0"><dataflow id="8b032490-948e-4983-b632-d16653755fcd" role="top"><name>Fetch_today_s_xkcd_comic</name><inputPorts /><outputPorts><port><name>todaysXkcd</name><annotations /></port></outputPorts><processors><processor><name>getPage</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>1.0</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="">
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<localworkerName>org.embl.ebi.escience.scuflworkers.java.WebPageFetcher</localworkerName>
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<script>URL inputURL = null;
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if (base != void) {
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inputURL = new URL(new URL(base), url);
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else {
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inputURL = new URL(url);
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URLConnection con = inputURL.openConnection();
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InputStream in = con.getInputStream();
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InputStreamReader isr = new InputStreamReader(in);
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Reader inReader = new BufferedReader(isr);
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StringBuffer buf = new StringBuffer();
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int ch;
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while ((ch = inReader.read()) > -1) {
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buf.append((char)ch);
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}
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inReader.close();
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contents = buf.toString();
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//String NEWLINE = System.getProperty("line.separator");
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//
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//URL inputURL = null;
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//if (base != void) {
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// inputURL = new URL(new URL(base), url);
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//} else {
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// inputURL = new URL(url);
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//}
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//StringBuffer result = new StringBuffer();
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//BufferedReader reader = new BufferedReader(new InputStreamReader(inputURL.openStream()));
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//String line = null;
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//while ((line = reader.readLine()) != null) {
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// result.append(line);
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// result.append(NEWLINE);
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//}
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//
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//contents = result.toString();
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</script>
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<dependencies />
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<classLoaderSharing>workflow</classLoaderSharing>
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<localDependencies />
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<artifactDependencies />
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<inputs>
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<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
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<handledReferenceSchemes />
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<translatedElementType>java.lang.String</translatedElementType>
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<allowsLiteralValues>true</allowsLiteralValues>
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<name>url</name>
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<depth>0</depth>
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<mimeTypes>
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<string>'text/x-taverna-web-url'</string>
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</mimeTypes>
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</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
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<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
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<handledReferenceSchemes />
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<translatedElementType>java.lang.String</translatedElementType>
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<allowsLiteralValues>true</allowsLiteralValues>
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<name>base</name>
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<depth>0</depth>
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<mimeTypes>
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<string>'text/x-taverna-web-url'</string>
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</mimeTypes>
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</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
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</inputs>
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<outputs>
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<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
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<granularDepth>0</granularDepth>
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<name>contents</name>
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<depth>0</depth>
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<mimeTypes>
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<string>'text/plain,text/html'</string>
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</mimeTypes>
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</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
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</outputs>
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</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>1.0</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="">
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<maxJobs>1</maxJobs>
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</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>1.0</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>1.0</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>1.0</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="">
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<backoffFactor>1.0</backoffFactor>
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<initialDelay>1000</initialDelay>
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<maxDelay>5000</maxDelay>
