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simpleWorkflow.t2flow
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<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow" version="1" producedBy="taverna-2.4.0"><dataflow id="673b9394-9206-4395-b9bb-1f48e52cec51" role="top"><name>Matchbox_Evaluation</name><inputPorts><port><name>bc_dirlist_file_path</name><depth>0</depth><granularDepth>0</granularDepth><annotations><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
<annotationAssertions>
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.ExampleValue">
<text>C:\Users\munterberger\Desktop\mb_content.txt</text>
</annotationBean>
<date>2013-07-23 13:59:01.517 UTC</date>
<creators />
<curationEventList />
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
</annotationAssertions>
</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
<annotationAssertions>
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
<text>Path to textfile containing paths to barcode directories.</text>
</annotationBean>
<date>2012-10-01 13:31:43.327 UTC</date>
<creators />
<curationEventList />
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
</annotationAssertions>
</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port></inputPorts><outputPorts><port><name>results</name><annotations /></port><port><name>matches</name><annotations /></port><port><name>report</name><annotations /></port><port><name>evlog</name><annotations /></port></outputPorts><processors><processor><name>matchbox_evaluate</name><inputPorts><port><name>matchbox</name><depth>0</depth></port></inputPorts><outputPorts><port><name>cid</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>fm</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>iid</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>md</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>prec</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>rec</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>log</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>1.4</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="matchbox" to="matchbox" /></inputMap><outputMap><map from="rec" to="rec" /><map from="fm" to="fm" /><map from="md" to="md" /><map from="iid" to="iid" /><map from="prec" to="prec" /><map from="cid" to="cid" /><map from="log" to="log" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
<inputs>
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
<name>matchbox</name>
<depth>0</depth>
<mimeTypes>
<string>text/plain</string>
</mimeTypes>
<handledReferenceSchemes />
<translatedElementType>java.lang.String</translatedElementType>
<allowsLiteralValues>true</allowsLiteralValues>
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
<name>groundtruth</name>
<depth>0</depth>
<mimeTypes>
<string>text/plain</string>
</mimeTypes>
<handledReferenceSchemes />
<translatedElementType>java.lang.String</translatedElementType>
<allowsLiteralValues>true</allowsLiteralValues>
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
</inputs>
<outputs>
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
<name>cid</name>
<depth>0</depth>
<mimeTypes />
<granularDepth>0</granularDepth>
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
<name>md</name>
<depth>0</depth>
<mimeTypes />
<granularDepth>0</granularDepth>
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
<name>iid</name>
<depth>0</depth>
<mimeTypes />
<granularDepth>0</granularDepth>
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
<name>prec</name>
<depth>0</depth>
<mimeTypes />
<granularDepth>0</granularDepth>
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
<name>rec</name>
<depth>0</depth>
<mimeTypes />
<granularDepth>0</granularDepth>
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
<name>fm</name>
<depth>0</depth>
<mimeTypes />
<granularDepth>0</granularDepth>
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
<name>log</name>
<depth>0</depth>
<mimeTypes />
<granularDepth>0</granularDepth>
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
</outputs>
<classLoaderSharing>workflow</classLoaderSharing>
<localDependencies>
<string>tb-lsdr-matchboxeval-lib-1.0-SNAPSHOT.jar</string>
<string>combinatoricslib-0.2.jar</string>
</localDependencies>
<artifactDependencies />
<script>import eu.scape_project.tb.lsdr.MatchboxEval;
MatchboxEval me = new MatchboxEval(matchbox,groundtruth);
me.evaluate();
cid = me.getTruePositives();
iid = me.getFalsePositives();
md = me.getFalseNegatives();
prec = me.getPrecision();
rec = me.getRecall();
fm = me.getFmeasure();
log = me.getLog();</script>
<dependencies />
</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>1.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
<maxJobs>1</maxJobs>
</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</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>1.4</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>1.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
<backoffFactor>1.0</backoffFactor>
<initialDelay>1000</initialDelay>
<maxDelay>5000</maxDelay>
<maxRetries>0</maxRetries>
