*/
public class EnsemblSymbol extends EnsemblXref
{
+ private static final String GENE = "gene";
+ private static final String TYPE = "type";
+ private static final String ID = "id";
+
/**
* Constructor given the target domain to fetch data from
*
* @return
* @throws IOException
*/
- protected String parseSymbolResponse(BufferedReader br)
- throws IOException
+ protected String parseSymbolResponse(BufferedReader br) throws IOException
{
JSONParser jp = new JSONParser();
String result = null;
while (rvals.hasNext())
{
JSONObject val = (JSONObject) rvals.next();
- String id = val.get("id").toString();
- if (id != null && isGeneIdentifier(id))
+ String id = val.get(ID).toString();
+ String type = val.get(TYPE).toString();
+ if (id != null && GENE.equals(type))
{
result = id;
break;
return result;
}
- protected URL getUrl(String id, Species species)
+ /**
+ * Constructs the URL for the REST symbol endpoint
+ *
+ * @param id
+ * the accession id (Ensembl or external)
+ * @param species
+ * a species name recognisable by Ensembl
+ * @param type
+ * an optional type to filter the response (gene, transcript,
+ * translation)
+ * @return
+ */
+ protected URL getUrl(String id, Species species, String... type)
{
- String url = getDomain() + "/xrefs/symbol/" + species.toString() + "/"
- + id + "?content-type=application/json";
+ StringBuilder sb = new StringBuilder();
+ sb.append(getDomain()).append("/xrefs/symbol/")
+ .append(species.toString()).append("/").append(id)
+ .append(CONTENT_TYPE_JSON);
+ for (String t : type)
+ {
+ sb.append("&object_type=").append(t);
+ }
try
{
+ String url = sb.toString();
return new URL(url);
} catch (MalformedURLException e)
{
* @param identifier
* @return
*/
- public List<String> getIds(String identifier)
+ public List<String> getGeneIds(String identifier)
{
List<String> result = new ArrayList<String>();
List<String> ids = new ArrayList<String>();
{
for (String query : queries)
{
- for (Species taxon : Species.values())
+ for (Species taxon : Species.getModelOrganisms())
{
- if (taxon.isModelOrganism())
+ URL url = getUrl(query, taxon, GENE);
+ if (url != null)
{
- URL url = getUrl(query, taxon);
- if (url != null)
- {
- br = getHttpResponse(url, ids);
- }
- String geneId = parseSymbolResponse(br);
- if (geneId != null)
+ br = getHttpResponse(url, ids);
+ if (br != null)
{
- result.add(geneId);
+ String geneId = parseSymbolResponse(br);
+ System.out.println(url + " returned " + geneId);
+ if (geneId != null && !result.contains(geneId))
+ {
+ result.add(geneId);
+ }
}
}
}