Type a folder to store temporary files
Type a folder to store the temporary files. Add a trailing slash!
net.sourceforge.taverna.scuflworkers.ui.AskWorker
1 ,2 ,3 ,4 ,5 ,6
org.embl.ebi.escience.scuflworkers.java.SplitByRegex
workflows.xml?num=100&page=
org.embl.ebi.escience.scuflworkers.java.StringConcat
What should be the name of the index?
Please enter a name to use
net.sourceforge.taverna.scuflworkers.ui.AskWorker
workflows.xml
org.embl.ebi.escience.scuflworkers.java.StringConcat
.txt
org.embl.ebi.escience.scuflworkers.java.StringConcat
http://sandbox.myexperiment.org/
http://(.+)/(.+)
2
org.embl.ebi.escience.scuflworkers.java.RegularExpressionStringList
<?xml version="1.0" encoding="UTF-8"?> <config xmlns='http://aid.org/' xmlns:xsi='http://www.w3.org/2001/XMLSchema-instance' xsi:schemaLocation='http://aid.org/ file:config.xsd' > <Name>My Experiment2</Name> <IndexOverwrite>true</IndexOverwrite> <IndexAnalyzer>STANDARD</IndexAnalyzer> <SRBused>false</SRBused> <MergeFactor>300</MergeFactor> <MaxBufferedDocs>30</MaxBufferedDocs> <DocType FileType="medline"> <FileExtension>med</FileExtension> <DocTypeAnalyzer>STANDARD</DocTypeAnalyzer> <Field Name="AU"> <Index>TOKENIZED</Index> <Store>true</Store> <Termvector>NO</Termvector> <Description>"Author field of Medline"</Description> </Field> <Field Name="TI"> <Index>TOKENIZED</Index> <Store>true</Store> <Termvector>YES</Termvector> <Description>"Title field of Medline"</Description> </Field> <Field Name="AB"> <Index>TOKENIZED</Index> <Store>true</Store> <Termvector>YES</Termvector> <Description>"Abstract field of Medline"</Description> </Field> <Field Name="FAU"> <Index>TOKENIZED</Index> <Store>true</Store> <Termvector>NO</Termvector> <Description>"First Author field of Medline"</Description> </Field> <Field Name="MH"> <Index>TOKENIZED</Index> <Store>true</Store> <Termvector>NO</Termvector> <Description>"MESH Heading field of Medline"</Description> </Field> <Field Name="PMID"> <Index>TOKENIZED</Index> <Store>true</Store> <Termvector>NO</Termvector> <Description>"PMID field of Medline"</Description> </Field> <Field Name="SO"> <Index>TOKENIZED</Index> <Store>true</Store> <Termvector>NO</Termvector> <Description>"SO field of Medline"</Description> </Field> </DocType> <DocType FileType="txt"> <FileExtension>txt</FileExtension> <FileExtension>xml</FileExtension> <DocTypeAnalyzer>STANDARD</DocTypeAnalyzer> <Field Name="path"> <Index>TOKENIZED</Index> <Store>true</Store> <Termvector>NO</Termvector> <Description>"path"</Description> </Field> <Field Name="content"> <Index>TOKENIZED</Index> <Store>true</Store> <Termvector>YES</Termvector> <Description>"content"</Description> </Field> <Field Name="title"> <Index>TOKENIZED</Index> <Store>true</Store> <Termvector>YES</Termvector> <Description>"title"</Description> </Field> <Field Name="summary"> <Index>TOKENIZED</Index> <Store>false</Store> <Termvector>NO</Termvector> <Description>"summary"</Description> </Field> </DocType> <DocType FileType="pdf"> <FileExtension>pdf</FileExtension> <DocTypeAnalyzer>STANDARD</DocTypeAnalyzer> <Field Name="path"> <Index>TOKENIZED</Index> <Store>true</Store> <Termvector>NO</Termvector> <Description>"path"</Description> </Field> <Field Name="content"> <Index>TOKENIZED</Index> <Store>true</Store> <Termvector>YES</Termvector> <Description>"content"</Description> </Field> <Field Name="title"> <Index>TOKENIZED</Index> <Store>true</Store> <Termvector>YES</Termvector> <Description>"title"</Description> </Field> <Field Name="summary"> <Index>TOKENIZED</Index> <Store>false</Store> <Termvector>NO</Termvector> <Description>"summary"</Description> </Field> </DocType> <DocType FileType="msword"> <DocTypeAnalyzer>STANDARD</DocTypeAnalyzer> <FileExtension>doc</FileExtension> <Field Name="path"> <Index>TOKENIZED</Index> <Store>true</Store> <Termvector>NO</Termvector> <Description>"path"</Description> </Field> <Field Name="content"> <Index>TOKENIZED</Index> <Store>true</Store> <Termvector>YES</Termvector> <Description>"content"</Description> </Field> <Field Name="summary"> <Index>TOKENIZED</Index> <Store>false</Store> <Termvector>NO</Termvector> <Description>"summary"</Description> </Field> </DocType> </config>