</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</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="matchbox" depth="0" /></dot></strategy></iteration></iterationStrategyStack></processor><processor><name>matchbox</name><inputPorts><port><name>barcode_path</name><depth>0</depth></port></inputPorts><outputPorts><port><name>STDOUT</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations /><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>external-tool-activity</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.activities.externaltool.ExternalToolActivity</class><inputMap><map from="barcode_path" to="barcode_path" /></inputMap><outputMap><map from="STDOUT" to="STDOUT" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.externaltool.ExternalToolActivityConfigurationBean xmlns="">
<mechanismType>D0A4CDEB-DD10-4A8E-A49C-8871003083D8</mechanismType>
<mechanismName>fuel</mechanismName>
<mechanismXML><?xml version="1.0" encoding="UTF-8"?>
<sshInvocation><sshNode><host>fue.onb.ac.at</host><port>22</port><directory>/tmp/</directory><linkCommand>/bin/ln -s %%PATH_TO_ORIGINAL%% %%TARGET_NAME%%</linkCommand><copyCommand>/bin/cp %%PATH_TO_ORIGINAL%% %%TARGET_NAME%%</copyCommand></sshNode></sshInvocation>
</mechanismXML>
<externaltoolid>eb15da53-92d0-4dac-aa40-3101b4500997</externaltoolid>
<useCaseDescription>
<usecaseid />
<description />
<command>RANDOM=`tr -dc "[:alpha:]" < /dev/urandom | head -c 20`
PATHID=matchbox
TMPDIR=/tmp/${PATHID}${RANDOM}
mkdir ${TMPDIR}
cd /opt/scape/darling/
/usr/bin/python ./FindDuplicates.py %%barcode_path%% --featdir ${TMPDIR} all</command>
<preparingTimeoutInSeconds>1200</preparingTimeoutInSeconds>
<executionTimeoutInSeconds>1800</executionTimeoutInSeconds>
<tags>
<string>barcode_path</string>
</tags>
<REs />
<queue__preferred />
<queue__deny />
<static__inputs />
<inputs>
<entry>
<string>barcode_path</string>
<de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
<tag>barcode_path</tag>
<file>false</file>
<tempFile>false</tempFile>
<binary>false</binary>
<charsetName>UTF-8</charsetName>
<forceCopy>false</forceCopy>
<list>false</list>
<concatenate>false</concatenate>
<mime />
</de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
</entry>
</inputs>
<outputs />
<includeStdIn>false</includeStdIn>
<includeStdOut>true</includeStdOut>
<includeStdErr>true</includeStdErr>
<validReturnCodes>
<int>0</int>
</validReturnCodes>
</useCaseDescription>
<edited>false</edited>
</net.sf.taverna.t2.activities.externaltool.ExternalToolActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
<maxJobs>4</maxJobs>
</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</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>1.4</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>1.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
<backoffFactor>1.0</backoffFactor>
<initialDelay>1000</initialDelay>
<maxDelay>5000</maxDelay>
<maxRetries>0</maxRetries>
</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</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="barcode_path" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>read_bc_dirlist_file</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>1.4</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="">
<inputs>
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
<name>fileurl</name>
<depth>0</depth>
<mimeTypes>
<string>'text/plain'</string>
</mimeTypes>
<handledReferenceSchemes />
<translatedElementType>java.lang.String</translatedElementType>
<allowsLiteralValues>true</allowsLiteralValues>
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
</inputs>
<outputs>
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
<name>filecontents</name>
<depth>0</depth>
<mimeTypes>
<string>'text/plain'</string>
</mimeTypes>
<granularDepth>0</granularDepth>
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
</outputs>
<classLoaderSharing>workflow</classLoaderSharing>
<localDependencies />
<artifactDependencies />
<script>BufferedReader getReader (String fileUrl) throws IOException {
InputStreamReader reader;
try {
reader = new FileReader(fileUrl);
}
catch (FileNotFoundException e) {
// try a real URL instead
URL url = new URL(fileUrl);
reader = new InputStreamReader (url.openStream());
}
return new BufferedReader(reader);
}
StringBuffer sb = new StringBuffer(4000);
BufferedReader in = getReader(fileurl);
String str;
String lineEnding = System.getProperty("line.separator");
while ((str = in.readLine()) != null) {
sb.append(str);
sb.append(lineEnding);
}
in.close();
filecontents = sb.toString();
</script>
<dependencies />
<localworkerName>net.sourceforge.taverna.scuflworkers.io.TextFileReader</localworkerName>
</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
<maxJobs>1</maxJobs>
</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</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>1.4</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>1.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
<backoffFactor>1.0</backoffFactor>
<initialDelay>1000</initialDelay>
<maxDelay>5000</maxDelay>
