JAL-3076 fetch Ensembl sequence as JSON instead of Fasta

[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 b19f557..e6b1264 100644 (file)
--- 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;
@@ -153,22 +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
@@ -222,25 +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;
   }
 
   /**
@@ -332,8 +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);