-<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.3.0"><dataflow id="
cb69bc38-61c3-481a-be99-c8644f2c0d07" role="top"><name>Workflow169</name><inputPorts /><outputPorts><port><name>csv_ouput</name><annotations /></port></outputPorts><processors><processor><name>Syn_Exp_Occ_Ret</name><inputPorts><port><name>csvData</name><depth>0</depth></port></inputPorts><outputPorts><port><name>csv_output</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>dataflow-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.dataflow.DataflowActivity</class><inputMap><map from="csvData" to="csvData" /></inputMap><outputMap><map from="csv_output" to="csv_output" /></outputMap><configBean encoding="dataflow"><dataflow ref="62f3f979-79ca-4566-8cd7-22af322c4c7e" /></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="">
\r+<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.3.0"><dataflow id="
3e5d0d2d-efec-4e0f-b271-dba90a4cb8ed" role="top"><name>Workflow169</name><inputPorts /><outputPorts><port><name>csv_ouput</name><annotations /></port></outputPorts><processors><processor><name>Syn_Exp_Occ_Ret</name><inputPorts><port><name>csvData</name><depth>0</depth></port></inputPorts><outputPorts><port><name>csv_output</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>dataflow-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.dataflow.DataflowActivity</class><inputMap><map from="csvData" to="csvData" /></inputMap><outputMap><map from="csv_output" to="csv_output" /></outputMap><configBean encoding="dataflow"><dataflow ref="ba529013-0329-4a22-be72-26b854e18f51" /></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="">
\r <maxJobs>1</maxJobs>\r
</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="">\r
<backoffFactor>1.0</backoffFactor>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>2d2d9854-192c-4bf1-b17c-6605821b4423</identification>\r
+ <identification>54255d6f-d137-4c44-bd4e-f0677240d1fb</identification>\r
</annotationBean>\r
- <date>2012-04-03 17:02:05.350 CEST</date>\r
+ <date>2012-04-04 13:28:10.609 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>8ec6ae8e-b2d8-4dd6-b2ee-85e1ecaec132</identification>\r
+ <identification>30e5587b-c517-4f97-b5b4-c1d849c8409c</identification>\r
</annotationBean>\r
- <date>2012-03-29 17:02:21.736 CEST</date>\r
+ <date>2012-05-31 16:21:12.520 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>71f1ee5f-1682-4671-8ef4-b0cc2f24f426</identification>\r
+ <identification>481193bb-155a-4448-81bb-24c8e77a6801</identification>\r
</annotationBean>\r
- <date>2012-03-29 15:00:58.820 CEST</date>\r
+ <date>2012-04-03 09:40:45.595 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>07ee1f3f-058e-4e82-bd20-87dc918f28f9</identification>\r
+ <identification>1d561bf9-612a-4495-8fae-97b7ae7ba5a5</identification>\r
</annotationBean>\r
- <date>2012-04-05 16:44:16.906 CEST</date>\r
+ <date>2012-05-31 16:08:56.393 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>54255d6f-d137-4c44-bd4e-f0677240d1fb</identification>\r
+ <identification>564898e6-4513-422e-813a-30ee68f758c6</identification>\r
</annotationBean>\r
- <date>2012-04-04 13:28:10.609 CEST</date>\r
+ <date>2012-06-01 11:03:43.571 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>481193bb-155a-4448-81bb-24c8e77a6801</identification>\r
+ <identification>3afc9d06-7ba4-4066-8518-64681aa8c895</identification>\r
</annotationBean>\r
- <date>2012-04-03 09:40:45.595 CEST</date>\r
+ <date>2012-06-01 11:06:35.849 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>cb69bc38-61c3-481a-be99-c8644f2c0d07</identification>\r
+ <identification>515c2ace-4328-4238-b1b1-3bba5dbf6fe9</identification>\r
</annotationBean>\r
- <date>2012-04-05 17:19:57.234 CEST</date>\r
+ <date>2012-04-05 16:36:32.184 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>849fce1d-83e1-40b7-a9f5-0f3118ae8f3b</identification>\r
+ <identification>7141ca11-cb68-4bba-a7da-2068196cffc2</identification>\r
</annotationBean>\r
- <date>2012-04-05 17:17:02.201 CEST</date>\r
+ <date>2012-04-05 17:15:12.67 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>10eeee30-f2f0-4767-9250-2a38399aaf9b</identification>\r
+ <identification>d67c97fb-616a-4238-ba6f-046b357ca433</identification>\r
</annotationBean>\r
- <date>2012-04-05 16:35:06.424 CEST</date>\r
+ <date>2012-05-31 17:53:06.966 CEST</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>2a26f643-5165-4bd7-bfad-fb347e640fb3</identification>\r
+ </annotationBean>\r
+ <date>2012-04-05 17:17:21.673 CEST</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>75550ad7-6efa-4891-8173-2d6c663f1c56</identification>\r
+ </annotationBean>\r
+ <date>2012-05-29 12:17:46.774 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>dd57c2b7-168e-4fa0-8e47-8853f4bc10dd</identification>\r
+ <identification>f7823f43-d92a-40f8-b6e9-9badd6595340</identification>\r
</annotationBean>\r
- <date>2012-04-04 11:56:57.497 CEST</date>\r
+ <date>2012-05-31 16:53:13.368 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>33506dd6-1341-4215-836d-d946e9d75b2e</identification>\r
+ <identification>6da3d3fa-470a-4440-b57e-5c80e3e69eaa</identification>\r
</annotationBean>\r
- <date>2012-04-05 16:36:13.129 CEST</date>\r
+ <date>2012-03-30 15:17:02.946 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>fda4c32f-fb52-4c55-a0b4-596f82a58cb7</identification>\r
+ <identification>0c79a1bd-2742-4e96-b446-2621854569ed</identification>\r
</annotationBean>\r
- <date>2012-04-04 13:49:03.799 CEST</date>\r
+ <date>2012-05-31 17:58:12.463 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>9e4fc010-46ed-40d2-a0b5-72791c02a3cc</identification>\r
+ <identification>3c881109-da28-46e8-833b-9c50bb3f16fa</identification>\r
</annotationBean>\r
- <date>2012-04-04 13:30:35.947 CEST</date>\r
+ <date>2012-06-01 11:02:08.848 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>5bd9cfb1-20a4-445d-b0db-47809641d791</identification>\r
+ <identification>9d482c0b-8c79-42ac-8504-c8edf1b3b348</identification>\r
</annotationBean>\r
- <date>2012-04-04 13:40:15.842 CEST</date>\r
+ <date>2012-04-05 16:47:39.691 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>7141ca11-cb68-4bba-a7da-2068196cffc2</identification>\r
+ <identification>849fce1d-83e1-40b7-a9f5-0f3118ae8f3b</identification>\r
</annotationBean>\r
- <date>2012-04-05 17:15:12.67 CEST</date>\r
+ <date>2012-04-05 17:17:02.201 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>2a26f643-5165-4bd7-bfad-fb347e640fb3</identification>\r
+ <identification>79e01ca8-6b67-412c-b8dc-28d17d45f549</identification>\r
</annotationBean>\r
- <date>2012-04-05 17:17:21.673 CEST</date>\r
+ <date>2012-06-01 11:19:58.847 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>6da3d3fa-470a-4440-b57e-5c80e3e69eaa</identification>\r
+ <identification>8ec6ae8e-b2d8-4dd6-b2ee-85e1ecaec132</identification>\r
</annotationBean>\r
- <date>2012-03-30 15:17:02.946 CEST</date>\r
+ <date>2012-03-29 17:02:21.736 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>8426bef1-e9a8-4e7c-a88d-97b01a3aa456</identification>\r
+ <identification>10eeee30-f2f0-4767-9250-2a38399aaf9b</identification>\r
</annotationBean>\r
- <date>2012-04-05 16:43:30.110 CEST</date>\r
+ <date>2012-04-05 16:35:06.424 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>d72c319e-e7e1-48e8-85e1-37ebe66b92cd</identification>\r
+ <identification>68dca16a-b312-4184-a0f3-f2b29e14bc18</identification>\r
</annotationBean>\r
- <date>2012-03-29 15:10:59.480 CEST</date>\r
+ <date>2012-05-29 12:23:03.410 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>515c2ace-4328-4238-b1b1-3bba5dbf6fe9</identification>\r
+ <identification>ff2ff7ee-4e8e-4ceb-8d53-96bb4b7bc917</identification>\r
</annotationBean>\r
- <date>2012-04-05 16:36:32.184 CEST</date>\r
+ <date>2012-05-31 16:15:02.700 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>9d482c0b-8c79-42ac-8504-c8edf1b3b348</identification>\r
+ <identification>cb69bc38-61c3-481a-be99-c8644f2c0d07</identification>\r
</annotationBean>\r
- <date>2012-04-05 16:47:39.691 CEST</date>\r
+ <date>2012-04-05 17:19:57.234 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
</annotationAssertions>\r
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow><dataflow id="124b440e-f7ef-445f-901b-b3d04ca3e2a7" role="nested"><name>Workflow20</name><inputPorts><port><name>sciName</name><depth>0</depth><granularDepth>0</granularDepth><annotations /></port><port><name>next</name><depth>0</depth><granularDepth>0</granularDepth><annotations /></port></inputPorts><outputPorts><port><name>next</name><annotations /></port><port><name>max1000_csv_output</name><annotations /></port></outputPorts><processors><processor><name>Transform_XML</name><inputPorts><port><name>xslFileURL</name><depth>0</depth></port><port><name>inString</name><depth>0</depth></port></inputPorts><outputPorts><port><name>outputStr</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="inString" to="inString" /><map from="xslFileURL" to="xslFileURL" /></inputMap><outputMap><map from="outputStr" to="outputStr" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">\r
- <inputs>\r
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
- <name>xslFileURL</name>\r
- <depth>0</depth>\r
- <mimeTypes>\r
- <string>'text/plain'</string>\r
- </mimeTypes>\r
- <handledReferenceSchemes />\r
- <translatedElementType>java.lang.String</translatedElementType>\r
- <allowsLiteralValues>true</allowsLiteralValues>\r
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
- <name>outFileURL</name>\r
- <depth>0</depth>\r
- <mimeTypes>\r
- <string>'text/plain'</string>\r
- </mimeTypes>\r
- <handledReferenceSchemes />\r
- <translatedElementType>java.lang.String</translatedElementType>\r
- <allowsLiteralValues>true</allowsLiteralValues>\r
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
- <name>inString</name>\r
- <depth>0</depth>\r
- <mimeTypes>\r
- <string>'text/plain'</string>\r
- </mimeTypes>\r
- <handledReferenceSchemes />\r
- <translatedElementType>java.lang.String</translatedElementType>\r
- <allowsLiteralValues>true</allowsLiteralValues>\r
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
- <name>outputExt</name>\r
- <depth>0</depth>\r
- <mimeTypes>\r
- <string>'text/plain'</string>\r
- </mimeTypes>\r
- <handledReferenceSchemes />\r
- <translatedElementType>java.lang.String</translatedElementType>\r
- <allowsLiteralValues>true</allowsLiteralValues>\r
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
- </inputs>\r
- <outputs>\r
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
- <name>outputStr</name>\r
- <depth>0</depth>\r
- <mimeTypes />\r
- <granularDepth>0</granularDepth>\r
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
- </outputs>\r
- <classLoaderSharing>workflow</classLoaderSharing>\r
- <localDependencies />\r
- <artifactDependencies />\r
- <script>import java.io.BufferedReader;\r
-import java.io.BufferedWriter;\r
-import java.io.FileInputStream;\r
-import java.io.FileNotFoundException;\r
-import java.io.FileReader;\r
-import java.io.FileWriter;\r
-import java.io.IOException;\r
-import java.io.InputStreamReader;\r
-import java.io.OutputStreamWriter;\r
-import java.io.StringWriter;\r
-import java.io.StringReader;\r
-import java.io.Writer;\r
-import java.net.URL;\r
-import java.util.HashMap;\r
-import java.util.Map;\r
-\r
-import javax.xml.transform.Result;\r
-import javax.xml.transform.Source;\r
-import javax.xml.transform.SourceLocator;\r
-import javax.xml.transform.Templates;\r
-import javax.xml.transform.Transformer;\r
-import javax.xml.transform.TransformerConfigurationException;\r
-import javax.xml.transform.TransformerException;\r
-import javax.xml.transform.TransformerFactory;\r
-import javax.xml.transform.stream.StreamResult;\r
-import javax.xml.transform.stream.StreamSource;\r
-\r
-BufferedReader getReader (String fileUrl) throws IOException {\r
- InputStreamReader reader;\r
- try {\r
- reader = new FileReader(fileUrl);\r
- }\r
- catch (FileNotFoundException e) {\r
- // try a real URL instead\r
- URL url = new URL(fileUrl);\r
- reader = new InputStreamReader (url.openStream());\r
- }\r
- return new BufferedReader(reader);\r
- }\r
- \r
-BufferedWriter getWriter (String fileUrl) throws IOException {\r
- Writer writer;\r
- try {\r
- writer = new FileWriter(fileUrl);\r
- }\r
- catch (FileNotFoundException e) {\r
- // try a real URL instead\r
- URL url = new URL(fileUrl);\r
- writer = new OutputStreamWriter (url.openConnection().getOutputStream());\r
- }\r
- return new BufferedWriter(writer);\r
- }\r
- \r
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-if (outFileURL != void) {\r
- outFilename = outFileURL;\r
-}\r
-\r
-String ext;\r
-if (outputExt != void) {\r
- ext = outputExt;\r
-}\r
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-\r
-\r
-// Create transformer factory\r
-TransformerFactory factory = TransformerFactory.newInstance();\r
-\r
-// Use the factory to create a template containing the xsl file\r
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-\r
-// Use the template to create a transformer\r
-Transformer xformer = template.newTransformer();\r
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-// Prepare the input and output files\r
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-Source source = new StreamSource(sourceReader);\r
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-Result result = new StreamResult(resultStr);\r
-\r
-// Apply the xsl file to the source file and write the result to the\r
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-if ((outFilename != null) && !outFilename.equals("")) {\r
-\r
- BufferedWriter out = getWriter(outFilename);\r
-\r
- out.write(outputStr);\r
- out.close();\r
-}\r
-sourceReader.close();\r
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- <dependencies />\r
- <localworkerName>net.sourceforge.taverna.scuflworkers.xml.XSLTWorker</localworkerName>\r
-</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
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<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.HostInstitution">\r
- <text>UserNameHere</text>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>ff2a2f11-018f-4f0d-954e-7d08e03e117c</identification>\r
</annotationBean>\r
- <date>2012-01-13 17:08:38.768 CET</date>\r
+ <date>2012-05-31 16:23:14.600 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
</annotationAssertions>\r
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- <value>http://ww2.bgbm.org/temp/biovel/gbifResponse_to_csv.xsl</value>\r
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- <initialDelay>1000</initialDelay>\r
- <maxDelay>5000</maxDelay>\r
- <maxRetries>0</maxRetries>\r
-</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>gbifOccurrence</name><inputPorts><port><name>format</name><depth>0</depth></port><port><name>scientificname</name><depth>0</depth></port><port><name>next</name><depth>0</depth></port></inputPorts><outputPorts><port><name>responseBody</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>rest-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.rest.RESTActivity</class><inputMap><map from="next" to="next" /><map from="format" to="format" /><map from="scientificname" to="scientificname" /></inputMap><outputMap><map from="responseBody" to="responseBody" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean xmlns="">\r
- <httpMethod>GET</httpMethod>\r
- <urlSignature>http://data.gbif.org/ws/rest/occurrence/list?scientificname={scientificname}&format={format}&startindex={next}&maxresults=1000</urlSignature>\r
- <acceptsHeaderValue>application/xml</acceptsHeaderValue>\r
- <contentTypeForUpdates>application/xml</contentTypeForUpdates>\r
- <outgoingDataFormat>String</outgoingDataFormat>\r
- <sendHTTPExpectRequestHeader>false</sendHTTPExpectRequestHeader>\r
- <showRedirectionOutputPort>false</showRedirectionOutputPort>\r
- <escapeParameters>true</escapeParameters>\r
- <otherHTTPHeaders />\r
- <activityInputs>\r
- <entry>\r
- <string>next</string>\r
- <java-class>java.lang.String</java-class>\r
- </entry>\r
- <entry>\r
- <string>format</string>\r
- <java-class>java.lang.String</java-class>\r
- </entry>\r
- <entry>\r
- <string>scientificname</string>\r
- <java-class>java.lang.String</java-class>\r
- </entry>\r
- </activityInputs>\r
-</net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean></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="">\r
- <maxJobs>1</maxJobs>\r
-</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="">\r
- <backoffFactor>1.0</backoffFactor>\r
- <initialDelay>1000</initialDelay>\r
- <maxDelay>5000</maxDelay>\r
- <maxRetries>0</maxRetries>\r
-</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="format" depth="0" /><port name="scientificname" depth="0" /><port name="next" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>format_value</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.3</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="">\r
- <value>darwin</value>\r
-</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="">\r
- <maxJobs>1</maxJobs>\r
-</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="">\r
- <backoffFactor>1.0</backoffFactor>\r
- <initialDelay>1000</initialDelay>\r
- <maxDelay>5000</maxDelay>\r
- <maxRetries>0</maxRetries>\r
-</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>next</name><inputPorts><port><name>xml_text</name><depth>0</depth></port></inputPorts><outputPorts><port><name>nodelist</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>xpath-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.xpath.XPathActivity</class><inputMap><map from="xml_text" to="xml_text" /></inputMap><outputMap><map from="nodelist" to="nodelist" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.xpath.XPathActivityConfigurationBean xmlns="">\r
- <xmlDocument><?xml version="1.0" encoding="UTF-8"?>\r
-<?xml-stylesheet type="text/xsl" href="http://data.gbif.org/ws/rest/taxon/stylesheet"?><gbif:gbifResponse xmlns:gbif="http://portal.gbif.org/ws/response/gbif" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:tc="http://rs.tdwg.org/ontology/voc/TaxonConcept#" xmlns:tn="http://rs.tdwg.org/ontology/voc/TaxonName#" xsi:schemaLocation="http://portal.gbif.org/ws/response/gbif http://data.gbif.org/ws/rest/taxon/schema http://purl.org/dc/elements/1.1/ http://data.gbif.org/schema/dc.xsd http://purl.org/dc/terms/ http://data.gbif.org/schema/dcterms.xsd http://www.w3.org/1999/02/22-rdf-syntax-ns# http://data.gbif.org/schema/rdf.xsd http://www.w3.org/2002/07/owl# http://data.gbif.org/schema/owl.xsd http://rs.tdwg.org/ontology/voc/Common# http://data.gbif.org/schema/tcom.xsd http://rs.tdwg.org/ontology/voc/TaxonOccurrence# http://data.gbif.org/schema/TaxonOccurrence.xsd http://rs.tdwg.org/ontology/voc/TaxonConcept# http://data.gbif.org/schema/TaxonConcept.xsd http://rs.tdwg.org/ontology/voc/TaxonName# http://data.gbif.org/schema/TaxonName.xsd">\r
- <gbif:header>\r
- <gbif:help>http://data.gbif.org/ws/rest/taxon/help\r
-</gbif:help>\r
- <gbif:request>list</gbif:request>\r
- <gbif:statements>-\r
-\r
-This document contains data shared through the GBIF Network - see http://data.gbif.org/ for more information.\r
- \r
-All usage of these data must be in accordance with the GBIF Data Use Agreement - see http://www.gbif.org/DataProviders/Agreements/DUA\r
-\r
--\r
-</gbif:statements>\r
- <gbif:stylesheet>http://data.gbif.org/ws/rest/taxon/stylesheet</gbif:stylesheet>\r
- <gbif:parameter name="maxresults" value="100"/>\r
- <gbif:parameter name="request" value="list"/>\r
- <gbif:parameter name="service" value="taxon"/>\r
- <gbif:parameter name="format" value="brief"/>\r
- <gbif:parameter name="scientificname" value="Plantae"/>\r
- <gbif:nextRequestUrl>http://data.gbif.org/ws/rest/taxon/list?startindex=100&amp;maxresults=100&amp;format=brief&amp;scientificname=Plantae</gbif:nextRequestUrl>\r
-<gbif:summary start="0" totalMatched="100" next="100" totalReturned="100"/>\r
- </gbif:header><gbif:dataProviders>\r
-\r
-\r
-<gbif:dataProvider gbifKey="116" rdf:about="http://data.gbif.org/ws/rest/provider/get/116">\r
- <gbif:name>Museo Nacional de Costa Rica</gbif:name>\r
- <gbif:dataResources>\r
- <gbif:dataResource gbifKey="566" rdf:about="http://data.gbif.org/ws/rest/resource/get/566">\r
- <gbif:name>herbario</gbif:name>\r
- <gbif:taxonConcepts>\r
- <tc:TaxonConcept gbifKey="51456466" status="unconfirmed" rdf:about="http://data.gbif.org/ws/rest/taxon/get/51456466">\r
- <tc:hasName>\r
- <tn:TaxonName>\r
- <tn:nameComplete>Plantae</tn:nameComplete>\r
- <tn:rankString>kingdom</tn:rankString>\r
- <tn:scientific>true</tn:scientific>\r
- </tn:TaxonName>\r
- </tc:hasName>\r
- <tc:accordingToString>herbario</tc:accordingToString>\r
- <tc:accordingTo rdf:resource="http://data.gbif.org/ws/rest/resource/get/566"/>\r
- <tc:primary>true</tc:primary>\r
- </tc:TaxonConcept> \r
- </gbif:taxonConcepts>\r
- </gbif:dataResource> \r
- </gbif:dataResources>\r
- </gbif:dataProvider>\r
-<gbif:dataProvider gbifKey="318" rdf:about="http://data.gbif.org/ws/rest/provider/get/318">\r
- <gbif:name>Arizona State University, Global Institute for Sustainability</gbif:name>\r
- <gbif:dataResources>\r
- <gbif:dataResource gbifKey="676" rdf:about="http://data.gbif.org/ws/rest/resource/get/676">\r
- <gbif:name>Arizona State University Vascular Plant Herbarium</gbif:name>\r
- <gbif:citation/>\r
- <gbif:taxonConcepts>\r
- <tc:TaxonConcept gbifKey="52007005" status="unconfirmed" rdf:about="http://data.gbif.org/ws/rest/taxon/get/52007005">\r
- <tc:hasName>\r
- <tn:TaxonName>\r
- <tn:nameComplete>Plantae</tn:nameComplete>\r
- <tn:rankString>kingdom</tn:rankString>\r
- <tn:scientific>true</tn:scientific>\r
- </tn:TaxonName>\r
- </tc:hasName>\r
- <tc:accordingToString>Arizona State University Vascular Plant Herbarium</tc:accordingToString>\r
- <tc:accordingTo rdf:resource="http://data.gbif.org/ws/rest/resource/get/676"/>\r
- <tc:primary>true</tc:primary>\r
- </tc:TaxonConcept> \r
- </gbif:taxonConcepts>\r
- </gbif:dataResource> \r
- </gbif:dataResources>\r
- </gbif:dataProvider>\r
-<gbif:dataProvider gbifKey="112" rdf:about="http://data.gbif.org/ws/rest/provider/get/112">\r
- <gbif:name>Mokpo Museum of Natural History</gbif:name>\r
- <gbif:dataResources>\r
- <gbif:dataResource gbifKey="570" rdf:about="http://data.gbif.org/ws/rest/resource/get/570">\r
- <gbif:name>Mokpo Museum of Natural History Plant</gbif:name>\r
- <gbif:citation/>\r
- <gbif:taxonConcepts>\r
- <tc:TaxonConcept gbifKey="51473457" status="unconfirmed" rdf:about="http://data.gbif.org/ws/rest/taxon/get/51473457">\r
- <tc:hasName>\r
- <tn:TaxonName>\r
- <tn:nameComplete>Plantae</tn:nameComplete>\r
- <tn:rankString>kingdom</tn:rankString>\r
- <tn:scientific>true</tn:scientific>\r
- </tn:TaxonName>\r
- </tc:hasName>\r
- <tc:accordingToString>Mokpo Museum of Natural History Plant</tc:accordingToString>\r
- <tc:accordingTo rdf:resource="http://data.gbif.org/ws/rest/resource/get/570"/>\r
- <tc:primary>true</tc:primary>\r
- </tc:TaxonConcept> \r
- </gbif:taxonConcepts>\r
- </gbif:dataResource> \r
- </gbif:dataResources>\r
- </gbif:dataProvider>\r
-<gbif:dataProvider gbifKey="139" rdf:about="http://data.gbif.org/ws/rest/provider/get/139">\r
- <gbif:name>NLBIF</gbif:name>\r
- <gbif:dataResources>\r
- <gbif:dataResource gbifKey="693" rdf:about="http://data.gbif.org/ws/rest/resource/get/693">\r
- <gbif:name>Natural History Museum Rotterdam</gbif:name>\r
- <gbif:citation>NLBIF, Natural History Museum Rotterdam</gbif:citation>\r
- <gbif:taxonConcepts>\r
- <tc:TaxonConcept gbifKey="52066103" status="unconfirmed" rdf:about="http://data.gbif.org/ws/rest/taxon/get/52066103">\r
- <tc:hasName>\r
- <tn:TaxonName>\r
- <tn:nameComplete>Plantae</tn:nameComplete>\r
- <tn:rankString>kingdom</tn:rankString>\r
- <tn:scientific>true</tn:scientific>\r
- </tn:TaxonName>\r
- </tc:hasName>\r
- <tc:accordingToString>Natural History Museum Rotterdam</tc:accordingToString>\r
- <tc:accordingTo rdf:resource="http://data.gbif.org/ws/rest/resource/get/693"/>\r
- <tc:primary>true</tc:primary>\r
- </tc:TaxonConcept> \r
- </gbif:taxonConcepts>\r
- </gbif:dataResource> \r
- </gbif:dataResources>\r
- </gbif:dataProvider>\r
-<gbif:dataProvider gbifKey="57" rdf:about="http://data.gbif.org/ws/rest/provider/get/57">\r
- <gbif:name>GBIF-Spain</gbif:name>\r
- <gbif:dataResources>\r
- <gbif:dataResource gbifKey="262" rdf:about="http://data.gbif.org/ws/rest/resource/get/262">\r
- <gbif:name>Institut d'Ecologia Litoral: IEL_Phyto</gbif:name>\r
- <gbif:citation>Gomis, C. (2005). Institut d'Ecologia Litoral Phytoplankton Collections on line databases.</gbif:citation>\r
- <gbif:taxonConcepts>\r
- <tc:TaxonConcept gbifKey="50817295" status="unconfirmed" rdf:about="http://data.gbif.org/ws/rest/taxon/get/50817295">\r
- <tc:hasName>\r
- <tn:TaxonName>\r
- <tn:nameComplete>Plantae</tn:nameComplete>\r
- <tn:rankString>kingdom</tn:rankString>\r
- <tn:scientific>true</tn:scientific>\r
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+ <identification>9e4fc010-46ed-40d2-a0b5-72791c02a3cc</identification>\r
+ </annotationBean>\r
+ <date>2012-04-04 13:30:35.947 CEST</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>2d2d9854-192c-4bf1-b17c-6605821b4423</identification>\r
+ </annotationBean>\r
+ <date>2012-04-03 17:02:05.350 CEST</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>1e206c8e-dd6c-4d41-9585-6891681a4a4b</identification>\r
+ </annotationBean>\r
+ <date>2012-06-01 10:57:40.69 CEST</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>550115ca-14f6-4dae-a760-77d52d99a372</identification>\r
+ </annotationBean>\r
+ <date>2012-05-31 17:58:51.374 CEST</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>33506dd6-1341-4215-836d-d946e9d75b2e</identification>\r
+ </annotationBean>\r
+ <date>2012-04-05 16:36:13.129 CEST</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>e7109cae-4abe-4c5c-ae55-68ceafe4a272</identification>\r
+ </annotationBean>\r
+ <date>2012-05-31 17:11:10.639 CEST</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>71f1ee5f-1682-4671-8ef4-b0cc2f24f426</identification>\r
+ </annotationBean>\r
+ <date>2012-03-29 15:00:58.820 CEST</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>b4ecfa15-da32-43f1-ba9f-5c37be218fe2</identification>\r
+ </annotationBean>\r
+ <date>2012-05-31 18:02:50.672 CEST</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>b8db6aa4-8f44-40dc-a61c-cbce4a2745ba</identification>\r
+ </annotationBean>\r
+ <date>2012-05-29 12:18:50.504 CEST</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>ff0d9290-60f4-487c-aa50-5593cff0fbc5</identification>\r
+ </annotationBean>\r
+ <date>2012-05-31 17:21:46.820 CEST</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>f70f7736-8e3f-4c3a-bc5d-1251d400dafc</identification>\r
+ </annotationBean>\r
+ <date>2012-05-29 12:25:03.618 CEST</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>8426bef1-e9a8-4e7c-a88d-97b01a3aa456</identification>\r
+ </annotationBean>\r
+ <date>2012-04-05 16:43:30.110 CEST</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>07ee1f3f-058e-4e82-bd20-87dc918f28f9</identification>\r
+ </annotationBean>\r
+ <date>2012-04-05 16:44:16.906 CEST</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>fda4c32f-fb52-4c55-a0b4-596f82a58cb7</identification>\r
+ </annotationBean>\r
+ <date>2012-04-04 13:49:03.799 CEST</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>d7b0c0f2-f703-4245-b29e-809ee0e952b6</identification>\r
+ </annotationBean>\r
+ <date>2012-05-29 13:42:58.175 CEST</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>5bd9cfb1-20a4-445d-b0db-47809641d791</identification>\r
+ </annotationBean>\r
+ <date>2012-04-04 13:40:15.842 CEST</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow><dataflow id="370ad085-8ced-4374-ba09-ebf615d24880" role="nested"><name>Workflow32</name><inputPorts><port><name>sciName</name><depth>0</depth><granularDepth>0</granularDepth><annotations /></port></inputPorts><outputPorts><port><name>csv_output</name><annotations /></port></outputPorts><processors><processor><name>Merge_String_List_to_a_String</name><inputPorts><port><name>seperator</name><depth>0</depth></port><port><name>stringlist</name><depth>1</depth></port></inputPorts><outputPorts><port><name>concatenated</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="seperator" to="seperator" /><map from="stringlist" to="stringlist" /></inputMap><outputMap><map from="concatenated" to="concatenated" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">\r
<inputs>\r
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
<name>stringlist</name>\r
<translatedElementType>java.lang.String</translatedElementType>\r
<allowsLiteralValues>true</allowsLiteralValues>\r
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ <name>seperator</name>\r
+ <depth>0</depth>\r
+ <mimeTypes>\r
+ <string>'text/plain'</string>\r
+ </mimeTypes>\r
+ <handledReferenceSchemes />\r
+ <translatedElementType>java.lang.String</translatedElementType>\r
+ <allowsLiteralValues>true</allowsLiteralValues>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
</inputs>\r
<outputs>\r
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
- <name>value</name>\r
+ <name>concatenated</name>\r
<depth>0</depth>\r
- <mimeTypes />\r
+ <mimeTypes>\r
+ <string>'text/plain'</string>\r
+ </mimeTypes>\r
<granularDepth>0</granularDepth>\r
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
</outputs>\r
<localDependencies />\r
<artifactDependencies />\r
<script>String seperatorString = "\n";\r
-\r
+if (seperator != void) {\r
+ seperatorString = seperator;\r
+}\r
StringBuffer sb = new StringBuffer();\r
for (Iterator i = stringlist.iterator(); i.hasNext();) {\r
String item = (String) i.next();\r
sb.append(seperatorString);\r
}\r
}\r
-value = sb.toString();\r
+concatenated = sb.toString();\r
</script>\r
<dependencies />\r
<localworkerName>org.embl.ebi.escience.scuflworkers.java.StringListMerge</localworkerName>\r
+</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="">\r
+ <maxJobs>1</maxJobs>\r
+</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="">\r
+ <backoffFactor>1.0</backoffFactor>\r
+ <initialDelay>1000</initialDelay>\r
+ <maxDelay>5000</maxDelay>\r
+ <maxRetries>0</maxRetries>\r
+</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="seperator" depth="0" /><port name="stringlist" depth="1" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>no_separator</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="">\r
+ <value />\r
+</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="">\r
+ <maxJobs>1</maxJobs>\r
+</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="">\r
+ <backoffFactor>1.0</backoffFactor>\r
+ <initialDelay>1000</initialDelay>\r
+ <maxDelay>5000</maxDelay>\r
+ <maxRetries>0</maxRetries>\r
+</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>gbif_occurrence_max1000</name><inputPorts><port><name>sciName</name><depth>0</depth></port><port><name>next</name><depth>0</depth></port></inputPorts><outputPorts><port><name>next</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>max1000_csv_output</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>dataflow-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.dataflow.DataflowActivity</class><inputMap><map from="next" to="next" /><map from="sciName" to="sciName" /></inputMap><outputMap><map from="next" to="next" /><map from="max1000_csv_output" to="max1000_csv_output" /></outputMap><configBean encoding="dataflow"><dataflow ref="124b440e-f7ef-445f-901b-b3d04ca3e2a7" /></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="">\r
+ <maxJobs>1</maxJobs>\r
+</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.Loop</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.LoopConfiguration xmlns="">\r
+ <conditionXML><activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
\r
+ <inputs>
\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
\r
+ <name>next</name>
\r
+ <depth>0</depth>
\r
+ <mimeTypes class="java.util.Collections$EmptyList" reference="../../net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean/mimeTypes" />
\r
+ <handledReferenceSchemes class="java.util.Collections$EmptyList" reference="../../net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean/mimeTypes" />
\r
+ <translatedElementType>java.lang.String</translatedElementType>
\r
+ <allowsLiteralValues>true</allowsLiteralValues>
\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
\r
+ </inputs>
\r
+ <outputs>
\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
\r
+ <name>loop</name>
\r
+ <depth>0</depth>
\r
+ <mimeTypes />
\r
+ <granularDepth>0</granularDepth>
\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
\r
+ <name>next</name>
\r
+ <depth>0</depth>
\r
+ <mimeTypes />
\r
+ <granularDepth>0</granularDepth>
\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
\r
+ </outputs>
\r
+ <classLoaderSharing>workflow</classLoaderSharing>
\r
+ <localDependencies />
\r
+ <artifactDependencies />
\r
+ <script>loop = "" + ! next.matches("");</script>
\r
+ <dependencies />
\r
+</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations /></activity></conditionXML>\r
+ <runFirst>true</runFirst>\r
+ <properties>\r
+ <property name="compareValue" value="" />\r
+ <property name="comparePort" value="next" />\r
+ <property name="delay" value="0.5" />\r
+ <property name="comparison" value="custom" />\r
+ <property name="isFeedBack" value="true" />\r
+ </properties>\r
+</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.LoopConfiguration></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="">\r
+ <backoffFactor>1.0</backoffFactor>\r
+ <initialDelay>1000</initialDelay>\r
+ <maxDelay>5000</maxDelay>\r
+ <maxRetries>0</maxRetries>\r
+</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="sciName" depth="0" /><port name="next" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>next_value</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.3</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="">\r
+ <value>0</value>\r
+</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="">\r
+ <maxJobs>1</maxJobs>\r
+</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="">\r
+ <backoffFactor>1.0</backoffFactor>\r
+ <initialDelay>1000</initialDelay>\r
+ <maxDelay>5000</maxDelay>\r
+ <maxRetries>0</maxRetries>\r
+</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>sink</name><inputPorts><port><name>inputlist</name><depth>1</depth></port></inputPorts><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="inputlist" to="inputlist" /></inputMap><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">\r
+ <inputs>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ <name>inputlist</name>\r
+ <depth>1</depth>\r
+ <mimeTypes>\r
+ <string>l('')</string>\r
+ </mimeTypes>\r
+ <handledReferenceSchemes />\r
+ <translatedElementType>[B</translatedElementType>\r
+ <allowsLiteralValues>true</allowsLiteralValues>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ </inputs>\r
+ <outputs />\r
+ <classLoaderSharing>workflow</classLoaderSharing>\r
+ <localDependencies />\r
+ <artifactDependencies />\r
+ <script>outputlist = inputlist;</script>\r
+ <dependencies />\r
+ <localworkerName>org.embl.ebi.escience.scuflworkers.java.EchoList</localworkerName>\r
</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.HostInstitution">\r
- <text>UserNameHere</text>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.HostInstitution">\r
+ <text>UserNameHere</text>\r
+ </annotationBean>\r
+ <date>2011-12-05 17:26:34.170 CET</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></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="">\r
+ <maxJobs>1</maxJobs>\r
+</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="">\r
+ <backoffFactor>1.0</backoffFactor>\r
+ <initialDelay>1000</initialDelay>\r
+ <maxDelay>5000</maxDelay>\r
+ <maxRetries>0</maxRetries>\r
+</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="inputlist" depth="1" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>Merge_String_List_to_a_String</processor><port>seperator</port></sink><source type="processor"><processor>no_separator</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>Merge_String_List_to_a_String</processor><port>stringlist</port></sink><source type="processor"><processor>gbif_occurrence_max1000</processor><port>max1000_csv_output</port></source></datalink><datalink><sink type="processor"><processor>gbif_occurrence_max1000</processor><port>sciName</port></sink><source type="dataflow"><port>sciName</port></source></datalink><datalink><sink type="processor"><processor>gbif_occurrence_max1000</processor><port>next</port></sink><source type="processor"><processor>next_value</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>sink</processor><port>inputlist</port></sink><source type="processor"><processor>gbif_occurrence_max1000</processor><port>next</port></source></datalink><datalink><sink type="dataflow"><port>csv_output</port></sink><source type="processor"><processor>Merge_String_List_to_a_String</processor><port>concatenated</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>eeab83cc-69df-4a18-a6ad-e33a5cc51f35</identification>\r
+ </annotationBean>\r
+ <date>2012-01-13 16:59:53.791 CET</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>aec72d1d-786a-4ccc-afb5-c712166bc3e2</identification>\r
+ </annotationBean>\r
+ <date>2012-01-31 16:33:25.857 CET</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>46828567-904f-4105-96ef-0bf268ada001</identification>\r
+ </annotationBean>\r
+ <date>2012-01-02 17:06:50.222 CET</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>5b4051bf-2a2a-46e8-a998-f80a766dd667</identification>\r
+ </annotationBean>\r
+ <date>2012-01-02 15:59:00.308 CET</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>7f0f8712-195f-48d2-9fce-5d5ff7832312</identification>\r
+ </annotationBean>\r
+ <date>2012-01-25 16:57:56.63 CET</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>d8d8cbfe-4a10-4903-b5d6-a1dbd68a1e0f</identification>\r
+ </annotationBean>\r
+ <date>2012-01-02 17:43:58.338 CET</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>7cbd63e4-d73d-42d9-9133-4f359b06efb5</identification>\r
+ </annotationBean>\r
+ <date>2012-01-02 14:51:19.40 CET</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>82083c79-a4c9-4d8c-bf19-3e89ff2276e6</identification>\r
+ </annotationBean>\r
+ <date>2012-01-02 15:05:39.350 CET</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>98429027-b6ab-4c7a-8952-f92ce82af604</identification>\r
+ </annotationBean>\r
+ <date>2012-01-13 16:44:12.623 CET</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
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+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>e2b4ef4f-5ce6-47fd-9aed-3042a7d27529</identification>\r
+ </annotationBean>\r
+ <date>2012-01-02 16:20:24.718 CET</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>54d71067-a78a-4e3b-a54f-d47f75bd2adf</identification>\r
+ </annotationBean>\r
+ <date>2012-01-31 16:10:34.267 CET</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>7a284b5d-ac86-416b-a639-27e9dc335bd6</identification>\r
+ </annotationBean>\r
+ <date>2012-02-07 17:40:29.204 CET</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>5dbd6255-5adc-46fb-a4c6-ed77d56af267</identification>\r
+ </annotationBean>\r
+ <date>2012-01-02 17:16:27.428 CET</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>f41b5d1f-a3a6-4fcb-a52a-748150c35471</identification>\r
+ </annotationBean>\r
+ <date>2012-02-07 17:22:31.525 CET</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>fc6e1c60-48ee-4b31-b03c-56578917a502</identification>\r
+ </annotationBean>\r
+ <date>2012-02-07 17:54:50.374 CET</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>df805bf7-d2c5-436b-a770-ba2258ed78c5</identification>\r
+ </annotationBean>\r
+ <date>2012-01-31 16:39:08.415 CET</date>\r
+ <creators />\r
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+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
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+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
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+ </annotationBean>\r
+ <date>2012-01-02 17:50:56.83 CET</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
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+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
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+ </annotationBean>\r
+ <date>2012-01-02 17:35:34.596 CET</date>\r
+ <creators />\r
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+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>feaf6e99-716b-4cc9-81b0-7255ea5a38f7</identification>\r
+ </annotationBean>\r
+ <date>2012-01-02 16:03:20.221 CET</date>\r
+ <creators />\r
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+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>97a86075-f1f7-4e46-a383-cec4b7b16ec4</identification>\r
+ </annotationBean>\r
+ <date>2012-01-31 16:24:57.958 CET</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>9b4884d3-e15c-4b7d-b142-29bf6a7dd990</identification>\r
+ </annotationBean>\r
+ <date>2012-02-07 17:48:17.932 CET</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>9995fb53-fe1e-4aee-88c8-60bb5f2f34cf</identification>\r
+ </annotationBean>\r
+ <date>2012-01-05 16:27:19.428 CET</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>68e10646-ec25-46ff-a748-a4ceb7eb8962</identification>\r
+ </annotationBean>\r
+ <date>2012-01-31 17:02:32.988 CET</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>6e0d1517-2294-4837-b994-80604a634cd0</identification>\r
+ </annotationBean>\r
+ <date>2012-01-02 15:55:00.474 CET</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>4f8dd224-cc83-4af5-bbd2-dedfd09b43fe</identification>\r
</annotationBean>\r
- <date>2011-12-05 16:37:45.485 CET</date>\r
+ <date>2012-01-02 17:14:37.644 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
</annotationAssertions>\r
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></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="">\r
- <maxJobs>1</maxJobs>\r
-</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="">\r
- <backoffFactor>1.0</backoffFactor>\r
- <initialDelay>1000</initialDelay>\r
- <maxDelay>5000</maxDelay>\r
- <maxRetries>0</maxRetries>\r
-</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="stringlist" depth="1" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>Transform_XML</processor><port>xslFileURL</port></sink><source type="processor"><processor>gbifResponse_to_csv_xsl</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>Transform_XML</processor><port>inString</port></sink><source type="processor"><processor>gbifOccurrence</processor><port>responseBody</port></source></datalink><datalink><sink type="processor"><processor>gbifOccurrence</processor><port>format</port></sink><source type="processor"><processor>format_value</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>gbifOccurrence</processor><port>scientificname</port></sink><source type="dataflow"><port>sciName</port></source></datalink><datalink><sink type="processor"><processor>gbifOccurrence</processor><port>next</port></sink><source type="dataflow"><port>next</port></source></datalink><datalink><sink type="processor"><processor>next</processor><port>xml_text</port></sink><source type="processor"><processor>gbifOccurrence</processor><port>responseBody</port></source></datalink><datalink><sink type="processor"><processor>list_to_single_value</processor><port>stringlist</port></sink><source type="processor"><processor>next</processor><port>nodelist</port></source></datalink><datalink><sink type="dataflow"><port>next</port></sink><source type="processor"><processor>list_to_single_value</processor><port>value</port></source></datalink><datalink><sink type="dataflow"><port>max1000_csv_output</port></sink><source type="processor"><processor>Transform_XML</processor><port>outputStr</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>0405ad51-49d4-499c-bba3-01dbac5fb318</identification>\r
+ <identification>96030fe2-efe7-4c53-a562-a358b87d4770</identification>\r
</annotationBean>\r
- <date>2012-02-07 17:37:21.427 CET</date>\r
+ <date>2012-04-04 11:55:49.744 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>65d843f2-dc3a-45f3-a8b7-94138384a01a</identification>\r
+ <identification>9b1c8f07-a857-4d04-b260-b13bcf331662</identification>\r
</annotationBean>\r
- <date>2012-02-07 18:14:49.842 CET</date>\r
+ <date>2012-01-31 16:03:53.673 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>3d7cc7af-f5a9-428f-a77d-2867c98c66a7</identification>\r
+ <identification>2547dd85-519d-4636-8ee9-3b380ad378ab</identification>\r
</annotationBean>\r
- <date>2012-02-07 17:48:00.763 CET</date>\r
+ <date>2012-02-07 17:38:22.701 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>428913bf-040a-43f2-9500-bb904c8c5aa6</identification>\r
+ <identification>7be40bed-1839-4117-81ff-49391e0fe35a</identification>\r
</annotationBean>\r
- <date>2012-02-07 17:54:40.933 CET</date>\r
+ <date>2012-01-02 17:52:39.889 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>124b440e-f7ef-445f-901b-b3d04ca3e2a7</identification>\r
+ <identification>25217334-644c-43ed-bd13-7a3b2a03d5c1</identification>\r
</annotationBean>\r
- <date>2012-03-02 16:39:23.274 CET</date>\r
+ <date>2012-01-31 16:20:23.935 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>801315c9-0a96-46b3-927b-b74e186f7ece</identification>\r
+ <identification>097d3ac1-d144-4f87-81f4-6b995a524fee</identification>\r
</annotationBean>\r
- <date>2012-02-09 17:39:14.181 CET</date>\r
+ <date>2012-02-07 17:42:08.823 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>f653d906-88de-417d-bf3e-61ed29fd6733</identification>\r
+ <identification>e0b1887f-8e9c-43d7-bb75-ee3b5e382834</identification>\r
</annotationBean>\r
- <date>2012-02-07 18:09:00.574 CET</date>\r
+ <date>2012-01-31 16:29:30.593 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>88fdb5ec-112f-40ce-be72-3c9bf4d888b0</identification>\r
+ <identification>a364b26a-abf3-425d-b166-ab27bf0381c5</identification>\r
