X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblLookup.java;h=9b56d6bfe91560cacb1cbb8e9997cfe8a79de196;hb=9d2408483e451285fd555c3cd6e0273977acbaa7;hp=c5945aea124abf085fa84a0e23b66d84004c3892;hpb=b8058f3f849f44740a695c83e96bdca3a197af5c;p=jalview.git

diff --git a/src/jalview/ext/ensembl/EnsemblLookup.java b/src/jalview/ext/ensembl/EnsemblLookup.java
index c5945ae..9b56d6b 100644
--- a/src/jalview/ext/ensembl/EnsemblLookup.java
+++ b/src/jalview/ext/ensembl/EnsemblLookup.java
@@ -1,27 +1,52 @@
+/*
+ * 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.bin.Cache;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.GeneLociI;
+import jalview.datamodel.GeneLocus;
+import jalview.datamodel.Mapping;
+import jalview.util.MapList;
 
-import java.io.BufferedReader;
 import java.io.IOException;
 import java.net.MalformedURLException;
 import java.net.URL;
 import java.util.Arrays;
+import java.util.Collections;
 import java.util.List;
+import java.util.Map;
 
-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.
+ * A client for the Ensembl /lookup REST endpoint, used to find the gene
+ * identifier given a gene, transcript or protein identifier, or to extract the
+ * species or chromosomal coordinates from the same service response
  * 
  * @author gmcarstairs
- *
  */
 public class EnsemblLookup extends EnsemblRestClient
 {
+  private static final String SPECIES = "species";
 
   /**
    * Default constructor (to use rest.ensembl.org)
@@ -57,17 +82,26 @@ public class EnsemblLookup extends EnsemblRestClient
   protected URL getUrl(List<String> ids) throws MalformedURLException
   {
     String identifier = ids.get(0);
-    return getUrl(identifier);
+    return getUrl(identifier, null);
   }
 
   /**
+   * Gets the url for lookup of the given identifier, optionally with objectType
+   * also specified in the request
+   * 
    * @param identifier
+   * @param objectType
    * @return
    */
-  protected URL getUrl(String identifier)
+  protected URL getUrl(String identifier, String objectType)
   {
     String url = getDomain() + "/lookup/id/" + identifier
-            + "?content-type=application/json";
+            + CONTENT_TYPE_JSON;
+    if (objectType != null)
+    {
+      url += "&" + OBJECT_TYPE + "=" + objectType;
+    }
+
     try
     {
       return new URL(url);
@@ -83,78 +117,169 @@ public class EnsemblLookup extends EnsemblRestClient
     return true;
   }
 
-  @Override
-  protected String getRequestMimeType(boolean multipleIds)
+  /**
+   * Returns the gene id related to the given identifier (which may be for a
+   * gene, transcript or protein), or null if none is found
+   * 
+   * @param identifier
+   * @return
+   */
+  public String getGeneId(String identifier)
   {
-    return "application/json";
+    return getGeneId(identifier, null);
   }
 
-  @Override
-  protected String getResponseMimeType()
+  /**
+   * Returns the gene id related to the given identifier (which may be for a
+   * gene, transcript or protein), or null if none is found
+   * 
+   * @param identifier
+   * @param objectType
+   * @return
+   */
+  public String getGeneId(String identifier, String objectType)
   {
-    return "application/json";
+    return parseGeneId(getResult(identifier, objectType));
   }
 