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<maxRetries>0</maxRetries>
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</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>1.0</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>xkcdURL</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>1.0</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="">
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<value>http://xkcd.com/</value>
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</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>1.0</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="">
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<maxJobs>1</maxJobs>
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</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>1.0</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>1.0</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>1.0</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="">
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<backoffFactor>1.0</backoffFactor>
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<initialDelay>1000</initialDelay>
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<maxDelay>5000</maxDelay>
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<maxRetries>0</maxRetries>
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</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>1.0</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>getImageLinks</name><inputPorts><port><name>document</name><depth>0</depth></port></inputPorts><outputPorts><port><name>imagelinks</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>1.0</version></raven><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap><map from="document" to="document" /></inputMap><outputMap><map from="imagelinks" to="imagelinks" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
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<localworkerName>org.embl.ebi.escience.scuflworkers.java.ExtractImageLinks</localworkerName>
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<script>String lowerCaseContent = document.toLowerCase();
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int index = 0;
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List imagelinks = new ArrayList();
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while ((index = lowerCaseContent.indexOf("<img", index)) != -1) {
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if ((index = lowerCaseContent.indexOf("src", index)) == -1)
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break;
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if ((index = lowerCaseContent.indexOf("=", index)) == -1)
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break;
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index++;
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String remaining = document.substring(index);
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StringTokenizer st = new StringTokenizer(remaining, "\t\n\r\">#");
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String strLink = st.nextToken();
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imagelinks.add(strLink);
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}
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</script>
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<dependencies />
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<classLoaderSharing>workflow</classLoaderSharing>
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<localDependencies />
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<artifactDependencies />
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<inputs>
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<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
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<handledReferenceSchemes />
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<translatedElementType>java.lang.String</translatedElementType>
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<allowsLiteralValues>true</allowsLiteralValues>
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<name>document</name>
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<depth>0</depth>
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<mimeTypes>
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<string>'text/html'</string>
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</mimeTypes>
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</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
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</inputs>
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<outputs>
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<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
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<granularDepth>1</granularDepth>
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<name>imagelinks</name>
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<depth>1</depth>
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<mimeTypes>
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<string>l('text/x-taverna-web-url')</string>
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</mimeTypes>
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</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
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</outputs>
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</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>1.0</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="">
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<maxJobs>1</maxJobs>
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</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>1.0</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>1.0</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>1.0</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="">
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<backoffFactor>1.0</backoffFactor>
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<initialDelay>1000</initialDelay>
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<maxDelay>5000</maxDelay>
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<maxRetries>0</maxRetries>
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</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>1.0</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="document" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>findComicURL</name><inputPorts><port><name>regex</name><depth>0</depth></port><port><name>stringlist</name><depth>1</depth></port></inputPorts><outputPorts><port><name>filteredlist</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>1.0</version></raven><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap><map from="regex" to="regex" /><map from="stringlist" to="stringlist" /></inputMap><outputMap><map from="filteredlist" to="filteredlist" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