</annotationBean>\r
- <date>2012-02-08 15:37:15.977 CET</date>\r
+ <date>2012-01-02 17:04:19.721 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
</annotationAssertions>\r
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow><dataflow id="62f3f979-79ca-4566-8cd7-22af322c4c7e" role="nested"><name>Workflow38</name><inputPorts><port><name>csvData</name><depth>0</depth><granularDepth>0</granularDepth><annotations /></port></inputPorts><outputPorts><port><name>csv_output</name><annotations /></port></outputPorts><processors><processor><name>syn_expansion</name><inputPorts><port><name>synRequest</name><depth>1</depth></port></inputPorts><outputPorts><port><name>synResponse</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>dataflow-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.dataflow.DataflowActivity</class><inputMap><map from="synRequest" to="synRequest" /></inputMap><outputMap><map from="synResponse" to="synResponse" /></outputMap><configBean encoding="dataflow"><dataflow ref="adac59f0-935b-498d-b4ef-af755de705ed" /></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="">\r
- <maxJobs>1</maxJobs>\r
-</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="">\r
- <backoffFactor>1.0</backoffFactor>\r
- <initialDelay>1000</initialDelay>\r
- <maxDelay>5000</maxDelay>\r
- <maxRetries>0</maxRetries>\r
-</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="synRequest" depth="1" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Wrap_strings_in_query_element</name><inputPorts><port><name>string2</name><depth>0</depth></port><port><name>string1</name><depth>0</depth></port></inputPorts><outputPorts><port><name>output</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="string2" to="string2" /><map from="string1" to="string1" /></inputMap><outputMap><map from="output" to="output" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">\r
- <inputs>\r
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
- <name>string1</name>\r
- <depth>0</depth>\r
- <mimeTypes>\r
- <string>'text/plain'</string>\r
- </mimeTypes>\r
- <handledReferenceSchemes />\r
- <translatedElementType>java.lang.String</translatedElementType>\r
- <allowsLiteralValues>true</allowsLiteralValues>\r
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
- <name>string2</name>\r
- <depth>0</depth>\r
- <mimeTypes>\r
- <string>'text/plain'</string>\r
- </mimeTypes>\r
- <handledReferenceSchemes />\r
- <translatedElementType>java.lang.String</translatedElementType>\r
- <allowsLiteralValues>true</allowsLiteralValues>\r
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
- </inputs>\r
- <outputs>\r
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
- <name>output</name>\r
- <depth>0</depth>\r
- <mimeTypes />\r
- <granularDepth>0</granularDepth>\r
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
- </outputs>\r
- <classLoaderSharing>workflow</classLoaderSharing>\r
- <localDependencies />\r
- <artifactDependencies />\r
- <script>output = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<syncheck>\n<query>\n" + string1 + string2 + "</query>\n</syncheck>";</script>\r
- <dependencies />\r
- <localworkerName>org.embl.ebi.escience.scuflworkers.java.StringConcat</localworkerName>\r
-</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>8fd4d664-f4f1-48b8-a9a6-36c420e7214e</identification>\r
+ </annotationBean>\r
+ <date>2012-01-13 15:45:48.22 CET</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>273737ec-425c-4577-8d2a-963156312cfd</identification>\r
+ </annotationBean>\r
+ <date>2012-01-02 15:56:51.418 CET</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>a87dd75f-af3c-44ad-9718-b7125a22089f</identification>\r
+ </annotationBean>\r
+ <date>2012-01-02 17:21:03.648 CET</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>d3e29f08-a44b-4bb2-9896-4f325e0499d3</identification>\r
+ </annotationBean>\r
+ <date>2012-01-13 17:09:46.986 CET</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>8dc4d420-1edf-473f-b111-d6510f6f026e</identification>\r
+ </annotationBean>\r
+ <date>2012-01-02 17:47:36.491 CET</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>dedef59b-8e8b-4e4d-8903-5f8c54422215</identification>\r
+ </annotationBean>\r
+ <date>2012-01-02 16:04:37.936 CET</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>d705a674-a106-4328-b611-2deb72c4620b</identification>\r
+ </annotationBean>\r
+ <date>2012-01-31 16:22:50.732 CET</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>0a796aad-5444-420c-a88c-c1ef2411601b</identification>\r
+ </annotationBean>\r
+ <date>2012-01-25 16:54:33.283 CET</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>89f2b55a-52b9-43e9-a4a7-04fe6baca933</identification>\r
+ </annotationBean>\r
+ <date>2012-03-02 16:39:26.106 CET</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>b5b6d740-cc89-4450-8e5b-44fcac2bfee2</identification>\r
+ </annotationBean>\r
+ <date>2012-01-02 15:00:31.584 CET</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>eb452b59-dcaf-4db0-8f72-244455633870</identification>\r
+ </annotationBean>\r
+ <date>2012-01-13 15:40:37.647 CET</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>818abfc6-bd93-4bbd-9c36-68b73b0af681</identification>\r
+ </annotationBean>\r
+ <date>2012-02-08 15:37:32.562 CET</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>69821203-d769-45ce-a3bb-145a9964679f</identification>\r
+ </annotationBean>\r
+ <date>2012-01-02 15:04:12.378 CET</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>b87d4830-e4c0-4665-972b-b60353b71873</identification>\r
+ </annotationBean>\r
+ <date>2012-01-02 16:29:06.484 CET</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>533cbe09-7d47-4443-a85e-7a85ba750924</identification>\r
+ </annotationBean>\r
+ <date>2012-02-07 17:33:24.631 CET</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.HostInstitution">\r
- <text>UserNameHere</text>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>370ad085-8ced-4374-ba09-ebf615d24880</identification>\r
</annotationBean>\r
- <date>2012-02-10 15:51:36.322 CET</date>\r
+ <date>2012-04-05 16:42:41.998 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
</annotationAssertions>\r
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></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="">\r
- <maxJobs>1</maxJobs>\r
-</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="">\r
- <backoffFactor>1.0</backoffFactor>\r
- <initialDelay>1000</initialDelay>\r
- <maxDelay>5000</maxDelay>\r
- <maxRetries>0</maxRetries>\r
-</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><dot><port name="string2" depth="0" /><port name="string1" depth="0" /></dot></strategy></iteration></iterationStrategyStack></processor><processor><name>occ_retrieval</name><inputPorts><port><name>sciNameList</name><depth>1</depth></port></inputPorts><outputPorts><port><name>csv_output</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>dataflow-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.dataflow.DataflowActivity</class><inputMap><map from="sciNameList" to="sciNameList" /></inputMap><outputMap><map from="csv_output" to="csv_output" /></outputMap><configBean encoding="dataflow"><dataflow ref="215a1834-28df-4b7d-b6c2-48f559140fa2" /></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="">\r
- <maxJobs>1</maxJobs>\r
-</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="">\r
- <backoffFactor>1.0</backoffFactor>\r
- <initialDelay>1000</initialDelay>\r
- <maxDelay>5000</maxDelay>\r
- <maxRetries>0</maxRetries>\r
-</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="sciNameList" depth="1" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>SynCheckGUI</name><inputPorts><port><name>synreqres_list</name><depth>1</depth></port></inputPorts><outputPorts><port><name>out</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="synreqres_list" to="synreqres_list" /></inputMap><outputMap><map from="out" to="out" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">\r
- <inputs>\r
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
- <name>synreqres_list</name>\r
- <depth>1</depth>\r
- <mimeTypes>\r
- <string>text/plain</string>\r
- </mimeTypes>\r
- <handledReferenceSchemes />\r
- <translatedElementType>java.lang.String</translatedElementType>\r
- <allowsLiteralValues>true</allowsLiteralValues>\r
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
- </inputs>\r
- <outputs>\r
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
- <name>out</name>\r
- <depth>1</depth>\r
- <mimeTypes />\r
- <granularDepth>1</granularDepth>\r
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
- </outputs>\r
- <classLoaderSharing>workflow</classLoaderSharing>\r
- <localDependencies>\r
- <string>DCWorkflow.jar</string>\r
- </localDependencies>\r
- <artifactDependencies />\r
- <script>import org.bgbm.biovel.datacleaning.syncheck.SynCheckDialog;\r
-Frame f = new JFrame();\r
-\r
-SynCheckDialog scd = new SynCheckDialog(f,true, synreqres_list);\r
-scd.setLocationRelativeTo(null);\r
-scd.show();\r
-\r
-out = scd.getUniqueNameList();\r
-</script>\r
- <dependencies />\r
-</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></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="">\r
- <maxJobs>1</maxJobs>\r
-</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="">\r
- <backoffFactor>1.0</backoffFactor>\r
- <initialDelay>1000</initialDelay>\r
- <maxDelay>5000</maxDelay>\r
- <maxRetries>0</maxRetries>\r
-</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="synreqres_list" depth="1" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>DCDataParser</name><inputPorts><port><name>csvData</name><depth>0</depth></port></inputPorts><outputPorts><port><name>synonymRequest</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="csvData" to="csvData" /></inputMap><outputMap><map from="synonymRequest" to="synonymRequest" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">\r
- <inputs>\r
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
- <name>csvData</name>\r
- <depth>0</depth>\r
- <mimeTypes>\r
- <string>text/plain</string>\r
- </mimeTypes>\r
- <handledReferenceSchemes />\r
- <translatedElementType>java.lang.String</translatedElementType>\r
- <allowsLiteralValues>true</allowsLiteralValues>\r
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
- </inputs>\r
- <outputs>\r
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
- <name>synonymRequest</name>\r
- <depth>1</depth>\r
- <mimeTypes />\r
- <granularDepth>1</granularDepth>\r
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
- <name>incorrectRecords</name>\r
- <depth>0</depth>\r
- <mimeTypes />\r
- <granularDepth>0</granularDepth>\r
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
- </outputs>\r
- <classLoaderSharing>workflow</classLoaderSharing>\r
- <localDependencies />\r
- <artifactDependencies />\r
- <script>\r
-\r
-import java.io.BufferedReader;\r
-import java.io.ByteArrayInputStream;\r
-import java.io.StringReader;\r
-import java.util.StringTokenizer;\r
-import java.util.HashSet;\r
-import java.util.Iterator;\r
-import java.io.StringWriter;\r
-import javax.xml.stream.XMLOutputFactory;\r
-import javax.xml.stream.XMLStreamWriter;\r
-import javax.xml.transform.OutputKeys;\r
-import javax.xml.transform.Transformer;\r
-import javax.xml.transform.TransformerFactory;\r
-import javax.xml.transform.stream.StreamResult;\r
-import javax.xml.transform.stream.StreamSource;\r
-\r
-\r
-\r
-\r
-class SynonymCheckData {\r
- public boolean atomised = false;\r
- public String sciName = "";\r
- public String authorship = "";\r
- public String genusPart = "";\r
- public String infragenericEpithet = "";\r
- public String specificEpithet = "";\r
- public String infraspecificEpithet = "";\r
- public String uninomial = "";\r
-\r
- public SynonymCheckData() {\r
- clear();\r
- }\r
-\r
- public void clear() {\r
- atomised = false;\r
- sciName = "";\r
- authorship = "";\r
- genusPart = "";\r
- infragenericEpithet = "";\r
- specificEpithet = "";\r
- infraspecificEpithet = "";\r
- uninomial = "";\r
- }\r
-\r
- public int hashCode() {\r
- return sciName.hashCode();\r
- }\r
- public boolean equals(Object obj) {\r
- \r
- if ( this == obj ) return true;\r
- \r
- if ( !(obj instanceof SynonymCheckData) ) return false;\r
- \r
- SynonymCheckData scd = (SynonymCheckData) obj;\r
- \r
- return scd.sciName.equals(this.sciName);\r
- }\r
-}\r
-\r
-\r
- \r
-private final static String DELIMITER = ",";\r
- \r
-private final static String AUTHORSHIP_HDR = "authorship";\r
-private final static String GENUSPART_HDR = "genusPart";\r
-private final static String INFRAGENERICEPITHET_HDR = "infragenericEpithet";\r
-private final static String SPECIFICEPITHET_HDR = "specificEpithet";\r
-private final static String INFRASPECIFICEPITHET_HDR = "infraspecificEpithet";\r
-private final static String NAMECOMPLETE_HDR = "nameComplete";\r
-private final static String UNINOMIAL_HDR = "uninomial";\r
-private final static String TAXONNAME_HDR = "taxonName";\r
- \r
-private static StringBuilder incorrectRecordsBldr = new StringBuilder();\r
- \r
-public static String[] split(String record, String delimiter, int noOfElements) throws Exception {\r
- \r
- String[] data = new String[noOfElements];\r
- boolean wasDelimiter=true; \r
- String token=""; \r
- int token_count = 0;\r
- \r
- StringTokenizer st=new StringTokenizer(record,delimiter,true); \r
-\r
- while(st.hasMoreTokens()) { \r
- token=st.nextToken().trim(); \r
- if(token_count >= noOfElements) {\r
- throw new Exception("No. of elements in record does not match no. of header elements");\r
- }\r
- if(token.equals(delimiter)) { \r
- if(wasDelimiter) \r
- { \r
- token=""; \r
- data[token_count] = token;\r
- token_count++;\r
- } \r
- wasDelimiter = true; \r
- }\r
- else \r
- { \r
- wasDelimiter = false; \r
- data[token_count] = token;\r
- token_count++;\r
- } \r
- } \r
-\r
- \r
- return data;\r
-}\r
- \r
-public static List synReq(HashSet hs) throws Exception {\r
- \r
- if(hs.isEmpty())\r
- return null;\r
- List synReqList = new ArrayList();\r
- \r
- XMLOutputFactory xof = XMLOutputFactory.newInstance();\r
- XMLStreamWriter xtw;\r
- \r
- Iterator itr = hs.iterator();\r
- \r
- while(itr.hasNext()) {\r
- SynonymCheckData scd = (SynonymCheckData)itr.next();\r
- if(scd.sciName.equals(""))\r
- continue;\r
- StringWriter out = new StringWriter();\r
- xtw = xof.createXMLStreamWriter(out); \r
- //xtw.writeStartDocument("utf-8", "1.0"); \r
- xtw.writeStartElement("synonymRequest");\r
- xtw.writeAttribute("id", scd.sciName);\r
-\r
- xtw.writeStartElement("taxonName");\r
- if(!scd.authorship.equals("")) {\r
- xtw.writeStartElement(AUTHORSHIP_HDR);\r
- xtw.writeCharacters(scd.authorship);\r
- xtw.writeEndElement();\r
- }\r
-\r
- xtw.writeStartElement("name");\r
-\r
- xtw.writeStartElement(NAMECOMPLETE_HDR);\r
- xtw.writeCharacters(scd.sciName);\r
- xtw.writeEndElement();\r
-\r
- \r
- if(!scd.uninomial.equals("")) {\r
- xtw.writeStartElement("atomisedName");\r
-\r
- xtw.writeStartElement(UNINOMIAL_HDR);\r
- xtw.writeCharacters(scd.uninomial);\r
- xtw.writeEndElement();\r
-\r
- xtw.writeEndElement(); // end atomisedName element\r
- } else if(!scd.genusPart.equals("")){\r
- xtw.writeStartElement("atomisedName");\r
- xtw.writeStartElement("subGenus");\r
-\r
- xtw.writeStartElement(GENUSPART_HDR);\r
- xtw.writeCharacters(scd.genusPart);\r
- xtw.writeEndElement();\r
-\r
- if(!scd.infragenericEpithet.equals("")) {\r
- xtw.writeStartElement(INFRASPECIFICEPITHET_HDR);\r
- xtw.writeCharacters(scd.infragenericEpithet);\r
- xtw.writeEndElement();\r
- }\r
- \r
- if(!scd.specificEpithet.equals("")) {\r
- xtw.writeStartElement(SPECIFICEPITHET_HDR);\r
- xtw.writeCharacters(scd.specificEpithet);\r
- xtw.writeEndElement();\r
- }\r
-\r
- if(!scd.infraspecificEpithet.equals("")){\r
- xtw.writeStartElement(INFRASPECIFICEPITHET_HDR);\r
- xtw.writeCharacters(scd.infraspecificEpithet);\r
- xtw.writeEndElement();\r
- }\r
-\r
- xtw.writeEndElement(); // end subGenus element\r
- xtw.writeEndElement(); // end atomisedName element\r
- }\r
- \r
- xtw.writeEndElement(); // end name element\r
- xtw.writeEndElement(); // end taxonName element\r
- xtw.writeEndElement(); // end synonymRequest element \r
- xtw.writeEndDocument(); \r
- xtw.flush();\r
-\r
- \r
- // Transform XML to get new with indentation.\r
- TransformerFactory factory = TransformerFactory.newInstance();\r
- \r
- Transformer transformer = factory.newTransformer();\r
- transformer.setOutputProperty(OutputKeys.INDENT, "yes");\r
- transformer.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");\r
- \r
- StringWriter indented_out = new StringWriter();\r
- transformer.transform(new StreamSource(new StringReader(out.toString())), new StreamResult(indented_out));\r
- synReqList.add(indented_out.toString()); \r
- out.flush();\r
- } \r
- xtw.close();\r
- return synReqList;\r
-}\r
- \r
- \r
-int authorship_index = -1; \r
-int genus_part_index = -1;\r
-int infrageneric_epithet_index = -1;\r
-int specific_epithet_index = -1;\r
-int infraspecific_epithet_index = -1;\r
-int name_complete_index = -1;\r
-int uninomial_index = -1;\r
-int taxon_name_index = -1;\r
- \r
-int line_count = 0;\r
-int header_index = 0;\r
- \r
-BufferedReader br = new BufferedReader(new StringReader(csvData));\r
-String line;\r
-HashSet sci_names_hs = new HashSet();\r
-SynonymCheckData scd;\r
-String[] recordData;\r
-while((line = br.readLine()) != null) { \r
- if (line.length() > 0) { \r
- try {\r
- StringTokenizer st = new StringTokenizer(line, DELIMITER); \r
- if(line_count == 0) { \r
- while(st.hasMoreTokens()) { \r
- String token = st.nextToken().trim();\r
- if(token.equals(AUTHORSHIP_HDR)) {\r
- authorship_index = header_index;\r
- } \r
- if(token.equals(GENUSPART_HDR)) {\r
- genus_part_index = header_index;\r
- } \r
- if(token.equals(INFRAGENERICEPITHET_HDR)) {\r
- infrageneric_epithet_index = header_index;\r
- } \r
- if(token.equals(SPECIFICEPITHET_HDR)) {\r
- specific_epithet_index = header_index;\r
- } \r
- if(token.equals(INFRASPECIFICEPITHET_HDR)) {\r
- infraspecific_epithet_index = header_index;\r
- } \r
- if(token.equals(NAMECOMPLETE_HDR)) {\r
- name_complete_index = header_index;\r
- }\r
- if(token.equals(TAXONNAME_HDR)) {\r
- taxon_name_index = header_index;\r
- }\r
- header_index++;\r
- }\r
- }\r
- else {\r
- recordData = split(line, DELIMITER, header_index);\r
- if(recordData == null)\r
- continue;\r
- scd = new SynonymCheckData();\r
- if(genus_part_index >= 0 && !recordData[genus_part_index].equals("") \r
- && ((infrageneric_epithet_index >= 0 && !recordData[infrageneric_epithet_index].equals("")) \r
- || (specific_epithet_index >= 0 && !recordData[specific_epithet_index].equals("")) \r
- || (infraspecific_epithet_index >= 0 && !recordData[infraspecific_epithet_index].equals("")))) {\r
- scd.atomised = true; \r
- scd.genusPart = recordData[genus_part_index];\r
- scd.infragenericEpithet = (infrageneric_epithet_index >= 0)?recordData[infrageneric_epithet_index]:"";\r
- scd.specificEpithet = (specific_epithet_index >= 0)?recordData[specific_epithet_index]:"";\r
- scd.infraspecificEpithet = (infrageneric_epithet_index >= 0)?recordData[infraspecific_epithet_index]:"";\r
- \r
- scd.sciName = scd.genusPart;\r
- if(!scd.infragenericEpithet.equals(""))\r
- scd.sciName = scd.sciName + " " + scd.infragenericEpithet;\r
- if(!scd.specificEpithet.equals(""))\r
- scd.sciName = scd.sciName + " " + scd.specificEpithet;\r
- if(!scd.infraspecificEpithet.equals(""))\r
- scd.sciName = scd.sciName + " " + scd.infraspecificEpithet;\r
-\r
- } else if(uninomial_index >=0 && !recordData[uninomial_index].equals("")) {\r
- scd.atomised = true;\r
- scd.uninomial = recordData[uninomial_index];\r
- scd.sciName = scd.uninomial;\r
- } else if(name_complete_index >=0 && !recordData[name_complete_index].equals("")) {\r
- scd.sciName = recordData[name_complete_index];\r
- } else if(taxon_name_index >= 0 && !recordData[taxon_name_index].equals("")){\r
- scd.sciName = recordData[taxon_name_index];\r
- }\r
- if(authorship_index >= 0 && !recordData[authorship_index].equals("")) {\r
- scd.authorship = recordData[authorship_index];\r
- }\r
- \r
- sci_names_hs.add(scd); \r
- }\r
- line_count++;\r
- } catch(Exception e) {\r
- incorrectRecordsBldr.append(line).append(":").append(e.getMessage());\r
- }\r
- } \r
-} \r
- \r
-synonymRequest = synReq(sci_names_hs);\r
-incorrectRecords = incorrectRecordsBldr.toString();\r
-</script>\r
- <dependencies />\r
-</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></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="">\r
- <maxJobs>1</maxJobs>\r
-</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="">\r
- <backoffFactor>1.0</backoffFactor>\r
- <initialDelay>1000</initialDelay>\r
- <maxDelay>5000</maxDelay>\r
- <maxRetries>0</maxRetries>\r
-</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="csvData" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Merge_String_List_to_a_String</name><inputPorts><port><name>seperator</name><depth>0</depth></port><port><name>stringlist</name><depth>1</depth></port></inputPorts><outputPorts><port><name>concatenated</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="seperator" to="seperator" /><map from="stringlist" to="stringlist" /></inputMap><outputMap><map from="concatenated" to="concatenated" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">\r
- <inputs>\r
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
- <name>stringlist</name>\r
- <depth>1</depth>\r
- <mimeTypes>\r
- <string>l('text/plain')</string>\r
- </mimeTypes>\r
- <handledReferenceSchemes />\r
- <translatedElementType>java.lang.String</translatedElementType>\r
- <allowsLiteralValues>true</allowsLiteralValues>\r
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
- <name>seperator</name>\r
- <depth>0</depth>\r
- <mimeTypes>\r
- <string>'text/plain'</string>\r
- </mimeTypes>\r
- <handledReferenceSchemes />\r
- <translatedElementType>java.lang.String</translatedElementType>\r
- <allowsLiteralValues>true</allowsLiteralValues>\r
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
- </inputs>\r
- <outputs>\r
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
- <name>concatenated</name>\r
- <depth>0</depth>\r
- <mimeTypes>\r
- <string>'text/plain'</string>\r
- </mimeTypes>\r
- <granularDepth>0</granularDepth>\r
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
- </outputs>\r
- <classLoaderSharing>workflow</classLoaderSharing>\r
- <localDependencies />\r
- <artifactDependencies />\r
- <script>String seperatorString = "\n";\r
-if (seperator != void) {\r
- seperatorString = seperator;\r
-}\r
-StringBuffer sb = new StringBuffer();\r
-for (Iterator i = stringlist.iterator(); i.hasNext();) {\r
- String item = (String) i.next();\r
- sb.append(item);\r
- if (i.hasNext()) {\r
- sb.append(seperatorString);\r
- }\r
-}\r
-concatenated = sb.toString();\r
-</script>\r
- <dependencies />\r
- <localworkerName>org.embl.ebi.escience.scuflworkers.java.StringListMerge</localworkerName>\r
-</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="">\r
- <maxJobs>1</maxJobs>\r
-</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="">\r
- <backoffFactor>1.0</backoffFactor>\r
- <initialDelay>1000</initialDelay>\r
- <maxDelay>5000</maxDelay>\r
- <maxRetries>0</maxRetries>\r
-</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="seperator" depth="0" /><port name="stringlist" depth="1" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>no_separator</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="">\r
- <value />\r
-</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="">\r
- <maxJobs>1</maxJobs>\r
-</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="">\r
- <backoffFactor>1.0</backoffFactor>\r
- <initialDelay>1000</initialDelay>\r
- <maxDelay>5000</maxDelay>\r
- <maxRetries>0</maxRetries>\r
-</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></processors><conditions /><datalinks><datalink><sink type="processor"><processor>syn_expansion</processor><port>synRequest</port></sink><source type="processor"><processor>DCDataParser</processor><port>synonymRequest</port></source></datalink><datalink><sink type="processor"><processor>Wrap_strings_in_query_element</processor><port>string2</port></sink><source type="processor"><processor>syn_expansion</processor><port>synResponse</port></source></datalink><datalink><sink type="processor"><processor>Wrap_strings_in_query_element</processor><port>string1</port></sink><source type="processor"><processor>DCDataParser</processor><port>synonymRequest</port></source></datalink><datalink><sink type="processor"><processor>occ_retrieval</processor><port>sciNameList</port></sink><source type="processor"><processor>SynCheckGUI</processor><port>out</port></source></datalink><datalink><sink type="processor"><processor>SynCheckGUI</processor><port>synreqres_list</port></sink><source type="processor"><processor>Wrap_strings_in_query_element</processor><port>output</port></source></datalink><datalink><sink type="processor"><processor>DCDataParser</processor><port>csvData</port></sink><source type="dataflow"><port>csvData</port></source></datalink><datalink><sink type="processor"><processor>Merge_String_List_to_a_String</processor><port>seperator</port></sink><source type="processor"><processor>no_separator</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>Merge_String_List_to_a_String</processor><port>stringlist</port></sink><source type="processor"><processor>occ_retrieval</processor><port>csv_output</port></source></datalink><datalink><sink type="dataflow"><port>csv_output</port></sink><source type="processor"><processor>Merge_String_List_to_a_String</processor><port>concatenated</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>62f4cd4d-508e-409c-8e06-3fef4020fa97</identification>\r
+ </annotationBean>\r
+ <date>2012-02-07 17:25:22.963 CET</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>6baa5e11-586d-4f13-b6f4-92c61c10ec9a</identification>\r
+ </annotationBean>\r
+ <date>2012-01-13 15:29:27.496 CET</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>974e04bd-3efb-424a-9e35-2cd9f4fcd274</identification>\r
+ </annotationBean>\r
+ <date>2012-01-02 17:23:23.829 CET</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>56cae6e8-a10e-44dc-86d9-dde7c69beee3</identification>\r
+ </annotationBean>\r
+ <date>2012-01-31 15:45:44.504 CET</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>cdf9c220-fb85-4262-bf44-77fc3302797e</identification>\r
+ <identification>2764b0d8-8242-40ea-b0a3-ddf550e8dc59</identification>\r
</annotationBean>\r
- <date>2012-03-29 17:02:17.600 CEST</date>\r
+ <date>2012-01-02 16:21:21.874 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>a61e3cdd-fe61-41f9-95af-c70859ad4797</identification>\r
+ <identification>8f681f37-c9a0-4f78-b668-0df9c735e332</identification>\r
</annotationBean>\r
- <date>2012-04-04 13:30:30.994 CEST</date>\r
+ <date>2012-01-13 15:24:58.691 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>2f0ef2c4-0d2f-41b1-a08c-cf5b114c4e4c</identification>\r
+ <identification>8a58b613-ac30-4ec1-9877-8221a6654ff4</identification>\r
</annotationBean>\r
- <date>2012-03-29 14:59:02.824 CEST</date>\r
+ <date>2012-01-03 12:48:44.529 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>97c631bc-c4d3-452a-93d2-4610c3808892</identification>\r
+ <identification>3322b5a3-1530-4824-9300-ba6a6b18b7f1</identification>\r
</annotationBean>\r
- <date>2012-04-05 16:35:01.668 CEST</date>\r
+ <date>2012-01-31 16:27:20.693 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>d9fbd0bb-0b5c-4ae1-a3e6-24b25fe15d8c</identification>\r
+ <identification>c818b2a9-90a8-4fc2-9c42-8066af346cba</identification>\r
</annotationBean>\r
- <date>2012-03-29 14:30:40.331 CEST</date>\r
+ <date>2012-01-31 15:47:04.807 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>771b9e2d-2de0-4b86-be30-ad834dac02b1</identification>\r
+ <identification>d044d916-0adb-4065-b39f-8357372e42cc</identification>\r
</annotationBean>\r
- <date>2012-04-05 17:04:49.990 CEST</date>\r
+ <date>2012-01-13 15:44:17.623 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>c937ca39-cd89-4ad1-8d74-161ccb7b3961</identification>\r
+ <identification>d4040120-4a6d-4a24-8bf4-73dd22e762c3</identification>\r
</annotationBean>\r
- <date>2012-04-03 09:40:40.891 CEST</date>\r
+ <date>2012-01-02 16:46:06.131 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>c08d7865-55d5-452b-aae4-88c1c5754d24</identification>\r
+ <identification>4337a0e1-a09d-4b68-8660-637490e21edb</identification>\r
</annotationBean>\r
- <date>2012-04-04 13:48:50.594 CEST</date>\r
+ <date>2012-01-31 15:58:55.276 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>fd8fb852-f3e8-4a57-a600-7a28c8c68961</identification>\r
+ <identification>1e0e6327-6000-40bb-bb2f-fb8f118350f0</identification>\r
</annotationBean>\r
- <date>2012-03-28 17:50:15.876 CEST</date>\r
+ <date>2012-02-07 18:14:57.3 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>efd208a7-5a9b-4f0a-a5a4-4beb3a8cb586</identification>\r
+ <identification>32faa1ef-391d-4360-8bb4-cc7f25b963a1</identification>\r
</annotationBean>\r
- <date>2012-03-29 11:37:04.382 CEST</date>\r
+ <date>2012-01-02 17:19:44.583 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>3702c3a9-3bac-4f53-bb8d-9fbbd457e077</identification>\r
+ <identification>b123cffa-dcf7-4e76-85e6-0dc999f97104</identification>\r
</annotationBean>\r
- <date>2012-03-29 11:45:10.791 CEST</date>\r
+ <date>2012-02-07 18:09:06.414 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>27df675c-6b6a-4f3d-bf15-7598ff5f87b4</identification>\r
+ <identification>8218cf20-6aa4-4a85-a62a-da0b401991cd</identification>\r
</annotationBean>\r
- <date>2012-04-05 16:57:33.422 CEST</date>\r
+ <date>2012-02-09 17:39:17.418 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>5c3c3a95-e017-404d-adb6-e7b91394df43</identification>\r
+ <identification>5f7faf68-279b-4c53-84ca-6746a5fa7832</identification>\r
</annotationBean>\r
- <date>2012-04-05 16:44:06.65 CEST</date>\r
+ <date>2012-01-31 16:40:24.470 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
</annotationAssertions>\r
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow><dataflow id="0415afc4-0331-4b83-a035-65ba8fea18f8" role="nested"><name>Workflow77</name><inputPorts><port><name>taxonID</name><depth>0</depth><granularDepth>0</granularDepth><annotations /></port></inputPorts><outputPorts><port><name>response</name><annotations /></port></outputPorts><processors><processor><name>Empty_Response_Service</name><inputPorts /><outputPorts><port><name>emptyResponse</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap /><outputMap><map from="emptyResponse" to="emptyResponse" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">\r
+ <inputs />\r
+ <outputs>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
+ <name>emptyResponse</name>\r
+ <depth>0</depth>\r
+ <mimeTypes />\r
+ <granularDepth>0</granularDepth>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
+ </outputs>\r
+ <classLoaderSharing>workflow</classLoaderSharing>\r
+ <localDependencies />\r
+ <artifactDependencies />\r
+ <script>emptyResponse = "";</script>\r
+ <dependencies />\r
+</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></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="">\r
+ <maxJobs>1</maxJobs>\r
+</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="">\r
+ <backoffFactor>1.0</backoffFactor>\r
+ <initialDelay>1000</initialDelay>\r
+ <maxDelay>5000</maxDelay>\r
+ <maxRetries>0</maxRetries>\r
+</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></processors><conditions /><datalinks><datalink><sink type="dataflow"><port>response</port></sink><source type="processor"><processor>Empty_Response_Service</processor><port>emptyResponse</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>b36d4cfa-6510-4d81-883e-eada09b56f2d</identification>\r
+ <identification>286d48b2-6e7f-4e69-88ec-c75c4ab1b21d</identification>\r
</annotationBean>\r
- <date>2012-03-29 14:25:21.10 CEST</date>\r
+ <date>2012-05-31 13:55:06.606 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>b4c96465-61be-4e99-bd05-52ba51a75f42</identification>\r
+ <identification>0415afc4-0331-4b83-a035-65ba8fea18f8</identification>\r
</annotationBean>\r
- <date>2012-04-03 17:01:10.410 CEST</date>\r
+ <date>2012-05-31 13:56:59.167 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
</annotationAssertions>\r
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow><dataflow id="12806644-8a59-4917-a0bf-a32566bfe2ff" role="nested"><name>Workflow1</name><inputPorts><port><name>synResponse</name><depth>0</depth><granularDepth>0</granularDepth><annotations /></port><port><name>nameStatus</name><depth>0</depth><granularDepth>0</granularDepth><annotations /></port></inputPorts><outputPorts><port><name>colResponse</name><annotations /></port></outputPorts><processors><processor><name>COLSynCheck_REST</name><inputPorts><port><name>sciId</name><depth>0</depth></port></inputPorts><outputPorts><port><name>responseBody</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>rest-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.rest.RESTActivity</class><inputMap><map from="sciId" to="sciId" /></inputMap><outputMap><map from="responseBody" to="responseBody" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean xmlns="">\r
+ <httpMethod>GET</httpMethod>\r
+ <urlSignature>http://www.catalogueoflife.org/webservice?response=full&id={sciId}</urlSignature>\r
+ <acceptsHeaderValue>application/xml</acceptsHeaderValue>\r
+ <contentTypeForUpdates>application/xml</contentTypeForUpdates>\r
+ <outgoingDataFormat>String</outgoingDataFormat>\r
+ <sendHTTPExpectRequestHeader>false</sendHTTPExpectRequestHeader>\r
+ <showRedirectionOutputPort>false</showRedirectionOutputPort>\r
+ <escapeParameters>true</escapeParameters>\r
+ <otherHTTPHeaders />\r
+ <activityInputs>\r
+ <entry>\r
+ <string>sciId</string>\r
+ <java-class>java.lang.String</java-class>\r
+ </entry>\r
+ </activityInputs>\r
+</net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean></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="">\r
+ <maxJobs>1</maxJobs>\r
+</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="">\r
+ <backoffFactor>1.0</backoffFactor>\r
+ <initialDelay>1000</initialDelay>\r
+ <maxDelay>5000</maxDelay>\r
+ <maxRetries>0</maxRetries>\r
+</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="sciId" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>taxon_id_xpath</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>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="">\r
+ <value>/results/result[1]/sn_id</value>\r
+</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="">\r
+ <maxJobs>1</maxJobs>\r
+</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="">\r
+ <backoffFactor>1.0</backoffFactor>\r
+ <initialDelay>1000</initialDelay>\r
+ <maxDelay>5000</maxDelay>\r
+ <maxRetries>0</maxRetries>\r
+</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>FirstElement_From_XPath</name><inputPorts><port><name>xmltext</name><depth>0</depth></port><port><name>xpath</name><depth>0</depth></port></inputPorts><outputPorts><port><name>nodeVal</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="xmltext" to="xmltext" /><map from="xpath" to="xpath" /></inputMap><outputMap><map from="nodeVal" to="nodeVal" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">\r
+ <inputs>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ <name>xpath</name>\r
+ <depth>0</depth>\r
+ <mimeTypes>\r
+ <string>text/plain</string>\r
+ </mimeTypes>\r
+ <handledReferenceSchemes />\r
+ <translatedElementType>java.lang.String</translatedElementType>\r
+ <allowsLiteralValues>true</allowsLiteralValues>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ <name>xmltext</name>\r
+ <depth>0</depth>\r
+ <mimeTypes>\r
+ <string>text/plain</string>\r
+ </mimeTypes>\r
+ <handledReferenceSchemes />\r
+ <translatedElementType>java.lang.String</translatedElementType>\r
+ <allowsLiteralValues>true</allowsLiteralValues>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ </inputs>\r
+ <outputs>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
+ <name>nodeVal</name>\r
+ <depth>0</depth>\r
+ <mimeTypes />\r
+ <granularDepth>0</granularDepth>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
+ </outputs>\r
+ <classLoaderSharing>workflow</classLoaderSharing>\r
+ <localDependencies />\r
+ <artifactDependencies />\r
+ <script>import org.dom4j.Document;\r
+import org.dom4j.Node;\r
+import org.dom4j.io.SAXReader;\r
+\r
+SAXReader reader = new SAXReader(false);\r
+reader.setIncludeInternalDTDDeclarations(false);\r
+reader.setIncludeExternalDTDDeclarations(false);\r
+\r
+Document document = reader.read(new StringReader(xmltext));\r
+List nodelist = document.selectNodes(xpath);\r
+\r
+// Process the elements in the nodelist\r
+ArrayList outputList = new ArrayList();\r
+ArrayList outputXmlList = new ArrayList();\r
+\r
+String val = null;\r
+String xmlVal = null;\r
+for (Iterator iter = nodelist.iterator(); iter.hasNext();) {\r
+ Node element = (Node) iter.next();\r
+ xmlVal = element.asXML();\r
+ val = element.getStringValue();\r
+ if (val != null && !val.equals("")) {\r
+ outputList.add(val);\r
+ outputXmlList.add(xmlVal);\r
+ }\r
+break;\r
+}\r
+\r
+//List nodelist=outputList;\r
+nodeVal = val;\r
+</script>\r
+ <dependencies />\r
+</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></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="">\r
+ <maxJobs>1</maxJobs>\r
+</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="">\r
+ <backoffFactor>1.0</backoffFactor>\r
+ <initialDelay>1000</initialDelay>\r
+ <maxDelay>5000</maxDelay>\r
+ <maxRetries>0</maxRetries>\r
+</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="xmltext" depth="0" /><port name="xpath" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>COLSynCheck_REST</processor><port>sciId</port></sink><source type="processor"><processor>FirstElement_From_XPath</processor><port>nodeVal</port></source></datalink><datalink><sink type="processor"><processor>FirstElement_From_XPath</processor><port>xmltext</port></sink><source type="dataflow"><port>synResponse</port></source></datalink><datalink><sink type="processor"><processor>FirstElement_From_XPath</processor><port>xpath</port></sink><source type="processor"><processor>taxon_id_xpath</processor><port>value</port></source></datalink><datalink><sink type="dataflow"><port>colResponse</port></sink><source type="processor"><processor>COLSynCheck_REST</processor><port>responseBody</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>bc9c65e4-9cda-4d92-a6bf-6f6859c69cff</identification>\r
+ <identification>12806644-8a59-4917-a0bf-a32566bfe2ff</identification>\r
</annotationBean>\r
- <date>2012-04-05 17:16:56.281 CEST</date>\r
+ <date>2012-02-10 12:40:34.784 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>d8130c5a-ea4b-4e89-a9c4-c7d95b0b4776</identification>\r
+ <identification>126219a1-2553-4015-a3cb-56f21d51f599</identification>\r
</annotationBean>\r
- <date>2012-04-05 16:43:25.356 CEST</date>\r
+ <date>2012-01-23 17:18:47.464 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>db6f1b58-c356-4583-aeaf-18eedb3c8afc</identification>\r
+ <identification>f856eeda-c416-44e3-b84a-3a0b3b8cd10d</identification>\r
</annotationBean>\r
- <date>2012-04-05 17:15:05.428 CEST</date>\r
+ <date>2012-01-23 17:37:08.778 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>e85227ec-8378-4cad-9a88-15a4a0f643c0</identification>\r
+ <identification>3114c079-dc39-46d0-8feb-99dc0f686512</identification>\r
</annotationBean>\r
- <date>2012-03-29 13:52:07.195 CEST</date>\r
+ <date>2012-01-23 17:33:51.189 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>f080c4b4-30ee-42eb-8897-0084d7779196</identification>\r
+ <identification>6be0b511-0710-45a1-a809-31681f072659</identification>\r
</annotationBean>\r
- <date>2012-03-29 13:41:32.443 CEST</date>\r
+ <date>2012-01-23 17:30:31.962 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>4f535006-c1b1-4c88-ad65-a45415c76407</identification>\r
+ <identification>9b2ea773-b806-4c88-9dd8-8d952d8a0755</identification>\r
</annotationBean>\r
- <date>2012-04-05 17:18:36.51 CEST</date>\r
+ <date>2012-01-24 14:32:22.796 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>b237f1c3-1d6f-4bee-b2e8-dddc87536337</identification>\r
+ <identification>07ec689f-59aa-4be9-8481-5f8e3f6000cf</identification>\r
</annotationBean>\r
- <date>2012-04-05 16:47:36.9 CEST</date>\r
+ <date>2012-01-23 17:45:21.174 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>ae40be70-6c12-45e5-be8b-81f0b8b735ba</identification>\r
+ <identification>ca3ec15d-1ea5-4bf2-a81f-136065d1d38b</identification>\r
</annotationBean>\r
- <date>2012-03-29 12:03:32.626 CEST</date>\r
+ <date>2012-01-23 17:48:54.281 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>62f3f979-79ca-4566-8cd7-22af322c4c7e</identification>\r
+ <identification>75f5a83c-3008-466a-ad20-33e95ba9ff15</identification>\r
</annotationBean>\r
- <date>2012-04-05 17:19:48.164 CEST</date>\r
+ <date>2012-01-23 17:38:12.894 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>5d68a44d-bf06-405c-806f-b228e4617031</identification>\r
+ <identification>cff680af-4261-4881-8faa-0c3f155a4f1b</identification>\r
</annotationBean>\r
- <date>2012-03-29 11:03:32.312 CEST</date>\r
+ <date>2012-01-23 17:27:35.142 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>9c9f8b53-94a2-4e2f-8352-5871b5c93cc5</identification>\r
+ <identification>1d63adfb-85c4-4ce2-a039-13daee06364a</identification>\r
</annotationBean>\r
- <date>2012-03-29 11:44:28.869 CEST</date>\r
+ <date>2012-01-23 17:41:34.44 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>4cf702a6-80f8-4d6f-92a1-79d0e2b6dc90</identification>\r
+ <identification>8eb05b48-f79d-4448-80a7-d45520247aee</identification>\r
</annotationBean>\r
- <date>2012-04-04 11:56:51.717 CEST</date>\r
+ <date>2012-01-24 14:00:38.765 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>8b188a00-3e4f-4262-bc22-696d31481b79</identification>\r
+ <identification>0bc37d95-ca84-4270-9a68-a33a6563caa4</identification>\r
</annotationBean>\r
- <date>2012-04-04 13:40:07.98 CEST</date>\r
+ <date>2012-01-23 17:32:43.771 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>1feeb8b4-0d6c-4436-9a45-088052d4765a</identification>\r
+ <identification>91226a57-267d-49c5-adc4-fab3dda2880a</identification>\r
</annotationBean>\r
- <date>2012-04-05 16:36:08.95 CEST</date>\r
+ <date>2012-01-23 18:00:29.942 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>fc0831b0-d5d1-4849-b27e-45393915f6bb</identification>\r
+ <identification>09763558-ce78-4cf7-bde5-1a202ba7953c</identification>\r
</annotationBean>\r
- <date>2012-03-29 14:55:49.410 CEST</date>\r
+ <date>2012-01-23 17:47:09.64 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
</annotationAssertions>\r
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow><dataflow id="c9988367-0549-456b-a037-a518f41268dc" role="nested"><name>Workflow56</name><inputPorts><port><name>taxonID</name><depth>0</depth><granularDepth>0</granularDepth><annotations /></port></inputPorts><outputPorts><port><name>response</name><annotations /></port></outputPorts><processors><processor><name>GBIF_Taxon_Search</name><inputPorts><port><name>taxonID</name><depth>0</depth></port></inputPorts><outputPorts><port><name>responseBody</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>rest-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.rest.RESTActivity</class><inputMap><map from="taxonID" to="taxonID" /></inputMap><outputMap><map from="responseBody" to="responseBody" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean xmlns="">\r
+ <httpMethod>GET</httpMethod>\r
+ <urlSignature>http://ecat-dev.gbif.org/ws/usage/{taxonID}</urlSignature>\r
+ <acceptsHeaderValue>application/json</acceptsHeaderValue>\r
+ <contentTypeForUpdates>application/xml</contentTypeForUpdates>\r
+ <outgoingDataFormat>String</outgoingDataFormat>\r
+ <sendHTTPExpectRequestHeader>false</sendHTTPExpectRequestHeader>\r
+ <showRedirectionOutputPort>false</showRedirectionOutputPort>\r
+ <escapeParameters>true</escapeParameters>\r
+ <otherHTTPHeaders />\r
+ <activityInputs>\r
+ <entry>\r
+ <string>taxonID</string>\r
+ <java-class>java.lang.String</java-class>\r
+ </entry>\r
+ </activityInputs>\r
+</net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean></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="">\r
+ <maxJobs>1</maxJobs>\r
+</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="">\r
+ <backoffFactor>1.0</backoffFactor>\r
+ <initialDelay>1000</initialDelay>\r
+ <maxDelay>5000</maxDelay>\r
+ <maxRetries>0</maxRetries>\r
+</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="taxonID" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>gbifTaxonSearchParser</name><inputPorts><port><name>gbifTaxonSerachJSON</name><depth>0</depth></port></inputPorts><outputPorts><port><name>synTaxonIDList</name><depth>1</depth><granularDepth>1</granularDepth></port><port><name>datasetName</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>acceptedNameResponse</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="gbifTaxonSerachJSON" to="gbifTaxonSerachJSON" /></inputMap><outputMap><map from="datasetName" to="datasetName" /><map from="synTaxonIDList" to="synTaxonIDList" /><map from="acceptedNameResponse" to="acceptedNameResponse" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">\r
+ <inputs>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ <name>gbifTaxonSerachJSON</name>\r
+ <depth>0</depth>\r
+ <mimeTypes>\r
+ <string>text/plain</string>\r
+ </mimeTypes>\r
+ <handledReferenceSchemes />\r
+ <translatedElementType>java.lang.String</translatedElementType>\r
+ <allowsLiteralValues>true</allowsLiteralValues>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ </inputs>\r
+ <outputs>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
+ <name>synTaxonIDList</name>\r
+ <depth>1</depth>\r
+ <mimeTypes />\r
+ <granularDepth>1</granularDepth>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
