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()
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
/**
* 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
*/
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));
}
/**
*
* @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;
}
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);
}
/**
- * 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
*