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Posted to commits@taverna.apache.org by st...@apache.org on 2015/02/17 21:43:44 UTC
[40/51] [partial] incubator-taverna-engine git commit: temporarily
empty repository
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-integration-tests/src/test/resources/t2flow/FetchTodaysXkcdComic.t2flow
----------------------------------------------------------------------
diff --git a/taverna-integration-tests/src/test/resources/t2flow/FetchTodaysXkcdComic.t2flow b/taverna-integration-tests/src/test/resources/t2flow/FetchTodaysXkcdComic.t2flow
deleted file mode 100644
index 4aeef6f..0000000
--- a/taverna-integration-tests/src/test/resources/t2flow/FetchTodaysXkcdComic.t2flow
+++ /dev/null
@@ -1,343 +0,0 @@
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.3.0"><dataflow id="24e3ca77-bca1-47a6-8f5e-0549801eb27e" 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>1.3</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="">
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <name>url</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/x-taverna-web-url'</string>
- </mimeTypes>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <name>base</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/x-taverna-web-url'</string>
- </mimeTypes>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <name>contents</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain,text/html'</string>
- </mimeTypes>
- <granularDepth>0</granularDepth>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <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 />
- <localworkerName>org.embl.ebi.escience.scuflworkers.java.WebPageFetcher</localworkerName>
-</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>1.3</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>1.3</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>1.3</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>1.3</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>1.3</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>1.3</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://xkcd.com/</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>1.3</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>1.3</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>1.3</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>1.3</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>1.3</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>1.3</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="">
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <name>document</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/html'</string>
- </mimeTypes>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <name>imagelinks</name>
- <depth>1</depth>
- <mimeTypes>
- <string>l('text/x-taverna-web-url')</string>
- </mimeTypes>
- <granularDepth>1</granularDepth>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <script>String lowerCaseContent = document.toLowerCase();
-int index = 0;
-List imagelinks = new ArrayList();
-while ((index = lowerCaseContent.indexOf("<img", index)) != -1) {
- if ((index = lowerCaseContent.indexOf("src", index)) == -1)
- break;
- if ((index = lowerCaseContent.indexOf("=", index)) == -1)
- break;
- index++;
- String remaining = document.substring(index);
- StringTokenizer st = new StringTokenizer(remaining, "\t\n\r\">#");
- String strLink = st.nextToken();
- imagelinks.add(strLink);
-}
-
-</script>
- <dependencies />
- <localworkerName>org.embl.ebi.escience.scuflworkers.java.ExtractImageLinks</localworkerName>
-</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>1.3</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>1.3</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>1.3</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>1.3</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>1.3</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>1.3</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="">
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <name>stringlist</name>
- <depth>1</depth>
- <mimeTypes>
- <string>l('text/plain')</string>
- </mimeTypes>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <name>regex</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <name>filteredlist</name>
- <depth>1</depth>
- <mimeTypes>
- <string>l('text/plain')</string>
- </mimeTypes>
- <granularDepth>1</granularDepth>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <script>filteredlist = new ArrayList();
-for (Iterator i = stringlist.iterator(); i.hasNext();) {
- String item = (String) i.next();
- if (item.matches(regex)) {
- filteredlist.add(item);
- }
-}
-</script>
- <dependencies />
- <localworkerName>org.embl.ebi.escience.scuflworkers.java.FilterStringList</localworkerName>
-</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>1.3</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>1.3</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>1.3</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>1.3</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>1.3</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>1.3</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>.*/comics/.*</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>1.3</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>1.3</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>1.3</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>1.3</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>1.3</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>1.3</version></raven><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMa
p><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="">
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <name>url</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/x-taverna-web-url'</string>
- </mimeTypes>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <name>base</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/x-taverna-web-url'</string>
- </mimeTypes>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <name>image</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'image/*'</string>
- </mimeTypes>
- <granularDepth>0</granularDepth>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <script>URL inputURL = null;
-if (base != void) {
- inputURL = new URL(new URL(base), url);
-} else {
- inputURL = new URL(url);
-}
-
-byte[] contents;
-if (inputURL.openConnection().getContentLength() == -1) {
- // Content size unknown, must read first...