+ <name>datasetName</name>\r
+ <depth>0</depth>\r
+ <mimeTypes />\r
+ <granularDepth>0</granularDepth>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
+ <name>acceptedNameResponse</name>\r
+ <depth>0</depth>\r
+ <mimeTypes />\r
+ <granularDepth>0</granularDepth>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
+ </outputs>\r
+ <classLoaderSharing>workflow</classLoaderSharing>\r
+ <localDependencies>\r
+ <string>json-simple-1.1.1.jar</string>\r
+ </localDependencies>\r
+ <artifactDependencies />\r
+ <script>import java.util.Iterator;\r
+import org.json.simple.JSONArray;\r
+import org.json.simple.JSONObject;\r
+import org.json.simple.parser.JSONParser;\r
+\r
+StringBuilder synResponseBuilder = new StringBuilder();\r
+\r
+synTaxonIDList = new ArrayList();\r
+JSONParser parser = new JSONParser();\r
+\r
+Object obj = parser.parse(gbifTaxonSerachJSON);\r
+JSONObject jsonObject = (JSONObject) obj;\r
+ \r
+JSONObject dataObject = (JSONObject)jsonObject.get("data");\r
+JSONArray synonyms = (JSONArray) dataObject.get("synonyms");\r
+Iterator iterator = synonyms.iterator();\r
+\r
+while (iterator.hasNext()) {\r
+ JSONObject dataObject = (JSONObject)iterator.next();\r
+ Number taxonID = (Number)dataObject.get("taxonID");\r
+ synTaxonIDList.add(String.valueOf( taxonID));\r
+}\r
+\r
+datasetName = (String) dataObject.get("datasetName");\r
+\r
+JSONObject dataObject = (JSONObject)jsonObject.get("data");\r
+String canonicalName = (String) dataObject.get("canonicalName");\r
+String taxonomicStatus = (String) dataObject.get("taxonomicStatus");\r
+String rank = (String) dataObject.get("rank");\r
+\r
+synResponseBuilder.append("<acceptedName>");\r
+synResponseBuilder.append("<taxonName><authorship></authorship><name>");\r
+synResponseBuilder.append("<nameComplete>").append(canonicalName).append("</nameComplete>");\r
+synResponseBuilder.append("<atomisedName>");\r
+synResponseBuilder.append("<subGenus>");\r
+synResponseBuilder.append("<genusPart></genusPart><specificEpithet></specificEpithet><infraspecificEpithet></infraspecificEpithet>");\r
+synResponseBuilder.append("</subGenus>");\r
+synResponseBuilder.append("</atomisedName>");\r
+synResponseBuilder.append("<nameStatus>").append("Accepted").append("</nameStatus>");\r
+synResponseBuilder.append("</name>");\r
+synResponseBuilder.append("<rank>").append(rank).append("</rank>");\r
+synResponseBuilder.append("</taxonName>");\r
+synResponseBuilder.append("<source><name></name><url></url></source><info><url></url></info>");\r
+synResponseBuilder.append("</acceptedName>");\r
+\r
+acceptedNameResponse = synResponseBuilder.toString();\r
+</script>\r
+ <dependencies />\r
+</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></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="">\r
+ <maxJobs>1</maxJobs>\r
+</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="">\r
+ <backoffFactor>1.0</backoffFactor>\r
+ <initialDelay>1000</initialDelay>\r
+ <maxDelay>5000</maxDelay>\r
+ <maxRetries>0</maxRetries>\r
+</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="gbifTaxonSerachJSON" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>gbifSynSearch</name><inputPorts><port><name>synTaxonID</name><depth>0</depth></port></inputPorts><outputPorts><port><name>synResponse</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>dataflow-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.dataflow.DataflowActivity</class><inputMap><map from="synTaxonID" to="synTaxonID" /></inputMap><outputMap><map from="synResponse" to="synResponse" /></outputMap><configBean encoding="dataflow"><dataflow ref="9b888ae9-ece1-4b74-b177-5b915c9cc381" /></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="">\r
+ <maxJobs>1</maxJobs>\r
+</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="">\r
+ <backoffFactor>1.0</backoffFactor>\r
+ <initialDelay>1000</initialDelay>\r
+ <maxDelay>5000</maxDelay>\r
+ <maxRetries>0</maxRetries>\r
+</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="synTaxonID" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Merge_String_List_to_a_String</name><inputPorts><port><name>stringlist</name><depth>1</depth></port></inputPorts><outputPorts><port><name>concatenated</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="stringlist" to="stringlist" /></inputMap><outputMap><map from="concatenated" to="concatenated" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">\r
+ <inputs>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ <name>stringlist</name>\r
+ <depth>1</depth>\r
+ <mimeTypes>\r
+ <string>l('text/plain')</string>\r
+ </mimeTypes>\r
+ <handledReferenceSchemes />\r
+ <translatedElementType>java.lang.String</translatedElementType>\r
+ <allowsLiteralValues>true</allowsLiteralValues>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ <name>seperator</name>\r
+ <depth>0</depth>\r
+ <mimeTypes>\r
+ <string>'text/plain'</string>\r
+ </mimeTypes>\r
+ <handledReferenceSchemes />\r
+ <translatedElementType>java.lang.String</translatedElementType>\r
+ <allowsLiteralValues>true</allowsLiteralValues>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ </inputs>\r
+ <outputs>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
+ <name>concatenated</name>\r
+ <depth>0</depth>\r
+ <mimeTypes>\r
+ <string>'text/plain'</string>\r
+ </mimeTypes>\r
+ <granularDepth>0</granularDepth>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
+ </outputs>\r
+ <classLoaderSharing>workflow</classLoaderSharing>\r
+ <localDependencies />\r
+ <artifactDependencies />\r
+ <script>String seperatorString = "\n";\r
+if (seperator != void) {\r
+ seperatorString = seperator;\r
+}\r
+StringBuffer sb = new StringBuffer();\r
+for (Iterator i = stringlist.iterator(); i.hasNext();) {\r
+ String item = (String) i.next();\r
+ sb.append(item);\r
+ if (i.hasNext()) {\r
+ sb.append(seperatorString);\r
+ }\r
+}\r
+concatenated = sb.toString();\r
+</script>\r
+ <dependencies />\r
+ <localworkerName>org.embl.ebi.escience.scuflworkers.java.StringListMerge</localworkerName>\r
+</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="">\r
+ <maxJobs>1</maxJobs>\r
+</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="">\r
+ <backoffFactor>1.0</backoffFactor>\r
+ <initialDelay>1000</initialDelay>\r
+ <maxDelay>5000</maxDelay>\r
+ <maxRetries>0</maxRetries>\r
+</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="stringlist" depth="1" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Concat_Response</name><inputPorts><port><name>datasetName</name><depth>0</depth></port><port><name>accNameRes</name><depth>0</depth></port><port><name>synRes</name><depth>0</depth></port></inputPorts><outputPorts><port><name>concatResponse</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="datasetName" to="datasetName" /><map from="synRes" to="synRes" /><map from="accNameRes" to="accNameRes" /></inputMap><outputMap><map from="concatResponse" to="concatResponse" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">\r
+ <inputs>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ <name>accNameRes</name>\r
+ <depth>0</depth>\r
+ <mimeTypes>\r
+ <string>text/plain</string>\r
+ </mimeTypes>\r
+ <handledReferenceSchemes />\r
+ <translatedElementType>java.lang.String</translatedElementType>\r
+ <allowsLiteralValues>true</allowsLiteralValues>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ <name>datasetName</name>\r
+ <depth>0</depth>\r
+ <mimeTypes>\r
+ <string>text/plain</string>\r
+ </mimeTypes>\r
+ <handledReferenceSchemes />\r
+ <translatedElementType>java.lang.String</translatedElementType>\r
+ <allowsLiteralValues>true</allowsLiteralValues>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ <name>synRes</name>\r
+ <depth>0</depth>\r
+ <mimeTypes>\r
+ <string>text/plain</string>\r
+ </mimeTypes>\r
+ <handledReferenceSchemes />\r
+ <translatedElementType>java.lang.String</translatedElementType>\r
+ <allowsLiteralValues>true</allowsLiteralValues>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ </inputs>\r
+ <outputs>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
+ <name>concatResponse</name>\r
+ <depth>0</depth>\r
+ <mimeTypes />\r
+ <granularDepth>0</granularDepth>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
+ </outputs>\r
+ <classLoaderSharing>workflow</classLoaderSharing>\r
+ <localDependencies />\r
+ <artifactDependencies />\r
+ <script>import javax.xml.parsers.DocumentBuilderFactory;\r
+import javax.xml.parsers.DocumentBuilder;\r
+import javax.xml.transform.Transformer;\r
+import javax.xml.transform.TransformerFactory;\r
+import javax.xml.transform.OutputKeys;\r
+import javax.xml.transform.stream.StreamResult;\r
+import javax.xml.transform.dom.DOMSource;\r
+import org.xml.sax.InputSource;\r
+\r
+StringBuilder concatResponseBuilder = new StringBuilder();\r
+\r
+concatResponseBuilder.append("<synonymResponse checklist=\"").append(datasetName).append("\">");\r
+concatResponseBuilder.append(accNameRes);\r
+concatResponseBuilder.append(synRes);\r
+concatResponseBuilder.append("</synonymResponse>"); \r
+\r
+\r
+\r
+DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();\r
+DocumentBuilder db = dbf.newDocumentBuilder();\r
+InputSource is = new InputSource(new StringReader(concatResponseBuilder.toString()));\r
+Transformer transformer = TransformerFactory.newInstance().newTransformer();\r
+transformer.setOutputProperty(OutputKeys.INDENT, "yes");\r
+transformer.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");\r
+StreamResult result = new StreamResult(new StringWriter());\r
+DOMSource source = new DOMSource(db.parse(is));\r
+transformer.transform(source, result);\r
+concatResponse = result.getWriter().toString();</script>\r
+ <dependencies />\r
+</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></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="">\r
+ <maxJobs>1</maxJobs>\r
+</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="">\r
+ <backoffFactor>1.0</backoffFactor>\r
+ <initialDelay>1000</initialDelay>\r
+ <maxDelay>5000</maxDelay>\r
+ <maxRetries>0</maxRetries>\r
+</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="datasetName" depth="0" /><port name="accNameRes" depth="0" /><port name="synRes" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>GBIF_Taxon_Search</processor><port>taxonID</port></sink><source type="dataflow"><port>taxonID</port></source></datalink><datalink><sink type="processor"><processor>gbifTaxonSearchParser</processor><port>gbifTaxonSerachJSON</port></sink><source type="processor"><processor>GBIF_Taxon_Search</processor><port>responseBody</port></source></datalink><datalink><sink type="processor"><processor>gbifSynSearch</processor><port>synTaxonID</port></sink><source type="processor"><processor>gbifTaxonSearchParser</processor><port>synTaxonIDList</port></source></datalink><datalink><sink type="processor"><processor>Merge_String_List_to_a_String</processor><port>stringlist</port></sink><source type="processor"><processor>gbifSynSearch</processor><port>synResponse</port></source></datalink><datalink><sink type="processor"><processor>Concat_Response</processor><port>datasetName</port></sink><source type="processor"><processor>gbifTaxonSearchParser</processor><port>datasetName</port></source></datalink><datalink><sink type="processor"><processor>Concat_Response</processor><port>accNameRes</port></sink><source type="processor"><processor>gbifTaxonSearchParser</processor><port>acceptedNameResponse</port></source></datalink><datalink><sink type="processor"><processor>Concat_Response</processor><port>synRes</port></sink><source type="processor"><processor>Merge_String_List_to_a_String</processor><port>concatenated</port></source></datalink><datalink><sink type="dataflow"><port>response</port></sink><source type="processor"><processor>Concat_Response</processor><port>concatResponse</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>cc2ba98d-9d65-4882-a1ff-b64e73082de9</identification>\r
+ <identification>c9988367-0549-456b-a037-a518f41268dc</identification>\r
</annotationBean>\r
- <date>2012-03-29 15:33:31.887 CEST</date>\r
+ <date>2012-05-31 13:53:34.400 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
</annotationAssertions>\r
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow><dataflow id="85ba17c1-2e24-49d8-a00b-84acb2a1cf61" role="nested"><name>Workflow33</name><inputPorts><port><name>sciName</name><depth>0</depth><granularDepth>0</granularDepth><annotations /></port></inputPorts><outputPorts><port><name>csv_output</name><annotations /></port></outputPorts><processors><processor><name>slwArtDataBank_to_csv_xsl</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="">\r
- <value>http://ww2.bgbm.org/temp/biovel/slwArtDataBank_to_csv.xsl</value>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow><dataflow id="61896bb4-e33f-49fa-8792-11bd2c8e3efe" role="nested"><name>Workflow11</name><inputPorts><port><name>synRequest</name><depth>0</depth><granularDepth>0</granularDepth><annotations /></port></inputPorts><outputPorts><port><name>synResponse</name><annotations /></port></outputPorts><processors><processor><name>COLRest_Service</name><inputPorts><port><name>sciName</name><depth>0</depth></port></inputPorts><outputPorts><port><name>responseBody</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>rest-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.rest.RESTActivity</class><inputMap><map from="sciName" to="sciName" /></inputMap><outputMap><map from="responseBody" to="responseBody" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean xmlns="">\r
+ <httpMethod>GET</httpMethod>\r
+ <urlSignature>http://www.catalogueoflife.org/webservice?response=full&name={sciName}</urlSignature>\r
+ <acceptsHeaderValue>application/xml</acceptsHeaderValue>\r
+ <contentTypeForUpdates>application/xml</contentTypeForUpdates>\r
+ <outgoingDataFormat>String</outgoingDataFormat>\r
+ <sendHTTPExpectRequestHeader>false</sendHTTPExpectRequestHeader>\r
+ <showRedirectionOutputPort>false</showRedirectionOutputPort>\r
+ <escapeParameters>true</escapeParameters>\r
+ <otherHTTPHeaders />\r
+ <activityInputs>\r
+ <entry>\r
+ <string>sciName</string>\r
+ <java-class>java.lang.String</java-class>\r
+ </entry>\r
+ </activityInputs>\r
+</net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean></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="">\r
+ <maxJobs>1</maxJobs>\r
+</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="">\r
+ <backoffFactor>1.0</backoffFactor>\r
+ <initialDelay>1000</initialDelay>\r
+ <maxDelay>5000</maxDelay>\r
+ <maxRetries>0</maxRetries>\r
+</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="sciName" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>name_status_xpath</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>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="">\r
+ <value>/results/result[1]/name_status</value>\r
</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="">\r
<maxJobs>1</maxJobs>\r
</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="">\r
<initialDelay>1000</initialDelay>\r
<maxDelay>5000</maxDelay>\r
<maxRetries>0</maxRetries>\r
-</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>slwOccurrence</name><inputPorts><port><name>scientificNameFilter</name><depth>0</depth></port></inputPorts><outputPorts><port><name>responseBody</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>rest-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.rest.RESTActivity</class><inputMap><map from="scientificNameFilter" to="scientificNameFilter" /></inputMap><outputMap><map from="responseBody" to="responseBody" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean xmlns="">\r
- <httpMethod>GET</httpMethod>\r
- <urlSignature>http://slwgeo.artdata.slu.se:8080/geoserver/wfs?&VERSION=1.0.0&SERVICE=WFS&REQUEST=GetFeature&TYPENAME=SLW:SwedishSpeciesDarwinCore_1.5&Filter={scientificNameFilter}</urlSignature>\r
- <acceptsHeaderValue>application/xml</acceptsHeaderValue>\r
- <contentTypeForUpdates>application/xml</contentTypeForUpdates>\r
- <outgoingDataFormat>String</outgoingDataFormat>\r
- <sendHTTPExpectRequestHeader>false</sendHTTPExpectRequestHeader>\r
- <showRedirectionOutputPort>false</showRedirectionOutputPort>\r
- <escapeParameters>true</escapeParameters>\r
- <otherHTTPHeaders />\r
- <activityInputs>\r
- <entry>\r
- <string>scientificNameFilter</string>\r
- <java-class>java.lang.String</java-class>\r
- </entry>\r
- </activityInputs>\r
-</net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean></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="">\r
+</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>NameStatusConditional</name><inputPorts><port><name>nameStatus</name><depth>0</depth></port></inputPorts><outputPorts><port><name>synpass_flags</name><depth>1</depth><granularDepth>1</granularDepth></port><port><name>synfail_flags</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="nameStatus" to="nameStatus" /></inputMap><outputMap><map from="synpass_flags" to="synpass_flags" /><map from="synfail_flags" to="synfail_flags" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">\r
+ <inputs>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ <name>nameStatus</name>\r
+ <depth>0</depth>\r
+ <mimeTypes>\r
+ <string>text/plain</string>\r
+ </mimeTypes>\r
+ <handledReferenceSchemes />\r
+ <translatedElementType>java.lang.String</translatedElementType>\r
+ <allowsLiteralValues>true</allowsLiteralValues>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ </inputs>\r
+ <outputs>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
+ <name>synpass_flags</name>\r
+ <depth>1</depth>\r
+ <mimeTypes />\r
+ <granularDepth>1</granularDepth>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
+ <name>synfail_flags</name>\r
+ <depth>1</depth>\r
+ <mimeTypes />\r
+ <granularDepth>1</granularDepth>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
+ </outputs>\r
+ <classLoaderSharing>workflow</classLoaderSharing>\r
+ <localDependencies />\r
+ <artifactDependencies />\r
+ <script>import java.util.ArrayList;\r
+\r
+ArrayList synpass_flags = new ArrayList();\r
+ArrayList synfail_flags = new ArrayList();\r
+\r
+if (nameStatus.equals("synonym")) {\r
+ synpass_flags.add(nameStatus); \r
+} else {\r
+ synfail_flags.add(nameStatus); \r
+}</script>\r
+ <dependencies />\r
+</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></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="">\r
+ <maxJobs>1</maxJobs>\r
+</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="">\r
+ <backoffFactor>1.0</backoffFactor>\r
+ <initialDelay>1000</initialDelay>\r
+ <maxDelay>5000</maxDelay>\r
+ <maxRetries>0</maxRetries>\r
+</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="nameStatus" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>if_synonym</name><inputPorts><port><name>nameStatus</name><depth>0</depth></port><port><name>synResponse</name><depth>0</depth></port></inputPorts><outputPorts><port><name>colResponse</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>dataflow-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.dataflow.DataflowActivity</class><inputMap><map from="nameStatus" to="nameStatus" /><map from="synResponse" to="synResponse" /></inputMap><outputMap><map from="colResponse" to="colResponse" /></outputMap><configBean encoding="dataflow"><dataflow ref="12806644-8a59-4917-a0bf-a32566bfe2ff" /></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="">\r
+ <maxJobs>1</maxJobs>\r
+</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="">\r
+ <backoffFactor>1.0</backoffFactor>\r
+ <initialDelay>1000</initialDelay>\r
+ <maxDelay>5000</maxDelay>\r
+ <maxRetries>0</maxRetries>\r
+</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="nameStatus" depth="0" /><port name="synResponse" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>if_not_synonym</name><inputPorts><port><name>nameStatus</name><depth>0</depth></port><port><name>colResponseIN</name><depth>0</depth></port></inputPorts><outputPorts><port><name>colResponse</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>dataflow-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.dataflow.DataflowActivity</class><inputMap><map from="colResponseIN" to="colResponseIN" /><map from="nameStatus" to="nameStatus" /></inputMap><outputMap><map from="colResponse" to="colResponse" /></outputMap><configBean encoding="dataflow"><dataflow ref="89482956-6a9c-4300-ace2-d8cebb2c4750" /></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="">\r
<maxJobs>1</maxJobs>\r
</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="">\r
<backoffFactor>1.0</backoffFactor>\r
<initialDelay>1000</initialDelay>\r
<maxDelay>5000</maxDelay>\r
<maxRetries>0</maxRetries>\r
-</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="scientificNameFilter" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>slw_filter_generator</name><inputPorts><port><name>sciName</name><depth>0</depth></port></inputPorts><outputPorts><port><name>filter</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="sciName" to="sciName" /></inputMap><outputMap><map from="filter" to="filter" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">\r
+</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="nameStatus" depth="0" /><port name="colResponseIN" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Merge_String_List_to_a_String</name><inputPorts><port><name>stringlist</name><depth>1</depth></port></inputPorts><outputPorts><port><name>concatenated</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="stringlist" to="stringlist" /></inputMap><outputMap><map from="concatenated" to="concatenated" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">\r
<inputs>\r
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
- <name>sciName</name>\r
+ <name>stringlist</name>\r
+ <depth>1</depth>\r
+ <mimeTypes>\r
+ <string>l('text/plain')</string>\r
+ </mimeTypes>\r
+ <handledReferenceSchemes />\r
+ <translatedElementType>java.lang.String</translatedElementType>\r
+ <allowsLiteralValues>true</allowsLiteralValues>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ <name>seperator</name>\r
<depth>0</depth>\r
<mimeTypes>\r
- <string>text/plain</string>\r
+ <string>'text/plain'</string>\r
</mimeTypes>\r
<handledReferenceSchemes />\r
<translatedElementType>java.lang.String</translatedElementType>\r
</inputs>\r
<outputs>\r
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
- <name>filter</name>\r
+ <name>concatenated</name>\r
<depth>0</depth>\r
- <mimeTypes />\r
+ <mimeTypes>\r
+ <string>'text/plain'</string>\r
+ </mimeTypes>\r
<granularDepth>0</granularDepth>\r
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
</outputs>\r
<classLoaderSharing>workflow</classLoaderSharing>\r
<localDependencies />\r
<artifactDependencies />\r
- <script>\r
-filter = "<Filter><PropertyIsLike wildCard='*' singleChar='.' escape='!'><PropertyName>scientificName</PropertyName><Literal>*" + sciName + "*</Literal></PropertyIsLike></Filter>";</script>\r
+ <script>String seperatorString = "\n";\r
+if (seperator != void) {\r
+ seperatorString = seperator;\r
+}\r
+StringBuffer sb = new StringBuffer();\r
+for (Iterator i = stringlist.iterator(); i.hasNext();) {\r
+ String item = (String) i.next();\r
+ sb.append(item);\r
+ if (i.hasNext()) {\r
+ sb.append(seperatorString);\r
+ }\r
+}\r
+concatenated = sb.toString();\r
+</script>\r
<dependencies />\r
-</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></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="">\r
+ <localworkerName>org.embl.ebi.escience.scuflworkers.java.StringListMerge</localworkerName>\r
+</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="">\r
<maxJobs>1</maxJobs>\r
</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="">\r
<backoffFactor>1.0</backoffFactor>\r
<initialDelay>1000</initialDelay>\r
<maxDelay>5000</maxDelay>\r
<maxRetries>0</maxRetries>\r
-</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="sciName" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Transform_XML_String</name><inputPorts><port><name>inString</name><depth>0</depth></port><port><name>xslFileURL</name><depth>0</depth></port></inputPorts><outputPorts><port><name>outputStr</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="inString" to="inString" /><map from="xslFileURL" to="xslFileURL" /></inputMap><outputMap><map from="outputStr" to="outputStr" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">\r
+</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="stringlist" depth="1" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Flatten_List</name><inputPorts><port><name>inputlist</name><depth>2</depth></port></inputPorts><outputPorts><port><name>outputlist</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="inputlist" to="inputlist" /></inputMap><outputMap><map from="outputlist" to="outputlist" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">\r
<inputs>\r
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
- <name>xslFileURL</name>\r
- <depth>0</depth>\r
+ <name>inputlist</name>\r
+ <depth>2</depth>\r
<mimeTypes>\r
- <string>'text/plain'</string>\r
+ <string>l(l(''))</string>\r
</mimeTypes>\r
<handledReferenceSchemes />\r
- <translatedElementType>java.lang.String</translatedElementType>\r
+ <translatedElementType>[B</translatedElementType>\r
<allowsLiteralValues>true</allowsLiteralValues>\r
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ </inputs>\r
+ <outputs>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
+ <name>outputlist</name>\r
+ <depth>1</depth>\r
+ <mimeTypes>\r
+ <string>l('')</string>\r
+ </mimeTypes>\r
+ <granularDepth>1</granularDepth>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
+ </outputs>\r
+ <classLoaderSharing>workflow</classLoaderSharing>\r
+ <localDependencies />\r
+ <artifactDependencies />\r
+ <script>flatten(inputs, outputs, depth) {\r
+ for (i = inputs.iterator(); i.hasNext();) {\r
+ element = i.next();\r
+ if (element instanceof Collection && depth > 0) {\r
+ flatten(element, outputs, depth - 1);\r
+ } else {\r
+ outputs.add(element);\r
+ }\r
+ }\r
+}\r
+\r
+outputlist = new ArrayList();\r
+\r
+flatten(inputlist, outputlist, 1);</script>\r
+ <dependencies />\r
+ <localworkerName>org.embl.ebi.escience.scuflworkers.java.FlattenList</localworkerName>\r
+</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="">\r
+ <maxJobs>1</maxJobs>\r
+</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="">\r
+ <backoffFactor>1.0</backoffFactor>\r
+ <initialDelay>1000</initialDelay>\r
+ <maxDelay>5000</maxDelay>\r
+ <maxRetries>0</maxRetries>\r
+</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="inputlist" depth="2" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>colRes_to_SynRes_xsl</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="">\r
+ <value>http://www.myexperiment.org/files/697/download/colres_to_synres.xsl</value>\r
+</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="">\r
+ <maxJobs>1</maxJobs>\r
+</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="">\r
+ <backoffFactor>1.0</backoffFactor>\r
+ <initialDelay>1000</initialDelay>\r
+ <maxDelay>5000</maxDelay>\r
+ <maxRetries>0</maxRetries>\r
+</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>Transform_XML_with_parameters</name><inputPorts><port><name>xsltString</name><depth>0</depth></port><port><name>sourceString</name><depth>0</depth></port><port><name>paramList</name><depth>1</depth></port></inputPorts><outputPorts><port><name>outputString</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="xsltString" to="xsltString" /><map from="paramList" to="paramList" /><map from="sourceString" to="sourceString" /></inputMap><outputMap><map from="outputString" to="outputString" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">\r
+ <inputs>\r
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
- <name>outFileURL</name>\r
+ <name>sourceString</name>\r
<depth>0</depth>\r
<mimeTypes>\r
- <string>'text/plain'</string>\r
+ <string>text/plain</string>\r
</mimeTypes>\r
<handledReferenceSchemes />\r
<translatedElementType>java.lang.String</translatedElementType>\r
<allowsLiteralValues>true</allowsLiteralValues>\r
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
- <name>inString</name>\r
+ <name>xsltString</name>\r
<depth>0</depth>\r
<mimeTypes>\r
- <string>'text/plain'</string>\r
+ <string>text/plain</string>\r
</mimeTypes>\r
<handledReferenceSchemes />\r
<translatedElementType>java.lang.String</translatedElementType>\r
<allowsLiteralValues>true</allowsLiteralValues>\r
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
- <name>outputExt</name>\r
- <depth>0</depth>\r
+ <name>paramList</name>\r
+ <depth>1</depth>\r
<mimeTypes>\r
- <string>'text/plain'</string>\r
+ <string>text/plain</string>\r
</mimeTypes>\r
<handledReferenceSchemes />\r
<translatedElementType>java.lang.String</translatedElementType>\r
</inputs>\r
<outputs>\r
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
- <name>outputStr</name>\r
+ <name>outputString</name>\r
<depth>0</depth>\r
<mimeTypes />\r
<granularDepth>0</granularDepth>\r
<classLoaderSharing>workflow</classLoaderSharing>\r
<localDependencies />\r
<artifactDependencies />\r
- <script>import java.io.BufferedReader;\r
-import java.io.BufferedWriter;\r
-import java.io.FileInputStream;\r
-import java.io.FileNotFoundException;\r
-import java.io.FileReader;\r
-import java.io.FileWriter;\r
-import java.io.IOException;\r
-import java.io.InputStreamReader;\r
-import java.io.OutputStreamWriter;\r
-import java.io.StringWriter;\r
-import java.io.StringReader;\r
-import java.io.Writer;\r
-import java.net.URL;\r
-import java.util.HashMap;\r
-import java.util.Map;\r
-\r
-import javax.xml.transform.Result;\r
+ <script>//From a proposal by Mikolaj Rybinski\r
import javax.xml.transform.Source;\r
-import javax.xml.transform.SourceLocator;\r
-import javax.xml.transform.Templates;\r
import javax.xml.transform.Transformer;\r
-import javax.xml.transform.TransformerConfigurationException;\r
-import javax.xml.transform.TransformerException;\r
import javax.xml.transform.TransformerFactory;\r
import javax.xml.transform.stream.StreamResult;\r
import javax.xml.transform.stream.StreamSource;\r
\r
-BufferedReader getReader (String fileUrl) throws IOException {\r
+param(paramstr) {\r
+ nameAndValue = paramstr.split("=");\r
+ if (nameAndValue.length != 2) {\r
+ throw new RuntimeException("Wrong parameter format: \"" + paramstr + "\".");\r
+ }\r
+ name = nameAndValue[0].trim();\r
+ value = nameAndValue[1].trim();\r
+ return this;\r
+}\r
+\r
+if ((sourceString == void) || (sourceString == null)) {\r
+ throw new RuntimeException("sourceString must be specified");\r
+}\r
+\r
+if ((xsltString == void) || (xsltString == null)) {\r
+ throw new RuntimeException("xsltString must be specified");\r
+}\r
+\r
+Source inSource = new StreamSource(new StringReader(sourceString));\r
+Source xslSource = new StreamSource(new StringReader(xsltString));\r
+\r
+// the factory pattern supports different XSLT processors\r
+// e.g. set the "javax.xml.transform.TransformerFactory" system property\r
+TransformerFactory tnfFact = TransformerFactory.newInstance();\r
+Transformer tnf = tnfFact.newTransformer(xslSource);\r
+\r
+if (paramList != void) {\r
+ for (String paramstr : paramList) {\r
+ p = param(paramstr);\r
+ tnf.setParameter(p.name, p.value);\r
+ }\r
+}\r
+\r
+Writer outputWriter = new StringWriter();\r
+tnf.transform(inSource, new StreamResult(outputWriter));\r
+outputString = outputWriter.toString();</script>\r
+ <dependencies />\r
+ <localworkerName>net.sourceforge.taverna.scuflworkers.xml.XSLTWorkerWithParameters</localworkerName>\r
+</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="">\r
+ <maxJobs>1</maxJobs>\r
+</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="">\r
+ <backoffFactor>1.0</backoffFactor>\r
+ <initialDelay>1000</initialDelay>\r
+ <maxDelay>5000</maxDelay>\r
+ <maxRetries>0</maxRetries>\r
+</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="xsltString" depth="0" /><port name="sourceString" depth="0" /><port name="paramList" depth="1" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Read_Text_File_2</name><inputPorts><port><name>fileurl</name><depth>0</depth></port></inputPorts><outputPorts><port><name>filecontents</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="fileurl" to="fileurl" /></inputMap><outputMap><map from="filecontents" to="filecontents" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">\r
+ <inputs>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ <name>fileurl</name>\r
+ <depth>0</depth>\r
+ <mimeTypes>\r
+ <string>'text/plain'</string>\r
+ </mimeTypes>\r
+ <handledReferenceSchemes />\r
+ <translatedElementType>java.lang.String</translatedElementType>\r
+ <allowsLiteralValues>true</allowsLiteralValues>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ <name>encoding</name>\r
+ <depth>0</depth>\r
+ <mimeTypes>\r
+ <string>'text/plain'</string>\r
+ </mimeTypes>\r
+ <handledReferenceSchemes />\r
+ <translatedElementType>java.lang.String</translatedElementType>\r
+ <allowsLiteralValues>true</allowsLiteralValues>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ </inputs>\r
+ <outputs>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
+ <name>filecontents</name>\r
+ <depth>0</depth>\r
+ <mimeTypes>\r
+ <string>'text/plain'</string>\r
+ </mimeTypes>\r
+ <granularDepth>0</granularDepth>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
+ </outputs>\r
+ <classLoaderSharing>workflow</classLoaderSharing>\r
+ <localDependencies />\r
+ <artifactDependencies />\r
+ <script>BufferedReader getReader (String fileUrl, String encoding) throws IOException {\r
InputStreamReader reader;\r
try {\r
- reader = new FileReader(fileUrl);\r
- }\r
- catch (FileNotFoundException e) {\r
- // try a real URL instead\r
- URL url = new URL(fileUrl);\r
- reader = new InputStreamReader (url.openStream());\r
- }\r
- return new BufferedReader(reader);\r
- }\r
- \r
-BufferedWriter getWriter (String fileUrl) throws IOException {\r
- Writer writer;\r
- try {\r
- writer = new FileWriter(fileUrl);\r
+ if (encoding == null) {\r
+ reader = new FileReader(fileUrl);\r
+ } else {\r
+ reader = new InputStreamReader(new FileInputStream(fileUrl),encoding); \r
+ }\r
}\r
catch (FileNotFoundException e) {\r
// try a real URL instead\r
URL url = new URL(fileUrl);\r
- writer = new OutputStreamWriter (url.openConnection().getOutputStream());\r
+ if (encoding == null) {\r
+ reader = new InputStreamReader (url.openStream());\r
+ } else {\r
+ reader = new InputStreamReader (url.openStream(), encoding);\r
+ }\r
}\r
- return new BufferedWriter(writer);\r
+ return new BufferedReader(reader);\r
}\r
- \r
-String xslFilename = xslFileURL;\r
-String outFilename;\r
-if (outFileURL != void) {\r
- outFilename = outFileURL;\r
-}\r
-\r
-String ext;\r
-if (outputExt != void) {\r
- ext = outputExt;\r
-}\r
-\r
-\r
-\r
-// Create transformer factory\r
-TransformerFactory factory = TransformerFactory.newInstance();\r
-\r
-// Use the factory to create a template containing the xsl file\r
-Templates template = factory.newTemplates(new StreamSource(getReader(xslFilename)));\r
\r
-// Use the template to create a transformer\r
-Transformer xformer = template.newTransformer();\r
-\r
-// Prepare the input and output files\r
-Reader sourceReader = new StringReader(inString);\r
-Source source = new StreamSource(sourceReader);\r
-StringWriter resultStr = new StringWriter();\r
-Result result = new StreamResult(resultStr);\r
\r
-// Apply the xsl file to the source file and write the result to the\r
-// output file\r
-xformer.transform(source, result);\r
\r
-outputStr = resultStr.toString();\r
+StringBuffer sb = new StringBuffer(4000);\r
\r
-if ((outFilename != null) && !outFilename.equals("")) {\r
+if (encoding == void) {\r
+ encoding = null;\r
+}\r
\r
- BufferedWriter out = getWriter(outFilename);\r
+BufferedReader in = getReader(fileurl, encoding);\r
+String str;\r
+String lineEnding = System.getProperty("line.separator");\r
\r
- out.write(outputStr);\r
- out.close();\r
+while ((str = in.readLine()) != null) {\r
+ sb.append(str);\r
+ sb.append(lineEnding);\r
}\r
-sourceReader.close();\r
+in.close();\r
+filecontents = sb.toString();\r
+ \r
</script>\r
<dependencies />\r
- <localworkerName>net.sourceforge.taverna.scuflworkers.xml.XSLTWorker</localworkerName>\r
-</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
- <annotationAssertions>\r
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.HostInstitution">\r
- <text>UserNameHere</text>\r
- </annotationBean>\r
- <date>2012-01-13 17:08:38.768 CET</date>\r
- <creators />\r
- <curationEventList />\r
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
- </annotationAssertions>\r
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></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="">\r
- <maxJobs>1</maxJobs>\r
-</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="">\r
- <backoffFactor>1.0</backoffFactor>\r
- <initialDelay>1000</initialDelay>\r
- <maxDelay>5000</maxDelay>\r
- <maxRetries>0</maxRetries>\r
-</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="inString" depth="0" /><port name="xslFileURL" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>slwOccurrence</processor><port>scientificNameFilter</port></sink><source type="processor"><processor>slw_filter_generator</processor><port>filter</port></source></datalink><datalink><sink type="processor"><processor>slw_filter_generator</processor><port>sciName</port></sink><source type="dataflow"><port>sciName</port></source></datalink><datalink><sink type="processor"><processor>Transform_XML_String</processor><port>inString</port></sink><source type="processor"><processor>slwOccurrence</processor><port>responseBody</port></source></datalink><datalink><sink type="processor"><processor>Transform_XML_String</processor><port>xslFileURL</port></sink><source type="processor"><processor>slwArtDataBank_to_csv_xsl</processor><port>value</port></source></datalink><datalink><sink type="dataflow"><port>csv_output</port></sink><source type="processor"><processor>Transform_XML_String</processor><port>outputStr</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
- <annotationAssertions>\r
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>1c711ced-b003-47e0-bd32-3abd5705da83</identification>\r
- </annotationBean>\r
- <date>2012-03-22 09:26:09.603 CET</date>\r
- <creators />\r
- <curationEventList />\r
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
- </annotationAssertions>\r
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
- <annotationAssertions>\r
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>7d53acd3-c1d9-4ab0-9552-7dd5b3955adf</identification>\r
- </annotationBean>\r
- <date>2012-03-21 17:55:21.599 CET</date>\r
- <creators />\r
- <curationEventList />\r
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
- </annotationAssertions>\r
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
- <annotationAssertions>\r
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>0ae246b3-cb94-4c25-851c-d306d21ad467</identification>\r
- </annotationBean>\r
- <date>2012-03-20 17:37:48.845 CET</date>\r
- <creators />\r
- <curationEventList />\r
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
- </annotationAssertions>\r
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
- <annotationAssertions>\r
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>1db7de4d-ac2e-4ce8-aa12-e50f2535dd51</identification>\r
- </annotationBean>\r
- <date>2012-03-20 17:01:09.185 CET</date>\r
- <creators />\r
- <curationEventList />\r
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
- </annotationAssertions>\r
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
- <annotationAssertions>\r
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>85ba17c1-2e24-49d8-a00b-84acb2a1cf61</identification>\r
- </annotationBean>\r
- <date>2012-03-22 09:26:26.82 CET</date>\r
- <creators />\r
- <curationEventList />\r
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
- </annotationAssertions>\r
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
- <annotationAssertions>\r
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>f4b19cf9-23f9-483a-ad3c-bfd981052f51</identification>\r
- </annotationBean>\r
- <date>2012-03-20 16:53:37.766 CET</date>\r
- <creators />\r
- <curationEventList />\r
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
- </annotationAssertions>\r
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
- <annotationAssertions>\r
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>15151ee4-7e16-4331-acb4-34a735cf3631</identification>\r
- </annotationBean>\r
- <date>2012-03-20 16:54:42.882 CET</date>\r
- <creators />\r
- <curationEventList />\r
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
- </annotationAssertions>\r
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
- <annotationAssertions>\r
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>a6cc5fd4-fe4a-461f-a371-bc5b87bc0513</identification>\r
- </annotationBean>\r
- <date>2012-03-20 16:48:17.526 CET</date>\r
- <creators />\r
- <curationEventList />\r
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
- </annotationAssertions>\r
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
- <annotationAssertions>\r
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>986b70a2-9f54-4b20-80a8-aead9fdd537d</identification>\r
- </annotationBean>\r
- <date>2012-03-21 17:56:36.196 CET</date>\r
- <creators />\r
- <curationEventList />\r
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
- </annotationAssertions>\r
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
- <annotationAssertions>\r
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>1dd9b6f5-24e8-4ea7-875f-4e98f9d135e4</identification>\r
- </annotationBean>\r
- <date>2012-03-21 13:25:11.607 CET</date>\r
- <creators />\r
- <curationEventList />\r
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
- </annotationAssertions>\r
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
- <annotationAssertions>\r
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>c0f096ee-4813-461c-a55a-6d153f3d06fb</identification>\r
- </annotationBean>\r
- <date>2012-03-21 13:13:48.453 CET</date>\r
- <creators />\r
- <curationEventList />\r
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
- </annotationAssertions>\r
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
- <annotationAssertions>\r
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>62e3c568-62d4-405a-85e1-59356b885e27</identification>\r
- </annotationBean>\r
- <date>2012-03-20 17:00:24.471 CET</date>\r
- <creators />\r
- <curationEventList />\r
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
- </annotationAssertions>\r
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
- <annotationAssertions>\r
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>1f00c813-cd52-4caa-8030-892cccb3ab13</identification>\r
- </annotationBean>\r
- <date>2012-03-20 17:39:54.780 CET</date>\r
- <creators />\r
- <curationEventList />\r
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
- </annotationAssertions>\r
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
- <annotationAssertions>\r
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>eafd7ab2-9c8f-4bfc-bac6-31e87a14286c</identification>\r
- </annotationBean>\r
- <date>2012-03-20 16:59:03.163 CET</date>\r
- <creators />\r
- <curationEventList />\r
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
- </annotationAssertions>\r
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
- <annotationAssertions>\r
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>c2694978-40f8-4032-af83-fce1617d630e</identification>\r
- </annotationBean>\r
- <date>2012-03-20 16:44:25.215 CET</date>\r
- <creators />\r
- <curationEventList />\r
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
- </annotationAssertions>\r
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow><dataflow id="adac59f0-935b-498d-b4ef-af755de705ed" role="nested"><name>Workflow202</name><inputPorts><port><name>synRequest</name><depth>1</depth><granularDepth>1</granularDepth><annotations /></port></inputPorts><outputPorts><port><name>synResponse</name><annotations /></port></outputPorts><processors><processor><name>col_synonyms</name><inputPorts><port><name>synRequest</name><depth>0</depth></port></inputPorts><outputPorts><port><name>synResponse</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>dataflow-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.dataflow.DataflowActivity</class><inputMap><map from="synRequest" to="synRequest" /></inputMap><outputMap><map from="synResponse" to="synResponse" /></outputMap><configBean encoding="dataflow"><dataflow ref="d18fe496-419c-4f13-9a5e-9ea550bc3a1e" /></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="">\r
+ <localworkerName>net.sourceforge.taverna.scuflworkers.io.TextFileReader</localworkerName>\r
+</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="">\r
<maxJobs>1</maxJobs>\r
</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="">\r
<backoffFactor>1.0</backoffFactor>\r
<initialDelay>1000</initialDelay>\r
<maxDelay>5000</maxDelay>\r
<maxRetries>0</maxRetries>\r
-</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="synRequest" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>CoL_Copyright</name><inputPorts><port><name>synRequest</name><depth>1</depth></port></inputPorts><outputPorts><port><name>synRequest</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>dataflow-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.dataflow.DataflowActivity</class><inputMap><map from="synRequest" to="synRequest" /></inputMap><outputMap><map from="synRequest" to="synRequest" /></outputMap><configBean encoding="dataflow"><dataflow ref="5563c4db-2322-4ce6-92a1-341f62a3490e" /></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="">\r