<maxRetries>0</maxRetries>
</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</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>split_bc_dirlist</name><inputPorts><port><name>regex</name><depth>0</depth></port><port><name>string</name><depth>0</depth></port></inputPorts><outputPorts><port><name>split</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>1.4</version></raven><class>net.sf.taverna.t2.activities.localworker.LocalworkerActivity</class><inputMap><map from="regex" to="regex" /><map from="string" to="string" /></inputMap><outputMap><map from="split" to="split" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean xmlns="">
<inputs>
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
<name>string</name>
<depth>0</depth>
<mimeTypes>
<string>'text/plain'</string>
</mimeTypes>
<handledReferenceSchemes />
<translatedElementType>java.lang.String</translatedElementType>
<allowsLiteralValues>true</allowsLiteralValues>
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
<name>regex</name>
<depth>0</depth>
<mimeTypes>
<string>'text/plain'</string>
</mimeTypes>
<handledReferenceSchemes />
<translatedElementType>java.lang.String</translatedElementType>
<allowsLiteralValues>true</allowsLiteralValues>
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
</inputs>
<outputs>
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
<name>split</name>
<depth>1</depth>
<mimeTypes>
<string>l('text/plain')</string>
</mimeTypes>
<granularDepth>1</granularDepth>
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
</outputs>
<classLoaderSharing>workflow</classLoaderSharing>
<localDependencies />
<artifactDependencies />
<script>List split = new ArrayList();
if (!string.equals("")) {
String regexString = ",";
if (regex != void) {
regexString = regex;
}
String[] result = string.split(regexString);
for (int i = 0; i < result.length; i++) {
split.add(result[i]);
}
}
</script>
<dependencies />
<localworkerName>org.embl.ebi.escience.scuflworkers.java.SplitByRegex</localworkerName>
</net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
<maxJobs>1</maxJobs>
</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</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>1.4</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>1.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
<backoffFactor>1.0</backoffFactor>
<initialDelay>1000</initialDelay>
<maxDelay>5000</maxDelay>
<maxRetries>0</maxRetries>
</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean encoding="xstream"><null xmlns="" /></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy><cross><port name="regex" depth="0" /><port name="string" depth="0" /></cross></strategy></iteration></iterationStrategyStack></processor><processor><name>newline</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>1.4</version></raven><class>net.sf.taverna.t2.activities.stringconstant.StringConstantActivity</class><inputMap /><outputMap><map from="value" to="value" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean xmlns="">
<value>\n</value>
</net.sf.taverna.t2.activities.stringconstant.StringConstantConfigurationBean></configBean><annotations /></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
<maxJobs>1</maxJobs>
</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</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>1.4</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>1.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
<backoffFactor>1.0</backoffFactor>
<initialDelay>1000</initialDelay>
<maxDelay>5000</maxDelay>
<maxRetries>0</maxRetries>
</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</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>parse_matchbox_stdout</name><inputPorts><port><name>matchbox_stdout</name><depth>0</depth></port><port><name>barcode_path</name><depth>0</depth></port></inputPorts><outputPorts><port><name>duplicates_result</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>duplicates_matches</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>1.4</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="barcode_path" to="barcode_path" /><map from="matchbox_stdout" to="matchbox_stdout" /></inputMap><outputMap><map from="duplicates_result" to="duplicates_result" /><map from="duplicates_matches" to="duplicates_matches" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
<inputs>
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
<name>barcode_path</name>
<depth>0</depth>
<mimeTypes>
<string>text/plain</string>
</mimeTypes>
<handledReferenceSchemes />
<translatedElementType>java.lang.String</translatedElementType>
<allowsLiteralValues>true</allowsLiteralValues>
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
<name>matchbox_stdout</name>
<depth>0</depth>
<mimeTypes>
<string>text/plain</string>
</mimeTypes>
<handledReferenceSchemes />
<translatedElementType>java.lang.String</translatedElementType>
<allowsLiteralValues>true</allowsLiteralValues>
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
</inputs>
<outputs>
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
<name>duplicates_result</name>
