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a |
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b/test/resources/simpleWorkflow.t2flow |
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1 |
<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="">
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2 |
<annotationAssertions>
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3 |
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
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4 |
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.ExampleValue">
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5 |
<text>C:\Users\munterberger\Desktop\mb_content.txt</text>
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6 |
</annotationBean>
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7 |
<date>2013-07-23 13:59:01.517 UTC</date>
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8 |
<creators />
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9 |
<curationEventList />
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10 |
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
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11 |
</annotationAssertions>
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12 |
</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
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13 |
<annotationAssertions>
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14 |
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
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15 |
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
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16 |
<text>Path to textfile containing paths to barcode directories.</text>
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17 |
</annotationBean>
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18 |
<date>2012-10-01 13:31:43.327 UTC</date>
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19 |
<creators />
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20 |
<curationEventList />
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21 |
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
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22 |
</annotationAssertions>
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23 |
</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="">
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24 |
<inputs>
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25 |
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
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26 |
<name>matchbox</name>
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27 |
<depth>0</depth>
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28 |
<mimeTypes>
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29 |
<string>text/plain</string>
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30 |
</mimeTypes>
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31 |
<handledReferenceSchemes />
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32 |
<translatedElementType>java.lang.String</translatedElementType>
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33 |
<allowsLiteralValues>true</allowsLiteralValues>
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34 |
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
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35 |
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
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36 |
<name>groundtruth</name>
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37 |
<depth>0</depth>
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38 |
<mimeTypes>
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39 |
<string>text/plain</string>
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40 |
</mimeTypes>
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41 |
<handledReferenceSchemes />
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42 |
<translatedElementType>java.lang.String</translatedElementType>
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43 |
<allowsLiteralValues>true</allowsLiteralValues>
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44 |
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
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45 |
</inputs>
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46 |
<outputs>
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47 |
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
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48 |
<name>cid</name>
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49 |
<depth>0</depth>
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50 |
<mimeTypes />
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51 |
<granularDepth>0</granularDepth>
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52 |
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
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53 |
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
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54 |
<name>md</name>
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55 |
<depth>0</depth>
