*/
package jalview.ext.ensembl;
-import jalview.bin.Cache;
-import jalview.javascript.json.JSON;
-import jalview.util.JSONUtils;
-import jalview.util.Platform;
-import jalview.util.StringUtils;
-
import java.io.BufferedReader;
import java.io.DataOutputStream;
import java.io.IOException;
import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.io.Reader;
import java.net.HttpURLConnection;
import java.net.MalformedURLException;
import java.net.ProtocolException;
import org.json.simple.parser.ParseException;
+import jalview.util.Platform;
+import jalview.util.StringUtils;
+
/**
* Base class for Ensembl REST service clients
*
static
{
- Cache.addJ2SDirectDatabaseCall("http://rest.ensembl");
- Cache.addJ2SDirectDatabaseCall("https://rest.ensembl");
+ Platform.addJ2SDirectDatabaseCall("http://rest.ensembl");
+ Platform.addJ2SDirectDatabaseCall("https://rest.ensembl");
}
private static final int DEFAULT_READ_TIMEOUT = 5 * 60 * 1000; // 5 minutes
* @see https://github.com/Ensembl/ensembl-rest/wiki/Change-log
* @see http://rest.ensembl.org/info/rest?content-type=application/json
*/
- private static final String LATEST_ENSEMBLGENOMES_REST_VERSION = "9.0";
+ private static final String LATEST_ENSEMBLGENOMES_REST_VERSION = "13.0";
- private static final String LATEST_ENSEMBL_REST_VERSION = "9.0";
+ private static final String LATEST_ENSEMBL_REST_VERSION = "13.0";
private static final String REST_CHANGE_LOG = "https://github.com/Ensembl/ensembl-rest/wiki/Change-log";
* in milliseconds
* @return
* @throws IOException
+ * @throws ParseException
*/
- private BufferedReader getHttpResponse(URL url, List<String> ids,
- int readTimeout) throws IOException
+ private Object getJSON(URL url, List<String> ids, int readTimeout)
+ throws IOException, ParseException
{
+
if (readTimeout < 0)
{
readTimeout = DEFAULT_READ_TIMEOUT;
HttpURLConnection connection = null;
int responseCode = 0;
- if (Platform.isJS())
- {
- JSON.setAjax(url);
- }
+ Platform.setAjaxJSON(url);
while (retriesLeft > 0)
{
InputStream response = connection.getInputStream();
- if (Platform.isJS())
- {
- return JSON.getJSONReader(response);
- }
-
- // System.out.println(getClass().getName() + " took "
- // + (System.currentTimeMillis() - now) + "ms to fetch");
+ // Platform.timeCheck(null, Platform.TIME_MARK);
+ Object ret = Platform.parseJSON(response);
+ // Platform.timeCheck("EnsemblRestClient.getJSON " + url,
+ // Platform.TIME_MARK);
- return new BufferedReader(new InputStreamReader(response, "UTF-8"));
+ return ret;
}
/**
url = getUrl(ids);
}
- Reader br = null;
- try
- {
- Platform.timeCheck(null, Platform.TIME_MARK);
-
- br = (url == null ? null : getHttpResponse(url, ids, msDelay));
+ Object json = (url == null ? null : getJSON(url, ids, msDelay));
- Object ret = (br == null ? null : JSONUtils.parse(br));
-
- Platform.timeCheck("EnsemblRestClient.getJSON " + url,
- Platform.TIME_MARK);
-
- if (ret != null && mapKey != null)
- {
- ret = ((Map<String, Object>) ret).get(mapKey);
- }
- if (ret == null)
- {
- return null;
- }
- switch (mode)
- {
- case MODE_ARRAY:
- case MODE_MAP:
- break;
- case MODE_ITERATOR:
- ret = ((List<Object>) ret).iterator();
- break;
- }
- return ret;
-
- } finally
+ if (json != null && mapKey != null)
{
- if (br != null)
- {
- try
- {
- br.close();
- } catch (IOException e)
- {
- // ignore
- }
- }
+ json = ((Map<String, Object>) json).get(mapKey);
+ }
+ if (json == null)
+ {
+ return null;
+ }
+ switch (mode)
+ {
+ case MODE_ARRAY:
+ case MODE_MAP:
+ break;
+ case MODE_ITERATOR:
+ json = ((List<Object>) json).iterator();
+ break;
}
+ return json;
}
/**