--- a +++ b/scripts/ctrpfullscrape.java @@ -0,0 +1,52 @@ +import java.util.*; +import java.io.*; +import java.net.*; +public class ctrpfullscrape { + public static void main(String[] args) throws Exception { + Scanner in = new Scanner(new File("fullctrpids.csv")); + PrintWriter out = new PrintWriter(new File("ctrpdata.csv")); + String useless = in.nextLine(); + int count = 0; + while(in.hasNext()) { + System.out.println(count); + count++; + String id = in.nextLine(); + String source = getURLSource("https://clinicaltrialsapi.cancer.gov/v1/clinical-trials?nct_id=" + id); + int index = source.indexOf("display_order"); + if (index > 0) { + int partsbeg = source.indexOf("minimum_target_accrual_number"); + int partsend = source.indexOf(",", partsbeg); + int biobeg = source.indexOf("biomarkers\":"); + int bioend = partsbeg; + String parts = source.substring(partsbeg + 31, partsend); + String bios = source.substring(biobeg + 12, bioend - 2); + out.print(id + "," + parts + ",\"" + bios + "\""); + 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(); + } + } +}