taverna-t2flow 0.2.0 → 0.3.0

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Files changed (26) hide show
  1. data/CHANGES.rdoc +16 -0
  2. data/README.rdoc +30 -21
  3. data/Rakefile +54 -0
  4. data/lib/t2flow/model.rb +7 -0
  5. data/lib/t2flow/parser.rb +7 -2
  6. data/taverna-t2flow.gemspec +76 -0
  7. data/test/fixtures/1000.t2flow +244 -0
  8. data/test/fixtures/1001.t2flow +321 -0
  9. data/test/fixtures/1002.t2flow +474 -0
  10. data/test/fixtures/1003.t2flow +292 -0
  11. data/test/fixtures/1004.t2flow +73 -0
  12. data/test/fixtures/996.t2flow +193 -0
  13. data/test/fixtures/997.t2flow +359 -0
  14. data/test/fixtures/998.t2flow +324 -0
  15. data/test/fixtures/999.t2flow +604 -0
  16. data/test/fixtures/basic.t2flow +94 -0
  17. data/test/fixtures/coordinated.t2flow +63 -0
  18. data/test/fixtures/linked.t2flow +88 -0
  19. data/test/fixtures/nested.t2flow +270 -0
  20. data/test/fixtures/processors.t2flow +174 -0
  21. data/test/run_tests.rb +7 -0
  22. data/test/test_bogus_workflows.rb +80 -0
  23. data/test/test_helper.rb +50 -0
  24. data/test/test_starter_pack_workflows.rb +132 -0
  25. metadata +121 -69
  26. data/ChangeLog.rdoc +0 -7
data/test/fixtures/1002.t2flow ADDED
@@ -0,0 +1,474 @@
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+ <workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.1.0"><dataflow id="f0fac9a7-7943-4191-a0d3-7e8e09044e43" 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>1.0</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>NM_000059</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>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>1.0</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>NP_000050</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>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>1.0</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="">
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+ <localworkerName>net.sourceforge.taverna.scuflworkers.ncbi.NucleotideINSDSeqXMLWorker</localworkerName>
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+ <script>if ((id == void) || (id == null) || id.equals("")) {
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+ throw new RunTimeException("port id must have a non-empty value");
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+ }
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+
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+ URL url = new URL ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=gbc&amp;db=nucleotide&amp;retmode=xml&amp;id=" + id);
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+
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+ BufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));
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+ StringWriter writer = new StringWriter();
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+
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+ char[] buffer = new char[1024];
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+ while (true) {
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+ int r = reader.read(buffer);
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+ if (r &lt;= 0) {
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+ break;
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+ }
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+ writer.write(buffer, 0, r);
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+ }
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+ outputText = writer.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>id</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>0</granularDepth>
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+ <name>outputText</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.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="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>1.0</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="">
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+ <localworkerName>net.sourceforge.taverna.scuflworkers.ncbi.NucleotideFastaWorker</localworkerName>
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+ <script>if ((id == void) || (id == null) || id.equals("")) {
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+ throw new RunTimeException("port id must have a non-empty value");
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+ }
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+
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+ URL url = new URL ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=fasta&amp;db=nucleotide&amp;retmode=text&amp;id=" + id);
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+
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+ BufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));
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+ StringWriter writer = new StringWriter();
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+
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+ char[] buffer = new char[1024];
85
+ while (true) {
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+ int r = reader.read(buffer);
87
+ if (r &lt;= 0) {
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+ break;
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+ }
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+ writer.write(buffer, 0, r);
