Phenotype to pubmed

Value

Wsdl

Wsdl Operation

Value

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;

Script

String[] split = input.split("\n");
Vector nonEmpty = new Vector();

for (int i = 0; i < split.length; i++){
   if (!(split[i].equals("")))
   {
       nonEmpty.add(split[i].trim());
   }
}

String[] non_empty = new String[nonEmpty.size()];

for (int i = 0; i < non_empty.length; i ++)
{
   non_empty[i] = nonEmpty.elementAt(i);
}

String output = "";

for (int i = 0; i < non_empty.length; i++)
{
	output = output + (String) (non_empty[i] + "\n");
}

Script

String id = id.trim();
String abstract_text = abstract_text.trim();
String[] abstract_array = abstract_text.split("\n");

String abstract_amended = "";

if(abstract_array.length > 1)
{
	abstract_amended = abstract_array[0] + " ";
	for(int i = 1; i < abstract_array.length; i++)
	{
		abstract_amended = abstract_amended + abstract_array[i] + " "; 
	}
}
else
{
	abstract_amended = abstract_array[0];
}


String date_text = date_text.trim();

String output = "";

output = id + "\t" + date_text + "\t" + abstract_amended;

Value

Value

Script

String[] split = abstracts.split("\n");
String phenotype_term = phenotype.trim();

Vector nonEmpty = new Vector();

for (int i = 0; i < split.length; i++) 
{		
	String trimmed = split[i].trim();
//	String mytext = split[i].substring(split[i].indexOf(0), split[i].indexOf(" AND "));
	nonEmpty.add(trimmed);	
}

String output = ">> " + phenotype_term + "\n";

for (int i = 0; i < nonEmpty.size(); i++)
{
	output = output + (String) (nonEmpty.elementAt(i) + "\n");
}

Script

String seperatorString = "\n";
if (seperator != void) {
	seperatorString = seperator;
}
StringBuffer sb = new StringBuffer();
for (Iterator i = stringlist.iterator(); i.hasNext();) {
	String item = (String) i.next();
	sb.append(item);
	if (i.hasNext()) {
		sb.append(seperatorString);
	}
}
concatenated = sb.toString();

Value

Script

String seperatorString = "\n";
if (seperator != void) {
	seperatorString = seperator;
}
StringBuffer sb = new StringBuffer();
for (Iterator i = stringlist.iterator(); i.hasNext();) {
	String item = (String) i.next();
	sb.append(item);
	if (i.hasNext()) {
		sb.append(seperatorString);
	}
}
concatenated = sb.toString();

Script

String seperatorString = "\n";
if (seperator != void) {
	seperatorString = seperator;
}
StringBuffer sb = new StringBuffer();
for (Iterator i = stringlist.iterator(); i.hasNext();) {
	String item = (String) i.next();
	sb.append(item);
	if (i.hasNext()) {
		sb.append(seperatorString);
	}
}
concatenated = sb.toString();