ADR-S

Script

String inputString = string;
StringBuffer sb = new StringBuffer();
String[] list = inputString.split("\n");
for (String item : list) {
	sb.append(", " + item);
}

concatenated = sb.toString();
// remove first comma
concatenated = concatenated.replaceFirst(", ", "");

fail = false;
if(concatenated.equals("")){
fail = true;
}

Script

import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.FileWriter;
import java.io.IOException;
import java.io.InputStreamReader;
import java.io.OutputStreamWriter;
import java.io.StringWriter;
import java.io.Writer;
import java.net.URL;
import java.util.HashMap;
import java.util.Map;

import javax.xml.transform.Result;
import javax.xml.transform.Source;
import javax.xml.transform.SourceLocator;
import javax.xml.transform.Templates;
import javax.xml.transform.Transformer;
import javax.xml.transform.TransformerConfigurationException;
import javax.xml.transform.TransformerException;
import javax.xml.transform.TransformerFactory;
import javax.xml.transform.stream.StreamResult;
import javax.xml.transform.stream.StreamSource;

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);
	}
	
BufferedWriter getWriter (String fileUrl) throws IOException {
		Writer writer;
		try {
			writer = new FileWriter(fileUrl);
		}
		catch (FileNotFoundException e) {
			// try a real URL instead
			URL url = new URL(fileUrl);
			writer = new OutputStreamWriter (url.openConnection().getOutputStream());
		}
		return new BufferedWriter(writer);
	}


// write geneDiseaseOutput to tmpFile

BufferedWriter out = new BufferedWriter(new FileWriter("./intersectingPathwaysTmp.xml"));
out.write(intersectingPathways);
out.close();


// XSL MERGE
//String xslFilename = "/home/abauer/Dropbox/signal_substantiation/TavernaWorkflow_Cytoscape/files/EUADR_merge.xsl";;
String xslFilename = "http://ibi.imim.es/eu-adr/EUADR_convertIntersectingPathways.xsl";

// Create transformer factory
TransformerFactory factory = TransformerFactory.newInstance();

// Use the factory to create a template containing the xsl file
Templates template = factory.newTemplates(new StreamSource(getReader(xslFilename)));

// Use the template to create a transformer
Transformer xformer = template.newTransformer();

// Prepare the input and output files
Source source = new StreamSource(getReader("./intersectingPathwaysTmp.xml"));
StringWriter resultStr = new StringWriter();
Result result = new StreamResult(resultStr);

// Apply the xsl file to the source file and write the result to the
// output file
xformer.transform(source, result);

// write output to tmp file
BufferedWriter resultWrite = new BufferedWriter(new FileWriter("./intersectingPathwaysANNA.html"));
resultWrite.write(resultStr.toString());
resultWrite.close();

EUADR_intersectingPathways = resultStr.toString();
// change the name of the graph
String name = "the drug " + atc + " and the event " + event;

EUADR_intersectingPathways = EUADR_intersectingPathways.replace("TESTANNATEST", name);



// open browser
/*File tmpFile2 = new File("intersectingPathways.html");
String path = tmpFile2.getAbsolutePath();
Runtime rt = Runtime.getRuntime();
Process pr = rt.exec("firefox " + path);
*/

// delete all tmp files
File tmpFile1 = new File("./intersectingPathways.xml");
tmpFile1.delete();

Script

String size = intersectionList.size().toString();
String result = "YES, this drug-event pair is connected through pathways.\n" +
"There are " + size + " pathways in which drug and event proteins are expressed.\n\n" + 
"To inspect the results in more detail:\n" + 
"1) Save the intersectingPathways as .html file\n" + 
"2) Open the file in a web browser";

if (intersectionList.size() == 0) result = "NO, there are no pathways to which drug and event proteins are annotated that are expressed in the same tissue";


if(failDisease.equals("true")){
	result = "There are no proteins annotated to the event.";
}

if(failDrug.equals("true")){
	result = "There are no proteins annotated to the drug.";
}

else if(failDisease.equals("true") && failDrug.equals("true")){
	result = "There are no proteins annotated to the event or drug. \n Both lists are empty";
}

Script

import org.dom4j.Document;
import org.dom4j.Node;
import org.dom4j.io.SAXReader;

SAXReader reader = new SAXReader(false);
reader.setIncludeInternalDTDDeclarations(false);
reader.setIncludeExternalDTDDeclarations(false);

Document document = reader.read(new StringReader(xmltext));
List nodelist = document.selectNodes(xpath);

// Process the elements in the nodelist
ArrayList outputList = new ArrayList();
ArrayList outputXmlList = new ArrayList();

String val = null;
String xmlVal = null;
for (Iterator iter = nodelist.iterator(); iter.hasNext();) {
	Node element = (Node) iter.next();
	xmlVal = element.asXML();
	val = element.getStringValue();
	if (val != null && !val.equals("")) {
		outputList.add(val);
		outputXmlList.add(xmlVal);
	}

}

List nodelist=outputList;
List nodelistAsXML=outputXmlList;

Value

Script

import javax.swing.JOptionPane;

JOptionPane.showMessageDialog(null, (message == void ? null : message), (title == void ? null : "Drug-event connection through pathways"),	JOptionPane.INFORMATION_MESSAGE);

answer = "answer";

Script

String inputString = string;
StringBuffer sb = new StringBuffer();
String[] list = inputString.split("\n");
for (String item : list) {
	sb.append(", " + item);
}

concatenated = sb.toString();
// remove first comma
concatenated = concatenated.replaceFirst(", ", "");

fail = false;
if(concatenated.equals("")){
fail = true;
}

Wsdl

Wsdl Operation