develop merge

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

diff --git a/src/jalview/ext/ensembl/EnsemblLookup.java b/src/jalview/ext/ensembl/EnsemblLookup.java
new file mode 100644 (file)
index 0000000..c5945ae
--- /dev/null
+++ b/src/jalview/ext/ensembl/EnsemblLookup.java
@@ -0,0 +1,160 @@
+package jalview.ext.ensembl;
+
+import jalview.datamodel.AlignmentI;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.Arrays;
+import java.util.List;
+
+import org.json.simple.JSONObject;
+import org.json.simple.parser.JSONParser;
+import org.json.simple.parser.ParseException;
+
+/**
+ * A client for the Ensembl lookup REST endpoint; used to find the Parent gene
+ * identifier given a transcript identifier.
+ * 
+ * @author gmcarstairs
+ *
+ */
+public class EnsemblLookup extends EnsemblRestClient
+{
+
+  /**
+   * Default constructor (to use rest.ensembl.org)
+   */
+  public EnsemblLookup()
+  {
+    super();
+  }
+
+  /**
+   * Constructor given the target domain to fetch data from
+   * 
+   * @param
+   */
+  public EnsemblLookup(String d)
+  {
+    super(d);
+  }
+
+  @Override
+  public String getDbName()
+  {
+    return "ENSEMBL";
+  }
+
+  @Override
+  public AlignmentI getSequenceRecords(String queries) throws Exception
+  {
+    return null;
+  }
+
+  @Override
+  protected URL getUrl(List<String> ids) throws MalformedURLException
+  {
+    String identifier = ids.get(0);
+    return getUrl(identifier);
+  }
+
+  /**
+   * @param identifier
+   * @return
+   */
+  protected URL getUrl(String identifier)
+  {
+    String url = getDomain() + "/lookup/id/" + identifier
+            + "?content-type=application/json";
+    try
+    {
+      return new URL(url);
+    } catch (MalformedURLException e)
+    {
+      return null;
+    }
+  }
+
+  @Override
+  protected boolean useGetRequest()
+  {
+    return true;
+  }
+
+  @Override
+  protected String getRequestMimeType(boolean multipleIds)
+  {
+    return "application/json";
+  }
+
+  @Override
+  protected String getResponseMimeType()
+  {
+    return "application/json";
+  }
+
+  /**
+   * Calls the Ensembl lookup REST endpoint and retrieves the 'Parent' for the
+   * given identifier, or null if not found
+   * 
+   * @param identifier
+   * @return
+   */
+  public String getParent(String identifier)
+  {
+    List<String> ids = Arrays.asList(new String[] { identifier });
+  
+    BufferedReader br = null;
+    try
+    {
+      URL url = getUrl(identifier);
+      if (url != null)
+      {
+        br = getHttpResponse(url, ids);
+      }
+      return (parseResponse(br));
+    } catch (IOException e)
+    {
+      // ignore
+      return null;
+    } finally
+    {
+      if (br != null)
+      {
+        try
+        {
+          br.close();
+        } catch (IOException e)
+        {
+          // ignore
+        }
+      }
+    }
+  }
+
+  /**
+   * Parses "Parent" from the JSON response and returns the value, or null if
+   * not found
+   * 
+   * @param br
+   * @return
+   * @throws IOException
+   */
+  protected String parseResponse(BufferedReader br) throws IOException
+  {
+    String parent = null;
+    JSONParser jp = new JSONParser();
+    try
+    {
+      JSONObject val = (JSONObject) jp.parse(br);
+      parent = val.get("Parent").toString();
+    } catch (ParseException e)
+    {
+      // ignore
+    }
+    return parent;
+  }
+
+}