return true;
}
- @Override
- protected String getRequestMimeType(boolean multipleIds)
- {
- return "application/json";
- }
-
- @Override
- protected String getResponseMimeType()
- {
- return "application/json";
- }
-
/**
* Calls the Ensembl xrefs REST endpoint and retrieves any cross-references
* ("primary_id") for the given identifier (Ensembl accession id) and database
*/
public List<DBRefEntry> getCrossReferences(String identifier)
{
- List<DBRefEntry> result = new ArrayList<DBRefEntry>();
- List<String> ids = new ArrayList<String>();
+ List<DBRefEntry> result = new ArrayList<>();
+ List<String> ids = new ArrayList<>();
ids.add(identifier);
BufferedReader br = null;
throws IOException
{
JSONParser jp = new JSONParser();
- List<DBRefEntry> result = new ArrayList<DBRefEntry>();
+ List<DBRefEntry> result = new ArrayList<>();
try
{
JSONArray responses = (JSONArray) jp.parse(br);
while (rvals.hasNext())
{
JSONObject val = (JSONObject) rvals.next();
- String dbname = val.get("dbname").toString();
- if (GO_GENE_ONTOLOGY.equals(dbname))
- {
- continue;
- }
+ String db = val.get("dbname").toString();
String id = val.get("primary_id").toString();
- if (dbname != null && id != null)
+ if (db != null && id != null
+ && !GO_GENE_ONTOLOGY.equals(db))
{
- dbname = DBRefUtils.getCanonicalName(dbname);
- DBRefEntry dbref = new DBRefEntry(dbname, getXRefVersion(), id);
+ db = DBRefUtils.getCanonicalName(db);
+ DBRefEntry dbref = new DBRefEntry(db, getXRefVersion(), id);
result.add(dbref);
}
}
protected URL getUrl(String identifier)
{
String url = getDomain() + "/xrefs/id/" + identifier
- + "?content-type=application/json&all_levels=1";
+ + CONTENT_TYPE_JSON + "&all_levels=1";
try
{
return new URL(url);