Merge remote-tracking branch 'origin/develop' into imp/JAL-2774

[jalview.git] / src / jalview / ext / ensembl / EnsemblLookup.java

diff --git a/src/jalview/ext/ensembl/EnsemblLookup.java b/src/jalview/ext/ensembl/EnsemblLookup.java
index 6483401..31da9c0 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblLookup.java
+++ b/src/jalview/ext/ensembl/EnsemblLookup.java
@@ -43,6 +43,13 @@ import org.json.simple.parser.ParseException;
 public class EnsemblLookup extends EnsemblRestClient
 {
 
+  private static final String OBJECT_TYPE_TRANSLATION = "Translation";
+  private static final String PARENT = "Parent";
+  private static final String OBJECT_TYPE_TRANSCRIPT = "Transcript";
+  private static final String ID = "id";
+  private static final String OBJECT_TYPE_GENE = "Gene";
+  private static final String OBJECT_TYPE = "object_type";
+
   /**
    * Default constructor (to use rest.ensembl.org)
    */
@@ -87,7 +94,7 @@ public class EnsemblLookup extends EnsemblRestClient
   protected URL getUrl(String identifier)
   {
     String url = getDomain() + "/lookup/id/" + identifier
-            + "?content-type=application/json";
+            + CONTENT_TYPE_JSON;
     try
     {
       return new URL(url);
@@ -122,7 +129,7 @@ public class EnsemblLookup extends EnsemblRestClient
    * @param identifier
    * @return
    */
-  public String getParent(String identifier)
+  public String getGeneId(String identifier)
   {
     List<String> ids = Arrays.asList(new String[] { identifier });
 
@@ -155,8 +162,10 @@ public class EnsemblLookup extends EnsemblRestClient
   }
 
   /**
-   * Parses "Parent" from the JSON response and returns the value, or null if
-   * not found
+   * Parses the JSON response and returns the gene identifier, or null if not
+   * found. If the returned object_type is Gene, returns the id, if Transcript
+   * returns the Parent. If it is Translation (peptide identifier), then the
+   * Parent is the transcript identifier, so we redo the search with this value.
    * 
    * @param br
    * @return
@@ -164,17 +173,42 @@ public class EnsemblLookup extends EnsemblRestClient
    */
   protected String parseResponse(BufferedReader br) throws IOException
   {
-    String parent = null;
+    String geneId = null;
     JSONParser jp = new JSONParser();
     try
     {
       JSONObject val = (JSONObject) jp.parse(br);
-      parent = val.get("Parent").toString();
+      String type = val.get(OBJECT_TYPE).toString();
+      if (OBJECT_TYPE_GENE.equalsIgnoreCase(type))
+      {
+        geneId = val.get(ID).toString();
+      }
+      else if (OBJECT_TYPE_TRANSCRIPT.equalsIgnoreCase(type))
+      {
+        geneId = val.get(PARENT).toString();
+      }
+      else if (OBJECT_TYPE_TRANSLATION.equalsIgnoreCase(type))
+      {
+        String transcriptId = val.get(PARENT).toString();
+        try
+        {
+          geneId = getGeneId(transcriptId);
+        } catch (StackOverflowError e)
+        {
+          /*
+           * unlikely data condition error!
+           */
+          System.err
+                  .println("** Ensembl lookup "
+                          + getUrl(transcriptId).toString()
+                          + " looping on Parent!");
+        }
+      }
     } catch (ParseException e)
     {
       // ignore
     }
-    return parent;
+    return geneId;
   }
 
 }