Merge branch 'develop' into bug/JAL-98consensusMemory

[jalview.git] / src / jalview / ext / ensembl / EnsemblRestClient.java

diff --git a/src/jalview/ext/ensembl/EnsemblRestClient.java b/src/jalview/ext/ensembl/EnsemblRestClient.java
index 30dcee8..5903f69 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblRestClient.java
+++ b/src/jalview/ext/ensembl/EnsemblRestClient.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ext.ensembl;
 
 import jalview.io.FileParse;
@@ -30,6 +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
@@ -52,10 +76,10 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
   private final static long VERSION_RETEST_INTERVAL = 1000L * 3600; // 1 hr
 
   private static final Regex TRANSCRIPT_REGEX = new Regex(
-            "(ENS)([A-Z]{3}|)T[0-9]{11}$");
+          "(ENS)([A-Z]{3}|)T[0-9]{11}$");
 
   private static final Regex GENE_REGEX = new Regex(
-            "(ENS)([A-Z]{3}|)G[0-9]{11}$");
+          "(ENS)([A-Z]{3}|)G[0-9]{11}$");
 
   static
   {
@@ -166,7 +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
@@ -176,8 +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();
@@ -188,9 +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;
@@ -207,7 +238,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
           throws IOException
   {
     URL url = getUrl(ids);
-  
+
     BufferedReader reader = getHttpResponse(url, ids);
     if (reader == null)
     {
@@ -219,21 +250,38 @@ 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();
-  
+
     /*
      * POST method allows multiple queries in one request; it is supported for
      * sequence queries, but not for overlap
@@ -249,13 +297,16 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
     connection.setDoInput(true);
     connection.setDoOutput(multipleIds);
 
+    connection.setConnectTimeout(CONNECT_TIMEOUT_MS);
+    connection.setReadTimeout(readTimeout);
+
     if (multipleIds)
     {
       writePostBody(connection, ids);
     }
-  
+
     int responseCode = connection.getResponseCode();
-  
+
     if (responseCode != 200)
     {
       /*
@@ -272,7 +323,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
     // + (System.currentTimeMillis() - now) + "ms to fetch");
 
     checkRateLimits(connection);
-  
+
     BufferedReader reader = null;
     reader = new BufferedReader(new InputStreamReader(response, "UTF-8"));
     return reader;
@@ -325,7 +376,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
       // remaining, limit, reset));
     }
   }
-  
+
   /**
    * Rechecks if Ensembl is responding, unless the last check was successful and
    * the retest interval has not yet elapsed. Returns true if Ensembl is up,