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+ }
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+ outputText = writer.toString();
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+ </script>
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+ <dependencies />
95
+ <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>
100
+ <handledReferenceSchemes />
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+ <translatedElementType>java.lang.String</translatedElementType>
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+ <allowsLiteralValues>true</allowsLiteralValues>
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+ <name>id</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>
112
+ <granularDepth>0</granularDepth>
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+ <name>outputText</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.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="">
123
+ <backoffFactor>1.0</backoffFactor>
124
+ <initialDelay>1000</initialDelay>
125
+ <maxDelay>5000</maxDelay>
126
+ <maxRetries>0</maxRetries>
127
+ </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="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>1.0</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="">
128
+ <localworkerName>net.sourceforge.taverna.scuflworkers.ncbi.NucleotideGBSeqWorker</localworkerName>
129
+ <script>if ((id == void) || (id == null) || id.equals("")) {
130
+ throw new RunTimeException("port id must have a non-empty value");
131
+ }
132
+
133
+ URL url = new URL ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=gb&amp;db=nucleotide&amp;retmode=xml&amp;id=" + id);
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+
135
+ BufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));
136
+ StringWriter writer = new StringWriter();
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+
138
+ char[] buffer = new char[1024];
139
+ while (true) {
140
+ int r = reader.read(buffer);
141
+ if (r &lt;= 0) {
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+ break;
143
+ }
144
+ writer.write(buffer, 0, r);
145
+ }
146
+ outputText = writer.toString();
147
+ </script>
148
+ <dependencies />
149
+ <classLoaderSharing>workflow</classLoaderSharing>
150
+ <localDependencies />
151
+ <artifactDependencies />
152
+ <inputs>
153
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
154
+ <handledReferenceSchemes />
155
+ <translatedElementType>java.lang.String</translatedElementType>
156
+ <allowsLiteralValues>true</allowsLiteralValues>
157
+ <name>id</name>
158
+ <depth>0</depth>
159
+ <mimeTypes>
160
+ <string>'text/plain'</string>
161
+ </mimeTypes>
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+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
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+ </inputs>
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+ <outputs>
165
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
166
+ <granularDepth>0</granularDepth>
167
+ <name>outputText</name>
168
+ <depth>0</depth>
169
+ <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.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="">
177
+ <backoffFactor>1.0</backoffFactor>
178
+ <initialDelay>1000</initialDelay>
179
+ <maxDelay>5000</maxDelay>
180
+ <maxRetries>0</maxRetries>
181
+ </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="id" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Get_Nucleotide_TinySeq_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>1.0</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="">
182
+ <localworkerName>net.sourceforge.taverna.scuflworkers.ncbi.NucleotideTinySeqXMLWorker</localworkerName>
183
+ <script>if ((id == void) || (id == null) || id.equals("")) {
184
+ throw new RunTimeException("port id must have a non-empty value");
185
+ }
186
+
187
+ URL url = new URL ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=fasta&amp;db=nucleotide&amp;retmode=xml&amp;id=" + id);
188
+
189
+ BufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));
190
+ StringWriter writer = new StringWriter();
191
+
192
+ char[] buffer = new char[1024];
193
+ while (true) {
194
+ int r = reader.read(buffer);
195
+ if (r &lt;= 0) {
196
+ break;
197
+ }
198
+ writer.write(buffer, 0, r);
199
+ }
200
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201
+ </script>
202
+ <dependencies />
203
+ <classLoaderSharing>workflow</classLoaderSharing>
204
+ <localDependencies />
205
+ <artifactDependencies />
206
+ <inputs>
207
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
208
+ <handledReferenceSchemes />
209
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210
+ <allowsLiteralValues>true</allowsLiteralValues>
211
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212
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214
+ <string>'text/plain'</string>
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216
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217
+ </inputs>
218
+ <outputs>
219
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
220
+ <granularDepth>0</granularDepth>
221
+ <name>outputText</name>
222
+ <depth>0</depth>
223
+ <mimeTypes>
224
+ <string>'text/plain'</string>
225
+ </mimeTypes>
226
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
227
+ </outputs>
228
+ </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="">
229