<depth>0</depth>
<mimeTypes />
<granularDepth>0</granularDepth>
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
<name>duplicates_matches</name>
<depth>0</depth>
<mimeTypes />
<granularDepth>0</granularDepth>
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
</outputs>
<classLoaderSharing>workflow</classLoaderSharing>
<localDependencies />
<artifactDependencies />
<script>#!Pairtree pt = new Pairtree();
#!String id = pt.mapToId("/mnt/abonas/linktree/", barcode_path.substring(0,barcode_path.lastIndexOf("/")));
String duplicates_result = "";
String duplicates_matches = "";
duplicates_result += barcode_path+ ":\n";
duplicates_matches += barcode_path + "\t";
StringTokenizer st = new StringTokenizer(matchbox_stdout, "\n");
boolean startDuplicates = false;
boolean hasDuplicates = false;
while (st.hasMoreTokens()) {
String token = st.nextToken();
if (startDuplicates) {
if (token.contains("=>")) {
duplicates_result += token + "\n";
hasDuplicates = true;
}
}
if (token.contains("=== List of detected duplicates ===")) {
startDuplicates = true;
}
}
if(hasDuplicates)
duplicates_matches += "1";
else
duplicates_matches += "0";</script>
<dependencies />
</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>1.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
<maxJobs>1</maxJobs>
</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</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>1.4</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>1.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
<backoffFactor>1.0</backoffFactor>
<initialDelay>1000</initialDelay>
<maxDelay>5000</maxDelay>
<maxRetries>0</maxRetries>
</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</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="matchbox_stdout" depth="0" /><port name="barcode_path" depth="0" /></dot></strategy></iteration></iterationStrategyStack></processor><processor><name>report</name><inputPorts><port><name>cid</name><depth>0</depth></port><port><name>fm</name><depth>0</depth></port><port><name>iid</name><depth>0</depth></port><port><name>md</name><depth>0</depth></port><port><name>prec</name><depth>0</depth></port><port><name>rec</name><depth>0</depth></port></inputPorts><outputPorts><port><name>report</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>1.4</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map from="rec" to="rec" /><map from="fm" to="fm" /><map from="md" to="md" /><map from="iid" to="iid" /><map from="prec" to="prec" /><map from="cid" to="cid" /></inputMap><outputMap><map from="report" to="report" /></outputMap><configBean encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean xmlns="">
<inputs>
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
<name>prec</name>
<depth>0</depth>
<mimeTypes>
<string>text/plain</string>
</mimeTypes>
<handledReferenceSchemes />
<translatedElementType>java.lang.String</translatedElementType>
<allowsLiteralValues>true</allowsLiteralValues>
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
<name>md</name>
<depth>0</depth>
<mimeTypes>
<string>text/plain</string>
</mimeTypes>
<handledReferenceSchemes />
<translatedElementType>java.lang.String</translatedElementType>
<allowsLiteralValues>true</allowsLiteralValues>
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
<name>iid</name>
<depth>0</depth>
<mimeTypes>
<string>text/plain</string>
</mimeTypes>
<handledReferenceSchemes />
<translatedElementType>java.lang.String</translatedElementType>
<allowsLiteralValues>true</allowsLiteralValues>
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
<name>fm</name>
<depth>0</depth>
<mimeTypes>
<string>text/plain</string>
</mimeTypes>
<handledReferenceSchemes />
<translatedElementType>java.lang.String</translatedElementType>
<allowsLiteralValues>true</allowsLiteralValues>
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
<name>cid</name>
<depth>0</depth>
<mimeTypes>
<string>text/plain</string>
</mimeTypes>
<handledReferenceSchemes />
<translatedElementType>java.lang.String</translatedElementType>
<allowsLiteralValues>true</allowsLiteralValues>
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
<name>rec</name>
<depth>0</depth>
<mimeTypes>
<string>text/plain</string>
</mimeTypes>
<handledReferenceSchemes />
<translatedElementType>java.lang.String</translatedElementType>
<allowsLiteralValues>true</allowsLiteralValues>
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
</inputs>
<outputs>
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
<name>report</name>
<depth>0</depth>
<mimeTypes />
<granularDepth>0</granularDepth>
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
</outputs>
<classLoaderSharing>workflow</classLoaderSharing>
<localDependencies />
<artifactDependencies />
<script>report = "Correctly identified duplicates (true positives): "+cid+"\n"+
"Incorrectly identified duplicates (false positives): "+iid+"\n"+
"Missed duplicates (false negatives): "+md+"\n"+
"Precision: "+prec+"%\n"+
"Recall: "+rec+"%\n"+
"F-Measure: "+fm+"%\n";</script>
<dependencies />
