Triplify UniProt text search results [myexperiments:uniprotkb_search2rdf]

Script

output = "http://www.uniprot.org/" + string1 + "/?query=" + string2.replace(" ","+") + "&limit=100000&format=list";

Script

URL inputURL = null;
if (base != void) {
  inputURL = new URL(new URL(base), url);
}
else {
  inputURL = new URL(url);
}
URLConnection con = inputURL.openConnection();
InputStream in = con.getInputStream();

InputStreamReader isr = new InputStreamReader(in);
Reader inReader = new BufferedReader(isr);

StringBuffer buf = new StringBuffer();
int ch;
while ((ch = inReader.read()) > -1) {
  buf.append((char)ch);
}
inReader.close();
contents = buf.toString();


//String NEWLINE = System.getProperty("line.separator");
//
//URL inputURL = null;
//if (base != void) {
//	inputURL = new URL(new URL(base), url);
//} else {
//	inputURL = new URL(url);
//}
//StringBuffer result = new StringBuffer();
//BufferedReader reader = new BufferedReader(new InputStreamReader(inputURL.openStream()));
//String line = null;
//while ((line = reader.readLine()) != null) {
//	result.append(line);
//	result.append(NEWLINE);
//}
//
//contents = result.toString();

Script

List split = new ArrayList();
if (!string.equals("")) {
	String regexString = ",";
	if (regex != void) {
		regexString = regex;
	}
	String[] result = string.split(regexString);
	for (int i = 0; i < result.length; i++) {
		split.add(result[i]);
	}
}

Value

Script

output = "http://bio2rdf.org/" + string1 + ":" + string2;

Script

search = search.replace(" ","_");
Integer count = 0;

search_ntriples = "";
count_ntriples = "";

for (Iterator i = stringlist.iterator(); i.hasNext();) {
	String id = (String) i.next();
	count = count + 1;
search_ntriples = search_ntriples + "\n   .";
}

if (count != 0) {
count_ntriples =                  "\n  \""+count+"\" .";
count_ntriples = count_ntriples + "\n    .";
count_ntriples = count_ntriples + "\n    .";
}