+ <maxJobs>1</maxJobs>
230
+ </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="">
231
+ <backoffFactor>1.0</backoffFactor>
232
+ <initialDelay>1000</initialDelay>
233
+ <maxDelay>5000</maxDelay>
234
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235
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236
+ <localworkerName>net.sourceforge.taverna.scuflworkers.ncbi.ProteinFastaWorker</localworkerName>
237
+ <script>if ((id == void) || (id == null) || id.equals("")) {
238
+ throw new RunTimeException("port id must have a non-empty value");
239
+ }
240
+
241
+ URL url = new URL ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=fasta&amp;db=protein&amp;retmode=text&amp;id=" + id);
242
+
243
+ BufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));
244
+ StringWriter writer = new StringWriter();
245
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246
+ char[] buffer = new char[1024];
247
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248
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249
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250
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251
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252
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253
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254
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255
+ </script>
256
+ <dependencies />
257
+ <classLoaderSharing>workflow</classLoaderSharing>
258
+ <localDependencies />
259
+ <artifactDependencies />
260
+ <inputs>
261
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
262
+ <handledReferenceSchemes />
263
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264
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265
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266
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267
+ <mimeTypes>
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+ <string>'text/plain'</string>
269
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271
+ </inputs>
272
+ <outputs>
273
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
274
+ <granularDepth>0</granularDepth>
275
+ <name>outputText</name>
276
+ <depth>0</depth>
277
+ <mimeTypes>
278
+ <string>'text/plain'</string>
279
+ </mimeTypes>
280
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281
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282
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283
+ <maxJobs>1</maxJobs>
284
+ </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="">
285
+ <backoffFactor>1.0</backoffFactor>
286
+ <initialDelay>1000</initialDelay>
287
+ <maxDelay>5000</maxDelay>
288
+ <maxRetries>0</maxRetries>
289
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290
+ <localworkerName>net.sourceforge.taverna.scuflworkers.ncbi.ProteinINSDSeqXMLWorker</localworkerName>
291
+ <script>if ((id == void) || (id == null) || id.equals("")) {
292
+ throw new RunTimeException("port id must have a non-empty value");
293
+ }
294
+
295
+ URL url = new URL ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=gbc&amp;db=protein&amp;retmode=xml&amp;id=" + id);
296
+
297
+ BufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));
298
+ StringWriter writer = new StringWriter();
299
+
300
+ char[] buffer = new char[1024];
301
+ while (true) {
302
+ int r = reader.read(buffer);
303
+ if (r &lt;= 0) {
304
+ break;
305
+ }
306
+ writer.write(buffer, 0, r);
307
+ }
308
+ outputText = writer.toString();
309
+ </script>
310
+ <dependencies />
311
+ <classLoaderSharing>workflow</classLoaderSharing>
312
+ <localDependencies />
313
+ <artifactDependencies />
314
+ <inputs>
315
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
316
+ <handledReferenceSchemes />
317
+ <translatedElementType>java.lang.String</translatedElementType>
318
+ <allowsLiteralValues>true</allowsLiteralValues>
319
+ <name>id</name>
320
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+ <string>'text/plain'</string>
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325
+ </inputs>
326
+ <outputs>
327
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
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+ <granularDepth>0</granularDepth>
329
+ <name>outputText</name>
330
+ <depth>0</depth>
331
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332
+ <string>'text/plain'</string>
333
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334
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336
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337
+ <maxJobs>1</maxJobs>
338
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339
+ <backoffFactor>1.0</backoffFactor>
340
+ <initialDelay>1000</initialDelay>
341
+ <maxDelay>5000</maxDelay>
342
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343
+ </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="id" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Get_Protein_TinySeq_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>1.0</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="">
344
+ <localworkerName>net.sourceforge.taverna.scuflworkers.ncbi.ProteinTinySeqXMLWorker</localworkerName>
345
+ <script>if ((id == void) || (id == null) || id.equals("")) {
346
+ throw new RunTimeException("port id must have a non-empty value");
347
+ }
348
+
349
+ URL url = new URL ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=fasta&amp;db=protein&amp;retmode=xml&amp;id=" + id);
