*/
package jalview.ws.ebi;
+import java.util.Locale;
+
import jalview.datamodel.DBRefSource;
import jalview.util.MessageManager;
import jalview.util.Platform;
* the query formatted as db:query1;query2;query3
* @param format
* the format wanted
- * @param extension
+ * @param ext
* for the temporary file to hold response (without separator)
* @return the file holding the response
* @throws OutOfMemoryError
{
String url = buildUrl(ids, database, format);
InputStream is = null;
+ BufferedReader br = null;
try
{
URL rcall = new URL(url);
Platform.streamToFile(is, outFile);
return null;
}
- BufferedReader br = new BufferedReader(new InputStreamReader(is));
+ br = new BufferedReader(new InputStreamReader(is));
String rtn;
List<String> arl = new ArrayList<>();
while ((rtn = br.readLine()) != null)
{
}
}
+ if (br != null)
+ {
+ try
+ {
+ br.close();
+ } catch (IOException e)
+ {
+ }
+ }
}
return null;
}
if (database.equalsIgnoreCase(DBRefSource.EMBL)
|| database.equalsIgnoreCase(DBRefSource.EMBLCDS))
{
- url = "https://www.ebi.ac.uk/ena/data/view/" + ids.toLowerCase()
- + (format != null ? "&" + format : "");
+ url = "https://www.ebi.ac.uk/ena/browser/api/embl/"
+ + ids.toLowerCase(Locale.ROOT) + "?download=true&gzip=true";
}
else
{
url = "https://www.ebi.ac.uk/Tools/dbfetch/dbfetch/"
- + database.toLowerCase() + "/" + ids.toLowerCase()
+ + database.toLowerCase(Locale.ROOT) + "/" + ids.toLowerCase(Locale.ROOT)
+ (format != null ? "/" + format : "");
}
return url;