X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblRestClient.java;h=540fc980d290f4114e124c7b51b4cd6f9818da13;hb=refs%2Fheads%2Ffeature%2FJAL-4274_configurable_bitmap_export_preferences;hp=bf151bf685c02c1e89f8d41baa7c406fc2ff0556;hpb=b3d9eaf8829a3aeb2bbc522315207a7940b0844e;p=jalview.git

diff --git a/src/jalview/ext/ensembl/EnsemblRestClient.java b/src/jalview/ext/ensembl/EnsemblRestClient.java
index bf151bf..540fc98 100644
--- a/src/jalview/ext/ensembl/EnsemblRestClient.java
+++ b/src/jalview/ext/ensembl/EnsemblRestClient.java
@@ -20,9 +20,6 @@
  */
 package jalview.ext.ensembl;
 
-import jalview.util.Platform;
-import jalview.util.StringUtils;
-
 import java.io.BufferedReader;
 import java.io.DataOutputStream;
 import java.io.IOException;
@@ -39,6 +36,9 @@ import javax.ws.rs.HttpMethod;
 
 import org.json.simple.parser.ParseException;
 
+import jalview.util.Platform;
+import jalview.util.StringUtils;
+
 /**
  * Base class for Ensembl REST service clients
  * 
@@ -69,9 +69,9 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
    * @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 = "10.0";
+  private static final String LATEST_ENSEMBLGENOMES_REST_VERSION = "15.2";
 
-  private static final String LATEST_ENSEMBL_REST_VERSION = "10.0";
+  private static final String LATEST_ENSEMBL_REST_VERSION = "15.2";
 
   private static final String REST_CHANGE_LOG = "https://github.com/Ensembl/ensembl-rest/wiki/Change-log";
 
@@ -211,7 +211,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
       return pingString != null;
     } catch (Throwable t)
     {
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "Error connecting to " + pingUrl + ": " + t.getMessage());
     } finally
     {
@@ -313,16 +313,16 @@ 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 
        */
-      System.err.println("Response code " + responseCode);// + " for " + url);
+      jalview.bin.Console.errPrintln("Response code " + responseCode);// + " for " + url);
       return null;
     }
 
     InputStream response = connection.getInputStream();
 
-    Platform.timeCheck(null, Platform.TIME_MARK);
+    // Platform.timeCheck(null, Platform.TIME_MARK);
     Object ret = Platform.parseJSON(response);
-    Platform.timeCheck("EnsemblRestClient.getJSON " + url,
-            Platform.TIME_MARK);
+    // Platform.timeCheck("EnsemblRestClient.getJSON " + url,
+    // Platform.TIME_MARK);
 
     return ret;
   }
@@ -338,7 +338,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
   protected HttpURLConnection tryConnection(URL url, List<String> ids,
           int readTimeout) throws IOException, ProtocolException
   {
-    // System.out.println(System.currentTimeMillis() + " " + url);
+    // jalview.bin.Console.outPrintln(System.currentTimeMillis() + " " + url);
 
     HttpURLConnection connection = (HttpURLConnection) url.openConnection();
 
@@ -387,14 +387,14 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
         int retrySecs = Integer.valueOf(retryDelay);
         if (retrySecs > 0 && retrySecs < 10)
         {
-          System.err.println(
+          jalview.bin.Console.errPrintln(
                   "Ensembl REST service rate limit exceeded, waiting "
                           + retryDelay + " seconds before retrying");
           Thread.sleep(1000 * retrySecs);
         }
       } catch (NumberFormatException | InterruptedException e)
       {
-        System.err.println("Error handling Retry-After: " + e.getMessage());
+        jalview.bin.Console.errPrintln("Error handling Retry-After: " + e.getMessage());
       }
     }
   }
@@ -566,7 +566,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
         }
       } catch (NumberFormatException e)
       {
-        System.err.println("Error in REST version: " + e.toString());
+        jalview.bin.Console.errPrintln("Error in REST version: " + e.toString());
       }
 
       /*
@@ -578,14 +578,14 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
               expected) == 1;
       if (laterVersion)
       {
-        System.err.println(String.format(
+        jalview.bin.Console.errPrintln(String.format(
                 "EnsemblRestClient expected %s REST version %s but found %s, see %s",
                 getDbSource(), expected, version, REST_CHANGE_LOG));
       }
       info.restVersion = version;
     } catch (Throwable t)
     {
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "Error checking Ensembl REST version: " + t.getMessage());
     }
   }
@@ -617,7 +617,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
       domainData.get(getDomain()).dataVersion = versions.get(0).toString();
     } catch (Throwable e)
     {// could be IOException | ParseException e) {
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "Error checking Ensembl data version: " + e.getMessage());
     }
   }