</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>1.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig xmlns="">
<maxJobs>1</maxJobs>
</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</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>1.4</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>1.4</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig xmlns="">
<backoffFactor>1.0</backoffFactor>
<initialDelay>1000</initialDelay>
<maxDelay>5000</maxDelay>
<maxRetries>0</maxRetries>
</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.4</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="cid" depth="0" /><port name="fm" depth="0" /><port name="iid" depth="0" /><port name="md" depth="0" /><port name="prec" depth="0" /><port name="rec" depth="0" /></dot></strategy></iteration></iterationStrategyStack></processor></processors><conditions /><datalinks><datalink><sink type="processor"><processor>matchbox_evaluate</processor><port>matchbox</port></sink><source type="processor"><processor>parse_matchbox_stdout</processor><port>duplicates_result</port></source></datalink><datalink><sink type="processor"><processor>matchbox</processor><port>barcode_path</port></sink><source type="processor"><processor>split_bc_dirlist</processor><port>split</port></source></datalink><datalink><sink type="processor"><processor>read_bc_dirlist_file</processor><port>fileurl</port></sink><source type="dataflow"><port>bc_dirlist_file_path</port></source></datalink><datalink><sink type="processor"><processor>split_bc_dirlist</processor><port>regex</port></sink><source type="processor"><processor>newline</processor><port>value</port></source></datalink><datalink><sink type="processor"><processor>split_bc_dirlist</processor><port>string</port></sink><source type="processor"><processor>read_bc_dirlist_file</processor><port>filecontents</port></source></datalink><datalink><sink type="processor"><processor>parse_matchbox_stdout</processor><port>matchbox_stdout</port></sink><source type="processor"><processor>matchbox</processor><port>STDOUT</port></source></datalink><datalink><sink type="processor"><processor>parse_matchbox_stdout</processor><port>barcode_path</port></sink><source type="processor"><processor>split_bc_dirlist</processor><port>split</port></source></datalink><datalink><sink type="processor"><processor>report</processor><port>cid</port></sink><source type="processor"><processor>matchbox_evaluate</processor><port>cid</port></source></datalink><datalink><sink type="processor"><processor>report</processor><port>fm</port></sink><source type="processor"><processor>matchbox_evaluate</processor><port>fm</port></source></datalink><datalink><sink type="processor"><processor>report</processor><port>iid</port></sink><source type="processor"><processor>matchbox_evaluate</processor><port>iid</port></source></datalink><datalink><sink type="processor"><processor>report</processor><port>md</port></sink><source type="processor"><processor>matchbox_evaluate</processor><port>md</port></source></datalink><datalink><sink type="processor"><processor>report</processor><port>prec</port></sink><source type="processor"><processor>matchbox_evaluate</processor><port>prec</port></source></datalink><datalink><sink type="processor"><processor>report</processor><port>rec</port></sink><source type="processor"><processor>matchbox_evaluate</processor><port>rec</port></source></datalink><datalink><sink type="dataflow"><port>results</port></sink><source type="processor"><processor>parse_matchbox_stdout</processor><port>duplicates_result</port></source></datalink><datalink><sink type="dataflow"><port>matches</port></sink><source type="processor"><processor>parse_matchbox_stdout</processor><port>duplicates_matches</port></source></datalink><datalink><sink type="dataflow"><port>report</port></sink><source type="processor"><processor>report</processor><port>report</port></source></datalink><datalink><sink type="dataflow"><port>evlog</port></sink><source type="processor"><processor>matchbox_evaluate</processor><port>log</port></source></datalink></datalinks><annotations><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
<annotationAssertions>
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
<identification>2efd4378-62f5-41ea-bf6f-dd7d50cd732e</identification>
</annotationBean>
<date>2012-10-01 13:08:54.255 UTC</date>
<creators />
<curationEventList />
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
</annotationAssertions>
</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
<annotationAssertions>
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
<identification>6d1c206f-f442-49d3-97b3-50cd4ac66b5f</identification>
</annotationBean>
<date>2012-09-26 15:20:31.846 UTC</date>
<creators />
<curationEventList />
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
</annotationAssertions>
</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
<annotationAssertions>
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
<identification>801043a1-195a-4b7d-8dd4-c1ebfa8d3b41</identification>
</annotationBean>
<date>2012-10-01 12:37:43.3 UTC</date>
<creators />