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56 |
<mimeTypes />
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57 |
<granularDepth>0</granularDepth>
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58 |
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
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59 |
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
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60 |
<name>iid</name>
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61 |
<depth>0</depth>
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62 |
<mimeTypes />
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63 |
<granularDepth>0</granularDepth>
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64 |
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
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65 |
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
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66 |
<name>prec</name>
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67 |
<depth>0</depth>
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68 |
<mimeTypes />
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69 |
<granularDepth>0</granularDepth>
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70 |
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
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71 |
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
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72 |
<name>rec</name>
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73 |
<depth>0</depth>
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74 |
<mimeTypes />
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75 |
<granularDepth>0</granularDepth>
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76 |
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
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77 |
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
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78 |
<name>fm</name>
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79 |
<depth>0</depth>
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80 |
<mimeTypes />
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|
81 |
<granularDepth>0</granularDepth>
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|
82 |
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
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83 |
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
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|
84 |
<name>log</name>
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|
85 |
<depth>0</depth>
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|
86 |
<mimeTypes />
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|
87 |
<granularDepth>0</granularDepth>
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|
88 |
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
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|
89 |
</outputs>
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|
90 |
<classLoaderSharing>workflow</classLoaderSharing>
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|
91 |
<localDependencies>
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|
92 |
<string>tb-lsdr-matchboxeval-lib-1.0-SNAPSHOT.jar</string>
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93 |
<string>combinatoricslib-0.2.jar</string>
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94 |
</localDependencies>
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|
95 |
<artifactDependencies />
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|
96 |
<script>import eu.scape_project.tb.lsdr.MatchboxEval;
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97 |
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98 |
MatchboxEval me = new MatchboxEval(matchbox,groundtruth);
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99 |
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|
100 |
me.evaluate();
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|
101 |
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|
102 |
cid = me.getTruePositives();
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|
103 |
iid = me.getFalsePositives();
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104 |
md = me.getFalseNegatives();
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105 |
prec = me.getPrecision();
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|
106 |
rec = me.getRecall();
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|
107 |
fm = me.getFmeasure();
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108 |
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|
109 |
log = me.getLog();</script>
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|
110 |
<dependencies />
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|
111 |
</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="">
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112 |
<maxJobs>1</maxJobs>
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113 |
</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="">
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|
114 |
<backoffFactor>1.0</backoffFactor>
