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=56d63bb968a38d3621722ea3a25cb2068b8b6c3e;hpb=c389306ad8eca96fe2476197d7ae63f94c4ee483;p=jalview.git diff --git a/src/jalview/ext/ensembl/EnsemblRestClient.java b/src/jalview/ext/ensembl/EnsemblRestClient.java index 56d63bb..e65e7ba 100644 --- a/src/jalview/ext/ensembl/EnsemblRestClient.java +++ b/src/jalview/ext/ensembl/EnsemblRestClient.java @@ -20,18 +20,9 @@ */ 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; @@ -44,6 +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 * @@ -51,22 +46,29 @@ 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 { - 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 @@ -74,16 +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"; @@ -192,11 +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 @@ -207,7 +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; @@ -216,22 +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; @@ -282,10 +293,12 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher * in milliseconds * @return * @throws IOException + * @throws ParseException */ - private BufferedReader getHttpResponse(URL url, List ids, - int readTimeout) throws IOException + private Object getJSON(URL url, List ids, int readTimeout) + throws IOException, ParseException { + if (readTimeout < 0) { readTimeout = DEFAULT_READ_TIMEOUT; @@ -294,10 +307,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher HttpURLConnection connection = null; int responseCode = 0; - if (Platform.isJS()) - { - JSON.setAjax(url); - } + Platform.setAjaxJSON(url); while (retriesLeft > 0) { @@ -319,21 +329,18 @@ 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(); - 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; } /** @@ -426,7 +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(); @@ -515,50 +522,26 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher 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) ret).get(mapKey); - } - if (ret == null) - { - return null; - } - switch (mode) - { - case MODE_ARRAY: - case MODE_MAP: - break; - case MODE_ITERATOR: - ret = ((List) ret).iterator(); - break; - } - return ret; - - } finally + if (json != null && mapKey != null) { - if (br != null) - { - try - { - br.close(); - } catch (IOException e) - { - // ignore - } - } + json = ((Map) json).get(mapKey); + } + if (json == null) + { + return null; + } + switch (mode) + { + case MODE_ARRAY: + case MODE_MAP: + break; + case MODE_ITERATOR: + json = ((List) json).iterator(); + break; } + return json; } /**