+</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="fileurl" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>CreateID</name><inputPorts><port><name>name</name><depth>0</depth></port></inputPorts><outputPorts><port><name>id_param</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="name" to="name" /></inputMap><outputMap><map from="id_param" to="id_param" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">\r
+ <inputs>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ <name>name</name>\r
+ <depth>0</depth>\r
+ <mimeTypes>\r
+ <string>text/plain</string>\r
+ </mimeTypes>\r
+ <handledReferenceSchemes />\r
+ <translatedElementType>java.lang.String</translatedElementType>\r
+ <allowsLiteralValues>true</allowsLiteralValues>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ </inputs>\r
+ <outputs>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
+ <name>id_param</name>\r
+ <depth>0</depth>\r
+ <mimeTypes />\r
+ <granularDepth>0</granularDepth>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
+ </outputs>\r
+ <classLoaderSharing>workflow</classLoaderSharing>\r
+ <localDependencies />\r
+ <artifactDependencies />\r
+ <script>\r
+id_param = "syncheckid=" + name</script>\r
+ <dependencies />\r
+</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></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="">\r
<maxJobs>1</maxJobs>\r
</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="">\r
<backoffFactor>1.0</backoffFactor>\r
<initialDelay>1000</initialDelay>\r
<maxDelay>5000</maxDelay>\r
<maxRetries>0</maxRetries>\r
-</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="synRequest" depth="1" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>col_synonyms</processor><port>synRequest</port></sink><source type="processor"><processor>CoL_Copyright</processor><port>synRequest</port></source></datalink><datalink><sink type="processor"><processor>CoL_Copyright</processor><port>synRequest</port></sink><source type="dataflow"><port>synRequest</port></source></datalink><datalink><sink type="dataflow"><port>synResponse</port></sink><source type="processor"><processor>col_synonyms</processor><port>synResponse</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
- <annotationAssertions>\r
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>84ed7c23-96be-4857-9359-fbdeb4913ee4</identification>\r
- </annotationBean>\r
- <date>2012-04-05 17:14:44.460 CEST</date>\r
- <creators />\r
- <curationEventList />\r
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
- </annotationAssertions>\r
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
- <annotationAssertions>\r
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>0be667cb-a8b6-4a96-b475-8df60635bac4</identification>\r
- </annotationBean>\r
- <date>2012-04-05 17:18:28.866 CEST</date>\r
- <creators />\r
- <curationEventList />\r
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
- </annotationAssertions>\r
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
- <annotationAssertions>\r
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>adac59f0-935b-498d-b4ef-af755de705ed</identification>\r
- </annotationBean>\r
- <date>2012-04-05 17:19:33.342 CEST</date>\r
- <creators />\r
- <curationEventList />\r
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
- </annotationAssertions>\r
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
- <annotationAssertions>\r
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>9e67bd5b-c212-434c-be79-c4e27a006e8e</identification>\r
- </annotationBean>\r
- <date>2012-04-05 17:15:44.133 CEST</date>\r
- <creators />\r
- <curationEventList />\r
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
- </annotationAssertions>\r
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow><dataflow id="370ad085-8ced-4374-ba09-ebf615d24880" role="nested"><name>Workflow32</name><inputPorts><port><name>sciName</name><depth>0</depth><granularDepth>0</granularDepth><annotations /></port></inputPorts><outputPorts><port><name>csv_output</name><annotations /></port></outputPorts><processors><processor><name>Merge_String_List_to_a_String</name><inputPorts><port><name>seperator</name><depth>0</depth></port><port><name>stringlist</name><depth>1</depth></port></inputPorts><outputPorts><port><name>concatenated</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="seperator" to="seperator" /><map from="stringlist" to="stringlist" /></inputMap><outputMap><map from="concatenated" to="concatenated" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">\r
+</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="name" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Transform_XML_2</name><inputPorts><port><name>xslFileURL</name><depth>0</depth></port><port><name>inString</name><depth>0</depth></port></inputPorts><outputPorts><port><name>outputStr</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="inString" to="inString" /><map from="xslFileURL" to="xslFileURL" /></inputMap><outputMap><map from="outputStr" to="outputStr" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">\r
<inputs>\r
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
- <name>stringlist</name>\r
- <depth>1</depth>\r
+ <name>xslFileURL</name>\r
+ <depth>0</depth>\r
<mimeTypes>\r
- <string>l('text/plain')</string>\r
+ <string>'text/plain'</string>\r
</mimeTypes>\r
<handledReferenceSchemes />\r
<translatedElementType>java.lang.String</translatedElementType>\r
<allowsLiteralValues>true</allowsLiteralValues>\r
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
- <name>seperator</name>\r
+ <name>outFileURL</name>\r
<depth>0</depth>\r
<mimeTypes>\r
<string>'text/plain'</string>\r
<translatedElementType>java.lang.String</translatedElementType>\r
<allowsLiteralValues>true</allowsLiteralValues>\r
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
- </inputs>\r
- <outputs>\r
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
- <name>concatenated</name>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ <name>inString</name>\r
+ <depth>0</depth>\r
+ <mimeTypes>\r
+ <string>'text/plain'</string>\r
+ </mimeTypes>\r
+ <handledReferenceSchemes />\r
+ <translatedElementType>java.lang.String</translatedElementType>\r
+ <allowsLiteralValues>true</allowsLiteralValues>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ <name>outputExt</name>\r
<depth>0</depth>\r
<mimeTypes>\r
<string>'text/plain'</string>\r
</mimeTypes>\r
+ <handledReferenceSchemes />\r
+ <translatedElementType>java.lang.String</translatedElementType>\r
+ <allowsLiteralValues>true</allowsLiteralValues>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ </inputs>\r
+ <outputs>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
+ <name>outputStr</name>\r
+ <depth>0</depth>\r
+ <mimeTypes />\r
<granularDepth>0</granularDepth>\r
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
</outputs>\r
<classLoaderSharing>workflow</classLoaderSharing>\r
<localDependencies />\r
<artifactDependencies />\r
- <script>String seperatorString = "\n";\r
-if (seperator != void) {\r
- seperatorString = seperator;\r
-}\r
-StringBuffer sb = new StringBuffer();\r
-for (Iterator i = stringlist.iterator(); i.hasNext();) {\r
- String item = (String) i.next();\r
- sb.append(item);\r
- if (i.hasNext()) {\r
- sb.append(seperatorString);\r
+ <script>import java.io.BufferedReader;\r
+import java.io.BufferedWriter;\r
+import java.io.FileInputStream;\r
+import java.io.FileNotFoundException;\r
+import java.io.FileReader;\r
+import java.io.FileWriter;\r
+import java.io.IOException;\r
+import java.io.InputStreamReader;\r
+import java.io.OutputStreamWriter;\r
+import java.io.StringWriter;\r
+import java.io.Writer;\r
+import java.net.URL;\r
+import java.util.HashMap;\r
+import java.util.Map;\r
+\r
+import javax.xml.transform.Result;\r
+import javax.xml.transform.Source;\r
+import javax.xml.transform.SourceLocator;\r
+import javax.xml.transform.Templates;\r
+import javax.xml.transform.Transformer;\r
+import javax.xml.transform.TransformerConfigurationException;\r
+import javax.xml.transform.TransformerException;\r
+import javax.xml.transform.TransformerFactory;\r
+import javax.xml.transform.stream.StreamResult;\r
+import javax.xml.transform.stream.StreamSource;\r
+\r
+BufferedReader getReader (String fileUrl) throws IOException {\r
+ InputStreamReader reader;\r
+ try {\r
+ reader = new FileReader(fileUrl);\r
+ }\r
+ catch (FileNotFoundException e) {\r
+ // try a real URL instead\r
+ URL url = new URL(fileUrl);\r
+ reader = new InputStreamReader (url.openStream());\r
+ }\r
+ return new BufferedReader(reader);\r
}\r
-}\r
-concatenated = sb.toString();\r
+ \r
+BufferedWriter getWriter (String fileUrl) throws IOException {\r
+ Writer writer;\r
+ try {\r
+ writer = new FileWriter(fileUrl);\r
+ }\r
+ catch (FileNotFoundException e) {\r
+ // try a real URL instead\r
+ URL url = new URL(fileUrl);\r
+ writer = new OutputStreamWriter (url.openConnection().getOutputStream());\r
+ }\r
+ return new BufferedWriter(writer);\r
+ }\r
+ \r
+String xslFilename = xslFileURL;\r
+\r
+\r
+\r
+// Create transformer factory\r
+TransformerFactory factory = TransformerFactory.newInstance();\r
+\r
+// Use the factory to create a template containing the xsl file\r
+Templates template = factory.newTemplates(new StreamSource(getReader(xslFilename)));\r
+\r
+// Use the template to create a transformer\r
+Transformer xformer = template.newTransformer();\r
+\r
+// Prepare the input and output files\r
+Reader sourceReader = new StringReader(inString);\r
+Source source = new StreamSource(sourceReader);\r
+StringWriter resultStr = new StringWriter();\r
+Result result = new StreamResult(resultStr);\r
+\r
+// Apply the xsl file to the source file and write the result to the\r
+// output file\r
+xformer.transform(source, result);\r
+outputStr = resultStr.toString();\r
+sourceReader.close();\r
</script>\r
<dependencies />\r
- <localworkerName>org.embl.ebi.escience.scuflworkers.java.StringListMerge</localworkerName>\r
-</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="">\r
- <maxJobs>1</maxJobs>\r
-</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="">\r
- <backoffFactor>1.0</backoffFactor>\r
- <initialDelay>1000</initialDelay>\r
- <maxDelay>5000</maxDelay>\r
- <maxRetries>0</maxRetries>\r
-</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="seperator" depth="0" /><port name="stringlist" depth="1" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>no_separator</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="">\r
- <value />\r
-</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="">\r
+ <localworkerName>net.sourceforge.taverna.scuflworkers.xml.XSLTWorker</localworkerName>\r
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.HostInstitution">\r
+ <text>UserNameHere</text>\r
+ </annotationBean>\r
+ <date>2012-01-24 15:55:03.158 CET</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></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="">\r
<maxJobs>1</maxJobs>\r
</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="">\r
<backoffFactor>1.0</backoffFactor>\r
<initialDelay>1000</initialDelay>\r
<maxDelay>5000</maxDelay>\r
<maxRetries>0</maxRetries>\r
-</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>gbif_occurrence_max1000</name><inputPorts><port><name>sciName</name><depth>0</depth></port><port><name>next</name><depth>0</depth></port></inputPorts><outputPorts><port><name>next</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>max1000_csv_output</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>dataflow-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.dataflow.DataflowActivity</class><inputMap><map from="next" to="next" /><map from="sciName" to="sciName" /></inputMap><outputMap><map from="next" to="next" /><map from="max1000_csv_output" to="max1000_csv_output" /></outputMap><configBean encoding="dataflow"><dataflow ref="124b440e-f7ef-445f-901b-b3d04ca3e2a7" /></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="">\r
- <maxJobs>1</maxJobs>\r
-</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.Loop</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.LoopConfiguration xmlns="">\r
- <conditionXML><activity xmlns="http://taverna.sf.net/2008/xml/t2flow"><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap /><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
\r
- <inputs>
\r
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
\r
- <name>next</name>
\r
- <depth>0</depth>
\r
- <mimeTypes class="java.util.Collections$EmptyList" reference="../../net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean/mimeTypes" />
\r
- <handledReferenceSchemes class="java.util.Collections$EmptyList" reference="../../net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean/mimeTypes" />
\r
- <translatedElementType>java.lang.String</translatedElementType>
\r
- <allowsLiteralValues>true</allowsLiteralValues>
\r
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
\r
- </inputs>
\r
- <outputs>
\r
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
\r
- <name>loop</name>
\r
- <depth>0</depth>
\r
- <mimeTypes />
\r
- <granularDepth>0</granularDepth>
\r
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
\r
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
\r
- <name>next</name>
\r
- <depth>0</depth>
\r
- <mimeTypes />
\r
- <granularDepth>0</granularDepth>
\r
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
\r
- </outputs>
\r
- <classLoaderSharing>workflow</classLoaderSharing>
\r
- <localDependencies />
\r
- <artifactDependencies />
\r
- <script>loop = "" + ! next.matches("");</script>
\r
- <dependencies />
\r
-</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations /></activity></conditionXML>\r
- <runFirst>true</runFirst>\r
- <properties>\r
- <property name="compareValue" value="" />\r
- <property name="comparePort" value="next" />\r
- <property name="delay" value="0.5" />\r
- <property name="comparison" value="custom" />\r
- <property name="isFeedBack" value="true" />\r
- </properties>\r
-</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.LoopConfiguration></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="">\r
- <backoffFactor>1.0</backoffFactor>\r
- <initialDelay>1000</initialDelay>\r
- <maxDelay>5000</maxDelay>\r
- <maxRetries>0</maxRetries>\r
-</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="sciName" depth="0" /><port name="next" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>next_value</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.3</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="">\r
- <value>0</value>\r
+</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="xslFileURL" depth="0" /><port name="inString" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>synReq_to_colReq_xsl</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="">\r
+ <value>http://www.myexperiment.org/files/690/download/synreq_to_colreq.xsl</value>\r
</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="">\r
<maxJobs>1</maxJobs>\r
</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="">\r
<initialDelay>1000</initialDelay>\r
<maxDelay>5000</maxDelay>\r
<maxRetries>0</maxRetries>\r
-</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>sink</name><inputPorts><port><name>inputlist</name><depth>1</depth></port></inputPorts><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="inputlist" to="inputlist" /></inputMap><outputMap /><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">\r
+</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>FirstElement_From_XPath</name><inputPorts><port><name>xmltext</name><depth>0</depth></port><port><name>xpath</name><depth>0</depth></port></inputPorts><outputPorts><port><name>nodeVal</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="xmltext" to="xmltext" /><map from="xpath" to="xpath" /></inputMap><outputMap><map from="nodeVal" to="nodeVal" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">\r
<inputs>\r
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
- <name>inputlist</name>\r
- <depth>1</depth>\r
+ <name>xpath</name>\r
+ <depth>0</depth>\r
+ <mimeTypes>\r
+ <string>text/plain</string>\r
+ </mimeTypes>\r
+ <handledReferenceSchemes />\r
+ <translatedElementType>java.lang.String</translatedElementType>\r
+ <allowsLiteralValues>true</allowsLiteralValues>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ <name>xmltext</name>\r
+ <depth>0</depth>\r
<mimeTypes>\r
- <string>l('')</string>\r
+ <string>text/plain</string>\r
</mimeTypes>\r
<handledReferenceSchemes />\r
- <translatedElementType>[B</translatedElementType>\r
+ <translatedElementType>java.lang.String</translatedElementType>\r
<allowsLiteralValues>true</allowsLiteralValues>\r
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
</inputs>\r
- <outputs />\r
+ <outputs>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
+ <name>nodeVal</name>\r
+ <depth>0</depth>\r
+ <mimeTypes />\r
+ <granularDepth>0</granularDepth>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
+ </outputs>\r
<classLoaderSharing>workflow</classLoaderSharing>\r
<localDependencies />\r
<artifactDependencies />\r
- <script>outputlist = inputlist;</script>\r
+ <script>import org.dom4j.Document;\r
+import org.dom4j.Node;\r
+import org.dom4j.io.SAXReader;\r
+\r
+SAXReader reader = new SAXReader(false);\r
+reader.setIncludeInternalDTDDeclarations(false);\r
+reader.setIncludeExternalDTDDeclarations(false);\r
+\r
+Document document = reader.read(new StringReader(xmltext));\r
+List nodelist = document.selectNodes(xpath);\r
+\r
+// Process the elements in the nodelist\r
+ArrayList outputList = new ArrayList();\r
+ArrayList outputXmlList = new ArrayList();\r
+\r
+String val = "";\r
+String xmlVal = "";\r
+for (Iterator iter = nodelist.iterator(); iter.hasNext();) {\r
+ Node element = (Node) iter.next();\r
+ xmlVal = element.asXML();\r
+ val = element.getStringValue();\r
+ if (val != null && !val.equals("")) {\r
+ outputList.add(val);\r
+ outputXmlList.add(xmlVal);\r
+ }\r
+break;\r
+}\r
+\r
+//List nodelist=outputList;\r
+nodeVal = val;\r
+</script>\r
<dependencies />\r
- <localworkerName>org.embl.ebi.escience.scuflworkers.java.EchoList</localworkerName>\r
-</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></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="">\r
+ <maxJobs>1</maxJobs>\r
+</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="">\r
+ <backoffFactor>1.0</backoffFactor>\r
+ <initialDelay>1000</initialDelay>\r
+ <maxDelay>5000</maxDelay>\r
+ <maxRetries>0</maxRetries>\r
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<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.HostInstitution">\r
- <text>UserNameHere</text>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>26d4175a-6fd8-4d00-a553-882be923f88c</identification>\r
</annotationBean>\r
- <date>2011-12-05 17:26:34.170 CET</date>\r
+ <date>2012-05-31 17:10:13.753 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
</annotationAssertions>\r
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- <backoffFactor>1.0</backoffFactor>\r
- <initialDelay>1000</initialDelay>\r
- <maxDelay>5000</maxDelay>\r
- <maxRetries>0</maxRetries>\r
-</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="inputlist" depth="1" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>Merge_String_List_to_a_String</processor><port>seperator</port></sink><source type="processor"><processor>no_separator</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>Merge_String_List_to_a_String</processor><port>stringlist</port></sink><source type="processor"><processor>gbif_occurrence_max1000</processor><port>max1000_csv_output</port></source></datalink><datalink><sink type="processor"><processor>gbif_occurrence_max1000</processor><port>sciName</port></sink><source type="dataflow"><port>sciName</port></source></datalink><datalink><sink type="processor"><processor>gbif_occurrence_max1000</processor><port>next</port></sink><source type="processor"><processor>next_value</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>sink</processor><port>inputlist</port></sink><source type="processor"><processor>gbif_occurrence_max1000</processor><port>next</port></source></datalink><datalink><sink type="dataflow"><port>csv_output</port></sink><source type="processor"><processor>Merge_String_List_to_a_String</processor><port>concatenated</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>feaf6e99-716b-4cc9-81b0-7255ea5a38f7</identification>\r
+ <identification>3a9f1b0b-5d5a-45a0-b134-d5dafc51ea40</identification>\r
</annotationBean>\r
- <date>2012-01-02 16:03:20.221 CET</date>\r
+ <date>2012-01-24 14:17:11.136 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>c818b2a9-90a8-4fc2-9c42-8066af346cba</identification>\r
+ <identification>f88ebd38-9ab7-4f03-ab29-75fe55ee240a</identification>\r
</annotationBean>\r
- <date>2012-01-31 15:47:04.807 CET</date>\r
+ <date>2012-02-14 17:10:41.962 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>7be40bed-1839-4117-81ff-49391e0fe35a</identification>\r
+ <identification>13e365c6-a1f5-4e3a-99a4-d39a147367c7</identification>\r
</annotationBean>\r
- <date>2012-01-02 17:52:39.889 CET</date>\r
+ <date>2012-01-23 15:39:42.940 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>98429027-b6ab-4c7a-8952-f92ce82af604</identification>\r
+ <identification>1bae1054-0ea5-436e-bc01-c2c8838ba066</identification>\r
</annotationBean>\r
- <date>2012-01-13 16:44:12.623 CET</date>\r
+ <date>2012-01-23 15:47:21.97 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>eeab83cc-69df-4a18-a6ad-e33a5cc51f35</identification>\r
+ <identification>2023d475-cce4-4812-bf43-fffa5fecf9cb</identification>\r
</annotationBean>\r
- <date>2012-01-13 16:59:53.791 CET</date>\r
+ <date>2012-02-14 13:54:46.413 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>df805bf7-d2c5-436b-a770-ba2258ed78c5</identification>\r
+ <identification>8c0fc6dc-bc1c-4cff-bd47-99e6a3a0fb62</identification>\r
</annotationBean>\r
- <date>2012-01-31 16:39:08.415 CET</date>\r
+ <date>2012-06-01 11:31:19.315 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>69821203-d769-45ce-a3bb-145a9964679f</identification>\r
+ <identification>3ab53f67-d243-4e40-8627-83028ef002df</identification>\r
</annotationBean>\r
- <date>2012-01-02 15:04:12.378 CET</date>\r
+ <date>2012-02-10 12:44:20.333 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>97a86075-f1f7-4e46-a383-cec4b7b16ec4</identification>\r
+ <identification>4f5b0cf0-f3e4-4a48-b3bc-4d3d6770a4c3</identification>\r
</annotationBean>\r
- <date>2012-01-31 16:24:57.958 CET</date>\r
+ <date>2012-01-25 17:19:33.836 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>4f8dd224-cc83-4af5-bbd2-dedfd09b43fe</identification>\r
+ <identification>d18fe496-419c-4f13-9a5e-9ea550bc3a1e</identification>\r
</annotationBean>\r
- <date>2012-01-02 17:14:37.644 CET</date>\r
+ <date>2012-02-23 17:14:42.676 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>8a58b613-ac30-4ec1-9877-8221a6654ff4</identification>\r
+ <identification>850e16e9-453e-416e-a7b1-ced1da71519f</identification>\r
</annotationBean>\r
- <date>2012-01-03 12:48:44.529 CET</date>\r
+ <date>2012-01-23 15:12:06.888 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>f41b5d1f-a3a6-4fcb-a52a-748150c35471</identification>\r
+ <identification>654ddd4b-3aee-4576-8bf7-939c9d470b9d</identification>\r
</annotationBean>\r
- <date>2012-02-07 17:22:31.525 CET</date>\r
+ <date>2012-01-23 15:14:53.241 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>96030fe2-efe7-4c53-a562-a358b87d4770</identification>\r
+ <identification>d004275f-4245-4a1c-b83a-ab166234a56d</identification>\r
</annotationBean>\r
- <date>2012-04-04 11:55:49.744 CEST</date>\r
+ <date>2012-06-01 11:33:15.588 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>a87dd75f-af3c-44ad-9718-b7125a22089f</identification>\r
+ <identification>e376fad1-bf30-4908-b97b-894900c25efa</identification>\r
</annotationBean>\r
- <date>2012-01-02 17:21:03.648 CET</date>\r
+ <date>2012-01-23 15:03:45.120 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>8dc4d420-1edf-473f-b111-d6510f6f026e</identification>\r
+ <identification>eb74b582-81c7-4049-8ab5-43b3ec96b920</identification>\r
</annotationBean>\r
- <date>2012-01-02 17:47:36.491 CET</date>\r
+ <date>2012-01-24 14:32:42.660 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>53f8a5ae-069d-4470-8da0-2df125dc5ec8</identification>\r
+ <identification>a58dbeb8-48e1-4b31-a1ea-57761cb4f712</identification>\r
</annotationBean>\r
- <date>2012-01-02 17:50:56.83 CET</date>\r
+ <date>2012-01-25 17:22:12.481 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>5dbd6255-5adc-46fb-a4c6-ed77d56af267</identification>\r
+ <identification>9f2c7ca2-e117-46e8-8d95-d5a9f8219570</identification>\r
</annotationBean>\r
- <date>2012-01-02 17:16:27.428 CET</date>\r
+ <date>2012-01-23 14:57:41.971 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>818abfc6-bd93-4bbd-9c36-68b73b0af681</identification>\r
+ <identification>56c300cd-9209-44ef-9874-3efa78d77df3</identification>\r
</annotationBean>\r
- <date>2012-02-08 15:37:32.562 CET</date>\r
+ <date>2012-02-10 12:41:11.317 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>7a284b5d-ac86-416b-a639-27e9dc335bd6</identification>\r
+ <identification>61896bb4-e33f-49fa-8792-11bd2c8e3efe</identification>\r
</annotationBean>\r
- <date>2012-02-07 17:40:29.204 CET</date>\r
+ <date>2012-06-01 11:43:43.712 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>b123cffa-dcf7-4e76-85e6-0dc999f97104</identification>\r
+ <identification>7d54ce42-e540-4c40-b7f1-2209c6638804</identification>\r
</annotationBean>\r
- <date>2012-02-07 18:09:06.414 CET</date>\r
+ <date>2012-02-10 12:40:38.13 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>54d71067-a78a-4e3b-a54f-d47f75bd2adf</identification>\r
+ <identification>a0866021-3699-4383-b41c-6b8d0866305e</identification>\r
</annotationBean>\r
- <date>2012-01-31 16:10:34.267 CET</date>\r
+ <date>2012-01-23 15:01:00.405 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>7cbd63e4-d73d-42d9-9133-4f359b06efb5</identification>\r
+ <identification>c07ee8d5-7314-45dc-a7b9-f136f9762905</identification>\r
</annotationBean>\r
- <date>2012-01-02 14:51:19.40 CET</date>\r
+ <date>2012-01-24 14:25:37.176 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>3322b5a3-1530-4824-9300-ba6a6b18b7f1</identification>\r
+ <identification>20cf832b-88c5-4214-ac8b-cd46f8159b7d</identification>\r
</annotationBean>\r
- <date>2012-01-31 16:27:20.693 CET</date>\r
+ <date>2012-01-23 15:08:03.570 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>b5b6d740-cc89-4450-8e5b-44fcac2bfee2</identification>\r
+ <identification>6ad09a10-0f7c-43c2-b807-ebf6c0fd776e</identification>\r
</annotationBean>\r
- <date>2012-01-02 15:00:31.584 CET</date>\r
+ <date>2012-01-23 15:14:07.562 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>8218cf20-6aa4-4a85-a62a-da0b401991cd</identification>\r
+ <identification>337a348a-0d6e-4969-bea0-0778605f5574</identification>\r
</annotationBean>\r
- <date>2012-02-09 17:39:17.418 CET</date>\r
+ <date>2012-06-01 11:00:50.619 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>9b1c8f07-a857-4d04-b260-b13bcf331662</identification>\r
+ <identification>b7e9c698-3b8f-418e-b732-c02b07b2d8dc</identification>\r
</annotationBean>\r
- <date>2012-01-31 16:03:53.673 CET</date>\r
+ <date>2012-02-14 13:50:23.444 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>eb452b59-dcaf-4db0-8f72-244455633870</identification>\r
+ <identification>d6cabd36-4763-4a7c-bd19-afb1547696b9</identification>\r
</annotationBean>\r
- <date>2012-01-13 15:40:37.647 CET</date>\r
+ <date>2012-01-25 16:08:29.517 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>2764b0d8-8242-40ea-b0a3-ddf550e8dc59</identification>\r
+ <identification>0f6b20ae-e472-4fbd-8ce2-a9671157fb01</identification>\r
</annotationBean>\r
- <date>2012-01-02 16:21:21.874 CET</date>\r
+ <date>2012-05-31 17:26:20.364 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>62f4cd4d-508e-409c-8e06-3fef4020fa97</identification>\r
+ <identification>7e933e2c-4286-4303-a56e-4cea981e3195</identification>\r
</annotationBean>\r
- <date>2012-02-07 17:25:22.963 CET</date>\r
+ <date>2012-01-27 15:45:49.310 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>d044d916-0adb-4065-b39f-8357372e42cc</identification>\r
+ <identification>2bcaf5f3-a086-4ab8-bfe6-4e7640a6ce45</identification>\r
</annotationBean>\r
- <date>2012-01-13 15:44:17.623 CET</date>\r
+ <date>2012-01-23 15:10:26.350 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>dedef59b-8e8b-4e4d-8903-5f8c54422215</identification>\r
+ <identification>08117860-fcd2-4342-b938-efe94165feb0</identification>\r
</annotationBean>\r
- <date>2012-01-02 16:04:37.936 CET</date>\r
+ <date>2012-01-24 13:53:17.262 CET</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>54039e3d-8d1c-4a40-a818-9cd8bcbf64b7</identification>\r
+ </annotationBean>\r
+ <date>2012-01-23 15:05:53.745 CET</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>907a23a5-7ea9-4901-8103-68bb6a45044e</identification>\r
+ </annotationBean>\r
+ <date>2012-02-13 13:36:37.936 CET</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>3f6fdae5-1039-4d5d-b016-09a7d0b7808f</identification>\r
+ </annotationBean>\r
+ <date>2012-02-10 16:33:33.703 CET</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>65b317eb-1a04-45d0-afc4-196506a33934</identification>\r
+ </annotationBean>\r
+ <date>2012-02-13 13:36:08.651 CET</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>c273ba6e-577c-4078-a967-8bc0a6ce0ccb</identification>\r
+ </annotationBean>\r
+ <date>2012-02-23 16:20:00.241 CET</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>7614477b-fc8e-4262-be98-03a72347ecd1</identification>\r
+ </annotationBean>\r
+ <date>2012-01-24 14:02:21.343 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
</annotationAssertions>\r
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow><dataflow id="b8467b4d-a015-44b2-aba8-437c606b0d3c" role="nested"><name>Workflow35</name><inputPorts><port><name>datasetID</name><depth>0</depth><granularDepth>0</granularDepth><annotations /></port><port><name>synReq</name><depth>0</depth><granularDepth>0</granularDepth><annotations /></port></inputPorts><outputPorts><port><name>response</name><annotations /></port></outputPorts><processors><processor><name>GBIF_Name_Search</name><inputPorts><port><name>datasetID</name><depth>0</depth></port><port><name>sciName</name><depth>0</depth></port></inputPorts><outputPorts><port><name>responseBody</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>rest-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.rest.RESTActivity</class><inputMap><map from="datasetID" to="datasetID" /><map from="sciName" to="sciName" /></inputMap><outputMap><map from="responseBody" to="responseBody" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean xmlns="">\r
+ <httpMethod>GET</httpMethod>\r
+ <urlSignature>http://ecat-dev.gbif.org/ws/usage/?rkey={datasetID}&q={sciName}&pagesize=100</urlSignature>\r
+ <acceptsHeaderValue>application/json</acceptsHeaderValue>\r
+ <contentTypeForUpdates>application/xml</contentTypeForUpdates>\r
+ <outgoingDataFormat>String</outgoingDataFormat>\r
+ <sendHTTPExpectRequestHeader>false</sendHTTPExpectRequestHeader>\r
+ <showRedirectionOutputPort>false</showRedirectionOutputPort>\r
+ <escapeParameters>true</escapeParameters>\r
+ <otherHTTPHeaders />\r
+ <activityInputs>\r
+ <entry>\r
+ <string>datasetID</string>\r
+ <java-class>java.lang.String</java-class>\r
+ </entry>\r
+ <entry>\r
+ <string>sciName</string>\r
+ <java-class>java.lang.String</java-class>\r
+ </entry>\r
+ </activityInputs>\r
+</net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean></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="">\r
+ <maxJobs>1</maxJobs>\r
+</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="">\r
+ <backoffFactor>1.0</backoffFactor>\r
+ <initialDelay>1000</initialDelay>\r
+ <maxDelay>5000</maxDelay>\r
+ <maxRetries>0</maxRetries>\r
+</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="datasetID" depth="0" /><port name="sciName" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>gbifNameSearchParser</name><inputPorts><port><name>gbifNameSerachJSON</name><depth>0</depth></port></inputPorts><outputPorts><port><name>taxonIDList</name><depth>1</depth><granularDepth>1</granularDepth></port><port><name>emptyTaxonIDList</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="gbifNameSerachJSON" to="gbifNameSerachJSON" /></inputMap><outputMap><map from="taxonIDList" to="taxonIDList" /><map from="emptyTaxonIDList" to="emptyTaxonIDList" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">\r
+ <inputs>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ <name>gbifNameSerachJSON</name>\r
+ <depth>0</depth>\r
+ <mimeTypes>\r
+ <string>text/plain</string>\r
+ </mimeTypes>\r
+ <handledReferenceSchemes />\r
+ <translatedElementType>java.lang.String</translatedElementType>\r
+ <allowsLiteralValues>true</allowsLiteralValues>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ </inputs>\r
+ <outputs>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
+ <name>taxonIDList</name>\r
+ <depth>1</depth>\r
+ <mimeTypes />\r
+ <granularDepth>1</granularDepth>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
+ <name>emptyTaxonIDList</name>\r
+ <depth>1</depth>\r
+ <mimeTypes />\r
+ <granularDepth>1</granularDepth>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
+ </outputs>\r
+ <classLoaderSharing>workflow</classLoaderSharing>\r
+ <localDependencies>\r
+ <string>json-simple-1.1.1.jar</string>\r
+ </localDependencies>\r
+ <artifactDependencies />\r
+ <script>import java.util.Iterator;\r
+import org.json.simple.JSONArray;\r
+import org.json.simple.JSONObject;\r
+import org.json.simple.parser.JSONParser;\r
+\r
+String taxonID = null;\r
+taxonIDList = new ArrayList();\r
+emptyTaxonIDList = new ArrayList();\r
+\r
+gbifChkList = new ArrayList();\r
+JSONParser parser = new JSONParser();\r
+\r
+Object obj = parser.parse(gbifNameSerachJSON);\r
+JSONObject jsonObject = (JSONObject) obj;\r
+ \r
+JSONArray data = (JSONArray) jsonObject.get("data");\r
+Iterator iterator = data.iterator();\r
+while (iterator.hasNext()) {\r
+ JSONObject dataObject= (JSONObject)iterator.next();\r
+ Boolean isSynonym = (Boolean)dataObject.get("isSynonym");\r
+ String taxonomicStatus = (String)dataObject.get("taxonomicStatus");\r
+ String rank = (String)dataObject.get("rank");\r
+ if(rank.equals("species")) { \r
+ if(taxonomicStatus.equals("Accepted") && !isSynonym.booleanValue()) {\r
+ Number taxonIDNumber = (Number)dataObject.get("taxonID");\r
+ taxonID = String.valueOf(taxonIDNumber);\r
+ \r
+ }\r
+ if(taxonomicStatus.equals("Synonym") && isSynonym.booleanValue()) {\r
+ Number taxonIDNumber = (Number)dataObject.get("higherTaxonID");\r
+ taxonID = String.valueOf(taxonIDNumber);\r
+ \r
+ }\r
+ break;\r
+ }\r
+}\r
+if(taxonID != null) {\r
+ taxonIDList.add(taxonID); \r
+} else {\r
+ emptyTaxonIDList.add(""); \r
+}\r
+\r
+</script>\r
+ <dependencies />\r
+</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></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="">\r
+ <maxJobs>1</maxJobs>\r
+</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="">\r
+ <backoffFactor>1.0</backoffFactor>\r
+ <initialDelay>1000</initialDelay>\r
+ <maxDelay>5000</maxDelay>\r
+ <maxRetries>0</maxRetries>\r
+</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="gbifNameSerachJSON" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>synReq_to_GBIFReq.xsl</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="">\r
+ <value>http://ww2.bgbm.org/temp/biovel/synreq_to_gbifreq.xsl</value>\r
+</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="">\r
+ <maxJobs>1</maxJobs>\r
+</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="">\r
+ <backoffFactor>1.0</backoffFactor>\r
+ <initialDelay>1000</initialDelay>\r
+ <maxDelay>5000</maxDelay>\r
+ <maxRetries>0</maxRetries>\r
+</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>Transform_StringXML</name><inputPorts><port><name>inString</name><depth>0</depth></port><port><name>xslFileURL</name><depth>0</depth></port></inputPorts><outputPorts><port><name>outputStr</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="inString" to="inString" /><map from="xslFileURL" to="xslFileURL" /></inputMap><outputMap><map from="outputStr" to="outputStr" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">\r
+ <inputs>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ <name>xslFileURL</name>\r
+ <depth>0</depth>\r
+ <mimeTypes>\r
+ <string>'text/plain'</string>\r
+ </mimeTypes>\r
+ <handledReferenceSchemes />\r
+ <translatedElementType>java.lang.String</translatedElementType>\r
+ <allowsLiteralValues>true</allowsLiteralValues>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ <name>outFileURL</name>\r
+ <depth>0</depth>\r
+ <mimeTypes>\r
+ <string>'text/plain'</string>\r
+ </mimeTypes>\r
+ <handledReferenceSchemes />\r
+ <translatedElementType>java.lang.String</translatedElementType>\r
+ <allowsLiteralValues>true</allowsLiteralValues>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ <name>inString</name>\r
+ <depth>0</depth>\r
+ <mimeTypes>\r
+ <string>'text/plain'</string>\r
+ </mimeTypes>\r
+ <handledReferenceSchemes />\r
+ <translatedElementType>java.lang.String</translatedElementType>\r
+ <allowsLiteralValues>true</allowsLiteralValues>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ <name>outputExt</name>\r
+ <depth>0</depth>\r
+ <mimeTypes>\r
+ <string>'text/plain'</string>\r
+ </mimeTypes>\r
+ <handledReferenceSchemes />\r
+ <translatedElementType>java.lang.String</translatedElementType>\r
+ <allowsLiteralValues>true</allowsLiteralValues>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ </inputs>\r
+ <outputs>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
+ <name>outputStr</name>\r
+ <depth>0</depth>\r
+ <mimeTypes />\r
+ <granularDepth>0</granularDepth>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
+ </outputs>\r
+ <classLoaderSharing>workflow</classLoaderSharing>\r
+ <localDependencies />\r
+ <artifactDependencies />\r
+ <script>import java.io.BufferedReader;\r
+import java.io.BufferedWriter;\r
+import java.io.FileInputStream;\r
+import java.io.FileNotFoundException;\r
+import java.io.FileReader;\r
+import java.io.FileWriter;\r
+import java.io.IOException;\r
+import java.io.InputStreamReader;\r
+import java.io.OutputStreamWriter;\r
+import java.io.StringWriter;\r
+import java.io.Writer;\r
+import java.net.URL;\r
+import java.util.HashMap;\r
+import java.util.Map;\r
+\r
+import javax.xml.transform.Result;\r
+import javax.xml.transform.Source;\r
+import javax.xml.transform.SourceLocator;\r
+import javax.xml.transform.Templates;\r
+import javax.xml.transform.Transformer;\r
+import javax.xml.transform.TransformerConfigurationException;\r
+import javax.xml.transform.TransformerException;\r
+import javax.xml.transform.TransformerFactory;\r
+import javax.xml.transform.stream.StreamResult;\r
+import javax.xml.transform.stream.StreamSource;\r
+\r
+BufferedReader getReader (String fileUrl) throws IOException {\r
+ InputStreamReader reader;\r
+ try {\r
+ reader = new FileReader(fileUrl);\r
+ }\r
+ catch (FileNotFoundException e) {\r
+ // try a real URL instead\r
+ URL url = new URL(fileUrl);\r
+ reader = new InputStreamReader (url.openStream());\r
+ }\r
+ return new BufferedReader(reader);\r
+ }\r
+ \r
+BufferedWriter getWriter (String fileUrl) throws IOException {\r
+ Writer writer;\r
+ try {\r
+ writer = new FileWriter(fileUrl);\r
+ }\r
+ catch (FileNotFoundException e) {\r
+ // try a real URL instead\r
+ URL url = new URL(fileUrl);\r
+ writer = new OutputStreamWriter (url.openConnection().getOutputStream());\r
+ }\r
+ return new BufferedWriter(writer);\r
+ }\r
+ \r
+String xslFilename = xslFileURL;\r
+\r
+\r
+\r
+// Create transformer factory\r
+TransformerFactory factory = TransformerFactory.newInstance();\r
+\r
+// Use the factory to create a template containing the xsl file\r
+Templates template = factory.newTemplates(new StreamSource(getReader(xslFilename)));\r
+\r
+// Use the template to create a transformer\r
+Transformer xformer = template.newTransformer();\r
+\r
+// Prepare the input and output files\r
+Reader sourceReader = new StringReader(inString);\r
+Source source = new StreamSource(sourceReader);\r
+StringWriter resultStr = new StringWriter();\r
+Result result = new StreamResult(resultStr);\r
+\r
+// Apply the xsl file to the source file and write the result to the\r
+// output file\r
+xformer.transform(source, result);\r
+outputStr = resultStr.toString();\r
+sourceReader.close();\r
+</script>\r
+ <dependencies />\r
+ <localworkerName>net.sourceforge.taverna.scuflworkers.xml.XSLTWorker</localworkerName>\r
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>b87d4830-e4c0-4665-972b-b60353b71873</identification>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.HostInstitution">\r
+ <text>UserNameHere</text>\r
</annotationBean>\r
- <date>2012-01-02 16:29:06.484 CET</date>\r
+ <date>2012-01-24 15:55:03.158 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
</annotationAssertions>\r
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></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="">\r
+ <maxJobs>1</maxJobs>\r
+</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="">\r
+ <backoffFactor>1.0</backoffFactor>\r
+ <initialDelay>1000</initialDelay>\r
+ <maxDelay>5000</maxDelay>\r
+ <maxRetries>0</maxRetries>\r
+</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="inString" depth="0" /><port name="xslFileURL" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>taxon_search</name><inputPorts><port><name>taxonID</name><depth>0</depth></port></inputPorts><outputPorts><port><name>response</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>dataflow-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.dataflow.DataflowActivity</class><inputMap><map from="taxonID" to="taxonID" /></inputMap><outputMap><map from="response" to="response" /></outputMap><configBean encoding="dataflow"><dataflow ref="c9988367-0549-456b-a037-a518f41268dc" /></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="">\r
+ <maxJobs>1</maxJobs>\r
+</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="">\r
+ <backoffFactor>1.0</backoffFactor>\r
+ <initialDelay>1000</initialDelay>\r
+ <maxDelay>5000</maxDelay>\r
+ <maxRetries>0</maxRetries>\r
+</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="taxonID" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>empty_taxon_search</name><inputPorts><port><name>taxonID</name><depth>0</depth></port></inputPorts><outputPorts><port><name>response</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>dataflow-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.dataflow.DataflowActivity</class><inputMap><map from="taxonID" to="taxonID" /></inputMap><outputMap><map from="response" to="response" /></outputMap><configBean encoding="dataflow"><dataflow ref="0415afc4-0331-4b83-a035-65ba8fea18f8" /></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="">\r
+ <maxJobs>1</maxJobs>\r
+</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="">\r
+ <backoffFactor>1.0</backoffFactor>\r
+ <initialDelay>1000</initialDelay>\r
+ <maxDelay>5000</maxDelay>\r
+ <maxRetries>0</maxRetries>\r
+</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="taxonID" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Flatten_List</name><inputPorts><port><name>inputlist</name><depth>2</depth></port></inputPorts><outputPorts><port><name>outputlist</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="inputlist" to="inputlist" /></inputMap><outputMap><map from="outputlist" to="outputlist" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">\r
+ <inputs>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ <name>inputlist</name>\r
+ <depth>2</depth>\r
+ <mimeTypes>\r
+ <string>l(l(''))</string>\r
+ </mimeTypes>\r
+ <handledReferenceSchemes />\r
+ <translatedElementType>[B</translatedElementType>\r
+ <allowsLiteralValues>true</allowsLiteralValues>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ </inputs>\r
+ <outputs>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
+ <name>outputlist</name>\r
+ <depth>1</depth>\r
+ <mimeTypes />\r
+ <granularDepth>1</granularDepth>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
+ </outputs>\r
+ <classLoaderSharing>workflow</classLoaderSharing>\r
+ <localDependencies />\r
+ <artifactDependencies />\r
+ <script>flatten(inputs, outputs, depth) {\r
+ for (i = inputs.iterator(); i.hasNext();) {\r
+ element = i.next();\r
+ if (element instanceof Collection && depth > 0) {\r
+ flatten(element, outputs, depth - 1);\r
+ } else {\r
+ outputs.add(element);\r
+ }\r
+ }\r
+}\r
+\r
+outputlist = new ArrayList();\r
+\r
+flatten(inputlist, outputlist, 1);</script>\r
+ <dependencies />\r
+ <localworkerName>org.embl.ebi.escience.scuflworkers.java.FlattenList</localworkerName>\r
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>2547dd85-519d-4636-8ee9-3b380ad378ab</identification>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.HostInstitution">\r
+ <text>UserNameHere</text>\r
</annotationBean>\r
- <date>2012-02-07 17:38:22.701 CET</date>\r
+ <date>2012-05-31 14:23:14.813 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
</annotationAssertions>\r
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></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="">\r
+ <maxJobs>1</maxJobs>\r
+</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="">\r
+ <backoffFactor>1.0</backoffFactor>\r
+ <initialDelay>1000</initialDelay>\r
+ <maxDelay>5000</maxDelay>\r
+ <maxRetries>0</maxRetries>\r
+</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="inputlist" depth="2" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Merge_String_List_to_a_String</name><inputPorts><port><name>stringlist</name><depth>1</depth></port></inputPorts><outputPorts><port><name>concatenated</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="stringlist" to="stringlist" /></inputMap><outputMap><map from="concatenated" to="concatenated" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">\r