<curationEventList />
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
</annotationAssertions>
</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
<annotationAssertions>
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
<identification>81553fe0-9aa5-4fc7-a775-19e96144f650</identification>
</annotationBean>
<date>2012-10-02 09:38:25.821 UTC</date>
<creators />
<curationEventList />
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
</annotationAssertions>
</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
<annotationAssertions>
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
<identification>673b9394-9206-4395-b9bb-1f48e52cec51</identification>
</annotationBean>
<date>2014-04-28 09:04:23.655 UTC</date>
<creators />
<curationEventList />
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
</annotationAssertions>
</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
<annotationAssertions>
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
<identification>506fc52e-7052-4f57-8c15-83821665c03e</identification>
</annotationBean>
<date>2012-10-02 09:56:29.495 UTC</date>
<creators />
<curationEventList />
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
</annotationAssertions>
</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
<annotationAssertions>
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
<text>Matchbox evaluation against ground truth. The evaluation process first
creates the matchbox output and ground truth lists. It then counts each page
tuple from the matchbox output that is in the ground truth as correctly
identified tuple (true positive). Those that are not in the ground truth are
counted as incorrectly identified tuples (false positives), and finally,
those that are in the ground truth but not in the matchbox output are counted
as missed tuples (false negatives).
The precision is then calculated as the number of true positives (i.e. the
number of items correctly labeled as duplicate page pairs) divided by the
total number of elements assumed to be duplicate page pairs (i.e. the sum of
true positives and false positives, which are items incorrectly labeled as
being duplicate page pairs ). Recall is then defined as the number of
true positives divided by the total number of elements of duplicate page
pairs (i.e. the sum of true positives and false negatives, which are items
have not been labeled as being duplicate page pairs but actually should have
been).
The ground truth contains single page instances without duplicates and
n-tuples (duplicates, triples, quadruples, etc.). n-tuples with n>2 are
expanded, the result is a list of 2-tuples which is used to determine the
number of missed duplicates (false negatives).</text>
</annotationBean>
<date>2012-10-02 12:36:08.934 UTC</date>
<creators />
<curationEventList />
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
</annotationAssertions>
</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
<annotationAssertions>
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
<identification>e26a0bd8-eb71-4fd3-9bc6-238d71792ed3</identification>
</annotationBean>
<date>2012-10-01 12:46:11.91 UTC</date>
<creators />
<curationEventList />
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
</annotationAssertions>
</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
<annotationAssertions>
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
<identification>857c050a-49b5-4606-bcdb-220455d64291</identification>
</annotationBean>
<date>2012-10-01 12:33:52.730 UTC</date>
<creators />
<curationEventList />
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
</annotationAssertions>
</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
<annotationAssertions>
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
<identification>f85240d9-2108-4057-8c42-78eef7ecf441</identification>
</annotationBean>
<date>2012-10-01 12:27:16.65 UTC</date>
<creators />
<curationEventList />
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
</annotationAssertions>
</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
<annotationAssertions>
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
<identification>79894ee6-b109-41b7-95db-8178b7eb4121</identification>
</annotationBean>
<date>2012-10-02 09:56:58.139 UTC</date>
<creators />
<curationEventList />
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
</annotationAssertions>
</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
<annotationAssertions>
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
<identification>66473d1e-e539-497e-874b-28f42198a8f3</identification>
</annotationBean>
<date>2012-09-26 15:18:43.167 UTC</date>
<creators />
<curationEventList />
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
</annotationAssertions>
</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
<annotationAssertions>
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
<identification>eaa27b27-7bc6-4461-875e-499f30946c6a</identification>
</annotationBean>
<date>2013-07-23 13:59:10.99 UTC</date>
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