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|
|
115 |
<initialDelay>1000</initialDelay>
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|
|
116 |
<maxDelay>5000</maxDelay>
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|
117 |
<maxRetries>0</maxRetries>
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|
118 |
</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="">
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119 |
<mechanismType>D0A4CDEB-DD10-4A8E-A49C-8871003083D8</mechanismType>
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|
120 |
<mechanismName>fuel</mechanismName>
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|
121 |
<mechanismXML><?xml version="1.0" encoding="UTF-8"?>
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|
122 |
<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>
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123 |
</mechanismXML>
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|
124 |
<externaltoolid>eb15da53-92d0-4dac-aa40-3101b4500997</externaltoolid>
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|
125 |
<useCaseDescription>
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|
126 |
<usecaseid />
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|
127 |
<description />
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|
128 |
<command>RANDOM=`tr -dc "[:alpha:]" < /dev/urandom | head -c 20`
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129 |
PATHID=matchbox
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|
130 |
TMPDIR=/tmp/${PATHID}${RANDOM}
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|
131 |
mkdir ${TMPDIR}
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|
132 |
cd /opt/scape/darling/
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|
133 |
/usr/bin/python ./FindDuplicates.py %%barcode_path%% --featdir ${TMPDIR} all</command>
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134 |
<preparingTimeoutInSeconds>1200</preparingTimeoutInSeconds>
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|
135 |
<executionTimeoutInSeconds>1800</executionTimeoutInSeconds>
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|
136 |
<tags>
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|
137 |
<string>barcode_path</string>
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|
138 |
</tags>
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|
139 |
<REs />
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|
140 |
<queue__preferred />
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|
141 |
<queue__deny />
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|
142 |
<static__inputs />
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|
143 |
<inputs>
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|
144 |
<entry>
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|
145 |
<string>barcode_path</string>
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|
146 |
<de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
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147 |
<tag>barcode_path</tag>
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148 |
<file>false</file>
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|
149 |
<tempFile>false</tempFile>
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|
150 |
<binary>false</binary>
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|
151 |
<charsetName>UTF-8</charsetName>
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|
152 |
<forceCopy>false</forceCopy>
|
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|
153 |
<list>false</list>
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|
154 |
<concatenate>false</concatenate>
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|
155 |
<mime />
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|
156 |
</de.uni__luebeck.inb.knowarc.usecases.ScriptInputUser>
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|
157 |
</entry>
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|
158 |
</inputs>
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|
159 |
<outputs />
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|
160 |
<includeStdIn>false</includeStdIn>
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|
161 |
<includeStdOut>true</includeStdOut>
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|
162 |
<includeStdErr>true</includeStdErr>
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|
163 |
<validReturnCodes>
|
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|
164 |
<int>0</int>
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|
165 |
</validReturnCodes>
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|
166 |
</useCaseDescription>
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|
167 |
<edited>false</edited>
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|
168 |
</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="">
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169 |
<maxJobs>4</maxJobs>
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|
170 |
</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="">
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|
171 |
<backoffFactor>1.0</backoffFactor>
|
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|
172 |
