From 21be5363b2f7b61aade8a4b4caf54da28d8cd82a Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 13 Oct 2016 16:43:52 +0100
Subject: [PATCH] JAL-2253 2 second timeout on ping URL, default 5 minutes on
 others

---
 src/jalview/ext/ensembl/EnsemblRestClient.java |   43 ++++++++++++++++++++----
 1 file changed, 37 insertions(+), 6 deletions(-)

diff --git a/src/jalview/ext/ensembl/EnsemblRestClient.java b/src/jalview/ext/ensembl/EnsemblRestClient.java
index b7b1985..5903f69 100644
--- a/src/jalview/ext/ensembl/EnsemblRestClient.java
+++ b/src/jalview/ext/ensembl/EnsemblRestClient.java
@@ -50,6 +50,10 @@ import com.stevesoft.pat.Regex;
  */
 abstract class EnsemblRestClient extends EnsemblSequenceFetcher
 {
+  private static final int DEFAULT_READ_TIMEOUT = 5 * 60 * 1000; // 5 minutes
+
+  private static final int CONNECT_TIMEOUT_MS = 10 * 1000; // 10 seconds
+
   /*
    * update these constants when Jalview has been checked / updated for
    * changes to Ensembl REST API
@@ -186,7 +190,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
    */
   private boolean checkEnsembl()
   {
-    HttpURLConnection conn = null;
+    BufferedReader br = null;
     try
     {
       // note this format works for both ensembl and ensemblgenomes
@@ -196,8 +200,9 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
 
       /*
        * expect {"ping":1} if ok
+       * if ping takes more than 2 seconds to respond, treat as if unavailable
        */
-      BufferedReader br = getHttpResponse(ping, null);
+      br = getHttpResponse(ping, null, 2 * 1000);
       JSONParser jp = new JSONParser();
       JSONObject val = (JSONObject) jp.parse(br);
       String pingString = val.get("ping").toString();
@@ -208,9 +213,15 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
               + t.getMessage());
     } finally
     {
-      if (conn != null)
+      if (br != null)
       {
-        conn.disconnect();
+        try
+        {
+          br.close();
+        } catch (IOException e)
+        {
+          // ignore
+        }
       }
     }
     return false;
@@ -239,17 +250,34 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
   }
 
   /**
+   * Gets a reader to the HTTP response, using the default read timeout of 5
+   * minutes
+   * 
+   * @param url
+   * @param ids
+   * @return
+   * @throws IOException
+   */
+  protected BufferedReader getHttpResponse(URL url, List<String> ids)
+          throws IOException
+  {
+    return getHttpResponse(url, ids, DEFAULT_READ_TIMEOUT);
+  }
+
+  /**
    * Writes the HTTP request and gets the response as a reader.
    * 
    * @param url
    * @param ids
    *          written as Json POST body if more than one
+   * @param readTimeout
+   *          in milliseconds
    * @return
    * @throws IOException
    *           if response code was not 200, or other I/O error
    */
-  protected BufferedReader getHttpResponse(URL url, List<String> ids)
-          throws IOException
+  protected BufferedReader getHttpResponse(URL url, List<String> ids,
+          int readTimeout) throws IOException
   {
     // long now = System.currentTimeMillis();
     HttpURLConnection connection = (HttpURLConnection) url.openConnection();
@@ -269,6 +297,9 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
     connection.setDoInput(true);
     connection.setDoOutput(multipleIds);
 
+    connection.setConnectTimeout(CONNECT_TIMEOUT_MS);
+    connection.setReadTimeout(readTimeout);
+
     if (multipleIds)
     {
       writePostBody(connection, ids);
-- 
1.7.10.2