import jalview.datamodel.GeneLociI;
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;
/**
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
* @param br
* @return
*/
- protected String parseGeneId(JSONObject val)
+ 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))
public String getSpecies(String identifier)
{
String species = null;
- JSONObject json = getResult(identifier, null);
+ Map<String, Object> json = getResult(identifier, null);
if (json != null)
{
Object o = json.get(SPECIES);
}
/**
- * Calls the /lookup/id rest service and returns the response as a JSONObject,
+ * Calls the /lookup/id rest service and returns the response as a Map<String, Object>,
* or null if any error
*
* @param identifier
* (optional)
* @return
*/
- protected JSONObject getResult(String identifier, String objectType)
+ @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, objectType);
-
- if (url != null)
- {
- br = getHttpResponse(url, ids);
- }
- return br == null ? null : (JSONObject) (new JSONParser().parse(br));
- } catch (IOException | ParseException e)
+ return (Map<String, Object>) getJSON(getUrl(identifier, objectType), ids, -1, MODE_MAP, null);
+ }
+ catch (IOException | ParseException e)
{
System.err.println("Error parsing " + identifier + " lookup response "
+ e.getMessage());
return null;
- } finally
- {
- if (br != null)
- {
- try
- {
- br.close();
- } catch (IOException e)
- {
- // ignore
- }
- }
}
}
* @param json
* @return
*/
- GeneLociI parseGeneLoci(JSONObject json)
+ GeneLociI parseGeneLoci(Map<String, Object> json)
{
if (json == null)
{