<initialDelay>1000</initialDelay>
|
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|
173 |
<maxDelay>5000</maxDelay>
|
|
|
174 |
<maxRetries>0</maxRetries>
|
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|
175 |
</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="">
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|
176 |
<inputs>
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|
177 |
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
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|
178 |
<name>fileurl</name>
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|
179 |
<depth>0</depth>
|
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|
180 |
<mimeTypes>
|
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|
181 |
<string>'text/plain'</string>
|
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|
182 |
</mimeTypes>
|
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|
183 |
<handledReferenceSchemes />
|
|
|
184 |
<translatedElementType>java.lang.String</translatedElementType>
|
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|
185 |
<allowsLiteralValues>true</allowsLiteralValues>
|
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|
186 |
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
|
|
|
187 |
</inputs>
|
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|
188 |
<outputs>
|
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|
189 |
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
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|
190 |
<name>filecontents</name>
|
|
|
191 |
<depth>0</depth>
|
|
|
192 |
<mimeTypes>
|
|
|
193 |
<string>'text/plain'</string>
|
|
|
194 |
</mimeTypes>
|
|
|
195 |
<granularDepth>0</granularDepth>
|
|
|
196 |
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
|
|
|
197 |
</outputs>
|
|
|
198 |
<classLoaderSharing>workflow</classLoaderSharing>
|
|
|
199 |
<localDependencies />
|
|
|
200 |
<artifactDependencies />
|
|
|
201 |
<script>BufferedReader getReader (String fileUrl) throws IOException {
|
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|
202 |
InputStreamReader reader;
|
|
|
203 |
try {
|
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|
204 |
reader = new FileReader(fileUrl);
|
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|
205 |
}
|
|
|
206 |
catch (FileNotFoundException e) {
|
|
|
207 |
// try a real URL instead
|
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|
208 |
URL url = new URL(fileUrl);
|
|
|
209 |
reader = new InputStreamReader (url.openStream());
|
|
|
210 |
}
|
|
|
211 |
return new BufferedReader(reader);
|
|
|
212 |
}
|
|
|
213 |
|
|
|
214 |
|
|
|
215 |
|
|
|
216 |
StringBuffer sb = new StringBuffer(4000);
|
|
|
217 |
|
|
|
218 |
BufferedReader in = getReader(fileurl);
|
|
|
219 |
String str;
|
|
|
220 |
String lineEnding = System.getProperty("line.separator");
|
|
|
221 |
|
|
|
222 |
while ((str = in.readLine()) != null) {
|
|
|
223 |
sb.append(str);
|
|
|
224 |
sb.append(lineEnding);
|
|
|
225 |
}
|
|
|
226 |
in.close();
|
|
|
227 |
filecontents = sb.toString();
|
|
|
228 |
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229 |
</script>
|
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|
230 |
<dependencies />
|
|
|
231 |
<localworkerName>net.sourceforge.taverna.scuflworkers.io.TextFileReader</localworkerName>
|
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|
232 |
</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="">
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233 |
<maxJobs>1</maxJobs>
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234 |
</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="">
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235 |
<backoffFactor>1.0</backoffFactor>
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236 |
<initialDelay>1000</initialDelay>
|
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237 |
<maxDelay>5000</maxDelay>
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238 |
<maxRetries>0</maxRetries>
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239 |
</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="">
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240 |
<inputs>
|
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|
241 |
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
|
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|
242 |
<name>string</name>
|
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|
243 |
<depth>0</depth>
|
|
|
244 |
<mimeTypes>
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|
245 |
<string>'text/plain'</string>
|
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|
246 |
</mimeTypes>
|
|
|
247 |
<handledReferenceSchemes />
|
|
|
248 |
<translatedElementType>java.lang.String</translatedElementType>
|
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|
249 |
<allowsLiteralValues>true</allowsLiteralValues>
|
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|
250 |
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
|
|
|
251 |
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
|
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|
252 |
<name>regex</name>
|
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|
253 |
<depth>0</depth>
|
|
|
254 |
