*/
package jalview.ext.ensembl;
+import jalview.io.DataSourceType;
import jalview.io.FileParse;
import jalview.util.StringUtils;
*/
abstract class EnsemblRestClient extends EnsemblSequenceFetcher
{
+ private static final int DEFAULT_READ_TIMEOUT = 5 * 60 * 1000; // 5 minutes
+
+ private static final int CONNECT_TIMEOUT_MS = 10 * 1000; // 10 seconds
+
/*
* update these constants when Jalview has been checked / updated for
- * changes to Ensembl REST API
+ * changes to Ensembl REST API (ref JAL-2105)
* @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 = "4.6";
+ private static final String LATEST_ENSEMBLGENOMES_REST_VERSION = "5.0";
- private static final String LATEST_ENSEMBL_REST_VERSION = "4.7";
+ private static final String LATEST_ENSEMBL_REST_VERSION = "5.0";
private static final String REST_CHANGE_LOG = "https://github.com/Ensembl/ensembl-rest/wiki/Change-log";
private final static long VERSION_RETEST_INTERVAL = 1000L * 3600; // 1 hr
+ private static final Regex PROTEIN_REGEX = new Regex(
+ "(ENS)([A-Z]{3}|)P[0-9]{11}$");
+
private static final Regex TRANSCRIPT_REGEX = new Regex(
"(ENS)([A-Z]{3}|)T[0-9]{11}$");
/**
* Answers true if the query matches the regular expression pattern for an
+ * Ensembl protein stable identifier
+ *
+ * @param query
+ * @return
+ */
+ public boolean isProteinIdentifier(String query)
+ {
+ return query == null ? false : PROTEIN_REGEX.search(query);
+ }
+
+ /**
+ * Answers true if the query matches the regular expression pattern for an
* Ensembl gene stable identifier
*
* @param query
*/
private boolean checkEnsembl()
{
- HttpURLConnection conn = null;
+ BufferedReader br = null;
try
{
// note this format works for both ensembl and ensemblgenomes
/*
* expect {"ping":1} if ok
+ * if ping takes more than 2 seconds to respond, treat as if unavailable
*/
- BufferedReader br = getHttpResponse(ping, null);
+ br = getHttpResponse(ping, null, 2 * 1000);
JSONParser jp = new JSONParser();
JSONObject val = (JSONObject) jp.parse(br);
String pingString = val.get("ping").toString();
+ t.getMessage());
} finally
{
- if (conn != null)
+ if (br != null)
{
- conn.disconnect();
+ try
+ {
+ br.close();
+ } catch (IOException e)
+ {
+ // ignore
+ }
}
}
return false;
// request failed
return null;
}
- FileParse fp = new FileParse(reader, url.toString(), "HTTP_POST");
+ FileParse fp = new FileParse(reader, url.toString(), DataSourceType.URL);
return fp;
}
/**
+ * Gets a reader to the HTTP response, using the default read timeout of 5
+ * minutes
+ *
+ * @param url
+ * @param ids
+ * @return
+ * @throws IOException
+ */
+ protected BufferedReader getHttpResponse(URL url, List<String> ids)
+ throws IOException
+ {
+ return getHttpResponse(url, ids, DEFAULT_READ_TIMEOUT);
+ }
+
+ /**
* Writes the HTTP request and gets the response as a reader.
*
* @param url
* @param ids
* written as Json POST body if more than one
+ * @param readTimeout
+ * in milliseconds
* @return
* @throws IOException
* if response code was not 200, or other I/O error
*/
- protected BufferedReader getHttpResponse(URL url, List<String> ids)
- throws IOException
+ protected BufferedReader getHttpResponse(URL url, List<String> ids,
+ int readTimeout) throws IOException
{
// long now = System.currentTimeMillis();
HttpURLConnection connection = (HttpURLConnection) url.openConnection();
connection.setDoInput(true);
connection.setDoOutput(multipleIds);
+ connection.setConnectTimeout(CONNECT_TIMEOUT_MS);
+ connection.setReadTimeout(readTimeout);
+
if (multipleIds)
{
writePostBody(connection, ids);
boolean laterVersion = StringUtils.compareVersions(version, expected) == 1;
if (laterVersion)
{
- System.err.println(String.format(
- "Expected %s REST version %s but found %s, see %s",
- getDbSource(), expected, version, REST_CHANGE_LOG));
+ System.err
+ .println(String
+ .format("EnsemblRestClient expected %s REST version %s but found %s, see %s",
+ getDbSource(), expected, version,
+ REST_CHANGE_LOG));
}
info.restVersion = version;
} catch (Throwable t)