Merge branch 'develop' into trialMerge

[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 8daf234..8ee6aaf 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblRestClient.java
+++ b/src/jalview/ext/ensembl/EnsemblRestClient.java
@@ -1,5 +1,26 @@
+/*
+ * 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.DataSourceType;
 import jalview.io.FileParse;
 import jalview.util.StringUtils;
 
@@ -30,6 +51,10 @@ 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
@@ -166,7 +191,7 @@ 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 +201,9 @@ 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 +214,15 @@ 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;
@@ -214,22 +246,39 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
       // request failed
       return null;
     }
-    FileParse fp = new FileParse(reader, url.toString(), "HTTP_POST");
+    FileParse fp = new FileParse(reader, url.toString(), DataSourceType.URL);
     return fp;
   }
 
   /**
+   * 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();
@@ -249,6 +298,9 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
     connection.setDoInput(true);
     connection.setDoOutput(multipleIds);
 
+    connection.setConnectTimeout(CONNECT_TIMEOUT_MS);
+    connection.setReadTimeout(readTimeout);
+
     if (multipleIds)
     {
       writePostBody(connection, ids);