Merge branch 'develop' into releases/Release_2_10_2_Branch

[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 2437588..ad6c70c 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblRestClient.java
+++ b/src/jalview/ext/ensembl/EnsemblRestClient.java
@@ -88,8 +88,8 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
   static
   {
     domainData = new HashMap<String, EnsemblInfo>();
-    domainData.put(ENSEMBL_REST, new EnsemblInfo(ENSEMBL_REST,
-            LATEST_ENSEMBL_REST_VERSION));
+    domainData.put(ENSEMBL_REST,
+            new EnsemblInfo(ENSEMBL_REST, LATEST_ENSEMBL_REST_VERSION));
     domainData.put(ENSEMBL_GENOMES_REST, new EnsemblInfo(
             ENSEMBL_GENOMES_REST, LATEST_ENSEMBLGENOMES_REST_VERSION));
   }
@@ -211,8 +211,8 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
     {
       // 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");
+      URL ping = new URL(
+              getDomain() + "/info/ping?content-type=application/json");
 
       /*
        * expect {"ping":1} if ok
@@ -225,8 +225,8 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
       return pingString != null;
     } catch (Throwable t)
     {
-      System.err.println("Error connecting to " + PING_URL + ": "
-              + t.getMessage());
+      System.err.println(
+              "Error connecting to " + PING_URL + ": " + t.getMessage());
     } finally
     {
       if (br != null)
@@ -250,8 +250,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
    * @return
    * @throws IOException
    */
-  protected FileParse getSequenceReader(List<String> ids)
-          throws IOException
+  protected FileParse getSequenceReader(List<String> ids) throws IOException
   {
     URL url = getUrl(ids);
 
@@ -261,7 +260,8 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
       // request failed
       return null;
     }
-    FileParse fp = new FileParse(reader, url.toString(), DataSourceType.URL);
+    FileParse fp = new FileParse(reader, url.toString(),
+            DataSourceType.URL);
     return fp;
   }
 
@@ -303,8 +303,8 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
      * sequence queries, but not for overlap
      */
     boolean multipleIds = ids != null && ids.size() > 1;
-    connection.setRequestMethod(multipleIds ? HttpMethod.POST
-            : HttpMethod.GET);
+    connection.setRequestMethod(
+            multipleIds ? HttpMethod.POST : HttpMethod.GET);
     connection.setRequestProperty("Content-Type",
             getRequestMimeType(multipleIds));
     connection.setRequestProperty("Accept", getResponseMimeType());
@@ -379,8 +379,8 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
                 + (1000 * Integer.valueOf(retryDelay));
       } catch (NumberFormatException e)
       {
-        System.err.println("Unexpected value for Retry-After: "
-                + retryDelay);
+        System.err
+                .println("Unexpected value for Retry-After: " + retryDelay);
       }
     }
     else
@@ -424,7 +424,8 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
     /*
      * recheck if Ensembl is up if it was down, or the recheck period has elapsed
      */
-    boolean retestAvailability = (now - info.lastAvailableCheckTime) > AVAILABILITY_RETEST_INTERVAL;
+    boolean retestAvailability = (now
+            - info.lastAvailableCheckTime) > AVAILABILITY_RETEST_INTERVAL;
     if (!info.restAvailable || retestAvailability)
     {
       info.restAvailable = checkEnsembl();
@@ -434,7 +435,8 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
     /*
      * refetch Ensembl versions if the recheck period has elapsed
      */
-    boolean refetchVersion = (now - info.lastVersionCheckTime) > VERSION_RETEST_INTERVAL;
+    boolean refetchVersion = (now
+            - info.lastVersionCheckTime) > VERSION_RETEST_INTERVAL;
     if (refetchVersion)
     {
       checkEnsemblRestVersion();
@@ -475,7 +477,8 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
     byte[] thepostbody = postBody.toString().getBytes();
     connection.setRequestProperty("Content-Length",
             Integer.toString(thepostbody.length));
-    DataOutputStream wr = new DataOutputStream(connection.getOutputStream());
+    DataOutputStream wr = new DataOutputStream(
+            connection.getOutputStream());
     wr.write(thepostbody);
     wr.flush();
     wr.close();
@@ -494,8 +497,8 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
     URL url = null;
     try
     {
-      url = new URL(getDomain()
-              + "/info/rest?content-type=application/json");
+      url = new URL(
+              getDomain() + "/info/rest?content-type=application/json");
       BufferedReader br = getHttpResponse(url, null);
       JSONObject val = (JSONObject) jp.parse(br);
       String version = val.get("release").toString();
@@ -525,20 +528,19 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
        * if so warn; we don't worry if it is earlier (this indicates Jalview has
        * been tested in advance against the next pending REST version)
        */
-      boolean laterVersion = StringUtils.compareVersions(version, expected) == 1;
+      boolean laterVersion = StringUtils.compareVersions(version,
+              expected) == 1;
       if (laterVersion)
       {
-        System.err
-                .println(String
-                        .format("EnsemblRestClient expected %s REST version %s but found %s, see %s",
-                                getDbSource(), expected, version,
-                                REST_CHANGE_LOG));
+        System.err.println(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("Error checking Ensembl REST version: "
-              + t.getMessage());
+      System.err.println(
+              "Error checking Ensembl REST version: " + t.getMessage());
     }
   }
 
@@ -558,16 +560,16 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
     URL url = null;
     try
     {
-      url = new URL(getDomain()
-              + "/info/data?content-type=application/json");
+      url = new URL(
+              getDomain() + "/info/data?content-type=application/json");
       BufferedReader br = getHttpResponse(url, null);
       JSONObject val = (JSONObject) jp.parse(br);
       JSONArray versions = (JSONArray) val.get("releases");
       domainData.get(getDomain()).dataVersion = versions.get(0).toString();
     } catch (Throwable t)
     {
-      System.err.println("Error checking Ensembl data version: "
-              + t.getMessage());
+      System.err.println(
+              "Error checking Ensembl data version: " + t.getMessage());
     }
   }