<mimeTypes>
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|
255 |
<string>'text/plain'</string>
|
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|
256 |
</mimeTypes>
|
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|
257 |
<handledReferenceSchemes />
|
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|
258 |
<translatedElementType>java.lang.String</translatedElementType>
|
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|
259 |
<allowsLiteralValues>true</allowsLiteralValues>
|
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|
260 |
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
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|
261 |
</inputs>
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262 |
<outputs>
|
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|
263 |
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
|
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|
264 |
<name>split</name>
|
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|
265 |
<depth>1</depth>
|
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|
266 |
<mimeTypes>
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|
267 |
<string>l('text/plain')</string>
|
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|
268 |
</mimeTypes>
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|
269 |
<granularDepth>1</granularDepth>
|
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|
270 |
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
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|
271 |
</outputs>
|
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|
272 |
<classLoaderSharing>workflow</classLoaderSharing>
|
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|
273 |
<localDependencies />
|
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|
274 |
<artifactDependencies />
|
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|
275 |
<script>List split = new ArrayList();
|
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|
276 |
if (!string.equals("")) {
|
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|
277 |
String regexString = ",";
|
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|
278 |
if (regex != void) {
|
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|
279 |
regexString = regex;
|
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|
280 |
}
|
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|
281 |
String[] result = string.split(regexString);
|
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|
282 |
for (int i = 0; i < result.length; i++) {
|
|
|
283 |
split.add(result[i]);
|
|
|
284 |
}
|
|
|
285 |
}
|
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|
286 |
</script>
|
|
|
287 |
<dependencies />
|
|
|
288 |
<localworkerName>org.embl.ebi.escience.scuflworkers.java.SplitByRegex</localworkerName>
|
|
|
289 |
</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="">
|
|
|
290 |
<maxJobs>1</maxJobs>
|
|
|
291 |
</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="">
|
|
|
292 |
<backoffFactor>1.0</backoffFactor>
|
|
|
293 |
<initialDelay>1000</initialDelay>
|
|
|
294 |
<maxDelay>5000</maxDelay>
|
|
|
295 |
<maxRetries>0</maxRetries>
|
|
|
296 |
</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="">
|
|
|
297 |
<value>\n</value>
|
|
|
298 |
</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="">
|
|
|
299 |
<maxJobs>1</maxJobs>
|
|
|
300 |
</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="">
|
|
|
301 |
<backoffFactor>1.0</backoffFactor>
|
|
|
302 |
<initialDelay>1000</initialDelay>
|
|
|
303 |
<maxDelay>5000</maxDelay>
|
|
|
304 |
<maxRetries>0</maxRetries>
|
|
|
305 |
</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="">
|
|
|
306 |
<inputs>
|
|
|
307 |
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
|
|
|
308 |
<name>barcode_path</name>
|
|
|
309 |
<depth>0</depth>
|
|
|
310 |
<mimeTypes>
|
|
|
311 |
<string>text/plain</string>
|
|
|
312 |
</mimeTypes>
|
|
|
313 |
<handledReferenceSchemes />
|
|
|
314 |
<translatedElementType>java.lang.String</translatedElementType>
|
|
|
315 |
<allowsLiteralValues>true</allowsLiteralValues>
|
|
|
316 |
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
|
|
|
317 |
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
|
|
|
318 |
<name>matchbox_stdout</name>
|
|
|
319 |
<depth>0</depth>
|
|
|
320 |
<mimeTypes>
|
|
|
321 |
<string>text/plain</string>
|
|
|
322 |
</mimeTypes>
|
|
|
323 |
<handledReferenceSchemes />
|
|
|
324 |
<translatedElementType>java.lang.String</translatedElementType>
|
|
|
325 |
<allowsLiteralValues>true</allowsLiteralValues>
|
|
|
326 |
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
|
|
|
327 |
</inputs>
|
|
|
328 |
<outputs>
|
|
|
329 |
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
|
|
|
330 |
<name>duplicates_result</name>
|
|
|
331 |
<depth>0</depth>
|
|
|
332 |
<mimeTypes />
|
|
|
333 |
<granularDepth>0</granularDepth>
|
|
|
334 |
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
|
|
|
335 |
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
|
|
|
336 |
<name>duplicates_matches</name>
|
|
|
337 |
<depth>0</depth>
|
|
|
338 |
<mimeTypes />
|
|
|
339 |
<granularDepth>0</granularDepth>
|
|
|
340 |
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
|
|
|
