Example-Java-Client.md

+# JARs
+
+- [json-smart](jars/json-smart-1.2.jar)
+
+# Example Client (RestClient.java)
+
+```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("/feature/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;
+    connection.setRequestProperty("Content-Type", "application/json");
+
+    InputStream response = connection.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
+
+```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-basic" depends="compile" description="Runs the BasicRestClient class">
+        <java fork="true" classname="BasicRestClient">
+            <classpath>
+                <path refid="classpath"/>
+                <path location="build"/>
+            </classpath>
+        </java>
+    </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>
+```
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