org.embl.ebi.escience.scuflworkers.java.WebPageFetcher
http://sandbox.myexperiment.org/
org.embl.ebi.escience.scuflworkers.java.WebPageFetcher
net.sourceforge.taverna.scuflworkers.io.TextFileWriter
/tmp/workflows.xsl
net.sourceforge.taverna.scuflworkers.io.TextFileWriter
/tmp/workflows.xsl
/tmp/bla
/tmp/workflows.xml
html
net.sourceforge.taverna.scuflworkers.xml.XSLTWorker
--
org.embl.ebi.escience.scuflworkers.java.SplitByRegex
workflows.xsl
org.embl.ebi.escience.scuflworkers.java.StringConcat
<xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform"><xsl:template match="workflow"><xsl:value-of select="@uri"/> -- </xsl:template></xsl:stylesheet>
org.embl.ebi.escience.scuflworkers.java.StringConcat
net.sourceforge.taverna.scuflworkers.io.TextFileWriter
/tmp/
org.embl.ebi.escience.scuflworkers.java.StringConcat
Use this method to add a single file to a named index using a specified config. The indexName in the argument will override that in the configfile
http://aida.science.uva.nl:9999/axis/services/IndexWS?wsdl
addToIndexWithConfig
title.out
org.embl.ebi.escience.scuflworkers.java.StringConcat
net.sourceforge.taverna.scuflworkers.io.TextFileWriter
getTitle.xsl
org.embl.ebi.escience.scuflworkers.java.StringConcat
<xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform"><xsl:template match="workflow"><xsl:value-of select="title"/> </xsl:template></xsl:stylesheet>
xml
net.sourceforge.taverna.scuflworkers.xml.XSLTWorker
net.sourceforge.taverna.scuflworkers.io.TextFileReader
import java.util.regex.*;
String pStr = "<(.*?)>(.*)";
Pattern idPattern = Pattern.compile(pStr, Pattern.UNIX_LINES | Pattern.DOTALL);
Matcher idMatcher = idPattern.matcher(in.replaceAll("\n"," "));
boolean matched = idMatcher.matches();
if (matched) {
out = idMatcher.group(2).trim();
}
else {
print("didn't match id");
Failure = true;
FailureMessage = "Couldn't extract from " + in;
}
in
out
org.embl.ebi.escience.scuflworkers.java.StringConcat
out = "_(" + in.replaceAll("\n", "").trim().replaceAll(tmp+"workflow.xml\\?id=","") + ")";
in
tmp
out
Completed
Write_XSL_File
Transform_XML
Scheduled
Running
Completed
Transform_XML
Read_Text_File
Scheduled
Running
getDescription.xsl
org.embl.ebi.escience.scuflworkers.java.StringConcat
xml
net.sourceforge.taverna.scuflworkers.xml.XSLTWorker
<xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform"><xsl:template match="workflow"><xsl:value-of select="description"/> </xsl:template></xsl:stylesheet>
net.sourceforge.taverna.scuflworkers.io.TextFileWriter
description.out
org.embl.ebi.escience.scuflworkers.java.StringConcat
net.sourceforge.taverna.scuflworkers.io.TextFileReader
import java.util.regex.*;
String pStr = "<(.*?)>(.*)";
Pattern idPattern = Pattern.compile(pStr, Pattern.UNIX_LINES | Pattern.DOTALL);
Matcher idMatcher = idPattern.matcher(in.replaceAll("\n"," "));
boolean matched = idMatcher.matches();
if (matched) {
out = idMatcher.group(2);
}
else {
print("didn't match id");
Failure = true;
FailureMessage = "Couldn't extract from " + in;
}
in
out
Completed
Write_XSL_File
Transform_XML
Scheduled
Running
Completed
Transform_XML
Read_Text_File
Scheduled
Running
text/html
text/xml
Completed
Write_Text_File
Extract_Workflows
Scheduled
Running
Completed
save_extract_workflow_XSLT
Extract_Workflows
Scheduled
Running
Completed
save_workflow
extractTitle
Scheduled
Running
Completed
save_workflow
extractDescription
Scheduled
Running
text/html
text/xml