341 |
</outputs>
|
|
|
342 |
<classLoaderSharing>workflow</classLoaderSharing>
|
|
|
343 |
<localDependencies />
|
|
|
344 |
<artifactDependencies />
|
|
|
345 |
<script>#!Pairtree pt = new Pairtree();
|
|
|
346 |
#!String id = pt.mapToId("/mnt/abonas/linktree/", barcode_path.substring(0,barcode_path.lastIndexOf("/")));
|
|
|
347 |
String duplicates_result = "";
|
|
|
348 |
String duplicates_matches = "";
|
|
|
349 |
duplicates_result += barcode_path+ ":\n";
|
|
|
350 |
duplicates_matches += barcode_path + "\t";
|
|
|
351 |
StringTokenizer st = new StringTokenizer(matchbox_stdout, "\n");
|
|
|
352 |
boolean startDuplicates = false;
|
|
|
353 |
boolean hasDuplicates = false;
|
|
|
354 |
while (st.hasMoreTokens()) {
|
|
|
355 |
String token = st.nextToken();
|
|
|
356 |
if (startDuplicates) {
|
|
|
357 |
if (token.contains("=>")) {
|
|
|
358 |
duplicates_result += token + "\n";
|
|
|
359 |
hasDuplicates = true;
|
|
|
360 |
}
|
|
|
361 |
|
|
|
362 |
}
|
|
|
363 |
if (token.contains("=== List of detected duplicates ===")) {
|
|
|
364 |
startDuplicates = true;
|
|
|
365 |
}
|
|
|
366 |
}
|
|
|
367 |
if(hasDuplicates)
|
|
|
368 |
duplicates_matches += "1";
|
|
|
369 |
else
|
|
|
370 |
duplicates_matches += "0";</script>
|
|
|
371 |
<dependencies />
|
|
|
372 |
</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="">
|
|
|
373 |
<maxJobs>1</maxJobs>
|
|
|
374 |
</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="">
|
|
|
375 |
<backoffFactor>1.0</backoffFactor>
|
|
|
376 |
<initialDelay>1000</initialDelay>
|
|
|
377 |
<maxDelay>5000</maxDelay>
|
|
|
378 |
<maxRetries>0</maxRetries>
|
|
|
379 |
</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="">
|
|
|
380 |
<inputs>
|
|
|
381 |
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
|
|
|
382 |
<name>prec</name>
|
|
|
383 |
<depth>0</depth>
|
|
|
384 |
<mimeTypes>
|
|
|
385 |
<string>text/plain</string>
|
|
|
386 |
</mimeTypes>
|
|
|
387 |
<handledReferenceSchemes />
|
|
|
388 |
<translatedElementType>java.lang.String</translatedElementType>
|
|
|
389 |
<allowsLiteralValues>true</allowsLiteralValues>
|
|
|
390 |
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
|
|
|
391 |
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
|
|
|
392 |
<name>md</name>
|
|
|
393 |
<depth>0</depth>
|
|
|
394 |
<mimeTypes>
|
|
|
395 |
<string>text/plain</string>
|
|
|
396 |
</mimeTypes>
|
|
|
397 |
<handledReferenceSchemes />
|
|
|
398 |
<translatedElementType>java.lang.String</translatedElementType>
|
|
|
399 |
<allowsLiteralValues>true</allowsLiteralValues>
|
|
|
400 |
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
|
|
|
401 |
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
|
|
|
402 |
<name>iid</name>
|
|
|
403 |
<depth>0</depth>
|
|
|
404 |
<mimeTypes>
|
|
|
405 |
<string>text/plain</string>
|
|
|
406 |
</mimeTypes>
|
|
|
407 |
<handledReferenceSchemes />
|
|
|
408 |
<translatedElementType>java.lang.String</translatedElementType>
|
|
|
409 |
<allowsLiteralValues>true</allowsLiteralValues>
|
|
|
410 |
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
|
|
|
411 |
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
|
|
|
412 |
<name>fm</name>
|
|
|
413 |
<depth>0</depth>
|
|
|
414 |
<mimeTypes>
|
|
|
415 |
<string>text/plain</string>
|
|
|
416 |
</mimeTypes>
|
|
|
417 |
<handledReferenceSchemes />
|
|
|
418 |
<translatedElementType>java.lang.String</translatedElementType>
|
|
|
419 |
<allowsLiteralValues>true</allowsLiteralValues>
|
|
|
420 |
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
|
|
|
421 |
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
|
|
|
422 |
<name>cid</name>
|
|
|
423 |
<depth>0</depth>
|
|
|
424 |
<mimeTypes>
|
|
|
425 |
<string>text/plain</string>
|
|
|
426 |
</mimeTypes>
|
|
|
427 |
<handledReferenceSchemes />
|
|
|
428 |
<translatedElementType>java.lang.String</translatedElementType>
|
|
|
429 |
<allowsLiteralValues>true</allowsLiteralValues>
|
|
|
430 |
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
|
|
|
431 |
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
|
|
|
432 |
<name>rec</name>
|
|
|
433 |
<depth>0</depth>
|
|
|
434 |
<mimeTypes>
|
|
|
435 |
<string>text/plain</string>
|
|
|
436 |
</mimeTypes>
|
|
|
437 |
<handledReferenceSchemes />
|
|
|
438 |
<translatedElementType>java.lang.String</translatedElementType>
|
|
|
439 |
<allowsLiteralValues>true</allowsLiteralValues>
|
|
|
440 |
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
|
|
|
441 |
</inputs>
|
|
|
442 |
<outputs>
|
|
|
443 |
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
|
|
|
444 |
<name>report</name>
|
|
|
445 |
<depth>0</depth>
|
|
|
446 |
<mimeTypes />
|
|
|
447 |
<granularDepth>0</granularDepth>
|
|
|
448 |
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
|
|
|
449 |
</outputs>
|
|
|
450 |
<classLoaderSharing>workflow</classLoaderSharing>
|
|
|
451 |
<localDependencies />
|
|
|
452 |
<artifactDependencies />
|
|
|
453 |
<script>report = "Correctly identified duplicates (true positives): "+cid+"\n"+
|
|
|
454 |
"Incorrectly identified duplicates (false positives): "+iid+"\n"+
|
|
|
455 |
"Missed duplicates (false negatives): "+md+"\n"+
|
|
|
456 |
"Precision: "+prec+"%\n"+
|
|
|
457 |
"Recall: "+rec+"%\n"+
|
|
|
458 |
"F-Measure: "+fm+"%\n";</script>
|
|
|
459 |
<dependencies />