- byte[] buffer = new byte[1024];
- int bytesRead = 0;
- int totalBytesRead = 0;
- InputStream is = inputURL.openStream();
- while (bytesRead != -1) {
- totalBytesRead += bytesRead;
- bytesRead = is.read(buffer, 0, 1024);
- }
- contents = new byte[totalBytesRead];
-} else {
- contents = new byte[inputURL.openConnection().getContentLength()];
-}
-int bytesRead = 0;
-int totalBytesRead = 0;
-InputStream is = inputURL.openStream();
-while (bytesRead != -1) {
- bytesRead = is.read(contents, totalBytesRead, contents.length - totalBytesRead);
- totalBytesRead += bytesRead;
- if (contents.length==totalBytesRead) break;
-}
-
-image = contents;
-</script>
- <dependencies />
- <localworkerName>org.embl.ebi.escience.scuflworkers.java.WebImageFetcher</localworkerName>
-</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>1.3</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>1.3</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>1.3</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>1.3</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>1.3</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><datali
nk><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_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>24e3ca77-bca1-47a6-8f5e-0549801eb27e</identification>
- </annotationBean>
- <date>2011-07-12 14:11:15.348 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><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.DescriptiveTitle">
- <text>Fetch today's xkcd comic</text>
- </annotationBean>
- <date>2009-12-15 20:39:06.623 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><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>8b032490-948e-4983-b632-d16653755fcd</identification>
- </annotationBean>
- <date>2010-07-04 18:16:02.491 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><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.FreeTextDescription">
- <text>Use the local services and some filtering operations to fetch the comic strip image from http://xkcd.com/
-
-Based on the FetchDailyDilbert workflow.</text>
- </annotationBean>
- <date>2011-07-12 14:11:12.608 BST</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.Author">
- <text>Tom Oinn, Stian Soiland-Reyes</text>
- </annotationBean>
- <date>2009-12-15 20:38:58.43 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></dataflow></workflow>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-integration-tests/src/test/resources/t2flow/GBSeqTest.t2flow
----------------------------------------------------------------------
diff --git a/taverna-integration-tests/src/test/resources/t2flow/GBSeqTest.t2flow b/taverna-integration-tests/src/test/resources/t2flow/GBSeqTest.t2flow
deleted file mode 100644
index 196a4bc..0000000
--- a/taverna-integration-tests/src/test/resources/t2flow/GBSeqTest.t2flow
+++ /dev/null
@@ -1,518 +0,0 @@
-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.3.0"><dataflow id="c00b121a-0114-471a-bd29-03597414879c" role="top"><name>GBSeq_test</name><inputPorts /><outputPorts><port><name>nuc_fasta</name><annotations /></port><port><name>nuc_xml</name><annotations /></port><port><name>nuc_insd</name><annotations /></port><port><name>nuc_tiny</name><annotations /></port><port><name>prot_fasta</name><annotations /></port><port><name>protein_xml</name><annotations /></port><port><name>prot_insd</name><annotations /></port><port><name>prot_tiny</name><annotations /></port></outputPorts><processors><processor><name>nuc_id</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>1.3</version></raven><class>net.sf.taverna.t2.activities.stringconstant.St
ringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
- <value>NM_000059</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>1.3</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>1.3</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>1.3</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>1.3</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>1.3</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>protein_id</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>1.3</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>NP_000050</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>1.3</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>1.3</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>1.3</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>1.3</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>1.3</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>Get_Nucleotide_INSDSeq_XML</name><inputPorts><port><name>id</name><depth>0</depth></port></inputPorts><outputPorts><port><name>outputText</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>1.3</version></raven><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap><map from="id" to="id" /></
inputMap><outputMap><map from="outputText" to="outputText" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <name>id</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <name>outputText</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- <granularDepth>0</granularDepth>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <script>if ((id == void) || (id == null) || id.equals("")) {
- throw new RunTimeException("port id must have a non-empty value");
-}
-
-URL url = new URL ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=gbc&db=nucleotide&retmode=xml&id=" + id);
-
-BufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));
