Merge branch 'develop' into features/filetypeEnum

[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 e651ddf..653d5d5 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblRestClient.java
+++ b/src/jalview/ext/ensembl/EnsemblRestClient.java
@@ -1,5 +1,6 @@
 package jalview.ext.ensembl;
 
+import jalview.io.DataSourceType;
 import jalview.io.FileParse;
 import jalview.util.StringUtils;
 
@@ -35,9 +36,11 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
    * changes to Ensembl REST API
    * @see https://github.com/Ensembl/ensembl-rest/wiki/Change-log
    */
-  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 = "4.6";
+
+  private static final String REST_CHANGE_LOG = "https://github.com/Ensembl/ensembl-rest/wiki/Change-log";
 
   private static Map<String, EnsemblInfo> domainData;
 
@@ -155,30 +158,40 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
   protected abstract String getResponseMimeType();
 
   /**
-   * Tries to connect to Ensembl's REST 'ping' endpoint, and returns true if
-   * successful, else false
+   * Checks Ensembl's REST 'ping' endpoint, and returns true if response
+   * indicates available, else false
    * 
+   * @see http://rest.ensembl.org/documentation/info/ping
    * @return
    */
   private boolean checkEnsembl()
   {
+    HttpURLConnection conn = null;
     try
     {
       // note this format works for both ensembl and ensemblgenomes
       // info/ping.json works for ensembl only (March 2016)
       URL ping = new URL(getDomain()
               + "/info/ping?content-type=application/json");
-      HttpURLConnection conn = (HttpURLConnection) ping.openConnection();
-      int rc = conn.getResponseCode();
-      conn.disconnect();
-      if (rc >= 200 && rc < 300)
-      {
-        return true;
-      }
+
+      /*
+       * expect {"ping":1} if ok
+       */
+      BufferedReader br = getHttpResponse(ping, null);
+      JSONParser jp = new JSONParser();
+      JSONObject val = (JSONObject) jp.parse(br);
+      String pingString = val.get("ping").toString();
+      return pingString != null;
     } catch (Throwable t)
     {
       System.err.println("Error connecting to " + PING_URL + ": "
               + t.getMessage());
+    } finally
+    {
+      if (conn != null)
+      {
+        conn.disconnect();
+      }
     }
     return false;
   }
@@ -196,7 +209,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
     URL url = getUrl(ids);
   
     BufferedReader reader = getHttpResponse(url, ids);
-    FileParse fp = new FileParse(reader, url.toString(), "HTTP_POST");
+    FileParse fp = new FileParse(reader, url.toString(), DataSourceType.URL);
     return fp;
   }
 
@@ -443,9 +456,8 @@ 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)