|
|
|
460 |
</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="">
|
|
|
461 |
<maxJobs>1</maxJobs>
|
|
|
462 |
</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="">
|
|
|
463 |
<backoffFactor>1.0</backoffFactor>
|
|
|
464 |
<initialDelay>1000</initialDelay>
|
|
|
465 |
<maxDelay>5000</maxDelay>
|
|
|
466 |
<maxRetries>0</maxRetries>
|
|
|
467 |
</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="">
|
|
|
468 |
<annotationAssertions>
|
|
|
469 |
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
|
|
|
470 |
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
|
|
|
471 |
<identification>2efd4378-62f5-41ea-bf6f-dd7d50cd732e</identification>
|
|
|
472 |
</annotationBean>
|
|
|
473 |
<date>2012-10-01 13:08:54.255 UTC</date>
|
|
|
474 |
<creators />
|
|
|
475 |
<curationEventList />
|
|
|
476 |
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
|
|
|
477 |
</annotationAssertions>
|
|
|
478 |
</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
|
|
|
479 |
<annotationAssertions>
|
|
|
480 |
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
|
|
|
481 |
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
|
|
|
482 |
<identification>6d1c206f-f442-49d3-97b3-50cd4ac66b5f</identification>
|
|
|
483 |
</annotationBean>
|
|
|
484 |
<date>2012-09-26 15:20:31.846 UTC</date>
|
|
|
485 |
<creators />
|
|
|
486 |
<curationEventList />
|
|
|
487 |
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
|
|
|
488 |
</annotationAssertions>
|
|
|
489 |
</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
|
|
|
490 |
<annotationAssertions>
|
|
|
491 |
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
|
|
|
492 |
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
|
|
|
493 |
<identification>801043a1-195a-4b7d-8dd4-c1ebfa8d3b41</identification>
|
|
|
494 |
</annotationBean>
|
|
|
495 |
<date>2012-10-01 12:37:43.3 UTC</date>
|
|
|
496 |
<creators />
|
|
|
497 |
<curationEventList />
|
|
|
498 |
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
|
|
|
499 |
</annotationAssertions>
|
|
|
500 |
</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
|
|
|
501 |
<annotationAssertions>
|
|
|
502 |
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
|
|
|
503 |
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
|
|
|
504 |
<identification>81553fe0-9aa5-4fc7-a775-19e96144f650</identification>
|
|
|
505 |
</annotationBean>
|
|
|
506 |
<date>2012-10-02 09:38:25.821 UTC</date>
|
|
|
507 |
<creators />
|
|
|
508 |
<curationEventList />
|
|
|
509 |
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
|
|
|
510 |
</annotationAssertions>
|
|
|
511 |
</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
|
|
|
512 |
<annotationAssertions>
|
|
|
513 |
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
|
|
|
514 |
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
|
|
|
515 |
<identification>673b9394-9206-4395-b9bb-1f48e52cec51</identification>
|
|
|
516 |
</annotationBean>
|
|
|
517 |
<date>2014-04-28 09:04:23.655 UTC</date>
|
|
|
518 |
<creators />
|
|
|
519 |
<curationEventList />
|
|
|
520 |
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
|
|
|
521 |
</annotationAssertions>
|
|
|
522 |
</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
|
|
|
523 |
<annotationAssertions>
|
|
|
524 |
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
|
|
|
525 |
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
|
|
|
526 |
<identification>506fc52e-7052-4f57-8c15-83821665c03e</identification>
|
|
|
527 |
</annotationBean>
|
|
|
528 |
<date>2012-10-02 09:56:29.495 UTC</date>
|
|
|
529 |
<creators />
|
|
|
530 |
<curationEventList />
|
|
|
531 |
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
|
|
|
532 |
</annotationAssertions>
|
|
|
533 |
</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
|
|
|
534 |
<annotationAssertions>
|
|
|
535 |
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
|
|
|
536 |
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.FreeTextDescription">
|
|
|
537 |
<text>Matchbox evaluation against ground truth. The evaluation process first
|
|
|
538 |
creates the matchbox output and ground truth lists. It then counts each page
|
|
|
539 |
tuple from the matchbox output that is in the ground truth as correctly
|
|
|
540 |
identified tuple (true positive). Those that are not in the ground truth are
|
|
|
541 |
counted as incorrectly identified tuples (false positives), and finally,
|
|
|
542 |
those that are in the ground truth but not in the matchbox output are counted
|
|
|
543 |
as missed tuples (false negatives).
|
|
|
544 |
The precision is then calculated as the number of true positives (i.e. the
|
|
|
545 |
number of items correctly labeled as duplicate page pairs) divided by the
|
|
|
546 |
total number of elements assumed to be duplicate page pairs (i.e. the sum of
|
|
|
547 |
true positives and false positives, which are items incorrectly labeled as
|
|
|
548 |
being duplicate page pairs ). Recall is then defined as the number of
|
|
|
549 |
true positives divided by the total number of elements of duplicate page
|
|
|
550 |
pairs (i.e. the sum of true positives and false negatives, which are items
|
|
|
551 |
have not been labeled as being duplicate page pairs but actually should have
|
|
|
552 |
been).
