EUADR - Literature Analysis

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);
	}

//URL of MedLine articles
String urlmedline= "http://www.ncbi.nlm.nih.gov/pubmed/";
// write getListPublis to tmpFile

BufferedWriter out = new BufferedWriter(new FileWriter("./getlistpublisTmp.xml"));
out.write(listpubli);
out.close();


// XSL MERGE
//String xslFilename = "/home/abauer/Dropbox/signal_substantiation/TavernaWorkflow_Cytoscape/files/EUADR_merge.xsl";;
String xslFilename = "http://lesimisped.free.fr/EUADR_webservice/EUADR_ConvertToHTML.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("./getlistpublisTmp.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("./getListPubli.html"));
resultWrite.write(resultStr.toString());
resultWrite.close();

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

//EAUDR_listpublis = EAUDR_listpublis.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("./convertHTML.xml");
tmpFile1.delete();