-StringWriter writer = new StringWriter();
-
-char[] buffer = new char[1024];
- while (true) {
- int r = reader.read(buffer);
- if (r <= 0) {
- break;
- }
- writer.write(buffer, 0, r);
- }
-outputText = writer.toString();
-</script>
- <dependencies />
- <localworkerName>net.sourceforge.taverna.scuflworkers.ncbi.NucleotideINSDSeqXMLWorker</localworkerName>
-</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>1.3</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>1.3</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>1.3</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>1.3</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>1.3</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="id" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Get_Nucleotide_FASTA</name><inputPorts><port><name>id</name><depth>0</depth></port></inputPorts><outputPorts><port><name>outputText</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>1.3</version></raven><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivit
y</class><inputMap><map from="id" to="id" /></inputMap><outputMap><map from="outputText" to="outputText" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <name>id</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <name>outputText</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- <granularDepth>0</granularDepth>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <script>if ((id == void) || (id == null) || id.equals("")) {
- throw new RunTimeException("port id must have a non-empty value");
-}
-
-URL url = new URL ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=fasta&db=nucleotide&retmode=text&id=" + id);
-
-BufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));
-StringWriter writer = new StringWriter();
-
-char[] buffer = new char[1024];
- while (true) {
- int r = reader.read(buffer);
- if (r <= 0) {
- break;
- }
- writer.write(buffer, 0, r);
- }
-outputText = writer.toString();
-</script>
- <dependencies />
- <localworkerName>net.sourceforge.taverna.scuflworkers.ncbi.NucleotideFastaWorker</localworkerName>
-</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>1.3</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>1.3</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>1.3</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>1.3</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>1.3</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="id" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Get_Nucleotide_GBSeq_XML</name><inputPorts><port><name>id</name><depth>0</depth></port></inputPorts><outputPorts><port><name>outputText</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>1.3</version></raven><class>net.sf.taverna.t2.activities.localworker.LocalworkerAct
ivity</class><inputMap><map from="id" to="id" /></inputMap><outputMap><map from="outputText" to="outputText" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
- <inputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- <name>id</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- <handledReferenceSchemes />
- <translatedElementType>java.lang.String</translatedElementType>
- <allowsLiteralValues>true</allowsLiteralValues>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
- </inputs>
- <outputs>
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- <name>outputText</name>
- <depth>0</depth>
- <mimeTypes>
- <string>'text/plain'</string>
- </mimeTypes>
- <granularDepth>0</granularDepth>
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
- </outputs>
- <classLoaderSharing>workflow</classLoaderSharing>
- <localDependencies />
- <artifactDependencies />
- <script>if ((id == void) || (id == null) || id.equals("")) {
- throw new RunTimeException("port id must have a non-empty value");
-}
-
-URL url = new URL ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=gb&db=nucleotide&retmode=xml&id=" + id);
-
-BufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));
-StringWriter writer = new StringWriter();
-
-char[] buffer = new char[1024];
- while (true) {
- int r = reader.read(buffer);
- if (r <= 0) {
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-BufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));
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-char[] buffer = new char[1024];
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- <string>'text/plain'</string>
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- <script>if ((id == void) || (id == null) || id.equals("")) {
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-}
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-URL url = new URL ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=fasta&db=protein&retmode=text&id=" + id);
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-BufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));
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-char[] buffer = new char[1024];
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- <string>'text/plain'</string>
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- <granularDepth>0</granularDepth>
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- <script>if ((id == void) || (id == null) || id.equals("")) {
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-}
-
-URL url = new URL ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=gbc&db=protein&retmode=xml&id=" + id);
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-BufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));