|
|
|
553 |
The ground truth contains single page instances without duplicates and
|
|
|
554 |
n-tuples (duplicates, triples, quadruples, etc.). n-tuples with n>2 are
|
|
|
555 |
expanded, the result is a list of 2-tuples which is used to determine the
|
|
|
556 |
number of missed duplicates (false negatives).</text>
|
|
|
557 |
</annotationBean>
|
|
|
558 |
<date>2012-10-02 12:36:08.934 UTC</date>
|
|
|
559 |
<creators />
|
|
|
560 |
<curationEventList />
|
|
|
561 |
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
|
|
|
562 |
</annotationAssertions>
|
|
|
563 |
</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
|
|
|
564 |
<annotationAssertions>
|
|
|
565 |
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
|
|
|
566 |
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
|
|
|
567 |
<identification>e26a0bd8-eb71-4fd3-9bc6-238d71792ed3</identification>
|
|
|
568 |
</annotationBean>
|
|
|
569 |
<date>2012-10-01 12:46:11.91 UTC</date>
|
|
|
570 |
<creators />
|
|
|
571 |
<curationEventList />
|
|
|
572 |
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
|
|
|
573 |
</annotationAssertions>
|
|
|
574 |
</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
|
|
|
575 |
<annotationAssertions>
|
|
|
576 |
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
|
|
|
577 |
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
|
|
|
578 |
<identification>857c050a-49b5-4606-bcdb-220455d64291</identification>
|
|
|
579 |
</annotationBean>
|
|
|
580 |
<date>2012-10-01 12:33:52.730 UTC</date>
|
|
|
581 |
<creators />
|
|
|
582 |
<curationEventList />
|
|
|
583 |
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
|
|
|
584 |
</annotationAssertions>
|
|
|
585 |
</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
|
|
|
586 |
<annotationAssertions>
|
|
|
587 |
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
|
|
|
588 |
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
|
|
|
589 |
<identification>f85240d9-2108-4057-8c42-78eef7ecf441</identification>
|
|
|
590 |
</annotationBean>
|
|
|
591 |
<date>2012-10-01 12:27:16.65 UTC</date>
|
|
|
592 |
<creators />
|
|
|
593 |
<curationEventList />
|
|
|
594 |
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
|
|
|
595 |
</annotationAssertions>
|
|
|
596 |
</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
|
|
|
597 |
<annotationAssertions>
|
|
|
598 |
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
|
|
|
599 |
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
|
|
|
600 |
<identification>79894ee6-b109-41b7-95db-8178b7eb4121</identification>
|
|
|
601 |
</annotationBean>
|
|
|
602 |
<date>2012-10-02 09:56:58.139 UTC</date>
|
|
|
603 |
<creators />
|
|
|
604 |
<curationEventList />
|
|
|
605 |
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
|
|
|
606 |
</annotationAssertions>
|
|
|
607 |
</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
|
|
|
608 |
<annotationAssertions>
|
|
|
609 |
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
|
|
|
610 |
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
|
|
|
611 |
<identification>66473d1e-e539-497e-874b-28f42198a8f3</identification>
|
|
|
612 |
</annotationBean>
|
|
|
613 |
<date>2012-09-26 15:18:43.167 UTC</date>
|
|
|
614 |
<creators />
|
|
|
615 |
<curationEventList />
|
|
|
616 |
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
|
|
|
617 |
</annotationAssertions>
|
|
|
618 |
</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
|
|
|
619 |
<annotationAssertions>
|
|
|
620 |
<net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
|
|
|
621 |
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
|
|
|
622 |
<identification>eaa27b27-7bc6-4461-875e-499f30946c6a</identification>
|
|
|
623 |
</annotationBean>
|
|
|
624 |
<date>2013-07-23 13:59:10.99 UTC</date>
|
|
|
625 |
<creators />
|
|
|
626 |
<curationEventList />
|
|
|
627 |
</net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
|
|
|
628 |
</annotationAssertions>
|
|
|
629 |
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630 |
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<identification>8538abb1-b420-4d8e-be5f-64da636f59c1</identification>
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<date>2012-10-02 09:37:23.56 UTC</date>
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636 |
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641 |
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<date>2012-10-01 12:40:56.91 UTC</date>
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647 |
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669 |
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670 |
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680 |
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681 |
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686 |
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691 |
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702 |
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703 |
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|
707 |
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709 |
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|
710 |
<text>Matchbox Evaluation</text>
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711 |
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|
712 |
<date>2012-10-02 09:38:19.704 UTC</date>
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|
713 |
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714 |
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715 |
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716 |
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|
719 |
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720 |
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|
721 |
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723 |
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724 |
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725 |
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727 |
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729 |
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733 |
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734 |
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735 |
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736 |
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741 |
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742 |
<annotationBean class="net.sf.taverna.t2.annotation.annotationbeans.Author">
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|
|
743 |
<text>Sven Schlarb</text>
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744 |
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745 |
<date>2012-10-02 12:36:16.119 UTC</date>
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746 |
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747 |
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748 |
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749 |
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753 |
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756 |
<date>2012-09-26 15:09:52.547 UTC</date>
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758 |
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760 |
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769 |
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795 |
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796 |
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801 |
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804 |
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806 |
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807 |
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810 |
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811 |
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812 |
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815 |
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816 |
</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow> |