JAL-2783 accept Ensembl query of the form "human:braf"

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

diff --git a/src/jalview/ext/ensembl/EnsemblSymbol.java b/src/jalview/ext/ensembl/EnsemblSymbol.java
index e2e38b5..411a244 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblSymbol.java
+++ b/src/jalview/ext/ensembl/EnsemblSymbol.java
@@ -25,6 +25,7 @@ import java.io.IOException;
 import java.net.MalformedURLException;
 import java.net.URL;
 import java.util.ArrayList;
+import java.util.Collections;
 import java.util.Iterator;
 import java.util.List;
 
@@ -42,6 +43,11 @@ import org.json.simple.parser.ParseException;
  */
 public class EnsemblSymbol extends EnsemblXref
 {
+  private static final String COLON = ":";
+  private static final String GENE = "gene";
+  private static final String TYPE = "type";
+  private static final String ID = "id";
+
   /**
    * Constructor given the target domain to fetch data from
    * 
@@ -73,8 +79,9 @@ public class EnsemblSymbol extends EnsemblXref
       while (rvals.hasNext())
       {
         JSONObject val = (JSONObject) rvals.next();
-        String id = val.get("id").toString();
-        if (id != null && isGeneIdentifier(id))
+        String id = val.get(ID).toString();
+        String type = val.get(TYPE).toString();
+        if (id != null && GENE.equals(type))
         {
           result = id;
           break;
@@ -87,12 +94,30 @@ public class EnsemblSymbol extends EnsemblXref
     return result;
   }
 
-  protected URL getUrl(String id, Species species)
+  /**
+   * Constructs the URL for the REST symbol endpoint
+   * 
+   * @param id
+   *          the accession id (Ensembl or external)
+   * @param species
+   *          a species name recognisable by Ensembl
+   * @param type
+   *          an optional type to filter the response (gene, transcript,
+   *          translation)
+   * @return
+   */
+  protected URL getUrl(String id, String species, String... type)
   {
-    String url = getDomain() + "/xrefs/symbol/" + species.toString() + "/"
-            + id + "?content-type=application/json";
+    StringBuilder sb = new StringBuilder();
+    sb.append(getDomain()).append("/xrefs/symbol/").append(species)
+            .append("/").append(id).append(CONTENT_TYPE_JSON);
+    for (String t : type)
+    {
+      sb.append("&object_type=").append(t);
+    }
     try
     {
+      String url = sb.toString();
       return new URL(url);
     } catch (MalformedURLException e)
     {
@@ -101,41 +126,40 @@ public class EnsemblSymbol extends EnsemblXref
   }
 
   /**
-   * Calls the Ensembl xrefs REST 'symbol' endpoint and retrieves any gene ids
-   * for the given identifier, for any known model organisms
+   * Calls the Ensembl xrefs REST 'symbol' endpoint and retrieves gene id(s) for
+   * the given identifier. If the identifier has the format species:symbol then
+   * the gene id for the specified species is returned, else any matched gene ids
+   * for model organisms. If lookup fails, the returned list is empty.
    * 
    * @param identifier
    * @return
    */
-  public List<String> getIds(String identifier)
+  public List<String> getGeneIds(String identifier)
   {
-    List<String> result = new ArrayList<String>();
-    List<String> ids = new ArrayList<String>();
-    ids.add(identifier);
+    List<String> result = new ArrayList<>();
+    List<String> ids = Collections.<String> emptyList();
+    List<String> species = getSpecies(identifier);
 
-    String[] queries = identifier.split(getAccessionSeparator());
+    String symbol = identifier.substring(identifier.indexOf(COLON) + 1);
     BufferedReader br = null;
     try
     {
-      for (String query : queries)
-      {
-        for (Species taxon : Species.getModelOrganisms())
+      for (String taxon : species)
         {
-          URL url = getUrl(query, taxon);
+        URL url = getUrl(symbol, taxon, GENE);
           if (url != null)
           {
             br = getHttpResponse(url, ids);
             if (br != null)
             {
               String geneId = parseSymbolResponse(br);
-              if (geneId != null)
+              if (geneId != null && !result.contains(geneId))
               {
                 result.add(geneId);
               }
             }
           }
         }
-      }
     } catch (IOException e)
     {
       // ignore
@@ -155,4 +179,27 @@ public class EnsemblSymbol extends EnsemblXref
     return result;
   }
 
+  /**
+   * Answers a list of species names which is
+   * <ul>
+   * <li>the species in the identifier if it is of the form species:symbol</li>
+   * <li>else a fixed list of 'model organism' species</li>
+   * </ul>
+   * 
+   * @param identifier
+   * @return
+   */
+  private List<String> getSpecies(String identifier)
+  {
+    int pos = identifier.indexOf(COLON);
+    if (pos > 0)
+    {
+      return Collections.singletonList(identifier.substring(0, pos));
+    }
+    else
+    {
+      return Species.getModelOrganisms();
+    }
+  }
+
 }