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<localworkerName>org.embl.ebi.escience.scuflworkers.java.FilterStringList</localworkerName>
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<script>filteredlist = new ArrayList();
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for (Iterator i = stringlist.iterator(); i.hasNext();) {
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String item = (String) i.next();
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if (item.matches(regex)) {
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filteredlist.add(item);
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}
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}
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</script>
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<dependencies />
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<classLoaderSharing>workflow</classLoaderSharing>
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<localDependencies />
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<artifactDependencies />
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<inputs>
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<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
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<handledReferenceSchemes />
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<translatedElementType>java.lang.String</translatedElementType>
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<allowsLiteralValues>true</allowsLiteralValues>
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<name>stringlist</name>
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166
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<depth>1</depth>
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<mimeTypes>
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<string>l('text/plain')</string>
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</mimeTypes>
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</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
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<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
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<handledReferenceSchemes />
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<translatedElementType>java.lang.String</translatedElementType>
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<allowsLiteralValues>true</allowsLiteralValues>
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<name>regex</name>
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<depth>0</depth>
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<mimeTypes>
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<string>'text/plain'</string>
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</mimeTypes>
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</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
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</inputs>
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<outputs>
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<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
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<granularDepth>1</granularDepth>
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<name>filteredlist</name>
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<depth>1</depth>
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187
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+
<mimeTypes>
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188
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+
<string>l('text/plain')</string>
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189
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</mimeTypes>
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190
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+
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
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191
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</outputs>
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192
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+
</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>1.0</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="">
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193
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<maxJobs>1</maxJobs>
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</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>1.0</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>1.0</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>1.0</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="">
|
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195
|
+
<backoffFactor>1.0</backoffFactor>
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196
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+
<initialDelay>1000</initialDelay>
|
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197
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<maxDelay>5000</maxDelay>
|
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198
|
+
<maxRetries>0</maxRetries>
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199
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+
</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>1.0</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="regex" depth="0" /><port name="stringlist" depth="1" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>comicURLRegex</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>1.0</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="">
|
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200
|
+
<value>.*/comics/.*</value>
|
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201
|
+
</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>1.0</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="">
|
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202
|
+
<maxJobs>1</maxJobs>
|
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203
|
+
</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>1.0</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>1.0</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>1.0</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="">
|
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204
|
+
<backoffFactor>1.0</backoffFactor>
|
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205
|
+
<initialDelay>1000</initialDelay>
|
|
206
|
+
<maxDelay>5000</maxDelay>
|
|
207
|
+
<maxRetries>0</maxRetries>
|
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208
|
+
