--- a
+++ b/scripts/ctsamplemetamap.java
@@ -0,0 +1,65 @@
+import java.util.*;
+import java.io.*;
+import gov.nih.nlm.nls.skr.*;
+public class ctsamplemetamap {
+  static GenericObject gj = new GenericObject();
+  public static void main(String[] args) throws Exception {
+    Scanner in = new Scanner(new File("ctsampleinds.csv"));
+    PrintWriter out = new PrintWriter(new File("sample_output_full.csv"));
+    int count = 0;
+    for (int j = 0; j < 339; j++) {
+      System.out.println(count);
+      count++;
+      String line = in.nextLine();
+      boolean inQuotes = false;
+      boolean inApos = false;
+      ArrayList<String> terms = new ArrayList<String>();
+      String term = "";
+      for (int i = 0; i < line.length(); i++) {
+        if (line.charAt(i) != ',' || inQuotes) {
+          if (line.charAt(i) == '\"') inQuotes = !inQuotes;
+          else term = term + line.charAt(i);
+        }
+        else {
+          if (!inQuotes) {terms.add(term); term = "";}
+        }
+      }
+      terms.add(term);
+      out.print(terms.get(0) + "," + terms.get(1) + ",\"[");
+      ArrayList<String> indications = new ArrayList<String>();
+      String indication = "";
+      for (int i = 1; i < terms.get(2).length()-1; i++) {
+        if (terms.get(2).charAt(i) != ',' || inApos) {
+          if (terms.get(2).charAt(i) == '\'') inApos = !inApos;
+          else indication = indication + terms.get(2).charAt(i);
+        }
+        else {
+          if (!inApos) {indications.add(indication); indication = "";}
+        }
+      }
+      indications.add(indication);
+      for (int i = 0; i < indications.size(); i++) {
+        String ind = indications.get(i);
+        PrintWriter tmp = new PrintWriter(new File("input.txt"));
+        tmp.print(ind);
+        tmp.close();
+        out.print('\'' + getMetamap() + "\'");
+        if (i < indications.size()-1) out.print(",");
+      }
+      out.print("]\"");
+      out.println();
+    }
+    in.close();
+    out.close();
+  }
+  static String getMetamap() {
+    gj.setField("Email_Address", "neilmalur@hotmail.com");
+    gj.setFileField("UpLoad_File", "./input.txt");
+    //gj.setField("APIText", input);
+    //gj.setField("Batch_Command", "MTI -opt1L_DCMS -E");
+    gj.setField("Batch_Command", "metamap -pcI");
+    gj.setField("BatchNotes", "SKR Web API test");
+    gj.setField("SilentEmail", true);
+    return gj.handleSubmission();
+  }
+}