   /**
-   * Calls the Ensembl lookup REST endpoint and retrieves the 'Parent' for the
+   * 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.
+   * 
+   * @param br
+   * @return
+   */
+  protected String parseGeneId(Map<String, Object> val)
+  {
+    if (val == null)
+    {
+      return null;
+    }
+    String geneId = null;
+    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);
+    }
+
+    return geneId;
+  }
+
+  /**
+   * Calls the Ensembl lookup REST endpoint and retrieves the 'species' for the
    * given identifier, or null if not found
    * 
    * @param identifier
    * @return
    */
-  public String getParent(String identifier)
+  public String getSpecies(String identifier)
   {
-    List<String> ids = Arrays.asList(new String[] { identifier });
-  
-    BufferedReader br = null;
-    try
+    String species = null;
+    Map<String, Object> json = getResult(identifier, null);
+    if (json != null)
     {
-      URL url = getUrl(identifier);
-      if (url != null)
+      Object o = json.get(SPECIES);
+      if (o != null)
       {
-        br = getHttpResponse(url, ids);
+        species = o.toString();
       }
-      return (parseResponse(br));
-    } catch (IOException e)
+    }
+    return species;
+  }
+
+  /**
+   * Calls the /lookup/id rest service and returns the response as a Map<String, Object>,
+   * or null if any error
+   * 
+   * @param identifier
+   * @param objectType
+   *          (optional)
+   * @return
+   */
+  @SuppressWarnings("unchecked")
+  protected Map<String, Object> getResult(String identifier, String objectType)
+  {
+    List<String> ids = Arrays.asList(new String[] { identifier });
+
+    try
     {
-      // ignore
-      return null;
-    } finally
+      return (Map<String, Object>) getJSON(getUrl(identifier, objectType), ids, -1, MODE_MAP, null);
+    } 
+    catch (IOException | ParseException e)
     {
-      if (br != null)
-      {
-        try
-        {
-          br.close();
-        } catch (IOException e)
-        {
-          // ignore
-        }
-      }
+      System.err.println("Error parsing " + identifier + " lookup response "
+              + e.getMessage());
+      return null;
     }
   }
 
   /**
-   * Parses "Parent" from the JSON response and returns the value, or null if
-   * not found
+   * Calls the /lookup/id rest service for the given id, and if successful,
+   * parses and returns the gene's chromosomal coordinates
    * 
-   * @param br
+   * @param geneId
    * @return
-   * @throws IOException
    */
-  protected String parseResponse(BufferedReader br) throws IOException
+  public GeneLociI getGeneLoci(String geneId)
   {
-    String parent = null;
-    JSONParser jp = new JSONParser();
+    return parseGeneLoci(getResult(geneId, OBJECT_TYPE_GENE));
+  }
+
+  /**
+   * Parses the /lookup/id response for species, asssembly_name,
+   * seq_region_name, start, end and returns an object that wraps them, or null
+   * if unsuccessful
+   * 
+   * @param json
+   * @return
+   */
+  GeneLociI parseGeneLoci(Map<String, Object> json)
+  {
+    if (json == null)
+    {
+      return null;
+    }
+
     try
     {
-      JSONObject val = (JSONObject) jp.parse(br);
-      parent = val.get("Parent").toString();
-    } catch (ParseException e)
+      final String species = json.get("species").toString();
+      final String assembly = json.get("assembly_name").toString();
+      final String chromosome = json.get("seq_region_name").toString();
+      String strand = json.get("strand").toString();
+      int start = Integer.parseInt(json.get("start").toString());
+      int end = Integer.parseInt(json.get("end").toString());
+      int fromEnd = end - start + 1;
+      boolean reverseStrand = "-1".equals(strand);
+      int toStart = reverseStrand ? end : start;
+      int toEnd = reverseStrand ? start : end;
+      List<int[]> fromRange = Collections.singletonList(new int[] { 1,
+          fromEnd });
+      List<int[]> toRange = Collections.singletonList(new int[] { toStart,
+          toEnd });
+      final Mapping map = new Mapping(
+              new MapList(fromRange, toRange, 1, 1));
+      return new GeneLocus(species == null ? "" : species, assembly,
+              chromosome, map);
+    } catch (NullPointerException | NumberFormatException e)
     {
-      // ignore
+      Cache.log.error("Error looking up gene loci: " + e.getMessage());
+      e.printStackTrace();
     }
-    return parent;
+    return null;
   }
 
 }