Push 1793 latest to spike branch

[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 cd792b5..0968663 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblLookup.java
+++ b/src/jalview/ext/ensembl/EnsemblLookup.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ext.ensembl;
 
 import jalview.datamodel.AlignmentI;
@@ -13,8 +33,36 @@ 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
 {
+  private static final String SPECIES = "species";
+
+  private static final String PARENT = "Parent";
+
+  /**
+   * 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()
@@ -41,7 +89,7 @@ public class EnsemblLookup extends EnsemblRestClient
    */
   protected URL getUrl(String identifier)
   {
-    String url = ENSEMBL_REST + "/lookup/id/" + identifier
+    String url = getDomain() + "/lookup/id/" + identifier
             + "?content-type=application/json";
     try
     {
@@ -79,8 +127,30 @@ public class EnsemblLookup extends EnsemblRestClient
    */
   public String getParent(String identifier)
   {
+    return getAttribute(identifier, PARENT);
+  }
+
+  /**
+   * Calls the Ensembl lookup REST endpoint and retrieves the 'species' for the
+   * given identifier, or null if not found
+   * 
+   * @param identifier
+   * @return
+   */
+  public String getSpecies(String identifier)
+  {
+    return getAttribute(identifier, SPECIES);
+  }
+
+  /**
+   * @param identifier
+   * @param attribute
+   * @return
+   */
+  protected String getAttribute(String identifier, String attribute)
+  {
     List<String> ids = Arrays.asList(new String[] { identifier });
-  
+
     BufferedReader br = null;
     try
     {
@@ -89,7 +159,7 @@ public class EnsemblLookup extends EnsemblRestClient
       {
         br = getHttpResponse(url, ids);
       }
-      return (parseResponse(br));
+      return (parseResponse(br, attribute));
     } catch (IOException e)
     {
       // ignore
@@ -110,22 +180,23 @@ public class EnsemblLookup extends EnsemblRestClient
   }
 
   /**
-   * Parses "Parent" from the JSON response and returns the value, or null if
-   * not found
+   * Parses the value of 'attribute' from the JSON response and returns the
+   * value, or null if not found
    * 
    * @param br
+   * @param attribute
    * @return
    * @throws IOException
    */
-  protected String parseResponse(BufferedReader br) throws IOException
+  protected String parseResponse(BufferedReader br, String attribute) throws IOException
   {
     String parent = null;
     JSONParser jp = new JSONParser();
     try
     {
       JSONObject val = (JSONObject) jp.parse(br);
-      parent = val.get("Parent").toString();
-    } catch (ParseException e)
+      parent = val.get(attribute).toString();
+    } catch (ParseException | NullPointerException e)
     {
       // ignore
     }