--- a +++ b/scripts/ctsampleconditions.java @@ -0,0 +1,62 @@ +import java.util.*; +import java.io.*; +import java.net.*; +public class ctsampleconditions { + public static void main(String[] args) throws Exception { + Scanner in = new Scanner(new File("example_ct.csv")); + PrintWriter out = new PrintWriter(new File("ctsampleconds.csv")); + String useless = in.nextLine(); + int count = 0; + while(in.hasNext()) { + System.out.println(count); + count++; + String id = in.nextLine().split(",")[0]; + String source = getURLSource("https://www.clinicaltrials.gov/ct2/show/record/"+id+"?term="+id+"&rank=1"); + int index = source.indexOf("<td", source.indexOf("Condition ")); + int end = source.indexOf("/td", index); + if (index > 0) { + ArrayList<Integer> startinds = new ArrayList<Integer>(); + ArrayList<Integer> endinds = new ArrayList<Integer>(); + while (index > 0 && index < end) { + if (source.charAt(index-1) == 'x') { + startinds.add(index); + endinds.add(source.indexOf("<", index)); + } + index = source.indexOf("\">", index+1); + } + ArrayList<String> strings = new ArrayList<String>(); + for (int i = 0; i < startinds.size(); i++) strings.add(source.substring(startinds.get(i) + 2, endinds.get(i)).replaceAll("\"", "").replaceAll("\r\n", "").replaceAll("\n\r", "")); + out.print(id + ","); + for (int i = 0; i < strings.size(); i++) { + out.print("\"" + strings.get(i) + "\""); + if (i < strings.size() - 1) out.print(","); + } + out.println(); + } + } + in.close(); + out.close(); + } + public static String getURLSource(String url) throws IOException + { + URL urlObject = new URL(url); + URLConnection urlConnection = urlObject.openConnection(); + urlConnection.setRequestProperty("User-Agent", "Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.11 (KHTML, like Gecko) Chrome/23.0.1271.95 Safari/537.11"); + try { + return toString(urlConnection.getInputStream());}catch(Exception e) {return "";} + } + private static String toString(InputStream inputStream) throws IOException + { + try (BufferedReader bufferedReader = new BufferedReader(new InputStreamReader(inputStream, "UTF-8"))) + { + String inputLine; + StringBuilder stringBuilder = new StringBuilder(); + while ((inputLine = bufferedReader.readLine()) != null) + { + stringBuilder.append(inputLine); + } + + return stringBuilder.toString(); + } + } +}