+ <inputs>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ <name>stringlist</name>\r
+ <depth>1</depth>\r
+ <mimeTypes>\r
+ <string>l('text/plain')</string>\r
+ </mimeTypes>\r
+ <handledReferenceSchemes />\r
+ <translatedElementType>java.lang.String</translatedElementType>\r
+ <allowsLiteralValues>true</allowsLiteralValues>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ <name>seperator</name>\r
+ <depth>0</depth>\r
+ <mimeTypes>\r
+ <string>'text/plain'</string>\r
+ </mimeTypes>\r
+ <handledReferenceSchemes />\r
+ <translatedElementType>java.lang.String</translatedElementType>\r
+ <allowsLiteralValues>true</allowsLiteralValues>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ </inputs>\r
+ <outputs>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
+ <name>concatenated</name>\r
+ <depth>0</depth>\r
+ <mimeTypes>\r
+ <string>'text/plain'</string>\r
+ </mimeTypes>\r
+ <granularDepth>0</granularDepth>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
+ </outputs>\r
+ <classLoaderSharing>workflow</classLoaderSharing>\r
+ <localDependencies />\r
+ <artifactDependencies />\r
+ <script>String seperatorString = "\n";\r
+if (seperator != void) {\r
+ seperatorString = seperator;\r
+}\r
+StringBuffer sb = new StringBuffer();\r
+for (Iterator i = stringlist.iterator(); i.hasNext();) {\r
+ String item = (String) i.next();\r
+ sb.append(item);\r
+ if (i.hasNext()) {\r
+ sb.append(seperatorString);\r
+ }\r
+}\r
+concatenated = sb.toString();\r
+</script>\r
+ <dependencies />\r
+ <localworkerName>org.embl.ebi.escience.scuflworkers.java.StringListMerge</localworkerName>\r
+</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="">\r
+ <maxJobs>1</maxJobs>\r
+</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="">\r
+ <backoffFactor>1.0</backoffFactor>\r
+ <initialDelay>1000</initialDelay>\r
+ <maxDelay>5000</maxDelay>\r
+ <maxRetries>0</maxRetries>\r
+</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="stringlist" depth="1" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>GBIF_Name_Search</processor><port>datasetID</port></sink><source type="dataflow"><port>datasetID</port></source></datalink><datalink><sink type="processor"><processor>GBIF_Name_Search</processor><port>sciName</port></sink><source type="processor"><processor>Transform_StringXML</processor><port>outputStr</port></source></datalink><datalink><sink type="processor"><processor>gbifNameSearchParser</processor><port>gbifNameSerachJSON</port></sink><source type="processor"><processor>GBIF_Name_Search</processor><port>responseBody</port></source></datalink><datalink><sink type="processor"><processor>Transform_StringXML</processor><port>inString</port></sink><source type="dataflow"><port>synReq</port></source></datalink><datalink><sink type="processor"><processor>Transform_StringXML</processor><port>xslFileURL</port></sink><source type="processor"><processor>synReq_to_GBIFReq.xsl</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>taxon_search</processor><port>taxonID</port></sink><source type="processor"><processor>gbifNameSearchParser</processor><port>taxonIDList</port></source></datalink><datalink><sink type="processor"><processor>empty_taxon_search</processor><port>taxonID</port></sink><source type="processor"><processor>gbifNameSearchParser</processor><port>emptyTaxonIDList</port></source></datalink><datalink><sink type="processor"><processor>Merge_String_List_to_a_String</processor><port>stringlist</port></sink><source type="processor"><processor>Flatten_List</processor><port>outputlist</port></source></datalink><datalink><sink type="merge"><processor>Flatten_List</processor><port>inputlist</port></sink><source type="processor"><processor>empty_taxon_search</processor><port>response</port></source></datalink><datalink><sink type="merge"><processor>Flatten_List</processor><port>inputlist</port></sink><source type="processor"><processor>taxon_search</processor><port>response</port></source></datalink><datalink><sink type="dataflow"><port>response</port></sink><source type="processor"><processor>Merge_String_List_to_a_String</processor><port>concatenated</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
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<creators />\r
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<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>d3e29f08-a44b-4bb2-9896-4f325e0499d3</identification>\r
+ <identification>878f934b-8a3e-4fff-9ad3-90543f6b1820</identification>\r
</annotationBean>\r
- <date>2012-01-13 17:09:46.986 CET</date>\r
+ <date>2012-05-30 15:27:24.675 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>a364b26a-abf3-425d-b166-ab27bf0381c5</identification>\r
- </annotationBean>\r
- <date>2012-01-02 17:04:19.721 CET</date>\r
- <creators />\r
- <curationEventList />\r
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
- </annotationAssertions>\r
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow><dataflow id="5563c4db-2322-4ce6-92a1-341f62a3490e" role="nested"><name>Workflow23</name><inputPorts><port><name>synRequest</name><depth>1</depth><granularDepth>1</granularDepth><annotations /></port></inputPorts><outputPorts><port><name>synRequest</name><annotations /></port></outputPorts><processors><processor><name>CoL_Copyright_Interaction</name><inputPorts /><outputPorts><port><name>answer</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>interaction-activity</artifact><version>0.1.2</version></raven><class>net.sf.taverna.t2.activities.interaction.InteractionActivity</class><inputMap /><outputMap><map from="answer" to="answer" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.interaction.InteractionActivityConfigurationBean xmlns="">\r
- <inputs />\r
- <outputs>\r
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
- <name>answer</name>\r
- <depth>0</depth>\r
- <mimeTypes />\r
- <granularDepth>0</granularDepth>\r
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
- </outputs>\r
- <presentationOrigin>http://ww2.bgbm.org/temp/biovel/col_copyright.html</presentationOrigin>\r
- <interactionActivityType>LocallyPresentedHtml</interactionActivityType>\r
-</net.sf.taverna.t2.activities.interaction.InteractionActivityConfigurationBean></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="">\r
- <maxJobs>1</maxJobs>\r
-</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="">\r
- <backoffFactor>1.0</backoffFactor>\r
- <initialDelay>1000</initialDelay>\r
- <maxDelay>5000</maxDelay>\r
- <maxRetries>0</maxRetries>\r
-</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>GBIF_Agreement_Conditional</name><inputPorts><port><name>copyright_answer</name><depth>0</depth></port><port><name>synReqIn</name><depth>1</depth></port></inputPorts><outputPorts><port><name>synReqOut</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="copyright_answer" to="copyright_answer" /><map from="synReqIn" to="synReqIn" /></inputMap><outputMap><map from="synReqOut" to="synReqOut" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">\r
- <inputs>\r
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
- <name>copyright_answer</name>\r
- <depth>0</depth>\r
- <mimeTypes>\r
- <string>text/plain</string>\r
- </mimeTypes>\r
- <handledReferenceSchemes />\r
- <translatedElementType>java.lang.String</translatedElementType>\r
- <allowsLiteralValues>true</allowsLiteralValues>\r
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
- <name>synReqIn</name>\r
- <depth>1</depth>\r
- <mimeTypes>\r
- <string>text/plain</string>\r
- </mimeTypes>\r
- <handledReferenceSchemes />\r
- <translatedElementType>java.lang.String</translatedElementType>\r
- <allowsLiteralValues>true</allowsLiteralValues>\r
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
- </inputs>\r
- <outputs>\r
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
- <name>synReqOut</name>\r
- <depth>1</depth>\r
- <mimeTypes />\r
- <granularDepth>1</granularDepth>\r
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
- </outputs>\r
- <classLoaderSharing>workflow</classLoaderSharing>\r
- <localDependencies />\r
- <artifactDependencies />\r
- <script>if(copyright_answer.equals("Yes")) {\r
- synReqOut = synReqIn; \r
-} else {\r
- synReqOut = new ArrayList(); \r
-}\r
-\r
-</script>\r
- <dependencies />\r
-</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></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="">\r
- <maxJobs>1</maxJobs>\r
-</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="">\r
- <backoffFactor>1.0</backoffFactor>\r
- <initialDelay>1000</initialDelay>\r
- <maxDelay>5000</maxDelay>\r
- <maxRetries>0</maxRetries>\r
-</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="copyright_answer" depth="0" /><port name="synReqIn" depth="1" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>GBIF_Agreement_Conditional</processor><port>copyright_answer</port></sink><source type="processor"><processor>CoL_Copyright_Interaction</processor><port>answer</port></source></datalink><datalink><sink type="processor"><processor>GBIF_Agreement_Conditional</processor><port>synReqIn</port></sink><source type="dataflow"><port>synRequest</port></source></datalink><datalink><sink type="dataflow"><port>synRequest</port></sink><source type="processor"><processor>GBIF_Agreement_Conditional</processor><port>synReqOut</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
- <annotationAssertions>\r
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>c6db23cf-d2a1-4898-addb-fb7eafd3b6b0</identification>\r
+ <identification>0b277055-2b51-48b7-8793-3b6379e395f9</identification>\r
</annotationBean>\r
- <date>2012-04-05 17:13:18.721 CEST</date>\r
+ <date>2012-05-31 12:53:00.670 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>fe0524a8-3d93-4759-a0cc-2537bb2a577d</identification>\r
+ <identification>3ba54c98-e4d8-42c5-a22e-d0a1028ccb83</identification>\r
</annotationBean>\r
- <date>2012-04-05 16:34:35.523 CEST</date>\r
+ <date>2012-05-31 10:49:50.251 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>5563c4db-2322-4ce6-92a1-341f62a3490e</identification>\r
+ <identification>afbf7fa0-d01f-44e3-8468-4cd0ac74577b</identification>\r
</annotationBean>\r
- <date>2012-04-05 17:18:25.865 CEST</date>\r
+ <date>2012-05-31 14:02:27.138 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>c13b55dc-e9e8-4809-887b-cd90764fa7c0</identification>\r
+ <identification>b2549055-01c9-4460-8c6c-7fd2aa2443ae</identification>\r
</annotationBean>\r
- <date>2012-04-05 16:41:23.996 CEST</date>\r
+ <date>2012-05-31 10:05:51.430 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>25f616d8-fa88-4d60-8127-8228cf93c5a3</identification>\r
+ <identification>32645248-6c44-4435-a348-cdf417f52e56</identification>\r
</annotationBean>\r
- <date>2012-04-05 16:31:27.376 CEST</date>\r
+ <date>2012-05-30 15:14:59.556 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>1f4e6dc3-c3d1-40c2-9278-8f6396184737</identification>\r
+ <identification>c9dbc8d5-d665-4bf2-b6ad-a0941fb85605</identification>\r
</annotationBean>\r
- <date>2012-04-05 16:53:48.103 CEST</date>\r
+ <date>2012-05-31 12:42:33.597 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>5e20399a-7e4f-4807-b510-1f15cdc22dd8</identification>\r
+ <identification>6eb4fe80-f745-4726-a4ef-ab1796a9dc07</identification>\r
</annotationBean>\r
- <date>2012-04-05 16:41:48.618 CEST</date>\r
+ <date>2012-05-31 14:13:54.299 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>25760699-c10c-4abe-ac58-2277f17a319b</identification>\r
+ <identification>fda28d76-34ae-401a-88cf-16f2d100dc94</identification>\r
</annotationBean>\r
- <date>2012-04-05 16:47:29.177 CEST</date>\r
+ <date>2012-05-30 15:16:25.384 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>adf2df6f-6ffa-490f-9b73-d8e46adac00b</identification>\r
+ <identification>ca4c901c-2d01-4e13-a6bd-3a3a633d9299</identification>\r
</annotationBean>\r
- <date>2012-04-05 16:54:07.336 CEST</date>\r
+ <date>2012-05-31 10:42:32.948 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>5a705158-54cb-4a67-aaa7-7f99030fdb84</identification>\r
+ <identification>8c5df190-a49a-4e67-aab9-68cca577c368</identification>\r
</annotationBean>\r
- <date>2012-04-05 17:12:59.464 CEST</date>\r
+ <date>2012-05-30 16:06:55.686 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>7f0d77bf-4336-4f46-8e55-d65a37d07ca3</identification>\r
+ <identification>4337a0e1-a09d-4b68-8660-637490e21edb</identification>\r
+ </annotationBean>\r
+ <date>2012-01-31 15:58:55.276 CET</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>416607f5-ecab-4866-ac2b-966286db8332</identification>\r
+ </annotationBean>\r
+ <date>2012-03-22 09:26:32.315 CET</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>3322b5a3-1530-4824-9300-ba6a6b18b7f1</identification>\r
</annotationBean>\r
- <date>2012-03-22 12:04:20.911 CET</date>\r
+ <date>2012-01-31 16:27:20.693 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>c5da4161-0b70-4e67-9704-cc2d26b6cf6e</identification>\r
+ <identification>6e0d1517-2294-4837-b994-80604a634cd0</identification>\r
</annotationBean>\r
- <date>2012-03-21 13:03:44.642 CET</date>\r
+ <date>2012-01-02 15:55:00.474 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>592c1eb2-fa84-4e1d-933a-e93df9414942</identification>\r
+ <identification>dedef59b-8e8b-4e4d-8903-5f8c54422215</identification>\r
</annotationBean>\r
- <date>2012-04-05 16:34:58.572 CEST</date>\r
+ <date>2012-01-02 16:04:37.936 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>3322b5a3-1530-4824-9300-ba6a6b18b7f1</identification>\r
+ <identification>53f8a5ae-069d-4470-8da0-2df125dc5ec8</identification>\r
</annotationBean>\r
- <date>2012-01-31 16:27:20.693 CET</date>\r
+ <date>2012-01-02 17:50:56.83 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>0d8d4ebe-a6f7-4e1c-b300-26d6bcda0d9f</identification>\r
+ <identification>592c1eb2-fa84-4e1d-933a-e93df9414942</identification>\r
</annotationBean>\r
- <date>2012-04-04 13:48:20.742 CEST</date>\r
+ <date>2012-04-05 16:34:58.572 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>34bdb8db-644c-4792-b591-dd8406ef7d78</identification>\r
+ <identification>9995fb53-fe1e-4aee-88c8-60bb5f2f34cf</identification>\r
</annotationBean>\r
- <date>2012-03-21 12:12:06.884 CET</date>\r
+ <date>2012-01-05 16:27:19.428 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>38415ea5-cbce-41ed-bc16-1d582af4c523</identification>\r
+ <identification>b176d4c2-c954-4fd4-971d-5f55f1c2ef09</identification>\r
</annotationBean>\r
- <date>2012-04-04 13:39:59.914 CEST</date>\r
+ <date>2012-02-09 17:39:20.187 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>b87d4830-e4c0-4665-972b-b60353b71873</identification>\r
+ <identification>b5b6d740-cc89-4450-8e5b-44fcac2bfee2</identification>\r
</annotationBean>\r
- <date>2012-01-02 16:29:06.484 CET</date>\r
+ <date>2012-01-02 15:00:31.584 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>62f4cd4d-508e-409c-8e06-3fef4020fa97</identification>\r
+ <identification>24937535-5952-412a-bd44-beebd29db137</identification>\r
</annotationBean>\r
- <date>2012-02-07 17:25:22.963 CET</date>\r
+ <date>2012-03-21 12:17:01.846 CET</date>\r
<creators />\r
<curationEventList />\r
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<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
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+ <identification>40ab0272-4c88-4606-9f3a-2ebc309e017b</identification>\r
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- <date>2012-02-07 18:07:20.452 CET</date>\r
+ <date>2012-02-08 15:46:10.571 CET</date>\r
<creators />\r
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</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
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+ <identification>eeab83cc-69df-4a18-a6ad-e33a5cc51f35</identification>\r
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- <date>2012-03-21 12:22:38.39 CET</date>\r
+ <date>2012-01-13 16:59:53.791 CET</date>\r
<creators />\r
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<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
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- <date>2012-01-31 16:24:57.958 CET</date>\r
+ <date>2012-01-03 12:48:44.529 CET</date>\r
<creators />\r
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<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
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+ <identification>7f0d77bf-4336-4f46-8e55-d65a37d07ca3</identification>\r
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- <date>2012-01-13 15:44:17.623 CET</date>\r
+ <date>2012-03-22 12:04:20.911 CET</date>\r
<creators />\r
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<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
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- <date>2012-01-02 15:00:31.584 CET</date>\r
+ <date>2012-04-05 16:47:32.81 CEST</date>\r
<creators />\r
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<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
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+ <date>2012-01-31 16:03:53.673 CET</date>\r
<creators />\r
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<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>3c13925e-8808-471e-9f19-e40364e1406c</identification>\r
+ <identification>69821203-d769-45ce-a3bb-145a9964679f</identification>\r
</annotationBean>\r
- <date>2012-02-10 13:01:39.855 CET</date>\r
+ <date>2012-01-02 15:04:12.378 CET</date>\r
<creators />\r
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</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>00826864-df38-4222-a06b-ac5fd4d79e9a</identification>\r
+ <identification>46828567-904f-4105-96ef-0bf268ada001</identification>\r
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- <date>2012-03-28 17:45:02.966 CEST</date>\r
+ <date>2012-01-02 17:06:50.222 CET</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
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+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
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+ <date>2012-01-02 17:16:27.428 CET</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
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+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
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+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
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+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
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<creators />\r
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</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
</annotationAssertions>\r
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+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
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+ <creators />\r
+ <curationEventList />\r
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+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
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+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
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+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
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+ </annotationBean>\r
+ <date>2012-03-28 17:45:02.966 CEST</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
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+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
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+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
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+ <creators />\r
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+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
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+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
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+ <creators />\r
+ <curationEventList />\r
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+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
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+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
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+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
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+ </annotationBean>\r
+ <date>2012-03-21 12:22:38.39 CET</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
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+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>2a24fc15-ccdc-46a3-ac3c-56715818d2c9</identification>\r
+ </annotationBean>\r
+ <date>2012-04-04 13:30:18.779 CEST</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>0d8d4ebe-a6f7-4e1c-b300-26d6bcda0d9f</identification>\r
+ </annotationBean>\r
+ <date>2012-04-04 13:48:20.742 CEST</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
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+ <identification>b87d4830-e4c0-4665-972b-b60353b71873</identification>\r
</annotationBean>\r
- <date>2012-02-07 17:54:59.874 CET</date>\r
+ <date>2012-01-02 16:29:06.484 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>0fa06dee-52dd-4af0-815c-92a4fca15a38</identification>\r
+ <identification>273737ec-425c-4577-8d2a-963156312cfd</identification>\r
</annotationBean>\r
- <date>2012-03-22 09:26:12.858 CET</date>\r
+ <date>2012-01-02 15:56:51.418 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>98429027-b6ab-4c7a-8952-f92ce82af604</identification>\r
+ <identification>a364b26a-abf3-425d-b166-ab27bf0381c5</identification>\r
</annotationBean>\r
- <date>2012-01-13 16:44:12.623 CET</date>\r
+ <date>2012-01-02 17:04:19.721 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>32faa1ef-391d-4360-8bb4-cc7f25b963a1</identification>\r
+ <identification>6baa5e11-586d-4f13-b6f4-92c61c10ec9a</identification>\r
</annotationBean>\r
- <date>2012-01-02 17:19:44.583 CET</date>\r
+ <date>2012-01-13 15:29:27.496 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>d6aa2f1a-4945-4c03-a5c1-83e8c5d71cbb</identification>\r
+ <identification>df805bf7-d2c5-436b-a770-ba2258ed78c5</identification>\r
</annotationBean>\r
- <date>2012-02-07 18:09:14.553 CET</date>\r
+ <date>2012-01-31 16:39:08.415 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>14e0d5c9-4a24-47df-a07b-e532cec4ca5c</identification>\r
+ <identification>56cae6e8-a10e-44dc-86d9-dde7c69beee3</identification>\r
</annotationBean>\r
- <date>2012-03-02 16:39:52.276 CET</date>\r
+ <date>2012-01-31 15:45:44.504 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>7be40bed-1839-4117-81ff-49391e0fe35a</identification>\r
+ <identification>c5da4161-0b70-4e67-9704-cc2d26b6cf6e</identification>\r
</annotationBean>\r
- <date>2012-01-02 17:52:39.889 CET</date>\r
+ <date>2012-03-21 13:03:44.642 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>416607f5-ecab-4866-ac2b-966286db8332</identification>\r
+ <identification>f41b5d1f-a3a6-4fcb-a52a-748150c35471</identification>\r
</annotationBean>\r
- <date>2012-03-22 09:26:32.315 CET</date>\r
+ <date>2012-02-07 17:22:31.525 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>7cbd63e4-d73d-42d9-9133-4f359b06efb5</identification>\r
+ <identification>92eb7f21-c6c2-4b1b-9200-1628662427a6</identification>\r
</annotationBean>\r
- <date>2012-01-02 14:51:19.40 CET</date>\r
+ <date>2012-03-21 12:06:31.153 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>dedef59b-8e8b-4e4d-8903-5f8c54422215</identification>\r
+ <identification>bb48ba73-aa77-42a1-9019-d72ebc20dfd0</identification>\r
</annotationBean>\r
- <date>2012-01-02 16:04:37.936 CET</date>\r
+ <date>2012-02-07 18:07:20.452 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>eeab83cc-69df-4a18-a6ad-e33a5cc51f35</identification>\r
+ <identification>f356c7e2-888e-4a2d-85f8-4bc7b6b059cd</identification>\r
</annotationBean>\r
- <date>2012-01-13 16:59:53.791 CET</date>\r
+ <date>2012-02-07 18:13:43.986 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>feaf6e99-716b-4cc9-81b0-7255ea5a38f7</identification>\r
+ <identification>6be02b9a-7aaa-4e2f-9b42-b0b24ae2053d</identification>\r
</annotationBean>\r
- <date>2012-01-02 16:03:20.221 CET</date>\r
+ <date>2012-02-10 13:02:19.116 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
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+ <identification>b5feb718-54f5-402c-88a6-73874036974b</identification>\r
</annotationBean>\r
- <date>2012-01-31 15:58:55.276 CET</date>\r
+ <date>2012-03-02 16:39:31.246 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>8fd4d664-f4f1-48b8-a9a6-36c420e7214e</identification>\r
+ <identification>c919e20c-7881-47e8-afb1-b6233038e6d5</identification>\r
</annotationBean>\r
- <date>2012-01-13 15:45:48.22 CET</date>\r
+ <date>2012-03-29 17:02:07.640 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
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<creators />\r
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<creators />\r
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<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
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<creators />\r
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<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
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<creators />\r
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<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
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<creators />\r
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<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
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- <date>2012-04-05 16:47:32.81 CEST</date>\r
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<creators />\r
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<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
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- <date>2012-02-10 13:02:19.116 CET</date>\r
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<creators />\r
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- <date>2012-04-04 13:30:18.779 CEST</date>\r
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<creators />\r
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<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>eb452b59-dcaf-4db0-8f72-244455633870</identification>\r
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</annotationBean>\r
- <date>2012-01-13 15:40:37.647 CET</date>\r
+ <date>2012-04-04 11:56:34.34 CEST</date>\r
<creators />\r
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</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
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<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
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<creators />\r
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<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
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<creators />\r
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<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
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- <date>2012-04-04 11:56:34.34 CEST</date>\r
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<creators />\r
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<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
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- <date>2012-04-05 16:43:22.12 CEST</date>\r
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<creators />\r
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<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
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<creators />\r
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<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
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- <date>2012-01-31 15:45:44.504 CET</date>\r
+ <date>2012-04-05 16:57:22.614 CEST</date>\r
<creators />\r
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</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
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<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
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<creators />\r
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<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
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<creators />\r
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<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
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</annotationBean>\r
- <date>2012-01-02 17:06:50.222 CET</date>\r
+ <date>2012-04-05 16:43:22.12 CEST</date>\r
<creators />\r
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</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>c919e20c-7881-47e8-afb1-b6233038e6d5</identification>\r
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</annotationBean>\r
- <date>2012-03-29 17:02:07.640 CEST</date>\r
+ <date>2012-01-31 16:29:30.593 CET</date>\r
<creators />\r
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<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
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- <date>2012-04-03 17:00:50.954 CEST</date>\r
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<creators />\r
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</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
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<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
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<creators />\r
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</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
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</annotationBean>\r
- <date>2012-02-07 17:53:12.962 CET</date>\r
+ <date>2012-04-04 13:39:59.914 CEST</date>\r
<creators />\r
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</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
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- <date>2012-04-05 16:57:22.614 CEST</date>\r
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<creators />\r
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</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
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+ <date>2012-01-02 17:35:34.596 CET</date>\r
<creators />\r
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</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>e0b1887f-8e9c-43d7-bb75-ee3b5e382834</identification>\r
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</annotationBean>\r
- <date>2012-01-31 16:29:30.593 CET</date>\r
+ <date>2012-02-07 18:15:01.509 CET</date>\r
<creators />\r
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</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
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+ <date>2012-01-02 17:21:03.648 CET</date>\r
<creators />\r
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</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
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</annotationBean>\r
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+ <date>2012-01-02 17:14:37.644 CET</date>\r
<creators />\r
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</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
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</annotationBean>\r
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+ <date>2012-04-03 17:00:50.954 CEST</date>\r
<creators />\r
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</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
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</annotationBean>\r
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+ <date>2012-01-25 16:54:33.283 CET</date>\r
<creators />\r
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</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
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</annotationBean>\r
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+ <date>2012-01-13 15:44:17.623 CET</date>\r
<creators />\r
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</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
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- <date>2012-02-08 15:46:10.571 CET</date>\r
+ <date>2012-01-02 16:46:06.131 CET</date>\r
<creators />\r
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</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
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- <date>2012-01-31 16:10:34.267 CET</date>\r
+ <date>2012-03-21 11:58:50.611 CET</date>\r
<creators />\r
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</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
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+ <date>2012-03-22 09:26:12.858 CET</date>\r
<creators />\r
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</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
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+ <date>2012-02-10 13:01:39.855 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
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</annotationBean>\r
- <date>2012-01-13 15:29:27.496 CET</date>\r
+ <date>2012-02-07 17:54:59.874 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
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</annotationBean>\r
- <date>2012-02-09 17:39:20.187 CET</date>\r
+ <date>2012-01-31 16:20:23.935 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>5f7faf68-279b-4c53-84ca-6746a5fa7832</identification>\r
+ <identification>34bdb8db-644c-4792-b591-dd8406ef7d78</identification>\r
</annotationBean>\r
- <date>2012-01-31 16:40:24.470 CET</date>\r
+ <date>2012-03-21 12:12:06.884 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>9f8d21c5-2523-4485-a181-01e6de804d4d</identification>\r
+ <identification>62f4cd4d-508e-409c-8e06-3fef4020fa97</identification>\r
</annotationBean>\r
- <date>2012-01-02 17:35:34.596 CET</date>\r
+ <date>2012-02-07 17:25:22.963 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>d4040120-4a6d-4a24-8bf4-73dd22e762c3</identification>\r
+ <identification>14e0d5c9-4a24-47df-a07b-e532cec4ca5c</identification>\r
</annotationBean>\r
- <date>2012-01-02 16:46:06.131 CET</date>\r
+ <date>2012-03-02 16:39:52.276 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
</annotationAssertions>\r
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow><dataflow id="cb4b094a-0513-4723-9a8a-6313e81b11c4" role="nested"><name>Workflow144</name><inputPorts><port><name>synRequest</name><depth>0</depth><granularDepth>0</granularDepth><annotations /></port></inputPorts><outputPorts><port><name>col_copyright_conditional</name><annotations /></port></outputPorts><processors><processor><name>Col_Copyright_Conditional</name><inputPorts><port><name>copyright_answer</name><depth>0</depth></port></inputPorts><outputPorts><port><name>col_copyright_conditional</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="copyright_answer" to="copyright_answer" /></inputMap><outputMap><map from="col_copyright_conditional" to="col_copyright_conditional" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">\r
+ <inputs>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ <name>copyright_answer</name>\r
+ <depth>0</depth>\r
+ <mimeTypes>\r
+ <string>text/plain</string>\r
+ </mimeTypes>\r
+ <handledReferenceSchemes />\r
+ <translatedElementType>java.lang.String</translatedElementType>\r
+ <allowsLiteralValues>true</allowsLiteralValues>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ </inputs>\r
+ <outputs>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
+ <name>col_copyright_conditional</name>\r
+ <depth>0</depth>\r
+ <mimeTypes />\r
+ <granularDepth>0</granularDepth>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
+ </outputs>\r
+ <classLoaderSharing>workflow</classLoaderSharing>\r
+ <localDependencies />\r
+ <artifactDependencies />\r
+ <script>\r
+//col_copyright_conditional = new ArrayList();\r
+if(copyright_answer.equals("Yes")) {\r
+ col_copyright_conditional = "true"; \r
+}\r
+\r
+</script>\r
+ <dependencies />\r
+</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></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="">\r
+ <maxJobs>1</maxJobs>\r
+</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="">\r
+ <backoffFactor>1.0</backoffFactor>\r
+ <initialDelay>1000</initialDelay>\r
+ <maxDelay>5000</maxDelay>\r
+ <maxRetries>0</maxRetries>\r
+</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="copyright_answer" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>CoL_Copyright_Interaction</name><inputPorts /><outputPorts><port><name>answer</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>interaction-activity</artifact><version>0.1.2</version></raven><class>net.sf.taverna.t2.activities.interaction.InteractionActivity</class><inputMap /><outputMap><map from="answer" to="answer" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.interaction.InteractionActivityConfigurationBean xmlns="">\r
+ <inputs />\r
+ <outputs>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
+ <name>answer</name>\r
+ <depth>0</depth>\r
+ <mimeTypes />\r
+ <granularDepth>0</granularDepth>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
+ </outputs>\r
+ <presentationOrigin>http://ww2.bgbm.org/temp/biovel/col_copyright.html</presentationOrigin>\r
+ <interactionActivityType>LocallyPresentedHtml</interactionActivityType>\r
+</net.sf.taverna.t2.activities.interaction.InteractionActivityConfigurationBean></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="">\r
+ <maxJobs>1</maxJobs>\r
+</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="">\r
+ <backoffFactor>1.0</backoffFactor>\r
+ <initialDelay>1000</initialDelay>\r
+ <maxDelay>5000</maxDelay>\r
+ <maxRetries>0</maxRetries>\r
+</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></processors><conditions /><datalinks><datalink><sink type="processor"><processor>Col_Copyright_Conditional</processor><port>copyright_answer</port></sink><source type="processor"><processor>CoL_Copyright_Interaction</processor><port>answer</port></source></datalink><datalink><sink type="dataflow"><port>col_copyright_conditional</port></sink><source type="processor"><processor>Col_Copyright_Conditional</processor><port>col_copyright_conditional</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>d5d43373-3338-4d0e-8f11-62fc2c73afae</identification>\r
+ <identification>90834f91-f80e-4426-b4b0-bbb6dcbb7dc2</identification>\r
</annotationBean>\r
- <date>2012-03-21 17:56:47.842 CET</date>\r
+ <date>2012-05-31 17:56:41.645 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>4f8dd224-cc83-4af5-bbd2-dedfd09b43fe</identification>\r
+ <identification>af069788-606d-4b1a-a033-d9c153256e49</identification>\r
</annotationBean>\r
- <date>2012-01-02 17:14:37.644 CET</date>\r
+ <date>2012-06-01 11:32:35.248 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>25217334-644c-43ed-bd13-7a3b2a03d5c1</identification>\r
+ <identification>f35144b6-2ce9-4593-87c6-70e1dcf132be</identification>\r
</annotationBean>\r
- <date>2012-01-31 16:20:23.935 CET</date>\r
+ <date>2012-06-01 11:00:08.42 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>aec72d1d-786a-4ccc-afb5-c712166bc3e2</identification>\r
+ <identification>f0aa610f-483e-4c68-9c42-a0b755cef545</identification>\r
</annotationBean>\r
- <date>2012-01-31 16:33:25.857 CET</date>\r
+ <date>2012-06-01 11:19:31.141 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>92eb7f21-c6c2-4b1b-9200-1628662427a6</identification>\r
+ <identification>64789f83-fd1c-4184-92f4-1d8543a1e36f</identification>\r
</annotationBean>\r
- <date>2012-03-21 12:06:31.153 CET</date>\r
+ <date>2012-05-31 17:31:21.932 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>d3e29f08-a44b-4bb2-9896-4f325e0499d3</identification>\r
+ <identification>011b4c31-e36d-49d1-a83b-f39abdd63d9d</identification>\r
</annotationBean>\r
- <date>2012-01-13 17:09:46.986 CET</date>\r
+ <date>2012-06-01 11:12:58.985 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>62eace58-eeb6-495b-80e8-a94fadcc7316</identification>\r
+ <identification>42f8e3b2-dbb0-4335-a380-35867968834a</identification>\r
</annotationBean>\r
- <date>2012-02-08 13:41:58.660 CET</date>\r
+ <date>2012-06-01 11:15:35.7 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>82083c79-a4c9-4d8c-bf19-3e89ff2276e6</identification>\r
+ <identification>cb4b094a-0513-4723-9a8a-6313e81b11c4</identification>\r
</annotationBean>\r
- <date>2012-01-02 15:05:39.350 CET</date>\r
+ <date>2012-06-01 11:45:03.50 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>702db05d-4a74-48b1-9b61-9ee90a1de8f4</identification>\r
+ <identification>a51024e5-a87d-4bfa-8b05-d19438370ade</identification>\r
</annotationBean>\r
- <date>2012-02-08 15:37:36.668 CET</date>\r
+ <date>2012-05-31 18:01:29.938 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>974e04bd-3efb-424a-9e35-2cd9f4fcd274</identification>\r
+ <identification>b79ec55e-c1b6-4f9d-856d-cbac48fbb1d2</identification>\r
</annotationBean>\r
- <date>2012-01-02 17:23:23.829 CET</date>\r
+ <date>2012-06-01 11:18:39.371 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>f41b5d1f-a3a6-4fcb-a52a-748150c35471</identification>\r
+ <identification>5245ddfd-3682-46a3-aa4c-44d06531088b</identification>\r
</annotationBean>\r
- <date>2012-02-07 17:22:31.525 CET</date>\r
+ <date>2012-06-01 11:40:04.780 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>e2b4ef4f-5ce6-47fd-9aed-3042a7d27529</identification>\r
+ <identification>883a39f0-67e5-46c3-9f8b-0a9305948eff</identification>\r
</annotationBean>\r
- <date>2012-01-02 16:20:24.718 CET</date>\r
+ <date>2012-06-01 11:30:15.15 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>e772224a-94c3-42a0-81e7-a7aedc37aff8</identification>\r
+ <identification>ccbf0253-8206-404e-be25-d93c9de7bb39</identification>\r
</annotationBean>\r
- <date>2012-03-21 11:58:50.611 CET</date>\r
+ <date>2012-06-01 10:55:27.720 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>9b1c8f07-a857-4d04-b260-b13bcf331662</identification>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>bf1aa85d-138a-41a7-a605-3b34468e2d6f</identification>\r
+ </annotationBean>\r
+ <date>2012-05-31 17:32:15.224 CEST</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow><dataflow id="124b440e-f7ef-445f-901b-b3d04ca3e2a7" role="nested"><name>Workflow20</name><inputPorts><port><name>sciName</name><depth>0</depth><granularDepth>0</granularDepth><annotations /></port><port><name>next</name><depth>0</depth><granularDepth>0</granularDepth><annotations /></port></inputPorts><outputPorts><port><name>next</name><annotations /></port><port><name>max1000_csv_output</name><annotations /></port></outputPorts><processors><processor><name>Transform_XML</name><inputPorts><port><name>xslFileURL</name><depth>0</depth></port><port><name>inString</name><depth>0</depth></port></inputPorts><outputPorts><port><name>outputStr</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="inString" to="inString" /><map from="xslFileURL" to="xslFileURL" /></inputMap><outputMap><map from="outputStr" to="outputStr" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">\r
+ <inputs>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ <name>xslFileURL</name>\r
+ <depth>0</depth>\r
+ <mimeTypes>\r
+ <string>'text/plain'</string>\r
+ </mimeTypes>\r
+ <handledReferenceSchemes />\r
+ <translatedElementType>java.lang.String</translatedElementType>\r
+ <allowsLiteralValues>true</allowsLiteralValues>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ <name>outFileURL</name>\r
+ <depth>0</depth>\r
+ <mimeTypes>\r
+ <string>'text/plain'</string>\r
+ </mimeTypes>\r
+ <handledReferenceSchemes />\r
+ <translatedElementType>java.lang.String</translatedElementType>\r
+ <allowsLiteralValues>true</allowsLiteralValues>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ <name>inString</name>\r
+ <depth>0</depth>\r
+ <mimeTypes>\r
+ <string>'text/plain'</string>\r
+ </mimeTypes>\r
+ <handledReferenceSchemes />\r
+ <translatedElementType>java.lang.String</translatedElementType>\r
+ <allowsLiteralValues>true</allowsLiteralValues>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ <name>outputExt</name>\r
+ <depth>0</depth>\r
+ <mimeTypes>\r
+ <string>'text/plain'</string>\r
+ </mimeTypes>\r
+ <handledReferenceSchemes />\r
+ <translatedElementType>java.lang.String</translatedElementType>\r
+ <allowsLiteralValues>true</allowsLiteralValues>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ </inputs>\r
+ <outputs>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
+ <name>outputStr</name>\r
+ <depth>0</depth>\r
+ <mimeTypes />\r
+ <granularDepth>0</granularDepth>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
+ </outputs>\r
+ <classLoaderSharing>workflow</classLoaderSharing>\r
+ <localDependencies />\r
+ <artifactDependencies />\r
+ <script>import java.io.BufferedReader;\r
+import java.io.BufferedWriter;\r
+import java.io.FileInputStream;\r
+import java.io.FileNotFoundException;\r
+import java.io.FileReader;\r
+import java.io.FileWriter;\r
+import java.io.IOException;\r
+import java.io.InputStreamReader;\r
+import java.io.OutputStreamWriter;\r
+import java.io.StringWriter;\r
+import java.io.StringReader;\r
+import java.io.Writer;\r
+import java.net.URL;\r
+import java.util.HashMap;\r
+import java.util.Map;\r
+\r
+import javax.xml.transform.Result;\r
+import javax.xml.transform.Source;\r
+import javax.xml.transform.SourceLocator;\r
+import javax.xml.transform.Templates;\r
+import javax.xml.transform.Transformer;\r
+import javax.xml.transform.TransformerConfigurationException;\r
+import javax.xml.transform.TransformerException;\r
+import javax.xml.transform.TransformerFactory;\r
+import javax.xml.transform.stream.StreamResult;\r
+import javax.xml.transform.stream.StreamSource;\r
+\r
+BufferedReader getReader (String fileUrl) throws IOException {\r
