Example Java Client

JARs

Install the following JARs locally to compile this example

• json-smart

Compiling and Running

javac -cp json-smart-1.2.jar RestClient.java
java -cp .:json-smart1.2.jar RestClient

Example Client (RestClient.java)

import java.net.URL;
import java.net.URLConnection;
import java.net.HttpURLConnection;
import java.net.MalformedURLException;
import java.io.BufferedReader;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.IOException;
import java.io.Reader;
import net.minidev.json.*;
import net.minidev.json.parser.*;
 
public class RestClient {

  public static final String SERVER = "http://rest.ensembl.org";
  public static final JSONParser PARSER = new JSONParser(JSONParser.MODE_JSON_SIMPLE);
  
  public static int requestCount = 0;
  public static long lastRequestTime = System.currentTimeMillis();
 
  public static void main(String[] args) throws Exception {
    String species, symbol;
    if(args.length == 2) {
      species = args[0];
      symbol = args[1];
    }
    else if(args.length == 1) {
      species = args[0];
      symbol = "BRAF";
    }
    else {
      species = "human";
      symbol = "BRAF";
    }
    
    JSONArray variants = getVariants(species, symbol);
    for(Object variantObject: variants) {
      JSONObject variant = (JSONObject)variantObject;
      String srName = (String)variant.get("seq_region_name");
      Number start = (Number)variant.get("start");
      Number end = (Number)variant.get("end");
      Number strand = (Number)variant.get("strand");
      String id = (String)variant.get("id");
      String consequence = (String)variant.get("id");
      String output = String.format("%s:%d-%d:%d ==> %s (%s)", srName, start, end, strand, id, consequence);
      System.out.println(output);
    }
  }

  public static JSONArray getVariants(String species, String symbol) throws ParseException, MalformedURLException, IOException, InterruptedException {
    String id = getGeneID(species, symbol);
    return (JSONArray) getJSON("/overlap/id/"+id+"?feature=variation");
  }
  
  public static String getGeneID(String species, String symbol) throws ParseException, MalformedURLException, IOException, InterruptedException {
    String endpoint = "/xrefs/symbol/"+species+"/"+symbol+"?object_type=gene";
    JSONArray genes = (JSONArray) getJSON(endpoint);
    if(genes.isEmpty()) {
      throw new RuntimeException("Got nothing for endpoint "+endpoint);
    }
    JSONObject gene = (JSONObject)genes.get(0);
    return (String)gene.get("id");
  }

  public static Object getJSON(String endpoint) throws ParseException, MalformedURLException, IOException, InterruptedException {
    String jsonString = getContent(endpoint);
    return PARSER.parse(jsonString);
  }

  public static String getContent(String endpoint) throws MalformedURLException, IOException, InterruptedException {
    
    if(requestCount == 15) { // check every 15
      long currentTime = System.currentTimeMillis();
      long diff = currentTime - lastRequestTime;
      //if less than a second then sleep for the remainder of the second
      if(diff < 1000) {
        Thread.sleep(1000 - diff);
      }
      //reset
      lastRequestTime = System.currentTimeMillis();
      requestCount = 0;
    }
    
    URL url = new URL(SERVER+endpoint);
    URLConnection connection = url.openConnection();
    HttpURLConnection httpConnection = (HttpURLConnection)connection;
    httpConnection.setRequestProperty("Content-Type", "application/json");
    requestCount++;

    InputStream response = httpConnection.getInputStream();
    int responseCode = httpConnection.getResponseCode();

    if(responseCode != 200) {
      if(responseCode == 429 && httpConnection.getHeaderField("Retry-After") != null) {
        double sleepFloatingPoint = Double.valueOf(httpConnection.getHeaderField("Retry-After"));
        double sleepMillis = 1000 * sleepFloatingPoint;
        Thread.sleep((long)sleepMillis);
        return getContent(endpoint);
      }
      throw new RuntimeException("Response code was not 200. Detected response was "+responseCode);
    }

    String output;
    Reader reader = null;
    try {
      reader = new BufferedReader(new InputStreamReader(response, "UTF-8"));
      StringBuilder builder = new StringBuilder();
      char[] buffer = new char[8192];
      int read;
      while ((read = reader.read(buffer, 0, buffer.length)) > 0) {
        builder.append(buffer, 0, read);
      }
      output = builder.toString();
    } 
    finally {
      if (reader != null) {
        try {
          reader.close(); 
        } 
        catch (IOException logOrIgnore) {
          logOrIgnore.printStackTrace();
        }
      }
    }
  
    return output;
  }
}

build.xml

<project default="run-basic">
    <path id="classpath">
        <fileset dir="." includes="*.jar"/>
    </path>
  
    <target name="clean" description="Cleanup any compiled files">
        <delete dir="build"/>
    </target>
    
    <target name="compile" description="Compiles the 2 rest clients into classes">
        <mkdir dir="build"/>
        <javac srcdir="." destdir="build" classpathref="classpath" includeantruntime="false"/>
    </target>

    <target name="run" depends="compile" description="Runs the advanced RestClient class">
        <java fork="true" classname="RestClient">
            <classpath>
                <path refid="classpath"/>
                <path location="build"/>
            </classpath>
        </java>
    </target>

</project>

How To Build

Once you have downloaded the json-smart JAR, created the RestClient.java file and the build.xml run the following command.

ant run

To run outside of the ant environment you will need the following command

java -classpath json-smart-1.2.jar:build RestClient