X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblRestClient.java;h=617ab21791de423b8f9467a8aac7e26cde274752;hb=00b73137cd165c4781c388b1230566986aed9213;hp=9dea886a2726461dfbb7c5d1628dbeb173667f1a;hpb=948bd3bcbacc509da0cefaae3eedd97300a6ccce;p=jalview.git

diff --git a/src/jalview/ext/ensembl/EnsemblRestClient.java b/src/jalview/ext/ensembl/EnsemblRestClient.java
index 9dea886..617ab21 100644
--- a/src/jalview/ext/ensembl/EnsemblRestClient.java
+++ b/src/jalview/ext/ensembl/EnsemblRestClient.java
@@ -20,8 +20,6 @@
  */
 package jalview.ext.ensembl;
 
-import jalview.io.DataSourceType;
-import jalview.io.FileParse;
 import jalview.util.StringUtils;
 
 import java.io.BufferedReader;
@@ -62,21 +60,18 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
 
   /*
    * update these constants when Jalview has been checked / updated for
-   * changes to Ensembl REST API (ref JAL-2105)
+   * changes to Ensembl REST API, and updated JAL-3018
    * @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 = "6.0";
+  private static final String LATEST_ENSEMBLGENOMES_REST_VERSION = "10.0";
 
-  private static final String LATEST_ENSEMBL_REST_VERSION = "6.1";
+  private static final String LATEST_ENSEMBL_REST_VERSION = "10.0";
 
   private static final String REST_CHANGE_LOG = "https://github.com/Ensembl/ensembl-rest/wiki/Change-log";
 
   private static Map<String, EnsemblData> domainData;
 
-  // @see https://github.com/Ensembl/ensembl-rest/wiki/Output-formats
-  private static final String PING_URL = "http://rest.ensembl.org/info/ping.json";
-
   private final static long AVAILABILITY_RETEST_INTERVAL = 10000L; // 10 seconds
 
   private final static long VERSION_RETEST_INTERVAL = 1000L * 3600; // 1 hr
@@ -156,22 +151,28 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
   protected abstract boolean useGetRequest();
 
   /**
-   * Return the desired value for the Content-Type request header
-   * 
-   * @param multipleIds
+   * Returns the desired value for the Content-Type request header. Default is
+   * application/json, override if required to vary this.
    * 
    * @return
    * @see https://github.com/Ensembl/ensembl-rest/wiki/HTTP-Headers
    */
-  protected abstract String getRequestMimeType(boolean multipleIds);
+  protected String getRequestMimeType()
+  {
+    return "application/json";
+  }
 
   /**
-   * Return the desired value for the Accept request header
+   * Return the desired value for the Accept request header. Default is
+   * application/json, override if required to vary this.
    * 
    * @return
    * @see https://github.com/Ensembl/ensembl-rest/wiki/HTTP-Headers
    */
-  protected abstract String getResponseMimeType();
+  protected String getResponseMimeType()
+  {
+    return "application/json";
+  }
 
   /**
    * Checks Ensembl's REST 'ping' endpoint, and returns true if response
@@ -225,25 +226,20 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
   }
 
   /**
-   * returns a reader to a Fasta response from the Ensembl sequence endpoint
+   * Returns a reader to a (Json) response from the Ensembl sequence endpoint.
+   * If the request failed the return value may be null.
    * 
    * @param ids
    * @return
    * @throws IOException
    */
-  protected FileParse getSequenceReader(List<String> ids) throws IOException
+  protected BufferedReader getSequenceReader(List<String> ids)
+          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(),
-            DataSourceType.URL);
-    return fp;
+    return reader;
   }
 
   /**
@@ -262,7 +258,8 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
   }
 
   /**
-   * Sends the HTTP request and gets the response as a reader
+   * Sends the HTTP request and gets the response as a reader. Returns null if
+   * the HTTP response code was not 200.
    * 
    * @param url
    * @param ids
@@ -271,7 +268,6 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
    *          in milliseconds
    * @return
    * @throws IOException
-   *           if response code was not 200, or other I/O error
    */
   protected BufferedReader getHttpResponse(URL url, List<String> ids,
           int readTimeout) throws IOException
@@ -335,8 +331,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
     boolean multipleIds = ids != null && ids.size() > 1;
     connection.setRequestMethod(
             multipleIds ? HttpMethod.POST : HttpMethod.GET);
-    connection.setRequestProperty("Content-Type",
-            getRequestMimeType(multipleIds));
+    connection.setRequestProperty("Content-Type", getRequestMimeType());
     connection.setRequestProperty("Accept", getResponseMimeType());
 
     connection.setUseCaches(false);