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-char[] buffer = new char[1024];
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-
-URL url = new URL ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=fasta&db=protein&retmode=xml&id=" + id);
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-BufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));
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-char[] buffer = new char[1024];
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-URL url = new URL ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=gb&db=protein&retmode=xml&id=" + id);
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-BufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));
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-char[] buffer = new char[1024];
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- int r = reader.read(buffer);
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-outputText = writer.toString();
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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>1.3</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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- <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>1.3</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="id" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>Get_Nucleotide_INSDSeq_XML</processor><port>id</port></sink><source type="processor"><processor>nuc_id</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>Get_Nucleotide_FASTA</processor><port>id</port></sink><source type="processor"><processor>nuc_id</processor><port>value</port></source></datalink><datalink><sink type="pr
ocessor"><processor>Get_Nucleotide_GBSeq_XML</processor><port>id</port></sink><source type="processor"><processor>nuc_id</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>Get_Nucleotide_TinySeq_XML</processor><port>id</port></sink><source type="processor"><processor>nuc_id</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>Get_Protein_FASTA</processor><port>id</port></sink><source type="processor"><processor>protein_id</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>Get_Protein_INSDSeq_XML</processor><port>id</port></sink><source type="processor"><processor>protein_id</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>Get_Protein_TinySeq_XML</processor><port>id</port></sink><source type="processor"><processor>protein_id</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>Ge
t_Protein_GBSeq_XML</processor><port>id</port></sink><source type="processor"><processor>protein_id</processor><port>value</port></source></datalink><datalink><sink type="dataflow"><port>nuc_fasta</port></sink><source type="processor"><processor>Get_Nucleotide_FASTA</processor><port>outputText</port></source></datalink><datalink><sink type="dataflow"><port>nuc_xml</port></sink><source type="processor"><processor>Get_Nucleotide_GBSeq_XML</processor><port>outputText</port></source></datalink><datalink><sink type="dataflow"><port>nuc_insd</port></sink><source type="processor"><processor>Get_Nucleotide_INSDSeq_XML</processor><port>outputText</port></source></datalink><datalink><sink type="dataflow"><port>nuc_tiny</port></sink><source type="processor"><processor>Get_Nucleotide_TinySeq_XML</processor><port>outputText</port></source></datalink><datalink><sink type="dataflow"><port>prot_fasta</port></sink><source type="processor"><processor>Get_Protein_FASTA</processor><port>outputText</por
t></source></datalink><datalink><sink type="dataflow"><port>protein_xml</port></sink><source type="processor"><processor>Get_Protein_GBSeq_XML</processor><port>outputText</port></source></datalink><datalink><sink type="dataflow"><port>prot_insd</port></sink><source type="processor"><processor>Get_Protein_INSDSeq_XML</processor><port>outputText</port></source></datalink><datalink><sink type="dataflow"><port>prot_tiny</port></sink><source type="processor"><processor>Get_Protein_TinySeq_XML</processor><port>outputText</port></source></datalink></datalinks><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.DescriptiveTitle">
- <text>GBSeq test</text>
- </annotationBean>
- <date>2009-12-15 20:30:12.959 GMT</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.FreeTextDescription">
- <text>This workflow retrieves nucleotide and protein sequences with the literature and references associated
-to them given a protein and a nucleotide id.</text>
- </annotationBean>
- <date>2009-12-15 20:30:23.505 GMT</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><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>f0fac9a7-7943-4191-a0d3-7e8e09044e43</identification>
- </annotationBean>
- <date>2010-07-04 18:16:42.290 BST</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>c00b121a-0114-471a-bd29-03597414879c</identification>
- </annotationBean>
- <date>2011-07-12 14:07:08.97 BST</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>af08cba7-dd16-404c-b20b-fd3cb7ccf7aa</identification>
- </annotationBean>
- <date>2011-07-12 14:06:02.422 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><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.Author">
- <text>Franck Tanoh</text>
- </annotationBean>
- <date>2011-07-12 14:07:04.790 BST</date>
- <creators />
- <curationEventList />
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
- </annotationAssertions>
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></dataflow></workflow>
\ No newline at end of file