initial commit of WormsAPI for making API requests to the Worms database

src/biotree/WormsAPI.java

+package biotree;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.net.HttpURLConnection;
+import java.net.URL;
+
+public class WormsAPI {
+	
+	public static void main(String[] args) throws IOException {
+		//small test
+		System.out.println(nameToID("Neogobius melanostomus"));
+	}
+	
+	/**
+	 * Search the WORMS database by scientific name to return Aphia (taxon) ID.
+	 * This must be an exact name or it will fail. Use fuzzyNameToID if the name 
+	 * is not exact.
+	 * @param scientificName Scientific name of taxon (family, genus, species, etc)
+	 * @return Aphia (taxon) ID of given scientific name.
+	 * @throws IOException
+	 */
+	public static int nameToID(String scientificName) throws IOException{
+		scientificName = repSpaces(scientificName);
+		String resp = makeRequest(String.format("http://marinespecies.org/rest/AphiaIDByName/%s?marine_only=false", scientificName));
+		
+		return Integer.parseInt(resp);
+	}
+	
+	/**
+	 * Search the WORMS database by fuzzy scientific name (a slightly misspelled name).
+	 * This has the advantage of being more flexible but it can be less accurate and it
+	 * is slower. If you have the actual scientific name, use nameToID() instead.
+	 * @param fuzzyName Fuzzy scientific name of taxon (family, genus, species, etc)
+	 * @return Aphia (taxon) ID of given scientific name.
+	 * @throws IOException
+	 */
+	public static int fuzzyNameToID(String fuzzyName) throws IOException{
+		fuzzyName = repSpaces(fuzzyName);
+		String resp = makeRequest(String.format("http://marinespecies.org/rest/AphiaRecordsByMatchNames?scientificnames%5B%5D=%s&marine_only=true", fuzzyName));
+		
+		//TODO: finish this function.
+		return 123123;
+	}
+	
+	/**
+	 * Perform a GET request to the given URL and return the content of the response.
+	 * @param url The URL to which to make a request.
+	 * @return The content returned by the server (if successful).
+	 * @throws IOException
+	 */
+	private static String makeRequest(String url) throws IOException {
+		//create new URL instance
+		URL urll = new URL(url);
+		//create and set up connection
+		HttpURLConnection con = (HttpURLConnection) urll.openConnection();
+		con.setRequestMethod("GET");
+		
+		int status = con.getResponseCode();
+		
+		BufferedReader in = new BufferedReader(
+				  new InputStreamReader(con.getInputStream()));
+		String inputLine;
+		StringBuffer content = new StringBuffer();
+		while ((inputLine = in.readLine()) != null) {
+		    content.append(inputLine);
+		}
+		in.close();
+		con.disconnect();
+		
+		return content.toString();
+	}
+	
+	/**
+	 * Helper to replace a space with the correct one for URLs.
+	 * @param in Input string
+	 * @return String with spaces replaced by "%20" for spaces in URLs.
+	 */
+	private static String repSpaces(String in) {
+		return in.replaceAll(" ", "%20");
+	}
+}