*/
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.bin.Cache;
+import jalview.util.Platform;
+import jalview.util.StringUtils;
+
/**
* Base class for Ensembl REST service clients
*
*/
abstract class EnsemblRestClient extends EnsemblSequenceFetcher
{
+ private static final int HTTP_OK = 200;
+
+ private static final int HTTP_OVERLOAD = 429;
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
+ /*
+ * constants for http retries and timeout;
+ * not final so they can be changed by a Groovy script
+ */
+ private static int PING_TIMEOUT_MS = 2 * 1000;
- private static final int CONNECT_TIMEOUT_MS = 10 * 1000; // 10 seconds
+ private static long PING_RETEST_INTERVAL = 10 * 1000L; // 10 seconds
- private static final int MAX_RETRIES = 3;
+ private static int DEFAULT_READ_TIMEOUT = 5 * 60 * 1000; // 5 minutes
- private static final int HTTP_OK = 200;
+ private static int CONNECT_TIMEOUT_MS = 10 * 1000; // 10 seconds
- private static final int HTTP_OVERLOAD = 429;
+ private static int MAX_RETRIES = 3;
/*
* update these constants when Jalview has been checked / updated for
* @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 = "12.0";
- private static final String LATEST_ENSEMBL_REST_VERSION = "9.0";
+ private static final String LATEST_ENSEMBL_REST_VERSION = "12.0";
private static final String REST_CHANGE_LOG = "https://github.com/Ensembl/ensembl-rest/wiki/Change-log";
private static Map<String, EnsemblData> domainData;
- private final static long AVAILABILITY_RETEST_INTERVAL = 10000L; // 10 seconds
-
private final static long VERSION_RETEST_INTERVAL = 1000L * 3600; // 1 hr
protected static final String CONTENT_TYPE_JSON = "?content-type=application/json";
* @see http://rest.ensembl.org/documentation/info/ping
* @return
*/
- @SuppressWarnings("unchecked")
boolean checkEnsembl()
{
- BufferedReader br = null;
String pingUrl = getDomain() + "/info/ping" + CONTENT_TYPE_JSON;
+ for (int i = 0 ; i < MAX_RETRIES ; i++)
+ {
+ if (pingEnsembl(pingUrl))
+ {
+ if (i > 0)
+ {
+ Cache.log.info("Ensembl ping responded on attempt " + (i+1));
+ }
+ return true;
+ }
+ }
+ Cache.log.error("Ensembl ping failed after " + MAX_RETRIES + " retries");
+ return false;
+ }
+
+ /**
+ * Connects to Ensembl REST service's 'ping' URL and answers true if
+ * successful, false if no reply, or no reply within the 2 second timeout
+ *
+ * @param pingUrl
+ * @return
+ */
+ @SuppressWarnings("unchecked")
+ protected boolean pingEnsembl(String pingUrl)
+ {
try
{
// note this format works for both ensembl and ensemblgenomes
* if ping takes more than 2 seconds to respond, treat as if unavailable
*/
Map<String, Object> val = (Map<String, Object>) getJSON(
- new URL(pingUrl), null, 2 * 1000, MODE_MAP, null);
+ new URL(pingUrl), null, PING_TIMEOUT_MS, MODE_MAP, null);
if (val == null)
{
return false;
return pingString != null;
} catch (Throwable t)
{
- System.err.println(
+ Cache.log.error(
"Error connecting to " + pingUrl + ": " + t.getMessage());
- } finally
- {
- if (br != null)
- {
- try
- {
- br.close();
- } catch (IOException e)
- {
- // ignore
- }
- }
+ return false;
}
- return false;
}
protected final static int MODE_ARRAY = 0;
* 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)
{
* note: a GET request for an invalid id returns an error code e.g. 415
* but POST request returns 200 and an empty Fasta response
*/
- System.err.println("Response code " + responseCode);// + " for " + url);
+ Cache.log.error("Response code " + responseCode);// + " for " + url);
return null;
}
InputStream response = connection.getInputStream();
- if (Platform.isJS())
- {
- return JSON.getJSONReader(response);
- }
+ // Platform.timeCheck(null, Platform.TIME_MARK);
+ Object ret = Platform.parseJSON(response);
+ // Platform.timeCheck("EnsemblRestClient.getJSON " + url,
+ // Platform.TIME_MARK);
- // System.out.println(getClass().getName() + " took "
- // + (System.currentTimeMillis() - now) + "ms to fetch");
-
- return new BufferedReader(new InputStreamReader(response, "UTF-8"));
+ return ret;
}
/**
* recheck if Ensembl is up if it was down, or the recheck period has elapsed
*/
boolean retestAvailability = (now
- - info.lastAvailableCheckTime) > AVAILABILITY_RETEST_INTERVAL;
+ - info.lastAvailableCheckTime) > PING_RETEST_INTERVAL;
if (!info.restAvailable || retestAvailability)
{
info.restAvailable = checkEnsembl();
url = getUrl(ids);
}
- Reader br = null;
- try
- {
- Platform.timeCheck(null, Platform.TIME_MARK);
-
- br = (url == null ? null : getHttpResponse(url, ids, msDelay));
-
- Object ret = (br == null ? null : JSONUtils.parse(br));
-
- Platform.timeCheck("EnsemblRestClient.getJSON " + url,
- Platform.TIME_MARK);
+ Object json = (url == null ? null : getJSON(url, ids, msDelay));
- 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;
}
/**
git://source.jalview.org / jalview.git / blobdiff