350
+
351
+ BufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));
352
+ StringWriter writer = new StringWriter();
353
+
354
+ char[] buffer = new char[1024];
355
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356
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357
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358
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359
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360
+ writer.write(buffer, 0, r);
361
+ }
362
+ outputText = writer.toString();
363
+ </script>
364
+ <dependencies />
365
+ <classLoaderSharing>workflow</classLoaderSharing>
366
+ <localDependencies />
367
+ <artifactDependencies />
368
+ <inputs>
369
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
370
+ <handledReferenceSchemes />
371
+ <translatedElementType>java.lang.String</translatedElementType>
372
+ <allowsLiteralValues>true</allowsLiteralValues>
373
+ <name>id</name>
374
+ <depth>0</depth>
375
+ <mimeTypes>
376
+ <string>'text/plain'</string>
377
+ </mimeTypes>
378
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
379
+ </inputs>
380
+ <outputs>
381
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
382
+ <granularDepth>0</granularDepth>
383
+ <name>outputText</name>
384
+ <depth>0</depth>
385
+ <mimeTypes>
386
+ <string>'text/plain'</string>
387
+ </mimeTypes>
388
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
389
+ </outputs>
390
+ </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="">
391
+ <maxJobs>1</maxJobs>
392
+ </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="">
393
+ <backoffFactor>1.0</backoffFactor>
394
+ <initialDelay>1000</initialDelay>
395
+ <maxDelay>5000</maxDelay>
396
+ <maxRetries>0</maxRetries>
397
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398
+ <localworkerName>net.sourceforge.taverna.scuflworkers.ncbi.ProteinGBSeqWorker</localworkerName>
399
+ <script>if ((id == void) || (id == null) || id.equals("")) {
400
+ throw new RunTimeException("port id must have a non-empty value");
401
+ }
402
+
403
+ URL url = new URL ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=gb&amp;db=protein&amp;retmode=xml&amp;id=" + id);
404
+
405
+ BufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));
406
+ StringWriter writer = new StringWriter();
407
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408
+ char[] buffer = new char[1024];
409
+ while (true) {
410
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411
+ if (r &lt;= 0) {
412
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413
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414
+ writer.write(buffer, 0, r);
415
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416
+ outputText = writer.toString();
417
+ </script>
418
+ <dependencies />
419
+ <classLoaderSharing>workflow</classLoaderSharing>
420
+ <localDependencies />
421
+ <artifactDependencies />
422
+ <inputs>
423
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
424
+ <handledReferenceSchemes />
425
+ <translatedElementType>java.lang.String</translatedElementType>
426
+ <allowsLiteralValues>true</allowsLiteralValues>
427
+ <name>id</name>
428
+ <depth>0</depth>
429
+ <mimeTypes>
430
+ <string>'text/plain'</string>
431
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432
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
433
+ </inputs>
434
+ <outputs>
435
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
436
+ <granularDepth>0</granularDepth>
437
+ <name>outputText</name>
438
+ <depth>0</depth>
439
+ <mimeTypes>
440
+ <string>'text/plain'</string>
441
+ </mimeTypes>
442
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
443
+ </outputs>
444
+ </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="">
445
+ <maxJobs>1</maxJobs>
446
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447
+ <backoffFactor>1.0</backoffFactor>
448
+ <initialDelay>1000</initialDelay>
449
+ <maxDelay>5000</maxDelay>
450
+ <maxRetries>0</maxRetries>
451
+ </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="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="processor"><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>Get_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</port></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="">
452
+ <annotationAssertions>
453
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
454
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.DescriptiveTitle">
455
+ <text>GBSeq test</text>
456
+ </annotationBean>
457
+ <date>2009-12-15 20:30:12.959 GMT</date>
458
+ <creators />
459
+ <curationEventList />
460
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
461
+ </annotationAssertions>
462
+ </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
463
+ <annotationAssertions>
464
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
465
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
466
+ <text>This workflow retrieves nucleotide and protein sequences with the literature and references associated
467
+ to them given a protein and a nucleotide id.</text>
468
+ </annotationBean>
469
+ <date>2009-12-15 20:30:23.505 GMT</date>
470
+ <creators />
471
+ <curationEventList />
472
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
473
+ </annotationAssertions>
474
+ </net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></dataflow></workflow>