X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblLookup.java;h=9b56d6bfe91560cacb1cbb8e9997cfe8a79de196;hb=a395b6d73484b2827f3e80295631e69dd8841c47;hp=5a616f06083b4ede39f2a4981ecf338d169ba3c6;hpb=6461d42898d6c7b253c7ccceeeee629b559d2479;p=jalview.git

diff --git a/src/jalview/ext/ensembl/EnsemblLookup.java b/src/jalview/ext/ensembl/EnsemblLookup.java
index 5a616f0..9b56d6b 100644
--- a/src/jalview/ext/ensembl/EnsemblLookup.java
+++ b/src/jalview/ext/ensembl/EnsemblLookup.java
@@ -20,22 +20,27 @@
  */
 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.function.Function;
+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
+ * 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
  */
@@ -43,14 +48,6 @@ public class EnsemblLookup extends EnsemblRestClient
 {
   private static final String SPECIES = "species";
 
-  private static final String PARENT = "Parent";
-
-  private static final String OBJECT_TYPE_TRANSLATION = "Translation";
-  private static final String OBJECT_TYPE_TRANSCRIPT = "Transcript";
-  private static final String ID = "id";
-  private static final String OBJECT_TYPE_GENE = "Gene";
-  private static final String OBJECT_TYPE = "object_type";
-
   /**
    * Default constructor (to use rest.ensembl.org)
    */
@@ -85,17 +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_JSON;
+    if (objectType != null)
+    {
+      url += "&" + OBJECT_TYPE + "=" + objectType;
+    }
+
     try
     {
       return new URL(url);
@@ -111,33 +117,66 @@ 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 returns
-   * <ul>
-   * <li>the 'id' for the identifier if its type is "Gene"</li>
-   * <li>the 'Parent' if its type is 'Transcript'</li>
-   * <ul>
-   * If the type is 'Translation', does a recursive call to this method, passing
-   * in the 'Parent' (transcript id).
+   * 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 identifier
+   * @param br
    * @return
    */
-  public String getGeneId(String identifier)
+  protected String parseGeneId(Map<String, Object> val)
   {
-    return getResult(identifier, br -> parseGeneId(br));
+    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;
   }
 
   /**
@@ -149,120 +188,98 @@ public class EnsemblLookup extends EnsemblRestClient
    */
   public String getSpecies(String identifier)
   {
-    return getResult(identifier, br -> getAttribute(br, SPECIES));
+    String species = null;
+    Map<String, Object> json = getResult(identifier, null);
+    if (json != null)
+    {
+      Object o = json.get(SPECIES);
+      if (o != null)
+      {
+        species = o.toString();
+      }
+    }
+    return species;
   }
 
   /**
-   * Calls the /lookup/id rest service and delegates parsing of the JSON
-   * response to the supplied parser
+   * Calls the /lookup/id rest service and returns the response as a Map<String, Object>,
+   * or null if any error
    * 
    * @param identifier
-   * @param parser
+   * @param objectType
+   *          (optional)
    * @return
    */
-  protected String getResult(String identifier,
-          Function<BufferedReader, String> parser)
+  @SuppressWarnings("unchecked")
+  protected Map<String, Object> getResult(String identifier, String objectType)
   {
     List<String> ids = Arrays.asList(new String[] { identifier });
 
-    BufferedReader br = null;
     try
     {
-      URL url = getUrl(identifier);
-      if (url != null)
-      {
-        br = getHttpResponse(url, ids);
-      }
-      return br == null ? null : parser.apply(br);
-    } catch (IOException e)
+      return (Map<String, Object>) getJSON(getUrl(identifier, objectType), ids, -1, MODE_MAP, null);
+    } 
+    catch (IOException | ParseException e)
     {
-      // ignore
+      System.err.println("Error parsing " + identifier + " lookup response "
+              + e.getMessage());
       return null;
-    } finally
-    {
-      if (br != null)
-      {
-        try
-        {
-          br.close();
-        } catch (IOException e)
-        {
-          // ignore
-        }
-      }
     }
   }
 
   /**
-   * Answers the value of 'attribute' from the JSON response, 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 attribute
+   * @param geneId
    * @return
    */
-  protected String getAttribute(BufferedReader br, String attribute)
+  public GeneLociI getGeneLoci(String geneId)
   {
-    String value = null;
-    JSONParser jp = new JSONParser();
-    try
-    {
-      JSONObject val = (JSONObject) jp.parse(br);
-      value = val.get(attribute).toString();
-    } catch (ParseException | NullPointerException | IOException e)
-    {
-      // ignore
-    }
-    return value;
+    return parseGeneLoci(getResult(geneId, OBJECT_TYPE_GENE));
   }
 
   /**
-   * 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.
+   * 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 br
+   * @param json
    * @return
    */
-  protected String parseGeneId(BufferedReader br)
+  GeneLociI parseGeneLoci(Map<String, Object> json)
   {
-    String geneId = null;
-    JSONParser jp = new JSONParser();
+    if (json == null)
+    {
+      return null;
+    }
+
     try
     {
-      JSONObject val = (JSONObject) jp.parse(br);
-      String type = val.get(OBJECT_TYPE).toString();
-      if (OBJECT_TYPE_GENE.equalsIgnoreCase(type))
-      {
-        geneId = val.get(ID).toString();
-      }
-      else if (OBJECT_TYPE_TRANSCRIPT.equalsIgnoreCase(type))
-      {
-        geneId = val.get(PARENT).toString();
-      }
-      else if (OBJECT_TYPE_TRANSLATION.equalsIgnoreCase(type))
-      {
-        String transcriptId = val.get(PARENT).toString();
-        try
-        {
-          geneId = getGeneId(transcriptId);
-        } catch (StackOverflowError e)
-        {
-          /*
-           * unlikely data condition error!
-           */
-          System.err
-                  .println("** Ensembl lookup "
-                          + getUrl(transcriptId).toString()
-                          + " looping on Parent!");
-        }
-      }
-    } catch (ParseException | IOException 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 geneId;
+    return null;
   }
 
 }