Merge branch 'develop' into releases/Release_2_11_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 ed1b4fa..c6b794a 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblLookup.java
+++ b/src/jalview/ext/ensembl/EnsemblLookup.java
@@ -49,11 +49,6 @@ public class EnsemblLookup extends EnsemblRestClient
   private static final String SPECIES = "species";
 
   /**
-   * keep track of last identifier retrieved to break loops
-   */
-  private String lastId;
-
-  /**
    * Default constructor (to use rest.ensembl.org)
    */
   public EnsemblLookup()
@@ -122,21 +117,9 @@ public class EnsemblLookup extends EnsemblRestClient
     return true;
   }
 
-  @Override
-  protected String getRequestMimeType(boolean multipleIds)
-  {
-    return "application/json";
-  }
-
-  @Override
-  protected String getResponseMimeType()
-  {
-    return "application/json";
-  }
-
   /**
    * Returns the gene id related to the given identifier (which may be for a
-   * gene, transcript or protein)
+   * gene, transcript or protein), or null if none is found
    * 
    * @param identifier
    * @return
@@ -148,7 +131,7 @@ public class EnsemblLookup extends EnsemblRestClient
 
   /**
    * Returns the gene id related to the given identifier (which may be for a
-   * gene, transcript or protein)
+   * gene, transcript or protein), or null if none is found
    * 
    * @param identifier
    * @param objectType
@@ -156,34 +139,7 @@ public class EnsemblLookup extends EnsemblRestClient
    */
   public String getGeneId(String identifier, String objectType)
   {
-    List<String> ids = Arrays.asList(new String[] { identifier });
-
-    BufferedReader br = null;
-    try
-    {
-      URL url = getUrl(identifier, objectType);
-      if (url != null)
-      {
-        br = getHttpResponse(url, ids);
-      }
-      return br == null ? null : parseResponse(br);
-    } catch (IOException e)
-    {
-      // ignore
-      return null;
-    } finally
-    {
-      if (br != null)
-      {
-        try
-        {
-          br.close();
-        } catch (IOException e)
-        {
-          // ignore
-        }
-      }
-    }
+    return parseGeneId(getResult(identifier, objectType));
   }
 
   /**
@@ -194,36 +150,32 @@ public class EnsemblLookup extends EnsemblRestClient
    * 
    * @param br
    * @return
-   * @throws IOException
    */
-  protected String parseResponse(BufferedReader br) throws IOException
+  protected String parseGeneId(JSONObject val)
   {
+    if (val == null)
+    {
+      return null;
+    }
     String geneId = null;
-    JSONParser jp = new JSONParser();
-    try
+    String type = val.get(OBJECT_TYPE).toString();
+    if (OBJECT_TYPE_GENE.equalsIgnoreCase(type))
     {
-      JSONObject val = (JSONObject) jp.parse(br);
-      String type = val.get(OBJECT_TYPE).toString();
-      if (OBJECT_TYPE_GENE.equalsIgnoreCase(type))
-      {
-        // got the gene - just returns its id
-        geneId = val.get(JSON_ID).toString();
-      }
-      else if (OBJECT_TYPE_TRANSCRIPT.equalsIgnoreCase(type))
-      {
-        // got the transcript - return its (Gene) Parent
-        geneId = val.get(PARENT).toString();
-      }
-      else if (OBJECT_TYPE_TRANSLATION.equalsIgnoreCase(type))
-      {
-        // got the protein - get its Parent, restricted to type Transcript
-        String transcriptId = val.get(PARENT).toString();
-        geneId = getGeneId(transcriptId, OBJECT_TYPE_TRANSCRIPT);
-      }
-    } catch (ParseException e)
+      // got the gene - just returns its id
+      geneId = val.get(JSON_ID).toString();
+    }
+    else if (OBJECT_TYPE_TRANSCRIPT.equalsIgnoreCase(type))
     {
-      // ignore
+      // got the transcript - return its (Gene) Parent
+      geneId = val.get(PARENT).toString();
     }
+    else if (OBJECT_TYPE_TRANSLATION.equalsIgnoreCase(type))
+    {
+      // got the protein - get its Parent, restricted to type Transcript
+      String transcriptId = val.get(PARENT).toString();
+      geneId = getGeneId(transcriptId, OBJECT_TYPE_TRANSCRIPT);
+    }
+
     return geneId;
   }
 
@@ -265,18 +217,8 @@ public class EnsemblLookup extends EnsemblRestClient
     BufferedReader br = null;
     try
     {
-
       URL url = getUrl(identifier, objectType);
 
-      if (identifier.equals(lastId))
-      {
-        System.err.println("** Ensembl lookup " + url.toString()
-                + " looping on Parent!");
-        return null;
-      }
-
-      lastId = identifier;
-
       if (url != null)
       {
         br = getHttpResponse(url, ids);
@@ -303,46 +245,6 @@ public class EnsemblLookup extends EnsemblRestClient
   }
 
   /**
-   * 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,
-   * specifying that object_type should be Transcript.
-   * 
-   * @param jsonObject
-   * @return
-   */
-  protected String parseGeneId(JSONObject json)
-  {
-    if (json == null)
-    {
-      // e.g. lookup failed with 404 not found
-      return null;
-    }
-
-    String geneId = null;
-    String type = json.get(OBJECT_TYPE).toString();
-    if (OBJECT_TYPE_GENE.equalsIgnoreCase(type))
-    {
-      // got the gene - just returns its id
-      geneId = json.get(JSON_ID).toString();
-    }
-    else if (OBJECT_TYPE_TRANSCRIPT.equalsIgnoreCase(type))
-    {
-      // got the transcript - return its (Gene) Parent
-      geneId = json.get(PARENT).toString();
-    }
-    else if (OBJECT_TYPE_TRANSLATION.equalsIgnoreCase(type))
-    {
-      // got the protein - look up its Parent, restricted to type Transcript
-      String transcriptId = json.get(PARENT).toString();
-      geneId = parseGeneId(getResult(transcriptId, OBJECT_TYPE_TRANSCRIPT));
-    }
-
-    return geneId;
-  }
-
-  /**
    * Calls the /lookup/id rest service for the given id, and if successful,
    * parses and returns the gene's chromosomal coordinates
    *