JAL-2189 apply license

[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 72efdc1..b7b1985 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;
@@ -34,10 +54,11 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
    * update these constants when Jalview has been checked / updated for
    * changes to Ensembl REST API
    * @see https://github.com/Ensembl/ensembl-rest/wiki/Change-log
+   * @see http://rest.ensembl.org/info/rest?content-type=application/json
    */
   private static final String LATEST_ENSEMBLGENOMES_REST_VERSION = "4.6";
 
-  private static final String LATEST_ENSEMBL_REST_VERSION = "4.6";
+  private static final String LATEST_ENSEMBL_REST_VERSION = "4.7";
 
   private static final String REST_CHANGE_LOG = "https://github.com/Ensembl/ensembl-rest/wiki/Change-log";
 
@@ -51,10 +72,10 @@ 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
   {
@@ -206,8 +227,13 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
           throws IOException
   {
     URL url = getUrl(ids);
-  
+
     BufferedReader reader = getHttpResponse(url, ids);
+    if (reader == null)
+    {
+      // request failed
+      return null;
+    }
     FileParse fp = new FileParse(reader, url.toString(), "HTTP_POST");
     return fp;
   }
@@ -227,7 +253,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
   {
     // 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
@@ -247,25 +273,26 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
     {
       writePostBody(connection, ids);
     }
-  
-    InputStream response = connection.getInputStream();
+
     int responseCode = connection.getResponseCode();
-  
+
     if (responseCode != 200)
     {
       /*
        * note: a GET request for an invalid id returns an error code e.g. 415
        * but POST request returns 200 and an empty Fasta response 
        */
-      throw new IOException(
-              "Response code was not 200. Detected response was "
-                      + responseCode);
+      System.err.println("Response code " + responseCode + " for " + url);
+      return null;
     }
+    // get content
+    InputStream response = connection.getInputStream();
+
     // System.out.println(getClass().getName() + " took "
     // + (System.currentTimeMillis() - now) + "ms to fetch");
 
     checkRateLimits(connection);
-  
+
     BufferedReader reader = null;
     reader = new BufferedReader(new InputStreamReader(response, "UTF-8"));
     return reader;
@@ -318,7 +345,7 @@ 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,