JAL-1705 fetch Uniprot and PDB xrefs for Ensembl protein products

[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 f81bce2..2fd7fa3 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblRestClient.java
+++ b/src/jalview/ext/ensembl/EnsemblRestClient.java
@@ -122,6 +122,24 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
   {
     URL url = getUrl(ids);
   
+    BufferedReader reader = getHttpResponse(url, ids);
+    FileParse fp = new FileParse(reader, url.toString(), "HTTP_POST");
+    return fp;
+  }
+
+  /**
+   * Writes the HTTP request and gets the response as a reader.
+   * 
+   * @param url
+   * @param ids
+   *          written as Json POST body if more than one
+   * @return
+   * @throws IOException
+   *           if response code was not 200, or other I/O error
+   */
+  protected BufferedReader getHttpResponse(URL url, List<String> ids)
+          throws IOException
+  {
     HttpURLConnection connection = (HttpURLConnection) url.openConnection();
   
     /*
@@ -153,15 +171,14 @@ 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 
        */
-      throw new RuntimeException(
+      throw new IOException(
               "Response code was not 200. Detected response was "
                       + responseCode);
     }
   
     BufferedReader reader = null;
     reader = new BufferedReader(new InputStreamReader(response, "UTF-8"));
-    FileParse fp = new FileParse(reader, url.toString(), "HTTP_POST");
-    return fp;
+    return reader;
   }
 
   /**