X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblRestClient.java;h=e65e7ba108b5c74aad94adc09b5c02a444be988e;hb=refs%2Fheads%2Ffeature%2FJAL-3730ensemblPingRetries;hp=b605232e039403d9473f4b34bf7724260ac86cc1;hpb=577b0bf651763fe609eb6d6343754662023b3eac;p=jalview.git diff --git a/src/jalview/ext/ensembl/EnsemblRestClient.java b/src/jalview/ext/ensembl/EnsemblRestClient.java index b605232..e65e7ba 100644 --- a/src/jalview/ext/ensembl/EnsemblRestClient.java +++ b/src/jalview/ext/ensembl/EnsemblRestClient.java @@ -20,10 +20,6 @@ */ package jalview.ext.ensembl; -import jalview.util.Platform; -import jalview.util.StringUtils; - -import java.io.BufferedReader; import java.io.DataOutputStream; import java.io.IOException; import java.io.InputStream; @@ -39,6 +35,10 @@ import javax.ws.rs.HttpMethod; 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 * @@ -46,6 +46,9 @@ import org.json.simple.parser.ParseException; */ abstract class EnsemblRestClient extends EnsemblSequenceFetcher { + private static final int HTTP_OK = 200; + + private static final int HTTP_OVERLOAD = 429; static { @@ -53,15 +56,19 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher 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 @@ -69,16 +76,14 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher * @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 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"; @@ -187,11 +192,34 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher * @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 @@ -202,7 +230,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher * if ping takes more than 2 seconds to respond, treat as if unavailable */ Map val = (Map) 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; @@ -211,22 +239,10 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher 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; @@ -313,16 +329,16 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher * 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(); - Platform.timeCheck(null, Platform.TIME_MARK); + // Platform.timeCheck(null, Platform.TIME_MARK); Object ret = Platform.parseJSON(response); - Platform.timeCheck("EnsemblRestClient.getJSON " + url, - Platform.TIME_MARK); + // Platform.timeCheck("EnsemblRestClient.getJSON " + url, + // Platform.TIME_MARK); return ret; } @@ -417,7 +433,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher * 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();