JAL-1705 return Ensembl genes for model species for a gene name

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

diff --git a/src/jalview/ext/ensembl/EnsemblSymbol.java b/src/jalview/ext/ensembl/EnsemblSymbol.java
new file mode 100644 (file)
index 0000000..5b3baa1
--- /dev/null
+++ b/src/jalview/ext/ensembl/EnsemblSymbol.java
@@ -0,0 +1,121 @@
+package jalview.ext.ensembl;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+
+import org.json.simple.JSONArray;
+import org.json.simple.JSONObject;
+import org.json.simple.parser.JSONParser;
+import org.json.simple.parser.ParseException;
+
+public class EnsemblSymbol extends EnsemblXref
+{
+  /**
+   * Returns the first "id" value in gene identifier format from the JSON
+   * response, or null if none found
+   * 
+   * @param br
+   * @return
+   * @throws IOException
+   */
+  protected String parseResponse(BufferedReader br)
+          throws IOException
+  {
+    JSONParser jp = new JSONParser();
+    String result = null;
+    try
+    {
+      JSONArray responses = (JSONArray) jp.parse(br);
+      Iterator rvals = responses.iterator();
+      while (rvals.hasNext())
+      {
+        JSONObject val = (JSONObject) rvals.next();
+        String id = val.get("id").toString();
+        if (id != null && isGeneIdentifier(id))
+        {
+          result = id;
+          break;
+        }
+      }
+    } catch (ParseException e)
+    {
+      // ignore
+    }
+    return result;
+  }
+
+  protected URL getUrl(String id, Species species)
+  {
+    String url = ENSEMBL_REST + "/xrefs/symbol/" + species.toString() + "/"
+            + id
+            + "?content-type=application/json";
+    try
+    {
+      return new URL(url);
+    } catch (MalformedURLException e)
+    {
+      return null;
+    }
+  }
+
+  /**
+   * Calls the Ensembl xrefs REST 'symbol' endpoint and retrieves any gene ids
+   * for the given identifier, for any known model organisms
+   * 
+   * @param identifier
+   * @return
+   */
+  public List<String> getIds(String identifier)
+  {
+    List<String> result = new ArrayList<String>();
+    List<String> ids = new ArrayList<String>();
+    ids.add(identifier);
+  
+    String[] queries = identifier.split(getAccessionSeparator());
+    BufferedReader br = null;
+    try
+    {
+      for (String query : queries)
+      {
+        for (Species taxon : Species.values())
+        {
+          if (taxon.isModelOrganism())
+          {
+            URL url = getUrl(query, taxon);
+            if (url != null)
+            {
+              br = getHttpResponse(url, ids);
+            }
+            String geneId = parseResponse(br);
+            if (geneId != null)
+            {
+              result.add(geneId);
+            }
+          }
+        }
+      }
+    } catch (IOException e)
+    {
+      // ignore
+    } finally
+    {
+      if (br != null)
+      {
+        try
+        {
+          br.close();
+        } catch (IOException e)
+        {
+          // ignore
+        }
+      }
+    }
+    return result;
+  }
+
+}