JAL-1705 use GET for single queries; set gene name as description on

[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 52993e9..f81bce2 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblRestClient.java
+++ b/src/jalview/ext/ensembl/EnsemblRestClient.java
@@ -64,15 +64,17 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
    * 
    * @return
    */
-  public abstract boolean useGetRequest();
+  protected abstract boolean useGetRequest();
 
   /**
    * Return the desired value for the Content-Type request header
    * 
+   * @param multipleIds
+   * 
    * @return
    * @see https://github.com/Ensembl/ensembl-rest/wiki/HTTP-Headers
    */
-  public abstract String getRequestMimeType();
+  protected abstract String getRequestMimeType(boolean multipleIds);
 
   /**
    * Return the desired value for the Accept request header
@@ -80,7 +82,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
    * @return
    * @see https://github.com/Ensembl/ensembl-rest/wiki/HTTP-Headers
    */
-  public abstract String getResponseMimeType();
+  protected abstract String getResponseMimeType();
 
   /**
    * Tries to connect to Ensembl's REST 'ping' endpoint, and returns true if
@@ -115,7 +117,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
    * @return
    * @throws IOException
    */
-  public FileParse getSequenceReader(List<String> ids)
+  protected FileParse getSequenceReader(List<String> ids)
           throws IOException
   {
     URL url = getUrl(ids);
@@ -126,16 +128,18 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
      * POST method allows multiple queries in one request; it is supported for
      * sequence queries, but not for overlap
      */
-    connection.setRequestMethod(useGetRequest() ? HttpMethod.GET
-            : HttpMethod.POST);
-    connection.setRequestProperty("Content-Type", getRequestMimeType());
+    boolean multipleIds = ids.size() > 1;// useGetRequest();
+    connection.setRequestMethod(multipleIds ? HttpMethod.POST
+            : HttpMethod.GET);
+    connection.setRequestProperty("Content-Type",
+            getRequestMimeType(multipleIds));
     connection.setRequestProperty("Accept", getResponseMimeType());
 
     connection.setUseCaches(false);
     connection.setDoInput(true);
-    connection.setDoOutput(true);
+    connection.setDoOutput(multipleIds);
 
-    if (!useGetRequest())
+    if (multipleIds)
     {
       writePostBody(connection, ids);
     }
@@ -145,6 +149,10 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
   
     if (responseCode != 200)
     {
+      /*
+       * 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(
               "Response code was not 200. Detected response was "
                       + responseCode);
@@ -163,7 +171,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
    * 
    * @return
    */
-  public boolean isEnsemblAvailable()
+  protected boolean isEnsemblAvailable()
   {
     long now = System.currentTimeMillis();
     boolean retest = now - lastCheck > RETEST_INTERVAL;