+ InputStreamReader reader;\r
+ try {\r
+ reader = new FileReader(fileUrl);\r
+ }\r
+ catch (FileNotFoundException e) {\r
+ // try a real URL instead\r
+ URL url = new URL(fileUrl);\r
+ reader = new InputStreamReader (url.openStream());\r
+ }\r
+ return new BufferedReader(reader);\r
+ }\r
+ \r
+BufferedWriter getWriter (String fileUrl) throws IOException {\r
+ Writer writer;\r
+ try {\r
+ writer = new FileWriter(fileUrl);\r
+ }\r
+ catch (FileNotFoundException e) {\r
+ // try a real URL instead\r
+ URL url = new URL(fileUrl);\r
+ writer = new OutputStreamWriter (url.openConnection().getOutputStream());\r
+ }\r
+ return new BufferedWriter(writer);\r
+ }\r
+ \r
+String xslFilename = xslFileURL;\r
+String outFilename;\r
+if (outFileURL != void) {\r
+ outFilename = outFileURL;\r
+}\r
+\r
+String ext;\r
+if (outputExt != void) {\r
+ ext = outputExt;\r
+}\r
+\r
+\r
+\r
+// Create transformer factory\r
+TransformerFactory factory = TransformerFactory.newInstance();\r
+\r
+// Use the factory to create a template containing the xsl file\r
+Templates template = factory.newTemplates(new StreamSource(getReader(xslFilename)));\r
+\r
+// Use the template to create a transformer\r
+Transformer xformer = template.newTransformer();\r
+\r
+// Prepare the input and output files\r
+Reader sourceReader = new StringReader(inString);\r
+Source source = new StreamSource(sourceReader);\r
+StringWriter resultStr = new StringWriter();\r
+Result result = new StreamResult(resultStr);\r
+\r
+// Apply the xsl file to the source file and write the result to the\r
+// output file\r
+xformer.transform(source, result);\r
+\r
+outputStr = resultStr.toString();\r
+\r
+if ((outFilename != null) && !outFilename.equals("")) {\r
+\r
+ BufferedWriter out = getWriter(outFilename);\r
+\r
+ out.write(outputStr);\r
+ out.close();\r
+}\r
+sourceReader.close();\r
+</script>\r
+ <dependencies />\r
+ <localworkerName>net.sourceforge.taverna.scuflworkers.xml.XSLTWorker</localworkerName>\r
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.HostInstitution">\r
+ <text>UserNameHere</text>\r
</annotationBean>\r
- <date>2012-01-31 16:03:53.673 CET</date>\r
+ <date>2012-01-13 17:08:38.768 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
</annotationAssertions>\r
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow><dataflow id="12806644-8a59-4917-a0bf-a32566bfe2ff" role="nested"><name>Workflow1</name><inputPorts><port><name>synResponse</name><depth>0</depth><granularDepth>0</granularDepth><annotations /></port><port><name>nameStatus</name><depth>0</depth><granularDepth>0</granularDepth><annotations /></port></inputPorts><outputPorts><port><name>colResponse</name><annotations /></port></outputPorts><processors><processor><name>COLSynCheck_REST</name><inputPorts><port><name>sciId</name><depth>0</depth></port></inputPorts><outputPorts><port><name>responseBody</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>rest-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.rest.RESTActivity</class><inputMap><map from="sciId" to="sciId" /></inputMap><outputMap><map from="responseBody" to="responseBody" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean xmlns="">\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></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="">\r
+ <maxJobs>1</maxJobs>\r
+</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="">\r
+ <backoffFactor>1.0</backoffFactor>\r
+ <initialDelay>1000</initialDelay>\r
+ <maxDelay>5000</maxDelay>\r
+ <maxRetries>0</maxRetries>\r
+</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="xslFileURL" depth="0" /><port name="inString" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>gbifResponse_to_csv_xsl</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="">\r
+ <value>http://ww2.bgbm.org/temp/biovel/gbifResponse_to_csv.xsl</value>\r
+</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="">\r
+ <maxJobs>1</maxJobs>\r
+</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="">\r
+ <backoffFactor>1.0</backoffFactor>\r
+ <initialDelay>1000</initialDelay>\r
+ <maxDelay>5000</maxDelay>\r
+ <maxRetries>0</maxRetries>\r
+</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>gbifOccurrence</name><inputPorts><port><name>format</name><depth>0</depth></port><port><name>scientificname</name><depth>0</depth></port><port><name>next</name><depth>0</depth></port></inputPorts><outputPorts><port><name>responseBody</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>rest-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.rest.RESTActivity</class><inputMap><map from="next" to="next" /><map from="format" to="format" /><map from="scientificname" to="scientificname" /></inputMap><outputMap><map from="responseBody" to="responseBody" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean xmlns="">\r
<httpMethod>GET</httpMethod>\r
- <urlSignature>http://www.catalogueoflife.org/webservice?response=full&id={sciId}</urlSignature>\r
+ <urlSignature>http://data.gbif.org/ws/rest/occurrence/list?scientificname={scientificname}&format={format}&startindex={next}&maxresults=1000</urlSignature>\r
<acceptsHeaderValue>application/xml</acceptsHeaderValue>\r
<contentTypeForUpdates>application/xml</contentTypeForUpdates>\r
<outgoingDataFormat>String</outgoingDataFormat>\r
<otherHTTPHeaders />\r
<activityInputs>\r
<entry>\r
- <string>sciId</string>\r
- <java-class>java.lang.String</java-class>\r
+ <string>next</string>\r
+ <java-class>java.lang.String</java-class>\r
+ </entry>\r
+ <entry>\r
+ <string>format</string>\r
+ <java-class>java.lang.String</java-class>\r
+ </entry>\r
+ <entry>\r
+ <string>scientificname</string>\r
+ <java-class>java.lang.String</java-class>\r
+ </entry>\r
+ </activityInputs>\r
+</net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean></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="">\r
+ <maxJobs>1</maxJobs>\r
+</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="">\r
+ <backoffFactor>1.0</backoffFactor>\r
+ <initialDelay>1000</initialDelay>\r
+ <maxDelay>5000</maxDelay>\r
+ <maxRetries>0</maxRetries>\r
+</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="format" depth="0" /><port name="scientificname" depth="0" /><port name="next" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>format_value</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>1.3</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="">\r
+ <value>darwin</value>\r
+</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="">\r
+ <maxJobs>1</maxJobs>\r
+</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="">\r
+ <backoffFactor>1.0</backoffFactor>\r
+ <initialDelay>1000</initialDelay>\r
+ <maxDelay>5000</maxDelay>\r
+ <maxRetries>0</maxRetries>\r
+</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>next</name><inputPorts><port><name>xml_text</name><depth>0</depth></port></inputPorts><outputPorts><port><name>nodelist</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>xpath-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.xpath.XPathActivity</class><inputMap><map from="xml_text" to="xml_text" /></inputMap><outputMap><map from="nodelist" to="nodelist" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.xpath.XPathActivityConfigurationBean xmlns="">\r
+ <xmlDocument><?xml version="1.0" encoding="UTF-8"?>\r
+<?xml-stylesheet type="text/xsl" href="http://data.gbif.org/ws/rest/taxon/stylesheet"?><gbif:gbifResponse xmlns:gbif="http://portal.gbif.org/ws/response/gbif" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:tc="http://rs.tdwg.org/ontology/voc/TaxonConcept#" xmlns:tn="http://rs.tdwg.org/ontology/voc/TaxonName#" xsi:schemaLocation="http://portal.gbif.org/ws/response/gbif http://data.gbif.org/ws/rest/taxon/schema http://purl.org/dc/elements/1.1/ http://data.gbif.org/schema/dc.xsd http://purl.org/dc/terms/ http://data.gbif.org/schema/dcterms.xsd http://www.w3.org/1999/02/22-rdf-syntax-ns# http://data.gbif.org/schema/rdf.xsd http://www.w3.org/2002/07/owl# http://data.gbif.org/schema/owl.xsd http://rs.tdwg.org/ontology/voc/Common# http://data.gbif.org/schema/tcom.xsd http://rs.tdwg.org/ontology/voc/TaxonOccurrence# http://data.gbif.org/schema/TaxonOccurrence.xsd http://rs.tdwg.org/ontology/voc/TaxonConcept# http://data.gbif.org/schema/TaxonConcept.xsd http://rs.tdwg.org/ontology/voc/TaxonName# http://data.gbif.org/schema/TaxonName.xsd">\r
+ <gbif:header>\r
+ <gbif:help>http://data.gbif.org/ws/rest/taxon/help\r
+</gbif:help>\r
+ <gbif:request>list</gbif:request>\r
+ <gbif:statements>-\r
+\r
+This document contains data shared through the GBIF Network - see http://data.gbif.org/ for more information.\r
+ \r
+All usage of these data must be in accordance with the GBIF Data Use Agreement - see http://www.gbif.org/DataProviders/Agreements/DUA\r
+\r
+-\r
+</gbif:statements>\r
+ <gbif:stylesheet>http://data.gbif.org/ws/rest/taxon/stylesheet</gbif:stylesheet>\r
+ <gbif:parameter name="maxresults" value="100"/>\r
+ <gbif:parameter name="request" value="list"/>\r
+ <gbif:parameter name="service" value="taxon"/>\r
+ <gbif:parameter name="format" value="brief"/>\r
+ <gbif:parameter name="scientificname" value="Plantae"/>\r
+ <gbif:nextRequestUrl>http://data.gbif.org/ws/rest/taxon/list?startindex=100&amp;maxresults=100&amp;format=brief&amp;scientificname=Plantae</gbif:nextRequestUrl>\r
+<gbif:summary start="0" totalMatched="100" next="100" totalReturned="100"/>\r
+ </gbif:header><gbif:dataProviders>\r
+\r
+\r
+<gbif:dataProvider gbifKey="116" rdf:about="http://data.gbif.org/ws/rest/provider/get/116">\r
+ <gbif:name>Museo Nacional de Costa Rica</gbif:name>\r
+ <gbif:dataResources>\r
+ <gbif:dataResource gbifKey="566" rdf:about="http://data.gbif.org/ws/rest/resource/get/566">\r
+ <gbif:name>herbario</gbif:name>\r
+ <gbif:taxonConcepts>\r
+ <tc:TaxonConcept gbifKey="51456466" status="unconfirmed" rdf:about="http://data.gbif.org/ws/rest/taxon/get/51456466">\r
+ <tc:hasName>\r
+ <tn:TaxonName>\r
+ <tn:nameComplete>Plantae</tn:nameComplete>\r
+ <tn:rankString>kingdom</tn:rankString>\r
+ <tn:scientific>true</tn:scientific>\r
+ </tn:TaxonName>\r
+ </tc:hasName>\r
+ <tc:accordingToString>herbario</tc:accordingToString>\r
+ <tc:accordingTo rdf:resource="http://data.gbif.org/ws/rest/resource/get/566"/>\r
+ <tc:primary>true</tc:primary>\r
+ </tc:TaxonConcept> \r
+ </gbif:taxonConcepts>\r
+ </gbif:dataResource> \r
+ </gbif:dataResources>\r
+ </gbif:dataProvider>\r
+<gbif:dataProvider gbifKey="318" rdf:about="http://data.gbif.org/ws/rest/provider/get/318">\r
+ <gbif:name>Arizona State University, Global Institute for Sustainability</gbif:name>\r
+ <gbif:dataResources>\r
+ <gbif:dataResource gbifKey="676" rdf:about="http://data.gbif.org/ws/rest/resource/get/676">\r
+ <gbif:name>Arizona State University Vascular Plant Herbarium</gbif:name>\r
+ <gbif:citation/>\r
+ <gbif:taxonConcepts>\r
+ <tc:TaxonConcept gbifKey="52007005" status="unconfirmed" rdf:about="http://data.gbif.org/ws/rest/taxon/get/52007005">\r
+ <tc:hasName>\r
+ <tn:TaxonName>\r
+ <tn:nameComplete>Plantae</tn:nameComplete>\r
+ <tn:rankString>kingdom</tn:rankString>\r
+ <tn:scientific>true</tn:scientific>\r
+ </tn:TaxonName>\r
+ </tc:hasName>\r
+ <tc:accordingToString>Arizona State University Vascular Plant Herbarium</tc:accordingToString>\r
+ <tc:accordingTo rdf:resource="http://data.gbif.org/ws/rest/resource/get/676"/>\r
+ <tc:primary>true</tc:primary>\r
+ </tc:TaxonConcept> \r
+ </gbif:taxonConcepts>\r
+ </gbif:dataResource> \r
+ </gbif:dataResources>\r
+ </gbif:dataProvider>\r
+<gbif:dataProvider gbifKey="112" rdf:about="http://data.gbif.org/ws/rest/provider/get/112">\r
+ <gbif:name>Mokpo Museum of Natural History</gbif:name>\r
+ <gbif:dataResources>\r
+ <gbif:dataResource gbifKey="570" rdf:about="http://data.gbif.org/ws/rest/resource/get/570">\r
+ <gbif:name>Mokpo Museum of Natural History Plant</gbif:name>\r
+ <gbif:citation/>\r
+ <gbif:taxonConcepts>\r
+ <tc:TaxonConcept gbifKey="51473457" status="unconfirmed" rdf:about="http://data.gbif.org/ws/rest/taxon/get/51473457">\r
+ <tc:hasName>\r
+ <tn:TaxonName>\r
+ <tn:nameComplete>Plantae</tn:nameComplete>\r
+ <tn:rankString>kingdom</tn:rankString>\r
+ <tn:scientific>true</tn:scientific>\r
+ </tn:TaxonName>\r
+ </tc:hasName>\r
+ <tc:accordingToString>Mokpo Museum of Natural History Plant</tc:accordingToString>\r
+ <tc:accordingTo rdf:resource="http://data.gbif.org/ws/rest/resource/get/570"/>\r
+ <tc:primary>true</tc:primary>\r
+ </tc:TaxonConcept> \r
+ </gbif:taxonConcepts>\r
+ </gbif:dataResource> \r
+ </gbif:dataResources>\r
+ </gbif:dataProvider>\r
+<gbif:dataProvider gbifKey="139" rdf:about="http://data.gbif.org/ws/rest/provider/get/139">\r
+ <gbif:name>NLBIF</gbif:name>\r
+ <gbif:dataResources>\r
+ <gbif:dataResource gbifKey="693" rdf:about="http://data.gbif.org/ws/rest/resource/get/693">\r
+ <gbif:name>Natural History Museum Rotterdam</gbif:name>\r
+ <gbif:citation>NLBIF, Natural History Museum Rotterdam</gbif:citation>\r
+ <gbif:taxonConcepts>\r
+ <tc:TaxonConcept gbifKey="52066103" status="unconfirmed" rdf:about="http://data.gbif.org/ws/rest/taxon/get/52066103">\r
+ <tc:hasName>\r
+ <tn:TaxonName>\r
+ <tn:nameComplete>Plantae</tn:nameComplete>\r
+ <tn:rankString>kingdom</tn:rankString>\r
+ <tn:scientific>true</tn:scientific>\r
+ </tn:TaxonName>\r
+ </tc:hasName>\r
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+ <gbif:name>Vascular Plant Collection - University of Washington Herbarium (WTU)</gbif:name>\r
+ <gbif:citation>University of Washington Burke Museum. WTU Herbarium Vascular Plant Collection. Seattle, Washington.</gbif:citation>\r
+ <gbif:taxonConcepts>\r
+ <tc:TaxonConcept gbifKey="50316447" status="unconfirmed" rdf:about="http://data.gbif.org/ws/rest/taxon/get/50316447">\r
+ <tc:hasName>\r
+ <tn:TaxonName>\r
+ <tn:nameComplete>Plantae</tn:nameComplete>\r
+ <tn:rankString>kingdom</tn:rankString>\r
+ <tn:scientific>true</tn:scientific>\r
+ </tn:TaxonName>\r
+ </tc:hasName>\r
+ <tc:accordingToString>Vascular Plant Collection - University of Washington Herbarium (WTU)</tc:accordingToString>\r
+ <tc:accordingTo rdf:resource="http://data.gbif.org/ws/rest/resource/get/126"/>\r
+ <tc:primary>true</tc:primary>\r
+ </tc:TaxonConcept> \r
+ </gbif:taxonConcepts>\r
+ </gbif:dataResource> \r
+ </gbif:dataResources>\r
+ </gbif:dataProvider>\r
+<gbif:dataProvider gbifKey="26" rdf:about="http://data.gbif.org/ws/rest/provider/get/26">\r
+ <gbif:name>CABIDiGIR Provider</gbif:name>\r
+ <gbif:dataResources>\r
+ <gbif:dataResource gbifKey="167" rdf:about="http://data.gbif.org/ws/rest/resource/get/167">\r
+ <gbif:name>CABI Bioscience Fungus Collection</gbif:name>\r
+ <gbif:citation>IMI</gbif:citation>\r
+ <gbif:taxonConcepts>\r
+ <tc:TaxonConcept gbifKey="50432479" status="unconfirmed" rdf:about="http://data.gbif.org/ws/rest/taxon/get/50432479">\r
+ <tc:hasName>\r
+ <tn:TaxonName>\r
+ <tn:nameComplete>Plantae</tn:nameComplete>\r
+ <tn:rankString>kingdom</tn:rankString>\r
+ <tn:scientific>true</tn:scientific>\r
+ </tn:TaxonName>\r
+ </tc:hasName>\r
+ <tc:accordingToString>CABI Bioscience Fungus Collection</tc:accordingToString>\r
+ <tc:accordingTo rdf:resource="http://data.gbif.org/ws/rest/resource/get/167"/>\r
+ <tc:primary>true</tc:primary>\r
+ </tc:TaxonConcept> \r
+ </gbif:taxonConcepts>\r
+ </gbif:dataResource> \r
+ </gbif:dataResources>\r
+ </gbif:dataProvider>\r
+<gbif:dataProvider gbifKey="164" rdf:about="http://data.gbif.org/ws/rest/provider/get/164">\r
+ <gbif:name>The Danish Biodiversity Information Facility</gbif:name>\r
+ <gbif:dataResources>\r
+ <gbif:dataResource gbifKey="703" rdf:about="http://data.gbif.org/ws/rest/resource/get/703">\r
+ <gbif:name>Botany registration database by Danish botanists</gbif:name>\r
+ <gbif:citation/>\r
+ <gbif:taxonConcepts>\r
+ <tc:TaxonConcept gbifKey="52077210" status="unconfirmed" rdf:about="http://data.gbif.org/ws/rest/taxon/get/52077210">\r
+ <tc:hasName>\r
+ <tn:TaxonName>\r
+ <tn:nameComplete>Plantae</tn:nameComplete>\r
+ <tn:rankString>kingdom</tn:rankString>\r
+ <tn:scientific>true</tn:scientific>\r
+ </tn:TaxonName>\r
+ </tc:hasName>\r
+ <tc:accordingToString>Botany registration database by Danish botanists</tc:accordingToString>\r
+ <tc:accordingTo rdf:resource="http://data.gbif.org/ws/rest/resource/get/703"/>\r
+ <tc:primary>true</tc:primary>\r
+ </tc:TaxonConcept> \r
+ </gbif:taxonConcepts>\r
+ </gbif:dataResource> \r
+ <gbif:dataResource gbifKey="702" rdf:about="http://data.gbif.org/ws/rest/resource/get/702">\r
+ <gbif:name>University of Copenhagen's Arboretum</gbif:name>\r
+ <gbif:citation/>\r
+ <gbif:taxonConcepts>\r
+ <tc:TaxonConcept gbifKey="52071070" status="unconfirmed" rdf:about="http://data.gbif.org/ws/rest/taxon/get/52071070">\r
+ <tc:hasName>\r
+ <tn:TaxonName>\r
+ <tn:nameComplete>Plantae</tn:nameComplete>\r
+ <tn:rankString>kingdom</tn:rankString>\r
+ <tn:scientific>true</tn:scientific>\r
+ </tn:TaxonName>\r
+ </tc:hasName>\r
+ <tc:accordingToString>University of Copenhagen's Arboretum</tc:accordingToString>\r
+ <tc:accordingTo rdf:resource="http://data.gbif.org/ws/rest/resource/get/702"/>\r
+ <tc:primary>true</tc:primary>\r
+ </tc:TaxonConcept> \r
+ </gbif:taxonConcepts>\r
+ </gbif:dataResource> \r
+ </gbif:dataResources>\r
+ </gbif:dataProvider>\r
+<gbif:dataProvider gbifKey="30" rdf:about="http://data.gbif.org/ws/rest/provider/get/30">\r
+ <gbif:name>Canadian Biodiversity Information Facility</gbif:name>\r
+ <gbif:dataResources>\r
+ <gbif:dataResource gbifKey="512" rdf:about="http://data.gbif.org/ws/rest/resource/get/512">\r
+ <gbif:name>Royal Botanical Gardens Herbarium</gbif:name>\r
+ <gbif:citation>Royal Botanical Gardens Herbarium</gbif:citation>\r
+ <gbif:taxonConcepts>\r
+ <tc:TaxonConcept gbifKey="51196472" status="unconfirmed" rdf:about="http://data.gbif.org/ws/rest/taxon/get/51196472">\r
+ <tc:hasName>\r
+ <tn:TaxonName>\r
+ <tn:nameComplete>Plantae</tn:nameComplete>\r
+ <tn:rankString>kingdom</tn:rankString>\r
+ <tn:scientific>true</tn:scientific>\r
+ </tn:TaxonName>\r
+ </tc:hasName>\r
+ <tc:accordingToString>Royal Botanical Gardens Herbarium</tc:accordingToString>\r
+ <tc:accordingTo rdf:resource="http://data.gbif.org/ws/rest/resource/get/512"/>\r
+ <tc:primary>true</tc:primary>\r
+ </tc:TaxonConcept> \r
+ </gbif:taxonConcepts>\r
+ </gbif:dataResource> \r
+ <gbif:dataResource gbifKey="526" rdf:about="http://data.gbif.org/ws/rest/resource/get/526">\r
+ <gbif:name>Phragmites of Canada</gbif:name>\r
+ <gbif:citation>Phragmites of Canada</gbif:citation>\r
+ <gbif:taxonConcepts>\r
+ <tc:TaxonConcept gbifKey="51200628" status="unconfirmed" rdf:about="http://data.gbif.org/ws/rest/taxon/get/51200628">\r
+ <tc:hasName>\r
+ <tn:TaxonName>\r
+ <tn:nameComplete>Plantae</tn:nameComplete>\r
+ <tn:rankString>kingdom</tn:rankString>\r
+ <tn:scientific>true</tn:scientific>\r
+ </tn:TaxonName>\r
+ </tc:hasName>\r
+ <tc:accordingToString>Phragmites of Canada</tc:accordingToString>\r
+ <tc:accordingTo rdf:resource="http://data.gbif.org/ws/rest/resource/get/526"/>\r
+ <tc:primary>true</tc:primary>\r
+ </tc:TaxonConcept> \r
+ </gbif:taxonConcepts>\r
+ </gbif:dataResource> \r
+ </gbif:dataResources>\r
+ </gbif:dataProvider>\r
+<gbif:dataProvider gbifKey="6" rdf:about="http://data.gbif.org/ws/rest/provider/get/6">\r
+ <gbif:name>Australian Antarctic Data Centre</gbif:name>\r
+ <gbif:dataResources>\r
+ <gbif:dataResource gbifKey="77" rdf:about="http://data.gbif.org/ws/rest/resource/get/77">\r
+ <gbif:name>Antarctic Marine Protists species checklist</gbif:name>\r
+ <gbif:citation>Species list derived from the book Antarctic Marine Prostists (2005) edited by Fiona J. Scott and Harvey J. Marchant. (ISBN 0 642 56835 9)</gbif:citation>\r
+ <gbif:taxonConcepts>\r
+ <tc:TaxonConcept gbifKey="50248379" status="unconfirmed" rdf:about="http://data.gbif.org/ws/rest/taxon/get/50248379">\r
+ <tc:hasName>\r
+ <tn:TaxonName>\r
+ <tn:nameComplete>Plantae</tn:nameComplete>\r
+ <tn:rankString>kingdom</tn:rankString>\r
+ <tn:scientific>true</tn:scientific>\r
+ </tn:TaxonName>\r
+ </tc:hasName>\r
+ <tc:accordingToString>Antarctic Marine Protists species checklist</tc:accordingToString>\r
+ <tc:accordingTo rdf:resource="http://data.gbif.org/ws/rest/resource/get/77"/>\r
+ <tc:primary>true</tc:primary>\r
+ </tc:TaxonConcept> \r
+ </gbif:taxonConcepts>\r
+ </gbif:dataResource> \r
+ <gbif:dataResource gbifKey="76" rdf:about="http://data.gbif.org/ws/rest/resource/get/76">\r
+ <gbif:name>Australian Antarctic Division Herbarium</gbif:name>\r
+ <gbif:citation>Contact Dave Watts for details on citation details.</gbif:citation>\r
+ <gbif:taxonConcepts>\r
+ <tc:TaxonConcept gbifKey="50244776" status="unconfirmed" rdf:about="http://data.gbif.org/ws/rest/taxon/get/50244776">\r
+ <tc:hasName>\r
+ <tn:TaxonName>\r
+ <tn:nameComplete>Plantae</tn:nameComplete>\r
+ <tn:rankString>kingdom</tn:rankString>\r
+ <tn:scientific>true</tn:scientific>\r
+ </tn:TaxonName>\r
+ </tc:hasName>\r
+ <tc:accordingToString>Australian Antarctic Division Herbarium</tc:accordingToString>\r
+ <tc:accordingTo rdf:resource="http://data.gbif.org/ws/rest/resource/get/76"/>\r
+ <tc:primary>true</tc:primary>\r
+ </tc:TaxonConcept> \r
+ </gbif:taxonConcepts>\r
+ </gbif:dataResource> \r
+ </gbif:dataResources>\r
+ </gbif:dataProvider>\r
+<gbif:dataProvider gbifKey="31" rdf:about="http://data.gbif.org/ws/rest/provider/get/31">\r
+ <gbif:name>Canadian Museum of Nature</gbif:name>\r
+ <gbif:dataResources>\r
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+ <gbif:citation>Canadian Museum of Nature Herbarium (The National Herbarium of Canada)</gbif:citation>\r
+ <gbif:taxonConcepts>\r
+ <tc:TaxonConcept gbifKey="50295570" status="unconfirmed" rdf:about="http://data.gbif.org/ws/rest/taxon/get/50295570">\r
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+ <tn:scientific>true</tn:scientific>\r
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+ <tc:accordingToString>Canadian Museum of Nature Herbarium</tc:accordingToString>\r
+ <tc:accordingTo rdf:resource="http://data.gbif.org/ws/rest/resource/get/123"/>\r
+ <tc:primary>true</tc:primary>\r
+ </tc:TaxonConcept> \r
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+ </gbif:dataResource> \r
+ </gbif:dataResources>\r
+ </gbif:dataProvider>\r
+<gbif:dataProvider gbifKey="8" rdf:about="http://data.gbif.org/ws/rest/provider/get/8">\r
+ <gbif:name>Australian National Herbarium (CANB)</gbif:name>\r
+ <gbif:dataResources>\r
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+ <gbif:name>Australian National Herbarium (CANB)</gbif:name>\r
+ <gbif:citation>http://www.cpbr.gov.au/cpbr/herbarium</gbif:citation>\r
+ <gbif:taxonConcepts>\r
+ <tc:TaxonConcept gbifKey="50029604" status="unconfirmed" rdf:about="http://data.gbif.org/ws/rest/taxon/get/50029604">\r
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+ <tn:TaxonName>\r
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+ <tn:rankString>kingdom</tn:rankString>\r
+ <tn:scientific>true</tn:scientific>\r
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+ <tc:accordingToString>Australian National Herbarium (CANB)</tc:accordingToString>\r
+ <tc:accordingTo rdf:resource="http://data.gbif.org/ws/rest/resource/get/47"/>\r
+ <tc:primary>true</tc:primary>\r
+ </tc:TaxonConcept> \r
+ </gbif:taxonConcepts>\r
+ </gbif:dataResource> \r
+ </gbif:dataResources>\r
+ </gbif:dataProvider>\r
+<gbif:dataProvider gbifKey="75" rdf:about="http://data.gbif.org/ws/rest/provider/get/75">\r
+ <gbif:name>Illinois Natural History Survey</gbif:name>\r
+ <gbif:dataResources>\r
+ <gbif:dataResource gbifKey="225" rdf:about="http://data.gbif.org/ws/rest/resource/get/225">\r
+ <gbif:name>Illinois Natural History Survey</gbif:name>\r
+ <gbif:citation>INHS Insect Collection</gbif:citation>\r
+ <gbif:taxonConcepts>\r
+ <tc:TaxonConcept gbifKey="50581580" status="unconfirmed" rdf:about="http://data.gbif.org/ws/rest/taxon/get/50581580">\r
+ <tc:hasName>\r
+ <tn:TaxonName>\r
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+ <tn:rankString>kingdom</tn:rankString>\r
+ <tn:scientific>true</tn:scientific>\r
+ </tn:TaxonName>\r
+ </tc:hasName>\r
+ <tc:accordingToString>Illinois Natural History Survey</tc:accordingToString>\r
+ <tc:accordingTo rdf:resource="http://data.gbif.org/ws/rest/resource/get/225"/>\r
+ <tc:primary>true</tc:primary>\r
+ </tc:TaxonConcept> \r
+ </gbif:taxonConcepts>\r
+ </gbif:dataResource> \r
+ </gbif:dataResources>\r
+ </gbif:dataProvider>\r
+<gbif:dataProvider gbifKey="141" rdf:about="http://data.gbif.org/ws/rest/provider/get/141">\r
+ <gbif:name>Oregon State University</gbif:name>\r
+ <gbif:dataResources>\r
+ <gbif:dataResource gbifKey="622" rdf:about="http://data.gbif.org/ws/rest/resource/get/622">\r
+ <gbif:name>Vascular Plant Collection</gbif:name>\r
+ <gbif:citation>Oregon State University Herbarium (OSC)</gbif:citation>\r
+ <gbif:taxonConcepts>\r
+ <tc:TaxonConcept gbifKey="51680150" status="unconfirmed" rdf:about="http://data.gbif.org/ws/rest/taxon/get/51680150">\r
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+ <tn:rankString>kingdom</tn:rankString>\r
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+ <tc:accordingToString>Vascular Plant Collection</tc:accordingToString>\r
+ <tc:accordingTo rdf:resource="http://data.gbif.org/ws/rest/resource/get/622"/>\r
+ <tc:primary>true</tc:primary>\r
+ </tc:TaxonConcept> \r
+ </gbif:taxonConcepts>\r
+ </gbif:dataResource> \r
+ </gbif:dataResources>\r
+ </gbif:dataProvider>\r
+<gbif:dataProvider gbifKey="89" rdf:about="http://data.gbif.org/ws/rest/provider/get/89">\r
+ <gbif:name>Instituto de Investigaciones de la AmazonÃa Peruana</gbif:name>\r
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+ <tn:scientific>true</tn:scientific>\r
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+ <tc:accordingToString>HerbarioHerrerense</tc:accordingToString>\r
+ <tc:accordingTo rdf:resource="http://data.gbif.org/ws/rest/resource/get/325"/>\r
+ <tc:primary>true</tc:primary>\r
+ </tc:TaxonConcept> \r
+ </gbif:taxonConcepts>\r
+ </gbif:dataResource> \r
+ </gbif:dataResources>\r
+ </gbif:dataProvider>\r
+</gbif:dataProviders>\r
+</gbif:gbifResponse></xmlDocument>\r
+ <xpathExpression>/gbif:gbifResponse/gbif:header/gbif:summary/@next[1]</xpathExpression>\r
+ <xpathNamespaceMap>\r
+ <entry>\r
+ <string>tn</string>\r
+ <string>http://rs.tdwg.org/ontology/voc/TaxonName#</string>\r
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<maxDelay>5000</maxDelay>\r
<maxRetries>0</maxRetries>\r
-</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>FirstElement_From_XPath</name><inputPorts><port><name>xmltext</name><depth>0</depth></port><port><name>xpath</name><depth>0</depth></port></inputPorts><outputPorts><port><name>nodeVal</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="xmltext" to="xmltext" /><map from="xpath" to="xpath" /></inputMap><outputMap><map from="nodeVal" to="nodeVal" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">\r
+</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="xml_text" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>list_to_single_value</name><inputPorts><port><name>stringlist</name><depth>1</depth></port></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>localworker-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap><map from="stringlist" to="stringlist" /></inputMap><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">\r
<inputs>\r
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
- <name>xpath</name>\r
- <depth>0</depth>\r
- <mimeTypes>\r
- <string>text/plain</string>\r
- </mimeTypes>\r
- <handledReferenceSchemes />\r
- <translatedElementType>java.lang.String</translatedElementType>\r
- <allowsLiteralValues>true</allowsLiteralValues>\r
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
- <name>xmltext</name>\r
- <depth>0</depth>\r
+ <name>stringlist</name>\r
+ <depth>1</depth>\r
<mimeTypes>\r
- <string>text/plain</string>\r
+ <string>l('text/plain')</string>\r
</mimeTypes>\r
<handledReferenceSchemes />\r
<translatedElementType>java.lang.String</translatedElementType>\r
</inputs>\r
<outputs>\r
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
- <name>nodeVal</name>\r
+ <name>value</name>\r
<depth>0</depth>\r
<mimeTypes />\r
<granularDepth>0</granularDepth>\r
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
- </outputs>\r
- <classLoaderSharing>workflow</classLoaderSharing>\r
- <localDependencies />\r
- <artifactDependencies />\r
- <script>import org.dom4j.Document;\r
-import org.dom4j.Node;\r
-import org.dom4j.io.SAXReader;\r
-\r
-SAXReader reader = new SAXReader(false);\r
-reader.setIncludeInternalDTDDeclarations(false);\r
-reader.setIncludeExternalDTDDeclarations(false);\r
-\r
-Document document = reader.read(new StringReader(xmltext));\r
-List nodelist = document.selectNodes(xpath);\r
-\r
-// Process the elements in the nodelist\r
-ArrayList outputList = new ArrayList();\r
-ArrayList outputXmlList = new ArrayList();\r
-\r
-String val = null;\r
-String xmlVal = null;\r
-for (Iterator iter = nodelist.iterator(); iter.hasNext();) {\r
- Node element = (Node) iter.next();\r
- xmlVal = element.asXML();\r
- val = element.getStringValue();\r
- if (val != null && !val.equals("")) {\r
- outputList.add(val);\r
- outputXmlList.add(xmlVal);\r
- }\r
-break;\r
-}\r
-\r
-//List nodelist=outputList;\r
-nodeVal = val;\r
-</script>\r
- <dependencies />\r
-</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></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="">\r
- <maxJobs>1</maxJobs>\r
-</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="">\r
- <backoffFactor>1.0</backoffFactor>\r
- <initialDelay>1000</initialDelay>\r
- <maxDelay>5000</maxDelay>\r
- <maxRetries>0</maxRetries>\r
-</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="xmltext" depth="0" /><port name="xpath" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>COLSynCheck_REST</processor><port>sciId</port></sink><source type="processor"><processor>FirstElement_From_XPath</processor><port>nodeVal</port></source></datalink><datalink><sink type="processor"><processor>FirstElement_From_XPath</processor><port>xmltext</port></sink><source type="dataflow"><port>synResponse</port></source></datalink><datalink><sink type="processor"><processor>FirstElement_From_XPath</processor><port>xpath</port></sink><source type="processor"><processor>taxon_id_xpath</processor><port>value</port></source></datalink><datalink><sink type="dataflow"><port>colResponse</port></sink><source type="processor"><processor>COLSynCheck_REST</processor><port>responseBody</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
- <annotationAssertions>\r
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>3114c079-dc39-46d0-8feb-99dc0f686512</identification>\r
- </annotationBean>\r
- <date>2012-01-23 17:33:51.189 CET</date>\r
- <creators />\r
- <curationEventList />\r
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
- </annotationAssertions>\r
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
- <annotationAssertions>\r
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>91226a57-267d-49c5-adc4-fab3dda2880a</identification>\r
- </annotationBean>\r
- <date>2012-01-23 18:00:29.942 CET</date>\r
- <creators />\r
- <curationEventList />\r
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
- </annotationAssertions>\r
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
- <annotationAssertions>\r
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>126219a1-2553-4015-a3cb-56f21d51f599</identification>\r
- </annotationBean>\r
- <date>2012-01-23 17:18:47.464 CET</date>\r
- <creators />\r
- <curationEventList />\r
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
- </annotationAssertions>\r
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
- <annotationAssertions>\r
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>cff680af-4261-4881-8faa-0c3f155a4f1b</identification>\r
- </annotationBean>\r
- <date>2012-01-23 17:27:35.142 CET</date>\r
- <creators />\r
- <curationEventList />\r
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
- </annotationAssertions>\r
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
- <annotationAssertions>\r
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>8eb05b48-f79d-4448-80a7-d45520247aee</identification>\r
- </annotationBean>\r
- <date>2012-01-24 14:00:38.765 CET</date>\r
- <creators />\r
- <curationEventList />\r
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
- </annotationAssertions>\r
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
- <annotationAssertions>\r
- <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>9b2ea773-b806-4c88-9dd8-8d952d8a0755</identification>\r
- </annotationBean>\r
- <date>2012-01-24 14:32:22.796 CET</date>\r
- <creators />\r
- <curationEventList />\r
- </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
- </annotationAssertions>\r
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
+ </outputs>\r
+ <classLoaderSharing>workflow</classLoaderSharing>\r
+ <localDependencies />\r
+ <artifactDependencies />\r
+ <script>String seperatorString = "\n";\r
+\r
+StringBuffer sb = new StringBuffer();\r
+for (Iterator i = stringlist.iterator(); i.hasNext();) {\r
+ String item = (String) i.next();\r
+ sb.append(item);\r
+ if (i.hasNext()) {\r
+ sb.append(seperatorString);\r
+ }\r
+}\r
+value = sb.toString();\r
+</script>\r
+ <dependencies />\r
+ <localworkerName>org.embl.ebi.escience.scuflworkers.java.StringListMerge</localworkerName>\r
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
- <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>0bc37d95-ca84-4270-9a68-a33a6563caa4</identification>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.HostInstitution">\r
+ <text>UserNameHere</text>\r
</annotationBean>\r
- <date>2012-01-23 17:32:43.771 CET</date>\r
+ <date>2011-12-05 16:37:45.485 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
</annotationAssertions>\r
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></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="">\r
+ <maxJobs>1</maxJobs>\r
+</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="">\r
+ <backoffFactor>1.0</backoffFactor>\r
+ <initialDelay>1000</initialDelay>\r
+ <maxDelay>5000</maxDelay>\r
+ <maxRetries>0</maxRetries>\r
+</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="stringlist" depth="1" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>Transform_XML</processor><port>xslFileURL</port></sink><source type="processor"><processor>gbifResponse_to_csv_xsl</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>Transform_XML</processor><port>inString</port></sink><source type="processor"><processor>gbifOccurrence</processor><port>responseBody</port></source></datalink><datalink><sink type="processor"><processor>gbifOccurrence</processor><port>format</port></sink><source type="processor"><processor>format_value</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>gbifOccurrence</processor><port>scientificname</port></sink><source type="dataflow"><port>sciName</port></source></datalink><datalink><sink type="processor"><processor>gbifOccurrence</processor><port>next</port></sink><source type="dataflow"><port>next</port></source></datalink><datalink><sink type="processor"><processor>next</processor><port>xml_text</port></sink><source type="processor"><processor>gbifOccurrence</processor><port>responseBody</port></source></datalink><datalink><sink type="processor"><processor>list_to_single_value</processor><port>stringlist</port></sink><source type="processor"><processor>next</processor><port>nodelist</port></source></datalink><datalink><sink type="dataflow"><port>next</port></sink><source type="processor"><processor>list_to_single_value</processor><port>value</port></source></datalink><datalink><sink type="dataflow"><port>max1000_csv_output</port></sink><source type="processor"><processor>Transform_XML</processor><port>outputStr</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>1d63adfb-85c4-4ce2-a039-13daee06364a</identification>\r
+ <identification>65d843f2-dc3a-45f3-a8b7-94138384a01a</identification>\r
</annotationBean>\r
- <date>2012-01-23 17:41:34.44 CET</date>\r
+ <date>2012-02-07 18:14:49.842 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>6be0b511-0710-45a1-a809-31681f072659</identification>\r
+ <identification>0405ad51-49d4-499c-bba3-01dbac5fb318</identification>\r
</annotationBean>\r
- <date>2012-01-23 17:30:31.962 CET</date>\r
+ <date>2012-02-07 17:37:21.427 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>09763558-ce78-4cf7-bde5-1a202ba7953c</identification>\r
+ <identification>f653d906-88de-417d-bf3e-61ed29fd6733</identification>\r
</annotationBean>\r
- <date>2012-01-23 17:47:09.64 CET</date>\r
+ <date>2012-02-07 18:09:00.574 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>75f5a83c-3008-466a-ad20-33e95ba9ff15</identification>\r
+ <identification>3d7cc7af-f5a9-428f-a77d-2867c98c66a7</identification>\r
</annotationBean>\r
- <date>2012-01-23 17:38:12.894 CET</date>\r
+ <date>2012-02-07 17:48:00.763 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>07ec689f-59aa-4be9-8481-5f8e3f6000cf</identification>\r
+ <identification>88fdb5ec-112f-40ce-be72-3c9bf4d888b0</identification>\r
</annotationBean>\r
- <date>2012-01-23 17:45:21.174 CET</date>\r
+ <date>2012-02-08 15:37:15.977 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>ca3ec15d-1ea5-4bf2-a81f-136065d1d38b</identification>\r
+ <identification>124b440e-f7ef-445f-901b-b3d04ca3e2a7</identification>\r
</annotationBean>\r
- <date>2012-01-23 17:48:54.281 CET</date>\r
+ <date>2012-03-02 16:39:23.274 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>f856eeda-c416-44e3-b84a-3a0b3b8cd10d</identification>\r
+ <identification>801315c9-0a96-46b3-927b-b74e186f7ece</identification>\r
</annotationBean>\r
- <date>2012-01-23 17:37:08.778 CET</date>\r
+ <date>2012-02-09 17:39:14.181 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>12806644-8a59-4917-a0bf-a32566bfe2ff</identification>\r
+ <identification>428913bf-040a-43f2-9500-bb904c8c5aa6</identification>\r
</annotationBean>\r
- <date>2012-02-10 12:40:34.784 CET</date>\r
+ <date>2012-02-07 17:54:40.933 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
</annotationAssertions>\r
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow><dataflow id="adf2df6f-6ffa-490f-9b73-d8e46adac00b" role="nested"><name>Workflow23</name><inputPorts><port><name>sciNameIn</name><depth>1</depth><granularDepth>1</granularDepth><annotations /></port></inputPorts><outputPorts><port><name>sciName</name><annotations /></port></outputPorts><processors><processor><name>GBIF_Agreement_Interaction</name><inputPorts /><outputPorts><port><name>answer</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>interaction-activity</artifact><version>0.1.2</version></raven><class>net.sf.taverna.t2.activities.interaction.InteractionActivity</class><inputMap /><outputMap><map from="answer" to="answer" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.interaction.InteractionActivityConfigurationBean xmlns="">\r
- <inputs />\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow><dataflow id="85ba17c1-2e24-49d8-a00b-84acb2a1cf61" role="nested"><name>Workflow33</name><inputPorts><port><name>sciName</name><depth>0</depth><granularDepth>0</granularDepth><annotations /></port></inputPorts><outputPorts><port><name>csv_output</name><annotations /></port></outputPorts><processors><processor><name>slwArtDataBank_to_csv_xsl</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="">\r
+ <value>http://ww2.bgbm.org/temp/biovel/slwArtDataBank_to_csv.xsl</value>\r
+</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="">\r
+ <maxJobs>1</maxJobs>\r
+</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="">\r
+ <backoffFactor>1.0</backoffFactor>\r
+ <initialDelay>1000</initialDelay>\r
+ <maxDelay>5000</maxDelay>\r
+ <maxRetries>0</maxRetries>\r
+</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>slwOccurrence</name><inputPorts><port><name>scientificNameFilter</name><depth>0</depth></port></inputPorts><outputPorts><port><name>responseBody</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>rest-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.rest.RESTActivity</class><inputMap><map from="scientificNameFilter" to="scientificNameFilter" /></inputMap><outputMap><map from="responseBody" to="responseBody" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean xmlns="">\r
+ <httpMethod>GET</httpMethod>\r
+ <urlSignature>http://slwgeo.artdata.slu.se:8080/geoserver/wfs?&VERSION=1.0.0&SERVICE=WFS&REQUEST=GetFeature&TYPENAME=SLW:SwedishSpeciesDarwinCore_1.5&Filter={scientificNameFilter}</urlSignature>\r
+ <acceptsHeaderValue>application/xml</acceptsHeaderValue>\r
+ <contentTypeForUpdates>application/xml</contentTypeForUpdates>\r
+ <outgoingDataFormat>String</outgoingDataFormat>\r
+ <sendHTTPExpectRequestHeader>false</sendHTTPExpectRequestHeader>\r
+ <showRedirectionOutputPort>false</showRedirectionOutputPort>\r
+ <escapeParameters>true</escapeParameters>\r
+ <otherHTTPHeaders />\r
+ <activityInputs>\r
+ <entry>\r
+ <string>scientificNameFilter</string>\r
+ <java-class>java.lang.String</java-class>\r
+ </entry>\r
+ </activityInputs>\r
+</net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean></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="">\r
+ <maxJobs>1</maxJobs>\r
+</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="">\r
+ <backoffFactor>1.0</backoffFactor>\r
+ <initialDelay>1000</initialDelay>\r
+ <maxDelay>5000</maxDelay>\r
+ <maxRetries>0</maxRetries>\r
+</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="scientificNameFilter" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>slw_filter_generator</name><inputPorts><port><name>sciName</name><depth>0</depth></port></inputPorts><outputPorts><port><name>filter</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="sciName" to="sciName" /></inputMap><outputMap><map from="filter" to="filter" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">\r
+ <inputs>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ <name>sciName</name>\r
+ <depth>0</depth>\r
+ <mimeTypes>\r
+ <string>text/plain</string>\r
+ </mimeTypes>\r
+ <handledReferenceSchemes />\r
+ <translatedElementType>java.lang.String</translatedElementType>\r
+ <allowsLiteralValues>true</allowsLiteralValues>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ </inputs>\r
<outputs>\r
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
- <name>answer</name>\r
+ <name>filter</name>\r
<depth>0</depth>\r
<mimeTypes />\r
<granularDepth>0</granularDepth>\r
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
</outputs>\r
- <presentationOrigin>http://ww2.bgbm.org/temp/biovel/gbif_agreement.html</presentationOrigin>\r
- <interactionActivityType>LocallyPresentedHtml</interactionActivityType>\r
-</net.sf.taverna.t2.activities.interaction.InteractionActivityConfigurationBean></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="">\r
+ <classLoaderSharing>workflow</classLoaderSharing>\r
+ <localDependencies />\r
+ <artifactDependencies />\r
+ <script>\r
+filter = "<Filter><PropertyIsLike wildCard='*' singleChar='.' escape='!'><PropertyName>scientificName</PropertyName><Literal>*" + sciName + "*</Literal></PropertyIsLike></Filter>";</script>\r
+ <dependencies />\r
+</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></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="">\r
<maxJobs>1</maxJobs>\r
</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="">\r
<backoffFactor>1.0</backoffFactor>\r
<initialDelay>1000</initialDelay>\r
<maxDelay>5000</maxDelay>\r
<maxRetries>0</maxRetries>\r
-</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>GBIF_Agreement_Conditional</name><inputPorts><port><name>agreement_answer</name><depth>0</depth></port><port><name>sciNameIn</name><depth>1</depth></port></inputPorts><outputPorts><port><name>sciNameOut</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="agreement_answer" to="agreement_answer" /><map from="sciNameIn" to="sciNameIn" /></inputMap><outputMap><map from="sciNameOut" to="sciNameOut" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">\r
+</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="sciName" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Transform_XML_String</name><inputPorts><port><name>inString</name><depth>0</depth></port><port><name>xslFileURL</name><depth>0</depth></port></inputPorts><outputPorts><port><name>outputStr</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="inString" to="inString" /><map from="xslFileURL" to="xslFileURL" /></inputMap><outputMap><map from="outputStr" to="outputStr" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">\r
<inputs>\r
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
- <name>agreement_answer</name>\r
+ <name>xslFileURL</name>\r
<depth>0</depth>\r
<mimeTypes>\r
- <string>text/plain</string>\r
+ <string>'text/plain'</string>\r
</mimeTypes>\r
<handledReferenceSchemes />\r
<translatedElementType>java.lang.String</translatedElementType>\r
<allowsLiteralValues>true</allowsLiteralValues>\r
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
- <name>sciNameIn</name>\r
- <depth>1</depth>\r
+ <name>outFileURL</name>\r
+ <depth>0</depth>\r
<mimeTypes>\r
- <string>text/plain</string>\r
+ <string>'text/plain'</string>\r
+ </mimeTypes>\r
+ <handledReferenceSchemes />\r
+ <translatedElementType>java.lang.String</translatedElementType>\r
+ <allowsLiteralValues>true</allowsLiteralValues>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ <name>inString</name>\r
+ <depth>0</depth>\r
+ <mimeTypes>\r
+ <string>'text/plain'</string>\r
+ </mimeTypes>\r
+ <handledReferenceSchemes />\r
+ <translatedElementType>java.lang.String</translatedElementType>\r
+ <allowsLiteralValues>true</allowsLiteralValues>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ <name>outputExt</name>\r
+ <depth>0</depth>\r
+ <mimeTypes>\r
+ <string>'text/plain'</string>\r
</mimeTypes>\r
<handledReferenceSchemes />\r
<translatedElementType>java.lang.String</translatedElementType>\r
</inputs>\r