</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>1.0</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>getComicStrip</name><inputPorts><port><name>base</name><depth>0</depth></port><port><name>url</name><depth>0</depth></port></inputPorts><outputPorts><port><name>image</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>1.0</version></raven><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap><map from="base" to="base" /><map from="url" to="url" /></inputMap><outputMap><map from="image" to="image" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
|
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209
|
+
<localworkerName>org.embl.ebi.escience.scuflworkers.java.WebImageFetcher</localworkerName>
|
|
210
|
+
<script>URL inputURL = null;
|
|
211
|
+
if (base != void) {
|
|
212
|
+
inputURL = new URL(new URL(base), url);
|
|
213
|
+
} else {
|
|
214
|
+
inputURL = new URL(url);
|
|
215
|
+
}
|
|
216
|
+
|
|
217
|
+
byte[] contents;
|
|
218
|
+
if (inputURL.openConnection().getContentLength() == -1) {
|
|
219
|
+
// Content size unknown, must read first...
|
|
220
|
+
byte[] buffer = new byte[1024];
|
|
221
|
+
int bytesRead = 0;
|
|
222
|
+
int totalBytesRead = 0;
|
|
223
|
+
InputStream is = inputURL.openStream();
|
|
224
|
+
while (bytesRead != -1) {
|
|
225
|
+
totalBytesRead += bytesRead;
|
|
226
|
+
bytesRead = is.read(buffer, 0, 1024);
|
|
227
|
+
}
|
|
228
|
+
contents = new byte[totalBytesRead];
|
|
229
|
+
} else {
|
|
230
|
+
contents = new byte[inputURL.openConnection().getContentLength()];
|
|
231
|
+
}
|
|
232
|
+
int bytesRead = 0;
|
|
233
|
+
int totalBytesRead = 0;
|
|
234
|
+
InputStream is = inputURL.openStream();
|
|
235
|
+
while (bytesRead != -1) {
|
|
236
|
+
bytesRead = is.read(contents, totalBytesRead, contents.length - totalBytesRead);
|
|
237
|
+
totalBytesRead += bytesRead;
|
|
238
|
+
if (contents.length==totalBytesRead) break;
|
|
239
|
+
}
|
|
240
|
+
|
|
241
|
+
image = contents;
|
|
242
|
+
</script>
|
|
243
|
+
<dependencies />
|
|
244
|
+
<classLoaderSharing>workflow</classLoaderSharing>
|
|
245
|
+
<localDependencies />
|
|
246
|
+
<artifactDependencies />
|
|
247
|
+
<inputs>
|
|
248
|
+
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
|
|
249
|
+
<handledReferenceSchemes />
|
|
250
|
+
<translatedElementType>java.lang.String</translatedElementType>
|
|
251
|
+
<allowsLiteralValues>true</allowsLiteralValues>
|
|
252
|
+
<name>url</name>
|
|
253
|
+
<depth>0</depth>
|
|
254
|
+
<mimeTypes>
|
|
255
|
+
<string>'text/x-taverna-web-url'</string>
|
|
256
|
+
</mimeTypes>
|
|
257
|
+
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
|
|
258
|
+
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
|
|
259
|
+
<handledReferenceSchemes />
|
|
260
|
+
<translatedElementType>java.lang.String</translatedElementType>
|
|
261
|
+
<allowsLiteralValues>true</allowsLiteralValues>
|
|
262
|
+
<name>base</name>
|
|
263
|
+
<depth>0</depth>
|
|
264
|
+
<mimeTypes>
|
|
265
|
+
<string>'text/x-taverna-web-url'</string>
|
|
266
|
+
</mimeTypes>
|
|
267
|
+
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
|
|
268
|
+
</inputs>
|
|
269
|
+
<outputs>
|
|
270
|
+
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
|
|
271
|
+
<granularDepth>0</granularDepth>
|
|
272
|
+
<name>image</name>
|
|
273
|
+
<depth>0</depth>
|
|
274
|
+
<mimeTypes>
|
|
275
|
+
<string>'image/*'</string>
|
|
276
|
+
</mimeTypes>
|
|
277
|
+
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
|
|
278
|
+
</outputs>
|
|
279
|
+
</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>1.0</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="">
|
|
280
|
+
<maxJobs>1</maxJobs>
|
|
281
|
+
</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>1.0</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>1.0</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>1.0</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="">
|
|
282
|
+
<backoffFactor>1.0</backoffFactor>
|
|
283
|
+
<initialDelay>1000</initialDelay>
|
|
284
|
+
<maxDelay>5000</maxDelay>
|
|
285
|
+
<maxRetries>0</maxRetries>
|
|
286
|
+
</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>1.0</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="base" depth="0" /><port name="url" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>getPage</processor><port>url</port></sink><source type="processor"><processor>xkcdURL</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>getImageLinks</processor><port>document</port></sink><source type="processor"><processor>getPage</processor><port>contents</port></source></datalink><datalink><sink type="processor"><processor>findComicURL</processor><port>regex</port></sink><source type="processor"><processor>comicURLRegex</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>findComicURL</processor><port>stringlist</port></sink><source type="processor"><processor>getImageLinks</processor><port>imagelinks</port></source></datalink><datalink><sink type="processor"><processor>getComicStrip</processor><port>base</port></sink><source type="processor"><processor>xkcdURL</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>getComicStrip</processor><port>url</port></sink><source type="processor"><processor>findComicURL</processor><port>filteredlist</port></source></datalink><datalink><sink type="dataflow"><port>todaysXkcd</port></sink><source type="processor"><processor>getComicStrip</processor><port>image</port></source></datalink></datalinks><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
|
|
287
|
+
<annotationAssertions>
|
|
288
|
+
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
|
|
289
|
+
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
|
|
290
|
+
<text>Use the local java plugins and some filtering operations to fetch the comic strip image from http://xkcd.com/
|
|
291
|
+
|
|
292
|
+
Based on the FetchDailyDilbert workflow.</text>
|
|
293
|
+
</annotationBean>
|
|
294
|
+
<date>2009-12-15 20:39:17.683 GMT</date>
|
|
295
|
+
<creators />
|
|
296
|
+
<curationEventList />
|
|
297
|
+
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
|
|
298
|
+
</annotationAssertions>
|
|
299
|
+
</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
|
|
300
|
+
<annotationAssertions>
|
|
301
|
+
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
|
|
302
|
+
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.Author">
|
|
303
|
+
<text>Tom Oinn, Stian Soiland-Reyes</text>
|
|
304
|
+
</annotationBean>
|
|
305
|
+
<date>2009-12-15 20:38:58.43 GMT</date>
|
|
306
|
+
<creators />
|
|
307
|
+
<curationEventList />
|
|
308
|
+
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
|
|
309
|
+
</annotationAssertions>
|
|
310
|
+
</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
|
|
311
|
+
<annotationAssertions>
|
|
312
|
+
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
|
|
313
|
+
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.DescriptiveTitle">
|
|
314
|
+
<text>Fetch today's xkcd comic</text>
|
|
315
|
+
</annotationBean>
|
|
316
|
+
<date>2009-12-15 20:39:06.623 GMT</date>
|
|
317
|
+
<creators />
|
|
318
|
+
<curationEventList />
|
|
319
|
+
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
|
|
320
|
+
</annotationAssertions>
|
|
321
|
+
</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></dataflow></workflow>
|