Merge branch 'develop' into task/JAL-2196pdbeProperties

[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 f9cfe05..30dcee8 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblRestClient.java
+++ b/src/jalview/ext/ensembl/EnsemblRestClient.java
@@ -34,10 +34,13 @@ 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 = "4.4";
+  private static final String LATEST_ENSEMBLGENOMES_REST_VERSION = "4.6";
 
-  private static final String LATEST_ENSEMBL_REST_VERSION = "4.5";
+  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";
 
   private static Map<String, EnsemblInfo> domainData;
 
@@ -206,6 +209,11 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
     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;
   }
@@ -246,7 +254,6 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
       writePostBody(connection, ids);
     }
   
-    InputStream response = connection.getInputStream();
     int responseCode = connection.getResponseCode();
   
     if (responseCode != 200)
@@ -255,10 +262,12 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
        * 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");
 
@@ -453,9 +462,8 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
       if (laterVersion)
       {
         System.err.println(String.format(
-                "Expected %s REST version %s but found %s", getDbSource(),
-                expected,
-                version));
+                "Expected %s REST version %s but found %s, see %s",
+                getDbSource(), expected, version, REST_CHANGE_LOG));
       }
       info.restVersion = version;
     } catch (Throwable t)