<outputs>\r
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
- <name>sciNameOut</name>\r
- <depth>1</depth>\r
+ <name>outputStr</name>\r
+ <depth>0</depth>\r
<mimeTypes />\r
- <granularDepth>1</granularDepth>\r
+ <granularDepth>0</granularDepth>\r
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
</outputs>\r
<classLoaderSharing>workflow</classLoaderSharing>\r
<localDependencies />\r
<artifactDependencies />\r
- <script>if(agreement_answer.equals("Yes")) {\r
- sciNameOut = sciNameIn; \r
-} else {\r
- sciNameOut = new ArrayList(); \r
+ <script>import java.io.BufferedReader;\r
+import java.io.BufferedWriter;\r
+import java.io.FileInputStream;\r
+import java.io.FileNotFoundException;\r
+import java.io.FileReader;\r
+import java.io.FileWriter;\r
+import java.io.IOException;\r
+import java.io.InputStreamReader;\r
+import java.io.OutputStreamWriter;\r
+import java.io.StringWriter;\r
+import java.io.StringReader;\r
+import java.io.Writer;\r
+import java.net.URL;\r
+import java.util.HashMap;\r
+import java.util.Map;\r
+\r
+import javax.xml.transform.Result;\r
+import javax.xml.transform.Source;\r
+import javax.xml.transform.SourceLocator;\r
+import javax.xml.transform.Templates;\r
+import javax.xml.transform.Transformer;\r
+import javax.xml.transform.TransformerConfigurationException;\r
+import javax.xml.transform.TransformerException;\r
+import javax.xml.transform.TransformerFactory;\r
+import javax.xml.transform.stream.StreamResult;\r
+import javax.xml.transform.stream.StreamSource;\r
+\r
+BufferedReader getReader (String fileUrl) throws IOException {\r
+ InputStreamReader reader;\r
+ try {\r
+ reader = new FileReader(fileUrl);\r
+ }\r
+ catch (FileNotFoundException e) {\r
+ // try a real URL instead\r
+ URL url = new URL(fileUrl);\r
+ reader = new InputStreamReader (url.openStream());\r
+ }\r
+ return new BufferedReader(reader);\r
+ }\r
+ \r
+BufferedWriter getWriter (String fileUrl) throws IOException {\r
+ Writer writer;\r
+ try {\r
+ writer = new FileWriter(fileUrl);\r
+ }\r
+ catch (FileNotFoundException e) {\r
+ // try a real URL instead\r
+ URL url = new URL(fileUrl);\r
+ writer = new OutputStreamWriter (url.openConnection().getOutputStream());\r
+ }\r
+ return new BufferedWriter(writer);\r
+ }\r
+ \r
+String xslFilename = xslFileURL;\r
+String outFilename;\r
+if (outFileURL != void) {\r
+ outFilename = outFileURL;\r
+}\r
+\r
+String ext;\r
+if (outputExt != void) {\r
+ ext = outputExt;\r
}\r
\r
+\r
+\r
+// Create transformer factory\r
+TransformerFactory factory = TransformerFactory.newInstance();\r
+\r
+// Use the factory to create a template containing the xsl file\r
+Templates template = factory.newTemplates(new StreamSource(getReader(xslFilename)));\r
+\r
+// Use the template to create a transformer\r
+Transformer xformer = template.newTransformer();\r
+\r
+// Prepare the input and output files\r
+Reader sourceReader = new StringReader(inString);\r
+Source source = new StreamSource(sourceReader);\r
+StringWriter resultStr = new StringWriter();\r
+Result result = new StreamResult(resultStr);\r
+\r
+// Apply the xsl file to the source file and write the result to the\r
+// output file\r
+xformer.transform(source, result);\r
+\r
+outputStr = resultStr.toString();\r
+\r
+if ((outFilename != null) && !outFilename.equals("")) {\r
+\r
+ BufferedWriter out = getWriter(outFilename);\r
+\r
+ out.write(outputStr);\r
+ out.close();\r
+}\r
+sourceReader.close();\r
</script>\r
<dependencies />\r
-</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></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="">\r
+ <localworkerName>net.sourceforge.taverna.scuflworkers.xml.XSLTWorker</localworkerName>\r
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.HostInstitution">\r
+ <text>UserNameHere</text>\r
+ </annotationBean>\r
+ <date>2012-01-13 17:08:38.768 CET</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></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="">\r
<maxJobs>1</maxJobs>\r
</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="">\r
<backoffFactor>1.0</backoffFactor>\r
<initialDelay>1000</initialDelay>\r
<maxDelay>5000</maxDelay>\r
<maxRetries>0</maxRetries>\r
-</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="
agreement_answer" depth="0" /><port name="sciNameIn" depth="1" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>GBIF_Agreement_Conditional</processor><port>agreement_answer</port></sink><source type="processor"><processor>GBIF_Agreement_Interaction</processor><port>answer</port></source></datalink><datalink><sink type="processor"><processor>GBIF_Agreement_Conditional</processor><port>sciNameIn</port></sink><source type="dataflow"><port>sciNameIn</port></source></datalink><datalink><sink type="dataflow"><port>sciName</port></sink><source type="processor"><processor>GBIF_Agreement_Conditional</processor><port>sciNameOut</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
\r+</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="
inString" depth="0" /><port name="xslFileURL" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>slwOccurrence</processor><port>scientificNameFilter</port></sink><source type="processor"><processor>slw_filter_generator</processor><port>filter</port></source></datalink><datalink><sink type="processor"><processor>slw_filter_generator</processor><port>sciName</port></sink><source type="dataflow"><port>sciName</port></source></datalink><datalink><sink type="processor"><processor>Transform_XML_String</processor><port>inString</port></sink><source type="processor"><processor>slwOccurrence</processor><port>responseBody</port></source></datalink><datalink><sink type="processor"><processor>Transform_XML_String</processor><port>xslFileURL</port></sink><source type="processor"><processor>slwArtDataBank_to_csv_xsl</processor><port>value</port></source></datalink><datalink><sink type="dataflow"><port>csv_output</port></sink><source type="processor"><processor>Transform_XML_String</processor><port>outputStr</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
\r <annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>5e20399a-7e4f-4807-b510-1f15cdc22dd8</identification>\r
+ <identification>a6cc5fd4-fe4a-461f-a371-bc5b87bc0513</identification>\r
</annotationBean>\r
- <date>2012-04-05 16:41:48.618 CEST</date>\r
+ <date>2012-03-20 16:48:17.526 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>c13b55dc-e9e8-4809-887b-cd90764fa7c0</identification>\r
+ <identification>c2694978-40f8-4032-af83-fce1617d630e</identification>\r
</annotationBean>\r
- <date>2012-04-05 16:41:23.996 CEST</date>\r
+ <date>2012-03-20 16:44:25.215 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>fe0524a8-3d93-4759-a0cc-2537bb2a577d</identification>\r
+ <identification>7d53acd3-c1d9-4ab0-9552-7dd5b3955adf</identification>\r
</annotationBean>\r
- <date>2012-04-05 16:34:35.523 CEST</date>\r
+ <date>2012-03-21 17:55:21.599 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>adf2df6f-6ffa-490f-9b73-d8e46adac00b</identification>\r
+ <identification>1db7de4d-ac2e-4ce8-aa12-e50f2535dd51</identification>\r
</annotationBean>\r
- <date>2012-04-05 16:54:07.336 CEST</date>\r
+ <date>2012-03-20 17:01:09.185 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>1f4e6dc3-c3d1-40c2-9278-8f6396184737</identification>\r
+ <identification>85ba17c1-2e24-49d8-a00b-84acb2a1cf61</identification>\r
</annotationBean>\r
- <date>2012-04-05 16:53:48.103 CEST</date>\r
+ <date>2012-03-22 09:26:26.82 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>25f616d8-fa88-4d60-8127-8228cf93c5a3</identification>\r
+ <identification>0ae246b3-cb94-4c25-851c-d306d21ad467</identification>\r
</annotationBean>\r
- <date>2012-04-05 16:31:27.376 CEST</date>\r
+ <date>2012-03-20 17:37:48.845 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>25760699-c10c-4abe-ac58-2277f17a319b</identification>\r
+ <identification>62e3c568-62d4-405a-85e1-59356b885e27</identification>\r
</annotationBean>\r
- <date>2012-04-05 16:47:29.177 CEST</date>\r
+ <date>2012-03-20 17:00:24.471 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
</annotationAssertions>\r
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow><dataflow id="89482956-6a9c-4300-ace2-d8cebb2c4750" role="nested"><name>Workflow21</name><inputPorts><port><name>nameStatus</name><depth>0</depth><granularDepth>0</granularDepth><annotations /></port><port><name>colResponseIN</name><depth>0</depth><granularDepth>0</granularDepth><annotations /></port></inputPorts><outputPorts><port><name>colResponse</name><annotations /></port></outputPorts><processors><processor><name>AssignInputOutput</name><inputPorts><port><name>in</name><depth>0</depth></port></inputPorts><outputPorts><port><name>out</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="in" to="in" /></inputMap><outputMap><map from="out" to="out" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">\r
- <inputs>\r
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
- <name>in</name>\r
- <depth>0</depth>\r
- <mimeTypes>\r
- <string>text/plain</string>\r
- </mimeTypes>\r
- <handledReferenceSchemes />\r
- <translatedElementType>java.lang.String</translatedElementType>\r
- <allowsLiteralValues>true</allowsLiteralValues>\r
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
- </inputs>\r
- <outputs>\r
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
- <name>out</name>\r
- <depth>0</depth>\r
- <mimeTypes />\r
- <granularDepth>0</granularDepth>\r
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
- </outputs>\r
- <classLoaderSharing>workflow</classLoaderSharing>\r
- <localDependencies />\r
- <artifactDependencies />\r
- <script>out = in;</script>\r
- <dependencies />\r
-</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></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="">\r
- <maxJobs>1</maxJobs>\r
-</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="">\r
- <backoffFactor>1.0</backoffFactor>\r
- <initialDelay>1000</initialDelay>\r
- <maxDelay>5000</maxDelay>\r
- <maxRetries>0</maxRetries>\r
-</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="in" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>AssignInputOutput</processor><port>in</port></sink><source type="dataflow"><port>colResponseIN</port></source></datalink><datalink><sink type="dataflow"><port>colResponse</port></sink><source type="processor"><processor>AssignInputOutput</processor><port>out</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>6eadb547-663a-49c7-bdf8-a23b2d7f4123</identification>\r
+ <identification>1dd9b6f5-24e8-4ea7-875f-4e98f9d135e4</identification>\r
</annotationBean>\r
- <date>2012-01-24 14:07:22.177 CET</date>\r
+ <date>2012-03-21 13:25:11.607 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>810c97ff-1258-47ad-a9fa-c018449828ef</identification>\r
+ <identification>eafd7ab2-9c8f-4bfc-bac6-31e87a14286c</identification>\r
</annotationBean>\r
- <date>2012-01-24 14:06:51.959 CET</date>\r
+ <date>2012-03-20 16:59:03.163 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>89482956-6a9c-4300-ace2-d8cebb2c4750</identification>\r
+ <identification>c0f096ee-4813-461c-a55a-6d153f3d06fb</identification>\r
</annotationBean>\r
- <date>2012-01-24 14:27:28.355 CET</date>\r
+ <date>2012-03-21 13:13:48.453 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>724a8409-b76e-40b8-ab78-45fad288675b</identification>\r
+ <identification>15151ee4-7e16-4331-acb4-34a735cf3631</identification>\r
</annotationBean>\r
- <date>2012-01-24 14:06:25.755 CET</date>\r
+ <date>2012-03-20 16:54:42.882 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>b8e14154-831e-41ce-b590-9f6daaa9fa67</identification>\r
+ <identification>1c711ced-b003-47e0-bd32-3abd5705da83</identification>\r
</annotationBean>\r
- <date>2012-01-24 14:12:26.300 CET</date>\r
+ <date>2012-03-22 09:26:09.603 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>8da12769-2015-408b-a6e2-d331a50c9c96</identification>\r
+ <identification>f4b19cf9-23f9-483a-ad3c-bfd981052f51</identification>\r
</annotationBean>\r
- <date>2012-01-24 14:10:10.838 CET</date>\r
+ <date>2012-03-20 16:53:37.766 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>95364f28-7f90-498a-bc62-1d1ede09052c</identification>\r
+ <identification>986b70a2-9f54-4b20-80a8-aead9fdd537d</identification>\r
</annotationBean>\r
- <date>2012-01-24 14:08:22.102 CET</date>\r
+ <date>2012-03-21 17:56:36.196 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
</annotationAssertions>\r
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow><dataflow id="d18fe496-419c-4f13-9a5e-9ea550bc3a1e" role="nested"><name>Workflow11</name><inputPorts><port><name>synRequest</name><depth>0</depth><granularDepth>0</granularDepth><annotations /></port></inputPorts><outputPorts><port><name>synResponse</name><annotations /></port></outputPorts><processors><processor><name>COLRest_Service</name><inputPorts><port><name>sciName</name><depth>0</depth></port></inputPorts><outputPorts><port><name>responseBody</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>rest-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.rest.RESTActivity</class><inputMap><map from="sciName" to="sciName" /></inputMap><outputMap><map from="responseBody" to="responseBody" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean xmlns="">\r
- <httpMethod>GET</httpMethod>\r
- <urlSignature>http://www.catalogueoflife.org/webservice?response=full&name={sciName}</urlSignature>\r
- <acceptsHeaderValue>application/xml</acceptsHeaderValue>\r
- <contentTypeForUpdates>application/xml</contentTypeForUpdates>\r
- <outgoingDataFormat>String</outgoingDataFormat>\r
- <sendHTTPExpectRequestHeader>false</sendHTTPExpectRequestHeader>\r
- <showRedirectionOutputPort>false</showRedirectionOutputPort>\r
- <escapeParameters>true</escapeParameters>\r
- <otherHTTPHeaders />\r
- <activityInputs>\r
- <entry>\r
- <string>sciName</string>\r
- <java-class>java.lang.String</java-class>\r
- </entry>\r
- </activityInputs>\r
-</net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean></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="">\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>1f00c813-cd52-4caa-8030-892cccb3ab13</identification>\r
+ </annotationBean>\r
+ <date>2012-03-20 17:39:54.780 CET</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow><dataflow id="ba529013-0329-4a22-be72-26b854e18f51" role="nested"><name>Workflow38</name><inputPorts><port><name>csvData</name><depth>0</depth><granularDepth>0</granularDepth><annotations /></port></inputPorts><outputPorts><port><name>csv_output</name><annotations /></port></outputPorts><processors><processor><name>Wrap_strings_in_query_element</name><inputPorts><port><name>string1</name><depth>0</depth></port><port><name>string2</name><depth>0</depth></port></inputPorts><outputPorts><port><name>output</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="string2" to="string2" /><map from="string1" to="string1" /></inputMap><outputMap><map from="output" to="output" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">\r
+ <inputs>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ <name>string1</name>\r
+ <depth>0</depth>\r
+ <mimeTypes>\r
+ <string>'text/plain'</string>\r
+ </mimeTypes>\r
+ <handledReferenceSchemes />\r
+ <translatedElementType>java.lang.String</translatedElementType>\r
+ <allowsLiteralValues>true</allowsLiteralValues>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ <name>string2</name>\r
+ <depth>0</depth>\r
+ <mimeTypes>\r
+ <string>'text/plain'</string>\r
+ </mimeTypes>\r
+ <handledReferenceSchemes />\r
+ <translatedElementType>java.lang.String</translatedElementType>\r
+ <allowsLiteralValues>true</allowsLiteralValues>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ </inputs>\r
+ <outputs>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
+ <name>output</name>\r
+ <depth>0</depth>\r
+ <mimeTypes />\r
+ <granularDepth>0</granularDepth>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
+ </outputs>\r
+ <classLoaderSharing>workflow</classLoaderSharing>\r
+ <localDependencies />\r
+ <artifactDependencies />\r
+ <script>output = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<syncheck>\n<query>\n" + string1 + string2 + "</query>\n</syncheck>";</script>\r
+ <dependencies />\r
+ <localworkerName>org.embl.ebi.escience.scuflworkers.java.StringConcat</localworkerName>\r
+</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.HostInstitution">\r
+ <text>UserNameHere</text>\r
+ </annotationBean>\r
+ <date>2012-05-31 16:14:43.533 CEST</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></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="">\r
<maxJobs>1</maxJobs>\r
</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="">\r
<backoffFactor>1.0</backoffFactor>\r
<initialDelay>1000</initialDelay>\r
<maxDelay>5000</maxDelay>\r
<maxRetries>0</maxRetries>\r
-</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="sciName" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>name_status_xpath</name><inputPorts /><outputPorts><port><name>value</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>stringconstant-activity</artifact><version>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="">\r
- <value>/results/result[1]/name_status</value>\r
-</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="">\r
+</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><dot><port name="string1" depth="0" /><port name="string2" depth="0" /></dot></strategy></iteration></iterationStrategyStack></processor><processor><name>occ_retrieval</name><inputPorts><port><name>sciNameList</name><depth>1</depth></port></inputPorts><outputPorts><port><name>csv_output</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>dataflow-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.dataflow.DataflowActivity</class><inputMap><map from="sciNameList" to="sciNameList" /></inputMap><outputMap><map from="csv_output" to="csv_output" /></outputMap><configBean encoding="dataflow"><dataflow ref="215a1834-28df-4b7d-b6c2-48f559140fa2" /></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="">\r
<maxJobs>1</maxJobs>\r
</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="">\r
<backoffFactor>1.0</backoffFactor>\r
<initialDelay>1000</initialDelay>\r
<maxDelay>5000</maxDelay>\r
<maxRetries>0</maxRetries>\r
-</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>NameStatusConditional</name><inputPorts><port><name>nameStatus</name><depth>0</depth></port></inputPorts><outputPorts><port><name>synpass_flags</name><depth>1</depth><granularDepth>1</granularDepth></port><port><name>synfail_flags</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="nameStatus" to="nameStatus" /></inputMap><outputMap><map from="synpass_flags" to="synpass_flags" /><map from="synfail_flags" to="synfail_flags" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">\r
+</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="sciNameList" depth="1" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>SynCheckGUI</name><inputPorts><port><name>synreqres_list</name><depth>1</depth></port></inputPorts><outputPorts><port><name>out</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="synreqres_list" to="synreqres_list" /></inputMap><outputMap><map from="out" to="out" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">\r
<inputs>\r
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
- <name>nameStatus</name>\r
- <depth>0</depth>\r
+ <name>synreqres_list</name>\r
+ <depth>1</depth>\r
<mimeTypes>\r
<string>text/plain</string>\r
</mimeTypes>\r
</inputs>\r
<outputs>\r
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
- <name>synpass_flags</name>\r
- <depth>1</depth>\r
- <mimeTypes />\r
- <granularDepth>1</granularDepth>\r
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
- <name>synfail_flags</name>\r
+ <name>out</name>\r
<depth>1</depth>\r
<mimeTypes />\r
<granularDepth>1</granularDepth>\r
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
</outputs>\r
<classLoaderSharing>workflow</classLoaderSharing>\r
- <localDependencies />\r
+ <localDependencies>\r
+ <string>DCWorkflow.jar</string>\r
+ </localDependencies>\r
<artifactDependencies />\r
- <script>import java.util.ArrayList;\r
+ <script>import org.bgbm.biovel.datacleaning.syncheck.SynCheckDialog;\r
+Frame f = new JFrame();\r
\r
-ArrayList synpass_flags = new ArrayList();\r
-ArrayList synfail_flags = new ArrayList();\r
+SynCheckDialog scd = new SynCheckDialog(f,true, synreqres_list);\r
+scd.setLocationRelativeTo(null);\r
+scd.show();\r
\r
-if (nameStatus.equals("synonym")) {\r
- synpass_flags.add(nameStatus); \r
-} else {\r
- synfail_flags.add(nameStatus); \r
-}</script>\r
+out = scd.getUniqueNameList();\r
+</script>\r
<dependencies />\r
</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></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="">\r
<maxJobs>1</maxJobs>\r
<initialDelay>1000</initialDelay>\r
<maxDelay>5000</maxDelay>\r
<maxRetries>0</maxRetries>\r
-</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="nameStatus" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>if_synonym</name><inputPorts><port><name>nameStatus</name><depth>0</depth></port><port><name>synResponse</name><depth>0</depth></port></inputPorts><outputPorts><port><name>colResponse</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>dataflow-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.dataflow.DataflowActivity</class><inputMap><map from="nameStatus" to="nameStatus" /><map from="synResponse" to="synResponse" /></inputMap><outputMap><map from="colResponse" to="colResponse" /></outputMap><configBean encoding="dataflow"><dataflow ref="12806644-8a59-4917-a0bf-a32566bfe2ff" /></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="">\r
- <maxJobs>1</maxJobs>\r
-</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="">\r
- <backoffFactor>1.0</backoffFactor>\r
- <initialDelay>1000</initialDelay>\r
- <maxDelay>5000</maxDelay>\r
- <maxRetries>0</maxRetries>\r
-</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="nameStatus" depth="0" /><port name="synResponse" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>if_not_synonym</name><inputPorts><port><name>nameStatus</name><depth>0</depth></port><port><name>colResponseIN</name><depth>0</depth></port></inputPorts><outputPorts><port><name>colResponse</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>dataflow-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.dataflow.DataflowActivity</class><inputMap><map from="colResponseIN" to="colResponseIN" /><map from="nameStatus" to="nameStatus" /></inputMap><outputMap><map from="colResponse" to="colResponse" /></outputMap><configBean encoding="dataflow"><dataflow ref="89482956-6a9c-4300-ace2-d8cebb2c4750" /></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="">\r
+</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="synreqres_list" depth="1" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>DCSynExpInputParser</name><inputPorts><port><name>csvData</name><depth>0</depth></port></inputPorts><outputPorts><port><name>synonymRequest</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="csvData" to="csvData" /></inputMap><outputMap><map from="synonymRequest" to="synonymRequest" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">\r
+ <inputs>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ <name>csvData</name>\r
+ <depth>0</depth>\r
+ <mimeTypes>\r
+ <string>text/plain</string>\r
+ </mimeTypes>\r
+ <handledReferenceSchemes />\r
+ <translatedElementType>java.lang.String</translatedElementType>\r
+ <allowsLiteralValues>true</allowsLiteralValues>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ </inputs>\r
+ <outputs>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
+ <name>synonymRequest</name>\r
+ <depth>1</depth>\r
+ <mimeTypes />\r
+ <granularDepth>1</granularDepth>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
+ <name>incorrectRecords</name>\r
+ <depth>0</depth>\r
+ <mimeTypes />\r
+ <granularDepth>0</granularDepth>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
+ </outputs>\r
+ <classLoaderSharing>workflow</classLoaderSharing>\r
+ <localDependencies />\r
+ <artifactDependencies />\r
+ <script>import org.bgbm.biovel.datacleaning.syncheck.DCSynExpInputParser;\r
+import java.util.HashSet;\r
+ \r
+DCSynExpInputParser dcseip = new DCSynExpInputParser();\r
+HashSet sci_names_hs = dcseip.parse(csvData);\r
+synonymRequest = dcseip.synReq(sci_names_hs);\r
+incorrectRecords = dcseip.incorrectRecordsBldr.toString();\r
+</script>\r
+ <dependencies />\r
+</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></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="">\r
<maxJobs>1</maxJobs>\r
</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="">\r
<backoffFactor>1.0</backoffFactor>\r
<initialDelay>1000</initialDelay>\r
<maxDelay>5000</maxDelay>\r
<maxRetries>0</maxRetries>\r
-</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="nameStatus" depth="0" /><port name="colResponseIN" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Merge_String_List_to_a_String</name><inputPorts><port><name>stringlist</name><depth>1</depth></port></inputPorts><outputPorts><port><name>concatenated</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="stringlist" to="stringlist" /></inputMap><outputMap><map from="concatenated" to="concatenated" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">\r
+</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="csvData" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Merge_String_List_to_a_String</name><inputPorts><port><name>seperator</name><depth>0</depth></port><port><name>stringlist</name><depth>1</depth></port></inputPorts><outputPorts><port><name>concatenated</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="seperator" to="seperator" /><map from="stringlist" to="stringlist" /></inputMap><outputMap><map from="concatenated" to="concatenated" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">\r
<inputs>\r
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
<name>stringlist</name>\r
<initialDelay>1000</initialDelay>\r
<maxDelay>5000</maxDelay>\r
<maxRetries>0</maxRetries>\r
-</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="stringlist" depth="1" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Flatten_List</name><inputPorts><port><name>inputlist</name><depth>2</depth></port></inputPorts><outputPorts><port><name>outputlist</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="inputlist" to="inputlist" /></inputMap><outputMap><map from="outputlist" to="outputlist" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">\r
+</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="seperator" depth="0" /><port name="stringlist" depth="1" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>no_separator</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="">\r
+ <value />\r
+</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="">\r
+ <maxJobs>1</maxJobs>\r
+</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="">\r
+ <backoffFactor>1.0</backoffFactor>\r
+ <initialDelay>1000</initialDelay>\r
+ <maxDelay>5000</maxDelay>\r
+ <maxRetries>0</maxRetries>\r
+</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>GBIF_ChkList_Retriever</name><inputPorts /><outputPorts><port><name>responseBody</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>rest-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.rest.RESTActivity</class><inputMap /><outputMap><map from="responseBody" to="responseBody" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean xmlns="">\r
+ <httpMethod>GET</httpMethod>\r
+ <urlSignature>http://ecat-dev.gbif.org/ws/checklist</urlSignature>\r
+ <acceptsHeaderValue>application/json</acceptsHeaderValue>\r
+ <contentTypeForUpdates>application/xml</contentTypeForUpdates>\r
+ <outgoingDataFormat>String</outgoingDataFormat>\r
+ <sendHTTPExpectRequestHeader>false</sendHTTPExpectRequestHeader>\r
+ <showRedirectionOutputPort>false</showRedirectionOutputPort>\r
+ <escapeParameters>true</escapeParameters>\r
+ <otherHTTPHeaders />\r
+ <activityInputs />\r
+</net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean></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="">\r
+ <maxJobs>1</maxJobs>\r
+</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="">\r
+ <backoffFactor>1.0</backoffFactor>\r
+ <initialDelay>1000</initialDelay>\r
+ <maxDelay>5000</maxDelay>\r
+ <maxRetries>0</maxRetries>\r
+</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>GBIFCheckListParser</name><inputPorts><port><name>gbifChkListJSON</name><depth>0</depth></port></inputPorts><outputPorts><port><name>gbifChkList</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="gbifChkListJSON" to="gbifChkListJSON" /></inputMap><outputMap><map from="gbifChkList" to="gbifChkList" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">\r
<inputs>\r
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
- <name>inputlist</name>\r
- <depth>2</depth>\r
+ <name>gbifChkListJSON</name>\r
+ <depth>0</depth>\r
<mimeTypes>\r
- <string>l(l(''))</string>\r
+ <string>text/plain</string>\r
</mimeTypes>\r
<handledReferenceSchemes />\r
- <translatedElementType>[B</translatedElementType>\r
+ <translatedElementType>java.lang.String</translatedElementType>\r
<allowsLiteralValues>true</allowsLiteralValues>\r
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
</inputs>\r
<outputs>\r
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
- <name>outputlist</name>\r
+ <name>gbifChkList</name>\r
<depth>1</depth>\r
- <mimeTypes>\r
- <string>l('')</string>\r
- </mimeTypes>\r
+ <mimeTypes />\r
<granularDepth>1</granularDepth>\r
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
</outputs>\r
<classLoaderSharing>workflow</classLoaderSharing>\r
- <localDependencies />\r
+ <localDependencies>\r
+ <string>json-simple-1.1.1.jar</string>\r
+ <string>DCWorkflow.jar</string>\r
+ </localDependencies>\r
<artifactDependencies />\r
- <script>flatten(inputs, outputs, depth) {\r
- for (i = inputs.iterator(); i.hasNext();) {\r
- element = i.next();\r
- if (element instanceof Collection && depth > 0) {\r
- flatten(element, outputs, depth - 1);\r
- } else {\r
- outputs.add(element);\r
- }\r
- }\r
+ <script>import java.util.Iterator;\r
+import org.json.simple.JSONArray;\r
+import org.json.simple.JSONObject;\r
+import org.json.simple.parser.JSONParser;\r
+\r
+gbifChkList = new ArrayList();\r
+JSONParser parser = new JSONParser();\r
+\r
+Object obj = parser.parse(gbifChkListJSON);\r
+JSONObject jsonObject = (JSONObject) obj;\r
+ \r
+JSONArray data = (JSONArray) jsonObject.get("data");\r
+Iterator iterator = data.iterator();\r
+while (iterator.hasNext()) {\r
+ JSONObject dataObject= (JSONObject)iterator.next();\r
+ Number datasetID = (Number)dataObject.get("datasetID");\r
+ String title = (String)dataObject.get("title");\r
+ gbifChkList.add(title + ":" + String.valueOf(datasetID));\r
}\r
\r
-outputlist = new ArrayList();\r
\r
-flatten(inputlist, outputlist, 1);</script>\r
+</script>\r
<dependencies />\r
- <localworkerName>org.embl.ebi.escience.scuflworkers.java.FlattenList</localworkerName>\r
-</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="">\r
- <maxJobs>1</maxJobs>\r
-</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="">\r
- <backoffFactor>1.0</backoffFactor>\r
- <initialDelay>1000</initialDelay>\r
- <maxDelay>5000</maxDelay>\r
- <maxRetries>0</maxRetries>\r
-</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="inputlist" depth="2" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>colRes_to_SynRes_xsl</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="">\r
- <value>http://www.myexperiment.org/files/697/download/colres_to_synres.xsl</value>\r
-</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="">\r
+</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></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="">\r
<maxJobs>1</maxJobs>\r
</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="">\r
<backoffFactor>1.0</backoffFactor>\r
<initialDelay>1000</initialDelay>\r
<maxDelay>5000</maxDelay>\r
<maxRetries>0</maxRetries>\r
-</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>Transform_XML_with_parameters</name><inputPorts><port><name>xsltString</name><depth>0</depth></port><port><name>sourceString</name><depth>0</depth></port><port><name>paramList</name><depth>1</depth></port></inputPorts><outputPorts><port><name>outputString</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="xsltString" to="xsltString" /><map from="paramList" to="paramList" /><map from="sourceString" to="sourceString" /></inputMap><outputMap><map from="outputString" to="outputString" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">\r
+</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="gbifChkListJSON" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>DCSynExpInputDialog</name><inputPorts><port><name>gbifChkLists</name><depth>1</depth></port><port><name>synonymRequest</name><depth>1</depth></port></inputPorts><outputPorts><port><name>gbifSynReq</name><depth>1</depth><granularDepth>1</granularDepth></port><port><name>gbifSelChkListIDs</name><depth>1</depth><granularDepth>1</granularDepth></port><port><name>colCopyright</name><depth>1</depth><granularDepth>1</granularDepth></port><port><name>colSynReq</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="synonymRequest" to="synonymRequest" /><map from="gbifChkLists" to="gbifChkLists" /></inputMap><outputMap><map from="colSynReq" to="colSynReq" /><map from="colCopyright" to="colCopyright" /><map from="gbifSynReq" to="gbifSynReq" /><map from="gbifSelChkListIDs" to="gbifSelChkListIDs" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">\r
<inputs>\r
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
- <name>sourceString</name>\r
- <depth>0</depth>\r
- <mimeTypes>\r
- <string>text/plain</string>\r
- </mimeTypes>\r
- <handledReferenceSchemes />\r
- <translatedElementType>java.lang.String</translatedElementType>\r
- <allowsLiteralValues>true</allowsLiteralValues>\r
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
- <name>xsltString</name>\r
- <depth>0</depth>\r
+ <name>gbifChkLists</name>\r
+ <depth>1</depth>\r
<mimeTypes>\r
<string>text/plain</string>\r
</mimeTypes>\r
<allowsLiteralValues>true</allowsLiteralValues>\r
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
- <name>paramList</name>\r
+ <name>synonymRequest</name>\r
<depth>1</depth>\r
<mimeTypes>\r
<string>text/plain</string>\r
</inputs>\r
<outputs>\r
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
- <name>outputString</name>\r
- <depth>0</depth>\r
+ <name>colSynReq</name>\r
+ <depth>1</depth>\r
<mimeTypes />\r
- <granularDepth>0</granularDepth>\r
+ <granularDepth>1</granularDepth>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
+ <name>gbifSynReq</name>\r
+ <depth>1</depth>\r
+ <mimeTypes />\r
+ <granularDepth>1</granularDepth>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
+ <name>gbifSelChkListIDs</name>\r
+ <depth>1</depth>\r
+ <mimeTypes />\r
+ <granularDepth>1</granularDepth>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
+ <name>colCopyright</name>\r
+ <depth>1</depth>\r
+ <mimeTypes />\r
+ <granularDepth>1</granularDepth>\r
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
</outputs>\r
<classLoaderSharing>workflow</classLoaderSharing>\r
- <localDependencies />\r
+ <localDependencies>\r
+ <string>DCWorkflow.jar</string>\r
+ </localDependencies>\r
<artifactDependencies />\r
- <script>//From a proposal by Mikolaj Rybinski\r
-import javax.xml.transform.Source;\r
-import javax.xml.transform.Transformer;\r
-import javax.xml.transform.TransformerFactory;\r
-import javax.xml.transform.stream.StreamResult;\r
-import javax.xml.transform.stream.StreamSource;\r
-\r
-param(paramstr) {\r
- nameAndValue = paramstr.split("=");\r
- if (nameAndValue.length != 2) {\r
- throw new RuntimeException("Wrong parameter format: \"" + paramstr + "\".");\r
- }\r
- name = nameAndValue[0].trim();\r
- value = nameAndValue[1].trim();\r
- return this;\r
-}\r
+ <script>import org.bgbm.biovel.datacleaning.syncheck.DCSynExpInputDialog;\r
+Frame f = new JFrame();\r
\r
-if ((sourceString == void) || (sourceString == null)) {\r
- throw new RuntimeException("sourceString must be specified");\r
-}\r
+DCSynExpInputDialog dcseid = new DCSynExpInputDialog(f,true,gbifChkLists);\r
+dcseid.setLocationRelativeTo(null);\r
+dcseid.show();\r
+colSynReq = new ArrayList();\r
+colCopyright = new ArrayList();\r
+gbifSynReq = new ArrayList();\r
\r
-if ((xsltString == void) || (xsltString == null)) {\r
- throw new RuntimeException("xsltString must be specified");\r
+if(dcseid.isColSelected()) {\r
+ colSynReq = synonymRequest;\r
+ colCopyright.add("tocheck"); \r
}\r
\r
-Source inSource = new StreamSource(new StringReader(sourceString));\r
-Source xslSource = new StreamSource(new StringReader(xsltString));\r
-\r
-// the factory pattern supports different XSLT processors\r
-// e.g. set the "javax.xml.transform.TransformerFactory" system property\r
-TransformerFactory tnfFact = TransformerFactory.newInstance();\r
-Transformer tnf = tnfFact.newTransformer(xslSource);\r
-\r
-if (paramList != void) {\r
- for (String paramstr : paramList) {\r
- p = param(paramstr);\r
- tnf.setParameter(p.name, p.value);\r
- }\r
+if(!dcseid.getSelectedGBIFChkList().isEmpty()) {\r
+ gbifSynReq = synonymRequest; \r
}\r
-\r
-Writer outputWriter = new StringWriter();\r
-tnf.transform(inSource, new StreamResult(outputWriter));\r
-outputString = outputWriter.toString();</script>\r
+gbifSelChkListIDs = dcseid.getSelectedGBIFChkList();</script>\r
<dependencies />\r
- <localworkerName>net.sourceforge.taverna.scuflworkers.xml.XSLTWorkerWithParameters</localworkerName>\r
-</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="">\r
+</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></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="">\r
<maxJobs>1</maxJobs>\r
</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="">\r
<backoffFactor>1.0</backoffFactor>\r
<initialDelay>1000</initialDelay>\r
<maxDelay>5000</maxDelay>\r
<maxRetries>0</maxRetries>\r
-</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="xsltString" depth="0" /><port name="sourceString" depth="0" /><port name="paramList" depth="1" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Read_Text_File_2</name><inputPorts><port><name>fileurl</name><depth>0</depth></port></inputPorts><outputPorts><port><name>filecontents</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="fileurl" to="fileurl" /></inputMap><outputMap><map from="filecontents" to="filecontents" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">\r
+</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="gbifChkLists" depth="1" /><port name="synonymRequest" depth="1" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>gbif_syn_expansion</name><inputPorts><port><name>datasetID</name><depth>0</depth></port><port><name>synReq</name><depth>0</depth></port></inputPorts><outputPorts><port><name>response</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>dataflow-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.dataflow.DataflowActivity</class><inputMap><map from="datasetID" to="datasetID" /><map from="synReq" to="synReq" /></inputMap><outputMap><map from="response" to="response" /></outputMap><configBean encoding="dataflow"><dataflow ref="b8467b4d-a015-44b2-aba8-437c606b0d3c" /></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="">\r
+ <maxJobs>1</maxJobs>\r
+</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="">\r
+ <backoffFactor>1.0</backoffFactor>\r
+ <initialDelay>1000</initialDelay>\r
+ <maxDelay>5000</maxDelay>\r
+ <maxRetries>0</maxRetries>\r
+</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="synReq" depth="0" /><port name="datasetID" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Merge_String_List_to_a_String_2</name><inputPorts><port><name>stringlist</name><depth>1</depth></port></inputPorts><outputPorts><port><name>concatenated</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="stringlist" to="stringlist" /></inputMap><outputMap><map from="concatenated" to="concatenated" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">\r
<inputs>\r
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
- <name>fileurl</name>\r
- <depth>0</depth>\r
+ <name>stringlist</name>\r
+ <depth>1</depth>\r
<mimeTypes>\r
- <string>'text/plain'</string>\r
+ <string>l('text/plain')</string>\r
</mimeTypes>\r
<handledReferenceSchemes />\r
<translatedElementType>java.lang.String</translatedElementType>\r
<allowsLiteralValues>true</allowsLiteralValues>\r
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
- <name>encoding</name>\r
+ <name>seperator</name>\r
<depth>0</depth>\r
<mimeTypes>\r
<string>'text/plain'</string>\r
</inputs>\r
<outputs>\r
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
- <name>filecontents</name>\r
+ <name>concatenated</name>\r
<depth>0</depth>\r
<mimeTypes>\r
<string>'text/plain'</string>\r
<classLoaderSharing>workflow</classLoaderSharing>\r
<localDependencies />\r
<artifactDependencies />\r
- <script>BufferedReader getReader (String fileUrl, String encoding) throws IOException {\r
- InputStreamReader reader;\r
- try {\r
- if (encoding == null) {\r
- reader = new FileReader(fileUrl);\r
- } else {\r
- reader = new InputStreamReader(new FileInputStream(fileUrl),encoding); \r
- }\r
- }\r
- catch (FileNotFoundException e) {\r
- // try a real URL instead\r
- URL url = new URL(fileUrl);\r
- if (encoding == null) {\r
- reader = new InputStreamReader (url.openStream());\r
- } else {\r
- reader = new InputStreamReader (url.openStream(), encoding);\r
- }\r
- }\r
- return new BufferedReader(reader);\r
- }\r
-\r
-\r
-\r
-StringBuffer sb = new StringBuffer(4000);\r
-\r
-if (encoding == void) {\r
- encoding = null;\r
+ <script>String seperatorString = "\n";\r
+if (seperator != void) {\r
+ seperatorString = seperator;\r
}\r
-\r
-BufferedReader in = getReader(fileurl, encoding);\r
-String str;\r
-String lineEnding = System.getProperty("line.separator");\r
-\r
-while ((str = in.readLine()) != null) {\r
- sb.append(str);\r
- sb.append(lineEnding);\r
+StringBuffer sb = new StringBuffer();\r
+for (Iterator i = stringlist.iterator(); i.hasNext();) {\r
+ String item = (String) i.next();\r
+ sb.append(item);\r
+ if (i.hasNext()) {\r
+ sb.append(seperatorString);\r
+ }\r
}\r
-in.close();\r
-filecontents = sb.toString();\r
- \r
+concatenated = sb.toString();\r
</script>\r
<dependencies />\r
- <localworkerName>net.sourceforge.taverna.scuflworkers.io.TextFileReader</localworkerName>\r
+ <localworkerName>org.embl.ebi.escience.scuflworkers.java.StringListMerge</localworkerName>\r
</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="">\r
<maxJobs>1</maxJobs>\r
</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="">\r
<initialDelay>1000</initialDelay>\r
<maxDelay>5000</maxDelay>\r
<maxRetries>0</maxRetries>\r
-</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="fileurl" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>CreateID</name><inputPorts><port><name>name</name><depth>0</depth></port></inputPorts><outputPorts><port><name>id_param</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="name" to="name" /></inputMap><outputMap><map from="id_param" to="id_param" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">\r
+</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="stringlist" depth="1" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Flatten_List</name><inputPorts><port><name>inputlist</name><depth>2</depth></port></inputPorts><outputPorts><port><name>outputlist</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="inputlist" to="inputlist" /></inputMap><outputMap><map from="outputlist" to="outputlist" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">\r
<inputs>\r
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
- <name>name</name>\r
- <depth>0</depth>\r
+ <name>inputlist</name>\r
+ <depth>2</depth>\r
<mimeTypes>\r
- <string>text/plain</string>\r
+ <string>l(l(''))</string>\r
</mimeTypes>\r
<handledReferenceSchemes />\r
- <translatedElementType>java.lang.String</translatedElementType>\r
+ <translatedElementType>[B</translatedElementType>\r
<allowsLiteralValues>true</allowsLiteralValues>\r
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
</inputs>\r
<outputs>\r
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
- <name>id_param</name>\r
- <depth>0</depth>\r
- <mimeTypes />\r
- <granularDepth>0</granularDepth>\r
+ <name>outputlist</name>\r
+ <depth>1</depth>\r
+ <mimeTypes>\r
+ <string>l('')</string>\r
+ </mimeTypes>\r
+ <granularDepth>1</granularDepth>\r
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
</outputs>\r
<classLoaderSharing>workflow</classLoaderSharing>\r
<localDependencies />\r
<artifactDependencies />\r
- <script>\r
-id_param = "syncheckid=" + name</script>\r
+ <script>flatten(inputs, outputs, depth) {\r
+ for (i = inputs.iterator(); i.hasNext();) {\r
+ element = i.next();\r
+ if (element instanceof Collection && depth > 0) {\r
+ flatten(element, outputs, depth - 1);\r
+ } else {\r
+ outputs.add(element);\r
+ }\r
+ }\r
+}\r
+\r
+outputlist = new ArrayList();\r
+\r
+flatten(inputlist, outputlist, 1);</script>\r
<dependencies />\r
-</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></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="">\r
+ <localworkerName>org.embl.ebi.escience.scuflworkers.java.FlattenList</localworkerName>\r
+</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="">\r
<maxJobs>1</maxJobs>\r
</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="">\r
<backoffFactor>1.0</backoffFactor>\r
<initialDelay>1000</initialDelay>\r
<maxDelay>5000</maxDelay>\r
<maxRetries>0</maxRetries>\r
-</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="name" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Transform_XML_2</name><inputPorts><port><name>xslFileURL</name><depth>0</depth></port><port><name>inString</name><depth>0</depth></port></inputPorts><outputPorts><port><name>outputStr</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="inString" to="inString" /><map from="xslFileURL" to="xslFileURL" /></inputMap><outputMap><map from="outputStr" to="outputStr" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">\r
+</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="inputlist" depth="2" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Workflow144</name><inputPorts><port><name>synRequest</name><depth>0</depth></port></inputPorts><outputPorts><port><name>col_copyright_conditional</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>dataflow-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.dataflow.DataflowActivity</class><inputMap><map from="synRequest" to="synRequest" /></inputMap><outputMap><map from="col_copyright_conditional" to="col_copyright_conditional" /></outputMap><configBean encoding="dataflow"><dataflow ref="cb4b094a-0513-4723-9a8a-6313e81b11c4" /></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="">\r
+ <maxJobs>1</maxJobs>\r
+</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="">\r
+ <backoffFactor>1.0</backoffFactor>\r
+ <initialDelay>1000</initialDelay>\r
+ <maxDelay>5000</maxDelay>\r
+ <maxRetries>0</maxRetries>\r
+</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="synRequest" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Workflow11</name><inputPorts><port><name>synRequest</name><depth>0</depth></port></inputPorts><outputPorts><port><name>synResponse</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>dataflow-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.dataflow.DataflowActivity</class><inputMap><map from="synRequest" to="synRequest" /></inputMap><outputMap><map from="synResponse" to="synResponse" /></outputMap><configBean encoding="dataflow"><dataflow ref="61896bb4-e33f-49fa-8792-11bd2c8e3efe" /></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="">\r
+ <maxJobs>1</maxJobs>\r
+</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="">\r
+ <backoffFactor>1.0</backoffFactor>\r
+ <initialDelay>1000</initialDelay>\r
+ <maxDelay>5000</maxDelay>\r
+ <maxRetries>0</maxRetries>\r
+</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="synRequest" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>Beanshell</name><inputPorts><port><name>colSynReq</name><depth>1</depth></port><port><name>col_copyright_conditional</name><depth>1</depth></port></inputPorts><outputPorts><port><name>colSynReq</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="colSynReq" to="colSynReq" /><map from="col_copyright_conditional" to="col_copyright_conditional" /></inputMap><outputMap><map from="colSynReq" to="colSynReq" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">\r
<inputs>\r
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
- <name>xslFileURL</name>\r
- <depth>0</depth>\r
- <mimeTypes>\r
- <string>'text/plain'</string>\r
- </mimeTypes>\r
- <handledReferenceSchemes />\r
- <translatedElementType>java.lang.String</translatedElementType>\r
- <allowsLiteralValues>true</allowsLiteralValues>\r
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
- <name>outFileURL</name>\r
- <depth>0</depth>\r
- <mimeTypes>\r
- <string>'text/plain'</string>\r
- </mimeTypes>\r
- <handledReferenceSchemes />\r
- <translatedElementType>java.lang.String</translatedElementType>\r
- <allowsLiteralValues>true</allowsLiteralValues>\r
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
- <name>inString</name>\r
- <depth>0</depth>\r
+ <name>col_copyright_conditional</name>\r
+ <depth>1</depth>\r
<mimeTypes>\r
- <string>'text/plain'</string>\r
+ <string>text/plain</string>\r
</mimeTypes>\r
<handledReferenceSchemes />\r
<translatedElementType>java.lang.String</translatedElementType>\r
<allowsLiteralValues>true</allowsLiteralValues>\r
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
- <name>outputExt</name>\r
- <depth>0</depth>\r
+ <name>colSynReq</name>\r
+ <depth>1</depth>\r
<mimeTypes>\r
- <string>'text/plain'</string>\r
+ <string>text/plain</string>\r
</mimeTypes>\r
<handledReferenceSchemes />\r
<translatedElementType>java.lang.String</translatedElementType>\r
</inputs>\r
<outputs>\r
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
- <name>outputStr</name>\r
- <depth>0</depth>\r
+ <name>colSynReq</name>\r
+ <depth>1</depth>\r
<mimeTypes />\r
- <granularDepth>0</granularDepth>\r
+ <granularDepth>1</granularDepth>\r
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
</outputs>\r
<classLoaderSharing>workflow</classLoaderSharing>\r
<localDependencies />\r
<artifactDependencies />\r
- <script>import java.io.BufferedReader;\r
-import java.io.BufferedWriter;\r
-import java.io.FileInputStream;\r
-import java.io.FileNotFoundException;\r
-import java.io.FileReader;\r
-import java.io.FileWriter;\r
-import java.io.IOException;\r
-import java.io.InputStreamReader;\r
-import java.io.OutputStreamWriter;\r
-import java.io.StringWriter;\r
-import java.io.Writer;\r
-import java.net.URL;\r
-import java.util.HashMap;\r
-import java.util.Map;\r
-\r
-import javax.xml.transform.Result;\r
-import javax.xml.transform.Source;\r
-import javax.xml.transform.SourceLocator;\r
-import javax.xml.transform.Templates;\r
-import javax.xml.transform.Transformer;\r
-import javax.xml.transform.TransformerConfigurationException;\r
-import javax.xml.transform.TransformerException;\r
-import javax.xml.transform.TransformerFactory;\r
-import javax.xml.transform.stream.StreamResult;\r
-import javax.xml.transform.stream.StreamSource;\r
-\r
-BufferedReader getReader (String fileUrl) throws IOException {\r
- InputStreamReader reader;\r
- try {\r
- reader = new FileReader(fileUrl);\r
- }\r
- catch (FileNotFoundException e) {\r
- // try a real URL instead\r
- URL url = new URL(fileUrl);\r
- reader = new InputStreamReader (url.openStream());\r
- }\r
- return new BufferedReader(reader);\r
- }\r
- \r
-BufferedWriter getWriter (String fileUrl) throws IOException {\r
- Writer writer;\r
- try {\r
- writer = new FileWriter(fileUrl);\r
- }\r
- catch (FileNotFoundException e) {\r
- // try a real URL instead\r
- URL url = new URL(fileUrl);\r
- writer = new OutputStreamWriter (url.openConnection().getOutputStream());\r
- }\r
- return new BufferedWriter(writer);\r
- }\r
- \r
-String xslFilename = xslFileURL;\r
-\r
-\r
-\r
-// Create transformer factory\r
-TransformerFactory factory = TransformerFactory.newInstance();\r
-\r
-// Use the factory to create a template containing the xsl file\r
-Templates template = factory.newTemplates(new StreamSource(getReader(xslFilename)));\r
-\r
-// Use the template to create a transformer\r
-Transformer xformer = template.newTransformer();\r
-\r
-// Prepare the input and output files\r
-Reader sourceReader = new StringReader(inString);\r
-Source source = new StreamSource(sourceReader);\r
-StringWriter resultStr = new StringWriter();\r
-Result result = new StreamResult(resultStr);\r
-\r
-// Apply the xsl file to the source file and write the result to the\r
-// output file\r
-xformer.transform(source, result);\r
-outputStr = resultStr.toString();\r
-sourceReader.close();\r
-</script>\r
+ <script>\r
+if(col_copyright_conditional.isEmpty()){\r
+ colSynReq = new ArrayList();\r
+}</script>\r
<dependencies />\r
- <localworkerName>net.sourceforge.taverna.scuflworkers.xml.XSLTWorker</localworkerName>\r
-</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></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="">\r
+ <maxJobs>1</maxJobs>\r
+</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="">\r
+ <backoffFactor>1.0</backoffFactor>\r
+ <initialDelay>1000</initialDelay>\r
+ <maxDelay>5000</maxDelay>\r
+ <maxRetries>0</maxRetries>\r
+</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="colSynReq" depth="1" /><port name="col_copyright_conditional" depth="1" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>Wrap_strings_in_query_element</processor><port>string1</port></sink><source type="processor"><processor>DCSynExpInputParser</processor><port>synonymRequest</port></source></datalink><datalink><sink type="processor"><processor>Wrap_strings_in_query_element</processor><port>string2</port></sink><source type="processor"><processor>Flatten_List</processor><port>outputlist</port></source></datalink><datalink><sink type="processor"><processor>occ_retrieval</processor><port>sciNameList</port></sink><source type="processor"><processor>SynCheckGUI</processor><port>out</port></source></datalink><datalink><sink type="processor"><processor>SynCheckGUI</processor><port>synreqres_list</port></sink><source type="processor"><processor>Wrap_strings_in_query_element</processor><port>output</port></source></datalink><datalink><sink type="processor"><processor>DCSynExpInputParser</processor><port>csvData</port></sink><source type="dataflow"><port>csvData</port></source></datalink><datalink><sink type="processor"><processor>Merge_String_List_to_a_String</processor><port>seperator</port></sink><source type="processor"><processor>no_separator</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>Merge_String_List_to_a_String</processor><port>stringlist</port></sink><source type="processor"><processor>occ_retrieval</processor><port>csv_output</port></source></datalink><datalink><sink type="processor"><processor>GBIFCheckListParser</processor><port>gbifChkListJSON</port></sink><source type="processor"><processor>GBIF_ChkList_Retriever</processor><port>responseBody</port></source></datalink><datalink><sink type="processor"><processor>DCSynExpInputDialog</processor><port>gbifChkLists</port></sink><source type="processor"><processor>GBIFCheckListParser</processor><port>gbifChkList</port></source></datalink><datalink><sink type="processor"><processor>DCSynExpInputDialog</processor><port>synonymRequest</port></sink><source type="processor"><processor>DCSynExpInputParser</processor><port>synonymRequest</port></source></datalink><datalink><sink type="processor"><processor>gbif_syn_expansion</processor><port>datasetID</port></sink><source type="processor"><processor>DCSynExpInputDialog</processor><port>gbifSelChkListIDs</port></source></datalink><datalink><sink type="processor"><processor>gbif_syn_expansion</processor><port>synReq</port></sink><source type="processor"><processor>DCSynExpInputDialog</processor><port>gbifSynReq</port></source></datalink><datalink><sink type="processor"><processor>Merge_String_List_to_a_String_2</processor><port>stringlist</port></sink><source type="processor"><processor>gbif_syn_expansion</processor><port>response</port></source></datalink><datalink><sink type="processor"><processor>Workflow144</processor><port>synRequest</port></sink><source type="processor"><processor>DCSynExpInputDialog</processor><port>colCopyright</port></source></datalink><datalink><sink type="processor"><processor>Workflow11</processor><port>synRequest</port></sink><source type="processor"><processor>Beanshell</processor><port>colSynReq</port></source></datalink><datalink><sink type="processor"><processor>Beanshell</processor><port>colSynReq</port></sink><source type="processor"><processor>DCSynExpInputDialog</processor><port>colSynReq</port></source></datalink><datalink><sink type="processor"><processor>Beanshell</processor><port>col_copyright_conditional</port></sink><source type="processor"><processor>Workflow144</processor><port>col_copyright_conditional</port></source></datalink><datalink><sink type="merge"><processor>Flatten_List</processor><port>inputlist</port></sink><source type="processor"><processor>Merge_String_List_to_a_String_2</processor><port>concatenated</port></source></datalink><datalink><sink type="merge"><processor>Flatten_List</processor><port>inputlist</port></sink><source type="processor"><processor>Workflow11</processor><port>synResponse</port></source></datalink><datalink><sink type="dataflow"><port>csv_output</port></sink><source type="processor"><processor>Merge_String_List_to_a_String</processor><port>concatenated</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>304759d3-1bc2-41d9-b2bf-6c8530f6efa9</identification>\r
+ </annotationBean>\r
+ <date>2012-06-01 11:15:44.68 CEST</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>3702c3a9-3bac-4f53-bb8d-9fbbd457e077</identification>\r
+ </annotationBean>\r
+ <date>2012-03-29 11:45:10.791 CEST</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>1feeb8b4-0d6c-4436-9a45-088052d4765a</identification>\r
+ </annotationBean>\r
+ <date>2012-04-05 16:36:08.95 CEST</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>7a500a7d-6dc3-4e85-8305-3ad391c40f65</identification>\r
+ </annotationBean>\r
+ <date>2012-05-29 13:42:53.908 CEST</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>24981a7d-e414-45a8-b5f4-97f6fad75bba</identification>\r
+ </annotationBean>\r
+ <date>2012-05-31 16:08:48.525 CEST</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>6a721986-e87d-498d-aefd-09d09b460250</identification>\r
+ </annotationBean>\r
+ <date>2012-05-31 17:21:41.874 CEST</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>ba529013-0329-4a22-be72-26b854e18f51</identification>\r
+ </annotationBean>\r
+ <date>2012-06-01 11:48:11.292 CEST</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>f32affaa-9b9e-442b-a750-8a5ae4b2c154</identification>\r
+ </annotationBean>\r
+ <date>2012-05-31 17:53:41.222 CEST</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>405b2dac-63cb-4a7e-9548-ab4ea4f14aad</identification>\r
+ </annotationBean>\r
+ <date>2012-06-01 11:33:23.582 CEST</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>cdf9c220-fb85-4262-bf44-77fc3302797e</identification>\r
+ </annotationBean>\r
+ <date>2012-03-29 17:02:17.600 CEST</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>efd208a7-5a9b-4f0a-a5a4-4beb3a8cb586</identification>\r
+ </annotationBean>\r
+ <date>2012-03-29 11:37:04.382 CEST</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>cc2ba98d-9d65-4882-a1ff-b64e73082de9</identification>\r
+ </annotationBean>\r
+ <date>2012-03-29 15:33:31.887 CEST</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
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- <date>2012-01-24 15:55:03.158 CET</date>\r
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</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
</annotationAssertions>\r
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- <maxDelay>5000</maxDelay>\r
- <maxRetries>0</maxRetries>\r
-</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>FirstElement_From_XPath</name><inputPorts><port><name>xmltext</name><depth>0</depth></port><port><name>xpath</name><depth>0</depth></port></inputPorts><outputPorts><port><name>nodeVal</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="xmltext" to="xmltext" /><map from="xpath" to="xpath" /></inputMap><outputMap><map from="nodeVal" to="nodeVal" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">\r
- <inputs>\r
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
- <name>xpath</name>\r
- <depth>0</depth>\r
- <mimeTypes>\r
- <string>text/plain</string>\r
- </mimeTypes>\r
- <handledReferenceSchemes />\r
- <translatedElementType>java.lang.String</translatedElementType>\r
- <allowsLiteralValues>true</allowsLiteralValues>\r
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
- <name>xmltext</name>\r
- <depth>0</depth>\r
- <mimeTypes>\r
- <string>text/plain</string>\r
- </mimeTypes>\r
- <handledReferenceSchemes />\r
- <translatedElementType>java.lang.String</translatedElementType>\r
- <allowsLiteralValues>true</allowsLiteralValues>\r
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
- </inputs>\r
- <outputs>\r
- <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
- <name>nodeVal</name>\r
- <depth>0</depth>\r
- <mimeTypes />\r
- <granularDepth>0</granularDepth>\r
- </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
- </outputs>\r
- <classLoaderSharing>workflow</classLoaderSharing>\r
- <localDependencies />\r
- <artifactDependencies />\r
- <script>import org.dom4j.Document;\r
-import org.dom4j.Node;\r
-import org.dom4j.io.SAXReader;\r
-\r
-SAXReader reader = new SAXReader(false);\r
-reader.setIncludeInternalDTDDeclarations(false);\r
-reader.setIncludeExternalDTDDeclarations(false);\r
-\r
-Document document = reader.read(new StringReader(xmltext));\r
-List nodelist = document.selectNodes(xpath);\r
-\r
-// Process the elements in the nodelist\r
-ArrayList outputList = new ArrayList();\r
-ArrayList outputXmlList = new ArrayList();\r
-\r
-String val = "";\r
-String xmlVal = "";\r
-for (Iterator iter = nodelist.iterator(); iter.hasNext();) {\r
- Node element = (Node) iter.next();\r
- xmlVal = element.asXML();\r
- val = element.getStringValue();\r
- if (val != null && !val.equals("")) {\r
- outputList.add(val);\r
- outputXmlList.add(xmlVal);\r
- }\r
-break;\r
-}\r
-\r
-//List nodelist=outputList;\r
-nodeVal = val;\r
-</script>\r
- <dependencies />\r
-</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></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="">\r
- <maxJobs>1</maxJobs>\r
-</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="">\r
- <backoffFactor>1.0</backoffFactor>\r
- <initialDelay>1000</initialDelay>\r
- <maxDelay>5000</maxDelay>\r
- <maxRetries>0</maxRetries>\r
-</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="xmltext" depth="0" /><port name="xpath" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>COLRest_Service</processor><port>sciName</port></sink><source type="processor"><processor>Transform_XML_2</processor><port>outputStr</port></source></datalink><datalink><sink type="processor"><processor>NameStatusConditional</processor><port>nameStatus</port></sink><source type="processor"><processor>FirstElement_From_XPath</processor><port>nodeVal</port></source></datalink><datalink><sink type="processor"><processor>if_synonym</processor><port>nameStatus</port></sink><source type="processor"><processor>NameStatusConditional</processor><port>synpass_flags</port></source></datalink><datalink><sink type="processor"><processor>if_synonym</processor><port>synResponse</port></sink><source type="processor"><processor>COLRest_Service</processor><port>responseBody</port></source></datalink><datalink><sink type="processor"><processor>if_not_synonym</processor><port>nameStatus</port></sink><source type="processor"><processor>NameStatusConditional</processor><port>synfail_flags</port></source></datalink><datalink><sink type="processor"><processor>if_not_synonym</processor><port>colResponseIN</port></sink><source type="processor"><processor>COLRest_Service</processor><port>responseBody</port></source></datalink><datalink><sink type="processor"><processor>Merge_String_List_to_a_String</processor><port>stringlist</port></sink><source type="processor"><processor>Flatten_List</processor><port>outputlist</port></source></datalink><datalink><sink type="processor"><processor>Transform_XML_with_parameters</processor><port>xsltString</port></sink><source type="processor"><processor>Read_Text_File_2</processor><port>filecontents</port></source></datalink><datalink><sink type="processor"><processor>Transform_XML_with_parameters</processor><port>sourceString</port></sink><source type="processor"><processor>Merge_String_List_to_a_String</processor><port>concatenated</port></source></datalink><datalink><sink type="processor"><processor>Transform_XML_with_parameters</processor><port>paramList</port></sink><source type="processor"><processor>CreateID</processor><port>id_param</port></source></datalink><datalink><sink type="processor"><processor>Read_Text_File_2</processor><port>fileurl</port></sink><source type="processor"><processor>colRes_to_SynRes_xsl</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>CreateID</processor><port>name</port></sink><source type="processor"><processor>Transform_XML_2</processor><port>outputStr</port></source></datalink><datalink><sink type="processor"><processor>Transform_XML_2</processor><port>xslFileURL</port></sink><source type="processor"><processor>synReq_to_colReq_xsl</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>Transform_XML_2</processor><port>inString</port></sink><source type="dataflow"><port>synRequest</port></source></datalink><datalink><sink type="processor"><processor>FirstElement_From_XPath</processor><port>xmltext</port></sink><source type="processor"><processor>COLRest_Service</processor><port>responseBody</port></source></datalink><datalink><sink type="processor"><processor>FirstElement_From_XPath</processor><port>xpath</port></sink><source type="processor"><processor>name_status_xpath</processor><port>value</port></source></datalink><datalink><sink type="merge"><processor>Flatten_List</processor><port>inputlist</port></sink><source type="processor"><processor>if_not_synonym</processor><port>colResponse</port></source></datalink><datalink><sink type="merge"><processor>Flatten_List</processor><port>inputlist</port></sink><source type="processor"><processor>if_synonym</processor><port>colResponse</port></source></datalink><datalink><sink type="dataflow"><port>synResponse</port></sink><source type="processor"><processor>Transform_XML_with_parameters</processor><port>outputString</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>131afac6-f587-4b61-bb65-3f1ebe122bda</identification>\r
+ </annotationBean>\r
+ <date>2012-06-01 11:06:25.664 CEST</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>fe138fe6-063b-4ee2-a3b0-11cc1ddb1d96</identification>\r
+ </annotationBean>\r
+ <date>2012-05-31 16:25:51.890 CEST</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>5d68a44d-bf06-405c-806f-b228e4617031</identification>\r
+ </annotationBean>\r
+ <date>2012-03-29 11:03:32.312 CEST</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>d9fbd0bb-0b5c-4ae1-a3e6-24b25fe15d8c</identification>\r
+ </annotationBean>\r
+ <date>2012-03-29 14:30:40.331 CEST</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>771b9e2d-2de0-4b86-be30-ad834dac02b1</identification>\r
+ </annotationBean>\r
+ <date>2012-04-05 17:04:49.990 CEST</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>fc0831b0-d5d1-4849-b27e-45393915f6bb</identification>\r
+ </annotationBean>\r
+ <date>2012-03-29 14:55:49.410 CEST</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>8b2fddc8-881a-46d4-8830-26d02c16f297</identification>\r
+ </annotationBean>\r
+ <date>2012-05-31 17:57:04.999 CEST</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>b907f11d-0d2b-4c60-99d0-b49d6743029e</identification>\r
+ </annotationBean>\r
+ <date>2012-05-31 17:45:11.362 CEST</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>9c9f8b53-94a2-4e2f-8352-5871b5c93cc5</identification>\r
+ </annotationBean>\r
+ <date>2012-03-29 11:44:28.869 CEST</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>74414f96-5ade-4452-b80d-63c50e7fe0ed</identification>\r
+ </annotationBean>\r
+ <date>2012-05-31 16:53:07.453 CEST</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>4f535006-c1b1-4c88-ad65-a45415c76407</identification>\r
+ </annotationBean>\r
+ <date>2012-04-05 17:18:36.51 CEST</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>bc9c65e4-9cda-4d92-a6bf-6f6859c69cff</identification>\r
+ </annotationBean>\r
+ <date>2012-04-05 17:16:56.281 CEST</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>b4c96465-61be-4e99-bd05-52ba51a75f42</identification>\r
+ </annotationBean>\r
+ <date>2012-04-03 17:01:10.410 CEST</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>97c631bc-c4d3-452a-93d2-4610c3808892</identification>\r
+ </annotationBean>\r
+ <date>2012-04-05 16:35:01.668 CEST</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>6c3b8751-ec53-4741-a942-01283865a96a</identification>\r
+ </annotationBean>\r
+ <date>2012-06-01 11:32:44.573 CEST</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+ <annotationAssertions>\r
+ <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ <annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
+ <identification>12fb5fe4-1523-48be-be0d-cedafda3b609</identification>\r
+ </annotationBean>\r
+ <date>2012-06-01 10:57:34.556 CEST</date>\r
+ <creators />\r
+ <curationEventList />\r
+ </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
+ </annotationAssertions>\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>54039e3d-8d1c-4a40-a818-9cd8bcbf64b7</identification>\r
+ <identification>74230a5e-fcd6-41bf-a1d6-d4e7d6fb2658</identification>\r
</annotationBean>\r
- <date>2012-01-23 15:05:53.745 CET</date>\r
+ <date>2012-06-01 11:47:45.762 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>654ddd4b-3aee-4576-8bf7-939c9d470b9d</identification>\r
+ <identification>ae40be70-6c12-45e5-be8b-81f0b8b735ba</identification>\r
</annotationBean>\r
- <date>2012-01-23 15:14:53.241 CET</date>\r
+ <date>2012-03-29 12:03:32.626 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>13e365c6-a1f5-4e3a-99a4-d39a147367c7</identification>\r
+ <identification>db6f1b58-c356-4583-aeaf-18eedb3c8afc</identification>\r
</annotationBean>\r
- <date>2012-01-23 15:39:42.940 CET</date>\r
+ <date>2012-04-05 17:15:05.428 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>a0866021-3699-4383-b41c-6b8d0866305e</identification>\r
+ <identification>6b12cb26-c06f-48ea-ab4e-353915b67bf5</identification>\r
</annotationBean>\r
- <date>2012-01-23 15:01:00.405 CET</date>\r
+ <date>2012-05-29 12:17:41.27 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>d6cabd36-4763-4a7c-bd19-afb1547696b9</identification>\r
+ <identification>2b0f015c-fa70-4423-8d58-6dad4bb8b651</identification>\r
</annotationBean>\r
- <date>2012-01-25 16:08:29.517 CET</date>\r
+ <date>2012-06-01 11:18:44.605 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>20cf832b-88c5-4214-ac8b-cd46f8159b7d</identification>\r
+ <identification>cc5e9e4c-a539-44c7-b04e-69e4393e3500</identification>\r
</annotationBean>\r
- <date>2012-01-23 15:08:03.570 CET</date>\r
+ <date>2012-05-31 17:57:31.88 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>b7e9c698-3b8f-418e-b732-c02b07b2d8dc</identification>\r
+ <identification>e85227ec-8378-4cad-9a88-15a4a0f643c0</identification>\r
</annotationBean>\r
- <date>2012-02-14 13:50:23.444 CET</date>\r
+ <date>2012-03-29 13:52:07.195 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>f88ebd38-9ab7-4f03-ab29-75fe55ee240a</identification>\r
+ <identification>2a4a6728-39b3-4c0f-98a6-fc78db67bc3b</identification>\r
</annotationBean>\r
- <date>2012-02-14 17:10:41.962 CET</date>\r
+ <date>2012-06-01 11:19:40.72 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>2023d475-cce4-4812-bf43-fffa5fecf9cb</identification>\r
+ <identification>1588011a-0b72-4e26-908e-424559dedf16</identification>\r
</annotationBean>\r
- <date>2012-02-14 13:54:46.413 CET</date>\r
+ <date>2012-05-29 12:18:20.252 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
</annotationAssertions>\r
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow><dataflow id="89482956-6a9c-4300-ace2-d8cebb2c4750" role="nested"><name>Workflow21</name><inputPorts><port><name>nameStatus</name><depth>0</depth><granularDepth>0</granularDepth><annotations /></port><port><name>colResponseIN</name><depth>0</depth><granularDepth>0</granularDepth><annotations /></port></inputPorts><outputPorts><port><name>colResponse</name><annotations /></port></outputPorts><processors><processor><name>AssignInputOutput</name><inputPorts><port><name>in</name><depth>0</depth></port></inputPorts><outputPorts><port><name>out</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="in" to="in" /></inputMap><outputMap><map from="out" to="out" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">\r
+ <inputs>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ <name>in</name>\r
+ <depth>0</depth>\r
+ <mimeTypes>\r
+ <string>text/plain</string>\r
+ </mimeTypes>\r
+ <handledReferenceSchemes />\r
+ <translatedElementType>java.lang.String</translatedElementType>\r
+ <allowsLiteralValues>true</allowsLiteralValues>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ </inputs>\r
+ <outputs>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
+ <name>out</name>\r
+ <depth>0</depth>\r
+ <mimeTypes />\r
+ <granularDepth>0</granularDepth>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
+ </outputs>\r
+ <classLoaderSharing>workflow</classLoaderSharing>\r
+ <localDependencies />\r
+ <artifactDependencies />\r
+ <script>out = in;</script>\r
+ <dependencies />\r
+</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></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="">\r
+ <maxJobs>1</maxJobs>\r
+</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="">\r
+ <backoffFactor>1.0</backoffFactor>\r
+ <initialDelay>1000</initialDelay>\r
+ <maxDelay>5000</maxDelay>\r
+ <maxRetries>0</maxRetries>\r
+</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="in" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>AssignInputOutput</processor><port>in</port></sink><source type="dataflow"><port>colResponseIN</port></source></datalink><datalink><sink type="dataflow"><port>colResponse</port></sink><source type="processor"><processor>AssignInputOutput</processor><port>out</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>850e16e9-453e-416e-a7b1-ced1da71519f</identification>\r
+ <identification>6eadb547-663a-49c7-bdf8-a23b2d7f4123</identification>\r
</annotationBean>\r
- <date>2012-01-23 15:12:06.888 CET</date>\r
+ <date>2012-01-24 14:07:22.177 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>c273ba6e-577c-4078-a967-8bc0a6ce0ccb</identification>\r
+ <identification>724a8409-b76e-40b8-ab78-45fad288675b</identification>\r
</annotationBean>\r
- <date>2012-02-23 16:20:00.241 CET</date>\r
+ <date>2012-01-24 14:06:25.755 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>3f6fdae5-1039-4d5d-b016-09a7d0b7808f</identification>\r
+ <identification>95364f28-7f90-498a-bc62-1d1ede09052c</identification>\r
</annotationBean>\r
- <date>2012-02-10 16:33:33.703 CET</date>\r
+ <date>2012-01-24 14:08:22.102 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>e376fad1-bf30-4908-b97b-894900c25efa</identification>\r
+ <identification>b8e14154-831e-41ce-b590-9f6daaa9fa67</identification>\r
</annotationBean>\r
- <date>2012-01-23 15:03:45.120 CET</date>\r
+ <date>2012-01-24 14:12:26.300 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>7e933e2c-4286-4303-a56e-4cea981e3195</identification>\r
+ <identification>89482956-6a9c-4300-ace2-d8cebb2c4750</identification>\r
</annotationBean>\r
- <date>2012-01-27 15:45:49.310 CET</date>\r
+ <date>2012-01-24 14:27:28.355 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>907a23a5-7ea9-4901-8103-68bb6a45044e</identification>\r
+ <identification>810c97ff-1258-47ad-a9fa-c018449828ef</identification>\r
</annotationBean>\r
- <date>2012-02-13 13:36:37.936 CET</date>\r
+ <date>2012-01-24 14:06:51.959 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>6ad09a10-0f7c-43c2-b807-ebf6c0fd776e</identification>\r
+ <identification>8da12769-2015-408b-a6e2-d331a50c9c96</identification>\r
</annotationBean>\r
- <date>2012-01-23 15:14:07.562 CET</date>\r
+ <date>2012-01-24 14:10:10.838 CET</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
</annotationAssertions>\r
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow><dataflow id="adf2df6f-6ffa-490f-9b73-d8e46adac00b" role="nested"><name>Workflow23</name><inputPorts><port><name>sciNameIn</name><depth>1</depth><granularDepth>1</granularDepth><annotations /></port></inputPorts><outputPorts><port><name>sciName</name><annotations /></port></outputPorts><processors><processor><name>GBIF_Agreement_Interaction</name><inputPorts /><outputPorts><port><name>answer</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>interaction-activity</artifact><version>0.1.2</version></raven><class>net.sf.taverna.t2.activities.interaction.InteractionActivity</class><inputMap /><outputMap><map from="answer" to="answer" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.interaction.InteractionActivityConfigurationBean xmlns="">\r
+ <inputs />\r
+ <outputs>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
+ <name>answer</name>\r
+ <depth>0</depth>\r
+ <mimeTypes />\r
+ <granularDepth>0</granularDepth>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
+ </outputs>\r
+ <presentationOrigin>http://ww2.bgbm.org/temp/biovel/gbif_agreement.html</presentationOrigin>\r
+ <interactionActivityType>LocallyPresentedHtml</interactionActivityType>\r
+</net.sf.taverna.t2.activities.interaction.InteractionActivityConfigurationBean></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="">\r
+ <maxJobs>1</maxJobs>\r
+</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="">\r
+ <backoffFactor>1.0</backoffFactor>\r
+ <initialDelay>1000</initialDelay>\r
+ <maxDelay>5000</maxDelay>\r
+ <maxRetries>0</maxRetries>\r
+</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>GBIF_Agreement_Conditional</name><inputPorts><port><name>agreement_answer</name><depth>0</depth></port><port><name>sciNameIn</name><depth>1</depth></port></inputPorts><outputPorts><port><name>sciNameOut</name><depth>1</depth><granularDepth>1</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="agreement_answer" to="agreement_answer" /><map from="sciNameIn" to="sciNameIn" /></inputMap><outputMap><map from="sciNameOut" to="sciNameOut" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">\r
+ <inputs>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ <name>agreement_answer</name>\r
+ <depth>0</depth>\r
+ <mimeTypes>\r
+ <string>text/plain</string>\r
+ </mimeTypes>\r
+ <handledReferenceSchemes />\r
+ <translatedElementType>java.lang.String</translatedElementType>\r
+ <allowsLiteralValues>true</allowsLiteralValues>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ <name>sciNameIn</name>\r
+ <depth>1</depth>\r
+ <mimeTypes>\r
+ <string>text/plain</string>\r
+ </mimeTypes>\r
+ <handledReferenceSchemes />\r
+ <translatedElementType>java.lang.String</translatedElementType>\r
+ <allowsLiteralValues>true</allowsLiteralValues>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ </inputs>\r
+ <outputs>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
+ <name>sciNameOut</name>\r
+ <depth>1</depth>\r
+ <mimeTypes />\r
+ <granularDepth>1</granularDepth>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
+ </outputs>\r
+ <classLoaderSharing>workflow</classLoaderSharing>\r
+ <localDependencies />\r
+ <artifactDependencies />\r
+ <script>if(agreement_answer.equals("Yes")) {\r
+ sciNameOut = sciNameIn; \r
+} else {\r
+ sciNameOut = new ArrayList(); \r
+}\r
+\r
+</script>\r
+ <dependencies />\r
+</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></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="">\r
+ <maxJobs>1</maxJobs>\r
+</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="">\r
+ <backoffFactor>1.0</backoffFactor>\r
+ <initialDelay>1000</initialDelay>\r
+ <maxDelay>5000</maxDelay>\r
+ <maxRetries>0</maxRetries>\r
+</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="agreement_answer" depth="0" /><port name="sciNameIn" depth="1" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>GBIF_Agreement_Conditional</processor><port>agreement_answer</port></sink><source type="processor"><processor>GBIF_Agreement_Interaction</processor><port>answer</port></source></datalink><datalink><sink type="processor"><processor>GBIF_Agreement_Conditional</processor><port>sciNameIn</port></sink><source type="dataflow"><port>sciNameIn</port></source></datalink><datalink><sink type="dataflow"><port>sciName</port></sink><source type="processor"><processor>GBIF_Agreement_Conditional</processor><port>sciNameOut</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>56c300cd-9209-44ef-9874-3efa78d77df3</identification>\r
+ <identification>fe0524a8-3d93-4759-a0cc-2537bb2a577d</identification>\r
</annotationBean>\r
- <date>2012-02-10 12:41:11.317 CET</date>\r
+ <date>2012-04-05 16:34:35.523 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>1bae1054-0ea5-436e-bc01-c2c8838ba066</identification>\r
+ <identification>5e20399a-7e4f-4807-b510-1f15cdc22dd8</identification>\r
</annotationBean>\r
- <date>2012-01-23 15:47:21.97 CET</date>\r
+ <date>2012-04-05 16:41:48.618 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>65b317eb-1a04-45d0-afc4-196506a33934</identification>\r
+ <identification>c13b55dc-e9e8-4809-887b-cd90764fa7c0</identification>\r
</annotationBean>\r
- <date>2012-02-13 13:36:08.651 CET</date>\r
+ <date>2012-04-05 16:41:23.996 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>2bcaf5f3-a086-4ab8-bfe6-4e7640a6ce45</identification>\r
+ <identification>25760699-c10c-4abe-ac58-2277f17a319b</identification>\r
</annotationBean>\r
- <date>2012-01-23 15:10:26.350 CET</date>\r
+ <date>2012-04-05 16:47:29.177 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>08117860-fcd2-4342-b938-efe94165feb0</identification>\r
+ <identification>adf2df6f-6ffa-490f-9b73-d8e46adac00b</identification>\r
</annotationBean>\r
- <date>2012-01-24 13:53:17.262 CET</date>\r
+ <date>2012-04-05 16:54:07.336 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>7d54ce42-e540-4c40-b7f1-2209c6638804</identification>\r
+ <identification>25f616d8-fa88-4d60-8127-8228cf93c5a3</identification>\r
</annotationBean>\r
- <date>2012-02-10 12:40:38.13 CET</date>\r
+ <date>2012-04-05 16:31:27.376 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>4f5b0cf0-f3e4-4a48-b3bc-4d3d6770a4c3</identification>\r
+ <identification>1f4e6dc3-c3d1-40c2-9278-8f6396184737</identification>\r
</annotationBean>\r
- <date>2012-01-25 17:19:33.836 CET</date>\r
+ <date>2012-04-05 16:53:48.103 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
</annotationAssertions>\r
-</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
+</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow><dataflow id="9b888ae9-ece1-4b74-b177-5b915c9cc381" role="nested"><name>Workflow10</name><inputPorts><port><name>synTaxonID</name><depth>0</depth><granularDepth>0</granularDepth><annotations /></port></inputPorts><outputPorts><port><name>synResponse</name><annotations /></port></outputPorts><processors><processor><name>GBIF_Taxon_Search</name><inputPorts><port><name>taxonID</name><depth>0</depth></port></inputPorts><outputPorts><port><name>responseBody</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>rest-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.rest.RESTActivity</class><inputMap><map from="taxonID" to="taxonID" /></inputMap><outputMap><map from="responseBody" to="responseBody" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean xmlns="">\r
+ <httpMethod>GET</httpMethod>\r
+ <urlSignature>http://ecat-dev.gbif.org/ws/usage/{taxonID}</urlSignature>\r
+ <acceptsHeaderValue>application/json</acceptsHeaderValue>\r
+ <contentTypeForUpdates>application/xml</contentTypeForUpdates>\r
+ <outgoingDataFormat>String</outgoingDataFormat>\r
+ <sendHTTPExpectRequestHeader>false</sendHTTPExpectRequestHeader>\r
+ <showRedirectionOutputPort>false</showRedirectionOutputPort>\r
+ <escapeParameters>true</escapeParameters>\r
+ <otherHTTPHeaders />\r
+ <activityInputs>\r
+ <entry>\r
+ <string>taxonID</string>\r
+ <java-class>java.lang.String</java-class>\r
+ </entry>\r
+ </activityInputs>\r
+</net.sf.taverna.t2.activities.rest.RESTActivityConfigurationBean></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="">\r
+ <maxJobs>1</maxJobs>\r
+</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="">\r
+ <backoffFactor>1.0</backoffFactor>\r
+ <initialDelay>1000</initialDelay>\r
+ <maxDelay>5000</maxDelay>\r
+ <maxRetries>0</maxRetries>\r
+</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="taxonID" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>gbifTaxonSearchParser</name><inputPorts><port><name>gbifSynTaxonSearchJSON</name><depth>0</depth></port></inputPorts><outputPorts><port><name>synResponse</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="gbifSynTaxonSearchJSON" to="gbifSynTaxonSearchJSON" /></inputMap><outputMap><map from="synResponse" to="synResponse" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">\r
+ <inputs>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ <name>gbifSynTaxonSearchJSON</name>\r
+ <depth>0</depth>\r
+ <mimeTypes>\r
+ <string>text/plain</string>\r
+ </mimeTypes>\r
+ <handledReferenceSchemes />\r
+ <translatedElementType>java.lang.String</translatedElementType>\r
+ <allowsLiteralValues>true</allowsLiteralValues>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>\r
+ </inputs>\r
+ <outputs>\r
+ <net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
+ <name>synResponse</name>\r
+ <depth>0</depth>\r
+ <mimeTypes />\r
+ <granularDepth>0</granularDepth>\r
+ </net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>\r
+ </outputs>\r
+ <classLoaderSharing>workflow</classLoaderSharing>\r
+ <localDependencies>\r
+ <string>json-simple-1.1.1.jar</string>\r
+ </localDependencies>\r
+ <artifactDependencies />\r
+ <script>import java.util.Iterator;\r
+import org.json.simple.JSONArray;\r
+import org.json.simple.JSONObject;\r
+import org.json.simple.parser.JSONParser;\r
+\r
+synList = new ArrayList();\r
+StringBuilder synResponseBuilder = new StringBuilder();\r
+JSONParser parser = new JSONParser();\r
+\r
+Object obj = parser.parse(gbifSynTaxonSearchJSON);\r
+JSONObject jsonObject = (JSONObject) obj;\r
+ \r
+JSONObject dataObject = (JSONObject)jsonObject.get("data");\r
+String canonicalName = (String) dataObject.get("canonicalName");\r
+String datasetName = (String) dataObject.get("datasetName");\r
+String taxonomicStatus = (String) dataObject.get("taxonomicStatus");\r
+String rank = (String) dataObject.get("rank");\r
+\r
+synResponseBuilder.append("<synonym>");\r
+synResponseBuilder.append("<taxonName><authorship></authorship><name>");\r
+synResponseBuilder.append("<nameComplete>").append(canonicalName).append("</nameComplete>");\r
+synResponseBuilder.append("<atomisedName>");\r
+synResponseBuilder.append("<subGenus>");\r
+synResponseBuilder.append("<genusPart></genusPart><specificEpithet></specificEpithet><infraspecificEpithet></infraspecificEpithet>");\r
+synResponseBuilder.append("</subGenus>");\r
+synResponseBuilder.append("</atomisedName>");\r
+synResponseBuilder.append("<nameStatus>").append(taxonomicStatus).append("</nameStatus>");\r
+synResponseBuilder.append("</name>");\r
+synResponseBuilder.append("<rank>").append(rank).append("</rank>");\r
+synResponseBuilder.append("</taxonName>");\r
+synResponseBuilder.append("<source><name></name><url></url></source><info><url></url></info>");\r
+synResponseBuilder.append("</synonym>");\r
+ \r
+\r
+synResponse = synResponseBuilder.toString();\r
+\r
+</script>\r
+ <dependencies />\r
+</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></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="">\r
+ <maxJobs>1</maxJobs>\r
+</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="">\r
+ <backoffFactor>1.0</backoffFactor>\r
+ <initialDelay>1000</initialDelay>\r
+ <maxDelay>5000</maxDelay>\r
+ <maxRetries>0</maxRetries>\r
+</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="gbifSynTaxonSearchJSON" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>GBIF_Taxon_Search</processor><port>taxonID</port></sink><source type="dataflow"><port>synTaxonID</port></source></datalink><datalink><sink type="processor"><processor>gbifTaxonSearchParser</processor><port>gbifSynTaxonSearchJSON</port></sink><source type="processor"><processor>GBIF_Taxon_Search</processor><port>responseBody</port></source></datalink><datalink><sink type="dataflow"><port>synResponse</port></sink><source type="processor"><processor>gbifTaxonSearchParser</processor><port>synResponse</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>7614477b-fc8e-4262-be98-03a72347ecd1</identification>\r
+ <identification>9b888ae9-ece1-4b74-b177-5b915c9cc381</identification>\r
</annotationBean>\r
- <date>2012-01-24 14:02:21.343 CET</date>\r
+ <date>2012-05-31 10:44:07.573 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>d18fe496-419c-4f13-9a5e-9ea550bc3a1e</identification>\r
+ <identification>2b1c6652-51c5-461a-8fff-44cb1d48eac6</identification>\r
</annotationBean>\r
- <date>2012-02-23 17:14:42.676 CET</date>\r
+ <date>2012-05-31 10:05:29.814 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>c07ee8d5-7314-45dc-a7b9-f136f9762905</identification>\r
+ <identification>b2b36695-4605-43f5-9abb-3edb59937bfb</identification>\r
</annotationBean>\r
- <date>2012-01-24 14:25:37.176 CET</date>\r
+ <date>2012-05-31 10:28:58.722 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>eb74b582-81c7-4049-8ab5-43b3ec96b920</identification>\r
+ <identification>4ebbd8f4-5d17-40e9-84b6-bf6c9483004c</identification>\r
</annotationBean>\r
- <date>2012-01-24 14:32:42.660 CET</date>\r
+ <date>2012-05-31 10:03:40.298 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>3ab53f67-d243-4e40-8627-83028ef002df</identification>\r
+ <identification>d804bf47-d57f-417d-a724-43fde250064d</identification>\r
</annotationBean>\r
- <date>2012-02-10 12:44:20.333 CET</date>\r
+ <date>2012-05-31 10:04:20.439 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>a58dbeb8-48e1-4b31-a1ea-57761cb4f712</identification>\r
+ <identification>6eb50bb0-c45f-4281-88c7-d7d0142fef05</identification>\r
</annotationBean>\r
- <date>2012-01-25 17:22:12.481 CET</date>\r
+ <date>2012-05-31 10:42:30.250 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>3a9f1b0b-5d5a-45a0-b134-d5dafc51ea40</identification>\r
+ <identification>3a4e4aea-879c-4dde-8988-5d920d7d979b</identification>\r
</annotationBean>\r
- <date>2012-01-24 14:17:11.136 CET</date>\r
+ <date>2012-05-31 10:19:15.89 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationAssertions>\r
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">\r
- <identification>9f2c7ca2-e117-46e8-8d95-d5a9f8219570</identification>\r
+ <identification>9f87d608-1374-4019-95ac-4e6333cbc129</identification>\r
</annotationBean>\r
- <date>2012-01-23 14:57:41.971 CET</date>\r
+ <date>2012-05-31 10:20:40.459 CEST</date>\r
<creators />\r
<curationEventList />\r
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>\r
BGBM BDI Projects / biovel.git / commitdiff